AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i027_Fumarate_Hydratase_hpyl_reg_300.orf -o027_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00716	174	AE000511

Motif number 1

TGCGAACGGATAATAACCCTCTTTTGTGTA	1	51	1	TAATAACCCT	    0.993902	-124
CCTAATTTTTTAAACACCATTTCCACAATT	1	83	0	TAAACACCAT	    0.988834	-92
ACCTTCTACTTAAAAACCCTAATTTTTTAA	1	100	0	TAAAAACCCT	    0.997577	-75
AAATTTGATTTTAAAACCTTAAAAAAATAG	1	143	0	TTAAAACCTT	    0.983539	-32
          **********

Masking position 6
Map Score:   6.12564

Number of sites scoring better than the average of aligned sites = 316
Number in coding regions = 262
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 2

  CGTTTTGACCTTTACATTAAGATAACAAGAA	1	9	1	CCTTCTTAAG	    0.974683	-166
TAATAACCCTCTTTTGTGTAAAAATTGTGGAAA	1	61	1	CTTTTTAAAA	    0.977527	-114
CTTAAAAACCCTAATTTTTTAAACACCATTTCC	1	89	0	CTATTTTAAA	    0.987937	-86
ACTCTTATACCTTCTACTTAAAAACCCTAATTT	1	105	0	CTTTCTAAAA	    0.985717	-70
AGAGTTTATGCTATTTTTTTAAGGTTTTAAAAT	1	133	1	CTATTTTAAG	    0.985044	-42
         GCTAATCCTTTGAAATTTGATTTT	1	161	0	CTATCTTGAA	    0.979248	-14
          *** * * *****

Masking position 5
Map Score:   5.55515

Number of sites scoring better than the average of aligned sites = 239
Number in coding regions = 184
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

          **********

No masking
Map Score:   -1.89414e-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:   -1.89414e-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:   -1.89414e-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