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

 Blastx evalue: 1e-74
 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/289193670/tempfiles/temptarget.fasta
 Chromosome: KN982505.1:subseq_1414612,107890_ Strand: -
 Positions:
 -Exon 1  57688        57890
 -Exon 2  56436        56648
 -Exon 3  54204        54321
 -Exon 4  49949        50557

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSNGSVTVVALLQASUYLCILQASK <---Intron---> LEELRVKLEKEGYSNI
        ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| <   1039bp   > ||/|||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSKGSVTVVALLQASUYLCILQASK                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccgtaaagcgcacgtagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttacagctcttcttacggatgttacca                taatgtataaagacat
        ggatggtcgtctctagaaagcgcaccctgacacgcaatatagaccgtagtgttttaccacgcaggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR <---Intron---> CGLLVYHLGLPFSFLTLPYVEEAIKIVYC
        |||||||||||||||| |||||||||||||||||||||||||||||||||||||| <   2114bp   > |||||||||||||||| ||||||||| ||
Target  SYIVVNHQGISSRLKYPHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR                CGLLVYHLGLPFSFLTFPYVEEAIKIAYC
        ttaggaccgattctatcccaaagtgcacgtccggacaggtactagaaggtcatga                tgccgtccgtctttcatctggggaaagtt
        catttaaagtccgtaacataaatcaatctaaaaaaacatgcttaggaaatttaag                ggtttaatgtctcttctcataactatcag
        tttttttaacttaagtattgtgtagtttttaaaacaatcgttatacatcccatc                atcttattttgttccatcataaactgttct
                                                                                                            

Query   EKKCGNCSLT <---Intron---> TLKDEDFCKSVSLATVDETVEAPQPHYHHEHHHNQGHQHLGSSELSENQQPGAPDAPTHPAPPGLHHHHKHKGQ
        |||||||||| <   3646bp   > ||||||||||||||||| |||||| |//||||||||||||||||| ||||||||||||||||||||||||||||
Target  EKKCGNCSLT                TLKDEDFCKSVSLATVDGTVEAPQLHHYHEHHHNQGHQHLGSSELPENQQPGAPDAPTHPAPPGLHHHHKHKGQ
        gaatgattca                acagggttaagttgagggagggccccctcgcccacgccccgaagccgacccggcggcaccgccgcccccacagc
        aaaggagctc                ctaaaatgagtctcctagctaccataaaaaaaaaagaaatgggatcaaaacgccacccaccccgtaaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctctcgttctgatgctcctgtagtgaaaaattttttttacttcctgcgta
                                                                                                            

Query   HRQGHPESUDMPGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLLAEENITESCQURLPPAAU
        |||||||/ || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Target  HRQGHPENRDMLGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAU
        cacgccgacgacgaggtccccaactcaataactctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggaaagttctctccggt
        agagacaagattggagtaataaatggaggtaattgatcaacatccgggggaggatttaacgcctcgagaaatcctgggagtgcaaatcacgaggtccccg
        tggtcagcatgaatataataaggcaagatataactagcataggttgcaccttatgataaagtaccagtaaccatatcagatgaggcatattgatgtatca
                *               *                      *                 *           *              *      *

Query   QISQQLVPTEVSTNURUKSKAKKUEUSSN
        ||||||/|||||||||||/||||||||||
Target  QISQQLIPTEVSTNURUKNKAKKUEUSSN
        caacccacaggaaatctaaagaatgttta
        atgaattccatgcagggaaacaagagcca
        aatggtacaactctatagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 689 ; UGA-SECIS: 698

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KN982505.1:subseq_1414612,107890_ Strand = - Positions = 49259 - 49195
 Found by:  Infernal (score=33.35) Covels (score=20.32)
 Stem2 length = 10   Apical loop length = 10   Insertion in stem2 = 1, 0
 Free Energy = -12.3

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

 Blastx evalue: 1e-74
 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/289193670/tempfiles/temptarget.fasta
 Chromosome: KN982505.1:subseq_1414612,107890_ Strand: -
 Positions:
 -Exon 1  57688        57890
 -Exon 2  56436        56648
 -Exon 3  54204        54321
 -Exon 4  49949        50557

