AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_tpal_reg_100.orf -o183_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	RTP00433	150	AE000520

Motif number 1

GGACGATACTTCCAGGTGGCTGTGCAATTG	1	34	1	TCCAGGTGGC	    0.973286	-117
TGCAATTGTATCCAGATGGTGCAGGTCGTA	1	56	1	TCCAGATGGT	     0.96749	-95
GGTCGTAAGACACCGGTGGTGCATGCAGTA	1	79	1	CACCGGTGGT	    0.996299	-72
CAAAAAGACGCCCCGGGGGCAAAGGACGCT	1	131	0	CCCCGGGGGC	    0.975869	-20
          **********

Masking position 5
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

          GCCAGCCGCTCAGCGGATTGGA	1	1	1	GCAGCCGCCA	    0.993461	-150
CCGGTGTCTTACGACCTGCACCATCTGGATAC	1	63	0	ACACCTGCCC	    0.995634	-88
ATCAACGGTTACTGCATGCACCACCGGTGTCT	1	86	0	ACGCATGCCC	    0.982567	-65
CCCCGGGGGCAAAGGACGCTCATCTTGCTCAT	1	119	0	AAGGACGCCA	    0.993357	-32
        CAAAAAGACGCCCCGGGGGCAAAG	1	137	0	AAAGACGCCC	    0.996808	-14
          ** ****** **

Masking position 8
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