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

 Blastx evalue: e-127
 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/307483547/tempfiles/temptarget.fasta
 Chromosome: CEMB01002674.1 Strand: -
 Positions:
 -Exon 1  99973        100839

 Redox box: no

Query   MLHSVGAQTLQALSQVAACVLLLPRFLLTAVMLWLLDFLCIRKKLLLTAAAAAAATLGEEQELAAEDGDSSEGTCPPDDPPLCVSDSNRMFTLESLKAVW
        /|||||| |||||||||||||||||||||||||||||||||||||||||| |           |     /|  | |||||||||||||||||||||||||
Target  LLHSVGAHTLQALSQVAACVLLLPRFLLTAVMLWLLDFLCIRKKLLLTAAPAGPGEEEAAAAEAEAAPAASGPTAPPDDPPLCVSDSNRMFTLESLKAVW
        ccctgggcatcgcacgggtgccccctccaggactctgtttacaacccaggcggcgggggggggggggcggagcagccggccctgtgtacatacgtcaggt
        ttactgcactactgatccgttttcgtttcctttgttattgtgaatttcccccgcgaaaccccacacccccggcccccaacctgtcacagttctactactg
        ggccgggccgacccggcccgcggccccggcggcgcgccgcccagccggcccggcagaggggaaaaaaaagccggctgccggccggcgccgcggggcgcgg
                                                                                                            

Query   HGQKLDFFKAAHVGATAPNPEVVQLDGRTRQRILDYARGKRPLILNFGSCTUPPFMARLRAFERLAARFVDIADFLLVYIEEAHPSDGWVSSDAAYDIPR
        ||||||||||||||| ||||||/|||||||/|||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||/||/
Target  HGQKLDFFKAAHVGAAAPNPEVIQLDGRTRRRILDYARGKRPLILNFGSCTUPPFMARLRAFQRLAARFVDIADFLLVYIEEAHPSDGWVSSDAAYEIPK
        cgcacgttaggcgggggcacggaccggcacccacgtgcgacccacatgatatcctagcccgtcccggctggaggtccgtagggcctggtgatgggtgaca
        agaatattaccatgccccacattataggcgggttaacggagctttatgggcgccttcgtgctagtccgttatcattttataacaccaggtgcaccaatca
        cggggcccgggccggggccggccggcggggcccgccgccggggccccccccagccgccgcccgcgccccccccccggcccgggcggccgccgccccgccg
                                                           *                                                

Query   HQCLQDRLRAAQLMKEGAPGCPLAVDTMDNASSAAYGAYFERLYIIQERKVMYQGGRGPEGYKISELRRWLDQYKSSLRAGPSTVVVQV
        |||||||||||||// |||||||||||||||||||||||||||||/||/ ||||||||||||||/||| |||/||| |/ |||||||||
Target  HQCLQDRLRAAQLLQAGAPGCPLAVDTMDNASSAAYGAYFERLYIVQEQVVMYQGGRGPEGYKIAELRSWLDRYKSRLQGGPSTVVVQV
        cctccgcccggccccgggcgtccgggaagagtaggtggttgcctagcgcggatcggcgcggtaaggccatcgctaacccggcaagggcg
        aagtaagtgccattacgccggctctactaaccgccagcatagtattaaatttaaggggcagaatcatgggtagaaggtaggcgctttat
        cgcggcggggggccgcccgccggccccgcccgccccgtccgcccccggggggcgcgcgcgccgccgcccgccgcgcccgcgcccgccgg
                                                                                                 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 742 ; UGA-SECIS: 1153

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CEMB01002674.1 Strand = - Positions = 99230 - 99156
 Found by:  Infernal (score=29.17) Covels (score=24.0)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 1
 Free Energy = -17.83

         ..(((((((.......(((((((((((((((...............)))))))).)))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccag-gcCuGAUGuuuuuucaugaccggc
         ((((((((((--....{[[{((((((((((.................))))))).)))}]]}..--...))))))))))
 target  CUAGUGUUUC--UGUGUGACGACCGGUUUUGAAAUGGCGAAUGCCAGGGAAUCGAGUCUGAUGU--ACCGAGACACUAG
                         ****           ^^^                        ****