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

 Blastx evalue: 5e-23
 Query name: gi|301336158|ref|NP_001180385.1| selenoprotein L [Oncorhynchus mykiss]
 Query range: 1-307  (total 307)

 Target: /data/www-rg/seblastian_results/8939461/tempfiles/temptarget.fasta
 Chromosome: CM007938.1:subseq_60558200,102920_ Strand: -
 Positions:
 -Exon 1  53786        53891
 -Exon 2  53357        53435
 -Exon 3  53013        53066
 -Exon 4  52852        52897
 -Exon 5  52627        52754
 -Exon 6  51230        51344
 -Exon 7  50571        50693
 -Exon 8  50294        50431
 -Exon 9  49979        50110

 Redox box: YES

Query   MAEDISEAEDTLIYGLTGLNTMGRILLENGKQEAAG <---Intron---> SIEDFVPNKITTLFGLMTCAANFYNS <---Intron---> IGVKKR
        |||||||||||||||||||||||||||||||||||| <   350bp    > |||||||||||||||||||||||||| <   290bp    > ||||||
Target  MAEDISEAEDTLIYGLTGLNTMGRILLENGKQEAAG                SIEDFVPNKITTLFGLMTCAANFYNS                IGVKKR
        agggaaggggacatgtagtaaagaaccgagacgggg                taggtgcaaaaattgcaatggattaa                aggaaa
        tcaatgacaacttagtcgtactggtttaagaaacc                gctaattcaatccttgttcgccataag                tgtaag
        gtatctgagttttttaacgttgaacatatcgaaaa                tctattcatatatataagtttccccc                tttgggg
                                                                                                            

Query   IDAEDVWKKSYH <---Intron---> HAKVQEQVEELLQLE <---Intron---> EEWDAFLDRIDTELKTSDKRLTGGPTSQNLSADTPLTDARS
        |||||||||||| <   115bp    > ||||||||||||||| <    97bp    > |||||||||||||||||||||||||||||||||||||||||
Target  IDAEDVWKKSYH                HAKVQEQVEELLQLE                EEWDAFLDRIDTELKTSDKRLTGGPTSQNLSADTPLTDARS
        agggggtaattc                cgagcgcgggccctg                ggtggtcgcagagcaaagaccaggcatcacaggaccaggaa
        tacaatgaacaa                acataaataattata                aagacttagtacatacgaagtcggcccaatgcacctcacgg
        cctacggggtt                ctcggagaaggcgggg                gagtctgccactgggatcagcaacatagtgtttaccatcgt
                                                                                                            

Query   GE <---Intron---> NVTLGMYFGKGENLLLVLIRHFGULPUREHVAELATQQ <---Intron---> GLLDSQSARVLVVSFGCREGAQIWLDQT
        || <   1282bp   > |||||||||||||||||||||||||||||||||||||| <   536bp    > ||||||||||||||||||||||||||||
Target  GE                NVTLGMYFGKGENLLLVLIRHFGULPUREHVAELATQQ                GLLDSQSARVLVVSFGCREGAQIWLDQT
        gg                agacgattgaggacccgcacctgtcctcgcgggcgacc                gccgtctgcgcggttgtcgggcatcgca
        ga                atctgtatgagaattttttgatggtcggaatcatccaa                gttacaccgttttctgggagcatgtaac
        a                gtgtgagctgaggtgggcgcactaaagacgcgtgtgcag                atattgatgaggcctctgattgtgatgg
                                                 *  *                                                       

Query   GCKYDMLLDPERK <---Intron---> IYKAFGLGSSYSNVMNFDSLLQYAEYVVLGQEFPDIPPRFLEDFYQ <---Intron---> MGGDFVLDE
        ||||||||||||| <   139bp    > |||||||||||||||||||||||||||||||||||||||||||||| <   183bp    > |||||||||
Target  GCKYDMLLDPERK                IYKAFGLGSSYSNVMNFDSLLQYAEYVVLGQEFPDIPPRFLEDFYQ                MGGDFVLDE
        gtatgaccgcgaa                atagtgtgttttagaatgttcctggtggtgcgtcgaccctcggttc                agggtgcgg
        ggaaatttacaga                taactgtgccacattatacttaacaatttgaatcatccgttaataa                tggatttaa
        ccgccggtcaggg                tcgatcgatctatggtcccgtatagttgacagttccaatcgacctg                gtgctcgta
                                                                                                            

Query   GGTVILSHPCKNPMDRPEVAQMVATISSVGRPTSF
        |||||||||||||||||||||||||||||||||||
Target  GGTVILSHPCKNPMDRPEVAQMVATISSVGRPTSF
        ggagactcctaacagacgggcaggaattggccaat
        ggctttcacgaactagcatcattcctcctggccgt
        cgagccttccgtagcgtaaagggtccattcttccc
                                           
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 65 ; UGA-SECIS: 491

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007938.1:subseq_60558200,102920_ Strand = - Positions = 49913 - 49832
 Found by:  Infernal (score=22.92) Covels (score=22.25)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -19.74

         ..(((((((.......(((((((((((((((.................)))))))))))))))...........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         ..(((((((.......{[[(((((((([((...................))]))))))))]]}.......-...)))))))..
 target  CCUUGGCUUAUGUGGAUGAAGACACUGAUCACACUCAUAACCUCAUGAAGAGCAGUGUCUGAUGGGAACU-CACAAGCCAAUG
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