Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009759.1 Corchorus capsularis cultivar CVL-1 contig09780, 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: 33790
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:169 original size:16 final size:16
Alignment explanation
Indices: 140--181 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
130 CAAATAAATA
*
140 ATATATTAATTAATTT
1 ATATATTTATTAATTT
* *
156 TTATTTTTATTAATTT
1 ATATATTTATTAATTT
172 ATATATTTAT
1 ATATATTTAT
182 ATATTTATGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATATTTATTAATTT
Found at i:188 original size:24 final size:24
Alignment explanation
Indices: 144--201 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
134 TAAATAATAT
* * *
144 ATTAAT-TAATTTTTATTTTTATTA
1 ATTAATAT-ATTTATATATTTATGA
*
168 ATTTATATATTTATATATTTATGA
1 ATTAATATATTTATATATTTATGA
192 ATTAATATAT
1 ATTAATATAT
202 ATTTTAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTAATATATTTATATATTTATGA
Found at i:3972 original size:39 final size:39
Alignment explanation
Indices: 3923--3999 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
3913 GTATGGTAAT
*
3923 TTTTCCTAAATTTCCATGTCTAACTTAGTAAGACCAAAA
1 TTTTCCTAAATTTCCATGTCTAACTTAGTAAGAACAAAA
* *
3962 TTTTCTTAAATTTCCATGTTTAACTTAGTAAGAACAAA
1 TTTTCCTAAATTTCCATGTCTAACTTAGTAAGAACAAA
4000 TTATATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (39 bp):
TTTTCCTAAATTTCCATGTCTAACTTAGTAAGAACAAAA
Found at i:4749 original size:1 final size:1
Alignment explanation
Indices: 4743--4776 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
4733 GTGTAGTAGC
4743 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4777 GTTGTGTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14647 original size:31 final size:31
Alignment explanation
Indices: 14545--14650 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
14535 GCTAAATAAC
* *
14545 CAATTCAGGATATAACGTTTGCCTG-AACGAT
1 CAATTCAGGATATAACG-TTACATGAAACGAT
** * *
14576 CAATTTGGGATATAACGTTCCA-GAAACG-C
1 CAATTCAGGATATAACGTTACATGAAACGAT
14605 CAATTCAGGATATAACGTTACATGAAACGAT
1 CAATTCAGGATATAACGTTACATGAAACGAT
*
14636 CAAATCAGGATATAA
1 CAATTCAGGATATAA
14651 GTGATGACGT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 20 0.32
30 13 0.21
31 29 0.47
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (31 bp):
CAATTCAGGATATAACGTTACATGAAACGAT
Found at i:14708 original size:11 final size:11
Alignment explanation
Indices: 14694--14747 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
14684 TGACGTAATT
14694 GCCACGTGGAC
1 GCCACGTGGAC
*
14705 GCCACGTAGAC
1 GCCACGTGGAC
* * *
14716 GCTACATGGAT
1 GCCACGTGGAC
* *
14727 GACACGTTGAC
1 GCCACGTGGAC
14738 GCCACGTGGA
1 GCCACGTGGA
14748 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.24, C:0.30, G:0.31, T:0.15
Consensus pattern (11 bp):
GCCACGTGGAC
Found at i:14747 original size:22 final size:22
Alignment explanation
Indices: 14694--14748 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
14684 TGACGTAATT
* *
14694 GCCACGTGGACGCCACGTAGAC
1 GCCACGTGGATGACACGTAGAC
* * *
14716 GCTACATGGATGACACGTTGAC
1 GCCACGTGGATGACACGTAGAC
14738 GCCACGTGGAT
1 GCCACGTGGAT
14749 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (22 bp):
GCCACGTGGATGACACGTAGAC
Found at i:14782 original size:11 final size:11
Alignment explanation
Indices: 14761--14830 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
14751 TTAAAATAAA
*
14761 AAATGAAAAAT
1 AAATAAAAAAT
*
14772 TAATAAAAAAT
1 AAATAAAAAAT
*
14783 AAAATAAAAATAA
1 -AAATAAAAA-AT
14796 AAATAAAATAAAT
1 AAAT-AAA-AAAT
* *
14809 TAATAAAAAACG
1 AAATAAAAAA-T
14821 AAATAAAAAA
1 AAATAAAAAA
14831 AATAAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
11 12 0.26
12 24 0.52
13 8 0.17
14 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:14786 original size:17 final size:17
Alignment explanation
Indices: 14755--14818 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
14745 GGATTTTTAA
14755 AATAAAAAATGAAAAATT
1 AATAAAAAAT-AAAAATT
**
14773 AATAAAAAATAAAATAAA
1 AATAAAAAATAAAA-ATT
*
14791 AATAAAAATAAAATAAATT
1 AATAAAAA-ATAA-AAATT
14810 AATAAAAAA
1 AATAAAAAA
14819 CGAAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 4 0.11
