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

 Blastx evalue: 2e-35
 Query name: gi|1034142209|ref|XP_016794961.1| PREDICTED: selenoprotein O isoform X1 [Pan troglodytes]
 Query range: 1-694  (total 694)

 Target: /data/www-rg/seblastian_results/185945971/tempfiles/temptarget.fasta
 Chromosome: LOCP02000762.1:subseq_312434,200000_ Strand: +
 Positions:
 -Exon 1  49982        50562
 -Exon 2  57995        58198
 -Exon 3  59420        59600
 -Exon 4  60316        60446
 -Exon 5  60819        61099
 -Exon 6  64049        64199
 -Exon 7  65075        65260
 -Exon 8  65400        65601
 -Exon 9  65627        65812

 Redox box: YES

Query   MAAHRAALGASLAAARLL-PLSRCSPSPA---PRSTLSGAAMEPAPRWLAGLRFDNRALRALPVETPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLV
        ||/ /|  |||| ||| | ||  | | ||     /   | ||/ |||||||||||||||| ||||||||||||||| || ||||||/||/| ||||||||
Target  MASLKATFGASLTAARTLSPLLGCLPLPALCSASAAARGTAMDSAPRWLAGLRFDNRALRELPVETPPPGPEGAPSTPRLVPGACFSRVRPAPLRQPRLV
        agtcagatggtcaggcactcccgtccccgcttgtgggcgagagtgcctcggcctgacgccgccggacccgcgggctacccgcggttacgccgcccccccg
        tcctacctgcctcccgctccttggtctcctgccccccggcctacccggtcgtgtaagctgatctaccccgcagcccccgttcgcgtggtgccctgacgtt
        gcgcgtgtgtccgccccggggctccggcgccttggccccccgcgaccgggggccccccctggcggggggccaccgcgggcgcgcccccgtcgcggggcgg
                                                                                                            

Query   ALSEPALALLGLGAPP----AREA-EAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSR <---I
        ||||| ||||||| ||    |||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||| <   7
Target  ALSEPTLALLGLGPPPDDAAAREAREAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSR      
        gctgcacgccgcgcccgggggcggcgggggcttagagcccgggcggctttgcctgctggccgggggatcgggtaggggctgcccagggcactta      
        ctcacctcttgtgcccaacccgacgacacctttggacttcgcacccagaggaatgatcgatgagcctatgatgcccgaggatatagcgccctcg      
        ggggcgggggcgcggcccccccggcgcgcgccccccggggccgccgccccccgtcgccgggccctcgcgcggcgcccgcggggcgccctgccc       
                                                                                                            

Query   ntron---> QADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIR <---Intron---> FGSFEI
        432bp   > |||||||||||||||||||||||||/|||||||||||/||| |||||||||| | | |||||| ||/| <   1221bp   > ||||||
Target            QADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSQSTVERDVFYDGNPKQEPCAVVLRVAPTFLR                FGSFEI
                  cgggcagcctaacgtctaggatccgacaacgggtgatctaggcggttggacacgctgggccggcatca                tgttga
                  acaggattgcgtgattggacttatgtcccgcgcgtccacctagattaagacaaacgctttgtcccttg                tgctat
                 agccccgcgccccggcgccgcgccgccccggggcccgggcgggtcgcccaccggggcgcggtaccccc                gcgccgc
                                                                                                            

Query   FKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDSVQRNAAFFRE <---Intron---> VTQRTARMVAEWQCVGFCHGVLNTDNMSIL
        || ||| ||||||||||||||||/||||/ /|||||||||| |||||||||||| <   715bp    > ||/||||||||||||||||||||||||||/
Target  FKPADERTGRAGPSVGRNDIRVQMLDYVVGTFYPEIQAAHAGDSVQRNAAFFRE                VTRRTARMVAEWQCVGFCHGVLNTDNMSIV
        tacgggcagcggcaggaagacgcacgtgggattcgacggcgggagcaaggttcg                gaccagcagggtctggttcggcaagaaaag
        taccaagcggcgcgtggaatgtattaattgctacataccacgagtagaccttga                tcggccgttcagagtgtgagttacaatgtt
        cgcgtgcggcacctgggtccccgggccggcgcctgcgttcccccgggcaccctg                gatcgcgggcgggccccccccccgccgccg
                                                                                                            

