├── .gitignore ├── LICENSE ├── README.md ├── annotations ├── Yeast_ARS_locations.bed ├── Yeast_centromeres.bed ├── Yeast_other_features.bed ├── Yeast_snRNA_genes.bed ├── Yeast_tRNA_genes.bed └── sacCer3_annotations.csv ├── computeLengthHistogram.R ├── config ├── annotation_config.yaml └── config.yaml ├── misc ├── Figure_3.png ├── Figure_4.png ├── Figure_5.png ├── Figure_6.png ├── Figure_7.png └── Figure_8.png ├── plot2DO.R ├── plot2DO_setup.R ├── sample_BAM_files └── README.md └── source ├── plot2DO_core.R ├── plot2DO_data.R ├── plot2DO_io.R ├── plot2DO_main.R └── plot2DO_plots.R /.gitignore: -------------------------------------------------------------------------------- 1 | wget.exe 2 | sample_BAM_files/*.bam 3 | sample_BAM_files/*.bed 4 | to_be_removed 5 | output 6 | annotations/*chromInfo.txt 7 | .Rhistory 8 | .ipynb_checkpoints 9 | plot2DO_tests* 10 | plotting_tests* 11 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2017 Razvan V. Chereji 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## plot2DO: Plot 2D Occupancies 2 | Micrococcal nuclease digestion followed by deep sequencing (MNase-seq) is the most used method to investigate nucleosome organization on a genome-wide scale. We present **plot2DO**, a flexible tool for evaluating the quality of MNase-seq and MNase-ChIP-seq data, and for visualizing the distribution of nucleosomes near the functional regions of the genome. Apart from MNase-seq data analysis, **plot2DO** was also used to investigate DNA fragments obtained in other types of experiments, such as ChIP-seq, ATAC-seq, and chemical cleavage mapping. In principle, **plot2DO** can be used to analyze the amount of DNA that is obtained from different regions of the genome, and the corresponding distribution of fragment sizes for each region, independent of the protocol that is used to generate the short DNA fragments. 3 | 4 | **plot2DO** is an open source package written in R, which can be used for computing and visualizing the two-dimensional (2D) occupancies of genomic data (e.g. MNase-seq, MNase-ChIP-seq, etc.). Instead of using the typical one-dimensional (1D) occupancy/coverage, obtained by stacking all the mapped reads regardless of their lengths, many times it is more informative to compute the relative occupancy given by DNA fragments of specific lengths in a matrix form. 5 | 6 | 7 | ## Download 8 | The easiest way to download this package is by using the GitHub interface (click the green **Clone or download** button). If you want to download the package from the terminal, then you need to install first a `git` client of your choice (follow the instructions from `http://git-scm.com/download`). After `git` has been installed, run the following command from the folder where you want to download the **plot2DO** package: 9 | ``` 10 | $ git clone https://github.com/rchereji/plot2DO.git 11 | ``` 12 | Note that it is important to put the provided `annotations` folder in the same main folder as the **plot2DO** script (*i.e.* the file `plot2DO.R` should be located outside of the `annotations` folder). 13 | 14 | In order to be able to run **plot2DO**, you will need to have R (version >= 3.5.0) installed on your computer, together with a few R packages. To install the R statistical computing environment, download the latest precompiled binary distributions from the following website: `http://cran.r-project.org`. To install all other dependencies, run the provided R script `plot2DO_setup.R`: 15 | ``` 16 | $ Rscript plot2DO_setup.R 17 | ``` 18 | 19 | The GNU `wget` package may be required (if the sequencing reads are provided in a BED-formatted file), and it is not installed by default in Windows and macOS, and should be downloaded and installed separately. The Windows binary executable file can be obtained from the following website: `https://www.gnu.org/software/wget/faq.html#download`. To install `wget` on a Mac computer, first install the Homebrew package manager (`https://brew.sh`), by running the following command in the terminal: 20 | ``` 21 | $ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" 22 | ``` 23 | After Homebrew has been installed, run the following command to install the `wget` package: 24 | ``` 25 | $ brew install wget 26 | ``` 27 | 28 | ## Usage 29 | After the R packages have been installed, you can execute **plot2DO** from a terminal. To list all the available options of **plot2DO**, run the following command: 30 | ``` 31 | $ Rscript plot2DO.R --help 32 | Usage: plot2DO.R [options] 33 | 34 | 35 | Options: 36 | -f FILE, --file=FILE 37 | Name of the file containing aligned sequencing data [options: BAM or BED file] 38 | 39 | -t TYPE, --type=TYPE 40 | Type of distribution to plot [options: occ, dyads, fivePrime_ends, threePrime_ends; default = occ] 41 | 42 | -g GENOME, --genome=GENOME 43 | Genome version 44 | [options: sacCer3 (default) (S. cerevisiae); EF2 (S. pombe); dm3, dm6 (D. melanogaster); 45 | ce10, ce11 (C. elegans); mm9, mm10 (M. musculus); 46 | hg18, hg19, hg38 (H. sapiens); tair10 (A. thaliana)] 47 | 48 | -r REFERENCE, --reference=REFERENCE 49 | Reference points to be aligned [options: TSS (default), TTS, Plus1] 50 | 51 | -s SITES, --sites=SITES 52 | User-provided sites to be aligned (BED file) 53 | 54 | -a ALIGN, --align=ALIGN 55 | Points of the provided intervals to be aligned? [options: center (default), fivePrime, threePrime] 56 | 57 | --siteLabel=SITELABEL 58 | Label for the aligned sites [default = Sites] 59 | 60 | -l MINLENGTH, --minLength=MINLENGTH 61 | The smallest DNA fragment to be considered [default = 50] 62 | 63 | -L MAXLENGTH, --maxLength=MAXLENGTH 64 | The largest DNA fragment to be considered [default = 200] 65 | 66 | -u UPSTREAM, --upstream=UPSTREAM 67 | Length of the upstream region to be plotted [default = 1000] 68 | 69 | -d DOWNSTREAM, --downstream=DOWNSTREAM 70 | Length of the downstream region to be plotted [default = 1000] 71 | 72 | -m COLORSCALEMAX, --colorScaleMax=COLORSCALEMAX 73 | Maximum value on the color scale (e.g. 0.02) 74 | 75 | --simplifyPlot=SIMPLIFYPLOT 76 | Simplify the plot (show only the 2D heat map) [options: on, off (default)] 77 | 78 | --squeezePlot=SQUEEZEPLOT 79 | Simplify the plot and squeeze the heat map [options: on, off (default)] 80 | 81 | -h, --help 82 | Show this help message and exit 83 | ``` 84 | 85 | Almost all arguments of **plot2DO** are optional. If an argument is not specified, it will take its default value, as indicated above. The only required argument for **plot2DO** is the name of the file that contains the aligned genomic data (in BAM or BED format), which is provided using the `-f/--file` argument. A minimal example, which generates the default 2D occupancy (2DO) plot (around TSS, all DNA fragments with the lengths between 50 - 200 bp, 2kb windows centered on TSS, yeast DNA), is given below: 86 | ``` 87 | $ Rscript plot2DO.R --file=yeast_SRR2045610.bam 88 | ``` 89 | where `yeast_SRR2045610.bam` is a test BAM file containing paired-end reads, which were aligned to the yeast genome. This command will generate Figure 1. 90 | 91 | |![](misc/Figure_3.png)| 92 | |:--:| 93 | | **Figure 1.** *The three panels that are generated by plot2DO: (1) 2D occupancy (2DO) plot (central heat map) indicating the relative coverage of the DNA fragments of specified lengths, at different locations relative to the reference points (transcription start sites (TSSs) in this case). The red color indicates a high coverage, while dark blue indicates zero coverage. (2) One-dimensional occupancy (top panel), generated by stacking DNA fragments of all lengths shown in the heat map. (3) Fragment length histogram (right panel) indicating the percentage corresponding to each DNA fragment size, from the whole sample of sequenced reads.* | 94 | 95 | By default, **plot2DO** aligns the TSSs, and plots the coverage obtained by stacking the footprints of the of the entire fragments that were sequenced (Fig. 1). One may want to plot the distribution of the DNA fragments at other locations from the genome (e.g. +1 nucleosomes), or to plot the distribution of the fragment centers (nucleosome dyads) instead of the coverage of the entire fragments. When multiple samples are compared, the color scale needs to be specified in a consistent way for all plots. These options are all possible using the following command line flags: 96 | ``` 97 | $ Rscript plot2DO.R --file=yeast_SRR2045610.bam --type=dyads --reference=Plus1 --type=dyads 98 | ``` 99 | This command will generate Figure 2. 100 | 101 | |![](misc/Figure_4.png)| 102 | |:--:| 103 | | **Figure 2.** *Distribution of nucleosome dyads near the typical positions of +1 nucleosomes. This special case of 2DO plot is also known as a V-plot* | 104 | 105 | Apart from the usual alignments, using the TSS, TTS or +1 nucleosomes as reference points, one can also align specific lists of reference points, provided in the form of a BED file. For convenience, we provide some of the yeast features that one may want to examine (tRNA genes, origins of replication, centromeres), and below are two examples of how one can use **plot2DO** to inspect a specific list of loci. 106 | ``` 107 | $ Rscript plot2DO.R --file=yeast_SRR2045610.bam --sites=annotations/Yeast_tRNA_genes.bed --align=fivePrime --siteLabel=tRNA --simplifyPlot=on 108 | $ Rscript plot2DO.R --file=yeast_SRR2045610.bam --sites=annotations/Yeast_centromeres.bed --align=threePrime --siteLabel=centromere --simplifyPlot=on 109 | 110 | ``` 111 | Notice that using the `--simplifyPlot=on` option, it is possible to plot only the 2DO panel without the panels showing the one-dimensional occupancy and the histogram of fragment lengths, and this makes it easier to combine multiple such panels in a single figure (Fig. 3). 112 | 113 | |![](misc/Figure_5.png)| 114 | |:--:| 115 | | **Figure 3.** *2D occupancy plots showing the distribution of sequencing data near the yeast (A) tRNA genes, aligned at their 5' ends, and (B) centromeres, aligned at their 3' ends.* | 116 | 117 | **plot2DO** can process sequencing data from multiple organisms, such as *Saccharomyces cerevisiae*, *Drosophila melanogaster*, *Caenorhabditis elegans*, *Mus musculus* and *Homo sapiens*. The following genome versions are available for these organisms: yeast — sacCer3; fly — dm3, dm6; worm — ce10, ce11; mouse — mm9, mm10; human — hg18, hg19, hg38. For the multicellular organisms the alignment of +1 nucleosomes is not possible, as the locations of these nucleosomes could vary from cell type to cell type, and these positions should be identified separately in each cell type. Here are a few examples of commands used to examine the distribution of reads at the TSSs of the aforementioned higher organisms: 118 | ``` 119 | $ Rscript plot2DO.R --file=fly_SRR2038265.bam -g dm3 -m 0.015 --simplifyPlot=on --minLength=100 --maxLength=200 120 | $ Rscript plot2DO.R --file=mouse_SRR572708.bam -g mm10 -m 0.015 --simplifyPlot=on --minLength=100 --maxLength=200 121 | $ Rscript plot2DO.R --file=human_SRR1781839.bam -g hg19 -m 0.015 --simplifyPlot=on --minLength=100 --maxLength=200 122 | ``` 123 | The figures resulted from these commands are shown in Figure 4. 124 | 125 | |![](misc/Figure_6.png)| 126 | |:--:| 127 | | **Figure 4.** *2D occupancy plots showing the degree of chromatin digestion and the distribution of sequencing data near the TSS in (A) fly, (B) mouse, and (C) human.* | 128 | 129 | If one wants to check only a small genomic region (e.g. +1 nucleosomes), the `--squeezePlot=on` option is very handy. Below are a few examples: 130 | ``` 131 | $ Rscript plot2DO.R -f yeast_50U_MNase_SRR3649301.bam -g sacCer3 -r Plus1 -m 0.03 -u 100 -d 100 --squeezePlot=on 132 | $ Rscript plot2DO.R -f yeast_100U_MNase_SRR3649296.bam -g sacCer3 -r Plus1 -m 0.03 -u 100 -d 100 --squeezePlot=on 133 | $ Rscript plot2DO.R -f yeast_200U_MNase_SRR3649297.bam -g sacCer3 -r Plus1 -m 0.03 -u 100 -d 100 --squeezePlot=on 134 | $ Rscript plot2DO.R -f yeast_300U_MNase_SRR3649298.bam -g sacCer3 -r Plus1 -m 0.03 -u 100 -d 100 --squeezePlot=on 135 | $ Rscript plot2DO.R -f yeast_400U_MNase_SRR3649299.bam -g sacCer3 -r Plus1 -m 0.03 -u 100 -d 100 --squeezePlot=on 136 | ``` 137 | The figures resulted from these commands are shown as panels in Figure 5. 138 | 139 | |![](misc/Figure_7.png)| 140 | |:--:| 141 | | **Figure 5.** *A titration of MNase produces different levels of chromatin digestion, and different sizes for the undigested fragments of DNA. Plus 1 nucleosomes are particularly sensitive to MNase, as they are located adjacent to the nucleosome free regions (the most accessible regions of the genome).* | 142 | 143 | 144 | ## Quality check of MNase-seq data 145 | **plot2DO** is very useful for inspecting the degree of digestion in MNase-seq and MNase-ChIP-seq experiments. Figure 6 shows three examples of 2DO plots that originate from an under-digested sample, a properly-digested sample, and an over-digested sample. 146 | 147 | |![](misc/Figure_8.png)| 148 | |:--:| 149 | | **Figure 6.** *Plot2DO offers a quick quality check for MNase-seq experiments. The left panel shows an under-digested MNase-seq sample: untrimmed linkers are still attached to nucleosomes (fragment length > 147 bp) and short fragments, protected by other proteins found in the promoters, are still not fully digested by MNase. The middle panel shows a properly digested MNase-seq sample: most of the undigested fragments originate from well trimmed nucleosome core particles, and have a length of about 147 bp. The right panel shows an over-digested MNase-seq sample: nucleosome core particles are invaded by MNase, and most of the undigested fragments have a length smaller than 147 bp.* | 150 | 151 | 152 | ## Data used in examples 153 | The data that were used in the examples above were downloaded from GEO database. The corresponding accession numbers are listed below: 154 | 155 | | Filename | GEO accession number for the raw data | 156 | | ------------- | ------------- | 157 | | yeast_SRR2045610.bam | [GSM1700669](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1700669) | 158 | | yeast_50U_MNase_SRR3649301.bam | [GSM2193286](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193286) | 159 | | yeast_100U_MNase_SRR3649296.bam | [GSM2193281](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193281) | 160 | | yeast_200U_MNase_SRR3649297.bam | [GSM2193282](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193282) | 161 | | yeast_300U_MNase_SRR3649298.bam | [GSM2193283](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193283) | 162 | | yeast_400U_MNase_SRR3649299.bam | [GSM2193284](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193284) | 163 | | fly_SRR2038265.bam | [GSM1694824](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1694824) | 164 | | mouse_SRR5116996.bam | [GSM2430825](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2430825) | 165 | | human_SRR1781839.bam | [GSM1425454](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1425454) | 166 | 167 | 168 | ## Extra functions 169 | Reasonable minimum (`--minLength`) and maximum (`--maxLength`) fragment sizes to be displayed in the 2D occupancy plot can be obtained by inspecting the histogram of all DNA fragment lengths that are present in the sample. This can be done using the additional function **computeLengthHistogram**. The available options are shown below: 170 | ``` 171 | $ Rscript computeLengthHistogram.R --help 172 | Usage: computeLengthHistogram.R [options] 173 | 174 | 175 | Options: 176 | -f FILES, --files=FILES 177 | Data file names, separated by commas only (BAM format) 178 | 179 | -l MINLENGTH, --minLength=MINLENGTH 180 | The smallest DNA fragment to be considered [default = 0] 181 | 182 | -L MAXLENGTH, --maxLength=MAXLENGTH 183 | The largest DNA fragment to be considered [default = 500] 184 | 185 | -s STATISTICS, --statistics=STATISTICS 186 | Include statistics in the plot [options: on, off; default = on] 187 | 188 | -o OUTPUTS, --outputs=OUTPUTS 189 | Types of outputs to be generated, separated by commas only [options: pdf, csv, RData; default = pdf,csv,RData] 190 | 191 | -h, --help 192 | Show this help message and exit 193 | ``` 194 | 195 | 196 | ## License 197 | **plot2DO** is freely available under the MIT License. 198 | 199 | 200 | ## Citation 201 | If you use this program in your research, please cite **plot2DO** as: 202 | Beati P., Chereji R.V. (2020) Creating 2D Occupancy Plots Using plot2DO. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY 203 | DOI: https://doi.org/10.1007/978-1-0716-0301-7_5 204 | -------------------------------------------------------------------------------- /annotations/Yeast_ARS_locations.bed: -------------------------------------------------------------------------------- 1 | chrI 650 1791 ARS102 0 . 2 | chrI 7997 8547 ARS103 0 . 3 | chrI 30946 31183 ARS104 0 . 4 | chrI 41808 42182 ARS105 0 . 5 | chrI 70257 70489 ARS106 0 . 6 | chrI 124349 124597 ARS107 0 . 7 | chrI 146701 147688 ARS108 0 . 8 | chrI 159907 160127 ARS109 0 . 9 | chrI 176157 176404 ARS110 0 . 10 | chrI 214888 215644 ARS111 0 . 11 | chrI 222880 224046 ARS112 0 . 12 | chrII 28942 29160 ARS230 0 . 13 | chrII 63193 63427 ARS202 0 . 14 | chrII 170088 170336 ARS207 0 . 15 | chrII 198232 198472 ARS231 0 . 16 | chrII 237684 237918 ARS208 0 . 17 | chrII 254206 255370 ARS209 0 . 18 | chrII 326140 326375 ARS211 0 . 19 | chrII 379221 379912 ARS212 0 . 20 | chrII 389212 390371 ARS213 0 . 21 | chrII 407876 408108 ARS214 0 . 22 | chrII 417784 418079 ARS215 0 . 23 | chrII 486707 486954 ARS216 0 . 24 | chrII 622671 622939 ARS220 0 . 25 | chrII 631939 632251 ARS221 0 . 26 | chrII 704296 704566 ARS222 0 . 27 | chrII 741558 741847 ARS224 0 . 28 | chrII 757437 757667 ARS225 0 . 29 | chrII 792164 792388 ARS228 0 . 30 | chrIII 838 1551 ARS300 0 . 31 | chrIII 11146 11401 ARS301 0 . 32 | chrIII 14575 14849 ARS302 0 . 33 | chrIII 14871 15213 ARS303 0 . 34 | chrIII 15214 16274 ARS320 0 . 35 | chrIII 30200 30657 ARS304 0 . 36 | chrIII 39159 39706 ARS305 0 . 37 | chrIII 74458 74677 ARS306 0 . 38 | chrIII 108780 109295 ARS307 0 . 39 | chrIII 114321 114939 ARS308 0 . 40 | chrIII 131985 132328 ARS309 0 . 41 | chrIII 166503 167348 ARS310 0 . 42 | chrIII 194265 194513 ARS313 0 . 43 | chrIII 197378 197609 ARS314 0 . 44 | chrIII 224816 225061 ARS315 0 . 45 | chrIII 272852 273095 ARS316 0 . 46 | chrIII 292388 292921 ARS317 0 . 47 | chrIII 294404 295034 ARS318 0 . 48 | chrIII 315354 316239 ARS319 0 . 49 | chrIV 137 1392 ARS400 0 . 50 | chrIV 15493 15739 ARS403 0 . 51 | chrIV 45918 46271 ARS404 0 . 52 | chrIV 85945 86176 ARS405 0 . 53 | chrIV 123617 123901 ARS406 0 . 54 | chrIV 212420 212668 ARS409 0 . 55 | chrIV 253791 254039 ARS410 0 . 56 | chrIV 256530 256633 ARS411 0 . 57 | chrIV 316388 316971 ARS412 0 . 58 | chrIV 329566 329814 ARS413 0 . 59 | chrIV 408075 408316 ARS414 0 . 60 | chrIV 434784 435989 ARS415 0 . 61 | chrIV 462354 463192 ARS416 0 . 62 | chrIV 483852 484096 ARS417 0 . 63 | chrIV 505343 505584 ARS450 0 . 64 | chrIV 555230 555466 ARS418 0 . 65 | chrIV 567496 567742 ARS419 0 . 66 | chrIV 628579 629921 ARS420 0 . 67 | chrIV 639867 640115 ARS421 0 . 68 | chrIV 702887 703132 ARS422 0 . 69 | chrIV 748392 748637 ARS451 0 . 70 | chrIV 753167 753398 ARS423 0 . 71 | chrIV 806052 806277 ARS425 0 . 72 | chrIV 899051 899596 ARS427 0 . 73 | chrIV 913790 914038 ARS428 0 . 74 | chrIV 921692 921939 ARS429 0 . 75 | chrIV 1016634 1016931 ARS430 0 . 76 | chrIV 1057838 1058085 ARS431 0 . 77 | chrIV 1109964 1110204 ARS452 0 . 78 | chrIV 1159262 1159510 ARS432 0 . 79 | chrIV 1166010 1166232 ARS453 0 . 80 | chrIV 1240882 1241110 ARS433 0 . 81 | chrIV 1276225 1276452 ARS434 0 . 82 | chrIV 1302592 1302831 ARS435 0 . 83 | chrIV 1305757 1306312 ARS436 0 . 84 | chrIV 1379641 1380100 ARS439 0 . 85 | chrIV 1404290 1404524 ARS440 0 . 86 | chrIV 1454509 1455087 ARS442 0 . 87 | chrIV 1461862 1462173 ARS443 0 . 88 | chrIV 1486918 1487161 ARS446 0 . 89 | chrIX 7470 8793 ARS902 0 . 90 | chrIX 16141 16784 ARS904 0 . 91 | chrIX 105822 106048 ARS909 0 . 92 | chrIX 113237 113806 ARS910 0 . 93 | chrIX 136098 136338 ARS911 0 . 94 | chrIX 175038 175358 ARS912 0 . 95 | chrIX 214679 214922 ARS913 0 . 96 | chrIX 245698 245935 ARS923 0 . 97 | chrIX 247583 247803 ARS914 0 . 98 | chrIX 248396 248850 ARS915 0 . 99 | chrIX 313861 314035 ARS918 0 . 100 | chrIX 341857 342099 ARS919 0 . 101 | chrIX 357160 357396 ARS920 0 . 102 | chrIX 362924 363221 ARS921 0 . 103 | chrIX 411821 412056 ARS922 0 . 104 | chrV 4097 4185 ARS502 0 . 105 | chrV 6464 7230 ARS503 0 . 106 | chrV 8786 10019 ARS504 0 . 107 | chrV 59283 59516 ARS507 0 . 108 | chrV 93978 94218 ARS508 0 . 109 | chrV 145541 145783 ARS510 0 . 110 | chrV 173638 173875 ARS511 0 . 111 | chrV 212383 212631 ARS512 0 . 112 | chrV 257958 258737 ARS513 0 . 113 | chrV 287507 287752 ARS514 0 . 114 | chrV 316600 316807 ARS515 0 . 115 | chrV 353509 353755 ARS516 0 . 116 | chrV 406752 406953 ARS517 0 . 117 | chrV 438934 439182 ARS518 0 . 118 | chrV 442416 442735 ARS519 0 . 119 | chrV 498422 499348 ARS520 0 . 120 | chrV 520772 521030 ARS521 0 . 121 | chrV 549566 549814 ARS522 0 . 122 | chrV 569025 570090 ARS523 0 . 123 | chrVI 5251 6155 ARS600 0 . 124 | chrVI 32473 32995 ARS601 0 . 125 | chrVI 32667 33247 ARS602 0 . 126 | chrVI 68693 68871 ARS603 0 . 127 | chrVI 118637 118957 ARS603.5 0 . 128 | chrVI 127751 128071 ARS604 0 . 129 | chrVI 135985 136085 ARS605 0 . 130 | chrVI 167614 168048 ARS606 0 . 131 | chrVI 199395 199505 ARS607 0 . 132 | chrVI 216357 216704 ARS608 0 . 133 | chrVI 256277 256431 ARS609 0 . 134 | chrVI 269417 270035 ARS610 0 . 135 | chrVII 64281 64529 ARS702 0 . 136 | chrVII 112079 112317 ARS704 0 . 137 | chrVII 117561 117854 ARS706 0 . 138 | chrVII 163177 163443 ARS707 0 . 139 | chrVII 187464 187796 ARS709 0 . 140 | chrVII 203914 204155 ARS710 0 . 141 | chrVII 231907 231981 ARS701 0 . 142 | chrVII 241085 241353 ARS712 0 . 143 | chrVII 285948 286242 ARS714 0 . 144 | chrVII 288451 288512 ARS715 0 . 145 | chrVII 352695 352916 ARS716 0 . 146 | chrVII 388658 388891 ARS717 0 . 147 | chrVII 421090 421338 ARS718 0 . 148 | chrVII 484930 485157 ARS719 0 . 149 | chrVII 508729 508977 ARS720 0 . 150 | chrVII 568490 568737 ARS721 0 . 151 | chrVII 574622 574915 ARS722 0 . 152 | chrVII 575484 576346 ARS723 0 . 153 | chrVII 581436 582213 ARS724 0 . 154 | chrVII 659809 660053 ARS727 0 . 155 | chrVII 715273 715555 ARS728 0 . 156 | chrVII 777966 778214 ARS729 0 . 157 | chrVII 834491 834734 ARS731 0 . 158 | chrVII 888349 888597 ARS737 0 . 159 | chrVII 977728 977976 ARS733 0 . 160 | chrVII 999447 999692 ARS734 0 . 161 | chrVII 1002239 1002522 ARS735 0 . 162 | chrVII 1083795 1084863 ARS736 0 . 163 | chrVIII 5471 6401 ARS801 0 . 164 | chrVIII 7536 7783 ARS802 0 . 165 | chrVIII 64259 64493 ARS805 0 . 166 | chrVIII 116179 116421 ARS806 0 . 167 | chrVIII 133357 133600 ARS807 0 . 168 | chrVIII 140349 141274 ARS808 0 . 169 | chrVIII 168541 168782 ARS809 0 . 170 | chrVIII 212720 213185 ARS810 0 . 171 | chrVIII 214718 215183 ARS811 0 . 172 | chrVIII 245719 245967 ARS813 0 . 173 | chrVIII 286770 287128 ARS814 0 . 174 | chrVIII 296447 297385 ARS815 0 . 175 | chrVIII 392148 392390 ARS818 0 . 176 | chrVIII 447622 447855 ARS820 0 . 177 | chrVIII 501756 501996 ARS822 0 . 178 | chrVIII 556001 556331 ARS824 0 . 179 | chrX 65 577 ARS1001 0 . 180 | chrX 7445 7943 ARS1002 0 . 181 | chrX 16124 16762 ARS1003 0 . 182 | chrX 23662 24158 ARS1004 0 . 183 | chrX 67469 67950 ARS1005 0 . 184 | chrX 99367 99803 ARS1006 0 . 185 | chrX 113233 113834 ARS1007 0 . 186 | chrX 204029 204917 ARS1008 0 . 187 | chrX 228552 229043 ARS1009 0 . 188 | chrX 298776 299256 ARS1010 0 . 189 | chrX 337281 337529 ARS1011 0 . 190 | chrX 374880 375122 ARS1012 0 . 191 | chrX 375706 376227 ARS1013 0 . 192 | chrX 417195 417440 ARS1014 0 . 193 | chrX 442556 442965 ARS1015 0 . 194 | chrX 454584 455555 ARS1016 0 . 195 | chrX 459337 459895 ARS1017 0 . 196 | chrX 540546 540780 ARS1018 0 . 197 | chrX 612846 613278 ARS1019 0 . 198 | chrX 654375 654614 ARS1020 0 . 199 | chrX 683634 684122 ARS1021 0 . 200 | chrX 711896 712142 ARS1022 0 . 201 | chrX 729983 730513 ARS1023 0 . 202 | chrX 737034 737275 ARS1024 0 . 203 | chrX 744408 745008 ARS1025 0 . 204 | chrXI 7528 8309 ARS1102 0 . 205 | chrXI 55671 55917 ARS1103 0 . 206 | chrXI 88789 89287 ARS1104 0 . 207 | chrXI 98329 98567 ARS1125 0 . 208 | chrXI 152934 153172 ARS1106 0 . 209 | chrXI 196042 196287 ARS1126 0 . 210 | chrXI 213439 213743 ARS1127 0 . 211 | chrXI 329682 329930 ARS1109 0 . 212 | chrXI 388970 389264 ARS1112 0 . 213 | chrXI 417185 417417 ARS1113 0 . 214 | chrXI 448020 448254 ARS1114 0 . 215 | chrXI 462699 463742 ARS1115 0 . 216 | chrXI 517017 517265 ARS1116 0 . 217 | chrXI 581833 582070 ARS1118 0 . 218 | chrXI 612241 612473 ARS1120 0 . 219 | chrXI 642727 642973 ARS1123 0 . 220 | chrXII 30209 31384 ARS1202 0 . 221 | chrXII 91419 91660 ARS1206 0 . 222 | chrXII 138185 139164 ARS1207 0 . 223 | chrXII 150947 151389 ARS1208 0 . 224 | chrXII 156648 156884 ARS1209 0 . 225 | chrXII 231179 231421 ARS1211 0 . 226 | chrXII 289220 289468 ARS1212 0 . 227 | chrXII 373156 373399 ARS1213 0 . 228 | chrXII 384534 384725 ARS1214 0 . 229 | chrXII 412668 412896 ARS1215 0 . 230 | chrXII 450485 450725 ARS1216 0 . 231 | chrXII 458991 459097 ARS1200-1 0 . 232 | chrXII 468128 468234 ARS1200-2 0 . 233 | chrXII 512867 513115 ARS1217 0 . 234 | chrXII 602939 603155 ARS1218 0 . 235 | chrXII 623198 623861 ARS1219 0 . 236 | chrXII 659824 660072 ARS1220 0 . 237 | chrXII 720784 721418 ARS1221 0 . 238 | chrXII 744943 745179 ARS1223 0 . 239 | chrXII 794021 794269 ARS1226 0 . 240 | chrXII 888570 888810 ARS1238 0 . 241 | chrXII 919800 920994 ARS1228 0 . 242 | chrXII 930891 931064 ARS1230 0 . 243 | chrXII 1007186 1007475 ARS1232 0 . 244 | chrXII 1013795 1014022 ARS1233 0 . 245 | chrXII 1023973 1024212 ARS1234 0 . 246 | chrXIII 31688 31935 ARS1303 0 . 247 | chrXIII 39824 40187 ARS1304 0 . 248 | chrXIII 94217 94463 ARS1305 0 . 249 | chrXIII 137300 137548 ARS1307 0 . 250 | chrXIII 183794 184037 ARS1308 0 . 251 | chrXIII 263063 263296 ARS1309 0 . 252 | chrXIII 286784 287068 ARS1310 0 . 253 | chrXIII 370978 371222 ARS1312 0 . 254 | chrXIII 468179 468469 ARS1316 0 . 255 | chrXIII 477606 478301 ARS1317 0 . 256 | chrXIII 503389 503771 ARS1319 0 . 257 | chrXIII 535597 535844 ARS1320 0 . 258 | chrXIII 542881 542978 ARS1321 0 . 259 | chrXIII 553422 554331 ARS1322 0 . 260 | chrXIII 611275 611489 ARS1323 0 . 