AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_sum_all033_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241046
 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
#3	rbsU	300	sigma regulatory family protein - PP2C phosphatase (RsbW antagonist)

Motif 1
TATACTGCGTAAGAAACAAAACACTAGAGGA	3	225	1
CTATTTTTCAAAAAAGAAAAAAGTAAAAAAG	2	105	1
AAGATTTAGTAAAAAGAAAAAATGAATCCAT	1	173	1
ACGGCCTTCAAAGAAGTTAAAAAACTATGTC	2	21	1
GGCAACCTGAAAAAAGAAAGAATTATGCCGG	0	142	0
TGTGATTTAAAAGAAGTTAGAGAATAATATT	3	80	1
TATTGTGAGTAAAAAACAAAAGCTTTAACAA	3	20	1
ATCTTGAAAAATGAAGCAAAACTTTCAATTT	1	147	0
GATCGAGATGAAAAAATAAGATCTTCGTTGC	3	125	1
TTTATAAAATAAGAAATACGATTTAATCGTT	1	81	0
GGTTTTCCCTAAGAAAAACGACAAAACAATT	0	177	0
AAATATCATTAAGACGTAAAATCCTTAGGCC	1	44	0
ATTTAATAGAAAGAATTTAAAAAATATTATC	1	120	0
CGATCTTCTAATGAATGAAAATATTATTCTC	3	99	0
AAGATATAGCAAGAATAAAAGAAATAGTAGG	3	172	1
          ATGAAAACAAAATAGATTATA	2	185	0
          ****** ****
MAP Score: 20.4885

Motif 2
GAGATTTCTCTTGCGATAATTAGAACAGAAACCGTACATT	0	10	1
TTATTGGCAACCTGAAAAAAGAAAGAATTATGCCGGTGAT	0	138	0
TGGTTTTCCCTAAGAAAAACGACAAAACAATTTATTGGCA	0	169	0
TATCAAATACTTTTTATAAAATAAGAAATACGATTTAATC	1	84	0
TTCAATTTAATAGAAAGAATTTAAAAAATATTATCAAATA	1	115	0
TTTTACTAAATCTTGAAAAATGAAGCAAAACTTTCAATTT	1	147	0
TTTTCAAGATTTAGTAAAAAGAAAAAATGAATCCATCCAG	1	168	1
CTGAACGGCCTTCAAAGAAGTTAAAAAACTATGTCGCTTC	2	17	1
CACAACACTATATATATAATTTAAAATTAATAATTTAGAA	2	54	0
GAAAAATAGTTTTGCATAAACACAACACTATATATATAAT	2	74	0
CAAAACTATTTTTCAAAAAAGAAAAAAGTAAAAAAGTGTA	2	100	1
ATAAGTATTGTGAGTAAAAAACAAAAGCTTTAACAATTTT	3	15	1
TACTAAGATATAGCAAGAATAAAAGAAATAGTAGGTGTCT	3	168	1
TTTTTATACTGCGTAAGAAACAAAACACTAGAGGAAAGAC	3	221	1
          *    * **   *****  *
MAP Score: 16.3497

Motif 3
GTTTTGCTTCATTTTTCAAGATTTAGTAAAAAGAAAAAAT	1	156	1
CATCCATGTGATTTAAAAGAAGTTAGAGAATAATATTTTC	3	74	1
CAAGCAATTGATTTACTAAGATATAGCAAGAATAAAAGAA	3	155	1
TAAATTATTAATTTTAAATTATATATATAGTGTTGTGTTT	2	57	1
ATGCAAAACTATTTTTCAAAAAAGAAAAAAGTAAAAAAGT	2	97	1
AATCACATGGATGTTTGAGAATATAGACAATAAAAATTGT	3	47	0
ATTATCAAATACTTTTTATAAAATAAGAAATACGATTTAA	1	86	0
AAAATAACTGATTTTATATTACGTATTCATTCATATAATC	2	152	1
AATAGAAAGAATTTAAAAAATATTATCAAATACTTTTTAT	1	107	0
TCTTAATGATATTTAAATACAACGATTAAATCGTATTTCT	1	61	1
TCCTGAACGGCCTTCAAAGAAGTTAAAAAACTATGTCGCT	2	15	1
ATGAAGCAAAACTTTCAATTTAATAGAAAGAATTTAAAAA	1	128	0
          ****   *  *  **   **
MAP Score: 10.2491

