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

 Blastx evalue: 9e-43
 Query name: gi|908522648|ref|XP_003453272.2| PREDICTED: selenoprotein N [Oreochromis niloticus]
 Query range: 1-557  (total 557)

 Target: /data/www-rg/seblastian_results/420972990/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000021.1:subseq_1465313,104006_ Strand: +
 Positions:
 -Exon 1  49138        49326
 -Exon 2  50030        50147
 -Exon 3  50238        50368
 -Exon 4  50715        50930
 -Exon 5  51021        51145
 -Exon 6  51795        51932
 -Exon 7  52013        52094
 -Exon 8  52280        52468
 -Exon 9  52550        52655
 -Exon 10 53267        53379
 -Exon 11 53472        53573
 -Exon 12 53848        54012

 Redox box: no

Query   MAADVDKRIPEEEKKISPQNGKQSPGSRSWICRGMWTLLVVCAVPLFAFGIKYYQDAQLLKRH <---Intron---> EESVRTLGAEGLFLFSSLDTD
        |||||||/  |/  /|/||/  /|||| ||| /|/|||||| |||| |||||||||||||||| <   703bp    > |||/|||||||||||||||||
Target  MAADVDKKNTEDGSRITPQSEHRSPGSGSWISKGLWTLLVVGAVPLLAFGIKYYQDAQLLKRH                EESIRTLGAEGLFLFSSLDTD
        agggggaaaagggaaaaccagccacgtgttatagctaccgggggcccgtgaattcggcccacc                ggaacacggggctcttttgag
        tccataaaacaagggtccagaaggcgcgcgtcagtgcttttgctcttctgtaaaaacattaga                aagtgctgcagttttcctaca
        gcacgtaaccgtgcatgggtgcgcgctacgccggggtatactcgttcctgcgtcatcgcgatt                ggtcatgtaggttccccgtcc
                                                                                                            

Query   HDFYLSPEEFKPIAEKLTG <---Intron---> ITNPADFEEEVIHDPNGETLTLEAKMQPLLLDSMTKSKDGFLG <---Intron---> VSHSSL
        || |||||||||||||||| <    90bp    > || | |||||| ||||||||||||||||||||||||||||||| <   346bp    > ||||||
Target  HDNYLSPEEFKPIAEKLTG                ITPPVDFEEEVTHDPNGETLTLEAKMQPLLLDSMTKSKDGFLG                VSHSSL
        cgatcacggtacaggacag                aaccggtggggacgcaggatatggaacccccgtaaaaaggtcg                gtcatc
        aaaatgcaatactcaatc                gtccctataaatcaacagactctacatactttactcagaagttg                tcagct
        ccttctgggtactagaca                atacggctggagcttctagtacggcaggggggccgagcgttctg                gtcctg
                                                                                                            

Query   SGLRSWKSPAVPSSSFSASQFRVFLPPKNKIEVGDTWWVIPSELNIFTGYLPNNRYHPPTPRG-RE <---Intron---> VVIHSLLSMFHPRPFIKT
        |||||||||||||||||||||| |||||||//|||||||||||||||||||||||||||/|/| /| <    90bp    > |/|||||/|||||||||/
Target  SGLRSWKSPAVPSSSFSASQFRAFLPPKNKVDVGDTWWVIPSELNIFTGYLPNNRYHPPSPKGNKE                VLIHSLLNMFHPRPFIKS
        agccttaacggctttttgactagtcccaaagggggattgacagcaatagtccaactccctcagaag                gcactttaatcccctaat
        ggtgcgagcctcccctccgatgcttccaaatatgacggttcgatattcgatcaagaaccccagaaa                tttacttattacgcttac
        ttgccggcaagtatcccccgcggcgcagcgctgacggggtccgcccccgcgcctgccggaagccag                tccccggtgcctgcccaa
                                                                                                            

Query   RFAPQGTVACIRASNDFYYDIVFR <---Intron---> IHAEFQLNDIPDFPFWFTPGQFTGNIVLSKDASHVRLFHLYVPNNR <---Intron---
        |||||||||||||||||||||||| <   649bp    > |||||||||/||||||||||||||||/||||||||| | |||||/| <    80bp    
Target  RFAPQGTVACIRASNDFYYDIVFR                IHAEFQLNDVPDFPFWFTPGQFTGNIILSKDASHVRHFQLYVPNDR              
        ctgccgaggtacgaagtttgagta                acggtccaggcgtctttacgctagaaactaggtcgcctcctgcaga              
        gtccagctcgtgcgaataaatttg                tacatataatcatctgtccgatcgatttcaaccatgatatatcaag              
        ttttgcacccttcccctttcccc                gtcaacgccttactccgccgcgctccctgtatattcatcacccctc               
                                                                                                            

