_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 7e-23 Query name: gi|755469480|gb|AHB30480.2| thioredoxin reductase 3 [Oplegnathus fasciatus] Query range: 6-602 (total 602) Target: /data/www-rg/seblastian_results/973169487/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 41323 41424 -Exon 2 50009 50069 -Exon 3 50968 51077 -Exon 4 53731 53835 -Exon 5 54049 54121 -Exon 6 55016 55131 -Exon 7 57588 57706 -Exon 8 58306 58531 -Exon 9 59220 59312 -Exon 10 65794 65870 -Exon 11 66606 66762 -Exon 12 67375 67482 -Exon 13 72110 72205 -Exon 14 75851 75985 -Exon 15 76125 76190 Redox box: no Query SDTGKNELKSRIQQLIDSNQVVVFSKSYCPFCVK <---Intron---> VKDLFKELKVECNVVELDLIE <---Intron---> DGTNYQEMLLEMT | / ||/ |/ ||/ //||/|||/||| / < 8584bp > ||/|| | |/||//||| / < 898bp > /| / ||/| ||| Target SRAAREELRRRLLGLIEGHRVVIFSKTYCPHSAR VKELFSSLGVDCNILELDQAD EGASVQEVLSEMT tcggcggccccccgcaggccggataaattccagc gagctttcgggtaatgcgcgg gggagcggctgaa cgccgaatgggttgttagagttttgacagcagcg taattcctgtagattataac aagcgtaattcatc ccgccggggccggcctgcccgccccgcccgccgg taactttgatctccgattat tggctcggtaaggc Query GQKTVPNVFINKTHIGGCDKTLQ <---Intron---> AHKDGSLQQLLSGENEAYDYDLIVIGGGSGGLACSK <---Intron---> EAALLGKKA |/|||//|/|/ |/|||| | | < 2653bp > ||/ | ||||| // ||||||||||||||||/|// < 213bp > |||/||/| Target NQRTVPSIFVNRVHVGGCDHTFQ AHQSGLLQQLLQ-QDLAYDYDLIVIGGGSGGLSCAQ EAAVLGRKV acaagcaatgaagcgggtgcatc gccagttccccc-cgcgtgtgcagagggtggcttgc ggggcgaag aagctcgtttagtatgggaacta caaggttaatta-aatcaaaattttgggcggtcgca accttggat cggtgccctgtagcgcttcctcg atgttaaggccg-gcggcccccccccgccgccgctg acccggggc Query MVLDYVVPTPKGTTWG <---Intron---> LGGTCVNVGCIPKKLMHQTALLGTAMQDARKFGWEFDE <---Intron---> TVKHNWETMKMAVN ||||/|||/|/|| || < 894bp > |||||||||||||||||| |||| |/ |/||||||/ / < 2456bp > Target MVLDFVVPSPRGTAWG LGGTCVNVGCIPKKLMHQAALLGQALTDSRKFGWEYSQ -------------- agcgtggctccgagtg cggatgaggtacaacaccggccgcgcagtaatgtgtac -------------- tttatttcccggccg gtggcgtatggtcaattaaccttgactcacgatggaaga -------------- gtgccgcaccccgcg tttcgtgttctcgggggcgtggaggggcccggccggctg -------------- Query NYIGSLNWGYRVALRDKNVNYVNAYAEFIEPHKIKAINKRGKETFYTAAKFVLATGERPRYLGIPGDKEYCITS <---Intron---> DDLFSLSYCP || |//|/| |||||||/|||/||||||||||/|||||| < 599bp > |||||| ||| Target ----------------------------------KATNEKGQEALYTAAKFVIATGQRPRYLGIPGDREYCITS DDLFSLPYCP ----------------------------------agaagagcggctaggatgagagcaccttgacggagttaaa ggcttccttc ----------------------------------accaaagaactacccatttccgagcgatgtcgagaagtcg aattctcagc ----------------------------------gactgaagggtcttggtccgaagggccgacgacagcccc cccgcggcccg Query GKTLVIGASYVALECGGFLAGLGLDVTVMVRSILLRGFDQDMANRAGEHMEEHGVKFLRKYVPVK <---Intron---> VEELEAGTPGRLKVTAKST | |||/||||||||| ||||||||/|||||||/|||||||/|| / | /// ||/||||/|||/ < 688bp > |//|| | |||||| |||| Target GTTLVVGASYVALECAGFLAGLGLEVTVMVRSVLLRGFDQEMAEKVGACLQQLGVRFLRKFVPVE VQQLEKGLPGRLKVVAKST gaacggggttggcgtggtcggcgcggagagctgcccgtgcgaggagggtccccggctccatgcgg gcccgagccgacagggata gcctttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcgtaatgtgttgattcta taataagtcggtattcacc cgcgggcgccggggtaccgccgcggcacggcggcggcccgggcgggcccgggccgccgcgcgcgg cgggggcgcggggcgtacg Query ETDEIIEGEYNT <---Intron---> VLIAVGRDACTDKIGLDKTGVKVNPK <---Intron---> NGKIPVNDEEQTNVPHIYAIGDILEGKWEL | | /|| ||| < 6481bp > ||/|/|||/|| |/||/| || // | < 735bp > |||||| ||||/||//||/||/|||| /| Target EGTETMEGVYNT VLLAIGRDSCTKKLGLEKIGVNISEK TGKIPVNGEEQTSVPYVYAVGDVLEGKPQL ggagaagggtaa gttgagcgttaaatgcgaaggaaaga agaacgagggcaagctgtgggggcggaccc agcactagtaac tttctggacgcaatgtaatgtatgaa cgatctagaaacgtcatactgattagacat agagaggctccg tgaatttcccgggaggggttgtctg ggcgcaatcgggctgctcctcgccggcgggc Query TPVAIQAGKLLARRLYGGSKLK <---Intron---> CDYVNVPTTVFTPLEYGACGLSEERATELYGKDNIE <---Intron---> VFHSLFWPLE ||||//|||||||||/|| | < 612bp > |||||||| |||||||| || |||/| |/ /|/ < 4627bp > |/|/|||||| Target TPVAVRAGKLLARRLFGGRSEK CDYVNVPTVVFTPLEYGCCGYSEEKAGEVCQAENLG VYHTLFWPLE acgggcggaccgcactggctga tgtgagcaggtactgtgttgttggaggggtcggacg gtcacttccg cctctgcgattcggttgggcaa gaatatcctttcctaaggggacaaacgatgacaatg taacttgcta cgccgggcggggagttgcaagg tcccccccggcgcggccctgcagggtcggcgggtgt ccccgcgtcg Query FTVPNRDNNKCYGKIICNKLDS <---Intron---> DRVIGFHYLGPNAGEVTQGFGAAMKCGATKEQLDSTIGIHPTCAE <---Intron---> I /|| |||| || ||||||||/ < 3645bp > ||||||| |||||||/|||| |||||| ||/ ||/|||||||| | < 139bp > / Target WTVACRDNNTCYAKIICNKLDN DRVIGFHVLGPNAGEITQGFAAAMKCGLTKQLLDATIGIHPTCGE V taggtagaaattgaaataacga gcgagtcgcgcagggaacgtgggaatgcaacccggaagaccatgg g gctcggaaacgacattgaataa agttgtattgcacgatcagtccctaggtcaattacctgtaccgga t gagccaccctccggacctagcc tggaatcccagccggctggtctcggtgcaggggtcccgcccgtag g Query FTTLEVTKSSGGDITQAGCUG |||||/||/|| |||| |||| Target FTTLEITKASGLDITQKGCUG taatgaaagtgcgaacagttg tcctatcaccgtatcaagggg cccggccgggagccgggccac * Sequence until next stop: TAG * Distance CDS-SECIS: 137 ; UGA-SECIS: 140 ------- SECIS element -- id:1 -- grade:B ---- Chromosome = your_sequence Strand = + Positions = 76328 - 76398 Found by: Infernal (score=17.61) Covels (score=12.55) Stem2 length = 10 Apical loop length = 11 Insertion in stem2 = 0, 0 Free Energy = -14.7 Type = 1 ..(((((((.......(((((((((((((((................))))))))))))))).........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc ...(((({(---....{[[{((((({(((((.........-----..)))))})))))}]]}.....-...)}))))... target CUCGCUGCC---UCCUUGACGUCUUCGCUCAGAGCCGCCA-----GGUGAGCCAAGACCGACCUCUG-CCCGCCAGCUCC **** ^^ ****