Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016863.1 Corchorus olitorius cultivar O-4 contig16896, 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: 8649
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:138 original size:48 final size:48
Alignment explanation
Indices: 1--213 Score: 277
Period size: 48 Copynumber: 4.4 Consensus size: 48
* * **
1 TTGTTTTCAGTATTTTATTCCCGTTTTGCCCTTCCCGGTCGGGTGGTG
1 TTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTG
* *
49 TTGTTTTCAA-AGTTTTCATTCCCGTTTTACCCTTCCTGGTCGGAAGGTG
1 TTGTTTTCAATA--TTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTG
* *
98 TTGTTTTCAATGTTTCACTCCCGTTTTGCCCTTCCCGGTCGGAAGG-G
1 TTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTG
* * *
145 TTTGTCTTCAATATTTCATTCCTGTTTTGCCCTTCTCGGTCGGAAGGTG
1 -TTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTG
*
194 TCGTTTTCAATATTTCATTC
1 TTGTTTTCAATATTTCATTC
214 ATGTCTTCAA
Statistics
Matches: 143, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
47 2 0.01
48 99 0.69
49 42 0.29
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (48 bp):
TTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTG
Found at i:2717 original size:7 final size:7
Alignment explanation
Indices: 2705--2742 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
2695 ATTCCCATTC
2705 GAAAGAA
1 GAAAGAA
2712 GAAAGAA
1 GAAAGAA
2719 GAAAGAA
1 GAAAGAA
*
2726 GAAAAAA
1 GAAAGAA
2733 GAAA-AA
1 GAAAGAA
2739 GAAA
1 GAAA
2743 ACTTGGCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:2868 original size:14 final size:15
Alignment explanation
Indices: 2849--2899 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
2839 AGTCACATGC
2849 TTTCAAAAAA-GATT
1 TTTCAAAAAATGATT
*
2863 TTTCAAAAAAATGGTT
1 TTTC-AAAAAATGATT
*
2879 TTTC-AAAAATG-GT
1 TTTCAAAAAATGATT
2892 TTTCAAAA
1 TTTCAAAA
2900 TTTGTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 14 0.44
15 6 0.19
16 7 0.22
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (15 bp):
TTTCAAAAAATGATT
Found at i:2907 original size:13 final size:13
Alignment explanation
Indices: 2869--2899 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
2859 GATTTTTCAA
2869 AAAAATGGTTTTTC
1 AAAAATGG-TTTTC
2883 AAAAATGGTTTTC
1 AAAAATGGTTTTC
2896 AAAA
1 AAAA
2900 TTTGTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (13 bp):
AAAAATGGTTTTC
Found at i:4533 original size:35 final size:35
Alignment explanation
Indices: 4403--4536 Score: 126
Period size: 35 Copynumber: 3.8 Consensus size: 35
4393 TTTCAAACGC
* *
4403 TTCAATTCATTTCAGTTGACCCACGGTGGTCC-TA
1 TTCAATTCATTTCAGTTGACCCAGGGTGATCCTTA
* * * * * *
4437 TTTCAATTTATTTTAGTTTGATCCATGGTGATCTTTC
1 -TTCAATTCATTTCAG-TTGACCCAGGGTGATCCTTA
* * * *
4474 TTCAATTCACTTCAGTTAATCCAGGGCGATCCTTA
1 TTCAATTCATTTCAGTTGACCCAGGGTGATCCTTA
*
4509 TTCAATTCATTTCAATTGACCCAGGGTG
1 TTCAATTCATTTCAGTTGACCCAGGGTG
4537 GTCCAATTTC
Statistics
Matches: 77, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
35 51 0.66
36 25 0.32
37 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (35 bp):
TTCAATTCATTTCAGTTGACCCAGGGTGATCCTTA
Found at i:4585 original size:20 final size:21
Alignment explanation
Indices: 4547--4587 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4537 GTCCAATTTC
4547 AGTTTATTTCAGTTTGATCCA
1 AGTTTATTTCAGTTTGATCCA
4568 AGTTTATTTCAG-TTGATCCA
1 AGTTTATTTCAGTTTGATCCA
4588 GGGCGATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (21 bp):
AGTTTATTTCAGTTTGATCCA
Found at i:4615 original size:36 final size:36
Alignment explanation
Indices: 4568--4904 Score: 450
Period size: 36 Copynumber: 9.4 Consensus size: 36
4558 GTTTGATCCA
4568 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
