AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i007_Pyrimidine_Nucleotides_Biosynthesis_bsub_reg_300.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	nadB	102	L-aspartate oxidase

Motif number 1

GAACGGATGGAGGAAGACCGG          	1	1	0	AGAAGACCGG	    0.992298	-102
AGAGTTTTTTATGGAGAACGGATGGAGGAAG	1	16	0	ATGAGAACGG	    0.981594	-87
CAAGGATAAAATAAACTCAAGAGTTTTTTAT	1	35	0	ATAACTCAAG	    0.972201	-68
TGACACCTATATTTACACAAGGATAAAATAA	1	52	0	ATTACACAAG	    0.976869	-51
AAATATAGGTGTCAAGACAGGTGTAAACAAC	1	69	1	GTAAGACAGG	    0.994646	-34
CAAGACAGGTGTAAACAACAGGAGGATGGCA	1	81	1	GTAACAACAG	    0.984316	-22
          ** ********

Masking position 5
Map Score:   6.03065

Number of sites scoring better than the average of aligned sites = 800
Number in coding regions = 708
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

CCGGTCTTCCTCCATCCGTTCTCCATAAAA	1	11	1	TCCATCCGTT	     0.99441	-92
GTTTATTTTATCCTTGTGTAAATATAGGTG	1	50	1	TCCTTGTGTA	    0.959102	-53
TCCTGTTGTTTACACCTGTCTTGACACCTA	1	74	0	TACACCTGTC	     0.86874	-29
    ATGCCATCCTCCTGTTGTTTACACCT	1	87	0	TCCTCCTGTT	    0.996874	-16
          **********

Masking position 9
Map Score:   4.37952

Number of sites scoring better than the average of aligned sites = 391
Number in coding regions = 321
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 3

TTATGGAGAACGGATGGAGGAAGACCGG  	1	9	0	CGGATGGAGG	    0.992013	-94
CCTATATTTACACAAGGATAAAATAAACTC	1	48	0	CACAAGGATA	    0.983803	-55
GGTGTCAAGACAGGTGTAAACAACAGGAGG	1	76	1	CAGGTGTAAA	    0.972951	-27
GTGTAAACAACAGGAGGATGGCAT      	1	89	1	CAGGAGGATG	    0.997389	-14
          **********

Masking position 8
Map Score:   1.83764

Number of sites scoring better than the average of aligned sites = 857
Number in coding regions = 757
Number in noncoding regions = 100
Number of orfs with sites within 600 bp upstream = 104
Fraction of orfs with sites within 600 bp upstream = 0.0167041


Motif number 4

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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