Query name: gi|170671712|ref|NP_001116249.1| thioredoxin reductase 3 [Gallus gallus] Query range: 1-606 (total 606) Target: /data/www-rg/seblastian_results/477427173/tempfiles/temptarget.fasta Chromosome: SJPD01000007.1:subseq_20875190,114209_ Strand: + Positions: -Exon 1 30492 30614 -Exon 2 47818 47878 -Exon 3 50028 50137 -Exon 4 50994 51113 -Exon 5 53097 53169 -Exon 6 54931 55050 -Exon 7 56066 56208 -Exon 8 57537 57652 -Exon 9 57759 57984 -Exon 10 58178 58270 -Exon 11 59118 59194 -Exon 12 61455 61611 -Exon 13 62145 62252 -Exon 14 62662 62757 -Exon 15 64072 64206 -Exon 16 66040 66105 Redox box: no Query MPPPGQTQLPDWDGLKLRVRTLIATHRVMIFSKSYCPYCHR <---Intron---> VKELFSSLGVQYYALELDVTD <---Intron---> DGPSIQ |||||| /||||| ||||||/||/ ||||/|||||||/| / < 17203bp > ||/|| ||||/| ||||| | < 2149bp > /||||| Target MPPPGQVRLPDWDALKLRVRSLISNHRVMVFSKSYCPFCRK VKDLFHSLGVEYSALELDKID EGPSIQ acccgcgcccgtggcaccgcacaaaccgagtaaattcttca gagctcttgggtagtgcgaag ggcaac tcccgatgtcagactatgtggttgaagttttgagagctgga taattactgtaagctataat aagcgta ggtacgcgggcgcgggccggccccccccgctcgccctttag gattttggagacttggtcgt taacttg Query QVLAELTNQRTVPNVFINGKHIGGCDATYK <---Intron---> AYENGTLQRILGDVKDAET--YDYDLIVIGGGSGGLACSK <---Intron--- /|| ||| ||||||||/|| |/|||| |// < 856bp > || /| ||//||| | || ||||||||||||||||||| < 1983bp Target EVLLELTGQRTVPNVFVNGTHVGGCDQTFQ AYHSGLLQKLLGDGKGEETEAYDYDLIVIGGGSGGLACSK ggtcgtagcaagcagtgagacgggtgcatc gtcagttcactgggagggaggtgtgcagagggtggcgtta atttatcgagctcatttagcatgggaacta caaggttaattgagagaacacaaaattttgggcggtcgca aaacagtcgatcttttataatgtattaatg tcttaagagtagtcataggacttttattttatttatattg Query > EAATLGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALKDSRAYGWQYDEQV <---Intron---> K > ||||||||||||||||||||||/|| < 1761bp > ||||||||||||||||||||||||||/||| /||/||/|| < 1015bp > | Target EAATLGKKVMVLDYVVPTPLGTTWG LGGTCVNVGCIPKKLMHQAALLGQALQDSRKFGWEYDQQV K gggatgaagagcgtggcaccgaatg cggatgaggtacaacaccggctgcgtcgtaatgtgtgccg a accctgaattttaattccctgccg gtggcgtatggtcaattaaccttgactaacgatggaaaaa ta atccaggggggatttaaaagttag attcttatttcttgaggtgactacgagacaggtcggttga ta Query HNWEIMVEAVQNYIGSLNWGYRLSLREKSVTYQNSYGEFVEPHKIK <---Intron---> ATNRKGQVTYHTAETFVLATGERPRYLGIPGDKEYCIT |||| ||||/||/|||||||||//||||/||| |/||||| |||| < 1328bp > ||||||| |//||/ ||/|||||||||||||||||||| Target HNWETMVEAIQNHIGSLNWGYRVALREKTVTYLNAYGEFVGSHKIK ATNRKGQETFYTAQAFVIATGERPRYLGIPGDKEYCIT catgaagggacacagttatgtcggtcgaagatcagtggtggtcaaa gaaaagcgattagcgtgagaggaccttgacggagttaa aagacttactaaatgctaggagtctgaactcatacagattgcaata ccagagaactaccactttccgagcgatgtcgaaaagtc ccggcgtaatattaacgcgttgacgtggttacctctggttgccgcg accaaaaatctatgatctctaaatatatcaacaactta Query S <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKIGAHMETHGVTFIRKFVPTQ <---Int | < 106bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||/ ||/|||||| ||/|||| / < 193 Target S DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAERAGAYMETHGVKFIKKFVPIE a ggctttcttcgaatggggttggcgtggtcggcgtggagagctatccgtgcgaggagggtagacggataaatgcag g aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcagcgcatacagtattaattcta tttccagccttagtgtgattcatgattatttcatgtcatggctcattcttaagagaatctgatttagccggttttg Query ron---> VERLEDGTPGRLKVTAKSTEGPEFFEGEYNT <---Intron---> VLIAIGRDACTRNIGLQTIGVKINEK <---Intron---> NGK bp > | /|||| |||||| |||||| / | |||| < 847bp > ||||/||||||/|||| |||||||| < 2260bp > ||| Target VIKLEDGMPGRLKVVAKSTEGLQIIEEEYNT VLIAVGRDACTKNIGLDKIGVKINEK NGK gaatgggacgacagggataggtcaagggtaa gtagggcggtaaaagtgaaggaaaga aga ttataagtcggtattcaccagtattaaaaac tttctggacgcaatgtaatgtataaa aga tagggtcgtaacagtaactaaagttaaatct tgatttttttgattcacattgatta gtga Query VPVNDEERTNVPYVYAIGDILDGKLELTPVAIQAGKLLARRLYGGSSTK <---Intron---> CDYINVPTTVFTPLEYGSCGLAEEKAIEEYGKQNL /||||||/| ||||||/||||/||||||||||||||||||||/|||| | < 533bp > ||||||||||||||||| ||| ||/|/|/ |//|/ Target IPVNDEEQTIVPYVYAVGDILEGKLELTPVAIQAGKLLARRLFGGSSIK CDYINVPTTVFTPLEYGCCGLPEERAVEQLGQENI acgagggcaagctgtggggatggacgcacggacggactgcactggataa tgtaagcaagtaccgtgttgtcggcgggccgcgaa tctaaaaacttcatactgattagatatcctctacgattcggttgggcta gaatatcccttcctaaggggtcaagctaatgaaat atgttaaactgttctttcttgaagtataatcagacggaccattagcaag ttcctcatagtatgatattaaaaacttaataaata Query E <---Intron---> VYHSLFWPLEWTVPGRDNNTCYAKIICNKLDG <---Intron---> NRVVGFHVLGPNAGEVTQGFAAAIKCGLTKELLDE | < 409bp > |||/||||||||/| |||||||||/|||||| < 1314bp > |||/|||||||||||/|||||||||||/|||||/| Target E VYHTLFWPLEWTIPSRDNNTCYAKVICNKLDK NRVIGFHVLGPNAGEITQGFAAAIKCGITKELLNE g gtcatttccgtaacaagaaattgagataacga acgagtcgcgcagggaacgtgggaatgaaagtcag a taacttgctagctcggaaacgacattgaataa agttgtattgcacgatcagtccctaggtcaattaa g atttgcgatagaaccaccctttaaccctgtca ctgaattttgtttgatcgataaaagtccggaatta Query TIGIHPTCAE <---Intron---> VFTTMDITKSSGQDITQRGCUG |||||||||| < 1833bp > ||||||||||||/|||| |||| Target TIGIHPTCAE VFTTMDITKSSGKDITQSGCUG aagaccatgg gtaaagaaattgagaacagttg ctgtaccgca ttcctatcaccgaatcaggggg attatattag cctagctagtagatctgtccat * Sequence until next stop: TAA * Distance CDS-SECIS: 216 ; UGA-SECIS: 219 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = SJPD01000007.1:subseq_20875190,114209_ Strand = + Positions = 66322 - 66405 Found by: Infernal (score=26.1) Covels (score=25.18) Stem2 length = 9 Apical loop length = 18 Insertion in stem2 = 0, 0 Free Energy = -12.62 ..(((((((.......(((((((((((((((................)))))))))))))))..............))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-----u-uuucaugaccggc ..((((({(.......{[[(((({((((((..................))))))}))))]]}..........-...)}))))).. target CACUCAAGUGCAUUUUUGAAGUUUUGGCUCUGAACCUCAUCUAGAGGCGAGUCAUAGCUGAUAAUUUCUAUG-CAAAGUUGGGAA **** ^^ ****