Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168291.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_518, 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: 24209
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:219 original size:21 final size:20
Alignment explanation
Indices: 193--270 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 20
183 AATTCATGCC
193 TGATTACTATTAAGTTATCA
1 TGATTACTATTAAGTTATCA
213 TTGATTACTATTATA-TTATCGA
1 -TGATTACTATTA-AGTTATC-A
*
235 TGATTTACTATT-AGTTGT-A
1 TGA-TTACTATTAAGTTATCA
*
254 CTGATTACTTTTAAGTT
1 -TGATTACTATTAAGTT
271 TTCAAATGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.16
20 8 0.16
21 23 0.47
22 10 0.20
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (20 bp):
TGATTACTATTAAGTTATCA
Found at i:299 original size:13 final size:13
Alignment explanation
Indices: 281--305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271 TTCAAATGTA
281 TAATTACTATTAT
1 TAATTACTATTAT
294 TAATTACTATTA
1 TAATTACTATTA
306 AACGTGGAAA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTACTATTAT
Found at i:3325 original size:27 final size:27
Alignment explanation
Indices: 3282--3338 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3272 CTAAAGAATG
*
3282 AAATTGGGTCTCAAGCCTGAATGAATCA
1 AAATTGGGTCTCAAGCCCGAATGAA-CA
*
3310 AAATTGGG-CTTC-AGCCCGATTGAACA
1 AAATTGGGTC-TCAAGCCCGAATGAACA
3336 AAA
1 AAA
3339 ATCAGGTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 5 0.19
27 11 0.42
28 10 0.38
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
AAATTGGGTCTCAAGCCCGAATGAACA
Found at i:3730 original size:101 final size:103
Alignment explanation
Indices: 3627--4022 Score: 353
Period size: 102 Copynumber: 3.9 Consensus size: 103
3617 TAAAATTTGA
* *
3627 AAAAAGGCTCTTTTTGATAAAGGCTCAACAACTTT-AAAATT-TGCATC-TAAAAAAAGCTCATC
1 AAAAAGGCTCTTTTTGATAAAGGCTCAACAACTTTAAAAATTATTCATCTTAAAAAAGGCTCATC
* *
3689 TTTGTAGAGGCTCAACAACTTTAAAAATTTTTATCTTG
66 TTTGTAGAGGCTTAACAACTTTAAAAATTTTTATATTG
* * * * * **
3727 AAAAAGGCT-TATCTTGGTAGAGGCTCAACAACTTTAAAAATT-TTCATATTGAAAAAGGCTTTT
1 AAAAAGGCTCT-TTTTGATAAAGGCTCAACAACTTTAAAAATTATTCATCTTAAAAAAGGCTCAT
** * *
3790 CTAGGTAGAGGTTTAACAATTTTAAAAATTTTTATATTG
65 CTTTGTAGAGGCTTAACAACTTTAAAAATTTTTATATTG
* * * * * * * * **
3829 GAAAATGCTATTTTTG-TAGAGGTTTAACAACTTTAAAAATT-CTCATCTTAGAAAATGTTTC-T
1 AAAAAGGCTCTTTTTGATAAAGGCTCAACAACTTTAAAAATTATTCATCTTA-AAAAAGGCTCAT
* * * * *
3891 TTTTGTAGAGGTTTAACAACTTTAAAAATTCTCATATTA
65 CTTTGTAGAGGCTTAACAACTTTAAAAATTTTTATATTG
* * * * *
3930 AAAAAGGCTC-CTTTAAGTAAAAGCTCAATAACTTTAAAAATTATTC-TCTTGAAAAAGGCTCAT
1 AAAAAGGCTCTTTTTGA-TAAAGGCTCAACAACTTTAAAAATTATTCATCTTAAAAAAGGCTCAT
* * *
3993 TTTTGTATAAGCTTAACAACTTTAAAAATT
65 CTTTGTAGAGGCTTAACAACTTTAAAAATT
4023 CTTCTTTTAG
Statistics
