Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168178.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_416, 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: 27856
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Found at i:9223 original size:20 final size:19
Alignment explanation
Indices: 9198--9271 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
9188 TATAAACTTA
*
9198 AAAGTGAAATTTTATATCT
1 AAAGTGAAATTTTATACCT
*
9217 GAAAGTG-ATTATTTATACCT
1 -AAAGTGAAAT-TTTATACCT
*
9237 AAAAT-AATTATTTTATACCT
1 AAAGTGAA--ATTTTATACCT
9257 AAAAGTGAAATTTTA
1 -AAAGTGAAATTTTA
9272 AAAAAATGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 7 0.16
20 29 0.67
21 5 0.12
22 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (19 bp):
AAAGTGAAATTTTATACCT
Found at i:13145 original size:14 final size:14
Alignment explanation
Indices: 13126--13163 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
13116 TAATATTATT
13126 AAATACAAAATACG
1 AAATACAAAATACG
*
13140 AAATACAAAATATG
1 AAATACAAAATACG
*
13154 AAATATAAAA
1 AAATACAAAA
13164 AAATACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.68, C:0.08, G:0.05, T:0.18
Consensus pattern (14 bp):
AAATACAAAATACG
Found at i:13186 original size:29 final size:27
Alignment explanation
Indices: 13154--13207 Score: 90
Period size: 29 Copynumber: 1.9 Consensus size: 27
13144 ACAAAATATG
13154 AAATATAAAAAAATACTAAAAATAATACA
1 AAATATAAAAAAATAC-AAAAA-AATACA
13183 AAATATAAAAAAATACAAAAAAATA
1 AAATATAAAAAAATACAAAAAAATA
13208 GAACGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 4 0.16
28 5 0.20
29 16 0.64
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (27 bp):
AAATATAAAAAAATACAAAAAAATACA
Found at i:13197 original size:17 final size:17
Alignment explanation
Indices: 13140--13202 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
13130 ACAAAATACG
13140 AAATACAAAATATGAAATA
1 AAATACAAAATAT-AAA-A
*
13159 TAA-A-AAAATACTAAAA
1 AAATACAAAATA-TAAAA
13175 ATAATACAAAATATAAAA
1 A-AATACAAAATATAAAA
13193 AAATACAAAA
1 AAATACAAAA
13203 AAATAGAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.03
17 20 0.53
18 9 0.24
19 8 0.21
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (17 bp):
AAATACAAAATATAAAA
Found at i:14325 original size:20 final size:21
Alignment explanation
Indices: 14292--14331 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
14282 GTTAATTTTT
*
14292 AAAATGAAATTTAAAAATAAA
1 AAAATGAAACTTAAAAATAAA
*
14313 AAAAT-AAACTTAATAATAA
1 AAAATGAAACTTAAAAATAA
14332 TACCAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAATGAAACTTAAAAATAAA
Found at i:14737 original size:211 final size:208
Alignment explanation
Indices: 14340--14720 Score: 472
Period size: 211 Copynumber: 1.8 Consensus size: 208
14330 AATACCAAAA
* * * *
14340 TAATAAAAATGCAAGAAAAGAAAATTTTTATTCGACGATGAGATTCAACAGTATTCCGAGTAGTG
