The kent program hgGcPercent will measure what you want to measure from your 


hgGcPercent - Calculate GC Percentage in 20kb windows
   hgGcPercent [options] database nibDir
     nibDir can be a .2bit file, a directory that contains a
     database.2bit file, or a directory that contains *.nib files.
     Loads gcPercent table with counts from sequence.
   -win=<size> - change windows size (default 20000)
   -noLoad - do not load mysql table - create bed file
   -file=<filename> - output to <filename> (stdout OK) (implies -noLoad)
   -chr=<chrN> - process only chrN from the nibDir
   -noRandom - ignore randome chromosomes from the nibDir
   -noDots - do not display ... progress during processing
   -doGaps - process gaps correctly (default: gaps are not counted as GC)
   -wigOut - output wiggle ascii data ready to pipe to wigEncode
   -overlap=N - overlap windows by N bases (default 0)
   -verbose=N - display details to stderr during processing
   -bedRegionIn=input.bed   Read in a bed file for GC content in specific 
regions and write to bedRegionsOut
   -bedRegionOut=output.bed Write a bed file of GC content in specific regions 
from bedRegionIn

  calculate GC percent in 5 base windows using a 2bit assembly (dp2):
    hgGcPercent -wigOut -doGaps -win=5 -file=stdout -verbose=0 \
      dp2 /cluster/data/dp2 \
    | wigEncode stdin gc5Base.wig gc5Base.wib

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