AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i310_mixed24_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

TGTATAGGATTATTTTGGTTGCACCCTTAG	1	19	0	TATTTTGGTT	    0.974624	-282
GTCCGGTAGTTCAGTTGGTTAGAATGCCTG	1	55	1	TCAGTTGGTT	    0.920903	-246
GAAAACATGATCGTTTCGTTTACATTAATG	1	129	0	TCGTTTCGTT	     0.97925	-172
GAAACGATCATGTTTTCGTTTTTTTTGTGT	1	142	1	TGTTTTCGTT	    0.993489	-159
GTTTTTTTTGTGTTTTCTTTTACTGTATCT	1	159	1	TGTTTTCTTT	    0.959361	-142
GTTGAAAGGAGGTTTTGGTTC         	1	290	1	GGTTTTGGTT	    0.982393	-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

TCCTATACAAATATGGTCCGGTAGTTCAGTT	1	40	1	ATAGGTCCGG	    0.982363	-261
TTAGAATGCCTGCCTGTCACGCAGGAGGTCG	1	73	1	TGCTGTCACG	    0.947126	-228
CCTGTCACGCAGGAGGTCGCGGGTTCGAGTC	1	85	1	AGGGGTCGCG	    0.992819	-216
AGGTCGCGGGTTCGAGTCCCGTCCGGACCGC	1	98	1	TTCAGTCCCG	     0.96919	-203
TTTACATTAATGGCGGTCCGGACGGGACTCG	1	110	0	TGGGGTCCGG	    0.996093	-191
GGAATATCCAAGATGTTCCCGATATAAAGAA	1	213	0	AGAGTTCCCG	    0.979915	-88
          *** *******

Masking position 7
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	    0.986845	-232
AACCCGCGACCTCCTGCGTGACAGGCAGGC	1	80	0	CTCCTGCGTG	    0.996375	-221
TTTACTGTATCTTCTGCTTGGTGTCATAGC	1	177	1	CTTCTGCTTG	    0.991765	-124
TTCAACCCTGCTTATGCCTATTTGTGCTCT	1	266	0	CTTATGCCTA	    0.954151	-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