AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID039_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391369
 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
CGCCCATGCTTTTTCGCCAGGGAACCGTT  	0	8	0
TTTGCTTTTTTCTGCGCCACGGAAATCAATA	0	64	1
CCTGAAGATATGTGCGACGAGCTTTTCATAA	0	96	1
GCGACGTCATTATGCGTCAGATTTATGACAG	0	129	0
TAAGCCCTGCTCTGCGTCCGATGAGCAAGGC	1	11	0
TCCCAAAATCTTTCTGTCGCGATTCAACGAT	2	14	1
AGGCTGCAAACATGCGTCAGGGGGTGTAAAA	2	61	1
TGACGTAATTTCTGCCTCGGAGGTATTTAAA	2	123	1
          * *********
MAP Score: 8.02788

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
    AACGGTTCCCTGGCGAAAAAGCATGG	0	6	1
AAATGGCACATCTGTTTGGGTATAATCGCG	0	37	0
TGCTTTTTTCTGCGCCACGGAAATCAATAA	0	66	1
CCTGAAGATATGTGCGACGAGCTTTTCATA	0	96	1
GACGTCATTATGCGTCAGATTTATGACAGA	0	128	0
TAAGCCCTGCTCTGCGTCCGATGAGCAAGG	1	12	0
CCAAAATCTTTCTGTCGCGATTCAACGATA	2	16	1
GCTGCAAACATGCGTCAGGGGGTGTAAAAC	2	63	1
TGACGTAATTTCTGCCTCGGAGGTATTTAA	2	123	1
          **********
MAP Score: 2.41216