data1.txt
@NS500278
AGATCNGAA
+
=CCGGGCGG   1

@NS500278
TACAGNGAG
+
CCCGGGGGG   2

@NS500278
CATTGNACC
+
CCCGGGGGG   3

data2.txt

@NS500278
AGATCNGAA
+
=CCGGGCGG   1

@NS500278
CATTGNACC
+
CCCG#GGG#   2

@NS500278
TACAGNGAG
+
CC=GGG#GG   2


output:

@NS500278
AGATCNGAA
+
=GGGGGCCG	 1:data1.txt.out	1:data2.txt.out	count:2

@NS500278
CATTGNACC
+
CCCGGGGGG 3:data1.txt.out	 2:data2.txt.out	count:5

@NS500278
TACAGNGAG
+
CCCGGGGGG 2:data1.txt.out	 2:data2.txt.out	count:4