AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i252_chemotaxis1_hpyl_reg_100.orf -o252_hpyl_100.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	    0.923485	-132
ATTTTCCTTTCATCAAACTCATCTCAACCA	1	12	1	CATCAAACTC	    0.992239	-121
GCGCTATTCTAGTCAAAATCGCCTTATTTT	1	54	1	AGTCAAAATC	    0.987545	-79
AAAATCATAGCGCAAAAATAAGGCGATTTT	1	68	0	CGCAAAAATA	    0.876497	-65
AGTCATTATTATTGAAAATCATAGCGCAAA	1	82	0	ATTGAAAATC	    0.974613	-51
TCCAAACTCCCTTCAAACTAGTTTTAAAAA	1	111	0	CTTCAAACTA	    0.980382	-22
         ACTCCAAACTCCCTTCAAACT	1	122	0	CTCCAAACTC	    0.993459	-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

TCTCAACCAACAATAATAGAAGCGCTATTCT	1	33	1	CAATAATAGA	    0.986757	-100
GCGATTTTGACTAGAATAGCGCTTCTATTAT	1	45	0	CTAGAATAGG	    0.986686	-88
AATCATAGCGCAAAAATAAGGCGATTTTGAC	1	65	0	CAAAAATAAG	    0.986494	-68
TTATTATTGAAAATCATAGCGCAAAAATAAG	1	76	0	AAATCATAGG	    0.973592	-57
CTATGATTTTCAATAATAATGACTTTTTAAA	1	88	1	CAATAATAAG	    0.921246	-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

CCTTTCATCAAACTCATCTCAACCAACAAT	1	17	1	AACTCATCTC	    0.973508	-116
TTTGACTAGAATAGCGCTTCTATTATTGTT	1	41	0	ATAGCGCTTC	    0.875238	-92
ATTCTAGTCAAAATCGCCTTATTTTTGCGC	1	59	1	AAATCGCCTT	    0.836507	-74
ACTCCCTTCAAACTAGTTTTAAAAAGTCAT	1	106	0	AACTAGTTTT	    0.918723	-27
    ACTCCAAACTCCCTTCAAACTAGTTT	1	117	0	AACTCCCTTC	    0.990887	-16
          **********

Masking position 9
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