AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_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	gmd	25	GDP-D-mannose dehydratase
#2	wcaA	34	putative regulator
#3	BIME92	24	BIME
#4	wza	300	putative polysaccharide export protein

Motif number 1

TTATATTCGGAAGTTAATTTCCGTAATAAC	4	12	1	AAGTTAATTT	    0.856844	-289
TACACTGATTTAGTTTAATTTTTCACACCC	4	71	0	TAGTTTAATT	    0.846217	-230
TAAACTAAATCAGTGTATTGGTAGCTAAAA	4	84	1	CAGTGTATTG	    0.940405	-217
AGGCTATTGACAGAATAATTCAGACTGGTC	4	148	0	CAGAATAATT	    0.819969	-153
ATTTCATCCGCAGGCTATTGACAGAATAAT	4	159	0	CAGGCTATTG	    0.940822	-142
GGACTGATGCCAGTTAAATTTTTATTCAAT	4	200	1	CAGTTAAATT	    0.960198	-101
ATTTACCTTGCAGTTAATTGAATAAAAATT	4	216	0	CAGTTAATTG	    0.925968	-85
AATTAACTGCAAGGTAAATGTGCATGGCGA	4	227	1	AAGGTAAATG	    0.907456	-74
TAATAGTGCACAGGATAATTACTCTGCCAA	4	266	1	CAGGATAATT	    0.947485	-35
          **********

Masking position 7
Map Score:   7.42019

Number of sites scoring better than the average of aligned sites = 1311
Number in coding regions = 1098
Number in noncoding regions = 213
Number of orfs with sites within 600 bp upstream = 210
Fraction of orfs with sites within 600 bp upstream = 0.0337295


Motif number 2

      CGACGCCTGCATTCGCACCGCCCC	3	5	1	GCCTGCATTC	    0.713024	-20
CACCCTCTCAGCATGCAGTCGTTGATGAGA	4	46	0	GCATGCAGTC	    0.896706	-255
GGTCTTTCAGGCATCCAGACACGCTACCGC	4	122	0	GCATCCAGAC	    0.975744	-179
TCTGTCAATAGCCTGCGGATGAAATCAATT	4	164	1	GCCTGCGGAT	    0.979771	-137
TGCACATTTACCTTGCAGTTAATTGAATAA	4	221	0	CCTTGCAGTT	    0.964608	-80
AGCAATGTCGCCATGCACATTTACCTTGCA	4	234	0	CCATGCACAT	    0.951434	-67
          **********

Masking position 4
Map Score:   4.98282

Number of sites scoring better than the average of aligned sites = 718
Number in coding regions = 668
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

 AAGCAAACCAGCTCATAAGCCGGGAGAACAA	2	10	1	AGCTCAAGCC	    0.992326	-25
GTGTATTGGTAGCTAAAAAGCCAGGGGCGGTA	4	96	1	AGCTAAAGCC	    0.973522	-205
CAATTTTTTTAGGACTGATGCCAGTTAAATTT	4	189	1	AGGACTAGCC	    0.984841	-112
AATGTCGCCATGCACATTTACCTTGCAGTTAA	4	229	0	TGCACATACC	    0.928761	-72
CACTATTAATAGCAATGTCGCCATGCACATTT	4	242	0	AGCAATTGCC	    0.983797	-59
          ****** * ***

Masking position 2
Map Score:   0.946717

Number of sites scoring better than the average of aligned sites = 605
Number in coding regions = 552
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

          **********

No masking
Map Score:   9.53751e-15

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:   9.53751e-15

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:   9.53751e-15

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