Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020320.1 Corchorus olitorius cultivar O-4 contig20353, 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: 8241
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1057 original size:3 final size:3
Alignment explanation
Indices: 1049--1089 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1039 CACATGAACT
1049 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1090 CATAATCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:4305 original size:22 final size:22
Alignment explanation
Indices: 4280--4900 Score: 197
Period size: 22 Copynumber: 28.5 Consensus size: 22
4270 ATTACGCTAT
*
4280 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
4302 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
4324 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * * **
4346 TTTCGA-GATCTTTTTAT-AAA
1 TTTTGATAACCTTCCTATGAAA
** *
4366 TTTCTTTTAACCTTCTTATGAAA
1 TTT-TGATAACCTTCCTATGAAA
* * * *
4389 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
**
4411 TTTT-A-AAGATCTCACTATGAAA
1 TTTTGATAACCT-TC-CTATGAAA
* * *
4433 TTTCGATAA-CTTCCCAATAAAA
1 TTTTGATAACCTT-CCTATGAAA
*
4455 TTTTGATAA-CTAAT-CTATGAGA
1 TTTTGATAACCT--TCCTATGAAA
* * *
4477 TGTTGATAA-CTTACATATG-AT
1 TTTTGATAACCTT-CCTATGAAA
* *
4498 TTATTGATAACC-ACATTATGAAA
1 TT-TTGATAACCTTC-CTATGAAA
* * *
4521 ATTT-AAAAACTTCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* ** *
4542 TTGTT-AGTAATCACCCTCTGAAA
1 TT-TTGA-TAACCTTCCTATGAAA
* *
4565 TTTTGATAATC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * *
4587 TTGTAATAACC-TCGTTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
*
4609 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
4632 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
4655 TTTTGATAACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* * *
4677 TCTTGATAA--TTACTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
*
4696 TTTTGATAGCCTCTCCCTATGAAA
1 TTTTGATAACCT-T-CCTATGAAA
* * *
4720 TTTTGATCTA-CATACTATGAAA
1 TTTTGAT-AACCTTCCTATGAAA
* * *
4742 TTTTGATAACCCTCTTGTGAAA
1 TTTTGATAACCTTCCTATGAAA
* **
4764 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
* *
4786 TTTTGATAACGTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
4808 TTTTGATATCC-TCC-CTGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
4828 TTTTGATTA-C-TCCATAATAAAA
1 TTTTGATAACCTTCC-T-ATGAAA
* *
4850 GTTTAATAACCTTCC--T--AA
1 TTTTGATAACCTTCCTATGAAA
* * *
4868 -TTTGGTAACCATACTATGAAA
1 TTTTGATAACCTTCCTATGAAA
4889 TTTTGATAACCT
1 TTTTGATAACCT
4901 CTCCAGAAAT
Statistics
Matches: 434, Mismatches: 118, Indels: 94
0.67 0.18 0.15
Matches are distributed among these distances:
17 10 0.02
18 2 0.00
19 15 0.03
20 24 0.06
21 29 0.07
22 263 0.61
23 72 0.17
24 19 0.04
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:4632 original size:23 final size:23
Alignment explanation
Indices: 4606--4685 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
4596 CCTCGTTATG
4606 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
4629 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
4652 AAATTTTGAT-AACC-TCCTTATG
1 AAATTTTGATAAACCTTCC-TATA
*
4674 AAATCTTGATAA
1 AAATTTTGATAA
4686 TTACTACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.31
23 33 0.65
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCCTATA
Found at i:4739 original size:65 final size:64
Alignment explanation
Indices: 4629--4750 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 64
4619 CCTTCCTATA
* *
4629 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAATTACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATACTTATGAAATCTTGATAATTACTAC
** * * *
4693 AAATTTTGATAGCCTCTCCCTATGAAATTTTGATCTACATAC-TATGAAATTTTGATAA
1 AAATTTTGATAAAC-CTCCCTATAAAATTTTGAT-AACATACTTATGAAATCTTGATAA
4751 CCCTCTTGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
64 12 0.24
65 33 0.67
66 4 0.08
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (64 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATACTTATGAAATCTTGATAATTACTAC
Found at i:4948 original size:22 final size:22
Alignment explanation
Indices: 4916--5039 Score: 126
Period size: 22 Copynumber: 5.6 Consensus size: 22
4906 GAAATACCAT
4916 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCTCTC
* * * *
4938 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTC
*
4960 TATGAAATTTTGATAA-TTACAT-
1 TATGAAATTTTGATAACCT-C-TC
* *
4982 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTCTC
* **
5004 TTTGAAATTTTGATAACAACTC
1 TATGAAATTTTGATAACCTCTC
5026 TATGAAATTTTGAT
1 TATGAAATTTTGAT
5040 CATCTTCCTA
Statistics
Matches: 80, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
22 78 0.98
23 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTC
Found at i:5027 original size:66 final size:66
Alignment explanation
Indices: 4913--5039 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
4903 CCAGAAATAC
* * * **
4913 CATTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTATGAAATTTTGATAATT
1 CATTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACAACTCTATGAAATTTTGATAATT
4978 A
66 A
* * *
4979 CATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACTCTATGAAATTTTGAT
1 CATTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACAACTCTATGAAATTTTGAT
5040 CATCTTCCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (66 bp):
CATTATGAAATTTTGATAACCTCGCTATAAAATTTTGATAACAACTCTATGAAATTTTGATAATT
A
Found at i:6001 original size:35 final size:36
Alignment explanation
Indices: 5954--6038 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
5944 GGCCTGGCAC
*
5954 GGCCCAAGCGCCCAGTCCAGGCGCG-GG-CCAGCGCAT
1 GGCCC-AGCGCCCAGGCCAGGCGCGCGGTCCAGC-CAT
* * *
5990 GGCCCAGCGCCCAGGCCTGGCGCGCGGTCTAGCCCT
1 GGCCCAGCGCCCAGGCCAGGCGCGCGGTCCAGCCAT
6026 GGCCCAGCGCCCA
1 GGCCCAGCGCCCA
6039 AGTTTGGGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 17 0.40
36 22 0.51
37 4 0.09
ACGTcount: A:0.13, C:0.45, G:0.35, T:0.07
Consensus pattern (36 bp):
GGCCCAGCGCCCAGGCCAGGCGCGCGGTCCAGCCAT
Done.