AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i105_Manganese_Transport_tpal_reg_100.orf -o105_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	RTP00321	174	AE000520
#2	RTP00320	147	AE000520

Motif number 1

GGCGCGCGTATGCACTGCTGGCAAATATAGC 	1	10	0	TGCACCTGGC	    0.987998	-165
GCAGTGCATACGCGCGCCTTGTGTAAAACTTT	1	24	1	CGCGCCTTGT	      0.9978	-151
ACCTCTTTGTCGCGGTTTTTGTTTTCGACGTA	1	64	0	CGCGGTTTGT	    0.974815	-111
TTCAGACACACGCACGTATGATCT        	2	3	0	CGCACATGAT	    0.935701	-145
ACAACAGTGCTGCACGATTTGTTTCAGACACA	2	25	0	TGCACTTTGT	    0.987764	-123
GCTTGAATATCGCGCCGATTGCGCAGTGCTCT	2	87	0	CGCGCATTGC	    0.992673	-61
 CTACCGTAATGAACAACTTGTTGCTGCCTTC	2	127	0	TGAACCTTGT	    0.959336	-21
          *****  *****

Masking position 9
Map Score:   6.4717

Number of sites scoring better than the average of aligned sites = 643
Number in coding regions = 616
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

CAAAAACCGCGACAAAGAGGTAAGAAAAAAA	1	75	1	GACAAAGGGT	    0.958898	-100
TGAAGAGGTAGGTAATGGGGTTGCTATTTTT	1	101	0	GGTAATGGGT	    0.997424	-74
TGACTGTGCAGGTGAAGAGGTAGGTAATGGG	1	113	0	GGTGAAGGGT	    0.993732	-62
CAGTCACAATGGTCATGTCGTCATGGGTAGT	1	138	1	GGTCATGCGT	    0.984736	-37
TGTCGTCATGGGTAGTGCGATCCGCACTGAA	1	153	1	GGTAGTGGAT	    0.970955	-22
          ******* ***

Masking position 11
Map Score:   2.28871

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 96
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

AGGCGCGCGTATGCACTGCTGGCAAATATA	1	13	0	ATGCACTGCT	     0.93884	-162
ATGTCGTCATGGGTAGTGCGATCCGCACTG	1	152	1	GGGTAGTGCG	    0.968661	-23
          TTTCAGTGCGGATCGCACTA	1	165	0	TTTCAGTGCG	     0.96635	-10
GAAACAAATCGTGCAGCACTGTTGTAAATA	2	32	1	GTGCAGCACT	    0.972105	-116
CGCGCCGATTGCGCAGTGCTCTTAATGGAT	2	79	0	GCGCAGTGCT	    0.992191	-69
GCAACAAGTTGTTCATTACGGTAG      	2	134	1	GTTCATTACG	    0.906574	-14
          **********

Masking position 5
Map Score:   1.1999

Number of sites scoring better than the average of aligned sites = 1309
Number in coding regions = 1208
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 4

TTTACACAAGGCGCGCGTATGCACTGCTGG	1	21	0	GCGCGCGTAT	    0.957211	-154
GAAGAGGTAGGTAATGGGGTTGCTATTTTT	1	101	0	GTAATGGGGT	    0.813761	-74
CATTGTGACTGTGCAGGTGAAGAGGTAGGT	1	119	0	GTGCAGGTGA	    0.934813	-56
 AGATCATACGTGCGTGTGTCTGAAACAAA	2	10	1	GTGCGTGTGT	    0.979168	-138
AAATCGTGCAGCACTGTTGTAAATAACACG	2	37	1	GCACTGTTGT	    0.889368	-111
GATACGATAAGTAATCGTGTTATTTACAAC	2	52	0	GTAATCGTGT	    0.934079	-96
CGATTGCGCAGTGCTCTTAATGGATACGAT	2	74	0	GTGCTCTTAA	    0.838663	-74
CTTCCAGGAGGTGCTTGAATATCGCGCCGA	2	101	0	GTGCTTGAAT	    0.851204	-47
          **********

Masking position 1
Map Score:   0.999091

Number of sites scoring better than the average of aligned sites = 2531
Number in coding regions = 2348
Number in noncoding regions = 183
Number of orfs with sites within 600 bp upstream = 142
Fraction of orfs with sites within 600 bp upstream = 0.0228076


Motif number 5

TCTGTTTAAAGTTTTACACAAGGCGCGCGT	1	33	0	GTTTTACACA	    0.959757	-142
AACAGAATACGTCGAAAACAAAAACCGCGA	1	57	1	GTCGAAAACA	    0.982585	-118
ACGTGCGTGTGTCTGAAACAAATCGTGCAG	2	18	1	GTCTGAAACA	    0.981837	-130
GTGCAGCACTGTTGTAAATAACACGATTAC	2	42	1	GTTGTAAATA	    0.941507	-106
          **********

Masking position 6
Map Score:   0.0350303

Number of sites scoring better than the average of aligned sites = 30
Number in coding regions = 29
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 6

          **********

No masking
Map Score:   -5.09159e-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:   -5.09159e-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 8

          **********

No masking
Map Score:   -5.09159e-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