AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icspA_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	HP0698	187	H. pylori predicted coding region HP0698
#2	HP0699	39	H. pylori predicted coding region HP0699

Motif number 1

TGCTCAATCCTTTTTATGAAAGAGGCTTTATG	1	14	1	TTTTATGAAG	    0.929487	-174
TGCTAAAAGCTTGGGTTGATTTAACTCAAGCA	1	54	1	TTGGTTGATT	    0.991315	-134
TTGAAGAAAATTTGCTTGAGTTAAATCAACCC	1	66	0	TTTGTTGATT	    0.989531	-122
GCAGCCAAATTTGTTAGGATTGAAGAAAATTT	1	85	0	TTGTAGGATG	    0.961991	-103
CCTAACAAATTTGGCTGCAAATTAAAAAATTT	1	99	1	TTGGTGCAAT	    0.920265	-89
CTTTTTTCTTTTTTTTTGATTTAATACTAGGT	1	134	1	TTTTTTGATT	    0.983496	-54
CTTTTCCTTGTTAGGTGGAATTAAAATTATAC	1	164	0	TTAGTGGATT	    0.965707	-24
AAACCCCTTATTTTATTGAAAGTATAGTGATA	2	15	0	TTTTTTGAAG	    0.973225	-25
          **** **** **

Masking position 9
Map Score:   7.73732

Number of sites scoring better than the average of aligned sites = 804
Number in coding regions = 685
Number in noncoding regions = 119
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 2

TCTTTCATAAAAAGGATTGAGCAATC    	1	7	0	AAAGGATTGA	    0.965189	-181
TTTTTATGAAAGAGGCTTTATGCCTCTTGG	1	24	1	AGAGGCTTTA	    0.957826	-164
TCTTGGTGCTAAAAGCTTGGGTTGATTTAA	1	48	1	AAAAGCTTGG	    0.967005	-140
TTAGGATTGAAGAAAATTTGCTTGAGTTAA	1	74	0	AGAAAATTTG	    0.970938	-114
CTTCAATCCTAACAAATTTGGCTGCAAATT	1	92	1	AACAAATTTG	    0.936529	-96
GCTGCAAATTAAAAAATTTAAGCTTTTTTC	1	112	1	AAAAAATTTA	    0.961753	-76
          **********

Masking position 7
Map Score:   3.66381

Number of sites scoring better than the average of aligned sites = 1029
Number in coding regions = 919
Number in noncoding regions = 110
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 3

AGCCTCTTTCATAAAAAGGATTGAGCAATC	1	11	0	ATAAAAAGGA	    0.988972	-177
ATTAAATCAAAAAAAAAGAAAAAAGCTTAA	1	129	0	AAAAAAAGAA	    0.957576	-59
TTAATTCCACCTAACAAGGAAAAGCT    	1	172	1	CTAACAAGGA	    0.977883	-16
TACTTTCAATAAAATAAGGGGTTTTTT   	2	23	1	AAAATAAGGG	    0.967566	-17
          **********

Masking position 6
Map Score:   1.37316

Number of sites scoring better than the average of aligned sites = 326
Number in coding regions = 239
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 94
Fraction of orfs with sites within 600 bp upstream = 0.015098


Motif number 4

          **********

No masking
Map Score:   -4.52315e-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:   -4.52315e-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:   -4.52315e-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