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

 Blastx evalue: 2e-19
 Query name: gi|45766836|gb|AAH09611.2| Selenoprotein T [Homo sapiens]
 Query range: 43-195  (total 195)

 Target: /var/www/seblastian_output/614846018/tempfiles/temptarget.fasta
 Chromosome: gi|511782578|gb|CM001956.1|subseq(39963998,230600) Strand: -
 Positions:
 -Exon 1  105224       105345
 -Exon 2  104219       104345
 -Exon 3  102206       102293
 -Exon 4  100000       100121

 Redox box: no

Query   FQICVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYR <---Intron---> HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKV
        |   ||||||||||||||||||||||||||||||||||||| <   878bp    > |||||||||||||||||||||||||||||||||||||||||||
Target  FFCSVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYR                HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKV
        tttagttgtacgtggtacgaacctcgacagggatccccata                cagttctgtacgtagtaaggagctgttgacgcaatctgcgaag
        ttggtcggaggttaaatgttgagacatgtagaaatcactag                atccttcttattttgttttgaactcttgtaccgtgaggaaaa 
        tcctccattgggtggcggtccggcaccctaagtcctaaat                acaatcaaccaaaaacaattcgttttctcgattccgggcaatg 
              *                                                                                             

Query    <---Intron---> YACMMVFFLSNMIENQCMSTGAFEITLNDV <---Intron---> PVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHR
         <   1925bp   > |||||||||||||||||||||||||||||| <   2084bp   > ||||||||||||||||||||||||||||||||||||||
Target                  YACMMVFFLSNMIENQCMSTGAFEITLNDV                PVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHR
                        tgtaagtttaaaagactataggtgaatagg                cgttacgtgccctacccgcacgagaacagcagtacccc
                       tacgttttttgattaaagtccgctatctaa                tctgcatacgatcctaattattaaatatatatactcaag
                       ctatggtccgccgtgcgtgaatatgatatt                atggtggattttacgaattattctaggctgtgtacacta
                                                                                                            

Query   S
        |
Target  S
        t
        c
        a
         
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1036 ; UGA-SECIS: 1474

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782578|gb|CM001956.1|subseq(39963998,230600) Strand = - Positions = 98963 - 98889
 Found by:  Infernal (score=30.25) Covels (score=39.15)
 Stem2 length = 11   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -14.32

         ..(((((((.......(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..([((([(---(...{[[{(({(((((((((.............)))))))))}))}]]}.....-..))])))])..
 target  GUGACUGAC---AUUAUGAAGGCCUGUACUGAAGACAGCAAGCUGUUAGUACAGACCAGAUGCUUU-CUUGGCAGGCUC
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