AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i288_ecoli_mtub_100.orf -o288_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -x5 -e 
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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	moxR	138	moxR

Motif number 1

CGACGCCGCGGTGGTGCCCGGCAAATCACA	1	17	0	GTGGTGCCCG	    0.997517	-122
CCTGGATTCCGTCGACGCCGCGGTGGTGCC	1	29	0	GTCGACGCCG	    0.996464	-110
GCGGGGCAGCGACGCGCCCGCGTTCAACTA	1	69	0	GACGCGCCCG	     0.99765	-70
CGACATGACCAACGTCGCGGGGCAGCGACG	1	85	0	AACGTCGCGG	    0.975717	-54
CGCGACGTTGGTCATGTCGGCAGTCGTGTC	1	96	1	GTCATGTCGG	    0.989331	-43
CATGTCGGCAGTCGTGTCCGATTGAGCTGT	1	108	1	GTCGTGTCCG	    0.999129	-31
          **********

Masking position 8
Map Score:   11.9424

Number of sites scoring better than the average of aligned sites = 1014
Number in coding regions = 970
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

ATTTGCCGGGCACCACCGCGGCGTCGACGG	1	21	1	CACCACCGCG	     0.99392	-118
GCCTGGAATAGTTGAACGCGGGCGCGTCGC	1	61	1	GTTGAACGCG	    0.939257	-78
CGTCGCGGGGCAGCGACGCGCCCGCGTTCA	1	73	0	CAGCGACGCG	    0.982449	-66
CTGCCGACATGACCAACGTCGCGGGGCAGC	1	89	0	GACCAACGTC	    0.964577	-50
CTCAATCGGACACGACTGCCGACATGACCA	1	104	0	CACGACTGCC	    0.978664	-35
   CAAAATCCTCCACAGCTCAATCGGACA	1	122	0	CTCCACAGCT	    0.957321	-17
          **********

Masking position 8
Map Score:   3.61907

Number of sites scoring better than the average of aligned sites = 6603
Number in coding regions = 6417
Number in noncoding regions = 186
Number of orfs with sites within 600 bp upstream = 189
Fraction of orfs with sites within 600 bp upstream = 0.0303566


Motif number 3

          **********

No masking
Map Score:   -9.70439e-14

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 4

          **********

No masking
Map Score:   -9.70439e-14

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:   -9.70439e-14

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