AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_Ribosomal_Operon_5_hpyl_reg_300.orf -o218_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	RHP01413	99	AE000511
#2	RHP01414	124	AE000511

Motif number 1

     TTCTTAAACAAACCATTTAAAAATTAGCC	1	6	1	AAAACCATTA	    0.941396	-94
AACCATTTAAAAATTAGCCTTAAAATCAGTCTTT	1	21	1	AAATCCTTAA	    0.994673	-79
CATTATACTTAAAATAGCCTTTAAAAAGACTGAT	1	45	0	AAATCCTTAA	    0.994635	-55
TTATTGAAATAAACTTTGCATTATACTTAAAATA	1	63	0	AAATGCATAT	    0.947235	-37
          AAAATCCCCTAAAATCGCCATGCT	2	1	1	AAATCCTAAA	     0.99222	-124
GCCATGCTTGAAATTTAGAAAAAAGAAAATTGTA	2	27	1	AAATGAAAAA	    0.883947	-98
TAAGTAAATCAATTTGCGCTACAATTTTCTTTTT	2	46	0	AATTGCTAAA	    0.947213	-79
TGATTTACTTAAAAATAGCATGAATAGGGTAGGA	2	69	1	AAAAGCATAA	    0.982991	-56
CCTAAAAATTAAAATAAGCTTCTATCCTACCCTA	2	93	0	AAATGCTTTA	    0.981111	-32
         AAAAGATTCCTAAAAATTAAAATAA	2	110	0	AAAACCTAAA	    0.982992	-15
          *** *  **** **

Masking position 2
Map Score:   17.6935

Number of sites scoring better than the average of aligned sites = 1132
Number in coding regions = 928
Number in noncoding regions = 204
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 2

AAAGACTGATTTTAAGGCTAATTTTTAAAT	1	25	0	TTTAAGGCTA	    0.994654	-75
ATCAGTCTTTTTAAAGGCTATTTTAAGTAT	1	45	1	TTAAAGGCTA	    0.980576	-55
CTATTTTAAGTATAATGCAAAGTTTATTTC	1	62	1	TATAATGCAA	    0.841699	-38
TATTTCAATAATTAAGGATACACA      	1	86	1	ATTAAGGATA	    0.973402	-14
TCATGCTATTTTTAAGTAAATCAATTTGCG	2	62	0	TTTAAGTAAA	    0.784544	-63
ATCCTACCCTATTCATGCTATTTTTAAGTA	2	74	0	ATTCATGCTA	    0.928487	-51
          **********

Masking position 5
Map Score:   5.09022

Number of sites scoring better than the average of aligned sites = 923
Number in coding regions = 799
Number in noncoding regions = 124
Number of orfs with sites within 600 bp upstream = 117
Fraction of orfs with sites within 600 bp upstream = 0.0187922


Motif number 3

          **********

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 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