AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons034_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240088
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0324	103	T. pallidum predicted coding region TP0324
#1	TP0327	56	cationic outer membrane protein (ompH)
#2	TP0328	55	DNA mismatch repair protein (mutS)
#3	TP0472	74	excinuclease ABC, subunit C (uvrC)
#4	TP0473	64	T. pallidum predicted coding region TP0473
#5	TP0474	140	conserved hypothetical protein

Motif 1
GTGTAGCAAAAAACGCGCCCGGAATACAGAAC	0	71	0
ATTCTTTGCAATGAGCACCCGGGTAGGGGGTT	0	42	1
ACTTGGAGAAAAGCGCACACCGTGCTAGCATC	5	67	1
GCCCGTTTTGAAACGGTCCGGGGCTGCGTCCA	1	18	1
GACCGTTTCAAAACGGGCACGGAACG      	1	4	0
GCCGTGCAATATGCGCCAGCGGGACTTGGAGA	5	44	1
    TGCACCGTGAGCACCGCGTCTCCTGCCT	2	6	1
TCTGTGCTTCTTAAGCCCGCGGTAATTACGCG	5	11	1
TTCGCCCATCAAAAGTGCGCCGCT        	4	2	0
GGCGCATATTGCACGGCCCGCGTAATTACCGC	5	29	0
CTTTCGCCGTATGCGGTGCCCCG         	4	51	1
CACCGCGGGTATGCGTTCGCCCATCAAAAGTG	4	17	0
        GTGGACGCTCCTGGGCCAACACGT	2	41	0
CCGTGCTAGCATCAGGCGCCCGCGTTCCGGTA	5	86	1
CATACGGCGAAAGATCACCGCGGGTATGCGTT	4	32	0
TGTCACGCGCAGAAGCATGCCGGCTTATTTTG	3	13	0
GTTTTTTGCTACACTTAGCGGGCT        	0	89	1
          * **** *****
MAP Score: 23.7892

Motif 2
AAAAAACGCGCCCGGAATACAGAACCCCCTACCCGGGTGCTCATTG	0	50	0
CTGTATTCCGGGCGCGTTTTTTGCTACACTTAGCGGGCT       	0	74	1
TGGACGCAGCCCCGGACCGTTTCAAAACGGGCACGGAACG      	1	4	0
CCGTGAGCACCGCGTCTCCTGCCTCCTACGTGTTGGCCCAGGAGCG	2	14	1
ACCAAAATAAGCCGGCATGCTTCTGCGCGTGACAGGAAAAACAGTT	3	11	1
ACCGCGGGTATGCGTTCGCCCATCAAAAGTGCGCCGCT        	4	2	0
CGAACGCATACCCGCGGTGATCTTTCGCCGTATGCGGTGCCCCG  	4	30	1
GCGGTAATTACGCGGGCCGTGCAATATGCGCCAGCGGGACTTGGAG	5	29	1
CCGGAACGCGGGCGCCTGATGCTAGCACGGTGTGCGCTTTTCTCCA	5	70	0
TCCCCTAATGCCCGAAAATGTACGTACCGGAACGCGGGCGCCTGAT	5	96	0
          ****           * ***    **
MAP Score: 17.8445

Motif 3
GGCACCTATTCTTTGCAATGAGCACCCGGGTAGGGGGTTCTGTA	0	35	1
GACGCAGCCCCGGACCGTTTCAAAACGGGCACGGAACG      	1	4	0
GTGGACGCTCCTGGGCCAACACGTAGGAGGCAGGAGACGCGGTG	2	21	0
CCAAAATAAGCCGGCATGCTTCTGCGCGTGACAGGAAAAACAGT	3	12	1
        AGCGGCGCACTTTTGATGGGCGAACGCATACCCGCG	4	2	1
GCACCGCATACGGCGAAAGATCACCGCGGGTATGCGTTCGCCCA	4	26	0
        GTCTGTGCTTCTTAAGCCCGCGGTAATTACGCGGGC	5	2	1
CCAAGTCCCGCTGGCGCATATTGCACGGCCCGCGTAATTACCGC	5	29	0
AAAGCGCACACCGTGCTAGCATCAGGCGCCCGCGTTCCGGTACG	5	76	1
GCCCGCGTTCCGGTACGTACATTTTCGGGCATTAGGGGAAAGAT	5	103	1
          * * **         *****   *
MAP Score: 13.6455

