AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jfarR.reg -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 = 	182

Input sequences:
#1	farR 108 bp farR 240 1-723 CDS

Motif number 1

ATACAAATACAATACAAATAATTTCAATCA	1	29	0	AATACAAATA	    0.994369	-80
TCCTGTAAATAATACAAATACAATACAAAT	1	40	0	AATACAAATA	    0.994369	-69
GTATCTCATTAATACGAATTTAACCATTAT	1	84	0	AATACGAATT	    0.750231	-25
GTATTAATGAGATACTAAAA          	1	99	1	GATACTAAAA	    0.972882	-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

    TATGTGATCAATTTCACTTGATTGAA	1	7	1	ATCAATTTCA	    0.984738	-102
ATACAATACAAATAATTTCAATCAAGTGAA	1	23	0	AATAATTTCA	    0.990034	-86
TTGTATTTGTATTATTTACAGGATGAATTT	1	47	1	ATTATTTACA	    0.929158	-62
CATTATGCCCGATAAATTCATCCTGTAAAT	1	60	0	GATAAATTCA	    0.986888	-49
GGGCATAATGGTTAAATTCGTATTAATGAG	1	80	1	GTTAAATTCG	    0.979843	-29
          **********

Masking position 4
Map Score:   5.67261

Number of sites scoring better than the average of aligned sites = 395
Number in coding regions = 317
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


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