Matches: 235, Mismatches: 52, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
99 1 0.00
100 33 0.14
101 86 0.37
102 112 0.48
103 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (103 bp):
AAAAAGGCTCTTTTTGATAAAGGCTCAACAACTTTAAAAATTATTCATCTTAAAAAAGGCTCATC
TTTGTAGAGGCTTAACAACTTTAAAAATTTTTATATTG
Found at i:3751 original size:51 final size:51
Alignment explanation
Indices: 3647--4081 Score: 307
Period size: 51 Copynumber: 8.6 Consensus size: 51
3637 TTTTTGATAA
* * * * *
3647 AGGCTCAACAACTTT-AAAATT-TGCATC-TAAAAAAAGCTCATCTTTGTAG
1 AGGCTTAACAACTTTAAAAATTCT-TATCTTGAAAAAGGCTTATCTTTGTAG
* * *
3696 AGGCTCAACAACTTTAAAAATTTTTATCTTGAAAAAGGCTTATCTTGGTAG
1 AGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAAGGCTTATCTTTGTAG
* * * **
3747 AGGCTCAACAACTTTAAAAATT-TTCATATTGAAAAAGGCTTTTCTAGGTAG
1 AGGCTTAACAACTTTAAAAATTCTT-ATCTTGAAAAAGGCTTATCTTTGTAG
* * * * * * *
3798 AGGTTTAACAATTTTAAAAATTTTTATATTGGAAAATGC-TATTTTTGTAG
1 AGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAAGGCTTATCTTTGTAG
* * * * * *
3848 AGGTTTAACAACTTTAAAAATTCTCATCTT-AGAAAATGTTTCTTTTTGTAG
1 AGGCTTAACAACTTTAAAAATTCTTATCTTGA-AAAAGGCTTATCTTTGTAG
* * * * * *
3899 AGGTTTAACAACTTTAAAAATTCTCATATTAAAAAAGGC-T-CCTTTAAGTAA
1 AGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAAGGCTTATCTTT--GTAG
* * * * * * * *
3950 AAGCTCAATAACTTTAAAAATTATTCTCTTGAAAAAGGCTCATTTTTGTAT
1 AGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAAGGCTTATCTTTGTAG
* * * *
4001 AAGCTTAACAACTTTAAAAATTCTTCT-TTTAGAAAAGG--TATCTCTAGGTAG
1 AGGCTTAACAACTTTAAAAATTCTTATCTTGA-AAAAGGCTTATCT-T-TGTAG
* *
4052 ACGCTTAACAAGTTTAAAAATTCTTATCTT
1 AGGCTTAACAACTTTAAAAATTCTTATCTT
4082 TTCTCGAACC
Statistics
Matches: 316, Mismatches: 54, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
49 21 0.07
50 55 0.17
51 232 0.73
52 5 0.02
53 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (51 bp):
AGGCTTAACAACTTTAAAAATTCTTATCTTGAAAAAGGCTTATCTTTGTAG
Found at i:3966 original size:152 final size:153
Alignment explanation
Indices: 3626--4075 Score: 430
Period size: 152 Copynumber: 3.0 Consensus size: 153
3616 TTAAAATTTG
** * * * * *
3626 AAAAAAGGCTCTT-TTTGATAAAGGCTCAACAACTTT-AAAATT-TGCAT-CTAAAAAAAGCTCA
1 AAAAAAGGCTCTTCTAAG-TAAAAGCTCAACAACTTTAAAAATTAT-TATATTGAAAAAGGCTCA
* * * * * *
3687 TCTTTGTAGAGGCTCAACAACTTTAAAAATTTTTATCTT-GAAAAAGGCTTATCTTGGTAGAGGC
64 TTTTTGTAGAGGCTTAACAACTTTAAAAATTCTCATCTTAG-AAAAGGTTTCTCTTGGTAGAGGC
* *
3751 TCAACAACTTTAAAAATTTTCATATT
128 TTAACAACTTTAAAAATTCTCATATT
* * * * * * * * * * *
3777 GAAAAAGGCTTTTCTAGGTAGAGGTTTAACAATTTTAAAAATTTTTATATTGGAAAATGCT-ATT
1 AAAAAAGGCTCTTCTAAGTAAAAGCTCAACAACTTTAAAAATTATTATATTGAAAAAGGCTCATT
* * * * *
3841 TTTGTAGAGGTTTAACAACTTTAAAAATTCTCATCTTAGAAAATGTTTCTTTTTGTAGAGGTTTA
