Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168212.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_447, 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: 26564
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:2891 original size:22 final size:22
Alignment explanation
Indices: 2849--2895 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2839 AAAAAAGTAA
*
2849 ATTTATTTCATTTAAATTATTAC
1 ATTTATTTCATTTAAAATATT-C
*
2872 ATTTATTT-TTTTAAAATATTC
1 ATTTATTTCATTTAAAATATTC
2893 ATT
1 ATT
2896 ACTCTTACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
23 8 0.36
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTATTTCATTTAAAATATTC
Found at i:3886 original size:20 final size:20
Alignment explanation
Indices: 3861--3901 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3851 ATGCATTAAT
*
3861 TTTGAGAAATGTGTTACAAA
1 TTTGAGAAACGTGTTACAAA
*
3881 TTTGAGAAACGTGTTAGAAA
1 TTTGAGAAACGTGTTACAAA
3901 T
1 T
3902 ATGCCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (20 bp):
TTTGAGAAACGTGTTACAAA
Found at i:5365 original size:31 final size:32
Alignment explanation
Indices: 5327--5387 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
5317 TTTTTTAATG
5327 ATTACTTGCTCAA-TTTTTTTTTTTAAATTTT
1 ATTACTTGCTCAATTTTTTTTTTTTAAATTTT
5358 ATTACTTGCTCAATTTTTTTTTTTTAAATT
1 ATTACTTGCTCAATTTTTTTTTTTTAAATT
5388 CTATCTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (32 bp):
ATTACTTGCTCAATTTTTTTTTTTTAAATTTT
Found at i:6013 original size:2 final size:2
Alignment explanation
Indices: 6000--6035 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5990 TTTCTCCTTT
* *
6000 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6036 AACCTCGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:12636 original size:1 final size:1
Alignment explanation
Indices: 12632--12660 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
12622 ATAATTTTCG
12632 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12661 GTAGCTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15071 original size:15 final size:14
Alignment explanation
Indices: 15046--15090 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
15036 AAGAATATAT
15046 TTTATTATTTATTAAA
1 TTTA-TATTTA-TAAA
15062 TTTATATTTATAAA
1 TTTATATTTATAAA
*
15076 TATTATATTAATAAA
1 T-TTATATTTATAAA
15091 AATATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 18 0.67
16 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATATTTATAAA
Found at i:15104 original size:16 final size:17
Alignment explanation
Indices: 15073--15104 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15063 TTATATTTAT
15073 AAATATTATATTAATAA
1 AAATATTATATTAATAA
15090 AAATATTAT-TTAATA
1 AAATATTATATTAATA
15105 TCATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATTATATTAATAA
Found at i:15688 original size:15 final size:16
Alignment explanation
Indices: 15660--15689 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15650 ATTATATAAT
15660 AATTAAACAATCATTC
1 AATTAAACAATCATTC
15676 AATTAAA-AATCATT
1 AATTAAACAATCATT
15690 GTTAATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAACAATCATTC
Found at i:16048 original size:40 final size:40
Alignment explanation
Indices: 16002--16084 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
15992 AATTCCTTTT
16002 TAATAATATGATTTTAATACATCTTAAAGGACAATATGAA
1 TAATAATATGATTTTAATACATCTTAAAGGACAATATGAA
16042 TAATAATATGATTTTAATACATCTTAAAGGACAATATGAA
1 TAATAATATGATTTTAATACATCTTAAAGGACAATATGAA
16082 TAA
1 TAA
16085 AACTAAGTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (40 bp):
TAATAATATGATTTTAATACATCTTAAAGGACAATATGAA
Found at i:16229 original size:31 final size:30
Alignment explanation
Indices: 16194--16257 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
