AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i166_bsub_mtub_100.orf -o166_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	ygaL	300	similar to nitrate ABC transporter (binding protein)
#2	ytlA	150	ytlA

Motif number 1

ATTGTTGAAAAACCTTGTTGTAACAGCTTT	1	74	1	AACCTTGTTG	    0.932305	-227
CTTGTTGTAACAGCTTTTTATGACACTTAA	1	87	1	CAGCTTTTTA	    0.937078	-214
ATCACTTACTCTGCTTGTTTCGCAAATAGA	1	145	0	CTGCTTGTTT	    0.971897	-156
GATTTTTGATATCCTTGTTTATCACTTACT	1	165	0	ATCCTTGTTT	    0.982204	-136
GATATGTCAACTCTTTTTTAAATACGATTT	1	190	0	CTCTTTTTTA	     0.88881	-111
 AACAGCCGCCTCCTTTTTTCTATATGCTT	2	10	1	CTCCTTTTTT	    0.990144	-141
ACATCCGGAGAACCTGGTTAGGCATTCACA	2	56	1	AACCTGGTTA	    0.864525	-95
TAGGCATTCACACATTTTTATACCCATCAT	2	74	1	CACATTTTTA	    0.845201	-77
TCAAGTTAATATCCTTTTTTGCTTTACATA	2	108	0	ATCCTTTTTT	    0.977206	-43
 ATAGACAACCTCCTTATTTCGCATCAAGT	2	132	0	CTCCTTATTT	    0.961215	-19
          **********

Masking position 5
Map Score:   12.8588

Number of sites scoring better than the average of aligned sites = 1371
Number in coding regions = 995
Number in noncoding regions = 376
Number of orfs with sites within 600 bp upstream = 424
Fraction of orfs with sites within 600 bp upstream = 0.0681015


Motif number 2

AATAATTATAAAATAATATTGAC       	1	4	0	AAATAATATT	    0.954569	-297
AACTATTTTATAATAATTATAAAATAATAT	1	15	0	TAATAATTAT	    0.918474	-286
AATTATTATAAAATAGTTATCTCTATTAAT	1	27	1	AAATAGTTAT	    0.945616	-274
TTATGACACTTAATAATTTTTGGAGAAATA	1	104	1	TAATAATTTT	    0.954569	-197
ATTTTTGGAGAAATAATTTTTCCTTCTCTA	1	119	1	AAATAATTTT	     0.97475	-182
AGGATATCAAAAATCGTATTTAAAAAAGAG	1	180	1	AAATCGTATT	    0.863138	-121
          **********

Masking position 4
Map Score:   5.08718

Number of sites scoring better than the average of aligned sites = 214
Number in coding regions = 143
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

TTACAACAAGGTTTTTCAACAATTTCGATACT	1	65	0	GTTTTCAACA	    0.957808	-236
TACTCTGCTTGTTTCGCAAATAGAGAAGGAAA	1	137	0	GTTTGCAAAA	    0.984616	-164
TGATATCCTTGTTTATCACTTACTCTGCTTGT	1	157	0	GTTTTCACTA	    0.819304	-144
TGATAAACAAGGATATCAAAAATCGTATTTAA	1	171	1	GGATTCAAAA	    0.921973	-130
ATCAAAAATCGTATTTAAAAAAGAGTTGACAT	1	185	1	GTATTAAAAA	    0.705497	-116
GAATTAACATGTTATTCAAACAAAAAAACAAT	1	230	1	GTTATCAAAA	    0.964147	-71
TTTGGAGTAAGGAAAGCATATAGAAAAAAGGA	2	21	0	GGAAGCATAA	    0.871044	-130
GGAGAACCTGGTTAGGCATTCACACATTTTTA	2	62	1	GTTAGCATTA	    0.893727	-89
CATACGATATGTAAAGCAAAAAAGGATATTAA	2	101	1	GTAAGCAAAA	    0.967465	-50
CAACCTCCTTATTTCGCATCAAGTTAATATCC	2	124	0	ATTTGCATCA	    0.624862	-27
          **** ***** *

Masking position 8
Map Score:   5.1528

Number of sites scoring better than the average of aligned sites = 1160
Number in coding regions = 961
Number in noncoding regions = 199
Number of orfs with sites within 600 bp upstream = 225
Fraction of orfs with sites within 600 bp upstream = 0.0361388


Motif number 4

TATATCGATTAATAGAGATAACTATTTTAT	1	34	0	AATAGAGATA	    0.969573	-267
TTGTTTCGCAAATAGAGAAGGAAAAATTAT	1	131	0	AATAGAGAAG	    0.956188	-170
TTTAAAAAAGAGTTGACATATCGGAATAAT	1	198	1	AGTTGACATA	    0.942801	-103
GAATAATTTGAATTAACATGTTATTCAAAC	1	221	1	AATTAACATG	    0.868286	-80
 CTCTGTTCTAGTAGAGATGAGAGCCTTCG	1	282	0	AGTAGAGATG	    0.987263	-19
          **********

Masking position 6
Map Score:   1.24894

Number of sites scoring better than the average of aligned sites = 176
Number in coding regions = 143
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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