AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i248_cell_division_bbur_reg_100.orf -o248_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	RBB00684	79	3615
#2	RBB00663	114	3615
#3	RBB00659	46	3615
#4	RBB00657	36	3615

Motif number 1

AAATATTTTAAAAAAAGGTCAATT         	1	2	0	AAAAAGCAAT	    0.964161	-78
TTCATATTATAATAAATAAAAATATTTTAAAAA	1	21	0	ATAAAAAAAT	    0.978261	-59
CCAATTACTGATAAATCTACAATTTCATATTAT	1	44	0	AAAATTCAAT	    0.975965	-36
     TTAAAATTAAAAACCAATTACTGATAAA	1	62	0	ATAAAACAAT	    0.988774	-18
TAGTATACCAAATAATTATCAATTTAAAAAAAA	2	42	1	ATAATACAAT	    0.984106	-73
TTATCAATTTAAAAAAAAAAAATTATTTGATAT	2	57	1	AAAAAAAAAT	    0.969125	-58
TTTCAAGCTAAATTATATCAAATAATTTTTTTT	2	71	0	ATTATTAAAT	    0.866438	-44
ATCCTTTAGGAGTTAATTTCAAGCTAAATTATA	2	87	0	ATTAATCAAG	    0.834184	-28
TAAAAATGAAAGAAAAAATAAATACATTGCTCA	3	21	1	AAAAAAAAAT	    0.968692	-26
      ATTTAATAATCTGCAATAAAATAGGAG	4	5	1	ATAATTCAAT	    0.983423	-32
          * **** * ****

Masking position 5
Map Score:   15.9325

Number of sites scoring better than the average of aligned sites = 750
Number in coding regions = 511
Number in noncoding regions = 239
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

TTTTTTTAAAATATTTTTATTTATTATAAT	1	19	1	ATATTTTTAT	    0.875977	-61
CTACAATTTCATATTATAATAAATAAAAAT	1	31	0	ATATTATAAT	    0.527017	-49
TCAGTAATTGGTTTTTAATTTTAA      	1	66	1	GTTTTTAATT	     0.85465	-14
AACCTTACTAATATTAGTATACCAAATAAT	2	28	1	ATATTAGTAT	    0.598612	-87
TTTTAAATTGATAATTATTTGGTATACTAA	2	41	0	ATAATTATTT	    0.941217	-74
ATTATATCAAATAATTTTTTTTTTTTAAAT	2	63	0	ATAATTTTTT	    0.932361	-52
TTTTTCTTTCATTTTTATTTCTCGCTA   	3	8	0	ATTTTTATTT	    0.942014	-39
TTTGAGCAATGTATTTATTTTTTCTTTCAT	3	26	0	GTATTTATTT	    0.949858	-21
TTTATTGCAGATTATTAAAT          	4	1	0	ATTATTAAAT	    0.749208	-36
GTTTGTTCTCCTATTTTATTGCAGATTATT	4	15	0	CTATTTTATT	     0.85137	-22
          **********

Masking position 5
Map Score:   7.92114

Number of sites scoring better than the average of aligned sites = 4077
Number in coding regions = 2553
Number in noncoding regions = 1524
Number of orfs with sites within 600 bp upstream = 220
Fraction of orfs with sites within 600 bp upstream = 0.0353357


Motif number 3

          **********

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 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