261 | chrXIII 634481 634715 ARS1324 0 . 262 | chrXIII 649309 649552 ARS1325 0 . 263 | chrXIII 758224 758471 ARS1327 0 . 264 | chrXIII 772631 772879 ARS1328 0 . 265 | chrXIII 805117 805338 ARS1329 0 . 266 | chrXIII 815342 815567 ARS1330 0 . 267 | chrXIII 837764 837928 ARS1331 0 . 268 | chrXIII 897805 898040 ARS1332 0 . 269 | chrXIII 917896 918366 ARS1333 0 . 270 | chrXIII 923015 923494 ARS1335 0 . 271 | chrXIV 28469 28700 ARS1405 0 . 272 | chrXIV 61599 61895 ARS1406 0 . 273 | chrXIV 89531 89804 ARS1407 0 . 274 | chrXIV 96247 96463 ARS1409 0 . 275 | chrXIV 126599 126805 ARS1410 0 . 276 | chrXIV 169568 169805 ARS1411 0 . 277 | chrXIV 196057 196292 ARS1412 0 . 278 | chrXIV 250315 250931 ARS1413 0 . 279 | chrXIV 279880 280112 ARS1414 0 . 280 | chrXIV 321921 322213 ARS1415 0 . 281 | chrXIV 325054 325267 ARS1416 0 . 282 | chrXIV 412267 412496 ARS1417 0 . 283 | chrXIV 449347 449591 ARS1419 0 . 284 | chrXIV 498991 499235 ARS1420 0 . 285 | chrXIV 545971 546205 ARS1421 0 . 286 | chrXIV 561111 561388 ARS1422 0 . 287 | chrXIV 568219 568524 ARS1423 0 . 288 | chrXIV 609463 609710 ARS1424 0 . 289 | chrXIV 616311 617125 ARS1425 0 . 290 | chrXIV 635664 635904 ARS1426 0 . 291 | chrXIV 691486 691730 ARS1427 0 . 292 | chrXV 35669 35904 ARS1531 0 . 293 | chrXV 72638 72873 ARS1507 0 . 294 | chrXV 85197 85445 ARS1508 0 . 295 | chrXV 113845 114085 ARS1509 0 . 296 | chrXV 166976 167221 ARS1510 0 . 297 | chrXV 277530 277778 ARS1511 0 . 298 | chrXV 309359 309925 ARS1512 0 . 299 | chrXV 337280 337528 ARS1513 0 . 300 | chrXV 436574 437190 ARS1501 0 . 301 | chrXV 566410 566643 ARS1516 0 . 302 | chrXV 600886 600960 ARS1502 0 . 303 | chrXV 616670 617517 ARS1518 0 . 304 | chrXV 656633 656876 ARS1519 0 . 305 | chrXV 729740 729969 ARS1521 0 . 306 | chrXV 766618 766862 ARS1523 0 . 307 | chrXV 783345 783563 ARS1524 0 . 308 | chrXV 874194 874437 ARS1526 0 . 309 | chrXV 908296 908544 ARS1528 0 . 310 | chrXV 981462 981697 ARS1529 0 . 311 | chrXVI 18370 19069 ARS1603 0 . 312 | chrXVI 42977 43212 ARS1604 0 . 313 | chrXVI 73039 73283 ARS1605 0 . 314 | chrXVI 116506 116765 ARS1607 0 . 315 | chrXVI 162341 162632 ARS1608 0 . 316 | chrXVI 220088 220167 ARS1611 0 . 317 | chrXVI 260931 261727 ARS1612 0 . 318 | chrXVI 289485 289705 ARS1614 0 . 319 | chrXVI 331699 332100 ARS1617 0 . 320 | chrXVI 384542 384789 ARS1618 0 . 321 | chrXVI 418138 418364 ARS1619 0 . 322 | chrXVI 422786 422885 ARS1620 0 . 323 | chrXVI 456563 456810 ARS1633 0 . 324 | chrXVI 511624 511944 ARS1621 0 . 325 | chrXVI 563828 564066 ARS1622 0 . 326 | chrXVI 565052 565294 ARS1634 0 . 327 | chrXVI 633874 634122 ARS1623 0 . 328 | chrXVI 684389 684637 ARS1624 0 . 329 | chrXVI 695438 695686 ARS1625 0 . 330 | chrXVI 749099 749345 ARS1626 0 . 331 | chrXVI 776926 777156 ARS1635 0 . 332 | chrXVI 819160 819399 ARS1627 0 . 333 | chrXVI 842653 842900 ARS1628 0 . 334 | chrXVI 850512 850629 ARS1629 0 . 335 | chrXVI 880861 881108 ARS1630 0 . 336 | chrXVI 932983 933229 ARS1631 0 . 337 | chrXVI 942084 943032 ARS1632 0 . 338 | -------------------------------------------------------------------------------- /annotations/Yeast_centromeres.bed: -------------------------------------------------------------------------------- 1 | chrI 151465 151582 CEN1 0 + 2 | chrII 238207 238323 CEN2 0 + 3 | chrIII 114385 114501 CEN3 0 + 4 | chrIV 449711 449821 CEN4 0 + 5 | chrV 151987 152104 CEN5 0 + 6 | chrVI 148510 148627 CEN6 0 + 7 | chrVII 496920 497038 CEN7 0 - 8 | chrVIII 105586 105703 CEN8 0 - 9 | chrIX 355629 355745 CEN9 0 + 10 | chrX 436307 436425 CEN10 0 - 11 | chrXI 440129 440246 CEN11 0 - 12 | chrXII 150828 150947 CEN12 0 - 13 | chrXIII 268031 268149 CEN13 0 + 14 | chrXIV 628758 628875 CEN14 0 + 15 | chrXV 326584 326702 CEN15 0 - 16 | chrXVI 555957 556073 CEN16 0 + 17 | -------------------------------------------------------------------------------- /annotations/Yeast_other_features.bed: -------------------------------------------------------------------------------- 1 | chrI 130799 131983 CYS3 0 + 2 | chrI 1 801 TEL01L 0 - 3 | chrI 1 62 TEL01L-TR 0 - 4 | chrI 63 336 TEL01L-XR 0 - 5 | chrI 337 801 TEL01L-XC 0 - 6 | chrI 532 544 TEL01L-XC_binding_site 0 - 7 | chrI 650 1791 ARS102 0 . 8 | chrI 753 763 TEL01L-XC_nucleotide_match 0 - 9 | chrI 7997 8547 ARS103 0 . 10 | chrI 22230 22552 YALWdelta1 0 + 11 | chrI 24000 27968 FLO9 0 - 12 | chrI 30946 31183 ARS104 0 . 13 | chrI 41808 42182 ARS105 0 . 14 | chrI 65778 67520 CLN3 0 - 15 | chrI 70257 70489 ARS106 0 . 16 | chrI 87286 87752 YAL030W_mRNA 0 + 17 | chrI 99305 99868 HRA1 0 + 18 | chrI 99305 99868 HRA1 0 + 19 | chrI 100225 101145 MAK16 0 - 20 | chrI 124349 124597 ARS107 0 . 21 | chrI 138831 138992 YALCdelta2 0 - 22 | chrI 139152 139254 tP(UGG)A 0 + 23 | chrI 139152 139187 tP(UGG)A 0 + 24 | chrI 139219 139254 tP(UGG)A 0 + 25 | chrI 142174 143160 YAL003W_mRNA 0 + 26 | chrI 142367 142468 snR18 0 + 27 | chrI 142367 142468 snR18 0 + 28 | chrI 146701 147688 ARS108 0 . 29 | chrI 147594 151166 YAL001C_mRNA 0 - 30 | chrI 151465 151582 CEN1 0 + 31 | chrI 151465 151474 CEN1 0 + 32 | chrI 151475 151557 CEN1 0 + 33 | chrI 151558 151582 CEN1 0 + 34 | chrI 159907 160127 ARS109 0 . 35 | chrI 159935 159945 ARS109_nucleotide_match_1 0 - 36 | chrI 159952 159966 ARS109_nucleotide_match_2 0 + 37 | chrI 160105 160237 YARCdelta3 0 - 38 | chrI 160238 166162 YARCTy1-1 0 - 39 | chrI 160238 160574 YARCdelta4 0 - 40 | chrI 165826 166162 YARCdelta5 0 - 41 | chrI 166267 166339 tA(UGC)A 0 + 42 | chrI 166267 166339 tA(UGC)A 0 + 43 | chrI 169375 170295 ADE1 0 + 44 | chrI 176157 176404 ARS110 0 . 45 | chrI 181141 181254 tL(CAA)A 0 + 46 | chrI 181141 181178 tL(CAA)A 0 + 47 | chrI 181211 181254 tL(CAA)A 0 + 48 | chrI 182522 182603 tS(AGA)A 0 - 49 | chrI 182522 182603 tS(AGA)A 0 - 50 | chrI 182620 182959 YARWsigma1 0 + 51 | chrI 183142 183474 YARWdelta6 0 + 52 | chrI 189426 189757 YARWdelta7 0 + 53 | chrI 209448 209778 YARCdelta8 0 - 54 | chrI 214888 215644 ARS111 0 . 55 | chrI 222880 224046 ARS112 0 . 56 | chrI 225460 226863 PHO11 0 + 57 | chrI 229411 230218 TEL01R 0 + 58 | chrI 229411 229871 TEL01R-XC 0 + 59 | chrI 229451 229461 TEL01R-XC_nucleotide_match 0 + 60 | chrI 229670 229682 TEL01R-XC_binding_site 0 + 61 | chrI 230121 230218 TEL01R-TR 0 + 62 | chrM 731 802 tP(UGG)Q 0 + 63 | chrM 731 802 tP(UGG)Q 0 + 64 | chrM 6546 8194 15S_rRNA 0 + 65 | chrM 6546 8194 15S_rRNA 0 + 66 | chrM 9374 9447 tW(UCA)Q 0 + 67 | chrM 9374 9447 tW(UCA)Q 0 + 68 | chrM 13818 26701 Q0045_mRNA 0 + 69 | chrM 13818 26701 COX1 0 + 70 | chrM 13818 23167 Q0070_mRNA 0 + 71 | chrM 13818 21935 Q0065_mRNA 0 + 72 | chrM 13818 19996 Q0060_mRNA 0 + 73 | chrM 13818 18830 Q0055_mRNA 0 + 74 | chrM 24156 25255 Q0075_mRNA 0 + 75 | chrM 35373 35444 tE(UUC)Q 0 + 76 | chrM 35373 35444 tE(UUC)Q 0 + 77 | chrM 36540 43647 Q0105_mRNA 0 + 78 | chrM 36540 43647 COB 0 + 79 | chrM 36540 42251 Q0120_mRNA 0 + 80 | chrM 36540 40265 Q0115_mRNA 0 + 81 | chrM 36540 38579 Q0110_mRNA 0 + 82 | chrM 48201 48290 tS(UGA)Q2 0 + 83 | chrM 48201 48290 tS(UGA)Q2 0 + 84 | chrM 58009 62447 21S_rRNA 0 + 85 | chrM 58009 60724 21S_rRNA 0 + 86 | chrM 61868 62447 21S_rRNA 0 + 87 | chrM 63862 63937 tT(UGU)Q1 0 + 88 | chrM 63862 63937 tT(UGU)Q1 0 + 89 | chrM 64415 64490 tC(GCA)Q 0 + 90 | chrM 64415 64490 tC(GCA)Q 0 + 91 | chrM 64596 64670 tH(GUG)Q 0 + 92 | chrM 64596 64670 tH(GUG)Q 0 + 93 | chrM 66095 66179 tL(UAA)Q 0 + 94 | chrM 66095 66179 tL(UAA)Q 0 + 95 | chrM 66210 66285 tQ(UUG)Q 0 + 96 | chrM 66210 66285 tQ(UUG)Q 0 + 97 | chrM 67061 67134 tK(UUU)Q 0 + 98 | chrM 67061 67134 tK(UUU)Q 0 + 99 | chrM 67309 67381 tR(UCU)Q1 0 + 100 | chrM 67309 67381 tR(UCU)Q1 0 + 101 | chrM 67468 67542 tG(UCC)Q 0 + 102 | chrM 67468 67542 tG(UCC)Q 0 + 103 | chrM 68322 68396 tD(GUC)Q 0 + 104 | chrM 68322 68396 tD(GUC)Q 0 + 105 | chrM 69203 69288 tS(GCU)Q1 0 + 106 | chrM 69203 69288 tS(GCU)Q1 0 + 107 | chrM 69289 69362 tR(ACG)Q2 0 + 108 | chrM 69289 69362 tR(ACG)Q2 0 + 109 | chrM 69846 69921 tA(UGC)Q 0 + 110 | chrM 69846 69921 tA(UGC)Q 0 + 111 | chrM 70162 70237 tI(GAU)Q 0 + 112 | chrM 70162 70237 tI(GAU)Q 0 + 113 | chrM 70824 70907 tY(GUA)Q 0 + 114 | chrM 70824 70907 tY(GUA)Q 0 + 115 | chrM 71433 71503 tN(GUU)Q 0 + 116 | chrM 71433 71503 tN(GUU)Q 0 + 117 | chrM 72630 72705 tM(CAU)Q1 0 + 118 | chrM 72630 72705 tM(CAU)Q1 0 + 119 | chrM 73758 74513 COX2 0 + 120 | chrM 74495 75984 Q0255_mRNA 0 + 121 | chrM 77431 77505 tF(GAA)Q 0 + 122 | chrM 77431 77505 tF(GAA)Q 0 + 123 | chrM 78089 78162 tT(XXX)Q2 0 - 124 | chrM 78089 78162 tT(XXX)Q2 0 - 125 | chrM 78533 78608 tV(UAC)Q 0 + 126 | chrM 78533 78608 tV(UAC)Q 0 + 127 | chrM 85035 85112 tM(CAU)Q2 0 + 128 | chrM 85035 85112 tM(CAU)Q2 0 + 129 | chrM 85295 85777 RPM1 0 + 130 | chrM 85295 85777 RPM1 0 + 131 | chrV 1 6473 TEL05L 0 - 132 | chrV 1 6278 TEL05L-YP 0 - 133 | chrV 65 75 TEL05L-YP_nucleotide_match 0 + 134 | chrV 1468 2062 TEL05L-YP_repeat_region 0 + 135 | chrV 4097 4185 ARS502 0 . 136 | chrV 4185 5114 YEL076C-A_mRNA 0 - 137 | chrV 6279 6473 TEL05L-XC 0 - 138 | chrV 6425 6435 TEL05L-XC_nucleotide_match 0 - 139 | chrV 6464 7230 ARS503 0 . 140 | chrV 8786 10019 ARS504 0 . 141 | chrV 31694 33466 CAN1 0 - 142 | chrV 52150 52320 snR80 0 - 143 | chrV 52150 52320 snR80 0 - 144 | chrV 59283 59516 ARS507 0 . 145 | chrV 61352 61433 snR67 0 + 146 | chrV 61352 61433 snR67 0 + 147 | chrV 61699 61789 snR53 0 + 148 | chrV 61699 61789 snR53 0 + 149 | chrV 61890 61960 tG(GCC)E 0 - 150 | chrV 61890 61960 tG(GCC)E 0 - 151 | chrV 62081 62756 YELWdelta1 0 + 152 | chrV 62142 62474 YELWdelta2 0 + 153 | chrV 86604 86685 tS(AGA)E 0 + 154 | chrV 86604 86685 tS(AGA)E 0 + 155 | chrV 93978 94218 ARS508 0 . 156 | chrV 99490 99664 YELCdelta3 0 - 157 | chrV 100133 100204 tM(CAU)E 0 + 158 | chrV 100133 100204 tM(CAU)E 0 + 159 | chrV 100769 101251 CUP5 0 + 160 | chrV 117667 118035 RPR1 0 - 161 | chrV 117667 118035 RPR1 0 - 162 | chrV 118230 118551 YELCtau1 0 - 163 | chrV 131082 131153 tQ(UUG)E2 0 - 164 | chrV 131082 131153 tQ(UUG)E2 0 - 165 | chrV 131772 132551 YEL012W_mRNA 0 + 166 | chrV 135425 135497 tK(CUU)E1 0 - 167 | chrV 135425 135497 tK(CUU)E1 0 - 168 | chrV 135612 135939 YELCdelta4 0 - 169 | chrV 137324 137639 YELWdelta5 0 + 170 | chrV 138221 138553 YELWdelta6 0 + 171 | chrV 138666 138737 tR(UCU)E 0 + 172 | chrV 138666 138737 tR(UCU)E 0 + 173 | chrV 145541 145783 ARS510 0 . 174 | chrV 148176 148599 YEL003W_mRNA 0 + 175 | chrV 151987 152104 CEN5 0 + 176 | chrV 151987 151996 CEN5 0 + 177 | chrV 151997 152079 CEN5 0 + 178 | chrV 152080 152104 CEN5 0 + 179 | chrV 157736 159118 YER003C_mRNA 0 - 180 | chrV 166237 166885 YER007C-A_mRNA 0 - 181 | chrV 167427 167586 snR14 0 - 182 | chrV 167427 167586 snR14 0 - 183 | chrV 173638 173875 ARS511 0 . 184 | chrV 176705 176856 YERWdelta7 0 + 185 | chrV 177099 177170 tE(UUC)E1 0 + 186 | chrV 177099 177170 tE(UUC)E1 0 + 187 | chrV 183731 184700 YER014C-A_mRNA 0 - 188 | chrV 207357 207428 tH(GUG)E1 0 + 189 | chrV 207357 207428 tH(GUG)E1 0 + 190 | chrV 212383 212631 ARS512 0 . 191 | chrV 238460 239774 YER044C-A_mRNA 0 - 192 | chrV 249109 249331 YERCdelta8 0 - 193 | chrV 249445 249752 YERWdelta9 0 + 194 | chrV 249930 250270 YERCsigma1 0 - 195 | chrV 250286 250357 tQ(UUG)E1 0 + 196 | chrV 250286 250357 tQ(UUG)E1 0 + 197 | chrV 257958 258737 ARS513 0 . 198 | chrV 266512 268113 FCY2 0 - 199 | chrV 269423 270185 YER056C-A_mRNA 0 - 200 | chrV 287507 287752 ARS514 0 . 201 | chrV 287745 288062 YERCdelta10 0 - 202 | chrV 288443 288524 tS(UGA)E 0 - 203 | chrV 288443 288524 tS(UGA)E 0 - 204 | chrV 306323 307196 YER074W_mRNA 0 + 205 | chrV 307653 308123 YER074W-A_mRNA 0 + 206 | chrV 312023 312095 tA(UGC)E 0 - 207 | chrV 312023 312095 tA(UGC)E 0 - 208 | chrV 312274 312445 YERWdelta11 0 + 209 | chrV 316600 316807 ARS515 0 . 210 | chrV 322212 322762 SRG1 0 + 211 | chrV 322212 322762 SRG1 0 + 212 | chrV 339864 342167 MET6 0 - 213 | chrV 347912 348400 YER093C-A_mRNA 0 - 214 | chrV 353399 353735 YERWdelta12 0 + 215 | chrV 353509 353755 ARS516 0 . 216 | chrV 354136 354850 YERWdelta13 0 + 217 | chrV 354360 354730 YERCtau2 0 - 218 | chrV 354851 354917 YERCsigma2 0 - 219 | chrV 354934 355005 tE(UUC)E2 0 + 220 | chrV 354934 355005 tE(UUC)E2 0 + 221 | chrV 396769 397653 YER117W_mRNA 0 + 222 | chrV 406752 406953 ARS517 0 . 223 | chrV 424698 424883 snR4 0 + 224 | chrV 424698 424883 snR4 0 + 225 | chrV 431129 431220 snR52 0 - 226 | chrV 431129 431220 snR52 0 - 227 | chrV 431490 431822 YERCdelta14 0 - 228 | chrV 432495 433958 YER133W_mRNA 0 + 229 | chrV 434541 434612 tH(GUG)E2 0 - 230 | chrV 434541 434612 tH(GUG)E2 0 - 231 | chrV 434631 434971 YERCsigma3 0 - 232 | chrV 435128 435447 YERCdelta15 0 - 233 | chrV 435752 435824 tK(CUU)E2 0 - 234 | chrV 435752 435824 tK(CUU)E2 0 - 235 | chrV 435946 436277 YERCdelta16 0 - 236 | chrV 436279 436605 YERCtau3 0 - 237 | chrV 438700 438773 tV(AAC)E1 0 + 238 | chrV 438700 438773 tV(AAC)E1 0 + 239 | chrV 438934 439182 ARS518 0 . 240 | chrV 441987 442508 SCR1 0 + 241 | chrV 441987 442508 SCR1 0 + 242 | chrV 442416 442735 ARS519 0 . 243 | chrV 442734 443072 YERWdelta17 0 + 244 | chrV 443202 443275 tI(AAU)E1 0 - 245 | chrV 443202 443275 tI(AAU)E1 0 - 246 | chrV 443397 449320 YERCTy1-1 0 - 247 | chrV 443397 443733 YERCdelta19 0 - 248 | chrV 444834 445139 YERWdelta21 0 + 249 | chrV 447722 447722 YER138C 0 - 250 | chrV 448984 449320 YERCdelta20 0 - 251 | chrV 469457 469530 tV(AAC)E2 0 + 252 | chrV 469457 469530 tV(AAC)E2 0 + 253 | chrV 487331 487402 tE(UUC)E3 0 - 254 | chrV 487331 487402 tE(UUC)E3 0 - 255 | chrV 487834 488165 YERWdelta22 0 + 256 | chrV 492352 492424 tR(ACG)E 0 - 257 | chrV 492352 492424 tR(ACG)E 0 - 258 | chrV 492695 498421 YERCTy1-2 0 - 259 | chrV 492695 492833 YERCdelta23 0 - 260 | chrV 496822 496822 YER160C 0 - 261 | chrV 498084 498421 YERCdelta24 0 - 262 | chrV 498422 499348 ARS520 0 . 263 | chrV 520772 521030 ARS521 0 . 264 | chrV 527082 529418 RAD3 0 + 265 | chrV 548421 549517 YER179W_mRNA 0 + 266 | chrV 549566 549814 ARS522 0 . 267 | chrV 551285 551358 tI(AAU)E2 0 - 268 | chrV 551285 551358 tI(AAU)E2 0 - 269 | chrV 551442 551773 YERWdelta25 0 + 270 | chrV 552040 552267 YERCdelta26 0 - 271 | chrV 563928 564024 YERComega1 0 - 272 | chrV 568791 569024 YERWomega2 0 + 273 | chrV 569025 570090 ARS523 0 . 274 | chrV 569599 576874 TEL05R 0 + 275 | chrV 569599 570060 TEL05R-XC 0 + 276 | chrV 569637 569647 TEL05R-XC_nucleotide_match 0 + 277 | chrV 569856 569868 TEL05R-XC_binding_site 0 + 278 | chrV 570061 570329 TEL05R-XR 0 + 279 | chrV 570330 576874 TEL05R-YP 0 + 280 | chrV 574898 575324 TEL05R-YP_repeat_region 0 - 281 | chrV 576714 576724 TEL05R-YP_nucleotide_match 0 - 282 | chrX 1 7767 TEL10L 0 - 283 | chrX 1 60 TEL10L-TR 0 - 284 | chrX 61 6931 TEL10L-YP 0 - 285 | chrX 65 577 ARS1001 0 . 286 | chrX 271 281 TEL10L-YP_nucleotide_match 0 + 287 | chrX 466 6130 YJL225C_mRNA 0 - 288 | chrX 1667 2369 TEL10L-YP_repeat_region 0 + 289 | chrX 6932 7304 TEL10L-XR 0 - 290 | chrX 6998 7227 TEL10L-XR_insertion 0 - 291 | chrX 7305 7767 TEL10L-XC 0 - 292 | chrX 7445 7943 ARS1002 0 . 293 | chrX 7498 7510 TEL10L-XC_binding_site 0 - 294 | chrX 7719 7729 TEL10L-XC_nucleotide_match 0 - 295 | chrX 16124 16762 ARS1003 0 . 296 | chrX 23662 24158 ARS1004 0 . 297 | chrX 50139 50443 YJL205C_mRNA 0 - 298 | chrX 59100 59172 tT(AGU)J 0 - 299 | chrX 59100 59172 tT(AGU)J 0 - 300 | chrX 59505 59784 YJLWdelta1 0 + 301 | chrX 67469 67950 ARS1005 0 . 302 | chrX 73787 74611 YJL191W_mRNA 0 + 303 | chrX 75933 76474 YJL189W_mRNA 0 + 304 | chrX 90786 91657 YJL177W_mRNA 0 + 305 | chrX 99367 99803 ARS1006 0 . 306 | chrX 109966 111159 TPK1 0 - 307 | chrX 113233 113834 ARS1007 0 . 308 | chrX 115939 116010 tE(UUC)J 0 - 309 | chrX 115939 116010 tE(UUC)J 0 - 310 | chrX 139566 139691 snR128 0 - 311 | chrX 139566 139691 snR128 0 - 312 | chrX 139761 139950 snR190 0 - 313 | chrX 139761 139950 snR190 0 - 314 | chrX 156550 157273 YJL136C_mRNA 0 - 315 | chrX 197313 197385 tA(AGC)J 0 - 316 | chrX 197313 197385 tA(AGC)J 0 - 317 | chrX 197401 197494 YJLWsigma1 0 + 318 | chrX 197545 203768 YJLWTy4-1 0 + 319 | chrX 197545 197915 YJLWtau1 0 + 320 | chrX 198999 198999 YJL113W 0 + 321 | chrX 203398 203768 YJLWtau2 0 + 322 | chrX 203783 204114 YJLCdelta3 0 - 323 | chrX 204029 204917 ARS1008 0 . 324 | chrX 204735 204806 tD(GUC)J1 0 + 325 | chrX 204735 204806 tD(GUC)J1 0 + 326 | chrX 228094 228479 snR37 0 - 327 | chrX 228094 228479 snR37 0 - 328 | chrX 228552 229043 ARS1009 0 . 329 | chrX 233939 234011 tR(ACG)J 0 + 330 | chrX 233939 234011 tR(ACG)J 0 + 331 | chrX 268799 269815 ARG3 0 + 332 | chrX 298776 299256 ARS1010 0 . 333 | chrX 337281 337529 ARS1011 0 . 334 | chrX 349130 349233 snR60 0 - 335 | chrX 349130 349233 snR60 0 - 336 | chrX 354244 354332 tY(GUA)J1 0 + 337 | chrX 354244 354282 tY(GUA)J1 0 + 338 | chrX 354297 354332 tY(GUA)J1 0 + 339 | chrX 354538 355204 YJLCdelta4 0 - 340 | chrX 354844 355175 YJLCdelta5 0 - 341 | chrX 355374 355445 tR(UCU)J1 0 + 342 | chrX 355374 355445 tR(UCU)J1 0 + 343 | chrX 355456 355527 tD(GUC)J2 0 + 344 | chrX 355456 355527 tD(GUC)J2 0 + 345 | chrX 365784 368373 YJL041W_mRNA 0 + 346 | chrX 374424 374495 tD(GUC)J3 0 - 347 | chrX 374424 374495 tD(GUC)J3 0 - 348 | chrX 374506 374577 tR(UCU)J2 0 - 349 | chrX 374506 374577 tR(UCU)J2 0 - 350 | chrX 374844 374935 YJLCdelta6 0 - 351 | chrX 374880 375122 ARS1012 0 . 352 | chrX 375706 376227 ARS1013 0 . 353 | chrX 377598 377870 YJLCdelta7 0 - 354 | chrX 378360 378433 tV(AAC)J 0 + 355 | chrX 378360 378433 tV(AAC)J 0 + 356 | chrX 386368 387438 YJL031C_mRNA 0 - 357 | chrX 391043 391115 tM(CAU)J1 0 - 358 | chrX 391043 391115 tM(CAU)J1 0 - 359 | chrX 395931 396592 YJL024C_mRNA 0 - 360 | chrX 396726 396796 tG(GCC)J1 0 - 361 | chrX 396726 396796 tG(GCC)J1 0 - 362 | chrX 414966 415038 tK(CUU)J 0 + 363 | chrX 414966 415038 tK(CUU)J 0 + 364 | chrX 415931 416036 tW(CCA)J 0 - 365 | chrX 415931 415966 tW(CCA)J 0 - 366 | chrX 416001 416036 tW(CCA)J 0 - 367 | chrX 416266 416441 YJLWtau3 0 + 368 | chrX 416506 416650 YJLWdelta8 0 + 369 | chrX 416899 417026 YJLWdelta9 0 + 370 | chrX 417195 417440 ARS1014 0 . 371 | chrX 421946 422295 YJLWtau4 0 + 372 | chrX 422601 422887 YJLWdelta10 0 + 373 | chrX 422937 423009 tM(CAU)J2 0 + 374 | chrX 422937 423009 tM(CAU)J2 0 + 375 | chrX 424432 424515 tL(UAA)J 0 - 376 | chrX 424432 424515 tL(UAA)J 0 - 377 | chrX 425157 431237 CYR1 0 + 378 | chrX 435163 435926 YJL001W_mRNA 0 + 379 | chrX 436307 436425 CEN10 0 - 380 | chrX 436307 436331 CEN10 0 - 381 | chrX 436332 436415 CEN10 0 - 382 | chrX 436416 436425 CEN10 0 - 383 | chrX 442556 442965 ARS1015 0 . 384 | chrX 454584 455555 ARS1016 0 . 385 | chrX 459337 459895 ARS1017 0 . 386 | chrX 468555 469579 YJR021C_mRNA 0 - 387 | chrX 472463 478384 YJRWTy1-1 0 + 388 | chrX 472463 472800 YJRWdelta11 0 + 389 | chrX 474062 474062 YJR027W 0 + 390 | chrX 478051 483972 YJRWTy1-2 0 + 391 | chrX 478051 478384 YJRWdelta12 0 + 392 | chrX 479645 479645 YJR029W 0 + 393 | chrX 483635 483972 YJRWdelta13 0 + 394 | chrX 517813 517884 tM(CAU)J3 0 - 395 | chrX 517813 517884 tM(CAU)J3 0 - 396 | chrX 517959 518099 YJRWdelta14 0 + 397 | chrX 524012 524093 tS(AGA)J 0 - 398 | chrX 524012 524093 tS(AGA)J 0 - 399 | chrX 526335 526664 CYC1 0 + 400 | chrX 531516 531675 YJRCdelta15 0 - 401 | chrX 531828 531898 tG(GCC)J2 0 + 402 | chrX 531828 531898 tG(GCC)J2 0 + 403 | chrX 537741 538041 YJRCdelta16 0 - 404 | chrX 538103 538434 YJRWdelta17 0 + 405 | chrX 538555 538626 tR(CCU)J 0 + 406 | chrX 538555 538626 tR(CCU)J 0 + 407 | chrX 540546 540780 ARS1018 0 . 408 | chrX 540766 541087 YJRWdelta18 0 + 409 | chrX 541095 541427 YJRCdelta19 0 - 410 | chrX 541508 541579 tD(GUC)J4 0 + 411 | chrX 541508 541579 tD(GUC)J4 0 + 412 | chrX 542956 543044 tY(GUA)J2 0 - 413 | chrX 542956 542991 tY(GUA)J2 0 - 414 | chrX 543006 543044 tY(GUA)J2 0 - 415 | chrX 543448 543770 YJRWdelta20 0 + 416 | chrX 580205 581239 YJR079W_mRNA 0 + 417 | chrX 608305 608858 YJR094W-A_mRNA 0 + 418 | chrX 612846 613278 ARS1019 0 . 419 | chrX 617919 618019 tL(UAG)J 0 + 420 | chrX 617919 617956 tL(UAG)J 0 + 421 | chrX 617976 618019 tL(UAG)J 0 + 422 | chrX 637790 638168 YJR112W-A_mRNA 0 + 423 | chrX 654375 654614 ARS1020 0 . 424 | chrX 663749 663942 snR3 0 + 425 | chrX 663749 663942 snR3 0 + 426 | chrX 678957 683285 ECM17 0 - 427 | chrX 683634 684122 ARS1021 0 . 428 | chrX 702027 703068 YJR145C_mRNA 0 - 429 | chrX 711896 712142 ARS1022 0 . 430 | chrX 729983 730513 ARS1023 0 . 431 | chrX 737034 737275 ARS1024 0 . 432 | chrX 744408 745008 ARS1025 0 . 433 | chrX 744902 745751 TEL10R 0 + 434 | chrX 744902 745361 TEL10R-XC 0 + 435 | chrX 744940 744950 TEL10R-XC_nucleotide_match 0 + 436 | chrX 745159 745171 TEL10R-XC_binding_site 0 + 437 | chrX 745362 745662 TEL10R-XR 0 + 438 | chrX 745663 745751 TEL10R-TR 0 + 439 | chrII 259578 265494 YBRWTy1-2 0 + 440 | chrII 393123 394742 YBR078W_mRNA 0 + 441 | chrII 1 6608 TEL02L 0 - 442 | chrII 1 5848 TEL02L-YP 0 - 443 | chrII 81 91 TEL02L-YP_nucleotide_match 0 + 444 | chrII 1479 2414 TEL02L-YP_repeat_region 0 + 445 | chrII 2907 5009 YBL111C_mRNA 0 - 446 | chrII 5849 6138 TEL02L-XR 0 - 447 | chrII 6139 6608 TEL02L-XC 0 - 448 | chrII 6339 6351 TEL02L-XC_binding_site 0 - 449 | chrII 6560 6570 TEL02L-XC_nucleotide_match 0 - 450 | chrII 8848 9092 YBLWdelta1 0 + 451 | chrII 9093 9424 YBLWdelta2 0 + 452 | chrII 9425 9518 YBLWdelta3 0 + 453 | chrII 9583 9666 tL(UAA)B1 0 + 454 | chrII 9583 9666 tL(UAA)B1 0 + 455 | chrII 28942 29160 ARS230 0 . 456 | chrII 29644 35602 YBLWTy2-1 0 + 457 | chrII 29644 29975 YBLWdelta4 0 + 458 | chrII 31228 31228 YBL100W-B 0 + 459 | chrII 35271 35602 YBLWdelta5 0 + 460 | chrII 35604 35796 YBLWdelta6 0 + 461 | chrII 35851 36221 YBLCtau1 0 - 462 | chrII 36398 36488 tF(GAA)B 0 + 463 | chrII 36398 36434 tF(GAA)B 0 + 464 | chrII 36453 36488 tF(GAA)B 0 + 465 | chrII 46565 47180 YBL091C-A_mRNA 0 - 466 | chrII 59822 60739 YBL087C_mRNA 0 - 467 | chrII 63193 63427 ARS202 0 . 468 | chrII 81043 84261 ILS1 0 - 469 | chrII 88190 88277 snR56 0 + 470 | chrII 88190 88277 snR56 0 + 471 | chrII 110125 110539 YBL059C-A_mRNA 0 - 472 | chrII 110594 111244 YBL059W_mRNA 0 + 473 | chrII 125125 126119 YBL050W_mRNA 0 + 474 | chrII 142112 142868 YBL040C_mRNA 0 - 475 | chrII 168423 169376 YBL027W_mRNA 0 + 476 | chrII 170088 170336 ARS207 0 . 477 | chrII 170623 171038 YBL026W_mRNA 0 + 478 | chrII 174920 177526 MCM2 0 - 479 | chrII 185998 186474 YBL018C_mRNA 0 - 480 | chrII 197016 197320 YBLCdelta7 0 - 481 | chrII 197494 197567 tI(AAU)B 0 + 482 | chrII 197494 197567 tI(AAU)B 0 + 483 | chrII 197629 197699 tG(GCC)B 0 - 484 | chrII 197629 197699 tG(GCC)B 0 - 485 | chrII 197714 198054 YBLWsigma1 0 + 486 | chrII 198232 198472 ARS231 0 . 487 | chrII 220895 221036 YBLWdelta8 0 + 488 | chrII 221037 226952 YBLWTy1-1 0 + 489 | chrII 221037 221370 YBLWdelta9 0 + 490 | chrII 222635 222635 YBL005W-B 0 + 491 | chrII 226621 226952 YBLWdelta10 0 + 492 | chrII 227075 227156 tS(AGA)B 0 + 493 | chrII 227075 227156 tS(AGA)B 0 + 494 | chrII 237684 237918 ARS208 0 . 495 | chrII 238207 238323 CEN2 0 + 496 | chrII 238207 238216 CEN2 0 + 497 | chrII 238217 238298 CEN2 0 + 498 | chrII 238299 238323 CEN2 0 + 499 | chrII 254206 255370 ARS209 0 . 500 | chrII 258670 258976 YBRCdelta11 0 - 501 | chrII 259578 259909 YBRWdelta12 0 + 502 | chrII 261174 261174 YBR012W-B 0 + 503 | chrII 265163 265494 YBRWdelta13 0 + 504 | chrII 266178 266256 YBRCdelta14 0 - 505 | chrII 266378 266450 tT(AGU)B 0 + 506 | chrII 266378 266450 tT(AGU)B 0 + 507 | chrII 307185 307345 snR161 0 - 508 | chrII 307185 307345 snR161 0 - 509 | chrII 307587 308887 TLC1 0 + 510 | chrII 307587 308887 TLC1 0 + 511 | chrII 326140 326375 ARS211 0 . 512 | chrII 326792 326865 tV(UAC)B 0 - 513 | chrII 326792 326865 tV(UAC)B 0 - 514 | chrII 327069 327394 YBRWdelta15 0 + 515 | chrII 327390 327704 YBRWdelta16 0 + 516 | chrII 332831 333812 YBR048W_mRNA 0 + 517 | chrII 347603 347686 tL(UAA)B2 0 + 518 | chrII 347603 347686 tL(UAA)B2 0 + 519 | chrII 350459 350751 YBRWdelta17 0 + 520 | chrII 350827 350898 tQ(UUG)B 0 + 521 | chrII 350827 350898 tQ(UUG)B 0 + 522 | chrII 365976 366600 YBR062C_mRNA 0 - 523 | chrII 379221 379912 ARS212 0 . 524 | chrII 389212 390371 ARS213 0 . 525 | chrII 405878 405949 tR(UCU)B 0 + 526 | chrII 405878 405949 tR(UCU)B 0 + 527 | chrII 405960 406031 tD(GUC)B 0 + 528 | chrII 405960 406031 tD(GUC)B 0 + 529 | chrII 406628 407169 YBR082C_mRNA 0 - 530 | chrII 407876 408108 ARS214 0 . 531 | chrII 414186 415261 YBR084C-A_mRNA 0 - 532 | chrII 417784 418079 ARS215 0 . 533 | chrII 426333 427058 YBR090C_mRNA 0 - 534 | chrII 462139 462579 YBR111W-A_mRNA 0 + 535 | chrII 467248 469620 RAD16 0 + 536 | chrII 479338 480323 YBR119W_mRNA 0 + 537 | chrII 486707 486954 ARS216 0 . 538 | chrII 530869 532182 SUP45 0 - 539 | chrII 591712 592774 YBR181C_mRNA 0 - 540 | chrII 600553 602360 YBR186W_mRNA 0 + 541 | chrII 604508 605508 YBR189W_mRNA 0 + 542 | chrII 606270 607140 YBR191W_mRNA 0 + 543 | chrII 622671 622939 ARS220 0 . 544 | chrII 631939 632251 ARS221 0 . 545 | chrII 643007 643078 tC(GCA)B 0 - 546 | chrII 643007 643078 tC(GCA)B 0 - 547 | chrII 643488 643858 YBRCtau2 0 - 548 | chrII 643859 644002 YBRWdelta18 0 + 549 | chrII 644362 644603 YBRCdelta19 0 - 550 | chrII 645167 645238 tE(UUC)B 0 + 551 | chrII 645167 645238 tE(UUC)B 0 + 552 | chrII 650368 651192 MET8 0 + 553 | chrII 653356 655317 YBR215W_mRNA 0 + 554 | chrII 662499 663303 YBR219C_mRNA 0 - 555 | chrII 679549 680050 YBR230C_mRNA 0 - 556 | chrII 680688 681862 LSR1 0 - 557 | chrII 680688 681862 LSR1 0 - 558 | chrII 704296 704566 ARS222 0 . 559 | chrII 726618 727074 YBR255C-A_mRNA 0 - 560 | chrII 741558 741847 ARS224 0 . 561 | chrII 757437 757667 ARS225 0 . 562 | chrII 792164 792388 ARS228 0 . 563 | chrII 812379 813184 TEL02R 0 + 564 | chrII 812379 812848 TEL02R-XC 0 + 565 | chrII 812417 812427 TEL02R-XC_nucleotide_match 0 + 566 | chrII 812636 812648 TEL02R-XC_binding_site 0 + 567 | chrII 812849 813137 TEL02R-XR 0 + 568 | chrII 813138 813184 TEL02R-TR 0 + 569 | chrIV 1 904 TEL04L 0 - 570 | chrIV 1 154 TEL04L-TR 0 - 571 | chrIV 137 1392 ARS400 0 . 572 | chrIV 155 434 TEL04L-XR 0 - 573 | chrIV 435 904 TEL04L-XC 0 - 574 | chrIV 635 647 TEL04L-XC_binding_site 0 - 575 | chrIV 856 866 TEL04L-XC_nucleotide_match 0 - 576 | chrIV 15493 15739 ARS403 0 . 577 | chrIV 45918 46271 ARS404 0 . 578 | chrIV 46216 46226 ARS404_nucleotide_match 0 - 579 | chrIV 65242 65765 YDL219W_mRNA 0 + 580 | chrIV 83548 83618 tG(GCC)D1 0 + 581 | chrIV 83548 83618 tG(GCC)D1 0 + 582 | chrIV 85945 86176 ARS405 0 . 583 | chrIV 117664 118517 YDL191W_mRNA 0 + 584 | chrIV 123617 123901 ARS406 0 . 585 | chrIV 164987 167254 CDC9 0 - 586 | chrIV 212420 212668 ARS409 0 . 