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

 Blastx evalue: 7e-22
 Query name: gi|1007775267|ref|XP_015825407.1| PREDICTED: selenoprotein N isoform X1 [Nothobranchius furzeri]
 Query range: 28-566  (total 566)

 Target: /data/www-rg/seblastian_results/987093708/tempfiles/temptarget.fasta
 Chromosome: CM007953.1:subseq_51205938,105569_ Strand: -
 Positions:
 -Exon 1  56900        57034
 -Exon 2  55446        55563
 -Exon 3  55197        55327
 -Exon 4  54677        54889
 -Exon 5  53001        53125
 -Exon 6  52778        52915
 -Exon 7  52528        52609
 -Exon 8  51490        51678
 -Exon 9  51218        51323
 -Exon 10 50829        50941
 -Exon 11 50358        50459
 -Exon 12 49994        50158

 Redox box: no

Query   SWFYRGIWALLGLCSVPLLAFGIKYYQDALFLKRHVRSTAGMRVL <---Intron---> EESVGALGAEGFFLFSSLDTDHDLYLSPEEFKPIAEKLT
        ||    /  ||    |||||||  ||||/  ||||| ||/      <   1336bp   > | // ||| || ||||||||/||||||||||| /|||||
Target  SWIIGAMSTLLMFIIVPLLAFGYTYYQDSQLLKRHVSSTSVSMFY                EVALKALGTEGLFLFSSLDTNHDLYLSPEEFKLVAEKLT
        ttaaggatatcataagcccgtgtattcgtcccaccgatatgtatt                gggtagcgaggctcttttgaacgctcacggtacgggaca
        cgttgctcctttttttcttctgacaaaacattagatgccctctta                atctactgcagttttcctacaaatatgcaatattcaatc
        tgctaagaagtgctttcttcttcattgcagatattataatacgtc                agcgaagccgcctccccgcactcgctttggcaccagaca
                                                                                                            

Query   G <---Intron---> ITAPVDQEEEDIHDPNGETLVLEARMQPLLLDSMTKSKDSFLG <---Intron---> VSHSSLSGLRSWTSPAVPSSSFFA
        | <   118bp    > |/ | | |||  |||||||| |||/|||| ||/|||||| ||| <   307bp    > |/|||||||||| |||||| || |
Target  G                ISPPADFEEEVTHDPNGETLTLEAKMQPLQLDTMTKSKDGFLG                VTHSSLSGLRSWQSPAVPSMSFSA
        g                atccggtggggacgcaggacacggaacccccgaaaaaaggtcg                gacatcagccttcacggctatttg
                        gtccccataaatcaacagactctacatactatactcagaagttg                tcagctggtgcgagcctcctctcc
                        gcataattggagctcctagcacggcgggtggtcagggcgccccg                ttttcgtggtcggtttgccgcctc
                                                                                                            

Query   SQFRVFLPPKNKLEVGDTWWVIPSELNIFTGYLPNNRYHPPSPKGKE <---Intron---> VLIHSLLSMFHPRPFIKSRFAPQGTVACIRASSDFYY
        |||| ||||||| ||||||||| ||||||||||||||||||/|/||| <   1551bp   > |||||||||||||||||||||||||||||||/|||| 
Target  SQFRAFLPPKNKGEVGDTWWVIQSELNIFTGYLPNNRYHPPAPRGKE                VLIHSLLSMFHPRPFIKSRFAPQGTVACIRAASDFYL
        actagtcccaaagggggattgacagcaatagtccaactcccgccgag                gcactccaatcccctaatctgccgaggtacggagttc
        gatgcttccaaagatgacggttagatattcgatcaagaaccccggaa                tttacttgttacgcttacgtccagctcgtgccgatat
        cgcgccgccacagaggccggctgtgcccctgcgactcccttaaaaag                tctccgatgctagcccgtttctgaagcccacctctta
                                                                                                            

