Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014284.1 Corchorus olitorius cultivar O-4 contig14317, 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: 19542
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2133 original size:49 final size:47
Alignment explanation
Indices: 2058--2197 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 47
2048 CAAGCAATCC
* *
2058 TTTACTTTTAC-TGCACCTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* * *
2105 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
*
2154 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
2198 TTGGCACGCT
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
47 20 0.25
48 20 0.25
49 40 0.49
50 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.51
Consensus pattern (47 bp):
TTTAATTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:7243 original size:20 final size:18
Alignment explanation
Indices: 7202--7245 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
7192 TTACAATTCA
7202 ATTATTTTATTTTTGATG
1 ATTATTTTATTTTTGATG
* *
7220 ATTACTTTTATATTTTTATT
1 ATTA-TTTTAT-TTTTGATG
7240 ATTATT
1 ATTATT
7246 ATATGATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
ATTATTTTATTTTTGATG
Found at i:7330 original size:10 final size:10
Alignment explanation
Indices: 7315--7343 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
7305 CCATATTAAC
7315 AATTTTATTT
1 AATTTTATTT
7325 AATTTTATTT
1 AATTTTATTT
7335 -ATTTTATTT
1 AATTTTATTT
7344 CCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
AATTTTATTT
Found at i:10281 original size:89 final size:91
Alignment explanation
Indices: 10163--10332 Score: 281
Period size: 89 Copynumber: 1.9 Consensus size: 91
10153 GTTTGCAGGG
* *
10163 TTAAAAAAATGATGTTTTACTCATGTCATGAATTCATATAACAATTATATACTAAGTCAAATCT-
1 TTAAAAAAATAATGTCTTACTCATGTCATGAATTCATATAACAATTATATACTAAGTCAAATCTC
*
10227 TTAATCTTTAAGAAAAAGTTATCAGT
66 TCAATCTTTAAGAAAAAGTTATCAGT
*
10253 TTAAAAAAA-AATGTCTTACTCATGTCATGAATTCATATAACAATTATGTACTAAGTCAAATCTC
1 TTAAAAAAATAATGTCTTACTCATGTCATGAATTCATATAACAATTATATACTAAGTCAAATCTC
*
10317 TCAATTTTTAAGAAAA
66 TCAATCTTTAAGAAAA
10333 TCCAAGCATG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 51 0.69
90 23 0.31
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (91 bp):
TTAAAAAAATAATGTCTTACTCATGTCATGAATTCATATAACAATTATATACTAAGTCAAATCTC
TCAATCTTTAAGAAAAAGTTATCAGT
Found at i:10412 original size:14 final size:15
Alignment explanation
Indices: 10385--10417 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
10375 TGACTAAAAA
10385 TAATATTAATTAAAT
1 TAATATTAATTAAAT
*
10400 TAATATTCA-TAAAT
1 TAATATTAATTAAAT
10414 TAAT
1 TAAT
10418 TCTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTAATTAAAT
Found at i:15950 original size:26 final size:26
Alignment explanation
Indices: 15921--15978 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
15911 AATGCAATGC
15921 ATGCAAACA-AAA-AGAAAATGAAAAA
1 ATGCAAACATAAACA-AAAATGAAAAA
15946 TATGCAAACATAAACAAAAATGAAAAA
1 -ATGCAAACATAAACAAAAATGAAAAA
15973 ATGCAA
1 ATGCAA
15979 TTTTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 15 0.50
27 14 0.47
28 1 0.03
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.12
Consensus pattern (26 bp):
ATGCAAACATAAACAAAAATGAAAAA
Found at i:16275 original size:19 final size:18
Alignment explanation
Indices: 16247--16282 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16237 AGAATTAAAT
16247 TAAAAGAAAACATAAAAAC
1 TAAAAGAAAA-ATAAAAAC
*
16266 TAAAATAAAAATAAAAA
1 TAAAAGAAAAATAAAAA
16283 TAAGTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
TAAAAGAAAAATAAAAAC
Done.