Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167927.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_190, 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: 54398
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:384 original size:24 final size:24
Alignment explanation
Indices: 352--399 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
342 AACCGTGAGC
352 AAACTTTTGAAACTTGGGCATTGT
1 AAACTTTTGAAACTTGGGCATTGT
376 AAACTTTTGAAACTTGGGCATTGT
1 AAACTTTTGAAACTTGGGCATTGT
400 GGGATAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (24 bp):
AAACTTTTGAAACTTGGGCATTGT
Found at i:2448 original size:22 final size:22
Alignment explanation
Indices: 2420--2463 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2410 CTAAATCTTC
*
2420 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
2442 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
2464 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5905 original size:18 final size:18
Alignment explanation
Indices: 5879--5913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5869 TAATCCATGA
*
5879 GAACCAGAAGCTTTACCT
1 GAACCAGAAACTTTACCT
*
5897 GAACTAGAAACTTTACC
1 GAACCAGAAACTTTACC
5914 CAAAGAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (18 bp):
GAACCAGAAACTTTACCT
Found at i:6175 original size:23 final size:23
Alignment explanation
Indices: 6085--6169 Score: 134
Period size: 23 Copynumber: 3.6 Consensus size: 23
6075 TTGAAAGGGT
* *
6085 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAA-A-AAG
6110 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
6133 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
6156 TCGGCAATGAAGGC
1 TCGGCAATGAAGGC
6170 TGAAAATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
23 38 0.66
24 1 0.02
25 19 0.33
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (23 bp):
TCGGCAATGAAGGCCTAAAAAAG
Found at i:6345 original size:22 final size:22
Alignment explanation
Indices: 6317--6360 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6307 CTAAATCTTC
*
6317 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
6339 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
6361 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:8415 original size:25 final size:26
Alignment explanation
Indices: 8376--8424 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
8366 TTGGAATTTC
8376 TGTGGAAAAACTAAGA-AATAAAACAG
1 TGTGGAAAAACTAAGAGAA-AAAACAG
8402 TGTGG-AAAACTAAGAGAAAAAAC
1 TGTGGAAAAACTAAGAGAAAAAAC
8425 TGAATGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.14
Consensus pattern (26 bp):
TGTGGAAAAACTAAGAGAAAAAACAG
Found at i:8597 original size:22 final size:22
Alignment explanation
Indices: 8569--8612 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
8559 ATTTTTTGTC
* *
8569 CTTAATTCTGGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
8591 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
8613 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:11867 original size:22 final size:22
Alignment explanation
Indices: 11842--11885 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11832 ATTTTTTGTC
*
11842 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
11864 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
11886 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:19454 original size:43 final size:43
Alignment explanation
Indices: 19391--19474 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
19381 GGAGAGCCTG
* * * *
19391 TATAAGATTAAATTAACATTTAACCACACCTTTAGCCATCAAA
1 TATAAGAATAAATGAACATTTAACCACACCATTAACCATCAAA
* *
19434 TATAAGAATAAATGACCATTTAACGACACCATTAACCATCA
1 TATAAGAATAAATGAACATTTAACCACACCATTAACCATCA
19475 TATTTAGCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (43 bp):
TATAAGAATAAATGAACATTTAACCACACCATTAACCATCAAA
Found at i:28238 original size:42 final size:41
Alignment explanation
Indices: 28187--28271 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 41
28177 TACAAATTAC
* *
28187 ATCTTAATTACA-TATAAATATAATATTTTTATTAAGT-TAAT
1 ATCTTAATTAAAGTATAAA-ATAATAATTTTATTAA-TATAAT
*
28228 ATCTTAAATTAAAGTATTAAATAATAATTTTATTAATATAAT
1 ATCTT-AATTAAAGTATAAAATAATAATTTTATTAATATAAT
28270 AT
1 AT
28272 ATATATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
41 6 0.16
42 27 0.71
43 5 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (41 bp):
ATCTTAATTAAAGTATAAAATAATAATTTTATTAATATAAT
Found at i:29598 original size:25 final size:24
Alignment explanation
Indices: 29569--29640 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
29559 GTTTTTTTCC
29569 AATATTTTAATTTGTTTAAAAAAAT
1 AATATTTTAATTT-TTTAAAAAAAT
*
29594 AATATTTCT--TTTATTTGTAAAAAAT
1 AATATTT-TAATTT-TTT-AAAAAAAT
* *
29619 CATATTTCAATTTTTTAAAAAA
1 AATATTTTAATTTTTTAAAAAA
29641 CAATTTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
24 11 0.29
25 23 0.61
26 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (24 bp):
AATATTTTAATTTTTTAAAAAAAT
Found at i:30429 original size:20 final size:20
Alignment explanation
Indices: 30388--30448 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
