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

 Blastx evalue: 4e-54
 Query name: gi|1041069759|ref|XP_017262405.1| PREDICTED: type I iodothyronine deiodinase [Kryptolebias marmoratus]
 Query range: 1-247  (total 248)

 Target: /data/www-rg/seblastian_results/878476641/tempfiles/temptarget.fasta
 Chromosome: KV884771.1:subseq_62576,100000_ Strand: +
 Positions:
 -Exon 1  49994        50330
 -Exon 2  50422        50565
 -Exon 3  51105        51304
 -Exon 4  51677        51736

 Redox box: no

Query   MLPQKLLVYLSTACNYCYVVGLFILFNILYFISPSLARKQILKLGVKLEMTQNTKFKYDDWGPTFMSLTFVKAASHGMWLSLGQEAFVGREAPDPPVVTV
        |  |||// ||| ||  ||/ | /   |//|||||| /| |///  |  |||| ||||/|||||| |  ||||||  ||||||||||/ /|||| ||||/
Target  MFLQKLMLCLSTVCNVFYVIALNLTVRIMHFISPSLTKKHIIRMNEKTTMTQNPKFKYEDWGPTFNSFNFVKAASWHMWLSLGQEAFLEKEAPDSPVVTM
        attcacactttagtagttgagcacagaaactatcacaaacaaaaagaaaaacacatatggtgcatattatgaggttcatctcgcggtcgaggcgtcggaa
        tttaatttgtcctgattattctatctgttattccgtcaaattgtaaacctcaacataaaaggcctactattacccgatgtctgaacttaaaccaccttct
        gtgaatgctggaactccctaactcgcgtgtctaacccggcccagtagatgcgtcatgtatgtggtccttccacccgcgggtcaagttgaaatgcatgccg
                                                                                                            

Query   DGERTSIRSFCRG <---Intron---> NRPLVLSFGSCTUPPFLFKLDEFKQLVRDFGDVADFLVVYIAEAHSTD <---Intron---> GWAFTNN
        ||//|||  / |  <    91bp    > ||||||||||||||||///|/||||||/|| ||||||||||||||||| <   539bp    > |||| ||
Target  DGKKTSIFQYLRD                NRPLVLSFGSCTUPPFMYRLEEFKQLVKDFSDVADFLVVYIAEAHSTD                GWAFNNN
        ggaaaaatcttag                aaccgtatgatatcctatacggtaccgagtaggggtcggtagggctag                gtgtaaa
        agaacgttaatg                aagctttgtgggcgccttagtaataattaatgatcattttatcacacc                aggctaaa
        cagagtccgcga                ccgggggttacccacgtgtatggcaaccgccctggcttgtcccgataa                ttgctccc
                                                 *                                                          

Query   IDISEHQSLQDRLSAAQMLVQMEPLCPVVVDDMSNAASVKYGAQPERLYVLQAGKVIYK <---Intron---> GAMGPFGYLPLEVRAVLQKI
         ||  |/||/||||||//||| |||||||||////  //|||| ||||||||||||/|| <   372bp    > | /|| || |||||/ |/|/
Target  YDIKHHRSLEDRLSAARILVQKEPLCPVVVDEINDVTAIKYGALPERLYVLQAGKVVYK                GGVGPCGYSPLEVRSFLEKM
        tgaacccacggactggcacgcagcctcgggggaaggagaatggccgactgccggaggta                ggggctgtaccggcttcgaa
        aataaaggtaagtcccgtttaaactgctttaataatcctaagctcagtattacgattaa                ggtgcggagctatgcttaat
        tccgcctcggcggcaagcgtgggcgtggtgtaattctcagtttatagttgggtgacgcg                gcggttcctagggtacgggg
                                                                                                       
 Sequence until next stop: 
AATTAA
 N  * 

 Distance CDS-SECIS: 211 ; UGA-SECIS: 574

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884771.1:subseq_62576,100000_ Strand = + Positions = 51948 - 52014
 Found by:  Infernal (score=35.42) Covels (score=20.85)
 Stem2 length = 10   Apical loop length = 10   Insertion in stem2 = 0, 0
 Free Energy = -22.1

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[{((((((((({(........-----..)})))))))))}]]}..--..-.)))))))..
 target  CACUGUUUC---CUAGUGACGGCUACAGAUGAAACCGUU-----GGCCUCUGUAGCCAGAUGA--CG-CGAAACAGAG
                         ****           ^^^                       ****                 
_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 4e-54
 Query name: gi|1041069759|ref|XP_017262405.1| PREDICTED: type I iodothyronine deiodinase [Kryptolebias marmoratus]
 Query range: 1-247  (total 248)

