AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ideoR_tpal_opreg_300.orf -g0.528 -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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP0261	114	catabolite gene activator, putative

Motif number 1

TTTCCTGGAAAAGGCGTGCGAACGATCTCT	1	16	1	AAGGCGTGCG	    0.998881	-99
ACGATCTCTGCAGGTGTGCGCGCAGGAGCG	1	37	1	CAGGTGTGCG	    0.999315	-78
GGTGTGCGCGCAGGAGCGCGTGACGTGAAT	1	49	1	CAGGAGCGCG	    0.996561	-66
          **********

Masking position 2
Map Score:   7.08392

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 74
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TGCAGAGATCGTTCGCACGCCTTTTCCAGGA	1	18	0	GTCGCACGCC	    0.998542	-97
ACGCGCTCCTGCGCGCACACCTGCAGAGATC	1	39	0	GGCGCACACC	    0.998565	-76
GTGCGCGCAGGAGCGCGTGACGTGAATTCTG	1	52	1	GGCGCGTGAC	     0.99853	-63
AAAAAGACTTAAGTGCATGACCGTTCTATCG	1	84	1	AGTGCATGAC	    0.986559	-31
          * *********

Masking position 6
Map Score:   4.66822

Number of sites scoring better than the average of aligned sites = 519
Number in coding regions = 470
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

    CCACCTTTCCTGGAAAAGGCGTGCGA	1	7	1	TTCCTGGAAA	    0.789922	-108
CGTGACGTGAATTCTGGAAAAAGACTTAAG	1	67	1	ATTCTGGAAA	     0.78886	-48
          **********

Masking position 5
Map Score:   0.818982

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 7
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

GCCTTTTCCAGGAAAGGTGG          	1	1	0	GGAAAGGTGG	      0.9944	-114
CACCTTTCCTGGAAAAGGCGTGCGAACGAT	1	12	1	GGAAAAGGCG	    0.986561	-103
ACACCTGCAGAGATCGTTCGCACGCCTTTT	1	24	0	AGATCGTTCG	    0.823003	-91
CATTTTCGATAGAACGGTCATGCACTTAAG	1	91	0	AGAACGGTCA	    0.913691	-24
          **********

Masking position 3
Map Score:   1.89105

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 207
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 5

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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