AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_mthe_reg_100.orf -o150_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	RTH00559	35	M.thermo
#2	RTH00866	17	M.thermo
#3	RTH00917	212	M.thermo

Motif number 1

TGAAATTTAATTTGAATTAAGACAATATTT	3	59	0	TTTGAATTAA	    0.982221	-154
TTCAAATTAAATTTCATAAAATGACTCAAT	3	73	1	ATTTCATAAA	    0.841637	-140
TCATAAAATGACTCAATTAACATCAGGAGG	3	86	1	ACTCAATTAA	    0.956901	-127
AACTAATCCCATTCAGTTAACCAAGCCTTT	3	122	0	ATTCAGTTAA	    0.956897	-91
AGTTTATGATATTCAACTAATCCCATTCAG	3	136	0	ATTCAACTAA	    0.956895	-77
ATCATAAACTTTTGAATAAAATAGTAAAAG	3	156	1	TTTGAATAAA	    0.958957	-57
GAAATAGACCTTTGCATTAATAGG      	3	199	1	TTTGCATTAA	    0.973555	-14
          **********

Masking position 9
Map Score:   6.57728

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 40
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 2

  CCACCCCCAACATCCTTTTTCAGGAGAGT	1	9	1	AACATCCTTT	     0.96439	-27
     TGGCTAACTCTCCTGAAAAAGGATGT	1	20	0	AACTCTCCTA	    0.977061	-16
     CTGTTATCTCCCCTTTT         	2	2	0	ATCTCCCCTT	    0.992129	-16
TTCACCCATCAACATCCATATGATTGCCGAT	3	13	1	AACATCCATT	    0.938876	-200
ATGATTGCCGATCACCCTTAAAGACTTAAAT	3	32	1	ATCACCCTTA	    0.987679	-181
AGCCTTTTGAATCCCTCCTGATGTTAATTGA	3	98	0	ATCCCTCCTA	    0.972827	-115
          ********* *

Masking position 9
Map Score:   3.41699

Number of sites scoring better than the average of aligned sites = 711
Number in coding regions = 660
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

     CCACCCCCAACATCCTTTTTCAGGAG	1	6	1	CCCAACACCT	    0.997732	-30
    AATTCACCCATCAACATCCATATGATT	3	7	1	CCCATCACAT	    0.996499	-206
CATATGATTGCCGATCACCCTTAAAGACTTA	3	29	1	CCGATCACCT	     0.99757	-184
          ******* ***

Masking position 7
Map Score:   2.51747

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 24
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

GCTAACTCTCCTGAAAAAGGATGTTGGGGG	1	14	0	CTGAAAAAGG	    0.967158	-22
ATCAGGAGGGATTCAAAAGGCTTGGTTAAC	3	107	1	ATTCAAAAGG	    0.992301	-106
TTACTATTTTATTCAAAAGTTTATGATATT	3	153	0	ATTCAAAAGT	    0.988141	-60
   CCTATTAATGCAAAGGTCTATTTCGCG	3	196	0	ATGCAAAGGT	    0.986952	-17
          **********

Masking position 5
Map Score:   3.05843

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 29
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

AATTAAGACAATATTTAAGTCTTTAAGGGT	3	45	0	ATATTTAAGT	    0.980407	-168
TCATTTTATGAAATTTAATTTGAATTAAGA	3	67	0	AAATTTAATT	    0.928459	-146
AAAGTTTATGATATTCAACTAATCCCATTC	3	138	0	ATATTCAACT	    0.981814	-75
ATTTCGCGGTATATTTATCTTTTACTATTT	3	174	0	ATATTTATCT	    0.971538	-39
          **********

Masking position 5
Map Score:   2.04713

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 23
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 6

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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 8

          **********

No masking
Map Score:   2.79544e-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