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

 Blastx evalue: 3e-33
 Query name: gi|229442427|gb|AAI72935.1| selenoprotein N, 1 [synthetic construct]
 Query range: 1-338  (total 338)

 Target: /data/www-rg/seblastian_results/398662502/tempfiles/temptarget.fasta
 Chromosome: KK951189.1:subseq_426542,15422_ Strand: -
 Positions:
 -Exon 1  7618         7730
 -Exon 2  6909         7046
 -Exon 3  5068         5149
 -Exon 4  4479         4667
 -Exon 5  3970         4075
 -Exon 6  2792         2904
 -Exon 7  2599         2700
 -Exon 8  1000         1167

 Redox box: no

Query   RLLSMFHPRPFVKTRFAPQGTVACLTAISDSYYTVMFR <---Intron---> IHAEFQLSEPPDFPFWFSPGQFTGHIILSKDATHIRDFRLFVPNHR
        |||||||||||||||||||| ||||||||| ||||||| <   571bp    > ||||||||||||||||||||||||||||||||||/|||||||||||
Target  RLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFR                IHAEFQLSEPPDFPFWFSPGQFTGHIILSKDATHVRDFRLFVPNHR
        cccaatcccctgaactgccggggtcagaagtttagatc                acggtccagccgtcttttcgctagcaactaggacgcgtcctgcaca
        gttgttacgcttacgtccagctcgtcctgataactttg                tacatatgaccatctgtccgatcgatttcaaccatgatgtttcaag
        gcgcgccggccggcctctggtgccgcccttccccggc                gctcgcgccgactcccgcttcgccccccccatcccctccgccgccc 
                                                                                                            

Query    <---Intron---> SLNVDMEWLYGASETSNMEVDIGYVPQ <---Intron---> MELEAVGPSVPSVILDEDGNMIDSRLPSGEPLQFVFEEIKW
         <   1759bp   > ||||||||||||||/|||||||||/|| <   400bp    > |||||/||||||||||||||/||||||||||||||||||||
Target                  SLNVDMEWLYGASESSNMEVDIGYIPQ                MELEALGPSVPSVILDEDGNLIDSRLPSGEPLQFVFEEIKW
                        tcaggagtctggagaaaagggagtacc                agcggcgctgctgacggggacagaccctggccctgtggaat
                        ctatatagtagcgaggatatatgatca                tatactgcctcctttaaagattaggtccgactatttaatag
                       gtgtgcggggcgctgcccgggccccacg                ggggcgccagctgcgtgtccgccccgcgggccgtgtggcgg
                                                                                                            

Query   HQELSWEEAARRLEVAMYPFKK <---Intron---> VNYLPFTEAFDRARAEKKLVHSILLWGALDDQSCUG <---Intron---> SGRTLRETVL
         ||||||||||||||||||||| <   403bp    > | |||||||||/|/|/ ||||||||||||||||||| <   1065bp   > ||||||||||
Target  QQELSWEEAARRLEVAMYPFKK                VTYLPFTEAFDQAKAKNKLVHSILLWGALDDQSCUG                SGRTLRETVL
        ccgcatggggcccgggatctaa                gatcctaggtgcgagaaacgctacctggcggctttg                tgcaccgagc
        aaatggaaccggtatctactaa                tcatctcactaacacaaattactttggctaaacgg                gcggctgactt
        ggggcgggtcgcgggcgcccgg                ctcggccgctcacgcgcgggcgcggggcgccgcca                taggtcggccg
                                                                                *                           

Query   ESPPILTLLNESFISTWSLVKELEDLQ <---Intron---> TQQENPLHRQLAGLHLEKYSFPVEMMICLPNGTV <---Intron---> VHHINAN
        || ||| |||||||||||||||||||| <    91bp    >   |/|| |//|| ||||||||||||||||||||| <   1431bp   > |||||||
Target  ESSPILALLNESFISTWSLVKELEDLQ                NNQDNPSHKKLADLHLEKYSFPVEMMICLPNGTV                VHHINAN
        gatcacgccagataaattcgagcggcc                aacgactcaacggcccgatatcggaaatccagag                gccaaga
        agccttcttaagttgcgcttaataata                aaaaaccaaatcatataaagtctatttgtcagct                taataca
        atgcccccccgccccagcggggggcgg                ccgccgccgggtcgcgggccccggggccgccctg                ccccccc
                                                                                                            

Query   YFLDITSMKPEDMENNNVFSFSSSFEDPSTATYMQFLREGLRRGLPLLQP
        ||||||||||||/| /|||||||/|||||||||||||/||||||||||||
Target  YFLDITSMKPEDIE-SNVFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP
        tttgaataacggag-aagtatttatggctagatactcaggcccgcccccc
        attatcctacaata-gattgtccctaacccccatattaagtgggtcttac
        ccgccccggcgctg-ccccccgcctacgcacccggcgggctgccgcccgc
                                                          
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 706 ; UGA-SECIS: 1090

------- SECIS element -- id:1 -- grade:C ----
 Chromosome = KK951189.1:subseq_426542,15422_ Strand = - Positions = 293 - 221
 Found by:  Covels (score=0.47) SECISearch1.0 (pattern=loose+)
 Stem2 length = 8   Apical loop length = 11   Insertion in stem2 = 0, 0
 Free Energy = -6.19

         ..(((((((............(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg-----UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ....({((((...........([[(({{(((((((------...........)))))))}}))]])..--...))))})--..
 target  GCUGUCUGGGAAaguuuACUGUGAAGCUGGCUUCU------GCCCUUAGCAAGGGAGUCCCCUGAGGG--GUCCCUGAA--GU
                              ****                 ^^                  ****