AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00120_hpyl_reg_100.orf -o00120_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	HP1376	171	(3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ)

Motif number 1

AACGCTTTGCATAGAAACCGCTTATGCA    	1	7	0	AAGAACCGCT	    0.995621	-165
GCCATAAGCTTCAAGAAACGCTTTGCATAGAA	1	23	0	TAAAAACGCT	    0.986867	-149
TTGTATTTGCAAAAACACCGATGCATTGCGCC	1	52	0	AAACACCGAT	    0.984866	-120
ATTATACCATAAGAAAACCGCTCGCTTGTATT	1	77	0	AGAAACCGCT	    0.995671	-95
TTATTCTAAAAAAATAACCGCTATTATACCAT	1	99	0	AAAAACCGCT	    0.998844	-73
TTTTTTTAGAATAACCAACGCTAAAAATAGCG	1	117	1	AAACAACGCT	    0.996461	-55
AACCAACGCTAAAAATAGCGCTTTAATTGAAT	1	129	1	AAATAGCGCT	     0.98378	-43
          AAAATAAACTCCTTGTTTTGGA	1	160	0	AAAAAACTCC	    0.925575	-12
          * ** *******

Masking position 7
Map Score:   17.4012

Number of sites scoring better than the average of aligned sites = 594
Number in coding regions = 534
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 2

AGCGGTTTCTATGCAAAGCGTTTCTTGAAG	1	17	1	ATGCAAAGCG	    0.992223	-155
AAAAACACCGATGCATTGCGCCATAAGCTT	1	44	0	ATGCATTGCG	    0.953143	-128
TGTTTTTGCAAATACAAGCGAGCGGTTTTC	1	67	1	AATACAAGCG	     0.97899	-105
ATTATACCATAAGAAAACCGCTCGCTTGTA	1	79	0	AAGAAAACCG	    0.967302	-93
TTTCTTATGGTATAATAGCGGTTATTTTTT	1	93	1	TATAATAGCG	    0.953092	-79
TTAAAGCGCTATTTTTAGCGTTGGTTATTC	1	125	0	ATTTTTAGCG	    0.928267	-47
TTTTGGATTCAATTAAAGCGCTATTTTTAG	1	137	0	AATTAAAGCG	    0.988881	-35
          **********

Masking position 9
Map Score:   8.43986

Number of sites scoring better than the average of aligned sites = 1088
Number in coding regions = 1010
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 3

ATAAGCGGTTTCTATGCAAAGCGTTTCTTGA	1	14	1	TTATGCAAAG	    0.953331	-158
CGCTCGCTTGTATTTGCAAAAACACCGATGC	1	60	0	TTTTGCAAAA	    0.967714	-112
ATAACCGCTATTATACCATAAGAAAACCGCT	1	87	0	TATACCATAA	    0.726578	-85
TTAGCGTTGGTTATTCTAAAAAAATAACCGC	1	110	0	TATTCTAAAA	    0.794267	-62
GCGCTTTAATTGAATCCAAAACAAGGAGTTT	1	146	1	TAATCCAAAA	    0.989341	-26
          * *********

Masking position 8
Map Score:   1.23241

Number of sites scoring better than the average of aligned sites = 579
Number in coding regions = 525
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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