Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017292.1 Corchorus olitorius cultivar O-4 contig17325, 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: 30534
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:468 original size:28 final size:28
Alignment explanation
Indices: 436--562 Score: 152
Period size: 27 Copynumber: 4.6 Consensus size: 28
426 AAGTGAACTT
* *
436 AAAATGACCAAAATGCCCCCGGATATGC
1 AAAATGACCAAAATGCCCCTGGACATGC
464 AAAATGACCAAAATG-CCCTGGACATGC
1 AAAATGACCAAAATGCCCCTGGACATGC
* **
491 AAAATGACCAAAATACCCCTGGATGTGC
1 AAAATGACCAAAATGCCCCTGGACATGC
* **
519 -AAATGACTAAAATGCCCCTAAACATGC
1 AAAATGACCAAAATGCCCCTGGACATGC
*
546 AAAA-GACTAAAATGCCC
1 AAAATGACCAAAATGCCC
563 ACCTAGGTGA
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
27 58 0.67
28 28 0.33
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGACATGC
Found at i:502 original size:55 final size:55
Alignment explanation
Indices: 436--562 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 55
426 AAGTGAACTT
**
436 AAAATGACCAAAATGCCCCCGGATATGCAAAATGACCAAAATG-CCCTGGACATGC
1 AAAATGACCAAAATGCCCCCGGATATGC-AAATGACCAAAATGCCCCTAAACATGC
* * * *
491 AAAATGACCAAAATACCCCTGGATGTGCAAATGACTAAAATGCCCCTAAACATGC
1 AAAATGACCAAAATGCCCCCGGATATGCAAATGACCAAAATGCCCCTAAACATGC
*
546 AAAA-GACTAAAATGCCC
1 AAAATGACCAAAATGCCC
563 ACCTAGGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
54 24 0.38
55 39 0.62
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.16
Consensus pattern (55 bp):
AAAATGACCAAAATGCCCCCGGATATGCAAATGACCAAAATGCCCCTAAACATGC
Found at i:1269 original size:136 final size:136
Alignment explanation
Indices: 1106--1365 Score: 466
Period size: 136 Copynumber: 1.9 Consensus size: 136
1096 GAATGCTTTG
*
1106 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
* *
1171 ATGTGCTTTTCCATAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAACCTTGGTTCCATCCAAG
66 ATGTGCTTTTCCATAAACCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAG
1236 GAGCAT
131 GAGCAT
*
1242 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCTATCCAAGCAGC
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
* *
1307 ATGTGCTTTTCCATAAACCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCA
66 ATGTGCTTTTCCATAAACCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCA
1366 CTCAAGCAAC
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 118 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (136 bp):
GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
ATGTGCTTTTCCATAAACCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAG
GAGCAT
Found at i:1408 original size:69 final size:69
Alignment explanation
Indices: 1106--1396 Score: 444
Period size: 69 Copynumber: 4.2 Consensus size: 69
1096 GAATGCTTTG
* *
1106 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1 GCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1171 ATGT
66 ATGT
* * *
1175 GCTTTTCCATAAGCCAAACTCGTTTCCATACGGGTCAGTTCAAACCTTGGTTCCATCCAAGGAGC
1 GCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1240 A--T
66 ATGT
* *
1242 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCTATCCAAGCAGC
1 GCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1307 ATGT
66 ATGT
* * *
1311 GCTTTTCCATAAACCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCA-CTCAAGCAA
1 GCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC-CAAGCAG
* *
1375 CAGGG
65 CATGT
1380 GCTTTTCCATAAGCCAA
1 GCTTTTCCATAAGCCAA
1397 GTTCATTTCC
Statistics
Matches: 201, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
67 62 0.31
68 1 0.00
69 138 0.69
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (69 bp):
GCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
ATGT
Found at i:1516 original size:69 final size:67
Alignment explanation
Indices: 1431--1567 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 67
1421 TTCCAAGACT
* * *
