AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i053_Altronate_Metabolism_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	yjmC	104	similar to malate dehydrogenase
#2	yjmE	24	similar to D-mannonate hydrolase
#3	yjmG	47	similar to hexuronate transporter
#4	yjmH	87	similar to transcriptional regulator (LacI family)
#5	yjmI	76	similar to tagaturonate reductase

Motif number 1

ACTCTCCAAGCGAAACCCCTACAAACACATTT	1	50	0	CAACCCCTAC	    0.988972	-55
          GCAAGTGCCTCCTTCCTTTTCA	1	93	0	GAATGCCTCC	    0.972303	-12
          GCTCGCACCTCCGGATTCAGTC	2	13	0	GTCCACCTCC	    0.954954	-12
     CTCAACCTCACCCCTATGTTGGTTCAG	3	31	0	CTCCCCCTAT	    0.949084	-17
TATCATCAAACATACCGCCTCTCCCACTATAT	4	18	0	CTACGCCTCT	    0.992245	-70
CCTTCCTTATCATACCGGCTGCGATTATTTAC	4	59	0	CTACGGCTGC	     0.96336	-29
          CTAATTCCCTTCCTTATCATAC	4	76	0	CAATCCCTTC	    0.952122	-12
         CCTTATTGCCTCCCTCTCACTTT	5	64	0	CTATGCCTCC	    0.995448	-13
          * ** *******

Masking position 10
Map Score:   6.46846

Number of sites scoring better than the average of aligned sites = 895
Number in coding regions = 764
Number in noncoding regions = 131
Number of orfs with sites within 600 bp upstream = 155
Fraction of orfs with sites within 600 bp upstream = 0.0248956


Motif number 2

ATTTTAAATATTCTTTATATTATATTG    	1	7	0	TTCTTATATT	     0.92478	-98
ACATTTTATTTACAAATTATTTTAAATATTC	1	25	0	TACAATTATT	    0.881042	-80
CCCCTACAAACACATTTTATTTACAAATTAT	1	36	0	CACATTTATT	    0.975766	-69
CTCCTTCCTTTTCAGTTTTTTGGGCACTCTC	1	76	0	TTCATTTTTT	    0.917931	-29
CCTATGTTGGTTCAGTTTCTGTTGCACCGCT	3	15	0	TTCATTTCTG	    0.903728	-33
TACCGCCTCTCCCACTATATTTCCAGA    	4	7	0	CCCATATATT	    0.936824	-81
TGCGATTATTTACTGTATATTGTATCATCAA	4	41	0	TACTTATATT	    0.904232	-47
TTGCCTCCCTCTCACTTTATGCACACGTTAA	5	51	0	CTCATTTATG	    0.967631	-26
          **** ******

Masking position 8
Map Score:   4.89457

Number of sites scoring better than the average of aligned sites = 952
Number in coding regions = 742
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 239
Fraction of orfs with sites within 600 bp upstream = 0.0383874


Motif number 3

TGTGTTTGTAGGGGTTTCGCTTGGAGAGTG	1	53	1	GGGGTTTCGC	    0.980936	-52
TCAGTTTTTTGGGCACTCTCCAAGCGAAAC	1	66	0	GGGCACTCTC	    0.996689	-39
AAAAGGAAGGAGGCACTTGC          	1	95	1	AGGCACTTGC	    0.972739	-10
GTTTTTCAGCGGGCATTCTTTATACAGAAA	5	17	1	GGGCATTCTT	    0.981892	-60
          **********

Masking position 7
Map Score:   1.21671

Number of sites scoring better than the average of aligned sites = 240
Number in coding regions = 222
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

          **********

No masking
Map Score:   2.86649e-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:   2.86649e-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:   2.86649e-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