Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019050.1 Corchorus olitorius cultivar O-4 contig19083, 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: 23160
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1930 original size:90 final size:90
Alignment explanation
Indices: 1774--1946 Score: 328
Period size: 90 Copynumber: 1.9 Consensus size: 90
1764 TGTGTTGCAC
1774 TTTCTACTATCGAAGCGGAGTTCATTGCAGCAATGGAAGCGTGCAAGGAGATACTTTGGATAAAG
1 TTTCTACTATCGAAGCGGAGTTCATTGCAGCAATGGAAGCGTGCAAGGAGATACTTTGGATAAAG
1839 AAGTACGTTGAGGAGCTCTGTTGAA
66 AAGTACGTTGAGGAGCTCTGTTGAA
* *
1864 TTTCTACTATCGAAGCGGAGTTCATTGCAGCAATGGAAGCGTGCAAGGAGATGCTTTGGATGAAG
1 TTTCTACTATCGAAGCGGAGTTCATTGCAGCAATGGAAGCGTGCAAGGAGATACTTTGGATAAAG
1929 AAGTACGTTGAGGAGCTC
66 AAGTACGTTGAGGAGCTC
1947 GGTCTCAACA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (90 bp):
TTTCTACTATCGAAGCGGAGTTCATTGCAGCAATGGAAGCGTGCAAGGAGATACTTTGGATAAAG
AAGTACGTTGAGGAGCTCTGTTGAA
Found at i:2270 original size:32 final size:32
Alignment explanation
Indices: 2183--2245 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2173 CTGATTATTC
*
2183 AGGCAAAAATCAACAAACAAATGATCAAAACT
1 AGGCAAAAATCAACTAACAAATGATCAAAACT
2215 AGGCAAAAATCAACTAACAAATGATCAAAAC
1 AGGCAAAAATCAACTAACAAATGATCAAAAC
2246 AGAGCATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.13
Consensus pattern (32 bp):
AGGCAAAAATCAACTAACAAATGATCAAAACT
Found at i:2586 original size:21 final size:20
Alignment explanation
Indices: 2548--2598 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2538 AGACCAAAGG
2548 AAGAAGAAG-ACAGAGGACT
1 AAGAAGAAGAACAGAGGACT
*
2567 AAGAAGACAGAACAGGGGACT
1 AAGAAGA-AGAACAGAGGACT
*
2588 AAAAAGAAGAA
1 AAGAAGAAGAA
2599 AGAAGAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 15 0.54
ACGTcount: A:0.57, C:0.10, G:0.29, T:0.04
Consensus pattern (20 bp):
AAGAAGAAGAACAGAGGACT
Found at i:8512 original size:22 final size:23
Alignment explanation
Indices: 8476--8520 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
8466 ACATATATAT
8476 ATATATTATTAAATAGA-AAATAA
1 ATATATTATTAAATA-ATAAATAA
8499 ATATATT-TTAAATAATAAATAA
1 ATATATTATTAAATAATAAATAA
8521 TGAGTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 13 0.62
23 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
ATATATTATTAAATAATAAATAA
Found at i:11348 original size:94 final size:94
Alignment explanation
Indices: 11240--11427 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
11230 CAAGTGTGTT
11240 TTGTGTTTCCAGTTAGCAATTTGTTTATCCAAACATGTTTCCTGCTTTCAAAAATTTGACAACAT
1 TTGTGTTTCCAGTTAGCAATTTGTTTATCCAAACATGTTTCCTGCTTTCAAAAATTTGACAACAT
*
11305 AACGAAAATAAAGTAAAACGAAACAAAAA
66 AACGAAAACAAAGTAAAACGAAACAAAAA
11334 TTGTGTTTCCAGTTAGCAATTTGTTTATCCAAACATGTTTCCTGCTTTCAAAAATTTGACAACAT
1 TTGTGTTTCCAGTTAGCAATTTGTTTATCCAAACATGTTTCCTGCTTTCAAAAATTTGACAACAT
*
11399 AACGAAAACAAAGTAAAATGAAACAAAAA
66 AACGAAAACAAAGTAAAACGAAACAAAAA
