AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00072_hpyl_reg_300.orf -o00072_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	HP0688	143	H. pylori predicted coding region HP0688
#2	HP0690	281	acetyl coenzyme A acetyltransferase (thiolase) (fadA)

Motif number 1

AACGATATAACTAAAAATTAGAAAAACTTTAA	1	30	0	CTAAAATAGA	    0.979359	-114
GACTTTTAATCTAAAAACGATATAACTAAAAA	1	45	0	CTAAAACATA	    0.985018	-99
CGTTTTTAGATTAAAAGTCAGCACTATAGCGC	1	58	1	TTAAAATAGC	    0.902132	-86
TTGTTATATAATAAAAGCGAGACAAGAATGTT	1	101	1	ATAAAACAGA	    0.985018	-43
   AATTCTATTAAAACCCTGAAACTAGGCAA	2	8	1	TTAAAACTGA	    0.865882	-274
GAGTGGGGATCTAAAATCAAGCAGATATGCAC	2	91	0	CTAAAACAGC	    0.991719	-191
TAGATCCCCACTCAAAGCTATATTGTGCAATA	2	110	1	CTCAAACATA	    0.932025	-172
TCAATCCAAAACAAAACCTAAAATAAAATCCA	2	194	1	ACAAAACAAA	    0.789045	-88
AAAACCTAAAATAAAATCCAACCTGTTAGGGT	2	206	1	ATAAAACAAC	    0.927379	-76
TGTCAATCACCTAAAAGTGATACTATGAATAA	2	237	1	CTAAAATATA	    0.948852	-45
          ****** * ***

Masking position 6
Map Score:   11.1647

Number of sites scoring better than the average of aligned sites = 816
Number in coding regions = 710
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 2

TAATCTAAAAACGATATAACTAAAAATTAGAAA	1	38	0	ACGATAAAAA	    0.911129	-106
GCACTATAGCGCTATAAGACTAATTGTTATATA	1	78	1	GCTATAGAAA	    0.937673	-66
AAGACTAATTGTTATATAATAAAAGCGAGACAA	1	93	1	GTTATAAAAA	    0.969861	-51
TATAATAAAAGCGAGACAAGAATGTTAAAAAAT	1	107	1	GCGAGAAAAT	    0.937539	-37
AGACAAGAATGTTAAAAAATGAAAGGAGCGTGT	1	120	1	GTTAAAAAAA	    0.944261	-24
TTTTTAAAGCGTTAGAGAAACATGAGCCTAAAG	2	59	1	GTTAGAAAAT	    0.879288	-223
TTTGAGTGGGGATCTAAAATCAAGCAGATATGC	2	93	0	GATCTAAAAA	    0.720137	-189
AAGCTATATTGTGCAATAATCATTGAACGATAA	2	124	1	GTGCAAAAAT	    0.831208	-158
TAATCATTGAACGATAAGAATAATATTTTTGTG	2	140	1	ACGATAGAAA	    0.815099	-142
TAATATTTTTGTGAAAAAAATAAACGGATCGCC	2	160	1	GTGAAAAAAA	    0.969898	-122
TCACCTAAAAGTGATACTATGAATAATAAATCA	2	243	1	GTGATATAAA	    0.906185	-39
          ****** **  **

Masking position 6
Map Score:   6.88229

Number of sites scoring better than the average of aligned sites = 764
Number in coding regions = 663
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 3

CCCTGAAACTAGGCAAAGACTGCTTAGAAA	2	24	1	AGGCAAAGAC	    0.997588	-258
ATCAACTTAAAGGCAAAGAC          	2	272	1	AGGCAAAGAC	    0.997588	-10
          **********

Masking position 5
Map Score:   1.66018

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 9
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 4

       TGGGTTTGAATGCTCCGCATTAA	1	4	1	GTTTGAATGC	    0.908515	-140
AATTAGAAAAACTTTAATGCGGAGCATTCA	1	17	0	ACTTTAATGC	    0.948515	-127
GTCTTATAGCGCTATAGTGCTGACTTTTAA	1	68	0	GCTATAGTGC	    0.981452	-76
GCACTATAGCGCTATAAGACTAATTGTTAT	1	78	1	GCTATAAGAC	    0.876751	-66
GAAACATGAGCCTAAAGTGCATATCTGCTT	2	75	1	CCTAAAGTGC	    0.917028	-207
TTTTGTTTTGGATTGAGGGCGATCCGTTTA	2	180	0	GATTGAGGGC	    0.936058	-102
TAATAAATCAACTTAAAGGCAAAGAC    	2	266	1	ACTTAAAGGC	    0.944625	-16
          **********

Masking position 6
Map Score:   1.92754

Number of sites scoring better than the average of aligned sites = 1292
Number in coding regions = 1217
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 5

          **********

No masking
Map Score:   -4.02005e-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:   -4.02005e-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 7

          **********

No masking
Map Score:   -4.02005e-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