AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_tpal_reg_100.orf -o179_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	RTP00880	18	AE000520
#2	RTP00792	152	AE000520

Motif number 1

CCCTGCAACGCACTTGCAATGGCTTCAGCA	2	13	0	CACTTGCAAT	    0.950734	-140
GTTCCCGTACCTCCTCCCATCCCTGCGGTG	2	61	0	CTCCTCCCAT	    0.989081	-92
GGGGCAGCACCTGTTCCCGTACCTCCTCCC	2	73	0	CTGTTCCCGT	    0.998385	-80
GGAACAGGTGCTGCCCCAGTTATTGCAAAG	2	86	1	CTGCCCCAGT	    0.984465	-67
TCAAAGCACCAAGTTCCCGTGCAATCTTTG	2	111	0	AAGTTCCCGT	    0.989658	-42
GGTGCTTTGACAGTTGCCGTAGTCACGAAG	2	131	1	CAGTTGCCGT	    0.996916	-22
          **********

Masking position 10
Map Score:   10.1922

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 221
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

CGTTGCAGGGCGCGAACATGGTGTTCATCA	2	33	1	CGCGAACATG	    0.996789	-120
GGAGGAGGTACGGGAACAGGTGCTGCCCCA	2	74	1	CGGGAACAGG	    0.999053	-79
AAAGATTGCACGGGAACTTGGTGCTTTGAC	2	112	1	CGGGAACTTG	    0.998659	-41
TTCGTGACTACGGCAACTGTCAAAGCACCA	2	130	0	CGGCAACTGT	    0.992365	-23
          **********

Masking position 5
Map Score:   8.74971

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 13
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 3

      GATACGGTCTATGCTCGG        	1	3	0	CGTCTAGCTC	    0.992304	-16
ATGTTCGCGCCCTGCAACGCACTTGCAATGGC	2	20	0	CTGCAAGCAC	    0.995562	-133
TTTGCAATAACTGGGGCAGCACCTGTTCCCGT	2	83	0	CGGGGCGCAC	    0.993726	-70
ACTACGGCAACTGTCAAAGCACCAAGTTCCCG	2	122	0	CGTCAAGCAC	    0.998245	-31
          * ***** ****

Masking position 9
Map Score:   1.69941

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 102
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

CACTTGCAATGGCTTCAGCATC        	2	3	0	GGCTTCAGCA	     0.99143	-150
CGCGAACATGGTGTTCATCACCGCAGGGAT	2	43	1	GTGTTCATCA	     0.97017	-110
GGATGGGAGGAGGTACGGGAACAGGTGCTG	2	69	1	AGGTACGGGA	    0.968552	-84
          GGCTTCGTGACTACGGCAAC	2	143	0	GGCTTCGTGA	    0.995021	-10
          **********

Masking position 4
Map Score:   1.45211

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 71
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 5

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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