AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iompR_bsub_opreg_100.orf -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yrpD	300	similar to hypothetical proteins from B. subtilis

Motif number 1

GGAAAGAGAGAAAACACTGTAATCAGATAT	1	30	0	AAAACACTGT	    0.967769	-271
TATTGAAATAGAAAAGCTATAGAGAGGGGG	1	73	0	GAAAAGCTAT	    0.986655	-228
AGTCTCGATTGAAAAGTTATCGTAACATTT	1	110	1	GAAAAGTTAT	     0.96958	-191
CTTGTATTATAAAACATTATGAAAATAATT	1	240	0	AAAACATTAT	     0.95219	-61
TTATAATTAGAAAACGCTATCATCTTGTAT	1	263	0	AAAACGCTAT	    0.977382	-38
          **********

Masking position 4
Map Score:   5.05993

Number of sites scoring better than the average of aligned sites = 230
Number in coding regions = 203
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

GGGAGAAATAAGAGGGGAAAGAGAGAAAAC	1	45	0	AGAGGGGAAA	    0.996304	-256
AAAGCTATAGAGAGGGGGGAGAAATAAGAG	1	61	0	AGAGGGGGGA	    0.998384	-240
AATTATAATGATAGGGGGAAATAATG    	1	285	1	ATAGGGGGAA	    0.996303	-16
          **********

Masking position 3
Map Score:   4.03889

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 8
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

GTAATCAGATATGTGTGTATAACTCAATTG	1	12	0	ATGTGTGTAT	    0.979379	-289
ATCTCCTGTGAAGTGTAAATGTTACGATAA	1	126	0	AAGTGTAAAT	     0.92411	-175
CACATTATGACTTTGTGCATCTGGCAAACG	1	177	0	CTTTGTGCAT	    0.974682	-124
CAAAGTCATAATGTGTAAATTCTGTATCTA	1	192	1	ATGTGTAAAT	    0.945016	-109
AATTCTGTATCTATGTGCATGTTTATTATG	1	209	1	CTATGTGCAT	    0.974809	-92
          **********

Masking position 6
Map Score:   2.91769

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 117
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

AGAAATAAGAGGGGAAAGAGAGAAAACACT	1	42	0	GGGGAAAGAG	    0.995092	-259
TAGAGAGGGGGGAGAAATAAGAGGGGAAAG	1	54	0	GGAGAAATAA	    0.990586	-247
ATAATGATAGGGGGAAATAATG        	1	289	1	GGGGAAATAA	    0.996528	-12
          **********

Masking position 5
Map Score:   2.81573

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 40
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

GATATGTGTGTATAACTCAATTGT      	1	5	0	TATAACTCAA	    0.984128	-296
TCTATTTCAATAAAACACAAGTCTCGATTG	1	91	1	TAAAACACAA	    0.984262	-210
CATAATGTTTTATAATACAAGATGATAGCG	1	249	1	TATAATACAA	    0.975738	-52
          **********

Masking position 5
Map Score:   1.15638

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 25
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 6

TAGCTTTTCTATTTCAATAAAACACAAGTC	1	84	1	ATTTCAATAA	     0.97632	-217
TTATGAAAATAATTCCATAATAAACATGCA	1	224	0	AATTCCATAA	    0.984734	-77
TTATGGAATTATTTTCATAATGTTTTATAA	1	234	1	ATTTTCATAA	     0.97632	-67
          **********

Masking position 7
Map Score:   0.720179

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 28
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 7

          **********

No masking
Map Score:   7.91135e-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 8

          **********

No masking
Map Score:   7.91135e-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 9

          **********

No masking
Map Score:   7.91135e-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