AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i103_Ferrous_Iron_Transporter_hpyl_reg_100.orf -o103_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	RHP00118	143	AE000511

Motif number 1

CAAGAATGTTAAAAAATGAAAGGAGCGTGT	1	12	0	AAAAAATGAA	    0.917253	-132
TGTTATATAATAAAAGCGAGACAAGAATGT	1	33	0	TAAAAGCGAG	    0.993834	-111
TTTTATTATATAACAATTAGTCTTATAGCG	1	48	1	TAACAATTAG	    0.974395	-96
GTTTTTAGATTAAAAGTCAGCACTATAGCG	1	76	0	TAAAAGTCAG	    0.986399	-68
ACTTTTAATCTAAAAACGATATAACTAAAA	1	89	1	TAAAAACGAT	    0.973859	-55
ACGATATAACTAAAAATTAGAAAAACTTTA	1	104	1	TAAAAATTAG	    0.990474	-40
          **********

Masking position 5
Map Score:   8.24676

Number of sites scoring better than the average of aligned sites = 456
Number in coding regions = 374
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

TATATAACAATTAGTCTTATAGCGCTATAGTG	1	54	1	TTAGTTATAG	    0.992356	-90
AGATTAAAAGTCAGCACTATAGCGCTATAAGA	1	68	0	TCAGCTATAG	    0.995468	-76
TATATCGTTTTTAGATTAAAAGTCAGCACTAT	1	80	0	TTAGAAAAAG	    0.940547	-64
TTTCTAATTTTTAGTTATATCGTTTTTAGATT	1	95	0	TTAGTTATCG	    0.983403	-49
GTTTGAATGCTCCGCATTAAAGTTTTTCTAAT	1	119	0	TCCGCTAAAG	    0.985732	-25
          *****  *****

Masking position 9
Map Score:   3.07077

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 95
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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