AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilacI_ecoli_bsub_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	    0.990187	-46
CCCGTATTTCGCGTAAGGAAATCCATT      	2	35	1	GCGTAAGATC	    0.971391	-17
          GCGCAACGCAATTAATGTGAGTT	3	1	1	GCGCAACATT	    0.997427	-122
GGAATTGTGAGCGGATAACAATTTCACACAGGA	3	93	1	GCGGATAATT	    0.928616	-30
CCATCGAATGGCGCAAAACCTTTCGCGGTATGG	4	13	1	GCGCAAACTT	    0.994104	-64
ATGATAGCGCCCGGAAGAGAGTCAATTCAGGGT	4	47	1	CCGGAAGATC	    0.938758	-30
TGTACTGTGCGCGCAACGACATTTTGTCCGAGT	5	25	0	GCGCAACCTT	    0.997375	-52
GCACAGTACAGCGCAACTTATTTTGTTAAAAAC	5	48	1	GCGCAACATT	    0.997426	-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

CAATGTCGGATGCGGCGCGAGCGCCTTATC	1	16	1	TGCGGCGCGA	    0.966205	-50
   AATGGATTTCCTTACGCGAAATACGGG	2	35	0	TTCCTTACGC	    0.977729	-17
TCACATTAATTGCGTTGCGC          	3	1	0	TGCGTTGCGC	    0.994751	-122
AATGGCGCAAAACCTTTCGCGGTATGGCAT	4	19	1	AACCTTTCGC	    0.892757	-58
ATTGACTCTCTTCCGGGCGCTATCATGCCA	4	43	0	TTCCGGGCGC	    0.982958	-34
     TTCAGTACCTCACGACTCGGACAAA	5	6	1	TACCTCACGA	     0.92651	-71
AGTTGCGCTGTACTGTGCGCGCAACGACAT	5	36	0	TACTGTGCGC	    0.982578	-41
TTTAACAAAATAAGTTGCGCTGTACTGTGC	5	48	0	TAAGTTGCGC	    0.962305	-29
          **********

Masking position 8
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	    0.968672	-64
TGCGATCACTCCGTTATGATATGTTGGTCGGAT	1	43	0	CCGTATGATG	    0.978265	-23
GAAATACGGGCAGACATGGCCTGCCCGGTTATT	2	12	0	CAGCATGGTG	    0.672334	-40
CATAAAGTGTAAAGCCTGGGGTGCCTAATGAGT	3	39	0	AAACCTGGTG	    0.869012	-84
ATACGAGCCGGAAGCATAAAGTGTAAAGCCTGG	3	53	0	GAACATAATG	     0.78089	-70
GAAAGGTTTTGCGCCATTCGATGGTG       	4	4	0	GCGCATTCTG	    0.960202	-73
AAAACCTTTCGCGGTATGGCATGATAGCGCCCG	4	27	1	GCGTATGGTG	    0.986141	-50
     ATTCACCACCCTGAATTGACTCTCTTCC	4	59	0	CCACCTGATG	    0.966929	-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

TCAATGTCGGATGCGGCGCGAGCGCCTTAT	1	15	1	ATGCGGCGCG	     0.96208	-51
CGAGCGCCTTATCCGACCAACATATCATAA	1	33	1	ATCCGACCAA	    0.937434	-33
      TAATAACCGGGCAGGCCATGTCTG	2	5	1	AACCGGGCAG	    0.986269	-47
CTTACGCGAAATACGGGCAGACATGGCCTG	2	22	0	ATACGGGCAG	    0.992246	-30
TCCACACAACATACGAGCCGGAAGCATAAA	3	66	0	ATACGAGCCG	    0.992322	-57
ACGACATTTTGTCCGAGTCGTGAGGTACTG	5	13	0	GTCCGAGTCG	    0.953299	-64
          **********

Masking position 5
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