Output_id:  SelO.2.selenocysteine
----------  ---------------------
-Species        Saimiri boliviensis                          -Taxid 27679
-Target         /cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa
-Chromosome (+) gi|357434206|gb|JH378157.1|
-Program        genewise
-Query name     gi|32880229|ref|NP_113642.1| Human SelO, introduced manually in the profile. The protein originally hit in nr contained an additional stretch of aminoacids, which did not fit in the profile.
-Query range    128-669    length:669   coverage: 0.81
-Profile range  263-1108   length:1108  coverage: 0.76    sec_position: [1106]
-Average sequence identity with profile: 0.4225   (ignoring gaps: 0.5243)
-State          kept

------- alignment -------
Query   ALLPGAEPAAHCYCGHQFGQFAGQLGDGAAMYLGEVCTATGERWELQLKGAGPTPFSR <---Intron---> QADGRKVLRSSIREFLCSEAMFHLGV
        ||||||||||||||||||| ||||||||||||||||||| |||||||||||||||||| <   4026bp   > |||||||||||||||||||||||||/
Target  ALLPGAEPAAHCYCGHQFGHFAGQLGDGAAMYLGEVCTAAGERWELQLKGAGPTPFSR                QADGRKVLRSSIREFLCSEAMFHLGI
        gcccgggcggctttgcctgctggccgggggatcgggtaggggctgcccagggcactta                cgggcagcctaacgtctaggatccga
        cttcgcacccagaggaatgatcgatgagcctatgatgcccgaggatatagcgccctcg                acaggattgcgtgattggacttatgt
        gcgttcgccgccccccgcccccggggccccgcacggcggccgcggggcgccgcgccc                agcctcgcggactggcgccacgccggc
                                                                                                            

Query   PTTRAGACVTSESTVVRDVFYDGNPKYEQCTVVLRVASTFIR <---Intron---> FGSFEIFKSADEHTGRAGPSVGRNDIRVQLLDYVISSFYPEI
        ||||||||||||||| ||||||||||||/||||||/|||||| <   1686bp   > |||||||||||||/|||||||||/|||||||/||||||||||
Target  PTTRAGACVTSESTVARDVFYDGNPKYEKCTVVLRIASTFIR                FGSFEIFKSADEHSGRAGPSVGRSDIRVQLLNYVISSFYPEI
        caacgggtgatgtaggcggttggacatgataggtcagtataa                tgttgatatgggctgcggcaggaagacgcccatgaatttcga
        cccgcgcgtccacctcgattaagacaaaagctttgtcccttg                tgctattaccaaacggcgcgtgggatgtattaattgctacat
        ccagttcccatgcgggttgcttttcataacatggtatctca                gtactgttgcatgcagcacccgggcctcgggccccccccctgc
                                                                                                            

Query   QAAHASDSVQRNAAFFRE <---Intron---> VTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDR <---Intron---> YDPDHV
        |||||||||||||||||| <   1421bp   > |||||||||||||||||||||||||||||||||||||||||||| <   276bp    > ||||||
Target  QAAHASDSVQRNAAFFRE                VTRRTARMVAEWQCVGFCHGVLNTDNMSILGLTIDYGPFGFLDR                YDPDHV
        cggcgagagcaaggttcg                gaccagcagggtctggttcggcaagaaaacgcaagtgctgtcga                tgcgcg
        accacgagtagaccttga                tcggccgttcagagtgtgagttacaatgttgtctaagctgttag                aacaat
        gttcccctggatccccgg                gggcgggggcgggcacccccgtccccgccgggccctgccccgc                gcccccg
                                                                                                            

Query   CNASDNTGRYAYSKQPEVCRWNLRKLAEALQPELPLELGEAILAEEFDAEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLETMHLTG <---Intron-
        |||||||||||||||||||/|||/|||||||||||||||||||||||| ||||||||||||||||||||||||||||||||/|||||| <   3717bp 
Target  CNASDNTGRYAYSKQPEVCKWNLQKLAEALQPELPLELGEAILAEEFDTEFQRHYLQKMRRKLGLVQVELEEDGALVSKLLQTMHLTG            
        tagtgaagctgtaaccggtataccacgggcccgcccgcgggacgggtgagtcactccaacaacgcgcggcgggggcgtacccaaccag            
        gaccaacggacagaacatgagataatcactacatctatgacttcaatacatagaataatggatgttatataaagcttcattactatc             
        cccacctcccaccggcggcggcggggtgggggggcgggcgccgcggtccgcagccggggagagccggggggacggggcgcggcgcgc             
                                                                                                            

