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

 Blastx evalue: 8e-24
 Query name: gi|168693656|ref|NP_001108227.1| selenoprotein S [Macaca mulatta]
 Query range: 1-190  (total 190)

 Target: /var/www/seblastian_output/627913407/tempfiles/temptarget.fasta
 Chromosome: gi|511782564|gb|CM001970.1|subseq(19629328,202995) Strand: -
 Positions:
 -Exon 1  102920       102995
 -Exon 2  102123       102257
 -Exon 3  100838       100944
 -Exon 4  100175       100264
 -Exon 5  100002       100080
 -Exon 6  98328        98410

 Redox box: no

Query   MEREEDSLSARPALETEGLRFLHVTV <---Intron---> GSLLASYGWYIVFSCILLYVVFQKLSARLRALRQRQLERAAASVE <---Intron--
        |||||||||||||||||||||||||| <   662bp    > ||||||||||||||||||||||||||||||||||||||||||||| <   1178bp  
Target  MEREEDSLSARPALETEGLRFLHVTV                GSLLASYGWYIVFSCILLYVVFQKLSARLRALRQRQLERAAASVE             
        agcgggtttgccgcgaggcctccgag                gttcgatgttagtatacctggtcactgccagtacaccgcgggtgg             
        tagaaactccgcctacagtgttatc                tgcttcgaggatttggtttatttaatccgtgctgagatagccccta             
        gggagtcgcgggcggcgagccgccg                gctggcctcgccccccctccgctggtccggacgggggggatgttga             
                                                                                                            

Query   -> PDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQL <---Intron---> EEEKRRQKIEMWDSMQEGKSYKGNAKKPQE <---Intron--->
         > |||||||||||||||||||||||||/|||||||||| <   573bp    > |||||||||||||||||||||||||||||| <    94bp    >
Target     PDVVVKRQEALAAARLKMQEELNAQIEKHKEKLKQL                EEEKRRQKIEMWDSMQEGKSYKGNAKKPQE               
           cggggaccggtgggctaacggcagcagacagacacc                gggaaacaagatgaacggaatagagaaccg               
           catttagaactcccgtataaatacataaaaaataat                aaaaggaatatgagtaagagaagacaacaa               
           tttttaaaataattagagaaaatgatagtgaagag                taaaagaggtaggccgaacatcaataggtgg               
                                                                                                            

Query    EDSPGPSTSSVVVKRKSDRKPLRGGGY <---Intron---> NPLSGEGGGSCSWRPGRRGPSSGGUS
         ||||||||||||||||||||||||||| <   1591bp   > ||||||||||||||||||||||||||
Target   EDSPGPSTSSVVVKRKSDRKPLRGGGY                NPLSGEGGGSCSWRPGRRGPSSGGUS
         ggacgctattgggacatgcactcgggt                acttgggggatttacgcagcttggta
         aagcgccccctttagacagactgggg                aactcgagggggcggcggggcccgggg
         acttgtctatccgagagcagggggtt                tctgttaatacccgatacacaattaac
                                                                            * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 350 ; UGA-SECIS: 353

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|511782564|gb|CM001970.1|subseq(19629328,202995) Strand = - Positions = 97977 - 97898
 Found by:  Infernal (score=19.41) Covels (score=36.61)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -4.79

         ..(((((((.........(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(({((({(.........{[[{(({{(((((((.................)))))))}}))}]]}..--....)})))})).
 target  GUGACAGGUUGCGUUGAAUGAUGUCUUCCUUAUCAAUGGUGAGCCCACCAGUGAGGAUUACUGAUGU--GGACAGUUGAUGG
                           ****            ^^                         ****