AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_hpyl_reg_300.orf -o215_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	RHP01243	241	AE000511
#2	RHP01245	116	AE000511
#3	RHP01250	19	AE000511

Motif number 1

AGCTTGTTTGTTAAAAAACCAATAAGGATTTGA	1	13	0	TTAAACCAAT	    0.975515	-229
ATAACCCCATTTAACCCGCCATTATTAACCCGC	1	101	0	TTAACCCATT	    0.971004	-141
TTATTTTGAATAAAAAATTCTTTTAATGTGGAT	1	130	1	TAAAATCTTT	    0.869784	-112
TAAATTGAGATTAAATCCACATTAAAAGAATTT	1	144	0	TTAAAACATT	    0.971746	-98
TAATCTCAATTTAAAGTTACATTTTAGCAAATA	1	164	1	TTAAAACATT	    0.971746	-78
TCCTTAAAAATTGAACGCTCTTTTTAAAATAAA	1	213	0	TTGAATCTTT	    0.953943	-29
ACCTAAAGGTTTAATTAACCTTTAAAGGTTACC	2	11	0	TTAATCCTTT	    0.965321	-106
TTAGGTGTTTGTGAAACACCTATAAACGCAATA	2	38	1	GTGAACCTAT	    0.848619	-79
       AGCTTAAAAATCCTTTCTT       	3	4	0	TTAAACCTTT	    0.993603	-16
          *****   *****

Masking position 4
Map Score:   8.56202

Number of sites scoring better than the average of aligned sites = 890
Number in coding regions = 735
Number in noncoding regions = 155
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 2

GTTAAAAAACCAATAAGGATTTGATC     	1	6	0	CAATAAGATT	    0.945269	-236
AACAAACAAGCTAAAAGTATTCCAAAATAAG	1	34	1	CTAAAAGATT	    0.915854	-208
AAAATAAGCTTAATAACAATTGCGAGTGGTT	1	57	1	TAATAACATT	    0.819536	-185
TAAATCCACATTAAAAGAATTTTTTATTCAA	1	135	0	TTAAAAGATT	    0.903808	-107
TAAAGTTACATTTTAGCAAATACTCACTATA	1	175	1	TTTTAGCAAT	     0.56836	-67
ATACTCACTATAATAAGCGTTTATTTTAAAA	1	194	1	TAATAAGGTT	    0.945269	-48
AGCGTTCAATTTTTAAGGAATAGAA      	1	227	1	TTTTAAGAAT	    0.885489	-15
    GGTAACCTTTAAAGGTTAATTAAACCT	2	7	1	CTTTAAAGTT	    0.891717	-110
TTAATTAAACCTTTAGGTGTTTGTGAAACAC	2	26	1	CTTTAGGGTT	    0.942251	-91
TTTATTGCGTTTATAGGTGTTTCACAAACAC	2	42	0	TTATAGGGTT	    0.964486	-75
GAGATCTAAATTATAAATATTTTATTGCGTT	2	62	0	TTATAAAATT	    0.922072	-55
ACAACAAATTCTATAAAGGATAGAGATCTAA	2	84	0	CTATAAAGAT	    0.849512	-33
          ******* ***

Masking position 5
Map Score:   10.6583

Number of sites scoring better than the average of aligned sites = 1623
Number in coding regions = 1396
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 183
Fraction of orfs with sites within 600 bp upstream = 0.0293929


Motif number 3

CTAAAAGTATTCCAAAATAAGCTTAATAAC	1	44	1	TCCAAAATAA	    0.986954	-198
GAATTTTTTATTCAAAATAACCCCATTTAA	1	120	0	TTCAAAATAA	    0.973422	-122
TGAGATTAAATCCACATTAAAAGAATTTTT	1	142	0	TCCACATTAA	    0.975017	-100
AAAATGTAACTTTAAATTGAGATTAAATCC	1	159	0	TTTAAATTGA	    0.807119	-83
GAACGCTCTTTTTAAAATAAACGCTTATTA	1	204	0	TTTAAAATAA	    0.946625	-38
AGGATAGAGATCTAAATTATAAATATTTTA	2	69	0	TCTAAATTAT	    0.853819	-48
 AAGCCAGTCTCCACAACAAATTCTATAAA	2	98	0	TCCACAACAA	    0.939997	-19
          **********

Masking position 6
Map Score:   6.43178

Number of sites scoring better than the average of aligned sites = 278
Number in coding regions = 241
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

          **********

No masking
Map Score:   6.63809e-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:   6.63809e-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:   6.63809e-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