AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i125_Multidrug_Resistance_Pump_2_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	emrA	126	multidrug resistance secretion protein

Motif number 1

AAAAATGACTGGCCAGCATCGCAACATGCT	1	48	1	GGCCAGCATC	    0.999392	-79
TTGCCAAAAAGGCCAGCATGTTGCGATGCT	1	62	0	GGCCAGCATG	     0.99967	-65
TGGCCTTTTTGGCAAGCAGGTCGGCTCAGC	1	77	1	GGCAAGCAGG	    0.998931	-50
          **********

Masking position 5
Map Score:   7.73765

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 36
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

          CGCGTCATCTCGCTCAAAAA	1	1	1	CGCGTCATCT	    0.989193	-126
GAAAAAATGACTGGCCAGCATCGCAACATG	1	46	1	CTGGCCAGCA	    0.990147	-81
TTTTGGCAAGCAGGTCGGCTCAGCCGATGA	1	83	1	CAGGTCGGCT	    0.997373	-44
ATCTTCTTAACTCATCGGCTGAGCCGACCT	1	94	0	CTCATCGGCT	    0.994099	-33
          **********

Masking position 6
Map Score:   3.08064

Number of sites scoring better than the average of aligned sites = 802
Number in coding regions = 770
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

TTTATAAATCTGGATTTTTGAGCGAGATGA	1	15	0	TGGATTTTTG	    0.983968	-112
ATGCTGGCCAGTCATTTTTTCTTTTATAAA	1	37	0	GTCATTTTTT	    0.976421	-90
GCAACATGCTGGCCTTTTTGGCAAGCAGGT	1	68	1	GGCCTTTTTG	    0.996153	-59
          **********

Masking position 5
Map Score:   0.359353

Number of sites scoring better than the average of aligned sites = 328
Number in coding regions = 241
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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:   -2.03625e-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