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use warnings;
use strict;
...
    }
}
close FILE1 || die "Failed to close $file1 : $!";

@SQ    SN:TMEM200B    LN:293
@SQ    SN:B3GAT2-2_P001    LN:204
Seq1Perfect    0    B3GAT2-2_P001    1    37    500M400D300M200I100M  
+  *    0    0    GGTTGGTTTTTATTTTTTGGAAGAGTTTTAGATTATAGGTGTTGTCGTCGTT
+AGCGAAGAAGAGTACGTCGGGTTGCGCGCGTTGGTGTTGGTGTTTTTGGCGTAGTTAGGCGAGGTTCGC
+GTTGCGTTGTTTAGTGGCGCGCGGTAGTTCGGGTCGTTTGTAGCGTCGCGGCGTGGGTACGTGTAGGTG
+AGTGTTGGGTAGTT    &a==aa=====a======aaaaaaa====aaa==a=aaa=a==a=$a=$a=
+=aa$aaaaaaaaa=a$a=$aaa==a$a$a$a==aa=a==aa=a=====aa$a=aa==aaa$aaaa==$a
+$a==a$a==a===aa=aa$a$a$aa=aa==$aaa=$a===a=aa$a=$a$aa$a=aaa=a$a=a=aaa=
+aaa=a==aaa=aa==