Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168363.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_583, 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: 22377
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:1281 original size:19 final size:19
Alignment explanation
Indices: 1257--1298 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1247 TAAAACAAAG
*
1257 AAAAGAATAA-CAAAGAAAA
1 AAAAGAAAAAGCAAA-AAAA
1276 AAAAGAAAAAGCAAAAAAA
1 AAAAGAAAAAGCAAAAAAA
1295 AAAA
1 AAAA
1299 AAAGCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAGCAAAAAAA
Found at i:1291 original size:16 final size:16
Alignment explanation
Indices: 1268--1318 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1258 AAAGAATAAC
1268 AAAG-AAAAAAAAGAA
1 AAAGCAAAAAAAAGAA
*
1283 AAAGCAAAAAAAAAAA
1 AAAGCAAAAAAAAGAA
*
1299 AAAGCAAAAAGAGAGAA
1 AAAGCAAAAA-AAAGAA
1316 AAA
1 AAA
1319 AAATGCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 4 0.13
16 20 0.65
17 7 0.23
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAGCAAAAAAAAGAA
Found at i:1624 original size:31 final size:31
Alignment explanation
Indices: 1575--1703 Score: 104
Period size: 31 Copynumber: 4.2 Consensus size: 31
1565 TGGTACCAAG
* * *
1575 GAATTTAGC-CAGTATAGCTAGCATCGAA-GA
1 GAATTAAGCTCAGTTTAGCTAGCA-CAAAGGA
* * *
1605 GAATTAAGCTCAGTCTAGCTTA-CACCAAGAA
1 GAATTAAGCTCAGTTTAGC-TAGCACAAAGGA
* *
1636 GAATTAAG-TCTAGTTTAGCTAGCATAAATGA
1 GAATTAAGCTC-AGTTTAGCTAGCACAAAGGA
* * *
1667 GAGTTAAGCCCAGTTTAGTTAGCACAAAGGA
1 GAATTAAGCTCAGTTTAGCTAGCACAAAGGA
1698 GAATTA
1 GAATTA
1704 CACCTAGTCA
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
30 15 0.19
31 60 0.77
32 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (31 bp):
GAATTAAGCTCAGTTTAGCTAGCACAAAGGA
Found at i:1711 original size:62 final size:62
Alignment explanation
Indices: 1575--1711 Score: 138
Period size: 62 Copynumber: 2.2 Consensus size: 62
1565 TGGTACCAAG
* * * * *
1575 GAATTTAGCC-AGTATAGCTAGCATCGAAGAGAATTAAGCTCAGTCTAGCTTACACCAAGAA
1 GAATTAAGCCTAGTTTAGCTAGCATCAAAGAGAATTAAGCCCAGTCTAGCTTACACAAAGAA
* * * *
1636 GAATTAAGTCTAGTTTAGCTAGCAT-AAATGAGAGTTAAGCCCAGTTTAG-TTAGCACAAAGGA
1 GAATTAAGCCTAGTTTAGCTAGCATCAAA-GAGAATTAAGCCCAGTCTAGCTTA-CACAAAGAA
1698 GAATTACA-CCTAGT
1 GAATTA-AGCCTAGT
1712 CAAGCTTGGC
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
61 13 0.21
62 48 0.77
