AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i073_ecoli_mtub_300.orf -o073_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	fabA	68	beta-hydroxydecanoyl thioester dehydrase, trans-2-decenoyl-ACP isomerase
#2	b0955	185	putative ATP-dependent protease
#3	fabB	98	3-oxoacyl-[acyl-carrier-protein] synthase I

Motif number 1

CGGACTTGTTCAGCGTACACGTGTTAGCTA	1	12	1	CAGCGTACAC	    0.992254	-57
GCACGCAGGATAGCTAACACGTGTACGCTG	1	22	0	TAGCTAACAC	    0.925113	-47
CAATAAAATAAGGCTTACAGAGAAC     	1	54	1	AGGCTTACAG	     0.99027	-15
TATTCTGTAAAGAGTTACACGGTAACATTG	2	19	0	AGAGTTACAC	    0.887457	-167
ATGGGCGTTAAAGCTCACAGGATGGAGATT	2	76	0	AAGCTCACAG	    0.954535	-110
CGGACTTGTTCGGCGTACAAGTGTACGCTA	3	33	1	CGGCGTACAA	    0.962287	-66
GAATGCACAATAGCGTACACTTGTACGCCG	3	43	0	TAGCGTACAC	    0.982717	-56
TGTGCATTCGAAACTTACTCTATGTGCGAC	3	64	1	AAACTTACTC	    0.869199	-35
ACTCTATGTGCGACTTACAGAGGTATTGA 	3	80	1	CGACTTACAG	    0.975776	-19
          **********

Masking position 7
Map Score:   11.3687

Number of sites scoring better than the average of aligned sites = 823
Number in coding regions = 720
Number in noncoding regions = 103
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 2

ACACGTGTACGCTGAACAAGTCCGA     	1	6	0	GCTGAACAAG	    0.989359	-63
TTCTTCACTGGCCTAAAAAGCTGATATTCT	2	43	0	GCCTAAAAAG	    0.993568	-143
TTTGACAACAGACTAAAAAACATCAACT  	2	168	1	GACTAAAAAA	    0.907284	-18
ACACTTGTACGCCGAACAAGTCCGATCAGC	3	27	0	GCCGAACAAG	    0.997301	-72
          **********

Masking position 5
Map Score:   3.4273

Number of sites scoring better than the average of aligned sites = 255
Number in coding regions = 224
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

ATTGAAGCACGCAGGATAGCTAACACGTGT	1	28	0	GCAGGATAGC	    0.992584	-41
GTAACTCTTTACAGAATATCAGCTTTTTAG	2	31	1	ACAGAATATC	    0.940007	-155
ACCGTAACCGGCACTACAGCACACGTAGAA	2	127	0	GCACTACAGC	    0.928922	-59
AGTTTCGAATGCACAATAGCGTACACTTGT	3	49	0	GCACAATAGC	    0.995552	-50
          **********

Masking position 6
Map Score:   2.43871

Number of sites scoring better than the average of aligned sites = 152
Number in coding regions = 138
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

          TCGGACTTGTTCAGCGTACA	1	1	1	TCGGACTTGT	    0.993494	-68
GACTTGTTCAGCGTACACGTGTTAGCTATC	1	14	1	GCGTACACGT	    0.980668	-55
CGGTATAATCGCGGCTTTGACAACAGACTA	2	153	1	GCGGCTTTGA	     0.90036	-33
AAATGGCTGATCGGACTTGTTCGGCGTACA	3	22	1	TCGGACTTGT	    0.993494	-77
GACTTGTTCGGCGTACAAGTGTACGCTATT	3	35	1	GCGTACAAGT	    0.976743	-64
          **********

Masking position 3
Map Score:   3.09186

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 250
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


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


Motif number 7

          **********

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