AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_SecDF_bbur_reg_100.orf -o118_borburg_100.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	RBB00112	194	3615
#2	RBB00111	23	3615
#3	RBB00109	85	3615

Motif number 1

TCTTTAAATTATAAAGACAAAGAATTT         	1	2	0	ATAAAAAATT	     0.99215	-193
AATTTTTATTATATAATGTAAATATTGACTAATCTT	1	34	0	ATATAAAATT	    0.936058	-161
CAAAATATACAAAACCAGTAAAAATTTTTATTATAT	1	56	0	AAAACAAATT	    0.981149	-139
CTATGCATCAAAAAATACAAAATATACAAAACCAGT	1	73	0	AAAAAAAATA	    0.945499	-122
TAAGATTAACATAAACTTAATACATTCGCTATAGTA	1	120	0	ATAAAATATT	    0.936067	-75
TAATTTACATATAACAATATAAGATTAACATAAACT	1	139	0	ATAACTAATT	    0.945799	-56
ACCCCTTTCTATAAATAAAAATAATTTACATATAAC	1	160	0	ATAAAAAATT	     0.99202	-35
TTTTATTTATAGAAAGGGGTAAAATTTTT       	1	176	1	AGAAATAATT	    0.948481	-19
     AGTTAAAAAAAAGGTATTGTTTAAAGGTAAA	3	6	1	AAAAATAGTT	    0.949041	-80
TGTTTAAAGGTAAAATTAGAACTGTTAGCTAATAAT	3	28	1	TAAAAAAGTT	    0.857412	-58
TAAAATTTTTAAAAAATACCATTATTAGCTAACAGT	3	48	0	AAAAACAATT	    0.959821	-38
GGTATTTTTTAAAAATTTTAAGGATTTGTATA    	3	64	1	AAAAAAAATT	    0.992316	-22
          *****    **  ***

Masking position 3
Map Score:   18.2246

Number of sites scoring better than the average of aligned sites = 1191
Number in coding regions = 762
Number in noncoding regions = 429
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 2

GTCTTTATAATTTAAAGATTAGTCAATATT	1	20	1	TTTAAAGATT	     0.94047	-175
TATTATATAATGTAAATATTGACTAATCTT	1	34	0	TGTAAATATT	    0.971658	-161
ATACAAAACCAGTAAAAATTTTTATTATAT	1	56	0	AGTAAAAATT	    0.942353	-139
TTACTGGTTTTGTATATTTTGTATTTTTTG	1	71	1	TGTATATTTT	    0.828334	-124
TATTGTTATATGTAAATTATTTTTATTTAT	1	156	1	TGTAAATTAT	    0.905057	-39
TATAGAAAGGGGTAAAATTTTT        	1	183	1	GGTAAAATTT	    0.961958	-12
          ATTAAAGTTTCACCGGCAAG	2	1	1	ATTAAAGTTT	    0.852587	-23
TAATTTTACCTTTAAACAATACCTTTTTTT	3	16	0	TTTAAACAAT	    0.704679	-70
ATTGTTTAAAGGTAAAATTAGAACTGTTAG	3	26	1	GGTAAAATTA	    0.780609	-60
AATGGTATTTTTTAAAAATTTTAAGGATTT	3	61	1	TTTAAAAATT	     0.95014	-25
          **********

Masking position 6
Map Score:   9.7292

Number of sites scoring better than the average of aligned sites = 1788
Number in coding regions = 1193
Number in noncoding regions = 595
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 3

          **********

No masking
Map Score:   -2.53363e-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:   -2.53363e-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:   -2.53363e-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