Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013945.1 Corchorus capsularis cultivar CVL-1 contig13966, 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: 33355
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:17762 original size:26 final size:27
Alignment explanation
Indices: 17733--17784 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
17723 ATTTCTTGAT
17733 TACTAATTACCAT-TTTTTACTCTTTG
1 TACTAATTACCATATTTTTACTCTTTG
*
17759 TACTGATTACCATATTTTTACTCTTT
1 TACTAATTACCATATTTTTACTCTTT
17785 TTTACTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54
Consensus pattern (27 bp):
TACTAATTACCATATTTTTACTCTTTG
Found at i:17775 original size:28 final size:28
Alignment explanation
Indices: 17733--17797 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
17723 ATTTCTTGAT
*
17733 TACTAATTACCAT-TTTTTACTC-TTTG
1 TACTGATTACCATATTTTTACTCTTTTG
*
17759 TACTGATTACCATATTTTTACTCTTTTT
1 TACTGATTACCATATTTTTACTCTTTTG
17787 TACTGATTACC
1 TACTGATTACC
17798 CCTTTTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 12 0.34
27 9 0.26
28 14 0.40
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (28 bp):
TACTGATTACCATATTTTTACTCTTTTG
Found at i:17796 original size:54 final size:52
Alignment explanation
Indices: 17732--17908 Score: 161
Period size: 54 Copynumber: 3.4 Consensus size: 52
17722 TATTTCTTGA
* *
17732 TTACTAATTACCATTTTTTACTCTTTGTACTGATTACCATATTTTTACTCTTTT
1 TTACTGATCACCATTTTTTACTCTTT-TACTGATTACCATA-TTTTACTCTTTT
* ** * *
17786 TTACTGATTACC--CCTTT--TC--TTACTGAATACCACATTTTACTCTTTT
1 TTACTGATCACCATTTTTTACTCTTTTACTGATTACCATATTTTACTCTTTT
* * * *
17832 TTACTGATCACCATTTCTTACTCTTTATCACTAATTACTC-TCTTTTACCCTTTT
1 TTACTGATCACCATTTTTTACTCTTT-T-ACTGATTAC-CATATTTTACTCTTTT
17886 TTACTGATCACCATTTTTTACTC
1 TTACTGATCACCATTTTTTACTC
17909 ATTTCTTACT
Statistics
Matches: 99, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
46 23 0.23
47 12 0.12
48 3 0.03
50 4 0.04
52 4 0.04
53 1 0.01
54 51 0.52
55 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.51
Consensus pattern (52 bp):
TTACTGATCACCATTTTTTACTCTTTTACTGATTACCATATTTTACTCTTTT
Found at i:17803 original size:17 final size:18
Alignment explanation
Indices: 17781--17823 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
17771 TATTTTTACT
* *
17781 CTTTTTTACTGATTACCC
1 CTTTTTTACTGAATACCA
17799 CTTTTCTTACTGAATACCA
1 CTTTT-TTACTGAATACCA
17818 CATTTT
1 C-TTTT
17824 ACTCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (18 bp):
CTTTTTTACTGAATACCA
Found at i:17810 original size:19 final size:18
Alignment explanation
Indices: 17781--17816 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17771 TATTTTTACT
*
17781 CTTTTTTACTGATTACCC
1 CTTTTTTACTGAATACCC
17799 CTTTTCTTACTGAATACC
1 CTTTT-TTACTGAATACC
17817 ACATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (18 bp):
CTTTTTTACTGAATACCC
Found at i:17844 original size:27 final size:27
Alignment explanation
Indices: 17799--17918 Score: 93
Period size: 27 Copynumber: 4.4 Consensus size: 27
17789 CTGATTACCC
*
17799 CTTTTCTTACTGAAT-ACCACATTTTACT
1 CTTTT-TTACTG-ATCACCACTTTTTACT
17827 CTTTTTTACTGATCACCA-TTTCTTACT
1 CTTTTTTACTGATCACCACTTT-TTACT
* * * * * *
17854 CTTTATCACTAATTA-CTCTCTTTTACC
1 CTTTTTTACTGATCACCACT-TTTTACT
*
17881 CTTTTTTACTGATCACCATTTTTTACT
1 CTTTTTTACTGATCACCACTTTTTACT
*
17908 CATTTCTTACT
1 C-TTTTTTACT
17919 CTTTTTACTG
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
26 5 0.07
27 49 0.69
28 17 0.24
