Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168132.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_375, 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: 30256
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
File 2 of 2
Found at i:25332 original size:22 final size:21
Alignment explanation
Indices: 25283--25390 Score: 68
Period size: 22 Copynumber: 5.2 Consensus size: 21
25273 ATATTATAAA
*
25283 ATAATTAT-A-TATAATATAT
1 ATAATTATAATTATAATTTAT
25302 -TAATATATAATTATAATTTAT
1 ATAAT-TATAATTATAATTTAT
** *
25323 ATAATTTATAAGAATAATTTGT
1 ATAA-TTATAATTATAATTTAT
*
25345 ATTAATTATTAA-AATAA-TTA-
1 A-TAATTA-TAATTATAATTTAT
25365 ACT-ATTATAATTATAATTTAAT
1 A-TAATTATAATTATAATTT-AT
25387 ATAA
1 ATAA
25391 ATAAATTCTT
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
18 7 0.10
19 11 0.16
20 5 0.07
21 13 0.19
22 27 0.39
23 7 0.10
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (21 bp):
ATAATTATAATTATAATTTAT
Found at i:25560 original size:12 final size:12
Alignment explanation
Indices: 25513--25566 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
25503 ATAATCAATT
*
25513 TATTACTTATTA
1 TATTAATTATTA
25525 TATTTAATTATAATA
1 TA-TTAATTAT--TA
25540 TATAATAATTATTA
1 TAT--TAATTATTA
25554 TATTAATTATTA
1 TATTAATTATTA
25566 T
1 T
25567 TACTTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 12 0.33
13 7 0.19
14 6 0.17
15 4 0.11
16 7 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTAATTATTA
Found at i:25560 original size:15 final size:15
Alignment explanation
Indices: 25519--25568 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
25509 AATTTATTAC
25519 TTATTATATT--TAA
1 TTATTATATTAATAA
*
25532 TTATAATATATAATAA
1 TTATTATAT-TAATAA
*
25548 TTATTATATTAATTA
1 TTATTATATTAATAA
25563 TTATTA
1 TTATTA
25569 CTTTATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
15 11 0.35
16 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTATATTAATAA
Found at i:26161 original size:18 final size:18
Alignment explanation
Indices: 26110--26174 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
26100 AGATTTAAAA
26110 AATTAATCTATTTAATTTAT
1 AATTAAT-TATTTAA-TTAT
26130 AATCT--TTA-TTAATTAT
1 AAT-TAATTATTTAATTAT
*
26146 AATTAATTATTTAATTTT
1 AATTAATTATTTAATTAT
*
26164 AATAAATTATT
1 AATTAATTATT
26175 GCTATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.03
16 7 0.18
17 7 0.18
18 19 0.49
19 1 0.03
20 3 0.08
21 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTAATTATTTAATTAT
Found at i:26467 original size:15 final size:16
Alignment explanation
Indices: 26425--26499 Score: 68
Period size: 15 Copynumber: 4.8 Consensus size: 16
26415 ACTGTAAATC
*
26425 ATATTATTGTTATATTA
1 ATATTATT-TTAAATTA
* * *
26442 TTATTAATTTAATTTA
1 ATATTATTTTAAATTA
26458 A-ATTATTTTAAATTA
1 ATATTATTTTAAATTA
26473 ATATTA--TT-AATTA
1 ATATTATTTTAAATTA
26486 ATATTATATTTAAA
1 ATATTAT-TTTAAA
26500 ATTTGAAGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.24
14 2 0.04
15 13 0.28
16 12 0.26
17 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
ATATTATTTTAAATTA
Found at i:26484 original size:13 final size:13
Alignment explanation
Indices: 26468--26492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26458 AATTATTTTA
26468 AATTAATATTATT
1 AATTAATATTATT
26481 AATTAATATTAT
1 AATTAATATTAT
26493 ATTTAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATATTATT
