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

 Blastx evalue: 2e-04
 Query name: gi|212549578|ref|NP_001131081.1| thioredoxin reductase 1, cytoplasmic [Equus caballus]
 Query range: 2-499  (total 499)

 Target: /data/www-rg/seblastian_results/606870016/tempfiles/temptarget.fasta
 Chromosome: PKMU01001697.1:subseq_33060,127307_ Strand: +
 Positions:
 -Exon 1  48710        48793
 -Exon 2  49976        50048
 -Exon 3  50168        50287
 -Exon 4  51047        51189
 -Exon 5  51315        51430
 -Exon 6  53590        53815
 -Exon 7  57746        57838
 -Exon 8  60500        60576
 -Exon 9  63529        63685
 -Exon 10 65716        65823
 -Exon 11 68332        68427
 -Exon 12 70990        71124
 -Exon 13 77242        77307

 Redox box: no

Query   NGSEDLPESYDYDLIIIGGGSGGLAAAK <---Intron---> EAAKYNKKVMVLDFVTPTPLGTRWG <---Intron---> LGGTCVNVGCIPKKL
         | / / /|||||||/||||||||||/| <   1182bp   > ||||| |||||||/||||| ||||| <   119bp    > |||||||||||||||
Target  KGHDHMQDSYDYDLIVIGGGSGGLAASK                EAAKYGKKVMVLDYVTPTPQGTRWG                LGGTCVNVGCIPKKL
        agcgcacgttgtgcagagggtggcggta                gggatgaagagcgtgacaccgaatg                cggatgaggtacaac
        agaaataacaaaattttgggcggtccca                accaagaattttaatccccagcgg                gtggcgtatggtcaat
        gattcggtctcttctctagttatgttcg                gtcgtcgaggggcctttttgatag                ttaggtatgttataag
                                                                                                            

Query   MHQAALLGQALRDSRNYGWNVEEMV <---Intron---> KHDWEKMTEAVQNHIGSLNWGYRVALREKKVTYENAYGQFIGPHRIK <---Intron-
        |||||||||||/||| /||  || | <   759bp    > || || |||||||/||||||||||/|||||||||||/|/|/||| || <   125bp  
Target  MHQAALLGQALQDSRKFGWQFEEKV                KHSWETMTEAVQNYIGSLNWGYRVSLREKKVTYENAFGEFVGPHTIK            
        accggtcgcgtcgtcatgtctggag                acatgaaagggcatagtcatgtagttagaagatgagtggtggccaaa            
        taaccttgactaacgatggataaa                taaggactcactaaatgctaggagtctgaaatcaaactgattgcacta            
        gcgatgaaacaatacgtaggtgga                caccggagaattgtctctccgccggtgagggcatgttcaattggcatg            
                                                                                                            

Query   --> TTNNKGKEKIYSAEKFLIATGERPRYLDIPGDKEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVR
          >  |||||||| |/||||||||||||||| /||||||||/| <   2159bp   > |||||||||||||||||||||||||||||||/|||||||||
Target      ATNNKGKEKFYTAEKFLIATGERPRYLGVPGDKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVR
            gaaaagagattaggatcagaggacctcggcggagttaaa                ggcttccttcgaacggggttggcgtggtcggcgtggagagc
            ccaaagaaataccaatttccgagcgatgtcgaaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttg
            aatcaaagatcaggatgtcttaggccgtctacgacctc                tttcctgtctaagcggtatcctctattattatttgtatagga
                                                                                                            

Query   SILLRGFDQDMANKIGEHMEEHGVKFIKQFVPIK <---Intron---> VEQIEAGTPGQLRVVAQSTKGDETIEGEYNT <---Intron---> VLL
        |||||||||/||||||||||||||||||/||||| <   3930bp   > ||||| ||||/|/|/|||| | | ||||||| <   2661bp   > |||
Target  SILLRGFDQEMANKIGEHMEEHGVKFIKEFVPIK                VEQIEEGTPGKLKVIAQSTDGREIIEGEYNT                VLL
        tactagtgcgagaaaggcaggcggataagtgcaa                ggcagggacgacagagctaggagaagggtaa                gtt
        ctttggtaaatcaatgaataaagtattaattcta                taataagccgatattcaccaggattagaaac                ttt
        cctaaattgagacatgatgaatacgttagtgata                cagtaaattcagacacgcaccgaatagacct                gga
                                                                                                            

Query   AIGRDACTRKIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSTVK <---Intr
        |/||||||| |||/ |||||||/ <   2952bp   > /|||||/|||||||||||||||/||||||||||||||||||||||| |/|/| <   2030
Target  AVGRDACTRTIGLDRVGVKINER                SGKIPVSDEEQTNVPYIYAIGDVLEGKLELTPVAIQAGRLLAQRLYAGATLK         
        gggaggtaaaagtgagggaaaga                tgaacgagggcaagctatgagggtggacgcacggacggattgcactgggata         
        ctggacgcgctgtagtgtataag                cgatctgaaaacatcatactgattagatatcctctacggttcagtacgccta         
        aaaatacagattacataggcta                aaaattcttgaaatgttttctatgggggggcgagacaataggtagtttaacag         
                                                                                                            

Query   on---> CDYENVPTTVFTPLEYGACGLSEENAVEKFGEENIE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKIICNIKDN <---Intr
        bp   > ||| |||||||||||||||| ||| |/||||||||| <   2508bp   > ||||||||||||/||||||||||||||||/|| <   2562
Target         CDYVNVPTTVFTPLEYGACGFSEETALEKFGEENIE                VYHSYFWPLEWTVPSRDNNKCYAKIICNIQDN         
               tgtgagcaagtaccgtggtgttggagtgatgggaag                gtcatttccgtagctagaaattgaaataacga         
               gaatatcccttcctaagcggtcaacctaatgaaata                taagatgctagctccgaaaagacattgataaa         
               cctgttacaacaagatactacaagaagggtggattg                tctttcgagggtcatacccactagaccttatt         
                                                                                                            

Query   on---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAE <---Intron---> IFTTLSVTKRSGGNILQTGCUG
        bp   > |||/||||||||||||||||/||/|||||| |||/|||||||||| <   6117bp   > |||||||||||||||||/||||
Target         ERVIGFHVLGPNAGEVTQGFSAAIKCGLTKAQLDNTIGIHPVCAE                IFTTLSVTKRSGGNILQSGCUG
               gcgagtcgcgcaggggacgttggaatgcaagctgaaagaccgtgg                ataactgaactggaacctgttg
               agttgtattgcacgatcagtccctaggtcacataactgtactgca                ttcctctcagcggattacgggg
               gatttctgttattaatcggtgaccatagaagggccaaattattag                accggagggtttatctgtccat
                                                                                                * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 252 ; UGA-SECIS: 255

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = PKMU01001697.1:subseq_33060,127307_ Strand = + Positions = 77560 - 77636
 Found by:  Infernal (score=24.43) Covels (score=28.37)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -13.63

         ..(((((((........(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcg-UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ....((({(........([[(((((({(((((.................)))))}))))))]])..--.--.)})))....
 target  UCUACAGGAUGCUUCCAUGAUGUCGCAGCCUAAACCCAGUAUUUUCUGGUAGGCAGCGAUGGAAGA--A--CUGCUGGCAC
                          ****           ^^                          ****