vmatchPattern() what went wrong?

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I think I'm using the right function,and there is no error message. But I didn't get the result.Here is what I did.

library(BSgenome)
bd<-DNAString("CAGGTAG")
dna <- readDNAStringSet("sequence.txt")
zld_bindingsite<-vmatchPattern(bd,dna, max.mismatch=0)

And my result is: MIndex object of length 5050 $dm3_cytoBand_101F1 range=chr4:69669-90134 5'pad=0 3'pad=0 strand=+repeatMasking=none IRanges of length 0

$dm3_cytoBand_102A1 range=chr4:90135-128922 5'pad=0 3'pad=0 strand=+ repeatMasking=none IRanges of length 0

$dm3_cytoBand_102A2 range=chr4:128923-130909 5'pad=0 3'pad=0 strand=+ repeatMasking=none IRanges of length 0

... <5047 more elements>

and DNAStringSet looks fine.

head(dna)
A DNAStringSet instance of length 6
width seq                                                     names               
[1] 20466 AATTGTCCTTATTAATTGACGATGCT...ATTATGCGCCTGATTTAAAGTACAAA dm3_cytoBand_101F...
[2] 38788 ATGTGTAAATATATCACCTTACCGTC...CATGCTAATCACTCGCTTTTAAATAG dm3_cytoBand_102A...
[3]  1987 CAACTTGGGCCACCTTCATCACCAAT...GACAATCCTGTATATCCTATAACACT dm3_cytoBand_102A...
[4] 24243 AGAGCCTTATGTAATCCACCTCATTT...TTCACTTGTAATTTTAAATTGTTCAG dm3_cytoBand_102A...
[5] 38787 AAATGTTCGCAAGTCAGAGCAAGGCT...AGCGGGAGCTTCTAAGACTTTGTTTT dm3_cytoBand_102A...
[6]  1987 TCGTGTTTTGCTCGTTCACAAAATCC...ATTATTAAAATACTTTCAAAAATAAA dm3_cytoBand_102

asked 2 mins ago

lxcfuji

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