AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iaraC_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	HP1492	138	conserved hypothetical nifU-like protein
#2	HP1496	54	general stress protein (ctc)
#3	HP1498	54	H. pylori predicted coding region HP1498

Motif number 1

TAGAACAAGGTTTTTATGACGAT       	1	4	0	TTTTTATGAC	    0.859382	-135
CAAGGGCTAATTGGATAGAATAAGACCACT	1	36	0	TTGGATAGAA	    0.938077	-103
CAAACAACGCTTTTTAAGAGTGGCTCAAGG	1	61	0	TTTTTAAGAG	    0.976665	-78
AAAAGCGTTGTTTGATAAAAATGGCTCATT	1	77	1	TTTGATAAAA	      0.7611	-62
TAAAGTAAAATTTTAAAGAGAGTTTTAAAA	1	118	1	TTTTAAAGAG	    0.986125	-21
          TTTTTAAAACTCTCTTTAAA	1	129	0	TTTTTAAAAC	    0.738571	-10
          TTTTTAAGGGTTTTTTGGAT	2	1	1	TTTTTAAGGG	     0.95719	-54
TAAGGGTTTTTTGGATAGAATAAGCCCTTA	2	15	1	TTGGATAGAA	    0.938077	-40
CCTTATTTTATTTTAAAGGATTGAC     	2	40	1	TTTTAAAGGA	    0.947201	-15
ACTTAAAACTTTTGATAGAGTGCAT     	3	6	0	TTTGATAGAG	    0.987203	-49
TTTATCGTGGTTTGAATAAGGGTTTAAA  	3	37	1	TTTGAATAAG	    0.890952	-18
          **********

Masking position 2
Map Score:   16.6418

Number of sites scoring better than the average of aligned sites = 2547
Number in coding regions = 2240
Number in noncoding regions = 307
Number of orfs with sites within 600 bp upstream = 212
Fraction of orfs with sites within 600 bp upstream = 0.0340508


Motif number 2

TCATAAAAACCTTGTTCTAATAGTGGTCTT	1	15	1	CTTGTTCTAA	    0.985712	-124
TAATAGTGGTCTTATTCTATCCAATTAGCC	1	32	1	CTTATTCTAT	    0.997167	-107
ATAAAAATGGCTCATTATATGGTATCTTAA	1	91	1	CTCATTATAT	    0.961063	-48
AAAATAAGGGCTTATTCTATCCAAAAAACC	2	19	0	CTTATTCTAT	    0.997167	-36
AGAATAAGCCCTTATTTTATTTTAAAGGAT	2	31	1	CTTATTTTAT	    0.985397	-24
  TTTAAACCCTTATTCAAACCACGATAAA	3	37	0	CTTATTCAAA	    0.978951	-18
          **********

Masking position 5
Map Score:   13.3242

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 45
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

ACTATTAGAACAAGGTTTTTATGACGAT  	1	9	0	CAAGGTTTTT	    0.979792	-130
AAGAGTGGCTCAAGGGCTAATTGGATAGAA	1	46	0	CAAGGGCTAA	    0.980584	-93
      TTTTTAAGGGTTTTTTGGATAGAA	2	5	1	TAAGGGTTTT	    0.993298	-50
TAAAATAAAATAAGGGCTTATTCTATCCAA	2	25	0	TAAGGGCTTA	    0.761644	-30
TCAAAAGTTTTAAGTTTTTATCGTGGTTTG	3	21	1	TAAGTTTTTA	    0.931687	-34
GTGGTTTGAATAAGGGTTTAAA        	3	43	1	TAAGGGTTTA	     0.98364	-12
          **********

Masking position 3
Map Score:   12.0734

Number of sites scoring better than the average of aligned sites = 411
Number in coding regions = 359
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 4

AGAATAAGACCACTATTAGAACAAGGTTTT	1	20	0	CACTATTAGA	    0.968821	-119
GCCCTTGAGCCACTCTTAAAAAGCGTTGTT	1	59	1	CACTCTTAAA	    0.995125	-80
 TTTTTAAAACTCTCTTTAAAATTTTACTT	1	120	0	CTCTCTTTAA	    0.964275	-19
CTATCCAAAAAACCCTTAAAAA        	2	3	0	AACCCTTAAA	    0.934324	-52
       ATGCACTCTATCAAAAGTTTTAA	3	4	1	CACTCTATCA	    0.963524	-51
TTATTCAAACCACGATAAAAACTTAAAACT	3	26	0	CACGATAAAA	    0.943355	-29
          **********

Masking position 6
Map Score:   4.37231

Number of sites scoring better than the average of aligned sites = 566
Number in coding regions = 503
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 5

          **********

No masking
Map Score:   2.86649e-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:   2.86649e-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:   2.86649e-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