Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024299.1 Corchorus olitorius cultivar O-4 contig24332, 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: 6222
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:189 original size:48 final size:48
Alignment explanation
Indices: 118--217 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
108 AGACTTAATT
118 TTAACGCATGAAGTATTTTCCAGCTTTTAATACTCTTAACAACATCAA
1 TTAACGCATGAAGTATTTTCCAGCTTTTAATACTCTTAACAACATCAA
* *
166 TTAACGCATGGAGTATTTTCCAGCTTTTAATTCTCTTAACAACATCAA
1 TTAACGCATGAAGTATTTTCCAGCTTTTAATACTCTTAACAACATCAA
214 TTAA
1 TTAA
218 TGGAGTTAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (48 bp):
TTAACGCATGAAGTATTTTCCAGCTTTTAATACTCTTAACAACATCAA
Found at i:2474 original size:24 final size:24
Alignment explanation
Indices: 2437--2493 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2427 GTTGCCTTTT
* *
2437 GTTTCGGTTTTGTAAGCTTTGTCA
1 GTTTCGGCTATGTAAGCTTTGTCA
2461 GTTTCGGCTATGTAAGCTTTGTCA
1 GTTTCGGCTATGTAAGCTTTGTCA
2485 GTTTCGGCT
1 GTTTCGGCT
2494 TTGCCTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.46
Consensus pattern (24 bp):
GTTTCGGCTATGTAAGCTTTGTCA
Found at i:2717 original size:13 final size:13
Alignment explanation
Indices: 2701--2735 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
2691 TGATATGACG
2701 TCGGCACATGATA
1 TCGGCACATGATA
2714 TCGGCACATGATA
1 TCGGCACATGATA
2727 TCGGCACAT
1 TCGGCACAT
2736 ATTTAGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (13 bp):
TCGGCACATGATA
Found at i:4426 original size:17 final size:17
Alignment explanation
Indices: 4404--4439 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4394 ATTACAATCC
4404 AAAAATTCAAGTACAAG
1 AAAAATTCAAGTACAAG
4421 AAAAATTCAAGTACAAG
1 AAAAATTCAAGTACAAG
4438 AA
1 AA
4440 TGAATGAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAAATTCAAGTACAAG
Found at i:5855 original size:421 final size:421
Alignment explanation
Indices: 5071--6111 Score: 1859
Period size: 421 Copynumber: 2.5 Consensus size: 421
5061 GAGGGAGTAT
* *
5071 CCAAAATTGACTTTAAAAGATGTTTTAATCCATATATTAATTGAATAAACCCCGTCTCTATGATT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
*
5136 TTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTCTAC
66 TTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
**
5201 CCAAATTATTTCTCATCATCCCCAAATAATCATATGCACCATCCCTAAATTCTTTAGAGATGGAC
131 CCAAATTATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGAC
* *
5266 ATTTTTTTTCATATACCCAAAATTAAATTAAAAGGTGTTTTAATCCATATATTAATTGAATAAAC
196 ATTATTTCTCATATACCCAAAATTAAATTAAAAGGTGTTTTAATCCATATATTAATTGAATAAAC
5331 CCCGTCTATATGATTTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAG
261 CCCGTCTATATGATTTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAG
5396 TAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAAT
326 TAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAAT
5461 TCTTTAGAGATGGACATTTGTTCTCATATAC
391 TCTTTAGAGATGGACATTTGTTCTCATATAC
*
5492 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTAAATAAACCCCGTCTATATGATT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
* *
5557 TT-GTGTCATCTAATAATTAAACAAAATGCAAAATCCAGTATCCCCAAAGTAATTTACTTTATAC
66 TTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
*
5621 CCAAATTATGTCTCATCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGAC
131 CCAAATTATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGAC
**
5686 ATTATTTCTCATATACCCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAA
196 ATTATTTCTCATATACCCAAAATT-AAATTAAAAGGTGTTTTAATCCATATATTAATTGAATAAA
5751 CCCCGTCTATATGATTTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
260 CCCCGTCTATATGATTTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
*
5816 GTAATATACTTTATACGCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAA
325 GTAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAA
*
5881 TTCTTTAGAGATGGACATTTTTTCTCATATAC
390 TTCTTTAGAGATGGACATTTGTTCTCATATAC
* *
5913 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATATATCCTCGTCTATATGAT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATA-AACCCCGTCTATATGAT
*
5978 TTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATA
65 TTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATA
* * * *
6043 CTCTAATTGTTTCTCAGCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGA
130 CCCAAATTATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGA
6108 CATT
195 CATT
6112 TGTATCAATA
Statistics
Matches: 591, Mismatches: 26, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
420 143 0.24
421 308 0.52
422 18 0.03
423 122 0.21
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (421 bp):
CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
TTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
CCAAATTATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGAC
ATTATTTCTCATATACCCAAAATTAAATTAAAAGGTGTTTTAATCCATATATTAATTGAATAAAC
CCCGTCTATATGATTTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAG
TAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAAT
TCTTTAGAGATGGACATTTGTTCTCATATAC
Found at i:5885 original size:211 final size:211
Alignment explanation
Indices: 5071--6112 Score: 1836
Period size: 210 Copynumber: 4.9 Consensus size: 211
5061 GAGGGAGTAT
* *
5071 CCAAAATTGACTTTAAAAGATGTTTTAATCCATATATTAATTGAATAAACCCCGTCTCTATGATT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
* *
5136 TTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTCTAC
66 TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
* *
5201 CCAAATTATTTCTCATCATCCCCAAATAATCATATGCACCATCCCTAAATTCTTTAGAGATGGAC
131 CCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
*
5266 ATTTTTTTTCATATAC
196 ATTTTTTCTCATATAC
**
5282 CCAAAATT-AAATTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
5346 TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
66 TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
5411 CCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
131 CCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
*
5476 ATTTGTTCTCATATAC
196 ATTTTTTCTCATATAC
*
5492 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTAAATAAACCCCGTCTATATGATT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
* * *
5557 TT-GTGTCATCTAATAATTAAACAAAATGCAAAATCCAGTATCCCCAAAGTAATTTACTTTATAC
66 TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
* * *
5621 CCAAATTATGTCTCATCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGAC
131 CCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
*
5686 ATTATTTCTCATATAC
196 ATTTTTTCTCATATAC
5702 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
5767 TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
66 TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
*
5832 GCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
131 CCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
5897 ATTTTTTCTCATATAC
196 ATTTTTTCTCATATAC
* *
5913 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATATATCCTCGTCTATATGAT
1 CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATA-AACCCCGTCTATATGAT
5978 TTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATA
65 TTTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATA
* * * *
6043 CTCTAATTGTTTCTCAGCATCCCCAAATAATCATATGCACCATCCCCGAATTCTTTAGAGATGGA
130 CCCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGA
6108 CATTT
195 CATTT
6113 GTATCAATAG
Statistics
Matches: 792, Mismatches: 36, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
210 401 0.51
211 245 0.31
212 146 0.18
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (211 bp):
CCAAAATTGACTTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATT
TTAGTGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTATAC
CCAAATTGTTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATGGAC
ATTTTTTCTCATATAC
Done.