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use strict;
use warnings;
...
__DATA__
.06669701$-.1672469$.02157899$.0346167$.65879324$.91614802$.45012441$r
+s11080516
[... I have abbreviated your data for this post ...]

$ perl overlapping_lines.pl
.06669701$-.1672469$.02157899$.0346167$.65879324$.91614802$.45012441$r
+s11080516
...
-.03866776$-.05004879$.00185491$.00145606$.38131545$.36141448$.1755140
+3$rs11080557
-.004521$.01312692$.00033174$.00070174$.77873394$.88615378$.63499741$r
+s1108056
.0339248$.02398934$.00276444$.00303152$.80478053$.55026576$.67512938$r
+s11080561