AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons032_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240071
 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)
#4	TP0569	24	aminopeptidase P
#5	TP0570	26	T. pallidum predicted coding region TP0570

Motif 1
GAACGTAGCGGGAGAGAGGAGGATGTTCGCC	0	38	1
TCGCACCGTTGAAAGAAGGGGCGGTTT    	1	55	1
AGCCTTTAGAAAAAGGAGGAGCTC       	2	3	0
CCCCTTCCTTGCGAAGAGGAGTATGCCAAAC	2	83	0
TCTTCGCAAGGAAGGGGGGAGGGC       	2	97	1
GATGTCCGCGGGCAAGAGGAGGGAATT    	3	104	1
          * *********
MAP Score: 8.7682

Motif 2
ATTAGGCGTTTAGCGCGCGCCGTCAAGTTTTTCTCAC	2	45	1
CGCCGTCAAGTTTTTCTCACCGTTTGGCATACTCCTC	2	62	1
GCCTAATAATTGCCTCGCAGCCTTTAGAAAAAGGAGG	2	15	0
ACATCCGGTGTAGGTCGCACCGTTGAAAGAAGGGGCG	1	41	1
CGCAGGCAGACTCTCCGCTCCCTAAGGCA        	1	2	0
     GTGTGTGCGTTGCCGCGCCAAGAGCG      	5	5	1
CCGTTTGGCATACTCCTCTTCGCAAGGAAGGGGGGAG	2	81	1
TGATCAAAAATCAAGATCTGCGTATAACACCAATCAA	3	20	0
CATCCTCCTCTCTCCCGCTACGTTCTAGTGTCGTTCA	0	26	0
          *    *** ****  **
MAP Score: 7.34962

Motif 3
  CGGTAATGCCGAGCCTTGAACGACACTAGAAC	0	8	1
AGAACGTAGCGGGAGAGAGGAGGATGTTCGCCC 	0	37	1
   TGCCTTAGGGAGCGGAGAGTCTGCCTGCGGC	1	7	1
CGGTGTAGGTCGCACCGTTGAAAGAAGGGGCGGT	1	46	1
ATAATTGCCTCGCAGCCTTTAGAAAAAGGAGGAG	2	13	0
AAACTTGACGGCGCGCGCTAAACGCCTAATAATT	2	41	0
GAGGAGTATGCCAAACGGTGAGAAAAACTTGACG	2	65	0
CTCCCCCCTTCCTTGCGAAGAGGAGTATGCCAAA	2	84	0
AAAAGATGTCCGCGGGCAAGAGGAGGGAATT   	3	100	1
GTGTGCGTTGCCGCGCCAAGAGCG          	5	12	1
          *** ***  *** *
MAP Score: 5.41293

Motif 4
     CGGTAATGCCGAGCCTTGAACGACA	0	5	1
CGACACTAGAACGTAGCGGGAGAGAGGAGG	0	30	1
    TGCCTTAGGGAGCGGAGAGTCTGCCT	1	6	1
GCGGAGAGTCTGCCTGCGGCACATCCGGTG	1	21	1
CATCCGGTGTAGGTCGCACCGTTGAAAGAA	1	42	1
CTTTTTCTAAAGGCTGCGAGGCAATTATTA	2	19	1
TTAGGCGTTTAGCGCGCGCCGTCAAGTTTT	2	46	1
TCTGAAAAGATGTCCGCGGGCAAGAGGAGG	3	96	1
 GTGTGTGCGTTGCCGCGCCAAGAGCG   	5	9	1
          **********
MAP Score: 4.6461

Motif 5
CGACACTAGAACGTAGCGGGAGAGAGGAGGAT	0	30	1
    TGCCTTAGGGAGCGGAGAGTCTGCCTGC	1	6	1
GCACCGTTGAAAGAAGGGGCGGTTT       	1	57	1
CGCAGCCTTTAGAAAAAGGAGGAGCTC     	2	5	0
CCCCTTCCTTGCGAAGAGGAGTATGCCAAACG	2	82	0
TCCTCTTCGCAAGGAAGGGGGGAGGGC     	2	94	1
GATGTCCGCGGGCAAGAGGAGGGAATT     	3	104	1
          * **** *****
MAP Score: 4.59577

Motif 6
TCCCGCTACGTTCTAGTGTCGTTCAAGGCTCGGC	0	17	0
GAACGTAGCGGGAGAGAGGAGGATGTTCGCCC  	0	38	1
GCCTTAGGGAGCGGAGAGTCTGCCTGCGGCACAT	1	11	1
CCTGCGGCACATCCGGTGTAGGTCGCACCGTTGA	1	33	1
GCACCGTTGAAAGAAGGGGCGGTTT         	1	57	1
AGCCTTTAGAAAAAGGAGGAGCTC          	2	0	0
CTTCCTTGCGAAGAGGAGTATGCCAAACGGTGAG	2	77	0
TCTTCGCAAGGAAGGGGGGAGGGC          	2	97	1
TTTTCCTGTTGATTGGTGTTATACGCAGATCTTG	3	12	1
CATTAGCTTAGGCGGGTGCACTGCATGTGGTGTC	3	64	1
GGTGCACTGCATGTGGTGTCTGAAAAGATGTCCG	3	78	1
GATGTCCGCGGGCAAGAGGAGGGAATT       	3	104	1
     AATTGAATCGGTGTTCTGCGTAGT     	4	5	1
          *   ******** *
MAP Score: 1.5327