Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168330.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_553, 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: 23131
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:1455 original size:114 final size:114
Alignment explanation
Indices: 1255--1640 Score: 663
Period size: 114 Copynumber: 3.4 Consensus size: 114
1245 TTTTTTGTAG
*
1255 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTT-TCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTT--ATTTCT-AAGGAA
1318 AATTGATACTTTCAACTTTTCCCAAAAAT-TTTTTTTGAAATTTA-TTCTTAA
63 AATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTC-TAA
1369 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTATTTCTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTTGAAATTTATTTCTAAGGAAAA
1434 TTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
65 TTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
*
1484 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATTTCTAAGGAAAAT
*
1549 TGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCTAA
66 TGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
*
1598 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTT
1641 TGGAATTTTT
Statistics
Matches: 264, Mismatches: 3, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
114 195 0.74
115 53 0.20
116 16 0.06
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (114 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATTTCTAAGGAAAAT
TGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
Found at i:1492 original size:56 final size:56
Alignment explanation
Indices: 1255--1639 Score: 632
Period size: 56 Copynumber: 6.7 Consensus size: 56
1245 TTTTTTGTAG
*
1255 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGAAATTT--ATTTCT-AA
1314 GGAAAATTGATACTTTCAACTTTTCCCAAAAAT-TTTTTTTGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTC-TAA
1369 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATA--TTTTTTTGAAATTTATTTCTAA
1428 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
1484 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTTGAAATTTATTTCTAA
*
1542 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
1598 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTT
1640 TTGGAATTTT
Statistics
Matches: 313, Mismatches: 3, Indels: 22
0.93 0.01 0.07
Matches are distributed among these distances:
54 2 0.01
55 27 0.09
56 107 0.34
57 40 0.13
58 68 0.22
59 66 0.21
60 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAATTTATTTCTAA
Found at i:1728 original size:1 final size:1
Alignment explanation
Indices: 1722--1786 Score: 103
Period size: 1 Copynumber: 65.0 Consensus size: 1
1712 TCTAATAAAT
* * *
1722 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAATAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1787 CCTGGAGCGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:1760 original size:31 final size:31
Alignment explanation
Indices: 1722--1786 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1712 TCTAATAAAT
1722 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAA
*
1753 AAAAAAATAAATAAAAAAAAAAAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAA
1784 AAA
1 AAA
1787 CCTGGAGCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (31 bp):
AAAAAAATAAAAAAAAAAAAAAAAAAAAAAA
Found at i:2657 original size:17 final size:17
Alignment explanation
