Dear japhy,
Thanks so much for your answer to my posting. I just have a question. Your code works well in generalize version of array like this: 
my @instances = ( 'AAAAA  ATCGA',
                  'ATCGA  AAAAA',
                  'ATAAA  AAAAA',
                 );

[download]
But how can I make it more generalize for cases like this? 
my @instances2 = ( 'AAAAA  ATCGA',
                   'ATCGA',
                   'ATAAA  AAAAA',
                 );
# consensus :       ATAAA  A[AT][CA][GA]A

[download]
Or this: 
my @instances3 = ( 'AAAAA  ATCGA TTTT',
                   'ATCGA        TATA ',
                   'ATAAA  AAAAA ATTA ',
                 );
# consensus :      ATAAA  A[AT][CA][GA]A TTTA

[download]
Cause, currently it gives warning when encountering two cases like that.

Regards,
Edward

In reply to Re^2: Finding Consensus String by monkfan
in thread Finding Consensus String by monkfan

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