Why is it hard to align longer DNA sequences?

Question

[sushi]

I often find excess nucleotide bases or gaps after MSA. Why could be the possible reason for this?

Answer 1

[Carlo Yague]

What do you align ? Homologs ? and what tool do you use for multiple sequence alignment (MSA) ?

The most obvious answer is that during evoution, indels occured between the multiple sequences you align, so when you align them, you see gaps or insertions. That would be the biological reason.

Alternatively, there is a possible technical reason if the gap penalty of your MSA algorithm is set too low.

[sushi]

I use MEGA software for MSA. Is it okay if I trim the unaligned sequences from both ends?

This is noted, thank you very much for answering my question.