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

 Blastx evalue: 8e-26
 Query name: gi|1041103057|ref|XP_017274552.1| PREDICTED: selenoprotein O isoform X1 [Kryptolebias marmoratus]
 Query range: 1-691  (total 691)

 Target: /data/www-rg/seblastian_results/695861312/tempfiles/temptarget.fasta
 Chromosome: JACSYO010000740.1:subseq_83486,100000_ Strand: +
 Positions:
 -Exon 1  50000        50553
 -Exon 2  50829        51032
 -Exon 3  51119        51296
 -Exon 4  51682        51812
 -Exon 5  52008        52285
 -Exon 6  52432        52600
 -Exon 7  53469        53654
 -Exon 8  53930        54086
 -Exon 9  54355        54576

 Redox box: YES

Query   MAYLGPRLGTSRLFIPRVSAARLLGTVRMDDMGLAVSRSPLERLDFDNVVLRRLPLDPSEEPGARQVKGACFSRVKPQPLSNPRFVAVSPEALALLGLHA
        ||||||||| ||/|/| ||| | |||  | ||| | |||||||| |||| |/||||| ||||| ||||||||||||||||/ ||||/|| /|||||||  
Target  MAYLGPRLGPSRIFVPGVSAFRRLGTAGMADMGQATSRSPLERLHFDNVALKRLPLDSSEEPGVRQVKGACFSRVKPQPLTKPRFVSVSHDALALLGLTG
        agttgcccgctcatgcggtgtaccgaggaggagcgaactccgccctgaggcaacccgttggcggccgaggtttcgaccccaacctgtgtcggcgccgcag
        tcatgcgtgccgtttcgtcctggtgccgtcatgaccggcctagtataatctagtctaccaacgtgatagcgtcgtacactcacgttctcaactcttgtcg
        gttaatggagaccccctgcccacccgccgccgtgggttcggggcccccccggatcgcgcggcggtggaagcccggggggccgcccgcggcccgggggccg
                                                                                                            

Query   DQVVKDPLGPEYLSGSRVMPGSEPAAHCYCGHQFGHFAGQLGDGAACYLGEVKVPPGQDPELLRENPSGRWEIQVKGAGLTPYSR <---Intron--->
        |/|  ||||||||||||//|||||||||||||||| |||||||||||||||| |||| /|//||||||||||||||||||||||| <   275bp    >
Target  DEVASDPLGPEYLSGSRILPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVTVPPGLEPQMLRENPSGRWEIQVKGAGLTPYSR               
        ggggagccgcgtcagtaaccgtgcggctttgcctgctggccgggggtttgggagccgcgccaccgacagctgacgagggcactta               
        aatcgactgcaatggcgttcgcacccagaggaatgatcgatgagccgatgatctccgtacattgaacggggatatagcgtccacg               
        cgcgccgcgggcgcgcacgcacgcttccccccgcagcccggccggcccgggggggccagcagggacgctgggtggaatagtttc                
                                                                                                            

Query    QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVTSDTKVIRDVYYSGHPKHERCSVVLRLAPTFLR <---Intron---> FGSFEIFKPADELTG
         ||||||||||||||||||| | ||||||||||||||||/||/|||||||/|//||||||/|/|||||| <    86bp    > |||||||| ||| ||
Target   QADGRKVLRSSIREFLCSEVMHFLGVPTTRAGSVVTSDSKVVRDVYYSGNPRYERCSVVVRIAPTFLR                FGSFEIFKRADENTG
         cgggcagcctaaagtctaggactcggcaaaggtggatgaaggcggttagacctgattgggcagcatca                tgttgatacgggaag
         acaggattgcgtgattggattattgtcccgcgcttccagattgataaggacgaaggctttgtcccttg                tgctattagcaaacg
        gattctgcgcccaagcgccgggccctccccaaccagccccgcaatccctgttccggccgcctttcccc                gcactaccggccgcac
                                                                                                            

Query   RQGPSYGQDEIRAQMLDYVIEMFYPEIQQNYPNQVERNVAFFRE <---Intron---> VMYRTARLVAQWQCVGFCHGVLNTDNMSVLGLTLDYGPYG
        |||||||/|||| ||/||||||||||||||/|//|||||||||| <   385bp    > || |||||||||||||||||||||||||/|||||||||||
Target  RQGPSYGRDEIRGQMMDYVIEMFYPEIQQNHPDRVERNVAFFRE                VMRRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPYG
        ccgcatgcggacgcaagtgagattcgaccaccgaggaaggttcg                gaccagccggctctggttcggcaagaaaacgcacgtgctg
        gagcgaggaatggattaattattacataaaacagtagatcttga                ttggccgttcagagtgtgagttacaatgttgtctaagcag
        cgtcctagtgcgtgggttctggtctgcggtcacggggcgtccag                ggccgtacgtgggtgtcctacgcaccgccgacggcctatc
                                                                                                            

