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

 Blastx evalue: 4e-28
 Query name: gi|260081569|gb|ACX31205.1| deiodinase 1, partial [Ovis aries]
 Query range: 10-146  (total 146)

 Target: /data/www-rg/seblastian_results/193621989/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  56543        56696
 -Exon 2  52295        52494
 -Exon 3  50009        50065

 Redox box: no

Query   FMQGNRPLVLNFGSCTUPSFIFKFDQFKRLIEEFGSVADFLIIYIEEAHASD <---Intron---> GWAFKNNVDIKNHRNLQDRLRAAHLLLDRSPQ
        |/ |||||||||||||||||||||||||||||/||||||||||||||||||| <   4048bp   > ||||||||||||||||||||||||||||||||
Target  FVLGNRPLVLNFGSCTUPSFIFKFDQFKRLIEDFGSVADFLIIYIEEAHASD                GWAFKNNVDIKNHRNLQDRLRAAHLLLDRSPQ
        tgtgaactgcatgatatcttatatgctaacaggtgtgggtcaatagggcgtg                gtgtaaaggaaaccaccgctcggccccgaacc
        tttgagctttatgggcgcctttataatagttaatgctcattttataacacc                aggctaaatataaagataagtgccatttaggca
        ttaccacgggttatccatattcatcacgattatttcaattcctccaaataa                tcgttgccgccgtcgtcgccggaccgggcgccg
                        *                                                                                   

Query   CPVVVDTMKNQSSSCYAALPERLYVLQEGRILYK <---Intron---> GKPGPWNYHPEEVRAVLEK
        ||||||||||||||||||||||||||/||||||| <   2229bp   > |||||||||||||||||||
Target  CPVVVDTMKNQSSSCYAALPERLYVLREGRILYK                GKPGPWNYHPEEVRAVLEK
        tcggggaaaacaatttggccgcctgccggaacta                gacgctatccgggcggcga
        gctttactaaaggcgacctcagtattgaggttaa                gacgcgaaacaatgcttaa
        ccggacaggcgccgccaagaggccgcggcgcgcg                tatttgcctagattttgag
                                                                             
 Sequence until next stop: 
CTCCACAGTTAA
 L  H  S  * 

 Distance CDS-SECIS: 869 ; UGA-SECIS: 1229

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 49139 - 49069
 Found by:  Infernal (score=33.75) Covels (score=27.83)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -12.42
 Type = 1

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ...((((((.--....{[[{(({(((((((.........-----...)))))))}))}]]}.....-...))))))...
 target  UUCAUAUUUG--UUCAUGACGGCCACAGCCUAAAGUACA-----CACGGCUGUGACUUGAUUUGAA-AGAAAAUGUUUU
                         ****           ^^^                       ****