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

 Blastx evalue: e-144
 Query name: gi|1002602070|ref|XP_015680165.1| PREDICTED: thyroxine 5-deiodinase [Protobothrops mucrosquamatus]
 Query range: 1-289  (total 289)

 Target: /data/www-rg/seblastian_results/685150299/tempfiles/temptarget.fasta
 Chromosome: SJPD01000003.1:subseq_52409709,100818_ Strand: +
 Positions:
 -Exon 1  49952        50842

 Redox box: no

Query   MLHSVGAQTLQALSQVAACVLLLPRFLLTAVMLWLLDFLCIRKKLLLT---AAAAAAATLGEE--QELAAEDG-DSSEGT-CPPDDPPLCVSDSNRMFTL
        ||||/|| | ||| |||||||||||||||| |||||||||||||||||   ||||||| / ||  /|  | || ////|   ||||||||||||||||||
Target  MLHSLGAHTWQALGQVAACVLLLPRFLLTAAMLWLLDFLCIRKKLLLTATAAAAAAAAAVTEEGAREREAADGEEAADGAGSPPDDPPLCVSDSNRMFTL
        acctcggcatcgcgcgggtgccccctccaggactccgtctacaacccagaggggggggggaggggcgcgggggggggggggtccggccctgtgtacatac
        ttactgcacgactgatccgttttcgtttcccttgttattgtgaatttcccccccccccctcaagcgagaccagaaccagcgcccaacctgtcacagttct
        ggcggcgccgggccggcccggggcccgggcggcgcgtcgctcggggggggggggggggcgcgggcggggggcgagggccccctccctggcgccgccgcgg
                                                                                                            

Query   ESLKAVWHGQKLDFFKAAHVGATAPNPEVVQLDGRTRQRILDYARGKRPLILNFGSCTUPPFMARLRAFERLAARFVDIADFLLVYIEEAHPSDGWVSSD
        |||||||||||||||||||||| ||||||/||||||| |||||||||||||||||||||||||||||||||||| |||/|||||||||||||||||||||
Target  ESLKAVWHGQKLDFFKAAHVGAAAPNPEVIQLDGRTRTRILDYARGKRPLILNFGSCTUPPFMARLRAFERLAAGFVDVADFLLVYIEEAHPSDGWVSSD
        gtcaggtcgcacgttaggcgggggcacggaccggcacacacgtgcgacccacatgatatcctagcccgtgccgggtgggggtccgtagggcctggtgatg
        actactgagaatattaccatgccccacattataggcgcgttaacggagctttatgggcgccttcgtgctagtccgttatcattttataacaccaggtgca
        ggcgcggcgaggcccgggccggggccggccggcgggggccgccgccggggccccccccagccgccgcccgcgcgccgcgcccggcccgggcgcccgccgc
                                                                  *                                         

Query   AAYDIPRHQCLQDRLRAAQLMKEGAPGCPLAVDTMDNASSAAYGAYFERLYIIQERKVMYQGGRGPEGYKISELRRWLDQYKSS-LRAGPSTVVVQV
        ||||||/||||||||||||||/ |||||||||||||||||||||||||||||/|||||/|||||||||||||||| |||||/|  |/ |||||||||
Target  AAYDIPKHQCLQDRLRAAQLMQRGAPGCPLAVDTMDNASSAAYGAYFERLYIVQERKVVYQGGRGPEGYKISELRHWLDQYRSRLLQGGPSTVVVQV
        ggtgacacctccgcccggccaccggcgtccgggaagagtaggtggttgcctagcgaaggtcggcgcggtaatgcactcgctaaccccggcaagggcg
        ccaatcaaagtaagtgccattaggccggctctactaaccgccagcatagtattaagattaaggggcagaatcatgagtaaagggttaggcgctttat
        ccccccgcgcggcagggggcggacggccggccccgcccgccccggccgcccccggggggcgcccgcgccgccacgcgacgcgcccggcgccggccgg
                                                                                                         
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 622 ; UGA-SECIS: 1036

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SJPD01000003.1:subseq_52409709,100818_ Strand = + Positions = 51465 - 51544
 Found by:  Infernal (score=26.63) Covels (score=17.44)
 Stem2 length = 10   Apical loop length = 22   Insertion in stem2 = 0, 1
 Free Energy = -16.75

         ..(((((((.......(((((((((((((((....................)))))))).)))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-----cuuuuuggggcgggccag-gcCuGAUGuuuuuucaugaccggc
         ((((((((((--....{[[{((((((((((......................))))))).)))}]]}..--...))))))))))
 target  CUAGUGUUUC--UUUGUGAUGACCGGUUUUGAAAUGGUGACUGCAAUGCCAGGAAAUCGAGUCUGAUGU--UCUGAGAUACUAG
                         ****           ^^^                             ****