AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID048_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391439
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	tap	45	methyl-accepting chemotaxis protein IV, peptide sensor receptor
#1	tar	144	methyl-accepting chemotaxis protein II, aspartate sensor receptor
#2	motA	126	proton conductor component of motor; no effect on switching

Motif 1
CGATGATCTGCGCATCGGGTTTTTTATTTC	1	40	1
ATTTCAATTTCGCGGCGGGTGGCATCAGCA	1	65	1
GGCAAAAAAAAGCAGCGGTACGTCGTTACC	2	41	0
GCAACATTCCAGCAGCGGTAACGACGTACC	2	25	1
CGATGCGCAGATCATCGGGTTCATTTCAAT	1	27	0
TTATCGGCAAGGAGGGGGGAAACTTTATTG	1	93	0
  CAACGCTCCCCATCAGGCGGCAATGACC	0	27	0
AGGATGTTCAGTCGTCAGGCGTTAACGCGC	2	77	0
TTCAATTGAGGAAATCGGGAGAA       	1	3	0
CGTTAACGCGCGATTGGGGCAAAAAAAAGC	2	58	0
CGCGGCGGGTGGCATCAGCAATAAAGTTTC	1	75	1
          **********
MAP Score: 8.07926

Motif 2
ATTGCCGCCTGATGGGGAGCGTTG      	0	31	1
TTCAATTGAGGAAATCGGGAGAA       	1	3	0
TCAATTTCGCGGCGGGTGGCATCAGCAATA	1	68	1
TTATCGGCAAGGAGGGGGGAAACTTTATTG	1	93	0
CTTGTTTTCAGGAAGGTGCCTT        	1	132	1
        CTGATACGGTGAGGCGCAACAT	2	2	1
TACCGCTGCTGGAATGTTGCGCCTCACCGT	2	15	0
GTTAACGCGCGATTGGGGCAAAAAAAAGCA	2	57	0
TGTTGACCATGACAGGATGTTCAGTCGTCA	2	90	0
GGTCAACAGTGGAAGGATGATGTC      	2	112	1
          **********
MAP Score: 2.60098