AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i243_regulatory_tpal_reg_300.orf -o243_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	RTP00740	47	AE000520
#2	RTP00743	169	AE000520

Motif number 1

GCTGCACCTCGCGCTCGAGGCG          	1	1	0	GCCTCGAGCG	     0.99767	-47
AGCGCGAGGTGCAGCCGAGGCGCCGCTGCCAC	1	18	1	GCGCCGAGCG	    0.999328	-30
        CTGCGCCAGTGGCAGCGGCGCCTC	1	34	0	GCCCAGTGCA	    0.991827	-14
GTACATACCAGATGCCGTCGCGGGAGGACAGG	2	50	0	GAGCCGTGCG	    0.999006	-120
AGTCGCAGATGATCCCGTTTCGGTGAATCTGG	2	130	1	GACCCGTTCG	    0.996455	-40
          ** ***** ***

Masking position 7
Map Score:   8.55033

Number of sites scoring better than the average of aligned sites = 181
Number in coding regions = 171
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

ATCGTGTACATACCAGATGCCGTCGCGGGA	2	57	0	TACCAGATGC	    0.997629	-113
ATCATTCTGTTCCCAAATTCTCAACTACGT	2	88	0	TCCCAAATTC	    0.990647	-82
GCACTTTTAGTCGCAGATGATCCCGTTTCG	2	122	1	TCGCAGATGA	    0.983893	-48
GGTTTTCAAATACCAGATTCACCGAAACGG	2	144	0	TACCAGATTC	    0.996338	-26
          **********

Masking position 5
Map Score:   5.46638

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 46
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

CTCGAGCGCGAGGTGCAGCCGAGGCGCCGC	1	14	1	AGGTGCAGCC	    0.981855	-34
GGTGCAGCCGAGGCGCCGCTGCCACTGGCG	1	25	1	AGGCGCCGCT	    0.994415	-23
GTGATAGGTAAAGCGCTTCTTTTCCCGGAA	2	21	0	AAGCGCTTCT	    0.927765	-149
TGTACATACCAGATGCCGTCGCGGGAGGAC	2	53	0	AGATGCCGTC	    0.973457	-117
CTGCGACTAAAAGTGCCTTCATCATTCTGT	2	108	0	AAGTGCCTTC	    0.960651	-62
AGGCACTTTTAGTCGCAGATGATCCCGTTT	2	120	1	AGTCGCAGAT	    0.911729	-50
          **********

Masking position 1
Map Score:   4.95724

Number of sites scoring better than the average of aligned sites = 800
Number in coding regions = 726
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 4

GGTAAAGCGCTTCTTTTCCCGGAAATCCCG	2	15	0	TTCTTTTCCC	    0.996634	-155
GCCTTCATCATTCTGTTCCCAAATTCTCAA	2	94	0	TTCTGTTCCC	    0.997727	-76
          **********

Masking position 6
Map Score:   1.30601

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 4
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 5

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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:   2.93755e-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