Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013576.1 Corchorus olitorius cultivar O-4 contig13609, 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: 26468
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:2325 original size:21 final size:21
Alignment explanation
Indices: 2300--2341 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2290 TTAGAAACCC
2300 TAGTACCACTTAG-ATCCAATT
1 TAGTACCACTT-GTATCCAATT
2321 TAGTACCACTTGTATCCAATT
1 TAGTACCACTTGTATCCAATT
2342 GGGCTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (21 bp):
TAGTACCACTTGTATCCAATT
Found at i:2792 original size:17 final size:17
Alignment explanation
Indices: 2754--2792 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2744 AAGCCACAAT
2754 AAATTTTTAAATCTTCA
1 AAATTTTTAAATCTTCA
* * *
2771 GAATTTTTAGATCTTGA
1 AAATTTTTAAATCTTCA
2788 AAATT
1 AAATT
2793 GAAAGTTGCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (17 bp):
AAATTTTTAAATCTTCA
Found at i:4395 original size:65 final size:66
Alignment explanation
Indices: 4314--4461 Score: 185
Period size: 66 Copynumber: 2.3 Consensus size: 66
4304 ACAAAGTTTG
* * * * *
4314 CCCTTTGACCGAAAGGGGATTTTTGGAAA-CTAGAGTAAACTGAAATGCGAA-AATGA-TGAAAC
1 CCCTTTGACCGAAAGGGGATTTTTGGAAATCAAAAGAAAACTCAAATGC-AAGAATGACAG-AAC
4376 TGA
64 TGA
* * *
4379 CCCTTTCACCGAAAGGGTATTTTTGGAAATCAAAAGAAAACTCAAATGCAAGAATGACAGAATTG
1 CCCTTTGACCGAAAGGGGATTTTTGGAAATCAAAAGAAAACTCAAATGCAAGAATGACAGAACTG
4444 A
66 A
4445 CCCTTTGACCGAAAGGG
1 CCCTTTGACCGAAAGGG
4462 TAATTTGGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
65 29 0.41
66 41 0.58
67 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (66 bp):
CCCTTTGACCGAAAGGGGATTTTTGGAAATCAAAAGAAAACTCAAATGCAAGAATGACAGAACTG
A
Found at i:4580 original size:68 final size:66
Alignment explanation
Indices: 4314--4741 Score: 249
Period size: 68 Copynumber: 6.5 Consensus size: 66
4304 ACAAAGTTTG
* * * * * * * * *
4314 CCCTTTGACCGAAAGGGGATTTTTGGAAACTAG-AGTA--AACTGAAATGCGAAAATGATGAAAC
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-AAGAAATACTTACTTAAATGC-AAAAAGACGAAAA
4376 TGA
64 TGA
* * ** * *
4379 CCCTTTC-ACCGAAAGGGTATTTTTGGAAATCA-AAAGA-AAACTCAAATGCAAGAATGAC-AGA
1 CCC-TTCGACCGAAAGGGTATTTTTGGAAA-AAGAAATACTTACTTAAATGCAA-AAAGACGA-A
*
4440 ATTGA
62 AATGA
* * * ** * * ** *
4445 CCCTTTGACCGAAAGGGTA-ATTTGGGAAAACTAA-ACTAACTTAGACATG-GAAAAGTTGAAAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACTTACTTA-A-ATGCAAAAAGACGAAAA
4507 TGA
64 TGA
* * * **
4510 CCCTTCGACCAAAATGGCATTTTTGGAAAAAGAAAGTACTTGACTTAGGTGCAAAAAGACGAAAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAA-TACTT-ACTTAAATGCAAAAAGACGAAAA
*
4575 CGA
64 TGA
* * *
4578 CCCTCCGACTGAAAGGGTATTTTTGGAAACACG-AAT-C-TA---AAATGCAAAAAGACGAAAAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-AAGAAATACTTACTTAAATGCAAAAAGACGAAAAT
4637 GA
65 GA
* * * * *
4639 CCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAACACTAAACTTAAATGCAAATAGATGAAAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAAAG-AAATACT-TACTTAAATGCAAAAAGACGAAAA
4704 TGA
64 TGA
* *
4707 CCCTTCGATCGAAAGGGTATTTTTGGAAATAGAAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAA
