Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168199.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_435, 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: 26972
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:2522 original size:16 final size:17
Alignment explanation
Indices: 2488--2539 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2478 CTTTATTTCT
*
2488 ATTTTTCAAAAACAAAAA
1 ATTTTGCAAAAA-AAAAA
2506 A-TTTG-AAAAAAAGAAA
1 ATTTTGCAAAAAAA-AAA
2522 ATTTTGCAAAAAAAAAA
1 ATTTTGCAAAAAAAAAA
2539 A
1 A
2540 AAAAAGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 2 0.07
16 9 0.30
17 11 0.37
18 8 0.27
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (17 bp):
ATTTTGCAAAAAAAAAA
Found at i:4548 original size:18 final size:19
Alignment explanation
Indices: 4525--4563 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4515 AATTAGAATT
* *
4525 AATATATTTTTAT-TGAAA
1 AATATATATTAATATGAAA
4543 AATATATATTAATATGAAA
1 AATATATATTAATATGAAA
4562 AA
1 AA
4564 ATTACCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AATATATATTAATATGAAA
Found at i:7059 original size:221 final size:221
Alignment explanation
Indices: 6670--7099 Score: 702
Period size: 221 Copynumber: 1.9 Consensus size: 221
6660 TGTTCGGTCC
*
6670 ATCACCTAATTACATGGAATCAATTAATTAACTAATATACCTTTTTTGTAATTGAAGCTATCAAA
1 ATCACCTAATTACATGGAATCAATTAATTAACTAATATACCTTTTTTGTAACTGAAGCTATCAAA
* * * *
6735 AATTAAATCTGATTTTTTTACGTCCAAAGGTTATTTTGGTCATTTTTTTCATTAGAGACTACCAA
66 AATTAAATCCGATCTTTTTACATCCAAAGGTTATTTTGGTCATTTTTTTCATTAAAGACTACCAA
* *
6800 TAAATAGCCAAGGGCATTTTAGACTTTTGGACTGACCTTACATGTCTGATCAACTTAATG-CTAC
131 CAAATAGCCAAGGGCATTTTAGACTTTTAGACTGACCTTACATGTCTGATCAACTTAATGTC-AC
*
6864 AGTACCACGTTAGCTTAACTTCGATCA
195 AGTACCACGTCAGCTTAACTTCGATCA
* * *
6891 ATCACCTAATTACATGGAATCAATTAATTAACTAATATACCTTTTTTTTTACTGAAGTTATCAAA
1 ATCACCTAATTACATGGAATCAATTAATTAACTAATATACCTTTTTTGTAACTGAAGCTATCAAA
6956 AATTAAATCCGA-CTTTTTACATCCAAAGGTTATTTTGGTCATCTTTTTTCATTAAAGACTACCA
66 AATTAAATCCGATCTTTTTACATCCAAAGGTTATTTTGGTCAT-TTTTTTCATTAAAGACTACCA
* * *
7020 ACAAATAGCTAGGGGCATTTTAGACTTTTAGATTGACCTTACATGTCTGATCAACTTAATGTCAC
130 ACAAATAGCCAAGGGCATTTTAGACTTTTAGACTGACCTTACATGTCTGATCAACTTAATGTCAC
7085 AGTACCACGTCAGCT
195 AGTACCACGTCAGCT
7100 CAACCACCTT
Statistics
Matches: 193, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
220 28 0.15
221 164 0.85
222 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (221 bp):
ATCACCTAATTACATGGAATCAATTAATTAACTAATATACCTTTTTTGTAACTGAAGCTATCAAA
AATTAAATCCGATCTTTTTACATCCAAAGGTTATTTTGGTCATTTTTTTCATTAAAGACTACCAA
CAAATAGCCAAGGGCATTTTAGACTTTTAGACTGACCTTACATGTCTGATCAACTTAATGTCACA
GTACCACGTCAGCTTAACTTCGATCA
Found at i:8648 original size:25 final size:25
Alignment explanation
Indices: 8588--8660 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
8578 TGTATAAAAA
* * *
8588 ATAATTTCAAAATATAAAAAAGTA-
1 ATAATTTTAAGATATAAAAAAATAT
* *
8612 AGAGTTTT-AGATATAAAAAAATAT
