AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_Sulfate_trans-Cys_Synthase_mthe_reg_100.orf -o109_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	RTH00068	49	M.thermo
#2	RTH00701	136	M.thermo

Motif number 1

          CTTCAGAAAAAGTCGGGGTC	1	40	0	CTTCAGAAAA	     0.99199	-10
TGAGGGAGTTATTCCCAGAAC         	2	2	0	ATTCCCAGAA	    0.974627	-135
GGAATAACTCCCTCAGAGTAGTCCTTCTTT	2	17	1	CCTCAGAGTA	    0.991707	-120
GTTCTCATTCCTTCACAGAACCGATATGTA	2	67	1	CTTCACAGAA	    0.994822	-70
ACCTCCATTAACTCAGAACACCTATATCGA	2	109	0	ACTCAGAACA	    0.972153	-28
          **********

Masking position 7
Map Score:   5.08777

Number of sites scoring better than the average of aligned sites = 325
Number in coding regions = 290
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

AGTTAACATACTACTTTATTTTTAAGACCC	1	15	1	CTACTTTATT	    0.952632	-35
TTTAAGACCCCGACTTTTTCTGAAG     	1	35	1	CGACTTTTTC	    0.971927	-15
CAGAGTAGTCCTTCTTTATCTTTCAGGACG	2	30	1	CTTCTTTATC	    0.992345	-107
TAACTCAGAACACCTATATCGACATGGACA	2	101	0	CACCTATATC	    0.951527	-36
GGTCTTTAACCTCCATTAACTCAGAACACC	2	117	0	CTCCATTAAC	    0.963741	-20
          GGTCTTTAACCTCCATTAAC	2	127	0	GGTCTTTAAC	    0.945007	-10
          **********

Masking position 7
Map Score:   4.44482

Number of sites scoring better than the average of aligned sites = 483
Number in coding regions = 437
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

AGAACATGGGATCGTCCTGAAAGATAAAGAA	2	41	0	ATCGTCCTGA	    0.993335	-96
CCTTCACAGAACCGATATGTATATATGTCCA	2	76	1	ACCGATATGA	    0.989994	-61
GAACACCTATATCGACATGGACATATATACA	2	93	0	ATCGACATGA	    0.996812	-44
          ********* *

Masking position 1
Map Score:   0.381094

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 16
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

TTTAAGACCCCGACTTTTTCTGAAG     	1	35	1	CGACTTTTTC	    0.957742	-15
CTACTCTGAGGGAGTTATTCCCAGAAC   	2	8	0	GGAGTTATTC	    0.990287	-129
CTCCCTCAGAGTAGTCCTTCTTTATCTTTC	2	24	1	GTAGTCCTTC	    0.983711	-113
ACGATCCCATGTTCTCATTCCTTCACAGAA	2	57	1	GTTCTCATTC	    0.976955	-80
          **********

Masking position 5
Map Score:   0.364728

Number of sites scoring better than the average of aligned sites = 147
Number in coding regions = 138
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 5

          **********

No masking
Map Score:   4.57179e-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:   4.57179e-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:   4.57179e-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