AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -imetR_hpyl_opreg_100.orf -g0.389 -x5 
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 =  	0.389
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HP0181	257	H. pylori predicted coding region HP0181

Motif number 1

TATAATACACTAAAACAATCTCAAGGTTTC	1	22	0	TAAAACAATC	    0.992175	-236
CTAAAATTCTTAAATTAAAATATAGCTATA	1	48	0	TAAATTAAAA	    0.853849	-210
AAACTACCCTTAAAAAAATCAATCTAAAAT	1	71	0	TAAAAAAATC	    0.971898	-187
TAACACAACTTAAAAAAAACTACCCTTAAA	1	87	0	TAAAAAAAAC	    0.978282	-171
CCATTACTCTTAAATCATGCCAATTCACAC	1	143	0	TAAATCATGC	    0.930217	-115
CATAGCGTCTTAAAACAAACACCCATTACT	1	165	0	TAAAACAAAC	     0.99398	-93
TAAATCAATATAATTCAAACCCTAAACCCA	1	229	0	TAATTCAAAC	     0.96731	-29
 AAGTAACGCTAAATCAATATAATTCAAAC	1	239	0	TAAATCAATA	    0.966648	-19
          **********

Masking position 7
Map Score:   13.3799

Number of sites scoring better than the average of aligned sites = 293
Number in coding regions = 245
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

AATCTCAAGGTTTCAAAATTTAGCC       	1	4	0	TTTAAAATTA	    0.840782	-254
CTTGAGATTGTTTTAGTGTATTATAGCTATAT	1	27	1	TTTAGTGTAT	     0.97211	-231
TATATTTTAATTTAAGAATTTTAGATTGATTT	1	54	1	TTTAGAATTT	     0.98132	-204
GATTGATTTTTTTAAGGGTAGTTTTTTTTAAG	1	77	1	TTTAGGGTAT	     0.98101	-181
AGGGTAGTTTTTTTTAAGTTGTGTTATTATTT	1	91	1	TTTTAAGTTT	    0.916013	-167
AGACTTGAAATTTGAAAATAATAACACAACTT	1	106	0	TTTAAAATAT	    0.970687	-152
ATTGGCATGATTTAAGAGTAATGGGTGTTTGT	1	149	1	TTTAGAGTAT	    0.992964	-109
          *** ****** *

Masking position 9
Map Score:   6.32816

Number of sites scoring better than the average of aligned sites = 388
Number in coding regions = 305
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

GCTATATTTTAATTTAAGAATTTTAGATTG	1	52	1	AATTTAAGAA	     0.86036	-206
TAGATTGATTTTTTTAAGGGTAGTTTTTTT	1	75	1	TTTTTAAGGG	    0.920688	-183
CAAATTTCAAGTCTAAAGAGTGTGAATTGG	1	124	1	GTCTAAAGAG	    0.904486	-134
GAATTGGCATGATTTAAGAGTAATGGGTGT	1	147	1	GATTTAAGAG	    0.992703	-111
ATGGGTGTTTGTTTTAAGACGCTATGACTA	1	169	1	GTTTTAAGAC	    0.726964	-89
CTTTATGCGAGATATATGAGAGAAAGGTTT	1	200	1	GATATATGAG	    0.911293	-58
          **********

Masking position 6
Map Score:   2.31725

Number of sites scoring better than the average of aligned sites = 663
Number in coding regions = 574
Number in noncoding regions = 89
Number of orfs with sites within 600 bp upstream = 75
Fraction of orfs with sites within 600 bp upstream = 0.0120463


Motif number 4

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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:   -2.60469e-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