Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168128.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_371, 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: 30509
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:630 original size:9 final size:9
Alignment explanation
Indices: 616--665 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
606 ATATCTCTTT
616 TTTTTTTTC
1 TTTTTTTTC
625 TTTTTTTTCTC
1 -TTTTTTT-TC
636 TTTTTTTTC
1 TTTTTTTTC
* *
645 TTTTCTTTA
1 TTTTTTTTC
*
654 ATTTTTTTC
1 TTTTTTTTC
663 TTT
1 TTT
666 GTTTCTTCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 17 0.52
10 14 0.42
11 2 0.06
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:630 original size:11 final size:11
Alignment explanation
Indices: 609--645 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
599 CCCATTCATA
609 TCTCTTTTTTTT
1 TCTC-TTTTTTT
*
621 TTTCTTTTTTT
1 TCTCTTTTTTT
632 TCTCTTTTTTT
1 TCTCTTTTTTT
643 TCT
1 TCT
646 TTTCTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 20 0.87
12 3 0.13
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TCTCTTTTTTT
Found at i:659 original size:20 final size:19
Alignment explanation
Indices: 615--661 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
605 CATATCTCTT
**
615 TTTTTTTTTCTTTTTTTTC
1 TTTTTTTTTCTTTTTTTAA
634 TCTTTTTTTTCTTTTCTTTAA
1 T-TTTTTTTTCTTTT-TTTAA
655 TTTTTTT
1 TTTTTTT
662 CTTTGTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 19 0.79
21 4 0.17
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTTCTTTTTTTAA
Found at i:7621 original size:30 final size:30
Alignment explanation
Indices: 7571--7629 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
7561 ATGATTCAAT
*
7571 TAAGTAAAAATAAATATTTAAAAATTTAAC
1 TAAGCAAAAATAAATATTTAAAAATTTAAC
* * *
7601 TAAGCAAAGATAAATGTTTAAGAATTTAA
1 TAAGCAAAAATAAATATTTAAAAATTTAA
7630 TTGCATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.32
Consensus pattern (30 bp):
TAAGCAAAAATAAATATTTAAAAATTTAAC
Found at i:9060 original size:32 final size:31
Alignment explanation
Indices: 8984--9061 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 31
8974 ATTATTTTAT
*
8984 AATTAATTTTT-AT-TTAAAATTAATTATAA
1 AATTACTTTTTAATATTAAAATTAATTATAA
**
9013 AA-TACATTTAAAATATTAAAACTTTAA-TATAA
1 AATTAC-TTTTTAATATTAAAA--TTAATTATAA
9045 AATTACTTTTTAATATT
1 AATTACTTTTTAATATT
9062 TTAAAATCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
28 2 0.05
29 5 0.13
30 2 0.05
31 6 0.16
32 16 0.42
33 7 0.18
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTACTTTTTAATATTAAAATTAATTATAA
Found at i:16313 original size:17 final size:16
Alignment explanation
Indices: 16276--16325 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
16266 CTAATAACCT
16276 AACTAAAAGAAA-TAAA
1 AACT-AAAGAAACTAAA
16292 GAACTAAAGAAACTTAAA
1 -AACTAAAGAAAC-TAAA
*
16310 AACT-TAGAAACTAAA
1 AACTAAAGAAACTAAA
16325 A
1 A
16326 GAAAGAAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.17
16 13 0.43
17 8 0.27
18 4 0.13
ACGTcount: A:0.66, C:0.10, G:0.08, T:0.16
Consensus pattern (16 bp):
AACTAAAGAAACTAAA
Found at i:18036 original size:3 final size:3
Alignment explanation
Indices: 18028--18076 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
18018 GTATTGGTAT
*
18028 TTA TTA TTA CTA -TA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18072 TTA TT
1 TTA TT
18077 TTTCTTTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18560 original size:22 final size:22
Alignment explanation
Indices: 18525--18569 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
18515 AGTTGGGATT
* *
18525 GAAATTCTGGAAAAGGTTTGGAA
1 GAAATTCTAGAAAA-ATTTGGAA
18548 GAAA-TCTAGAAAAATTTGGAA
1 GAAATTCTAGAAAAATTTGGAA
18569 G
1 G
18570 TTTCTGGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.24
Consensus pattern (22 bp):
GAAATTCTAGAAAAATTTGGAA
Found at i:19039 original size:10 final size:10
Alignment explanation
Indices: 19024--19048 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19014 TTTTAAGTTT
19024 TTATTTTATA
1 TTATTTTATA
19034 TTATTTTATA
1 TTATTTTATA
19044 TTATT
1 TTATT
