AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_hpyl_reg_100.orf -o215_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	RHP01243	241	AE000511
#2	RHP01245	116	AE000511
#3	RHP01250	19	AE000511

Motif number 1

     GATCAAATCCTTATTGGTTTTTTAAC	1	6	1	AATCTTATTG	    0.942692	-236
CTTATTTTGGAATACTTTTAGCTTGTTTGTT	1	34	0	AATCTTTTAG	    0.912022	-208
AACCACTCGCAATTGTTATTAAGCTTATTTT	1	57	0	AATGTTATTA	    0.812216	-185
TTGAATAAAAAATTCTTTTAATGTGGATTTA	1	135	1	AATCTTTTAA	    0.899487	-107
TATAGTGAGTATTTGCTAAAATGTAACTTTA	1	175	0	ATTGCTAAAA	    0.556367	-67
TTTTAAAATAAACGCTTATTATAGTGAGTAT	1	194	0	AACCTTATTA	    0.942692	-48
      TTCTATTCCTTAAAAATTGAACGCT	1	227	0	ATTCTTAAAA	    0.880454	-15
AGGTTTAATTAACCTTTAAAGGTTACC    	2	7	0	AACTTTAAAG	    0.886921	-110
GTGTTTCACAAACACCTAAAGGTTTAATTAA	2	26	0	AACCCTAAAG	    0.939542	-91
GTGTTTGTGAAACACCTATAAACGCAATAAA	2	42	1	AACCCTATAA	    0.962778	-75
AACGCAATAAAATATTTATAATTTAGATCTC	2	62	1	AATTTTATAA	    0.918498	-55
TTAGATCTCTATCCTTTATAGAATTTGTTGT	2	84	1	ATCTTTATAG	    0.843175	-33
          *** *******

Masking position 1
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 2

TTTAGCTTGTTTGTTAAAAAACCAATAAGG	1	19	0	TTGTTAAAAA	    0.719249	-223
TTCCAAAATAAGCTTAATAACAATTGCGAG	1	53	1	AGCTTAATAA	    0.937597	-189
GGGACAATGCGGGTTAATAATGGCGGGTTA	1	93	1	GGGTTAATAA	    0.936095	-149
TAATAATGGCGGGTTAAATGGGGTTATTTT	1	107	1	GGGTTAAATG	    0.828053	-135
GATTAAATCCACATTAAAAGAATTTTTTAT	1	139	0	ACATTAAAAG	    0.870571	-103
    TTCTATTCCTTAAAAATTGAACGCTC	1	226	0	TCCTTAAAAA	    0.954238	-16
      GGTAACCTTTAAAGGTTAATTAAA	2	5	1	ACCTTTAAAG	    0.951667	-112
ATATTTTATTGCGTTTATAGGTGTTTCACA	2	47	0	GCGTTTATAG	    0.929136	-70
TAGATCTCTATCCTTTATAGAATTTGTTGT	2	85	1	TCCTTTATAG	    0.911725	-32
          AGCTTAAAAATCCTTTCTT 	3	10	0	AGCTTAAAAA	    0.956537	-10
          **********

Masking position 5
Map Score:   7.36735

Number of sites scoring better than the average of aligned sites = 1544
Number in coding regions = 1353
Number in noncoding regions = 191
Number of orfs with sites within 600 bp upstream = 153
Fraction of orfs with sites within 600 bp upstream = 0.0245744


Motif number 3

AGCTTGTTTGTTAAAAAACCAATAAGGATT	1	16	0	TTAAAAAACC	    0.943179	-226
AAAAGTATTCCAAAATAAGCTTAATAACAA	1	46	1	CAAAATAAGC	    0.978577	-196
ATTTTTTATTCAAAATAACCCCATTTAACC	1	118	0	CAAAATAACC	    0.983606	-124
AAATACTCACTATAATAAGCGTTTATTTTA	1	192	1	TATAATAAGC	    0.903212	-50
GCGTTTATTTTAAAAAGAGCGTTCAATTTT	1	210	1	TAAAAAGAGC	    0.913956	-32
ACCTAAAGGTTTAATTAACCTTTAAAGGTT	2	14	0	TTAATTAACC	    0.817758	-103
ATAGGTGTTTCACAAACACCTAAAGGTTTA	2	31	0	CACAAACACC	    0.860343	-86
          **********

Masking position 4
Map Score:   3.41445

Number of sites scoring better than the average of aligned sites = 886
Number in coding regions = 779
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


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