AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00410_mthe_reg_300.orf -o00410_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	MTH1116	146	glutamate decarboxylase
#2	MTH1117	43	phosphoenolpyruvate synthase
#3	MTH1119	132	ribosomal protein L10

Motif number 1

TGAGGAGGAGTCTCTGCTCGGCCCTTGCAACCG	1	17	0	TCTCGCTGCC	    0.985505	-130
AGCAGAGACTCCTCCTCAAGGCCGCACAGGAAC	1	32	1	CCTCTCAGCC	    0.996375	-115
CCGCACAGGAACTCCTCTAAACTATTTTTGGGC	1	53	1	ACTCTCTACT	    0.922029	-94
AGTACTTTTTCCTCGGGTAGACCCTTTCATCCA	1	93	0	CCTCGGTGCC	    0.994623	-54
       GTCCCTCCTCTGAAATTCGGCGAGAA	1	131	0	CCTCTCTAAT	    0.972705	-16
          CCTCACCCAGTACACCCTCGCCA	2	1	1	CCTCCCCGAC	    0.986827	-43
CCCAGTACACCCTCGCCATAGACAGGTACAATG	2	16	1	CCTCCCAAAC	    0.982516	-28
   AAATAATCCTCCTGTGATCCTGTGAGAATA	3	113	0	CCTCTGTACC	    0.992959	-20
          **** *** * **

Masking position 3
Map Score:   9.59593

Number of sites scoring better than the average of aligned sites = 1003
Number in coding regions = 972
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

TCTGCTCGGCCCTTGCAACCGTCTTCC        	1	3	0	CCTTGACTTT	    0.995721	-144
CACAGGAACTCCTCTAAACTATTTTTGGGCGTAAA	1	56	1	CCTCTACTTT	    0.990351	-91
TCGGGTAGACCCTTTCATCCATTTTTACGCCCAAA	1	79	0	CCTTTACTTT	     0.99645	-68
     GTGTTCATTGTACCTGTCTATGGCGAGGGT	2	24	0	CATTGACTTA	    0.950978	-20
ATCTCGGTAACCATTAATAAATATTGTCTTGGACA	3	64	0	CCATTAATTT	    0.959015	-69
CCGAGATACTCATTTCATAGTTATTCTCACAGGAT	3	92	1	CATTTAATTT	    0.969742	-41
          ***** * *  * **

Masking position 7
Map Score:   3.74344

Number of sites scoring better than the average of aligned sites = 159
Number in coding regions = 137
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

GGAGGAGTCTCTGCTCGGCCCTTGCAACCG	1	17	0	CTGCTCGGCC	    0.995456	-130
AGAGGAGTTCCTGTGCGGCCTTGAGGAGGA	1	41	0	CTGTGCGGCC	    0.994093	-106
TTTCATCCATTTTTACGCCCAAAAATAGTT	1	72	0	TTTTACGCCC	    0.961903	-75
AGTACTTGAACTTCTCGCCGAATTTCAGAG	1	120	1	CTTCTCGCCG	    0.975416	-27
   CCTCACCCAGTACACCCTCGCCATAGA	2	8	1	CAGTACACCC	    0.945273	-36
          **********

Masking position 6
Map Score:   2.0002

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 190
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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