*
4604 AGTTTATTTCAGTTGACCCAGGGC-AGT-CTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGA-TCCTTTCTTC
*
4639 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
* *
4675 AGTTTATTTCAATTGATCCAGGGCGGT-CTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
* *
4710 AGTTTATTTCAGTTGATCTAGGGCGATCTTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
* * *
4746 AATTTATTTCAATTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
* *
4782 AGTTTATTTCACTTGATCCAGGGCGATCTTTTCTTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
* * *
4818 AGTTTATTTCAATTGATCCAGGACGAT-CTTTCCTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
* * * *
4853 AATTTACTTCAGTAGATCCAGGGCGAT-CTTCTCTGC
1 AGTTTATTTCAGTTGATCCAGGGCGATCCTT-TCTTC
*
4889 AGTTTATTTCAATTGA
1 AGTTTATTTCAGTTGA
4905 CTGCAAAATG
Statistics
Matches: 266, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
35 95 0.36
36 171 0.64
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.42
Consensus pattern (36 bp):
AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTC
Found at i:4641 original size:92 final size:90
Alignment explanation
Indices: 4484--4658 Score: 235
Period size: 92 Copynumber: 1.9 Consensus size: 90
4474 TTCAATTCAC
**
4484 TTCAGTTAATCCAGGGCGATCCTTATTCAATTCATTTCAATTGACCCAGGGTGGTCCAATTTCAG
1 TTCAGTTAATCCAGGGCGATCCTTATTCAATTCATTTCAATTGACCCAGGGCAGTCCAATTTCAG
4549 TTTATTTCAGTTTGATCCAAGTTTAT
66 TTTATTTCAG-TTGATCCAAGTTTAT
* * * * * **
4575 TTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCAGT-CTTTCTTC
1 TTCAGTTAATCCAGGGCGATCC-TTATTCAATTCATTTCAATTGACCCAGGGCAGTCCAAT-TTC
4639 AGTTTATTTCAGTTGATCCA
64 AGTTTATTTCAGTTGATCCA
4659 GGGCGATCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 31 0.42
92 42 0.58
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (90 bp):
TTCAGTTAATCCAGGGCGATCCTTATTCAATTCATTTCAATTGACCCAGGGCAGTCCAATTTCAG
TTTATTTCAGTTGATCCAAGTTTAT
Found at i:4654 original size:71 final size:71
Alignment explanation
Indices: 4568--4904 Score: 523
Period size: 71 Copynumber: 4.7 Consensus size: 71
4558 GTTTGATCCA
* * *
4568 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGC-AGTC
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGA-TC
4632 TTTCTTC
65 TTTCTTC
*
4639 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGGTCT
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCT
4704 TTCTTC
66 TTCTTC
* *
4710 AGTTTATTTCAGTTGATCTAGGGCGATCTTTTCTTCAATTTATTTCAATTGATCCAGGGCGATCT
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC-
4775 TTTCTTC
65 TTTCTTC
* *
4782 AGTTTATTTCACTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGACGATCT
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCT
*
4847 TTCCTC
66 TTCTTC
* * * * *
4853 AATTTACTTCAGTAGATCCAGGGCGATCTTCTCTGCAGTTTATTTCAATTGA
1 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGA
4905 CTGCAAAATG
Statistics
Matches: 246, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
71 179 0.73
72 67 0.27
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.42
Consensus pattern (71 bp):
AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCT
TTCTTC
Found at i:4754 original size:107 final size:106
Alignment explanation
Indices: 4568--4904 Score: 505
Period size: 107 Copynumber: 3.2 Consensus size: 106
4558 GTTTGATCCA
* *
4568 AGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGC-AGTC
1 AGTTTATTTCAATTGATCCAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA-TC
*
4632 TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
64 TTTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* *
4675 AGTTTATTTCAATTGATCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATCTT
