Entering edit mode
2.4 years ago
lukhanyomakhabane
▴
30
Hello good people Below is an REPET annotation file.gff out, there are transposable elements classified as match or match part. Do we consider both match and match part or it is advisable to only consider those transposable elements with match in terms of TE content. Does Match imply that its a complete match? what are about partial match? I tried to search but nothing, your help would be greatly appreciated.
supercontig_1.1 REPET_FLF match 100739 100920 0.0 - . ID=ms1;Target=Mivi-B-P10.18-Map3_NoCat+496+684;target_length=686;target_description=SSRs:coverage:0.03<0.95;alignlength=182;alignident=0.943182;tegaps=0.745665;alignscore=1424
supercontig_1.1 REPET_FLF match_part 100739 100920 0.0 - . ID=mp1-1;Target=Mivi-B-P10.18-Map3_NoCat+496+684;Parent=ms1;alignlength=182;alignident=0.943182;tegaps=0.745665;alignscore=1424
supercontig_1.1 REPET_FLF match 555 1143 0.0 + . ID=ms2;Target=Mivi-B-P23.13-Map4_classII-TIR-incomp+4+592;target_length=595;target_description=struct:TIRs 11nt;alignlength=589;alignident=0.976231;tegaps=0.010084;alignscore=5638
supercontig_1.1 REPET_FLF match_part 555 1143 0.0 + . ID=mp2-1;Target=Mivi-B-P23.13-Map4_classII-TIR-incomp+4+592;Parent=ms2;alignlength=589;alignident=0.976231;tegaps=0.010084;alignscore=5638
supercontig_1.1 REPET_FLF match 218 2048 0.0 + . ID=ms4;Target=Mivi-B-R21-Map15_classII-TIR-incomp+1+1278;target_length=1278;target_description=struct:TIRs 243nt - profiles:HMMER PF03108.8_MuDR_Tase_21.8 39nt
