AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i006_bsub_mtub_100.orf -o006_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	pyrB	145	aspartate carbamoyltransferase

Motif number 1

ACCCTTCCAAGCCTCTCTGGACTTTCATTA	1	18	0	GCCTCTCTGG	    0.994753	-128
ATTGAAGCTTCCTTCTCTTCATAACCCTTC	1	41	0	CCTTCTCTTC	    0.995346	-105
AGAGAAGGAAGCTTCAATGCTGCCCTCTAT	1	53	1	GCTTCAATGC	    0.953956	-93
TTCAATGCTGCCCTCTATTTAACCATACCC	1	65	1	CCCTCTATTT	     0.99282	-81
  GTTCTTTCCCCTCTCTTTTCAACTTAAG	1	128	0	CCCTCTCTTT	    0.996802	-18
          **********

Masking position 4
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	    0.991593	-112
AGATAGACTCGGGGTATGGTTAAATAGAGG	1	76	0	GGGGTATGGT	     0.99473	-70
AAAAAACCCCGGTCTAAGATAGACTCGGGG	1	92	0	GGTCTAAGAT	    0.977781	-54
TGAAAAGAGAGGGGAAAGAAC         	1	135	1	GGGGAAAGAA	    0.992209	-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	    0.981066	-121
GGCTTGGAAGGGTTATGAAGAGAAGGAAGC	1	35	1	GGTTATGAAG	    0.982777	-111
CTCGGGGTATGGTTAAATAGAGGGCAGCAT	1	69	0	GGTTAAATAG	    0.975965	-77
TTCAACTTAAGGCTGAAAAAAAACCCCGGT	1	109	0	GGCTGAAAAA	    0.977151	-37
TTCAGCCTTAAGTTGAAAAGAGAGGGGAAA	1	122	1	AGTTGAAAAG	    0.975351	-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