AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ioxyR_hpyl_opreg_100.orf -g0.389 -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 =  	0.389
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HP0243	205	neutrophil activating protein (napA) (bacterioferritin)

Motif number 1

ATAAAACAAAATTTTAAAAAGATTAAATAATA	1	47	1	ATTTAAAAGA	    0.978808	-159
GTTTATCAATATTTGACAAAAATAAGATCAAA	1	93	1	ATTTAAAAAA	    0.988858	-113
GACAAAAATAAGATCAAAAAAATTTTTTATTA	1	107	1	AGATAAAAAA	    0.980669	-99
ACACCAAAAGAGTTAATAAAAAATTTTTTTGA	1	120	0	AGTTAAAAAA	    0.986722	-86
TAGGCTTTTATTTTCATAAAAACCTTGATCGC	1	158	0	TTTTAAAAAA	    0.564992	-48
GCCTAAAACAATTTTAAAAAAAGGACTTTTG 	1	185	1	ATTTAAAAAA	    0.882389	-21
          **** * *****

Masking position 6
Map Score:   12.6507

Number of sites scoring better than the average of aligned sites = 173
Number in coding regions = 138
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

ATCCCCCTTAAAAATGAGTTTTACTATAAAA	1	22	1	AAAATGATTT	    0.865212	-184
GTTTTACTATAAAACAAAATTTTAAAAAGAT	1	39	1	AAAACAAATT	    0.985474	-167
TTAAAAAGATTAAATAATATTAAATTGAATG	1	60	1	TAAATAAATT	    0.930135	-146
ATATTTGACAAAAATAAGATCAAAAAAATTT	1	101	1	AAAATAAATC	    0.978942	-105
AAATAAGATCAAAAAAATTTTTTATTAACTC	1	112	1	AAAAAAATTT	    0.850176	-94
GGTTTTTATGAAAATAAAAGCCTAAAACAAT	1	166	1	AAAATAAAGC	    0.925862	-40
ATAAAAGCCTAAAACAATTTTAAAAAAAGGA	1	179	1	AAAACAATTT	     0.87087	-27
CAATTTTAAAAAAAGGACTTTTG        	1	193	1	AAAAGGATTT	    0.949562	-13
          ******* ***

Masking position 7
Map Score:   11.2463

Number of sites scoring better than the average of aligned sites = 825
Number in coding regions = 654
Number in noncoding regions = 171
Number of orfs with sites within 600 bp upstream = 136
Fraction of orfs with sites within 600 bp upstream = 0.0218439


Motif number 3

          **********

No masking
Map Score:   -2.46258e-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 4

          **********

No masking
Map Score:   -2.46258e-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 5

          **********

No masking
Map Score:   -2.46258e-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