Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168403.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_619, 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: 21421
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Found at i:177 original size:4 final size:4
Alignment explanation
Indices: 128--302 Score: 55
Period size: 4 Copynumber: 43.5 Consensus size: 4
118 TCTTGTGTAT
* * * *
128 TTTA TGTA TTT- TATTA TTTA -TTA TTATA TGTA TAT- TTTA CTTA TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA
* * *
175 TTTA TTTA TTT- TTTT TGTTA -ATA TTTA TATGTA TTTTA TTTA TATA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA T-T-TA -TTTA TTTA TTTA
* * * *
221 GTTC TATA TTTA TTATA TATTA -TAA TTTA TTTA -TTA -TTA TTTA TTT-
1 TTTA TTTA TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
267 TTTC TTGTA -ATA TTTT TTTA TTTA TCTTA TTGTA TT
1 TTTA TT-TA TTTA TTTA TTTA TTTA T-TTA TT-TA TT
303 ATCTGTTAAT
Statistics
Matches: 126, Mismatches: 25, Indels: 39
0.66 0.13 0.21
Matches are distributed among these distances:
3 24 0.19
4 74 0.59
5 23 0.18
6 4 0.03
7 1 0.01
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:248 original size:17 final size:18
Alignment explanation
Indices: 138--266 Score: 57
Period size: 17 Copynumber: 7.6 Consensus size: 18
128 TTTATGTATT
138 TTAT-TATTTATTATTATA
1 TTATATATTTATTA-TATA
*
156 TGTATAT-TTTACTTATTTA
1 T-TATATATTTA-TTATATA
* * *
175 TTTATTTATTT-TT-TTTG
1 -TTATATATTTATTATATA
*
192 TTA-ATATTTA-TATGTA
1 TTATATATTTATTATATA
*
208 TT-T-TATTTA-TATA-G
1 TTATATATTTATTATATA
*
222 TTCTATATTTATTATATA
1 TTATATATTTATTATATA
240 TTATA-ATTTATT-TATTA
1 TTATATATTTATTATA-TA
*
257 TTATTTATTT
1 TTATATATTT
267 TTTCTTGTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
14 2 0.02
15 16 0.19
16 15 0.17
17 20 0.23
18 11 0.13
19 14 0.16
20 8 0.09
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATATATTTATTATATA
Found at i:255 original size:14 final size:14
Alignment explanation
Indices: 233--266 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
223 TCTATATTTA
*
233 TTATATATTATAAT
1 TTATTTATTATAAT
*
247 TTATTTATTATTAT
1 TTATTTATTATAAT
261 TTATTT
1 TTATTT
267 TTTCTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTATTATAAT
Found at i:512 original size:13 final size:13
Alignment explanation
Indices: 494--528 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
484 AGAAGAGTCC
*
494 AGATTGGATTCAA
1 AGATTGAATTCAA
507 AGATTGAATTCAA
1 AGATTGAATTCAA
520 AGATTGAAT
1 AGATTGAAT
529 CTCCGTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (13 bp):
AGATTGAATTCAA
Found at i:1330 original size:25 final size:25
Alignment explanation
Indices: 1300--1361 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 25
1290 ATTTATTTAA
1300 TATTTTTTTATCTTTATCTTATT-TT
1 TATTTTTTTATCTTTATCTT-TTCTT
*
1325 TA---TTTT-TGTTTA-CTTTTCTT
1 TATTTTTTTATCTTTATCTTTTCTT
1345 TATTTTTTTATCTTTAT
1 TATTTTTTTATCTTTAT
1362 TATTTTCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
19 2 0.07
20 7 0.24
21 5 0.17
22 4 0.14
23 4 0.14
24 5 0.17
25 2 0.07
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.76
Consensus pattern (25 bp):
TATTTTTTTATCTTTATCTTTTCTT
Found at i:1331 original size:26 final size:26
Alignment explanation
Indices: 1302--1351 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1292 TTATTTAATA
1302 TTTT-TTTATCTTTATC-TTATTTTTAT
1 TTTTGTTTA-CTTT-TCTTTATTTTTAT
1328 TTTTGTTTACTTTTCTTTATTTTT
1 TTTTGTTTACTTTTCTTTATTTTT
1352 TTATCTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.09
26 16 0.73
27 4 0.18
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTGTTTACTTTTCTTTATTTTTAT
Found at i:1536 original size:117 final size:116
Alignment explanation
Indices: 1403--1798 Score: 634
Period size: 117 Copynumber: 3.4 Consensus size: 116
1393 TAAATAAAAA
*
1403 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
1 TCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
1468 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTT
66 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTT
*
1519 CCAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAA
1 TCAAAAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAA
*
1584 AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTTCTTAAAAAATAAATTT
65 AATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTTCTTTAAAAATAAATTT
* *
1637 TCAAAAAAAAGATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAA
1 TC-AAAAAAAGA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC--A
* * *
1702 AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAATTT
62 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTT
* *
