AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_Uracil_Utilization_tpal_reg_100.orf -o008_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	RTP00166	135	AE000520
#2	RTP00167	41	AE000520
#3	RTP00169	57	AE000520

Motif number 1

AAGTTTGAACGCAAGTCAGCT         	1	2	0	GCAAGTCAGC	    0.974427	-134
ACCGCTTTTGGCGAGGCGTTGTTTGCAATG	1	81	1	GCGAGGCGTT	     0.98449	-55
GGCGTTGTTTGCAATGCTGCTAATGAGCGC	1	95	1	GCAATGCTGC	    0.992961	-41
     GGCGAGCAATGCGTCAAAGTGTTGT	2	6	1	GCAATGCGTC	    0.998529	-36
AAGCGGTACCGTAATGCGTCCGTTAATGTC	3	22	0	GTAATGCGTC	    0.992397	-36
          **********

Masking position 4
Map Score:   7.14009

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 185
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

  AGCTGACTTGCGTTCAAACTTTCTGGGA	1	9	1	TGCGTTCAAA	    0.974399	-127
TTTTTTAGAATGTGCTCGAGTTGAGTAGCA	1	51	1	TGTGCTCGAG	     0.98598	-85
AAGAGGGTTATGCGCTCATTAGCAGCATTG	1	106	0	TGCGCTCATT	    0.969517	-30
CATAACCCTCTTTGTCCGAGGT        	1	124	1	TTTGTCCGAG	    0.952275	-12
 GGCGAGCAATGCGTCAAAGTGTTGTTGAT	2	10	1	TGCGTCAAAG	    0.975157	-32
GGTACCGTAATGCGTCCGTTAATGTCGGTA	3	18	0	TGCGTCCGTT	    0.989519	-40
          **********

Masking position 1
Map Score:   5.14449

Number of sites scoring better than the average of aligned sites = 733
Number in coding regions = 695
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

CATTCTAAAAAAGCCGCTGCATATTCCCAG	1	33	0	AAGCCGCTGC	    0.996965	-103
GCCTCGCCAAAAGCGGTTGCTACTCAACTC	1	68	0	AAGCGGTTGC	    0.998612	-68
GACGACCACCAAGCGGTACCGTAATGCGTC	3	32	0	AAGCGGTACC	    0.995511	-26
          **********

Masking position 2
Map Score:   3.10382

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 = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

CCGTTAATGTCGGTACGGTACG        	3	3	0	CGGTACGGTA	    0.998609	-55
GACCACCAAGCGGTACCGTAATGCGTCCGT	3	29	0	CGGTACCGTA	    0.998609	-29
          **********

Masking position 5
Map Score:   1.61687

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 5

TAAAAAAGCCGCTGCATATTCCCAGAAAGTTTG	1	25	0	GCTGCAATCC	    0.995632	-111
GCCAAAAGCGGTTGCTACTCAACTCGAGCACAT	1	60	0	GTTGCTCTAC	    0.912035	-76
TGTTTGCAATGCTGCTAATGAGCGCATAACCCT	1	100	1	GCTGCTATAC	     0.93379	-36
GCGTCAAAGTGTTGTTGATTCTCGCTGGTTT  	2	21	1	GTTGTTATCC	    0.989094	-21
          ****** ** * *

Masking position 9
Map Score:   1.28684

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 70
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

TTTTTAGAATGTGCTCGAGTTGAGTAGCAAC	1	52	1	GTGTCGAGTT	    0.980588	-84
AACCGCTTTTGGCGAGGCGTTGTTTGCAATG	1	80	1	GGCAGGCGTT	    0.984582	-56
CGAGCAATGCGTCAAAGTGTTGTTGATTCTC	2	13	1	GTCAAGTGTT	    0.988703	-29
CCGCTTGGTGGTCGTCGTGTTA         	3	46	1	GTCTCGTGTT	    0.995815	-12
          *** *******

Masking position 10
Map Score:   0.227105

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 45
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 7

          **********

No masking
Map Score:   3.08538e-14

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:   3.08538e-14

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 9

          **********

No masking
Map Score:   3.08538e-14

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