AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i233_protein_modification____tpal_reg_100.orf -o233_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	RTP00651	75	AE000520
#2	RTP00654	39	AE000520
#3	RTP00655	46	AE000520

Motif number 1

      ACCGCGCACCGCACAGTTTTACGGG	1	5	1	CGCACCGACA	    0.952299	-71
ACCGCACAGTTTTACGGGAGAACATGCGGTA	1	18	1	TTTACGGAGA	    0.899016	-58
TACGGGAGAACATGCGGTAGAAATTATTTGT	1	30	1	CATGCGGAGA	    0.963585	-46
TGGGGGCGTGCGTACCGTACAGG        	1	63	1	CGTACCGACA	    0.610458	-13
  TCAAATCCTGTGCCGGAGAGGAAAAAATA	2	21	0	TGTGCCGAGA	    0.880817	-19
CATCGAAAAACTCATTGAAGATGT       	3	4	0	CTCATTGAGA	    0.956495	-43
CGGCTACAAGCTCATCGAAAAACTCATTGAA	3	16	0	CTCATCGAAA	     0.95647	-31
          ******* ***

Masking position 9
Map Score:   8.86601

Number of sites scoring better than the average of aligned sites = 623
Number in coding regions = 563
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 2

GTAAAACTGTGCGGTGCGCGGT        	1	3	0	GCGGTGCGCG	    0.998202	-73
ATTTGTCATGGGGGCGTGCGTACCGTACAG	1	55	1	GGGGCGTGCG	     0.99765	-21
GCTTGTAGCCGCGGCCTACTT         	3	36	1	GCGGCCTACT	    0.992957	-11
          **********

Masking position 4
Map Score:   1.65079

Number of sites scoring better than the average of aligned sites = 239
Number in coding regions = 216
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

GTTCTCCCGTAAAACTGTGCGGTGCGCGGT	1	11	0	AAAACTGTGC	    0.995128	-65
AGGAAAAAATAACCCGGTGCT         	2	2	0	AACCCGGTGC	    0.997203	-38
       TCAAATCCTGTGCCGGAGAGGAA	2	27	0	AATCCTGTGC	    0.998145	-13
          **********

Masking position 2
Map Score:   4.66098

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 20
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

CTCATCGAAAAACTCATTGAAGATGT    	3	7	0	AACTCATTGA	    0.994308	-40
CGCGGCTACAAGCTCATCGAAAAACTCATT	3	19	0	AGCTCATCGA	    0.997401	-28
          **********

Masking position 6
Map Score:   0.310387

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 16
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:   7.34864e-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 6

          **********

No masking
Map Score:   7.34864e-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 7

          **********

No masking
Map Score:   7.34864e-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