Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023096.1 Corchorus olitorius cultivar O-4 contig23129, 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: 18974
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 CCTAATTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:633 original size:26 final size:26
Alignment explanation
Indices: 582--640 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
572 TTTATTACTA
*
582 TACTAAAATTTCTAAGAATTCAAGGT
1 TACTAAAAGTTCTAAGAATTCAAGGT
* *
608 TGCTAAAAGTTCTAAGAATGT-GAGGT
1 TACTAAAAGTTCTAAGAAT-TCAAGGT
634 TACTAAA
1 TACTAAA
641 TTTATGCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (26 bp):
TACTAAAAGTTCTAAGAATTCAAGGT
Found at i:2258 original size:27 final size:26
Alignment explanation
Indices: 2239--2306 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
2229 TTTGATATTG
2239 ATGAAAGGTTACTAAAATTTGTAAGA
1 ATGAAAGGTTACTAAAATTTGTAAGA
* *
2265 ATGCAAGGTTACTAAAATTTTTAAGA
1 ATGAAAGGTTACTAAAATTTGTAAGA
*
2291 AT-ATGAGGTTACTAAA
1 ATGA-AAGGTTACTAAA
2307 TTTATGTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (26 bp):
ATGAAAGGTTACTAAAATTTGTAAGA
Found at i:4371 original size:20 final size:20
Alignment explanation
Indices: 4333--4410 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
4323 ATCTCAAGAG
* * *
4333 TTTATAAGATTAATGAAAAT
1 TTTATAAGATTATTAAAAAC
*
4353 TTTATAAGTTTATTAAAAAAC
1 TTTATAAGATTATT-AAAAAC
* * *
4374 TTTATAATATTAGTT-AAGAG
1 TTTATAAGATTA-TTAAAAAC
4394 TTTATAAGATTATTAAA
1 TTTATAAGATTATTAAA
4411 TAAATTGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 28 0.61
21 14 0.30
22 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTATAAGATTATTAAAAAC
Found at i:4378 original size:41 final size:41
Alignment explanation
Indices: 4333--4410 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
4323 ATCTCAAGAG
* *
4333 TTTATAAGATTAATGAAAATTTTATAAGTTTATTAAAAAAC
1 TTTATAAGATTAATGAAAAGTTTATAAGATTATTAAAAAAC
* * * *
4374 TTTATAATATTAGTTAAGAGTTTATAAGATTATTAAA
1 TTTATAAGATTAATGAAAAGTTTATAAGATTATTAAA
4411 TAAATTGATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (41 bp):
TTTATAAGATTAATGAAAAGTTTATAAGATTATTAAAAAAC
Found at i:4488 original size:19 final size:20
Alignment explanation
Indices: 4437--4490 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
4427 CTAAAAAAGT
*
4437 TTAATAAAGTTACTACAATA
1 TTAATAACGTTACTACAATA
*
4457 TTAATAACATTACTACAA-A
1 TTAATAACGTTACTACAATA
* *
4476 TTATTAAGGTTACTA
1 TTAATAACGTTACTA
4491 AAAACCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (20 bp):
TTAATAACGTTACTACAATA
Found at i:4582 original size:21 final size:21
Alignment explanation
Indices: 4527--4624 Score: 58
Period size: 21 Copynumber: 4.6 Consensus size: 21
4517 ATAAAGTTAT
* *
4527 TAAAAAGCTTAATAAGACTT-T
1 TAAAAATCTTAATAAGA-TTAC
* **
4548 TAAAATTCACAATAAGATTAC
1 TAAAAATCTTAATAAGATTAC
* *
4569 TAAAAATCTTAATAAGGTTAGG
1 TAAAAATCTTAATAAGATTA-C
* *
4591 T-AAAATACTTAATAAGGTGAC
1 TAAAAAT-CTTAATAAGATTAC
4612 TGAAAAAT-TTAAT
1 T-AAAAATCTTAAT
4625 TTATATAAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.03
21 40 0.67
22 13 0.22
23 5 0.08
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (21 bp):
TAAAAATCTTAATAAGATTAC
Found at i:4759 original size:20 final size:20
Alignment explanation
Indices: 4736--4789 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
4726 AAAGGTTTTC
*
4736 AAGGTTATTAAAAAATTTAT
1 AAGGTTATTAAAAAATTTAA
* * *
4756 AAGGTGATTAATAACTTTAA
1 AAGGTTATTAAAAAATTTAA
*
4776 AATGTTATTGAAAA
1 AAGGTTATT-AAAA
4790 GCTTAGCATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (20 bp):
AAGGTTATTAAAAAATTTAA
Found at i:6336 original size:16 final size:16
