What is this 5-column sequencing format from 2009?
This is an early Solexa/Illumina sequencer format. The columns are the identifier to location on the flowcell.  I believe the &quot;.&quot; was the original placeholder for an unread base, which has been replaced by and &quot;N&quot; in current Illumina sequencing output.
From on http://www.crg.eu/en/content/processing-and-analysis-illumina-sequencing-data.

seq.txt (Gerald)
4 1 23 1566 ACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCG
The first 4 columns are an ID that provides location details of the cluster in the flow cell, followed by the read sequence. Seq.txt file size typically ranges between 250 Megabytes and 1 Gigabyte. One file is generated per lane.