AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00460_bbur_reg_100.orf -o00460_bbur_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	BB0599	51	cysteinyl-tRNA synthetase (cysS)
#2	BB0620	226	beta-glucosidase, putative

Motif number 1

AAAAAATCTAATTTATTATTAAGTACGT  	1	9	0	ATTTATTATT	    0.981343	-43
AATAAATTAGATTTTTTATTTTTTCAATTT	1	22	1	ATTTTTTATT	    0.984376	-30
CATCAGCTTAAACTTTTATTAAGTGTATAA	2	91	1	AACTTTTATT	    0.959696	-136
AACATTGACAAAGCATTATTGAATTTATAC	2	115	0	AAGCATTATT	    0.918764	-112
TATTATTCAAAAGTATTATTATAAAGTATA	2	144	1	AAGTATTATT	    0.974323	-83
TTAGCAAGCCATTTTGTATTATACTTTATA	2	163	0	ATTTTGTATT	    0.953325	-64
CTAATTTAGTAATTTATATTTATTAGCAAG	2	185	0	AATTTATATT	    0.912951	-42
CTAAATTAGCATTTATTATTTATATGGTTA	2	206	1	ATTTATTATT	    0.981343	-21
          **********

Masking position 8
Map Score:   13.5469

Number of sites scoring better than the average of aligned sites = 894
Number in coding regions = 556
Number in noncoding regions = 338
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 2

AAAAAATAAAAAATCTAATTTATTATTAAGTA	1	14	0	AAATCTATTA	    0.915252	-38
TACAACCTCTAATGCTGATGGAGGGACTTGAA	2	12	1	AATGCTATGA	     0.99399	-215
AATAAAAGTTTAAGCTGATGTAGCTCAGTTGG	2	79	0	TAAGCTATGA	    0.956268	-148
TAAATTCAATAATGCTTTGTCAATGTTATTAT	2	118	1	AATGCTTGTA	    0.953729	-109
ACTTTATAATAATACTTTTGAATAATAACATT	2	139	0	AATACTTTGA	    0.944399	-88
ATAAATAATAAATGCTAATTTAGTAATTTATA	2	197	0	AATGCTATTA	     0.99058	-30
          ****** *** *

Masking position 6
Map Score:   3.81682

Number of sites scoring better than the average of aligned sites = 197
Number in coding regions = 147
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

AATCTAATTTATTATTAAGTACGT      	1	5	0	ATTATTAAGT	    0.942226	-47
AGATTTTTTATTTTTTCAATTTTGAGAAAT	1	30	1	TTTTTTCAAT	    0.909235	-22
        ACATTTCTCAAAATTGAAAAAA	1	40	0	ATTTCTCAAA	    0.891086	-12
AGCTTAAACTTTTATTAAGTGTATAAATTC	2	95	1	TTTATTAAGT	    0.856651	-132
TTGACAAAGCATTATTGAATTTATACACTT	2	111	0	ATTATTGAAT	    0.937506	-116
TTCAATAATGCTTTGTCAATGTTATTATTC	2	122	1	CTTTGTCAAT	    0.724532	-105
TGTCAATGTTATTATTCAAAAGTATTATTA	2	135	1	ATTATTCAAA	    0.965202	-92
ATTCAAAAGTATTATTATAAAGTATAATAC	2	148	1	ATTATTATAA	    0.734186	-79
ATAAATATAAATTACTAAATTAGCATTTAT	2	192	1	ATTACTAAAT	    0.947839	-35
          **********

Masking position 6
Map Score:   5.96375

Number of sites scoring better than the average of aligned sites = 1486
Number in coding regions = 968
Number in noncoding regions = 518
Number of orfs with sites within 600 bp upstream = 116
Fraction of orfs with sites within 600 bp upstream = 0.0186315


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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 6

          **********

No masking
Map Score:   -2.39152e-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