<p>I find that in hg19 fasta file, the sequence contains capital letters(ATGC) and lowercase letters(atgc), so I am wondering is there any difference between these 2 kinds of letters, or is there any special meanings?</p>

See http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/

> Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.