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

Motif number 1

AAATTTGCTAAACTACAATCAAATCAATTTAGGGA	1	19	0	AATAAAAATC	    0.991748	-181
ATAACTAATTAAGTCAAACCAAAACCAACACAAAA	1	51	0	AATAAAAAAC	    0.961676	-149
TGACTTAATTAGTTATAAAAGAATAACCAAATTCT	1	70	1	AGTAAGAATA	    0.973806	-130
AAGAATAACCAAATTCTACTAAATACATACAAAAT	1	88	1	AATTAAAATA	    0.973847	-112
AAGAAATACTAATAACAATTAAATATTAAGTTATT	1	120	0	AAAAAAAATA	    0.973839	-80
TATAGCATAGAAATTTAAAGAAATACTAATAACAA	1	137	0	AATAAAAATA	    0.994299	-63
AATTCAAGTTAAGTTAAAAGGAATAGAAAA     	1	180	1	AATAAGAATA	     0.99163	-20
          ** *  **  *****

Masking position 8
Map Score:   9.38952

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 72
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

TTATCCTCCCTAAATTGATTTGATTGTAGT	1	13	1	TAAATTGATT	    0.932088	-187
GGTTTTGGTTTGACTTAATTAGTTATAAAA	1	60	1	TGACTTAATT	    0.959772	-140
TATAAAAGAATAACCAAATTCTACTAAATA	1	83	1	TAACCAAATT	    0.956085	-117
CAAATTCTACTAAATACATACAAAATAACT	1	97	1	TAAATACATA	    0.889873	-103
ACATACAAAATAACTTAATATTTAATTGTT	1	112	1	TAACTTAATA	    0.983406	-88
CATAGAAATTTAAAGAAATACTAATAACAA	1	137	0	TAAAGAAATA	    0.890048	-63
CTATTCCTTTTAACTTAACTTGAATTGTAA	1	176	0	TAACTTAACT	    0.959772	-24
          **********

Masking position 3
Map Score:   4.88356

Number of sites scoring better than the average of aligned sites = 132
Number in coding regions = 77
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

TTGCTAAACTACAATCAAATCAATTTAGGG	1	20	0	ACAATCAAAT	    0.866957	-180
AAGAATAACCAAATTCTACTAAATACATAC	1	88	1	AAATTCTACT	    0.859986	-112
TCTACTAAATACATACAAAATAACTTAATA	1	102	1	ACATACAAAA	    0.946752	-98
AAATTTAAAGAAATACTAATAACAATTAAA	1	132	0	AAATACTAAT	    0.962952	-68
AATCATTATAGCATAGAAATTTAAAGAAAT	1	148	0	GCATAGAAAT	    0.974077	-52
AACTTAACTTGAATTGTAATCATTATAGCA	1	165	0	GAATTGTAAT	    0.948327	-35
AAGTTAAAAGGAATAGAAAA          	1	190	1	GAATAGAAAA	    0.931208	-10
          **********

Masking position 3
Map Score:   4.59474

Number of sites scoring better than the average of aligned sites = 427
Number in coding regions = 384
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


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