AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i043_5_1_3_1_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 
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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	dam	106	DNA adenine methylase
#2	yjeQ	64	orf, hypothetical protein

Motif number 1

AACGATAAACCATTGCGGGAGATAACCTTGA	1	11	0	CATTGCGGAG	    0.997364	-96
AATGGTTTATCGTTGCGGGAGTTGCCTGAAG	1	28	1	CGTTGCGGAG	    0.999099	-79
CAGCATCCAGCGCTTCAGGCAACTCCCGCAA	1	40	0	CGCTTCGGCA	    0.983649	-67
AAGCGCTGGATGCTGTCGGAGCTTTCTCCAC	1	56	1	TGCTGTGGAG	    0.986011	-51
GAGCTTTCTCCACAGCCGGAGAAGGTGTAAT	1	74	1	CACAGCGGAG	    0.995689	-33
      GCGGCGCTGCTGGCCTTTGGAGAGT	2	50	0	CGCTGCGGCC	    0.998479	-15
          ****** ****

Masking position 8
Map Score:   13.0079

Number of sites scoring better than the average of aligned sites = 2021
Number in coding regions = 1941
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 2

TTATCTCCCGCAATGGTTTATCGTTGCGGG	1	17	1	CAATGGTTTA	    0.900557	-90
CTGAAGCGCTGGATGCTGTCGGAGCTTTCT	1	53	1	GGATGCTGTC	    0.979132	-54
CCACAGCCGGAGAAGGTGTAATTAGTTAGT	1	83	1	AGAAGGTGTA	     0.96179	-24
GGGGCGACCAGGAGTCTGTACGATTGAGTA	2	13	1	GGAGTCTGTA	    0.984443	-52
GGAGTCTGTACGATTGAGTAAAAATAAACT	2	23	1	CGATTGAGTA	    0.949989	-42
GCTGGCCTTTGGAGAGTTTATTTTTACTCA	2	37	0	GGAGAGTTTA	    0.958677	-28
          **********

Masking position 3
Map Score:   1.52292

Number of sites scoring better than the average of aligned sites = 1356
Number in coding regions = 1217
Number in noncoding regions = 139
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 3

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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