AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_mthe_reg_100.orf -o198_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	RTH01062	171	M.thermo
#2	RTH01098	51	M.thermo

Motif number 1

         GGGACCGTAGGGTAGCTTGGT	1	2	1	GGACCGTAGG	    0.991384	-170
CTTTTCAACTGGAACGGGGATGGTCAGCAC	1	64	1	GGAACGGGGA	    0.994716	-108
GGTCAGCACCGGAACGCTGGAGACCCGAGT	1	85	1	GGAACGCTGG	    0.997617	-87
CGCCGAGATTTGAACTCGGGTCTCCAGCGT	1	98	0	TGAACTCGGG	    0.977055	-74
CGATTTGATGGGACCGCCGAGATTTGAACT	1	112	0	GGACCGCCGA	    0.996685	-60
          **********

Masking position 3
Map Score:   6.73756

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 113
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

 GGGACCGTAGGGTAGCTTGGTCCATCCTCC	1	10	1	GGTAGCTTGG	    0.986917	-162
TCTTGGATTCGATTTGATGGGACCGCCGAGA	1	120	0	GTTTGATGGG	    0.960042	-52
CATTAAAATAGAGGTTCTTGGATTCGATTTG	1	135	0	GGGTTCTTGG	     0.99264	-37
CTATTTTAATGTTTTTCTTGGAGGCAT    	1	155	1	GTTTTCTTGG	     0.99204	-17
TGAAAAATAGTGGTTTATTAGAGT       	2	4	0	TGTTTATTAG	    0.924595	-48
TTTCAGTCTAGAGTTTATTATGAGGTGTTTT	2	30	1	GGTTTATTAT	    0.924595	-22
          * *********

Masking position 8
Map Score:   2.75168

Number of sites scoring better than the average of aligned sites = 365
Number in coding regions = 337
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

CGAATCCAAGAACCTCTATTTTAATGTTTT	1	140	1	AACCTCTATT	    0.994697	-32
 ACTCTAATAAACCACTATTTTTCAGTCTA	2	10	1	AACCACTATT	    0.990737	-42
ACCTCATAATAAACTCTAGACTGAAAAATA	2	26	0	AAACTCTAGA	    0.970765	-26
          **********

Masking position 8
Map Score:   1.08151

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 16
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

GGGTAGCTTGGTCCATCCTCCCAGCCATTG	1	20	1	GTCCATCCTC	    0.992146	-152
TTCCGGTGCTGACCATCCCCGTTCCAGTTG	1	69	0	GACCATCCCC	    0.992933	-103
          **********

Masking position 5
Map Score:   0.589466

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 18
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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:   -1.68098e-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