AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_hpyl_reg_300.orf -o217_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	RHP00824	120	AE000511
#2	RHP00825	19	AE000511
#3	RHP01620	71	AE000511

Motif number 1

GATACTTTTGAAATTTAAGCGGTAAGTTGG	1	14	0	AAATTTAAGC	    0.989309	-107
AAAACAAATGGTATTTTAGCCGATAGTGTT	1	48	0	GTATTTTAGC	    0.976576	-73
TTATAGCAACAAATTAAAACAAATGGTATT	1	63	0	AAATTAAAAC	    0.861172	-58
TTCAAATGCTCTATTATAGCAACAAATTAA	1	76	0	CTATTATAGC	    0.947752	-45
  TTTTAGTCAATTTTTAGCATTCTTTAGC	3	9	1	AATTTTTAGC	    0.989309	-63
ACATAAACACAGATTTTAGCTAAAGAATGC	3	27	0	AGATTTTAGC	    0.989675	-45
GTTTATGTTTAATTTTTATCAAGGGAGTTT	3	49	1	AATTTTTATC	    0.934684	-23
          **********

Masking position 8
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

GTGTTGTAGGATACTTTTGAAATTTAAGCG	1	23	0	ATACTTTTGA	    0.936431	-98
ATTTTAGCCGATAGTGTTGTAGGATACTTT	1	36	0	ATAGTGTTGT	    0.806858	-85
AAAACAAATGGTATTTTAGCCGATAGTGTT	1	48	0	GTATTTTAGC	    0.884168	-73
CATTTGTTTTAATTTGTTGCTATAATAGAG	1	68	1	AATTTGTTGC	    0.952494	-53
CCTTTGCGATAAGCTTTTGTCATTCAAATG	1	98	0	AAGCTTTTGT	     0.92127	-23
          AAACCTTTGCGATAAGCTTT	1	111	0	AAACCTTTGC	    0.961964	-10
  TTTTAGTCAATTTTTAGCATTCTTTAGC	3	9	1	AATTTTTAGC	    0.956655	-63
AATTTTTAGCATTCTTTAGCTAAAATCTGT	3	19	1	ATTCTTTAGC	    0.978534	-53
          **********

Masking position 7
Map Score:   4.77512

Number of sites scoring better than the average of aligned sites = 1342
Number in coding regions = 1215
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

     TATCCAACTTACCGCTTAAATTTCA	1	6	1	AACTTACCGC	    0.980377	-115
CATTTGTTTTAATTTGTTGCTATAATAGAG	1	68	1	AATTTGTTGC	    0.956699	-53
GAATGACAAAAGCTTATCGCAAAGGTTT  	1	103	1	AGCTTATCGC	    0.991717	-18
  TTTTAGTCAATTTTTAGCATTCTTTAGC	3	9	1	AATTTTTAGC	    0.978882	-63
ACATAAACACAGATTTTAGCTAAAGAATGC	3	27	0	AGATTTTAGC	    0.965959	-45
          **********

Masking position 5
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