63 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (62 bp):
GAATTAAGCCTAGTTTAGCTAGCATCAAAGAGAATTAAGCCCAGTCTAGCTTACACAAAGAA
Found at i:1812 original size:49 final size:48
Alignment explanation
Indices: 1744--2077 Score: 303
Period size: 49 Copynumber: 6.8 Consensus size: 48
1734 TTTTTTAAAA
* * *
1744 AAAGTTTTTTGCTTGTCTTTATATG-AGCCTTTTTCAAAGTGAGATTTTT
1 AAAGTTTGTTGCTTATCTTTATA-GAAG-CTTTTTCAAAATGAGATTTTT
* * *
1793 AAAGTTTATTACTTATCTTTATAGAAGCTTTATTCAAAATGAGATTATT
1 AAAGTTTGTTGCTTATCTTTATAGAAGCTTT-TTCAAAATGAGATTTTT
* * * *
1842 AAAGTTTGTTGCCTATCTTTAAAGAAGTTATTTTCAAAATAAGATTTCTT
1 AAAGTTTGTTGCTTATCTTTATAGAAGCT-TTTTCAAAATGAGATTT-TT
* * * ** *
1892 AAAATTTGTTG-TCTATATTTATAGGAGTCTTCCTCCAAATGAGATTTTT
1 AAAGTTTGTTGCT-TATCTTTATAGAAG-CTTTTTCAAAATGAGATTTTT
* * * *
1941 AAAGTTTTTTGTTTATCTTTATAGGAGTCTTTTTCAAAAAGAGATTTTT
1 AAAGTTTGTTGCTTATCTTTATAGAAG-CTTTTTCAAAATGAGATTTTT
* * * * *
1990 AAAGTTTGTTGCCTATATTTATAGAATCCATTTTCAAAATAAGATTTTT
1 AAAGTTTGTTGCTTATCTTTATAGAA-GCTTTTTCAAAATGAGATTTTT
* * * *
2039 AAAGTTTGTTGCCTATCTTCATACAAGCCCTTTTCAAAA
1 AAAGTTTGTTGCTTATCTTTATAGAAG-CTTTTTCAAAA
2078 AGAAAAAAAA
Statistics
Matches: 233, Mismatches: 43, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
48 5 0.02
49 188 0.81
50 39 0.17
51 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.46
Consensus pattern (48 bp):
AAAGTTTGTTGCTTATCTTTATAGAAGCTTTTTCAAAATGAGATTTTT
Found at i:2029 original size:148 final size:148
Alignment explanation
Indices: 1778--2054 Score: 407
Period size: 148 Copynumber: 1.9 Consensus size: 148
1768 GAGCCTTTTT
*
1778 CAAAGTGAGATTTTTAAAGTTTATTACTTATCTTTATAGAAGCTTTATTCAAAATGAGATTATTA
1 CAAAGTGAGATTTTTAAAGTTTATTACTTATCTTTATAGAAGCTTTATTCAAAAAGAGATTATTA
* * *
1843 AAGTTTGTTGCCTATCTTTAAAGAAGTTATTTTCAAAATAAGATTTCTTAAAATTTGTTGTCTAT
66 AAGTTTGTTGCCTATATTTAAAGAAGTCATTTTCAAAATAAGATTT-TTAAAATTTGTTGCCTAT
1908 ATTTATAGGAGTCTTCCTC
130 ATTTATAGGAGTCTTCCTC
* ** * *
1927 CAAA-TGAGATTTTTAAAGTTTTTTGTTTATCTTTATAGGAGTCTTT-TTCAAAAAGAGATTTTT
1 CAAAGTGAGATTTTTAAAGTTTATTACTTATCTTTATAGAAG-CTTTATTCAAAAAGAGATTATT
* *
1990 AAAGTTTGTTGCCTATATTTATAGAA-TCCATTTTCAAAATAAGATTTTTAAAGTTTGTTGCCTA
65 AAAGTTTGTTGCCTATATTTAAAGAAGT-CATTTTCAAAATAAGATTTTTAAAATTTGTTGCCTA
2054 T
129 T
2055 CTTCATACAA
Statistics
Matches: 115, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
147 17 0.15
148 90 0.78
149 8 0.07
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (148 bp):
