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

 Blastx evalue: 1e-21
 Query name: gi|928046123|ref|XP_013872017.1| PREDICTED: selenoprotein O [Austrofundulus limnaeus]
 Query range: 1-691  (total 691)

 Target: /data/www-rg/seblastian_results/113928887/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000027.1:subseq_151128,104823_ Strand: +
 Positions:
 -Exon 1  50000        50553
 -Exon 2  50697        50900
 -Exon 3  50996        51173
 -Exon 4  51520        51650
 -Exon 5  51767        52044
 -Exon 6  52169        52337
 -Exon 7  53757        53942
 -Exon 8  54207        54363
 -Exon 9  54602        54823

 Redox box: YES

Query   MAYLGPRVWTSRLFIPGVSVFRLLGSGSMDDMGLTASRSPLERLDFDNVVLRKLPLDPSEEPGVRQVKGACFSRVKPQPLSNPRFVAVSPEALTLLGLHA
        |||| ||/  ||/|/||/|  ||  |  ||||||  |||||||||||||||/||||| ||||||||||||||| |||||| |||||||| ||| ||||/ 
Target  MAYLRPRLGLSRIFLPGMSAVRLFCSVGMDDMGLAVSRSPLERLDFDNVVLKKLPLDTSEEPGVRQVKGACFSLVKPQPLVNPRFVAVSHEALALLGLNG
        agttacccgctcatccgatggactttggaggagcggactccgccgtgaggcaacccgatggcggccgaggtttcgaccccgacctgggtcggcgccgcag
        tcatgcgtgtcgtttcgtcctgttgctgtaatgtctggcctagtataatttaatctaccaacgtgatagcgtcttacacttacgttctcaactcttgtag
        gttaatggagatcccctgcgcgcctgcggccgtgtgttcggggcctcccgtaatcgcccggcggggggagtccgggggggctcgcgtgctacgggggcct
                                                                                                            

Query   DEVLKDPLGPEYLSGSRVMPGSEPAAHCYCGHQFGNFAGQLGDGAACYLGEVKAPPSQDPELLRENPCGRWEIQVKGAGLTPFSR <---Intron--->
        /||/ |||||||||||/|||||||||||||||||| ||||||||||||||||| ||  ||| ||/|| ||||||||||||||||| <   143bp    >
Target  EEVMNDPLGPEYLSGSKVMPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVKVPPGHDPEQLRDNPSGRWEIQVKGAGLTPFSR               
        gggaagccgcgtcagtagacgtgcggctttgcctgctggccgggggttcgggagccgcgcgcccgacagctgacgagggcactta               
        aattaactgcaatggcattcgcacccagaggaatgatcgatgagccgatgatatccgaacaatgaacggggatatagcgtcctcg               
        ggcgctgcaggtccacatgtacgtttccccacgtagccgggccggacccgggggaccctcggggttgctgggtggaatagtttc                
                                                                                                            

Query    QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVTSDSRVIRDVYYSGXPQHERCSVVLRIAPTFLR <---Intron---> FGSFEIFKAADEFTG
         ||||||||||||||||||| |||||/|||||||/|||||/||||||||| |/|||||||||||||||| <    95bp    > |||||||| |||/||
Target   QADGRKVLRSSIREFLCSEVMFFLGIPTTRAGSIVTSDSKVIRDVYYSGHPRHERCSVVLRIAPTFLR                FGSFEIFKQADEYTG
         cgggcagcctaaagtctaggattcgacaaaggtagatgaagacggttagccccgattggccagcatca                tgttgatacgggtag
         acaggattgcgtgattggatttttgtcccgcgcttccagattgataaggacgaaggctttgtcccttg                tgctattaacaaacg
        gattctacgtgtaagcgccgggccgttcccaacccgctccgcaatgcccgttccgactgcctctcccc                gtgttgccggccgccc
                                                                                                            

Query   RQGPSYGRDEIRGQMLDYVIEVFYPEIQQNYPDRVERNVAFFRE <---Intron---> VMYRTARLVAQWQCVGFCHGVLNTDNMSVQGLTLDYGPYG
        |/||| |||||||||/|||||/|||||||||||||||||||||| <   346bp    > || |||||||||||||||||||||||||/ ||||||||||
Target  RRGPSCGRDEIRGQMMDYVIEMFYPEIQQNYPDRVERNVAFFRE                VMLRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPYG
        ccgcatgcggaagcaagtgagattcgaccatcgaggaaggttag                gaccagccggctctggttcggcaagaaaacgcacgtgctg
        gggcggggaatggattaattattacataaaacagtagatcttga                tttgccgttcagagtgtgagttacaatgttgtctaagcag
        cctcctattgcaagggttctggtccgcggtcctggggtgtccag                ggctgtacgtgggtctcctacgcaccgccgacggtttatc
                                                                                                            

