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

 Blastx evalue: 6e-05
 Query name: gi|379698834|ref|NP_001243891.1| thioredoxin reductase 1, cytoplasmic [Oryctolagus cuniculus]
 Query range: 90-499  (total 499)

 Target: /data/www-rg/seblastian_results/584242931/tempfiles/temptarget.fasta
 Chromosome: JSZB01004433.1:subseq_330000,180000_ Strand: -
 Positions:
 -Exon 1  78783        78938
 -Exon 2  78285        78400
 -Exon 3  76667        76892
 -Exon 4  74208        74300
 -Exon 5  73541        73617
 -Exon 6  71263        71419
 -Exon 7  65139        65246
 -Exon 8  64139        64234
 -Exon 9  59245        59379
 -Exon 10 49580        49645

 Redox box: no

Query   FEDTVEHDWEKMTEAVQNHIGSLNWGYRVALREKKVVYENAYGEFIGPHQIK <---Intron---> ATNNKGKEKIYSAERFLIATGERPRYLGIPGD
        |   |/|||||||||||||||||||||||||||||| ||||||||/|||/|| <   382bp    >  |||||||||||||||||||||||||||||||
Target  FSCAVKHDWEKMTEAVQNHIGSLNWGYRVALREKKVTYENAYGEFVGPHRIK                TTNNKGKEKIYSAERFLIATGERPRYLGIPGD
        tttggacgtgaaagggcacagtcatgtcggccgaagatgagtggtggccaaa                aaaaagagaattggatcagaggaccttgacgg
        tcgctaaagaatcactaaatgctaggagtctgaaatcaaacagattgcagta                ccaaagaaataccagtttccgagcgatgtcga
        tttatatcgaagcatggcctctgcgccgaatggaacctgtgcggtctctgtg                aatcacaaactaagatgttttagatcgctttc
                                                                                                            

Query   KEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGAHMEEHGVKFIRQFVPIK <
        /|||||| <   1392bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||//||||| <
Target  REYCISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGVKFIKEFVPIK  
        agttaaa                ggcttccttcgaacggggttggtgtggtcggagtggagagctaccagtgcgagaaaggcaggcggataagtgcaa  
        gaagtgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattaattcta  
        aacccc                tttttcatccgtgcggtaagtttgattatttcttatcttgggctctaatcgcgccataatgagtgcgtagataaaa  
                                                                                                            

Query   ---Intron---> VEQIEAGTPGRLRVVAKSTNSEETIEGEYNT <---Intron---> VLLAIGRDACTRKIGLETVGVKINEK <---Intron--
           2366bp   > ||||||||||||||||/||/| ||||||||| <   590bp    > |||||||||||||||||||||||||| <   2121bp  
Target                VEQIEAGTPGRLRVVAQSTSSGETIEGEYNT                VLLAIGRDACTRKIGLETVGVKINEK             
                      ggcagggacgccagggctaaaggaagggtaa                gtcgagaggtaaaagtgagggaaaga             
                      taatacgccggtgttcaccgggactagaaac                tttctggacgcgatgtactgtataaa             
                      taataagaccagggaggccctcaccaagttg                gggaaaattcaaattgatggagata              
                                                                                                            

Query   -> TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYAGSTVK <---Intron---> CDYENVPTTVFTPLEYGACGLSEEKAVEK
         > |||||||||||||||||||||||||||||||||||||||||||||||||||| <   6016bp   > |||||||||||||||||/|||||||||||
Target     TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYAGSTVK                CDYENVPTTVFTPLEYGSCGLSEEKAVEK
           agaacgagggcaagctatgaggatggacgcacggacggatcgcactggtaga                tgtgagcaagtactgtgttgctggaggga
           cgatctcaaaacatcatactgattagatatcctctacggttcagtacgccta                gaaaatcccttcctaagcggtcaaactaa
          gtaaatcataggctgatccctttaggggggccaaacgaaaggtgggtccctcg                tctattaatgtttgacttttttagatgga
                                                                                                            

Query   FGEENVE <---Intron---> VYHSFFWPLEWTIPSRDNNRCYAKIVCNLKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLT
        |||||/| <   904bp    > /|||/|||||| |||||||/||||||||/||| <   4759bp   > |||||||||||||||||||||||/|||||
Target  FGEENIE                IYHSYFWPLEWAIPSRDNNKCYAKIVCNIKDN                ERVVGFHVLGPNAGEVTQGFAAAVKCGLT
        tgggaag                atcatttccgtgactagaaattgaagtaaaga                gcgggtcgcgcaggggacgtggggatgca
        tgaaata                taagatgctagctccgaaaagacattgataaa                agttgtattgcacgatcagtccctaggtc
        cgaatta                tcttccgggagataaatccattaaacttcact                aaggcccggtattgatagctgcacgtggc
                                                                                                            

Query   KTQLDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGDILQAGCUG
        | |||||||||||||| <   9599bp   > ||||||||||||||||||||||
Target  KQQLDSTIGIHPVCAE                VFTTLSVTKRSGGDILQAGCUG
        acccgaaagaccgtgg                gtaactgaactgggaccggttg
        aaatagctgtactgca                ttcctctcagcggattacgggg
        ggggccccgcctccag                gcatgggcgccgacccgtccat
                                                            * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 209 ; UGA-SECIS: 212

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JSZB01004433.1:subseq_330000,180000_ Strand = - Positions = 49370 - 49286
 Found by:  Infernal (score=24.81) Covels (score=21.91)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 1, 0
 Free Energy = -20.12

         ..(((((((.....................((((((((((.(((((................)))))))))))))))........)))))))..
 model   uucggucaugcg--------------UuaAUGAcGgccug-gcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((((...................([[{(((((((.(((..........-----...))))))))))}]])----..)))))))))..
 target  CAUUCGGCAGCGCAUUGAGGGAUGCGUCCAUGAAGUCACUGGUCUCAAGCCACGU-----GGUGGGCAGUGACCGAA----CAGCUGUCGGAGC
                                       ****            ^^                         ****