├── __init__.py ├── src ├── __init__.py ├── __pycache__ │ ├── wish.cpython-36.pyc │ ├── blast.cpython-36.pyc │ ├── crispr.cpython-36.pyc │ ├── s2star.cpython-36.pyc │ ├── Variables.cpython-36.pyc │ ├── __init__.cpython-36.pyc │ └── neighborhood.cpython-36.pyc ├── tools │ ├── WIsH.h │ ├── mm.h │ ├── tools.cpp │ ├── kmer_count_multithreads.h │ ├── mm.cpp │ └── ctpl_stl.h ├── neighborhood.py ├── Variables.py ├── wish.py ├── args.py ├── crispr.py ├── blast.py └── s2star.py ├── .gitignore ├── __pycache__ └── predictor.cpython-36.pyc ├── cmd.sh ├── setup.py ├── VirHostMatcher-Net.py ├── predictor.py ├── README.md └── test └── mVCs ├── SRS019128_WUGC_scaffold_25110.fasta ├── SRS045127_LANL_scaffold_39500.fasta ├── SRS016086_WUGC_scaffold_24100.fasta ├── SRS057205_LANL_scaffold_13380.fasta ├── SRS011452_WUGC_scaffold_3640.fasta ├── SRS050752_LANL_scaffold_33630.fasta ├── SRS023352_LANL_scaffold_83757.fasta ├── SRS022602_Baylor_scaffold_3690.fasta ├── SRS014271_WUGC_scaffold_25970.fasta ├── SRS018739_WUGC_scaffold_56127.fasta ├── SRS018656_WUGC_scaffold_13330.fasta └── SRS058053_LANL_scaffold_6657.fasta /__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | build/ 2 | data/ 3 | src/tools-1.0* 4 | src/tools.cpython* 5 | __pycache__/* 6 | src/__pycache__/* 7 | -------------------------------------------------------------------------------- /src/__pycache__/wish.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/wish.cpython-36.pyc -------------------------------------------------------------------------------- /__pycache__/predictor.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/__pycache__/predictor.cpython-36.pyc -------------------------------------------------------------------------------- /src/__pycache__/blast.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/blast.cpython-36.pyc -------------------------------------------------------------------------------- /src/__pycache__/crispr.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/crispr.cpython-36.pyc -------------------------------------------------------------------------------- /src/__pycache__/s2star.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/s2star.cpython-36.pyc -------------------------------------------------------------------------------- /src/__pycache__/Variables.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/Variables.cpython-36.pyc -------------------------------------------------------------------------------- /src/__pycache__/__init__.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/__init__.cpython-36.pyc -------------------------------------------------------------------------------- /src/__pycache__/neighborhood.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WeiliWw/VirHostMatcher-Net/HEAD/src/__pycache__/neighborhood.cpython-36.pyc -------------------------------------------------------------------------------- /cmd.sh: -------------------------------------------------------------------------------- 1 | rm -R build/ 2 | #swig -python -c++ -Isrc tools.i 3 | #python setup.py build_ext 4 | CC=g++ python setup.py install --install-platlib=./src/ 5 | 6 | -------------------------------------------------------------------------------- /src/tools/WIsH.h: -------------------------------------------------------------------------------- 1 | //#define OPENMP 2 | #define WIsH_VERSION_MAJOR 1 3 | #define WIsH_VERSION_MINOR 0 4 | int wish(std::string genomeDir, std::string modelDir, std::string resultDir, std::string command, 5 | unsigned int threads); 6 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import os 2 | import numpy 3 | from distutils.sysconfig import get_config_vars 4 | from distutils.core import setup, Extension 5 | 6 | # Remove the "-Wstrict-prototypes" compiler option, which isn't valid for C++. 7 | cfg_vars = get_config_vars() 8 | for key, value in cfg_vars.items(): 9 | if type(value) == str: 10 | cfg_vars[key] = value.replace("-Wstrict-prototypes", "") 11 | 12 | 13 | 14 | 15 | MOD = "tools" 16 | version = "1.0" 17 | 18 | setup(name=MOD, 19 | version = version, 20 | ext_modules=[Extension(name = MOD, 21 | sources = ["./src/tools/tools.cpp", "./src/tools/WIsH.cpp", "./src/tools/mm.cpp"], 22 | # extra_compile_args=['-fPIC','-pthread','-std=c++11'])], 23 | extra_compile_args=['-w','-std=c++11'])], 24 | include_dirs=[numpy.get_include(),"./src/tools/"] 25 | ) 26 | 27 | -------------------------------------------------------------------------------- /src/neighborhood.py: -------------------------------------------------------------------------------- 1 | ''' 2 | This code is used to generate positive and negative SV's, given interaction matrix, 3 | intra virus and virus-host s2star matrices 4 | ''' 5 | 6 | import pandas as pd 7 | 8 | def neighborhood_calculator(df_query_virus, df_interaction): 9 | ''' 10 | ####df_query_host: s2star matrix: (Query Viruses) * Hosts 11 | df_query_virus: s2star matrix: Q * (B + Q) 12 | df_interaction: binary matrix: (Bench + Query Viruses) * Hosts 13 | ''' 14 | print('----Start calculating network neighborhood feature values...----') 15 | pos_interaction = df_interaction.apply(lambda x: x/sum(x) ,axis=0).fillna(0) 16 | pos_SV = df_query_virus.dot(pos_interaction) 17 | neg_interaction = (1 - df_interaction).apply(lambda x: x/sum(x), 18 | axis=0).fillna(0) 19 | neg_SV = df_query_virus.dot(neg_interaction) 20 | print('----Finished Calculating network neighborhood feature values----') 21 | return pos_SV, neg_SV 22 | 23 | -------------------------------------------------------------------------------- /src/tools/mm.h: -------------------------------------------------------------------------------- 1 | #ifndef MM_H 2 | #define MM_H 3 | 4 | 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | #include 12 | #include 13 | #include 14 | 15 | 16 | class mm 17 | { 18 | int verbosity; 19 | 20 | std::string modelName; 21 | unsigned int order; 22 | 23 | double alpha; 24 | 25 | std::vector lowerOrderCounts,orderCounts; 26 | std::vector pc; // pseudo count probabilities 27 | std::vector p; 28 | 29 | void initArrays(); 30 | int read(std::string modelFile); 31 | 32 | 33 | void computeModelProb(); 34 | 35 | 36 | size_t hashKmer(std::string::iterator kmer, unsigned int k); 37 | static std::string mapToAlphabet(std::string seq); 38 | void countKmers(std::string genome); 39 | size_t lastNucl(size_t k); 40 | 41 | size_t head(size_t k); 42 | 43 | 44 | public: 45 | mm(std::string modelFile, int verb); 46 | mm(unsigned int k,double a, int verb); 47 | ~mm(); 48 | 49 | void printParameters(); 50 | std::string getName(); 51 | 52 | int write(std::string modelDir); 53 | int trainOn(std::string genomeFile); 54 | static std::vector readGenome(std::string genomeFile); 55 | double evaluate(std::vector); 56 | }; 57 | 58 | #endif // MM_H 59 | -------------------------------------------------------------------------------- /src/Variables.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Preset variables 3 | ''' 4 | import os 5 | from . import args 6 | 7 | args = args.parse_arguments() 8 | _path = args.data_dir 9 | #_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) 10 | 11 | # intercept, s2star/wish, posSV, negSV, crispr 12 | REGRESSION_COEFFICIENTS = [-1.85696213, 17.13324415, 4.27680508, -27.73515517, 0.12533108] 13 | REGRESSION_COEFFICIENTS_SHORT = [39.58978537, 27.69902541, 6.40628182, -15.18968327, 0.20333482] 14 | # INTERMEDIATE_RESULT = os.path.join(_path, 'intermediate_res/') 15 | # DB_HOST_PREFIX = os.path.join(_path, 'data/host_db_prefix/hostGenomes.fna') 16 | DB_HOST_CRISPR_PREFIX = os.path.join(_path, 'crispr_db_prefix/allCRISPRs') 17 | HASH_TABLE = os.path.join(_path, 'tables/genome2header.pkl') 18 | WISH_HOST_MODELS = os.path.join(_path, 'host_wish_model/') 19 | TAXA_INFO = os.path.join(_path, 'tables/hostTaxa.pkl') 20 | PRED_THRE = os.path.join(_path, 'tables/predThre.csv') 21 | # TABLES: intermediate s2 values and the interaction 0-1 matrix 22 | # TABLES = os.path.join(_path, 'data/tables/tables.h5') 23 | 24 | TABLE_HOST = os.path.join(_path, 'tables/host62493_s2_mat.pkl') 25 | TABLE_BENCH = os.path.join(_path, 'tables/bench_s2_mat.pkl') 26 | TABLE_INTER = os.path.join(_path, 'tables/df_interaction.csv') 27 | 28 | # D2STAR_HASH = os.path.join(_path, 'data/hash/') 29 | # S2STAR_BENCH_HOST = os.path.join(_path, 'data/tables/relationMat_352by31986.csv') 30 | # PSEUDO_HOST = os.path.join(_path, 'data/pseudo_host/') 31 | # PSEUDO_VIRUS = os.path.join(_path, 'data/pseudo_virus/') 32 | 33 | # try: 34 | # os.stat(INTERMEDIATE_RESULT) 35 | # except: 36 | # os.mkdir(INTERMEDIATE_RESULT) 37 | -------------------------------------------------------------------------------- /src/wish.py: -------------------------------------------------------------------------------- 1 | ''' 2 | This code generates likelihood generated from WIsH 3 | ''' 4 | import os 5 | import pandas as pd 6 | from . import tools 7 | from .Variables import WISH_HOST_MODELS 8 | 9 | ''' 10 | Preset variables 11 | ''' 12 | host_model_dir = WISH_HOST_MODELS 13 | # output_dir = INTERMEDIATE_RESULT 14 | 15 | ''' 16 | Function: Fit query viruses into host models and return likelihood matrix 17 | -------- 18 | Parameters: 19 | query_virus_dir 20 | virus_index 21 | host_index 22 | ''' 23 | 24 | def wish_llkd_calculator(query_virus_dir, virus_index, host_index, output_dir, numThreads): 25 | #def wish_llkd_calculator(query_virus_dir, numThreads, output_dir, host_model_dir = WISH_HOST_MODELS): 26 | # import src.wish 27 | # src.wish.wish_llkd_calculator('test_query/', 8, 'tmp', '/home/rcf-40/weiliw/panasas/v-h-WIsH/host2695_model/') 28 | print('----Fitting models in WIsH...----') 29 | tools.wish(query_virus_dir, host_model_dir, output_dir, 'predict', numThreads) 30 | print('----WIsH calculation finished.----') 31 | llkh = pd.read_csv(os.path.join(output_dir, 'llikelihood.matrix'),header=0,index_col=0) 32 | return llkh.T.loc[virus_index][host_index] 33 | ''' 34 | def wish_llkd_calculator(query_virus_dir, virus_index, host_index, numThreads): 35 | print('----Fitting models in WIsH. This may take up to a few hours...----') 36 | tools.wish(['wish','-c','predict','-m',host_model_dir,'-g',query_virus_dir, 37 | '-r',output_dir,'-b', '-t',str(numThreads)]) 38 | print(' WIsH finished. ') 39 | llkh = pd.read_table(os.path.join(output_dir, 'llikelihood.matrix')) 40 | return llkh.T.loc[virus_index][host_index] 41 | ''' 42 | -------------------------------------------------------------------------------- /src/tools/tools.cpp: -------------------------------------------------------------------------------- 1 | #include "Python.h" 2 | #include 3 | #include "kmer_count_multithreads.h" 4 | #include "WIsH.h" 5 | #include 6 | #include 7 | 8 | static PyObject *wish(PyObject *self, PyObject *args) 9 | { 10 | char *genomeDir, *modelDir, *resultDir, *command; 11 | unsigned int thread; 12 | int res; 13 | if (!PyArg_ParseTuple(args, "ssssi", &genomeDir, &modelDir, &resultDir, &command, &thread)) 14 | return NULL; 15 | res = wish(genomeDir,modelDir,resultDir,command,thread); 16 | return PyLong_FromLong(res); 17 | } 18 | 19 | 20 | static PyObject *kmer_count(PyObject *self, PyObject *args) 21 | { 22 | char* filename; 23 | int K; 24 | int Num_Threads; 25 | bool Reverse; 26 | if (!PyArg_ParseTuple(args, "siii", &filename, &Num_Threads, &Reverse, &K)) 27 | return NULL; 28 | //npy_intp SIZE = pow(4, K); 29 | //std::vector count_res; 30 | std::vector> count_array; 31 | //std::cout<(count_res.data())); 46 | return result; 47 | } 48 | 49 | static PyMethodDef module_methods[] = { 50 | {"kmer_count", kmer_count, METH_VARARGS, ""}, 51 | {"wish", wish, METH_VARARGS, ""}, 52 | {NULL, NULL, 0, NULL} 53 | }; 54 | 55 | static struct PyModuleDef toolsmodule = { 56 | PyModuleDef_HEAD_INIT, 57 | "tools", /* name of module */ 58 | "", /* module documentation, may be NULL */ 59 | -1, /* size of per-interpreter state of the module, 60 | or -1 if the module keeps state in global variables. */ 61 | module_methods 62 | }; 63 | 64 | PyMODINIT_FUNC PyInit_tools(void) 65 | { 66 | import_array(); 67 | return PyModule_Create(&toolsmodule); 68 | } 69 | 70 | -------------------------------------------------------------------------------- /src/tools/kmer_count_multithreads.h: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include "ctpl_stl.h" 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | 11 | 12 | std::atomic X; 13 | bool VALID = true; 14 | std::unordered_map nuc2num = { 15 | {'W',-1}, {'w',-1}, {'S',-1}, {'s',-1}, {'M',-1}, 16 | {'m',-1}, {'K',-1}, {'k',-1}, {'R',-1}, {'r',-1}, 17 | {'Y',-1}, {'y',-1}, {'B',-1}, {'b',-1}, {'D',-1}, 18 | {'d',-1}, {'H',-1}, {'h',-1}, {'V',-1}, 19 | {'v',-1}, {'N',-1}, {'n',-1}, 20 | {'N', -1}, {'A', 0}, {'C', 1 }, {'G', 2}, {'T', 3}, 21 | {'n', -1}, {'a', 0}, {'c', 1}, {'g', 2}, {'t', 3} 22 | }; 23 | 24 | int revcomp(int num, int K){ 25 | int nuc_rc = 0; 26 | int shift; 27 | for (int i=0; i>shift)&3) * pow(4, i); 30 | } 31 | return nuc_rc; 32 | } 33 | 34 | 35 | void count_one_read(int id, int K, std::string one_read, std::vector> &count_array, bool Reverse) { 36 | int length = one_read.length(); 37 | int mask = pow(2, (2*(K-1)))-1; 38 | int num = 0; 39 | int nuc_num = 0; 40 | std::unordered_map::iterator search; 41 | int j = 0; 42 | char nuc; 43 | int rev = 0; 44 | for (int i=0;i second; 53 | } 54 | if (nuc_num == -1){ 55 | num = 0; 56 | rev = 0; 57 | j = 0; 58 | } 59 | else{ 60 | if (j < (K-1)){ 61 | num = num * 4 + nuc_num; 62 | if (Reverse) rev = (rev >> 2) + (3-nuc_num) * pow(4, K-1); 63 | j += 1; 64 | } 65 | else{ 66 | num = (num&mask)<<2; 67 | num += nuc_num; 68 | count_array[num] ++; 69 | if (Reverse) { 70 | rev = (rev >> 2) + (3-nuc_num) * pow(4, K-1); 71 | count_array[rev] ++; 72 | } 73 | } 74 | } 75 | } 76 | } 77 | 78 | std::vector> count(std::string filename, int K, int Num_Threads, bool Reverse) { 79 | ::VALID = true; 80 | const int SIZE = pow(4, K); 81 | std::vector> count_array(SIZE); 82 | std::ifstream fs(filename); 83 | char temp_char[5000]; 84 | std::string temp; 85 | std::string one_read; 86 | //int Num_Threads = std::thread::hardware_concurrency(); 87 | ctpl::thread_pool p(Num_Threads); 88 | while (::VALID) { 89 | fs.getline(temp_char, 5000, '\n'); 90 | std::string temp(temp_char); 91 | if(temp[0] == '>'){ 92 | one_read = one_read + "N"; 93 | } 94 | else{ 95 | one_read = one_read + temp; 96 | } 97 | if (one_read.length() >= 5000){ 98 | p.push([one_read, K, Reverse, &count_array](int id){count_one_read(id, K, one_read, count_array, Reverse);}); 99 | one_read = one_read.substr(one_read.length()-K+1); 100 | } 101 | if (fs.eof()) break; 102 | fs.clear(); 103 | } 104 | p.push([one_read, K, Reverse, &count_array](int id){count_one_read(id, K, one_read, count_array, Reverse);}); 105 | fs.close(); 106 | p.stop(true); 107 | if (!::VALID) count_array[0] = -1; 108 | return count_array; 109 | } 110 | -------------------------------------------------------------------------------- /VirHostMatcher-Net.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # ============================================================================= 3 | # Sanity check 4 | # ============================================================================= 5 | import os 6 | import sys 7 | import src.args 8 | 9 | args = src.args.parse_arguments() 10 | #args = parser.parse_args(['-q','test_query/','-t','8','-o','tmp','--short-contig']) 11 | 12 | query_virus_dir = os.path.abspath(os.path.expanduser(args.query_virus_dir)) 13 | if not os.path.isdir(query_virus_dir): 14 | sys.exit('Query directory error: no such directory '+ query_virus_dir) 15 | 16 | 17 | output_dir = os.path.abspath(os.path.expanduser(args.output_dir)) 18 | if not os.path.isdir(output_dir): 19 | print("Specified output directory does not exist!\n" 20 | "Creating {}".format(output_dir) 21 | ) 22 | os.makedirs(output_dir) 23 | 24 | genome_list = args.genome_list 25 | if genome_list is not None: 26 | if not os.path.isfile(genome_list): 27 | sys.exit('Genome ID file error: no such file '+ genome_list) 28 | 29 | intermediate_dir = os.path.abspath(os.path.expanduser(args.intermediate_dir)) 30 | 31 | 32 | # Basic checks on the data directory 33 | data_dir = args.data_dir 34 | if not os.path.isdir(data_dir): 35 | sys.exit( 36 | "Please provide a valid path to a directory with all required data" 37 | ) 38 | 39 | for subname in ['tables', 'crispr_db_prefix', 'host_wish_model']: 40 | subdir = os.path.join(data_dir, subname) 41 | if not os.path.isdir(subdir): 42 | sys.exit( 43 | "\nError: The data directory you provided is malformatted.\n" 44 | "More info: " 45 | "https://github.com/WeiliWw/VirHostMatcher-Net#download\n" 46 | ) 47 | 48 | # ============================================================================= 49 | # Prediction 50 | # ============================================================================= 51 | print('Loading packages...') 52 | 53 | import pandas as pd 54 | from predictor import HostPredictor 55 | 56 | predictor = HostPredictor(query_virus_dir, args.short_contig, intermediate_dir, genome_list, args.num_Threads) 57 | 58 | output_dir_features = os.path.join(output_dir, 'feature_values') 59 | try: 60 | os.stat(output_dir_features) 61 | except: 62 | os.mkdir(output_dir_features) 63 | 64 | output_dir_pred = os.path.join(output_dir, 'predictions') 65 | try: 66 | os.stat(output_dir_pred) 67 | except: 68 | os.mkdir(output_dir_pred) 69 | 70 | 71 | if args.short_contig: 72 | predictor.wish.to_csv(os.path.join(output_dir_features,'feature_values_wish.csv'), float_format='%.4f') 73 | else: 74 | predictor.s2star.to_csv(os.path.join(output_dir_features,'feature_values_s2star.csv'), float_format='%.4f') 75 | 76 | print('Writing feature scores to {}...'.format(output_dir_features)) 77 | predictor.crispr.to_csv(os.path.join(output_dir_features,'feature_values_crispr.csv'), float_format='%.4f') 78 | predictor.posSV.to_csv(os.path.join(output_dir_features,'feature_values_posSV.csv'), float_format='%.4f') 79 | predictor.negSV.to_csv(os.path.join(output_dir_features,'feature_values_negSV.csv'), float_format='%.4f') 80 | # predictor.blast.to_csv(os.path.join(output_dir_features,'feature_values_blast.csv'), float_format='%.5f') 81 | 82 | predictor.getScores() 83 | predictor.prediction(args.topN, output_dir_pred) 84 | 85 | ## write predictions 86 | # for query,preds in dict_pred.items(): 87 | # preds.to_csv(os.path.join(output_dir_pred, (query+'_prediction.csv'))) 88 | 89 | print('---- Predictions are written to ',output_dir,' ----') 90 | -------------------------------------------------------------------------------- /src/args.py: -------------------------------------------------------------------------------- 1 | # Make arguments accessible from modules 2 | # see https://stackoverflow.com/a/41324084 3 | import argparse 4 | import os 5 | 6 | def parse_arguments(): 7 | # Define default data dir to be the same as before 8 | up_one = os.path.dirname(os.path.dirname((os.path.abspath(__file__)))) 9 | # Append data to it 10 | DEFAULT_DATA_DIR = os.path.join(up_one, 'data') 11 | 12 | parser = argparse.ArgumentParser( 13 | description="VirHostMatcher-Net: A network-based tool for predicting " 14 | "hosts given query viruses", 15 | formatter_class=argparse.ArgumentDefaultsHelpFormatter) 16 | 17 | optionalArgs = parser._action_groups.pop() 18 | optionalArgs.title= "Optional Arguments" 19 | 20 | requiredArgs = parser.add_argument_group("Required Arguments") 21 | requiredArgs.add_argument('-q', 22 | dest='query_virus_dir', 23 | required=True, 24 | type=str, 25 | help="Directory containing query virus genomes with " 26 | ".fasta, .fa or .fna suffixes. One genome per file." 27 | ) 28 | requiredArgs.add_argument('-o', 29 | dest='output_dir', 30 | type=str, 31 | required=True, 32 | help="Output directory. It is created if it doesn't " 33 | "exist" 34 | ) 35 | optionalArgs.add_argument('-t', 36 | dest='num_Threads', 37 | required=False, 38 | type=int, 39 | default=1, 40 | help='Number of threads to use.' 41 | ) 42 | optionalArgs.add_argument('--short-contig', 43 | action='store_true', 44 | required=False, 45 | help="Predict hosts for short viral contigs. " 46 | "(WIsH model files are required in this mode" 47 | ) 48 | optionalArgs.add_argument('-n', 49 | dest='topN', 50 | metavar='topN', 51 | required=False, 52 | type=int, 53 | default=1, 54 | help="Number of top predictions written to the output " 55 | "files. All predictions will be output if there is a tie " 56 | "in score" 57 | ) 58 | optionalArgs.add_argument('-i', 59 | dest='intermediate_dir', 60 | default='./intermediate_res', 61 | type=str, 62 | required=False, 63 | help="Directory storing intermediate result." 64 | ) 65 | optionalArgs.add_argument('-l', 66 | dest='genome_list', 67 | required=False, 68 | default=None, 69 | help="Location of the file containing host " 70 | "NCBI genome names of interest" 71 | ) 72 | optionalArgs.add_argument('-d', 73 | dest='data_dir', 74 | type=str, 75 | required=False, 76 | default=DEFAULT_DATA_DIR, 77 | help="Directory where models, blast and CRISPRs are " 78 | "located." 79 | ) 80 | 81 | parser._action_groups.append(optionalArgs) 82 | 83 | return parser.parse_args() 84 | -------------------------------------------------------------------------------- /src/crispr.py: -------------------------------------------------------------------------------- 1 | ''' 2 | This code generates feature values of CRISPR 3 | ''' 4 | 5 | import os 6 | import math 7 | import pandas as pd 8 | from Bio.Blast.Applications import NcbiblastnCommandline 9 | from .Variables import DB_HOST_CRISPR_PREFIX, TAXA_INFO 10 | from numpy import isnan 11 | ''' 12 | Preset variables and load tables 13 | ''' 14 | 15 | db_host_crispr_prefix = DB_HOST_CRISPR_PREFIX 16 | # output_dir = INTERMEDIATE_RESULT 17 | taxa_info_file = TAXA_INFO 18 | #hash_table_file = HASH_TABLE 19 | 20 | db_host_crispr_prefix = os.path.expanduser(db_host_crispr_prefix) 21 | #hash_table = pd.read_pickle(hash_table_file) 22 | 23 | #dict_genome = hash_table.set_index(1).to_dict()[0] 24 | taxa_info = pd.read_pickle(taxa_info_file) 25 | # taxa_info = taxa_info.set_index('hostNCBIName') 26 | 27 | ''' 28 | Function: Run blast for a single query virus and return CRISPR signal 29 | -------- 30 | Parameters: 31 | item: query file 32 | query_virus_dir 33 | numThreads 34 | ''' 35 | 36 | def crisprSingle(item, query_virus_dir, output_dir, numThreads): 37 | query_name = item.split('.')[0] 38 | query_file = os.path.join(query_virus_dir, item) 39 | output_file = os.path.join(output_dir, query_name) + '.crispr' 40 | crispr_call = NcbiblastnCommandline(query=query_file,db=db_host_crispr_prefix,out=output_file,outfmt="6 qacc sacc evalue", evalue=1,gapopen=10,penalty=-1, 41 | gapextend=2,word_size=7,dust='no', 42 | task='blastn-short',perc_identity=90,num_threads=numThreads) 43 | crispr_call() 44 | ''' 45 | Parse blast results 46 | ''' 47 | if os.stat(output_file).st_size == 0: 48 | ind = False 49 | return ind, None 50 | else: 51 | query_res = pd.read_table(output_file,header = None) 52 | # Sanity check for blastn output format 53 | query_res = query_res[query_res[1].apply(lambda x: x.count("|")) == 2] 54 | if query_res.shape[0] == 0: 55 | return False, None 56 | query_res[0] = query_name 57 | query_res[1] = query_res[1].apply(lambda x: x.split('|')[-2]) 58 | #query_res[1] = [dict_genome[k] for k in list(query_res[1])] 59 | query_res[2] = -query_res[2].apply(math.log) 60 | df_crispr = query_res.groupby([0,1]).max().unstack(fill_value=0) 61 | ind = True 62 | return ind, df_crispr.set_index([[query_name]]) 63 | 64 | ''' 65 | Function: Gather available CRISPR signals 66 | -------- 67 | Parameters: 68 | query_virus_dir 69 | numThreads 70 | ''' 71 | def crispr_calculator(query_virus_dir, output_dir, numThreads): 72 | query_cont = [] 73 | query_list = [f for f in os.listdir(query_virus_dir) 74 | if f.lower().endswith(('.fasta', '.fa', '.fna'))] 75 | crispr_output_dir = os.path.join(output_dir, 'CRISPR/') 76 | try: 77 | os.stat(crispr_output_dir) 78 | except: 79 | os.mkdir(crispr_output_dir) 80 | for item in query_list: 81 | print('----Calculating crispr feature values for ',item,' ----') 82 | ind, df = crisprSingle(item, query_virus_dir, crispr_output_dir, numThreads) 83 | if ind: 84 | query_cont.append(df) 85 | print('----CRISPR intermediate files are stored in ',crispr_output_dir,' ----') 86 | if query_cont == []: 87 | return pd.DataFrame() # Return an empty data frame if no match for any queries 88 | else: 89 | df_concat = pd.concat(query_cont,axis =1,sort=False).groupby(axis=1,level=1,sort=False).sum().fillna(0) 90 | return df_concat 91 | 92 | ''' 93 | Function: Augment signals to the entire matrix and generate values at genus level 94 | -------- 95 | Parameters: 96 | df_input 97 | virus_index: query index 98 | host_index 99 | ''' 100 | 101 | def uniGenus(df_input, virus_index, host_index): 102 | df_pseudo = pd.DataFrame(index=virus_index, columns=host_index).fillna(0) 103 | df_full = pd.concat([df_pseudo, df_input],sort=False).groupby(level=0,sort=False).sum().fillna(0) 104 | df_full = df_full.loc[virus_index][host_index] 105 | df_full.loc['hostGenus'] = taxa_info.loc[host_index]['hostGenus'] 106 | dict_genera = {} 107 | for i in df_full: 108 | col = df_full[i].rename(None) 109 | genus = col['hostGenus'] 110 | if type(genus) is not str: # not a genus name 111 | if isnan(genus): continue 112 | if genus in dict_genera: 113 | dict_genera[genus] = pd.concat([dict_genera[genus], col],axis=1,sort=False).max(axis=1) 114 | else: dict_genera[genus] = col 115 | for i in df_full: 116 | genus = df_full[i]['hostGenus'] 117 | if type(genus) is not str: 118 | if isnan(genus): continue 119 | df_full[i] = dict_genera[genus] 120 | return df_full.loc[virus_index,:] 121 | ''' 122 | def uniGenus(df_input, host_index): 123 | virus_index = df_input.index 124 | df_pseudo = pd.DataFrame(index=virus_index, columns=host_index).fillna(0) 125 | df_full = pd.concat([df_pseudo, df_input]).groupby(level=0).sum().fillna(0) 126 | df_full = df_full.loc[virus_index][host_index] 127 | df_full.loc['hostGenus'] = taxa_info.loc[host_index]['hostGenus'] 128 | for genera in taxa_info.loc[host_index]['hostGenus'].unique(): 129 | if pd.notnull(genera): 130 | idx = (df_full.loc['hostGenus'] == genera) 131 | df_full.loc[virus_index,idx] = df_full.loc[virus_index,idx].max(axis=1) 132 | return df_full.loc[virus_index,:] 133 | ''' 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | -------------------------------------------------------------------------------- /src/tools/mm.cpp: -------------------------------------------------------------------------------- 1 | #include "mm.h" 2 | 3 | mm::mm(std::string modelFile, int verb) 4 | { 5 | verbosity = verb; 6 | modelName = modelFile.substr(0, modelFile.find_last_of(".")); 7 | unsigned int slashPos; 8 | if ((slashPos = modelName.find_last_of('/'))!