AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons035_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238582
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0582	68	CT465 hypothetical protein
#1	CPn0583	219	CT466 hypothetical protein
#2	atoC	208	2-Component Regulator
#3	tctD	196	HTH Transcriptional Regulatory Protein + Receiver Doman

Motif 1
CCGGCATAATTCTTTCTTTTTTCAGGTTGCCAAT	1	142	1
AATAAATTGTTTTGTCGTTTTTCTTAGGGAAAAC	1	173	1
GGCCTAAGGATTTTACGTCTTAATGATATTTAAA	2	44	1
ATACAACGATTAAATCGTATTTCTTATTTTATAA	2	77	1
GATAATATTTTTTAAATTCTTTCTATTAAATTGA	2	120	1
TTCTATTAAATTGAAAGTTTTGCTTCATTTTTCA	2	140	1
ATGGATTCATTTTTTCTTTTTACTAAATCTTGAA	2	170	0
CTATGTCGCTTCTAAATTATTAATTTTAAATTAT	3	45	1
ACTTACACTTTTTTACTTTTTTCTTTTTTGAAAA	3	109	0
ACTGATTTTATATTACGTATTCATTCATATAATC	3	158	1
TCATATAATCTATTTTGTTTTCAT          	3	182	1
          * * **** ** **
MAP Score: 12.4901

Motif 2
ACCGGCATAATTCTTTCTTTTTTCAGGTTGCCAATAA	1	141	1
AATAAATTGTTTTGTCGTTTTTCTTAGGGAAAACCAA	1	173	1
ATTTTACGTCTTAATGATATTTAAATACAACGATTAA	2	53	1
TTAAATCGTATTTCTTATTTTATAAAAAGTATTTGAT	2	86	1
TAAAAAGTATTTGATAATATTTTTTAAATTCTTTCTA	2	108	1
ATTTTTTAAATTCTTTCTATTAAATTGAAAGTTTTGC	2	126	1
TTGAAAGTTTTGCTTCATTTTTCAAGATTTAGTAAAA	2	150	1
GATGGATTCATTTTTTCTTTTTACTAAATCTTGAAAA	2	168	0
CGCTTCTAAATTATTAATTTTAAATTATATATATAGT	3	51	1
CTTTTTTACTTTTTTCTTTTTTGAAAAATAGTTTTGC	3	99	0
TAATATAAAATCAGTTATTTTTCAAAGGTCACTTACA	3	136	0
          **  *  *****  * *
MAP Score: 11.6857

Motif 3
AAAGTATTTGATAATATTTTTTAAATTCTTTCTATTA	2	111	1
CCTTTGAAAAATAACTGATTTTATATTACGTATTCAT	3	145	1
ATTCATTCATATAATCTATTTTGTTTTCAT       	3	176	1
TCGCTTCTAAATTATTAATTTTAAATTATATATATAG	3	50	1
CAGGTTGCCAATAAATTGTTTTGTCGTTTTTCTTAGG	1	164	1
GATCACCGGCATAATTCTTTCTTTTTTCAGGTTGCCA	1	137	1
TCAAAGGTCACTTACACTTTTTTACTTTTTTCTTTTT	3	115	0
ATCCTTAGGCCAAATAATTTTTCAATTGGAGATTGTA	2	18	0
TTTAGAAGCGACATAGTTTTTTAACTTCTTTGAAGGC	3	24	0
TTCTTTTTTGAAAAATAGTTTTGCATAAACACAACAC	3	86	0
TTTAAATTATATATATAGTGTTGTGTTTATGCAAAAC	3	69	1
          ****    ****   **
MAP Score: 7.48425

Motif 4
AGAAAAACGACAAAACAATTTATTGGCAACC	1	166	0
TCTCCAATTGAAAAATTATTTGGCCTAAGGA	2	23	1
CTTATTTTATAAAAAGTATTTGATAATATTT	2	99	1
AAAGAAGTTAAAAAACTATGTCGCTTCTAAA	3	30	1
TATGTCGCTTCTAAATTATTAATTTTAAATT	3	46	1
TGTGTTTATGCAAAACTATTTTTCAAAAAAG	3	90	1
ATTCATTCATATAATCTATTTTGTTTTCAT 	3	176	1
          ***** *****
MAP Score: 4.71842

Motif 5
ACTCGTCGCTTACCAACATACTATAAATCC	0	33	1
CATTCCGCCACACCGGCATAAAGTGAGCCA	1	52	0
CGAGTCCGATCACCGGCATAATTCTTTCTT	1	130	1
TCCCTAAGAAAAACGACAAAACAATTTATT	1	173	0
TCTTAGGGAAAACCAAAGTAACACCCCGAT	1	194	1
AATAATTTAGAAGCGACATAGTTTTTTAAC	3	36	0
      ATGAAAACAAAATAGATTATATGA	3	182	0
          **********
MAP Score: 1.34205