AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i074_Fatty_Acid_Metabolism_bsub_reg_100.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	yusL	267	similar to 3-hydroxyacyl-CoA dehydrogenase

Motif number 1

GCTGCTTCCCACGGCTGCTT          	1	1	0	ACGGCTGCTT	    0.992229	-267
GGACAATCATAATGCAGCTGCTTCCCACGG	1	17	0	AATGCAGCTG	    0.984468	-251
TGTTTTTTATACTGCTGATTTTGACTTGTC	1	54	1	ACTGCTGATT	    0.982524	-214
ACTCAGCATTACGGCGGCGGAAAACGGACA	1	80	0	ACGGCGGCGG	    0.990912	-188
CCGCCGCCGTAATGCTGAGTCGGACCGGCA	1	90	1	AATGCTGAGT	    0.952514	-178
GGCGAGCGTAAAGGGAGATGCCGGTCCGAC	1	108	0	AAGGGAGATG	    0.913143	-160
CGCCGCGCTGACTGCCGCTGAAGACGGATT	1	134	1	ACTGCCGCTG	    0.988201	-134
ACTGCCGCTGAAGACGGATTTTTTTTCTCT	1	144	1	AAGACGGATT	    0.843034	-124
          **********

Masking position 1
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

GCATTATGATTGTCCCATGTTATGTTTTTT	1	32	1	TGTCCCATGT	    0.904398	-236
GATTTTGACTTGTCCGTTTTCCGCCGCCGT	1	70	1	TGTCCGTTTT	    0.983733	-198
GGGAGATGCCGGTCCGACTCAGCATTACGG	1	96	0	GGTCCGACTC	    0.992436	-172
AGAGAAAAAAAATCCGTCTTCAGCGGCAGT	1	144	0	AATCCGTCTT	    0.916244	-124
GGGCTTAAGTTGCCCGACTTTTATAGGCTT	1	195	1	TGCCCGACTT	    0.991875	-73
AAAGATTTCCGGTTCGACTTCAATAGCTAA	1	244	0	GGTTCGACTT	    0.982209	-24
          **********

Masking position 5
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

ATTGTCCCATGTTATGTTTTTTATACTGCT	1	40	1	GTTATGTTTT	    0.981849	-228
GCTGAAGACGGATTTTTTTTCTCTCGTACC	1	150	1	GATTTTTTTT	    0.962227	-118
TAGCTAATTTGTTATTTTTTTGTATGAAGC	1	221	0	GTTATTTTTT	    0.984699	-47
AGTCGAACCGGAAATCTTTTAAG       	1	255	1	GAAATCTTTT	    0.954619	-13
          **********

Masking position 5
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