1 AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATC-T
*
4740 TTCTTCAATTTATTTCAATTGATCCAGGGCGATCTTTTCTTC
65 TTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
* * *
4782 AGTTTATTTCACTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGACGATCT
1 AGTTTATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCT
* * * * *
4847 TTCCTCAATTTACTTCAGTAGATCCAGGGCGATCTTCTCTGC
65 TTCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
4889 AGTTTATTTCAATTGA
1 AGTTTATTTCAATTGA
4905 CTGCAAAATG
Statistics
Matches: 209, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
106 32 0.15
107 145 0.69
108 32 0.15
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.42
Consensus pattern (106 bp):
AGTTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTT
TCTTCAATTTATTTCAGTTGATCCAGGGCGATCTTTTCTTC
Found at i:5208 original size:30 final size:30
Alignment explanation
Indices: 5168--5914 Score: 900
Period size: 30 Copynumber: 25.1 Consensus size: 30
5158 CTTTATCAGT
* *
5168 TTTATTTTAATCCTGTTTGAGGATCATTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
5198 CTTATGTTAATCCTGCTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * *
5228 TTTATTTTAATCATGTTTGAGGAGCACTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
5258 TTTGTGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
5288 TTTATGTTAATCCTGGTTGAGGAT-A--G-
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
** *
5314 -TT-CCTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
5342 TTCATTTTAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
5372 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
5402 TTCATGTTAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
5432 TTCATTTTAATCCTGGTTGAGGATCAATGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
5462 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
5492 TTTATGTTAATCCTGTTTAAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
5522 TTTATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
5552 TTTATTTTAATCCTGGTTGAGGATCAATGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
5582 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
5612 TTTATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* **
5642 TTTATTCTAATCCTGGTTGAGGATCATCAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
5672 TTCATTTTAATCCTGGTTGAGGATCATTG-
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
5701 TTTCATTTTAATCCTGGTTAAGGATCATTGC
1 TTT-ATTTTAATCCTGGTTGAGGATCATTGC
* *
5732 TTCATTTTAATCCTGATTGAGGAT-ATTCGC
1 TTTATTTTAATCCTGGTTGAGGATCATT-GC
**
5762 TCCATTTTAATCCTGGTTGAGGAT-ATTTGC
1 TTTATTTTAATCCTGGTTGAGGATCA-TTGC
* * **
5792 ATCATTTTAATCCTGGTTGAGGATTGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
5822 TTTATTTTAATCATGGTTGAAGACCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
5852 TTTATTTTAATCCTGGTTGAGGATCATCGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * * * *
5882 TATATTTTTATCCTGATTTAGGATTATTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
5912 TTT
1 TTT
5915 GGTTTATTTG
Statistics
Matches: 621, Mismatches: 85, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
24 17 0.03
25 3 0.00
27 2 0.00
29 7 0.01
30 588 0.95
31 4 0.01
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.45
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:6412 original size:27 final size:26
Alignment explanation
Indices: 6374--6430 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
6364 TTTCCAAAAA
*
6374 TTCAGGGGCATTTTGGTCATTTGTACG
1 TTCAGGGGCATTTAGGTCATTT-TACG
*
6401 TTCAGGGGCATTTAGGTCATTTTAGG
1 TTCAGGGGCATTTAGGTCATTTTACG
6427 TTCA
1 TTCA
6431 CTTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCATTTAGGTCATTTTACG
Done.