I want to find the positions in seq1 were there is a '-' character

index

and delete those positions in seq2.

substr

Is it possible to do it without a for loop??

Possibly, but why do you have this constraint?

Read the docs that I pointed to, try it with your own code, then, if you still have problems, post the code you have tried, along with actual and expected output.

Also, please do not post general Perl questions in the 'PerlMonks Discussion' section. Read Where should I post X?.