Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168117.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_361, 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: 31443
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:2518 original size:290 final size:290
Alignment explanation
Indices: 1723--2582 Score: 894
Period size: 294 Copynumber: 2.9 Consensus size: 290
1713 TTTTCTGGAC
* * ** * * * *
1723 AAAAATGCCTTGAATAATCCCAATAAAAAAATCATAA--ATTATTTAAGGCATTTTTGGCAGAAA
1 AAAAATGCCTTGAATGATCACAA-AAAAAAAAGAGAAGGATTATTAAAAGCATTTTTAGCAGAAA
* * * * * * * * *
1786 ATGCCTCGAATAAGCCTCTCTAAAATTTGAAGGAGATTATTGAAGGCATTTTTGACCAAAAATAA
65 ACGCCTCAAATAATCATTTCAAAAAATT-AAGG-GATTATTAAAGGCATTTTTGGCC--AAATAA
* * * ** ** * * * *
1851 T-TTCAATAATTCAAGAATTATGAAAGGTGTTTATGGTCAGAAATGCTTTCAATAACCCCATTCA
126 TCTTCAATAATCCAGGATTTATTCAAGGCATTTTTGGTCAGAAACGCCTTCAATAATCCCATTCA
* * * * ** *
1915 ATATTTTGTTAAAAATTATTCAAGATGTTTTTTGGGCCAAAACGCCTTCAATAATCTCCTTATAA
191 ATATTTTGTTAGAGATTATTCAAGGTATTTTTTGGGAAAAAACGCCTTCAATAATCTCCTCATAA
** * *
1980 ATGCCTAAAGGAAATTATTCAAGGTGTTTTATTAT
256 ATGCCTAAAGGGGATTATTCAAGGTGTTTTATCAA
*
2015 AAAAATGCCTTGAATGATCACAAAAAAAAAATGAGAAAGGATTATTAAAAGCATTTTTGGCAGAA
1 AAAAATGCCTTGAATGATCACAAAAAAAAAA-GAG-AAGGATTATTAAAAGCATTTTTAGCAGAA
* ** *
2080 AACGCCTCGAATAATCAGTTTCAAAAAATTAAGGGATTATTAAAGGTGTTTTTGG-CAAAAAATA
64 AACGCCTCAAATAATCA-TTTCAAAAAATTAAGGGATTATTAAAGGCATTTTTGGCCAAATAAT-
* * ***
2144 CCTTCAATAATCCAGGATTTATTCAAGTCATTTTTTGTCAGAAACGCCTTCAATAATGTAATTCA
127 -CTTCAATAATCCAGGATTTATTCAAGGCATTTTTGGTCAGAAACGCCTTCAATAATCCCATTCA
* * *
2209 ATATTTTGTTAGGGATTATTCAAGGTATTTTTTGGGTAAAAACGCCTTCAATAATCTTCTCATAA
191 ATATTTTGTTAGAGATTATTCAAGGTATTTTTTGGGAAAAAACGCCTTCAATAATCTCCTCATAA
* *
2274 ATGCTTGAAGGGGATTATTCAAGGTGTTTTATCAA
256 ATGCCTAAAGGGGATTATTCAAGGTGTTTTATCAA
* * * *
2309 AAAAATGGCTTGAATGATC-CAAAAAAAAAA-AG-AGGATTATTGAAGGCATTTTTATCA-AAAA
1 AAAAATGCCTTGAATGATCACAAAAAAAAAAGAGAAGGATTATTAAAAGCATTTTTAGCAGAAAA
* * *
2370 TGCTTCAAATAATC-TCTTCAAAAAAATTGGAGGGGATTATTAAAGGCATTTTTGGCCAAATACA
66 CGCCTCAAATAATCAT-TTC-AAAAAATT--AAGGGATTATTAAAGGCATTTTTGGCCAAATA-A
2434 TCTTCAATAATCCAGGATTTATTCAAGGCATTTTTGG-CTAGAAACGCCTTCAATAATCCCATTC
126 TCTTCAATAATCCAGGATTTATTCAAGGCATTTTTGGTC-AGAAACGCCTTCAATAATCCCATTC
* * * ** **
2498 AATATTTTGATAGAGATTATTCAAGGCATTTTCTAAGAAAAAATACCTTCAATAATCTCCTCATA
190 AATATTTTGTTAGAGATTATTCAAGGTATTTTTTGGGAAAAAACGCCTTCAATAATCTCCTCATA
2563 AATGCCTAAAGGGGATTATT
255 AATGCCTAAAGGGGATTATT
2583 TAAAGCCTTT
Statistics
Matches: 475, Mismatches: 78, Indels: 32
0.81 0.13 0.05
Matches are distributed among these distances:
286 1 0.00
287 3 0.01
288 23 0.05
289 22 0.05
290 151 0.32
291 20 0.04
292 24 0.05
293 14 0.03
294 167 0.35
295 41 0.09
296 9 0.02
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (290 bp):
AAAAATGCCTTGAATGATCACAAAAAAAAAAGAGAAGGATTATTAAAAGCATTTTTAGCAGAAAA
