AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons032_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240066
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0477	60	glucose-6-phosphate 1-dehydrogenase, putative
#1	TP0478	72	glucose-6-phosphate 1-dehydrogenase (zwf)
#2	TP0479	111	T. pallidum predicted coding region TP0479
#3	TP0568	121	4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda)

Motif 1
          CGGTAATGCCGAGCCTTGAAC	0	0	1
GAACGACACTAGAACGTAGCGGGAGAGAGGA	0	27	1
GAACGTAGCGGGAGAGAGGAGGATGTTCGCC	0	38	1
    TGCCTTAGGGAGCGGAGAGTCTGCCTG	1	6	1
CACCGGATGTGCCGCAGGCAGACTCTCCGCT	1	20	0
CATCCGGTGTAGGTCGCACCGTTGAAAGAAG	1	42	1
GCACCGTTGAAAGAAGGGGCGGTTT      	1	57	1
CGCAGCCTTTAGAAAAAGGAGGAGCTC    	2	6	0
TTAGGCGTTTAGCGCGCGCCGTCAAGTTTTT	2	46	1
AGAGGAGTATGCCAAACGGTGAGAAAAACTT	2	69	0
CCCCTTCCTTGCGAAGAGGAGTATGCCAAAC	2	83	0
CCTCTTCGCAAGGAAGGGGGGAGGGC     	2	95	1
CTTTTCAGACACCACATGCAGTGCACCCGCC	3	74	0
GATGTCCGCGGGCAAGAGGAGGGAATT    	3	104	1
          ****** ****
MAP Score: 14.164

Motif 2
          CGGTAATGCCGAGCCTTGAACGACACTA	0	0	1
TAGAACGTAGCGGGAGAGAGGAGGATGTTCGCCC    	0	36	1
CGACCTACACCGGATGTGCCGCAGGCAGACTCTCCGCT	1	20	0
CATCCGGTGTAGGTCGCACCGTTGAAAGAAGGGGCGGT	1	42	1
CTTTTTCTAAAGGCTGCGAGGCAATTATTAGGCGTTTA	2	19	1
TTAGGCGTTTAGCGCGCGCCGTCAAGTTTTTCTCACCG	2	46	1
TACTCCTCTTCGCAAGGAAGGGGGGAGGGC        	2	91	1
AAAGGACATTAGCTTAGGCGGGTGCACTGCATGTGGTG	3	58	1
AAGATGTCCGCGGGCAAGAGGAGGGAATT         	3	102	1
          ***  * ****  *   *
MAP Score: 12.8694

Motif 3
AACGACACTAGAACGTAGCGGGAGAGAGGAGGAT	0	28	1
TCGCACCGTTGAAAGAAGGGGCGGTTT       	1	55	1
CGGGTGCACTGCATGTGGTGTCTGAAAAGATGTC	3	76	1
ACTCCTCTTCGCAAGGAAGGGGGGAGGGC     	2	92	1
ATGTCCGCGGGCAAGAGGAGGGAATT        	3	105	1
 TGCCTTAGGGAGCGGAGAGTCTGCCTGCGGCAC	1	9	1
TAGGCGTTTAGCGCGCGCCGTCAAGTTTTTCTCA	2	47	1
          *** * ** *** *
MAP Score: 9.24042

Motif 4
AGAACGTAGCGGGAGAGAGGAGGATGTTCG	0	37	1
   TGCCTTAGGGAGCGGAGAGTCTGCCTG	1	7	1
TCGCACCGTTGAAAGAAGGGGCGGTTT   	1	55	1
GCCTTTAGAAAAAGGAGGAGCTC       	2	3	0
CCCTTCCTTGCGAAGAGGAGTATGCCAAAC	2	83	0
CTCCTCTTCGCAAGGAAGGGGGGAGGGC  	2	93	1
ATGTCCGCGGGCAAGAGGAGGGAATT    	3	105	1
          **********
MAP Score: 7.16798

Motif 5
CGACACTAGAACGTAGCGGGAGAGAGGAGGA	0	30	1
    TGCCTTAGGGAGCGGAGAGTCTGCCTG	1	6	1
GCGGAGAGTCTGCCTGCGGCACATCCGGTGT	1	21	1
CATCCGGTGTAGGTCGCACCGTTGAAAGAAG	1	42	1
GCACCGTTGAAAGAAGGGGCGGTTT      	1	57	1
CTTTTTCTAAAGGCTGCGAGGCAATTATTAG	2	19	1
TTAGGCGTTTAGCGCGCGCCGTCAAGTTTTT	2	46	1
CCTCTTCGCAAGGAAGGGGGGAGGGC     	2	95	1
AAAGGACATTAGCTTAGGCGGGTGCACTGCA	3	58	1
TCCCTCCTCTTGCCCGCGGACATCTTTTCAG	3	97	0
          *** *******
MAP Score: 6.62199

Motif 6
AACGTAGCGGGAGAGAGGAGGATGTTCGCC	0	39	1
 TGCCTTAGGGAGCGGAGAGTCTGCCTGCG	1	9	1
ACCGTTGAAAGAAGGGGCGGTTT       	1	59	1
AGCCTTTAGAAAAAGGAGGAGCTC      	2	4	0
TCTTCGCAAGGAAGGGGGGAGGGC      	2	97	1
GTCCGCGGGCAAGAGGAGGGAATT      	3	107	1
          **********
MAP Score: 3.99097