Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168451.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_662, 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: 20322
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:292 original size:3 final size:3
Alignment explanation
Indices: 284--314 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
274 TTACTGGGAA
284 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
315 AAGATATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1014 original size:27 final size:27
Alignment explanation
Indices: 976--1032 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
966 ATCTACCTTG
*
976 AGCTTTTGGTCACTCCCATTATTATGA
1 AGCTTTCGGTCACTCCCATTATTATGA
*
1003 AGCTTTCGGTCACTCCCATTCTTATGA
1 AGCTTTCGGTCACTCCCATTATTATGA
1030 AGC
1 AGC
1033 ATTCAGAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (27 bp):
AGCTTTCGGTCACTCCCATTATTATGA
Found at i:3088 original size:273 final size:273
Alignment explanation
Indices: 2601--3142 Score: 1003
Period size: 273 Copynumber: 2.0 Consensus size: 273
2591 GGGTGTGAGC
* * *
2601 AACTGGCATATCTCTTTTCGACTCCCCTTGCTCGAAGTTTGGAGCATCTGGAAGTACTCGTAGTA
1 AACTGGCATATCTCTTTTCGACTCCCCTTGCTCAAAGTTTGGAGCATCTGGAAGTACTCGAAATA
*
2666 AGCTATTGCGATTCTTTGGAACATGTAATCTTCGATGAAGCAGAAAAGGAGGATCAAATAGTTTC
66 AGCCATTGCGATTCTTTGGAACATGTAATCTTCGATGAAGCAGAAAAGGAGGATCAAATAGTTTC
2731 AAACATGAATGGCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCGGAA
131 AAACATGAATGGCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCGGAA
*
2796 GATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGTATCTGTTGAGATA
196 GATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCTGTTGAGATA
*
2861 ACTGGTTGTGCGA
261 ACTGATTGTGCGA
*
2874 AACTGGCATATCTCTTTTCGACTCCCCTTGCTCAAAGTTTGGAGCATCTGGAAGTGCTCGAAATA
1 AACTGGCATATCTCTTTTCGACTCCCCTTGCTCAAAGTTTGGAGCATCTGGAAGTACTCGAAATA
*
2939 AGCCATTGCGATTCTTTGGAACATGTAATCTTCGATGAAGCAGAAAATGAGGATCAAATAGTTTC
66 AGCCATTGCGATTCTTTGGAACATGTAATCTTCGATGAAGCAGAAAAGGAGGATCAAATAGTTTC
*
3004 AAACATGGATGGCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCGGAA
131 AAACATGAATGGCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCGGAA
3069 GATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCTGTTGAGATA
196 GATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCTGTTGAGATA
3134 ACTGATTGT
261 ACTGATTGT
3143 TCTCAACTAA
Statistics
Matches: 260, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
273 260 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (273 bp):
AACTGGCATATCTCTTTTCGACTCCCCTTGCTCAAAGTTTGGAGCATCTGGAAGTACTCGAAATA
AGCCATTGCGATTCTTTGGAACATGTAATCTTCGATGAAGCAGAAAAGGAGGATCAAATAGTTTC
AAACATGAATGGCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCGGAA
GATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCTGTTGAGATA
ACTGATTGTGCGA
Found at i:6411 original size:15 final size:16
Alignment explanation
Indices: 6392--6437 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
6382 AGAAAATGTT
6392 GGAAGAGAAAGAAAAA
1 GGAAGAGAAAGAAAAA
*
6408 -GAAGGGAAA-AAAAA
1 GGAAGAGAAAGAAAAA
6422 GGAA-AGAAAAGAAAAA
1 GGAAGAG-AAAGAAAAA
6438 AAGGGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
GGAAGAGAAAGAAAAA
Found at i:8565 original size:276 final size:276
Alignment explanation
Indices: 8065--8606 Score: 952
Period size: 276 Copynumber: 2.0 Consensus size: 276
8055 AGGTGTGAGC
* *
8065 AACTGGATATCTCTTTTCGACTCCCTTGCTCGAAGTTTGAGCATCTGGGAGTCGCTCCGAAATAA
1 AACTGGATATCTCTTTTCGACTCCCTTGCTCAAAGTTTGAGCATCTGCGAGTCGCTCCGAAATAA
8130 GCCCATTGCGATTCTTTGGAACATTTAATCTTCGATGAAGCAGAAAATGAGGATCAAATAGTTTC
66 GCCCATTGCGATTCTTTGGAACATTTAATCTTCGATGAAGCAGAAAATGAGGATCAAATAGTTTC
8195 AAAACAATGAATGGCCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCG
131 AAAACAATGAATGGCCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCG
*
8260 GAAGATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGTATCTGTTGAG
196 GAAGATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCTGTTGAG
8325 ATAAATGGTTGTGCGA
261 ATAAATGGTTGTGCGA
8341 AACTGGCATATCTCTTTTCGACTCCCCTTGCTCAAAGTTTGGAGCATCTGCGAGT-GCT-CGAAA
1 AACTGG-ATATCTCTTTTCGACT-CCCTTGCTCAAAGTTT-GAGCATCTGCGAGTCGCTCCGAAA
8404 TAAG-CCATTGCGATTCTTTGGAACATTTAATCTTCGATGAAGCAGAAAATGAGGATCAAATAGT
63 TAAGCCCATTGCGATTCTTTGGAACATTTAATCTTCGATGAAGCAGAAAATGAGGATCAAATAGT
*
8468 TTC-AAAC-ATGGATGG-CTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGAATAATTAAA
128 TTCAAAACAATGAATGGCCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAG-ATAATT-AA
8530 TTGCGGAAGATTGAAATATGTGTTTCCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCT
191 TTGCGGAAGATTGAAATATGTGTTT-CCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCT
8595 GTTGAGATAAAT
255 GTTGAGATAAAT
8607 TATTGTTCTC
Statistics
Matches: 256, Mismatches: 4, Indels: 12
0.94 0.01 0.04
Matches are distributed among these distances:
273 37 0.14
274 13 0.05
275 31 0.12
276 119 0.46
277 25 0.10
278 18 0.07
279 13 0.05
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (276 bp):
AACTGGATATCTCTTTTCGACTCCCTTGCTCAAAGTTTGAGCATCTGCGAGTCGCTCCGAAATAA
GCCCATTGCGATTCTTTGGAACATTTAATCTTCGATGAAGCAGAAAATGAGGATCAAATAGTTTC
AAAACAATGAATGGCCTATCCTCTCCGCTGGCCTAAGTTGAGAACTCTCAAGATAATTAATTGCG
GAAGATTGAAATATGTGTTTCCAATCACTTTGGCTCAAGGACTTCCTTATTTGGAATCTGTTGAG
ATAAATGGTTGTGCGA
Found at i:9262 original size:15 final size:14
Alignment explanation
Indices: 9242--9330 Score: 62
Period size: 15 Copynumber: 6.4 Consensus size: 14
9232 GAAACGGGAT
9242 GAAAAAGAGAGAAAA
1 GAAAAAGA-AGAAAA
9257 GAAAAAGAAGAAAA
1 GAAAAAGAAGAAAA
* *
9271 TG--TAGGAAGCAAAA
1 -GAAAAAGAAG-AAAA
**
9285 GAAAAAGAAGGGAA
1 GAAAAAGAAGAAAA
9299 -AAAAA-AAGAAAA
1 GAAAAAGAAGAAAA
*
9311 G-AAAAGAAAAAAA
1 GAAAAAGAAGAAAA
9324 GGAAAAA
1 -GAAAAA
9331 TGAAACTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
12 9 0.16
13 17 0.30
14 13 0.23
15 18 0.32
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.02
Consensus pattern (14 bp):
GAAAAAGAAGAAAA
Found at i:9304 original size:20 final size:20
Alignment explanation
Indices: 9281--9335 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
9271 TGTAGGAAGC
**
9281 AAAAGAAAAAGAAGGGAAAA
1 AAAAGAAAAAGAAAAGAAAA
9301 AAAA-AGAAAAGAAAAGAAAA
1 AAAAGA-AAAAGAAAAGAAAA
*
9321 AAAGGAAAAATGAAA
1 AAAAGAAAAA-GAAA
9336 CTATTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.03
20 23 0.79
21 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAGAAAAGAAAA
Found at i:11107 original size:23 final size:24
Alignment explanation
Indices: 11080--11136 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
11070 TTTAACCGTG
11080 TTATTATTTTCAA-TAA-TTTAAAT
1 TTATTATTTTCAATTAACTTT-AAT
11103 TTATT-TTTT-AATTAACTTTAAT
1 TTATTATTTTCAATTAACTTTAAT
*
11125 TTTTTATATTTC
1 TTATTAT-TTTC
11137 CTTAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 2 0.07
22 14 0.50
23 9 0.32
24 3 0.11
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTATTTTCAATTAACTTTAAT
Found at i:11122 original size:17 final size:18
Alignment explanation
Indices: 11097--11130 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11087 TTTCAATAAT
11097 TTAAATTT-ATTTTTTAA
1 TTAAATTTAATTTTTTAA
*
11114 TTAACTTTAATTTTTTA
1 TTAAATTTAATTTTTTA
11131 TATTTCCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTAAATTTAATTTTTTAA
Found at i:13970 original size:22 final size:22
Alignment explanation
Indices: 13943--13993 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
13933 AAATTTTTAA
*
13943 AAAAATTGTGTTGGATAC-CCAT
1 AAAAATTGTGTTGGAGACTCC-T
* *
13965 AAAAATTTTTTTGGAGACTCCT
1 AAAAATTGTGTTGGAGACTCCT
13987 AAAAATT
1 AAAAATT
13994 AAAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
AAAAATTGTGTTGGAGACTCCT
Found at i:18606 original size:18 final size:20
Alignment explanation
Indices: 18570--18607 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
18560 AAAATTATAT
18570 TTTTAATAAGTTTTAATTAA
1 TTTTAATAAGTTTTAATTAA
*
18590 TTTTAA-AA-TTTTTATTAA
1 TTTTAATAAGTTTTAATTAA
18608 AAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTAATAAGTTTTAATTAA
Found at i:18868 original size:16 final size:17
Alignment explanation
Indices: 18844--18887 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
18834 TTATTTCTAT
*
18844 TTTTCAAAAA-CAAAAA
1 TTTTGAAAAATCAAAAA
*
18860 TTTTGAAAAATGAAAAA
1 TTTTGAAAAATCAAAAA
18877 TTTTGCAAAAA
1 TTTTG-AAAAA
18888 AAAGAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 10 0.42
18 5 0.21
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (17 bp):
TTTTGAAAAATCAAAAA
Found at i:18869 original size:17 final size:18
Alignment explanation
Indices: 18849--18888 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
18839 TCTATTTTTC
18849 AAAAACAAAAATTTTG-A
1 AAAAACAAAAATTTTGCA
**
18866 AAAATGAAAAATTTTGCA
1 AAAAACAAAAATTTTGCA
18884 AAAAA
1 AAAAA
18889 AAGAAGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (18 bp):
AAAAACAAAAATTTTGCA
Done.