AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iglpR_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	HP0654	296	conserved hypothetical protein
#2	HP0655	82	protective surface antigen D15
#3	HP0664	37	H. pylori predicted coding region HP0664

Motif number 1

TTAAACCAACACAAAGGAGATACT      	1	5	0	ACAAAGGAGA	    0.918284	-292
TAATTATAGCATAAATGATAATGAAAAAGT	1	44	1	ATAAATGATA	    0.862962	-253
AAAAATTTACAAAAATGAGAAAGAACACCG	1	96	1	AAAAATGAGA	    0.976663	-201
AATTAGGTAAAAAAAGGGGTTGGCATCAAT	1	177	1	AAAAAGGGGT	    0.935244	-120
AATAGGGGGTTAAAAGGGGATATTTTTATA	1	204	1	TAAAAGGGGA	    0.821657	-93
TTTTAGATTTAAGAATGCTTTTTACATATT	1	235	0	AAGAATGCTT	    0.903858	-62
TCTTAAATCTAAAAATGCTACAATGTTTAT	1	251	1	AAAAATGCTA	    0.982914	-46
AATCATTCTTAAAAACGCTAAAAATTA   	2	8	0	AAAAACGCTA	    0.974856	-75
TAGCGTTTTTAAGAATGATTAGTTATAATA	2	18	1	AAGAATGATT	    0.883109	-65
GATTAGTTATAATAACGCTACTAACAACAC	2	34	1	AATAACGCTA	    0.859383	-49
CAATCAGCTTAAAAAGGATATAAA      	3	24	1	AAAAAGGATA	     0.98294	-14
          **********

Masking position 5
Map Score:   12.6688

Number of sites scoring better than the average of aligned sites = 1110
Number in coding regions = 925
Number in noncoding regions = 185
Number of orfs with sites within 600 bp upstream = 164
Fraction of orfs with sites within 600 bp upstream = 0.0263412


Motif number 2

AGTTGTCCCATAATTATAGCATAAATGATA	1	34	1	TAATTATAGC	    0.907626	-263
GATAAAGCTTAGATTTTATCATAAAAATCT	1	137	1	AGATTTTATC	    0.963097	-160
TTAAAGATAAACATTGTAGCATTTTTAGAT	1	257	0	ACATTGTAGC	     0.97713	-40
         TAATTTTTAGCGTTTTTAAGA	2	2	1	AATTTTTAGC	    0.933612	-81
GCTTGAGTGTTGTTAGTAGCGTTATTATAA	2	40	0	TGTTAGTAGC	    0.912542	-43
TTTCCTTAATAGATTTTAGCTTGAGTGTTG	2	58	0	AGATTTTAGC	    0.989655	-25
CTTTTTAAGCTGATTGTATCCAATTTCGT 	3	10	0	TGATTGTATC	    0.969246	-28
          **********

Masking position 8
Map Score:   6.48742

Number of sites scoring better than the average of aligned sites = 548
Number in coding regions = 467
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 3

CATACTCTCATTTACTTTTTCATTATCATT	1	57	0	TTTACTTTTT	     0.94222	-240
CTTGATAAAGCTTAGATTTTATCATAAAAA	1	134	1	CTTAGATTTT	     0.93445	-163
ATTCTCATTAAATAGATTTTTATGATAAAA	1	150	0	AATAGATTTT	    0.927041	-147
AAGAATGCTTTTTACATATTATATAAAAAT	1	225	0	TTTACATATT	    0.863821	-72
TTGTAGCATTTTTAGATTTAAGAATGCTTT	1	244	0	TTTAGATTTA	    0.953376	-53
TAAATTGCCCTTTCGTTTTAAAGATAAACA	1	274	0	TTTCGTTTTA	    0.890279	-23
TTTAAGAATGATTAGTTATAATAACGCTAC	2	25	1	ATTAGTTATA	    0.765506	-58
TGATTTCCTTAATAGATTTTAGCTTGAGTG	2	61	0	AATAGATTTT	    0.927041	-22
      TTTATATCCTTTTTAAGCTGATTG	3	24	0	TATCCTTTTT	    0.807004	-14
          **********

Masking position 7
Map Score:   5.67226

Number of sites scoring better than the average of aligned sites = 1025
Number in coding regions = 825
Number in noncoding regions = 200
Number of orfs with sites within 600 bp upstream = 162
Fraction of orfs with sites within 600 bp upstream = 0.0260199


Motif number 4

ATGAGAGTATGAAAATTTTTAAAAATTTAC	1	76	1	GAAAATTTTT	    0.710337	-221
TCTCATTTTTGTAAATTTTTAAAAATTTTC	1	86	0	GTAAATTTTT	    0.944578	-211
TTCTCATTAAATAGATTTTTATGATAAAAT	1	149	0	ATAGATTTTT	    0.887788	-148
GGTTAAAAGGGGATATTTTTATATAATATG	1	211	1	GGATATTTTT	    0.961688	-86
          **********

Masking position 5
Map Score:   0.813754

Number of sites scoring better than the average of aligned sites = 163
Number in coding regions = 141
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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