_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:3     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/968245476/tempfiles/temptarget.fasta
 Chromosome: KZ836210.1:subseq_102694526,100131_ Strand: -
 Positions:
 -Exon 1  50689        50816
 -Exon 2  50003        50129
 -Exon 3  47639        47726
 -Exon 4  45393        45514

 Redox box: no

Query   MLFSCSVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYR <---Intron---> HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPTIWQWGQDN
        /|| ||||||||||||||||||||||||||||||||||||||| <   559bp    > ||||||||||||||||||||||||||||||||/||||||/|
Target  LLFFCSVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYR                HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQEN
        cttttagttgtacgtggtacgaacctcgacagggatccccata                cagttctgtacgtagtaaggagctgttgacgcaatctgcga
        ttttggtcggaggttaaatgttgagacatgtagaaatcactag                atccttcttattttgttttgaactcttgtaccgtgaggaaa
        tatccttcattgggtggcggtacggcaccctaaatcctacat                acagtcgaccaaaaacaattcgttttctcgattccgggtaat
                *                                                                                           

Query   K <---Intron---> VYACMMVFFLSNMIENQCMSTGAFEITLND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPH
        | <   2276bp   > |||||||||||||||||||||||||||||| <   2124bp   > |||||||||||||||||||||||||||||||||||||
Target  K                VYACMMVFFLSNMIENQCMSTGAFEITLND                VPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPH
        a                gtgtaagtttaaaagactataggtgaatag                gcgttacgtgccctacccgcacgagaacagcagtacc
        a                tacgttttttgattaaagtccgctatcta                atctgcatacgatcctaattattaaatatatatactca
        g                ctatggtccgccgtgcgtgaatatgatgt                tgtggtggattccacgagttattctaggctgtgtacat
                                                                                                            

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

 Distance CDS-SECIS: 562 ; UGA-SECIS: 1000

------- SECIS element -- id:3 -- grade:A ----
 Chromosome = KZ836210.1:subseq_102694526,100131_ Strand = - Positions = 44830 - 44756
 Found by:  Infernal (score=30.25) Covels (score=39.15) SECISearch1.0 (pattern=default)
 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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