last four column of the output

[gorliver]

There are four columns with sequences in the output tabular file. It seems no document about these sequences.

@seq8
35738 35771 16 2.1 16 88 0 50 11 23 0 64 1.26 TTCTTCATCTTTTAAC TTCTTCTTCTTTTTACTTCTTCATCTTTTAACTT AGTAACTGAACGATTATGATTTTACTGTAATATATCTACTACAAGTTTTT TCTCTTTAAATCTCATATGAAGATGATAAAACACATCAATGGAGGAAAGA

I wonder what these sequences are?
Thank you.

[kcamnairb]

I am not even able to find documentation on what any of the columns represent.

[gorliver]

I am not even able to find documentation on what any of the columns represent.
Some of the columns are documented here:
https://tandem.bu.edu/trf/trf.definitions.html

[yzhernand]

Sorry, I'm no longer in Gary's lab so I don't get too many chances to address things in this repo too often.

You're right, those columns are not documented and they should be. They are: the consensus pattern, the repeat sequence, the left flanking sequence, right flanking sequence.

A '.' (dot) for either flanking sequence means there is no sequence in that region (length 0).

[yzhernand]

Also, the rest of the columns are documented in the README on this repo as well: https://github.com/Benson-Genomics-Lab/TRF#table-explanation