AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i077_Lipopolysaccharide_Biosynthesis_2__mthe_reg_300.orf -o077_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH00306	48	M.thermo
#2	RTH00146	60	M.thermo
#3	RTH01779	194	M.thermo

Motif number 1

     GTGGTCTGTCTTCACATGCAAGGGA	1	6	1	CTGTCTTCAC	    0.945049	-43
CAGTCCAGTCCAGTCCAGTCCATCCTATCC	3	103	0	CAGTCCAGTC	    0.998795	-92
CAGTCCAGTCCAGTCCAGTCCAGTCCAGTC	3	113	0	CAGTCCAGTC	    0.998795	-82
TTTATCAGTCCAGTCCAGTCCAGTCCAGTC	3	123	0	CAGTCCAGTC	    0.998795	-72
TCTGCATTCACTGTCTACTCCAGGATCTTT	3	151	0	CTGTCTACTC	    0.994129	-44
          **********

Masking position 4
Map Score:   12.4232

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 25
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

TCCTCACGCTTAACTCCCTTGCATGTGAAG	1	20	0	TAACTCCCTT	    0.900394	-29
       GGCATCATCTCCTCACGCTTAAC	1	36	0	ATCATCTCCT	     0.97065	-13
CTCTGATGAGTTAATCCCTATGAGGAATGC	2	28	0	TTAATCCCTA	    0.898942	-33
       TCAATCATCCTTTCTCTGATGAG	2	48	0	ATCATCCTTT	    0.929409	-13
TCCTATCCTATTCCTCCCTTAAACCTACAG	3	81	0	TTCCTCCCTT	    0.993774	-114
AGTCCAGTCCATCCTATCCTATTCCTCCCT	3	92	0	ATCCTATCCT	    0.838195	-103
        TTTTCATCTCTCCATGTTCGAG	3	183	0	TTCATCTCTC	    0.959016	-12
          **********

Masking position 5
Map Score:   3.59339

Number of sites scoring better than the average of aligned sites = 1442
Number in coding regions = 1347
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 3

CAAGGGAGTTAAGCGTGAGGAGATGATGCC  	1	29	1	AAGCGGAGAG	    0.980739	-20
GGAATGCCGGGACCTCCAGAAGTG        	2	3	0	GACCTCAGAG	    0.989805	-58
TCCTCCCTTAAACCTACAGCAGTAAAAATCTG	3	68	0	AACCTCAGAG	    0.992604	-127
CTGATAAAAGATCCTGGAGTAGACAGTGAATG	3	145	1	ATCCTGAGAG	    0.897321	-50
GTGAATGCAGATCCTCGAACATGGAGAGATGA	3	170	1	ATCCTGAAAT	    0.675149	-25
          ***** *** **

Masking position 8
Map Score:   2.17954

Number of sites scoring better than the average of aligned sites = 476
Number in coding regions = 460
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

GTCCCGGCATTCCTCATAGGGATTAACTCA	2	22	1	TCCTCATAGG	    0.992412	-39
AGGGATTAACTCATCAGAGAAAGGATGATT	2	39	1	TCATCAGAGA	    0.978249	-22
GCACCCCACATCATCATACGAAAAGTTTAA	3	36	0	TCATCATACG	    0.988372	-159
TGAATGCAGATCCTCGAACATGGAGAGATG	3	171	1	TCCTCGAACA	    0.958242	-24
          **********

Masking position 4
Map Score:   1.107

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 161
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   -2.53363e-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:   -2.53363e-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:   -2.53363e-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