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

 Blastx evalue: 7e-22
 Query name: gi|170671714|ref|NP_001116250.1| thioredoxin reductase 3 [Canis lupus familiaris]
 Query range: 374-586  (total 586)

 Target: /data/www-rg/seblastian_results/659376628/tempfiles/temptarget.fasta
 Chromosome: KZ836502.1:subseq_398879,169347_ Strand: +
 Positions:
 -Exon 1  90844        90920
 -Exon 2  91493        91649
 -Exon 3  95469        95576
 -Exon 4  116793       116888
 -Exon 5  119210       119344
 -Exon 6  119559       119624

 Redox box: no

Query   VLLAIGRDSCTRKIGLEKIGVKINEK <---Intron---> SGKIPVNDVEQTNVPYVYAVGDILEGKLELTPVAIQAGKLLARRLFAGRLEK <---I
        |||||||||||||||||||||||||| <   572bp    > |||||||||||||||||||||||||||||||||||||||||||||||| ||| <   3
Target  VLLAIGRDSCTRKIGLEKIGVKINEK                SGKIPVNDVEQTNVPYVYAVGDILEGKLELTPVAIQAGKLLARRLFAGCLEK      
        gttgagcgttaaaagtgaaggaaaga                agaacgagggcaagctgtggggacggacgcacggacggatcgcactggttga      
        tttctggacgcgatgtaatgtataaa                ggatctaataacatcatactgattagatatcctctacgattcggttcggtaa      
        taaatttcccagaacgggttcactg                gtcaaaactgagctgcttttcgttggtatgcactcagacgggtcatttctgag      
                                                                                                            

Query   ntron---> CDYVNVPTTVFTPLEYGCCGLSEEKAIEMYKKENLE <---Intron---> VYHTLFWPLEWTVAGRDNNTCYAKIICNKLDN <---I
        819bp   > ||||||||||| ||||||||||||||||/||||||| <  21216bp   > |||||||||||||| |||||||||||||| || <   2
Target            CDYVNVPTTVFAPLEYGCCGLSEEKAIEVYKKENLE                VYHTLFWPLEWTVASRDNNTCYAKIICNKFDN      
                  tgtgagcaagtgctgtgttgttggagaggtaagacg                gtcatttccgtaggaagaaattgaaataatga      
                  gaatatcccttcctaaggggtcaaactataaaaata                taacttgctagctcggaaacgacattgaataa      
                  ttttttatagtttgaccctagcagattagtaagttg                gtttgcgttagagccaccttttagatctacct      
                                                                                                            

Query   ntron---> YRVIGFHVLGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGLDITQKGCUG
        321bp   > |||||||||||||||/||||||||||||||||||||||||||||| <   214bp    > ||||||||||||||||||||||
Target            YRVIGFHVLGPNAGEITQGFAAAMKCGLTKQLLDDTIGIHPTCGE                VFTTLEITKSSGLDITQKGCUG
                  tcgagtcgcgcagggaacgtgggaatgcaacccggaagaccatgg                gtaatgaaattgcgaacagttg
                  agttgtattgcacgatcagtccctaggtcaattaactgtaccgga                ttcctatcaccgtatcaagggg
                  tggaactttagtctgccagtgcagatgcaggattcctattcattg                gtatgacggggaaccggaccac
                                                                                                   * 
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 212 ; UGA-SECIS: 215

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KZ836502.1:subseq_398879,169347_ Strand = + Positions = 119837 - 119914
 Found by:  Infernal (score=29.18) Covels (score=23.67)
 Stem2 length = 11   Apical loop length = 15   Insertion in stem2 = 0, 0
 Free Energy = -13.18

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..(((({{((......{[[{(((((((((((...............)))))))))))}]]}.....-..))}}))))..
 target  AGUUGGGCUGCCUCCUUGACGUUUUAGCUCGGAACCCGUUGUGAGGUGAGCUAAGGCCGAUGCUCU-UCCAUGUCAGAA
                         ****            ^^                       ****