The ^ character has meaning within a regex (anchor the following stuff at the beginning of line). If you want this ^ character be interpreted without the contextual meaning, ie literally, you need to "escape it" with a "\".

I'm not really sure what you are trying to do here. A simple example with a)I have this "X" and b)I what that "Y" would be helpful. BTW:

 
[a]|[c]|[t]|[g]{6} #looks like a char set 
[actg]{6}
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