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

 Blastx evalue: 0.0
 Query name: gi|984143962|ref|XP_015332391.1| PREDICTED: thyroxine 5-deiodinase [Marmota marmota marmota]
 Query range: 1-302  (total 303)

 Target: /data/www-rg/seblastian_results/836164525/tempfiles/temptarget.fasta
 Chromosome: QVIC01000918.1: Strand: -
 Positions:
 -Exon 1  50000        50902

 Redox box: no

Query   MPRQAASRLVVGEGEGPPGASGPTATMLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHFLGRRRRQPEPEVELNSEGEEVPPDDPPIC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
Target  MPRQAASRLVVGEGEGPPGASGPTATMLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHFLG-RRRQPEPEVELNSEGEEVPPDDPPIC
        acccggtctgggggggccggtgcagaacctcccctcactgcagttcgctcctcgagtactccgtctacactcg-cccccgcgggcaagggggccggccat
        tcgacccgtttgagagccgccgccccttgctttactgtgcacccgttttcgttgcctttgttattgtgaattg-gggacacatatagagaatccaacctg
        gtcgccggggcaacggcggcggcgccgcccggtccggctcgccgccgccgccacgccgcgccccgcccgtcgc-cccgcacaggcttgcgggccccaccc
                                                                                                            

Query   VSDDNRLCTLASLKAVWHGQKLDFFKQAHEGGPAPNSEVVLPEGFRSQRILDYAQGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEA
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  VSDDNRLCTLASLKAVWHGQKLDFFKQAHEGGPAPNSEVVLPEGFRSQRILDYAQGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEA
        gtggacctacgtcaggtcgcatgttacgcgggcgcatgggccggtcaccatgtgcgacccgcatgatatcctagcaagtcccgaatccgggtcaataggg
        tcaaagtgctcctactgagaatattaacaaggcccacatttcagtggagttaacagagctttatgggcgccttcgtgctagttcaaagatattttataac
        gcccccgccgggcgcggtcgggtccggacgcaagccgggcgtgccgcgccactcagccaggctcccccaagcggcgcccgtgccgcgcccctcccctgaa
                                                                            *                               

Query   HPSDGWITTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGTRP
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  HPSDGWITTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGTRP
        cctggtaaagtctaaccccacggcgaggagcccggcgtgcgcgaagataatgtggttgcctgacagaaatcggcgcggtcgtgccatcgctggctcgacc
        accaggtccaccattcaaggtaagtgccgttaagccggctttactcacggccagcatagtattaggcttaaggggcagaatcatgcgtagaaaatagcgc
        ttcccgccaccgcctcacgcggcgccaaggggataaccagcgccgctccctatccccgcccccgttccgcgactcatccgcaggctgggcttgggcctgc
                                                                                                            

Query   RR
        ||
Target  RR
        cc
        gg
        tg
          
 Sequence until next stop: 
TTTTAA
 F  * 

 Distance CDS-SECIS: 543 ; UGA-SECIS: 942

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = QVIC01000918.1: Strand = - Positions = 49456 - 49387
 Found by:  Infernal (score=18.39) Covels (score=28.11)
 Stem2 length = 8   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -13.63

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(({[(((---(...([[{(({((({(((.................)))})))}))}]])----..-))))]}))..
 target  GCCCCACUG---CUGAUGACGAACUAUCUCUAACUGGUCUUGACCACGAGCUGGCUCCGAA----CU-GCAGGAGGCU
                         ****           ^^                        ****