Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006878.1 Corchorus capsularis cultivar CVL-1 contig06899, 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: 17538
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Found at i:2511 original size:18 final size:18
Alignment explanation
Indices: 2488--2523 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2478 TGGTTTTTTC
2488 TCCATGCTTATATTCAAG
1 TCCATGCTTATATTCAAG
2506 TCCATGCTTATATTCAAG
1 TCCATGCTTATATTCAAG
2524 ATCATTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
TCCATGCTTATATTCAAG
Found at i:4651 original size:13 final size:12
Alignment explanation
Indices: 4627--4662 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
4617 GAGGAAGTAT
4627 ACATTTAGATAA
1 ACATTTAGATAA
4639 ACATTTGAGATAA
1 ACATTT-AGATAA
4652 ACATTTAGATA
1 ACATTTAGATA
4663 CAATTGACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (12 bp):
ACATTTAGATAA
Found at i:12535 original size:111 final size:113
Alignment explanation
Indices: 12392--12607 Score: 280
Period size: 111 Copynumber: 1.9 Consensus size: 113
12382 ATCCTACTCC
* *
12392 TTTTTACTGATTACCATTTTCTACCTTCTTCTTTTACT-AACTACCCTTTTCTTACT-ATTTTTA
1 TTTTTACTGATTACCATTTACTACCTTCTTCTTTTACTGAA-TACCATTTT-TTACTCATTTTTA
* * * *
12455 TTGATTACCA-TTTTTACT-TTTTTTACTGATTACCCTTTTCTTACTTTG
64 CTGAATACCATTTTTTACTCTTTTCTACTGATTACCATTTTCTTACTTTG
* * * *
12503 TTTTTACTGATTACCCTTTACTTA-CTTTTTCTTTTACTGAATACCATTTTTTTCTCTTTTTTAC
1 TTTTTACTGATTACCATTTAC-TACCTTCTTCTTTTACTGAATACCATTTTTTACTCATTTTTAC
12567 TGAATACCATTTTTTACTCTTTTCTACTGATTACCATTTTC
65 TGAATACCATTTTTTACTCTTTTCTACTGATTACCATTTTC
12608 ATTTTACTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
110 4 0.04
111 54 0.60
112 12 0.13
113 20 0.22
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (113 bp):
TTTTTACTGATTACCATTTACTACCTTCTTCTTTTACTGAATACCATTTTTTACTCATTTTTACT
GAATACCATTTTTTACTCTTTTCTACTGATTACCATTTTCTTACTTTG
Found at i:12566 original size:27 final size:27
Alignment explanation
Indices: 12386--12606 Score: 196
Period size: 27 Copynumber: 8.0 Consensus size: 27
12376 TAATCTATCC
* *
12386 TACTCCTTTTTACTGATTACCATTTTC
1 TACTCTTTTTTACTGATTACCATTTTT
* * *
12413 TACCTTCTTCTTTTACTAACTACCCTTTTCT
1 TA-C-TCTT-TTTTACTGATTACCATTTT-T
* *
12444 TACT-ATTTTTATTGATTACCA-TTTT
1 TACTCTTTTTTACTGATTACCATTTTT
*
12469 TACT-TTTTTTACTGATTACCCTTTTCT
1 TACTCTTTTTTACTGATTACCATTTT-T
* * *
12496 TACTTTGTTTTTACTGATTACCCTTTACT
1 TACTCT-TTTTTACTGATTACCATTT-TT
* *
12525 TACTTTTTCTTTTACTGAATACCATTTTT
1 TAC-TCTT-TTTTACTGATTACCATTTTT
* *
12554 TTCTCTTTTTTACTGAATACCATTTTT
1 TACTCTTTTTTACTGATTACCATTTTT
*
12581 TACTCTTTTCTACTGATTACCATTTT
1 TACTCTTTTTTACTGATTACCATTTT
12607 CATTTTACTA
Statistics
Matches: 161, Mismatches: 22, Indels: 22
0.79 0.11 0.11
Matches are distributed among these distances:
25 19 0.12
26 6 0.04
27 61 0.38
28 6 0.04
29 31 0.19
30 36 0.22
31 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.56
Consensus pattern (27 bp):
TACTCTTTTTTACTGATTACCATTTTT
Found at i:12590 original size:57 final size:56
Alignment explanation
Indices: 12392--12607 Score: 198
Period size: 57 Copynumber: 3.9 Consensus size: 56
12382 ATCCTACTCC
* * *
12392 TTTTTACTGATTACCATTTTCTACCTTCTTCTTTTACT-AACTACCCTTTTCTTACTA
1 TTTTTACTGATTACCATTTTTTACCTT-TTCTTTTACTGAA-TACCATTTTCTTACTT
* * *
12449 TTTTTATTGATTACCA-TTTTTA-C-TTT-TTTTACTGATTACCCTTTTCTTACTTT
1 TTTTTACTGATTACCATTTTTTACCTTTTCTTTTACTGAATACCATTTTCTTAC-TT
* * * *
12502 GTTTTTACTGATTACCCTTTACTTACTTTTTCTTTTACTGAATACCATTTT-TTTCTCT
1 -TTTTTACTGATTACCATTT-TTTACCTTTTCTTTTACTGAATACCATTTTCTTACT-T
* *
12560 TTTTTACTGAATACCATTTTTTACTCTTTTC---TACTGATTACCATTTTC
1 TTTTTACTGATTACCATTTTTTAC-CTTTTCTTTTACTGAATACCATTTTC
12608 ATTTTACTAA
Statistics
Matches: 132, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
