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

 Blastx evalue: 5e-05
 Query name: gi|379698834|ref|NP_001243891.1| thioredoxin reductase 1, cytoplasmic [Oryctolagus cuniculus]
 Query range: 1-499  (total 499)

 Target: /data/www-rg/seblastian_results/790677170/tempfiles/temptarget.fasta
 Chromosome: KZ294002.1:subseq_1337875,80123_ Strand: -
 Positions:
 -Exon 1  58354        58440
 -Exon 2  56602        56674
 -Exon 3  55003        55122
 -Exon 4  50113        50255
 -Exon 5  49621        49736
 -Exon 6  47526        47751
 -Exon 7  38469        38561
 -Exon 8  37841        37917
 -Exon 9  37067        37223
 -Exon 10 31909        32016
 -Exon 11 29061        29156
 -Exon 12 25003        25137
 -Exon 13 13037        13102

 Redox box: no

Query   MNGSEDLPPSYDYDLIIIGGGSGGLAAAK <---Intron---> EAAKYGKKVMVLDFVTPTPLGTRWG <---Intron---> LGGTCVNVGCIPKK
        |||||||| |||/|||||||||||||||| <   1679bp   > ||||| ||||||||||||||||||| <   1479bp   > ||||||||||||||
Target  MNGSEDLPESYDFDLIIIGGGSGGLAAAK                EAAKYDKKVMVLDFVTPTPLGTRWG                LGGTCVNVGCIPKK
        aagtggccgttgtgcaaagggtggcggga                gggatgaagagtgtgacaccgaatg                cggatgaggtacaa
        tagcaatcacaatattttgggcggtccca                accaaaaattttattcccctgcgg                gtggcgtatggtcaa
        gtctgttcgtttcctcctatcaaggttcg                gacatcggtgcgttctacttatag                ttaagtgtgtcataa
                                                                                                            

Query   LMHQAALLGQALQDSRNYGWKFEDTV <---Intron---> EHDWEKMTEAVQNHIGSLNWGYRVALREKKVVYENAYGEFIGPHQIK <---Intron
        ||||||||||||/||||||| ||| | <   4747bp   > /|||||||||||||||||||||||||||||||||||/|/|||||/|| <   376bp 
Target  LMHQAALLGQALKDSRNYGWNFEDNV                KHDWEKMTEAVQNHIGSLNWGYRVALREKKVVYENAFGQFIGPHRIK           
        caccggttgcgcagtcatgtatggag                acgtgaaagggcacagtcatgtcggccgaaggtgagtgctagccaaa           
        ttaaccttgactaacgaaggataaa                taaagaatcactaaatgctaggagtctgaaattaaactgattgcagta           
        agcaatgaaacgactcctcgccgct                tatcgaagaatagtctctgcgcctataggaggctgcttgatcattgtg           
                                                                                                            

Query   ---> ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMV
           > ||||||||| ||||||||||||||||||||||||||||  <   1869bp   > ||||||||||||||||||||||||||||||||||||||||
Target       ATNNKGKEKFYSAERFLIATGERPRYLGIPGDKEYCISR                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMV
             gaaaagagatttggctcagaggaccttgacggagttaaa                ggctttcttcgaacggggttggtgtggtcggagtggagag
             ccaaagaaataccagtttccgagcgatgtcgaaaagtgg                aattctcagcgactttgccatctagcgttcgtgtatcttt
             aatcacaaattaagatctcttagatcgcccgcggcccc                attatcatccgtgcggtaactctgattattttttgtcttgg
                                                                                                            

Query   RSILLRGFDQDMANKIGAHMEEHGVKFIRQFVPIK <---Intron---> VEQIEAGTPGRLRVVAKSTNSEETIEGEYNT <---Intron---> VL
        ||||||||||||||||| ||||||/|||/|||||| <   8964bp   > /||||||||||||| |/|||||| ||||||| <   551bp    > ||
Target  RSILLRGFDQDMANKIGEHMEEHGIKFIKQFVPIK                IEQIEAGTPGRLRVTAQSTNSEEIIEGEYNT                VL
        ctaccagtgcgagaaaggcaggcgaataactgcaa                agcagggacgccagagctaaaggaagggtaa                gc
        gctttggtaaatcaatgaataaagtattaattcta                taatacgccggtgtccaccagaattagaaac                tt
        gttcgaatcgcgctattacgaattcgtaggtaata                taataagaacacggatgccttgactaagttg                ag
                                                                                                            

Query   LAIGRDACTRKIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYAGSTVK <---Int
        ||||||/||| ||||||||||||| <   617bp    > |||||||||||||||||||||||||||||||||||||||||||||||||||| <   505
Target  LAIGRDSCTRNIGLETVGVKINEK                TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYAGSTVK        
        cgagagttaaaagtgagggaaaga                agaacgagggcaagctatgaggatggacgcacggacggatcgcactggtaga        
        tctggacgcgatgtactgtataaa                cgatctcaaaacatcatactgattagatatcctctacggttcagtacgccta        
        gaaaatttaattcaatggggata                atcaatcgtaagctgtcctctttaggaggatcagccgaaaggcggtttcctcg        
                                                                                                            

Query   ron---> CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENVE <---Intron---> VYHSFFWPLEWTIPSRDNNRCYAKIVCNLKDN <---Int
        0bp   > ||||||||||||||||||||||||||||||||||/| <   2752bp   > ||||||||||||/||||||/|||||||||||| <   392
Target          CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE                VYHSFFWPLEWTVPSRDNNKCYAKIVCNLKDN        
                tgtgagcaagtactgtggtgctggagggatgggaag                gtcatttccgtagctagaaattgaagtacaga        
                gaaaatcccttcctaagcggtcaaactaatgaaata                taagttgctagctccgaaaagacattgataaa        
                tctattaatatttgattttctaaggtagatgggctg                tcttctgagagataaatccattaaacttgact        
                                                                                                            

Query   ron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKTQLDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGDILQAGCUG
        3bp   > |||||||||||||||||||||||||||||| |||||||||||||| <  11900bp   > ||||||||||||||||||||||
Target          ERVVGFHVLGPNAGEVTQGFAAALKCGLTKRQLDSTIGIHPVCAE                VFTTLSVTKRSGGDILQAGCUG
                gcgggtcgcgcaggggacgtgggcatgcaaaccgaaagaccgtgg                gtaactgaactgggaccggttg
                agttgtattgcacgatcagtccctaggtcagatagctgtactgca                ttcctctcagcggattacgggg
                attgcttagcattaacggccatgcgtagcggggccgtacctctag                gcaggggcgctgccctgtccat
                                                                                                 * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 227 ; UGA-SECIS: 230

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KZ294002.1:subseq_1337875,80123_ Strand = - Positions = 12809 - 12731
 Found by:  Infernal (score=27.45) Covels (score=22.57)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -13.31

         ..(((((((............((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg-----UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((({((............([[[((((((.((((......---........))))))))))]]])..--....))}))))..
 target  UGCAUCAGAGUGAUGCGUCCAUGAAGUCGCCAGCCUCAAGCC---CGAGUGGUGGGCGGUGAUGGAACA--GCUGUCAGAUGAG
                              ****            ^^                        ****