 Redox box: YES

Query   MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSNGSVTVVALLQASUYLCILQASK <---Intron---> LEELRVKLEKEGYSNI
        ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| <   1039bp   > ||/|||||||||||||
Target  MWRSLGLALALCLLPSGGTESQDQSSFCKQPPAWSIRDQDPMLDSKGSVTVVALLQASUYLCILQASK                LEDLRVKLEKEGYSNI
        ataacgcgcgctccctggagacgcatttacccgtaaagcgcacgtagtgagggcccgattctaccgta                tggccgacgaggttaa
        tgggtgtctctgttccggcagaaagctgaacccggtgaaacttacagctcttcttacggatgttacca                taatgtataaagacat
        ggatggtcgtctctagaaagcgcaccctgacacgcaatatagaccgtagtgttttaccacgcaggat                agacgaaaggaaatttt
                                                                  *                                         

Query   SYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR <---Intron---> CGLLVYHLGLPFSFLTLPYVEEAIKIVYC
        |||||||||||||||| |||||||||||||||||||||||||||||||||||||| <   2114bp   > |||||||||||||||| ||||||||| ||
Target  SYIVVNHQGISSRLKYPHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDR                CGLLVYHLGLPFSFLTFPYVEEAIKIAYC
        ttaggaccgattctatcccaaagtgcacgtccggacaggtactagaaggtcatga                tgccgtccgtctttcatctggggaaagtt
        catttaaagtccgtaacataaatcaatctaaaaaaacatgcttaggaaatttaag                ggtttaatgtctcttctcataactatcag
        tttttttaacttaagtattgtgtagtttttaaaacaatcgttatacatcccatc                atcttattttgttccatcataaactgttct
                                                                                                            

Query   EKKCGNCSLT <---Intron---> TLKDEDFCKSVSLATVDETVEAPQPHYHHEHHHNQGHQHLGSSELSENQQPGAPDAPTHPAPPGLHHHHKHKGQ
        |||||||||| <   3646bp   > ||||||||||||||||| |||||| |//||||||||||||||||| ||||||||||||||||||||||||||||
Target  EKKCGNCSLT                TLKDEDFCKSVSLATVDGTVEAPQLHHYHEHHHNQGHQHLGSSELPENQQPGAPDAPTHPAPPGLHHHHKHKGQ
        gaatgattca                acagggttaagttgagggagggccccctcgcccacgccccgaagccgacccggcggcaccgccgcccccacagc
        aaaggagctc                ctaaaatgagtctcctagctaccataaaaaaaaaagaaatgggatcaaaacgccacccaccccgtaaaaaaaga
        agatacctcg                tcatacttatatgttgtaatatagctctcgttctgatgctcctgtagtgaaaaattttttttacttcctgcgta
                                                                                                            

Query   HRQGHPESUDMPGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLLAEENITESCQURLPPAAU
        |||||||/ || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Target  HRQGHPENRDMLGSEGLQHLQKKLURKRCINQLLCKLPKDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAU
        cacgccgacgacgaggtccccaactcaataactctatcagtgtgcaatttctcccatgaagtgaatctagacctttatcgccgggaaagttctctccggt
        agagacaagattggagtaataaatggaggtaattgatcaacatccgggggaggatttaacgcctcgagaaatcctgggagtgcaaatcacgaggtccccg
        tggtcagcatgaatataataaggcaagatataactagcataggttgcaccttatgataaagtaccagtaaccatatcagatgaggcatattgatgtatca
                *               *                      *                 *           *              *      *

Query   QISQQLVPTEVSTNURUKSKAKKUEUSSN
        ||||||/|||||||||||/||||||||||
Target  QISQQLIPTEVSTNURUKNKAKKUEUSSN
        caacccacaggaaatctaaagaatgttta
        atgaattccatgcagggaaacaagagcca
        aatggtacaactctatagtgaagaaatac
                      * *      * *   
 Sequence until next stop: 
TAA
 * 

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

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = KN982505.1:subseq_1414612,107890_ Strand = - Positions = 49689 - 49618
 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
                         ****           ^^^                       ****