Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167924.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_188, 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: 54654
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:1211 original size:19 final size:19
Alignment explanation
Indices: 1189--1231 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1179 AAAAAAATTA
1189 TATTA-AAATAAAATTTTAT
1 TATTACAAATAAAA-TTTAT
* *
1208 TATTACATATAGAATTTAT
1 TATTACAAATAAAATTTAT
1227 TATTA
1 TATTA
1232 TATATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTACAAATAAAATTTAT
Found at i:2658 original size:2 final size:2
Alignment explanation
Indices: 2643--2682 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2633 ACACACACAC
* *
2643 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2683 GCGAGTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6484 original size:2 final size:2
Alignment explanation
Indices: 6471--6503 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6461 ATATGTGTAT
*
6471 TA TA TA TG 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 TA TA T
6504 TTTTAGGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7536 original size:21 final size:24
Alignment explanation
Indices: 7498--7540 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
7488 TTTATTTTAA
7498 ATTTAATAAAACTAACATATTTGT
1 ATTTAATAAAACTAACATATTTGT
7522 ATTTAA-AAAA-T-ACATATTT
1 ATTTAATAAAACTAACATATTT
7541 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 4 0.21
24 6 0.32
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTTAATAAAACTAACATATTTGT
Found at i:7709 original size:19 final size:19
Alignment explanation
Indices: 7677--7722 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
7667 GAAATACCAT
7677 TGAGTAT-A-GGTACAAGA
1 TGAGTATAATGGTACAAGA
*
7694 TGAGTATAATGGTACAATA
1 TGAGTATAATGGTACAAGA
*
7713 TGAATATAAT
1 TGAGTATAAT
7723 ATAAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 1 0.04
19 17 0.68
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (19 bp):
TGAGTATAATGGTACAAGA
Found at i:11140 original size:17 final size:16
Alignment explanation
Indices: 11095--11139 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
11085 TTTTAAGTTG
*
11095 AAATTATTTTATTAAT
1 AAATTATTTTTTTAAT
*
11111 AAATAATTTTTTTATAT
1 AAATTATTTTTTTA-AT
11128 AAATT-TTTTTTT
1 AAATTATTTTTTT
11140 TGCATCTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATTATTTTTTTAAT
Found at i:12944 original size:20 final size:19
Alignment explanation
Indices: 12891--12936 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
12881 AAGTAAATTT
12891 AAAAAAAATAAAAAAGAAGA
1 AAAAAAAATAAAAAAGAA-A
**
12911 AAAAAACTTAAAAAAGAAA
1 AAAAAAAATAAAAAAGAAA
12930 AAAAAAA
1 AAAAAAA
12937 GATGAAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAAAATAAAAAAGAAA
Found at i:12944 original size:29 final size:29
Alignment explanation
Indices: 12889--12962 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
12879 AAAAGTAAAT
12889 TTAAAAAA-AATAAAAAAGAAGAAAAAAAC
1 TTAAAAAAGAA-AAAAAAGAAGAAAAAAAC
* *
12918 TTAAAAAAGAAAAAAAA-AAGATGAAAAGC
1 TTAAAAAAGAAAAAAAAGAAGA-AAAAAAC
*
12947 ATAAAAATAGAAAAAA
1 TTAAAAA-AGAAAAAA
12963 GTTGAGTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.10
29 25 0.64
30 10 0.26
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.11
Consensus pattern (29 bp):
TTAAAAAAGAAAAAAAAGAAGAAAAAAAC
Found at i:14967 original size:25 final size:25
Alignment explanation
Indices: 14930--14990 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
14920 ATTCATAAAA
**
14930 AAATCATTTTCAACATGTGATTTTG
1 AAATCATTTTCAACATGCAATTTTG
*
14955 AAGTCATTTTCAACATGCAATTTTG
1 AAATCATTTTCAACATGCAATTTTG
*
14980 AAATTATTTTC
1 AAATCATTTTC
14991 TTATGTCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (25 bp):
AAATCATTTTCAACATGCAATTTTG
Found at i:17818 original size:19 final size:19
Alignment explanation
Indices: 17781--17820 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17771 TAGCAAGTTG
* **
17781 TTAAATATGCATATGCAAT
1 TTAAAAATGCATAAACAAT
17800 TTAAAAATGCATAAACAAT
