Give your dataset, here's one option:

use strict;
use warnings;

local $/ = 'HDR';

while (<DATA>) {
    chomp;
    s/\n+$//;
    print substr( $_, 47, ( length $_ ) - 77 ), "\n" if /\S/;
}

__DATA__
HDR.S287878877.DDDDD.DDDDDDXXXXXXXXXXXXXXXXXXXXXXX1STR HYTRES NAME PLA
+CE DEST
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG11111111111111111111122222222222222222222222222223
+33333333333333333333333333444444444444444444444444444444444455
5555555555555555555555555555566666666666666777777777777FTRDDDDDDDDDDFF
+FFFFFFFFFFFFFFF
HDR.S287878877.DDDDD.DDDDDDXXXXXXXXXXXXXXXXXXXXXXX1STR HYTRES NAME PLA
+CE DEST
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG11111111111111111111122222222222222222222222222223
+33333333333333333333333333444444444444444444444444444444444455
5555555555555555555555555555566666666666666777777777777FTRDDDDDDDDDDFF
+FFFFFFFFFFFFFFF
[download]

Output:

1STR HYTRES NAME PLACE DEST
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG11111111111111111111122222222222222222222222222223
+33333333333333333333333333444444444444444444444444444444444455
5555555555555555555555555555566666666666666777777777777
1STR HYTRES NAME PLACE DEST
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
GGGGGGGGGGGGGGGGGGGG11111111111111111111122222222222222222222222222223
+33333333333333333333333333444444444444444444444444444444444455
5555555555555555555555555555566666666666666777777777777
[download]