Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168085.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_332, 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: 34227
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:554 original size:3 final size:3
Alignment explanation
Indices: 548--573 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
538 TTTTTTTCAT
548 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
574 TCTGCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3876 original size:16 final size:15
Alignment explanation
Indices: 3849--3887 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
3839 GTACTATTAA
3849 AAAATAG-CCTTTTC
1 AAAATAGCCCTTTTC
*
3863 AAAATAGCCACTTTTT
1 AAAATAGCC-CTTTTC
3879 AAAATAGCC
1 AAAATAGCC
3888 TCACCGGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.32
15 1 0.05
16 14 0.64
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (15 bp):
AAAATAGCCCTTTTC
Found at i:5539 original size:17 final size:17
Alignment explanation
Indices: 5499--5531 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5489 TAAAAATCGA
5499 TGTAAAAAAAAGAGGTC
1 TGTAAAAAAAAGAGGTC
5516 TGTAAAAAAAAGAGGT
1 TGTAAAAAAAAGAGGT
5532 TAGTAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.18
Consensus pattern (17 bp):
TGTAAAAAAAAGAGGTC
Found at i:10346 original size:10 final size:9
Alignment explanation
Indices: 10326--10368 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
10316 TAATATGCTT
*
10326 AAAAAATAA
1 AAAAAAGAA
*
10335 AAAAATGAA
1 AAAAAAGAA
10344 AAAAAAGAGA
1 AAAAAAGA-A
10354 AAAAAAGAA
1 AAAAAAGAA
10363 AAAAAA
1 AAAAAA
10369 AAAGACTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:10517 original size:16 final size:16
Alignment explanation
Indices: 10484--10563 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 16
10474 CCCATTGATG
10484 TATTGATTTATTT-GTT
1 TATT-ATTTATTTAGTT
*
10500 TATTATTTATTTATTT
1 TATTATTTATTTAGTT
*
10516 TATTATTTTTTTAAGATT
1 TATTATTTATTT-AG-TT
*
10534 TATCATGATTATTTA-TT
1 TATTAT--TTATTTAGTT
10551 TATTTATTT-TTTA
1 TA-TTATTTATTTA
10564 TTCTTGTTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
15 12 0.23
16 19 0.37
17 5 0.10
18 10 0.19
19 1 0.02
20 5 0.10
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.69
Consensus pattern (16 bp):
TATTATTTATTTAGTT
Found at i:11076 original size:10 final size:10
Alignment explanation
Indices: 11061--11102 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
11051 CTTGAATCCT
11061 AGAGAGAGAA
1 AGAGAGAGAA
11071 AGAGAGA-AA
1 AGAGAGAGAA
11080 AGA-AGAGGAA
1 AGAGAGA-GAA
11090 A-AGAGAGAA
1 AGAGAGAGAA
11099 AGAG
1 AGAG
11103 GAGGAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.11
9 10 0.36
10 15 0.54
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAA
Found at i:11361 original size:3 final size:3
Alignment explanation
Indices: 11353--11389 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
11343 TGCGTCAAGA
11353 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11390 GCTTATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:23323 original size:19 final size:20
Alignment explanation
Indices: 23301--23359 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
23291 ATATCATATT
23301 ATGCAATAAATATAA-AATC
1 ATGCAATAAATATAATAATC
23320 ATGCAAT-AATAATAATAATC
1 ATGCAATAAAT-ATAATAATC
* *
