Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024519.1 Corchorus olitorius cultivar O-4 contig24552, 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: 19195
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2016 original size:7 final size:7
Alignment explanation
Indices: 2004--2058 Score: 67
Period size: 7 Copynumber: 7.4 Consensus size: 7
1994 GTTAAAATAA
2004 TATATAT
1 TATATAT
2011 TATATAT
1 TATATAT
2018 TATATAT
1 TATATAT
2025 TATAT-T
1 TATATAT
2031 ATATTATAT
1 -TA-TATAT
2040 TATATTATT
1 TATA-TA-T
2049 TATATAT
1 TATATAT
2056 TAT
1 TAT
2059 TTGAAACACC
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.02
7 27 0.63
8 9 0.21
9 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATATAT
Found at i:2021 original size:5 final size:5
Alignment explanation
Indices: 2006--2053 Score: 66
Period size: 5 Copynumber: 10.0 Consensus size: 5
1996 TAAAATAATA
2006 TATAT TATA- TAT-T ATATAT TATAT TATAT TATAT TATAT TAT-T TATAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT
2054 ATTATTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 7 0.18
5 31 0.79
6 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:3856 original size:24 final size:24
Alignment explanation
Indices: 3810--3856 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3800 TTAATATACC
3810 CTAATCCTTTTTAAAAAATAAATA
1 CTAATCCTTTTTAAAAAATAAATA
3834 CTAATCC-TTTTACAAAAATAAAT
1 CTAATCCTTTTTA-AAAAATAAAT
3857 CTTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (24 bp):
CTAATCCTTTTTAAAAAATAAATA
Found at i:5637 original size:14 final size:14
Alignment explanation
Indices: 5618--5665 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
5608 TTTCACCTCC
5618 TATGCACTTGCACA
1 TATGCACTTGCACA
* *
5632 TATGCA-TT-AACC
1 TATGCACTTGCACA
*
5644 TATTCACTTGCACA
1 TATGCACTTGCACA
5658 TATGCACT
1 TATGCACT
5666 AAATATACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (14 bp):
TATGCACTTGCACA
Found at i:9370 original size:2 final size:2
Alignment explanation
Indices: 9347--9429 Score: 54
Period size: 2 Copynumber: 45.0 Consensus size: 2
9337 ATGTTTTCTG
* * *
9347 AT AT AT TT AT AA AT -T AT A- AT AT AT AT A- AT -T AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
9385 AT AT TT AT A- AT AT AT A- AT AT AT AT AA AA AT AT TT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9424 AT AT AT
1 AT AT AT
9430 TAAAATCCTA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
1 7 0.11
2 55 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9372 original size:20 final size:19
Alignment explanation
Indices: 9347--9408 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
9337 ATGTTTTCTG
9347 ATATATTTATAAATTAT-A-
1 ATATATTTAT-AATTATAAT
9365 ATATA--TATAATTATATAT
1 ATATATTTATAATTATA-AT
*
9383 AAATATTTATAATATATAAT
1 ATATATTTATAAT-TATAAT
9403 ATATAT
1 ATATAT
9409 AAAAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.17
16 3 0.08
17 1 0.03
18 9 0.25
20 13 0.36
21 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATTTATAATTATAAT
Found at i:9381 original size:10 final size:9
Alignment explanation
Indices: 9349--9429 Score: 61
Period size: 9 Copynumber: 9.7 Consensus size: 9
9339 GTTTTCTGAT
*
9349 ATATTTATA
1 ATATATATA
9358 A-AT-TATA
1 ATATATATA
9365 ATATATATA
1 ATATATATA
9374 ATTATATATA
1 A-TATATATA
*
9384 A-ATAT-TT
1 ATATATATA
9391 ATAATATATA
1 AT-ATATATA
9401 ATATATATA
1 ATATATATA
9410 A-A-A-AT-
1 ATATATATA
*
9415 ATTTATATA
1 ATATATATA
9424 ATATAT
1 ATATAT
9430 TAAAATCCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
5 1 0.02
6 2 0.03
7 9 0.16
8 11 0.19
9 23 0.40
10 12 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATATA
Found at i:9386 original size:26 final size:26
Alignment explanation
Indices: 9349--9429 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
9339 GTTTTCTGAT
*
9349 ATATTTATAAAT-TATAAT-ATATATA
1 ATATATATAAATAT-TAATAATATATA
*
9374 ATTATATATAAATATTTATAATATATA
1 A-TATATATAAATATTAATAATATATA
9401 ATATATATAAAAATATTTATATAATATAT
1 ATATATAT--AAATA-TTA-ATAATATAT
9430 TAAAATCCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.02
26 20 0.43
27 9 0.20
28 5 0.11
29 2 0.04
30 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATATATAAATATTAATAATATATA
Found at i:9427 original size:28 final size:27
Alignment explanation
Indices: 9365--9428 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
9355 ATAAATTATA
*
9365 ATAT-ATATAATTATATATAAATATTT
1 ATATAATATAATTATATAAAAATATTT
9391 ATA-ATATATAATATATATAAAAATATTT
1 ATATA-ATATAAT-TATATAAAAATATTT
9419 ATATAATATA
1 ATATAATATA
9429 TTAAAATCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 7 0.21
28 22 0.67
29 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATAATATAATTATATAAAAATATTT
Found at i:9429 original size:30 final size:27
Alignment explanation
Indices: 9367--9421 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
9357 AAATTATAAT
*
9367 ATATATAATTATATATAAATATTTATA
1 ATATATAATTATATAAAAATATTTATA
9394 ATATATAATATATATAAAAATATTTATA
1 ATATATAAT-TATATAAAAATATTTATA
9422 TAATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATAATTATATAAAAATATTTATA
Found at i:14807 original size:27 final size:27
Alignment explanation
Indices: 14769--14822 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
14759 AATTCAACAT
14769 TCATAGAATAACAAAGGAGAAAAAGAA
1 TCATAGAATAACAAAGGAGAAAAAGAA
14796 TCATAGAATAACAAAGGAGAAAAAGAA
1 TCATAGAATAACAAAGGAGAAAAAGAA
14823 GTTATACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.63, C:0.07, G:0.19, T:0.11
Consensus pattern (27 bp):
TCATAGAATAACAAAGGAGAAAAAGAA
Found at i:18971 original size:27 final size:28
Alignment explanation
Indices: 18935--19008 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
18925 TCCGGCATTT
* *
18935 AAGGGCAAAACTGTAATTTAATC-AACC
1 AAGGGTAAAACTGTAATTTAAGCTAACC
* * *
18962 AGGGGTAAAA-TGGTAATTTTAGCTGACC
1 AAGGGTAAAACT-GTAATTTAAGCTAACC
*
18990 AAGGGTAAAACAGTAATTT
1 AAGGGTAAAACTGTAATTT
19009 TGACATCTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.03
27 17 0.46
28 19 0.51
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (28 bp):
AAGGGTAAAACTGTAATTTAAGCTAACC
Done.