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

 Blastx evalue: 4e-78
 Query name: gi|316983151|ref|NP_001186909.1| selenoprotein O precursor [Pongo abelii]
 Query range: 1-669  (total 669)

 Target: /var/www/seblastian_output/735732449/tempfiles/temptarget.fasta
 Chromosome: gi|511782574|gb|CM001960.1|subseq(32647652,110791) Strand: +
 Positions:
 -Exon 1  45302        45861
 -Exon 2  50002        50205
 -Exon 3  52260        52440
 -Exon 4  53865        53995
 -Exon 5  54284        54564
 -Exon 6  59218        59368
 -Exon 7  60121        60306
 -Exon 8  60396        60552
 -Exon 9  60630        60791

 Redox box: YES

Query   MAAYRAALGALLAAARLLPLGRCRPSPALRSTLSGAAMEPAPRWLAGLRFDNRALRALPVEAPPPGPEGAPSAPRPVPGACFTRVQPTPLRQPRLVALSE
        |||||||||  |||||||||||| ||||  |||||||||||| ||||||||||||||||||||||||||| ||||||||||||||/||||||||||||||
Target  MAAYRAALGGSLAAARLLPLGRCHPSPAPGSTLSGAAMEPAPCWLAGLRFDNRALRALPVEAPPPGPEGAQSAPRPVPGACFTRVRPTPLRQPRLVALSE
        aggtaggcggtcgggcccccgctcctcgcgtattgggagcgcttcggcctgacgccgccgggcccgcgggctgcccgcggttacgccacccccccggctg
        tccagcctggctcccgttctgggacccccgcctcgcctacccggtcgtgtaagctgctctaccccgcagcacccgctcgcgtcgtgccctgacgttctca
        gcgcgttcgtgcgtcacgccccccggcgcctcggcccggcgtcgggggccccccgcggcggggtttcgccgcggcggcgcccccggccgggggctggggg
                                                                                                            

Query   PALALLGLGAPPAREAEAEAE--LFFSGNAILPGAEPAAHCYWGHQFDQLAGQLGEGSAMYLGEVCTATGERWELQLKGAGPTPFSR <---Intron--
        |||||||||||||||||||||  |||||||/||||||||||| |||| | |||||/|/||||||||||||||||||||||||||||| <   4140bp  
Target  PALALLGLGAPPAREAEAEAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSR             
        cgcgccgcggccgcgggggggggcttagagcccgggcggctttgcctgctggccgggggattgggtagaggctgcccagggcactta             
        cctcttgtgccccgacacacacctttggacttcgcacccagaggaatgatcgatgagcctatgatgcccgaggatatagcgccctcg             
        cggaggcgcggcacgcgcgcgcggcccccgcggctgccgccccccgccgccgggcccccgcgcggcggccgcggagcgctgcgccc              
                                                                                                            

Query   -> QADGRKVLRSSIREFLCSEAMFHLGIPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIR <---Intron---> FGSFEIFKSADEH
         > |||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||/|||||| <   2054bp   > |||||||||||||
Target     QADGRKVLRSSIREFLCSEAMFHLGVPTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRIASTFIR                FGSFEIFKSADEH
           cgggcagcctaacgtctaggatccggcaacgggtgatgtaggcggttggacatgctaggtcagtataa                tgttgatatgggc
           acaggattgcgtgattggacttatgtcccgcgcgtccaccttgattaagacaaaagctttgtcccttg                tgctattaccaaa
          agcctcgcggaccggcgccacgccggcccagctctcgcgcgggccgcttttcataacgtggtatctcag                tactgttgcatgc
                                                                                                            

Query   TGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASNNVQRNAAFFREV <---Intron---> TRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYG
        |||||||||||||||||||||||||||||||||||/ ||||||||||| <   1424bp   > ||||| ||||||||||||||||||||||||||||||
Target  TGRAGPSVGRNDIRVQLLDYVISSFYPEIQAAHASDRVQRNAAFFREV                TRRTAWMVAEWQCVGFCHGVLNTDNMSILGLTIDYG
        agcggcaggaagacgcccgtgaatttcgacggcgagcgcaaggttcgg                accagtagggtctggttcggcaagaaaacgcaagtg
        cggcgcgtggaatgtattaattgctacataccacgagtagaccttga                tcggccgttcagagtgtgagttacaatgttgtctaag
        agtacccgggcctcgggtctcccctctgcgttcctccggacccccgg                gggcgggggcgggcgcccccgccctcgccggcccccg
                                                                                                            

