AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_bbur_reg_100.orf -o150_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	RBB00641	21	3615
#2	RBB00640	85	3615
#3	RBB00638	183	3615

Motif number 1

 GGGGTTTGGAGAAATATATAT        	1	10	1	AGAAATATAT	    0.932302	-12
          AAAAGGAATTTAAATGAATA	2	1	1	AAAAGGAATT	    0.829427	-85
AAATGAATACAAAAGGAAAAGTCGTTGGAG	2	22	1	AAAAGGAAAA	    0.902358	-64
CTCAACTATTAGAAATAATACAACCA    	3	7	0	AGAAATAATA	     0.87932	-177
ATAGTTGAGAATAAGTATATTCTTTAAAGA	3	28	1	ATAAGTATAT	    0.815033	-156
TATTCTTTAAAGAAGTATTATTGTGCCAAC	3	45	1	AGAAGTATTA	    0.949544	-139
TACAATATTAAAAAACATATCAAGTTGGCA	3	68	0	AAAAACATAT	    0.879802	-116
TTTTAATATCAAAAATTTTACAATATTAAA	3	86	0	AAAAATTTTA	     0.78963	-98
TTTTGATATTAAAAATTTATTTTATGCTTT	3	102	1	AAAAATTTAT	    0.612658	-82
AAAACTTTAAAAAAGCATAAAATAAATTTT	3	113	0	AAAAGCATAA	    0.946545	-71
ATTAGCAAACAAAACTTTAAAAAAGCATAA	3	123	0	AAAACTTTAA	    0.764134	-61
CATATAAGATAAAAATAATAACCTAACACT	3	154	0	AAAAATAATA	    0.920764	-30
          **********

Masking position 4
Map Score:   11.3298

Number of sites scoring better than the average of aligned sites = 3967
Number in coding regions = 2578
Number in noncoding regions = 1389
Number of orfs with sites within 600 bp upstream = 221
Fraction of orfs with sites within 600 bp upstream = 0.0354963


Motif number 2

AGTAACTAAGTTTCCATTAACTCCAACGAC	2	42	0	TTTCCATTAA	    0.943454	-44
GGTTGTATTATTTCTAATAGTTGAGAATAA	3	12	1	TTTCTAATAG	    0.918081	-172
TTTCTAATAGTTGAGAATAAGTATATTCTT	3	22	1	TTGAGAATAA	    0.900073	-162
TATCAAAAATTTTACAATATTAAAAAACAT	3	80	0	TTTACAATAT	    0.929163	-104
TGTAAAATTTTTGATATTAAAAATTTATTT	3	94	1	TTGATATTAA	    0.913602	-90
ATATTAAAAATTTATTTTATGCTTTTTTAA	3	107	1	TTTATTTTAT	    0.801773	-77
AAAGTTTTGTTTGCTAATAAGTGTTAGGTT	3	135	1	TTGCTAATAA	    0.960388	-49
GGTTATTATTTTTATCTTATATGATAAGGA	3	161	1	TTTATCTTAT	    0.856465	-23
          **********

Masking position 9
Map Score:   4.77344

Number of sites scoring better than the average of aligned sites = 1131
Number in coding regions = 723
Number in noncoding regions = 408
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 3

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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