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

 Blastx evalue: e-132
 Query name: gi|13242866|gb|AAB35616.2| type 3 iodothyronine deiodinase [Homo sapiens]
 Query range: 49-278  (total 278)

 Target: /data/www-rg/seblastian_results/235370033/tempfiles/temptarget.fasta
 Chromosome: gi|432098262|gb|KB109558.1|:subseq_2992989,100689_ Strand: +
 Positions:
 -Exon 1  50000        50689

 Redox box: no

Query   RRRGKPEPEVELNSEGEEVPPDDPPICVSDDNRLCTLASLKAVWHGQKLDFFKQAHEGGPAPNSEVVLPDGFQSQHILDYAQGNRPLVLNFGSCTUPPFM
        ||||/|/||/||||/ ||||||||||||||||||||/||||||||||||| |||||||||||||/||||/||| |||||||/|/||||||||||||||||
Target  RRRGRPQPEMELNSDEEEVPPDDPPICVSDDNRLCTMASLKAVWHGQKLDLFKQAHEGGPAPNSQVVLPEGFQYQHILDYARGDRPLVLNFGSCTUPPFM
        accgccccgagcaagggggccggccatgtggacctaagtcaggtcgcacgctacgcgggcgcatcggccggtctccacgtgcggcccgcatgatatccta
        gggggcacatatagaaaatccaacctgtcaaagtgctcctactgagaatattaacaaggcccacatttcagtaaaattaacggagctttatgggcgcctt
        gcgttcataggcctcggggccccgcccgcccccgccggggggggccaggtccgggcgcccgcccggcgcaccgcgcccccgagcggggctcccccaagcg
                                                                                                       *    

Query   ARMSAFQRLVTKYQRDVDFLIIYIEEAHPSDGWVTTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGG
        ||||||/|||||||| |||||||||||||||||||||/||||||||||/|||||||||||| |||||||||| ||||||||||||||||/||| ||||||
Target  ARMSAFRRLVTKYQRHVDFLIIYIEEAHPSDGWVTTDTPYIIPQHRSLDDRVSAARVLQQGVPGCALVLDTMTNSSSSAYGAYFERLYVVQSGIIMYQGG
        gcaagtcccgaatcccggtcaatagggcctggtgaagactaaccccacggcgaggcgcccggcgtgcgcgaaaataatgtggttgcctggcagaaatcgg
        cgtgctggttcaaagatattttataacaccaggtccaccattcaaggtaagtgccgttaagtcggctttactcacggccagcatagtattaggtttaagg
        gagcccgcgccgcgccgctcccccgggcccccgcctccccccagcgcgccgcccggtgggggccctgcgccgccccccccccccgcccccgccccgcgcc
                                                                                                            

Query   RGPDGYQVSELRTWLERYDEQLHGARPRRV
        |||||||||||||||||||/||| | || |
Target  RGPDGYQVSELRTWLERYDDQLHSALPRPV
        cgcggtcgtgccattgctggcccagccccg
        ggcagaatcatgcgtagaaaatagctcgct
        cctcccgcgggccgggctttggcctgcggg
                                      
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 550 ; UGA-SECIS: 952

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|432098262|gb|KB109558.1|:subseq_2992989,100689_ Strand = + Positions = 51240 - 51309
 Found by:  Infernal (score=15.52) Covels (score=19.78)
 Stem2 length = 8   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -20.13

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ((((({(((---(...([[{((({(({(((.................)))}))})))}]])----..-))))})))))
 target  GCCCCGCUG---CUGAUGAUGAGCUGCCUCUAACUGGUCUUGACCACGAGCUGCUUCUGAA----UU-GCAGGGGGGC
                         ****           ^^                        ****