11428 CAAAAAACAA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (94 bp):
TTGTGTTTCCAGTTAGCAATTTGTTTATCCAAACATGTTTCCTGCTTTCAAAAATTTGACAACAT
AACGAAAACAAAGTAAAACGAAACAAAAA
Found at i:11576 original size:2 final size:2
Alignment explanation
Indices: 11569--11597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11559 CTTTTATTAA
11569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11598 ACACTAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15394 original size:19 final size:19
Alignment explanation
Indices: 15365--15413 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
15355 AGGAATTACA
*
15365 CTGCTAAGAAGAAGTTTCT
1 CTGCTGAGAAGAAGTTTCT
* *
15384 TTGCTGGGAAGAAGTTTCT
1 CTGCTGAGAAGAAGTTTCT
15403 CTGCTGAGAAG
1 CTGCTGAGAAG
15414 TCGTGCTGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (19 bp):
CTGCTGAGAAGAAGTTTCT
Found at i:17187 original size:38 final size:37
Alignment explanation
Indices: 17114--17251 Score: 195
Period size: 37 Copynumber: 3.7 Consensus size: 37
17104 AACTATAACC
*
17114 TGATGGGAACTTTTCCAATTTGAAAACCTTGAAAACT
1 TGATGGGAACTTTCCCAATTTGAAAACCTTGAAAACT
* * *
17151 TGATGAGAACTTTCCCAATTTGAAAAACTTTAAAAACT
1 TGATGGGAACTTTCCCAATTTG-AAAACCTTGAAAACT
* * *
17189 TGACGGGAACTTTCCCAATTTGAAAACCATGAAGACT
1 TGATGGGAACTTTCCCAATTTGAAAACCTTGAAAACT
*
17226 TGATGGGAACTTTCCGAATTTGAAAA
1 TGATGGGAACTTTCCCAATTTGAAAA
17252 GAGCTAAATT
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
37 55 0.62
38 33 0.38
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (37 bp):
TGATGGGAACTTTCCCAATTTGAAAACCTTGAAAACT
Found at i:17279 original size:52 final size:52
Alignment explanation
Indices: 17218--17330 Score: 208
Period size: 52 Copynumber: 2.2 Consensus size: 52
17208 TTGAAAACCA
* *
17218 TGAAGACTTGATGGGAACTTTCCGAATTTGAAAAGAGCTAAATTGAATACTT
1 TGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
17270 TGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
1 TGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
17322 TGAAAACTT
1 TGAAAACTT
17331 TGAAGGAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (52 bp):
TGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATACTT
Found at i:20789 original size:77 final size:77
Alignment explanation
Indices: 20662--20816 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
20652 ACTATACTAA
20662 TTTTGTTGGGTGCAATCTTGTTACAACCTTGTCCATTTTTGTCCCTATATGATCCTATGGCTGCA
1 TTTTGTTGGGTGCAATCTTGTTACAACCTTGTCCATTTTTGTCCCTATATGATCCTATGGCTGCA
20727 AACCGCCTGTTT
66 AACCGCCTGTTT
20739 TTTTGTTGGGTGCAATCTTGTTACAACCTTGTCCATTTTTGTCCCTATATGATCCTATGGCTGCA
1 TTTTGTTGGGTGCAATCTTGTTACAACCTTGTCCATTTTTGTCCCTATATGATCCTATGGCTGCA
*
20804 AACTGCCTGTTT
66 AACCGCCTGTTT
20816 T
1 T
20817 GAGCATCTTC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.43
Consensus pattern (77 bp):
TTTTGTTGGGTGCAATCTTGTTACAACCTTGTCCATTTTTGTCCCTATATGATCCTATGGCTGCA
AACCGCCTGTTT
Done.