├── LICENSE ├── PerlLib ├── Fasta_reader.pm └── overlapping_nucs.ph ├── README.md ├── TransposonWeb ├── TransposonDB.mysqldump └── cgi-bin │ ├── TE_report.cgi │ ├── TransposonDB.cgi │ ├── TransposonPerlLib │ ├── Mysql_connect.pm │ └── TransposonDB_API.pm │ ├── cgi_stub │ ├── genbank_to_TransposonDB_loader.cgi │ ├── illustrate_region.cgi │ ├── list_database_entries.cgi │ └── truncate_transposonDB.dbi ├── docs ├── TransposonPSI_documentation.asciidoc └── TransposonPSI_documentation.html ├── misc └── repeatIllustration │ ├── m2fmt_self_to_miropeats_fmt.pl │ ├── miropeats_illustrator.pl │ ├── mirorepeats.example.out │ ├── nucmer_coords_genome_tiler.pl │ ├── repeat_illustrator.pl │ └── repfind_illustrator.pl ├── scripts ├── .#BPbtab.1.1.1.1 ├── BPbtab ├── TBLASTN_hit_chainer.pl ├── TBLASTN_hit_chainer_nonoverlapping_genome_DP_extraction.pl ├── TPSI_btab_to_gff3.pl ├── TPSI_chains_to_fasta.pl ├── TPSI_chains_to_gff3.pl ├── m2fmt_tier_hits.pl └── transposon_db_m2fmt_to_gff3.pl ├── test ├── runMe.sh └── target_test_genome_seq.fasta ├── transposonPSI.pl ├── transposonPSIcreate ├── BPbtab ├── CACTA │ ├── cacta.chkp │ └── cacta.refSeq ├── DDE_tp1 │ ├── DDE_1.chkp │ └── DDE_1.refSeq ├── ISC1316 │ ├── isc1316.chkp │ └── isc1316.refSeq ├── ISa-element │ ├── ISa.chkp │ └── ISa.refSeq ├── ISb-element │ ├── ISb.chkp │ └── ISb.refSeq ├── LINE │ ├── line.chkp │ └── line.refSeq ├── MuDR │ ├── MuDR.chkp │ └── MuDR.refSeq ├── P-element │ ├── P_element.chkp │ └── P_element.refSeq ├── PSIBLAST │ ├── create_PSI_BLAST_profile.pl │ └── run_PSI_BLAST.pl ├── TPSI_library │ ├── ISa.chkp │ ├── ISa.refSeq │ ├── ISb.chkp │ ├── ISb.refSeq │ ├── MuDR.chkp │ ├── MuDR.refSeq │ ├── P_element.chkp │ ├── P_element.refSeq │ ├── TY1_Copia.chkp │ ├── TY1_Copia.refSeq │ ├── cacta.chkp │ ├── cacta.refSeq │ ├── gypsy.chkp │ ├── gypsy.refSeq │ ├── hAT.chkp │ ├── hAT.refSeq │ ├── isc1316.chkp │ ├── isc1316.refSeq │ ├── line.chkp │ ├── line.refSeq │ ├── mariner.chkp │ └── mariner.refSeq ├── TY1_Copia │ ├── TY1_Copia.chkp │ └── TY1_Copia.refSeq ├── chainMatches.pl ├── chain_summarizer.pl ├── create_transposon_psiProfile.pl ├── gypsy │ ├── gypsy.chkp │ └── gypsy.refSeq ├── hAT_element │ ├── hAT.chkp │ └── hAT.refSeq ├── ltr_Roo │ ├── ltr_Roo.chkp │ └── ltr_Roo.refSeq ├── mariner │ ├── mariner.chkp │ └── mariner.refSeq ├── mariner_ant1 │ ├── mariner_ant1.chkp │ └── mariner_ant1.refSeq └── transposonPSI.pl ├── transposon_ORF_lib └── transposon_db.pep └── transposon_PSI_LIB ├── DDE_1.chk ├── DDE_1.chkp ├── DDE_1.refSeq ├── ISa.chk ├── ISa.chkp ├── ISa.refSeq ├── ISb.chk ├── ISb.chkp ├── ISb.refSeq ├── MuDR.chk ├── MuDR.chkp ├── MuDR.refSeq ├── P_element.chk ├── P_element.chkp ├── P_element.refSeq ├── TY1_Copia.chk ├── TY1_Copia.chkp ├── TY1_Copia.refSeq ├── TyrRecombinaseCrypton.chk ├── TyrRecombinaseCrypton.chkp ├── TyrRecombinaseCrypton.refSeq ├── cacta.chk ├── cacta.chkp ├── cacta.refSeq ├── gypsy.chk ├── gypsy.chkp ├── gypsy.refSeq ├── hAT.chk ├── hAT.chkp ├── hAT.refSeq ├── helitron.chk 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