_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
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 Blastx evalue: 2e-54
 Query name: gi|823464937|ref|XP_012430774.1| PREDICTED: type I iodothyronine deiodinase-like [Taeniopygia guttata]
 Query range: 1-225  (total 225)

 Target: /data/www-rg/seblastian_results/965063916/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  52944        53274
 -Exon 2  51284        51427
 -Exon 3  50024        50223

 Redox box: no

Query   MSGIRVVLQKILILLQVSLSVVVGKTLMILFPNAMKRYILKMGEKSRMNQNPKFSYENWGPTFFSFKYLQFVLKVKWKRLEDEAYEGHPAPNTPVVTLGG
        ||||||/|||| |||||/||||||||/||||||||||||||||||||||/||||||||||||||||||||||||||||||||||||| |||||||||| |
Target  MSGIRVLLQKIXILLQVTLSVVVGKTMMILFPNAMKRYILKMGEKSRMNKNPKFSYENWGPTFFSFKYLQFVLKVKWKRLEDEAYEGQPAPNTPVVTLSG
        atgaagcccaanacccgactggggaaaaactcagaaatacaaggaaaaaaacatatgatgcattatattctgcagataacggggtggccgcaacggacag
        tcgtgtttaatttttatctctttgactttttcactagattatgaaggtaaacatgaaaggccttgtaatatttatagagtaaacaagacccaccttctgg
        gaccgggagacgctggttgttggcaaggagcctcgaaccaggcagcagcgtagcccacgccttcccgtggtggggggggggtaccgagttccnaggcccg
                                                                                                            

Query   EVCHLLDFMKD <---Intron---> NRPLILNFGSCTUPSFMLKFDEFNKLIKDFSSIADFLIIYIEEAHAVD <---Intron---> GWAFKNNVI
        |||||||| || <   1516bp   > ||||||||||||||||||||||||/||||||||||||||||||||||| <   1060bp   > |||||||||
Target  EVCHLLDFXKD                NRPLILNFGSCTUPSFMLKFDEFNQLIKDFSSIADFLIIYIEEAHAVD                GWAFKNNVI
        ggtcccgtnag                acctacatgatatcttacatggtaccaagtataggtcaatagggcggg                gtgtaaaga
        atgattatta                aagctttatgggcgcctttataataattaatgctcattttataacact                aggctaaatt
        attccgtcga                tcatacgctacccatatgaattgccgccatccaaatctccctgattaa                tagttactct
                                               *                                                            

Query   IKNHRSLEDRKIAAQFLQKSHPLCPVVLDTMENLSSSKYAALPERLYVLQGGKVIYR
        ||||||||||||||||||//|||||||||||||||||||||||||||/||||||||/
Target  IKNHRSLEDRKIAAQFLQENHPLCPVVLDTMENLSSSKYAALPERLYMLQGGKVIYK
        aaacaacggcaaggctccgaccctcggtgaagacaatatggccgcctaccggagata
        taaaggtaagatccattaaaactgctttactaatggcaacctcagtattaggattaa
        tatcactataataaattgatctatagtactgacgctaactggagaccgggaggcccg
                                                                 
 Sequence until next stop: 
GTAAAAATATCAGCACCAATGAGCACAGGGTACAGAGATTCTTAA
 V  K  I  S  A  P  M  S  T  G  Y  R  D  S  * 

 Distance CDS-SECIS: 1026 ; UGA-SECIS: 1329

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 48997 - 48930
 Found by:  Infernal (score=35.94) Covels (score=26.08)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -15.7

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (((((((((---....{[[{(((({(((((.........-----...)))))}))))}]]}..--....)))))))))
 target  UGAAUAUUU---GUUAUGAUGGUCCCAGCUUAAANCACU-----GGUGGCUGUGACCUGAUUC--UAGAAAAUAUUUA
                         ****           ^^^                       ****