_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 1e-04 Query name: gi|987312895|gb|AMD78106.1| thioredoxin reductase 3 [Clarias batrachus] Query range: 1-600 (total 600) Target: /data/www-rg/seblastian_results/200044427/tempfiles/temptarget.fasta Chromosome: CM008312.1:subseq_32732757,112496_ Strand: - Positions: -Exon 1 62380 62496 -Exon 2 58791 58851 -Exon 3 56448 56557 -Exon 4 55388 55495 -Exon 5 55036 55108 -Exon 6 54813 54932 -Exon 7 54379 54521 -Exon 8 53998 54113 -Exon 9 53128 53353 -Exon 10 52450 52542 -Exon 11 52286 52362 -Exon 12 51388 51544 -Exon 13 51131 51238 -Exon 14 50927 51022 -Exon 15 50027 50161 -Exon 16 49837 49902 Redox box: no Query MPPVQTDKG--QIRSRIQELIDNHLVVVFSKSYCPYCKK <---Intron---> VKEFFKEVNVTYEVLELDLIE <---Intron---> NGAIYQDV ||||/ | | ||//||||||| / |||||||||||| | < 3528bp > ||| | //|| //||||/| < 2233bp > ||/ /||/ Target MPPVEIDAGRDQIKARIQELIDTNSVVVFSKSYCPYCTK VKELFNDLNVECNIIELDLME NGSNFQDL accggagggcgcaagcacgcagaatgggtaaattcttaa gagctagtaggtaaagcgtag agtatcgc tcctatacggaatacgtaattacacttttgagagcagca taattaatatagattatatt aagcataat gggagccccgcgtatgagggtcccgcggttacctcctgg aagatttgtgatcctagtgg gtccccgtg Query LMEMTGQKTVPNVFVNKTHVGGSDKTMQ <---Intron---> AYKDGHLKQLLGEESTAYDYDLIVIGGGSGGLACSK <---Intron---> EAAA |||||||||||||||||||||| | |// < 952bp > |/||| |/||||//| ||||||||||||||||||| < 279bp > ||| Target LMEMTGQKTVPNVFVNKTHVGGCDNTIK AHKDGLLQQLLGDKSEVYDYDLIVIGGGSGGLACSK EAAN cagaagcaagcagtgaaacgggtgaaaa gcaggccccccggaaggtgtgcagagggtggcgtta ggga ttatcgaactcatttaacatgggaacta caaagttaattgaagataaaattttgggcggtcgca acca ggggtagacctcccccgctctcttccag ataccgcggggacgcggcttcgtcaaaccacgccag aaat Query LGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQTAMLRTALEDARKFGWEFSEEV <---Intron---> SHNWETM ||||||||||||||| ||/|| < 103bp > ||||||||||||||||||||// |||/|||||||||||/| < 291bp > ||||||| Target LGKKVMVLDYVVPTPKGTTWG LGGTCVNVGCIPKKLMHQTALMGTALQDARKFGWEFSEQV SHNWETM tgaagagcgtggcacagaatg cggatgaggtacaataccagcagagtcggcatgtgtagcg acatgaa tgaattttaattcccagccg gtggcgtatggtcaattaaccttgcctaacgatggatgaa tgaagact ggggcgtgtttccatgctcg tgtcttgcacttagaagcgtaagtgcgatttatcggctga gctcggag Query KTAVNNYIGSLNWGYRVSLRDKNVNYVNAYGEFVEPHKIK <---Intron---> ATNKRGKETFYTAAKFVLATGERPRYLGIPGDKEYCITS <--- ||||||||||||||||||||||||||||/| ||||||||| < 265bp > |||/||||||/|||||||||||||||||||||||||||| < Target KTAVNNYIGSLNWGYRVSLRDKNVNYVNSYAEFVEPHKIK ATNRRGKETFHTAAKFVLATGERPRYLGIPGDKEYCITS aaggaatagttatgtagaccgaagatgattggtggccaaa gaaacgagatcaggatgcgaggccctcgacggagttaaa acctaaatgctaggagtgtgaaataatacacattacaata ccagggaactacccatttccgagcgatgtcgaaaagtcg gtagtcctttgcgtcagtcacgccctcctcagtggtcacg catgttggatcaacatgggtagggccgcccatagcccc Query Intron---> DDLFYLSYCPGKTLVIGASYVALECGGFLAGLGLDVTIMVRSILLRGFDQDMANRAGDHMETHGVKFLRKFVPIK <---Intron--- 644bp > |||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/| < 585bp Target DDLFSLPYCPGKTLVIGASYVALECGGFLAGLGLDVTIMVRSILLRGFDQDMANRAGDHMETHGVKFLRKFVPVK ggctttcttcgaacgaggttggcgtggtcggcgcggaaagctaccagtgcgagacgggcagacggatccatgcga aattctcagcgactttgccatctagggttcgtgtatctttgctttggtaaatcagcgaatacagtattgattcta ttcgccacttttgaagcaaactttgccgcgttggatccagacctggacccgcgcctaaccggatgcaccgattttg Query > IEQLEAGSPGRLKVTAKSTETDEIIEGEFNT <---Intron---> VLIAVGRDACTGTIGLDKAGVIVNSK <---Intron---> NGKIPVNDG > /|/||||/|||||||||||||||| |||/|| < 87bp > ||||||||||| ||||/||| || | < 741bp > |||||||| Target VEELEAGTPGRLKVTAKSTETDEIFEGEYNT VLIAVGRDACTEKIGLDQAGVKVNPK NGKIPVNDE gggcgggacgatagagatagaggatgggtaa gtagggcggtagaagcgcgggagaca agaacgagg taatacgccggtatccaccacaattagaaac tttctggacgcaatgtaacgtataca agatctaaa gagtattttcagaatcgcaattgctaaacct ggatttttccaagcattgttggctg gtggcaactg Query EQTNIPHVYAIGDILEGKWELTPVAIQAGRLLARRLYAGSSVK <---Intron---> CDYVNVPTTVFTPLEYGSCGLSEEKSIELYGEENLE <--- |||||||/|||||||||||||||||||||/|||||||||/|/| < 149bp > |||||||||||||||||||| ||///||||/|||| < Target EQTNIPHIYAIGDILEGKWELTPVAIQAGKLLARRLYAGASLK CDYVNVPTTVFTPLEYGSCGHPEERAVELYGQENLE gcaaaccatgaggacggatgcacggacggaccgcactgggtca tgtgagcaagtactgtgatgccggagggctgcgacg aacatcatactgattagagatcctctacgattcggtacgccta gaatatcccttcctaaggggacaagctatagaaata agcctaccttcaccggcggagatgttgtgaggtcgctaaatgg tctgttcctgccaggtccttcagagtaaatagacgg Query Intron---> IFHSLFWPLEYTIPNRDNNRCYAKIICNKLDD <---Intron---> DRVIGFHYLGPNAGEVTQGFGAAMKCGVTKEQLDTTIGIHP 108bp > //||||||||||/||||||||||||||||||| < 765bp > /||||||||||||||||||||||||||||||||| |||||| Target VYHSLFWPLEYTVPNRDNNRCYAKIICNKLDD NRVIGFHYLGPNAGEVTQGFGAAMKCGVTKEQLDNTIGIHP gtcacttccgtagcaagaaattgaaataatgg acgagtcttgcaggggacgtgggaatggaagccgaaagacc taagttgctaactcagaaaggacattgaataa agttgtaatgcacgatcagtgcctaggtcaaataactgtac ttctgtgtggccactgcccaccagatccgact ctgttcttgccccggctgcttttggtgccgaggttctgacc Query TCAE <---Intron---> IFTTMEVTKRSGGDIKQAGCUG |||| < 124bp > ||||||||||||||| |||||| Target TCAE IFTTMEVTKRSGGDITQAGCUG atgg ataaaggaactgggaacggttg cgca ttcctatcagcggatcacgggg cctg cccagggcggattcctgtacat * Sequence until next stop: TAA * Distance CDS-SECIS: 530 ; UGA-SECIS: 533 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = CM008312.1:subseq_32732757,112496_ Strand = - Positions = 49306 - 49231 Found by: Infernal (score=33.0) Covels (score=27.79) Stem2 length = 10 Apical loop length = 19 Insertion in stem2 = 0, 0 Free Energy = -16.51 ..(((((((.......(((((((((((((((.................)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc .((((((((.--....{[[{((((((((((...................))))))))))}]]}..--....)))))))). target CUCUAAGUGC--UAUGUGAUGUUUUAGCUCUUAACCUAAAUGCUAAGGUGGGCUAAAGCUGAUGU--UCUCUGCUUAGAC **** ^^ ****