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

 Blastx evalue: 5e-98
 Query name: gi|984109117|ref|XP_015345952.1| PREDICTED: selenoprotein P isoform X1 [Marmota marmota marmota]
 Query range: 1-371  (total 371)

 Target: /data/www-rg/seblastian_results/435075257/tempfiles/temptarget.fasta
 Chromosome: QVIC01001039.1: Strand: +
 Positions:
 -Exon 1  50000        50202
 -Exon 2  51222        51434
 -Exon 3  53477        53594
 -Exon 4  55943        56521

 Redox box: YES

Query   MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRIKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1019bp   > ||||||||||||||||
Target  MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR                LEDLRIKLEKEGYSNI
        ataacgcgcgcttcctggagacggatatacccgtaaagcacacatcgtgagggcccgattctaccgta                tggccaatgaggttaa
        tgggtgtctctgttcaggcagagaattgaaccaggtgaaactaacagctcttcttacggatgttaccg                taatgtataaagacat
        gggcgatcgtcttcctaaagcgtaccttgacacgcaatataggccttagtgttttatcacgctggac                agacgaaagaaaatttt
                                                                  *                                         

Query   SYIVVNHQGISSQLKYIHLKNKVSDHIPVYQQEENQKDVWTLLNGYKDDFLIYDR <---Intron---> CGHLVYHLGLPYSFLTFPYVEDAIKIAYC
        |||||||||||||| ||||||||| ||||||||||| |||||||||||||||||| <   2042bp   > |||||||||||||||| |||| |||||||
Target  SYIVVNHQGISSQLNYIHLKNKVSXHIPVYQQEENQTDVWTLLNGYKDDFLIYDR                CGHLVYHLGLPYSFLTSPYVEXAIKIAYC
        ttaggaccgattctataccaaagtncacgtccggacaggtactagtaggtcatga                tgccgtccgtctttcatctggngaaagtt
        catttaaagtccataatataaatcaatctaaaaaaacatgcttagaaaatttaag                ggattaatgtcacttcccataactatcag
        cttttttaacttaaccattatgtactttttaaaacaatcgacatacatcccatc                atcttattttgtcccatcataatctgttct
                                                                                                            

Query   EDRCGNCSFR <---Intron---> TLENEDFCRNVSLPTVEKTIEALQPHHHHSHQHLGSSELSKNQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS
        |||||||||| <   2348bp   > |||||||||||||| ||||||||||||||/||||||||||/|||||||||||||||||||||||||||||||||
Target  EDRCGNCSFR                TLENEDFCRNVSLPXVEKTIEALQPHHHHNHQHLGSSELSENQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS
        ggatgattta                acgaggttaagttcaggaaaggcccccccaccccgaagctgacccggggactacgccgccccaacagctacgat
        aagggagctg                ctaaaatggatctcntaactactacaaaaaaaatgggatcaaaacgccacccaccctataaaaaaagaagagac
        acatacctcg                ttatacctatatgctgaaatgtggatctcctgttgctgtagtgaaaaatttactttacttctagcgcgtggtca
                                                                                                            

Query   ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAEENVIESCQURKPPAAUQRSQ
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/|/|||||||| |||||||||
Target  ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAQESVIESCQURMPPAAUQRSQ
        gatcaggaggtcctcgcaactcagtgactctattagccggtaatttctcccatgaagtgaatctggacctttatcgcagcgagagttctcaccggtcaac
        aggatcggagtatctcagatgaaggtaatagattaacacccgggggaggatttaagacctcgagcaatcctgggagtgcaagttacgaggtccccgagga
        gcaggaatataatataagaccagatataagtggcatagatttctctttatgataaagtaccagttaccatatcagatgaggtctattgaagtatcaaatg
          *                                                          *           *              *      *    

Query   QLDPTEVGTNUSUKNKAKK
        |||||||||||||||||||
Target  QLDPTEVGTNUSUKNKAKK
        ccgcagggaatataaagaa
        ataccatgcagggaaacaa
        gttcaatcctacaatgaag
                  * *      
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 745 ; UGA-SECIS: 763

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = QVIC01001039.1: Strand = + Positions = 57267 - 57332
 Found by:  Infernal (score=24.86) Covels (score=16.28)
 Stem2 length = 10   Apical loop length = 8   Insertion in stem2 = 1, 0
 Free Energy = -15.3

         ..(((((((.......((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....([[{((((((.{((((.....--.-----..))))}))))))}]])..--..-.)))))))..
 target  UUUCCAUAG---UCAAUGAUGGUUUAAUAGGGAAAUU--A-----AACCCUCUAAACUUGAACU--CC-UUUAUGGAUA
                         ****            ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 5e-98
 Query name: gi|984109117|ref|XP_015345952.1| PREDICTED: selenoprotein P isoform X1 [Marmota marmota marmota]
 Query range: 1-371  (total 371)

