AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icpxR6_bbur_opreg_100.orf -g0.282 -x5 
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 =  	0.282
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	BB0104	39	periplasmic serine protease DO (htrA)
#2	BB0107	28	N-utilization substance protein B (nusB)
#3	BB0108	79	basic membrane protein
#4	BB0109	136	acetyl-CoA C-acetyltransferase (fadA)

Motif number 1

         ATTTTAAATTAATCAAATATTT	1	2	1	TTTTAAATAA	    0.893764	-38
TATAAATAATATTTAAATATTTGATTAATTT	1	16	0	ATTTAAAATT	     0.86405	-24
        TTTTATAAATAATATTTAAATAT	1	27	0	TTATAAAAAT	    0.870702	-13
AAATTATATAAATAAAAATATGTT       	2	4	0	AATAAAATAT	    0.970162	-25
          AATAAAATTATATAAATAAAA	2	18	0	AATAAAATAT	    0.970186	-11
AAATCTAGTTAATAAAACATTT         	3	2	0	AATAAAAATT	    0.865418	-78
TTACCCACTAATTTAACAAAATTTTACATTT	3	33	0	ATTTAACAAA	    0.790413	-47
CATAACCTCTTATTAAAGAATCACTTACCCA	3	57	0	TATTAAAAAT	    0.973719	-23
          TTTAAAATTATAACATTTTAG	4	1	1	TTTAAAATAT	    0.937292	-136
TTAGCTTGTTTATTAAATAATTCAGGTTAAA	4	28	1	TATTAAAAAT	    0.973653	-109
TATTTAATAAAAATAAACTATTTAACCTGAA	4	48	0	AAATAAATAT	    0.928219	-89
AGTTTATTTTTATTAAATAAACTTAGTTTTT	4	60	1	TATTAAAAAA	    0.933821	-77
AATAGATCATATAAAAACTAAGTTTATTTAA	4	72	0	ATAAAAATAA	    0.693599	-65
AAACTTATTGAATTATACAATACAATAGATC	4	95	0	AATTATAAAT	    0.833387	-42
CTAAAGTCTTAATAAACTTATTGAATTATAC	4	108	0	AATAAACTAT	    0.897397	-29
          ******* ***

Masking position 5
Map Score:   21.0929

Number of sites scoring better than the average of aligned sites = 4839
Number in coding regions = 3073
Number in noncoding regions = 1766
Number of orfs with sites within 600 bp upstream = 249
Fraction of orfs with sites within 600 bp upstream = 0.0399936


Motif number 2

ATATTTAAATATTTGATTAATTTAAAAT    	1	7	0	ATTGTTAATT	    0.852111	-33
AAATATTTAAATATTATTTATAAAA       	1	25	1	AATTTTTATA	    0.699412	-15
ACATATTTTTATTTATATAATTTTATT     	2	12	1	ATTAATAATT	     0.58347	-17
TTACATTTAAATCTAGTTAATAAAACATTT  	3	9	0	ACTATTAATA	     0.90967	-71
TAAATGTAAAATTTTGTTAAATTAGTGGGTAA	3	32	1	ATTTTTAAAT	    0.763024	-48
AACAAGCTAAAATGTTATAATTTTAAA     	4	6	0	ATGTATAATT	    0.641558	-131
ATAACATTTTAGCTTGTTTATTAAATAATTCA	4	20	1	ACTTTTTATT	    0.968486	-117
AAACTATTTAACCTGAATTATTTAATAAACAA	4	33	0	ACTGATTATT	     0.90049	-104
AATTCAGGTTAAATAGTTTATTTTTATTAAAT	4	46	1	AATATTTATT	    0.934175	-91
TCATATAAAAACTAAGTTTATTTAATAAAAAT	4	65	0	ATAATTTATT	    0.836688	-72
TTTTTATATGATCTATTGTATTGTATAATTCA	4	86	1	ACTATGTATT	    0.939488	-51
GTCTTAATAAACTTATTGAATTATACAATACA	4	102	0	ATTATGAATT	    0.917183	-35
          * *** ******

Masking position 10
Map Score:   9.07048

Number of sites scoring better than the average of aligned sites = 1978
Number in coding regions = 1180
Number in noncoding regions = 798
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 3

AATCAAATATTTAAATATTATTTATAAAA 	1	21	1	TTAAATATTA	    0.787438	-19
TTTTTATTTATATAATTTTATT        	2	17	1	TATAATTTTA	    0.561054	-12
GATTTAAATGTAAAATTTTGTTAAATTAGT	3	28	1	TAAAATTTTG	    0.579896	-52
      AACATAACCTCTTATTAAAGAATC	3	66	0	TAACCTCTTA	    0.953594	-14
TTTAAAATTATAACATTTTAGCTTGTTTAT	4	11	1	TAACATTTTA	    0.542942	-126
TTAATAAAAATAAACTATTTAACCTGAATT	4	46	0	TAAACTATTT	    0.856869	-91
 AATTACTCCTAAAGTCTTAATAAACTTAT	4	118	0	TAAAGTCTTA	    0.870739	-19
          **********

Masking position 6
Map Score:   4.43056

Number of sites scoring better than the average of aligned sites = 603
Number in coding regions = 373
Number in noncoding regions = 230
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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:   -2.59896e-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