Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168247.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_479, 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: 25501
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:546 original size:59 final size:59
Alignment explanation
Indices: 452--814 Score: 403
Period size: 59 Copynumber: 6.1 Consensus size: 59
442 AAATCCTCTT
* * *
452 TTTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCAAAAAATA
1 TTTTTTTGGAAAATTTAATTTTAAGGAAAATTGATACTTTCAACTTTTCCCAAAAAATA
* * *
511 TTTTTTTGGAAACTTTAATTTTGAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAATT
1 TTTTTTTGGAAAATTTAATTTTAAGGAAAATTGATACTTTCAACTTTTCC-C-AAAAAATA
* **
572 TTTTTTTTGAAAATTT-ATTCTTAAGGAAAATTGATACTTTCAACTTTTCCCTTAAAATA
1 TTTTTTTGGAAAATTTAATT-TTAAGGAAAATTGATACTTTCAACTTTTCCCAAAAAATA
* ** * * * *
631 TTTTTTTAGAATTTTTAATTTCAAGGAAAATTGATACTTTCAACCTTTCCTTAGAAAAA-C
1 TTTTTTTGGAAAATTTAATTTTAAGGAAAATTGATACTTTCAACTTTTCC-CA-AAAAATA
* **
691 CTTTTTT-GAAAATTT-ATTCTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATA
1 TTTTTTTGGAAAATTTAATT-TTAAGGAAAATTGATACTTTCAACTTTTCCCAAAAAATA
*** ** *
749 TTTTTTTTGGATTTTTTAATTTCGAGGAAAATTGATACTTTCAAC-TTTCCCCAAAAATA
1 -TTTTTTTGGAAAATTTAATTTTAAGGAAAATTGATACTTTCAACTTTTCCCAAAAAATA
808 TTTTTTT
1 TTTTTTT
815 TGGATTTTAT
Statistics
Matches: 257, Mismatches: 36, Indels: 23
0.81 0.11 0.07
Matches are distributed among these distances:
57 5 0.02
58 11 0.04
59 143 0.56
60 41 0.16
61 57 0.22
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (59 bp):
TTTTTTTGGAAAATTTAATTTTAAGGAAAATTGATACTTTCAACTTTTCCCAAAAAATA
Found at i:583 original size:120 final size:120
Alignment explanation
Indices: 407--815 Score: 545
Period size: 120 Copynumber: 3.4 Consensus size: 120
397 TTTGTACAAG
* *
407 GGAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAAATCCTCTTTTTTTTTTGAAAATTTATTT
1 GGAAAATTGATACTTTCAACTTTTCCTC---AAAAAAA-----TTTTTTTTTTGAAAATTTATTC
* * ** *
472 TTAAGAAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTGGAAACTTTAATTTTGA
58 TTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAATTTTTAATTTCGA
535 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTTTGAAAATTTATTCTTAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTTTGAAAATTTATTCTTAAGGAA
* * *
600 AATTGATACTTTCAACTTTTCCCTTAAAATATTTTTTTAGAATTTTTAATTTCAA
66 AATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAATTTTTAATTTCGA
* * * **
655 GGAAAATTGATACTTTCAACCTTTCCTTAGAAAAA--CCTTTTTTGAAAATTTATTCTTAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTTTGAAAATTTATTCTTAAGGAA
* *
718 AATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGGATTTTTTAATTTCGA
66 AATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAATTTTTAATTTCGA
* *
774 GGAAAATTGATACTTTCAAC-TTTCCCCAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTT
816 GGATTTTATT
Statistics
Matches: 252, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
118 65 0.26
119 41 0.16
120 112 0.44
125 7 0.03
128 27 0.11
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (120 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTTTGAAAATTTATTCTTAAGGAA
AATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAATTTTTAATTTCGA
Found at i:664 original size:179 final size:177
Alignment explanation
Indices: 478--814 Score: 448
Period size: 179 Copynumber: 1.9 Consensus size: 177
468 ATTTTTAAGA
* * * *
478 AAAATTGATACTTTCAACTTTTCC-CA-AAAAATATTTTTTTGGAAACTTTAATT-TTGAGGAAA
1 AAAATTGATACTTTCAACCTTTCCTCAGAAAAA-ACTTTTTT-GAAAATTT-ATTCTTAAGGAAA
* *
540 ATTGATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTTTGAAAATTT-ATTCTTAAGGAAAATT
63 ATTGATACTTTCAACTTTTCCTCAAAAAAA-TTTTTTTTGGAAAATTTAATT-TCAAGGAAAATT
**
604 GATACTTTCAACTTTTCCCTTAAAATATTTTTTTAGAATTTTTAATTTCAAGG
126 GATACTTTCAAC-TTTCCCCAAAAATATTTTTTTAGAATTTTTAATTTCAAGG
* *
657 AAAATTGATACTTTCAACCTTTCCTTAGAAAAACCTTTTTTGAAAATTTATTCTTAAGGAAAATT
1 AAAATTGATACTTTCAACCTTTCCTCAGAAAAAACTTTTTTGAAAATTTATTCTTAAGGAAAATT
* * *** *
722 GATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGGATTTTTTAATTTCGAGGAAAATTGATAC
66 GATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGGAAAATTTAATTTCAAGGAAAATTGATAC
787 TTTCAACTTTCCCCAAAAATATTTTTTT
131 TTTCAACTTTCCCCAAAAATATTTTTTT
815 TGGATTTTAT
Statistics
Matches: 138, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
177 19 0.14
178 38 0.28
179 69 0.50
180 7 0.05
181 5 0.04
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (177 bp):
AAAATTGATACTTTCAACCTTTCCTCAGAAAAAACTTTTTTGAAAATTTATTCTTAAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAAAATTTTTTTTGGAAAATTTAATTTCAAGGAAAATTGATAC
TTTCAACTTTCCCCAAAAATATTTTTTTAGAATTTTTAATTTCAAGG
Found at i:854 original size:18 final size:19
Alignment explanation
Indices: 831--900 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 19
821 TTATTTAAAG
831 AAAATAAA-ATAATAAAAC
1 AAAATAAAGATAATAAAAC
849 AAAATAAAG-TGAA-AATAA-
1 AAAATAAAGAT-AATAA-AAC
*
867 AAAATAAAGAAAAGTAAAAC
1 AAAATAAAGATAA-TAAAAC
*
887 AAAAATAAATATAA
1 -AAAATAAAGATAA
901 AAATAAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
18 22 0.54
19 6 0.15
20 2 0.05
21 11 0.27
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.16
Consensus pattern (19 bp):
AAAATAAAGATAATAAAAC
Found at i:1881 original size:22 final size:22
Alignment explanation
Indices: 1826--1903 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
1816 ATATTAATGA
*
1826 AAATAAATCAGATAAA-CAAAA-
1 AAAT-AATCAGATAAATTAAAAT
1847 AAATTAA-CAGATAAATTAAAATT
1 AAA-TAATCAGATAAATTAAAA-T
*
1870 AAATAAT-AGATAAATTATAAT
1 AAATAATCAGATAAATTAAAAT
*
1891 ATATAATCAGATA
1 AAATAATCAGATA
1904 CATATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 8 0.17
21 16 0.33
22 21 0.44
23 3 0.06
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (22 bp):
AAATAATCAGATAAATTAAAAT
Found at i:1964 original size:31 final size:28
Alignment explanation
Indices: 1929--1997 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 28
1919 TAACAGAAAA
*
1929 AAATAATAATAATAAGGATATATATAATAAT
1 AAATAATAATAATAA--ATAAATA-AATAAT
* *
1960 AAATAGTAGTAATAAATAAATAAATAAT
1 AAATAATAATAATAAATAAATAAATAAT
1988 AAATACATAA
1 AAATA-ATAA
1998 GATAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 11 0.34
29 8 0.25
31 13 0.41
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAATAAATAAATAAT
