AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___tpal_reg_100.orf -o190_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	RTP00381	170	AE000520
#2	RTP00767	126	AE000520

Motif number 1

TTTTCAAAATACGCATCCGCCAGCGCCTGA	1	15	0	ACGCATCCGC	    0.908685	-156
TATTTTGAAAACGGATACACGTCAAATTAC	1	34	1	ACGGATACAC	    0.978271	-137
AAAGAAGAACACCGGGACACGGCGGAGAAA	1	70	1	ACCGGGACAC	    0.914567	-101
TGGCTGCGCTCGCGCTCCACCACCGTGATC	1	114	0	CGCGCTCCAC	    0.973858	-57
TGGAGCGCGAGCGCAGCCACGTCGAGCACA	1	125	1	GCGCAGCCAC	    0.943615	-46
ATTATCATTAAGGGAACGAAGAATACA   	1	154	1	AGGGAACGAA	    0.818456	-17
TGAAAACGACCCGGAACGACTGCAAT    	2	7	0	CCGGAACGAC	    0.971429	-120
TGTTGCCCTGAGCAAACCACAGATACTCCC	2	45	0	AGCAAACCAC	    0.932223	-82
TGGTTTGCTCAGGGCAACACCCTGTCGATG	2	56	1	AGGGCAACAC	    0.958689	-71
TTTGATCGATAGCCATCGACAGGGTGTTGC	2	69	0	AGCCATCGAC	    0.955121	-58
ATCCTTTCGGCGCGAGACACACAGCGTAAG	2	101	0	CGCGAGACAC	     0.97494	-26
          **********

Masking position 9
Map Score:   10.1513

Number of sites scoring better than the average of aligned sites = 1131
Number in coding regions = 1037
Number in noncoding regions = 94
Number of orfs with sites within 600 bp upstream = 75
Fraction of orfs with sites within 600 bp upstream = 0.0120463


Motif number 2

GACGTGTATCCGTTTTCAAAATACGCATCC	1	27	0	CGTTTTCAAA	     0.86733	-144
GCCGTGTCCCGGTGTTCTTCTTTGTTCAGG	1	63	0	GGTGTTCTTC	       0.977	-108
TAAACGAAAGCGTTTTCTCCGCCGTGTCCC	1	83	0	CGTTTTCTCC	    0.993206	-88
GCTCCACCACCGTGATCTTAAACGAAAGCG	1	101	0	CGTGATCTTA	    0.916029	-70
 TGTATTCTTCGTTCCCTTAATGATAATGT	1	152	0	CGTTCCCTTA	    0.903315	-19
CGTTCCGGGTCGTTTTCACCTGTTGGGGGA	2	19	1	CGTTTTCACC	    0.979899	-108
GAGTATCTGTGGTTTGCTCAGGGCAACACC	2	47	1	GGTTTGCTCA	    0.946057	-80
          GGTGCTATCCTTTCGGCGCG	2	117	0	GGTGCTATCC	    0.801847	-10
          **********

Masking position 3
Map Score:   6.53258

Number of sites scoring better than the average of aligned sites = 616
Number in coding regions = 572
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

         GCTTTCAGGCGCTGGCGGATGC	1	2	1	CTTTCGGCGC	    0.964498	-169
AAAACGCTTTCGTTTAAGATCACGGTGGTGG	1	97	1	CGTTTAGATC	    0.855175	-74
GACGTGGCTGCGCTCGCGCTCCACCACCGTG	1	117	0	CGCTCCGCTC	    0.987978	-54
  ATTGCAGTCGTTCCGGGTCGTTTTCACCT	2	9	1	CGTTCGGGTC	    0.982922	-118
GTCGTTTTCACCTGTTGGGGGAGTATCTGTG	2	27	1	CCTGTGGGGG	     0.90435	-100
CAGGGCAACACCCTGTCGATGGCTATCGATC	2	65	1	CCCTGCGATG	    0.892683	-62
ATCGATCAAACCCTTACGCTGTGTGTCTCGC	2	89	1	CCCTTCGCTG	    0.982116	-38
  GGTGCTATCCTTTCGGCGCGAGACACACA	2	108	0	CCTTTGGCGC	    0.991547	-19
          ***** *****

Masking position 8
Map Score:   3.05439

Number of sites scoring better than the average of aligned sites = 991
Number in coding regions = 919
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

CCGTGATCTTAAACGAAAGCGTTTTCTCCG	1	92	0	AAACGAAAGC	    0.983596	-79
CACGGTGGTGGAGCGCGAGCGCAGCCACGT	1	117	1	GAGCGCGAGC	    0.976125	-54
AAACGACCCGGAACGACTGCAAT       	2	4	0	GAACGACTGC	    0.983237	-123
GTAAGGGTTTGATCGATAGCCATCGACAGG	2	76	0	GATCGATAGC	    0.989381	-51
TCTCGCGCCGAAAGGATAGCACC       	2	114	1	AAAGGATAGC	    0.967773	-13
          **********

Masking position 2
Map Score:   3.15981

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 99
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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:   2.93755e-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