AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i253_chemotaxis2_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	motA	126	proton conductor component of motor; no effect on switching

Motif number 1

GGTACGTCGTTACCGCTGCTGGAATGTTGC	1	26	0	TACCGCTGCT	    0.994574	-101
GGTAACGACGTACCGCTGCTTTTTTTTGCC	1	42	1	TACCGCTGCT	    0.994574	-85
GACATCATCCTTCCACTGTTGACCATGACA	1	107	0	TTCCACTGTT	    0.993198	-20
          **********

Masking position 7
Map Score:   6.90797

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 41
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

         CTGATACGGTGAGGCGCAACA	1	2	1	TGATACGGTG	    0.988973	-125
TTACCGCTGCTGGAATGTTGCGCCTCACCG	1	17	0	TGGAATGTTG	    0.988742	-110
AAAAAAGCAGCGGTACGTCGTTACCGCTGC	1	37	0	CGGTACGTCG	    0.978052	-90
CTGTTGACCATGACAGGATGTTCAGTCGTC	1	92	0	TGACAGGATG	    0.988907	-35
TGGTCAACAGTGGAAGGATGATGTC     	1	112	1	TGGAAGGATG	    0.995859	-15
          **********

Masking position 5
Map Score:   5.15496

Number of sites scoring better than the average of aligned sites = 547
Number in coding regions = 515
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

TGGAATGTTGCGCCTCACCGTATCAG    	1	7	0	CGCCTCACCG	    0.997632	-120
GCAGCGGTACGTCGTTACCGCTGCTGGAAT	1	31	0	GTCGTTACCG	    0.996142	-96
GCCCCAATCGCGCGTTAACGCCTGACGACT	1	69	1	CGCGTTAACG	    0.997219	-58
          **********

Masking position 7
Map Score:   2.84838

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 251
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   -2.03625e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -2.03625e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -2.03625e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0