18 20 0.53
19 12 0.32
20 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAAAAATAAAAATT
Found at i:14788 original size:5 final size:5
Alignment explanation
Indices: 14778--14836 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
14768 AAATTAATAA
* * *
14778 AAAAT AAAAT AAAAAT AAAAAT AAAAT AAATT AATAA- AAAAC GAAAT
1 AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT
14825 AAAA- AAAAT AAA
1 AAAAT AAAAT AAA
14837 TTTTGTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
4 6 0.13
5 27 0.60
6 12 0.27
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20795 original size:31 final size:31
Alignment explanation
Indices: 20760--20864 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
20750 TCCGTCTAAA
* *
20760 TATATCCTGATTTGATCGTTTCATGTAAAGT
1 TATATCCTGAATTGATCGTTTCATGCAAAGT
* * *
20791 TATATCCTGAATTG-GCGTTTC-TGGAACGT
1 TATATCCTGAATTGATCGTTTCATGCAAAGT
** *
20820 TATATCCCAAATTGATCG-TTCAGGCAAACGT
1 TATATCCTGAATTGATCGTTTCATGCAAA-GT
20851 TATATCCTGAATTG
1 TATATCCTGAATTG
20865 GTTATTTAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
29 21 0.36
30 11 0.19
31 27 0.46
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (31 bp):
TATATCCTGAATTGATCGTTTCATGCAAAGT
Found at i:28901 original size:19 final size:20
Alignment explanation
Indices: 28864--28901 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28854 ATGCCTTCTT
*
28864 TTAACAAAAGGTTAGAATGA
1 TTAACAAAAGGTTAAAATGA
28884 TTAACAAAA-GTTAAAATG
1 TTAACAAAAGGTTAAAATG
28902 CCTTCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (20 bp):
TTAACAAAAGGTTAAAATGA
Found at i:30975 original size:12 final size:12
Alignment explanation
Indices: 30958--30982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30948 TCACGAATGT
30958 CCCAATGATATC
1 CCCAATGATATC
30970 CCCAATGATATC
1 CCCAATGATATC
30982 C
1 C
30983 TTGAGTATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (12 bp):
CCCAATGATATC
Found at i:31153 original size:66 final size:66
Alignment explanation
Indices: 31072--31201 Score: 260
Period size: 66 Copynumber: 2.0 Consensus size: 66
31062 TAGTCTGGAA
31072 AATAAAGGAAAATATTAAAATTATAAATAATGAAAGTGAAAATTAAATAATAACTTCTTGAGATG
1 AATAAAGGAAAATATTAAAATTATAAATAATGAAAGTGAAAATTAAATAATAACTTCTTGAGATG
31137 T
66 T
31138 AATAAAGGAAAATATTAAAATTATAAATAATGAAAGTGAAAATTAAATAATAACTTCTTGAGAT
1 AATAAAGGAAAATATTAAAATTATAAATAATGAAAGTGAAAATTAAATAATAACTTCTTGAGAT
31202 TTCCTACATC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (66 bp):
AATAAAGGAAAATATTAAAATTATAAATAATGAAAGTGAAAATTAAATAATAACTTCTTGAGATG
T
Found at i:31273 original size:2 final size:2
Alignment explanation
Indices: 31266--31298 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31256 AATTAATGTG
31266 AT AT AT AT 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 AT AT AT AT A
31299 CATGGTTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32282 original size:31 final size:31
Alignment explanation
Indices: 32236--32296 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
32226 ATATTAAACT
*
32236 AATAAGGATATAATAGGAATATT-AAAAGTTA
1 AATAAGGATACAATAGGAAT-TTCAAAAGTTA
* *
32267 AATAAGGGTACAATAGGTATTTCAAAAGTT
1 AATAAGGATACAATAGGAATTTCAAAAGTT
32297 TCTCAAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (31 bp):
AATAAGGATACAATAGGAATTTCAAAAGTTA
Found at i:32452 original size:60 final size:60
Alignment explanation
Indices: 32359--32520 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
32349 GCTAATTGTT
*** *
32359 CAAATAAGGGCCTAACGTTTGAT-AAAATGCTCAAATAAGGGTTTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTG-TCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
32419 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
1 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
*
32479 CAAATAAGGGCCTAACGTTTGCCAAAATGCTC-AATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCC
32521 TATCTCACGC
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 11 0.11
60 85 0.89
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGAC
Found at i:32499 original size:29 final size:30
Alignment explanation
Indices: 32358--32522 Score: 128
