Reference genome alphabets

[seq_GA]

Hi,
I have a very basic question. Why small parts of the erference genome have small letters and some parts have bbig letters as below? Thanks.

atgcatttgggccaATGCATGatgcAAATTTTGCA

[orctyr]

capital letters means: assemblied by surely short reads of pair-end relationship
lowercase means: assemblied by gap close precedure, maybe not such precisely.

[kmcarr]

Without knowing what software produced your sequence there is no way to know for sure. Some possibilities: 1) lowercase are lower quality consensus base calls, 2) lowercase represents repeat regions masked by repeatmasker.

Was there a README file or other documentation provided with the reference?

[n00c]

RepeatMasker, most likely.