AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00071_hpyl_reg_100.orf -o00071_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP0690	281	acetyl coenzyme A acetyltransferase (thiolase) (fadA)

Motif number 1

GGCAAAGACTGCTTAGAAAGAAATTTTTTAAA	1	35	1	GCTTAGAAAA	    0.883097	-247
AGAAACATGAGCCTAAAGTGCATATCTGCTTG	1	74	1	GCCTAAAGCA	    0.956416	-208
TTGAGTGGGGATCTAAAATCAAGCAGATATGC	1	93	0	ATCTAAAAAA	    0.967093	-189
TTAGATCCCCACTCAAAGCTATATTGTGCAAT	1	109	1	ACTCAAAGAT	    0.833216	-173
ATCGCCCTCAATCCAAAACAAAACCTAAAATA	1	187	1	ATCCAAAAAA	    0.943317	-95
CCAAAACAAAACCTAAAATAAAATCCAACCTG	1	199	1	ACCTAAAAAA	    0.992277	-83
GGTGTCAATCACCTAAAAGTGATACTATGAAT	1	235	1	ACCTAAAAGA	    0.975331	-47
TAATAAATCAACTTAAAGGCAAAGAC      	1	266	1	ACTTAAAGAA	    0.980091	-16
          ********  **

Masking position 7
Map Score:   5.31625

Number of sites scoring better than the average of aligned sites = 675
Number in coding regions = 584
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

CTTATCGTTCAATGATTATTGCACAATATA	1	128	0	AATGATTATT	    0.781024	-154
TTTTTCACAAAAATATTATTCTTATCGTTC	1	148	0	AAATATTATT	    0.855056	-134
AGGGCGATCCGTTTATTTTTTTCACAAAAA	1	165	0	GTTTATTTTT	    0.913857	-117
CTTTAAGTTGATTTATTATTCATAGTATCA	1	254	0	ATTTATTATT	    0.957851	-28
          **********

Masking position 5
Map Score:   0.156661

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 60
Number in noncoding regions = 21
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:   8.97716e-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:   8.97716e-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:   8.97716e-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