AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i284_hypothetical9_bbur_reg_300.orf -o284_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	RBB00992	109	4091
#2	RBB00993	35	4091
#3	RBB00995	46	4091

Motif number 1

ATATTGATAAATCAAATTTTATAGAAATA  	1	9	0	ATCAATTTTA	    0.961411	-101
TTGATTTATCAATATATTTTATTATTAGATT	1	25	1	AATAATTTTA	    0.986022	-85
AACGCTATTTATTGGATTTTAATCTAATAAT	1	45	0	ATTGATTTTA	    0.962708	-65
TACTCCTCAAATTTTATTTTATATCAAAAAT	1	82	0	ATTTATTTTA	    0.982849	-28
TTAGGCTTTTAATTCTTTTTAAAGGC     	2	6	0	AATTTTTTTA	    0.971125	-30
         TAATAATTATTAGGCTTTTAAT	2	24	0	AATATTATTA	    0.940502	-12
GAAAGGAGAGTATTTATATTAA         	3	2	0	TATTATATTA	    0.911032	-45
      AATTAACTTATATTATACAATACAG	3	32	0	AACTATATTA	    0.970096	-15
          **** ******

Masking position 11
Map Score:   11.9941

Number of sites scoring better than the average of aligned sites = 1078
Number in coding regions = 633
Number in noncoding regions = 445
Number of orfs with sites within 600 bp upstream = 130
Fraction of orfs with sites within 600 bp upstream = 0.0208802


Motif number 2

AATATATTGATAAATCAAATTTTATAGAAA	1	13	0	TAAATCAAAT	    0.929456	-97
ATCTAATAATAAAATATATTGATAAATCAA	1	25	0	AAAATATATT	    0.744404	-85
TTATTAGATTAAAATCCAATAAATAGCGTT	1	46	1	AAAATCCAAT	    0.958663	-64
TTTTATATCAAAAATAAAACCAACGCTATT	1	67	0	AAAATAAAAC	    0.971789	-43
TTTTTGATATAAAATAAAATTTGAGGAGTA	1	83	1	AAAATAAAAT	    0.988831	-27
        TTAATATAAATACTCTCCTTTC	3	3	1	AATATAAATA	    0.833098	-44
TGTATTGTATAATATAAGTTAATT      	3	33	1	AATATAAGTT	    0.869817	-14
          **********

Masking position 4
Map Score:   6.37158

Number of sites scoring better than the average of aligned sites = 2621
Number in coding regions = 1686
Number in noncoding regions = 935
Number of orfs with sites within 600 bp upstream = 172
Fraction of orfs with sites within 600 bp upstream = 0.0276261


Motif number 3

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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:   1.51646e-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