_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 1e-27 Query name: gi|315138999|ref|NP_001186707.1| selenoprotein N precursor [Taeniopygia guttata] Query range: 37-533 (total 533) Target: /data/www-rg/seblastian_results/598126556/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: - Positions: -Exon 1 58898 59021 -Exon 2 57771 57901 -Exon 3 57123 57335 -Exon 4 56337 56461 -Exon 5 55563 55700 -Exon 6 54427 54508 -Exon 7 53355 53543 -Exon 8 52307 52412 -Exon 9 51256 51368 -Exon 10 50515 50616 -Exon 11 49997 50164 Redox box: no Query QQELALKSLGNEGLFLFSSLDTNKDLYLSPEEFKPIAEKLTG <---Intron---> VPAVSESEEEETPDPDGETLSIVAKFQPLLMETMTKSKDGFL ||||||||| ||||||||||||||||||||||||||||||| < 996bp > | |||||||||||||||||||||||||||||||||||||||| Target NQELALKSLGKEGLFLFSSLDTNKDLYLSPEEFKPIAEKLTG VAAVSESEEEETPDPDGETLSIVAKFQPLLMETMTKSKDGFL acgcgcattgaggctctttcgaaagctcacggtacaggacag ggggtgtggggacgcgggactaggatcctcagaaaaaaggtt aaatctactgaagttttcctacaaatatgcaatactcaatc gtcctcacaaaaccacagactcttcatactttactcagaagtt cgggtggcggggggcccncgcccgcgcgcaggcacttggca gttagagtagggggtatggtgccgcgcgcgcgaagggcgttcg Query G <---Intron---> ISHVALSGLRNWTAPAAPMSVLLARQFKAFLPPKDNLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKE <---Intron- | < 435bp > ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 661bp Target G ISHXALSGLRNWTAPAAPMSVLLARQFKAFLPPKDNLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKE g atcngctgcaatagcggcaagccgactagtcccagacgcggcttaacagcaatagtctaaattccccagag g tcatctcgtgagcccccctgtttcgatacttccaaatatgacggttcgatattcgatcaagtaccccagaa a ttcgtgtgcgcgacaaccgtcgtcggcacccttgctgttgtcggatctggccctgtccccgtctatcgcag Query --> VIIHKLLSMFHPRPFVRTRFAPQGAVACIQASSSFYYTIAFR <---Intron---> IHAEFQLNEPPNFPFWFSPGQFTGYIVLSKDSSHIRDF > |/||/|||||||||||||||||||||||/||||||||||||| < 636bp > | ||||||||||||||||||||||||||||||||/||| Target VLIHRLLSMFHPRPFVRTRFAPQGAVACLQASSSFYYTIAFR IXAEFQLNEPPNFPFWFSPGQFTGYIVLSKDSSHVRDF gcacaccaatcccctgcactgccggggtccgaaatttaagtc acggtccagccatcttttcgctagtagctagttcgagt tttagttgttacgcttgcgtccagctcgtacgggtaactctg tacatataaccatctgtccgatcgatttcaaccatgat gcccgggcgccgccccggcccggacgccggccccccccaac gcntacggcgaaccccgccgggcatctcgcgctcccgcc Query RLFVPNNR <---Intron---> SLNVDMEWLYGASESSNMEVDIGYLPQ <---Intron---> MELESTGPSVPTVIHDENGNVLDSRDPSGEPIQ |||||||| < 1054bp > ||||||||||||||||||||||||||| < 883bp > |||||||||||/|||||/| || |||||||||| Target RLFVPNNR SLNVDMEWLYGASESSNMEVDIGYLPQ MELESTGPSVPSVIHDEDGKVLASRDPSGEPIQ actgcaaa tcaggagtctggagaaaagggagtccc agcgtagctgctgacggggagcgaagctggcac gtttcaag ctatatagtagcgaggatatatgatca tataccgcctccttaaaagattcggaccgacta gctttcc gcgcgcgggccggcgcccgggctacgcg gggacagcggcggcctgcggcgccgccgggccg Query FVFEEITWQQEIPWQEAAHRLEVAMYPFKK <---Intron---> ISYLPFTEAFERAQAEKKLVHSILLWGALDDQSCUG <---Intron---> SG ||||||||||/||||||||||||||||||| < 942bp > /||||||||||||||||||||||||||||||||||| < 938bp > || Target FVFEEITWQQQIPWQEAAHRLEVAMYPFKK VSYLPFTEAFERAQAEKKLVHSILLWGALDDQSCUG SG tgtggaatcccactcgggcacgggatctaa gttcctaggtgagcggaacgctacctggcggctttg tg tttaatcgaaatcgaaccagtatctactaa tcatctcactagcacaaattactttggctaaacgg gcg tgtggccggggccgggaccggggcgtatgg cccgccaactgaaaagggggcccgggtcgtcgcca tgg * Query RTLRETVLESSPILALLNESFISSWSLVKELEELQ <---Intron---> SNRENEFYSKLAKLHLEKYNFPVEMIICLPNGTV <---Intron---> ||||||||||||||||||||||||||||||||||| < 639bp > |||||| /|||||||||||||||||||||| ||| < 350bp > Target RTLRETVLESSPILALLNESFISSWSLVKELEELQ SNRENELHSKLAKLHLEKYNFPVEMIICLPXGTV caccgagcgatcacgccagataaatttgagcggcc aaagagccaacgacccgatatcggaaatccagag gctgacttagccttcttaagttgggcttaataata gagaaatagatcatataaaatctatttgtcagct atcgaccgatgccccgccgcccccgcggggggggg ccagtgcccagcggcggaccctgggcccccncgg Query IHHINANYFLDITSMKPEDVESSIFSFSTNFEDPSTATYLQFLKEGLHRAKPYLQP |||||||||||||||||||||||||||| ||||||||||||||||||||||||||| Target IHHINANYFLDITSMKPEDVESSIFSFSANFEDPSTATYLQFLKEGLHRAKPYLQP accaagattcgaataacggggaaatattgatggctagatcctcaggccagactccc taatacaattatcctacaataggttgtccataacccccatattaagtagcacatac tccctcctcgctttggtattacccttcacttactatatccgcggaggcaaaacggc Sequence until next stop: TAA * Distance CDS-SECIS: 1805 ; UGA-SECIS: 2189 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = - Positions = 48191 - 48121 Found by: Infernal (score=18.18) Covels (score=25.81) Stem2 length = 10 Apical loop length = 10 Insertion in stem2 = 0, 0 Free Energy = -39.72 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc (((((((((.......{[[{(((({((((((........-----..))))))}))))}]]}..--....))))))))) target CCCCUCCCGUGCCUGGUGACGCCCCGGCCCGAAACCCGC-----GGCGGGCCCGGGCCGAUGU--CGGCCGGGAGGGG **** ^^^ ****