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

 Blastx evalue: 1e-23
 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/50092001/tempfiles/temptarget.fasta
 Chromosome: NW_018334967.1:subseq_229490,66461_ Strand: -
 Positions:
 -Exon 1  37080        37155
 -Exon 2  36314        36448
 -Exon 3  34142        34248
 -Exon 4  30181        30270
 -Exon 5  30002        30080
 -Exon 6  28104        28186

 Redox box: no

Query   MERDGDQLSARPTLETEGLRFLHVTV <---Intron---> GSLLATYGWYIVFSCILLYVVFQKLSTRLRALRQRHLDQAAAALE <---Intron--
        |||||||||||| || |||||||||| <   631bp    > ||||||||||||||||||||||||||||||||||||||||||||| <   2065bp  
Target  MERDGDQLSARPALEAEGLRFLHVTV                GSLLATYGWYIVFSCILLYVVFQKLSTRLRALRQRHLDQAAAALE             
        agcgggcctgccgcggggcctccgag                gtccgatgttagtatacctggtcactactagtacactgcggggcg             
        tagagaatccgcctacagtgttatc                tgcttccaggatttggtttatttaatccgtgctgagataacccct              
        gggcgtggcggccggcgggtctccg                gccggctccgccccccctccgctggtccggggggggcatatcttg              
                                                                                                            

Query   -> PDIVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ <---Intron---> LEEEKRRQKIEMWDSMQEGKSYKGNTRKPQ <---Intron---> 
         > ||/|||||||||||||||||||||||||||||||| <   3871bp   > |||||||||||||||||||||||||||||| <   100bp    > 
Target     PDVVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ                LEEEKRRQKIEMWDSMQEGKSYKGNTRKPQ                
           cggggaccggtgggctaacggtagcggacagatac                cgggaaacaagatgaacggaatagaaaacc                
          acatttagaactcccgtataaatacataaaaaatga                taaaaggaatatgagtaagagaagacgaca                
          atttttagggtaatttgagaaggtaataatagaaag                taaaagaggtaggtcgaaaattaataagtg                
                                                                                                            

Query   EEDSPGPSTSSVIPKRKSDRKPLRGGG <---Intron---> YNPLSGEGGGTCSWRPGRRGPSSGGUG
        ||||||||||||||||||||||||||| <   1815bp   > |||||||| ||||||||||||||||||
Target  EEDSPGPSTSSVIPKRKSDRKPLRGGG                YNPLSGEGSGTCSWRPGRRGPSSGGUG
        gggacgctattgacacatgaactcggg                tacttgggagatttacgcagcttggtg
        aaagcgcccccttcagacagactggg                gaactcgagggcgcggcggggcccgggg
        aacttgtttaaccgaaatcagtgaaa                tcttgttattacccgatacaacattaac
                                                                            * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 347 ; UGA-SECIS: 350

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = NW_018334967.1:subseq_229490,66461_ Strand = - Positions = 27756 - 27677
 Found by:  Infernal (score=27.05) Covels (score=42.41)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -11.49

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