which code is giving you always the same key? it seems not probable to me. In case post your code , your data and your output.
Here mines:
#cat gen1.txt
@gi
AGAT
+
AAAA 1:1.txt
@gi
CATT
+
AAAAA 3:1.txt
#cat gen2.txt
@gi
AGAT
+
AAAA 1:2.txt
@gi
TACA
+
AAAA 2:2.txt
perl -lane "BEGIN{$/=''}map{$h{$_}{s}.=' '.$F[4];$h{$_}{c}+=$1 if $F[
+4]=~/(\d+):/}join qq(\n),@F[0..3];
END{print map{qq($_ $h{$_}{c} $h{$_}{s}\n\n)} keys %h}"
+ gen1.txt gen2.txt
@gi
AGAT
+
AAAA 2 1:1.txt 1:2.txt
@gi
CATT
+
AAAAA 3 3:1.txt
@gi
TACA
+
AAAA 2 2:2.txt
L*
There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.
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