AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_tpal_reg_300.orf -o183_tpal_300.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	RTP00433	150	AE000520

Motif number 1

CAATTGCACAGCCACCTGGAAGTATCGTCC	1	34	0	GCCACCTGGA	    0.973696	-117
TACGACCTGCACCATCTGGATACAATTGCA	1	56	0	ACCATCTGGA	    0.967793	-95
TACTGCATGCACCACCGGTGTCTTACGACC	1	79	0	ACCACCGGTG	    0.996258	-72
AGCGTCCTTTGCCCCCGGGGCGTCTTTTTG	1	131	1	GCCCCCGGGG	    0.976249	-20
          **********

Masking position 6
Map Score:   7.37294

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 39
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TCCAATCCGCTGAGCGGCTGGC          	1	1	0	TGGCGGCTGC	    0.993736	-150
GTATCCAGATGGTGCAGGTCGTAAGACACCGG	1	63	1	GGGCAGGTGT	    0.995812	-88
AGACACCGGTGGTGCATGCAGTAACCGTTGAT	1	86	1	GGGCATGCGT	    0.982181	-65
ATGAGCAAGATGAGCGTCCTTTGCCCCCGGGG	1	119	1	TGGCGTCCTT	    0.993636	-32
CTTTGCCCCCGGGGCGTCTTTTTG        	1	137	1	GGGCGTCTTT	    0.996943	-14
          ** ****** **

Masking position 5
Map Score:   4.84623

Number of sites scoring better than the average of aligned sites = 320
Number in coding regions = 297
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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