1431 AAACTTGTTTCCATACGAGCCAGTTCAAACCTTGGTTCCATCCAAATAGCATGTGCTTTTCCATA
1 AAACTCGTTTCCATACGAGCCAGTTCAAACCTTGGTTCCACCCAAATAGCATGT--TTTTCCACA
1496 AGCC
64 AGCC
* * *
1500 AAACTCGTTTGCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGTAGCATGTTTTTCCACAAG
1 AAACTCGTTTCCATACGAGCCAGTTCAAACCTTGGTTCCACCCAAATAGCATGTTTTTCCACAAG
1565 CC
66 CC
1567 A
1 A
1568 CGGTTCGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
67 13 0.21
69 49 0.79
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (67 bp):
AAACTCGTTTCCATACGAGCCAGTTCAAACCTTGGTTCCACCCAAATAGCATGTTTTTCCACAAG
CC
Found at i:1686 original size:35 final size:35
Alignment explanation
Indices: 1606--2045 Score: 533
Period size: 35 Copynumber: 12.7 Consensus size: 35
1596 TCTTCTCGAT
* *
1606 ATGACTCGGTGTAGCATCTCCAAAG-T---TTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
* * * *
1637 ATAACTCAGTGTAGCATCTTCAAAGTTGAA-TCAAA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTC-AG
1672 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
* * *
1707 ATGACTCAGTGTAGAATCTTCAAAGTTGAA-TCCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACT-CAG
* *
1742 ATGACTCAGTGTAGCATCTTCAAAGATGAACTCAA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
* *
1777 ATGACGT-AGTGTAGCATCTTCAAAGTTGAA-TCCAG
1 ATGAC-TCGGTGTAGCATCTTCAAAGATGAACT-CAG
1812 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
* *
1847 ATGACTCAGTGTAGCATCTTCAAAGTTGAA-TCCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACT-CAG
1882 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
* * *
1917 ATGACTCAGTGTAGCGTCTAT-AAAGTTGAA-TCCAG
1 ATGACTCGGTGTAGCATCT-TCAAAGATGAACT-CAG
* *
1952 ATGACTCGGAGTAGCATCTTCAAAGATGAACTCGG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
* *
1987 ATGACTCGGTGTAGCATATTCAAAGATGAATTCAGG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCA-G
2023 ATGACTCGGTGTAGCATCTTCAA
1 ATGACTCGGTGTAGCATCTTCAA
2046 TATGGACTCA
Statistics
Matches: 355, Mismatches: 35, Indels: 33
0.84 0.08 0.08
Matches are distributed among these distances:
31 22 0.06
32 1 0.00
34 8 0.02
35 293 0.83
36 31 0.09
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (35 bp):
ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAG
Found at i:1728 original size:70 final size:70
Alignment explanation
Indices: 1606--2045 Score: 676
Period size: 70 Copynumber: 6.3 Consensus size: 70
1596 TCTTCTCGAT
* * *
1606 ATGACTCGGTGTAGCATCTCCAAAG-T---TTCAGATAACTCAGTGTAGCATCTTCAAAGTTGAA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCTTCAAAGTTGAA
* *
1667 TCAAA
66 TCCAG
*
1672 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGAATCTTCAAAGTTGAA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCTTCAAAGTTGAA
1737 TCCAG
66 TCCAG
* *
1742 ATGACTCAGTGTAGCATCTTCAAAGATGAACTCAAATGACGT-AGTGTAGCATCTTCAAAGTTGA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGAC-TCAGTGTAGCATCTTCAAAGTTGA
1806 ATCCAG
65 ATCCAG
1812 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCTTCAAAGTTGAA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCTTCAAAGTTGAA
1877 TCCAG
66 TCCAG
*
1882 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCGTCTAT-AAAGTTGA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCT-TCAAAGTTGA
1946 ATCCAG
65 ATCCAG
* * * * *
1952 ATGACTCGGAGTAGCATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATATTCAAAGATGAA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCTTCAAAGTTGAA
*
2017 TTCAGG
66 TCCA-G
2023 ATGACTCGGTGTAGCATCTTCAA
1 ATGACTCGGTGTAGCATCTTCAA
2046 TATGGACTCA
Statistics
Matches: 345, Mismatches: 20, Indels: 13
0.91 0.05 0.03
Matches are distributed among these distances:
66 24 0.07
67 1 0.00
69 2 0.01
70 293 0.85
71 25 0.07
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (70 bp):
ATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCAGTGTAGCATCTTCAAAGTTGAA
TCCAG
Found at i:2474 original size:26 final size:27