= modelName.size()) 9 | modelName = modelName.substr(slashPos+1,modelName.size()); 10 | 11 | read(modelFile); 12 | } 13 | 14 | mm::mm(unsigned int k,double a, int verb) 15 | { 16 | verbosity = verb; 17 | order = k; 18 | alpha = a; 19 | initArrays(); 20 | } 21 | 22 | void mm::printParameters() 23 | { 24 | std::cout<<"Parameters for model "< (1<<(2*(order)),0); 39 | orderCounts = std::vector(1<<(2*(order+1)),0); 40 | p = std::vector(1<<(2*(order+1)),0); 41 | pc = std::vector(4,0.25); 42 | } 43 | 44 | int mm::trainOn(std::string genomeFile) 45 | { 46 | modelName = genomeFile.substr(0, genomeFile.find_last_of(".")); 47 | unsigned int slashPos; 48 | if ((slashPos = modelName.find_last_of('/'))!= modelName.size()) 49 | modelName = modelName.substr(slashPos+1,modelName.size()); 50 | 51 | 52 | std::vector genomeChunks = readGenome(genomeFile); 53 | 54 | if (!genomeChunks.size()) 55 | return -1; 56 | 57 | for (size_t i = 0 ; i < genomeChunks.size() ; i++) 58 | { 59 | countKmers(genomeChunks[i]); 60 | } 61 | 62 | computeModelProb(); 63 | 64 | return 0; 65 | } 66 | 67 | 68 | std::string mm::mapToAlphabet(std::string seq) 69 | { 70 | bool seenUnknown = false; 71 | std::string res; 72 | for (size_t i = 0 ; i < seq.size() ; i++) 73 | { 74 | switch (seq[i]) { 75 | case 'A': 76 | res.push_back(0); 77 | break; 78 | case 'T': 79 | res.push_back(1); 80 | break; 81 | case 'C': 82 | res.push_back(2); 83 | break; 84 | case 'G': 85 | res.push_back(3); 86 | break; 87 | default: 88 | seenUnknown=true; 89 | break; 90 | } 91 | 92 | } 93 | 94 | /*if (seenUnknown) 95 | std::cout<< "Warning: there are letters in genome not in {A,T,C,G}."<= order) 128 | lowerOrderCounts[hashKmer(genome.end() - order,order)]++; 129 | } 130 | 131 | size_t mm::head(size_t k) 132 | { 133 | return k>>2; 134 | } 135 | 136 | 137 | size_t mm::lastNucl(size_t k) 138 | { 139 | return k&3; 140 | } 141 | 142 | 143 | 144 | void mm::computeModelProb() 145 | { 146 | for (size_t k=0; k0 && verbosity > 1) 150 | std::cout <<"OUPS ! Positive log-probability : "<< p[k] <(&p[0]),p.size() * sizeof(p[0])); 173 | fout.close(); 174 | return 0; 175 | } 176 | 177 | 178 | int mm::read(std::string modelFile) 179 | { 180 | std::ifstream fin(modelFile.c_str(), std::ios::in|std::ios::binary); 181 | if (!fin.good()) 182 | return -1; 183 | 184 | fin.seekg(0,fin.end); 185 | size_t sizep = static_cast(fin.tellg()) - sizeof(alpha) - sizeof(order); 186 | 187 | 188 | p = std::vector(sizep / sizeof(double)); 189 | 190 | fin.seekg(0,std::ios::beg); 191 | fin.read(reinterpret_cast(&order),sizeof(order)); 192 | fin.read(reinterpret_cast(&alpha),sizeof(alpha)); 193 | 194 | 195 | 196 | fin.read(reinterpret_cast(p.data()),p.size() * sizeof(double)); 197 | fin.close(); 198 | 199 | return 0; 200 | } 201 | 202 | std::vector mm::readGenome(std::string genomeFile) 203 | { 204 | std::ifstream fin(genomeFile.c_str(), std::ios::in); 205 | 206 | if (!fin.good()) 207 | return std::vector(); 208 | 209 | std::vector genomeChunks; 210 | std::string line; 211 | 212 | while(std::getline(fin,line)) 213 | { 214 | if(!line.empty()) 215 | { 216 | if (line[0]=='>') 217 | { 218 | genomeChunks.push_back(std::string()); 219 | } else { 220 | if (!genomeChunks.size()) 221 | { 222 | std::cout<<"Corrupted Fasta file: "< genomeChunks) 234 | { 235 | double ll = 0; 236 | size_t length = 0; 237 | for (size_t i = 0 ; i < genomeChunks.size() ; i++) 238 | { 239 | size_t start = order; 240 | for (size_t pos = start; pos= 0.7 and pred['hostSuperkingdom'][0] == 'Bacteria': 127 | ind = (pred['score'][0] - 0.31)//0.001 - 1 128 | pred['acc_phylum'] = [pred_thre['hostPhylum'][ind]] + [None for i in range(len(pred)-1)] 129 | if pred['hostClass'][0]: 130 | pred['acc_class'] = [pred_thre['hostClass'][ind]] + [None for i in range(len(pred)-1)] 131 | if pred['hostOrder'][0]: 132 | pred['acc_order'] = [pred_thre['hostOrder'][ind]] + [None for i in range(len(pred)-1)] 133 | if pred['hostFamily'][0]: 134 | pred['acc_family'] = [pred_thre['hostFamily'][ind]] + [None for i in range(len(pred)-1)] 135 | if pred['hostGenus'][0]: 136 | pred['acc_genus'] = [pred_thre['hostGenus'][ind]] + [None for i in range(len(pred)-1)] 137 | pred.to_csv(os.path.join(output_dir_pred, (query+'_prediction.csv')), float_format='%.4f') 138 | #return dict_pred 139 | 140 | 141 | 142 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # README 2 | 3 | VirHostMatcher-Net is a network-based computational tool for predicting virus-host interactions. Current version predicts hosts of given viruses from a database of 62,493 Bacteria and Archaea candidates. VirHostMatcher-Net has two modes: predicting for complete genomes and predicting for short viral contigs. 4 | 5 | ### Update on 2021/04/10: Please check the message below before usage! 6 | ***Important:*** We corrected a critical bug in the software: the coefficients for SV+ and SV- (see Equation 6 in the paper) were mistakenly swapped when the software was published. Note this does not impact the results in the paper: we computed the feature values separately without the software (because the computation/simulation used in the study was too time-consuming for a single run by the software, especially for the blast feature that we evaluated in the study), and directly applied the coefficients to calculate the final score. 7 | 8 | ## Citation 9 | Wang *et al.* "A network-based integrated framework for predicting virus–prokaryote interactions" NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa044, https://doi.org/10.1093/nargab/lqaa044. 10 | 11 | 12 | ### Dependencies 13 | 14 | VirHostMatcher-Net requires Python 3.4+ together with the following packages and `BLAST`. 15 | 16 | * Python packages 17 | + [Biopython](http://biopython.org/wiki/Download) 18 | + [pandas](https://pandas.pydata.org/) 19 | + [numpy](https://www.scipy.org/scipylib/download.html) 20 | 21 | We recommend to use [Miniconda](https://conda.io/miniconda.html) to install all dependencies. After installing Miniconda, simply run 22 | ``` 23 | conda install numpy pandas Biopython 24 | conda install -c bioconda blast # skip this line if you've already installed BLAST 25 | ``` 26 | 27 | Alternatively, users may want to install Python3.X and dependencies manually. 28 | 29 | ## Installation 30 | In addition to dependencies, VirHostMatcher-Net requires to build local modules and download database. 31 | 32 | ### Building local dependent modules 33 | ##### Linux: 34 | ``` 35 | git clone https://github.com/WeiliWw/VirHostMatcher-Net.git 36 | cd VirHostMatcher-Net 37 | CC=g++ python setup.py install --install-platlib=./src/ 38 | 39 | ## Optional 40 | # Include the VirHostmatcher-Net directory in your $PATH 41 | # The main script is executable 42 | export PATH=/path/to/VirHostMatcher-Net/:$PATH 43 | VirHostMatcher.py -h 44 | ``` 45 | ##### MacOS 46 | ``` 47 | git clone https://github.com/WeiliWw/VirHostMatcher-Net.git 48 | cd VirHostMatcher-Net 49 | MACOSX_DEPLOYMENT_TARGET=10.9 CC=g++ python setup.py install --install-platlib=./src/ 50 | ``` 51 | 52 | ### Data preparation 53 | The prediction model of VirHostMatcher-Net depends on a large amount of data: BLAST index files of all bacteria and their CRISPRs, WIsH models(short viral contig mode) and hash files for calculating s*2, etc. 54 | 55 | #### Download 56 | There are two packs of files for downloading, based on your use case: if you intend to use the software on complete genomes or long contigs, you can download "Pack 1" below which is much smaller than "Pack 2". The data can be directly downloaded from [Google Drive](https://drive.google.com/drive/folders/1lkL6gtKJPqgQUxW2dcE2MnUvd2-mPKcD?usp=sharing), or you can use `curl` in the commandline to download the files from Google Drive (see below, credit to [this genius post](https://stackoverflow.com/a/48133859/9250524)). 57 | 58 | ##### Pack 1: Complete genome mode alone 59 | At the directory of VirHostMatcher-Net, run 60 | ``` 61 | # download 62 | fileid="185U3ZLYe1uNmB5oCaIlb0IQNURnlyXcN" 63 | filename="data_VirHostMatcher-Net_complete_genome_mode_alone.tar.gz" 64 | curl -c ./cookie -s -L "https://drive.google.com/uc?export=download&id=${fileid}" > /dev/null 65 | curl -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} 66 | # extract 67 | tar xf data_VirHostMatcher-Net_complete_genome_mode_alone.tar.gz 68 | ``` 69 | 70 | ##### Pack 2: Complete genome mode and short viral contig mode 71 | > Note: The extracted `data` folder takes up 125G of disk space. 72 | 73 | At the directory of VirHostMatcher-Net, run 74 | ``` 75 | # download 76 | fileid="1ZWTn_WIkSbtr6guyAPNnmmYai-qmh93P" 77 | filename="data_VirHostMatcher-Net_both_modes.tar.gz" 78 | curl -c ./cookie -s -L "https://drive.google.com/uc?export=download&id=${fileid}" > /dev/null 79 | curl -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} 80 | # extract 81 | tar xf data_VirHostMatcher-Net_both_modes.tar.gz 82 | ``` 83 | 84 | 85 | #### Required format of query sequences 86 | VirHostMatcher-Net accepts files in FASTA format. 87 | 88 | 89 | ## Usage 90 | python VirHostMatcher-Net.py [-h] -q QUERY_VIRUS_DIR [-t NUM_THREADS] [--short-contig] -o 91 | OUTPUT_DIR [-n topN] [-i INTERMEDIATE_DIR] [-l GENOME_LIST] 92 | #### Options 93 | -h, --help show this help message and exit 94 | -q QUERY_VIRUS_DIR Directory containing query virus genomes with .fasta or 95 | .fa suffix 96 | -t NUM_THREADS Number of threads to use. Default = 1 97 | --short-contig Predict hosts for short viral contigs. WIsH model files 98 | are required in this mode 99 | -o OUTPUT_DIR Output directory 100 | -n topN Number of top predictions written to the output files. 101 | All predictions will be output if there is a tie in 102 | score. Default = 1 103 | -i INTERMEDIATE_DIR Directory storing intermediate result. Default = 104 | ./intermediate_res 105 | -l GENOME_LIST Location of the file containing host NCBI genome names of 106 | interest 107 | 108 | ### Examples 109 | 110 | #### Predict hosts of virus genomes 111 | ``` 112 | mkdir output 113 | python VirHostMatcher-Net.py -q ./test/VGs -o output -i tmp -n 3 -t 8 114 | ``` 115 | 116 | #### Predict hosts of viral contigs 117 | ``` 118 | mkdir output2 119 | python VirHostMatcher-Net.py -q ./test/mVCs --short-contig -o output2 -n 3 -t 8 -l genome_list/marine_host_list.txt 120 | ``` 121 | 122 | 123 | 124 | In both modes, VirHostMatcher-Net outputs a prediction file for each query virus to the specified directory. A prediction file is in .csv format where each row represents one candidate host with detailed taxanomic information, a prediction score, values (*_val) and percentiles (*_pct) of each feature. The feature percentile of a virus-host pair is defined as the percentile of this feature score among all scores between that virus and all the candidate hosts. A very high percentile (i.e. >95%) suggests significance of the feature on contributing to the prediction. In the output, the percentile of SV-, with a negative coefficient, is reversed to keep consistent with other feature percentiles. Tables of feature values are stored in a subdirectory `feature_values` under the output directory. 125 | 126 | Users can use a subset of candidate hosts for prediction by the option `-l` to specify a list of NCBI genome names. Two example lists of 4034 marine hosts and 9097 human-associated hosts can be found in the directory `genome_list`. 127 | 128 | ### Training and validation data 129 | Training and validation data are shared in [Google Drive](https://drive.google.com/drive/folders/1ilhe-xPQa89jZL8C33NgHNcymz-hkTEC?usp=sharing). 130 | 131 | ### Bug reports 132 | Please open a Github issue or contact Weili Wang weiliw@usc.edu 133 | 134 | ----------------------------------------------------------------------------------------------- 135 | ## Copyright and License Information 136 | Copyright (C) 2019 University of Southern California, Weili Wang and Fengzhu Sun 137 | 138 | This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. 139 | 140 | This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 141 | 142 | You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. 143 | -------------------------------------------------------------------------------- /src/s2star.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Generates necessary results of s2star 3 | ''' 4 | import os, sys, pickle 5 | import pandas as pd 6 | #from sklearn.metrics.pairwise import cosine_similarity 7 | import numpy as np 8 | #from . import tools 9 | from .tools import kmer_count 10 | from .Variables import TABLE_HOST, TABLE_BENCH, TABLE_INTER 11 | ''' 12 | Preset variables 13 | ### to be checked! 14 | ''' 15 | # output_dir = INTERMEDIATE_RESULT #'./intermediate_res/' 16 | # tables = TABLES 17 | # original_interaction_file = S2STAR_BENCH_HOST 18 | # hash_dir = D2STAR_HASH #'/home/rcf-40/weiliw/panasas/v-h- 19 | # pseudo_host = PSEUDO_HOST #'./prepare_data/pseudo_host/' 20 | # pseudo_virus = PSEUDO_VIRUS #'./prepare_data/pseudo_virus/' 21 | 22 | ''' 23 | Helper functions for calculating s2star 24 | ''' 25 | Alphabeta = ['A', 'C', 'G', 'T'] 26 | Alpha_dict = dict(zip(Alphabeta, range(4))) 27 | 28 | def get_transition(count_array): 29 | shape = len(count_array) 30 | transition_array = count_array.reshape(shape//4, 4) 31 | with np.errstate(divide='ignore', invalid='ignore'): 32 | transition_array = (transition_array / np.sum(transition_array, 1)[:, np.newaxis]) 33 | transition_array[np.isnan(transition_array)] = 0 34 | return transition_array 35 | 36 | 37 | def get_expect(a_M_count, a_trans, K, M): 38 | a_expect = a_M_count 39 | for _ in range(K-M): 40 | a_trans = np.tile(a_trans, (4, 1)) 41 | a_expect = (a_expect[:,np.newaxis] * a_trans).flatten() 42 | return a_expect 43 | 44 | def get_f(a_K_count, a_expect): 45 | with np.errstate(divide='ignore', invalid='ignore'): 46 | f = (a_K_count-a_expect)/np.sqrt(a_expect) 47 | f[np.isnan(f)]=0 48 | return f 49 | 50 | def get_all_f(Dir, K, order, Reverse, numThreads): 51 | M = order + 1 52 | sequence_list = [f for f in os.listdir(Dir) 53 | if f.lower().endswith(('.fasta', '.fa', '.fna'))] 54 | f_matrix = np.ones((len(sequence_list), 4**K)) 55 | flag = False 56 | for i, seq in enumerate(sequence_list): 57 | seqfile = os.path.join(Dir, seq) 58 | K_count = np.array(kmer_count(seqfile, numThreads, Reverse, K)) 59 | if K_count[0] == -1: # sanity check for the fasta files 60 | print('The query file {} contains invalid chars, please make sure it is a valid fasta file.'.format(seq)) 61 | flag = True 62 | if np.sum(K_count) == 0: 63 | print('The query file {} is empty, please double check the file.'.format(seq)) 64 | flag = True 65 | M_count = np.array(kmer_count(seqfile, numThreads, Reverse, M)) 66 | trans = get_transition(M_count) 67 | expect = get_expect(M_count, trans, K, M) 68 | f_matrix[i] = get_f(K_count, expect) 69 | name_list = [x.rsplit('.', 1)[0] for x in sequence_list] 70 | if flag: sys.exit('Program terminated. Please check error info above.') 71 | return f_matrix, name_list 72 | 73 | def cosine_similarity(f1, f2): 74 | n1 = np.linalg.norm(f1,axis=1,keepdims=True) 75 | n2 = np.linalg.norm(f2,axis=1,keepdims=True) 76 | norms = np.dot(f1,f2.T) 77 | prod = np.dot(f1,f2.T) 78 | return prod/(np.dot(n1,n2.T)) 79 | 80 | 81 | ''' 82 | Function: Calculate distances within query viruses 83 | -------- 84 | Parameters: 85 | query_virus_dir = './test_query/' 86 | 87 | ''' 88 | 89 | 90 | 91 | def s2_query(query_virus_dir, ifShort, numThreads): 92 | print('----Start calculating s2* part I... ----') 93 | virus_mat, virus_list = get_all_f(query_virus_dir, 6, 2, True, numThreads) 94 | # s2_intra_mat = cosine_similarity(virus_mat, virus_mat) 95 | print('----Finished calculating s2* part I----') 96 | print('----Start calculating s2* part II... ----') 97 | ## read bench file 98 | bench_mat, bench_list = pickle.load(open(TABLE_BENCH, 'rb')) 99 | s2_virus_bench_mat = cosine_similarity(virus_mat, bench_mat) 100 | print('----Finished calculating s2* part II----') 101 | if ifShort: 102 | return pd.DataFrame(s2_virus_bench_mat, index=virus_list, columns=bench_list), None 103 | else: 104 | ## read host mat file 105 | print('----Start calculating s2* part III... ----') 106 | host_mat, host_list = pickle.load(open(TABLE_HOST, 'rb')) 107 | s2_host_virus_mat = cosine_similarity(virus_mat, host_mat) 108 | print('----Finished calculating s2* part III----') 109 | ## return three matrices 110 | return pd.DataFrame(s2_virus_bench_mat, index=virus_list, columns=bench_list), pd.DataFrame(s2_host_virus_mat, index=virus_list, columns=host_list) 111 | 112 | 113 | 114 | ''' 115 | def intra_query(query_virus_dir): 116 | print('----Start calculating s2* part I. This may take a few seconds...----') 117 | tools.cafe(['CAFE','-F1',query_virus_dir, '-F2', query_virus_dir, 118 | '-K', '6', '-M', '2', '-D', 'D2star', '-S', hash_dir, 119 | '-R', '-O', output_dir + 'intra_query_virus']) 120 | print('----Finished calculating s2* part I----') 121 | # Read results and return the df 122 | results_file = output_dir + 'intra_query_virus.D2star.plain' 123 | results = pd.read_csv(results_file, index_col=0) 124 | return 1 - 2*results 125 | 126 | ''' 127 | ''' 128 | Function: Calculate distances between query viruses and 352 'benchmark' 129 | viruses 130 | -------- 131 | Parameters: 132 | query_virus_dir 133 | 134 | ''' 135 | 136 | 137 | # def query_bench(query_virus_dir): 138 | # print('----Start calculating s2* part II. This may take a few minutes...----') 139 | # tools.cafe(['CAFE','-F1',query_virus_dir, '-F2', pseudo_virus, 140 | # '-K', '6', '-M', '2', '-D', 'D2star', '-S', hash_dir, 141 | # '-R', '-O', output_dir + 'between_query_virus_bench']) 142 | # print('----Finished calculating s2* part II----') 143 | # # Read results and return the df 144 | # results_file = output_dir + 'between_query_virus_bench.D2star.plain' 145 | # results = pd.read_csv(results_file, index_col=0) 146 | # return 1 - 2*results 147 | 148 | 149 | ''' 150 | Function: Calculate distances between query viruses and candidate hosts 151 | -------- 152 | Parameters: 153 | query_virus_dir 154 | 155 | ''' 156 | # def query_host(query_virus_dir): 157 | # print('----Start calculating s2* part III. This may take up to a few hours...----') 158 | # tools.cafe(['CAFE','-F1',query_virus_dir, '-F2', pseudo_host, 159 | # '-K', '6', '-M', '2', '-D', 'D2star', '-S', hash_dir, 160 | # '-R', '-O', output_dir + 'inter_query_virus_hosts']) 161 | # print('----Finished calculating s2* part III----') 162 | # # Read results and return the df 163 | # results_file = output_dir + 'inter_query_virus_hosts.D2star.plain' 164 | # results = pd.read_csv(results_file, index_col=0) 165 | # return 1 - 2*results 166 | 167 | 168 | ''' 169 | Function: Combine previous d2star results and return virus-virus and virus-host 170 | distance matrices and interaction matrix 171 | -------- 172 | Parameters: 173 | query_virus_dir 174 | 175 | ''' 176 | 177 | # 178 | #def s2star_caclculator(query_virus_dir, ifShort, numThreads): 179 | # mat_original_interaction = pd.read_hdf(tables,'interaction') # 352 by 31k 180 | # if ifShort: 181 | # print('----Calculation of s2* is split into two parts----') 182 | # else: 183 | # print('----Calculation of s2* is split into three parts----') 184 | # mat_intra_query, mat_query_bench, s2star_query_host = s2_query(query_virus_dir, ifShort, numThreads) 185 | ## mat_intra_query = intra_query(query_virus_dir) 186 | ## mat_query_bench = query_bench(query_virus_dir) 187 | # host_index = mat_original_interaction.columns 188 | # query_index = mat_intra_query.index 189 | # virus_index = mat_original_interaction.index.union(query_index) 190 | # s2star_query_virus = pd.concat([mat_query_bench, 191 | # mat_intra_query],sort=False).groupby(level=0,sort=False).sum() 192 | # # rearrange df 193 | # if not ifShort: 194 | # # rearrange df 195 | # s2star_query_host = s2star_query_host.loc[query_index, host_index] 196 | # s2star_query_virus = s2star_query_virus.loc[query_index, virus_index] 197 | # pseudo_interaction = pd.DataFrame(index=virus_index, columns=host_index).fillna(0) 198 | # df_interaction = pd.concat([mat_original_interaction,pseudo_interaction]).groupby(level=0).sum().fillna(0) 199 | # df_interaction = df_interaction.loc[virus_index][host_index] 200 | # return s2star_query_host, s2star_query_virus, df_interaction 201 | # 202 | def s2star_caclculator(query_virus_dir, ifShort, numThreads): 203 | mat_original_interaction = pd.read_csv(TABLE_INTER) # 352 by 31k 204 | if ifShort: 205 | print('----Calculation of s2* is split into two parts----') 206 | else: 207 | print('----Calculation of s2* is split into three parts----') 208 | mat_query_bench, s2star_query_host = s2_query(query_virus_dir, ifShort, numThreads) 209 | host_index = mat_original_interaction.columns 210 | query_index = mat_query_bench.index 211 | virus_index = query_index.tolist() + mat_original_interaction.index.tolist() 212 | #s2star_query_virus = pd.concat([mat_query_bench, 213 | # mat_intra_query], sort=False).groupby(level=0, sort=False).sum().loc[query_index, virus_index] 214 | if not ifShort: 215 | s2star_query_host = s2star_query_host.loc[query_index, host_index] 216 | #s2star_query_virus = s2star_query_virus.loc[query_index, virus_index] 217 | #pseudo_interaction = pd.DataFrame(index=virus_index, columns=host_index).fillna(0) 218 | #df_interaction = pd.concat([mat_original_interaction,pseudo_interaction]).groupby(level=0).sum().fillna(0) 219 | #df_interaction = df_interaction.loc[virus_index][host_index] 220 | #s2star_query_virus.values[[np.arange(s2star_query_virus.shape[0])]*2] = 0 221 | return s2star_query_host, mat_query_bench, mat_original_interaction 222 | 223 | 224 | -------------------------------------------------------------------------------- /src/tools/ctpl_stl.h: -------------------------------------------------------------------------------- 1 | /********************************************************* 2 | * 3 | * Copyright (C) 2014 by Vitaliy Vitsentiy 4 | * 5 | * Licensed under the Apache License, Version 2.0 (the "License"); 6 | * you may not use this file except in compliance with the License. 7 | * You may obtain a copy of the License at 8 | * 9 | * http://www.apache.org/licenses/LICENSE-2.0 10 | * 11 | * Unless required by applicable law or agreed to in writing, software 12 | * distributed under the License is distributed on an "AS IS" BASIS, 13 | * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | * See the License for the specific language governing permissions and 15 | * limitations under the License. 16 | * 17 | *********************************************************/ 18 | 19 | 20 | #ifndef __ctpl_stl_thread_pool_H__ 21 | #define __ctpl_stl_thread_pool_H__ 22 | 23 | #include 24 | #include 25 | #include 26 | #include 27 | #include 28 | #include 29 | #include 30 | #include 31 | #include 32 | 33 | 34 | 35 | // thread pool to run user's functors with signature 36 | // ret func(int id, other_params) 37 | // where id is the index of the thread that runs the functor 38 | // ret is some return type 39 | 40 | 41 | namespace ctpl { 42 | 43 | namespace detail { 44 | template 45 | class Queue { 46 | public: 47 | bool push(T const & value) { 48 | std::unique_lock lock(this->mutex); 49 | this->q.push(value); 50 | return true; 51 | } 52 | // deletes the retrieved element, do not use for non integral types 53 | bool pop(T & v) { 54 | std::unique_lock lock(this->mutex); 55 | if (this->q.empty()) 56 | return false; 57 | v = this->q.front(); 58 | this->q.pop(); 59 | return true; 60 | } 61 | bool empty() { 62 | std::unique_lock lock(this->mutex); 63 | return this->q.empty(); 64 | } 65 | private: 66 | std::queue q; 67 | std::mutex mutex; 68 | }; 69 | } 70 | 71 | class thread_pool { 72 | 73 | public: 74 | 75 | thread_pool() { this->init(); } 76 | thread_pool(int nThreads) { this->init(); this->resize(nThreads); } 77 | 78 | // the destructor waits for all the functions in the queue to be finished 79 | ~thread_pool() { 80 | this->stop(true); 81 | } 82 | 83 | // get the number of running threads in the pool 84 | int size() { return static_cast(this->threads.size()); } 85 | 86 | // number of idle threads 87 | int n_idle() { return this->nWaiting; } 88 | std::thread & get_thread(int i) { return *this->threads[i]; } 89 | 90 | // change the number of threads in the pool 91 | // should be called from one thread, otherwise be careful to not interleave, also with this->stop() 92 | // nThreads must be >= 0 93 | void resize(int nThreads) { 94 | if (!this->isStop && !this->isDone) { 95 | int oldNThreads = static_cast(this->threads.size()); 96 | if (oldNThreads <= nThreads) { // if the number of threads is increased 97 | this->threads.resize(nThreads); 98 | this->flags.resize(nThreads); 99 | 100 | for (int i = oldNThreads; i < nThreads; ++i) { 101 | this->flags[i] = std::make_shared>(false); 102 | this->set_thread(i); 103 | } 104 | } 105 | else { // the number of threads is decreased 106 | for (int i = oldNThreads - 1; i >= nThreads; --i) { 107 | *this->flags[i] = true; // this thread will finish 108 | this->threads[i]->detach(); 109 | } 110 | { 111 | // stop the detached threads that were waiting 112 | std::unique_lock lock(this->mutex); 113 | this->cv.notify_all(); 114 | } 115 | this->threads.resize(nThreads); // safe to delete because the threads are detached 116 | this->flags.resize(nThreads); // safe to delete because the threads have copies of shared_ptr of the flags, not originals 117 | } 118 | } 119 | } 120 | 121 | // empty the queue 122 | void clear_queue() { 123 | std::function * _f; 124 | while (this->q.pop(_f)) 125 | delete _f; // empty the queue 126 | } 127 | 128 | // pops a functional wrapper to the original function 129 | std::function pop() { 130 | std::function * _f = nullptr; 131 | this->q.pop(_f); 132 | std::unique_ptr> func(_f); // at return, delete the function even if an exception occurred 133 | std::function f; 134 | if (_f) 135 | f = *_f; 136 | return f; 137 | } 138 | 139 | // wait for all computing threads to finish and stop all threads 140 | // may be called asynchronously to not pause the calling thread while waiting 141 | // if isWait == true, all the functions in the queue are run, otherwise the queue is cleared without running the functions 142 | void stop(bool isWait = false) { 143 | if (!isWait) { 144 | if (this->isStop) 145 | return; 146 | this->isStop = true; 147 | for (int i = 0, n = this->size(); i < n; ++i) { 148 | *this->flags[i] = true; // command the threads to stop 149 | } 150 | this->clear_queue(); // empty the queue 151 | } 152 | else { 153 | if (this->isDone || this->isStop) 154 | return; 155 | this->isDone = true; // give the waiting threads a command to finish 156 | } 157 | { 158 | std::unique_lock lock(this->mutex); 159 | this->cv.notify_all(); // stop all waiting threads 160 | } 161 | for (int i = 0; i < static_cast(this->threads.size()); ++i) { // wait for the computing threads to finish 162 | if (this->threads[i]->joinable()) 163 | this->threads[i]->join(); 164 | } 165 | // if there were no threads in the pool but some functors in the queue, the functors are not deleted by the threads 166 | // therefore delete them here 167 | this->clear_queue(); 168 | this->threads.clear(); 169 | this->flags.clear(); 170 | } 171 | 172 | template 173 | auto push(F && f, Rest&&... rest) ->std::future { 174 | auto pck = std::make_shared>( 175 | std::bind(std::forward(f), std::placeholders::_1, std::forward(rest)...) 