AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i308_mixed22_hpyl_reg_300.orf -o308_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	RHP00800	59	AE000511
#2	RHP00801	100	AE000511

Motif number 1

TATTTTAACCCATTTTTTAGGAAACTC     	1	43	1	CATTTTTGGA	    0.993469	-17
AAACTCATCGCGCTTTTAGGGCCTAGCGGGAG	2	12	1	CGTTTTAGGC	    0.997304	-89
ATAGAAAGAGCGCTTTTACCGCTCCCGCTAGG	2	33	0	CGTTTTACGC	    0.990572	-68
TTTCAGCGTCCAATTCTTGGGCTAATTCAATA	2	62	0	CATTCTTGGC	    0.997304	-39
ACGCTGAAATCTTTTCTTTGGATTCT      	2	85	1	CTTTCTTGGA	    0.989375	-16
          ** ***** ***

Masking position 7
Map Score:   6.68935

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 264
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

AAAAAATGGGTTAAAATAGCCTTATTATAA	1	31	0	TTAAAATAGC	       0.991	-29
CCGCTAGGCCCTAAAAGCGCGATGAGTTTC	2	11	0	CTAAAAGCGC	    0.983223	-90
GCTAATTCAATAGAAAGAGCGCTTTTACCG	2	44	0	TAGAAAGAGC	    0.990501	-57
GCTCTTTCTATTGAATTAGCCCAAGAATTG	2	54	1	TTGAATTAGC	    0.985322	-47
          **********

Masking position 5
Map Score:   3.32274

Number of sites scoring better than the average of aligned sites = 343
Number in coding regions = 320
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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