AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i284_hypothetical9_hpyl_reg_100.orf -o284_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	RHP00574	245	AE000511

Motif number 1

GGCAATTTCACTCTTTAATGGTTTTTAAAGGGAGCG	1	15	0	CCTAAGGTTT	     0.98877	-231
AAAAAGCTCATCTTGTAAGGCAATTTCACTCTTTAA	1	33	0	TTTAAGCTTT	    0.985246	-213
ACAAGATGAGCTTTTTTGTGGTTTTTATTAAAAACG	1	53	1	CTTTGGGTTT	     0.99264	-193
AAAACGATCCTTTTTTAGCGGAGTTTTTCTAAAAAA	1	83	1	TTTAGGGTTT	    0.992902	-163
CGGAGTTTTTCTAAAAAAAGGGTTTTTTACTCACTT	1	101	1	CAAAAGGTTT	    0.903522	-145
CCTTAAGATGCTTGATTGTGTTGTTTAAATCAAGAG	1	137	0	CTTTGGTTTT	    0.954263	-109
CACAATCAAGCATCTTAAGGCAATTTAAAATAAAAT	1	153	1	CTTAAGCTTT	    0.995116	-93
GCTTTAGGGTCATGCTAGCGCTATTTTATTTTAAAT	1	175	0	CTTAGGCTTT	    0.996202	-71
TATAGATTAATTTAATAAGGGGCTTTAGGGTCATGC	1	196	0	TTTAAGGTTT	     0.99088	-50
          * *  *** **  ***

Masking position 14
Map Score:   16.076

Number of sites scoring better than the average of aligned sites = 488
Number in coding regions = 404
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

ACAAGATGAGCTTTTTTGTGGTTTTTATTA	1	53	1	CTTTTTTGTG	    0.948635	-193
TTTTTGTGGTTTTTATTAAAAACGATCCTT	1	65	1	TTTTATTAAA	    0.809371	-181
TAAAAACGATCCTTTTTTAGCGGAGTTTTT	1	81	1	CCTTTTTTAG	    0.952911	-165
GTAAAAAACCCTTTTTTTAGAAAAACTCCG	1	101	0	CTTTTTTTAG	    0.972705	-145
ACTCACTTCTCTTGATTTAAACAACACAAT	1	129	1	CTTGATTTAA	    0.952964	-117
CCTTAAGATGCTTGATTGTGTTGTTTAAAT	1	143	0	CTTGATTGTG	    0.943655	-103
GCTAGCGCTATTTTATTTTAAATTGCCTTA	1	168	0	TTTTATTTTA	    0.837485	-78
CCCTAAAGCCCCTTATTAAATTAATCTATA	1	202	1	CCTTATTAAA	    0.915774	-44
          **********

Masking position 6
Map Score:   7.24301

Number of sites scoring better than the average of aligned sites = 1846
Number in coding regions = 1518
Number in noncoding regions = 328
Number of orfs with sites within 600 bp upstream = 206
Fraction of orfs with sites within 600 bp upstream = 0.0330871


Motif number 3

GGTTTTTAAAGGGAGCGTTTT         	1	2	0	GGGAGCGTTT	    0.990353	-244
GCCTTACAAGATGAGCTTTTTTGTGGTTTT	1	48	1	ATGAGCTTTT	    0.976304	-198
CCGCTAAAAAAGGATCGTTTTTAATAAAAA	1	74	0	AGGATCGTTT	    0.987182	-172
CCTTTTTTAGCGGAGTTTTTCTAAAAAAAG	1	91	1	CGGAGTTTTT	    0.976664	-155
TTCTAAAAAAAGGGTTTTTTACTCACTTCT	1	109	1	AGGGTTTTTT	    0.963001	-137
TAATTTAATAAGGGGCTTTAGGGTCATGCT	1	195	0	AGGGGCTTTA	    0.982526	-51
          **********

Masking position 8
Map Score:   7.41635

Number of sites scoring better than the average of aligned sites = 824
Number in coding regions = 746
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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