AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238378
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0363	300	chemotaxis histidine kinase (cheA)
#1	TP0365	21	chemotaxis protein (cheX)
#2	TP0519	300	response regulatory protein (atoC)
#3	TP0872	75	flagellar filament cap protein (fliD)
#4	TP0875	39	conserved hypothetical protein
#5	TP0876	46	conserved hypothetical protein
#6	TP0907	62	conserved hypothetical protein
#7	TP0911	21	conserved hypothetical protein

Motif 1
ACCCAAGACGACCGCGCGTGGGTAGAAAGCTG	0	33	1
TGGGTAGAAAGCTGCGAGAGGGTCTGGTTTTG	0	51	1
CTACTCCTCTACCGAGCGGTGGGGGTCTACGT	0	99	0
CTCCTTGTATGCCGCGGGACTGGTCCTACTCC	0	124	0
CAAGGAGTAACCACCGAGGGCGAGAAACCGAC	0	149	1
GACAAACGTACCTGCGCGCGGGCCATGGCGGA	0	183	1
GTCAAGGGATGCAGCGGGTGGCGGGGTCTTTT	0	238	1
TTGACCAAAGGCTGAGAATGCGGGAAGATT  	0	280	1
          GCCGCGCGTGGGGTTTTTTTGA	3	0	1
CTCGAAAGCTGCGGAGAGTGGATCAAGACTCC	3	45	0
         CGCGGCGAGTCTACCGTTTTTAA	4	26	0
TTGCAAAAAGGCAAAGAGGGCGGGGTGT    	5	28	1
CTGCAACAAGGCCGCAAGACGGAAAAGGAGCC	6	11	0
          ** ***** ***
MAP Score: 24.289

Motif 2
         GGCTGGCGTGTCCGCCAATCGATAC	0	1	1
CTACCCACGCGCGGTCGTCTTGGGTATCGATTGG	0	24	0
GTAGAAAGCTGCGAGAGGGTCTGGTTTTGATAAA	0	54	1
CTACTCCTCTACCGAGCGGTGGGGGTCTACGTTT	0	97	0
CTCCTTGTATGCCGCGGGACTGGTCCTACTCCTC	0	122	0
GTACCTGCGCGCGGGCCATGGCGGAGTCTATTCT	0	190	1
TCTATTCTCGGCTGATGGAAGTGTCAAGGGATGC	0	216	1
GTCAAGGGATGCAGCGGGTGGCGGGGTCTTTTGG	0	238	1
TTGACCAAAGGCTGAGAATGCGGGAAGATT    	0	280	1
CACTACTAAAACTGAAGGTACGGGGTTAGGGTTA	2	102	1
TGTGTCCTCTACTGTTGGACGGGGTACGTGTTTT	2	180	1
          GCCGCGCGTGGGGTTTTTTTGAAG	3	0	1
CTCCTCGAAAGCTGCGGAGAGTGGATCAAGACTC	3	46	0
TTGCAAAAAGGCAAAGAGGGCGGGGTGT      	5	28	1
CTTGTTGCAGGCGGTGTGTGGTGGGTTATGGATA	6	33	1
      GGTGGCGGTAGTGTGCGTCTG       	7	3	0
          ** * ***  ****
MAP Score: 20.5557

Motif 3
CGGCCTTGTTGCAGGCGGTGTGTGGTGGGTTATGG	6	29	1
AAACGTACCTGCGCGCGGGCCATGGCGGAGTCTAT	0	186	1
CTCTACTGTTGGACGGGGTACGTGTTTTACTCTCC	2	186	1
AAGTGTCAAGGGATGCAGCGGGTGGCGGGGTCTTT	0	234	1
     TTAGCGCATGAGGAGTGGTGT         	1	5	1
          GGTGGCGGTAGTGTGCGTCTG    	7	6	0
TAAAACTGAAGGTACGGGGTTAGGGTTAACCTTAA	2	108	1
ACTCCTCGAAAGCTGCGGAGAGTGGATCAAGACTC	3	46	0
GTAGAAAGCTGCGAGAGGGTCTGGTTTTGATAAAA	0	54	1
TCTACCGAGCGGTGGGGGTCTACGTTTGGATCCAC	0	89	0
CCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCGC	0	108	1
TTGCAAAAAGGCAAAGAGGGCGGGGTGT       	5	28	1
TCAGTATTTCGGATACAGGAGAGGGAATTGATGCC	2	35	1
GTCTATTCTCGGCTGATGGAAGTGTCAAGGGATGC	0	215	1
     GCCGCGCGTGGGGTTTTTTTGAAGGGAACT	3	5	1
GTATGTCTTAGGTGGGTGGATATTTTTTCTTGTAA	2	253	0
          **  ****   ****
MAP Score: 16.3761

