AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i331_bsub_mtub_300.orf -o331_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	kdgK	37	2-keto-3-deoxygluconate kinase
#2	kdgR	221	transcriptional regulator (LacI family)

Motif number 1

TAAGAGGAGGTTGGGAAGAG          	1	28	1	TTGGGAAGAG	    0.992356	-10
TAAAATTTTCTTTGAAACCGTTACCAAAAT	2	57	0	TTTGAAACCG	    0.990934	-165
AGGATAAATAGTGAAAAGAGTCAACGAAAA	2	86	1	GTGAAAAGAG	    0.950861	-136
ATTTTAAAATTTGGGAAGAGTTTTTTTAAT	2	135	0	TTGGGAAGAG	    0.992356	-87
TGAAACCGATTTCAAAACCGTTACAACAAA	2	176	0	TTCAAAACCG	    0.968792	-46
ATCTCATATATTTGAAACCGATTTCAAAAC	2	188	0	TTTGAAACCG	    0.990934	-34
          **********

Masking position 6
Map Score:   8.40546

Number of sites scoring better than the average of aligned sites = 351
Number in coding regions = 302
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 2

GAAACCGTTACCAAAATATTTTCATTCAAG	2	44	0	CCAAAATATT	    0.987007	-178
ACTATTTATCCTAAAATTTTCTTTGAAACC	2	68	0	CTAAAATTTT	    0.979533	-154
ATATGTCAATTCATTATTTTTTCGTTGACT	2	104	0	TCATTATTTT	     0.86298	-118
AAAAACTCTTCCCAAATTTTAAAATTATGG	2	140	1	CCCAAATTTT	    0.991561	-82
CAAAAGAATACCATAATTTTAAAATTTGGG	2	150	0	CCATAATTTT	    0.987007	-72
GCTCCTGTATCTCATATATTTGAAACCGAT	2	196	0	CTCATATATT	    0.919392	-26
          **********

Masking position 6
Map Score:   7.7076

Number of sites scoring better than the average of aligned sites = 395
Number in coding regions = 328
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 3

CTAGGTGCCCTCAACTAAGAGGAGGTTGGG	1	13	1	TCAACTAAGA	    0.972056	-25
CAGCATCACTTGAATGAAAATATTTTGGTA	2	36	1	TGAATGAAAA	    0.971389	-186
GGTAACGGTTTCAAAGAAAATTTTAGGATA	2	62	1	TCAAAGAAAA	    0.989075	-160
GTGAAAAGAGTCAACGAAAAAATAATGAAT	2	96	1	TCAACGAAAA	    0.995757	-126
          **********

Masking position 4
Map Score:   3.6543

Number of sites scoring better than the average of aligned sites = 182
Number in coding regions = 156
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

TGATGCTGAAATCCTAACCAAGGGGGAAAT	2	14	0	ATCCTAACCA	    0.908126	-208
TTTCTTTGAAACCGTTACCAAAATATTTTC	2	51	0	ACCGTTACCA	    0.996154	-171
TTTTTCGTTGACTCTTTTCACTATTTATCC	2	87	0	ACTCTTTTCA	    0.953783	-135
TATTAAAAAAACTCTTCCCAAATTTTAAAA	2	134	1	ACTCTTCCCA	    0.980892	-88
CGATTTCAAAACCGTTACAACAAAAGAATA	2	170	0	ACCGTTACAA	    0.975649	-52
TATATTTGAAACCGATTTCAAAACCGTTAC	2	182	0	ACCGATTTCA	    0.937762	-40
          **********

Masking position 1
Map Score:   4.78091

Number of sites scoring better than the average of aligned sites = 634
Number in coding regions = 570
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 5

        TCCTAGGTGCCCTCAACTAAGAG	1	3	1	CTAGGTCCCT	    0.983241	-35
TATTTTCATTCAAGTGATGCTGAAATCCTAA	2	27	0	CAAGTGTGCT	    0.989939	-195
ACTCTTTTCACTATTTATCCTAAAATTTTCT	2	76	0	CTATTTTCCT	     0.97723	-146
         TCAAGTGCTCCTGTATCTCATA	2	210	0	CAAGTGTCCT	    0.996223	-12
          ****** ****

Masking position 3
Map Score:   0.19411

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 90
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 6

          **********

No masking
Map Score:   1.23224e-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 7

          **********

No masking
Map Score:   1.23224e-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 8

          **********

No masking
Map Score:   1.23224e-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