Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168243.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_475, 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: 25656
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Found at i:2839 original size:17 final size:18
Alignment explanation
Indices: 2803--2840 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2793 TATTATTCAT
* *
2803 AAAAGTCATGATTATACA
1 AAAAGTCATAACTATACA
2821 AAAAGTCATAACTAT-CA
1 AAAAGTCATAACTATACA
2838 AAA
1 AAA
2841 TAGAAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (18 bp):
AAAAGTCATAACTATACA
Found at i:12000 original size:2 final size:2
Alignment explanation
Indices: 11987--12020 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11977 TTGGTCTTTG
*
11987 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12021 GAATATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12628 original size:34 final size:34
Alignment explanation
Indices: 12581--12657 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
12571 ATGAGAATAT
*
12581 GAAGATGAAAATGAAGAGCATTCAACTTGGCAAA
1 GAAGATCAAAATGAAGAGCATTCAACTTGGCAAA
* *
12615 GATGATCAAAATGAAGATCATTCAACTTGGCAAA
1 GAAGATCAAAATGAAGAGCATTCAACTTGGCAAA
12649 GAAGATCAA
1 GAAGATCAA
12658 CTCTCAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (34 bp):
GAAGATCAAAATGAAGAGCATTCAACTTGGCAAA
Found at i:13806 original size:2 final size:2
Alignment explanation
Indices: 13799--13823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13789 TTAAATATCC
13799 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13824 CTGTCCGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18589 original size:2 final size:2
Alignment explanation
Indices: 18582--18626 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18572 GGCAATTATC
18582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18624 AT A
1 AT A
18627 CAAACAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19328 original size:105 final size:103
Alignment explanation
Indices: 19211--19399 Score: 227
Period size: 105 Copynumber: 1.8 Consensus size: 103
19201 AAAATAAGAT
* * * * * * *
19211 GAGAAGATTTTGTGAGATTTTAAAGT-ATAAAGACTACTTTTTTTACATAAGAAATGTAGTCTTT
1 GAGAAGAATTTGTGACATTTT--AGTAAAAAACACTACGTTTCTTACATAAGAAATGTAAT-TTT
19275 TGTAGTTTTTTATTATAAAAATTTTTTTAGAAAAGTAAAAA
63 TGTAGTTTTTTATTATAAAAATTTTTTTAGAAAAGTAAAAA
* * *
19316 GAGAAGAATTTGTTACATTTTGGTACAAAAACACTACGTTTCTTATATAAGAAATGTAATTTTTG
1 GAGAAGAATTTGTGACATTTTAGTA-AAAAACACTACGTTTCTTACATAAGAAATGTAATTTTTG
* *
19381 TAGTTTTTTGTTGTAAAAA
65 TAGTTTTTTATTATAAAAA
19400 AAATTCTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
103 2 0.03
104 22 0.31
105 46 0.66
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (103 bp):
GAGAAGAATTTGTGACATTTTAGTAAAAAACACTACGTTTCTTACATAAGAAATGTAATTTTTGT
AGTTTTTTATTATAAAAATTTTTTTAGAAAAGTAAAAA
Found at i:19400 original size:105 final size:102
Alignment explanation
Indices: 19243--19429 Score: 243
Period size: 105 Copynumber: 1.8 Consensus size: 102
19233 AAGTATAAAG
* * * * *
19243 ACTACTTTTTTTACATAAGAAATGTAGTCTTTTGTAGTTTTTTATTAT-AAAAATTTTTTTAGAA
1 ACTACGTTTCTTACATAAGAAATGTAATCTTTTGTAGTTTTTTATTATAAAAAAATTCTTTA-AA
19307 AAGTAAAAAGAGAAGAATTTGTTACATTTTGGTACAAAAAC
65 AAGT--AAAGAGAAG-ATTTGTTACATTTTGGTACAAAAAC
* * *
19348 ACTACGTTTCTTATATAAGAAATGTAAT-TTTTGTAGTTTTTTGTTGTAAAAAAAATTCTTTAAA
1 ACTACGTTTCTTACATAAGAAATGTAATCTTTTGTAGTTTTTTATTAT-AAAAAAATTCTTTAAA
19412 AAGTAAAGAGAAGATTTG
65 AAGTAAAGAGAAGATTTG
19430 GTTAGATTCA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
102 5 0.07
103 9 0.12
104 17 0.24
105 30 0.42
106 11 0.15
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (102 bp):
