Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168185.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_422, 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: 27437
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
File 2 of 2
Found at i:25676 original size:23 final size:23
Alignment explanation
Indices: 25636--25679 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
25626 TTTAATTAAA
*
25636 ATATATTATATTTAAAACTAACC
1 ATATATTAGATTTAAAACTAACC
25659 ATATAATTAGATTT-AAACTAA
1 ATAT-ATTAGATTTAAAACTAA
25680 TAAACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATATTAGATTTAAAACTAACC
Found at i:26021 original size:26 final size:25
Alignment explanation
Indices: 25992--26047 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
25982 TATAATTTAA
25992 TATAAATAATAT-TAATATATTATATT
1 TATAAATAATATATAAT-TATTA-ATT
*
26018 TATAAATTATATATAATTATTAATT
1 TATAAATAATATATAATTATTAATT
26043 TATAA
1 TATAA
26048 TCTTATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.29
26 16 0.57
27 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATAAATAATATATAATTATTAATT
Found at i:26115 original size:22 final size:24
Alignment explanation
Indices: 26087--26134 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
26077 GTGATGTTAT
* *
26087 TTAATAATTATATAA-A-TATAAA
1 TTAATAATAATACAATATTATAAA
26109 TTAATAATAATACAATATTATAAA
1 TTAATAATAATACAATATTATAAA
26133 TT
1 TT
26135 GACTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAATAATAATACAATATTATAAA
Found at i:26556 original size:29 final size:27
Alignment explanation
Indices: 26524--26625 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 27
26514 AAATTAAGTA
*
26524 ATATTAAAATATATTATCTAACAATATTT
1 ATATT-AAATATATTAT-TAATAATATTT
* **
26553 ATATTATATTATATTATTTAATTAATAAAT
1 ATATTA-AATATATTA-TTAA-TAATATTT
* *
26583 A-ATTAAATATTAATATTAATTATATTT
1 ATATTAAATA-TATTATTAATAATATTT
26610 ATATTAAATATATTAT
1 ATATTAAATATATTAT
26626 AATTAATTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
27 11 0.19
28 16 0.28
29 24 0.41
30 7 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
ATATTAAATATATTATTAATAATATTT
Found at i:26569 original size:15 final size:15
Alignment explanation
Indices: 26551--26657 Score: 66
Period size: 15 Copynumber: 7.1 Consensus size: 15
26541 CTAACAATAT
26551 TTATATTATATTATA
1 TTATATTATATTATA
26566 TTAT-TTA-ATTA-A
1 TTATATTATATTATA
*
26578 TAAATAATTAAATATTAATA
1 T-TAT-ATT--ATATT-ATA
26598 TTA-ATTATATTTATA
1 TTATATTATA-TTATA
*
26613 TTA-AATATATTATAA
1 TTATATTATATTAT-A
*
26628 TTA-ATTATAATATAA
1 TTATATTATATTAT-A
26643 TTATATT-TATTATA
1 TTATATTATATTATA
26657 T
1 T
26658 GTAATAATAT
Statistics
Matches: 75, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.03
13 6 0.08
14 9 0.12
15 42 0.56
16 5 0.07
17 4 0.05
18 3 0.04
19 2 0.03
20 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATTATATTATA
Found at i:26592 original size:57 final size:56
Alignment explanation
Indices: 26530--26655 Score: 139
Period size: 57 Copynumber: 2.2 Consensus size: 56
26520 AGTAATATTA
*
26530 AAATATATTATCTAACAATATTTATATTATATTATATTAT-TTAATTAATAA-ATAATT
1 AAATATATTAT-TAACAATATTTATATTA-AATATATTATATTAATT-ATAATATAATT
* **
26587 AAATATTAATATTAATTATATTTATATTAAATATATTATAATTAATTATAATATAATT
1 AAATA-TATTATTAACAATATTTATATTAAATATATTAT-ATTAATTATAATATAATT
* *
26645 ATATTTATTAT
1 AAATATATTAT
26656 ATGTAATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
56 9 0.16
57 29 0.50
58 20 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (56 bp):
AAATATATTATTAACAATATTTATATTAAATATATTATATTAATTATAATATAATT
Found at i:26618 original size:36 final size:36
Alignment explanation
Indices: 26553--26683 Score: 104
Period size: 36 Copynumber: 3.4 Consensus size: 36
26543 AACAATATTT
* *
26553 ATATTATATTATATTAT-TTAATTAATAAATAATTAA
1 ATATTATATTA-ATTATATTTATTATTAAATAATTAA
26589 ATATTAATATTAATTATATTTA-TATTAAATATATTATA
1 ATATT-ATATTAATTATATTTATTATTAAATA-ATTA-A
*
26627 ATTAATTATAATATAATTATATTTATTATATGTAATAATATAA
1 A-T-ATTAT-AT-TAATTATATTTATTAT-T-AAATAAT-TAA
*
26670 ATTATAATATTAAT
1 A-TATTATATTAAT
26684 AATTTGATAT
Statistics
Matches: 79, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
36 18 0.23
37 13 0.16
38 2 0.03
39 3 0.04
40 9 0.11
41 14 0.18
42 7 0.09
43 7 0.09
44 6 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (36 bp):
ATATTATATTAATTATATTTATTATTAAATAATTAA
Found at i:26654 original size:39 final size:39
Alignment explanation
Indices: 26567--26679 Score: 110
Period size: 39 Copynumber: 2.9 Consensus size: 39
26557 TATATTATAT
*
26567 TATTTA-ATTA-ATA-AATAATTAAATATTAATATTAATTA
1 TATTTATATTATATATAATAATTAATTA-TAATA-TAATTA
*
26605 TATTTATATTAAATATATTATAATTAATTATAATATAATTA
1 TATTTATATT--ATATATAATAATTAATTATAATATAATTA
*
26646 TA-TT-TATTATATGTAATAATATAAATTATAATAT
1 TATTTATATTATATATAATAAT-T-AATTATAATAT
26680 TAATAATTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
37 10 0.16
38 7 0.11
39 18 0.28
40 2 0.03
41 9 0.14
42 8 0.12
43 10 0.16
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (39 bp):
TATTTATATTATATATAATAATTAATTATAATATAATTA
Found at i:26955 original size:27 final size:28
Alignment explanation
Indices: 26936--26992 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
26926 ATATTTGAAT
*
26936 AATTATCAATAATAA-AAATAATTATTA
1 AATTATCAATAATAACAAATAATTAATA
*
26963 AATTATTAATAATAACAAATAAGTT-ATA
1 AATTATCAATAATAACAAATAA-TTAATA
26991 AA
1 AA
26993 CAATTGTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 14 0.54
28 10 0.38
29 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (28 bp):
AATTATCAATAATAACAAATAATTAATA
Done.