AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i027_ecoli_bsub_100.orf -o027_ecoli_bsub_100.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	citG	300	fumarate hydratase

Motif number 1

TATCAAATGGTAAATAATAAGTGAGCTAAAA	1	67	1	TAAATATAAG	    0.883669	-76
TAACGAAAGCAAAACAGAAAGAAAAAATTAA	1	104	1	AAAACAAAAG	    0.982638	-39
AAACAGAAAGAAAAAATTAATCAGGTGAGGA	1	115	1	AAAAAATAAT	    0.843369	-28
GGCTAGCTGGAAAACAAGAAGAAATTGAACA	2	72	1	AAAACAGAAG	    0.962258	-229
GGACAAATCCAAAATACAAATATTCAAAGGA	2	162	1	AAAATAAAAT	    0.970635	-139
ATCTTGAATTAAAATTAAAATCTGCCAAGAT	2	204	1	AAAATTAAAT	    0.872807	-97
CCAAGATCGAAAAATAAAAAGGATTTTTTGT	2	228	1	AAAATAAAAG	    0.985563	-73
          ****** ****

Masking position 4
Map Score:   5.00081

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 135
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 2

ACCATTTGATAACAAATGTTTGGTCTTTCG	1	48	0	AACAAATGTT	    0.793927	-95
AACATTTGTTATCAAATGGTAAATAATAAG	1	58	1	ATCAAATGGT	     0.92117	-85
CATAATGCTGTTCAAATGATCTAATGAGCT	2	102	0	TTCAAATGAT	    0.964831	-199
TCTCTTATACATCAAAGGAGTACGGCAGGA	2	135	1	ATCAAAGGAG	    0.953709	-166
AATACAAATATTCAAAGGATTCCCGCGTAT	2	174	1	TTCAAAGGAT	    0.988234	-127
GATCGAAAAATAAAAAGGATTTTTTGTGTC	2	232	1	TAAAAAGGAT	    0.835748	-69
TAACGGTTGCTTCAATAGATCATAATTCGC	2	266	0	TTCAATAGAT	     0.80985	-35
          **********

Masking position 5
Map Score:   4.61409

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 232
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

GTTTTTTTACATGGCACGAAAGACCAAACATTTGTT	1	32	1	AGCAGAAACA	    0.990822	-111
AAAAAAACTTACTCCATGAAATACTCTA        	2	3	0	ATCAGAAACC	    0.996017	-298
TCAAAGGAGTACGGCAGGACAAATCCAAAATACAAA	2	146	1	AGCAGAAATC	    0.996017	-155
TTTTAATTTTAATTCAAGATATACGCGGGAATCCTT	2	188	0	ATCAGAAACC	    0.996017	-113
TAATTCGCCAATGACACAAAAAATCCTTTTTATTTT	2	238	0	AGCAAAAATC	    0.979558	-63
          * * ** ** * ** *

Masking position 9
Map Score:   2.84055

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 17
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 4

TCTTTCGTGCCATGTAAAAAAACCGCCCCG	1	25	0	CATGTAAAAA	    0.940895	-118
GAAAGCAAAACAGAAAGAAAAAATTAATCA	1	108	1	CAGAAAGAAA	    0.959341	-35
TAGAGTATTTCATGGAGTAAGTTTTTTTAT	2	11	1	CATGGAGTAA	    0.941719	-290
CCTCCGCTTTCATAAAAAAACTTACTCCAT	2	22	0	CATAAAAAAA	    0.946956	-279
AGCTGGAAAACAAGAAGAAATTGAACAGCT	2	76	1	CAAGAAGAAA	    0.972877	-225
          **********

Masking position 6
Map Score:   0.768375

Number of sites scoring better than the average of aligned sites = 253
Number in coding regions = 207
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

CGCCCCGAAGGGCGGCTCTGT         	1	2	0	GGCGGCTCTG	    0.975206	-141
CGCCCTTCGGGGCGGTTTTTTTACATGGCA	1	18	1	GGCGGTTTTT	    0.986122	-125
GCTTTCGTTAAGCAACTTTTAGCTCACTTA	1	84	0	AGCAACTTTT	    0.879714	-59
TTTCGATCTTGGCAGATTTTAATTTTAATT	2	210	0	GGCAGATTTT	    0.982336	-91
TTGTGTCATTGGCGAATTATGATCTATTGA	2	255	1	GGCGAATTAT	    0.944144	-46
          **********

Masking position 7
Map Score:   0.724425

Number of sites scoring better than the average of aligned sites = 1089
Number in coding regions = 968
Number in noncoding regions = 121
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 6

          **********

No masking
Map Score:   -1.88842e-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:   -1.88842e-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:   -1.88842e-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