AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i261_twitching_mobility_hpyl_reg_100.orf -o261_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

Purged sequences:
RHP00808	16	AE000511

Input sequences:
#1	RHP00809	24	AE000511
#2	RHP00810	101	AE000511

Motif number 1

 AGACAAAAGACTAAGGATTAATCA     	1	10	1	ACTAAGGATT	    0.945265	-15
CACCACTCTTTTTAAGGAATTTGT      	2	5	0	TTTAAGGAAT	    0.985295	-97
CTTATAAGGGTTTTAGTTTTAGCATGTTAG	2	43	0	TTTTAGTTTT	    0.975114	-59
CTAAAACCCTTATAAGTTATGGATAAAAAC	2	57	1	TATAAGTTAT	    0.972495	-45
TACCCTATTCTTTAAGTTTTTATCCATAAC	2	72	0	TTTAAGTTTT	     0.99225	-30
          **********

Masking position 5
Map Score:   5.51261

Number of sites scoring better than the average of aligned sites = 316
Number in coding regions = 248
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 2

       TGATTAATCCTTAGTCTTTTGTC	1	12	0	TTAATCCTTA	    0.956546	-13
AGGGTTTTAGTTTTAGCATGTTAGCATTCA	2	37	0	TTTTAGCATG	    0.955483	-65
TCTTTAAGTTTTTATCCATAACTTATAAGG	2	64	0	TTTATCCATA	    0.989884	-38
   GCGTTTATTTTACCCTATTCTTTAAGT	2	85	0	TTTTACCCTA	    0.988014	-17
          **********

Masking position 2
Map Score:   1.26085

Number of sites scoring better than the average of aligned sites = 394
Number in coding regions = 340
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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