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

 Blastx evalue: 2e-46
 Query name: gi|226443071|ref|NP_001140181.1| selenoprotein V [Pan troglodytes]
 Query range: 1-346  (total 346)

 Target: /data/www-rg/seblastian_results/512041747/tempfiles/temptarget.fasta
 Chromosome: KN982046.1:subseq_6385479,103088_ Strand: +
 Positions:
 -Exon 1  41939        42320
 -Exon 2  49986        50412
 -Exon 3  52552        52576
 -Exon 4  52684        52737
 -Exon 5  52846        52920
 -Exon 6  53014        53088

 Redox box: YES

Query   MNNQARTPAPSSARTSTSVRASTPTRTPTPLRTPTPVRTRTPIRTLTPVLTPSPAGTPPLVLTPAPAQIPTLVPTPALARIPRLVPPPAPAWIPTPVPTP
        ||||||||||||||||||||||| ||||||||||||||||||||| |||| ||||  | || ||||| ||| ||||||||||||||||| |||||||| |
Target  MNNQARTPAPSSARTSTSVRASTLTRTPTPLRTPTPVRTRTPIRTQTPVLIPSPARPPALVQTPAPAHIPTQVPTPALARIPRLVPPPARAWIPTPVPAP
        aaacgcacgcttgcatatgcgtacacacacccacacgcacacacacacgcactcgcccgcgcacgcgcacacgcacgcgcacccgcccgcgtacacgcgc
        taaacgcccccccgcccctgccctcgcccctgcccctgcgcctgcacctttccccgcccttacccccatccatcccctcgtcgttccccgcgtccctccc
        gtcgggcacccgggcacacgttcgcgagtacgtgtacatgcccgcgtacatgtgcgtctgcgtctacccctgcgtttgcgactgtgtttgcgcttgcttt
                                                                                                            

Query   VPVRNPTPVPTPARTLTPPVRVPAPAPA <---Intron---> QLLAGIRAALPVLDSYLAPALPLDPPPEPAPELPLLPEEDPEPAPSLKLIPSVSSE
         ||||||||||||||||||||||||||| <   7665bp   > |/||||| ||| |||| ||||||||||||||| || ||||||||||||||||||||
Target  APVRNPTPVPTPARTLTPPVRVPAPAPA                QVLAGIRTALPALDSYPAPALPLDPPPEPAPEPPLSPEEDPEPAPSLKLIPSVSSE
        gcgcacacgcacgcacaccgcgcgcgcg                cgcggacagccgtgttcgcgcctgcccgcgcgccttcgggcgcgcacacactgtag
        cctgaccctccccgctccctgtccccc                cattcgtgcctcctacacccctctacccacccacctccaaacacccgtattcctcga
        tccgcatgcgtgtgcgttacgcacaca                cgcgggtgcgcccgcccgagcatgtgcgatcgggtggcggctggggcggccggcccg
                                                                                                            

Query   AGPAPGPLPTRTPLAANSPGPTLDFTFRADPSATGLADPPIPSPVPSPILGTIPSAISLQNSTETFPSSSENFALDKRVLIRVTYC <---Intron---
        |||| ||||  ||||||| |||||||||||||||||||| /|||||/|||||||||/||||||||| |/||||||||||||||||| <   2139bp   
Target  AGPALGPLPAHTPLAANSSGPTLDFTFRADPSATGLADPHMPSPVPAPILGTIPSALSLQNSTETFVSTSENFALDKRVLIRVTYC              
        ggcgcgcccgcaccggattgcacgtataggctgagcggccacacgcgcacgaactgcttcatagatgtaagatgcgaagcacgatt              
        cgcctgctccacctccaccgcctatctgcaccccgtcacatcgctcccttgctccctctaaccacttccgaatctaagtttgtcag              
        cgccggctctcttgcgcacgccgccccgacggccggatccgccttcgctggccggcccagtggaccccccgccggcggcgtagcc               
                                                                                                            

Query   > GLUSYSLR <---Intron---> YILLKKSLEQQFPNHLLF <---Intron---> EEDRAAQATGEFEVFVNGRLVHSKK <---Intron--->
        > |||||||| <   107bp    > ||||| ||||||||/||| <   108bp    > ||||||||||||||||||||||||| <    93bp    >
Target    GLUSYSLR                YILLKNSLEQQFPNYLLF                EEDRAAQATGEFEVFVNGRLVHSKK               
          gctatacc                taccaaacgcctcatcct                gggaggcgaggtggtgagacgctaa               
          gtggagtg                atttaagtaaatcaattt                aaagccaccgatatttaggttacaa               
         tccactctg                ctagaccgggatatcact                ggcatcgtaggtggtgcgagctcgg               
            *                                                                                               

Query    RGDGFVNESRLQKIVSVIDEEIKKR
         ||||||||| |||||||| ||||||
Target   RGDGFVNESGLQKIVSVIYEEIKKR
         agggtgagtgccaagagatggaaaa
         ggagttaacgtaattgttaaataag
         gttctgcgcgggatgctctggcgag
                                  
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1003 ; UGA-SECIS: 1222

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KN982046.1:subseq_6385479,103088_ Strand = + Positions = 54092 - 54164
 Found by:  Infernal (score=26.68) Covels (score=34.0)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -27.23

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(((((((((--((..{[[{((((((((((.................))))))))))}]]}..--))-))))))))).
 target  GAGUCUCAGC--CGGAUGAUGAGAAGGGCUGAAAUGUUGCCAAGUCAGGUCCUUUUCUGAUGG--UG-GUUGGGGCUG
                         ****           ^^^                       ****