AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_hpyl_reg_300.orf -o198_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	RHP01107	98	AE000511

Motif number 1

      AGTAAAATCCTTTTGTGATAGGGT	1	5	1	AAATCCTTTT	    0.956246	-94
GTGATAGGGTAAGTCCTTTTATTATAATAG	1	25	1	AAGTCCTTTT	    0.984632	-74
ATCCTAGCCTAAAATCTATTATAATAAAAG	1	40	0	AAAATCTATT	     0.91218	-59
TTATTCTATCAAATCCTAGCCTAAAATCTA	1	52	0	AAATCCTAGC	    0.984998	-47
TAGAATAAACAAATCAAATTCAATAAGGTA	1	74	1	AAATCAAATT	     0.91218	-25
          **********

Masking position 2
Map Score:   5.908

Number of sites scoring better than the average of aligned sites = 994
Number in coding regions = 846
Number in noncoding regions = 148
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 2

  AGTAAAATCCTTTTGTGATAGGGTAAGTC	1	9	1	CCTTTTGTAT	    0.997103	-90
TAGGGTAAGTCCTTTTATTATAATAGATTTT	1	29	1	CCTTTTATAT	    0.995712	-70
   TAAATTACCTTATTGAATTTGATTTGTT	1	81	0	CCTTATTGAT	    0.991042	-18
          ******** **

Masking position 10
Map Score:   1.75521

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 90
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

CTTACCCTATCACAAAAGGATTTTACT   	1	8	0	CACAAAAGGA	    0.995833	-91
AATCTATTATAATAAAAGGACTTACCCTAT	1	28	0	AATAAAAGGA	    0.990527	-71
TGATAGAATAAACAAATCAAATTCAATAAG	1	71	1	AACAAATCAA	     0.96989	-28
          **********

Masking position 5
Map Score:   0.8604

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 87
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


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