Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168258.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_489, 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: 25140
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:103 original size:21 final size:22
Alignment explanation
Indices: 76--139 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
66 AAATTTCAAA
*
76 AAAAAAAATCTAAAAAATTTTT
1 AAAAAAATTCTAAAAAATTTTT
*
98 AAAAAAATTCT-AAAAACTTTT
1 AAAAAAATTCTAAAAAATTTTT
* *
119 -AAACAATTCAAAAATAATTTT
1 AAAAAAATTCTAAAA-AATTTT
140 AGAAATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.23
21 12 0.34
22 15 0.43
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAAAATTCTAAAAAATTTTT
Found at i:201 original size:19 final size:18
Alignment explanation
Indices: 160--334 Score: 84
Period size: 19 Copynumber: 9.3 Consensus size: 18
150 TTGAAAATTA
* * *
160 AAAAAATTTAAAAAACTTG
1 AAAAAATCT-AAAAATTTT
179 AAAAAATCCTAAAAATTTT
1 AAAAAAT-CTAAAAATTTT
** * *
198 AAAATTTTTTAACAATTTT
1 AAAA-AATCTAAAAATTTT
* *
217 GTAAAAATCTAAAAATAATT
1 -AAAAAATCTAAAAAT-TTT
* *
237 AAAAATTCTAAAATAATTT
1 AAAAAATCTAAAA-ATTTT
*
256 AAAGAAA-CTTAAAATTTTT
1 AAA-AAATC-TAAAAATTTT
*
275 CAAAAAATCTCAAAATTTTT
1 -AAAAAATCT-AAAAATTTT
* * *
295 AGAAAATCAAAAAATTTA
1 AAAAAATCTAAAAATTTT
* *
313 AAAAAAT-TCAAAAGTTT
1 AAAAAATCTAAAAATTTT
330 AAAAA
1 AAAAA
335 GAATGAAGAT
Statistics
Matches: 117, Mismatches: 29, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
17 11 0.09
18 13 0.11
19 65 0.56
20 28 0.24
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAAATCTAAAAATTTT
Found at i:335 original size:9 final size:9
Alignment explanation
Indices: 153--334 Score: 62
Period size: 9 Copynumber: 19.3 Consensus size: 9
143 AATTTTTTTG
*
153 AAAATTAAA
1 AAAATTTAA
162 AAAATTTAA
1 AAAATTTAA
*
171 AAAACTTGAA
1 AAAA-TTTAA
*
181 AAAATCCTAA
1 AAAAT-TTAA
*
191 AAATTTTAA
1 AAAATTTAA
**
200 AATTTTTTAA
1 AA-AATTTAA
* * *
210 CAATTTTGTA
1 AAAATTT-AA
*
220 AAAATCTAA
1 AAAATTTAA
*
229 AAATAATT-A
1 AAA-ATTTAA
238 AAAATTCTAA
1 AAAATT-TAA
248 AATAATTTAA
1 AA-AATTTAA
*
258 AGAAACTTAA
1 A-AAATTTAA
**
268 AATTTTTCAA
1 AAAATTT-AA
*
278 AAAATCTCAA
1 AAAAT-TTAA
** *
288 AATTTTTAG
1 AAAATTTAA
*
297 AAAA-TCAA
1 AAAATTTAA
305 AAAATTTAA
1 AAAATTTAA
* *
314 AAAAATTCA
1 AAAATTTAA
*
323 AAAGTTTAA
1 AAAATTTAA
332 AAA
1 AAA
335 GAATGAAGAT
Statistics
Matches: 123, Mismatches: 38, Indels: 24
0.66 0.21 0.13
Matches are distributed among these distances:
8 8 0.07
9 57 0.46
10 52 0.42
11 6 0.05
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:453 original size:20 final size:19
Alignment explanation
Indices: 424--488 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
414 ATATAATTTT
*
424 TTTTTGAAAAGATATAAAAA
1 TTTTT-AAAAAATATAAAAA
*
444 TTTTTAAAAAATTGTAAAAAA
1 TTTTTAAAAAA-TAT-AAAAA
* * *
465 GTTTTAAAAATTCTAAAAA
1 TTTTTAAAAAATATAAAAA
484 TTTTT
1 TTTTT
489 CATATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
19 14 0.38
20 9 0.24
21 14 0.38
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (19 bp):
TTTTTAAAAAATATAAAAA
Found at i:455 original size:11 final size:10
Alignment explanation
Indices: 438--487 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
428 TGAAAAGATA
*
438 TAAAAATTTT
1 TAAAAAATTT
*
448 TAAAAAATTG
1 TAAAAAATTT
458 TAAAAAAGTTT
1 TAAAAAA-TTT
*
469 T-AAAAATTC
1 TAAAAAATTT
478 T-AAAAATTT
1 TAAAAAATTT
487 T
1 T
488 TCATATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 20 0.59
11 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:548 original size:33 final size:33
Alignment explanation
Indices: 484--545 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
474 ATTCTAAAAA
*
484 TTTTTCATATTTTTTGAATCTTACAATTTTAAT
