AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i206_nucleases_bbur_reg_300.orf -o206_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00127	300	3615

Motif number 1

CAAAGCTTGATAATTAAAATTTTAACAAAA	1	42	1	TAATTAAAAT	    0.946218	-259
ATTAAAATTTTAACAAAAATAAATCAAAAT	1	54	1	TAACAAAAAT	    0.951369	-247
TAACAAAAATAAATCAAAATAATTTTTCAA	1	64	1	AAATCAAAAT	    0.885054	-237
CTTAAAACAATTTGAAAAATTATTTTGATT	1	75	0	TTTGAAAAAT	    0.873986	-226
TTTCAAATTGTTTTAAGAATTTAATAAAAA	1	88	1	TTTTAAGAAT	       0.731	-213
TTTAAGAATTTAATAAAAATGCAGATAAAA	1	99	1	TAATAAAAAT	    0.978457	-202
ATAAAAATGCAGATAAAAAATCCTTCCAAA	1	111	1	AGATAAAAAA	    0.720037	-190
TTTCGCTAGTTTTTAAAAATCTCTCGTGTG	1	160	0	TTTTAAAAAT	    0.929279	-141
ATTTCAAGTTAGACAAAAATTTATTAATAT	1	232	1	AGACAAAAAT	    0.905284	-69
AGACAAAAATTTATTAATATTGATAGAAAA	1	242	1	TTATTAATAT	    0.594115	-59
ATTAATATTGATAGAAAAATTTTACATTAA	1	254	1	ATAGAAAAAT	    0.933916	-47
TAAGGACAAAAAATTAAAATTC        	1	289	1	AAATTAAAAT	    0.917068	-12
          **********

Masking position 6
Map Score:   12.1331

Number of sites scoring better than the average of aligned sites = 3938
Number in coding regions = 2547
Number in noncoding regions = 1391
Number of orfs with sites within 600 bp upstream = 197
Fraction of orfs with sites within 600 bp upstream = 0.0316415


Motif number 2

TGGAGTTGGATAGCTTGATATGTAT      	1	5	0	TAGCTTGTAT	    0.974625	-296
CAATTTACCAAAGCTTGATAATTAAAATTTT	1	34	1	AAGCTTGTAA	    0.986238	-267
CTTGTGAAATAAGCTTTGGAAGGATTTTTTA	1	124	0	AAGCTTTGAA	    0.961507	-177
CTCGTGTGCTTTGCTTGTGAAATAAGCTTTG	1	137	0	TTGCTTGGAA	     0.97551	-164
AGATTTTTAAAAACTAGCGAAATAACACTCT	1	168	1	AAACTAGGAA	    0.930845	-133
AATTTTTGTCTAACTTGAAATCATGAGTGTC	1	222	0	TAACTTGAAT	    0.880386	-79
          ******* ***

Masking position 5
Map Score:   2.60494

Number of sites scoring better than the average of aligned sites = 287
Number in coding regions = 204
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

          **********

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 4

          **********

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 5

          **********

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