AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i193_dna_polymerase_bbur_reg_100.orf -o193_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	RBB00205	220	3615

Motif number 1

      AGGGTAAAATTTAACATATTCTTTATTA	1	5	1	TAAAATTAAA	    0.953263	-216
AATTGTTTGATAAAATAATAAAGAATATGTTAAA	1	20	0	TAAAATATAA	    0.992809	-201
TATTTTATCAAACAATTCTAACAAGCAAAAACCG	1	37	1	AACAATTTAA	    0.839091	-184
ATACAAACTGTAAAATACCACCAAAAATACATGC	1	79	1	TAAAATACAA	    0.995454	-142
TGAACATAAATAAAATAGCATGTATTTTTGGTGG	1	96	0	TAAAATACAA	    0.995286	-125
ATGTTCAAATTAAAATAATCTTTAAAGAAAAATA	1	123	1	TAAAATATCA	    0.967105	-98
ATCTTTAAAGAAAAATATCAATCAAAAAGACAAT	1	140	1	AAAAATACAA	    0.985755	-81
CAATCAAAAAGACAATATTATAAAAATGTGAATT	1	158	1	GACAATATAA	     0.94036	-63
TAACGACAATTAAAATATAATTCACATTTTTATA	1	176	0	TAAAATAAAA	    0.976477	-45
TCTAGCATATTAAAATATCTTTAACGACAATTAA	1	197	0	TAAAATACTA	    0.961814	-24
          ******* **   *

Masking position 6
Map Score:   18.2634

Number of sites scoring better than the average of aligned sites = 581
Number in coding regions = 365
Number in noncoding regions = 216
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 2

ATTGTTTGATAAAATAATAAAGAATATGTT	1	23	0	AAAATAATAA	    0.825921	-198
AACAATTCTAACAAGCAAAAACCGACTTTA	1	47	1	ACAAGCAAAA	    0.955895	-174
AACCGACTTTACTATACAAACTGTAAAATA	1	66	1	ACTATACAAA	    0.834722	-155
TAATTTGAACATAAATAAAATAGCATGTAT	1	105	0	ATAAATAAAA	    0.764073	-116
TATTTATGTTCAAATTAAAATAATCTTTAA	1	118	1	CAAATTAAAA	    0.950234	-103
AAATAATCTTTAAAGAAAAATATCAATCAA	1	135	1	TAAAGAAAAA	     0.85782	-86
AAGAAAAATATCAATCAAAAAGACAATATT	1	147	1	TCAATCAAAA	    0.941963	-74
AAAAGACAATATTATAAAAATGTGAATTAT	1	164	1	ATTATAAAAA	    0.891024	-57
ATCTTTAACGACAATTAAAATATAATTCAC	1	185	0	ACAATTAAAA	    0.981646	-36
     TCTAGCATATTAAAATATCTTTAAC	1	206	0	CATATTAAAA	    0.896328	-15
          **********

Masking position 4
Map Score:   7.97802

Number of sites scoring better than the average of aligned sites = 4121
Number in coding regions = 2698
Number in noncoding regions = 1423
Number of orfs with sites within 600 bp upstream = 204
Fraction of orfs with sites within 600 bp upstream = 0.0327658


Motif number 3

TTCTAACAAGCAAAAACCGACTTTACTATA	1	52	1	CAAAAACCGA	    0.967158	-169
AAAATACCACCAAAAATACATGCTATTTTA	1	90	1	CAAAAATACA	    0.990984	-131
TTAATTTGAACATAAATAAAATAGCATGTA	1	106	0	CATAAATAAA	    0.940998	-115
AAATATCAATCAAAAAGACAATATTATAAA	1	152	1	CAAAAAGACA	    0.989293	-69
          **********

Masking position 5
Map Score:   1.80418

Number of sites scoring better than the average of aligned sites = 142
Number in coding regions = 85
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

AATAATAAAGAATATGTTAAATTTTACCCT	1	11	0	AATATGTTAA	    0.966589	-210
ATTGTTTGATAAAATAATAAAGAATATGTT	1	23	0	AAAATAATAA	    0.855303	-198
TTTACTATACAAACTGTAAAATACCACCAA	1	73	1	AAACTGTAAA	    0.978146	-148
AAATTAAAATAATCTTTAAAGAAAAATATC	1	129	1	AATCTTTAAA	    0.857911	-92
TCTTTAAAGAAAAATATCAATCAAAAAGAC	1	141	1	AAAATATCAA	    0.952687	-80
CAATATTATAAAAATGTGAATTATATTTTA	1	170	1	AAAATGTGAA	    0.978438	-51
          **********

Masking position 5
Map Score:   3.60215

Number of sites scoring better than the average of aligned sites = 737
Number in coding regions = 482
Number in noncoding regions = 255
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 5

          **********

No masking
Map Score:   2.72438e-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:   2.72438e-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 7

          **********

No masking
Map Score:   2.72438e-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