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

 Blastx evalue: 9e-19
 Query name: gi|928073769|ref|XP_013886755.1| PREDICTED: uncharacterized protein LOC106534608 [Austrofundulus limnaeus]
 Query range: 4-258  (total 263)

 Target: /data/www-rg/seblastian_results/477781085/tempfiles/temptarget.fasta
 Chromosome: SSNR01000243.1:subseq_90496,101205_ Strand: +
 Positions:
 -Exon 1  44764        44854
 -Exon 2  45315        45393
 -Exon 3  45466        45519
 -Exon 4  46940        46985
 -Exon 5  47652        47779
 -Exon 6  48021        48135
 -Exon 7  49997        50119
 -Exon 8  50522        50665

 Redox box: YES

Query   DVSEETLTSSLNLLVSLGKVLLQNAKQDAAA <---Intron---> SLQTFIPHKITTLFGLITAGADFYRS <---Intron---> VGVKTKTEAEA
         || ||||| | |||/|||||||||||/||| <   460bp    > ||//|/|||||||||||||  ||||| <    72bp    > /|||||||||/
Target  SVSPETLTSGLTLLVNLGKVLLQNAKQEAAA                SLESFVPHKITTLFGLITASEDFYRS                IGVKTKTEAES
        agtcgataagcactgatgagtccagacgggg                tcgttgccaaaattgcaagaggttaa                aggaaaagggt
        gtccactcggtctttatgatttaacaaacc                cctacttcaatccttgttccgaatagg                tgtacacacac
        cttggtactcgtggctgtatacatcagaca                ccggttattacctatcgcactaccca                ctaggagtaagc
                                                                                                            

Query   VWKKFYH <---Intron---> HEAVREQTEELLQLE <---Intron---> NEWDSFLQSVDGGL-----QLSGGKMADSLSPDCVLTDARSGA <-
        /|/| || <   1420bp   > | ||||| ||||||| <   666bp    >  ||||||/||  ||     |||||  || |||||/| |||||  < 
Target  IWQKSYH                HAAVREQVEELLQLE                TEWDSFLESVVEGLQTTDEQLSGGTTADRLSPDCLLIDARSGK   
        atcattc                cgggagcgggccccg                agtgttcgaggggccaaggcctggaaggccacgtccaggcaga   
        tgaacaa                acctgaataattata                cagacttagttagtaccaaatcggcccagtgcagtttacggga   
        tgggct                ctaagaggaggtgggg                tggcctggcgcatggaatgggaaaataccgttctgcttagta    
                                                                                                            

Query   --Intron---> NVSLGHFLGRGQKLLLVLIRHFGULPURDHVAELQTSR <---Intron---> DLLEARSVRVLVVSFGSTEGAQLWLKQTGCTFE
          241bp    > ///||  ||/ |||||||||||||||||||||||/ || <   1861bp   > |||||||//|||||||| |||||||/||||||/
Target               SITLGQVLGQSQKLLLVLIRHFGULPURDHVAELEASR                DLLEARSMQVLVVSFGSVEGAQLWLEQTGCTFK
                     aaacgcgcgcacacccgcaactgtcctcgcgggcggac                gccggctacgtggttgaggggcctcgcagtata
                     gtctgattgagaattttttgatggtcggaatcatacgg                attacgctattttctggtagcatgtaacggcta
                    gcatttgcgtgtgggggtttattaaggaaccgtgggctg                ccggtgcggcagtctttgaatggggagtaccca
                                            *  *                                                            

Query   MLLDPQRK <---Intron---> IYRSFGLGSSYAKVMKFGCLLQFSEYRTANIDFPDFPPRLLEDLYQVQ
        |||||||| <   402bp    >  ||| |||||| ||||||||||/||/| || | |||||||/|||||||
Target  MLLDPQRK                TYRSLGLGSSYFKVMKFGCLLQYSEFRIANRDLPDFPPRLIEDLYQVQ
        accgccaa                ataatgcgttttagaatgtctcttgtaagaagccgtccccaggctcgc
        tttacaga                caggtgtgccatattatggttaacatgtcagatcatccgttaataata
        gggctggg                ccgtggccgcccgggacccgggcagcatacatcttctttgaacccgaa
                                                                                
 Sequence until next stop: 
AACACAAAATAA
 N  T  K  * 

 Distance CDS-SECIS: 736 ; UGA-SECIS: 1036

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SSNR01000243.1:subseq_90496,101205_ Strand = + Positions = 51402 - 51479
 Found by:  Infernal (score=24.4) Covels (score=27.04)
 Stem2 length = 9   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -9.23

         ..(((((((.......(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ....(((((.--....{[[{({(((([(((...................)))]))))})}]]}......-.-.)))))....
 target  UUGACUCACA--UCAAUGACGCCACGACUUGAACUCAUGACAUCAUGAAGAGGUGUGACUGAUGCUGCA-A-CGUGAGGAAA
                         ****           ^^                          ****