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

 Blastx evalue: 6e-30
 Query name: gi|46048169|ref|NP_840073.2| methionine-R-sulfoxide reductase B1-A [Danio rerio] >gi|292495073|sp|Q802G6.3|MSB1A_DANRE RecName: Full=Methionine-R-sulfoxide reductase B1-A; Short=MsrB; Short=MsrB1-A; AltName: Full=Selenoprotein X-A; Short=SePR; Short=SelX-A [Danio rerio] >gi|45501381|gb|AAH67380.1| Selenoprotein X, 1 [Danio rerio]
 Query range: 1-103  (total 110)

 Target: /data/www-rg/seblastian_results/3721324/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  14763        14817
 -Exon 2  13372        13514
 -Exon 3  13131        13241

 Redox box: no

Query   MSFCSFSGGEIYKDHFESG <---Intron---> MYVCAQCGYELFSSRSKYEHSSPWPAFTETIHEDSVSKQEERWGAYK <---Intron---> VR
        |||| | |||||||||/ | <   1248bp   > ||||//| / |||||||/ ||||||||| || ||||/|  |   |/| <   130bp    > | 
Target  MSFCQFVGGEIYKDHFKPG                MYVCSKCNHPLFSSRSKFAHSSPWPAFTNTIREDSVTKMMETLTAFK                VL
        atttctggggatagctacg                atgttatacccttactatgcttctcgtaaaaaggagaaaagacagta                gc
        tctgattggataaaatac                gtatgcagaacttcggcatcacccgcctcactgaagtcattactccta                tt
        gtttgttctgccgttcaa                tgtaccgtctagcctccgcccgtcgtttccccagccccggggtcctcg                tt
                                                                                                            

Query   CGKCGNGLGHEFVNDGPKHGLSRFUIFSSSLKFIP
        |||||||||||||||||/ |/||||||| ||||/|
Target  CGKCGNGLGHEFVNDGPEEGVSRFUIFSHSLKFVP
        tgatgagcgcgtgaggcggggtcttatactcatgc
        ggaggagtgaattaagcaagtcgtgttgactattc
        tcgccctgtcgtgtccaagagattaactcgcgtcc
                                *          
 Sequence until next stop: 
AACAAAGGTGAGATAAACACAGACAGGAGTGAGGAAATTTAG
 N  K  G  E  I  N  T  D  R  S  E  E  I  * 

 Distance CDS-SECIS: 723 ; UGA-SECIS: 753

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 12407 - 12331
 Found by:  Infernal (score=27.57) Covels (score=27.61)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -20.91

         ..(((((((.......(((((((((((((((.................))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ....(((((.--....{[[{((((((((((...................))))))))))}]]}.....-.-.)))))....
 target  UCGAGGUCAA--UUGGUGACGUGGGCAGGGGAAAGUCCUGAGAAGGACAUCCUGUCCACUGAUGUAUC-U-CUGACCAGCC
                         ****           ^^^                         ****