Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168256.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_487, 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: 25241
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Found at i:203 original size:2 final size:2
Alignment explanation
Indices: 196--224 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
186 TATATGTGAG
196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
225 TATTAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1650 original size:2 final size:2
Alignment explanation
Indices: 1643--1677 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1633 TTAACTTTTC
1643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1678 AACATAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5683 original size:4 final size:4
Alignment explanation
Indices: 5676--5749 Score: 55
Period size: 4 Copynumber: 18.5 Consensus size: 4
5666 ATCCACAAAC
* *
5676 AAAT AAAT AAAAT AACT AAAT AAA- AAA- AAGAT AAAT AAA- AGAAT GAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT
* * *
5724 GAAT GAAT AAAT GAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
5750 GTAGGGTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
3 6 0.10
4 47 0.80
5 6 0.10
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:8907 original size:14 final size:14
Alignment explanation
Indices: 8888--8914 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8878 TCATTTTATG
8888 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
8902 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
8915 TGAGTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:9341 original size:29 final size:30
Alignment explanation
Indices: 9303--9379 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
9293 ATTATTAAAT
* * *
9303 TTTAAGTAAGATTTTATATTTTTA-TTGTA
1 TTTAAATAAGATTTTATATTTTGATTTATA
9332 TTTAAATAAG-TTTTATATTTTGATTTATA
1 TTTAAATAAGATTTTATATTTTGATTTATA
9361 TTTAAATAA-ATTTT-TATTT
1 TTTAAATAAGATTTTATATTT
9380 CATGGAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.40
29 26 0.60
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (30 bp):
TTTAAATAAGATTTTATATTTTGATTTATA
Found at i:9460 original size:23 final size:23
Alignment explanation
Indices: 9429--9482 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
9419 AATTAAAAAT
* * *
9429 TTAAGAATTTATCTGGATATCAA
1 TTAAAAATTTATCTGAATATAAA
* *
9452 TTAAAAA-TTATTTGAATGTAAA
1 TTAAAAATTTATCTGAATATAAA
9474 TTAAAAATT
1 TTAAAAATT
9483 AAAAATTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (23 bp):
TTAAAAATTTATCTGAATATAAA
Found at i:9564 original size:3 final size:3
Alignment explanation
Indices: 9554--9593 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
9544 GGGATTTATT
9554 ATA A-A ATA ATA TATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA ATA
9594 CGGTGGCCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9571 original size:10 final size:10
Alignment explanation
Indices: 9553--9593 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
9543 AGGGATTTAT
*
9553 TATAAAATAA
1 TATATAATAA
9563 TATATAATAA
1 TATATAATAA
9573 TA-ATAATAA
1 TATATAATAA
*
9582 TAAATAATAA
1 TATATAATAA
9592 TA
1 TA
9594 CGGTGGCCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TATATAATAA
Found at i:9579 original size:16 final size:16
Alignment explanation
Indices: 9554--9593 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
9544 GGGATTTATT
9554 ATAA-AATAAT-ATATA
1 ATAATAATAATAATA-A
9569 ATAATAATAATAATAA
1 ATAATAATAATAATAA
9585 ATAATAATA
1 ATAATAATA
9594 CGGTGGCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.17
16 16 0.70
17 3 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATAATAATAATAA
Found at i:21558 original size:20 final size:20
Alignment explanation
Indices: 21533--21572 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21523 AAATACAACA
**
21533 ATTACATGTGTTAAAAAATT
1 ATTACATGTGCAAAAAAATT
21553 ATTACATGTGCAAAAAAATT
1 ATTACATGTGCAAAAAAATT
