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

 Blastx evalue: e-163
 Query name: gi|169790985|ref|NP_001116122.1| type III iodothyronine deiodinase [Ovis aries] >gi|182702120|sp|Q6DN07.2|IOD3_SHEEP RecName: Full=Type III iodothyronine deiodinase; AltName: Full=5DIII; AltName: Full=DIOIII; AltName: Full=Type 3 DI; AltName: Full=Type-III 5'-deiodinase >gi|50346346|gb|AAT74923.1| type 3 iodothyronine deiodinase [Ovis aries]
 Query range: 1-278  (total 278)

 Target: /data/www-rg/seblastian_results/844197/tempfiles/temptarget.fasta
 Chromosome: gi|431839086|gb|KB031153.1|:subseq_22406677,142000_ Strand: +
 Positions:
 -Exon 1  41760        42593

 Redox box: no

Query   MLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHLLGRRRRGQPEIEVELNSDGEEVPPDDPPVCVSDDNRLCTLASLRAVWHGQKLDFF
        ||||||||||||||||||||||||||||||||| |||||||||  |||||||||| ||| |||||||||||||/ |||||||||||||/|||||||||||
Target  MLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLCLLDFLCIRKRFLGRRRRGQPEPEVEFNSDGEEVPPDDPPIFVSDDNRLCTLASLKAVWHGQKLDFF
        acctcccctcactgcagttcgctcctcgagtactccgtctacactcgccccgccgcgggtaagggggccggccatgtggacctacgtcaggtcgcatgtt
        ttgctttactgtgcacccgttttcgttgcctttgttattgtgagttggggggacacatatagagaatccaacctttcaaagtgctcctactgagaatatt
        gcccggtccggcccggcgccgccgccccgccgccgcccgcccgtcgccccgtgtacaggccctcgggccccgtccgcccccgcgggggagggccgggtcc
                                                                                                            

Query   KQAHEGGPAPNSEVVLPDGFQNQHILDYARGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHPSDGWVTTDSPYSIPQHRSLEDRV
        |||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/|/||||||
Target  KQAHEGGPAPNSEVVLPDGFQNQHILDYARGDRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEAHPSDGWVTTDSPYSIPKHQSLEDRV
        acgcgggcgcatgggccggtcaccacgtgcggcccgcatgatatcctagcaagtcccgaatccgggtcaatagggcctggtgaagtctaacaccatggcg
        aacaaggcccacatttcagtaaaattaacggagctttatgggcgccttcgtgctagttcaaagatattttataacaccaggtccaccagtcaaagtaagt
        gggcgctgtcccggcgccccgcgcccccgagccgggtccccccaaacggcgcccgcgccgcgccgctcccccaggcccccgccaccccccggcacggcgc
                                                   *                                                        

Query   SAARVLQQGAPECALVLDTMTNSSSSAYGAYFERLYIIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGPQPRRV
        ||||||||||| |||||||| |||||||||||||||/|||| |||||||||||||||||||||||||||||  ||| |
Target  SAARVLQQGAPSCALVLDTMANSSSSAYGAYFERLYVIQSGIIMYQGGRGPDGYQVSELRTWLERYDEQLHSGQPRPV
        aggcgcccggcatgcgcgaagataatgtggttgcctgacagaaatcggcgcggtcgtgccattgctggcccagccccg
        gccgttaagccggctttactcacggccagcatagtattaggtttaaggggcagaatcatgcgtagaaaataggacgct
        tggtgtgataccttccgccgcccccgctccccgcgcccgtcctgcgtctcatccgcaggccgggcttgggcctgttag
                                                                                      
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 614 ; UGA-SECIS: 1016

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|431839086|gb|KB031153.1|:subseq_22406677,142000_ Strand = + Positions = 43208 - 43277
 Found by:  Infernal (score=17.08) Covels (score=21.5)
 Stem2 length = 8   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -14.63

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((([(((---(...([[{((({(({(((.................)))}))})))}]])----..-))))])))..
 target  GCCCCACUG---CUGAUGACGAACUGUCUCUAACUGGUCUUGACCACGAGCUGCUUCUGAA----UU-GCAGGGGGUC
                         ****           ^^                        ****