# [Tutor] number of mismatches in a string

Hs Hs ilhs_hs at yahoo.com
Fri Mar 2 20:11:30 CET 2012

```Hi:
I have the following table and I am interested in calculating mismatch ratio. I am not completely clear how to do this and any help is deeply appreciated.

Length     Matches
77      24A0T9T36

71      25^T9^T37

60      25^T9^T26
62      42A19

In length column I have length of the character string.
In the second column I have the matches my reference string.

In fist case, where 77 is length, in matches from left to right, first 24 matched my reference string following by a extra character A, a null (does not account to proble) and extra T, 9 matches, extra T and 36 matches.  Totally there are 3 mismatches

In case 2, I lost 2 characters (^ = loss of character compared to reference sentence)   -

TOMISAGOODBOY
T^MISAGOOD^OY   (here I lost 2 characters)  = I have 2 mismatches
TOMISAGOOODBOOY (here I have 2 extra characters O and O) = I have two mismatches

In case 4: I have 42 matches, extra A and 19 matches = so I have 1 mismatch

How can that mismatch number from matches string.
1. I have to count how many A or T or G or C (believe me only these 4 letters will appear in this, i will not see Z or B or K etc)
2. ^T or ^A or ^G or ^C will also be a mismatch

desired output:

Length     Matches   mismatches
77      24A0T9T36    3

71      25^T9^T37     2

60      25^T9^T26     2
62      42A19             1
10      6^TTT1           3

thanks
Hs.
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