AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i233_protein_modification____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	ydiA	300	alternate gene name: ydxA; similar to thiamin-monophosphate kinase

Motif number 1

CTAAGGGTGCAACCAAAATAATCCTATACA	1	19	1	AACCAAAATA	    0.974538	-282
CAGGCATTCTAACCAACTGAACTACCGGAC	1	55	0	AACCAACTGA	     0.92065	-246
CATTAATGTAAACGAAACGATCATGTTTTC	1	129	1	AACGAAACGA	     0.97918	-172
ACACAAAAAAAACGAAAACATGATCGTTTC	1	142	0	AACGAAAACA	    0.993467	-159
AGATACAGTAAAAGAAAACACAAAAAAAAC	1	159	0	AAAGAAAACA	    0.959226	-142
         GAACCAAAACCTCCTTTCAAC	1	290	0	AACCAAAACC	    0.982333	-11
          **********

Masking position 5
Map Score:   5.93158

Number of sites scoring better than the average of aligned sites = 324
Number in coding regions = 285
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

AACTGAACTACCGGACCATATTTGTATAGGA	1	40	0	CCGGACCTAT	    0.982242	-261
CGACCTCCTGCGTGACAGGCAGGCATTCTAA	1	73	0	CGTGACAGCA	    0.946777	-228
GACTCGAACCCGCGACCTCCTGCGTGACAGG	1	85	0	CGCGACCCCT	     0.99277	-216
GCGGTCCGGACGGGACTCGAACCCGCGACCT	1	98	0	CGGGACTGAA	    0.968984	-203
CGAGTCCCGTCCGGACCGCCATTAATGTAAA	1	110	1	CCGGACCCCA	    0.996066	-191
TTCTTTATATCGGGAACATCTTGGATATTCC	1	213	1	CGGGAACTCT	    0.979778	-88
          ******* ***

Masking position 5
Map Score:   3.18142

Number of sites scoring better than the average of aligned sites = 450
Number in coding regions = 410
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

TTGGTTAGAATGCCTGCCTGTCACGCAGGA	1	69	1	TGCCTGCCTG	    0.987553	-232
AACCCGCGACCTCCTGCGTGACAGGCAGGC	1	80	0	CTCCTGCGTG	     0.99657	-221
TTTACTGTATCTTCTGCTTGGTGTCATAGC	1	177	1	CTTCTGCTTG	     0.99221	-124
TTCAACCCTGCTTATGCCTATTTGTGCTCT	1	266	0	CTTATGCCTA	    0.956542	-35
          **********

Masking position 5
Map Score:   1.34217

Number of sites scoring better than the average of aligned sites = 357
Number in coding regions = 321
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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