AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -igcvA_hpyl_opreg_300.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	HP0992	199	H. pylori predicted coding region HP0992

Motif number 1

AAATTTGCTAAACTACAATCAAATCAATTTAGGG	1	20	0	AATAACAAAT	    0.993786	-180
ATAACTAATTAAGTCAAACCAAAACCAACACAAA	1	52	0	AATAACAAAA	    0.990102	-148
TTAGTTATAAAAGAATAACCAAATTCTACTAAAT	1	78	1	AAAAACAAAT	    0.983263	-122
AAATTCTACTAAATACATACAAAATAACTTAATA	1	98	1	AATATCAAAA	    0.947081	-102
AAGAAATACTAATAACAATTAAATATTAAGTTAT	1	121	0	AAAAATAAAT	     0.95202	-79
TATAGCATAGAAATTTAAAGAAATACTAATAACA	1	138	0	AATAAGAAAT	    0.988207	-62
CTTTTAACTTAACTTGAATTGTAATCATTATAGC	1	166	0	AATAATGTAA	    0.774282	-34
AATTCAAGTTAAGTTAAAAGGAATAGAAAA    	1	180	1	AATAAGGAAT	    0.979381	-20
          ** *  ** *****

Masking position 7
Map Score:   10.2295

Number of sites scoring better than the average of aligned sites = 308
Number in coding regions = 225
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 2

TTGGTTTGACTTAATTAGTTATAAAAGAAT	1	64	1	TTAATTAGTT	     0.96119	-136
TAGAATTTGGTTATTCTTTTATAACTAATT	1	76	0	TTATTCTTTT	    0.729422	-124
TATTTTGTATGTATTTAGTAGAATTTGGTT	1	94	0	GTATTTAGTA	    0.981411	-106
AAATATTAAGTTATTTTGTATGTATTTAGT	1	105	0	TTATTTTGTA	    0.950023	-95
CTAATAACAATTAAATATTAAGTTATTTTG	1	117	0	TTAAATATTA	    0.848345	-83
ATATTTAATTGTTATTAGTATTTCTTTAAA	1	129	1	GTTATTAGTA	    0.934525	-71
AACTTGAATTGTAATCATTATAGCATAGAA	1	160	0	GTAATCATTA	    0.957261	-40
          **********

Masking position 2
Map Score:   4.57624

Number of sites scoring better than the average of aligned sites = 152
Number in coding regions = 110
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

GTAGTTTAGCAAATTTTGTGTTGGTTTTGG	1	38	1	AAATTTTGTG	      0.9353	-162
AAGAATAACCAAATTCTACTAAATACATAC	1	88	1	AAATTCTACT	     0.96425	-112
AATAACAATTAAATATTAAGTTATTTTGTA	1	115	0	AAATATTAAG	    0.957255	-85
AAATTTAAAGAAATACTAATAACAATTAAA	1	132	0	AAATACTAAT	    0.957252	-68
TATTTCTTTAAATTTCTATGCTATAATGAT	1	147	1	AATTTCTATG	    0.956467	-53
          **********

Masking position 4
Map Score:   1.40933

Number of sites scoring better than the average of aligned sites = 234
Number in coding regions = 188
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

          **********

No masking
Map Score:   -2.7468e-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:   -2.7468e-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:   -2.7468e-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