AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00071_hpyl_reg_300.orf -o00071_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	    0.980409	-114
GACTTTTAATCTAAAAACGATATAACTAAAAA	1	45	0	CTAAAACATA	    0.985784	-99
CGTTTTTAGATTAAAAGTCAGCACTATAGCGC	1	58	1	TTAAAATAGC	    0.906737	-86
TTGTTATATAATAAAAGCGAGACAAGAATGTT	1	101	1	ATAAAACAGA	    0.985784	-43
   AATTCTATTAAAACCCTGAAACTAGGCAA	2	8	1	TTAAAACTGA	     0.87195	-274
GAGTGGGGATCTAAAATCAAGCAGATATGCAC	2	91	0	CTAAAACAGC	    0.992145	-191
TAGATCCCCACTCAAAGCTATATTGTGCAATA	2	110	1	CTCAAACATA	    0.935325	-172
TCAATCCAAAACAAAACCTAAAATAAAATCCA	2	194	1	ACAAAACAAA	    0.797779	-88
AAAACCTAAAATAAAATCCAACCTGTTAGGGT	2	206	1	ATAAAACAAC	    0.930887	-76
TGTCAATCACCTAAAAGTGATACTATGAATAA	2	237	1	CTAAAATATA	    0.951377	-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

TTTCTAATTTTTAGTTATATCGTTTTTAGATTA	1	38	1	TTTTTATCGT	    0.916445	-106
TATATAACAATTAGTCTTATAGCGCTATAGTGC	1	78	0	TTTCTATAGC	    0.941503	-66
TTGTCTCGCTTTTATTATATAACAATTAGTCTT	1	93	0	TTTTTATAAC	    0.971759	-51
ATTTTTTAACATTCTTGTCTCGCTTTTATTATA	1	107	0	ATTTTCTCGC	    0.941377	-37
ACACGCTCCTTTCATTTTTTAACATTCTTGTCT	1	120	0	TTTTTTTAAC	    0.947709	-24
CTTTAGGCTCATGTTTCTCTAACGCTTTAAAAA	2	59	0	ATTTTCTAAC	     0.88627	-223
GCATATCTGCTTGATTTTAGATCCCCACTCAAA	2	93	1	TTTTTAGATC	    0.733535	-189
TTATCGTTCAATGATTATTGCACAATATAGCTT	2	124	0	ATTTTTGCAC	    0.840463	-158
CACAAAAATATTATTCTTATCGTTCAATGATTA	2	140	0	TTTCTATCGT	    0.825056	-142
GGCGATCCGTTTATTTTTTTCACAAAAATATTA	2	160	0	TTTTTTTCAC	    0.971808	-122
TGATTTATTATTCATAGTATCACTTTTAGGTGA	2	243	0	TTTATATCAC	    0.911741	-39
          **  ** ******

Masking position 8
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	    0.997809	-258
ATCAACTTAAAGGCAAAGAC          	2	272	1	AGGCAAAGAC	    0.997809	-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

TTAATGCGGAGCATTCAAACCCA       	1	4	0	GCATTCAAAC	    0.912084	-140
TGAATGCTCCGCATTAAAGTTTTTCTAATT	1	17	1	GCATTAAAGT	    0.950257	-127
TTAAAAGTCAGCACTATAGCGCTATAAGAC	1	68	1	GCACTATAGC	    0.982166	-76
ATAACAATTAGTCTTATAGCGCTATAGTGC	1	78	0	GTCTTATAGC	     0.88135	-66
AAGCAGATATGCACTTTAGGCTCATGTTTC	2	75	0	GCACTTTAGG	    0.920366	-207
TAAACGGATCGCCCTCAATCCAAAACAAAA	2	180	1	GCCCTCAATC	     0.93868	-102
    GTCTTTGCCTTTAAGTTGATTTATTA	2	266	0	GCCTTTAAGT	    0.946901	-16
          **********

Masking position 8
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