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.51
Consensus pattern (27 bp):
CTTTTTTACTGATCACCACTTTTTACT
Found at i:17914 original size:65 final size:65
Alignment explanation
Indices: 17843--17973 Score: 192
Period size: 65 Copynumber: 2.0 Consensus size: 65
17833 TACTGATCAC
*
17843 CATTTCTTACTCTTTATCACTAATTACTCTCTT-TTACCCTTTTTTACTGATCACCATTTTTTAC
1 CATTTCTTACTCTTT-TCACTAATTACTCTCTTCTTACCCTTTTTTACTGATCACCACTTTTTAC
17907 T
65 T
* * * * *
17908 CATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACT
1 CATTTCTTACTCTTTTCACTAATTACTCTCTTCTTACCCTTTTTTACTGATCACCACTTTTTACT
17973 C
1 C
17974 TTCTTCTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 14 0.24
65 45 0.76
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.54
Consensus pattern (65 bp):
CATTTCTTACTCTTTTCACTAATTACTCTCTTCTTACCCTTTTTTACTGATCACCACTTTTTACT
Found at i:17955 original size:37 final size:37
Alignment explanation
Indices: 17866--17955 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
17856 TTATCACTAA
* *
17866 TTACTCTCTTTTACCCTTTTTTACTGATCACCATTTT
1 TTACTCTTTTTTACTCTTTTTTACTGATCACCATTTT
* *
17903 TTACTCATTTCTTACTC-TTTTTACTGATTACTC-TTTT
1 TTACTC-TTTTTTACTCTTTTTTACTGATCAC-CATTTT
17940 CTTACTCTTTTTTACT
1 -TTACTCTTTTTTACT
17956 GATTACCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
37 31 0.69
38 14 0.31
ACGTcount: A:0.16, C:0.24, G:0.02, T:0.58
Consensus pattern (37 bp):
TTACTCTTTTTTACTCTTTTTTACTGATCACCATTTT
Found at i:17960 original size:28 final size:27
Alignment explanation
Indices: 17903--17975 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
17893 TCACCATTTT
17903 TTACTCATTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTACTGA
*
17930 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCATTTCTTACTC-TTTTTACTGA
17958 TTAC-CACTTT-TTACTCTT
1 TTACTCA-TTTCTTACTCTT
17976 CTTCTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 2 0.05
27 23 0.55
28 17 0.40
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.58
Consensus pattern (27 bp):
TTACTCATTTCTTACTCTTTTTACTGA
Found at i:17972 original size:38 final size:36
Alignment explanation
Indices: 17930--18012 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 36
17920 TTTTTACTGA
* *
17930 TTACTCTT-TTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTCTTCTTACTC-ATTTTACTGACTACCA--TT
**
17968 TTACTCTTCTTCTTTTTCATTTTACTGACTACCATT
1 TTACTCTTCTTCTTACTCATTTTACTGACTACCATT
18004 TTACTCTTC
1 TTACTCTTC
18013 GAATTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
36 11 0.28
38 22 0.55
39 7 0.17
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.57
Consensus pattern (36 bp):
TTACTCTTCTTCTTACTCATTTTACTGACTACCATT
Found at i:18148 original size:22 final size:20
Alignment explanation
Indices: 18121--18485 Score: 142
Period size: 20 Copynumber: 17.1 Consensus size: 20
18111 TGAATCTGGA
18121 TTACTGATTACCCTTTTTACTT
1 TTACTGATTA-CC-TTTTACTT
* *
18143 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
*
18162 CTTACTGATTA-CTATTACTCT
1 -TTACTGATTACCTTTTACT-T
18183 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
* *
18205 TTACTAATTACCATTTTACCCT
1 TTACTGATTACC-TTTTA-CTT
* *
18227 TTACAGA-TACCTTTTAAATTT
1 TTACTGATTACCTTTT--ACTT
*
18248 TTATTGATTACCTTTTTACTTTTTT
1 TTACTGATTACC-TTTTAC----TT
* *
18273 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
18292 CTTACTGATT-TCTATTACTCT
1 -TTACTGATTACCTTTTACT-T
18313 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
* * *
18335 TTGCTAATTACCATTTTACCCT
