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

 Blastx evalue: 1e-33
 Query name: gi|169790989|ref|NP_001116124.1| type I iodothyronine deiodinase [Macaca mulatta]
 Query range: 1-249  (total 249)

 Target: /var/www/seblastian_output/759369003/tempfiles/temptarget.fasta
 Chromosome: gi|511782573|gb|CM001961.1|subseq(78925275,215869) Strand: -
 Positions:
 -Exon 1  115533       115869
 -Exon 2  105407       105550
 -Exon 3  103696       103895
 -Exon 4  100000       100065

 Redox box: no

Query   MGLPQSGLWVKKLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTGMTRNPHFSHDNWIPTFFSTQYFWFVLKVRWQRLEDTTELGGLAPNCPVVRL
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  MGLPQSGLWVKKLWVLLEVAVHVVVGKVLLILFPDRVKRNILAMGEKTGMTRNPHFSHDNWIPTFFSTQYFWFVLKVRWQRLEDTTELGGLAPNCPVVRL
        agccctgctgaactgccggggcggggagccattcgagacaacgaggaagaaaacctacgatacattaacttttgtagctcccggaagcggcgcatcggcc
        tgtcacgtgtaatgtttatctatttgattttttcagtagattctgaacgtcgacatgaaagtccttgcaatgtttatggagtaaccatggtccagcttgt
        gggcgaggggggcggcgggtctgcgtagtgagtacacggccgcgcggctgcgcctcccccgcgctcccgtcgccggctggaagcgtgagtgcaccagccc
                                                                                                            

Query   SGQRCNIWDFMQG <---Intron---> NRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSIADFLIIYIEEAHASD <---Intron---> GWAFKNN
        ||||||||||||| <   9982bp   > |||||||||||||||||||||||||||||||||||||||||||||||| <   1511bp   > |||||||
Target  SGQRCNIWDFMQG                NRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSIADFLIIYIEEAHASD                GWAFKNN
        tgcataatgtacg                aaccgcatgatatcttatatgctaacaggtataggtcaatagggcgtg                gtgtaaa
        cgaggatgatta                gagctttatgggcgcctttataatagttaatgctcattttataacacca                ggctaaa
        aaggcctgctga                ctgagggttattcatatgcatcacggttacttcaattcctctaaataat                cgttgcc
                                                 *                                                          

Query   MDIRNHRNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRILYKG <---Intron---> KSGPWNYNPEEVRAVLEKLYS
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   3630bp   > |||||||||||||||||||||
Target  MDIRNHRNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYVIQEGRILYKG                KSGPWNYNPEEVRAVLEKLYS
        agaaaccaccgcccggccccgaacctcggggaacacaacctggccgactgacggaactag                atgctatacgggcggcgacta
        tatgaagataagtaccatttcggcagctttactaaaggatacctcagtattaaggttaag                acgcgaaacaatgcttaatag
        gccatcgctgccggactaggcgccgctgggtcggcgccgccaagtggccacggcgcccg                tacctgcctagattttgagcct
                                                                                                         
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 944 ; UGA-SECIS: 1313

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782573|gb|CM001961.1|subseq(78925275,215869) Strand = - Positions = 99055 - 98985
 Found by:  Infernal (score=33.03) Covels (score=29.16)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -12.32

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ...((((((.--....{[[{(({(((((((.........-----...)))))))}))}]]}.....-...))))))...
 target  UAUAUAUUUG--UUUAUGAUGGCCACAGCCUAAAGUACA-----CACGGCUGUGACUUGAUUCAAA-AGAAAAUGUUAU
                         ****           ^^^                       ****