AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i075_Fatty_Acid_Oxidation_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	fadA	156	fadA

Motif number 1

          GGCGGTCGAGCCTATCCGGGCGA	1	1	1	GGCGGCGACT	    0.993688	-156
GAGCCTATCCGGGCGACGATGCGCGCCGCAGCG	1	18	1	GGGCGCGACG	    0.999378	-139
CCTGTTGGTTGGGCAAGGTATCGCTGCGGCGCG	1	39	0	GGGCAGGTCG	    0.992433	-118
CCAACAGGTTGGCCGGGGGCCCTGTTAGGGTGC	1	64	1	GGCCGGGGCT	    0.998267	-93
GGCCCTGTTAGGGTGCCGGTACGGGACCTAGTC	1	81	1	GGGTGCGGCG	    0.998782	-76
CCACAAAAGGGGGTTTGGATCCTTCTTCAAGAC	1	111	0	GGGTTGGACT	    0.988516	-46
          ***** ***  **

Masking position 8
Map Score:   9.82327

Number of sites scoring better than the average of aligned sites = 3203
Number in coding regions = 2949
Number in noncoding regions = 254
Number of orfs with sites within 600 bp upstream = 246
Fraction of orfs with sites within 600 bp upstream = 0.0395117


Motif number 2

GGCGGTCGAGCCTATCCGGGCGACGATGCG	1	11	1	CCTATCCGGG	     0.96153	-146
ACCTTGCCCAACCAACAGGTTGGCCGGGGG	1	53	1	ACCAACAGGT	    0.954984	-104
GTACCGGCACCCTAACAGGGCCCCCGGCCA	1	73	0	CCTAACAGGG	    0.996572	-84
TGTTAGGGTGCCGGTACGGGACCTAGTCTT	1	86	1	CCGGTACGGG	    0.559024	-71
CCACAAATTCCACAAAAGGGGGTTTGGATC	1	123	0	CACAAAAGGG	    0.974565	-34
          **********

Masking position 8
Map Score:   4.78925

Number of sites scoring better than the average of aligned sites = 2359
Number in coding regions = 2127
Number in noncoding regions = 232
Number of orfs with sites within 600 bp upstream = 208
Fraction of orfs with sites within 600 bp upstream = 0.0334083


Motif number 3

CCCGGATAGGCTCGACCGCC          	1	1	0	CTCGACCGCC	     0.99292	-156
GTCGAGCCTATCCGGGCGACGATGCGCGCC	1	15	1	TCCGGGCGAC	    0.960705	-142
CGATACCTTGCCCAACCAACAGGTTGGCCG	1	49	1	CCCAACCAAC	    0.995064	-108
TAACAGGGCCCCCGGCCAACCTGTTGGTTG	1	61	0	CCCGGCCAAC	    0.993468	-96
AGACTAGGTCCCGTACCGGCACCCTAACAG	1	85	0	CCGTACCGGC	    0.977016	-72
GAAGAAGGATCCAAACCCCCTTTTGTGGAA	1	116	1	CCAAACCCCC	    0.972283	-41
          **********

Masking position 7
Map Score:   6.52684

Number of sites scoring better than the average of aligned sites = 9995
Number in coding regions = 9305
Number in noncoding regions = 690
Number of orfs with sites within 600 bp upstream = 538
Fraction of orfs with sites within 600 bp upstream = 0.0864118


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