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

 Blastx evalue: 2e-16
 Query name: gi|928073769|ref|XP_013886755.1| PREDICTED: uncharacterized protein LOC106534608 [Austrofundulus limnaeus]
 Query range: 5-261  (total 263)

 Target: /data/www-rg/seblastian_results/419056145/tempfiles/temptarget.fasta
 Chromosome: JACSYO010001682.1:subseq_2826963,100000_ Strand: -
 Positions:
 -Exon 1  55758        55845
 -Exon 2  54566        54644
 -Exon 3  54404        54457
 -Exon 4  53758        53803
 -Exon 5  52934        53061
 -Exon 6  52656        52770
 -Exon 7  51421        51543
 -Exon 8  50741        50893

 Redox box: YES

Query   VSEETLTSSLNLLVSLGKVLLQNAKQDAAA <---Intron---> SLQTFIPHKITTLFGLITAGADFYRS <---Intron---> VGVKTKTEAEAV
        ||||||| /|  /|/||//||| |||/|   <   1113bp   > ||/ |/| ||||| ||| || |||/| <   108bp    > /||| |/||||/
Target  VSEETLTRALTQMVNLGRLLLQTAKQEAEE                SLEKFVPFKITTLLGLIQAGTDFYKS                IGVKKKSEAEAI
        gtggataagcacagacgcccccagacgggg                tcgatgctaaaatcgcacggagttaa                aggaaaagggga
        tcaactcgctcattatggtttaccaaaca                actaattctatccttgttacgcataag                tgtaaagacact
        ggggtagatgtggccgcactgggcgggga                gcgggtcatgcctaccgcacaaccca                caaggggtaagct
                                                                                                            

Query   WKKFYH <---Intron---> HEAVREQTEELLQLE <---Intron---> NEWDSFLQSVDGGL-----QLSGGKMADSLSPDCVLTDARSGA <--
        |/| || <   600bp    > | ||||| ||||||| <   696bp    > /|||/||/||| ||     ||||||/|||||||   || /||  <  
Target  WQKSYH                HAAVREQVEELLQLE                SEWDAFLESVDRGLQMTDIQLSGGKIADSLSPDTPFTDGQSGE    
        tcattc                cgggagcgggccccg                agtggtcgaggagccaagacctggaaggacacgactaggcagg    
        gaacaa                acctgaataattata                gagacttagtaggtatcatatcggatcagtgcacctcagagga    
        gggtt                ctaagagggagcggcg                tggcccggtgcatgggacagggaagcaccgcttcgcttagta     
                                                                                                            

Query   -Intron---> NVSLGHFLGRGQKLLLVLIRHFGULPURDHVAELQTSR <---Intron---> DLLEARSVRVLVVSFGSTEGAQLWLKQTGCTFEM
         163bp    > /|/|| /||/||/ ||||||||||||||||||||/ // <   1112bp   >  /||||||||||||||  |||||| /||||| /|
Target              SVTLGKYLGQGQRPLLVLIRHFGULPURDHVAELEANQ                AVLEARSVRVLVVSFGGVEGAQLWREQTGCTLDM
                    agacgatcgcgcacccgcaactgtcctcgcgggcggac                ggcggctgcgtggttggggggcttcgcagtacga
                    gtctgaatgagagctttttgatggtcggaatcatacaa                cttacgctgttttctggtagcatggaacggctat
                   gtgcgtgcgtgtgggggcccattaaagaaccgcgggatg                tcggtgaggcggttcgtgggtggggggtactccg
                                           *  *                                                             

Query   LLDPQRK <---Intron---> IYRSFGLGSSYAKVMKFGCLLQFSEYRTANIDFPDFPPRLLEDLYQVQMEN
        ||||||| <   527bp    > /|||||||||||||||||||| /|||  |/  ||/ | |||||/||||///
Target  LLDPQRK                VYRSFGLGSSYAKVMKFGCLLLYSEYGAADRGFPNVPFRLLEDMYQVQVDD
        ccgccaa                gtaatgcgtttgagaatgtcccttgtggggagtcagctcccggatcgcggg
        ttacaga                taggtgtgccacattatggtttacaagccaggtcatctgttaataatataa
        ggtagag                acgctccctcccggggcccgggcggcatgcaccctcctcggatgcgaaacc
                                                                                  
 Sequence until next stop: 
ACAGCAGCAAATACTTTGGCGTTGAGGTGCTGA
 T  A  A  N  T  L  A  L  R  C  * 

 Distance CDS-SECIS: 907 ; UGA-SECIS: 1216

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010001682.1:subseq_2826963,100000_ Strand = - Positions = 49833 - 49756
 Found by:  Infernal (score=28.16) Covels (score=30.13)
 Stem2 length = 9   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -14.21

         ..(((((((.......(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         (((({({(((--....{[[{((((((({((...................))})))))))}]]}......-.-)))})}))))
 target  UUGACUCACG--UUUAUGACGUCACGUCUCGCACUCAUGACACCAUGAGGAAACGUGACCGAUGCAGAA-C-UGUAAAUCAA
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