AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imarR_ecoli_hinf_300.orf -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	marR	268	multiple antibiotic resistance protein; repressor of mar operon
#2	marB	31	multiple antibiotic resistance protein

Motif number 1

GTTATCAGCGAAAAGTATAAGGGGTAAACAAGG	1	37	1	AAAAGTAAGG	    0.892247	-232
AGGCTAGCTAAAGAGTGACACTTTATCCTTGTT	1	63	0	AAGAGTCATT	    0.896765	-206
GTTTTGTTCAATGCGATGCAAGGCTAGCTAAAG	1	83	0	ATGCGACAGG	    0.934388	-186
CGTTTTGCTAAATCGGTTCAAGTTTTGTTCAAT	1	104	0	AATCGGCAGT	    0.826673	-165
CGATTTAGCAAAACGTGGCATCGGTCAATTCAT	1	122	1	AAACGTCACG	    0.987976	-147
TGCAGGGGATAATATTGCCCAGGCAAGTATAAG	1	163	0	AATATTCCGG	    0.795191	-106
CTGGCAAGTAATTAGTTGCAGGGGATAATATTG	1	179	0	ATTAGTCAGG	    0.980601	-90
TACTTTTCACATTAGTTGCCCTGGCAAGTAATT	1	199	0	ATTAGTCCTG	    0.899162	-70
AACTAATGTGAAAAGTACCAGCGATCTGTTCAA	1	215	1	AAAAGTCACG	    0.986098	-54
GACCCAATGGAATAATTTCATTGAACAGATCGC	1	235	0	AATAATCATG	    0.850791	-34
   ATGGATTAAGCGACCCAATGGAATAATTTC	1	249	0	AAGCGACATG	     0.95318	-20
      TTGAAAACGTGACAACGTCACTGAGGC	2	5	1	AAACGTCACG	    0.987966	-27
          ******  ** **

Masking position 1
Map Score:   11.6816

Number of sites scoring better than the average of aligned sites = 1835
Number in coding regions = 1668
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 195
Fraction of orfs with sites within 600 bp upstream = 0.0313203


Motif number 2

CTTTAGCTAGCCTTGCATCGCATTGAACAA	1	83	1	CCTTGCATCG	    0.512383	-186
TTTAGCAAAACGTGGCATCGGTCAATTCAT	1	125	1	CGTGGCATCG	    0.621191	-144
ATAATATTGCCCAGGCAAGTATAAGTCAAA	1	158	0	CCAGGCAAGT	    0.913944	-111
CAATATTATCCCCTGCAACTAATTACTTGC	1	179	1	CCCTGCAACT	    0.889378	-90
CATTAGTTGCCCTGGCAAGTAATTAGTTGC	1	193	0	CCTGGCAAGT	    0.878422	-76
   TTGAAAACGTGACAACGTCACTGAGGC	2	8	1	CGTGACAACG	    0.864615	-24
          **********

Masking position 7
Map Score:   9.10421

Number of sites scoring better than the average of aligned sites = 967
Number in coding regions = 921
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

TATCCTGTGTATCTGGGTTATCAGCGAAAA	1	21	1	ATCTGGGTTA	    0.758235	-248
GTTTTGCTAAATCGGTTCAAGTTTTGTTCA	1	106	0	ATCGGTTCAA	    0.953173	-163
GAATGAATTGACCGATGCCACGTTTTGCTA	1	127	0	ACCGATGCCA	     0.93892	-142
ACTTATACTTGCCTGGGCAATATTATCCCC	1	162	1	GCCTGGGCAA	    0.992712	-107
CTAATTACTTGCCAGGGCAACTAATGTGAA	1	197	1	GCCAGGGCAA	    0.981788	-72
AGTACCAGCGATCTGTTCAATGAAATTATT	1	228	1	ATCTGTTCAA	     0.92829	-41
TGACAACGTCACTGAGGCAATC        	2	20	1	ACTGAGGCAA	    0.918451	-12
          **********

Masking position 10
Map Score:   2.69557

Number of sites scoring better than the average of aligned sites = 3592
Number in coding regions = 3381
Number in noncoding regions = 211
Number of orfs with sites within 600 bp upstream = 210
Fraction of orfs with sites within 600 bp upstream = 0.0337295


Motif number 4

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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:   -3.38628e-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