52 21 0.16
53 4 0.03
54 30 0.23
55 3 0.02
56 12 0.09
57 38 0.29
58 7 0.05
59 17 0.13
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (56 bp):
TTTTTACTGATTACCATTTTTTACCTTTTCTTTTACTGAATACCATTTTCTTACTT
Found at i:12634 original size:7 final size:7
Alignment explanation
Indices: 12618--12737 Score: 59
Period size: 7 Copynumber: 16.7 Consensus size: 7
12608 ATTTTACTAA
*
12618 TTACTAT
1 TTACTCT
12625 TTACTCT
1 TTACTCT
12632 TTA-TCATT
1 TTACTC--T
*
12640 TTACTTT
1 TTACTCT
**
12647 TTACTGA
1 TTACTCT
12654 TTACTCT
1 TTACTCT
*
12661 TTACTTT
1 TTACTCT
12668 TTAC-CATT
1 TTACTC--T
*
12676 TTACCCT
1 TTACTCT
**
12683 TTACTGA
1 TTACTCT
12690 TTACTCT
1 TTACTCT
12697 TTACT-T
1 TTACTCT
12703 CTTACAAT-T
1 -TTAC--TCT
12712 TTACTCT
1 TTACTCT
**
12719 TTACTGA
1 TTACTCT
12726 TTACTCT
1 TTACTCT
12733 TTACT
1 TTACT
12738 TTTTTTACCA
Statistics
Matches: 86, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
6 4 0.05
7 65 0.76
8 13 0.15
9 4 0.05
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.55
Consensus pattern (7 bp):
TTACTCT
Found at i:12642 original size:29 final size:29
Alignment explanation
Indices: 12591--12671 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
12581 TACTCTTTTC
12591 TACTGATTAC-CATTT-TCATTTTACTAAT
1 TACTGATTACTC-TTTATCATTTTACTAAT
**
12619 TACT-ATTTACTCTTTATCATTTTACTTTT
1 TACTGA-TTACTCTTTATCATTTTACTAAT
*
12648 TACTGATTACTCTTTA-CTTTTTAC
1 TACTGATTACTCTTTATCATTTTAC
12672 CATTTTACCC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.02
28 18 0.39
29 26 0.57
30 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.02, T:0.56
Consensus pattern (29 bp):
TACTGATTACTCTTTATCATTTTACTAAT
Found at i:12650 original size:36 final size:36
Alignment explanation
Indices: 12597--12759 Score: 202
Period size: 36 Copynumber: 4.5 Consensus size: 36
12587 TTTCTACTGA
* * * *
12597 TTACCATTTT-CATTTTACTAATTACTATTTACTCT
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
*
12632 TTATCATTTTACTTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
** *
12668 TTACCATTTTACCCTTTACTGATTACTCTTTACTTC
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
* *
12704 TTACAATTTTACTCTTTACTGATTACTCTTTACTTTTT
1 TTACCATTTTACTTTTTACTGATTACTCTTTAC--TTT
12742 TTACCATTTTACCTTTTT
1 TTACCATTTTA-CTTTTT
12760 TAACTTAATT
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
35 9 0.08
36 84 0.76
38 12 0.11
39 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (36 bp):
TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
Found at i:12837 original size:40 final size:40
Alignment explanation
Indices: 12789--12870 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
12779 CATCTTTTGA
** *
12789 TCTTAATTACTGATTTACTGACT-ACTTCTTTTACTTTTAC
1 TCTTAATTACCAATTTACTG-CTCACTTCTTTTACTCTTAC
*
12829 TCTTAATTACCAATTTACTGCTCCCTTCTTTTACTCTTAC
1 TCTTAATTACCAATTTACTGCTCACTTCTTTTACTCTTAC
12869 TC
1 TC
12871 CATTCTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.21, C:0.26, G:0.04, T:0.50
Consensus pattern (40 bp):
TCTTAATTACCAATTTACTGCTCACTTCTTTTACTCTTAC
Found at i:12884 original size:40 final size:40
Alignment explanation
Indices: 12793--12884 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
12783 TTTTGATCTT
* * *
12793 AATTACTGATTTACTGACTACTTCTTTTACTTTTACTCTT
1 AATTACTAATTTACTGACTACTTCTTTTACTCTTACTCTC
* *
12833 AATTACCAATTTACTG-CTCCCTTCTTTTACTCTTACTC-C
1 AATTACTAATTTACTGACT-ACTTCTTTTACTCTTACTCTC
*
12872 ATTCTACTAATTT
1 AAT-TACTAATTT
12885 CTTCTTTTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.23, C:0.25, G:0.03, T:0.49
Consensus pattern (40 bp):
AATTACTAATTTACTGACTACTTCTTTTACTCTTACTCTC
Found at i:13085 original size:38 final size:38
Alignment explanation
Indices: 13042--13538 Score: 834
Period size: 38 Copynumber: 13.1 Consensus size: 38
