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

 Blastx evalue: 2e-32
 Query name: gi|169234651|ref|NP_001108448.1| selenoprotein N [Bos taurus] >gi|296490034|tpg|DAA32147.1| TPA: selenoprotein N, 1 [Bos taurus]
 Query range: 14-557  (total 557)

 Target: /data/www-rg/seblastian_results/361022014/tempfiles/temptarget.fasta
 Chromosome: gi|432034144|gb|KB168745.1|:subseq_1989667,100134_ Strand: -
 Positions:
 -Exon 1  58743        58857
 -Exon 2  53043        53189
 -Exon 3  50006        50139
 -Exon 4  47829        48041
 -Exon 5  47539        47663
 -Exon 6  46902        47039
 -Exon 7  45217        45298
 -Exon 8  44644        44832
 -Exon 9  44201        44306
 -Exon 10 43069        43181
 -Exon 11 42874        42975
 -Exon 12 41503        41670

 Redox box: no

Query   SGPAAPPAPPPRRARALALLGALLAAAAAAAAARAFARY <---Intron---> SEAQAAARQDSALKTLGTEGLFLFSSLDTDRDMYISPEEFKPIAE
        | |//|    |||||   || /   /// //     |   <   5553bp   >             ||||||||||||||||||||/|/||||| |/||
Target  SFPSSPRPQAPRRARVTVLLSSPSISSSPSSLLLLGASX                XXXXXXXXXXXXLKTLGTEGLFLFSSLDTDRDLYLSPEEFGPLAE
        ttcatcaccgcccgcgagccttcaatttcttctccggat                nnnnnnnnnnnncaacgaggctcttttgagcgctcacggtgccgg
        ctcgccgcaccggcgtctttcccgtccccccttttgcg                nnnnnnnnnnnnctactgcagttttcctacagatatgcaatgctca
        atatcggcgtccgttctccccccccattattgaggaat                nnnnnnnnnnnntggcgggacccccccgcccgtgccccggcgcccg
                                                                                                            

Query   KLTG <---Intron---> STPTANYEEEELPPDPSEETLTIEARFQPLLPESMTKSKDGFLG <---Intron---> VSRLALSGLRNWTTAASPSA
        |||| <   2903bp   > |||||/|||||||||||||||||||||||||||||||||||||| <   1964bp   > |||||||||||||||||| |
Target  KLTG                STPTASYEEEELPPDPSEETLTIEARFQPLLPESMTKSKDGFLG                VSRLALSGLRNWTTAASPRA
        acag                tacagatggggcccgcaggacaaggctcccccgtaaaaaggtcg                gtccgctgccataaggtccg
        atc                gcccccgaaaaatccacgaactctacgtacttcactcagaagttg                tcgtctcgtgagccccccgc
        gga                gattacccgggggctcccggaccaacacgtgcggcgcgcatgcag                cccgcgtccccgacacgata
                                                                                                            

Query   VFAARHFRPFLPPQGHVELGEPWWIIPSELSVFTGYLSNNRFYPPPPKGKE <---Intron---> VIIHRLLSMFHPRPFVKTRFAPQGAVACLTAIS
         ||||||||||||/|  |||||||||||||||||||||||||||||||||| <   165bp    > ||||||||||||||||||||||||||||/||/|
Target  QFAARHFRPFLPPRGQAELGEPWWIIPSELSVFTGYLSNNRFYPPPPKGKE                VIIHRLLSMFHPRPFVKTRFAPQGAVACVTAVS
        ctggcctcctccccgcggcggcttaacagcagtagtttaacttccccagag                gaaccccaatcccctgaactgccggggtgagga
        atccgatgcttccggacatgacggttcgatgttcgatcaagtaccccagaa                tttagttgttacgcttacgtccagctcgtcctg
        gtcccccgccccggcgaggcgcggccctggccccctgccccccgaacgagg                ccccgggcgccggccggcctcgggagccgagcc
                                                                                                            

