AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -itorR_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	HP0404	80	protein kinase C inhibitor (SP:P16436)
#2	HP0406	25	H. pylori predicted coding region HP0406
#3	HP0407	103	biotin sulfoxide reductase (bisC)

Motif number 1

ATTATAGCTTTTTAAAAATAAAATATAAGGA	1	17	0	TTTAAAATAA	    0.951303	-64
TTTATTAAAGTTGTATTATAGCTTTTTAAAA	1	31	0	TTGTATATAG	    0.909974	-50
AAGGTTTTTCTTTTATTAAAGTTGTATTATA	1	42	0	TTTTATAAAG	    0.643212	-39
TAAAACTATTTTTAAGGAAAAAT        	2	13	1	TTTAAGAAAA	    0.919871	-13
          TTTTAAATTAACGCCCATGCT	3	1	1	TTTTAATTAA	    0.921463	-103
TTAGCGGTAATTTTAGGTGAATCTATGTTAG	3	41	1	TTTTAGTGAA	    0.943403	-63
ACACCCCAAATTCTAACATAGATTCACCTAA	3	53	0	TTCTAAATAG	    0.914218	-51
ATTTGGGGTGTTTTAACAGAATGCAAGCTTG	3	73	1	TTTTAAAGAA	    0.882592	-31
GAATGCAAGCTTGAAGGAGAATC        	3	91	1	TTGAAGAGAA	    0.948076	-13
          ****** ****

Masking position 5
Map Score:   8.44234

Number of sites scoring better than the average of aligned sites = 1513
Number in coding regions = 1171
Number in noncoding regions = 342
Number of orfs with sites within 600 bp upstream = 266
Fraction of orfs with sites within 600 bp upstream = 0.0427241


Motif number 2

TAAAGTTGTATTATAGCTTTTTAAAAATAAAA	1	25	0	TTATGCTTTT	    0.964325	-56
TTTGCTCCCTTTTAAGGTTTTTCTTTTATTAA	1	54	0	TTTAGGTTTT	    0.986652	-27
TGAGGGCTTATTAGCGGTAATTTTAGGTGAAT	3	31	1	TTAGGGTATT	    0.987633	-73
TATGTTAGAATTTGGGGTGTTTTAACAGAATG	3	64	1	TTTGGGTTTT	    0.995069	-40
          **** *** ***

Masking position 8
Map Score:   1.05138

Number of sites scoring better than the average of aligned sites = 423
Number in coding regions = 367
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

ATATTTTATTTTTAAAAAGCTATAATACAA	1	22	1	TTTAAAAAGC	    0.975514	-59
TTAAAAGGGAGCAAAAAAGC          	1	71	1	GCAAAAAAGC	    0.981419	-10
TAAAATTACCGCTAATAAGCCCTCAGCATG	3	26	0	GCTAATAAGC	    0.621879	-78
          **********

Masking position 5
Map Score:   1.85027

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 180
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

          **********

No masking
Map Score:   -2.32047e-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:   -2.32047e-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:   -2.32047e-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