1756 TC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1799 CTACGCAAGA
Statistics
Matches: 261, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
116 39 0.15
117 92 0.35
118 23 0.09
119 74 0.28
121 33 0.13
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (116 bp):
TCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAA
ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTT
Found at i:1575 original size:59 final size:58
Alignment explanation
Indices: 1403--1798 Score: 600
Period size: 57 Copynumber: 6.8 Consensus size: 58
1393 TAAATAAAAA
*
1403 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* *
1461 TC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTT
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAATTT
* * *
1519 CCAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT
1 TCAAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* *
1578 TC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTTCTTAAAAAATAAATTT
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTT-AAAAATAAATTT
* *
1637 TCAAAAAAAAGATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
1 TC-AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
*
1697 TCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TC-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
*
1756 TC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1799 CTACGCAAGA
Statistics
Matches: 312, Mismatches: 18, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
57 100 0.32
58 34 0.11
59 86 0.28
60 51 0.16
61 15 0.05
62 26 0.08
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (58 bp):
TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
Found at i:1729 original size:178 final size:175
Alignment explanation
Indices: 1406--1796 Score: 660
Period size: 178 Copynumber: 2.2 Consensus size: 175
1396 ATAAAAATCA
* * *
1406 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAGAAATAAATTTTCAAAAAAT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTTCAAAAAAG
* *
1470 ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTCCAAAAAAAGGATTTT
66 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTCCAAAAAAAAGATTTT
*
1535 TGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
131 TGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
1580 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTTCTTAAAAAATAAATTTTCAAAAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCCTT-AAAAATAAATTTTC--AAAA
*
1645 AAGATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAATTTTCAAAAAAAAGA
63 AAGA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTCCAAAAAAAAGA
1709 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
127 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1758 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1797 CCCTACGCAA
Statistics
Matches: 204, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
174 34 0.17
175 7 0.03
176 13 0.06
178 118 0.58
179 32 0.16
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (175 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCCTTAAAAATAAATTTTCAAAAAAG
ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTCCAAAAAAAAGATTTT
TGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:7707 original size:22 final size:20
Alignment explanation
Indices: 7682--7727 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
7672 TAAAAAAACA
7682 ATTTAATTGGAAAAAAAGAAAT
1 ATTTAATT--AAAAAAAGAAAT
*
7704 ATTTCATTAAAAAAAGAAAT
1 ATTTAATTAAAAAAAGAAAT
7724 ATTT
1 ATTT
7728 GAACTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.70
22 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.33
Consensus pattern (20 bp):
ATTTAATTAAAAAAAGAAAT
Found at i:18468 original size:7 final size:7
Alignment explanation
Indices: 18441--18487 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
18431 GCAAGGTTAC
18441 TAAAAA-
1 TAAAAAT
18447 TAGAAAAT
1 TA-AAAAT
18455 TACAAAAT
1 TA-AAAAT
18463 TAAAAAT
1 TAAAAAT
18470 TAAAAA-
1 TAAAAAT
18476 T-AAAAT
1 TAAAAAT
18482 TAAAAA
1 TAAAAA
18488 AATTAAAGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
5 4 0.11
6 4 0.11
7 19 0.53
8 9 0.25
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAAAAT
Found at i:18490 original size:14 final size:14
Alignment explanation
Indices: 18442--18488 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
18432 CAAGGTTACT
18442 AAAAATAGAAAATTA
1 AAAAATA-AAAATTA
*
18457 CAAAATTAAAAATT-
1 -AAAAATAAAAATTA
18471 AAAAAT-AAAATTA
1 AAAAATAAAAATTA
18484 AAAAA
1 AAAAA
18489 ATTAAAGGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.21
13 10 0.36
15 6 0.21
16 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAAATAAAAATTA
Done.