Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024321.1 Corchorus olitorius cultivar O-4 contig24354, 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: 9843
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:349 original size:201 final size:199
Alignment explanation
Indices: 1--390 Score: 591
Period size: 201 Copynumber: 1.9 Consensus size: 199
* *
1 CGTGTGGGGTTTAAGGGTTGACATGTGTCCCTTTAGGAAATATGTATTAATATTAAATATTTAAT
1 CGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGAAATATGTATTAATATTAAATATTTAAT
* * *
66 TAATTATGAAATGGAGTATGTGTCAACTTCTTAACCCACTTATGGAGTCTAAAATTTACACTAAC
66 TAATTATAAAATGGAGTATGTGTCAACTTCCTAACCCACTTATGGAGTCCAAAATTTACACTAAC
* * * *
131 AGTGAATTGTATAATAATCCTATAAGAAAAAGTATACAATACACCGTCAGTGGAGTTTAGCAGAC
131 AGTGAATAGTATAATAATCATATAAGAAAAAGTATACAATAAACCGTCACTGGAGTTTAGCAGAC
196 TGCA
196 TGCA
* *
200 CGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTT
1 CGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGAAATATGTATTAATATT-AA-ATATTTA
* * * *
265 CTTAATTATAAAATGGGGTATGTGTCAACTTCCTAACCCGCTTATGGAGTCCAAAATTTACACTG
64 ATTAATTATAAAATGGAGTATGTGTCAACTTCCTAACCCACTTATGGAGTCCAAAATTTACACTA
* * * *
330 ACAGTGTATAGTATAATAATCATATAAGAAGAATTGTACAATAAACCGTCACTGGAGTTTA
129 ACAGTGAATAGTATAATAATCATATAAGAAAAAGTATACAATAAACCGTCACTGGAGTTTA
391 TTCGACTTGC
Statistics
Matches: 170, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
199 51 0.30
200 2 0.01
201 117 0.69
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (199 bp):
CGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGAAATATGTATTAATATTAAATATTTAAT
TAATTATAAAATGGAGTATGTGTCAACTTCCTAACCCACTTATGGAGTCCAAAATTTACACTAAC
AGTGAATAGTATAATAATCATATAAGAAAAAGTATACAATAAACCGTCACTGGAGTTTAGCAGAC
TGCA
Found at i:1527 original size:20 final size:20
Alignment explanation
Indices: 1502--1561 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1492 TTCAACAATC
1502 TTACATTCTTACTTAATACT
1 TTACATTCTTACTTAATACT
*
1522 TTACATTTTTCAAC--AAT-C-
1 TTACATTCTT--ACTTAATACT
*
1540 TTATATTCTTACTTAATACT
1 TTACATTCTTACTTAATACT
1560 TT
1 TT
1562 GAATTTTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
16 2 0.06
18 11 0.35
19 2 0.06
20 14 0.45
22 2 0.06
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (20 bp):
TTACATTCTTACTTAATACT
Found at i:1548 original size:38 final size:38
Alignment explanation
Indices: 1492--1569 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
1482 TTTCAACAAA
1492 TTCAACAATCTTACATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
*
1530 TTCAACAATCTTATATTCTTACTTAATACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
1568 TT
1 TT
1570 GGTAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.01, T:0.50
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:3853 original size:48 final size:47
Alignment explanation
Indices: 3763--3897 Score: 184
Period size: 49 Copynumber: 2.8 Consensus size: 47
3753 ATCTTTTACA
3763 TTTCC-TGCACTTTTTCTCAATTTTTACAACAAAATTGAATCTTTAT-T
1 TTTCCTTGCACTTTTTCTCAATTTTTA-AACAAAATTG-ATCTTTATCT
*
3810 TTTCCTTGCACATTTTTCTCAATTTTTAAGACAAAATTGATCTTTTTCT
1 TTTCCTTGCAC-TTTTTCTCAATTTTTAA-ACAAAATTGATCTTTATCT
