AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i069_Serine_Metabolism_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	yloW	138	similar to phosphoglycerate dehydrogenase
#2	ylpA	25	similar to L-serine dehydratase

Motif number 1

GCTTTTAAGTGCGGCAGCGCTGTAACGCGC	1	42	1	GCGGCAGCGC	    0.906225	-97
AATTAGTCTAGAAGCAAAGCGCTAATAAGC	1	96	1	GAAGCAAAGC	    0.992544	-43
TCCTCCTTATGAACCAGAGCTTATTAGCGC	1	114	0	GAACCAGAGC	    0.992755	-25
GGTTCATAAGGAGGAATAGC          	1	129	1	GAGGAATAGC	    0.992544	-10
CGAAAAGGGTCAGGAGGAGCCAGTT     	2	11	1	CAGGAGGAGC	    0.985426	-15
          **********

Masking position 9
Map Score:   5.94628

Number of sites scoring better than the average of aligned sites = 815
Number in coding regions = 760
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

ACATAAGAATAGAAGGGCAAATTGCCCTT 	1	10	0	AGAAGGGCAA	    0.995485	-129
GATCAGATATAAAATGGCAAGCGGGCGCGT	1	66	0	AAAATGGCAA	    0.989542	-73
AGTCTAGAAGCAAAGCGCTAATAAGCTCTG	1	100	1	CAAAGCGCTA	    0.978982	-39
        CGAAAAGGGTCAGGAGGAGCCA	2	3	1	AAAAGGGTCA	    0.987567	-23
          **********

Masking position 4
Map Score:   2.74957

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 222
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

CCCTTCTATTCTTATGTCTGCTTTTAAGTG	1	23	1	CTTATGTCTG	    0.988901	-116
CTTATGTCTGCTTTTAAGTGCGGCAGCGCT	1	33	1	CTTTTAAGTG	    0.975627	-106
CGCTTGCCATTTTATATCTGATCAATTAGT	1	73	1	TTTATATCTG	    0.964711	-66
TGAACCAGAGCTTATTAGCGCTTTGCTTCT	1	105	0	CTTATTAGCG	    0.973095	-34
          **********

Masking position 5
Map Score:   0.742721

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 174
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

     GCTATTCCTCCTTATGAACCAGAGC	1	124	0	TCCTCCTTAT	    0.995733	-15
   AACTGGCTCCTCCTGACCCTTTTCG  	2	9	0	TCCTCCTGAC	    0.998036	-17
          **********

Masking position 4
Map Score:   0.520105

Number of sites scoring better than the average of aligned sites = 30
Number in coding regions = 17
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 5

          **********

No masking
Map Score:   5.92755e-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:   5.92755e-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 7

          **********

No masking
Map Score:   5.92755e-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