AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -irpoE_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	HP1015	111	H. pylori predicted coding region HP1015
#2	HP1017	97	amino acid permease (rocE)
#3	HP1018	47	H. pylori predicted coding region HP1018

Motif number 1

TGGATAATGTTTTGCAAGAAATATCT    	1	7	0	TTTGCAAGAA	    0.954582	-105
AACTCTTTGTTTTGGTGGATGTGGATAATG	1	28	0	TTTGGTGGAT	     0.82912	-84
AACAAGCATTTTTTAATGAATTGCAACTCT	1	52	0	TTTTAATGAA	    0.967366	-60
       TATTTTAAAAGAAGTTTTTAGCG	2	4	1	TTTAAAAGAA	    0.961456	-94
TTTAAGGTTTTTTTAAAGAACGCTAAAAAC	2	24	0	TTTTAAAGAA	    0.991143	-74
TTTTTAAGCGTTTTAAGGTTTTTTTAAAGA	2	35	0	TTTTAAGGTT	    0.968084	-63
         TTTTTAAAGATTAAATAGTAA	2	87	0	TTTTAAAGAT	     0.98987	-11
CTTTTCTTAATTTTGAAGTTTAGCAAATTT	3	12	1	TTTTGAAGTT	    0.946015	-36
GTTTAGCAAATTTTAAGGAAGTAACCATG 	3	29	1	TTTTAAGGAA	    0.991583	-19
          **********

Masking position 3
Map Score:   16.1354

Number of sites scoring better than the average of aligned sites = 1092
Number in coding regions = 949
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 125
Fraction of orfs with sites within 600 bp upstream = 0.0200771


Motif number 2

AATGTTTTGCAAGAAATATCT         	1	2	0	AAGAAATATC	    0.937843	-110
ATTTCTTGCAAAACATTATCCACATCCACC	1	15	1	AAACATTATC	    0.939051	-97
CCACCAAAACAAAGAGTTGCAATTCATTAA	1	40	1	AAAGAGTTGC	    0.955401	-72
CAAAGGGGCGAAAAAATAGCCCAACAAGCA	1	74	0	AAAAAATAGC	    0.990211	-38
        TAACAGAATAGCCCCACACAAA	1	100	0	ACAGAATAGC	    0.962737	-12
AAAACGCTTAAAAAACTATCGCTTGATCAA	2	51	1	AAAAACTATC	    0.966366	-47
GTTACTTCCTTAAAATTTGCTAAACTTCAA	3	24	0	TAAAATTTGC	    0.859494	-24
          **********

Masking position 5
Map Score:   4.52198

Number of sites scoring better than the average of aligned sites = 791
Number in coding regions = 697
Number in noncoding regions = 94
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 3

TTTTTTAAAGAACGCTAAAAACTTCTTTTA	2	16	0	AACGCTAAAA	    0.991989	-82
AAAACCTTAAAACGCTTAAAAAACTATCGC	2	43	1	AACGCTTAAA	    0.995441	-55
     TTTTTAAAGATTAAATAGTAAAAGA	2	83	0	AAAGATTAAA	    0.967051	-15
          **********

Masking position 8
Map Score:   2.30653

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 156
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

AAAAATGCTTGTTGGGCTATTTTTTCGCCC	1	69	1	GTTGGGCTAT	    0.996507	-43
GCCCCTTTGTGTGGGGCTATTCTGTTA   	1	95	1	GTGGGGCTAT	    0.997247	-17
          **********

Masking position 8
Map Score:   1.40584

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 7
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

AATTCATTAAAAAATGCTTGTTGGGCTATT	1	60	1	AAAATGCTTG	    0.987989	-52
CGTTCTTTAAAAAAACCTTAAAACGCTTAA	2	32	1	AAAAACCTTA	    0.967813	-66
TTAAATAGTAAAAGAGCTTGATCAAGCGAT	2	68	0	AAAGAGCTTG	    0.980462	-30
          **********

Masking position 3
Map Score:   0.2981

Number of sites scoring better than the average of aligned sites = 162
Number in coding regions = 135
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 6

          **********

No masking
Map Score:   -4.09683e-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:   -4.09683e-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:   -4.09683e-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