AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_profile020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234368
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0356	103	370aa long hypothetical protein
#1	PH1578	50	248aa long hypothetical protein
#2	PH1579	59	173aa long hypothetical protein
#3	PH1904	90	106aa long hypothetical protein

Motif 1
TTAGAAAAGGAAACTAGGATAAGAGGTGGG	0	16	0
ACACGTTAATAAACTTCTCTCTTGCAAAAT	0	54	0
 ATAGTCTCCCTACTTGGTTAGTGTACTGA	0	84	0
TTGAGATTCGAAATTACCCTTTTAAACTTG	1	13	1
TTACCCTTTTAAACTTGCCTTCCAACTGAT	1	26	1
TGATTGAGAGGGACTTGGCTGAGCG     	2	44	1
         TCAACTTCCCTCGAATAGTTA	3	1	1
TGGCTATTTAAAAATTGCTTTAGAGGATTA	3	52	0
          **********
MAP Score: 4.54196

Motif 2
ACCCTTTTAAACTTGCCTTCCAACTGATAG	1	28	1
ATGAGGCCTCGATTGGCTGAATCGATGATT	2	19	1
ATTGAGAGGGACTTGGCTGAGCG       	2	46	1
GCTATTTAAAAATTGCTTTAGAGGATTAAC	3	50	0
          **********
MAP Score: 0.432096