AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_hpyl_reg_100.orf -o150_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	RHP00251	121	AE000511
#2	RHP00533	22	AE000511
#3	RHP00535	20	AE000511
#4	RHP00538	110	AE000511

Motif number 1

TTAACGAGTTTTTTAACGATTTGTCTTGTTTT	1	21	0	TTTAACGATT	    0.975879	-101
AAACCAAGCTTTTTAACGAGTTTTTTAACGAT	1	33	0	TTTAACGATT	    0.975879	-89
GTTTAATGAGTTTTTAAAACTTAATTGCTACA	1	61	1	TTTTAAAATT	    0.964191	-61
TCTCTAAGCCTTATTGAAAATTTCCTTAATTG	1	91	0	TTATGAAATT	    0.952208	-31
TCAATAAGGCTTAGAGAAACTTTTTC      	1	106	1	TTAAGAAATT	     0.97778	-16
CGCTCCTTGATTAATATAATTT          	2	1	0	TTATATAATT	    0.792454	-22
TCGCTTAAAATTTGAGAATATTCAAGCG    	4	7	0	TTTAGAATTT	    0.900648	-104
ATTCTCAAATTTTAAGCGATTTTTTGTTAAGA	4	20	1	TTTAGCGATT	    0.977695	-91
CTCGCATTTGTTATAAAAACATTAACTCTATC	4	50	0	TTAAAAAAAT	    0.851084	-61
CAAATGCGAGTTTCAAATATTTTGTAGGATTT	4	72	1	TTTAAATATT	    0.925068	-39
          *** ***** **

Masking position 2
Map Score:   11.422

Number of sites scoring better than the average of aligned sites = 1412
Number in coding regions = 1145
Number in noncoding regions = 267
Number of orfs with sites within 600 bp upstream = 194
Fraction of orfs with sites within 600 bp upstream = 0.0311597


Motif number 2

AAAACAAGACAAATCGTTAAAAAACTCGTT	1	21	1	AAATCGTTAA	    0.994779	-101
ATCGTTAAAAAACTCGTTAAAAAGCTTGGT	1	33	1	AACTCGTTAA	    0.995391	-89
AAGTTTTAAAAACTCATTAAACCAAGCTTT	1	53	0	AACTCATTAA	    0.989708	-69
TCTTAACAAAAAATCGCTTAAAATTTGAGA	4	22	0	AAATCGCTTA	    0.963855	-89
ATTTGTTATAAAAACATTAACTCTATCTTA	4	47	0	AAAACATTAA	    0.964252	-64
          **********

Masking position 8
Map Score:   8.05916

Number of sites scoring better than the average of aligned sites = 148
Number in coding regions = 141
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

          ATTGTAAAAGAAAACAAGACAAAT	1	1	1	ATTAAAGAAA	    0.979805	-121
AATTTCCTTAATTGTAGCAATTAAGTTTTAAAAA	1	71	0	ATTAGAATAA	    0.985994	-51
        AAATTATATTAATCAAGGAGCG    	2	3	1	ATTATAATAA	    0.946603	-20
       TCAATCTAAGGAGATAAATA       	3	4	1	ATAAGAGAAA	    0.964248	-17
CATTAACTCTATCTTAACAAAAAATCGCTTAAAA	4	29	0	ATTAAAAAAA	    0.982447	-82
ATTTTGTAGGATTTTAGGAAAGAAATAGGTT   	4	90	1	ATTAGAAAAA	    0.992428	-21
          **  *** *** **

Masking position 6
Map Score:   5.51634

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 82
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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:   2.79544e-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