Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023925.1 Corchorus olitorius cultivar O-4 contig23958, 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: 28212
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5528 original size:34 final size:32
Alignment explanation
Indices: 5490--5558 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5480 AAGAAATTCA
5490 AATAAAAAAAATCATCAA-AAATCAAATCAAAGTC
1 AATAAAAAAAA--ATCAACAAATCAAATCAAA-TC
5524 AATAAAAAAAAATCAATCAAATCAAATCAAATC
1 AATAAAAAAAAATCAA-CAAATCAAATCAAATC
5557 AA
1 AA
5559 AATCAAAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 5 0.15
33 4 0.12
34 24 0.73
ACGTcount: A:0.67, C:0.14, G:0.01, T:0.17
Consensus pattern (32 bp):
AATAAAAAAAAATCAACAAATCAAATCAAATC
Found at i:5541 original size:4 final size:5
Alignment explanation
Indices: 5508--5565 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
5498 AAATCATCAA
* **
5508 AAATC AAATC AAAGTC -AATA AAAAA AAATC -AATC AAATC AAATC AAATC
1 AAATC AAATC AAA-TC AAATC AAATC AAATC AAATC AAATC AAATC AAATC
5557 AAAATC AAA
1 -AAATC AAA
5566 GGAAAATGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 5 0.11
5 33 0.73
6 7 0.16
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.17
Consensus pattern (5 bp):
AAATC
Found at i:5553 original size:39 final size:35
Alignment explanation
Indices: 5493--5564 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 35
5483 AAATTCAAAT
*
5493 AAAAAAAATCATCAAAAATCAAATCAAAGTCAATA
1 AAAAAAAATCATCAAAAATCAAATCAAAATCAATA
5528 AAAAAAAATCAATCAAATCAAATCAAATCAAAATCAA
1 AAAAAAAATC-ATC-AA--AAATCAAATCAAAATCAA
5565 AGGAAAATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 10 0.31
36 3 0.09
37 2 0.06
39 17 0.53
ACGTcount: A:0.67, C:0.15, G:0.01, T:0.17
Consensus pattern (35 bp):
AAAAAAAATCATCAAAAATCAAATCAAAATCAATA
Found at i:6257 original size:50 final size:50
Alignment explanation
Indices: 6179--6321 Score: 198
Period size: 50 Copynumber: 2.9 Consensus size: 50
6169 CGATAAGATT
*
6179 GCATTCCATTTGTGAGCCCAAGAG-CAAAATTCGCTTTTCAAAGTAAAATC
1 GCATTCCATTTGTGAGTCCAAG-GTCAAAATTCGCTTTTCAAAGTAAAATC
* * * * * *
6229 GCTTTCCATTTGTGAGTTCAAGGTCAAAATTTGCTTTTCGAAGTAAGATT
1 GCATTCCATTTGTGAGTCCAAGGTCAAAATTCGCTTTTCAAAGTAAAATC
*
6279 GCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 GCATTCCATTTGTGAGTCCAAGGTCAAAATTCGCTTTTCAAAG
6322 GACATTGAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 79 0.99
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (50 bp):
GCATTCCATTTGTGAGTCCAAGGTCAAAATTCGCTTTTCAAAGTAAAATC
Found at i:7188 original size:50 final size:50
Alignment explanation
Indices: 7095--7273 Score: 290
Period size: 50 Copynumber: 3.6 Consensus size: 50
7085 TGCATTACCT
7095 TTTTAAGATTGAATTGGT--ACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
7143 TTTTAAGATTGAATTGGTAGACGGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
7193 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * * *
7243 TTTTAATATTAAATTGGGAGACAATTCAAAG
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAG
7274 AAGTTGATCG
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 18 0.15
50 103 0.85
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:7532 original size:27 final size:27
Alignment explanation
Indices: 7494--7589 Score: 104
Period size: 28 Copynumber: 3.5 Consensus size: 27
7484 ATTTACTGTT
* *
7494 ATTTTGGTCATTTGGATGGCTAGGGGC
1 ATTTTGGTCATTTGGATGCCCAGGGGC
* **
7521 ATTTTGGTCATTTTGTACACCCAGGGGC
1 ATTTTGGTCA-TTTGGATGCCCAGGGGC
*
7549 ATTTTGGTCATTTTG-TGCACCCAGGGGC
1 ATTTTGGTCATTTGGATG--CCCAGGGGC
7577 ATTTTGGTCATTT
1 ATTTTGGTCATTT
7590 CAAGAACCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
27 13 0.23
28 44 0.77
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.40
Consensus pattern (27 bp):
ATTTTGGTCATTTGGATGCCCAGGGGC
Found at i:7547 original size:28 final size:28
Alignment explanation
Indices: 7515--7589 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
7505 TTGGATGGCT
7515 AGGGGCATTTTGGTCATTTTGTACACCC
1 AGGGGCATTTTGGTCATTTTGTACACCC
*
7543 AGGGGCATTTTGGTCATTTTGTGCACCC
1 AGGGGCATTTTGGTCATTTTGTACACCC
7571 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
7590 CAAGAACCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGTACACCC
Found at i:12921 original size:31 final size:31
Alignment explanation
Indices: 12886--12945 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12876 ATTGGACGAA
* *
12886 ATAAAAGGTTTCGTACTAAATTGGTATTTTC
1 ATAAAAGGTTTCGTACCAAATTGGGATTTTC
*
12917 ATAAAAGGTTTGGTACCAAATTGGGATTT
1 ATAAAAGGTTTCGTACCAAATTGGGATTT
12946 CAGCCTCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (31 bp):
ATAAAAGGTTTCGTACCAAATTGGGATTTTC
Found at i:15566 original size:3 final size:3
Alignment explanation
Indices: 15558--15585 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15548 CGTCTCCCCT
15558 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
15586 AATTGAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:21840 original size:30 final size:29
Alignment explanation
Indices: 21781--21850 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
21771 TGCCAACGGT
* ** *
21781 CAAATAAGCCTCTGAACTTCAATTTTGGC
1 CAAATAAGCCCCTGAACACCAAATTTGGC
21810 CAAATAAGCCCCTGAACCACCAAATTTGGC
1 CAAATAAGCCCCTGAA-CACCAAATTTGGC
* *
21840 CAGATTAGCCC
1 CAAATAAGCCC
21851 TTCTGCTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACACCAAATTTGGC
Found at i:22097 original size:29 final size:30
Alignment explanation
Indices: 22042--22111 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
22032 CATAGCAGAA
* * *
22042 GGGCTTATTTTGTCAAAATTGGTAGTTCAG
1 GGGCTTATTTGGCCAAAATTGGAAGTTCAG
22072 GGGCTTATTTGGCCAAAATT-GAAGTTCAG
1 GGGCTTATTTGGCCAAAATTGGAAGTTCAG
22101 GGGCTTATTTG
1 GGGCTTATTTG
22112 ACCGTTGGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (30 bp):
GGGCTTATTTGGCCAAAATTGGAAGTTCAG
Found at i:22297 original size:33 final size:34
Alignment explanation
Indices: 22255--22321 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
22245 GAATACATAC
*
22255 GATTTTACTATGTATTTTATTCCACCA-TAAAAA
1 GATTTTACTATGTATATTATTCCACCATTAAAAA
22288 GATTTTACTATGTATATTATTCCACCATTAAAAA
1 GATTTTACTATGTATATTATTCCACCATTAAAAA
22322 ATCGAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (34 bp):
GATTTTACTATGTATATTATTCCACCATTAAAAA
Done.