Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024770.1 Corchorus olitorius cultivar O-4 contig24803, 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: 26634
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:215 original size:11 final size:11
Alignment explanation
Indices: 172--209 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
162 TTCCTATATA
*
172 AAATAAATTAT
1 AAATTAATTAT
183 CAAA-TAATTAT
1 -AAATTAATTAT
194 AAATTAATTAT
1 AAATTAATTAT
205 AAATT
1 AAATT
210 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:584 original size:28 final size:31
Alignment explanation
Indices: 527--587 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
517 CAATATTTAT
* *
527 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
558 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
586 TT
1 TT
588 ATAGTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:7439 original size:31 final size:31
Alignment explanation
Indices: 7404--7520 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
7394 GTGTTTTGGG
7404 GCCCTTATTTGAGCTTATTTGAAAAGTTGAA
1 GCCCTTATTTGAGCTTATTTGAAAAGTTGAA
* *
7435 GCCCTTATTTG-GTCTTTAATTTGTTGAAATTGTGTTTTG-G
1 GCCCTTATTTGAG-C-TT-A--T-TTGAAA---AG--TTGAA
7475 GACCCTTATTTGAGCTTATTTGAAAAGTTGAA
1 G-CCCTTATTTGAGCTTATTTGAAAAGTTGAA
7507 GCCCTTATTTGAGC
1 GCCCTTATTTGAGC
7521 CTTTAATCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 28
0.68 0.04 0.28
Matches are distributed among these distances:
30 1 0.01
31 28 0.41
32 3 0.04
33 2 0.03
35 1 0.01
36 12 0.18
37 1 0.01
39 2 0.03
40 3 0.04
41 14 0.21
42 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.43
Consensus pattern (31 bp):
GCCCTTATTTGAGCTTATTTGAAAAGTTGAA
Found at i:7493 original size:72 final size:73
Alignment explanation
Indices: 7376--7527 Score: 279
Period size: 72 Copynumber: 2.1 Consensus size: 73
7366 TAAATATGTA
*
7376 CTTTAATTTGTTGAAATTGTGTTTTGGGGCCCTTATTTGAGCTTATTTGAAAAGTTGAAGCCCTT
1 CTTTAATTTGTTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTATTTGAAAAGTTGAAGCCCTT
*
7441 ATTTG-GT
66 ATTTGAGC
7448 CTTTAATTTGTTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTATTTGAAAAGTTGAAGCCCTT
1 CTTTAATTTGTTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTATTTGAAAAGTTGAAGCCCTT
7513 ATTTGAGC
66 ATTTGAGC
7521 CTTTAAT
1 CTTTAAT
7528 CTTTCTTTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 69 0.90
73 8 0.10
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.45
Consensus pattern (73 bp):
CTTTAATTTGTTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTATTTGAAAAGTTGAAGCCCTT
ATTTGAGC
Found at i:7498 original size:36 final size:36
Alignment explanation
Indices: 7386--7499 Score: 89
Period size: 36 Copynumber: 3.2 Consensus size: 36
7376 CTTTAATTTG
*
7386 TTGAAATTGTGTTTTGGGGCCCTTATTTGAGCTTAT
1 TTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTAT
* *
7422 TTGAAA---AG--TT-GAAGCCCTTATTTG-GTCTTTAATTT
1 TTGAAATTGTGTTTTGGGA-CCCTTATTTGAG-C-TT-A--T
7457 GTTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTAT
1 -TTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTAT
7494 TTGAAA
1 TTGAAA
7500 AGTTGAAGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 28
0.64 0.05 0.30
Matches are distributed among these distances:
30 2 0.03
31 13 0.22
32 2 0.03
33 2 0.03
35 1 0.02
36 18 0.31
37 1 0.02
39 2 0.03
40 2 0.03
41 13 0.22
42 3 0.05
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (36 bp):
TTGAAATTGTGTTTTGGGACCCTTATTTGAGCTTAT
Found at i:7749 original size:31 final size:31
Alignment explanation
Indices: 7712--7777 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
7702 AAAAGCAATT
*
7712 AATTTAGAT-CATGTATCAATAAGATTGGGTC
1 AATTTAG-TCCATGTACCAATAAGATTGGGTC
*
7743 AATTTAGTCCATGTACCCATAAGATTGGGTC
1 AATTTAGTCCATGTACCAATAAGATTGGGTC
7774 AATT
1 AATT
7778 GAATCCAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (31 bp):
AATTTAGTCCATGTACCAATAAGATTGGGTC
