AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons035_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238571
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0583	219	CT466 hypothetical protein
#1	atoC	208	2-Component Regulator
#2	tctD	196	HTH Transcriptional Regulatory Protein + Receiver Doman

Motif 1
AATGTACGGTTTCTGTTCTAATTATCGCAAGAGAAATCTC	0	10	0
ATCACCGGCATAATTCTTTCTTTTTTCAGGTTGCCAATAA	0	138	1
TGCCAATAAATTGTTTTGTCGTTTTTCTTAGGGAAAACCA	0	169	1
GATTAAATCGTATTTCTTATTTTATAAAAAGTATTTGATA	1	84	1
TATTTGATAATATTTTTTAAATTCTTTCTATTAAATTGAA	1	115	1
AAATTGAAAGTTTTGCTTCATTTTTCAAGATTTAGTAAAA	1	147	1
CTGGATGGATTCATTTTTTCTTTTTACTAAATCTTGAAAA	1	168	0
GAAGCGACATAGTTTTTTAACTTCTTTGAAGGCCGTTCAG	2	17	0
TTCTAAATTATTAATTTTAAATTATATATATAGTGTTGTG	2	54	1
ATTATATATATAGTGTTGTGTTTATGCAAAACTATTTTTC	2	74	1
TACACTTTTTTACTTTTTTCTTTTTTGAAAAATAGTTTTG	2	100	0
          *  *****   ** *    *
MAP Score: 14.7795

Motif 2
CAATCTCCAATTGAAAAATTATTTGGCCTAA	1	20	1
TAAGTGACCTTTGAAAAATAACTGATTTTAT	2	138	1
TTACTAAATCTTGAAAAATGAAGCAAAACTT	1	154	0
CAAATACTTTTTATAAAATAAGAAATACGAT	1	90	0
TTTTTCTTTTTTGAAAAATAGTTTTGCATAA	2	95	0
TTCAAAGAAGTTAAAAAACTATGTCGCTTCT	2	27	1
TGAATACGTAATATAAAATCAGTTATTTTTC	2	150	0
TAGAAAGAATTTAAAAAATATTATCAAATAC	1	114	0
TTTAGTAAAAAGAAAAAATGAATCCATCCAG	1	177	1
TATATATATAATTTAAAATTAATAATTTAGA	2	55	0
AATCGTTGTATTTAAATATCATTAAGACGTA	1	57	0
ATTGGCAACCTGAAAAAAGAAAGAATTATGC	0	145	0
          ********* *
MAP Score: 11.9297

Motif 3
CACCGGCATAATTCTTTCTTTTTTCAGGTTGCCA	0	140	1
GGATGGATTCATTTTTTCTTTTTACTAAATCTTG	1	172	0
ATTCATTCATATAATCTATTTTGTTTTCAT    	2	176	1
AAAGTATTTGATAATATTTTTTAAATTCTTTCTA	1	111	1
TATTTTTTAAATTCTTTCTATTAAATTGAAAGTT	1	125	1
ATTAAATCGTATTTCTTATTTTATAAAAAGTATT	1	85	1
CACTTTTTTACTTTTTTCTTTTTTGAAAAATAGT	2	104	0
TCGCTTCTAAATTATTAATTTTAAATTATATATA	2	50	1
CAGGTTGCCAATAAATTGTTTTGTCGTTTTTCTT	0	164	1
TTAATTTTAAATTATATATATAGTGTTGTGTTTA	2	64	1
AACTGATTTTATATTACGTATTCATTCATATAAT	2	157	1
TCAAAGGTCACTTACACTTTTTTACTTTTTTCTT	2	118	0
TGGCCTAAGGATTTTACGTCTTAATGATATTTAA	1	43	1
          *** * * **** *
MAP Score: 7.43807