AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_mixed21_tpal_reg_300.orf -o307_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	RTP00131	190	AE000520
#2	RTP00159	29	AE000520

Motif number 1

GGAATTCCACTCCCCGCACTCAGGGCAACGC	1	46	0	TCCCCGCACC	    0.986623	-145
AGCACGAACATCGCCGGAGGACAACGAGGGT	1	88	0	TCGCCGGAGA	    0.985682	-103
GATGCCTTTTTTACAGCACGAACATCGCCGG	1	102	0	TTACAGCACA	    0.977695	-89
GGGAACGCCTGTACAGGAGAAGAAGATGCCT	1	126	0	GTACAGGAGA	    0.975778	-65
TCCTGCGCGCGCACAGCACACAGCGGGAACG	1	150	0	GCACAGCACC	    0.995588	-41
TGCTGTGCGCGCGCAGGATGCGCAGCGTATT	1	163	1	GCGCAGGATC	    0.985315	-28
GACGAATAGTTTGCAGCAGCCTCTTT     	2	14	1	TTGCAGCAGC	    0.993025	-16
          ********* *

Masking position 8
Map Score:   8.29071

Number of sites scoring better than the average of aligned sites = 979
Number in coding regions = 896
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 2

AAGTGGCTTGGGCGTTGCCCTGAGTGCGGG	1	35	1	GGCGTTGCCC	     0.99667	-156
AAGAGACACCCTCGTTGTCCTCCGGCGATG	1	81	1	CTCGTTGTCC	    0.988192	-110
GTTGTCCTCCGGCGATGTTCGTGCTGTAAA	1	94	1	GGCGATGTTC	    0.986777	-97
CTCCTGTACAGGCGTTCCCGCTGTGTGCTG	1	138	1	GGCGTTCCCG	     0.97425	-53
          **********

Masking position 6
Map Score:   3.78268

Number of sites scoring better than the average of aligned sites = 126
Number in coding regions = 113
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

          GTGGGGTGTGGTTACGTTCA	1	1	1	GTGGGGTGTG	    0.999012	-190
TTCATCCTAAGTGGCTTGGGCGTTGCCCTG	1	27	1	GTGGCTTGGG	    0.987824	-164
TGCCCTGAGTGCGGGGAGTGGAATTCCTTC	1	50	1	GCGGGGAGTG	    0.995758	-141
CGTTCCCGCTGTGTGCTGTGCGCGCGCAGG	1	150	1	GTGTGCTGTG	    0.992821	-41
          **********

Masking position 3
Map Score:   4.78517

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 84
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   3.71914e-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:   3.71914e-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:   3.71914e-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