AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -iarcA_mgen_opreg_100.orf -g0.317 -x5 
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 =  	0.317
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MG272	249	dihydrolipoamide acetyltransferase (pdhC)

Motif number 1

AGGTACCTAGCTCTAAAAAATAAAGCTAGGTAA	1	29	0	CTTAAAATAA	    0.995799	-221
TCTTCCATCACTTTAATTTATGAAATGAGGTAC	1	56	0	CTTAATTTGA	    0.932716	-194
GCAACAGCTGCTGTAAAAAGTAAGACAAAATTT	1	130	1	CTTAAAATAA	    0.995823	-120
CAAAATTTTTGTCTAACAACTAAAAAGCCAGTA	1	155	1	GTTAAAATAA	    0.978653	-95
TAGTAGTGATCTATAACAAATAAAAAAAGCCAG	1	194	0	CTTAAAATAA	    0.995228	-56
TAGATCACTACTATTAAATTTAAACTTTAAGTA	1	214	1	CTTTAATTAA	    0.955364	-36
TAAATTTAAACTTTAAGTACTATCAATACGAT 	1	228	1	CTTAATATAT	    0.955608	-22
          ** *** ** ***

Masking position 6
Map Score:   11.0568

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 41
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

CACTTTTTTAAAATATAGTTACCTAGCTTT	1	11	1	AAATATAGTT	    0.883564	-239
TCTAAAAAATAAAGCTAGGTAACTATATTT	1	21	0	AAAGCTAGGT	    0.996238	-229
TTTATTTTTTAGAGCTAGGTACCTCATTTC	1	38	1	AGAGCTAGGT	    0.991702	-212
TAACAACTAAAAAGCCAGTAACTAAACTGG	1	168	1	AAAGCCAGTA	     0.98775	-82
ACAAATAAAAAAAGCCAGTTTAGTTACTGG	1	182	0	AAAGCCAGTT	     0.99622	-68
          **********

Masking position 7
Map Score:   7.49018

Number of sites scoring better than the average of aligned sites = 71
Number in coding regions = 62
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

TACCTAGCTTTATTTTTTAGAGCTAGGTAC	1	30	1	TATTTTTTAG	    0.882884	-220
ATTGGCAGCATTTCTTGTTGTCTTCCATCA	1	79	0	TTTCTTGTTG	    0.977605	-171
AGTTACTGGCTTTTTAGTTGTTAGACAAAA	1	161	0	TTTTTAGTTG	    0.986736	-89
AAACTGGCTTTTTTTATTTGTTATAGATCA	1	191	1	TTTTTATTTG	    0.979644	-59
          **********

Masking position 5
Map Score:   1.78311

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 85
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

ACAAGAAATGCTGCCAATGCAAGTGCGAAT	1	91	1	CTGCCAATGC	    0.994016	-159
GCCAATGCAAGTGCGAATGCGCTAAGTGCA	1	103	1	GTGCGAATGC	    0.996738	-147
AATGCGCTAAGTGCAACAGCTGCTGTAAAA	1	118	1	GTGCAACAGC	    0.989929	-132
          **********

Masking position 6
Map Score:   0.792833

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 10
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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:   1.23224e-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