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

 Blastx evalue: e-169
 Query name: gi|929422743|ref|XP_005534729.2| PREDICTED: type III iodothyronine deiodinase [Pseudopodoces humilis] >gi|929446211|ref|XP_005498001.2| PREDICTED: type III iodothyronine deiodinase [Zonotrichia albicollis] >gi|930231625|ref|XP_005431762.2| PREDICTED: type III iodothyronine deiodinase [Geospiza fortis] >gi|959049526|ref|XP_014727444.1| PREDICTED: thyroxine 5-deiodinase [Sturnus vulgaris] >gi|998697921|ref|XP_015486574.1| PREDICTED: thyroxine 5-deiodinase [Parus major] >gi|1020981260|ref|XP_005063161.2| PREDICTED: thyroxine 5-deiodinase [Ficedula albicollis]
 Query range: 1-274  (total 274)

 Target: /data/www-rg/seblastian_results/976825418/tempfiles/temptarget.fasta
 Chromosome: CM003715.1:subseq_51026976,100497_ Strand: +
 Positions:
 -Exon 1  49715        50536

 Redox box: no

Query   MLHSVGVHTLQLLTQAAACILLFPRFLLTAVMLWLLDFLCIRKKMLTMPTAEEAASASEEPPPDDPPVCVSDSNRMFTLESLKAVWHGQKLDFFKSAHVG
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  MLHSVGVHTLQLLTQAAACILLFPRFLLTAVMLWLLDFLCIRKKMLTMPTAEEAASASEEPPPDDPPVCVSDSNRMFTLESLKAVWHGQKLDFFKSAHVG
        acctgggcatcccacgggtacctcctccaggactccgtctaaaaacaacagggggagaggcccggccgtgtgtacatacgtcaggtcgcacgttatgcgg
        ttactgtactattcacccgttttcgtttcctttgttattgtgaattctcccaaccgcgaacccaacctgtcacagttctactactgagaatattaccatg
        gccccctccgggctggcccccatcccgcccggcgcgttgctgggggggcgggggccccgggcccccgccgcccccgcgggggacggcggggcccgggcgt
                                                                                                            

Query   SLAPNPEVIQLDGQKRLRILDFARGKRPLILNFGSCTUPPFMARLRSFQRLAAHFVDIADFLLVYIEEAHPSDGWVSSDAAYNIPKHQCLQDRLRAAQLM
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  SLAPNPEVIQLDGQKRLRILDFARGKRPLILNFGSCTUPPFMARLRSFQRLAAHFVDIADFLLVYIEEAHPSDGWVSSDAAYNIPKHQCLQDRLRAAQLM
        ttgcacggaccggcaaccacgtgcgaaccacatgatatcctagccattcccggctggaggtccgtagggcctggtgatgggtaacacctccgaccggcca
        ctccacattatagaagtgttatcggagctttatgggcgccttcgtgctagtccattatcattttataacaccaggtgcaccaatcaaagtaagtgccatt
        cgctccggcggcggggcccgcccccgaccccccccccacgcgccggccgcgcgccgctcccgggccaaacccccgccgtacccccgcgccgcgggatggg
                                             *                                                              

Query   REGAPDCPLAVDTMDNASSAAYGAYFERLYIIQEEKVMYQGGRGPEGYKISELRSWLDQYKTRLQSPSTVVIQV
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  REGAPDCPLAVDTMDNASSAAYGAYFERLYIIQEEKVMYQGGRGPEGYKISELRSWLDQYKTRLQSPSTVVIQV
        agggcgtccgggaagagtaggtggttgactaacggagatcggagcggtaatgcaatcgctaacccacaaggacg
        gagccagctctactaaccgccagcatagtattaaaattaaggggcagaatcatgggtaaaacgtagcgctttat
        gaggttccgcgccgcttccccctcccggccctggggggcgacaaagccgcggggcgacgcacgcgcccggccag
                                                                                  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 436 ; UGA-SECIS: 844

------- SECIS element -- id:1 -- grade:B ----
 Chromosome = CM003715.1:subseq_51026976,100497_ Strand = + Positions = 50973 - 51053
 Found by:  Infernal (score=31.53) Covels (score=12.65)
 Stem2 length = 10   Apical loop length = 23   Insertion in stem2 = 0, 1
 Free Energy = -13.2

         ..(((((((.......(((((((((((((((.....................)))))))).)))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC------cuuuuuggggcgggccag-gcCuGAUGuuuuuucaugaccggc
         (((((((((.--....{[[{((((((((((.......................))))))).)))}]]}..--....)))))))))
 target  CUAGUAUUUC--UUUGUGAUGACCGAUUUUGAAAUGGGUUUCUCUAAUGCCAGGAAAUCGCGUCUGAUGU--UGUCAAAUACUAG
                         ****           ^^^                              ****