Indices: 2637--2711 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
2627 ATAATATAAT
*
2637 TAAAAATAATTTAAAAA
1 TAAAAATAATATAAAAA
* **
2654 TAAAAATAAGATAAACC
1 TAAAAATAATATAAAAA
2671 TAAAAAATAATATAAAAAA
1 T-AAAAATAATAT-AAAAA
*
2690 TAAAATAATAATATAATAA
1 T-AAA-AATAATATAAAAA
2709 TAA
1 TAA
2712 TACTATATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
17 14 0.30
18 12 0.26
19 13 0.28
20 8 0.17
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (17 bp):
TAAAAATAATATAAAAA
Found at i:2767 original size:8 final size:8
Alignment explanation
Indices: 2657--2786 Score: 54
Period size: 8 Copynumber: 15.1 Consensus size: 8
2647 TTAAAAATAA
2657 AAATAAGAT
1 AAATAA-AT
2666 AAACCTAAA-
1 AAA--TAAAT
2675 AAATAATAT
1 AAATAA-AT
2684 AAA-AAAT
1 AAATAAAT
2691 AAA-ATAAT
1 AAATA-AAT
2699 -AATATAAT
1 AAATA-AAT
2707 -AATAATACT
1 AAATAA-A-T
*
2716 ATATAATAT
1 AAATAA-AT
2725 AAATAAATT
1 AAATAAA-T
2734 ACATATAAAT
1 A-A-ATAAAT
* *
2744 ATTAACAAAA
1 A--AATAAAT
2754 AAATAAAT
1 AAATAAAT
2762 AAATAAAT
1 AAATAAAT
*
2770 AACTAAAT
1 AAATAAAT
*
2778 AAATCAAT
1 AAATAAAT
2786 A
1 A
2787 TATACATATG
Statistics
Matches: 98, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
7 12 0.12
8 44 0.45
9 18 0.18
10 15 0.15
11 9 0.09
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (8 bp):
AAATAAAT
Found at i:2776 original size:12 final size:12
Alignment explanation
Indices: 2657--2786 Score: 54
Period size: 12 Copynumber: 10.1 Consensus size: 12
2647 TTAAAAATAA
2657 AAATAAGATAAACCT
1 AAATAA-ATAAA--T
2672 AAA-AAATAATAT
1 AAATAAATAA-AT
2684 AAA-AAATAAA-
1 AAATAAATAAAT
2694 ATAAT-AATATAAT
1 A-AATAAATA-AAT
*
2707 -AATAATACTATAT
1 AAATAA-A-TAAAT
2720 AATATAAATAAATT
1 AA-ATAAATAAA-T
*
2734 ACATATAAATATTAAC
1 A-A-ATAAATA--AAT
*
2750 AAAAAAATAAAT
1 AAATAAATAAAT
*
2762 AAATAAATAACT
1 AAATAAATAAAT
*
2774 AAATAAATCAAT
1 AAATAAATAAAT
2786 A
1 A
2787 TATACATATG
Statistics
Matches: 92, Mismatches: 9, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
10 1 0.01
11 10 0.11
12 36 0.39
13 10 0.11
14 15 0.16
15 17 0.18
16 1 0.01
17 2 0.02
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:3007 original size:20 final size:20
Alignment explanation
Indices: 2984--3048 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
2974 TCTTTGAATC
2984 TTAATGTAAATCTCTAAATT
1 TTAATGTAAATCTCTAAATT
** *
3004 TTAAAATAAGAATCTTTGAAATT
1 TTAATGT-A-AATCTCT-AAATT
* *
3027 TTGATGTGAATCTCTAAATT
1 TTAATGTAAATCTCTAAATT
3047 TT
1 TT
3049 TTGAATGAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 12 0.35
21 7 0.21
22 6 0.18
23 9 0.26
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (20 bp):
TTAATGTAAATCTCTAAATT
Found at i:3062 original size:43 final size:43
Alignment explanation
Indices: 2947--3072 Score: 123
Period size: 43 Copynumber: 2.9 Consensus size: 43
2937 GTGTCTACAG
* *
2947 AAATCTTTAAAATTTTTTGACTATGA-ATCTTTG-AATCTTAATGT
1 AAATCTCT-AAATTTTTTGA--ATGAGATCTTTGAAATTTTAATGT
** * *
2991 AAATCTCTAAA-TTTTAAAATAAGAATCTTTGAAATTTTGATGT
1 AAATCTCTAAATTTTTTGAATGAG-ATCTTTGAAATTTTAATGT
*
3034 GAATCTCTAAATTTTTTGAATGAGATCTTTGAAAATTTT
1 AAATCTCTAAATTTTTTGAATGAGATCTTTG-AAATTTT
3073 TCAAATGCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
40 3 0.04
42 12 0.18
43 29 0.43
44 23 0.34
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (43 bp):
AAATCTCTAAATTTTTTGAATGAGATCTTTGAAATTTTAATGT
Found at i:3234 original size:18 final size:20
