AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i059_Sulfate_trans-cys_synthase_mthe_reg_300.orf -o059_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	    0.963067	-10
GAGGGAGTTATTCCCAGAAC          	2	1	0	TTCCCAGAAC	    0.992629	-136
AAAGAAGGACTACTCTGAGGGAGTTATTCC	2	17	0	TACTCTGAGG	    0.957643	-120
TTCTCATTCCTTCACAGAACCGATATGTAT	2	68	1	TTCACAGAAC	    0.988725	-69
AACCTCCATTAACTCAGAACACCTATATCG	2	110	0	AACTCAGAAC	    0.952463	-27
CTGATAAAGATATCCGGAAG          	3	1	0	TATCCGGAAG	    0.924775	-91
AATGTATTTTTTCACTGAACATCAGATTCA	3	39	0	TTCACTGAAC	    0.988725	-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	    0.953258	-36
TTTTAAGACCCCGACTTTTTCTGAAG      	1	34	1	CCCTTTTTCT	    0.988139	-16
TCAGAGTAGTCCTTCTTTATCTTTCAGGACGA	2	29	1	CCCTTTATCT	    0.996356	-108
TTAACTCAGAACACCTATATCGACATGGACAT	2	100	0	ACCTATATCG	    0.946276	-37
 GGTCTTTAACCTCCATTAACTCAGAACACCT	2	116	0	CCCATTAACT	    0.921959	-21
       CTTCCGGATATCTTTATCAGTTTGT	3	4	1	CCATATCTTT	    0.928328	-88
TATCACCATTCCATATATCTCTCTCCCCAATA	3	68	0	CCATATCTCT	    0.974902	-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

CAGAAAAAGTCGGGGTCTTAAAAATAAAGT	1	27	0	CGGGGTCTTA	    0.943266	-23
       GTTCTGGGAATAACTCCCTCAGA	2	4	1	CTGGGAATAA	    0.959136	-133
CCTATATCGACATGGACATATATACATATC	2	89	0	CATGGACATA	     0.98309	-48
ACATCAGATTCATGGACAAACTGATAAAGA	3	21	0	CATGGACAAA	    0.988239	-71
ATCTGATGTTCAGTGAAAAAATACATTATT	3	42	1	CAGTGAAAAA	    0.942143	-50
          **********

Masking position 10
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

CCCTCAGAGTAGTCCTTCTTTATCTTTCAG	2	26	1	AGTCCTTCTT	    0.960869	-111
TTTCAGGACGATCCCATGTTCTCATTCCTT	2	50	1	ATCCCATGTT	    0.939459	-87
CCATGTTCTCATTCCTTCACAGAACCGATA	2	63	1	ATTCCTTCAC	    0.928296	-74
TATGTATATATGTCCATGTCGATATAGGTG	2	91	1	TGTCCATGTC	    0.982246	-46
TTTATCAGTTTGTCCATGAATCTGATGTTC	3	23	1	TGTCCATGAA	    0.950421	-69
 GTTATCACCATTCCATATATCTCTCTCCC	3	73	0	ATTCCATATA	    0.914398	-19
          **********

Masking position 7
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