Alignment explanation
Indices: 2440--2513 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
2430 TAGGGTCTCC
* * *
2440 CAGGTGCATTTCGGTCATTTTTACACT
1 CAGGGGCATTTTGGTCATTTTCACACT
* *
2467 -AGGGGCATTTTGGTCATTTGCATACT
1 CAGGGGCATTTTGGTCATTTTCACACT
*
2493 CAGGGGCGTTTTGGTCATTTT
1 CAGGGGCATTTTGGTCATTTT
2514 GGCATTTTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.41
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTTCACACT
Found at i:10427 original size:21 final size:21
Alignment explanation
Indices: 10397--10442 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
10387 CACCTGGGCG
*
10397 CCCACATGG-TTGCCTTGAGCA
1 CCCACATGGTTTGCCTTAAG-A
*
10418 CCCACTTGGTTTGCCTTAAGA
1 CCCACATGGTTTGCCTTAAGA
10439 CCCA
1 CCCA
10443 GCTGGGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.26
Consensus pattern (21 bp):
CCCACATGGTTTGCCTTAAGA
Found at i:11518 original size:29 final size:27
Alignment explanation
Indices: 11461--11511 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
11451 ATGATTTAGG
*
11461 GGTTACTAACTCCCTTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTTCTTTTGA
*
11488 GGTTACTAACACTCTTTTTT-TTTT
1 GGTTACTAACACCCTTTTTTCTTTT
11512 CCAGAGGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.55
Consensus pattern (27 bp):
GGTTACTAACACCCTTTTTTCTTTTGA
Found at i:11578 original size:3 final size:3
Alignment explanation
Indices: 11570--11638 Score: 122
Period size: 3 Copynumber: 23.0 Consensus size: 3
11560 GTTACTAACC
11570 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11618 TTA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA
11639 ATTAAAGAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:13739 original size:21 final size:21
Alignment explanation
Indices: 13715--13759 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
13705 GACAAGTTTC
*
13715 TGAT-TCGACCTCCTTGAAGGT
1 TGATGTCGACC-CCATGAAGGT
13736 TGATGTCGACCCCATGAAGGT
1 TGATGTCGACCCCATGAAGGT
13757 TGA
1 TGA
13760 AACAGAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (21 bp):
TGATGTCGACCCCATGAAGGT
Found at i:17661 original size:21 final size:21
Alignment explanation
Indices: 17631--17676 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17621 CACCTGGGCG
*
17631 CCCACATGG-TTGCCTTGAGCA
1 CCCACATGGTTTGCCTTAAG-A
*
17652 CCCACTTGGTTTGCCTTAAGA
1 CCCACATGGTTTGCCTTAAGA
17673 CCCA
1 CCCA
17677 GCTGAGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.26
Consensus pattern (21 bp):
CCCACATGGTTTGCCTTAAGA
Found at i:20652 original size:19 final size:18
Alignment explanation
Indices: 20619--20654 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20609 TTGAAATTAT
20619 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
20637 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
20655 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:27732 original size:11 final size:11
Alignment explanation
Indices: 27716--27741 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27706 AGATAATTTC
27716 TTTTCTTCTAG
1 TTTTCTTCTAG
27727 TTTTCTTCTAG
1 TTTTCTTCTAG
27738 TTTT
1 TTTT
27742 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:28522 original size:16 final size:15
Alignment explanation
Indices: 28501--28542 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
28491 TTACTTTGCT
28501 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
28517 TTGTTTTATGTTTAA
1 TTGTTTTCTGTTTAA
*
28532 TTGCTTTCTGT
1 TTGTTTTCTGT
28543 CAATCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:30422 original size:14 final size:14
Alignment explanation
Indices: 30403--30444 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
30393 TTCTTTCAGA
30403 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
30417 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
**
30431 TTTCCTTCTTCTTC
1 TTTTTTTCTTCTTC
30445 CTCTCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Done.