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

Motif number 1

AAGTATTTTGAAAATTCCTCCCTACA     	1	6	0	AAAATTCTCC	    0.912228	-295
AGGAATTTTCAAAATACTTCCTATTTCCTTA	1	18	1	AAAATACTCC	    0.963255	-283
TTTCCTTAAGAAAATGAATTTAAAAATCAAA	1	41	1	AAAATGATTT	    0.553878	-260
AATGAATTTAAAAATCAAACTTAAAAAATGA	1	53	1	AAAATCAACT	    0.954144	-248
TCAAACTTAAAAAATGAGTTTTATCATTAAA	1	67	1	AAAATGATTT	    0.678081	-234
TTTTATCATTAAAATAAAATCTTAAAACGAT	1	85	1	AAAATAAATC	    0.961988	-216
TTAAAACGATAAAATCAAGCCATTAAAATCC	1	106	1	AAAATCAGCC	    0.960444	-195
TCAAGCCATTAAAATCCCTTTTTTAAAAAAT	1	120	1	AAAATCCTTT	    0.941344	-181
TAGGAAAGCCAAAAACAGATCATAATCCCCT	1	173	1	AAAAACAATC	    0.874059	-128
CCTAGATCTTAAATTAAAACCCACTAGCCTT	1	201	1	AAATTAAACC	    0.734366	-100
ATCCGCATGACAAATCCCTTCAAAAATGATA	1	249	1	CAAATCCTTC	    0.912249	-52
AATCCCTTCAAAAATGATATAATAGACTTGA	1	261	1	AAAATGAATA	    0.823999	-40
   TTTCCTTAAAATGAGTTCATCAAGTCTA	1	283	0	AAAATGATTC	    0.968922	-18
          ******* ***

Masking position 3
Map Score:   16.8971

Number of sites scoring better than the average of aligned sites = 1174
Number in coding regions = 1031
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 2

TGTAGGGAGGAATTTTCAAAATACTTCCTA	1	11	1	AATTTTCAAA	    0.938263	-290
TAAGAAAATGAATTTAAAAATCAAACTTAA	1	47	1	AATTTAAAAA	     0.88618	-254
TTTAAAAATCAAACTTAAAAAATGAGTTTT	1	59	1	AAACTTAAAA	    0.949619	-242
ATTTTATTTTAATGATAAAACTCATTTTTT	1	75	0	AATGATAAAA	     0.92826	-226
ATTAAAATAAAATCTTAAAACGATAAAATC	1	92	1	AATCTTAAAA	    0.983511	-209
GGGATCACTCAATTTTTTAAAAAAGGGATT	1	132	0	AATTTTTTAA	    0.936212	-169
TGGCTTTCCTAAATTTTTAATAGGGATCAC	1	154	0	AAATTTTTAA	    0.822632	-147
TATTCTCACTAATCTTATAAGGCTAGTGGG	1	220	0	AATCTTATAA	    0.979763	-81
TCCCTTCAAAAATGATATAATAGACTTGAT	1	263	1	AATGATATAA	    0.913066	-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

AAATAAAATCTTAAAACGATAAAATCAAGC	1	96	1	TTAAAACGAT	    0.904995	-205
AAAAAGGGATTTTAATGGCTTGATTTTATC	1	113	0	TTTAATGGCT	    0.876124	-188
CAATTTTTTAAAAAAGGGATTTTAATGGCT	1	123	0	AAAAAGGGAT	    0.875572	-178
CCTAAATTTTTAATAGGGATCACTCAATTT	1	147	0	TAATAGGGAT	    0.963005	-154
CTCACTAATCTTATAAGGCTAGTGGGTTTT	1	216	0	TTATAAGGCT	    0.962415	-85
TATATCATTTTTGAAGGGATTTGTCATGCG	1	252	0	TTGAAGGGAT	    0.972298	-49
GATGAACTCATTTTAAGGAAA         	1	290	1	TTTTAAGGAA	    0.808948	-11
          **********

Masking position 5
Map Score:   2.10678

Number of sites scoring better than the average of aligned sites = 1532
Number in coding regions = 1325
Number in noncoding regions = 207
Number of orfs with sites within 600 bp upstream = 168
Fraction of orfs with sites within 600 bp upstream = 0.0269836


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