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

 Blastx evalue: 5e-74
 Query name: gi|817324763|ref|XP_012289265.1| PREDICTED: selenoprotein P [Aotus nancymaae]
 Query range: 1-381  (total 381)

 Target: /var/www/seblastian_output/306852442/tempfiles/temptarget.fasta
 Chromosome: KN995513.1:subseq_156602,21351_ Strand: +
 Positions:
 -Exon 1  1000         1202
 -Exon 2  2276         2488
 -Exon 3  4620         4737
 -Exon 4  7743         8351

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSSGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1073bp   > ||||||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSSGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        ataacgcgtgctccctggagacgcatttacccgtaaagcgcacatagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttacggctcttcttacggatgttaccg                taatgtataaagacat
        ggacggtcgtctcccaaaagcgcaccatgacacgcaatataggccttagtgttttaccacgctggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYVIINHQGLSSQLRYTHLKNHVSKHIPVYQQEENQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLTFPYVEEAIKIAYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2131bp   > |||||||||||||||||||||||||||||
Target  SYVIINHQGLSSQLRYTHLKNHVSKHIPVYQQEENQPDVWTLLNGNKDDFLIYDR                CGRLVYHLGLPYSFLTFPYVEEAIKIAYC
        ttgaaaccgcttctataccaacgtacacgtccggaccggtactagaaggtcatga                tgccgtccgtctttcatctggggaaagtt
        catttaaagtccatgacataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtcacttctcataactatcag
        tttttttaacttaaacattgtctagtttttgaaacaatcgttatacatcccatca                tcttattttgttccatcataaactgttct
                                                                                                            

Query   EKKCGNCSLTT <---Intron---> LKDEDFCKNVSLATVNKTTEAPQPHHHHKHHQNHGHQHLGSSELSKNKQPGAPDAPTHLTPSDLHHHHKHKGQ
        ||||||||||| <   3005bp   > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EKKCGNCSLTT                LKDEDFCKNVSLATVNKTTEAPQPHHHHKHHQNHGHQHLGSSELSKNKQPGAPDAPTHLTPSDLHHHHKHKGQ
        gaatgattcaa                cagggttaagttgagaaaaggcccccccacccacgccccgaagctaaaccggcggcaccactgcccccacagc
        aaaggagctc                ctaaaatgaatctcctaaccaccacaaaaaaaaaagaaatgggatcaaaacgccacccatcccataaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctcttgttgttatgctcctgtagtgaaaaatttttcttacttcctgcgta
                                                                                                            

Query   HRQGHPENUYVPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPSAAU
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HRQGHPENUYVPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPSAAU
        cacgccgattgcgaggtccccaactcaataactctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggaaagttctctctggt
        agagacaagatcggagtaacgaatgaaggtaattgatcaacatccgggggaggatttaacgcctcgagaaatcctgggagtgcaaatcacgaggtccccg
        tggtcagcatgaatataataacgcaagatataacaagcataggttgcacattatgataaagtaccagtaaccatatcagatgaggtatattgatgtgtca
                *               *         *            * *               *           *              *      *

Query   QTSQQLIPTEASTNUSUKNKAKKUEUPSN
        |||||||||||||||||||||||||||||
Target  QTSQQLIPTEASTNUSUKNKAKKUEUPSN
        caacccacaggaaatataaagaatgtcta
        acgaattccacgcagggaaacaagagcca
        gatggtacaactctacagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 259 ; UGA-SECIS: 268

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KN995513.1:subseq_156602,21351_ Strand = + Positions = 8611 - 8680
 Found by:  Infernal (score=29.62) Covels (score=31.44)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -8.9

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

 Blastx evalue: 5e-74
 Query name: gi|817324763|ref|XP_012289265.1| PREDICTED: selenoprotein P [Aotus nancymaae]
 Query range: 1-381  (total 381)

 Target: /var/www/seblastian_output/306852442/tempfiles/temptarget.fasta
 Chromosome: KN995513.1:subseq_156602,21351_ Strand: +
 Positions:
 -Exon 1  1000         1202
 -Exon 2  2276         2488
 -Exon 3  4620         4737
 -Exon 4  7743         8351

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSSGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1073bp   > ||||||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSSGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        ataacgcgtgctccctggagacgcatttacccgtaaagcgcacatagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttacggctcttcttacggatgttaccg                taatgtataaagacat
        ggacggtcgtctcccaaaagcgcaccatgacacgcaatataggccttagtgttttaccacgctggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYVIINHQGLSSQLRYTHLKNHVSKHIPVYQQEENQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPYSFLTFPYVEEAIKIAYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2131bp   > |||||||||||||||||||||||||||||
Target  SYVIINHQGLSSQLRYTHLKNHVSKHIPVYQQEENQPDVWTLLNGNKDDFLIYDR                CGRLVYHLGLPYSFLTFPYVEEAIKIAYC
        ttgaaaccgcttctataccaacgtacacgtccggaccggtactagaaggtcatga                tgccgtccgtctttcatctggggaaagtt
        catttaaagtccatgacataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtcacttctcataactatcag
        tttttttaacttaaacattgtctagtttttgaaacaatcgttatacatcccatca                tcttattttgttccatcataaactgttct
                                                                                                            

Query   EKKCGNCSLTT <---Intron---> LKDEDFCKNVSLATVNKTTEAPQPHHHHKHHQNHGHQHLGSSELSKNKQPGAPDAPTHLTPSDLHHHHKHKGQ
        ||||||||||| <   3005bp   > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EKKCGNCSLTT                LKDEDFCKNVSLATVNKTTEAPQPHHHHKHHQNHGHQHLGSSELSKNKQPGAPDAPTHLTPSDLHHHHKHKGQ
        gaatgattcaa                cagggttaagttgagaaaaggcccccccacccacgccccgaagctaaaccggcggcaccactgcccccacagc
        aaaggagctc                ctaaaatgaatctcctaaccaccacaaaaaaaaaagaaatgggatcaaaacgccacccatcccataaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctcttgttgttatgctcctgtagtgaaaaatttttcttacttcctgcgta
                                                                                                            

Query   HRQGHPENUYVPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPSAAU
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HRQGHPENUYVPGSEGLQHPRNKLUQKRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPSAAU
        cacgccgattgcgaggtccccaactcaataactctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggaaagttctctctggt
        agagacaagatcggagtaacgaatgaaggtaattgatcaacatccgggggaggatttaacgcctcgagaaatcctgggagtgcaaatcacgaggtccccg
        tggtcagcatgaatataataacgcaagatataacaagcataggttgcacattatgataaagtaccagtaaccatatcagatgaggtatattgatgtgtca
                *               *         *            * *               *           *              *      *

Query   QTSQQLIPTEASTNUSUKNKAKKUEUPSN
        |||||||||||||||||||||||||||||
Target  QTSQQLIPTEASTNUSUKNKAKKUEUPSN
        caacccacaggaaatataaagaatgtcta
        acgaattccacgcagggaaacaagagcca
        gatggtacaactctacagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 704 ; UGA-SECIS: 713

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = KN995513.1:subseq_156602,21351_ Strand = + Positions = 9056 - 9121
 Found by:  Infernal (score=24.3) Covels (score=17.9)
 Stem2 length = 9   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -5.3

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