1 ATAATTTTAAGATATAAAAAAATAT
8636 ATAATTTTAAGATATAAAAAAATAT
1 ATAATTTTAAGATATAAAAAAATAT
8661 GAACAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 13 0.32
24 11 0.28
25 16 0.40
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (25 bp):
ATAATTTTAAGATATAAAAAAATAT
Found at i:8795 original size:32 final size:31
Alignment explanation
Indices: 8754--8831 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
8744 ATCCAAATAA
8754 AACCCAAACGAAGCCTAAA-CATTAGATTTCTG
1 AACCCAAACGAAGCCTAAATC--TAGATTTCTG
* *
8786 AACCAAAACGAAGCCTAAATCTAGATTTTTG
1 AACCCAAACGAAGCCTAAATCTAGATTTCTG
*
8817 AACCCAAACAAAGCC
1 AACCCAAACGAAGCC
8832 CAAAGTCTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 22 0.54
32 18 0.44
33 1 0.02
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.19
Consensus pattern (31 bp):
AACCCAAACGAAGCCTAAATCTAGATTTCTG
Found at i:11118 original size:24 final size:25
Alignment explanation
Indices: 11091--11139 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
11081 ATTTTAATTG
*
11091 CGTTTATAAAATTAA-AAAAATTTT
1 CGTTAATAAAATTAATAAAAATTTT
* *
11115 CGTTAATATATTTAATAAAAATTTT
1 CGTTAATAAAATTAATAAAAATTTT
11140 TATAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
CGTTAATAAAATTAATAAAAATTTT
Found at i:11516 original size:3 final size:3
Alignment explanation
Indices: 11508--11551 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
11498 TAAAGGTTTG
11508 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11552 AAGACTCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:14019 original size:298 final size:288
Alignment explanation
Indices: 13268--14027 Score: 629
Period size: 300 Copynumber: 2.6 Consensus size: 288
13258 GTAAATAATT
* * * * *
13268 GAGAAGAATAATAAAATTCA-TATAAATTTGT-TTAAAATAAGTTAGAAGTGA-CGTAATACCTT
1 GAGAA-AA-AATAAAA-TCAGTAT-AATTTGTAGTAAAATGAGTTAAAAGT-ATTGTAACACCTT
* * ** * *
13330 AAGATAGAATTATAAAAATTTTAAATATAATGAAAGGTAAGAA-TAAATGTAA-AAAGATATTTT
61 AAAAAAGAATTATAAAAATTTT-AATATAATGAAACTTAA-AAGTAAATATAAGAAA-ATATTAT
* * * *
13393 TTTAACATAAATGATTGAGTTG-TTACATAAAATTTAAATTAATTATTATTCATGTAAATATTTT
123 TTT-ACATAAATAATT-AATTGAAT-CGTAAAATTTAAATTAATTATTATTCATGTAAATATTTT
* *
13457 TAGGCCAATGACTAAAAAAATACTTAAAAGTAAAAAAAGACAGTGTTAAAAAATTAATTTTTGAA
185 TAGGCCAATGACTAAAAAAATACTTAAAACTAAAAAAAGACAATGTTAAAAAATTAATTTTTGAA
*** *
13522 AATAAAAATATTAAAAAAATTATTAATGTAAACATGTGT
250 AATAAAAATATTAAAAAAATTATTAACACAAACATGTGA
** * * * * * *
13561 GAGAAATTATAAAATTAGTATAATTTGTTGTAAAATGGGTTAAAAGTGTTATAACA--TGAAAAG
1 GAGAAAAAATAAAATCAGTATAATTTGTAGTAAAATGAGTTAAAAGTATTGTAACACCTTAAAA-
* * * * *
13624 ACAAAATTATAAAAATTTTAACATAA--ATAATTTAGAAAAGAATAAGTATAAGAAGATATTATT
65 A-AGAATTATAAAAATTTTAATATAATGA-AACTT--AAAAG--TAAATATAAGAAAATATTATT
* * * **
13687 TTAGCATAAATAA-TAA-AGAATAAGTATAAAAATTTAAATTAATTATTGTTTTTGTAAATA-TT
124 TTA-CATAAATAATTAATTGAAT-CG--T-AAAATTTAAATTAATTATTATTCATGTAAATATTT
* *
13749 TTAGGCC-ATGACT-AAAAAATATTTTAAAGACTAAAAGAATAAAAGACAATGTT-AAAAATTCA
