AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i015_Glycolysis_2_tpal_reg_100.orf -o015_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00425	101	AE000520

Motif number 1

TCTCTATTCAGCTGGAGCGCTCGGTCGTAG	1	35	0	GCTGGAGCGC	    0.997515	-67
TAGAGATCTGGCTGATGCTCGCCGGGGCAG	1	59	1	GCTGATGCTC	     0.99557	-43
GCTGATGCTCGCCGGGGCAGGGAGCGGGTG	1	69	1	GCCGGGGCAG	    0.997728	-33
GGGGCAGGGAGCGGGTGCTGAGGTACGTGT	1	82	1	GCGGGTGCTG	    0.998806	-20
          **********

Masking position 4
Map Score:   6.75632

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 228
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

          GGACTATCGCTATGCGTTAC	1	1	1	GGACTATCGC	    0.976071	-101
CTCGGTCGTAGGCCTGTAACGCATAGCGAT	1	16	0	GGCCTGTAAC	    0.981635	-86
ACAGGCCTACGACCGAGCGCTCCAGCTGAA	1	29	1	GACCGAGCGC	    0.985147	-73
GCGAGCATCAGCCAGATCTCTATTCAGCTG	1	51	0	GCCAGATCTC	     0.96477	-51
TGCTCGCCGGGGCAGGGAGCGGGTGCTGAG	1	74	1	GGCAGGGAGC	    0.995384	-28
          **********

Masking position 1
Map Score:   4.42113

Number of sites scoring better than the average of aligned sites = 497
Number in coding regions = 449
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

GGCCTGTAACGCATAGCGATAGTCC     	1	6	0	GCATAGCGAT	    0.996276	-96
CAGGCCTACGACCGAGCGCTCCAGCTGAAT	1	30	1	ACCGAGCGCT	    0.987498	-72
CGCTCCAGCTGAATAGAGATCTGGCTGATG	1	46	1	GAATAGAGAT	    0.977574	-56
GCTCGCCGGGGCAGGGAGCGGGTGCTGAGG	1	75	1	GCAGGGAGCG	    0.993035	-27
          **********

Masking position 6
Map Score:   1.91904

Number of sites scoring better than the average of aligned sites = 603
Number in coding regions = 568
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 4

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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