Found at i:26484 original size:29 final size:31
Alignment explanation
Indices: 26425--26499 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
26415 ACTGTAAATC
* *
26425 ATATTATTGTTATATTATTATTAATTTAATTTA
1 ATATTATT-TTAAATTAATATTAATTTAA-TTA
26458 A-ATTATTTTAAATTAATATT-A-TTAATTA
1 ATATTATTTTAAATTAATATTAATTTAATTA
26486 ATATTATATTTAAA
1 ATATTAT-TTTAAA
26500 ATTTGAAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 4 0.11
29 9 0.24
30 7 0.18
31 11 0.29
32 6 0.16
33 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
ATATTATTTTAAATTAATATTAATTTAATTA
Found at i:28071 original size:34 final size:33
Alignment explanation
Indices: 28033--28117 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
28023 TTATGACTAT
*
28033 TAATAATAATT-GTAATATTAAATATTAATAGATA
1 TAATAATAATTAATAA-ATTAAATA-TAATAGATA
* *
28067 TAATAATAGTTAATAAATTAAATATAATAGTTAAA
1 TAATAATAATTAATAAATTAAATATAATAG--ATA
*
28102 TTATAATAATTAATAA
1 TAATAATAATTAATAA
28118 CTAAATGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 6 0.14
34 18 0.42
35 19 0.44
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (33 bp):
TAATAATAATTAATAAATTAAATATAATAGATA
Found at i:28165 original size:17 final size:17
Alignment explanation
Indices: 28135--28251 Score: 66
Period size: 17 Copynumber: 6.7 Consensus size: 17
28125 TTTATCATTA
28135 TAATATATATTAATTTATT
1 TAAT-TATA-TAATTTATT
28154 TAATTATATAA--TA-T
1 TAATTATATAATTTATT
*
28168 T-ATTATATATTTAATATT
1 TAATTATATAATT--TATT
*
28186 TAAATTAAAT-ATTTA-T
1 T-AATTATATAATTTATT
*
28202 TATATTATAATAAATATTATA
1 TA-ATTAT-AT-AAT-TTATT
* *
28223 TAATTATATTATTAATT
1 TAATTATATAATTTATT
28240 TAATTATATAAT
1 TAATTATATAAT
28252 AATAGTAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 28
0.67 0.08 0.25
Matches are distributed among these distances:
13 8 0.11
14 2 0.03
15 3 0.04
16 6 0.08
17 23 0.30
18 8 0.11
19 10 0.13
20 14 0.18
21 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTATATAATTTATT
Found at i:28197 original size:20 final size:22
Alignment explanation
Indices: 28159--28219 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
28149 TTATTTAATT
* * *
28159 ATATAATATTATTATATATTTA
1 ATATATTATAATTAAATATTTA
28181 ATAT-TTA-AATTAAATATTTA
1 ATATATTATAATTAAATATTTA
*
28201 TTATATTATAA-TAAATATT
1 ATATATTATAATTAAATATT
28220 ATATAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 14 0.42
21 13 0.39
22 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATATTATAATTAAATATTTA
Found at i:28230 original size:20 final size:21
Alignment explanation
Indices: 28174--28219 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28164 ATATTATTAT
*
28174 ATATTTAATAT-TTA-AATTAA
1 ATATTTATTATATTATAA-TAA
28194 ATATTTATTATATTATAATAA
1 ATATTTATTATATTATAATAA
28215 ATATT
1 ATATT
28220 ATATAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 11 0.48
22 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTATTATATTATAATAA
Found at i:28233 original size:25 final size:25
Alignment explanation
Indices: 28126--28251 Score: 70
Period size: 25 Copynumber: 5.0 Consensus size: 25
28116 AACTAAATGT
* * *
28126 TTATCATTATAATATATATTAATTTAT
1 TTAT-ATTATAATAAATATT-ATATAA
*
28153 TTA-ATTAT-ATAATATTATTATATAT
1 TTATATTATAATAA-A-TATTATATAA
28178 TTAATATT-TAAATTAAATA-T-T-T-A
1 TT-ATATTAT-AA-TAAATATTATATAA
28201 TTATATTATAATAAATATTATATAA
1 TTATATTATAATAAATATTATATAA
**
28226 TTATATTATTAATTTA-ATTATATAA
1 TTATATTA-TAATAAATATTATATAA
