Output_id:  TR.25.selenocysteine
----------  --------------------
-Species        Saimiri boliviensis                          -Taxid 27679
-Target         /cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa
-Chromosome (-) gi|357434094|gb|JH378269.1|
-Program        exonerate
-Query name     gi|27807131|ref|NP_777051.1| thioredoxin reductase 2 precursor [Bos taurus] gi|190359067|sp|Q9N2I8.2|TRXR2_BOVIN RecName: Full=Thioredoxin reductase 2, mitochondrial_ AltName: Full=Thioredoxin reductase TR3_ Flags: Precursor gi|5360756|dbj|BAA82153.1| th
-Query range    6-511      length:511   coverage: 0.99
-Profile range  6-1345     length:1345  coverage: 1.0    sec_position: [1344]
-Average sequence identity with profile: 0.4623   (ignoring gaps: 0.5544)
-State          kept

------- alignment -------
Query   GAAARFRGRAPGGARGAA <---Intron---> GRQCYDLLVIGGGSGGLACAKEA <---Intron---> AQLGKKVAVLDYVEPSPQG <---Int
        |/     ||||||| |   <  123639bp  > |// ||||||||||||||||||| <  10552bp   > ||||/||||/|||||||/| <   786
Target  GSQRVAEGRAPGGAEGTT                GQRDYDLLVIGGGSGGLACAKEA                AQLGRKVAVVDYVEPSPRG        
        gtcaggggcgcgggggaa                gccgtgccgagggtggcgtgagg                gccgaagggggtggctccg        
        gcagtcaggccggcagc                cgagaaattttgggcggtcgcaa                ccatggatcttaatacccg         
        gagggtaaatataggcc                atggcttcggtcgatccgttcga                tcggagggcggccgattca         
                                                                                                            

Query   ron---> TRWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAPHYGWGVAQ-APHSW <---Intron---> ATLADAVQNHVKSLNWGHRIQLQDR <-
        bp    > ||||||||||||||||||||||||||||/||||||||| |||  || | <   802bp    >   /|/||||||||||||||/|| || < 
Target          TRWGLGGTCVNVGCIPKKLMHQAALLGGLIRDAPHYGWEVAQPVPHDW                RKMAEAVQNHVKSLNWGHRVQLHDR   
                actgcggatgaggtacaacaccggccggcacggcctgtgggccgccgt                aaaggggcacgattatgccgcccga   
               gcgggtggcgtatggtcaattaaccttggttgaccaaggatcactcaag                gatcactaaatactaggagtataag   
               ccggccgcccccccctcggggcggagggcgcacccttcgggcgcggtc                ggggaattatcgacgcgcctcggcc    
                                                                                                            

Query   --Intron---> KVKYFNVKASFVDTHTVCGVSKGGEE <---Intron---> TLLSAEHIVIATGGRPRYPTH <---Intron---> IEGALEYG
          2210bp   > ||||||||| ||| ||| ||/|||/| <   493bp    >  ||||/||||||||||||| | <   4489bp   > /|||||||
Target               KVKYFNVKAGFVDEHTVRGVAKGGKE                ILLSADHIVIATGGRPRYPAH                VEGALEYG
                     agattagaggtgggcagcgggaggag                acctggcagagaggccatcgc                ggggtgtg
                     ataatatacgttaaactggtcaggaa                tttccaatttccgggcgacca                tagctaag
                    gacgctccatcttcgcatcttcatgag                tggatccccctcaggggccac                cattgata
                                                                                                            

Query   ITSDDLFWLKESPGKT <---Intron---> LVVGASY <---Intron---> VALECAGLLTGLGLDTTVMIRSVPLRAFDQ <---Intron--->
        |||||/|||||||||| <  10285bp   > ||||||| <   1019bp   > ||||||| |||||||||||/||/||| ||| <   2004bp   >
Target  ITSDDIFWLKESPGKT                LVVGASY                VALECAGFLTGLGLDTTVMMRSIPLRGFDQ               
        aaaggattcagtcgaa                tggggat                ggcgtggtcagcgcgaagaacaacccgtgc               
        tcgaattgtaaccgac                tttgcg                atctagcgttcgtgtacctttggtctggtaa               
        cactcccggggctaa                gggcgcc                cgcggttccccgcggccacggaccccccccg               
                                                                                                            