587 | chrIV 217600 218367 YDL136W_mRNA 0 + 588 | chrIV 229906 230527 YDL130W_mRNA 0 + 589 | chrIV 239019 239606 YDL125C_mRNA 0 - 590 | chrIV 253791 254039 ARS410 0 . 591 | chrIV 253995 255126 YDL115C_mRNA 0 - 592 | chrIV 256530 256633 ARS411 0 . 593 | chrIV 267698 268699 YDL108W_mRNA 0 + 594 | chrIV 276872 280165 CDC2 0 + 595 | chrIV 306926 307789 YDL083C_mRNA 0 - 596 | chrIV 308424 309388 YDL082W_mRNA 0 + 597 | chrIV 312951 314748 YDL079C_mRNA 0 - 598 | chrIV 316388 316971 ARS412 0 . 599 | chrIV 322226 322988 YDL075W_mRNA 0 + 600 | chrIV 323217 323471 snR63 0 - 601 | chrIV 323217 323471 snR63 0 - 602 | chrIV 329566 329814 ARS413 0 . 603 | chrIV 337487 338070 YDL064W_mRNA 0 + 604 | chrIV 359577 359672 tK(UUU)D 0 + 605 | chrIV 359577 359613 tK(UUU)D 0 + 606 | chrIV 359637 359672 tK(UUU)D 0 + 607 | chrIV 399340 400638 YDL029W_mRNA 0 + 608 | chrIV 408075 408316 ARS414 0 . 609 | chrIV 410379 410451 tA(AGC)D 0 + 610 | chrIV 410379 410451 tA(AGC)D 0 + 611 | chrIV 431108 431517 YDL012C_mRNA 0 - 612 | chrIV 434264 434336 tT(AGU)D 0 - 613 | chrIV 434264 434336 tT(AGU)D 0 - 614 | chrIV 434423 434739 YDLCdelta1 0 - 615 | chrIV 434784 435989 ARS415 0 . 616 | chrIV 437149 437518 YDLWtau1 0 + 617 | chrIV 437772 437853 tS(AGA)D1 0 + 618 | chrIV 437772 437853 tS(AGA)D1 0 + 619 | chrIV 449711 449821 CEN4 0 + 620 | chrIV 449711 449720 CEN4 0 + 621 | chrIV 449721 449796 CEN4 0 + 622 | chrIV 449797 449821 CEN4 0 + 623 | chrIV 456836 458103 YDR005C_mRNA 0 - 624 | chrIV 461842 462516 TRP1 0 + 625 | chrIV 462354 463192 ARS416 0 . 626 | chrIV 462596 462606 ARS416_nucleotide_match 0 - 627 | chrIV 483852 484096 ARS417 0 . 628 | chrIV 488797 488870 tV(UAC)D 0 - 629 | chrIV 488797 488870 tV(UAC)D 0 - 630 | chrIV 491515 492324 YDR025W_mRNA 0 + 631 | chrIV 505343 505584 ARS450 0 . 632 | chrIV 512986 513258 YDRCdelta2 0 - 633 | chrIV 513259 513590 YDRCdelta3 0 - 634 | chrIV 513692 519647 YDRCTy2-1 0 - 635 | chrIV 513692 514020 YDRCdelta4 0 - 636 | chrIV 518063 518063 YDR034C-D 0 - 637 | chrIV 519316 519647 YDRCdelta5 0 - 638 | chrIV 519743 519826 tL(UAA)D 0 + 639 | chrIV 519743 519826 tL(UAA)D 0 + 640 | chrIV 520173 520475 YDRCdelta6a 0 - 641 | chrIV 520477 520805 YDRWdelta7 0 + 642 | chrIV 520806 520833 YDRCdelta6b 0 - 643 | chrIV 520972 521043 tQ(UUG)D1 0 + 644 | chrIV 520972 521043 tQ(UUG)D1 0 + 645 | chrIV 541602 541700 snR47 0 - 646 | chrIV 541602 541700 snR47 0 - 647 | chrIV 555230 555466 ARS418 0 . 648 | chrIV 567496 567742 ARS419 0 . 649 | chrIV 568882 568953 tR(UCU)D 0 + 650 | chrIV 568882 568953 tR(UCU)D 0 + 651 | chrIV 568964 569035 tD(GUC)D 0 + 652 | chrIV 568964 569035 tD(GUC)D 0 + 653 | chrIV 569234 569770 YDR059C_mRNA 0 - 654 | chrIV 579458 580452 YDR064W_mRNA 0 + 655 | chrIV 619969 620041 tR(ACG)D 0 - 656 | chrIV 619969 620041 tR(ACG)D 0 - 657 | chrIV 628579 629921 ARS420 0 . 658 | chrIV 629876 630605 YDR092W_mRNA 0 + 659 | chrIV 639867 640115 ARS421 0 . 660 | chrIV 645153 645224 tQ(UUG)D2 0 - 661 | chrIV 645153 645224 tQ(UUG)D2 0 - 662 | chrIV 645502 651419 YDRCTy1-1 0 - 663 | chrIV 645502 645835 YDRCdelta7 0 - 664 | chrIV 649821 649821 YDR098C-B 0 - 665 | chrIV 651086 651419 YDRCdelta8 0 - 666 | chrIV 651420 651503 YDRCsigma1 0 - 667 | chrIV 651682 651980 YDRCdelta9 0 - 668 | chrIV 668007 668080 tI(AAU)D 0 - 669 | chrIV 668007 668080 tI(AAU)D 0 - 670 | chrIV 668096 668436 YDRWsigma2 0 + 671 | chrIV 668543 668784 YDRWdelta10 0 + 672 | chrIV 702887 703132 ARS422 0 . 673 | chrIV 713340 715379 YDR129C_mRNA 0 - 674 | chrIV 733618 733924 YDR139C_mRNA 0 - 675 | chrIV 748392 748637 ARS451 0 . 676 | chrIV 753167 753398 ARS423 0 . 677 | chrIV 802731 802802 tQ(UUG)D3 0 - 678 | chrIV 802731 802802 tQ(UUG)D3 0 - 679 | chrIV 802905 803235 YDRWdelta11 0 + 680 | chrIV 806052 806277 ARS425 0 . 681 | chrIV 871821 877779 YDRWTy2-2 0 + 682 | chrIV 871821 872152 YDRWdelta13 0 + 683 | chrIV 873405 873405 YDR210W-B 0 + 684 | chrIV 877448 877779 YDRWdelta14 0 + 685 | chrIV 878303 884220 YDRCTy1-2 0 - 686 | chrIV 882622 882622 YDR210C-D 0 - 687 | chrIV 884361 884493 tI(UAU)D 0 + 688 | chrIV 884361 884397 tI(UAU)D 0 + 689 | chrIV 884458 884493 tI(UAU)D 0 + 690 | chrIV 899051 899596 ARS427 0 . 691 | chrIV 913790 914038 ARS428 0 . 692 | chrIV 917571 921647 SIR4 0 + 693 | chrIV 921692 921939 ARS429 0 . 694 | chrIV 945351 945673 YDRWdelta12 0 + 695 | chrIV 945955 946295 YDRCsigma3 0 - 696 | chrIV 946312 946400 tY(GUA)D 0 + 697 | chrIV 946312 946350 tY(GUA)D 0 + 698 | chrIV 946365 946400 tY(GUA)D 0 + 699 | chrIV 980974 981055 tS(AGA)D2 0 - 700 | chrIV 980974 981055 tS(AGA)D2 0 - 701 | chrIV 981171 987125 YDRWTy2-3 0 + 702 | chrIV 981171 981502 YDRWdelta19 0 + 703 | chrIV 982755 982755 YDR261W-B 0 + 704 | chrIV 986794 987125 YDRWdelta20 0 + 705 | chrIV 987150 992642 YDRCTy1-3 0 - 706 | chrIV 987150 987483 YDRCdelta21 0 - 707 | chrIV 991044 991044 YDR261C-D 0 - 708 | chrIV 992309 992642 YDRCdelta22 0 - 709 | chrIV 992740 992815 YDRCsigma4 0 - 710 | chrIV 992832 992902 tG(GCC)D2 0 + 711 | chrIV 992832 992902 tG(GCC)D2 0 + 712 | chrIV 1016634 1016931 ARS430 0 . 713 | chrIV 1017207 1017278 tE(CUC)D 0 - 714 | chrIV 1017207 1017278 tE(CUC)D 0 - 715 | chrIV 1023137 1023477 YDRWsigma5 0 + 716 | chrIV 1057838 1058085 ARS431 0 . 717 | chrIV 1072746 1073488 YDR305C_mRNA 0 - 718 | chrIV 1075472 1075544 tV(CAC)D 0 - 719 | chrIV 1075472 1075544 tV(CAC)D 0 - 720 | chrIV 1095370 1095461 tF(GAA)D 0 - 721 | chrIV 1095370 1095405 tF(GAA)D 0 - 722 | chrIV 1095425 1095461 tF(GAA)D 0 - 723 | chrIV 1095767 1101692 YDRWTy1-4 0 + 724 | chrIV 1095767 1096104 YDRWdelta23 0 + 725 | chrIV 1097369 1097369 YDR316W-B 0 + 726 | chrIV 1101355 1101692 YDRWdelta24 0 + 727 | chrIV 1103758 1104947 YDR318W_mRNA 0 + 728 | chrIV 1109964 1110204 ARS452 0 . 729 | chrIV 1150842 1150941 tX(XXX)D 0 - 730 | chrIV 1150842 1150941 tX(XXX)D 0 - 731 | chrIV 1151039 1151368 YDRWdelta25 0 + 732 | chrIV 1159262 1159510 ARS432 0 . 733 | chrIV 1159447 1159461 ARS432_nucleotide_match 0 - 734 | chrIV 1166010 1166232 ARS453 0 . 735 | chrIV 1166167 1166181 ARS453_nucleotide_match 0 - 736 | chrIV 1175134 1175812 YDRCsigma6 0 - 737 | chrIV 1175316 1175647 YDRWdelta26 0 + 738 | chrIV 1175829 1175901 tM(CAU)D 0 + 739 | chrIV 1175829 1175901 tM(CAU)D 0 + 740 | chrIV 1201750 1201822 tK(CUU)D1 0 + 741 | chrIV 1201750 1201822 tK(CUU)D1 0 + 742 | chrIV 1206704 1212621 YDRWTy1-5 0 + 743 | chrIV 1206704 1207037 YDRWdelta27 0 + 744 | chrIV 1208302 1208302 YDR365W-B 0 + 745 | chrIV 1212288 1212621 YDRWdelta28 0 + 746 | chrIV 1212848 1213614 YDR367W_mRNA 0 + 747 | chrIV 1215016 1217580 XRS2 0 - 748 | chrIV 1236558 1238004 YDR381W_mRNA 0 + 749 | chrIV 1238312 1238850 YDR381C-A_mRNA 0 - 750 | chrIV 1240882 1241110 ARS433 0 . 751 | chrIV 1257008 1257079 tG(CCC)D 0 - 752 | chrIV 1257008 1257079 tG(CCC)D 0 - 753 | chrIV 1266366 1266898 YDR397C_mRNA 0 - 754 | chrIV 1276225 1276452 ARS434 0 . 755 | chrIV 1302592 1302831 ARS435 0 . 756 | chrIV 1305630 1305712 tS(AGA)D3 0 + 757 | chrIV 1305630 1305712 tS(AGA)D3 0 + 758 | chrIV 1305757 1306312 ARS436 0 . 759 | chrIV 1319387 1319841 YDR424C_mRNA 0 - 760 | chrIV 1352466 1352538 tK(CUU)D2 0 - 761 | chrIV 1352466 1352538 tK(CUU)D2 0 - 762 | chrIV 1352644 1352975 YDRWdelta29 0 + 763 | chrIV 1352976 1353226 YDRWdelta30 0 + 764 | chrIV 1354829 1355553 YDR447C_mRNA 0 - 765 | chrIV 1359923 1360798 YDR450W_mRNA 0 + 766 | chrIV 1379641 1380100 ARS439 0 . 767 | chrIV 1401770 1402564 YDR471W_mRNA 0 + 768 | chrIV 1402919 1403042 snR13 0 + 769 | chrIV 1402919 1403042 snR13 0 + 770 | chrIV 1404290 1404524 ARS440 0 . 771 | chrIV 1450198 1450853 YDR500C_mRNA 0 - 772 | chrIV 1454509 1455087 ARS442 0 . 773 | chrIV 1461715 1461829 tL(CAA)D 0 - 774 | chrIV 1461715 1461758 tL(CAA)D 0 - 775 | chrIV 1461792 1461829 tL(CAA)D 0 - 776 | chrIV 1461862 1462173 ARS443 0 . 777 | chrIV 1486918 1487161 ARS446 0 . 778 | chrIV 1492477 1493026 snR84 0 - 779 | chrIV 1492477 1493026 snR84 0 - 780 | chrIV 1506606 1507362 YDR535C_mRNA 0 - 781 | chrIV 1518484 1518807 YDRWdelta31 0 + 782 | chrIV 1524625 1531933 TEL04R 0 + 783 | chrIV 1524625 1525089 TEL04R-XC 0 + 784 | chrIV 1524663 1524673 TEL04R-XC_nucleotide_match 0 + 785 | chrIV 1524882 1524894 TEL04R-XC_binding_site 0 + 786 | chrIV 1525090 1525370 TEL04R-XR 0 + 787 | chrIV 1525371 1525466 TEL04R-TR 0 + 788 | chrIV 1525467 1531933 TEL04R-YP 0 + 789 | chrIV 1530081 1530507 TEL04R-YP_repeat_region 0 - 790 | chrIV 1531900 1531910 TEL04R-YP_nucleotide_match 0 - 791 | chrIX 1 7784 TEL09L 0 - 792 | chrIX 1 77 TEL09L-TR 0 - 793 | chrIX 78 6948 TEL09L-YP 0 - 794 | chrIX 288 298 TEL09L-YP_nucleotide_match 0 + 795 | chrIX 483 6147 YIL177C_mRNA 0 - 796 | chrIX 1684 2386 TEL09L-YP_repeat_region 0 + 797 | chrIX 6949 7321 TEL09L-XR 0 - 798 | chrIX 7015 7244 TEL09L-XR_insertion 0 - 799 | chrIX 7322 7784 TEL09L-XC 0 - 800 | chrIX 7470 8793 ARS902 0 . 801 | chrIX 7515 7527 TEL09L-XC_binding_site 0 - 802 | chrIX 7736 7746 TEL09L-XC_nucleotide_match 0 - 803 | chrIX 16141 16784 ARS904 0 . 804 | chrIX 37385 38983 SUC2 0 + 805 | chrIX 47690 47973 YIL156W-B_mRNA 0 + 806 | chrIX 68708 69528 YIL148W_mRNA 0 + 807 | chrIX 97111 97246 snR68 0 + 808 | chrIX 97111 97246 snR68 0 + 809 | chrIX 98527 99416 YIL133C_mRNA 0 - 810 | chrIX 105822 106048 ARS909 0 . 811 | chrIX 113237 113806 ARS910 0 . 812 | chrIX 136098 136338 ARS911 0 . 813 | chrIX 142928 144085 HIS5 0 + 814 | chrIX 155222 155765 YIL111W_mRNA 0 + 815 | chrIX 166415 167444 YIL106W_mRNA 0 + 816 | chrIX 175031 175103 tT(AGU)I1 0 + 817 | chrIX 175031 175103 tT(AGU)I1 0 + 818 | chrIX 175038 175358 ARS912 0 . 819 | chrIX 183440 183513 tI(AAU)I1 0 - 820 | chrIX 183440 183513 tI(AAU)I1 0 - 821 | chrIX 196653 197023 YILCtau1 0 - 822 | chrIX 197140 197488 YILCdelta1 0 - 823 | chrIX 197592 197663 tE(CUC)I 0 + 824 | chrIX 197592 197663 tE(CUC)I 0 + 825 | chrIX 205220 210647 YILWTy3-1 0 + 826 | chrIX 205220 205559 YILWsigma1 0 + 827 | chrIX 206486 206486 YIL082W-A 0 + 828 | chrIX 210308 210647 YILWsigma2 0 + 829 | chrIX 210665 210738 tI(AAU)I2 0 + 830 | chrIX 210665 210738 tI(AAU)I2 0 + 831 | chrIX 214679 214922 ARS913 0 . 832 | chrIX 222937 225954 YIL073C_mRNA 0 - 833 | chrIX 231553 232369 YIL069C_mRNA 0 - 834 | chrIX 245698 245935 ARS923 0 . 835 | chrIX 246220 246552 YILWdelta2 0 + 836 | chrIX 247583 247803 ARS914 0 . 837 | chrIX 248396 248850 ARS915 0 . 838 | chrIX 248850 248931 tS(UGA)I 0 + 839 | chrIX 248850 248931 tS(UGA)I 0 + 840 | chrIX 256226 257063 YIL052C_mRNA 0 - 841 | chrIX 290419 291669 BCY1 0 - 842 | chrIX 300228 300300 tK(CUU)I 0 - 843 | chrIX 300228 300300 tK(CUU)I 0 - 844 | chrIX 300409 300727 YILCdelta3 0 - 845 | chrIX 313861 314035 ARS918 0 . 846 | chrIX 316768 317932 YIL018W_mRNA 0 + 847 | chrIX 324303 324374 tD(GUC)I1 0 - 848 | chrIX 324303 324374 tD(GUC)I1 0 - 849 | chrIX 324391 324734 YILWsigma3 0 + 850 | chrIX 324831 325164 YILWdelta4 0 + 851 | chrIX 325748 325820 tT(AGU)I2 0 + 852 | chrIX 325748 325820 tT(AGU)I2 0 + 853 | chrIX 335666 336212 YIL009C-A_mRNA 0 - 854 | chrIX 335936 335936 YIL009C-A_mRNA 0 - 855 | chrIX 336349 336420 tD(GUC)I2 0 - 856 | chrIX 336349 336420 tD(GUC)I2 0 - 857 | chrIX 336708 336897 YILCdelta5 0 - 858 | chrIX 341857 342099 ARS919 0 . 859 | chrIX 347946 348505 YIL004C_mRNA 0 - 860 | chrIX 355629 355745 CEN9 0 + 861 | chrIX 355629 355638 CEN9 0 + 862 | chrIX 355639 355720 CEN9 0 + 863 | chrIX 355721 355745 CEN9 0 + 864 | chrIX 357160 357396 ARS920 0 . 865 | chrIX 362924 363221 ARS921 0 . 866 | chrIX 370417 370488 tE(UUC)I 0 + 867 | chrIX 370417 370488 tE(UUC)I 0 + 868 | chrIX 393884 397082 ICR1 0 - 869 | chrIX 393884 397082 ICR1 0 - 870 | chrIX 395999 396939 PWR1 0 + 871 | chrIX 395999 396939 PWR1 0 + 872 | chrIX 411821 412056 ARS922 0 . 873 | chrIX 419615 420736 LYS1 0 - 874 | chrIX 426201 426425 YIRCdelta6 0 - 875 | chrIX 439068 439888 TEL09R 0 + 876 | chrIX 439068 439533 TEL09R-XC 0 + 877 | chrIX 439106 439116 TEL09R-XC_nucleotide_match 0 + 878 | chrIX 439325 439337 TEL09R-XC_binding_site 0 + 879 | chrIX 439534 439815 TEL09R-XR 0 + 880 | chrIX 439816 439888 TEL09R-TR 0 + 881 | chrVI 131061 131503 RUF20 0 - 882 | chrVI 131061 131503 RUF20 0 - 883 | chrVI 1 5530 TEL06L 0 - 884 | chrVI 1 4684 TEL06L-YP 0 - 885 | chrVI 891 1269 TEL06L-YP_repeat_region 0 + 886 | chrVI 4685 4819 TEL06L-TR 0 - 887 | chrVI 4820 5067 TEL06L-XR 0 - 888 | chrVI 5068 5530 TEL06L-XC 0 - 889 | chrVI 5251 6155 ARS600 0 . 890 | chrVI 5261 5273 TEL06L-XC_binding_site 0 - 891 | chrVI 5482 5492 TEL06L-XC_nucleotide_match 0 - 892 | chrVI 5482 5492 ARS600_nucleotide_match 0 - 893 | chrVI 32473 32995 ARS601 0 . 894 | chrVI 32667 33247 ARS602 0 . 895 | chrVI 32708 32718 ARS601_nucleotide_match 0 + 896 | chrVI 32960 32970 ARS602_nucleotide_match 0 - 897 | chrVI 53260 54696 YFL039C_mRNA 0 - 898 | chrVI 55366 55986 YPT1 0 - 899 | chrVI 57815 58521 RUF21 0 - 900 | chrVI 57815 58521 RUF21 0 - 901 | chrVI 63016 63993 YFL034C-B_mRNA 0 - 902 | chrVI 64243 64932 YFL034C-A_mRNA 0 - 903 | chrVI 68693 68871 ARS603 0 . 904 | chrVI 68829 68839 ARS603_nucleotide_match_1 0 + 905 | chrVI 68845 68855 ARS603_nucleotide_match_2 0 - 906 | chrVI 75179 76147 YFL031W_mRNA 0 + 907 | chrVI 100581 100901 YFLWdelta1 0 + 908 | chrVI 101376 101478 tP(UGG)F 0 + 909 | chrVI 101376 101411 tP(UGG)F 0 + 910 | chrVI 101443 101478 tP(UGG)F 0 + 911 | chrVI 118637 118957 ARS603.5 0 . 912 | chrVI 118678 118688 ARS603.5_nucleotide_match 0 - 913 | chrVI 119429 123106 SMC1 0 + 914 | chrVI 127751 128071 ARS604 0 . 915 | chrVI 127869 127879 ARS604_nucleotide_match 0 + 916 | chrVI 135985 136085 ARS605 0 . 917 | chrVI 136037 136047 ARS605_nucleotide_match 0 - 918 | chrVI 137486 137559 tN(GUU)F 0 - 919 | chrVI 137486 137559 tN(GUU)F 0 - 920 | chrVI 137663 137912 YFLWdelta2 0 + 921 | chrVI 137913 143871 YFLWTy2-1 0 + 922 | chrVI 137913 138240 YFLWdelta3 0 + 923 | chrVI 139497 139497 YFL002W-A 0 + 924 | chrVI 143540 143871 YFLWdelta4 0 + 925 | chrVI 143872 143947 YFLWdelta5 0 + 926 | chrVI 144203 144523 YFLWtau1 0 + 927 | chrVI 144524 144822 YFLCdelta6 0 - 928 | chrVI 148510 148627 CEN6 0 + 929 | chrVI 148510 148519 CEN6 0 + 930 | chrVI 148520 148602 CEN6 0 + 931 | chrVI 148603 148627 CEN6 0 + 932 | chrVI 157916 158007 tF(GAA)F 0 - 933 | chrVI 157916 157951 tF(GAA)F 0 - 934 | chrVI 157971 158007 tF(GAA)F 0 - 935 | chrVI 158376 158686 YFRWdelta7 0 + 936 | chrVI 161804 162135 YFRCdelta8 0 - 937 | chrVI 162228 162298 tG(GCC)F1 0 + 938 | chrVI 162228 162298 tG(GCC)F1 0 + 939 | chrVI 167437 167525 tY(GUA)F1 0 + 940 | chrVI 167437 167475 tY(GUA)F1 0 + 941 | chrVI 167490 167525 tY(GUA)F1 0 + 942 | chrVI 167614 168048 ARS606 0 . 943 | chrVI 167726 167736 ARS606_nucleotide_match 0 - 944 | chrVI 180974 181044 tG(GCC)F2 0 - 945 | chrVI 180974 181044 tG(GCC)F2 0 - 946 | chrVI 191513 191613 tS(GCU)F 0 - 947 | chrVI 191513 191557 tS(GCU)F 0 - 948 | chrVI 191577 191613 tS(GCU)F 0 - 949 | chrVI 191685 191854 YFRCdelta9 0 - 950 | chrVI 199299 199813 RUF22 0 - 951 | chrVI 199299 199813 RUF22 0 - 952 | chrVI 199395 199505 ARS607 0 . 953 | chrVI 199416 199426 ARS607_nucleotide_match 0 + 954 | chrVI 201960 203433 YFR024C-A_mRNA 0 - 955 | chrVI 203743 204750 HIS2 0 - 956 | chrVI 204924 204996 tA(AGC)F 0 - 957 | chrVI 204924 204996 tA(AGC)F 0 - 958 | chrVI 206922 207138 YFRWdelta10 0 + 959 | chrVI 210619 210707 tY(GUA)F2 0 - 960 | chrVI 210619 210654 tY(GUA)F2 0 - 961 | chrVI 210669 210707 tY(GUA)F2 0 - 962 | chrVI 216357 216704 ARS608 0 . 963 | chrVI 216484 216494 ARS608_nucleotide_match 0 + 964 | chrVI 220507 221418 YFR031C-A_mRNA 0 - 965 | chrVI 221714 221967 RUF23 0 + 966 | chrVI 221714 221967 RUF23 0 + 967 | chrVI 226688 226760 tK(CUU)F 0 - 968 | chrVI 226688 226760 tK(CUU)F 0 - 969 | chrVI 241998 242999 YFR045W_mRNA 0 + 970 | chrVI 253592 255049 HXK1 0 - 971 | chrVI 256277 256431 ARS609 0 . 972 | chrVI 256375 256385 ARS609_nucleotide_match 0 - 973 | chrVI 269417 270035 ARS610 0 . 974 | chrVI 269731 270161 TEL06R 0 + 975 | chrVI 269731 270112 TEL06R-XC 0 + 976 | chrVI 269770 269780 TEL06R-XC_nucleotide_match 0 + 977 | chrVI 269989 270001 TEL06R-XC_binding_site 0 + 978 | chrVI 270113 270161 TEL06R-TR 0 + 979 | chrXI 1 807 TEL11L 0 - 980 | chrXI 1 67 TEL11L-TR 0 - 981 | chrXI 68 346 TEL11L-XR 0 - 982 | chrXI 347 807 TEL11L-XC 0 - 983 | chrXI 538 550 TEL11L-XC_binding_site 0 - 984 | chrXI 759 769 TEL11L-XC_nucleotide_match 0 - 985 | chrXI 7528 8309 ARS1102 0 . 986 | chrXI 25215 26159 URA1 0 + 987 | chrXI 38811 38911 snR64 0 + 988 | chrXI 38811 38911 snR64 0 + 989 | chrXI 46735 46806 tT(CGU)K 0 - 990 | chrXI 46735 46806 tT(CGU)K 0 - 991 | chrXI 55671 55917 ARS1103 0 . 992 | chrXI 74236 74518 YKLWdelta1 0 + 993 | chrXI 74624 74697 tN(GUU)K 0 + 994 | chrXI 74624 74697 tN(GUU)K 0 + 995 | chrXI 82947 83550 YKL190W_mRNA 0 + 996 | chrXI 83808 84115 YKLCdelta2 0 - 997 | chrXI 84208 84291 tL(UAA)K 0 + 998 | chrXI 84208 84291 tL(UAA)K 0 + 999 | chrXI 88789 89287 ARS1104 0 . 1000 | chrXI 98329 98567 ARS1125 0 . 1001 | chrXI 109269 110129 YKL180W_mRNA 0 + 1002 | chrXI 141018 141089 tE(UUC)K 0 - 1003 | chrXI 141018 141089 tE(UUC)K 0 - 1004 | chrXI 152934 153172 ARS1106 0 . 1005 | chrXI 154991 158232 YKL157W_mRNA 0 + 1006 | chrXI 154991 158232 APE2 0 + 1007 | chrXI 158613 159212 YKL156W_mRNA 0 + 1008 | chrXI 162487 162558 tR(UCU)K 0 - 1009 | chrXI 162487 162558 tR(UCU)K 0 - 1010 | chrXI 162831 163169 YKLWdelta3 0 + 1011 | chrXI 196042 196287 ARS1126 0 . 1012 | chrXI 202644 202983 YKLCsigma1 0 - 1013 | chrXI 202999 203071 tK(CUU)K 0 + 1014 | chrXI 202999 203071 tK(CUU)K 0 + 1015 | chrXI 213439 213743 ARS1127 0 . 1016 | chrXI 219395 219723 YKLCdelta4 0 - 1017 | chrXI 219895 219967 tA(AGC)K1 0 + 1018 | chrXI 219895 219967 tA(AGC)K1 0 + 1019 | chrXI 282891 284455 YKL081W_mRNA 0 + 1020 | chrXI 283185 283279 snR38 0 + 1021 | chrXI 283185 283279 snR38 0 + 1022 | chrXI 302334 302625 YKLCdelta5 0 - 1023 | chrXI 302918 303023 tW(CCA)K 0 + 1024 | chrXI 302918 302953 tW(CCA)K 0 + 1025 | chrXI 302988 303023 tW(CCA)K 0 + 1026 | chrXI 308144 308217 tV(AAC)K1 0 - 1027 | chrXI 308144 308217 tV(AAC)K1 0 - 1028 | chrXI 313401 313472 tH(GUG)K 0 - 1029 | chrXI 313401 313472 tH(GUG)K 0 - 1030 | chrXI 313602 313919 YKLCdelta6 0 - 1031 | chrXI 314193 314524 YKLWdelta7 0 + 1032 | chrXI 329682 329930 ARS1109 0 . 1033 | chrXI 347214 349136 ELM1 0 - 1034 | chrXI 364776 364876 snR69 0 + 1035 | chrXI 364776 364876 snR69 0 + 1036 | chrXI 379680 379753 tV(AAC)K2 0 + 1037 | chrXI 379680 379753 tV(AAC)K2 0 + 1038 | chrXI 388970 389264 ARS1112 0 . 1039 | chrXI 417185 417417 ARS1113 0 . 1040 | chrXI 430198 430632 YKL006C-A_mRNA 0 - 1041 | chrXI 431030 431138 snR87 0 - 1042 | chrXI 431030 431138 snR87 0 - 1043 | chrXI 431906 432720 YKL006W_mRNA 0 + 1044 | chrXI 437778 438544 YKL002W_mRNA 0 + 1045 | chrXI 440129 440246 CEN11 0 - 1046 | chrXI 440129 440153 CEN11 0 - 1047 | chrXI 440154 440236 CEN11 0 - 1048 | chrXI 440237 440246 CEN11 0 - 1049 | chrXI 440608 442722 VPS1 0 - 1050 | chrXI 446799 448036 YKR004C_mRNA 0 - 1051 | chrXI 448020 448254 ARS1114 0 . 1052 | chrXI 448521 450167 YKR005C_mRNA 0 - 1053 | chrXI 458140 458471 YKRCdelta8 0 - 1054 | chrXI 458557 458670 tL(CAA)K 0 + 1055 | chrXI 458557 458594 tL(CAA)K 0 + 1056 | chrXI 458627 458670 tL(CAA)K 0 + 1057 | chrXI 462699 463742 ARS1115 0 . 1058 | chrXI 490286 490416 YKRCdelta9 0 - 1059 | chrXI 490464 490787 YKRWdelta10 0 + 1060 | chrXI 490968 491040 tR(ACG)K 0 + 1061 | chrXI 490968 491040 tR(ACG)K 0 + 1062 | chrXI 513332 513403 tD(GUC)K 0 - 1063 | chrXI 513332 513403 tD(GUC)K 0 - 1064 | chrXI 513532 513846 YKRCdelta11 0 - 1065 | chrXI 517017 517265 ARS1116 0 . 1066 | chrXI 517453 517784 YKRCdelta12 0 - 1067 | chrXI 517988 518060 tA(AGC)K2 0 + 1068 | chrXI 517988 518060 tA(AGC)K2 0 + 1069 | chrXI 551657 552242 YKR057W_mRNA 0 + 1070 | chrXI 559016 559366 snR42 0 - 1071 | chrXI 559016 559366 snR42 0 - 1072 | chrXI 578965 579060 tK(UUU)K 0 + 1073 | chrXI 578965 579001 tK(UUU)K 0 + 1074 | chrXI 579025 579060 tK(UUU)K 0 + 1075 | chrXI 581833 582070 ARS1118 0 . 1076 | chrXI 612241 612473 ARS1120 0 . 1077 | chrXI 617996 618750 YKR094C_mRNA 0 - 1078 | chrXI 625864 626205 YKR095W-A_mRNA 0 + 1079 | chrXI 640540 642504 SIR1 0 + 1080 | chrXI 642727 642973 ARS1123 0 . 1081 | chrXI 665430 665668 YKRWomega1 0 + 1082 | chrXI 665904 666816 TEL11R 0 + 1083 | chrXI 665904 666364 TEL11R-XC 0 + 1084 | chrXI 665942 665952 TEL11R-XC_nucleotide_match 0 + 1085 | chrXI 666161 666173 TEL11R-XC_binding_site 0 + 1086 | chrXI 666365 666608 TEL11R-XR 0 + 1087 | chrXI 666609 666816 TEL11R-TR 0 + 1088 | chrXV 784857 786744 YOR239W_mRNA 0 + 1089 | chrXV 1 847 TEL15L 0 - 1090 | chrXV 1 117 TEL15L-TR 0 - 1091 | chrXV 118 388 TEL15L-XR 0 - 1092 | chrXV 389 847 TEL15L-XC 0 - 1093 | chrXV 579 591 TEL15L-XC_binding_site 0 - 1094 | chrXV 799 809 TEL15L-XC_nucleotide_match 0 - 1095 | chrXV 2894 3223 YOLCdelta1 0 - 1096 | chrXV 3809 3986 YOLWtau1 0 + 1097 | chrXV 18302 18561 YOLCdelta2 0 - 1098 | chrXV 25273 26976 HXT11 0 + 1099 | chrXV 35669 35904 ARS1531 0 . 1100 | chrXV 72638 72873 ARS1507 0 . 1101 | chrXV 80348 81190 YOL127W_mRNA 0 + 1102 | chrXV 85197 85445 ARS1508 0 . 1103 | chrXV 92026 92850 YOL121C_mRNA 0 - 1104 | chrXV 93395 94402 YOL120C_mRNA 0 - 1105 | chrXV 110962 111033 tG(UCC)O 0 - 1106 | chrXV 110962 111033 tG(UCC)O 0 - 1107 | chrXV 113294 113626 YOLCdelta3 0 - 1108 | chrXV 113802 113874 tT(AGU)O1 0 + 1109 | chrXV 113802 113874 tT(AGU)O1 0 + 1110 | chrXV 113845 114085 ARS1509 0 . 1111 | chrXV 117703 123628 YOLWTy1-1 0 + 1112 | chrXV 117703 118040 YOLWdelta4 0 + 1113 | chrXV 119305 119305 YOL103W-B 0 + 1114 | chrXV 123291 123628 YOLWdelta5 0 + 1115 | chrXV 136088 136183 snR58 0 - 1116 | chrXV 136088 136183 snR58 0 - 1117 | chrXV 166976 167221 ARS1510 0 . 1118 | chrXV 226611 226681 tG(GCC)O1 0 - 1119 | chrXV 226611 226681 tG(GCC)O1 0 - 1120 | chrXV 226696 227037 YOLWsigma1 0 + 1121 | chrXV 227096 227293 YOLWdelta6 0 + 1122 | chrXV 227851 228178 YOLCdelta7 0 - 1123 | chrXV 228331 228404 tN(GUU)O1 0 + 1124 | chrXV 228331 228404 tN(GUU)O1 0 + 1125 | chrXV 234346 234546 snR81 0 + 1126 | chrXV 234346 234546 snR81 0 + 1127 | chrXV 240204 241310 YOL048C_mRNA 0 - 1128 | chrXV 241614 242747 YOL047C_mRNA 0 - 1129 | chrXV 259489 259578 snR50 0 + 1130 | chrXV 259489 259578 snR50 0 + 1131 | chrXV 274673 274773 tS(GCU)O 0 + 1132 | chrXV 274673 274709 tS(GCU)O 0 + 1133 | chrXV 274729 274773 tS(GCU)O 0 + 1134 | chrXV 277530 277778 ARS1511 0 . 1135 | chrXV 282164 282234 tG(GCC)O2 0 + 1136 | chrXV 282164 282234 tG(GCC)O2 0 + 1137 | chrXV 288192 288280 tY(GUA)O 0 + 1138 | chrXV 288192 288230 tY(GUA)O 0 + 1139 | chrXV 288245 288280 tY(GUA)O 0 + 1140 | chrXV 300683 301021 YOLCdelta8 0 - 1141 | chrXV 301097 301198 tP(UGG)O1 0 + 1142 | chrXV 301097 301132 tP(UGG)O1 0 + 1143 | chrXV 301163 301198 tP(UGG)O1 0 + 1144 | chrXV 309359 309925 ARS1512 0 . 1145 | chrXV 313078 315387 TOP1 0 - 1146 | chrXV 326584 326702 CEN15 0 - 1147 | chrXV 326584 326608 CEN15 0 - 1148 | chrXV 326609 326692 CEN15 0 - 1149 | chrXV 326693 326702 CEN15 0 - 1150 | chrXV 337280 337528 ARS1513 0 . 1151 | chrXV 340299 340371 tR(ACG)O 0 - 1152 | chrXV 340299 340371 tR(ACG)O 0 - 1153 | chrXV 340598 340898 YORCdelta9 0 - 1154 | chrXV 354041 354113 tT(AGU)O2 0 - 1155 | chrXV 354041 354113 tT(AGU)O2 0 - 1156 | chrXV 354128 354466 YORWsigma2 0 + 1157 | chrXV 354681 354958 YORWdelta10 0 + 1158 | chrXV 407948 408134 snR9 0 - 1159 | chrXV 407948 408134 snR9 0 - 1160 | chrXV 409765 409864 snR62 0 - 1161 | chrXV 409765 409864 snR62 0 - 1162 | chrXV 436574 437190 ARS1501 0 . 1163 | chrXV 438175 438483 YORCdelta11 0 - 1164 | chrXV 438643 438738 tK(UUU)O 0 + 1165 | chrXV 438643 438679 tK(UUU)O 0 + 1166 | chrXV 438703 438738 tK(UUU)O 0 + 1167 | chrXV 464450 464551 tP(UGG)O2 0 + 1168 | chrXV 464450 464485 tP(UGG)O2 0 + 1169 | chrXV 464516 464551 tP(UGG)O2 0 + 1170 | chrXV 487439 487512 tN(GUU)O2 0 + 1171 | chrXV 487439 487512 tN(GUU)O2 0 + 1172 | chrXV 505794 506767 YOR096W_mRNA 0 + 1173 | chrXV 552298 552887 YOR122C_mRNA 0 - 1174 | chrXV 566410 566643 ARS1516 0 . 1175 | chrXV 571958 572029 tD(GUC)O 0 + 1176 | chrXV 571958 572029 tD(GUC)O 0 + 1177 | chrXV 594354 594425 tG(CCC)O 0 - 1178 | chrXV 594354 594425 tG(CCC)O 0 - 1179 | chrXV 594512 594819 YORWdelta12 0 + 1180 | chrXV 594820 600733 YORWTy1-2 0 + 1181 | chrXV 594820 595151 YORWdelta13 0 + 1182 | chrXV 596417 596417 YOR142W-B 0 + 1183 | chrXV 600402 600733 YORWdelta14 0 + 1184 | chrXV 600886 600960 ARS1502 0 . 1185 | chrXV 616670 617517 ARS1518 0 . 1186 | chrXV 656633 656876 ARS1519 0 . 1187 | chrXV 663812 663885 tV(AAC)O 0 - 1188 | chrXV 663812 663885 tV(AAC)O 0 - 1189 | chrXV 664003 664324 YORCdelta15 0 - 1190 | chrXV 664325 664469 YORWdelta16 0 + 1191 | chrXV 664813 665145 YORWdelta17 0 + 1192 | chrXV 678191 678793 YOR182C_mRNA 0 - 1193 | chrXV 680685 680866 snR36 0 - 1194 | chrXV 680685 680866 snR36 0 - 1195 | chrXV 703429 703582 YORCdelta18 0 - 1196 | chrXV 703612 703762 YORWdelta19 0 + 1197 | chrXV 703772 704062 YORWtau2 0 + 1198 | chrXV 704063 710023 YORCTy2-1 0 - 1199 | chrXV 704063 704395 YORCdelta20 0 - 1200 | chrXV 708439 708439 YOR192C-B 0 - 1201 | chrXV 709691 710023 YORCdelta21 0 - 1202 | chrXV 710024 710107 YORWtau3 0 + 1203 | chrXV 710201 710272 tM(CAU)O1 0 + 1204 | chrXV 710201 710272 tM(CAU)O1 0 + 1205 | chrXV 722911 724725 DED1 0 + 1206 | chrXV 729740 729969 ARS1521 0 . 1207 | chrXV 759326 759529 snR35 0 - 1208 | chrXV 759326 759529 snR35 0 - 1209 | chrXV 766618 766862 ARS1523 0 . 1210 | chrXV 778555 779405 YOR234C_mRNA 0 - 1211 | chrXV 780107 780596 snR17a 0 + 1212 | chrXV 780107 780120 snR17a 0 + 1213 | chrXV 780278 780596 snR17a 0 + 1214 | chrXV 783345 783563 ARS1524 0 . 1215 | chrXV 785688 785688 YOR239W_mRNA 0 + 1216 | chrXV 832332 832521 snR8 0 + 1217 | chrXV 832332 832521 snR8 0 + 1218 | chrXV 841958 842182 snR31 0 - 1219 | chrXV 841958 842182 snR31 0 - 1220 | chrXV 842403 842606 snR5 0 + 1221 | chrXV 842403 842606 snR5 0 + 1222 | chrXV 854187 854259 tA(UGC)O 0 - 1223 | chrXV 854187 854259 tA(UGC)O 0 - 1224 | chrXV 854275 854614 YORWsigma3 0 + 1225 | chrXV 867098 867852 YOR293W_mRNA 0 + 1226 | chrXV 874194 874437 ARS1526 0 . 1227 | chrXV 900250 901194 YOR312C_mRNA 0 - 1228 | chrXV 908296 908544 ARS1528 0 . 1229 | chrXV 911784 912436 YOR318C_mRNA 0 - 1230 | chrXV 921535 922905 PRO2 0 - 1231 | chrXV 968991 969301 YORWsigma4 0 + 1232 | chrXV 969293 969431 YORWdelta22 0 + 1233 | chrXV 970286 976244 YORWTy2-2 0 + 1234 | chrXV 970286 970617 YORWdelta23 0 + 1235 | chrXV 971872 971872 YOR343W-B 0 + 1236 | chrXV 975913 976244 YORWdelta24 0 + 1237 | chrXV 976421 976493 tM(CAU)O2 0 + 1238 | chrXV 976421 976493 tM(CAU)O2 0 + 1239 | chrXV 980259 980590 YORCdelta25 0 - 1240 | chrXV 980683 980787 tP(UGG)O3 0 + 1241 | chrXV 980683 980718 tP(UGG)O3 0 + 1242 | chrXV 980752 980787 tP(UGG)O3 0 + 1243 | chrXV 981462 981697 ARS1529 0 . 