1 TTACTGATTACC-TTTTA-CTT
*
18357 TTA-AGA-TACCTTTTTACTTT
1 TTACTGATTACC-TTTTAC-TT
18377 TTACTGATTACCTTTCTACTTTT
1 TTACTGATTACCTTT-TAC--TT
* *
18400 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
18419 CTTACTGATT-TCTATTACTCT
1 -TTACTGATTACCTTTTACT-T
18440 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
*
18462 TTACTGATTGCCCTTTTTACTT
1 TTACTGATT-ACC-TTTTACTT
18484 TT
1 TT
18486 TGGAACTTAA
Statistics
Matches: 270, Mismatches: 34, Indels: 78
0.71 0.09 0.20
Matches are distributed among these distances:
19 12 0.04
20 97 0.36
21 26 0.10
22 92 0.34
23 32 0.12
24 1 0.00
25 10 0.04
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTT
Found at i:18295 original size:130 final size:127
Alignment explanation
Indices: 18121--18466 Score: 579
Period size: 130 Copynumber: 2.7 Consensus size: 127
18111 TGAATCTGGA
* *
18121 TTACTGATTACCCTTTTTAC--TTTTACTGTTTACTATTACTTCTTACTGATTACTATTACTCTT
1 TTACTGATTA-CCTTTCTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTT
18184 TACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCTTTTAAATTT
65 TACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTA-AGATACCTTTTAAATTT
* *
18248 TTATTGATTACCTTTTTACTTTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCT
1 TTACTGATTACCTTTCTAC--TTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCT
* * *
18313 TTACTGATTATCACTTTACTCTTTGCTAATTACCATTTTACCCTTTAAGATACCTTTTTACTTT
64 TTACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTAAGATACCTTTTAAATTT
18377 TTACTGATTACCTTTCTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTT
1 TTACTGATTACCTTTCTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTT
18442 ACTGATTATCACTTTACTCTTTACT
66 ACTGATTATCACTTTACTCTTTACT
18467 GATTGCCCTT
Statistics
Matches: 207, Mismatches: 8, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
126 9 0.04
127 79 0.38
129 32 0.15
130 87 0.42
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (127 bp):
TTACTGATTACCTTTCTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTT
ACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTAAGATACCTTTTAAATTT
Found at i:25307 original size:14 final size:14
Alignment explanation
Indices: 25288--25321 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
25278 GCATATTAAC
25288 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
25302 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
25316 ATTAGT
1 TTTAGT
25322 ATCATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:26547 original size:48 final size:48
Alignment explanation
Indices: 26487--27135 Score: 881
Period size: 48 Copynumber: 13.5 Consensus size: 48
26477 TGTCTAATAA
* *
26487 AGTTTTGCCCTTCCCGGTCGGAAGGTGTC-GTCTTCAGTGTCTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTG-CAGTCTTCGGTGTTTATTTCC
* * * * *
26535 AGATTTGCCCTTCCTGGTCAGAAGGTGTAGTCTTCGGTCTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* *
26583 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTGTA-TTAC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* * * *
26630 AGATTTGCCCTTCCCGGTCGGAAGGTGCCGTCTTCAGTGTCTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* * * *
26678 AGATTTGCCCTTCCCGGTCGAAAGGTGCAGTCTTCGATCTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* *
26726 AGTTTTGCCCTTCCCGGTAGGAAGGTGCAGTCTTTGGTGTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
** * *
26774 AGTTTTGCCCTTCCCGGTCGGAAGGTGCCCTCTTCAGTGTCTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* * *