Period size: 31 Copynumber: 5.5 Consensus size: 30
32348 GGCTAATTGT
32358 TCAAATAAGGGCCTAACGTTTGATAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-TAAAATGC
** * **
32389 TCAAATAAGGGTTTGATC-TTT-TAATTTGAC
1 TCAAATAAGGGCCT-AACGTTTGTAAAATG-C
32419 -CAAATAAGGGCCTAACGTTTGTCAAAATGC
1 TCAAATAAGGGCCTAACGTTTGT-AAAATGC
* * **
32449 TCAAATAAGGGCCCGATC-TTTG-AATTTGAC
1 TCAAATAAGGG-CCTAACGTTTGTAAAATG-C
*
32479 -CAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTG-TAAAATGC
32509 TC-AATAAGGGCCTA
1 TCAAATAAGGGCCTA
32523 TCTCACGCGT
Statistics
Matches: 104, Mismatches: 18, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
28 6 0.06
29 37 0.36
30 17 0.16
31 38 0.37
32 6 0.06
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACGTTTGTAAAATGC
Found at i:32590 original size:31 final size:31
Alignment explanation
Indices: 32552--32680 Score: 122
Period size: 31 Copynumber: 4.2 Consensus size: 31
32542 TGACACCAGG
32552 CCCTTATTTGAGCATTTTCGATAACGTTAGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGA
* * *
32583 CCCTTATTTGAGTATTTTTGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGA
* * * **
32614 CCCTTATTCG-GTCATATT--A-AAAGATCGGA
1 CCCTTATTTGAG-CATTTTCGATAACG-TTAGA
* *
32643 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGA
32674 CCCTTAT
1 CCCTTAT
32681 CTGGCCAAAT
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
28 3 0.04
29 17 0.22
30 2 0.03
31 51 0.67
32 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGA
Found at i:32651 original size:60 final size:61
Alignment explanation
Indices: 32581--32741 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 61
32571 GATAACGTTA
* * * *
32581 GACCCTTATTTGAGTATTTTTGATAACGTTAGGCCCTTATTC-GGTCATATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTCTGGCCAAATTAAAAGATCG
*
32641 GACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTA-TCTGGCCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTCTGGCCAAATTAAAAGATCG
** *
32701 GGTCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATT
1 GACCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATT
32742 TTAGCAATCT
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
59 2 0.02
60 85 0.96
61 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (61 bp):
GACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTCTGGCCAAATTAAAAGATCG
Found at i:32827 original size:4 final size:4
Alignment explanation
Indices: 32818--32870 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
32808 CATTTTAGTG
* * * * * *
32818 TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA TGTA TATG TATG
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
32866 TATA T
1 TATA T
32871 GATCATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:32871 original size:6 final size:6
Alignment explanation
Indices: 32818--32870 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
32808 CATTTTAGTG
* * * * * *
32818 TATATA TATATA TATATA TATATA TGTATG TATGTA TGTATA TGTATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
32866 TATAT
1 TATAT
32871 GATCATTAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:32871 original size:10 final size:10
Alignment explanation
Indices: 32816--32871 Score: 62
Period size: 10 Copynumber: 5.8 Consensus size: 10
32806 ATCATTTTAG
*
32816 TGTATATATA
1 TGTATATGTA
* *
32826 TATATATATA
1 TGTATATGTA
*
32836 TATATATGTA
1 TGTATATGTA
32846 TG--TATGTA
1 TGTATATGTA
32854 TGTATATGTA
1 TGTATATGTA
32864 TGTATATG
1 TGTATATG
32872 ATCATTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
8 8 0.20
10 33 0.80
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (10 bp):
TGTATATGTA
Found at i:33624 original size:2 final size:2
Alignment explanation
Indices: 33617--33642 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33607 CATAATGTTA
33617 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
33643 GTACACAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33770 original size:2 final size:2
Alignment explanation
Indices: 33763--33790 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33753 TCTTATTAGA
33763 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
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
Done.