AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i273_hypothetical18_hpyl_reg_100.orf -o273_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	RHP01302	205	AE000511

Motif number 1

TTTTAAAGGATTAAAAAGCTAAAATACTGCTTCTT	1	55	0	TAAACTAAAT	    0.992817	-151
TTTAATCCTTTAAAAATACTGAAAAATTGAAGTTT	1	75	1	TAAACTAAAA	    0.996863	-131
ACTCCAAATTTTAAAAAACTTCAATTTTTCAGTAT	1	90	0	TAAACTCAAT	    0.989357	-116
CCTAAAAGCCAGAAAAAACTCCAAATTTTAAAAAA	1	107	0	AAAACTCAAA	    0.977974	-99
TAAAAGAATTTAAAACCCCCTAAAAGCCAGAAAAA	1	125	0	TAAACCAAAA	    0.989878	-81
ATAGTCTTGTTAGAATACCTTAAAAGAATTTAAAA	1	145	0	TGAACTAAAA	    0.989878	-61
  TTTGTTCCTTAATTTCCTTAAAACTATCTCAAT	1	183	0	TAATCTAAAA	    0.985069	-23
          * ***   ** ****

Masking position 4
Map Score:   11.4423

Number of sites scoring better than the average of aligned sites = 294
Number in coding regions = 261
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 2

AGAAGCAGTATTTTAGCTTTTTAATCCTTT	1	56	1	TTTTAGCTTT	    0.899267	-150
TTCAGTATTTTTAAAGGATTAAAAAGCTAA	1	68	0	TTAAAGGATT	    0.948393	-138
AACTTCAATTTTTCAGTATTTTTAAAGGAT	1	79	0	TTTCAGTATT	    0.945414	-127
TACTGAAAAATTGAAGTTTTTTAAAATTTG	1	91	1	TTGAAGTTTT	    0.976477	-115
TTTTTAAAATTTGGAGTTTTTTCTGGCTTT	1	108	1	TTGGAGTTTT	    0.949239	-98
TTTAAATTCTTTTAAGGTATTCTAACAAGA	1	146	1	TTTAAGGTAT	    0.971611	-60
TTGAGATAGTTTTAAGGAAATTAAGGAACA	1	184	1	TTTAAGGAAA	    0.843751	-22
          **********

Masking position 5
Map Score:   4.72287

Number of sites scoring better than the average of aligned sites = 1263
Number in coding regions = 1023
Number in noncoding regions = 240
Number of orfs with sites within 600 bp upstream = 211
Fraction of orfs with sites within 600 bp upstream = 0.0338901


Motif number 3

          **********

No masking
Map Score:   -2.46258e-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 4

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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