28251 T
1 T
28252 AATAGTAATT
Statistics
Matches: 81, Mismatches: 5, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
21 6 0.07
22 8 0.10
23 4 0.05
24 5 0.06
25 33 0.41
26 12 0.15
27 8 0.10
28 2 0.02
29 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATATTATAATAAATATTATATAA
Found at i:28531 original size:25 final size:25
Alignment explanation
Indices: 28478--28540 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
28468 TAATGATTAT
* * **
28478 TAAATTAATAATTTAATTTATATTTA
1 TAAATTAAT-ATTCAAATTATATACA
28504 TAAATTAATATTCAAATTATATACA
1 TAAATTAATATTCAAATTATATACA
28529 TAAATTATATAT
1 TAAATTA-ATAT
28541 AATTAGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAATTAATATTCAAATTATATACA
Found at i:28640 original size:24 final size:24
Alignment explanation
Indices: 28609--28728 Score: 95
Period size: 24 Copynumber: 4.9 Consensus size: 24
28599 TTGTATACAA
28609 ATAAATTATATA-ATATTAATAAT
1 ATAAATTATATATATATTAATAAT
28632 ATAATATTAT-TATATATTAA-ATAT
1 ATAA-ATTATATATATATTAATA-AT
* * *
28656 TTAAATTAAATATTTATTATATAAT
1 ATAAATTATATATATATTA-ATAAT
*
28681 ATAATATTATATAATTATATTATTAAT
1 ATAA-ATTATAT-A-TATATTAATAAT
* *
28708 -TTAATTATATAATAAATTAAT
1 ATAAATTATAT-ATATATTAAT
28729 TTTATTAAAC
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
23 11 0.14
24 32 0.41
25 15 0.19
26 9 0.12
27 5 0.06
28 6 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATAAATTATATATATATTAATAAT
Found at i:28700 original size:13 final size:13
Alignment explanation
Indices: 28612--28720 Score: 64
Period size: 13 Copynumber: 8.2 Consensus size: 13
28602 TATACAAATA
*
28612 AATTATATAATATT
1 AATTATATTATA-T
* *
28626 AATAATATAATATT
1 AATTATATTATA-T
* *
28640 ATTATATATTAAAT
1 AAT-TATATTATAT
* * *
28654 ATTTAAATTAAAT
1 AATTATATTATAT
28667 -ATT-TATTATAT
1 AATTATATTATAT
28678 AATATAATATTATAT
1 AAT-T-ATATTATAT
28693 AATTATATTAT-T
1 AATTATATTATAT
28705 AATT-TAATTATAT
1 AATTAT-ATTATAT
28718 AAT
1 AAT
28721 AAATTAATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 15
0.77 0.09 0.15
Matches are distributed among these distances:
11 7 0.09
12 14 0.18
13 21 0.27
14 20 0.25
15 17 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTATATTATAT
Found at i:28712 original size:17 final size:17
Alignment explanation
Indices: 28692--28736 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
28682 TAATATTATA
* *
28692 TAATTATATTATTAATT
1 TAATTATATTAATAAAT
28709 TAATTATA-TAATAAAT
1 TAATTATATTAATAAAT
*
28725 TAATTTTATTAA
1 TAATTATATTAA
28737 ACAATTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTATATTAATAAAT
Found at i:28720 original size:8 final size:8
Alignment explanation
Indices: 28612--28720 Score: 56
Period size: 8 Copynumber: 14.4 Consensus size: 8
28602 TATACAAATA
28612 AATTATAT
1 AATTATAT
28620 AA-TAT-T
1 AATTATAT
*
28626 AATAATAT
1 AATTATAT
28634 AA-TAT-T
1 AATTATAT
28640 -ATTATAT
1 AATTATAT
*
28647 -ATTAAAT
1 AATTATAT
* *
28654 ATTTAAATT
1 AATTATA-T
*
28663 AAATAT-T
1 AATTATAT
*
28670 TATTATAT
1 AATTATAT
28678 AA-TATA-
1 AATTATAT
28684 ATATTATAT
1 A-ATTATAT
28693 AATTATAT
1 AATTATAT
* *
28701 TATTAATTT
1 AATT-ATAT
28710 AATTATAT
1 AATTATAT
28718 AAT
1 AAT
28721 AAATTAATTT
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
5 1 0.01
6 8 0.11
7 24 0.32
8 32 0.42
9 11 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTATAT
Found at i:28801 original size:13 final size:14