ACTACGTTTCTTACATAAGAAATGTAATCTTTTGTAGTTTTTTATTATAAAAAAATTCTTTAAAA
AGTAAAGAGAAGATTTGTTACATTTTGGTACAAAAAC
Found at i:19795 original size:19 final size:20
Alignment explanation
Indices: 19771--19812 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
19761 GTTTTTATAT
*
19771 TTAAAACATAGT-AAATAAA
1 TTAAAACAAAGTAAAATAAA
*
19790 TTAAAATAAAGTAAAATAAA
1 TTAAAACAAAGTAAAATAAA
19810 TTA
1 TTA
19813 GATATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
TTAAAACAAAGTAAAATAAA
Found at i:19796 original size:10 final size:10
Alignment explanation
Indices: 19783--19812 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
19773 AAAACATAGT
19783 AAATAAATTA
1 AAATAAATTA
*
19793 AAATAAAGTA
1 AAATAAATTA
19803 AAATAAATTA
1 AAATAAATTA
19813 GATATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AAATAAATTA
Found at i:21043 original size:24 final size:24
Alignment explanation
Indices: 21007--21053 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20997 TTCTGTAATC
21007 AGCCACTCCTTCCCTCTAGAAACT
1 AGCCACTCCTTCCCTCTAGAAACT
* * *
21031 AGCCGCTCTTTCCCTCTGGAAAC
1 AGCCACTCCTTCCCTCTAGAAAC
21054 CAACCCCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.40, G:0.13, T:0.26
Consensus pattern (24 bp):
AGCCACTCCTTCCCTCTAGAAACT
Found at i:22121 original size:22 final size:22
Alignment explanation
Indices: 22096--22140 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
22086 AAGATCATGT
*
22096 TTAG-AAATTTTATAGATTATAC
1 TTAGAAAATTTGA-AGATTATAC
22118 TTAGAAAATTTGAAGATTATAC
1 TTAGAAAATTTGAAGATTATAC
22140 T
1 T
22141 CGAAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.42
Consensus pattern (22 bp):
TTAGAAAATTTGAAGATTATAC
Found at i:22213 original size:84 final size:83
Alignment explanation
Indices: 22125--22450 Score: 277
Period size: 84 Copynumber: 3.9 Consensus size: 83
22115 TACTTAGAAA
* * * *
22125 ATTTGAAGATTATACTCGAAGATTTTACAAATATCGACTCTAAAATAGATTTAGCTTAGAAGACT
1 ATTTGAAGATTATGCTCGAAGATCTTACAAATTTCGACTCTAAAATAGATTTAGCTCAGAAGACT
*
22190 TATGAATCTTACCAAAACG
66 TACGAATCTTACCAAAA-G
* * * * *
22209 ATTTGAAGATTATGCCTAGATG-TCTTATAAATTTTGACTCTAAAATTGATTTAGCT-AGGAAGA
1 ATTTGAAGATTATG-CTCGAAGATCTTACAAATTTCGACTCTAAAATAGATTTAGCTCA-GAAGA
* * *** *
22272 CTTACAAATTTTACTTGGAGG
64 CTTACGAATCTTAC-CAAAAG
* * * * * * *
22293 ATTTGAAGATTATGCTTGAA-AGTCTTATAAATCTCAACTCTAAAACATATTCAGCTCA-AA-AC
1 ATTTGAAGATTATGCTCGAAGA-TCTTACAAATTTCGACTCTAAAATAGATTTAGCTCAGAAGAC
*
22355 TTACGAATATTACCCAAAAG
65 TTACGAATCTTA-CCAAAAG
* * * * * *
22375 ACTT-AGAGATTATGCCCAAAGATCTTACAAATTTTGACTCTAAAATAAATTTAGCTCAAAAGAC
1 ATTTGA-AGATTATGCTCGAAGATCTTACAAATTTCGACTCTAAAATAGATTTAGCTCAGAAGAC
22439 TTACGAATCTTA
65 TTACGAATCTTA
22451 TCTAGAAGAC
Statistics
Matches: 189, Mismatches: 42, Indels: 22
0.75 0.17 0.09
Matches are distributed among these distances:
81 1 0.01
82 57 0.30
83 11 0.06
84 113 0.60
85 7 0.04
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (83 bp):
ATTTGAAGATTATGCTCGAAGATCTTACAAATTTCGACTCTAAAATAGATTTAGCTCAGAAGACT
TACGAATCTTACCAAAAG
Found at i:24553 original size:4 final size:4
Alignment explanation
Indices: 24535--24594 Score: 58
Period size: 4 Copynumber: 16.2 Consensus size: 4
24525 CTTTTAAATC
*
24535 TTAT TTAT CTA- TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTA- TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
**
24578 TTGC TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT T
24595 GATGCAATTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 14 0.29
4 34 0.71
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:24579 original size:28 final size:29
Alignment explanation
