Plasmid, M13 primer that is 5' to the insert site is called the reverse primer and the M13 primer that is 3' to the insert is called the forward primer.
PCR, forward primer has the same sequence as the 5' to 3' template and is 5' to the region being amplifying. While the reverse primer sequence is complementary to the 5' to 3' sequence and is 3' to the region being amplified. Seems opposite of sequencing primer notation.
I used the forward sequencing primer the first time and the sequence matched my reference but when I sequenced with the T3 priming site primer (5' to the insert) I got the complementary sequence to my reference.
Edited by Epigeneticist, 08 January 2013 - 09:18 PM.