_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       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: 142-499  (total 499)

 Target: /data/www-rg/seblastian_results/86226763/tempfiles/temptarget.fasta
 Chromosome: QVIC01000007.1: Strand: -
 Positions:
 -Exon 1  68004        68119
 -Exon 2  65901        66126
 -Exon 3  63514        63606
 -Exon 4  62878        62954
 -Exon 5  62104        62260
 -Exon 6  56957        57064
 -Exon 7  53999        54094
 -Exon 8  50003        50137
 -Exon 9  38061        38126

 Redox box: no

Query   ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILL
        ||||||||| ||||||||||||||||||||||||||||| <   1877bp   > |||||||||||||||||||||||||||||||||||||||||||||
Target  ATNNKGKEKFYSAERFLIATGERPRYLGIPGDKEYCISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILL
        gaaaagagatttggctcagaggaccttgacggagttaaa                ggctttcttcgaacggggttggtgtggtcggagtggagagctacc
        ccaaagaaataccagtttccgagcgatgtcgaaaagtgg                aattctcagcgactttgccatctagcgttcgtgtatctttgcttt
        aatcacaaattaagatctcttagatcgcccgcggcccc                tttatcatccgtgcggtaactctgattattttttgtcttgggctcg
                                                                                                            

Query   RGFDQDMANKIGAHMEEHGVKFIRQFVPIK <---Intron---> VEQIEAGTPGRLRVVAKSTNSEETIEGEYNT <---Intron---> VLLAIGR
        |||||||||||| ||||||/|||/|||||| <   2294bp   > /||||||||||||| |/|||||| ||||||| <   559bp    > |||||||
Target  RGFDQDMANKIGEHMEEHGIKFIKQFVPIK                IEQIEAGTPGRLRVTAQSTNSEEIIEGEYNT                VLLAIGR
        agtgcgagaaaggcaggcgaataactgcaa                agcagggacgccagagctaaaggaagggtaa                gccgaga
        ggtaaatcaatgaataaagtattaattcta                taatacgccggtgtccaccagaattagaaac                tttctgg
        aatcgcgctattacgaattcgtaggtaata                taataagaacacggatgccttgactaagttg                aggaaaa
                                                                                                            

Query   DACTRKIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYAGSTVK <---Intron--
        |/||| ||||||||||||| <   617bp    > ||||||||||||||||||||||/||||||||||||||||||||||||||||| <   5039bp  
Target  DSCTRNIGLETVGVKINEK                TGKIPVTDEEQTNVPYIYAIGDVLEGKLELTPVAIQAGRLLAQRLYAGSTVK             
        gttaaaagtgagggaaaga                agaacgagggcaagctatgagggtggacgcacggacggatcgcactggtaga             
        acgcgatgtactgtataaa                cgatctcaaaacatcatactgattagatatcctctacggttcagtacgccta             
        tttaattcaatggggata                atcaatcgtaagctgtcctctttaggaggatcagccgaaaggcggtttcctcg             
                                                                                                            

Query   -> CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENVE <---Intron---> VYHSFFWPLEWTIPSRDNNRCYAKIVCNLKDN <---Intron--
         > ||||||||||||||||||||||||||||||||||/| <   2862bp   > ||||||||||||/||||||/|||||||||||| <   3861bp  
Target     CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE                VYHSFFWPLEWTVPSRDNNKCYAKIVCNLKDN             
           tgtgagcaagtactgtggtgctggagggatgggaag                gtcatttccgtagctagaaattgaagtacaga             
           gaaaatcccttcctaagcggtcaaactaatgaaata                taagttgctagctccgaaaagacattgataaa             
           tctattaacatttgatttcctaaggtagatgggctg                tcttctgagagataaatccattaaacttgact             
                                                                                                            

Query   -> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKTQLDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGDILQAGCUG
         > |||||||||||||||||||||||||||||| |||||||||||||| <  11876bp   > ||||||||||||||||||||||
Target     ERVVGFHVLGPNAGEVTQGFAAALKCGLTKRQLDSTIGIHPVCAE                VFTTLSVTKRSGGDILQAGCUG
           gcgggtcgcgcaggggacgtgggcatgcaaaccgaaagaccgtgg                gtaactgaactgggaccggttg
           agttgtattgcacgatcagtccctaggtcagatagctgtactgca                ttcctctcagcggattacgggg
           attgcttagcattaacggccatgcgtagtggggccgtacccctag                gcaggggcgctgccctgtccat
                                                                                            * 
 Sequence until next stop: 
TAA
 * 

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

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = QVIC01000007.1: Strand = - Positions = 37833 - 37755
 Found by:  Infernal (score=27.18) Covels (score=24.38)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -13.71

         ..(((((((............((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg-----UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((([((............([[[((((((.((((......---........))))))))))]]])..--....))]))))..
 target  UGCAUCGGAGUGAUGCGUCCAUGAAGUCACCAGCCUCAAGCC---CGAGUGGUGGGCGGUGAUGGAACA--GCUGUCAGAUGAG
                              ****            ^^                        ****