[Genome] Lowercase in .net.axt vs .fa files

[Martin Frith]

Hello:

the .net.axt files include lowercase sequence, but this does not seem
to correspond to annotated repeats, or to lowercase sequence in the
original chromosome files.

For example:

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsFr2/axtNet/chr10.hg18.fr2.net.axt.gz

includes:

0 chr10 82862 84100 chrUn 370283108 370284351 + 70025
GCATactataaaaatgctttaaaac--gCAGCA...
gtacgtTATATAAGAAGTTTAATATTGACAAGA...

but the corresponding region is uppercase in:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr10.fa.gz

and this region of hg18 has no annotated repeats in the genome browser.

So where does the lowercase in the .net.axt files come from?

Have a nice day,
Martin Frith
http://www.cbrc.jp/~martin/