AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons031_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240064
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0726	57	flagellar protein (flbD)
#1	TP0727	70	flagellar hook protein (flgE)
#2	TP0728	75	flagellar hook assembly scaffolding protein (flgD)

Motif 1
AGGTGGCGTGATGGGGATGAGGG          	0	44	1
GGTTTGTGAACAGAGAAAGAGAGATTAGGAAAA	1	19	1
AAGAGAGATTAGGAAAATGAGTCACATGAGGAG	1	35	1
AATGAGTCACATGAGGAGGACACAGAGCAT   	1	50	1
CCTACCCTGTAGGGGGGTCAGCGTACACAACCG	2	28	1
CCGGTGAAAAAAGAGGAGGGCCGGGGC      	2	58	1
          * ***** *** *
MAP Score: 4.88906

Motif 2
ATACATTTTCACACAGTCGACACA      	0	4	0
AATGTATCTTAAGCGGCAGGTGGCGTGATG	0	27	1
GTGGCGTGATGGGGATGAGGG         	0	46	1
ACAGAGAAAGAGAGATTAGGAAAATGAGTC	1	28	1
GGAAAATGAGTCACATGAGGAGGACACAGA	1	46	1
       ATAGGCGCGCCGGTTTTGCCTAC	2	3	1
TGACCCCCCTACAGGGTAGGCAAAACCGGC	2	18	0
CTACCCTGTAGGGGGGTCAGCGTACACAAC	2	29	1
GGGTCAGCGTACACAACCGGTGAAAAAAGA	2	42	1
ACCGGTGAAAAAAGAGGAGGGCCGGGGC  	2	57	1
          **********
MAP Score: 1.11518