AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifadR_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	HP0836	300	H. pylori predicted coding region HP0836

Motif number 1

AGTATTTTGAAAATTCCTCCCTACA        	1	3	0	AAATTCCCCA	    0.969625	-298
AGGAATTTTCAAAATACTTCCTATTTCCTTAAG	1	18	1	AAAATACCCA	    0.962025	-283
TTTGATTTTTAAATTCATTTTCTTAAGGAAATA	1	39	0	AAATTCATTT	    0.915248	-262
AATGAATTTAAAAATCAAACTTAAAAAATGAGT	1	53	1	AAAATCACTA	    0.972351	-248
TCAAACTTAAAAAATGAGTTTTATCATTAAAAT	1	67	1	AAAATGATTA	    0.899273	-234
TTTTATCATTAAAATAAAATCTTAAAACGATAA	1	85	1	AAAATAATCT	    0.963021	-216
TTAAAACGATAAAATCAAGCCATTAAAATCCCT	1	106	1	AAAATCACCT	    0.990921	-195
TCAAGCCATTAAAATCCCTTTTTTAAAAAATTG	1	120	1	AAAATCCTTT	    0.925983	-181
TAGGAAAGCCAAAAACAGATCATAATCCCCTAG	1	173	1	AAAAACATCT	    0.915399	-128
CCTAGATCTTAAATTAAAACCCACTAGCCTTAT	1	201	1	AAATTAACCA	    0.916307	-100
ATCCGCATGACAAATCCCTTCAAAAATGATATA	1	249	1	CAAATCCTCA	    0.930098	-52
   TTTCCTTAAAATGAGTTCATCAAGTCTATT	1	281	0	AAAATGATCT	    0.966246	-20
          *******  ** *

Masking position 3
Map Score:   16.3079

Number of sites scoring better than the average of aligned sites = 1914
Number in coding regions = 1685
Number in noncoding regions = 229
Number of orfs with sites within 600 bp upstream = 160
Fraction of orfs with sites within 600 bp upstream = 0.0256987


Motif number 2

TGTAGGGAGGAATTTTCAAAATACTTCCTA	1	11	1	AATTTTCAAA	     0.93552	-290
TAAGAAAATGAATTTAAAAATCAAACTTAA	1	47	1	AATTTAAAAA	    0.881416	-254
TTTAAAAATCAAACTTAAAAAATGAGTTTT	1	59	1	AAACTTAAAA	    0.947353	-242
ATTTTATTTTAATGATAAAACTCATTTTTT	1	75	0	AATGATAAAA	    0.925108	-226
ATTAAAATAAAATCTTAAAACGATAAAATC	1	92	1	AATCTTAAAA	    0.982742	-209
GGGATCACTCAATTTTTTAAAAAAGGGATT	1	132	0	AATTTTTTAA	    0.933384	-169
TGGCTTTCCTAAATTTTTAATAGGGATCAC	1	154	0	AAATTTTTAA	     0.81576	-147
TATTCTCACTAATCTTATAAGGCTAGTGGG	1	220	0	AATCTTATAA	    0.978822	-81
TCCCTTCAAAAATGATATAATAGACTTGAT	1	263	1	AATGATATAA	    0.909312	-38
          **********

Masking position 2
Map Score:   11.6601

Number of sites scoring better than the average of aligned sites = 821
Number in coding regions = 652
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 3

TTAAATTCATTTTCTTAAGGAAATAGGAAGTA	1	32	0	TTTTAAGGAA	    0.929652	-269
TTTAAGATTTTATTTTAATGATAAAACTCATT	1	79	0	TTTTAATGAT	    0.842958	-222
TAAAATAAAATCTTAAAACGATAAAATCAAGC	1	94	1	TTAAAACGAT	    0.870043	-207
CTCAATTTTTTAAAAAAGGGATTTTAATGGCT	1	123	0	TAAAAGGGAT	    0.893013	-178
TTCCTAAATTTTTAATAGGGATCACTCAATTT	1	147	0	TTATAGGGAT	    0.988616	-154
TTTAATTTAAGATCTAGGGGATTATGATCTGT	1	187	0	GTTAGGGGAT	    0.828684	-114
TTCTCACTAATCTTATAAGGCTAGTGGGTTTT	1	216	0	TTATAAGGCT	    0.933634	-85
TGAAGGGATTTGTCATGCGGATATTCTCACTA	1	239	0	TTATGCGGAT	    0.913836	-62
ATTATATCATTTTTGAAGGGATTTGTCATGCG	1	252	0	TTGAAGGGAT	    0.955928	-49
TTGATGAACTCATTTTAAGGAAA         	1	288	1	CTTTAAGGAA	    0.780514	-13
          * * ********

Masking position 10
Map Score:   3.62442

Number of sites scoring better than the average of aligned sites = 1422
Number in coding regions = 1209
Number in noncoding regions = 213
Number of orfs with sites within 600 bp upstream = 169
Fraction of orfs with sites within 600 bp upstream = 0.0271442


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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