AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i295_mixed10_hpyl_reg_100.orf -o295_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	RHP01336	120	AE000511

Motif number 1

AAAGAAAATTTTCAAAATGTG         	1	2	0	TTCAAAATGT	    0.919436	-119
AAATTTTCTTTAAAAAAACCGCTAATTGTT	1	21	1	TAAAAAAACC	    0.972048	-100
TACAAAATCGTTTAAAAACTAACAATTAGC	1	41	0	TTTAAAAACT	    0.944337	-80
TTTTTTGGCTTACAAAATCGTTTAAAAACT	1	51	0	TACAAAATCG	    0.989708	-70
CAAAAAAGGATACAATACCCTTAAGGATTT	1	74	1	TACAATACCC	    0.960175	-47
ATAAAATAAATATAAAATCCTTAAGGGTAT	1	88	0	TATAAAATCC	    0.993937	-33
ACTGCCTTACTATAAAATAAATATAAAATC	1	99	0	TATAAAATAA	    0.864564	-22
          **********

Masking position 5
Map Score:   6.71435

Number of sites scoring better than the average of aligned sites = 1607
Number in coding regions = 1405
Number in noncoding regions = 202
Number of orfs with sites within 600 bp upstream = 148
Fraction of orfs with sites within 600 bp upstream = 0.0237713


Motif number 2

          **********

No masking
Map Score:   -7.57276e-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 3

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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