16184 TAATAGGATT
*
16194 AATATCATAA-ATAATTTTTAAATTATAATAA
1 AATAT-ATAATATAATATTTAAATTATAA-AA
* *
16225 AATATTTAATATAATATTTAAATTTTAAAA
1 AATATATAATATAATATTTAAATTATAAAA
16255 AAT
1 AAT
16258 TTTAATGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AATATATAATATAATATTTAAATTATAAAA
Found at i:16261 original size:29 final size:31
Alignment explanation
Indices: 16204--16278 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
16194 AATATCATAA
*
16204 ATAATTTTTAAATTATAATAAAATATTTAAT
1 ATAATATTTAAATTATAATAAAATATTTAAT
*
16235 ATAATATTTAAATTTTAA-AAAAT-TTTAAT
1 ATAATATTTAAATTATAATAAAATATTTAAT
* * *
16264 GTGATATTTGAATTA
1 ATAATATTTAAATTA
16279 ATCACTCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 17 0.45
30 5 0.13
31 16 0.42
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (31 bp):
ATAATATTTAAATTATAATAAAATATTTAAT
Found at i:16327 original size:21 final size:21
Alignment explanation
Indices: 16303--16350 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
16293 AAGTATCAAA
*
16303 TTAATTAAT-AAATTTATAATT
1 TTAA-TAATAAAATTTAAAATT
*
16324 TTAATATTAAAATTTAAAATT
1 TTAATAATAAAATTTAAAATT
*
16345 TAAATA
1 TTAATA
16351 TTATATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATAATAAAATTTAAAATT
Found at i:16351 original size:21 final size:21
Alignment explanation
Indices: 16312--16353 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16302 ATTAATTAAT
* *
16312 AAATTTATAATTTTAATATTA
1 AAATTTAAAATTTAAATATTA
16333 AAATTTAAAATTTAAATATTA
1 AAATTTAAAATTTAAATATTA
16354 TATTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTAAAATTTAAATATTA
Found at i:16367 original size:28 final size:28
Alignment explanation
Indices: 16312--16370 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
16302 ATTAATTAAT
*
16312 AAATTTATAATTTTAATATTAAAATTTA
1 AAATTTATAATATTAATATTAAAATTTA
16340 AAATTTA-AATATT-ATATTAAATATTTTA
1 AAATTTATAATATTAATATTAAA-A-TTTA
16368 AAA
1 AAA
16371 AATGTAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.29
27 6 0.21
28 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATTTATAATATTAATATTAAAATTTA
Found at i:18522 original size:30 final size:30
Alignment explanation
Indices: 18486--18547 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
18476 TTTTTTAATG
* **
18486 ATTACTTGCTTAATTTTTTTTTTAAATTCT
1 ATTACTTGCTCAATTTGGTTTTTAAATTCT
18516 ATTACTTGCTCAATTTGGTTTTTAAATTCT
1 ATTACTTGCTCAATTTGGTTTTTAAATTCT
18546 AT
1 AT
18548 CTTTTTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.58
Consensus pattern (30 bp):
ATTACTTGCTCAATTTGGTTTTTAAATTCT
Found at i:19495 original size:2 final size:2
Alignment explanation
Indices: 19460--19486 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19450 TCTTTCTCTT
19460 TA 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 TA T
19487 TTTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19814 original size:25 final size:24
Alignment explanation
Indices: 19786--19849 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 24
19776 AAAAAATAAT
*
19786 ATTATTAAATACAAAATACAAAAAA
1 ATTATAAAATACAAAATAC-AAAAA
* *
19811 ATTATAAAATCCAAAATACCAAAA
1 ATTATAAAATACAAAATACAAAAA
19835 A-TATAAAATACAAAA
1 ATTATAAAATACAAAA
19850 AAAACAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 13 0.37
24 5 0.14
25 17 0.49
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (24 bp):
ATTATAAAATACAAAATACAAAAA
Found at i:20986 original size:20 final size:21
Alignment explanation
Indices: 20954--20993 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20944 GTTAATTTTT
20954 AAAATAAACTTTAAAAATAAA
1 AAAATAAACTTTAAAAATAAA
*
20975 AAAATAAA-TTTAATAATAA
1 AAAATAAACTTTAAAAATAA
20994 TACTAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAAACTTTAAAAATAAA
Done.