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

 Blastx evalue: 4e-54
 Query name: gi|998709415|ref|XP_015492457.1| PREDICTED: type I iodothyronine deiodinase [Parus major]
 Query range: 1-247  (total 247)

 Target: /data/www-rg/seblastian_results/235354464/tempfiles/temptarget.fasta
 Chromosome: CM003718.2:subseq_26330195,101344_ Strand: +
 Positions:
 -Exon 1  48178        48511
 -Exon 2  50019        50162
 -Exon 3  51148        51347
 -Exon 4  51815        51877

 Redox box: no

Query   MMLGIRVFLQKILILLQVTLTVVVGKTLMILFPNAMKRYILKMGEKSRMNRNPKFSYENWGPTFFSFKYLQFVLKVKWKRLEDEAYEGHPAPNTPVVTLG
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  MMLGIRVFLQKILILLQVTLTVVVGKTLMILFPNAMKRYILKMGEKSRMNRNPKFSYENWGPTFFSFKYLQFVLKVKWKRLEDEAYEGHPAPNTPVVTLG
        aatgaagtccaacacccgacaggggaacaactcagaaatacaaggaaaaacacatatgatgcattatattctgcagataacggggtggccgcaacggacg
        tttgtgtttaatttttatctctttgactttttcactagattatgaaggtagacatgaaaggccttgtaatatttatagagtaaacaagacccaccttctg
        gggccgacagacgttggttgttttcaaggagccccgaaccaggtagcagcgtagcccacgcgttcccatgatggggggggggtaccgactcccgaggccc
                                                                                                            

Query   GEVCHVLDFMKD <---Intron---> NRPLILNFGSCTUPSFMLKFDEFNKLIKDFSSIADFLIIYIEEAHAVD <---Intron---> GWAFKNNI
        |||||||||||| <   1507bp   > |||||||||||||||||||||||||||||||||||||||||||||||| <   985bp    > ||||||||
Target  GEVCHVLDFMKD                NRPLILNFGSCTUPSFMLKFDEFNKLIKDFSSIADFLIIYIEEAHAVD                GWAFKNNI
        gggtcgcgtaag                acctacatgatatcttacatggtaacaagtataggtcaatagggcggg                gtgtaaaa
        gatgattatta                aagctttatgggcgcctttataataattaatgctcattttataacact                aggctaaat
        gattccgtcga                tcatacgttacccatatgaattgccgccatccaaatctccctgattaa                tagttactc
                                                *                                                           

Query   IIKNHRSLEDRKAAAQILQKNHPLCPVVLDTMENLSSSKYAALPERLYMLQGGKVLYK <---Intron---> GGVGPWNYHPQEIRAILEKLK
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   467bp    > |||||||||||||||||||||
Target  IIKNHRSLEDRKAAAQILQKNHPLCPVVLDTMENLSSSKYAALPERLYMLQGGKVLYK                GGVGPWNYHPQEIRAILEKLK
        aaaacaacggcagggcaccaaccctcggtgaagacaatatggccgcctaccggagcta                ggggctatcccgacgacgaca
        ttaaaggtaagacccattaaaactgctttactaatggcaacctcagtattaggattaa                ggtgcgaaacaatgcttaata
        ttatcactataataaattgatctgtagtactgacgctaactggaaaccgtaaggcccg                aaggcgtcccgaatccgaaga
                                                                                                       
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 484 ; UGA-SECIS: 850

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM003718.2:subseq_26330195,101344_ Strand = + Positions = 52362 - 52429
 Found by:  Infernal (score=33.05) Covels (score=21.35)
 Stem2 length = 8   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -14.04

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (((((((((---....{[[{(((({((((..........-----....))))}))))}]]}..--....)))))))))
 target  UGAGUAUUU---GUUAUGAUGGUCCCAGCAUAAAGCACU-----GGCGGCUGCGACCUGAUUC--UAGAAAAUAUUUA
                         ****           ^^^                       ****