Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168421.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_635, 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: 20959
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:3924 original size:63 final size:63
Alignment explanation
Indices: 3805--3925 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
3795 TTGAAAAAAC
* * *
3805 AAATACCTTCAATAATCCCCCCTAATTTTTTTGAGGGTACTATTGAAGGCGTTTTTTGACCAA
1 AAATACCTTCAATAATCCCCCCTAATTTTTTTAAGGGTACTATTAAAAGCGTTTTTTGACCAA
* * *
3868 AAATACTTTCAATAATCCCCTCTAATTTTTTTAAAGGAG-ATTATTAAAAGCGTTTTTT
1 AAATACCTTCAATAATCCCCCCTAATTTTTTT-AAGG-GTACTATTAAAAGCGTTTTTT
3926 TGCAAAAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 30 0.60
64 19 0.38
65 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (63 bp):
AAATACCTTCAATAATCCCCCCTAATTTTTTTAAGGGTACTATTAAAAGCGTTTTTTGACCAA
Found at i:3932 original size:63 final size:62
Alignment explanation
Indices: 3805--3948 Score: 159
Period size: 63 Copynumber: 2.3 Consensus size: 62
3795 TTGAAAAAAC
* * * *
3805 AAATACCTTCAATAATCCCCCCTAATTTTTTTGAGGGTACTATTGAAGGCGTTTTTTGACCAA
1 AAATACTTTCAATAATCCCCCCTAATTTTTTTAAGGGTACTATTAAAAGCGTTTTTTGA-CAA
* *
3868 AAATACTTTCAATAATCCCCTCTAATTTTTTTAAAGGAG-ATTATTAAAAGCGTTTTTTTG-CAA
1 AAATACTTTCAATAATCCCCCCTAATTTTTTT-AAGG-GTACTATTAAAAGCG-TTTTTTGACAA
3931 AAA-ACGCTTTCAATAATC
1 AAATA--CTTTCAATAATC
3949 TCTTTCATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 36 0.51
64 25 0.36
65 8 0.11
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (62 bp):
AAATACTTTCAATAATCCCCCCTAATTTTTTTAAGGGTACTATTAAAAGCGTTTTTTGACAA
Found at i:4124 original size:64 final size:64
Alignment explanation
Indices: 3773--4177 Score: 226
Period size: 64 Copynumber: 6.4 Consensus size: 64
3763 CTATTTGCAA
* * ** * *
3773 AGAGGATTATTGAAGGCGTTTTTTGAAAAAACAAATACCTTCAATAATCCCCCCTAATTTTTTT-
1 AGAGAATTATTGAAGGCGTTTTTTG-TAAAA-AAATGTCTTCAATAATCCTCTCTAATTTTTTTA
3837 G
64 G
* * * * * *
3838 AGGGTACTATTGAAGGCGTTTTTTG-ACCAAAAAT-ACTTTCAATAATCCCCTCTAATTTTTTTA
1 AGAGAATTATTGAAGGCGTTTTTTGTA-AAAAAATGTC-TTCAATAATCCTCTCTAATTTTTTTA
*
3901 A
64 G
* * * * * * *
3902 AG-GAGATTATTAAAAGCGTTTTTT-TGCAAAAAACG-CTTTCAATAAT-CTCTTTCA-TTTTAT
1 AGAGA-ATTATTGAAGGCGTTTTTTGT-AAAAAAATGTC-TTCAATAATCCTCTCTAATTTTTTT
3962 ATG
63 A-G
* *** * * * *
3965 AGA-AGATTATTGAAGGCATTTTGACT-AAAAAACGTCGTCAATAATCCTTTCTAATTTTTTTGG
1 AGAGA-ATTATTGAAGGCGTTTTTTGTAAAAAAATGTCTTCAATAATCCTCTCTAATTTTTTTAG
* * * ** * ** *
4028 AGGGGATTATTG-ATGATTTTTTTTTGCCAAAAATGTCTTCAATAATCCTCTATAATTTTTTTAG
1 AGAGAATTATTGAAGGCGTTTTTTGT-AAAAAAATGTCTTCAATAATCCTCTCTAATTTTTTTAG
* * * * *
4092 AGAGAATTATTGAAGGCGTTTTCTGTAAAAAAATGTTTTTAGTAATCC-CTTTCAATTTTTTATA
1 AGAGAATTATTGAAGGCGTTTTTTGTAAAAAAATGTCTTCAATAATCCTCTCT-AATTTTTT-TA
4156 -
64 G
4156 AGAG-ATTATTGAAGGCGTTTTT
1 AGAGAATTATTGAAGGCGTTTTT
4178 AGACAAAAAT
Statistics
Matches: 263, Mismatches: 58, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
62 30 0.11
63 89 0.34
64 112 0.43
65 32 0.12
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (64 bp):
AGAGAATTATTGAAGGCGTTTTTTGTAAAAAAATGTCTTCAATAATCCTCTCTAATTTTTTTAG
Found at i:5888 original size:14 final size:14
Alignment explanation
Indices: 5869--5907 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
5859 TATGTTATTT
*
5869 TTAATTTTTTAATA
1 TTAATTTTTTAACA
5883 TTAA-TTTTTAACA
1 TTAATTTTTTAACA
5896 TTAATTTTTTAA
1 TTAATTTTTTAA
5908 GCCATTAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTTTTTAACA
Found at i:8560 original size:3 final size:3
Alignment explanation
Indices: 8549--8579 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
8539 TTTTTTTTTT
8549 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8580 CAAACCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:11285 original size:31 final size:31
Alignment explanation
Indices: 11239--11316 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
