AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i042_Transketolase_hpyl_reg_100.orf -o042_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	RHP00489	66	AE000511
#2	RHP00492	46	AE000511

Motif number 1

TATATTATAACTAAAAGGGGGTTTT     	1	6	0	CTAAAAGGGG	    0.985943	-61
CCATTTTTAGCTAAAATAAAATCTATATTA	1	29	0	CTAAAATAAA	    0.939787	-38
TTATTTTAGCTAAAAATGGCATGGGTTTTA	1	40	1	TAAAAATGGC	    0.994631	-27
    TTTGTGTTAAAATGACTCTCAAAAAC	2	7	1	TTAAAATGAC	    0.991521	-40
TCAAAAACCTTAAAAATGGAAAAATTTG  	2	29	1	TAAAAATGGA	    0.991713	-18
          **********

Masking position 5
Map Score:   6.41571

Number of sites scoring better than the average of aligned sites = 657
Number in coding regions = 581
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 2

          AAAACCCCCTTTTAGTTATA	1	1	1	AAAACCCCCT	    0.989234	-66
TTAGCTAAAATAAAATCTATATTATAACTA	1	23	0	TAAAATCTAT	    0.966553	-44
   TCCTTGCTAAAACCCATGCCATTTTTA	1	50	0	TAAAACCCAT	    0.994655	-17
AATGACTCTCAAAAACCTTAAAAATGGAAA	2	21	1	AAAAACCTTA	    0.959344	-26
          **********

Masking position 4
Map Score:   2.22049

Number of sites scoring better than the average of aligned sites = 1265
Number in coding regions = 1086
Number in noncoding regions = 179
Number of orfs with sites within 600 bp upstream = 134
Fraction of orfs with sites within 600 bp upstream = 0.0215226


Motif number 3

          **********

No masking
Map Score:   -5.44113e-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 4

          **********

No masking
Map Score:   -5.44113e-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 5

          **********

No masking
Map Score:   -5.44113e-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