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

 Blastx evalue: 1e-92
 Query name: gi|1044366702|ref|XP_017388639.1| PREDICTED: selenoprotein P isoform X2 [Cebus capucinus imitator]
 Query range: 1-381  (total 381)

 Target: /data/www-rg/seblastian_results/32125515/tempfiles/temptarget.fasta
 Chromosome: KV389506.1:subseq_2207742,100551_ Strand: -
 Positions:
 -Exon 1  56008        56210
 -Exon 2  54732        54944
 -Exon 3  52489        52606
 -Exon 4  49943        50551

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSTGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1063bp   > ||||||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSTGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccgtaaagcgcacatagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttaccgctcttcttacggatgttaccg                taatgtataaagacat
        ggacggtcgtctcccaaaagcgcaccatgacacgcaatataggccttagtgttttactacgctggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYIIVNHQGLSSQLRYTHLKNQVSEHIPVYQQEENQPDVWALLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPFSFLTFPYVEEAIKIAYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2125bp   > |||||||||||||||||||||||||||||
Target  SYIIVNHQGLSSQLRYTHLKNQVSEHIPVYQQEENQPDVWALLNGNKDDFLIYDR                CGRLVYHLGLPFSFLTFPYVEEAIKIAYC
        ttaagaccgcttctataccaacgtgcacgtccggaccggtgctagaaggtcatga                tgccgtccgtctttcatctggggaaagtt
        catttaaagtccatgacataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtctcttctcataactatcag
        tttttttaacttaaacattgtgtagtttttgaaacaatcgttatacatcccatc                atcttattttgttccaacataaactgttct
                                                                                                            

Query   EKKCGNCSLT <---Intron---> TLKDEDFCKNVSLATVNKTTEAPQPHHHHKHHRNHGHQHLGSSELSKNQQPGAPDAPTHLTPSDLHHHHKHKGQ
        |||||||||| <   1937bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EKKCGNCSLT                TLKDEDFCKNVSLATVNKTTEAPQPHHHHKHHRNHGHQHLGSSELSKNQQPGAPDAPTHLTPSDLHHHHKHKGQ
        gaatgattca                acagggttaagttgagaaaaggcccccccacccacgccccgaagctaacccggcggcaccactgcccccacagc
        aaaggagctc                ctaaaatgaatctcctaaccaccacaaaaaaagaagaaatgggatcaaaacgccacccatcccataaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctcttgttcttatgctcctgtagtgaaaaatttttcttatttcctgcgta
                                                                                                            

Query   HRQGHPENUYIPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCTENLPSLCSUQGLRAEENITESCQURLPPAAU
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HRQGHPENUYIPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCTENLPSLCSUQGLRAEENITESCQURLPPAAU
        cacgccgattacgaggtccccaactcaataactctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggaaagttctctccggt
        agagacaagatcggagtaacgaatgaaggtaattgatcaacatccgggggaggatttaacgcctcgagcaatcctgggagtgcaaatcacgaggtccccg
        tggtcagcataaatataataacgcaagatataacaagcataggttgcacattatgataaggtaccagtaactatatcagatgaggtatattgatgtatca
                *               *         *            * *               *           *              *      *

Query   KTSQQLIPTEASTNUSUKNMAKKUEUPSN
        |||||||||||||||||||||||||||||
Target  KTSQQLIPTEASTNUSUKNMAKKUEUPSN
        aaacccacaggaaatataaagaatgtcta
        acgaattccacgcagggaatcaagagcca
        gatggtataactctacagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 265 ; UGA-SECIS: 274

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV389506.1:subseq_2207742,100551_ Strand = - Positions = 49677 - 49608
 Found by:  Infernal (score=31.58) Covels (score=32.57)
 Stem2 length = 11   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -12.54

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..({(((((---....{[[{((((((((([(.....-.........)])))))))))}]]}----....)))))})..
 target  CUACUUGCU---UUAAUGAGAACAGAAACAUAAACU-AUGACCUAGGGGUUUCUGUUGGAU----AAUUAGCAAUUUA
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 1e-92
 Query name: gi|1044366702|ref|XP_017388639.1| PREDICTED: selenoprotein P isoform X2 [Cebus capucinus imitator]
 Query range: 1-381  (total 381)

