AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_hpyl_reg_300.orf -o034_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	RHP00509	259	AE000511

Motif number 1

AAACTTTGTTATTATTTAAGGTGTGATTTGAT	1	32	0	ATTTTAAGGT	    0.836315	-228
ACCACTAATATTTATTTTAAACTTTGTTATTA	1	50	0	TTTTTTAAAC	     0.93792	-210
ATATTAGTGGTTTTTATTAAGAACGCTTGTCT	1	71	1	TTTTATAAGA	    0.897541	-189
TTTATGGCCATTTATTCTAAAAAGACAAGCGT	1	93	0	TTTTTTAAAA	     0.96378	-167
AATAGCCATAATTCTTGTAGGTATGCCCCCAT	1	124	1	ATTTTTAGGT	    0.973204	-136
CTTTTTAGGAATTTTTATAGGAAAATGGGGGC	1	148	0	ATTTTTAGGA	    0.989764	-112
TTATAACAATATCTTTTTAGGAATTTTTATAG	1	160	0	ATCTTTAGGA	    0.953841	-100
CTAAAAAGATATTGTTATAAGACACATTAATA	1	172	1	ATTTTTAAGA	    0.984227	-88
ATTAATAGTTTTTCTTGTATAATTCTAGGCTG	1	197	1	TTTTTTATAA	    0.934663	-63
CTGAATTCAATTTATTTTATACGATATTAAGG	1	226	1	TTTTTTATAC	    0.890123	-34
          *** ** *****

Masking position 5
Map Score:   12.0977

Number of sites scoring better than the average of aligned sites = 497
Number in coding regions = 417
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 2

ATGGCTATTTTATGGCCATTTATTCTAAAAA	1	102	0	TATGCCATTT	    0.991583	-158
CTACAAGAATTATGGCTATTTTATGGCCATT	1	113	0	TATGCTATTT	     0.98705	-147
TTCTTGTAGGTATGCCCCCATTTTCCTATAA	1	135	1	TATGCCCCAT	    0.991133	-125
     GGTAATATGTCTCCTTAATATCGTAT	1	244	0	TATGCTCCTT	    0.994519	-16
          **** ******

Masking position 3
Map Score:   3.30348

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 15
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

TTGTTATTATTTAAGGTGTGATTTGATTTT	1	29	0	TTAAGGTGTG	    0.992367	-231
AGAAAAACTATTAATGTGTCTTATAACAAT	1	182	0	TTAATGTGTC	    0.988729	-78
TTATACGATATTAAGGAGACATATTACC  	1	242	1	TTAAGGAGAC	    0.987172	-18
          **********

Masking position 4
Map Score:   0.841349

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 15
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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 6

          **********

No masking
Map Score:   -3.81261e-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