Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023988.1 Corchorus olitorius cultivar O-4 contig24021, 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: 32022
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--50 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1 CTC
4 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46 CT CT C
1 CT CT C
51 CGTTATCGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4798 original size:11 final size:11
Alignment explanation
Indices: 4782--4829 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
4772 TTGACAGCGC
4782 AACAAAAACAA
1 AACAAAAACAA
*
4793 AACAAAAACGA
1 AACAAAAACAA
4804 AACAAAAACAA
1 AACAAAAACAA
*
4815 AAAAAAAACGAA
1 AACAAAAAC-AA
4827 AAC
1 AAC
4830 GATGCCAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 28 0.88
12 4 0.12
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:4808 original size:22 final size:22
Alignment explanation
Indices: 4782--4827 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
4772 TTGACAGCGC
*
4782 AACAAAAACAAAACAAAAACGA
1 AACAAAAACAAAAAAAAAACGA
4804 AACAAAAACAAAAAAAAAACGA
1 AACAAAAACAAAAAAAAAACGA
4826 AA
1 AA
4828 ACGATGCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.80, C:0.15, G:0.04, T:0.00
Consensus pattern (22 bp):
AACAAAAACAAAAAAAAAACGA
Found at i:4831 original size:6 final size:6
Alignment explanation
Indices: 4782--4829 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
4772 TTGACAGCGC
* *
4782 AACAAA AAC-AA AACAAA AAC-GA AACAAA AACAAA AA-AAA AACGAA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA
4827 AAC
1 AAC
4830 GATGCCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 14 0.39
6 22 0.61
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:12238 original size:58 final size:56
Alignment explanation
Indices: 12129--12315 Score: 245
Period size: 58 Copynumber: 3.3 Consensus size: 56
12119 TCAGGAATAT
*
12129 AAGAAAGAGTAATCAAGAGATTAGTTTAATTTAGAGGTAATTAAACTAAAAAGAGTAA
1 AAGAAAGAGTAATC-AGAGATTAGTTTAATTCAGA-GTAATTAAACTAAAAAGAGTAA
* *
12187 AAGAAAGAGTAATCAGTA-ATAAGTTTAATTCAGAGTAATTAAACTAAAAAAAG-AA
1 AAGAAAGAGTAATCAG-AGATTAGTTTAATTCAGAGTAATTAAACTAAAAAGAGTAA
* *
12242 ATAAAAAGAGTAATCAGAAGATTAGTTTAATTCAAGAGTAATTAAGCTAAAAAGAGTAA
1 A-AGAAAGAGTAATCAG-AGATTAGTTTAATTC-AGAGTAATTAAACTAAAAAGAGTAA
12301 AAGGAAA-AGTAATCA
1 AA-GAAAGAGTAATCA
12316 AGAGTAAAAG
Statistics
Matches: 114, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
55 3 0.03
56 33 0.29
57 28 0.25
58 44 0.39
59 6 0.05
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (56 bp):
AAGAAAGAGTAATCAGAGATTAGTTTAATTCAGAGTAATTAAACTAAAAAGAGTAA
Found at i:12321 original size:22 final size:22
Alignment explanation
Indices: 12293--12625 Score: 247
Period size: 22 Copynumber: 15.5 Consensus size: 22
12283 TTAAGCTAAA
12293 AAGAGTAAAAGGAAAAGTAATC
1 AAGAGTAAAAGGAAAAGTAATC
* *
12315 AAGAGTAAAAGGAAGAGTCATC
1 AAGAGTAAAAGGAAAAGTAATC
*
12337 AAGAGTAAAAGGAAGAGTAATC
1 AAGAGTAAAAGGAAAAGTAATC
*
12359 AAGAGTAAAAGGAAGAGTAATC
1 AAGAGTAAAAGGAAAAGTAATC
*
12381 -AGAAGTAGAA-GAAAGAGTAATC
1 AAG-AGTAAAAGGAAA-AGTAATC
12403 -AGAAGTAAAA-GAAAGAGTAATC
1 AAG-AGTAAAAGGAAA-AGTAATC
** ***
12425 -AGAAG-ATTAGTTTAA-T--TC
1 AAG-AGTAAAAGGAAAAGTAATC
**
12443 AAGAGT---A-GTTAAGCTAA-C
1 AAGAGTAAAAGGAAAAG-TAATC
*
12461 AAAGAGTAAAAGGAAGAGTAATC
1 -AAGAGTAAAAGGAAAAGTAATC
* *
12484 AAAAGTAGAAGGAAAAGTAATC
1 AAGAGTAAAAGGAAAAGTAATC
*
12506 AAGAGTAAAAGGAAGAGTAATC
1 AAGAGTAAAAGGAAAAGTAATC
*
12528 AAGAGTAAAAGAAAAAGTAATC
1 AAGAGTAAAAGGAAAAGTAATC
12550 -AGAAGT-AAAGGAAAGAGTAATC
1 AAG-AGTAAAAGGAAA-AGTAATC
*
12572 -AGAAGTAACA-GAAAGAGTAATC
1 AAG-AGTAAAAGGAAA-AGTAATC
12594 AAGAGTAAAA-GAAAGAGTAATC
