my @file1_lines = qw(
   xxtcgtatccgaggga
   cgcgcgggggagg
   jjsjjjjsjjjdtcgtat
   aaaaaaacccaaan
   ggtcgtatffaadda
   gggctggalllslllssdkk
   );

my @file2_lines = qw(
   tcgtat
   gctgga
   );

my $replace_pattern = join('.*|', @file2_lines) . '.*';

my @output_array;
for my $line (@file1_lines)
{
   my $output_line = $line;
   $output_line =~ s/$replace_pattern//;
   push @output_array, $output_line;
}

say for @output_array;