How to interpret contig-alignment.psa produced by velvet I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using velvetg out-dir/ -alignment yes, velvet produces contig-alignment.psa which is a file in a strange format. 
The file for every contig contains zero or more records of 7 integers, and I cannot understand their meaning.

The following is an excerpt of the file, and you can see the entire file here:

&gt;contig_1
1    193    1939    1939    6   194 2
195 244 1   1   6   22  71
&gt;contig_2
1   84  1   1   6   59  142
86  170 1935    1935    6   22  106
172 285 1935    1935    6   108 221
&gt;contig_3
1   98  2   2   6   1   98
100 321 2   2   6   100 321
334 415 1204    1204    6   1   82
&gt;contig_15
1   23  3   3   6   84  106
It looks like you are trying to do a transcript isoform expression analysis. Velvet is a genome assembler, and really not designed for this task. The tools you are looking for are kallisto and salmon.