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copied!<p>This is a tough one. I think this might work:</p> <pre><code>s/((?<!a)a|(?<!a|t)t)((?<!t)\1|t){3,6}(?!\2|t)/\U$&/gi </code></pre> <p>Essentially, what I'm doing is:</p> <ol> <li>Get an <code>a</code> not preceded by an <code>a</code>. Or a <code>t</code> not preceded by an <code>a</code> or <code>t</code>. <ul> <li><code>((?<!a)a|(?<!a|t)t)</code></li> </ul></li> <li>Get 3-6 more of the first match, or <code>t's</code> not preceded by a <code>t</code> <ul> <li><code>((?<!t)\1|t){3,6}</code></li> </ul></li> <li>Make sure it is not followed by the last item in the sequence or a <code>t</code>. <ul> <li><code>(?!\2|t)/</code></li> </ul></li> </ol> <p>And the perl code:</p> <pre><code>$syb = "aaatcgacgatcgatcaatttcgaaaaaggattttttatgcacgcacggggattaaaaactgaaaattttactgaaaaaaaasttttttts"; $syb =~ s/((?<!a)a|(?<!a|t)t)((?<!t)\1|t){3,6}(?!\2|t)/\U$&/gi; print $syb; </code></pre> <hr> <p><strong>Edit</strong> taking a queue from qtax I've removed capturing groups from mine and chars from his:</p> <pre><code>s/(?:(?<!a)a|(?<!a|t)t)(?:(?<!t)a|t){3,6}(?!(?<=a)a|t)/\U$&/gi </code></pre> <p><strong>Edit:</strong> reducing the regex by 5 chars.</p> <pre><code>s/(?<!a|t(?=t))(?:a|t(?!a)){3,6}(?:a(?!a)|t)(?!t)/\U$&/gi </code></pre> <p>with commments </p> <pre><code>s/ # Look behind for a char not an 'a' nor a 't' followed by a 't' (?<!a|t(?=t)) # Capture 3-6 'a's or 't's not followed by 'a's (?:a|t(?!a)){3,6} # Capture an 'a' not followed by an 'a', or a 't' (?:a(?!a)|t) #make sure none of this is followed by a 't'. (?!t) /\U$&/gix; </code></pre>

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