If you want to use split, you need to apply lookbehind and lookahead assertions in the regex, to keep the letters A, G, C and T out of the match: 

my @info = split /(?<=[ATGC])N+(?=[ATGC])/, $line;

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In reply to Re^4: Splitting only on internal pattern, not at start or end of string by hdb
in thread Splitting only on internal pattern, not at start or end of string by BiologySwede

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