176 | ); 177 | auto _f = new std::function([pck](int id) { 178 | (*pck)(id); 179 | }); 180 | this->q.push(_f); 181 | std::unique_lock lock(this->mutex); 182 | this->cv.notify_one(); 183 | return pck->get_future(); 184 | } 185 | 186 | // run the user's function that excepts argument int - id of the running thread. returned value is templatized 187 | // operator returns std::future, where the user can get the result and rethrow the catched exceptins 188 | template 189 | auto push(F && f) ->std::future { 190 | auto pck = std::make_shared>(std::forward(f)); 191 | auto _f = new std::function([pck](int id) { 192 | (*pck)(id); 193 | }); 194 | this->q.push(_f); 195 | std::unique_lock lock(this->mutex); 196 | this->cv.notify_one(); 197 | return pck->get_future(); 198 | } 199 | 200 | 201 | private: 202 | 203 | // deleted 204 | thread_pool(const thread_pool &);// = delete; 205 | thread_pool(thread_pool &&);// = delete; 206 | thread_pool & operator=(const thread_pool &);// = delete; 207 | thread_pool & operator=(thread_pool &&);// = delete; 208 | 209 | void set_thread(int i) { 210 | std::shared_ptr> flag(this->flags[i]); // a copy of the shared ptr to the flag 211 | auto f = [this, i, flag/* a copy of the shared ptr to the flag */]() { 212 | std::atomic & _flag = *flag; 213 | std::function * _f; 214 | bool isPop = this->q.pop(_f); 215 | while (true) { 216 | while (isPop) { // if there is anything in the queue 217 | std::unique_ptr> func(_f); // at return, delete the function even if an exception occurred 218 | (*_f)(i); 219 | if (_flag) 220 | return; // the thread is wanted to stop, return even if the queue is not empty yet 221 | else 222 | isPop = this->q.pop(_f); 223 | } 224 | // the queue is empty here, wait for the next command 225 | std::unique_lock lock(this->mutex); 226 | ++this->nWaiting; 227 | this->cv.wait(lock, [this, &_f, &isPop, &_flag](){ isPop = this->q.pop(_f); return isPop || this->isDone || _flag; }); 228 | --this->nWaiting; 229 | if (!isPop) 230 | return; // if the queue is empty and this->isDone == true or *flag then return 231 | } 232 | }; 233 | this->threads[i].reset(new std::thread(f)); // compiler may not support std::make_unique() 234 | } 235 | 236 | void init() { this->nWaiting = 0; this->isStop = false; this->isDone = false; } 237 | 238 | std::vector> threads; 239 | std::vector>> flags; 240 | detail::Queue *> q; 241 | std::atomic isDone; 242 | std::atomic isStop; 243 | std::atomic nWaiting; // how many threads are waiting 244 | 245 | std::mutex mutex; 246 | std::condition_variable cv; 247 | }; 248 | 249 | } 250 | 251 | #endif // __ctpl_stl_thread_pool_H__ 252 | -------------------------------------------------------------------------------- /test/mVCs/SRS019128_WUGC_scaffold_25110.fasta: -------------------------------------------------------------------------------- 1 | >SRS019128_WUGC_scaffold_25110 2 | AACTTATGTGATTTGCTAAAATATTTCTATTATAACCTTCCGGAGTGGCC 3 | CCTCCCATAAATTCTTCTGGATTTTTAAGTTTAAATACAGTATCAGTTAT 4 | AAAATATTTAGCATTATCACATAAATAATATCTATAATCTTTAATTGTAA 5 | GAGGACATATTACATCTATAGCAGCTTCATATACTTGAATCGTAGGTAAT 6 | GTTCCATGGACACTACGCATCATATTTTTATAAATTTCAGGTGAAACAGC 7 | ATAATTCATCATATATGGTAAATTTGCAGCTATACATTTGTCAAATAAAT 8 | CTAATTTATTATATGATTCGATTACTCTTGGATGTAATACTATATTAGAT 9 | ATTATTATCCAGCATTTATGACTTTTCGTATACTCACTTATATCGGATGT 10 | CTCTAATACAGTCCATTCAAATTCACGATTAAATACTTTATAATTCCATT 11 | TTTCCTTAAGAGTACCATTAGCGTTCATATCATCTTTATGGAAATTATCA 12 | CTAATATTAATCATTGGTTTAGTAAGCTCTGTATCAAAGAATTTTACTTT 13 | TCTATCTCTGACATAAATATCAAAACATGCACTATTAAGTATATCATTTG 14 | GAGTACCATTTAAGTCTCCACTAAAATCAGTTTTAAGCTTTTGAATAAAT 15 | GTTGGATCTTTTACTACACTTAGTCCAATAGTTTTACCAGTAACAAGTTC 16 | AAATCCATTCCCAGTTATAGTTTGTTTTACTGGATTATATGGGAATACTG 17 | CAGCAAATGCTTTCTCTCCATTTTCTAAACCTATACTATTAGCAACAAAT 18 | TTAATTTTTATGTTCTTAATACTATTAGGTTTAATAAATCCAGTTGGTAA 19 | TCCATATGTATAAACTCCAATACCAACTTCATCTATTCTAGGAACATCTA 20 | CTTCATTTACTATTTCAACCATTCGTAGTGATGCCTTAACTTCAAGATCT 21 | ATATTAAGATCTTCAGTTATAGTTCTAGTAGCAAAAGTAAATCCATCTGG 22 | GTAACGAAGTGTTACTTTAAATAAGTTTGGAGCAGTTCCAACTTTAAGAT 23 | TATCCGGAAATGGAGCTAAATCAGCTTGAGTAACAGTTTGATTATAAGTT 24 | CTTTCAAGTTTATAAGTATGCCATACAGTATTTATATTTCCATTTTTATA 25 | CGTAGCAAGTCTTATATTGATATTATAAACCTTTACTTTCATATAAATAC 26 | TAGTATTATTTTCATCATTATCTACTCTACGAGTTTGTTCATAACCAACA 27 | GGTATAGTAATAATATAATCATAACTTCCAGATAAATATCTATGAGTTTC 28 | TGTTTTATATATAGTTTGGTCACCATTAGAATCTACTAAGTAGTATTTAA 29 | TAGTTACCTTTTTAATAGGTGTTGGATTAGCACTTGTACTTACCTTAAGT 30 | GGTACATTATATGTGTAATCATTATCCACCGTAAGATCATCTGGAAACTC 31 | TGTAAAATTTGGTACATCAACATCATATCCAGAAGGAAATGATGGATGTG 32 | ATATTATTTCATTTCTAGCAGAAGTTATAGTCATTTTAGCGTTTTCTGGT 33 | TTCTTTATTATAAGTTCAACTGGAGTTGCTAAATTAGGATGTTTACATAT 34 | AAATTTTAATGTATATGCCTCTTTAACAACATTTACTTTATTAACTCCAT 35 | GTTTCTTTGGTGTAAAGGTACTATCTTCAAGAATATAACCAGTTGGTATA 36 | TGATATACTATATTTTGACTTCCTTGAGTCTTAAATGTTTCTCGACTAAG 37 | TTCCACTCCACGGTGATAATATATAAAAGTATGATTATATATTAGAAGTT 38 | CTTCGTCTAATGTAGCCCATTTAAGTATTTCTTCATCACGTTTCCATACT 39 | GGATATTCTCCCCAATATATATTAGATAGACGTTTACCAGCTTTATGTGG 40 | GTTATCGTCTACCCATGAAGGTTTCTTTATTTTCATAAGATTATCTCCTT 41 | ATCTTGCCCATACAACTTGAGACGGACAATATATTTTACCTTTTTCAGCT 42 | TCATCAAAAGTTTTACATGTTAATCCCCAATATACAGCTTCAGTGCTATT 43 | TGCATTTGATATTGTAAATAATTCTTTATTCTTAAGATCAAAATAGCATA 44 | ATACAACTCTCAAATCGTTAATATTTGATTCATATTGAGGGAATGTAGTA 45 | TCATCTGGGTTTGGCATATATGTACATGGAATATATCCCCCAATTTTACA 46 | TTTCTTAGCTTCTGGCATTAATACTTTATCTTCATATGCTTTTTCTGCAT 47 | CGTAGTAATCATCTATATCATCAAATACTTCATTTATTATACTACCAATA 48 | TCTTCCATTTCATATCCAGGATCTCTTTTAATATATAGTTTTTGAATTTT 49 | ATCTAAAAATTTACTATAAACTGTAGGGTCATAAATACTAGGAATATCTA 50 | TAATAGGTTTTTCGAATGTTATTTTAAATTCTCCATTGATTTTTACTAAT 51 | CCATTTGATTTAGGACGATATCTCTCAGTACATTCTTCAATTGATAATCC 52 | ATTATTTTGCTCATCAATTACTGAATAATACAATAATTTAAAGTATTCAG 53 | TATCATTATAATAACCACTAAATGCTTCTTCTGGATCAACCCATATTTGA 54 | TAAATTCCAGCTGTAGTAAATCCCATATCAGTTGGATAAGGAATATCTGC 55 | ACAGTTAATTTGACATAGCATAAGCATTTGATTTCTACCATTATCACACA 56 | TTGGTATTTCAGTTTTAGCAGTCATAAAAGGAACTCCTCCAACTTTACTA 57 | TCAGTAAGTCCTGCACCTTTAGTAAATTTCATATAACTACATTTCTTTTT 58 | CTTATTTTGATTTCTAATAAGATTTGCAGTTATAAATATATCATCTAACA 59 | CATCTTTAGTTAATTGAGGTTTTGGTTCTTTGGGTTTTTCTGGCTCTTTC 60 | TTTTTACTTCCAAATATTCCAAAGAATTCCATTCCTATTTTTTCACTCAT 61 | GTTAATTCACTCCTCTTTCTATTCTAAAGTTTTTACATACTTCTTTTACA 62 | TTATCAAAATTAGTATGAATTAATCCCATTTTAGTATTAATTAATGGAAT 63 | TTTTACAGTATCTTCCATCTCTTTACAAATATAATTCATATATTCTCTTA 64 | ATACTAAAGTCTTTAAATCATTTTCATTTATACTAACTGTTCCCTTGAAT 65 | GCTATTCCATATATTCTAATTATCTTTTCTGGAGTAATACCAGGTTTACT 66 | ACTCTTTTTATATGTTATAAATGGATAATATGTAAATCCATTATATGTTT 67 | TCCATTCATTTCTTCCAGTGTGTTGTTCATATGTGTATTTAAAATCGTGA 68 | CCTTTAACTACTATATTAAGAAAGCTACATTCTTCGGTTGGAGTAAATAC 69 | ATATTTAGCTCTACTTAAATATTCGCTAAAATCTATACTATTTCTATATT 70 | TATCCCATATTACTATATAACTATCACTAGGAAGCATCATTCCAATATCT 71 | TCAAGTTTAATTTCATTAACTTTATCTCTAACGTATGGTATTAAATCTCC 72 | ATTAGCAGTTCCTCTATTAGAATCCCATTCTACAAACATATAGAAATCCA 73 | TAATATCTAAAGTTTCATCAGATTCAATACCTCCATATCTCACCCATTTT 74 | ACTTCTACTTCTTTATTACCATGATATACTGGCATTATATCACCTCCATT 75 | TAATAAATGAAAGGCCGTTAGCTATAAAATGCTAACGGCCTATAAATTTA 76 | AATATAATCTTGTACATCTTTAAATACATCATCTATTATTTCTTTTATAT 77 | TATTAATAAAGTTTCTACTACCAGTAAAATATTCTTTTGGAATAACATCA 78 | TTTATATTATCTGTAAAAGCATATTTAGCTAAGAAATCTAAGAATTCTTG 79 | ATAATTTCTTATAGATTTAATAGCTGTAGTGAATTCTTTATTATTTATAT 80 | CATTAATATAGTTATTATTAAGTAAGTTTCTAACTTTATCTTGTAAAGCA 81 | TTACTTAAATTATTCATGACATTCATATTTAATGATACTGTGTATATATG 82 | TTTAAGCTTATTCTTATAATTATCATCAAGATATCTAGAATAATTTTCTA 83 | ATGCAGTCTTATTAGTATCATTAAAATGTGGAAGATTATCATACACAAAC 84 | TTTAATTCATCTCCAGTTAAATTATTATTTAATATATTATTAATCATATT 85 | AGTAATATTTCTATCCGGACTCGTTACAGTATCTGTAGTATAATGAATCT 86 | TTCTATCATATGTCTGTATATTATAAGTTCCACCATTTATATGTTCAAAG 87 | TTTATTATAGAGTTTACAGCTTTATCAAATGATGAACGTTTATTATTTTG 88 | TAATATATCATCAAATGTTTTACTATCAGTAAATCTCCATACTTCATCTT 89 | TAAATAATAATGGAATTAAGTATTTATTAATAAATAACTTATTAAATCCA 90 | TTAGTATCATTATATGTTATACAGTATTCATCTTTATCTCTGTAATATTT 91 | CTTTAAGAAACTATTCATATTAAGATAATTAGCATCTTTAAGAACAGCTT 92 | CATTATAATCTGTAGGAGATATTCCACTATCAATATCTATACATGGGTCT 93 | AAATATACTGTAGTATTAGCTGGTAAATTACTAGATTTAATCCAAGGACC 94 | TTGTTTATGCTTAAAGTCTTCGATATAATCAGCATTTGTATGATCTAATA 95 | CTTCTATTTGACCTATTATATCAGTATATTTATTAAAATGTGGTTTATTT 96 | CCTATATTACGCATATGATCAATTATAAAGTTTATACCGTTTATATCATT 97 | AGGATCCATAAATCCATAAGTTTGTATTATATAATTCTTATCATATTGCT 98 | TTCTATAATCAATTAAATCACCAAATGATTTAGTTCCAGTTTCCCATGTA 99 | TCTACTGGATCAAATAGATTTACAATAAATTTATCAGCCATAACTCTTTC 100 | ATTAAAGTATCCAACATTATCTGCATCTACTTTAGTAGTGTCAACTGATA 101 | AATTATATCCATACATATAATCATCTAATGCTGGGAAATATATAGAAACT 102 | GATGGTCTAGGTAATAACCCATCAATATCATAGTTCTTCATAAAGTTCAT 103 | ATCTATATATTCGGTAGATAATAACTTTACTCTATCAGTACATTCTTCTC 104 | CCTGCTTATCAAATGCAATGAATCTATTATCTCTAAGTAATCTTGTAGTA 105 | AGTTTTGGAAGTTCTACTGGATTCATTAATGATATATCGGGAGCATTATA 106 | ATAATAAGTATCTTCATCTCCCATCCATATTTTAGTATGTCCTCCAAACT 107 | TTACATTTTCATATTTAGAATACCATGGTCCTAGTTTATATCCATCTTCT 108 | ATTGGAGCGGTATATTGTACTCCATAAGGATATTCAAGTTCTAATGATCT 109 | ATAACCATTAACAAAGTTTACACCCTTTATATTAGATTTCCATGGAAAAT 110 | CACTATATTTATCTATACAACAGTCAGTTCCTTTATAAAGATCTCTAGTA 111 | ATCTTACCACTTTGTCTACTATTCCATATAGTACCGTCTTTACGTTGTAT 112 | CTTATTATACGGATAATCAGTAAATATTATACGAGGTTTATTATATTTAA 113 | ATACATTCTTAAATTTAGCTTCTATCCATTCTACATCATCCCATGGATCT 114 | GTTACTCTTTTATTACGAGCAACATATGGTTTAAGTCTACCCTCATTATC 115 | TAAGTCAGTCCCACGGTCTATATTATGAGTCTCGAAATATTCATCTTCAA 116 | TAGCCTTTATTTCAGATTCCTTCATAGTAAACTTCATAAATTCTCTAGGG 117 | TCCACTATTAGAATATCAGCATCAAATTTCTTTATTATTTTATAGTCTTG 118 | CTCGAATAAACGATTTCCTATAAATAATGCAGGATATTTTTGTAATGGGT 119 | TCCATACATGGAATTGATATTTAAGATGCCAGAACACATCTTCATAGTCA 120 | GATGGAATTAGTCCATACTTACTCTTATTTTCTCTGTAGAAATAATTATA 121 | AGATGCTAGTTCATCTATTTTGATATAATAAGTTCTTATCATATCAAATG 122 | ATGATTGTCTTAATGTATATGGATGAAGTATTTCTTTAAGAAGAAGTAAT 123 | TTATTCTTAATAACTTCTCCTATAGTAACTTCGTTTACTTTATTAATAGT 124 | AAGTATTTCATTTATAACCTTTTCAAGCTCTCCAAGTATAAATAATACTT 125 | CATTATTTTTTATACTATCTTTAGCAATTGGTTTAAAACTATTAATAAAT 126 | TCTATAAGCTCATTAAGTTTTATATTATCTACAATATTTCCAAGATTCTT 127 | ATAAGTAGGGTGAGGTTCTTGACTAGCTTTAAGAAGTGCTTGTCTTCTTT 128 | TATTTATTTCTGCTAATCTTTTATTAACCTCAGTTATATTTCCATCAATA 129 | CCTGGGGTATCTATAACTTGCTCCTTATATTCTCTAGTAACACGTTCTTT 130 | TTTATATGTGGTAATATATCTATAAATCTTTTCTACTTCTTCTACATATT 131 | CTTGAATAGCTTTACTATCAGGTGTCCATGCGTTATATCTATTAAGTTGA 132 | TTTATATATTTAATGTATTCATTCTTAATATATGTAGGAACACTTACATT 133 | TTTATATGGAAGCTTTTTATAATGTTTAAGCCCATACCTATCTTCTACTT 134 | GCATATTTTGTTTTATAGCAGATTTAGGAACTAATGTAAAGTCTAGAACC 135 | ATTTGATTTTCTGTATTTACTTTAAGATGGAAGAAATCCATAAATTCTGT 136 | AAATATATAGTTATTTTCAAGTCCTATTACAATAGCACTCTTAATTTCAT 137 | CATTACTAAAATCATCAAGATCAGCTTGTGATTTAAAGTCTCTAGTACTT 138 | CCATAAACATGTTTAAGCTTTTCATGAGCATTTTTACTAAATACAAGACC 139 | CCATATAGATTTAAACCAGTCTGTAAAGTTATTTCCATTAACACCAATTG 140 | CATCTTTAACCATAGAAGGATCTGCCTTATATTTAGCTAATACTGCAGCA 141 | GACGCATGGCTTAGAGTCAACTTTATACCAGTTTCCCATTCACTAAAGTT 142 | ATCTATAGTAATAACTGTAGAGGATTTAAATTCATCAAAAATTGGATCTG 143 | TAACATTTAGTATACCAGCAGTAGTTATATTATTATAAAACATTTCAAGT 144 | AATGATTTTATATTAAATAATTTAGCAGGTTCTAAGTCTTGTCCATAACG 145 | ATATTTCTTATGCCACGTATAACTAAGTGTACATTTTATATCTCCATTAT 146 | ACCAACTAATATTAATAACAGATGTAAATGGAAAGCTATTAGTAGGTCTA 147 | AGTGGCCTCTCAGCTGGAACTTCTTTAGTTTTATGTACTCTTTCTAATTC 148 | GTATTTTATACGTCTCTTAGTAATTTCATTACCAACTGTAGTATCATTAG 149 | TAAGAGTAGGATTATTATTTGATATTCCATTCTCTATATTAGTATTCCAT 150 | GTTCTATACGCAGTAATAACAGATGGATCTGTAAATTTTGTGGTTTTAGC 151 | CTCTTCTATAGAATTCCATTTATTTAATGTGTTAACTGGAATATCTCCAA 152 | GACCATCTTTTTTAGGAACTGTATACATTTTAATAACTATTTTTGTAGTT 153 | TCATTATGTTTTGCATTATTAAATATCTTTGTAGTATGTTTAAAATAGTC 154 | AATTATTTGACTCATATTATACACTTTATTAACATCTAATACAAGTTTAT 155 | TCCCAATGTTATAGTAATCATAACCAGCAGTTATCTCATTAGCTATTACA 156 | TCTTGCTCATCACCTGTATATGCATATACTACAAGTCCCCATATATCATC 157 | TATAATAGAATCTCCAATATTACTTGTCATATCTTTACATAAATAGAATA 158 | TATTATTAGCATTATCATTTATCTTTTTATCTATAACAGCGTCTTTAGTA 159 | AATGGAATACTAACATCATAATCAATTCCAGTTGTTTCTATTTTGAAATT 160 | AAGATCATCTTTTCTTATAGTAGCACTACCACATTTATCACAGTACTGTT 161 | TTATAATAGATTTTAAATCAAAAAAAGTCTGTTCGTTAGGTTTAGTATAA 162 | TTCTTTATTCCATGAAAATTAGCAGAAACTGCTAATTCCTTACCAGCTAT 163 | ATCTAATACTGGACTTATACTAAATGTAAGATCTACTCCAAGATTAATCT 164 | TTCTTTCTGGTATATATGTTTCTGTAATATCTTCTTTAGTTTCTGATAAC 165 | TTAGTTTCTAGATCAACAGTTTTAGTCTTCCATACAGTTTTATATGTAGG 166 | TGGTTTTGGATATATTTTACTAGCATTTATTTCAGCTATATGATCATCTA 167 | GCAAATCTATTTGAACTTTATTATCATTTATTCTTTGACGCCACGCTTTA 168 | ACTTCTGGATGAGTTTCTGGAAGTTTATTACTATAACCATAATATTTATC 169 | TAGTACTATTGCAGTATTATCTAGCTCTACTATATGTGGGAATGAATTTT 170 | GGATTACTTTCAATACATCAAGATCGTGTTCATATCCATATTTTATTATA 171 | TCATCGGTACACATACAAGTATTACTTAATAAATATTCATATAATCTATC 172 | AGTTCTACAAGCATATTTACGCATATGTTTTGCAGCACGTTGATTTTTAT 173 | TTAAAGCTTCATAATATGTAGTATCAGGTTTAACAAAATCACCTTTACCA 174 | TAAGGTTTTATAAACATAAATACTTTCTTTATATTAGGATTTTGTTTCAC 175 | TTCTATATTATGCTTTCCTACACGTTCTACATATTTACCTACTGGATTAC 176 | TATATAGATTTTCTACATAATACGTTCCATCTTTAAGCAGAACTAATGCA 177 | GTAGTAGTCATAATACTATCAGGATCATATATATTATAACGTCCATTTTC 178 | CATATTAAACCATTTAGGTCTCATCCCCATATCACGCCATCCAAATGATT 179 | TATGACCAGGAATATCTGGAAATGAATCTAATGATATATTACTATAATCT 180 | AATTCTATATATGGATAAGCAAAACATAGTCCTGCTAAGTGAGGGTCATC 181 | TGGATCTACGCTTAGTATTGGATCTTTTGGATCTTCCGATGCTTTATTAT 182 | CTTTATTAATAAAAATCTTAAGAAGTTTATCATCTTTATACTTTTCAATC 183 | CACGAAGGATGAATCTTATCAGAAGCCCATCCGTACTCATTTATATACAT 184 | AGAACTTACAAAGTTATGATTATTCTCTACAATACCATCAAAGAAACCTT 185 | CCATTTCAGCTTCTTTAAAGAAATAATATAGTTTTCCATTATGATTGTAT 186 | TTAATTGTATTTTTATTAATATCGTATAGTTCAAATAACTTATTATTAAT 187 | AATTACTATATTACGTCTATCCATATCATATTCATTACGTTCATATGTAA 188 | TTGGGATAGGATTCATACTAAATACATCAGGTAGTATTACATATTTATCA 189 | CAATATTCTAGTATTTCATCATATAAATCTAATTTCTTAAGATCATCTCT 190 | AATATCCCAATGCAGATCATTTTCTATATTAGCTACATCAAATATAGTCC 191 | CAACCCATTCTGCGTTTACTGTTGTAAGCATAGGTTTAGGAATAGAATTT 192 | TCATATGCATAACGAAATACATTATCAAAGATAATATCACGATATATACG 193 | TAAATTATCTCCTAATTTCATATAAAAACCTCCTTTTTAGGTAATAAAAT 194 | TGTTTAAATTAACAGTTTCATTGTTCGAAATTGAGGATATTAAAAACCAG 195 | ATGAACAAGAAAAGTTACTAAATGGAATAAAAAATTCCTTCGTATACTCT 196 | AAAAATAAAAAATATAAATGGATGTTAAGTCCATTTATATTTTAATATTA 197 | TTATTTATTTAGATCATCTAGAAGATTATCTAATTGTTTTTCTGTTTCTT 198 | CTAGAATTTTTTGATTCTTTTCATGATTTTCTTTAGCAGATTTAGCTTCC 199 | TGAGCTTCTACTACAACTTCTAGATCTTTTTTAGTTTCTTCTAAAACTTC 200 | AACCACTTTTTCTAGATCTTTAGTTGTTTCTTCCATTTTCTTGATTTCTT 201 | CATCAAGTTTTTCATGTCTTTCTTTAATACTATTTAAAGTATCAATTTTA 202 | GTTTCTTCAAGATCTTTCCAAACTTCTTTAGATCTCTCCTTCATTTGTTC 203 | ATTAATATTTTTTAAACTATCAGTAGTTTTTTCTACTACATTATTTACAA 204 | ATTCATCATCGAAAGTTTCATTAATCTTCTTTCCAACTTCCTTTGATTTC 205 | TTCCAAGCCATGTATCCACCTACTACTATTCCTACACCTACACCAACTGC 206 | TATTGCTTTTAATATATCTTTCATTTTATTTCCTCCTAA 207 | 208 | -------------------------------------------------------------------------------- /test/mVCs/SRS045127_LANL_scaffold_39500.fasta: -------------------------------------------------------------------------------- 1 | >SRS045127_LANL_scaffold_39500 2 | AAGTCCATTGTCATTTGAAGAATATGCTGGTTCATCAAGTTAAAACACCA 3 | AAAGGGATTCAGAAGAAGACATTTGCACAAGATGTAGCTTCATTAGATAA 4 | GTGGTACTTGCCTATAAGAGTAAAAGTGCTTGATATAGGCTGTGTGGAAG 5 | ATTTTTCTAATGAGTTAGTAGATGAAGTAGAAATGTTCTCATTTCCTGCA 6 | TCCTTATCAATATTCACTTGTACTTAATAGGAGAAATAAATGGCTAATGA 7 | ACAACCATTGAACCTTGATGCGTTTTTCATGTCTCGTAATGAGATTGCTA 8 | ATCGTCATGGGGGTAAACTTGAGCTTCAAGCACTAGCACGTGTTCGTGAA 9 | CACATGGTAGAGGAAGCTTCAAAAAAGCAAATTCAGGAAACAGTTAAGCC 10 | TATAGTTAAGGAAGAAACTGCTCCTGTAAAACCTAATGTAAACCAAGACA 11 | AAAAGGAGAAATAAATGTCTAACTGTTTCGTAGATATGTCACACCCTATG 12 | TATGGTTACAACGCACAAGACAAAGATTCTAAAATCATTGTGTCTATCAC 13 | AGAGGAAATTCGTCCTTGTGTACGTTGGAAGACAAGCAAACAAGTTCAGA 14 | TTCCATCTGGTACACTTGTGAGCTACGTGCGTAAGGATGTCCCAGAAGAC 15 | CAAATCAACTGTGCACCAATCAAGTGCTTGAACACAGGTACTTTGTATGT 16 | TAATCCTGCTGATAAGAAAGCTTCAGCTAAATTCCAAGTACGTTCGGATG 17 | CAGATGATTTTGCACTAGGTTTCAATATGTTGTACTTGAATCTTCCTAAA 18 | GAGGGTAGATATGAGTTTAAAGCTATTGTGTCTGATTTCAAAGACTTGGC 19 | TCAAACAAACTCTTATGTGTACACTTACACATTCAGTACATCAGCACCTG 20 | GATTTGTTCTTCGTACTGTAGACTTTGCTGATACTAAGGTAATGACACAA 21 | ACTGGTACTGGTTGGAAACCTTCTGACCATGGTATTGTGGTTACTTATGA 22 | AGTAACTTATAAGGGTGAAGATGCACTCACAGGTCACATTGGATTCTCAA 23 | GTCCATCTATTGTGAATGACCGTTCAGAGCTTCGTAAGTTCTCAAATGTG 24 | TTGCTTTCATGTTTGACTTCATTCACTCACAATGTATCTGTGCCAGCTTC 25 | AGATGCTCGTTGCTTTGGTAGACAGTACGATAAATCTCAAGTAGAGATTA 26 | CAAAAGAAATTACAGCTACAACTACATCATGTAATGACTATTGGTTGAAC 27 | CCACTTCAATCTATGTCTAAGAAAATGACTAGTGGTGTTCCTGTGACAGA 28 | TAGCTTCACTGTTGAAGAAATCACAGTAGATGGTAAGAAATATGGTTCAT 29 | TGATAATTCCTGACCTTTACTATGAGGACTGTAACTCAATCATTGTATCA 30 | TCTGACCGTTGTGCTTGTACTTATTTGTCAAGTATGCCATTGTCACCAGG 31 | TGTAGAGCTTGAAGATGATGAGTTCATTGCTTTGACTCAACAATATCATG 32 | GATACTCTAGAGGTACAGTTCTAGTAAACCCAATGTACATTGGTGAAAAA 33 | CTGATTGTAACCTACAATGGTGAGCGTGATGTTGAGTTGATTGTAGCAAA 34 | TGATAAACGTTTGCGTAACACTCATTTCCGTGTGATTCAAGAAGTTGAAA 35 | ATACACGTGGAATTAAAGAATACTATGTATTCAATAATGTTCTTGTAACA 36 | GAGAACTCACGTGAATTTGGTTCAGATGGTGAAGTAACATTGTCTCTATC 37 | ATTCACTGTGTCACGCGATGAAAATGATAACTTCTATGAAATCCGTAGAA 38 | ATGTTGAGGATGTAGCTTAACTGTAGGAGAAAAGTATGGCAATTAGAACC 39 | ATTAAGGTTGATATTACAGGTTTAAAGGAAATTGAGAAAGCCCAAAAAGC 40 | TGTGTCAACTCTTAGGGATTCTGTGTTAGACTTTGAGAAGAGACTTAAAA 41 | AGATGGGCGGGAAGAATACTTCCACGCTCTCTTTTAATGTCAACTTGAAA 42 | TTGAACACAGATAAAGCACTAAGTGATTATCTTGCATTAAAAAGACAAAT 43 | TGAAAATATTCCTATCAAAGTAGGAACTAAAAAGGGGTCTACTAGTGATT 44 | CTAATGTGCCTACTGTGGATAAAACAAAAGCATCTAGACCTACAGGTAAG 45 | TCAACTGATTATGTTAAGGTTCGTGACCAAGATTATCAATCATGGAGAAA 46 | CCTTCATAAAGTTATTCAAGATACCTCAAATGCTACAATAAACTTGACTA 47 | ACAGAATGGTGAGTCTTGGTGCTATAAACCCAGCAAAAGGGTTACTCTCT 48 | GTGTTTAACAAGGTCAACTCTACTGTGTTAGGTATTCAGAATAACCTTAT 49 | GGGCTTTGTGGGTAATAAACTCACTGGTGCTATTGGTAATGCTGTTCAAG 50 | GAACTCTTAGTGCTGTTACTGGAGGAATTGGTCAGCTTAAGGATGAAGCC 51 | AATAACCTTGGTGATGCTATGCAGATTTATAGAATCAATATGCACGCTCT 52 | AGGTTTTGATGAGAAAGAAACCAATAAGTCAATCAAGAGACTTGGTGACT 53 | ATGGTAAGGATTCTGTGTTTGATGCAACTGACTTGCTAGAACAAGCATCT 54 | ACATATACTGCTTATAACAGACGAGATAGTGAAGAGATAGTTAAAGCCTA 55 | TGTAGGTCTACTTGCACAGACTAAAAATCCTGTTCAGGGTCTTAAAACTG 56 | TCGGTATTCAAACTTCACAAATGCTTGCTTCAGGCTACCTAAACCAACAA 57 | GACTTTAGGTTTATTCGTGAGAGATTCTCTGCATTAGGGGCTTCTGCTGT 58 | AAATAATGCCCTAACAGAATTAGCTAAGTCTAAGGGTTATAAAAACATTA 59 | TAGATGCTACAAGACATAAAGCTATTACTGCTGATGAGTTTTTGGACTTA 60 | GTTAAACAAGTAGGTAGTCAAGAAGACTTCCAAAAATTAGTTACATCTAT 61 | TGTTACACCTAGACAAGCATTGGCTAACTTTAAAGAAACTCTTTCTAACC 62 | TCCTTGTATTTGATGAGATTGATGATGAAGGTAATGCTAAACCTGGTGCA 63 | CTTAACCAAGTGTATGTGGCTACTAGAGACTTCATCAAAGGTATTACAGA 64 | AATTGTAGGTACTAATAAGTTTAAAGAGTATGTCACTAAATTAGGTAATG 65 | CTATTGGCGAAACAATTAAGCAAGTTAACCAGTTTGGTGCATCTTGGAAA 66 | TTAGCTTTTGGTAAACAATCACTAGAAGCTATTGATGAGTTCTCTAAAGA 67 | GTTCATGAAAGGTGTGAAAGGTTTAGATGTAGCTCCTTTGTTCTTTAACA 68 | TAACCAAAGAAATGCTCAATACAGTAAAAAATTCAGGCAAGTCTTTTGGT 69 | GATTTTGCTAAGGATTTAGTCACTAGTATTTCTAGTATTACAGTAAGTTT 70 | AGTAAATCTTTCTACACAGTTTGTTCAAGGTGGTGGACTAAGTGTTTTCT 71 | CAAATTACCTAGATGTATTTGATAGTTTAGGTAAATTGGCTGTCAAATCT 72 | GGTTCTGTGAAAGACTTTATTGACATCTATAAAGAATTATCATCGACACT 73 | TAATCAAATTGTCCTTTCCATTAAGCCAACTGATGTTAAGAGTGTGACTG 74 | ACTCAATTAGGTCACTTGTTGTGCAGGTTCTTGGATTTATTGAAAATATT 75 | ACAGGTAAGACAACACTTATCTCAGATGCTTCAGCTATCTTCACAAGTAT 76 | AATAAACACTTTATCAAACATTGTTAATAAACTAAGTAAGTTTAATCCTC 77 | AATCAGTCAACAAGGTTTTAGGATATCTTAAGAATACAATCAATGGTATT 78 | CTTAAACATATTGAACCTATTATTGTTGAATTGGGTCAAGGAGCTATCAC 79 | AGCACTTTCATCTTCTAGTGGGGAAAACTTCTTTAGAGCACTTGGTAATT 80 | TTATTAAGTCAGTTACATCAGCTATTAAAGCTTTCCTTACTTCTATTGGT 81 | GGTTCTGTTGAAGGTGGATTTAAGAAGATTTTAGATTTCTTAACTACACT 82 | TGTAAACTTTGCTTCTAAGGTTGCTGATGTATTAGGTGTAGCTGGTAAGT 83 | ATGTTGTAATAGGCTTTATAGGAACTAAGTTTGCTTCATGGGCTACAAAT 84 | ATTATCTCATCATTATTAACCGTGGCTACTGCTATGTCCTCTGTGACCAA 85 | TGGGAAAATTAACCCACTAGGTCTAGGTAGCAACTTTAGTAATTCTGCTT 86 | TAGCAAGACAAGGGCTAACTTCATCTAGTGTAAACACTGCATATAGTGGT 87 | CTTTCTAGAGCATCAAAAAATAATCCCTATGGTATGTCAAGAGTTGCTAG 88 | AAACAAAGCAGTAAGAAACGCTAGAATTGGTGCTGGTGCTCTATTTGGAG 89 | CAGACCTAGCATTAGGAGCTGTAAACAATTCTGTACAAAATTCAACTACT 90 | GCTTCACAGGGGTTGAAAGACTTCACAGATGTATTGTCTAGCACTGCTTC 91 | ATGGGCTTCTTCTGGTGCTTTAATTGGTAGTGCTTTTAGTCCTGTAGGTA 92 | CTGCTATAGGTGGAGGTATTGGTGCACTTATAGGTCTAGGTTCTAGCCTT 93 | TATGGTATTTTCAATAGGGAAAATGAGAATAAGAAACTAGAAGAGGAAGC 94 | TAAAAAAGAAGCAGAAAAGCAATCTAAAGAAGAATGGTTACAGCAACAAG 95 | CACACCTTAAAGAAATTTCTGAGCAAAATAGCCAAATCAGAGATACTTAC 96 | TTCAAGTCCATCACAAAAGATACATCATTGGTTGATAGTGTTGTTGGTGC 97 | TAACTCCACCATTGAAGCAATTAAGAATAACTCTAACACTACTGTGGAAG 98 | GAGCATTGTCTCAATTAGGTATTGAGGTAGCTAAAGTTCCACAGAATGTT 99 | GATAGTCTTTTTGTGAAGATTGGAGACCAAGTTAAGAGTTGGAAAGACCT 100 | CAAAGATGCTACAGGTTATACTGATGAACAATTACTTCAAGCCTTACAAC 101 | TAGCTAAGTCTGCTGTGGGTGAAAAAGTTGTAGAATTTGTCAATGAAACT 102 | GGTCAAGAGGTTGTAGCTCAAGTACAGACACTCACTGATGGAGAGCAACA 103 | TAGACAATCTTCTAATGTGGATACCTTCACAGGTAAACTTGGTGAATTAG 104 | GTCTTAAACTTCAAGAAGGAAAAGAGTTCATCTTCAAAGATATTTCTTCA 105 | ACTGTGGAGCAATTAGAAGCAGTTAAGAAAAATAGTAGCCTGACTGGTGA 106 | TGCTAAGAGTAAAGCTCTTGATGAAGTCCTTACTAAGTTAGGGTTTGATA 107 | CTACAGAATTTGTAGGTAAAACCATTGCTGAGAAGATGGAGATTGTTAAC 108 | CAGATTATCAAAGATGGTAAAATTCTTGGTGGTACTTCTGACCATCAGTT 109 | TTCAGGTATTAAAGACCAAATCACTGCTAAGATAAGTGACTATAAGGATT 110 | CACTTGGAGGGGTTGTTGAGCGTATAGGTAATACTGAGCTTGATGGTTTC 111 | TTAGCAATATTGAATGATGCTGAAAAACTCAATAGTGAAGGTGGAGATAA 112 | AGCCAATGCTGGTAAGATTATTGAGTTTCAGAATAAAGTTTTAGATTATC 113 | TTAACAAAGGTTACTTGAAAGTAGATGAAGCTTCTAAACTGTTTGAAAAA 114 | GCAGGTATTAGTGATGTTTCTATAAAAGACCTTGGAAATGGTAAGTATGA 115 | ATTTGAAAAAACTGTCACAGAGTTCGTTGCAAAAGGTACTAAGTACATAA 116 | ATGATGGCTCTACAGGGTTGAAGAAGGTTACTTACACAGAAGAGGAGAAA 117 | CATAATCTCTTTGAAAGTGCTAATGCTTTATCTTACATGGTTAATCAGTT 118 | CCTAAGAAATGCTGTAGATGTTATTGAGGGAGCAAAAGCAGAGCTTAGAA 119 | AAGCTAATAAATTTGAAGAGCTTAGTGAAGCTACACATGAGCAAAACCTG 120 | ATGGAAGAGAAAATCAATAGCTCATTCAGATATGCAGGTGGACTCATTCC 121 | TGAATATCACTCTGAGGGTCTTCCTGTAGGAATTAACTGGAGAAGAAGAG 122 | GTACTGACACTGTGCCTGCAATGCTTACTCCTGGTGAGTATGTTCTTCGT 123 | AAAAAGGCTGTAGATAGTCTTGGTACTAACTTGCTCAATAACCTTAACAA 124 | GTATGGGGTAGGTGCTTTGCAAAATATTGCAAAATCTACTATAATAAATA 125 | ATGTATATAACACAAATAATGCCCAAATCAACCAAAATATTGATAACAAG 126 | TCTCAATATCTAAATGGTATGTTTGGTGTGGATAAATTGATGAGGTATGT 127 | TTAATGTTTGCGTGTGATGAAAACTTATCAAAGCCCAAACGATATATCCA 128 | ATTCAATGACCTAGTGTTCCTTGGTAGAAAATCTATTGATGAACAGTCAG 129 | AGAGTATTAGTTTGCGTGAGAGTAAAACCTCACGCACTTTTACCAATGGG 130 | TCTTATGTTGGTAATATTGGTAGTAAGTCACTTATTGATAGCAACTCAAT 131 | ATCACTTAAAATTGCACTGAAGACTAGTAATTGGTCTGAAGAGCACGTAC 132 | AAGCCCATTATGACTTCATCATGGAGCAGTTAGTCACTCCAGGCAAGTTA 133 | TGGGCTATAAATACTGGGCTACAACTTGTGTGGTGTAATGCTTATGTGAC 134 | AAGTATTCAACCTAATAAAGATTGGGTTATCACTGATGATGATTACCTTG 135 | TGTTTAGAGTTGAATTTGACAATCCTGATGGTGTGTGGTACAAGGCTGAT 136 | GAAGCTAAGACCTACTTAGAATCATTTGACAACTGTGACTTCTTAGATAT 137 | GAAGGCTGGTTGTGTGGGTAAATCAAGACATTGTTGTAATGGTCTACCTA 138 | ATTGCAATAACATCTGTGAGTGTTGTGAGGATGATTGTGGTGATATGGAA 139 | GGTATGATTGACTTGTGCTCTGCTCAGTCTAACATTAAGTTCATGAATGA 140 | TTTCTTTGAAGAGTGTAACTCTAAGTGGAGAGTTGTATATAACTGTTCCA 141 | AGGGTAAATGCTCTCAATCACTACAAGACTTCTATAAAAACACAGTGTGT 142 | GATAACTGCGTGCATGAGGTTATGAATGGTCAATTCCTTTCTGATACAGT 143 | TCTTGATAGTCACAGATGGAGCTTTGCTTTAGAAGGACATTTCAAAGACC 144 | CAGTAGTGAGAATCAATGACATTGACTTCAAAATTAGTGGTGAGTATAAT 145 | GGTGTACTTACAGCTAACTATAAAGGTGAAATTAGGTTTGCTAAGTCTTG 146 | GGATTGTATTGAGTATAGCTACACTGAAGTATCACTTTCTGTGCTTACAA 147 | TATGTGCTGAAATGCCCTATATCAAGAAAGGACTAAACACTGTGTCAGTA 148 | AGTGGGGTTGTGAGTGAGAATGCTTGTATTTTTATAGACTATGAGGGTGT 149 | TACATTATGATTGGTTATATTGAGAATACAGTAAGCTCTGGACTAGGTTC 150 | AGCAATCATAGCAAAAGAAGACTTCTTAGGGGATATTTCTGTGGAGTATT 151 | CCCTTATGGAAGTTCCTGCAATTAAGTTGACCTTGCCTATCAGATATACA 152 | AAAATGCTCAATGGTAATAGTCATGTTGTTGTGAAGACTGATGATTGGAC 153 | TTACAGAGGGTATGTAGGTAACAAGGTCAATAACTTCCAAGATATGACTG 154 | TAAGTGTGGAAACTTCTCATATCATTGGTAGATTAGGCAAAAGAACCTTA 155 | CCTACAAACGTTACAGTAAAAGCTAGGTCTGTGGTATCTGCTGTGGAACA 156 | AGCTATGGGATATTGGAAGGGTGAACAGCACAAGGATGATTTACTGAATG 157 | AGTTTAAGGTTGAATACCTTGATGATTATGCTAGTAAGAACTTGATTGAG 158 | TATGAGTTTTCTAATGAGTCATTCCTTGAATTTTTAACAAAGGTGTGTGA 159 | AAAGACTACAGCACTATATTGGAGAGTAAGTAGACAAGACCCTTATCTAA 160 | TTCAGTTTGGCATCTTTGGTCATAAGAGAGATGTTCTAATCAATGAGCAC 161 | ACAAAGCTGATTGCCTTAGATGAAGTTGAGGAAAACTATGAGGATACTGT 162 | AAATATAGCTGTGGCTATGTCAGATAAGTCTGATAGTGGAGCTAGTTCCC 163 | TTACCCTTAGAGACATTTTTCATAACCCTAAATTCATGCTTAAGGGTTTC 164 | CCTGTGATTAAGACTGGTAACAAGGTAAATTCACAACGTTACTATGACTA 165 | TCCACAACTACCTGTGTTTGCTCCTGAAATCATTGGTGATGAGTTTGCAG 166 | TTATGGATGAAGAAGGTATTGCCCTTGAAGCTGGTGAGCTTTATTGGGGT 167 | ACTGTGACAGATAATGACACACAATCCATTGCTGATGATAATAGAGAGAT 168 | TACAGATTCAGATAGATTAAGAGCCACTGAACAGCTCTATAGAACGGCTA 169 | TAAGACGCTTGATTAACTCTCGTAGGAAAGTTACCTATGACATCACTATA 170 | GAGCCATTAGAGCCTAAATCAGTGGGTGTAGGGGATAGGGTGATGTTTAC 171 | CCTTAATGCTGGTGTGTGGGAATTAACTGCTTGTTCTAAGTATTATGAGA 172 | AGGTGTTAAAGCAAAGTGATTGGTTCTTTGTGACACATATCACTGATGAG 173 | TATGGTGTTGGTAATTCACATATACAGAAGTTAAAATTATCTAAGTTCTT 174 | ATATAGTGATAGAGATATTACTGTGAACCAATAGGAGGGAATATGTCAAA 175 | TAGCTATGTGAAACTAGTAAACTCTGTAGCAAGAACAAAAGCTAGGGTAA 176 | TTCAACAATCAAAACAACGTAGAGGTGGAGTAACAGACCTTTATGCCCTA 177 | GATTATGTTTCAAGCTTTAGCACATCAAAGGCTTGTGCTCCCTATGGAGA 178 | TGAGAACGTAGAAGAATCAGAGTCAAAGGATGTACAGGTAAGAATAAAAA 179 | AATTAGTTAAAGCTATTAAGAAAGAAATACCTGAAGCTAAAGCTAATGGT 180 | GTTTCAGCTATTGTTGGATTCTTTGGTATTGAAAGTAATGTCAGAGCAAA 181 | ACGTTATGAAACTGATGATTTGACTGGTAACAAATATGGTACTGTTGCAG 182 | AAGAACCTACTGCTGAAAACCTTGTAGGTTCATGGAGTGCATTTGCTAGT 183 | ATGTACAAGAACTTACAGCTTGCTGAAGAGGTATATAGAGTAGGAGATAA 184 | ACACTGGATTGGTATTGGTTTAGGGCAATGGACTGGTGTTAGATGTAAAG 185 | CTCTATTTGACTTTGCTAAGAAAGACAAGCGAAGAAGTATTTGGAGCTTT 186 | GGTACACAATTTAAGTTTATGCTTAGTGAGGAAGGTAGGAGTAATGTTGT 187 | AAGGGAAGTTGCAAGTAGTGATAGTGACATTGCTGAATTATCTCTTAGAT 188 | TCCTTAAGGACTGGGGAGGACAAGAAGGTAATAAGCCACAAGAGCGTATT 189 | GACTTTGCTAATAAACATAGAGACTTCATTCAATCTGTGCTAGAAGACAA 190 | TGACACAGACAAGAAAGAAGATGATAAGCCTAACCCAGAGGATGTAGTTC 191 | CAATAAATAAAGAGTCTAGGTCTGCATCATTCCGTGTGTTAGTTCCTTCT 192 | GACCTTGATAGATTCCAAAGATGGTTCTTGAAGTTCATTGTGGAACAGAA 193 | TAAGAGTGAGTGTGACGGAGGTAAAGTAAACCCTATTGCTGATGTACATT 194 | TAACTGTGTCAGCTAAGAATGAATCTACTGGAGATACTGCTGAAATAGAC 195 | CTTACTGAAATATTTAGAAGACAGTGGGGGTGTAATTGGATTGGTGATGA 196 | TGCTAGTGGAGAAGGTATCTTTCCTAACAACAAACCACTAGAAGGTTATG 197 | ACCTAATGTATTCAGCATGGTACTTAAATGATGTTCAACGTAATGCTTTG 198 | TTCAGTGCTGGTGAAAAGATATTCACTGTGTATGCACTAGGGGAAGCAAA 199 | AATTACACTTAGAAACTTCTTAAAATATAGTCACATTAACTAGGAGATAA 200 | CATGAGCCTTTATGGAACATATAAGAACACCTTGCACAGAAAGAATCACA 201 | GGGAAGCAAAACAGTTCAAGTTAGAAGCTCACTTAGAGAATCATCCAACT 202 | GATTACCAATCTGTGATAGCAAATGAAAAGCTAAAAAGTGAAGTCTTTTG 203 | GCTTGAATATAAACTCAAACAAGTAATAAAGGAGATGGAAGCTGATGGTA 204 | CGTGGTAAAGTTAGAAAAGACCTTGTTCATAGAATGAGAAACAGAATACT 205 | TGCTGAAGACATTGTTGAACAATTCATCTTGCAACTAATCAAGAGTAATG 206 | ACAAAGGTGGAGCTGAAGAGTTCATTCACACAGAGAATTTTACCCTACAA 207 | CTAGAGGATAAGATTGTTGTGTGTTTTAGAAAAGATAACAAGATTGAGCT 208 | TGATGGAGAAGAGTTTATGTATGACTTCACACATCTTACTCATTTGTGTT 209 | TGAGTTTACTAGAAGACAAATTTTAGGTATAATTATTATGACAAATGCTT 210 | ATAAGATAGCCCAACAATATG 211 | 212 | -------------------------------------------------------------------------------- /test/mVCs/SRS016086_WUGC_scaffold_24100.fasta: -------------------------------------------------------------------------------- 1 | >SRS016086_WUGC_scaffold_24100 2 | TTTTCAGCTAAGAAGATAGCATTATTGTATTTATACAAATCAGTTAATGC 3 | CATTTCTTGTAATTGATGTAACAAAGCTTGTTCAAGCTTAGCTACTTCAC 4 | GTACAGTATCAGCATTGATTTCACCAATCTTCATGGAATCTAATTTACCA 5 | AAGATATAGTCATATTCCTTGATAGCATTTTCTTTACCAGTCTTAAGATC 6 | AGTAAGCTTTTCTTTCTTATTAGTATCTAGTGTTTTCAATAATTCACTAG 7 | CATCTTCTAAAGTAACTTCACGAGTTTCAGTAACAGGGTTTTCGACTTTC 8 | TCGATCAATTGCATATAAGTCAAATGATCTTCTTTACCCATTACAGAACC 9 | ACGAATACCAGACTCTAATACATTGAAGTTTTCATTGACAGTTTTAATTA 10 | CACCGTCAAGATCTTCTTTAGAGTTATGGTAGAAGTTTTCATAGATTTTG 11 | CTAATAGATTTGAATGCATCTTTAACTGCTGGAGTATACTTAGCTTCTTC 12 | GAAGAATAACTTCTTAAGTTTAAGTCCTTTACAGTCAGCTTGGTTAGCAA 13 | ATTCTTTTAAGAAACGTTTATCTTTAGAACTTACATAAGCCAATGTAGAT 14 | ACAGCATCATTATAGGATTTACCATATGCTTCTACAATAGACTTTAAGTT 15 | CTTACGGTATACGTTATATAAGTTTTCGCTTACGGCTTTGTATTTGATTA 16 | CATTACCATCAGCGTTTAACACACCACGGTAGAATTCTTGTAACCCTTTA 17 | GCTTCGTGGTTACGGATATCTTCTACTAGGGAATACATAAATTGCTTACG 18 | GGAAATATCGCATTTACCAGTAACCAACTTATTATCAGTAGCATCCATAA 19 | TATAACTAAAGGAGAATTGTTTATTTTCCATAAGTTACCTCATAAAAAAA 20 | TATTTATAAGGTATGAGGATGTACCCCATACCTTATAAATTATTTTACAT 21 | AATAGTCAGTTTACGAGTAAACTAAAATTATTTAGCAGCTTTGATGTAAG 22 | CAGTACGTGCAAGACGCAATACTAATTGAGCTGCAGCGATTTGACCTTTG 23 | ATAGTAGTGTTTGTTACTTTAGTCAATTCAACAACACCTTCACGGTAAGT 24 | AGTATATTTTTTGCTTTCTTTTTCGTTAGGGTTTTTGAACAAAGACTCAG 25 | TTAATTTCAAAGCAGCGTCAGCGATTTTAGCTGTAGCATTGATAGCTTTC 26 | ATAGCAGCATCGCCATTTGTTAATACACGAACGATATCAGTTTCTTCTTT 27 | ACCAAATGTAGAATCGATTTCTTCACCGATAAGACCTTTGATTACAGTAG 28 | AAGTGTTGAATTCGCCATCGTTAGCTTTTTTAACTTTTACAGCTGCAGCA 29 | ACTGCTTTCTTAACTTCTTTAGCATCAGTGTTATCTACTTTACCAGTAGA 30 | AGATTGTGCTACCATTTTTTGGATATCAGCTGGAGTAATAGAGCATTCAA 31 | TTGCTTCGAAGCAAGATTTGCTATCTTTTACCCATTTGATTTCAGTTTCA 32 | GCTGCATTTTTGTTTTCTTTAACTTTGTCTTTGTATTTTTCTAAGACTTT 33 | TTTGTTATCAGAAGCAAAACGGCCTAAGATTTTAGCTACCATATTGGATA 34 | CGAAAGCTTTAATTTTAGCGTACCATTTTTTAACGAATTCGATAACTTTT 35 | TTACCAACTTTTTTAAGTGTGTCAAGAACGCCTTCTTGGATTGCTTCTAC 36 | GTCAGCGCCTTCGTGAACCATAGCCATTTCACGGAAGTCAGCAACTACTA 37 | AATCAGTGAATGTTTCTTTATCGAATTCAGCACATTCCATCATGATTGCG 38 | TCCATGCCATATTCGTTAGCATACATTTCTTTATTTTCTAATACAATACC 39 | GTCATCTAAAACGGATTCAGTGAAGAATGCCATATTAATTAGCCTCCATT 40 | TAATTAAAAAGTATTAACGTTAATATTTTTCCTATAAAAGGAAGATGCTC 41 | TATACATATTTGTTATTAGATTATATCTAAATCAAGCAATTCTGCATCTT 42 | CTAATTCATAAGATTCGTTTTTACCGTCTTTAAGTTTAAGCAAGAATACA 43 | CAAATGTCATGTACAACTTTCATATTCTCACGAATAGCACGAAGTTGTTC 44 | CACATGGACAGAAGCAATAAAACGAGAAAGTTGAAGTCTGAAGACGGCTA 45 | CAGATGCTAACCATGCACCAGTAAACTTAGCTTCGATGATTTGCTCAATT 46 | TGTTTAATCAACTCAGCCAAACCAGTCATTTGTAAACGTTGGATCTTTAA 47 | CCAGTCAAAGTCTAAGAACTTAATCATTTCATCAATATGTGTAGAGATGA 48 | ATGCTTGACCGATTTCTTGTTTACCAAAAGAGTTATTCTTAATAGCTCTA 49 | TCGAAAAGATCACCACTTTGCAATTGGCGTCTAGTTGTCATAGGGCTTAA 50 | AGAGTCAAAGAAGTGTTGGATTTGACCATAGATGTTTTTGAGTGGGGATG 51 | CAATAAACGTAGTGAAGATATTGATATGGTCAAATAATGGTTTACCATAT 52 | AAAGTGTGTACAGTAAAGCGTTTAGAGTATTTCTTTTCAGCATTAGCTCT 53 | AATGATACGTACATTGTTTTCGTCTTCTACTACACGTTGAAGATCACCTA 54 | CAGCAGTACTTTCATACCACTTTTCAGCATTCTTGATCAATGTTTTAACT 55 | AAGCCATTTTCAAAGTAGTCATTCTTAGATGCTTCGTTTACCCACCAGCA 56 | TTCTACTGCTACTTCGGAAGTACCTTCAGCGATAAGCTCTTGTTCTTTAT 57 | CGAATAACTCTTGGATTTGAGCATCATAAGATTCAATAATAGAATCTAAT 58 | GCTTTGATATTATCCTCGGCTTTCTCAATCAAGGCACCAATGTCGTCGAC 59 | TAATAATAGTTCGTCCATTTTTAATTCCTTTACTAAACAATAACGAATTC 60 | AATATCTAATTGATTTTCTTCAGTATTAGCAGTATTGACATTCAAGAACT 61 | CAGGGATACGTCCCACAATCATTTCATCTCTACGATAAATATGCTGTATA 62 | CCAGGACCATAACCATTGAATTCTAGGAACTCAAAGTACACTAATACATC 63 | TTTATACTTATCAGTAATGTAAGTGATAAGATTTGGTATATGAAGATCAT 64 | TGATTTGAGTAGTGTCTTCGATATATAATCGAATATCATTCTTAATCAAT 65 | GTAATTATCTCTTTAGTGCTAGTATTGATAAACTTAACACGGAATCGTAA 66 | ACTTAAGTTAGTTCTATTCAATGGTTTACCATCCTCTACATAGAATAGTT 67 | TAGATGGGCCATATGTATTGAATAACTTAAAGTCGATACCAAATGAGTCT 68 | TCTAGTACATTCAAACACTGATTGATATGTACACGTTTCTTTTCTAAATC 69 | TAAGATAAACTTTTGTAATTTCATCTCAGTATTAATGAAAGACCAACCAA 70 | CCATAGGAACTTTATCTATAGTATAGCTTAGTGTACCATTATCCAACTTA 71 | GTGACTTTAACTTTAGATTCGATAATGTCAGAGTAGTTATACATAAAGTC 72 | TACACCACCACGAGTGTTGTAGATATTAGTAAGACTATATCCACCAAGAA 73 | TACCGCTAGTGAAGATTTGTTCAGACTTATATGTACCAGCATTCTCTCCA 74 | TCTTTATTCTTAATGAATGTAAAGATCTTGAACTGTGTATTGTTTGGCAT 75 | ATAACCATACAAGTCATTATCAGAACCAGCTTCTTTAAGATTCAAGATCT 76 | TAAGTTGGTTTAGTGTATCAATAGAGTTATCTGTTTCCATATCAAACTCG 77 | TATAAGAAAGAGAACTCTGTTTCATTGTACTTCTTGAACTTACCTTGAGT 78 | CCAACGTGTAGGTTTACCATCTTTATAGAATACACCTAAGACTTTAAGAT 79 | CTACACCAGTAATCTCTTCAGGATCTAGTTCATTATCTCTGTGGATTACA 80 | CCGATATTTCTATCAATGTTTTGAACTAGCTTAACTGTACACTTATAAGT 81 | ATTCTTATCAGTAAAGTATTCTCTCTTCCAGTTAAGATTATTACAAATGA 82 | ATTGGTATTTGGAAGCCTTATTGATATACTCAAACTCAAGAGCTTTCTTG 83 | GTATCCATATAGTTGATATAATATGAAGCATACAAAGGACTCTTATTGAT 84 | TACAATCATAAATGGATTGAAGTATAAGAACTTAATCTTATTTATAGACT 85 | CTAATTCATCTTTTGAGCTATTATATATAACCTTACCGTTACCACCAGCT 86 | TCATACTGAATAGTATTACCAGTATTGAAGATATAGTTTTCACTAGATAC 87 | ATTATCAAAGTCACGTCTAATCAATTCTATAGGAACTGTATTAGTTGGAA 88 | TCATTTGTGTATCAGTGCTTGATAAAAGATAAGCATAGTATAGACGGTAT 89 | AATGGAGATTCCATTTTCTTGAAGAAGTATAGCTTATTCTTAGGCAAGCC 90 | ATAGCTTAAAGAGTTAAAGAAGTTATTAACGTCTTTAGAGTTGGTTACAC 91 | TACCACGAGCTAATGCTTCTTTAGGAATCATTTGTTTTAACTCATCAATA 92 | GTTTTCTTATCCAAACCATCTTCAGATGCAGGTAAACCTAATGGATCACC 93 | TAATGGTGTAATAACCATGAATAGACGGTCATAGTTAAATCTATCACTGA 94 | TAGGATATAACTGGATAGGATCTATATACTTAAAGTTACCTTCGGAACCC 95 | TTGGTTGTATATAGATTGACAGAAATCTCAGAGTTCATACCAGGAATATT 96 | AGACGTATCACTAAATACAAGTCTAATAGTCTTCTCATCTATATATGTAT 97 | AACTACAGTAGTTGACTTCGCTACCAGTATGTAAACCCTCATATATTGGG 98 | GTTAACTTAACTGGTTGGCTACCATAGTTCTTAATAGTTACATCGAAACC 99 | AGCTAATTGGTCATCGAATGTAAACTGATAAGTTTTATTCTCAATAGGGT 100 | TTCTATTAAGAATTGTAGCAGTATTCTTAGTATACTTGTATTGACGTATA 101 | CGGCATCTTACTGCAATCTTTTGTTCATTCTCATCAAGAATACGACCTAC 102 | AGGTGGTAAGTATGGGTCAATGATTTCAAATGAATCAATAATTGGATTAT 103 | AAGCAGATAAGTCATACTGAGCAGTGTAAACATAATCGCCGTCTGGTAAT 104 | ACCACACGACGAATCAGGATATCATATTCAGTATGGAATTCAAATCCACC 105 | AATATTAATAGCTACCTCTCTATCAAACGTAAATACATCATTACGCATAT 106 | TAGCTAATAGTACATCTTCAGAGATAGTAAATACTATATCCATATATGCA 107 | GGTCTAGCATTAATATTTTTAATACCTAAACCTAAAGCATGAGCAATAAT 108 | ATTCTTTTCGAATTTAGCTCTAGTTGGAATAGCTTCATTACCAAACTCCG 109 | AAGCCATGATGATATTATTTTGTAGAGTTGTAGAGAATACATCACTTAGA 110 | TAACCAAATATACCCATAGATAGGGTAAGATCATCTTCTTGGATATGCTT 111 | TTTCTTAACGGACTCAATATATGCATTGAGATCATAAATATTAGAGTTCG 112 | TCAATAGTTCATTAGCCATTAATCTCCCCCTTCCTAAACGTTATATTTTT 113 | CACGGTATCTAGTATACTCTTGTAAATTCTTTTGGGCACCAGCTTGGTCT 114 | TTAGGGTTTCTATCAGTGAATTTAAATGAATCGTTTGGAGCTTTCCATTT 115 | AAGTTTATAGAACTTATACTGACCTTGACCTTCACCATTAAGCCCGGCAA 116 | TATATGGAGCCTGCATCCAATCACCAGACCAACCTTCTAATTCATCTATA 117 | TAACCACCACCAGCAGTATCACCACCAGAATATAGACTACAAAGACGATT 118 | GAACTCGTGTAGAGTATCGACTTCCATATCAAAAACAAATGTAGATTTAA 119 | AGCTAACAGTAAATCTTAAATCAGAACCGTCTGCCATGTCACTAAATACA 120 | TCACGTGGTACTGTCTTAGGGTACACACCAACATACTTAGCCCAATAGAT 121 | AATATCTTCACCACCAGAATCTTCAGATACTATGAACTTATACATGGACA 122 | TTTGGTCATGGATAATACGTTGCATAGCATAAGACTTGTTAGGTTGATTG 123 | ATACGACCAAAGTGCTTCAATCTAGAATATTCGTCAAACAGCTTGAAAAA 124 | CATGTAGACCTCTAGATACTTAGTATCTAGAAACTCTACACTGAATTCAT 125 | GGTTTTCATCACTCTCTATTGAAGTACCTCGATAGAATACAGAAGAACCT 126 | AAGATGTTTCTAGAAGTCTCATAGTCATTAGATACACTAATAGCTGGTAA 127 | GTCTACATTAGAAACTTTCTGGTTTGAAAGAAGATTAATGAATGGCTCAG 128 | AACGATTTTGTGAATAGCATAGTTGATGCAACACTTCTGGATACTTAGTT 129 | GCTGCTTCTATAAATAATGGATTACTAGCCACAGACTCAATGAATGTTTT 130 | AGACATATCATTACGTCCGTTTCTACCAATAGTAAAGTCCTTATCATGTA 131 | AGAAGATTTGTAAATCTGGTTTAGTAAAGAATATATACTCTTTAGTAACC 132 | CCTACACGATTATACGGATCCATCTTAGAGAACCTAGCAAATCTATGATA 133 | TCTATCTAGAGATGTCGGATTATATATACCATTCTTTTTAATGAATTGCA 134 | ACATCATTTGGGAATCAACCGTAGGCTTAAGATTCTTGTATTCTTGATTA 135 | GTCTCGGTTAAACTTTTACCCTGTCTGATGTCATTAGTTTCATCAGGCAT 136 | TCTCAGTCTCCTTTCTTTATAGGATTATAGAAATGTTTCAAAGATATCTT 137 | TAATTGTATACTATAAATATGAATAAGAGATAAGAGTCTAGCTGATAACT 138 | CATTAGAGTTAACTCTCCCTCCACGTTTTTGTTTATTGGACATCAGTTAA 139 | AGGAAGAGGTAACCACTATGAGCAGCTATGATTATGATACTAACGAGATT 140 | ATTACGGGTTATGGTGATACATATGATATGAGCTATTTAGGCAACTATGT 141 | AGAGACTGACGACTCCATTAAAGTAAATCAGGTAGCTAAGACAAACTTTA 142 | GACCAGCAGCTCCAGGAGAAGTTCTTATTGACCAAGACGGTAATGTTTAT 143 | TATTCAAGCAGAATCGTTAAGAAATTAAGAAAAGATCTTTTAGCAAACGC 144 | TGTTCTTGTAGATGAGTTATTGTCCTTAATTGGCCCTGGTAAAGACTACA 145 | ATGATGGAAGTGAAGACGTTATGAGAACACCTGAAGCAAAATGTTGCACA 146 | TATAAAGAACGTATGGAACTCGCTAGAGATTATGCCGAAGAAGACGGTTA 147 | TTATGAAGATATTTTAGATTGCATTAATGATGCAGAACCAAAGTCTATAT 148 | TTATTAAGTAACTATTTTATATTCGGCTAGGCTTTTATTTTTTGCCTAAA 149 | TTGGGCTGTTTTAACATAGTAGTAAATTTCAATATTGAATTTAGAATACG 150 | TATTTTAAGGAGGACTATAATGTCTTACATTCAAGAATCAATCCTCAGTG 151 | ACATTATTAATGTGTATGATAATGTAACCGCTGATGATTTCAGTTTAGAC 152 | AAATTATTACCTACCCAGGCTGGTGGATATAAGTCTTTCAAGTCTATTAA 153 | TAGTGCAACTAAAGACTTGGTGCTCACATTCCCAGTTATGTTTAGCCGTA 154 | ATATGGAATTAGCAACAGCTGAGCTAATTGCTAAAGCACTTGAAGCTAAG 155 | TATGCTAACTTAGTTAAAATGCTTTTAACTGCTATGGCAATCACTAATGC 156 | TACAGATGCTATTGATTACGTTAAGAATATCCATAGCAATATGCAGTTTA 157 | ATAATGGCATTGATGTAGATGACTATCTCACAATCAATAGCAAACTAACT 158 | AAAGAATCTGGTGCGATGGTTATGTTTACACCTGGTACTAAAGCTGTATA 159 | TGAAAACTACAAGCATAGTTTAAAGCACAGTCTACCAATTGCTAATCAAA 160 | TTATTAGCGAAGCCGACTCTAAACGTGATGAAAATAAAAGCAGTAAAAGC 161 | AAAGATGATAAGCCAGGATCTGTCAAATTTGACCAAGATGCTAAACTTGA 162 | TAAAGCTAACCAACAAATGCCTTTGATGATGAAAGTTAACTTCATCTCTA 163 | AAGCAACAGGTCGTCCTATTACTACATCTGCATACTTAGGTATCAAATGT 164 | AAACTATTTGACGTAGCAGGTTTAGATATCATTCAACGTATTGTATCTAA 165 | GAACTCTTCTGCTATTAGCTTATTCAACTTTATCCGTGCTACATCTCAAG 166 | AAATTGGTTTCTGGAGAGACTTTGTATTTGCATTAAGCAAAGCTAAAGTC 167 | GATGCTATTTCCAATGCTCGTAATGGCTCTTCTTCTAAAATGTGGAAAGC 168 | ATTAGAGCAACGTGCTACCAAATCCAAACTTAACCAATTCTTTCGTCAAA 169 | AGAATGATGCCACAGCTATCACTTCTTTATTGGTAACTACAGATGAAGTT 170 | GAAGAATTGAAAAAGAATAATGACATTGATCTTTCCAGATCTAATGTGGC 171 | TAGAAAGATTATGTCTGACTACAACTTACTTTGTATTGGTATTGTAGATG 172 | AAACTACAGAGTCTGTAGCTTTAATCTTTGATACAGGTGATGATGAATAC 173 | GAATTAGTACGATTCAAATCCTTGAAGAAAGATAAAGACATGGATGCTAA 174 | GCAAATCGTTAACCTATTAACTAAAATGGCCTAGGAGGAGGACACATGAC 175 | TAAATACTTTAAAGAAGCCTGCTCCTATATGGATTTGGGTGACAGAGAAA 176 | CATTAGAAATCGTATCTTCTGTAAATGAAGCAGACCAACGATTGATCATG 177 | ATGAATGTATCCAACAAGATCTATGACTTCGTTAAACTTAAAGCTAATGA 178 | AGTAGACTTTGGTGATATTCCATTATCCAAAGGTGATGTACAACGTTTAC 179 | GTCACTATAAACTAGTTAAACAAACACTAGAAGCTTTAGAACGTCTTTGT 180 | GCTTCTCGTAATATCCAATCTAAAGCATTGAAAACTACTAAAGAAGCATT 181 | AGCTAACTTAGAGAAAGATAAATATGCTTACGTTGGTGCATTCATGCGTA 182 | ACTTGGATTACCCTTGCACTATTTATAACTTTGCTGTATTGTCTATCATT 183 | GCTTCTACTAGTATGATGGTATCTGCTATTACAGAATACATCATGGATAA 184 | CGAGGGTACAACTAAGTTTGCTATGGATTCTAAACACTTCAATGTATTAG 185 | ATGACAATGTAGTTATTAAGAATCTTGAACGCTTTAATGAAAACTCTCGT 186 | AATGGTAAACTTGCTAAAGCATTATCCTTATTCACTAAAGCACATGCTCG 187 | TGGTATCTTAGGTACTATGGCAGCAGTATCTATGATTGGTGCTGGTATTT 188 | ACTTGATCTTCAATATCATTCCTATCTTACGTGAGATTGCTTACTACTTC 189 | TACTTCTGTAGAACTAGCTTAGCTGAATATCTTGAAGTACAAGCAAGTAT 190 | GCTAGAAATCAATGCTTCTAAGATTGAATATGATGACGATATGAAAGATG 191 | CTGCAGCTTACCAACGTGACGTTGCAGTTAAGTTCCGTCGTTATGCTGAT 192 | AAATTAGACATCAATGATAAAGCTGCTACAGCTAAGATGGCTAAAGAAAT 193 | CAAAGAAGAAGATTCTCAAACTAAATTTAAACATGATGACATTAGTGACA 194 | GCATTCCTGATTCTGCTGGTGCTAATAGCAGTCTATTCTAGGAGGTTAAC 195 | TAATGAATATTAAAAATAAACCTAGAGGAATTACATCTGGTTCTTTATTT 196 | TTTGAAGCAGTACAATCCGCTAGACGTGAAGAAATTGTAAAAGGTTTAAA 197 | AGAATTAGAATACCAACCTGTACATGAATCTGCGGCTGCAGCTAATATGT 198 | ACGATCGTATTGTTAATCGTAATAAGATGACTAAACGTCATCAAGACTTC 199 | TCTAATGCTGTACGTAATGGTCTTATCTTTGAAGCATTGAATGTATTATT 200 | CGAAGCATCTGCTAGTCATCCAATGATGTCTGAAGATAACCGTGTAATCA 201 | GAAACAAAGTTATCTCCAATTTCATTGAGCAAACTGGTTCTGATAAAATC 202 | TTATCTACATTAAGCAAAACAAATGCATTCACTGCACAAATTGCTAAGTA 203 | TGTAACAGAAACACACAAAGCTATCATGGAAGATAATGAAGAAGCTTTGA 204 | ATTCCAATGATGTGAATGATGAACCTAAAGTTTCTCCAGATGACACTGAA 205 | ACATTCGTTGATAAAGTAAACTCTGATGAAAACAAAGAAGAAATCCAAGA 206 | CATTGGTGATTCTGTAAAAACTCATGTAGCTAATGGTATTGAACAATTCA 207 | TCATTGCTAATATCGAAGATAAAGAACACATCAAAGACGTATTACAAAAC 208 | GTTGAAGATAAAGTTGCAACTATCCAAGCAGCTAATGCTGAAGAGGAAGA 209 | AGAGATTAAAGAATCTGCTATCCAACGTGGTAGATTGCAAATTAAGAAAC 210 | GTTTGGATACTCGTAAAGTAGGTTTATATGAAGCTATGGTTCGTGACCTA 211 | TCTAAGAAAGCTTTAACTAACCCAGGTTATGGTATGATTACTGAATCTGG 212 | TACATTAGATATGGATAAAATCACAGCAGCTTGTGAAGCTACACTAACTA 213 | TGATGGTATTATCTGAAGCATTAGGA 214 | 215 | -------------------------------------------------------------------------------- /test/mVCs/SRS057205_LANL_scaffold_13380.fasta: -------------------------------------------------------------------------------- 1 | >SRS057205_LANL_scaffold_13380 2 | TATCATCAACAAAGTCAACTAGACCATAGTGTTTCATACGTTCATATTCA 3 | TCGAATAGTCTGAACCACATATACACTTCTAGATACTTTGTATCTTCAAA 4 | TTCAACAGAGAACTCATGATTCTCATCGGATTCATATGAAGTACCACGAT 5 | AGAATAAAGAAGATCCAAGAATATTTTTAGATGTCTCATAGTCACTAGCT 6 | GTATTGATATCTGGTAAATCTACATTAGATCTCTTATAGTTAGATAAGAG 7 | ATTAACGAATGGTCTACCACAAGCTGAGTAGCTTAGACTTTGTAATACAT 8 | CATTATATCTTTTAAATGCTTCAACCATTAAGGCATTATTAGCAATAGAT 9 | GGATTCAATGTAGGTCCTTTGAATAACTGCAAGTCTGGTGTAGTAAAGAA 10 | TATAAATTCTCTAGTAGCACCCATCCAGTTATTAGGATCTAATCTTTCAT 11 | ATCTAGCAAACTTTTGATATTTCTCTATCTGGCTTACTCGTCCAGGACCA 12 | ATACCAAGACCATTTGCTTTTACATATTTTAACAGACCAGCTGTTGATTC 13 | ATCAAACTCTGGTCTAGTAGTCTGATCAAGTAAACTTGGTTTAGCAACTA 14 | TATTATCAAGACTATTACCAACACTGTTAATAGCCCCGGCTGTTTCATTA 15 | CCTATTTTAGTAATAGCACCGCCAACTTGCCCAACAGTATTAATATATAG 16 | TGTATTCTTTACTGAACTGACTGTATCAGAAGCAGCATTCTTACCTTTAT 17 | CTATGACATTACCAACTGCTCCAGAAACTCCAGACGCAGCATTATCTATG 18 | GCTGTTCCAATAAGGGATTTATCATCTGCCATTGCATATATTCCCCCTTT 19 | CTTATTTAATTTAATCTTATGTTAAAATGGCTAACTTCTATCGTAATTGT 20 | ATATTATTATAGTGAAATAGGATAAAGCATATAGATATACACTCTTATAT 21 | CACAGCTTTCAGTTATTTGTTTTACTATACTTTTTAAAGCGAGGCTGATG 22 | ATTATGAGAGATTATATCGAAGACATTTTAGATGGTGAGTTACCTAAATT 23 | AGAAGAAGCTAAATATTCATGTAACGTTTATACTATAGCAATTGAGTCTG 24 | ATGATGAATCAATCAACCTTGAGCTTGTTAAAGTAGATGATTACAATGAA 25 | GTAGTAGAGCTTTATAACTCACTAATCGATGACCTTATCGAAAGAGGTCA 26 | AACTAACAACTATTCTCATACCCTCAAATGTATGAATAAAAGATTTTTCA 27 | AAATTTAATGAGAAAAATCTATATGCTTTATTTTTTTTTCTTATTTACCC 28 | ATTTTAACATAAGATTAAAGTCATATATGATACTATAAGGAGGTACTTTA 29 | AATGATCCTTAAGGATTTAATTACAGACGTTTTAGACGCTGCCGATGGTA 30 | CTGAAATTGGTAAATTTATTTCCAAGAAGAATCCATCTATCAAGTCTATT 31 | ACTCGAGCAAATAAAGATTTAACTATGACATTTCCTGTCATGGCTTCTAA 32 | TACTGTAGATCCAGCATCTGCACAATTAGTTTCTAGAGCATTGGAGCGTA 33 | AGTTTGTTACATTAACTCAAATGCTATTATCTGCTATTTCCATTACATCT 34 | TCTAAAGATGCTATTGATCATCTTAAAAATATTCATTCTAATCTAGATCT 35 | ATCTAGTTTATTTGACGTTGATGATTATCTTGCAATTAGCCAAGAAGCTA 36 | CAGCTAGTCATATTTTTGATGCAGATGAAATTAAAGCTGTATATGAAGCA 37 | TTTAGACAAGAACGTTTACATGCTAAACCTATCAATCATTTACATGAAAC 38 | GCTAATGGATGATATGATGGCTCGTATGCGTCAAGATCCAAAATTTAATG 39 | CAAACGTTGCTGATGCAAGATTTAATAATCTTAGTGATGACGATAAAGCT 40 | AGAGCAGTAAATCTTTTGAATACAGATACGGCTACTCGAAATAGAGATTT 41 | AACTCGTCAAAATAGAAGTCTAACTCAACAGCTTAATGATATTGAGCGCA 42 | ATGAAGGTAGAATGAGAAGAAATTTCGCAAGAACTCAATCTCAATCTAAT 43 | AGACGTATTAATGATTTACGCCAAAGTAATGACAATTTACAATCTCGTTT 44 | AGATGATATCCGTAATAATACTAGAGCTGGTTTAACCAAATTAGCTAAAG 45 | ATCAAGACTATAAGAAAGCTAATGAATTACAACCTACATTGTTACAAATT 46 | CAATTCATTAGTACTAATGATAATAATGATCCTATCACTGTAGATGCATA 47 | TGTTGGTATTAAGACTAAAATCTATTGTGTAGATTCCGCTGATATCGCTA 48 | ATCATATCGTATCTAAACGTAGCTATAATTTCAGCTTATATAACTTAATC 49 | AAAGCTACAAGTGGTGAAATCGAATTCTGGAGAGACTTCGTATTTGCTAT 50 | TAAGAAAGCTAAGATTGATGCTGTGTCTAATACACACCGTGGTTCTTCTT 51 | CCAAACTTTGGAAAGTATTAGAACGTCGTGCATTAGCATCTAAAATCAAT 52 | CGTTTCATGTCTGCTCGTAATGATGCAACAGCTATCACTACTTTGATGAT 53 | GTCTGCATATGATGTAGAGATGCTTCGTAAAATGGAAGACATCGATATCT 54 | CTGATTCTCGTGTAGCTCGTAAGTTAATGGATGACTATAACTTAGTTGGT 55 | ATCGTTATCGTTGATGACTCCACTGAATCTGCTAAAATCATCTTTGATAC 56 | AGGTGATGATGAGTATGAACCATACACATTCAAAACTTTGAAACGTGATG 57 | ATAAAATGGACTATAAACAAATGATTCAATTACTAGCTGGAGGTAAATAG 58 | TAATGCAAAAGTATGTATTAAAAGAATTCGTTGAAGCCAGCAAGTTAATG 59 | GATCTTACTGACAAAGAAACCTATATCACTGTCGGTGTAGTTAATGAAGC 60 | TGAACAACGTGAAGTCTTGTTAGGTGTAACTAATAAACTATATGAAAAAA 61 | TTGAAGCTAAAGTAACTGATGTTGACTTTGGTACAATTCCTCAATCTAGA 62 | GGTGATTTCTTAAAGATTGATAATATTGATATGGTAACTGAAGCTATTAG 63 | TGATATGAAGAAAATCTATCAAGAATATAAGCAACCTCTTACGTATATCA 64 | ATATCTTAACTGATGCAATCAATAACTTGGTTGAATTGAAAAATGAATTC 65 | CAACGTTGTTATGCATCCAATACTAGCTTAGGTATTGTATTATATAATAC 66 | AACAGCTATGTCTGTAATCAGTGGTGTATCTTTACTTATTGCTTCCACTA 67 | TCGATTTCATCGTAGATCCTAAAACAAAATCTATCGAAGTATCTGTAGAC 68 | CGTGTAGGCGTATCTAGAAGTAAAGAACTTCTTCAATTACAAACTCTAGC 69 | TGAATTCAATAACCTTTGTAAAGGTAACAAACTTAAAAAGGTATTGAATG 70 | ACTTGATTAAAGTAAGTGCTAAGAACTTAGCTGGTACATCTGTATTAGCA 71 | GTTATCGGTGTAAGTATTGGTCTTATCTTTACTATCGTTCCGATCATGCG 72 | TGAATTGATCTACTACTTCTACTATTGTAGAGCAAGTGTAGCTGAGTACT 73 | TTGAAACTCAAATTGCAATGTTGTCTTTAAATGCTGCACGATTAGAGACA 74 | GCTGGTGACCCTAAAACAGCAAACGAACAACGTAAATATGTAGATCGTTT 75 | CCGTAAGATTGCTGACTATCTCGCAGTTGATGCAAAAGAAGCTTCCAATA 76 | AAGCTGAAGCAAATGTAAAACAAGACGAAAAAGAAAAATATAAAATCGAC 77 | GATGTAACTGAAAGTCTTCCAGACTCCGCTGCATCTTCTTTATTCTAATG 78 | AAAGGAGCATAGAAAAGATGCATTTTTCTAGAAAACAAATTAGAGAGTCT 79 | AATACCTTGAAGATGGTAAAACAAGCTGAAAAGGCTACTCTTGAAAAACA 80 | ACTTAATGAGTCTAAGACTATTATTCCTGAAGTGGGACGTGTTGCTATGA 81 | ATGAAAGCTCCTTGGCTCGATCTAAACGTTCTTTAAATCTTCGTATGGCT 82 | GCTAAAGCTATGATTAAAGAACACTTCTTAACTGAAGCTATTAAATATAT 83 | CTATAACGAATGTATGATTCCTGATCTTCAAAAGGAATCTACTAATATCA 84 | TTCGTGATACAGTAATCCGTGGATTCATTAAAGAGAACGGTGTTGAAAAT 85 | ATTATCCGTACTTTCAATACTAAATCTTTATTCTTAGCTGACATTGCTAA 86 | AGCAGTCAAAGAAGCTACAGATGATGTAGTTAAAGCTAATGAAGATAAAC 87 | TTAAAAATCCTGATACTAAAGTAGATGATATCACTGTAGATCCTGAATAT 88 | CAAGATTCTTTCATTGATAAAATGGGTCAACAAAAAGAAGAAATTGAAGA 89 | TGTTGGTGCTATGGTACAATCTCACGTTGCTAATAACGTAGAAGACTTCA 90 | TTGCTTCCAATGTTGAAGATAAACAACAAATCAAAGAGATCCTTGATGAA 91 | GTAAAAGAAAAAGTAGCTAATATTAAAGCTGCAAATGCTGACGTAGCAGA 92 | GGACATCAAGGAATCCATGATTATCGGCGCTAAGCGAAAAATCTATAACG 93 | TAAAGAGTGCTAAGAAGAGCATTCTAGAAGCTATGGTTAAACATTTAGCT 94 | AAACGTGTAATTGCTGAAAACCATACAGAATTCCTGACTGAATCTAAAAC 95 | TATCAATACTGATAAGATTGTAGAAACAGCAGAATGTATGTTGACTATGC 96 | TAGTACTCTCTGAAGCACTAGGATTCAAATTGAATGAACAAGAAGTTCGT 97 | GCAATGTACAAATAAAAATAAAAAAAATAATAGTTCCCCATCTGGTTAAA 98 | CCAGATGGGGATCATTCTTTTAGTTTTTTATTATTAATCATAAACCTCCT 99 | TTCTTATTGATGAAGATGTATACCATCATCTAGATGGACTCCTAGCACAT 100 | CTTCTTCGTCAAATAATTGACCACAATCTACTGCTAAATCTAATTCTTCG 101 | TATAACATATTTTTCACCTCATAATTAATACTAACACACTAAATGATATA 102 | CTAAGATTATTCTTCTTCTGTTTCCTCCTCTTCTAACTTATCCATTACTG 103 | CTACGAGTACAGCTACTGCTGCATCTATCTCTAATTGTGTAGGCATATTG 104 | CCACCTCCTAACTAAATAACTATATCATATATTCACCTTAATAATATACA 105 | GTTATAGAATGCTAGAATTACAAAAAATAAATACCCCATAGGACTCGCGG 106 | ATCCTATGGGGTATTGTGACGTATTATTAGATTGACTTAAAAGAACTTAT 107 | GCGTCTTAAATTAGACTTATTAAAGTGTTGTCTCCAATACGATAAACAGT 108 | ATGGAAAAGTTCAATGTTATCCATTAAGAATTTATATTGCTGAGCTGTTA 109 | AAGTTTCTAGAATAGTATCCTTATCAGAGGTGTATTGTGTGCGTATGTTA 110 | GATAAGAATACATCATCATTAGTAAGATTACCTTTTTGCCAAGCATATCG 111 | TCCTTCTTCACAGAAGGCAAATCCTGGGAATGCTTTAACATAGTTAGCAT 112 | CCCAATAGGATGCATTTAACATTTTTCTTTTGATATCATAAAATGTATCA 113 | AGCTGTTTATGATTGTAAGACATTGTGATCACCTAAATAAGATCTTCAGG 114 | ATCATAGAAATCCTGAGTATCTTCCTTTTCTTCCTTCTCAGTTACAGGGA 115 | TGTCAAGTTCGACACCACGTTTTTCCATGATTTCCTTGATTTTTTGATTA 116 | TCACCATACCCCTTTTCTAATAGGATATGAGTCAAATCATGTGGACCTTG 117 | CTCCGTTAGGAAAGAGAAACCTTTATTAGGTTGCATAGTTCCATCGGATT 118 | GAACTACCCACTTACGTAGTTCAATTTTATAAGCTCTGTCATTCCAGCTC 119 | ATTTCAGAAATCTTTAGAATAGAGTTTCCTCTTTCATCAAAGACTTCATC 120 | AATACCGTCTGGGTTGATATTAAATTTGAATTCCATAGATCCTCCAAAAA 121 | ATAATAATAGACTGGGGAGATTAATCCCCAGTCATATTAGAATCAATTAT 122 | TTTTGTGGACGGAATAAACCATCGGATACAACTTGACGGCTTACATATTT 123 | CTTAAGCAAGCGTTTAGTTACATCAGGATGCAATTGTTTGATTTCAAGAA 124 | GACGACCAGAGTAGCTATTAGTATTTACTGGAGCACCAGGAATTACTACA 125 | TAGTCATATTGGTTACCATAGATGAAACCAAGAATAGATTCAATTGTAGC 126 | ACCATATACTACCAAGTTGCTGTTACCAGAACCATCAGACGCATATGCAT 127 | AAGTTACACATTGAGTACGGAATTTGTCATGGTTTTCATTGTCTTTACCG 128 | AAGTCAATGATTGTATCTTTCAAGATATCAATTGCTTCATTAGTAAGACG 129 | GAAGCCCATAACTGTTTCAGATACAGTACCGTTTTTAACTAATTGACGGA 130 | TGTTAGAAGTACCATTGAATTTAGCAACCATTTCAAGTTCTTTAGTAGCT 131 | GCATTTTGACCAATGCTTTCTAAACCGATTTGTTCAATAGCTTTCAAACG 132 | AGTATCGTGTTCGTTATCAGAACCATTGAATGCAAATACCAATGCAATAC 133 | CGATTTGTGGGCTGTTAGTGAATACCATATCACGGCAACCTACATAGTCA 134 | GCAAAGATGTTACCAAGACGATTAGTGAGAAGTTCACATAATTCGCTTGT 135 | AGCGATTGTTTTTGTTTTGTAATCGCTTTCAAATGTTTCAGGAGTAACTT 136 | TAAGTTCAATGCGTTTTGCATTACCTTTATCGTTACCTTCTTTATCTCGA 137 | CGAGTTTCACGAGAAGCACGTTGAAGTACTTCGCCTAAAGATTGGAATCC 138 | ATTGTCGACTTGTGGAATTCCATTGATCAATTGATTTGACATAGCTATGT 139 | CCTCCTTTAAAATATAAAAGAAATTATTCTACTGTTAGGATCATAGTAAA 140 | TATTAATCACCTAACTTCACCATTATAATATATCAATATATCTAAGTTTA 141 | GAAGACATGTAATCCAGGAAGGTCATCCATGCCTACATATTTAACTATAA 142 | AGGTTCGGTCATTCTTATCTTGAATAAAGAAGAAATTACCTCTAGCCTTA 143 | TATAATAAGATATCATGATAATATTCAACGATGTTATAATCTACTATACG 144 | ATCTTGTACTATAGCTTCAAGAGCAAATAAGTCACCAGGTCGTAATTGAG 145 | CACCGTCTTTGACTTCAAATAATACATTGATTACTCTGAAGTTGTAATGG 146 | AACCAGTACATGAATAGAATATTCTGTAATGCTATCTTAATAGCTTGATC 147 | TGTATCATCGTATTCTAATCCACGACTATCACAGATAGAAATAAGAGTGT 148 | CATAAACACGTGAGTCTAACTTAACAAATGATACAATATTCTTGAGTGGA 149 | TCATTTAAATATAAGTCTACACTGAAAGCATAGTCTTTGCTTGCAATGTC 150 | ATACATCATAAGATCATAAGCTCTCTTATATTGTCTCATAGAACTGTCGT 151 | TATCGAACTCACCTTTACATACATACTTACCAAACTTCTTCTTAGGATCT 152 | GGATTATCAATATTAATCCGACTAGCAAAGTATGGATAGTTATTTGCTTC 153 | ATATGGACAATAGATATTGATACATAATTCCTTTTCCCCATTCTTTAGAG 154 | TACACACTTCGAAAAACATCTTACAGTGTATCTCTAAAGGCATATACTCA 155 | TCATTATTGAATTTATCAATCAATAACTTATCTCCTATTACAGGAGTAAC 156 | CTTATAGAAGTCTTTGTCTTTTCTAGATACTATTCTATATAGTTCAGTAA 157 | TCTGACCGAATTTATCTTTCTTACAAAGCTTCTGTCCGACATTATACATT 158 | TTTATATTCACCTCCTTAATCATAGTTATAATATATGAGCGAATAGTATT 159 | TATAAGAGTCCTACTTATCTAGTAAGTAGGACTCATTATATTATAATACT 160 | TGCATAGCTATCTTAGCATATTTACCAGCATGTTTTAGTGTAGGTGCCGT 161 | AATAACAAAGGAGTCATCACAGAATTCGCTACGTTGATAATAATTAGAGA 162 | AGTTGAATTGTCTATCATTCTTAAGTACTACTTTGAGATACTTATGGAAA 163 | TCATTCAATACTCTAGCTCTAATCTTAACTAATTCTTTATCTTTCTTAGT 164 | ACGATCTTGTTTAGTAAGATCTTCTGTAATCTTAAGATTTAGATAATACA 165 | TCTTAGCTAGTTCATATTTCATTGCTTCAGTATTCTTAGCTCTATCATAC 166 | TCCATAAGCAATCTATGAGATTCCATATATGTAGCTTGATAGTTCTTATT 167 | CTTTAAGAAGTTCTTAACGAATAGGTTACCTTTATTATCGAACTCGAAGC 168 | CAATACCTTTTTCTTGTAATAACTTAGCAGTCATACTTCTATGGAATAAT 169 | GTATTAGCTCGGTTATAGGCTCTATTCATATTGATAGGATTGAATTCCAT 170 | GTAAGGATTCCAACCGAATTCTAATAAAGCTTGTTTATATTCATCAGATT 171 | GAGTTCTAGAATACTCTAGACTTAAATATCTTACATTAGACATCCAGTCT 172 | AGAATAGCTTTCTTATCATAAGATTTACCTTCATAGATATTCTTATAATC 173 | TTTCAACCACTGATCAGCTTTAGATTTCCACTTATCTGGAATAGAACCAA 174 | ATGTGCAATTACGTTTGAATACCTCAATCTCGTGAGGAATATAGAACGGT 175 | GTAGTATTTGGTAAGTTTCTAACTGGCTGTGCATCTTCTATAGCAGATTC 176 | TACCATAGGGAAGTAATAGTAATCATCAAATCCCTTATTAGTAAATACAC 177 | TCTTTAGGAAGTTATACATAGTTTCATTATTGCAACCAAATGCTTCCATT 178 | AATCTCATATCGGAGATACGGATTAATGAGATATCCATAGATTGTAAGTT 179 | ATTCCATTGAGCATCTAATTCTTCTTCACTATCACAAGGTAAGATAACAA 180 | AGATACCAGAGTTTAGAGACCAAGCTTGAAGATATTCAATCTCACGTTTC 181 | TTACCACGGAGTTCAATACCATAATCTCTGGCTCTATCTAAATCAGATAA 182 | TTGTAAACCAGATTCACTTAAAGCCAAATCATCATAAGGGATCTCAGAGT 183 | TAAGATATTTAGATCGTAATTCTTTAAATCTTTCGCTATTAGATTTACCA 184 | TAGATCTCAATAGACATATCATCGCTATGACGTTTCATATCAGCAGAGAG 185 | ATTATTATAATCATTCCAGTCATCCATTAATTGCTCTTCGGATGTATATT 186 | TGTCATCAAGTACTTTATACATGCCAGAGTCATTAATTTCTTTAACCTTC 187 | TTGTTATTAGTATCTTGAGTATCATCTTCATTAGATATAATCTCTTTAGC 188 | TTTAACAAAAGCTGGAGCTTCAATCTCTAGAATAGTATCATAAGATTTAG 189 | ATCTTATACCAGACTCTAAGTCAATAGCAAAGTATCCATTATGATCTTCC 190 | ATGATCATAGTACCTTCAGGGAATTCTTTTAGTTTAGACTTTGCAGTATT 191 | AACTTCTAGAATATCACATAAAGGCATAGCCGTATTATATAACTCAGATT 192 | CAATAGAATAGATCATATTCATTAGAGTTAACTTATTCTCTCTATCTAAA 193 | TCAGCTTCAATAAAGTCATCATCATACTCTAATTGATCTCTAGATAGCAT 194 | TACTTTACCAGTAATCTCTTCATATAGATTGATTGCATTCTCCCAAGTAA 195 | CTCTATCTCGTTTATGTCTATAAGACTTATAGAATTTATCTTGTAAGAAT 196 | GGCTCTTTATCTACAATCTCAGTCTCTTCATTATCAGATTTAACTCTTAG 197 | CTTAGTAGACTTCTTATCATCAACTACACCAAAGCCATCTTTCTCTCCAC 198 | TGAAAGAGTGTTTATGTGGAGTATATTGGACTAGCATATTACCATCCATG 199 | GTACCAACAATACCACCTACAGCACCAACACCCATATGCTCTCTAGCAGC 200 | ATATTCTTTTAAGTCAGATAGACGTCTAATGATATCATATTCTATAGGAA 201 | TATCTTCATTATCTTCTTCAGAGTCTTCTGCATTATCTAGAGTGAAGAAT 202 | CTATCATCGTATACCGCAGATTCATTGATTCTAATAACTTTATTATCCGT 203 | ATTAGGCTCATTAATCTCTTGATCTTTAAGCAATGCTAATACTTCCATGA 204 | GTTGGACAAACTTATTATCTACTAATCTTAGATAGTTATATTCACCAAGC 205 | TTAATAAGCTCAGCTTCTTTACTAACTTGCTTAGCACGATATTCATCCAT 206 | TTGACGATTATTAGGATTATCCCCACCGTCCTTAACTTCGATAATCAAAT 207 | TATAAGGAACGTAGTAAATATCCGTAATCCATTGTCTAGAATTACCATAT 208 | TGATCGGTATAATCAATAACTGGACCTGGCATAATAATATCTTTAGAGCT 209 | ACAGTGTAAAACTTTATCCATAAACTCTATAGCTTTATGCTCATAAGATC 210 | CAGTGTAAGTAAACTTAGTACCATCACTATATACATAAGTACCACTAATG 211 | CTACGATTAGCTAACATCTTAGCTTGGTGTGCTGCATCATCTAATAGAGA 