Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167873.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_141, 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: 67063
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:3797 original size:30 final size:30
Alignment explanation
Indices: 3761--3819 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
3751 GAGGATAGGA
3761 TAATAATCATTTTATATCATATTTGGTTTG
1 TAATAATCATTTTATATCATATTTGGTTTG
3791 TAATAATCATTTTATATCATATTTGGTTT
1 TAATAATCATTTTATATCATATTTGGTTT
3820 ATATCTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (30 bp):
TAATAATCATTTTATATCATATTTGGTTTG
Found at i:4813 original size:20 final size:19
Alignment explanation
Indices: 4784--4823 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4774 GGTGAAAAGG
*
4784 AGAGAGAAAAGAGACTAAAA
1 AGAGAGAAAAAAGA-TAAAA
*
4804 AGAGATAAAAAAGATAAAA
1 AGAGAGAAAAAAGATAAAA
4823 A
1 A
4824 TAAATAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (19 bp):
AGAGAGAAAAAAGATAAAA
Found at i:4823 original size:9 final size:10
Alignment explanation
Indices: 4790--4823 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
4780 AAGGAGAGAG
4790 AAAAGAGACTA
1 AAAAGAGA-TA
4801 AAAAGAGATA
1 AAAAGAGATA
4811 AAAA-AGATA
1 AAAAGAGATA
4820 AAAA
1 AAAA
4824 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 6 0.26
11 8 0.35
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (10 bp):
AAAAGAGATA
Found at i:7381 original size:42 final size:42
Alignment explanation
Indices: 7295--7378 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
7285 TTGCTTCTTT
* * *
7295 ATATAAACACTATTATATGAGAAAGAAACGGTTCCGATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
7337 ATATAAACACTATTATACGAGAAAG-AACAGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
7378 A
1 A
7379 ATACTGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.38
42 24 0.62
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (42 bp):
ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
Found at i:13846 original size:23 final size:24
Alignment explanation
Indices: 13784--13849 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 24
13774 TTTTTCAATT
* *
13784 TAAAATAGAGAATAATAAGAGTAAA
1 TAAAATA-AGAAAAATAACAGTAAA
13809 TAAAAATAA-ACAAAATAACA-TAAA
1 T-AAAATAAGA-AAAATAACAGTAAA
13833 TAAAATAAGAAAAATAA
1 TAAAATAAGAAAAATAA
13850 AGTCAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 14 0.39
24 7 0.19
25 9 0.25
26 6 0.17
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (24 bp):
TAAAATAAGAAAAATAACAGTAAA
Found at i:14486 original size:52 final size:50
Alignment explanation
Indices: 14344--14486 Score: 126
Period size: 52 Copynumber: 2.8 Consensus size: 50
14334 TTTATTTTCG
* * *
14344 TTTTAATGAAAATTGATTCTGAAATCAAATTCCAAAATCTCTCCCTATCA
1 TTTTAATGAAAATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCA
* ** * * * *
14394 ATTTAATGTGAATTGATTATAGAATTAAATTTCGACAATCTCTCCAC-ATCA
1 TTTTAATGAAAATTGATTCTGGAATTAAA-TTCAAAAATCTCTCC-CTATCA
** *
14445 TTTTTAATGCCAATTGATTCTGGAATTAAATCTAAAAAATCT
1 -TTTTAATGAAAATTGATTCTGGAATTAAAT-TCAAAAATCT
14487 TTCAATTACG
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
50 22 0.31
51 18 0.25
52 32 0.44
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (50 bp):
TTTTAATGAAAATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCA
Found at i:18979 original size:27 final size:27
Alignment explanation
Indices: 18941--18997 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
18931 GGATCAAGGT
18941 ATTTAGTATTAAATGATGTTAGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
*
18968 ATTTAGTATTAAATGATGTTTGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
18995 ATT
1 ATT
18998 CAATTAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (27 bp):
