AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i285_ecoli_bsub_100.orf -o285_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	citC	291	citrate lyase synthetase (citrate (pro-3S)-lyase ligase

Motif number 1

TTGACGGATGTAATTAAAATGTTGAATCAA	1	41	1	TAATTAAAAT	    0.975493	-251
ATTAAAATGTTGAATCAAAATACATAGATA	1	53	1	TGAATCAAAA	    0.972655	-239
GCCACGATCATAATTAATATCTATGTATTT	1	70	0	TAATTAATAT	    0.875382	-222
ATTGATTTAATGAATAAAATTTGCCACGAT	1	92	0	TGAATAAAAT	    0.973182	-200
TTTTATTCATTAAATCAATTAAATCACTTA	1	103	1	TAAATCAATT	    0.918411	-189
GTAATTACATTAATTAAAAAACTTAAAATC	1	150	1	TAATTAAAAA	    0.973296	-142
AATCATTAAATAAATAAAAAACCACTAACT	1	176	1	TAAATAAAAA	    0.984549	-116
CTATGTGAAATAAATCAAAATTTCACGCCG	1	206	1	TAAATCAAAA	    0.984326	-86
          **********

Masking position 7
Map Score:   14.226

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 139
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 128
Fraction of orfs with sites within 600 bp upstream = 0.0205589


Motif number 2

CTCTTTGACGGATGTAATTAAAATGTTGAA	1	37	1	GATGTAATTA	    0.963309	-255
AATTAATATCTATGTATTTTGATTCAACAT	1	59	0	TATGTATTTT	    0.813959	-233
TGATTTAATTGATTTAATGAATAAAATTTG	1	99	0	GATTTAATGA	    0.889151	-193
TTAAACCTGCGAGTCATTTCGTAATTACAT	1	130	1	GAGTCATTTC	    0.853032	-162
TTTTTTAATTAATGTAATTACGAAATGACT	1	141	0	AATGTAATTA	    0.809658	-151
AGTGGTTTTTTATTTATTTAATGATTTTAA	1	172	0	TATTTATTTA	    0.876777	-120
GTGAAATTTTGATTTATTTCACATAGAGTT	1	202	0	GATTTATTTC	    0.956742	-90
TACTCCTTAGGATGTATAGCGAAAGGAGAA	1	239	1	GATGTATAGC	    0.937387	-53
GGGGGTGATCGAGGTATATCTTTTTCTCCT	1	262	0	GAGGTATATC	    0.932109	-30
          **********

Masking position 6
Map Score:   6.65838

Number of sites scoring better than the average of aligned sites = 1021
Number in coding regions = 854
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 197
Fraction of orfs with sites within 600 bp upstream = 0.0316415


Motif number 3

TTGTCCCGAGCCTCTTTGACGGATGTAATT	1	26	1	CCTCTTTGAC	    0.964212	-266
ATAAAATTTGCCACGATCATAATTAATATC	1	79	0	CCACGATCAT	    0.937775	-213
AAATAAAAAACCACTAACTCTATGTGAAAT	1	187	1	CCACTAACTC	      0.9529	-105
ATATCTTTTTCTCCTTTCGCTATACATCCT	1	247	0	CTCCTTTCGC	    0.942837	-45
AAAAGATATACCTCGATCACCCCCTTTCTC	1	268	1	CCTCGATCAC	    0.989839	-24
CCTCGATCACCCCCTTTCTCCCAA      	1	278	1	CCCCTTTCTC	    0.992178	-14
          **********

Masking position 4
Map Score:   3.57164

Number of sites scoring better than the average of aligned sites = 1085
Number in coding regions = 1001
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 4

          **********

No masking
Map Score:   -4.80737e-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 5

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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