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

 Blastx evalue: 3e-60
 Query name: gi|965788681|ref|XP_011965380.2| PREDICTED: selenoprotein O isoform X2 [Ovis aries musimon]
 Query range: 119-682  (total 682)

 Target: /data/www-rg/seblastian_results/409461170/tempfiles/temptarget.fasta
 Chromosome: NW_018342064.1:subseq_1891769,79625_ Strand: -
 Positions:
 -Exon 1  49402        49619
 -Exon 2  38646        38849
 -Exon 3  37639        37819
 -Exon 4  36177        36307
 -Exon 5  35564        35844
 -Exon 6  31332        31482
 -Exon 7  30495        30680
 -Exon 8  30270        30426
 -Exon 9  30000        30170

 Redox box: YES

Query   REAREAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTEAGERWELQLKGAGPTPFSR <---Intron---> QADGRKVLRSS
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <  10552bp   > |||||||||||
Target  REAREAEAALFFSGNALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTEAGERWELQLKGAGPTPFSR                QADGRKVLRSS
        cggcgggggcttagagcccgggcggctttgcctgctggccgggggatcgggtaggggctgcccagggcactta                cgggcagccta
        gacgacacctttggacttcgcacccagaggaatgatcgatgagcctatgatgcacgaggatatagcgccctcg                acaggattgcg
        cggcgcgcgccccccggggccgcctccccccgccgcggggcccccgcgcggccgccgcggggcgcggcgccc                ggccccgggcct
                                                                                                            

Query   IREFLCSEAMFHLGIPTTRAGSCVSSQSTVVRDAFYDGNPRPEPCAVVLRLAPTFLR <---Intron---> FGSFEIFKPRDEHTGRAGPSVGRDDIR
        /|||||||||| |||||||||/||/|||||||| ||||||||||||||||||||||| <   826bp    > |||||||||||||||||||||||||||
Target  VREFLCSEAMFRLGIPTTRAGACVTSQSTVVRDVFYDGNPRPEPCAVVLRLAPTFLR                FGSFEIFKPRDEHTGRAGPSVGRDDIR
        gcgtctaggatccgacaacgggtgatctaggcggttggacccgctgggcccgcatca                tgttgatacaggcagcggcaggaggac
        tgattggacttgtgtcccgcgcgtccaccttgattaagacgcacgctttgtcccttg                tgctattacgaaacggcgcgtggaatg
        ccgcgccgcgccgccccggcccccgcgcccgtcccccgccgcggccgggcgccacc                gcagcgccgcacgcgccacctgggcccg
                                                                                                            

Query   LQMLDYVISTFYPEIQASHPGDHVQRHAAFFRE <---Intron---> VTRRTARLVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDR <---In
        |||||||||||||||||/|||| |||||||||| <   1331bp   > |||||||||||||||||||||||||||||||||||||||||||| <   33
Target  LQMLDYVISTFYPEIQAAHPGDPVQRHAAFFRE                VTRRTARLVAEWQCVGFCHGVLNTDNMSIVGLTIDYGPFGFLDR       
        ccacgtgaaattcgacggccggcgcacggttcg                gaccagccgggtctggttcggcaagaaaaggcaagtgctgtcga       
        tattaattgctacataccacgactagaccttga                tcggccgttcagagtgtgagttacaatgttgtctaagctgttag       
        gggcctcccccccgcggtctgccgggcccccgg                gtgcgcgggtgggcgcccccgccgccgccggcccccgctccgc        
                                                                                                            