23340 ATTCAAATAAATATATTAAT
1 ATGC-AATAAATATAATAAT
23360 AATCATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.09
19 11 0.32
20 7 0.21
21 10 0.29
22 3 0.09
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.32
Consensus pattern (20 bp):
ATGCAATAAATATAATAATC
Found at i:23540 original size:41 final size:41
Alignment explanation
Indices: 23406--23650 Score: 281
Period size: 39 Copynumber: 6.1 Consensus size: 41
23396 ATGCTAATAG
* * *
23406 ACATGCAATTAAATGTATAATCATGAAATTAACAATA-AAA
1 ACATGCAAATAAATATATAATCATGCAATTAACAATATAAA
* *
23446 ATCA-CCAAATAAATATATAATAATGCAATTAACAATATAAA
1 A-CATGCAAATAAATATATAATCATGCAATTAACAATATAAA
* *
23487 TCATGCAAAT--ATATATAATCACGCAATTAACAATATAAA
1 ACATGCAAATAAATATATAATCATGCAATTAACAATATAAA
*
23526 ACATGCAAAT--ATATATTATCATGCAATTAACAATATAAA
1 ACATGCAAATAAATATATAATCATGCAATTAACAATATAAA
* *
23565 ACTTGCAATTAAATATATAATCATGCAATTAACAATATAAA
1 ACATGCAAATAAATATATAATCATGCAATTAACAATATAAA
* * * * *
23606 A-AAGCCTACTAAAGATATAATCAAGCAATTAACAATAT-AA
1 ACATG-CAAATAAATATATAATCATGCAATTAACAATATAAA
23646 ACATG
1 ACATG
23651 GAATCACAAA
Statistics
Matches: 176, Mismatches: 22, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
39 71 0.40
40 35 0.20
41 70 0.40
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (41 bp):
ACATGCAAATAAATATATAATCATGCAATTAACAATATAAA
Found at i:23550 original size:18 final size:18
Alignment explanation
Indices: 23480--23551 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
23470 GCAATTAACA
23480 ATATA-AATCATGCAAAT
1 ATATATAATCATGCAAAT
* *
23497 ATATATAATCACGCAATT
1 ATATATAATCATGCAAAT
* *
23515 AACAATATAAAACATGCAAAT
1 -A-TATAT-AATCATGCAAAT
*
23536 ATATATTATCATGCAA
1 ATATATAATCATGCAA
23552 TTAACAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
17 5 0.12
18 18 0.43
19 5 0.12
20 5 0.12
21 9 0.21
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATATAATCATGCAAAT
Found at i:23689 original size:20 final size:20
Alignment explanation
Indices: 23664--23728 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
23654 TCACAAAAAT
23664 AAATAAATTGATAATCATGC
1 AAATAAATTGATAATCATGC
*
23684 AAATAAATTGATAATCATGT
1 AAATAAATTGATAATCATGC
* * * *
23704 AAATATATTAATAGTCACGC
1 AAATAAATTGATAATCATGC
23724 AAATA
1 AAATA
23729 TATTAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (20 bp):
AAATAAATTGATAATCATGC
Found at i:23726 original size:40 final size:41
Alignment explanation
Indices: 23662--23756 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
23652 AATCACAAAA
* * * * *
23662 ATAAATAAATTGATAATCATGCAAATAAATTGAT-AATCAT
1 ATAAATATATTAATAATCACGCAAATAAATTAATAAATCAC
* * *
23702 GTAAATATATTAATAGTCACGCAAATATATTAATAAATCAC
1 ATAAATATATTAATAATCACGCAAATAAATTAATAAATCAC
*
23743 ACAAATATATTAAT
1 ATAAATATATTAAT
23757 CATACAAATA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
40 27 0.61
41 17 0.39
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (41 bp):
ATAAATATATTAATAATCACGCAAATAAATTAATAAATCAC
Found at i:23729 original size:20 final size:21
Alignment explanation
Indices: 23704--23756 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
23694 ATAATCATGT
* *
23704 AAATATATTAAT-AGTCACGC
1 AAATATATTAATAAATCACAC
23724 AAATATATTAATAAATCACAC
1 AAATATATTAATAAATCACAC
23745 AAATATATTAAT
1 AAATATATTAAT
23757 CATACAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (21 bp):