Alignment explanation
Indices: 28783--28831 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
28773 AATATTTAGA
28783 TAATTAA-TAATAT
1 TAATTAATTAATAT
28796 TAATTAATTAATAT
1 TAATTAATTAATAT
*
28810 TCTATTATATTAA-A-
1 T-AATTA-ATTAATAT
28824 TAATTAAT
1 TAATTAAT
28832 AAGAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 2 0.06
13 11 0.35
14 8 0.26
15 5 0.16
16 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTAATTAATAT
Found at i:29424 original size:25 final size:25
Alignment explanation
Indices: 29377--29424 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29367 TTAATTAAAA
* *
29377 TATAAATATTTAATTAAATTATTAT
1 TATAAATAATTAATTAAACTATTAT
* *
29402 TATAATTAATTAATTATACTATT
1 TATAAATAATTAATTAAACTATT
29425 TATTTTAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATAAATAATTAATTAAACTATTAT
Found at i:29881 original size:16 final size:16
Alignment explanation
Indices: 29798--29882 Score: 54
Period size: 18 Copynumber: 5.1 Consensus size: 16
29788 TTATCTAAAT
29798 TATTATTATAAAA-AT-
1 TATTATT-TAAAATATA
29813 TATTGA-TTAATAAGTATA
1 TATT-ATTTAA-AA-TATA
29831 TATTCATTTTAATAATATA
1 TATT-A-TTTAA-AATATA
29850 TA-T-TTTAAAAGTTATA
1 TATTATTTAAAA--TATA
29866 TATTATTTAAAATATA
1 TATTATTTAAAATATA
29882 T
1 T
29883 TTAAGACTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
14 5 0.09
15 12 0.21
16 12 0.21
17 3 0.05
18 13 0.22
19 6 0.10
20 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (16 bp):
TATTATTTAAAATATA
Found at i:30010 original size:22 final size:22
Alignment explanation
Indices: 29971--30027 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
29961 TTGAAATATA
29971 TTATTATAATAAAATAATTAAT
1 TTATTATAATAAAATAATTAAT
*
29993 TTATTA-AATAATATTAATT-AT
1 TTATTATAATAA-AATAATTAAT
*
30014 TAATTATTAATAAA
1 TTATTA-TAATAAA
30028 TTATATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 12 0.40
22 13 0.43
23 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTATAATAAAATAATTAAT
Found at i:30033 original size:27 final size:27
Alignment explanation
Indices: 29997--30091 Score: 72
Period size: 27 Copynumber: 3.5 Consensus size: 27
29987 ATTAATTTAT
29997 TAAATAATATTAATTATTAATTATTAA
1 TAAATAATATTAATTATTAATTATTAA
* **
30024 TAAATTATA-TAACAATATAATTATT-A
1 TAAATAATATTAATTAT-TAATTATTAA
* * *
30050 TATATATTATTCTAATTATT-GTTATT-A
1 TAAATAATA-T-TAATTATTAATTATTAA
30077 TAAATAATTATTAAT
1 TAAATAA-TATTAAT
30092 AACAATAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
26 16 0.31
27 28 0.54
28 3 0.06
29 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (27 bp):
TAAATAATATTAATTATTAATTATTAA
Found at i:30035 original size:56 final size:58
Alignment explanation
Indices: 29965--30110 Score: 144
Period size: 56 Copynumber: 2.6 Consensus size: 58
29955 TATAAATTGA
*
29965 AATATATTATTATAATAAAATAATTAATTTATTAAATAATA-T-TAATTATTAATTATT
1 AATAAATTATTATAATAAAATAATTAATTTATTAAATAATATTCTAATTATT-ATTATT
* * * * *
30022 AATAAATTA-TATAACAATATAATT-A-TTA-TATATATTATTCTAATTATTGTTATT
1 AATAAATTATTATAATAAAATAATTAATTTATTAAATAATATTCTAATTATTATTATT
* *
30076 -ATAAATAATTATTAATAACAATAATTATTTTATTA
1 AATAAATTATTA-TAATAA-AATAATTAATTTATTA
30111 TTAAAATAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
53 14 0.20
54 11 0.15
55 14 0.20
56 19 0.27
57 8 0.11
58 3 0.04
59 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (58 bp):
AATAAATTATTATAATAAAATAATTAATTTATTAAATAATATTCTAATTATTATTATT
Done.