AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00460_bbur_reg_300.orf -o00460_bbur_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	BB0599	51	cysteinyl-tRNA synthetase (cysS)
#2	BB0620	226	beta-glucosidase, putative

Motif number 1

  ACGTACTTAATAATAAATTAGATTTTTT	1	9	1	AATAATAAAT	    0.982073	-43
AAATTGAAAAAATAAAAAATCTAATTTATT	1	22	0	AATAAAAAAT	    0.985334	-30
TTATACACTTAATAAAAGTTTAAGCTGATG	2	91	0	AATAAAAGTT	    0.962288	-136
GTATAAATTCAATAATGCTTTGTCAATGTT	2	115	1	AATAATGCTT	    0.923495	-112
TATACTTTATAATAATACTTTTGAATAATA	2	144	0	AATAATACTT	    0.975527	-83
TATAAAGTATAATACAAAATGGCTTGCTAA	2	163	1	AATACAAAAT	    0.956428	-64
CTTGCTAATAAATATAAATTACTAAATTAG	2	185	1	AATATAAATT	    0.915871	-42
TAACCATATAAATAATAAATGCTAATTTAG	2	206	0	AATAATAAAT	    0.982073	-21
          **********

Masking position 4
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

GTACTTAATAATAAATTAGATTTTTTATTTTT	1	13	1	ATATTAGATT	    0.924979	-39
GTTCAAGTCCCTCCATCAGCATTAGAGGTTGT	2	13	0	CTATCAGCAT	    0.995555	-214
ACCAACTGAGCTACATCAGCTTAAACTTTTAT	2	78	1	CTATCAGCTT	     0.99365	-149
AGTAATTTATATTTATTAGCAAGCCATTTTGT	2	176	0	ATATTAGCAA	    0.965543	-51
ATATAAATTACTAAATTAGCATTTATTATTTA	2	196	1	CTATTAGCAT	    0.995209	-31
          **  ********

Masking position 6
Map Score:   4.22858

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 39
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

          **********

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 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