Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012298.1 Corchorus olitorius cultivar O-4 contig12331, 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: 36371
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:367 original size:204 final size:201
Alignment explanation
Indices: 1--396 Score: 722
Period size: 204 Copynumber: 2.0 Consensus size: 201
1 ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
1 ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
*
66 TTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTAAA
66 CTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTAAA
131 TTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC-AATTTATTTATCA
131 TTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCAAATTTATTTATCA
195 ATGGTGA
195 ATGGTGA
*
202 ATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
1 ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
*
267 CTATTATATATATAGAACTATACCTAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATT
66 CTATTATATATA-A-AACTATACC-AAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATT
332 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCAAATTTATTTAT
128 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCAAATTTATTTAT
397 TATTAAGAAA
Statistics
Matches: 188, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
201 75 0.40
202 1 0.01
203 16 0.09
204 96 0.51
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (201 bp):
ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
CTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTAAA
TTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCAAATTTATTTATCAA
TGGTGA
Found at i:509 original size:24 final size:24
Alignment explanation
Indices: 466--511 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
456 ACGTTTGCAC
*
466 AAATCCTACGAATTTGAATTAAAA
1 AAATCCTAAGAATTTGAATTAAAA
490 AAATACCTAAGAATTT-AATTAA
1 AAAT-CCTAAGAATTTGAATTAA
512 TGTAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATCCTAAGAATTTGAATTAAAA
Found at i:561 original size:39 final size:38
Alignment explanation
Indices: 502--576 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 38
492 ATACCTAAGA
502 ATTTAATTAATGTAAGTATTTAAGTTATTATAGTATAAC
1 ATTTAATTAATGTAAGTATTTAAGTTATTATA-TATAAC
* *
541 ATTTAATTAATGTAATTATTTTAGTTATTATATATA
1 ATTTAATTAATGTAAGTATTTAAGTTATTATATATA
577 TTACATAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (38 bp):
ATTTAATTAATGTAAGTATTTAAGTTATTATATATAAC
Found at i:857 original size:96 final size:96
Alignment explanation
Indices: 723--916 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 96
713 GTTTACCCTT
723 TAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTTTTGA
1 TAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTTTTGA
*
788 AGTTTAGACTTATATAGTATATAGATATAGA
66 AGTTTAGACTTATATAATATATAGATATAGA
819 TAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTTTTGA
1 TAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTTTTGA
884 AGTTTAGACTTATATAATATATAGATATAGA
66 AGTTTAGACTTATATAATATATAGATATAGA
915 TA
1 TA
917 TAGATATAGA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (96 bp):
TAAATGAATACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATATTTCAGGTCAATGGTTTTGA
AGTTTAGACTTATATAATATATAGATATAGA
Found at i:913 original size:6 final size:6
Alignment explanation
Indices: 902--964 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
892 CTTATATAAT
902 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
950 ATATAG ATATAG ATA
1 ATATAG ATATAG ATA
965 GATATATACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:1700 original size:17 final size:18
Alignment explanation
Indices: 1678--1717 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1668 CAAACCTCTT
*
1678 CCGCCACC-CCTCCACCG
1 CCGCCACCACCACCACCG
1695 CCGCCACCACCACCACCG
1 CCGCCACCACCACCACCG
1713 -CGCCA
1 CCGCCA
1718 AGCCTTCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.17, C:0.68, G:0.12, T:0.03
Consensus pattern (18 bp):
CCGCCACCACCACCACCG
Found at i:4956 original size:42 final size:42
Alignment explanation
Indices: 4900--5093 Score: 210
Period size: 42 Copynumber: 4.3 Consensus size: 42
4890 AGAGAATGTG
4900 TAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAA
1 TAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAA
4942 TAAATACATTGTCTTCCCTATTTACAAATTGAAAT-CTTTATTTAGAGAA
1 TAAATACATTGTCTTCCCTATTTACAAATTGAAATAC---A---A-A-AA
*
4991 TGTGTAAATACATTGTCTTCCCTATTTACAAATTGAAATACATAAA
1 ----TAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAA
* * *
5037 TAAATACATTATCTACCCTATTTACAAATTGAAATACAGAAA
1 TAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAA
*
5079 TCAAATTAGATTGTC
1 T-AAA-TACATTGTC
5094 AAATCTCTAA
Statistics
Matches: 131, Mismatches: 6, Indels: 28
0.79 0.04 0.17
Matches are distributed among these distances:
41 1 0.01
42 75 0.57
43 3 0.02
44 8 0.06
46 2 0.02
47 2 0.02
48 1 0.01
49 2 0.02
51 1 0.01
53 35 0.27
54 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.36
Consensus pattern (42 bp):
TAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAA
Found at i:5042 original size:95 final size:95
Alignment explanation
Indices: 4879--5071 Score: 359
Period size: 95 Copynumber: 2.0 Consensus size: 95
4869 GCTCAATTTT
