AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i027_Fumarate_Hydratase_hpyl_reg_100.orf -o027_hpyl_100.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	    0.993787	-124
CCTAATTTTTTAAACACCATTTCCACAATT	1	83	0	TAAACACCAT	    0.988625	-92
ACCTTCTACTTAAAAACCCTAATTTTTTAA	1	100	0	TAAAAACCCT	    0.997532	-75
AAATTTGATTTTAAAACCTTAAAAAAATAG	1	143	0	TTAAAACCTT	    0.983233	-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

TTCTTGTTATCTTAATGTAAAGGTCAAAACG  	1	9	0	CTTAAGAAGG	    0.976518	-166
TTTCCACAATTTTTACACAAAAGAGGGTTATTA	1	61	0	TTTTAAAAAG	    0.979177	-114
GGAAATGGTGTTTAAAAAATTAGGGTTTTTAAG	1	89	1	TTTAAAATAG	    0.988848	-86
AAATTAGGGTTTTTAAGTAGAAGGTATAAGAGT	1	105	1	TTTTAGAAAG	    0.986793	-70
ATTTTAAAACCTTAAAAAAATAGCATAAACTCT	1	133	0	CTTAAAATAG	      0.9861	-42
AAAATCAAATTTCAAAGGATTAGC         	1	161	1	TTCAAGATAG	    0.980809	-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

AGATAACAAGAAAATTCTTGTTGCGAACGG	1	30	1	AAAATTCTTG	    0.984762	-145
CTTTTGTGTAAAAATTGTGGAAATGGTGTT	1	71	1	AAAATTGTGG	    0.994372	-104
TGGTGTTTAAAAAATTAGGGTTTTTAAGTA	1	94	1	AAAATTAGGG	    0.990126	-81
          **********

Masking position 4
Map Score:   1.48619

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 58
Number in noncoding regions = 12
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:   -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


Motif number 6

          **********

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