AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239443
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0489	300	conserved hypothetical protein
#1	TP0492	23	DNA primase (dnaG)
#2	TP0708	65	T. pallidum predicted coding region TP0708
#3	TP0709	55	RNA polymerase sigma-28 factor
#4	TP1012	204	RNA polymerase sigma-43 factor (sigA)
#5	TP1025	300	ribosomal protein L13 (rplM)

Motif 1
CCCCTATGGAGTACGGTTGTGGTCTCGGGTGGGCGCAG	5	129	1
TGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGATT	0	252	1
TCGGGAGATTTTGCGCGGGAGGCGGTGGTGGGCGCGGT	5	44	1
TGCGGAAGGATTTCAGTGGCGGAGGAGGGGAC      	0	278	1
ATGCACTGCGGTTCTTGCGTGGTGCTGCGCCAGTCGGC	5	168	1
CTCTTGTCACTTTCTTGAGTGCAGGATGTTCTTTTCGT	0	226	1
AAGTTGGCTTGTTCGTTTGGGGAGTTTCCCGAGTGGTC	0	41	1
TTCCCGAGTGGTCAAAGGGAGCAGACTGTAAATCTGTT	0	66	1
AGAATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAG	4	100	1
         TGTAATCTCGAGGTCTAGGGTTCGAATCC	0	1	1
AGTCATATCTTCACGTTTGCGCCGTATGCCTACACGCA	4	28	1
AAATCAGCTATAACAGTAGAGGGCACGGGA        	3	35	1
AAGGACCTGTTTCCAAGCGTGTAGTGTGAGCT      	2	4	0
         GGAGCTAGTCTGCAGCTGGTTTTTTGTTT	2	46	0
GCAAACATGCGTGATCGTGCGCCCACGCGCAAGCTACC	5	245	1
TGCACAGAGGGTCCAGTGGCGTGATAGGGACACCGAAC	4	141	1
CGTCTTCCGTTTGCTTTTGGGTAGTGTCTGACTTGTCT	0	145	1
GCGCCCACGCGCAAGCTACCGGAGCGTGTGGATAAAGG	5	263	1
GCGGTTTTGGTTGGTGTGCTGCTGATGGGAGCGGCGGT	5	77	1
          ** *  * * ** *  **
MAP Score: 29.3396

Motif 2
CGTTTGGGGAGTTTCCCGAGTGGTCAAAGGGAGCAGACTGT	0	54	1
AGGCGTTTTTGCTAGCTGCTGTGCCTCTTGTCACTTTCTTG	0	202	1
TGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGATTTCA	0	252	1
GGTGCGGAAGGATTTCAGTGGCGGAGGAGGGGAC       	0	276	1
TGAAATCAGCTATAACAGTAGAGGGCACGGGA         	3	33	1
TGCGCCCCGCGCGGTGCGTGTAGGCATACGGCGCAAACGTG	4	39	0
GAAGAATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAGG	4	98	1
TATGCACAGAGGGTCCAGTGGCGTGATAGGGACACCGAACA	4	139	1
AGACGATCGGGAGATTTTGCGCGGGAGGCGGTGGTGGGCGC	5	38	1
AGGCGGTGGTGGGCGCGGTTTTGGTTGGTGTGCTGCTGATG	5	63	1
GTGTGCTGCTGATGGGAGCGGCGGTTTTCGCTCTTCTTTCC	5	90	1
TTCCCCTATGGAGTACGGTTGTGGTCTCGGGTGGGCGCAGG	5	127	1
AGCACCACGCAAGAACCGCAGTGCATCCTGCGCCCACCCGA	5	153	0
TGCGGTTCTTGCGTGGTGCTGCGCCAGTCGGCGGTATTTTT	5	174	1
          * *  * *  * **    ***
MAP Score: 25.0769

