Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023007.1 Corchorus olitorius cultivar O-4 contig23040, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33096
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4261 original size:19 final size:19
Alignment explanation
Indices: 4237--4276 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4227 TTTATAGCTG
4237 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
4256 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
4275 AG
1 AG
4277 TTAGAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (19 bp):
AGATTTAGAGTACAAGATC
Found at i:4286 original size:17 final size:18
Alignment explanation
Indices: 4241--4286 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
4231 TAGCTGAGAT
4241 TTAGAGTACAAGATCAGA
1 TTAGAGTACAAGATCAGA
4259 TTTAGAGTACAAGATCAG-
1 -TTAGAGTACAAGATCAGA
*
4277 TTAGAATACA
1 TTAGAGTACA
4287 TAAGTAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (18 bp):
TTAGAGTACAAGATCAGA
Found at i:8746 original size:19 final size:19
Alignment explanation
Indices: 8722--8761 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8712 TTTATAGCTG
8722 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
8741 AGATTTAGAGTACAAGATC
1 AGATTTAGAGTACAAGATC
8760 AG
1 AG
8762 TTAGAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (19 bp):
AGATTTAGAGTACAAGATC
Found at i:8771 original size:17 final size:18
Alignment explanation
Indices: 8726--8771 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
8716 TAGCTGAGAT
8726 TTAGAGTACAAGATCAGA
1 TTAGAGTACAAGATCAGA
8744 TTTAGAGTACAAGATCAG-
1 -TTAGAGTACAAGATCAGA
*
8762 TTAGAATACA
1 TTAGAGTACA
8772 TAAGTAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (18 bp):
TTAGAGTACAAGATCAGA
Found at i:21705 original size:15 final size:16
Alignment explanation
Indices: 21675--21714 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
21665 TTACTTTGCT
21675 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
21691 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
21706 TTGCTTTCT
1 TTGTTTTCT
21715 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:24192 original size:9 final size:9
Alignment explanation
Indices: 24159--24186 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24149 GAACTAATTC
24159 CTGTTTAGT
1 CTGTTTAGT
24168 CTGTTTAGT
1 CTGTTTAGT
24177 CTGTTTAGT
1 CTGTTTAGT
24186 C
1 C
24187 ATTTTAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (9 bp):
CTGTTTAGT
Found at i:26270 original size:21 final size:21
Alignment explanation
Indices: 26241--26282 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
26231 GTTGTGTGTT
*
26241 TCTCAATTGGCACTTCAACAA
1 TCTCAATTGACACTTCAACAA
*
26262 TCTCTATTGACACTTCAACAA
1 TCTCAATTGACACTTCAACAA
26283 CCTGTGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (21 bp):
TCTCAATTGACACTTCAACAA
Found at i:32979 original size:14 final size:14
Alignment explanation
Indices: 32962--32988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32952 ATTATTACCT
32962 ATATAAATAAATAA
1 ATATAAATAAATAA
32976 ATATAAATAAATA
1 ATATAAATAAATA
32989 TAATCTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATAAATAAATAA
Done.