66 TTTGTAGAGGCTTAACAACTTTAAAAATTCTCATCTTAGAAAAGGTTTCTCTTGGTAGAGGCTTA
3906 ACAACTTTAAAAATTCTCATATT
131 ACAACTTTAAAAATTCTCATATT
* * *
3929 AAAAAAGGCTCCTT-TAAGTAAAAGCTCAATAACTTTAAAAATTATTCTCTTGAAAAAGGCTCAT
1 AAAAAAGGCT-CTTCTAAGTAAAAGCTCAACAACTTTAAAAATTATTATATTGAAAAAGGCTCAT
* * * * * *
3993 TTTTGTATAAGCTTAACAACTTTAAAAATTCTTC-TTTTAGAAAAGGTATCTCTAGGTAGACGCT
65 TTTTGTAGAGGCTTAACAACTTTAAAAATTC-TCATCTTAGAAAAGGTTTCTCTTGGTAGAGGCT
*
4057 TAACAAGTTTAAAAATTCT
129 TAACAACTTTAAAAATTCT
4076 TATCTTTTCT
Statistics
Matches: 239, Mismatches: 52, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
151 25 0.10
152 130 0.54
153 82 0.34
154 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (153 bp):
AAAAAAGGCTCTTCTAAGTAAAAGCTCAACAACTTTAAAAATTATTATATTGAAAAAGGCTCATT
TTTGTAGAGGCTTAACAACTTTAAAAATTCTCATCTTAGAAAAGGTTTCTCTTGGTAGAGGCTTA
ACAACTTTAAAAATTCTCATATT
Found at i:4923 original size:12 final size:12
Alignment explanation
Indices: 4905--4938 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4895 TTCTTACTTT
4905 TTCTTTTTTTT-
1 TTCTTTTTTTTG
*
4916 TTGTTTTTTTTG
1 TTCTTTTTTTTG
4928 TTCTTTTTTTT
1 TTCTTTTTTTT
4939 AAACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (12 bp):
TTCTTTTTTTTG
Found at i:11953 original size:8 final size:8
Alignment explanation
Indices: 11940--11964 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11930 TTGAAACCAA
11940 TATATTTG
1 TATATTTG
11948 TATATTTG
1 TATATTTG
11956 TATATTTG
1 TATATTTG
11964 T
1 T
11965 CATTGAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TATATTTG
Found at i:13408 original size:16 final size:17
Alignment explanation
Indices: 13375--13408 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13365 AATATTTTTT
*
13375 AGTCTAATTATAAAAAA
1 AGTCTAATAATAAAAAA
13392 AGTCTAATAATAAAAAA
1 AGTCTAATAATAAAAAA
13409 TTTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (17 bp):
AGTCTAATAATAAAAAA
Found at i:13671 original size:17 final size:17
Alignment explanation
Indices: 13649--13681 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13639 TAATTTTTTA
*
13649 GTCTAATTATAAAAAAG
1 GTCTAATAATAAAAAAG
13666 GTCTAATAATAAAAAA
1 GTCTAATAATAAAAAA
13682 ATTCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (17 bp):
GTCTAATAATAAAAAAG
Found at i:13732 original size:22 final size:22
Alignment explanation
Indices: 13707--13748 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13697 AAATTATAAC
* *
13707 AAAAGAGTTTAATATTAAAAAT
1 AAAAGAATTTAAAATTAAAAAT
*
13729 AAAATAATTTAAAATTAAAA
1 AAAAGAATTTAAAATTAAAA
13749 TTTATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAAGAATTTAAAATTAAAAAT
Found at i:13740 original size:16 final size:17
Alignment explanation
Indices: 13716--13749 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13706 CAAAAGAGTT
