Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018579.1 Corchorus olitorius cultivar O-4 contig18612, 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: 39825
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:8649 original size:38 final size:38
Alignment explanation
Indices: 8533--8649 Score: 130
Period size: 38 Copynumber: 3.1 Consensus size: 38
8523 GTTTGTCATC
** * *
8533 TAAGTAAACCTGCTTAGGTCTCCATTTGGAGTTGTCATT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAGTT-TCGTT
* *
8572 TAAGTAAACCTGCTTAGGTCTTTGTTTAGAATGTT-GTT
1 TAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT-TTCGTT
*
8610 TAA-TCAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTT
1 TAAGT-AAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTT
8648 TA
1 TA
8650 CTTAGGTCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 3 0.05
38 34 0.52
39 28 0.42
40 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (38 bp):
TAAGTAAACCTGCTTAGGTCTCTGTTTAGAGTTTCGTT
Found at i:14488 original size:21 final size:20
Alignment explanation
Indices: 14463--14518 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
14453 GAATTGATTG
14463 AAATTTCGGTTTGGGCCTTA
1 AAATTTCGGTTTGGGCCTTA
***
14483 ATAATTGATGTTTGGG-CTTA
1 A-AATTTCGGTTTGGGCCTTA
*
14503 AGATTTCGGTTTGGGC
1 AAATTTCGGTTTGGGC
14519 TTCATGGGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 10 0.37
20 6 0.22
21 11 0.41
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (20 bp):
AAATTTCGGTTTGGGCCTTA
Found at i:14516 original size:19 final size:19
Alignment explanation
Indices: 14465--14520 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
14455 ATTGATTGAA
*
14465 ATTTCGGTTTGGGCCTTAAT
1 ATTTCGGTTTGGG-CTTAAG
*
14485 AATT-GATGTTTGGGCTTAAG
1 ATTTCG--GTTTGGGCTTAAG
14505 ATTTCGGTTTGGGCTT
1 ATTTCGGTTTGGGCTT
14521 CATGGGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 11 0.37
20 11 0.37
21 8 0.27
ACGTcount: A:0.16, C:0.11, G:0.29, T:0.45
Consensus pattern (19 bp):
ATTTCGGTTTGGGCTTAAG
Found at i:17540 original size:41 final size:41
Alignment explanation
Indices: 17455--17548 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
17445 AATAAAATCT
* * * * * *
17455 TAAATCAGGGGCGAAATTGAATTAATAAATAAATATTACTC
1 TAAATCAGGGACAAAATTGAATCAATAAACAAACATAACTC
*
17496 TAAATCAGGGACAAAATTGAATCAATTAACAAACATAAAC-C
1 TAAATCAGGGACAAAATTGAATCAATAAACAAACAT-AACTC
17537 TAAATCAGGGAC
1 TAAATCAGGGAC
17549 TATATTGGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (41 bp):
TAAATCAGGGACAAAATTGAATCAATAAACAAACATAACTC
Found at i:20573 original size:29 final size:30
Alignment explanation
Indices: 20532--20757 Score: 162
Period size: 29 Copynumber: 7.7 Consensus size: 30
20522 TCCAAAATGA
*
20532 GCAAAAA-AGACCAAAATGCCCCCAG-ATAT
1 GCAAAAATA-ACCAAAATGCCCCCGGAATAT
* * ** *
20561 GCACAAACAACCAAAATGCCCATGG-ATGT
1 GCAAAAATAACCAAAATGCCCCCGGAATAT
20590 GCAAAAA-AGACCAAAATGCCCCCGGAATAT
1 GCAAAAATA-ACCAAAATGCCCCCGGAATAT
* * *
20620 ACAAAAATGACCAAAATG-CCCCTGAATAT
1 GCAAAAATAACCAAAATGCCCCCGGAATAT
* * *
20649 GCAAAAATGACCAAAATG-CCCCTGAATGT
1 GCAAAAATAACCAAAATGCCCCCGGAATAT
* * * *
20678 GCAGAAATGACCAAAATG-CCCCTGAATGT
1 GCAAAAATAACCAAAATGCCCCCGGAATAT
* * ** *
