AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i124_Multidrug_Resistance_Pump_1_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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	cof	87	orf, hypothetical protein
#2	ybaO	65	putative LRP-like transcriptional regulator
#3	mdlA	29	ATP-binding component of a transport system

Motif number 1

TGATTGAGTATCACCTGATATATACGGAAG	1	49	0	TCACCTGATA	    0.951946	-39
      TCTGTGACACGGTTAATGGTGATT	1	74	0	TGACACGGTT	    0.988971	-14
AACCGGGCAATTGCCCGGTGCTGGAAGGGA	2	16	0	TTGCCCGGTG	    0.994809	-50
CACCGGGCAATTGCCCGGTTTTTTTTGCGT	2	26	1	TTGCCCGGTT	    0.996948	-40
CGTTGTGTCCTGACCTGATTCTGGATAT  	3	9	0	TGACCTGATT	    0.989271	-21
          **********

Masking position 9
Map Score:   5.70374

Number of sites scoring better than the average of aligned sites = 940
Number in coding regions = 862
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 2

AATAGTTAAATAATATTGTTCCGGGTTTAT	1	11	0	TAATATTGTT	    0.968138	-77
TATACGGAAGTAATAGTGAATAGTTAAATA	1	29	0	TAATAGTGAA	    0.988097	-59
GTGACACGGTTAATGGTGATTGAGTATCAC	1	65	0	TAATGGTGAT	    0.991945	-23
          **********

Masking position 3
Map Score:   1.13746

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 99
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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:   -1.11255e-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