AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i042_Transketolase_mjan_reg_100.orf -o042_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ00065	39	M_jannaschii_chromosome
#2	RMJ03270	23	M_jannaschii_chromosome
#3	RMJ00927	156	M_jannaschii_chromosome

Motif number 1

ATAATTAATTTATTATTTTTGTTT      	1	5	0	TATTATTTTT	    0.995829	-35
ATAATAAATTAATTATTTTGGGTGAAAAAT	1	19	1	AATTATTTTG	    0.974806	-21
        AATTTTATTTTTTGGTGATTTA	2	3	1	TTTTATTTTT	    0.990652	-21
ATTTACTATCTATTATTTTTAGGTGTAAGT	3	20	1	TATTATTTTT	    0.995829	-137
TATGACTAACAATTATTTTAGCATAACATC	3	56	1	AATTATTTTA	    0.962415	-101
ATTATGGATTTTTTGTTTTTGCTTTTTTTA	3	86	1	TTTTGTTTTT	    0.970256	-71
TGAGTAATGATATTATTTTTTAAATCTTAA	3	125	1	TATTATTTTT	    0.995829	-32
          **********

Masking position 6
Map Score:   18.7141

Number of sites scoring better than the average of aligned sites = 639
Number in coding regions = 389
Number in noncoding regions = 250
Number of orfs with sites within 600 bp upstream = 215
Fraction of orfs with sites within 600 bp upstream = 0.0345326


Motif number 2

AATTAATTATTTTGGGTGAAAAATC     	1	25	1	TTTGGGTGAA	    0.950811	-15
 AATTTTATTTTTTGGTGATTTAA      	2	10	1	TTTTGGTGAT	    0.977227	-14
ATCTATTATTTTTAGGTGTAAGTTTTAAAT	3	27	1	TTTAGGTGTA	    0.977215	-130
TAACAATTATTTTAGCATAACATCATTATG	3	62	1	TTTAGCATAA	    0.785091	-95
CATAACATCATTATGGATTTTTTGTTTTTG	3	77	1	TTATGGATTT	    0.880727	-80
GATTTTTTGTTTTTGCTTTTTTTATTAATT	3	92	1	TTTTGCTTTT	    0.951134	-65
GTTTCACCTTTTTAAGATTTAAAAAATAAT	3	136	0	TTTAAGATTT	    0.821981	-21
          **********

Masking position 2
Map Score:   3.59382

Number of sites scoring better than the average of aligned sites = 1756
Number in coding regions = 1504
Number in noncoding regions = 252
Number of orfs with sites within 600 bp upstream = 224
Fraction of orfs with sites within 600 bp upstream = 0.0359782


Motif number 3

 AAACAAAAATAATAAATTAATTATTTTGG	1	10	1	TAATAAATTA	    0.713928	-30
 TTAAATCACCAAAAAATAAAATT      	2	5	0	CAAAAAATAA	     0.89226	-19
CCTCTATTTACTATCTATTATTTTTAGGTG	3	15	1	CTATCTATTA	    0.928741	-142
TTAGTCATATTTAAAACTTACACCTAAAAA	3	35	0	TTAAAACTTA	    0.944443	-122
TTAAATATGACTAACAATTATTTTAGCATA	3	51	1	CTAACAATTA	    0.977585	-106
TATCATTACTCAATGAATTAATAAAAAAAG	3	107	0	CAATGAATTA	    0.930835	-50
ATATTATTTTTTAAATCTTAAAAAGGTGAA	3	134	1	TTAAATCTTA	    0.875445	-23
          **********

Masking position 3
Map Score:   4.48271

Number of sites scoring better than the average of aligned sites = 851
Number in coding regions = 595
Number in noncoding regions = 256
Number of orfs with sites within 600 bp upstream = 246
Fraction of orfs with sites within 600 bp upstream = 0.0395117


Motif number 4

TTAATTATTTTGGGTGAAAAATC       	1	27	1	TGGGTGAAAA	    0.988982	-13
CTATTATTTTTAGGTGTAAGTTTTAAATAT	3	29	1	TAGGTGTAAG	    0.988982	-128
AAATCTTAAAAAGGTGAAACT         	3	146	1	AAGGTGAAAC	    0.988982	-11
          **********

Masking position 8
Map Score:   0.282824

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 24
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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 7

          **********

No masking
Map Score:   -2.39152e-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