_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:2 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 2e-66 Query name: gi|965980787|ref|XP_014956797.1| PREDICTED: selenoprotein P isoform X1 [Ovis aries] Query range: 1-386 (total 386) Target: /data/www-rg/seblastian_results/120150215/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 50000 50202 -Exon 2 51204 51416 -Exon 3 53399 53516 -Exon 4 55290 55379 -Exon 5 55452 55985 Redox box: YES Query MWRGLGLALALCLLLTGGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| < 1001bp > |||||||||||||||| Target MWRGLGLALALCLLLTRGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR LEDLRVKLEKEGYSNI atagcgcgcgctcccaagagacgcatttacccgtaaagcgcacattgtgagggcccgattctaccgta tggccgacgaggttaa tgggtgtctctgtttcggcagagagcagaacccggtaaaacttacagctcttcttacggatgttaccg taatgtataaagacat ggacgggtgtccccacaaagcgcaccttgatacgcagtactggccttagcgttttaccacgctggct aggcgaaaggaaattcc * Query SYVVVNHQEISSRLKYAHLKNKVSEHIPVYQQEEDQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLTFTYVEDSIKTVYC |||||||||||||||| ||||||||||||||||/||||||||||||||||||||| < 1982bp > ||||||||||||||||||||||||||||| Target SYVVVNHQEISSRLKYVHLKNKVSEHIPVYQQEDDQPDVWTLLNGNKDDFLIYDR CGRLVYHLGLPYSFLTFTYVEDSIKTVYC ttgggaccgattctatgccaaagtgcacgtccgggccggtactagaaggtcatga tgccgtccgtctttcatatgggtaaagtt catttaaaatccgtaatataaatcaatctaaaaaaacatgcttagaaaatttaag gggttaatgtcacttctcataactactag tttttttaacttaaatgttatgtaattttcaaaccaatcgtcatatatcccatc atcctattttgttccatcataatctgttct Query EDKCGNCSLK <---Intron---> TQEDEDFCKNVSLATKEKTAEASQRHHHPH <---Intron---> PHPHHGHQLHENAHLSESPKPDTPDTPE |||||||||| < 1773bp > | |||||||||||||||||||||||||| | < 72bp > ||||||||||||||||||| |||||||| Target EDKCGNCSLK TLEDEDFCKNVSLATKEKTAEASQRHHHHH PHPHHGHQLHENAHLSESPNPDTPDTPE ggatgattca acggggttaagtcgaagaagggtccccccc cccccgccccgagcctgtcacgacgacg aaaggagcta ctaaaatgaatctccaaaccaccagaaaaa cacaagaataaacatcaccacaccacca atatacctcg agatacctatatgtcggaatgtagatctct ctctcgtgttattttagtacacaatctg Query NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQG accctgccccccacagccacgctgatgacggagatcctcccaactcaataactctctcagtgtgtaatttctcccgtgaagtgaatctagacctttatcg accccgtaaaaagaagaagagacaagacctggaatatctcaaatggaggtaattgatcaacacctgggggaggatttaacgcctcgagcaatcctgggag tcttatttccctgcgtcaagtcatcttaaaatataatttaaggcaagacatgacagtcataattgtcctcctatgataaagtaccagtaaccctatcagc * * * * Query LLAEENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN |||||||||||||||||||||||||||||||||||||||||||||||||| Target LLAEENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN ctgggagagttctctccggtcgggcccacaggaaatataaagaatatcta ttcaaattacgaggtccccgaccgaataccacgcagggaaacatgagcca tgaggcctatagatgtatcagaatggctcaacccgacaatgcagaaatat * * * * * * * Sequence until next stop: TAA * Distance CDS-SECIS: 243 ; UGA-SECIS: 252 ------- SECIS element -- id:2 -- grade:A ---- Chromosome = your_sequence Strand = + Positions = 56229 - 56300 Found by: Infernal (score=28.33) Covels (score=28.55) Stem2 length = 10 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -11.34 Type = 1 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ...({((((.--....{[[{((((((((({(.....-.........)})))))))))}]]}..--..-.))))