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

 Blastx evalue: 1e-75
 Query name: gi|171451963|dbj|BAG15906.1| iodothyronine deiodinase type I [Paralichthys olivaceus]
 Query range: 1-247  (total 248)

 Target: /data/www-rg/seblastian_results/453466224/tempfiles/temptarget.fasta
 Chromosome: OMLM01002656.1:subseq_0,69324_ Strand: -
 Positions:
 -Exon 1  26832        27168
 -Exon 2  26604        26747
 -Exon 3  26011        26210
 -Exon 4  25601        25660

 Redox box: no

Query   MWLQKLLVYVSTAGMLCFMVGLSAILRVMHFISPSLSKKQILRMGEKTTMTQNQKFRYEDWGLTFLSFDFIKTASQHMWLSLGQEAFVGGEAPDSPVVTM
        |/||||/|| ||| | |/|/||/ /||//||||||||||/||||||| ||||| /|/||||| || || |/|/||/||||||||||||| /|||||||||
Target  MFLQKLMVYFSTASMFCYMIGLTVVLRIVHFISPSLSKKRILRMGEKITMTQNPRFKYEDWGPTFESFMFVKSASKHMWLSLGQEAFVGRDAPDSPVVTM
        atccacagtttagtatttaagcaggcaagctatcacaaacacaaggaaaaacacatatggtgcatgttatgatgtacatctcgcggtggaggcgtcggaa
        tttaatttatccccttgattgtctttgttattccgtgaagttgtgaatctcaacgtaaaaggcctacttttacccaatgtctgaacttggaccaccttct
        gtgaaggcttgagcgtccgaactcaggtgtttaacccggcccagtagccgcgtcatgtgtgtggtgccgtcacatgtgggtcaagttgaactacatgccg
                                                                                                            

Query   EGKKSSVCKFIRG <---Intron---> SRPLVLSFGSCTUPPFIYKLDEFKQLVRDFSDVADFMVVYIAEAHSTD <---Intron---> GWAFTNN
        /|||/|/||///| <    84bp    > /|||||||||||||||//||/||||||/|||||/||/||||||||||| <   393bp    > |||||||
Target  DGKKTSICKYMKG                NRPLVLSFGSCTUPPFMFKLEEFKQLVKDFSDVSDFLVVYIAEAHSTD                GWAFTNN
        ggaaaaatataag                aaccgtatgatatcctatacggtaccgagtaggtgtcggtagggctag                gtgtaaa
        agaacgtgaata                gagctttgtgggcgcctttataataattaatgatcattttatcacacc                aggctcaa
        cagaacccgcga                tcgggggttattcacgtgcatggcgaccgccccgtcttgcccagttaa                tcgcttcc
                                                 *                                                          

Query   FDINQHRSLEERLSAAQILVQQEPLCPVVVDEMNDVSAIKYGALPERLYVLQAGKVIYK <---Intron---> GGMGPWGYNPLEVRSLLEKM
        /||||||/||/|/||||||| /||||||||||||| /|||||||||||||||||||/|| <   350bp    > || ||||||| |||| ||||
Target  YDINQHRTLEDRISAAQILVLKEPLCPVVVDEMNDATAIKYGALPERLYVLQAGKVVYK                GGTGPWGYNPQEVRSFLEKM
        tgaacccacggaatggcacgcagcctcgggggaaggagaatggccgactgccggaggta                ggagctgtaccggcttcgaa
        aataaagctaagtcccattttaactgctttaataaccctaagctcagtattacgattaa                ggcgcggaacaatgcttaat
        tcccgcctggcgctaagcgtaagggcagtgtggttcccagtttgtaagcgggtgatccg                agggtgcctagggtacgggg
                                                                                                       
 Sequence until next stop: 
AAATAA
 K  * 

 Distance CDS-SECIS: 588 ; UGA-SECIS: 951

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = OMLM01002656.1:subseq_0,69324_ Strand = - Positions = 25012 - 24939
 Found by:  Infernal (score=31.49) Covels (score=25.3)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -9.83

         ..(((((((.......(((((((((((((((...............))))))))))))))).............)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu----u-uuucaugaccggc
         ..(((((((---....{[[((((((((((..........-----....))))))))))]]}.........-...)))))))..
 target  GUUGCUUUU---UGUAUGAGGAUUACAGUGCAAACCCCU-----GGUAACUGUAAUUUGAUAUAUGAUGA-CCUAAAAGUACC
                         ****           ^^^                       ****                      
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 1e-75
 Query name: gi|171451963|dbj|BAG15906.1| iodothyronine deiodinase type I [Paralichthys olivaceus]
 Query range: 1-247  (total 248)

