AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons033_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240076
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0659	33	flagellar hook-associated protein 3 (flgL)
#1	TP0660	105	flagellar hook-associated protein 1 (flgK)

Motif 1
TTCAGATAGTGCACGGTATGAGGAAGGGAGG         	0	12	1
          GGTGCGGTACCTCGGGGGAGGAGCAGAGCG	1	0	1
CGGTACCTCGGGGGAGGAGCAGAGCGCGAGTATCCACAGG	1	14	1
GGAGCAGAGCGCGAGTATCCACAGGGCGAGAGGGAGGTTC	1	29	1
CAGGGCGAGAGGGAGGTTCCTGATGGGGCTGCTGCGCGTA	1	50	1
GCTGCGCGTACCCTCCATTCTTATAGGGAGAACAC     	1	80	1
          **     * *  *  *****
MAP Score: 5.87421

Motif 2
CACGGTATGAGGAAGGGAGG          	0	23	1
CGGTACCTCGGGGGAGGAGCAGAGCGCGAG	1	14	1
TCCACAGGGCGAGAGGGAGGTTCCTGATGG	1	46	1
CTATAAGAATGGAGGGTACGCGCAGCAGCC	1	76	0
          **********
MAP Score: 5.79323

Motif 3
TGCACGGTATGAGGAAGGGAGG         	0	21	1
GGTACCTCGGGGGAGGAGCAGAGCGCGAGTA	1	15	1
TATCCACAGGGCGAGAGGGAGGTTCCTGATG	1	44	1
          * *********
MAP Score: 1.05986