------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|408541484|gb|JH947448.1|:subseq_2058201,200269_ Strand = + Positions = 103397 - 103477
 Found by:  Infernal (score=21.85) Covels (score=39.96)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -5.42

         ..(((((((.........(((((((((((((((.................))))))))))))))).........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         .(({((({(.........{[[{(({{(((((((.................)))))))}}))}]]}.....-.-.)})))})).
 target  GUGACAAGUUGCGUUGAAUGAUGUCUUCCUUAUAAAUGGUGAACUCACCAAUAAGGAUUACUGAUGAUAG-A-CAGUUGAUGG
                           ****           ^^^                         ****                  

SEQUENCIA FASTA

>SECIS.1 chromosome:gi|408541484|gb|JH947448.1|:subseq_2058201,200269_ strand:+ positions:103397-103477
GUGACAAGUUGCGUUGAAUGAUGUCUUCCUUAUAAAUGGUGAACUCACCAAUAAGGAUUACUGAUGAUAGACAGUUGAUGG


Selenoprotein id: 1         Category: known selenoprotein 
Protein prediction
Predicted by: exonerate Blastx evalue: 5e-22
Query protein: 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]
Positions on query: 2-190 Query length: 190

Target name: gi|408541484|gb|JH947448.1|:subseq_2058201,200269_
Positions on target: 84953-85025,85477-85611,88866-88972,99967-100056,100150-100228,102983-103065 Strand: +


  Query   ERDGDQLSARPTLETEGLRFLHVTV <---Intron---> GSLLATYGWYIVFSCILLYVVFQKLSTRL
          ||||//| ||| ||||||||||||| <   451bp    > |/|||/|||||| | |/| |  |||||||
  Target  ERDGERLLARPALETEGLRFLHVTV                GALLASYGWYIVVSVIVLVVAVQKLSTRL
          gcgggcccgccgcgaggcctccgag                ggccgatgttaggagagcggggcactacc
          agagagttcgcctacagtgttatc                tgcttcgaggatttgttttttctaatccgt
          agtgaggccaggggcaggccgccc                gccggcttcgccccccccccggggacctgg
                                                                                
  
  Query   RALRQRHLDQAAAALE <---Intron---> PDIVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ <-
          | ||||    /|| /| <   3254bp   > || |||/||||||||/||||||| | ||||||||| < 
  Target  RVLRQRQRSISAAPVE                PDTVVKQQEALAAARMKMQEELNVQAEKHKEKLRQ   
          cgtccaccaaaggcgg                cgaggaccggtgggcaaacggtagcggacagacac   
          gttgagaggtgccct                acacttaaaactcccgtataaatatacaaaaaatga   
          acggggggtctgccg                atttttgaaataatttgagaaaatgatagtgagaag   
                                                                                
  
  Query   --Intron---> LEEEKRRQKIEMWDSMQEGKSYKGNTRKPQ <---Intron---> EEDSPGPSTSS
           10994bp   > ||||||||||||||||||||||||||/||| <    93bp    > ||// ||||||
  Target               LEEEKRRQKIEMWDSMQEGKSYKGNTKKPQ                EENNSGPSTSS
                       cgggaaacaagatgaacggaatagaaaacc                ggaatgctatt
                       taaaaggaatatgagtaagagaagacaaca                aaaacgccccc
                       taaagaaggtaggccgaaaaccaatcagtg                agtctgttaaa
                                                                                
  
  Query   VIPKRKSDRKPLRGGG <---Intron---> YNPLSGEGGGTCSWRPGRRGPSSGGUG
          / || | ||||||||| <   2754bp   > |||||||| |||||||||||||/||||
  Target  LPPKHKPDRKPLRGGG                YNPLSGEGSGTCSWRPGRRGPSTGGUG
          cccacacgaactcggg                tacctgggagatttacgcagctaggtg
          tccaaacagactggg                gaactcgagggcgcggcggggcccgggg
          tcgatatcagagtat                tcctgtgaaccgccggtacacaattaac