AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_tpal_reg_100.orf -o113_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	RTP00139	102	AE000520

Motif number 1

TCTGCCGCTAACAGCAAGTGAGTACGGGCG	1	12	0	ACAGCAAGTG	    0.989964	-91
TATCCCCTCCATCGAAAGCGGCATCTGCCG	1	35	0	ATCGAAAGCG	    0.994609	-68
GATGGAGGGGATAGAGCGCGTGCACGTGCT	1	52	1	ATAGAGCGCG	    0.994251	-51
CGCGTACCAAAAAGCACGTGCACGCGCTCT	1	64	0	AAAGCACGTG	    0.992585	-39
GAAAACGGTCAACGTACGCGTACCAAAAAG	1	80	0	AACGTACGCG	    0.967544	-23
          **********

Masking position 1
Map Score:   8.31746

Number of sites scoring better than the average of aligned sites = 519
Number in coding regions = 485
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

AACAGCAAGTGAGTACGGGCGT        	1	3	0	GAGTACGGGC	    0.987591	-100
CTCACTTGCTGTTAGCGGCAGATGCCGCTT	1	20	1	GTTAGCGGCA	    0.975379	-83
CCCCTCCATCGAAAGCGGCATCTGCCGCTA	1	32	0	GAAAGCGGCA	     0.99422	-71
GGAGGGGATAGAGCGCGTGCACGTGCTTTT	1	55	1	GAGCGCGTGC	     0.70289	-48
AACGGTCAACGTACGCGTACCAAAAAGCAC	1	77	0	GTACGCGTAC	    0.499698	-26
       CAGGAAAACGGTCAACGTACGCG	1	90	0	GAAAACGGTC	    0.979281	-13
          **********

Masking position 6
Map Score:   8.06053

Number of sites scoring better than the average of aligned sites = 847
Number in coding regions = 790
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

          ACGCCCGTACTCACTTGCTG	1	1	1	ACGCCCGTAC	    0.985991	-102
CTGCCGCTAACAGCAAGTGAGTACGGGCGT	1	11	0	CAGCAAGTGA	    0.987787	-92
CCATCGAAAGCGGCATCTGCCGCTAACAGC	1	27	0	CGGCATCTGC	    0.990181	-76
GCGTACCAAAAAGCACGTGCACGCGCTCTA	1	63	0	AAGCACGTGC	    0.998217	-40
          **********

Masking position 8
Map Score:   1.79333

Number of sites scoring better than the average of aligned sites = 887
Number in coding regions = 830
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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