1 AAGAGTAAAAGGAAA-AGTAATC
12616 -AGAAGTAAAA
1 AAG-AGTAAAA
12626 TAAAGAGTAA
Statistics
Matches: 265, Mismatches: 26, Indels: 40
0.80 0.08 0.12
Matches are distributed among these distances:
15 4 0.02
16 1 0.00
17 1 0.00
18 5 0.02
19 8 0.03
20 1 0.00
21 19 0.07
22 218 0.82
23 8 0.03
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.15
Consensus pattern (22 bp):
AAGAGTAAAAGGAAAAGTAATC
Found at i:12330 original size:12 final size:12
Alignment explanation
Indices: 12293--12378 Score: 58
Period size: 12 Copynumber: 7.7 Consensus size: 12
12283 TTAAGCTAAA
12293 AAGAGTAAAAGG
1 AAGAGTAAAAGG
* **
12305 AAAAGT--AATC
1 AAGAGTAAAAGG
12315 AAGAGTAAAAGG
1 AAGAGTAAAAGG
* **
12327 AAGAGT--CATC
1 AAGAGTAAAAGG
12337 AAGAGTAAAAGG
1 AAGAGTAAAAGG
**
12349 AAGAGT--AATC
1 AAGAGTAAAAGG
12359 AAGAGTAAAAGG
1 AAGAGTAAAAGG
12371 AAGAGTAA
1 AAGAGTAA
12379 TCAGAAGTAG
Statistics
Matches: 52, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
10 22 0.42
12 30 0.58
ACGTcount: A:0.56, C:0.05, G:0.27, T:0.13
Consensus pattern (12 bp):
AAGAGTAAAAGG
Found at i:12346 original size:44 final size:44
Alignment explanation
Indices: 12293--12636 Score: 276
Period size: 44 Copynumber: 8.0 Consensus size: 44
12283 TTAAGCTAAA
* *
12293 AAGAGTAAAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTCATC
1 AAGAGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATC
* *
12337 AAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGGAAGAGTAATC
1 AAGAGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATC
*
12381 -AGAAGTAGAA-GAAAGAGTAATC-AGAAGTAAAAGAAAGAGTAATC
1 AAG-AGTAAAAGGAAA-AGTAATCAAG-AGTAAAAGAAAGAGTAATC
** *** * *
12425 -AGAAG-ATTAGTTTAA-T--TCAAGAGT-A--GTTAAG-CTAA-C
1 AAG-AGTAAAAGGAAAAGTAATCAAGAGTAAAAG-AAAGAGTAATC
* * *
12461 AAAGAGTAAAAGGAAGAGTAATCAAAAGTAGAAGGAAA-AGTAATC
1 -AAGAGTAAAAGGAAAAGTAATCAAGAGTA-AAAGAAAGAGTAATC
* *
12506 AAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGAAAAAGTAATC
1 AAGAGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATC
*
12550 -AGAAGT-AAAGGAAAGAGTAATC-AGAAGTAACAGAAAGAGTAATC
1 AAG-AGTAAAAGGAAA-AGTAATCAAG-AGTAAAAGAAAGAGTAATC
*
12594 AAGAGTAAAA-GAAAGAGTAATC-AGAAGTAAAATAAAGAGTAAT
1 AAGAGTAAAAGGAAA-AGTAATCAAG-AGTAAAAGAAAGAGTAAT
12637 ATTAGAGTAA
Statistics
Matches: 248, Mismatches: 28, Indels: 48
0.77 0.09 0.15
Matches are distributed among these distances:
36 1 0.00
37 6 0.02
38 9 0.04
39 2 0.01
40 5 0.02
41 9 0.04
42 1 0.00
43 28 0.11
44 180 0.73
45 7 0.03
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (44 bp):
AAGAGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATC
Found at i:12371 original size:66 final size:66
Alignment explanation
Indices: 12296--12625 Score: 337
Period size: 66 Copynumber: 5.1 Consensus size: 66
12286 AGCTAAAAAG
* * *
12296 AGTAAAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTCATCAAGAGTAAAAGGAAGAGTAATCA-
1 AGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATCAAGAGTAAAAGAAAGAGTAATCAG
12360 A
66 A
* *
12361 GAGTAAAAGGAAGAGTAATC-AGAAGTAGAAGAAAGAGTAATC-AGAAGTAAAAGAAAGAGTAAT
1 -AGTAAAAGGAAAAGTAATCAAG-AGTAAAAGAAAGAGTAATCAAG-AGTAAAAGAAAGAGTAAT
12424 CAGA
63 CAGA
** *** * * *
12428 AG-ATTAGTTTAA-T--TCAAGAGT---AGTTAAG-CTAA-CAAAGAGTAAAAGGAAGAGTAATC
1 AGTAAAAGGAAAAGTAATCAAGAGTAAAAG-AAAGAGTAATC-AAGAGTAAAAGAAAGAGTAATC
*
12484 AAA
64 AGA
* * *
12487 AGTAGAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGAAAAAGTAATCAG
1 AGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATCAAGAGTAAAAGAAAGAGTAATCAG
12552 A
66 A
*
12553 AGT-AAAGGAAAGAGTAATC-AGAAGTAACAGAAAGAGTAATCAAGAGTAAAAGAAAGAGTAATC
1 AGTAAAAGGAAA-AGTAATCAAG-AGTAAAAGAAAGAGTAATCAAGAGTAAAAGAAAGAGTAATC
12616 AGA
