Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012112.1 Corchorus olitorius cultivar O-4 contig12145, 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: 16086
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:2135 original size:27 final size:27
Alignment explanation
Indices: 2077--2178 Score: 105
Period size: 28 Copynumber: 3.7 Consensus size: 27
2067 AGTAAACTTA
* *
2077 AAATGACCAAAACACCCCTGAATGTGC
1 AAATGACCAAAATACCCCTGAACGTGC
* *
2104 AAAATGACCAAAATACCCTTGGACGTGC
1 -AAATGACCAAAATACCCCTGAACGTGC
* * *
2132 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACCAAAATACCCCTGAACGTGC
* *
2159 AAACGACCCAAAATCCCCCT
1 AAATGA-CCAAAATACCCCT
2179 AGGTGACCCT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 27 0.44
28 34 0.56
ACGTcount: A:0.40, C:0.30, G:0.14, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATACCCCTGAACGTGC
Found at i:3096 original size:69 final size:69
Alignment explanation
Indices: 3023--3429 Score: 697
Period size: 69 Copynumber: 5.9 Consensus size: 69
3013 CTTTAATGTA
*** * * * * * *
3023 TGGATGGAACCAATATTTAAACTGACTCGCATGGAAACAAGTTTGACTTATGGAAAAGTCTATAT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
3088 GGCT
66 GGCT
3092 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
3157 GGCT
66 GGCT
* * *
3161 TGGATGGAACCAAGGATTAAACTGACTTGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTACGT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
3226 GGCT
66 GGCT
*
3230 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAACCTATGT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
3295 GGCT
66 GGCT
3299 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
3364 GGCT
66 GGCT
3368 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
3430 AACATTCGGA
Statistics
Matches: 321, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 321 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (69 bp):
TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
GGCT
Found at i:4299 original size:51 final size:51
Alignment explanation
Indices: 4231--4369 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 51
4221 AAAAGCGAGC
* * * * **
4231 TTTTGGTCTTGGTCTCACAAATGGAGTGTAATCTTATTTTTGACGAGCAAA
1 TTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTTGAAAAGCAAA
* *
4282 TTTTGATCTTGGACTCACAAATGGAACGCAAT-TTCA-TTTTGAAAAGCGAA
1 TTTTGATCTTGGACTCACAAATGGAATGCAATCTT-ATTTTTGAAAAGCAAA
*
4332 TTTTGATCTT-GACCTCATAAATGGAATGCAATCTTATT
1 TTTTGATCTTGGA-CTCACAAATGGAATGCAATCTTATT
4370 ATAAAACTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
49 2 0.03
50 41 0.55
51 31 0.42
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (51 bp):
TTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTTGAAAAGCAAA
Found at i:5005 original size:5 final size:5
Alignment explanation
Indices: 4983--5017 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
4973 AATTATCTTT
4983 TTTGA CTTTGA TTTTGA TTTGA TTTGA TTTGA TTT
1 TTTGA -TTTGA -TTTGA TTTGA TTTGA TTTGA TTT
5018 TTTTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (5 bp):
TTTGA
Found at i:5019 original size:22 final size:21
Alignment explanation
Indices: 4983--5055 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
4973 AATTATCTTT
*
4983 TTTGACTTTGATTTTGATTTGA
1 TTTGA-TTTGATTTTTATTTGA
*
5005 TTTGATTTGATTTTTTTTTTGA
1 TTTGATTTGA-TTTTTATTTGA
* * *
5027 ATTGAATTGAATTTTTCTTT-A
1 TTTGATTTG-ATTTTTATTTGA
5048 TTTGATTT
1 TTTGATTT
5056 TTTTGATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 12 0.29
22 29 0.69
23 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (21 bp):
TTTGATTTGATTTTTATTTGA
Found at i:5459 original size:6 final size:6
Alignment explanation
Indices: 5443--5490 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
5433 TCCAAGTGCT
* *
5443 TTTTTC ATTTTC TTTTTC ATTTTTTC TTTTTC TTTTT- TTTTTA TTTTT
1 TTTTTC TTTTTC TTTTTC --TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
5491 TATTATTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
8 6 0.16
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:5460 original size:12 final size:12
Alignment explanation
Indices: 5443--5489 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 12
5433 TCCAAGTGCT
5443 TTTTTCATTTTC
1 TTTTTCATTTTC
5455 TTTTTCATTTTTTC
1 TTTTTCA--TTTTC
5469 TTTTTC-TTTT-
1 TTTTTCATTTTC
*
5479 TTTTTTATTTT
1 TTTTTCATTTT
5490 TTATTATTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 5 0.16
11 8 0.26
12 7 0.23
14 11 0.35
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCATTTTC
Found at i:5467 original size:14 final size:13
Alignment explanation
Indices: 5450--5484 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
5440 GCTTTTTTCA
5450 TTTTCTTTTTCATT
1 TTTTCTTTTTC-TT
5464 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
5477 TTTT-TTTT
1 TTTTCTTTT
5485 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 6 0.29
14 11 0.52
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:5467 original size:20 final size:20
Alignment explanation
Indices: 5442--5479 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5432 TTCCAAGTGC
5442 TTTTTTCATTTTCTTTTTCA
1 TTTTTTCATTTTCTTTTTCA
*
5462 TTTTTTCTTTTTCTTTTT
1 TTTTTTCATTTTCTTTTT
5480 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCATTTTCTTTTTCA
Found at i:5490 original size:12 final size:12
Alignment explanation
Indices: 5442--5491 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
5432 TTCCAAGTGC
5442 TTTTTTCATTTT
1 TTTTTTCATTTT
*
5454 CTTTTTCATTTTT
1 TTTTTTCA-TTTT
5467 TCTTTTTC-TTTT
1 T-TTTTTCATTTT
5479 TTTTTT-ATTTT
1 TTTTTTCATTTT
5490 TT
1 TT
5492 ATTATTGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 11 0.33
12 12 0.36
13 4 0.12
14 6 0.18
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCATTTT
Found at i:9456 original size:15 final size:16
Alignment explanation
Indices: 9426--9465 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
9416 TTACTTTGCT
9426 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
9442 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
9457 TTGCTTTCT
1 TTGTTTTCT
9466 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:11528 original size:29 final size:30
Alignment explanation
Indices: 11481--11540 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
11471 GAAGTTCGTG
* *
11481 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
11512 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
11541 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:15126 original size:8 final size:8
Alignment explanation
Indices: 15113--15161 Score: 64
Period size: 8 Copynumber: 6.0 Consensus size: 8
15103 GATTCCTTTC
15113 CATTTTTT
1 CATTTTTT
15121 CATTTTTT
1 CATTTTTT
*
15129 CATTTTTC
1 CATTTTTT
15137 CATTTTCTTT
1 CA-TTT-TTT
15147 C-TTTTTT
1 CATTTTTT
15154 CATTTTTT
1 CATTTTTT
15162 TCTTCAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 4 0.11
8 26 0.72
9 3 0.08
10 3 0.08
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (8 bp):
CATTTTTT
Found at i:15143 original size:7 final size:8
Alignment explanation
Indices: 15109--15142 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
15099 TATTGATTCC
15109 TTTCCATT
1 TTTCCATT
*
15117 TTTTCATT
1 TTTCCATT
*
15125 TTTTCATT
1 TTTCCATT
15133 TTTCCATT
1 TTTCCATT
15141 TT
1 TT
15143 CTTTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTCCATT
Done.