AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i247_regulatory_cassete2_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	atoS	214	sensor protein AtoS for response regulator AtoC

Motif number 1

TGCTTCTTTTCGTACAACCCTGAAAGCCTCG	1	17	0	CTACAACCCT	    0.872123	-198
CTGAGGCGGAGCTTCGCCCCTTTGAAATACC	1	49	0	GTTCGCCCCT	    0.941067	-166
CACACTCCATCGGTCACCTGAGGCGGAGCTT	1	66	0	CGTCACCTGA	    0.927351	-149
TTTACCGCTACCTTAACCACACTCCATCGGT	1	83	0	CTTAACCACA	    0.942625	-132
CGGTAACACGCTTTTACCGCTACCTTAACCA	1	95	0	CTTTACCGCT	    0.991926	-120
CGGTAAAAGCGTGTTACCGCAATGTTCTCTC	1	107	1	GGTTACCGCA	    0.968698	-108
TCTGGAATATGATACACCGCCGAGAAATCAT	1	141	1	GTACACCGCC	    0.968652	-74
GAAATCATCACCTTAACCTCTGATAATCGTC	1	164	1	CTTAACCTCT	    0.966634	-51
TGATAATCGTCATATACCGGACAAGACTAGT	1	184	1	CTATACCGGA	    0.951524	-31
          * *********

Masking position 8
Map Score:   5.82993

Number of sites scoring better than the average of aligned sites = 4387
Number in coding regions = 4113
Number in noncoding regions = 274
Number of orfs with sites within 600 bp upstream = 317
Fraction of orfs with sites within 600 bp upstream = 0.0509155


Motif number 2

CGTACAACCCTGAAAGCCTCGCGCTAC   	1	8	0	TGAAAGCCTC	    0.995654	-207
TACACCGCCGAGAAATCATCACCTTAACCT	1	153	1	AGAAATCATC	    0.982658	-62
        GCTGAAATCCACTAGTCTTGTC	1	203	0	TGAAATCCAC	    0.993571	-12
          **********

Masking position 5
Map Score:   1.89589

Number of sites scoring better than the average of aligned sites = 67
Number in coding regions = 59
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

          **********

No masking
Map Score:   -1.32571e-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 4

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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