Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023232.1 Corchorus olitorius cultivar O-4 contig23265, 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: 22756
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:5314 original size:27 final size:27
Alignment explanation
Indices: 5278--5406 Score: 181
Period size: 27 Copynumber: 4.8 Consensus size: 27
5268 GACTGTTGCC
5278 GCAGTGGATCCTTCCACTTCGACCCCA
1 GCAGTGGATCCTTCCACTTCGACCCCA
* * *
5305 GTAGTGGATCCTCCCACTTCGAGCCCA
1 GCAGTGGATCCTTCCACTTCGACCCCA
5332 GCAGTGGATCC-TCGCACTTCGACCCCA
1 GCAGTGGATCCTTC-CACTTCGACCCCA
*
5359 GCAGTGGATGC-TCACACTTCGACCCCA
1 GCAGTGGATCCTTC-CACTTCGACCCCA
*
5386 GCAGTGGATCCTCCCACTTCG
1 GCAGTGGATCCTTCCACTTCG
5407 CCTCGGGTCG
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 88 0.98
28 1 0.01
ACGTcount: A:0.19, C:0.39, G:0.22, T:0.21
Consensus pattern (27 bp):
GCAGTGGATCCTTCCACTTCGACCCCA
Found at i:7813 original size:32 final size:32
Alignment explanation
Indices: 7776--7960 Score: 221
Period size: 32 Copynumber: 5.8 Consensus size: 32
7766 GTGTGAAAAG
*
7776 AAAACGCCCTTATTTAGCGACGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
** * * *
7808 AAAACGCCCCAATTCAGCGGCGTTTAGAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
* *
7840 ATAACGCCTTTATTTAGCGGCGTCTAATA-AAC
1 AAAACGCCCTTATTTAGCGGCGTCTAA-AGAAC
*
7872 AAAACGCCCTTATTTAGCGGCGTCTGAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
**
7904 AAAACGCTTTTATTTAGCGGCGTCTAATA-AAC
1 AAAACGCCCTTATTTAGCGGCGTCTAA-AGAAC
* *
7936 AAAACGCCTTTATTTAGGGGCGTCT
1 AAAACGCCCTTATTTAGCGGCGTCT
7961 TCAGATCAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.01
32 126 0.98
33 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
Found at i:7942 original size:96 final size:96
Alignment explanation
Indices: 7776--7960 Score: 255
Period size: 96 Copynumber: 1.9 Consensus size: 96
7766 GTGTGAAAAG
* *
7776 AAAACGCCCTTATTTAGCGACGTCTAAAGAACAAAACGCCCCAATTCAGCGGCGTTTAGAGAACA
1 AAAACGCCCTTATTTAGCGACGTCTAAAGAACAAAACGCCCCAATTCAGCGGCGTCTAGAAAACA
*
7841 TAACGCCTTTATTTAGCGGCGTCTAATAAAC
66 AAACGCCTTTATTTAGCGGCGTCTAATAAAC
* * **** *
7872 AAAACGCCCTTATTTAGCGGCGTCTGAAGAACAAAACGCTTTTATTTAGCGGCGTCTA-ATAAAC
1 AAAACGCCCTTATTTAGCGACGTCTAAAGAACAAAACGCCCCAATTCAGCGGCGTCTAGA-AAAC
*
7936 AAAACGCCTTTATTTAGGGGCGTCT
65 AAAACGCCTTTATTTAGCGGCGTCT
7961 TCAGATCAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 76 0.99
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (96 bp):
AAAACGCCCTTATTTAGCGACGTCTAAAGAACAAAACGCCCCAATTCAGCGGCGTCTAGAAAACA
AAACGCCTTTATTTAGCGGCGTCTAATAAAC
Found at i:7971 original size:64 final size:64
Alignment explanation
Indices: 7776--7971 Score: 252
Period size: 64 Copynumber: 3.1 Consensus size: 64
7766 GTGTGAAAAG
* * ** *
7776 AAAACGCCCTTATTTAGCGACGTCTAA-AGAACAAAACGCCCCAATTCAGCGGCGT-TTAGAGAA
1 AAAACGCCTTTATTTAGCGGCGTCTAATA-AACAAAACGCCCTTATTTAGCGGCGTCTTA-AGAA
7839 C
64 C
* *
7840 ATAACGCCTTTATTTAGCGGCGTCTAATAAACAAAACGCCCTTATTTAGCGGCGTCTGAAGAAC
1 AAAACGCCTTTATTTAGCGGCGTCTAATAAACAAAACGCCCTTATTTAGCGGCGTCTTAAGAAC
* * * * *
7904 AAAACGCTTTTATTTAGCGGCGTCTAATAAACAAAACGCCTTTATTTAGGGGCGTCTTCAGATC
1 AAAACGCCTTTATTTAGCGGCGTCTAATAAACAAAACGCCCTTATTTAGCGGCGTCTTAAGAAC
7968 AAAA
1 AAAA
7972 TGCCGCTATA
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
64 113 0.97
65 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
AAAACGCCTTTATTTAGCGGCGTCTAATAAACAAAACGCCCTTATTTAGCGGCGTCTTAAGAAC
Found at i:8094 original size:65 final size:64
Alignment explanation
Indices: 7973--8105 Score: 162
Period size: 65 Copynumber: 2.0 Consensus size: 64
7963 AGATCAAAAT
** *
7973 GCCGCTATATTTAACTGCTTTTAAAAAAAATATAGTGTTAAATACATATATAGCGGCGTCTAA-A
1 GCCGCTATATTTAACTGCTTCCAAAAAAAATATAGTATTAAATACA-ATATAGCGGCGT-TAAGA
8037 C
64 C
* * *
8038 GCCGCTATATTTAATTGCTTCCAAAAATAAATATAGTATTAAATTGC-ATATGGCGGCGTTAAGA
1 GCCGCTATATTTAACTGCTTCCAAAAA-AAATATAGTATTAAA-TACAATATAGCGGCGTTAAGA
8102 C
64 C
8103 GCC
1 GCC
8106 CCCAAATAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
64 3 0.05
65 40 0.68
66 14 0.24
67 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (64 bp):