1 TTAAAAATGCATAAACAAT
17819 TT
1 TT
17821 GTAAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (19 bp):
TTAAAAATGCATAAACAAT
Found at i:31086 original size:124 final size:123
Alignment explanation
Indices: 30846--31098 Score: 280
Period size: 124 Copynumber: 2.0 Consensus size: 123
30836 AAAATGAATA
* * * * * * *
30846 GATTATTCAAGATATTTTTGACCAAAAACGCTTTGAATAATCCCCTCATAAACATTGAAGGGGAT
1 GATTATTCAAGATATTTTTGACAAAAAACACCTTGAATAATCACCTCATAAAAATTGAACGAGAT
* *
30911 TATTCAAAGTGTTTTTGACAAAAAAAACTTGAATAACCTCATTCAATTTTTTGTAAGG
66 TATTCAAAGTGTTTTTGACAAAAAAAACTTAAAAAACCTCATTCAATTTTTTGTAAGG
* *
30969 GATTATTCAAGGCAT-TTTTTGACAAAAAATACCTTGAATAATCATCTCATAAAAATTGAACGAG
1 GATTATTCAA-G-ATATTTTTGACAAAAAACACCTTGAATAATCACCTCATAAAAATTGAACGAG
*** *
31033 ATTATTC-AAGATGTTTTTTG-CTAAAAACGCCTTAAAAAA-CTCTATTCAATTTTTTTGTAAAG
64 ATTATTCAAAG-TG-TTTTTGAC-AAAAAAAACTTAAAAAACCTC-ATTCAA-TTTTTTGTAAGG
31095 GATT
1 GATT
31099 CTTTAAAACA
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
123 13 0.12
124 54 0.50
125 26 0.24
126 15 0.14
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (123 bp):
GATTATTCAAGATATTTTTGACAAAAAACACCTTGAATAATCACCTCATAAAAATTGAACGAGAT
TATTCAAAGTGTTTTTGACAAAAAAAACTTAAAAAACCTCATTCAATTTTTTGTAAGG
Found at i:31177 original size:127 final size:125
Alignment explanation
Indices: 30951--31178 Score: 264
Period size: 127 Copynumber: 1.8 Consensus size: 125
30941 GAATAACCTC
* **
30951 ATTCAATTTTTTGTAAGGGATTATTCAAGGCATTTTTTGACAAAAAATACCTTGAATAATCATCT
1 ATTCAATTTTTTGTAAAGGATTATTCAAAACATTTTTTGACAAAAAATACCTTGAATAATCATCT
* * **
31016 CATAAAAATTGAACGAGATTATTCAAGATGTTTTTTGCTAAAAACGCCTTAAAAAACTCT
66 CATAAAAATTAAAAGAGATTATTCAAGACATTTTTTGCTAAAAACGCCTTAAAAAACTCT
* * ** *
31076 ATTCAATTTTTTTGTAAAGGATTCTTTAAAACATTTTTTTGGTAAAAAATTA-TTTGAATAATC-
1 ATTCAA-TTTTTTGTAAAGGATTATTCAAAACA-TTTTTTGACAAAAAA-TACCTTGAATAATCA
* *
31139 TC-CAATAAAAATTTAAAAGGGATTATTCAAGGCATTTTTT
63 TCTC-ATAAAAA-TTAAAAGAGATTATTCAAGACATTTTTT
31179 ATAATTATTC
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
125 7 0.08
126 30 0.36
127 45 0.54
128 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (125 bp):
ATTCAATTTTTTGTAAAGGATTATTCAAAACATTTTTTGACAAAAAATACCTTGAATAATCATCT
CATAAAAATTAAAAGAGATTATTCAAGACATTTTTTGCTAAAAACGCCTTAAAAAACTCT
Found at i:36960 original size:22 final size:23
Alignment explanation
Indices: 36921--36976 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
36911 TAATAATTTT
* *
36921 TTTAACATATTATTAATTT-TCATA
1 TTTAA-ATTTTATCAATTTATCA-A
36945 TTT-AATTTTATCAATTTATCAA
1 TTTAAATTTTATCAATTTATCAA
36967 TTTAAATTTT
1 TTTAAATTTT
36977 TTATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 15 0.54
23 10 0.36
24 3 0.11
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAAATTTTATCAATTTATCAA
Found at i:37380 original size:16 final size:16
Alignment explanation
Indices: 37359--37393 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37349 CATTGATTTT
37359 TTTATTTAAT-TTTAAA
1 TTTATTT-ATGTTTAAA
37375 TTTATTTATGTTTAAA
1 TTTATTTATGTTTAAA
37391 TTT
1 TTT
37394 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTATTTATGTTTAAA
Found at i:38923 original size:103 final size:103
Alignment explanation
Indices: 38741--38951 Score: 332
Period size: 103 Copynumber: 2.0 Consensus size: 103
38731 ATTTTTTTTA
* *
38741 ATGAAATGCTACAAACATCGTGATACATCTTTTTCTCTTTAAAAGAAGTTTGAAAAATATGTTAG
1 ATGAAATGCTACAAACATCGTGATACATCTTTTTCCCTTTAAAAGAAGTTTAAAAAATATGTTAG
*
38806 GGAATTATGTGATGGCAAATTTTTAGTAAGTTTAGAAT
66 GGAATTATGCGATGGCAAATTTTTAGTAAGTTTAGAAT
* * * * *
38844 ATGAAATGCTAGAAACTTCGTGATACCTCTTTTTCCCTTTTAGAGAAGTTTAAAAAATATGTTAG
1 ATGAAATGCTACAAACATCGTGATACATCTTTTTCCCTTTAAAAGAAGTTTAAAAAATATGTTAG
* *
38909 GGGATTATGCGATGGTAAATTTTTAGTAAGTTTAGAAT
66 GGAATTATGCGATGGCAAATTTTTAGTAAGTTTAGAAT
38947 ATGAA
1 ATGAA
38952 CTGTGAATGA
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (103 bp):
ATGAAATGCTACAAACATCGTGATACATCTTTTTCCCTTTAAAAGAAGTTTAAAAAATATGTTAG
GGAATTATGCGATGGCAAATTTTTAGTAAGTTTAGAAT
Found at i:40521 original size:4 final size:4
Alignment explanation