Query   DIVFR <---Intron---> IHAEFQLNDVPNFPFWFTPGQFTGNIVLSKDASHVRRFHLYVPNER <---Intron---> SLNVDMEWLYGASESSN
        ||||| <    85bp    > |||||||||||/||||||||||||||/||/|/||||/| |||||/| <   168bp    > /|||||||||||/|/||
Target  DIVFR                IHAEFQLNDVPDFPFWFTPGQFTGNIILSRDSSHVRQFTLYVPNDR                TLNVDMEWLYGATENSN
        gagta                acggtccaggcgtctttacgctagaaactcgttcgcctactgcaga                acaggagtctggagaaa
        atttg                tacatataatcatctgtccgatcgatttcgaccatgatctatcaag                ctatatagtagccaaga
        ctcc                gctagtgcttcaccccgccgcgctccccccgcccccagcccccccc                gtgtgcgggctactgctt
                                                                                                            

Query   MEVDIGYLPQ <---Intron---> LELQSTGPSTPSVITDEEGNVVDSRDGSSEPIQFIFEEINWNTEISQEEAFGRVEATLYPFKK <---Intron
        |||||||||| <   849bp    > /|||/ |||||| | |||||//||| | |/||||/||/|/| /|||/|||  |/| | ||||| <   166bp 
Target  MEVDIGYLPQ                MELQAAGPSTPSFIQDEEGNIIDSRGGGSDPIQFVFEDIHWTSEISREEAARRLEVTFYPFKK           
        agggagtccc                agccgggctacttacggggaaagacgggagcactgtggactatgaacggggcccggattctaa           
        tatatgatca                tataccgcccccttaaaagattaggggggactatttaatagccatggaaccggtatctactaa           
        gggctacgag                ggggcttcctccccgtgggttctcagaccctcgtccgcccggtgcccggttcccgccccccgg           
                                                                                                            

Query   ---> VSYLPFSEAFERAEAEKKLVHSILLWGALDDQSCUG <---Intron---> SGRTLRETVLESSPVLALLNQSFISSWSLVKELENMQ <---I
           > ||||||||||/||/ | ||||||||||||||||||| <   276bp    > |||||||||||||||||||||||/||||||||||/|| <   3
Target       VSYLPFSEAFQRAQEESKLVHSILLWGALDDQSCUG                SGRTLRETVLESSPVLALLNQSFVSSWSLVKELEDMQ      
             gttccttggtccgcggaacgctacctggcggctttg                tgcaccgagcgatcgcgccacatgaattcgagcggac      
             tcatctcactagcaaagattactttggctaaacgg                gcggctgacttagccttcttaagttgggcttaataata      
             gacgccagctgaagagcgggcccccggaatcacca                tgggtcggacgatgccgcgccgtccccgcgcagggcgg      
                                               *                                                            

Query   ntron---> ADEQNPALSEKARLHLEKYNFPVEMMVALPNGTI <---Intron---> LHHINANYFLDQTAMKPEDEGATFSFSSGFEDPSTSTYIS
        69bp    > |//|||  |//|||||| |||||||||||||||| <   199bp    > /||||||||||||/||||/| |||||| |||||||/|||/
Target            ANKQNPVESQRARLHLENYNFPVEMMVALPNGTI                VHHINANYFLDQTSMKPEEEAATFSFSGGFEDPSTATYIN
                  gaacacggacagccccgatatcggaaggccagaa                gccaagattcgcataacgggggatattggtggctagataa
                  caaaactagagcgtataaaatctatttctcagct                taatacaattaacctacaaaccctgtcggtaacccccata
                  tcggcgtgtggccacggtcctaaagggggccctt                tcccttcccgcggcgggggatcatcctggcgcacttgccc
                                                                                                            

Query   FLKEGLEKAKEIMEQ
        ||||||||||| / |
Target  FLKEGLEKAKEHLAQ
        tcaggcgagagccgc
        ttaagtaacaaatca
        ccagtggacggcgag
                       
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 629 ; UGA-SECIS: 1010

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007953.1:subseq_51205938,105569_ Strand = - Positions = 49364 - 49291
 Found by:  Infernal (score=38.65) Covels (score=29.24)
 Stem2 length = 11   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -24.79

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (((({(((((--(...{[[{(((((((((((................)))))))))))}]]}..--.)-)))))}))))
 target  GUUUCAGCAG--UUUGUGACGGCCUUGCCUGAAAGUCCAAAGUUGGCUGGGUAGGGCCUGAUGU--CA-UUGCUUAAGC
                         ****           ^^^                        ****