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

 Blastx evalue: 2e-52
 Query name: gi|315630400|ref|NP_001186857.1| selenoprotein P precursor [Callithrix jacchus]
 Query range: 1-381  (total 381)

 Target: /data/www-rg/seblastian_results/66099169/tempfiles/temptarget.fasta
 Chromosome: gi|408541724|gb|JH947208.1|:subseq_9873781,108344_ Strand: -
 Positions:
 -Exon 1  58142        58344
 -Exon 2  55534        55746
 -Exon 3  53699        53816
 -Exon 4  49895        50509

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSSCKHPPAWSIRDQDPMLNSSGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        ||||||||||||||| ||||||  || || || | ||//||||||/|||||||||||||||||||||| <   2395bp   > ||||||||||||||||
Target  MWRSLGLALALCLLPLGGTESQGPSSYCKQPPPWRIREEDPMLNSNGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccctaaagggcacatagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttctggcagagcgcagaacccggtgaaacttacagctcttcttacggatgttaccg                taatgtataaagacat
        ggacggtcgtcttccgaaggcggaccttaatacgaaggataggccttagtgttttatcacgcacgac                agacgaaagaaatttta
                                                                  *                                         

Query   SYIIVNHQGLSSQLRYTHLKNQVSEHIPVYQQEENQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPFSFLTFPYVEEAIKIAYC
        ||//|||||/ |||/| /|||/|||||||||||||| |||||||||||||||||| <   1717bp   > |||||||/|||/||||||||| |||| ||
Target  SYVVVNHQGVESQLKYLYLKNKVSEHIPVYQQEENQTDVWTLLNGNKDDFLIYDR                CGRLVYHIGLPYSFLTFPYVEAAIKITYC
        ttgggaccgggtctatttcaaagtgcacgtccggacaggtactagaaggtcatga                tgccgtcagtcttttatctggggaaaatt
        catttaaagtacataatataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtcacttctcatacctatcag
        ctatcttaatgtaaacactatgtagtttttaaaacaatcgttatacatcccatt                atcttgtcttgttccattatgatctgttct
                                                                                                            

Query   EKKCGNCPLT <---Intron---> TLNDEDFCKNVSLATVNKTTEAPQPHHHHKHHHNHRHQHLGSSELSKNQQPGAPDAPTHLTPLDLYHHHKHKGQ
        ||||||| |  <   3189bp   > || || ||/||/ | |//|||||/| ||| |     /         /||||| |||     || |/|||| || 
Target  EKKCGNCSLM                TLQDEIFCQNVTSANVDETTEAPEPDHHHGHDRPSHNHEHSHQHQGENQQPGEPDAHQQPPPLGLHHHHKLKGH
        gaatgattca                accggattcagatgagggaaggcgcgcccgcgccacacgctccccggacccggcggcccccccgcccccacagc
        aaaggagctt                ctaaattgaatcccataaccaccacaaaagaagcgaaaaacaaaagaaaacgacacaaaccctgtaaaaataga
        aggtacttcg                tcatacctatctgttgtaatgctaatctcttcacttttgtatataggtgaacaatttggcttacttcccgcgct
                                                                                                            

Query   HRQGHPENUYMPGSEGLQHP--RNKLUQRRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPA
         || ||||| || ||| |    / ||||/|| |||| |||||| ||| |||||||||||||||||||| ||/|||||||||||  || / || |||||||
Target  QRQSHPENUDMPESEGSQLSLLQKKLUQKRCKNQLLCKLPKDSGLAPSSUCUHCRHLIFEKTGSAITUHCKDNLPSLCSUQGLLVEEKVIESUQURLPPA
        cacaccgatgacgaggtcctcccaactcaataaccctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggagagttctccccg
        agagacaagatcagagcatcttaaatgaaggaaattgatcaacgtccgggggaggatttaacgcctcgagaaatcctgggagtttaaattacgaggtccc
        aggtcagcatgagtgtaatctagagcaagatatagccggcataggtttcacattatgataaagtaccactacccaaatcagatggggactatagatgtat
                *                 *         *            * *               *           *            * *     

Query   AUQTSQQLIPTEASTNUSUKNKAKKUECSSN
        ||| |||| |||||| |||||||/ |/ /||
Target  AUQASQQLKPTEASTTUSUKNKAEMUKUASN
        gtcgacccacaggaaatataaaggatatgta
        cgacgaataccacgccgggaaacatgagcca
        cagatggtgcaaccccatagtgaagagatac
         *              * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 629 ; UGA-SECIS: 638

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|408541724|gb|JH947208.1|:subseq_9873781,108344_ Strand = - Positions = 49265 - 49201
 Found by:  Infernal (score=29.59) Covels (score=25.34)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -15.7

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((({((---....([[{(((((((((.......--.-----....)))))))))}]])..--..-.))}))))..
 target  UUGCCACAG---UCAAUGAUGGUUUAUAGGUAAACU--A-----AGUACUAUAAACCUGAACU--CC-UCUAUGGUUA
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 2e-52
 Query name: gi|315630400|ref|NP_001186857.1| selenoprotein P precursor [Callithrix jacchus]
 Query range: 1-381  (total 381)

