AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i304_ecoli_bsub_300.orf -o304_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	yfdE	34	putative enzyme
#2	b2372	69	putative receptor protein
#3	b2373	53	putative enzyme
#4	b2374	300	putative enzyme

Motif number 1

          TTCGGCATTTATGTAAAATC	1	25	0	TTCGGCATTT	    0.959166	-10
GGGCTTCTGGCTCCCAATTTATAAAAATTT	3	20	1	CTCCCAATTT	    0.906694	-34
GATTAATAACCTCGAAATTTTTATAAATTG	3	34	0	CTCGAAATTT	    0.972296	-20
CAGAGAGAGTCGCGACATTTGTGATGTTAT	4	59	0	CGCGACATTT	    0.960423	-242
ATTACCACGAATCAATATTTATCATATTCT	4	89	1	ATCAATATTT	    0.842826	-212
TCTTTTCGTCCTCACTACTTACCATGCAGA	4	119	1	CTCACTACTT	    0.951409	-182
AAATCATTTCATCGCCACTTCCAATTCCTT	4	149	0	ATCGCCACTT	    0.965779	-152
TGAAATGATTTTCAGCACTTGATACAGGAT	4	168	1	TTCAGCACTT	    0.883361	-133
CGTAGCTGCACTCGATATTTTTAAAATCCT	4	193	0	CTCGATATTT	    0.980502	-108
          **********

Masking position 7
Map Score:   7.68863

Number of sites scoring better than the average of aligned sites = 956
Number in coding regions = 854
Number in noncoding regions = 102
Number of orfs with sites within 600 bp upstream = 106
Fraction of orfs with sites within 600 bp upstream = 0.0170254


Motif number 2

TAAAAATTTCGAGGTTATTAATC        	3	41	1	GGGTTATTAA	    0.980299	-13
GTAAGAAGCGCCGGTGATTTACAAGCAAGGG	4	18	0	CGGTGATTTA	    0.973954	-283
CGATATTTTGCGGGTTATTTATAGAAGATAT	4	224	1	CGGTTATTTA	    0.984555	-77
TGTTAATTTAGCGTTTATTTAAGGCGTAATA	4	252	0	GGTTTATTTA	    0.983348	-49
AATTAAATATGTGTTAATTTAGCGTTTATTT	4	263	0	GGTTAATTTA	    0.976308	-38
CAATACCTATTAGTTAATTAAATATGTGTTA	4	278	0	TGTTAATTAA	    0.847462	-23
          * *********

Masking position 5
Map Score:   4.73561

Number of sites scoring better than the average of aligned sites = 221
Number in coding regions = 186
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

TACTGACATCGTCTCCTCTTGCCAACTCATTA	2	12	1	GTCTCCCTTC	    0.986924	-58
TTTCCGATAAGGGTCCCCTCACCATCGCATAA	2	41	0	GGGTCCCTCC	    0.986383	-29
  TATTAACGGGGGCTTCTGGCTCCCAATTTA	3	9	1	GGGGCTCTGC	     0.98488	-45
GTAAATCACCGGCGCTTCTTACAGTTGTAAGA	4	27	1	GGCGCTCTTC	    0.995314	-274
CATCACAAATGTCGCGACTCTCTCTGATTACC	4	63	1	GTCGCGCTCC	    0.993871	-238
AAATCATTTCATCGCCACTTCCAATTCCTTTC	4	147	0	ATCGCCCTTC	    0.972891	-154
AAATATCGTCGTAGCTGCACTCGATATTTTTA	4	200	0	GTAGCTCACC	    0.916628	-101
          ****** *** *

Masking position 5
Map Score:   5.87045

Number of sites scoring better than the average of aligned sites = 794
Number in coding regions = 756
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 4

TGTAAAATCAATAACATGATTAA       	1	4	0	ATAACATGAT	    0.928133	-31
AGTTGGCAAGAGGAGACGATGTCAGTAT  	2	9	0	AGGAGACGAT	    0.955914	-61
TTTACAAGCAAGGGTATGATT         	4	2	0	AGGGTATGAT	    0.958212	-299
GACGAAAAGAAGAATATGATAAATATTGAT	4	99	0	AGAATATGAT	    0.956514	-202
GGAAGTGGCGATGAAATGATTTTCAGCACT	4	157	1	ATGAAATGAT	    0.876182	-144
AATGATTTTCAGCACTTGATACAGGATTTT	4	171	1	AGCACTTGAT	    0.897131	-130
          **********

Masking position 9
Map Score:   1.18745

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 242
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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