AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_profile005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240425
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0082	300	formate hydrogenlyase transcriptional activator (fhlA)
#1	TP0246	145	T. pallidum predicted coding region TP0246
#2	TP0247	50	N-acetylmuramoyl-L-alanine amidase (amiA)
#3	TP0277	127	carboxyl-terminal protease (ctp)
#4	TP0704	142	single-stranded-DNA-specific exonuclease (recJ)
#5	TP0936	171	hemolysin, putative

Motif 1
ACCCGGCAGTGCGTTGCATGCGAGGTTCACACGG	5	58	1
TTTTAAAATAGCGTTTGGTGCGAG          	5	157	1
   ATGTGATGCGAAGCGTGCGCAAGAGAATTTT	1	7	1
CGCCACCTTTGCGGGGGATGCGCATTTTCGTTGT	1	73	1
GGTGCGTGTGGCCGTTCTGGCGGGTCCTCTTGCG	4	85	1
CACGCGGGGCGCGTGTGTGGTGCGTGTGGCCGTT	4	67	1
ACGGAAAGCGTCGCGGCACGCGGGGCGCGTGTGT	4	51	1
CTTTCAAAAGGAGAGTGCAGCGAGCACAAAGCAG	5	113	0
     GCGTAGCCCTTCCTCCGAGAGAGTACCAC	4	123	0
CCAGAGAGCAGTACGTCTTGAGCGTAAGGAGTAA	0	261	1
AGTCCATGTGGGGAAGGGAGTGCGCTGGTGATCA	3	64	0
AAAGGTTTTTGTGTCTCAGCCGCAGCCATTGAAA	0	80	0
AGCAAGATTATTGCTGCGGGAGAGAACTGGTTCT	0	217	0
GCGTGCGCAAGAGAATTTTGCGCGTTTTTTTTCC	1	22	1
TGCTTATTGTGAGTAGGGAGAGGGGACAGGT   	2	29	1
TGATCGGTTTGTGTTTGTTCCGCAGGAGGGG   	1	124	1
GCGAAAGTCCTTAAGTCGCGCGAGGTCATGACAC	0	168	1
CTTGCTAACCGAAACGCCAGAGAGCAGTACGTCT	0	245	1
GTGGCGATATTCCGTGCTTCAGCGGAAAAAAAAC	1	45	0
ACTCTCCTTTTGAAAGGCAGCGCGCCTTTTAAAA	5	131	1
ACAGTCTTCCGAGGAAGACGAGCGC         	3	112	1
CTTAAGGACTTTCGCGCACGTGGGTGAGCAACTA	0	149	0
          ***  **  *****
MAP Score: 24.3078

Motif 2
TCTTTCAATGGCTGCGGCTGAGACACAAAAAC	0	78	1
CAAGATTATTGCTGCGGGAGAGAACTGGTTCT	0	217	0
TACGTCTTGAGCGTAAGGAGTAATACGGTACA	0	272	1
   ATGTGATGCGAAGCGTGCGCAAGAGAATT	1	7	1
CGCCACCTTTGCGGGGGATGCGCATTTTCGTT	1	73	1
         TGTGGTGCGTGGACGTATGTGCT	2	1	1
TGCTTATTGTGAGTAGGGAGAGGGGACAGGT 	2	29	1
ACACTCATGGGCGGATGATGGA          	3	0	0
AGTCCATGTGGGGAAGGGAGTGCGCTGGTGAT	3	66	0
ACAGTCTTCCGAGGAAGACGAGCGC       	3	112	1
GTCGCGGCACGCGGGGCGCGTGTGTGGTGCGT	4	60	1
GGGCGCGTGTGTGGTGCGTGTGGCCGTTCTGG	4	73	1
GGGTCCTCTTGCGTCGGGTGGTACTCTCTCGG	4	106	1
TGGTACTCTCTCGGAGGAAGGGCTACGC    	4	124	1
ACCCGGCAGTGCGTTGCATGCGAGGTTCACAC	5	58	1
CTTTCAAAAGGAGAGTGCAGCGAGCACAAAGC	5	115	0
TTTTAAAATAGCGTTTGGTGCGAG        	5	157	1
          **** ***** *
MAP Score: 23.8889

Motif 3
TTTGGTAGTTGCTCACCCACGTGCGCGAAAGT	0	144	1
CGCGACTTAAGGACTTTCGCGCACGTGGGTGA	0	156	0
GCAAGAACCAGTTCTCTCCCGCAGCAATAATC	0	214	1
AAGACGTACTGCTCTCTGGCGTTTCGGTTAGC	0	248	0
GAGAGCAGTACGTCTTGAGCGTAAGGAGTAAT	0	264	1
AACGCGCAAAATTCTCTTGCGCACGCTTCGCA	1	16	0
GCGATATTCCGTGCTTCAGCGGAAAAAAAACG	1	44	0
CGGAATATCGCCACCTTTGCGGGGGATGCGCA	1	65	1
TGCGGGGGATGCGCATTTTCGTTGTGTACCTA	1	82	1
          CCCCTCCTGCGGAACAAACACA	1	133	0
GTCTCAGAACACTCATGGGCGGATGATGGA  	3	8	0
TCTGTTGTCTGATCACCAGCGCACTCCCTTCC	3	55	1
     GCGCTCGTCTTCCTCGGAAGACTGTGG	3	110	0
GTGCCGCGACGCTTTCCGTCGGCGAAGCCATC	4	38	0
GCCACACGCACCACACACGCGCCCCGCGTGCC	4	65	0
GTGCGTGTGGCCGTTCTGGCGGGTCCTCTTGC	4	86	1
GTTCTGGCGGGTCCTCTTGCGTCGGGTGGTAC	4	98	1
GCGTCGGGTGGTACTCTCTCGGAGGAAGGGCT	4	116	1
CTCGCATGCAACGCACTGCCGGGTAAGACATA	5	50	0
          ** **** ****
MAP Score: 16.6913