64 AGA
12619 AGTAAAA
1 AGTAAAA
12626 TAAAGAGTAA
Statistics
Matches: 216, Mismatches: 29, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
58 1 0.00
59 27 0.12
60 10 0.05
61 1 0.00
62 5 0.02
63 10 0.05
64 1 0.00
65 20 0.09
66 136 0.63
67 5 0.02
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.15
Consensus pattern (66 bp):
AGTAAAAGGAAAAGTAATCAAGAGTAAAAGAAAGAGTAATCAAGAGTAAAAGAAAGAGTAATCAG
A
Found at i:12531 original size:169 final size:168
Alignment explanation
Indices: 12246--12594 Score: 592
Period size: 169 Copynumber: 2.1 Consensus size: 168
12236 AAAGAAATAA
12246 AAAGAGTAATCAGAAGATTAGTTTAATTCAAGAGTAATTAAGCTAAAAAGAGTAAAAGGAAAAGT
1 AAAGAGTAATCAGAAGATTAGTTTAATTCAAGAGTAATTAAGCTAAAAAGAGTAAAAGGAAAAGT
* * * * *
12311 AATCAAGAGTAAAAGGAAGAGTCATCAAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGGAAGAG
66 AATCAAAAGTAAAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGAAAAAG
12376 TAATCAGAAGTAGAA-GAAAGAGTAATCAGAAGTAAAAG
131 TAATCAGAAGTA-AAGGAAAGAGTAATCAGAAGTAAAAG
* *
12414 AAAGAGTAATCAGAAGATTAGTTTAATTCAAGAGTAGTTAAGCTAACAAAGAGTAAAAGGAAGAG
1 AAAGAGTAATCAGAAGATTAGTTTAATTCAAGAGTAATTAAGCTAA-AAAGAGTAAAAGGAAAAG
*
12479 TAATCAAAAGTAGAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGAAAAA
65 TAATCAAAAGTAAAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGAAAAA
*
12544 GTAATCAGAAGTAAAGGAAAGAGTAATCAGAAGTAACAG
130 GTAATCAGAAGTAAAGGAAAGAGTAATCAGAAGTAAAAG
12583 AAAGAGTAATCA
1 AAAGAGTAATCA
12595 AGAGTAAAAG
Statistics
Matches: 170, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
168 47 0.28
169 123 0.72
ACGTcount: A:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (168 bp):
AAAGAGTAATCAGAAGATTAGTTTAATTCAAGAGTAATTAAGCTAAAAAGAGTAAAAGGAAAAGT
AATCAAAAGTAAAAGGAAAAGTAATCAAGAGTAAAAGGAAGAGTAATCAAGAGTAAAAGAAAAAG
TAATCAGAAGTAAAGGAAAGAGTAATCAGAAGTAAAAG
Found at i:14406 original size:2 final size:2
Alignment explanation
Indices: 14399--14424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14389 CTCACCTGAA
14399 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
14425 GCAGGTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14673 original size:21 final size:20
Alignment explanation
Indices: 14631--14673 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
14621 AATAACAATT
* *
14631 AAAAGAAAGCAATTAAACTA
1 AAAACAAAGCAAGTAAACTA
*
14651 AAAACAAAGCAAAGTAAAGTA
1 AAAACAAAGC-AAGTAAACTA
14672 AA
1 AA
14674 TCTAAACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAACAAAGCAAGTAAACTA
Found at i:17820 original size:22 final size:20
Alignment explanation
Indices: 17790--17830 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
17780 AAAATGCTCC
*
17790 TAATGTAAATTAAGAAATGATT
1 TAATCTAAA-TAA-AAATGATT
17812 TAATCTAAATAAAAATGAT
1 TAATCTAAATAAAAATGAT
17831 ATAGGCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (20 bp):
TAATCTAAATAAAAATGATT
Found at i:20762 original size:28 final size:28
Alignment explanation
Indices: 20723--20796 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
20713 ATCACTTGAG
* *
20723 GGGGCATTTTGGTCATTTTGCATATCCA
1 GGGGCATTTTGGTCATTTTACACATCCA
*
20751 GGGGCATTTTGGTCATTTTACACATCTA
1 GGGGCATTTTGGTCATTTTACACATCCA
* *
20779 GGGGTATTTCGGTCATTT
1 GGGGCATTTTGGTCATTT
20797 CAAGTGCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.41
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTACACATCCA
Found at i:25994 original size:2 final size:2
Alignment explanation
Indices: 25987--26025 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25977 GATCTAACTA
25987 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
26026 CAGAATTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Done.