AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i248_cell_division_bbur_reg_300.orf -o248_borburg_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	RBB00684	79	3615
#2	RBB00663	114	3615
#3	RBB00659	46	3615
#4	RBB00657	36	3615

Motif number 1

AAATATTTTAAAAAAAGGTCAATT         	1	2	0	AAAAAACAAT	    0.990523	-78
TTCATATTATAATAAATAAAAATATTTTAAAAA	1	21	0	AATAAAAAAT	    0.984738	-59
CCAATTACTGATAAATCTACAATTTCATATTAT	1	44	0	ATAAATCAAT	    0.968751	-36
     TTAAAATTAAAAACCAATTACTGATAAA	1	62	0	ATTAAACAAT	    0.977539	-18
TAGTATACCAAATAATTATCAATTTAAAAAAAA	2	42	1	AATAATCAAT	    0.988809	-73
TTATCAATTTAAAAAAAAAAAATTATTTGATAT	2	57	1	AAAAAAAAAT	     0.98155	-58
TTTCAAGCTAAATTATATCAAATAATTTTTTTT	2	71	0	AATTATAAAT	    0.889791	-44
TAAAAATGAAAGAAAAAATAAATACATTGCTCA	3	21	1	AGAAAAAAAT	    0.942222	-26
      ATTTAATAATCTGCAATAAAATAGGAG	4	5	1	AATAATCAAT	    0.990457	-32
          ******   ****

Masking position 5
Map Score:   16.4807

Number of sites scoring better than the average of aligned sites = 491
Number in coding regions = 333
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

ATTATAATAAATAAAAATATTTTAAAAAAA	1	19	0	ATAAAAATAT	    0.920707	-61
TTATTATAATATGAAATTGTAGATTTATCA	1	39	1	ATGAAATTGT	    0.955212	-41
          TTAAAATTAAAAACCAATTA	1	70	0	TTAAAATTAA	     0.92999	-10
ATTTTTTTTTTTTAAATTGATAATTATTTG	2	50	0	TTTAAATTGA	    0.886468	-65
ATTTAAAAAAAAAAAATTATTTGATATAAT	2	63	1	AAAAAATTAT	    0.919839	-52
ATAATTTAGCTTGAAATTAACTCCTAAAGG	2	88	1	TTGAAATTAA	    0.954327	-27
 TAGCGAGAAATAAAAATGAAAGAAAAAAT	3	10	1	ATAAAAATGA	    0.949067	-37
AAAATGAAAGAAAAAATAAATACATTGCTC	3	23	1	AAAAAATAAA	    0.772944	-24
          **********

Masking position 5
Map Score:   6.71517

Number of sites scoring better than the average of aligned sites = 2041
Number in coding regions = 1315
Number in noncoding regions = 726
Number of orfs with sites within 600 bp upstream = 156
Fraction of orfs with sites within 600 bp upstream = 0.0250562


Motif number 3

ATAAATAAAAATATTTTAAAAAAAGGTCAAT	1	12	0	ATATTTTAAA	    0.917653	-68
CTACAATTTCATATTATAATAAATAAAAATA	1	30	0	ATATTATAAA	    0.981711	-50
AACCTTACTAATATTAGTATACCAAATAATT	2	28	1	ATATTAGTAA	    0.940169	-87
ATTTCAAGCTAAATTATATCAAATAATTTTT	2	74	0	AAATTATATA	    0.856581	-41
ATTAACTCCTAAAGGATAAAAC         	2	103	1	AAAGGATAAA	     0.92871	-12
ATTTTATTGCAGATTATTAAAT         	4	2	0	AGATTATTAA	    0.913191	-35
CTGCAATAAAATAGGAGAACAAACTT     	4	21	1	ATAGGAGAAA	    0.942383	-16
          ********* *

Masking position 3
Map Score:   3.15309

Number of sites scoring better than the average of aligned sites = 573
Number in coding regions = 337
Number in noncoding regions = 236
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

          **********

No masking
Map Score:   -4.23894e-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 5

          **********

No masking
Map Score:   -4.23894e-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:   -4.23894e-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