AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i219_Ribosomal_Operon_6_hpyl_reg_300.orf -o219_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	RHP01627	100	AE000511
#2	RHP01474	247	AE000511

Motif number 1

   AAATTCTTGACAACCAGTTAATTCGTCTTATATAATACTAT	1	8	1	TGCAAATTAT	    0.985178	-93
TGCTTAACAATGGCTACAAATGAAATAGTATTATATAAGACGAA	1	32	0	TGCAAATTAT	    0.985764	-69
AAGCAATGATTTTAAGCTATGGAAAAGAGGTGATAGCAGT    	1	71	1	TTCAAATGAT	    0.970143	-30
TTTTTATTTCCTAATTCCATTAAAATTTCCTTTTTTAGTTAGTG	2	66	1	CTCAAATTTT	    0.985758	-182
GACGGCTATTCTAACATGAAATAAACGCCGTTTTATATTAAATC	2	124	1	CTTAAATTTT	    0.885531	-124
CCGTTTTATATTAAATCTAAAGAAAAATATTTTTAGATGTGCTA	2	151	1	TTCAAATTTT	    0.991892	-97
GAATACCCATTTGTTACAAGATAAGCTTTTTTATCAAAAATAAT	2	195	1	TTCAAATTAT	    0.991892	-53
       TTGTTACCCCTATGTCATCATTATTTTTGATAAAAAA	2	221	0	TTCACATTTT	    0.970143	-27
          **    * *   **      ****

Masking position 14
Map Score:   6.49382

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 191
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

AAATAGTATTATATAAGACGAATTAACTGG	1	24	0	ATATAAGACG	    0.942714	-77
GGAAATAAAAATATAAAACCCGGTCGCAAG	2	47	0	ATATAAAACC	    0.979584	-201
TACACACTAACTAAAAAAGGAAATTTTAAT	2	84	0	CTAAAAAAGG	     0.94149	-164
TTATTTCATGTTAGAATAGCCGTCATGATA	2	118	0	TTAGAATAGC	    0.865302	-130
TTTAGATTTAATATAAAACGGCGTTTATTT	2	142	0	ATATAAAACG	    0.973355	-106
TTTAGATGTGCTAGAATACCCATTTGTTAC	2	182	1	CTAGAATACC	    0.958359	-66
ATTATTTTTGATAAAAAAGCTTATCTTGTA	2	209	0	ATAAAAAAGC	    0.962255	-39
          **********

Masking position 5
Map Score:   5.3362

Number of sites scoring better than the average of aligned sites = 397
Number in coding regions = 344
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 3

TACTATTTCATTTGTAGCCATTGTTAAGCAA	1	46	1	TTTGTAGCAT	    0.986358	-55
TTGTAGCCATTGTTAAGCAATGATTTTAAGC	1	57	1	TGTTAAGCAT	    0.974845	-44
TAAGCAATGATTTTAAGCTATGGAAAAGAGG	1	70	1	TTTTAAGCAT	    0.979056	-31
AAAATTTCCTTTTTTAGTTAGTGTGTAGTAA	2	87	1	TTTTTAGTAG	    0.934012	-161
TTTTAGTTAGTGTGTAGTAATATCATGACGG	2	98	1	TGTGTAGTAT	    0.963776	-150
AAGAAAAATATTTTTAGATGTGCTAGAATAC	2	170	1	TTTTTAGAGT	     0.88922	-78
          ******** **

Masking position 6
Map Score:   2.82502

Number of sites scoring better than the average of aligned sites = 303
Number in coding regions = 266
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   -7.8627e-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:   -7.8627e-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:   -7.8627e-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