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

 Blastx evalue: 5e-18
 Query name: gi|48257067|gb|AAH07489.3| TXNRD2 protein [Homo sapiens]
 Query range: 190-485  (total 485)

 Target: /var/www/seblastian_output/606925018/tempfiles/temptarget.fasta
 Chromosome: gi|511782574|gb|CM001960.1| Strand: +
 Positions:
 -Exon 1  69163        69252
 -Exon 2  72035        72209
 -Exon 3  84693        84829
 -Exon 4  87435        87530
 -Exon 5  87882        87974
 -Exon 6  89697        89768
 -Exon 7  89947        90044
 -Exon 8  90900        91026

 Redox box: no

Query   VALECAGFLTGIGLDTTIMMRSIPLRGFDQ <---Intron---> QMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTV
        |||||||||||||||||/|/|||||||||| <   2782bp   > |||||||||||||||||||||||||||||||| ||||||| |||||||||||||
Target  VALECAGFLTGIGLDTTVMIRSIPLRGFDQ                QMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGHLQVTWEDHTTGKEDTGTFDTV
        ggcgtggtcagagcgaagaacaacccgtgc                cattagagcagtcgactcagtgctcgaaccggcccgatggcaagaggagatgag
        tctagcgttcgtgtacctttggtctggtaa                atcctttaatccagcgttgggcccgtggtcagatatcgaaaccgaaacgctact
        gcggttccctgcggctccgacccccccccg                agccgcagcgattccgcggctcccacggcttccggccggccctcggcacccctc
                                                                                                            

Query   LWAIG <---Intron---> RVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEG <---Intron---> RPELTPIAIMAGRLLVQ
        ||||| <  12483bp   > |||||||||||||||||||||||||||||| ||||||||||||||| <   2605bp   > |||||| ||||||||||
Target  LWAIG                RVPDTRSLNLEKAGVDTSPDTQKILVDSREGTSVPHIYAIGDVVEG                RPELTPTAIMAGRLLVQ
        ctgag                cgcgaaacatgaggggaacgacaacggtcggatgccatgagggggg                ccgcacagaaggaccgc
        tgct                ggtcacggtataacgtacgcacaatttacgagcctcatactgattag                gcatccccttcggttta
        ggca                taaaccatgtgggtgattccctggcggccgacctgcccccttcggg                ggtggacgtcgtggcggg
                                                                                                            

Query   RLFGGSSDLMDYDNV <---Intron---> PTTVFTPLEYGCVGLSEEEAVARHGQEHVEV <---Intron---> YHAHYKPLEFTVAGRDASQCYV
        ||||||||||||||| <   351bp    > ||||||||||||||||||||||||||||||| <   1722bp   > ||||||||||||||||||||||
Target  RLFGGSSDLMDYDNV                PTTVFTPLEYGCVGLSEEEAVARHGQEHVEV                YHAHYKPLEFTVAGRDASQCYV
        cctggttgcagtgag                caagtaccgtgtggctggggggccgcgcggg                tcgctaccgtagggcggtcttg
        gttggccattaaaat                cccttcctaaggtgtcaaactcgagaaatat                aacaaactatctcggaccagat
        gcccgcacggctctt                ctccccgggtctgggcgggagtccgggttgc                tccttagggcggtagtacgtta
                                                                                                            

Query   KM <---Intron---> VCLREPPQLVLGLHFLGPNAGEVTQGFALGIKC <---Intron---> GASYAQVMRTVGIHPTCSEEVVKLRISKRSGLD
        || <   178bp    > ||||||||||||||||||||||||||||||||| <   855bp    > |||||||||||||||||||||||||||||||||
Target  KM                VCLREPPQLVLGLHFLGPNAGEVTQGFALGIKC                GASYAQVMRTVGIHPTCSEEVVKLRISKRSGLD
        aa                gtcagccccgcgcctcgcaggggacgtgcgaat                ggttgcgacaggaccattggggaccatactgcg
        at                tgtgaccatttgtattgcacgatcagtctgtag                gccacattgctgtaccgcaattatgtcagcgta
        gg                gcgggcgggggcgcctcccacattaattggcg                tgcccgggggcgtctcaccggacggcccgcacgc
                                                                                                            

Query   PTVTGCUG
        ||||||||
Target  PTVTGCUG
        cagagttg
        cctcgggg
        cggaccag
              * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1441 ; UGA-SECIS: 1444

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782574|gb|CM001960.1| Strand = + Positions = 92468 - 92538
 Found by:  Infernal (score=41.5) Covels (score=35.39)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -21.73

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .({((((((---....([[{((({((((((.................))))))})))}]])----....))))))}).
 target  UGCUGCCAG---AUAAUGACGACCUGGGUGGAAACCCACCCUGUGGGCACCCAUGUCCGAG----CCCCCUGGCAUUU
                         ****           ^^^                       ****