AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_hpyl_reg_300.orf -o228_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	RHP01398	117	AE000511

Motif number 1

ATGATTGAGATTATTTTTGATTAGGATCAA	1	13	0	TTATTTTTGA	    0.984593	-105
CAATCATACACTAATTTTAATAGAAAAAAG	1	36	1	CTAATTTTAA	    0.980258	-82
AAAAGTGAAACCATTTTTAAGCCATTTTTG	1	61	1	CCATTTTTAA	    0.995778	-57
CATTTTTAAGCCATTTTTGAATACAATAAG	1	72	1	CCATTTTTGA	    0.996025	-46
TAAGAGTATTTTATTTTTAAGGTTAGAACA	1	98	1	TTATTTTTAA	    0.984421	-20
          **********

Masking position 5
Map Score:   12.574

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 74
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

    GGTTGATCCTAATCAAAAATAATCTC	1	7	1	TCCTAATCAA	    0.988742	-111
TTTCACTTTTTTCTATTAAAATTAGTGTAT	1	41	0	TTCTATTAAA	     0.97384	-77
AATACTCTTATTGTATTCAAAAATGGCTTA	1	78	0	TTGTATTCAA	    0.668648	-40
          **********

Masking position 5
Map Score:   1.84036

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 41
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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:   -2.59896e-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