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

 Blastx evalue: e-113
 Query name: gi|1012031160|ref|XP_015989189.1| PREDICTED: selenoprotein P [Rousettus aegyptiacus]
 Query range: 1-392  (total 392)

 Target: /data/www-rg/seblastian_results/951136036/tempfiles/temptarget.fasta
 Chromosome: LOCP02001250.1:subseq_1008,200000_ Strand: +
 Positions:
 -Exon 1  48938        49140
 -Exon 2  50029        50241
 -Exon 3  51519        51636
 -Exon 4  54185        54826

 Redox box: YES

Query   MWRSLGLALALCLLPWGGTESQEQSSFCKQPPAWSIGDQDPMLNSYGSVTVVALLQASUYFCILQSSS <---Intron---> LEDLRVKLEEQGFSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   888bp    > ||||||||||||||||
Target  MWRSLGLALALCLLPWGGTESQEQSSFCKQPPAWSIGDQDPMLNSYGSVTVVALLQASUYFCILQSSS                LEDLRVKLEEQGFSNI
        ataacgtgcgctccctggagacgcatttacccgtaaggcgcacattgtgagggcccgattttacctta                tggccgacggcgttaa
        tgggtgtctctgttcgggcagaaagctgaacccggtgaaacttacagctcttcttacggatgttaccg                taatgtataaagtcat
        ggacgcgcgtctcctggaagcggaccttggtacgcagtacaggcattattgttttaccactctaaat                tgatgaaagggattttt
                                                                  *                                         

Query   SYAIVNHQGISSRLKYMHLKNKVSEHISVYQQEENQTDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPFSSLSFLYVEEAIKIAYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1277bp   > |||||||||||||||||||||||||||||
Target  SYAIVNHQGISSRLKYMHLKNKVSEHISVYQQEENQTDVWTLLNGNKDDFLIYDR                CGRLVYHLGLPFSSLSFLYVEEAIKIAYC
        ttgagaccgattctataccaaagtgcatgtccggacaggtactagaaggtcatga                tgccgtccgtcttacatttggggaaagtt
        cacttaaagtccgtaatataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtctcgtgttataactatcag
        tttttttaacttaaacgttatgtagtttttaaaacaatcgtcatacatcccatc                atcttatcttgtctcatcataaactgttct
                                                                                                            

Query   EDKCGNCSLT <---Intron---> TLEDEGICKNVSLVTVEQTTETPQPHHHHHHQHRHRHHQHHHKHEHQHIRNGQLSENKQPEALSAPENPPPLGL
        |||||||||| <   2548bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EDKCGNCSLT                TLEDEGICKNVSLVTVEQTTETPQPHHHHHHQHRHRHHQHHHKHEHQHIRNGQLSENKQPEALSAPENPPPLGL
        ggatgattca                acggggataagttgaggcaagaccccccccccccccccccccacgcccaaagcctgaaccggcagcgaccccgc
        aaaggagctc                ctaaagtgaatcttctaaccaccacaaaaaaaagagaaaaaaaaaaaatgagatcaaaacactgccaaccctgt
        acatacctgg                cgatacctatatgttgaaatgtagattttttgtctctcgttcgcgtgctgtcgtagtgaaaaatatgtctcact
                                                                                                            

Query   HNHHKLKDPQIHSHSNNCYMPESENLQLSLSQKKLCGKRCINPLLCKLLKDSKLAPSSCCCHCRHLVFEKTGPATTUQCKEKLPSLCSUQGLWAEENVIE
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HNHHKLKDPQIHSHSNNCYMPESENLQLSLSQKKLCGKRCINPLLCKLLKDSKLAPSSCCCHCRHLVFEKTGPATTUQCKEKLPSLCSUQGLWAEENVIE
        caccacagccacactaattacgagatcctctcaactgaataactctatcagtatgcaatttctcccgtgaagcgaatctagacctttatcgctgggagag
        aaaaataacatagacaagatcagaatatctcaaatggaggtacttgattaacatccgggggaggatttaacgccccgagaaatcctgggagtgcaaatta
        tcctgcgcaaacttaccctgaatatgaattaagactagatataaccggcataggtttcccctcatgataaagtaccagtaaacctatcaggtgaggccta
                                                                                    *           *           

Query   SUQURLPPAAUQASQQLEPTEARTNUSUKNKAKMUKUPSN
        ||||||||||||||||||||||||||||||||||||||||
Target  SUQURLPPAAUQASQQLEPTEARTNUSUKNKAKMUKUPSN
        ttctctccggtcgacccgcaggcaatataaagaatatcta
        cgaggtccccgacgaataccacgcagggaaacatgagcca
        tagatgtatcagatggcgcaaccatacaatgaagaaatac
         * *      *              * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 263 ; UGA-SECIS: 272

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = LOCP02001250.1:subseq_1008,200000_ Strand = + Positions = 55090 - 55161
 Found by:  Infernal (score=28.25) Covels (score=31.91)
 Stem2 length = 11   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -10.84

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({((((.--....{[[{((((((((([(.....-.........)])))))))))}]]}..--..-.))))})...
 target  UCUACUUGCG--UUAAUGAGAACAGGAACAUAAACU-AUGACCUAGGGGUUUCUGUUGGAUAG--UU-AGCAAUUUAG
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: e-113
 Query name: gi|1012031160|ref|XP_015989189.1| PREDICTED: selenoprotein P [Rousettus aegyptiacus]
 Query range: 1-392  (total 392)

