AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00940_hpyl_reg_300.orf -o00940_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

TGAAGGCTTGATTTTTAAAGTTAGGCTTAAT	2	17	1	ATTTTAAAGT	    0.601544	-87
AAAATCTCAGAATTTTAACATAAAAGATTAA	2	43	0	ATTTTAACAT	     0.95116	-61
TAAATATAAAATATATAAAATCTCAGAATTT	2	59	0	AATATAAAAT	    0.731296	-45
TATATATTTTATATTTATCGTTAGGTTTTAG	2	73	1	AATTTATCGT	    0.859641	-31
GTTAGGTTTTAGGTTTAAAGTT         	2	92	1	AGTTTAAAGT	    0.898944	-12
TTTTAAAGAGAGTTTTAAAAA          	3	1	0	ATTTTAAAAA	    0.962387	-138
CTTAAAGTAAAATTTTAAAGAGAGTTTTAAA	3	13	0	ATTTTAAAGA	     0.97077	-126
CATTATATGGTATCTTAAAGTAAAATTTTAA	3	26	0	TTCTTAAAGT	    0.853924	-113
ATAATGAGCCATTTTTATCAAACAACGCTTT	3	51	1	ATTTTATCAA	    0.890723	-88
CCCTTGAGCCACTCTTAAAAAGCGTTGTTTG	3	69	0	ATCTTAAAAA	    0.933467	-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

TTCTTTTTTCATGGCTTGTCT         	1	2	0	ATGGCTTGTC	    0.934577	-25
  GGTTTTTGAAGGCTTGATTTTTAAAGTT	2	9	1	AAGGCTTGAT	    0.973472	-95
TTTTTAAAGTTAGGCTTAATCTTTTATGTT	2	28	1	TAGGCTTAAT	    0.941935	-76
   TTTTTAAAACTCTCTTTAAAATTTTAC	3	8	1	AACTCTCTTT	    0.778868	-131
TTTGATAAAAATGGCTCATTATATGGTATC	3	43	0	ATGGCTCATT	    0.977551	-96
TTTATCAAACAACGCTTTTTAAGAGTGGCT	3	64	1	AACGCTTTTT	    0.958198	-75
GAGTGGCTCAAGGGCTAATTGGATAGAATA	3	86	1	AGGGCTAATT	    0.961174	-53
GTTCTAATAGTGGTCTTATTCTATCCAATT	3	102	0	TGGTCTTATT	    0.893647	-37
          **********

Masking position 6
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

        GACTTTTCTTTTTTCATGGCTT	1	15	0	CTTTTCTTTT	    0.953314	-12
TAGGCTTAATCTTTTATGTTAAAATTCTGA	2	38	1	CTTTTATGTT	    0.985937	-66
GATTTTATATATTTTATATTTATCGTTAGG	2	68	1	ATTTTATATT	    0.942949	-36
TTATCGTTAGGTTTTAGGTTTAAAGTT   	2	87	1	GTTTTAGGTT	    0.957169	-17
TCTCTTTAAAATTTTACTTTAAGATACCAT	3	21	1	ATTTTACTTT	    0.945005	-118
          **********

Masking position 5
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

    AGACAAGCCATGAAAAAAGAAAAGTC	1	7	1	GCCATGAAAA	    0.964635	-20
TAAAAATCAAGCCTTCAAAAACC       	2	4	0	GCCTTCAAAA	    0.984297	-100
ATTAAGCCTAACTTTAAAAATCAAGCCTTC	2	18	0	ACTTTAAAAA	    0.876925	-86
TTTAAAGAGAGTTTTAAAAA          	3	1	0	GTTTTAAAAA	    0.916987	-138
TTTTAAAACTCTCTTTAAAATTTTACTTTA	3	12	1	CTCTTTAAAA	    0.948112	-127
CCTTGAGCCACTCTTAAAAAGCGTTGTTTG	3	69	0	CTCTTAAAAA	    0.981162	-70
       ATCGTCATAAAAACCTTGTTCTA	3	126	0	GTCATAAAAA	     0.98034	-13
          **********

Masking position 7
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