1. Run GetGaps.pm on each masked chromosome file
   - A minimum gap size of 20 base pairs was used in selection.
   - The output gives a unique identifier for each gap, the chromosome, start and end points of the gap, and gap size.

2. Run flanks_ed.pl on individual chromosomes (modified by Susan Strickler from bioperl script written by Heikki Lehvaslaiho).
   - This script was modified from the original so a file containing a list of gap ranges can be accepted (rather than one gap range).
   - The gap range file must be a comma-delimited list, i.e., SL2.30ch00_000001:119288..125011,SL2.30ch00_000002:126061..128865, etc.  This list is derived from the GetGaps.pm output.
   - Each gap plus 200 bp on either side was extracted.
   - Output is in fasta format.

3. Run flanks2primer3.pl (written by Susan Strickler)  
   - Takes flanks_ed.pl output and reformats it for primer3 input.
   - Adds 10 bp to either side of gap so primer will not anneal directly beside gap (better for sequencing).
   - A PCR product size of 60-10,000 base pairs was used.  These may not be the realized size from experimental results.

4. Run primer3 

5. Run pull_out_primer.pl (written by Adri Mills)
   - Makes a list of primers and other relevent info.

10/15/10
Files used: SL2.30chxx.repeats.softmasked.stringent.itag0 - genomic sequence
	    gaps_20.txt  - gap coordinates for gaps greater than or equal to 20 bp.