Query   FMDR <---Intron---> FDPDFICNASDSSGRYSYQAQPAICRWNLVKLAEALAPELPPDRAEAVMEEYLDLFNRFYLENMRKKLGLLTKEEPEDEI
        |||| <   116bp    > |||||||||||/| ||||||||||||||||||||||||||||||||| //||/ |/| ||||||||||||| | |||||/
Target  FMDR                FDPDFICNASDNSARYSYQAQPAICRWNLVKLAEALAPELPPDRAEAAIDEYMALYNGFYLENMRKKLGLLKKGEPEDEV
        taga                tgcgtatagtgatgctttcgccgatatacgacgggcgcgcccgcggggaggtagctagttcgaaaaacgttaaggcgggg
        ttag                tacattgaccaaccgacaacacctgggattatcactccatccagcacctaaatctaagtataatgaatgttaagacaaat
        cgc                gttacctccctccctacccgcgatccggcggggagtccaggaacttaccttgcgtgtccccagtgggggcggggcgtgcgc
                                                                                                            

Query   LITELLQTMHNTG <---Intron---> ADFTNTFRSLSQISCPTEGEAE-GHEGLKKTTDLLLEQCASLEELKAANKPTMDLR <---Intron--->
        ||||||||||||| <   124bp    > |||||||||||||||||||| | | / /|| ||||||||||||||||||| ||| | <   1419bp   >
Target  LITELLQTMHNTG                ADFTNTFRSLSQISCPTEGEGEAGEDLIKKATDLLLEQCASLEELKAANKLTMDPR               
        caagttcaacaag                ggtaaatcatacattcagggggggggcaaagagcccgctgttggcaggaacaagcc               
        ttcattactaac                gcatcactggtgatcgccagagacgaattaaccatttaagcctaataccaatctacg               
        gctggggcgcca                ttccccccccgtgtctctgaacgaggcccgacactggggtccaggcgtccacagtc                
                                                                                                            

Query    ELSMLLSMAQSNPTLFQMVSDRVTIARQLDKLGKLKDLMETSEEELRTKQAEEWSSWITHYR <---Intron---> KRLARELEGQSDVQSVQEERV
         ||/|||||||||| ||||/||| |||||||/| |||||||||/|||/|| ||||| ||| || <   264bp    > ||||/|||||||||/||||||
Target   ELAMLLSMAQSNPALFQMISDRATIARQLDRLRKLKDLMETSQEELKTKHAEEWSHWITRYR                KRLAQELEGQSDVQAVQEERV
         gcgacctagcaacgctcaatgagaagactgacaacagcagaacggcaaacgggtactaacta                accgcgcggcaggcggcggag
         atctttctcagaccttattcagcctcgatagtgataattacgaaatacaacaaggagtcgag                agtcaatagagatactaaagt
        tggggcccgtactaggcggcacgaatgggacacgagacgggccggggacattgggccgcact                ggtgtgggacgctggcgggggg
                                                                                                            

Query   RVMNSSNPRVVLRNYIAQNAIEAAENGDFSE <---Intron---> VQRVLEVLQKPFSSQPGLELPVWVGEPGTTAQAERDEGEE-QQHGASASAART
        |||/|/||||/|||||||||||||| ||||| <   238bp    > |||||/||/|||||||||||||| |/  /  / ||||||| ||  || | || 
Target  RVMDSTNPRVILRNYIAQNAIEAAEIGDFSE                VQRVLKVLEKPFSSQPGLELPVWAGKGESAERGERDEGEEQQQEAASTSTARN
        agagaaaccgacaatagcagaggggaggttg                gccgcagcgactttccgcgccgtggaggtggcggagggggcccgggtatagaa
        gttagcacgtttgaatcaactaccatgatca                tagttattaactccacgtatctgcgagaccaggagaagaaaaaacccccccga
        gggcctcttgacgcctcgtatgttgtacctg                cggccatgggtctggattaatgggcaagataagggcaagaagagtgtatacat
                                                                                                            

Query   PLPYDSKPPAWAQQICVTUSS
        |/|||||||/|| /|||||||
Target  PVPYDSKPPSWAHEICVTUSS
        cgctgaaccttgcgatgattt
        ctcaagacccgcaatgtcgcc
        tcccccgtgtgctactcaatg
                          *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 548 ; UGA-SECIS: 554

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000027.1:subseq_151128,104823_ Strand = + Positions = 55372 - 55452
 Found by:  Infernal (score=25.23) Covels (score=19.8)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -10.62

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