Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024431.1 Corchorus olitorius cultivar O-4 contig24464, 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: 9951
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:212 original size:2 final size:2
Alignment explanation
Indices: 205--243 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
195 CTTTAAACTT
*
205 TA TA TA TA TA TA TA TA TA TA TG TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
244 CAAATGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2335 original size:31 final size:32
Alignment explanation
Indices: 2274--2338 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
2264 ACGAGTTTTG
* *
2274 TAAAACTTTTGAATCGCCTATTATATCCTTAT
1 TAAAACTTTTGAATCGCCTATCATACCCTTAT
*
2306 TAAAA-TTTTGAATCGCCTATCATGCCCTTAT
1 TAAAACTTTTGAATCGCCTATCATACCCTTAT
2337 TA
1 TA
2339 TTCGAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.42
Consensus pattern (32 bp):
TAAAACTTTTGAATCGCCTATCATACCCTTAT
Found at i:2584 original size:23 final size:21
Alignment explanation
Indices: 2550--2598 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
2540 GTTAAGTGAA
2550 TAAAAAATATTTTAAAATTA-T
1 TAAAAAATATTTT-AAATTACT
*
2571 TAAAAAAGTAATTTTTAATTACT
1 TAAAAAA-T-ATTTTAAATTACT
2594 TAAAA
1 TAAAA
2599 TAAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAAATATTTTAAATTACT
Found at i:2634 original size:18 final size:18
Alignment explanation
Indices: 2595--2632 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2585 TTAATTACTT
2595 AAAATAAAAAAGAAAACG
1 AAAATAAAAAAGAAAACG
2613 AAAATAAAAAA-AAAA-G
1 AAAATAAAAAAGAAAACG
2629 AAAA
1 AAAA
2633 AAAGTAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 4 0.20
18 11 0.55
ACGTcount: A:0.84, C:0.03, G:0.08, T:0.05
Consensus pattern (18 bp):
AAAATAAAAAAGAAAACG
Found at i:4606 original size:164 final size:163
Alignment explanation
Indices: 4364--4785 Score: 650
Period size: 164 Copynumber: 2.6 Consensus size: 163
4354 AAATTACCGT
* ** ** * *
4364 ATGAACAAACCCTAAAATTTCTAGAAATTTCCCAAATACCCAGAAACAATTCATAGCAATAACTG
1 ATGAACAAACACT-AAATTTCCCGAAAAATCGCAAATACCCATAAACAATTCATAGCAATAACTG
4429 ATAATAAAACACTTTTTTACCAAAACCCATAAAAAAACATCTATTTTAACCCAAATTCCCTATCA
65 ATAAT-AAACACTTTTTTACCAAAACCCATAAAAAAACATCTATTTTAACCCAAATTCCCTATCA
4494 TTTTAACTCATAAAACCTAATTCCCAATCAAACTG
129 TTTTAACTCATAAAACCTAATTCCCAATCAAACTG
4529 ATGAACAAACACTAAATTTCCCGAAAAATCGCAAATACCCATAAACAATTCATAGCAATAACTGA
1 ATGAACAAACACTAAATTTCCCGAAAAATCGCAAATACCCATAAACAATTCATAGCAATAACTGA
* * * * *
4594 TAATAGAACACTTTTTTACCAAAGCCCATAACAAAATATCTATTTTAACCCAAATTTCCTATTAT
66 TAATA-AACACTTTTTTACCAAAACCCATAAAAAAACATCTATTTTAACCCAAATTCCCTATCAT
4659 TTTAACTCATAAAACCTAATTCCCAATCAAACTG
130 TTTAACTCATAAAACCTAATTCCCAATCAAACTG
* *
4693 ATGAACAAACACTAAATTTCCCGAAAAATCGCAAATACCCATAAATAATTCATACCAATTAA-TG
1 ATGAACAAACACTAAATTTCCCGAAAAATCGCAAATACCCATAAACAATTCATAGCAA-TAACTG
* *
4757 ATAATAAA-ACCTTTTTAGCAAAACCCATA
65 ATAATAAACACTTTTTTACCAAAACCCATA
4786 TCAGAAAACC
Statistics
Matches: 238, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
162 18 0.08
163 3 0.01
164 202 0.85
165 15 0.06
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (163 bp):
ATGAACAAACACTAAATTTCCCGAAAAATCGCAAATACCCATAAACAATTCATAGCAATAACTGA
TAATAAACACTTTTTTACCAAAACCCATAAAAAAACATCTATTTTAACCCAAATTCCCTATCATT
TTAACTCATAAAACCTAATTCCCAATCAAACTG
Found at i:5294 original size:29 final size:32
Alignment explanation
Indices: 5230--5297 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 32
5220 AGACGGTCTG
* * *
5230 CCCCAAATTGACGCGAATTGAAAACGTTTTGA
1 CCCCAAATAGACGCAAATTGAAAACGTTGTGA
5262 -CCCAAATAGAC-CAAATTG-AAACGTTGT-A
1 CCCCAAATAGACGCAAATTGAAAACGTTGTGA
5290 CCCCAAAT
1 CCCCAAAT
5298 TAGCCCGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 15 0.47
30 6 0.19
31 10 0.31
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (32 bp):
CCCCAAATAGACGCAAATTGAAAACGTTGTGA
Found at i:8415 original size:2 final size:2
Alignment explanation
Indices: 8404--8439 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
8394 TACTATTTAG
8404 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8440 CACTTACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8849 original size:18 final size:18
Alignment explanation
Indices: 8823--8867 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
8813 CTTCAGTACT
*
8823 CTCTGCTTTTTTTTTCGC
1 CTCTTCTTTTTTTTTCGC
8841 CTCTTCTTTTTTTTTCGC
1 CTCTTCTTTTTTTTTCGC
*
8859 TTCTTCTTT
1 CTCTTCTTT
8868 CCTCTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.67
Consensus pattern (18 bp):
CTCTTCTTTTTTTTTCGC
Done.