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

 Blastx evalue: 2e-18
 Query name: gi|6649223|gb|AAF21431.1|AF166126_1 selenoprotein Zf1 [Homo sapiens]
 Query range: 1-277  (total 277)

 Target: /data/www-rg/seblastian_results/9964626/tempfiles/temptarget.fasta
 Chromosome: LOCP02000599.1:subseq_602831,200000_ Strand: -
 Positions:
 -Exon 1  71051        71083
 -Exon 2  68983        69157
 -Exon 3  58405        58541
 -Exon 4  55032        55127
 -Exon 5  54482        54574
 -Exon 6  52783        52854
 -Exon 7  52513        52610
 -Exon 8  50000        50126

 Redox box: no

Query   MRSIPLRGFDQ <---Intron---> QMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIG <---Intron---
        ||||||||||| <   1893bp   > ||||/| |/||| ||/||||| | ||//||||||||||||  /|/||  ||||/|||/| <  10441bp   
Target  MRSIPLRGFDQ                QMSSLVTEYMASQGTQFLRGCTPLRVKKLPDGQLQVTWEDLESGREDMDTFDTILWAVG              
        acaacccgtgc                catttgagtagtcgactcagtaccagaaccggcccgatggcgtgaggagatgaactggg              
        tggtctggtaa                atccttcaatccagcattgggcctgtaatcagatatcgaatacggaatactacttgct               
        gccctggctcg                agacgcagcgttgccgcggtcccgagggcgtcgtgccggccgtcggcgccccccggca               
                                                                                                            

Query   > RVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVE <---Intron---> GRPELTPTAIMAGRLLVQRLFGGSSDLMDYDN <---
        > |||/|| ||||| ||/ /||/|||||| ||||||||||||||  | <   3277bp   > |||||||||||||||| ||| | ||||||| | <   
Target    RVPETRGLNLEKVGVNINPDSQKILVDDREATSVPHIYAIGDAAE                GRPELTPTAIMAGRLLAQRLCGQSSDLMDYSN     
          cgcgaagcatgagggaaacgacaacgggcggatgccatgaggggg                gccgcacagaaggaccgccctgcttgcagtaa     
         ggtcacggtataatgtatacagaatttaagaccctcatactgacca                ggcatccccttcggttcagtggaccattaaga     
         tgtaacatgtgggtaaccctctggtgtccgacccccttttcatagg                cgtgggcatcgaggcgcggcccgcacggccct     
                                                                                                            

Query   Intron---> VPTTVFTPLEYGCVGLSEEEAVARHGQEHVE <---Intron---> VYHAHYKPLEFTVAGRDASQCYVK <---Intron---> MV
        457bp    > ||||||||||||||||||||||||||/|||| <   1627bp   > ||||/||||||||| |||||||/| <   172bp    > ||
Target             VPTTVFTPLEYGCVGLSEEEAVARHGEEHVE                VYHAYYKPLEFTVAERDASQCYIK                MV
                   gcaagtaccgtgtggctggggggccgggcgg                gtcgttaccgtagggcggtcttaa                ag
                   tcccttcctaaggtgtcaaactcgagaaata                taacaaactatctcagaccagata                tt
                   ccgacctagatctgggagggtgactaggtgg                tttctcaaggcagtagtgcgtccg                gg
                                                                                                            

Query   CLREPPQLVLGLHFLGPNAGEVTQGFALGIK <---Intron---> CGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
        ||||||||||||||||||||||||||||||| <   2386bp   > ||||||||||||||||||/||| |||||||||||||||||||
Target  CLREPPQLVLGLHFLGPNAGEVTQGFALGIK                CGASYAQVMRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG
        tccgccccgcgcctcgcaggggacgtgcgaa                tggttgcgacaggaccatgggggaccatactgcgcagagttg
        gtgaccatttgtattgcacgatcagtctgta                ggccacattgctgtaccgcaatcatgtcagcgtacctcgggg
        cggacaggggcgcccccctcattaattggc                gtgcctaggggagcccccctgggcggtctgcacgcccggccag
                                                                                               * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1259 ; UGA-SECIS: 1262

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = LOCP02000599.1:subseq_602831,200000_ Strand = - Positions = 48740 - 48668
 Found by:  Infernal (score=31.95) Covels (score=35.14)
 Stem2 length = 9   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -17.39

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (((((((((---....([[{((({(({((((................))))}))})))}]])..--..-.)))))))))
 target  GGAUGCCAG---ACAAUGACGACCUGCGCAGAAACCCACCCUGUGGGCUGCCCAUGUCCGAGCC--CC-CCUGGUGUUU
                         ****           ^^^                        ****