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

 Blastx evalue: 0.0
 Query name: gi|942053820|ref|XP_014333626.1| PREDICTED: thyroxine 5-deiodinase [Bos mutus]
 Query range: 1-301  (total 301)

 Target: /data/www-rg/seblastian_results/473993881/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  49895        50797

 Redox box: no

Query   MSRQAAPRWVVGEGRGALGGAATMLRSLLLHSLRLCSQTASCLVLFPRFLGTAFMLWLLDFLCIRKHLLGRRRRGQPEIEVELNSDGEEVPPDDPPVCVS
        | ||||||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  MPRQAAPRWVVGEGRGALGGAATMLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHLLGRRRRGQPEIEVELNSDGEEVPPDDPPVCVS
        acccggcctgggggaggcggggaacctcccctcactgcagttcgctcctcgagtactccgtctacactcgccccgccgagggcaagggggccggccgtgt
        tcgacccggttgagggctggcccttgctttactgtgcacccgttttcgttgcctttgttattgtgaattggggggacatatatagagaatccaacctgtc
        gtcgccggggggatggtggccccggccggtccggcccggcgccgccgccgcgccgcggaccgcccgcagctacgtggacaggcccccaggccccgtccgc
                                                                                                            

Query   DDNRLCTLASLRAVWHGQKLDFFKQAHEGGPAPNSEVVLPDGFQNQHILDYARGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHP
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  DDNRLCTLASLRAVWHGQKLDFFKQAHEGGPAPNSEVVLPDGFQNQHILDYARGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHP
        ggacctatgtcaggtcgcatgttacgcgggcgcatgggccggtcaccacgtgcgacccgcatgatatcctagcaagtcccgaatccgggtcaatagggcc
        aaagtgctcctgctgagaatattaacaaggcccacatttcagtaaaattaacggagctttatgggcgccttcgtgctagttcaaagatattttataacac
        tcccgccgggggccgccgggtccgggtacgggtctggcgccccgcgccccccaaccgggccctcccaagcggcgcccgcgccgtgccccccccccgagct
                                                                          *                                 

Query   SDGWVTTDSPYSIPQHRSLEDRVSAARVLQQGAPECALVLDTMTNSSSSAYGAYFERLYIIQSGTIMYQGGRGPDGYQVSEVRTWLERYDEQLHGPQPRR
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/||||||||||||||||||
Target  SDGWVTTDSPYSIPQHRSLEDRVSAARVLQQGAPECALVLDTMTNSSSSAYGAYFERLYIIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGPQPRR
        tggtgaagtctaaccccacggcgaggcgcccggcgtgcgcgaaaataatgtggttgcctaacagaaatcggcgcggtcgtgccatcgctggcccgccccc
        caggtccaccagtcaaggtaagtgccgttaagccagctttactcacggccagcatagtattaggcttaaggggcagaatcatgcgtagaaaatagcacgg
        cccgccactccccggcacggcgcccgcaggagtgactcgccagcccccgccccccgcccccgtcctgcgccccccccgccggccgggcttgggccggcta
                                                                                                            

Query   V
        |
Target  V
        g
        t
        g
         
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 608 ; UGA-SECIS: 1010

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 51406 - 51486
 Found by:  Infernal (score=21.4) Covels (score=23.4)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -14.8
 Type = 1

         ..(((((((..........(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcg---UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         (({((((((..........{[[{(((((({(((.................)))}))))))}]]}.....-...))))))}))
 target  UUACGAGCCCCACUGCUGAUGACGAGCUGUCUCUAACUGGCCUCGACCACGAGCUGGUUCUGAUUUGCA-GGAGGCUCGCAG
                            ****           ^^                        ****