AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00940_hpyl_reg_100.orf -o00940_hpyl_100.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

Motif number 1

   AGACAAGCCATGAAAAAAGAAAAGTC     	1	8	1	CCTAAAAAAA	    0.976257	-19
ATTAAGCCTAACTTTAAAAATCAAGCCTTCAAAA	2	14	0	ACTAAAATAA	    0.997811	-90
CAGAATTTTAACATAAAAGATTAAGCCTAACTTT	2	33	0	ACTAAAATAA	    0.997811	-71
AATATAAAATATATAAAATCTCAGAATTTTAACA	2	54	0	ATTAAACTAG	    0.955298	-50
CTAAAACCTAACGATAAATATAAAATATATAAAA	2	70	0	ACAAAAATAA	     0.99118	-34
         AACTTTAAACCTAAAACCTAACGAT	2	89	0	ACTAAACTAA	    0.997361	-15
          ** * *** ** **

Masking position 7
Map Score:   10.3678

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 54
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

CTAACTTTAAAAATCAAGCCTTCAAAAACC  	2	9	0	AATAAGCCTT	    0.988459	-95
TTAACATAAAAGATTAAGCCTAACTTTAAAAA	2	28	0	AATAAGCCTA	     0.99647	-76
AAAATCTCAGAATTTTAACATAAAAGATTAAG	2	42	0	ATTTAACATA	    0.932558	-62
CTAACGATAAATATAAAATATATAAAATCTCA	2	65	0	AATAAATATA	    0.956977	-39
  AACTTTAAACCTAAAACCTAACGATAAATA	2	84	0	ACTAAACCTA	    0.993524	-20
          * ** *******

Masking position 7
Map Score:   3.00123

Number of sites scoring better than the average of aligned sites = 177
Number in coding regions = 140
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

GCTTGATTTTTAAAGTTAGGCTTAATCTTT	2	22	1	TAAAGTTAGG	    0.994863	-82
ATTTTATATTTATCGTTAGGTTTTAGGTTT	2	78	1	TATCGTTAGG	    0.996515	-26
          **********

Masking position 6
Map Score:   0.698585

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 6
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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:   -7.57276e-14

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