AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iilvY_ecoli_opreg_100.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

GTGATTCCTCGTGATGTTGTGCTTCTTATT	1	12	1	GTGATGTTGT	    0.995888	-138
GATGTTGTGCTTCTTATTGTTCGGTTCGCG	1	24	1	TTCTTATTGT	    0.926906	-126
TAAATTTCCTGTCATATAGTGAATTCAATC	1	61	0	GTCATATAGT	    0.977417	-89
ATTGCGGAAATTGATATATTCACAACGTCA	1	90	1	TTGATATATT	    0.890758	-60
AAATTGCAATGTGACGTTGTGAATATATCA	1	101	0	GTGACGTTGT	    0.995038	-49
GCCCTCGATGTTGACGTTGCAAAAATTGCA	1	123	0	TTGACGTTGC	    0.979045	-27
          **********

Masking position 7
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	    0.985408	-102
CTATATGACAGGAAATTTATTGCGGAAATT	1	72	1	GGAAATTTAT	    0.983594	-78
AATTTATTGCGGAAATTGATATATTCACAA	1	85	1	GGAAATTGAT	    0.995613	-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