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

Motif number 1

        AGTATCTCCTTTGTGTTGGTTTAAG	1	3	1	TTCCTTTGTG	    0.918665	-294
TGGTTTAAGTTGTCCCATAATTATAGCATAAAT	1	27	1	TTCCTAATTA	    0.908531	-270
TTACTTTTTCATTATCATTTATGCTATAATTAT	1	43	0	ATACTTTATG	    0.836297	-254
GCCGGTGTTCTTTCTCATTTTTGTAAATTTTTA	1	95	0	TTCCTTTTTG	    0.977025	-202
AAGCTTAGATTTTATCATAAAAATCTATTTAAT	1	141	1	TTACTAAAAA	    0.656972	-156
TATATAAAAATATCCCCTTTTAACCCCCTATTG	1	203	0	TTCCTTTTAA	    0.964341	-94
AGATAAACATTGTAGCATTTTTAGATTTAAGAA	1	250	0	TTACTTTTTA	    0.986413	-47
TGCTACAATGTTTATCTTTAAAACGAAAGGGCA	1	266	1	TTACTTAAAA	    0.885269	-31
     TAATTTTTAGCGTTTTTAAGAATGATTA	2	6	1	TTACTTTTTA	    0.986408	-77
GAGTGTTGTTAGTAGCGTTATTATAACTAATCA	2	33	0	ATACTTATTA	    0.913948	-50
        TTTATATCCTTTTTAAGCTGATTGT	3	23	0	TTACTTTTTA	    0.986311	-15
          * ** * ******

Masking position 8
Map Score:   12.8583

Number of sites scoring better than the average of aligned sites = 651
Number in coding regions = 518
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 114
Fraction of orfs with sites within 600 bp upstream = 0.0183103


Motif number 2

AAATGATAATGAAAAAGTAAATGAGAGTAT	1	56	1	GAAAAAGTAA	    0.850263	-241
ATTTTTATGATAAAATCTAAGCTTTATCAA	1	135	0	TAAAATCTAA	    0.979673	-162
ATTTTATCATAAAAATCTATTTAATGAGAA	1	149	1	AAAAATCTAT	    0.827634	-148
TATTTTTATATAATATGTAAAAAGCATTCT	1	224	1	TAATATGTAA	    0.891709	-73
AAAAGCATTCTTAAATCTAAAAATGCTACA	1	243	1	TTAAATCTAA	    0.932632	-54
ATGTTTATCTTTAAAACGAAAGGGCAATTT	1	273	1	TTAAAACGAA	    0.914033	-24
AGTAGCGTTATTATAACTAATCATTCTTAA	2	26	0	TTATAACTAA	    0.872033	-57
ACACTCAAGCTAAAATCTATTAAGGAAATC	2	60	1	TAAAATCTAT	    0.963842	-23
ACAATCAGCTTAAAAAGGATATAAA     	3	23	1	TAAAAAGGAT	    0.845723	-15
          **********

Masking position 5
Map Score:   8.07671

Number of sites scoring better than the average of aligned sites = 720
Number in coding regions = 567
Number in noncoding regions = 153
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 3

CATTTACTTTTTCATTATCATTTATGCTAT	1	49	0	TTCATTATCA	    0.935116	-248
TTAGCCGGTGTTCTTTCTCATTTTTGTAAA	1	101	0	TTCTTTCTCA	     0.92831	-196
ATAAAATCTAAGCTTTATCAAGCCATTAGC	1	126	0	AGCTTTATCA	    0.958087	-171
CTTTTTTTACCTAATTCTCATTAAATAGAT	1	163	0	CTAATTCTCA	    0.736418	-134
ATATGTAAAAAGCATTCTTAAATCTAAAAA	1	236	1	AGCATTCTTA	    0.985596	-61
TAAACATTGTAGCATTTTTAGATTTAAGAA	1	250	0	AGCATTTTTA	    0.929137	-47
ATTATAACTAATCATTCTTAAAAACGCTAA	2	17	0	ATCATTCTTA	    0.977344	-66
TGTTGTTAGTAGCGTTATTATAACTAATCA	2	33	0	AGCGTTATTA	    0.923744	-50
          **********

Masking position 10
Map Score:   6.75692

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 311
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

AATTTTTAAAAATTTTCATACTCTCATTTA	1	73	0	AATTTTCATA	    0.939781	-224
CATTTTTGTAAATTTTTAAAAATTTTCATA	1	83	0	AATTTTTAAA	     0.94415	-214
TAAAAGGGGATATTTTTATATAATATGTAA	1	214	1	TATTTTTATA	    0.928386	-83
AACATTGTAGCATTTTTAGATTTAAGAATG	1	248	0	CATTTTTAGA	     0.95407	-49
AAAATGCTACAATGTTTATCTTTAAAACGA	1	262	1	AATGTTTATC	    0.928297	-35
         TAATTTTTAGCGTTTTTAAGA	2	2	1	AATTTTTAGC	    0.974508	-81
          **********

Masking position 5
Map Score:   3.52075

Number of sites scoring better than the average of aligned sites = 333
Number in coding regions = 284
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


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