AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_bsub_mtub_300.orf -o319_bsub_mtub_300.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	comGB	52	probably part of the DNA transport machinery
#2	comGA	300	late competence gene

Motif number 1

CTGGTTGTTAAAGGATCAAGCCAGGTTATTAAAGAG	1	17	1	AAACAACGGT	    0.993856	-36
AAGCCAGGTTATTAAAGAGGCTCGGTGAA       	1	34	1	ATAGAGCGGT	    0.992697	-19
AGATCGCCTAATGCAACAATACCGGTCATTTGGTCA	2	20	0	ATACAAAGGT	    0.982039	-281
TGAAAATGGAATCTAGCAGGCATGGTGACCATGTCT	2	99	1	ATACAGCGGT	    0.997766	-202
CCTATAAATAAAAAAGCAGACATGGTCACCATGCCT	2	116	0	AAACAGCGGT	    0.997916	-185
CATATTGTAGAAAAAGAAGAAAAGGTAATCAAACAG	2	252	0	AAAAAGAGGT	    0.968757	-49
          **  * *** *  ***

Masking position 8
Map Score:   7.79922

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 56
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

GTCAATAAGCGAAAACAGCATAATGAAAATG	2	76	1	GAAAAAGCAT	      0.9667	-225
ACAGCATAATGAAAATGGAATCTAGCAGGCA	2	90	1	GAAAAGGAAT	    0.995762	-211
TTTCTGGCAAGAAAAAAGACTTTCAACTGAA	2	176	0	GAAAAAGACT	    0.960675	-125
GTTATATGCTGAAAAACCAATTCTTTCTGGC	2	199	0	GAAAACCAAT	     0.94988	-102
ATCAAACAGGGAAAACGTGATTTTGTGAGAT	2	230	0	GAAAAGTGAT	      0.9667	-71
AGAAAAAGAAGAAAAGGTAATCAAACAGGGA	2	249	0	GAAAAGTAAT	    0.987561	-52
TGCGTTGAAAGGAGAGGGAATCAAA      	2	286	1	GGAGAGGAAT	    0.956981	-15
          ***** *****

Masking position 5
Map Score:   6.45906

Number of sites scoring better than the average of aligned sites = 747
Number in coding regions = 661
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 3

CTTGATCCTTTAACAACCAGACTTTT       	1	4	0	TAACAACCGT	    0.988446	-49
CGAGCCTCTTTAATAACCTGGCTTGATCCTTTA	1	25	0	TAATAACCGT	    0.994762	-28
GAAAATGACCAAATGACCGGTATTGTTGCATTA	2	15	1	AAATGACCGT	    0.992369	-286
TGTTTTCGCTTATTGACCAGTATCTTTCTCAAC	2	60	0	TATTGACCGT	     0.99237	-241
GGGAAAATTATAATGACAGGGGTACATTCAGTT	2	150	1	TAATGACAGT	    0.987951	-151
          ******** *  *

Masking position 6
Map Score:   4.83583

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 43
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

GGTATTGTTGCATTAGGCGATCTTTCCGTT	2	33	1	CATTAGGCGA	    0.991701	-268
AGATACTGGTCAATAAGCGAAAACAGCATA	2	68	1	CAATAAGCGA	    0.987748	-233
ATTCCATTTTCATTATGCTGTTTTCGCTTA	2	81	0	CATTATGCTG	    0.967243	-220
TCTTTTTCTACAATATGCGTTGAAAGGAGA	2	271	1	CAATATGCGT	    0.987747	-30
          **********

Masking position 5
Map Score:   2.33926

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 123
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

CCAGTATCTTTCTCAACGGAAAGATCGCCT	2	47	0	TCTCAACGGA	    0.994976	-254
GAAAAAAGACTTTCAACTGAATGTACCCCT	2	167	0	TTTCAACTGA	    0.988665	-134
TTCCCTCTCCTTTCAACGCATATTGTAGAA	2	276	0	TTTCAACGCA	    0.992326	-25
          **********

Masking position 5
Map Score:   1.95462

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 13
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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 8

          **********

No masking
Map Score:   -1.17788e-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