AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_mixed18_hpyl_reg_100.orf -o303_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP01210	111	AE000511
#2	RHP01211	72	AE000511
#3	RHP01212	53	AE000511

Motif number 1

TTATTTAGCCAAAAACCATTTTGATCAAAG	1	41	1	AAAAACCATT	    0.995697	-71
TAGAAGATTTAAAAAGGCTTTT        	1	100	1	AAAAAGGCTT	    0.990799	-12
   GCGTTTTAAAAACCTTTGAGGGTTAAA	2	8	1	AAAAACCTTT	    0.985861	-65
TTTAAAACTCAAAAAGGATTGATA      	2	59	1	AAAAAGGATT	    0.995697	-14
CTTTTTCAAAAATAACCATTTCTTGTCTTT	3	28	0	AATAACCATT	    0.982893	-26
GTTATTTTTGAAAAAGGATTGA        	3	42	1	AAAAAGGATT	    0.995697	-12
          **********

Masking position 5
Map Score:   14.3731

Number of sites scoring better than the average of aligned sites = 235
Number in coding regions = 183
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 2

ATGCTCTTGATTTTAGAGCTTTGATCAAAAT	1	58	0	TTTTAGACTT	    0.984277	-54
  AAAAGCCTTTTTAAATCTTCTAATAAATT	1	93	0	TTTTAAACTT	    0.992855	-19
CCTCAAAGGTTTTTAAAACGC          	2	1	0	TTTTAAACGC	     0.99296	-72
TTTTACACTATTTTAACCCTCAAAGGTTTTT	2	18	0	TTTTAACCTC	     0.99296	-55
ATAGTAAAGATTTTAAAACTCAAAAAGGATT	2	48	1	TTTTAAACTC	    0.996816	-25
          ******* ***

Masking position 5
Map Score:   9.75683

Number of sites scoring better than the average of aligned sites = 235
Number in coding regions = 203
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

TCAAAGCTCTAAAATCAAGAGCATAGAAAA	1	65	1	AAAATCAAGA	    0.987339	-47
ATAGTGTAAAATAGTAAAGATTTTAAAACT	2	38	1	ATAGTAAAGA	    0.954932	-35
AAAGATTTTAAAACTCAAAAAGGATTGATA	2	53	1	AAACTCAAAA	    0.966768	-20
TTATCCTAAAAAAGACAAGAAATGGTTATT	3	18	1	AAAGACAAGA	    0.988261	-36
          **********

Masking position 7
Map Score:   1.86124

Number of sites scoring better than the average of aligned sites = 164
Number in coding regions = 151
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

GATCGTCATGGAGCATGAATGAGATGGCCTTT	1	11	1	GAGCTGAATA	    0.948761	-101
CTTGATTTTAGAGCTTTGATCAAAATGGTTTT	1	52	0	GAGCTTGATA	     0.97578	-60
CTAAAATCAAGAGCATAGAAAATTTATTAGAA	1	73	1	GAGCTAGAAA	    0.988306	-39
          GCGTTTTAAAAACCTTTGAGGG	2	1	1	GCGTTTAAAA	    0.949483	-72
AGGGTTAAAATAGTGTAAAATAGTAAAGATTT	2	29	1	TAGTTAAAAA	    0.942111	-44
AATCCTTTTTGAGTTTTAAAATCTTTACTATT	2	47	0	GAGTTTAAAT	    0.926928	-26
  GGTTTTGTTATCCTAAAAAAGACAAGAAAT	3	9	1	TATCTAAAAA	    0.878613	-45
AAGAAATGGTTATTTTTGAAAAAGGATTGA  	3	34	1	TATTTTGAAA	     0.85466	-20
          **** ***** *

Masking position 9
Map Score:   5.06426

Number of sites scoring better than the average of aligned sites = 1886
Number in coding regions = 1704
Number in noncoding regions = 182
Number of orfs with sites within 600 bp upstream = 129
Fraction of orfs with sites within 600 bp upstream = 0.0207196


Motif number 5

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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:   1.87173e-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