Motif 4
AGAAGGGTGAGTTGGGTGGCACCTATTCTTTG	0	18	1
TGAGCACCCGGGTAGGGGGTTCTGTATTCCGG	0	53	1
GGGGTTCTGTATTCCGGGCGCGTTTTTTGCTA	0	68	1
         CGTTCCGTGCCCGTTTTGAAACG	1	1	1
GTTTTGAAACGGTCCGGGGCTGCGTCCACCAG	1	22	1
TGGGCCAACACGTAGGAGGCAGGAGACGCGGT	2	22	0
AGCCGGCATGCTTCTGCGCGTGACAGGAAAAA	3	20	1
CACGATTCTTGGTGGGGGCATGACCC      	3	58	1
GCGCACTTTTGATGGGCGAACGCATACCCGCG	4	14	1
GATCTTTCGCCGTATGCGGTGCCCCG      	4	48	1
GCCCGCGGTAATTACGCGGGCCGTGCAATATG	5	25	1
CGGGCCGTGCAATATGCGCCAGCGGGACTTGG	5	41	1
ATGCTAGCACGGTGTGCGCTTTTCTCCAAGTC	5	66	0
CGTACCGGAACGCGGGCGCCTGATGCTAGCAC	5	88	0
ATTTTCGGGCATTAGGGGAAAGATCTC     	5	123	1
          *********  *
MAP Score: 11.0495

Motif 5
CCTATTCTTTGCAATGAGCACCCGGGTAGGGGGTTC	0	39	1
GCTAAGTGTAGCAAAAAACGCGCCCGGAATACAGAA	0	72	0
         TGCACCGTGAGCACCGCGTCTCCTGCC	2	1	1
        AACCAAAATAAGCCGGCATGCTTCTGCG	3	2	1
AACAGTTTCACGATTCTTGGTGGGGGCATGACCC  	3	50	1
    AGCGGCGCACTTTTGATGGGCGAACGCATACC	4	6	1
CCGCATACGGCGAAAGATCACCGCGGGTATGCGTTC	4	31	0
    GTCTGTGCTTCTTAAGCCCGCGGTAATTACGC	5	6	1
TCCCGCTGGCGCATATTGCACGGCCCGCGTAATTAC	5	32	0
CACCGTGCTAGCATCAGGCGCCCGCGTTCCGGTACG	5	84	1
          ***      *******
MAP Score: 6.60228

Motif 6
ATTCTTTGCAATGAGCACCCGGGTAGGGGG	0	42	1
GTAGCAAAAAACGCGCCCGGAATACAGAAC	0	71	0
CCGTTTCAAAACGGGCACGGAACG      	1	4	0
CCGTTTTGAAACGGTCCGGGGCTGCGTCCA	1	20	1
AGGAGACGCGGTGCTCACGGTGCA      	2	4	0
      GTGGACGCTCCTGGGCCAACACGT	2	41	0
TTTTCCTGTCACGCGCAGAAGCATGCCGGC	3	21	0
     GGGTCATGCCCCCACCAAGAATCGT	3	59	0
          AGCGGCGCACTTTTGATGGG	4	0	1
CGCACTTTTGATGGGCGAACGCATACCCGC	4	15	1
GGGCGAACGCATACCCGCGGTGATCTTTCG	4	27	1
          CGGGGCACCGCATACGGCGA	4	54	0
TGTGCTTCTTAAGCCCGCGGTAATTACGCG	5	13	1
CGCGGTAATTACGCGGGCCGTGCAATATGC	5	28	1
GCCGTGCAATATGCGCCAGCGGGACTTGGA	5	44	1
GGACTTGGAGAAAAGCGCACACCGTGCTAG	5	65	1
TGCTAGCATCAGGCGCCCGCGTTCCGGTAC	5	89	1
          **********
MAP Score: 6.30505

