AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iilvY_ecoli_hinf_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
#2	HI0681	300	transcriptional activator (ilvY)

Motif number 1

CTATATGACAGGAAATTTATTGCGGAAATT	1	72	1	GGAAATTTAT	    0.981015	-78
AATTTATTGCGGAAATTGATATATTCACAA	1	85	1	GGAAATTGAT	    0.959193	-65
TTAGTTTTCTGGTATTTTTCAAAATACGCT	2	23	1	GGTATTTTTC	    0.902412	-278
AAAGAAGGGAGCTAATTTATTCTTTCTTCA	2	75	0	GCTAATTTAT	    0.840788	-226
CTGAAAAATTGGAAATTTGTAGGAAATTTT	2	110	1	GGAAATTTGT	    0.943978	-191
GAAATTTGTAGGAAATTTTCGTCTGTTTGA	2	121	1	GGAAATTTTC	    0.788565	-180
TTTGCTTAACGGAAATTTTCTGAACTCGCT	2	155	0	GGAAATTTTC	    0.788565	-146
CTGAAAAATTGGAAATTTGCTTAACGGAAA	2	170	0	GGAAATTTGC	     0.58991	-131
          **********

Masking position 4
Map Score:   15.8751

Number of sites scoring better than the average of aligned sites = 161
Number in coding regions = 140
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

TGTTGACGTTGCAAAAATTGCAATGTGACGT	1	114	0	GAAAAATTGC	    0.849191	-36
          TAAAAAGTGCGGTTAGTTTTC	2	1	1	TAAAAGTGCG	    0.968433	-300
TCTGGTATTTTTCAAAATACGCTAAATTTTA	2	30	1	TCAAAATACG	    0.941342	-271
CTTTCTTCAATTTAAAGTGCGGGTAAAATTT	2	53	0	TTAAAGTGCG	    0.864297	-248
TTTTTCAGGCGGCAAAGAAGGGAGCTAATTT	2	87	0	GCAAAGAAGG	    0.950047	-214
CTTTGCCGCCTGAAAAATTGGAAATTTGTAG	2	101	1	TAAAAATTGG	    0.964707	-200
CCTTATTTCCTGAAAAATTGGAAATTTGCTT	2	178	0	TAAAAATTGG	    0.964707	-123
CAGGAAATAAGGCAAAGTAGGGCGTGTTTTC	2	197	1	GCAAAGTAGG	    0.992655	-104
CTCGTGCAAAGCAAAAGTAGGCAAAAAGAAA	2	224	0	GAAAAGTAGG	    0.993932	-77
CACGAGCAAAGAAAAAGTAGGTCGCCATCGG	2	249	1	GAAAAGTAGG	    0.993934	-52
          * *********

Masking position 6
Map Score:   14.3291

Number of sites scoring better than the average of aligned sites = 523
Number in coding regions = 461
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 3

GGAGCTAATTTATTCTTTCTTCAATTTAAAGT	2	66	0	TATTCTTTTC	    0.931334	-235
TTAACGGAAATTTTCTGAACTCGCTACGCTCA	2	148	0	TTTTCTGACC	    0.969591	-153
AAATTGGAAATTTGCTTAACGGAAATTTTCTG	2	163	0	TTTGCTTACG	    0.943105	-138
GTAGGGCGTGTTTTCTTTTTGCCTACTTTTGC	2	213	1	TTTTCTTTTC	    0.982136	-88
TTTGCCTACTTTTGCTTTGCACGAGCAAAGAA	2	230	1	TTTGCTTTCC	    0.992641	-71
GCGACCTACTTTTTCTTTGCTCGTGCAAAGCA	2	242	0	TTTTCTTTCC	    0.993891	-59
          ******** * *

Masking position 6
Map Score:   4.93815

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 176
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 4

AATAAGAAGCACAACATCACGAGGAATCAC	1	12	0	ACAACATCAC	    0.990931	-138
TGATATATTCACAACGTCACATTGCAATTT	1	101	1	ACAACGTCAC	    0.995995	-49
TGCAATTTTTGCAACGTCAACATCGAGGGC	1	123	1	GCAACGTCAA	    0.988043	-27
          **********

Masking position 4
Map Score:   2.00203

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 44
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

GCTTCTTATTGTTCGGTTCGCGTTTGCGAG	1	32	1	GTTCGGTTCG	    0.990598	-118
    TAAAAAGTGCGGTTAGTTTTCTGGTA	2	7	1	GTGCGGTTAG	    0.997081	-294
TCAATTTAAAGTGCGGGTAAAATTTAGCGT	2	48	0	GTGCGGGTAA	    0.990556	-253
          **********

Masking position 8
Map Score:   0.823274

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 29
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:   8.764e-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 7

          **********

No masking
Map Score:   8.764e-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 8

          **********

No masking
Map Score:   8.764e-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