_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: e-134
 Query name: gi|927115335|ref|XP_013919774.1| PREDICTED: type II iodothyronine deiodinase isoform X1 [Thamnophis sirtalis]
 Query range: 1-280  (total 280)

 Target: /data/www-rg/seblastian_results/667560816/tempfiles/temptarget.fasta
 Chromosome: ULFQ01000009.1:subseq_2948485,116340_ Strand: +
 Positions:
 -Exon 1  50000        50221
 -Exon 2  65768        66385

 Redox box: no

Query   MGLLSIDLLITLQILPVFFSNCLFLALYDSVVLLKHMVLLLSCSKAARGEWRRMLTSEGLRCVWNSFLLDAYKQ <---Intron---> VKLGGDAPNS
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <  15546bp   > |||||/||||
Target  MGLLSIDLLITLQILPVFFSNCLFLALYDSVVLLKHMVLLLSCSKAARGEWRRMLTSEGLRCVWNSFLLDAYKQ                VKLGGEAPNS
        agttaagctaaccaccgtttatctcgctgtggctacagcccattaggcggtcaacatggtctgtaatccggtac                gatggggcat
        tgttgtatttctattctttcagtttctaacttttaatttttggcaccggagggttccagtggtgagtttacaaa                tatggaccac
        gcgactcggcatgcggttcccctcccctcggccggcggttgtccgtatcagaggcaagcacccgtctcatccgg                gagtaatttc
                                                                                                            

Query   NVIHIPNGTAESSSNCRWKSSMGKYGSECHLLDFAKSDRPLVINFGSATUPPFTNQLSAFGKLVEEFSSVADFLLVYIDEAHPSDGWAAPGISSSFEVKK
        |||||||||||||||||||||||||||||||||||||/||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  NVIHIPNGTAESSSNCRWKSSMGKYGSECHLLDFAKSERPLVINFGSATUPPFTNQLSAFGKLVEEFSSVADFLLVYIDEAHPSDGWAAPGISSSFEVKK
        agacacagaggaaaatataatagatgagtcctgtgatgcccgaatgtgatcctaacctgtgatgggttagggtctgtagggcctggtggcgattttggaa
        attatcagccagggagggagctgaaggagattatcacagctttatgcccgcctcaatcctgattaatcgtcattttataacaccaggcccgtccctataa
        ttccatttttacccccagaccgaatatactcactcaagcatacctgatcatccacggtctcgggagcttgtctgaccttgtcaatcgttttcatatacga
                                                         *                                                  

Query   HRNQEDRCAAAHQLLKKFSLPPQCQIVADCMDNNANVAYGVSFERVCIIQRQKIAYLGGKGPFFYNLQEVRLWLEQNFRKRUNPNVPDKNSRGLSF
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/||| ||||||
Target  HRNQEDRCAAAHQLLKKFSLPPQCQIVADCMDNNANVAYGVSFERVCIIQRQKIAYLGGKGPFFYNLQEVRLWLEQNFRKRUNPNLPDKKSRGLSF
        caacggatgggccccaatttccctcagggtagaagaggtggttgcgtaacacaagtcggagctttaccggcctcgcataaatacatcgaatagctt
        agaaaaggcccaattaatctccagattcagtaaacatcagtctagtgttagaatcatggagcttaataatgtgtaaatgaggacatcaaacggtct
        tgcaacattttcgtagattgaagcgagttcgcttctgttacctgtactaaaaattcgggacctccttagtatgggaccgaaatataatggaaagct
                                                                                         *              
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1414 ; UGA-SECIS: 1456

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = ULFQ01000009.1:subseq_2948485,116340_ Strand = + Positions = 67800 - 67884
 Found by:  Infernal (score=16.54) Covels (score=16.96)
 Stem2 length = 12   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -9.95

         ..(((((((..................((((((((((.(((((...............))))).))))))))))........)))))))..
 model   uucggucaugcg-----------UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc
         ..((((({((.................([[{((((((((((((.....-.........))))))))))))}]])----..-))})))))..
 target  UGUAUUGGAUCACAGAAGGAACAAUCAUGAGGACAUUACCUUGCAUUC-UUUCUGCACUGAGGUAAUGUCGGAG----CA-AUGUAAUGAA
                                    ****                                       ****