Alignment explanation
Indices: 3194--3231 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3184 TTTTGAAAAC
*
3194 TTTGAAATTTTATTGTGAAA
1 TTTGAAATTATATTGTGAAA
3214 TTTGAAATTAT-TTGTGAA
1 TTTGAAATTATATTGTGAA
3232 TTTTTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTGAAATTATATTGTGAAA
Found at i:3444 original size:40 final size:38
Alignment explanation
Indices: 3393--3486 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 38
3383 CTATAAATTT
* *
3393 TTTTAA-AATCTTTGTA-TTGTTTGTGAATCTTTTGAACTC
1 TTTTAAGAATCTTTG-AGTTGTTTGTG-AGCTTTTGAA-TA
*
3432 TTTTAAGAATCTTTGAGTTTTTTGTGAGCTTTTGAATA
1 TTTTAAGAATCTTTGAGTTGTTTGTGAGCTTTTGAATA
3470 TTTTAAAGAATCTTTGA
1 TTTT-AAGAATCTTTGA
3487 AAGTTTTTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
38 5 0.10
39 28 0.57
40 16 0.33
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (38 bp):
TTTTAAGAATCTTTGAGTTGTTTGTGAGCTTTTGAATA
Found at i:11616 original size:17 final size:19
Alignment explanation
Indices: 11585--11620 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
11575 TTGCCATTAC
11585 ATTTTTTAAATTTTCATTG
1 ATTTTTTAAATTTTCATTG
11604 ATTTTTT-AA-TTTCATTG
1 ATTTTTTAAATTTTCATTG
11621 TTCTAATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (19 bp):
ATTTTTTAAATTTTCATTG
Found at i:14784 original size:20 final size:21
Alignment explanation
Indices: 14759--14799 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
14749 CATACTATCG
*
14759 ATTTTTTATA-TTTTAAATTT
1 ATTTTTCATATTTTTAAATTT
14779 ATTTTTCATATTTTTAAATTT
1 ATTTTTCATATTTTTAAATTT
14800 TTCACGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTTCATATTTTTAAATTT
Found at i:14950 original size:21 final size:20
Alignment explanation
Indices: 14911--14958 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
14901 TAAGTGGAGG
14911 GAAAAATAATGTTTTAAAAA
1 GAAAAATAATGTTTTAAAAA
** *
14931 GAAAAATTGTGTTTTGAAAA
1 GAAAAATAATGTTTTAAAAA
*
14951 GATAAATA
1 GAAAAATA
14959 TCTATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (20 bp):
GAAAAATAATGTTTTAAAAA
Found at i:15024 original size:14 final size:14
Alignment explanation
Indices: 15005--15041 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14995 TAGACATATG
*
15005 TATTTTTAATATTA
1 TATTTTTAATAATA
*
15019 TATTTTTTATAATA
1 TATTTTTAATAATA
15033 TATTTTTAA
1 TATTTTTAA
15042 ATTTTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTTAATAATA
Found at i:22413 original size:119 final size:119
Alignment explanation
Indices: 22199--22437 Score: 383
Period size: 119 Copynumber: 2.0 Consensus size: 119
22189 TTCTTGTATC
* * *
22199 ACCCTAGATCACTGTGGAAAGATAGTAATTACTTGTCCCTACCTCAAAACTTGCCAATATAATTG
1 ACCCTAGATCACTATGGAAAGATAGTAATTACCTGTCCCTACCTCAAAACTTACCAATATAATTG
* *
22264 CTTCAGTGATGATAATGTAAGGTACTTTTTTGTTTCTTTTGTCTTTTCAAACTA
66 CTTCAGTGATGATAACGTAAAGTACTTTTTTGTTTCTTTTGTCTTTTCAAACTA
*
22318 ACCCTTGATCACTATGGAAAGATAGTAATTACCTGTCCCCT-CCTCAAAACTTACCAATATAATT
1 ACCCTAGATCACTATGGAAAGATAGTAATTACCTGT-CCCTACCTCAAAACTTACCAATATAATT
*
22382 GCTTCAGTGATGATCACGTAAAGTA-TCTTTTTGTTTCTTTTGTCTTTTCAAACTA
65 GCTTCAGTGATGATAACGTAAAGTACT-TTTTTGTTTCTTTTGTCTTTTCAAACTA
22437 A
1 A
22438 GTACCTACTA
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
118 1 0.01
119 106 0.95
120 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (119 bp):
ACCCTAGATCACTATGGAAAGATAGTAATTACCTGTCCCTACCTCAAAACTTACCAATATAATTG
CTTCAGTGATGATAACGTAAAGTACTTTTTTGTTTCTTTTGTCTTTTCAAACTA
Done.