Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013233.1 Corchorus olitorius cultivar O-4 contig13266, 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: 57955
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:25032 original size:16 final size:16
Alignment explanation
Indices: 24999--25030 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
24989 ATTTACAACA
24999 ATTATTATAGTATTAT
1 ATTATTATAGTATTAT
25015 ATTATTAT--TATTAT
1 ATTATTATAGTATTAT
25029 AT
1 AT
25031 ATAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTATTATAGTATTAT
Found at i:26510 original size:21 final size:21
Alignment explanation
Indices: 26485--26567 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
26475 TATCTTAGAT
26485 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
26506 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
26527 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
26549 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
26568 TTACTAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:26518 original size:25 final size:25
Alignment explanation
Indices: 26487--26535 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
26477 TCTTAGATAT
*
26487 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
26512 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
26536 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:28376 original size:10 final size:10
Alignment explanation
Indices: 28361--28398 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
28351 CCTCCCTTGT
28361 TTCAACACAC
1 TTCAACACAC
28371 TTCAACACAC
1 TTCAACACAC
*
28381 TTCAACACAT
1 TTCAACACAC
28391 TTCAACAC
1 TTCAACAC
28399 GCTAAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (10 bp):
TTCAACACAC
Found at i:29651 original size:4 final size:4
Alignment explanation
Indices: 29642--29668 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29632 GACATGTCAT
29642 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
29669 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:29673 original size:2 final size:2
Alignment explanation
Indices: 29666--29693 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29656 AAATAAATAA
29666 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
29694 TTTGAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34256 original size:5 final size:5
Alignment explanation
Indices: 34246--34271 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34236 AGTATCTATA
34246 AGGAG AGGAG AGGAG AGGAG AGGAG A
1 AGGAG AGGAG AGGAG AGGAG AGGAG A
34272 CGAGCGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (5 bp):
AGGAG
Found at i:34808 original size:11 final size:11
Alignment explanation
Indices: 34792--34817 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34782 AACAATTTTA
34792 TCGCAAGTATG
1 TCGCAAGTATG
34803 TCGCAAGTATG
1 TCGCAAGTATG
34814 TCGC
1 TCGC
34818 TTATGCTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (11 bp):
TCGCAAGTATG
Found at i:35443 original size:40 final size:39
Alignment explanation
Indices: 35385--35751 Score: 203
Period size: 40 Copynumber: 9.3 Consensus size: 39
35375 TCTTCCGACT
* *
35385 GGAAGGGCAATACT-GGAAATAAAACAACACCTTCCAGTAG
1 GGAAGGGCAA-ACTGGGAAA-AAAACAACACCTTCCGGTGG
* * * *
35425 AGAAGGGCAAACTGGGAAAGAGATAACACCTTCTC-GTGG
1 GGAAGGGCAAACTGGGAAAAAAACAACACCTTC-CGGTGG
* * *
35464 GAAAGGGCAAACTGAGATAAATAAATAACACCTTCCGGTGG
1 GGAAGGGCAAACTGGGA-AAA-AAACAACACCTTCCGGTGG
* *
35505 GGAAGGGCAAAAC-AGGAATTAAAACAACACCTTCCGGTGG
1 GGAAGGGC-AAACTGGGAA-AAAAACAACACCTTCCGGTGG
* *
35545 GGAAGGGCAAA-TGGGAAAAGTAAACAACACCTTTCGATGG
1 GGAAGGGCAAACTGGGAAAA--AAACAACACCTTCCGGTGG
* * *** * *
35585 GGAAGGACAAA-TTGGAATACTGACAACACCTTCCGATGA
1 GGAAGGGCAAACTGGGAA-AAAAACAACACCTTCCGGTGG
* **** * * *
35624 GGAAGGGCAAA-TTGGAATGCTGACAACACTTTCCGATGA
1 GGAAGGGCAAACTGGGAA-AAAAACAACACCTTCCGGTGG
* *** * *
35663 GGATGGGCAAACT-GG--ATTGACAACACCTTCCGATGA
1 GGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGG
