AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i035_bsub_mtub_100.orf -o035_bsub_mtub_100.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	yckG	231	similar to D-arabino 3-hexulose 6-phosphate formaldehyde lyase
#2	araA	207	L-arabinose isomerase

Motif number 1

CCTTAGTAACCTTTTTGTATGTTAGATACGTATCAT	1	22	1	CTTTATTTAA	    0.891697	-210
TATCATCACTTACTTACTTTTTTGCAGACTCTTTTT	1	52	1	TTTTTTTTGA	    0.877787	-180
TTTTTGCAGACTCTTTTTTCATTATACTCACTCATA	1	70	1	CTTTTCTTAA	    0.951336	-162
AGATTTCTTTCGCTTGATTTTATGAGTGAGTATAAT	1	90	0	CTTTTTATGG	     0.97481	-142
TTCTATAGGTTCCTTCTTTTGTTGAGAAGTAGGCAC	1	173	0	TTTTTTTTGG	    0.906001	-59
TTTCGAATTATTGTTCATTCTATAGGTTCCTTCTTT	1	190	0	TTTTTCATAG	    0.942251	-42
CAGAGCCCGGCTTTTTATTCAATAGGACGGCCAGCC	2	22	0	CTTTTCATAG	     0.97459	-186
TACTGTCAATCTTTTCTTTTAAAAAAAGCCGGGGGC	2	57	0	CTTTTTAAAA	    0.896132	-151
GTATAATAGTCAATTACTATAATAAAATTGTTCGTA	2	90	1	CTTTATATAA	    0.933792	-118
TATAATAAAATTGTTCGTACAAAATATTTATTTATA	2	107	1	TTTTACAAAA	    0.521898	-101
TATTTGAAAGCGTTTTATTTTATGAGAAAGGGGCAG	2	177	1	CTTTTTATGG	     0.97459	-31
          *  **  *** *** *

Masking position 8
Map Score:   8.54233

Number of sites scoring better than the average of aligned sites = 1276
Number in coding regions = 993
Number in noncoding regions = 283
Number of orfs with sites within 600 bp upstream = 327
Fraction of orfs with sites within 600 bp upstream = 0.0525217


Motif number 2

TATAATGAAAAAAGAGTCTGCAAAAAAGTA	1	66	0	AAAGAGTCTG	    0.970766	-166
AATCAAGCGAAAGAAATCTGATTGTCTCTC	1	107	1	AAGAAATCTG	    0.916574	-125
TGTTGACTTCAAAGTGCCTACTTCTCAACA	1	160	1	AAAGTGCCTA	    0.924357	-72
TCAACAAAAGAAGGAACCTATAGAATGAAC	1	184	1	AAGGAACCTA	     0.95771	-48
CCTATTGAATAAAAAGCCGGGCTCTGCCCC	2	32	1	AAAAAGCCGG	    0.985476	-176
TTTCTTTTAAAAAAAGCCGGGGGCAGAGCC	2	51	0	AAAAAGCCGG	    0.985476	-157
ATGATAGGAAAATAAACCTATAAATAAATA	2	131	0	AATAAACCTA	    0.877809	-77
          **********

Masking position 2
Map Score:   5.32111

Number of sites scoring better than the average of aligned sites = 1455
Number in coding regions = 1211
Number in noncoding regions = 244
Number of orfs with sites within 600 bp upstream = 195
Fraction of orfs with sites within 600 bp upstream = 0.0313203


Motif number 3

TACAAAAAGGTTACTAAGGGGGGATTCTAT 	1	10	0	TTATAAGGGG	    0.961628	-222
AGTCAACAAGTTACTTGGAGGATACTGTGAG	1	137	0	TTATTGGAGG	    0.970983	-95
CTTCTTTTGTTGAGAAGTAGGCACTTTGAAG	1	166	0	TGAAAGTAGG	    0.945918	-66
GGCTTTTTATTCAATAGGACGGCCAGCCCGA	2	19	0	TCATAGGACG	    0.972251	-189
TACAAAATATTTATTTATAGGTTTATTTTCC	2	124	1	TTATTATAGG	    0.886938	-84
TATTTTCCTATCATTAGTACGTATCTTTTGT	2	147	1	TCATAGTACG	    0.944336	-61
TTTTATTTTATGAGAAAGGGGCAGTTTAC  	2	189	1	TGAAAAGGGG	    0.921688	-19
          *** *******

Masking position 3
Map Score:   1.41249

Number of sites scoring better than the average of aligned sites = 533
Number in coding regions = 349
Number in noncoding regions = 184
Number of orfs with sites within 600 bp upstream = 198
Fraction of orfs with sites within 600 bp upstream = 0.0318021


Motif number 4

AAGGTTACTAAGGGGGGATTCTAT      	1	5	0	AGGGGGGATT	    0.938931	-227
AAAGTAAGTAAGTGATGATACGTATCTAAC	1	42	0	AGTGATGATA	    0.943714	-190
TGATTTTATGAGTGAGTATAATGAAAAAAG	1	82	0	AGTGAGTATA	    0.973422	-150
TGGAGGATACTGTGAGGAGAGACAATCAGA	1	123	0	TGTGAGGAGA	    0.979658	-109
AACAAGTTACTTGGAGGATACTGTGAGGAG	1	134	0	TTGGAGGATA	    0.933915	-98
TAATTCGAAAAGGGAGTGGATCAACA    	1	216	1	AGGGAGTGGA	    0.945824	-16
          **********

Masking position 4
Map Score:   1.34642

Number of sites scoring better than the average of aligned sites = 506
Number in coding regions = 356
Number in noncoding regions = 150
Number of orfs with sites within 600 bp upstream = 167
Fraction of orfs with sites within 600 bp upstream = 0.026823


Motif number 5

TATTGAATAAAAAGCCGGGCTCTGCCCCCG	2	34	1	AAAGCCGGGC	    0.997973	-174
TCTTTTAAAAAAAGCCGGGGGCAGAGCCCG	2	49	0	AAAGCCGGGG	    0.997973	-159
          **********

Masking position 3
Map Score:   0.543252

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 26
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 6

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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