1 TAATAAAAATGCAAGAAAAGAAAATTTTTATCCGACGATGAGATTCAAAAGTATTCCAAGTAGAG
* * *
14405 ATGCCTACAAAATCTCTAAGTGAGAAGATTTTTTTTTAAATACTACCAGTGTATTGGAGTATTTA
66 ATGCCTACAAAATCTCTAAGTGAGAAGATTTTTTGTAAAATACTACCAGTGTATTGGAATATTTA
*
14470 TAAAAAAATTTTCTTCAATACAATAAAAATTTTCTTTTTTTAAAAGTAATAAATAAAAATTGATT
131 TAAAAAAA--TTCTTCAATACAATAAAAATTTTCTTTTTTCAAAAGTAATAAATAAAAATTGATT
14535 AGTTAAAAATATAAG
194 AGTTAAAAATATAAG
* * * *
14550 TAATAAAAATGAGAAGAAAAG-AAA-TTTTATCCGATGATGGGATTCTAAAAGTATTTCAAGTAG
1 TAATAAAAATG-CAAGAAAAGAAAATTTTTATCCGACGATGAGATTC-AAAAGTATTCCAAGTAG
* * *
14613 AGATGCTTTA-AAGAATC-CTAGGTGAGAAAGATTTTTTGTAAAATATTACCAGTGTATTGGAAT
64 AGATGC-CTACAA-AATCTCTAAGTGAG-AAGATTTTTTGTAAAATACTACCAGTGTATTGGAAT
* * *
14676 ATTTAT-AGAAAA-TCTTCAATATAAT-TAAATTTT-TTTTCTTCAAAA
126 ATTTATAAAAAAATTCTTCAATACAATAAAAATTTTCTTTT-TTCAAAA
14721 TTTCAATTAC
Statistics
Matches: 147, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
205 4 0.03
206 13 0.09
207 12 0.08
209 18 0.12
210 48 0.33
211 52 0.35
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (208 bp):
TAATAAAAATGCAAGAAAAGAAAATTTTTATCCGACGATGAGATTCAAAAGTATTCCAAGTAGAG
ATGCCTACAAAATCTCTAAGTGAGAAGATTTTTTGTAAAATACTACCAGTGTATTGGAATATTTA
TAAAAAAATTCTTCAATACAATAAAAATTTTCTTTTTTCAAAAGTAATAAATAAAAATTGATTAG
TTAAAAATATAAG
Found at i:15503 original size:4 final size:4
Alignment explanation
Indices: 15494--15529 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
15484 ACAAAGGTAA
15494 AAAT AAAT -AAT AAAT AAAT AAA- AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
15530 AATTCACACG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 9 0.31
4 20 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:15507 original size:7 final size:7
Alignment explanation
Indices: 15492--15531 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
15482 GTACAAAGGT
15492 AAAAATA
1 AAAAATA
*
15499 AATAATA
1 AAAAATA
15506 AATAAATA
1 AA-AAATA
15514 AAAAATA
1 AAAAATA
15521 AAAAATA
1 AAAAATA
15528 AAAA
1 AAAA
15532 TTCACACGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:15510 original size:11 final size:11
Alignment explanation
Indices: 15494--15529 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
15484 ACAAAGGTAA
15494 AAATAAATAAT
1 AAATAAATAAT
*
15505 AAATAAATAAA
1 AAATAAATAAT
*
15516 AAATAAAAAAT
1 AAATAAATAAT
15527 AAA
1 AAA
15530 AATTCACACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:26835 original size:49 final size:46
Alignment explanation
Indices: 26763--27169 Score: 490
Period size: 49 Copynumber: 8.5 Consensus size: 46
26753 TACGCAACAA
* *
26763 CCTCTGCTGAGAGGAGCCCTTTCAAGATGGAATTTTTAAAGTTGTTGAG
1 CCTCTACTGAGAGGAG-CTTTTCAAGAT-GAA-TTTTAAAGTTGTTGAG
* *
26812 CCTCTACTGAGAAGAGCTTTTTCAAGATTAATTTTTAAAGTTGTTGAG
1 CCTCTACTGAGAGGAGC-TTTTCAAGATGAA-TTTTAAAGTTGTTGAG
* * *
26860 CCTCTGCTGAGAGGAGTCATTTTCAAGATGGATTTTAAAGTTATTGAG