Indices: 24539--24594 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
24529 TAAATCTTAT
*
24539 TTATCTATTATTTATTTATTTATTTATTA
1 TTATCTATTATTTACTTATTTATTTATTA
*
24568 TTAT-TATTATTTGCTTATTTATTTATT
1 TTATCTATTATTTACTTATTTATTTATT
24595 GATGCAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (29 bp):
TTATCTATTATTTACTTATTTATTTATTA
Found at i:24854 original size:61 final size:59
Alignment explanation
Indices: 24676--25425 Score: 604
Period size: 60 Copynumber: 12.6 Consensus size: 59
24666 AAAATTATAT
* * * *
24676 ATATTTTT-AGGAAAAGTTGAAAAGCATAAATTTTTCTTAAAAATAAAATTTTCAAAAAAA
1 ATATTTTTGAGGAAAAGTTG-AAAGTATCAATTTTT-TTGAAAATAAAAATTTCAAAAAAA
** * * * ** *
24736 GCATTTTTGAGGAAGAGTTAAAAATATCAACTTTCCTT-AAAATAAAAATTCCAAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTTTTGAAAATAAAAATTTC-AAAAAAA
* *
24796 ATATTTTTGAGGAAAAGTTGATAGTATCAATTTTTTTAAAAAATAAAAATTTTC-AAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTT-GAAAATAAAAA-TTTCAAAAAAA
** * * *
24856 GCATTTTTGAGGAAGAA-TTGAAAATATTAATTTTTCTCGAAAATAAAAA--T-AAAAAAA
1 ATATTTTTGAGGAA-AAGTTGAAAGTATCAATTTTT-TTGAAAATAAAAATTTCAAAAAAA
* * *
24913 ATATTTTTGAAGACAAGTTAAAAGTATCAATTTTCTTTGAAAATAAAAAAAAATTTCAAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTGAAAAT----AAAAATTTC--AAAAAA
24978 A
59 A
* * * *
24979 ATATTTTTAAGAAAAATTTGAAAGTAAT-AATTTTTCTTGAAAATAAATATTTCAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGT-ATCAATTTTT-TTGAAAATAAAAATTTCAAAAAAA
** *
25039 GGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAGAATAAAATTTTCAAAAAAA
1 -ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTT-TTGAA-AATAAAAATTTCAAAAAAA
* * * * * *
25100 ATATTTTTAAGAAAAAGTTAAAAGTATCAATTTTTCT-----CAAAAA--TAAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAAAATTTCAAAAAAA
* * * * * *
25152 ATATTTTTGAGAAAAATTTGAAAGTATCAGTTTTCCTTGAAAATGAAAATTTCAAGAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAAAAATTTCAAAAAAA
* ** * * **
25212 ATAGTTTTGAAAAAAAAGTTGAAAGTATCGATTTTCTTGAAAATAAAAATTTCAAATAATG
1 ATATTTTTG-AGGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAAAATTTCAAA-AAAA
* * *
25273 A-ATTTTTGAGAAAAAGTTTGAAAATATCAAATTTTCTTGAAAATAAAAGATTTCAAAAAAGA
1 ATATTTTTGAGGAAAAG-TTGAAAGTATC-AATTTTTTTGAAAATAAAA-ATTTCAAAAAA-A
* * *
25335 A-ATTTTTGAGGTAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAA-TTAAAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAAAAATTTCAAAAAAA
* *
25392 ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTT
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
25426 CTTTATATAG
Statistics
Matches: 559, Mismatches: 90, Indels: 84
0.76 0.12 0.11
Matches are distributed among these distances:
52 38 0.07
53 1 0.00
54 4 0.01
56 2 0.00
57 40 0.07
58 42 0.08
59 26 0.05
60 189 0.34
61 140 0.25
62 33 0.06
63 1 0.00
65 1 0.00
66 40 0.07
67 2 0.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (59 bp):
ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAAAATTTCAAAAAAA
Found at i:24966 original size:67 final size:66
Alignment explanation
Indices: 24895--25025 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 66
24885 ATTTTTCTCG
*
24895 AAAATAAAAATAAAAAAAATATTTTTGAAG-ACAAGTTAAAAGT-ATCAA-TTTTCTTTGAAAAT
1 AAAATAAAAA-AAAAAAAATATTTTT-AAGAAAAAGTTAAAAGTAAT-AATTTTTC-TTGAAAAT
24957 AAAAA
62 AAAAA
*** * *
24962 AAAATTTCAAAAAAAAAATATTTTTAAGAAAAATTTGAAAGTAATAATTTTTCTTGAAAATAAA
1 AAAATAAAAAAAAAAAAATATTTTTAAGAAAAAGTTAAAAGTAATAATTTTTCTTGAAAATAAA
25026 TATTTCAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
65 3 0.05
66 38 0.69
67 14 0.25
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (66 bp):
AAAATAAAAAAAAAAAAATATTTTTAAGAAAAAGTTAAAAGTAATAATTTTTCTTGAAAATAAAA
A
Done.