Output_id:  SPS.2.selenocysteine
----------  --------------------
-Species        Saimiri boliviensis                          -Taxid 27679
-Target         /cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa
-Chromosome (+) gi|357434222|gb|JH378141.1|
-Program        genewise
-Query name     gi|168480154|ref|NP_001108204.1| selenophosphate synthetase 2 [Bos taurus]
-Query range    1-449      length:451   coverage: 1.0
-Profile range  1-1547     length:1549  coverage: 1.0    sec_position: [696]
-Average sequence identity with profile: 0.2624   (ignoring gaps: 0.376)
-State          kept

------- alignment -------
Query   MAEVAATGAGGEAMAAVAAGEGSSGPVGLPQGRGFSSYRPFEPQALGLSPSWRLTGFSGMKGUGCKVPQETLLKLLAGLTRPEVLPAPGRGLVGGLEETA
        ||| /|||| ||||||/|| |||||| ||  || ||/|||||||||||| ||||||||||||||||||||||||||||||||/| |  | || || || /
Target  MAEASATGACGEAMAAMAAAEGSSGPAGLTLGRNFSNYRPFEPQALGLSASWRLTGFSGMKGUGCKVPQETLLKLLAGLTRPDVRPPLGGGLEGGQEEAS
        agggtgaggtgggaggagggggttgcggtacgcattatcctgccgtgcagatccagttgaagtgtagccgaccaccggcaccggccccgggcgggcgggt
        tcaccccgcggactcctcccagccgccgtctggatcaagctacactgtgcgggtcgtcgtaggggatcaacttattcgtcgcatgcctgggtaggaaacc
        ggacggccccaggggggatgaccgctgcgtgcgcccccgccgcgggtccgcggggccccggcaccgcgggggcacggaggggcggcagcgcggctgaggg
                                                                      *                                     

Query   QEAGLPVRAEPSPPFPTLGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMPEEEREKITPLMIK
        || |    | ||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||/||||/|
Target  QETG----AGPSPTFPALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEEEREKVTPLMVK
        cgag----ggcacatcgcgagagttgaccacggctcgcaagtttctgggctaagcagtgagcagctgagaagtgaatatcagacaaagggcgagaccaga
        aacg----cgcgcctcctgtgtacgttctgaggtcttaccattacttaacattggtcgcattgatactgtcagaatttttgtgagtgaaagaatccttta
        gaca----gccccttacgccggctccccggtgcgggggtacctccggatccgggcattccggttcccgcttgtccggggccccgtgtggacagagacgca
                                                                                                            

Query   GFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFILPDSAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKIKMVVSREEVELGYQEAMFNMAT
        ||||||||||||||||||||||||||||||||||||||||/||||||||||||||||||||||||||||||||||||/|||/||||||| ||||||||||
Target  GFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKVKMVISREEVELAYQEAMFNMAT
        gtcgggggggaggaggcaggactaaaggggaggtccagtaacgaggggggtgtaactgacgggagcctcgacgataagaagataggggcgtcggataaga
        gtgaccaaggcctcggacttacgtttggtccttgacaatttcagcttgattttcactgcatctacaagtaacaggaatatttcgaatatcaaacttatcc
        ctgtgtgaagtagctgatgcctgtactatctgacgatacagcccggtgtgggacagaacgttctccagctttaagtaagggccaagggggtgacgctgtc
                                                                                                            

Query   LNRIAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAISKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGE
        ||| |||||||||||||||||||||||||||||||||||||||||||||||||||/||||||||||/|||||||||||||||||||||||||||||||||
Target  LNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGRFGLLRGTSAETSGGLLICLPREQAARFCSEIKSSKYGE
        caaagggtacatagcggagaagtgatgctcacgaccaaggttgacaccaagaagggaagagctgcccgatggatggtcatccagcggctttgaattatgg
        tagcccgttactacacccatcgtgttgacaatcaaagaatctttaatcttcatcctgacgggtgttggcccaccggtttgtcgaaccgtgcataccaaga
        ccattatagcattctgcatcactctaaccgctgaaaacagctttttgaatcggtcccgctactgttgacgtactgaagttgtaaggtctttacaccgtag
                                                                                                            

Query   GHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGATATPLVPENSSASSEP
        |||||||||||||||||||||||||||||||||||  | |/||/|||||
Target  GHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGATAAALAPDNSNASSEP
        gccgtaggaggagacagcaagaccgaggcccggagggcgcgatagttgc
        gaacgttgttaagagccgttaacgttattcggccccctccaacacccac
        tcaggctctgagacagcgctcgtattacattgcattctttctatcctgt
                                                         
------- positions -------
Exon 1    10046722     10048056

--------- SECIS ---------
>SPS.2.selenocysteine.esecis:str.1 chromosome:gi|357434222|gb|JH378141.1| strand:+ positions:10048611-10048708 species:"Saimiri boliviensis" target:/cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa distance_from_sec_uga:1700 distance_from_cds:554
GACCUGCAAC CAUGUGGC UUGGUCUCUGUUA AUGAC GUCUCUCCCUCC AA ACCCCAUUAAGGA CUGGGAGAGGC AGAG CAA GCCUCAG AGCCCAGGCC
.......... .....((( ((((.(((((... .(((( (((((((((((( .. ..........))) ..))))))))) )))) ... ....))) )).)))))))

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