AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_tpal_reg_300.orf -o228_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	RTP00558	177	AE000520

Motif number 1

GATTTTGTCGTGGGTGCGCGCCCT      	1	5	0	TGGGTGCGCG	    0.995121	-173
TACTCCACGAATCGAACGCGTGCCAGTGCG	1	43	1	ATCGAACGCG	    0.964246	-135
ATCGAACGCGTGCCAGTGCGGTACACTGCG	1	53	1	TGCCAGTGCG	    0.997022	-125
TTGGGGGAAGATGCAGCGCGCAGTGTACCG	1	71	0	ATGCAGCGCG	    0.996761	-107
CTTCCCCCAATACCAGCGCGAGCTTGCCCT	1	91	1	TACCAGCGCG	    0.996786	-87
GCTTGCCCTCAAGCTGTGCGCCATACTTTT	1	112	1	AAGCTGTGCG	    0.991335	-66
GAGACGGTGCAGCATGTGCGGGAAAAGTAT	1	134	0	AGCATGTGCG	    0.983351	-44
          **********

Masking position 8
Map Score:   15.3273

Number of sites scoring better than the average of aligned sites = 1027
Number in coding regions = 954
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 2

TTGATTTTGTCGTGGGTGCGCGCCCT    	1	7	0	CGTGGGTGCG	    0.990753	-171
TCGCGCTGGTATTGGGGGAAGATGCAGCGC	1	82	0	ATTGGGGGAA	    0.988999	-96
TGGCGCACAGCTTGAGGGCAAGCTCGCGCT	1	105	0	CTTGAGGGCA	    0.992856	-73
CGGTGCAGCATGTGCGGGAAAAGTATGGCG	1	130	0	TGTGCGGGAA	    0.986758	-48
          CGTGGGGGTATTTCGTATAC	1	168	0	CGTGGGGGTA	    0.997813	-10
          **********

Masking position 3
Map Score:   6.90962

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 200
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

ATCAACGTGTGTACTCCACGAATCGAACGC	1	32	1	GTACTCCACG	    0.991798	-146
TGCCAGTGCGGTACACTGCGCGCTGCATCT	1	63	1	GTACACTGCG	    0.998557	-115
GGGGTATTTCGTATACTGCCGAGACGGTGC	1	154	0	GTATACTGCC	    0.992796	-24
          **********

Masking position 3
Map Score:   1.29991

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 82
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

GTATTGGGGGAAGATGCAGCGCGCAGTGTA	1	74	0	AAGATGCAGC	     0.99704	-104
TACTGCCGAGACGGTGCAGCATGTGCGGGA	1	141	0	ACGGTGCAGC	    0.997487	-37
          **********

Masking position 5
Map Score:   0.602563

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 20
Number in noncoding regions = 1
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:   1.87173e-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:   1.87173e-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 7

          **********

No masking
Map Score:   1.87173e-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