AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jmarR.reg -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 = 	137

Input sequences:
#1	marR 268 bp marR 125 1-378 CDS

Motif number 1

GTATCTGGGTTATCAGCGAAAAGTATAAGGGGTAA	1	29	1	TTCAGAAGTA	    0.983399	-240
TAGCCTTGCATCGCATTGAACAAAACTTGAACCGA	1	90	1	TGCAGAAAAA	    0.978621	-179
TAGCAAAACGTGGCATCGGTCAATTCATTCATTTG	1	127	1	TGCAGGAATT	    0.989533	-142
GGGGATAATATTGCCCAGGCAAGTATAAGTCAAAT	1	157	0	TGCCGGAGTA	      0.9967	-112
AAGTAATTAGTTGCAGGGGATAATATTGCCCAGGC	1	172	0	TGCAGGAATA	    0.995416	-97
TTCACATTAGTTGCCCTGGCAAGTAATTAGTTGCA	1	192	0	TGCCGGAGTA	      0.9967	-77
AATGGAATAATTTCATTGAACAGATCGCTGGTACT	1	228	0	TTCAGAAGAT	    0.918165	-41
          * ***  **  ****

Masking position 12
Map Score:   9.50671

Number of sites scoring better than the average of aligned sites = 260
Number in coding regions = 230
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

GTATCTGGGTTATCAGCGAAAAGTATAAGG	1	29	1	TATCAGCGAA	     0.93565	-240
TTAGCTAGCCTTGCATCGCATTGAACAAAA	1	85	1	TTGCATCGCA	    0.954933	-184
TAGCAAAACGTGGCATCGGTCAATTCATTC	1	127	1	TGGCATCGGT	    0.959759	-142
GACTTATACTTGCCTGGGCAATATTATCCC	1	161	1	TGCCTGGGCA	    0.761831	-108
AAGTAATTAGTTGCAGGGGATAATATTGCC	1	177	0	TTGCAGGGGA	    0.983473	-92
ACTAATTACTTGCCAGGGCAACTAATGTGA	1	196	1	TGCCAGGGCA	    0.569802	-73
ATGTGAAAAGTACCAGCGATCTGTTCAATG	1	220	1	TACCAGCGAT	    0.961678	-49
          **********

Masking position 1
Map Score:   6.89202

Number of sites scoring better than the average of aligned sites = 2814
Number in coding regions = 2705
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 3

CAAGTTTTGTTCAATGCGATGCAAGGCTAG	1	89	0	TCAATGCGAT	    0.940517	-180
AATGAATTGACCGATGCCACGTTTTGCTAA	1	126	0	CCGATGCCAC	     0.96926	-143
CTTATACTTGCCTGGGCAATATTATCCCCT	1	163	1	CCTGGGCAAT	     0.96413	-106
GCAATATTATCCCCTGCAACTAATTACTTG	1	178	1	CCCCTGCAAC	    0.974904	-91
TAATTACTTGCCAGGGCAACTAATGTGAAA	1	198	1	CCAGGGCAAC	    0.990723	-71
AGCGATCTGTTCAATGAAATTATTCCATTG	1	234	1	TCAATGAAAT	    0.869956	-35
ATTAAGCGACCCAATGGAATAATTTCATTG	1	245	0	CCAATGGAAT	    0.973223	-24
          **********

Masking position 9
Map Score:   3.55057

Number of sites scoring better than the average of aligned sites = 1445
Number in coding regions = 1353
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 4

TAAAGAGTGACACTTTATCCTTGTTTACCC	1	58	0	CACTTTATCC	    0.985768	-211
TAAAGTGTCACTCTTTAGCTAGCCTTGCAT	1	71	1	CTCTTTAGCT	    0.974343	-198
AAACTTGAACCGATTTAGCAAAACGTGGCA	1	112	1	CGATTTAGCA	    0.945076	-157
TCCATTGGGTCGCTTAATCCAT        	1	257	1	CGCTTAATCC	    0.893224	-12
          **********

Masking position 5
Map Score:   0.916873

Number of sites scoring better than the average of aligned sites = 606
Number in coding regions = 570
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

TTCAAGTTTTGTTCAATGCGATGCAAGGCT	1	91	0	GTTCAATGCG	    0.991419	-178
ACGTGGCATCGGTCAATTCATTCATTTGAC	1	134	1	GGTCAATTCA	    0.966757	-135
GCAAGTATAAGTCAAATGAATGAATTGACC	1	144	0	GTCAAATGAA	    0.949105	-125
CCAGCGATCTGTTCAATGAAATTATTCCAT	1	232	1	GTTCAATGAA	    0.992207	-37
          **********

Masking position 5
Map Score:   1.32603

Number of sites scoring better than the average of aligned sites = 176
Number in coding regions = 159
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 6

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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