1244 | chrXV 1026843 1028048 RAD17 0 + 1245 | chrXV 1083922 1091291 TEL15R 0 + 1246 | chrXV 1083922 1084367 TEL15R-XC 0 + 1247 | chrXV 1083960 1083970 TEL15R-XC_nucleotide_match 0 + 1248 | chrXV 1084179 1084191 TEL15R-XC_binding_site 0 + 1249 | chrXV 1084368 1084620 TEL15R-XR 0 + 1250 | chrXV 1084621 1091273 TEL15R-YP 0 + 1251 | chrXV 1089233 1089659 TEL15R-YP_repeat_region 0 - 1252 | chrXV 1091052 1091062 TEL15R-YP_nucleotide_match 0 - 1253 | chrXV 1091274 1091291 TEL15R-TR 0 + 1254 | chrIII 1 360 TEL03L-TR 0 - 1255 | chrIII 1 1098 TEL03L 0 - 1256 | chrIII 361 639 TEL03L-XR 0 - 1257 | chrIII 640 1098 TEL03L-XC 0 - 1258 | chrIII 829 841 TEL03L-XC_binding_site 0 - 1259 | chrIII 838 1551 ARS300 0 . 1260 | chrIII 1050 1060 TEL03L-XC_nucleotide_match 0 - 1261 | chrIII 1050 1060 ARS300_nucleotide_match 0 - 1262 | chrIII 1179 4322 YCLWTy5-1 0 + 1263 | chrIII 1179 1429 YCLWomega1 0 + 1264 | chrIII 4073 4322 YCLWomega2 0 + 1265 | chrIII 11146 14849 HML 0 + 1266 | chrIII 11146 11401 ARS301 0 . 1267 | chrIII 11257 11267 ARS301_nucleotide_match 0 + 1268 | chrIII 11509 12238 HML_region 0 + 1269 | chrIII 12239 12943 HML_region_1 0 + 1270 | chrIII 12944 13690 HML_region_2 0 + 1271 | chrIII 13282 13809 HMLALPHA1 0 + 1272 | chrIII 13691 13929 HML_region_3 0 + 1273 | chrIII 13930 14017 HML_region_4 0 + 1274 | chrIII 14575 14849 ARS302 0 . 1275 | chrIII 14701 14711 ARS302_nucleotide_match 0 + 1276 | chrIII 14871 15213 ARS303 0 . 1277 | chrIII 15186 15196 ARS303_nucleotide_match 0 - 1278 | chrIII 15214 16274 ARS320 0 . 1279 | chrIII 15298 15308 ARS320_nucleotide_match 0 + 1280 | chrIII 30200 30657 ARS304 0 . 1281 | chrIII 30429 30439 ARS304_nucleotide_match 0 - 1282 | chrIII 39159 39706 ARS305 0 . 1283 | chrIII 39579 39589 ARS305_nucleotide_match 0 - 1284 | chrIII 74458 74677 ARS306 0 . 1285 | chrIII 74521 74531 ARS306_nucleotide_match 0 + 1286 | chrIII 82462 82533 tE(UUC)C 0 - 1287 | chrIII 82462 82533 tE(UUC)C 0 - 1288 | chrIII 82700 83036 YCLWdelta15 0 + 1289 | chrIII 83055 83194 YCLCdelta1 0 - 1290 | chrIII 84069 84294 YCLWdelta2a 0 + 1291 | chrIII 84295 84626 YCLWdelta3 0 + 1292 | chrIII 84630 84718 YCLWdelta2b 0 + 1293 | chrIII 84811 90769 YCLWTy2-1 0 + 1294 | chrIII 84811 85142 YCLWdelta4 0 + 1295 | chrIII 86392 86392 YCL019W 0 + 1296 | chrIII 90438 90769 YCLWdelta5 0 + 1297 | chrIII 90859 90972 tL(CAA)C 0 + 1298 | chrIII 90859 90896 tL(CAA)C 0 + 1299 | chrIII 90929 90972 tL(CAA)C 0 + 1300 | chrIII 101317 101788 YCL012C_mRNA 0 - 1301 | chrIII 107023 107417 YCL005W-A_mRNA 0 + 1302 | chrIII 107504 107712 snR43 0 - 1303 | chrIII 107504 107712 snR43 0 - 1304 | chrIII 108780 109295 ARS307 0 . 1305 | chrIII 108960 108970 ARS307_nucleotide_match 0 - 1306 | chrIII 110808 111675 YCL002C_mRNA 0 - 1307 | chrIII 114321 114939 ARS308 0 . 1308 | chrIII 114385 114501 CEN3 0 + 1309 | chrIII 114385 114394 CEN3 0 + 1310 | chrIII 114395 114476 CEN3 0 + 1311 | chrIII 114477 114501 CEN3 0 + 1312 | chrIII 123577 123648 tP(AGG)C 0 - 1313 | chrIII 123577 123648 tP(AGG)C 0 - 1314 | chrIII 124134 124465 YCRCdelta6 0 - 1315 | chrIII 127716 127789 tN(GUU)C 0 + 1316 | chrIII 127716 127789 tN(GUU)C 0 + 1317 | chrIII 131985 132328 ARS309 0 . 1318 | chrIII 132046 132056 ARS309_nucleotide_match 0 + 1319 | chrIII 142364 142546 snR33 0 - 1320 | chrIII 142364 142546 snR33 0 - 1321 | chrIII 142701 142771 tG(GCC)C 0 - 1322 | chrIII 142701 142771 tG(GCC)C 0 - 1323 | chrIII 142758 143080 YCRCdelta7 0 - 1324 | chrIII 149482 149809 YCRWdelta8 0 + 1325 | chrIII 149920 149991 tM(CAU)C 0 + 1326 | chrIII 149920 149991 tM(CAU)C 0 + 1327 | chrIII 150220 150551 YCRWdelta9 0 + 1328 | chrIII 150695 151055 YCRCtau1 0 - 1329 | chrIII 151284 151356 tK(CUU)C 0 - 1330 | chrIII 151284 151356 tK(CUU)C 0 - 1331 | chrIII 151521 151851 YCRWdelta10 0 + 1332 | chrIII 166503 167348 ARS310 0 . 1333 | chrIII 166663 166673 ARS310_nucleotide_match_1 0 + 1334 | chrIII 166700 166710 ARS310_nucleotide_match_2 0 - 1335 | chrIII 166756 166766 ARS310_nucleotide_match_3 0 - 1336 | chrIII 168301 168372 tQ(UUG)C 0 - 1337 | chrIII 168301 168372 tQ(UUG)C 0 - 1338 | chrIII 169573 169888 YCRWdelta11 0 + 1339 | chrIII 172950 173440 YCR028C-A_mRNA 0 - 1340 | chrIII 177183 177282 snR65 0 + 1341 | chrIII 177183 177282 snR65 0 + 1342 | chrIII 177500 178220 YCR031C_mRNA 0 - 1343 | chrIII 178610 178798 snR189 0 - 1344 | chrIII 178610 178798 snR189 0 - 1345 | chrIII 194265 194513 ARS313 0 . 1346 | chrIII 197378 197609 ARS314 0 . 1347 | chrIII 198671 201177 MATALPHA 0 + 1348 | chrIII 198671 199400 MATALPHA_region 0 + 1349 | chrIII 199401 200103 MATALPHA_region_1 0 + 1350 | chrIII 200104 200850 MATALPHA_region_2 0 + 1351 | chrIII 200442 200969 MATALPHA1 0 + 1352 | chrIII 200851 201089 MATALPHA_region_3 0 + 1353 | chrIII 201090 201177 MATALPHA_region_4 0 + 1354 | chrIII 224816 225061 ARS315 0 . 1355 | chrIII 227942 228042 tS(CGA)C 0 + 1356 | chrIII 227942 227978 tS(CGA)C 0 + 1357 | chrIII 227998 228042 tS(CGA)C 0 + 1358 | chrIII 272852 273095 ARS316 0 . 1359 | chrIII 291373 291712 YCRWdelta12 0 + 1360 | chrIII 291922 292167 YCRWomega3 0 + 1361 | chrIII 292388 295034 HMR 0 + 1362 | chrIII 292388 292921 ARS317 0 . 1363 | chrIII 292674 292684 ARS317_nucleotide_match 0 - 1364 | chrIII 293032 293736 HMR_region 0 + 1365 | chrIII 293737 294378 HMR_region_1 0 + 1366 | chrIII 293835 294321 YCR097W_mRNA 0 + 1367 | chrIII 293835 294321 HMRA1 0 + 1368 | chrIII 294379 294617 HMR_region_2 0 + 1369 | chrIII 294404 295034 ARS318 0 . 1370 | chrIII 294824 294834 ARS318_nucleotide_match 0 + 1371 | chrIII 295003 295330 YCRWdelta13 0 + 1372 | chrIII 295484 295556 tT(AGU)C 0 + 1373 | chrIII 295484 295556 tT(AGU)C 0 + 1374 | chrIII 295958 296190 YCRCdelta14 0 - 1375 | chrIII 315354 316239 ARS319 0 . 1376 | chrIII 315783 316620 TEL03R 0 + 1377 | chrIII 315783 316239 TEL03R-XC 0 + 1378 | chrIII 315821 315831 TEL03R-XC_nucleotide_match 0 + 1379 | chrIII 315821 315831 ARS319_nucleotide_match 0 + 1380 | chrIII 316040 316052 TEL03R-XC_binding_site 0 + 1381 | chrIII 316240 316521 TEL03R-XR 0 + 1382 | chrIII 316522 316620 TEL03R-TR 0 + 1383 | chrVII 1 781 TEL07L 0 - 1384 | chrVII 1 34 TEL07L-TR 0 - 1385 | chrVII 35 317 TEL07L-XR 0 - 1386 | chrVII 318 781 TEL07L-XC 0 - 1387 | chrVII 512 524 TEL07L-XC_binding_site 0 - 1388 | chrVII 733 743 TEL07L-XC_nucleotide_match 0 - 1389 | chrVII 838 1079 YGLWomega1 0 + 1390 | chrVII 15159 16307 ADH4 0 + 1391 | chrVII 27921 31636 YGL251C_mRNA 0 - 1392 | chrVII 62075 63002 YGL232W_mRNA 0 + 1393 | chrVII 64281 64529 ARS702 0 . 1394 | chrVII 64444 64458 ARS702_nucleotide_match 0 - 1395 | chrVII 72749 73158 YGL226C-A_mRNA 0 - 1396 | chrVII 73829 73902 tV(AAC)G3 0 - 1397 | chrVII 73829 73902 tV(AAC)G3 0 - 1398 | chrVII 110625 110696 tH(GUG)G1 0 - 1399 | chrVII 110625 110696 tH(GUG)G1 0 - 1400 | chrVII 110855 111225 YGLWtau1 0 + 1401 | chrVII 111226 111505 YGLCdelta1 0 - 1402 | chrVII 111506 111698 YGLWdelta2 0 + 1403 | chrVII 112079 112317 ARS704 0 . 1404 | chrVII 112125 112139 ARS704_nucleotide_match 0 + 1405 | chrVII 114939 115269 YGLWdelta3 0 + 1406 | chrVII 115488 115583 tK(UUU)G1 0 + 1407 | chrVII 115488 115524 tK(UUU)G1 0 + 1408 | chrVII 115548 115583 tK(UUU)G1 0 + 1409 | chrVII 117561 117854 ARS706 0 . 1410 | chrVII 122269 122341 tK(CUU)G1 0 + 1411 | chrVII 122269 122341 tK(CUU)G1 0 + 1412 | chrVII 156543 157285 YGL183C_mRNA 0 - 1413 | chrVII 163177 163443 ARS707 0 . 1414 | chrVII 163236 163250 ARS707_nucleotide_match 0 + 1415 | chrVII 167352 170571 YGL178W_mRNA 0 + 1416 | chrVII 185714 185786 tK(CUU)G2 0 - 1417 | chrVII 185714 185786 tK(CUU)G2 0 - 1418 | chrVII 187464 187796 ARS709 0 . 1419 | chrVII 191129 191806 CUP2 0 + 1420 | chrVII 203914 204155 ARS710 0 . 1421 | chrVII 203972 203986 ARS710_nucleotide_match 0 + 1422 | chrVII 204982 205337 YGLWtau2 0 + 1423 | chrVII 205521 205634 tL(CAA)G1 0 + 1424 | chrVII 205521 205558 tL(CAA)G1 0 + 1425 | chrVII 205591 205634 tL(CAA)G1 0 + 1426 | chrVII 231907 231981 ARS701 0 . 1427 | chrVII 241085 241353 ARS712 0 . 1428 | chrVII 249869 252738 YGL137W_mRNA 0 + 1429 | chrVII 285948 286242 ARS714 0 . 1430 | chrVII 286004 286018 ARS714_nucleotide_match 0 + 1431 | chrVII 287350 287455 tW(CCA)G1 0 - 1432 | chrVII 287350 287385 tW(CCA)G1 0 - 1433 | chrVII 287420 287455 tW(CCA)G1 0 - 1434 | chrVII 288451 288512 ARS715 0 . 1435 | chrVII 310967 311927 YGL103W_mRNA 0 + 1436 | chrVII 316788 317055 snR82 0 + 1437 | chrVII 316788 317055 snR82 0 + 1438 | chrVII 318697 318860 YGLWdelta4 0 + 1439 | chrVII 319009 319341 YGLCdelta5 0 - 1440 | chrVII 319423 319762 YGLCsigma1 0 - 1441 | chrVII 319781 319852 tH(GUG)G2 0 + 1442 | chrVII 319781 319852 tH(GUG)G2 0 + 1443 | chrVII 320355 320707 YGLCtau3 0 - 1444 | chrVII 327904 328224 YGLWdelta6 0 + 1445 | chrVII 328583 328654 tE(UUC)G1 0 + 1446 | chrVII 328583 328654 tE(UUC)G1 0 + 1447 | chrVII 345986 346230 snR10 0 + 1448 | chrVII 345986 346230 snR10 0 + 1449 | chrVII 346406 346904 YGL087C_mRNA 0 - 1450 | chrVII 352695 352916 ARS716 0 . 1451 | chrVII 364335 365996 YGL076C_mRNA 0 - 1452 | chrVII 365163 365251 snR39 0 - 1453 | chrVII 365163 365251 snR39 0 - 1454 | chrVII 366374 366469 snR39B 0 - 1455 | chrVII 366374 366469 snR39B 0 - 1456 | chrVII 388658 388891 ARS717 0 . 1457 | chrVII 388832 388846 ARS717_nucleotide_match 0 - 1458 | chrVII 401527 401598 tE(UUC)G2 0 - 1459 | chrVII 401527 401598 tE(UUC)G2 0 - 1460 | chrVII 401616 401894 YGLWsigma2 0 + 1461 | chrVII 401959 402290 YGLWdelta7 0 + 1462 | chrVII 405004 405145 YGLWdelta8 0 + 1463 | chrVII 405146 405207 YGLWdelta9 0 + 1464 | chrVII 405208 405453 YGLCsigma3 0 - 1465 | chrVII 405470 405541 tR(UCU)G1 0 + 1466 | chrVII 405470 405541 tR(UCU)G1 0 + 1467 | chrVII 412294 412367 tV(AAC)G1 0 - 1468 | chrVII 412294 412367 tV(AAC)G1 0 - 1469 | chrVII 412456 412725 YGLWdelta10 0 + 1470 | chrVII 421090 421338 ARS718 0 . 1471 | chrVII 421265 421279 ARS718_nucleotide_match 0 - 1472 | chrVII 423092 423205 tL(CAA)G2 0 + 1473 | chrVII 423092 423129 tL(CAA)G2 0 + 1474 | chrVII 423162 423205 tL(CAA)G2 0 + 1475 | chrVII 435625 436351 YGL033W_mRNA 0 + 1476 | chrVII 439091 439638 YGL030W_mRNA 0 + 1477 | chrVII 440716 440807 tF(GAA)G 0 - 1478 | chrVII 440716 440751 tF(GAA)G 0 - 1479 | chrVII 440771 440807 tF(GAA)G 0 - 1480 | chrVII 446412 448535 TRP5 0 - 1481 | chrVII 484930 485157 ARS719 0 . 1482 | chrVII 485096 485110 ARS719_nucleotide_match 0 - 1483 | chrVII 496920 497038 CEN7 0 - 1484 | chrVII 496920 496944 CEN7 0 - 1485 | chrVII 496945 497028 CEN7 0 - 1486 | chrVII 497029 497038 CEN7 0 - 1487 | chrVII 497133 498034 YGR001C_mRNA 0 - 1488 | chrVII 508729 508977 ARS720 0 . 1489 | chrVII 531610 531681 tD(GUC)G1 0 + 1490 | chrVII 531610 531681 tD(GUC)G1 0 + 1491 | chrVII 535211 535542 YGRWdelta11 0 + 1492 | chrVII 535607 535759 YGRCdelta12 0 - 1493 | chrVII 535760 541685 YGRWTy1-1 0 + 1494 | chrVII 535760 536097 YGRWdelta13 0 + 1495 | chrVII 537362 537362 YGR027W-B 0 + 1496 | chrVII 541348 541685 YGRWdelta14 0 + 1497 | chrVII 541850 541921 tE(UUC)G3 0 + 1498 | chrVII 541850 541921 tE(UUC)G3 0 + 1499 | chrVII 543553 544205 YGR029W_mRNA 0 + 1500 | chrVII 544577 544648 tD(GUC)G2 0 - 1501 | chrVII 544577 544648 tD(GUC)G2 0 - 1502 | chrVII 545370 545566 snR46 0 + 1503 | chrVII 545370 545566 snR46 0 + 1504 | chrVII 555812 556672 YGR034W_mRNA 0 + 1505 | chrVII 561662 561743 tS(AGA)G 0 - 1506 | chrVII 561662 561743 tS(AGA)G 0 - 1507 | chrVII 561843 567760 YGRCTy1-2 0 - 1508 | chrVII 561843 562176 YGRCdelta15 0 - 1509 | chrVII 566162 566162 YGR038C-B 0 - 1510 | chrVII 567427 567760 YGRCdelta16 0 - 1511 | chrVII 568490 568737 ARS721 0 . 1512 | chrVII 568646 568660 ARS721_nucleotide_match 0 - 1513 | chrVII 568740 574700 YGRCTy2-1 0 - 1514 | chrVII 568740 569072 YGRCdelta17 0 - 1515 | chrVII 574369 574700 YGRCdelta18 0 - 1516 | chrVII 574622 574915 ARS722 0 . 1517 | chrVII 575484 576346 ARS723 0 . 1518 | chrVII 581436 582213 ARS724 0 . 1519 | chrVII 609584 609696 snR48 0 + 1520 | chrVII 609584 609696 snR48 0 + 1521 | chrVII 644860 646815 GCD2 0 - 1522 | chrVII 659809 660053 ARS727 0 . 1523 | chrVII 659986 660000 ARS727_nucleotide_match 0 - 1524 | chrVII 661749 661820 tT(UGU)G1 0 + 1525 | chrVII 661749 661820 tT(UGU)G1 0 + 1526 | chrVII 700675 700756 tL(GAG)G 0 + 1527 | chrVII 700675 700756 tL(GAG)G 0 + 1528 | chrVII 700953 701048 tK(UUU)G2 0 - 1529 | chrVII 700953 700988 tK(UUU)G2 0 - 1530 | chrVII 701012 701048 tK(UUU)G2 0 - 1531 | chrVII 701104 701350 YGRWdelta19 0 + 1532 | chrVII 707108 707179 tC(GCA)G 0 - 1533 | chrVII 707108 707179 tC(GCA)G 0 - 1534 | chrVII 707195 712545 YGRWTy3-1 0 + 1535 | chrVII 707195 707534 YGRWsigma4 0 + 1536 | chrVII 708460 708460 YGR109W-B 0 + 1537 | chrVII 712206 712545 YGRWsigma5 0 + 1538 | chrVII 713084 713384 YGRCdelta20 0 - 1539 | chrVII 715273 715555 ARS728 0 . 1540 | chrVII 715315 715329 ARS728_nucleotide_match 0 + 1541 | chrVII 726974 727730 YGR118W_mRNA 0 + 1542 | chrVII 731137 731210 tN(GUU)G 0 + 1543 | chrVII 731137 731210 tN(GUU)G 0 + 1544 | chrVII 735542 735872 YGRWdelta21 0 + 1545 | chrVII 735982 736322 YGRWsigma6 0 + 1546 | chrVII 736340 736411 tR(UCU)G3 0 + 1547 | chrVII 736340 736411 tR(UCU)G3 0 + 1548 | chrVII 739122 739195 tI(AAU)G 0 + 1549 | chrVII 739122 739195 tI(AAU)G 0 + 1550 | chrVII 774040 774162 YGRWdelta22 0 + 1551 | chrVII 774349 774421 tA(AGC)G 0 + 1552 | chrVII 774349 774421 tA(AGC)G 0 + 1553 | chrVII 777966 778214 ARS729 0 . 1554 | chrVII 778014 778028 ARS729_nucleotide_match 0 + 1555 | chrVII 778784 779112 YGRWdelta23 0 + 1556 | chrVII 779116 779224 YGRWdelta24 0 + 1557 | chrVII 779225 779515 YGRCdelta25 0 - 1558 | chrVII 779616 779687 tG(UCC)G 0 + 1559 | chrVII 779616 779687 tG(UCC)G 0 + 1560 | chrVII 793237 793559 YGRWdelta26 0 + 1561 | chrVII 794417 794489 tA(UGC)G 0 + 1562 | chrVII 794417 794489 tA(UGC)G 0 + 1563 | chrVII 811447 817397 YGRWTy2-2 0 + 1564 | chrVII 811447 811778 YGRWdelta27 0 + 1565 | chrVII 813031 813031 YGR161W-B 0 + 1566 | chrVII 817074 817397 YGRWdelta28 0 + 1567 | chrVII 817393 823306 YGRCTy1-3 0 - 1568 | chrVII 817393 817724 YGRCdelta29 0 - 1569 | chrVII 821710 821710 YGR161C-D 0 - 1570 | chrVII 822975 823306 YGRCdelta30 0 - 1571 | chrVII 823482 823555 tV(AAC)G2 0 + 1572 | chrVII 823482 823555 tV(AAC)G2 0 + 1573 | chrVII 828723 828794 tR(UCU)G2 0 - 1574 | chrVII 828723 828794 tR(UCU)G2 0 - 1575 | chrVII 834491 834734 ARS731 0 . 1576 | chrVII 834650 834664 ARS731_nucleotide_match 0 - 1577 | chrVII 845281 845602 YGRWsigma7 0 + 1578 | chrVII 845649 845719 tG(GCC)G1 0 + 1579 | chrVII 845649 845719 tG(GCC)G1 0 + 1580 | chrVII 857378 857491 tL(CAA)G3 0 - 1581 | chrVII 857378 857421 tL(CAA)G3 0 - 1582 | chrVII 857454 857491 tL(CAA)G3 0 - 1583 | chrVII 859063 859476 YGR183C_mRNA 0 - 1584 | chrVII 875951 876279 YGRWdelta31 0 + 1585 | chrVII 876394 876466 tK(CUU)G3 0 + 1586 | chrVII 876394 876466 tK(CUU)G3 0 + 1587 | chrVII 878710 878815 tW(CCA)G2 0 - 1588 | chrVII 878710 878745 tW(CCA)G2 0 - 1589 | chrVII 878780 878815 tW(CCA)G2 0 - 1590 | chrVII 888349 888597 ARS737 0 . 1591 | chrVII 888413 888427 ARS737_nucleotide_match 0 + 1592 | chrVII 920575 921788 YGR214W_mRNA 0 + 1593 | chrVII 930953 931023 tG(GCC)G2 0 - 1594 | chrVII 930953 931023 tG(GCC)G2 0 - 1595 | chrVII 931171 931540 YGRCtau3 0 - 1596 | chrVII 931688 932019 YGRWdelta32 0 + 1597 | chrVII 939459 939672 snR7-L 0 - 1598 | chrVII 939459 939672 snR7-L 0 - 1599 | chrVII 939494 939672 snR7-S 0 - 1600 | chrVII 939494 939672 snR7-S 0 - 1601 | chrVII 945145 947019 YGR225W_mRNA 0 + 1602 | chrVII 970771 973734 PFK1 0 - 1603 | chrVII 977728 977976 ARS733 0 . 1604 | chrVII 977891 977905 ARS733_nucleotide_match 0 - 1605 | chrVII 999447 999692 ARS734 0 . 1606 | chrVII 1002239 1002522 ARS735 0 . 1607 | chrVII 1004216 1004287 tT(UGU)G2 0 + 1608 | chrVII 1004216 1004287 tT(UGU)G2 0 + 1609 | chrVII 1083635 1090940 TEL07R 0 + 1610 | chrVII 1083635 1084092 TEL07R-XC 0 + 1611 | chrVII 1083673 1083683 TEL07R-XC_nucleotide_match 0 + 1612 | chrVII 1083795 1084863 ARS736 0 . 1613 | chrVII 1083891 1083903 TEL07R-XC_binding_site 0 + 1614 | chrVII 1084093 1084346 TEL07R-XR 0 + 1615 | chrVII 1084347 1090940 TEL07R-YP 0 + 1616 | chrVII 1084864 1090591 YGR296W_mRNA 0 + 1617 | chrVII 1088964 1089390 TEL07R-YP_repeat_region 0 - 1618 | chrVII 1090780 1090790 TEL07R-YP_nucleotide_match 0 - 1619 | chrXII 650824 656743 YLRWTy1-3 0 + 1620 | chrXII 1 75 TEL12L-TR1 0 - 1621 | chrXII 1 12085 TEL12L 0 - 1622 | chrXII 76 5661 TEL12L-YP1 0 - 1623 | chrXII 284 294 TEL12L-YP1_nucleotide_match 0 + 1624 | chrXII 585 4301 YLL067C_mRNA 0 - 1625 | chrXII 1681 2215 TEL12L-YP1_repeat_region 0 + 1626 | chrXII 5662 5723 TEL12L-TR2 0 - 1627 | chrXII 5724 11196 TEL12L-YP2 0 - 1628 | chrXII 5921 5931 TEL12L-YP2_nucleotide_match 0 + 1629 | chrXII 6120 9836 YLL066C_mRNA 0 - 1630 | chrXII 7324 7750 TEL12L-YP2_repeat_region 0 + 1631 | chrXII 11197 11358 TEL12L-TR3 0 - 1632 | chrXII 11359 11625 TEL12L-XR 0 - 1633 | chrXII 11626 12085 TEL12L-XC 0 - 1634 | chrXII 11816 11828 TEL12L-XC_binding_site 0 - 1635 | chrXII 12037 12047 TEL12L-XC_nucleotide_match 0 - 1636 | chrXII 30209 31384 ARS1202 0 . 1637 | chrXII 39804 40414 YLL050C_mRNA 0 - 1638 | chrXII 91419 91660 ARS1206 0 . 1639 | chrXII 92050 92381 YLLCdelta1 0 - 1640 | chrXII 92548 92650 tP(UGG)L 0 + 1641 | chrXII 92548 92583 tP(UGG)L 0 + 1642 | chrXII 92615 92650 tP(UGG)L 0 + 1643 | chrXII 138185 139164 ARS1207 0 . 1644 | chrXII 150828 150947 CEN12 0 - 1645 | chrXII 150828 150852 CEN12 0 - 1646 | chrXII 150853 150937 CEN12 0 - 1647 | chrXII 150938 150947 CEN12 0 - 1648 | chrXII 150947 151389 ARS1208 0 . 1649 | chrXII 156648 156884 ARS1209 0 . 1650 | chrXII 167944 168025 tS(AGA)L 0 - 1651 | chrXII 167944 168025 tS(AGA)L 0 - 1652 | chrXII 168043 168380 YLRCsigma1 0 - 1653 | chrXII 198784 199389 snR30 0 + 1654 | chrXII 198784 199389 snR30 0 + 1655 | chrXII 214883 214955 tA(UGC)L 0 - 1656 | chrXII 214883 214955 tA(UGC)L 0 - 1657 | chrXII 215080 215417 YLRCdelta2 0 - 1658 | chrXII 220668 221005 YLRCdelta3 0 - 1659 | chrXII 221006 221266 YLRWdelta4 0 + 1660 | chrXII 231179 231421 ARS1211 0 . 1661 | chrXII 242232 243349 YLR048W_mRNA 0 + 1662 | chrXII 248717 250978 YLR054C_mRNA 0 - 1663 | chrXII 263194 263948 YLR061W_mRNA 0 + 1664 | chrXII 285736 286559 YLR078C_mRNA 0 - 1665 | chrXII 289220 289468 ARS1212 0 . 1666 | chrXII 326513 327415 YLR093C_mRNA 0 - 1667 | chrXII 348427 348510 snR79 0 - 1668 | chrXII 348427 348510 snR79 0 - 1669 | chrXII 365810 366144 YLRCdelta5 0 - 1670 | chrXII 366235 366346 snR6 0 + 1671 | chrXII 366235 366346 snR6 0 + 1672 | chrXII 373156 373399 ARS1213 0 . 1673 | chrXII 373999 374338 YLRWsigma2 0 + 1674 | chrXII 374355 374427 tR(ACG)L 0 + 1675 | chrXII 374355 374427 tR(ACG)L 0 + 1676 | chrXII 384534 384725 ARS1214 0 . 1677 | chrXII 398530 399433 YLR128W_mRNA 0 + 1678 | chrXII 412668 412896 ARS1215 0 . 1679 | chrXII 427132 427203 tD(GUC)L1 0 + 1680 | chrXII 427132 427203 tD(GUC)L1 0 + 1681 | chrXII 448650 448721 tQ(UUG)L 0 - 1682 | chrXII 448650 448721 tQ(UUG)L 0 - 1683 | chrXII 448842 449028 YLRWdelta6 0 + 1684 | chrXII 450485 450725 ARS1216 0 . 1685 | chrXII 451575 458432 RDN37-1 0 - 1686 | chrXII 451575 451785 RDN37-1 0 - 1687 | chrXII 451575 451785 ETS2-1 0 - 1688 | chrXII 451575 451785 ETS2-1 0 - 1689 | chrXII 451786 455181 RDN37-1 0 - 1690 | chrXII 451786 455181 RDN25-1 0 - 1691 | chrXII 451786 455181 RDN25-1 0 - 1692 | chrXII 455182 455413 RDN37-1 0 - 1693 | chrXII 455182 455413 ITS2-1 0 - 1694 | chrXII 455182 455413 ITS2-1 0 - 1695 | chrXII 455414 455571 RDN58-1 0 - 1696 | chrXII 455414 455571 RDN58-1 0 - 1697 | chrXII 455414 455571 RDN37-1 0 - 1698 | chrXII 455572 455932 RDN37-1 0 - 1699 | chrXII 455572 455932 ITS1-1 0 - 1700 | chrXII 455572 455932 ITS1-1 0 - 1701 | chrXII 455933 457732 RDN37-1 0 - 1702 | chrXII 455933 457732 RDN18-1 0 - 1703 | chrXII 455933 457732 RDN18-1 0 - 1704 | chrXII 457733 458432 RDN37-1 0 - 1705 | chrXII 457733 458432 ETS1-1 0 - 1706 | chrXII 457733 458432 ETS1-1 0 - 1707 | chrXII 458433 459675 NTS2-1 0 - 1708 | chrXII 458991 459097 ARS1200-1 0 . 1709 | chrXII 459078 459088 ARS1200-1_nucleotide_match 0 - 1710 | chrXII 459676 459796 RDN5-1 0 + 1711 | chrXII 459676 459796 RDN5-1 0 + 1712 | chrXII 459797 460711 NTS1-2 0 - 1713 | chrXII 460712 467569 RDN37-2 0 - 1714 | chrXII 460712 460922 RDN37-2 0 - 1715 | chrXII 460712 460922 ETS2-2 0 - 1716 | chrXII 460712 460922 ETS2-2 0 - 1717 | chrXII 460923 464318 RDN37-2 0 - 1718 | chrXII 460923 464318 RDN25-2 0 - 1719 | chrXII 460923 464318 RDN25-2 0 - 1720 | chrXII 464319 464550 RDN37-2 0 - 1721 | chrXII 464319 464550 ITS2-2 0 - 1722 | chrXII 464319 464550 ITS2-2 0 - 1723 | chrXII 464551 464708 RDN58-2 0 - 1724 | chrXII 464551 464708 RDN58-2 0 - 1725 | chrXII 464551 464708 RDN37-2 0 - 1726 | chrXII 464709 465069 RDN37-2 0 - 1727 | chrXII 464709 465069 ITS1-2 0 - 1728 | chrXII 464709 465069 ITS1-2 0 - 1729 | chrXII 465070 466869 RDN37-2 0 - 1730 | chrXII 465070 466869 RDN18-2 0 - 1731 | chrXII 465070 466869 RDN18-2 0 - 1732 | chrXII 466870 467569 RDN37-2 0 - 1733 | chrXII 466870 467569 ETS1-2 0 - 1734 | chrXII 466870 467569 ETS1-2 0 - 1735 | chrXII 467570 468812 NTS2-2 0 - 1736 | chrXII 468128 468234 ARS1200-2 0 . 1737 | chrXII 468215 468225 ARS1200-2_nucleotide_match 0 - 1738 | chrXII 468813 468931 RDN5-2 0 + 1739 | chrXII 468813 468931 RDN5-2 0 + 1740 | chrXII 472465 472583 RDN5-3 0 + 1741 | chrXII 472465 472583 RDN5-3 0 + 1742 | chrXII 475976 481897 YLRCTy1-1 0 - 1743 | chrXII 475976 476310 YLRCdelta7 0 - 1744 | chrXII 480296 480296 YLR157C-B 0 - 1745 | chrXII 481563 481897 YLRCdelta8 0 - 1746 | chrXII 482045 482163 RDN5-4 0 + 1747 | chrXII 482045 482163 RDN5-4 0 + 1748 | chrXII 485697 485815 RDN5-5 0 + 1749 | chrXII 485697 485815 RDN5-5 0 + 1750 | chrXII 489349 489469 RDN5-6 0 + 1751 | chrXII 489349 489469 RDN5-6 0 + 1752 | chrXII 512867 513115 ARS1217 0 . 1753 | chrXII 522663 523288 YLR185W_mRNA 0 + 1754 | chrXII 547853 548769 YLR199C_mRNA 0 - 1755 | chrXII 550194 550636 YLR202C_mRNA 0 - 1756 | chrXII 563792 564531 YLR211C_mRNA 0 - 1757 | chrXII 592519 592619 tL(UAG)L1 0 - 1758 | chrXII 592519 592562 tL(UAG)L1 0 - 1759 | chrXII 592582 592619 tL(UAG)L1 0 - 1760 | chrXII 592706 593035 YLRCdelta9 0 - 1761 | chrXII 593145 599062 YLRWTy1-2 0 + 1762 | chrXII 593145 593478 YLRWdelta10 0 + 1763 | chrXII 594743 594743 YLR227W-B 0 + 1764 | chrXII 598729 599062 YLRWdelta11 0 + 1765 | chrXII 599268 599544 YLRWdelta12 0 + 1766 | chrXII 599570 599844 YLRCtau1 0 - 1767 | chrXII 602939 603155 ARS1218 0 . 1768 | chrXII 605300 605432 tI(UAU)L 0 - 1769 | chrXII 605300 605335 tI(UAU)L 0 - 1770 | chrXII 605396 605432 tI(UAU)L 0 - 1771 | chrXII 623198 623861 ARS1219 0 . 1772 | chrXII 628383 628497 tL(CAA)L 0 + 1773 | chrXII 628383 628420 tL(CAA)L 0 + 1774 | chrXII 628454 628497 tL(CAA)L 0 + 1775 | chrXII 650824 651157 YLRWdelta13 0 + 1776 | chrXII 656410 656743 YLRWdelta14 0 + 1777 | chrXII 656934 657006 tA(AGC)L 0 - 1778 | chrXII 656934 657006 tA(AGC)L 0 - 1779 | chrXII 657022 657365 YLRWsigma3 0 + 1780 | chrXII 657449 657767 YLRWdelta15 0 + 1781 | chrXII 659824 660072 ARS1220 0 . 1782 | chrXII 687859 687932 tV(AAC)L 0 - 1783 | chrXII 687859 687932 tV(AAC)L 0 - 1784 | chrXII 688119 688368 YLRCdelta16 0 - 1785 | chrXII 688369 688664 YLRWdelta17 0 + 1786 | chrXII 694378 694800 YLR275W_mRNA 0 + 1787 | chrXII 712537 713158 YLR287C-A_mRNA 0 - 1788 | chrXII 720784 721418 ARS1221 0 . 1789 | chrXII 731668 732000 YLRCdelta18 0 - 1790 | chrXII 732090 732190 tL(UAG)L2 0 + 1791 | chrXII 732090 732127 tL(UAG)L2 0 + 1792 | chrXII 732147 732190 tL(UAG)L2 0 + 1793 | chrXII 734501 734671 YLRCdelta19 0 - 1794 | chrXII 734802 734875 tI(AAU)L1 0 + 1795 | chrXII 734802 734875 tI(AAU)L1 0 + 1796 | chrXII 744151 744851 YLR306W_mRNA 0 + 1797 | chrXII 744943 745179 ARS1223 0 . 1798 | chrXII 752224 756993 CDC25 0 - 1799 | chrXII 765266 766358 YLR316C_mRNA 0 - 1800 | chrXII 784354 784453 tS(GCU)L 0 + 1801 | chrXII 784354 784389 tS(GCU)L 0 + 1802 | chrXII 784410 784453 tS(GCU)L 0 + 1803 | chrXII 786442 787333 YLR329W_mRNA 0 + 1804 | chrXII 793552 793870 YLRWsigma4 0 + 1805 | chrXII 793918 793989 tD(GUC)L2 0 + 1806 | chrXII 793918 793989 tD(GUC)L2 0 + 1807 | chrXII 794021 794269 ARS1226 0 . 1808 | chrXII 794486 794575 snR61 0 - 1809 | chrXII 794486 794575 snR61 0 - 1810 | chrXII 794697 794794 snR55 0 - 1811 | chrXII 794697 794794 snR55 0 - 1812 | chrXII 794937 795024 snR57 0 - 1813 | chrXII 794937 795024 snR57 0 - 1814 | chrXII 796899 797088 YLRWdelta20 0 + 1815 | chrXII 797178 797249 tE(UUC)L 0 + 1816 | chrXII 797178 797249 tE(UUC)L 0 + 1817 | chrXII 818073 818403 YLRCdelta21 0 - 1818 | chrXII 818609 818680 tR(CCG)L 0 + 1819 | chrXII 818609 818680 tR(CCG)L 0 + 1820 | chrXII 819312 820142 YLR344W_mRNA 0 + 1821 | chrXII 855878 857317 YLR367W_mRNA 0 + 1822 | chrXII 856710 856920 snR44 0 + 1823 | chrXII 856710 856920 snR44 0 + 1824 | chrXII 875376 875471 tK(UUU)L 0 + 1825 | chrXII 875376 875412 tK(UUU)L 0 + 1826 | chrXII 875436 875471 tK(UUU)L 0 + 1827 | chrXII 888570 888810 ARS1238 0 . 1828 | chrXII 899180 899382 snR34 0 + 1829 | chrXII 899180 899382 snR34 0 + 1830 | chrXII 919800 920994 ARS1228 0 . 1831 | chrXII 930891 931064 ARS1230 0 . 1832 | chrXII 931065 931755 YLR406C_mRNA 0 - 1833 | chrXII 941192 947150 YLRWTy2-1 0 + 1834 | chrXII 941192 941523 YLRWdelta22 0 + 1835 | chrXII 942776 942776 YLR410W-B 0 + 1836 | chrXII 946819 947150 YLRWdelta23 0 + 1837 | chrXII 962972 963055 tL(UAA)L 0 - 1838 | chrXII 962972 963055 tL(UAA)L 0 - 1839 | chrXII 963230 963545 YLRWdelta24 0 + 1840 | chrXII 975983 976056 tN(GUU)L 0 - 1841 | chrXII 975983 976056 tN(GUU)L 0 - 1842 | chrXII 976258 981700 YLRCTy2-2 0 - 1843 | chrXII 976258 976589 YLRCdelta25 0 - 1844 | chrXII 981369 981700 YLRCdelta26 0 - 1845 | chrXII 987062 988113 YLR426W_mRNA 0 + 1846 | chrXII 1007186 1007475 ARS1232 0 . 1847 | chrXII 1013795 1014022 ARS1233 0 . 1848 | chrXII 1023973 1024212 ARS1234 0 . 