AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -imetR_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	HP0181	257	H. pylori predicted coding region HP0181

Motif number 1

GCTATAATACACTAAAACAATCTCAAGGTTTC	1	22	0	ACTAAACAAC	    0.974671	-236
ATCTAAAATTCTTAAATTAAAATATAGCTATA	1	48	0	CTTAAATAAA	    0.948115	-210
AAAAACTACCCTTAAAAAAATCAATCTAAAAT	1	71	0	CTTAAAAAAC	    0.988033	-187
AATAACACAACTTAAAAAAAACTACCCTTAAA	1	87	0	CTTAAAAAAC	    0.988033	-171
ACCCATTACTCTTAAATCATGCCAATTCACAC	1	143	0	CTTAAACATC	    0.981896	-115
GTCATAGCGTCTTAAAACAAACACCCATTACT	1	165	0	CTTAAACAAC	    0.996706	-93
TAATTCAAACCCTAAACCCAAACCTTTCTCTC	1	217	0	CCTAAACCAA	    0.968554	-41
   AAGTAACGCTAAATCAATATAATTCAAAC	1	239	0	GCTAAACAAA	    0.957065	-19
          ****** *** *

Masking position 6
Map Score:   13.6686

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 328
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

TCTCAAGGTTTCAAAATTTAGCC       	1	4	0	TCAAAATTTA	    0.804997	-254
ATACACTAAAACAATCTCAAGGTTTCAAAA	1	18	0	ACAATCTCAA	    0.833806	-240
CTTAAAAAAAACTACCCTTAAAAAAATCAA	1	79	0	ACTACCCTTA	     0.95934	-179
GAAAATAATAACACAACTTAAAAAAAACTA	1	95	0	ACACAACTTA	    0.930482	-163
ATGCCAATTCACACTCTTTAGACTTGAAAT	1	127	0	ACACTCTTTA	     0.97978	-131
CTTAAAACAAACACCCATTACTCTTAAATC	1	157	0	ACACCCATTA	    0.940828	-101
AGACGCTATGACTATCTTTATGCGAGATAT	1	185	1	ACTATCTTTA	    0.947641	-73
TCAATATAATTCAAACCCTAAACCCAAACC	1	225	0	TCAAACCCTA	    0.925242	-33
          **********

Masking position 10
Map Score:   4.91239

Number of sites scoring better than the average of aligned sites = 831
Number in coding regions = 721
Number in noncoding regions = 110
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 3

      GGCTAAATTTTGAAACCTTGAGAT	1	5	1	AAATTTTGAA	    0.939202	-253
AATCAATCTAAAATTCTTAAATTAAAATAT	1	55	0	AAATTCTTAA	    0.913832	-203
TCAAGTCTAAAGAGTGTGAATTGGCATGAT	1	130	1	AGAGTGTGAA	    0.985056	-128
AGATAGTCATAGCGTCTTAAAACAAACACC	1	172	0	AGCGTCTTAA	    0.969307	-86
GTTTGGGTTTAGGGTTTGAATTATATTGAT	1	226	1	AGGGTTTGAA	    0.978724	-32
          **********

Masking position 5
Map Score:   1.50931

Number of sites scoring better than the average of aligned sites = 330
Number in coding regions = 288
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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:   -2.60469e-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