AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i132_Transmembrane_Transport_6_tpal_reg_100.orf -o132_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	RTP00337	109	AE000520

Motif number 1

ACTCGGCAACGCACTCCCTACGAAACTTTG	1	16	0	GCACTCCCTA	    0.993877	-94
CGCGCAGGCCACACCACCCTCCTGAACTCG	1	41	0	ACACCACCCT	    0.979228	-69
TGGCCTGCGCGCACTCAGGTACATACCGCG	1	60	1	GCACTCAGGT	    0.978237	-50
GTAGAGACGAGCACTACCTTAACCGCGGTA	1	83	0	GCACTACCTT	     0.99798	-27
GTAGTGCTCGTCTCTACCGTTGTC      	1	96	1	TCTCTACCGT	    0.982895	-14
          **********

Masking position 4
Map Score:   5.06719

Number of sites scoring better than the average of aligned sites = 401
Number in coding regions = 355
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 2

CCACCCTCCTGAACTCGGCAACGCACTCCC	1	28	0	GAACTCGGCA	    0.992009	-82
GCACTACCTTAACCGCGGTATGTACCTGAG	1	73	0	AACCGCGGTA	    0.533571	-37
          GACAACGGTAGAGACGAGCA	1	100	0	GACAACGGTA	     0.97249	-10
          **********

Masking position 2
Map Score:   1.52442

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 33
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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