1 CCTCTACTGAGAGGAG-C-TTTTCAAGATGAATTTTAAAGTTGTTGAG
26908 CCTCTACTGAGAGGAGCTTTTCAAGATGAGATTTTAAAGTTGTTGAG
1 CCTCTACTGAGAGGAGCTTTTCAAGATGA-ATTTTAAAGTTGTTGAG
* * *
26955 CCTCTATTGAGAGGAGCCTTTTTTAAGATGAGATTTTAATGTTGTTGAG
1 CCTCTACTGAGAGGAG-C-TTTTCAAGATGA-ATTTTAAAGTTGTTGAG
** * *
27004 CCTCTGTTGAGAGGAGCTTTTCAAGATGATTTTTAAAGTCGTTGAG
1 CCTCTACTGAGAGGAGCTTTTCAAGATGAATTTTAAAGTTGTTGAG
* *
27050 CCTCTACTGAGAGGAGCCTTTTTTAAGATGAGATTTTAATGTTGTTGAG
1 CCTCTACTGAGAGGAG-C-TTTTCAAGATGA-ATTTTAAAGTTGTTGAG
** * *
27099 CCTCTGTTGAGAGGAGCTTTTCAAGATGATTTTTAAAGTCGTTGAG
1 CCTCTACTGAGAGGAGCTTTTCAAGATGAATTTTAAAGTTGTTGAG
27145 CCTCTACTGAGAGGAGTCTATTTCA
1 CCTCTACTGAGAGGAG-CT-TTTCA
27170 GATTTTAAAT
Statistics
Matches: 313, Mismatches: 35, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
46 67 0.21
47 57 0.18
48 83 0.27
49 106 0.34
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (46 bp):
CCTCTACTGAGAGGAGCTTTTCAAGATGAATTTTAAAGTTGTTGAG
Found at i:26970 original size:95 final size:95
Alignment explanation
Indices: 26763--27160 Score: 532
Period size: 95 Copynumber: 4.2 Consensus size: 95
26753 TACGCAACAA
* * *
26763 CCTCTGCTGAGAGGAGCC-CTTTCAAGATG-GAATTTTTAAAGTTGTTGAGCCTCTACTGAGAAG
1 CCTCTACTGAGAGGAGCCATTTTCAAGATGAG-A-TTTTAAAGTTGTTGAGCCTCTACTGAGAGG
* *
26826 AGCTTTTTCAAGATTAATTTTTAAAGTTGTTGAG
64 AGC-TTTTCAAGATGAA-TTTTAAAGTCGTTGAG
* * *
26860 CCTCTGCTGAGAGGAGTCATTTTCAAGATG-GATTTTAAAGTTATTGAGCCTCTACTGAGAGGAG
1 CCTCTACTGAGAGGAGCCATTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG
*
26924 CTTTTCAAGATGAGATTTTAAAGTTGTTGAG
66 CTTTTCAAGATGA-ATTTTAAAGTCGTTGAG
* * * * **
26955 CCTCTATTGAGAGGAGCCTTTTTTAAGATGAGATTTTAATGTTGTTGAGCCTCTGTTGAGAGGAG
1 CCTCTACTGAGAGGAGCCATTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG
*
27020 CTTTTCAAGATGATTTTTAAAGTCGTTGAG
66 CTTTTCAAGATGAATTTTAAAGTCGTTGAG
* * * **
27050 CCTCTACTGAGAGGAGCCTTTTTTAAGATGAGATTTTAATGTTGTTGAGCCTCTGTTGAGAGGAG
1 CCTCTACTGAGAGGAGCCATTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG
*
27115 CTTTTCAAGATGATTTTTAAAGTCGTTGAG
66 CTTTTCAAGATGAATTTTAAAGTCGTTGAG
27145 CCTCTACTGAGAGGAG
1 CCTCTACTGAGAGGAG
27161 TCTATTTCAG
Statistics
Matches: 281, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
95 177 0.63
96 75 0.27
97 18 0.06
98 11 0.04
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (95 bp):
CCTCTACTGAGAGGAGCCATTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG
CTTTTCAAGATGAATTTTAAAGTCGTTGAG
Found at i:27078 original size:144 final size:142
Alignment explanation
Indices: 26763--27169 Score: 554
Period size: 144 Copynumber: 2.8 Consensus size: 142
26753 TACGCAACAA
* * * *
26763 CCTCTGCTGAGAGGAGCCCTTTCAAGATG-GAATTTTTAAAGTTGTTGAGCCTCTACTGAGAAGA
1 CCTCTACTGAGAGGAGCCTTTTCAAGATGAG-A-TTTTAAAGTTGTTGAGCCTCTATTGAGAGGA
*
26827 GCTTTTTCAAGATTAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTCATTTTCAAGATGGA
