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

 Blastx evalue: 1e-67
 Query name: gi|401712800|gb|AFP99133.1| deiodinase 1 [Sebastiscus marmoratus]
 Query range: 1-247  (total 248)

 Target: /data/www-rg/seblastian_results/973034433/tempfiles/temptarget.fasta
 Chromosome: JACSYO010002145.1:subseq_2047519,100000_ Strand: +
 Positions:
 -Exon 1  49994        50330
 -Exon 2  50446        50589
 -Exon 3  51184        51383
 -Exon 4  51819        51878

 Redox box: no

Query   MSLHRFMVYLSTACLFCFMITINFMLLILHYISPGLARKLILKLGESSTMTQNPNFKYEDWGLTFGSMKFIRAASHHLWLSLGQDAFMGGEAPDTPVVTM
        ||||| |||||||||||||| ||  ||//  ||| | /|/|||/|| /||||||| ||/|||||| |/ |// | ||/|/|||||||/| |||||||| |
Target  MSLHRLMVYLSTACLFCFMIGINVALLVMRLISPSLTKKMILKMGEKTTMTQNPNLKYDDWGLTFASINFVKTAGHHMWMSLGQDAFVGVEAPDTPVVNM
        atccacagtttagtttttaagaaggctgaccatcacaaaaacaaggaaaaacacacatggtgcatgaaatgaaggccatatcgcggtgggggcgacggaa
        tctagtttatcccgttgtttgtatcttttgttccgtcaatttatgaacctcaacataaaaggtctcgtattaccgaatgtctgaacttgtaccaccttat
        gtgcagggcggtacgttcgaactcgcgcgtctaatccgggccagtagcggcgtcccgtccgtggcccttcgactatcgggtcaatccggcatgcatgccg
                                                                                                            

Query   EGKKTSICKYLKD <---Intron---> NRPLVLSFGSCTUPPFMYKLEEFKQLVKDFSDVADFLVIYIAEAHSKD <---Intron---> GWAFANN
        || |||||||||| <   115bp    > ||||||||||||||||//||||||||||||||||||/|/|/||||| | <   594bp    > |||| ||
Target  EGTKTSICKYLKD                NRPLVLSFGSCTUPPFIFKLEEFKQLVKDFSDVADFVVVYVAEAHSTD                GWAFTNN
        ggaaaaatattag                aaccgtatgatatcctatacggtaccgagtaggggtgggtggggctag                gtgtaaa
        agcacgtgaata                aagctttgtgggcgcctttataataattaatgatcattttatcacacc                aggctcaa
        gggactccgcga                ccgggggttgcctacgcccatggcgaccgcctcagcttgccccggtaa                ttgccccc
                                                 *                                                          

Query   FDINQHQSLEDRLSAAQIVVQKEPLCPVVVDEMNDLSTIKYGAMPERLYVLQAGKVVYK <---Intron---> GSVGPWGYSPMEVRSFLEKM
        |||||||/||||||||||/||||||||||||/|/|/| |||||/||||||||||||||| <   435bp    > | /|||||  ||||||||||
Target  FDINQHQNLEDRLSAAQILVQKEPLCPVVVDDMSDVSAIKYGALPERLYVLQAGKVVYK                GGLGPWGYDLMEVRSFLEKM
        tgaacccacggcctggcatgcagcctcgggggaaggtgaatggccgactgccggaggta                ggtgctgtgcaggcttcgaa
        tataaaaataagtcccatttaaactgctttaatgatcctaagctcagtattacgattaa                ggtgcggaattatgcttaat
        tcccgcgcggcggccggcgtgggcgcggcgccgccgtcagcctgcggccgggcgatccg                gcggtgtctggggtgcgggg
                                                                                                       
 Sequence until next stop: 
AAATAA
 K  * 

 Distance CDS-SECIS: 595 ; UGA-SECIS: 958

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010002145.1:subseq_2047519,100000_ Strand = + Positions = 52474 - 52546
 Found by:  Infernal (score=34.43) Covels (score=29.05)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -11.2

         ..(((((((.......(((((((((((((((...............)))))))))))))))............)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu---u-uuucaugaccggc
         ..(((((((---....{[[{(((((((((..........-----....)))))))))}]]}........-...)))))))..
 target  GGUGUUUUU---AAUAUGACGAUUACGGUGCAAACCUCU-----GGUAACUGUAAUCUGAUGGAUUACU-UGGAAAAACAGC
                         ****           ^^^                       ****                     
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 1e-67
 Query name: gi|401712800|gb|AFP99133.1| deiodinase 1 [Sebastiscus marmoratus]
 Query range: 1-247  (total 248)