Motif 3
GGGAGTTTCCCGAGTGGTCAAAGGGAGCAGACTGTAAATCTG	0	60	1
TCACACTACACGCTTGGAAACAGGTCCTTGACGAAACAAAAA	2	13	1
TCTTCTTTCCCCTATGGAGTACGGTTGTGGTCTCGGGTGGGC	5	121	1
GTTGTGGTCTCGGGTGGGCGCAGGATGCACTGCGGTTCTTGC	5	144	1
CGGGAGATTTTGCGCGGGAGGCGGTGGTGGGCGCGGTTTTGG	5	45	1
GAACAGATCTCCTCTGGTTTATCGTAAATGGCATGATAT   	4	175	1
GACTTGTCTTTCCCTGGCGTTTCGTTCCAGGCGTTTTTGCTA	0	174	1
CGGTAGCTTGCGCGTGGGCGCACGATCACGCATGTTTGCCAC	5	242	0
ACGTTTGCGCCGTATGCCTACACGCACCGCGCGGGGCGCATT	4	40	1
GCTACCGGAGCGTGTGGATAAAGGAGCAGAGGG         	5	277	1
CTGCGGTTCTTGCGTGGTGCTGCGCCAGTCGGCGGTATTTTT	5	173	1
GGCGCGGTTTTGGTTGGTGTGCTGCTGATGGGAGCGGCGGTT	5	74	1
ATGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGATTTCA	0	251	1
GGGAAAGGGAGGTATGCACAGAGGGTCCAGTGGCGTGATAGG	4	127	1
CTTTCGTCTTCCGTTTGCTTTTGGGTAGTGTCTGACTTGTCT	0	141	1
TCCAGTGGCGTGATAGGGACACCGAACAGATCTCCTCTGGTT	4	152	1
CGGTGCGGAAGGATTTCAGTGGCGGAGGAGGGGAC       	0	275	1
          **  ***     **  *  * *
MAP Score: 21.0681

Motif 4
TTCCCGAGTGGTCAAAGGGAGCAGACTGTAAATCTGTT	0	66	1
TCAAGGATTCGAACCTTGGAAGACAACGCCAACAGATT	0	96	0
TCAAGAAAGTGACAAGAGGCACAGCAGCTAGCAAAAAC	0	206	0
CTCTTGTCACTTTCTTGAGTGCAGGATGTTCTTTTCGT	0	226	1
TGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGATT	0	252	1
TGCGGAAGGATTTCAGTGGCGGAGGAGGGGAC      	0	278	1
         GGAGCTAGTCTGCAGCTGGTTTTTTGTTT	2	46	0
AAATCAGCTATAACAGTAGAGGGCACGGGA        	3	35	1
AGTCATATCTTCACGTTTGCGCCGTATGCCTACACGCA	4	28	1
GCCGTATGCCTACACGCACCGCGCGGGGCGCATTCTAT	4	48	1
AGAATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAG	4	100	1
CGTGGGAAAGGGAGGTATGCACAGAGGGTCCAGTGGCG	4	124	1
         CGCAGCTTGACACAGAATGATTTTTATGA	5	1	1
AGACGATCGGGAGATTTTGCGCGGGAGGCGGTGGTGGG	5	38	1
CGCGGGAGGCGGTGGTGGGCGCGGTTTTGGTTGGTGTG	5	57	1
TTGGTGTGCTGCTGATGGGAGCGGCGGTTTTCGCTCTT	5	87	1
TATGGAGTACGGTTGTGGTCTCGGGTGGGCGCAGGATG	5	133	1
TGCGGTTCTTGCGTGGTGCTGCGCCAGTCGGCGGTATT	5	174	1
GCAAACATGCGTGATCGTGCGCCCACGCGCAAGCTACC	5	245	1
GCGCCCACGCGCAAGCTACCGGAGCGTGTGGATAAAGG	5	263	1
CGGAGCGTGTGGATAAAGGAGCAGAGGG          	5	282	1
          *      *******  **
MAP Score: 10.7917

Motif 5
CTCTTGTCACTTTCTTGAGTGCAGGATGTTCTTTTCGTG	0	226	1
TGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGATTT	0	252	1
TGCGGAAGGATTTCAGTGGCGGAGGAGGGGAC       	0	278	1
AGTCATATCTTCACGTTTGCGCCGTATGCCTACACGCAC	4	28	1
ATGTATAGAATGCGCCCCGCGCGGTGCGTGTAGGCATAC	4	51	0
AGAATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAGG	4	100	1
AGACGATCGGGAGATTTTGCGCGGGAGGCGGTGGTGGGC	5	38	1
CGCGGGAGGCGGTGGTGGGCGCGGTTTTGGTTGGTGTGC	5	57	1
GGTTGTGGTCTCGGGTGGGCGCAGGATGCACTGCGGTTC	5	143	1
CGGTTCTTGCGTGGTGCTGCGCCAGTCGGCGGTATTTTT	5	176	1
          *  *    **** **  **
MAP Score: 10.4982

