I need to compare some BACend sequences against contigs sequences. First i made the comparison without masking the BACend sequences and then I masked them for SSR and simple repeats.
When I masked the BACends no alignment was made. I compared the results with and without masking and found the alignments without masking didn't occur between SSR or simple repeats.
Then, I don't understand why the alignments between unmasked BACends and the contigs are not the same as alignments between masked BACends and contigs at the same e-value. I even used a less astringent e-value without success.
Can somebody explain what is happenning?