First off, please use the <code> tag when including code.
Second, We need a little terminology consistency :). You talk about looking for A/C/G/T in 'arrays 4-7'. I assume that you really mean 'columns' here, but need to be sure. The statement " If an '=' sign exist, then I need to skip that array and still keep count of the array number." does not seem to correlate at all to the output example you have provided. You then mention that 48 arrays will be present. Do you really mean 48 rows of data, or 48 blocks of rows of data?
Third, your code does not appear to do anything like what you ask. You dereference an array without brackets, you define $skip_strain but never apply it.