Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168372.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_591, 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: 22080
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Found at i:11401 original size:31 final size:31
Alignment explanation
Indices: 11355--11424 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
11345 AATTTCCAGA
* * ** *
11355 TTCCGACG-AAATTCCGGCGAAGTTTGAATT
1 TTCCGGCGAAAATTCCGGCCAACCTTGAAGT
11385 TTCCGGCGAAAATTCCGGCCAACCTTGAAGT
1 TTCCGGCGAAAATTCCGGCCAACCTTGAAGT
11416 TTCCGGCGA
1 TTCCGGCGA
11425 CCTACCCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGGCCAACCTTGAAGT
Found at i:11499 original size:19 final size:20
Alignment explanation
Indices: 11475--11518 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
11465 TTCCGGCAAC
11475 TTCCGACGA-AATTTCCAGA
1 TTCCGACGACAATTTCCAGA
*
11494 TTCCGACGACATTTTCCAGA
1 TTCCGACGACAATTTCCAGA
*
11514 ATCCG
1 TTCCG
11519 GCACCGGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (20 bp):
TTCCGACGACAATTTCCAGA
Found at i:12062 original size:27 final size:27
Alignment explanation
Indices: 11974--12062 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
11964 AAAAAAAAAT
11974 ATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTTAGGGAAAAGTTGAAAGTATCA
* * * * **
12001 ATTTTCCTTAAGAATAAATTTCCAAAAAAT--
1 A-TTT--TTAGGGA-AAAGTT-GAAAGTATCA
12031 ATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTTAGGGAAAAGTTGAAAGTATCA
12058 ATTTT
1 ATTTT
12063 CCTTAAGAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 5 0.12
27 11 0.26
28 3 0.07
29 3 0.07
30 6 0.14
31 5 0.12
32 5 0.12
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (27 bp):
ATTTTTAGGGAAAAGTTGAAAGTATCA
Found at i:12087 original size:119 final size:116
Alignment explanation
Indices: 11965--12357 Score: 525
Period size: 119 Copynumber: 3.4 Consensus size: 116
11955 AAATTTCAAA
11965 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTCCAAAAAA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTCCAAAAAA
*
12030 TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
66 TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
12081 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTCAAAAA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAG-AATAAATTTCCAAAAA
12145 A-AGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
65 ATA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
** * *
12198 AGAAAAAAAGGGTTTTT-GAGGAAAAGTTAAAAGTATCAATTTTTCTTGAA-AATCAAAATTTCC
1 A-AAAAAAA-TATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTT-AAGAAT--AAATTTCC
* *
12261 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATAAATTTTTCTTAAAAATAAATTTTC
60 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
12318 -AAAAAGAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
12358 CTACACAAGA
Statistics
Matches: 246, Mismatches: 15, Indels: 33
0.84 0.05 0.11
Matches are distributed among these distances:
115 27 0.11
116 64 0.26
117 6 0.02
118 55 0.22
119 74 0.30
120 5 0.02
121 14 0.06
122 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (116 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTCCAAAAAA
TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:12116 original size:59 final size:59
Alignment explanation
Indices: 11965--12357 Score: 489
Period size: 59 Copynumber: 6.7 Consensus size: 59
11955 AAATTTCAAA
*
11965 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAA-TTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
* *
12023 -CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
12081 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAG-AATAAATTTTC
*** * *
12140 AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
** * * * *
12198 AGAAAAAAAGGGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTGAA-AATCAAAATTTC
1 A-AAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAGAAT-AAATTTTC
* * * * *
12260 -CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATAAATTTTTCTTAAAAATAAATTTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
* *
12318 ---AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
12358 CTACACAAGA
Statistics
Matches: 301, Mismatches: 24, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
56 35 0.12
57 52 0.17
58 20 0.07
59 140 0.47
60 45 0.15
61 5 0.02
62 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (59 bp):
AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTC
Found at i:12273 original size:178 final size:172
Alignment explanation
Indices: 11968--12357 Score: 538
Period size: 178 Copynumber: 2.2 Consensus size: 172
11958 TTTCAAAAAA
* * *
11968 AAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTCCAAAAAATA
1 AAAAAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAAAA
* * *
12032 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAATATTTTTG
65 TTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAAGAATAAAATTTCAAAAAAAATATTTTTA
* *
12097 GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
130 GGGAAAAGTTGAAAGTATAAATTTTCCTTAAAAATAAATTTTC
*
12140 AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT-CAGAAAA
1 --AAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCA-AAAA
* *
12204 AAAGGGTTTTT-GAGGAAAAGTTAAAAGTATCAATTTTTCTTGAA-AATCAAAATTTC-CAAAAA
62 AAA---TTTTTAG-GGAAAAGTTAAAAGTATCAATTTTCCTT-AAGAAT-AAAATTTCAAAAAAA
*
12266 ATATTTTTAGGGAAAAGTTGAAAGTATAAATTTTTCTTAAAAATAAATTTTC
121 ATATTTTTAGGGAAAAGTTGAAAGTATAAATTTTCCTTAAAAATAAATTTTC
12318 AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
12358 CTACACAAGA
Statistics
Matches: 194, Mismatches: 13, Indels: 17
0.87 0.06 0.08
Matches are distributed among these distances:
174 7 0.04
175 84 0.43
176 6 0.03
177 1 0.01
178 87 0.45
179 9 0.05
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (172 bp):
AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAAAAT
TTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAAGAATAAAATTTCAAAAAAAATATTTTTAG
GGAAAAGTTGAAAGTATAAATTTTCCTTAAAAATAAATTTTC
Done.