Maybe you need to think of the problem in reverse ie the target is the source and the source the target and see where that works.

target = [ACT]GCTATC[GC]
source = TGCTATCA
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Then you can apply each character or group in the target as a regex to the source. The answer should be the same if as in examples they are the same length.

If not then you may need to keep some form of pointer to the actual place in the sequence (this looks like gene/DNA sequences).