**** * *
35699 GGAAGGGCAAACTGGGAATGTTGACAACACCTTCCGATGA
1 GGAAGGGCAAACTGGGAA-AAAAACAACACCTTCCGGTGG
35739 GGAAGGGCAAACT
1 GGAAGGGCAAACT
35752 AGAAATGCTG
Statistics
Matches: 276, Mismatches: 35, Indels: 32
0.80 0.10 0.09
Matches are distributed among these distances:
36 30 0.11
37 2 0.01
38 1 0.00
39 101 0.37
40 111 0.40
41 27 0.10
42 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (39 bp):
GGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGG
Found at i:35622 original size:39 final size:39
Alignment explanation
Indices: 35528--35793 Score: 306
Period size: 40 Copynumber: 6.8 Consensus size: 39
35518 AGGAATTAAA
* * * * *
35528 ACAACACCTTCCGGTGGGGAAGGGCAAATGGGAAAAG-TAA
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-AATGCT-G
* * * *
35568 ACAACACCTTTCGATGGGGAAGGACAAATTGGAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAATGCTG
35607 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAATGCTG
* * *
35646 ACAACACTTTCCGATGAGGATGGGCAAACTGG-AT--TG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGGAATGCTG
* *
35682 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGTTG
1 ACAACACCTTCCGATGAGGAAGGGCAAA-TTGGAATGCTG
* *
35722 ACAACACCTTCCGATGAGGAAGGGCAAACTAGAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAA-TTGGAATGCTG
* *
35762 ACAACACTTTCCGATGAGGAAGGGTAAATTGG
1 ACAACACCTTCCGATGAGGAAGGGCAAATTGG
35794 GAAAAGTAAC
Statistics
Matches: 196, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
36 28 0.14
37 2 0.01
38 4 0.02
39 68 0.35
40 94 0.48
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (39 bp):
ACAACACCTTCCGATGAGGAAGGGCAAATTGGAATGCTG
Found at i:35738 original size:115 final size:115
Alignment explanation
Indices: 35568--35781 Score: 340
Period size: 115 Copynumber: 1.9 Consensus size: 115
35558 GGAAAAGTAA
* * *
35568 ACAACACCTTTCGATGGGGAAGGACAAATTGGAATACTGACAACACCTTCCGATGAGGAAGGGCA
1 ACAACACCTTCCGATGAGGAAGGACAAATGGGAATACTGACAACACCTTCCGATGAGGAAGGGCA
* *
35633 AA-TTGGAATGCTGACAACACTTTCCGATGAGGATGGGCAAACTGGATTG
66 AACTAGAAATGCTGACAACACTTTCCGATGAGGATGGGCAAACTGGATTG
* **
35682 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGTTGACAACACCTTCCGATGAGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGACAAA-TGGGAATACTGACAACACCTTCCGATGAGGAAGGGC
35747 AAACTAGAAATGCTGACAACACTTTCCGATGAGGA
65 AAACTAGAAATGCTGACAACACTTTCCGATGAGGA
35782 AGGGTAAATT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 25 0.28
115 36 0.40
116 29 0.32
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.19
Consensus pattern (115 bp):
ACAACACCTTCCGATGAGGAAGGACAAATGGGAATACTGACAACACCTTCCGATGAGGAAGGGCA
AACTAGAAATGCTGACAACACTTTCCGATGAGGATGGGCAAACTGGATTG
Found at i:35844 original size:50 final size:47
Alignment explanation
Indices: 35761--35895 Score: 121
Period size: 47 Copynumber: 2.8 Consensus size: 47
35751 TAGAAATGCT
* * * * * *
35761 GACAACACTTTCCGATGAGGAAGGGTAAATTGGGAAAAGTAACA-ACTTTG
1 GACAACACCTTCTGATGGGGAAGGGCAATTTGGGAAAAG---CAGAC-TTA
*
35811 GACAACACCTTCTGATGGGGAAGGGCAATTTGGGTAAAGCAGACTTA
1 GACAACACCTTCTGATGGGGAAGGGCAATTTGGGAAAAGCAGACTTA
* * *
35858 AACAACACCTTCCT-ATGGGGAAGGGCAATCTGGAAAAA
1 GACAACACCTT-CTGATGGGGAAGGGCAATTTGGGAAAA
35896 CAAACAAGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
47 35 0.49
48 4 0.06
50 33 0.46
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (47 bp):
GACAACACCTTCTGATGGGGAAGGGCAATTTGGGAAAAGCAGACTTA
Found at i:37280 original size:21 final size:21
Alignment explanation
Indices: 37256--37322 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
37246 AATCTTCATC
37256 AATATTCATCAACTTTACAAG
1 AATATTCATCAACTTTACAAG
* * **
37277 AATAAATCAT-AAATCTT-CATC
1 AAT-ATTCATCAACT-TTACAAG
37298 AATATTCATCAACTTTACAAG
1 AATATTCATCAACTTTACAAG
37319 AATA
1 AATA
37323 AAGAGCTATC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 7 0.21
21 20 0.59
22 7 0.21
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (21 bp):
AATATTCATCAACTTTACAAG
Found at i:37283 original size:42 final size:42
Alignment explanation
