AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00120_hpyl_reg_300.orf -o00120_hpyl_300.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)
#2	HP1377	300	H. pylori predicted coding region HP1377

Motif number 1

   TGCATAAGCGGTTTCTATGCAAAGCGTT	1	8	1	GCGTTTCTAT	    0.835478	-164
GCGCAATGCATCGGTGTTTTTGCAAATACAA	1	53	1	TCGTGTTTTT	    0.959628	-119
AGAAAACCGCTCGCTTGTATTTGCAAAAACA	1	67	0	TCGTTGTATT	    0.875154	-105
ATACAAGCGAGCGGTTTTCTTATGGTATAAT	1	78	1	GCGTTTTCTT	    0.957744	-94
TGGTATAATAGCGGTTATTTTTTTAGAATAA	1	100	1	GCGTTATTTT	    0.987995	-72
GCTATTTTTAGCGTTGGTTATTCTAAAAAAA	1	117	0	GCGTGGTTAT	    0.964201	-55
TTCAATTAAAGCGCTATTTTTAGCGTTGGTT	1	129	0	GCGTATTTTT	    0.973475	-43
CCAAAACAAGGAGTTTATTTT          	1	161	1	GAGTTATTTT	    0.877904	-11
TGGTGCGGCTGGGCTTGATTTGGAGAAATGG	2	39	0	GGGTTGATTT	    0.942445	-262
GAGATTTACTGGGATTATTTTTCTTGATTTG	2	95	1	GGGTTATTTT	    0.966179	-206
TCTTGATTTGTGGTTTTATTTTGCTCATTCC	2	116	1	TGGTTTATTT	    0.746934	-185
AAATCAATTTTCGCTAGTTTTGGATATAATC	2	208	0	TCGTAGTTTT	    0.943894	-93
AAATCATTGAGCGCTGGTTTTAAGGCGGTCT	2	277	1	GCGTGGTTTT	    0.992474	-24
          *** *******

Masking position 5
Map Score:   18.7637

Number of sites scoring better than the average of aligned sites = 1871
Number in coding regions = 1696
Number in noncoding regions = 175
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 2

AAGAAACGCTTTGCATAGAAACCGCTTATGCA 	1	10	0	TTGATAAACC	    0.832488	-162
TGCATCGGTGTTTTTGCAAATACAAGCGAGCGG	1	59	1	TTTTGAATAC	    0.912228	-113
TAGCGGTTATTTTTTTAGAATAACCAACGCTAA	1	108	1	TTTTTAATAA	    0.875186	-64
AAAATAGCGCTTTAATTGAATCCAAAACAAGGA	1	140	1	TTTATAATCC	    0.984239	-32
CTGACATTATTTGGTGGGAATAAGAA       	2	4	0	TTGTGAATAA	    0.776208	-297
GTCAGCACCATTTCTCCAAATCAAGCCCAGCCG	2	32	1	TTTTCAATCA	    0.956451	-269
TGTGGTTTTATTTTGCTCATTCCTCAACTCCTT	2	124	1	TTTGCATTCC	    0.814957	-177
ATGATGGAAGTTTAACCGAATCATTATAAAATA	2	161	0	TTTACAATCA	    0.964387	-140
TTCGCTAGTTTTGGATATAATCCCAATAACTTA	2	197	0	TTGATAATCC	     0.97507	-104
ATCAAACAATTTTGGTAAAATCAATTTTCGCTA	2	223	0	TTTGTAATCA	    0.956698	-78
ACCAAAATTGTTTGATATAATACAGAGTTTAGC	2	240	1	TTTATAATAC	    0.958235	-61
          *** **  *****

Masking position 9
Map Score:   8.40733

Number of sites scoring better than the average of aligned sites = 775
Number in coding regions = 657
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 90
Fraction of orfs with sites within 600 bp upstream = 0.0144555


Motif number 3

CCGATGCATTGCGCCATAAGCTTCAAGAAA	1	37	0	GCGCCATAAG	    0.969997	-135
AAAAAAATAACCGCTATTATACCATAAGAA	1	94	0	CCGCTATTAT	    0.891056	-78
AGAATAACCAACGCTAAAAATAGCGCTTTA	1	124	1	ACGCTAAAAA	    0.919277	-48
GCTAAAAATAGCGCTTTAATTGAATCCAAA	1	136	1	GCGCTTTAAT	    0.927117	-36
 TTCTTATTCCCACCAAATAATGTCAGCAC	2	10	1	CCACCAAATA	    0.794398	-291
AAGCCCAGCCGCACCAAAAAGACGCCACCT	2	54	1	GCACCAAAAA	    0.942577	-247
ACGCCACCTACCGCTAAAATGAGATTTACT	2	75	1	CCGCTAAAAT	    0.978559	-226
    AAAAGACCGCCTTAAAACCAGCGCTC	2	285	0	CCGCCTTAAA	    0.971838	-16
          **********

Masking position 4
Map Score:   5.19936

Number of sites scoring better than the average of aligned sites = 1060
Number in coding regions = 986
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 4

          **********

No masking
Map Score:   -8.99385e-14

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:   -8.99385e-14

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:   -8.99385e-14

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