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

 Blastx evalue: 4e-05
 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: 85-499  (total 499)

 Target: /data/www-rg/seblastian_results/641475766/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  75626        75796
 -Exon 2  75124        75239
 -Exon 3  73251        73476
 -Exon 4  71483        71575
 -Exon 5  70832        70908
 -Exon 6  69183        69339
 -Exon 7  62322        62429
 -Exon 8  59844        59939
 -Exon 9  55650        55784
 -Exon 10 50000        50065

 Redox box: no

Query   NYGWNVEETVKHDWERMTEAVQNHIGSLNWGYRVALREKKVTYENAYGEFVGPHRIK <---Intron---> ATNNKGKEKIYSAERFLIATGERPRYL
         /|  /   ||||||||||||||||||||||||||||||||||||/||||||||||| <   386bp    > |||||||||||||||||||||||||||
Target  EHGVCLSRAVKHDWERMTEAVQNHIGSLNWGYRVALREKKVTYENSYGEFVGPHRIK                ATNNKGKEKIYSAERFLIATGERPRYL
        gcggtctcggacgtgaaagggcacagtcatgtcggccgaagatgattggtggccaaa                gaaaagagaattggatcagaggacctt
        aagtgtcgctaaagagtcactaaatgctaggagtctgaaatcaaacagattgcagta                ccaaagaaataccagtttccgagcgat
        gttcttttatgtcggagaggcgcctctccgcccgcgggagcccgcgcggtggtcgtg                aattacaggtcaagatctcttaggttg
                                                                                                            

Query   GIPGDKEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMQEHGIKFIRQFV
        |||||||||||| <   1647bp   > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/||
Target  GIPGDKEYCISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMQEHGIKFIREFV
        gacggagttaaa                ggctttcttcgaacggggttggtgtggtcggagtggagagctaccagtgcgagaaaggcacgcgaataagtg
        gtcgaaaagtgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattgatt
        tcttcaactcc                ttttctattcgtgcggcaactttgattattttttaccttgaactcaaatcgcgccattatgaattcgcaagta
                                                                                                            

Query   PIK <---Intron---> VEQIEAGTPGRLRVIAKSTDSDQTIEGEYNT <---Intron---> VLLAIGRDACTRKIGLENVGVKINEK <---Int
        ||| <   1675bp   > ||||||||||||||/||||/ |||||||||| <   574bp    > |||||||||||||||||||||||||| <   149
Target  PIK                VEQIEAGTPGRLRVVAKSTNGDQTIEGEYNT                VLLAIGRDACTRKIGLENVGVKINEK        
        caa                ggcagggacgccagggataaggcaagggtaa                gtcgagaggtaaaagtgagggaaaga        
        cta                taatacgccggtgttcaccagaactagaaac                tttctggacgcgatgtaatgtataaa        
        aag                taataagaacagagatgctttcaccaagttg                aggaatattcgaatcaacgaagata         
                                                                                                            

Query   ron---> TGKIPVTEEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSTVK <---Intron---> CDYENVPTTVFTPLEYGSCGLSEE
        2bp   > |||||||||||||||||||||||||||||||||||||||||||||||||||| <   6753bp   > ||||||||||||||||||||||||
Target          TGKIPVTEEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSTVK                CDYENVPTTVFTPLEYGSCGLSEE
                agaacgagggcaagctatgaggatggacgcacggacggaccgcattggtaga                tgtgagcaagtactgtgttgctgg
                cgatctcaaaacatcatactgattagatatcctctacggttcagtaggccta                gaaaatcccttcctaagcggtcaa
               gtaaatcagaggccgtcctccttaagggggcccgccgaagggtgggttccccg                cctactggttcttgatgtttttgg
                                                                                                            

Query   KAVEKFGEENVE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKVVCNIKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAAL
        |||||||||||| <   2382bp   > |||||||||||||||||||||||||||||||| <   4059bp   > |||||||/||||||||||||||||
Target  KAVEKFGEENVE                VYHSYFWPLEWTIPSRDNNKCYAKVVCNIKDN                ERVVGFHILGPNAGEVTQGFAAAL
        agggatgggagg                gtcatttctgtaactagaaattgaggtaaaga                gcgggtcacgcaggggacgtgggc
        actaatgaaata                taagatgctagctccgaaaagacattgataaa                agttgtattgcacgatcagtccct
        atggatgaattg                tcttctgagaggtgaatccattaaacctcact                attgcccagtattaggcggcaaac
                                                                                                            

Query   KCGLTKDQLDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGGNILQTGCUG
        ||||||||||||||||||||| <   5584bp   > ||||||||||||||||||||||
Target  KCGLTKDQLDSTIGIHPVCAE                VFTTLSVTKRSGGNILQTGCUG
        atgcaagccgaaagaccgtgg                gtaactgaactggaaccagttg
        aggtcaaatagctgtactgca                ttcctctcagcggattacgggg
        atggcgcggccccgcctttag                gcgtgggcgccgacccgctcat
                                                                 * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 230 ; UGA-SECIS: 233

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 49769 - 49691
 Found by:  Infernal (score=23.79) Covels (score=18.09)
 Stem2 length = 10   Apical loop length = 15   Insertion in stem2 = 1, 0
 Free Energy = -15.98

         ..(((((((.......((((((((((.(((((...............)))))))))))))))...........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         .(((({([(((.....([[[((((((.((((......--.........))))))))))]]]).......-.)))])})))).
 target  CAGAGUGAUGCGUCCAUGAAGUCAUCAGCCCCAAGCC--CCUCGCGGUGGGUGGUGAUGGAACCGUCAA-AGCAGUUUUCUC
                         ****            ^^                        ****