AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_bbur_reg_100.orf -o054_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

Motif number 1

       GATTAGTATTTTAGCATAATTTT	1	4	1	TAGTATTTTA	    0.952116	-175
TATTTTAGCATAATTTTTTGTTTATGTTTT	1	17	1	TAATTTTTTG	    0.864595	-162
TTTTTTGTTTATGTTTTTGATTTGAAGTTT	1	30	1	ATGTTTTTGA	    0.960372	-149
TTTTGATTTGAAGTTTTTTAGAACTTTTAT	1	44	1	AAGTTTTTTA	    0.991402	-135
TTTATTTTTTCAATTTTTTATATTTATATT	1	69	1	CAATTTTTTA	    0.970639	-110
TATTTATATTATATTTTTAATATTATTAAA	1	89	1	ATATTTTTAA	    0.946325	-90
AAAACATCAACTATTTTTAATAATATTAAA	1	104	0	CTATTTTTAA	     0.92225	-75
AAAATAGTTGATGTTTTTTAATATAAACTA	1	117	1	ATGTTTTTTA	    0.987462	-62
ATATAAACTATAGTATTTTAATATATGACA	1	137	1	TAGTATTTTA	    0.952116	-42
CTTTACAATCAAGTTTTTAAAAACTCATTT	2	37	0	AAGTTTTTAA	    0.983736	-28
          **********

Masking position 6
Map Score:   18.2755

Number of sites scoring better than the average of aligned sites = 1108
Number in coding regions = 767
Number in noncoding regions = 341
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 2

AAACAAAAAATTATGCTAAAATACTAATC 	1	10	0	TTATGCTAAA	    0.984305	-169
TTTTTTATATTTATATTATATTTTTAATAT	1	82	1	TTATATTATA	    0.913195	-97
CTATTTTTAATAATATTAAAAATATAATAT	1	94	0	TAATATTAAA	     0.93904	-85
ATACTATAGTTTATATTAAAAAACATCAAC	1	123	0	TTATATTAAA	    0.979107	-56
GAAAATTGTCATATATTAAAATACTATAGT	1	143	0	ATATATTAAA	    0.956782	-36
TCATGCTTAAACATGCTTAAATA       	2	4	0	ACATGCTTAA	    0.920918	-61
CTCATTTAACTCATGCTTAAACATGCTTAA	2	14	0	TCATGCTTAA	    0.961303	-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

TCAAATCAAAAACATAAACAAAAAATTATG	1	25	0	AACATAAACA	    0.983321	-154
AGTTCTAAAAAACTTCAAATCAAAAACATA	1	39	0	AACTTCAAAT	    0.893627	-140
AAAAATTGAAAAAATAAAAGTTCTAAAAAA	1	57	0	AAAATAAAAG	    0.878175	-122
ATATAATATAAATATAAAAAATTGAAAAAA	1	73	0	AATATAAAAA	    0.968766	-106
TATTTTTAATAATATTAAAAATATAATATA	1	93	0	AATATTAAAA	    0.904194	-86
TATATTAAAAAACATCAACTATTTTTAATA	1	112	0	AACATCAACT	    0.979951	-67
GATGTTTTTTAATATAAACTATAGTATTTT	1	126	1	AATATAAACT	    0.973213	-53
          **********

Masking position 7
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