_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 3e-58
 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/651974896/tempfiles/temptarget.fasta
 Chromosome: NW_018330451.1:subseq_498805,10263_ Strand: -
 Positions:
 -Exon 1  5941         6143
 -Exon 2  5004         5216
 -Exon 3  3487         3604
 -Exon 4  1957         2037
 -Exon 5  1366         1905

 Redox box: YES

Query   MWRGLGLALALCLLLTGGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| <   724bp    > ||||||||||||||||
Target  MWRGLGLALALCLLLAGGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        atagcgtgcgctcccgggagacgcatttacccgtaaagcgcacattgtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgtttcggcagagagcagaacccggtaaaacttacagctcttcttacggatgttaccg                taatgtataaagacat
        ggacgggcgtctccataaagcgcaccctggtacgcagtgctggccttagcgttttaccacgctggat                aggcgaaaggaaattcc
                                                                  *                                         

Query   SYVVVNHQEISSRLKYAHLKNKVSEHIPVYQQEEDQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLTFTYVEDSIKTVYC
        |||||||| ||||||| |||||||||||||||||/|||||||||||||||||||| <   1399bp   > |||||||||||||||||||||||||||||
Target  SYVVVNHQGISSRLKYVHLKNKVSEHIPVYQQEENQPDVWTLLNGNKDDFLIYDR                CGRLVYHLGLPYSFLTFTYVEDSIKTVYC
        ttgggaccgattctatgccaaagtgcacgtccggaccggtactagaaggtcatga                tgccgtccgtcttttatatgggtaaagtt
        catttaaagtccgtaatataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtcacttctcataactactag
        cttttttaacttaaatgttatgtaattttcaaaacaatcgtcacatatcccatc                atcctattttgttccatcataacctgttct
                                                                                                            

Query   EDKCGNCSLK <---Intron---> TQEDEDFCKNVSLATKEKTAEASQRHHH <---Intron---> PHPHPHHGHQLHENAHLSESPKPDTPDTPE
        |||||||||| <   1449bp   > | ||||||||||||||||||||||| || <    51bp    > |||||||||||||||||||||||| |||||
Target  EDKCGNCSLK                TLEDEDFCKNVSLATKEKTAEASQR-HH                PHPHPHHGHQLHENAHLSESPKPDAPDTPE
        ggatgattca                acggggttaagtcgaagaagggtcc-cc                cccccccgccccgagcctgtcacggcgacg
        aaaggagcta                ctaaaatgaatctccaaaccaccag-aa                cacacaagaataaacatcaccacaccacca
        atatacctcg                agatacctatatgtcggaatgtaga-tc                ctctcttgtgttattttagtaaacaatctg
                                                                                                            

Query   NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQG
        |||||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||| |/|||||||||
Target  NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSESLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCKEDLPSLCSUQG
        accctgccccccacagccacgctgatgacggagatcctcccaactcaataactctctcagtgtgtaatttctcctgtgaagtgaatctaggcctctatcg
        accccgtaaaaagaagaagagacaagacctggagtatctcaaatggaggtaattgatcaacacctgggggaggatttaacgcctcgagaaatcctgggag
        tcttgtttccctgcgtcaagtcatcttaaaatataatttaaggcaagacatgacagtcataattgtcctcctatgataaagtaccagtaaccctatcagc
                                                    *         *                              *           *  

Query   LLAEENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN
        ||||||||||||||||||||||||||||||/ ||||||||/ |/||||||
Target  LLAEENVIESUQURLPPAAUQAAGQQLNPTKPSTKUSUKNQDKLUKUPSN
        ctgggagagttctctccggtcgggcccacaacaaatataacgactatcta
        ttcaaattacgaggtccccgaccgaataccacgcagggaaaaatgagcca
        tgaggcctatagaagtatcagaatggcccaacccgacaatgcagaaatat
                  * *      *               * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 248 ; UGA-SECIS: 257

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = NW_018330451.1:subseq_498805,10263_ Strand = - Positions = 1117 - 1046
 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

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({((((.--....{[[{((((((((({(.....-.........)})))))))))}]]}..--..-.))))})...
 target  UCUACUUGCA--UUAAUGAGAACAGAAACGUAAACU-AUAACCUAGGGGUUUCUGUUGGAUAG--UU-GGCAACUUAG
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 3e-58
 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/651974896/tempfiles/temptarget.fasta
 Chromosome: NW_018330451.1:subseq_498805,10263_ Strand: -
 Positions:
 -Exon 1  5941         6143
 -Exon 2  5004         5216
 -Exon 3  3487         3604
 -Exon 4  1957         2037
 -Exon 5  1366         1905

