AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ifadR_tpal_opreg_100.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	TP0145	109	long-chain-fatty-acid--CoA ligase

Motif number 1

TATAGTCCCCGGCGGGGAGAGGCT       	1	4	0	GCGGGGAGAG	     0.99734	-106
TCTCCCCGCCGGGGACTATAGCATAGCTCTA	1	15	1	GGGACTATAG	    0.988335	-95
CCCTGGATAGGAGCTCTAGAGCTATGCTATA	1	31	0	GGCTCTAGAG	    0.993165	-79
TGTACCCCTCACCCTGGATAGGAGCTCTAGA	1	42	0	ACCTGGATAG	    0.879407	-68
TATCCAGGGTGAGGGGTACAGTGCTGCTGTC	1	53	1	GGGGGTACAG	    0.996621	-57
CACTCCCTTTGAGCAAGACAGCAGCACTGTA	1	69	0	GGCAAGACAG	    0.981086	-41
          GCGGGCGAGTGTACCGAATGC	1	99	0	GGGGCGAGTG	    0.994607	-11
          * *********

Masking position 8
Map Score:   9.40489

Number of sites scoring better than the average of aligned sites = 727
Number in coding regions = 628
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 2

GGAGCTCTAGAGCTATGCTATAGTCCCCGG	1	23	0	AGCTATGCTA	    0.985423	-87
GCATAGCTCTAGAGCTCCTATCCAGGGTGA	1	35	1	AGAGCTCCTA	      0.9946	-75
TGAGGGGTACAGTGCTGCTGTCTTGCTCAA	1	62	1	AGTGCTGCTG	    0.996506	-48
          **********

Masking position 1
Map Score:   0.694744

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 56
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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