AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_3_5_1_28_tpal_reg_300.orf -o262_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	RTP00651	75	AE000520
#2	RTP00654	39	AE000520

Motif number 1

TCCCGTAAAACTGTGCGGTGCGCGGT    	1	7	0	CTGTGCGGTG	    0.991849	-69
CTACCGCATGTTCTCCCGTAAAACTGTGCG	1	20	0	TTCTCCCGTA	    0.995434	-56
GACAAATAATTTCTACCGCATGTTCTCCCG	1	32	0	TTCTACCGCA	    0.993523	-44
         CCTGTACGGTACGCACGCCCC	1	65	0	CTGTACGGTA	    0.996944	-11
TTATTTTTTCCTCTCCGGCACAGGATTTGA	2	20	1	CTCTCCGGCA	    0.998686	-20
          **********

Masking position 4
Map Score:   10.0243

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 82
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 2

          ACCGCGCACCGCACAGTTTT	1	1	1	ACCGCGCACC	    0.984749	-75
ACCGCATGTTCTCCCGTAAAACTGTGCGGT	1	18	0	CTCCCGTAAA	    0.916258	-58
AATAATTTCTACCGCATGTTCTCCCGTAAA	1	28	0	ACCGCATGTT	    0.949602	-48
GGTACGCACGCCCCCATGACAAATAATTTC	1	49	0	CCCCCATGAC	    0.992247	-27
GGAAAAAATAACCCGGTGCT          	2	1	0	ACCCGGTGCT	    0.992249	-39
      TCAAATCCTGTGCCGGAGAGGAAA	2	26	0	ATCCTGTGCC	    0.984718	-14
          **********

Masking position 3
Map Score:   2.93001

Number of sites scoring better than the average of aligned sites = 1644
Number in coding regions = 1485
Number in noncoding regions = 159
Number of orfs with sites within 600 bp upstream = 117
Fraction of orfs with sites within 600 bp upstream = 0.0187922


Motif number 3

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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