CGCCTCAAATAATCATTTCAAAAAATTAAGGGATTATTAAAGGCATTTTTGGCCAAATAATCTTC
AATAATCCAGGATTTATTCAAGGCATTTTTGGTCAGAAACGCCTTCAATAATCCCATTCAATATT
TTGTTAGAGATTATTCAAGGTATTTTTTGGGAAAAAACGCCTTCAATAATCTCCTCATAAATGCC
TAAAGGGGATTATTCAAGGTGTTTTATCAA
Found at i:3465 original size:22 final size:22
Alignment explanation
Indices: 3435--3478 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3425 AAAATGAACA
3435 AATGAATGAATGATATAA-TATG
1 AATGAATG-ATGATATAAGTATG
* *
3457 AATGCATGATGATTTAAGTATG
1 AATGAATGATGATATAAGTATG
3479 TACAACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.34
Consensus pattern (22 bp):
AATGAATGATGATATAAGTATG
Found at i:3629 original size:7 final size:7
Alignment explanation
Indices: 3550--3644 Score: 55
Period size: 7 Copynumber: 13.4 Consensus size: 7
3540 TGGGGTAACT
*
3550 TTTAAGG
1 TTTAGGG
*
3557 TTTAGGTT
1 TTTAGG-G
3565 TTTAGGG
1 TTTAGGG
*
3572 CTTAGGG
1 TTTAGGG
**
3579 TTTAGAT
1 TTTAGGG
*
3586 TTTAGAG
1 TTTAGGG
**
3593 TTTAAAG
1 TTTAGGG
* *
3600 CTTAGGT
1 TTTAGGG
*
3607 TTTAGAG
1 TTTAGGG
*
3614 TTTAAGG
1 TTTAGGG
*
3621 TTTGGGG
1 TTTAGGG
*
3628 TTTAGGA
1 TTTAGGG
3635 TTTAGGG
1 TTTAGGG
3642 TTT
1 TTT
3645 CATGGAATTA
Statistics
Matches: 64, Mismatches: 23, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
7 58 0.91
8 6 0.09
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:12437 original size:21 final size:23
Alignment explanation
Indices: 12411--12466 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 23
12401 CATTTTCTAA
*
12411 CAAAAAACATCTTA-AA-TAATC
1 CAAAAAAAATCTTATAAGTAATC
12432 CAAAAAAAATCTTATAAGTAATC
1 CAAAAAAAATCTTATAAGTAATC
12455 CTAAAAAAAATC
1 C-AAAAAAAATC
12467 AAACTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 13 0.42
22 2 0.06
23 6 0.19
24 10 0.32
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (23 bp):
CAAAAAAAATCTTATAAGTAATC
Found at i:12970 original size:62 final size:61
Alignment explanation
Indices: 12907--13045 Score: 201
Period size: 62 Copynumber: 2.3 Consensus size: 61
12897 ACATTTTTTA
* * **
12907 TTAAGATATTTTTAAATCAAAAATATCTT-AAATAATCTCCTGATATATTTTTAAAAAAATTAT
1 TTAAGATATTTTTAAATAAAAAACA-CTTCAAATAATCTCCT--TATATTTAAAAAAAAATTAT
12970 TTAAGAT-TTTTTAAATAAAAAACACTTCAAATAATCTCCTTATATTTAAAAAAAAATTAT
1 TTAAGATATTTTTAAATAAAAAACACTTCAAATAATCTCCTTATATTTAAAAAAAAATTAT
13030 TTAAGATATTTTTAAA
1 TTAAGATATTTTTAAA
13046 AATAATCTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 25 0.36
61 11 0.16
62 27 0.39
63 7 0.10
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (61 bp):
TTAAGATATTTTTAAATAAAAAACACTTCAAATAATCTCCTTATATTTAAAAAAAAATTAT
Found at i:17449 original size:12 final size:11
Alignment explanation
Indices: 17425--17454 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17415 TCAAATGTAT
17425 AAATTTTAAAA
1 AAATTTTAAAA
17436 AAATTTTAAAA
1 AAATTTTAAAA
*
17447 AAAATTTA
1 AAATTTTA
17455 TATATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATTTTAAAA
Done.