 Target: /data/www-rg/seblastian_results/435075257/tempfiles/temptarget.fasta
 Chromosome: QVIC01001039.1: Strand: +
 Positions:
 -Exon 1  50000        50202
 -Exon 2  51222        51434
 -Exon 3  53477        53594
 -Exon 4  55943        56521

 Redox box: YES

Query   MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRIKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1019bp   > ||||||||||||||||
Target  MWRSLGLALALCFLPYGGTESQGENFICKQPPDWSIRDQNPMQNSHGSVTVVALLQASUYLCILQASR                LEDLRIKLEKEGYSNI
        ataacgcgcgcttcctggagacggatatacccgtaaagcacacatcgtgagggcccgattctaccgta                tggccaatgaggttaa
        tgggtgtctctgttcaggcagagaattgaaccaggtgaaactaacagctcttcttacggatgttaccg                taatgtataaagacat
        gggcgatcgtcttcctaaagcgtaccttgacacgcaatataggccttagtgttttatcacgctggac                agacgaaagaaaatttt
                                                                  *                                         

Query   SYIVVNHQGISSQLKYIHLKNKVSDHIPVYQQEENQKDVWTLLNGYKDDFLIYDR <---Intron---> CGHLVYHLGLPYSFLTFPYVEDAIKIAYC
        |||||||||||||| ||||||||| ||||||||||| |||||||||||||||||| <   2042bp   > |||||||||||||||| |||| |||||||
Target  SYIVVNHQGISSQLNYIHLKNKVSXHIPVYQQEENQTDVWTLLNGYKDDFLIYDR                CGHLVYHLGLPYSFLTSPYVEXAIKIAYC
        ttaggaccgattctataccaaagtncacgtccggacaggtactagtaggtcatga                tgccgtccgtctttcatctggngaaagtt
        catttaaagtccataatataaatcaatctaaaaaaacatgcttagaaaatttaag                ggattaatgtcacttcccataactatcag
        cttttttaacttaaccattatgtactttttaaaacaatcgacatacatcccatc                atcttattttgtcccatcataatctgttct
                                                                                                            

Query   EDRCGNCSFR <---Intron---> TLENEDFCRNVSLPTVEKTIEALQPHHHHSHQHLGSSELSKNQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS
        |||||||||| <   2348bp   > |||||||||||||| ||||||||||||||/||||||||||/|||||||||||||||||||||||||||||||||
Target  EDRCGNCSFR                TLENEDFCRNVSLPXVEKTIEALQPHHHHNHQHLGSSELSENQQPGAADTPSNPAPLDLHHHKKHKGQYRQGNS
        ggatgattta                acgaggttaagttcaggaaaggcccccccaccccgaagctgacccggggactacgccgccccaacagctacgat
        aagggagctg                ctaaaatggatctcntaactactacaaaaaaaatgggatcaaaacgccacccaccctataaaaaaagaagagac
        acatacctcg                ttatacctatatgctgaaatgtggatctcctgttgctgtagtgaaaaatttactttacttctagcgcgtggtca
                                                                                                            

Query   ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAEENVIESCQURKPPAAUQRSQ
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/|/|||||||| |||||||||
Target  ESUQMAGSEGLQLSLAQRKLCQKGCVNQLQCKLFKDPQAASSSCCCHCRHLIFEKRESAITUQCAENLPSLCSUQGLRAQESVIESCQURMPPAAUQRSQ
        gatcaggaggtcctcgcaactcagtgactctattagccggtaatttctcccatgaagtgaatctggacctttatcgcagcgagagttctcaccggtcaac
        aggatcggagtatctcagatgaaggtaatagattaacacccgggggaggatttaagacctcgagcaatcctgggagtgcaagttacgaggtccccgagga
        gcaggaatataatataagaccagatataagtggcatagatttctctttatgataaagtaccagttaccatatcagatgaggtctattgaagtatcaaatg
          *                                                          *           *              *      *    

Query   QLDPTEVGTNUSUKNKAKK
        |||||||||||||||||||
Target  QLDPTEVGTNUSUKNKAKK
        ccgcagggaatataaagaa
        ataccatgcagggaaacaa
        gttcaatcctacaatgaag
                  * *      
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 277 ; UGA-SECIS: 295

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = QVIC01001039.1: Strand = + Positions = 56799 - 56881
 Found by:  Infernal (score=23.62) Covels (score=32.57)
 Stem2 length = 11   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -12.04

         ..(((((((..........(((((((((((((((...............)))))))))))))))............)))))))..
 model   uucggucaugcg---UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu---u-uuucaugaccggc
         ..(((((((..........{[[{((((((((([(.....-.........)])))))))))}]]}........-...)))))))..
 target  AGUAUUCUAUUUGCAUUGAUGAGAACAGAAACAUAAACU-AUGACCUAGGGGUUUCUGUUGGAUAGUUAGUA-ACUUAGAAUGGA
                            ****           ^^^                       ****