CAAAGTGAGATTTTTAAAGTTTATTACTTATCTTTATAGAAGCTTTATTCAAAAAGAGATTATTA
AAGTTTGTTGCCTATATTTAAAGAAGTCATTTTCAAAATAAGATTTTTAAAATTTGTTGCCTATA
TTTATAGGAGTCTTCCTC
Found at i:2760 original size:153 final size:153
Alignment explanation
Indices: 2508--2818 Score: 559
Period size: 153 Copynumber: 2.0 Consensus size: 153
2498 TTTTTATGCA
2508 TTAAAAATTTTTTGCACTTCAAAAAATGTAAATTATAAAATGTCTTTAAGGGTACTTTTATAATT
1 TTAAAAATTTTTTGCACTTCAAAAAATGTAAATTATAAAATGTCTTTAAGGGTACTTTTATAATT
* *
2573 TGACATTTTTTAAATCGAATTTTTTAATGATTTTTTATGCTTAAGAATCCATATCACACAATGGA
66 TGACATTTTTGAAATCGAATTTTTTAATGATTTTTTATGCTTAAGAATCCAGATCACACAATGGA
2638 AGGTGTGATATTACAAAAATACC
131 AGGTGTGATATTACAAAAATACC
* * *
2661 TTAAAAATTTTTTGCACTTCGAAAAATGTAAATTATAAAATGTCTTTAGGGGTATTTTTATAATT
1 TTAAAAATTTTTTGCACTTCAAAAAATGTAAATTATAAAATGTCTTTAAGGGTACTTTTATAATT
*
2726 TGACATTTTTGAAATCGAATTTTTTAATGATTTTTTATGCTTAAGAATCCAGATCACACAGTGGA
66 TGACATTTTTGAAATCGAATTTTTTAATGATTTTTTATGCTTAAGAATCCAGATCACACAATGGA
2791 AGGTGTGATATTACAAAAATACC
131 AGGTGTGATATTACAAAAATACC
*
2814 CTAAA
1 TTAAA
2819 CCCTAAAACC
Statistics
Matches: 151, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (153 bp):
TTAAAAATTTTTTGCACTTCAAAAAATGTAAATTATAAAATGTCTTTAAGGGTACTTTTATAATT
TGACATTTTTGAAATCGAATTTTTTAATGATTTTTTATGCTTAAGAATCCAGATCACACAATGGA
AGGTGTGATATTACAAAAATACC
Found at i:4995 original size:57 final size:58
Alignment explanation
Indices: 4902--5034 Score: 182
Period size: 57 Copynumber: 2.3 Consensus size: 58
4892 TTTCTTTTTA
* * *
4902 AAAAAAATGATATTTCAAAATTATTTCTCAAAATTTTGAAATTATTCTTTGTC-TAAGG
1 AAAAAATTGATATTTCAAAATTATTCCTCAAAATTTTGAAATTATT-TTTCTCTTAAGG
4960 AAAAAATTGATATTTCAAAATT-TTCCTCAAAATTTTGAAATTATTTTTCTCTTTAAGG
1 AAAAAATTGATATTTCAAAATTATTCCTCAAAATTTTGAAATTATTTTTCTC-TTAAGG
* *
5018 -AAAGATTGATACTTCAA
1 AAAAAATTGATATTTCAA
5035 CTTCTTAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
56 5 0.07
57 37 0.54
58 26 0.38
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (58 bp):
AAAAAATTGATATTTCAAAATTATTCCTCAAAATTTTGAAATTATTTTTCTCTTAAGG
Found at i:5156 original size:56 final size:55
Alignment explanation
Indices: 5036--5223 Score: 174
Period size: 56 Copynumber: 3.5 Consensus size: 55
5026 ATACTTCAAC
* *
5036 TTCTTAATTT-TTGAAATTATTTTTGTTCAAGAAAAAAATTAATATTTTAACTTT
1 TTCTTAATTTCTTGAAATTACTTTTGTTCAAGAAAAAAATTAATATTTCAACTTT
* *
