Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022232.1 Corchorus olitorius cultivar O-4 contig22265, 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: 19914
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5556 original size:29 final size:29
Alignment explanation
Indices: 5496--5578 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
5486 ACAAACAAAT
* * *
5496 ATTCTATCAATCAAATAACAA-ATAATTGCA
1 ATTCAATCAATC-AATAGCAAGAT-ATGGCA
5526 ATTCAATCAATCAATAGCAAGATATGGCA
1 ATTCAATCAATCAATAGCAAGATATGGCA
* *
5555 ATTCAAATCAA-CAATTGAAAGATA
1 ATTC-AATCAATCAATAGCAAGATA
5579 GAATAAGCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 27 0.59
30 19 0.41
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (29 bp):
ATTCAATCAATCAATAGCAAGATATGGCA
Found at i:6518 original size:12 final size:12
Alignment explanation
Indices: 6502--6567 Score: 59
Period size: 11 Copynumber: 5.7 Consensus size: 12
6492 GGAGCAAAGG
*
6502 AAGAAGAAGAAG
1 AAGAAGAAGAAA
*
6514 AAGAAGAA-AGA
1 AAGAAGAAGAAA
6525 AAGAAAGAAAGAAA
1 AAG-AAG-AAGAAA
*
6539 AAAAAGAA-AAA
1 AAGAAGAAGAAA
6550 AAGAAGAA-AAA
1 AAGAAGAAGAAA
6561 AA-AAGAA
1 AAGAAGAA
6568 AAGTAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
10 5 0.11
11 19 0.41
12 13 0.28
13 5 0.11
14 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:6526 original size:4 final size:4
Alignment explanation
Indices: 6517--6568 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
6507 GAAGAAGAAG
* *
6517 AAGA AAGA AAGA AAGA AAGAA AAAA AAGA AAAA AAG- AAGA AA-A AA-A
1 AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAGA
6563 AAGA AA
1 AAGA AA
6569 AGTAAAAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 9 0.22
4 29 0.71
5 3 0.07
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:6544 original size:21 final size:20
Alignment explanation
Indices: 6508--6569 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
6498 AAGGAAGAAG
* *
6508 AAGAAGAAGAAGAAAGAAAGA
1 AAGAAGAA-AAAAAAGAAAAA
6529 AAGAAAGAAAAAAAAGAAAAA
1 AAG-AAGAAAAAAAAGAAAAA
6550 AAGAAGAAAAAAAAAGAAAA
1 AAGAAG-AAAAAAAAGAAAA
6570 GTAAAAAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.08
21 29 0.78
22 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAGAAGAAAAAAAAGAAAAA
Found at i:6559 original size:9 final size:9
Alignment explanation
Indices: 6502--6560 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
6492 GGAGCAAAGG
*
6502 AAGAAGAAG
1 AAGAAGAAA
6511 AAGAAGAAGA
1 AAGAAGAA-A
6521 AAGAAAGAAAGA
1 AAG-AAG-AA-A
*
6533 AAGAAAAAA
1 AAGAAGAAA
6542 AAGAA-AAA
1 AAGAAGAAA
6550 AAGAAGAAA
1 AAGAAGAAA
6559 AA
1 AA
6561 AAAAGAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 8 0.18
9 19 0.43
10 5 0.11
11 5 0.11
12 7 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:6569 original size:8 final size:8
Alignment explanation
Indices: 6517--6583 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 8
6507 GAAGAAGAAG
*
6517 AAGAAAGA
1 AAGAAAAA
*
6525 AAGAAAGA
1 AAGAAAAA
6533 AAGAAAAAA
1 AAG-AAAAA
6542 AAGAAAAA
1 AAGAAAAA
6550 AAGAAGAAA
1 AAGAA-AAA
*
6559 AAAAAAGAA
1 AAGAAA-AA
*
6568 AAGTAAAA
1 AAGAAAAA
*
6576 AGGAAAAA
1 AAGAAAAA
6584 TATATTGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
8 30 0.60
9 20 0.40
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (8 bp):
AAGAAAAA
Found at i:6575 original size:6 final size:5
Alignment explanation
Indices: 6505--6575 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
6495 GCAAAGGAAG
*
6505 AAGAA GAAGAA GAAG-A AAG-A AAG-A AAG-A AAGAA AA-AA AAGAA AAAAA
1 AAGAA -AAGAA -AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
*
6552 GAAGAA AAAAA AAGAA AAGTAA AA
1 -AAGAA AAGAA AAGAA AAG-AA AA
6576 AGGAAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
4 19 0.33
5 21 0.37
6 17 0.30
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (5 bp):
AAGAA
Found at i:6582 original size:21 final size:19
Alignment explanation
Indices: 6520--6583 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 19
6510 GAAGAAGAAG
6520 AAAGAAAGAAAGAAAGAAAAA
1 AAAGAAA-AAA-AAAGAAAAA
6541 AAAGAAAAAAAGAAGAAAAAA
1 AAAGAAAAAAA-AAG-AAAAA
*
6562 AAAGAAAAGTAAAAAGGAAAA
1 AAAGAAAA--AAAAAGAAAAA
6583 A
1 A
6584 TATATTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 6 0.16
21 25 0.66
22 3 0.08
23 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAAAAAGAAAAA
Found at i:7981 original size:13 final size:13
Alignment explanation
Indices: 7963--8010 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
7953 CTATTTTATT
7963 ATTGTTTTATTAA
1 ATTGTTTTATTAA
*
7976 ATTGTTTAATTAA
1 ATTGTTTTATTAA
* *
7989 ATGGTTTTAAGTAA
1 ATTGTTTT-ATTAA
8003 ATTGTTTT
1 ATTGTTTT
8011 GGGTGTATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTGTTTTATTAA
Found at i:14723 original size:70 final size:69
Alignment explanation
Indices: 14593--14753 Score: 259
Period size: 70 Copynumber: 2.3 Consensus size: 69
14583 CAGATCTTGG
*
14593 CCAAGTCCTGTCCAGGACTTGGGCTGTTAGGAACACAGAAATACAGGACAAGACCTGGGCAGGAG
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTAGGAACACAGAAATACAGGACAAGACCTGGGCAGGAG
*
14658 TTAC
66 TGAC
* * *
14662 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGCAGAAATACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTT-AGGAACACAGAAATACAGGACAAGACCTGGGCAGGA
14727 GTGAC
65 GTGAC
*
14732 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
14754 TGCGGGAGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 26 0.31
70 58 0.69
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (69 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTAGGAACACAGAAATACAGGACAAGACCTGGGCAGGAG
TGAC
Done.