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

 Blastx evalue: 1e-04
 Query name: gi|387598071|ref|NP_001248375.1| thioredoxin reductase 1, cytoplasmic isoform 5 [Homo sapiens]
 Query range: 55-461  (total 461)

 Target: /data/www-rg/seblastian_results/326308881/tempfiles/temptarget.fasta
 Chromosome: KN979385.1:subseq_15432774,201163_ Strand: +
 Positions:
 -Exon 1  133955       134101
 -Exon 2  134510       134625
 -Exon 3  136440       136665
 -Exon 4  139600       139692
 -Exon 5  140609       140685
 -Exon 6  141763       141919
 -Exon 7  145394       145501
 -Exon 8  148388       148483
 -Exon 9  151026       151160
 -Exon 10 161098       161163

 Redox box: no

Query   TVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIK <---Intron---> ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEY
        ||||||||||||||||||||||||||||||||||||||||||||||||| <   408bp    > |||||||||||||||||||||||||||||||||||
Target  TVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIK                ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEY
        agacgtgaaagggcacagttatgtcggccgaaggtgagtgctagccaaa                gaaaagagaattggatcagaggaccttgacggagt
        ctaaagagttactaaatgctaggagtctgaaattaaacagattgcagta                ccaaagaaataccagtttccgagcgatgtcgaaaa
        atgttgcagaatagtctctgtgccaaagggaatctgttcggttttcgtg                aattacaaattaagatctcttaaatcgccttcaac
                                                                                                            

Query   CISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK <---
        |||| <   1814bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   
Target  CISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK     
        taaa                ggctttcttcgaacggggttggtgtggtcggagtggagagataccagtgcgagaaaggcaggcgaataactgcaa     
        gtgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattgattcta     
        ctc                ttttccgtccgtgcgctaactctggttattttttatcttgtgctttaatcgcgccattacgaatccgtaagtaata     
                                                                                                            

Query   Intron---> VEQIEAGTPGRLRVVAQSTNSEEIIEGEYNT <---Intron---> VMLAIGRDACTRKIGLETVGVKINEK <---Intron---> 
        2934bp   > /|||||||||||||||||||||||||||||| <   916bp    > |/|||||||||||||||||||||||| <   1077bp   > 
Target             IEQIEAGTPGRLRVVAQSTNSEEIIEGEYNT                VLLAIGRDACTRKIGLETVGVKINEK                
                   agcagggacgccagggctaaaggaagggtaa                gtcgagaggtaaaagtgagggaaaga                
                   taatacgccggtgttcaccagaattagaaac                tttctggacgcgatgtactgtataaa                
                   taataggaacacaaatgccttgactaagttg                gggaaaattcaaatcaatagggata                g
                                                                                                            

Query   TGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVK <---Intron---> CDYENVPTTVFTPLEYGACGLSEEKAVEKFGE
        |||||||||||||||||||||||||||||||||||||||||||||||||||| <   3474bp   > |||/||||||||||||||||||||||||||||
Target  TGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVK                CDYDNVPTTVFTPLEYGACGLSEEKAVEKFGE
        agaacgagggcaagctatgaggatggaggcacggacggatcgcactggtaga                tgtgagcaagtactgtggtgctggagggatgg
        cgatctcaaaacatcatactgattaaatatcctctacggttcagtacgccta                gaaaatcccttcctaagcggtcaaactaatga
        taaatcataagctgtcctctctaggtgggccatacgaaaggtggctatctcg                tctcttactatttgattttcttggatgggtga
                                                                                                            

Query   ENIE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKIICNTKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQ
        |||| <   2886bp   > |||||||||||||||||||||||||||||||| <   2542bp   > ||||||||||||||||||||||||||||||||
Target  ENIE                VYHSYFWPLEWTIPSRDNNKCYAKIICNTKDN                ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQ
        gaag                gtcatttctgtaactagaaattgaaataaaga                gcgggtcgcgcaggggacgtgggcatgcaaac
        aata                taagatgctagctccgaaaagacattgacaaa                agttgtattgcacgatcagtccctaggtcaaa
        attg                tcttctgagaggtaaatccattaaactttact                attgctcagtattaataaccatacatagcagg
                                                                                                            

Query   LDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGASILQAGCUG
        ||||||||||||| <   9937bp   > ||||||||||||||||||||||
Target  LDSTIGIHPVCAE                VFTTLSVTKRSGASILQAGCUG
        cgaaagaccgtgg                gtaattgaactggaaccggttg
        tagctgtactgca                ttcctctcagcgcgttacgggg
        gccgtacctctag                acaagtgcgctgacccgtccat
                                                         * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 217 ; UGA-SECIS: 220

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KN979385.1:subseq_15432774,201163_ Strand = + Positions = 161381 - 161467
 Found by:  Infernal (score=27.22) Covels (score=23.03)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -16.19

         ..(((((((......................((((((((((.(((((...............)))))))))))))))........)))))))..
 model   uucggucaugcg---------------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(((((((((.....................([[[((((((.((((......---........))))))))))]]])----...))))))))).
 target  UAUUUGGCAGGGCAUCGAAGGGAUGCAUCCAUGAAGUCACCAGUCUCAAGCC---CAUGGGGUAGGCGGUGAUGGAA----CAACUGUCAAAUC
                                        ****            ^^                        ****