Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022208.1 Corchorus olitorius cultivar O-4 contig22241, 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: 18274
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:1316 original size:30 final size:30
Alignment explanation
Indices: 1262--1321 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1252 GAAGTTCGTG
* *
1262 TTTGAAGATTTATTGAAGACAATTTGAAGA
1 TTTGAAGATTCATTGAAGACAATTTCAAGA
*
1292 TTTGAAGA-TCATTGAAGAATAATTTCAAGA
1 TTTGAAGATTCATTGAAG-ACAATTTCAAGA
1322 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGATTCATTGAAGACAATTTCAAGA
Found at i:2618 original size:37 final size:35
Alignment explanation
Indices: 2552--2621 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
2542 GAGTGTTTTC
2552 TTAATTATTTTCTCAATTTATTATCTGCTTTCTGA
1 TTAATTATTTTCTCAATTTATTATCTGCTTTCTGA
* *
2587 TTAATTGTTTTCTTTAATTTTATTGAT-TGCTTTCT
1 TTAATTATTTTC-TCAA-TTTATT-ATCTGCTTTCT
2622 TAGATAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 11 0.37
36 3 0.10
37 14 0.47
38 2 0.07
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.61
Consensus pattern (35 bp):
TTAATTATTTTCTCAATTTATTATCTGCTTTCTGA
Found at i:3441 original size:22 final size:22
Alignment explanation
Indices: 3413--3522 Score: 123
Period size: 22 Copynumber: 5.0 Consensus size: 22
3403 TAAAAAGAGC
*
3413 AAAAGAAAAAGTAATCAGAAGT
1 AAAAGAAAGAGTAATCAGAAGT
* *
3435 AGAAGAAAGAGTAATCAGGAGT
1 AAAAGAAAGAGTAATCAGAAGT
* * *
3457 AAAAGGAAGAGTAATCGGAATT
1 AAAAGAAAGAGTAATCAGAAGT
* *
3479 AGAAGAAAGAGTAATTAGAAGT
1 AAAAGAAAGAGTAATCAGAAGT
*
3501 AAAAGAAAGTGTAAAT-AGAAGT
1 AAAAGAAAGAGT-AATCAGAAGT
3523 TAGTTTAATT
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
22 69 0.96
23 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.25, T:0.16
Consensus pattern (22 bp):
AAAAGAAAGAGTAATCAGAAGT
Found at i:3482 original size:44 final size:44
Alignment explanation
Indices: 3413--3522 Score: 141
Period size: 44 Copynumber: 2.5 Consensus size: 44
3403 TAAAAAGAGC
* *
3413 AAAAGAAAAAGTAATCAGAAGTAGAAGAAAGAGTAATCAGGAGT
1 AAAAGAAAGAGTAATCAGAAGTAGAAGAAAGAGTAATCAGAAGT
* * * *
3457 AAAAGGAAGAGTAATCGGAATTAGAAGAAAGAGTAATTAGAAGT
1 AAAAGAAAGAGTAATCAGAAGTAGAAGAAAGAGTAATCAGAAGT
*
3501 AAAAGAAAGTGTAAAT-AGAAGT
1 AAAAGAAAGAGT-AATCAGAAGT
3523 TAGTTTAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 52 0.95
45 3 0.05
ACGTcount: A:0.55, C:0.03, G:0.25, T:0.16
Consensus pattern (44 bp):
AAAAGAAAGAGTAATCAGAAGTAGAAGAAAGAGTAATCAGAAGT
Found at i:3569 original size:54 final size:54
Alignment explanation
Indices: 3522--3742 Score: 336
Period size: 54 Copynumber: 4.1 Consensus size: 54
3512 TAAATAGAAG
*
3522 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGTAAACAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
* * * *
3576 TTAGTTTAATTCAGAGCAGTTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
* ** *
3630 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGCGAACGGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
*
3684 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAA-AGAGTAAGCAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGA-AGTAAACAGTAA
3738 TTAGT
1 TTAGT
3743 AATTAAACTA
Statistics
Matches: 148, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.01
54 147 0.99
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (54 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