Query   > SLNVDMEWLYGASESSNMEVDIGYLPQ <---Intron---> LELQSAGPSTPSIITDEQGNIIDRRDSSSEPIQFVFEEIHWTSEISQEEAARRME
        > ||||||||||||||||||||||||||| <   185bp    > ||||| ||||||/| ||/||||| || | ||||||||/||||||/||/|| ||//
Target    SLNVDMEWLYGASESSNMEVDIGYLPQ                LELQSTGPSTPSVIMDEEGNIIDSRDGSREPIQFVFEDIHWTSELSQQEATRRLD
          tcaggagtctggagaaaagggagtccc                tgcctagctactgaaggggaaagacggacgcactgtggactatgcaccggacccg
          ctatatagtagcgaggatatatgatca                tataccgccccctttaaagattaggagggactatttaatagccatgaaaccggta
         gtgtgcggggcgctgcccgggcttcgag                agggcacactccccgtggccccccaccctggcgcctgcccgcagctgaactcggt
                                                                                                            

Query   VTFYPFKK <---Intron---> VSYLPFSEAFERAEAEQKLVHSILLWGALDDQSCUG <---Intron---> SGRTLRETVLESSPVLALLNQSFI
        |||||||/ <    81bp    > |||||||||||||||| ||||||||||||||||||| <   611bp    > ||||||||||||||||||||||||
Target  VTFYPFKR                VSYLPFSEAFERAEAENKLVHSILLWGALDDQSCUG                SGRTLRETVLESSPVLALLNQSFI
        gattctaa                gttccttggtgcggggaacgctacctggtggctttg                tgcaccgagcgatcgcgccacata
        tctactag                tcatctcactagcacaaattactttggctaaacgg                gcggctgacttagccttcttaagtt
        ctccccgg                gccgttagctaacaaataggtctgtgaaaccgcca                tggatcggacgatgccatgccgcca
                                                                  *                                         

Query   SSWSLVKELENLQ <---Intron---> ADEQNPALSEKARLHLEKYSFPVEMMVALPNGTI <---Intron---> VHHINANFFLDQTAMKPEEEE
        |||||||||||/| <    92bp    > |||||  |||||||||| |/|||||||||||||| <   274bp    > |||||||/|||||/|||||| 
Target  SSWSLVKELENMQ                ADEQNRELSEKARLHLESYNFPVEMMVALPNGTI                VHHINANYFLDQTSMKPEEEG
        aattcgagcgaac                gggcacgcagagctccgatatcggaaggccagaa                gccaagattcgcataacgggg
        gggcttaataata                caaaagatgaacgtatagaatctatttctcagct                taatacaattaacctacaaag
        ccgtgcagggcgg                ttggccggcagtaacggtccctgggggcgttatt                cccctcctcgcagcgaaggaa
                                                                                                            

Query   ATFSFSGGFEDPSTSTYISFLKEGLEKAKEYLAQ
        |||||| |||||||||||||||||||||||||||
Target  ATFSFSSGFEDPSTSTYISFLKEGLEKAKEYLAQ
        gatattagtggctatataatcaggtgagagtcgc
        cctgtcggtaacccccatgttaagtaacaaatca
        atcccctctgcccacttcccggaggaacggtgag
                                          
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 492 ; UGA-SECIS: 873

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000021.1:subseq_1465313,104006_ Strand = + Positions = 54505 - 54584
 Found by:  Infernal (score=35.06) Covels (score=32.38)
 Stem2 length = 9   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -20.49

         ..(((((((........(((((((((((((((................))))))))))))))).........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ...((((((((......{[[(({({(((((((................)))))))})}))]]}.....-.))))))))...
 target  UGUGUCUCAGCCGUUUGUGAAGACUUUGCCUGAAAGCCCUCUAUGGGCUGGGCGACGCCUGAUGUUAU-UGCUGAGGCUGC
                          ****           ^^^                        ****