AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i015_Glycolysis_2_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	pykA	42	pyruvate kinase
#2	pfk	183	6-phosphofructokinase

Motif number 1

GGAATGTCACAAAAAATAAACGTGAGCCAA	2	26	0	AAAAAATAAA	    0.946196	-158
TTGTTTTTAAATAAAATTTAAGGAATGTCA	2	47	0	ATAAAATTTA	    0.955352	-137
TTTTATTTAAAAACAATTTATTTAATTGTA	2	61	1	AAACAATTTA	    0.985873	-123
CTTACCTATTATACAATTAAATAAATTGTT	2	72	0	ATACAATTAA	    0.985873	-112
ATTGCCCTAAAAACAATGAAAAGGGATCTC	2	119	0	AAACAATGAA	    0.983261	-65
          **********

Masking position 5
Map Score:   5.96321

Number of sites scoring better than the average of aligned sites = 268
Number in coding regions = 203
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 2

TGAAATCTTCAGCCTTCAGCTGTACA        	1	3	0	AGCTTCAGTA	    0.997809	-40
TGAAGGCTGAAGATTTCAGAAGGAAGTGAACCAA	1	19	1	AGTTTCAGGA	    0.997808	-24
CGTGAGCCAAAGGCTTCACGTTTAT         	2	2	0	AGCTTCATTA	    0.991351	-182
ATAATAGGTAAGGTTTCATAGGGAGGATGGAGAT	2	90	1	AGTTTCAGGA	    0.997809	-94
          ** *****   ***

Masking position 8
Map Score:   3.59997

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 29
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

CCTTCTGAAATCTTCAGCCTTCAGCTGTAC	1	12	0	TCTTCAGCCT	    0.988541	-31
   TTGGTTCACTTCCTTCTGAAATCTTCA	1	26	0	ACTTCCTTCT	    0.960459	-17
TGAAAAGGGATCTCCATCCTCCCTATGAAA	2	103	0	TCTCCATCCT	    0.995186	-81
TGGAGATCCCTTTTCATTGTTTTTAGGGCA	2	117	1	TTTTCATTGT	    0.906145	-67
          TCTCCATTCACCTCAGCAAC	2	174	0	TCTCCATTCA	     0.98311	-10
          **********

Masking position 3
Map Score:   2.99525

Number of sites scoring better than the average of aligned sites = 1041
Number in coding regions = 917
Number in noncoding regions = 124
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 4

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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