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

 Blastx evalue: 4e-24
 Query name: gi|301601637|ref|NP_001180421.1| selenoprotein J [Oryzias latipes]
 Query range: 196-339  (total 340)

 Target: /data/www-rg/seblastian_results/562828455/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  170          293
 -Exon 2  560          637
 -Exon 3  796          935
 -Exon 4  1136         1225

 Redox box: no

Query   AARFLEHFILNGADPGALEAVLNQLNDLKRKQPQDLDKAVVG <---Intron---> HIHQVKEHLSKTPQEIIPTVFPNTUG <---Intron---> 
        / ||||||||||/|| ||/ ||/||||  |||||||||||/| <   266bp    > || ||||/|||||/|/|||||||||| <   158bp    > 
Target  SPRFLEHFILNGSDPKALDTVLHQLNDPNRKQPQDLDKAVIG                HILQVKENLSKTPKELIPTVFPNTUG                
        tcatcgctacagtgcagtgagccccagcaaacccgcgaggag                caccgagattaacagcacagtcaatg                
        ccgttaatttagcacactacttaataacagaacaataactt                gattataaatcaccaattccttcacg                g
        tcgcggtccgttttaacgcagctgttcgcaggagtgcagct                gcttggggtacgtcagacctgtacaa                t
                                                                                          *                 

Query   LPGAFQAALHGVLTAKNFETAVRDTMSCGGCTCSRGSFIGACLGAQ <---Intron---> VGLEGIPASWREKTLRYNSVLEHAKKITKH
        |||||||||||||||| /| |||||||||||||||||||||||||| <   200bp    > /| ||||/||  |||||/||||||||||||
Target  LPGAFQAALHGVLTAKQYEQAVRDTMSCGGCTCSRGSFIGACLGAQ                IGFEGIPSSWASKTLRYDSVLEHAKKITKH
        tcggtcggccggcagactgcggagaaatggtataagttaggtcggc                agtggactttgtaacctgtgtgcgaaaaac
        tcgctacctagttccaaaaactgactgggggcggggcttgcgtgca                tgtagtcccgccactgaacttaacaatcaa
        gatgcaaggcacgacggcggtcaccgctgacctcaacccgcttttg                tatgatatcgacatgatcagggccggatac
                                                                                                    
 Sequence until next stop: 
CACCAGTAG
 H  Q  * 

 Distance CDS-SECIS: 85 ; UGA-SECIS: 316

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 1311 - 1377
 Found by:  Infernal (score=29.07) Covels (score=25.14)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -12.22

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({((((---....{[[{((((((((((..........-----...))))))))))}]]}..--.--.))))})...
 target  ACAGAACAG---UGAAUGAAGGUUUUUGUCUAAACUGUUA-----GACGGCAGGAGCCAGAUGU--U--UUUGUCUCUG
                         ****           ^^^                        ****