11229 TGAGACTTTG
*
11239 GGCTTTGTTTGGGTTCAAAAATCT-AGATTTA
1 GGCTTCGTTTGGGTTCAAAAATCTAAG-TTTA
* *
11270 GGCTTCGTTTTGGTTCAGAAATCTAATGTTTA
1 GGCTTCGTTTGGGTTCAAAAATCTAA-GTTTA
11302 GGCTTCGTTTGGGTT
1 GGCTTCGTTTGGGTT
11317 TTATTTGGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 21 0.51
32 19 0.46
33 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.44
Consensus pattern (31 bp):
GGCTTCGTTTGGGTTCAAAAATCTAAGTTTA
Found at i:11452 original size:23 final size:24
Alignment explanation
Indices: 11410--11469 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
11400 TTCTTTGTTC
* *
11410 ATATTTTTTATATCTTAAAATTAT
1 ATATTTTTTATATCTAAAAACTAT
*
11434 ATATTTTTTATATC-AAAAACTCT
1 ATATTTTTTATATCTAAAAACTAT
11457 -TACTTTTTTATAT
1 ATA-TTTTTTATAT
11470 TTTGAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.06
23 16 0.50
24 14 0.44
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTTTTATATCTAAAAACTAT
Found at i:13372 original size:219 final size:219
Alignment explanation
Indices: 12988--13416 Score: 684
Period size: 219 Copynumber: 2.0 Consensus size: 219
12978 AAGGTGGTTG
* * ** *
12988 AGCTGACGTGGTACTGTGACATTAAGTTGATTAGACATGTAAGGTTGGTCTAAAAGTCTAAAATG
1 AGCTAACGTGGTACTGTGACATTAAGTTGATCAGACATGTAAGGTCAGTCCAAAAGTCTAAAATG
* * *
13053 CCCCTGGCTATTTATGGTAGTCTTTAATGAAAAAAGATGACCAAAATAACTTTGGATGTAAAAAA
66 CCCCTGGCTATTTATGGTAGTATCTAATGAAAAAAGATGACCAAAATAACTTTGGACGTAAAAAA
* *
13118 TCATATTTAATTTTTGATAGCTTCAGTTAAAAAAAAAGTATATTAGTTAATTAATTGATTCCATG
131 TCAGATTTAATTTTTGATAGCTTCAATTAAAAAAAAAGTATATTAGTTAATTAATTGATTCCATG
13183 TAATTAGGTGATGGATCGAAGTTA
196 TAATTAGGTGATGGATCGAAGTTA
13207 AGCTAACGTGGTACTGTGACATTAAGTTTGATCAGACATGTAAGGTCAGTCCAAAAGTCTAAAAT
1 AGCTAACGTGGTACTGTGACATTAAG-TTGATCAGACATGTAAGGTCAGTCCAAAAGTCTAAAAT
* * *
13272 GCCCTTGGTTATTTGTTGGTAGTATCTAATGAAAAAA-ATGACC-AAATAACCTTTGGACGT-AA
65 GCCCCTGGCTATTT-ATGGTAGTATCTAATGAAAAAAGATGACCAAAATAA-CTTTGGACGTAAA
*
13334 AAATCAGATTTAATTTTTGATAGCTTCAATTAAAAAAAAGGTATATTAGTTAATTAATTGATTCC
128 AAATCAGATTTAATTTTTGATAGCTTCAATTAAAAAAAAAGTATATTAGTTAATTAATTGATTCC
13399 ATGTAATTAGGTGATGGA
193 ATGTAATTAGGTGATGGA
13417 CCAAACATTT
Statistics
Matches: 193, Mismatches: 14, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
219 113 0.59
220 61 0.32
221 19 0.10
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (219 bp):
AGCTAACGTGGTACTGTGACATTAAGTTGATCAGACATGTAAGGTCAGTCCAAAAGTCTAAAATG
CCCCTGGCTATTTATGGTAGTATCTAATGAAAAAAGATGACCAAAATAACTTTGGACGTAAAAAA
TCAGATTTAATTTTTGATAGCTTCAATTAAAAAAAAAGTATATTAGTTAATTAATTGATTCCATG
TAATTAGGTGATGGATCGAAGTTA
Found at i:15498 original size:15 final size:16
Alignment explanation
Indices: 15478--15507 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15468 AAAACTATAA
15478 TTTTATTTTT-TATTT
1 TTTTATTTTTATATTT
15493 TTTTATTTTTATATT
1 TTTTATTTTTATATT
15508 ATATATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTTTATATTT
Found at i:18235 original size:57 final size:59
Alignment explanation
Indices: 18171--18288 Score: 213
Period size: 57 Copynumber: 2.0 Consensus size: 59
18161 TTTTCAATTT
18171 CTCAAATCTAGATAAAATTTAGAAAAATGTTTTTAACTTGGGTA-TTTC-ATGATAATC
1 CTCAAATCTAGATAAAATTTAGAAAAATGTTTTTAACTTGGGTATTTTCAATGATAATC
*
18228 CTCAAATCTAGATAAAATTTAGAAAAATGTTTTTGACTTGGGTATTTTCAATGATAATC
1 CTCAAATCTAGATAAAATTTAGAAAAATGTTTTTAACTTGGGTATTTTCAATGATAATC
18287 CT
1 CT
18289 TAAAACCAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 43 0.74
58 4 0.07
59 11 0.19
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (59 bp):
CTCAAATCTAGATAAAATTTAGAAAAATGTTTTTAACTTGGGTATTTTCAATGATAATC
Found at i:18496 original size:13 final size:13
Alignment explanation
Indices: 18478--18514 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
18468 GTGATGTAAC
18478 ATGAAGCAAATTA
1 ATGAAGCAAATTA
18491 ATGAAGCAAATTA
1 ATGAAGCAAATTA
*
18504 ATGATGCAAAT
1 ATGAAGCAAAT
18515 ATAAACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGAAGCAAATTA
Done.