184 TTAGGCCAATGACTAAAAAAATA-CTTAAA-ACT---A-AA-AAAAGACAATGTTAAAAAATTAA
*
13811 TTTTTGAAAATAAATAATCTTCAAAAAAAATTATTAACACAAACATGTGA
242 TTTTTGAAAATAAA-AATATT--AAAAAAATTATTAACACAAACATGTGA
* *
13861 GAGAAAAAATAAAATGCA-TATCATTTGTAGTAAAATGAGTTAAAA-TCATTGTAACACCTTAAT
1 GAGAAAAAATAAAAT-CAGTATAATTTGTAGTAAAATGAGTTAAAAGT-ATTGTAACACCTTAAA
* *
13924 AAAGAATTATGAAAATTTTAAGTATAATGAAACTTAAAAGTAAACATAAGAAAATATTATTTTGA
64 AAAGAATTATAAAAATTTTAA-TATAATGAAACTTAAAAGTAAATATAAGAAAATATTATTTT-A
13989 CATAAATAATTCAATTGACATCGTAAAATTTAAATTAAT
127 CATAAATAATT-AATTGA-ATCGTAAAATTTAAATTAAT
14028 CATTTGTCCT
Statistics
Matches: 369, Mismatches: 59, Indels: 73
0.74 0.12 0.15
Matches are distributed among these distances:
288 1 0.00
289 7 0.02
290 18 0.05
291 56 0.15
292 14 0.04
293 41 0.11
294 31 0.08
296 1 0.00
297 24 0.07
298 61 0.17
299 4 0.01
300 91 0.25
301 9 0.02
302 10 0.03
303 1 0.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (288 bp):
GAGAAAAAATAAAATCAGTATAATTTGTAGTAAAATGAGTTAAAAGTATTGTAACACCTTAAAAA
AGAATTATAAAAATTTTAATATAATGAAACTTAAAAGTAAATATAAGAAAATATTATTTTACATA
AATAATTAATTGAATCGTAAAATTTAAATTAATTATTATTCATGTAAATATTTTTAGGCCAATGA
CTAAAAAAATACTTAAAACTAAAAAAAGACAATGTTAAAAAATTAATTTTTGAAAATAAAAATAT
TAAAAAAATTATTAACACAAACATGTGA
Found at i:14237 original size:14 final size:14
Alignment explanation
Indices: 14218--14254 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14208 CTTTAAAGGC
* *
14218 TAAAAAGTTAATGT
1 TAAAAAATTAATAT
14232 TAAAAAATTAATAT
1 TAAAAAATTAATAT
14246 TAAAAAATT
1 TAAAAAATT
14255 CAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (14 bp):
TAAAAAATTAATAT
Found at i:16137 original size:63 final size:62
Alignment explanation
Indices: 16070--16418 Score: 260
Period size: 63 Copynumber: 5.5 Consensus size: 62
16060 CTAAAAACAT
* * *
16070 TTTTTTACAGAAAATACCTTCAATAATCCTCTCTAAAAAAATTATAAAGGATTATTGAAGGCG
1 TTTTTTACAAAAAATACCTTCAATAATCCTCTC-AAAAAAATTAGAAGGGATTATTGAAGGCG
* * ** *
16133 TTTTTGACCAAAAAATACCATCAATAATTCC-CTCAAAAAAATTAGAAAAGATTATTGAAGACG
1 TTTTTTA-CAAAAAATACCTTCAATAA-TCCTCTCAAAAAAATTAGAAGGGATTATTGAAGGCG
* * * * *
16196 TTTTTTAGTAAAAAATACCTTCAATAATCTTCTCATATAAAA-T-GAAGGAGATTATTGAAAGTG
1 TTTTTTA-CAAAAAATACCTTCAATAATCCTCTCA-AAAAAATTAGAAGG-GATTATTGAAGGCG
* ** * ** * *
16259 TTTTTTTACAGAAAACGCCTTTAATAAT-CTCCTTTAAAAAATTAGAGGGGATTATTGAAAGCAG
1 -TTTTTTACAAAAAATACCTTCAATAATCCT-CTCAAAAAAATTAGAAGGGATTATTGAAGGC-G
* * * * *
16323 TTTTGGT-CAAAAAACACCTTTAATAATCCCCTCAAAAAAATTTA-AGGGGGATTATTGAAGGCA
1 TTTT-TTACAAAAAATACCTTCAATAATCCTCTCAAAAAAA-TTAGA-AGGGATTATTGAAGGC-
*
16386 TTT
62 --G
* *
16389 TTTTTTTCAAAAAATGCCTTCAATAATCCT
1 TTTTTTACAAAAAATACCTTCAATAATCCT
16419 ATTTGCAAAT
Statistics
Matches: 227, Mismatches: 42, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
62 11 0.05
63 132 0.58
64 57 0.25
65 4 0.02
66 23 0.10
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (62 bp):
TTTTTTACAAAAAATACCTTCAATAATCCTCTCAAAAAAATTAGAAGGGATTATTGAAGGCG
Done.