Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023383.1 Corchorus olitorius cultivar O-4 contig23416, 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: 20661
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:578 original size:52 final size:52
Alignment explanation
Indices: 518--622 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
508 AAAAAAGATT
*
518 GCAGGACAACTTCGGCCTAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
570 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
1 GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
622 G
1 G
623 GAAAGAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (52 bp):
GCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGC
Found at i:612 original size:22 final size:22
Alignment explanation
Indices: 576--619 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
566 TTGCGCAGGA
*
576 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
598 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
620 GCGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:2703 original size:26 final size:26
Alignment explanation
Indices: 2654--2700 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2644 CTTAAAAATT
2654 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATGGATGAGATGGA
2680 TGAAAAAC-TTGAT-GAT-AGATG
1 TGAAAAACTTTGATGGATGAGATG
2701 ATGCGCCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (26 bp):
TGAAAAACTTTGATGGATGAGATGGA
Found at i:4941 original size:20 final size:21
Alignment explanation
Indices: 4904--4948 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
4894 AATTTTGTGT
4904 TTTGCGTCAAAGAAAAAAAAA
1 TTTGCGTCAAAGAAAAAAAAA
* *
4925 TTTGCGTTAAA-AAAAAAAAT
1 TTTGCGTCAAAGAAAAAAAAA
4945 TTTG
1 TTTG
4949 TTCCTGCGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (21 bp):
TTTGCGTCAAAGAAAAAAAAA
Found at i:8057 original size:21 final size:21
Alignment explanation
Indices: 8008--8051 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
7998 CGCCCATTCA
*
8008 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGTCAAGC
*
8029 CCGTGCCACCACCGGTCATGC
1 CCGTGCCACCACCGGTCAAGC
8050 CC
1 CC
8052 TAGCCATCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.14
Consensus pattern (21 bp):
CCGTGCCACCACCGGTCAAGC
Found at i:12607 original size:15 final size:15
Alignment explanation
Indices: 12587--12615 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12577 TGGAGGTTCG
12587 AAATCAACAAGCTCA
1 AAATCAACAAGCTCA
12602 AAATCAACAAGCTC
1 AAATCAACAAGCTC
12616 CACTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAACAAGCTCA
Found at i:13249 original size:33 final size:33
Alignment explanation
Indices: 13202--13282 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
13192 GTGTTTTAGA
* * *
13202 TGTTTTTTGCGATGATACTAAACCTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG
* * *
13235 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG
13268 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
13283 AACAAATTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 4 0.10
33 37 0.90
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTATTTGAGG
Found at i:13294 original size:33 final size:31
Alignment explanation
Indices: 13229--13333 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 31
13219 CTAAACCTAA
*
13229 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
1 TTTG-GTGTTGTTTGTGATGAAAC-AAATCTGT
13262 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
1 TTT-GGTGTTGTTTGTGATGAAACAAA-TCTGT
**
13295 TTTGGATGTTAATTGTGATGAAAACAAATCTGT
1 TTTGG-TGTTGTTTGTGATG-AAACAAATCTGT
13328 TTTGGT
1 TTTGGT
13334 TGATCATAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
32 6 0.09
33 51 0.78
34 8 0.12
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.45
Consensus pattern (31 bp):
TTTGGTGTTGTTTGTGATGAAACAAATCTGT
Found at i:18137 original size:21 final size:21
Alignment explanation
Indices: 18113--18183 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
18103 CTTAGGCAAT
18113 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
18134 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
18155 TCCAATGACCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
18176 TCCAATGA
1 TCCAATGA
18184 ACTCCTAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:19005 original size:34 final size:33
Alignment explanation
Indices: 18952--19016 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
18942 TTTAGCATCC
*
18952 AAAACAGAATTTGTTTCATCACAAACAACACCT
1 AAAACAGAATTTGTGTCATCACAAACAACACCT
*
18985 AAAACAGATTTTAGTGTCATCACAAACAACAC
1 AAAACAGAATTT-GTGTCATCACAAACAACAC
19017 TCAAATTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (33 bp):
AAAACAGAATTTGTGTCATCACAAACAACACCT
Found at i:19065 original size:34 final size:32
Alignment explanation
Indices: 18952--19070 Score: 98
Period size: 34 Copynumber: 3.6 Consensus size: 32
18942 TTTAGCATCC
18952 AAAACAGAATTT-GT-TTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTATT-ATCACAAACAACA-CT
* *
18985 AAAACAGATTTTAGTGTCATCACAAACAACACT
1 AAAACAGA-TTTAGTATTATCACAAACAACACT
** * *
19018 CAAATTAGGTTTAGTATTATTCGCAAACAACATCT
1 -AAAACAGATTTAGTATTA-TCACAAACAACA-CT
*
19053 AAAACAGATTTAGAATTA
1 AAAACAGATTTAGTATTA
19071 CTCTTTGAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
32 1 0.01
33 20 0.29
34 45 0.65
35 3 0.04
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (32 bp):
AAAACAGATTTAGTATTATCACAAACAACACT
Done.