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

 Blastx evalue: 1e-62
 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/969463925/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000014.1:subseq_2346940,101317_ Strand: +
 Positions:
 -Exon 1  49994        50327
 -Exon 2  50416        50559
 -Exon 3  51115        51314
 -Exon 4  52451        52510

 Redox box: no

Query   MWLQKLLVYVSTAGMLCFMVGLSAILRVMHFISPSLSKKQILRMGEKTTMTQNQKFRYEDWGLTFLSFDFIKTASQHMWLSLGQEAFVGGEAPDSPVVTM
        |/||/||/|/|||  ||||/ |/ | |//|||||||/|| ||/|||/ |||||  |/|||||||  |  ||||/ /|||/||||||||||||||||||/|
Target  MFLQRLLLYMSTAWNLCFMLSLNLICRILHFISPSLAKKVILKMGERITMTQNPNFKYEDWGLT-TSTTFIKTSLKHMWVSLGQEAFVGGEAPDSPVVSM
        attcaccttatagtacttactcacataatctatcacgaagacaaggaaaaacacatatggtgca-ataataaattacatgtcgcggtgggggcgtcggaa
        tttagtttatcccgatgtttctattggttattccgtcaatttatgagtctcaacataaaaggtc-ccccttacctaatgtctgaacttggaccaccttgt
        gtgaggtgcggaagttttgaagtcacgcgcttaattcggaccagtagccgcgccttatatgtga-gtagccacgggcgggttaagttgatatacatgccg
                                                                                                            

Query   EGKKSSVCKFIRG <---Intron---> SRPLVLSFGSCTUPPFIYKLDEFKQLVRDFSDVADFMVVYIAEAHSTD <---Intron---> GWAFTNN
        ||/|||/||///| <    88bp    > /|||||||||||||||//||/||||||/|| |||||/|/||||||||| <   555bp    > |||||||
Target  EGEKSSICKYLKG                NRPLVLSFGSCTUPPFMFKLEEFKQLVKDFRDVADFLVIYIAEAHSTD                GWAFTNN
        gggataatatcag                aaccgtatgatatcctatacggtaccgagtcggggtcgatagggctag                gtgtaaa
        agaacgtgaata                gagctttgtgggcgcctttataataattaatgatcattttatcacacc                aggctcaa
        gagaatccgcga                ccaggggttgtccacgtgcatggcgaccgccttatcttgccctgacaa                ttgctccc
                                                 *                                                          

Query   FDINQHRSLEERLSAAQILVQQEPLCPVVVDEMNDVSAIKYGALPERLYVLQAGKVIYK <---Intron---> GGMGPWGYNPLEVRSLLEKM
        |||||||/|||||||||||||/||||||||||| / /|||||||||||||||||||/|| <   1136bp   > | /||||||| |||| ||||
Target  FDINQHRNLEERLSAAQILVQKEPLCPVVVDEMKNAAAIKYGALPERLYVLQAGKVVYK                GQLGPWGYNPQEVRSFLEKM
        tgaacccacggattggcacgcagcctcgggggaaagggaatggccgactgccggaggta                gccgctgtaccggcttcgaa
        tataaagataagtcccatttaaactgctttaataaccctaagctcagtattacgattaa                gatgcggaacaatgcttaat
        tcctgcgcggaggctagcgagagtgtagtgtagatatcagtttgaggttgggtgatgcg                tgggtgcctaaggtacgggg
                                                                                                       
 Sequence until next stop: 
AAATAA
 K  * 

 Distance CDS-SECIS: 602 ; UGA-SECIS: 965

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000014.1:subseq_2346940,101317_ Strand = + Positions = 53113 - 53181
 Found by:  Infernal (score=41.12) Covels (score=31.57)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -18.04

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((((((((--....{[[{(((((((((..........-----....)))))))))}]]}..--...))))))))..
 target  GGCUGCUUUU--UAUAUGAUGAUUACAGUGCAAACCUCU-----GGUAACUGUAAUCUGAUGA--CUUAAAAGUAGGC
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 1e-62
 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/969463925/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000014.1:subseq_2346940,101317_ Strand: +
 Positions:
 -Exon 1  49994        50327
 -Exon 2  50416        50559
 -Exon 3  51115        51314
 -Exon 4  52451        52510

