AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i342_weak3_mthe_reg_300.orf -o342_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	RTH01601	134	M.thermo
#2	RTH01432	19	M.thermo

Motif number 1

AAAAATACCTGATGATGGATC          	1	1	0	GTGATGGATC	    0.995827	-134
AGAATGAGCCGCGGTTTGTTGCTAAAAATAC	1	24	0	GGGTTTGTTG	    0.980946	-111
GGATGGAGCAGCTGATGGTTGTGAGGAGAAT	1	50	0	GTGATGGTTG	    0.998866	-85
AAAAATAGTTGGTGATGGATGGAGCAGCTGA	1	66	0	GTGATGGATG	    0.998863	-69
          * *********

Masking position 6
Map Score:   6.46468

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 99
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

CGCGGTTTGTTGCTAAAAATACCTGATGAT	1	16	0	TGCTAAAAAT	    0.993204	-119
CGGCTCATTCTCCTCACAACCATCAGCTGC	1	44	1	TCCTCACAAC	    0.987307	-91
ATGGGGCTATTGCTAAAAATAGTTGGTGAT	1	81	0	TGCTAAAAAT	    0.993204	-54
   GATGTCACCCTAAAAACTGAAGTCCAA	1	118	0	CCCTAAAAAC	    0.992515	-17
          **********

Masking position 6
Map Score:   4.98741

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 33
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

TAGCAACAAACCGCGGCTCATTCTCCTCACAA	1	31	1	CGCGCTCATT	    0.988426	-104
TCACAACCATCAGCTGCTCCATCCATCACCAA	1	57	1	CGCGCTCCAT	    0.998278	-78
CTATTTTTAGCAATAGCCCCATATTAATATTG	1	89	1	CATGCCCCAT	    0.989022	-46
ACCCTAAAAACTGAAGTCCAATATTAATATGG	1	107	0	CGAGTCCAAT	    0.986065	-28
     TTTGCCTCCCGTCTCATTG        	2	3	0	CCCGTCTCAT	     0.97844	-17
          * ** *******

Masking position 12
Map Score:   2.39524

Number of sites scoring better than the average of aligned sites = 485
Number in coding regions = 450
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

TAGCAACAAACCGCGGCTCATTCTCCTCAC	1	31	1	CCGCGGCTCA	    0.999134	-104
TCACAACCATCAGCTGCTCCATCCATCACC	1	57	1	CAGCTGCTCC	    0.992391	-78
    TTTGCCTCCCGTCTCATTG       	2	4	0	TCCCGTCTCA	    0.988279	-16
          **********

Masking position 8
Map Score:   0.773343

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 69
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   -1.53887e-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:   -1.53887e-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:   -1.53887e-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