AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i321_mixed6_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	pabC	119	4-amino-4-deoxychorismate lyase

Motif number 1

GGCCCGCAAGCGGACCTTTTATAAGGGTGG	1	22	0	CGGACCTTTT	    0.997232	-98
GGTCCGCTTGCGGGCCTTTTTTCTTAGCTT	1	36	1	CGGGCCTTTT	    0.998209	-84
AGCTTTTATTCCGACTTGTTCCGTAGTGAA	1	61	1	CCGACTTGTT	    0.994919	-59
         ACCGGCTCCTTATCAGAGAAT	1	109	0	CCGGCTCCTT	    0.994382	-11
          **********

Masking position 9
Map Score:   6.25057

Number of sites scoring better than the average of aligned sites = 284
Number in coding regions = 213
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

GACCTTTTATAAGGGTGGAAAATGACAAC 	1	10	0	AAGGGTGGAA	     0.99159	-110
ACCCTTATAAAAGGTCCGCTTGCGGGCCTT	1	24	1	AAGGTCCGCT	    0.987726	-96
GCTAAGAAAAAAGGCCCGCAAGCGGACCTT	1	34	0	AAGGCCCGCA	    0.995525	-86
CACTACGGAACAAGTCGGAATAAAAGCTAA	1	59	0	CAAGTCGGAA	    0.950757	-61
AGAGAATTGTTAGTGTGGCAGCATGTTCAC	1	86	0	TAGTGTGGCA	    0.952719	-34
          **********

Masking position 2
Map Score:   2.60995

Number of sites scoring better than the average of aligned sites = 1736
Number in coding regions = 1556
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 195
Fraction of orfs with sites within 600 bp upstream = 0.0313203


Motif number 3

          **********

No masking
Map Score:   9.48026e-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:   9.48026e-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:   9.48026e-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