20707 GCAAAAAATGACCATAATG-CCCTTGAATGT
1 GC-AAAAATAACCAAAATGCCCCCGGAATAT
* *
20737 GAAAAAATGACCAAAATGCCC
1 GCAAAAATAACCAAAATGCCC
20758 ATGGATTTTT
Statistics
Matches: 171, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.01
29 124 0.73
30 46 0.27
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (30 bp):
GCAAAAATAACCAAAATGCCCCCGGAATAT
Found at i:20602 original size:58 final size:59
Alignment explanation
Indices: 20504--20757 Score: 271
Period size: 58 Copynumber: 4.3 Consensus size: 59
20494 CTAGAGCATT
* * * ** *
20504 CAAAAACGACCAAGATGCTCCAAAATGAGCAAAAAAGACCAAAATGCCCCCAG-ATATG
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCCAGAATATG
* ** * * * *
20562 CACAAACAACCAAAATGCCCATGGATGTGCAAAAAAGACCAAAATGCCCCCGGAATATA
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCCAGAATATG
* * * *
20621 CAAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATG-CCCCTGAATGTG
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCCAGAATATG
* * ** *
20679 CAGAAATGACCAAAATGCCCCTGAATGTGCAAAAAATGACCATAATG-CCCTTGAATGTG
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAA-GACCAAAATGCCCCCAGAATATG
*
20738 AAAAAATGACCAAAATGCCC
1 CAAAAATGACCAAAATGCCC
20758 ATGGATTTTT
Statistics
Matches: 166, Mismatches: 28, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
58 85 0.51
59 81 0.49
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.15
Consensus pattern (59 bp):
CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCCAGAATATG
Found at i:20652 original size:59 final size:58
Alignment explanation
Indices: 20504--20757 Score: 260
Period size: 59 Copynumber: 4.3 Consensus size: 58
20494 CTAGAGCATT
* * * ** * * *
20504 CAAAAACGACCAAGATGCTCCAAAATGAGCAAAAAAGACCAAAATGCCCC-CAGATATG
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCTGA-ATATA
* ** * * *
20562 CACAAACAACCAAAATGCCCATGGATGTGCAAAAAAGACCAAAATGCCCCCGGAATATA
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATG-CCCCTGAATATA
* * * *
20621 CAAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGAATGTG
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCTGAATATA
* * * *
20679 CAGAAATGACCAAAATGCCCCTGAATGTGCAAAAAATGACCATAATGCCCTTGAATGTGA
1 CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAA-GACCAAAATGCCCCTGAATAT-A
20739 -AAAAATGACCAAAATGCCC
1 CAAAAATGACCAAAATGCCC
20758 ATGGATTTTT
Statistics
Matches: 164, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
58 79 0.48
59 84 0.51
60 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.15
Consensus pattern (58 bp):
CAAAAATGACCAAAATGCCCCTGAATGTGCAAAAAAGACCAAAATGCCCCTGAATATA
Found at i:20662 original size:88 final size:87
Alignment explanation
Indices: 20533--20763 Score: 284
Period size: 88 Copynumber: 2.6 Consensus size: 87
20523 CCAAAATGAG
* * * **
20533 CAAAAAAGACCAAAATGCCCC-CAGATATGCACAAACAACCAAAATGCCCATGGATGTGCAAAAA
1 CAAAAATGACCAAAATGCCCCTGA-ATATGCAAAAATGACCAAAATGCCCATGGATGTGCAAAAA
20597 AGACCAAAATGCCCCCGGAATATA
65 AGACCAAAATG-CCCCGGAATATA
* * * *
20621 CAAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGAATGTGCAGAAAT
1 CAAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCATGGATGTGCAAAAAA
* * *
20686 GACCAAAATGCCCCTGAATGTG
66 GACCAAAATGCCCCGGAATATA
* * * *
