AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i075_bsub_mtub_100.orf -o075_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	fadA	156	fadA

Motif number 1

          GGCGGTCGAGCCTATCCGGGCGA	1	1	1	GGCGGCGACT	    0.993635	-156
GAGCCTATCCGGGCGACGATGCGCGCCGCAGCG	1	18	1	GGGCGCGACG	    0.999369	-139
CCTGTTGGTTGGGCAAGGTATCGCTGCGGCGCG	1	39	0	GGGCAGGTCG	    0.992296	-118
CCAACAGGTTGGCCGGGGGCCCTGTTAGGGTGC	1	64	1	GGCCGGGGCT	     0.99824	-93
GGCCCTGTTAGGGTGCCGGTACGGGACCTAGTC	1	81	1	GGGTGCGGCG	     0.99876	-76
CCACAAAAGGGGGTTTGGATCCTTCTTCAAGAC	1	111	0	GGGTTGGACT	    0.988341	-46
          ***** ***  **

Masking position 8
Map Score:   9.82327

Number of sites scoring better than the average of aligned sites = 214
Number in coding regions = 191
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

GGCGGTCGAGCCTATCCGGGCGACGATGCG	1	11	1	CCTATCCGGG	    0.960116	-146
ACCTTGCCCAACCAACAGGTTGGCCGGGGG	1	53	1	ACCAACAGGT	    0.956899	-104
GTACCGGCACCCTAACAGGGCCCCCGGCCA	1	73	0	CCTAACAGGG	    0.996653	-84
TGTTAGGGTGCCGGTACGGGACCTAGTCTT	1	86	1	CCGGTACGGG	    0.556788	-71
CCACAAATTCCACAAAAGGGGGTTTGGATC	1	123	0	CACAAAAGGG	    0.975167	-34
          **********

Masking position 8
Map Score:   4.78925

Number of sites scoring better than the average of aligned sites = 354
Number in coding regions = 275
Number in noncoding regions = 79
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

          GGCGGTCGAGCCTATCCGGG	1	1	1	GGCGGTCGAG	    0.992688	-156
GGCGCGCATCGTCGCCCGGATAGGCTCGAC	1	15	0	GTCGCCCGGA	    0.959482	-142
CGGCCAACCTGTTGGTTGGGCAAGGTATCG	1	49	0	GTTGGTTGGG	    0.994815	-108
CAACCAACAGGTTGGCCGGGGGCCCTGTTA	1	61	1	GTTGGCCGGG	    0.993521	-96
CTGTTAGGGTGCCGGTACGGGACCTAGTCT	1	85	1	GCCGGTACGG	    0.975901	-72
TTCCACAAAAGGGGGTTTGGATCCTTCTTC	1	116	0	GGGGGTTTGG	    0.970918	-41
          **********

Masking position 4
Map Score:   6.52684

Number of sites scoring better than the average of aligned sites = 789
Number in coding regions = 699
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


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