Found at i:4670 original size:483 final size:481
Alignment explanation
Indices: 3717--4680 Score: 1716
Period size: 483 Copynumber: 2.0 Consensus size: 481
3707 ACTAAAGAGT
*
3717 AAAAGAAAGAGTAAGCAGTAATTAGTAATTAAACTAAAAAAGTAAAAAGTAGTAATAAGTAAAAT
1 AAAAGAAAGAGTAAGCAGTAATTAGTAATTAAAATAAAAAAGTAAAAAGTAGTAATAAGTAAAAT
*
3782 GGGCTTAATTCGAAGTAATCCATAGTGAAATAATGGGTTAACATTATTAAAAGTCGTTAAATATC
66 GAGCTTAATTCGAAGTAATCCATAGTGAAATAATGGGTTAACATTATTAAAAGTCGTTAAATATC
3847 TTTAAACTTGGCATGAATTAATTTAAGCATTAAGAATAGAAACAACCAATAATAGAAACCCATAG
131 TTTAAACTTGGCATGAATTAATTTAAGCATTAAGAATAGAAACAACCAATAATAGAAACCCATAG
*
3912 CTAGTTCTAGACTAGTCAGTGCCGTCATTTCAATGAGCGTCGTGGGGGTGCTAATCATTCCCCAC
196 CTAGTTCTAGACTAGTCAGTGCCGTCATTTCAACGAGCGTCGTGGGGGTGCTAATCATTCCCCAC
3977 GCGTACCCGACTCCCGAACCTTTTAGACTCTGGTTAGAAGACCGTTTATTAGGTTTAGTCTTACC
261 GCGTACCCGACTCCCGAACCTTTTAGACTCTGGTTAGAAGACCGTTTATTAGGTTTAGTCTTACC
*
4042 TTTCCCAAGCTTAGATTAACATTAGGCCTAATAATCTAATAGGTGGCTAATCACACCTAGGTTAA
326 TTTCCCAAGCTTAGAGTAACATTAGGCCTAATAATCTAATAGGTGGCTAATCACACCTAGGTTAA
4107 AAAAGATTAGTGGCGACTCCCATCCATAGATAGATTCCAGTAGTTTCCCCACGTCGTGGGCGGCG
391 AAAAGATTAGTGGCGACTCCCATCCATAGATAGATTCCAGTAGTTTCCCCACGTCGTGGGCGGCG
* ***
4172 GGTCCCTTTGGGCCCGCGCGTTGCGA
456 CGTCCCCCCGGGCCCGCGCGTTGCGA
4198 AAAAGAAAGAGTAAGCAGTAATTAGTAATTAAAATAAAAAAAAGTAAAAAGTAGTAATAAGTAAA
1 AAAAGAAAGAGTAAGCAGTAATTAGTAATTAAAAT--AAAAAAGTAAAAAGTAGTAATAAGTAAA
* *
4263 ATGAGCTTAATTCGGAGTAATCCATAGTGAAATAATGGGTTAACGTTATTAAAAGTCGTTAAATA
64 ATGAGCTTAATTCGAAGTAATCCATAGTGAAATAATGGGTTAACATTATTAAAAGTCGTTAAATA
4328 TCTTTAAACTTGGCATGAA-TAGATTTAAGCATTAAGAATAGAAACAACCAATAATAGAAACCCA
129 TCTTTAAACTTGGCATGAATTA-ATTTAAGCATTAAGAATAGAAACAACCAATAATAGAAACCCA
* * *
4392 TAGCTAGTTCTAGACTAGTCAGTGCCGTCATTTCGACGGGCGTCGTGGGGGTGCTAATCGTTCCC
193 TAGCTAGTTCTAGACTAGTCAGTGCCGTCATTTCAACGAGCGTCGTGGGGGTGCTAATCATTCCC
* *
4457 CATGCGTACCCGACTCCCGAACCTTTTAGACTCTGGTTAGAAGACCGTTTATTAGGTTTAGTGTT
258 CACGCGTACCCGACTCCCGAACCTTTTAGACTCTGGTTAGAAGACCGTTTATTAGGTTTAGTCTT
4522 ACCTTTCCCAAGCTTAG-GTAACATTAGGCCTAATAATCTAATAGGTGGCTAATCACACCTAGGT
323 ACCTTTCCCAAGCTTAGAGTAACATTAGGCCTAATAATCTAATAGGTGGCTAATCACACCTAGGT
* *
4586 TAAAAAAAGATTAGTGGCGACTCTCATCCATAGATAGATTCCAGTAGTTTCCCCACGTCGTGTGC
388 T-AAAAAAGATTAGTGGCGACTCCCATCCATAGATAGATTCCAGTAGTTTCCCCACGTCGTGGGC
*
4651 GGCGCGTCCCCCCGGGCCCGTGCGTTGCGA
452 GGCGCGTCCCCCCGGGCCCGCGCGTTGCGA
4681 CAAATTTCTC
Statistics
Matches: 461, Mismatches: 18, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
481 34 0.07
482 49 0.11
483 378 0.82
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (481 bp):
AAAAGAAAGAGTAAGCAGTAATTAGTAATTAAAATAAAAAAGTAAAAAGTAGTAATAAGTAAAAT
GAGCTTAATTCGAAGTAATCCATAGTGAAATAATGGGTTAACATTATTAAAAGTCGTTAAATATC
TTTAAACTTGGCATGAATTAATTTAAGCATTAAGAATAGAAACAACCAATAATAGAAACCCATAG
CTAGTTCTAGACTAGTCAGTGCCGTCATTTCAACGAGCGTCGTGGGGGTGCTAATCATTCCCCAC
GCGTACCCGACTCCCGAACCTTTTAGACTCTGGTTAGAAGACCGTTTATTAGGTTTAGTCTTACC
TTTCCCAAGCTTAGAGTAACATTAGGCCTAATAATCTAATAGGTGGCTAATCACACCTAGGTTAA
AAAAGATTAGTGGCGACTCCCATCCATAGATAGATTCCAGTAGTTTCCCCACGTCGTGGGCGGCG
CGTCCCCCCGGGCCCGCGCGTTGCGA
Found at i:6391 original size:21 final size:21
Alignment explanation
Indices: 6343--6391 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
6333 ACTAAACAAT
6343 CCCACATAAATAGGCACAAAA
1 CCCACATAAATAGGCACAAAA
* *
6364 ACTACATAAAATAGG-ACAAAA
