if ($intron_from_boundary[$i] >= -6) { $left_of_boundary = 3; #$right_of_boundary = 6; $left_of_boundary = $left_of_boundary - intron_from_bound +ary[$i]; $new_left = 51 - $left_of_boundary; $seq = substr( $col7[$i], $new_left, 9); $matchID = $ID[$i] . "\t" . $intron_from_boundary[$i] +. "\t" . "on the negative strand"; }