AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i239_ecoli_bsub_300.orf -o239_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	yjdH	180	putative 2-component sensor protein
#2	yufL	120	similar to two-component sensor histidine kinase [YufM]

Motif number 1

GTGCTGTATGAAGATTCCGGGGCTATGCTT	1	46	0	AAGATTCCGG	    0.987345	-135
ACAGCACTGGCAGTTTCCGTTGCCAGAGTC	1	69	1	CAGTTTCCGT	    0.959998	-112
CCTTGTGTGACAAATTTCTTAAGCATTATC	1	155	0	CAAATTTCTT	    0.876941	-26
          CAGCTTCCTTGTGTGACAAA	1	171	0	CAGCTTCCTT	    0.989536	-10
CTGCTTTGTGAAGATTTGGGCCCGTAATTC	2	48	0	AAGATTTGGG	    0.916072	-73
TCTCAAAATGCTGCTTTGTGAAGATTTGGG	2	58	0	CTGCTTTGTG	    0.886542	-63
CTTACGTTTTATGATTCCTGCGTACTACTT	2	91	0	ATGATTCCTG	    0.967036	-30
       ATAAAACTTCCTTACGTTTTATG	2	108	0	AAACTTCCTT	    0.933473	-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

ATACTGATGAGAGAGGGAAGGTC        	1	3	0	GAGAGGAAGG	    0.993955	-178
AATTCAAAGGGAGTAAGAATGATTGGCTATA	1	109	0	GAGTAAAATG	    0.972193	-72
CCCGCCTCATCAGAGATAATGCTTAAGAAAT	1	141	1	CAGAGAAATG	    0.986137	-40
TCGTAAAAAGGAGAAAAAATGGAATAATTTA	2	19	0	GAGAAAAATG	    0.991394	-102
GCAGCATTTTGAGAGTAAAGTAGTACGCAGG	2	74	1	GAGAGTAAGT	     0.95507	-47
          ****** ****

Masking position 8
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

GTATGAAGATTCCGGGGCTATGCTTATAGC	1	41	0	TCCGGGGCTA	    0.996675	-140
ACTGGCAGTTTCCGTTGCCAGAGTCTCTTC	1	74	1	TCCGTTGCCA	    0.991037	-107
TTTTACGAATTACGGGCCCAAATCTTCACA	2	42	1	TACGGGCCCA	    0.993561	-79
          **********

Masking position 10
Map Score:   0.469867

Number of sites scoring better than the average of aligned sites = 162
Number in coding regions = 151
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


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