Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168378.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_597, 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: 21926
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:955 original size:33 final size:33
Alignment explanation
Indices: 905--998 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
895 AGTACATATT
* *
905 TTAATCTTAAGGAGTAATTAAATTTAATTAAAC
1 TTAAGCTTAAGGGGTAATTAAATTTAATTAAAC
938 TTAAGCTTAAGGGGTAATTAAATTTAATTAAAC
1 TTAAGCTTAAGGGGTAATTAAATTTAATTAAAC
971 TTAAGCTTAAGGGGTAATTAAATTTAAT
1 TTAAGCTTAAGGGGTAATTAAATTTAAT
999 ATCTATAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (33 bp):
TTAAGCTTAAGGGGTAATTAAATTTAATTAAAC
Found at i:6869 original size:20 final size:18
Alignment explanation
Indices: 6821--6871 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
6811 TTGATCTATG
6821 TCATAATTTAAATATAAT
1 TCATAATTTAAATATAAT
* *
6839 T-ATTATATTAAGTATGAAAT
1 TCATAAT-TTAAATAT--AAT
6859 TCATAATTTAAAT
1 TCATAATTTAAAT
6872 TTACATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 4 0.16
18 8 0.32
20 9 0.36
21 4 0.16
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (18 bp):
TCATAATTTAAATATAAT
Found at i:10990 original size:110 final size:110
Alignment explanation
Indices: 10780--10980 Score: 269
Period size: 110 Copynumber: 1.8 Consensus size: 110
10770 AGCTAAGAAT
* **
10780 GGATATAGCTACTTTCAAAATGACGAATGATAAAAAAAATTGGATGAAGAAAAGAGTGATAGTGC
1 GGATATAGCTACTTTCAAAATGACGAATGAGAAAAAAAATTAAATGAAGAAAAGAGTGATAGTGC
* *
10845 TGCTATTTATGTTTAATGATGATGATATCATTTTGACGATTTGAA
66 TGCTAGTTATATTTAATGATGATGATATCATTTTGACGATTTGAA
* * * * * *
10890 GGATATGGCTGCTTTTAAAATGACGAATAGGGAGAAAAAATTAAATGAAGAAAAGAGTGATATTG
1 GGATATAGCTACTTTCAAAATGACGAAT-GAGAAAAAAAATTAAATGAAGAAAAGAGTGATAGTG
* *
10955 TTGCT-GTTATATTTGATGATGATGAT
65 CTGCTAGTTATATTTAATGATGATGAT
10981 GTTGTTTTGA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
110 43 0.56
111 34 0.44
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (110 bp):
GGATATAGCTACTTTCAAAATGACGAATGAGAAAAAAAATTAAATGAAGAAAAGAGTGATAGTGC
TGCTAGTTATATTTAATGATGATGATATCATTTTGACGATTTGAA
Found at i:14402 original size:25 final size:25
Alignment explanation
Indices: 14374--14423 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
14364 CCTAGGTAAG
*
14374 TTGGTTTCATATCCAAATGCCAAAC
1 TTGGTTTCATATACAAATGCCAAAC
*
14399 TTGGTTTCATATACAATTGCCAAAC
1 TTGGTTTCATATACAAATGCCAAAC
14424 ATCCATCGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (25 bp):
TTGGTTTCATATACAAATGCCAAAC
Found at i:16781 original size:19 final size:18
Alignment explanation
Indices: 16757--16792 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16747 GTTTTAAACG
16757 AAAATATGATATGAAAATA
1 AAAATATGATAT-AAAATA
*
16776 AAAATATTATATAAAAT
1 AAAATATGATATAAAAT
16793 TATATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAATATGATATAAAATA
Found at i:17559 original size:15 final size:15
Alignment explanation
Indices: 17539--17569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17529 GTGGAATGGG
17539 GAAAGGAAAGGAAAA
1 GAAAGGAAAGGAAAA
*
17554 GAAAGGAGAGGAAAA
1 GAAAGGAAAGGAAAA
17569 G
1 G
17570 CTGTTCTGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (15 bp):
GAAAGGAAAGGAAAA
Found at i:18210 original size:3 final size:3
Alignment explanation
Indices: 18202--18265 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
18192 TGCTAGCATG
18202 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18250 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
18266 AAAGAGCTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19108 original size:14 final size:14
Alignment explanation
Indices: 19089--19115 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19079 TATATTTAGT
19089 AATTTTAATATTTA
1 AATTTTAATATTTA
19103 AATTTTAATATTT
1 AATTTTAATATTT
19116 GTAATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTTTAATATTTA
Found at i:19462 original size:27 final size:27
Alignment explanation
Indices: 19404--19463 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
19394 TGATCAAAAA
* * * *
19404 TAAAAAATTCAAAACTTGAATTATAAT
1 TAAAATATTAAAAACTTAAATAATAAT
* *
19431 AAAAATATTAAAAACTTAAATAATTAT
1 TAAAATATTAAAAACTTAAATAATAAT
19458 TAAAAT
1 TAAAAT
19464 TTTATTACAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAATATTAAAAACTTAAATAATAAT
Done.