AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i289_moxr_protein_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yieN	198	putative 2-component regulator

Motif number 1

AAATATGAAATGTGTGCTTAGTCCCTTGGCCC	1	28	1	TGTGGCTTGT	    0.996748	-171
TGCGCTTTTTTGTGGGCCAAGGGACTAAGCAC	1	41	0	TGTGGCCAGG	    0.995383	-158
TCGTGCATACTGTGCGCTTTTTTGTGGGCCAA	1	53	0	TGTGGCTTTT	    0.992707	-146
GGTATTTTTCTTTGAGCCAGGTTAATGTGGCC	1	113	0	TTTGGCCAGT	    0.995349	-86
ATACCCCCCCTTTGAGACTATTTTAGCCACCA	1	140	1	TTTGGACTTT	    0.963079	-59
          **** **** **

Masking position 3
Map Score:   5.29367

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 156
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

          AGACTAGTCTTTCGTTGAAA	1	1	1	AGACTAGTCT	    0.498925	-198
TGCATACTGTGCGCTTTTTTGTGGGCCAAG	1	52	0	GCGCTTTTTT	    0.930853	-147
GCATTTAGGAGTACGATTTTGCCGTTAATC	1	83	0	GTACGATTTT	    0.944271	-116
TCTCAAAGGGGGGGTATTTTTCTTTGAGCC	1	127	0	GGGGTATTTT	    0.952991	-72
CCCCCCTTTGAGACTATTTTAGCCACCAGC	1	144	1	AGACTATTTT	    0.953995	-55
TTGCGAGTATAGACGTTTCTTGCTGGTGGC	1	165	0	AGACGTTTCT	     0.95781	-34
          **********

Masking position 8
Map Score:   2.14542

Number of sites scoring better than the average of aligned sites = 1089
Number in coding regions = 860
Number in noncoding regions = 229
Number of orfs with sites within 600 bp upstream = 240
Fraction of orfs with sites within 600 bp upstream = 0.038548


Motif number 3

AAAAGCGCACAGTATGCACGATTAACGGCA	1	64	1	AGTATGCACG	    0.989845	-135
GAGCCAGGTTAATGTGGCCGCATTTAGGAG	1	102	0	AATGTGGCCG	    0.987777	-97
GTAAATTGCGAGTATAGACGTTTCTTGCTG	1	170	0	AGTATAGACG	     0.98408	-29
          **********

Masking position 1
Map Score:   0.0993902

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 68
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          **********

No masking
Map Score:   -2.59896e-14

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:   -2.59896e-14

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:   -2.59896e-14

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