AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_bbur_reg_300.orf -o054_borburg_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	RBB00743	178	3615
#2	RBB00715	64	3615

Motif number 1

      GATTAGTATTTTAGCATAATTTTT	1	5	1	AGTATTTTAG	    0.957071	-174
ATTTTAGCATAATTTTTTGTTTATGTTTTT	1	18	1	AATTTTTTGT	    0.913848	-161
TTTTTGTTTATGTTTTTGATTTGAAGTTTT	1	31	1	TGTTTTTGAT	    0.961611	-148
TTTGATTTGAAGTTTTTTAGAACTTTTATT	1	45	1	AGTTTTTTAG	    0.987685	-134
TTATTTTTTCAATTTTTTATATTTATATTA	1	70	1	AATTTTTTAT	    0.980718	-109
ATTTATATTATATTTTTAATATTATTAAAA	1	90	1	TATTTTTAAT	    0.947982	-89
AAACATCAACTATTTTTAATAATATTAAAA	1	103	0	TATTTTTAAT	    0.947982	-76
AAATAGTTGATGTTTTTTAATATAAACTAT	1	118	1	TGTTTTTTAA	    0.980675	-61
TATAAACTATAGTATTTTAATATATGACAA	1	138	1	AGTATTTTAA	    0.953815	-41
TTTACAATCAAGTTTTTAAAAACTCATTTA	2	36	0	AGTTTTTAAA	    0.974982	-29
          **********

Masking position 5
Map Score:   18.2755

Number of sites scoring better than the average of aligned sites = 1076
Number in coding regions = 724
Number in noncoding regions = 352
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

AAACAAAAAATTATGCTAAAATACTAATC 	1	10	0	TTATGCTAAA	    0.983832	-169
TTTTTTATATTTATATTATATTTTTAATAT	1	82	1	TTATATTATA	    0.909762	-97
CTATTTTTAATAATATTAAAAATATAATAT	1	94	0	TAATATTAAA	    0.936558	-85
ATACTATAGTTTATATTAAAAAACATCAAC	1	123	0	TTATATTAAA	    0.978349	-56
GAAAATTGTCATATATTAAAATACTATAGT	1	143	0	ATATATTAAA	    0.954974	-36
TCATGCTTAAACATGCTTAAATA       	2	4	0	ACATGCTTAA	    0.917737	-61
CTCATTTAACTCATGCTTAAACATGCTTAA	2	14	0	TCATGCTTAA	      0.9599	-51
          **********

Masking position 3
Map Score:   8.33763

Number of sites scoring better than the average of aligned sites = 417
Number in coding regions = 261
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

CATAATTTTTTGTTTATGTTTTTGATTTGA	1	25	1	TGTTTATGTT	    0.981501	-154
TATGTTTTTGATTTGAAGTTTTTTAGAACT	1	39	1	ATTTGAAGTT	    0.883185	-140
TTTTTTAGAACTTTTATTTTTTCAATTTTT	1	57	1	CTTTTATTTT	    0.866437	-122
TTTTTTCAATTTTTTATATTTATATTATAT	1	73	1	TTTTTATATT	    0.965419	-106
TATATTATATTTTTAATATTATTAAAAATA	1	93	1	TTTTAATATT	    0.894662	-86
TATTAAAAATAGTTGATGTTTTTTAATATA	1	112	1	AGTTGATGTT	    0.977771	-67
AAAATACTATAGTTTATATTAAAAAACATC	1	126	0	AGTTTATATT	    0.970491	-53
          **********

Masking position 6
Map Score:   7.39056

Number of sites scoring better than the average of aligned sites = 626
Number in coding regions = 420
Number in noncoding regions = 206
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 4

          **********

No masking
Map Score:   -3.30951e-14

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:   -3.30951e-14

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:   -3.30951e-14

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