AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i105_Manganese_Transport_tpal_reg_300.orf -o105_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	RTP00321	174	AE000520
#2	RTP00320	147	AE000520

Motif number 1

GGCGCGCGTATGCACTGCTGGCAAATATAGC 	1	10	0	TGCACCTGGC	    0.988999	-165
GCAGTGCATACGCGCGCCTTGTGTAAAACTTT	1	24	1	CGCGCCTTGT	    0.997986	-151
ACCTCTTTGTCGCGGTTTTTGTTTTCGACGTA	1	64	0	CGCGGTTTGT	    0.976892	-111
TTCAGACACACGCACGTATGATCT        	2	3	0	CGCACATGAT	    0.940807	-145
ACAACAGTGCTGCACGATTTGTTTCAGACACA	2	25	0	TGCACTTTGT	    0.988785	-123
GCTTGAATATCGCGCCGATTGCGCAGTGCTCT	2	87	0	CGCGCATTGC	    0.993287	-61
 CTACCGTAATGAACAACTTGTTGCTGCCTTC	2	127	0	TGAACCTTGT	     0.96264	-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

TTTTTTTCTTACCTCTTTGTCGCGGTTTTTG	1	75	0	ACCCTTTGTC	     0.95943	-100
AAAAATAGCAACCCCATTACCTACCTCTTCA	1	101	1	ACCCATTACC	    0.997459	-74
CCCATTACCTACCTCTTCACCTGCACAGTCA	1	113	1	ACCCTTCACC	    0.993816	-62
ACTACCCATGACGACATGACCATTGTGACTG	1	138	0	ACGCATGACC	    0.984939	-37
TTCAGTGCGGATCGCACTACCCATGACGACA	1	153	0	ATCCACTACC	    0.971335	-22
          *** *******

Masking position 1
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	    0.939222	-162
ATGTCGTCATGGGTAGTGCGATCCGCACTG	1	152	1	GGGTAGTGCG	    0.968863	-23
          TTTCAGTGCGGATCGCACTA	1	165	0	TTTCAGTGCG	    0.966566	-10
GAAACAAATCGTGCAGCACTGTTGTAAATA	2	32	1	GTGCAGCACT	    0.972285	-116
CGCGCCGATTGCGCAGTGCTCTTAATGGAT	2	79	0	GCGCAGTGCT	    0.992243	-69
GCAACAAGTTGTTCATTACGGTAG      	2	134	1	GTTCATTACG	    0.907137	-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

CCAGCAGTGCATACGCGCGCCTTGTGTAAA	1	21	1	ATACGCGCGC	    0.960552	-154
AAAAATAGCAACCCCATTACCTACCTCTTC	1	101	1	ACCCCATTAC	    0.827871	-74
ACCTACCTCTTCACCTGCACAGTCACAATG	1	119	1	TCACCTGCAC	     0.94042	-56
TTTGTTTCAGACACACGCACGTATGATCT 	2	10	0	ACACACGCAC	    0.981003	-138
CGTGTTATTTACAACAGTGCTGCACGATTT	2	37	0	ACAACAGTGC	     0.89846	-111
GTTGTAAATAACACGATTACTTATCGTATC	2	52	1	ACACGATTAC	    0.939723	-96
ATCGTATCCATTAAGAGCACTGCGCAATCG	2	74	1	TTAAGAGCAC	     0.85123	-74
TCGGCGCGATATTCAAGCACCTCCTGGAAG	2	101	1	ATTCAAGCAC	    0.862954	-47
          **********

Masking position 10
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

ACGCGCGCCTTGTGTAAAACTTTAAACAGA	1	33	1	TGTGTAAAAC	    0.963142	-142
TCGCGGTTTTTGTTTTCGACGTATTCTGTT	1	57	0	TGTTTTCGAC	    0.984153	-118
CTGCACGATTTGTTTCAGACACACGCACGT	2	18	0	TGTTTCAGAC	    0.983471	-130
GTAATCGTGTTATTTACAACAGTGCTGCAC	2	42	0	TATTTACAAC	    0.946513	-106
          **********

Masking position 5
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