AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i184_thi_operon_mthe_reg_100.orf -o184_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	RTH01046	227	M.thermo
#2	RTH00600	21	M.thermo
#3	RTH00364	23	M.thermo

Motif number 1

       TTCCTGATTTTCCATCTGCTCTG	1	4	1	CTGATTTTCC	    0.987663	-224
GATTTTCCATCTGCTCTGAGGTGGTCTGAA	1	16	1	CTGCTCTGAG	    0.937173	-212
CTGAGGTGGTCTGAACTATCAACTGAATTT	1	31	1	CTGAACTATC	    0.971014	-197
GAACTATCAACTGAATTTTCTGCATCCAAC	1	43	1	CTGAATTTTC	    0.975428	-185
TCCCTCATCACTGATTTTCCCTGCACTAAC	1	96	1	CTGATTTTCC	    0.987663	-132
CTGATTTTCCCTGCACTAACCTGAAGGACA	1	106	1	CTGCACTAAC	    0.969971	-122
TGAAGTATTACTGATTTGATCAGTTGGCTG	1	134	0	CTGATTTGAT	    0.925245	-94
          **********

Masking position 7
Map Score:   7.45098

Number of sites scoring better than the average of aligned sites = 386
Number in coding regions = 343
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

TCTGCATCCAACCACTAATGAACTGTTATG	1	61	1	ACCACTAATG	    0.982801	-167
TGCAGGGAAAATCAGTGATGAGGGATATCT	1	91	0	ATCAGTGATG	    0.993514	-137
AACTGATCAAATCAGTAATACTTCACCGGA	1	139	1	ATCAGTAATA	    0.985014	-89
TTTACACCCCATGAGTAATGGTTACCTAGG	1	206	0	ATGAGTAATG	    0.989839	-22
          **********

Masking position 6
Map Score:   3.66228

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 24
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

CTGCTCTGAGGTGGTCTGAACTATCAACTG	1	26	1	GTGGTCTGAA	    0.921881	-202
TTCATTAGTGGTTGGATGCAGAAAATTCAG	1	53	0	GTTGGATGCA	    0.984886	-175
AATCAGTGATGAGGGATATCTCATAACAGT	1	82	0	GAGGGATATC	    0.936519	-146
GATTTGATCAGTTGGCTGTCCTTCAGGTTA	1	122	0	GTTGGCTGTC	     0.98139	-106
ACCATTACTCATGGGGTGTAAAAT      	1	214	1	ATGGGGTGTA	    0.941898	-14
TATTAAGATTGAGGGATCCAAA        	3	12	1	GAGGGATCCA	    0.967029	-12
          **********

Masking position 7
Map Score:   0.577946

Number of sites scoring better than the average of aligned sites = 1237
Number in coding regions = 1169
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 4

          **********

No masking
Map Score:   -1.75204e-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 5

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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