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

 Blastx evalue: 5e-22
 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/756513734/tempfiles/temptarget.fasta
 Chromosome: LOCP02000395.1:subseq_794803,200000_ Strand: -
 Positions:
 -Exon 1  55883        56010
 -Exon 2  55211        55337
 -Exon 3  52455        52542
 -Exon 4  50000        50121

 Redox box: no

Query   MLFSCSVSUGYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYR <---Intron---> HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPTIWQWGQDN
        /|   ||||||||||||||||| |||||||||||||||||||| <   545bp    > ||||||||||||||||||||||||||||||||/||||||/|
Target  LLLFSSVSUGYRRVFEEYMRVIRQRYPDIRIEGENYLPQPIYR                HIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQEN
        ctcttagttgtacgtggtacgaacctcgacagggatccccata                cagttctgtacgtagtaaggagctgttgacgcaatctgcga
        ttttcgtcggaggttaaatgttgagacatgtagaaatcactag                atccttcttattttgttttgaactcttgtaccgtgaggaaa
        tgtccttcattgggtggcgattgggcaccctaagtcctaaat                acaatcgaccaaaaacaattcgttttctcgattccgagcaac
                *                                                                                           

Query   K <---Intron---> VYACMMVFFLSNMIENQCMSTGAFEITLND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPH
        | <   2668bp   > |||||||||||||||||||||||||||||| <   2333bp   > |||||||||||||||||||||||||||||||||||||
Target  K                VYACMMVFFLSNMIENQCMSTGAFEITLND                VPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPH
        a                gtgtaagtttaaaagactataggtgaatag                gcgttacgtgccctacccgcacgagaacagcagtacc
        a                tacgttttttgattaaagtccgctatcta                atctgcatacgatcctaattattaaatatatatactca
        g                ctatggtccgccgtgcgtggatatgatgt                tatggtggattctacgagttattctaggctgtgtacat
                                                                                                            

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

 Distance CDS-SECIS: 567 ; UGA-SECIS: 1005

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = LOCP02000395.1:subseq_794803,200000_ Strand = - Positions = 49432 - 49358
 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
                         ****                                     ****