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

 Blastx evalue: 2e-84
 Query name: gi|929119538|ref|XP_014071376.1| PREDICTED: type I iodothyronine deiodinase [Salmo salar] >gi|825310428|gb|AKJ23335.1| deiodinase 1 [Salmo salar]
 Query range: 1-249  (total 249)

 Target: /data/www-rg/seblastian_results/390909097/tempfiles/temptarget.fasta
 Chromosome: CM007939.1:subseq_51031302,101077_ Strand: +
 Positions:
 -Exon 1  49991        50330
 -Exon 2  50447        50590
 -Exon 3  50875        51074
 -Exon 4  51679        51741

 Redox box: no

Query   MILIWKLFIYLSMPCLFCFAFMQFIFLTLLNLISRSLTKKLILKMGEKVTMTQNPKFKYEDWGPTFMSWNFVKTILGHMWTNVGQEAFVGNSAPDSPVIT
        |||||| |||||||||||||||||/||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/||||||||
Target  MILIWKWFIYLSMPCLFCFAFMQFVFLTLLNLISRSLTKKLILKMGEKVTMTQNPKFKYEDWGPTFMSWNFVKTILGHMWTNVGQEAFVGNNAPDSPVIT
        aatatattatctactttttgtactgtcaccatatcataaacataaggagaaacacatatggtgcatattatgaaacgcataaggcggtggaagcgtcgaa
        ttttgagttatctcgttgtcttattttcttattcggtcaatttatgaatctcaacataaaaggccttcgattacttgatgcatgaacttgaaccaccttc
        gaaagagcttgagatatctgcgatctcgtgtgtaacgcgatcaagcagatgcgtggcgtatgagttgagttcgccagcggttctaattgccttccaagta
                                                                                                            

Query   LDGKITSIYNYLKD <---Intron---> NRPLVLTFGSCTUPPFMYKLCEFKQLVKDFSDVADFLVVYIAEAHSTD <---Intron---> GWVFAN
        |||||||||||||| <   116bp    > ||||||/||||||||||||||||||||||| ||||||||||||||||| <   284bp    > ||||||
Target  LDGKITSIYNYLKD                NRPLVLSFGSCTUPPFMYKLCEFKQLVKDFGDVADFLVVYIAEAHSTD                GWVFAN
        tggaaaaatattag                aaccgtatgatatcctatactgtaccgagtgggggtcggtagggctag                gtgtga
        tagatcgtaaata                aagctttgtgggcgccttaatgataattaatgatcattttatcacacc                aggttca
        gccgtctccctga                ccaagggttatttacgcgtatcgcgaccgccctgaccggcctcggtaa                ctgctcc
                                                  *                                                         

Query   NVDITKHRNQEERLAAAQFLVKEDPLCPIVVDEMKDTTASKYGAIPERLYVLQAGKVVYK <---Intron---> GKIGPWGYSPEEVRSFLEKMK
        | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   604bp    > ||||| |||||||||||||||
Target  NFDITKHRNQEERLAAAQFLVKEDPLCPIVVDEMKDTTASKYGAIPERLYVLQAGKVVYK                GKIGPRGYSPEEVRSFLEKMK
        atgaaaccacggccgggctcgaggcctcaggggaagaagaatggacgcctgccggaggta                gaagcagtacgggcttcgaaa
        atatcaagaaaagtcccatttaaactgctttaataacccgaagctcagtattacgattaa                gatgcggagcaatgcttaata
        ctcttacacgggggtaagcgcagccgcccagtagaccattattttagggtgggaagtttg                agtgaaccctgggcccggagg
                                                                                                         
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 571 ; UGA-SECIS: 937

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007939.1:subseq_51031302,101077_ Strand = + Positions = 52313 - 52381
 Found by:  Infernal (score=39.27) Covels (score=29.2)
 Stem2 length = 10   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -19.5

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ((((((((((--....{[[{((((((((((.........-----...))))))))))}]]}..--...))))))))))
 target  AACUGCUUUU--UCCAUGAUGAUUACAGUGCAAACCUCU-----GGUCAUUGUAAUUUGAUGA--ACUGAAAGCAGUU
                         ****           ^^^                       ****