_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:3     SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: 4e-29
 Query name: gi|144953869|ref|NP_001039579.2| selenoprotein S [Bos taurus] >gi|172045703|sp|Q2KI76.2|SELS_BOVIN RecName: Full=Selenoprotein S; Short=SelS; AltName: Full=VCP-interacting membrane protein >gi|296475585|tpg|DAA17700.1| TPA: selenoprotein S [Bos taurus]
 Query range: 1-190  (total 190)

 Target: /data/www-rg/seblastian_results/89059383/tempfiles/temptarget.fasta
 Chromosome: KZ836350.1:subseq_19789446,103423_ Strand: -
 Positions:
 -Exon 1  56809        56884
 -Exon 2  55964        56098
 -Exon 3  53396        53502
 -Exon 4  49865        50033
 -Exon 5  47420        47502

 Redox box: no

Query   MERDGDQLSARPTLETEGLRFLHVTV <---Intron---> GSLLATYGWYIVFSCILLYVVFQKLSTRLRALRQRHLDQAAAALE <---Intron--
        |||||  ||||| ||||| |/||||| <   710bp    > ||||||||||||||||||||||||||||||||||| ||/||||/| <   2461bp  
Target  MERDGQLLSARPALETEGFRYLHVTV                GSLLATYGWYIVFSCILLYVVFQKLSTRLRALRQRQLDRAAAAVE             
        agcggccctgccgcgaggtctccgag                gtccgatgttagtatacctggtcactaccagtacaccgcgggggg             
        tagagattccgcctacagtgatatc                tgcttccaggatttggtttatttaatccgtgctgagatagcccct              
        gggcggggcgggcgggggtccgccg                gccgactccgccccccctccggtggtccgggcgaggggcatattg              
                                                                                                            

Query   -> PDIVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ <---Intron---> LEEEKRRQKIEMWDSMQEGKSYKGNTRKPQEEDSPGPSTSSVIPKR
         > ||/|||||||||||||||||||||||||||||||| <   3362bp   > |||/|||||||||||||||||||| |||| ||||||||||||/| |
Target     PDVVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ                LEEQKRRQKIEMWDSMQEGKSYKGPTRKPPEEDSPGPSTSSVLPNR
           cggggaccggtgggctaacggtagcggacagacac                cggcaaacaagatgaacggaatagcaaaccgggacgctattgccac
          acatttagaactcccgtataaatacataaaaaatga                taaaaggaatatgagtaagagaagccgaccaaagcgcccccttcag
          acttttaaggtaatttgagaaaataatagtgaaaag                taaaagaggtaggccgaagatcaataagtcaacttgtttagcgaca
                                                                                                            

Query   KSDRKPLRGGG <---Intron---> YNPLSGEGGGTCSWRPGRRGPSSGGUG
        ||||||||||| <   2362bp   > |||||||||| ||||||||||||||||
Target  KSDRKPLRGGG                YNPLSGEGGGACSWRPGRRGPSSGGUG
        atgaacccggg                tacttggggggtttacgcagcttggtg
        acagactggg                gaactcgagggcgcggcggggcccgggg
        atcggtggat                tccggttaatacctgatacacgagtaac
                                                            * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 349 ; UGA-SECIS: 352

------- SECIS element -- id:3 -- grade:A ----
 Chromosome = KZ836350.1:subseq_19789446,103423_ Strand = - Positions = 47070 - 46991
 Found by:  Infernal (score=24.28) Covels (score=41.01) SECISearch1.0 (pattern=default)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -6.59

         ..(((((((.........(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .(({((({(.........{[[{(({{(((((((.................)))))))}}))}]]}..--....)})))})).
 target  GUGACAGGUUGCGUUGAAUGAUGUCUUCCUUGUAAAUGGUGAGCCCACCAGCGAGGAUUACUGAUGC--AGACAGUUGAUGG
                           ****           ^^^                         ****