20708 CAAAAAATGACCATAATGCCCTTGAATGTGAAAAAATGACCAAAATGCCCATGGAT
1 C-AAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCATGGAT
20764 TTTTGAAAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
87 10 0.08
88 112 0.91
89 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (87 bp):
CAAAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCATGGATGTGCAAAAAA
GACCAAAATGCCCCGGAATATA
Found at i:21555 original size:176 final size:176
Alignment explanation
Indices: 21261--21610 Score: 700
Period size: 176 Copynumber: 2.0 Consensus size: 176
21251 AAGAATAGCT
21261 TGTTGAAGACTATTTATTCCTTTTATTTGGAACTAATGTTCTTAATGCTATTGTTGATAGAAGTT
1 TGTTGAAGACTATTTATTCCTTTTATTTGGAACTAATGTTCTTAATGCTATTGTTGATAGAAGTT
21326 TGGGGCAAGTTAATTGCAATTTTTCGTTTTACTAGAATGAATGCTGTAAATAAATTCTTTCTTTG
66 TGGGGCAAGTTAATTGCAATTTTTCGTTTTACTAGAATGAATGCTGTAAATAAATTCTTTCTTTG
21391 TTTTATATAATTACTTTATTAATTTTGATATAAAGTATATGTTATA
131 TTTTATATAATTACTTTATTAATTTTGATATAAAGTATATGTTATA
21437 TGTTGAAGACTATTTATTCCTTTTATTTGGAACTAATGTTCTTAATGCTATTGTTGATAGAAGTT
1 TGTTGAAGACTATTTATTCCTTTTATTTGGAACTAATGTTCTTAATGCTATTGTTGATAGAAGTT
21502 TGGGGCAAGTTAATTGCAATTTTTCGTTTTACTAGAATGAATGCTGTAAATAAATTCTTTCTTTG
66 TGGGGCAAGTTAATTGCAATTTTTCGTTTTACTAGAATGAATGCTGTAAATAAATTCTTTCTTTG
21567 TTTTATATAATTACTTTATTAATTTTGATATAAAGTATATGTTA
131 TTTTATATAATTACTTTATTAATTTTGATATAAAGTATATGTTA
21611 GTTCAATTTT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 174 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (176 bp):
TGTTGAAGACTATTTATTCCTTTTATTTGGAACTAATGTTCTTAATGCTATTGTTGATAGAAGTT
TGGGGCAAGTTAATTGCAATTTTTCGTTTTACTAGAATGAATGCTGTAAATAAATTCTTTCTTTG
TTTTATATAATTACTTTATTAATTTTGATATAAAGTATATGTTATA
Found at i:22416 original size:22 final size:21
Alignment explanation
Indices: 22391--22444 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
22381 GAAGTTAGTG
22391 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
22413 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
22432 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
22445 TCGAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:23439 original size:50 final size:50
Alignment explanation
Indices: 23359--23466 Score: 198
Period size: 50 Copynumber: 2.2 Consensus size: 50
23349 TTTCTTGTGT
*
23359 TGTTGGGCTCATTTCCATCTATTTCTTTTTTGTTTCCACTTGGGCCATCA
1 TGTTGGGCTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
*
23409 TGTTGGGTTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
1 TGTTGGGCTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
23459 TGTTGGGC
1 TGTTGGGC
23467 CCATGGTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (50 bp):
TGTTGGGCTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
Found at i:24816 original size:10 final size:10
Alignment explanation
Indices: 24783--24818 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
24773 AGGTTATTTA
24783 AGATTTAATT
1 AGATTTAATT
* *
24793 ATACTTAATT
1 AGATTTAATT
24803 AGATTTAATT
1 AGATTTAATT
24813 AGATTT
1 AGATTT
24819 TTTTTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (10 bp):
AGATTTAATT
Found at i:38216 original size:26 final size:26
Alignment explanation
Indices: 38187--38246 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
