AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_sum_all057_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254289
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB1103	94	PAB1103
#1	ppa	64	PAB1104
#2	rpoE1	36	PAB1105

Motif 1
   TAGAAATCACCAAATGCTTTAGTGAGC	0	7	1
          CACTTCACCCAGGAATAATT	0	84	0
AGAGTCTCTTCATCTAACCCAGAGGTTTTC	1	13	1
        TCCCTCTCACCCCTATTTCGTT	1	52	0
          **********
MAP Score: 2.72695

Motif 2
TCTTAAATAACCTCTGCTCACTAAAGCATT	0	22	0
ACCCAGGAATAATTAGGCCACTCTAAAATT	0	68	0
          CACTTCACCCAGGAATAATT	0	84	0
AGAGTCTCTTCATCTAACCCAGAGGTTTTC	1	13	1
        TCCCTCTCACCCCTATTTCGTT	1	52	0
          CAGTTGCCCCTCCGGAAAAA	2	26	0
          **********
MAP Score: 0.13275