AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00053_hpyl_reg_300.orf -o00053_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -x5 -e 
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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP1483	26	gerC2 protein (gerC2)
#2	HP1490	103	hemolysin
#3	HP1491	138	phosphate permease

Motif number 1

ATTAAGCCTAACTTTAAAAATCAAGCCTTCA	2	17	0	ACTTTAAAAT	    0.595154	-87
TTAATCTTTTATGTTAAAATTCTGAGATTTT	2	43	1	ATGTTAAAAT	    0.950668	-61
AAATTCTGAGATTTTATATATTTTATATTTA	2	59	1	ATTTTATATT	    0.747258	-45
CTAAAACCTAACGATAAATATAAAATATATA	2	73	0	ACGATAAATT	     0.86939	-31
         AACTTTAAACCTAAAACCTAAC	2	92	0	ACTTTAAACT	    0.896777	-12
          TTTTTAAAACTCTCTTTAAAA	3	1	1	TTTTTAAAAT	    0.962959	-138
TTTAAAACTCTCTTTAAAATTTTACTTTAAG	3	13	1	TCTTTAAAAT	    0.970678	-126
TTAAAATTTTACTTTAAGATACCATATAATG	3	26	1	ACTTTAAGAA	    0.863744	-113
AAAGCGTTGTTTGATAAAAATGGCTCATTAT	3	51	0	TTGATAAAAT	    0.898283	-88
CAAACAACGCTTTTTAAGAGTGGCTCAAGGG	3	69	1	TTTTTAAGAT	    0.936205	-70
          ********* *

Masking position 6
Map Score:   12.411

Number of sites scoring better than the average of aligned sites = 1104
Number in coding regions = 861
Number in noncoding regions = 243
Number of orfs with sites within 600 bp upstream = 197
Fraction of orfs with sites within 600 bp upstream = 0.0316415


Motif number 2

         AGACAAGCCATGAAAAAAGAA	1	2	1	GACAAGCCAT	    0.925833	-25
AACTTTAAAAATCAAGCCTTCAAAAACC  	2	9	0	ATCAAGCCTT	    0.969765	-95
AACATAAAAGATTAAGCCTAACTTTAAAAA	2	28	0	ATTAAGCCTA	    0.934105	-76
GTAAAATTTTAAAGAGAGTTTTAAAAA   	3	8	0	AAAGAGAGTT	    0.754888	-131
GATACCATATAATGAGCCATTTTTATCAAA	3	43	1	AATGAGCCAT	    0.974407	-96
AGCCACTCTTAAAAAGCGTTGTTTGATAAA	3	64	0	AAAAAGCGTT	    0.952464	-75
TATTCTATCCAATTAGCCCTTGAGCCACTC	3	86	0	AATTAGCCCT	    0.955816	-53
AATTGGATAGAATAAGACCACTATTAGAAC	3	102	1	AATAAGACCA	    0.880133	-37
          **********

Masking position 5
Map Score:   4.30659

Number of sites scoring better than the average of aligned sites = 2268
Number in coding regions = 2048
Number in noncoding regions = 220
Number of orfs with sites within 600 bp upstream = 156
Fraction of orfs with sites within 600 bp upstream = 0.0250562


Motif number 3

AAGCCATGAAAAAAGAAAAGTC        	1	15	1	AAAAGAAAAG	    0.954913	-12
TCAGAATTTTAACATAAAAGATTAAGCCTA	2	38	0	AACATAAAAG	    0.986435	-66
CCTAACGATAAATATAAAATATATAAAATC	2	68	0	AATATAAAAT	    0.944862	-36
   AACTTTAAACCTAAAACCTAACGATAA	2	87	0	AACCTAAAAC	    0.958641	-17
ATGGTATCTTAAAGTAAAATTTTAAAGAGA	3	21	0	AAAGTAAAAT	    0.946872	-118
          **********

Masking position 6
Map Score:   2.06123

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 222
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 4

GACTTTTCTTTTTTCATGGCTTGTCT    	1	7	0	TTTTCATGGC	    0.968762	-20
       GGTTTTTGAAGGCTTGATTTTTA	2	4	1	TTTTGAAGGC	    0.986161	-100
GAAGGCTTGATTTTTAAAGTTAGGCTTAAT	2	18	1	TTTTTAAAGT	    0.889566	-86
          TTTTTAAAACTCTCTTTAAA	3	1	1	TTTTTAAAAC	    0.914096	-138
TAAAGTAAAATTTTAAAGAGAGTTTTAAAA	3	12	0	TTTTAAAGAG	    0.954048	-127
CAAACAACGCTTTTTAAGAGTGGCTCAAGG	3	69	1	TTTTTAAGAG	    0.982753	-70
TAGAACAAGGTTTTTATGACGAT       	3	126	1	TTTTTATGAC	    0.982639	-13
          **********

Masking position 6
Map Score:   9.59552

Number of sites scoring better than the average of aligned sites = 756
Number in coding regions = 649
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 5

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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:   1.23224e-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