AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i026_Fumarate_Reductase_hpyl_reg_100.orf -o026_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	RHP01144	214	AE000511

Motif number 1

AGGGGCTATTGTTTAAAATTTACATTTTTTAAACGCTAT	1	58	0	GTTAAATTTT	     0.96689	-157
AACAATAGCCCCTTTGAATTGAATTTTTTCTCAATTTAG	1	84	1	CTTTAATTTT	    0.990749	-131
AATTTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAATT	1	105	1	CATTAGTTTT	    0.989712	-110
AATTCTACTACATTTGAAATAATTTTTCTTATAAACAAA	1	125	0	CTTTAATTTT	    0.990749	-90
AAATGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGCG	1	149	1	GATTAGTTTT	    0.992149	-66
TGCGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAGGA	1	177	1	GTTTAGTTTA	     0.98369	-38
TTAATTTTGAGTTTTTAGGAGCAGTTTTT          	1	196	1	GTTTAGTTTT	     0.99657	-19
          * *** **      *** *

Masking position 7
Map Score:   9.00073

Number of sites scoring better than the average of aligned sites = 323
Number in coding regions = 280
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 2

GTTTAAAATTTACATTTTTTAAACGCTATT	1	57	0	TACATTTTTT	    0.898596	-158
ATTCAAAGGGGCTATTGTTTAAAATTTACA	1	73	0	GCTATTGTTT	     0.95382	-142
CCCTTTGAATTGAATTTTTTCTCAATTTAG	1	93	1	TGAATTTTTT	    0.920881	-122
TCTCAATTTAGGTTTTGTTTATAAGAAAAA	1	112	1	GGTTTTGTTT	    0.947205	-103
GTAGAATTAAGGCAGTGTTTTTGCGTCAAG	1	156	1	GGCAGTGTTT	    0.992692	-59
AGTTTTTAGGAGCAGTTTTT          	1	205	1	AGCAGTTTTT	    0.956022	-10
          **********

Masking position 6
Map Score:   2.90028

Number of sites scoring better than the average of aligned sites = 967
Number in coding regions = 861
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

TTACCACCTATAAAATAAGGATCGTTCA  	1	9	0	TAAAATAAGG	    0.990041	-206
CGCTATTAGATATAATAAGGGATAGTTACC	1	34	0	TATAATAAGG	    0.982173	-181
GAATTTTTTCTCAATTTAGGTTTTGTTTAT	1	104	1	TCAATTTAGG	    0.958066	-111
TCAAATGTAGTAGAATTAAGGCAGTGTTTT	1	147	1	TAGAATTAAG	    0.954683	-68
          **********

Masking position 6
Map Score:   1.43377

Number of sites scoring better than the average of aligned sites = 181
Number in coding regions = 141
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 4

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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