AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ideoR_bsub_opreg_100.orf -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	dra	105	deoxyribose-phosphate aldolase

Motif number 1

CAATGAAAGGTTTGAACGTG          	1	1	0	TTTGAACGTG	    0.983733	-105
CAAACCTTTCATTGAACAAAATTTCAATTA	1	17	1	ATTGAACAAA	    0.928965	-89
ATAACCGACTTTTGAACATATGTAAATTGG	1	47	0	TTTGAACATA	    0.940277	-59
TTAAGATATTTTTTAGCATAACCGACTTTT	1	64	0	TTTTAGCATA	    0.981472	-42
CTAAAAAATATCTTAACAAAAAAGGAAGTG	1	78	1	TCTTAACAAA	    0.972669	-28
          **********

Masking position 5
Map Score:   7.20448

Number of sites scoring better than the average of aligned sites = 579
Number in coding regions = 468
Number in noncoding regions = 111
Number of orfs with sites within 600 bp upstream = 136
Fraction of orfs with sites within 600 bp upstream = 0.0218439


Motif number 2

ATTTTGTTCAATGAAAGGTTTGAACGTG  	1	9	0	ATGAAAGGTT	    0.981694	-97
AAATTGGTAATTGAAATTTTGTTCAATGAA	1	24	0	TTGAAATTTT	    0.970359	-82
ATTACCAATTTACATATGTTCAAAAGTCGG	1	43	1	TACATATGTT	    0.632953	-63
CTTTTTTGTTAAGATATTTTTTAGCATAAC	1	72	0	AAGATATTTT	    0.839928	-34
CTTAACAAAAAAGGAAGTGTGCGAAGG   	1	89	1	AAGGAAGTGT	    0.936499	-17
          **********

Masking position 6
Map Score:   1.28755

Number of sites scoring better than the average of aligned sites = 1133
Number in coding regions = 915
Number in noncoding regions = 218
Number of orfs with sites within 600 bp upstream = 230
Fraction of orfs with sites within 600 bp upstream = 0.0369419


Motif number 3

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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