Query   GLTIDYGPFGFLDR <---Intron---> YDPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLG
        |||||||||||||| <   372bp    > |||||||||||| ||| | ||||||/||||||||||/||||| | |||||||/||||/|||| ||| |||
Target  GLTIDYGPFGFLDR                YDPDHVCNASDNAGRYTYRKQPEVCKWNLRKLAEALEPELPLALAEAILAEEYDAEFRRHYLHKMRSKLG
        gcaagtgctgtcga                tgcgcgtagtgaggctatcaccggtataccacgggcgcgcccgcgggacgggtgggtcactccaacaacg
        gtctaagctgttag                aacaatgaccaacggacagaacatgagatgatcactacatctctcacttcaaaacatggaataatggatg
        gcctccgccccgc                gcccccgccccctcgccgccgggggcggcggggcgcggcggcgggcgccgcggcccgccgccgcggccggc
                                                                                                            

Query   LVQVELEEDGALVSKLLETMHLTG <---Intron---> ADFTNTFSLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPR <---Intro
        ||| | |||  ||//||||| ||| <   2949bp   > ||||||| |||||||| |/|| |/ |  |  ||||||||||||||||||| <   875bp
Target  LVQTEQEEDAVLVARLLETMQLTG                ADFTNTFWLLSSFPVEPEAPGQADVLTALTAQCASLEELRLAFRPQMDPR          
        cgcagcgggggcggcccgaaccag                ggtaaattccattcggcggcgcgggtagcagctgttggcacgtcccagcc          
        ttacaaaaactttcgttactatc                gcatcactgttgctctacaccgacattcctccagcctaatgtctgcatacg          
        cggcggggccgggcgcggcgggc                ttccccccgggcccgggggagcatccgcggtagtccgggggccctcggct           
                                                                                                            

Query   n---> QLSMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAAELQSRNQGHWADWLQAYR <---Intron---> ARLDKDLEGAGDAAAW
            > ||||||||||||||||||/|//| | /||||||||||||||| ||| | |/ ||| ||| || <   139bp    >  ||/|| |||||   |
Target        QLSMMLMLAQSNPQLFALLGSQANITKELERVEQQSRLEQLSPAELLSTNKDHWAAWLQEYR                VRLEKDREGAGDTGTW
              cctaacacgctaccctgccgtcgaaaagcgcggcctccgccacggccaaaagctggtccgtc                gccgagagggggagat
              atctttttcacacattcttgcacatcaatagtaaacgtaatgccattgcaaaagccgtaaag                tgtaaagagcgacgcg
             ggccgggggggccggccggccgggccgggggtggggggggggcgggggcgcgccgccggggc                gcggagcggccgccccg
                                                                                                            

Query   QAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSEASTRLSLWSLGGGRP <---Intron---> QTPLTLLILQVRRVLKLLETPYHCEAGAATDAE
        ||| || |||/||||||||||| ||||||| ||||||   ||     | /| <    25bp    > | | /    |||||||||||||| /  |    /
Target  QAERVRTMHASNPKYVLRNYIAHNAIEAAENGDFSEARAHLSQLCPWGPQP                QNPTS--FPQVRRVLKLLETPYHRDGEAPEVPD
        cggcgcaacgaacatgccatagcagaggggaggttggagcctcctctgccc                cacat--tccgccgcaccgactcaggggcggcg
        acagtgctacgacaattgaatcaactaccaagatcacgcatcatgcggcac                aaccc--tcatggttattaccaagagaccatca
        gtgtgccgcccccgcgagcctaccccggcgcaccagaggcgcggtcgcagg                acccg--ccggaaggggggtgccgcggccgcgt
                                                                                                            

Query   ATEANGADGRQRSYSSKPPLWAAELCVTUSS
        | |  || | ||||||/||||||||||||||
Target  AAEPEGAAGGQRSYSSRPPLWAAELCVTUSS
        gggcggggggccttaaaccctgggctgattt
        ccacagccggagcagggcctgccatgtcgcc
        ttgtgggccgacccccgcgcggggccccacg
                                    *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 99 ; UGA-SECIS: 105

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = LOCP02000762.1:subseq_312434,200000_ Strand = + Positions = 65912 - 65982
 Found by:  Infernal (score=15.39) Covels (score=25.71)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -11.97

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..({({{((---(...{[[{((({((((((..................))))))})))}]]}----..-)))}})})..
 target  CACCGCCUC---UCCAUGACGGCAGAGACGUCCAGUCAGGACCUGACCCGUCUCCGUCCGAU----GC-GGACUCAGCA
                         ****           ^^                         ****