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

 Blastx evalue: 5e-22
 Query name: gi|170671714|ref|NP_001116250.1| thioredoxin reductase 3 [Canis lupus familiaris]
 Query range: 177-586  (total 586)

 Target: /data/www-rg/seblastian_results/313211994/tempfiles/temptarget.fasta
 Chromosome: JAEUCK010006363.1:subseq_881916,134337_ Strand: +
 Positions:
 -Exon 1  55059        55214
 -Exon 2  57171        57286
 -Exon 3  58054        58279
 -Exon 4  59471        59563
 -Exon 5  65077        65153
 -Exon 6  65744        65900
 -Exon 7  71008        71115
 -Exon 8  81976        82071
 -Exon 9  84203        84337
 -Exon 10 84718        84783

 Redox box: no

Query   YSQQVKHTWETMTEAIQNHIGSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK <---Intron---> ATNRKGQETCYTAAKFVLATGQRPRYLGIQGD
        |   |||||||||||||||||||||||||||||||||||||||||||||||| <   1956bp   > ||||||||||||||||||||||||||||||||
Target  YLFSVKHTWETMTEAIQNHIGSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK                ATNRKGQETCYTAAKFVLATGQRPRYLGIQGD
        ttttgacatgaaaggacacagtcatgtactcagagggtgattggtggccaaa                gaaaagcgattaggatgcgagcaccttgacgg
        attctaacgactcactaaatgctaggagtctgaactcatacagattaaaata                ccagagaacgacccatttccgagcgatgtaga
        tataagccggtgaaatacccctacgccggcggggcgctctctaatcattaag                actaaagatctttaatcagacagagtaacaat
                                                                                                            

Query   KEYCITS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTIMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFVPVL <
        ||||||| <   767bp    > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <
Target  KEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTIMVRSILLRGFDQEMAEKVGSYMEQHGVKFLRKFVPVL  
        agttaaa                ggcttccttcgaatggggttggcgtggtcggagtggaaagctacccgtgcgaggaggttagccggattaatgcgt  
        aaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcataaagtattgattctt  
        agcttt                ttctttgttctcagaggtatcttgataatctctcatcatggtgctttgttaggagagtccgaatttgcaaatatcg  
                                                                                                            

Query   ---Intron---> VQQLEKGSPGKLKVVAKSTEGPETIEEIYNT <---Intron---> VLLAIGRDSCTRKIGLEKIGVKINEK <---Intron--
           1191bp   > ||||||||||||||||||||||||||||||| <   5513bp   > |||||||||||||||||||||||||| <   590bp   
Target                VQQLEKGSPGKLKVVAKSTEGPETIEEIYNT                VLLAIGRDSCTRKIGLEKIGVKINEK             
                      gcctgagtcgacagggataggcgaaggataa                gttgagcgttaaaagtgaaggaaaga             
                      taataagccgatattcaccagcactaataac                tttctggacgcgatgtaatgtataaa             
                      tggggatataggaagtactaaaattaaatta                tggatttcctagaatgggttcactg              
                                                                                                            

Query   -> SGKIPVNDVEQTNVPYVYAVGDILEGKLELTPVAIQAGKLLARRLFAGRLEK <---Intron---> CDYVNVPTTVFTPLEYGCCGLSEEKAIEM
         > |||||||||||||||||||||||||||||||||||||||||||||||||||| <   5107bp   > |||||||||||||||||||||||||||||
Target     SGKIPVNDVEQTNVPYVYAVGDILEGKLELTPVAIQAGKLLARRLFAGRLEK                CDYVNVPTTVFTPLEYGCCGLSEEKAIEM
           agaacgagggcaagctgtggggacggacgcacggacggaccgcactggctga                tgtgagcaagtactgtgttgttggagaga
           ggatctaataacatcatactgattagatatcctctacgattcggttcggtaa                gaatatcccttcctaaggggtcaaactat
          gtcaaaattgagctgatttttgttggtatgcatttagacgggtaattgctaag                tttattatagtttgatcctaatagattag
                                                                                                            

Query   YKKENLE <---Intron---> VYHTLFWPLEWTVAGRDNNTCYAKIICNKLDN <---Intron---> YRVIGFHVLGPNAGEVTQGFAAAMKCGLT
        ||||||| <  10860bp   > |||||||||||||||||||||||||||||||| <   2131bp   > |||||||||||||||||||||||||||||
Target  YKKENLE                VYHTLFWPLEWTVAGRDNNTCYAKIICNKLDN                YRVIGFHVLGPNAGEVTQGFAAAMKCGLT
        taagacg                gtcatttccgtagggagaaattgaaataatga                tcgagtcgcgcaggggacgtgggaatgca
        aaaaata                taacttgctagctcggaaacgacattgaataa                agttgtattgcacgatcagtccctaggtc
        taagtca                gtttgcgttagagccacctttcagatctagcc                ttgaacttcactctgtcagttcagatgca
                                                                                                            

Query   KQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGLDITQKGCUG
        |||||||||||||||| <   380bp    > ||||||||||||||||||||||
Target  KQLLDDTIGIHPTCGE                VFTTLEITKSSGLDITQKGCUG
        acccggaagaccatgg                gtaacgaaattgcgaacagttg
        aattaactgtaccgga                ttcctatcaccgtatcaagggg
        ggatttctattccttg                gtgtggcagggaacctggccac
                                                            * 
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 207 ; UGA-SECIS: 210

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JAEUCK010006363.1:subseq_881916,134337_ Strand = + Positions = 84991 - 85065
 Found by:  Infernal (score=34.11) Covels (score=23.89)
 Stem2 length = 11   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -21.54

         ..(((((((.......(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..((((({(---(...{[[{(((((((((((.....-.........)))))))))))}]]}......-..))})))))..
 target  CAGGCUGCC---UCCUUGACGCCUUAGCUCGGAACC-GCUGUGAGGUGAGCUGAGGCCGAUGUCCUC-CAGGCCAGCUGC
                         ****            ^^                       ****