19049 GGTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTTTATA
Found at i:23308 original size:11 final size:10
Alignment explanation
Indices: 23286--23332 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
23276 CAAAAAAAAT
23286 AAAAAAG-GA
1 AAAAAAGTGA
*
23295 AAAAAATTGCA
1 AAAAAAGTG-A
23306 AAAAAAGTGA
1 AAAAAAGTGA
*
23316 AAAAAAGAGA
1 AAAAAAGTGA
23326 AAAAAAG
1 AAAAAAG
23333 AATACTTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 6 0.18
10 18 0.55
11 9 0.27
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.06
Consensus pattern (10 bp):
AAAAAAGTGA
Found at i:23332 original size:10 final size:10
Alignment explanation
Indices: 23266--23333 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
23256 AAAAAGGTGT
23266 GAAAAAAA-A
1 GAAAAAAAGA
23275 GCAAAAAAA-A
1 G-AAAAAAAGA
*
23285 -TAAAAAAG-
1 GAAAAAAAGA
**
23293 GAAAAAAATT
1 GAAAAAAAGA
*
23303 GCAAAAAAAGT
1 G-AAAAAAAGA
23314 GAAAAAAAGA
1 GAAAAAAAGA
23324 GAAAAAAAGA
1 GAAAAAAAGA
23334 ATACTTAAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
8 6 0.12
9 7 0.14
10 27 0.55
11 9 0.18
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (10 bp):
GAAAAAAAGA
Found at i:24611 original size:120 final size:120
Alignment explanation
Indices: 24487--24729 Score: 281
Period size: 120 Copynumber: 2.0 Consensus size: 120
24477 TCCTGGCTAT
* * * * * * * * *
24487 TTTATCTTTTTGACTCGTAGTTTCATCTCGATCATTTGATCTTGGCTTAGTCTATATCATTTTCT
1 TTTATCTTTTTGACTCGCAATTTCATCCCGACCATTCGATCTCGACTTAGTCCAGATCATTTTCT
* * * * *
24552 AACTTGCGATTTTAT-CTCGATTAGCCATCTTTGACCTTGACTCGATCTTGGTGGC
66 AACTCGCGATTTCATCCT-GATCAGCCATCTTCGACCTTGACTCGATCTTGGTCGC
* * *
24607 TTTATCTTTTTGACTTGCAATTTCATCCCGCCCATTCGATCTCGACTTAGTCCAGATTATTTTCT
1 TTTATCTTTTTGACTCGCAATTTCATCCCGACCATTCGATCTCGACTTAGTCCAGATCATTTTCT
* * * *
24672 GACTCGTGATTTCATCCTGGTCAGCCATCTTCGACCTTGACTCGGTCTTGGTCGC
66 AACTCGCGATTTCATCCTGATCAGCCATCTTCGACCTTGACTCGATCTTGGTCGC
24727 TTT
1 TTT
24730 TAGACTCGCG
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
120 99 0.98
121 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.43
Consensus pattern (120 bp):
TTTATCTTTTTGACTCGCAATTTCATCCCGACCATTCGATCTCGACTTAGTCCAGATCATTTTCT
AACTCGCGATTTCATCCTGATCAGCCATCTTCGACCTTGACTCGATCTTGGTCGC
Found at i:24775 original size:11 final size:11
Alignment explanation
Indices: 24759--24783 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24749 TAGTCATTTG
24759 ATTATTTTTAA
1 ATTATTTTTAA
24770 ATTATTTTTAA
1 ATTATTTTTAA
24781 ATT
1 ATT
24784 TTTATATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTTAA
Found at i:25184 original size:3 final size:3
Alignment explanation
Indices: 25171--25251 Score: 103
Period size: 3 Copynumber: 27.3 Consensus size: 3
25161 TATTGCATGC
* * *
25171 TAT TA- TAT TAT TAT TAT TA- TAGT TAT TGT TGT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
25215 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
25252 TTCCTTTCTT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.06
3 65 0.92
4 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:25686 original size:21 final size:21
Alignment explanation
Indices: 25652--25691 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
25642 GGATTTTGGA
25652 TTTAGATTTTGGTTTTTGGGG
1 TTTAGATTTTGGTTTTTGGGG
25673 TTTAG-TTTTAGGTTTTTGG
1 TTTAGATTTT-GGTTTTTGG
25692 AGTGGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.10, C:0.00, G:0.30, T:0.60
Consensus pattern (21 bp):
TTTAGATTTTGGTTTTTGGGG
Found at i:28227 original size:11 final size:10
Alignment explanation
Indices: 28191--28316 Score: 68
Period size: 11 Copynumber: 12.8 Consensus size: 10
28181 ATTTGAATCA
*
28191 TATTAAATAT
1 TATTTAATAT
* *
28201 TA-TTAAAAA
1 TATTTAATAT
28210 TATTTAATAT
1 TATTTAATAT
*
28220 TCATTTAATAA
1 T-ATTTAATAT
28231 TA-TTAATAT
1 TATTTAATAT
28240 TAATTTAATA-
1 T-ATTTAATAT
* *
28250 GATTGAATAT
1 TATTTAATAT
*
28260 TATTT--TAA
1 TATTTAATAT
28268 TA-TTAATAT
1 TATTTAATAT
* *
28277 TAATATAATAG
1 T-ATTTAATAT
28288 TATTTTAAT-T
1 TA-TTTAATAT
*
28298 CATTTAATAT
1 TATTTAATAT
28308 TATTATAAT
1 TATT-TAAT
28317 TGTAAATATT
