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

 Blastx evalue: 2e-10
 Query name: gi|1042356734|ref|XP_017322217.1| PREDICTED: selenoprotein O [Ictalurus punctatus]
 Query range: 1-689  (total 689)

 Target: /data/www-rg/seblastian_results/778086369/tempfiles/temptarget.fasta
 Chromosome: CM008317.1:subseq_13757946,107514_ Strand: -
 Positions:
 -Exon 1  56961        57514
 -Exon 2  55666        55869
 -Exon 3  55290        55467
 -Exon 4  53829        53959
 -Exon 5  53003        53280
 -Exon 6  52734        52902
 -Exon 7  51706        51891
 -Exon 8  50665        50821
 -Exon 9  50000        50230

 Redox box: YES

Query   MASNVLRLIRPYIFNSNPGLLRSYSMEGM-GTAIATSRSKLERLDFDNVVLRKLPVEESEAPGVRTVRGACFSRVMPQPLEKPRFVAVSGPAMALLGLSA
        ||// ||| || /      //      ||    / /||| |||| |||| |||||// ||||||||||||||||| ||||/ |||||||| |/ ||||| 
Target  MAASALRLTRPCLRYPGAVVVSRPRCSGMEDMGLGSSRSPLERLHFDNVALRKLPLDPSEAPGVRTVRGACFSRVQPQPLQSPRFVAVSGAALGLLGLSG
        aggagcccacctcctcgggggaaccttgaggagcgtactccgccctgaggccacccgctggcggcagcggtttagccccccacctgggtgggcgccgcag
        tccgctgtcgcgtgacgctttggcggcgtaatgtgcggcctagtataatctgatctaccaccgtgctggcgtcgtacactagcgttctcgcctgttgtgg
        gccttgcgcggtcgtcctgtgcgcctggggtgtgcgtctgggggccttcggggcggcgcgcggcccccgccccacggggggcggcgggccatgtggcccg
                                                                                                            

Query   EEVISDPLGAVYLSGSRVMPGSEPAAHCYCGHQFGHFAGQLGDGAACYLGEVKAPADQSPELLKENPSRRWEIQLKGSGLTPYSR <---Intron--->
        | |  ||||| ||||||/||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||/||/||||||| <   1091bp   >
Target  EAVEEDPLGAEYLSGSRLMPGSESAAHCYCGHQFGQFAGQLGDGAACYLGEVKAPADQSPELLKENPSGRWEIQVKGAGLTPYSR               
        ggggggccgggtcagtacacgtgtggctttgcctgctggccgggggttcgggagcggcacgccagacagatgacgagggcactta               
        actaaactgcaatggcgttcgcacccagaggaatgatcgatgagccgatgatacccaagcattaaacggggatatagcgtccacg               
        gggggcgggtgtgcccgggaccgcggccccatgccgccggggcagccccgggatgtcgctgggggcccagggcgggttagtctc                
                                                                                                            

Query    QADGRKVLRSSIREFLCSEAVFALGIPTTRAGSVVTSDSRVMRDVFYNGNPRMERCSVVLRIAPTFIR <---Intron---> FGSFEIFKQEDELTG
         |||||||||||||||||||||||||/|||||||||||||||||||||/|/|/|||||||||||||||| <   198bp    > ||||||||| || ||
Target   QADGRKVLRSSIREFLCSEAVFALGVPTTRAGSVVTSDSRVMRDVFYSGSPKMERCSVVLRIAPTFIR                FGSFEIFKQMDEFTG
         cgggcagtctaacgtctagggtgcggcaacggtggatgtcgaaggttagacaagattggtcagcataa                tgttgatacaggtag
         acaggattgcgtgattggacttctgtcccgcgcttccacgttgattagggcataggctttgtcccttg                tgctattaataatcg
        ggatgtatgtccctgtgctaactattgcctatctagcgtagcgatgtccctcagggctaggttgcctc                gttttgccaggtgtaa
                                                                                                            

Query   RQGPSYRYTEIRTQMLDYVIDTFYPEIQQSHSDPVERNTAFFRE <---Intron---> VTLRTARLVAHWQCVGFCHGVLNTDNMSILGLTLDYGPFG
        |||||| / |||||||||||/||||||||||||||||| ||||| <   1330bp   > | |||||||| |||||||||||||||||||||||||||||
Target  RQGPSYGHDEIRTQMLDYVIETFYPEIQQSHSDPVERNIAFFRE                VMLRTARLVAQWQCVGFCHGVLNTDNMSILGLTLDYGPFG
        ccgcatgcggaaacatgtgagattcgaccactgcggcaagttag                gacaagacggctctggttcggcaagaaaacgcatgtgctg
        gagcgagaaatgcattaattactacataagacactagatcttga                tttgccgttcagagtgtgagttacaatgttgtctaagctg
        agacctattgtatgggttctacccagcggccacaggacttctag                gggaacgggcggacgtcttacttattgtttgcagctactc
                                                                                                            