 Target: /data/www-rg/seblastian_results/951136036/tempfiles/temptarget.fasta
 Chromosome: LOCP02001250.1:subseq_1008,200000_ Strand: +
 Positions:
 -Exon 1  48938        49140
 -Exon 2  50029        50241
 -Exon 3  51519        51636
 -Exon 4  54185        54826

 Redox box: YES

Query   MWRSLGLALALCLLPWGGTESQEQSSFCKQPPAWSIGDQDPMLNSYGSVTVVALLQASUYFCILQSSS <---Intron---> LEDLRVKLEEQGFSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   888bp    > ||||||||||||||||
Target  MWRSLGLALALCLLPWGGTESQEQSSFCKQPPAWSIGDQDPMLNSYGSVTVVALLQASUYFCILQSSS                LEDLRVKLEEQGFSNI
        ataacgtgcgctccctggagacgcatttacccgtaaggcgcacattgtgagggcccgattttacctta                tggccgacggcgttaa
        tgggtgtctctgttcgggcagaaagctgaacccggtgaaacttacagctcttcttacggatgttaccg                taatgtataaagtcat
        ggacgcgcgtctcctggaagcggaccttggtacgcagtacaggcattattgttttaccactctaaat                tgatgaaagggattttt
                                                                  *                                         

Query   SYAIVNHQGISSRLKYMHLKNKVSEHISVYQQEENQTDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPFSSLSFLYVEEAIKIAYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1277bp   > |||||||||||||||||||||||||||||
Target  SYAIVNHQGISSRLKYMHLKNKVSEHISVYQQEENQTDVWTLLNGNKDDFLIYDR                CGRLVYHLGLPFSSLSFLYVEEAIKIAYC
        ttgagaccgattctataccaaagtgcatgtccggacaggtactagaaggtcatga                tgccgtccgtcttacatttggggaaagtt
        cacttaaagtccgtaatataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtctcgtgttataactatcag
        tttttttaacttaaacgttatgtagtttttaaaacaatcgtcatacatcccatc                atcttatcttgtctcatcataaactgttct
                                                                                                            

Query   EDKCGNCSLT <---Intron---> TLEDEGICKNVSLVTVEQTTETPQPHHHHHHQHRHRHHQHHHKHEHQHIRNGQLSENKQPEALSAPENPPPLGL
        |||||||||| <   2548bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EDKCGNCSLT                TLEDEGICKNVSLVTVEQTTETPQPHHHHHHQHRHRHHQHHHKHEHQHIRNGQLSENKQPEALSAPENPPPLGL
        ggatgattca                acggggataagttgaggcaagaccccccccccccccccccccacgcccaaagcctgaaccggcagcgaccccgc
        aaaggagctc                ctaaagtgaatcttctaaccaccacaaaaaaaagagaaaaaaaaaaaatgagatcaaaacactgccaaccctgt
        acatacctgg                cgatacctatatgttgaaatgtagattttttgtctctcgttcgcgtgctgtcgtagtgaaaaatatgtctcact
                                                                                                            

Query   HNHHKLKDPQIHSHSNNCYMPESENLQLSLSQKKLCGKRCINPLLCKLLKDSKLAPSSCCCHCRHLVFEKTGPATTUQCKEKLPSLCSUQGLWAEENVIE
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HNHHKLKDPQIHSHSNNCYMPESENLQLSLSQKKLCGKRCINPLLCKLLKDSKLAPSSCCCHCRHLVFEKTGPATTUQCKEKLPSLCSUQGLWAEENVIE
        caccacagccacactaattacgagatcctctcaactgaataactctatcagtatgcaatttctcccgtgaagcgaatctagacctttatcgctgggagag
        aaaaataacatagacaagatcagaatatctcaaatggaggtacttgattaacatccgggggaggatttaacgccccgagaaatcctgggagtgcaaatta
        tcctgcgcaaacttaccctgaatatgaattaagactagatataaccggcataggtttcccctcatgataaagtaccagtaaacctatcaggtgaggccta
                                                                                    *           *           

Query   SUQURLPPAAUQASQQLEPTEARTNUSUKNKAKMUKUPSN
        ||||||||||||||||||||||||||||||||||||||||
Target  SUQURLPPAAUQASQQLEPTEARTNUSUKNKAKMUKUPSN
        ttctctccggtcgacccgcaggcaatataaagaatatcta
        cgaggtccccgacgaataccacgcagggaaacatgagcca
        tagatgtatcagatggcgcaaccatacaatgaagaaatac
         * *      *              * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 699 ; UGA-SECIS: 708

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = LOCP02001250.1:subseq_1008,200000_ Strand = + Positions = 55526 - 55591
 Found by:  Infernal (score=26.44) Covels (score=16.12)
 Stem2 length = 9   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -10.9

         ..(((((((.......((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((---....([[{(((({(.((((......--.-----...)))))}))))}]])..--..-.))))))...
 target  UUUCCAUAG---UCAAUGAUGGUUCAAUAGGUAAACU--A-----AGUCCUAUAAACCUGAACU--UC-UUUAUGGUUA
                         ****            ^^^                       ****