Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168061.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_310, 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: 36228
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:1478 original size:232 final size:233
Alignment explanation
Indices: 1067--1721 Score: 740
Period size: 232 Copynumber: 2.8 Consensus size: 233
1057 ACATCACCTT
* * * *
1067 ATCTTAATTTAAAACTAATTTTAAACTAATTTATCTTTTCTAATTTATCT-AAAGTTAAAATGAA
1 ATCTCAATTTAAAACTAATTTTAAAGTAATTTATCTTTTC-AATTTATCTGTAA-TTAACATG-A
* * * *
1131 TATTTAAATTTATCACAATTTTTAAAAGTATTATTTAATATCTTTAATATTTTTGATAAATATTC
63 TATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTTAATATTTTTTATAAATAATC
* * * *
1196 CTTGTATTATCTTTAGTTTTTAAATATATTTCACAAAGGAAATGTGAAAAAAATATATAAATATC
128 CTTGCATTATCTTTAGTTTTTAAATATATTTCACAAAGAAAATATGAAAAAAATATATAAATACC
* * * *
1261 AGAACAATTTCAGGAAAGTTTCTCCTATATATC-A-C-CC-C
193 AAAACAACTTCAAGAAAGTTTCTCCT-TACATCAATCTCCTC
*
1299 ATCTCAATTTAAAACCAATTTTAAAGTAATTTATCTATTTCAATTTATCTGTAATTAACATGAGT
1 ATCTCAATTTAAAACTAATTTTAAAGTAATTTATCT-TTTCAATTTATCTGTAATTAACATGA-T
* *
1364 AGTTAAATTTATTACAACTTTTAAAAATATTATTTAATATCTTTAATATTTTTTATAAATAATCC
64 ATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTTAATATTTTTTATAAATAATCC
* * * * *
1429 TTACATTATCTTCAATTTTTAAATACATTTCACAAAGAAAATATGAAAAATATATATAAATACCA
129 TTGCATTATCTTTAGTTTTTAAATATATTTCACAAAGAAAATATGAAAAAAATATATAAATACCA
1494 AAACAACTTCAAGAAAGTTTCTCCTTACATCAAGTTTCTCCTGTATATC
194 AAACAACTTCAAGAAAGTTTCTCCTTACATCAA---TCTCC------TC
* * *
1543 ATCTCATTTCAATTTGAAACTAATTTGAAAGTAATTTATCTTTTTCAATCTATCTGT-A--AACA
1 A--TC---TCAATTTAAAACTAATTTTAAAGTAATTTATC-TTTTCAATTTATCTGTAATTAACA
* * *
1605 TTA-ATTTAAATTTATCACAACTTTTAAAAATATTATTTAAGATCTTT-A-ATTTTTTACAAATA
60 TGATATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTTAATATTTTTTATAAATA
* * *
1667 ATACTTGCATTATCTTTAGTTTTTAAATATATTTCACAAA-AAAAAATGCAAAAAA
125 ATCCTTGCATTATCTTTAGTTTTTAAATATATTTCACAAAGAAAATATGAAAAAAA
1722 GAAAATACAA
Statistics
Matches: 360, Mismatches: 41, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
231 6 0.02
232 188 0.52
233 6 0.02
236 1 0.00
237 2 0.01
241 12 0.03
242 48 0.13
243 1 0.00
244 43 0.12
246 8 0.02
248 1 0.00
249 43 0.12
250 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (233 bp):
ATCTCAATTTAAAACTAATTTTAAAGTAATTTATCTTTTCAATTTATCTGTAATTAACATGATAT
TTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTTAATATTTTTTATAAATAATCCTT
GCATTATCTTTAGTTTTTAAATATATTTCACAAAGAAAATATGAAAAAAATATATAAATACCAAA
ACAACTTCAAGAAAGTTTCTCCTTACATCAATCTCCTC
Found at i:1748 original size:244 final size:246
Alignment explanation
Indices: 1276--1752 Score: 624
Period size: 249 Copynumber: 1.9 Consensus size: 246
1266 AATTTCAGGA
*
1276 AAGTTTCTCCTATATATCACCCCATCTCAATTTAAAACCAATTTTAAAGTAATTTATCTATTTCA
1 AAGTTTCTCCTATATATCACCCCATCTCAATTTAAAACCAATTTGAAAGTAATTTATCTATTTCA
* * *
1341 ATTTATCTGTAATTAACATGAGTAGTTAAATTTATTACAACTTTTAAAAATATTATTTAATATCT
66 ATCTATCTGTAA-TAACATGAG-AGTTAAATTTATCACAACTTTTAAAAATATTATTTAAGATCT
* * *