Query    QMASLVTEHMAGHGTRILRGCAPEKVEKLPGQQLRVTWVDLTSDRKDAGTFDTVLWAIG <---Intron---> RVPETASLNLEKAGVHTNPVTGKI
         ||/|||||||| |||| |||| | /| /||  ||/||| | |/ //  ||| |||||/| <  11147bp   > |||/| ||||||||| |/| | ||
Target   QMSSLVTEHMASHGTRFLRGCTPSQVRRLPDGQLQVTWEDCTTGKEGTGTFSTVLWAVG                RVPDTRSLNLEKAGVDTSPNTQKI
         catttgagcagtcgactcagtactcgaaccggcccgatggtaagaggagataagctggg                cgcgaaacatgaggggaacaacaa
         atccttcaatccagcgttgggcccatggtcagatatcgaagccgaagcgctgcttgct                ggtcacggtataacgtacgcacaat
         agccgcggcgatcccgcgggccccacggcgccgggccggccctcggcgccccccggca                tataccatgtgggtgacttcctggc
                                                                                                            

Query   LVDAQETTSVPHIYAIGDVAE <---Intron---> GRPELTPTAIMAGRLLAQRLSGRTSDLMDYSS <---Intron---> VPTTVFTPLEYGCVG
        |||//| |||||||||||| | <   2584bp   > |||||||||/|||||||||| | /| ||||   <   346bp    > |||||||||||||||
Target  LVDSREATSVPHIYAIGDVVE                GRPELTPTAVMAGRLLAQRLFGGSSALMDYDK                VPTTVFTPLEYGCVG
        cggtcggatgccatgaggggg                gccgcacaggaggaccgccctggttgcagtga                gcaagtaccgtgtgg
        ttacgaccctcatactgatta                ggcatccccttcggttcagttggcccttaaaa                tcccttcctaaggtg
        ggccgacctgctctctccggg                ggtgggcgtcgtggcgaggcttgcacggcccg                tcgccccaggcccgg
                                                                                                            

Query   LSEEAAVARHGEEHVE <---Intron---> VYHAFYKPLEFTVPQRDASQCYIK <---Intron---> MVCLREPPQLVLGLHFLGPNAGEVIQGF
        |||| ||||||/| || <   1695bp   > |||| ||||||||| |||||||/| <   156bp    > |||||||||||||||||||||||| |||
Target  LSEEEAVARHGQERVE                VYHAHYKPLEFTVPGRDASQCYVK                MVCLREPPQLVLGLHFLGPNAGEVTQGF
        ctggggggccgcgcgg                gtcgctaccgtagcgcggtcttga                agtcagccccgcgcctcgcaggggacgt
        tcaaactcgagaagta                taacaaactatctcggaccagata                ttgtgaccatttgtattgcacgatcagt
        gtgagagtctgggttg                ctcgttaaggcagtggtgcgtcag                ggcgggcggaggcgccccccacattgat
                                                                                                            

Query   ALGIK <---Intron---> CGASYQQLMRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG
        |/||| <   827bp    > || || |/|/||||||||/||| |||||||||||||||||||
Target  AVGIK                CGVSYVQVMQTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
        gggaa                tggttgcgacaggaccattggggaccatactgcgcagagttg
        ctgta                ggtcatattactgtaccgcaattatgtcagcgtacctcgggg
        tgac                gtgcctaggggcgcctcgccgggcggcccgcacgccggaccag
                                                                     * 
------- positions -------
Exon 1    2379625      2379676
Exon 2    2255917      2255985
Exon 3    2245308      2245364
Exon 4    2244377      2244521
Exon 5    2243500      2243574
Exon 6    2241211      2241289
Exon 7    2240655      2240717
Exon 8    2236095      2236165
Exon 9    2225790      2225809
Exon 10   2224679      2224770
Exon 11   2222500      2222674
Exon 12   2211216      2211352
Exon 13   2208536      2208631
Exon 14   2208097      2208189
Exon 15   2206330      2206401
Exon 16   2206076      2206173
Exon 17   2205122      2205248

--------- SECIS ---------
>TR.25.selenocysteine.esecis:str.1 chromosome:gi|357434094|gb|JH378269.1| strand:- positions:2203627-2203724 species:"Saimiri boliviensis" target:/cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa distance_from_sec_uga:1400 distance_from_cds:1397
CACCCCCCCC AGGCUCCU GGUGCCAGAUG AUGAC GAUCUGGGUGG AA ACCCAUCCUGUGG GCACCCACGUC CGAG CCCGC UGGCAUUU CUGUAAUGCA
........(( ((....)) ))((((((..( .(((( (((.((((((. .. .(((((...)))) ))))))).))) )))) .)..) )))))... ..........

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