Query   DFYYTVMFR <---Intron---> IHAEFQLSEPPDFPFWFSPGQFTGHVVLSKDATHVRDFRLFVPNHR <---Intron---> SLNVDMEWLYGAS
        ||||||||| <   499bp    > |||||||||||||||||||||||||/|||||||||||||||||||| <   1603bp   > |||||||||||||
Target  DFYYTVMFR                IHAEFQLSEPPDFPFWFSPGQFTGHIVLSKDATHVRDFRLFVPNHR                SLNVDMEWLYGAS
        gtttagatc                acggtccagccgtcttttcgctagcagctaggacgcgtcctgcaca                tcaggagtctgga
        ataactttg                tacatatgaccatctgtccgatcgatttcaaccatgatgtttcaag                ctatatagtagcg
        cccccggc                gcccgcgccggcccccgcgccgccccccccatcccgtccgccgccc                gtgtgcggggtgct
                                                                                                            

Query   ESSNMEVDIGYIPQ <---Intron---> MELEALGPSVPSVILDEDGNLIDSRLPSGEPLQFVFEEIQWQQELSWEEAARRLEVAMYPFKK <---In
        |/|||||||||||| <   384bp    > ||||| |||/||||/|||||/||||||||||||||||||/||||||||||||||||||||| | <   33
Target  ENSNMEVDIGYIPQ                MELEATGPSIPSVIMDEDGNMIDSRLPSGEPLQFVFEEIRWQQELSWEEAARRLEVAMYPFMK       
        gaaaagggagtacc                agcggagctactgaaggggaaagaccctggccctgtggaatccgcatggggcccgggatctaa       
        aagatatatgatca                tataccgcctcctttaaagattaggtccgactatttaatggaaatggaaccggtatctactta       
        gcctgggccccacg                ggggcaccaaccgcgtgtccgtcccgcgggccgtgtggcggggggcgggtcgcgggcgcccgg       
                                                                                                            

Query   tron---> VTYLPFTEAFDQAKAKNKLVHSILLWGALDDQSCUG <---Intron---> SGRTLRETVLESSPILALLNESFISTWSLVKELEDLQ <
        7bp    > |||||||||||||||||||||||||||||||||||| <   1019bp   > ||||||||||||||/|||||||||||||||||||||/ <
Target           VTYLPFTEAFDQAKAKNKLVHSILLWGALDDQSCUG                SGRTLRETVLESSPVLALLNESFISTWSLVKELEDLR  
                 gatcctaggtgcgagaaacgctacctggcggctttg                tgcaccgagcgatcgcgccagataaattcgagcggcc  
                 tcatctcactaacacaaattactttggctaaacgg                gcggctgacttagccttcttaagttgcgcttaataatg  
                 cccgaccgcccacgcgcgggcgcggggcgccgcca                tcggtcgggcgatgcctgcccgcctccgcggggggcga  
                                                   *                                                        

Query   ---Intron---> NNQENPSHQKLAGLHLEKYSFPVEMMICLPNGTV <---Intron---> VHHINANYFLDITSMKPEDIENHVFSFSSTFEDPST
            93bp    > ||/|||||/||| ||||||||||||||||||||| <   1203bp   > |||||||/|||||||/|||/||  |||/||||||||
Target                NNRENPSHKKLADLHLEKYSFPVEMMICLPNGTV                VHHINANHFLDITSMRPEDVENSAFSFASTFEDPST
                      aacgactcaacggcccgatatcggaaatccagag                gccaagacttgaataacggggaagtatgtatggcta
                      aagaaccaaatcatataaagtctatttgtcagct                taatacaattatcctgcaataagctgtccctaaccc
                      ccggccccgggacgcgggccccggggccgctccg                cccccccccgccccggcgcggccccccacctacgcg
                                                                                                            

Query   ATYMQFLKEGLRRGLPLLQP
        |||/||||||||||||||||
Target  ATYLQFLKEGLRRGLPLLQP
        gatcctcaggcccgcccccc
        ccatattaagtgggtcttac
        cgcggcgggccgccgcccgc
                            
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1052 ; UGA-SECIS: 1436

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|432034144|gb|KB168745.1|:subseq_1989667,100134_ Strand = - Positions = 40450 - 40380
 Found by:  Infernal (score=40.48) Covels (score=30.36)
 Stem2 length = 10   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -30.4

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ...(((((((--((..{[[{((((((((((.........-----...))))))))))}]]}.....-)))))))))...
 target  CCAGCAGCUG--CGCAUGAUGGCUGGGUCUGAAAUCCUA-----GAGGGGCCCAGCUUGAUGUCCC-UGCAGUUGCCCC
                         ****           ^^^                       ****