AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_tpal_reg_300.orf -o119_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	RTP00575	175	AE000520

Motif number 1

TTTCTATACGCCGCGCTTCAGCGA          	1	1	0	CCGCGCTGCA	    0.964711	-175
GGCGATTGTCGCCCGGGTACGGGTGATAGGTAGG	1	37	1	GCCCGGTGGT	    0.993851	-139
TTCGGTGAACGCGCGCATGAGGGTAAGCAATAGC	1	87	1	GCGCGCTGGT	    0.911077	-89
AGCAATAGCCGCGCGCGTGTGTTTTTTTGCAGCA	1	112	1	GCGCGCTGTT	    0.995379	-64
GGGGCGGTATGCACGGTGCTGCAAAAAAACACAC	1	128	0	GCACGGGGCA	      0.9934	-48
TTAGCGACGTCCGCTGGGGCGGTATGCACGGTGC	1	143	0	CCGCTGGGGA	    0.984001	-33
        CGGCGCAGCTTAGCGACGTCCGCTGG	1	160	0	GCGCAGTGCA	    0.977816	-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

TCGCCCCTTTCTATACGCCGCGCTTCAGCG	1	12	0	CTATACGCCG	    0.965049	-164
ACCCGGGCGACAATCGCCCCTTTCTATACG	1	25	0	CAATCGCCCC	    0.998327	-151
TGACACCTACCTATCACCCGTACCCGGGCG	1	46	0	CTATCACCCG	    0.993278	-130
TGAGGGTAAGCAATAGCCGCGCGCGTGTGT	1	104	1	CAATAGCCGC	    0.986884	-72
AGCACCGTGCATACCGCCCCAGCGGACGTC	1	142	1	ATACCGCCCC	    0.986637	-34
          **********

Masking position 3
Map Score:   4.23553

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 175
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TATACGCCGCGCTTCAGCGA          	1	1	0	GCTTCAGCGA	    0.996759	-175
GTTCACCGAAACTTCACCTAATGACACCTA	1	67	0	ACTTCACCTA	      0.9632	-109
CTCATGCGCGCGTTCACCGAAACTTCACCT	1	78	0	CGTTCACCGA	    0.987471	-98
CGTGCATACCGCCCCAGCGGACGTCGCTAA	1	147	1	GCCCCAGCGG	    0.985179	-29
    CGGCGCAGCTTAGCGACGTCCGCTGG	1	160	0	AGCTTAGCGA	    0.965816	-16
          **********

Masking position 6
Map Score:   2.73676

Number of sites scoring better than the average of aligned sites = 255
Number in coding regions = 235
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


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


Motif number 6

          **********

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