 Redox box: YES

Query   MWRGLGLALALCLLLTGGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| <   724bp    > ||||||||||||||||
Target  MWRGLGLALALCLLLAGGTESQGQSSYCKQPPAWSIKDQDPMLNSYGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        atagcgtgcgctcccgggagacgcatttacccgtaaagcgcacattgtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgtttcggcagagagcagaacccggtaaaacttacagctcttcttacggatgttaccg                taatgtataaagacat
        ggacgggcgtctccataaagcgcaccctggtacgcagtgctggccttagcgttttaccacgctggat                aggcgaaaggaaattcc
                                                                  *                                         

Query   SYVVVNHQEISSRLKYAHLKNKVSEHIPVYQQEEDQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLTFTYVEDSIKTVYC
        |||||||| ||||||| |||||||||||||||||/|||||||||||||||||||| <   1399bp   > |||||||||||||||||||||||||||||
Target  SYVVVNHQGISSRLKYVHLKNKVSEHIPVYQQEENQPDVWTLLNGNKDDFLIYDR                CGRLVYHLGLPYSFLTFTYVEDSIKTVYC
        ttgggaccgattctatgccaaagtgcacgtccggaccggtactagaaggtcatga                tgccgtccgtcttttatatgggtaaagtt
        catttaaagtccgtaatataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtcacttctcataactactag
        cttttttaacttaaatgttatgtaattttcaaaacaatcgtcacatatcccatc                atcctattttgttccatcataacctgttct
                                                                                                            

Query   EDKCGNCSLK <---Intron---> TQEDEDFCKNVSLATKEKTAEASQRHHH <---Intron---> PHPHPHHGHQLHENAHLSESPKPDTPDTPE
        |||||||||| <   1449bp   > | ||||||||||||||||||||||| || <    51bp    > |||||||||||||||||||||||| |||||
Target  EDKCGNCSLK                TLEDEDFCKNVSLATKEKTAEASQR-HH                PHPHPHHGHQLHENAHLSESPKPDAPDTPE
        ggatgattca                acggggttaagtcgaagaagggtcc-cc                cccccccgccccgagcctgtcacggcgacg
        aaaggagcta                ctaaaatgaatctccaaaccaccag-aa                cacacaagaataaacatcaccacaccacca
        atatacctcg                agatacctatatgtcggaatgtaga-tc                ctctcttgtgttattttagtaaacaatctg
                                                                                                            

Query   NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSENLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCTENLPSLCSUQG
        |||||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||| |/|||||||||
Target  NPPPSGLHHHHHRHKGHQRQGHSDNCDTPVGSESLQLSLPQKKLURKRCINQLLUQFPKDSESALSSCCCHCRHLVFEKTGSAITUQCKEDLPSLCSUQG
        accctgccccccacagccacgctgatgacggagatcctcccaactcaataactctctcagtgtgtaatttctcctgtgaagtgaatctaggcctctatcg
        accccgtaaaaagaagaagagacaagacctggagtatctcaaatggaggtaattgatcaacacctgggggaggatttaacgcctcgagaaatcctgggag
        tcttgtttccctgcgtcaagtcatcttaaaatataatttaaggcaagacatgacagtcataattgtcctcctatgataaagtaccagtaaccctatcagc
                                                    *         *                              *           *  

Query   LLAEENVIESUQURLPPAAUQAAGQQLNPTEASTKUSUKNKAKMUKUPSN
        ||||||||||||||||||||||||||||||/ ||||||||/ |/||||||
Target  LLAEENVIESUQURLPPAAUQAAGQQLNPTKPSTKUSUKNQDKLUKUPSN
        ctgggagagttctctccggtcgggcccacaacaaatataacgactatcta
        ttcaaattacgaggtccccgaccgaataccacgcagggaaaaatgagcca
        tgaggcctatagaagtatcagaatggcccaacccgacaatgcagaaatat
                  * *      *               * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 697 ; UGA-SECIS: 706

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = NW_018330451.1:subseq_498805,10263_ Strand = - Positions = 668 - 603
 Found by:  Infernal (score=28.26) Covels (score=13.38)
 Stem2 length = 9   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -9.9

         ..(((((((.......((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((---....([[{(((({(.((((......--.-----...)))))}))))}]])..--..-.))))))...
 target  UUUCCAUAG---UCAAUGAUGGUUCAAUAGGCAAACC--A-----GGUCCUAUAAACCUGAAUU--UU-UUUAUGGUUA
                         ****            ^^^                       ****