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

 Blastx evalue: 5e-20
 Query name: gi|374349238|ref|NP_001243403.1| thioredoxin reductase 2, mitochondrial [Cavia porcellus]
 Query range: 126-524  (total 524)

 Target: /data/www-rg/seblastian_results/503724064/tempfiles/temptarget.fasta
 Chromosome: JSZB01015288.1:subseq_490000,135000_ Strand: -
 Positions:
 -Exon 1  81740        81813
 -Exon 2  79992        80070
 -Exon 3  79418        79480
 -Exon 4  75968        76038
 -Exon 5  68141        68160
 -Exon 6  67303        67394
 -Exon 7  65171        65345
 -Exon 8  55036        55172
 -Exon 9  52298        52393
 -Exon 10 51910        52002
 -Exon 11 50335        50406
 -Exon 12 50078        50175
 -Exon 13 48284        48410

 Redox box: no

Query   EKMAEAVQNHVKSLNWGHRVQLQDR <---Intron---> KVKYFNIKASFVNQHTVRGITKGGKE <---Intron---> MLLSAEHIVIATGGRPK
         |||||||||||||||||||||||| <   1669bp   > |||||||||||||/|||||/|| ||| <   511bp    >  |||||||||||||||/
Target  RKMAEAVQNHVKSLNWGHRVQLQDR                KVKYFNIKASFVNKHTVRGVTKDGKE                TLLSAEHIVIATGGRPR
        aaaggggcacgatcatgccgcccga                agattaaagatgaacagcggaaggag                acctggcagagaggcca
        gatcactaaatactaggagtataag                ataatatacgttaaactggtcaagaa                cttccaatttccgggcg
        gggagctaccggcgcggcgggggc                aacgctccgcctccgcatttcagtggg                tgtgtgccctttagggg
                                                                                                            

Query   YPTH <---Intron---> IEGALEYGITSDDIFWLKKSPGKT <---Intron---> LVVGASY <---Intron---> VALECAGFLTGIGLDIT
        || | <   3379bp   > /|||||||||||||||||/||||| <   7807bp   > ||||||| <   746bp    > |||||||||||/||| |
Target  YPMH                VEGALEYGITSDDIFWLKESPGKT                LVVGASY                VALECAGFLTGLGLDTT
        tcac                ggggtgtgaaaggattcagtcgaa                tggggat                ggcgtggtcagcgcgaa
        acta                tagctaagtcgaattgtaaccgac                tttgcg                atctagcgttcgtgtacc
        ccgc                tattgatacatccccgggactaa                gggcgcc                cgcggtccccggcagccc
                                                                                                            

Query   VMMRSIPLRGFDQ <---Intron---> QMSSLVTEHMESHGTRFLRGCIPSRIRKLPDGQLQVTWEDGISGKEDMGTFDTVLWAIG <---Intron-
        /|||||||||||| <   1957bp   > |||||||||| /||||||||||| |/ /||||||||||||  / ||/ |||||||||/| <   9998bp 
Target  IMMRSIPLRGFDQ                QMSSLVTEHMAAHGTRFLRGCIPLRVGRLPDGQLQVTWEDLTASKENTGTFDTVLWAVG            
        aaacaacccgtgc                catttgagcaggcgactcagtactaggaccggcccgatggcagaagaagatgagctggg            
        tttggtctggtaa                atccttcaatccagcgttgggtctgtggtcagatatcgaatccgaaacgctacttgct             
        cggcccccgctcg                ggatgcagcgattccgcggccccgagggcgtcgggccggcctccggcacccctgggca             
                                                                                                            

Query   --> RVPETRCLNLEKAGVNINPKNQKIVVDSQEATSIPHIYAIGDVAE <---Intron---> GRPELTPTAIMAGRLLAQRLFGQSSDLMDYDN <-
          > | |||  | ||||||/ /| /||//||/|||||/|||/||||||| <   2642bp   > |||||||||/|||/||||||  |||||||||| < 
Target      RAPETGSLALEKAGVSTDPHSQKVLVDAQEATSVPHIFAIGDVAE                GRPELTPTAVMAGKLLAQRLCHQSSDLMDYDN   
            cgcgagacgcgagggaagccacagcgggcggatgccatgaggggg                gccgcacaggaggactgccctccttgcagtga   
           ggccacggtctaacgtgcacagaatttacaaccctcattctgatca                ggcatccccttcgattcagtgaaccattaaaa   
           cgtagcatgtggggagttccccggcggccgacccctcccccacaag                ggcggacgtaggagcacggcccgcacggttct   
                                                                                                            

Query   --Intron---> VPTTVFTPLEYGCVGLSEEEAVARHGQEHVE <---Intron---> VYHAYYKPLEFTVAERDASQCYIK <---Intron---> 
          295bp    > ||||||||||||||||||| ||||||||||| <   1503bp   > |||||||||||||||||||||||| <   159bp    > 
Target               VPTTVFTPLEYGCVGLSEEAAVARHGQEHVE                VYHAYYKPLEFTVAERDASQCYIK                
                     gcaagtaccgtgtggctggggggccgcgcgg                gtcgttaccgtagggcggtcttaa                
                     tcccttcctaaggtgtcaacctcgagaaata                taacaaactatctcagaccagata                
                     ccggcccaggcccgggagggtgtctgggtgg                ttcattacggcagtagcaagccag                
                                                                                                            

Query   MVCLREPPQLVLGLHFLGPNAGEVTQGFALGIK <---Intron---> CGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
        ||||||||||||||||||||||||||||||||| <   1667bp   > || || ||||||||||||/||| |||||||||||||||||||
Target  MVCLREPPQLVLGLHFLGPNAGEVTQGFALGIK                CGTSYQQVMRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG
        agtccgccccgcgcctcgcaggggacgtgcgaa                tgattccgacaggaccatgggggaccatactgcgcagagttg
        ttgtgaccatttgtattgcacgatcagtctgta                ggccaaattgctgtaccgcaatcatgtcagcgtacctcgggg
        ggtgggcaggggcgctccctacactaattggc                gcgcccggggcagcctcccggggtggcccgcacgcctggccag
                                                                                                 * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1256 ; UGA-SECIS: 1259

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JSZB01015288.1:subseq_490000,135000_ Strand = - Positions = 47027 - 46954
 Found by:  Infernal (score=36.63) Covels (score=33.98)
 Stem2 length = 9   Apical loop length = 15   Insertion in stem2 = 0, 0
 Free Energy = -20.36

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((((((((--....([[{((({(({((((...............))))}))})))}]])..--...))))))))..
 target  CCGAUGCCAG--ACAAUGACGACCUGCGCAGAAACCCACCUGUGGGCUGCCCAUGUCUGAGCC--CGACUGGCAUUUC
                         ****           ^^^                       ****