 Target: /data/www-rg/seblastian_results/453466224/tempfiles/temptarget.fasta
 Chromosome: OMLM01002656.1:subseq_0,69324_ Strand: -
 Positions:
 -Exon 1  26832        27168
 -Exon 2  26604        26747
 -Exon 3  26011        26210
 -Exon 4  25601        25660

 Redox box: no

Query   MWLQKLLVYVSTAGMLCFMVGLSAILRVMHFISPSLSKKQILRMGEKTTMTQNQKFRYEDWGLTFLSFDFIKTASQHMWLSLGQEAFVGGEAPDSPVVTM
        |/||||/|| ||| | |/|/||/ /||//||||||||||/||||||| ||||| /|/||||| || || |/|/||/||||||||||||| /|||||||||
Target  MFLQKLMVYFSTASMFCYMIGLTVVLRIVHFISPSLSKKRILRMGEKITMTQNPRFKYEDWGPTFESFMFVKSASKHMWLSLGQEAFVGRDAPDSPVVTM
        atccacagtttagtatttaagcaggcaagctatcacaaacacaaggaaaaacacatatggtgcatgttatgatgtacatctcgcggtggaggcgtcggaa
        tttaatttatccccttgattgtctttgttattccgtgaagttgtgaatctcaacgtaaaaggcctacttttacccaatgtctgaacttggaccaccttct
        gtgaaggcttgagcgtccgaactcaggtgtttaacccggcccagtagccgcgtcatgtgtgtggtgccgtcacatgtgggtcaagttgaactacatgccg
                                                                                                            

Query   EGKKSSVCKFIRG <---Intron---> SRPLVLSFGSCTUPPFIYKLDEFKQLVRDFSDVADFMVVYIAEAHSTD <---Intron---> GWAFTNN
        /|||/|/||///| <    84bp    > /|||||||||||||||//||/||||||/|||||/||/||||||||||| <   393bp    > |||||||
Target  DGKKTSICKYMKG                NRPLVLSFGSCTUPPFMFKLEEFKQLVKDFSDVSDFLVVYIAEAHSTD                GWAFTNN
        ggaaaaatataag                aaccgtatgatatcctatacggtaccgagtaggtgtcggtagggctag                gtgtaaa
        agaacgtgaata                gagctttgtgggcgcctttataataattaatgatcattttatcacacc                aggctcaa
        cagaacccgcga                tcgggggttattcacgtgcatggcgaccgccccgtcttgcccagttaa                tcgcttcc
                                                 *                                                          

Query   FDINQHRSLEERLSAAQILVQQEPLCPVVVDEMNDVSAIKYGALPERLYVLQAGKVIYK <---Intron---> GGMGPWGYNPLEVRSLLEKM
        /||||||/||/|/||||||| /||||||||||||| /|||||||||||||||||||/|| <   350bp    > || ||||||| |||| ||||
Target  YDINQHRTLEDRISAAQILVLKEPLCPVVVDEMNDATAIKYGALPERLYVLQAGKVVYK                GGTGPWGYNPQEVRSFLEKM
        tgaacccacggaatggcacgcagcctcgggggaaggagaatggccgactgccggaggta                ggagctgtaccggcttcgaa
        aataaagctaagtcccattttaactgctttaataaccctaagctcagtattacgattaa                ggcgcggaacaatgcttaat
        tcccgcctggcgctaagcgtaagggcagtgtggttcccagtttgtaagcgggtgatccg                agggtgcctagggtacgggg
                                                                                                       
 Sequence until next stop: 
AAATAA
 K  * 

 Distance CDS-SECIS: 314 ; UGA-SECIS: 677

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = OMLM01002656.1:subseq_0,69324_ Strand = - Positions = 25286 - 25220
 Found by:  Infernal (score=29.19) Covels (score=15.86)
 Stem2 length = 8   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -18.44

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[((({((((((..........-----....))))))})))]]}..--..-.)))))))..
 target  CAGUGUUUC---UUAUUGAUGGCUACAGAUUAAACUUUU-----GGCCUCUGUAUCCAGAUGA--AG-UGAAACACAG
                         ****           ^^^                       ****