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

 Blastx evalue: e-176
 Query name: gi|169790985|ref|NP_001116122.1| thyroxine 5-deiodinase [Ovis aries] >gi|50346346|gb|AAT74923.1| type 3 iodothyronine deiodinase [Ovis aries]
 Query range: 13-278  (total 278)

 Target: /data/www-rg/seblastian_results/825932016/tempfiles/temptarget.fasta
 Chromosome: SJYR01002697.1:subseq_5018,100000_ Strand: -
 Positions:
 -Exon 1  99203        100000

 Redox box: no

Query   CAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHLLGRRRRGQPEIEVELNSDGEEVPPDDPPVCVSDDNRLCTLASLRAVWHGQKLDFFKQAHEGGPAPNS
        |||||||| ||||||||| ||||||||||||| |||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  CAQTASCLALFPRFLGTALMLWLLDFLCIRKHFLGRRRRGRPEIEVELNSDGEEVPPDDPPVCVSDDNRLCTLASLRAVWHGQKLDFFKQAHEGGPAPNS
        tgcagttcgctcctcgagcactccgtctacactcgccccgccgagggcaagggggccggccgtgtggacctatgtcaggtcgcatgttacgcgggcgcat
        gcacccgtcttcgttgcctttgttattgtgaattgggggggcatatatagagaatccaacctgtcaaagtgctcctgctgagaatattaacaaggcccac
        ccggcgccgccgccgcgccgcggaccgcccgccgctacgtggacaggcccccaggccccgcccgcccccgctgggggccgccgggtccgggtacgggcct
                                                                                                            

Query   EVVLPDGFQNQHILDYARGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHPSDGWVTTDSPYSIPQHRSLEDRVSAARVLQQGAPE
        ||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EVVLPDGFQNRHILDYARGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHPSDGWVTTDSPYSIPQHRSLEDRVSAARVLQQGAPE
        gggccggtcaccacgtgcgacccgcatgatatcctagcaagtcccgaatccgggtcaatagggcctggtgaagtctaaccccacggcgaggcgcccggcg
        atttcagtaagattaacggagctttatgggcgccttcgtgctagttcaaagatattttataacaccaggtccaccagtcaaggtaagtgccgttaagcca
        agcgccccgcgccccccaaccgggcccccccaagcggcgcccgcgccgtgccccccccccgagctcccgccgctccccggcacggcccccgcgggagtga
                                       *                                                                    

Query   CALVLDTMTNSSSSAYGAYFERLYIIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGPQPRRV
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  CALVLDTMTNSSSSAYGAYFERLYIIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGPQPRRV
        tgcgcgaaaataatgtggttgcctaacagaaatcggcgcggtcgtgccatcgctggcccgcccccg
        gctttactcacggccagcatagtattaggcttaaggggcagaatcatgcgtagaaaatagcacggt
        cgcgccggcccctgtcccccgcccccgtcctgcgccccccccgccggccgggcttgggccggctag
                                                                          
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 611 ; UGA-SECIS: 1013

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SJYR01002697.1:subseq_5018,100000_ Strand = - Positions = 98591 - 98511
 Found by:  Infernal (score=21.57) Covels (score=26.21)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -15.6

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