A Degenerate Primer Design Method Based on Ant Colony Optimization

Table 2

DNA sequence analysis at 500 bps and 600 bps under three conditions.

	ACOH	Primer 3	Oligo 7
500 bps up primer (3′- 5′)	CT[TA][TC][CG][TA]	[AC][AT]C[GC][ATC]	A[AG]CG[AT][GAT]
	G[GT]C[CT][CG]	[GA][AT]G[TC]C	AG[TC][CG]TG
	[TA]A[CTA]	[TG]G[AT][AG]C	[AT]A[AC][GCT]
	[CG]CTA	[CG][AT][AT]TC	[AT]G[TC]C
500 bps down primer (3′- 5′)	GAA[CA][CT][GT]	CT[TA][TA][GC]	C[CT]G[TA][TCG]
600 bps up primer (3′- 5′)	[CT][CT]G[TG]	C[GA][TA]G[GT]C[CT]	[CA]A[TA]GT
600 bps down primer (3′- 5′)	G[TG]ACGA[CGA]	G[TA][AG][CTA]	[GC][CT]GA[TAG]
	[TA]T[CA]	[CG]C[TA][CA]	[TA]GC[GA]A
	GGA[TC]A[GA]	G[TAG]A[TC]A[GA]	[TG][AG]A[TC][TA]
	GT[CA][CAT][CA]	G[TGA][CA][CAT]	[GA]G[TA][CA]
	[TG][TA]C[CA]	[CA][TG][TA]C	[CT][CGA]T[TA]C
	GAC[AG]	[CA][GA][AC][AG]	C[GA]ACA
	GC[AG]CGG[TG]	GC[AG]C[AG]G	GC[CAG][CT]G
	[TC]C[CAT]A	[TG][TC]C[CAT]	[GA][TG]TC[CT]
	[TA]G[TA][TC]G	A[TA]G[TA][TC]	[GA][GTA]GAC
	[GA]T[CA]	[GA][GA][TA][CAG]	[GA]G[TA][CA]