I'm working with pairwise whole genome alignment and retrieved some data from Ensembl, in the data there two types of symbols '-' and '.' . for example in this alignment:

http://www.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=714&db=core&g=ENSG00000184029&r=21%3A37951425-37973764

i think '-' represent gaps but i dont know what dots represent. in the example above there are dots in the vicinity of the sequence 'TTTAAAGAGAATATCCTTGTTCTTAGTAAATATGCCTT'

I appreciate if anybody could help me here
Answer by Ensembl Helpdesk:

> In this view:

> <a href="http://www.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=688--pan_troglodytes--17:62917953-63020080;db=core;r=17:64155265-64255264" target="_blank">http://www.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=688--pan_troglodytes--17:62917953-63020080;db=core;r=17:64155265-64255264</a>

> dashes ('-') represent gaps in the sequence of one genome relative to its counterpart in the pairwise view. You can think of them as indels (insertions/deletions when comparing the genomes).

> The dots are to represent that we were unable to find a match in that given region and this can be due to several region s such as the genome is fragmented (therefore regions are missing) or the match did not pass our threshold so we have not showed them in the alignment...

> This information should be in the help page of that view:

> <a href="http://www.ensembl.org/Help/View?id=202" target="_blank">http://www.ensembl.org/Help/View?id=202</a>

> We will be updating it for the next release.