5090 TT-TCTAATTTCTTGGAATTACTTTTGTTTTAAGAAAAAAATTAATATTTCAACTTT
1 TTCT-TAATTTCTTGAAATTACTTTTG-TTCAAGAAAAAAATTAATATTTCAACTTT
* * * * * * *
5146 TTCTTCATTTCTTAAAATT-GTTATT-TT-AAG-AAAAATTTGATATTTAAACATT
1 TTCTTAATTTCTTGAAATTACTT-TTGTTCAAGAAAAAAATTAATATTTCAACTTT
* *
5198 TTCTTCAATTT-TTGAAGTTATTTTTG
1 TTCTT-AATTTCTTGAAATTACTTTTG
5224 CTTTAAAAGA
Statistics
Matches: 110, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
52 31 0.28
53 10 0.09
54 10 0.09
55 15 0.14
56 43 0.39
57 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (55 bp):
TTCTTAATTTCTTGAAATTACTTTTGTTCAAGAAAAAAATTAATATTTCAACTTT
Found at i:5270 original size:51 final size:51
Alignment explanation
Indices: 5043--5326 Score: 144
Period size: 51 Copynumber: 5.3 Consensus size: 51
5033 AACTTCTTAA
* * * * * *
5043 TTTTTGAAATTATTTTTGTTCAAGAAAAAAATTAATATTTTAACTTTTTTCTAAT
1 TTTTTGAAATTATTTTTGTTTAAG--AAAAATTGAGATTTCAAGTTTGTTC--AT
* * * * * * *
5098 TTCTTGGAATTACTTTTGTTTTAAGAAAAAAATTAATATTTCAACTTTTTCTTCAT
1 TTTTTGAAATTATTTTTG-TTTAAG--AAAAATTGAGATTTCAA--GTTTGTTCAT
* * * * * * * * *
5154 TTCTTAAAATT-GTTAT-TTTAAGAAAAATTTGATATTTAAACATTTTCTTCAA
1 TTTTTGAAATTATTTTTGTTTAAGAAAAA-TTGAGATTT-CA-AGTTTGTTCAT
* *
5206 TTTTTGAAGTTATTTTTGCTTTAA-AAGAAATTGAGATTTCAAG-TTGTTCCT
1 TTTTTGAAATTATTTTTG-TTTAAGAA-AAATTGAGATTTCAAGTTTGTTCAT
* * * *
5257 TTTTTAAAATTATTTTTGTTTAAGGAAAATTTGATATTTCAAGTTTTTTTCAT
1 TTTTTGAAATTATTTTTGTTTAA-GAAAAATTGAGATTTCAAG-TTTGTTCAT
5310 TTTTTGAAATTATTTTT
1 TTTTTGAAATTATTTTT
5327 TATTTTATTT
Statistics
Matches: 183, Mismatches: 32, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
50 5 0.03
51 40 0.22
52 28 0.15
53 33 0.18
54 11 0.06
55 26 0.14
56 34 0.19
58 6 0.03
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.52
Consensus pattern (51 bp):
TTTTTGAAATTATTTTTGTTTAAGAAAAATTGAGATTTCAAGTTTGTTCAT
Found at i:8843 original size:126 final size:125
Alignment explanation
Indices: 8664--8928 Score: 284
Period size: 126 Copynumber: 2.1 Consensus size: 125
8654 CATGCTAAAT
* * * * * * *
8664 ATGCCTTTAATAATCCATAGAAAAAATATGGAACGGATTCTTGAATGCGTTTTTAGGT-GAAAGC
1 ATGCCTTCAATAATCCATACAAAAAATATGAAACGGATTCTTGAAAGCATTTTT--GTCCAAAAC
*
8728 ACCTTTAATAATCCA-ATCAATAAATTTTTA-ATAGAAATTATTGAAGGCAATTTTTGTAAAAA
64 ACCTTTAATAATCCATA-CAATAAATTTTTAGAT-GAAATTATTGAAGGCAATTTTGGTAAAAA
* * * *
8790 ATGCCTTCAATAATCCATACACAATATTTGAAATGGATTCTTGAAAGCATTTTTGTCCCAAAACA
