Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168277.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_505, 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: 24618
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Found at i:3818 original size:3 final size:3
Alignment explanation
Indices: 3805--3835 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
3795 TAAATAGCTC
3805 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
3836 TTTTGTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:4908 original size:29 final size:28
Alignment explanation
Indices: 4884--4945 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
4874 TTTTTATTTT
4884 TATATA-AAATTTTACTTTTAATTTATA
1 TATATATAAATTTTACTTTTAATTTATA
* * * *
4911 TATATATGACTTTTATTTTTAATTTTTA
1 TATATATAAATTTTACTTTTAATTTATA
4939 TATATAT
1 TATATAT
4946 GTGAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (28 bp):
TATATATAAATTTTACTTTTAATTTATA
Found at i:4931 original size:28 final size:28
Alignment explanation
Indices: 4893--4946 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
4883 TTATATAAAA
4893 TTTTACTTTTAATTTATATATATATGAC
1 TTTTACTTTTAATTTATATATATATGAC
* *
4921 TTTTATTTTTAATTTTTATATATATG
1 TTTTACTTTTAATTTATATATATATG
4947 TGAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTACTTTTAATTTATATATATATGAC
Found at i:6415 original size:51 final size:52
Alignment explanation
Indices: 6313--6467 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 52
6303 ATAACCATAT
* * * * * *
6313 AAACTTGCCCATTAAGAATCC-CTCTCCTCTTAGAATCCTTCTCCTGTAAGTC
1 AAACTTACCTATTAAGAATCCTCT-TTCTCTTAGAATTCTTCTCTTGCAAGTC
* * * *
6365 AAACTTGCCTATTAAGAATTCT-TTTTTTTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTCTTGCAAGTC
* *
6416 AAACTTACCTATTAAGAATCCTCTTTCTCTTATAATTCTTCTTTTGCAAGTC
1 AAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTCTTGCAAGTC
6468 TTCTTGTCCA
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 42 0.48
52 45 0.52
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
AAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTCTTGCAAGTC
Found at i:6508 original size:11 final size:11
Alignment explanation
Indices: 6492--6531 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
6482 GCAATATCTG
6492 ACAAATCCCAA
1 ACAAATCCCAA
* *
6503 ACAAATCTCTA
1 ACAAATCCCAA
6514 ACAAATCCCAA
1 ACAAATCCCAA
*
6525 ATAAATC
1 ACAAATC
6532 TCTTATGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (11 bp):
ACAAATCCCAA
Found at i:6517 original size:22 final size:22
Alignment explanation
Indices: 6492--6534 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6482 GCAATATCTG
6492 ACAAATCCCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
*
6514 ACAAATCCCAAATAAATCTCT
1 ACAAATCCCAAACAAATCTCT
6535 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:6791 original size:23 final size:25
Alignment explanation
Indices: 6752--6816 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
6742 GAACTTGTTT
**
6752 CTTCCCATGTCTCAAACC-AT-GCA
1 CTTCCCACATCTCAAACCTATAGCA
* * *
6775 CTTCCCACATCTTAAACCTTTAGCT
1 CTTCCCACATCTCAAACCTATAGCA
6800 CTTCCCACATCTCAAAC
1 CTTCCCACATCTCAAAC
6817 TTTCAGCTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 15 0.44
24 1 0.03
25 18 0.53
ACGTcount: A:0.26, C:0.40, G:0.05, T:0.29
Consensus pattern (25 bp):
CTTCCCACATCTCAAACCTATAGCA
Found at i:6831 original size:24 final size:25
Alignment explanation
Indices: 6775--6851 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
6765 AAACCATGCA
*
6775 CTTCCCACATCTTAAACCTTTAGCT
1 CTTCCCACATCTCAAACCTTTAGCT
6800 CTTCCCACATCTCAAA-CTTTCAGCT
1 CTTCCCACATCTCAAACCTTT-AGCT
* * *
6825 CTT-CCACGTCTCGAACCTTTGGCT
1 CTTCCCACATCTCAAACCTTTAGCT
6849 CTT
1 CTT
6852 TTCACATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 20 0.43
25 26 0.57
ACGTcount: A:0.19, C:0.38, G:0.08, T:0.35
Consensus pattern (25 bp):
CTTCCCACATCTCAAACCTTTAGCT
Found at i:6881 original size:25 final size:25
Alignment explanation
Indices: 6789--6900 Score: 73
Period size: 25 Copynumber: 4.5 Consensus size: 25
6779 CCACATCTTA
* * * * *
6789 AACCTTTAGCTCTTCCCACATCTCA
1 AACCTTCAACTCTTCTCACATTTCG
* * * *
6814 AACTTTCAGCTCTTC-CACGTCTCG
1 AACCTTCAACTCTTCTCACATTTCG
*** * *
6838 AACCTTTGGCTCTTTTCACATTTTG
1 AACCTTCAACTCTTCTCACATTTCG
*
6863 AATCTTCAACTCTTCTCACATTTCG
1 AACCTTCAACTCTTCTCACATTTCG
*
6888 AACCTTCAGCTCT
