AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iilvY_ecoli_opreg_300.orf -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	ilvY	149	positive regulator for ilvC

Motif number 1

AATAAGAAGCACAACATCACGAGGAATCAC	1	12	0	ACAACATCAC	    0.995358	-138
CGCGAACCGAACAATAAGAAGCACAACATC	1	24	0	ACAATAAGAA	    0.918154	-126
GATTGAATTCACTATATGACAGGAAATTTA	1	61	1	ACTATATGAC	    0.974552	-89
TGACGTTGTGAATATATCAATTTCCGCAAT	1	90	0	AATATATCAA	    0.878246	-60
TGATATATTCACAACGTCACATTGCAATTT	1	101	1	ACAACGTCAC	    0.994401	-49
TGCAATTTTTGCAACGTCAACATCGAGGGC	1	123	1	GCAACGTCAA	    0.976394	-27
          **********

Masking position 4
Map Score:   6.75687

Number of sites scoring better than the average of aligned sites = 1072
Number in coding regions = 974
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 2

TTCGCGTTTGCGAGATTGAATTCACTATAT	1	48	1	CGAGATTGAA	    0.984935	-102
CTATATGACAGGAAATTTATTGCGGAAATT	1	72	1	GGAAATTTAT	    0.983451	-78
AATTTATTGCGGAAATTGATATATTCACAA	1	85	1	GGAAATTGAT	    0.995506	-65
          **********

Masking position 5
Map Score:   1.83422

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 61
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

          **********

No masking
Map Score:   -6.86222e-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 4

          **********

No masking
Map Score:   -6.86222e-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:   -6.86222e-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