AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_tpal_reg_100.orf -o194_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	RTP00762	73	AE000520
#2	RTP00763	58	AE000520
#3	RTP00764	108	AE000520

Motif number 1

TCTGCAAGCAGCGGCAACGGATTCTGTAAA	1	31	0	GCGGCAACGG	     0.99384	-43
GCCGCTGCTTGCAGAAAAGGTTGGGTATTT	1	46	1	GCAGAAAAGG	    0.987002	-28
GCCTCTCTACGCAGCAAGAGTTTTATCCTT	2	18	0	GCAGCAAGAG	    0.983286	-41
GCGTAGAGAGGCAGGTGCGGAACGAATAGG	2	36	1	GCAGGTGCGG	    0.986707	-23
GCCGCAAGACGCAGACCCAGATCA      	3	5	0	GCAGACCCAG	     0.99262	-104
GCGTCTTGCGGCAGGCACGCTGGTGAACGC	3	23	1	GCAGGCACGC	    0.977054	-86
TTGGTGAATTGCAGACACAGGATTTTGCAC	3	85	1	GCAGACACAG	    0.997328	-24
          **********

Masking position 4
Map Score:   12.3904

Number of sites scoring better than the average of aligned sites = 401
Number in coding regions = 375
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

         CTCGGTCAGGTGTACGACGGTTTA	1	2	1	TCGGAGTGTA	    0.922887	-72
AACCTTTTCTGCAAGCAGCGGCAACGGATTCTG	1	35	0	GCAAAGGGCA	    0.993607	-39
AACTCTTGCTGCGTAGAGAGGCAGGTGCGGAAC	2	26	1	GCGTAGGGCA	    0.998237	-33
ATCTGGGTCTGCGTCTTGCGGCAGGCACGCTGG	3	13	1	GCGTTGGGCA	    0.995957	-96
CTTGCGGCAGGCACGCTGGTGAACGCAGATTAC	3	27	1	GCACTGTGAA	    0.933542	-82
CAGATTACAAGCGCGCAGTGGTATTCTTGTCTC	3	52	1	GCGCAGGGTA	    0.997675	-57
TGTCTGCAATTCACCAAGAGACAAGAATACCAC	3	69	0	TCACAGGACA	    0.956247	-40
          ****  ** ****

Masking position 13
Map Score:   7.56125

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 414
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

CAGGTGTACGACGGTTTACAGAATCCGTTG	1	17	1	ACGGTTTACA	    0.926033	-57
ATCCGTTGCCGCTGCTTGCAGAAAAGGTTG	1	39	1	GCTGCTTGCA	    0.989389	-35
ATCTGGGTCTGCGTCTTGCGGCAGGCACGC	3	13	1	GCGTCTTGCG	    0.983639	-96
GCTGGTGAACGCAGATTACAAGCGCGCAGT	3	41	1	GCAGATTACA	    0.972912	-68
TTGTCTCTTGGTGAATTGCAGACACAGGAT	3	78	1	GTGAATTGCA	    0.920323	-31
TGCAGACACAGGATTTTGCACAATA     	3	94	1	GGATTTTGCA	    0.930549	-15
          **********

Masking position 6
Map Score:   1.68015

Number of sites scoring better than the average of aligned sites = 806
Number in coding regions = 765
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

GATTCTGTAAACCGTCGTACACCTGACCGA	1	12	0	ACCGTCGTAC	    0.979977	-62
ATCTGCGTTCACCAGCGTGCCTGCCGCAAG	3	27	0	ACCAGCGTGC	    0.998123	-82
CGCGCTTGTAATCTGCGTTCACCAGCGTGC	3	37	0	ATCTGCGTTC	    0.970606	-72
AACGCAGATTACAAGCGCGCAGTGGTATTC	3	48	1	ACAAGCGCGC	    0.988645	-61
          **********

Masking position 1
Map Score:   2.10184

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 207
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 5

          **********

No masking
Map Score:   -3.31523e-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:   -3.31523e-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:   -3.31523e-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