1849 | chrXII 1024189 1024837 YLR445W_mRNA 0 + 1850 | chrXII 1028854 1029768 YLR448W_mRNA 0 + 1851 | chrXII 1036093 1038753 LEU3 0 + 1852 | chrXII 1052071 1052144 tI(AAU)L2 0 - 1853 | chrXII 1052071 1052144 tI(AAU)L2 0 - 1854 | chrXII 1052303 1052632 YLRCdelta27 0 - 1855 | chrXII 1064281 1078177 TEL12R 0 + 1856 | chrXII 1064281 1064747 TEL12R-XC 0 + 1857 | chrXII 1064319 1064329 TEL12R-XC_nucleotide_match 0 + 1858 | chrXII 1064538 1064550 TEL12R-XC_binding_site 0 + 1859 | chrXII 1064748 1065030 TEL12R-XR 0 + 1860 | chrXII 1065031 1065155 TEL12R-TR2 0 + 1861 | chrXII 1065156 1071645 TEL12R-YP2 0 + 1862 | chrXII 1066572 1067501 YLR464W_mRNA 0 + 1863 | chrXII 1069605 1070031 TEL12R-YP2_repeat_region 0 - 1864 | chrXII 1071424 1071434 TEL12R-YP2_nucleotide_match 0 - 1865 | chrXII 1071646 1071653 TEL12R-TR1 0 + 1866 | chrXII 1071654 1078177 TEL12R-YP1 0 + 1867 | chrXII 1076268 1076694 TEL12R-YP1_repeat_region 0 - 1868 | chrXII 1078087 1078097 TEL12R-YP1_nucleotide_match 0 - 1869 | chrXIV 519163 525062 YNLWTy1-2 0 + 1870 | chrXIV 1 7428 TEL14L 0 - 1871 | chrXIV 1 6617 TEL14L-YP 0 - 1872 | chrXIV 172 182 TEL14L-YP_nucleotide_match 0 + 1873 | chrXIV 371 6098 YNL339C_mRNA 0 - 1874 | chrXIV 1572 1998 TEL14L-YP_repeat_region 0 + 1875 | chrXIV 6618 6691 TEL14L-TR 0 - 1876 | chrXIV 6692 6963 TEL14L-XR 0 - 1877 | chrXIV 6964 7428 TEL14L-XC 0 - 1878 | chrXIV 7159 7171 TEL14L-XC_binding_site 0 - 1879 | chrXIV 7380 7390 TEL14L-XC_nucleotide_match 0 - 1880 | chrXIV 28469 28700 ARS1405 0 . 1881 | chrXIV 44447 45214 DAL82 0 + 1882 | chrXIV 48287 49216 YNL312W_mRNA 0 + 1883 | chrXIV 61599 61895 ARS1406 0 . 1884 | chrXIV 61958 62943 YNL302C_mRNA 0 - 1885 | chrXIV 63570 64562 YNL301C_mRNA 0 - 1886 | chrXIV 89210 89306 snR40 0 + 1887 | chrXIV 89210 89306 snR40 0 + 1888 | chrXIV 89531 89804 ARS1407 0 . 1889 | chrXIV 96241 96312 tG(UCC)N 0 - 1890 | chrXIV 96241 96312 tG(UCC)N 0 - 1891 | chrXIV 96247 96463 ARS1409 0 . 1892 | chrXIV 96451 96609 YNLWtau1 0 + 1893 | chrXIV 96610 96941 YNLCdelta1 0 - 1894 | chrXIV 96610 102523 YNLCTy1-1 0 - 1895 | chrXIV 100927 100927 YNL284C-B 0 - 1896 | chrXIV 102192 102523 YNLCdelta2 0 - 1897 | chrXIV 102632 102700 YNLCsigma1 0 - 1898 | chrXIV 102716 102789 tN(GUU)N1 0 + 1899 | chrXIV 102716 102789 tN(GUU)N1 0 + 1900 | chrXIV 104805 104877 tT(AGU)N1 0 + 1901 | chrXIV 104805 104877 tT(AGU)N1 0 + 1902 | chrXIV 126599 126805 ARS1410 0 . 1903 | chrXIV 144280 145281 YNL265C_mRNA 0 - 1904 | chrXIV 169568 169805 ARS1411 0 . 1905 | chrXIV 185460 186349 YNL246W_mRNA 0 + 1906 | chrXIV 196057 196292 ARS1412 0 . 1907 | chrXIV 202428 204872 KEX2 0 + 1908 | chrXIV 230105 230672 snR19 0 - 1909 | chrXIV 230105 230672 snR19 0 - 1910 | chrXIV 250315 250931 ARS1413 0 . 1911 | chrXIV 279880 280112 ARS1414 0 . 1912 | chrXIV 321921 322213 ARS1415 0 . 1913 | chrXIV 325054 325267 ARS1416 0 . 1914 | chrXIV 331322 332154 YNL162W_mRNA 0 + 1915 | chrXIV 347766 348521 RPC31 0 - 1916 | chrXIV 350940 351383 YNL147W_mRNA 0 + 1917 | chrXIV 366033 366412 YNL138W-A_mRNA 0 + 1918 | chrXIV 374869 374959 tF(GAA)N 0 + 1919 | chrXIV 374869 374905 tF(GAA)N 0 + 1920 | chrXIV 374924 374959 tF(GAA)N 0 + 1921 | chrXIV 379558 380831 YNL130C_mRNA 0 - 1922 | chrXIV 412267 412496 ARS1417 0 . 1923 | chrXIV 413639 416281 YNL112W_mRNA 0 + 1924 | chrXIV 443006 443119 tL(CAA)N 0 + 1925 | chrXIV 443006 443043 tL(CAA)N 0 + 1926 | chrXIV 443076 443119 tL(CAA)N 0 + 1927 | chrXIV 443398 444315 YNL096C_mRNA 0 - 1928 | chrXIV 449347 449591 ARS1419 0 . 1929 | chrXIV 457704 461990 TOP2 0 + 1930 | chrXIV 493956 495001 YNL069C_mRNA 0 - 1931 | chrXIV 498991 499235 ARS1420 0 . 1932 | chrXIV 519099 519169 tD(GUC)N 0 - 1933 | chrXIV 519099 519169 tD(GUC)N 0 - 1934 | chrXIV 519163 519496 YNLWdelta3 0 + 1935 | chrXIV 524729 525062 YNLWdelta4 0 + 1936 | chrXIV 534079 534982 YNL050C_mRNA 0 - 1937 | chrXIV 545268 545877 YNL044W_mRNA 0 + 1938 | chrXIV 545971 546205 ARS1421 0 . 1939 | chrXIV 546423 546714 YNLWsigma2 0 + 1940 | chrXIV 546738 547077 YNLWsigma3 0 + 1941 | chrXIV 547094 547196 tP(UGG)N1 0 + 1942 | chrXIV 547094 547129 tP(UGG)N1 0 + 1943 | chrXIV 547161 547196 tP(UGG)N1 0 + 1944 | chrXIV 557020 557783 YNL038W_mRNA 0 + 1945 | chrXIV 560693 560765 tT(AGU)N2 0 - 1946 | chrXIV 560693 560765 tT(AGU)N2 0 - 1947 | chrXIV 561111 561388 ARS1422 0 . 1948 | chrXIV 561607 561977 YNLWtau2 0 + 1949 | chrXIV 562033 562364 YNLCdelta5 0 - 1950 | chrXIV 562364 567660 YNLCTy2-1 0 - 1951 | chrXIV 567660 567992 YNLCdelta6 0 - 1952 | chrXIV 568115 568217 tP(UGG)N2 0 + 1953 | chrXIV 568115 568150 tP(UGG)N2 0 + 1954 | chrXIV 568182 568217 tP(UGG)N2 0 + 1955 | chrXIV 568219 568524 ARS1423 0 . 1956 | chrXIV 569867 569940 tI(AAU)N1 0 - 1957 | chrXIV 569867 569940 tI(AAU)N1 0 - 1958 | chrXIV 585587 585926 NME1 0 + 1959 | chrXIV 585587 585926 NME1 0 + 1960 | chrXIV 586090 586175 snR66 0 + 1961 | chrXIV 586090 586175 snR66 0 + 1962 | chrXIV 602312 602385 tI(AAU)N2 0 + 1963 | chrXIV 602312 602385 tI(AAU)N2 0 + 1964 | chrXIV 609463 609710 ARS1424 0 . 1965 | chrXIV 609686 611665 YNL012W_mRNA 0 + 1966 | chrXIV 616311 617125 ARS1425 0 . 1967 | chrXIV 622915 624621 YNL004W_mRNA 0 + 1968 | chrXIV 628758 628875 CEN14 0 + 1969 | chrXIV 628758 628767 CEN14 0 + 1970 | chrXIV 628768 628850 CEN14 0 + 1971 | chrXIV 628851 628875 CEN14 0 + 1972 | chrXIV 631846 631917 tP(AGG)N 0 - 1973 | chrXIV 631846 631917 tP(AGG)N 0 - 1974 | chrXIV 631998 632114 YNRCdelta7 0 - 1975 | chrXIV 632119 632489 YNRCtau3 0 - 1976 | chrXIV 632599 632672 tN(GUU)N2 0 + 1977 | chrXIV 632599 632672 tN(GUU)N2 0 + 1978 | chrXIV 635664 635904 ARS1426 0 . 1979 | chrXIV 691486 691730 ARS1427 0 . 1980 | chrXIV 714048 715388 LYS9 0 - 1981 | chrXIV 716120 716284 snR49 0 + 1982 | chrXIV 716120 716284 snR49 0 + 1983 | chrXIV 721120 723112 YNR053C_mRNA 0 - 1984 | chrXIV 721938 722211 snR191 0 - 1985 | chrXIV 721938 722211 snR191 0 - 1986 | chrXIV 726134 726217 tL(UAA)N 0 - 1987 | chrXIV 726134 726217 tL(UAA)N 0 - 1988 | chrXIV 726234 726574 YNRWsigma4 0 + 1989 | chrXIV 726614 726945 YNRCdelta8 0 - 1990 | chrXIV 727363 727661 YNRCdelta9 0 - 1991 | chrXIV 783278 784333 TEL14R 0 + 1992 | chrXIV 783278 783740 TEL14R-XC 0 + 1993 | chrXIV 783316 783326 TEL14R-XC_nucleotide_match 0 + 1994 | chrXIV 783535 783547 TEL14R-XC_binding_site 0 + 1995 | chrXIV 783741 784037 TEL14R-XR 0 + 1996 | chrXIV 784038 784333 TEL14R-TR 0 + 1997 | chrXVI 1 7223 TEL16L 0 - 1998 | chrXVI 1 6524 TEL16L-YP 0 - 1999 | chrXVI 81 91 TEL16L-YP_nucleotide_match 0 + 2000 | chrXVI 280 6007 YPL283C_mRNA 0 - 2001 | chrXVI 1481 1907 TEL16L-YP_repeat_region 0 + 2002 | chrXVI 6525 6777 TEL16L-XR 0 - 2003 | chrXVI 6778 7223 TEL16L-XC 0 - 2004 | chrXVI 6954 6966 TEL16L-XC_binding_site 0 - 2005 | chrXVI 7175 7185 TEL16L-XC_nucleotide_match 0 - 2006 | chrXVI 18370 19069 ARS1603 0 . 2007 | chrXVI 42977 43212 ARS1604 0 . 2008 | chrXVI 55657 55858 YPLCdelta1 0 - 2009 | chrXVI 56169 56274 tW(CCA)P 0 - 2010 | chrXVI 56169 56204 tW(CCA)P 0 - 2011 | chrXVI 56239 56274 tW(CCA)P 0 - 2012 | chrXVI 56290 56358 YPLWsigma1 0 + 2013 | chrXVI 56409 56451 YPLWdelta2 0 + 2014 | chrXVI 56452 62375 YPLWTy1-1 0 + 2015 | chrXVI 56452 56788 YPLWdelta3 0 + 2016 | chrXVI 58053 58053 YPL257W-B 0 + 2017 | chrXVI 62039 62375 YPLWdelta4 0 + 2018 | chrXVI 62389 62720 YPLWdelta5 0 + 2019 | chrXVI 62724 63006 YPLWdelta6 0 + 2020 | chrXVI 73039 73283 ARS1605 0 . 2021 | chrXVI 75699 76239 YPL249C-A_mRNA 0 - 2022 | chrXVI 79711 82356 GAL4 0 - 2023 | chrXVI 95372 96258 YPL241C_mRNA 0 - 2024 | chrXVI 116506 116765 ARS1607 0 . 2025 | chrXVI 138698 139409 YPL218W_mRNA 0 + 2026 | chrXVI 162341 162632 ARS1608 0 . 2027 | chrXVI 166256 167398 TPK2 0 + 2028 | chrXVI 173152 174702 YPL198W_mRNA 0 + 2029 | chrXVI 173827 173904 snR59 0 + 2030 | chrXVI 173827 173904 snR59 0 + 2031 | chrXVI 210192 210263 tE(UUC)P 0 - 2032 | chrXVI 210192 210263 tE(UUC)P 0 - 2033 | chrXVI 210451 210771 YPLWdelta7 0 + 2034 | chrXVI 211577 211898 YPLWdelta8 0 + 2035 | chrXVI 218630 220088 YPL175W_mRNA 0 + 2036 | chrXVI 220088 220167 ARS1611 0 . 2037 | chrXVI 259714 260931 PEP4 0 - 2038 | chrXVI 260931 261727 ARS1612 0 . 2039 | chrXVI 281056 281517 snR17b 0 - 2040 | chrXVI 281056 281373 snR17b 0 - 2041 | chrXVI 281504 281517 snR17b 0 - 2042 | chrXVI 282122 282970 YPL143W_mRNA 0 + 2043 | chrXVI 289485 289705 ARS1614 0 . 2044 | chrXVI 305298 306137 YPL129W_mRNA 0 + 2045 | chrXVI 331699 332100 ARS1617 0 . 2046 | chrXVI 338848 338919 tM(CAU)P 0 - 2047 | chrXVI 338848 338919 tM(CAU)P 0 - 2048 | chrXVI 345264 347389 YPL109C_mRNA 0 - 2049 | chrXVI 377291 378395 YPL090C_mRNA 0 - 2050 | chrXVI 384542 384789 ARS1618 0 . 2051 | chrXVI 404950 406044 YPL081W_mRNA 0 + 2052 | chrXVI 406636 407539 YPL079W_mRNA 0 + 2053 | chrXVI 412254 415362 YPL075W_mRNA 0 + 2054 | chrXVI 418138 418364 ARS1619 0 . 2055 | chrXVI 422786 422885 ARS1620 0 . 2056 | chrXVI 435893 435964 tC(GCA)P1 0 - 2057 | chrXVI 435893 435964 tC(GCA)P1 0 - 2058 | chrXVI 436068 436249 YPLWdelta9 0 + 2059 | chrXVI 436250 436587 YPLCdelta10 0 - 2060 | chrXVI 436594 436731 YPLWdelta11 0 + 2061 | chrXVI 436890 443112 YPLCTy4-1 0 - 2062 | chrXVI 436890 437260 YPLCtau1 0 - 2063 | chrXVI 442742 443112 YPLCtau2 0 - 2064 | chrXVI 456563 456810 ARS1633 0 . 2065 | chrXVI 458799 459678 YPL052W_mRNA 0 + 2066 | chrXVI 459006 459006 YPL052W_mRNA 0 + 2067 | chrXVI 492018 493037 YPL031C_mRNA 0 - 2068 | chrXVI 498096 499292 ERG10 0 + 2069 | chrXVI 511624 511944 ARS1621 0 . 2070 | chrXVI 555957 556073 CEN16 0 + 2071 | chrXVI 555957 555966 CEN16 0 + 2072 | chrXVI 555967 556048 CEN16 0 + 2073 | chrXVI 556049 556073 CEN16 0 + 2074 | chrXVI 560198 560289 tF(GAA)P1 0 - 2075 | chrXVI 560198 560233 tF(GAA)P1 0 - 2076 | chrXVI 560253 560289 tF(GAA)P1 0 - 2077 | chrXVI 560481 560812 YPRWdelta12 0 + 2078 | chrXVI 563828 564066 ARS1622 0 . 2079 | chrXVI 565052 565294 ARS1634 0 . 2080 | chrXVI 571845 572173 YPRCdelta13 0 - 2081 | chrXVI 572269 572339 tG(GCC)P1 0 + 2082 | chrXVI 572269 572339 tG(GCC)P1 0 + 2083 | chrXVI 582062 582134 tK(CUU)P 0 + 2084 | chrXVI 582062 582134 tK(CUU)P 0 + 2085 | chrXVI 582373 582734 YPR010C-A_mRNA 0 - 2086 | chrXVI 622540 622631 tF(GAA)P2 0 - 2087 | chrXVI 622540 622575 tF(GAA)P2 0 - 2088 | chrXVI 622595 622631 tF(GAA)P2 0 - 2089 | chrXVI 623527 624202 YPR028W_mRNA 0 + 2090 | chrXVI 633874 634122 ARS1623 0 . 2091 | chrXVI 637379 639019 HTS1 0 - 2092 | chrXVI 654166 654847 YPR043W_mRNA 0 + 2093 | chrXVI 677812 678320 YPR063C_mRNA 0 - 2094 | chrXVI 684389 684637 ARS1624 0 . 2095 | chrXVI 689565 689646 tS(UGA)P 0 + 2096 | chrXVI 689565 689646 tS(UGA)P 0 + 2097 | chrXVI 695438 695686 ARS1625 0 . 2098 | chrXVI 718700 718806 snR51 0 - 2099 | chrXVI 718700 718806 snR51 0 - 2100 | chrXVI 718887 719050 snR70 0 - 2101 | chrXVI 718887 719050 snR70 0 - 2102 | chrXVI 719148 719242 snR41 0 - 2103 | chrXVI 719148 719242 snR41 0 - 2104 | chrXVI 728947 729528 YPR098C_mRNA 0 - 2105 | chrXVI 744284 744355 tT(UGU)P 0 + 2106 | chrXVI 744284 744355 tT(UGU)P 0 + 2107 | chrXVI 745828 746835 RPC40 0 - 2108 | chrXVI 749099 749345 ARS1626 0 . 2109 | chrXVI 769207 769302 tK(UUU)P 0 - 2110 | chrXVI 769207 769242 tK(UUU)P 0 - 2111 | chrXVI 769266 769302 tK(UUU)P 0 - 2112 | chrXVI 769319 769659 YPRWsigma2 0 + 2113 | chrXVI 775765 775836 tC(GCA)P2 0 - 2114 | chrXVI 775765 775836 tC(GCA)P2 0 - 2115 | chrXVI 776093 776413 YPRWdelta14 0 + 2116 | chrXVI 776667 776796 YPRCdelta15 0 - 2117 | chrXVI 776926 777156 ARS1635 0 . 2118 | chrXVI 777084 777098 ARS1635_nucleotide_match 0 - 2119 | chrXVI 777832 778154 YPRWdelta16 0 + 2120 | chrXVI 794965 795767 YPR132W_mRNA 0 + 2121 | chrXVI 804511 804638 YPRWdelta17 0 + 2122 | chrXVI 804645 810562 YPRCTy1-2 0 - 2123 | chrXVI 804645 804978 YPRCdelta18 0 - 2124 | chrXVI 808964 808964 YPR137C-B 0 - 2125 | chrXVI 810229 810562 YPRCdelta19 0 - 2126 | chrXVI 810676 810749 tN(GUU)P 0 + 2127 | chrXVI 810676 810749 tN(GUU)P 0 + 2128 | chrXVI 819160 819399 ARS1627 0 . 2129 | chrXVI 819529 819602 tI(AAU)P1 0 + 2130 | chrXVI 819529 819602 tI(AAU)P1 0 + 2131 | chrXVI 821732 821903 snR45 0 + 2132 | chrXVI 821732 821903 snR45 0 + 2133 | chrXVI 833689 834245 YPR153W_mRNA 0 + 2134 | chrXVI 842653 842900 ARS1628 0 . 2135 | chrXVI 844412 850340 YPRWTy1-3 0 + 2136 | chrXVI 844412 844749 YPRWdelta20 0 + 2137 | chrXVI 846014 846014 YPR158W-B 0 + 2138 | chrXVI 850003 850340 YPRWdelta21 0 + 2139 | chrXVI 850357 850512 YPRCdelta22 0 - 2140 | chrXVI 850512 850629 ARS1629 0 . 2141 | chrXVI 850629 856554 YPRCTy1-4 0 - 2142 | chrXVI 850629 850966 YPRCdelta23 0 - 2143 | chrXVI 854952 854952 YPR158C-D 0 - 2144 | chrXVI 856217 856554 YPRCdelta24 0 - 2145 | chrXVI 856545 856885 YPRWsigma3 0 + 2146 | chrXVI 856902 856974 tA(AGC)P 0 + 2147 | chrXVI 856902 856974 tA(AGC)P 0 + 2148 | chrXVI 860379 860449 tG(GCC)P2 0 + 2149 | chrXVI 860379 860449 tG(GCC)P2 0 + 2150 | chrXVI 880296 880369 tI(AAU)P2 0 - 2151 | chrXVI 880296 880369 tI(AAU)P2 0 - 2152 | chrXVI 880386 880726 YPRWsigma4 0 + 2153 | chrXVI 880861 881108 ARS1630 0 . 2154 | chrXVI 881487 881830 YPRCtau3 0 - 2155 | chrXVI 883239 883595 YPR170W-B_mRNA 0 + 2156 | chrXVI 911257 911800 YPR187W_mRNA 0 + 2157 | chrXVI 932983 933229 ARS1631 0 . 2158 | chrXVI 933071 933404 YPRWtau4 0 + 2159 | chrXVI 942084 943032 ARS1632 0 . 2160 | chrXVI 942396 948010 TEL16R 0 + 2161 | chrXVI 942396 942771 TEL16R-XC 0 + 2162 | chrXVI 942434 942444 TEL16R-XC_nucleotide_match 0 + 2163 | chrXVI 942624 942636 TEL16R-XC_binding_site 0 + 2164 | chrXVI 942810 948010 TEL16R-YP 0 + 2165 | chrXVI 943032 943896 YPR202W_mRNA 0 + 2166 | chrXVI 945966 946500 TEL16R-YP_repeat_region 0 - 2167 | chrXVI 947890 947900 TEL16R-YP_nucleotide_match 0 - 2168 | chrVIII 130730 131446 ARD1 0 - 2169 | chrVIII 1 5505 TEL08L 0 - 2170 | chrVIII 1 34 TEL08L-TR 0 - 2171 | chrVIII 35 4951 TEL08L-YP 0 - 2172 | chrVIII 246 256 TEL08L-YP_nucleotide_match 0 + 2173 | chrVIII 445 3311 YHL050C_mRNA 0 - 2174 | chrVIII 1649 1943 TEL08L-YP_repeat_region 0 + 2175 | chrVIII 4952 5051 TEL08L-XR 0 - 2176 | chrVIII 5052 5505 TEL08L-XC 0 - 2177 | chrVIII 5236 5248 TEL08L-XC_binding_site 0 - 2178 | chrVIII 5457 5467 TEL08L-XC_nucleotide_match 0 - 2179 | chrVIII 5471 6401 ARS801 0 . 2180 | chrVIII 7536 7783 ARS802 0 . 2181 | chrVIII 7994 8225 YHLComega1 0 - 2182 | chrVIII 62755 62826 tH(GUG)H 0 + 2183 | chrVIII 62755 62826 tH(GUG)H 0 + 2184 | chrVIII 62961 64157 SPO11 0 - 2185 | chrVIII 64259 64493 ARS805 0 . 2186 | chrVIII 85298 85371 tV(AAC)H 0 - 2187 | chrVIII 85298 85371 tV(AAC)H 0 - 2188 | chrVIII 85388 85538 YHLCsigma1 0 - 2189 | chrVIII 85539 91761 YHLWTy4-1 0 + 2190 | chrVIII 85539 85909 YHLWtau1 0 + 2191 | chrVIII 86995 86995 YHL009W-B 0 + 2192 | chrVIII 91391 91761 YHLWtau2 0 + 2193 | chrVIII 91772 92099 YHLCdelta1 0 - 2194 | chrVIII 92240 92390 YHLWdelta2 0 + 2195 | chrVIII 104277 105091 YHL001W_mRNA 0 + 2196 | chrVIII 105586 105703 CEN8 0 - 2197 | chrVIII 105586 105610 CEN8 0 - 2198 | chrVIII 105611 105693 CEN8 0 - 2199 | chrVIII 105694 105703 CEN8 0 - 2200 | chrVIII 107826 108122 YHR001W-A_mRNA 0 + 2201 | chrVIII 116107 116179 tT(AGU)H 0 - 2202 | chrVIII 116107 116179 tT(AGU)H 0 - 2203 | chrVIII 116179 116421 ARS806 0 . 2204 | chrVIII 116421 116752 YHRCdelta3 0 - 2205 | chrVIII 116763 117061 YHRCdelta4 0 - 2206 | chrVIII 126521 127492 YHR010W_mRNA 0 + 2207 | chrVIII 129481 130448 YHR012W_mRNA 0 + 2208 | chrVIII 133026 133107 tS(AGA)H 0 - 2209 | chrVIII 133026 133107 tS(AGA)H 0 - 2210 | chrVIII 133201 133442 YHRCdelta5 0 - 2211 | chrVIII 133357 133600 ARS807 0 . 2212 | chrVIII 133565 133684 YHRCdelta6 0 - 2213 | chrVIII 133685 134009 YHRWdelta7 0 + 2214 | chrVIII 134321 134392 tQ(UUG)H 0 + 2215 | chrVIII 134321 134392 tQ(UUG)H 0 + 2216 | chrVIII 136881 138455 YHR016C_mRNA 0 - 2217 | chrVIII 140349 141274 ARS808 0 . 2218 | chrVIII 146242 146314 tA(AGC)H 0 - 2219 | chrVIII 146242 146314 tA(AGC)H 0 - 2220 | chrVIII 146331 146671 YHRCsigma2 0 - 2221 | chrVIII 146844 147114 YHRWtau3 0 + 2222 | chrVIII 147871 148669 YHR021C_mRNA 0 - 2223 | chrVIII 168541 168782 ARS809 0 . 2224 | chrVIII 187173 187679 YHR039C-A_mRNA 0 - 2225 | chrVIII 189131 189864 YHR041C_mRNA 0 - 2226 | chrVIII 212409 213118 RUF5-1 0 + 2227 | chrVIII 212409 213118 RUF5-1 0 + 2228 | chrVIII 212535 212720 CUP1-1 0 - 2229 | chrVIII 212720 213185 ARS810 0 . 2230 | chrVIII 214407 215116 RUF5-2 0 + 2231 | chrVIII 214407 215116 RUF5-2 0 + 2232 | chrVIII 214718 215183 ARS811 0 . 2233 | chrVIII 237848 237939 tF(GAA)H1 0 - 2234 | chrVIII 237848 237883 tF(GAA)H1 0 - 2235 | chrVIII 237903 237939 tF(GAA)H1 0 - 2236 | chrVIII 245719 245967 ARS813 0 . 2237 | chrVIII 251101 252225 YHR076W_mRNA 0 + 2238 | chrVIII 252374 255756 YHR077C_mRNA 0 - 2239 | chrVIII 262192 262553 YHR079C-A_mRNA 0 - 2240 | chrVIII 286770 287128 ARS814 0 . 2241 | chrVIII 296447 297385 ARS815 0 . 2242 | chrVIII 297385 298609 YHR097C_mRNA 0 - 2243 | chrVIII 314874 315968 YHR101C_mRNA 0 - 2244 | chrVIII 354815 356081 YHR123W_mRNA 0 + 2245 | chrVIII 358478 358569 tF(GAA)H2 0 - 2246 | chrVIII 358478 358513 tF(GAA)H2 0 - 2247 | chrVIII 358533 358569 tF(GAA)H2 0 - 2248 | chrVIII 358672 358850 YHRCdelta8 0 - 2249 | chrVIII 358850 359067 YHRCtau4 0 - 2250 | chrVIII 359079 359372 YHRWdelta9 0 + 2251 | chrVIII 362115 362765 FUR1 0 + 2252 | chrVIII 381540 381727 snR32 0 + 2253 | chrVIII 381540 381727 snR32 0 + 2254 | chrVIII 381990 382751 YHR141C_mRNA 0 - 2255 | chrVIII 388893 388995 tP(UGG)H 0 - 2256 | chrVIII 388893 388928 tP(UGG)H 0 - 2257 | chrVIII 388960 388995 tP(UGG)H 0 - 2258 | chrVIII 389177 389509 YHRCdelta10 0 - 2259 | chrVIII 389613 389845 YHRCdelta11 0 - 2260 | chrVIII 392148 392390 ARS818 0 . 2261 | chrVIII 411228 411317 snR71 0 + 2262 | chrVIII 411228 411317 snR71 0 + 2263 | chrVIII 447622 447855 ARS820 0 . 2264 | chrVIII 463920 464147 YHRCdelta12 0 - 2265 | chrVIII 466549 466863 YHRWdelta13 0 + 2266 | chrVIII 466884 466975 YHRCsigma3 0 - 2267 | chrVIII 466990 467061 tT(UGU)H 0 + 2268 | chrVIII 466990 467061 tT(UGU)H 0 + 2269 | chrVIII 475706 475778 tV(CAC)H 0 - 2270 | chrVIII 475706 475778 tV(CAC)H 0 - 2271 | chrVIII 484845 486179 ERG9 0 + 2272 | chrVIII 498571 498859 YHR199C-A_mRNA 0 - 2273 | chrVIII 501756 501996 ARS822 0 . 2274 | chrVIII 504476 505530 YHR203C_mRNA 0 - 2275 | chrVIII 530049 530379 YHRCdelta14 0 - 2276 | chrVIII 543610 549637 YHRCTy1-1 0 - 2277 | chrVIII 543610 543941 YHRCdelta15 0 - 2278 | chrVIII 547930 547930 YHR214C-B 0 - 2279 | chrVIII 549306 549637 YHRCdelta16 0 - 2280 | chrVIII 556001 556331 ARS824 0 . 2281 | chrVIII 556105 562643 TEL08R 0 + 2282 | chrVIII 556105 556575 TEL08R-XC 0 + 2283 | chrVIII 556143 556153 TEL08R-XC_nucleotide_match 0 + 2284 | chrVIII 556362 556374 TEL08R-XC_binding_site 0 + 2285 | chrVIII 556576 556831 TEL08R-XR 0 + 2286 | chrVIII 556832 556985 TEL08R-TR2 0 + 2287 | chrVIII 556986 562456 TEL08R-YP 0 + 2288 | chrVIII 558014 559924 YHR218W_mRNA 0 + 2289 | chrVIII 560417 560843 TEL08R-YP_repeat_region 0 - 2290 | chrVIII 562236 562246 TEL08R-YP_nucleotide_match 0 - 2291 | chrVIII 562457 562643 TEL08R-TR1 0 + 2292 | chrXIII 1 6344 TEL13L 0 - 2293 | chrXIII 1 51 TEL13L-TR1 0 - 2294 | chrXIII 52 5537 TEL13L-YP 0 - 2295 | chrXIII 262 272 TEL13L-YP_nucleotide_match 0 + 2296 | chrXIII 461 4684 YML133C_mRNA 0 - 2297 | chrXIII 1665 2091 TEL13L-YP_repeat_region 0 + 2298 | chrXIII 5538 5585 TEL13L-TR2 0 - 2299 | chrXIII 5586 5874 TEL13L-XR 0 - 2300 | chrXIII 5875 6344 TEL13L-XC 0 - 2301 | chrXIII 6075 6087 TEL13L-XC_binding_site 0 - 2302 | chrXIII 6296 6306 TEL13L-XC_nucleotide_match 0 - 2303 | chrXIII 22048 23683 YML124C_mRNA 0 - 2304 | chrXIII 31688 31935 ARS1303 0 . 2305 | chrXIII 39824 40187 ARS1304 0 . 2306 | chrXIII 67768 67938 snR85 0 - 2307 | chrXIII 67768 67938 snR85 0 - 2308 | chrXIII 82275 82849 YML094W_mRNA 0 + 2309 | chrXIII 94217 94463 ARS1305 0 . 2310 | chrXIII 97941 99400 YML085C_mRNA 0 - 2311 | chrXIII 115734 118898 HMG1 0 - 2312 | chrXIII 123227 124172 YML073C_mRNA 0 - 2313 | chrXIII 131825 131896 tR(UCU)M2 0 - 2314 | chrXIII 131825 131896 tR(UCU)M2 0 - 2315 | chrXIII 131989 132321 YMLCdelta1 0 - 2316 | chrXIII 137300 137548 ARS1307 0 . 2317 | chrXIII 139063 140214 YML067C_mRNA 0 - 2318 | chrXIII 162194 164176 YML056C_mRNA 0 - 2319 | chrXIII 163535 163620 snR54 0 - 2320 | chrXIII 163535 163620 snR54 0 - 2321 | chrXIII 168349 168681 YMLCdelta2 0 - 2322 | chrXIII 168795 168883 tY(GUA)M1 0 + 2323 | chrXIII 168795 168833 tY(GUA)M1 0 + 2324 | chrXIII 168848 168883 tY(GUA)M1 0 + 2325 | chrXIII 183794 184037 ARS1308 0 . 2326 | chrXIII 183898 183968 tG(GCC)M 0 - 2327 | chrXIII 183898 183968 tG(GCC)M 0 - 2328 | chrXIII 184170 190083 YMLWTy1-1 0 + 2329 | chrXIII 184170 184501 YMLWdelta3 0 + 2330 | chrXIII 185766 185766 YML045W 0 + 2331 | chrXIII 189752 190083 YMLWdelta4 0 + 2332 | chrXIII 196068 196170 tP(UGG)M 0 - 2333 | chrXIII 196068 196103 tP(UGG)M 0 - 2334 | chrXIII 196135 196170 tP(UGG)M 0 - 2335 | chrXIII 196332 202234 YMLWTy1-2 0 + 2336 | chrXIII 196332 196668 YMLWdelta5 0 + 2337 | chrXIII 197933 197933 YML039W 0 + 2338 | chrXIII 201919 202234 YMLWdelta6 0 + 2339 | chrXIII 205642 206293 YML036W_mRNA 0 + 2340 | chrXIII 209525 212155 YML034W_mRNA 0 + 2341 | chrXIII 214189 216156 NDC1 0 + 2342 | chrXIII 222987 223828 YML026C_mRNA 0 - 2343 | chrXIII 224406 225365 YML025C_mRNA 0 - 2344 | chrXIII 225889 226697 YML024W_mRNA 0 + 2345 | chrXIII 236588 238731 YML017W_mRNA 0 + 2346 | chrXIII 259158 259239 tS(AGA)M 0 - 2347 | chrXIII 259158 259239 tS(AGA)M 0 - 2348 | chrXIII 263063 263296 ARS1309 0 . 2349 | chrXIII 268031 268149 CEN13 0 + 2350 | chrXIII 268031 268040 CEN13 0 + 2351 | chrXIII 268041 268124 CEN13 0 + 2352 | chrXIII 268125 268149 CEN13 0 + 2353 | chrXIII 286784 287068 ARS1310 0 . 2354 | chrXIII 290049 290224 YMRCtau1 0 - 2355 | chrXIII 290801 290872 tE(UUC)M 0 + 2356 | chrXIII 290801 290872 tE(UUC)M 0 + 2357 | chrXIII 297278 297364 snR78 0 + 2358 | chrXIII 297278 297364 snR78 0 + 2359 | chrXIII 297506 297593 snR77 0 + 2360 | chrXIII 297506 297593 snR77 0 + 2361 | chrXIII 297725 297833 snR76 0 + 2362 | chrXIII 297725 297833 snR76 0 + 2363 | chrXIII 297918 298006 snR75 0 + 2364 | chrXIII 297918 298006 snR75 0 + 2365 | chrXIII 298138 298225 snR74 0 + 2366 | chrXIII 298138 298225 snR74 0 + 2367 | chrXIII 298307 298412 snR73 0 + 2368 | chrXIII 298307 298412 snR73 0 + 2369 | chrXIII 298554 298651 snR72 0 + 2370 | chrXIII 298554 298651 snR72 0 + 2371 | chrXIII 321147 321219 tA(AGC)M1 0 - 2372 | chrXIII 321147 321219 tA(AGC)M1 0 - 2373 | chrXIII 337788 339277 YMR033W_mRNA 0 + 2374 | chrXIII 352280 352370 tF(GAA)M 0 + 2375 | chrXIII 352280 352316 tF(GAA)M 0 + 2376 | chrXIII 352335 352370 tF(GAA)M 0 + 2377 | chrXIII 353871 354731 MCM1 0 + 2378 | chrXIII 357005 362918 YMRCTy1-3 0 - 2379 | chrXIII 357005 357336 YMRCdelta7 0 - 2380 | chrXIII 361322 361322 YMR045C 0 - 2381 | chrXIII 362587 362918 YMRCdelta8 0 - 2382 | chrXIII 363064 363135 tH(GUG)M 0 + 2383 | chrXIII 363064 363135 tH(GUG)M 0 + 2384 | chrXIII 370978 371222 ARS1312 0 . 2385 | chrXIII 372445 372518 tV(AAC)M1 0 - 2386 | chrXIII 372445 372518 tV(AAC)M1 0 - 2387 | chrXIII 372697 378622 YMRCTy1-4 0 - 2388 | chrXIII 372697 373034 YMRCdelta9 0 - 2389 | chrXIII 377020 377020 YMR050C 0 - 2390 | chrXIII 378285 378622 YMRCdelta10 0 - 2391 | chrXIII 378727 379061 YMRCdelta11 0 - 2392 | chrXIII 379072 379198 YMRWdelta12 0 + 2393 | chrXIII 379303 379408 tW(CCA)M 0 - 2394 | chrXIII 379303 379338 tW(CCA)M 0 - 2395 | chrXIII 379373 379408 tW(CCA)M 0 - 2396 | chrXIII 420588 420661 tV(AAC)M2 0 - 2397 | chrXIII 420588 420661 tV(AAC)M2 0 - 2398 | chrXIII 424989 426059 YMR079W_mRNA 0 + 2399 | chrXIII 463128 463461 YMRCdelta13 0 - 2400 | chrXIII 463554 463625 tD(GUC)M 0 + 2401 | chrXIII 463554 463625 tD(GUC)M 0 + 2402 | chrXIII 468179 468469 ARS1316 0 . 2403 | chrXIII 477606 478301 ARS1317 0 . 2404 | chrXIII 480621 480693 tK(CUU)M 0 - 2405 | chrXIII 480621 480693 tK(CUU)M 0 - 2406 | chrXIII 481214 481547 YMRCdelta14 0 - 2407 | chrXIII 481571 481808 YMRWdelta15 0 + 2408 | chrXIII 499456 500688 YMR116C_mRNA 0 - 2409 | chrXIII 499984 500072 snR24 0 - 2410 | chrXIII 499984 500072 snR24 0 - 2411 | chrXIII 503192 503389 YMRWdelta16 0 + 2412 | chrXIII 503389 503771 ARS1319 0 . 2413 | chrXIII 503771 504141 YMRWtau2 0 + 2414 | chrXIII 504346 504677 YMRWdelta17 0 + 2415 | chrXIII 504895 505008 tL(CAA)M 0 + 2416 | chrXIII 504895 504932 tL(CAA)M 0 + 2417 | chrXIII 504965 505008 tL(CAA)M 0 + 2418 | chrXIII 517539 520446 YMR125W_mRNA 0 + 2419 | chrXIII 535597 535844 ARS1320 0 . 2420 | chrXIII 536207 537609 YMR133W_mRNA 0 + 2421 | chrXIII 542881 542978 ARS1321 0 . 2422 | chrXIII 550206 551207 YMR142C_mRNA 0 - 2423 | chrXIII 551928 552903 YMR143W_mRNA 0 + 2424 | chrXIII 553422 554331 ARS1322 0 . 2425 | chrXIII 572883 572955 tM(CAU)M 0 - 2426 | chrXIII 572883 572955 tM(CAU)M 0 - 2427 | chrXIII 573112 573338 YMRCdelta18 0 - 2428 | chrXIII 586636 586709 tV(AAC)M3 0 - 2429 | chrXIII 586636 586709 tV(AAC)M3 0 - 2430 | chrXIII 611275 611489 ARS1323 0 . 2431 | chrXIII 626349 626654 snR83 0 + 2432 | chrXIII 626349 626654 snR83 0 + 2433 | chrXIII 634481 634715 ARS1324 0 . 2434 | chrXIII 649309 649552 ARS1325 0 . 2435 | chrXIII 651145 651910 YMR194W_mRNA 0 + 2436 | chrXIII 652275 652532 snR11 0 + 2437 | chrXIII 652275 652532 snR11 0 + 2438 | chrXIII 652594 652887 YMR194C-B_mRNA 0 - 2439 | chrXIII 665845 667044 YMR201C_mRNA 0 - 2440 | chrXIII 667288 667456 RNA170 0 - 2441 | chrXIII 667288 667456 RNA170 0 - 2442 | chrXIII 671887 674766 PFK2 0 - 2443 | chrXIII 720960 721403 YMR225C_mRNA 0 - 2444 | chrXIII 732414 733141 YMR230W_mRNA 0 + 2445 | chrXIII 747892 747963 tR(UCU)M1 0 - 2446 | chrXIII 747892 747963 tR(UCU)M1 0 - 2447 | chrXIII 753225 754220 YMR242C_mRNA 0 - 2448 | chrXIII 758224 758471 ARS1327 0 . 2449 | chrXIII 762110 763113 snR86 0 - 2450 | chrXIII 762110 763113 snR86 0 - 2451 | chrXIII 768369 768441 tA(AGC)M2 0 - 2452 | chrXIII 768369 768441 tA(AGC)M2 0 - 2453 | chrXIII 768548 768879 YMRWdelta19 0 + 2454 | chrXIII 772631 772879 ARS1328 0 . 2455 | chrXIII 805117 805338 ARS1329 0 . 2456 | chrXIII 808246 808317 tQ(CUG)M 0 - 2457 | chrXIII 808246 808317 tQ(CUG)M 0 - 2458 | chrXIII 808537 808906 YMRCtau3 0 - 2459 | chrXIII 809000 809233 YMRWdelta20 0 + 2460 | chrXIII 815342 815567 ARS1330 0 . 2461 | chrXIII 837450 837764 YMRWdelta21 0 + 2462 | chrXIII 837764 837928 ARS1331 0 . 2463 | chrXIII 837928 838016 tY(GUA)M2 0 + 2464 | chrXIII 837928 837966 tY(GUA)M2 0 + 2465 | chrXIII 837981 838016 tY(GUA)M2 0 + 2466 | chrXIII 854795 855293 YMR292W_mRNA 0 + 2467 | chrXIII 865559 867091 ADE4 0 - 2468 | chrXIII 897805 898040 ARS1332 0 . 2469 | chrXIII 917896 918366 ARS1333 0 . 2470 | chrXIII 923015 923494 ARS1335 0 . 