Query   --> ADFTNTFYLLSSFPVELESPGLAEFLARLMEQCASLEELRLAFRPQMDPR <---Intron---> QLSMMLMLAQSNPQLFALMGTRAGIARELE
          > ||||||||||||| |/ ||||||||||||||||||||||||||||||||| <   937bp    > ||||||||||||||||||||||||||||||
Target      ADFTNTFYLLSSFLVDPESPGLAEFLARLMEQCASLEELRLAFRPQMDPR                QLSMMLMLAQSNPQLFALMGTRAGIARELE
            ggtaaatttcattcggcgtcgcggtcgacagctgtcggcacgtcccagcc                cctaatacgctaccctgcagacggagagcg
           gcatcactattgctttacaccgtcattcgttaagcctaatgtctgcatacg                atctttttcacacattcttgcgcgtcgata
           ttccaccccggtccggtggagcgggcgcgggggttcgggggaccgcggtc                gggcgggggagacgggtgcgccgacccgggg
                                                                                                            

Query   RVEQQSRLEQLSAAELQSRNQGHWADWLQAYR <---Intron---> ARLDKDLEGAGDAAAWQAEHVRVMHANNPKYVLRNYIAQNAIEAAERGDFSE
        ||||||/|||||||||||||| ||| |||||| <    74bp    > ||||||||||||||||||| |||| |/|||||||||||||||||||||||||
Target  RVEQQSQLEQLSAAELQSRNQDHWATWLQAYR                ARLDKDLEGAGDAAAWQAERVRVMRASNPKYVLRNYIAQNAIEAAERGDFSE
        cggcctccgccagggccaaacgctgatccgta                gccgagcggggggggtcggcgcgacgaacatgcaatagcagaggggcggttg
        gtaaacataatgccataggaaaagccgtacag                cgtaaatagcgacccgacagtgttgcgacaattgaatcaactaccaggatca
        tggggtggagacgcgggcgcgccgccgtggc                acggcgcggttatttcggcgtgtggcccccgtgggcccagcccgtcgtgccag
                                                                                                            

Query   --- <---Intron---> VRRVLKLLETPYHCEAGAATDAEATEADGADGRQRSYSSKPPLWAAELCVTUSS
            <    67bp    > ||||||||||||||||||||/ ||||| || | |||||||||||||||||||||
Target  AST                VRRVLKLLETPYHCEAGAATEPEATEARGATGGQRSYSSKPPLWAAELCVTUSS
        gaa                gccgcaccgactctgggggagcggaggaggaggccttaaaccctgggctgattt
        cgc                tggttattaccaagacgcccacaccacggccggagcaggacctgccatgtcgcc
        aca                tggaggaggctcccgagccagcgcagcagattggtccccgcacgaaagtggaag
                                                                              *  
------- positions -------
Exon 1    6482340      6482512
Exon 2    6486539      6486742
Exon 3    6488429      6488609
Exon 4    6490031      6490161
Exon 5    6490438      6490718
Exon 6    6494436      6494586
Exon 7    6495524      6495709
Exon 8    6495784      6495949
Exon 9    6496017      6496178

--------- SECIS ---------
>SelO.2.selenocysteine.esecis:loose.1 chromosome:gi|357434206|gb|JH378157.1| strand:+ positions:6496801-6496907 species:"Saimiri boliviensis" target:/cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa distance_from_sec_uga:628 distance_from_cds:622
GGGCCCCCAG CAGGGAC CCAGGCCUGGGAG AUGAG CUGGCUGCGG AA CUUGAGCACGAGGCUGAAG AUGCUGUGG AUGAU GUUCAUGACG GGCGCCG CCUUCUCCGU
((((((.... ..))).) ))..(((((.((( .(((( ....(((((( .. (((.(((.....))).))) ...)))))) .)))) .)))....)) ))).... ..........

--------- 3' seq --------
Total sequence length available downstream >= 3000
Sequence until first stop codon: 
TAA
 *