AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_hpyl_reg_100.orf -o217_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	RHP00824	120	AE000511
#2	RHP00825	19	AE000511
#3	RHP01620	71	AE000511

Motif number 1

CCAACTTACCGCTTAAATTTCAAAAGTATC	1	14	1	GCTTAAATTT	    0.989154	-107
AACACTATCGGCTAAAATACCATTTGTTTT	1	48	1	GCTAAAATAC	     0.97624	-73
AATACCATTTGTTTTAATTTGTTGCTATAA	1	63	1	GTTTTAATTT	    0.859432	-58
TTAATTTGTTGCTATAATAGAGCATTTGAA	1	76	1	GCTATAATAG	    0.947025	-45
GCTAAAGAATGCTAAAAATTGACTAAAA  	3	9	0	GCTAAAAATT	    0.989154	-63
GCATTCTTTAGCTAAAATCTGTGTTTATGT	3	27	1	GCTAAAATCT	    0.989525	-45
AAACTCCCTTGATAAAAATTAAACATAAAC	3	49	0	GATAAAAATT	    0.933789	-23
          **********

Masking position 6
Map Score:   9.154

Number of sites scoring better than the average of aligned sites = 761
Number in coding regions = 655
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 2

GTGTTGTAGGATACTTTTGAAATTTAAGCGGTA	1	20	0	ACTTTTGAAT	    0.990443	-101
CATTTGTTTTAATTTGTTGCTATAATAGAGCAT	1	68	1	ATTGTTGCAT	    0.942379	-53
CCTTTGCGATAAGCTTTTGTCATTCAAATGCTC	1	95	0	ACTTTTGTAT	    0.983352	-26
          AAACCTTTGCGATAAGCTTTTGT	1	108	0	ACCTTTGCAT	    0.994868	-13
AATTTTTAGCATTCTTTAGCTAAAATCTGTGTT	3	19	1	ACTTTAGCAA	    0.968773	-53
     TTAAAACTCCCTTGATAAAAATTAAACA	3	54	0	ACCCTTGAAA	     0.95423	-18
          *  ******* **

Masking position 7
Map Score:   3.75663

Number of sites scoring better than the average of aligned sites = 349
Number in coding regions = 316
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

TGAAATTTAAGCGGTAAGTTGGATA     	1	6	0	GCGGTAAGTT	    0.980696	-115
CTCTATTATAGCAACAAATTAAAACAAATG	1	68	0	GCAACAAATT	    0.957386	-53
  AAACCTTTGCGATAAGCTTTTGTCATTC	1	103	0	GCGATAAGCT	    0.991853	-18
GCTAAAGAATGCTAAAAATTGACTAAAA  	3	9	0	GCTAAAAATT	    0.979225	-63
GCATTCTTTAGCTAAAATCTGTGTTTATGT	3	27	1	GCTAAAATCT	    0.966505	-45
          **********

Masking position 6
Map Score:   3.22964

Number of sites scoring better than the average of aligned sites = 324
Number in coding regions = 284
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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:   -7.57276e-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