AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i173_1_17_4_2_mthe_reg_100.orf -o173_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	RTH01486	123	M.thermo
#2	RTH00930	246	M.thermo

Motif number 1

CGATATGAATGCCTTATTAAATGAATAATA	2	102	1	GCCTTATTAA	    0.983813	-145
ATTATTTAAACCCTTATAAAGGTGTTATTA	2	140	1	CCCTTATAAA	    0.995722	-107
TGCCGCGCCCCCCTTAAAAATCATCGGCTG	2	172	0	CCCTTAAAAA	     0.98606	-75
ATGTTCACCACCCATATTAAAGGTGCCGCG	2	195	0	CCCATATTAA	    0.980169	-52
         CTCCTTATAGAATCTAATGTC	2	236	0	TCCTTATAGA	    0.955683	-11
          **********

Masking position 5
Map Score:   5.94367

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 89
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

CTGGGATCATTCCATCGGCCTGTTCCCTGT	1	44	1	TCCATCGGCC	    0.987481	-80
AGTCAGAGCCCTCATCATCCACAAGGAAAC	1	94	0	CTCATCATCC	    0.988628	-30
TAAGGGGCTCTGCATCATCCTCTCTGTTTT	2	47	0	TGCATCATCC	    0.991242	-200
AAAGGTGTTATTAATCAGCCGATGATTTTT	2	157	1	TTAATCAGCC	    0.982818	-90
TAATTTTATGTTCACCACCCATATTAAAGG	2	202	0	TTCACCACCC	    0.986499	-45
          **********

Masking position 4
Map Score:   3.89282

Number of sites scoring better than the average of aligned sites = 263
Number in coding regions = 247
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

GTGGATGATGAGGGCTCTGACTACACCGAT	1	102	1	AGGGCTCTGA	    0.992602	-22
GGGAAATTAAGGGGCTCTGCATCATCCTCT	2	54	0	GGGGCTCTGC	    0.997587	-193
ATTTTTAAGGGGGGCGCGGCACCTTTAATA	2	181	1	GGGGCGCGGC	    0.975878	-66
          **********

Masking position 5
Map Score:   3.11222

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 14
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

ACAGGCCGATGGAATGATCCCAGCTGTCCAGCT	1	34	0	GGAAGATCCG	    0.988024	-90
TCATTCCATCGGCCTGTTCCCTGTCAGCAAGTA	1	50	1	GGCCGTTCCG	    0.996384	-74
GTACCAGTTTGAACGTTTCCTTGTGGATGATGA	1	80	1	GAACTTTCCG	    0.990871	-44
CCCTCTATACGAACAGTTCCACGATATGAATGC	2	81	1	GAACGTTCCG	    0.998238	-166
CCACCCATATTAAAGGTGCCGCGCCCCCCTTAA	2	185	0	TAAAGTGCCG	    0.955958	-62
          **** *****  *

Masking position 9
Map Score:   1.80477

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 143
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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