AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i160_Porphyrin_Biosynthesis_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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	yjaD	94	orf, hypothetical protein
#2	hemE	39	uroporphyrinogen decarboxylase

Motif number 1

TCTCACTGAGCAGTTTTTGAATACAAACTT	1	23	0	CAGTTTTTGA	    0.934761	-72
AAAAACTGCTCAGTGAGAAATGTAAAAACC	1	35	1	CAGTGAGAAA	    0.973443	-60
TTAAACATGCCAGTGATGCAAAGGTAGTGC	1	68	1	CAGTGATGCA	    0.987521	-27
GATGCAAAGGTAGTGCAAGAGCT       	1	82	1	TAGTGCAAGA	    0.970676	-13
GTCAGGCGGTCAGTGTATCA          	2	1	0	CAGTGTATCA	    0.992641	-39
GGCTGTTCCTTAGTGCGTCAGGCGGTCAGT	2	17	0	TAGTGCGTCA	    0.990886	-23
          **********

Masking position 4
Map Score:   5.59228

Number of sites scoring better than the average of aligned sites = 1305
Number in coding regions = 1203
Number in noncoding regions = 102
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 2

          **********

No masking
Map Score:   -6.15168e-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 3

          **********

No masking
Map Score:   -6.15168e-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:   -6.15168e-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