Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018980.1 Corchorus olitorius cultivar O-4 contig19013, 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: 36780
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:1766 original size:178 final size:178
Alignment explanation
Indices: 1441--1771 Score: 612
Period size: 178 Copynumber: 1.9 Consensus size: 178
1431 AATCTCCATT
1441 TATGTTAACGTGTTATATTATTGAAAATACCAACTTCGCTTTAATTGAAAATAAAAATTATAGAC
1 TATGTTAACGTGTTATATTATTGAAAATACCAACTTCGCTTTAATTGAAAATAAAAATTATAGAC
* *
1506 AATTAAAACTATAAATGAGTACTAAAACTACAACAAAATCATCCATGATACATTCAAGGTTCTAA
66 AATTAAAACTATAAATGAGTACTAAAACTACAAAAAAATCACCCATGATACATTCAAGGTTCTAA
1571 TAATCTAATTATATTGCGAGTTACAACTTTATTAACAAATCTTCTAAG
131 TAATCTAATTATATTGCGAGTTACAACTTTATTAACAAATCTTCTAAG
1619 TATGTTAACGTGTTATATTATTGAAAATACCAACTTCGCTTTAATTGAAAAATAAAAATTATAGA
1 TATGTTAACGTGTTATATTATTGAAAATACCAACTTCGCTTTAATTG-AAAATAAAAATTATAGA
1684 CAATTAAAACTATAAATGAGTACTAAAACTACAAAAGAAATCACCCATGATACATTCAAGGTTCT
65 CAATTAAAACTATAAATGAGTACTAAAACTACAAAA-AAATCACCCATGATACATTCAAGGTTCT
1749 AATAATCTAA-T-TATTGCGAGTTA
129 AATAATCTAATTATATTGCGAGTTA
1772 TAACAAACTT
Statistics
Matches: 149, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
178 59 0.40
179 53 0.36
180 37 0.25
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (178 bp):
TATGTTAACGTGTTATATTATTGAAAATACCAACTTCGCTTTAATTGAAAATAAAAATTATAGAC
AATTAAAACTATAAATGAGTACTAAAACTACAAAAAAATCACCCATGATACATTCAAGGTTCTAA
TAATCTAATTATATTGCGAGTTACAACTTTATTAACAAATCTTCTAAG
Found at i:2929 original size:99 final size:99
Alignment explanation
Indices: 2758--2952 Score: 354
Period size: 99 Copynumber: 2.0 Consensus size: 99
2748 ACCAACCTGC
* *
2758 GTAAACAAATTATTAGAAAAAGTCTTACATTCCTACTTAATTTAATTAATTCTAAAATAAACCCT
1 GTAAACAAATTATTAGAAAAAATCTTACATTCATACTTAATTTAATTAATTCTAAAATAAACCCT
2823 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAATGA
66 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAATGA
**
2857 GTAAACAAATTATTAGAAAAAATCTTACATTCATACTTAATTTAATTAATTCTAAAATAAATTCT
1 GTAAACAAATTATTAGAAAAAATCTTACATTCATACTTAATTTAATTAATTCTAAAATAAACCCT
2922 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAA
66 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAA
2953 ATAAATATGC
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (99 bp):
GTAAACAAATTATTAGAAAAAATCTTACATTCATACTTAATTTAATTAATTCTAAAATAAACCCT
TAAAGTAAATTAAAAGGAAAAGAAGAAAGAATGA
Found at i:2994 original size:67 final size:67
Alignment explanation
Indices: 2922--3055 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
2912 AATAAATTCT
2922 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
1 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
2987 GG
66 GG
* *
2989 TAAAGTAAATTAAAAGGAAAAGAAGGAAGAAATAAATTTGCTACAAAATAGCCTACATAATAATC
1 TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
3054 GG
66 GG
3056 CTTAGAAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (67 bp):
TAAAGTAAATTAAAAGGAAAAGAAGAAAGAAATAAATATGCTACAAAATAGCCTACATAATAATC
GG
Found at i:5482 original size:6 final size:6
Alignment explanation
Indices: 5471--5495 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5461 AGGTAGGGGG
5471 GCAAAT GCAAAT GCAAAT GCAAAT G
1 GCAAAT GCAAAT GCAAAT GCAAAT G
5496 GCATTGCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (6 bp):
GCAAAT
Found at i:5578 original size:7 final size:7
Alignment explanation
Indices: 5566--5597 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
5556 GACCAACGGC
5566 AATGGCA
1 AATGGCA
5573 AATGGCA
1 AATGGCA
5580 AATGGCA
1 AATGGCA
5587 AATGGCA
1 AATGGCA
5594 AATG
1 AATG
5598 CGAAGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.16
Consensus pattern (7 bp):
AATGGCA
Found at i:5754 original size:4 final size:4
Alignment explanation
Indices: 5745--5771 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5735 ATGAAATGAA
5745 CATT CATT CATT CATT CATT CATT CAT
1 CATT CATT CATT CATT CATT CATT CAT
5772 GTTGTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
CATT
Found at i:7399 original size:8 final size:8
Alignment explanation
Indices: 7386--7412 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
7376 CAGAAATAGG
7386 AAAAAGAA
1 AAAAAGAA
7394 AAAAAGAA
1 AAAAAGAA
7402 AAAAAGAA
1 AAAAAGAA
7410 AAA
1 AAA
7413 GAATGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:12747 original size:6 final size:6
Alignment explanation
Indices: 12736--12762 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12726 TGCTTTTCTA
12736 TGAAGC TGAAGC TGAAGC TGAAGC TGA
1 TGAAGC TGAAGC TGAAGC TGAAGC TGA
