AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_Sulfate_trans-Cys_Synthase_mthe_reg_300.orf -o109_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	RTH00068	49	M.thermo
#2	RTH00701	136	M.thermo
#3	RTH00799	91	M.thermo

Motif number 1

GACCCCGACTTTTTCTGAAG          	1	40	1	TTTTCTGAAG	    0.963516	-10
GAGGGAGTTATTCCCAGAAC          	2	1	0	TTCCCAGAAC	     0.99272	-136
AAAGAAGGACTACTCTGAGGGAGTTATTCC	2	17	0	TACTCTGAGG	    0.958156	-120
TTCTCATTCCTTCACAGAACCGATATGTAT	2	68	1	TTCACAGAAC	    0.988866	-69
AACCTCCATTAACTCAGAACACCTATATCG	2	110	0	AACTCAGAAC	    0.953035	-27
CTGATAAAGATATCCGGAAG          	3	1	0	TATCCGGAAG	    0.925601	-91
AATGTATTTTTTCACTGAACATCAGATTCA	3	39	0	TTCACTGAAC	    0.988866	-53
          **********

Masking position 8
Map Score:   8.19376

Number of sites scoring better than the average of aligned sites = 367
Number in coding regions = 340
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

CAGTTAACATACTACTTTATTTTTAAGACCCC	1	14	1	ACCTTTATTT	    0.951218	-36
TTTTAAGACCCCGACTTTTTCTGAAG      	1	34	1	CCCTTTTTCT	    0.987601	-16
TCAGAGTAGTCCTTCTTTATCTTTCAGGACGA	2	29	1	CCCTTTATCT	    0.996191	-108
TTAACTCAGAACACCTATATCGACATGGACAT	2	100	0	ACCTATATCG	    0.943962	-37
 GGTCTTTAACCTCCATTAACTCAGAACACCT	2	116	0	CCCATTAACT	    0.918668	-21
       CTTCCGGATATCTTTATCAGTTTGT	3	4	1	CCATATCTTT	    0.925299	-88
TATCACCATTCCATATATCTCTCTCCCCAATA	3	68	0	CCATATCTCT	    0.974179	-24
          **  ********

Masking position 8
Map Score:   4.78788

Number of sites scoring better than the average of aligned sites = 504
Number in coding regions = 466
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 3

ACTTTATTTTTAAGACCCCGACTTTTTCTG	1	27	1	TAAGACCCCG	    0.939888	-23
TCTGAGGGAGTTATTCCCAGAAC       	2	4	0	TTATTCCCAG	     0.95666	-133
GATATGTATATATGTCCATGTCGATATAGG	2	89	1	TATGTCCATG	    0.982078	-48
TCTTTATCAGTTTGTCCATGAATCTGATGT	3	21	1	TTTGTCCATG	    0.987519	-71
AATAATGTATTTTTTCACTGAACATCAGAT	3	42	0	TTTTTCACTG	    0.938703	-50
          **********

Masking position 1
Map Score:   1.77902

Number of sites scoring better than the average of aligned sites = 394
Number in coding regions = 371
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

CTGAAAGATAAAGAAGGACTACTCTGAGGG	2	26	0	AAGAAGGACT	    0.958583	-111
AAGGAATGAGAACATGGGATCGTCCTGAAA	2	50	0	AACATGGGAT	    0.936006	-87
TATCGGTTCTGTGAAGGAATGAGAACATGG	2	63	0	GTGAAGGAAT	    0.924258	-74
CACCTATATCGACATGGACATATATACATA	2	91	0	GACATGGACA	    0.981185	-46
GAACATCAGATTCATGGACAAACTGATAAA	3	23	0	TTCATGGACA	    0.947558	-69
GGGAGAGAGATATATGGAATGGTGATAAC 	3	73	1	TATATGGAAT	    0.909653	-19
          **********

Masking position 4
Map Score:   1.23121

Number of sites scoring better than the average of aligned sites = 656
Number in coding regions = 617
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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