21573 TACATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (20 bp):
ATTACATGTGCAAAAAAATT
Found at i:21575 original size:18 final size:20
Alignment explanation
Indices: 21533--21577 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21523 AAATACAACA
* *
21533 ATTACATGTGTTAAAAAATT
1 ATTACATGTGTCAAAAAAAT
21553 ATTACATGTG-CAAAAAAAT
1 ATTACATGTGTCAAAAAAAT
21572 -TTACAT
1 ATTACAT
21578 TGATGTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 7 0.30
20 10 0.43
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (20 bp):
ATTACATGTGTCAAAAAAAT
Found at i:21825 original size:17 final size:17
Alignment explanation
Indices: 21785--21826 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
21775 ACATATTTTA
*
21785 AAAAAATTAAAAAATTTG
1 AAAAAA-TAAAAAATTAG
*
21803 ATAAAATAAAAAATTAG
1 AAAAAATAAAAAATTAG
21820 AAAAAAT
1 AAAAAAT
21827 TCTAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAAAATAAAAAATTAG
Found at i:22502 original size:7 final size:7
Alignment explanation
Indices: 22492--22533 Score: 57
Period size: 7 Copynumber: 5.6 Consensus size: 7
22482 TTTGGGAATG
22492 TTTTTAA
1 TTTTTAA
22499 TTTTTATA
1 TTTTTA-A
22507 TTGTTTTAA
1 -T-TTTTAA
22516 TTTTTAA
1 TTTTTAA
22523 TTTTTAA
1 TTTTTAA
22530 TTTT
1 TTTT
22534 CATTATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 23 0.72
8 2 0.06
9 2 0.06
10 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:22542 original size:14 final size:14
Alignment explanation
Indices: 22492--22533 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 14
22482 TTTGGGAATG
22492 TTTTTAATTTTTATA
1 TTTTTAATTTTTA-A
22507 TTGTTTTAATTTTTAA
1 -T-TTTTAATTTTTAA
22523 TTTTTAATTTT
1 TTTTTAATTTT
22534 CATTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.40
15 1 0.04
16 2 0.08
17 12 0.48
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTAATTTTTAA
Found at i:22677 original size:22 final size:21
Alignment explanation
Indices: 22646--22690 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
22636 AATTAGCAAA
*
22646 TTTTTTTAATTCTTTAGTTTT
1 TTTTTTTAATTCTTTAGTCTT
*
22667 TTTTTTATAATTTTTTAGTCTT
1 TTTTTT-TAATTCTTTAGTCTT
22689 TT
1 TT
22691 AGAATTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTTTAATTCTTTAGTCTT
Found at i:22774 original size:19 final size:20
Alignment explanation
Indices: 22746--22793 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
22736 TTTTTAAATT
22746 AGATTGTTTTGAAATTTTT-G
1 AGATT-TTTTGAAATTTTTAG
*
22766 GGATTTTTTGAAATTTTTAG
1 AGATTTTTTGAAATTTTTAG
22786 AGATTTTT
1 AGATTTTT
22794 AAATTTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (20 bp):
AGATTTTTTGAAATTTTTAG
Found at i:22880 original size:22 final size:21
Alignment explanation
Indices: 22838--22899 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
22828 TTGAAAAATT
* * *
22838 TAAAAATTTTTCATATTTTTGG
1 TAAATATTTTTAAGATTTTT-G
22860 TAAATATTTTT-AGATTATTTG
1 TAAATATTTTTAAGATT-TTTG
*
22881 TGAAT-TTTTTAAGATTTTT
1 TAAATATTTTTAAGATTTTT
22900 TTTAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 8 0.23
21 14 0.40
22 13 0.37
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (21 bp):
TAAATATTTTTAAGATTTTTG
Found at i:22891 original size:20 final size:20
Alignment explanation
Indices: 22852--22909 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
22842 AATTTTTCAT
*
22852 ATTTTTGGTAAATATTTTT-AG
1 ATTTTT-GTGAAT-TTTTTAAG
22873 ATTATTTGTGAATTTTTTAAG
1 ATT-TTTGTGAATTTTTTAAG
* *
22894 ATTTTTTTTAATTTTT
1 ATTTTTGTGAATTTTT
22910 CTTCTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.50
21 13 0.41
22 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (20 bp):
ATTTTTGTGAATTTTTTAAG
Found at i:24088 original size:21 final size:19
Alignment explanation
Indices: 24056--24106 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
24046 TCAGTGCTCC
*
24056 AAAAAGAAA-GAGAGAAAAT
1 AAAAA-AAATGAGAGAGAAT
*
24075 AAAAAAATTGAGAGAGAAT
1 AAAAAAAATGAGAGAGAAT
24094 AAAAAAAATGAGA
1 AAAAAAAATGAGA
24107 TGCCAATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAAAAAATGAGAGAGAAT
Done.