File: test.hhm

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HHsearch 1.5
NAME  name
FAM   fam
LENG  2 match states, 2 columns in multiple alignment
NEFF  10
PCT   False
SEQ
#
NULL   5346	8263	5863
HMM    A	C	E
       M->M	M->I	M->D	I->M	I->I	D->M	D->D	Neff	Neff_I	Neff_D
       321    	3321   	3321   	*	*	*	*	*	*	*	
A 1    0      	1000   	1584   	1
       321    	3321   	3321   	1000   	1000   	1000   	1000   	*      	*      	*      	

C 2    0      	1000   	1584   	2
       152    	3321   	*	1000   	1000   	0      	*	*      	*      	*      	

//