AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID039_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391208
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	phoB	189	positive response regulator for pho regulon, sensor is PhoR (or CreC)
#1	phoR	57	positive and negative sensor protein for pho regulon
#2	cpxR	146	transcriptional regulator in 2-component system

Motif 1
   AACGGTTCCCTGGCGAAAAAGCATGGGC	0	7	1
TTATTGATTTCCGTGGCGCAGAAAAAAGCAA	0	65	0
TCTGTCATAAATCTGACGCATAATGACGTCG	0	128	1
GCGATCATTAATGCGACGTCATTATGCGTCA	0	141	0
CGCCTTGCTCATCGGACGCAGAGCAGGGCTT	1	10	1
GTTTTACACCCCCTGACGCATGTTTGCAGCC	2	62	0
AAATTACGTCATCAGACGTCGCTAATCCATG	2	103	0
GTTTAAATACCTCCGAGGCAGAAATTACGTC	2	124	0
          *** *******
MAP Score: 9.18955

Motif 2
ATCTGTTTGGGTATAATCGCGCCCATGCTTTTT	0	25	0
TAAATCTGACGCATAATGACGTCGCATTAATGA	0	135	1
ACTCTCTATCGTTGAATCGCGACAGAAAGATTT	2	19	0
GATTCAGGCTGCAAACATGCGTCAGGGGGTGTA	2	56	1
GTCAGGGGGTGTAAAACAACGTAAAGTCATGGA	2	76	1
TAAAGTCATGGATTAGCGACGTCTGATGACGTA	2	97	1
         TGTTTAAATACCTCCGAGGCAGAA	2	132	0
          *** **  *****
MAP Score: 2.93981

Motif 3
GCCACGGAAATCAATAACCTGAAGATATGTGCGA	0	79	1
GACGAGCTTTTCATAAATCTGTCATAAATCTGAC	0	111	1
CATAAATCTGTCATAAATCTGACGCATAATGACG	0	122	1
TAGGTTGCGATCATTAATGCGACGTCATTATGCG	0	144	0
TGCCCTGTTGTAATAAATAGGTTGCGATCATTAA	0	161	0
          **** ***  ** *
MAP Score: 2.06943