Output_id:  SelW.4.selenocysteine
----------  ---------------------
-Species        Saimiri boliviensis                          -Taxid 27679
-Target         /cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa
-Chromosome (-) gi|357434082|gb|JH378281.1|
-Program        exonerate
-Query name     ref|NP_874363.1| selenoprotein V [Homo sapiens]
-Query range    1-346      length:346   coverage: 1.0
-Profile range  1-433      length:494   coverage: 0.88    sec_positions: [288, 291]
-Average sequence identity with profile: 0.1574   (ignoring gaps: 0.2653)
-State          kept

------- alignment -------
Query   MNNQARTPAPSSARTSTSVRASTPTRTPTPLRTPTPVRTRTPIRTLTPVLTPSPAGTSPLVLTPAPAQIPTLVPTPALARIPRLVPPPAPAWIPTPVPTP
        ||||||||||||||||||||||||||||||/||||  ||||||||||| |    |||  || |||||/|   ||||     |   | | || / |  |  
Target  MNNQARTPAPSSARTSTSVRASTPTRTPTPVRTPTAARTRTPIRTLTPSL----AGTPALVPTPAPARISRPVPTPVPTPAPARTPTPIPALVRTLTPVR
        aaacgcacgcttgcatatgcgtacacacacgcacaggcacacacacactc----ggacgcgcacgcgcatccgcacgcacgcgcacacacgcgcacacgc
        taaacgcccccccgcccctgcccccgcccctgcccccgcgcctgctccct----cgcccttccccccgtcgctccctccccccgcccctccttgctcctg
        gtcgggcccccgcgcaggcgttcgcgagtacgtgcgcgtgcccgcgcatg----cgtctgcgtatgcgcctgcatatgtttccgcatgcgtgtgcgtacg
                                                                                                            

Query   VPVRNP <---Intron---> TPVPTPARTLTPPVRVPAPAPAQLLAGIRAALPVLDSYLAPALPLDPPPEPAPELP--LLPEEDPEPAPSLKLIPSVS
        /|     <    52bp    >                   |||| /|||||| || |||| | ||| || |||||| |  /  ||||||||||||/||||
Target  LPAPAR                XXXXXXXXXXXXXXXXXXPAPALVLAGIRAMLPFLDSYPASALPWDPLPEPAPEPPVSVSSEEDPEPAPSLKLVPSVS
        ccgcgc                nnnnnnnnnnnnnnnnnncgcgcgcggacgaccttgttcgtgcctgcccgcgcgccgtgttgggcgcgcacacgctgt
        tccccg                nnnnnnnnnnnnnnnnnncccctttcgtgcttcttacacccctcgactcacccacctctccaaacacccgtattcctc
        caccc                nnnnnnnnnnnnnnnnnncacataagcgtgcgcccgcccgcgcgtgtgcgattgggtgtgacggctggggcggccggcc
                                                                                                            

Query   SEAGPAPGPLPTRTPLAANSPGPTLDFTFRADPSAIGLADPPIPSPVPSPILGTIPSAISLQNCTETFPSSSENFALDKRVLIRVTYU <---Intron-
         | |||| ||| ||||| | ||||||  |/||||| ||||  ||  ||/|| |||||| || |  |/| |/|||||||||| |||||  <   1884bp 
Target  GETGPAPEPLPARTPLATNPPGPTLD--FKADPSATGLADHTIPGSVPAPIPGTIPSAASLPNSAESFVSASENFALDKRVPIRVTYC            
        ggagcgcgcccgcaccgaaccgcacg--taggctgagcggcaacgtgcgcacgaactggttcatggatgtgagatgcgaagcacgatt            
        gacgcccactccgcctccaccgccta--tacaccccgtcaactcgctccctcgctccccctcaccagttccgaatctaagtctgtcag            
        cgtgccggctcgccagcgcacgcgac--cgacggctgggtcctcctctgccggccggcccagttcaccccccgccggcggcttagtc             
                                                                                               *            

Query   --> GLUSYSLR <---Intron---> YILLKKSLEQQFPNHLLF <---Intron---> EEDRAAQATGEFEVFVNGRLVHSKK <---Intron--
          > |||||||| <   106bp    > ||||||||||/||/ ||| <    85bp    > ||||||||||/|||||/|||||||| <    93bp   
Target      GLUSYSLR                YILLKKSLEQRFPDRLLF                EEDRAAQATGDFEVFVDGRLVHSKK             
            gctatacc                taccaaacgcctcgccct                gggaggcgaggtggtgggacgctaa             
            gtggagtg                atttaagtaagtcagttt                aaagccaccgatatttaggttacaa             
           tccactctg                ctagagcgggatatcact                gacatcgtagttagtatgagctcag             
              *                                                                                             

Query   -> RGDGFVNESRLQKIVSVIDEEIKKR
         > ||||||/|//|||||||||| ||||
Target     RGDGFVDEAKLQKIVSVIDEVIKKR
           agggtggggaccaagagagggaaaa
           ggagttaacataattgttaattaag
           gtcctgtgcgggatgctttggcggg
                                    
------- positions -------
Exon 1    1023176      1023480
Exon 2    1022632      1023123
Exon 3    1020723      1020747
Exon 4    1020563      1020616
Exon 5    1020403      1020477
Exon 6    1020235      1020309

--------- SECIS ---------
>SelW.4.selenocysteine.esecis:loosest.1 chromosome:gi|357434082|gb|JH378281.1| strand:- positions:1018898-1019006 species:"Saimiri boliviensis" target:/cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa distance_from_sec_uga:1447 distance_from_cds:1228
UGAGGCAGGA GAAUUGC UUGAACCCAGGAG GUGAG GUUGCAGUGAG CC GAGAUCGCCCCACUGCACUCCAG CCUGGGCAAC AGAG CAAGACU CUGUCUC AAAAAAAGAA
(((((((((. ...(((( (((....)))).. .(((( (((((.((((. .. ....)))).(((..((......) ).)))))))) )))) )))...) ))))))) ).........

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