AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i042_Transketolase_hpyl_reg_300.orf -o042_hpyl_300.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

     AAAACCCCCTTTTAGTTATAATATA	1	6	1	CCCCTTTTAG	    0.985235	-61
TAATATAGATTTTATTTTAGCTAAAAATGG	1	29	1	TTTATTTTAG	     0.93695	-38
TAAAACCCATGCCATTTTTAGCTAAAATAA	1	40	0	GCCATTTTTA	    0.994358	-27
GTTTTTGAGAGTCATTTTAACACAAA    	2	7	0	GTCATTTTAA	    0.991097	-40
  CAAATTTTTCCATTTTTAAGGTTTTTGA	2	29	0	TCCATTTTTA	    0.991293	-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

AAAATCTATATTATAACTAAAAGGGGGTTTT	1	11	0	TTTAACTAAA	     0.98686	-56
CCCATGCCATTTTTAGCTAAAATAAAATCTA	1	34	0	TTTAGCTAAA	    0.992645	-33
          TCCTTGCTAAAACCCATGCCA	1	56	0	TCTTGCTAAA	    0.994442	-11
          TTTGTGTTAAAATGACTCTCA	2	1	1	TTGTGTTAAA	    0.971262	-46
          ** ********

Masking position 8
Map Score:   4.21563

Number of sites scoring better than the average of aligned sites = 183
Number in coding regions = 155
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

TTATAACTAAAAGGGGGTTTT         	1	2	0	AAGGGGGTTT	    0.985672	-65
TTAGTTATAATATAGATTTTATTTTAGCTA	1	22	1	TATAGATTTT	    0.957778	-45
CTAAAAATGGCATGGGTTTTAGCAAGGA  	1	49	1	CATGGGTTTT	    0.995192	-18
TTTCCATTTTTAAGGTTTTTGAGAGTCATT	2	21	0	TAAGGTTTTT	     0.98047	-26
          **********

Masking position 8
Map Score:   1.7062

Number of sites scoring better than the average of aligned sites = 1182
Number in coding regions = 1028
Number in noncoding regions = 154
Number of orfs with sites within 600 bp upstream = 124
Fraction of orfs with sites within 600 bp upstream = 0.0199165


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


Motif number 6

          **********

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