212 | TACTTTACCGTGTACTCTAATCATATTCTTTTTAAACTTAGCTCTCATTT 213 | CCTCTTTACATCTAGGATTAGAGCAAAGTCTATGGTATTTACCAGTCTTT 214 | TCATTCCAGTCTGTCTTATTACCGCATACGATACATTTACCAGAACCTGG 215 | GTGAGTTTTATCATATAAGAATTGCTCGGCAGA 216 | 217 | -------------------------------------------------------------------------------- /test/mVCs/SRS011452_WUGC_scaffold_3640.fasta: -------------------------------------------------------------------------------- 1 | >SRS011452_WUGC_scaffold_3640 2 | GCTTAACTTGGTACGTTCAGCATCAGTCATAAACCTGTGTGTCTCATCTT 3 | CATTTATTTCTGACGCTCCGTGCTTATGTGTCGCTGCCGCATAATTACCC 4 | TTTGCTTGATATACCGAATCGTGGTTGTGATTTCCTGCCGCCTTACCATT 5 | CCAATTTGTCTTTTCAGAATCCGTTACAAATCTATGTGTGATATCATCCG 6 | TGATGTCAGATGCCGAATGCTTATGTGAAGCAGGTGCATAATCCCCCTTT 7 | GGTTGATACGTAGAATCATGGTTATGGTTTCCTGCAGCCTTACTGTTCCA 8 | AGTCTCTTTTTCCGTATCGGTAACAAAGCGATGAGTACTATCAGGAGTTA 9 | TATCAGACGCATTATGACCGTGCGATGACGCCGCATAACTACCTGCAGGT 10 | TGATATACTCCGGCATGGTTGTGATTAGAAGGAGAAGCGCCAACCTCGCT 11 | CGCTGTGTAACTAGGTTTACTAGCAGCCTTCGCCCATGACGGCACATCAC 12 | TTGCAGGCATAGAGGTGGGGAAATCACTGATTTCAGATACCTTATGCGTA 13 | TGCGCTAATGGAGGCCGTGCATTACTTAGCCGATCATCGTTTCCTTGGCA 14 | TACCGTCCCTTCTGCACTACCAAAATTCTTATTAAAGGCAGAGTTTTTAG 15 | TGAATGCAGGTTCGTATGTACCGGTATGATTGTGACCTGATGGAGAAGCG 16 | CCTACTTCGCTTGCCGTATAGGTTGGTTTGGATGCAGCCTTCGCCCAAGA 17 | GTATACGTCACTAGCGGGCATAGAAGAAGGGAAATCACTGATTTCAGATA 18 | CTTTATGCGCATGTGCTAATGGAGGCCGTGCATTACTCAAACGCGAATCA 19 | TTTCCCTCACACACGGTCCCGGCAGAGCTTCCGAAATTCTTATTAAAAGC 20 | GGTAAGTTTGGTAATAATCTTCTCATATACTGCATCATGATTATGTGAGT 21 | CCAAAGCAGCTTTCAAAGCTTTTCCCTGCTCTGCAGAAAGAGCTTTACCA 22 | GTTCCTCCACTTGTCAGATTATTAACAATATCGGAAACATTAAGTTTCTT 23 | TCCTAGCTCTGTTGTCATAGTGGCAGCAAAATTCGGATCGTTGTTCAGGG 24 | CGTTCGCTAACTCAATCAGTGTATCAAGAGCGTCCGGAGCACCGGCTACC 25 | AGTTTGTCGATAGCTGCTTGTACTTTAGCGTCAACGCCGGATACTGCATT 26 | ATTCGCAGCTATCGCAGCGGCGTTCGCATCATCGGTAGCCTTCTTCGCTA 27 | AACCCGTTTGTATTACAGATGCATCCTTGGCCGCATTAGCATCATCTGTT 28 | GCTTTTTTAGCCAAAGCGGTTTGGACTTCCGATGCTGTCTTGGCTGCATT 29 | AGCATTGTTCGCTGCAGTCGTTGCAGCATCTTTTGCAGCATTGACACTAC 30 | CAGCGGCAGCATCGGCCTTGGCAGCTTTCTCACCTGCCAAGGTTGCTTTT 31 | TGATTTGCGAGTGTTGCTGCAGCATTTGCATTATCAGTAGCCGTCTTTAC 32 | AAGTCCTAGTTGTGCAGTTGCATCTTCTGTAGCTTGGTTCATCTCATCTA 33 | CAATGCCGCCATATTCAGCTTTACGAGCTTCTTCCGCTTTAACACGTTCC 34 | ACTTCCGCCTTAGCCCGGTTGGTCTCATCAACTTTACGTGCTGCTTCGGT 35 | AGATTTACGCTCATCTTCATTCTGAACTCTGATTGTTTCAGCAGAGGAAC 36 | GACCTGATTCAGCCGTGGCACGTGCGGTTTCGGCTGTTGTCCGTTTAGTC 37 | TCGGCAGATACGCGAGCATCCTCGGCGGTCTTGCGTGCATTCTCGGCATT 38 | AATACGAGCCGTTTCAGATTGATTACGGGTAGTTTCAGCAGAGACACGGG 39 | CAGTTTCATTATTGCCTCTTATGACTTCATCCGCTTTTCTTTTATTTTCC 40 | GCAGTAGCACGTTCGGATTCAGCGGTAGAACGACCTGTTTCAGCGGTTTT 41 | TCGTTTATCTTCTTCCTTTACACGTTCCGATTCAGCAGAGGAACGGCTTG 42 | TTTCGGCAGTCTTACGGGCATCTTCATTACTTTTACGTGTTTGTTCCTCC 43 | GAAACACGTTTTGTTTCTGTATCAACACGCCCAGTTTCAGCAGTTACCCG 44 | CTTGCCTTCCGCTATAACACGTGCTTCTTCGGTAGATTTGCGGGCATCTT 45 | CATTCTGGGCTCTTTTCGTTTCAGCAGAGGAACGTCCAGTTTCAGCCGTG 46 | GCACGTGCGGTTTCGGCAGACTTTCTCTTATCTTCTTCGGATGATCGCGT 47 | ACTTTCAGCTGATTTGCGGGCATTCTCATTAGTTACACGTTCGGATTCAG 48 | CATTGCCTCTCACTGTTTCAGCATTCTTTCTAGCTTGCTCATTAGATTCT 49 | CGTGTACCTTCGTCAGTAACACGTTTCTTTTCTGCATTGTCCCGTGCAGT 50 | TTCAGCAGAAGAACGACCTGTTTCGGCTGTCTTACGTGCATTTTCATTAG 51 | TGATACGAACGGATTCAGCAGCTTCCCGGGCCTGTTCTTCACGAGAACGT 52 | CCGGTTTCAGCCGTTTGCCTCGACTGCTCGGAAGCATTACGACGGGATTC 53 | AGCAGTTTCACGGGCTGATTCATTACCTTCAACAGTAGCTTCTAATTGCC 54 | GCATATCGGTAGTAGCAGTTTTGGCATCGCTTGTAGCTTTGAGCATATTA 55 | TCTAATGCCGTCTGAATCTTCTCTAGCCCGAATTTCAAGCTCGTTTTGAC 56 | ACCGTTTACTATCCTGTAACCGATGGTGTAGAAGCCTTTCATGTCGCTGG 57 | CTTCATTCAATTCTGATATTCTTTTCTTTTTTAATGGCATGGCAATCAAT 58 | TTAAGTCAATATAAAATTCTCCGTCCTCTGTTATAATGAACTCGCCCGCT 59 | TCGGATGAAAGCAAAAACTCCGTTTCTCTGATCCGGAAGCAAGTAAACAC 60 | GAGATTCAAAGTAAATTCCCACCAGACACCACCTCTTAACATAAAATTGT 61 | TTGTCTGGCAATCTTTATAGTAGCAAGGATAACTTTCACTCCATCCATCA 62 | CAGTATAATACCCTCTCCGCATCGGAATATTCATAACCTTCATTATCGGT 63 | CTTCATAGTCAGTTTAGTTAGATCATAGAGTAAGGCATCATAGCTCTGCC 64 | AAAAAGTTCGAATATCCGTTGCCCGCATCAGGCACTTTAAAGAAACTTCC 65 | TTTGTCTGAAACTTCACTATTTCACCGTCGTAGACAGCTCCATCCTGACG 66 | TTTGAAATTCTGTAGTAAGTTCTTTTTTACTGCCGGAGATTTCAGTATTT 67 | CAGCATTACTGCCTTTCAAAATGACTACACCATATTCCGATAAATCACGA 68 | TCATCTATTTCGTACCCCCTTGGTAGAGGAATGGAACAAACAGGTTCCTG 69 | GTATTCATAATTTGCTTCGCGGGGGAAGTCGTTGGCAAAAGTTATCCTCA 70 | CGACTTGAAATCCCGGATAGATTGTATAACTGTTCTGTGAGGAAAGACGT 71 | AAACGATAGGTTCTATCAAGAATAGGAAAATAAAAATCATGATATCCCAT 72 | ATCTGATAAAATAGCAACTAATCCACTAAATCCCAGATCGTCTTTACAGG 73 | CAAAATCAATACTCAATTCATAGGTGTTTAACGTCAAGCTAGAAAGGTCT 74 | ATTTCAATACCATCTTCTTCCGGCCAATCATTTTTATCATCCGATTCTTT 75 | GGCAGGAGGAAATGCCACAAGATTATCATAGCTTCCTTTTATAATAAATA 76 | TACCGAGAGTGGTATATGTATTCTCTCCATCTATAAAGCAAATTCCTTTC 77 | ATCTTACGAGCTTTATCCCTTTATCATTTATCTTTTCAATACCTGCTTTC 78 | ATCGACTTCATATCCTTTTCTATACCTTCCAATCTAGCTGTATTAGTATC 79 | AATATTCGAAAGGTGTCCAACAATGGTATTCATATTATCCTTGATAATTT 80 | TCACGTTTTCATTTATGGATGCAGATATGGTTTTAATATCTCCAACACCA 81 | GAAATGATACCTTGGAAAATGAGAGTATGAGACTGTAGCTCTGTTTTTAT 82 | GTCTGCTATCAAAACATTAGCCATTGTGAATCTACCATTCAATTCGTCTG 83 | CAGAATCTTGTGACATGGAAGCAAACCCTTTTTTTGATGCTTCGCGTTCC 84 | GAATCCTCATCAGTAGTCCACCCATACATCTCTGCCATGGCATCACGCTT 85 | TGCTTTCATCTCATCGGAAATCTTCTGTCCTTCCTTTTTCAGATCGTTAT 86 | ATTCATCTTCGGTTACCCCATCGTCCATTGCATTATATAGCTTCTCCCTC 87 | CACGCTATTAATCTGTCCATATATTCTTCTTTAAGCATGGAATTGAGAAT 88 | AGCATTTCGCATATAATCCTCGAAGTTGTCGGCAAAGTCTGCCGAATCGG 89 | CATCCATATCAGAAATTAAGTCCTGAAAGTCTGAACGAAGAGAATCGTAA 90 | TCAATAAGAGTTGTATCAGCTATTTGTTGTTCCAATACCTCTGCAACCTT 91 | CCCTACACCATTTGCAATTTGATCGGCAAATTTCTGCGTGTCTGAATCAA 92 | GTTGGGACCAGAAGATACCGGCATCCGATTGCAATTTTAAAAGTTGTTCA 93 | TCAGTCAAATCAAATAGACCGGTCATACGACCGCCCATTTTATTTTTAAA 94 | TTCATTTACCGACATGCCTAATGCTTTTGCAGCCTGCTTCCATCCTTCAC 95 | CGGACATATCATCTACTTCACTGTAACCTTTTGAATGAGATTTCCCAGAT 96 | GCACCGGAGTTCAAATACTGTTTGCCTAGTACTTTAGCATTCTCACTTTG 97 | CAATTTTATGTTAGCGATAGCTGCTTCATATACAGCATTTGCCGTGTCTC 98 | CCGTAAGAGTTTCCGCTAGCTCCAGTTGCTTCTCAATTACTCGATCAAGG 99 | ATATTGATATAGGATTCATACGCTTCTTTCGCTTTCTCGTATTTCTCGGT 100 | CGTATCATCCTTACCGAACATATCGAAGATTTTCATGGCTATCTGAACGG 101 | CTGCACCAATGATAGCTAGAATAACAGACGCCTTTTCAACTGTACTTATT 102 | GCATTAGCAGAGGTATCGGCAGCAGCTTCAACCCCTGCCATTGCAGTCAT 103 | TGTAAATGAGCCAATACTGCCAATAAGGGAAATGATCTCACCAGCCGGAC 104 | CACCAATCGACTTACCCAGTTCGTCTATGGTATCCGCTAACTCCGAAATC 105 | TGTGTTCTAACTTCTTTTTCTGCCTTCTTTACCTGATTGTCCTTTTTTAC 106 | AACCTTATCTTTTGCCGCATTATACTTTTCGGTTTTCTTCTTTACTAGAT 107 | CAAGTGCCTGCGCTTCGGACAAATAAGATTTTGTAGATTCAATCTTACCG 108 | GTTGCAGGATTATACTTGGATGAAGAAATCCCATTTTCAATCTTAGAGCC 109 | ACCTTTGACTGCTTCGGCCTTTACCTTGGCATTTTCTAACTCTATCTGTG 110 | CATTAGCTAGCTCTTCCTCCGCTTCTGCGAGTTCTTTCTTCTTATCAGAT 111 | AATGACTGAAACGGATTACGGGAATCCAGTTCGTCCATGATGGATTGAAT 112 | TGTACTCGTATATTCGCGAAGTTGATCGGGAGACAAAACTTGCGCTGCCG 113 | CACTTTTCGCATTTTCAAATTGAGTAAGAAGGGAATTCAATGTTTCAGTA 114 | GACGTTTCCTTTAAATTTTCAAAGGCACGTATATAGTCCGGAGATTTTTT 115 | CAACTGCTCATAATCAAACCCCATGAGGGATTCACCCTTCATTTTTGTAG 116 | CCTGTGCTATTGAACGGTCTGTCTGCTGAACTTTCTCCGTTTTGCCTTCC 117 | TTCTGAAACCTCTCCCTTTGAATACGAAGAGCTTCAATATCATCATTGAA 118 | CTTCTTCTCGATTGCAAGCCTTTCATCGGTGTAATTCTGGTACTGCTCCA 119 | AAAGAGCTTTAGATAAAGTTGCTTCCGCCTTTTCCCTTGTCTCAACAGCA 120 | ACCTTATCATATTCATTTAGCGTATCCTGCTTCTTCTGTGAAAGGTCATC 121 | TTTAGTTTTTGTTTTGGGAACAAAAACAAGGCCTTCCTCTTTATACTTCG 122 | GATGTTCTTTCTCCCACTCTTTACGCTCCGTGTCCTGTTGGTCCTTTACA 123 | TATTCAGCAGCACGACGATCATTGTCAGCTTTGGCTTTCCGATAATTAAG 124 | TTGAATTTGTTCCTGCTGTTTCTTGAAACCTTCGTCCATGGCATCAATCT 125 | TAGCTTGAGAGAGTTCAAGTTCAGCCTGTACAGCTTTCTCTATATCCTGT 126 | TGATTCTGCTCATCAATCTTCCGCTGGAGCTCGGCCTGCTCAACTTTAAG 127 | TTTATTCTCTTCCTCCTTTTTCTTTTTTTTGGAGTTCAATGTTTGTTTAT 128 | CATTCCCTGTCAATGTCGCCAAAGCAGATTCAGCCTCTTTCAACTCTTTA 129 | GCTTTATCTTCAAGAACAGACTTTACGGTTTTACCTGCATCCACTTTGGT 130 | TTTACCACTCCGCAAATCTTCAATTTCCTGTTTAAGCTTTTCCACCTTTG 131 | CAGTAGCATCGGTAACCTCTTTTGTAATATCAGGAACCTTATTTTTTTTA 132 | GCTTCTTCGTCTGCCTTACCTTTATTCAATGCTTGCGCTTCTTTCAACAA 133 | ACGAATATTATTCAGCATCTCTCCTTCCCCCATAAGATTACTGACGGAAC 134 | CATCATGTCTGATAGCAACTTGTTTCTTTCCTGATTTGTTGAAGCGTTCA 135 | AGAGCAGCTTGATACATAGCTATATCTTTTGCAATCTGTTCGGCTGTCAG 136 | ATTGATATATTCATTAGTATCATAGCCTAATTTTTCATGAATATCCTTAT 137 | AAGTATTCTCAAGCAGTTTGTTATTCGCAATCATGCGATCAATATAAACC 138 | TGAACGTCATTACCTATTCTTGTTTCCTCCGTTGATACACCTGGAACAAT 139 | ATTAGTCGTAGTTGTATATTGTTTCGTAAGAGTATCCACTATTTTTTGAG 140 | TTTCAGAAGATAACCCTCCACCAGACTTCAAATCATTCTTTATCATCTGC 141 | ATAATCGCAGAAATTTCCCTTTCAGAGCCTTTCTTACCCCTGAAATTATC 142 | CGAATCTCGAATAGCTTTTTCCAAATCTCCAGTAAGTTCACCCTGCTTAT 143 | CCGCCCAATCTTTTTGAGCTGTAGAATGAGAATCCGCAATAGCTCTATCA 144 | AGTGCCGCCTGTTTAGCGGCCGCACTAACAGCCCCGTATGCTCTCGCAAC 145 | ATCATCTAAAGCGTTTTTTTCATCACCTAACCCCTTTAAGTATTCACCAT 146 | ACTTATCTAAAATGGATTTCTTTGCATCATCGTAATCTTCTGTACCTTTC 147 | TTTGCCTTATCTAGTTTTCCGAACAAACGATCTATTTCTGCCTGTTCAGC 148 | ATTCGTTTCAGAATTGAATTCCTGTATACGTTTGTTCAATTTCACTTGGG 149 | CCTTCTCTGCATCCGTCTGATAAGTTACTAGCTTATAAATTCCATAAGAT 150 | AACCCAACTATAGCAGCCGCAGCCAATACATAAGGATTTGTAAGCATTGA 151 | CAAACCTAACGCTTTTGATGCTGCAGCTAATCTCGTCTTGGCAACAGTCA 152 | AAAAGTTTGTTGATCTCGTATTTACATTCTGCGATACTGTATTAAGTTGA 153 | GTAGCCGCAGTTTCTGCCACTTTGCTCGCAGTAGAAGAGTTCGTGTAGGC 154 | CGTTGTTGCATTTGTTCTAGCTGCTTCAAGTTGTTTGGCCGCAGAATATT 155 | TATTGCTCTCTGCTGTTGCAAGTTGTGTCTCCGCTATTTCTATACTTCTA 156 | GCGTTACCTGTTTTTAATGCAGCATTATATTTCATGTTAGCTGCCGCTAC 157 | CTCTAATTCAGCAGCTTCAAAATTAGCAGCCGCAAGACTTGCAGTATTAA 158 | TAGCCTCTTCGTATTGTGACTTAGCTTGCAATGCCTTTAAACGCAAAGAT 159 | TCTACATTTGCAGCAGCTTCCACACGCATAGATGCAATTAATTCCGCTTT 160 | TGCCTGCGTTAATCTTCCACTTGCTACAGCCTGTTCCAGATCAGCATTAG 161 | CAGACTTTTCCTTGGCAGGGATTAATTTCGAAAGTTCTGTAATCTCAGCA 162 | GTATATTTTATACCAGTTACCGTACTCTGAACAGATGCAACTGCGATAAT 163 | AGCAGCTTTCTGAACTCCATACATAGCTATGAGAGCAGCGAGAGCAGTGC 164 | CGACTTCCTGATAATGTTCAATTAAGTAAGCTGTACCATCAAGAGCTGTA 165 | TTAATAACTCCATCACTTGCCTGACCTAGCTCATTGAACATCATATCAAG 166 | ATTATCACCTATGTTAGAAATCTTACCAGATACGGATTTAGATTGTTCTT 167 | GCATGAGGTTGAAGAACATTCCTCCCTTATTGGTAAGGTTGTCAACAACC 168 | TGTTCCAACTTGTCAAAACCAATCTTACCCTCTGCAGCCAAATCCTTAAC 169 | TTTATCCTTATTAACTCCCATAACCTTTGCTAGTTCGGAGAAAATAGGTA 170 | CACCACGCCCGGCAAATTGATTCAAGTCCTGTGTCATAAGTTTGCCTTGC 171 | GTCATACTTGTACCATAAAGATAGACCAGGTCACCAATAGGCTGACTTAA 172 | TCCGGCTGCAATATTTCCAAGACGAGTAAGTTTCTCTATGACATCCTCGG 173 | AGGCTGTACCATAGGCCACGAGTTGAGTTGCACTTTGGGAAACACCTTTA 174 | AGGTCAAAAGGAGTGGTAGCGGCAAAGTTTACGAGTTCTCCCATCAACTT 175 | CTGTGCCTTTTCCCCAGATTGTAGCATTGAGGTAAATTTGATTTCAAGTT 176 | GTTGGAAAGTACCATAAACTGAAACCATTTCCGAAGCAAACCGTTTCGCC 177 | AGATCGATAGATAAGAAAGCCATACCGGCAGCCTTCATCTGTGAGAAAGA 178 | CCTAGCTACAGACTGACTAGCCGCATCTGTATGGTCCTGCATCATGTCAA 179 | TATTCTGAACGTATTTCTGAACGTTTCTCTGCATTTCAGAAATATCCAGA 180 | GTAGCCTTAATACCTATTGTTCCCTGTGTCTCCATCTTTACATGAATTGA 181 | GCAAAATATTCGTTAGCATGAAGTTCCTTTGACTTTTCTTTTTCTCCTTC 182 | TTCCTTTGGCTTAGTACCAGGAATAGCCGCATTGAGTAACATGATATTGG 183 | AATATGACCTTTCATTGACAACCTCCTCATAACTCATACGGTAGTATTTC 184 | ATCACTCCGCTAATTGTTGACCAAGGGCTGTCGCTTCTGGTGTATTCGTC 185 | GGTTTCGTTGTCTCGTTTAGACCTTTTAGGAAAATGATAGTGCTTAAAAA 186 | AAAAGTGGCATCCATAGTCTGTGCCATATAGTCCTGCAACTTCTTGTATT 187 | TGCGAACCGTTAATCTTTTCTTGATAAATCCACCAAACAGCTTTCTTTTC 188 | CAGACGCTACGAAAGATCGTCATTACTGCGATATCAGACATCCTATCCGC 189 | TTCCTCATAATATACAAGAGTGGCCGACACGCTTGTCCGACCGTTTAGCT 190 | TCGCCTGGTCTACTTCCTTCATATCCTTCGAAATAGAACCAATATCAAAC 191 | AACTGTGTAAACGTCAATGGCCTAACCATGAAAGGAATCATACCAAACCA 192 | AAGAAAAATAGGGCGCTCTGCAATAGTGTCGGCAACCTGCTTTTGTACAT 193 | TGTCTTTTTCCATCTTTACCTCAAATTAAAAAGTCCCGGCCCGTAATGAC 194 | CGGGACACCTGAAACAACCTTTTCGATGATGCCACAATGCTCGTTATCCC 195 | TACTCACATTTCAACAATCATCCTTTCACCCAAAAACTATGTAGCGGAAG 196 | CCGGATTCGAACCGGCGACACTTAGGCAGTAACCCGCAACCTAATGTTCT 197 | ACCACTGAACTATCCCGCTTCCCTTATCAGCCTTCCGGGACAGTGTAAAT 198 | CTTGTTACGTGCCCCACATACTTCCTCACCAGTCTTATTGAGATTAGCAA 199 | GTTTCTTGAATTCAAGATTGAAGTTAGGGAAACCAGATTTACCGATGTTT 200 | CCTGTTTTGGTGACTTTTACTTTCATACGGGCCCATTGGAAGATACGAGA 201 | CGGGAAATCTTGGAATTCTTTCGTTTTTAACTCCACGCCTTGATTAGTGA 202 | GAGTGAACCCGGGAGTTTCTTCATTCCACTCTCCGTTCTTCGTATATCCC 203 | ATAAGATATTTGTAGGCTTCCTCGCCCATGTCGTAAGTTTGGACTGTAAA 204 | GCCCTCACTACCGGCATCAGACGGAAGAGAAGCATAGAGAGTGTTCATAT 205 | CTTCGACCTCAATATCCGTATCTCCCGGTGCCTGATCGTTGAAAGACATT 206 | GAATCCTTCACAATAGCTTTAACAAGGAATTTGGCAGCTACCTTTTCAAA 207 | GTCTGGAAAGGTCCCGGCTGTTTCTCCGGATTCGAGAGCCGGAGATAATT 208 | TTAGGTATTCAATACCATATACTGCAGTTTTTGACATAACTAATTTATTT 209 | AATTGTAATACGATACTTTGATTTTATAGTTCTGATAACTCGTCCCGTCT 210 | TCATCAGGAAAGAACGAATCATCATAAAGAGAGAATTCAGCACCCAAACG 211 | AGCTGTATAGATATTTCCTTCGGCATCTTCCGTTTCTTTGAACAGAGGCA 212 | AAACAAGTGCTGAAATATGGTCTATCCTTCCGCTATCCGGTTCGCCTGTA 213 | TCTGCATCCTTCACATGAATGTTGATATTAGCATAACCGTACTGCAGACC 214 | GCTTTCTTGCGGAAATGAAAGATGATTGACTACAATGTATTCAGAACCAG 215 | AGAAATTAGTCTCTCTCCTGTTCTTGAAAATCCGCACACCAACATTTCCG 216 | GCTGCGAGTATTTTACAAATTTCAGTTATAGCCTGTTGTCCTGTCATTGA 217 | TTAAATCCCGCTTTAGAAAGAATCCTCCTAATCTTAGTTTGCACTTCCCG 218 | TTTCAGATACTTTTCAGTAGATGATAGTACATCATACCCTCGGTTTTCTA 219 | CAGGTCTGGCATAATTCATACCTGCTACAATTATCAAATCAAAACCAGAA 220 | TCACCAATCATCTCCTGAATCTTATAGTCAGCATGAAAAGCCTTTTTGT 221 | 222 | -------------------------------------------------------------------------------- /test/mVCs/SRS050752_LANL_scaffold_33630.fasta: -------------------------------------------------------------------------------- 1 | >SRS050752_LANL_scaffold_33630 2 | TGTTTTCTATTTTGACTTTCTTCTTCTATTGTAGCTCTTATAGAATTACT 3 | AAAATCTTCAGTATTAAAATATCCTATTTTAAGCATATCAAGAGATTCTT 4 | TTAATTTAGGAACTCTATTACGAAGAATATCTTGCCATGCTTTATCTAAA 5 | TCTTCTTGTTCTTTAATCCAATCTTCAACTTGAGTTGCAGCATTAGACAT 6 | TCTTGTCATAGTAAGATAATCAACTTGTTGAGCAATAAGGTCAACTCTAT 7 | CGTTATAATCATTTTGTGATTTAGGTTGAATATTTTCTAAATCAGCTTTT 8 | TTATCTTGAAGAGCAACTTGTTTATCAATTAAATCTTTAACATTATTAGG 9 | AGCTTCAGGAATATTTTTATCAGATTCGTTAATAAGTTTTTCAATATCAT 10 | TTAATATAGTCTGAATATCTCCAGAAAGTCTTTCTGCTTGATAATCTTTT 11 | CCAAGACTTTGATTAAAAATATTAATTATAGATTGTCTATTATTTTCAGA 12 | TAAAGGATTATTATCATTTAGAAATTTAAGAAGTCCTCTTTTTCTATCAT 13 | TATAAATTTTATTATATTGATTTTTAGCTTGTTCAGAAATATCTGGATTA 14 | TTATTAACTTCTTCTTGAGCTTGATTAATTTCATTTAGTAATTTAGAAAC 15 | ATGTTTATCAATAGCTTGTCTTCTATATTTATCTATTGAACTTATATCAA 16 | CATTATTTTTATTTATTTCATTTTGTATAGTATTAATTCTATCCCCAAAA 17 | GATTCAATTTCTAATTGTTCTCTTGTAAACTCTCTTGCAGCAATTTTGGC 18 | AGTATATTCACTTTCTATTTCACTATTATATAGTACGTTATAGAGATTTT 19 | CAGCATATATATCTTTAACTTTATCCATTTTAGCGAAAGCTTGATTAGTA 20 | AAATCTTCTTCAGATTTAGTAAGTTGAACACCAGCTTCTCTAAAATATTC 21 | TTTAAATTCAGGACTTGTAATATATTCTTTTAATAAATCATAAGTACCTG 22 | CTTCATAAGCGTTAATAGCTAAATTAGTAAAATAATCATCAATAACTTGT 23 | TGTTTTTTTATTTCAGCTTCTTCTGGAGTAAGTTTTCTATGAATATCGAC 24 | TCCTTCATCTTGAAGTCTTTCTCCAGTAATAGGATCTTCAACATAGTCAT 25 | CTGGAGAAATATAATCATTTAACATAGTAAGTTTATCAACAACATCTTTA 26 | TTTAAAGCAGCACGGTCTTGAATTTCTTTATTCATTATTTTTTCTTCAGC 27 | AGTAAGAGTATTTAATATATTAGCATCAGATTCTTTACCTTTTAATGTAT 28 | TAGCTTTAATACGCCTTTGTAAAGCAGAAAGTCCTTTACCAGCTCCTTGA 29 | AAAACCATACCTCCAACAGCTCCCCAAAATGCTTGTTCCCATATTTTATC 30 | GTCAGTAATATAACTTTCAATTGTACGAGGAATAAAATTAGGATCTAAAT 31 | ACATTTTAGCAACTTCTTTACCTTTTTCAGTTTGAATACCTTGATATGCT 32 | TCTTCAAAAGCTTCAGTAAGTTGCAAAGTACCAATAGTACTTAAAGGATG 33 | TTTAATAGCTTCTTTAAATTCATCTGTTCTATCTTTCCAAAAACTTCCTT 34 | TAGGAATATCTGTACTGGCACTTGGTTGACGTGTATTTGCATTAGCTTTT 35 | TTACGAAGATTTTCAATTGCTTGTTTATTAGAACGTCTAATTCTTGAAGT 36 | AGGTACTGCTTTACCAACTTTACCAAATAATTGACCAATACCTCTAAATT 37 | GCAAAATATCTTGACCAAGCATAGCATAATCATTAATAAAAGTTTTATCC 38 | GCAGATTCTCCAGCAATATATCTCGCTATTTGATCAATAGTTTTACCATT 39 | TAATTCAGGATTTCTTGCAAAGAAGTCTTTCCATTGTTGATTAGTATATC 40 | CTTCAAGTTCTTGTTTAGTAGATTCATAAGTTTCTGTCCAAACACCTCTT 41 | GCTTCCATATAATTTTCCATAGTACGAGAAAGAACAGCATTAGTAGTTAA 42 | ATTATTAATATATTTAACAGAATTATCAAGACGAGCAACTGAAGGAGCTT 43 | TAATACCAGCACCTTTCATAGCTTTATAAGTAAGTTTAGCTAAACCTCTT 44 | GTAGAAGCGTTATATGCTCTTCCTATTTTATTAATTTTCCCTAATGCTCC 45 | AATAGCTTTAGTAACACCAAGAGTAGGCAACATCATAGATAAAGTACTAA 46 | AAGCACTTACTCCATTATTAGCCCACCAACCAAAATCACCAAATGCAAAA 47 | GTAGCATTTGGATCTTTTTGATAAATCTCAAATTCATCTCTAATAGTATT 48 | TTGAATACCTTCAATATATTCACTTACTGGATTAGTATAGTCATTTTCAT 49 | CAGTAAAAACTTGTCCTACAGCATCTACAATATTACTAAGAGAAAGAAAT 50 | GAACCAAGAACAGCTTCATTAGCAACTCCTTGTATTATCATATTACCAAG 51 | TTGTTCAAAAGCAGATTGATTTTCTGCACGTTGACGTTTTAAACTTTCTT 52 | CAGAATCAATATTATTAACAGTAATATCTTGTTCTTCAAATTTTTCTATT 53 | TCACGAGGACTATATCGTGAAGTATATCTAAGTTTATTAGCCATTCTATT 54 | AACATCTTCAGCAAAATCATCACTCATTGTATTAGAAACAAGATAAGGGG 55 | ACTCTTTGGCCCCCTTTTTAGTTTTAGGATTATATTTAGGATTTCTTACT 56 | AATTCTCCATTATTTATAAAATCAATAACTTTACTCATATCTTATATATT 57 | TAATTTACTTCCTAAATCTTTACTTAAAACAGCATAATAACGTTCTAATA 58 | AATCAGGTCTTCCAATAGAAGTTGTTATAGTTTTTGCAATTTCAAAAATA 59 | CGTCCATTTAATCTTTCAATAGCATTTTCATTATCTAATTGTAAATTTCC 60 | TTGTACGAAATTATTTTGAATATCAATATATTCATTCATAGCTGAATAAA 61 | TATCTACGGCTGCTTCTCTATTAATGTTAATAGCTGTATTTCCATTTTTA 62 | TAAGTAAATATATTACCACCATTAGCTATTAATTGTTGAGCACCTAATGT 63 | AGGAGTTTCAGAACTTTCACTAAGATTAGATGTCATTGCGTAAGCGTCCA 64 | TTTTAGCAATATGATCTGAAGCCTTAGTATATGGATTATTTTCAAATGCT 65 | TCTTGAGCTTCATCATTAACTAATCCGGGAATAAAATAAGTTTTTGGAAT 66 | ACCTGTTGGTTTACCAGTATTATCTAATTTAGGATAAATCGTTATATTAG 67 | TACCAGTACCAAAAAAAGGATTATGTGCAGAATTAAATACAACTCTACCA 68 | TTTCCAACAGCTGCTACTATTTCATTACCTTTATCTTCTCTATCTTTAGT 69 | ATTTGTAATTTCTCTAAAAGTTCCATATTGGTCATCATTTTCTACAGCAA 70 | ACATTTTAGTATTTCCAAATCCATGAGCTATAGTTTTCCTTCTTAGTTCT 71 | TCTTGGTCAATATTAAGTCTAAGACGATATTCTGTTTCATCAATTTGACC 72 | AGTATTAAGTTGATGTAAAAGTAATTGTTGATAATTTGTTTCACCCGGAA 73 | GAGATTGATGACCTATAGTAATTTCATCATAATTATCAAGTTTAGTACTT 74 | ATTTTTTCTTGTTGTTTAATAAAATCATTAGAAAAATTAAGAAACTTTTT 75 | ATCGGCAGCTTTTTTATATCTATTATATAAATATATATTACCAAAACCAA 76 | CAGCTGCATTATGTGCAGGATTTAAATTATAATATAAAGGAACTGTATAT 77 | TTACTATCTTGTTGTGATCGAGGAATTATAGGATTATATTCAGCATCTAA 78 | TACTTGTACACTAATATTATCTACATTACCTTTAACAGCAGCATTAACAG 79 | TATTAGATAAAAGTAATATATTTTGATAATATTCTTTTGGAAGTCTAATA 80 | TAAGAAACACTTTTTCCGTCAATTTCTTTTCTTCCTGTATTAAAGCCTAA 81 | ACCAAGAAAACCTTCTTCATTATTAGAATTTAAAATTTGAATAGCTTGAT 82 | TATATTCATCTGTATTATTAAAACTAACATCATAATATTGACCTTTATCT 83 | CCAAATTCAATTTGAATATCTTTTAATAGTTTTTGGTCATATGGATTATC 84 | TTTGTTAAAACTACCTCCATTTTTCATTCTATTAACATAATCTACTAAAT 85 | ATTTATCATCTCCTTTTAAATCTTTAGTTAGATTATCATAATTCATTGTA 86 | GTTTCATTATATTCTCTAATAAGCTCATTACTTTTAACTCTAAAATCTAC 87 | AAGTTGTTGTTCTGTAGCACCATTATTTTTAAAAATTAAATATGCTCTTT 88 | CAAGAGTATTTTTCCAACCATCTGTACTTGCATTAGTCATATCGACATTA 89 | ACATCTCTACCAACAGCAGTTTTAAATAGATTATATAAATCATTCTGAAT 90 | ATTTTGTTTTTTACTCATTAATTCAGAAGTCATATTATAATTAAGAGTTA 91 | TTGGTTTAGTATCACTTGTTCTATTTAATGATTTTATATATTCATTATTA 92 | AGTTCAGCATTATTTTTAGCAGTTTCTGCTGATTGTTCAGCAGCTTTATA 93 | AGTTTTTAACCCATTTCCATAAGTAGTTTTACGAGTAGTATTATAATATT 94 | CAGCAGCATATAAAGCAGGAGATATTCTTTTATTTAAATATTGATCTGGA 95 | GTAAGAGTTATACCGTTATCATCAGTAACATCACTTATTATATTATATTC 96 | TCCGTTAGTAGCATTTACAGCTTTTTTATGTTTCCAAAGAGCAACATCAT 97 | AATCTTGTTGAAGACTTTCTTTAGCACCCGGAGTAGATTCGATAGCTGCT 98 | CTAATACCAGCTTCTATTTTACTTCTATCAAGTTTTTCAAAAGCATGAGT 99 | AGTATCGTCGTAATATTCTCCATCAAATACTTCATTTGGATTAGTAGTGG 100 | GATTACCATTTTTATCAAGCCAACGAACTTGATTATAACTACCAGATTCT 101 | CTTGCAGCCCATTGTAAACCCTTAGAAATCAAAGAAGATAAATCTACAAC 102 | AGCAGTAGGAGAAGTAGTAGGAGACCATTTTGTTCCACTAATAACTTTTC 103 | CAGTTTCTTCATCAACAATATCTTTATAATAATAAGGATTTTTTTCCAAA 104 | AAATATTCTTTATAATCTTCAGGAAGAGTTTTATCATTTATAACTCTATT 105 | TTTAAAATCAGTATAATCTTTTTGAGCTTGAAGTCTACCAATCATTCCAG 106 | CATTAGAAGCTAAATTACCAGCTTTAATAACTATATCATCTAAAGCTGCA 107 | GCAGAATTACCAAATACAGTATTATTATCAACAAGTTGTTGTATTTCAGA 108 | AATCTTTTGTTGTCTCCATTCATTTTCTGCTTCATTAAGATCTAATTTAG 109 | CCATTTCAGCTTGAAGATTAGAAGCAGTTTTAATAGCTTCTTTATGGCCT 110 | TGTTCAAGAGTATTAAAAGTATTTCCTAAAGTATTTAAATCTACTGTTGG 111 | AACATATTCTGTATTAATATAATTAAAACCTTTCATATAAACTATGTTTT 112 | TAATTGTTTTTATTTCCGTATGCTCTCAACCATGATTCTATCATATCATT 113 | TGTTATACCTCTTACACCAAGAGCTTTTAATATAATAGGATTAACATTAG 114 | GATTTGCAGCAGCAATAGCTCTAATATTATTTTCAGTAGCTAATCGTTTT 115 | TCAAGATTACCTATAGCATTTTGTACTCCAGCATTAATACTATTAATTAA 116 | CCTTATAGTATTTTCAGATTGTTTTTCGATAATAGCATTTTCAAAAGCAT 117 | TTTTCTTTTCTCTCCAAGCATTATAATTAGTAATATTTTGATTTGCAACA 118 | GCTTGTTGATTAAGTTTATCTCTATTAATTAATCCAGTTTCAATATTTTC 119 | TTTATCGCCGTAAAGATTATTAAGTAATTTAATAGTATTTAATCTACTAC 120 | GTTGTTTTCTACCTAATGCAACTCTTGAACTTGCAGTATTAGCATCAATT 121 | TGTCGTTCATATGCTTGTTGTTGATCTCTAATAGCATCAAGTTGAGGATT 122 | AATATTAATACTCGTTTTAAGTTTAGCAGGAATTAAATTAATAGGAGCTG 123 | CAATATATTTCATTTTATCTAATGCTTTTCTATTAGCATTATATCCTATA 124 | ATACTTCCAATAATATTTGAAGTAATACCAATACCATCACTAATTAAAGA 125 | ATTATAAGTTCGTTTATTCATAATATCTTGCTTATTATCATGTTTTCGTT 126 | TAGTATTTAAATCTACTCCAGTAGTAGGATTAAATCTACCTTTAGTATCA 127 | AGAATATCATATTTAACCTTTTCTACGGGGTTGCTATAATTAATAATTGG 128 | TTGATTTATTTTATTAGCTAATTCATCTTCAAGTCCTAAACTATAAATTT 129 | CTGGATTAAGAGTAACAATTTTTTCAATCTCTTCAGTACCACCATTTTTG 130 | AACTTTATTCGTTCCCCCGTAGAGGGAATCATTCTTAGAATTGTCTTACC 131 | ATTGCTTGTAACTGTATAAACTCCACCATTTTTAGCACGTTTACGAAGTT 132 | CTGGATATTTATCATAAACTTTAGCTTTAATATCATTGCGTCCATGAAGT 133 | CCTGCAAGTCTTAATGCATCAACAGCATCGGCTTTAGTAGGAATTGGATA 134 | ACTTCTATTTTTACCAGCAAAATCTTTTTTATCTACTTTAGGATAAGGTT 135 | TAGATTTAGAACCATAATCTTTAGAACGACTTAAACCACCCATACGTTTT 136 | TTATTTCTTTTTTTATAAAAATTATTAACTAAACTATCTCTATTAGCTAA 137 | ACCAGCTTCTCTATATATTTTATTAATTTCTTCTCTAACTTCATCATCAG 138 | TACCTTCAAGAATAGCTTTTTGCATAGGAACGTATTTTTCATCTTCAGGA 139 | TTAAAATATTCTCTTGCAGTTCTACCGCTTCCTCTATTATAAATCAAATT 140 | AGTAATTAATGCTTCTTTAGTTTCAGTAACATTTCCTTCATCATTATAAT 141 | ATTTACGAATAAAATCTATTCTTCGTTTCGCACTTTGGTTAGCACTTTTA 142 | ATTCTTTTAAATCTTAAATCTCTTTCATCTTCTTCAGTAATATATTCTCT 143 | TCCTTTAGAATCTTTTTTAATTTTATCATTAATATTACCTCCAGTATATC 144 | TATCTACTCCCATTCCAAAATTATCTTTATCAAAACCTTTACCTTTAGGA 145 | GCATACCATCTACGATTAATTCTATCAAATTCTATACTATCAGGATTTTC 146 | AGAATGATTAATTAATTTACCAACTTCAGTGGTATCATAATAAGGTGTAT 147 | AATCTGGACTAATAATAGGATTTTCTAAAGTAGAAATATTATTTGCTAAA 148 | CTTTGCATTTCTCTAATTTTTTCAAAACTATTTTTCTTAGTACCATATCT 149 | ACTTTTATTTTTTCTATTTCGATTATTCTTAGTACCATCATCGTTAATAT 150 | TATTAACATCTTTATATCTTTCTTGAGCATTAAAAACTTTATTAGGATTA 151 | TTTCCTTTCATAACTTTTTCAGCAGGAGATTCACCATTAAGAAAAGGAAC 152 | AGAACTAAACACTTTAACTTCAGTAGGAGATATGTGCATAACTTCTCCAT 153 | CTTCAACTTCTAAACCAGTACGAGGATTCTTGCCGATATCAATACCACCT 154 | TGTTCATGTTTTCTACCTTTCATATAGTAATAATTCTTTTTATTAGGAAT 155 | AGGTATAGCAACACCACCACGAACTATATTAGGTCTAAGTCTTTTATTAC 156 | TCATAATCTGTTATATTGTATATTTTGACGTTATATAAAGCCTTATAACG 157 | TTGTCTTATATTGAACTTGATTAATTATACAAGAAAGCATATTGAAATCA 158 | ATGTAGAGCTAATAATAGCTATTATTTACGCTTTTTCTTGCCTTTGCAGC 159 | CTCCCAATTTCATTTGAGCGAGTCTATCGGAGTATTGGTTATTATTAGGA 160 | ACTTGTTGATTAACATTTTGAGTAACAGGTTGAGTAGAAGAATAACTATT 161 | AGGAGTAAGAGAAGTTTTTTGTTCATAATCAAAACCATCAGCTTTTTTAA 162 | TCATTTTAGGAGTACTTGGACCACCAATTAAACTATTAGCAACAGATCCA 163 | ACACCAGAAGCAATTCCTCCAACAGTATCATTAAGATTATTACCAGTAAA 164 | TTGATTTGCGATAGTAGAACCGAAATTAGCTTTCTTTCTACCACCGCAAG 165 | CATACTTCTTTTGATTTTTAATTCTATCTGTATAATTACCTTGTTTAGTT 166 | TTCATTTTTCCACCATTTTTTAAAACAACTTTCTTTTTATATTCATCAAC 167 | ATAATCTTGATTAGCATAACTTTGAGTCATAGCTTGTGCAGCAGCTAAAC 168 | TATCTTGTCTATATTGTTCTTCTTGTTGCATTTTAAACGCTTTTTCTTCT 169 | GCTTTTCTTCTTTTAGCAGCACCAATAGCAGAACCTATAATACCACCAAC 170 | AGCTCCTATAATACTACCTAAAAATGCTTTATCACGTTTAACAATTTTAT 171 | TTTTCATAACTTACTTATTTTATAACTAAGAGATTCAAAATCAATACGTC 172 | TATCTTGCATTAAAAATTCAAATTCAACAATAAAGTAATTACCATAAAGT 173 | CTACTCATAACAGCAGCAGATTGATCTTCTTCATTGCCAATCATATTTCT 174 | AAGATAACTAAAATTCCAATTACCTAAATCCCAATAAGGTTTTTTATAAT 175 | TACCAAAAATATTTTTATGTTCATTAGGATCAATGCTTTCGTTATCAACA 176 | GTAATATTTATATCATTAGTGTTAACATTGTCATTATAAACTCTAAGTAT 177 | TTGACCAGCATAAGGAGTATCTAATTTCTTTACGGGGAATGGAACATCGC 178 | CTCTTACAGATTCATCTACTTTATATAATTTATAAGTAATATATTCTAAA 179 | AACTTAACAATGTCATATCCTTCATTAATAATAAAAGACAGTTTACAACT 180 | ATTATTAAATCCTTCAACAGCATTAGCATAACCATAAATATTAGCATAAG 181 | TACAATAATTATTAAATGCTTCAGTAAAATTATAAATAGTATCATATACT 182 | AAATTACCACTTTGAAAACCATTAATAAAATAAACTCTATTTTTACTATT 183 | ATAAGCATCTCTAAAATAATAACTATGAGTAGAAATAAAATTTTGAGTTT 184 | TATAATTATAACTAATAACTAAATTACGTTTTTGAGTAAAAATACTACTA 185 | TCTTCATTTTTTCTAAAAATATCATAATCGAATTTAATAAGTAAACGATT 186 | ATTTCTAATATCATTAGCAAATCTTACATTATTAGGTTTAGCTTTAACAA 187 | GCCATTCTACAATATCATTACTAATAATAGCTAATTGATTATTATCAAAT 188 | CTGTAAATATTATTATCGTCATTATTATAAAATATATAGCCAAATTGGTC 189 | AACAATAGCGCTTCGCTTATCTTGAAGACCTCCATAACCTAATTCAGAAG 190 | TAAATACTTCTTTATAAGCAACATCAAAAGCGTCTGGTTGATGAAGTTGA 191 | ATATTTTGGTCAATAGTTTTAAGTTCATTATTTAAATCAAATATAAAAAG 192 | ACTATGTTCAGTATGAACTAAAACTAAATTACCAATTCCAACTAAATTAG 193 | TAATAATACCTTTATTTTCAGTAATATTTTTATATGCTTCTAAAGAAAAC 194 | TTTCGCCAACTATTTTCTCTTGATTCATCTTGAATAACGTTACTTCTACG 195 | AATAGTTTTATTATAAACATCAATATCTTTAATATCTTCTCTATAATTAC 196 | TATAAGTTTTAGGATTAAATTGGTCAGCACTACCTTGTCTATTTTCAAAA 197 | AGATCAATAGAGTTAGCTGGTGTAACCATATAGCCTGTTCTATATTGAGC 198 | ACTATCATTTTCAGAAGCAGGTTTAGTTACATAAGATTGAGGTTTAGGTT 199 | CATTTTTAAAACATTTACTTTCATGAAAAACTGTATCAATAACAGGCATT 200 | TGTAAATAACACATAAACGGCCTATCATTTTCATAAGTTTTATTATGTTC 201 | CGGAGAAATAGTAGTAGGATAATATTGATATTCGGCGTTTTGCATAGTCA 202 | CAATACCATTTGTTTCATTAAATACAACACCTGTATCGGCATATATAATA 203 | GTGCCACTATAAGTATAAACACCATTAAGACCAGTATTAATAATTCCAGT 204 | ATTATTTTTGTTATAAAAAACATCAGTAAATTTAATAAGAGTTTTATTAT 205 | TATTATTATTATATATATTAGGATTATCTTTAACTAAAGAAACTCTATAC 206 | AAATTAATATCATTATTTTTCTTTTCAGTAGCATTAACAAAAAGATCATA 207 | TTTATTATCAATAACTATACATGTTCCTACACCAATACGATTATCTTTTA 208 | CAGAATTAGCAACAGCTAATTTATAATTAGGCATAGGATATAATTTTTCA 209 | AAACCATAATCTTGTAATTGAACCTTGTTCATATCAGTAACAAATCCAAA 210 | AGGAGCATTTCTTTGATAATAATTAATATTAGGAATATCATTATAATCGA 211 | AAACATTTTTACCTTCAATTCTAAGAAAATCAAAATCTAATTCTAAAGTA 212 | TCATCTATATCTAAATTATCACAATAAAAATTTATAGTATTAGAACTCAT 213 | CGTATTTAATGAATCTTTTTTAACTACATTATCAGTATTATCATATATTC 214 | TTAAATTGCCATTTATAATTTCTAATTCACTATAATTACCAGTAATACTT 215 | GCAACAGTATTTATTAATCCATCAATAATTCTTCCAGAAATACTTCCTCC 216 | GCCATTTTCAATAACACCATAAGCTAAATTTCCATCTGTTATTTTATTAT 217 | TAACTATTTTAGCATTATATATAGTGCCGGAATATAATTTTACAGTATTA 218 | TGATTATTAATTCCTTTACTAATAGTAACATTTACTAATAAATAGTCATT 219 | ATAATTAGTATCTCCTTTAACTATAATAGTATCTGTATTTCTAAAATCAT 220 | TAATAGTAAGTAGTCCAGTATATTTACTTCTTTTTTCAAATTTTTCATAA 221 | GAAATAAAATATCCAACATAATTATTAGGTATATTAATATTATTAAAATA 222 | AGGACGATAAACTCTATGACTATTAACATCTATGTTATTAAATGGAACTT 223 | TAAATAAAC 224 | 225 | -------------------------------------------------------------------------------- /test/mVCs/SRS023352_LANL_scaffold_83757.fasta: -------------------------------------------------------------------------------- 1 | >SRS023352_LANL_scaffold_83757 2 | TCCTTATAGGGGATTTTTCGTTATTAAAGAAATTTCAGTTGTATAATATA 3 | ACTGTAATTCTATGGTAGTTTAATTAATTTTACATAAAGGAGGATATTAC 4 | CATGAAAGAATTAAAATTGATGGATCAATATTGCGTTGAGGTTGTTGTAA 5 | AAGGTATCGCTAAAGATGATGCCAAAAAAGCAGCTGAGCTAATGGAGGCA 6 | TTCTTTATGCAACCATTAGACCATCTTACTGAAAGTGTTGGATATTTAGT 7 | TGAGCAGGTGGTTGATAATGATTTTATCAAAGACCTAATCTCTAAAGATC 8 | CTGTGCGTGTGGAGATGGACGAATTAGTCCGCCAAATAGGAATCGTATTA 9 | TTCTTACCACTCAATAGAGTGAAAGAATACGATTTGGTTATCGGTGGACT 10 | GTTAGCATCCGCTGTTGCTAAATATGTATCTGATAATAAAGATACATTAA 11 | AGCTAGCGGAGCCAATGTTTGATCTATTATCGGATGCTGGTCAGGTTAAA 12 | CAGCTGATGACTTTCGACGGTGTTAGATATGCCGATAGAGTCATCAATCT 13 | GTCCGAAGCAAAAGAAGAGCCAAAAAAGGCTGATAACAAAAAGCAACCTA 14 | AGACCAAGACCGAAAAGAAGGAGAAGCCTAAAGAGAAAAAGGTTGATCCT 15 | GAATTGCTCAAAGTAGTCAATTATGATTCCATCCCTAAGAAACTTAGGGT 16 | TGTAATCGAAAAAGGATTCGAAAATGCTAAGATAAAAGAAAATATCTTAG 17 | CACTCGCATCTAAGGCTGGCAAGCCGTTATATTATGATGCAAAAGCATCA 18 | AAAGATGGCTTGTTGGTATTGAAACAGGTGGATGAACAAGCAAACACCTA 19 | CACTTTGGAACTACCTTACACTAGTAAGATAGAGGTCGAAACTGATAAAG 20 | CTTCAGCTTAATTTATAAAGACGGGTAGCCAATCCCGTCTTTATTTTTTG 21 | TATTCTACAAGGACTTTAACTATCTTATGACGGTTAATTTTTCTTGGAGG 22 | AAGCACTATGGAAAATTTTGAATCATATACTAAGATAAGCGAGGAAGTAT 23 | TTGATTTTGGTAATAATCTGATTATGAAGATTACTGTAGCATTCAATACT 24 | ACAACACTAAGAAATGGTAATACTAAGTTTAGTCCATTACATAATGAGTA 25 | TACTATAGTTAATAGTGGTAATAAGATAACCACGAATCTTAGATATAAGT 26 | ACTATATGTCTTTGACTCAACGTGGTAATAATAATGTATCTATAGATTTA 27 | ACTTGGGAGAACTATGATGAGTTCTGTGAGCTAATAGATACTATTCTTGA 28 | AGTCTGTGATGTAAATGCAGAGGGTTCACCATTTGACTACGTACGTGGTA 29 | AAGATGGAGTATCTTATGACTTAAGATGTAATTCTAATACAGTAAGACCT 30 | ATGCTTATGAAAGACTACCGAGGTGCATCATTATACTGTGTACCTGTGGT 31 | TATTGATAATAAGAAGACTGGGTCATTCTATGCTGGTGTAAGTTTTGTAT 32 | TTAATGAGTCTTCAGAAGATTCATTCAATGTAACTATAAACCGCATCAAA 33 | GGATTTAAAAGATTCTTATCTACATATAATCCATTATTACATGCTAGTAC 34 | TATGGCTAAGTATATGGGTACAACTGGTTTACTTGGAACTAATAATATCT 35 | CATTATAAACAAAGAAATATCCACTATGAGGAATTTCCTCATAGTGGATT 36 | TTTTCTATTATACTGTGTACATAATTGGTTGATTGCCATTCGCTGGGTTG 37 | ACATAGTTCTCTTGTAAGAACTGTACAATCTCTTCACGTCTTGATGCTTG 38 | TTGTTCAAGAGAAGATAACTTAAGATCGATATTAGCAAATACTGTCTCAA 39 | TACCATCAAAGTGTTTTAAGTATTCAAATAACCAAGTTGCTACATCAGCT 40 | GTAGCCAATCGTTCAAATGTTTCCATCTTAGTTGGTTCAATAGTCATTAG 41 | GTTAGATGGGTGTTTAACGAATACACCTAGAGTCATTTGGTCTAGGATAT 42 | TGGATACTTGACCTGCCATATTCATAGTTACACGAACCATATTAGGCGGA 43 | ATGTATTCAACGTATACGTTATTATTAAACAATGATGCAATGTTTGAATA 44 | TTGTTGAGATAGCATCATATCATCAAAGCTTAATGCTTTAGCTGACATAA 45 | CGTATGTACCATATTGCTGTACACCAGTTCTTGTAGTATCCAAGTCTTCC 46 | CACATAAGATCTTTAACACCAAGAATTTCATAGTTCTCTGGAATATGTCT 47 | ATCAAGAAGATAATAGTCTCCACGTTGATCGTCTTTAGTCAACAAGACTC 48 | TAATCATATGAGGGAAATATCTACTAAACGTAGATAGTGTATCTGGAATG 49 | ATTACTTCACTAGCCCATTTATCTTTAGCTAGTTCAGGCGGTAATCCTAA 50 | TGGCTTTGTACCTAGACGTCGTTCGATCTTATTAATGACGTCTGTCATTC 51 | TATTATATGCCATGCCTATTTGCCTCCTTTAATGGTTATTTTGGTTATAT 52 | ATCATAATGTTGAGGTGATAGATATTATGCGTATTTCTTATGAAGTGGCC 53 | TCTAAATTAATGAGGAAAGCTGCTATTAAAGTTTATCTTAAGTACAACGG 54 | GATTATTAATCCATCCCACCCATACACTACATTACATGTTCTGGATACTC 55 | CATTACGAGAAGATCCAGATGCCTATGCAAATACATCTGTATTTGGTAAG 56 | ATCAGTGTAAGCTTACCAACCATATTCAAATATGGTGAAGATGAAGATAC 57 | TATAGAACGGTATATAACTAGAGTCACTGAGATTACTTTACATGAGTTAT 58 | CTCACTGTGAACAGGCTCTAGACATTTATCAATTACATTTCCAAAATAGA 59 | TTGGTTGATAAATGTGAGGCAGAGAATGAGTATAGAACTGGTACATTTAT 60 | GCTTAATAGGTTAGATGAATTAGCTAAACTATTAGGCTACCAAATAGATG 61 | TAGACTTTATAAAGACTTATTATATAGACGAGTATTCTGATCATAAGAAC 62 | TTTGTCTACAGAAATCCTGCTACATACCCTATATATTTGAACTATGTAAT 63 | GCTAGGGGATATGACTAATATCCCTAGAGATTGTGATCTATATACAGGGC 64 | TAAAAGAATTTGGTGATTTACCAGTAAGACGTAATGGTATATACATACCA 65 | TCCCATAAACTCTTTGAGTATTATGGTGAAGTATATGATAACTACTGGCC 66 | TATGGGTTGGAGATTTGTAACTCCAAATAAGATAGCTTTGATAGTAAAAC 67 | CTAGGTAGAGTCAATGACTCTACCTAGATTCTTTTTATTTTTTTCTTAGA 68 | AATTCTTTTCAGCGTAGCTTCTAATTTCTTTTAAGATGTAGTCTTCTGGT 69 | TTCATAACCAATGTAGAACCATCTTGGTTAAACATTTGGATTGTACCCTC 70 | TTTGGTAACAGCAACGCTATCATAAGAACTAATACCAAATGCTTCTGCCA 71 | TGATATCTAAGTTAGCAGATTCAGTTTTAATGAAGTCTTTAACTTGTGGG 72 | CAGTTAGTAATAGGGATAATAGAACCTTGGTAAGATTCTTCTACTATAAC 73 | TTGGTTACTATTTATAGAAGTTGTATCTACATCAGCAGATTCAGTAATAA 74 | GTTTTTCTACATAAGCTACTTTATGGGAAGGGTAGATTACACGGTCCCAA 75 | GTGATAACTTTAATATTTTTTACATAAGACTTACCACCATTAACTTGCAT 76 | AGTACCTAGAGCACGTAAACTGAAAGATGGTTTTTCTCCATCCATAAGGT 77 | CTCTATTGAAGTAGTCACCGTATTGGTTATTAGTGCCAGTAACGTGAGCT 78 | TTAATAAGATTACCCTCATTCCAGAGTTTAAGATATTTACAGCAAACTAA 79 | TACTGGATCGATAGTTTGTTGACGGGATAACTCTTGGCTCATAGGGTGAC 80 | CTAATTCACCTTTAAGATTACCAGTTTCAAGAAGCTCCATAGCACGACTA 81 | GCACGCAATTCTGGCAATAAGTCATTAGGTAAGTAAATACGTCTATTACG 82 | GTTTTGTACACCTAAGTCTTGTAAAATAGTTTGAGCAATGATCTTACCAT 83 | TATTCTCAGACACAATTTCAGAAGATGCGATAGCCATAGGAGCTTCGTGG 84 | ATAATGTATGGGATGTTTTTAATGGACATCTATATAGTACCTCCGATTCT 85 | TCTTATGGGATTAAAATTAACTATATGTTTCCCTTATAAGTGCATTCTGG 86 | GTAAATTAATTAGAGAACCTATATATAATCATCAATTATTCATAGAAAGT 87 | GAGGGTAAAACGTAAAAATGCTAAGACGACTAAGACAACGTAAAGCATAC 88 | TTAGAAAGTAAGCGTAAACCTAGTGGGGTTATCATGGCTTATGCTTATGA 89 | AAAAGCCAGGAGAAATCCTACAGAGGAAAATTTGAAAATTGCAATCGAGA 90 | ACCATTTAAACTTGGATGCTAACTTAGATGAATCAGTAGCTAAATCTATT 91 | GGTTTATATCTTGATGCATTAGAGATTAATAACCCTGTACATGTAAAGAA 92 | ATACTTTGGCCGAGTATTAGAAGGTGTACGTCGAGTACAAGATCCTGAAC 93 | GTATCCGTAGAAGTATGAAGAATATTCTTGCTAACCGTACGGATGCAATC 94 | AATGAAAGTACTGAACTTACTAAGCATCAAAAGAATGCTTATATTCATGC 95 | TGTAGAAAAGATTCTTAATGAGGCTAATGCTCTATGTACTTATGACCGAG 96 | TTATTAAGAATCATACAATGATTAATAAACGTTTCAATACAGATAAGCTT 97 | ATCTCTGAGAATGTATTCAATGAAGTACAATCTAAAGTGTATGCTATTAA 98 | GTTTGCTGAGTTAATTGATACTTACAAGCTTCCTATTGAAGATAAGTATA 99 | AGATTACTCTAGAAAACTATTTCTATTTATTAGATAAGTATAACTGTGAT 100 | TATGATAGATATGCTGTACTAGAAGCTATTACTGGATACTTCTTCGTTAG 101 | AGATACTGATAATGTATTACAAGAAAGCTTTAGAAAGATTATCAAGCATT 102 | CTTCTGTAGTTACTGAAGCTACTGAAGAAGATACTGATCATATTGATAAA 103 | GACTTCTATGATGACGGTGGTAATGAATTGCTCCGTAGTAATATTATCCG 104 | TACTTGGAGAGCATTAAAACTAGATGGCGAAACTGGTTTCAAATATAAAG 105 | AGTTTATCTGTAACTCTACTAAGCCAGAAGAGTTCGCTATGATTCTATCT 106 | AAGAGCCTAGTTCTATCTGACTATATTCGTAAAGAAATCTTTGATTTGGT 107 | TGTAACTAAAATATCTTCTCTCCAAGAGGGTTATGATTACAATCAATTAG 108 | TAGCTATCTTCAAAGGGTATGTAGAAGAATTAGAACGCCGTGATATGAAA 109 | GAGTATCTTTACGTATTAGGTGAACTATACTATGCTTTAGAATGTGATAT 110 | CAAAGGTATCTTTACTACACCTAGTAAGGCTAATCTAGATACTGCAGAAA 111 | AAGTACATATGGAAATGAGTTTCTTAGATACAGTTAAAGCTATTGGTGTA 112 | AAACTAGATAAGAAGCTCACTGAGTTATCTGATAATGAAAAGATGGCTAG 113 | TCGTACTTTTGATGCTGCTATTAAGAACTTAATGTCTGCTGTAACTAAAG 114 | ATACAGAAGATAATGCTAGGGAAGAAGTTATTGCTGATAAGTTTATCCCT 115 | AAAGCTTCTACTATTATTAAACTAGCTATCACTACTGGTGTATTATATAT 116 | GGTAGCACCAACGTTATCTGTAATTGGTTTATTTGGATGGTGGGTAACTA 117 | GACGTCAAGCTTCTGCTGATGAACGTAGAAAACTTATGGATGAATTAGAT 118 | ATCGAAATCAATATGTGTAACCGTTATCTTAAAGATGCCGAAGAAAAGAA 119 | CCAATTAGAAAAGATTCGTAATCTTATGAAGATTAAACAAAAACTTATCC 120 | GTGAAAAAGAAAAGCTTGGATATACTATGGTAGTTAAACACGGTGAAGCT 121 | ATTAGTAAATCTAAAGATGAGGATGATTAATAATGAGCTTGTTTAAATCA 122 | GAGATAGATCATCCATTATTTTTTAGTGATGATGATATATATGTAAACTT 123 | TGATAGATTTGACCGTGGTAAAGGATTCAATGTATGTTTTATACTAGGCT 124 | ACCCAGCATCTGGTAAGACAACACTATCATTCGAATTAGCTAAAAAGCAT 125 | AATGCTGAATTATTGAATTTGGACGCTATAATCTATCCACAAAGTATTGA 126 | TTGGTTGGTTGATTATTGTAAGAAGCACTATAAAACTTTTTATGAGTTTA 127 | TTAATAAGAACCCTAAATACCTAAAGTTCATTTATACATGGGCAAGAGTA 128 | TTTGCTGATGGGGAGAACCCTATGACCCCTGAAAAGAAACAGCTTACTAT 129 | TGAGCGTAGAAGATGGATTATTAAGATAATTGAATTCTGTATTTCTAAAC 130 | CACATAAGATAGTCATAGAAGGTGTAGATTTGTATCCTATATTTACAGTA 131 | CATCCAGAACTATGTGAATACCCTATAATTATTAAGGGTACTAGTAAACT 132 | TACATCAATGCTCCGATATGTGAAACGAGACCTTGAATCTGGAGTAGGGG 133 | TACGAAATGTATTAGATCTAATAGAGATGTATGGGCAACAGTCAACCAAG 134 | TTAAATGATTTTAGAATAAATATGAGAGTTTTTATGAAAGGATAATATAT 135 | GGGATTCCTTGACGAACTAACTAATTCTATTATCCTTGAAGCAGAGGATA 136 | ATAAGAAGAAAAAAGATACCCCTGCTGAAGATGATGATACAATGGAACCA 137 | GATGTTCCTGAAGATGGAGATGAAGTTCCAGAAGATGATGATACTCAAGA 138 | AGAACCACCAGCAGATGATACAGCTGATGACGACACCGATGATGATGTTG 139 | AACCAGATGATGGTGATGATGAAGTTCCTACTGATGACGATGATACTGAT 140 | ACCGGTGATGGTGATACAGATGGTGGGGATACTGCAGATGATGCACCAGA 141 | AGATGATGGAGTAGAACCTGACGAAGGTGATGATATTCCAGCGGATGATG 142 | ACGGTGGAGACACTGCTGATAGAGCCGCTGATGGTGGTGACGATACTGGT 143 | GATGATATTGAACCTGATACATCAGAAGATGGTGAAGATGTACCAACTGA 144 | AGACGGAGATGATGCTCCAGATGCTGGTACTGACGACACAGGTGATGATA 145 | CTGGTGATGGTGATGATATCGAACCAGATTCTGGTGAAGATGGAGACGAT 146 | ATTCCATCCGAAGATGGTGATGATGTACCTGATGCCGGAGGAGATGACGG 147 | TGGAGACACTGATGACTCTGGAGATGGTACAGGTGATGCTGGTACTGACG 148 | ATGGTAGTACTGGTGGAGACCCTAAATTAGATACTGATATCAAAGCCATT 149 | GAAGATAACCTTTTCAACAATCTAAAACCAGAACAGAAAAATATAGCAAT 150 | AAAAGAACTTAAGACTAGATGGATGGATTTGTATGATCAAATCAATCGGT 151 | TTATTACTAAGATCGATTATATTGCTAAGACTCCAGACAATATCAATATA 152 | GTACTACGTGTGACTAAACTTACGCAACAATTACGTGATACAGTTGAACA 153 | CTATATCATTAATACGTTTGCGACTAAGTCCTATATTGAGAATAAGTCTG 154 | AACTATTTTACTCGCTGCTTATATTAGATAGACTTGTCAAACTACTTGCT 155 | ACTACAGTTAAAGAAGACGATACAGAAAAAACTGAGTGACCAGTCTGCCC 156 | TGTTTAGCTAATATAACAATATATTAAAATGCGCTAATTTGAGCATTAAT 157 | GTTTAAATTAAACTATCCTGAAAGGAGACTACAAATATGCCAGTTGTAGG 158 | TAATCAATCTAGCGATGTTGTATCCAGCCGTTCTTTCCATAAAGGTGCTG 159 | AATACGAATTCGCTAATGCCATTGTAGAAATGGCGGAAAATATCGCAAGC 160 | GAAACACAAACAGACTTCTTTACTGAGTCTGCTCGTTTAATGCGTAATAA 161 | GGACGCTGCTCGTGCCCTTAAAAACTTCTTCGTAAATGAATCTGCTGATG 162 | CAGACGAATTTGCTGACAATCCAGCAGGTCTTCGTGACCACGAAATGATG 163 | ATGGAACAACTTTTCGAAAATGACCGTCAAGGTATCTTGGAATATGCTTC 164 | CATCGGTTCTTACAACCCTGTAATGGGTCTTGTGTTACCTTTACACAAAA 165 | ATATGATGATGAATAACGTTTTCGATAAAGGCGTTATTCCTAAAGCTGTA 166 | GCTAAAACTCCTAAGTTCACTTTGAGCATGGAAGTGCGCAAAATGATCGG 167 | TGTTGATGGTACTGAAATCGATATGTTCACAGAACAAAATCGTATTTTCG 168 | AATTGATGGAATCTTCTGCTCCTACACGTCGTGTATTCGTAGAAGTTAAC 169 | CCAACTAAACCTATCATCCCTGGTGGTGCTGACGAAAAAGCTATGCGTGA 170 | ATCCTTGAACTTGGCTCTTTATGGTGCTAAAGATGGTTTCAACAAAGCTT 171 | ATGATGCATACTCCATTACTACAGCTATCACTGGTATCGTAATCGACGGT 172 | ACTAACGCTCATGATGGCGATGCTATCGTAGTTGACTCCAAAGCTGTAAA 173 | TGCTGCTGGTGAAACTTACAAAACTGTAGGCGTTAAAACTGCAGCTAATA 174 | CTGGTGACTTGGTTATCGCTATTAGCCCTCGTCGCTTCGAACCTGGCTAT 175 | GGTGAATTAGATCGTCAAATCACTACTAAATTCAACTTCGTAAAACCTGG 176 | TACTACAGACGTAGTTGAAGGCTACATCACTGGTTACACTAAAAACAATC 177 | AATTCATGATTTCCTGTGTTGGTTCTGCTGACATTAAAGGTGTAATCATC 178 | GATTCCAAACGTGACACTTCCAACGCTATGATCGATACTCCATCCGTACG 179 | TTGGGATGCTGTAACTCAAATCGTAGAAATCCCTAATGCTAACCCTATCA 180 | ACGTTCCTATTTCTCCTGAAGAAGTAAAAGACGTTCAAGCATTATACAAC 181 | GTTGACCAATTGTCCAAAACTCTTGGCTTGATCAAAGACGTATTGGGTAA 182 | CTACAAAGATGACAAAATCCGTAAAGAATTGGACTTGTCCTTCAAAACTA 183 | TGCCTGCAGCTAACAAACTTGCAGCTACATTCGACTTCTGCCCACCAGAC 184 | ACTTATAACATGGATCCAGTAAACTGGAGACGTACAATGTTCATGGACCA 185 | ATTAGATATGTATGTAACTACATTGCTCCAAGTATTGAACGATCCTAACG 186 | TAACTGTTTCCGTTATCGGTGCTCCTGCATTGATTCGTCGTATTACTCCA 187 | GTAGAATACACTTACCAATCCCCATCCAGCATTGGTCCTGTAGAATTGGA 188 | TTACAAACGTACAGTTGTAACTTCCGACAAACGTGTTTACAACTTCGTTT 189 | CTTCCGATAAACTTCGTAACGATTCCAACTTGATCATCGTATTGAACCCT 190 | CGTAACACTGACCGTGTTATCTACACTATTTACGATTATCAATTGTACTT 191 | ATCCAACGAAATCCGTAACAAACAAAACTACGCTCTCCCAGCTGTACATG 192 | CGTTTGAACGTTTCCACTTCTTCTCCTATCAACCAGTACAAGGTCGTCTT 193 | CGTATCTTGAACGCTTCCGGTCTTCGTGATACAGTTCAAAATACTAAACC 194 | TGTAACTAAAGATTACAACGAACGTTACGACATGAACGATCATGGTTTCT 195 | ATGATTCCATCCGTCATGACGGCACTAAAGTTGTATCCCCAACTGGTTAC 196 | CCTTACCCTGTAAAATACGACTTGGCTTCCAACCCTCATTCCTACTCTGT 197 | AGAAGCTGAATTGACTCCAGCAGCTCAAGCAGCTAAAGCAGAATTGGATG 198 | CTATGCGTGCAGCAGGTGTAACTTCTAAAGTTGAACCATTCGAATTGGAT 199 | CGTGTAGTTCGTGAAACTGAAAAATAATATCCACATTCAGTAATACTATG 200 | CTGATGGTGAATTAGTATAGCATTCGTGGTTTATTGTAAAAGAGCAGGCC 201 | TATAGACTGAGAGTCTATAGGCTCACTCTTTGTTTTCACAAGGGGATAAG 202 | AATGGATAAAGCAAAAACAAATTATGATTTTAATGATCTCTTAACTATAA 203 | TTGATTCATTAAAACAAGATGCTGATCCTGATGTCCTTCGAAACTTTGCA 204 | TATGAATTAAACATGTTCTTCAGAGATGTCAAATGTGAGGGTGTCTTATA 205 | CACTAATAACACAGACTTAGACTTCTTTGGTGTGTATGTACAACCAGTCT 206 | TAAAAGAAAAGGATGTATATCCTTTACTTATATCTGATTATACTACTACT 207 | ATTGAGAAGTACTACGTTGAATTGGACTCTAAACTATTTAATCCATTGCT 208 | AGGTTTGACTAATAGAGAGATCCTCGCTATTATTCTACATGATATAGGTT 209 | CAATGATTAACTCATCTGGTCCAATAGATCGTGCTGTAAAAGAGATTGAT 210 | TTGTATCTTGATACTACAAATGATGTACTACGTACTACAGACAATGTAAA 211 | CTACGTAGCTATACTTACATTTGGATTGAAAGACTTATTACATAAATTAA 212 | CCTCAATCTTCACGGCGGACTTGACTAGCAACGTTGCTATTGATGACTTT 213 | ATTATGTCTTGTGGGTTCATTAACGAACTTAATAGTGCTATTAGTAAACT 214 | CAAAAAGTTTGGCTACTTAAACATGTTCTCCGAAGGTGGTTCTCCTTCTG 215 | CGATTATTGCATGGACAATCCGGATCTACAATGATATCAAAGGTCAACGT 216 | ATCCGTACTATACGTTTACTACGTAAAGCTGCTTCTTACACTCCAGTGCG 217 | TTTAGTTAAACGTGAAATGAATCATATGATTACTGCGTTATCTAGAATTG 218 | ATGATTCTTCTATCTTAGAATCTGTATTTGACGACGTTAAAATGAAATAC 219 | CAAAGTATGACCAAGAAATTCACAATGTCTTCTATTAAAGACATTGAGGA 220 | AGACTATTATGATTATGCTGTCACTCTTCAAAACGTTAATGACGAGGACG 221 | ATGCTCTATTACTCTTGCATAGAATTAATAGTCGTATGAGCGTTATCGAT 222 | GGTATTCTTAATGACGATAATCCTCAAATCTCTGACAGAGAACGTAAAGC 223 | ATTCGCTGATTTATATGAACGATATAACAAATTGCGTAATGACGTTGTAG 224 | CTAAGAAAGTATATAAACGTAACTATCGACGTATTTATGTAAACTACGGC 225 | GAAGATGACTAATAACAAAACAGGTTCTACCCCAAAGCA 226 | 227 | -------------------------------------------------------------------------------- /test/mVCs/SRS022602_Baylor_scaffold_3690.fasta: -------------------------------------------------------------------------------- 1 | >SRS022602_Baylor_scaffold_3690 2 | TAGGGGCGCCCCTAGTAGAGAGTATCGTTAATATCTAGATAAACTAAATA 3 | TCAGTTAACTGATTAAGCGGTGGCTACTTCAGTGCTTTTGCTCTCTTCAG 4 | CAGCTTCGCCTTTCAGCATAGCTTTGTAGATGTCAGCCAGACCTTTAACT 5 | TCGTACAGGAAGTAAGAAGAGAAGGAAGTGGCCGGCTCACGCAGAAGAGT 6 | CAGGATGTCTTTCAGTTTAGTGACACGGGCGCGAACAGCTTGGTTGTTCT 7 | CGATGAAACCTTTGCCCTCACGAGCGGTTTTGCTAACGGCCAGGTATTGT 8 | TTACGAGCAGAGGAAACAGCGCGTTGCAGTACCTTAGCAGCGTTAGAAGC 9 | TTCATCCAGTTTTTTGCGGATAACCATCATTTTGTCAATCAGACCCAGGA 10 | GAGAACCCAAGTCTTTTTCGATGGTGGCAATACCGAGGTTAGCCAGTTTA 11 | ACGTCTTCGCCGTCCTGTTTGAAGTTAGTAGAAACCACACCTGCGCGAAC 12 | ACCATTGCCTTCCAGATTTAAGGCAACCAGAACGCGTTTGTTGCGGGGCA 13 | GTTCATCAGACATCTTGATGGCCCAGTCTTTACCCAGTTTCACACCGGCT 14 | TTGGCAGCAGCTTCGTTACCAACAGTGTAACGACCACCAGAGAACGGAAC 15 | GGTGGCGATAACATCGTCAACGATTTGTTTACCTGCCTCATTGGCCAGTT 16 | CTTTGGCTTTGGCAGTTTTGAATACCATTTCGGTTTCTTCAGCCAGTTTC 17 | TTACCGATTTCGCCGAGTTTACGGGCATCCCAAGAAGCGGCTACTTCTTT 18 | AACGGCTTCAGAGAGCAGGGTAATGCAAGTAGTCGGAGATTCTTTCTTAC 19 | CGTCTACTACCAGGTTCAGAGCCAGGCTACGAGAAATCTTCACGTCAGGA 20 | GACAGGGTTTTGCCTTTAGCAGCACTGGCAGCTTCTTTAATGGATTCAAC 21 | GTATTTTTTCAGTTTGTCGAAATTGGCGAAGAGTTTGTTCCATAGGGCGC 22 | GACCTTTGTCGATAATCCAGGCAATACCATCCAAAATGGCATTCAGGATA 23 | CGTACAAAGAAGTCTTTCACTGACTGGATAGCGCCTTCAGTAGTCAGGGC 24 | AATAGCACCGGCAGAAGAGAAGGACTCTTGAGAGTAAGCCATAGCAGGCA 25 | TCTGAGCTTCACTCATGCCCAGAGACTTACCTACATAACGTACGTGTTCG 26 | TTAGCCAATTCGGCGTGAGCAATACCCATTCCACCCAATGCTTTAGCAGC 27 | ATACAGGTTTTTCAGGAGAGATTCGGTAGAAACAGCAGCTTCTTCAGCTT 28 | CTTCTACAGACTCCTCACCTTCGTGGTATTCGGCTTCTTCTTCTTGTACT 29 | TCCAGAAGAGCGGTGTTGAGTTCGTCAGCATCAGCGATGACTACTTCATC 30 | ACCAGCAGCATCTTCTTCTACTGCTACGGGCTCAGCAGGCTCTTCAGCGG 31 | CTGCTTCACCAGTTTCGGCAGCTTCTTCAGCAGCTTCTTCAGAAGCAGGA 32 | GCAGCTTCGCCTTCAGCGGCTTCAGGTTCTACGGCAGCCGGTTCTTCACC 33 | TGCGCCTTGTTCTACAGCGACTTCTTCGTCTTTGGTTTCTTCGGCGATAG 34 | CAGCCACGTCAGCTTCGGTACCATCAAGGTTAGTTACCTTAACGCCGGAA 35 | GCAATCAGGTCGAATAATGACATATTCAATATCCTTTTCAATGCAATTAA 36 | GTTTTAATAAAAGCTTTTGTTAAAAGTTAATCGTCTTAGTCCTTAGTGTA 37 | AACTGAGAAACCAAGCATTACTTTCCAACACTTCACTCTACGTAGAGCGA 38 | AGTAAGTCTCGAAAGAGACGAGCAACATACACCAAAGCCTGATTTAACAA 39 | GGCTTAAATCTGGTATAGTCATAAATGCATGTAAAATCTACTCGTGAATA 40 | AAAGAAGCTCTCCTTGCCCCCTAAAAGAGGGTAAGGAGAGGGTTTGTTTA 41 | TTACTCTTTTTCGTATTGTTCAGCCAATCTTACAAGTTCTGTACCGCTCT 42 | GATAAAGAGCAGCGTAATAGGCACGGTAAGCATTCACGTAGTATACAGCC 43 | AGTTTGTGTTCTAGACGATATACCAGTTTCTTCATGATAGAAGTAAGAAC 44 | AGCAGTATCAGTACCCATTACACCGCCGGAAATGAAAGCTTGCAAAGCAG 45 | CATAGCTGTTGTTACCATGATAGTGTTCTTTCAGTGAATCACTAAACGTG 46 | TTATTGGGTACTGAGAGTGCTTGATTCAGAAGCGTACCAGCAGCATAACC 47 | CATCTTAAAGGACAAGAAAAGAGGACCACAGAGAGCATAAAGAGCAAAGG 48 | GTACAGTCAGGCTACCTACTAGACGAGATAAATCGACTTTATTCCATTTG 49 | GTGATTTCAGCTCTTTGCTTATTCAAGTCAATATTCTTTTCAGAAAGCTC 50 | TTTTACCTGTTTCTTGAACTTAGCAGACAAACCATCTAGGTCTTTAGCAT 51 | TGGGTATCTGCTGCAAGAGTTTTACGAAAGACTCAAGCTCTTTAATCAGT 52 | TCGTCCTTAGTAATGGAAACACTTTTCACTTTGCTAGCAGCAGGGATAAT 53 | GAGACCATTATCTATATTCGGGTAGAGCTTACCTTCACCAGTAGGATACT 54 | TCAGTTCAATGGTAGAAGCATCGGAAATCTTAGATTCCCACTTTCTCATG 55 | CCTTTGTCAATACCAGTAGTAACAAAACAAGTACCAGGATTGAAGAACTG 56 | TTTGCTCTTCTCTCTTAACTCATTAGCTAAGGTTTCCTTATCCTTATCGT 57 | AATTAGTAACAGCGTAAGCTGTCAGTGCACTAATACCTTTTACGTAGGTA 58 | TTGAAGAAACCACCATCAGCAATCGCTGCTGCGTTAACACGAGAGAGATT 59 | GTCAATGACTTTAGCAATATCGGTTTTACCATTTACTGCTAAGGTAGCAC 60 | CATTCTTCAATACGAAGGATTTCTTCTCATTGTCTTCTACTTTCTTCAGG 61 | TACTCAATACTACGCTGTACACGTGTTAACAGGCGTTCAGCTTGATTGGC 62 | TTCACGACNTGTCAATGACTTTAGCAATATCGGTTTTACCATTTACTGCT 63 | AANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGAA 64 | GATGTCTTTAATGCCAGAGAAGAGCTTACGGAAGATGTTATCCGCTTCAG 65 | TAGAAAGCATATCGATGCGGGTATCGAGTTCTTCTACAGCTAAAACCACA 66 | TTGCTCTTAAATCCAGTAGATTCAGTAGAGACGTGGAGAGGAATCTTCTC 67 | CTCTACACCAAATCGCTGGTAAGCTAGAGAAACACGCTGAGACAAAGCAG 68 | TCACTTCAGTAGGACTGAGTCTATAACTGCTTTCTCTAGCCAATACGAGA 69 | TTAGCTTTCAGTGATTCCAGGGAGTCAATAGTACCCATGATACTGGATAA 70 | GAGTTTTACCTGGTCCTCATTCTCTTCAGTAATGAGTTTCTCAGGTACCG 71 | AGGGATGGATTTCCTCTGGTTGGGTAGTCTCCTCGGGAGTAATATCAAAT 72 | TCCTCTCTGGAGAGTAGTTCAAATAGCGCCATTTTCATTTAATCCTTTTA 73 | CTAATTAAAATGAATGAATTATCTAGATAAGAGAATAATCTCACAGTGTA 74 | TAGAGCTACTCTTCGTTAGAAGAGCAGCGAGTAATACTGGTATTAAGAGC 75 | TACTCTACTACCAAAAATAGGTAGTAGAGTAGTCTTTTCTATTACTTAGT 76 | GGACTGCTTATTGCTGTTACTACCAGTAGTAGTCTTTTTCTTAATTACGA 77 | TACGAGTACCAAATAAAGTCATTTAGTTAGCTCCTTATCCTATTAAGAAG 78 | ATTGTCTCTCGTAGTGTACGTATTGGTTTATCAGTACGCTACCATAGAGA 79 | ACGTAGAGTACATCAATCAGTTTACCAATACCCCCTACTTTCAAGCAGGC 80 | ATTAATCAGTTGTAGAGTACATCCTTCAGTATCAAAGAGCTTATCCAAGT 81 | CCTTCAACTCTACCGTAGGAGCGTTAGTTATCTCAGGATTCTTAAGATTA 82 | CCCCTTTCTGCTCGATTACTGAAGTAATCTTTAATCAGACCTAAGTGGTA 83 | AACACTACTATACCGATTAGGTGTAGTACTTACTCCTGCCTGGTACAATA 84 | CCTCACGAACCGTGTCACTAAACAAATCAAATACGTGTTTGTTGGCGTAC 85 | TTACTATTCCTAATCAGGAATTGGCGAGTTAAGTCTAGGTAGTTCTTACC 86 | CAATAGGTTAAGAGCCAGATTGATTACTGACTCTCTATTGGCAAAAGCTT 87 | CTTCACTACTGCCTTGGAACCAATGAGGGTGCTGGTAGTGCAAAGCGTAG 88 | AGGTAATCTACATCAGTGTTACCACGGATATAGAGCATGTCTCTATCGGG 89 | ATTAGCTATCGGAGACTTGTACTTCTCGTCGTAATAGTAGTAAGAAGGCG 90 | TATAGCGAAAGTCTTGTACTTCACGGGTTTTAGATAGACGAGGGATAGAG 91 | AATGAACCAATTGCTTGAACATGCATGGTATACTCTCCTTTTAGTAACGA 92 | GTGTCTAAAACACGTTTCTCGTGTTCGTGAATCTGATACTCGAGTTTGTC 93 | CAGTCTCTCTAATGCTTTCTCTTTCTGTCTTTCTAAAAGAGCATCACCTT 94 | GGCCATTAGCCAATTGGGTATTCATGTAGTCCAATTCAATCTTAATGGCT 95 | TCGACTTCTTCTTTAGCCAGTTTGTACTTGTTGTGGCGTCTATCCACTAG 96 | GTATACACCGGCGTAGTAGAAAGGATTGATGGAAGCAGAAACAAAGTTAT 97 | TCACGCTACCAGTAGGGTCTAACTTGAATTTGTTAAAGAGGGAGTTCTCC 98 | TCACCAGATTCCGTTACCGCTACATCAGGGATGTCTTTTAACTGTTTCTC 99 | AATGTCTTTTACGCTGGTACGAGACAGTACAGAAATGGTTTTAAAGAAAT 100 | TCAAGGTATTGGAATTGATGTACTTAATCTGGGCTTTAGAGAGGGATTTC 101 | TCTACCTTCATGCCACCATTGATTTCAGTCTGTTTAGCAATGATGAAACG 102 | GCAGTACTTCGGAATGAAGTCTGCAATGAAGTCAATATTGCTCGCTAGAG 103 | TAAGAATCTGGGCACGAGGATAGGTAATGGAGTCTTTGTCTACCGTAGCA 104 | GTAAAGTACTTATCCACTAAGGAAATCAGTTTATCAATGGTGCCTTCTGC 105 | ATTCACACTGATGTAAGCCAGAGCAGGGAATAGCTCCATTTTCTCAGTAC 106 | CATGGTAATGGCGTTTAATAGTCGCCAAACCAGACTGGTAATCACGATTG 107 | TCTTTAAAAGACAAATCTTTAGTGTTGTTAATACATTCAGTCACGACAGG 108 | AATCAAACCTTCCCGAATACGGGTACGGGTATCCGTTAGGGTTTCCGTGA 109 | TGTCTTCGGACTTGAAAAGATTAGCTACACCGCTAAATAATTCACCAATA 110 | TTCATTATCGCTTGTCCTAAGGAGGTTAATCAAGAATGGTAGAGAGTAGA 111 | GGCAGTATCTCTACTCTCTGGTATTACTCAGTATTACAGAATCGGTGCAC 112 | TACCCTGAGAGAGGAGTTTGAATACATCCATGTCGAAGTTCTTGTCATTG 113 | ACCTTCTTCTCCAGGTAGTTCATGGAGATTTCAGATACTTCTTCCAAACC 114 | ATGGTTGTAGATAAACACACGCTGGTAATCAGGATTGTAGACAATCAGTG 115 | TCATGCAGCCTGATTCCTCCATGAATTTATCACGGGCTCTCTTGTTTTTA 116 | TCCAAACGAGCACCAATAGCCGTTTCGATACGAGTAGCCGTGAGATTGGA 117 | GATAATCCAGGTATTGGCTACGGTACCGACTGAGAATTCACCGGTTAAGA 118 | GGGCAGCAGTTTTATTAGACTTATTGCGTTTCAATACTTCTTCGTAGTAA 119 | CCGGTAGTATCCTCTACTAGGTTACGGGCGCGGGCTTCTACCAAGTCACG 120 | GCAGAACAAGTAATCCCAGAAGGTATTGATGGTCTCACGATTCCAGAAGG 121 | CATTCCAGCGCTCGCTAAAGGTTCTGGGTTGTTTGGAGACACTGGCAATG 122 | GCTACCAGAGATACTGATTTCAATCCTACTAGAGTAGGCTTCAGCATCAA 123 | GGATACCGTAGCAGTCGCTTTATCACGAGAGATAGAGACATTCAAGAGCT 124 | TACCTACAGCTAGATTCTGTAGAGCATTGATGTCTTTACGCACATCATCA 125 | CTGGAGGTAGTGATGACATCGTGTTTCTCTTTAACGATAGTTTCATCTTT 126 | ATCGTTCTTACCGTATTCAGTACGGAAGGTATCTTCTCTCTTGATGTTGT 127 | CTTCAATAGAAGCATTGCCTCTCTCTACAGCTTCTTTAGCAGAACCAGTA 128 | ATGCCTTTTACCGCATCACTTAACCATTCACCAATCCCTTCAGTAGAAAG 129 | CTCAGTGACACCGGATTGATAAACTTCACCCAGTTTGGGGAAGCTTACTG 130 | GTAGCTGATAAGCGGCTTTTTCGTGAGAGAGACTAATGCCTTCAATGGCG 131 | TTAGTGGCCTTTGGAGTATATGAATTATTCGATATATTGGCTACCTGTAC 132 | CATGGTATCGAAGCCGAATTTAGCTATCTCAGCAGCTGCATCTCGTGTAG 133 | GAGAGTACTTACTTAAGATTTTGCCTACAGACACACCGTTAATGGTATTG 134 | TCAATAGAGAGGGCCACTACGTAGTAGCCGGCAAAGTTAGAGATTGCAGT 135 | GTGTACTAAGGTACCCATTTTCTCGTCATTTTGAATTTCTTTCTCAATGG 136 | CAATAACGGGTCTTAATTGCATTTCGGTGGAGTATTGACTCAATGACTTA 137 | GCACTGATGTCATGATAGTTGGCTGCAGCCATTTTAGCTACGTTAGCAGT 138 | CATTGCACTACTGGCTACTTTGGCAGCAGATAATCCATATTTCACTGGGT 139 | CCATATCAGAGTCCTTTTCTTACAGGTCATGTTTTAAATAAATGCTCAGA 140 | TACTGCTCTAACACCAGAGCAGTATCTAGCGGTATTATTCACAATTGTAT 141 | TTAGAAAGAGCAATGCAAATGAGTGATTTTGATTTAACCAAATACGGTGA 142 | TAAGGTATTTTCAGTAGACCAATTGTTAAACAAAGGGTATAATGAAGATA 143 | TCAGTAGAATGATAGACATGTTGGTGAAGAGTAAAACCGGTTTTACTTTA 144 | AGCGAGTCCATGACCAATACGTTCAAGGGACCGAACATCTTAACCAATAC 145 | CCCGATGCTTAAACCGAATACCAATAACAATGGTTACATTTTCACCACTA 146 | GGCCAGACCTCAACCTGACTGATGAAAATATTCAGGTAGAGAGAAGGCTG 147 | ATGCCTTTACTGACGGGTAATGCTAATTCCATCATGAGAGCGATTCGATT 148 | GATTCTCTCTCCTCGCTTAGGCGTATCGTTTAATCTACCAGGCTTTAGAA 149 | GTAATCCAGTGAGTAGACGGGGAAGATTACCCTGTCCACTAGTAGACCCT 150 | AACTATCCCTTTATTGCGGTTTCTGATAACAGCATAAAAACCTTAACCGG 151 | TTGGCCTTCCGGTCAACTGGGGGTAAGAGAATCGAATCCTGGTATCTTAA 152 | AAGAAGTACACATCATGGCTGATGGCCCTTCTACGTATAACGGGGTTTAC 153 | TCTTTAAACCTTTCTACCGTTTCCATGAGGGGTAATCCAGTAATGTATTT 154 | GTATTACTTCTGGATTCTCTACATTGGTTTTGTTTATTACCAGACCTACG 155 | GGGTGATCCCCTGGCCTGAGTATTTATACAATGGTAGAATGGATTATACA 156 | TGCCGTATCTATCGGCTCATAATGGATGAATCTAAAACCTATGTTACTGA 157 | GATTGCTGCTACGGGATATGCTATCCCCAGAAGCGTGGATATTGGTCCTT 158 | ATTTCGACTATCAGCAAGAGGAATCCAGACCTTTCATGTCTAAGACTACA 159 | GAGGTAGAATTCACTTGTGTGGGTGCTATCTATCTGGATGAAATCTTGAT 160 | TCAGCAATTTAACAGCACGGTTATGGCTTATCAGCCTGGCATGAGAGAAG 161 | TCGCTAAAAGCGGTAAAGGACAGGTAGTGAAAGGTAGAGGAGGAGATATG 162 | GTGGTTAAGGGTAGTTTTATTANTAAGAGTGGTAAAGGACAAGTCGTGAA 163 | AGGTAGGGGAGGAGACATGGTGGTTAAGGGTAGTTTTATTAAAGTACCCA 164 | AACGCTACCAGAACATCTTCAATAACCTCTGCTATCCTTTCATCAATCCC 165 | CGTACTCGTGAATTGGAGTGGTGGATAAGAGCTGATGTCTATAATGCCAA 166 | TAAGGAAATGATTAAGCTGGCGGATATTCAGTCCGGTCTCTACACGGGTA 167 | GAACCGGTAAGTAATGGAATGGAATAGAGTGAGTTTCGTAAGAAACGAAC 168 | GAAGTAATGGAGTGAAACGAAATGAGTAATGAGAATTTACTAGTCAGGAA 169 | CGTAGACAAATACGGTAGTTCTCCTGGCATGCTGCAAAGAGATGCTTTGC 170 | TCGCCATTAAAGAGATGTTGAATAACGAATACGGGATCATCAGTGCTGCT 171 | AACCCTGTATCGTTGCTATTAGAAACGTCCAGTATGCAGACGGCAGCGGC 172 | TGTCGGTAAGTACTGGTTGTTGAACAGACGCCAATACCCAGTCTCGGCAC 173 | AAACCTACGAGGATTTGTGGTATCACTTTAGTGAACAAGACTGGATTGGG 174 | GCATTTAGCTTACCTTCTACTGCAGAGTTTATTATCTCGTTTCATTACGA 175 | CGAACTCTTGCAGATGGTACAGCCAGTAAACGATGGGAGTGAAACTAAGC 176 | TATTGCGTATTCCTCGTGGCATGAGGATTACAGTAGGGGGTGTAGACTTC 177 | CTATTGGATTATCCGGTTAATATCGTGCAATTGAAACACGGTGGTTTTCG 178 | AGTGACTTACGATACCACTGAAAAGTCTCCTATTCAAGACTTAAGCAGTA 179 | ATGTAGTAGACCACCAAATCTTAACCTTTGGTGCCACTGGGGATGATGCG 180 | ATTAAACGCTTTAGCTTTACGCTACAGTTAGTACAGGTCACTGAGACGGT 181 | AGTAGAAGATGCGATTAATGCAGCTGGTCGAATTGAAATGGTGAAGAAGT 182 | TCCCAGATGACTACTACTTCTCACGAGTGTATACCGGTAATGATCAGACA 183 | GGCTGGACTGAGTTAACCACCACTCATTGCCCTGATGTTTACGATACCAC 184 | TAAACCGACTGCTTTCTTGAAGGTAATTGAAAACAACGATGACAATACCT 185 | TAACAGTTAGTATTCCGAAGATTTACAATAATATTCAGGTAGGTCCTGGA 186 | GGGATTATTACCTCTCCATTAGGGAGTAGACTGAAAACTGAAATCTACTC 187 | TACCTTAGGGTACTTAACCATGAATCTAGACGAATACGTACCCTCTCAGT 188 | TTAGTCATGACTTCTTTCCCTCAGGAGAGCGAAAAAGAGATTACAGTGGA 189 | TTGGGTAATTACAGCAGTGCATTAAAGAGTGTTAAGGCTGTTTCTATTTA 190 | CTCTCGTGACTTTATCTCTCAAGGAAGGAATAAGTTATCCTTCGAGGAAT 191 | TGAGACAAAGGGTAATCGATAACACGACTGGACCCAATGTGGTGCCTGTT 192 | TCCCATCAGTCTATTCGGGATAAGATTCAAGATAATCAGTTTAAGATTAT 193 | CAAGAGTGTGGACTACGTCACCAACCGTGTCTACTGGGCAATACGAGATG 194 | TACCTGACCCGACTAATGCCTCTCTGATTACTCCTGCAGCTGCTTCTATA 195 | GAAACACTCACTACGACGATTAGTGACTTAATCTCCACGGGGACAGTGAT 196 | TGATAATGGTAAACGAGTCACCATTACCCCTGATTCGATTTATCAGCTAA 197 | ACAATGGTAAACTCTCTATCATGAACAAAACGGAGATTGATAGAATAGTA 198 | GCGTTGTCTCCTGAGAATAAGGCTAAAACCGTTTCAGCTAAAGAGATGTT 199 | CTTCTCTCCTTTCCACTACGTAGTGGATACGGAGAATGCGACTATTAAGA 200 | TTCGTCCTTATTACCTAGACAAACCAGAGACTTTGTATAAGACTTATCTG 201 | GATAGCAATACGAAGCTAGACTTATCCTTAACCATTTCTCAGTATGCCAT 202 | TGAGAAGAAGGATAGCGGCTATGTCTTACATGTCACCATGAAGTCCAATG 203 | ACGAATACAAGCGTTTCGATAATAACTCATTGTGGGCTCAATTACTGGTA 204 | CACCCTTATCATGATAGAGGCTATACCTACATCATGGGTGAATTGACTGG 205 | TAGAACAGATGACAATGAGCCTATCTTCAGTTTTCCATTGAATACTCGAT 206 | TCGATATAGATGAAACCAATAGTCTTATCTTAACCAATGGGACACTGAAT 207 | AATGTCCGTGATGTCCACATCCCCATTGACTTAGAAACGAATGTAGAATT 208 | GATATTCGGCTTCTACGGAGATTACCCTAACTGGCAAAGAGCCCAATTGG 209 | ATAATAAGATTAACTTAAATCTCCTGGATAATGACCCTAAGGCTATCTTG 210 | AATGAAGGTATTCGGATTAAGCTAGGTAGCTATCTAGAGTACTTGTGGGT 211 | AAGAGCCCGTACCCATGCCAGTGATGTTACTTATCGTCGACATGATGCTG 212 | ATGTACCCTTAACCTATACGGAAGATGTATACGGAGCAGATGCGGCTACC 213 | GGCTCGATTCTCAATATCGTCAATGGTAAACCCCAGTATACGATTAAACA 214 | CCGTAAAGGGGAGAATGTACTGGATAGTAAGGGTAATATCGTCTATCGGT 215 | ATAAGAAAGGGGATATTTACCTAGATGAGAATGGTAATACGGTGATTTCT 216 | AAACCTAGAGAGATTATTCGTCGATTAGAGCTCACCATGGTGGATGCTAC 217 | CTATTGGTTTGCTACTGATGATATTGCTAAGGATTATCGTAAGGAATTGG 218 | TGGCTACGTTCATTGACTGGCTGACTGATGACCTACGTCCCTTGAATAGG 219 | AATACATTAGAGCAGACTAAGATTCTCTTCTATCCCTCTTCTACCATGGG 220 | CGAGATTAGAGTAATCTATAACGAGGGTATTGATACCTACATCAATGCTG 221 | CTCAATCTCTCTCTTTAGACTTAACCGTTGATAAGCAGATTTACTTAGAT 222 | TACGATATTCAAGAGAAGATTAAAGAGTCTTCTATCCGAGTGATTAAGGA 223 | AGAATTGAAGAAAGATACGGTATCCGTGTCGTCTATTCTTTCTCAATTGG 224 | TGAAGGAATACGGCTCCGATGTCATTGGTGTACAGCTAAGAAACTTAGGT 225 | AATACGGATAAGATTATCTCTTTTACCGTAGTAGAAGAAGGTAAGAAACC 226 | TACTATCCGTAAGAAACTGACTGTGAATAGTGATGAGACTTTGTCAGTAA 227 | GAGAGGACATTACCTTCAACTTTGTACTCCATAACCCTGACTCCGTCACG 228 | GATTAAGTCGTACATTACTTCGTAGTATCTTACATTCCCCAGATTCAATT 229 | AACGAATAAACGAATAACTGATACTACTA 230 | 231 | -------------------------------------------------------------------------------- /test/mVCs/SRS014271_WUGC_scaffold_25970.fasta: -------------------------------------------------------------------------------- 1 | >SRS014271_WUGC_scaffold_25970 2 | CATGATTATTCTTCTGAGGAAGAAGCTAAGACTTCTATCGCCACTGCATT 3 | ATATGGTGCATTTAAAGATGAGTTTAAAGATAAATTCACTCCAGCTCGTA 4 | TGATGGAAATCTGCAAAGAATATGTAGATAATTATGTAACCTTCAATAAT 5 | GATGAAGAAAATACTGAGGAAGAAGTTCACACAGCAGCTGATGAATTATA 6 | ATTTCGCGAAGGGTGATAAAATATGATTAATCAGCAACCTCGTTTTAATC 7 | AATTCTTAGAAGGCGTTCTGTATGGTTGTAATGACGCAGGAAGTATTCCA 8 | GATGCATTAGCATCTGGATATGCTGTAATAGCAGTAGTAGATATAGAAGA 9 | GGCCTACAAGTATGCTAATATACCAAACTTAGCAATCATGTCTAATCTAT 10 | TACCACCTCCAGAAGCAGTAACAGCTTATATTGATGGAGAAGCAGCTATT 11 | GGTCATCAGATCTATTATGAGTATTTATCTCATAAAGAACGTGAGTCTAC 12 | GATGGTCACTATTTTGCAAGCATTGTATGGTCACAGACCAAGTATTAGAT 13 | TTAGAAACTTCTTGATTTATACAGATTATGAACCAGATGTAGAGTTCAAT 14 | ATTCTATATACTCTAGGAGAGTTCTTTAAAAACACATTTGGTATTGTAAT 15 | GGCCCCATATAAACAATCTCATGCATATAATATTGGTACAGACCAATTTG 16 | ATTATGTTATTGCTAACCTACTATTCTCTAATGGTAAGATTAACAAGTAT 17 | GAGTTTGTGCGTATGCTTCCACAAGATGCAATGCCTACAGATATATCCTG 18 | CAGTGTTCTATTATCTGATATTAACTATCAACCATCTGGATTAGAAGATG 19 | GGTATAGAATTGTATGCAATTATGTAGCTCAACTTAGAGAAGAGATTGCA 20 | TCTAACTTTATCAAGAAATCTCCTATCATTCAATTGAATGATAAACTCAA 21 | TAAAGAAGTGGAGCAAAGTATCAATAATAAGATCTTTGAATCTCAATCTA 22 | GATTTGGTAATAAGTAAAAGATGAAGAGAACTCATAACGAGTTCTCTTTT 23 | CTTTTTTGTTTGGAGGATTTAAATAATGCCTATAGTTAGAACTGAAGAAG 24 | AATTAGAATATGCAAGACAACTTATTCTAAGTGATTTTATGAATTTTGGT 25 | TGGTTTAAAGTAGAGAACTCTAATCAAAAGGTAACTAGAGATCAATTAGA 26 | ATCTATTAAAGCCGGGGCTTATCAAGATATGTATGGAGAAGTTCAAGCAT 27 | TCTTTATAGCAAAAGCTTTATTGGATAATAAACAAAAATCCACTGAAGTG 28 | GAAGAAATTACAGAAGAAATGGAACCATTAGAGTATTCTGTAAAACAAGA 29 | AGTTGTAGCAAAGAATTATACTGATGAAGAAGATAAGATGCAAGATAATA 30 | AATTTGTAACGTATTATCTTGTAACTCAACAATATAAGAGTGGAGCATTT 31 | ACAGGAAAGCATCTTCCAACCCAAGATGATATTGATAGAAGTGTAGCATT 32 | AAATAAGAGTAGTAAATTCTCATATTTATTCTTAGATAATAGATGATATA 33 | ATCATATACTATAATCTTGAATAGAAGAAAAGGAGTGTGATTATATTGAA 34 | ACTTCAATTCATTAATATTAATGATATGAGATTGTTGGAATATGTAAAGG 35 | ATAAAGTAAGAGTAGAGAATGCACCTGTATTTAATTTCTATTCAATGTTG 36 | GATTTTGGATATAGAGTAGAAGCATTAAAGCCTCTTCCTAATATTATGCA 37 | GTATCTATCATATGCTAATTCTTTTAATGATGATAATTATACAGTTCAAT 38 | TTGATAAGGCTTATGCATATCAAATCCTATATAATGAAGCATCTTTCTTA 39 | GATCTTATGAAAATCATTAGTATGGTAGAGAATACAGAAACAGTTATAGT 40 | TGTAACAAACCATTCCCATCCTATAGTAGAAGCTATTGTAGATTCTCTTA 41 | TTAAATTTATCCAAGAACGATATGCTCTTCAAAGTTTTATTATAAATGAT 42 | TTAGATGATATCGACCAATTCGCTACATCTACTTTTGAAACAGAAGGTGG 43 | ATATCTAAACTATGTTGATGATCTTAAACGTATGGGTAGATATTGTGACC 44 | CACATCAATTACTGAAAGAATCTGAATTTTATATTTAAGGAGCATATATG 45 | GCTATATGGGAAAAGGATAGATATGTTGCTCCATATGAGTGGCTTATAAA 46 | TAGACACTTAAGAGAGTATGATCTATCCAAAGCTAATATAAGTCTCTTAT 47 | TAGAATATGGATTCATAACGAAAAAGAGATATGATGAAATATTTCATATG 48 | CCAAGAGAACAAAGGGAAATAACAGTAGGCCTAATGCAACGAGATGATCC 49 | TGAACTATCTAAAGGTTTGTCTAACTGTTTTAAAGATGCAAGAAGAAGAT 50 | TCTTTGAAATAAATCAGCTAAATCCAGATAATGTGTTATATATAGATAAA 51 | GACTCAATAACCACAATAGATACAGAGGTCCCATATACAAGATTATCCAA 52 | TAATCTTGAGTTTAAACTAAAGAATGAATACAGTAGTTTTTATAGATTAC 53 | AATTTATAGATTTTCTGTATTATTGTAATGGGACTGTTGAAAGGTTTCGT 54 | TTAAAAGGAGCTGGAAAACAAGTTCCTATTAAACATAAAAATCATTTAAT 55 | GCAATTCTTATTAGCTTTGGCTTATACTGCACAAACTGATAGTATAGAAA 56 | ATTGTATTTTAATGATAAAAGACTTCTATCATCAATATACTCATAGAATG 57 | CTAGAAACCAATTTCTATAGAGAGTTGAATAATCGTTGTATGTATAAAGT 58 | GATAAATACTGGATATCATACTTATTATACAGATGCATTGAATAGTATCG 59 | GATCTGAATTTATAGATATATCACACAATGCTGATATTTTAAGAATTCTT 60 | TATAGAATCTTTACTACTGAATATTTTTCAAAAAGATGAGGGCTATGGGA 61 | ACTTAATCCCATAGCCTTTTATTTTTTATCATTGTTATTGATAGGTTTTT 62 | GTTGATAAATAACACGATTATTTCCAGCTGCAAGAAGAGTGATATAGATA 63 | AAGCACTTACTAGATAAGATACTACCTAATCTATCATCACCATAATATAG 64 | TTCTAACTTCTTTCTAAATGCTTTAGACATGTTAGAAGCTACACTATCTT 65 | TAAGTTCTTGCATTAGAGCAATTTGTTCTTTTTCTGAAACATAATCGTTC 66 | ATAATATTTGGATGGAAGAATCCTACGTCTCTATTATAACATTCTTCAAT 67 | ATATAAATCTAATATCTTATCCAATTCTTTGAATTGATCAAATTCTATTA 68 | ATTCTAATAACTCTTTTTCTTTTTTGTGATCTAAATATTTATAAGCTAAG 69 | GTTAAGATATATAGAACAGTTGCCCATACAAATGGAAAGATATAATCTCC 70 | ACTAATAAGGAAGATTATAATAGATGCTAATAAAATATAGATCCCTTTAT 71 | GATCTAGTATATTTTTTATAATAGAATCTGTACCAATTCTTATATTTAAG 72 | AATAGGTTGTTAAAGAACCATTTTATATTATTTCGAAAATTATCATATTT 73 | GGAATAGAATTCAGCCATAGTTAAATTACCTCTCTAGTTTAGTTGACCAA 74 | TCATATAGTTTATCTCTTAGTTCTAAGAGCTTACTTGCTTGTTCTTCCTT 75 | AAATTTATATTTACCATCTAGAGAGTTGTTTAAATACATCATAAGCTTAT 76 | AAGCTATATCTCTATTTAGTCCATTAGGATATCTTTCTAATAGAGACCAC 77 | CATTTGCCAAAGATCATTTCTGGGTGAACGTATAGGTATTTATGATGATA 78 | CATTTGGTGGCATGTTTTACAAAGCATTACTACTGGAATATTATTTTGAG 79 | TATGTTCATATCTTAACAAATCTGATAAATCAAACTCAGTGATAGCTCCA 80 | TATGTATTTAAAATATGCTCTGTAATAATAATAGCAATATCATAGATATT 81 | AAGCATACAATGGTGCATTTCTAAAGATGCCATCTCTTCACCCTCATCAT 82 | TACCTGCTGTAATATTAGGATGGAATTGGCAACAATCTAAACCAATAGAA 83 | TATAGATATGCTTTATAATGCTTATAAGTTCTACTATGTCTGAATTCTCT 84 | AATAGCTGAATCTAGAAATGCTTTATATTCATCAAGGTCATAAGACCCTT 85 | CTTTAGTCAATGCAAATTCTACTGCATACTCTGAATTTGGAGAGGTTAAG 86 | AGCGGATTATGCTCTGCATTCTCTACAAATACATTTGGAAATACATTTGT 87 | CTGTGTATACATTCTGTTTAGCTCCCTTTATAATACTAACGGAATTATTT 88 | GTATGTTGCCCGCTGCAATTAGGACATATCCCTATAAAACTGCCCATCTC 89 | TGACATTAGATTAATTTTATAGGAATTTAGAAAGGAGAAGCTACTATGTC 90 | TTTACCTTTTTCTGAGGCTAAATTGACAACTCAAAATCCTTTCATAGATT 91 | TGGTGTTATATAATCTTAAGCTGTTGGCCTTTAATTCAATTATCAAAGAC 92 | CAGGCTAAAGCAGATAGATATGAAACTACTGAGTCTCTAAGGAATGCATC 93 | TTTATATATTGCATGCATAGAAAATCATATCGAATTAGATATGTTTAAAG 94 | GCATTCAATATCCTAGAGATTTATTAATAAAAGCTGGGTTAGATGAAAAA 95 | GAGCTTTGGGTTTATGAAAACTTTAAAGACAACTATTACATCCCAGATGA 96 | ATATAGACCTAAACTTACCGAATTATTAAGACAGTGGTTTATTGATACAT 97 | ATATGGATGATAAGGAGTTAAATCCTTATTATCGAAATCTTGTCGGATAT 98 | CCAGCGATTGATCAATGGGGTATTCCTGTAAGAGAGTTTGAATATATGTT 99 | CCCAGATTATCTAGAATATGATAAGACTGCAACATATATGCATGAACTTT 100 | CAAATGAAGTAATCAAAGAGTTATCTGGATTAGGTATCTTGGATGCTATC 101 | TTATCCCAATATCCAGATCATAAATATCTTAAATATAAAACTTATGGTAT 102 | TAATATTTATGAAGCTAGAAAGAAATTAGACTTCCAAATATTATGGTATC 103 | CAGAAGGTTCTGATGTAGACTATAGTGTTACAGAAGAATTCTTATTGAAG 104 | TATACTCAAAACCGTAAGTTTATGCTAGAAACAGTATATTCTTATGCTAT 105 | GGAATTAGAAGAGAAGAATTATCATGATATGATGATTATTTATCTCATCA 106 | TTTCTGTATTAGTAGATATACTTGTAGATATTCAATCTCATATTATCAAG 107 | AAAGATATTCTTGATAGACGTTGTATTGAATTTATCTTCTCTATGTATGG 108 | AGTTCCATATTATAGAGTAATTCCTATTGAATATCAAAAATCTTTAGCTA 109 | GAAACATTCATTCATTGTGCAAATACAAATCATCCACTACTGAGATGCTT 110 | AATATTATTAAACTCTTTGATACTAAAGATAAATACGGTATTAAGATCTT 111 | TAAGTATTGGCTTCTTAAAGAAAGAATTGCAGATTCTTATAATGGATTTG 112 | AATGGAAATCTAAGAAAGTTCTTAAAGGGAATTATAACCAAAATATTGAA 113 | GAAGAGCATATTACTGTAGATATTACCAAATCTCCAGAGCGTCAAATTAT 114 | ACCACATGATATTCTCATGTATAATACAAACGTTAATAAGAATATGGGTA 115 | AGAAGAACATTCTTCAATCTAAAGAATATAAACCTTCTAATTATAGCTTA 116 | GAAGCTAGAAGAGCTGCTGCATCTACTATTGCTGCTATTAAAGGTATTAA 117 | GTTCGACCTTACTTTATTTGGCGATTCTTTAAATACTACTTCTGGACTTG 118 | GTTATGCTGCTATTAATGGTGCATCACTATATGATATTGGTGGTAATTTA 119 | ACTTTAAAGAACAAAGAAACCAAACAAGACTTCAATGCTTCTATTAAAGT 120 | AAAGACTGCTTCTTATGTAAACCTTGCATTCCAAGAGATAGTTGGTAAAG 121 | ATCTAACTTTTGTTCCTAATCATCTTGGTTATGATTTGAATGGTGATCTA 122 | TTAGTAGATTATAATGGTGGACAATCTAAAGATATCAATGGCCATTTATA 123 | TTTTGATTATATTGGTATAATCCCATTCCCATTCGATTACTATCTTCAAA 124 | AAGGCAATGTGTTATTCGTTAGATTAGAAGATAAGTTCTTGGTTGAAGGT 125 | GTAGATTATGAGATCTATGATTATAACAAAATAAGATTCTTTAATGAGAT 126 | TCTTGATGGTAAAAAAGAAATTACTTACGATTTCTATTACGATAGATCTA 127 | CTAAAGATACTAAATTCAACGTTGATAAATCTTATAATTTCCAAACTAAA 128 | GTTAAGACTTATGAAGGTGCTAATTCTATTAATCTAGGAACTTTACCATT 129 | TGGTGATTTCTTCTTGAAAGAAAATCAATTAATTGTAACAGTAGACTCCG 130 | TGTTCTTAGCTCCTAATACTTATCATGTAGACTTAGCTACAAATGTGCTT 131 | ACTATTGATAACAGAATAGATACTATTGGTAAGAAAGTAAATTGTATATT 132 | CATTTATTCAACTTATTCTCAAGCTAGATTCTTTAAATCTACTACTATTA 133 | CAGAAACTGATAATCAAACTAAAATATATATCGATGAACCATTTAAAAAC 134 | TATTGTTTGAATGGGAATACTTTCTTTGTAATGATTGGAAAGAGATTCAT 135 | ATCTAATAAAGAATATGATATAAATATCTCTGAAATAGATGGTGGTTCAT 136 | ACATTACTCTTAAGAATAGTAATCTAGAAGCTGGAACTGCTATTGACTTT 137 | AACTTCATTTATTCTACTAATGCTATTAATGAGGATATTGAATTAAAGCG 138 | TAAGGTAATTAAATTAAAAGCTACAACAGATTACCAAAATGAGTTTAAGG 139 | TAACATATCCATTCAAGAACTATGTAGCTACTAAATATAAACACTATGTA 140 | AAATATTTAGATAAATATCTACCAGATGATTGGTATAGTATTACTAATAA 141 | CTCTCTAGTCATTGTAAATGATACTCTTGCTCTTCATAAAGATGATGAGT 142 | TAGAATTAGAATTGGTTTATATTGACAAAGATAGAACCAGACCAGAATTT 143 | AGTAATATTAAAGTTGCTATAACTCACTTAGTAGCAGGATCTGATAATCA 144 | AGACAGATTCCCTATTATCTTCCCAGTAGAAAACTACTTTACAAAAGGAA 145 | ATAAAGTATGTGTAGATATTGAAGGTTCTATGCTAACTGAAGGGATAGAT 146 | TATACTGTAAACTATAATAAGAAAAATATAAGATTACTTAAAAAGAAATT 147 | GTTCTTGAAAAAAGGTCAACAAGTAAATATTACATTCTTCTTTAATGGAG 148 | TTACAGAAAATACTTTGGTATTAAGCGAAGAAACTCATAAGATCTTTAAT 149 | CATGGAGATCCTAAGTTTAATATCAATTTCCCATTCTTCCCTTATATACA 150 | AACAGATCAAGGATTTATCACTATTAGTGAAAATTCTATTCATTCTAGTG 151 | ATGATATGGGTCTAACTAACCAGTTCCATGTTACTATGAATCCTAAGATG 152 | GTTTCTAATGCAGATATTAATGAAAACTTCTTATTCATTTATAATAAGCA 153 | TTATATTGATAATCCTAATCCAGCTCTTACAGTACAAACTTTAGAAAGTC 154 | CTATAAATGTATCTTCTGATGGATATATGGATATCAAAGTGCCATTCGAT 155 | TATTACTTTGAAAATAGATGGCCATATGTAGTTATGGACTCTTATGGGAA 156 | TACTATAGACGAATCTGAATATAGTATCTTCAATGGAAGCTTCTATTTTA 157 | CTAATCCTAAAAATGTAGCTAAATATGGAGACAAGATCTATATTAAATAT 158 | ATTTATAATACCAATGGTTCATCTACAGTAGGATATTCTTATGAAGAAGA 159 | TTATGCTTCCACAACAAATCTTAAATTCTGTAAGATTCCTATTGATAAAC 160 | TTTACGTTACTGACAGAATGAAAGATAGTTCAAACTATAAAGATTATGAT 161 | GTAATGGTTAAAGGCGATGGCTGGTGGGATGGTGTTGATTATAAAGATAA 162 | TAACCATCAACTAGTAAAAGATGCTATCTATAGAGAACCTTGGAACTATG 163 | CTAGAACCAAATACTATGGAATTAGTCAGATGATGGATGTATCTGCATAT 164 | TCTGCTCAAATGAGTTATTTCTACAGCATGTTATATGATGATATTATGCT 165 | TGAAGAGAAATTACTAGTTAAGGTTCCATCTATCTCTACTTCTCACCAAT 166 | TCAAATTAGCACACTTATTTATCTTTATGACTTCTTTGACTTACATGTTT 167 | AACGGCATTGAAGATTTCATTATTGATAATCCTGCTAAGACAATGCTTGT 168 | CCAAGGATTTAACTTTAGAACAAGTTTAGCTGATCTAAAAGAATATCTAA 169 | GAAAGAAACACAGGGAAGAAAAAGAATTCCCTATCTGGAACTTCATTACT 170 | CCTAAATCTCAAATCAAAGATTTAGCAGAGTTCATGAATATCTATAAAAC 171 | AAATATAGAAGTTCGTAGAACTATTTGTCAAAGAATGATTGATGCTCAAG 172 | ATTGGGAAGAATATAAAGTATGGAAAGATCTTTATGATTCTCTTATGACT 173 | TGGAAACTCACTATGAAATACTTTACTTTAAGCAATGGTGAGATTGCTAA 174 | GACATATACTGAATTCTTAAAGGATAAAGATTCTGTATTATATGATACTC 175 | TTAAAAAGGTAGATAAGATTATTTCTTCTGATGAAAAGATCGATACTATT 176 | ACTGGATTGATAGATGATATTATTTATATTCTAAATGAGTATATGGGTGA 177 | TATGAGATATATCTTTGATGGATATGCTGGTCATTCTGGTACTGAGATTA 178 | TGAAGTATATTATGCTCATGATCGAATTCTTTAAATCCTATAAGATCGTA 179 | TTCCTTACAAGAAATACTACTATGGAAATAATCTGGGGTAAAGATAGAGA 180 | TGAAGATACTACTATCAGACCTAATGATATGGCTTATATCAAAGAAATAG 181 | ATAAACGTCCTGAATATTATCCATTAGTAGAAAAAGTTCTTGATACAGAA 182 | GTTAATCATGTAGATGATAGATTTGATAAAGTTCCTTGGATGAGGGAAGA 183 | TTTGGTTATTAATTATAACAATGAACGTAAGTATATCACTATAGATCTTC 184 | CAGGCTCTTCCTATTTGTGGTCTGAAATGATTACCAAAGAAATTGATGGT 185 | ACTGTAACAGCTCCTAGCAGAAAAGATTTCTCTATGGATATTATCAAATC 186 | TGATGTATTTACTTACGTTAAGAATCTTTTAAATAAAGATATCTTGACTG 187 | GTAGCTTAGCTCCTTTTGCATATGAGATATCTGCAATCATTACTGGTGAT 188 | ACAGATATTGATAAGAAAACTAATGATGATTCATTTGTTGGCGATTTAGC 189 | ATTCATTGGTCAGGATTTAGATCCTATCGAAATTCCTGGTAAGTTAAAAC 190 | TAGGTACTACTTATAAGGAATGGACAATTAATCTTAATCTCGCTGTAAAC 191 | AATGAATACAAGGATCTTTCTTATTATATGCAAAAGACTCTTAGAGATAC 192 | TTTGGCTACAGAAACTGTATTAAATAATACTATTAAATCAGATCTTGGAT 193 | CTATTGATAAAGCTCATAATATCGAAGGAATGTTTAAAGGCTGCAAGAGC 194 | CTAGCTAATATACCTGGGTCTGATATTATTCATATAGATACTTCTAAAGC 195 | TAAATCTGCTCTAGATTTATATGCTGGTTGTAGCTCTGTTGGTACTATCG 196 | ATGCTAGTTGGGTAAATACTGCTAATATTACTACAGCAGAAGAAGCATTC 197 | AATGGTTGTTCTAATGCTATTTCTATTGATATCTCTAGCTGGGATACATC 198 | TAAGTTTAAAAACATGGCATACATGTTTGAAGGTTGTACGAAATTAGTCA 199 | ATATTGAAGGTATATTAGATATGAGTTCGTGCAAATCTTATAGAAACATG 200 | TTTAGCGGATGTGATAACTTAGTTGGATTAAAAGTAATCAACCCACCAGA 201 | CGATTTTGAAGAAAAGACTGGTATTAGACATGATCAATACACAGTAGTTT 202 | CTAAAACATCTATTGATAAAGACTTTAGATTATCTATCATGATCAATAAT 203 | GATTATAAAGACTTTACAGGATACTTTGCTAAGAAAGATCCAGATGGAAC 204 | TATGAACACTATTCCTAATAATATCTTAACAGAGTTGAGAGGTTCTAAAG 205 | CATCTAATGTGTCTAGAATGTTTGAAACTTGTTTCTTAACAGCAATTCCT 206 | AATCTTAGAATCGATACTTCTAAGGTAGAAGATTTCTCTAACATGTTTAA 207 | CTGGAGTACTGGTATAACAACAATTGATACTACATGGATTGATACATCTT 208 | CTGCTACCAATATGAACGGTATGTTTGCTGGTACTGGTATCAGAACAATA 209 | GATATTTCTAGATTTGATACTTCCAAAGTTAAAGACTTCGGATACATGTT 210 | TAATAGATGTGATTATATAGATACAATTACTGGTATTATTGATATGAGTA 211 | GTTGTACTAATTGCGAAGGAATGTTTGCAGATTCTACTAAACTTAGAAAT 212 | GTAAAAATCTTTAATCCACCTCTAGACTTTGCAGAAAAATGTGGATTATC 213 | TAATGACCAATATGTAATAGTAAAATCTAAATAAAGTATGGAGGAATATT 214 | AACGTGGTTAATGATAAATACAAAATCCAGGAAGAGGTTATCTCTAATTC 215 | TGAAGAATTAGTATCTTTAGTAGAGGGCCATCCTAATGGATTAAAAACAG 216 | AAGTTATTATTAGAGATCATGATACTGGGTTAGAACTGTTCCGTGGTAGT 217 | AATAAAACTCTCATCTCTGGATCTGAATTTATTGCAATGCGGATGTTTGA 218 | TCTTCATGATAAATCTTTTGTAACTCCTACATATAACAACCGTTTACAAC 219 | TAGAAAATACAATCAATAATCCTAATCAAGAAGAGATTTTGAATAATTAC 220 | TTTGTTCATCTATTCTGTTTAGGCACTTCTGGTTGTAACCGTGAGTCTGC 221 | TTTAAAATATGAAGTAGATAATAAGAAATGGATTGATCCTGCAGACATGG 222 | TACCATTCCAATACGTTCCTGAAGATAAAGATCTTGATGCTGATCAACGC 223 | CAAGTATACTTTGGTCGTAAAGCTCTTAAAGATAAAAAGATGGTTGCTTA 224 | TTACTTTAAAAAGTTTGATAGCGATCCTACAGAACGTAAACAATTAGAAG 225 | ATGGTACTCCTATTGATGCTACAATCTATGATGATCAATCTGAATTACCA 226 | GCACAAATCATTGTAGAAAATACTTTGGTTATTACTAAAGATGACTGCCG 227 | TGATTATTTTATTAATACTACTGGTATTAATGATGCTAGATTCAATTGTA 228 | TCAGCTTATGCTTAGCATACAAAAAAGAAAGTGAAGATGGATATACCTAC 229 | TATCAAGATATCCGTCCAGCTACTAGAATCAACTTCCCTAATAAGTTCCT 230 | AAATGACTTAGGTGCTTCTTGGGATATTATTTACCGTATCTACTTCTAAT 231 | ACATAAGAATACCCCATAGGATTAATTTCCTATGGGG 232 | 233 | -------------------------------------------------------------------------------- /test/mVCs/SRS018739_WUGC_scaffold_56127.fasta: -------------------------------------------------------------------------------- 1 | >SRS018739_WUGC_scaffold_56127 2 | GAAGTTCTGGAATAGCTTTGTTGTATTTTGTTCCAGTATAGAAACATATT 3 | ACATCTAGAGTATCACTGTTTTTTATATCTAAAGAATCTGATAGATTTAA 4 | AACTCCTTTATAAATATTGATTGTATAATCTGCCCCATGAATTAATTCTT 5 | TTCTATTAAAGAAAACCTTAAATCTATTTCTTATATCAAGAATCATATAG 6 | TATGGTGATAATAGATTATACTGATATTTGTTGGTTTCGCATTCAAAATT 7 | TAATTCCATCTTTTGAACTGCATATTGCCCTTTATTATGGGCAAATACAA 8 | ATTTTAAATCCCTATCGGAAGATATTTGTAAATCAGTATTATCTTTGATA 9 | CGTATAGTATAATTATCTATACGATCATAATATCTAGCTGGAATTAGTTT 10 | TCCTTCTTTATCTATAATAAAGAATTGCATTTCTGTAAATTGCTTATATG 11 | GAAATGGTATAGTCACATCATATTTACTATGATATTCAAATACGTTGATT 12 | TTAGAATATATTTCATAAGGCTCTATATCTGCTTTTAATACAGTTATTAC 13 | AACCTTACCATCTACTTCATTATTTCCACCAACTATTGTTTCTGTATCAG 14 | TAAATAAAACATGGTCATTATTTGGTTCATCAGAGCAGTTAGGATCTCCA 15 | CTTATATAAGAAGAACCTCCTCCTGCTTTGATATCTCCTCCACCACCACC 16 | ATAATATCCAGCTCCTCCACCAGGAGCTCCACCTTTACAGGTAATAGTTG 17 | AGGTTTCTTTTAATCCATTGCCACCAGTATTTCTAGACCCATTAGATAAT 18 | CTTACAAATTCAGTAGAGATAGAATTCTTATCTAAACTACCGCCATATCC 19 | ACCAGCAGTTTGTGTACCAGACTTTCCAGAATATCCAGAATTATACCATT 20 | TATATTCTAATGCAGGATCTCCATTACTTTCATTTAAAGGTTCTCCTTCA 21 | TATCCTCCACCATCTAGTCCTTTTACTGGTTTTATAAGATAATCATCATT 22 | GTTTGTTCTTATTATAAAATCAGTTCCACCACCAGCACCAGCGGCTATCA 23 | TATAGAAATAGTTTTTATCATCACTAAAAATGGAGATAGCGGAAGATCCG 24 | CCACCTCCATAACCAACCATCTCATTCTTAGGTTTAAAAGAATCTCCACC 25 | TTTACCAAATCCTTTTCCACCTATACGACCTTTAGGTTTGCATCCTACAA 26 | ATACCCAAAGATGATCAATATTACTTACATCTAGAATGCCTTTGGTATAT 27 | CCACCTCTAGAGAAGATATTAGGATCTCTTGTTTGAGAACCAGCTCCATA 28 | ACATTCTACTTTTATAGATCGAATACCAGTAAGATTTATATATTCAGGTA 29 | TTCCATCATTAGGTCTAAAAACAAATACTTTATTCCCATTGTTTTGCTCT 30 | ACGATATTACCCATTATAAACTCCTTACTGTATTATTTTAACCGTGGCTC 31 | CTGCAGCTCCCCATGGTTTATTATTCATAGATTCAGTGTTTACTAATTCA 32 | ACTGTATGGGAGTGAGGATATTCTTTAATATAAATAGTTCTTAATTCAGG 33 | GCAATTGGTGAATGCATTTTGATCTATATGCTTAACTGATGCAGGAAGAG 34 | TTATTTCCTTAAGTACATCAGATCCTATAGCATAAGCTCCAATACGCTTT 35 | AAACCTTTTCCTTGTTGTCCTAATTCAGGCTCTATAGGTTCATCTATAAT 36 | CACTTCTTTTAATTTACTACAGTTATTAAAAGCTCCTTCTTCTATAATAT 37 | CAATAGAATTTGGAATTGTAACTTTAGTAAGTTCTGTATTGTCACTAAAA 38 | GAATTCTTATGGATTATACCACATGAATTAGGAATAGAAACTTCTTTTAT 39 | CTTAGTATTAGAAAATGCCCCACTACCAATATAAGAAATATTGTTATTAA 40 | GAGTTAATGAACTTAATGAAGTACAATTCTTAAATGCAGCAGGATATATT 41 | TCTGTTATTGTATCAGGAATGACTACATTGTTTAATTTATTAAATCCATA 42 | GAATTGGTAAGATTGTACTCTAGTCTTATTTGAATCGAAGGATACAGTTT 43 | CTATTGAATTTCTATTAACTTGTGTATTTTCCATAATATATTGATTAGAA 44 | GTCTTATCAAAGGTTATATTAATTATAGAATTAGGTTCAAATGCATTATC 45 | TGCTACCTTAGCCATATCAGGAATAAATATATTGTTTAATAATCCAAATG 46 | CATTTTCATCAACTTCTAAATTTGTTCCCTTTAAGATAATATTTTTTAAT 47 | CTAGCACAAGATACAAAGGCATAAGAATTTATCTTATTCAAATGCTTAGA 48 | GAAATCTACATATTTAAGATCACTCATACCCTTAAATGTATAAGCTAAAA 49 | TAGATCTAATATTACTTTTTTCTTCAAAACGTATACCAATAACTCCTCTT 50 | TTATCTGTAAAGAAACTTGAGAAGGTATTGTTTGGTTGAAGTCTTATAGA 51 | TATAGAGGTGGCATTGTTTGCTATTAATGCATACTTAAGACCAGGCATAT 52 | CTTCATGAAGAAAATCTATATCTGTATTATTATTAGGAGAAACCTTTTCC 53 | CAATCTACATAATAATCTTCTACCACACCTGATATAATATCTGTATCTTG 54 | TCTATCTGTATAATCTGTATACAAATATCCAGTTAAGAAATCTTGTTGTA 55 | CAGGATATTCTACTCTACTGTATAACGTACCAGATATCATAGTTCTAGAA 56 | TACCAGTGATTATAATCTTTTACATAAGTAAGATTTCCATATATAGCATC 57 | TACAGTAACATCTTTGATTTTATCTGTAGGTATAGGAGTTGAATACATTT 58 | CATCAAACATGATATCATCATGGTCAAATTTCTTATCAATATATTCATAA 59 | GGTCCTTCAATCCCATAATTATTCAAAGAAACTTTATGTTTATACAAATA 60 | TAAAATGGTTATGGTTTTACCTACTTTAAATTCTGATTCAGCTCTATATG 61 | TAGAAATTATGGTGTTTCCATCTATCTTATATCTATTAGGATTAATATAA 62 | GTTCCATTTATAAATATAATAGTATTTTCTTTTGTTATTATATTATTAGC 63 | AAAATAACTACTAGGAATAGTTACCCGATTATTTATTACGATAGGTAATT 64 | CATTCTTTTCAAAATCTATACGTTCAGTATATCCACCTTCAGATCCTTTA 65 | TTTTTTATAGAAATTACAGTGATATTTCTTCCTTTGGTAAAGTATAAATT 66 | AGGATCTCCAAAGGAAATACTATTATTAGCAGCATTATAAGAATACTTTT 67 | GTGATTGTTCTAATGATACACTGCCAACAAATACAATGAATGAAGATTTA 68 | GGTCCTATAAACTTATTCAACTTAAATACAGTTTGTCCATCATATTCAGC 69 | AGGTATTTGTTGAATATCTAATTCAAAATTAGAATCACTATTTATATTGA 70 | ATTTAGAATTCTTCATATCATTGAATATAATCATAGTATAATTAGCATAC 71 | TTAGCATGTCTTATATCTACGCCATTATTGAATCTAATAGTATGATTATC 72 | AATAAGATCAAATCTATCTTTACTAATATAGGTAGTATTTCCAAATAGTA 73 | AAAAATTATTTTTACTTAATTCATATGAAGTAAAAGGAGGATCAAAGGAT 74 | ACTATACCATCATCACCAGAAGATTTTGAATAAGAATAAACAAAGTTTAT 75 | TCCTGTATTACCCATATATTTATTTTCAAGAAGCTCTCCTTCTTCTTCAA 76 | ATTCAGCTCTTACATAAGGAAATACAAATACTAGATAATCATTTCTATCT 77 | TCTGTTTTGTATAACTTAGAATGATCAAATAAAGTAATGGCACTTCCATC 78 | TTCAGATGTAGTATAATCATTCTTCTTATCTAAATATATACCATCCTTAT 79 | TAAATACAAAGAAATACTTATCTCCCTTAGGATAAGATTTGTAAGGATAA 80 | GGAACATTTACAACATATTGTTCATTCTCATCAGCATATACTAAATTAGA 81 | AGACATATATACATCATGGTTATAAGGAACATGTAAGAAGTTATCATCAG 82 | ATTCGATATAGAATACTTCTATTCTGTCCCCAGGTCTAAAGGTAACAGCT 83 | GTATAGATTTTCTTATTTTTTATCTTATTAGTAAAAGTAGCTACATCTAT 84 | TTTATAAATAGAATTGTTTAAGAGTAATCCATTTCTAAATACTAAATATC 85 | TCTTAGGATCCCATCCTGTTTTAAATTCTTCTTCCAATTCCAGTATATTG 86 | GTATTAAAGTTTATAAAATACTTATGATATAAGAATTGCTTATTAGACCC 87 | TACATATACAGGAAGATCAGCATAGTATTTATTATCTTCTATTTTTACAT 88 | TTCCATTAGAATCTGTAATATATTTTACAGGATATAAATTATTTTCAGAT 89 | ATCTCTACAAATAATTGCATATCCTCATATTTAATACCACTACAGTGATG 90 | GCAATGATCTTTAAATTTTTCATTCAGTTCATCTAATACCAAATAATCAG 91 | AAATTCGTTGTATTCCATTACCCTTAATATTAGAGTGATCTATTTTTCCT 92 | TTGTACACTTCTTTTTCAATTACAGTAACAGAAGAGAACGCATCATGACC 93 | ATCAAATGGGTAGAAAAATACATTAACTGATCCATTTACCAAATTATACT 94 | TTGATGCTTCAGACTGTTTAAAGGTAACTGTACAGTTGATATCTTTATAG 95 | TTTTCAGCAATGGTATCATTGAATTTATTAAATATTTCTCCATATTCAAT 96 | ATTAATAAATCCATTCCTAAAGAAAGAAGCCCCACGCATAGGTTCTAGAT 97 | TATATCTTTGGAAATTAAGATCAGTAGTCTTTTTATTATCGGTTACAAGA 98 | GTATTTAAAGCAATAACTGTATTATCCGAATTTATATTGTAAGGGTACAA 99 | TTTATACTTGCTTTTATCATCCACATCATAACCAAGACCCAAATCTAAAT 100 | TATTATTTTTATCTCGATAATCAATAGTATTTACTCTTACATAAAATCCA 101 | TTACCTCTATACTGCTCTAGGATTATTTGTAGATTAAATTTACTAGAATA 102 | ATAGTTTCCTGGTATAGATAAATCCCATCCATTAACTTTATTAGATTTAG 103 | AGTCCTCAGTAGGAGAAAATACATCTATGATTAAATTATCGGTATTATAA 104 | TATTTTCTAATATTGTTTAAATATCTTTCTTTATCCCCTACAATAAGAGA 105 | ATATATAGGAGCAGTAGACTTCTTATCTATTAAAGAAAACAATGCAAATG 106 | GTTCTAAGTTATTTATTGTATTTACATCATTATCCGTTATCTCATAAGAT 107 | GTATCCTTTTCTCTAATCATAAAGTATGGATTAGAGAAAACAACCAAAGC 108 | ATCAAATACAATTCTAGTTACATCATTATTTGAAGCTCTATTAGTATATA 109 | CAGAAGATAAATCTATAACAGATGATCCCGTAAAAGAAATCCCATCACGA 110 | TCTTTCCCTCTATGTTTATCTAAATAACTTGCCCCATCATTATATTCATA 111 | ATCATATAGAGATCCTTCTTTAGATTCCAATTCTGAAATTGATATATTGT 112 | TCAATTTCATTTCGGCATCTAGATTCATACTAATATTGCTTGTAATTATA 113 | GTAGTATTGGTATTGTTTCTAGATGCTATAATATCATTTATCGGTTGTCT 114 | ATCTGAATAATCAAAATTAATATCAGTATTATAATTATTTGATTGAAACG 115 | GTATTTTAATAGTTCCATTGTATTTACTTAGCTTAGTAAACATATAATTT 116 | CTGTGCCTCCTAAGTAAAAATTATTACTAATATGTACCCCTATGCGAATT 117 | AACCGCATAGGGGATTTATTCATTAAGATTTAGGTATGATTATAGGAACT 118 | TCTAGTTTACATGTAAATTCTTTAGCATCGAATCCATATGAAGGAGTTAC 119 | TCTAGAGTAGATTTCAAAAGATTCTCCACTGGTGTCATGAATATCAACAT 120 | AATCCCATACATATAATCTTACAAAACCATTAATATCTGTAGGTTTCCAA 121 | GGAACAGATACTGTTATTTCTGCAGGGAATGTGATTTCGTAAGCATTCTT 122 | ATAAACTATAAGTCTACTAATTACCGTAATAGAAGACTTGATATTATATT 123 | CTCTAGTCTTAGTAGGAACTGTAAGTGTAGAAGTAAAGGAATTATCTTCT 124 | TTATTACCAACTGTTAGGTTAAATATAAATTCTCTAGTTACCCTGTTTAT 125 | ATATAGAATCTTAGAATTTAAAGGTTGTAAGAAATTGACAATATTCTTAC 126 | ATTTTATAGCTTCTAATCTATCTGTAATGGAAGACTTTACATAACTTCCA 127 | TACATAAATGAAGATCTAGATTTGATATGGAAATAATACCCATTAGTTAT 128 | AGTTTTATCTATATTAATATCACTTATTAATTTACTATATTTAAATATAA 129 | TATCATCACTATTAGCATTTTTAGTATTAAAAACAGTGCCATGGCTATAA 130 | GCTATTATATTATAATACGGCATAGCTGAAATATCAGTTTTTAATCTTTT 131 | ACCATTTCTAAATAAGCTTATATTATAAGTATCATTAGAATAGCTGATAG 132 | CTAATCGGAAATTATCCTTCTCAGCAATACTATTAAGACTAAAACTAATC 133 | ATAGAATAATTATTAGTCTTGGTTATAGTAGAAAGATCTTTCTTATATTC 134 | GGCCTCATCTCCAATATATACATTACAAAGAGGTTCTCCAAGATTAGTAT 135 | ATACTGTTATCAGGTTTATATATTTAATATCAGAAGATGGATTTATTCTA 136 | CTATCATAACTAAAATCAATGGTAGTTCTTCCTAATGTTTCTTTAGAAGA 137 | AGGAGTATAGCAATCAGATATATCTACTAAACAAGAACCAGAATAATTGG 138 | TATTAAACTGAGTTTGTTTACCTACTTCTTTGATATAAATATTTTCTTCT 139 | CCATCTATTCCAGTTGCATCAGAGAAATTGAATGGGATAGGAACTTCTAT 140 | TGTTTTAGTATTACTAAAGGTAGAATCTATATCTCCGCCTTTAAAAGGAT 141 | ATTCTAATTGTAAGCTTACTTTGTTTCCATCATAAATAATATCTTCATAC 142 | CATTCAGGAAGAGATCCATTTAAGAAATAGATAGGATAAGTTCTATAATA 143 | TCTATCATGGAAATCATCTCTTTCCATATCATATTGATATCTCCCTGAAT 144 | CATTTAGATGAACGGCTTTATTTAATTTTAAAACATTATAAGATTCACGA 145 | TAAGCAGTAGCTCTTTTTTCATAAATAGGATCAAACTTCATTTGCTGATA 146 | GCAAGCCATATAATCTAAAGCTCTTGCTAAGTTTTCTCCATAATGCTTAT 147 | CCTTATAATATCTTACATTAAAATCATCCATAAATTCCTGGAACTTTTCA 148 | TCCATTTCATAGAACTCTTCATACAACCCTATATATCCATTTATAAACCA 149 | TTTACTAGTTGGATGGATAGCATTGGCTTCGTTTGATAAAGAATCTTTTA 150 | ACCAAATACAAGAAATATATGAGGGGAATCTTTCTAATGGATCTCCAGAG 151 | TAGATAGATTTTATAATATTTCTATTATATATTTGACCAAATAGATCAGG 152 | AGTATATGTACCATTCTGATCGAATGCAACTATATTATCAAGAGTTATCT 153 | TATATTTTTTATCTATATTCAGATCATAAAGAATAAATCTTCTTCCTGTA 154 | GATAATTGATTCTTGATAACTTCATATCTTGTTGTTCTAGGATCTTCATA 155 | CTCATCCACAAATTTATAGATCATAATTGTGATTGTTTGATCTTTTTTAA 156 | AAGTTGCATTTTTATCAAACAATATAAGCTTATTACTTTCTATGACATAA 157 | TCTCTAGGAAGTAATTGCTTTTGATCAATATAAATAGTGAAATTAGTAAG 158 | ATCATAATTCATATCATTAGGAAGAGTAATAGAAGGGGTATCTTCTTCTA 159 | TTACTATCTTATTTTGAATAGGTTTAATATGAATTTTACCATACTGAGAA 160 | GATTTAAGAACTTTTACAAAATATATAAGAGCAATCTCTCCAGCATTTAC 161 | TACATCTTTAGGATTTACTAATATAACAGAGTTTGATTTTGCATCTATAT 162 | AATAATGATCAGGAGGTATAAACTTATCTCCTATTAAGAAAGAAGCAATG 163 | ATCTGATAATTATCAGATATATCTATATTTTTAGATACTGGAATAGATAT 164 | GGTTCCATCTTGTTTTGATACGAATTTAAATAGGGTAGTAGATATAAATT 165 | CATCATCAGCTTGATTTACATCAAAGGTCAAGATATCCATAGAAAATAGA 166 | TTATCATATATTCCATCTATGGTATTATAATCTAAAAATTCTATAAGATC 167 | ATCACCTATAATCTTATATGAATCAGGATCTACTGGTACTCCATTATTAT 168 | ATAGAATTATTGTATCATCAGGAGAAAGATAACTGTGATCCCACGAGCGG 169 | AAGTACATTTGAACTGTGGTATCATCTACAATTCTTTTTTCTTCAAATTG 170 | TCCATATCTCCAGCTATGTTTTAATACATTAGAATCAGATAAGGTACTTT 171 | CTTTAAAATTTAATGGTAGATTTTGTTCATATATACCATTAGTCATTAGA 172 | TTACAGTTTAAAGTAGATTCTTTATCTATATAATAGAAATAGATAGCATT 173 | TTGACCAGAATCGAATTTACCATGGATATTAAATTTGTATATAGGAATAT 174 | TGTCAGGTCTTTCCCCTATTAATTCTTCATAGATAATTGGGAAAGGTAGT 175 | CTTACAAATTCTACCTTAGAGACTTTTCCTTTAATATTCGGATCTCTATT 176 | TTTTATAATCAAAGTATAATATTCATCGGATTTAATAATTTGGATTTTTG 177 | ATAAGGGGATAAATTCTCCATTTACAAATATCATAAATCCATCTATCTTC 178 | TTATCTAATAAAAGATGATAAGCCAACCCTTCATTAAATTCAGAATTTTT 179 | AAATCCCAAATCATTTTCATGAATATTGTTTATTTTGATTACTGTATAAT 180 | TTCTATATTTAGAAACACGTTCTATATCTCTATTTATAAAATACTCCCTA 181 | TCTTCAAACCAAGTAATTCTTACTCTTTGGGGTAAATATCCTCGTTGAGC 182 | TTCATTTAAAAGATAGGCAGTTGATTCCATTTTATGATCAATTAGATCTT 183 | GAGTTTCTTCTTCTAATTGATTATTGTTTACTATATTAGATTCATCTAAT 184 | CTGTAATAATTTTCTATAGTATCTTCTGTTCCTATATACAAAGTAGGAGG 185 | AATAAAAGAATCCCTATATAAACAGCTATCAATAATTGTAATGTCGTCTA 186 | ATGATCCTCCATTAAACGTTGAAACATTGCCAAGATTATCTTCTCCATAT 187 | CCAATATATAATTCATCCCCAAATTTGATATCTTTGGTTATATTATTAGA 188 | AGTTACATTACAACCATCTACAAATATTCTAAAGATATTTTCATCTTTAG 189 | TAATTGTAAAATAATGCCATTTATTATTGAAAGTAAAATCACACACAGAA 190 | GAATAGAATTTTTCTGTTTCTGATAATCTTACTACAAAATATTCTGCATT 191 | CTCTATATATACATAACTTTCAAACTTATCATTATTCTTGAAAGAGAATA 192 | ATGGTATTTTAGTGTCTTTGTTTAGATTTTTCTTATCTATTTTATATTTA 193 | CAGTATAAGGTAAAATCATTGTTTCCATTAATATGTGCTCTTATTTTACT 194 | GGTGTCTTTTAATATCAATCCAGCTGATCTATCGTATCCTTTAAAATAAG 195 | CACAGGTAGATCCGTGGATAATGGATGAAGTATCTTCAAAAGATACTCCA 196 | CCCATATTTATTATATCAGTATTATTGCAACCAGTTTTATCGAAATGGAG 197 | GTTCAATAAATATTTTGACATAATACATCCCCTCTATATTTTATGCTATT 198 | GTTCCTAAAGTAGAAATAACGTCTTTTGTATATTCTACCATATCTTTTCC 199 | ACAAATCTTTTCAATAGTTTTCTGATTATTTAAATATCCACCAACGTATG 200 | CATCAGTAATCATAGCAGAGAAAGCGGGGAAGTATTCCATACCAAATACA 201 | GTTCCAGGACCATATTGCATCATCCATTTTTCTACTACTAAATCAAGAGT 202 | TACTGTCTTATCATTAAGATGAAGAGTATCTCTCATTGAATTTACAAATA 203 | CTTTAATATTATCATACGGATCAATAAAATCTTTAGCAGAATGCTTTCTA 204 | CCTTTAGCAGATTTTTCAATCAAGATATCAAGAATATTTGCTTCATTAGG 205 | AGATACATTACCAATCCTAATTGCATACTCACGGCAACGTTTATCATCAT 206 | CATATTGAACAATGCCTTTTAAGAAGTACATTGCTGCAAGATACATTAAC 207 | TTATTCTTATTAGATTCCTGAATAGAGATCTTTGCAAGATAATCAATAAT 208 | ATGAGTAAATGTTTTAGCAAAACAAGTAGTCAAAAGAAGAAGCAAATTTG 209 | TTCTTCTCAAGAAAATATCAAACTTCTTATGATAGATCATAGAAATACCA 210 | GCATTGATAAGATAAGAAGTAAGAGCTAAACTATTGATATCATAATCAAT 211 | TCCATTAGATAATTTCACGATACAAGTAGAGGTATCAATAAATGCTTTTA 212 | CCTTTCCTCTATCTTTACCTTTCATTTCTTTAGCACAAAATACTTTGAAA 213 | GATCTAGGAAGCGGTGCATCACAATCTAAAAGAACAGTGTTTGTAGATTT 214 | AAGAATACGAATCAAAGGTTCTTCAATTCGTTGATGTTTTAAAGTTCCAA 215 | TTACGTTTGTATTAAATTCATCTGTATTTTTATCTATAATAGGATCATTC 216 | ATGAGAGCATCCAATAATATCTTCTGATATTTAGGATATTGTTTGTAAAA 217 | ATACGAGTCGGAATAAGACTTTAAGTCCTTGTTATCCATGTTAAATAAAT 218 | CCTCCTATTAAATAATCTAAGTAGTTATTTTAATGTCCCCTTTAGAATTA 219 | TATGATGGTTTAAACAATTTATTAAGCTTATATAAGGGGAGAGAGATAAA 220 | TGGATTTACAAGATATATTAGATCTTCATTTAGAGATAACCTCTAATGAT 221 | AGATATACATATAATGGTAAAAATGTACCTAGAGTAACAGAAGTTATCTC 222 | TAAAATGATCAATGAAGAAAAGATAATCAACTGGGCTAACTGCCTTGGTT 223 | TTAAAAAGAAAAGATATAGGGATGCTTTAGAAGAAGCAGCTAATTTTGGT 224 | ACTAGAGTTCATAGTGGTATAGAATATTATTTAAAAGGAGAAAAACTTCC 225 | TTTAGATACTCCTAAAACTCCTATGAATTCTTTTAAAGAATGGTGGAAAT 226 | CTATAAACAATGGAAATACCATAACCGTTTTAGGCCAAGAACAAAAACTA 227 | ACTTGTGAATGGTATGGAGGAACATATGATTGTTTATTAGATATAAATGG 228 | TCGTATTTTTCTTGTAGATTTTAAAACTTCCAACCACGTAACCTATAAAT 229 | ATTATCTTCAACTAGCCGCTTATTCAAAAGTTCTAAGAGAAGAGAAGAAT 230 | ATAAATATAGATGGAGTAATCATACTCCAAATAGATAAATATAAACTAAA 231 | GTATAGAGAATACGTGTTAGACTTTAATATACCTGAGCATAAATCATATT 232 | TTGATTTATGTGAAAGAACT 233 | 234 | -------------------------------------------------------------------------------- /test/mVCs/SRS018656_WUGC_scaffold_13330.fasta: -------------------------------------------------------------------------------- 1 | >SRS018656_WUGC_scaffold_13330 2 | GGCAAAATCGATCCAGAGCATATCAGACCAATCTGGACAGATGATGATCT 3 | TTATACAATTCACGTTGATCTGGACGTAGCAGCTGCTAAGAAAGAACTTC 4 | AGGGAACCAACACTGGAGCTAATTTCGGAGAGAATTTTGTCGTAGCCGAG 5 | GGAATGATCAATACTGTTCTGTATGCAAAAGAAAATTACAAAGGAACTGG 6 | TACTCCAGACGCCTTTATGACACCACATATGCTGAACCAGATGCTTCTTG 7 | CAAGAGATCTGAATGGCAGACGTATTTACGCGTCCAGACAGGAACTGGCT 8 | ACTGCTCTTAATGTCGGCACCATCCATACTGTTGAGCAGTTCGAGGGCAA 