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

 Blastx evalue: 1e-83
 Query name: gi|226443071|ref|NP_001140181.1| selenoprotein V [Pan troglodytes]
 Query range: 1-346  (total 346)

 Target: /data/www-rg/seblastian_results/189475217/tempfiles/temptarget.fasta
 Chromosome: gi|511782587|gb|CM001946.1|subseq(34073123,102811) Strand: +
 Positions:
 -Exon 1  49592        50412
 -Exon 2  52274        52298
 -Exon 3  52406        52459
 -Exon 4  52569        52643
 -Exon 5  52737        52811

 Redox box: YES

Query   MNNQARTPAPSSARTSTSVRASTPTRTPTPLRTPTPVRTRTPIRTLTPVLTPSPAGTPPLVLTPAPAQIPTLVPTPALARIPRLVPPPAPAWIPTPVPTP
        ||||||||||||||||||||||||||||||||||||||||||||| |||||||||  | ||  |||| ||| |||||||||| |||||| ||||||||||
Target  MNNQARTPAPSSARTSTSVRASTPTRTPTPLRTPTPVRTRTPIRTQTPVLTPSPARLPALVQPPAPAHIPTQVPTPALARIPGLVPPPARAWIPTPVPTP
        aaacgcacgcttgcatatgcgtacacacacccacacgcacacacacacgcactcgcccgcgcccgcgcacacgcacgcgcacgcgcccgcgtacacgcac
        taaacgcccccccgcccctgcccccgcccctgcccctgcgcctgcaccttcccccgtccttacccccatccatcccctcgtcgttccccgcgtccctccc
        gtcgggcacccgggcacacgttcgcgagtacgcgtacgtgcccgcgtacgtgtgcgtctgcgtctacccctgcgtctgcgactgtggttgcgcttgcgtt
                                                                                                            

Query   VPVRNPTPVPTPARTLTPPVRVPAPA----PAQLLAGIRAALPVLDSYLAPALPLDPPPEPAPELPLLPEEDPEPAPSLKLIPSVSSEAGPAPGPLPTRT
          ||||||| ||||||||||||||||    |||/||||| ||| |||| | ||||||||||||| |  |||||||||||||||||||||||| || |  |
Target  ARVRNPTPVRTPARTLTPPVRVPAPAPAPDPAQVLAGIRTALPALDSYTARALPLDPPPEPAPEPPFSPEEDPEPAPSLKLIPSVSSEAGPALGPFPAHT
        gcgcacacgcacgcacaccgcgcgcgcgcgcgcgcggacagccgtgttagcgcctgcccgcgcgccttcgggcgcgcacacactgtagggcgcgctcgca
        cgtgaccctgcccgctccctgtcccccccaccattcgtgcctcctacaccgctctacccacccacctccaaacacccgtattcctcgacgcctgctccac
        tccgcatgcgtgtgcgttacgcacacacacccgcgggtgcgcccgcccgcgcatgtgcgattgggttgcggctggggcggccggcccgtgccgcctctct
                                                                                                            

Query   PLAANSPGPTLDFTFRADPSATGLADPPIPSPVPSPILGTIPSAISLQNSTETFPSSSENFALDKRVLIRVTYC <---Intron---> GLUSYSLR <
        |||||| |||||||||||||||||||| ||||||/|||||||| /||||||||  |/||||||||||||||||| <   1861bp   > |||||||| <
Target  PLAANSSGPTLDFTFRADPSATGLADPHIPSPVPAPILGTIPSTLSLQNSTETLVSTSENFALDKRVLIRVTYC                GLUSYSLR  
        ccggattgcacgtataggctgagcggccacacgcgcacgaactacttcatagatgtaagatgcgaagcacgatt                gctatacc  
        ctccaccgcctatctgcaccccgtcacatcgctcccttgctccctctaaccacttccgaatctaagtttgtcag                gtggagtg  
        tgcgcacgccgccccgacggctggatcctcctccgccggccggcccagttgacgccccaccggcggcgtagcc                tccactctg  
                                                                                                    *       

Query   ---Intron---> YILLKKSLEQQFPNHLLF <---Intron---> EEDRAAQATGEFEVFVNGRLVHSKK <---Intron---> RGDGFVNESRL
           107bp    > ||||| |||||||||||| <   109bp    > ||||||||||||||||||||||||| <    93bp    > ||||||||| |
Target                YILLKNSLEQQFPNHLLF                EEDRAAQATGEFEVFVNGRLVHSKK                RGDGFVNESGL
                      taccaaacgcctcaccct                gggaggcgaggtggtgagacgctaa                agggtgagtgc
                      atttaagtaaatcaattt                aaagccaccgatatttaggttacaa                ggagttaacgt
                      ctagaccgggatatcact                ggcatcgtaggtggtgcgagctcgg                gttctgcgtgg
                                                                                                            

Query   QKIVSVIDEEIKKR
        ||||||| ||||||
Target  QKIVSVIYEEIKKR
        caagagatggaaaa
        aattgttaaataag
        gatgccctggcgag
                      
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 981 ; UGA-SECIS: 1200

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782587|gb|CM001946.1|subseq(34073123,102811) Strand = + Positions = 53793 - 53865
 Found by:  Infernal (score=24.27) Covels (score=34.0)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -23.83

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