Motif 4
ATTGGCAACCTGAAAAAAGAAAGAATTATGCC	0	144	0
CTAAGAAAAACGACAAAACAATTTATTGGCAA	0	168	0
CGTTTTTCTTAGGGAAAACCAAAGTAACACCC	0	188	1
CAATCTCCAATTGAAAAATTATTTGGCCTAAG	1	20	1
CAAATACTTTTTATAAAATAAGAAATACGATT	1	89	0
AATAGAAAGAATTTAAAAAATATTATCAAATA	1	115	0
TTCAAGATTTAGTAAAAAGAAAAAATGAATCC	1	170	1
TTCAAAGAAGTTAAAAAACTATGTCGCTTCTA	2	27	1
TATATATATAATTTAAAATTAATAATTTAGAA	2	54	0
TGTTGTGTTTATGCAAAACTATTTTTCAAAAA	2	87	1
TTTTCAAAAAAGAAAAAAGTAAAAAAGTGTAA	2	109	1
GTAAGTGACCTTTGAAAAATAACTGATTTTAT	2	137	1
TGAATACGTAATATAAAATCAGTTATTTTTCA	2	149	0
AAGTATTGTGAGTAAAAAACAAAAGCTTTAAC	3	17	1
CATCCATGTGATTTAAAAGAAGTTAGAGAATA	3	74	1
GAAGATCGAGATGAAAAAATAAGATCTTCGTT	3	122	1
CTTACGCAGTATAAAAAAATTTCCTTAAGGAG	3	206	0
          *** **** ***
MAP Score: 6.47741

Motif 5
TTTGTCGTTTTTCTTAGGGAAAACCAAAGT	0	183	1
AGACGTAAAATCCTTAGGCCAAATAATTTT	1	34	0
ATTGTCTATATTCTCAAACATCCATGTGAT	3	56	1
AGTAGGTGTCTCCTTAAGGAAATTTTTTTA	3	197	1
AGTGTTTTGTTTCTTACGCAGTATAAAAAA	3	220	0
AAGACGTTCCTTCTCAAGGATGACAAGCCT	3	256	1
CGGCGCTCTATTCTTAAGGCTTGTCATCCT	3	272	0
          **********
MAP Score: 5.64115

Motif 6
TCAGGTTGCCAATAAATTGTTTTGTCGTTTTTCTT	0	163	1
TCCTTAGGCCAAATAATTTTTCAATTGGAGATTGT	1	19	0
GATTAAATCGTATTTCTTATTTTATAAAAAGTATT	1	84	1
AAGTATTTGATAATATTTTTTAAATTCTTTCTATT	1	112	1
CCTGGATGGATTCATTTTTTCTTTTTACTAAATCT	1	174	0
GCTTCTAAATTATTAATTTTAAATTATATATATAG	2	52	1
TTACACTTTTTTACTTTTTTCTTTTTTGAAAAATA	2	106	0
TCATTCATATAATCTATTTTGTTTTCAT       	2	178	1
AAAATTGTTAAAGCTTTTGTTTTTTACTCACAATA	3	20	0
CAAAAGCTTTAACAATTTTTATTGTCTATATTCTC	3	36	1
GCTTGCAACGAAGATCTTATTTTTTCATCTCGATC	3	125	0
AGACACCTACTATTTCTTTTATTCTTGCTATATCT	3	173	0
TGTCTCCTTAAGGAAATTTTTTTATACTGCGTAAG	3	203	1
TCTTTCCTCTAGTGTTTTGTTTCTTACGCAGTATA	3	225	0
          **  * **** ** *
MAP Score: 0.450585