AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i026_Fumarate_Reductase_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	frdA	294	fumarate reductase, anaerobic, flavoprotein subunit

Motif number 1

CTGCCCACCGCTGTTTGATTCCTGCGTAAA	1	44	0	CTGTTTGATT	    0.897495	-251
AAAGCACGATCTGATGGTTTAGTAATTAAA	1	83	1	CTGATGGTTT	    0.979237	-212
ATTATCACTGAAGATGATTAATTTAATTAC	1	104	0	AAGATGATTA	    0.798308	-191
TTTAGTGCGCAAGAGGGCTAAATTATCACT	1	125	0	AAGAGGGCTA	    0.908669	-170
ACAGTATAGTCTGATGGATAAGTCTGAAAT	1	172	0	CTGATGGATA	    0.989951	-123
TATAAAGGAGCAGTGGAATAGCGTTCGCAG	1	208	1	CAGTGGAATA	    0.932284	-87
AAGTACGTGGCTGTGGGATAAAAACAATCT	1	264	1	CTGTGGGATA	    0.983658	-31
GACATTCCTCCAGATTGTTTTTATCCCACA	1	275	0	CAGATTGTTT	    0.915161	-20
          **********

Masking position 9
Map Score:   6.62357

Number of sites scoring better than the average of aligned sites = 2606
Number in coding regions = 2412
Number in noncoding regions = 194
Number of orfs with sites within 600 bp upstream = 217
Fraction of orfs with sites within 600 bp upstream = 0.0348538


Motif number 2

AAAAAGCACGATCTGATGGTTTAGTAATTA	1	81	1	ATCTGATGGT	     0.98285	-214
TGATGGATAAGTCTGAAATTTGACGAGATC	1	161	0	GTCTGAAATT	    0.930854	-134
CAACAGTATAGTCTGATGGATAAGTCTGAA	1	174	0	GTCTGATGGA	    0.984419	-121
CAGGGTAAGTACCTGAAAGTTACGGTCTGC	1	234	0	ACCTGAAAGT	    0.963577	-61
CAGGTACTTACCCTGAAGTACGTGGCTGTG	1	249	1	CCCTGAAGTA	    0.947107	-46
GATAAAAACAATCTGGAGGAATGTC     	1	280	1	ATCTGGAGGA	    0.974901	-15
          **********

Masking position 4
Map Score:   4.23421

Number of sites scoring better than the average of aligned sites = 765
Number in coding regions = 677
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 3

 GAAGTCTACTCGCAACGCGACGGCGAGAC	1	10	1	TCGCAACGCG	    0.976493	-285
TTTAGTCACTGCCCACCGCTGTTTGATTCC	1	52	0	GCCCACCGCT	    0.996045	-243
GCGAACGCTATTCCACTGCTCCTTTATAGG	1	206	0	TTCCACTGCT	    0.972671	-89
AGTTACGGTCTGCGAACGCTATTCCACTGC	1	217	0	TGCGAACGCT	    0.962189	-78
ATTGTTTTTATCCCACAGCCACGTACTTCA	1	262	0	TCCCACAGCC	    0.988085	-33
          **********

Masking position 5
Map Score:   1.23777

Number of sites scoring better than the average of aligned sites = 1004
Number in coding regions = 961
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

CAGATCGTGCTTTTTTTAGTCACTGCCCAC	1	66	0	TTTTTTTAGT	    0.985938	-229
GCACGATCTGATGGTTTAGTAATTAAATTA	1	86	1	ATGGTTTAGT	    0.965626	-209
ACGAGATCGATTTTTTTAGTGCGCAAGAGG	1	139	0	TTTTTTTAGT	    0.985938	-156
          **********

Masking position 8
Map Score:   0.827287

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 14
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -4.02005e-14

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:   -4.02005e-14

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:   -4.02005e-14

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