Alignment explanation
Indices: 6315--6349 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
6305 ACAATTCAGA
6315 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
6331 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
6347 AAG
1 AAG
6350 TATTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:6518 original size:41 final size:41
Alignment explanation
Indices: 6445--6808 Score: 426
Period size: 41 Copynumber: 8.9 Consensus size: 41
6435 TTTTTGTTTG
* * * *
6445 TTCAAGATTAAGTAACCGAGACCCTTGAATTAAAGTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
*
6486 TTCAGGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
6527 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
*
6568 TTCAGGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
*
6609 TTCAAGATTGAGTCATCGAGACCCTTGAATTACATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
*** * *
6650 TTCAAGAACAAGTCATCGA-AACTTTGAATTAAATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
*** *
6690 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
*** * * * * *
6734 TTCAAGACCAAGTCGTCAAGACCCTTGAATGAGATTGTCAA
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
** ** *
6775 TTCAAGATCAAGTCAT-TTGACTCTTGAATTAAAT
1 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAAT
6809 CAAATCAAAC
Statistics
Matches: 289, Mismatches: 30, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
40 50 0.17
41 200 0.69
42 2 0.01
43 2 0.01
44 35 0.12
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (41 bp):
TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:7488 original size:2 final size:2
Alignment explanation
Indices: 7483--7507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7473 ACGTAATGAA
7483 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
7508 GTTTTCATAC
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:8595 original size:4 final size:4
Alignment explanation
Indices: 8586--8615 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
8576 TGAAGTAGTA
8586 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
8616 TTGAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:10107 original size:13 final size:13
Alignment explanation
Indices: 10089--10113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10079 TTCAATGTTC
10089 TAAATATTATTTA
1 TAAATATTATTTA
10102 TAAATATTATTT
1 TAAATATTATTT
10114 GGAATTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:11840 original size:34 final size:33
Alignment explanation
Indices: 11777--11841 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
11767 ACTTACAACC
*
11777 AATGAAGTTACACGACCTTCAACACGCCTTTCT
1 AATGAAGTTAAACGACCTTCAACACGCCTTTCT
* * *
11810 AATGAAGTTAAACGGGCCTTCATCATGCCTTT
1 AATGAAGTTAAAC-GACCTTCAACACGCCTTT
11842 ACCAGTTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (33 bp):
AATGAAGTTAAACGACCTTCAACACGCCTTTCT
Found at i:14023 original size:23 final size:23
Alignment explanation
Indices: 13997--14043 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13987 ACAAGTAAGC
13997 ACAACAAATCTACTTAATCACAT
1 ACAACAAATCTACTTAATCACAT
*
14020 ACAACAAATCTGCTTAATCACAT
1 ACAACAAATCTACTTAATCACAT
14043 A
1 A
14044 AGATATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.26
Consensus pattern (23 bp):
ACAACAAATCTACTTAATCACAT
Found at i:16840 original size:21 final size:21
Alignment explanation
Indices: 16790--16834 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16780 GAGACACTGC
* *
16790 CCACCTGGGTTCTCAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
*
16811 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTGCTCAAGCAAA
16832 CCA
1 CCA
16835 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGCAAA
Done.