* * *
3859 TTTCATTGCACTTTTTATCAATTTTTATACAAAATTGAT
1 TTTCCTTGCACTTTTTCTCAATTTTTAAACAAAATTGAT
3898 TGGCACGCTC
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
47 16 0.20
48 28 0.35
49 36 0.45
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.50
Consensus pattern (47 bp):
TTTCCTTGCACTTTTTCTCAATTTTTAAACAAAATTGATCTTTATCT
Found at i:4801 original size:29 final size:29
Alignment explanation
Indices: 4766--4821 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
4756 TAAAATTCTG
*
4766 TCTACCAATATACGTGCTACATAATTCCA
1 TCTACCAATAAACGTGCTACATAATTCCA
*
4795 TCTACCAATAAACGTGTTACATAATTC
1 TCTACCAATAAACGTGCTACATAATTC
4822 TTTAGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
TCTACCAATAAACGTGCTACATAATTCCA
Found at i:7291 original size:299 final size:299
Alignment explanation
Indices: 6739--7336 Score: 984
Period size: 299 Copynumber: 2.0 Consensus size: 299
6729 TATATATATA
* *
6739 CTATATATTATTTTTAGTGACTATGGCAATTACTTAAAGGTCAAATTGAGGATTAATGTGGTGTC
1 CTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGTC
* *
6804 TCCTTTCGGCTTTTTTTGGTCATTTTTCACTTTCCGGGTGACTAAAAAGGCCCTCAATGAATTTA
66 TCCTTTCGGCTTTTTTTGATCATTTCTCACTTTCCGGGTGACTAAAAAGGCCCTCAATGAATTTA
*
6869 CTCTCTTACTTTTCCTGCTGCCCTTTTTTGTAATTTACTATTTTTATGATTAAGTGTGTTTTAAT
131 CTCTCTTACTTTTCATGCTGCCCTTTTTTGTAATTTACTATTTTTATGATTAAGTGTGTTTTAAT
* *
6934 TACATATTAACTGTGTGTGAATATTAGGATTACCGGTTCAACTCTCTTGCCGGAATTCCAAAGGA
196 TACATATTAACTGTGTGTGAATATTAGGATTACCAGTTCAACTCTCTTGCCAGAATTCCAAAGGA
*
6999 TTGGTGCTATAAATGTATCTGCAATAATGATTAATTCAT
261 ATGGTGCTATAAATGTATCTGCAATAATGATTAATTCAT
7038 CTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGTC
1 CTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGTC
* * * *
7103 TCCTTTTGGCTTTTTTTGATC-TTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTT
66 TCCTTTCGGCTTTTTTTGATCATTTCTCACTTTCCGGGTGACTAAAAAGGCCCTCAATGAATTTA
*
7167 CTCTCTTACTTTTCATGTTGCCCTTTTTTGTAATTTACTATTTTTATGATTAAGTGTGTTTTAAT
131 CTCTCTTACTTTTCATGCTGCCCTTTTTTGTAATTTACTATTTTTATGATTAAGTGTGTTTTAAT
* * * *
7232 TACATATTAATTTTGTGTGGATATTAGGATTTACCAGTTCAACTC-CTTCGCTAGAATTCCAAAG
196 TACATATTAACTGTGTGTGAATATTAGGA-TTACCAGTTCAACTCTCTT-GCCAGAATTCCAAAG
* * *
7296 GAATGGTGTTATAAATGTATTTGCAATAATGGTTAATTCAT
259 GAATGGTGCTATAAATGTATCTGCAATAATGATTAATTCAT
7337 GGATAAACTA
Statistics
Matches: 277, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
298 131 0.47
299 146 0.53
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (299 bp):
CTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGTC
TCCTTTCGGCTTTTTTTGATCATTTCTCACTTTCCGGGTGACTAAAAAGGCCCTCAATGAATTTA
CTCTCTTACTTTTCATGCTGCCCTTTTTTGTAATTTACTATTTTTATGATTAAGTGTGTTTTAAT
TACATATTAACTGTGTGTGAATATTAGGATTACCAGTTCAACTCTCTTGCCAGAATTCCAAAGGA
ATGGTGCTATAAATGTATCTGCAATAATGATTAATTCAT
Found at i:8911 original size:6 final size:6
Alignment explanation
Indices: 8900--8926 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8890 CTTATATAAT
8900 ATAAAG ATAAAG ATAAAG ATAAAG ATA
1 ATAAAG ATAAAG ATAAAG ATAAAG ATA
8927 TATATGGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
ATAAAG
Done.