AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilacI_ecoli_opreg_300.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
#4	lacI	76	transcriptional repressor of the lac operon
#5	mhpR	76	transcriptional regulator for mhp operon

Motif number 1

GTCGGATGCGGCGCGAGCGCCTTATCCGACCAA	1	20	1	GCGCGAGCTT	    0.989639	-46
CCCGTATTTCGCGTAAGGAAATCCATT      	2	35	1	GCGTAAGATC	    0.969825	-17
          GCGCAACGCAATTAATGTGAGTT	3	1	1	GCGCAACATT	    0.997282	-122
GGAATTGTGAGCGGATAACAATTTCACACAGGA	3	93	1	GCGGATAATT	    0.924889	-30
CCATCGAATGGCGCAAAACCTTTCGCGGTATGG	4	13	1	GCGCAAACTT	    0.993774	-64
ATGATAGCGCCCGGAAGAGAGTCAATTCAGGGT	4	47	1	CCGGAAGATC	    0.935524	-30
TGTACTGTGCGCGCAACGACATTTTGTCCGAGT	5	25	0	GCGCAACCTT	    0.997227	-52
GCACAGTACAGCGCAACTTATTTTGTTAAAAAC	5	48	1	GCGCAACATT	    0.997281	-29
          *******  * **

Masking position 12
Map Score:   12.1452

Number of sites scoring better than the average of aligned sites = 627
Number in coding regions = 564
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

GATAAGGCGCTCGCGCCGCATCCGACATTG	1	16	0	TCGCGCCGCA	    0.964606	-50
CCCGTATTTCGCGTAAGGAAATCCATT   	2	35	1	GCGTAAGGAA	    0.976662	-17
          GCGCAACGCAATTAATGTGA	3	1	1	GCGCAACGCA	    0.994495	-122
ATGCCATACCGCGAAAGGTTTTGCGCCATT	4	19	0	GCGAAAGGTT	    0.888083	-58
TGGCATGATAGCGCCCGGAAGAGAGTCAAT	4	43	1	GCGCCCGGAA	    0.982136	-34
TTTGTCCGAGTCGTGAGGTACTGAA     	5	6	0	TCGTGAGGTA	     0.92318	-71
ATGTCGTTGCGCGCACAGTACAGCGCAACT	5	36	1	GCGCACAGTA	    0.981739	-41
GCACAGTACAGCGCAACTTATTTTGTTAAA	5	48	1	GCGCAACTTA	    0.960528	-29
          **********

Masking position 3
Map Score:   7.29862

Number of sites scoring better than the average of aligned sites = 3007
Number in coding regions = 2815
Number in noncoding regions = 192
Number of orfs with sites within 600 bp upstream = 191
Fraction of orfs with sites within 600 bp upstream = 0.0306778


Motif number 3

CGCGCCGCATCCGACATTGATTGC         	1	2	0	CCGCATTGTG	    0.969688	-64
TGCGATCACTCCGTTATGATATGTTGGTCGGAT	1	43	0	CCGTATGATG	    0.976346	-23
GAAATACGGGCAGACATGGCCTGCCCGGTTATT	2	12	0	CAGCATGGTG	    0.682011	-40
CATAAAGTGTAAAGCCTGGGGTGCCTAATGAGT	3	39	0	AAACCTGGTG	    0.859113	-84
ATACGAGCCGGAAGCATAAAGTGTAAAGCCTGG	3	53	0	GAACATAATG	    0.765536	-70
GAAAGGTTTTGCGCCATTCGATGGTG       	4	4	0	GCGCATTCTG	    0.956717	-73
AAAACCTTTCGCGGTATGGCATGATAGCGCCCG	4	27	1	GCGTATGGTG	    0.984894	-50
     ATTCACCACCCTGAATTGACTCTCTTCC	4	59	0	CCACCTGATG	    0.965842	-18
          *** *****  **

Masking position 7
Map Score:   4.43397

Number of sites scoring better than the average of aligned sites = 1577
Number in coding regions = 1460
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 95
Fraction of orfs with sites within 600 bp upstream = 0.0152586


Motif number 4

ATAAGGCGCTCGCGCCGCATCCGACATTGA	1	15	0	CGCGCCGCAT	    0.959192	-51
TTATGATATGTTGGTCGGATAAGGCGCTCG	1	33	0	TTGGTCGGAT	      0.9328	-33
CAGACATGGCCTGCCCGGTTATTA      	2	5	0	CTGCCCGGTT	    0.985196	-47
CAGGCCATGTCTGCCCGTATTTCGCGTAAG	2	22	1	CTGCCCGTAT	    0.991648	-30
TTTATGCTTCCGGCTCGTATGTTGTGTGGA	3	66	1	CGGCTCGTAT	    0.991718	-57
CAGTACCTCACGACTCGGACAAAATGTCGT	5	13	1	CGACTCGGAC	    0.949778	-64
          **********

Masking position 6
Map Score:   3.4435

Number of sites scoring better than the average of aligned sites = 1147
Number in coding regions = 1054
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 5

          **********

No masking
Map Score:   -1.88842e-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 6

          **********

No masking
Map Score:   -1.88842e-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 7

          **********

No masking
Map Score:   -1.88842e-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