AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_sum_all042_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243117
 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
ATGTATCTTAAGCGGCAGGTGGCGTGATGGGG	0	28	1
AGGTGGCGTGATGGGGATGAGGG         	0	44	1
GAACAGAGAAAGAGAGATTAGGAAAATGAGTC	1	26	1
TAGGAAAATGAGTCACATGAGGAGGACACAGA	1	44	1
CAACCGGTGAAAAAAGAGGAGGGCCGGGGC  	2	55	1
          **  ********
MAP Score: 4.73499

Motif 2
AGGTGGCGTGATGGGGATGAGGG        	0	44	1
AAGAGAGATTAGGAAAATGAGTCACATGAGG	1	35	1
AATGAGTCACATGAGGAGGACACAGAGCAT 	1	50	1
CCTACCCTGTAGGGGGGTCAGCGTACACAAC	2	28	1
CCGGTGAAAAAAGAGGAGGGCCGGGGC    	2	58	1
          * *********
MAP Score: 3.34698

Motif 3
ATGTATCTTAAGCGGCAGGTGGCGTGATGGGGAT	0	28	1
ATGAGTCACATGAGGAGGACACAGAGCAT     	1	51	1
GCCTACCCTGTAGGGGGGTCAGCGTACACAACCG	2	27	1
CGGTGAAAAAAGAGGAGGGCCGGGGC        	2	59	1
          ** ** ** * ***
MAP Score: 0.552353

Motif 4
GAAAATGTATCTTAAGCGGCAGGTGGCGTGATGG	0	24	1
GAAAATGAGTCACATGAGGAGGACACAGAGCAT 	1	47	1
ACAGGGTAGGCAAAACCGGCGCGCCTAT      	2	4	0
GTTTTGCCTACCCTGTAGGGGGGTCAGCGTACAC	2	22	1
CAACCGGTGAAAAAAGAGGAGGGCCGGGGC    	2	55	1
          ** *  *** ****
MAP Score: 0.420666