1 CCCACAT-AAATAGGCACAAAA
6385 CCCACAT
1 CCCACAT
6392 TCGATTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.53, C:0.27, G:0.08, T:0.12
Consensus pattern (21 bp):
CCCACATAAATAGGCACAAAA
Found at i:11043 original size:34 final size:34
Alignment explanation
Indices: 11000--11071 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
10990 ATGTTTCTAA
11000 TGATACATGCTTCATATTTTGAATATGATTAATT
1 TGATACATGCTTCATATTTTGAATATGATTAATT
11034 TGATACATGCTTCATATTTTGAATATGATTAATT
1 TGATACATGCTTCATATTTTGAATATGATTAATT
11068 TGAT
1 TGAT
11072 TTTCTGCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TGATACATGCTTCATATTTTGAATATGATTAATT
Found at i:12180 original size:60 final size:60
Alignment explanation
Indices: 12087--12204 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 60
12077 TGTAGTTTTA
* * * * *
12087 CTTTTATTGATTGGGGTGCTTGTTTGGTATGGTGAACCTAACTTAATTTTGTATCGTCAT
1 CTTTTATTGATCGGGGTGCTTATTTGGTATGGTGAACCTAACTGAATCTTGTAACGTCAT
* *
12147 CTTTTATTGATCGTGGTGCTTATTTGGTATGGTGAACTTAACTGAATCTTGTAACGTC
1 CTTTTATTGATCGGGGTGCTTATTTGGTATGGTGAACCTAACTGAATCTTGTAACGTC
12205 CTCATGTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (60 bp):
CTTTTATTGATCGGGGTGCTTATTTGGTATGGTGAACCTAACTGAATCTTGTAACGTCAT
Found at i:13940 original size:89 final size:89
Alignment explanation
Indices: 13818--13997 Score: 306
Period size: 89 Copynumber: 2.0 Consensus size: 89
13808 AATTTTGAAC
* * * *
13818 TCCACAAGCGGATTGTGGAGTTGACATATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTT
1 TCCACAAACGGATTGTGGAGTTGACACAAGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTC
13883 AATCTAGTCCCTAGAAGACACATG
66 AATCTAGTCCCTAGAAGACACATG
*
13907 TCCACAAACGGGTTGTGGAGTTGACACAAGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTC
1 TCCACAAACGGATTGTGGAGTTGACACAAGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTC
*
13972 AATCTAGTCCCTAGAGGACACATG
66 AATCTAGTCCCTAGAAGACACATG
13996 TC
1 TC
13998 ACCCTTCCGG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (89 bp):
TCCACAAACGGATTGTGGAGTTGACACAAGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTC
AATCTAGTCCCTAGAAGACACATG
Found at i:16771 original size:31 final size:31
Alignment explanation
Indices: 16733--16832 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
16723 AACATGACTG
*
16733 AATTGAGCAGAATTTGAAAGGTTTAGGACCA
1 AATTGAGCAGAATCTGAAAGGTTTAGGACCA
* * *
16764 AATTGAGCCG-GTCAGAAA-GTTTAGGACCA
1 AATTGAGCAGAATCTGAAAGGTTTAGGACCA
* *
16793 AATCGAGCAG-ACCGTGAAAGGTTTAGGACCA
1 AATTGAGCAGAATC-TGAAAGGTTTAGGACCA
16824 AATTGAGCA
1 AATTGAGCA
16833 TTTAGCCGAC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 20 0.35
30 9 0.16
31 28 0.49
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (31 bp):
AATTGAGCAGAATCTGAAAGGTTTAGGACCA
Found at i:16789 original size:29 final size:31
Alignment explanation
Indices: 16748--16832 Score: 111
Period size: 29 Copynumber: 2.8 Consensus size: 31
16738 AGCAGAATTT
* **
16748 GAAAGGTTTAGGACCAAATTGAGCCGGTC-A
1 GAAAGGTTTAGGACCAAATTGAGCAGACCGA
* *
16778 GAAA-GTTTAGGACCAAATCGAGCAGACCGT
1 GAAAGGTTTAGGACCAAATTGAGCAGACCGA
16808 GAAAGGTTTAGGACCAAATTGAGCA
1 GAAAGGTTTAGGACCAAATTGAGCA
16833 TTTAGCCGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.43
30 8 0.17
31 19 0.40
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.19
Consensus pattern (31 bp):
GAAAGGTTTAGGACCAAATTGAGCAGACCGA
Done.