Motif 6
TGGCTTGTTCGTTTGGGGAGTTTCCCGAGTGGT	0	45	1
CTGTAAATCTGTTGGCGTTGTCTTCCAAGGTTC	0	91	1
TTCCGTTTGCTTTTGGGTAGTGTCTGACTTGTC	0	149	1
TGACTTGTCTTTCCCTGGCGTTTCGTTCCAGGC	0	173	1
TGTCACTTTCTTGAGTGCAGGATGTTCTTTTCG	0	230	1
AGGATGTTCTTTTCGTGCGCGTGCGCGCGGTGC	0	248	1
GCGGAAGGATTTCAGTGGCGGAGGAGGGGAC  	0	279	1
GCTATAACAGTAGAGGGCACGGGA         	3	41	1
ATATCTTCACGTTTGCGCCGTATGCCTACACGC	4	32	1
TCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGA	4	104	1
GATCGGGAGATTTTGCGCGGGAGGCGGTGGTGG	5	42	1
CGCGGGAGGCGGTGGTGGGCGCGGTTTTGGTTG	5	57	1
CGGTTTTGGTTGGTGTGCTGCTGATGGGAGCGG	5	78	1
TGCTGCTGATGGGAGCGGCGGTTTTCGCTCTTC	5	93	1
CTTTCCCCTATGGAGTACGGTTGTGGTCTCGGG	5	125	1
GTGGTCTCGGGTGGGCGCAGGATGCACTGCGGT	5	147	1
ACTGCGGTTCTTGCGTGGTGCTGCGCCAGTCGG	5	172	1
TAGCTTGCGCGTGGGCGCACGATCACGCATGTT	5	248	0
          *** **** ** *
MAP Score: 9.06292

Motif 7
TAAGTTGGCTTGTTCGTTTGGGGAGTTTCCCGA	0	40	1
GCAAACGGAAGACGAAAGTGGGGAGTCAAGGAT	0	126	0
CTTCCGTTTGCTTTTGGGTAGTGTCTGACTTGT	0	148	1
TTGTCACTTTCTTGAGTGCAGGATGTTCTTTTC	0	229	1
ATGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGA	0	251	1
 AGAAAAATACGGGAATGTAGGCA         	1	9	1
GTTTCCAAGCGTGTAGTGTGAGCT         	2	1	0
AGCTATAACAGTAGAGGGCACGGGA        	3	40	1
CGCCCCGCGCGGTGCGTGTAGGCATACGGCGCA	4	45	0
ATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGG	4	103	1
GAGACGATCGGGAGATTTTGCGCGGGAGGCGGT	5	37	1
TTGCGCGGGAGGCGGTGGTGGGCGCGGTTTTGG	5	54	1
GGGCGCGGTTTTGGTTGGTGTGCTGCTGATGGG	5	73	1
TGGTGTGCTGCTGATGGGAGCGGCGGTTTTCGC	5	88	1
CTTCTTTCCCCTATGGAGTACGGTTGTGGTCTC	5	122	1
TACGGTTGTGGTCTCGGGTGGGCGCAGGATGCA	5	140	1
GATGCACTGCGGTTCTTGCGTGGTGCTGCGCCA	5	167	1
GGCAAACATGCGTGATCGTGCGCCCACGCGCAA	5	244	1
CCACACGCTCCGGTAGCTTGCGCGTGGGCGCAC	5	261	0
          ** * * ******
MAP Score: 3.60702

Motif 8
TGGGGAGTTTCCCGAGTGGTCAAAGGGAGCAGACTGT	0	58	1
ATGTTCTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGA	0	251	1
GGAAGGATTTCAGTGGCGGAGGAGGGGAC        	0	281	1
TCAGCTATAACAGTAGAGGGCACGGGA          	3	38	1
ATGCCTACACGCACCGCGCGGGGCGCATTCTATACAT	4	53	1
ATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGGAGGT	4	103	1
GGGAGGTATGCACAGAGGGTCCAGTGGCGTGATAGGG	4	133	1
CGGGAGATTTTGCGCGGGAGGCGGTGGTGGGCGCGGT	5	45	1
TGGTGTGCTGCTGATGGGAGCGGCGGTTTTCGCTCTT	5	88	1
CTTCTTTCCCCTATGGAGTACGGTTGTGGTCTCGGGT	5	122	1
CGGTTGTGGTCTCGGGTGGGCGCAGGATGCACTGCGG	5	142	1
GGAGCGTGTGGATAAAGGAGCAGAGGG          	5	283	1
          *    * * **** ***
MAP Score: 2.04163