_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 9e-94 Query name: gi|930235540|ref|XP_014162892.1| PREDICTED: selenoprotein P isoform X2 [Geospiza fortis] Query range: 1-357 (total 357) Target: /data/www-rg/seblastian_results/940527054/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: - Positions: -Exon 1 52995 53074 -Exon 2 51699 51911 -Exon 3 50000 50117 -Exon 4 48494 49153 Redox box: YES Query MWNSRGSVTVVALLQASULLCLQQASS <---Intron---> LEDLRLKLENEGLVNISYVVVNHQGAQSRREFHLLKEHVSDYITVYQQDEHQEDVWT ||/|||||||||||||||||||/|||| < 1083bp > |||||/|||||||||||||/||||||||||||||||| |||||||||||| |||||| Target MWSSRGSVTVVALLQASULLCLRQASS LEDLRVKLENEGLVNISYVIVNHQGAQSRREFHLLKERVSDYITVYQQDEQQEDVWT atatcgtgagggcccgattttcccgta tggccgatgaggtgaattgagaccggctcagtcccagcgtgtaagtccggccgggta tggcggctcttcttacggttgtgaccg taatgtataaagttatcatttaaagcacggatattaagtcaatctaaaaaaaaatgc ggccacggaggtccgtcaggcgggtc tggcgaagagtaagcccgtgtcctgatacggatcaaaattaccttccgatggagtcgt * Query TLNGNKDDFLIYDR <---Intron---> CGRLVYHLGMPYSFLHFQYVEESIKIAYCENKCGNCSYM <---Intron---> EPDIDGVCENITKKA |||||||||||||| < 1581bp > ||||||||||||||||||||||||||||||||||||||| < 846bp > ||| ||||||||||| Target TLNGNKDDFLIYDR CGRLVYHLGMPYSFLHFQYVEESIKIAYCENKCGNCSYM EPDTDGVCENITKKA atagaaggtcatga tgccgtccgactttcctctgggtaaagttgaatgattta gcgagggtgaaaaag ctagaaaatttaag gggttaatgtcacttataataactatcagaaaggagcat acacagtgaatcaac tatacgtctcctc acctcgttgtgccccgttgtgaactgtactacgtacctcg gtttttttacctaaa Query VEELSEIEHEPTDQHSHPNPHRHGHHHRRHHHRHRHQGSRDPKHENHQAAAEADRHHPHSAWRHRLFGRHRHNQTGSQEHVDTAPPGEIVEIPQDKKLRK |||||||| /||||||| |||||||||||||| | /||||||||||||||| /|||| | |||||||||||/| ||||||||||||||||||||||||| Target VEELSEIESKPTDQHSHRNPHRHGHHHRRHHHHHHQKGSRDPKHENHQAAAETERHHPPSGWRHRLFGRHRHDQIGSQEHVDTAPPGEIVEIPQDKKLRK gggctgagtacagcctccaccacgccccccccccccagacgcacgaccggggagaccccagtccactgccacgcagacgcggagccggaggaccgaacca taatcatacaccaaacagacagagaaaggaaaaaaaagggacaaaaaacccacagaaccggggagttggagaaatggaaataccccgattatcaaaatga taggagaacggacgtctccacatacccccccctctggctttcacgccgtttatgatttcccgccgctcccactgattggcactctaaatgataataaaag Query KGKNSCKNQLTUNWQTGSDSTSGSUSCHCRHLLFEELGNSVTUQCRGALPNSCRUHGQQAAEDVTESUQCRLLSAVUHSSPAGASETSDTUQUQEKARNU ||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||| |||||||||||||||||||||||| Target KGKTICKNQLTUNWQTGSDSTSSSUSCHCRHLLFEELGNSVTUQCRGALPNSCRUHGQLAAEDVTESUQCRLLSAAUHSSPAGASETSDTUQUQEKARNU agaaataactatatcagtgtataatttctcccctggcgatgatctcggccattatcgccgggggagttctccctggtcttcgggagaagatctcgagaat agactgaaatcgagacgcacccgggcgaggatttaatgactcgagggctcacgggagatccaatcacgaggttcccgaccccgcgacgacgagaaacgag agacccacgatatggaaactcttcactttactgtagagttccagttaaaattcgacgggaagcctgtagctgcttcataaaaaatattccagagagagca * * * * * * * * * Query SUKTN ||||| Target SUKTN ttaaa cgaca caaac * Sequence until next stop: TAA * Distance CDS-SECIS: 306 ; UGA-SECIS: 315 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = - Positions = 48187 - 48116 Found by: Infernal (score=36.54) Covels (score=35.74) Stem2 length = 11 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -23.64 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ..(({(((((--....{[[(((((((((([(.....-.........)]))))))))))]]}..--..