AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_hpyl_reg_100.orf -o034_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	RHP00509	259	AE000511

Motif number 1

AAACTTTGTTATTATTTAAGGTGTGATTTGAT	1	32	0	ATTTTAAGGT	    0.978292	-228
ATATTAGTGGTTTTTATTAAGAACGCTTGTCT	1	71	1	TTTTATAAGA	    0.883473	-189
ATGGCCATTTATTCTAAAAAGACAAGCGTTCT	1	90	0	ATTTAAAAGA	    0.974451	-170
AATAGCCATAATTCTTGTAGGTATGCCCCCAT	1	124	1	ATTTTTAGGT	    0.984068	-136
CTTTTTAGGAATTTTTATAGGAAAATGGGGGC	1	148	0	ATTTTTAGGA	    0.991156	-112
TTATAACAATATCTTTTTAGGAATTTTTATAG	1	160	0	ATCTTTAGGA	    0.982255	-100
CTAAAAAGATATTGTTATAAGACACATTAATA	1	172	1	ATTTTTAAGA	    0.983564	-88
TCAGCCTAGAATTATACAAGAAAAACTATTAA	1	198	0	ATTTAAAGAA	    0.937871	-62
TCTCCTTAATATCGTATAAAATAAATTGAATT	1	229	0	ATCTAAAAAT	    0.559427	-31
          *** ** *****

Masking position 5
Map Score:   12.0191

Number of sites scoring better than the average of aligned sites = 412
Number in coding regions = 339
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 2

  ACTTGCCCCATACAGACTAAAATCAAATC	1	9	1	CATACAACTA	    0.947875	-251
CTTAAATAATAACAAAGTTTAAAATAAATAT	1	44	1	AACAAATTTA	    0.862466	-216
CAAAGTTTAAAATAAATATTAGTGGTTTTTA	1	56	1	AATAAAATTA	    0.974376	-204
AAGCGTTCTTAATAAAAACCACTAATATTTA	1	68	0	AATAAAACCA	    0.908257	-192
ATATTGTTATAAGACACATTAATAGTTTTTC	1	180	1	AAGACAATTA	    0.986456	-80
AGAATTATACAAGAAAAACTATTAATGTGTC	1	192	0	AAGAAAACTA	    0.978252	-68
TTCTAGGCTGAATTCAATTTATTTTATACGA	1	219	1	AATTCATTTA	    0.798267	-41
CGATATTAAGGAGACATATTACC        	1	247	1	GAGACAATTA	    0.957276	-13
          ****** ****

Masking position 6
Map Score:   5.97167

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 169
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

ACAAAGTTTAAAATAAATATTAGTGGTTTT	1	55	1	AAATAAATAT	    0.862414	-205
CATTTATTCTAAAAAGACAAGCGTTCTTAA	1	87	0	AAAAAGACAA	    0.953867	-173
TTTTTAGAATAAATGGCCATAAAATAGCCA	1	102	1	AAATGGCCAT	    0.973221	-158
AATGGCCATAAAATAGCCATAATTCTTGTA	1	113	1	AAATAGCCAT	    0.990011	-147
AAAAATTCCTAAAAAGATATTGTTATAAGA	1	164	1	AAAAAGATAT	    0.965879	-96
ATACGATATTAAGGAGACATATTACC    	1	244	1	AAGGAGACAT	    0.962447	-16
          **********

Masking position 2
Map Score:   4.62656

Number of sites scoring better than the average of aligned sites = 429
Number in coding regions = 384
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

TTTAGAATAAATGGCCATAAAATAGCCATA	1	104	1	ATGGCCATAA	    0.994323	-156
TGGCCATAAAATAGCCATAATTCTTGTAGG	1	115	1	ATAGCCATAA	    0.991572	-145
CTAAAAAGATATTGTTATAAGACACATTAA	1	172	1	ATTGTTATAA	     0.94081	-88
          **********

Masking position 7
Map Score:   0.578893

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 47
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 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


Motif number 7

          **********

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