AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yveM	258	similar to capsular polysaccharide biosynthesis

Motif number 1

GGAGGCACTCGGCTCTGCTGTGGGCAGCTGA	1	47	1	GGTCTGCTGT	    0.972196	-212
TAAGGCAGCAACTTCAGCTGCCCACAGCAGA	1	60	0	ACTCAGCTGC	    0.972263	-199
TGAAGTTGCTGCCTTAGATGCTGGTCGTCGC	1	75	1	GCTTAGATGC	    0.798769	-184
GCGTGAGGATGGGTTAAATGCCCACTTATCT	1	113	1	GGTTAAATGC	    0.972559	-146
ACGTATTGTCGGTTTAGCTGCTGCCGATTTT	1	158	1	GGTTAGCTGC	    0.998669	-101
TTCTTTTATCGGTTTAGCTGCGGCGGTTTTC	1	199	0	GGTTAGCTGC	    0.998669	-60
          ** ********

Masking position 4
Map Score:   12.2207

Number of sites scoring better than the average of aligned sites = 358
Number in coding regions = 316
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

CACTCGGCTCTGCTGTGGGCAGCTGAAGTT	1	52	1	TGCTGTGGGC	    0.961508	-207
GGGCAGCTGAAGTTGCTGCCTTAGATGCTG	1	68	1	AGTTGCTGCC	    0.995368	-191
TTGCTGCCTTAGATGCTGGTCGTCGCTGGC	1	80	1	AGATGCTGGT	    0.968228	-179
AGATGCTGGTCGTCGCTGGCGGGGCGTGAG	1	90	1	CGTCGCTGGC	    0.978542	-169
TTGTCGGTTTAGCTGCTGCCGATTTTTTGG	1	163	1	AGCTGCTGCC	    0.963932	-96
TTATCGGTTTAGCTGCGGCGGTTTTCGTCT	1	195	0	AGCTGCGGCG	    0.624546	-64
          **********

Masking position 5
Map Score:   8.14746

Number of sites scoring better than the average of aligned sites = 992
Number in coding regions = 913
Number in noncoding regions = 79
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 3

TTGATACAGGTCAGGAGACATCACCTTTAC	1	16	0	TCAGGAGACA	    0.976247	-243
GACCTGTATCAATGGAGGCACTCGGCTCTG	1	34	1	AATGGAGGCA	     0.96359	-225
ACTCGGCTCTGCTGTGGGCAGCTGAAGTTG	1	53	1	GCTGTGGGCA	    0.947816	-206
GACCAGCATCTAAGGCAGCAACTTCAGCTG	1	71	0	TAAGGCAGCA	       0.914	-188
ATATATGAGATAAGTGGGCATTTAACCCAT	1	121	0	TAAGTGGGCA	    0.983584	-138
CTGCCGATTTTTTGGAGAGACGAAAACCGC	1	178	1	TTTGGAGAGA	    0.895892	-81
GATAAAAGAATTAGGGGGGAAAAGGTTGAG	1	220	1	TTAGGGGGGA	    0.984775	-39
          **********

Masking position 10
Map Score:   3.69183

Number of sites scoring better than the average of aligned sites = 1321
Number in coding regions = 1090
Number in noncoding regions = 231
Number of orfs with sites within 600 bp upstream = 228
Fraction of orfs with sites within 600 bp upstream = 0.0366206


Motif number 4

CTCCTGACCTGTATCAATGGAGGCACTCGGCT	1	29	1	GTATCAGGAG	    0.962597	-230
ATGTATATATGAGATAAGTGGGCATTTAACCC	1	123	0	GAGATATGGG	    0.948132	-136
AGCTGCTGCCGATTTTTTGGAGAGACGAAAAC	1	173	1	GATTTTGGAG	    0.970058	-86
ACCGATAAAAGAATTAGGGGGGAAAAGGTTGA	1	217	1	GAATTAGGGG	    0.995096	-42
GGAAAAGGTTGAGTTACCGGAGAAGACTGTCA	1	237	1	GAGTTAGGAG	    0.996572	-22
          ******  ****

Masking position 10
Map Score:   1.09888

Number of sites scoring better than the average of aligned sites = 163
Number in coding regions = 135
Number in noncoding regions = 28
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:   3.15071e-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:   3.15071e-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:   3.15071e-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