Broadly speaking, an apparatus and associated method of operation is provided for controlling alignment signal transmission in an electronic communication process. More specifically, a programmable control is provided for controlling transmission of alignment signals in either a Serial Attached SCSI (SAS) or Serial ATA (SATA) communication process. The programmable control includes a counter operated to sequentially modify a count value. When the count value is equal to a programmed alignment trigger value, the programmable control is configured to generate and transmit an alignment signal through the initiator transceiver to the target transceiver. Thus, the apparatus and associated method of operation controls a rate at which alignment signals are transmitted in a SAS/SATA communication process.