AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifarR_ecoli_opreg_100.orf -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	farR	108	transcriptional regulator of succinylCoA synthetase operon

Motif number 1

TGATTGAAATTATTTGTATTGTATTTGTAT	1	29	1	TATTTGTATT	    0.994229	-80
ATTTGTATTGTATTTGTATTATTTACAGGA	1	40	1	TATTTGTATT	    0.994229	-69
ATAATGGTTAAATTCGTATTAATGAGATAC	1	84	1	AATTCGTATT	    0.758849	-25
          TTTTAGTATCTCATTAATAC	1	99	0	TTTTAGTATC	    0.970833	-10
          **********

Masking position 4
Map Score:   6.6407

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 25
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

ATCAAGTGAAATTGATCACATA          	1	1	0	ATTATCAATA	    0.994802	-108
CATCCTGTAAATAATACAAATACAATACAAAT	1	40	0	ATATACAATA	    0.925033	-69
TGCCCGATAAATTCATCCTGTAAATAATACAA	1	53	0	ATTATCCGTA	    0.991816	-56
ATTAATACGAATTTAACCATTATGCCCGATAA	1	75	0	ATTAACCTTA	    0.982778	-34
TTAAATTCGTATTAATGAGATACTAAAA    	1	91	1	ATTATGAATA	    0.981935	-18
          *** **** ***

Masking position 2
Map Score:   2.70741

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 181
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 3

          **********

No masking
Map Score:   1.37435e-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 4

          **********

No masking
Map Score:   1.37435e-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:   1.37435e-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