Found at i:1989 original size:15 final size:16
Alignment explanation
Indices: 1952--2009 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 16
1942 AAGGATATAT
1952 ATAAT-AATAAAT-AG
1 ATAATAAATAAATAAG
1966 TAGTAATAAATAAATAA-
1 -A-TAATAAATAAATAAG
*
1983 ATAATAAATACATAAG
1 ATAATAAATAAATAAG
1999 ATAA-AAATAAA
1 ATAATAAATAAA
2010 AGAAATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 20 0.54
16 9 0.24
17 7 0.19
18 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (16 bp):
ATAATAAATAAATAAG
Found at i:2707 original size:21 final size:23
Alignment explanation
Indices: 2660--2707 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2650 ATATTATTGT
*
2660 TATACTTAATATGAATGTACTATG
1 TATACTTAATA-GAATGTACTAAG
2684 TATACTTAATA-AAT-TACTAAG
1 TATACTTAATAGAATGTACTAAG
2705 TAT
1 TAT
2708 GATTATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
24 11 0.48
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (23 bp):
TATACTTAATAGAATGTACTAAG
Found at i:13382 original size:105 final size:105
Alignment explanation
Indices: 13268--13460 Score: 262
Period size: 105 Copynumber: 1.8 Consensus size: 105
13258 AATCCACTTT
* * *
13268 AAAGGTTAGGCAGACTTATTCTTGAATGCTTTAAGGGTT-GTCGAAACTTGTTTTTGAATGCTTC
1 AAAGGTTAGGCAAACTTATTCTTGAATGCTTCAAGGGTTAG-CGAAACTTGTTCTTGAATGCTTC
* *
13332 AAGACTCTTGTTGACTTGATCTTGGATGTAAAATCTGCTTC
65 AAGACTCTTATTAACTTGATCTTGGATGTAAAATCTGCTTC
* * * * *
13373 AAAGGTTAGGCAAACTTGTTCTTGAATTCTTCAAGGGTTAGCTAAATTTGTTCTTGAATGCTTTA
1 AAAGGTTAGGCAAACTTATTCTTGAATGCTTCAAGGGTTAGCGAAACTTGTTCTTGAATGCTTCA
**
13438 AGGGTCTTATTAACTTGATCTTG
66 AGACTCTTATTAACTTGATCTTG
13461 AACAAACGAA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
105 74 0.99
106 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (105 bp):
AAAGGTTAGGCAAACTTATTCTTGAATGCTTCAAGGGTTAGCGAAACTTGTTCTTGAATGCTTCA
AGACTCTTATTAACTTGATCTTGGATGTAAAATCTGCTTC
Found at i:13412 original size:32 final size:32
Alignment explanation
Indices: 13367--13442 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
13357 ATGTAAAATC
*
13367 TGCTTCAAAGGTTAGGC-AAACTTGTTCTTGAA
1 TGCTTCAAGGGTTA-GCTAAACTTGTTCTTGAA
* *
13399 TTCTTCAAGGGTTAGCTAAATTTGTTCTTGAA
1 TGCTTCAAGGGTTAGCTAAACTTGTTCTTGAA
*
13431 TGCTTTAAGGGT
1 TGCTTCAAGGGT
13443 CTTATTAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 2 0.05
32 36 0.95
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (32 bp):
TGCTTCAAGGGTTAGCTAAACTTGTTCTTGAA
Found at i:15694 original size:49 final size:48
Alignment explanation
Indices: 15631--15766 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 48
15621 TAAAATCTAA
* *
15631 AAAAAGCTCCTCTCAGCAGAGGCTTAACAATTTTTAAAATCTTATCTTG
1 AAAAAGCTCATCTCAGCAGAGGCTTAACAATTTTTAAAATC-CATCTTG
* * *
15680 AAAAAGCTCATCTCAGTAGAGGCCTAACAA-CTTTAAAATCCATCTTG
1 AAAAAGCTCATCTCAGCAGAGGCTTAACAATTTTTAAAATCCATCTTG
* * * *
15727 AAAAAGCTCTTTTCAGCAGAGGCTCAACAATTTTAAAAAT
1 AAAAAGCTCATCTCAGCAGAGGCTTAACAATTTTTAAAAT
15767 TTCATATGTT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
47 31 0.42
48 16 0.22
49 27 0.36
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (48 bp):
AAAAAGCTCATCTCAGCAGAGGCTTAACAATTTTTAAAATCCATCTTG
Done.