AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i055_Arginine_Metabolism_bbur_reg_100.orf -o055_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	RBB00743	178	3615
#2	RBB00715	64	3615
#3	RBB00576	27	3615

Motif number 1

AAAAATTATGCTAAAATACTAATC      	1	5	0	CTAAAATACT	    0.943136	-174
AAAAACATAAACAAAAAATTATGCTAAAAT	1	18	0	ACAAAAAATT	    0.921186	-161
AAAACTTCAAATCAAAAACATAAACAAAAA	1	31	0	ATCAAAAACA	    0.963483	-148
AATAAAAGTTCTAAAAAACTTCAAATCAAA	1	45	0	CTAAAAAACT	    0.985261	-134
TAATATAAATATAAAAAATTGAAAAAATAA	1	70	0	ATAAAAAATT	    0.984143	-109
TTTTAATAATATTAAAAATATAATATAAAT	1	90	0	ATTAAAAATA	    0.959431	-89
TTTTAATATTATTAAAAATAGTTGATGTTT	1	103	1	ATTAAAAATA	    0.959431	-76
ATAGTTTATATTAAAAAACATCAACTATTT	1	118	0	TTAAAAAACA	    0.981171	-61
TTGTCATATATTAAAATACTATAGTTTATA	1	138	0	TTAAAATACT	    0.938891	-41
CAATCAAGTTTTTAAAAACTCATTTAACTC	2	32	0	TTTAAAAACT	    0.965563	-33
TTAATTTCACATAAAAAATACTG       	3	4	0	ATAAAAAATA	    0.981213	-24
          **********

Masking position 5
Map Score:   22.1753

Number of sites scoring better than the average of aligned sites = 1161
Number in coding regions = 733
Number in noncoding regions = 428
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

ATTAGTATTTTAGCATAATTTTTTGTTTAT	1	12	1	TAGCATAATT	    0.762528	-167
TTCAAATCAAAAACATAAACAAAAAATTAT	1	26	0	AAACATAAAC	    0.985539	-153
AAGTTCTAAAAAACTTCAAATCAAAAACAT	1	40	0	AAACTTCAAA	    0.921432	-139
AAAAAATTGAAAAAATAAAAGTTCTAAAAA	1	58	0	AAAAATAAAA	    0.838485	-121
AATATAATATAAATATAAAAAATTGAAAAA	1	74	0	AAATATAAAA	    0.944388	-105
ATAATATTAAAAATATAATATAAATATAAA	1	85	0	AAATATAATA	    0.886459	-94
TTATATTAAAAAACATCAACTATTTTTAAT	1	113	0	AAACATCAAC	    0.959398	-66
TGATGTTTTTTAATATAAACTATAGTATTT	1	125	1	TAATATAAAC	      0.8759	-54
ATGCTTAAACATGCTTAAATA         	2	2	0	ATGCTTAAAT	    0.756489	-63
CATTTAACTCATGCTTAAACATGCTTAAAT	2	12	0	ATGCTTAAAC	    0.831301	-53
GAGTTTTTAAAAACTTGATTGTAAAGGTTG	2	41	1	AAACTTGATT	     0.70537	-24
AAATTTAATTTCACATAAAAAATACTG   	3	8	0	TCACATAAAA	    0.762004	-20
          AAATTTAATTTCACATAAAA	3	18	0	AAATTTAATT	    0.803887	-10
          **********

Masking position 8
Map Score:   10.2347

Number of sites scoring better than the average of aligned sites = 3036
Number in coding regions = 1999
Number in noncoding regions = 1037
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 3

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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