AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_3_5_1_28_hpyl_reg_100.orf -o262_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

Purged sequences:
RHP00199	16	AE000511

Input sequences:
#1	RHP00200	23	AE000511
#2	RHP00203	107	AE000511

Motif number 1

  TAAGCCCTAATTAAGGAATGAAC     	1	9	1	AATTAAGGAA	    0.988088	-15
GTAGGCTTAAAATTCAGAAAGGGTGTTTTT	2	26	1	AATTCAGAAA	    0.984542	-82
GAAAGGGTGTTTTTAAGCAAGATTAGGTTA	2	42	1	TTTTAAGCAA	    0.975789	-66
ATTAATAAAATTTTAATAAAACTTGTGATT	2	73	0	TTTTAATAAA	    0.967352	-35
CCTTCTCATTAATTAATAAAATTTTAATAA	2	84	0	AATTAATAAA	    0.984314	-24
          **********

Masking position 6
Map Score:   6.5895

Number of sites scoring better than the average of aligned sites = 164
Number in coding regions = 103
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 2

ATTTTAAGCCTACATTCTCAGCGAATCA  	2	9	0	TACATTCTCA	    0.996967	-99
AAGATTAGGTTACAATCACAAGTTTTATTA	2	60	1	TACAATCACA	    0.990562	-48
        GATCCCTTCTCATTAATTAATA	2	96	0	TCCCTTCTCA	    0.995716	-12
          **********

Masking position 10
Map Score:   3.42432

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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:   -1.46782e-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