ATTTAGTATTAAATGATGTTAGCCCAC
Found at i:21842 original size:15 final size:17
Alignment explanation
Indices: 21817--21849 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21807 TTAAATTAAC
21817 AAAAAATATT-AATATG
1 AAAAAATATTAAATATG
21833 AAAAAA-ATTAAATATG
1 AAAAAATATTAAATATG
21849 A
1 A
21850 TATTAGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAAAATATTAAATATG
Found at i:22521 original size:30 final size:30
Alignment explanation
Indices: 22485--22543 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
22475 CGGGATAGGA
22485 TAATAATCATTTTATATCATATTTGGTTTG
1 TAATAATCATTTTATATCATATTTGGTTTG
22515 TAATAATCATTTTATATCATATTTGGTTT
1 TAATAATCATTTTATATCATATTTGGTTT
22544 ATATCTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (30 bp):
TAATAATCATTTTATATCATATTTGGTTTG
Found at i:23513 original size:9 final size:9
Alignment explanation
Indices: 23501--23539 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
23491 GGGTGAAAAG
23501 AGAGATAAA
1 AGAGATAAA
23510 AGAGAATTAAA
1 AGAG-A-TAAA
23521 AGAGATAAA
1 AGAGATAAA
*
23530 AAAGATAAA
1 AGAGATAAA
23539 A
1 A
23540 ATAAATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 17 0.63
10 2 0.07
11 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (9 bp):
AGAGATAAA
Found at i:29540 original size:14 final size:14
Alignment explanation
Indices: 29489--29533 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
29479 ATATAAGAGT
*
29489 AAATAAAAATAAACA
1 AAATAAAAA-AAATA
* *
29504 AAATAACATAAATA
1 AAATAAAAAAAATA
29518 AAATAAAAAAAATA
1 AAATAAAAAAAATA
29532 AA
1 AA
29534 GTCAAAACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAAAAAAAATA
Found at i:30166 original size:52 final size:50
Alignment explanation
Indices: 30034--30166 Score: 124
Period size: 52 Copynumber: 2.6 Consensus size: 50
30024 TTTTAATAAA
* * * **
30034 AATTGATTCTGAAATCAAATTCCAAAATCTCTCCCTATCAATTTAATGTG
1 AATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCAATTTAATGCC
* * * * *
30084 AATTGATTATAGAATTAAATTTCGACAATCTCTCCAC-ATCATTTTTAATGCC
1 AATTGATTCTGGAATTAAA-TTCAAAAATCTCTCC-CTATCA-ATTTAATGCC
*
30136 AATTGATTCTGGAATTAAATCTAAAAAATCT
1 AATTGATTCTGGAATTAAAT-TCAAAAATCT
30167 TTCAATTACG
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
50 15 0.23
51 18 0.28
52 32 0.49
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (50 bp):
AATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCAATTTAATGCC
Found at i:36641 original size:9 final size:9
Alignment explanation
Indices: 36607--36646 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
36597 GGGTGAAAAG
36607 AAAGATAAA
1 AAAGATAAA
*
36616 AGAGAATAAA
1 AAAG-ATAAA
36626 AAGAGATAAA
1 AA-AGATAAA
36636 AAAGATAAA
1 AAAGATAAA
36645 AA
1 AA
36647 TAAATAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.44
10 13 0.48
11 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (9 bp):
AAAGATAAA
Found at i:38198 original size:43 final size:44
Alignment explanation
Indices: 38110--38195 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
38100 ATTGCTTCTT
* * * *
38110 TATATAAACAGTATTATATGAGAAAGAAACAGTTTCGATTGAAA
1 TATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAAA
38154 TATA-AAACACTATTATACGAGAAAG-AACAGTTCCAATTGAAA
1 TATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAAA
38196 ATACTGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 15 0.39
43 19 0.50
44 4 0.11
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (44 bp):
TATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAAA
Found at i:44677 original size:23 final size:23
Alignment explanation
Indices: 44629--44691 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
44619 TTTCAATTTA
* *
44629 AAATAAGAAATAATAAGAGTAAAT
1 AAATAAGAAAAAATAACA-TAAAT
*
44653 AAA-AATAAACAAATAACATAAAT
1 AAATAAGAAA-AAATAACATAAAT
