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

 Blastx evalue: 5e-21
 Query name: gi|852788923|ref|XP_012885371.1| PREDICTED: selenoprotein T [Dipodomys ordii]
 Query range: 1-155  (total 155)

 Target: /data/www-rg/seblastian_results/788355928/tempfiles/temptarget.fasta
 Chromosome: NW_018336329.1:subseq_89422,65435_ Strand: +
 Positions:
 -Exon 1  29994        30121
 -Exon 2  31029        31155
 -Exon 3  33139        33226
 -Exon 4  35314        35435

 Redox box: no

Query   MLFSCSVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYR <---Intron---> HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPTIWQWGQDN
        /||  |||||||||||||||||||||||||||||/|||||/|| <   907bp    > |||||||||||/||||||||||||||||||||/||||||/|
Target  LLFFRSVSUGYRRVFEEYMRVISQRYPDIRIEGESYLPQPVYR                HIASFLSVFKLILIGLIIVGKDPFAFFGMQAPSIWQWGQEN
        ccttcagttgtacgtggtacgaacctcgacagggatccccgta                cagttctgtacatagtaaggagctgttgacgcaatctgcga
        ttttggtcggaggttaaatgttgagacatgtagagatcactag                atccttcttattttgttttgaactcttgtaccgtgaggaaa
        tatcctccaccgggtggcggtccggctcccagggccccgagc                acaatcgaccgcaaacaattcgttttctcgattccgggcaat
                *                                                                                           

Query   K <---Intron---> VYACMMVFFLSNMIENQCMSTGAFEITLND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPH
        | <   1983bp   > |||||||||||||||||||||||||||||| <   2087bp   > |||||||||||||||||||||||||||||||||||||
Target  K                VYACMMVFFLSNMIENQCMSTGAFEITLND                VPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPH
        a                gtgtaagtttaaaagactataggtgaatag                gcgttatgtgccctacccgcacgagaacagcagtacc
        a                tacgttttttgattaaagtccgctatcta                atctgcatacgatcctaattattaaatatatatactca
        g                ctatggaccgccgtgcgtgaatatgatgt                tatggtggattctacgagttattctaggctgtgtacac
                                                                                                            

Query   HRS
        |||
Target  HRS
        cct
        agc
        taa
           
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 616 ; UGA-SECIS: 1054

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = NW_018336329.1:subseq_89422,65435_ Strand = + Positions = 36052 - 36126
 Found by:  Infernal (score=31.45) Covels (score=38.5)
 Stem2 length = 12   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -21.02

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