Output_id:  TR.10.selenocysteine
----------  --------------------
-Species        Saimiri boliviensis                          -Taxid 27679
-Target         /cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa
-Chromosome (+) gi|357434224|gb|JH378139.1|
-Program        exonerate
-Query name     gi|37542493|gb|AAL15432.1| MODIFIED thioredoxin reductase 1 [Homo sapiens]
-Query range    1-649      length:649   coverage: 1.0
-Profile range  1-1345     length:1345  coverage: 1.0    sec_position: [1344]
-Average sequence identity with profile: 0.4237   (ignoring gaps: 0.5521)
-State          kept

------- alignment -------
Query   MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKD <---Intron---> HHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTE <-
        ||| ||||||  || ||||||||  |||||  | <  27924bp   > ||| |||||||  |||||||| ||||||||| |||||||||||||||| < 
Target  MGCMEGKAVAVGAPPELQTKGKNDRGRRRSQVD                HHPSKTLPENPTAFTSTATADPRALLQAYIDSHSVVIFSRSTCTRCTE   
        agtaggaggggggccgccaagaagcgcactcgg                cccaaatcgacagtaaagaggcagcccgtagactggataatatactag   
        tggtagactctgcccatacagaaagggggcat                aaacgactcaaccctcgccccacgcttacatagacttttggccgcggca   
        gccggcgggggccacgggcacgccagaggcgc                ttcttatgagccaacccgctatcacgagctactctgccccgcacacttg   
                                                                                                            

Query   --Intron---> VKKLFKSLCVPYFVLELDQTE <---Intron---> DGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLK <---Intron---
          5382bp   > ||||||||||||||||||||| <  25541bp   > ||||||| ||||||||||| ||||||||||/||||| <  26280bp   
Target               VKKLFKSLCVPYFVLELDQTE                DGRALEGALSELAAETDLPAVFVKQRKIGGYGPTLK              
                     gaattatctgcttgcgcgcag                ggcgcgggctgtgggagccggtgacaaaggtgcata              
                     taattactgtcatttataac                aaggctagctcatccacatcctttaagatggagccta              
                     aggatgtgtttttgtattaa                gctgcgaagcgagcgaccggtgtgagagaccttacgg              
                                                                                                            

Query   > AYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAK <---Intron---> EAAQYGKKVMVLDFVTPTPLGTRWG <---Intron---> 
        > ||||||||||||||||||||/|||||||||||||||||||| <   2423bp   > ||||||||||||||||||||||||| <   2289bp   > 
Target    AYQEGRLQKLLKMNGPEDLPESYDYDLIIIGGGSGGLAAAK                EAAQYGKKVMVLDFVTPTPLGTRWG                
          gtcggaccaccaaagcggccgttgtgcaaagggtggcggga                gggctgaagagcgtgacaccgaatg                
          caaaggtaattatagcaatcacaaaattttgggcggtccca                accaagaattttattcccctgcgg                g
          ttggcatagaaagtctgtttgctctctcctatccacgattg                aacatcggggcgctctccttatag                t
                                                                                                            

Query   LGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETV <---Intron---> KHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPH
        |||||||||||||||||||||||||||||||||||||||| <   2981bp   > ||||||||||||||||||||||||||||||||||||||||||||
Target  LGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETV                KHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPH
        cggatgaggtacaacaccggttgcgccgtcatgtagggag                acgtgaaagggcacagttatgtcggccgaaggtgagtgctagcc
        tggcgtatggtcaattaaccttgactaacgaaggataac                taaagagttactaaatgctaggagtctgaaattaaacagattgca
        caaatgtgtcataaggcactaaaacaactactagacgga                tgttgcagaatagtctctgtgccaatggggacctgttcgattttc
                                                                                                            

Query   RIK <---Intron---> ATNNKGKEKIYSAESFLIATGERPRYLGIPGDKEYCISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECA
        ||| <   399bp    > |||||||||||||| |||||||||||||||||||||||| <   2456bp   > ||||||||||||||/|||||||||||
Target  RIK                ATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISS                DDLFSLPYCPGKTLIVGASYVALECA
        aaa                gaaaagagaattggatcagaggaccttgacggagttaaa                ggctttcttcgaacagggttggtgtg
        gta                ccaaagaaataccagtttccgagcgatgtcgaaaagtgg                aattctcagcgactttgccatctagc
        gtg                aattacaagttaagatctcttaaatcgccttcaacccc                ttttccatccgggccctaactttgatt
                                                                                                            