Indices: 40512--40536 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40502 CCTTCATCTG
40512 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
40537 GTAAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:44212 original size:2 final size:2
Alignment explanation
Indices: 44205--44239 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
44195 AAGTGATGAG
*
44205 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44240 GCCAAGGCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:45886 original size:72 final size:72
Alignment explanation
Indices: 45743--45878 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 72
45733 GTGCTTTAGA
* * * *
45743 ACTTGTTTAATTTTTCCTGTTATATATGTGAAAGTAAGATATGATTTGAGTGCAAAGATGGGTGC
1 ACTTATTTAATTTTTCCTGTTATATATGTAAAAATAAGATATGATTTAAGTGCAAAGATGGGTGC
45808 CTGTGTT
66 CTGTGTT
45815 ACTTATTTAATTTTTCCTGTTATATATGTAAAAATAAGATATGATTTAAGTGCAAAGATGGGTG
1 ACTTATTTAATTTTTCCTGTTATATATGTAAAAATAAGATATGATTTAAGTGCAAAGATGGGTG
45879 TTTGTGTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (72 bp):
ACTTATTTAATTTTTCCTGTTATATATGTAAAAATAAGATATGATTTAAGTGCAAAGATGGGTGC
CTGTGTT
Found at i:46531 original size:13 final size:12
Alignment explanation
Indices: 46498--46530 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
46488 AATTATTTTC
46498 ATAATTTTATAT
1 ATAATTTTATAT
46510 ATAAGTTTTATAT
1 ATAA-TTTTATAT
46523 ATAATTTT
1 ATAATTTT
46531 TTTTAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
ATAATTTTATAT
Found at i:50794 original size:19 final size:19
Alignment explanation
Indices: 50724--50795 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
50714 ATTGGTGTTT
50724 AAAAATTATTAAAT--TAAG
1 AAAAATTA-TAAATAATAAG
* * *
50742 AAAAATGTGTAAAAAAAAAG
1 AAAAAT-TATAAATAATAAG
50762 AAAAA--ATGACAATAATAAG
1 AAAAATTAT-A-AATAATAAG
50781 AAAAATTATAAATAA
1 AAAAATTATAAATAA
50796 AAAATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
17 1 0.02
18 11 0.27
19 18 0.44
20 9 0.22
21 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAAATTATAAATAATAAG
Found at i:50836 original size:13 final size:12
Alignment explanation
Indices: 50776--50845 Score: 51
Period size: 13 Copynumber: 6.1 Consensus size: 12
50766 AATGACAATA
* *
50776 ATAAGAAAAATT
1 ATAATAAAAATG
50788 ATAAATAAAAA--
1 AT-AATAAAAATG
50799 AT-ATAAAAAT-
1 ATAATAAAAATG
* *
50809 ATAA-AACAATA
1 ATAATAAAAATG
50820 ATAATAAATAATG
1 ATAATAAA-AATG
50833 ATAATAAAAATG
1 ATAATAAAAATG
50845 A
1 A
50846 AAATCTCTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 7 0.15
10 7 0.15
11 7 0.15
12 9 0.19
13 18 0.38
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (12 bp):
ATAATAAAAATG
Found at i:51099 original size:8 final size:8
Alignment explanation
Indices: 51088--51115 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
51078 AGAAAATAAA
51088 AAAAAATG
1 AAAAAATG
51096 AAAAAATG
1 AAAAAATG
51104 AAAAAATG
1 AAAAAATG
51112 AAAA
1 AAAA
51116 CTTTTGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:51534 original size:19 final size:19
Alignment explanation
Indices: 51509--51551 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
51499 TAAGGCTCTC
*
51509 ATTTTTTTTTC-AAGTAAA
1 ATTTTTTTTTCTAAATAAA
51527 AGTTTTTTTTTCTAAATAAA
1 A-TTTTTTTTTCTAAATAAA
51547 ATTTT
1 ATTTT
51552 ATTGAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTTTTTTCTAAATAAA
Found at i:52046 original size:20 final size:20
Alignment explanation
Indices: 52009--52045 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
51999 TGTTATAAAA
*
52009 AAAACAATAATAATAAAAGG
1 AAAACAATAATAAAAAAAGG
52029 AAAACAA-AATAAAAAAA
1 AAAACAATAATAAAAAAA
52046 AAAAACTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAACAATAATAAAAAAAGG
Found at i:54598 original size:16 final size:16
Alignment explanation
Indices: 54573--54613 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
54563 AAGAACTTTA
* *
54573 TCATTTATTCATTTGT
1 TCATTCATTCATATGT
54589 TCATTCATTCATATGT
1 TCATTCATTCATATGT
54605 TCATTCATT
1 TCATTCATT
54614 TGCATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (16 bp):
TCATTCATTCATATGT
Done.