4879 AATCTTTATTTAGAGAATGTGTAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAATA
1 AATCTTTATTTAGAGAATGTGTAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAATA
* *
4944 AATACATTGTCTTCCCTATTTACAAATTGA
66 AATACATTATCTACCCTATTTACAAATTGA
*
4974 AATCTTTATTTAGAGAATGTGTAAATACATTGTCTTCCCTATTTACAAATTGAAATACATAAATA
1 AATCTTTATTTAGAGAATGTGTAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAATA
5039 AATACATTATCTACCCTATTTACAAATTGA
66 AATACATTATCTACCCTATTTACAAATTGA
5069 AAT
1 AAT
5072 ACAGAAATCA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (95 bp):
AATCTTTATTTAGAGAATGTGTAAATACATTGTCTTCCCTATTTACAAATTGAAATACAAAAATA
AATACATTATCTACCCTATTTACAAATTGA
Found at i:6366 original size:40 final size:41
Alignment explanation
Indices: 6321--6401 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 41
6311 CATGATAGTC
*
6321 ACGTTATATCTTGATTAATATGA-AAATTAATTTGCGTTAA
1 ACGTTATATCTTGATTAATATGAGAAATTAATTCGCGTTAA
*
6361 ACGTTATATCTTGATTAATATTATGAAATTAATTCGCGTTA
1 ACGTTATATCTTGATTAATATGA-GAAATTAATTCGCGTTA
6402 GACATTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 22 0.59
42 15 0.41
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (41 bp):
ACGTTATATCTTGATTAATATGAGAAATTAATTCGCGTTAA
Found at i:17065 original size:14 final size:14
Alignment explanation
Indices: 17046--17075 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17036 GATAGAATAC
17046 TGCATAATAAGTGT
1 TGCATAATAAGTGT
17060 TGCATAATAAGTGT
1 TGCATAATAAGTGT
17074 TG
1 TG
17076 TATCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (14 bp):
TGCATAATAAGTGT
Found at i:17745 original size:37 final size:37
Alignment explanation
Indices: 17704--17812 Score: 92
Period size: 37 Copynumber: 3.2 Consensus size: 37
17694 TTAGATAGAT
17704 CAAATTTCAAACATCTAGGCACATATCTTACTAAAAC
1 CAAATTTCAAACATCTAGGCACATATCTTACTAAAAC
* * * * * *
17741 CAAATTACGAA-A--T---C-C-TATATTA-GATAGAT
1 CAAATTTCAAACATCTAGGCACATATCTTACTA-AAAC
17770 CAAATTTCAAACATCTAGGCACATATCTTACTAAAAC
1 CAAATTTCAAACATCTAGGCACATATCTTACTAAAAC
17807 CAAATT
1 CAAATT
17813 ACGAAATCCT
Statistics
Matches: 50, Mismatches: 12, Indels: 20
0.61 0.15 0.24
Matches are distributed among these distances:
28 1 0.02
29 17 0.34
30 2 0.04
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 2 0.04
37 23 0.46
38 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.28
Consensus pattern (37 bp):
CAAATTTCAAACATCTAGGCACATATCTTACTAAAAC
Found at i:17762 original size:66 final size:66
Alignment explanation
Indices: 17656--17838 Score: 303
Period size: 66 Copynumber: 2.8 Consensus size: 66
17646 CTCCATTCAA
* * * * * * *
17656 GCACAAATCTTACCAAACCCGAATCAGGAAATCATATATTAGATAGATCAAATTTCAAACATCTA
1 GCACATATCTTACTAAAACCAAATTACGAAATCCTATATTAGATAGATCAAATTTCAAACATCTA
17721 G
66 G
17722 GCACATATCTTACTAAAACCAAATTACGAAATCCTATATTAGATAGATCAAATTTCAAACATCTA
1 GCACATATCTTACTAAAACCAAATTACGAAATCCTATATTAGATAGATCAAATTTCAAACATCTA
17787 G
66 G
17788 GCACATATCTTACTAAAACCAAATTACGAAATCCTATATTAGATAGATCAA
1 GCACATATCTTACTAAAACCAAATTACGAAATCCTATATTAGATAGATCAA
17839 GTTACAAATC
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 110 1.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (66 bp):
GCACATATCTTACTAAAACCAAATTACGAAATCCTATATTAGATAGATCAAATTTCAAACATCTA
G
Found at i:34249 original size:5 final size:5
Alignment explanation
Indices: 34235--34270 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
34225 TTTTTCTGTT
34235 TTTTG TTTTTG TTTTG TTTTCG TTTTG TTTTG TTTT
1 TTTTG -TTTTG TTTTG TTTT-G TTTTG TTTTG TTTT
34271 TGTTGCACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:34271 original size:6 final size:6
Alignment explanation
Indices: 34234--34274 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
34224 GTTTTTCTGT
*
34234 TTTTTG TTTTTG -TTTTG TTTTCG -TTTTG -TTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
34275 GCACTGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 14 0.45
6 17 0.55
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:34274 original size:11 final size:11
Alignment explanation
Indices: 34235--34270 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
34225 TTTTTCTGTT
34235 TTTTGTTTTTG
1 TTTTGTTTTTG
*
34246 TTTTGTTTTCG
1 TTTTGTTTTTG
34257 TTTTG-TTTTG
1 TTTTGTTTTTG
34267 TTTT
1 TTTT
34271 TGTTGCACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:34853 original size:13 final size:14
Alignment explanation
Indices: 34825--34852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34815 TGGAAAACGT
34825 ATGTTCTTGAAAAA
1 ATGTTCTTGAAAAA
34839 ATGTTCTTGAAAAA
1 ATGTTCTTGAAAAA
34853 TTGGAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATGTTCTTGAAAAA
Found at i:34902 original size:13 final size:13
Alignment explanation
Indices: 34872--34896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34862 TATGCGGTTG
34872 GATTTCAATGTAT
1 GATTTCAATGTAT
34885 GATTTCAATGTA
1 GATTTCAATGTA
34897 CTATTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GATTTCAATGTAT
Found at i:36337 original size:2 final size:2
Alignment explanation
Indices: 36330--36368 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
36320 CTCTTATAGA
*
36330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36369 GAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.