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

 Blastx evalue: 9e-05
 Query name: gi|33519426|ref|NP_877393.1| thioredoxin reductase 1, cytoplasmic isoform 2 [Homo sapiens] >gi|33519428|ref|NP_877419.1| thioredoxin reductase 1, cytoplasmic isoform 2 [Homo sapiens] >gi|33519430|ref|NP_877420.1| thioredoxin reductase 1, cytoplasmic isoform 2 [Homo sapiens] >gi|34782844|gb|AAH18122.2| Thioredoxin reductase 1 [Homo sapiens]
 Query range: 175-499  (total 499)

 Target: /var/www/seblastian_output/166474491/tempfiles/temptarget.fasta
 Chromosome: gi|511782582|gb|CM001952.1| Strand: +
 Positions:
 -Exon 1  170885       171127
 -Exon 2  173934       174026
 -Exon 3  175537       175613
 -Exon 4  176932       177088
 -Exon 5  181111       181218
 -Exon 6  184305       184400
 -Exon 7  190120       190254
 -Exon 8  200346       200411

 Redox box: no

Query   EYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK <---Intron---> VEQ
         /  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   2806bp   > /||
Target  SFFFSSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK                IEQ
        tttttaggctttcttcgaacggggttggtgtggtcggagtggagagataccagtgcgagaaaggcaggcgaataactgcaa                agc
        ctttcgaattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataaagtattgattcta                taa
        ttttcttttccgtccgtgcgctaactctggttattttttatcttgtgcttcaatcgcgccattacgaatccgtaagtaata                taa
                                                                                                            

Query   IEAGTPGRLRVVAQSTNSEEIIEGEYNT <---Intron---> VMLAIGRDACTRKIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNV
        || ||||||||||||| ||||||||||| <   1510bp   > |/|||||||||||||||||||||||| <   1318bp   > ||||||||||||||
Target  IEVGTPGRLRVVAQSTISEEIIEGEYNT                VLLAIGRDACTRKIGLETVGVKINEK                TGKIPVTDEEQTNV
        agggacgccagggctaaaggaagggtaa                gtcgagaggtaaaagtgagggaaaga                agaacgagggcaag
        tatgccggtgttcacctgaattagaaac                tttctggacgcgatgtactgtataaa                cgatctcaaaacat
        taggaacacaaatgccttgactaagttg                gggaaaattcaaatcaatagggata                gtaaatcataagctg
                                                                                                            

Query   PYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKC <---Intron---> DYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEV <---Intr
        ||||||||||||||||||||||||||||||||||||||| <   4022bp   > |||||||||||||||||||||||||||||||||||| <   3086
Target  PYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKC                DYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEV         
        ctatgaggatggaggcacggacggatcgcactggtagat                gtgagcaagtactgtggtgctggagggatgggaagg         
        catactgattaaatatcctctacggttcagtacgccta                gaaaatcccttcctaagcggtcaaactaatgaaatat         
        tcctctctaggtgggccatacgaaaggtggctatctcg                tctattactatttgactttcttggatgggtgaattgt         
                                                                                                            

Query   on---> YHSYFWPLEWTIPSRDNNKCYAKIICNTKDNE <---Intron---> RVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEV
        bp   > |||||||||||||||||||||||||||||||| <   5719bp   > |||||||||||||||||||||||||||||||||||||||||||||
Target         YHSYFWPLEWTIPSRDNNKCYAKIICNTKDNE                RVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEV
               tcatttctgtaactagaaattgaaataaagag                cgggtcgcgcaggggacgtgggcatgcaaaccgaaagaccgtggg
               aagatgctagctccgaaaagacattgacaaaa                gttgtattgcacgatcagtccctaggtcaaatagctgtactgcat
               cttctgagaggtaaatccattaaactttacta                ttgctcagtattaataaccatacatagcagggccatacctctaga
                                                                                                            

Query    <---Intron---> FTTLSVTKRSGASILQAGCUG
         <  10091bp   > |||||||||||||||||||||
Target                  FTTLSVTKRSGASILQAGCUG
                        taattgaactggaaccggttg
                        tcctctcagcgcgttacgggg
                        caagtgcgctgacccgtccat
                                           * 
 Sequence until next stop: 
TAA
 * 

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

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782582|gb|CM001952.1| Strand = + Positions = 200629 - 200715
 Found by:  Infernal (score=27.14) Covels (score=23.03)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 1, 0
 Free Energy = -16.29

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