AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i074_bsub_mtub_100.orf -o074_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	yusL	267	similar to 3-hydroxyacyl-CoA dehydrogenase

Motif number 1

          AAGCAGCCGTGGGAAGCAGC	1	1	1	AAGCAGCCGT	    0.992684	-267
CCGTGGGAAGCAGCTGCATTATGATTGTCC	1	17	1	CAGCTGCATT	    0.985651	-251
GACAAGTCAAAATCAGCAGTATAAAAAACA	1	54	0	AATCAGCAGT	    0.983802	-214
TGTCCGTTTTCCGCCGCCGTAATGCTGAGT	1	80	1	CCGCCGCCGT	    0.991291	-188
TGCCGGTCCGACTCAGCATTACGGCGGCGG	1	90	0	ACTCAGCATT	    0.955887	-178
GTCGGACCGGCATCTCCCTTTACGCTCGCC	1	108	1	CATCTCCCTT	     0.91934	-160
AATCCGTCTTCAGCGGCAGTCAGCGCGGCG	1	134	0	CAGCGGCAGT	    0.989086	-134
AGAGAAAAAAAATCCGTCTTCAGCGGCAGT	1	144	0	AATCCGTCTT	     0.84897	-124
          **********

Masking position 10
Map Score:   10.6806

Number of sites scoring better than the average of aligned sites = 2242
Number in coding regions = 2020
Number in noncoding regions = 222
Number of orfs with sites within 600 bp upstream = 142
Fraction of orfs with sites within 600 bp upstream = 0.0228076


Motif number 2

AAAAAACATAACATGGGACAATCATAATGC	1	32	0	ACATGGGACA	    0.907878	-236
ACGGCGGCGGAAAACGGACAAGTCAAAATC	1	70	0	AAAACGGACA	    0.984375	-198
CCGTAATGCTGAGTCGGACCGGCATCTCCC	1	96	1	GAGTCGGACC	    0.992734	-172
ACTGCCGCTGAAGACGGATTTTTTTTCTCT	1	144	1	AAGACGGATT	    0.919322	-124
AAGCCTATAAAAGTCGGGCAACTTAAGCCC	1	195	0	AAGTCGGGCA	    0.992198	-73
TTAGCTATTGAAGTCGAACCGGAAATCTTT	1	244	1	AAGTCGAACC	    0.982896	-24
          **********

Masking position 6
Map Score:   4.44683

Number of sites scoring better than the average of aligned sites = 642
Number in coding regions = 577
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

AGCAGTATAAAAAACATAACATGGGACAAT	1	40	0	AAAACATAAC	    0.982564	-228
GGTACGAGAGAAAAAAAATCCGTCTTCAGC	1	150	0	AAAAAAAATC	    0.963686	-118
GCTTCATACAAAAAAATAACAAATTAGCTA	1	221	1	AAAAAATAAC	    0.985303	-47
       CTTAAAAGATTTCCGGTTCGACT	1	255	0	AAAAGATTTC	    0.956298	-13
          **********

Masking position 6
Map Score:   2.01704

Number of sites scoring better than the average of aligned sites = 190
Number in coding regions = 141
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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