AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_tpal_reg_300.orf -o149_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	RTP00970	222	AE000520

Motif number 1

GCGGGGTATTTTTCTCTCGTTCCAAA      	1	5	0	TTCTCCGTTC	    0.972721	-218
AGAGAAAAATACCCCGCCGAGCGCGCTCGTAC	1	20	1	ACCCGCGAGC	    0.996556	-203
GGGCAGTGTATCAACGACGTGCCTGTGTACGA	1	46	0	TCACGCGTGC	    0.992747	-177
GAAAATAAATTTCCCCACGTTCGATAGTGCAG	1	80	1	TTCCCCGTTC	    0.996376	-143
GCAGTGGGGATTTCCCACGATGGTGCCTGCAA	1	108	1	TTCCCCGATG	    0.988899	-115
GTTCGGTCCCATGACGGCGTGCACCTCGCCGG	1	159	1	ATACGCGTGC	     0.99364	-64
CTAACCCTGAATACCGGCGAGGTGCACGCCGT	1	172	0	ATCCGCGAGG	    0.994604	-51
          ** *** *****

Masking position 8
Map Score:   10.7133

Number of sites scoring better than the average of aligned sites = 367
Number in coding regions = 342
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

ACGACGTGCCTGTGTACGAGCGCGCTCGGCGG	1	33	0	TGTGACAGCG	    0.992092	-190
TTTCAAGGGCAGTGTATCAACGACGTGCCTGT	1	52	0	AGTGATAACG	    0.964638	-171
GATAGTGCAGTGGGGATTTCCCACGATGGTGC	1	102	1	TGGGATTCCC	    0.983829	-121
TGCCTGCAAGAGTGGACTTGCCTGCACCGTTC	1	131	1	AGTGACTGCC	    0.972342	-92
CACGCCGTCATGGGACCGAACGGTGCAGGCAA	1	148	0	TGGGCCAACG	     0.99063	-75
CTTTTGAGGATGGGCCTATCCG          	1	211	1	TGGGCTTCCG	    0.990372	-12
          **** ** ****

Masking position 4
Map Score:   3.19474

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 256
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

CACGTCGTTGATACACTGCCCTTGAAAATA	1	57	1	ATACACTGCC	    0.958628	-166
GAAATCCCCACTGCACTATCGAACGTGGGG	1	92	0	CTGCACTATC	    0.993669	-131
CCACTCTTGCAGGCACCATCGTGGGAAATC	1	116	0	AGGCACCATC	    0.989254	-107
GTGGACTTGCCTGCACCGTTCGGTCCCATG	1	142	1	CTGCACCGTT	     0.98953	-81
          **********

Masking position 5
Map Score:   0.704272

Number of sites scoring better than the average of aligned sites = 372
Number in coding regions = 339
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

GAACGAGAGAAAAATACCCCGCCGAGCGCG	1	15	1	AAAATACCCC	    0.993286	-208
CCTTGAAAATAAATTTCCCCACGTTCGATA	1	76	1	AAATTTCCCC	    0.988223	-147
CAAAAGTCTCAACCTAACCCTGAATACCGG	1	187	0	AACCTAACCC	    0.985415	-36
          **********

Masking position 2
Map Score:   0.335022

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 33
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 5

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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