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

 Blastx evalue: 3e-38
 Query name: gi|1035271291|ref|XP_008310584.2| PREDICTED: selenoprotein O [Cynoglossus semilaevis]
 Query range: 1-691  (total 691)

 Target: /data/www-rg/seblastian_results/498653827/tempfiles/temptarget.fasta
 Chromosome: OMLM01015002.1:subseq_0,105491_ Strand: -
 Positions:
 -Exon 1  38008        38561
 -Exon 2  37574        37777
 -Exon 3  37282        37459
 -Exon 4  36778        36908
 -Exon 5  36372        36649
 -Exon 6  36009        36177
 -Exon 7  34569        34754
 -Exon 8  32845        33001
 -Exon 9  32365        32586

 Redox box: YES

Query   MAYFGHRLGLLHVFSANLSVFRLFRSAGMDSMGLGVSRSPLERLDFDNIALKKLPLDESEELGVRQVKGACFSRVKPQPLTKPRFVAVSHEALALLGLDG
        ||/ | ||||  /|   /|| ||  | ||//||| /||| |||||||||||/|||||  |/ |||||||||||||/||||| ||||||||||||||||||
Target  MAHVGPRLGLSRIFLPGVSVSRLLVSVGMENMGLAMSRSSLERLDFDNIALRKLPLDPCEDPGVRQVKGACFSRVQPQPLTNPRFVAVSHEALALLGLDG
        agcggcccgttcatccggtgtaccgtggagaagcgaacttcgccgtgaagcaacccgctggcggccgaggtttagcccccaacctgggtcggcgccgcgg
        tcatgcgtgtcgtttcgtctcgtttctgtaatgtctggcctagtataatctgatctacgaacgtgatagcgtcgtacactcacgttctcaactcttgtag
        gttaatggagaacccctgcgcaccctcggacgagtgttcgagtcctccctcgatcgctcgcggggggaattccgagggggcctgcgcggtacgggggcca
                                                                                                            

Query   EEVMNDPFGPEYLSGSRLMPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVKVPPGQDPKLLKENPNGRWEIQVKGAGMTPYSR <---Intron--->
        |||/||| ||||||||//||||||||||||||||||||||||||||||||||||||||||/||/|||/|||||||||||/||||| <   230bp    >
Target  EEVVNDPLGPEYLSGSKVMPGSEPAAHCYCGHQFGQFAGQLGDGAACYLGEVKVPPGQDPELLRENPSGRWEIQVKGAGLTPYSR               
        ggggagccgcgtcagtagacgtgcggctttgcctgctggccgggggttcgggagccgcgcgcccgacagctgacgagggtactta               
        aattaactgcaatggcattcgcacccagaggaatgatcgatgagccgatgatatccgaacattgaacggggatatagcgtccacg               
        ggtgctgcaagtctccacgtacgccgccccctaccgccgggacggcccggggggatcaccggggacgccgggaggagtagtttc                
                                                                                                            

Query    QADGRKVLRSSIREFLCSEAMFFLGIPTTRAGSVVTSDSEVMRDVYYSGKPRFEKCSVVLRVAPTFLR <---Intron---> FGSFEIFKKSDEFTG
         |||||||||||||||||||||||||/||||||||||||| |/||||||| || |/||||||/|||||| <   114bp    > ||||||||//|||||
Target   QADGRKVLRSSIREFLCSEAMFFLGVPTTRAGSVVTSDSRVIRDVYYSGNPRHERCSVVLRIAPTFLR                FGSFEIFKQADEFTG
         cgggcagcctaaagtctaggattcggcaaaggtggatgaagacggttagacccgattggccagcatca                tgttgatacgggtag
         acaggattgcgtgattggacttttgtcccgcgcttccaggttgataaggacgaaggctttgtcccttg                tgctattaacaatcg
        aactccacgccttaacgccgggccgtgtccaactagctccacagtgctcgctctggctgccctttgcc                gcaacaccggttgcac
                                                                                                            

Query   RQGPSYGLDEIRRQMLDYVIEMFYPEIQQNHTDRVERNVAFFRE <---Intron---> VMLRTARLVAQWQSVGFCHGVLNTDNMSILGLTLDYGPYG
        ||||||| |||| ||/||||| ||||||/// |||||||||||| <   373bp    > |/||||||||||| ||||||||||||||||||||||||||
Target  RQGPSYGRDEIRGQMMDYVIETFYPEIQRDYPDRVERNVAFFRE                VVLRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPYG
        ccgcatgcggacgcaagtgagattcgaccgtcgcggaaggttag                ggccagccggctctggttcggcaagaaaacgcacgtgctg
        gagcgaggaatggattaattactacatagaacagtagatcttga                tttgccgttcagagtgtgagttacaatgttgtctaagcag
        cgtcctattgcatgggccctggtctgcggtctcagagcgtccag                ggttatatgagggtatcttacgtaccgccgacggcttatc
                                                                                                            