13716 TAATATTAAAAATAAAA
1 TAATATTAAAAATAAAA
*
13733 TAAT-TTAAAATTAAAA
1 TAATATTAAAAATAAAA
13749 T
1 T
13750 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATATTAAAAATAAAA
Found at i:13748 original size:50 final size:45
Alignment explanation
Indices: 13653--13759 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 45
13643 TTTTTAGTCT
* *
13653 AATTATAAAAAAGGTCTAATAATAAAAAAATTCATTTAAATTAAA
1 AATTATAAAAAAGGTCTAATAATAAAAAAAATAATTTAAATTAAA
* *
13698 AATTATAACAAAAGAGTTTAATATTAAAAATAAAATAATTTAAAATTAAA
1 AATTATAA-AAAAG-GTCTAATAAT-AAAA-AAAATAATTT-AAATTAAA
*
13748 ATTTATAAAAAA
1 AATTATAAAAAA
13760 TTACTAATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
45 8 0.15
46 5 0.10
47 8 0.15
48 4 0.08
49 12 0.23
50 15 0.29
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (45 bp):
AATTATAAAAAAGGTCTAATAATAAAAAAAATAATTTAAATTAAA
Found at i:14345 original size:281 final size:277
Alignment explanation
Indices: 13828--14347 Score: 756
Period size: 281 Copynumber: 1.9 Consensus size: 277
13818 GGGTTTATTG
* * * * * *
13828 AATCACTTTTAGTATTTTTTTAGTCTAATTACAAGAAAGTCTAATAATAAAAAATTTATTTAAAT
1 AATCACTTTTAGTAATTTTTTAGTCTAATTAAAAAAAAATATAATAATAAAAAATTCATTTAAAT
* * * *
13893 TAAAAATTATTAAAAATGTACTAAAGATATCGTATTTAATCACTATTAACACTTAAAATTAAAAT
66 TAAAAATTATAAAAAATGTACTAAAAATATCGTAATCAATCACTATTAACACTTAAAATTAAAAT
* * *
13958 TTTAAAATTTTTAGTTTAATTTCTCATAAACTTTATTTTTAATTCTAGTTTATTTAAATTAAATT
131 TTTAAAATTTTTAGTTTAATTTCTCATAAACTTTAATTTTAATTCTAATTGATTTAAATTAAATT
* * *
14023 TAAATATATTAATAAAATTTATATATTTAAGGATAAATTTGTTATTATAAAGGTATTTAGATTGA
196 TAAATAAATTAATAAAAGTTATATATTTAAAGATAAATTTGTTATTATAAAGGTATTTAGATTGA
14088 TCACTATGAATTGTCTC
261 TCACTATGAATTGTCTC
*
14105 AATCATTTTTAGTAATTTTTTAGTCTAATTATAAAAAAAATATAATAATAAAAAATTCATTTAAA
1 AATCACTTTTAGTAATTTTTTAGTCTAATTA-AAAAAAAATATAATAATAAAAAATTCATTTAAA
*
14170 TTAAAAATTATAAAAAAAAT-TACTAAAAATAT-TTAATCAATCACTATTAACACTTAAAATTAA
65 TTAAAAATTAT--AAAAAATGTACTAAAAATATCGTAATCAATCACTATTAACACTTAAAATTAA
** * *
14233 AATTTTACGATTTTAAGTAGTTTAATTTCTCATAAATTTTAATTTTAATTTTAATTGATTTAAAT
128 AATTTTAAAATTTT---TAGTTTAATTTCTCATAAACTTTAATTTTAATTCTAATTGATTTAAAT
* *
14298 TAAATTTAGATAAATTAATAAAAGTTATATATTTAAAGATGAATTTGTTA
190 TAAATTTAAATAAATTAATAAAAGTTATATATTTAAAGATAAATTTGTTA
14348 ATGTAAATAT
Statistics
Matches: 213, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
277 29 0.14
278 79 0.37
279 11 0.05
280 6 0.03
281 88 0.41
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (277 bp):
AATCACTTTTAGTAATTTTTTAGTCTAATTAAAAAAAAATATAATAATAAAAAATTCATTTAAAT
TAAAAATTATAAAAAATGTACTAAAAATATCGTAATCAATCACTATTAACACTTAAAATTAAAAT
TTTAAAATTTTTAGTTTAATTTCTCATAAACTTTAATTTTAATTCTAATTGATTTAAATTAAATT
TAAATAAATTAATAAAAGTTATATATTTAAAGATAAATTTGTTATTATAAAGGTATTTAGATTGA
TCACTATGAATTGTCTC
Done.