regex: matching a repeating sequence

Question

I'm trying to construct a regular expression that will match a repeating DNA sequence of 2 characters. These characters can be the same.

The regex should match a repeating sequence of 2 characters at least 3 times and, here are some examples:

regex should match on:

ATATAT
GAGAGAGA
CCCCCC

and should not match on:

ACAC
ACGTACGT

So far I've come up with the following regular expressions:

[ACGT]{2}

this captures any sequence consisting of exactly two characters (A, C, G or T). Now I want to repeat this pattern at least three times, so I tried the following regular expressions:

[ACGT]{2}{3,}
([ACGT]{2}){3,}

Unfortunately, the first one raises a 'multiple repeat' error (Python), while the second one will simply match any sequence with 6 characters consisting of A, C, G and T.

Is there anyone that can help me out with this regular expression? Thanks in advance.

Jerry · Accepted Answer · 2013-12-12 08:47:32Z

8

You could perhaps make use of backreferences.

([ATGC]{2})\1{2,}

\1 is the backreference referring to the first capture group and will be what you have captured.

regex101 demo

edited Dec 12, 2013 at 8:47

answered Dec 12, 2013 at 8:42

Jerry

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6 Comments

Alec Teal Over a year ago

Will match ACAC (ACACACAC certainly) - not downvoting because I have no idea what the OP wants

thefourtheye Over a year ago

@AlecTeal Entire expression will not match match ACAC. :)

Alec Teal Over a year ago

@thefourtheye so the OP wants to reject only ACAC? This sounds like a job for simple if statements in that case, the comment stays because I am not convinced it does not apply.

thefourtheye Over a year ago

@AlecTeal He wants to match any two letter combination of AGCT and that should be repeated atleast twice.

Michael Molter Over a year ago

Cases like AAATTTAAATTTAAA aren't caught by this pattern.

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Alec Teal · Accepted Answer · 2013-12-12 08:41:08Z

0

One:

(AT){3}

Two

(GA){4}

Three

C{6}

Combining them!

(C{6}|(GA){4}|(AT){3})

answered Dec 12, 2013 at 8:41

Alec Teal

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11 Comments

thefourtheye Over a year ago

He wants to match something like ACACAC or any combination of letters in AGCT

Alec Teal Over a year ago

@thefourtheye I don't really follow

thefourtheye Over a year ago

He wants to match patterns like, ACACAC, ACACACAC, GCGCGC

Alec Teal Over a year ago

@thefourtheye then why is RedNaw's answer not the accepted one?

thefourtheye Over a year ago

Because he deleted it?

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