26822 TGATTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTCTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* *
26870 AGTTTTGCCCTTCCCGGTCGGAAGGTG-ATGTCTTCGATCTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCA-GTCTTCGGTGTTTATTTCC
26918 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* * * **
26966 AGTTTTGCCCTTCCCGCTCGGAAGGTGCCGTCTTCAGTGTCAATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* * *
27014 AGATTCGCCCTTCCCAGGTCGGAAGGTGCAGTCTTCGGTCTTTATTTCC
1 AGTTTTGCCCTTCCC-GGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
*
27063 AGTTTTGCCCTTCCCGGTCGTAAGGTGCAGTCTTCGGTGTTTATTTCC
1 AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
* * **
27111 TGTTTTGCCATTCCCGAACGGAAGG
1 AGTTTTGCCCTTCCCGGTCGGAAGG
27136 CGCTAGATTT
Statistics
Matches: 525, Mismatches: 71, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
47 43 0.08
48 441 0.84
49 41 0.08
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.36
Consensus pattern (48 bp):
AGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCC
Found at i:28478 original size:35 final size:35
Alignment explanation
Indices: 28431--28514 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
28421 ATTTTTAGGA
*
28431 ATTCAGACGACTCGGTGTAGCATCTTCAAAATTGG
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAATTGG
* * * *
28466 CTTCAGATGACTCAGTGTGGCATCTTCAAGATTGG
1 ATTCAGATGACTCGGTGTAGCATCTTCAAAATTGG
28501 ATTC-GATGAGCTCG
1 ATTCAGATGA-CTCG
28515 ATGCAGCACA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 5 0.12
35 36 0.88
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (35 bp):
ATTCAGATGACTCGGTGTAGCATCTTCAAAATTGG
Found at i:28552 original size:6 final size:6
Alignment explanation
Indices: 28543--28591 Score: 71
Period size: 6 Copynumber: 7.7 Consensus size: 6
28533 CAATTTAGAT
28543 TTAGGG TTAGGG TTAGGG TTAGGG TTTAGGG TTTAGGG TTTAGGG TTAG
1 TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG -TTAGGG -TTAGGG TTAG
28592 ACACTTTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 22 0.52
7 20 0.48
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:28573 original size:7 final size:7
Alignment explanation
Indices: 28542--28589 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
28532 ACAATTTAGA
28542 TTTAGGG
1 TTTAGGG
28549 -TTAGGG
1 TTTAGGG
28555 -TTAGGG
1 TTTAGGG
28561 -TTAGGG
1 TTTAGGG
28567 TTTAGGG
1 TTTAGGG
28574 TTTAGGG
1 TTTAGGG
28581 TTTAGGG
1 TTTAGGG
28588 TT
1 TT
28590 AGACACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 18 0.45
7 22 0.55
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:28580 original size:14 final size:13
Alignment explanation
Indices: 28542--28591 Score: 84
Period size: 14 Copynumber: 3.8 Consensus size: 13
28532 ACAATTTAGA
28542 TTTAGGGTTAGGG
1 TTTAGGGTTAGGG
28555 -TTAGGGTTAGGG
1 TTTAGGGTTAGGG
28567 TTTAGGGTTTAGGG
1 TTTAGGG-TTAGGG
28581 TTTAGGGTTAG
1 TTTAGGGTTAG
28592 ACACTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.34
13 10 0.29
14 13 0.37
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TTTAGGGTTAGGG
Found at i:32313 original size:19 final size:19
Alignment explanation
Indices: 32291--32329 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
32281 CCTCTTAGCA
32291 TTGTACTTGGGTCTTGAAT
1 TTGTACTTGGGTCTTGAAT
** *
32310 TTGTTGTTGGGTCTTTAAT
1 TTGTACTTGGGTCTTGAAT
32329 T
1 T
32330 AGTTTAGGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.08, G:0.26, T:0.54
Consensus pattern (19 bp):
TTGTACTTGGGTCTTGAAT
Done.