 Target: /data/www-rg/seblastian_results/878476641/tempfiles/temptarget.fasta
 Chromosome: KV884771.1:subseq_62576,100000_ Strand: +
 Positions:
 -Exon 1  49994        50330
 -Exon 2  50422        50565
 -Exon 3  51105        51304
 -Exon 4  51677        51736

 Redox box: no

Query   MLPQKLLVYLSTACNYCYVVGLFILFNILYFISPSLARKQILKLGVKLEMTQNTKFKYDDWGPTFMSLTFVKAASHGMWLSLGQEAFVGREAPDPPVVTV
        |  |||// ||| ||  ||/ | /   |//|||||| /| |///  |  |||| ||||/|||||| |  ||||||  ||||||||||/ /|||| ||||/
Target  MFLQKLMLCLSTVCNVFYVIALNLTVRIMHFISPSLTKKHIIRMNEKTTMTQNPKFKYEDWGPTFNSFNFVKAASWHMWLSLGQEAFLEKEAPDSPVVTM
        attcacactttagtagttgagcacagaaactatcacaaacaaaaagaaaaacacatatggtgcatattatgaggttcatctcgcggtcgaggcgtcggaa
        tttaatttgtcctgattattctatctgttattccgtcaaattgtaaacctcaacataaaaggcctactattacccgatgtctgaacttaaaccaccttct
        gtgaatgctggaactccctaactcgcgtgtctaacccggcccagtagatgcgtcatgtatgtggtccttccacccgcgggtcaagttgaaatgcatgccg
                                                                                                            

Query   DGERTSIRSFCRG <---Intron---> NRPLVLSFGSCTUPPFLFKLDEFKQLVRDFGDVADFLVVYIAEAHSTD <---Intron---> GWAFTNN
        ||//|||  / |  <    91bp    > ||||||||||||||||///|/||||||/|| ||||||||||||||||| <   539bp    > |||| ||
Target  DGKKTSIFQYLRD                NRPLVLSFGSCTUPPFMYRLEEFKQLVKDFSDVADFLVVYIAEAHSTD                GWAFNNN
        ggaaaaatcttag                aaccgtatgatatcctatacggtaccgagtaggggtcggtagggctag                gtgtaaa
        agaacgttaatg                aagctttgtgggcgccttagtaataattaatgatcattttatcacacc                aggctaaa
        cagagtccgcga                ccgggggttacccacgtgtatggcaaccgccctggcttgtcccgataa                ttgctccc
                                                 *                                                          

Query   IDISEHQSLQDRLSAAQMLVQMEPLCPVVVDDMSNAASVKYGAQPERLYVLQAGKVIYK <---Intron---> GAMGPFGYLPLEVRAVLQKI
         ||  |/||/||||||//||| |||||||||////  //|||| ||||||||||||/|| <   372bp    > | /|| || |||||/ |/|/
Target  YDIKHHRSLEDRLSAARILVQKEPLCPVVVDEINDVTAIKYGALPERLYVLQAGKVVYK                GGVGPCGYSPLEVRSFLEKM
        tgaacccacggactggcacgcagcctcgggggaaggagaatggccgactgccggaggta                ggggctgtaccggcttcgaa
        aataaaggtaagtcccgtttaaactgctttaataatcctaagctcagtattacgattaa                ggtgcggagctatgcttaat
        tccgcctcggcggcaagcgtgggcgtggtgtaattctcagtttatagttgggtgacgcg                gcggttcctagggtacgggg
                                                                                                       
 Sequence until next stop: 
AATTAA
 N  * 

 Distance CDS-SECIS: 394 ; UGA-SECIS: 757

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = KV884771.1:subseq_62576,100000_ Strand = + Positions = 52131 - 52204
 Found by:  Infernal (score=32.78) Covels (score=28.04)
 Stem2 length = 9   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -4.43

         ..(((((((.......(((((((((((((((...............)))))))))))))))............)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu---u-uuucaugaccggc
         .....((((.--....{[[{(((((((((..........-----....)))))))))}]]}........-...)))).....
 target  GCUACUUUGC--UUUAUGACGAUUACAGUGAAAACCUCU-----GGCAACUGUAAUUUGAUGAAAGAUG-ACCUAAAAGUAG
                         ****          ^^^                        ****