AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i299_mixed14_hpyl_reg_100.orf -o299_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	RHP00146	68	AE000511
#2	RHP00147	207	AE000511

Motif number 1

ATGCAAAATGACTTAAAACTAGCCCCTTT 	1	10	0	ACTTAAAACT	    0.966618	-59
TGATTGTAATCCTTAAAACTCATTTAGGAG	1	47	0	CCTTAAAACT	    0.972802	-22
TCTTAGTGGCGTTTAAGAATAAGTTAAGAT	2	15	0	GTTTAAGAAT	    0.922018	-193
CACTAAGAGCGCTAAAAAATGGGGTTTTTA	2	37	1	GCTAAAAAAT	     0.96258	-171
AAAAAATGGGGTTTTTAAATTTTCGCGCAA	2	50	1	GTTTTTAAAT	    0.586005	-158
TTAAAACGACCTTTATAAATAAAAATTAAA	2	98	0	CTTTATAAAT	    0.565472	-110
AAATTTTAGGGTTTAAAACGACCTTTATAA	2	110	0	GTTTAAAACG	    0.940778	-98
AAACCCTAAAATTTTAAAATACCATTTTTG	2	126	1	ATTTTAAAAT	    0.494081	-82
CAAACCAATCATTCAAAAATGGTATTTTAA	2	139	0	ATTCAAAAAT	    0.677264	-69
CTCAAAATAAGCTAAAAACTACCAACACCA	2	171	0	GCTAAAAACT	    0.965466	-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

    AAAGGGGCTAGTTTTAAGTCATTTTG	1	7	1	GCTAGTTTTA	    0.970871	-62
GCGCTCTTAGTGGCGTTTAAGAATAAGTTA	2	19	0	TGGCGTTTAA	    0.915159	-189
GCTAAAAAATGGGGTTTTTAAATTTTCGCG	2	47	1	GGGGTTTTTA	    0.959817	-161
TATTTATAAAGGTCGTTTTAAACCCTAAAA	2	107	1	GGTCGTTTTA	    0.993668	-101
ATTCAAAAATGGTATTTTAAAATTTTAGGG	2	129	0	GGTATTTTAA	    0.963405	-79
GTATGGTGTTGGTAGTTTTTAGCTTATTTT	2	168	1	GGTAGTTTTT	    0.972872	-40
          **********

Masking position 6
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

TAGTTTTAAGTCATTTTGCATTACAATACTCCT	1	19	1	TCATTGATTA	    0.869638	-50
TCCTTAAAACTCATTTAGGAGTATTGTAATGCA	1	35	0	TCATAGAGTA	    0.977241	-34
CGTTTAAGAATAAGTTAAGATTAAC        	2	3	0	TAATAAATTA	     0.95349	-205
ACGACCTTTATAAATAAAAATTAAATGATGATA	2	90	0	TAATAAATTA	    0.943561	-118
TACAAACCAATCATTCAAAAATGGTATTTTAAA	2	138	0	TCATAAAATG	    0.930579	-70
CTTAATCCTTTCACTCAAAATAAGCTAAAAACT	2	181	0	TCATAAATAA	    0.964888	-27
          *** * ** ****

Masking position 5
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

TGCAAAATGACTTAAAACTAGCCCCTTT  	1	9	0	CTTAAAACTA	     0.86916	-60
    ATTGATTGTAATCCTTAAAACTCATT	1	53	0	TGTAATCCTT	    0.917547	-16
          GTTAATCTTAACTTATTCTT	2	1	1	GTTAATCTTA	    0.923094	-207
TTAATCTTAACTTATTCTTAAACGCCACTA	2	12	1	CTTATTCTTA	    0.852206	-196
AAATGGGGTTTTTAAATTTTCGCGCAAAGC	2	53	1	TTTAAATTTT	    0.900032	-155
TGTATCATCATTTAATTTTTATTTATAAAG	2	88	1	TTTAATTTTT	    0.935245	-120
AAAATGGTATTTTAAAATTTTAGGGTTTAA	2	124	0	TTTAAAATTT	    0.900033	-84
      CTTGCTTAATCCTTTCACTCAAAA	2	194	0	CTTAATCCTT	    0.980618	-14
          **********

Masking position 4
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