 Target: /data/www-rg/seblastian_results/66099169/tempfiles/temptarget.fasta
 Chromosome: gi|408541724|gb|JH947208.1|:subseq_9873781,108344_ Strand: -
 Positions:
 -Exon 1  58142        58344
 -Exon 2  55534        55746
 -Exon 3  53699        53816
 -Exon 4  49895        50509

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSSCKHPPAWSIRDQDPMLNSSGSVTVVALLQASUYLCILQASR <---Intron---> LEDLRVKLEKEGYSNI
        ||||||||||||||| ||||||  || || || | ||//||||||/|||||||||||||||||||||| <   2395bp   > ||||||||||||||||
Target  MWRSLGLALALCLLPLGGTESQGPSSYCKQPPPWRIREEDPMLNSNGSVTVVALLQASUYLCILQASR                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccctaaagggcacatagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttctggcagagcgcagaacccggtgaaacttacagctcttcttacggatgttaccg                taatgtataaagacat
        ggacggtcgtcttccgaaggcggaccttaatacgaaggataggccttagtgttttatcacgcacgac                agacgaaagaaatttta
                                                                  *                                         

Query   SYIIVNHQGLSSQLRYTHLKNQVSEHIPVYQQEENQPDVWTLLNGNKDDFLIYDR <---Intron---> CGRLVYHLGLPFSFLTFPYVEEAIKIAYC
        ||//|||||/ |||/| /|||/|||||||||||||| |||||||||||||||||| <   1717bp   > |||||||/|||/||||||||| |||| ||
Target  SYVVVNHQGVESQLKYLYLKNKVSEHIPVYQQEENQTDVWTLLNGNKDDFLIYDR                CGRLVYHIGLPYSFLTFPYVEAAIKITYC
        ttgggaccgggtctatttcaaagtgcacgtccggacaggtactagaaggtcatga                tgccgtcagtcttttatctggggaaaatt
        catttaaagtacataatataaatcaatctaaaaaaacatgcttagaaaatttaag                gggttaatgtcacttctcatacctatcag
        ctatcttaatgtaaacactatgtagtttttaaaacaatcgttatacatcccatt                atcttgtcttgttccattatgatctgttct
                                                                                                            

Query   EKKCGNCPLT <---Intron---> TLNDEDFCKNVSLATVNKTTEAPQPHHHHKHHHNHRHQHLGSSELSKNQQPGAPDAPTHLTPLDLYHHHKHKGQ
        ||||||| |  <   3189bp   > || || ||/||/ | |//|||||/| ||| |     /         /||||| |||     || |/|||| || 
Target  EKKCGNCSLM                TLQDEIFCQNVTSANVDETTEAPEPDHHHGHDRPSHNHEHSHQHQGENQQPGEPDAHQQPPPLGLHHHHKLKGH
        gaatgattca                accggattcagatgagggaaggcgcgcccgcgccacacgctccccggacccggcggcccccccgcccccacagc
        aaaggagctt                ctaaattgaatcccataaccaccacaaaagaagcgaaaaacaaaagaaaacgacacaaaccctgtaaaaataga
        aggtacttcg                tcatacctatctgttgtaatgctaatctcttcacttttgtatataggtgaacaatttggcttacttcccgcgct
                                                                                                            

Query   HRQGHPENUYMPGSEGLQHP--RNKLUQRRCINQLLUKLPKDSELAPRSUCUHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPA
         || ||||| || ||| |    / ||||/|| |||| |||||| ||| |||||||||||||||||||| ||/|||||||||||  || / || |||||||
Target  QRQSHPENUDMPESEGSQLSLLQKKLUQKRCKNQLLCKLPKDSGLAPSSUCUHCRHLIFEKTGSAITUHCKDNLPSLCSUQGLLVEEKVIESUQURLPPA
        cacaccgatgacgaggtcctcccaactcaataaccctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggagagttctccccg
        agagacaagatcagagcatcttaaatgaaggaaattgatcaacgtccgggggaggatttaacgcctcgagaaatcctgggagtttaaattacgaggtccc
        aggtcagcatgagtgtaatctagagcaagatatagccggcataggtttcacattatgataaagtaccactacccaaatcagatggggactatagatgtat
                *                 *         *            * *               *           *            * *     

Query   AUQTSQQLIPTEASTNUSUKNKAKKUECSSN
        ||| |||| |||||| |||||||/ |/ /||
Target  AUQASQQLKPTEASTTUSUKNKAEMUKUASN
        gtcgacccacaggaaatataaaggatatgta
        cgacgaataccacgccgggaaacatgagcca
        cagatggtgcaaccccatagtgaagagatac
         *              * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 261 ; UGA-SECIS: 270

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = gi|408541724|gb|JH947208.1|:subseq_9873781,108344_ Strand = - Positions = 49633 - 49562
 Found by:  Infernal (score=26.2) Covels (score=32.24)
 Stem2 length = 11   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -10.24

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({((((.--....{[[{((((((((([(.....-.........)])))))))))}]]}..--..-.))))})...
 target  UCUAUUUGCA--UCAAUGAAAACAGAAGCAUAAACU-AUGACCUAGGGGUUUCUGUUAGAUAA--UU-AGCAAUUUAG
                         ****           ^^^                       ****                 