AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i027_ecoli_mtub_300.orf -o027_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	fumC	142	fumarase C= fumarate hydratase Class II; isozyme
#2	fumA	198	fumarase A = fumarate hydratase Class I; aerobic isozyme
#3	fum	30	fum
#4	Rv1099c	100	hypothetical protein Rv1099c

Motif number 1

TAAAAAAACCGCCCCGAAGGGCGGCTCTGT    	1	7	0	GCCCGAGGGG	    0.980297	-136
TTAAAGCAAGAATCCTACGGGAAGTAACCTGGAG	2	49	1	ATCCTCGGGG	     0.84455	-150
AGTACGACTTTTTGCGGCTCCAGGTTACTTCCCG	2	66	0	TTGCGCTCCG	    0.954686	-133
CTGGGCGGGTGTTCCGTTGCCCTGTTAAAAGCGA	2	141	0	GTCCGTGCCG	    0.996805	-58
CTGGTTTGGTTATGCTCTGGGCGGGTGTTCCGTT	2	157	0	TTGCTTGGGG	    0.958352	-42
         TGATCGGGTTCCTTGTGTGTCGTGG	3	16	0	GTCGGTTCCG	    0.911357	-15
ACAGCTGAGGGATCCGGTTCGTCGACGGCCGCGG	4	12	1	GTCCGTTCGG	    0.990564	-89
TTCGTCGACGGCCGCGGTGGCCAGCCACGACCCG	4	29	1	GCGCGTGGCG	    0.996398	-72
GATGGCCTGGTGTGCGACGGGTCGTGGCTGGCCA	4	46	0	TTGCGCGGGG	    0.990663	-55
GGGGCTTCCCGGCGCGATGGCCTGGTGTGCGACG	4	61	0	GCGCGTGGCG	     0.99639	-40
    GGCCAGGTTGCGGTCCGGGGCTTCCCGGCG	4	81	0	GTGCGTCCGG	    0.985154	-20
          * **** ****  *

Masking position 14
Map Score:   15.3742

Number of sites scoring better than the average of aligned sites = 3191
Number in coding regions = 3045
Number in noncoding regions = 146
Number of orfs with sites within 600 bp upstream = 130
Fraction of orfs with sites within 600 bp upstream = 0.0208802


Motif number 2

TAAAAAAACCGCCCCGAAGGGCGGCTCTGT  	1	9	0	GCCCGAGGGC	    0.990087	-134
TTTTTTACATGGCACGAAAGACCAAACATTTG	1	34	1	GCACGAAGAC	    0.915711	-109
TCCAGGTTACTTCCCGTAGGATTCTTGCTTTA	2	50	0	TCCCGAGGAT	    0.876184	-149
CTGGGCGGGTGTTCCGTTGCCCTGTTAAAAGC	2	143	0	GTCCGTGCCC	    0.983918	-56
GGCCGTCGACGAACCGGATCCCTCAGCTGTC 	4	10	0	GACCGATCCC	    0.957379	-91
TTCGTCGACGGCCGCGGTGGCCAGCCACGACC	4	29	1	GCGCGTGGCC	    0.995025	-72
GGCCAGCCACGACCCGTCGCACACCAGGCCAT	4	47	1	GCCCGCGCAC	    0.990818	-54
GGGGCTTCCCGGCGCGATGGCCTGGTGTGCGA	4	63	0	GCGCGTGGCC	    0.994475	-38
GGGAAGCCCCGGACCGCAACCTGGCC      	4	85	1	GACCGAACCT	    0.886359	-16
          * **** *****

Masking position 5
Map Score:   9.29806

Number of sites scoring better than the average of aligned sites = 1320
Number in coding regions = 1212
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 3

AATGGTAAATAATAAGTGAGCTAAAAGTTG	1	72	1	AATAAGTGAG	    0.981075	-71
ATTTCCACATTAAAACAGGGATTGATC   	2	8	0	TAAAACAGGG	    0.887615	-191
ATTCTTGCTTTAATAGTGGGATTAATTTCC	2	32	0	TAATAGTGGG	    0.940302	-167
CTTTTTTAACAAAAACTGAGACTAGTACGA	2	93	0	AAAAACTGAG	      0.9805	-106
GTTTTTGTTAAAAAAGTGTGTAGGATATTG	2	107	1	AAAAAGTGTG	    0.973132	-92
GTTGCCCTGTTAAAAGCGAGTAACAATATC	2	130	0	TAAAAGCGAG	    0.970982	-69
CAAACCAGGCAGTAAGTGAGAGAACA    	2	183	1	AGTAAGTGAG	    0.941006	-16
          **********

Masking position 5
Map Score:   5.57886

Number of sites scoring better than the average of aligned sites = 355
Number in coding regions = 279
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 4

TTTTCTTTCTGTTTTGCTTTCGTTAAGCAA	1	99	0	GTTTTGCTTT	    0.991199	-44
ACCTGATTAATTTTTTCTTTCTGTTTTGCT	1	111	0	TTTTTTCTTT	    0.948253	-32
TCCCGTAGGATTCTTGCTTTAATAGTGGGA	2	41	0	TTCTTGCTTT	     0.97712	-158
GCCTGGTTTGGTTATGCTCTGGGCGGGTGT	2	163	0	GTTATGCTCT	     0.96316	-36
          **********

Masking position 5
Map Score:   0.745262

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 107
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 5

          **********

No masking
Map Score:   -2.95996e-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:   -2.95996e-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:   -2.95996e-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