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

 Blastx evalue: 4e-73
 Query name: gi|1039408233|ref|XP_008416550.2| PREDICTED: selenoprotein P isoform X1 [Poecilia reticulata]
 Query range: 1-389  (total 389)

 Target: /data/www-rg/seblastian_results/110918236/tempfiles/temptarget.fasta
 Chromosome: SSNR01000009.1:subseq_0,100000_ Strand: -
 Positions:
 -Exon 1  23858        24060
 -Exon 2  23395        23607
 -Exon 3  23195        23312
 -Exon 4  22957        23101
 -Exon 5  22442        22923

 Redox box: YES

Query   MWVRLSLLLTLCLLHGGGAESEGGGPRCQPPSTWMIGEVEPMKGTAGQVTVVALLKASULFCLVQASR <---Intron---> IDGLRQKLETQGLNDV
        ||| ||||||||||||| |||/||||||| |  | ||| /|| |/ |/|||||||/|||| ||/|||/ <   250bp    >    |||/|| ||| ||
Target  MWVHLSLLLTLCLLHGGSAESDGGGPRCQLPPAWTIGEEQPMTGSMGRVTVVALLQASULLCLLQASK                FADLRQQLEGQGLKDV
        atgccacccactcccggaggaggggcctccccgtaagggccaagtagcgagggcccgatctttccgta                tggcccccggcgcagg
        tgtatgtttctgttagggcagagggcggatcccgctgaaactcgctggtcttcttacggttgttacca                tcatgaatagagtaat
        gggcccgcctccgctgctagttgcgtctgatacgcaggggcgggagcagaggcttgccaggcgggtc                actcgcggggtgcggtg
                                                                  *                                         

Query   VYMVINHQGEQAQRLHPMLAERLSDKISLYKQGEQQPDVWQALNGKKDDFIIYDR <---Intron---> CGRLTHHISLPYSVIGHGHIESAIKEAYC
        ||| |||||/|||/|||/||/||// |/||||  ||||||| |||/|||| |||| <    82bp    > |||||/ ||||||/| |||/|||||/ ||
Target  VYMAINHQGDQAQQLHPLLAQRLTENITLYKQDNQQPDVWQTLNGEKDDFFIYDR                CGRLTYRISLPYSIISHGHVESAIKKTYC
        gtagaaccggcgcccccttgcacagaaactacgacccggtcacaggaggttatga                tgccatcatccttaaacgcggagaaaatt
        tatctaaagaacaatacttcagtcaatctaaaaaaacatgactagaaaatttaag                gggtcagtctcacttgagatagctaacag
        ccgccccggtacggcctgaagattgccaccagctagtttggagtagatcccctt                gcattcccaccatcctttcttgtacgaccc
                                                                                                            

Query   NRMCGACSHE <---Intron---> TAETPEGCRATPNAQPEADAPAAVGDNTEHDHRRHHGHGHHGHGHHGHGHHG <---Intron---> HGHHGQ
        ||||| |||| <    93bp    > / || | |     |||/||     ||||||   ||||| |   ||||||||| <    33bp    > |||   
Target  NRMCGECSHE                STETAEVCTGNNAAQPDADVIHPAGDNTEHG--RHHGH-HSHRGHHGHGHHG                HGHDQN
        acatggttcg                aagagggtagaaggccggggaccgggaagcg--cccgc-caccgccgcgccg                cgcgca
        agtggagcaa                gcaccatgcgaaccacacattaccgaacaag--gaaga-agaggaagagaa                gagaaaa
        tcgtagcttg                ctgtaggcaacctagttatcctttacccact--tttct-ttcttttctctt                cttttac
                                                                                                            

