AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i027_ecoli_bsub_300.orf -o027_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 =  	0.47
 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	citG	300	fumarate hydratase

Motif number 1

TGATAACAAATGTTTGGTCTTTCGTGCCATGTAAAAAAAC	1	32	0	TTTTCTTTGT	    0.989862	-111
GTTAAGCAACTTTTAGCTCACTTATTATTTACCATTTGAT	1	68	0	TTTTCATTTT	    0.974466	-75
CTGATTAATTTTTTCTTTCTGTTTTGCTTTCGTTAAGCAA	1	99	0	TTTTCTTTGT	    0.989862	-44
CCCGTAGGATTCTTGCTTTAATAGTGGGATTAATTTCCAC	2	30	0	TTTTTATTGT	    0.974466	-169
          TGTTCTCTCACTTACTGCCTGGTTTGGTTA	2	179	0	TTTTCATCTT	    0.955774	-20
TCTAATGAGCTGTTCAATTTCTTCTTGTTTTCCAGCTAGC	3	73	0	TTTTTTTTTT	    0.937178	-228
AATATTTGTATTTTGGATTTGTCCTGCCGTACTCCTTTGA	3	146	0	TTTTTTTTGT	    0.974466	-155
AAAAAGGATTTTTTGTGTCATTGGCGAATTATGATCTATT	3	243	1	TTTTCATCGT	    0.982234	-58
          * **   *** *  **   *

Masking position 12
Map Score:   6.57423

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 66
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

TTCGGGGCGGTTTTTTTACATGGCACGAAA	1	23	1	TTTTTTTACA	    0.918297	-120
AGCTCACTTATTATTTACCATTTGATAACA	1	64	0	TTATTTACCA	    0.920531	-79
GAGCTAAAAGTTGCTTAACGAAAGCAAAAC	1	89	1	TTGCTTAACG	      0.8654	-54
TGATTAATTTTTTCTTTCTGTTTTGCTTTC	1	108	0	TTTCTTTCTG	    0.833923	-35
AATAGTGGGATTAATTTCCACATTAAAACA	2	21	0	TTAATTTCCA	    0.820931	-178
CGGCTCCAGGTTACTTCCCGTAGGATTCTT	2	56	0	TTACTTCCCG	    0.899372	-143
TCCTACACACTTTTTTAACAAAAACTGAGA	2	102	0	TTTTTTAACA	    0.854982	-97
ATGGAGTAAGTTTTTTTATGAAAGCGGAGG	3	22	1	TTTTTTTATG	    0.756007	-279
CAATTTCTTCTTGTTTTCCAGCTAGCCTTA	3	69	0	TTGTTTTCCA	    0.948204	-232
AAAATCCTTTTTATTTTTCGATCTTGGCAG	3	225	0	TTATTTTTCG	    0.844909	-76
          **********

Masking position 5
Map Score:   3.87716

Number of sites scoring better than the average of aligned sites = 1524
Number in coding regions = 1270
Number in noncoding regions = 254
Number of orfs with sites within 600 bp upstream = 283
Fraction of orfs with sites within 600 bp upstream = 0.0454545


Motif number 3

CTGCTCCTCACCTGATTAATTTTTTCTTTCT	1	119	0	CCTGATAATT	     0.95466	-24
  GATCAATCCCTGTTTTAATGTGGAAATTA	2	9	1	CCTGTTTAAT	    0.967919	-190
GTTCCGTTGCCCTGTTAAAAGCGAGTAACAA	2	134	0	CCTGTTAAAG	    0.978103	-65
GATCTAATGAGCTGTTCAATTTCTTCTTGTT	3	84	0	GCTGTTAATT	    0.979407	-217
ACATCATAATGCTGTTCAAATGATCTAATGA	3	105	0	GCTGTTAAAT	    0.985538	-196
          ****** ****

Masking position 6
Map Score:   2.76473

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 66
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

CCGCCCCGAAGGGCGGCTCTGT        	1	3	0	GGGCGGCTCT	    0.997066	-140
CCGCCCTTCGGGGCGGTTTTTTTACATGGC	1	17	1	GGGCGGTTTT	    0.993582	-126
GTTATGCTCTGGGCGGGTGTTCCGTTGCCC	2	153	0	GGGCGGGTGT	    0.997066	-46
          **********

Masking position 8
Map Score:   1.7557

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 17
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

GGTTACTTCCCGTAGGATTCTTGCTTTAAT	2	48	0	CGTAGGATTC	    0.986388	-151
TTTATGAAAGCGGAGGATACGAAGTGGCAC	3	36	1	CGGAGGATAC	    0.990775	-265
TACAAATATTCAAAGGATTCCCGCGTATAT	3	176	1	CAAAGGATTC	    0.969838	-125
CAACCGTTATGGAGGGATACATAA      	3	287	1	GGAGGGATAC	    0.965466	-14
          **********

Masking position 7
Map Score:   0.333082

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 65
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 6

          **********

No masking
Map Score:   -9.70439e-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:   -9.70439e-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 8

          **********

No masking
Map Score:   -9.70439e-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