Motif 4
CAATCGATACCCAAGACGACCGCGCGTGGGTAGAAA	0	25	1
ACCGCGCGTGGGTAGAAAGCTGCGAGAGGGTCTGGT	0	43	1
TGGATCCAAACGTAGACCCCCACCGCTCGGTAGAGG	0	90	1
TAGAGGAGTAGGACCAGTCCCGCGGCATACAAGGAG	0	120	1
ACCACCGAGGGCGAGAAACCGACCTGACAAACGTAC	0	158	1
ACCGACCTGACAAACGTACCTGCGCGCGGGCCATGG	0	175	1
ATGGAAGTGTCAAGGGATGCAGCGGGTGGCGGGGTC	0	230	1
TGACCAAAGGCTGAGAATGCGGGAAGATT       	0	281	1
GGAGAGTGGATCAAGACTCCAGCCGAGTTCCCTTCA	3	29	0
   AATGACTCCTCGAAAGCTGCGGAGAGTGGATCA	3	52	0
          CGCAGAGTGCTTCCTGTCTTGCAAAA	5	0	1
TGCAAAAAGGCAAAGAGGGCGGGGTGT         	5	29	1
CACACCGCCTGCAACAAGGCCGCAAGACGGAAAAGG	6	15	0
      CAGACGCACACTACCGCCACC         	7	4	1
          *  ***  ** *** *
MAP Score: 12.1848

Motif 5
TACCCAAGACGACCGCGCGTGGGTAGAAAGCTG	0	32	1
GTAGAAAGCTGCGAGAGGGTCTGGTTTTGATAA	0	54	1
TACTCCTCTACCGAGCGGTGGGGGTCTACGTTT	0	97	0
ACGTACCTGCGCGCGGGCCATGGCGGAGTCTAT	0	188	1
AAGGGATGCAGCGGGTGGCGGGGTCTTTTGGAC	0	241	1
     TTAGCGCATGAGGAGTGGTGT       	1	5	1
     GCCGCGCGTGGGGTTTTTTTGAAGGGAA	3	5	1
AAAAGGCAAAGAGGGCGGGGTGT          	5	33	1
GTTGCAGGCGGTGTGTGGTGGGTTATGGATAGA	6	36	1
          *** * ** ****
MAP Score: 8.81

Motif 6
CGCCAATCGATACCCAAGACGACCGCGCGTGGGTAGAAAGCTGCGA	0	22	1
CCCCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCGCGGCATACAA	0	106	1
CAAACGTACCTGCGCGCGGGCCATGGCGGAGTCTATTCTCGGCTGA	0	185	1
TGGCGGAGTCTATTCTCGGCTGATGGAAGTGTCAAGGGATGCAGCG	0	208	1
CTGATGGAAGTGTCAAGGGATGCAGCGGGTGGCGGGGTCTTTTGGA	0	227	1
GACGTTGCCTTGACCAAAGGCTGAGAATGCGGGAAGATT       	0	271	1
GACATCAGTGTGTCCTCTACTGTTGGACGGGGTACGTGTTTTACTC	2	172	1
CTTCCTGTCTTGCAAAAAGGCAAAGAGGGCGGGGTGT         	5	19	1
TTTCCGTCTTGCGGCCTTGTTGCAGGCGGTGTGTGGTGGGTTATGG	6	18	1
          *   *   *     **  * ***  *
MAP Score: 4.18172

Motif 7
ACGACCGCGCGTGGGTAGAAAGCTGCGAGAGGGTCTGGTTTTGA	0	40	1
AACGTAGACCCCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCG	0	98	1
GACAAACGTACCTGCGCGCGGGCCATGGCGGAGTCTATTCTCGG	0	183	1
GGAGTCTATTCTCGGCTGATGGAAGTGTCAAGGGATGCAGCGGG	0	212	1
TGTCAAGGGATGCAGCGGGTGGCGGGGTCTTTTGGACGTTGCCT	0	237	1
TGGACGTTGCCTTGACCAAAGGCTGAGAATGCGGGAAGATT   	0	269	1
TACTTCACTACTAAAACTGAAGGTACGGGGTTAGGGTTAACCTT	2	97	1
TTAAGGTGATTAAAGAACATGGCGGTGACATCAGTGTGTCCTCT	2	146	1
TCAGTGTGTCCTCTACTGTTGGACGGGGTACGTGTTTTACTCTC	2	176	1
GGAGAGTGGATCAAGACTCCAGCCGAGTTCCCTTCAAAAAAACC	3	21	0
TGCTTCCTGTCTTGCAAAAAGGCAAAGAGGGCGGGGTGT     	5	17	1
CGTCTTGCGGCCTTGTTGCAGGCGGTGTGTGGTGGGTTATGGAT	6	22	1
          *  **     *** * *     **
MAP Score: 0.149551