AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i299_mixed14_hpyl_reg_300.orf -o299_hpyl_300.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	RHP00146	68	AE000511
#2	RHP00147	207	AE000511

Motif number 1

ATGCAAAATGACTTAAAACTAGCCCCTTT 	1	10	0	ACTTAAAACT	    0.968854	-59
TGATTGTAATCCTTAAAACTCATTTAGGAG	1	47	0	CCTTAAAACT	    0.975331	-22
TCTTAGTGGCGTTTAAGAATAAGTTAAGAT	2	15	0	GTTTAAGAAT	    0.925774	-193
CACTAAGAGCGCTAAAAAATGGGGTTTTTA	2	37	1	GCTAAAAAAT	    0.966333	-171
AAAAAATGGGGTTTTTAAATTTTCGCGCAA	2	50	1	GTTTTTAAAT	    0.584093	-158
TTAAAACGACCTTTATAAATAAAAATTAAA	2	98	0	CTTTATAAAT	    0.562185	-110
AAATTTTAGGGTTTAAAACGACCTTTATAA	2	110	0	GTTTAAAACG	    0.945824	-98
AAACCCTAAAATTTTAAAATACCATTTTTG	2	126	1	ATTTTAAAAT	    0.495144	-82
CAAACCAATCATTCAAAAATGGTATTTTAA	2	139	0	ATTCAAAAAT	    0.673011	-69
CTCAAAATAAGCTAAAAACTACCAACACCA	2	171	0	GCTAAAAACT	    0.968961	-37
          **********

Masking position 3
Map Score:   11.2978

Number of sites scoring better than the average of aligned sites = 1440
Number in coding regions = 1204
Number in noncoding regions = 236
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


Motif number 2

CAAAATGACTTAAAACTAGCCCCTTT    	1	7	0	TAAAACTAGC	    0.972817	-62
TAACTTATTCTTAAACGCCACTAAGAGCGC	2	19	1	TTAAACGCCA	    0.920521	-189
CGCGAAAATTTAAAAACCCCATTTTTTAGC	2	47	0	TAAAAACCCC	    0.962473	-161
TTTTAGGGTTTAAAACGACCTTTATAAATA	2	107	0	TAAAACGACC	      0.9941	-101
CCCTAAAATTTTAAAATACCATTTTTGAAT	2	129	1	TTAAAATACC	    0.965832	-79
AAAATAAGCTAAAAACTACCAACACCATAC	2	168	0	AAAAACTACC	    0.974687	-40
          **********

Masking position 5
Map Score:   5.40115

Number of sites scoring better than the average of aligned sites = 883
Number in coding regions = 779
Number in noncoding regions = 104
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 3

AGGAGTATTGTAATGCAAAATGACTTAAAACTA	1	19	0	TAATCAATGA	    0.872927	-50
TGCATTACAATACTCCTAAATGAGTTTTAAGGA	1	35	1	TACTCTATGA	    0.975448	-34
        GTTAATCTTAACTTATTCTTAAACG	2	3	1	TAATTTATTA	    0.953277	-205
TATCATCATTTAATTTTTATTTATAAAGGTCGT	2	90	1	TAATTTATTA	    0.944114	-118
TTTAAAATACCATTTTTGAATGATTGGTTTGTA	2	138	1	CATTTTATGA	    0.924875	-70
AGTTTTTAGCTTATTTTGAGTGAAAGGATTAAG	2	181	1	TTATTTATGA	    0.962327	-27
          **** ** * ***

Masking position 9
Map Score:   1.51989

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 74
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

  AAAGGGGCTAGTTTTAAGTCATTTTGCA	1	9	1	TAGTTTTAAG	    0.861239	-60
AATGAGTTTTAAGGATTACAATCAAT    	1	53	1	AAGGATTACA	    0.912259	-16
AAGAATAAGTTAAGATTAAC          	2	1	0	TAAGATTAAC	    0.918131	-207
TAGTGGCGTTTAAGAATAAGTTAAGATTAA	2	12	0	TAAGAATAAG	    0.843443	-196
GCTTTGCGCGAAAATTTAAAAACCCCATTT	2	53	0	AAAATTTAAA	    0.893752	-155
CTTTATAAATAAAAATTAAATGATGATACA	2	88	0	AAAAATTAAA	    0.931007	-120
TTAAACCCTAAAATTTTAAAATACCATTTT	2	124	1	AAATTTTAAA	    0.893752	-84
TTTTGAGTGAAAGGATTAAGCAAG      	2	194	1	AAGGATTAAG	    0.979284	-14
          **********

Masking position 8
Map Score:   4.74785

Number of sites scoring better than the average of aligned sites = 1003
Number in coding regions = 739
Number in noncoding regions = 264
Number of orfs with sites within 600 bp upstream = 230
Fraction of orfs with sites within 600 bp upstream = 0.0369419


Motif number 5

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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 7

          **********

No masking
Map Score:   -1.17788e-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