AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i321_mixed6_bbur_reg_100.orf -o321_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	RBB00547	300	3615

Motif number 1

AAAAAGTCTAACAAAAAAATCTAAAATT        	1	3	0	AAAAAATAAA	    0.986802	-298
GGGAATCTACACAAAACTTATTAAAAAGTCTAACAA	1	25	0	AAAAATAAAA	    0.939786	-276
TTAAAATAAAACATAAATATGGGAATCTACACAAAA	1	45	0	AATAAATAAT	    0.946129	-256
AAGCAGTTTTAAAAAAGAATGTTAAAATAAAACATA	1	66	0	AAAAAATAAA	    0.986803	-235
AACTGCTTTTATTAAATAAATAGAATAAGCGTGATT	1	94	1	ATAAAAAAAT	    0.824073	-207
AGCGTGATTAAAAAAATCAATTATATTTTTTCATGT	1	121	1	AAAAAAATAT	    0.948816	-180
TTTATTATATAAAAAAACATGAAAAAATATAATTGA	1	137	0	AAAAAATAAA	    0.986809	-164
ATGTTTTTTTATATAATAAATGTTATTAAGTTGGAT	1	153	1	AATAAAATAT	    0.795534	-148
TATAAATACAACAAAACCTAATTTAACTTTAATATC	1	186	0	AAAAATATAA	    0.902052	-115
AACACACCGCAAATAATAATACGTAAAGCTCAATTT	1	225	0	AATAAATTAA	    0.946146	-76
TATATCTTTGATAAACCGATTTAAAAGGGGTATTT 	1	276	1	AAAACATAAA	    0.933667	-25
          * ****  **   ***

Masking position 5
Map Score:   13.6773

Number of sites scoring better than the average of aligned sites = 2374
Number in coding regions = 1483
Number in noncoding regions = 891
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 2

GTCTAACAAAAAAATCTAAAATT        	1	3	0	AAAATCAAAA	    0.931911	-298
AACTTATTAAAAAGTCTAACAAAAAAATCTA	1	16	0	AAAGTCAACA	      0.9557	-285
AAAGAATGTTAAAATAAAACATAAATATGGG	1	58	0	AAAATAAACA	    0.983825	-243
TTTTATTAAATAAATAGAATAAGCGTGATTA	1	100	1	TAAATAAATA	    0.915009	-201
AAAACATGAAAAAATATAATTGATTTTTTTA	1	129	0	AAAATAAATT	    0.941995	-172
TAACATTTATTATATAAAAAAACATGAAAAA	1	147	0	TATATAAAAA	    0.703625	-154
ATTTAACTTTAATATCCAACTTAATAACATT	1	171	0	AATATCAACT	    0.915465	-130
GTTGGATATTAAAGTTAAATTAGGTTTTGTT	1	182	1	AAAGTTAATT	    0.591689	-119
AATTTATATATAAATACAACAAAACCTAATT	1	199	0	TAAATAAACA	    0.964965	-102
CGGTTTATCAAAGATATAACTTCAACTACCT	1	263	0	AAGATAAACT	     0.91691	-38
          ****** ****

Masking position 5
Map Score:   9.40029

Number of sites scoring better than the average of aligned sites = 1586
Number in coding regions = 1016
Number in noncoding regions = 570
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 3

CTACACAAAACTTATTAAAAAGTCTAACAAA	1	24	0	CTATTAAAAA	    0.978229	-277
TTAATAAAAGCAGTTTTAAAAAAGAATGTTA	1	78	0	CGTTTTAAAA	    0.917361	-223
TAAAACTGCTTTTATTAAATAAATAGAATAA	1	91	1	TTATTAAATA	    0.801528	-210
TAGAATAAGCGTGATTAAAAAAATCAATTAT	1	114	1	GGATTAAAAA	    0.968907	-187
TAACATTTATTATATAAAAAAACATGAAAAA	1	147	0	TTATAAAAAA	    0.801528	-154
CTTTGATAAACCGATTTAAAAGGGGTATTT 	1	281	1	CGATTTAAAA	    0.978269	-20
          * *********

Masking position 5
Map Score:   2.2301

Number of sites scoring better than the average of aligned sites = 635
Number in coding regions = 425
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


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


Motif number 6

          **********

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