AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_dna_mismatch_repair_tpal_reg_100.orf -o205_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	RTP00865	103	AE000520
#2	RTP00868	56	AE000520
#3	RTP00869	55	AE000520

Motif number 1

TAGGCCGGTGGCAATTCCGACCAGATCGCTT	1	32	0	GCAATCCGAC	    0.998081	-72
GGTGGATTCCAGAACTCCGAGCTTATTGTC 	1	84	1	AGAATCCGAG	    0.955893	-20
TACCGAGTGCGCAAGCGCGCGCGC       	2	4	0	GCAACGCGCG	    0.994833	-53
TGTGATATGTGCAAATCCGCCTTACGTACCG	2	30	0	GCAATCCGCC	    0.999069	-27
CCGCGTGCGTGGATTCTCGCCCACCAGCA  	3	9	0	GGATCTCGCC	    0.963436	-47
GAAGTTGCTTGCGAAGCCGCGTGCGTGGATT	3	25	0	GCGAGCCGCG	    0.991255	-31
GGCTTCGCAAGCAACTTCGACAGAATAA   	3	38	1	GCAATTCGAC	    0.994342	-18
          **** ******

Masking position 8
Map Score:   11.647

Number of sites scoring better than the average of aligned sites = 310
Number in coding regions = 288
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

  GCGCGCGCGCTTGCGCACTCGGTACGTA	2	9	1	GCTTGCGCAC	    0.983409	-48
TGCAAATCCGCCTTACGTACCGAGTGCGCA	2	22	0	CCTTACGTAC	     0.97944	-35
TTGCGAAGCCGCGTGCGTGGATTCTCGCCC	3	18	0	GCGTGCGTGG	    0.967392	-38
TGTCGAAGTTGCTTGCGAAGCCGCGTGCGT	3	30	0	GCTTGCGAAG	    0.987398	-26
          **********

Masking position 4
Map Score:   3.63115

Number of sites scoring better than the average of aligned sites = 250
Number in coding regions = 239
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

GGTGGCAATTCCGACCAGATCGCTTTGATT	1	27	0	CCGACCAGAT	      0.9735	-77
GGTCGGAATTGCCACCGGCCTAACGGCTCT	1	41	1	GCCACCGGCC	    0.997004	-63
AGTTCTGGAATCCACCGGTAAGATTATCCA	1	70	0	TCCACCGGTA	    0.989934	-34
TGGATTCTCGCCCACCAGCA          	3	1	0	CCCACCAGCA	    0.997891	-55
          **********

Masking position 4
Map Score:   2.82852

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 90
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

TGAGACTCGTTACCGAAATCAAAGCGATCT	1	11	1	TACCGAAATC	     0.92988	-93
CCGGTAAGATTATCCAGAGCCGTTAGGCCG	1	56	0	TATCCAGAGC	    0.979383	-48
TGGATTCCAGAACTCCGAGCTTATTGTC  	1	86	1	AACTCCGAGC	    0.972836	-18
CCGCCTTACGTACCGAGTGCGCAAGCGCGC	2	15	0	TACCGAGTGC	    0.996046	-42
TTGCTTGCGAAGCCGCGTGCGTGGATTCTC	3	22	0	AGCCGCGTGC	    0.988435	-34
          **********

Masking position 10
Map Score:   2.43485

Number of sites scoring better than the average of aligned sites = 600
Number in coding regions = 558
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 5

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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:   3.50598e-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