AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -iaraC_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	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

       ATCGTCATAAAAACCTTGTTCTA	1	4	1	GTCATAAAAA	    0.859382	-135
AGTGGTCTTATTCTATCCAATTAGCCCTTG	1	36	1	TTCTATCCAA	    0.938077	-103
CCTTGAGCCACTCTTAAAAAGCGTTGTTTG	1	61	1	CTCTTAAAAA	    0.976665	-78
AATGAGCCATTTTTATCAAACAACGCTTTT	1	77	0	TTTTATCAAA	      0.7611	-62
TTTTAAAACTCTCTTTAAAATTTTACTTTA	1	118	0	CTCTTTAAAA	    0.986125	-21
TTTAAAGAGAGTTTTAAAAA          	1	129	1	GTTTTAAAAA	    0.738571	-10
ATCCAAAAAACCCTTAAAAA          	2	1	0	CCCTTAAAAA	     0.95719	-54
TAAGGGCTTATTCTATCCAAAAAACCCTTA	2	15	0	TTCTATCCAA	    0.938077	-40
     GTCAATCCTTTAAAATAAAATAAGG	2	40	0	TCCTTTAAAA	    0.947201	-15
     ATGCACTCTATCAAAAGTTTTAAGT	3	6	1	CTCTATCAAA	    0.987203	-49
  TTTAAACCCTTATTCAAACCACGATAAA	3	37	0	CTTATTCAAA	    0.890952	-18
          **********

Masking position 9
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

AAGACCACTATTAGAACAAGGTTTTTATGA	1	15	0	TTAGAACAAG	    0.984476	-124
GGCTAATTGGATAGAATAAGACCACTATTA	1	32	0	ATAGAATAAG	    0.996919	-107
TTAAGATACCATATAATGAGCCATTTTTAT	1	91	0	ATATAATGAG	    0.957783	-48
GGTTTTTTGGATAGAATAAGCCCTTATTTT	2	19	1	ATAGAATAAG	    0.996919	-36
ATCCTTTAAAATAAAATAAGGGCTTATTCT	2	31	0	ATAAAATAAG	    0.984134	-24
TTTATCGTGGTTTGAATAAGGGTTTAAA  	3	37	1	TTTGAATAAG	    0.977147	-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

   ATCGTCATAAAAACCTTGTTCTAATAG	1	8	1	TAAAAACCTT	    0.936498	-131
ATTCTATCCAATTAGCCCTTGAGCCACTCT	1	45	1	ATTAGCCCTT	    0.987998	-94
ATACCATATAATGAGCCATTTTTATCAAAC	1	86	0	ATGAGCCATT	    0.940481	-53
ATTCTATCCAAAAAACCCTTAAAAA     	2	6	0	AAAAACCCTT	    0.991938	-49
TTTGGATAGAATAAGCCCTTATTTTATTTT	2	24	1	ATAAGCCCTT	    0.997017	-31
TCAAACCACGATAAAAACTTAAAACTTTTG	3	22	0	ATAAAAACTT	    0.909974	-33
         TTTAAACCCTTATTCAAACCA	3	44	0	TTAAACCCTT	    0.992017	-11
          **********

Masking position 4
Map Score:   12.2445

Number of sites scoring better than the average of aligned sites = 759
Number in coding regions = 658
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

AACCTTGTTCTAATAGTGGTCTTATTCTAT	1	22	1	TAATAGTGGT	    0.990967	-117
CAACGCTTTTTAAGAGTGGCTCAAGGGCTA	1	57	0	TAAGAGTGGC	    0.987295	-82
CGTTGTTTGATAAAAATGGCTCATTATATG	1	82	1	TAAAAATGGC	    0.970884	-57
CTTTAAAATAAAATAAGGGCTTATTCTATC	2	28	0	AAATAAGGGC	    0.965089	-27
TTTTAAGTTTTTATCGTGGTTTGAATAAGG	3	28	1	TTATCGTGGT	    0.908227	-27
ATCGTGGTTTGAATAAGGGTTTAAA     	3	40	1	GAATAAGGGT	    0.963041	-15
          **********

Masking position 3
Map Score:   4.89013

Number of sites scoring better than the average of aligned sites = 336
Number in coding regions = 296
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


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