GCCGCTATATTTAACTGCTTCCAAAAAAAATATAGTATTAAATACAATATAGCGGCGTTAAGAC
Found at i:12588 original size:3 final size:3
Alignment explanation
Indices: 12576--12621 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
12566 TTCTTTACAA
12576 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12622 AGAGAATACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12805 original size:16 final size:16
Alignment explanation
Indices: 12780--12812 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12770 AAGATCTTAT
*
12780 AGTTTCTGTATGGTAC
1 AGTTTATGTATGGTAC
12796 AGTTTATGTATGGTAC
1 AGTTTATGTATGGTAC
12812 A
1 A
12813 CCTACTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (16 bp):
AGTTTATGTATGGTAC
Found at i:12846 original size:2 final size:2
Alignment explanation
Indices: 12839--12873 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12829 ACAATTAGAG
12839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12874 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16782 original size:12 final size:12
Alignment explanation
Indices: 16765--16791 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16755 CCACATCAAG
16765 TTTATAGTTAAA
1 TTTATAGTTAAA
16777 TTTATAGTTAAA
1 TTTATAGTTAAA
16789 TTT
1 TTT
16792 GTACCACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTATAGTTAAA
Found at i:19880 original size:24 final size:24
Alignment explanation
Indices: 19851--19896 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
19841 TACTACCACT
* *
19851 AGAATTCCATACTGATTCGGGACC
1 AGAATTCCATAATAATTCGGGACC
19875 AGAATTCCATAATAATTCGGGA
1 AGAATTCCATAATAATTCGGGA
19897 AGCTATGGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (24 bp):
AGAATTCCATAATAATTCGGGACC
Found at i:20056 original size:45 final size:45
Alignment explanation
Indices: 19967--20056 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
19957 GAAATTGTGT
* * * *
19967 AGATTTCTTGACTAATATGGGTCAAGCTTCCTTTTTTGGTTGCAC
1 AGATTTCTTGACTAATATGGGTCAAGCCTCCTCTTTTAGCTGCAC
* * *
20012 AGATTTTTTGGCTAGTATGGGTCAAGCCTCCTCTTTTAGCTGCAC
1 AGATTTCTTGACTAATATGGGTCAAGCCTCCTCTTTTAGCTGCAC
20057 GGTTCTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (45 bp):
AGATTTCTTGACTAATATGGGTCAAGCCTCCTCTTTTAGCTGCAC
Found at i:20227 original size:18 final size:18
Alignment explanation
Indices: 20188--20227 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20178 TTCTACTATG
* **
20188 TTTTGTTTTTGTTTTTGT
1 TTTTGTTTTCGTTTTTAC
20206 TTTTGTTTTCGTTTTTAC
1 TTTTGTTTTCGTTTTTAC
20224 TTTT
1 TTTT
20228 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.05, G:0.12, T:0.80
Consensus pattern (18 bp):
TTTTGTTTTCGTTTTTAC
Found at i:20235 original size:6 final size:6
Alignment explanation
Indices: 20188--20221 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
20178 TTCTACTATG
*
20188 TTTTGT TTTTGT TTTTGT TTTTGT TTTCGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
20222 ACTTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (6 bp):
TTTTGT
Found at i:20359 original size:21 final size:23
Alignment explanation
Indices: 20323--20364 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
20313 AACTTATAAA
*
20323 TCATAGTATAATTTTATATATAT
1 TCATAGTATAATTTTAGATATAT
20346 TCAT-GTAT-ATTTTAGATAT
1 TCATAGTATAATTTTAGATAT
20365 CTTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (23 bp):
TCATAGTATAATTTTAGATATAT
Found at i:20527 original size:16 final size:16
Alignment explanation
Indices: 20506--20537 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20496 TAAATCTAAG
20506 GCTAAAAGTCCAATTT
1 GCTAAAAGTCCAATTT
20522 GCTAAAAGTCCAATTT
1 GCTAAAAGTCCAATTT
20538 TAGCCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
GCTAAAAGTCCAATTT
Found at i:21896 original size:24 final size:25
Alignment explanation
Indices: 21867--21917 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
21857 ATAGAGTAAC
*
21867 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
21891 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
21916 AA
1 AA
21918 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Done.