Major steps of my program
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My program was written in ANSI C in UNIX. There are three major step.
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Base quality statistics.
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We use the base-calling software, PHRED, reads trace files, call the
bases, and calculate base quality statistics. We use the output of PHRED
as the input of my program. The output of PHRED is that. 
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Primer Prediction
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Using the output from PHRED as the input, the first step for the
prediction is to find the good region for primer selection. 
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Then find all the octamer primers that present in that region and find out
the template sequence around the location of primer. So, after that step,
we get another output with all the candidate primers, and the template
regions. We will use that result do further analysis.
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Analysis of template secondary structure.
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This part of program is under developed. We use the algorithm which is
used by OLIGO for determining self-complementarily of oligonucleotides.
The 5’-terminus of the oligonucleotide is progressively moved toward the
3’-terminus, and each step, a determination of the number of base pairs is
made. A minimum length of continuous complementarily is set to 3, a base
pairing occurring is more than 3, will be considered significant and will
be stored in memory. And calculate the DG for the conformation.  
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We use the nearest-neighbor data to predict free energies for the DNA
duplex.
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After we finished the calculation of the stability of the structure, will
find the free energy value of the most likely stability scondary structure
of the template sequence. We can use the eliminate the primer who is fall
into the template secondary structure. 
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After eliminating that kind of primer, we score the candidate primers to
find a optimal primer for next primer walking to extend the sequence. 
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