Query   tron---> YDPGHVCNASDTAGRYSYGKQPEVCRWNLQKLAEALDPALPLELAEAILAQEFDAEFGRHYLQKMRRKLGLVQTEQEGDGALVAQLLETMH
        2bp    > ||| ||||||||||||/| ||||||/||||||||||||||||||||||||/||||||||||||||||||||/|||||||||||||||||||
Target           YDPDHVCNASDTAGRYAYSKQPEVCKWNLQKLAEALDPALPLELAEAILAEEFDAEFGRHYLQKMRRKLGLMQTEQEGDGALVAQLLETMH
                 tgcgcgtagtgaggctgtaaccggtataccacgggcgcgcccgcgggacgggtgggtgcctccaaccacgcacagcgggggcggcccgaac
                 aacaatgaccaccggacagaacatgagataatcactacctctatcacttcaatacatggaataatggatgttacaaagagcttcattacta
                gccttcgccccctcgccgccggtggcggcggggcgcgctggccggcgccggggctcgccgccggggcgggccggtggggtccggcgcggcgc
                                                                                                            

Query   LTG <---Intron---> ADFTNSFYLLSSFPAAPESPDLDEFLAALTAQCASLEELRLAFRPQMDPR <---Intron---> QLAMMLMLAQSNPQL
        ||| <   4081bp   > ||||||||||||||||||||||||||| |||||||||||||||||||||| <   651bp    > ||/||||||||||||
Target  LTG                ADFTNSFYLLSSFPAAPESPDLDEFLATLTAQCASLEELRLAFRPQMDPR                QLSMMLMLAQSNPQL
        cag                ggtaattttcattcggcgtcgcggtcgacagctgtcggcacgtcccagcc                cctaacacgctaccc
        tc                gcatcactattgctccccaccataattcctccagcctaatgtctgcatacg                atctttttcacacat
        gc                gtccaccccggcccacgtgcacgtgcgcggtagtccgggggcccacggtc                gggcggcggggacggc
                                                                                                            

Query   LALIGTRASLARELERVEQQSRLEQLSEAELHSKNRSRWAAWLHDYR <---Intron---> ARLEKDREASGDVATWQAERTRVMRANNPKYVLRNYI
        ||||||||||||||||||||||||||||||| |/||| ||||| ||| <    68bp    > |||||||||||| | ||||| |/||||||||||||||
Target  LALIGTRASLARELERVEQQSRLEQLSEAELRSRNRSTWAAWLGDYR                ARLEKDREASGDAAAWQAERVRIMRANNPKYVLRNYI
        cgcagacgacgcgcgcggcctccgccagggccaaaaaatggtcggta                gccgagcggagggggtcggcgcaacgaacatgcaata
        tcttgcgcgtcgatagtaaacgtaatgacatgggaggcgccgtgaag                cgtaaagacggacccgacagtgttgcaacaattgaat
        ggcccgggcgtggggcggggtgggggcggggccgcgccgcggcccc                gcggggcggctccgccggtgggctgcccccgcgggccc
                                                                                                            

Query   AQGAIEAAENGDFSE <---Intron---> VRRVLKLLETPYGGEAEAAEPEGAAEASEVAAETSGAAGRRRSYSSKPPLWAAELCVTUSS
        |||||||||/||||| <    99bp    > ||||||||||||||| |||||| | |    |||| ||  ||||||||||||||||||||||
Target  AQGAIEAAESGDFSE                VRRVLKLLETPYGGEVEAAEPEEACE----AAETRGATDRRRSYSSKPPLWAAELCVTUSS
        gcggaggggaggttg                gccgcaccgactggggggggcgggtg----gggacggagcccttaaaccctgggctgattt
        cagctaccaggatca                tggttattaccaggataccacaacga----ccacggccagggcaggacctgccatgtcgcc
        ggcccatagtcccgg                gggggggggatctggggccgcggccg----ccgccgaccggcctccgcgcgggggcggacg
                                                                                                 *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 66 ; UGA-SECIS: 72

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = NW_018342064.1:subseq_1891769,79625_ Strand = - Positions = 29933 - 29863
 Found by:  Infernal (score=15.73) Covels (score=21.24)
 Stem2 length = 10   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -15.57

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...(({{((---....{[[{((((((((((..................))))))))))}]]}----..-.))}}))...
 target  CCCCGUCUC---UCCGUGACGGUGGAGACGUCCAGUCAGGACCUGACCCGUCUCUGCCCGAC----AC-UGACUCGCCA
                         ****           ^^                         ****