13032 TTAACTTTTG
* * * *
13042 ATTATCACTTTTACTAATTATTCTTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
*
13080 ATTATCAATTTTACTGATTACTAATACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
13118 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
*
13156 ATTATCAATTTTACTGATTACTATTGCTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
* * *
13194 CTTATCAATTTTACTGATTACTATTACTTTGGCTATTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
13232 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
*
13270 ATTATCAATTTTACTGATTACTATTACTTTG-GTCCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACT-CTTA
* * *
13308 ATTATCAATTTTACTGATTATTCTTACTTTGATTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
13346 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
* *
13384 CTTATCAATTTTACTGATTACTATTACTTTGGCTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
*
13422 ATTTTCAATTTTACTGATTACTATTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
13460 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
13498 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
1 ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
13536 ATT
1 ATT
13539 TTATTGGGGT
Statistics
Matches: 430, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
37 1 0.00
38 428 1.00
39 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.51
Consensus pattern (38 bp):
ATTATCAATTTTACTGATTACTATTACTTTGACTCTTA
Found at i:13121 original size:22 final size:22
Alignment explanation
Indices: 13096--13159 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
13086 AATTTTACTG
13096 ATTACTAATACTTTGACTCTTA
1 ATTACTAATACTTTGACTCTTA
*
13118 ATTA-TCAAT--TTT-A--C-TG
1 ATTACT-AATACTTTGACTCTTA
*
13134 ATTACTATTACTTTGACTCTTA
1 ATTACTAATACTTTGACTCTTA
13156 ATTA
1 ATTA
13160 TCAATTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 16
0.62 0.06 0.32
Matches are distributed among these distances:
16 7 0.23
17 2 0.06
18 3 0.10
19 2 0.06
20 3 0.10
21 2 0.06
22 12 0.39
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTACTAATACTTTGACTCTTA
Found at i:14404 original size:52 final size:50
Alignment explanation
Indices: 14341--14511 Score: 234
Period size: 51 Copynumber: 3.3 Consensus size: 50
14331 CAAAACTATC
* * * * *
14341 AAGATTCAATTTTTTATTGTTAAAATTACTAAAACCCAACTCTTACTACATA
1 AAGATTCAA-TTTTTATGGCTAAAATCACTAGAACTCAAC-CTTACTACATA
*
14393 AAGATTTAATTTTTTATGGCTAAAATCACTAGAACTCAACCTTTACTACATA
1 AAGATTCAA-TTTTTATGGCTAAAATCACTAGAACTCAACC-TTACTACATA
14445 AAGATTCAATTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
1 AAGATTCAATTTTTATGGCTAAAATCACTAGAACTCAA-CCTTACTACATA
*
14496 AAAATTCAATTTTTAT
1 AAGATTCAATTTTTAT
14512 TGTCAAGGTC
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
51 55 0.50
52 54 0.50
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.37
Consensus pattern (50 bp):
AAGATTCAATTTTTATGGCTAAAATCACTAGAACTCAACCTTACTACATA
Found at i:14511 original size:51 final size:52
Alignment explanation
Indices: 14341--14509 Score: 250
Period size: 52 Copynumber: 3.3 Consensus size: 52
14331 CAAAACTATC
* * * * * *
14341 AAGATTCAATTTTTTATTGTTAAAATTACTAAAACCCAACTCTTACTACATA
1 AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
* *
14393 AAGATTTAATTTTTTATGGCTAAAATCACTAGAACTCAACCTTTACTACATA
1 AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
14445 AAGATTCAA-TTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
1 AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
*
14496 AAAATTCAATTTTT
1 AAGATTCAATTTTT
14510 ATTGTCAAGG
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 49 0.47
52 56 0.53
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.37
Consensus pattern (52 bp):
AAGATTCAATTTTTTATGGCTAAAATCACTAGAACTCAACCCTTACTACATA
Done.