Indices: 37237--37324 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
37227 ATTGGAACCT
37237 TAAATCATAAATCTTCATCAATATTCATCAACTTTACAAGAA
1 TAAATCATAAATCTTCATCAATATTCATCAACTTTACAAGAA
37279 TAAATCATAAATCTTCATCAATATTCATCAACTTTACAAGAA
1 TAAATCATAAATCTTCATCAATATTCATCAACTTTACAAGAA
37321 TAAA
1 TAAA
37325 GAGCTATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (42 bp):
TAAATCATAAATCTTCATCAATATTCATCAACTTTACAAGAA
Found at i:46422 original size:41 final size:41
Alignment explanation
Indices: 46377--46542 Score: 212
Period size: 41 Copynumber: 4.0 Consensus size: 41
46367 GGTTCAATAT
*
46377 GGTTTGACTATCAAATTTT-GGATTTGATC-ATCAAACTTTGG
1 GGTTTGACTATCAAATTTTGGGGTTTGA-CAATCAAA-TTTGG
*
46418 GGTTTGACAATCAAATTTTGGGGTTTGACAATCAAATTTGG
1 GGTTTGACTATCAAATTTTGGGGTTTGACAATCAAATTTGG
* * * *
46459 GGTTTGACCATCAAACTTTGAGGTTTGACTATCAAAGTTT-G
1 GGTTTGACTATCAAATTTTGGGGTTTGACAATCAAA-TTTGG
*
46500 GGTTTGACTATCAAATTTTGGGGTTTGACCATCAAAATTTGG
1 GGTTTGACTATCAAATTTTGGGGTTTGACAATC-AAATTTGG
46542 G
1 G
46543 CAAAAACACA
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
41 89 0.81
42 21 0.19
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (41 bp):
GGTTTGACTATCAAATTTTGGGGTTTGACAATCAAATTTGG
Found at i:46430 original size:21 final size:20
Alignment explanation
Indices: 46377--46542 Score: 192
Period size: 21 Copynumber: 8.1 Consensus size: 20
46367 GGTTCAATAT
*
46377 GGTTTGACTATCAAATTTTG
1 GGTTTGACTATCAAATTTGG
*
46397 GATTTGA-TCATCAAACTTTGG
1 GGTTTGACT-ATCAAA-TTTGG
*
46418 GGTTTGACAATCAAATTTTGG
1 GGTTTGACTATCAAA-TTTGG
*
46439 GGTTTGACAATCAAATTTGG
1 GGTTTGACTATCAAATTTGG
* *
46459 GGTTTGACCATCAAACTTTGA
1 GGTTTGACTATCAAA-TTTGG
46480 GGTTTGACTATCAAAGTTT-G
1 GGTTTGACTATCAAA-TTTGG
46500 GGTTTGACTATCAAATTTTGG
1 GGTTTGACTATCAAA-TTTGG
*
46521 GGTTTGACCATCAAAATTTGG
1 GGTTTGACTATC-AAATTTGG
46542 G
1 G
46543 CAAAAACACA
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.01
20 49 0.38
21 75 0.59
22 3 0.02
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (20 bp):
GGTTTGACTATCAAATTTGG
Found at i:46474 original size:62 final size:61
Alignment explanation
Indices: 46377--46542 Score: 242
Period size: 62 Copynumber: 2.7 Consensus size: 61
46367 GGTTCAATAT
* * * *
46377 GGTTTGACTATCAAATTTTGGATTTGATCATCAAACTTTGGGGTTTGACAATCAAATTTTGG
1 GGTTTGACTATCAAATTTGGGGTTTGACCATCAAACTTTGGGGTTTGACAATCAAAGTTT-G
* * *
46439 GGTTTGACAATCAAATTTGGGGTTTGACCATCAAACTTTGAGGTTTGACTATCAAAGTTTG
1 GGTTTGACTATCAAATTTGGGGTTTGACCATCAAACTTTGGGGTTTGACAATCAAAGTTTG
*
46500 GGTTTGACTATCAAATTTTGGGGTTTGACCATCAAAATTTGGG
1 GGTTTGACTATCAAA-TTTGGGGTTTGACCATCAAACTTTGGG
46543 CAAAAACACA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
61 15 0.16
62 78 0.84
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (61 bp):
GGTTTGACTATCAAATTTGGGGTTTGACCATCAAACTTTGGGGTTTGACAATCAAAGTTTG
Found at i:48795 original size:13 final size:13
Alignment explanation
Indices: 48777--48802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48767 ATGATCTCAA
48777 CAAAAATCATCAC
1 CAAAAATCATCAC
48790 CAAAAATCATCAC
1 CAAAAATCATCAC
48803 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:52353 original size:6 final size:6
Alignment explanation
Indices: 52342--52370 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52332 ATTTCTTGCG
52342 CCATTA CCATTA CCATTA CCATTA CCATT
1 CCATTA CCATTA CCATTA CCATTA CCATT
52371 CCTCACGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
CCATTA
Found at i:55850 original size:21 final size:20
Alignment explanation
Indices: 55824--55889 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
55814 TTTAACATGA
*
55824 TTTGACTATCAAACTTTGGGG
1 TTTGACAATCAAA-TTTGGGG
* *
55845 TTTGACAATTAAAATTTGGGA
1 TTTGACAA-TCAAATTTGGGG
* *
55866 TTTAACCATCAAATATTGGGG
1 TTTGACAATCAAAT-TTGGGG
55887 TTT
1 TTT
55890 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 5 0.14
21 27 0.75
22 4 0.11
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (20 bp):
TTTGACAATCAAATTTGGGG
Done.