AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i125_Multidrug_Resistance_Pump_2_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0898	182	multidrug resistance protein A (emrA)

Motif number 1

TTAATGAATATTCTAAAGATATAGTCTCATT	1	19	0	TTCTAAAGTA	    0.977588	-164
CATCTCTTTATTTTCTAGATTAATGAATATT	1	38	0	TTTTCTAGTT	    0.977589	-145
GAGTTCCCCTTTTTAAAGTTTCATAATGACC	1	81	1	TTTTAAAGTT	    0.996871	-102
TTTTTGATAGTTTTAAAGGTTATCTCAAATA	1	123	1	TTTTAAAGTT	    0.996871	-60
AATATCTCATTTTTAAACATTATCCCAGCTT	1	150	1	TTTTAAACTT	    0.989069	-33
          ******** **

Masking position 7
Map Score:   7.7058

Number of sites scoring better than the average of aligned sites = 134
Number in coding regions = 105
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

     ATCAAATTAATGAGACTATATCTTT	1	6	1	ATTAATGAGA	    0.986374	-177
TATTTTCTAGATTAATGAATATTCTAAAGA	1	31	0	ATTAATGAAT	    0.872299	-152
TAATCTAGAAAATAAAGAGATGATGATTTC	1	47	1	AATAAAGAGA	    0.976345	-136
ATGAAACTTTAAAAAGGGGAACTCAAGGGA	1	75	0	AAAAAGGGGA	    0.957208	-108
TATCAAAAATAAAAATGAAGGGTCATTATG	1	102	0	AAAAATGAAG	    0.953852	-81
GATAATGTTTAAAAATGAGATATTTGAGAT	1	144	0	AAAAATGAGA	    0.992689	-39
          **********

Masking position 5
Map Score:   6.59083

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 145
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

TAAAGAGATGATGATTTCCCTTGAGTTCCC	1	59	1	ATGATTTCCC	    0.996296	-124
ATGATTTCCCTTGAGTTCCCCTTTTTAAAG	1	69	1	TTGAGTTCCC	     0.99565	-114
         AATGCCTTCCCTAAGCTGGGA	1	172	0	ATGCCTTCCC	    0.997228	-11
          **********

Masking position 6
Map Score:   3.43227

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 9
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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