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

 Blastx evalue: 4e-72
 Query name: gi|226958322|ref|NP_001152962.1| selenoprotein P precursor [Macaca mulatta]
 Query range: 1-381  (total 381)

 Target: /data/www-rg/seblastian_results/285635102/tempfiles/temptarget.fasta
 Chromosome: gi|511782589|gb|CM001944.1|subseq(41494945,107633) Strand: -
 Positions:
 -Exon 1  57431        57633
 -Exon 2  56182        56394
 -Exon 3  53948        54065
 -Exon 4  50000        50608

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSNGSVTVVALLQASUYLCILQASK <---Intron---> LEELRVKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1036bp   > ||/|||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSNGSVTVVALLQASUYLCILQASK                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccgtaaagcgcacgtagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttacagctcttcttacggatgttacca                taatgtataaagacat
        ggatggtcgtctctagaaagcgcaccctgacacgcaatatagaccttagtgctttaccacgcaggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR <---Intron---> CGLLVYHLGLPFSFLTLPYVEEAIKIVYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2116bp   > || |||||||||||||  |||||||||||
Target  SYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR                CGRLVYHLGLPFSFLTFSYVEEAIKIVYC
        ttaggaccgattctataccaaagtgcacgtccggacaggtactagaaggtcatga                tgccgtccgtctttcatttggggaaagtt
        catttaaagtccgtaacataaatcaatctaaaaaaacatgcttaggaaatttaag                gggttaatgtctcttctcataactattag
        tttttttaacttaaacattgtgtagtttttaaaacaatcgttatacatcccatc                atcttattttgttccatcacaaactgttct
                                                                                                            

Query   EKKCGNCSLT <---Intron---> TLKDEDFCKSVSLATVDETVEAPQPHYHHEHHHNQGHQHLGSSELSENQQPGAPDAPTHPAPPGLHHHHKHKGQ
        |||||||||| <   3339bp   > |||||||||||||||||| ||||||||||||||||||||||||/||||||||||||||||||| ||||||||||
Target  EKKCGNCSLT                TLKDEDFCKSVSLATVDEAVEAPQPHYHHEHHHNQGHQHLGSSKLSENQQPGAPDAPTHPAPPDLHHHHKHKGQ
        gaatgattca                acagggttaagttgagggggggcccctccgcccacgccccgaaactgacccggcggcaccgccgcccccacagc
        aaaggagctc                ctaaaatgagtctcctaactaccacaaaaaaaaaagaaatgggatcaaaacgccacccaccccataaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctcttgttctgatgctcctgtagtgaaaaattttttttacttcctgcgta
                                                                                                            

Query   HRQGHPESUDMPGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLLAEENITESCQURLPPAAU
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HRQGHPESUDMPGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLLAEENITESCQURLPPAAU
        cacgccgatgacgaggtccccaactcaataactctatcagtgcgcaatttctcccatgaagtgaatctagacctttatcgctgggaaagttctctccggt
        agagacaggatcggagtaataaatggaggtaattgatcaacatccgggggaggatttaacgcctcgagaaatcctgggagttcaaatcacgaggtccccg
        tggtcagcatgaatataataaggcaagatataactagcataggttgcaccctatgataaagtaccagtaaccatatcagatgaagcatattgatgtatca
                *               *                      *                 *           *              *      *

Query   QISQQLVPTEVSTNURUKSKAKKUEUSSN
        ||||||/||||||||||||||||||||||
Target  QISQQLIPTEVSTNURUKSKAKKUEUSSN
        caacccacaggaaatctaaagaatgttta
        atgaattccatgcagggagacaagagcca
        aatggtacaactctacagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

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

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782589|gb|CM001944.1|subseq(41494945,107633) Strand = - Positions = 49311 - 49236
 Found by:  Infernal (score=25.75) Covels (score=19.41)
 Stem2 length = 10   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -4.61

         ..(((((((...............((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg--------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..([(((((...............{[[{((((((.((((......--.-----...))))))))))}]]}----....)))))])..
 target  CUUAGUAAGUAUUUCCAUAGUCAAUGAUGGUUUAAUAGGUAAACC--A-----AACCCUGUAAACCUGAC----CUCCUUUACGGUU
                                 ****            ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 4e-72
 Query name: gi|226958322|ref|NP_001152962.1| selenoprotein P precursor [Macaca mulatta]
 Query range: 1-381  (total 381)