AAATATATTAATAAATCACAC
Found at i:23782 original size:16 final size:16
Alignment explanation
Indices: 23761--23806 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
23751 ATTAATCATA
23761 CAAATAAAATATTAAG
1 CAAATAAAATATTAAG
* * *
23777 CAAATAAATTATCATG
1 CAAATAAAATATTAAG
*
23793 CAAATATAATATTA
1 CAAATAAAATATTA
23807 GTCATGCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (16 bp):
CAAATAAAATATTAAG
Found at i:23797 original size:32 final size:33
Alignment explanation
Indices: 23744--23806 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
23734 ATAAATCACA
*
23744 CAAATATATTAATCATACAAATAAAATATTAAG
1 CAAATAAATTAATCATACAAATAAAATATTAAG
* *
23777 CAAATAAATT-ATCATGCAAATATAATATTA
1 CAAATAAATTAATCATACAAATAAAATATTA
23807 GTCATGCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.32
Consensus pattern (33 bp):
CAAATAAATTAATCATACAAATAAAATATTAAG
Found at i:23813 original size:20 final size:18
Alignment explanation
Indices: 23780--23817 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
23770 TATTAAGCAA
23780 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
23798 ATAATATTAGTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
23818 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Found at i:24468 original size:19 final size:19
Alignment explanation
Indices: 24444--24485 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
24434 TCTTTTGACA
*
24444 AAAAAATA-AAATTTAAACT
1 AAAAAATATAAATATAAA-T
24463 AAAAAATATAAATATAAAT
1 AAAAAATATAAATATAAAT
24482 AAAA
1 AAAA
24486 TTTAGGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAATATAAATATAAAT
Found at i:25674 original size:76 final size:76
Alignment explanation
Indices: 25538--25684 Score: 197
Period size: 76 Copynumber: 1.9 Consensus size: 76
25528 TAATACCAGG
* * * * *
25538 TTATATTTACAAGCGGCCAATGAGTTTTTGGTTTAAAAGTAAGGAAAATGTTTTAAAATTTTAAG
1 TTATATTTACAAGCGGCCAATGAATTTTTGATTTAAAAGTAAAGAAAAAGTTTCAAAATTTTAAG
25603 ATTTTATAAGA
66 ATTTTATAAGA
* ** *
25614 TTATATTTACAAGTGGCCAATGAATTTTTGATTTAGTAG-AAAGAAAAAGATTTCATAATTTTAA
1 TTATATTTACAAGCGGCCAATGAATTTTTGATTTAAAAGTAAAGAAAAAG-TTTCAAAATTTTAA
25678 GATTTTA
65 GATTTTA
25685 GATCCAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 8 0.13
76 53 0.87
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (76 bp):
TTATATTTACAAGCGGCCAATGAATTTTTGATTTAAAAGTAAAGAAAAAGTTTCAAAATTTTAAG
ATTTTATAAGA
Found at i:27429 original size:2 final size:2
Alignment explanation
Indices: 27422--27447 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27412 ACCTCAAGTA
27422 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
27448 AAATAATATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33255 original size:55 final size:56
Alignment explanation
Indices: 33171--33282 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 56
33161 TTAAATCTCG
* * **
33171 TCTTATTTTTAGAAAAGAAAGTTATATCAGCATG-AAAAGCATGTCAATAATTTGA
1 TCTTATTTTTAGAAAAGAAAGTAATATCAGCACGAAAAAGCATAACAATAATTTGA
33226 TCTTATTTTTAGAAAAGAAAGTAATATCAGCACGAAAAAGCATAACAATAATTTGA
1 TCTTATTTTTAGAAAAGAAAGTAATATCAGCACGAAAAAGCATAACAATAATTTGA
33282 T
1 T
33283 GCAAACAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 32 0.62
56 20 0.38
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (56 bp):
TCTTATTTTTAGAAAAGAAAGTAATATCAGCACGAAAAAGCATAACAATAATTTGA
Done.