 Redox box: no

Query   MWLQKLLVYVSTAGMLCFMVGLSAILRVMHFISPSLSKKQILRMGEKTTMTQNQKFRYEDWGLTFLSFDFIKTASQHMWLSLGQEAFVGGEAPDSPVVTM
        |/||/||/|/|||  ||||/ |/ | |//|||||||/|| ||/|||/ |||||  |/|||||||  |  ||||/ /|||/||||||||||||||||||/|
Target  MFLQRLLLYMSTAWNLCFMLSLNLICRILHFISPSLAKKVILKMGERITMTQNPNFKYEDWGLT-TSTTFIKTSLKHMWVSLGQEAFVGGEAPDSPVVSM
        attcaccttatagtacttactcacataatctatcacgaagacaaggaaaaacacatatggtgca-ataataaattacatgtcgcggtgggggcgtcggaa
        tttagtttatcccgatgtttctattggttattccgtcaatttatgagtctcaacataaaaggtc-ccccttacctaatgtctgaacttggaccaccttgt
        gtgaggtgcggaagttttgaagtcacgcgcttaattcggaccagtagccgcgccttatatgtga-gtagccacgggcgggttaagttgatatacatgccg
                                                                                                            

Query   EGKKSSVCKFIRG <---Intron---> SRPLVLSFGSCTUPPFIYKLDEFKQLVRDFSDVADFMVVYIAEAHSTD <---Intron---> GWAFTNN
        ||/|||/||///| <    88bp    > /|||||||||||||||//||/||||||/|| |||||/|/||||||||| <   555bp    > |||||||
Target  EGEKSSICKYLKG                NRPLVLSFGSCTUPPFMFKLEEFKQLVKDFRDVADFLVIYIAEAHSTD                GWAFTNN
        gggataatatcag                aaccgtatgatatcctatacggtaccgagtcggggtcgatagggctag                gtgtaaa
        agaacgtgaata                gagctttgtgggcgcctttataataattaatgatcattttatcacacc                aggctcaa
        gagaatccgcga                ccaggggttgtccacgtgcatggcgaccgccttatcttgccctgacaa                ttgctccc
                                                 *                                                          

Query   FDINQHRSLEERLSAAQILVQQEPLCPVVVDEMNDVSAIKYGALPERLYVLQAGKVIYK <---Intron---> GGMGPWGYNPLEVRSLLEKM
        |||||||/|||||||||||||/||||||||||| / /|||||||||||||||||||/|| <   1136bp   > | /||||||| |||| ||||
Target  FDINQHRNLEERLSAAQILVQKEPLCPVVVDEMKNAAAIKYGALPERLYVLQAGKVVYK                GQLGPWGYNPQEVRSFLEKM
        tgaacccacggattggcacgcagcctcgggggaaagggaatggccgactgccggaggta                gccgctgtaccggcttcgaa
        tataaagataagtcccatttaaactgctttaataaccctaagctcagtattacgattaa                gatgcggaacaatgcttaat
        tcctgcgcggaggctagcgagagtgtagtgtagatatcagtttgaggttgggtgatgcg                tgggtgcctaaggtacgggg
                                                                                                       
 Sequence until next stop: 
AAATAA
 K  * 

 Distance CDS-SECIS: 354 ; UGA-SECIS: 717

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = JXSJ01000014.1:subseq_2346940,101317_ Strand = + Positions = 52865 - 52931
 Found by:  Infernal (score=32.37) Covels (score=20.45)
 Stem2 length = 8   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -12.84

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..({(((((---....{[[{(({((((((..........-----....))))))}))}]]}..--..-.)))))})..
 target  CAGCGUUUC---UUAGUGACGGCUACAGAUUAAACCGUU-----GGCUUCUGUAACCAGAUGA--UG-UGAAACACGC
                         ****           ^^^                       ****