Query   PFGFLDRY <---Intron---> DPDHVCNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILADEFDAEFQRHYLQKMRRKLGLVQVELE
        |||||||| <   288bp    > ||||||||||||||||||||||||/|||/||||||||||||||||||||/||||||||||/||||||||||//|||
Target  PFGFLDRY                DPDHVCNASDNTGRYAYSKQPEVCKWNLQKLAEALQPELPLELGEAILAEEFDAEFQRHYMQKMRRKLGLVRLELE
        ctgtcgat                gcgcgtagtgaagctgtaaccggtataccacgggcccgcccgcgggacgggtgggtcactacaacaacgcgccgcg
        ctgttaga                acaatgaccaacggacagaacatgagataatcactacatctatgacttcaatacatagaataatggatgttgtata
        ccccgcg                cctccgctccccccccaccggcggcggcggggcgcggaggcgggcgccgcggttcgcagccggggcgggccgggggg
                                                                                                            

Query   EDGVLVSKLLETMHLTGA <---Intron---> DFTNTFYLLSSFPVEPESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQL <---Intron--->
        ||  |||||||||||||| <   4653bp   > ||||||/|||||||| ||||||||||||||||||||||||||||||||||| <   752bp    >
Target  EDKALVSKLLETMHLTGA                DFTNTFFLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPRQL               
        ggagcgtaccgaaccagg                gtaaattccattcggcgtcgcggtcgacagctgtcggcacgtcccagcccc               
        aaacttcattactatcgc                atcacttttgctctataccgtcattcgttaagcctaatgtctgcatacga                
        acggggcgcggcgcgct                tccacctcggcccagggggacgggcgcggggatccggggggccgcggtcgg                
                                                                                                            

Query    SMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSAADLQSRNQGHWADWLQAYRAR <---Intron---> LDKDLEGARDAAAWQAERVRV
         |||||||||||||||||||||||||||||||||||||||| |/||||||||||||||||||| <    89bp    > |||||||| ||||||||||||
Target   SMMLMLAQSNPQLFALMGTRAGIARELERVEQQSRLEQLSMAELQSRNQGHWADWLQAYRAR                LDKDLEGAGDAAAWQAERVRV
         taacacgctaccctgcagacggagagcgcggcctccgccaaggccacacgctggtccgtagc                cgagcggggggggtcggcgcg
        tctttttcacacattcttgcgcgtcgatagtaaacgtaatgtcataggaagagcagtacagcg                taaatagcgacccgacagtgt
        acgggggagacgggcacgccgacccggagtggggtgggggcgagggcgcgccgtcgggatacg                gcgcgaccgtttcggtgtgcg
                                                                                                            

Query   MHANNPKYVLRNYIAQNAIEAAERGDFSEVRR <---Intron---> VLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS
        |||/|||||||||||||||||||||||||||| <    77bp    > |||||| ||||||||||| |||||/||| ||||||||||||||||||||||
Target  MHASNPKYVLRNYIAQNAIEAAERGDFSEVRR                VLKLLENPYHCEAGAATDPEATEANGADSRQRSYSSKPPLWAAELCVTUSS
        acgaacatgcaatagcagaggggcggttggcc                gcaccgactctgggggagcggaggagggaaccttaaaccctgggctgattt
        tacgacaattgaatcaactaccaggatcatg                gttattaacaagacgcccacaccacagcaggagcaggacctgccatgtcgcc
        gcccccgcgggcccggcccgtcgcgccaggg                ggggaggctcccgggtcatcgcggccggccggcccctgcgcgacagcgaatg
                                                                                                        *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 117 ; UGA-SECIS: 123

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782574|gb|CM001960.1|subseq(32647652,110791) Strand = + Positions = 60909 - 60987
 Found by:  Infernal (score=20.78) Covels (score=25.77)
 Stem2 length = 9   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -21.11

         ..(((((((........(((((((((((((((................))))))))))))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         (((({{(((........([[{(((((((((....................)))))))))}]]).....-.-.)))}}))))
 target  GCACACCUGUCUUUCCAUGAUGGCAGAGACAUCCAGUCAGGACCUGACCCGUCUCUGUCUGAGGCCAG-C-UCAGCAGUGC
                          ****           ^^                         ****