Motif 4
AAACACTGCGTCATTGGTAGCGGTAACCAAAAC	0	17	1
TCAAGATCTTTCAATGGCTGCGGCTGAGACACA	0	72	1
   ATGTGATGCGAAGCGTGCGCAAGAGAATTT	1	7	1
CGCCACCTTTGCGGGGGATGCGCATTTTCGTTG	1	73	1
GTCTGTTGTCTGATCACCAGCGCACTCCCTTCC	3	54	1
AGTCTTCCGAGGAAGACGAGCGC          	3	114	1
ACGGAAAGCGTCGCGGCACGCGGGGCGCGTGTG	4	51	1
TGGTACTCTCTCGGAGGAAGGGCTACGC     	4	124	1
ACCCGGCAGTGCGTTGCATGCGAGGTTCACACG	5	58	1
ACTCTCCTTTTGAAAGGCAGCGCGCCTTTTAAA	5	131	1
TTTTAAAATAGCGTTTGGTGCGAG         	5	157	1
          ***  ** *****
MAP Score: 12.7198

Motif 5
AAACCGCTCCGTTATCCGGATGTACCTCAAGATCTTTC	0	46	1
CCTCAAGATCTTTCAATGGCTGCGGCTGAGACACAAAA	0	70	1
TCTTCACTACCTTCTTTGGTAGTTGCTCACCCACGTGC	0	130	1
CGCGAAAGTCCTTAAGTCGCGCGAGGTCATGACACCTC	0	167	1
TTTGCGCGTTTTTTTTCCGCTGAAGCACGGAATATCGC	1	38	1
AATATCGCCACCTTTGCGGGGGATGCGCATTTTCGTTG	1	68	1
TCGGTTTGTGTTTGTTCCGCAGGAGGGG          	1	127	1
TGTTCTGAGACTGTTTGCGCTCCTCGTCTGTTGTCTGA	3	29	1
TTGCCACAGTCTTCCGAGGAAGACGAGCGC        	3	107	1
TGGGCAGTCTCTTTAGAGGAAGATGGCTTCGCCGACGG	4	17	1
CCGACGGAAAGCGTCGCGGCACGCGGGGCGCGTGTGTG	4	48	1
GTGCGTGTGGCCGTTCTGGCGGGTCCTCTTGCGTCGGG	4	86	1
TCGGGTGGTACTCTCTCGGAGGAAGGGCTACGC     	4	119	1
TTGCATATGTCTTACCCGGCAGTGCGTTGCATGCGAGG	5	45	1
GCACTCTCCTTTTGAAAGGCAGCGCGCCTTTTAAAATA	5	129	1
          ***    *** *  ** *
MAP Score: 9.62607

Motif 6
TTTGGTAGTTGCTCACCCACGTGCGCGAAAGT	0	144	1
GAGGTGTCATGACCTCGCGCGACTTAAGGACT	0	173	0
GCAAGAACCAGTTCTCTCCCGCAGCAATAATC	0	214	1
AAGACGTACTGCTCTCTGGCGTTTCGGTTAGC	0	248	0
TACCGTATTACTCCTTACGCTCAAGACGTACT	0	270	0
AACGCGCAAAATTCTCTTGCGCACGCTTCGCA	1	16	0
          CCCCTCCTGCGGAACAAACACA	1	133	0
    ACCTGTCCCCTCTCCCTACTCACAATAA	2	32	0
GAGACTGTTTGCGCTCCTCGTCTGTTGTCTGA	3	35	1
CTGATCACCAGCGCACTCCCTTCCCCACATGG	3	63	1
          GCGCTCGTCTTCCTCGGAAGAC	3	115	0
CGTCGGCGAAGCCATCTTCCTCTAAAGAGACT	4	22	0
GCGTGCCGCGACGCTTTCCGTCGGCGAAGCCA	4	40	0
GCCACACGCACCACACACGCGCCCCGCGTGCC	4	65	0
GCGTGTGGCCGTTCTGGCGGGTCCTCTTGCGT	4	88	1
CGCATGCAACGCACTGCCGGGTAAGACATATG	5	48	0
TGCATGCGAGGTTCACACGGGTATCCAAAACG	5	72	1
TGTGCTCGCTGCACTCTCCTTTTGAAAGGCAG	5	119	1
ATTTTAAAAGGCGCGCTGCCTTTCAAAAGGAG	5	134	0
          ** *** *****
MAP Score: 6.67719