AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_tpal_reg_300.orf -o113_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	RTP00139	102	AE000520

Motif number 1

TCTGCCGCTAACAGCAAGTGAGTACGGGCG	1	12	0	ACAGCAAGTG	    0.989471	-91
TATCCCCTCCATCGAAAGCGGCATCTGCCG	1	35	0	ATCGAAAGCG	    0.994343	-68
GATGGAGGGGATAGAGCGCGTGCACGTGCT	1	52	1	ATAGAGCGCG	    0.993969	-51
CGCGTACCAAAAAGCACGTGCACGCGCTCT	1	64	0	AAAGCACGTG	    0.992571	-39
GAAAACGGTCAACGTACGCGTACCAAAAAG	1	80	0	AACGTACGCG	    0.968607	-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	    0.989144	-100
CTCACTTGCTGTTAGCGGCAGATGCCGCTT	1	20	1	GTTAGCGGCA	    0.978443	-83
CCCCTCCATCGAAAGCGGCATCTGCCGCTA	1	32	0	GAAAGCGGCA	    0.994828	-71
GGAGGGGATAGAGCGCGTGCACGTGCTTTT	1	55	1	GAGCGCGTGC	     0.68701	-48
GTGCTTTTTGGTACGCGTACGTTGACCGTT	1	77	1	GTACGCGTAC	    0.499769	-26
       CAGGAAAACGGTCAACGTACGCG	1	90	0	GAAAACGGTC	    0.980161	-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

  ACGCCCGTACTCACTTGCTGTTAGCGGC	1	9	1	ACTCACTTGC	    0.992648	-94
GCGTACCAAAAAGCACGTGCACGCGCTCTA	1	63	0	AAGCACGTGC	     0.99651	-40
AAAACGGTCAACGTACGCGTACCAAAAAGC	1	79	0	ACGTACGCGT	    0.874893	-24
          **********

Masking position 5
Map Score:   1.15296

Number of sites scoring better than the average of aligned sites = 682
Number in coding regions = 636
Number in noncoding regions = 46
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:   -1.9652e-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