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

 Blastx evalue: e-122
 Query name: gi|347360898|ref|NP_001117740.1| type II iodothyronine deiodinase [Oncorhynchus mykiss] >gi|16550970|gb|AAL25653.1| type II iodothyronine deiodinase [Oncorhynchus mykiss] >gi|16551140|gb|AAL25715.1| type II iodothyronine deiodinase [Oncorhynchus mykiss]
 Query range: 1-264  (total 264)

 Target: /data/www-rg/seblastian_results/729527008/tempfiles/temptarget.fasta
 Chromosome: CM007953.1:subseq_22471454,95559_ Strand: -
 Positions:
 -Exon 1  50003        50224
 -Exon 2  44987        45556

 Redox box: no

Query   MGAGSVDLLVTLQILPGFFSNCLFLALYDSVVLVKRLVSLLSCSGSGGGEWQRMLTSAGLRSIWNSFLLDAYKQ <---Intron---> VKLGFEAPNS
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   4446bp   > ||||||||||
Target  MGAGSVDLLVTLQILPGFFSNCLFLALYDSVVLVKRLVSLLSCSGSGGGEWQRMLTSAGLRSIWNSFLLDAYKQ                VKLGFEAPNS
        agggaggccgaccaccgtttatttcgctgtggcgaccgttcattgaggggtccacatggcctataatccggtac                gacgtggcat
        tgcggtatttctattcgttcagtttctaacttttagttcttggcgggggagagttcccgtgctgagtttacaaa                tatgtaccac
        gctccgcagctcgcgctcccctgccgcccggggggcagcagccgcccgagggcggcgagcgcagcccggtatag                tagttgaccc
                                                                                                            

Query   KVVKVPGSIRRRSSLTSTTGPHLGDECRLLDFESSDRPLVVNFGSATUPPFISHLPAFRRLVEEFSDVADFLLVYIDEAHPSDGWVAPAMGPRSFEVRKH
        |||||||||||/||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  KVVKVPGSIRRQSSLTSTTGPHLGDECRLLDFESSDRPLVVNFGSATUPPFISHLPAFRRLVEEFSDVADFLLVYIDEAHPSDGWVAPAMGPRSFEVRKH
        aggagcgaacccaataaaagcccgggtcccgtgttgcccggatgtgatcctaacccgtcccgggttggggtccgtagggcctggtggcgagccttggaac
        attatcggtggaggtcgccgcatgaaggttataccagctttatgcccgccttgatcctggttaatcatcattttataacaccaggtccctgcgctatgaa
        agcgtttccggaccgcccgcttcgcgccggccgggccttggcccgccaccccccgcccggggggcacgcccggccccgaccgcgggaccgcgcccgcggc
                                                       *                                                    

Query   RSLEERVVAAKKLIESFSLPSQCQLVADCMDNNANVAYGVSNERVCIVQRRKIAYLGGKGPFFYNLKDVRQYLEQSYGKR
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  RSLEERVVAAKKLIESFSLPSQCQLVADCMDNNANVAYGVSNERVCIVQRRKIAYLGGKGPFFYNLKDVRQYLEQSYGKR
        ctcggaggggaacagttacctctccgggtagaagaggtggtagagtagcaaaagtcggagctttacaggactcgcatgaa
        gctaagttccaattactgtccagattcagtaaacatcagtcaagtgttaggatcatggagcttaataatgaataagagag
        aagaaggggcgggtgcctgatgcgggcccgccttcgcctgccgggccgggggccctaggactcccggtgggtgagcccga
                                                                                        
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1323 ; UGA-SECIS: 1719

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007953.1:subseq_22471454,95559_ Strand = - Positions = 43663 - 43582
 Found by:  Infernal (score=22.71) Covels (score=27.7)
 Stem2 length = 8   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -16.26

         ..(((((((.........(((((((((((((((................)))))))))))))))..........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..(((({(((........{[[[{((((({(((..................)))})))))}]]]}......-..)))}))))..
 target  ACGGGGCUGGUGUGAGAAUGAAAACCACUGACUAAAGGGUUACUGACUCUGUUUGUGGUCGGAUGACAGA-CCUCACCUCCCU
                           ****           ^^^                        ****