Query   FMDR <---Intron---> FDPDFICNASDNSGRYSYQAQPTICRWNLVKLAEALAPELPPDRAEAVMDEYQDLFNRFYLENMRKKLGLLTKEEPEDEI
        |||| <   195bp    > ||||/||||||||||||||||| ||||||||||||||||||||/|||||||| ||/| ||||||||||||| |/||||||
Target  FMDR                FDPDYICNASDNSGRYSYQAQPAICRWNLVKLAEALAPELPPDQAEAVMDEYLDLYNGFYLENMRKKLGLLKKDEPEDEI
        taga                tgcgtatagtgatgctttcgccgatatacgacgggcgcgcccgcggggaggtcgctagttcgaaaaacgttaaggcggga
        ttag                tacaatgaccaacggacaacacctgggattatcactccatccaacacttaaatataagtataatgaatgttaaaacaaat
        tgc                gttgtctccccccccacccgcgatccggcgggaggtttaggagcgtgctgcgcgtgtccccggcgggggcggggcgagtgc
                                                                                                            

Query   LITELLQTMHNTG <---Intron---> ADFTNTFRSLSQVSCPTEEEAEGHEEL-KKTTDLVLEQCASLDELKAANKPTMDLR <---Intron--->
        ||||||| ||||| <   146bp    > ||||||||||||/||||| |/|| ||| || |||/|||||||/||||||||||| | <   868bp    >
Target  LITELLQAMHNTG                ADFTNTFRSLSQISCPTEGESEGDEELVKKATDLLLEQCASLEELKAANKPTMDTR               
        caagcccgacaag                ggtaaatcatacattcagggagggggcgaagagcccgctgttggcaggaacaagac               
        ttcattactaac                gcatcactggtgatcgccagagagaaattaaccatttaagcctaataccaacctacg               
        gcaggggcgtcc                ttcccccctcgtgtccctgaataacgggcgacaccggggtccaggcgcacactgta                
                                                                                                            

Query    ELSMLLSMAQSNPALFQMISDRVTIARQLDKLSKLKELMETSQEELKTRQAEEWSSWLTRYR <---Intron---> KRLARELEGQSDVQATQEERV
         ||/|||||||||||||||||||  ||/|||/| |/|/|||||||||||/|||||| |/|||| <   275bp    > ||||||||||||| | |||||
Target   ELAMLLSMAQSNPALFQMISDRTGIAKQLDRLGKMKDLMETSQEELKTKQAEEWSRWITRYR                KRLARELEGQSDVPAAQEERV
         gcgacctagcaacgctcaatgaagagactgacgaaagcagaacggcaaacgggtactaacta                accgcgcggcaggcggcggag
         atctttctcagaccttattcagcgtcaatagtgataattacgaaatacaacaaggggtcgag                agtcgatagagatcccaaagt
        cgggggctgtgccgagcggcacgcgtgggacaccagacgggccgaggacagagggccgcact                ggtgtggaacgttggcgggggg
                                                                                                            

Query   RVMDSTNPRVVLRNYIAQNAIEAAENSDFSE <---Intron---> VQRVLKVLQKPFSSQPGLELPAWVGGHGTASQAERDEGEE-QQHEASASAARN
        |||||||||||||||||||||||||| |||| <   268bp    > ||||||||/|||||||||| ||| ||     | ||||||/  |  |||| |||
Target  RVMDSTNPRVVLRNYIAQNAIEAAENGDFSE                VQRVLKVLEKPFSSQPGLERPAWAGGGEATKQGERDEGEDPPQEAASASTARN
        agagaaaccggcaatagcagaggggaggttg                gccgcagcgactttccgcgccgtggggggaacggagggggcccgggtgtagaa
        gttagcacgtttgaatcaactaccaagatca                tagttattaactccacgtagccgcgggaccaagagaagaaccaacccccccga
        gggccccccggcgcctcgtatgttgcatctg                cgaccgtggggcggggtgggtcggcccgccgaaggtaagcagaggccacacat
                                                                                                            

Query   PVPYNSRPPAWAQEICVTUSS
        ||||/||||||| ||||||||
Target  PVPYDSRPPAWAHEICVTUSS
        cgctgaaccgtgcgatgattt
        ctcaaggcccgcaatgtcgcc
        ttccccgcatgctactcaatg
                          *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 483 ; UGA-SECIS: 489

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010000740.1:subseq_83486,100000_ Strand = + Positions = 55060 - 55138
 Found by:  Infernal (score=23.38) Covels (score=19.71)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -5.43

         ..(((((((..........(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcg---UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .((((([((..........{[[{(({(((((((..................)))))))}))}]]}..--..-.))]))))).
 target  AUGUUUAACUAGCGAUUAAUGACGAUUCAGACAACAAGUCCUACAGUGACCUGUCUGACUCUGACAA--AC-UGUGAGGUGC
                            ****            ^^                        ****