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

 Blastx evalue: 1e-05
 Query name: gi|78191795|ref|NP_113802.2| thioredoxin reductase 1, cytoplasmic [Rattus norvegicus]
 Query range: 1-499  (total 499)

 Target: /data/www-rg/seblastian_results/110055341/tempfiles/temptarget.fasta
 Chromosome: CM004103.1:subseq_81589812,224304_ Strand: +
 Positions:
 -Exon 1  101672       101758
 -Exon 2  102659       102731
 -Exon 3  104292       104411
 -Exon 4  106239       106381
 -Exon 5  106782       106897
 -Exon 6  108713       108938
 -Exon 7  110872       110964
 -Exon 8  111458       111534
 -Exon 9  111901       112057
 -Exon 10 112147       112254
 -Exon 11 114161       114256
 -Exon 12 118633       118767
 -Exon 13 124239       124304

 Redox box: no

Query   MNDSKDAPKSYDFDLIIIGGGSGGLAAAK <---Intron---> EAAKFDKKVMVLDFVTPTPLGTRWG <---Intron---> LGGTCVNVGCIPKK
        || ||| |/|||||||||||||||||||| <   900bp    > |||||||||/||||||||||||||| <   1560bp   > ||||||||||||||
Target  MNGSKDPPESYDFDLIIIGGGSGGLAAAK                EAAKFDKKVLVLDFVTPTPLGTRWG                LGGTCVNVGCIPKK
        aagtagccgttgtgcaaagggtggcggga                gggatgaagcgtgtgacaccgaatg                cggatgaggtacaa
        tagcaaccacaatattttgggcggtccca                accataaattttattcccctgcgg                gtggcgtatggtcaa
        gtccatctgctcccgcctaacaaagaatg                gacatcgaggcgttcagtttgcag                tcaagtgcgtcatgg
                                                                                                            

Query   LMHQAALLGQALKDSRNYGWKLEDTV <---Intron---> KHDWEKMTESVQNHIGSLNWGYRVALREKKVVYENAYGKFIGPHKIM <---Intron
        |||||||||||||||||||||/|||| <   1827bp   > ||||||||||||||||||||||||||||||||||||||/|||||/|/ <   400bp 
Target  LMHQAALLGQALKDSRNYGWKVEDTV                KHDWEKMTESVQNHIGSLNWGYRVALREKKVVYENAYGRFIGPHRIV           
        caccggtcgcgcagtcatgtagggag                acgtgaaagtgcacagtcatgtcggccgaaggtgagtgatagccaag           
        ttaaccttgactaacgaaggataac                taaagaatcactaaatgctaggagtctgaaattaaacaggttgcagtt           
        ggcgatgcaatgacgcctcgacaca                ggtcggagaatggtcccggcgcccatcggagcctgttcggctttcgtg           
                                                                                                            

Query   ---> ATNNKGKEKVYSAERFLIATGERPRYLGIPGDKEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMV
           > |||||||||/||||||||||||||||||||||||||||| <   1815bp   > ||||||||||||||||||||||||||||||||||||||||
Target       ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMV
             gaaaagagaattggctcagaggacctcgacggagttaaa                ggctttcttcgaacggggttggtgtggtcggagtggagag
             ccaaagaaataccagtttccgagcgatgtcgaaaagtgg                aattctcagcgactttgccatctagcgttcgtgtatcttt
             gatcataaactaaggccccgtggcacgcctacagcccc                ttttccgtccgggcaattactccgataatgttccacctagg
                                                                                                            

Query   RSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTK <---Intron---> IEQIEAGTPGRLKVTAKSTNSEETIEDEFNT <---Intron---> VL
        ||||||||||||||||||||||||||||||||||| <   1933bp   > ||||||||||||/|||/||||||||| |||| <   493bp    > ||
Target  RSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTK                IEQIEAGTPGRLRVTAQSTNSEETIEGEFNT                VL
        ctaccagtgcgagaaaggcaggcgaataactgcaa                agcagggacgccagagctaaaggaagggtaa                gt
        gctttggtaaatcaatgaataaagtattgattcca                taatacgccggtgtccaccagaactagatac                tt
        gctcgaatcacgccactacgaattcgtaggccaga                tagcaagaacacggttacaccggcagcatca                gg
                                                                                                            

Query   LAVGRDSCTRTIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSTVK <---Int
        |||||||||||||||||||||||| <   366bp    > ||||||||||||||||||||||||||||||||||||||||||||||||| || <    89
Target  LAVGRDSCTRTIGLETVGVKINEK                TGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSNVK        
        cgggagttaaaagtgagggaaaga                agaacgagggcaagctatgaggacggacgcacggacggatcgcactggtaga        
        tctggacgcgctgtactgtataaa                cgatctcaaaacatcatactgattagatatcctctacggttcagtaggcata        
        ggaaatttgattcagcgcggaca                acagatcataggctgtccccctccggggaggtcaccgggaggtgggcacctca        
                                                                                                            

Query   ron---> CDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIE <---Intron---> VYHSFFWPLEWTVPSRDNNKCYAKVVCNLKDN <---Int
        bp    > |||||||||||||||||||||||||||||||||||| <   1906bp   > ||||||||||||||||||||||||//|||||/ <   437
Target          CDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIE                VYHSFFWPLEWTVPSRDNNKCYAKIICNLKDD        
                tgtgagcaagtactgtgttgctggagggatgggaag                gtcatttctgtagctcgaaattgaaatacagg        
                gaaaatcccttcctaaggggtcaaactaatgaaata                taagttgctagctccgaaaagacattgataaa        
                tctctcagtatttgatcttcctaaacagatgaatta                tcttctgagagacacgtccattaaaccctacc        
                                                                                                            

Query   ron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAE <---Intron---> IFTTLSVTKRSGGDILQSGCUG
        6bp   > ||||||||||||||||||||||||||||||||||||||||||||| <   5471bp   > ||||||||||||||||||||||
Target          ERVVGFHVLGPNAGEVTQGFAAALKCGLTKQQLDSTIGIHPVCAE                IFTTLSVTKRSGGDILQSGCUG
                gcgggtcgcgcaggggacgtgggcatgcaacccgaaagaccgtgg                ataattgaactgggacctgttg
                agttgtattgcacgatcagtccctaggtcaaatagctgtactgca                ttcctctcagcggattacgggg
                atcgcccggtactaggggctgcgcgtggcggggcccccccgctag                acaggagtgctgacccgtccat
                                                                                                 * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 231 ; UGA-SECIS: 234

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM004103.1:subseq_81589812,224304_ Strand = + Positions = 124536 - 124611
 Found by:  Infernal (score=32.98) Covels (score=27.9)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -20.06

         ..(((((((.......((((((((((.(((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .(((((([((......([[{(((((((.(((......---........))))))))))}]])......-.-))])))))).
 target  CACAGGCAUGCGUCCAUGAAGUCACUGGCCUCAAGCC---CAAGUGGUGGGCAGUGACAGAAGAGCUG-C-CGGGUCUGUU
                         ****            ^^                        ****                   