Found at i:11797 original size:22 final size:21
Alignment explanation
Indices: 11772--11825 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
11762 CTGCTTGTTT
11772 TTCTCATTCCAAAATCCACCGA
1 TTCTC-TTCCAAAATCCACCGA
* **
11794 TTCTC-TACAAAATCCATTGA
1 TTCTCTTCCAAAATCCACCGA
11814 TTCTCTTCCAAA
1 TTCTCTTCCAAA
11826 TCTGAAGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.63
21 5 0.19
22 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (21 bp):
TTCTCTTCCAAAATCCACCGA
Found at i:12755 original size:31 final size:31
Alignment explanation
Indices: 12715--12783 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
12705 TTTCAGCAAA
* *
12715 ATGTGTGTGTTAGTT-TTGATAATGAGTAAAT
1 ATGTATGTGTTACTTATT-ATAATGAGTAAAT
12746 ATGTATGTGTTACTTCATTATAATGAGTAAAT
1 ATGTATGTGTTACTT-ATTATAATGAGTAAAT
*
12778 AGGTAT
1 ATGTAT
12784 TCATAGCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 13 0.39
32 18 0.55
33 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (31 bp):
ATGTATGTGTTACTTATTATAATGAGTAAAT
Found at i:14542 original size:10 final size:11
Alignment explanation
Indices: 14521--14555 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
14511 CTTTTTTAAT
14521 TATTATTATTA
1 TATTATTATTA
14532 TATTA-TATTA
1 TATTATTATTA
14542 TA-TATTATTA
1 TATTATTATTA
14552 TATT
1 TATT
14556 TCTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 14 0.64
11 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:15176 original size:78 final size:78
Alignment explanation
Indices: 15042--15187 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 78
15032 AGGATCTTCA
*
15042 TTTGAGTCTTTTTCGTTGGTTTCGCATTGGGTTGTAGCTTTGGAGAGGAAAGGAGGCATCTTTTT
1 TTTGAGTCTTTTTCGTTGGTTTCGCATCGGGTTGTAGCTTTGGAGAGGAAAGGAGGCATCTTTTT
15107 AGTGCTGAAGGCG
66 AGTGCTGAAGGCG
* * *
15120 TTTGAGTCTTTTTCGTTGGTTTCGCGTCGGGTTGTAGCTTTGGAGAGGAAATGAGGCGTCTTTTT
1 TTTGAGTCTTTTTCGTTGGTTTCGCATCGGGTTGTAGCTTTGGAGAGGAAAGGAGGCATCTTTTT
15185 AGT
66 AGT
15188 ACTGGAGGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.15, C:0.12, G:0.33, T:0.40
Consensus pattern (78 bp):
TTTGAGTCTTTTTCGTTGGTTTCGCATCGGGTTGTAGCTTTGGAGAGGAAAGGAGGCATCTTTTT
AGTGCTGAAGGCG
Found at i:16127 original size:20 final size:21
Alignment explanation
Indices: 16102--16147 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
16092 ATAAGTATGG
*
16102 TGTTTTT-TATGTTTTAATTT
1 TGTTTTTATATGTGTTAATTT
*
16122 TGTTTTTATCTGTGTTAATTT
1 TGTTTTTATATGTGTTAATTT
16143 T-TTTT
1 TGTTTT
16148 ATCAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (21 bp):
TGTTTTTATATGTGTTAATTT
Found at i:20487 original size:3 final size:3
Alignment explanation
Indices: 20479--20519 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20469 AACCCAAAGT
20479 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
20520 GTACTTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22508 original size:3 final size:3
Alignment explanation
Indices: 22500--22538 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
22490 AATTATTTAT
22500 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22539 ATATCGCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:22513 original size:17 final size:16
Alignment explanation
Indices: 22491--22538 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
22481 TTTCTTTTCA
22491 ATTATTTATTTATTATT
1 ATTA-TTATTTATTATT
22508 ATTATTATATTATTATT
1 ATTATTAT-TTATTATT
22525 ATTATTA-TTATTAT
1 ATTATTATTTATTAT
22539 ATATCGCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 19 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATTATTTATTATT
Found at i:22523 original size:20 final size:20
Alignment explanation
Indices: 22491--22536 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
22481 TTTCTTTTCA
22491 ATTATTTATTTATTATTATT
1 ATTATTTATTTATTATTATT
22511 ATTATATTA-TTATTATTATT
1 ATTAT-TTATTTATTATTATT
22531 ATTATT
1 ATTATT
22537 ATATATCGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATTTATTTATTATTATT
Done.