Query   HGHHHHRHHGDHHGHYGDLEQSQQGAGQDHGQHVFDLPQLQQAVDTEQLLQEAVAAPVRPUVAEKGRUKSKFTUQGTAGSENETVPKASUCUHURR-VFG
        |||||  |||  ||      / |   |    ||  /   /|||| |/// |||  |||||| //| ||||||/|| |||||||  ||||||||||/ /||
Target  HGHHHGNHHGSDHGQSQQGVRPQDDGGLSQRQHQLESHHMQQAVLTQEMFQEADVAPVRPUGSDKARUKSKFSUQWTAGSENEAAPKASUCUHURKLLFG
        cgcccgaccgtgcgcaccggaccggggttcaccctgtccaccggcacgatcgggggcgactgtgagatatatatctaggtgagggcagatttctcacttg
        agaaagaaagcaagagaagtgcaaaggtcagaaatacaataacttcaattaacatcctgcggcaacggacatggagccgcaaacccacggggaggatttg
        tttctacctttttagtaattaagtttagtaggtgagaccggatacagggtggccacttatagacgcgaacgccagggaccgcactcaccacacacgggct
                                                                    *      *     *               * * *      

Query   EAGSEQSLGLUHCEEGLPASUQUQGLTSEAATNVRETUQURMPPAEUQQPQPDQ
         |||||  |||||/| ||||||| || |||  ||||||||| |||/||||/| |
Target  NAGSEQPRGLUHCDEALPASUQUHGLMSEADGNVRETUQURSPPADUQQPEPAQ
        aggagcccgctctgggtcgttctcgcaaggggagagatctctccggtcccgcgc
        acggaacggtgagaactcccgagagttgacagatgacgaggccccagaacacca
        catcggggtcacttgggcccagaccggtggctctggcagacgtttcaggtgacg
                  *         * *              * *      *       
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 865 ; UGA-SECIS: 886

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SSNR01000009.1:subseq_0,100000_ Strand = - Positions = 21576 - 21499
 Found by:  Infernal (score=23.05) Covels (score=20.2)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 1
 Free Energy = -13.13

         ..(((((((........((((((((((((.(((...............))))))))).)))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggc-ccuAAAcCcuuuuuggggcgggccagg-cCuGAUGuuu-uuucaugaccggc
         ..(((((((........{[[{((((((((.((......---........)))))))).))}]]}.....-...)))))))..
 target  AUAUUUUCUAUACUUAAUGAUGGUUUCAGUGGGAAGAC---AGCUGUCACCCUGAAAUCCUGAUGCCAG-CACAGAGAAUUU
                          ****            ^^                         ****                  
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 4e-73
 Query name: gi|1039408233|ref|XP_008416550.2| PREDICTED: selenoprotein P isoform X1 [Poecilia reticulata]
 Query range: 1-389  (total 389)

 Target: /data/www-rg/seblastian_results/110918236/tempfiles/temptarget.fasta
 Chromosome: SSNR01000009.1:subseq_0,100000_ Strand: -
 Positions:
 -Exon 1  23858        24060
 -Exon 2  23395        23607
 -Exon 3  23195        23312
 -Exon 4  22957        23101
 -Exon 5  22442        22923

 Redox box: YES

Query   MWVRLSLLLTLCLLHGGGAESEGGGPRCQPPSTWMIGEVEPMKGTAGQVTVVALLKASULFCLVQASR <---Intron---> IDGLRQKLETQGLNDV
        ||| ||||||||||||| |||/||||||| |  | ||| /|| |/ |/|||||||/|||| ||/|||/ <   250bp    >    |||/|| ||| ||
Target  MWVHLSLLLTLCLLHGGSAESDGGGPRCQLPPAWTIGEEQPMTGSMGRVTVVALLQASULLCLLQASK                FADLRQQLEGQGLKDV
        atgccacccactcccggaggaggggcctccccgtaagggccaagtagcgagggcccgatctttccgta                tggcccccggcgcagg
        tgtatgtttctgttagggcagagggcggatcccgctgaaactcgctggtcttcttacggttgttacca                tcatgaatagagtaat
        gggcccgcctccgctgctagttgcgtctgatacgcaggggcgggagcagaggcttgccaggcgggtc                actcgcggggtgcggtg
                                                                  *                                         

