Gila Lithwick gilal at
Wed Nov 5 14:55:28 UTC 2003


I ran the emboss program "palindrome" on the sequence K01964.

This sequence has an inverted repeat of length 11, occurring at 122-132 
and 4672-4682.  These inverted repeats have a mismatch at the first base 
(the entire 11 bases are defined as inverted repeats for several reasons).

I noticed two problems when I ran palindrome on this sequence:
1)The "maximum length of palindrome" is actually the maximum length +1. 
 (To search for a specific palindrome length the maximum length must be 
the minimum length +1).
2) When searching for a repeat of length 11 with at least one mismatch 
in the above example, the true inverted repeats are not found.  I 
imagine that this is because the mismatch is on the edge, however there 
is meaning for this type of hit.

Thank you,


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