Output_id:  TR.15.selenocysteine
----------  --------------------
-Species        Saimiri boliviensis                          -Taxid 27679
-Target         /cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa
-Chromosome (+) gi|357434057|gb|JH378306.1|
-Program        genewise
-Query name     gi|29476880|gb|AAH50032.1| MODIFIED TXNRD3 protein [Homo sapiens]
-Query range    121-683    length:683   coverage: 0.82
-Profile range  329-1345   length:1345  coverage: 0.76    sec_position: [1344]
-Average sequence identity with profile: 0.4715   (ignoring gaps: 0.5612)
-State          kept

------- alignment -------
Query   RVKELFSSLGVECNVLELDQVD <---Intron---> DGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQ <---Intron---> AYQSGLLQKL
        /||||||||| || |||||||| <   1023bp   > |||//|||| |||||||||||||||||||||||||| <   1728bp   > ||||||||||
Target  QVKELFSSLGTECYVLELDQVD                DGAKIQEVLLEITNQKTVPNIFVNKVHVGGCDQTFQ                AYQSGLLQKL
        cgagcttttgagttgtgcgcgg                gggaacggctgaaacaagcaatgaagcgggtgcatc                gtcagttcac
        ataattcctgcagattataat                aagcataatttatcaaactcatttaatatgggaacta                caaggttaat
        ggaactttgatattcgattat                ttgcgtaaggaacttgacgctttgtagtttatcatcg                atgttggagc
                                                                                                            

Query   LQEDLAYDYDLIIIGGGSGGLSCAK <---Intron---> EAAILGKKVMVLDFVVPSPQGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQ
        | || |||||||/|||||||||||| <   246bp    > |||||||||||||||||||||| || <   747bp    > ||||||||||||||||||
Target  LHEDSAYDYDLIVIGGGSGGLSCAK                EAAILGKKVMVLDFVVPSPQGTCWG                LGGTCVNVGCIPKKLMHQ
        ccggtgtgtgcagagggtggcttga                gggatgaagagcgtggctccgattg                cggatgaggtacaatacc
        taaaccaaaattttgggcggtcgca                accttgaattttatttcccagcgg                gtggcgtatggtcaattaa
        tcatgattttgccctttttctgtag                atctgagatgtacttcgatgcgcg                tttcttatattttgaggtg
                                                                                                            

Query   AALLGQALCDSRKFGWEYNQQV <---Intron---> RHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK <---Intron--->
        |||||||| ||||||||||||| <   3051bp   > /|||||||||||||| |||/|| |||||||||||||||||||||||| <   3925bp   >
Target  AALLGQALHDSRKFGWEYNQQV                KHNWETMTKAIQNHIRSLNFGYGLSLREKAVAYVNSYGEFVEHHKIK               
        ggctgcgtcgtaatgtgtaccg                acatgaaaagacacactcatgtgtttagagggtgattggtggccaaa               
        ccttgactaacgatggaaaaa                taaagactcactaaatgctatgagtctgaactcatacagattaaaata               
        tctgggaatcaggtcggttaa                ggccggggaaatgcccctactccggtggagtgctctctaattatcaag               
                                                                                                            

Query    ATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSIL
         |||| |||||||||||||||||||||||||||||||||| <   788bp    > ||||||||||||||||||||||||||||||||||||||||||||
Target   ATNKNGQETYYTAAQFVIATGERPRYLGIQGDKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGFGLDVTVMVRSIL
         gaaaagcgattaggctgagaggaccttgacggagttaaa                ggcttccttcgaatggggttggcgtggtcggtgcggagagctac
         ccaaagaacaacccatttccgagcgatgtagaaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttgctt
         actatagatttttagtcaagtagggtaacaataacttc                ttctttgttctcagagatctcccggtagtgtctcgtcatgacact
                                                                                                            