30378 TTATCAATGT
* *
30388 TGTCACATTAGCAATGGT-AA
1 TGTCACATTAGTAA-AGTCAA
30408 TGTCACATTAGTAAAGTCAA
1 TGTCACATTAGTAAAGTCAA
* *
30428 TGTCACATCAATAAAGTCAA
1 TGTCACATTAGTAAAGTCAA
30448 T
1 T
30449 ATGTGCATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.06
20 34 0.94
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTCACATTAGTAAAGTCAA
Found at i:32851 original size:18 final size:17
Alignment explanation
Indices: 32817--32870 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
32807 ATAGTAAATC
*
32817 TTTTTTTAAATTTTATT
1 TTTTTTTAAATTATATT
32834 TTTTTTTAAATTAATATT
1 TTTTTTTAAATT-ATATT
* *
32852 TCTTTTAAAATATATATT
1 TTTTTTTAAAT-TATATT
32870 T
1 T
32871 CAATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.38
18 19 0.59
19 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTAAATTATATT
Found at i:32857 original size:17 final size:18
Alignment explanation
Indices: 32837--32871 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
32827 TTTTATTTTT
*
32837 TTTTAAATTA-ATATTTC
1 TTTTAAAATATATATTTC
32854 TTTTAAAATATATATTTC
1 TTTTAAAATATATATTTC
32872 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATATATATTTC
Found at i:32892 original size:21 final size:22
Alignment explanation
Indices: 32854--32899 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
32844 TTAATATTTC
*
32854 TTTTAAAATATATATTTCAATT
1 TTTTAAAATATATATTTCAACT
32876 TTTTAAAA-ATAGT-TTTCAACT
1 TTTTAAAATATA-TATTTCAACT
32897 TTT
1 TTT
32900 AGAATTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTAAAATATATATTTCAACT
Found at i:33555 original size:20 final size:20
Alignment explanation
Indices: 33518--33556 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33508 TCACGTCAAA
* *
33518 AAAGTCAACGCTATATTAGC
1 AAAGTCAACGCCACATTAGC
*
33538 AAAGTCAATGCCACATTAG
1 AAAGTCAACGCCACATTAG
33557 TATGGTCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAGTCAACGCCACATTAGC
Found at i:46237 original size:20 final size:21
Alignment explanation
Indices: 46208--46249 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
46198 ATACAAAATT
46208 CAAAAAAAAAAAAAG-ACAAA
1 CAAAAAAAAAAAAAGAACAAA
* *
46228 CAAAAGAAAAGAAAGAACAAA
1 CAAAAAAAAAAAAAGAACAAA
46249 C
1 C
46250 CTTCAACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAAAAGAACAAA
Found at i:48971 original size:23 final size:26
Alignment explanation
Indices: 48945--49000 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
48935 ATCATTTTAA
48945 TTATAAC-TTATATTA-TAAAA-AAT
1 TTATAACTTTATATTACTAAAATAAT
*
48968 TTATAACTTTATGTTACTTAAAATAAT
1 TTATAACTTTATATTAC-TAAAATAAT
48995 TTATAA
1 TTATAA
49001 TAACTCAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 7 0.25
26 5 0.18
27 9 0.32
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (26 bp):
TTATAACTTTATATTACTAAAATAAT
Found at i:49820 original size:15 final size:16
Alignment explanation
Indices: 49802--49831 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49792 TTTTTTTGAA
49802 AAAAAATTA-AAAAAG
1 AAAAAATTACAAAAAG
49817 AAAAAATTACAAAAA
1 AAAAAATTACAAAAA
49832 AATTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAATTACAAAAAG
Found at i:49857 original size:25 final size:25
Alignment explanation
Indices: 49798--49859 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
49788 ATTTTTTTTT
49798 TGAAAAAAAATTAAAAAAGAAAAAA
1 TGAAAAAAAATTAAAAAAGAAAAAA
* * *
49823 TTACAAAAAAATT-TAAAAGAAAAAC
1 TGA-AAAAAAATTAAAAAAGAAAAAA
*
49848 TGAAATAAAATT
1 TGAAAAAAAATT
49860 TTTTTCATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 8 0.26
25 14 0.45
26 9 0.29
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (25 bp):
TGAAAAAAAATTAAAAAAGAAAAAA
Found at i:51426 original size:16 final size:16
Alignment explanation
Indices: 51405--51440 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
51395 CACTGTTATT
51405 TATTTA-TATTTTATAA
1 TATTTATTATTTTA-AA
51421 TATTTATTATTTTAAA
1 TATTTATTATTTTAAA
51437 TATT
1 TATT
51441 ATTGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATTATTTTAAA
Found at i:51792 original size:22 final size:22
Alignment explanation
Indices: 51767--51808 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
51757 TTATAATTTA
51767 TATTTAAATTATAATATTTTTG
1 TATTTAAATTATAATATTTTTG
**
51789 TATTTTTATTATAATATTTT
1 TATTTAAATTATAATATTTT
51809 ATATTATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTAAATTATAATATTTTTG
Found at i:53127 original size:15 final size:13
Alignment explanation
Indices: 53066--53164 Score: 56
Period size: 15 Copynumber: 7.0 Consensus size: 13
53056 CCCAAACTAT
*
53066 TTTAAATTCAAAA
1 TTTAAATTTAAAA
* *
53079 -TTCAATTTAATA
1 TTTAAATTTAAAA
* *
53091 CTTAAATTAAATTAA
1 TTTAAATTTAA--AA
53106 TTTTAAAATTTAACAA
1 -TTT-AAATTTAA-AA
53122 TTTAAATTTAAAA
1 TTTAAATTTAAAA
*
53135 TATTCGAATTTAAATAA
1 T-TT-AAATTT-AA-AA
53152 TTTAAATTTAAAA
1 TTTAAATTTAAAA
53165 CTAAATTAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
12 9 0.14
13 13 0.20
14 12 0.18
15 14 0.21
16 8 0.12
17 10 0.15
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (13 bp):
TTTAAATTTAAAA
Done.