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

 Blastx evalue: 1e-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: 181-499  (total 499)

 Target: /data/www-rg/seblastian_results/189715079/tempfiles/temptarget.fasta
 Chromosome: SJYR01000959.1:subseq_716558,100000_ Strand: +
 Positions:
 -Exon 1  3            227
 -Exon 2  1899         1991
 -Exon 3  2566         2642
 -Exon 4  4291         4447
 -Exon 5  11111        11218
 -Exon 6  13596        13691
 -Exon 7  17731        17865
 -Exon 8  23173        23238

 Redox box: no

Query   DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMQEHGIKFIRQFVPIK <---Intron---> VEQIEAGTP
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   1671bp   > |||||||||
Target  DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMQEHGIKFIRQFVPIK                VEQIEAGTP
        ggcttccttcgaacggggttggtgtggtcggagtggagagctaccagtgcgagaaaggcacgcgaataactgcaa                ggcagggac
        aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattgattcta                taatacgcc
        tttctattcgtgcggcaactttgattattttttaccttgaactcaaatcgcgccattatgaattcgcaagtaaaa                caataagaa
                                                                                                            

Query   GRLRVIAKSTDSDQTIEGEYNT <---Intron---> VLLAIGRDACTRKIGLENVGVKINEK <---Intron---> TGKIPVTEEEQTNVPYIYAI
        |||||/||||/||||||||||| <   574bp    > |||||||||||||||||||||||||| <   1648bp   > ||||||||||||||||||||
Target  GRLRVVAKSTNSDQTIEGEYNT                VLLAIGRDACTRKIGLENVGVKINEK                TGKIPVTEEEQTNVPYIYAI
        gccagggataaagcaagggtaa                gtcgagaggtaaaagtgagggaaaga                agaacgagggcaagctatga
        ggtgttcaccagaactagaaac                tttctggacgcgatgtaatgtataaa                cgatctcaaaacatcatact
        cagagatgctttcaccaagttg                aggaaaattcgaatcaacggagata                gtaaatcagaggctgtcctcc
                                                                                                            

Query   GDILEGKLELTPVAIQAGRLLAQRLYGGSTVK <---Intron---> CDYENVPTTVFTPLEYGSCGLSEEKAVEKFGEENVE <---Intron---> 
        |||||||||||||||||||||||||||||||| <   6663bp   > |||||||||||||||||||||||||||||||||||| <   2377bp   > 
Target  GDILEGKLELTPVAIQAGRLLAQRLYGGSTVK                CDYENVPTTVFTPLEYGSCGLSEEKAVEKFGEENVE                
        ggatggacgcacggacggaccgcactggtaga                tgtgagcaagtactgtgttgctggagggatgggagg                
        gattagatatcctctacggttcagtaggccta                gaaaatcccttcctaagcggtcaaactaatgaaata                
        ttaggggggcgcgccgacgggtgggttcctcg                cctactagttcttgatgtttttggatggatgaattg                
                                                                                                            

Query   VYHSYFWPLEWTIPSRDNNKCYAKVVCNIKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKDQLDSTIGIHPVCAE <---In
        |||||||||||||||||||||||||||||||| <   4039bp   > |||||||/||||||||||||||||||||||||||||||||||||| <   53
Target  VYHSYFWPLEWTIPSRDNNKCYAKVVCNIKDN                ERVVGFHILGPNAGEVTQGFAAALKCGLTKDQLDSTIGIHPVCAE       
        gtcatttctgtaactagaaattgaggtaaaga                gcgggtcacgcaggggacgtgggcatgcaagccgaaagaccgtgg       
        taagatgctagctccgaaaagacattgataaa                agttgtattgcacgatcagtccctaggtcaaatagctgtactgca       
        tcttctgagaggtacatccattaaacctcact                attgcccagtattaggcggcaagcatggcgcggccccgccctcag       
                                                                                                            

Query   tron---> VFTTLSVTKRSGGNILQTGCUG
        07bp   > |||||||||||||/||||||||
Target           VFTTLSVTKRSGGSILQTGCUG
                 gtaactgaactggaaccagttg
                 ttcctctcagcgggttacgggg
                 gcatgggcgccgacccgctcat
                                     * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 229 ; UGA-SECIS: 232

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SJYR01000959.1:subseq_716558,100000_ Strand = + Positions = 23468 - 23546
 Found by:  Infernal (score=25.46) Covels (score=19.73)
 Stem2 length = 10   Apical loop length = 15   Insertion in stem2 = 1, 0
 Free Energy = -18.58

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