AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_mixed11_tpal_reg_100.orf -o296_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	RTP00949	206	AE000520

Motif number 1

CAAAACTCCACGACACCCGCATTGAAGTATC	1	28	1	CGACCCCGCA	    0.997084	-179
CGGTGGGCGTCGACGCCGACACGTCTTGATT	1	73	0	CGACCCGACA	    0.977079	-134
TCGGCGTCGACGCCCACCGCAACGAAAAAAA	1	85	1	CGCCACCGCA	    0.997801	-122
GCGTTGCAAACTCTAGCCCCAGCTCCGGCCG	1	118	1	CTCTGCCCCA	    0.989785	-89
CTAGCCCCAGCTCCGGCCGGAACAGCAAACT	1	130	1	CTCCGCCGGA	    0.992351	-77
GGGATTAAAAAGCCTGCGGCAGGGAGTTTGC	1	154	0	AGCCGCGGCA	    0.964164	-53
CAGTATGATCCGCTTGCGCCAAATAATTTGG	1	184	0	CGCTGCGCCA	    0.996242	-23
          **** ******

Masking position 11
Map Score:   13.4243

Number of sites scoring better than the average of aligned sites = 491
Number in coding regions = 460
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

ATACTTCAATGCGGGTGTCGTGGAGTTTTG	1	28	0	GCGGGTGTCG	    0.990753	-179
ATCAAGACGTGTCGGCGTCGACGCCCACCG	1	74	1	GTCGGCGTCG	    0.960262	-133
TTTTTTCGTTGCGGTGGGCGTCGACGCCGA	1	85	0	GCGGTGGGCG	    0.991803	-122
GGCCGGAGCTGGGGCTAGAGTTTGCAACGC	1	118	0	GGGGCTAGAG	    0.966917	-89
GTTTGCTGTTCCGGCCGGAGCTGGGGCTAG	1	130	0	CCGGCCGGAG	    0.983848	-77
CAAACTCCCTGCCGCAGGCTTTTTAATCCC	1	155	1	GCCGCAGGCT	    0.986702	-52
CAAATTATTTGGCGCAAGCGGATCATACTG	1	185	1	GGCGCAAGCG	    0.987618	-22
          **********

Masking position 4
Map Score:   5.99731

Number of sites scoring better than the average of aligned sites = 1455
Number in coding regions = 1328
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 3

CCTCAATACGCAAAACTCCACGACACCCGC	1	18	1	CAAAACTCCA	    0.986761	-189
AAAGGGCGTTGCAAACTCTAGCCCCAGCTC	1	113	1	GCAAACTCTA	    0.986761	-94
AAACTCTAGCCCCAGCTCCGGCCGGAACAG	1	125	1	CCCAGCTCCG	    0.986319	-82
GGCCGGAACAGCAAACTCCCTGCCGCAGGC	1	144	1	GCAAACTCCC	     0.99591	-63
          **********

Masking position 4
Map Score:   2.13082

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 70
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

         CCTTGAGCCTCAATACGCAAAA	1	2	1	CTTGAGCCCA	    0.997187	-205
GCCGACACGTCTTGATTCACTGTTTGTCTCT	1	59	0	CTTGATTCCT	    0.977673	-148
GCGTTGCAAACTCTAGCCCCAGCTCCGGCCG	1	118	1	CTCTAGCCCA	    0.975748	-89
CCGCAGGCTTTTTAATCCCCAAATTATTTGG	1	166	1	TTTAATCCCA	    0.973488	-41
     CTCAGTATGATCCGCTTGCGCCAAAT	1	191	0	TATGATCCCT	    0.968674	-16
          ******** **

Masking position 5
Map Score:   2.14749

Number of sites scoring better than the average of aligned sites = 144
Number in coding regions = 132
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 5

          **********

No masking
Map Score:   1.44541e-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:   1.44541e-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 7

          **********

No masking
Map Score:   1.44541e-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