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

 Blastx evalue: 8e-09
 Query name: gi|928014420|ref|XP_013877637.1| PREDICTED: migration and invasion enhancer 1-like [Austrofundulus limnaeus]
 Query range: 9-46  (total 95)

 Target: /data/www-rg/seblastian_results/505444988/tempfiles/temptarget.fasta
 Chromosome: CM007947.1:subseq_46484811,106351_ Strand: +
 Positions:
 -Exon 1  55679        55792

 Redox box: no

Query   YCGRUGYEPRYRELAQVVQAEFPEAEVSGFVGRTGSFE
        / |/|||||||//| | |  ||| ||||||||| |  /
Target  FSGQUGYEPRYKKLQQAVAVEFPGAEVSGFVGRKGQLD
        tagctgtgcctaacccgggggtcggggtgtggcagccg
        tggaggaacgaaataactctatcgcatcgttggagata
        ctcaagcgcccgatggtctggttggggactaaaatggt
            *                                 
 Sequence until next stop: 
AACCAATCAATCACATTTATTTTATAA
 N  Q  S  I  T  F  I  L  * 

 Distance CDS-SECIS: 676 ; UGA-SECIS: 775

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007947.1:subseq_46484811,106351_ Strand = + Positions = 56469 - 56537
 Found by:  Infernal (score=30.78) Covels (score=23.64)
 Stem2 length = 11   Apical loop length = 10   Insertion in stem2 = 0, 0
 Free Energy = -26.1

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .((((((((.--....{[[{(((((((((((........-----..)))))))))))}]]}..--....)))))))).
 target  UCCAGGACUU--UAUAUGAUUACUGUAGACCAAAGCUGA-----AAGGUUUAUAGUAUGAUGA--CCCCAGUCCUGGC
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:3     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 7e-22
 Query name: gi|992185819|ref|XP_015458696.1| PREDICTED: migration and invasion enhancer 1-like [Astyanax mexicanus]
 Query range: 30-118  (total 118)

 Target: /data/www-rg/seblastian_results/505444988/tempfiles/temptarget.fasta
 Chromosome: CM007947.1:subseq_46484811,106351_ Strand: +
 Positions:
 -Exon 1  50021        50129
 -Exon 2  51221        51297
 -Exon 3  51406        51486

 Redox box: no

Query   VFSSGGUGYEPRYQELKRVVVAEFPEAAVSGFVGRQG <---Intron---> SFEIEINGQLVFSKLETSGFPYEDD <---Intron---> VMDAIQ
        |  ||||||||||||| ||| ||| || ||||||||| <   1091bp   > |||||||||/||||||||||||||| <   108bp    > /|||||
Target  VVLSGGUGYEPRYQELARVVTAEFTEAEVSGFVGRQG                SFEIEINGQVVFSKLETSGFPYEDD                IMDAIQ
        ggcaggtgtgcctcgcgcggaggtaggggtgtggacg                atgagaagcggttacgaagtctggg                aaggac
        tttgggggaacgaaatcgttccatcacatcgttgga                ggtatatagatttcatacggtcaaaa                ttacta
        tctctaagcgcctggcggtctgactagaggccaaga                cttgtgctgaatccgcaacccatacc                cgctag
              *                                                                                             

Query   KAHDGKPVEKITKSQPPCVIL
        ||||||||||||||/||||||
Target  KAHDGKPVEKITKSRPPCVIL
        agcggacggaaaaaccctgac
        acaagactaatcaggccgttt
        acttcgagggccgccgttccg
                             
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 264 ; UGA-SECIS: 510

------- SECIS element -- id:3 -- grade:A ----
 Chromosome = CM007947.1:subseq_46484811,106351_ Strand = + Positions = 51751 - 51817
 Found by:  Infernal (score=27.53) Covels (score=19.9)
 Stem2 length = 9   Apical loop length = 11   Insertion in stem2 = 0, 0
 Free Energy = -16.0

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .((((((((---....{[[{(((((((({(......-..-----...)}))))))))}]]}..--....)))))))).
 target  UCUAGGACU---UAUAUGAUUACUGUAGCCCAAAGC-UG-----AAAGUUUAUAGUAUGAUGA--CCCCAGUCCUGGC
                         ****           ^^^                       ****