AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i124_Multidrug_Resistance_Pump_1_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yheJ	109	yheJ
#2	yheI	119	similar to ABC transporter (ATP-binding protein)

Motif number 1

CATTACTTGAATAGGAAAAGGTTAA      	1	5	0	AAGGAAAAGG	    0.992538	-105
GTAATGATTGACAATAAAAGGTTTTGTTTAT	1	30	1	AAATAAAAGG	     0.98175	-80
AGATGAAATCAGAATGGAAGGAGGGTTTGCT	1	73	1	AAATGGAAGG	    0.986249	-37
AGACAAATACAGAGGCGAGGGCAGTTCGTGC	2	36	1	AAGGCGAGGG	    0.987637	-84
CTGCAAGGAAAAAATAGAAGGCGGCTGATGA	2	85	1	AAATAGAAGG	    0.993758	-35
AGGCGGCTGATGAGGAGATGGGGATAG    	2	103	1	TAGGAGATGG	    0.967232	-17
          * *********

Masking position 8
Map Score:   6.74485

Number of sites scoring better than the average of aligned sites = 525
Number in coding regions = 402
Number in noncoding regions = 123
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 2

AGTAATGATTGACAATAAAAGGTTTTGTTT	1	29	1	GACAATAAAA	    0.797604	-81
TTGTTTATATGATGATAAAAAGATGAAATC	1	53	1	GATGATAAAA	    0.988108	-57
ATGATAAAAAGATGAAATCAGAATGGAAGG	1	64	1	GATGAAATCA	    0.917593	-46
AGGTGTATGGGATGTGAAGACAAATACAGA	2	19	1	GATGTGAAGA	     0.95675	-101
TGCCAAACTGGATGAAAAAAGCTGCAAGGA	2	64	1	GATGAAAAAA	    0.991671	-56
AAAAAGCTGCAAGGAAAAAATAGAAGGCGG	2	79	1	AAGGAAAAAA	    0.849551	-41
GAAGGCGGCTGATGAGGAGATGGGGATAG 	2	101	1	GATGAGGAGA	    0.970402	-19
          **********

Masking position 2
Map Score:   4.98285

Number of sites scoring better than the average of aligned sites = 2220
Number in coding regions = 1917
Number in noncoding regions = 303
Number of orfs with sites within 600 bp upstream = 312
Fraction of orfs with sites within 600 bp upstream = 0.0501124


Motif number 3

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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:   2.93755e-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