1 TTTTTCATATTTTTTCAATCTTACAATTTTAAT
*
517 TTTTTACATA-TTTTTCAAT-TTATAATTTT
1 TTTTT-CATATTTTTTCAATCTTACAATTTT
546 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 9 0.35
33 13 0.50
34 4 0.15
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (33 bp):
TTTTTCATATTTTTTCAATCTTACAATTTTAAT
Found at i:555 original size:26 final size:25
Alignment explanation
Indices: 507--557 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
497 TTGAATCTTA
* * *
507 CAATTTTAATTTTTTACATATTTTT
1 CAATTTTAATTTTTAAAAAATTTTT
532 CAATTTATAATTTTTAAAAAATTTTT
1 CAATTT-TAATTTTTAAAAAATTTTT
558 TTGGATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (25 bp):
CAATTTTAATTTTTAAAAAATTTTT
Found at i:804 original size:18 final size:18
Alignment explanation
Indices: 781--825 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
771 AGAAAATCTA
781 ATTTTTATTAAAATTTTT
1 ATTTTTATTAAAATTTTT
*
799 ATTTTTA--AAATTTTTT
1 ATTTTTATTAAAATTTTT
*
815 ATATTTATTAA
1 ATTTTTATTAA
826 TTTTTTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 14 0.61
18 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTATTAAAATTTTT
Found at i:827 original size:17 final size:17
Alignment explanation
Indices: 784--832 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
774 AAATCTAATT
* *
784 TTTATTAAAATTTTTATT
1 TTTATT-AATTTTTTATA
*
802 TTTA-AAATTTTTTATA
1 TTTATTAATTTTTTATA
818 TTTATTAATTTTTTA
1 TTTATTAATTTTTTA
833 GAATTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 13 0.50
17 9 0.35
18 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTAATTTTTTATA
Found at i:874 original size:9 final size:9
Alignment explanation
Indices: 788--855 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
778 CTAATTTTTA
788 TTAAAATTT
1 TTAAAATTT
797 TT---ATTT
1 TTAAAATTT
803 TTAAAATTT
1 TTAAAATTT
* *
812 TTTATATTT
1 TTAAAATTT
*
821 ATT-AATTTT
1 -TTAAAATTT
*
830 TTAGAATTT
1 TTAAAATTT
839 TTAAAATTT
1 TTAAAATTT
*
848 TGAAAATT
1 TTAAAATT
856 ATCCTAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
6 6 0.13
8 2 0.04
9 36 0.78
10 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (9 bp):
TTAAAATTT
Found at i:1124 original size:29 final size:30
Alignment explanation
Indices: 1092--1159 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
1082 ATTTGTTTTG
1092 AATTTTTTAAAATTT-TAAGAAAAATTT-AA
1 AATTTTTTAAAATTTATAA-AAAAATTTAAA
**
1121 AATTTTTTAGTATTTATAAAAAAATTTAAA
1 AATTTTTTAAAATTTATAAAAAAATTTAAA
1151 AATTTTTTA
1 AATTTTTTA
1160 GAAACAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
AATTTTTTAAAATTTATAAAAAAATTTAAA
Found at i:1231 original size:18 final size:18
Alignment explanation
Indices: 1179--1231 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1169 TTAGTTTTTT
*
1179 TTTTTTTAGGAAATTTAAA
1 TTTTTTTA-AAAATTTAAA
*
1198 -ATTTTTAAAAATTTTAAA
1 TTTTTTTAAAAA-TTTAAA
1216 TTTTTTTAAAAATTTA
1 TTTTTTTAAAAATTTA
1232 TTTTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.10
18 16 0.55
19 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTTTTTAAAAATTTAAA
Found at i:10597 original size:4 final size:4
Alignment explanation
Indices: 10590--10622 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
10580 AGGAAGAAGG
*
10590 AAGA AAGA AAGA AAGA AATA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
10623 GTGTTTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:10662 original size:25 final size:25
Alignment explanation
Indices: 10634--10684 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
10624 TGTTTGTAGT
10634 AGTGACTTTAGTGATTATAGTTTCC
1 AGTGACTTTAGTGATTATAGTTTCC
10659 AGTGACTTTAGTGATTATAGTTTCC
1 AGTGACTTTAGTGATTATAGTTTCC
10684 A
1 A
10685 AAACATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (25 bp):
AGTGACTTTAGTGATTATAGTTTCC
Done.