AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i284_hypothetical9_bbur_reg_100.orf -o284_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	RBB00992	109	4091
#2	RBB00993	35	4091
#3	RBB00995	46	4091

Motif number 1

  TATTTCTATAAAATTTGATTTATCAATAT	1	9	1	TAAAATTGAT	    0.959646	-101
AATCTAATAATAAAATATATTGATAAATCAA	1	25	0	TAAAATTATT	    0.985367	-85
ATTATTAGATTAAAATCCAATAAATAGCGTT	1	45	1	TAAAATCAAT	    0.960999	-65
ATTTTTGATATAAAATAAAATTTGAGGAGTA	1	82	1	TAAAATAAAT	    0.982046	-28
     GCCTTTAAAAAGAATTAAAAGCCTAA	2	6	1	TAAAAAAATT	    0.969791	-30
ATTAAAAGCCTAATAATTATTA         	2	24	1	TAATAATATT	    0.937936	-12
         TTAATATAAATACTCTCCTTTC	3	2	1	TAATATAATA	    0.907205	-45
CTGTATTGTATAATATAAGTTAATT      	3	32	1	TAATATAGTT	    0.968716	-15
          ****** ****

Masking position 5
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

TTCTATAAAATTTGATTTATCAATATATTT	1	14	1	TTTGATTTAT	    0.982121	-96
TATTTTATTATTAGATTAAAATCCAATAAA	1	39	1	TTAGATTAAA	    0.759574	-71
ATAAATAGCGTTGGTTTTATTTTTGATATA	1	64	1	TTGGTTTTAT	    0.962815	-46
TGGTTTTATTTTTGATATAAAATAAAATTT	1	75	1	TTTGATATAA	    0.906051	-35
          **********

Masking position 6
Map Score:   1.56597

Number of sites scoring better than the average of aligned sites = 279
Number in coding regions = 181
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


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