AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_Galactose_Metabolism__mthe_reg_300.orf -o038_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	RTH00414	143	M.thermo

Motif number 1

TATATGAAATCAGACCATTAAAGCTATGCAAA	1	29	1	CAGCCATAAA	    0.997625	-115
TATGCAAAGGCAGACCACAAAGACCTACCCAC	1	53	1	CAGCCACAAG	    0.998979	-91
CCACAAAGACCTACCCACAAAAACAGGCCACC	1	67	1	CTACCACAAA	    0.994021	-77
CCCACAAAAACAGGCCACCAAACCTTATTTAC	1	80	1	CAGCCACAAA	    0.999401	-64
          *** **** ***

Masking position 7
Map Score:   7.82285

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 2
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

GATTAATATATGAAATCAGACCATTAAAGCTA	1	23	1	TGAACAGACC	    0.989432	-121
TAAAGCTATGCAAAGGCAGACCACAAAGACCT	1	47	1	CAAACAGACC	     0.99907	-97
AGGCAGACCACAAAGACCTACCCACAAAAACA	1	60	1	CAAACCTACC	    0.995404	-84
GACCTACCCACAAAAACAGGCCACCAAACCTT	1	74	1	CAAACAGGCC	    0.997957	-70
GAAATATAGACAGAATCATATCTGTGTGATAA	1	121	1	CAGACATATC	    0.976499	-23
          ****  ******

Masking position 4
Map Score:   6.90825

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 84
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          **********

No masking
Map Score:   -2.17836e-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 4

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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