AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i006_Pyrimidine_Biosynthesis_II_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	pyrB	145	aspartate carbamoyltransferase

Motif number 1

TAATGAAAGTCCAGAGAGGCTTGGAAGGGT	1	18	1	CCAGAGAGGC	    0.995207	-128
GAAGGGTTATGAAGAGAAGGAAGCTTCAAT	1	41	1	GAAGAGAAGG	     0.99577	-105
ATAGAGGGCAGCATTGAAGCTTCCTTCTCT	1	53	0	GCATTGAAGC	    0.957733	-93
GGGTATGGTTAAATAGAGGGCAGCATTGAA	1	65	0	AAATAGAGGG	    0.993473	-81
CTTAAGTTGAAAAGAGAGGGGAAAGAAC  	1	128	1	AAAGAGAGGG	    0.997094	-18
          **********

Masking position 7
Map Score:   7.74659

Number of sites scoring better than the average of aligned sites = 272
Number in coding regions = 186
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 2

AGGCTTGGAAGGGTTATGAAGAGAAGGAAG	1	34	1	GGGTTATGAA	    0.990922	-112
AGATAGACTCGGGGTATGGTTAAATAGAGG	1	76	0	GGGGTATGGT	    0.994308	-70
AAAAAACCCCGGTCTAAGATAGACTCGGGG	1	92	0	GGTCTAAGAT	    0.976035	-54
TGAAAAGAGAGGGGAAAGAAC         	1	135	1	GGGGAAAGAA	    0.991587	-11
          **********

Masking position 6
Map Score:   3.18668

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 108
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

AGTCCAGAGAGGCTTGGAAGGGTTATGAAG	1	25	1	GGCTTGGAAG	    0.979181	-121
GGCTTGGAAGGGTTATGAAGAGAAGGAAGC	1	35	1	GGTTATGAAG	    0.981062	-111
CTCGGGGTATGGTTAAATAGAGGGCAGCAT	1	69	0	GGTTAAATAG	    0.973589	-77
TTCAACTTAAGGCTGAAAAAAAACCCCGGT	1	109	0	GGCTGAAAAA	    0.974887	-37
TTCAGCCTTAAGTTGAAAAGAGAGGGGAAA	1	122	1	AGTTGAAAAG	    0.972919	-24
          **********

Masking position 4
Map Score:   2.93214

Number of sites scoring better than the average of aligned sites = 782
Number in coding regions = 683
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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