AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imarR_ecoli_hinf_100.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

CCTTGTTTACCCCTTATACTTTTCGCTGATAACC	1	36	0	CCTTACTTTC	    0.928446	-233
AACAAGGATAAAGTGTCACTCTTTAGCTAGCCTT	1	63	1	AATGACTTTT	    0.937775	-206
CTTTAGCTAGCCTTGCATCGCATTGAACAAAACT	1	83	1	CCTGTCGATT	    0.961865	-186
ATTGAACAAAACTTGAACCGATTTAGCAAAACGT	1	104	1	ACTGCCGTTT	    0.929494	-165
ATGAATTGACCGATGCCACGTTTTGCTAAATCGG	1	121	0	CGTGACGTTT	    0.995446	-148
CAATATTATCCCCTGCAACTAATTACTTGCCAGG	1	179	1	CCTGACTATT	    0.980412	-90
TTGAACAGATCGCTGGTACTTTTCACATTAGTTG	1	214	0	CGTGACTTTC	    0.991234	-55
GCGATCTGTTCAATGAAATTATTCCATTGGGTCG	1	235	1	CATGATTTTC	    0.862681	-34
GAAATTATTCCATTGGGTCGCTTAATCCAT    	1	249	1	CATGTCGTTA	    0.901193	-20
GCCTCAGTGACGTTGTCACGTTTTCAA       	2	4	0	CGTGACGTTT	    0.995446	-28
          ** **  *** ***

Masking position 4
Map Score:   11.6618

Number of sites scoring better than the average of aligned sites = 1156
Number in coding regions = 1059
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 2

AGGATAAAGTGTCACTCTTTAGCTAGCCTT	1	67	1	GTCACTCTTT	    0.878281	-202
GCTAAATCGGTTCAAGTTTTGTTCAATGCG	1	101	0	TTCAAGTTTT	    0.857466	-168
ATTGACCGATGCCACGTTTTGCTAAATCGG	1	121	0	GCCACGTTTT	    0.966543	-148
CGTGGCATCGGTCAATTCATTCATTTGACT	1	135	1	GTCAATTCAT	    0.897636	-134
ATATTGCCCAGGCAAGTATAAGTCAAATGA	1	155	0	GGCAAGTATA	    0.904602	-114
TAGTTGCCCTGGCAAGTAATTAGTTGCAGG	1	190	0	GGCAAGTAAT	    0.979927	-79
TACTTGCCAGGGCAACTAATGTGAAAAGTA	1	202	1	GGCAACTAAT	    0.917997	-67
ATTCCATTGGGTCGCTTAATCCAT      	1	255	1	GTCGCTTAAT	    0.854147	-14
CAGTGACGTTGTCACGTTTTCAA       	2	4	0	GTCACGTTTT	    0.987497	-28
          **********

Masking position 3
Map Score:   6.30526

Number of sites scoring better than the average of aligned sites = 1415
Number in coding regions = 1225
Number in noncoding regions = 190
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


Motif number 3

TGCATCGCATTGAACAAAACTTGAACCGAT	1	96	1	TGAACAAAAC	      0.9919	-173
TTGAACCGATTTAGCAAAACGTGGCATCGG	1	116	1	TTAGCAAAAC	    0.947585	-153
GCAACTAATGTGAAAAGTACCAGCGATCTG	1	213	1	TGAAAAGTAC	    0.949667	-56
ATAATTTCATTGAACAGATCGCTGGTACTT	1	227	0	TGAACAGATC	    0.986836	-42
          **********

Masking position 6
Map Score:   0.989314

Number of sites scoring better than the average of aligned sites = 261
Number in coding regions = 230
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

AAGAGTGACACTTTATCCTTGTTTACCCCT	1	56	0	CTTTATCCTT	    0.959079	-213
GCATCGGTCAATTCATTCATTTGACTTATA	1	139	1	ATTCATTCAT	    0.922641	-130
GTTCAATGAAATTATTCCATTGGGTCGCTT	1	242	1	ATTATTCCAT	    0.963415	-27
CATTGGGTCGCTTAATCCAT          	1	259	1	CTTAATCCAT	    0.989987	-10
          **********

Masking position 6
Map Score:   0.519338

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 115
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 5

   TGGTGGTTGTTATCCTGTGTATCTGGG	1	8	1	TGTTATCCTG	    0.966283	-261
TACTTTTCGCTGATAACCCAGATACACAGG	1	24	0	TGATAACCCA	    0.967768	-245
ACTTTATCCTTGTTTACCCCTTATACTTTT	1	47	0	TGTTTACCCC	    0.988062	-222
GCCTGGGCAATATTATCCCCTGCAACTAAT	1	172	1	TATTATCCCC	    0.981384	-97
          **********

Masking position 4
Map Score:   0.263181

Number of sites scoring better than the average of aligned sites = 293
Number in coding regions = 247
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


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


Motif number 7

          **********

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 8

          **********

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