1406 TTAATATTTTTTATAAATAATCCTTACATTATCTTCAATTTTTAAATACATTTCACAAAGAAAAT
129 TTAATATTTTTTACAAATAATACTTACATTATCTTCAATTTTTAAATACATTTCACAAAGAAAAA
* * *
1471 ATGAAAAATATATATAAATACCAAAACAACTTCAAGAAAGTTTCTCCTTACATC
194 ATGAAAAAAAAATACAAATACCAAAACAACTTC-AGAAAGTTTCTCCTTACATC
* * * * * * *
1525 AAGTTTCTCCTGTATATCATCTCATTTCAATTTGAAACTAATTTGAAAGTAATTTATCTTTTTCA
1 AAGTTTCTCCTATATATCACCCCATCTCAATTTAAAACCAATTTGAAAGTAATTTATCTATTTCA
* *
1590 ATCTATCTGT-A-AACATTA-ATTTAAATTTATCACAACTTTTAAAAATATTATTTAAGATCTTT
66 ATCTATCTGTAATAACATGAGAGTTAAATTTATCACAACTTTTAAAAATATTATTTAAGATCTTT
* * * *
1652 -A-ATTTTTTACAAATAATACTTGCATTATCTTTAGTTTTTAAATATATTTCACAAA-AAAAAAT
131 AATATTTTTTACAAATAATACTTACATTATCTTCAATTTTTAAATACATTTCACAAAGAAAAAAT
* * *
1714 GCAAAAAAGAAAATACAAATACGATAATAACTTCAGAAA
196 G--AAAAA-AAAATACAAATACCAAAACAACTTCAGAAA
1753 AACCCTCATT
Statistics
Matches: 199, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
241 7 0.04
242 48 0.24
243 11 0.06
244 60 0.30
246 6 0.03
248 1 0.01
249 66 0.33
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (246 bp):
AAGTTTCTCCTATATATCACCCCATCTCAATTTAAAACCAATTTGAAAGTAATTTATCTATTTCA
ATCTATCTGTAATAACATGAGAGTTAAATTTATCACAACTTTTAAAAATATTATTTAAGATCTTT
AATATTTTTTACAAATAATACTTACATTATCTTCAATTTTTAAATACATTTCACAAAGAAAAAAT
GAAAAAAAAATACAAATACCAAAACAACTTCAGAAAGTTTCTCCTTACATC
Found at i:2805 original size:2 final size:2
Alignment explanation
Indices: 2792--2839 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2782 AATTACTACA
*
2792 CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2833 CT CT CT C
1 CT CT CT C
2840 ACACACACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2844 original size:2 final size:2
Alignment explanation
Indices: 2839--2870 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2829 CTCTCTCTCT
2839 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2871 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5989 original size:16 final size:15
Alignment explanation
Indices: 5968--6022 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
5958 TTCAAGAACA
5968 GTTGTTCCATAAAAGT
1 GTTGTTCC-TAAAAGT
5984 GTTGTTTCCTAAAAGT
1 GTTG-TTCCTAAAAGT
* *
6000 GTTGTTCCGTGAAAGA
1 GTTGTTCC-TAAAAGT
6016 GTTGTTC
1 GTTGTTC
6023 TTTGAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 4 0.11
16 27 0.77
17 4 0.11
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (15 bp):
GTTGTTCCTAAAAGT
Found at i:6760 original size:35 final size:31
Alignment explanation
Indices: 6721--6788 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 31
6711 GTAATATAAG
*
6721 TGTTTCCCTAAAAATATGAGAATAAGTAATGTGAA
1 TGTTTCCCT-AAAATAT-AGAA-AAATAAT-TGAA
*
6756 TGTTTTCCTAAAATATAGAAAAATAATTGAA
1 TGTTTCCCTAAAATATAGAAAAATAATTGAA
6787 TG
1 TG
6789 GAACAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.19
32 6 0.19
33 4 0.13
34 7 0.23
35 8 0.26
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (31 bp):
TGTTTCCCTAAAATATAGAAAAATAATTGAA
Found at i:8408 original size:20 final size:18
Alignment explanation
Indices: 8383--8425 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
