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

 Blastx evalue: 6e-13
 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/694384753/tempfiles/temptarget.fasta
 Chromosome: KZ688257.1:subseq_119717,107660_ Strand: -
 Positions:
 -Exon 1  57585        57660
 -Exon 2  56759        56893
 -Exon 3  54686        54792
 -Exon 4  52169        52258
 -Exon 5  51745        51823
 -Exon 6  49961        50043

 Redox box: no

Query   MERDGDQLSARPTLETEGLRFLHVTV <---Intron---> GSLLATYGWYIVFSCILLYVVFQKLSTRLRALRQRHLDQAAAALE <---Intron--
        ||||||||| || ||||||||||||| <   691bp    > ||||||||||||||||||||||||| ||||||||| ||/|||||| <   1966bp  
Target  MERDGDQLSTRPALETEGLRFLHVTV                GSLLATYGWYIVFSCILLYVVFQKLFTRLRALRQRQLDRAAAALE             
        agcgggcctaccgcgaggcctccgag                gtccgatgttagtatacctggtcactaccagtacaccgcggggcg             
        tagagaatccgcctacagtgttatc                tgcttccaggatttggtttatttaattcgtgctgagatagcccct              
        gggcgtggcggacagcaggcctccg                gccggtctcgccctccttccgctggcccgggcggggggtatcttg              
                                                                                                            

Query   -> PDIVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ <---Intron---> LEEEKRRQKIEMWDSMQEGKSYKGNTRKPQ <---Intron---> 
         > |||||||||||||||||||/||||||||||||||| <   2427bp   > ||||||||||||||||/||||||||||||| <   345bp    > 
Target     PDIVVKRQEALAAARLKMQDELNAQVEKHKEKLRQ                LEEEKRRQKIEMWDSMREGKSYKGNTRKPQ                
           cgaggaccggtgggctaacggtagcggacagacac                cgggaaacaagatgaacggaatagaaaacc                
          acatttagaactcccgtataaatacataaaaaatga                taaaaggaatatgagtgagagaagacgaca                
          atttttaaggtaatttgagataataatagtggaaag                taagagaggtaggtcgaaaatcaataagtg                
                                                                                                            

Query   EEDSPGPSTSSVIPKRKSDRKPLRGGG <---Intron---> YNPLSGEGGGTCSWRPGRRGPSSGGUG
        |||||||||| ||||||||||||| || <   1701bp   > |||||||||||||||||||||||||||
Target  EEDSPGPSTSLVIPKRKSDRKPLRRGG                YNPLSGEGGGTCSWRPGRRGPSSGGUG
        gggacgctattgacacatgaactccgg                tacttgggggatttacgcagcttggtg
        aaagcgcccctttcagacagactggg                gaactcgagggcgcggcggggcccgggg
        aacttgtttaaccaaaatcagcggaa                tcctgttaatacccgatacatagttaac
                                                                            * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 345 ; UGA-SECIS: 348

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KZ688257.1:subseq_119717,107660_ Strand = - Positions = 49615 - 49528
 Found by:  Infernal (score=22.07) Covels (score=41.01)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -8.63

         ..(((((((..............(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcg-------UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .(((([({(..............{[[{(({{(((((((.................)))))))}}))}]]}......-...)})])))).
 target  UCUCUGUGACAGGUUGCGUUGAAUGAUGUCUUCCUUGUAAAUGGUGAGCCCACCAGCGAGGAUUACUGAUGCAGAG-AGUUGAAGGGGU
                                ****           ^^^                         ****