Query   FMDR <---Intron---> FDPEFICNASDNSGRYSYRAQPEICHWNLARLAEALNPDLPSDRAQAVLEEYSPLFNTFYLSNMRRKLGLLRKEEPEDEL
        |||| <   548bp    > |||/||||||||||||||/||| || ||||||||||/||||| ||| ||/|| |||||||| |||/|||||/||||||| 
Target  FMDR                FDPDFICNASDNSGRYSYKAQPAICRWNLARLAEALSPDLPSARAQDVLDEYLPLFNTFYLQNMRKKLGLLKKEEPEDET
        tagc                tgcgtatagtgatgctttagccgatctacgccgggcacgtctgcgcggcggtccctaattccaaaaacgccaaggcggga
        ttag                tacattgaccaacggacaacacctgggatcgtcactgcatcccgcaattaaatcttactataatgaatgttaaaacaaac
        cgc                tccacccttcttttgtcacacgaccccgcgtcaaacgcacgtaaatgtggtgcgcaccacttgcggaggtggagaaggtgc
                                                                                                            

Query   LITNLMQTMHNTG <---Intron---> ADFTNTFRCLSQISCPAEGDTVEDAELVKQATELLLQQCASLEELKAASKPNMDPR <---Intron--->
        |||/||||||||| <   100bp    > |||||||| |||||||/||/ |/  | /|||||||||||||||||| ||/| |||| <   842bp    >
Target  LITDLMQTMHNTG                ADFTNTFRSLSQISCPSEGEAVDQPEAIKQATELLLQQCASLEELKVASRPTMDPR               
        caagcacaacaag                ggtaaatcatacaatctggggggccggaacgagccccctgtcggtaggaacaagcc               
        ttcattactaac                gcatcactggtgatggccagactaacactaaccatttaagcctaatatcggcctacg               
        ccactggtgcct                tcccccccctgcgccttagagagcgtgtcggaaggcgggtccagggatctagtgct                
                                                                                                            

Query    EFSMLLSLAQSNPALFGMLSDRRTLARQLEKLSRLKELLESTETDLKNKQTEEWTCWIKQYR <---Intron---> QRLARECEGECDVKVVQEERV
         | /||||/|||||||| /|||| |/|/||/||||||||||/|| /|| ||||/|||||//|| <   884bp    > |||||||||  |/| ||||||
Target   ELAMLLSMAQSNPALFNILSDRTTVAQQLQKLSRLKELLETTEEELKAKQTEDWTCWIQKYR                QRLARECEGVNDIKTVQEERV
         gtgacctagcaacgctaattgcaaggccccactatagccgaagggcagacaggtattacata                cccgcgtgggagaaagcggag
         atctttctcagaccttattcagcctcaataatcgtaattaccaaatacaacaagcggtaaag                agtcgagagtaatactaaagt
        tggagggcgcgcctaccctgatggaatgggggctgaagtgataggggacggagcgccgaggc                ggttttgtaagtcagtgggaag
                                                                                                            

Query   RVMDSTNPRVVLRNYIAQNAIEAAENGDFSE <---Intron---> VQRVLKVLEKPFCAQE-----GWMVRRGSEEAQERDE-EEGQREAEEDVTGAE
        ||||/|||||||||||||||||||||||||| <   434bp    > |/||||||||||| ||     ||| | || |/ |||| |/|/ | | /  |||
Target  RVMDNTNPRVVLRNYIAQNAIEAAENGDFSE                VRRVLKVLEKPFCKQEGLEQPGWMGRGGSVESGERDEGEQGEAETEVEGGGAE
        agagaaaccggccatagcagaggggaggttg                gcagcagcgacttacggtgccgtagcggtggtggcggggcggggagggggggg
        gttaacacgtttgaatcaactaccaagatca                tggttattaactgaaagtaacggtggggctacgagaagaagacacatagggca
        gggccctatggcgcctcgtgtgaaatgccgg                tgatgaagagattggacggggcggcaatgggtaagcgcggggtgtggataaag
                                                                                                            

Query   NRVIVSYDSKPPAWAAQICVTUSS
        /|| | |||||| || /|||||||
Target  SRVFVPYDSKPPTWANEICVTUSS
        aagtgctgaaccatgagatgattt
        ggtttcaagacccgcaatgtcgcc
        cagtcttccgcacgatacttcaac
                             *  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 272 ; UGA-SECIS: 278

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM008317.1:subseq_13757946,107514_ Strand = - Positions = 49727 - 49645
 Found by:  Infernal (score=21.54) Covels (score=19.11)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -7.38

         ..(((((((...............(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcg--------UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...(({(((...............([[{(((({(((((..................)))))}))))}]])----....)))}))...
 target  UGUAUGCUUUUGACUGGUUAUAAAUGACGACUUAGACCACCAGUCUUAUAUAGGCAGGUCUCAGUCUGAA----AGACAGGGGUUGC
                                 ****           ^^                         ****