AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_bsub_mtub_100.orf -o279_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	ywbL	156	alternate gene name: ipa-27d; similar to hypothetical proteins

Motif number 1

TTTTACAGAACAGCCCTTTGAAGGAAAATGA	1	15	0	CAGCCCTTTA	    0.996519	-142
AGCAAAAAAGCTGTCCTTTTACAGAACAGCC	1	31	0	CTGTCCTTTA	    0.998572	-126
AGCTTTTTTGCTGTCCATCAAGGTTTTCAGA	1	50	1	CTGTCCATCA	    0.995656	-107
TCAAGGTTTTCAGACCTTCAAATTTTAATTG	1	67	1	CAGACCTTCA	    0.995151	-90
TAGCCAGTTCCTGTCCTTTGTCAATTAAAAT	1	88	0	CTGTCCTTTT	    0.995317	-69
          ********* *

Masking position 8
Map Score:   10.436

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 104
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

TTCCTTCAAAGGGCTGTTCTGTAAAAGGAC	1	20	1	GGGCTGTTCT	    0.990523	-137
GACAGCAAAAAAGCTGTCCTTTTACAGAAC	1	35	0	AAGCTGTCCT	    0.994612	-122
GACAGCTTTTTTGCTGTCCATCAAGGTTTT	1	47	1	TTGCTGTCCA	    0.995633	-110
TCATAGCCAGTTCCTGTCCTTTGTCAATTA	1	92	0	TTCCTGTCCT	    0.995465	-65
          **********

Masking position 5
Map Score:   4.786

Number of sites scoring better than the average of aligned sites = 193
Number in coding regions = 169
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

ACAGCCCTTTGAAGGAAAATGAACGA    	1	7	0	GAAGGAAAAT	    0.969495	-150
TGTCCTTTGTCAATTAAAATTTGAAGGTCT	1	78	0	CAATTAAAAT	    0.972303	-79
CAGGAACTGGCTATGATTATGTTATACAAT	1	106	1	CTATGATTAT	    0.924022	-51
TTATGTTATACAATGATAATCATTTTCAAT	1	122	1	CAATGATAAT	    0.992478	-35
TTCCTCCTATAATTGAAAATGATTATCATT	1	133	0	AATTGAAAAT	    0.932689	-24
          **********

Masking position 6
Map Score:   3.00368

Number of sites scoring better than the average of aligned sites = 1138
Number in coding regions = 980
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 178
Fraction of orfs with sites within 600 bp upstream = 0.0285898


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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:   -2.03625e-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