8373 GTTCGCTAAC
*
8383 GTTTTCGTTTTCTATTTTTT
1 GTTTTCGGTTTC-A-TTTTT
8403 GTTTTCGGTTTCATTTTT
1 GTTTTCGGTTTCATTTTT
8421 GTTTT
1 GTTTT
8426 AAAATTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 11 0.50
ACGTcount: A:0.05, C:0.09, G:0.14, T:0.72
Consensus pattern (18 bp):
GTTTTCGGTTTCATTTTT
Found at i:8698 original size:23 final size:22
Alignment explanation
Indices: 8668--8748 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
8658 TAAATATTAA
*
8668 ATTAATAAATATTATTATATTT
1 ATTAATAAATAATATTATATTT
8690 ATTATATAAATAATA-T-TA--T
1 ATTA-ATAAATAATATTATATTT
* *
8709 ATTAATAAATAACATTATAATAT
1 ATTAATAAATAATATTAT-ATTT
8732 ATTAATAAATAATATTA
1 ATTAATAAATAATATTA
8749 ATAATAACTA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 9 0.18
19 6 0.12
20 1 0.02
21 3 0.06
22 5 0.10
23 26 0.52
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAATAAATAATATTATATTT
Found at i:8711 original size:31 final size:29
Alignment explanation
Indices: 8619--8712 Score: 83
Period size: 31 Copynumber: 3.3 Consensus size: 29
8609 TACAGTAACG
8619 TTATAATTATTATATTA-ATA-AAATAATA
1 TTAT-ATTATTATATTATATATAAATAATA
*
8647 TT-T-TTATTATA-TAAATATTAAATTAATA
1 TTATATTATTATATTATATA-TAAA-TAATA
*
8675 -AATATTATTATATTTATTATATAAATAATA
1 TTATATTATTATA-TTA-TATATAAATAATA
8705 TTATATTA
1 TTATATTA
8713 ATAAATAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
24 2 0.04
25 11 0.21
27 4 0.08
28 8 0.15
29 8 0.15
30 5 0.09
31 12 0.23
32 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTATATTATTATATTATATATAAATAATA
Found at i:8716 original size:41 final size:41
Alignment explanation
Indices: 8621--8771 Score: 156
Period size: 41 Copynumber: 3.8 Consensus size: 41
8611 CAGTAACGTT
* *
8621 ATAATTATTATATTAATAAA-A-TAATATTTTTATTATAT--
1 ATAA-TATTATATTAATAAATATTATTATATTTATTATATAA
*
8659 A-AATATTAAATTAATAAATATTATTATATTTATTATATAA
1 ATAATATTATATTAATAAATATTATTATATTTATTATATAA
** *
8699 ATAATATTATATTAATAAATAACATTATAATATATTA-ATAA
1 ATAATATTATATTAATAAATATTATTAT-ATTTATTATATAA
* *
8740 ATAATATTA-A-TAATAACTATTATTTTATTTAT
1 ATAATATTATATTAATAAATATTATTATATTTAT
8772 ATTATTAATA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
36 14 0.15
37 3 0.03
38 21 0.22
39 12 0.13
40 2 0.02
41 36 0.38
42 7 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.48
Consensus pattern (41 bp):
ATAATATTATATTAATAAATATTATTATATTTATTATATAA
Found at i:11220 original size:16 final size:16
Alignment explanation
Indices: 11199--11229 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11189 TTCGAGAATA
*
11199 ATTATTTCGTGAAAGT
1 ATTATTCCGTGAAAGT
11215 ATTATTCCGTGAAAG
1 ATTATTCCGTGAAAG
11230 AATTGGTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (16 bp):
ATTATTCCGTGAAAGT
Found at i:16867 original size:20 final size:20
Alignment explanation
Indices: 16842--16890 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
16832 ATTAAAAAAA
*
16842 TTAAAAAATATATAATATTT
1 TTAAAAAATATATAAAATTT
16862 TT-AAAAAT-TATAAAATTT
1 TTAAAAAATATATAAAATTT
*
16880 TAAAAAAATAT
1 TTAAAAAATAT