1 ATGCCTTCAATAATCCATACAAAAAATATGAAACGGATTCTTGAAAGCATTTTTGT-CCAAAACA
* * * ** * *
8855 CCTTTAATATTCCATACAATATATTTTTAGGTGGGATTATTGAAGGCGATTTTGGTTAAAA
65 CCTTTAATAATCCATACAATAAATTTTTAGATGAAATTATTGAAGGCAATTTTGGTAAAAA
*
8916 ACGCCTTCAATAA
1 ATGCCTTCAATAA
8929 CATTTTGTTA
Statistics
Matches: 115, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
124 2 0.02
126 111 0.97
127 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (125 bp):
ATGCCTTCAATAATCCATACAAAAAATATGAAACGGATTCTTGAAAGCATTTTTGTCCAAAACAC
CTTTAATAATCCATACAATAAATTTTTAGATGAAATTATTGAAGGCAATTTTGGTAAAAA
Found at i:13349 original size:178 final size:178
Alignment explanation
Indices: 13131--13454 Score: 435
Period size: 178 Copynumber: 1.8 Consensus size: 178
13121 TCTTAATCAT
** *
13131 TTTTAAAAATAAATTATTGAAGGCGTTTGTTCCTAAAAAATACCTTCAATAATTATGTAC-AAAG
1 TTTTAAAAATAAATTATTGAAGGAATTTGTTCCTAAAAAATACCTTAAATAATTATGTACGAAA-
* *
13195 ATTAAAATGAATTAGTGGAGGTGTTTTTCTAGAAT-AA-ATGCTTTCACTAA-CTGTTTTAAAAT
65 ATTAAAAGGAATTAGTGAAGGTGTTTTTCTAGAATAAACAT-C-TTCACTAATC-GTTTTAAAAT
13257 TTAAGAAGTGAAATATTGAATGTGTTTTTTATTGGAATAATAATCCCAAAAA
127 TTAAGAAGTGAAATATTGAATGTGTTTTTTATTGGAATAATAATCCCAAAAA
* * * *
13309 TTTTAAAAA-AATATTATTGAAGGAATTTGTT-TTCAAAAAATGCTTTAAATAATTATGTACGTA
1 TTTTAAAAATAA-ATTATTGAAGGAATTTGTTCCT-AAAAAATACCTTAAATAATTATGTACGAA
*
13372 AATTAAAAGGAATTAGTGAAGGTGTTTTTCTAGAATAAACATCTTCATTAATCGTTTTAAAATTT
64 AATTAAAAGGAATTAGTGAAGGTGTTTTTCTAGAATAAACATCTTCACTAATCGTTTTAAAATTT
* * *
13437 GAGTAGTGGAATATTGAA
129 AAGAAGTGAAATATTGAA
13455 AGCGTTTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
177 3 0.02
178 116 0.91
179 6 0.05
180 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (178 bp):
TTTTAAAAATAAATTATTGAAGGAATTTGTTCCTAAAAAATACCTTAAATAATTATGTACGAAAA
TTAAAAGGAATTAGTGAAGGTGTTTTTCTAGAATAAACATCTTCACTAATCGTTTTAAAATTTAA
GAAGTGAAATATTGAATGTGTTTTTTATTGGAATAATAATCCCAAAAA
Found at i:21502 original size:34 final size:34
Alignment explanation
Indices: 21420--21511 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
21410 GACACCTCAA
* * * * *
21420 AGATACAAACACCGTTAAAATAGCGACATTTTTT
1 AGATACAAACGCTGCTAATATAGCGACATTTTTC
*
21454 AGATACAAACGCTGCTAATATAGTGACATTTTTC
1 AGATACAAACGCTGCTAATATAGCGACATTTTTC
* *
21488 ATATACAAATGCTGCTAATATAGC
1 AGATACAAACGCTGCTAATATAGC
21512 TTCGTTTTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (34 bp):
AGATACAAACGCTGCTAATATAGCGACATTTTTC
Done.