AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i247_regulatory_cassete2_ecoli_reg_300.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

CGAGGCTTTCAGGGTTGTACGAAAAGAAGCA	1	17	1	AGGGTTGTAG	     0.86328	-198
GGTATTTCAAAGGGGCGAAGCTCCGCCTCAG	1	49	1	AGGGGCGAAC	    0.936645	-166
AAGCTCCGCCTCAGGTGACCGATGGAGTGTG	1	66	1	TCAGGTGACG	    0.921986	-149
ACCGATGGAGTGTGGTTAAGGTAGCGGTAAA	1	83	1	TGTGGTTAAG	    0.938312	-132
TGGTTAAGGTAGCGGTAAAAGCGTGTTACCG	1	95	1	AGCGGTAAAG	    0.991285	-120
GAGAGAACATTGCGGTAACACGCTTTTACCG	1	107	0	TGCGGTAACC	    0.966275	-108
ATGATTTCTCGGCGGTGTATCATATTCCAGA	1	141	0	GGCGGTGTAC	    0.966225	-74
GACGATTATCAGAGGTTAAGGTGATGATTTC	1	164	0	AGAGGTTAAG	    0.964057	-51
ACTAGTCTTGTCCGGTATATGACGATTATCA	1	184	0	TCCGGTATAG	    0.947844	-31
          ********* *

Masking position 4
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

   GTAGCGCGAGGCTTTCAGGGTTGTACG	1	8	1	GAGGCTTTCA	    0.995632	-207
AGGTTAAGGTGATGATTTCTCGGCGGTGTA	1	153	0	GATGATTTCT	    0.982573	-62
GACAAGACTAGTGGATTTCAGC        	1	203	1	GTGGATTTCA	    0.993539	-12
          **********

Masking position 6
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