12763 CTTTGATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAGC
Found at i:15326 original size:6 final size:6
Alignment explanation
Indices: 15315--15339 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15305 CATGCTTTTA
15315 GAAAAT GAAAAT GAAAAT GAAAAT G
1 GAAAAT GAAAAT GAAAAT GAAAAT G
15340 GAGTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (6 bp):
GAAAAT
Found at i:17563 original size:10 final size:10
Alignment explanation
Indices: 17548--17580 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
17538 ACAACATCCC
17548 AAAAAAAGAA
1 AAAAAAAGAA
17558 AAAAAAAGAA
1 AAAAAAAGAA
*
17568 AGAAAAAGAA
1 AAAAAAAGAA
17578 AAA
1 AAA
17581 GAAACGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:23757 original size:19 final size:20
Alignment explanation
Indices: 23735--23774 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
23725 TATAAAAAAG
*
23735 AAGTAGTTAT-CTAAAGTAA
1 AAGTAGTTATAATAAAGTAA
23754 AAGTAGTTATAATAAAGTAA
1 AAGTAGTTATAATAAAGTAA
23774 A
1 A
23775 CTATCTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (20 bp):
AAGTAGTTATAATAAAGTAA
Found at i:25387 original size:11 final size:11
Alignment explanation
Indices: 25368--25408 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
25358 TAGAATTCAG
*
25368 AAATCAGAATC
1 AAATCAGAAGC
*
25379 AAATAAGAAGC
1 AAATCAGAAGC
25390 AAATCAGAAGC
1 AAATCAGAAGC
25401 AAA-CAGAA
1 AAATCAGAA
25409 AGTTCGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 5 0.19
11 22 0.81
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.10
Consensus pattern (11 bp):
AAATCAGAAGC
Found at i:28462 original size:24 final size:24
Alignment explanation
Indices: 28432--28483 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
28422 ATACACCATA
28432 AAATAGTATCAAGTTATGTATATG
1 AAATAGTATCAAGTTATGTATATG
*
28456 AAATAGTATCAAGTTTTGTATATG
1 AAATAGTATCAAGTTATGTATATG
28480 AAAT
1 AAAT
28484 TAAATGGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (24 bp):
AAATAGTATCAAGTTATGTATATG
Found at i:30282 original size:21 final size:21
Alignment explanation
Indices: 30242--30282 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30232 TGATCTTACA
* **
30242 CCATGAAACCTTTATTTCATG
1 CCATGAAACCTCTAAGTCATG
30263 CCATGAAACCTCTAAGTCAT
1 CCATGAAACCTCTAAGTCAT
30283 TCACTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (21 bp):
CCATGAAACCTCTAAGTCATG
Found at i:30371 original size:21 final size:20
Alignment explanation
Indices: 30337--30381 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
30327 TTCCATGAAG
30337 TCAAGGCTCGTTGCACATTC
1 TCAAGGCTCGTTGCACATTC
*
30357 TCAAGTGCTTGTTGCACATTC
1 TCAAG-GCTCGTTGCACATTC
30378 TCAA
1 TCAA
30382 ACGCTTCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (20 bp):
TCAAGGCTCGTTGCACATTC
Found at i:30387 original size:21 final size:21
Alignment explanation
Indices: 30346--30393 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
30336 GTCAAGGCTC
**
30346 GTTGCACATTCTCAAGTGCTT
1 GTTGCACATTCTCAAACGCTT
30367 GTTGCACATTCTCAAACGCTT
1 GTTGCACATTCTCAAACGCTT
*
30388 CTTGCA
1 GTTGCA
30394 TAGCAACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (21 bp):
GTTGCACATTCTCAAACGCTT
Found at i:31961 original size:126 final size:126
Alignment explanation
Indices: 31736--31987 Score: 441
Period size: 126 Copynumber: 2.0 Consensus size: 126
31726 ATTATTGAAA
31736 AGATATCGAACTAAATCTAACTTACCATATATCGATATCCCCTCCTACCCAGCTACTATGTGCTA
1 AGATATCGAACTAAATCTAACTTACCATATATCGATATCCCCTCCTACCCAGCTACTATGTGCTA
* * * *
31801 ATTCTTACTCATTAACTAATTGAGTTTTTATCAGGTTTATCGTCAGTGAAGTTTAGCAGAC
66 ATTCTTACCCATTAACTAATTGAGTTATTATCAGGTCTATCGTCAGTGAAATTTAGCAGAC
31862 AGATATCGAACTAAATCTAACTTACCATATATCGATATCCCCTCCTACCCAGCTACTATGTGCTA
1 AGATATCGAACTAAATCTAACTTACCATATATCGATATCCCCTCCTACCCAGCTACTATGTGCTA
* * *
31927 ATTCTTACCCATTAACTTATTGAGTTATTATCAGGTCTATCGTTAGTGAAATTTAGTAGAC
66 ATTCTTACCCATTAACTAATTGAGTTATTATCAGGTCTATCGTCAGTGAAATTTAGCAGAC
31988 TGCATGTGTG
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (126 bp):
AGATATCGAACTAAATCTAACTTACCATATATCGATATCCCCTCCTACCCAGCTACTATGTGCTA
ATTCTTACCCATTAACTAATTGAGTTATTATCAGGTCTATCGTCAGTGAAATTTAGCAGAC
Found at i:35967 original size:15 final size:16
Alignment explanation
Indices: 35939--35977 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35929 GAGGTTGACA
*
35939 AAAAGCAATTAAAC-AG
1 AAAA-CAATGAAACTAG
35955 AAAACAATGAAACTAG
1 AAAACAATGAAACTAG
35971 AAAACAA
1 AAAACAA
35978 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.67, C:0.13, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAACAATGAAACTAG
Done.