 Target: /data/www-rg/seblastian_results/973034433/tempfiles/temptarget.fasta
 Chromosome: JACSYO010002145.1:subseq_2047519,100000_ Strand: +
 Positions:
 -Exon 1  49994        50330
 -Exon 2  50446        50589
 -Exon 3  51184        51383
 -Exon 4  51819        51878

 Redox box: no

Query   MSLHRFMVYLSTACLFCFMITINFMLLILHYISPGLARKLILKLGESSTMTQNPNFKYEDWGLTFGSMKFIRAASHHLWLSLGQDAFMGGEAPDTPVVTM
        ||||| |||||||||||||| ||  ||//  ||| | /|/|||/|| /||||||| ||/|||||| |/ |// | ||/|/|||||||/| |||||||| |
Target  MSLHRLMVYLSTACLFCFMIGINVALLVMRLISPSLTKKMILKMGEKTTMTQNPNLKYDDWGLTFASINFVKTAGHHMWMSLGQDAFVGVEAPDTPVVNM
        atccacagtttagtttttaagaaggctgaccatcacaaaaacaaggaaaaacacacatggtgcatgaaatgaaggccatatcgcggtgggggcgacggaa
        tctagtttatcccgttgtttgtatcttttgttccgtcaatttatgaacctcaacataaaaggtctcgtattaccgaatgtctgaacttgtaccaccttat
        gtgcagggcggtacgttcgaactcgcgcgtctaatccgggccagtagcggcgtcccgtccgtggcccttcgactatcgggtcaatccggcatgcatgccg
                                                                                                            

Query   EGKKTSICKYLKD <---Intron---> NRPLVLSFGSCTUPPFMYKLEEFKQLVKDFSDVADFLVIYIAEAHSKD <---Intron---> GWAFANN
        || |||||||||| <   115bp    > ||||||||||||||||//||||||||||||||||||/|/|/||||| | <   594bp    > |||| ||
Target  EGTKTSICKYLKD                NRPLVLSFGSCTUPPFIFKLEEFKQLVKDFSDVADFVVVYVAEAHSTD                GWAFTNN
        ggaaaaatattag                aaccgtatgatatcctatacggtaccgagtaggggtgggtggggctag                gtgtaaa
        agcacgtgaata                aagctttgtgggcgcctttataataattaatgatcattttatcacacc                aggctcaa
        gggactccgcga                ccgggggttgcctacgcccatggcgaccgcctcagcttgccccggtaa                ttgccccc
                                                 *                                                          

Query   FDINQHQSLEDRLSAAQIVVQKEPLCPVVVDEMNDLSTIKYGAMPERLYVLQAGKVVYK <---Intron---> GSVGPWGYSPMEVRSFLEKM
        |||||||/||||||||||/||||||||||||/|/|/| |||||/||||||||||||||| <   435bp    > | /|||||  ||||||||||
Target  FDINQHQNLEDRLSAAQILVQKEPLCPVVVDDMSDVSAIKYGALPERLYVLQAGKVVYK                GGLGPWGYDLMEVRSFLEKM
        tgaacccacggcctggcatgcagcctcgggggaaggtgaatggccgactgccggaggta                ggtgctgtgcaggcttcgaa
        tataaaaataagtcccatttaaactgctttaatgatcctaagctcagtattacgattaa                ggtgcggaattatgcttaat
        tcccgcgcggcggccggcgtgggcgcggcgccgccgtcagcctgcggccgggcgatccg                gcggtgtctggggtgcgggg
                                                                                                       
 Sequence until next stop: 
AAATAA
 K  * 

 Distance CDS-SECIS: 331 ; UGA-SECIS: 694

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = JACSYO010002145.1:subseq_2047519,100000_ Strand = + Positions = 52210 - 52276
 Found by:  Infernal (score=32.45) Covels (score=18.92)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -19.14

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (({((((((---....{[[{(((((((((..........-----....)))))))))}]]}..--..-.))))))}))
 target  CUGUGUUUC---UUAGUGACGGCUGCAGAUUAAACCGUU-----GGCCUCUGUAGCCAGAUGA--AG-UGAAACGGAG
                         ****           ^^^                       ****