Query   VYMVINHQGEQAQRLHPMLAERLSDKISLYKQGEQQPDVWQALNGKKDDFIIYDR <---Intron---> CGRLTHHISLPYSVIGHGHIESAIKEAYC
        ||| |||||/|||/|||/||/||// |/||||  ||||||| |||/|||| |||| <    82bp    > |||||/ ||||||/| |||/|||||/ ||
Target  VYMAINHQGDQAQQLHPLLAQRLTENITLYKQDNQQPDVWQTLNGEKDDFFIYDR                CGRLTYRISLPYSIISHGHVESAIKKTYC
        gtagaaccggcgcccccttgcacagaaactacgacccggtcacaggaggttatga                tgccatcatccttaaacgcggagaaaatt
        tatctaaagaacaatacttcagtcaatctaaaaaaacatgactagaaaatttaag                gggtcagtctcacttgagatagctaacag
        ccgccccggtacggcctgaagattgccaccagctagtttggagtagatcccctt                gcattcccaccatcctttcttgtacgaccc
                                                                                                            

Query   NRMCGACSHE <---Intron---> TAETPEGCRATPNAQPEADAPAAVGDNTEHDHRRHHGHGHHGHGHHGHGHHG <---Intron---> HGHHGQ
        ||||| |||| <    93bp    > / || | |     |||/||     ||||||   ||||| |   ||||||||| <    33bp    > |||   
Target  NRMCGECSHE                STETAEVCTGNNAAQPDADVIHPAGDNTEHG--RHHGH-HSHRGHHGHGHHG                HGHDQN
        acatggttcg                aagagggtagaaggccggggaccgggaagcg--cccgc-caccgccgcgccg                cgcgca
        agtggagcaa                gcaccatgcgaaccacacattaccgaacaag--gaaga-agaggaagagaa                gagaaaa
        tcgtagcttg                ctgtaggcaacctagttatcctttacccact--tttct-ttcttttctctt                cttttac
                                                                                                            

Query   HGHHHHRHHGDHHGHYGDLEQSQQGAGQDHGQHVFDLPQLQQAVDTEQLLQEAVAAPVRPUVAEKGRUKSKFTUQGTAGSENETVPKASUCUHURR-VFG
        |||||  |||  ||      / |   |    ||  /   /|||| |/// |||  |||||| //| ||||||/|| |||||||  ||||||||||/ /||
Target  HGHHHGNHHGSDHGQSQQGVRPQDDGGLSQRQHQLESHHMQQAVLTQEMFQEADVAPVRPUGSDKARUKSKFSUQWTAGSENEAAPKASUCUHURKLLFG
        cgcccgaccgtgcgcaccggaccggggttcaccctgtccaccggcacgatcgggggcgactgtgagatatatatctaggtgagggcagatttctcacttg
        agaaagaaagcaagagaagtgcaaaggtcagaaatacaataacttcaattaacatcctgcggcaacggacatggagccgcaaacccacggggaggatttg
        tttctacctttttagtaattaagtttagtaggtgagaccggatacagggtggccacttatagacgcgaacgccagggaccgcactcaccacacacgggct
                                                                    *      *     *               * * *      

Query   EAGSEQSLGLUHCEEGLPASUQUQGLTSEAATNVRETUQURMPPAEUQQPQPDQ
         |||||  |||||/| ||||||| || |||  ||||||||| |||/||||/| |
Target  NAGSEQPRGLUHCDEALPASUQUHGLMSEADGNVRETUQURSPPADUQQPEPAQ
        aggagcccgctctgggtcgttctcgcaaggggagagatctctccggtcccgcgc
        acggaacggtgagaactcccgagagttgacagatgacgaggccccagaacacca
        catcggggtcacttgggcccagaccggtggctctggcagacgtttcaggtgacg
                  *         * *              * *      *       
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 345 ; UGA-SECIS: 366

------- SECIS element -- id:2 -- grade:B ----
 Chromosome = SSNR01000009.1:subseq_0,100000_ Strand = - Positions = 22096 - 22021
 Found by:  Infernal (score=22.79) Covels (score=21.56)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -16.38

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ((((({(((.......{[[({{((((((([(.....-.........)])))))))}})]]}.....-.-.)))})))))
 target  CUCUCGCCAUCCUUUAUGAAACCAGAUGCAGAAACU-ACGCUCUAGUGGCGUCUGUAUGAUGUCAG-G-CUGGGGGGAG
                         ****           ^^^                       ****