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

 Blastx evalue: 3e-04
 Query name: gi|27807129|ref|NP_777050.1| thioredoxin reductase 1, cytoplasmic [Bos taurus] >gi|190359068|sp|O62768.3|TRXR1_BOVIN RecName: Full=Thioredoxin reductase 1, cytoplasmic; Short=TR; AltName: Full=Thioredoxin reductase TR1 >gi|2997700|gb|AAC13914.1| thioredoxin reductase [Bos taurus] >gi|296487626|tpg|DAA29739.1| TPA: thioredoxin reductase 1 [Bos taurus]
 Query range: 93-499  (total 499)

 Target: /data/www-rg/seblastian_results/611286429/tempfiles/temptarget.fasta
 Chromosome: KZ688579.1:subseq_3526884,146227_ Strand: -
 Positions:
 -Exon 1  79647        79793
 -Exon 2  79122        79237
 -Exon 3  77329        77554
 -Exon 4  74973        75065
 -Exon 5  74307        74383
 -Exon 6  72862        73018
 -Exon 7  66326        66433
 -Exon 8  63426        63521
 -Exon 9  59879        60013
 -Exon 10 50000        50065

 Redox box: no

Query   TVKHDWERMTEAVQNHIGSLNWGYRVALREKKVTYENAYGEFVGPHRIK <---Intron---> ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEY
         |||||||||||||||||||||||||||||||||||||||/|||||||| <   409bp    > |||||||||||||||||||||||||||||||||||
Target  AVKHDWERMTEAVQNHIGSLNWGYRVALREKKVTYENAYGQFVGPHRIK                ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEY
        ggacgtgaaagggcacagtcatgtcggccgaagatgagtgctggccaaa                gaaaagagaattggatcagaggaccttgacggagt
        ctaaagagtcactaaatgctaggagtctgaaatcaaacagattgcagta                ccaaagaaataccagtttccgagcgatgtcgaaaa
        agatcggagaatcgtctctgcgcctgtgggagcctgcatggttgttgtg                acccacaggtttagatctcttagattgtcttcaac
                                                                                                            

Query   CISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMQEHGIKFIRQFVPIK <---
        |||| <   1567bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/|||||||||||||| <   
Target  CISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK     
        taaa                ggctttcttcgaacggggttggtgtggtcggagtggagagctaccagtgcgagaaaggcaggcgaataactgcaa     
        gtgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattgattcta     
        ccc                tttgctactcgtgcggtaactttgattatttcttatcttgagctcaaatcgcgccactatgaattcgtaagtaaaa     
                                                                                                            

Query   Intron---> VEQIEAGTPGRLRVIAKSTDSDQTIEGEYNT <---Intron---> VLLAIGRDACTRKIGLENVGVKINEK <---Intron---> 
        2263bp   > ||||||||||||||/||||||| |||||||| <   589bp    > ||||||||||||/|||||||||/||/ <   1288bp   > 
Target             VEQIEAGTPGRLRVVAKSTDSDITIEGEYNT                VLLAIGRDACTREIGLENVGVKLNEQ                
                   ggcagggacgccagggatagagaaagggtaa                gtcgagaggtaagagtgagggatagc                
                   taatacgccggtgttcaccagatctagaaac                tttctggacgcgatgtaatgtataaa                
                   taataagaacacggatgctttcaccaagttg                aggaaaatttagatcaacggagata                g
                                                                                                            

Query   TGKIPVTEEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSTVK <---Intron---> CDYENVPTTVFTPLEYGSCGLSEEKAVEKFGE
        |||||||/||||/|||||||||/|||||||||||||||||| /|||| |||| <   6428bp   > |||||||||||||||||/||||||||||||||
Target  TGKIPVTDEEQTSVPYIYAIGDVLEGKLELTPVAIQAGRLLVRRLYGSSTVK                CDYENVPTTVFTPLEYGACGLSEEKAVEKFGE
        agaacgagggcaagctatgagggtggacgcacggacggatcgcactgataga                tgtgagcaagtactgtggtgctggagggatgg
        cgatctcaaaacgtcatactgattagatatcctctacggtttggtaggccta                gaaaatcccttcctaagcggtcaaactaatga
        taaatcgtaggccgtcctctctgagggggccagacgaagggggggtgcctcg                tctattagctcttgatttttttagatggatga
                                                                                                            

Query   ENVE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKVVCNIKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKDQ
        ||/| <   2804bp   > ||||/|||||||||||||||||||/||||||/ <   3412bp   > ||||||||||||||||||||||||||||||||
Target  ENIE                VYHSHFWPLEWTIPSRDNNKCYAKIVCNIKDS                ERVVGFHVLGPNAGEVTQGFAAALKCGLTKDQ
        gaag                gtcacttctgtaactagaaattgaagtaaaga                gcgggtcgcgcaggggacgtgggcatgcaagc
        aata                taagatgctagctccgaaaagacattgataag                agttgtattgcacgatcagtccctaggtcaaa
        attg                tcttctgagaggtaaatccattaaacctcact                gttgcccagtattaatcgccaatcgcggcacg
                                                                                                            

Query   LDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGNILQTGCUG
        || |||||||||| <   9813bp   > |||||||||||| |||||||||
Target  LDGTIGIHPVCAE                VFTTLSVTKRSGENILQTGCUG
        cggaagaccgtgg                gtaactgaactggaaccagttg
        tagctgtactgca                ttcctctcagcgaattacgggg
        gccccacccccag                acaagggcgcgggcccgctcat
                                                         * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 221 ; UGA-SECIS: 224

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KZ688579.1:subseq_3526884,146227_ Strand = - Positions = 49778 - 49698
 Found by:  Infernal (score=24.16) Covels (score=23.79)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -16.41

         ..(((((((...............((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg--------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ....((((((..............([[[((((((.((((......---........))))))))))]]])..--..-))))))....
 target  CAGCGCUUCGCAGAGGGGCGUCCAUGAAGUCACCAGCCUCAAGCC---CGCGCGGUGGGUGGUGAUGGAACC--GU-CGAAGCAGUU
                                 ****            ^^                        ****