I believe you want that:

DL;H1_ENSP00000194530_chr2_202024 CCCC---GCCTTCTCGCTGCCCAGC--CCCGGGGAGGGAGG*

To became:

H1_ENSP00000194530_chr2_202024 CCCCGCCTTCTCGCTGCCCAGCCCCGGGGAGGGAGG

A very naive approach would be using tr and s to remove the undesired characters, like this:

# in a loop while reading
$_ =~ tr/-//d;
$_ =~ s/^DL\;//o;
$_ =~ s/\*$//o;
[download]

Of course, I'm unaware about any rule to remove those characters, since you didn't mentioned anything about it.