AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons029_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240013
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0075	118	sugar ABC transporter, permease protein (y4oQ)
#1	TP0076	39	sugar ABC transporter, permease protein (y4oR)
#2	TP0077	40	capsular polysaccharide biosynthesis protein (cap5D)
#3	TP0284	104	T. pallidum predicted coding region TP0284
#4	TP0562	170	spore coat polysaccharide biosynthesis protein (spsE)

Motif 1
TCTTCTTCTTGGGGGAAGAGAGGGCAGAAAAGATGCT	0	16	1
CGTGTTCTATCTGTGGAGCGCGTTACGTTGGGTAGCG	0	76	1
GCGTTACGTTGGGTAGCGTAAGAGGGGGAGTGC    	0	95	1
          GGGTTGCGTACGGGTTAGATAAGAGCA	1	0	1
GTACGGGTTAGATAAGAGCAGGAGCAGATAGC     	1	17	1
ACACTCTGCGCGGGTGAGTACGTGCAGCAGAT     	2	18	1
   ATTGCATGAGCTGAGTATGTGATGATTCTTTTTC	3	7	1
TTTTCTCACTCGGTTGAGTGATCTTCGGGGCTGTGCT	3	39	1
GTTCAGAAAAGTTTTGAGCAAGGTTCTCCTGC     	3	82	1
GGCCCTGCGGGTGCCGAGGATGAACGGC         	4	1	0
GGTTTGTATGGGTAAGAGGCAGGTGCTAAGATAGTGT	4	77	0
          ***  *** * * *  *
MAP Score: 13.6255

Motif 2
       AAAGTCTCTTCTTCTTGGGGGAAGAGAGGGCAGA	0	3	1
GGGCAGAAAAGATGCTGGATATGAGCGGAAACAGAATGACG	0	37	1
AACAGAATGACGTGTTCTATCTGTGGAGCGCGTTACGTTGG	0	66	1
TTCTATCTGTGGAGCGCGTTACGTTGGGTAGCGTAAGAGGG	0	80	1
CGCGTTACGTTGGGTAGCGTAAGAGGGGGAGTGC       	0	94	1
GGGTTGCGTACGGGTTAGATAAGAGCAGGAGCAGATAGC  	1	10	1
       AGGGATAAACACTCTGCGCGGGTGAGTACGTGCA	2	3	1
AACACTCTGCGCGGGTGAGTACGTGCAGCAGAT        	2	17	1
TTCTCACTCGGTTGAGTGATCTTCGGGGCTGTGCTTTTAAA	3	41	1
TTGCAGTACCGTCGTGTCGGCCCTGCGGGTGCCGAGGATGA	4	15	0
          *  *     ** * ****  *
MAP Score: 11.9901

Motif 3
TACCCAACGTAACGCGCTCCACAGATAGAACA	0	78	0
CACTCCCCCTCTTACGCTACCCAACGTAACGC	0	95	0
TTATCTAACCCGTACGCAACCC          	1	0	0
   AGGGATAAACACTCTGCGCGGGTGAGTAC	2	7	1
AGAATCATCACATACTCAGCTCATGCAAT   	3	7	0
CTGAACTTTAAAAGCACAGCCCCGAAGATCAC	3	56	0
     GCAGGAGAACCTTGCTCAAAACTTTTC	3	87	0
    GCCGTTCATCCTCGGCACCCGCAGGGCC	4	6	1
ACACTATCTTAGCACCTGCCTCTTACCCATAC	4	77	1
GCCTCTTACCCATACAAACCACGGCAAGGATT	4	94	1
ACCGATCAGGAAAGCTATACACCAATCACGCG	4	130	1
ACGCGTTTGGCGTACAATGCCCC         	4	157	1
          ***** **** *
MAP Score: 8.65176