Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168143.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_385, 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: 29562
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Found at i:683 original size:25 final size:27
Alignment explanation
Indices: 654--713 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
644 AAAATAACAT
654 TTTATTTTATTTGAAT-T-TATATTTA
1 TTTATTTTATTTGAATGTATATATTTA
*
679 TTTATTATTTATTTGAATGTATCTATTTA
1 TTTA-T-TTTATTTGAATGTATATATTTA
708 TTTATT
1 TTTATT
714 ATGAGTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 4 0.13
26 1 0.03
27 12 0.40
28 2 0.07
29 11 0.37
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTATTTTATTTGAATGTATATATTTA
Found at i:691 original size:27 final size:29
Alignment explanation
Indices: 659--715 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
649 AACATTTTAT
659 TTTATTTGAAT-T-TATATTTATTTATTA
1 TTTATTTGAATGTATATATTTATTTATTA
*
686 TTTATTTGAATGTATCTATTTATTTATTA
1 TTTATTTGAATGTATATATTTATTTATTA
715 T
1 T
716 GAGTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 11 0.41
28 1 0.04
29 15 0.56
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (29 bp):
TTTATTTGAATGTATATATTTATTTATTA
Found at i:2116 original size:24 final size:25
Alignment explanation
Indices: 2084--2178 Score: 72
Period size: 29 Copynumber: 3.7 Consensus size: 25
2074 ATTAATTGAC
*
2084 ATGTGAATGCAATCAAAACAAATA-
1 ATGTAAATGCAATCAAAACAAATAT
2108 ATGTAAATGCCAAT--AAA-AAATAT
1 ATGTAAATG-CAATCAAAACAAATAT
**
2131 ATGTAAATGTGATACAAAACAAATTGAGT
1 ATGTAAATGCAAT-CAAAACAAA-T-A-T
*
2160 GTGTAAATGCAAGTCAAAA
1 ATGTAAATGCAA-TCAAAA
2179 TGTATAGGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
22 7 0.13
23 12 0.22
24 8 0.15
25 7 0.13
26 3 0.05
27 1 0.02
28 1 0.02
29 15 0.27
30 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (25 bp):
ATGTAAATGCAATCAAAACAAATAT
Found at i:2242 original size:23 final size:22
Alignment explanation
Indices: 2216--2259 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2206 TTAGGTTTAA
2216 GGTTTAGATAAAGATTTAGATTC
1 GGTTTAGATAAAGATTT-GATTC
*
2239 GGTTTAGATAAGGATTTGATT
1 GGTTTAGATAAAGATTTGATT
2260 TTGAGATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (22 bp):
GGTTTAGATAAAGATTTGATTC
Found at i:4772 original size:63 final size:64
Alignment explanation
Indices: 4672--4818 Score: 156
Period size: 64 Copynumber: 2.3 Consensus size: 64
4662 AATAATCCAT
* * * ** * *
4672 GAATTATTCAAGGC--GTTTTTAACTAAAAACACCTTCAAT-AACCCATTCAATATTTTGTAAG
1 GAATTATTCAAGGCATTTTTTTAACTAAAAACACCTTCAATCAACCCATTAAAAAAATGGAAAG
** ** *
4733 GAATTATTCAAGGCATTTTTTTGGCTAAAAATGCCTTCAATCATCCCATTAAAAAAATGGAAAG
1 GAATTATTCAAGGCATTTTTTTAACTAAAAACACCTTCAATCAACCCATTAAAAAAATGGAAAG
*
4797 GGATTATTCAAGGCATTTTTTT
1 GAATTATTCAAGGCATTTTTTT
4819 TGTTTTTGCC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
61 14 0.20
63 20 0.29
64 36 0.51
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (64 bp):
GAATTATTCAAGGCATTTTTTTAACTAAAAACACCTTCAATCAACCCATTAAAAAAATGGAAAG
Found at i:21320 original size:21 final size:19
Alignment explanation
Indices: 21291--21333 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
21281 TATAAATAAT
*
21291 TTAATTATAGTTTTAATGTTA
1 TTAAATATA-TTTTAAT-TTA
*
21312 TTAAATATATTTTACTTTA
1 TTAAATATATTTTAATTTA
21331 TTA
1 TTA
21334 TTATTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
TTAAATATATTTTAATTTA
Found at i:21636 original size:55 final size:54
Alignment explanation
Indices: 21494--21637 Score: 148
Period size: 55 Copynumber: 2.6 Consensus size: 54
21484 AATCATCAAA
* * * *
21494 ATATAA-TAAAAAAATTAAAACATATAAGTTTATATTGACAATCTCTTATCGTC
1 ATATAAGTAAAAAAATTAAAACATATAAGTCTATACTAACAATCTCTAATCGTC
* * * * *
21547 AGTAAAAGTAAAAAAATTAAAGCATACAATTCTATACTAACAGTCTCTAA-CTGTC
1 A-TATAAGTAAAAAAATTAAAACATATAAGTCTATACTAACAATCTCTAATC-GTC
* *
21602 GATATAAGTAAGAAAATTAAAAAATATAAGTCTATA
1 -ATATAAGTAAAAAAATTAAAACATATAAGTCTATA
21638 TTGACGAATG
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
53 1 0.01
54 5 0.07
55 65 0.90
56 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (54 bp):
ATATAAGTAAAAAAATTAAAACATATAAGTCTATACTAACAATCTCTAATCGTC
Found at i:22681 original size:20 final size:20
Alignment explanation
Indices: 22656--22722 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
22646 ACCATTGGAT
22656 GAATTTACTCCAAGATCTAA
1 GAATTTACTCCAAGATCTAA
* * *
22676 GAATTTACTCTAAGGTCTAC
1 GAATTTACTCCAAGATCTAA
22696 GAATTTACTCCAAGATCTAA
1 GAATTTACTCCAAGATCTAA
*
22716 GGATTTA
1 GAATTTA
22723 TATCATTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
GAATTTACTCCAAGATCTAA
Found at i:23937 original size:2 final size:2
Alignment explanation
Indices: 23930--23961 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23920 TTGGACAAAC
23930 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
23962 TACTTAACTT
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27539 original size:19 final size:20
Alignment explanation
Indices: 27515--27560 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
27505 AAATTAATGA
27515 AAATATTA-TTTTTAAATAT
1 AAATATTATTTTTTAAATAT
27534 AAATATTATTTTTTAAATAT
1 AAATATTATTTTTTAAATAT
27554 AAATATT
1 AAATATT
27561 TAAAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTATTTTTTAAATAT
Found at i:28293 original size:16 final size:16
Alignment explanation
Indices: 28267--28308 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28257 TTTTTAATTC
* *
28267 ATAAGAAATAATTTTA
1 ATAATAAATAATATTA
28283 A-ATATAAATAATATTA
1 ATA-ATAAATAATATTA
28299 ATAATAAATA
1 ATAATAAATA
28309 TAAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
ATAATAAATAATATTA
Done.