AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iilvY_ecoli_bsub_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
#2	gltC	146	transcriptional regulator (LysR family)

Motif number 1

TTCGCGTTTGCGAGATTGAATTCACTATAT	1	48	1	CGAGATTGAA	    0.969497	-102
CTATATGACAGGAAATTTATTGCGGAAATT	1	72	1	GGAAATTTAT	    0.979858	-78
AATTTATTGCGGAAATTGATATATTCACAA	1	85	1	GGAAATTGAT	    0.996138	-65
CGGTATTATCGGAAATTGATCGGGGGAGAG	2	16	0	GGAAATTGAT	    0.996138	-131
AATCTCAAAATGAGATAGATGGATGTGAGA	2	122	1	TGAGATAGAT	    0.955456	-25
          **********

Masking position 5
Map Score:   7.09334

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 121
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

CAATAAGAAGCACAACATCACGAGGAATCA	1	13	0	CACAACATCA	    0.994168	-137
TTGATATATTCACAACGTCACATTGCAATT	1	100	1	CACAACGTCA	    0.997854	-50
TTGCAATTTTTGCAACGTCAACATCGAGGG	1	122	1	TGCAACGTCA	    0.993033	-28
          **********

Masking position 5
Map Score:   3.36164

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 45
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

TGTCATATAGTGAATTCAATCTCGCAAACGCGA	1	49	0	TGAATATCTC	    0.876138	-101
AATTTATTGCGGAAATTGATATATTCACAACGT	1	85	1	GGAAAATATA	    0.882954	-65
GGTCATAAAATCTAACAACTCTATAATCATTGT	2	45	1	TCTAACTCTA	    0.941392	-102
TTGTAGGTTTTCAAAACGATATAAACAATATAT	2	74	1	TCAAAATATA	    0.983046	-73
ATTCTTTTGATCTAAATTATATATTGTTTATAT	2	92	0	TCTAAATATA	    0.961565	-55
ATAATTTAGATCAAAAGAATCTCAAAATGAGAT	2	105	1	TCAAAATCTC	    0.987768	-42
   GTTTGTCTCACATCCATCTATCTCATTTTG	2	127	0	TCACAATCTA	    0.973636	-20
          *****   *****

Masking position 10
Map Score:   2.23766

Number of sites scoring better than the average of aligned sites = 221
Number in coding regions = 186
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 4

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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:   7.34864e-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