_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 7e-23 Query name: gi|961009001|ref|XP_014820571.1| PREDICTED: selenoprotein P [Calidris pugnax] Query range: 1-377 (total 396) Target: /data/www-rg/seblastian_results/888694830/tempfiles/temptarget.fasta Chromosome: ULFQ01000016.1:subseq_12358855,102464_ Strand: - Positions: -Exon 1 52271 52464 -Exon 2 51070 51282 -Exon 3 50003 50120 -Exon 4 47883 48341 Redox box: YES Query MWAGLGLVLALCLLPGGGAETQ-NCKEPPEWHIGEENPMLNSRGSVTVVALLQASUYLCLLQASR <---Intron---> LEDLRVKLENEGLVNISYV ||||||| | |||||||| | | |||||||/|| | ||/ |||/|||||||||||||||||||| < 988bp > ||||//|| / |||||/// Target MWAGLGLALVLCLLPGGGTEHQGRCKEPPEWNIGVEYPMIKSRGTVTVVALLQASUYLCLLQASR LEDLQLKLGSSGLVNITFI atggcgcgcgctcccgggagccgctagccgtaagggtcaaatagagagggcccgattctctcgta cggcccacgaagcgaaata tgcgtgtctttgttcgggcaaagggaaccagatgtaacttacggctcttcttacggatgttaccg taatatatggggttatctt ggtgaaacgcctccaaaaagtgtttaataagccgaatcgagaagagagttgcgtcacgctggtc atacgagggattagctccct * Query VVNHQGAHSQRKFHLLKESVSDYITVYQQDEQQPDVWTTLNGSKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLSFQYVEESIKVAYCESK |||||| || | ||/| ||/ | ||||/ ||||| || | ||||||||| < 949bp > ||||||||||||/|||| |||//|//|||| Target VVNHQGHQSQLKHQLLREKVSEDIPVYQQNATQPDVWATLKGKKDDFLIYDR CGRLVYHLGLPYTFLSFPYVEKAIQIAYCEDT ggaccgcctccaccccagagtggacgtccagaccggtgatagaaggtcatga tgccgtccgtctatcatctggagacagttgga ttaaagaacataaattgaatcaatctaaaaccacatgcctagaaaatttaag gggttaatgtcacttgtcataactatcagaac gctcaacacgggcataaagtaacttacaataaattcgttaacaattcgtcc gttttttctcatttcgttatagattgccttacc Query CGNCSYT <---Intron---> EPDIDGVCENITKSVDEKLAEIEPKPSGHHSHHHRGHGHGHGQGHRHRHHHHRGGSRHSKNEDHQASSESHRHHPHS ||||||| < 1661bp > | | / |/ | || | Target CGNCSYT --------------------------------------------------EHPHPHHHPHHHQHRHPHHHHHHHGHH tgattta --------------------------------------------------gcccccccccccccccccccccccgcc ggagcac --------------------------------------------------aacacaaacaaaaagacaaaaaaagaa catcaca --------------------------------------------------gtcctttcttttatttctttttttatt Query GRRHRVFGHSRHDQAGSQEQVDPAPPGESVEIPQDKRLUKKGKTSCKNQLTUNWQTASDSALSSUCCHCRHLLFEELGNSVTUQCRGALPNSCRUHGQLS / | ///|/ / | / | |||//| || |/|||| // |||| | ||||||/ // /| ||| ||/| || ||| Target PKGDRPEVNNQHNSSVLGLDPAKAARLPAAIALQGDRLUERGSGICKRHLSUNWQLSTGPISSSUCUHURHLLFEDQQSTSSUHCRGELPSSURUQGQLL caggccggaaccaaagtgcgcgaggcccggagtcggactgagagatacctatatcctagcataatttctcccttggccaaattctcggcctttatcgcct cagagcataaaaaggttgtaccaccgtccctctagagtgaggggtgagatggagatccgctcgggggaggatttaaaagcgcgagggatcccgggagatt cagtgaaactgtcctcgcgttcatctagatatgagcgcaaggtcccgctacacggcgatccctcacacaacggtatgacatcatttagcatcagaagggg * * * * * * * * Query AEDITESUQURLLTAAUQSPAAGASE |/// ||||||| |||| |||| | Target ADNVAESUQURLPTAAULSPAARRGE ggagggttctcccaggtctcggaagg caatcacgaggtccccgtccccggga accgtgtagatgaattagaaaaagta * * * Sequence until next stop: ACCTGA T * Distance CDS-SECIS: 1104 ; UGA-SECIS: 1131 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = ULFQ01000016.1:subseq_12358855,102464_ Strand = - Positions = 46778 - 46711 Found by: Infernal (score=27.0) Covels (score=15.17) Stem2 length = 11 Apical loop length = 9 Insertion in stem2 = 1, 1 Free Energy = -15.0 ..(((((((.......((((((((((.(((((...............))))))))).))))))........))))))).. model uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccagg-cCuGAUGuuuuuucaugaccggc (((((((((---....([[{((((((.(((((.....-..-----..))))))))).))}]])..--..-.))))))))) target UUGCCAUAG---UUCAUGAUGGUUUGGUAGGGAAAUC-GU-----ACCCCUAUAAAACCUGAAUU--AU-UUUAUGGUGA **** ^^^ ****