AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i239_ecoli_bsub_100.orf -o239_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	yjdH	180	putative 2-component sensor protein
#2	yufL	120	similar to two-component sensor histidine kinase [YufM]

Motif number 1

AAGCATAGCCCCGGAATCTTCATACAGCAC	1	46	1	CCGGAATCTT	    0.986083	-135
GACTCTGGCAACGGAAACTGCCAGTGCTGT	1	69	0	ACGGAAACTG	    0.956042	-112
GATAATGCTTAAGAAATTTGTCACACAAGG	1	155	1	AAGAAATTTG	    0.866122	-26
TTTGTCACACAAGGAAGCTG          	1	171	1	AAGGAAGCTG	    0.988523	-10
GAATTACGGGCCCAAATCTTCACAAAGCAG	2	48	1	CCCAAATCTT	    0.908192	-73
CCCAAATCTTCACAAAGCAGCATTTTGAGA	2	58	1	CACAAAGCAG	    0.876251	-63
AAGTAGTACGCAGGAATCATAAAACGTAAG	2	91	1	CAGGAATCAT	    0.963781	-30
CATAAAACGTAAGGAAGTTTTAT       	2	108	1	AAGGAAGTTT	    0.927089	-13
          **********

Masking position 5
Map Score:   6.61439

Number of sites scoring better than the average of aligned sites = 2529
Number in coding regions = 2318
Number in noncoding regions = 211
Number of orfs with sites within 600 bp upstream = 221
Fraction of orfs with sites within 600 bp upstream = 0.0354963


Motif number 2

        GACCTTCCCTCTCTCATCAGTAT	1	3	1	CCTTCCTCTC	    0.993506	-178
TATAGCCAATCATTCTTACTCCCTTTGAATT	1	109	1	CATTTTACTC	    0.970187	-72
ATTTCTTAAGCATTATCTCTGATGAGGCGGG	1	141	0	CATTTCTCTG	    0.985187	-40
TAAATTATTCCATTTTTTCTCCTTTTTACGA	2	19	1	CATTTTTCTC	    0.990758	-102
CCTGCGTACTACTTTACTCTCAAAATGCTGC	2	74	0	ACTTACTCTC	     0.95188	-47
          **** ******

Masking position 4
Map Score:   2.5638

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 138
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

          **********

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 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