Query   GFLAGIGLGVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK <---Intron---> VEQIEAGTPGRLRVVAQSTNSEEIIEGEYNT <--
        |||||||| |||||||||||||||||||||||||||||||||||||||| <   3064bp   > ||||||||||||||||||||||||||||||| <  
Target  GFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIK                VEQIEAGTPGRLRVVAQSTNSEEIIEGEYNT    
        gtcggagtggagagataccagtgcgagaaaggcaggcgaataactgcaa                ggcagggacgcccgggctaaaggaagggtaa    
        gttcgtgtatctttgctttggtaaatcaatgaataaagtattgattcta                taatacgccggtgttcaccagaattagaaac    
        attttctatcttgtgctttaatcgcgccattacggatccgtaagtgata                taataagaacactaatggcttgactaagttg    
                                                                                                            

Query   -Intron---> VMLAIGRDACTRKIGLETVGVKINEK <---Intron---> TGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLY
         1511bp   > |/|||||||||||||||||||||||| <   683bp    > ||||||||||||||||||||||||| ||||||||||||||||||||
Target              VLLAIGRDACTRKIGLETVGVKINEK                TGKIPVTDEEQTNVPYIYAIGDILEGKVELTPVAIQAGRLLAQRLY
                    gttgagaggtaaaagtgagggaaaga                agaacgagggcaagctatgaggatggaggcacggacggctcgcact
                    tttctggacgcgatgtactgtataaa                cgatctcaaaacatcatactgattagatatcctctacggttcagta
                    gggaaaattcaaatcaacagggata                gtaaatcataggctgtcctctttaggtgggtcatacgaaaggtggct
                                                                                                            

Query   AGSTVK <---Intron---> CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE <---Intron---> VYHSYFWPLEWTIPSRDNNKCYAKII
        |||||| <   526bp    > |||||||||||||||||||||||||||||||||||| <   2124bp   > ||||||||||||||||||||||||||
Target  AGSTVK                CDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIE                VYHSYFWPLEWTIPSRDNNKCYAKII
        ggtaga                tgtgagcaagtactgtggtgctggagggatgggaag                gtcatttctgtaactagaaattgaaa
        cgccta                gaaaatcccttcctaagcggtcaaactaatgaaata                taagatgctagctccgaaaagacatt
        atcttg                tctattgctatttgatactcttggatgggtgggttg                tcttctgagaggtaaatccattaaac
                                                                                                            

Query   CNTKDN <---Intron---> ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE <---Intron---> VFTTLSVTKRSGASILQ
        |||||| <   4243bp   > ||||||||||||||||||||||||||||||||||||||||||||| <   9340bp   > |||||||||||||||||
Target  CNTKDN                ERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE                VFTTLSVTKRSGASILQ
        taaaga                gcgggtcgcgcaggggacgtgggcatgcaaaccgaaagaccgtgg                gtaactgaactggaacc
        gacaaa                agttgtattgcacgatcagtccctaggtcaaatagctgtactgca                ttcctctcagcgcgtta
        tttact                attgctcagtattaataaccatagatagcaaggccatacctctag                acaactgcactgaccgg
                                                                                                            

Query   AGCUG
        |||||
Target  AGCUG
        ggttg
        cgggg
        tccat
           * 
------- positions -------
Exon 1    10442389     10442485
Exon 2    10470410     10470555
Exon 3    10475938     10475998
Exon 4    10501540     10501649
Exon 5    10527930     10528052
Exon 6    10530476     10530548
Exon 7    10532838     10532957
Exon 8    10535939     10536081
Exon 9    10536481     10536596
Exon 10   10539053     10539278
Exon 11   10542343     10542435
Exon 12   10543947     10544023
Exon 13   10544707     10544863
Exon 14   10545390     10545497
Exon 15   10547622     10547717
Exon 16   10551961     10552095
Exon 17   10561436     10561501

--------- SECIS ---------
>TR.10.selenocysteine.esecis:str.1 chromosome:gi|357434224|gb|JH378139.1| strand:+ positions:10561721-10561821 species:"Saimiri boliviensis" target:/cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa distance_from_sec_uga:222 distance_from_cds:219
CAUUUGGCAG GGCAUUGU AAGGAUGCAUCC AUGAA GUCACCAGUCUC AA GCCCAUGUGG UAGACAGUGAU GGAA CAACUGUCAA AUCAGUU UCAGCAUGAC
.((((((((( .(((((.. ...))))).... .(((( (((((..((((. .. (((.....)) ))))).))))) )))) ...))))))) ))..... (((...))).

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