AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00130_bbur_reg_100.orf -o00130_bbur_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	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

ATACACTTTATTATACTTTTTCATTATAATT	1	24	1	TTATACTTTT	    0.950669	-27
TACTTTTTCATTATAATTCTTATT       	1	37	1	TTATAATTTT	    0.986261	-14
GACAGATATTTTAAAATTATT          	2	1	0	TTAAAATTTT	    0.925667	-36
         ATTATTCTTAATAATGACAGAT	2	25	0	TTATTCTTAT	    0.893006	-12
CGTTGACAATTAATAATTATTTAATTACAAT	3	16	0	TAATAATTTT	    0.876014	-100
TGTCAACGAATGATTATTGATTGATTAATCA	3	39	1	TGATTATTAT	    0.819339	-77
ATATTTTGAATTTTAATTTGTTTTGATTAAT	3	62	0	TTTTAATTGT	     0.94082	-54
AAAATTCAAAATATAATTATTTATAAATAAA	3	79	1	ATATAATTTT	    0.930863	-37
AATATTCTTATTTTTATTTATAAATAATTAT	3	91	0	TTTTTATTAT	    0.941219	-25
        TTATAATATTCTTATTTTTATTT	3	103	0	ATAATATTTT	     0.61309	-13
GTTTGCCTTTTTATAATTTTTATTGTGATCT	4	122	1	TTATAATTTT	     0.98626	-179
CATTTTGGTGCTTTTATTTTTGTCTATTTAG	4	174	1	CTTTTATTTT	    0.798078	-127
TTTAGAAAAGTTATTATTGGTTATAAAATAT	4	200	1	TTATTATTGT	    0.954381	-101
CAATTAAAATTTTTAATTGATAGCTAACATC	4	231	0	TTTTAATTAT	    0.959391	-70
CAATTAAAAATTTTAATTGATAGCTAAAGTG	4	243	1	TTTTAATTAT	    0.959391	-58
          ******** **

Masking position 7
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

AATTTTTAATTGATAGCTAACATCATATTT	4	225	0	TGATAGCTAA	    0.990785	-76
AAATTTTAATTGATAGCTAAAGTGTAATTA	4	250	1	TGATAGCTAA	    0.990785	-51
TAAACAAAAGTCTTTGCTAATTACACTTTA	4	267	0	TCTTTGCTAA	    0.960249	-34
   AAGAATCTCCTAGCTAAACAAAAGTCT	4	284	0	TCCTAGCTAA	    0.989066	-17
          **********

Masking position 4
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	    0.952708	-30
CAAATTAAAATTCAAAATATAATTATTTATAA	3	73	1	TTAAAATATA	     0.97855	-43
AAGATCACAATAAAAATTATAAAAAGGCAAAC	4	122	0	TAAAATTATA	     0.76742	-179
ACATAACACATTTAAAAGATCACAATAAAAAT	4	137	0	TTAAAAGATA	    0.968906	-164
TTTGTCTATTTAGAAAAGTTATTATTGGTTAT	4	192	1	TAAAAAGTTT	    0.819125	-109
TATTATTGGTTATAAAATATGATGTTAGCTAT	4	211	1	TAAAAATATA	    0.972628	-90
TAGCTATCAATTAAAAATTTTAATTGATAGCT	4	236	1	TTAAAATTTA	    0.851261	-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	     0.94257	-40
ATAATGAAAAAGTATAATAAAGTGTATTAA	1	21	0	AGTATAATAA	     0.95741	-30
     AAAGTATTGTAATTAAATAATTATT	3	6	1	ATTGTAATTA	    0.959654	-110
TAAAATTCAAAATATAATTATTTATAAATA	3	78	1	AATATAATTA	    0.889344	-38
TCCCCAATTTAGTGAAATTATAAGCGTTTG	4	97	1	AGTGAAATTA	    0.968377	-204
TGATAGCTAAAGTGTAATTAGCAAAGACTT	4	260	1	AGTGTAATTA	    0.992008	-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