2471 | chrXIII 923541 924431 TEL13R 0 + 2472 | chrXIII 923541 924005 TEL13R-XC 0 + 2473 | chrXIII 923578 923588 TEL13R-XC_nucleotide_match 0 + 2474 | chrXIII 923796 923808 TEL13R-XC_binding_site 0 + 2475 | chrXIII 924006 924306 TEL13R-XR 0 + 2476 | chrXIII 924307 924431 TEL13R-TR 0 + 2477 | -------------------------------------------------------------------------------- /annotations/Yeast_snRNA_genes.bed: -------------------------------------------------------------------------------- 1 | chrI 142367 142468 snR18 0 + 2 | chrII 88190 88277 snR56 0 + 3 | chrII 307185 307345 snR161 0 - 4 | chrIII 107504 107712 snR43 0 - 5 | chrIII 142364 142546 snR33 0 - 6 | chrIII 177183 177282 snR65 0 + 7 | chrIII 178610 178798 snR189 0 - 8 | chrIV 323217 323471 snR63 0 - 9 | chrIV 541602 541700 snR47 0 - 10 | chrIV 1402919 1403042 snR13 0 + 11 | chrIV 1492477 1493026 snR84 0 - 12 | chrIX 97111 97246 snR68 0 + 13 | chrV 52150 52320 snR80 0 - 14 | chrV 61352 61433 snR67 0 + 15 | chrV 61699 61789 snR53 0 + 16 | chrV 167427 167586 snR14 0 - 17 | chrV 424698 424883 snR4 0 + 18 | chrV 431129 431220 snR52 0 - 19 | chrVII 316788 317055 snR82 0 + 20 | chrVII 345986 346230 snR10 0 + 21 | chrVII 365163 365251 snR39 0 - 22 | chrVII 366374 366469 snR39B 0 - 23 | chrVII 545370 545566 snR46 0 + 24 | chrVII 609584 609696 snR48 0 + 25 | chrVII 939459 939672 snR7-L 0 - 26 | chrVII 939494 939672 snR7-S 0 - 27 | chrVIII 381540 381727 snR32 0 + 28 | chrVIII 411228 411317 snR71 0 + 29 | chrX 139566 139691 snR128 0 - 30 | chrX 139761 139950 snR190 0 - 31 | chrX 228094 228479 snR37 0 - 32 | chrX 349130 349233 snR60 0 - 33 | chrX 663749 663942 snR3 0 + 34 | chrXI 38811 38911 snR64 0 + 35 | chrXI 283185 283279 snR38 0 + 36 | chrXI 364776 364876 snR69 0 + 37 | chrXI 431030 431138 snR87 0 - 38 | chrXI 559016 559366 snR42 0 - 39 | chrXII 198784 199389 snR30 0 + 40 | chrXII 348427 348510 snR79 0 - 41 | chrXII 366235 366346 snR6 0 + 42 | chrXII 794486 794575 snR61 0 - 43 | chrXII 794697 794794 snR55 0 - 44 | chrXII 794937 795024 snR57 0 - 45 | chrXII 856710 856920 snR44 0 + 46 | chrXII 899180 899382 snR34 0 + 47 | chrXIII 67768 67938 snR85 0 - 48 | chrXIII 163535 163620 snR54 0 - 49 | chrXIII 297278 297364 snR78 0 + 50 | chrXIII 297506 297593 snR77 0 + 51 | chrXIII 297725 297833 snR76 0 + 52 | chrXIII 297918 298006 snR75 0 + 53 | chrXIII 298138 298225 snR74 0 + 54 | chrXIII 298307 298412 snR73 0 + 55 | chrXIII 298554 298651 snR72 0 + 56 | chrXIII 499984 500072 snR24 0 - 57 | chrXIII 626349 626654 snR83 0 + 58 | chrXIII 652275 652532 snR11 0 + 59 | chrXIII 762110 763113 snR86 0 - 60 | chrXIV 89210 89306 snR40 0 + 61 | chrXIV 230105 230672 snR19 0 - 62 | chrXIV 586090 586175 snR66 0 + 63 | chrXIV 716120 716284 snR49 0 + 64 | chrXIV 721938 722211 snR191 0 - 65 | chrXV 136088 136183 snR58 0 - 66 | chrXV 234346 234546 snR81 0 + 67 | chrXV 259489 259578 snR50 0 + 68 | chrXV 407948 408134 snR9 0 - 69 | chrXV 409765 409864 snR62 0 - 70 | chrXV 680685 680866 snR36 0 - 71 | chrXV 759326 759529 snR35 0 - 72 | chrXV 780107 780596 snR17a 0 + 73 | chrXV 780107 780120 snR17a 0 + 74 | chrXV 780278 780596 snR17a 0 + 75 | chrXV 832332 832521 snR8 0 + 76 | chrXV 841958 842182 snR31 0 - 77 | chrXV 842403 842606 snR5 0 + 78 | chrXVI 173827 173904 snR59 0 + 79 | chrXVI 281056 281517 snR17b 0 - 80 | chrXVI 281056 281373 snR17b 0 - 81 | chrXVI 281504 281517 snR17b 0 - 82 | chrXVI 718700 718806 snR51 0 - 83 | chrXVI 718887 719050 snR70 0 - 84 | chrXVI 719148 719242 snR41 0 - 85 | chrXVI 821732 821903 snR45 0 + 86 | -------------------------------------------------------------------------------- /annotations/Yeast_tRNA_genes.bed: -------------------------------------------------------------------------------- 1 | chrI 139152 139254 tP(UGG)A 0 + 2 | chrI 166267 166339 tA(UGC)A 0 + 3 | chrI 181141 181254 tL(CAA)A 0 + 4 | chrI 182522 182603 tS(AGA)A 0 - 5 | chrII 9583 9666 tL(UAA)B1 0 + 6 | chrII 36398 36488 tF(GAA)B 0 + 7 | chrII 197494 197567 tI(AAU)B 0 + 8 | chrII 197629 197699 tG(GCC)B 0 - 9 | chrII 227075 227156 tS(AGA)B 0 + 10 | chrII 266378 266450 tT(AGU)B 0 + 11 | chrII 326792 326865 tV(UAC)B 0 - 12 | chrII 347603 347686 tL(UAA)B2 0 + 13 | chrII 350827 350898 tQ(UUG)B 0 + 14 | chrII 405878 405949 tR(UCU)B 0 + 15 | chrII 405960 406031 tD(GUC)B 0 + 16 | chrII 643007 643078 tC(GCA)B 0 - 17 | chrII 645167 645238 tE(UUC)B 0 + 18 | chrIII 82462 82533 tE(UUC)C 0 - 19 | chrIII 90859 90972 tL(CAA)C 0 + 20 | chrIII 123577 123648 tP(AGG)C 0 - 21 | chrIII 127716 127789 tN(GUU)C 0 + 22 | chrIII 142701 142771 tG(GCC)C 0 - 23 | chrIII 149920 149991 tM(CAU)C 0 + 24 | chrIII 151284 151356 tK(CUU)C 0 - 25 | chrIII 168301 168372 tQ(UUG)C 0 - 26 | chrIII 227942 228042 tS(CGA)C 0 + 27 | chrIII 295484 295556 tT(AGU)C 0 + 28 | chrIV 83548 83618 tG(GCC)D1 0 + 29 | chrIV 359577 359672 tK(UUU)D 0 + 30 | chrIV 410379 410451 tA(AGC)D 0 + 31 | chrIV 434264 434336 tT(AGU)D 0 - 32 | chrIV 437772 437853 tS(AGA)D1 0 + 33 | chrIV 488797 488870 tV(UAC)D 0 - 34 | chrIV 519743 519826 tL(UAA)D 0 + 35 | chrIV 520972 521043 tQ(UUG)D1 0 + 36 | chrIV 568882 568953 tR(UCU)D 0 + 37 | chrIV 568964 569035 tD(GUC)D 0 + 38 | chrIV 619969 620041 tR(ACG)D 0 - 39 | chrIV 645153 645224 tQ(UUG)D2 0 - 40 | chrIV 668007 668080 tI(AAU)D 0 - 41 | chrIV 802731 802802 tQ(UUG)D3 0 - 42 | chrIV 884361 884493 tI(UAU)D 0 + 43 | chrIV 946312 946400 tY(GUA)D 0 + 44 | chrIV 980974 981055 tS(AGA)D2 0 - 45 | chrIV 992832 992902 tG(GCC)D2 0 + 46 | chrIV 1017207 1017278 tE(CUC)D 0 - 47 | chrIV 1075472 1075544 tV(CAC)D 0 - 48 | chrIV 1095370 1095461 tF(GAA)D 0 - 49 | chrIV 1150842 1150941 tX(XXX)D 0 - 50 | chrIV 1175829 1175901 tM(CAU)D 0 + 51 | chrIV 1201750 1201822 tK(CUU)D1 0 + 52 | chrIV 1257008 1257079 tG(CCC)D 0 - 53 | chrIV 1305630 1305712 tS(AGA)D3 0 + 54 | chrIV 1352466 1352538 tK(CUU)D2 0 - 55 | chrIV 1461715 1461829 tL(CAA)D 0 - 56 | chrIX 175031 175103 tT(AGU)I1 0 + 57 | chrIX 183440 183513 tI(AAU)I1 0 - 58 | chrIX 197592 197663 tE(CUC)I 0 + 59 | chrIX 210665 210738 tI(AAU)I2 0 + 60 | chrIX 248850 248931 tS(UGA)I 0 + 61 | chrIX 300228 300300 tK(CUU)I 0 - 62 | chrIX 324303 324374 tD(GUC)I1 0 - 63 | chrIX 325748 325820 tT(AGU)I2 0 + 64 | chrIX 336349 336420 tD(GUC)I2 0 - 65 | chrIX 370417 370488 tE(UUC)I 0 + 66 | chrV 61890 61960 tG(GCC)E 0 - 67 | chrV 86604 86685 tS(AGA)E 0 + 68 | chrV 100133 100204 tM(CAU)E 0 + 69 | chrV 131082 131153 tQ(UUG)E2 0 - 70 | chrV 135425 135497 tK(CUU)E1 0 - 71 | chrV 138666 138737 tR(UCU)E 0 + 72 | chrV 177099 177170 tE(UUC)E1 0 + 73 | chrV 207357 207428 tH(GUG)E1 0 + 74 | chrV 250286 250357 tQ(UUG)E1 0 + 75 | chrV 288443 288524 tS(UGA)E 0 - 76 | chrV 312023 312095 tA(UGC)E 0 - 77 | chrV 354934 355005 tE(UUC)E2 0 + 78 | chrV 434541 434612 tH(GUG)E2 0 - 79 | chrV 435752 435824 tK(CUU)E2 0 - 80 | chrV 438700 438773 tV(AAC)E1 0 + 81 | chrV 443202 443275 tI(AAU)E1 0 - 82 | chrV 469457 469530 tV(AAC)E2 0 + 83 | chrV 487331 487402 tE(UUC)E3 0 - 84 | chrV 492352 492424 tR(ACG)E 0 - 85 | chrV 551285 551358 tI(AAU)E2 0 - 86 | chrVI 101376 101478 tP(UGG)F 0 + 87 | chrVI 137486 137559 tN(GUU)F 0 - 88 | chrVI 157916 158007 tF(GAA)F 0 - 89 | chrVI 162228 162298 tG(GCC)F1 0 + 90 | chrVI 167437 167525 tY(GUA)F1 0 + 91 | chrVI 180974 181044 tG(GCC)F2 0 - 92 | chrVI 191513 191613 tS(GCU)F 0 - 93 | chrVI 204924 204996 tA(AGC)F 0 - 94 | chrVI 210619 210707 tY(GUA)F2 0 - 95 | chrVI 226688 226760 tK(CUU)F 0 - 96 | chrVII 73829 73902 tV(AAC)G3 0 - 97 | chrVII 110625 110696 tH(GUG)G1 0 - 98 | chrVII 115488 115583 tK(UUU)G1 0 + 99 | chrVII 122269 122341 tK(CUU)G1 0 + 100 | chrVII 185714 185786 tK(CUU)G2 0 - 101 | chrVII 205521 205634 tL(CAA)G1 0 + 102 | chrVII 287350 287455 tW(CCA)G1 0 - 103 | chrVII 319781 319852 tH(GUG)G2 0 + 104 | chrVII 328583 328654 tE(UUC)G1 0 + 105 | chrVII 401527 401598 tE(UUC)G2 0 - 106 | chrVII 405470 405541 tR(UCU)G1 0 + 107 | chrVII 412294 412367 tV(AAC)G1 0 - 108 | chrVII 423092 423205 tL(CAA)G2 0 + 109 | chrVII 440716 440807 tF(GAA)G 0 - 110 | chrVII 531610 531681 tD(GUC)G1 0 + 111 | chrVII 541850 541921 tE(UUC)G3 0 + 112 | chrVII 544577 544648 tD(GUC)G2 0 - 113 | chrVII 561662 561743 tS(AGA)G 0 - 114 | chrVII 661749 661820 tT(UGU)G1 0 + 115 | chrVII 700675 700756 tL(GAG)G 0 + 116 | chrVII 700953 701048 tK(UUU)G2 0 - 117 | chrVII 707108 707179 tC(GCA)G 0 - 118 | chrVII 731137 731210 tN(GUU)G 0 + 119 | chrVII 736340 736411 tR(UCU)G3 0 + 120 | chrVII 739122 739195 tI(AAU)G 0 + 121 | chrVII 774349 774421 tA(AGC)G 0 + 122 | chrVII 779616 779687 tG(UCC)G 0 + 123 | chrVII 794417 794489 tA(UGC)G 0 + 124 | chrVII 823482 823555 tV(AAC)G2 0 + 125 | chrVII 828723 828794 tR(UCU)G2 0 - 126 | chrVII 845649 845719 tG(GCC)G1 0 + 127 | chrVII 857378 857491 tL(CAA)G3 0 - 128 | chrVII 876394 876466 tK(CUU)G3 0 + 129 | chrVII 878710 878815 tW(CCA)G2 0 - 130 | chrVII 930953 931023 tG(GCC)G2 0 - 131 | chrVII 1004216 1004287 tT(UGU)G2 0 + 132 | chrVIII 62755 62826 tH(GUG)H 0 + 133 | chrVIII 85298 85371 tV(AAC)H 0 - 134 | chrVIII 116107 116179 tT(AGU)H 0 - 135 | chrVIII 133026 133107 tS(AGA)H 0 - 136 | chrVIII 134321 134392 tQ(UUG)H 0 + 137 | chrVIII 146242 146314 tA(AGC)H 0 - 138 | chrVIII 237848 237939 tF(GAA)H1 0 - 139 | chrVIII 358478 358569 tF(GAA)H2 0 - 140 | chrVIII 388893 388995 tP(UGG)H 0 - 141 | chrVIII 466990 467061 tT(UGU)H 0 + 142 | chrVIII 475706 475778 tV(CAC)H 0 - 143 | chrX 59100 59172 tT(AGU)J 0 - 144 | chrX 115939 116010 tE(UUC)J 0 - 145 | chrX 197313 197385 tA(AGC)J 0 - 146 | chrX 204735 204806 tD(GUC)J1 0 + 147 | chrX 233939 234011 tR(ACG)J 0 + 148 | chrX 354244 354332 tY(GUA)J1 0 + 149 | chrX 355374 355445 tR(UCU)J1 0 + 150 | chrX 355456 355527 tD(GUC)J2 0 + 151 | chrX 374424 374495 tD(GUC)J3 0 - 152 | chrX 374506 374577 tR(UCU)J2 0 - 153 | chrX 378360 378433 tV(AAC)J 0 + 154 | chrX 391043 391115 tM(CAU)J1 0 - 155 | chrX 396726 396796 tG(GCC)J1 0 - 156 | chrX 414966 415038 tK(CUU)J 0 + 157 | chrX 415931 416036 tW(CCA)J 0 - 158 | chrX 422937 423009 tM(CAU)J2 0 + 159 | chrX 424432 424515 tL(UAA)J 0 - 160 | chrX 517813 517884 tM(CAU)J3 0 - 161 | chrX 524012 524093 tS(AGA)J 0 - 162 | chrX 531828 531898 tG(GCC)J2 0 + 163 | chrX 538555 538626 tR(CCU)J 0 + 164 | chrX 541508 541579 tD(GUC)J4 0 + 165 | chrX 542956 543044 tY(GUA)J2 0 - 166 | chrX 617919 618019 tL(UAG)J 0 + 167 | chrXI 46735 46806 tT(CGU)K 0 - 168 | chrXI 74624 74697 tN(GUU)K 0 + 169 | chrXI 84208 84291 tL(UAA)K 0 + 170 | chrXI 141018 141089 tE(UUC)K 0 - 171 | chrXI 162487 162558 tR(UCU)K 0 - 172 | chrXI 202999 203071 tK(CUU)K 0 + 173 | chrXI 219895 219967 tA(AGC)K1 0 + 174 | chrXI 302918 303023 tW(CCA)K 0 + 175 | chrXI 308144 308217 tV(AAC)K1 0 - 176 | chrXI 313401 313472 tH(GUG)K 0 - 177 | chrXI 379680 379753 tV(AAC)K2 0 + 178 | chrXI 458557 458670 tL(CAA)K 0 + 179 | chrXI 490968 491040 tR(ACG)K 0 + 180 | chrXI 513332 513403 tD(GUC)K 0 - 181 | chrXI 517988 518060 tA(AGC)K2 0 + 182 | chrXI 578965 579060 tK(UUU)K 0 + 183 | chrXII 92548 92650 tP(UGG)L 0 + 184 | chrXII 167944 168025 tS(AGA)L 0 - 185 | chrXII 214883 214955 tA(UGC)L 0 - 186 | chrXII 374355 374427 tR(ACG)L 0 + 187 | chrXII 427132 427203 tD(GUC)L1 0 + 188 | chrXII 448650 448721 tQ(UUG)L 0 - 189 | chrXII 592519 592619 tL(UAG)L1 0 - 190 | chrXII 605300 605432 tI(UAU)L 0 - 191 | chrXII 628383 628497 tL(CAA)L 0 + 192 | chrXII 656934 657006 tA(AGC)L 0 - 193 | chrXII 687859 687932 tV(AAC)L 0 - 194 | chrXII 732090 732190 tL(UAG)L2 0 + 195 | chrXII 734802 734875 tI(AAU)L1 0 + 196 | chrXII 784354 784453 tS(GCU)L 0 + 197 | chrXII 793918 793989 tD(GUC)L2 0 + 198 | chrXII 797178 797249 tE(UUC)L 0 + 199 | chrXII 818609 818680 tR(CCG)L 0 + 200 | chrXII 875376 875471 tK(UUU)L 0 + 201 | chrXII 962972 963055 tL(UAA)L 0 - 202 | chrXII 975983 976056 tN(GUU)L 0 - 203 | chrXII 1052071 1052144 tI(AAU)L2 0 - 204 | chrXIII 131825 131896 tR(UCU)M2 0 - 205 | chrXIII 168795 168883 tY(GUA)M1 0 + 206 | chrXIII 183898 183968 tG(GCC)M 0 - 207 | chrXIII 196068 196170 tP(UGG)M 0 - 208 | chrXIII 259158 259239 tS(AGA)M 0 - 209 | chrXIII 290801 290872 tE(UUC)M 0 + 210 | chrXIII 321147 321219 tA(AGC)M1 0 - 211 | chrXIII 352280 352370 tF(GAA)M 0 + 212 | chrXIII 363064 363135 tH(GUG)M 0 + 213 | chrXIII 372445 372518 tV(AAC)M1 0 - 214 | chrXIII 379303 379408 tW(CCA)M 0 - 215 | chrXIII 420588 420661 tV(AAC)M2 0 - 216 | chrXIII 463554 463625 tD(GUC)M 0 + 217 | chrXIII 480621 480693 tK(CUU)M 0 - 218 | chrXIII 504895 505008 tL(CAA)M 0 + 219 | chrXIII 572883 572955 tM(CAU)M 0 - 220 | chrXIII 586636 586709 tV(AAC)M3 0 - 221 | chrXIII 747892 747963 tR(UCU)M1 0 - 222 | chrXIII 768369 768441 tA(AGC)M2 0 - 223 | chrXIII 808246 808317 tQ(CUG)M 0 - 224 | chrXIII 837928 838016 tY(GUA)M2 0 + 225 | chrXIV 96241 96312 tG(UCC)N 0 - 226 | chrXIV 102716 102789 tN(GUU)N1 0 + 227 | chrXIV 104805 104877 tT(AGU)N1 0 + 228 | chrXIV 374869 374959 tF(GAA)N 0 + 229 | chrXIV 443006 443119 tL(CAA)N 0 + 230 | chrXIV 519099 519169 tD(GUC)N 0 - 231 | chrXIV 547094 547196 tP(UGG)N1 0 + 232 | chrXIV 560693 560765 tT(AGU)N2 0 - 233 | chrXIV 568115 568217 tP(UGG)N2 0 + 234 | chrXIV 569867 569940 tI(AAU)N1 0 - 235 | chrXIV 602312 602385 tI(AAU)N2 0 + 236 | chrXIV 631846 631917 tP(AGG)N 0 - 237 | chrXIV 632599 632672 tN(GUU)N2 0 + 238 | chrXIV 726134 726217 tL(UAA)N 0 - 239 | chrXV 110962 111033 tG(UCC)O 0 - 240 | chrXV 113802 113874 tT(AGU)O1 0 + 241 | chrXV 226611 226681 tG(GCC)O1 0 - 242 | chrXV 228331 228404 tN(GUU)O1 0 + 243 | chrXV 274673 274773 tS(GCU)O 0 + 244 | chrXV 282164 282234 tG(GCC)O2 0 + 245 | chrXV 288192 288280 tY(GUA)O 0 + 246 | chrXV 301097 301198 tP(UGG)O1 0 + 247 | chrXV 340299 340371 tR(ACG)O 0 - 248 | chrXV 354041 354113 tT(AGU)O2 0 - 249 | chrXV 438643 438738 tK(UUU)O 0 + 250 | chrXV 464450 464551 tP(UGG)O2 0 + 251 | chrXV 487439 487512 tN(GUU)O2 0 + 252 | chrXV 571958 572029 tD(GUC)O 0 + 253 | chrXV 594354 594425 tG(CCC)O 0 - 254 | chrXV 663812 663885 tV(AAC)O 0 - 255 | chrXV 710201 710272 tM(CAU)O1 0 + 256 | chrXV 854187 854259 tA(UGC)O 0 - 257 | chrXV 976421 976493 tM(CAU)O2 0 + 258 | chrXV 980683 980787 tP(UGG)O3 0 + 259 | chrXVI 56169 56274 tW(CCA)P 0 - 260 | chrXVI 210192 210263 tE(UUC)P 0 - 261 | chrXVI 338848 338919 tM(CAU)P 0 - 262 | chrXVI 435893 435964 tC(GCA)P1 0 - 263 | chrXVI 560198 560289 tF(GAA)P1 0 - 264 | chrXVI 572269 572339 tG(GCC)P1 0 + 265 | chrXVI 582062 582134 tK(CUU)P 0 + 266 | chrXVI 622540 622631 tF(GAA)P2 0 - 267 | chrXVI 689565 689646 tS(UGA)P 0 + 268 | chrXVI 744284 744355 tT(UGU)P 0 + 269 | chrXVI 769207 769302 tK(UUU)P 0 - 270 | chrXVI 775765 775836 tC(GCA)P2 0 - 271 | chrXVI 810676 810749 tN(GUU)P 0 + 272 | chrXVI 819529 819602 tI(AAU)P1 0 + 273 | chrXVI 856902 856974 tA(AGC)P 0 + 274 | chrXVI 860379 860449 tG(GCC)P2 0 + 275 | chrXVI 880296 880369 tI(AAU)P2 0 - 276 | -------------------------------------------------------------------------------- /computeLengthHistogram.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript 2 | library("optparse") 3 | 4 | options = list( 5 | make_option(c("-f", "--files"), type="character", default=NULL, 6 | help="Data file names, separated by commas only (BAM format)"), 7 | make_option(c("-l", "--minLength"), type="integer", default=0, 8 | help="The smallest DNA fragment to be considered [default = %default]"), 9 | make_option(c("-L", "--maxLength"), type="integer", default=500, 10 | help="The largest DNA fragment to be considered [default = %default]"), 11 | make_option(c("-s", "--statistics"), type="character", default="on", 12 | help="Include statistics in the plot [options: on, off; default = %default]"), 13 | make_option(c("-o", "--outputs"), type="character", default="pdf,csv,RData", 14 | help="Types of outputs to be generated, separated by commas only [options: pdf, csv, RData; default = %default]") 15 | ) 16 | 17 | opt_parser = OptionParser(option_list=options) 18 | opt = parse_args(opt_parser) 19 | 20 | 21 | if (is.null(opt$file)){ 22 | print_help(opt_parser) 23 | stop("At least the dataset file name must be supplied.", call.=FALSE) 24 | } 25 | 26 | minLength = opt$minLength 27 | maxLength = opt$maxLength 28 | 29 | ################## 30 | # Initialization # 31 | ################## 32 | # Load the necessary R packages 33 | suppressPackageStartupMessages({ 34 | library(GenomicRanges) 35 | library(rtracklayer) 36 | library(caTools) 37 | library(colorRamps) 38 | library(Rsamtools) 39 | library(ggplot2) 40 | library(gridExtra) 41 | }) 42 | 43 | # Data files 44 | bam.files = opt$files 45 | bam.files = strsplit(bam.files, ',')[[1]] 46 | noFiles = length(bam.files) 47 | 48 | for (f in 1:noFiles){ 49 | ######################################### 50 | # Import the paired-end sequencing data # 51 | ######################################### 52 | # Data file name 53 | inputFilename = bam.files[f] 54 | sample.name = sub(".bam", "", inputFilename) 55 | all_fields = c("rname", "pos", "isize") 56 | param = ScanBamParam(what = all_fields, 57 | flag = scanBamFlag(isPaired = TRUE, isProperPair = TRUE, 58 | isUnmappedQuery = FALSE, hasUnmappedMate = FALSE, 59 | isMinusStrand = FALSE, isMateMinusStrand = TRUE, 60 | isNotPassingQualityControls = FALSE)) 61 | bam = scanBam(inputFilename, param=param) 62 | 63 | # Keep only the proper reads, with the length > 0 64 | posStrandReads = (bam[[1]]$isize > 0) 65 | 66 | reads = GRanges(seqnames=Rle(bam[[1]]$rname[posStrandReads]), 67 | ranges = IRanges(start=bam[[1]]$pos[posStrandReads], width=bam[[1]]$isize[posStrandReads]), 68 | strand = "*") 69 | rm(bam) 70 | readLength = width(reads) 71 | TotalNoReads = length(reads) 72 | 73 | ######################################### 74 | # Compute the fragment length histogram # 75 | ######################################### 76 | output.files = toupper(opt$outputs) 77 | filesToGenerate = strsplit(output.files, ',')[[1]] 78 | 79 | # Compute the histogram 80 | h = hist(readLength, breaks=seq(from = 0.5, to = 1000.5, by = 1), plot=FALSE) 81 | 82 | # Create folder 83 | dir.create("Length_histograms", showWarnings = FALSE) 84 | 85 | if ("PDF" %in% filesToGenerate){ 86 | # Plot the histogram using ggplot2 87 | 88 | df = data.frame(x = h$mids, y = 100*h$density) 89 | myplot = ggplot(df, aes(x = x, y = y)) + geom_line(colour="#56B4E9") + 90 | scale_x_continuous(expand = c(0, 0), limits = c(minLength, maxLength)) + 91 | scale_y_continuous(expand = c(0, 0)) + theme_bw() + 92 | theme(panel.border = element_blank(), axis.line = element_line(colour = "black"), plot.margin = unit(c(0.5,0.5,0.25,0.25), "cm")) + 93 | theme(plot.title = element_text(hjust = 0.5)) + 94 | xlab("Fragment length (bp)") + 95 | ylab("Percentage (%)") + 96 | ggtitle(sample.name) + 97 | theme(axis.text=element_text(size=14), 98 | axis.title=element_text(size=18,face="bold"), 99 | plot.title=element_text(size=18,face="bold")) 100 | 101 | if (opt$statistics == 'on') { 102 | # Add table of quantiles 103 | mytable = data.frame(Percentile = c("5%", "10%", "25%", "50%", "75%", "90%", "95%"), 104 | Length = quantile(readLength, probs = c(0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95))) 105 | 106 | myplot = myplot + annotation_custom(tableGrob(mytable, rows=NULL), xmin=minLength + 0.65*(maxLength-minLength), xmax=minLength + 0.95*(maxLength-minLength), ymin=0.27*max(100*h$density), ymax=0.95*max(100*h$density)) 107 | 108 | suppressWarnings( 109 | ggsave(filename=paste("Length_histograms/Length_histogram.", sample.name, ".w_stats.pdf", sep=""), 110 | plot=myplot, 111 | width = 5, height = 4, units = "in")) 112 | } else { 113 | suppressWarnings( 114 | ggsave(filename=paste("Length_histograms/Length_histogram.", sample.name, ".pdf", sep=""), 115 | plot=myplot, 116 | width = 5, height = 4, units = "in")) 117 | } 118 | 119 | } 120 | 121 | if ("CSV" %in% filesToGenerate){ 122 | # Save the histogram in a CSV format 123 | write.csv(data.frame(Length=1:1000, Percentage=100*h$density), 124 | file=paste("Length_histograms/Length_histogram.", sample.name, ".csv", sep=""), 125 | row.names=FALSE) 126 | } 127 | 128 | if ("RDATA" %in% filesToGenerate){ 129 | fragmentLength = 1:1000 130 | Percentage = 100*h$density 131 | save(fragmentLength, Percentage, TotalNoReads, sample.name, file=paste("Length_histograms/Length_histogram.", sample.name, ".RData", sep="")) 132 | } 133 | } 134 | -------------------------------------------------------------------------------- /config/annotation_config.yaml: -------------------------------------------------------------------------------- 1 | 2 | annotations: 3 | sacCer3: 4 | chromosome_size: 5 | url: http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/chromInfo.txt.gz 6 | filter: 7 | - chrI 8 | - chrII 9 | - chrIII 10 | - chrIV 11 | - chrV 12 | - chrVI 13 | - chrVII 14 | - chrVIII 15 | - chrIX 16 | - chrX 17 | - chrXI 18 | - chrXII 19 | - chrXIII 20 | - chrXIV 21 | - chrXV 22 | - chrXVI 23 | path: annotations/sacCer3_chromInfo.txt 24 | file: 25 | path: annotations/sacCer3_annotations.csv 26 | EF2: 27 | chromosome_size: 28 | filter: 29 | - I 30 | - II 31 | - III 32 | path: annotations/EF2_chromInfo.txt 33 | mart: 34 | host: fungi.ensembl.org 35 | biomart: fungi_mart 36 | dataset: spombe_eg_gene 37 | attributes: 38 | - refseq_mrna 39 | - chromosome_name 40 | - strand 41 | - transcript_start 42 | - transcript_end 43 | attributeId: refseq_mrna 44 | vars: # required. format: "variable name: mart attribute name" 45 | strand: strand 46 | txStart: transcript_start 47 | txEnd: transcript_end 48 | chrName: chromosome_name 49 | tair10: 50 | chromosome_size: 51 | url: https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/araTha1.chrom.sizes 52 | filter: 53 | - 1 54 | - 2 55 | - 3 56 | - 4 57 | - 5 58 | path: annotations/tair10_chromInfo.txt 59 | mart: 60 | host: plants.ensembl.org 61 | biomart: plants_mart 62 | dataset: athaliana_eg_gene 63 | attributes: 64 | - ensembl_transcript_id 65 | - chromosome_name 66 | - strand 67 | - transcript_start 68 | - transcript_end 69 | attributeId: ensembl_transcript_id 70 | vars: # required. format: "variable name: mart attribute name" 71 | strand: strand 72 | txStart: transcript_start 73 | txEnd: transcript_end 74 | chrName: chromosome_name 75 | dm3: 76 | chromosome_size: 77 | url: http://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/chromInfo.txt.gz 78 | filter: 79 | - chr2L 80 | - chr2R 81 | - chr3L 82 | - chr3R 83 | - chr4 84 | - chrX 85 | path: annotations/dm3_chromInfo.txt 86 | mart: 87 | host: oct2014.archive.ensembl.org 88 | biomart: ENSEMBL_MART_ENSEMBL 89 | dataset: dmelanogaster_gene_ensembl 90 | attributes: 91 | - refseq_mrna 92 | - chromosome_name 93 | - strand 94 | - transcript_start 95 | - transcript_end 96 | attributeId: refseq_mrna 97 | vars: # required. format: "variable name: mart attribute name" 98 | strand: strand 99 | txStart: transcript_start 100 | txEnd: transcript_end 101 | chrName: chromosome_name 102 | dm6: 103 | chromosome_size: 104 | url: http://hgdownload.cse.ucsc.edu/goldenPath/dm6/database/chromInfo.txt.gz 105 | filter: 106 | - chr2L 107 | - chr2R 108 | - chr3L 109 | - chr3R 110 | - chr4 111 | - chrX 112 | - chrY 113 | path: annotations/dm6_chromInfo.txt 114 | mart: 115 | host: may2017.archive.ensembl.org 116 | biomart: ENSEMBL_MART_ENSEMBL 117 | dataset: dmelanogaster_gene_ensembl 118 | attributes: 119 | - refseq_mrna 120 | - chromosome_name 121 | - strand 122 | - transcript_start 123 | - transcript_end 124 | attributeId: refseq_mrna 125 | vars: # required. format: "variable name: mart attribute name" 126 | strand: strand 127 | txStart: transcript_start 128 | txEnd: transcript_end 129 | chrName: chromosome_name 130 | ce10: 131 | chromosome_size: 132 | url: http://hgdownload.cse.ucsc.edu/goldenPath/ce10/database/chromInfo.txt.gz 133 | filter: 134 | - chrI 135 | - chrII 136 | - chrIII 137 | - chrIV 138 | - chrV 139 | - chrX 140 | path: annotations/ce10_chromInfo.txt 141 | mart: 142 | host: may2012.archive.ensembl.org 143 | biomart: ENSEMBL_MART_ENSEMBL 144 | dataset: celegans_gene_ensembl 145 | attributes: 146 | - refseq_mrna 147 | - chromosome_name 148 | - strand 149 | - transcript_start 150 | - transcript_end 151 | attributeId: refseq_mrna 152 | vars: # required. format: "variable name: mart attribute name" 153 | strand: strand 154 | txStart: transcript_start 155 | txEnd: transcript_end 156 | chrName: chromosome_name 157 | ce11: 158 | chromosome_size: 159 | url: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/chromInfo.txt.gz 160 | filter: 161 | - chrI 162 | - chrII 163 | - chrIII 164 | - chrIV 165 | - chrV 166 | - chrX 167 | path: annotations/ce11_chromInfo.txt 168 | mart: 169 | host: jan2019.archive.ensembl.org 170 | biomart: ENSEMBL_MART_ENSEMBL 171 | dataset: celegans_gene_ensembl 172 | attributes: 173 | - refseq_mrna 174 | - chromosome_name 175 | - strand 176 | - transcript_start 177 | - transcript_end 178 | attributeId: refseq_mrna 179 | vars: # required. format: "variable name: mart attribute name" 180 | strand: strand 181 | txStart: transcript_start 182 | txEnd: transcript_end 183 | chrName: chromosome_name 184 | mm9: 185 | chromosome_size: 186 | url: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz 187 | filter: 188 | - chr1 189 | - chr2 190 | - chr3 191 | - chr4 192 | - chr5 193 | - chr6 194 | - chr7 195 | - chr8 196 | - chr9 197 | - chr10 198 | - chr11 199 | - chr12 200 | - chr13 201 | - chr14 202 | - chr15 203 | - chr16 204 | - chr17 205 | - chr18 206 | - chr19 207 | - chrX 208 | - chrY 209 | path: annotations/mm9_chromInfo.txt 210 | mart: 211 | host: may2012.archive.ensembl.org 212 | biomart: ENSEMBL_MART_ENSEMBL 213 | dataset: mmusculus_gene_ensembl 214 | attributes: 215 | - refseq_mrna 216 | - chromosome_name 217 | - strand 218 | - transcript_start 219 | - transcript_end 220 | attributeId: refseq_mrna 221 | vars: # required. format: "variable name: mart attribute name" 222 | strand: strand 223 | txStart: transcript_start 224 | txEnd: transcript_end 225 | chrName: chromosome_name 226 | mm10: 227 | chromosome_size: 228 | url: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz 229 | filter: 230 | - chr1 231 | - chr2 232 | - chr3 233 | - chr4 234 | - chr5 235 | - chr6 236 | - chr7 237 | - chr8 238 | - chr9 239 | - chr10 240 | - chr11 241 | - chr12 242 | - chr13 243 | - chr14 244 | - chr15 245 | - chr16 246 | - chr17 247 | - chr18 248 | - chr19 249 | - chrX 250 | - chrY 251 | path: annotations/mm10_chromInfo.txt 252 | mart: 253 | host: oct2018.archive.ensembl.org 254 | biomart: ENSEMBL_MART_ENSEMBL 255 | dataset: mmusculus_gene_ensembl 256 | attributes: 257 | - refseq_mrna 258 | - chromosome_name 259 | - strand 260 | - transcript_start 261 | - transcript_end 262 | attributeId: refseq_mrna 263 | vars: # required. format: "variable name: mart attribute name" 264 | strand: strand 265 | txStart: transcript_start 266 | txEnd: transcript_end 267 | chrName: chromosome_name 268 | hg18: 269 | chromosome_size: 270 | url: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz 271 | filter: 272 | - chr1 273 | - chr2 274 | - chr3 275 | - chr4 276 | - chr5 277 | - chr6 278 | - chr7 279 | - chr8 280 | - chr9 281 | - chr10 282 | - chr11 283 | - chr12 284 | - chr13 285 | - chr14 286 | - chr15 287 | - chr16 288 | - chr17 289 | - chr18 290 | - chr19 291 | - chr20 292 | - chr21 293 | - chr22 294 | - chrX 295 | - chrY 296 | path: annotations/hg18_chromInfo.txt 297 | mart: 298 | host: may2009.archive.ensembl.org 299 | biomart: ENSEMBL_MART_ENSEMBL 300 | dataset: hsapiens_gene_ensembl 301 | attributes: 302 | - refseq_mrna 303 | - chromosome_name 304 | - strand 305 | - transcript_start 306 | - transcript_end 307 | attributeId: refseq_mrna 308 | vars: # required. format: "variable name: mart attribute name" 309 | strand: strand 310 | txStart: transcript_start 311 | txEnd: transcript_end 312 | chrName: chromosome_name 313 | hg19: 314 | chromosome_size: 315 | url: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz 316 | filter: 317 | - chr1 318 | - chr2 319 | - chr3 320 | - chr4 321 | - chr5 322 | - chr6 323 | - chr7 324 | - chr8 325 | - chr9 326 | - chr10 327 | - chr11 328 | - chr12 329 | - chr13 330 | - chr14 331 | - chr15 332 | - chr16 333 | - chr17 334 | - chr18 335 | - chr19 336 | - chr20 337 | - chr21 338 | - chr22 339 | - chrX 340 | - chrY 341 | path: annotations/hg19_chromInfo.txt 342 | mart: 343 | host: grch37.ensembl.org 344 | biomart: ENSEMBL_MART_ENSEMBL 345 | dataset: hsapiens_gene_ensembl 346 | attributes: 347 | - refseq_mrna 348 | - chromosome_name 349 | - strand 350 | - transcript_start 351 | - transcript_end 352 | attributeId: refseq_mrna 353 | vars: # required. format: "variable name: mart attribute name" 354 | strand: strand 355 | txStart: transcript_start 356 | txEnd: transcript_end 357 | chrName: chromosome_name 358 | hg38: 359 | chromosome_size: 360 | url: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz 361 | filter: 362 | - chr1 363 | - chr2 364 | - chr3 365 | - chr4 366 | - chr5 367 | - chr6 368 | - chr7 369 | - chr8 370 | - chr9 371 | - chr10 372 | - chr11 373 | - chr12 374 | - chr13 375 | - chr14 376 | - chr15 377 | - chr16 378 | - chr17 379 | - chr18 380 | - chr19 381 | - chr20 382 | - chr21 383 | - chr22 384 | - chrX 385 | - chrY 386 | path: annotations/hg38_chromInfo.txt 387 | mart: 388 | host: jan2019.archive.ensembl.org 389 | biomart: ENSEMBL_MART_ENSEMBL 390 | dataset: hsapiens_gene_ensembl 391 | attributes: 392 | - refseq_mrna 393 | - chromosome_name 394 | - strand 395 | - transcript_start 396 | - transcript_end 397 | attributeId: refseq_mrna 398 | vars: # required. format: "variable name: mart attribute name" 399 | strand: strand 400 | txStart: transcript_start 401 | txEnd: transcript_end 402 | chrName: chromosome_name 403 | 404 | -------------------------------------------------------------------------------- /config/config.yaml: -------------------------------------------------------------------------------- 1 | application: 2 | paths: 3 | source: 4 | # config: 5 | reads: 6 | annotations: 7 | output: 8 | -------------------------------------------------------------------------------- /misc/Figure_3.