Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015803.1 Corchorus olitorius cultivar O-4 contig15836, 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: 12728
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3778 original size:27 final size:27
Alignment explanation
Indices: 3725--3781 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
3715 TAGTGTCACA
*
3725 AATTTTTGTGCTCCAGTTAGTCCCACT
1 AATTTTGGTGCTCCAGTTAGTCCCACT
*
3752 AATTTTGGTGCTCTAGTTAGTCCCACT
1 AATTTTGGTGCTCCAGTTAGTCCCACT
3779 AAT
1 AAT
3782 ATTTACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (27 bp):
AATTTTGGTGCTCCAGTTAGTCCCACT
Found at i:5547 original size:16 final size:16
Alignment explanation
Indices: 5512--5549 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5502 ATTATTTTTG
*
5512 GAAAAAACAGAAAAAG
1 GAAAAAACAGAAAAAA
5528 GAAAAAA-AGAAAAGAA
1 GAAAAAACAGAAAA-AA
5544 GAAAAA
1 GAAAAA
5550 TCAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
GAAAAAACAGAAAAAA
Found at i:8065 original size:15 final size:17
Alignment explanation
Indices: 8045--8079 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
8035 GAAGAAGAAG
8045 AAAAAAA-A-AGAGAGA
1 AAAAAAAGAGAGAGAGA
8060 AAAAAAAGAGAGAGAGA
1 AAAAAAAGAGAGAGAGA
8077 AAA
1 AAA
8080 GGCCTGCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 1 0.06
17 10 0.56
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAGAGAGAGA
Found at i:8080 original size:13 final size:13
Alignment explanation
Indices: 8046--8072 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8036 AAGAAGAAGA
8046 AAAAAAAAGAGAG
1 AAAAAAAAGAGAG
8059 AAAAAAAAGAGAG
1 AAAAAAAAGAGAG
8072 A
1 A
8073 GAGAAAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAG
Found at i:8209 original size:22 final size:21
Alignment explanation
Indices: 8184--8226 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
8174 GGGAAAAAGG
*
8184 GAAAAAGGAGAAGAAAAGAAAA
1 GAAAAAGGA-AAAAAAAGAAAA
8206 GAAAAAGGAAAAAAAAGAAAA
1 GAAAAAGGAAAAAAAAGAAAA
8227 AAGAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
GAAAAAGGAAAAAAAAGAAAA
Found at i:8221 original size:16 final size:16
Alignment explanation
Indices: 8194--8265 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
8184 GAAAAAGGAG
8194 AAGAAAAGAAAAGAAAA
1 AAGAAAA-AAAAGAAAA
*
8211 AGGAAAAAAAAGAAAA
1 AAGAAAAAAAAGAAAA
* *
8227 AAGAAAAAAAGGAAAT
1 AAGAAAAAAAAGAAAA
* *
8243 AAGAAATAAGAGAAAA
1 AAGAAAAAAAAGAAAA
*
8259 TAGAAAA
1 AAGAAAA
8266 TTATGGATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 39 0.87
17 6 0.13
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (16 bp):
AAGAAAAAAAAGAAAA
Found at i:8227 original size:22 final size:23
Alignment explanation
Indices: 8184--8234 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
8174 GGGAAAAAGG
*
8184 GAAAAAGGAGAAGAAAAG-AAAA
1 GAAAAAGGAGAAAAAAAGAAAAA
8206 GAAAAAGGA-AAAAAAAGAAAAAA
1 GAAAAAGGAGAAAAAAAG-AAAAA
8229 GAAAAA
1 GAAAAA
8235 AAGGAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.27
22 9 0.35
23 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
GAAAAAGGAGAAAAAAAGAAAAA
Found at i:8234 original size:29 final size:30
Alignment explanation
Indices: 8176--8233 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
8166 AAAAAATGGG
**
8176 GAAAAAGGGAAAAAGGAGAAGAAAAGAAAA
1 GAAAAAGGGAAAAAAAAGAAGAAAAGAAAA
8206 GAAAAA-GGAAAAAAAAGAA-AAAAGAAAA
1 GAAAAAGGGAAAAAAAAGAAGAAAAGAAAA
8234 AAAGGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 9 0.35
29 11 0.42
30 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (30 bp):
GAAAAAGGGAAAAAAAAGAAGAAAAGAAAA
Found at i:8246 original size:23 final size:24
