AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_hpyl_reg_100.orf -o198_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	RHP01107	98	AE000511

Motif number 1

ACCCTATCACAAAAGGATTTTACT      	1	5	0	AAAAGGATTT	    0.953103	-94
CTATTATAATAAAAGGACTTACCCTATCAC	1	25	0	AAAAGGACTT	    0.984941	-74
CTTTTATTATAATAGATTTTAGGCTAGGAT	1	40	1	AATAGATTTT	    0.912928	-59
TAGATTTTAGGCTAGGATTTGATAGAATAA	1	52	1	GCTAGGATTT	    0.986314	-47
TACCTTATTGAATTTGATTTGTTTATTCTA	1	74	0	AATTTGATTT	    0.912928	-25
          **********

Masking position 9
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

GACTTACCCTATCACAAAAGGATTTTACT  	1	9	0	ATCAAAAAGG	    0.996968	-90
AAAATCTATTATAATAAAAGGACTTACCCTA	1	29	0	ATAAAAAAGG	    0.995513	-70
AACAAATCAAATTCAATAAGGTAATTTA   	1	81	1	ATTCATAAGG	    0.990629	-18
          **** ******

Masking position 6
Map Score:   1.75521

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 83
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

TAAAAGGACTTACCCTATCACAAAAGGATT	1	16	0	TACCCTATCA	    0.995017	-83
TAAGTCCTTTTATTATAATAGATTTTAGGC	1	34	1	TATTATAATA	    0.491197	-65
TATCAAATCCTAGCCTAAAATCTATTATAA	1	46	0	TAGCCTAAAA	    0.965219	-53
TTGATTTGTTTATTCTATCAAATCCTAGCC	1	61	0	TATTCTATCA	    0.980003	-38
     TAAATTACCTTATTGAATTTGATTT	1	84	0	TACCTTATTG	    0.936305	-15
          **********

Masking position 6
Map Score:   1.88819

Number of sites scoring better than the average of aligned sites = 408
Number in coding regions = 338
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


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