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /misc/Figure_7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rchereji/plot2DO/2c904ab36dc27b30663b1d43ba626fb571f24f48/misc/Figure_7.png -------------------------------------------------------------------------------- /misc/Figure_8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rchereji/plot2DO/2c904ab36dc27b30663b1d43ba626fb571f24f48/misc/Figure_8.png -------------------------------------------------------------------------------- /plot2DO.R: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env Rscript 2 | 3 | # Check the minimum R version: R>=3.5.0 (required for Bioconductor 3.7) 4 | getRversion <- function() { 5 | rvs <- sub("R version ", "", R.version.string) 6 | pos <- gregexpr(" \\(", rvs)[[1]][1] 7 | rVersion <- substr(rvs, 1, pos-1) 8 | releaseDate <- substr(rvs, pos+2, nchar(rvs)-1) 9 | result <- list("version" = rVersion, "date" = releaseDate) 10 | return(result) 11 | } 12 | 13 | rvs <- getRversion() 14 | rVersion <- rvs$version 15 | releaseDate <- rvs$date 16 | if (rVersion < "3.5") { 17 | stop(paste0("Your R version is ", rVersion,", which is a bit too old (release date: ", releaseDate, ").\nTo run plot2DO, please upgrade R to a version >= 3.5.0.\nYou can download the latest version of R from https://www.r-project.org/")) 18 | } 19 | 20 | suppressPackageStartupMessages({ 21 | library(yaml) 22 | }) 23 | 24 | # Load default paths from config.yaml 25 | config <- yaml.load_file("config/config.yaml") 26 | 27 | sourceBasePath <- config$application$paths$source 28 | if(is.null(sourceBasePath)) { 29 | sourceBasePath <- file.path(getwd(), "source") 30 | } 31 | 32 | readsBasePath <- config$application$paths$reads 33 | if(is.null(readsBasePath)) { 34 | readsBasePath <- getwd() 35 | } 36 | 37 | outputBasePath <- config$application$paths$outTests 38 | if(is.null(outputBasePath)) { 39 | outputBasePath <- file.path(getwd(), "output") 40 | } 41 | 42 | annotationsBasePath <- config$application$paths$annotations 43 | if(is.null(annotationsBasePath)) { 44 | annotationsBasePath <- getwd() 45 | } 46 | 47 | configBasePath <- config$application$paths$config 48 | if(is.null(configBasePath)) { 49 | configBasePath <- file.path(getwd(), "config") 50 | } 51 | 52 | main <- file.path(sourceBasePath, "plot2DO_main.R") 53 | 54 | source(main) 55 | 56 | Main() 57 | 58 | -------------------------------------------------------------------------------- /plot2DO_setup.R: -------------------------------------------------------------------------------- 1 | # Libraries that are required: 2 | # CRAN: 3 | # c("colorRamps", "doParallel", "foreach", "ggplot2", "gridExtra", "optparse", "pracma", "reshape2", "yaml") 4 | # Bioconductor: 5 | # c("AnnotationHub", "biomaRt", "GenomicFeatures", "GenomicRanges", "GenomeInfoDb", "IRanges", "Rsamtools", "rtracklayer") 6 | # R core libraries (do not need installation): 7 | # c("grid", "parallel", "tools") 8 | 9 | 10 | noError = TRUE 11 | 12 | # Install CRAN packages 13 | cat("Checking and installing missing CRAN packages:\n") 14 | cranLibraries <- c("colorRamps", "doParallel", "foreach", "ggplot2", "gridExtra", "optparse", "pracma", "reshape2", "xml2", "yaml") 15 | foo <- sapply(cranLibraries, function(x) { 16 | if (requireNamespace(x, quietly = TRUE)){ 17 | result <- "was already available." 18 | } else { 19 | install.packages(x, repos="http://cloud.r-project.org") 20 | success <- requireNamespace(x, quietly = TRUE) 21 | if(success) { 22 | result <- "was successfully installed." 23 | } else { 24 | result <- "error: not available and cannot install!" 25 | noError = FALSE 26 | } 27 | } 28 | cat(" >", paste(x, result, sep = ".....")) 29 | cat("\n") 30 | }) 31 | 32 | 33 | 34 | # Install Bioconductor packages 35 | cat("\n") 36 | cat("Checking and installing missing Bioconductor packages:\n") 37 | bioconductorLibraries <- c("AnnotationHub", "biomaRt", "GenomicFeatures", "GenomicRanges", "GenomeInfoDb", "IRanges", "Rsamtools", "rtracklayer") 38 | if (!requireNamespace("BiocManager", quietly = TRUE)){ 39 | install.packages("BiocManager") 40 | } 41 | foo <- sapply(bioconductorLibraries, function(x) { 42 | if (requireNamespace(x, quietly = TRUE)){ 43 | result <- "was already available." 44 | } else { 45 | BiocManager::install(x) 46 | success <- requireNamespace(x, quietly = TRUE) 47 | if(success) { 48 | result <- "was successfully installed." 49 | } else { 50 | result <- "error: not available and cannot install!" 51 | noError = FALSE 52 | } 53 | } 54 | cat(" >", paste(x, result, sep = ".....")) 55 | cat("\n") 56 | }) 57 | 58 | cat("\nDone!") 59 | if (noError) { 60 | cat(" All the required packages are available now.\n") 61 | } else { 62 | cat(" Error(s) found! See above.\n") 63 | } 64 | -------------------------------------------------------------------------------- /sample_BAM_files/README.md: -------------------------------------------------------------------------------- 1 | ## Sample BAM files 2 | The data that were used in the examples were downloaded from GEO database. The corresponding accession numbers are listed below: 3 | 4 | | Filename | GEO accession number for the raw data | 5 | | ------------- | ------------- | 6 | | yeast_SRR2045610.bam | [GSM1700669](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1700669) | 7 | | yeast_50U_MNase_SRR3649301.bam | [GSM2193286](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193286) | 8 | | yeast_100U_MNase_SRR3649296.bam | [GSM2193281](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193281) | 9 | | yeast_200U_MNase_SRR3649297.bam | [GSM2193282](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193282) | 10 | | yeast_300U_MNase_SRR3649298.bam | [GSM2193283](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193283) | 11 | | yeast_400U_MNase_SRR3649299.bam | [GSM2193284](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2193284) | 12 | | fly_SRR2038265.bam | [GSM1694824](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1694824) | 13 | | mouse_SRR5116996.bam | [GSM2430825](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2430825) | 14 | | human_SRR1781839.bam | [GSM1425454](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1425454) | 15 | 16 | The size of the above data sets exceeds the allowed quota for a GitHub repository. Therefore, for convenience, we provide at the following website sets of 5 million paired-end reads randomly selected from the aforementioned data sets: 17 | 18 | https://goo.gl/W2AoW7 19 | 20 | 21 | #### *Important note* 22 | 23 | The figures shown in the examples were generated using all the reads from each GEO accession, so the figures generated using the sub-sampled data sets should look slightly different. These sub-sampled data sets are provided only to facilitate the testing of **plot2DO**, and should not be used for other purposes (*e.g.* in a publication). 24 | -------------------------------------------------------------------------------- /source/plot2DO_core.R: -------------------------------------------------------------------------------- 1 | suppressPackageStartupMessages({ 2 | library(GenomicRanges) 3 | library(IRanges) 4 | library(rtracklayer) 5 | library(pracma) 6 | library(doParallel) 7 | library(foreach) 8 | }) 9 | 10 | 11 | ComputeNormalizationFactors <- function(reads) { 12 | 13 | # Compute rescaling coefficients, such that after rescaling the average occupancy is 1, for each chromosome 14 | occ <- coverage(reads) 15 | chrLabel <- seqlevels(occ) 16 | coverageWeight <- lapply(chrLabel, function(chr) 1/mean(occ[[chr]])) 17 | names(coverageWeight) <- chrLabel 18 | return(coverageWeight) 19 | } 20 | 21 | 22 | noCores <- switch(Sys.info()[['sysname']], 23 | Windows = 1, # the parallel functions do not work in Windows... 24 | Linux = floor(detectCores(logical = FALSE) / 2), # logical = FALSE does not work in linux..., so we divide by 2 25 | Darwin = detectCores(logical = FALSE)) # Mac 26 | 27 | if(noCores > 1) { 28 | noCores <- min(noCores - 1, 8) # Do not use more than 8 cores (to prevent memory issues) 29 | } 30 | 31 | # Parallelized version, much faster (~100x faster on my macbook pro) 32 | ComputeCoverageMatrix <- function(lMin, lMax, beforeRef, afterRef, reads, 33 | coverageWeight, referenceGRanges, readLength, referenceGenome) 34 | { 35 | # For human and mouse data, limit the number of cores to 2 (increase this # according to the available memory that is available on your system) 36 | if (referenceGenome %in% c('mm9', 'mm10', 'hg18', 'hg19', 'hg38')){ 37 | noCores = min(c(2, noCores)) 38 | } 39 | 40 | occ <- coverage(reads) 41 | chrLabel <- seqlevels(occ) 42 | noChr <- length(chrLabel) 43 | 44 | registerDoParallel(cores=noCores) 45 | 46 | # For each fragment size, compute the corresponding coverage/occupancy 47 | #occMatrixTranspose <- foreach(l=lMin:lMax, .combine='cbind') %dopar% { 48 | occMatrixTranspose <- foreach(l=lMin:lMax, .export=c("AlignRegionsTranspose"), .packages=c('GenomicRanges', 'pracma'), .combine='cbind') %dopar% { 49 | # Keep only the reads with the specific length l 50 | goodReadsInd <- (readLength == l) 51 | goodReads <- reads[goodReadsInd] 52 | 53 | # Compute average occupancy 54 | occ <- coverage(goodReads, weight=coverageWeight) 55 | alignedRegionsTranspose <- AlignRegionsTranspose(occ, referenceGRanges) 56 | rowMeans(alignedRegionsTranspose) 57 | } 58 | occMatrix <- t(occMatrixTranspose) 59 | rownames(occMatrix) <- c() 60 | 61 | stopImplicitCluster() 62 | #registerDoSEQ() 63 | 64 | return(occMatrix) 65 | } 66 | 67 | AlignRegionsTranspose <- function(profile, referenceGRanges) 68 | { 69 | # Create Views with all the referenceGRanges 70 | chrName <- unique(as.character(seqnames(referenceGRanges))) 71 | myViews <- Views(profile[chrName], as(referenceGRanges, "IntegerRangesList")[chrName]) 72 | 73 | alignedProfilesList <- lapply(myViews, function(gr) viewApply(gr, as.vector)) 74 | alignedProfiles <- do.call("cbind", alignedProfilesList) 75 | 76 | ## Get the index of referenceGRanges, which were reorganized by as(referenceGRanges, "IntegerRangesList") 77 | listInd <- split(1:length(referenceGRanges), as.factor(seqnames(referenceGRanges))) 78 | idx <- do.call("c", listInd) 79 | 80 | alignedProfiles <- alignedProfiles[, order(idx)] 81 | 82 | ## Flip regions from the Crick strand 83 | crickInd <- which(strand(referenceGRanges) == "-") 84 | alignedProfiles[ , crickInd] <- flipud(alignedProfiles[ , crickInd]) 85 | 86 | return(alignedProfiles) 87 | } 88 | 89 | ConstructReferenceGRanges <- function(optSites, annotat, selectedReference, beforeRef, afterRef, genome, optAlign) { 90 | 91 | chrLen <- annotat$chrLen 92 | 93 | annotations <- annotat$annotations 94 | 95 | if (is.null(optSites)) { 96 | 97 | if(selectedReference == "Plus1" & genome != 'sacCer3') { 98 | print_help(opt_parser) 99 | stop("Plus1 annotations are available only for the sacCer3 genome. For other genomes, the available options for --reference are: TSS (default), TTS", call.=FALSE) 100 | } 101 | 102 | referencePos <- annotations[[selectedReference]] 103 | referenceChr <- annotations$Chr 104 | refStrand <- annotations$Strand 105 | 106 | validValues <- (! is.nan(referencePos)) 107 | referencePos <- referencePos[validValues] 108 | referenceChr <- referenceChr[validValues] 109 | refStrand <- refStrand[validValues] 110 | 111 | watson <- (refStrand == 1) 112 | 113 | } else { 114 | 115 | referenceFilename <- optSites 116 | referenceFilePath <- file.path(annotationsBasePath, referenceFilename) 117 | sites <- import.bed(referenceFilePath) 118 | 119 | if(genome == 'tair10') { 120 | seqlevelsStyle(sites) <- 'Ensembl' 121 | } else { 122 | # Make sure the chromosome names are following the 'UCSC' convention 123 | seqlevelsStyle(sites) <- 'UCSC' 124 | } 125 | 126 | switch(optAlign, 127 | "center" ={ fixAlign = "center" }, 128 | "fivePrime" ={ fixAlign = "start" }, 129 | "threePrime"={ fixAlign = "end" }) 130 | 131 | referenceGRanges <- resize(sites, width = 1, fix = fixAlign) 132 | 133 | referencePos <- start(referenceGRanges) 134 | referenceChr <- seqnames(referenceGRanges) 135 | refStrand <- strand(referenceGRanges) 136 | 137 | watson <- as.vector(strand(refStrand) != '-') # ('+' or '*') 138 | } 139 | 140 | leftEdge <- referencePos - beforeRef 141 | rightEdge <- referencePos + afterRef 142 | 143 | leftEdgeCrick <- referencePos - afterRef 144 | rightEdgeCrick <- referencePos + beforeRef 145 | 146 | leftEdge[!watson] <- leftEdgeCrick[!watson] 147 | rightEdge[!watson] <- rightEdgeCrick[!watson] 148 | 149 | wholeChr <- GRanges(seqnames=names(chrLen), IRanges(start=rep(1, length(chrLen)), end=chrLen)) 150 | 151 | referenceGRanges <- GRanges(seqnames=referenceChr, IRanges(start=leftEdge, end=rightEdge), strand=refStrand) 152 | result <- subsetByOverlaps(referenceGRanges, wholeChr, type="within", ignore.strand=TRUE) 153 | 154 | return(result) 155 | 156 | } 157 | 158 | 159 | CalculatePlotData <- function(params, reads, referenceGRanges) { 160 | 161 | # Compute the histogram 162 | readLength <- width(reads) 163 | h <- hist(readLength, breaks=seq(from = 0.5, to = max(readLength, 1000, params$lMax)+0.5, by = 1), plot=FALSE) 164 | lengthHist <- 100 * h$density[params$lMin:params$lMax] 165 | 166 | totalNoReads <- length(reads) 167 | 168 | resized_reads <- switch(params$plotType, 169 | "OCC" = reads, 170 | "DYADS" = resize(reads, width = 1, fix = "center"), 171 | "FIVEPRIME_ENDS" = resize(reads, width = 1, fix = "start"), 172 | "THREEPRIME_ENDS"= resize(reads, width = 1, fix = "end")) 173 | 174 | coverageWeight <- ComputeNormalizationFactors(resized_reads) 175 | 176 | occMatrix <- ComputeCoverageMatrix(params$lMin, params$lMax, params$beforeRef, params$afterRef, 177 | resized_reads, coverageWeight, referenceGRanges, readLength, params$genome) 178 | 179 | outputFilePath <- GetOutputMatrixFilePath(params$plotType, params$referencePointsBed, 180 | params$reference, params$siteLabel, 181 | params$lMin, params$lMax, params$sampleName) 182 | 183 | # Parameters to be saved: 184 | lMin <- params$lMin 185 | lMax <- params$lMax 186 | beforeRef <- params$beforeRef 187 | afterRef <- params$afterRef 188 | sampleName <- params$sampleName 189 | siteLabel <- params$siteLabel 190 | save(occMatrix, lMin, lMax, beforeRef, afterRef, totalNoReads, lengthHist, sampleName, siteLabel, file=outputFilePath) 191 | 192 | } 193 | 194 | -------------------------------------------------------------------------------- /source/plot2DO_data.R: -------------------------------------------------------------------------------- 1 | suppressPackageStartupMessages({ 2 | library(tools) 3 | library(AnnotationHub) 4 | library(yaml) 5 | library(biomaRt) 6 | library(Rsamtools) 7 | library(rtracklayer) 8 | library(GenomeInfoDb) 9 | library(GenomicFeatures) 10 | }) 11 | 12 | LoadReads <- function(inputFilename, genome, annotations){ 13 | 14 | inputType <- toupper(file_ext(inputFilename)) 15 | 16 | switch(inputType, 17 | BED={ 18 | reads <- BuildReadsGRangesFromBED(inputFilename, genome, annotations) 19 | }, 20 | BAM={ 21 | reads <- BuildReadsGRangesFromBAM(inputFilename, genome, annotations) 22 | }, 23 | { 24 | print_help(opt_parser) 25 | stop("File type not supported! Please provide a BED or BAM file as input.", call.=FALSE) 26 | } 27 | ) 28 | 29 | return(reads) 30 | 31 | } 32 | 33 | BuildReadsGRangesFromBED <- function(bedFilename, genome, annotations){ 34 | reads <- import.bed(bedFilename) 35 | 36 | if(genome == 'tair10') { 37 | seqlevelsStyle(reads) <- 'Ensembl' 38 | } else { 39 | # Make sure the chromosome names are following the 'UCSC' convention 40 | seqlevelsStyle(reads) <- 'UCSC' 41 | } 42 | 43 | genomeSeqInfo <- Seqinfo(seqnames = names(annotations$chrLen), 44 | seqlengths = as.numeric(annotations$chrLen), 45 | isCircular = rep(NA, length(annotations$chrLen)), 46 | genome = rep(genome, length(annotations$chrLen))) 47 | 48 | good.seq.levels <- intersect(seqlevels(reads), seqlevels(genomeSeqInfo)) 49 | 50 | result <- keepSeqlevels(reads, good.seq.levels, pruning.mode="coarse") 51 | seqlevels(result) <- good.seq.levels 52 | seqlevels(genomeSeqInfo) <- good.seq.levels 53 | seqinfo(result) <- genomeSeqInfo 54 | return(result) 55 | } 56 | 57 | BuildReadsGRangesFromBAM <- function(bamFilename, genome, annotations){ 58 | all_fields <- c("rname", "pos", "isize") 59 | param <- ScanBamParam(what = all_fields, 60 | flag = scanBamFlag(isPaired = TRUE, isProperPair = TRUE, 61 | isUnmappedQuery = FALSE, hasUnmappedMate = FALSE, 62 | isMinusStrand = FALSE, isMateMinusStrand = TRUE, 63 | isNotPassingQualityControls = FALSE)) 64 | 65 | bam <- scanBam(bamFilename, param=param) 66 | aln <- bam[[1]] 67 | rm(bam) 68 | 69 | posStrandReads <- aln$isize > 0 70 | reads <- GRanges(seqnames=Rle(aln$rname[posStrandReads]), 71 | ranges = IRanges(start = aln$pos[posStrandReads], 72 | width = aln$isize[posStrandReads])) 73 | 74 | if(genome == 'tair10') { 75 | seqlevelsStyle(reads) <- 'Ensembl' 76 | } else { 77 | # Make sure the chromosome names are following the 'UCSC' convention 78 | seqlevelsStyle(reads) <- 'UCSC' 79 | } 80 | 81 | genomeSeqInfo <- Seqinfo(seqnames = names(annotations$chrLen), 82 | seqlengths = as.numeric(annotations$chrLen), 83 | isCircular = rep(NA, length(annotations$chrLen)), 84 | genome = rep(genome, length(annotations$chrLen))) 85 | 86 | good.seq.levels <- intersect(seqlevels(reads), seqlevels(genomeSeqInfo)) 87 | 88 | result <- keepSeqlevels(reads, good.seq.levels, pruning.mode="coarse") 89 | seqlevels(result) <- good.seq.levels 90 | seqlevels(genomeSeqInfo) <- good.seq.levels 91 | seqinfo(result) <- genomeSeqInfo 92 | return(result) 93 | } 94 | 95 | 96 | CleanReads <- function(reads, chrLen, lMin, lMax){ 97 | 98 | # Size selection; keep reads with the length between lMin and lMax 99 | readLength <- width(reads) 100 | goodReadsInd <- ((readLength >= lMin) & (readLength <= lMax)) 101 | goodReadsLen <- reads[goodReadsInd] 102 | 103 | # Compute the raw coverage of these reads 104 | rawOcc <- coverage(goodReadsLen) 105 | 106 | # Discard regions where the raw coverage is very high -- sequencing artifacts 107 | # Compute the threshold occupancy for each chromosome 108 | thresholdFactor <- 10 109 | chrLabel <- seqlevels(rawOcc) 110 | chrCoverageThreshold <- lapply(chrLabel, function(chr) thresholdFactor * mean(rawOcc[[chr]])) 111 | names(chrCoverageThreshold) <- chrLabel 112 | 113 | badRanges <- sapply(names(chrCoverageThreshold), 114 | function(chr) { 115 | if(is.na(chrCoverageThreshold[[chr]])) { 116 | result <- rawOcc[[chr]] 117 | } else { 118 | result <- reduce(slice(rawOcc[[chr]], lower=chrCoverageThreshold[[chr]], rangesOnly=TRUE) + 500) 119 | } 120 | return(result) 121 | }) 122 | 123 | allSeqnames <- names(badRanges) 124 | badRegions <- sapply(allSeqnames, function(x) { 125 | badRange <- badRanges[[x]] 126 | if(length(badRange) == 0) { 127 | result <- NULL 128 | } else { 129 | result <- GRanges(seqnames = x, ranges = badRange, strand = '*') 130 | seqlevels(result) <- allSeqnames 131 | } 132 | return(result) 133 | }) 134 | 135 | badRegionsDF <- lapply(badRegions, function(gr) as.data.frame(gr)) 136 | badRegionsDFAll <- do.call(rbind, badRegionsDF) 137 | if (ncol(badRegionsDFAll) > 0 & nrow(badRegionsDFAll) > 0) { 138 | badRegionsAll <- makeGRangesFromDataFrame(badRegionsDFAll) 139 | badReadIndex <- overlapsAny(goodReadsLen, badRegionsAll, ignore.strand=TRUE) 140 | } else { 141 | # all chr are good; no regions with very high coverage 142 | badReadIndex <- rep(FALSE, length(goodReadsLen)) 143 | } 144 | 145 | goodReadsLenCov <- goodReadsLen[!badReadIndex] 146 | 147 | return(reads) 148 | } 149 | 150 | LoadGenomeAnnotation <- function(genome){ 151 | 152 | chrData <- GetChromosomeLength(genome) 153 | chrLen <- chrData[, 2] 154 | names(chrLen) <- chrData[, 1] 155 | 156 | annotations <- GetAnnotations(genome) 157 | 158 | result = list(chrLen = chrLen, annotations = annotations) 159 | return(result) 160 | 161 | } 162 | 163 | LoadGenomeAnnotation_v2 <- function(inputFilename, genome){ 164 | 165 | inputType <- toupper(file_ext(inputFilename)) 166 | 167 | switch(inputType, 168 | BED={ 169 | result = LoadGenomeAnnotation(genome) 170 | }, 171 | BAM={ 172 | # Read chrLen directly from the BAM file 173 | bam_file <- Rsamtools::BamFile(inputFilename) 174 | 175 | # Get the chromosome names/lengths 176 | chrLen <- seqlengths(bam_file) 177 | 178 | 179 | if(genome == 'tair10') { 180 | newChrNames <- mapSeqlevels(names(chrLen), "Ensembl") 181 | } else { 182 | # Rename to UCSC style 183 | newChrNames <- mapSeqlevels(names(chrLen), "UCSC") 184 | } 185 | 186 | names(chrLen) <- newChrNames 187 | 188 | # Filter the chromosomes 189 | configFilePath <- file.path(configBasePath, "annotation_config.yaml") 190 | config <- yaml.load_file(configFilePath) 191 | chrFilter <- config$annotations[[genome]]$chromosome_size$filter 192 | chrLen <- chrLen[chrFilter] 193 | 194 | annotations <- GetAnnotations(genome) 195 | 196 | result <- list(chrLen = chrLen, annotations = annotations) 197 | }, 198 | { 199 | print_help(opt_parser) 200 | stop("File type not supported! Please provide a BED or BAM file as input.", call.