AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i100_Ion_Transporter_tpal_reg_300.orf -o100_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	RTP00342	39	AE000520
#2	RTP00341	171	AE000520

Motif number 1

TAGAGAAGAATCACGCACTTCCTTCGCCTT       	1	4	0	TCCCTTCTGC	    0.985884	-36
AAGTGCGTGATTCTTCTCTACGTGTGCCG        	1	21	1	TTCCTACTGC	    0.986159	-19
GATCTTACCTGTGAGCAGCTCGTACTC          	2	1	0	GTCGCTCTTC	    0.988327	-171
CACCCGGGTTTCACCCTGCTCATTTTCCACCGTCACC	2	49	0	TCCGCTCTTC	    0.993223	-123
GGGGATGGATTTTCTCTCCTGCTTTGTACAACACCCG	2	80	0	TTCCCTGTGT	     0.93622	-92
GGAGAGAAAATCCATCCCCATGTCATCGATGATCTGC	2	98	1	TCCCCATTTC	    0.967511	-74
ACATATGCCGTTTTGCAGCAGATCATCGATGACATGG	2	115	0	TTCGCAGTTC	    0.984398	-57
GGTTAATAATGTAGACCTCACATATGCCGTTTTGCAG	2	134	0	GTCTCACTGC	    0.970829	-38
          **   * **** *  **

Masking position 13
Map Score:   5.26083

Number of sites scoring better than the average of aligned sites = 862
Number in coding regions = 812
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

CGGCACACGTAGAGAAGAATCACGCACTTCC	1	19	0	AGAGAAGATC	    0.986936	-21
AGCTGCTCACAGGTAAGATCCTAGCACGATC	2	18	1	AGGTAAGACC	    0.991329	-154
GAAAATGAGCAGGGTGAAACCCGGGTGTTGT	2	59	1	AGGGTGAACC	    0.985796	-113
ACAAAGCAGGAGAGAAAATCCATCCCCATGT	2	90	1	AGAGAAAACC	    0.994816	-82
          ******** **

Masking position 8
Map Score:   1.52617

Number of sites scoring better than the average of aligned sites = 79
Number in coding regions = 71
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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:   6.63809e-14

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