Query   FMDR <---Intron---> FDPDFICNASDNSGRYSYQAQPAICRWNLLKLAEALAPELPPDRAEVVMDEYLALYNDFYLQNMRKKLGLLKKEEPEDEM
        |||| <   128bp    > |||||||||||||||||||||||||||||/|||||||||||||/|| |||||//||| ||| |||||||||||||||||/
Target  FMDR                FDPDFICNASDNSGRYSYQAQPAICRWNLVKLAEALAPELPPDKAETVMDEYMSLYNGFYLNNMRKKLGLLKKEEPEDEI
        taga                tgcgtatagtgatgctttcgccgatatacgacgggcgcgtccgaggagaggtaactagttcaaaaaacgttaaggcggga
        ttag                tacattgaccaacggacaacacctgggattatcactccatccaacacttaaatgtaagtataatgaatgttaaaacaaat
        tgc                gttatttctcccctcccccgcgatacggcgggaggtttaggtacgtgttgtacgtgctaccgccgggagcagggggtgtac
                                                                                                            

Query   LITELLQTMHNTG <---Intron---> ADFTNTFRSLSQISCP----AKEEEELVRGATSLLLEQCASLEELKAANRPTMDPR <---Intron--->
        ||||||||||||| <   194bp    > ||||||||||||||||    // || ||/ || ||||||||| ||||||/|||||| <   1254bp   >
Target  LITELLQTMHNTG                ADFTNTFRSLSQISCPTEGESEREEHLVKHATDLLLEQCASLAELKAANKPTMDPR               
        caagcccaacaag                ggtaaatcatacattcagggagaggccgacgagcccgctgttggcaggaacaagcc               
        ttcattactaac                gcatcactggtgatcgccagagagaaattaaccatttaagcctcataccaacctacg               
        gctggggggcca                ttctccccctgtgtctctgaatgaagctcacctcaggggtacaagggactactgta                
                                                                                                            

Query    ELSMLLSMAQSNPSLFHMISDRMTISRQLDKLSKLKDLMETSQEELTAKQSEEWTSWITRYR <---Intron---> KRLSRELEGESDVRAVQEERL
         ||/||||||||||/|| /||||||//|||||||/||||||||||||  | / ||/ ||  || <   1567bp   > |||/|||||/ ||/| |/||/
Target   ELAMLLSMAQSNPALFQIISDRMTLARQLDKLSRLKDLMETSQEELKTKHAGEWSQWIKHYR                KRLARELEGQCDVQATQQERV
         gcgacctagcaacgctcaatgaaatgactgacaacagcagaacggcaaacgggtactaacta                accgcgcggctggcgaccgag
         atctttctcagaccttattcagtctcgataatggtaattacgaaatacaacgaggagtaaag                agtcgatagagataccaaagt
        tataggctgtgccaagcgtcacggaaggaacaccagacgggctgaggacattgggcggcgcc                ggtgtcgggcgttggcgggggg
                                                                                                            

Query   RVMYSTNPRVILRNYIAQNAIEAAENGDFSE <---Intron---> VRRVLQVLEKPFSSQPGLELPSWVGTGGTAEPGERDEDQEQQQEAATASSSSA
        ||| ||||||/|||||||||||||||||||| <   258bp    > |/|||/||/||||||||||||/||| | | | ||||| /||||||  ||||/|
Target  RVMDSTNPRVVLRNYIAQNAIEAAENGDFSE                VQRVLKVLKKPFSSQPGLELPAWVGGGSTTEQGERDEAEEQQQEA--ASSSAA
        agagaaaccggcaatagcagaggggaggttg                gccgcagtaactttccgcgccgtggggaaagcggagggggcccgg--gtttgg
        gttagcacgtttgaatcaactaccaagatca                tagttattaactccacgtatccgtggggccaagagaacaaaaaac--cccccc
        gggccccttggcgcctcgtaagttgtacctg                cggcagtgggtttggttggttgggcaccccagaggtagggaaaac--atatac
                                                                                                            

Query   RHPTPYDSKPPAWAQEICVTUSS
        |/  |||||||||| ||||||||
Target  RNSVPYDSKPPAWAHEICVTUSS
        aatgctgaaccgtgcgatgattt
        gactcaagacccgcaatgtcgcc
        atttctccgtatgctactcaaga
                            *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 437 ; UGA-SECIS: 443

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = OMLM01015002.1:subseq_0,105491_ Strand = - Positions = 31927 - 31845
 Found by:  Infernal (score=25.84) Covels (score=23.57)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -16.57

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