Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168213.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_448, 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: 26556
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:354 original size:14 final size:15
Alignment explanation
Indices: 335--364 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
325 TTTAATTTTA
335 AAAATTAA-TTGATT
1 AAAATTAATTTGATT
349 AAAATTAATTTGATT
1 AAAATTAATTTGATT
364 A
1 A
365 GTTCAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
AAAATTAATTTGATT
Found at i:462 original size:14 final size:13
Alignment explanation
Indices: 440--494 Score: 65
Period size: 13 Copynumber: 3.9 Consensus size: 13
430 TAAAATAAAA
440 TAAATAAAAATAT
1 TAAATAAAAATAT
*
453 TTAATAAAAATAT
1 TAAATAAAAATAT
466 TCAAATAATAAAATAT
1 T-AAAT-A-AAAATAT
482 TAAATTAAAAATA
1 TAAA-TAAAAATA
495 CTAATAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 13 0.36
14 9 0.25
15 5 0.14
16 9 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAAAAATAT
Found at i:478 original size:30 final size:31
Alignment explanation
Indices: 437--494 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
427 ATGTAAAATA
*
437 AAATAAATAAAAATATTTAA-TAAAAATATTC
1 AAATAAAT-AAAATATTAAATTAAAAATATTC
468 AAAT-AATAAAATATTAAATTAAAAATA
1 AAATAAATAAAATATTAAATTAAAAATA
495 CTAATAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 11 0.44
31 4 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (31 bp):
AAATAAATAAAATATTAAATTAAAAATATTC
Found at i:552 original size:18 final size:18
Alignment explanation
Indices: 525--560 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
515 AGACTATTTC
* *
525 ATATATTTTTTATTATAT
1 ATATAATTTTTATAATAT
543 ATATAATTTTTATAATAT
1 ATATAATTTTTATAATAT
561 TTTAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATAATTTTTATAATAT
Found at i:3383 original size:14 final size:14
Alignment explanation
Indices: 3364--3393 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3354 ACCCTCACCT
3364 AGAAAGTACATATC
1 AGAAAGTACATATC
3378 AGAAAGTACATATC
1 AGAAAGTACATATC
3392 AG
1 AG
3394 CCGCTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (14 bp):
AGAAAGTACATATC
Found at i:5736 original size:47 final size:49
Alignment explanation
Indices: 5640--5746 Score: 130
Period size: 47 Copynumber: 2.2 Consensus size: 49
5630 TTATATAACG
* *
5640 ATAAAAATTTTATTAATATTTTTATTAAAAATATTTGTTTAATAAATAT-
1 ATAAAAA-TTTATTAATATTTTTATAAAAAATATATGTTTAATAAATATA
* **
5689 ATCAAAATTTATTAAT-TTTTTA-AAAAAATTATATGTTTAATCTATATA
1 ATAAAAATTTATTAATATTTTTATAAAAAA-TATATGTTTAATAAATATA
5737 ATAAAAATTT
1 ATAAAAATTT
5747 TCAATCTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
46 5 0.10
47 21 0.42
48 18 0.36
49 6 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (49 bp):
ATAAAAATTTATTAATATTTTTATAAAAAATATATGTTTAATAAATATA
Found at i:10652 original size:27 final size:26
Alignment explanation
Indices: 10622--10679 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
10612 ACAAGATAAG
10622 ATAATATTATTTAATCTAATCATATTC
1 ATAATATTATTTAATCTAATCATA-TC
* * *
10649 ATAATATTATTTTATCTTATCTTATC
1 ATAATATTATTTAATCTAATCATATC
10675 ATAAT
1 ATAAT
10680 TTTGTGTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (26 bp):
ATAATATTATTTAATCTAATCATATC
Found at i:15126 original size:33 final size:33
Alignment explanation
Indices: 15084--15149 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
15074 TCATCATTCA
15084 AACTCTAGCTAACTTTTATATAAAAGAATAAAT
1 AACTCTAGCTAACTTTTATATAAAAGAATAAAT
15117 AACTCTAGCTAACTTTTATATAAAAGAATAAAT
1 AACTCTAGCTAACTTTTATATAAAAGAATAAAT
15150 TTTGAATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (33 bp):
AACTCTAGCTAACTTTTATATAAAAGAATAAAT
Found at i:17725 original size:16 final size:17
Alignment explanation
Indices: 17704--17738 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
17694 TCAAATTGAA
17704 TTATATATATTTTA-AT
1 TTATATATATTTTATAT
17720 TTATATATATTTTATAT
1 TTATATATATTTTATAT
17737 TT
1 TT
17739 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATATATTTTATAT
Found at i:17786 original size:20 final size:21
Alignment explanation
Indices: 17761--17811 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
17751 TAATATTTTT
*
17761 TATTAAAATTTATTTA-AATA
1 TATTAAAATTTATATATAATA
*
17781 TATTAATATTTATATATAATA
1 TATTAAAATTTATATATAATA
*
17802 TATAAAAATT
1 TATTAAAATT
17812 AAAAATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAAAATTTATATATAATA
Found at i:23108 original size:13 final size:13
Alignment explanation
Indices: 23045--23108 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
23035 ATAAATTTTG
* *
23045 AATTTTTATATAT
1 AATTTTAATATAA
*
23058 TATTTTAATATAA
1 AATTTTAATATAA
23071 AATTTTAATAT--
1 AATTTTAATATAA
23082 -A-TTTAA-AT-A
1 AATTTTAATATAA
23091 AATTTTAATATAA
1 AATTTTAATATAA
23104 AATTT
1 AATTT
23109 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 2 0.05
11 5 0.12
12 2 0.05
13 26 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTTAATATAA
Found at i:23251 original size:23 final size:23
Alignment explanation
Indices: 23225--23269 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
23215 TTTAATATCT
23225 AAATTAAATCAAATT-AAATAAAA
1 AAATT-AATCAAATTGAAATAAAA
*
23248 AAATTAATTAAATTGAAATAAA
1 AAATTAATCAAATTGAAATAAA
23270 TATTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATTAATCAAATTGAAATAAAA
Done.