AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i252_chemotaxis1_hpyl_reg_300.orf -o252_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e 
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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00236	132	AE000511

Motif number 1

AGTTTGATGAAAGGAAAATC          	1	1	0	AAGGAAAATC	    0.922681	-132
ATTTTCCTTTCATCAAACTCATCTCAACCA	1	12	1	CATCAAACTC	    0.992151	-121
GCGCTATTCTAGTCAAAATCGCCTTATTTT	1	54	1	AGTCAAAATC	    0.987405	-79
AAAATCATAGCGCAAAAATAAGGCGATTTT	1	68	0	CGCAAAAATA	    0.875266	-65
AGTCATTATTATTGAAAATCATAGCGCAAA	1	82	0	ATTGAAAATC	    0.974331	-51
TCCAAACTCCCTTCAAACTAGTTTTAAAAA	1	111	0	CTTCAAACTA	    0.980163	-22
         ACTCCAAACTCCCTTCAAACT	1	122	0	CTCCAAACTC	    0.993385	-11
          **********

Masking position 5
Map Score:   9.44772

Number of sites scoring better than the average of aligned sites = 798
Number in coding regions = 745
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

AGAATAGCGCTTCTATTATTGTTGGTTGAGA	1	33	0	TCTATTATTG	    0.987453	-100
ATAATAGAAGCGCTATTCTAGTCAAAATCGC	1	45	1	CCTATTCTAG	    0.987496	-88
GTCAAAATCGCCTTATTTTTGCGCTATGATT	1	65	1	CTTATTTTTG	    0.987316	-68
CTTATTTTTGCGCTATGATTTTCAATAATAA	1	76	1	CCTATGATTT	    0.975271	-57
TTTAAAAAGTCATTATTATTGAAAATCATAG	1	88	0	CTTATTATTG	    0.917231	-45
          * *********

Masking position 6
Map Score:   5.71701

Number of sites scoring better than the average of aligned sites = 268
Number in coding regions = 234
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

ATTGTTGGTTGAGATGAGTTTGATGAAAGG	1	17	0	GAGATGAGTT	    0.973508	-116
AACAATAATAGAAGCGCTATTCTAGTCAAA	1	41	1	GAAGCGCTAT	    0.875238	-92
GCGCAAAAATAAGGCGATTTTGACTAGAAT	1	59	0	AAGGCGATTT	    0.836507	-74
ATGACTTTTTAAAACTAGTTTGAAGGGAGT	1	106	1	AAAACTAGTT	    0.918723	-27
AAACTAGTTTGAAGGGAGTTTGGAGT    	1	117	1	GAAGGGAGTT	    0.990887	-16
          **********

Masking position 2
Map Score:   1.42554

Number of sites scoring better than the average of aligned sites = 1084
Number in coding regions = 997
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 4

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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:   5.21701e-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