AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i018_non-Oxidative_glucose_Metabolism_mthe_reg_100.orf -o018_mthe_100.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	RTH00146	60	M.thermo
#2	RTH01779	194	M.thermo

Motif number 1

GGATAGGATGGACTGGACTGGACTGGACTG	2	103	1	GACTGGACTG	    0.999314	-92
GACTGGACTGGACTGGACTGGACTGGACTG	2	118	1	GACTGGACTG	    0.999314	-77
GACTGGACTGGACTGGACTGATAAAAGATC	2	128	1	GACTGGACTG	    0.999314	-67
AAAGATCCTGGAGTAGACAGTGAATGCAGA	2	151	1	GAGTAGACAG	     0.98651	-44
          **********

Masking position 4
Map Score:   12.8363

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 6
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

         CACTTCTGGAGGTCCCGGCAT	1	2	1	ACTTCTGGAG	    0.978294	-59
CTTTTCGTATGATGATGTGGGGTGCGACAG	2	41	1	GATGATGTGG	    0.927533	-154
ACAGCAGTAAAAATCTGTCGCACCCCACAT	2	55	0	AAATCTGTCG	    0.893019	-140
ACAGATTTTTACTGCTGTAGGTTTAAGGGA	2	67	1	ACTGCTGTAG	    0.977942	-128
ACTGATAAAAGATCCTGGAGTAGACAGTGA	2	144	1	GATCCTGGAG	    0.992494	-51
GCAGATCCTCGAACATGGAGAGATGAAAA 	2	176	1	GAACATGGAG	    0.959896	-19
          **********

Masking position 6
Map Score:   2.617

Number of sites scoring better than the average of aligned sites = 956
Number in coding regions = 886
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 3

GTCCCGGCATTCCTCATAGGGATTAACTCA	1	22	1	TCCTCATAGG	    0.993757	-39
AGGGATTAACTCATCAGAGAAAGGATGATT	1	39	1	TCATCAGAGA	    0.981882	-22
GCACCCCACATCATCATACGAAAAGTTTAA	2	36	0	TCATCATACG	    0.990451	-159
TGAATGCAGATCCTCGAACATGGAGAGATG	2	171	1	TCCTCGAACA	    0.962534	-24
          **********

Masking position 4
Map Score:   1.7399

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 4

CTCTGATGAGTTAATCCCTATGAGGAATGC	1	28	0	TTAATCCCTA	     0.88357	-33
       TCAATCATCCTTTCTCTGATGAG	1	48	0	ATCATCCTTT	    0.976877	-13
CGCACCCCACATCATCATACGAAAAGTTTA	2	37	0	ATCATCATAC	    0.824066	-158
TCCTATCCTATTCCTCCCTTAAACCTACAG	2	81	0	TTCCTCCCTT	    0.978412	-114
TCCAGTCCAGTCCATCCTATCCTATTCCTC	2	95	0	TCCATCCTAT	    0.939201	-100
        TTTTCATCTCTCCATGTTCGAG	2	183	0	TTCATCTCTC	    0.962462	-12
          **********

Masking position 5
Map Score:   1.00165

Number of sites scoring better than the average of aligned sites = 1121
Number in coding regions = 1043
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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