=FALSE) 201 | } 202 | ) 203 | 204 | return(result) 205 | 206 | } 207 | 208 | GetChromosomeLength <- function(genome) { 209 | 210 | configFilePath <- file.path(configBasePath, "annotation_config.yaml") 211 | config <- yaml.load_file(configFilePath) 212 | 213 | genomeConfig <- config$annotations[[genome]] 214 | 215 | url <- genomeConfig$chromosome_size$url 216 | configFilePath <- genomeConfig$chromosome_size$path 217 | chrFilter <- as.data.frame(genomeConfig$chromosome_size$filter) 218 | 219 | if (! is.null(configFilePath)) { 220 | filePath <- file.path(annotationsBasePath, configFilePath) 221 | if(! file.exists(filePath)) { 222 | if(is.null(url)) { 223 | # error: no url from where to download chrom.sizes 224 | } else { 225 | fileExtension <- file_ext(url) 226 | destFileName <- paste0("tmp.", fileExtension) 227 | destfile <- file.path(annotationsBasePath, destFileName) 228 | content <- download.file(url, destfile, method = "wget", quiet = TRUE) 229 | compressed <- (fileExtension == "gz") 230 | if(compressed){ 231 | chrData <- read.table(gzfile(destfile), header = FALSE) 232 | } else { 233 | chrData <- read.table(destfile, header = FALSE) 234 | } 235 | 236 | #filter by chr list: 237 | chrDataToSave <- chrData[order(chrData$V1), c(1:2)] 238 | if (nrow(chrFilter) > 0 & ncol(chrFilter) > 0) { 239 | chrDataToSaveFilter <- merge(chrDataToSave, chrFilter, by=c(1)) 240 | } else { 241 | chrDataToSaveFilter <- chrDataToSave 242 | } 243 | 244 | annotationsFolder <- dirname(filePath) 245 | if (! file.exists(annotationsFolder)){ 246 | dir.create(annotationsFolder) 247 | } 248 | 249 | # save downloaded data 250 | write.table(chrDataToSaveFilter, filePath, quote = FALSE, col.names = FALSE, row.names = FALSE, sep="\t") 251 | # clean 252 | file.remove(destfile) 253 | } 254 | } 255 | result <- read.table(filePath, stringsAsFactors = FALSE, sep="\t") 256 | } else { 257 | # error: genomeConfig$chromosome_size$path is empty 258 | } 259 | return(result) 260 | } 261 | 262 | GetAnnotations <- function(genome) { 263 | 264 | configFilePath <- file.path(configBasePath, "annotation_config.yaml") 265 | config <- yaml.load_file(configFilePath) 266 | 267 | genomeConfig <- config$annotations[[genome]] 268 | 269 | mart <- genomeConfig$mart 270 | file <- genomeConfig$file 271 | 272 | if (! is.null(mart)) { 273 | 274 | if (is.null(mart$host)) { 275 | ensembl <- useMart(biomart = mart$biomart, dataset = mart$dataset) 276 | } else { 277 | ensembl <- useMart(host = mart$host, biomart = mart$biomart, dataset = mart$dataset) 278 | } 279 | 280 | annot <- getBM(mart$attributes, mart=ensembl) 281 | 282 | # exclude annotations with attr_id == '' 283 | annot <- annot[annot[mart$attributeId] != '', ] 284 | 285 | strand <- annot[[mart$vars$strand]] 286 | txStart <- annot[[mart$vars$txStart]] 287 | txEnd <- annot[[mart$vars$txEnd]] 288 | chrName <- annot[[mart$vars$chrName]] 289 | 290 | if(genome == 'tair10') { 291 | seqlevelsStyle(chrName) <- 'Ensembl' 292 | } else { 293 | # Make sure the chromosome names have the UCSC style 294 | seqlevelsStyle(chrName) <- 'UCSC' 295 | } 296 | 297 | TSS <- txStart 298 | TTS <- txEnd 299 | TSS[strand == -1] <- txEnd[strand == -1] 300 | TTS[strand == -1] <- txStart[strand == -1] 301 | 302 | annotations <- data.frame(Transcript = annot[mart$attributeId], 303 | Chr = chrName, 304 | Strand = strand, 305 | TSS = TSS, 306 | TTS = TTS, 307 | stringsAsFactors = FALSE) 308 | 309 | } else if (! is.null(file)) { 310 | 311 | annotationsFilePath <- file.path(annotationsBasePath, file$path) 312 | annotations <- read.csv(annotationsFilePath, header=TRUE, stringsAsFactors=FALSE) 313 | 314 | } 315 | 316 | return(annotations) 317 | } 318 | -------------------------------------------------------------------------------- /source/plot2DO_io.R: -------------------------------------------------------------------------------- 1 | suppressPackageStartupMessages({ 2 | library(optparse) 3 | library(tools) 4 | }) 5 | 6 | CreateOptionsParser <- function(){ 7 | 8 | options = list( 9 | make_option(c("-f", "--file"), type="character", default=NULL, 10 | help="Name of the file containing aligned sequencing data [options: BAM or BED file]"), 11 | make_option(c("-t", "--type"), type="character", default="occ", 12 | help="Type of distribution to plot [options: occ, dyads, fivePrime_ends, threePrime_ends; default = %default]"), 13 | make_option(c("-g", "--genome"), type="character", default="sacCer3", 14 | help="Genome version\n\t\t[options: sacCer3 (default) (S. cerevisiae); EF2 (S. pombe); dm3, dm6 (D. melanogaster);\n\t\tce10, ce11 (C. elegans); mm9, mm10 (M. musculus);\n\t\thg18, hg19, hg38 (H. sapiens); tair10 (A. thaliana)]"), 15 | make_option(c("-r", "--reference"), type="character", default="TSS", 16 | help="Reference points to be aligned [options: TSS (default), TTS, Plus1]"), 17 | make_option(c("-s", "--sites"), type="character", default=NULL, 18 | help="User-provided sites to be aligned (BED file)"), 19 | make_option(c("-a", "--align"), type="character", default="center", 20 | help="Points of the provided intervals to be aligned? [options: center (default), fivePrime, threePrime]"), 21 | make_option(c("--siteLabel"), type="character", default="Sites", 22 | help="Label for the aligned sites [default = %default]"), 23 | make_option(c("-l", "--minLength"), type="integer", default=50, 24 | help="The smallest DNA fragment to be considered [default = %default]"), 25 | make_option(c("-L", "--maxLength"), type="integer", default=200, 26 | help="The largest DNA fragment to be considered [default = %default]"), 27 | make_option(c("-u", "--upstream"), type="integer", default=1000, 28 | help="Length of the upstream region to be plotted [default = %default]"), 29 | make_option(c("-d", "--downstream"), type="integer", default=1000, 30 | help="Length of the downstream region to be plotted [default = %default]"), 31 | make_option(c("-m", "--colorScaleMax"), type="double", default=NULL, 32 | help="Maximum value on the color scale (e.g. 0.02)"), 33 | make_option(c("--simplifyPlot"), type="character", default="off", 34 | help="Simplify the plot (show only the 2D heat map) [options: on, off (default)]"), 35 | make_option(c("--squeezePlot"), type="character", default="off", 36 | help="Simplify the plot and squeeze the heat map [options: on, off (default)]") 37 | ) 38 | 39 | optParser = OptionParser(option_list=options) 40 | 41 | return(optParser) 42 | } 43 | 44 | LoadArguments <- function(commandLineArgs = NA){ 45 | 46 | optParser <- CreateOptionsParser() 47 | 48 | if(anyNA(commandLineArgs) | length(commandLineArgs) == 0) { 49 | opt <- parse_args(optParser) 50 | } else { 51 | opt <- parse_args(optParser, args = commandLineArgs) 52 | } 53 | 54 | if (is.null(opt$file)) { 55 | print_help(optParser) 56 | stop("At least the dataset file name must be supplied.", call.=FALSE) 57 | } 58 | 59 | if (opt$squeezePlot == "on"){ 60 | opt$simplifyPlot = "on" 61 | } 62 | 63 | return(opt) 64 | } 65 | 66 | InitializeParams <- function(opt) { 67 | 68 | # Type of plot 69 | plotType <- toupper(opt$type) 70 | plotType <- strsplit(plotType, ',')[[1]] 71 | 72 | # Genome 73 | genome <- opt$genome 74 | 75 | inputFilePath <- opt$file 76 | 77 | # Data file name 78 | inputFilename <- basename(inputFilePath) 79 | 80 | # Reference label 81 | if(is.null(opt$sites)) { 82 | siteLabel <- "" 83 | } else { 84 | siteLabel <- opt$siteLabel 85 | } 86 | 87 | if (! is.null(opt$colorScaleMax)) { 88 | colorScaleMax <- opt$colorScaleMax 89 | } else { 90 | colorScaleMax <- NULL 91 | } 92 | 93 | # Type of alignments, i.e. reference points 94 | selectedReference <- opt$reference 95 | 96 | # Size selection parameters: specify the interval of lengths to be analyzed 97 | lMin <- opt$minLength # the smallest DNA fragment to be considered 98 | lMax <- opt$maxLength # the largest DNA fragment to be considered 99 | 100 | # Window selection parameters 101 | beforeRef <- opt$upstream # length of the upstream region that will be plotted 102 | afterRef <- opt$downstream # length of the downstream region that will be plotted 103 | 104 | inputType = toupper(file_ext(inputFilename)) 105 | 106 | sampleName <- switch(inputType, 107 | BED={ 108 | sampleName <- sub(".bed", "", inputFilename) 109 | }, 110 | BAM={ 111 | sampleName <- sub(".bam", "", inputFilename) 112 | }) 113 | 114 | align <- opt$align 115 | 116 | referencePointsBed <- opt$sites 117 | 118 | if(opt$squeezePlot == "off") { 119 | squeezePlot <- FALSE 120 | } else { 121 | squeezePlot <- TRUE 122 | } 123 | 124 | if(opt$simplifyPlot == "on") { 125 | simplifyPlot <- TRUE 126 | } else { 127 | simplifyPlot <- FALSE 128 | } 129 | 130 | # if (opt$squeezePlot == "on") => opt$simplifyPlot = "on" 131 | if (squeezePlot){ 132 | simplifyPlot <- TRUE 133 | } 134 | 135 | result <- list(plotType = plotType, genome = genome, align = align, 136 | inputFilename = inputFilename, inputFilePath = inputFilePath, 137 | sampleName = sampleName, 138 | reference = selectedReference, siteLabel = siteLabel, 139 | referencePointsBed = referencePointsBed, 140 | lMin = lMin, lMax = lMax, 141 | beforeRef = beforeRef, afterRef = afterRef, 142 | colorScaleMax = colorScaleMax, 143 | squeezePlot = squeezePlot, simplifyPlot = simplifyPlot) 144 | 145 | return(result) 146 | } 147 | 148 | CreateOutputFolders <- function(plotType, sites, selectedReference, siteLabel) { 149 | # Create folder where figures are saved 150 | folderPath <- GetOutputBaseFolderPath(plotType, sites, selectedReference, siteLabel) 151 | dir.create(folderPath, showWarnings = FALSE, recursive = TRUE) 152 | return(folderPath) 153 | } 154 | 155 | # output helper functions: 156 | GetOutputBaseFolderPath <- function(plotType, sites, selectedReference, siteLabel){ 157 | 158 | folderNameHead <- paste0("2D_", tolower(plotType), "_") 159 | 160 | if (is.null(sites)) { 161 | folderName <- paste(folderNameHead, selectedReference, sep = "") 162 | } else { 163 | folderName <- paste(folderNameHead, siteLabel, sep="") 164 | } 165 | 166 | folderPath <- file.path(outputBasePath, folderName) 167 | 168 | return(folderPath) 169 | } 170 | 171 | GetOutputPlotFilePath <- function(plotType, sites, selectedReference, siteLabel, 172 | lMin, lMax, sampleName) { 173 | extension <- ".pdf" 174 | result <- GetOutputFilePathBase(plotType, sites, selectedReference, siteLabel, 175 | lMin, lMax, sampleName, extension) 176 | return(result) 177 | 178 | } 179 | 180 | GetOutputMatrixFilePath <- function(plotType, sites, selectedReference, siteLabel, 181 | lMin, lMax, sampleName){ 182 | 183 | extension <- ".RData" 184 | 185 | result <- GetOutputFilePathBase(plotType, sites, selectedReference, siteLabel, 186 | lMin, lMax, sampleName, extension) 187 | 188 | return(result) 189 | 190 | } 191 | 192 | GetOutputFilePathBase <- function(plotType, sites, selectedReference, siteLabel, 193 | lMin, lMax, sampleName, extension){ 194 | 195 | folder_base_path <- GetOutputBaseFolderPath(plotType, sites, selectedReference, siteLabel) 196 | 197 | fileNameHead <- paste0(plotType, "_matrix.") 198 | fileNameTail <- paste0(".", lMin, "_", lMax, ".", sampleName, extension) 199 | 200 | if (is.null(sites)) { 201 | fileName <- paste0(fileNameHead, selectedReference, fileNameTail) 202 | } else { 203 | fileName <- paste0(fileNameHead, siteLabel, fileNameTail) 204 | } 205 | 206 | filePath <- file.path(folder_base_path, fileName) 207 | 208 | return(filePath) 209 | 210 | } 211 | -------------------------------------------------------------------------------- /source/plot2DO_main.R: -------------------------------------------------------------------------------- 1 | io <- file.path(sourceBasePath, "plot2DO_io.R") 2 | data <- file.path(sourceBasePath, "plot2DO_data.R") 3 | core <- file.path(sourceBasePath, "plot2DO_core.R") 4 | plots <- file.path(sourceBasePath, "plot2DO_plots.R") 5 | source(io) 6 | source(data) 7 | source(core) 8 | source(plots) 9 | 10 | 11 | Main <- function(command_line_args=NA) 12 | { 13 | opt <- LoadArguments(command_line_args) 14 | 15 | params <- InitializeParams(opt) 16 | 17 | rm(opt) # deleted to be sure using initialized params 18 | 19 | # annotations <- LoadGenomeAnnotation(params$genome) 20 | annotations <- LoadGenomeAnnotation_v2(params$inputFilePath, params$genome) 21 | 22 | rawReads <- LoadReads(params$inputFilePath, params$genome, annotations) 23 | 24 | reads <- CleanReads(rawReads, annotations$chrLen, params$lMin, params$lMax) 25 | 26 | referenceGRanges <- ConstructReferenceGRanges(params$referencePointsBed, annotations, params$reference, 27 | params$beforeRef, params$afterRef, params$genome, params$align) 28 | 29 | outputFolderPath <- CreateOutputFolders(params$plotType, params$referencePointsBed, params$reference, params$siteLabel) 30 | 31 | CalculatePlotData(params, reads, referenceGRanges) 32 | 33 | plot <- PlotFigure(params) 34 | 35 | # check whether the unwanted file exists and remove it 36 | somethingToRemove <- file.exists("Rplots.pdf") 37 | if(somethingToRemove) { 38 | dummy <- file.remove("Rplots.pdf") 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /source/plot2DO_plots.R: -------------------------------------------------------------------------------- 1 | suppressPackageStartupMessages({ 2 | library(ggplot2) 3 | library(reshape2) 4 | library(colorRamps) 5 | library(grid) 6 | library(gridExtra) 7 | library(yaml) 8 | }) 9 | 10 | # Construct all plot labels and titles according to the type of plot/alignment 11 | GetPlotsLabels <- function(sampleName, type, reference, site, align) { 12 | 13 | typeLabel <- switch(type, 14 | "OCC" = "occupancy", 15 | "DYADS" = "dyad density", 16 | "FIVEPRIME_ENDS" = "density", 17 | "THREEPRIME_ENDS"= "density", 18 | "") 19 | 20 | referenceLabel <- switch(reference, 21 | "TSS" = "TSS", 22 | "TTS" = "TTS", 23 | "Plus1"= "+1 nuc.", 24 | "") 25 | 26 | 27 | if (site != "" & align != "") { 28 | siteLabel <- site 29 | alignLabel <- switch(align, 30 | "fivePrime" = "5'", 31 | "threePrime" = "3'", 32 | "center"= "center", 33 | "") 34 | } else { 35 | alignLabel <- "" 36 | siteLabel <- "" 37 | } 38 | 39 | # Construct axes labels 40 | heatmapYLabel <- "Fragment length (bp)" 41 | heatmapLegend <- "Relative coverage (%)" 42 | 43 | fragmentLengthXLabel <- "Fragment length (bp)" 44 | fragmentLengthYLabel <- "Percentage (%)" 45 | 46 | if (siteLabel != "" & alignLabel != "") { 47 | 48 | heatmapXLabel <- paste0("Position relative to ", alignLabel, " of ", siteLabel, " (bp)") 49 | averageXLabel <- paste0("Position relative to ", alignLabel, " of ", siteLabel, " (bp)") 50 | averageYLabel <- paste0("Average ", typeLabel) 51 | 52 | } else if (referenceLabel != "") { 53 | 54 | heatmapXLabel <- paste0("Position relative to ", referenceLabel, " (bp)") 55 | averageXLabel <- paste0("Position relative to ", referenceLabel, " (bp)") 56 | averageYLabel <- paste0("Average ", typeLabel) 57 | 58 | } 59 | 60 | heatmapLabels <- list(xTitle = heatmapXLabel, yTitle = heatmapYLabel, legendTitle = heatmapLegend, mainTitle = sampleName) 61 | averageLabels <- list(xTitle = averageXLabel, yTitle = averageYLabel, legendTitle = "", mainTitle = sampleName) 62 | fragmentLengthLabels <- list(xTitle = fragmentLengthXLabel, yTitle = fragmentLengthYLabel, legendTitle = "", mainTitle = "") 63 | 64 | result <- list(heatmap = heatmapLabels, average = averageLabels, fragmentLength = fragmentLengthLabels) 65 | 66 | return(result) 67 | 68 | } 69 | 70 | # Remove some of the labels, i.e. skip noSkippedTicks between consecutive labels 71 | FixTickLabels <- function(labels, noSkippedTicks, paddingLeft) { 72 | newLabels <- paste0(paddingLeft, labels) 73 | labelsToSkip <- setdiff(1:length(labels), seq(1, length(labels), noSkippedTicks + 1)) 74 | newLabels[labelsToSkip] <- "" 75 | return(newLabels) 76 | } 77 | 78 | GetHeatmapBreaksAndLabels <- function(occMatrix, colorScaleMax) { 79 | 80 | if (is.null(colorScaleMax)) { 81 | maxValue <- max(occMatrix) 82 | } else { 83 | maxValue <- colorScaleMax 84 | } 85 | 86 | if (maxValue > 0.1) { 87 | step <- 0.05 88 | } else if (maxValue > 0.05) { 89 | step <- 0.01 90 | } else if (maxValue > 0.01) { 91 | step <- 0.005 92 | } else { 93 | step <- 0.002 94 | } 95 | 96 | breaks <- seq(0, maxValue, step) 97 | labels <- breaks * 100 # Use percentages instead of fractional numbers 98 | limits <- c(0, maxValue) 99 | 100 | result <- list(breaks = breaks, labels = labels, limits = limits) 101 | 102 | return(result) 103 | } 104 | 105 | 106 | PlotHeatmap <- function(occMatrix, xTitle, yTitle, mainTitle, legendTitle, 107 | beforeRef, afterRef, lMin, lMax, 108 | customTheme, legendTitleTheme, legendLabelTheme, 109 | scaleXPosition, scaleYPosition, colorScaleMax) { 110 | 111 | occMatrixMelt <- melt(t(occMatrix)) 112 | 113 | breaksLabels <- GetHeatmapBreaksAndLabels(occMatrix, colorScaleMax) 114 | 115 | result <- ggplot(occMatrixMelt, aes(x = Var1, y = Var2, fill = value)) + 116 | geom_raster(aes(fill = value), interpolate = TRUE) + 117 | scale_color_gradientn(colors = matlab.like(100), aesthetics = "fill", 118 | breaks = breaksLabels$breaks, 119 | labels = breaksLabels$labels, 120 | limits = breaksLabels$limits) 121 | 122 | xBreaks <- seq(-beforeRef, afterRef, by=100) + beforeRef + 1 123 | if (length(xBreaks) >= 5){ 124 | xLabels <- FixTickLabels(as.character(seq(-beforeRef, afterRef, by=100)), 4, "") # skip 4 labels 125 | } else { 126 | xBreaks <- seq(-beforeRef, afterRef, by=10) + beforeRef + 1 127 | xLabels <- FixTickLabels(as.character(seq(-beforeRef, afterRef, by=10)), 4, "") # skip 4 labels 128 | } 129 | xLimits <- c(1, beforeRef + afterRef + 1) 130 | 131 | yBreaks <- seq(lMin, lMax, by=10) - lMin + 1 132 | yLabels <- FixTickLabels(as.character(seq(lMin, lMax, by=10)), 4, "") # skip 4 labels 133 | yLimits <- c(1, lMax - lMin + 1) 134 | 135 | guideColourbar <- guide_colourbar(title = legendTitle, reverse = FALSE, title.position = "left", 136 | frame.colour = "black", frame.linewidth = 0.5, 137 | ticks.colour = "black", ticks.linewidth = 0.5, 138 | label.position = "left", 139 | title.theme = legendTitleTheme, 140 | label.theme = legendLabelTheme, 141 | title.hjust = 0.5, 142 | barheight = 10, 143 | nbin = 1000) # necessary to shift zero tick to bottom 144 | 145 | result <- result + labs(x = xTitle, y = yTitle, title = mainTitle) 146 | 147 | scaleX <- scale_x_continuous(breaks = xBreaks, labels = xLabels, limits = xLimits, 148 | expand = c(0,0), position = scaleXPosition, 149 | sec.axis = dup_axis()) 150 | 151 | scaleY <- scale_y_continuous(breaks = yBreaks, labels = yLabels, limits = yLimits, 152 | expand = c(0,0), position = scaleYPosition, 153 | sec.axis = dup_axis()) 154 | 155 | result <- result + guides(fill = guideColourbar) + 156 | scaleY + scaleX + geom_vline(xintercept=beforeRef+1, linetype='longdash', color="white", size=0.4) + 157 | customTheme 158 | 159 | return(result) 160 | 161 | } 162 | 163 | PlotAverageOccupancy <- function(occMatrix, beforeRef, afterRef, xTitle, yTitle, mainTitle, customTheme) { 164 | 165 | avgOcc <- colSums(occMatrix) 166 | avgOcc.df <- as.data.frame(avgOcc) 167 | avgOcc.df$x <- seq(-beforeRef, afterRef, 1) 168 | 169 | deltaYBreaks = max(0.1, round(1.05 * max(avgOcc)/10, digits = 1)) 170 | yBreaks <- seq(0, 1.05 * max(avgOcc), deltaYBreaks) 171 | if (length(yBreaks) >= 8){ 172 | yLabels <- FixTickLabels(as.character(yBreaks), 1, " ") # yBreaks 173 | } else { 174 | yLabels <- FixTickLabels(as.character(yBreaks), 0, " ") # yBreaks 175 | } 176 | yLimits <- c(0, 1.05 * max(avgOcc)) 177 | 178 | xBreaks <- seq(-beforeRef, afterRef, 100) 179 | xLabels <- FixTickLabels(as.character(xBreaks), 4, "") # xBreaks 180 | xLimits <- c(-beforeRef, afterRef) 181 | 182 | xlineInterceps <- seq(-5000, 5000, by=500) 183 | 184 | result <- ggplot(data=avgOcc.df, aes(x = x, y = avgOcc)) + 185 | geom_line(color="blue") + 186 | scale_y_continuous(breaks = yBreaks, labels = yLabels, limits = yLimits, expand = c(0,0), 187 | sec.axis = dup_axis()) + 188 | scale_x_continuous(breaks = xBreaks, labels = xLabels, limits = xLimits, expand = c(0,0), 189 | sec.axis = dup_axis()) + 190 | geom_vline(xintercept = xlineInterceps, linetype = 'longdash', color = "lightgray", size = 0.4) + 191 | labs(x = xTitle, y = yTitle, title = mainTitle) + customTheme 192 | 193 | return(result) 194 | 195 | } 196 | 197 | PlotFragmentLength <- function(lengthHist, lMin, lMax, xTitle, yTitle, customTheme) { 198 | 199 | data <- as.data.frame(lengthHist) 200 | data$x <- seq(lMin, lMax, 1) 201 | 202 | xBreaks <- seq(lMin, lMax, 10) 203 | xLabels <- FixTickLabels(as.character(xBreaks), 4, "") # skip 4 labels 204 | xLimits <- c(lMin, lMax) 205 | 206 | yBreaks <- round(seq(min(lengthHist), 1.05 * max(lengthHist), 1), 2) 207 | if (length(yBreaks) == 1){ 208 | yBreaks <- round(seq(min(lengthHist), 1.05 * max(lengthHist), 0.2), 2) 209 | } 210 | yLabels <- yBreaks 211 | yLimits <- c(0, 1.05 * max(lengthHist)) 212 | 213 | xlineInterceps <- seq(0, 1000, by=50) 214 | 215 | result <- ggplot(data=data, aes(x = x, y = lengthHist)) + 216 | geom_line(color="blue") + 217 | scale_y_continuous(breaks = yBreaks, labels = yLabels, limits = yLimits, expand = c(0,0), 218 | sec.axis = dup_axis()) + 219 | scale_x_continuous(breaks = xBreaks, labels = xLabels, limits = xLimits, expand = c(0,0), 220 | sec.axis = dup_axis()) + 221 | geom_vline(xintercept = xlineInterceps, linetype = 'longdash', color = "lightgray", size = 0.4) + 222 | labs(x = xTitle, y = yTitle) + 223 | customTheme 224 | 225 | result <- result + coord_flip() 226 | 227 | return(result) 228 | } 229 | 230 | GetHeatmapLegend <- function(myggplot){ 231 | tmp <- ggplot_gtable(ggplot_build(myggplot)) 232 | leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box") 233 | legend <- tmp$grobs[[leg]] 234 | return(legend) 235 | } 236 | 237 | PlotFigure <- function(params) { 238 | 239 | suppressWarnings({ 240 | 241 | dataFilePath <- GetOutputMatrixFilePath(params$plotType, params$referencePointsBed, 242 | params$reference, params$siteLabel, 243 | params$lMin, params$lMax, params$sampleName) 244 | 245 | # Load data: 246 | load(dataFilePath) 247 | 248 | occMatrix[occMatrix < 0] = 0 # eliminate rounding errors 249 | if (! is.null(params$colorScaleMax)) { 250 | occMatrix[occMatrix > params$colorScaleMax] = params$colorScaleMax # override the default colorbar and set everything above the threshold with the threshold value 251 | } 252 | 253 | plotsConfig <- GetPlotsLabels(sampleName, params$plotType, params$reference, siteLabel, params$align) 254 | 255 | heatmapTitles <- plotsConfig$heatmap 256 | 257 | graphicalParams <- GetGraphicalParams(params$simplifyPlot, params$squeezePlot) 258 | 259 | heatmap <- PlotHeatmap(occMatrix, heatmapTitles$xTitle, heatmapTitles$yTitle, 260 | heatmapTitles$mainTitle, heatmapTitles$legendTitle, 261 | beforeRef, afterRef, lMin, lMax, 262 | graphicalParams$heatmapTheme, graphicalParams$legendTitleTheme, 263 | graphicalParams$legendLabelTheme, 264 | graphicalParams$scaleXPosition, graphicalParams$scaleYPosition, 265 | params$colorScaleMax) 266 | 267 | if(params$simplifyPlot) { 268 | avgOccupancy <- NA 269 | fragmentLength <- NA 270 | result.grob <- arrangeGrob(heatmap, 271 | ncol = ncol(graphicalParams$layout), nrow = nrow(graphicalParams$layout), 272 | layout_matrix = graphicalParams$layout, 273 | widths = graphicalParams$gridWidths, 274 | heights = graphicalParams$gridHeights) 275 | # grid.draw(result.grob) 276 | } else { 277 | 278 | averageTitles <- plotsConfig$average 279 | avgOccupancy <- PlotAverageOccupancy(occMatrix, beforeRef, afterRef, 280 | averageTitles$xTitle, averageTitles$yTitle, averageTitles$mainTitle, 281 | graphicalParams$avgOccupancyTheme) 282 | 283 | fragmentLengthTitles <- plotsConfig$fragmentLength 284 | fragmentLength <- PlotFragmentLength(lengthHist, lMin, lMax, 285 | fragmentLengthTitles$xTitle, fragmentLengthTitles$yTitle, 286 | graphicalParams$fragmentLengthTheme) 287 | 288 | # Separate legend from heatmap: 289 | legend <- GetHeatmapLegend(heatmap) 290 | heatmapWithoutLegend <- heatmap + theme(legend.position="none") 291 | 292 | result.grob <- arrangeGrob(avgOccupancy, heatmapWithoutLegend, 293 | fragmentLength, legend, 294 | ncol = ncol(graphicalParams$layout), nrow = nrow(graphicalParams$layout), 295 | layout_matrix = graphicalParams$layout, 296 | widths = graphicalParams$gridWidths, 297 | heights = graphicalParams$gridHeights) 298 | # grid.draw(result.grob) 299 | } 300 | 301 | plotFilePath <- GetOutputPlotFilePath(params$plotType, params$referencePointsBed, 302 | params$reference, siteLabel, 303 | lMin, lMax, sampleName) 304 | ggsave(plotFilePath, result.grob, width = graphicalParams$plotWidth, height = graphicalParams$plotHeight, 305 | units = "in", dpi = 300, scale = 1) 306 | 307 | }) 308 | 309 | return(result.grob) 310 | 311 | } 312 | 313 | GetGraphicalParams <- function(simplifyPlot, squeezePlot) { 314 | 315 | baseTheme <- theme_bw() + theme( 316 | panel.grid.major = element_blank(), 317 | panel.grid.minor = element_blank(), 318 | plot.title = element_text(size = 14, hjust = 0.5, face = "bold"), 319 | axis.text.x = element_text(size = 12, angle = 0, hjust = 0.5, vjust = 0.5, colour="black"), 320 | axis.text.y = element_text(size = 12, angle = 0, hjust = 0.5, vjust = 0.5, colour="black"), 321 | axis.title = element_text(size = 14, hjust = 0.5, vjust = 0.5), 322 | axis.ticks.length = unit(.15, "cm") 323 | ) 324 | 325 | legendTitleTheme <- element_text(size = 14, angle = 90, hjust = 0.5, vjust = 0.5, margin = margin(t = 0, r = 7, b = 0, l = 0)) 326 | legendLabelTheme <- element_text(size = 12, angle = 0, hjust = 0.5) 327 | 328 | if(simplifyPlot) { 329 | if(squeezePlot) { 330 | layout <- cbind(c(1, 1, 1), c(1, 1, 1)) 331 | gridWidths <- c(1, 1) 332 | gridHeights <- c(1, 1, 1) 333 | plotWidth <- 4 334 | plotHeight <- 5 335 | } else { 336 | layout <- cbind(c(1)) 337 | gridWidths <- c(1) 338 | gridHeights <- c(1) 339 | plotWidth <- 5 340 | plotHeight <- 4 341 | } 342 | 343 | scaleXPosition <- "bottom" 344 | scaleYPosition <- "left" 345 | 346 | heatmapTheme <- baseTheme + theme(legend.position="right", 347 | axis.ticks.x.top = element_blank(), 348 | axis.text.x.top = element_blank(), 349 | axis.title.x.top = element_blank(), 350 | axis.title.x.bottom = element_text(margin = margin(t = 10, r = 0, b = 0, l = 0)), 351 | axis.ticks.y.right = element_blank(), 352 | axis.text.y.right = element_blank(), 353 | axis.title.y.right = element_blank(), 354 | axis.title.y.left = element_text(margin = margin(t = 0, r = 10, b = 0, l = 0))) 355 | avgOccupancyTheme <- NA 356 | fragmentLengthTheme <- NA 357 | 358 | } else { 359 | 360 | layout <- cbind(c(NA, 4, 4), c(1,2,2), c(NA,3,3)) 361 | gridWidths <- c(0.5, 2, 1) 362 | gridHeights <- c(1.2, 1, 1) 363 | plotWidth <- 9 364 | plotHeight <- 7 365 | 366 | scaleXPosition <- "top" 367 | scaleYPosition <- "right" 368 | 369 | # i have to duplicate axis and add element text to align all the plots. 370 | # they should use that space but not be shown 371 | heatmapTheme <- baseTheme + theme(plot.title = element_blank(), 372 | axis.ticks.x.bottom = element_blank(), 373 | axis.ticks.y.left = element_blank(), 374 | axis.text.y.left = element_text(color="white"), 375 | axis.text.x.bottom = element_text(color="white"), 376 | axis.title.x.bottom = element_text(color="white"), 377 | axis.title.x.top = element_blank(), 378 | axis.title.y.left = element_text(color="white", margin = margin(t = 0, r = 10, b = 0, l = 0)), 379 | axis.title.y.right = element_blank()) 380 | 381 | avgOccupancyTheme <- baseTheme + theme(axis.ticks.x.top = element_blank(), 382 | axis.text.x.top = element_blank(), 383 | axis.title.x.top = element_blank(), 384 | axis.title.x.bottom = element_text(margin = margin(t = 12, r = 0, b = 0, l = 0)), 385 | axis.ticks.y.right = element_blank(), 386 | axis.text.y.right = element_text(color="white"), 387 | axis.title.y.right = element_blank(), 388 | axis.title.y.left = element_text(margin = margin(t = 0, r = 10, b = 0, l = 0))) 389 | 390 | fragmentLengthTheme <- baseTheme + theme(axis.ticks.x.top = element_blank(), 391 | axis.text.x.top = element_text(color="white"), 392 | axis.title.x.top = element_blank(), 393 | axis.ticks.y.right = element_blank(), 394 | axis.text.y.right = element_blank(), 395 | axis.title.y.right = element_blank(), 396 | axis.title.y.left = element_text(margin = margin(t = 0, r = 10, b = 0, l = 0))) 397 | } 398 | 399 | 400 | result = list(layout = layout, 401 | gridWidths = gridWidths, gridHeights = gridHeights, 402 | plotWidth = plotWidth, plotHeight = plotHeight, 403 | heatmapTheme = heatmapTheme, 404 | legendTitleTheme = legendTitleTheme, 405 | legendLabelTheme = legendLabelTheme, 406 | avgOccupancyTheme = avgOccupancyTheme, 407 | fragmentLengthTheme = fragmentLengthTheme, 408 | scaleXPosition = scaleXPosition, 409 | scaleYPosition = scaleYPosition) 410 | 411 | return(result) 412 | 413 | } 414 | --------------------------------------------------------------------------------