AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ilacI_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	HP0097	104	H. pylori predicted coding region HP0097
#2	HP0098	203	threonine synthase (thrC)

Motif number 1

CCTTATTCCTAATAAAATCTTAATTTTAAGTCAAA	1	24	1	AATAAACATT	    0.923962	-81
ATTTTAAGTCAAACTACACTATAATAAGGAAATTC	1	46	1	AAATACCAAT	    0.962055	-59
TAATAAGGAAATTCTAAACGAAAATTAAACTGAAT	1	67	1	ATTTAACAAT	    0.985071	-38
TTGCGGCAAAATTTTAAACCGCATTATAGTATTAT	2	45	1	ATTTAACATT	    0.981798	-159
GCATTATAGTATTATAAGCATAAATCAAAAATTAA	2	65	1	ATTTAACAAT	    0.988073	-139
CATAAATCAAAAATTAAACTGGATTAAAAAGACGA	2	83	1	AAATAACATT	    0.981892	-121
TAAAAGAGCGAATGTAACCTTAAATGGTTTTTTAA	2	131	0	AATTAACAAT	    0.982096	-73
CTACGACTTGAAATTATCCAAAAATAAAAAGGAAT	2	173	1	AAATATCAAT	    0.947884	-31
          *** *** *   ***

Masking position 6
Map Score:   11.068

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 97
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

GAATAAGGGCTTAAAAAAGAT         	1	2	0	TTAAAAAAGA	    0.873682	-103
AAATTAAGATTTTATTAGGAATAAGGGCTT	1	20	0	TTTATTAGGA	    0.869603	-85
AGTTTGACTTAAAATTAAGATTTTATTAGG	1	31	0	AAAATTAAGA	    0.729202	-74
AAACTACACTATAATAAGGAAATTCTAAAC	1	56	1	ATAATAAGGA	    0.987992	-49
AATTAAACTGAATGAAAGGAGTTTGA    	1	89	1	AATGAAAGGA	     0.89331	-16
AAATTTCATCATAGTAAGGCTGTGTT    	2	7	0	ATAGTAAGGC	    0.903815	-197
GCATTATAGTATTATAAGCATAAATCAAAA	2	65	1	ATTATAAGCA	    0.906573	-139
ATTAAACTGGATTAAAAAGACGATCAATCG	2	95	1	ATTAAAAAGA	    0.946711	-109
TTATCCAAAAATAAAAAGGAATCATTTT  	2	186	1	ATAAAAAGGA	    0.985247	-18
          **********

Masking position 7
Map Score:   8.52157

Number of sites scoring better than the average of aligned sites = 955
Number in coding regions = 740
Number in noncoding regions = 215
Number of orfs with sites within 600 bp upstream = 211
Fraction of orfs with sites within 600 bp upstream = 0.0338901


Motif number 3

AGTCAAACTACACTATAATAAGGAAATTCT	1	52	1	CACTATAATA	    0.781632	-53
CAAAAAATTTCATCATAGTAAGGCTGTGTT	2	11	0	CATCATAGTA	    0.974753	-193
TTTTAAACCGCATTATAGTATTATAAGCAT	2	56	1	CATTATAGTA	     0.89104	-148
CAATCGTTCTCATTAAAAAACCATTTAAGG	2	119	1	CATTAAAAAA	    0.910255	-85
          **********

Masking position 5
Map Score:   1.58235

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 23
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

TTAGGAATAAGGGCTTAAAAAAGAT     	1	6	0	GGGCTTAAAA	     0.99479	-99
TAGTGTAGTTTGACTTAAAATTAAGATTTT	1	37	0	TGACTTAAAA	    0.976586	-68
TTGCCGCAAAGGGCAAAAAATTTCATCATA	2	24	0	GGGCAAAAAA	     0.92077	-180
TACTATAATGCGGTTTAAAATTTTGCCGCA	2	46	0	CGGTTTAAAA	    0.973397	-158
AAAATTAAACTGGATTAAAAAGACGATCAA	2	92	1	TGGATTAAAA	     0.95944	-112
GGGTATGCTACGACTTGAAATTATCCAAAA	2	166	1	CGACTTGAAA	    0.959336	-38
          **********

Masking position 8
Map Score:   6.70245

Number of sites scoring better than the average of aligned sites = 733
Number in coding regions = 655
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 5

AAATTCTAAACGAAAATTAAACTGAATGAAA	1	75	1	CGAAAATAAA	    0.987794	-30
CCCTTTGCGGCAAAATTTTAAACCGCATTAT	2	41	1	CAAAATTTAA	    0.954744	-163
AAGCATAAATCAAAAATTAAACTGGATTAAA	2	80	1	CAAAAATAAA	     0.99279	-124
TGAAATTATCCAAAAATAAAAAGGAATCATT	2	181	1	CAAAAATAAA	    0.992822	-23
          ******* ***

Masking position 5
Map Score:   4.32376

Number of sites scoring better than the average of aligned sites = 89
Number in coding regions = 72
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 6

          **********

No masking
Map Score:   -8.21797e-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 7

          **********

No masking
Map Score:   -8.21797e-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 8

          **********

No masking
Map Score:   -8.21797e-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