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

 Blastx evalue: e-171
 Query name: gi|927120676|ref|XP_013931755.1| PREDICTED: type III iodothyronine deiodinase [Thamnophis sirtalis]
 Query range: 1-288  (total 288)

 Target: /data/www-rg/seblastian_results/593666952/tempfiles/temptarget.fasta
 Chromosome: ULFQ01000129.1:subseq_1422126,100788_ Strand: -
 Positions:
 -Exon 1  49973        50827

 Redox box: no

Query   MLHSVGAQTLQALSQVAAGVLLLPRFLLTAVMLWLLDFLCIRKKLLLTAAAAAAPGEEQELAAEDDGDSSDGTCPPDDPPLCVSDSNRMFTLESLKAVWH
        |||||||||||||||||| |||/||||||||||||||||||||||||   |||||||||||||| | |||||||||||||||||||||||||||||||||
Target  MLHSVGAQTLQALSQVAACVLLVPRFLLTAVMLWLLDFLCIRKKLLL--PAAAAPGEEQELAAE-DADSSDGTCPPDDPPLCVSDSNRMFTLESLKAVWH
        acctgggcatcgcacgggtgccgcctccaggactccgtctacaactc--cggggcgggcgtggg-gggtaggatccggccctgtgtacatacgtcaggtc
        ttactgcactactgatccgttttcgtttcctttgttattgtgaattt--ccccccgaaaatcca-acacgagcgccaacctgtcacagttctactactga
        gaccgccacgagccggcccgccgcccggctggcgcgttgccggacgg--cgggattggagggcg-cccgccgccggcctgccgccgccgcggggcacggc
                                                                                                            

Query   GQKLDFFKAAHVGATAPNPEVVQLDGRTRLRILDYARGKRPLILNFGSCTUPPFMARLRAFERLATRFVDIADFLLVYIEEAHPSDGWVSSDAAYDIPKH
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Target  GQKLDFFKAAHVGATAPNPEVVQLDGRTRLRILDYARGKRPLILNFGSCTUPPFMARLRAFERLATRFVDIADFLLVYIEEAHPSDGWVSSDAAYAIPKH
        gcacgttaggcgggagcacgggccggcacccacgtgcgaaccacatgatatcctagcccgtgccgactggaggttcgtagggcctggtgatgggtgacac
        gaatattaccatgccccacattataggcgtgttaacggagctttatgggcgccttcgtgctagtccgttatcattttataacaccaggtgcaccactcaa
        ggagctcgggcccgggccggccggcgcgggccgcccgcggggccccccccagccggcgcccgcgcgccgcccccggcccggtctcccgccgcccccccgc
                                                          *                                                 

Query   QCLQDRLRAAQLMKEGAPGCPLAVDTMDNASSAAYGAYFERIYIIQERKVIYQGGRGPEGYKISELRRWLDQYKSSLRAGPSTVIVQV
        ||||||||||||||||||||||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||||
Target  QCLQDRLRAAQLMKEGAPGCPLAVDTMDNASSAAYGAYFERIYIIQERKVMYQGGRGPEGYKISELRRWLDQYKSSLRAGPSTVIVQV
        cttcgcccggccaagggcgtccgggaagagtaggtggttgcataacgcagatcggcgcggtaatgcactcgctaaaccggcaagagcg
        agtaagtgccattaagccggctctactaaccgccagcatagtattaagattaaggggcagaatcatgggtaaaaggtgcgcgctttat
        gcagcggcatggggacggccggcgccgcccgtcccggccgccctcggggggcgccgccgccgccacgcgccgcgcccgcgccccccgg
                                                                                                
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 481 ; UGA-SECIS: 892

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = ULFQ01000129.1:subseq_1422126,100788_ Strand = - Positions = 49491 - 49413
 Found by:  Infernal (score=25.17) Covels (score=18.7)
 Stem2 length = 10   Apical loop length = 21   Insertion in stem2 = 0, 1
 Free Energy = -22.9

         ..(((((((.......(((((((((((((((...................)))))))).)))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC----cuuuuuggggcgggccag-gcCuGAUGuuuuuucaugaccggc
         ((((((((((--....([[{((((((((((.....................))))))).)))}]])..--...))))))))))
 target  CUAGCGUUUC--GUUAUGAUGACCGGUUUCGAAAUGGUUUUGGAGCGCCAGGAAACCGAGUCUGAAAU--UGGGAGAUGCUAG
                         ****           ^^^                            ****