Query   LRGFDQEMAEKVGSYMEQHGVKFLRKFIPVM <---Intron---> VQQLEKGSPGKLKVLAKSTEGTETIEGVYNT <---Intron---> VLLAIG
        |||||||||||||||||||||/|| |||||| <   1252bp   > |||||||||||||||||||||||||| |||| <   7816bp   > ||||||
Target  LRGFDQEMAEKVGSYMEQHGVRFLWKFIPVM                VQQLEKGSPGKLKVLAKSTEGTETIEEVYNT                VLLAIG
        ccgtgcgaggaggttagccggatctatacga                gcctgagtcgacagtgataggagaagggtaa                gttgag
        tggtaaatcaatgcataaagtgttgattctt                taataagccgatattcaccagcactaataac                tttctg
        ctctcaagagagtccgggttggcggacatgg                tagggatataggaagtattaaaaataactca                tgattt
                                                                                                            

Query   RDSCTRKIGLEKIGVKINEK <---Intron---> SGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEK <---Intron-
        |||||||||||||||||||| <   542bp    > ||||||||||||||||||||||||| ||||||||/|||||||/||||||||| <   5975bp 
Target  RDSCTRKIGLEKIGVKINEK                SGKIPVNDVEQTNVPYVYAVGDILEGKPELTPVAVQSGKLLARRLFGASLEK            
        cgttaaaagtgaaggaaaga                agaacgagggcaagctgtggggatggacgcacgggctgaccgcactggttga            
        gacgcgatgtaatgtataaa                ggatctaataacatcatactgattagacatcctctacgattcggttgcctaa            
        tcctagaacgggttcattg                ataaatattgagctgatctttgttggtgagctcccagacggatgactgctaag            
                                                                                                            

Query   --> CDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLE <---Intron---> IYHTLFWPLEWTVAGRENNTCYAKIICNKFDH <---Intron-
          > ||||||||||||||||||||||||||||/||||||| <   4466bp   > |||||||||||||||||||||||||||||||| <   2626bp 
Target      CDYINVPTTVFTPLEYGCCGLSEEKAIEIYKKENLE                IYHTLFWPLEWTVAGRENNTCYAKIICNKFDH            
            tgtaagcaagtaccgtgttgttggagagataagacg                atcatttccgtagggagaaattgaaataatgc            
            gaatatcccttcctaaggggtcaaactataaaaata                taacttgctagctcggaaacgacattgaataa            
            ttttttatggtttggttctaataggttaataagtaa                atttgcgttagaatcagccttcagacctatct            
                                                                                                            

Query   --> DRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGLDITQKGCUG
          > ||||||||||||||||||||||||||||||||||||||||||||| <   520bp    > ||||||||||||||||||||||
Target      DRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE                VFTTLEITKSSGLDITQKGCUG
            gcgagtcacgcaggggacgtgggaatgcaacccggaagaccatgg                gtaatgaaattgcgaacagttg
            agttgtattgcacgatcagtccctaggtcaattaactgtaccgga                ttcctatcaccgtatcaagggg
            tggagttttaatctgtcaatatagatgctagattcctatccatgg                gcgtgacaacgaacctgaccac
                                                                                             * 
------- positions -------
Exon 1    1052775      1052838
Exon 2    1053862      1053971
Exon 3    1055700      1055804
Exon 4    1056051      1056123
Exon 5    1056871      1056990
Exon 6    1060042      1060184
Exon 7    1064110      1064225
Exon 8    1065014      1065239
Exon 9    1066492      1066584
Exon 10   1074401      1074477
Exon 11   1075020      1075176
Exon 12   1081152      1081259
Exon 13   1085726      1085821
Exon 14   1088448      1088582
Exon 15   1089103      1089168

--------- SECIS ---------
>TR.15.selenocysteine.esecis:loosest.1 chromosome:gi|357434057|gb|JH378306.1| strand:+ positions:1089367-1089461 species:"Saimiri boliviensis" target:/cursos/BI/genomes/project_2013/Saimiri_boliviensis/genome.fa distance_from_sec_uga:201 distance_from_cds:198
GACUGCGAGA AGCAGUG GUACUGCUUCC UUGAC GCCUUAACUCG AA GCCCCGUUAUGAGG UGAGCCAAGGC UGAU UCU CGCAAGC GAGGACUGAG
........(( ((((((. ..)))))))). .(((( (((((..(((. .. (((.(.....).)) ))))..))))) )))) ((( ((....) ))))......

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