AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_tpal_reg_300.orf -o033_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	RTP00331	75	AE000520
#2	RTP00330	224	AE000520

Motif number 1

AAGCACTGGATGGGCTAGGGGGTTTCATCGCCT	1	24	1	TGGGTGGGGT	    0.995557	-52
AGAGTTTGATTGGGTTTGGTAGGCGATGAAACC	1	44	0	TGGGTGGAGG	    0.996411	-32
TAGTGGCGAGCGAAATTGGAGGAGCCTAAACCT	2	66	1	CGAATGGGGA	    0.923261	-159
TGTGTCTAACAGGGGTTGTAGGGCCGCGCGGGC	2	98	1	AGGGTGTGGG	    0.982793	-127
CGCGCGGGCTTGCGTTCGGTGGGTGAAATAATC	2	122	1	TGCGTGGGGG	     0.99868	-103
AAAACCTTTCTGCTATAGGCCGGATTATTTCAC	2	144	0	TGCTTGGCGG	    0.986968	-81
TCCCCGTATGCGGAATGGGGCGGACCTGCTGG 	2	203	1	CGGATGGCGG	    0.995305	-22
          **** * ** ***

Masking position 6
Map Score:   8.62306

Number of sites scoring better than the average of aligned sites = 147
Number in coding regions = 121
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

TGGTAGGCGATGAAACCCCCTAGCCCATCC	1	31	0	TGAAACCCCC	     0.97591	-45
AATCAAACTCTGAATGCCGG          	1	66	1	TGAATGCCGG	    0.950579	-10
CACTACTTTCGGAATCTCTCTTGATTTCTT	2	41	0	GGAATCTCTC	    0.839921	-184
AACAGGGGTTGTAGGGCCGCGCGGGCTTGC	2	105	1	GTAGGGCCGC	    0.964685	-120
CCCACCGAACGCAAGCCCGCGCGGCCCTAC	2	115	0	GCAAGCCCGC	    0.985415	-110
AAAGGTTTTGGGAAAGCCTGACAGAGAGGG	2	168	1	GGAAAGCCTG	    0.959718	-57
ACAGAGAGGGTGAAATCCCCGTATGCGGAA	2	188	1	TGAAATCCCC	    0.947491	-37
       CCAGCAGGTCCGCCCCATTCCGC	2	212	0	GCAGGTCCGC	     0.93387	-13
          **********

Masking position 3
Map Score:   5.14549

Number of sites scoring better than the average of aligned sites = 722
Number in coding regions = 663
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

CAGTGCTTTACCTCCGACAGT         	1	2	0	CCTCCGACAG	    0.993465	-74
ACCCAATCAAACTCTGAATGCCGG      	1	62	1	ACTCTGAATG	    0.956399	-14
ATCAAGAGAGATTCCGAAAGTAGTGGCGAG	2	46	1	ATTCCGAAAG	    0.915283	-179
GGCCCTACAACCCCTGTTAGACACAGGTTT	2	93	0	CCCCTGTTAG	    0.946934	-132
ATTATTTCACCCACCGAACGCAAGCCCGCG	2	124	0	CCACCGAACG	    0.962835	-101
GATTTCACCCTCTCTGTCAGGCTTTCCCAA	2	175	0	TCTCTGTCAG	    0.963042	-50
GAGGGTGAAATCCCCGTATGCGGAATGGGG	2	193	1	TCCCCGTATG	    0.966492	-32
          **********

Masking position 6
Map Score:   4.555

Number of sites scoring better than the average of aligned sites = 438
Number in coding regions = 400
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

AGGGGGTTTCATCGCCTACCAAACCCAATC	1	40	1	ATCGCCTACC	    0.980414	-36
CTCCTCCAATTTCGCTCGCCACTACTTTCG	2	60	0	TTCGCTCGCC	    0.990662	-165
GCCGGATTATTTCACCCACCGAACGCAAGC	2	129	0	TTCACCCACC	    0.996931	-96
ATACGGGGATTTCACCCTCTCTGTCAGGCT	2	182	0	TTCACCCTCT	    0.978892	-43
          **********

Masking position 2
Map Score:   2.37516

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 79
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

TCCGAAAGTAGTGGCGAGCGAAATTGGAGG	2	58	1	GTGGCGAGCG	    0.995287	-167
AGGGGTTGTAGGGCCGCGCGGGCTTGCGTT	2	108	1	GGGCCGCGCG	    0.867737	-117
TATGCGGAATGGGGCGGACCTGCTGG    	2	209	1	GGGGCGGACC	    0.615929	-16
          **********

Masking position 5
Map Score:   0.305521

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 57
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 6

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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 8

          **********

No masking
Map Score:   -3.38628e-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