AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilacI_ecoli_opreg_100.orf -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	lacA	65	thiogalactoside acetyltransferase
#2	lacY	51	galactoside permease (M protein)
#3	lacZ	122	beta-D-galactosidase

Motif number 1

  GCAATCAATGTCGGATGCGGCGCGAGCGCCTTA	1	9	1	TGCGATGCGC	    0.998064	-57
ATGATATGTTGGTCGGATAAGGCGCTCGCGCCGCA	1	26	0	GGCGATGCGC	    0.999124	-40
GGCCATGTCTGCCCGTATTTCGCGTAAGGAAATCC	2	24	1	GCCGATGCGT	    0.880687	-28
GTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTT	3	27	1	TCCTATGCAC	    0.922454	-96
CATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGG	3	52	0	GGAGATGTGT	    0.980784	-71
TATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGA	3	68	1	GCCGATGTGT	    0.996702	-55
          ** ** **   ****

Masking position 8
Map Score:   8.51966

Number of sites scoring better than the average of aligned sites = 1190
Number in coding regions = 747
Number in noncoding regions = 443
Number of orfs with sites within 600 bp upstream = 125
Fraction of orfs with sites within 600 bp upstream = 0.0200771


Motif number 2

TCGGATAAGGCGCTCGCGCCGCATCCGACA	1	19	0	CGCTCGCGCC	    0.978247	-47
        TGCGATCACTCCGTTATGATAT	1	54	0	CGATCACTCC	     0.98972	-12
   TAATAACCGGGCAGGCCATGTCTGCCC	2	8	1	CGGGCAGGCC	    0.994309	-44
ACGCGAAATACGGGCAGACATGGCCTGCCC	2	19	0	CGGGCAGACA	    0.980744	-33
AATGTGAGTTAGCTCACTCATTAGGCACCC	3	24	1	AGCTCACTCA	    0.963066	-99
AATTGTTATCCGCTCACAATTCCACACAAC	3	86	0	CGCTCACAAT	    0.937591	-37
          **********

Masking position 5
Map Score:   4.1622

Number of sites scoring better than the average of aligned sites = 2124
Number in coding regions = 1929
Number in noncoding regions = 195
Number of orfs with sites within 600 bp upstream = 138
Fraction of orfs with sites within 600 bp upstream = 0.0221651


Motif number 3

AATGAGTGAGCTAACTCACATTAATTGCGT	3	16	0	CTAACTCACA	    0.980843	-107
TATCCGCTCACAATTCCACACAACATACGA	3	80	0	CAATTCCACA	    0.993758	-43
GAGCGGATAACAATTTCACACAGGAAACAG	3	101	1	CAATTTCACA	    0.994748	-22
          **********

Masking position 3
Map Score:   1.41223

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 27
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

CCGCATCCGACATTGATTGC          	1	1	0	CATTGATTGC	    0.996454	-65
TACGGGCAGACATGGCCTGCCCGGTTATTA	2	11	0	CATGGCCTGC	    0.993321	-41
          AATGGATTTCCTTACGCGAA	2	42	0	AATGGATTTC	    0.964957	-10
AGCTAACTCACATTAATTGCGTTGCGC   	3	8	0	CATTAATTGC	    0.986059	-115
          **********

Masking position 3
Map Score:   3.00659

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 279
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

          **********

No masking
Map Score:   2.72438e-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:   2.72438e-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 7

          **********

No masking
Map Score:   2.72438e-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