Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014488.1 Corchorus olitorius cultivar O-4 contig14521, 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: 37622
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1609 original size:42 final size:42
Alignment explanation
Indices: 1533--1624 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1523 CGGGCGTGAC
* *
1533 AGAA-GACATTCCCGTAATTGACACTGATGCTGCGGTTAGGG
1 AGAAGGACATTCCCGCAATTGACACTGATGCTGCGGTTAGAG
* * *
1574 AGAAGGACATTCCCGCAGTTGAGACT-ATTGTTGCGGTTAGAG
1 AGAAGGACATTCCCGCAATTGACACTGA-TGCTGCGGTTAGAG
1616 AGAAGGACA
1 AGAAGGACA
1625 ACGACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
41 5 0.11
42 39 0.89
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (42 bp):
AGAAGGACATTCCCGCAATTGACACTGATGCTGCGGTTAGAG
Found at i:1856 original size:27 final size:26
Alignment explanation
Indices: 1818--1959 Score: 108
Period size: 27 Copynumber: 5.3 Consensus size: 26
1808 ATGCTCATGT
* *
1818 AGTTGGCACTCATGCTGAATTTCCCGC
1 AGTTGGGACTCATGCTGAA-ATCCCGC
* * *
1845 AGTTGGGACTCACGC-CAAAGCCTTCGC
1 AGTTGGGACTCATGCTGAAATCC--CGC
*
1872 AGTTGGGACTCATGCTGAAGCTCCCGC
1 AGTTGGGACTCATGCTGAA-ATCCCGC
* * *
1899 AGTTGGGACTCATGC-CAAAGCCTTCGT
1 AGTTGGGACTCATGCTGAAATCC--CGC
* *
1926 AGTTGGGACTTATGCTGAAGGTCCCGC
1 AGTTGGGACTCATGCTGAA-ATCCCGC
1953 AGTTGGG
1 AGTTGGG
1960 TTTTGTGTTG
Statistics
Matches: 89, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
25 4 0.04
26 4 0.04
27 73 0.82
28 4 0.04
29 4 0.04
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.25
Consensus pattern (26 bp):
AGTTGGGACTCATGCTGAAATCCCGC
Found at i:1900 original size:54 final size:54
Alignment explanation
Indices: 1818--1959 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
1808 ATGCTCATGT
* **
1818 AGTTGGCACTCATGCTGAATTTCCCGCAGTTGGGACTCACGCCAAAGCCTTCGC
1 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCACGCCAAAGCCTTCGC
* *
1872 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCATGCCAAAGCCTTCGT
1 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCACGCCAAAGCCTTCGC
* *
1926 AGTTGGGACTTATGCTGAAGGTCCCGCAGTTGGG
1 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGG
1960 TTTTGTGTTG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.25
Consensus pattern (54 bp):
AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCACGCCAAAGCCTTCGC
Found at i:5498 original size:14 final size:15
Alignment explanation
Indices: 5471--5501 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5461 AGTAGCAGAT
5471 AAAAGAATCAAATGA
1 AAAAGAATCAAATGA
5486 AAAAGAATC-AATGA
1 AAAAGAATCAAATGA
5500 AA
1 AA
5502 TCGAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.68, C:0.06, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAGAATCAAATGA
Found at i:5539 original size:21 final size:20
Alignment explanation
Indices: 5488--5545 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
5478 TCAAATGAAA
*
5488 AAGAATCAA-TGAAATCGAG
1 AAGAATCAAGTGAAATTGAG
**
5507 AAGAATTTAGTGAAAATTGAG
1 AAGAATCAAGTG-AAATTGAG
5528 AAGAATCAAGTGCAAATT
1 AAGAATCAAGTG-AAATT
5546 TGGGGAAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 7 0.23
20 2 0.06
21 22 0.71
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.22
Consensus pattern (20 bp):
AAGAATCAAGTGAAATTGAG
Found at i:7235 original size:37 final size:37
Alignment explanation
Indices: 7185--7279 Score: 172
Period size: 37 Copynumber: 2.6 Consensus size: 37
7175 TATTCACTGG
* *
7185 AAGTTTAGAAACAGACAAATGAAGGAGTTAACATTTC
1 AAGTTGAGAAACAGACAAATAAAGGAGTTAACATTTC
7222 AAGTTGAGAAACAGACAAATAAAGGAGTTAACATTTC
1 AAGTTGAGAAACAGACAAATAAAGGAGTTAACATTTC
7259 AAGTTGAGAAACAGACAAATA
1 AAGTTGAGAAACAGACAAATA
7280 TGATGAACTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (37 bp):
AAGTTGAGAAACAGACAAATAAAGGAGTTAACATTTC
Found at i:11585 original size:6 final size:6
Alignment explanation
Indices: 11545--11608 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
11535 ACTTTTCAGT
* * *
11545 AAAATA AAAA-A AGAAA-A AAGA-A AAAAGA AAAATA AATATA AAAATAA
1 AAAATA AAAATA A-AAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A
11592 AAAATAA AAAATA AAAA
1 AAAAT-A AAAATA AAAA
11609 AATGTCTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 8 0.16
6 29 0.58
7 13 0.26
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (6 bp):
AAAATA
Found at i:11588 original size:32 final size:32
Alignment explanation
Indices: 11546--11608 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
11536 CTTTTCAGTA
11546 AAATAAAAAAAGAAAAAAGAAAAAAGAAAAAT
1 AAATAAAAAAAGAAAAAAGAAAAAAGAAAAAT
* * * *
