AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i185_4_6_1_10_mthe_reg_100.orf -o185_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	RTH00539	117	M.thermo

Motif number 1

  GGTGTCGGGGGGATGCTGCTGGTGTCTG	1	9	1	GGGGATGCTG	    0.840904	-109
CTGCTGGTGTCTGGATACTGGTGTGTCTGA	1	26	1	CTGGATACTG	     0.66442	-92
TGGTGTGTCTGAGGATATGGCCAGGACCCG	1	44	1	GAGGATATGG	    0.987275	-74
AGGATATGGCCAGGACCCGGATCTTTTAAG	1	55	1	CAGGACCCGG	    0.657751	-63
TAAGGTGTTTCAGGATAGGCTACCCGGGTC	1	81	1	CAGGATAGGC	    0.957261	-37
ACTGTTGAATGGGGACCCGGGTAGCCTATC	1	94	0	GGGGACCCGG	    0.967404	-24
          **********

Masking position 5
Map Score:   10.3614

Number of sites scoring better than the average of aligned sites = 484
Number in coding regions = 454
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

CAGCAGCATCCCCCCGACACC          	1	1	0	CCCCCGCACC	    0.998772	-117
AGTATCCAGACACCAGCAGCATCCCCCCGAC	1	14	0	CACCAGAGCA	     0.96356	-104
CTGGCCATATCCTCAGACACACCAGTATCCA	1	37	0	CCTCAGCACA	    0.995173	-81
GGTAGCCTATCCTGAAACACCTTAAAAGATC	1	74	0	CCTGAACACC	    0.983892	-44
TGAATGGGGACCCGGGTAGCCTATCCTGAAA	1	88	0	CCCGGGAGCC	    0.991668	-30
CTACCCGGGTCCCCATTCAACAGTTGAA   	1	100	1	CCCCATCAAC	    0.981657	-18
          ****** ****

Masking position 1
Map Score:   6.33456

Number of sites scoring better than the average of aligned sites = 1284
Number in coding regions = 1207
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

AGCAGCATCCCCCCGACACC          	1	1	0	CCCCGACACC	    0.998931	-117
CACACCAGTATCCAGACACCAGCAGCATCC	1	21	0	TCCAGACACC	     0.99749	-97
TGGCCATATCCTCAGACACACCAGTATCCA	1	37	0	CTCAGACACA	    0.994361	-81
GTAGCCTATCCTGAAACACCTTAAAAGATC	1	74	0	CTGAAACACC	    0.985027	-44
TACCCGGGTCCCCATTCAACAGTTGAA   	1	101	1	CCCATTCAAC	     0.96815	-17
          **********

Masking position 8
Map Score:   8.44672

Number of sites scoring better than the average of aligned sites = 482
Number in coding regions = 459
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

          **********

No masking
Map Score:   -2.59896e-14

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:   -2.59896e-14

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:   -2.59896e-14

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