AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i342_weak3_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1263	103	homoserine acetyltransferase (met2)

Motif number 1

GCCGTCTAAACGGCTAAATTATCGCACATCA  	1	9	0	CGCTAAATTC	    0.999227	-95
GCCGTTTAGACGGCTAAAATTTCTTGACAAGCT	1	28	1	CGCTAAATTC	    0.999227	-76
ATCAGTAAGTCGATTAGCTTGTCAAGAAATTTT	1	43	0	CGTTAGCTTC	    0.996533	-61
ATCAGAATGGCGTTTAAACTATCAGTAAGTCGA	1	63	0	CGTTAAATTC	    0.998804	-41
          ** ***** * **

Masking position 6
Map Score:   8.67238

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 14
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

CGATAATTTAGCCGTTTAGACGGCTAAAAT	1	18	1	GCCGTTTAGA	    0.990536	-86
CAAGCTAATCGACTTACTGATAGTTTAAAC	1	55	1	GACTTACTGA	    0.987255	-49
TAGTTTAAACGCCATTCTGATTATTACGAT	1	75	1	GCCATTCTGA	    0.996858	-29
          **********

Masking position 10
Map Score:   1.33418

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 220
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TTTAAACTATCAGTAAGTCGATTAGCTTGT	1	54	0	CAGTAAGTCG	     0.99665	-50
TCGTAATAATCAGAATGGCGTTTAAACTAT	1	74	0	CAGAATGGCG	    0.996329	-30
          **********

Masking position 5
Map Score:   0.406242

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 88
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   -5.44113e-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:   -5.44113e-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:   -5.44113e-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