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

 Blastx evalue: 8e-18
 Query name: gi|13486927|dbj|BAA77602.2| thioredoxin reductase II beta [Homo sapiens]
 Query range: 199-494  (total 494)

 Target: /var/www/seblastian_output/19309516/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  61903        61992
 -Exon 2  64741        64915
 -Exon 3  77740        77876
 -Exon 4  80468        80563
 -Exon 5  80915        81007
 -Exon 6  82730        82801
 -Exon 7  82980        83077
 -Exon 8  83940        84066

 Redox box: no

Query   VALECAGFLTGIGLDTTIMMRSIPLRGFDQ <---Intron---> QMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTV
        |||||||||||||||||/|/|||||||||| <   2748bp   > |||||||||||||||/|||||||||||||||| ||||||| |||||||||||||
Target  VALECAGFLTGIGLDTTVMIRSIPLRGFDQ                QMSSMVIEHMASHGTQFLRGCAPSRVRRLPDGHLQVTWEDCTTGKEDTGTFDTV
        ggcgtggtcagagcgaagaacaacccgtgc                cattagagcagtcgactcagtgctcgaaccggcccgatggtaagaggagatgag
        tctagcgttcgtgtacctttggtctggtaa                atcctttaatccagcattgggcccgtggtcagatatcgaagccgaaacgctact
        gcggttccccgcggccccgacccccccccg                agccgcagcgattccgcggctcccacggcttccggccggccctcggcacccccc
                                                                                                            

Query   LWAIG <---Intron---> RVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEG <---Intron---> RPELTPTAIMAGRLLVQ
        ||||| <  12824bp   > |||||||||||||||||||||||||||||| ||||||||||||||| <   2591bp   > |||||||||||||||||
Target  LWAIG                RVPDTRSLNLEKAGVDTSPDTQKILVDSREGTSVPHIYAIGDVVEG                RPELTPTAIMAGRLLVQ
        ctgag                cgcgaaacatgaggggaacgacaacggtcggatgccatgagggggg                ccgcacagaaggaccgc
        tgct                ggtcacggtataacgtacgcacaatttacgagcctcatactgattag                gcatccccttcggttta
        ggca                taaaccatgtgggtgattccctggcggccgacctgcccccttcggg                ggtggacgccgtggcggg
                                                                                                            

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

Query   KM <---Intron---> VCLREPPQLVLGLHFLGPNAGEVTQGFALGIKC <---Intron---> GASYAQVMRTVGIHPTCSEEVVKLRISKRSGLD
        || <   178bp    > ||||||||||||||||||||||||||||||||| <   862bp    > |||||||||||||||||||||||||||||||||
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: 1454 ; UGA-SECIS: 1457

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 85521 - 85591
 Found by:  Infernal (score=39.6) Covels (score=35.39)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -22.5

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