AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_tpal_reg_300.orf -o179_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	RTP00880	18	AE000520
#2	RTP00792	152	AE000520

Motif number 1

TGCTGAAGCCATTGCAAGTGCGTTGCAGGG	2	13	1	ATTGCAAGTG	    0.953246	-140
CACCGCAGGGATGGGAGGAGGTACGGGAAC	2	61	1	ATGGGAGGAG	    0.989659	-92
GGGAGGAGGTACGGGAACAGGTGCTGCCCC	2	73	1	ACGGGAACAG	    0.998472	-80
CTTTGCAATAACTGGGGCAGCACCTGTTCC	2	86	0	ACTGGGGCAG	    0.985283	-67
CAAAGATTGCACGGGAACTTGGTGCTTTGA	2	111	1	ACGGGAACTT	    0.990205	-42
CTTCGTGACTACGGCAACTGTCAAAGCACC	2	131	0	ACGGCAACTG	    0.997081	-22
          **********

Masking position 1
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

TGATGAACACCATGTTCGCGCCCTGCAACG	2	33	0	CATGTTCGCG	    0.996901	-120
TGGGGCAGCACCTGTTCCCGTACCTCCTCC	2	74	0	CCTGTTCCCG	    0.999073	-79
GTCAAAGCACCAAGTTCCCGTGCAATCTTT	2	112	0	CAAGTTCCCG	    0.998695	-41
TGGTGCTTTGACAGTTGCCGTAGTCACGAA	2	130	1	ACAGTTGCCG	    0.992673	-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	    0.993308	-16
ATGTTCGCGCCCTGCAACGCACTTGCAATGGC	2	20	0	CTGCAAGCAC	    0.996146	-133
TTTGCAATAACTGGGGCAGCACCTGTTCCCGT	2	83	0	CGGGGCGCAC	    0.994491	-70
ACTACGGCAACTGTCAAAGCACCAAGTTCCCG	2	122	0	CGTCAAGCAC	     0.99847	-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

        GATGCTGAAGCCATTGCAAGTG	2	3	1	TGCTGAAGCC	    0.991487	-150
ATCCCTGCGGTGATGAACACCATGTTCGCG	2	43	0	TGATGAACAC	    0.971568	-110
CAGCACCTGTTCCCGTACCTCCTCCCATCC	2	69	0	TCCCGTACCT	    0.970024	-84
GTTGCCGTAGTCACGAAGCC          	2	143	1	TCACGAAGCC	     0.99526	-10
          **********

Masking position 7
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