AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_tpal_reg_100.orf -o119_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	RTP00575	175	AE000520

Motif number 1

          TCGCTGAAGCGCGGCGTATAGAAA	1	1	1	TGCAGCGCGG	    0.965944	-175
CCTACCTATCACCCGTACCCGGGCGACAATCGCC	1	37	0	ACCACCGGGC	    0.993785	-139
GCTATTGCTTACCCTCATGCGCGCGTTCACCGAA	1	87	0	ACCAGCGCGC	     0.91413	-89
TGCTGCAAAAAAACACACGCGCGCGGCTATTGCT	1	112	0	AACAGCGCGC	    0.995184	-64
GTGTGTTTTTTTGCAGCACCGTGCATACCGCCCC	1	128	1	TGCCCCGTGC	    0.993129	-48
GCACCGTGCATACCGCCCCAGCGGACGTCGCTAA	1	143	1	TCCCCAGCGG	    0.983393	-33
CCAGCGGACGTCGCTAAGCTGCGCCG        	1	160	1	TGCACTGCGC	    0.978364	-16
          * **  * ******

Masking position 4
Map Score:   11.2355

Number of sites scoring better than the average of aligned sites = 744
Number in coding regions = 693
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

CCCCTTTCTATACGCCGCGCTTCAGCGA  	1	9	0	TACGCCGCGC	    0.994755	-167
CGGCGTATAGAAAGGGGCGATTGTCGCCCG	1	22	1	AAAGGGGCGA	    0.932173	-154
CCTATCACCCGTACCCGGGCGACAATCGCC	1	37	0	GTACCCGGGC	    0.982566	-139
AAGTTTCGGTGAACGCGCGCATGAGGGTAA	1	83	1	GAACGCGCGC	    0.996494	-93
AGGGTAAGCAATAGCCGCGCGCGTGTGTTT	1	106	1	ATAGCCGCGC	    0.997407	-70
TGCTGCAAAAAAACACACGCGCGCGGCTAT	1	116	0	AAACACACGC	      0.9436	-60
CGGACGTCGCTAAGCTGCGCCG        	1	164	1	TAAGCTGCGC	    0.989632	-12
          **********

Masking position 9
Map Score:   10.303

Number of sites scoring better than the average of aligned sites = 1262
Number in coding regions = 1184
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 3

          **********

No masking
Map Score:   2.15595e-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 4

          **********

No masking
Map Score:   2.15595e-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 5

          **********

No masking
Map Score:   2.15595e-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