})... target UCUACUUGCA--UUAAUGAGAACAGAAACGUAAACU-AUAACCUAGGGGUUUCUGUUGGAUAG--UU-GGCAACUUAG **** ^^^ **** _________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 2e-66 Query name: gi|965980787|ref|XP_014956797.1| PREDICTED: selenoprotein P isoform X1 [Ovis aries] Query range: 1-386 (total 386) Target: /data/www-rg/seblastian_results/120150215/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 50000 50202 -Exon 2 51204 51416 -Exon 3 53399 53516 -Exon 4 55290 55379 -Exon 5 55452 55985 Redox box: YES Query MWRGLGLALALCLLLTGGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| < 1001bp > |||||||||||||||| Target MWRGLGLALALCLLLTRGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR LEDLRVKLEKEGYSNI atagcgcgcgctcccaagagacgcatttacccgtaaagcgcacattgtgagggcccgattctaccgta tggccgacgaggttaa tgggtgtctctgtttcggcagagagcagaacccggtaaaacttacagctcttcttacggatgttaccg taatgtataaagacat ggacgggtgtccccacaaagcgcaccttgatacgcagtactggccttagcgttttaccacgctggct aggcgaaaggaaattcc * Query SYVVVNHQEISSRLKYAHLKNKVSEHIPVYQQEEDQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLTFTYVEDSIKTVYC |||||||||||||||| ||||||||||||||||/||||||||||||||||||||| < 1982bp > ||||||||||||||||||||||||||||| Target SYVVVNHQEISSRLKYVHLKNKVSEHIPVYQQEDDQPDVWTLLNGNKDDFLIYDR CGRLVYHLGLPYSFLTFTYVEDSIKTVYC ttgggaccgattctatgccaaagtgcacgtccgggccggtactagaaggtcatga tgccgtccgtctttcatatgggtaaagtt catttaaaatccgtaatataaatcaatctaaaaaaacatgcttagaaaatttaag gggttaatgtcacttctcataactactag tttttttaacttaaatgttatgtaattttcaaaccaatcgtcatatatcccatc atcctattttgttccatcataatctgttct Query EDKCGNCSLK <---Intron---> TQEDEDFCKNVSLATKEKTAEASQRHHHPH <---Intron---> PHPHHGHQLHENAHLSESPKPDTPDTPE |||||||||| < 1773bp > | |||||||||||||||||||||||||| | < 72bp > ||||||||||||||||||| |||||||| Target EDKCGNCSLK TLEDEDFCKNVSLATKEKTAEASQRHHHHH PHPHHGHQLHENAHLSESPNPDTPDTPE ggatgattca acggggttaagtcgaagaagggtccccccc cccccgccccgagcctgtcacgacgacg aaaggagcta ctaaaatgaatctccaaaccaccagaaaaa cacaagaataaacatcaccacaccacca atatacctcg agatacctatatgtcggaatgtagatctct ctctcgtgttattttagtacacaatctg Query NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQG accctgccccccacagccacgctgatgacggagatcctcccaactcaataactctctcagtgtgtaatttctcccgtgaagtgaatctagacctttatcg accccgtaaaaagaagaagagacaagacctggaatatctcaaatggaggtaattgatcaacacctgggggaggatttaacgcctcgagcaatcctgggag tcttatttccctgcgtcaagtcatcttaaaatataatttaaggcaagacatgacagtcataattgtcctcctatgataaagtaccagtaaccctatcagc * * * * Query LLAEENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN |||||||||||||||||||||||||||||||||||||||||||||||||| Target LLAEENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN ctgggagagttctctccggtcgggcccacaggaaatataaagaatatcta ttcaaattacgaggtccccgaccgaataccacgcagggaaacatgagcca tgaggcctatagatgtatcagaatggctcaacccgacaatgcagaaatat * * * * * * * Sequence until next stop: TAA * Distance CDS-SECIS: 680 ; UGA-SECIS: 689 ------- SECIS element -- id:1 -- grade:B ---- Chromosome = your_sequence Strand = + Positions = 56666 - 56732 Found by: Infernal (score=29.41) Covels (score=13.38) Stem2 length = 9 Apical loop length = 10 Insertion in stem2 = 1, 0 Free Energy = -9.3 Type = 1 ..(((((((.......((((((((((.(((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ...((((((---....([[{(((({(.((((......--.-----...)))))}))))}]])..--....))))))... target UUUCCAUAG---UCAAUGAUGGUUCAAUAGGCAAACC--A-----GGUCCUAUAAACCUGAAUU--UUUUUUAUGGUUA **** ^^^ ****