38177 GTTTAGAATT
38187 TCCGTTTAAGAAAACCTGCTTAGGTC
1 TCCGTTTAAGAAAACCTGCTTAGGTC
* *
38213 TCCGTTTCAGTAAACCTGCTTAGGTC
1 TCCGTTTAAGAAAACCTGCTTAGGTC
*
38239 TCTGTTTA
1 TCCGTTTA
38247 GAATTTTCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (26 bp):
TCCGTTTAAGAAAACCTGCTTAGGTC
Found at i:38246 original size:65 final size:65
Alignment explanation
Indices: 38157--38342 Score: 257
Period size: 65 Copynumber: 2.9 Consensus size: 65
38147 TTTCGTCTAG
* *
38157 GTAAATCTGCTTAGGTCTCAGTTTAGAATTTCCGTTTAAGAAAACCTGCTTAGGTCTCCGTTTCA
1 GTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTTTAAGAAAACCTGCTTAGGTCTCCGTTTCA
* *
38222 GTAAACCTGCTTAGGTCTCTGTTTAGAATTTTCGTTTAGGAAAACCTGCTTAGGTCTCCGTTTCA
1 GTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTTTAAGAAAACCTGCTTAGGTCTCCGTTTCA
* * * * * * *
38287 ATAAACCTGCTTAGGTCTCTATCTA-AATTAACCATTCAAGTAAACCTGCTTAGGTC
1 GTAAACCTGCTTAGGTCTCTGTTTAGAATT-TCCGTTTAAGAAAACCTGCTTAGGTC
38343 CCTGTTTAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
64 4 0.04
65 103 0.96
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (65 bp):
GTAAACCTGCTTAGGTCTCTGTTTAGAATTTCCGTTTAAGAAAACCTGCTTAGGTCTCCGTTTCA
Found at i:38319 original size:26 final size:26
Alignment explanation
Indices: 38263--38319 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
38253 TCGTTTAGGA
* * *
38263 AAACCTGCTTAGGTCTCCGTTTCAAT
1 AAACCTGCTTAGGTCTCCATCTAAAT
*
38289 AAACCTGCTTAGGTCTCTATCTAAAT
1 AAACCTGCTTAGGTCTCCATCTAAAT
*
38315 TAACC
1 AAACC
38320 ATTCAAGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (26 bp):
AAACCTGCTTAGGTCTCCATCTAAAT
Found at i:38502 original size:39 final size:39
Alignment explanation
Indices: 38288--38521 Score: 256
Period size: 39 Copynumber: 6.0 Consensus size: 39
38278 TCCGTTTCAA
* * * *
38288 TAAACCTGCTTAGGTCTCTATCTA-AATTAACCATTCAAG
1 TAAACCTGCTTAGGTCTCTATTTAGAGTT-TCCATTTAAG
* * * * *
38327 TAAACCTGCTTAGGTCCCTGTTTAAAGTCTCCCTTTAAG
1 TAAACCTGCTTAGGTCTCTATTTAGAGTTTCCATTTAAG
* * * * *
38366 TAAACCTGTTTAGGTCTTTGTCTAAAGTTTCCATTTAAG
1 TAAACCTGCTTAGGTCTCTATTTAGAGTTTCCATTTAAG
*
38405 TAAACCTGCTTAGGTCTCTGTTTAGAG-TTCCATTTTAAG
1 TAAACCTGCTTAGGTCTCTATTTAGAGTTTCCA-TTTAAG
*
38444 TATACCTGCTTAGGTCTCTATTTAGAGTTTCCATTTAAG
1 TAAACCTGCTTAGGTCTCTATTTAGAGTTTCCATTTAAG
** * *
38483 TAAATTTGCTTAGATCTCTATTTAGAGTTTTCATTTAAG
1 TAAACCTGCTTAGGTCTCTATTTAGAGTTTCCATTTAAG
38522 AAAAAAAAAC
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
38 5 0.03
39 155 0.93
40 7 0.04
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (39 bp):
TAAACCTGCTTAGGTCTCTATTTAGAGTTTCCATTTAAG
Found at i:38942 original size:50 final size:50
Alignment explanation
Indices: 38880--38987 Score: 189
Period size: 50 Copynumber: 2.2 Consensus size: 50
38870 TTTCTTGTGT
* *
38880 TGTTGGGCTCATTTCTATCTATTTCTTTTTTGTTTCCACTTGGGCCATCA
1 TGTTGGGCTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
*
38930 TGTTGGGTTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
1 TGTTGGGCTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
38980 TGTTGGGC
1 TGTTGGGC
38988 CCATGGTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (50 bp):
TGTTGGGCTCATTTCCATCTATTTCCTTTTTGTTTCCACTTGGGCCATCA
Done.