16891 GAAAACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.40
19 12 0.48
20 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAAATATATAAAATTT
Found at i:16873 original size:18 final size:18
Alignment explanation
Indices: 16845--16905 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
16835 AAAAAAATTA
*
16845 AAAAATATATAATATTTTT
1 AAAAATATATAA-AATTTT
16864 AAAAAT-TATAAAATTTT
1 AAAAATATATAAAATTTT
* * *
16881 AAAAAAATATGAAAACTTA
1 AAAAATATAT-AAAATTTT
16900 AAAAAT
1 AAAAAT
16906 TAAAAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 10 0.29
18 8 0.23
19 17 0.49
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAATATATAAAATTTT
Found at i:16913 original size:18 final size:18
Alignment explanation
Indices: 16832--16914 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
16822 AATCTGAAAT
*
16832 ATTA-AAAAAATTAAAAA
1 ATTATAAAAATTTAAAAA
* * *
16849 ATATATAATATTTTTAAAA
1 AT-TATAAAAATTTAAAAA
*
16868 ATTATAAAATTTTAAAAA
1 ATTATAAAAATTTAAAAA
* * *
16886 AATATGAAAACTTAAAAA
1 ATTATAAAAATTTAAAAA
*
16904 ATTAAAAAAAT
1 ATTATAAAAAT
16915 CTCAAATTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
17 2 0.04
18 37 0.74
19 11 0.22
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
ATTATAAAAATTTAAAAA
Found at i:20458 original size:79 final size:79
Alignment explanation
Indices: 20327--20478 Score: 277
Period size: 79 Copynumber: 1.9 Consensus size: 79
20317 TGCAGCAAGC
*
20327 AATTCCACCATGTTAATGTCTATTCACAGAAAAATTAATTGTTCAAAAGATTCCATGACAAAGAA
1 AATTCCACCATGTTAATGTCTATCCACAGAAAAATTAATTGTTCAAAAGATTCCATGACAAAGAA
20392 AAAGAAGCCAAAGT
66 AAAGAAGCCAAAGT
* *
20406 AATTCCACCATGTTAATGTCTGTCCACGGAAAAATTAATTGTTCAAAAGATTCCATGACAAAGAA
1 AATTCCACCATGTTAATGTCTATCCACAGAAAAATTAATTGTTCAAAAGATTCCATGACAAAGAA
20471 AAAGAAGC
66 AAAGAAGC
20479 TAAACAACTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (79 bp):
AATTCCACCATGTTAATGTCTATCCACAGAAAAATTAATTGTTCAAAAGATTCCATGACAAAGAA
AAAGAAGCCAAAGT
Found at i:25975 original size:14 final size:15
Alignment explanation
Indices: 25949--25977 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25939 AATCAATGAA
25949 TATATTATTAAAATT
1 TATATTATTAAAATT
25964 TATATT-TTAAAATT
1 TATATTATTAAAATT
25978 ATAAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATTAAAATT
Found at i:26878 original size:26 final size:26
Alignment explanation
Indices: 26828--26878 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
26818 AAATATTTAA
* *
26828 TTTAAATTTGACTTTAAATTTATTAT
1 TTTAAATTTGACTTCAAATTGATTAT
26854 TTTAAATTTGA-TTCAAATTCGATTA
1 TTTAAATTTGACTTCAAATT-GATTA
26879 AATTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (26 bp):
TTTAAATTTGACTTCAAATTGATTAT
Found at i:31917 original size:28 final size:28
Alignment explanation
Indices: 31864--31918 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
31854 TCAAAATTAA
* * *
31864 ATTAATTAAATTATTTTATTTTATTTTT
1 ATTAATCAAATTAATTTATTTAATTTTT
31892 ATTAATCAAATTAAATTTA-TTAATTTT
1 ATTAATCAAATT-AATTTATTTAATTTT
31919 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTAATCAAATTAATTTATTTAATTTTT
Done.