 Target: /data/www-rg/seblastian_results/285635102/tempfiles/temptarget.fasta
 Chromosome: gi|511782589|gb|CM001944.1|subseq(41494945,107633) Strand: -
 Positions:
 -Exon 1  57431        57633
 -Exon 2  56182        56394
 -Exon 3  53948        54065
 -Exon 4  50000        50608

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSNGSVTVVALLQASUYLCILQASK <---Intron---> LEELRVKLEKEGYSNI
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1036bp   > ||/|||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSNGSVTVVALLQASUYLCILQASK                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccgtaaagcgcacgtagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttacagctcttcttacggatgttacca                taatgtataaagacat
        ggatggtcgtctctagaaagcgcaccctgacacgcaatatagaccttagtgctttaccacgcaggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR <---Intron---> CGLLVYHLGLPFSFLTLPYVEEAIKIVYC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2116bp   > || |||||||||||||  |||||||||||
Target  SYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR                CGRLVYHLGLPFSFLTFSYVEEAIKIVYC
        ttaggaccgattctataccaaagtgcacgtccggacaggtactagaaggtcatga                tgccgtccgtctttcatttggggaaagtt
        catttaaagtccgtaacataaatcaatctaaaaaaacatgcttaggaaatttaag                gggttaatgtctcttctcataactattag
        tttttttaacttaaacattgtgtagtttttaaaacaatcgttatacatcccatc                atcttattttgttccatcacaaactgttct
                                                                                                            

Query   EKKCGNCSLT <---Intron---> TLKDEDFCKSVSLATVDETVEAPQPHYHHEHHHNQGHQHLGSSELSENQQPGAPDAPTHPAPPGLHHHHKHKGQ
        |||||||||| <   3339bp   > |||||||||||||||||| ||||||||||||||||||||||||/||||||||||||||||||| ||||||||||
Target  EKKCGNCSLT                TLKDEDFCKSVSLATVDEAVEAPQPHYHHEHHHNQGHQHLGSSKLSENQQPGAPDAPTHPAPPDLHHHHKHKGQ
        gaatgattca                acagggttaagttgagggggggcccctccgcccacgccccgaaactgacccggcggcaccgccgcccccacagc
        aaaggagctc                ctaaaatgagtctcctaactaccacaaaaaaaaaagaaatgggatcaaaacgccacccaccccataaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctcttgttctgatgctcctgtagtgaaaaattttttttacttcctgcgta
                                                                                                            

Query   HRQGHPESUDMPGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLLAEENITESCQURLPPAAU
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HRQGHPESUDMPGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLLAEENITESCQURLPPAAU
        cacgccgatgacgaggtccccaactcaataactctatcagtgcgcaatttctcccatgaagtgaatctagacctttatcgctgggaaagttctctccggt
        agagacaggatcggagtaataaatggaggtaattgatcaacatccgggggaggatttaacgcctcgagaaatcctgggagttcaaatcacgaggtccccg
        tggtcagcatgaatataataaggcaagatataactagcataggttgcaccctatgataaagtaccagtaaccatatcagatgaagcatattgatgtatca
                *               *                      *                 *           *              *      *

Query   QISQQLVPTEVSTNURUKSKAKKUEUSSN
        ||||||/||||||||||||||||||||||
Target  QISQQLIPTEVSTNURUKSKAKKUEUSSN
        caacccacaggaaatctaaagaatgttta
        atgaattccatgcagggagacaagagcca
        aatggtacaactctacagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

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

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = gi|511782589|gb|CM001944.1|subseq(41494945,107633) Strand = - Positions = 49740 - 49669
 Found by:  Infernal (score=23.22) Covels (score=30.8)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -10.64

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({(((((--....{[[{((((((((({(.....-.........)})))))))))}]]}..--..-)))))})...
 target  UCUAUUUGCU--UUAAUGAGAAUAGAAACGUAAACU-AUGACCUAGGGGUUUCUGUUGGAUAG--UU-AGCAAUUUAG
                         ****           ^^^                       ****