11578 AAATATAAAAATAAAAAATAAAAAATAAAAA
1 AAATAAAAAAAGAAAAAAGAAAAAAGAAAAA
11609 AATGTCTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (32 bp):
AAATAAAAAAAGAAAAAAGAAAAAAGAAAAAT
Found at i:11594 original size:7 final size:7
Alignment explanation
Indices: 11545--11609 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
11535 ACTTTTCAGT
11545 AAAATAAA
1 AAAAT-AA
*
11553 AAAAGAA
1 AAAATAA
*
11560 AAAAGAA
1 AAAATAA
*
11567 AAAA-GA
1 AAAATAA
11573 AAAAT-A
1 AAAATAA
*
11579 AATAT-A
1 AAAATAA
11585 AAAATAA
1 AAAATAA
11592 AAAATAA
1 AAAATAA
11599 AAAATAA
1 AAAATAA
11606 AAAA
1 AAAA
11610 ATGTCTTCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
6 15 0.29
7 32 0.63
8 4 0.08
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.11
Consensus pattern (7 bp):
AAAATAA
Found at i:12722 original size:67 final size:67
Alignment explanation
Indices: 12614--12745 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 67
12604 GATCCTGGTA
* * *
12614 GTGGAGAATGAAATCAGGGAGGGAGGAAGAAAGAAGAGAAAAAAGAAAAA-AAAATGTAAAAAAA
1 GTGGAGAAAGAAATCAGGGAGGGAGGAAGAAAGAAAAGAAAAAAGAAAAAGAAAAAG-AAAAAAA
12678 GTC
65 GTC
*
12681 GTGGAGAAAGAAGTCAGGGAAGGGA-GAAGAAAGAAAAGAAAAAAGAAAAAGAAAAAGAAAAAAA
1 GTGGAGAAAGAAATCAGGG-AGGGAGGAAGAAAGAAAAGAAAAAAGAAAAAGAAAAAGAAAAAAA
12745 G
65 G
12746 AAATGTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
67 49 0.83
68 10 0.17
ACGTcount: A:0.61, C:0.02, G:0.30, T:0.06
Consensus pattern (67 bp):
GTGGAGAAAGAAATCAGGGAGGGAGGAAGAAAGAAAAGAAAAAAGAAAAAGAAAAAGAAAAAAAG
TC
Found at i:12729 original size:6 final size:6
Alignment explanation
Indices: 12705--12742 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
12695 CAGGGAAGGG
12705 AGAAGAA AG-AAA AGAAAAA AGAAAA AGAAAA AGAAAA A
1 AGAA-AA AGAAAA AG-AAAA AGAAAA AGAAAA AGAAAA A
12743 AAGAAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.14
6 18 0.62
7 7 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:12755 original size:19 final size:19
Alignment explanation
Indices: 12705--12748 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
12695 CAGGGAAGGG
12705 AGAAGAAAG-AAAAGAAAAA
1 AGAA-AAAGAAAAAGAAAAA
12724 AGAAAAAGAAAAAGAAAAAA
1 AGAAAAAGAAAAAG-AAAAA
12744 AGAAA
1 AGAAA
12749 TGTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAAAAGAAAAA
Found at i:19786 original size:11 final size:11
Alignment explanation
Indices: 19766--19800 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
19756 TTGACAGCGC
19766 AACAAAAACAA
1 AACAAAAACAA
*
19777 AACGAAAACAA
1 AACAAAAACAA
19788 AACAAAAACAA
1 AACAAAAACAA
19799 AA
1 AA
19801 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:26648 original size:56 final size:56
Alignment explanation
Indices: 26576--26689 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
26566 TTTATTTTGT
26576 AGAATAATTAAATAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAATAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
* *
26632 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAATAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
26688 AG
1 AG
26690 GAAACAGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (56 bp):
AGAATAATTAAATAGAGATAGGGGGATAGAATTTATTATAACATTTATTGTGTGAA
Found at i:27498 original size:26 final size:26
Alignment explanation
Indices: 27462--27520 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
27452 AAACCACTGT
27462 AAACCAATTGGTTTCATTGATGGAAC
1 AAACCAATTGGTTTCATTGATGGAAC
27488 AAACCAATTGGTTTCATTGATGGAAC
1 AAACCAATTGGTTTCATTGATGGAAC
27514 AAACCAA
1 AAACCAA
27521 GCTCAACCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (26 bp):
AAACCAATTGGTTTCATTGATGGAAC
Found at i:29509 original size:31 final size:29
Alignment explanation
Indices: 29474--29531 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
29464 AAAGTTCAAA
* *
29474 TAAGGGCCTGATATTTTGGGAAAAGGTCATT
1 TAAGGGCCTGA-A-CTTCGGAAAAGGTCATT
*
29505 TAAGGGGCTGAACTTCGGAAAAGGTCA
1 TAAGGGCCTGAACTTCGGAAAAGGTCA
29532 AATCAGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
30 1 0.04
31 10 0.42
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (29 bp):
TAAGGGCCTGAACTTCGGAAAAGGTCATT
Found at i:35487 original size:30 final size:31
Alignment explanation
Indices: 35451--35514 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
35441 CCGCAAACTA
*
35451 CAATTTAGGTTCTAACGTTAGC-TCTTGTGT
1 CAATTTAGGATCTAACGTTAGCGTCTTGTGT
* *
35481 CAATTTAGGATCTAACGTTATCGTGTTGTGT
1 CAATTTAGGATCTAACGTTAGCGTCTTGTGT
35512 CAA
1 CAA
35515 AACAGGTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (31 bp):
CAATTTAGGATCTAACGTTAGCGTCTTGTGT
Done.