Motif 7
ATAGGTGCCACCCAACTCACCCTTCTTCCAAA	0	12	0
CTATTCTTTGCAATGAGCACCCGGGTAGGGGG	0	40	1
GTAGGGGGTTCTGTATTCCGGGCGCGTTTTTT	0	64	1
TTTTTTGCTACACTTAGCGGGCT         	0	90	1
GACCGTTTCAAAACGGGCACGGAACG      	1	4	0
GCCCGTTTTGAAACGGTCCGGGGCTGCGTCCA	1	18	1
TCACTCCTTGCCTGGTGGACGCAGCCCCGGAC	1	33	0
      TGCACCGTGAGCACCGCGTCTCCTGC	2	4	1
CCTGCCTCCTACGTGTTGGCCCAGGAGCGTCC	2	31	1
     AACCAAAATAAGCCGGCATGCTTCTGC	3	5	1
AACTGTTTTTCCTGTCACGCGCAGAAGCATGC	3	25	0
TTTCACGATTCTTGGTGGGGGCATGACCC   	3	55	1
TTCGCCCATCAAAAGTGCGCCGCT        	4	2	0
CACCGCGGGTATGCGTTCGCCCATCAAAAGTG	4	17	0
   CGGGGCACCGCATACGGCGAAAGATCACC	4	45	0
 GTCTGTGCTTCTTAAGCCCGCGGTAATTACG	5	9	1
AGCCCGCGGTAATTACGCGGGCCGTGCAATAT	5	24	1
GCGGGCCGTGCAATATGCGCCAGCGGGACTTG	5	40	1
CTGATGCTAGCACGGTGTGCGCTTTTCTCCAA	5	69	0
ACCGTGCTAGCATCAGGCGCCCGCGTTCCGGT	5	85	1
TCCGGTACGTACATTTTCGGGCATTAGGGGAA	5	111	1
          ** ** ******
MAP Score: 5.26457

Motif 8
TGCAATGAGCACCCGGGTAGGGGGTTCTGTATTCCGGGCGCGTTTTT	0	48	1
CTGTATTCCGGGCGCGTTTTTTGCTACACTTAGCGGGCT        	0	74	1
GTGGACGCAGCCCCGGACCGTTTCAAAACGGGCACGGAACG      	1	4	0
CATGCTTCTGCGCGTGACAGGAAAAACAGTTTCACGATTCTTGGTGG	3	26	1
CGAACGCATACCCGCGGTGATCTTTCGCCGTATGCGGTGCCCCG   	4	30	1
GCTTCTTAAGCCCGCGGTAATTACGCGGGCCGTGCAATATGCGCCAG	5	16	1
GCATCAGGCGCCCGCGTTCCGGTACGTACATTTTCGGGCATTAGGGG	5	94	1
          **** * *          *     ***
MAP Score: 3.89496

Motif 9
TTTGCAATGAGCACCCGGGTAGGGGGTTCTGTATTCCGGGCGCGTTTT	0	46	1
TCTGTATTCCGGGCGCGTTTTTTGCTACACTTAGCGGGCT        	0	73	1
    CGTTCCGTGCCCGTTTTGAAACGGTCCGGGGCTGCGTCCACCAG	1	6	1
GCGAACGCATACCCGCGGTGATCTTTCGCCGTATGCGGTGCCCCG   	4	29	1
TGCTTCTTAAGCCCGCGGTAATTACGCGGGCCGTGCAATATGCGCCAG	5	15	1
TGCTAGCACGGTGTGCGCTTTTCTCCAAGTCCCGCTGGCGCATATTGC	5	49	0
AGCATCAGGCGCCCGCGTTCCGGTACGTACATTTTCGGGCATTAGGGG	5	93	1
          *  **** *  *           * * *
MAP Score: 3.31574

Motif 10
ACAGAACCCCCTACCCGGGTGCTCATTGCAAAGAATAG	0	40	0
GTTCTGTATTCCGGGCGCGTTTTTTGCTACACTTAGCG	0	71	1
          CGTTCCGTGCCCGTTTTGAAACGGTCCG	1	0	1
CGTTTTGAAACGGTCCGGGGCTGCGTCCACCAGGCAAG	1	21	1
          TGCACCGTGAGCACCGCGTCTCCTGCCT	2	0	1
     GTGGACGCTCCTGGGCCAACACGTAGGAGGCAG	2	32	0
TTTCACGATTCTTGGTGGGGGCATGACCC         	3	55	1
GGCGAAAGATCACCGCGGGTATGCGTTCGCCCATCAAA	4	21	0
TGTGCTTCTTAAGCCCGCGGTAATTACGCGGGCCGTGC	5	13	1
GGTAATTACGCGGGCCGTGCAATATGCGCCAGCGGGAC	5	31	1
GATGCTAGCACGGTGTGCGCTTTTCTCCAAGTCCCGCT	5	61	0
GTACGTACCGGAACGCGGGCGCCTGATGCTAGCACGGT	5	85	0
GCCCGCGTTCCGGTACGTACATTTTCGGGCATTAGGGG	5	103	1
          *   *****  * *  **
MAP Score: 2.32817