Statistics
Matches: 85, Mismatches: 19, Indels: 23
0.67 0.15 0.18
Matches are distributed among these distances:
7 2 0.02
8 4 0.05
9 29 0.34
10 20 0.24
11 30 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
TATTTAATAT
Found at i:28238 original size:20 final size:19
Alignment explanation
Indices: 28190--28278 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 19
28180 AATTTGAATC
*
28190 ATATTAAATATTA-TTAAAA
1 ATATT-AATATTATTTAATA
28209 ATATTTAATATTCATTTAATA
1 ATA-TTAATATT-ATTTAATA
28230 ATATTAATATTAATTTAATA
1 ATATTAATATT-ATTTAATA
*
28250 GAT-TGAATATTATTT--TA
1 -ATATTAATATTATTTAATA
28267 ATATTAATATTA
1 ATATTAATATTA
28279 ATATAATAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
16 2 0.03
17 10 0.16
19 13 0.21
20 26 0.43
21 10 0.16
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATTAATATTATTTAATA
Found at i:28304 original size:37 final size:37
Alignment explanation
Indices: 28228--28309 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
28218 ATTCATTTAA
* *
28228 TAATATTAATATTAATTTAATAGATTGAATATTATTT
1 TAATATTAATATTAATATAATAGATTGAATATCATTT
*
28265 TAATATTAATATTAATATAATAGTATTTTAAT-TCA-TT
1 TAATATTAATATTAATATAATAG-A-TTGAATATCATTT
28302 TAATATTA
1 TAATATTA
28310 TTATAATTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 32 0.80
38 3 0.08
39 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
TAATATTAATATTAATATAATAGATTGAATATCATTT
Found at i:28308 original size:31 final size:28
Alignment explanation
Indices: 28276--28366 Score: 57
Period size: 31 Copynumber: 3.2 Consensus size: 28
28266 AATATTAATA
28276 TTAATATAATAGTATTTTAATTCATTTAATA
1 TTAATATAATAGTATTTTAA-T-A-TTAATA
* *
28307 TTATTATAATTGTA----AATATTAAT-
1 TTAATATAATAGTATTTTAATATTAATA
*
28330 TCATAATATAATATATTATTTTAATATTAATA
1 T--TAATAT-A-ATAGTATTTTAATATTAATA
28362 TTAAT
1 TTAAT
28367 TTTATAAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 19
0.66 0.07 0.27
Matches are distributed among these distances:
23 1 0.02
24 5 0.11
25 6 0.13
26 2 0.04
27 6 0.13
30 4 0.09
31 21 0.46
32 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TTAATATAATAGTATTTTAATATTAATA
Found at i:28326 original size:18 final size:18
Alignment explanation
Indices: 28303--28364 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
28293 TAATTCATTT
*
28303 AATATTATTATAATTGTA
1 AATATTATTATAATTATA
28321 AATATTAATTCATAA-TATA
1 AATATT-ATT-ATAATTATA
* *
28340 ATATATTATTTTAA-TATT
1 A-ATATTATTATAATTATA
28358 AATATTA
1 AATATTA
28365 ATTTTATAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.16
18 13 0.34
19 10 0.26
20 9 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATTATTATAATTATA
Found at i:28358 original size:11 final size:11
Alignment explanation
Indices: 28342--28478 Score: 63
Period size: 11 Copynumber: 12.5 Consensus size: 11
28332 ATAATATAAT
28342 ATATTATTTTA
1 ATATTATTTTA
*
28353 ATATTAATATTA
1 ATATT-ATTTTA
*
28365 ATTTTATAAGTTT-
1 ATATTAT---TTTA
* *
28378 ATAATACTTT-
1 ATATTATTTTA
*
28388 ATAGTATTTTA
1 ATATTATTTTA
28399 ATATTA-TTTA
1 ATATTATTTTA
*
28409 TATATTAATTTA
1 -ATATTATTTTA
*
28421 TTATTATTTT-
1 ATATTATTTTA
*
28431 A-A-TA-CTTA
1 ATATTATTTTA
*
28439 ATATTATCTTA
1 ATATTATTTTA
* *
28450 AGAATATTTTGA
1 ATATTATTTT-A
*
28462 ATAATATTTTA
1 ATATTATTTTA
28473 ATATTA
1 ATATTA
28479 AATACTGATT
Statistics
Matches: 96, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
7 2 0.02
8 3 0.03
9 2 0.02
10 17 0.18
11 43 0.45
12 23 0.24
13 4 0.04
14 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (11 bp):
ATATTATTTTA
Found at i:28475 original size:41 final size:41
Alignment explanation
Indices: 28425--28505 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
28415 AATTTATTAT
* * *
28425 TATTTTAATACTT-AATA-TTATCTTAAGAATATTTTGAATAA
1 TATTTTAATA-TTAAATACTGAT-TTAAAAATATTTTAAATAA
28466 TATTTTAATATTAAATACTGATTTAAAAATATTTTAAATA
1 TATTTTAATATTAAATACTGATTTAAAAATATTTTAAATA
28506 TGCTATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 2 0.06
41 30 0.86
42 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (41 bp):
TATTTTAATATTAAATACTGATTTAAAAATATTTTAAATAA
Done.