4742 ATAGAGCTTT
Statistics
Matches: 284, Mismatches: 54, Indels: 48
0.74 0.14 0.12
Matches are distributed among these distances:
60 1 0.00
61 46 0.16
62 2 0.01
63 1 0.00
64 3 0.01
65 72 0.25
66 52 0.18
67 9 0.03
68 91 0.32
69 7 0.02
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.23
Consensus pattern (66 bp):
CCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAATACTTACTTAAATGCAAAAAGACGAAAATG
A
Found at i:4661 original size:129 final size:129
Alignment explanation
Indices: 4502--4735 Score: 317
Period size: 129 Copynumber: 1.8 Consensus size: 129
4492 TGGAAAAGTT
* * ** ** **
4502 GAAATTGACCCTTCGACCAAAATGGCATTTTTGGAAAAAGAAAGTACTTGACTTAGGTGCAAAAA
1 GAAAATGACCCTTCGACCAAAAGGGCATTTTTGGAAAAAGAAAACACTAAACTTAAATGCAAAAA
4567 GACGAAAACGACCCTCCGA-CTGAAAGGGTATTTTTGGAAACACGAATCTAAAATGCAAAAAGAC
66 GACGAAAACGACCCTCCGATC-GAAAGGGTATTTTTGGAAACACGAATCTAAAATGCAAAAAGAC
* * * *
4631 GAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATAGAAAACACTAAACTTAAATGCAAATA
1 GAAAATGACCCTTCGACCAAAAGGGCATTTTTGGAAAAAGAAAACACTAAACTTAAATGCAAAAA
* * *
4696 GATGAAAATGACCCTTCGATCGAAAGGGTATTTTTGGAAA
66 GACGAAAACGACCCTCCGATCGAAAGGGTATTTTTGGAAA
4736 TAGAAAATAG
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
129 88 0.99
130 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (129 bp):
GAAAATGACCCTTCGACCAAAAGGGCATTTTTGGAAAAAGAAAACACTAAACTTAAATGCAAAAA
GACGAAAACGACCCTCCGATCGAAAGGGTATTTTTGGAAACACGAATCTAAAATGCAAAAAGAC
Found at i:5577 original size:15 final size:15
Alignment explanation
Indices: 5557--5593 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
5547 TTTAAAGAAG
5557 CCCAATCCCATTCAA
1 CCCAATCCCATTCAA
5572 CCCAATCCCATTCAA
1 CCCAATCCCATTCAA
*
5587 ACCAATC
1 CCCAATC
5594 TTGATTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (15 bp):
CCCAATCCCATTCAA
Found at i:9795 original size:2 final size:2
Alignment explanation
Indices: 9790--9814 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9780 AAGGGATTTA
9790 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9815 ACAAAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10245 original size:1 final size:1
Alignment explanation
Indices: 10200--10227 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
10190 TTAGGCTGAG
10200 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
10228 AAAAGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16087 original size:21 final size:21
Alignment explanation
Indices: 16048--16088 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16038 TGGATGGTAA
*
16048 GAAAACTTTTTCTCTCTTTTG
1 GAAAACTTTTTCTCCCTTTTG
16069 GAAAACTTTTTC-CACCTTTT
1 GAAAACTTTTTCTC-CCTTTT
16089 ACTGATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (21 bp):
GAAAACTTTTTCTCCCTTTTG
Found at i:26300 original size:2 final size:2
Alignment explanation
Indices: 26295--26343 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
26285 TATATATATA
26295 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
26337 TG TG TG T
1 TG TG TG T
26344 ATATCAATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Done.