AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_mixed18_tpal_reg_100.orf -o303_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	RTP00417	194	AE000520
#2	RTP00592	140	AE000520

Motif number 1

TTTCACTGATGGTCGAGTTCCGCT         	1	2	0	GGCGTTCCGC	    0.998241	-193
TTAGATGCCAACACGGATACCTCTCCAAAGGAG	1	51	1	ACCGTACCTC	    0.969628	-144
CCGCCGATCGGGAAGCAATCCGCACACATGATC	1	97	1	GGAGATCCGC	    0.938623	-98
CCTGCCCCACACGCTCCTTCCACGTGCGGTAAA	1	147	1	ACCTTTCCAC	    0.972626	-48
AAGAGCTCGAGCCCTTTTACCGCACGTGGAAGG	1	162	0	GCCTTACCGC	    0.992982	-33
GTACCCATTGTGCCTGTTTCCGCCGTTTTCTTA	2	29	0	TGCTTTCCGC	    0.985756	-112
TCACCGTCTTACCCGCCTTCCGGACAACCATGC	2	70	0	ACCGTTCCGG	    0.989154	-71
          ** **  ******

Masking position 10
Map Score:   6.7473

Number of sites scoring better than the average of aligned sites = 296
Number in coding regions = 271
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

TTCACTGATGGTCGAGTTCCGCT       	1	4	0	GTCGAGTTCC	    0.956322	-191
CTTCCCGATCGGCGGGTTGCAGATCTATCT	1	82	0	GGCGGGTTGC	    0.994501	-113
CAACCCGCCGATCGGGAAGCAATCCGCACA	1	93	1	ATCGGGAAGC	    0.912654	-102
    AGATGTGATGGGTAGCTTTAAGAAAA	2	7	1	GATGGGTAGC	    0.988928	-134
AAACAGGCACAATGGGTACGCAAGCCCGCA	2	43	1	AATGGGTACG	    0.911368	-98
TTGTCCGGAAGGCGGGTAAGACGGTGAGTA	2	76	1	GGCGGGTAAG	    0.977851	-65
CGGGTAAGACGGTGAGTACCTTAGTACTTA	2	88	1	GGTGAGTACC	    0.981865	-53
          **********

Masking position 6
Map Score:   6.42937

Number of sites scoring better than the average of aligned sites = 308
Number in coding regions = 266
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

AAAATAATCATATCTCGTTTTAGATGCCAA	1	32	1	TATCTCGTTT	    0.979755	-163
GTTGCAGATCTATCTCCTTTGGAGAGGTAT	1	67	0	TATCTCCTTT	    0.979773	-128
AAAAGAGCTCGAGCCCTTTTACCGCACGTG	1	167	0	GAGCCCTTTT	    0.987787	-28
AAAAGGGCTCGAGCTCTTTTTCGTTTTC  	1	177	1	GAGCTCTTTT	    0.992799	-18
          **********

Masking position 8
Map Score:   2.683

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 41
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

GGAGAGGTATCCGTGTTGGCATCTAAAACG	1	47	0	CCGTGTTGGC	    0.990747	-148
AAAAGTATGATCATGTGTGCGGATTGCTTC	1	108	0	TCATGTGTGC	     0.97023	-87
CGTGGAAGGAGCGTGTGGGGCAGGTGATTG	1	141	0	GCGTGTGGGG	    0.987105	-54
CACGCTCCTTCCACGTGCGGTAAAAGGGCT	1	156	1	CCACGTGCGG	    0.692151	-39
TTCCGGACAACCATGCGGGCTTGCGTACCC	2	56	0	CCATGCGGGC	    0.968044	-85
          **********

Masking position 5
Map Score:   3.39574

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 217
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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