-- RUNTIME COMPARISON --
Compute mum candidates of length >= 100.
Result is identical for both programs.
 
			mummer3:		mummer2:

Ecoli K12/
Ecoli 0157: 		14 sec/66 MB		17 sec/133 MB

Ecoli 0157/
Ecoli K12: 		14 sec/77 MB		17 sec/155 MB

S cerevisae/
S pombe			42 sec/172 MB		50 sec/348 MB

S pombe/
S cerevisae		41 sec/176 MB		52 sec/358 MB



-- CORRECTNESS COMPARISON --
Consider the two files

> N25
NNNNNNNNNNNNNNNNNNNNNNNNN

and nn.query

> n18
nnnnnnnnnnnnnnnnnn

------------------ First example:---------------
mummer3 -l 5 Data/nn.query Data/nn.subject
> N25
       1         1        18
       1         2        18
       1         3        18
       1         4        18
       1         5        18
       1         6        18
       1         7        18
       1         8        18

mummer2 -l 5 Data/nn.query Data/nn.subject
> N25
       1         1        18

I think the result of mummer3 is correct, since the 
string n18 occurs exactly once in n18. It occurs 8
times in N25. hence 8 MUM-candidates are reported.

---- second example -----

mummer3.x -l 5 Data/nn.subject Data/nn.query
> n18

Bigmum.sh  -l 5 Data/nn.subject Data/nn.query
> n18
New string is suffix of reference string
       8         1        18

Here n18 occurs several times in the N25, hence it is 
not a MUM-candidates and so nothing is to be reported.
Thus the result of mummer3 is correct.