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

 Blastx evalue: 9e-48
 Query name: gi|379656510|gb|AFD09496.1| glutathione peroxidase 4a [Oncorhynchus kisutch] >gi|589268206|emb|CCG28022.1| glutathione peroxidase 4a1 [Oncorhynchus mykiss]
 Query range: 1-200  (total 200)

 Target: /data/www-rg/seblastian_results/499808374/tempfiles/temptarget.fasta
 Chromosome: CM007935.1:subseq_17090989,99908_ Strand: -
 Positions:
 -Exon 1  52252        52344
 -Exon 2  50280        50374
 -Exon 3  50000        50144
 -Exon 4  49757        49908
 -Exon 5  49263        49287
 -Exon 6  48769        48828
 -Exon 7  45243        45272

 Redox box: no

Query   MSLWQIKRVLVFGTLASCGLVLVIGLYLFTM <---Intron---> SAPTEDWQTATSIYDFSAKDIDGNEVSLEKYR <---Intron---> GDVVI
        ||||||||||||||||||||||||||||||| <   1877bp   > |||||||||||||||||||||||||||||||| <   135bp    > |||||
Target  MSLWQIKRVLVFGTLASCGLVLVIGLYLFTM                SAPTEDWQTATSIYDFSAKDIDGNEVSLEKYR                GDVVI
        atttcaacgtgtgatgatgcgcgagttttaa                tgcaggtcagatatgttgagaggaggtcgata                gggga
        tctgatagttttgctcgggtttttgtattct                ccccaagacccctaatccaatagaatctaaag                gattt
        ggggatgtcaatgagactacttgtaatacag                tcgagcggacatttcctcgtttccggcggac                gattcc
                                                                                                            

Query   IVNVASKUGKTPVNYSQFAEMHAKYAEKGLRILAFPSNQFGSQ <---Intron---> EPGTEAQIKDFAKSYNAEFPMFSKIDVNGDNAHPLWKWLKE
        ||||||||||||||||||||||||||||||||||||||||||| <    91bp    > |||||||||||||||||||||||||||||||||||||||||
Target  IVNVASKUGKTPVNYSQFAEMHAKYAEKGLRILAFPSNQFGSQ                EPGTEAQIKDFAKSYNAEFPMFSKIDVNGDNAHPLWKWLKE
        agaggtatgaacgattctggacgatggagtcacgtctactgac                gcgaggcaagtgattaggtcataaaggaggagccctatcag
        ttatccaggacctaacatcatacaacaagtgttctccaatgga                acgcacataatcacaacatcttgatatagaacactgagtaa
        ccctctaagacgacttgtgggcggctgataccgcctccgcgtg                atctatgcgcttgacttgcagctgtcgcgtccccggggggg
               *                                                                                            

Query   QPNGKGFLGN <---Intron---> GIKWNFTK <---Intron---> FLINREGQVMKRYGPMDDPS <---Intron---> VVEKDLPKYL
        |||||||||| <   469bp    > |||||||| <   434bp    > |||||||||||||||||||| <   3496bp   > ||||||||||
Target  QPNGKGFLGN                GIKWNFTK                FLINREGQVMKRYGPMDDPS                VVEKDLPKYL
        ccagagtcga                gaatataa                tcaaaggcgaaatgcaggca                gggagccatc
        acagagttga                gtagatca                tttagagattagagctaacg                ttaaatcaat
        gccgaccga                tccggtcag                cgccagcgtggataagttct                ggggtttgcg
                                                                                                        
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 87 ; UGA-SECIS: 459

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007935.1:subseq_17090989,99908_ Strand = - Positions = 45155 - 45079
 Found by:  Infernal (score=31.99) Covels (score=32.85)
 Stem2 length = 9   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -16.35

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({({(((......{[[{(((((((((....................)))))))))}]]}..--...)))})})...
 target  CCAUUCCCCAGACCAGUGACGGUCUGUCCACAAACCCGCCUGACGGACAGGACAGACCUGAUGA--AAAUGGCGUGCAA
                         ****           ^^^                        ****