44676 AAATAAGAAAAAATAA
1 AAATAAGAAAAAATAA
44692 AGTCAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.17
Consensus pattern (23 bp):
AAATAAGAAAAAATAACATAAAT
Found at i:45329 original size:52 final size:50
Alignment explanation
Indices: 45187--45329 Score: 126
Period size: 52 Copynumber: 2.8 Consensus size: 50
45177 TTTATTTTCG
* * *
45187 TTTTAATGAAAATTGATTCTGAAATCAAATTCCAAAATCTCTCCCTATCA
1 TTTTAATGAAAATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCA
* ** * * * *
45237 ATTTAATGTGAATTGATTATAGAATTAAATTTCGACAATCTCTCCAC-ATCA
1 TTTTAATGAAAATTGATTCTGGAATTAAA-TTCAAAAATCTCTCC-CTATCA
** *
45288 TTTTTAATGCCAATTGATTCTGGAATTAAATCTAAAAAATCT
1 -TTTTAATGAAAATTGATTCTGGAATTAAAT-TCAAAAATCT
45330 TTCAATTACG
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
50 22 0.31
51 18 0.25
52 32 0.44
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (50 bp):
TTTTAATGAAAATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCA
Found at i:49796 original size:26 final size:27
Alignment explanation
Indices: 49760--49815 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
49750 TGGATCAGGT
49760 ATTTAGTATTAAATGATG-TAGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
*
49786 ATTTAGTATTAAATGATGTTTGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
49813 ATT
1 ATT
49816 CAATTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (27 bp):
ATTTAGTATTAAATGATGTTAGCCCAC
Found at i:52732 original size:42 final size:41
Alignment explanation
Indices: 52646--52729 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
52636 TTGCTTCTTT
* * *
52646 ATATAAACACTATTATATGAGAAAGAAACGGTTTCGATTGAA
1 ATATAAACACTATTATACGAGAAAGAAAC-GTTCCAATTGAA
52688 ATATAAACACTATTATACGAGAAAGAATA-GTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAA-ACGTTCCAATTGAA
52729 A
1 A
52730 ATACTGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 26 0.68
43 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (41 bp):
ATATAAACACTATTATACGAGAAAGAAACGTTCCAATTGAA
Found at i:59197 original size:23 final size:24
Alignment explanation
Indices: 59135--59200 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 24
59125 TTTTTCAATT
*
59135 TAAAATAAGAAATAATAAGAGTAAA
1 TAAAATAAGAAA-AATAACAGTAAA
59160 TAAAAATAA-ACAAAATAACA-TAAA
1 T-AAAATAAGA-AAAATAACAGTAAA
59184 TAAAATAAGAAAAATAA
1 TAAAATAAGAAAAATAA
59201 AGTCAAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 14 0.38
24 6 0.16
25 8 0.22
26 9 0.24
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (24 bp):
TAAAATAAGAAAAATAACAGTAAA
Found at i:59838 original size:52 final size:50
Alignment explanation
Indices: 59696--59838 Score: 126
Period size: 52 Copynumber: 2.8 Consensus size: 50
59686 TTTATTTTCG
* * *
59696 TTTTAATGAAAATTGATTCTGAAATCAAATTCCAAAATCTCTCCCTATCA
1 TTTTAATGAAAATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCA
* ** * * * *
59746 ATTTAATGTGAATTGATTATAGAATTAAATTTCGACAATCTCTCCAC-ATCA
1 TTTTAATGAAAATTGATTCTGGAATTAAA-TTCAAAAATCTCTCC-CTATCA
** *
59797 TTTTTAATGCCAATTGATTCTGGAATTAAATCTAAAAAATCT
1 -TTTTAATGAAAATTGATTCTGGAATTAAAT-TCAAAAATCT
59839 TTCAATTACG
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
50 22 0.31
51 18 0.25
52 32 0.44
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (50 bp):
TTTTAATGAAAATTGATTCTGGAATTAAATTCAAAAATCTCTCCCTATCA
Found at i:64327 original size:27 final size:27
Alignment explanation
Indices: 64289--64345 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
64279 GGATCAAGGT
64289 ATTTAGTATTAAATGATGTTAGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
*
64316 ATTTAGTATTAAATGATGTTTGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
64343 ATT
1 ATT
64346 CAATTAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (27 bp):
ATTTAGTATTAAATGATGTTAGCCCAC
Done.