AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i059_Sulfate_trans-cys_synthase_mthe_reg_100.orf -o059_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

GACCCCGACTTTTTCTGAAG          	1	40	1	TTTTCTGAAG	    0.991095	-10
         GTTCTGGGAATAACTCCCTCA	2	2	1	TTCTGGGAAT	    0.971832	-135
AAAGAAGGACTACTCTGAGGGAGTTATTCC	2	17	0	TACTCTGAGG	    0.990775	-120
TACATATCGGTTCTGTGAAGGAATGAGAAC	2	67	0	TTCTGTGAAG	    0.994239	-70
TCGATATAGGTGTTCTGAGTTAATGGAGGT	2	109	1	TGTTCTGAGT	    0.969094	-28
          **********

Masking position 4
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

GGGTCTTAAAAATAAAGTAGTATGTTAACT	1	15	0	AATAAAGTAG	    0.955378	-35
     CTTCAGAAAAAGTCGGGGTCTTAAA	1	35	0	GAAAAAGTCG	    0.973585	-15
CGTCCTGAAAGATAAAGAAGGACTACTCTG	2	30	0	GATAAAGAAG	    0.992804	-107
TGTCCATGTCGATATAGGTGTTCTGAGTTA	2	101	1	GATATAGGTG	    0.954333	-36
GGTGTTCTGAGTTAATGGAGGTTAAAGACC	2	117	1	GTTAATGGAG	    0.965865	-20
GTTAATGGAGGTTAAAGACC          	2	127	1	GTTAAAGACC	    0.948149	-10
          **********

Masking position 4
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	    0.993636	-96
CCTTCACAGAACCGATATGTATATATGTCCA	2	76	1	ACCGATATGA	     0.99047	-61
GAACACCTATATCGACATGGACATATATACA	2	93	0	ATCGACATGA	    0.996957	-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

     CTTCAGAAAAAGTCGGGGTCTTAAA	1	35	0	GAAAAAGTCG	    0.957742	-15
   GTTCTGGGAATAACTCCCTCAGAGTAG	2	8	1	GAATAACTCC	    0.990287	-129
GAAAGATAAAGAAGGACTACTCTGAGGGAG	2	24	0	GAAGGACTAC	    0.983711	-113
TTCTGTGAAGGAATGAGAACATGGGATCGT	2	57	0	GAATGAGAAC	    0.976955	-80
          **********

Masking position 6
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