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

 Blastx evalue: 3e-80
 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/564209009/tempfiles/temptarget.fasta
 Chromosome: WARS01000011.1:subseq_3311534,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  97883        98436
 -Exon 2  98926        99129
 -Exon 3  99232        99409
 -Exon 4  99743        99873
 -Exon 5  100002       100279
 -Exon 6  100371       100539
 -Exon 7  102357       102542
 -Exon 8  102840       102996
 -Exon 9  103121       103342

 Redox box: YES

Query   MAYLGPRVWTSRLFIPGVSVFRLLGSGSMDDMGLTASRSPLERLDFDNVVLRKLPLDPSEEPGVRQVKGACFSRVKPQPLSNPRFVAVSPEALTLLGLHA
        |||||||/  ||/|/||||| | |||  ||||||  ||| ||||||||||||||||| ||||||||||||||||||||||/|||||||| /|| ||||  
Target  MAYLGPRLRPSRIFLPGVSVIRRLGSVGMDDMGLAISRSSLERLDFDNVVLRKLPLDMSEEPGVRQVKGACFSRVKPQPLTNPRFVAVSHKALALLGLDG
        agttgcccactcatccggtgaaccgtggaggagcgaacttcgccgtgaggcaacccgatggcggccgaggtttcgaccccaacctgggtcagcgccgcgg
        tcatgcgtgccgtttcgtcttggtgctgtaatgtctggcctagtataatttgatctatcaacgtgatagcgtcgtacactcacgttctcaactcttgtag
        gttattggaaatctgctgcgcaccagcggccgtggctctggggccccctccgaccgcgcggccggggaagtccgggggggctcgcgtgccatgggggcca
                                                                                                            

Query   DEVLKDPLGPEYLSGSRVMPGSEPAAHCYCGHQFGNFAGQLGDGAACYLGEVKAPPSQDPELLRENPCGRWEIQVKGAGLTPFSR <---Intron--->
        /||/ |||||||||||/|||||||||||||||||| ||||||||||||||||/ || |||||||/|| ||||||||||||||/|| <   489bp    >
Target  EEVMNDPLGPEYLSGSKVMPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVRVPPGQDPELLRDNPSGRWEIQVKGAGLTPYSR               
        gggaagccgcgtcagtagacgtgcggctttgcctgctggccgggggttcgggagccgcgcgcccgacagctgacgagggcactta               
        aattaactgcaatggcattcgcacccagaggaatgatcgatgagccgatgatgtccgaacattgaacggggatatagcgtccacg               
        ggcgctgtaagtgcacatgcacgctcccccccgccgccgggccgaccccgggggacaatcagggtcgccgggaggagtagtttc                
                                                                                                            

Query    QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVTSDSRVIRDVYYSGXPQHERCSVVLRIAPTFLR <---Intron---> FGSFEIFKAADEFTG
         ||||||||||||||||||| |||||||||||||/||||||||||||||| |/|||||||||||||||| <   102bp    > ||||||||  |||||
Target   QADGRKVLRSSIREFLCSEVMFFLGVPTTRAGSIVTSDSRVIRDVYYSGHPRHERCSVVLRIAPTFLR                FGSFEIFKQTDEFTG
         cgggcagcctaaagtctaggattcggcaaaggtagatgaagacggttagccccgattggccagcatca                tgttgatacaggtag
         acaggattgcgtgattggatttttgtcccgcgcttccaggttgataaggacgaaggctttgtcccttg                tgctattaacaatcg
        aattctgcgcctaagctccgggccgttcccaacctgctccgcagtacccgctctgactgccttacctc                gtactgccgaccgcgc
                                                                                                            

Query   RQGPSYGRDEIRGQMLDYVIEVFYPEIQQNYPDRVERNVAFFRE <---Intron---> VMYRTARLVAQWQCVGFCHGVLNTDNMSVQGLTLDYGPYG
        |/||| | |||||||/||||| |||||||/|||||||||||||| <   333bp    > || |||||||||||||||||||||||||/ ||||||||||
Target  RRGPSCGLDEIRGQMMDYVIETFYPEIQQDYPDRVERNVAFFRE                VMLRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPYG
        ccgcatgcggacgcaagtgagattcgaccgtcgaggaaggttag                gaccagccggctctggttcggcaagaaaacgcacgtgctg
        gggcgggtaatggattaattactacataaaacagtagatcttga                tttgccgttcagagtgtgagttacaatgttgtctaagcag
        tgtcctactgctggggttctgatctgcagccatggggcgtccag                ggctgcttgtgggtgtcctacacactgccgacagcttatc
                                                                                                            

