AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i289_moxr_protein_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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	yieN	198	putative 2-component regulator

Motif number 1

GGGCCAAGGGACTAAGCACACATTTCATATTT	1	28	0	ACAAGCCACA	    0.997074	-171
GTGCTTAGTCCCTTGGCCCACAAAAAAGCGCA	1	41	1	CCTGGCCACA	    0.995839	-158
TTGGCCCACAAAAAAGCGCACAGTATGCACGA	1	53	1	AAAAGCCACA	    0.993437	-146
GGCCACATTAACCTGGCTCAAAGAAAAATACC	1	113	1	ACTGGCCAAA	    0.995815	-86
TGGTGGCTAAAATAGTCTCAAAGGGGGGGTAT	1	140	0	AAAGTCCAAA	    0.966673	-59
          ** **** ****

Masking position 10
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	     0.49917	-198
TGCATACTGTGCGCTTTTTTGTGGGCCAAG	1	52	0	GCGCTTTTTT	    0.939061	-147
GCATTTAGGAGTACGATTTTGCCGTTAATC	1	83	0	GTACGATTTT	    0.950967	-116
TCTCAAAGGGGGGGTATTTTTCTTTGAGCC	1	127	0	GGGGTATTTT	    0.958684	-72
CCCCCCTTTGAGACTATTTTAGCCACCAGC	1	144	1	AGACTATTTT	    0.951518	-55
TTGCGAGTATAGACGTTTCTTGCTGGTGGC	1	165	0	AGACGTTTCT	    0.961955	-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

TGCCGTTAATCGTGCATACTGTGCGCTTTT	1	64	0	CGTGCATACT	    0.989853	-135
CTCCTAAATGCGGCCACATTAACCTGGCTC	1	102	1	CGGCCACATT	    0.987842	-97
CAGCAAGAAACGTCTATACTCGCAATTTAC	1	170	1	CGTCTATACT	    0.984087	-29
          **********

Masking position 6
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