9 | AACCAGAACTACATCTGACAATAAAAAGAAGAAACTTGTTGCCATTATCG 10 | CAAATCTTGCAGACTATTCCCTGGGTGCAACTAAAGGCGGTGAGATTGCT 11 | CACTTCACACAGTTCGATATCGATTTCAACCAGGAGAAATCTCTGCTTGA 12 | AACCAGATGTTCTGGAGCACTGACAAGAGTGTACGCAGCAATTGTAGTCG 13 | AGGAGGATGTAACAACAGCTTCTTCTGATACATCTAGTCAGGACACAGTA 14 | AATTCTCAGGGCTGATTTTAAAGGGGAAAATTCAAAATGGCAAAGTTTTA 15 | CGGAACAATAGGATACATTCGAAACGTTGAAATAAGACCTGGCGTATATA 16 | AAGAAGAAGTTACAGAACGAAATTATTCTGGGGATTTGATTCGTAACATA 17 | CGCCAGTTGGAAGCTTCTGACAAAGTGAATGACGATATTAATATTTCGAA 18 | TGAAATCAGTATTATTGCTGATCCATTTGCCTATCAGAATTTTCATGCTA 19 | TGAGATACGTTGAATTTATGGGTGCTAAATGGAAAATTCATAAGGTTGAT 20 | GTTCAGTACCCTAGATTGACATTAATGGTTGGAGGTGTTTATAACGGAAA 21 | AGCGAAGACTACAACTTCATGAAATTTTGTGCCAGACGCTTGACAGCAGA 22 | AACGTCTATTTTCAACCTCCGGAAAACGTACGGATGAATTACCCCGCTAT 23 | TGTATACAGTCTTGACGACATCGATCCTGTATATGCAAATGGCGGGGTTT 24 | ATTTGTCCCCGATAAAGTATTCGGTGATTGTTATTGATGATGATCCGGAT 25 | ACCGAAATAGTAGGCAAAGTGTCTGCGTTACCATTATGTCGATTTGTTCG 26 | TCCGTACGTGTCCAATAATCTGAATCATTATGTATTTGAAATCTACTATT 27 | AAAGGAGGAATTTAAATGAGACTCTCATGGGATAAAGCCGGCGAACGTCT 28 | TTACGAGACCGGTGTCGACAGAGGCGTATTCTATCCGTTTACAACGGGCG 29 | GAAAATACGGAAGCGGTGTAGCCTGGAACGGTTTGACCGCTGTAAATGAA 30 | ACTCCATCCGGAGCAGAACCGACAGCATTATGGGCTAATAACAAAAAGTA 31 | TTTGACTTTAATGTCTGCCGAAGAGCTTGGCTTAACAATCGAAGCTTATA 32 | CATATCCGGACGAATTTGAAGCATGTGACGGCTCTGCTGAACTAGCAGAA 33 | GGTGTTACCATTGGTCAGCAGGATCGCGAACACTTTGGATTCTGTTATCG 34 | CTCTCTTATCGGAAACGATGACGTTGGTACCAAGCATGGTTATAAAATCC 35 | ATCTTGTTTACGATTGCCTTGCTTCACCGACCGATAAAGATCGAAGCACA 36 | GTAAATGATTCTCCGGATATTTCACCATTTTCCTGGGAAGTGACAACATC 37 | CCCAGTTGATGTTGACGATAGTAAATCAACATCAATGCTGACTATCGATT 38 | CCACAAAAATCGATCCTGCTAAGCTCAAGCTAATTGAGGATAAACTGTAT 39 | GGAACTACTGATGCAGAACCAGCACTTCTTCTTCCGAGTGAACTTGTCAC 40 | AATCCTTGAGTCTTAATTAAGGCGGTGGAATATGGGAAAATTGGAATGGG 41 | ATAAAATTGGTGAGCGGCGTTATGAGACTGGTGTCGACCATGTTGTGCTG 42 | TATAAGAACAACGGAAATAGTGCTTATGCCTGGAATGGAATCACAGGGAT 43 | TACTGAGAATCCATCTGGTGCTGAGCCATCAATCTTGTGGGCTAACAATA 44 | AAAAGTATATGACTTTGATGTCAGTTGAACAGTTAGGTTTAACCATTGAA 45 | GCGTACACATATCCCAACGAATTTCTTGGTTGTATTGGAAAAGAAGAACT 46 | GTCTCCGGGTGTACTTATCAGTCAGCAGGAGCATGAGCACTTTGGGCTGA 47 | GTTATAGAACACTTGTCGGTAACGATGAGCGTGGAAATGACTATGCGTAT 48 | AAAGTTCATTTGGTTTATAATTGCCTGGCTTCTCCAACAGAAGAGAACCA 49 | TGCTAGCACTAGCGATAGCCCGGATATTTCACCATTTTCCTGGGAGATTG 50 | ATACAACTCCAGTGGAGGTGGAAAACCGTCAGTCCACGTCGAAACTTACA 51 | TTTTCTTCATCTGATATGAAGAAGGCTGGAATGGCAAATGTGTTACGTGG 52 | AATCGAGGATGCATTGTACGGAACTCCCAAGACCAGTGCTTATCTCCCAA 53 | CGGTTTCCCAGGTAATGGATTTGATCGAGTTTCATAGCACGCTTAGAGAT 54 | TCAAATGGGAACGCAATAACCGATAGCTCTGGAAATAAGATGTTGTCAAA 55 | AGTTTATGAATAATTTCAAATGGAGAGCAGTATTCAGGTAAGCTGGCTGC 56 | TCTTCAGTCATGTAAAGGAGAGAAAATATGTTAGTAAAGACTATTACTTA 57 | TACGGATTATAACGGCGTTAGCAGAACAGAAGACTTCTACTTCAATCTGT 58 | CAAGACCAGAAATTATTGAGATGGAGTATTCGCCAGATGGAAGTCTTACG 59 | GAAATGATTGAGAAATTGGTTTCTCCGGCTGATACACCGACAATCATAAG 60 | ACTTATTAAAGATTTTATCCTCAAATCCTATGGTGAAAAGTCACCAGACG 61 | GAAAGAGACTGGTTAAATCTCCAGAATTAGCAACAGCATTTTCTCAGACA 62 | GAAGCTTACACTCAGCTTTTCATGGAATTAGTTACAGATTCTCAGAAAGC 63 | TTCTGATTTTATCAATGGGGTGTTACCGACTCTTACCCCGGAACAGAAGG 64 | CTCAAATTAAGAAAACTCTGGATGAAAAGGGTGTATCTGATTCAGTAACA 65 | ATTTGATAATGAAAATAATTTGGAGGGACTAAAAAAATGCTACAACTTGT 66 | CTTGCCCCGGATAGAAGGATGGGACGAAGAGAACGAAGAATTTGTCACCA 67 | TTGCGAAGGAGCAGAAACTTACATTAGAGCATTCTCTGGTCTCTCTTTCA 68 | AAATGGGAGTCGAAATGGCATAAACCGTTTCTAACCAAAGATACAAAAAG 69 | CGTTGAAGAAACATTGGATTATATTCGTTGTATGACTTTGACACAAAACG 70 | TCGATCCGAATACATACAAGCGGATCACGAATGAACACATCAATCAGGTT 71 | AACGCTTACATTGCAGATACTATGACTGCTACATGGTTTCGTAAGGATGC 72 | GGTTAAGAAACCGAGTAACGAAACTATAACCAGTGAGCGGATTTACTACT 73 | GGATGATTGCTTTAAATATTCCAGTAAAATTTGAAAAGTGGCATCTCAAT 74 | AGATTGCTGACGTTAATCAGAGTTTGCAATGAAGAATCGAAACCAAAGAA 75 | TAAAGTGGCGAGAAAAGATTTCTTAGACAGAAGACGTGCTATGAACAAAG 76 | CGCGTAAAGAAAAATGGAATACGAAAGGGTGATGTTTTATGAGTAAAAGA 77 | TCAGCAGAAGATCTGTTGAAAGTTTTACGTTCATGGGTTGGCTACGGTCG 78 | ATCAAATGGAAAACAGAAGATCATTATCGACATTTACAATAAAGATGATC 79 | CGACTCATTTACCAAGAGGTTATAAAGTTCAGTATGGAGATTCTTACTGT 80 | GATACTACCGTATCAGCCGCAGCTATTAAAGCCGCTATGAAAGATCTTAT 81 | CGGTAAAGAATGCGGTGTTGAAGAGCATGTAAAGATTTTCAAGAAGATGG 82 | GAATCTGGCAGGAAGACGGAACTATTGTTCCGAAAGCTGGTTATCCAATT 83 | GTGTATGGTTGGAGGAAAGCTGTGCAGCCTAACGATGCATATTCCGATCA 84 | TATTGGAGTTGTTGAATCCGTTAAGAACGGAACAATTGTGGCAATTGAAG 85 | GAAACCTTGGCGGTGAAGTAAAGAGGCGTTCAATTCCGGTTGGATGGGGC 86 | TATATCAGAGGATACGCCATTCCGAAATATGAGAGTAATGTTGGACAGAG 87 | CAGCGGCGAATCCAACAACGGTGGTAAGACTGAGTCCGGTTCAACAAAAC 88 | TTTCAAAGAAATCAAAATGGATTGGTGCAGTTACTGTAAACAGTGTACTG 89 | AATGTTCGTAAATGGGCAGGAATCGAGTACGATAAGTTAGTATCCAAGCC 90 | AGAGCTGAAGAATAACAATCCAGTGCATGTGTGCGACACCATTTATGATT 91 | CAAATGATGAACCGTGGTATTACATTTACCTTGATAAAGCTGATTATGGA 92 | TTTAGCAGCAACATTTACGGATTTGTAAAAGCAGAATACATTCGGAAACA 93 | GTAGGAGATAAGATGATTTCATTCAGACAAAAGGGCGATTTTTCAAAAGT 94 | CACAAGTTATTTCGAGAAACTGAAAGAGACTATGCGACTTGGAATTCTTG 95 | ACAAATATGGCAGGGAAGGAGTAAACGCCCTTTCGTCTGCCACTCCTGTA 96 | GAATCAGGTCTGACTGCCTCTTCGTGGTATTACGAGATAGAACATTCAAA 97 | CGGTTCTGCGGCTATACAATTTTACAATTCACATGTGAATAAAGGGGTTC 98 | CTATTGCGATTATATTGCAGTACGGACATGGCACCGGAACTGGAGGTTGG 99 | GTGCAGGGTAGAGACTATATCAATCCTGCTATCCAGCCTCTTTTTGACAA 100 | GATGGCAGAAGAAGTTTGGAAGGAGGTTACCAGTATATGAGTAAGACTGT 101 | TGACGAACGAGTCGTCGAAATGCGGTTTGATAATAAACAGTTCGAAAGTA 102 | ATGTTCAGACGAGTTTATCTACAATTGGAAAATTAAAACAGAGTTTGGAT 103 | TTACGGGGAGCCTCAAAAGGGCTGGAGAATGTAAGCGCAGCTGCAAAAAC 104 | ATGTAATTTGTCTGGTCTTACTGGAGCTGTGGAGACCGTCCAAGCAAAGT 105 | TTTCAGCACTTGAAGTTATGGCAGTAACCGCACTTGCTAATATTACTAAT 106 | TCAGCGGTGAATGCTGGAAAGCGAATCATTTCAGCATTGACCATTGAACC 107 | TGTACGTAGTGGTTTTGAAGAGTATGAGACACAGATTAATGCCATTCAGA 108 | CAATTTTAGCGAATACAGAAAGTAAAGGTAGTACATTACAGGATGTAAAC 109 | CAGGCACTTGATGAATTGAACCATTATGCTGATTTAACAATTTACAATTT 110 | TACGGAAATGACTCGTAATATTGGAACATTTACTGCGGCTGGTGTTGATC 111 | TGGAGACTTCCGTTTCTGCAATCAAAGGCATCGCAAACCTGGCTGCGGTT 112 | TCTGGTTCAACATCTCAGCAGGCAAGTACTGCAATGTATCAGCTTTCGCA 113 | GGCACTTGCGGCTGGAACAGTTAAGCTTCAAGACTGGAACTCAGTTGTAA 114 | ATGCGGGTATGGGCGGTCAGGTGTTCCAGGATGCACTAAAAGAAACAGCA 115 | CGAGTTCATGGAATTGCAATTGATCAGATGATTACCGATGAAGGCTCTTT 116 | CAGAGAGACACTGTCGAAAGGATGGCTTACTGCTGAAGTACTCACAGAGA 117 | CATTATCAAAATTTACAGGCGACTTAACCGAAAGCCAGCTCAAACAAATG 118 | GGTTATACGGATGAGCAGATCGCTTCAATAATCAAAATGGGGCAGACTGC 119 | CAATGATGCTGCAACAAAGGTGAAGACTCTATCGCAGTTATTTGATACGT 120 | CGAAAGAGGCTGCTCAGTCTGGATGGACACAAACCTGGGAATTAATCATC 121 | GGCGATTTCGATCAGGCAAAGGAATTGTTTACTGGAATATCAGATTCGGT 122 | AAGCAATATGCTCAATGCTTCCGCTGATCGTAGAAATAATTTGCTCGAAG 123 | GAGCGCTGTCAAATAATTGGGAAAAACTTATTTCCAAGATAAACGAAGCC 124 | GGGATTGAAACCAAAACTTTTGAAGAACAGTTAAAAGAAACCGCGACATC 125 | CCATGGGTTGGATGTAGAAGCTTTAATTGAACAATACGGATCATTGGAAA 126 | AAGTGTTTCGTTCCGGAGCAGCTTCTACAGATATTCTTAAAGAAGCAGTT 127 | AATAGTCTGCGTTCTGGAATGGTAGATTTAAGTAGTGTTAGCCGTGAATT 128 | GGATATGTGGTCTACTGGAGATGATGTGAAAAAAGTCCAGGAGGCATTAC 129 | AGAAACAAGGTCTTGATATTGGACAAACTGGTGTGGACGGAATTCTTGGA 130 | CCGGCAACCCAATCGGCAATAAAAGCATTCCAGGAGCTAAAAGGCATTGA 131 | GCCTACTGGCATTGTTGATGAATCGACTCTTAACGCGTTAAAAGAGGCGA 132 | CGTCTGAGACTAAGAATCTTACCGGAAATATTGATAAGCTTATTGATGGA 133 | ATTGATAAGCTGGGCGGAAGAGAAAAGCTGATCGAATCTTTCAAGAATAT 134 | TTTCAAAACTTTGGGTGATGTGGTTAAGCCTGTTAAAGAAGCTTTTAATG 135 | AAGTATTTCCACCAACTACTTCAAAGCAATTGAGTAAGTTGATCGATAAA 136 | TTCAAATCTTTTACGGATGGATTGAAAATCAGTGATGAGACCTCAGATAA 137 | ACTGAAAAGGACCTTCAAGGGTGTATTTTCGGCTGTGGATCTTTTGAAAA 138 | AAGGATTTTCTTCTATAATCAGTCCTATTGGAAAGTTTCTTGGTTCTGGA 139 | GGACTAAACGGAATCATCGATGGATTGCTGAACATAACAGCATCTGTCGG 140 | TGATTTTTTGACGTCTCTCAACGAAAGTGGAAATGTCAGCGAATTCTTAT 141 | CAAAACTATCTGACGGTATTTTTGATACATTCCGAGGAATTGCTGGAGTG 142 | ATAGATCCTGCTCTTGAGAAAGTAGAGTCACTGGGAGATGTATTTTCAGT 143 | TGTAAAAACGACAATCTGTAACGCAGCAACGAATATTTTCGACGCTGTGA 144 | AAAACGTGTTCTCTTGGATTAAAGAAAATGTTTCTGCTGGGGATCTATTT 145 | GCCGGATTAGCTAGTGGCGGAATATTCGCTGTAGCAAAGAAATTGTCCGG 146 | CGTATTGAGCACTATAAAAGAAGGAATAGAAGGTCTGTTTGAGAAGAAAA 147 | CATCAAAGATTGCAAAACAATTTTCTGATCTTCTGAACGGAGTGAAAGAT 148 | GCAATTTCATCATTCACAACTGGTATAAAAGTTGCTTCATTAATCGGTAT 149 | TGCAGCAGCTATTGCAATATTGTCAGTTGCACTGAATTCCATAGCAAAAA 150 | TTGATTCGGATAAAGTCGTTACATCTTTGTCTGCTATTGGAGTAATGCTC 151 | GGTGAACTTAGTGGCACTTTATTTGTAATCACAAAAGTGCTCTCTAAAAA 152 | TGGCTCTAAGGGGCTTATAAAAGCTGGGGCATCAATGGTGCTTATCGCTG 153 | CTGCGGTTAAAGTATTGGCAGACGCAATGGTCAAAATGGCAGATTTATCC 154 | TGGGAGAAAATCGGAAAAGGACTTACTGCTATGGGTGGAGGCCTTCTCGA 155 | ATTGTCAGCCGCAATGAAGATTATTAATGGTGCAAAAGTTTCCCTCTCGA 156 | CAAGTGTTGCAATGCTTGCACTGGCGAAGTCATGTCGGATGCTCGGAGAC 157 | GCGCTTGCTAAATTTTCAGTGTTTTCATGGGATGAAATCGGTCGAGGACT 158 | GTCTGCGATGGGCGGAGCTTTGGCGGAAATGACGGCATCATTAAGCGTTC 159 | TTAGCAAAGCTGGCGGTTTTGGAGCTTTACTTGGTGGTACTGGAATGCTG 160 | ATAGCTGTACAGTCTCTTGATGAAATTTCAGAAAATCTTGAAAGACTTGG 161 | TAACCTTTCCTGGGAACAGATCAAACGAGGTCTCGCCGCAATGGGTGGTG 162 | CTTTTGGTGAGTTTACTGCTTCGTTAGGAATATTAAGCGCGGTGGGTGGC 163 | TTCGGATCACTTTTAGGAGGAACTGGTCTTCTTGTGGCTGTACAATCTCT 164 | TGATGAAATATCAGAGAATCTCGAAAGACTCGGTGCTCTATCGTGGGATG 165 | AAATCGGTAAAGGTTTAGCTGCGATGGATGGTGCTTTGGGCGAGTTAACG 166 | GCTTCGCTTGGTATTCTTAGTGCGGTTGGTGGATTTGGCTCTCTTCTTGG 167 | AGCAACTGGTATTCTTATAGCCGTTCAAGCTTTAGAACCTATTGCAATAG 168 | CGCTTTCGAATATCGGTTCTCTTTCCTGGGAAGAAATTGGCAAAGGATTA 169 | GCGGGAATGGGTGGCGCACTTGCTGAGTTTACAGCAGCATTAAGCGTGTT 170 | AAGCCTTAGTGGAGGCTTCGGCTCGCTTCTGGGTGGAACTGCCGTTCTTA 171 | TTGCTGCTCAGTCATTAGAACCTATTGCTGCAACACTATCTGAAATTGGT 172 | GCCATGGATTGGGACGAGATTGCAAAAGGTCTTGTCGGAATGGGTGGCGC 173 | CTTAACGGAGGTTGGAGTTGTATCTGCCCTGGTTGGCAATCTTGGAGGTT 174 | TGGGTTCGCTTATCGGTAGCGCATCGCTTACTCTTGGCGTGCAAGGCTTA 175 | GGCGAACTTGCCAATGCATTGACGATTTTTGGCACCATGGATTGGGATGA 176 | AATCGGTCGTGGTTTAACAGCTATGGCTGGAGCTCTTGGTGAAACGGCAT 177 | TAGGCGGATTGCTGAATACCTTTTCCGGATTTGGCGCGGCTGCAATTGCT 178 | GCTATGGCTGAACCTCTTGGTAACCTGGCAGATTCGGTAAAGCGATGGTC 179 | TGGGGTTATTGTTCCAGATGGATTAGGAACACAACTAGGATCTCTTGCCA 180 | CAGGTGTTCAGAAATTTAATTTCAGTGGATGGGGGGCCGATGCTATTGGT 181 | GCGATGGCGATTCCACTTGGTGATTTAGCTGACTCAATTTCAAAATGGAA 182 | AGATGTAATTGTTCCAGACGGAATTGGAGATGGACTTAGTAATCTTGCAG 183 | ATGGCGTAAAAGCATTCAACTTCAGCGGATGGGGTGCGGATGCTATGGCA 184 | GATGTGGCAACACCGTTGGGAACCATGGCAGATTCCATTAAGAAATGGGA 185 | CGGAATCATTATCCCAGAGGATTTAGGAACCAATCTCAGCTATTTGGCAA 186 | ACGGTGTGTACGCATGGTCTACTGTTGGCCCATCCGATATTGTTGGCATC 187 | ACTGAGCCGTTAGGAACTTTTGCTGATTCTGTAAAGAAATGGAACGATGT 188 | GTCAATTCCATCTAATCTTGAAACTGCTTTGACTGGATTTGCAAACGGGA 189 | TTAATGCTTGCAATAACGTTTCTGTGGATAATGTAACGAATGTATGTACG 190 | AGTGTGAAAGATCTTGGTACTGCGGTTTCGGATATATCAACAATTGACTT 191 | TAGCGGAAGCGTTTCCAAATTGTCAGATTTCGCAGCTGCTATTGGAAATG 192 | TGAGCGTTTCGACCGACTCTTTCAAGATACTTGGAACGACTATTGTTACT 193 | GACTTTGCTACTTCTTTAAAGAGTGGAGTAAGCACGGTTTCAGAAGCTGG 194 | CGGTGAGCTGGCAGAAGCAGTTGCCACTGGAATGCGTAGGACGATTGATT 195 | CTATAGTGAAAACCGCGTCATCAATTGCGAACTCAGCGAAAAATTCGGTA 196 | GCAAATAAAAAGAGTAATTTTGTAACAGCTGGATCTTCTCTTATGCTTGG 197 | TCTTGCAGCAGGTCTTCGTTCCAGCATGGGCGTGGTCGCATCCGCATCTG 198 | GTTCGGCAGCATCAGCCGGTGCGAGTGCGTCTATGGCATATTATAGTAGC 199 | TTTTATAGTTCGGGTGTCTATCTTGTCAGCGGATTTGCAGCTGGCATCAG 200 | AGATAATATCAGTTCGGCAGCATCAGCCGCAGCACAGATGGCATCTGAAG 201 | CGTCAAAAGCAGCAAGAAGCAGTCTTGATATTAATTCGCCATCAAAAGTT 202 | TTCTATAAAATAGGTGGATTTGCTGGACAAGGTTTTGTGAATGCTTTGGT 203 | CGATTATAGTGAGGCTTCTTATGATGCTGGATCGAACATTGGATTATCAG 204 | CCAGGGAAGGATTAAGCCGGGCTATTTATAAAGCTACTGAGATAGTTTCA 205 | AATGGCATTGATAATGTTCCAACAATTCGACCGGTTCTTGATCTAAGTGC 206 | AGTAAGAGCTGGTGCAAATGAGATCGGTGGAATTCTTGGAATGGATCATG 207 | CTATCGGATTAAGTGGAAATCTCGGAGCCATCACGACAATGATGGCACAA 208 | AATCAAAATGGAAATTCTTCTGATGTTGTTGATGCTATTAATCGACTTGG 209 | AAAGAAACTTAACAACCTTGGTAATACTTATAACAATATCGGCGGTGTTA 210 | CTTATGATGATACGAGTGGCGTTAGCGATGCTATCGAGATATTAACAAGA 211 | GCAGTGGTAGTGGAAGGGAGGCGATAATAGTGGCTACTACTAAATCTGCG 212 | CCAACTATAGAAAAGTTCGGTTTGCAAACTGGTACAGAGCGTACTATTTT 213 | CGCAACTTGGAAATGGAGTAAATCGCACACAAAAGAGTATAAATGCATTT 214 | GGTATTATGCAACCGGAGACGGCGTCTGGTTCGTCGGTGCTGATACGACA 215 | GAAACTGTAAAACAGAGTACGTATACTGCTCCAGAGAACGCTACAAAGGT 216 | AAAGTTTAAAGTTAAGGCGATTGCCAAGACGCATAAAGTCAATAAAAAAG 217 | ATGTTGCGTATTGGACGGGAAAATTTTCAAGCGAGAAAAAATACAATTTC 218 | AAATCCAGTCCGCCGTCTAAACCATCGGCACCTGAAATCGGTATCAACGA 219 | GTATAATAAAACTCAGATCGATTTGAGCATTTCTAATTTGGATTCGAAAT 220 | GGACGGCTACCGGGGTTGAGTTTGAAGTTTACAAGGATGGCACAAGTGAT 221 | CCGTTCTATACAGGGTATTCCACAATTCAGAATCAATCTGCTGGAATATC 222 | CTGTACGATCGAAACTGGGTATAAGTATAAAGCTCGTTGCCGTGGATATA 223 | CAATGGACGACGAAGGCGCATGGTCTGATTATTCGAGTACTATCACTACT 224 | CAACCATCTTCGCCAGGAAAAATCACAACACTTAGAGCATTGTCGTCAAC 225 | TTCCATTACTATGGATTGGGATCGCGTTGCCAACTGCACGAGTTATGAGA 226 | TTCAGTACACTACTGAGAGACAATATTTCGATGCAAATCCCGACCAGGTG 227 | ACAAGCAAAACCATTGAATCCGAAGCCGGTCACGCTGAATTTACAGGGCT 228 | TGAATCTGGAAAAGAATATTTCTTTCGGGTAAGAGCGGTTAATAGTGCAG 229 | GAAACTCTGGATGGAGCGATGTGGCATCCGTTGTTATCGGAAAGGAACCC 230 | TCAGCACCTACGACCTGGTCATCTACAACAACAGCTATGGTCGGAGAATC 231 | GTTGATTCTATATTGGATTCATAATTCTCAAGACGGTTCTTATGAGAAAC 232 | ATGCTCAACTGGAATTGAACGTTGACGGTAGGATTACGACACAGACGATT 233 | CAAAATACGAAATCCGACGATGATCAAGGAAAAGCAAGTACATA 234 | 235 | -------------------------------------------------------------------------------- /test/mVCs/SRS058053_LANL_scaffold_6657.fasta: -------------------------------------------------------------------------------- 1 | >SRS058053_LANL_scaffold_6657 2 | GGTCCATTCACCATTGTGGTGAAGGCCGCAACTCTTACCGTTGACGACGC 3 | CAACGTCCAGGGTAAGGCTTCTGGCGAAAACTACAAGGTTGAGGACATCA 4 | CCCAGACCCAGAACCCAGCCGCAGCGGGTTCCACCGACCTGGATTCCCTG 5 | CGTCAGGCCAAGGGTAAGCTGATTCGCAAGGCCCTCGGCGGCGTTGTTCT 6 | GTTCGCCCCCATGACGGTTCCCGTGCCGGAAGTCTTCTTCACGGATGACG 7 | CCAAACTGGTGAACTTCCGCAATATGGGCTACTTCTCTCTCGGCTGGCTG 8 | CAGAAGTCCTCGGGCATTAACTTCTCCCGTGAGACCGAGCAGTCCGACGT 9 | CGAGTCGTTTGGTGCTCAGGAGCCGACCCGCACTGACTTCACTAAAGACG 10 | TTACGTCCGCGGCGTTCGTCATGCAAGAAACCTCCAAGGGCTCCCTTGAG 11 | TTCTACTACAACGTGGACCTCTCCAAGGCAAAGATTGGATCTAACTCGGA 12 | GCTGTCCTTCACCCAGGACAACATCCCGAAGGCGCGCTACCGCCGTATGC 13 | TGTACATCGCCGAGGACTCGTACAACGATCTTCCGATCTACATCATCAAG 14 | GTCATGCCGAAGGCTATCGTGTCCGAAGTTCAGGAGAACGCCTGGTCCGC 15 | GGATTCCGAGATTTCCTACTCAGTGACCTTGAAGGCTTCCCGTGACGACG 16 | AGCTCGACTACGCCGTCAAACACGTGTTCGGTGGTGAGGGCTGGAAAGCC 17 | CTGGCTGCTGACATGGGTTTCGTGGTGGGGTAACTGGAGTAACGTCTCCC 18 | CCGGTTATCCCACCAGCCGTAACACCTGGGGCTGCGAACGTTTTACGCGT 19 | GACCAGCCCCAACGCTGTTACATCCCCGAATGCGGTCACGTCACCGTAAA 20 | TCATACCTTTAGGAGATACCCAAATTGGCTTACACCCCACAGGAGTGGAA 21 | AGACAACTCAACCCAACACCCCGCATCAGCCGCGCGCTTCACGCATATGG 22 | AGCAAGGAATCAGCGGCGCACACACCCTGGCGCAGGCCGCCGCGGAATCC 23 | GTCACCGGCGTGCAGGCCAAGCAGGCCGAACTGGACAAGAAGATCGAGGG 24 | CATCGCGGCCCCCGCTAAGCCTACCGCGGAGGACATCGCTCCCGCTGTGC 25 | GTAGCTACCTGGAGGCCCACCCGGTCGCCGTCCAGGAGGACTCTCTTGCC 26 | GCAGCGGTAACCAAGGCCGTGCAGGAGCGGATTTCGCATCTGCCCCCGGC 27 | TGAACTCCCAGCTGACTTCAACACCACGGTCGAAAGCCTGGTCAAGGCCG 28 | AACTGGCCAAGGCGGCCCCGACTCCTTCAGGAGATGGTACCCCAGCGGCA 29 | CCGGCTGCCCCTGTCGACGAGGCGAAGATTCGGGAAATTGTCGACGCCGC 30 | CATCAAGTCGAAGATAGCCGAAGGCGACGGTGCCGCACCGACCGGTGACG 31 | CTCCGTCGGAAGACCCATTCCGCTGGTTTAATGCTGGTCAGCGCTACTGG 32 | TGTCCTGTCACCTACTGGTGGGCCGACCAACGCCAGCCCGGTTCTAAGTG 33 | GGACTATATCTTCGGCAACCTCGATATCATTGGCTTCGTCATCATCAACC 34 | CCCGAAGCGGATTCGGCGACAAGGTTGAGCCTGACTTCACCGACCTGACG 35 | ACGCAGCTGAAGAACAAGAACGTTCCCTGCGTTGGCTACGTGCGCACCAT 36 | CAAGGGCACCAAGTCTGTCGACGATGTCCTGGCCGAAATTCGCAAGTATC 37 | AGGAAGCCTACAAGCTTGAGGGTGTTTTCCTGGACGAAATGATCAACGGC 38 | TGGGCCCCGTCCGAGGCTGCCCTGATCGACCAGTACAAGGACTTGTACAA 39 | GAAGATCAAAGCCGAGTTCGGTAAAGGCTTCCTGGTTGTAGGCAACCCCG 40 | GCACCAACACCAAGCCTGAAATCTTGGAGTGCGCCGACATCCTCATGTCG 41 | TTCGAGAAGGCCGCCTCCGCGTACCTGGATGATGCCGCCGCACCGGTAAC 42 | CCCAGACCACTACCGCGCGGAATCGCCTCTGCGTTTCATCCACACAATCC 43 | ACAACCTGGAGTCCGTGGACCAGCTGCGCAAGGTTCTGGCCAAGGCGGAT 44 | GTCAGCAACGTCGGTTTCTTCTATGCGACCGATGATACGTTCAGCGGCGT 45 | TGAGGGTAGCGAAAACCAGGACAACAACCCTTGGGATTCCGTGCCTAGCG 46 | AGAAGTACCGCGCCATGCAGTTCCGCTGGTGCCGCCGCCAAGAGGAACCA 47 | GTTGAGCAGGTCATCGCCACCGGCGACCCTGGCGCCATCTGGGTACATGA 48 | CTCGGCGCTCGGCGAGGTTGTTGGCGGGGATATTACCGCCAACCTGCAGA 49 | AGGCTGTGAATGCCCCCAACATTCGCACCATCAAGATTCCCTCCGGCAAG 50 | CACAAGATCAAGACCGTCACGATGGACAAGATCGCCGGGAAGAAGATTAT 51 | TGGTGCGGGCCGCAACTTGACGCAGCTGGACTACGACAAGTCGGCAACGC 52 | AGGTTCCGTTCCTCGTGACCTCTGGCTCCGATAGTCACCGCTCTACCCTG 53 | CAGGGCTTCGCGGTCAACATGGACTGGAAGAGCGGAGACCCGGAGCGTAA 54 | TGCGTTCCAGGTGTCGAACGCCATGCTCATGGACTACATTGACCTGCTGA 55 | TCACCAACGCGGGAGCCAACGGCATCCTGCACCAGTCCGCAGCGGTCAAG 56 | GACAACCCGAAGGGCCTGGATGGCTCCAGTATTCGATTCCGCGACGTCGA 57 | CATTGACGGCTCTGGCCTTGCCGACAAGACCACCGGTTTTGGCATCCAAC 58 | TGAAGGGCAACGTCAACGATGTTTCCATGTTCGGTCTGCGCATCAAAGGC 59 | GTGAAGGGTGGTATGGGTGTCGGCGGCGTTTTCGACTCGGCGGCAGGCGT 60 | TGGTCCTAGTCGTGTCACCATCGAAGGCTCCTCCATCGGCACAGCGGAAT 61 | CCACCACGGCTTTCGAGCCGATTGGTTTCACCAAGGGCTGCGACAACATC 62 | ATTGTCCGCGGCAATCACCTGTGGTCGTTCGACAACGGCACCTCCCTCTC 63 | GGGAAGCGGATGCCTGTTCGAAGGCAACACCGTGTACCAGGGCTGGAACT 64 | TCGGTGTGTCTGTTGGCTCCGACGACGCGGATTTCCAGGCTGCCGTCGGT 65 | ACCCGTGTCATCGGCAACCTGTTCTACGACCTTGCGCTGGAGAACGAGAA 66 | GCGGCCCGATCGGGGCACCTTCGAGTATGCGGTGGTGCGTTTCGCAAAGG 67 | CCAAGCGCTGCGTTGTGGCCAACAACGTTTACGCTGGTCGTGCGAAGATT 68 | CTCCACCACTTCATCAAGGTCCAGGGACAAAACCACGGCTTCAACCAGGT 69 | TTACGGCAACGCCGTCGACCGTGAGGATTTCCTCAAGGAACCATTCAAGG 70 | GCCAGGTTGAAACCGACCAGGTACAGGAGTGGAAAACCTCTGTTCCGCTG 71 | ACCGGGTAGAATAAGAGCAGAATCGGGTTGAGGAGGACCATGAGTTTAGA 72 | GAAGCGAGTCGAAGCGCTGGAGGCTGCCGCACGCCCTGACGAGGGTTGGT 73 | CCCTGTCCGACTTCCGGGCCGACGTGTCCGAAGTCATTGGTGACAAGCGC 74 | GACCTCATTAAAGCCTTAGAGCGCATTGGTTCCATCTCAGAGCAAAAGGT 75 | TCTCCTCGACCAGGTGATCAAGGCCCAGAGCCAAGAGGTGGACCGTCTCA 76 | TCCAAGATGCTCAGCGCAGGGATAAGGCGAGTCGCGCCTTCACATCAATC 77 | ATGGACTGGTGGGACCAAAACTACCGGATTATTGTTGACGCTAAGGAGTC 78 | CCTGGCGTTGAATAAGCAGATCGTCGACACGGCCAACAACGCGACAACCA 79 | GTATCGATGCGTCCGCACGCTCTGCTCGTCAAGCTTCGGAAAACTTTGAG 80 | CGAGCCACCGCGCAGAAAATGCGCGATTTCGGCAACACTTTTGAAGCCGC 81 | GAAACGCGACCTGGCTAATACAGCGACCACGGCTTCCCGCAACCTCGCGG 82 | ACTCGGAGAAGAAAGTCGCGGCAGCGGTCGAAGCAGCGAAGAAGGCGGCC 83 | ACGGAGGCCGCGGCAGCTGAGATACGCAAAACCGACGGCAACCTGGCTGA 84 | GATGAAGCGCATCCAGGACCGGGTTAATGCCGCCGTCAACGCCGCCGCAC 85 | AAACCCTTACCAATGAGGTCAAAAAAGTCTTTGTTAATCCACCGGAGGGG 86 | TATAAGACCATCGGCGACGTGAAAGCCCGCGTCGAGGAGGCAAAGAAGGC 87 | AGCCAGCGACGCGCGTGCCGTGGCGGATGCCGCCATGCCGAAAAACATGG 88 | TGTCAGCAGCCGTAACCGACAACACAGCGGCACAGCGCTACGCTGGGGGC 89 | CGTCTGCGTGTTGGGGATGCTTCCGAGCCGGATGACGCCGTCAACAAGCG 90 | TCAGATGGAAATGATCATCAACGGCTTTAACGCCAAGGACGCGGACCTTG 91 | AGCGCAAAATCCAGGAAGCCAAGCAGGGGCAGCAGCAGGTCCGGCAGGAC 92 | CAAACCGTCAATGGTGTCCGGTTTATGCGCCGCGGTGACATGGTTTTTGT 93 | GACTACCGTATCCAATAGCGTCAAAACTTCAGACCTGGAGGGGATCAACA 94 | CTCCGCAGTGGGCCCGTCCGATGGCGGACGTACACGTTCATGCGGCTTGG 95 | GTGTGGGAAACTTACGGCGGGGGAAGAGTGGCTTCTGGGGGCTGGGTTAA 96 | CATTGGAACAGGAGGCCGAATCACCGGTTCGGTCTCGGAATACACCTACC 97 | GCGGGATCGAGTTTTCCGCGGCCTACATTGCAGCATAGGAGACGTAAATG 98 | GCTGTATCTTTCGAAAGCCTCGCACAAGAGGCGGAGCGCCGAGTAAAGCG 99 | TTCACGAGTTAAGACCCGCGAACCGTATGGAGTCACCCTGAGCGACGGCA 100 | CCGAAATCAAAATTCCCTACCCGGATGGTATCAAGGTGGCCCTGTCGATG 101 | GAAAACCCGGAGGCCAGCCCGACGGTGATGCTCCGCAACTTCATGGCGGA 102 | CGACCAGGCCGGTTACCGCCGCCTCATGGAGGAAATCGACTCCACTCACC 103 | AACAGTTTGAGTTTTTCGCAGTCCTCACTGAAGACATGTGGAACTTCTGG 104 | GGTGTTGAGGGTGGTTTGGGAAAATCCGAGCAATCTCGGACCTAGTTGAC 105 | AAGTACGCCAACGAACTGCTCCATGATTTCCGTGTCTACTACGGAGCGGA 106 | TTTAGTTGACTACATCCCCCCACTCAGCAGCTTCGACATACTGTATTCGC 107 | TGATTCTGCAGCTTCCGGCCCACCTGAAATTCAAGACGGCAATCACCAGT 108 | GACGAGGATGAGGCCAGGAAGTACGCAGCCAGCTTGTCCGAGCTGGACCT 109 | GAAGCGGATGCTGGAGGACGACAGGGACGCCGCTGTCGGAGAAGTGTCCC 110 | CGGAGGGTTGGACCCACGAGATCGAGATGTTGACGCAGATTGCTGACAGC 111 | ATCGATGCCCTCCGATTCACGATTGTCGGGATGCTGTCGAAGAAGAGCGA 112 | CAGTAGAAAGTTCGAGCGGAGAAACAGACCAATTACCGCCAGGGAGCGGA 113 | TGGTTAAAGAGAGGCTTGACTCCTTCGAGGAGAAGAAAGCCCACGGCCTC 114 | CTTGAACAGATGGGGTTTTAGATTAAAGACCGTCTTACGACGGTCTTTTT 115 | GCTTTTTAAAGGAGAACACATGGCTTTTGTCGTGGGTGAAGGTGCCGTCC 116 | GCATCTTTCCCAATGCTAAGCATTTTCACACAGAGCTGCGCGCTATCATG 117 | GCAAAAGCCAAGAAAGAAGCCAGCCAACTAGAAGTCGAACTACAGGTCGA 118 | CGACCGCGAATTAACCCTTGCGGAGAAGCGCATCGACCGGATGGACGGTC 119 | GCAAGGTTAACATCGACGTCCACCTCAACACAAACGAGGCGTGGGCCGAG 120 | TACGCTCAGCTCGTCGCAGACATTGAGCGCACACCTATTTTCGTCGACGT 121 | CGACGTGGACGAGGGTTCACTGCGCGACGCACGACGCGACGTCGAGAAAC 122 | TACGCGAGGAGAACGACCGCATTCACATGTATGTGGATGTGGACCGAAAC 123 | TGGGCCGATGATGAGCTCAAAGACTTCAAAGCCAAGCATGACAACACCGA 124 | CCTGGTGTACCGCCTGGTTGTCGACGCCCCGACGAAGTCACCACTAGAGC 125 | AGATCGTCTCCGCGCCGAAGATTCAGTTGCCGGACCCAAAGAAACTAGAG 126 | TCCGAATGGAATGCCCTCAACTTCGTCCCGAAGCTACTCAAACTCATGGA 127 | CGACCAATTTGAGGCCGGTATCCGACGCATCTACGACCCCTACGTTAACT 128 | TCACGGTGAAGCTAGGTCGTCTCATGCGCAAGCCGTTCGACGACCTCGGC 129 | AGCGCAATCAACGGCTCGAACAGCTTCAACGAGCTCTTTGCTAAAGGCGC 130 | GCAGAAGGTGTCGCAGAACGCGGCTCGGATTCGCTCGGCCGTTGCTTCGG 131 | CAGCCGAATCCTTTGACCCTCTCATCAACGGAGTTCGCCGAGTCCATGCG 132 | GCCATGCACGACATGCGGATGCGTAGCCTCCTGGAGTTCCAGTCGTTCCA 133 | GCGCGGAGCCATTGAGGCGGGGGCCCGGTTCCAAATCTTCTTTACCAACA 134 | AGCTTCTCGATGCTAGGGATAAGGTTCAAGAGTTCGGCTCCGCCATGAAA 135 | AACTTCGGCCTTAACCAGGTCGAAAAGGCCGTGTCCTCCTTGTCTGCGCA 136 | CTTCATTAACTTGCGTAACGTCATGCAGGGGGCCATCGCGAACCTCAACC 137 | CTCTCAAGTCACTGCGCTTGGCCGGTATTGACGTTGATGCTTTGATTCCG 138 | CGTAACTTCCCGGCAGCCCTAGCCCGGCAGCTTCAGCTGGGCTACTTCTA 139 | CGCTGTCGATACTCTCGGTGACAAGGTGCGACCAGCAATAACCAAGTTGA 140 | GCGACATCGGTCACCGGATGGCCAGCACAATCTCCCGCGGACTCATTGAC 141 | TCCCCGGTGTGGCACAGCGTGTCCAACGCCATGTACCGCATCGGCAACAC 142 | CCGCATCGCGCGCGGCCTACAGCGCGGCCTGGCATCCGCTCGCGGTGTGG 143 | CCACCGGCCTCGGCAACAAGATTTCCGAGACTCTTCTTCCTGGTTTGAAC 144 | CGCGCTGGTCGCGGGTTTGCTCGGTTCCTTGGCAACTCTAATGTCCTGTT 145 | CAGGTCACTGCGCGCTGGATTCGGTCGTGCCGGGGCCTACGTTTTGGGTT 146 | TCAGTCAGATCGCGCTGGGTGCGTTCTCCAAGGTCGCGCAGATGATCGGG 147 | GCAACCCTGCTTCCTGCCGTGGTTGCCTTGGGTGCTGGCCTCGCCGCCCT 148 | CGGCGGACAAGCTGTGATCGGCGGTGTGCTAGCTATCGGTGGTGCGCTCG 149 | TGAGCGTCGCACAAGGTGCGGCGCTGGCCACACCGGCTCTCATTGGTATG 150 | GCCGGAATCAGCTTTGCAGTCCTTAAGGTTGGCTTAAAAGATGTTAAGGC 151 | GGGCATAAGCGCCGCCTTCAACACCGAGTCCGCTGAGGAGTTCGAGAAGG 152 | CCATTCAAGGCATGGCGCCGTCGGTACAGAACGTGGCGCGTAGCCTGCGT 153 | GAAGTCTCTCCGGCGTGGCGTGAACTTAAGAAGCTCACTCAGGAGCGGTT 154 | ACTGGACAACCTCGGACCGTCGATCCGGGACGCGTTCCAAAACGTCATCC 155 | CTGAGTTCGGCGCCGGGATGCTGAACATCGCAACCCACTGGAACTCTGCG 156 | CTGAAGCTAGCCTTCGCCGAGATCGCCTCCCCCGCAGCCAAATCCGGCGT 157 | TGCGGAGATTGTACGCGGGGCTAGTGAAATGGCGGCGGCGATGCGGCCAG 158 | TCCTGGCAAACATGATCGCGGCATTTGGTTCACTTGCGGAGCAGGGTGCC 159 | AAGTTCATGGGTCCGCTTGGCCAGTACTTCGCGGACGCTTCCCAGCGTTT 160 | CCGCGAGTGGGCTGAAAGCTTGAAGGAGGTTGACCCCACCACGGGGATGT 161 | CCCGCTTCGACGAGATGATTCAGTCCGCAATCCGCAACGCAGGCTACCTG 162 | AAAGACATCCTCGGCGGCGTCTTCGGAACACTAGGTAACATCCTTCACGC 163 | TGGCCAGGAAGGCGGAGGTGGGATGCTCGCCGGTATGGCGGCAGCCGCAC 164 | AACAGCTTAAGGCAGCCACCGACGAGGGTACGCAGGGTTACGCGCAGCTC 165 | CTGAGCTTCATGCAGTCTGCTACGGCAGCTGCATCGCAGCTTGGACAGGT 166 | TCTTGGTCCTGTATTGTCGATTGTGACGACGGTCGGCGGCACTCTCGCTG 167 | ACTTCGCCGCGGGTGCTATTCCCGGTCTTGCAGCTGCACTCGGCGGTCTC 168 | GCTGAGGGTTTGCAGCCTGTGAGGGACGTCGCGGACAGCGTTGGCCGCGC 169 | CTTTGGTGACATGCTGGCAAGCTTCGCACCTGCGCTCTCTGCGCTTGGCG 170 | CGGCTGTAGCTCCGCTGATTGAAGGCTTGGTCAACGGCCTGTCCCTGGCT 171 | GGCCAAGGCTTGGCGCAGGCTCTCACCCCCATCATCGAGTCGCTTGGCCC 172 | CGCAATGGAGGCTATGAAACCTGTATTCGAGGCGGTCGGTAATGCCCTCG 173 | GTCAAATCTTCGTCGCCATGTCGCCGATCATCGCGTCGACGGTGAACACC 174 | CTCACCCAGATCATGCCTGTGGTGACAACGGTGTTTGACCTGATTGGCCA 175 | GATTGGCGCCAAGATTCTCGAAGTTTTGGCCCCGCTGTTCACCGGCCATG 176 | ATTCTGTGATCGTGCAGCTGGTCAACGCCCTACAGCCGCTGGCGGAAATC 177 | CTGGGTAACGCGATCCTCAACATCCTGAACGCGCTGGCCCCGGTCATGCC 178 | GGTGATTTCAGACGGCCTTGGGCAAATCCTGGGAGCAGTGATACCGCTCC 179 | TGGACCCGATTGGTCGACTCATTGGTCTTATCGGACAGGCCCTGGTTGAG 180 | GCAATTAACTGGGTCGTTCCGCTGATTCCTCCACTAGTGAGCATGATCGT 181 | GTCGATTGCTAACGCAGCTTCGGCGATCCTCGTTCCGGCCATGAACTTCC 182 | TTGTCGATGTAATCAAGGCCGCCTGGGACATCATCTCCGCAGTAATCGGG 183 | TTCGCAATCCGCAACGTCATCGCACCGGTGTTCGACTTCATGGATTGGTC 184 | TTTCCATAAACTCGCGGACGCCATCGGCTGGGGCGTCAACAACCTCGTTG 185 | TCCCCTACTTCAACTTCCTTGGCGACTCGCTACGCAAAACCGGCGACGGC 186 | TTCCGTTGGGTTGTTGACCATATTTTCCAGCCAGCCATCGACTGGCTGAA 187 | AGACATCTTCAAGGCTGGCGTCGACGGCATCAAGAACCACTGGAACCTAT 188 | TGAAGAAAATCTTCGCCGACCCGGTTCGTGCGTTCATCGACATTGTTGTG 189 | AACAAGGGCATTGTCGGAACGTGGAACCACATCAACGAGAAGTTCCTTGG 190 | CGGTAAACTCGGAAACCTGGCACCAGTGCCAGCCGTGGATGAGATGCGCT 191 | TCGCAACGGGTGGTGTGATGCCTGGCTACAGCCCAGGACGCGACCCGCAC 192 | AAATTCTGGAGCCCAACCGGCGGCAGCCTTGCTCTGTCCGGCGGCGAGGC 193 | TATCATGCGTCCCGAATGGACCAAGGCTGTTGGTGGCCCCGCTGCCGTCG 194 | AGGCCATGAACAATGTGGCCCGCAAACAGGGTGTCAAAGGCGTTCAGCGG 195 | ATGCTCGGCGAGGGTGCAGCCTACGCCAACGGCGGTGTTGTCGACCTTGA 196 | TGGTCGGATCGCTGCCTTGTTCGAAGCCCTTAAGCCTGAGCATGGTAAAC 197 | CCTATCAATACGGCGGCGACGGCAATCCCTCGTGGGACTGCTCTGGTATT 198 | TGGTCTGGCGTGGTTAACTTCCTCAACGGCCGAGACCTCCGCGCAGGCCG 199 | CCTGTTCAGCACCGAATCCGCGTTCGAACAGTTCGGCTTCAAGCCTGGCC 200 | TTGATGGTCGCGTCACCATTGGTATTATGCGTGGTGGCGGTGGCCCCAAC 201 | TCACACATGGCCGGAACCATTGACGGCGTCAACATCGAGTCCGCTGGTGA 202 | CCACGGCGTGCAGATTGGCGGCGGCGCTCGCGGCTCCGACAACCCCCTGT 203 | TCAGCCTTCACTACACCCTGGCCGACTACCTCGGCGAGTTCATCTCCGGT 204 | GGTAATGGCGGCAACGGCGGCGGCTTCTGGTCCCGCATGTTCAATAAGAT 205 | CAAGGAAGCTATTGGCGGAGCCTTCGATCCGATCCGCGACCAGATGAAAG 206 | GCTTCGCCGGTATTGCTGGCCAAGCCATGCACGCTCTCACCAACAAGGTT 207 | TTGGACGGCGTCAAAGACTTCATCTTCAGCAAGATTCCGCGCTTCGGCGG 208 | CGGTGCTGGCTCCTACGATGGCGCTGGCGGCGTGTCCGGCGACGTTGAGT 209 | CGTGGCGTGAAATGGCGATGGAGGCCATGCGCCGCAACGGGTTCAACGCC 210 | GACGACCCCGCGCAGGTCAACGCCATGCTGAAGCAGATTCAGTCCGAGTC 211 | TGGTGGTAACCCAGGAATCTCGCAGCAGATCGTTGATGTCAACGGCACTG 212 | GTGACAGTGCTGGCGTCGGCCTGTTGCAGATCATCCCCGGTACGTTCGCC 213 | GCGTACCGCGACCCGTCCTTGCCGGATGATCGCCGCGATCCGTGGGCCAA 214 | CATGAACGCGGCCCTACGCTACTACAAGTCGAAGTACGGCAACGACTTGA 215 | CTTCCATGTGGGGCCACGGCCACGGCTACGACAGCGGCGGCGAGGCCCTG 216 | GGTATCGGCTACATGCCGAAGTACACGCTAGAACCAGAGCGAGTGCTGTC 217 | CCCTGCACAAACCCGCGCGTTCAACTCGTTCGTGTTTGAACTCATGCCAG 218 | CCATGATCTCGGCGTACCAGCGCCAGCCTTACGATCTGCAGGAGGGCTTC 219 | CGCCGTCTGAACCTTGGCATCCAAGGTATCCGTGGCGACATGGCCAAGTA 220 | CCGTGACGACCAGGTTGACCGCATCTCAGGCTCCCTGCACGACGTGTTCA 221 | AGTCCCGCATCGACGGCACCATGAAGCTAGACCCGGTTGACCTGAACAAG 222 | ATTGTCCAGGGTGACCAGGGTGAAATCAACAAGGCTTTTGAACGCGGAAA 223 | CTACGCCCTGTCGAAGACCCTTGAGGCTTCCGCCGACCCGAGCGTGTACC 224 | TGGCTGCCGAGAAGGCCGCCAAGGAGCGCCTGGATAAAGAAGAGGACGAA 225 | GCCAAGCAGAAGGCTCGCGACGCTGCTCGCGAAGAACGGAAGAAAGCCAC 226 | TGAGGAATCCGATAAGAAGAAACAGGATGAGCTTCGTAAGCGCCATGAGG 227 | AGGAGCTCAAAGACCTCAACGACGAGCAGAAGAAAACTGTTGAGGCTCGC 228 | CATAAGGAGGAGGATGAGGCTCTACGCAAGGAGCTGAACGCCGACGAGGA 229 | GCGGATTCGTAAGGAGGAGCAGGCCGAGGACCAGCGGATTGCGAAGCTGA 230 | AGGAATCCGGGGAGTACTACTACGGGTACAAAGTTCTCGGAGACGACGGT 231 | ACCAATCCTTACGCTCGTGAGGAAACCACTGAAGAGAAGGTCGGCAAGGA 232 | AACCGTCAAGCAGCTTGGCTCCGTTACCGGCCTTGGTGCCCTGGCCAGCG 233 | AAATGGTCACCTTCTACGACGTTGTAAAATCAAGTCAAGAGGAGATCGCT 234 | GCTGCGATCCCCGCGTGGCAGGCGGCAGCCGCCGGTGACCCTTCCGGCCT 235 | GG 236 | 237 | --------------------------------------------------------------------------------