Query   FMDR <---Intron---> FDPDFICNASDSSGRYSYQAQPAICRWNLVKLAEALAPELPPDRAEAVMEEYLDLFNRFYLENMRKKLGLLTKEEPEDEI
        |||| <   128bp    > |||||||||||/|||||||||||||||||||||||||||||||||||||/||| |/| ||||||||||||| ||||||||
Target  FMDR                FDPDFICNASDNSGRYSYQAQPAICRWNLVKLAEALAPELPPDRAEAVMDEYLGLYNGFYLENMRKKLGLLKKEEPEDEI
        taga                tgcgtatagtgatgatttcgccgatatacgacgggcgcgcccgcggggaggtcgctagttcgaaaaacgtcaaggcggga
        ttag                tacattgaccaacggacaacacctgggattatcactccatccagcacttaaatgtaagtataatgaatgttaaaacaaat
        tgc                gttacccccccccacgcctgcgaaccggcgggaagtccaggaacgtgtcgcgcatgcccccggcgagggcagggagtgcgc
                                                                                                            

Query   LITELLQTMHNTG <---Intron---> ADFTNTFRSLSQISCPTEGEAEG-HEGLKKTTDLLLEQCASLEELKAANKPTMDLR <---Intron--->
        ||||||||||||| <    91bp    > ||||||||||| |||| |||/ |  | |||  |||||||||||||||||||||| | <   1817bp   >
Target  LITELLQTMHNTG                ADFTNTFRSLSLISCPAEGESAGDEEHLKKAVDLLLEQCASLEELKAANKPTMDPR               
        caagcccaacaag                ggtaaatcatacattcggggagggggccaagggcccgctgttggcaggaacaagcc               
        ttcattactaac                gcatcactggtgttcgccagagcgaaaataactatttaagcctaataccaacctacg               
        gctgtggcgcca                ttccccccccgtgtctctgaatggtggtagaaaccggggtccaagcgtatactgta                
                                                                                                            

Query    ELSMLLSMAQSNPTLFQMVSDRVTIARQLDKLGKLKDLMETSEEELRTKQAEEWSSWITHYR <---Intron---> KRLARELEGQSDVQSVQEERV
         ||/||||/||||| ||||/||| /||||||/| |||||||||/|||/|/|||||/ ||| || <   297bp    > ||||||||||||/|/|||/||
Target   ELAMLLSLAQSNPALFQMISDRASIARQLDRLSKLKDLMETSQEELKTRQAEEWNRWITRYR                KRLARELEGQSDMQAVQEQRV
         gcgacctcgcaacgttcaatgcgtagactgacaacagcagaacggcaaacgggtactaacta                accgcgtggcagacggcgcag
         atctttctcagaccttattcagcctcgatagtgataattacgaaatacgacaagaggtcgag                agtcgatagagatactaaagt
        tgggggctgtgccaagcggcacgagtgggacaccagacgggccgagggcagcgggccgcact                ggtacgggacgccggggggggg
                                                                                                            

Query   RVMNSSNPRVVLRNYIAQNAIEAAENGDFSE <---Intron---> VQRVLEVLQKPFSSQPGLELPVWVGEPGTTAQAERDEGEE-QQHGASASAART
        |||/|/||||/|||||||||||||||||||| <   124bp    > ||||| ||/|||||||||||| |||    | | |||||/| || |||| ||| 
Target  RVMDSTNPRVILRNYIAQNAIEAAENGDFSE                VQRVLRVLEKPFSSQPGLELPAWVGGGEDTQQGERDEGQEGQQEGASAPAARN
        agagaaaccgacaatagcagaggggaggttg                gccgcagcgactttccgcgccgtggggggaccggagggcggccgggtgcggaa
        gttagcacgtttgaatcaactaccaagatca                tagttgttaactccacgtatccgtgggaacaagagaagaagaaagccccccga
        gggccccttgacgccccgtatgttgtaccag                cggccgcaggtccagatggctagctttgccaaaggcaagggaagaatatacat
                                                                                                            

Query   PLPYDSKPPAWAQQICVTUSS
        |/|||||||||| /|||||||
Target  PVPYDSKPPAWASEICVTUSS
        cgctgaaccgtgagatgattt
        ctcaagacccgcgatgtcgcc
        tcctccgaatgctactcaaaa
                          *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 409 ; UGA-SECIS: 415

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000011.1:subseq_3311534,200000_:subseq_0,120000_ Strand = + Positions = 103752 - 103838
 Found by:  Infernal (score=22.59) Covels (score=19.85)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -10.37

         ..(((((((...............(((((((((((((((................))))))))))))))).........)))))))..
 model   uucggucaugcg--------UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..((((((((..............{[[{(({(((((((..................)))))))}))}]]}.....-..))))))))..
 target  GCGUGGUAUUUGACCAGCGAUUAAUGACGACUCAGACAACAAGUCCGGCAGUGACCUGUCUGACUCUGACAAAUA-AUGGUGUCACCU
                                 ****            ^^                        ****