AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00130_bbur_reg_300.orf -o00130_bbur_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	BB0314	50	octaprenyl-diphosphate synthase (ispB)
#2	BB0590	36	dimethyladenosine transferase (ksgA)
#3	BB0591	115	competence locus E, putative
#4	BB0709	300	conserved hypothetical protein

Motif number 1

AATTATAATGAAAAAGTATAATAAAGTGTAT	1	24	0	AAAAGTATAA	    0.949281	-27
       AATAAGAATTATAATGAAAAAGTA	1	37	0	AAAATTATAA	     0.98586	-14
          AATAATTTTAAAATATCTGTC	2	1	1	AAAATTTTAA	    0.923634	-36
ATCTGTCATTATTAAGAATAAT         	2	25	1	ATAAGAATAA	    0.890183	-12
ATTGTAATTAAATAATTATTAATTGTCAACG	3	16	1	AAAATTATTA	    0.872806	-100
TGATTAATCAATCAATAATCATTCGTTGACA	3	39	0	ATAATAATCA	    0.814975	-77
ATTAATCAAAACAAATTAAAATTCAAAATAT	3	62	1	ACAATTAAAA	    0.939173	-54
TTTATTTATAAATAATTATATTTTGAATTTT	3	79	0	AAAATTATAT	    0.928962	-37
ATAATTATTTATAAATAAAAATAAGAATATT	3	91	1	ATAATAAAAA	    0.939582	-25
AAATAAAAATAAGAATATTATAA        	3	103	1	AAAATATTAT	    0.606138	-13
AGATCACAATAAAAATTATAAAAAGGCAAAC	4	122	0	AAAATTATAA	    0.985859	-179
CTAAATAGACAAAAATAAAAGCACCAAAATG	4	174	0	AAAATAAAAG	     0.79333	-127
ATATTTTATAACCAATAATAACTTTTCTAAA	4	200	0	ACAATAATAA	    0.953093	-101
GATGTTAGCTATCAATTAAAAATTTTAATTG	4	231	1	ATAATTAAAA	    0.958238	-70
CACTTTAGCTATCAATTAAAATTTTTAATTG	4	243	0	ATAATTAAAA	    0.958238	-58
          ** ********

Masking position 5
Map Score:   21.4472

Number of sites scoring better than the average of aligned sites = 1673
Number in coding regions = 1037
Number in noncoding regions = 636
Number of orfs with sites within 600 bp upstream = 138
Fraction of orfs with sites within 600 bp upstream = 0.0221651


Motif number 2

AAATATGATGTTAGCTATCAATTAAAAATT	4	225	1	TTAGCTATCA	    0.992138	-76
TAATTACACTTTAGCTATCAATTAAAATTT	4	250	0	TTAGCTATCA	    0.992138	-51
TAAAGTGTAATTAGCAAAGACTTTTGTTTA	4	267	1	TTAGCAAAGA	    0.965941	-34
AGACTTTTGTTTAGCTAGGAGATTCTT   	4	284	1	TTAGCTAGGA	    0.990672	-17
          **********

Masking position 7
Map Score:   4.03789

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 5
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

    AATAATTTTAAAATATCTGTCATTATTA	2	7	1	TTAAAATATT	    0.950147	-30
CAAATTAAAATTCAAAATATAATTATTTATAA	3	73	1	TTAAAATATA	     0.97739	-43
AAGATCACAATAAAAATTATAAAAAGGCAAAC	4	122	0	TAAAATTATA	    0.766808	-179
ACATAACACATTTAAAAGATCACAATAAAAAT	4	137	0	TTAAAAGATA	    0.967192	-164
TTTGTCTATTTAGAAAAGTTATTATTGGTTAT	4	192	1	TAAAAAGTTT	     0.81077	-109
TATTATTGGTTATAAAATATGATGTTAGCTAT	4	211	1	TAAAAATATA	    0.971116	-90
TAGCTATCAATTAAAAATTTTAATTGATAGCT	4	236	1	TTAAAATTTA	    0.853316	-65
          ** ******* *

Masking position 6
Map Score:   5.40459

Number of sites scoring better than the average of aligned sites = 824
Number in coding regions = 551
Number in noncoding regions = 273
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 4

AGTATAATAAAGTGTATTAAAGGGATTGAT	1	11	0	AGTGTATTAA	    0.939114	-40
ATAATGAAAAAGTATAATAAAGTGTATTAA	1	21	0	AGTATAATAA	    0.954804	-30
     AAAGTATTGTAATTAAATAATTATT	3	6	1	ATTGTAATTA	    0.957179	-110
TAAAATTCAAAATATAATTATTTATAAATA	3	78	1	AATATAATTA	    0.883083	-38
TCCCCAATTTAGTGAAATTATAAGCGTTTG	4	97	1	AGTGAAATTA	    0.966419	-204
TGATAGCTAAAGTGTAATTAGCAAAGACTT	4	260	1	AGTGTAATTA	      0.9915	-41
          **********

Masking position 6
Map Score:   6.55759

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 34
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   1.44541e-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:   1.44541e-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:   1.44541e-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