 Target: /data/www-rg/seblastian_results/32125515/tempfiles/temptarget.fasta
 Chromosome: KV389506.1:subseq_2207742,100551_ Strand: -
 Positions:
 -Exon 1  56008        56210
 -Exon 2  54732        54944
 -Exon 3  52489        52606
 -Exon 4  49943        50551

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSTGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1063bp   > ||||||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSTGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccgtaaagcgcacatagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttaccgctcttcttacggatgttaccg                taatgtataaagacat
        ggacggtcgtctcccaaaagcgcaccatgacacgcaatataggccttagtgttttactacgctggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYIIVNHQGLSSQLRYTHLKNQVSEHIPVYQQEENQPDVWALLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPFSFLTFPYVEEAIKIAYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2125bp   > |||||||||||||||||||||||||||||
Target  SYIIVNHQGLSSQLRYTHLKNQVSEHIPVYQQEENQPDVWALLNGNKDDFLIYDR                CGRLVYHLGLPFSFLTFPYVEEAIKIAYC
        ttaagaccgcttctataccaacgtgcacgtccggaccggtgctagaaggtcatga                tgccgtccgtctttcatctggggaaagtt
        catttaaagtccatgacataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtctcttctcataactatcag
        tttttttaacttaaacattgtgtagtttttgaaacaatcgttatacatcccatc                atcttattttgttccaacataaactgttct
                                                                                                            

Query   EKKCGNCSLT <---Intron---> TLKDEDFCKNVSLATVNKTTEAPQPHHHHKHHRNHGHQHLGSSELSKNQQPGAPDAPTHLTPSDLHHHHKHKGQ
        |||||||||| <   1937bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EKKCGNCSLT                TLKDEDFCKNVSLATVNKTTEAPQPHHHHKHHRNHGHQHLGSSELSKNQQPGAPDAPTHLTPSDLHHHHKHKGQ
        gaatgattca                acagggttaagttgagaaaaggcccccccacccacgccccgaagctaacccggcggcaccactgcccccacagc
        aaaggagctc                ctaaaatgaatctcctaaccaccacaaaaaaagaagaaatgggatcaaaacgccacccatcccataaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctcttgttcttatgctcctgtagtgaaaaatttttcttatttcctgcgta
                                                                                                            

Query   HRQGHPENUYIPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCTENLPSLCSUQGLRAEENITESCQURLPPAAU
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HRQGHPENUYIPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCTENLPSLCSUQGLRAEENITESCQURLPPAAU
        cacgccgattacgaggtccccaactcaataactctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggaaagttctctccggt
        agagacaagatcggagtaacgaatgaaggtaattgatcaacatccgggggaggatttaacgcctcgagcaatcctgggagtgcaaatcacgaggtccccg
        tggtcagcataaatataataacgcaagatataacaagcataggttgcacattatgataaggtaccagtaactatatcagatgaggtatattgatgtatca
                *               *         *            * *               *           *              *      *

Query   KTSQQLIPTEASTNUSUKNMAKKUEUPSN
        |||||||||||||||||||||||||||||
Target  KTSQQLIPTEASTNUSUKNMAKKUEUPSN
        aaacccacaggaaatataaagaatgtcta
        acgaattccacgcagggaatcaagagcca
        gatggtataactctacagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 688 ; UGA-SECIS: 697

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = KV389506.1:subseq_2207742,100551_ Strand = - Positions = 49254 - 49189
 Found by:  Infernal (score=30.45) Covels (score=21.41)
 Stem2 length = 10   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -12.4

         ..(((((((.......((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((---....{[[{((((((.((((......--.-----...))))))))))}]]}..--..-.))))))...
 target  UUUCCAUAG---UCAAUGAUGGUUUAAUAGGUAAACU--A-----AACCCUAUAAACCUGACCU--CC-UUUAUGGUUA
                         ****            ^^^                       ****