AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_aful_reg_100.orf -o076_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -x5 -e 
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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG49475	219	Archaeoglobus_fulgidus
#2	RAG49513	126	Archaeoglobus_fulgidus

Motif number 1

CTTTTTTATTGGCACTCGTCTTGTTTCTGGTTTT	1	18	0	GGCCTCCTTT	    0.987675	-202
TTGGAGCCTCTTAGCTCCTTTTTTATTGGCACTC	1	35	0	TTACTCTTTT	    0.978977	-185
ACCGAGGCACGGCTCTAGGTTTGATTTGGAGCCT	1	60	0	GGCCTATTTA	     0.96275	-160
CCGTGCCTCGGTATCTCTGCTTAAACTCAAATTG	1	82	1	GTACTCCTTA	    0.975691	-138
ATGGTGATTATGACATCTCTTTTTCTCAAATATC	1	120	1	TGAATCTTTT	    0.899686	-100
TTAAAAACATTGAGCTCAGTCTATGGGTATGTCC	1	155	0	TGACTCTCTT	    0.955307	-65
TTAAAAATTTTGCTCTAAGTTTAAAAACATTGAG	1	175	0	TGCCTATTTA	    0.952551	-45
AAACGTCTCCGTACCTCCCCTTCTCCGCAAGGAG	2	44	0	GTACTCCTTT	    0.980179	-83
AACTCCGTTCTTAGCTACATTTTACTTGCACTCG	2	101	1	TTACTATTTA	    0.925218	-26
          *** ***  *** *

Masking position 6
Map Score:   7.2133

Number of sites scoring better than the average of aligned sites = 575
Number in coding regions = 533
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 2

AGCTAAGAGGCTCCAAATCAAACCTAGAGCCG	1	53	1	CTCAATCAAA	    0.973866	-167
GGTATCTCTGCTTAAACTCAAATTGAGTCATG	1	91	1	CTTACTCAAA	    0.995921	-129
TATGACATCTCTTTTTCTCAAATATCCGGACA	1	128	1	CTTTCTCAAA	    0.990222	-92
CTACATTTTACTTGCACTCGAA          	2	115	1	CTTACTCGAA	    0.993229	-12
          ***  *******

Masking position 8
Map Score:   1.9719

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 46
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

TAAAAAAGGAGCTAAGAGGCTCCAAATCAA	1	44	1	GCTAAGAGGC	     0.97681	-176
TTAAGCAGAGATACCGAGGCACGGCTCTAG	1	76	0	ATACCGAGGC	    0.975665	-144
CCCCTTCTCCGCAAGGAGGCAGTAGCCCTT	2	32	0	GCAAGGAGGC	    0.996315	-95
AGAAGGGGAGGTACGGAGACGTTTACAACC	2	54	1	GTACGGAGAC	    0.986621	-73
          **********

Masking position 7
Map Score:   1.14127

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 141
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

          **********

No masking
Map Score:   -2.60469e-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 5

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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