AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i097_Phosphate_Transport_hpyl_reg_300.orf -o097_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	RHP00872	138	AE000511

Motif number 1

TTTAAAGAGAGTTTTAAAAA          	1	1	0	GTTTTAAAAA	    0.630828	-138
TTTTAAAACTCTCTTTAAAATTTTACTTTA	1	12	1	CTCTTTAAAA	    0.982198	-127
AAAGCGTTGTTTGATAAAAATGGCTCATTA	1	52	0	TTGATAAAAA	    0.895456	-87
CCTTGAGCCACTCTTAAAAAGCGTTGTTTG	1	69	0	CTCTTAAAAA	    0.930382	-70
       ATCGTCATAAAAACCTTGTTCTA	1	126	0	GTCATAAAAA	    0.989728	-13
          **********

Masking position 5
Map Score:   8.16598

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 116
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

AAACTCTCTTTAAAATTTTACTTTAAGATACCAT	1	17	1	TAAATTTCTT	    0.934769	-122
TAAGATACCATATAATGAGCCATTTTTATCAAAC	1	40	1	TAAATAGCTT	    0.996711	-99
GCCATTTTTATCAAACAACGCTTTTTAAGAGTGG	1	58	1	TCAACACCTT	    0.983381	-81
TCTTATTCTATCCAATTAGCCCTTGAGCCACTCT	1	85	0	TCAATAGCTT	    0.996036	-54
GCTAATTGGATAGAATAAGACCACTATTAGAACA	1	99	1	TAAATAGCAC	    0.964719	-40
AGACCACTATTAGAACAAGGTTTTTATGACGAT 	1	116	1	TAAACAGTTT	    0.973609	-23
          ** *** ** * **

Masking position 5
Map Score:   4.12163

Number of sites scoring better than the average of aligned sites = 351
Number in coding regions = 307
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

ACCATATAATGAGCCATTTTTATCAAACAA	1	46	1	GAGCCATTTT	    0.996681	-93
ATTAGCCCTTGAGCCACTCTTAAAAAGCGT	1	75	0	GAGCCACTCT	    0.998489	-64
          **********

Masking position 6
Map Score:   0.769067

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 4
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   -9.70439e-14

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:   -9.70439e-14

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:   -9.70439e-14

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