-)))))})).. target UCUGCUUGCA--UUUGUGAGGACAGGAGCAUAAACU-AUGACCUAGGGGCUCCUGUCUGAUGU--UU-UGCAAUCAAG **** ^^^ **** _________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:2 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 9e-94 Query name: gi|930235540|ref|XP_014162892.1| PREDICTED: selenoprotein P isoform X2 [Geospiza fortis] Query range: 1-357 (total 357) Target: /data/www-rg/seblastian_results/940527054/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: - Positions: -Exon 1 52995 53074 -Exon 2 51699 51911 -Exon 3 50000 50117 -Exon 4 48494 49153 Redox box: YES Query MWNSRGSVTVVALLQASULLCLQQASS <---Intron---> LEDLRLKLENEGLVNISYVVVNHQGAQSRREFHLLKEHVSDYITVYQQDEHQEDVWT ||/|||||||||||||||||||/|||| < 1083bp > |||||/|||||||||||||/||||||||||||||||| |||||||||||| |||||| Target MWSSRGSVTVVALLQASULLCLRQASS LEDLRVKLENEGLVNISYVIVNHQGAQSRREFHLLKERVSDYITVYQQDEQQEDVWT atatcgtgagggcccgattttcccgta tggccgatgaggtgaattgagaccggctcagtcccagcgtgtaagtccggccgggta tggcggctcttcttacggttgtgaccg taatgtataaagttatcatttaaagcacggatattaagtcaatctaaaaaaaaatgc ggccacggaggtccgtcaggcgggtc tggcgaagagtaagcccgtgtcctgatacggatcaaaattaccttccgatggagtcgt * Query TLNGNKDDFLIYDR <---Intron---> CGRLVYHLGMPYSFLHFQYVEESIKIAYCENKCGNCSYM <---Intron---> EPDIDGVCENITKKA |||||||||||||| < 1581bp > ||||||||||||||||||||||||||||||||||||||| < 846bp > ||| ||||||||||| Target TLNGNKDDFLIYDR CGRLVYHLGMPYSFLHFQYVEESIKIAYCENKCGNCSYM EPDTDGVCENITKKA atagaaggtcatga tgccgtccgactttcctctgggtaaagttgaatgattta gcgagggtgaaaaag ctagaaaatttaag gggttaatgtcacttataataactatcagaaaggagcat acacagtgaatcaac tatacgtctcctc acctcgttgtgccccgttgtgaactgtactacgtacctcg gtttttttacctaaa Query VEELSEIEHEPTDQHSHPNPHRHGHHHRRHHHRHRHQGSRDPKHENHQAAAEADRHHPHSAWRHRLFGRHRHNQTGSQEHVDTAPPGEIVEIPQDKKLRK |||||||| /||||||| |||||||||||||| | /||||||||||||||| /|||| | |||||||||||/| ||||||||||||||||||||||||| Target VEELSEIESKPTDQHSHRNPHRHGHHHRRHHHHHHQKGSRDPKHENHQAAAETERHHPPSGWRHRLFGRHRHDQIGSQEHVDTAPPGEIVEIPQDKKLRK gggctgagtacagcctccaccacgccccccccccccagacgcacgaccggggagaccccagtccactgccacgcagacgcggagccggaggaccgaacca taatcatacaccaaacagacagagaaaggaaaaaaaagggacaaaaaacccacagaaccggggagttggagaaatggaaataccccgattatcaaaatga taggagaacggacgtctccacatacccccccctctggctttcacgccgtttatgatttcccgccgctcccactgattggcactctaaatgataataaaag Query KGKNSCKNQLTUNWQTGSDSTSGSUSCHCRHLLFEELGNSVTUQCRGALPNSCRUHGQQAAEDVTESUQCRLLSAVUHSSPAGASETSDTUQUQEKARNU ||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||| |||||||||||||||||||||||| Target KGKTICKNQLTUNWQTGSDSTSSSUSCHCRHLLFEELGNSVTUQCRGALPNSCRUHGQLAAEDVTESUQCRLLSAAUHSSPAGASETSDTUQUQEKARNU agaaataactatatcagtgtataatttctcccctggcgatgatctcggccattatcgccgggggagttctccctggtcttcgggagaagatctcgagaat agactgaaatcgagacgcacccgggcgaggatttaatgactcgagggctcacgggagatccaatcacgaggttcccgaccccgcgacgacgagaaacgag agacccacgatatggaaactcttcactttactgtagagttccagttaaaattcgacgggaagcctgtagctgcttcataaaaaatattccagagagagca * * * * * * * * * Query SUKTN ||||| Target SUKTN ttaaa cgaca caaac * Sequence until next stop: TAA * Distance CDS-SECIS: 1011 ; UGA-SECIS: 1020 ------- SECIS element -- id:2 -- grade:A ---- Chromosome = your_sequence Strand = - Positions = 47482 - 47414 Found by: Infernal (score=21.68) Covels (score=15.64) Stem2 length = 10 Apical loop length = 10 Insertion in stem2 = 0, 0 Free Energy = -15.1 ..(((((((.......((((((((((.(((((...............))))).))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc .((({((((---....([[{((((({{(((((........-----..)))))}})))))}]])..--..-.))))}))). target ACACCAUAA---UUAAUGAUGGUUUAAUAGGGAAAUUACU-----ACUCCUACAAAACCUGAAUC--UU-UUUAUUGUGA **** ^^^ ****