Alignment explanation
Indices: 8194--8258 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 24
8184 GAAAAAGGAG
8194 AAGAAAAGAA-AAGAAAAAGGAAAAAA
1 AAGAAAA-AAGAA-AAAAAGG-AAAAA
*
8220 AAGAAAAAAGAAAAAAAGG-AAAT
1 AAGAAAAAAGAAAAAAAGGAAAAA
* *
8243 AAGAAATAAGAGAAAA
1 AAGAAAAAAGAAAAAA
8259 TAGAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 17 0.49
25 9 0.26
26 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAGAAAAAAAGGAAAAA
Found at i:11561 original size:46 final size:46
Alignment explanation
Indices: 11505--11593 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
11495 CTGCTAAGCA
* * *
11505 GGCCTGGCCAGCGCTGGGCCGCACTGCTGCCAATGGGCAGCGTGCG
1 GGCCTAGCCAGCGCTGGGCCACACTGCCGCCAATGGGCAGCGTGCG
*
11551 GGCCTAGCCAGTGCTGGGCCACACTGCCGCCAATGGGCAGCGT
1 GGCCTAGCCAGCGCTGGGCCACACTGCCGCCAATGGGCAGCGT
11594 TGGGACCTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.13, C:0.35, G:0.38, T:0.13
Consensus pattern (46 bp):
GGCCTAGCCAGCGCTGGGCCACACTGCCGCCAATGGGCAGCGTGCG
Found at i:11603 original size:46 final size:46
Alignment explanation
Indices: 11511--11603 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
11501 AGCAGGCCTG
* * *
11511 GCCAGCGCTGGGCCGCACTGCTGCCAATGGGCAGCGTGCGGGCCTA
1 GCCAGCGCTGGGCCACACTGCCGCCAATGGGCAGCGTGCGGACCTA
*
11557 GCCAGTGCTGGGCCACACTGCCGCCAATGGGCAGCGTTG-GGACCTA
1 GCCAGCGCTGGGCCACACTGCCGCCAATGGGCAGCG-TGCGGACCTA
11603 G
1 G
11604 GCCCAAACGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 40 0.95
47 2 0.05
ACGTcount: A:0.15, C:0.33, G:0.38, T:0.14
Consensus pattern (46 bp):
GCCAGCGCTGGGCCACACTGCCGCCAATGGGCAGCGTGCGGACCTA
Found at i:11718 original size:22 final size:22
Alignment explanation
Indices: 11692--11733 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11682 CCAAAAAGGG
11692 AGAAA-AAAAAGAAGAGAAAAAT
1 AGAAAGAAAAAGAA-AGAAAAAT
*
11714 AGAAAGGAAAAGAAAGAAAA
1 AGAAAGAAAAAGAAAGAAAA
11734 GAAAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAAAGAAAGAAAAAT
Found at i:11752 original size:14 final size:13
Alignment explanation
Indices: 11684--11757 Score: 55
Period size: 14 Copynumber: 5.7 Consensus size: 13
11674 GGCCTAGCCC
*
11684 AAAAAGGGAGAAA
1 AAAAAGGAAGAAA
11697 AAAAA-GAAGAGAA
1 AAAAAGGAAGA-AA
* *
11710 AAATAGAAAGGAAA
1 AAAAAGGAA-GAAA
* *
11724 AGAAA-GAA-AAG
1 AAAAAGGAAGAAA
11735 AAAAAGGAAGGAAA
1 AAAAAGGAA-GAAA
11749 AAAAAGGAA
1 AAAAAGGAA
11758 AATAAGGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
11 6 0.13
12 7 0.15
13 13 0.28
14 18 0.39
15 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (13 bp):
AAAAAGGAAGAAA
Found at i:11758 original size:21 final size:21
Alignment explanation
Indices: 11698--11759 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
11688 AGGGAGAAAA
* *
11698 AAAAGAAGAGAAAAATAGAAAGG
1 AAAAGAA-A-AAAAAGAAAAAGG
*
11721 AAAAGAAAGAAAAGAAAAAGG
1 AAAAGAAAAAAAAGAAAAAGG
* *
11742 -AAGGAAAAAAAAGGAAAA
1 AAAAGAAAAAAAAGAAAAA
11760 TAAGGAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.45
21 10 0.30
22 1 0.03
23 7 0.21
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAAAAAGAAAAAGG
Found at i:11899 original size:27 final size:27
Alignment explanation
Indices: 11834--11900 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
11824 CTATTTTACA
** *
11834 CTTTGATGGGTAAAGTACTAAATCACC
1 CTTTGATGATTAAAGTACGAAATCACC
* * *
11861 C-TTAAGTTATTAAATTACGAAATCACC
1 CTTTGA-TGATTAAAGTACGAAATCACC
11888 CTTTGATGATTAA
1 CTTTGATGATTAA
11901 TTTTAAGAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
26 3 0.10
27 24 0.80
28 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (27 bp):
CTTTGATGATTAAAGTACGAAATCACC
Done.