AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i220_Ribosomal_Operon_7_hpyl_reg_300.orf -o220_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	RHP01312	55	AE000511
#2	RHP00471	290	AE000511

Motif number 1

TTTATTTTTTATTAATCGTTTTATTTTAGC	1	19	0	ATTAATCGTT	    0.987705	-37
TTAATAAAAAATAAATCGTTAGAAAGAAGT	1	34	1	ATAAATCGTT	    0.984677	-22
GAGTGCGATAAAGGGTCATTGGATGGTTTG	2	41	0	AAGGGTCATT	    0.766492	-250
TGTTTGCTATGATAATCGTTTAAAAGTAAT	2	84	0	GATAATCGTT	     0.94047	-207
TGGAGCGTTCAATGAGCGTTCTTATTTGTA	2	127	0	AATGAGCGTT	    0.947937	-164
CATTGGCTAAATGGAGCGTTCAATGAGCGT	2	138	0	ATGGAGCGTT	    0.979202	-153
CTTGACCGACAATAATCATTGGCTAAATGG	2	154	0	AATAATCATT	    0.786171	-137
CCTTATAATAATAAATCGTTCCAAATAATA	2	205	0	ATAAATCGTT	    0.984677	-86
ATTTATTATTATAAGGCGTTAGAGACGCTT	2	219	1	ATAAGGCGTT	     0.96301	-72
          **********

Masking position 9
Map Score:   14.107

Number of sites scoring better than the average of aligned sites = 775
Number in coding regions = 660
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 2

AAACGATTAATAAAAAATAAATCGTTAGAA	1	28	1	TAAAAAATAA	    0.877527	-28
AAATAAATCGTTAGAAAGAAGTTA      	1	42	1	TTAGAAAGAA	    0.917726	-14
GACAAGGATTTTACAAGTAA          	2	1	0	TTACAAGTAA	    0.942492	-290
TGATAATCGTTTAAAAGTAATAAAATAACT	2	75	0	TTAAAAGTAA	    0.964687	-216
CTGAATTTTTTTACAAATAAGAACGCTCAT	2	116	1	TTACAAATAA	    0.974595	-175
CATGTTTTGATTAAAATTACCTTGACCGAC	2	174	0	TTAAAATTAC	    0.871563	-117
TAATAAATCGTTCCAAATAATAGCATGTTT	2	197	0	TTCCAAATAA	    0.906115	-94
CTTTGGCTGTTTAAAAAGAGCCTAATTTAA	2	246	1	TTAAAAAGAG	    0.967644	-45
TAAGATTGCATTTAAATTAGGCTCTTTTTA	2	257	0	TTTAAATTAG	    0.742324	-34
AAATGCAATCTTAAAAGGAGAAGCACT   	2	274	1	TTAAAAGGAG	    0.966906	-17
          **********

Masking position 5
Map Score:   11.9106

Number of sites scoring better than the average of aligned sites = 516
Number in coding regions = 360
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 3

ATTAATCGTTTTATTTTAGCATGCACCA      	1	5	0	TTATTTACAC	    0.964126	-51
TGTCTTTCTTTTTTCAAACCATCCAATGACCCTT	2	27	1	TTTTAAACAC	     0.98155	-264
CGTTTAAAAGTAATAAAATAACTCTTTGAGTGCG	2	64	0	TAATAAAAAC	    0.944055	-227
TTTTAAACGATTATCATAGCAAACAAACTGAATT	2	89	1	TTATATACAC	    0.977299	-202
GCGTTCTTATTTGTAAAAAAATTCAGTTTGTTTG	2	108	0	TTGTAAAAAC	    0.924213	-183
AAGGTAATTTTAATCAAAACATGCTATTATTTGG	2	181	1	TAATAAACAC	    0.977365	-110
TGGAACGATTTATTATTATAAGGCGTTAGAGACG	2	212	1	TATTTTAAAC	    0.834352	-79
AAATTAGGCTCTTTTTAAACAGCCAAAGCGTCTC	2	240	0	CTTTTAACAC	    0.898045	-51
          **** *** **  *

Masking position 8
Map Score:   5.07416

Number of sites scoring better than the average of aligned sites = 518
Number in coding regions = 429
Number in noncoding regions = 89
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 4

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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:   -2.60469e-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