64 GCTTTTTCAAGATGAA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTC-TTTTCAAGATGGA
*
26892 TTTTAAAGTTATTGAG
127 TTTTAAAGTCATTGAG
26908 CCTCTACTGAGAGGAG-CTTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGC
1 CCTCTACTGAGAGGAGCCTTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAG-
* * *
26972 CTTTTTTAAGATGAGATTTTAATGTTGTTGAGCCTCTGTTGAGAGGAG-CTTTTCAAGAT-GATT
65 CTTTTTCAAGATGA-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTCTTTTCAAGATGGA-T
*
27035 TTTAAAGTCGTTGAG
128 TTTAAAGTCATTGAG
* * *
27050 CCTCTACTGAGAGGAGCCTTTTTTAAGATGAGATTTTAATGTTGTTGAGCCTCTGTTGAGAGGAG
1 CCTCTACTGAGAGGAGCC-TTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAG
* * *
27115 C-TTTTCAAGATGATTTTTAAAGTCGTTGAGCCTCTACTGAGAGGAGTCTATTTCA
65 CTTTTTCAAGATGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTCT-TTTCA
27170 GATTTTAAAT
Statistics
Matches: 235, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
141 30 0.13
142 53 0.23
143 38 0.16
144 97 0.41
145 17 0.07
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (142 bp):
CCTCTACTGAGAGGAGCCTTTTCAAGATGAGATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGC
TTTTTCAAGATGAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGTCTTTTCAAGATGGATTTT
AAAGTCATTGAG
Found at i:27450 original size:22 final size:22
Alignment explanation
Indices: 27419--27484 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 22
27409 TAATATTATT
*
27419 AAATATGAAATACAAAAATATA
1 AAATATGAAATACAAAAATACA
*
27441 AAATACGAAATACAAAAAAATACA
1 AAATATGAAATAC--AAAAATACA
*
27465 AAATATAAAATACAAAAATA
1 AAATATGAAATACAAAAATA
27485 ATACCAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.50
24 19 0.50
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (22 bp):
AAATATGAAATACAAAAATACA
Found at i:27462 original size:17 final size:17
Alignment explanation
Indices: 27440--27515 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 17
27430 ACAAAAATAT
*
27440 AAAATACGAAATACAAA
1 AAAATACAAAATACAAA
*
27457 AAAATACAAAATATAAA
1 AAAATACAAAATACAAA
27474 ATACAA-A-AATAATACCAAA
1 A-A-AATACAA-AATA-CAAA
27493 AATAATACAAAATACCAAA
1 AA-AATACAAAATA-CAAA
27512 AAAA
1 AAAA
27516 ATAGAATAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
17 18 0.37
18 11 0.22
19 18 0.37
20 2 0.04
ACGTcount: A:0.72, C:0.12, G:0.01, T:0.14
Consensus pattern (17 bp):
AAAATACAAAATACAAA
Found at i:27494 original size:12 final size:11
Alignment explanation
Indices: 27449--27504 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 11
27439 TAAAATACGA
27449 AATACAAAAA-
1 AATACAAAAAT
27459 AATACAAAATAT
1 AATACAAAA-AT
27471 AAAATACAAAAAT
1 --AATACAAAAAT
27484 AATACCAAAAAT
1 AATA-CAAAAAT
27496 AATACAAAA
1 AATACAAAA
27505 TACCAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.22
11 10 0.24
12 11 0.27
13 2 0.05
14 9 0.22
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (11 bp):
AATACAAAAAT
Done.