1 AACCTTCAACTCT
6901 GATACCACTT
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
24 18 0.27
25 49 0.73
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (25 bp):
AACCTTCAACTCTTCTCACATTTCG
Found at i:7486 original size:52 final size:51
Alignment explanation
Indices: 7402--7548 Score: 170
Period size: 52 Copynumber: 2.8 Consensus size: 51
7392 TATAACCATA
* * * * *
7402 CAAACTTGCCCATTAAAAAT-TCTTCTCCTTTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTT-T-CTTTTAGAATTCTTCTCCTGCAAAT
* *
7454 TAAACTTGCCTATTAAGAATCCCTTTCTTTTTAGAATTCTTCTCTTGCAAAT
1 CAAACTTGCCTATTAAGAATCCCTTTC-TTTTAGAATTCTTCTCCTGCAAAT
* *
7506 CAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCT
1 CAAACTTGCCTATTAAGAATCC-CTTTCTTTTAGAATTCTTCT
7549 TTTGCAAGTC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 1 0.01
52 73 0.89
53 8 0.10
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTTCTTTTAGAATTCTTCTCCTGCAAAT
Found at i:13545 original size:13 final size:13
Alignment explanation
Indices: 13527--13573 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
13517 TTTATATAAA
13527 TTTTATTTTTAAT
1 TTTTATTTTTAAT
* *
13540 TTTTATACATATAAT
1 TTTTAT--TTTTAAT
13555 TTTTATTTTTAAT
1 TTTTATTTTTAAT
13568 TTTTAT
1 TTTTAT
13574 ATATATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATTTTTAAT
Found at i:13553 original size:28 final size:28
Alignment explanation
Indices: 13520--13579 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
13510 TGTTACTTTT
13520 ATATAAATTTTATTTTTAATTTTTATAC
1 ATATAAATTTTATTTTTAATTTTTATAC
* *
13548 ATATAATTTTTATTTTTAATTTTTATAT
1 ATATAAATTTTATTTTTAATTTTTATAC
13576 ATAT
1 ATAT
13580 GTGAATTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
ATATAAATTTTATTTTTAATTTTTATAC
Found at i:15368 original size:15 final size:16
Alignment explanation
Indices: 15348--15380 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
15338 AAGGTTTAAT
*
15348 TTTTTTTTTATT-TTG
1 TTTTTTTATATTATTG
15363 TTTTTTTATATTATTG
1 TTTTTTTATATTATTG
15379 TT
1 TT
15381 GAAAATATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTTTATATTATTG
Found at i:15601 original size:28 final size:28
Alignment explanation
Indices: 15514--15602 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
15504 TATTTTATTT
* *
15514 TATTTCTAAAATTTTCACCATTTGGGTC
1 TATTTCTAAAATTTTCACTATTTAGGTC
* * * * *
15542 TATTT-AAAAATTTTC-TTTTTATAAGTTT
1 TATTTCTAAAATTTTCACTATT-T-AGGTC
15570 TATTTCTAAAATTTTCACTATTTAGGTC
1 TATTTCTAAAATTTTCACTATTTAGGTC
15598 TATTT
1 TATTT
15603 AGAAAAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
26 2 0.04
27 10 0.22
28 20 0.44
29 10 0.22
30 3 0.07
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (28 bp):
TATTTCTAAAATTTTCACTATTTAGGTC
Found at i:16143 original size:25 final size:27
Alignment explanation
Indices: 16079--16143 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 27
16069 AAATTTAGAA
*
16079 AAAAATTTC-TCACTTAAGAATTTTAT
1 AAAAATTTCATCATTTAAGAATTTTAT
* *
16105 AAAAATTT-ACCATTTGA-AATTTT-T
1 AAAAATTTCATCATTTAAGAATTTTAT
*
16129 TAAAATTTCATCATT
1 AAAAATTTCATCATT
16144 GGATAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.25
25 11 0.34
26 13 0.41
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (27 bp):
AAAAATTTCATCATTTAAGAATTTTAT
Found at i:16268 original size:25 final size:26
Alignment explanation
Indices: 16218--16268 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
16208 AAAATTTAAT
* *
16218 AATGCAAAAATACTTAAAAAATAAAA
1 AATGCAAAAATACTCAAAAAAGAAAA
16244 AATG-AAAAATA-TCAAAACAAGAAAA
1 AATGCAAAAATACTCAAAA-AAGAAAA
16269 CTGCTCGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.16
Consensus pattern (26 bp):
AATGCAAAAATACTCAAAAAAGAAAA
Found at i:17306 original size:43 final size:42
Alignment explanation
Indices: 17190--17572 Score: 234
Period size: 43 Copynumber: 9.1 Consensus size: 42
17180 ACATTAAAAA
* * * *
17190 CTCCTCTAAACAAAGGCTTCACAACTTTTGAGAAATAAATAAAG
1 CTCCTCTAAACAGAGG-TTAACAAC-TTTGAAAAATAAATAAGG
** * * * *
17234 CT-CTAGAAGCAGAGGCTCAACCACTTTTGAAACATAAATAAGG
1 CTCCTCTAAACAGAGG-TTAACAAC-TTTGAAAAATAAATAAGG
*
17277 CTCCTCTAAATAGAGGTTCAACAACTTTGAAAAATAAATAAGG
1 CTCCTCTAAACAGAGGTT-AACAACTTTGAAAAATAAATAAGG
* *
17320 --CCTCT------A--TTTACAACTTTAAAAAATAAATAAGG
1 CTCCTCTAAACAGAGGTTAACAACTTTGAAAAATAAATAAGG
* * * *
17352 CTCATTTAAACAAAGGCTT-ACGACTTTGAAAAATAAATAAGG
1 CTCCTCTAAACAGAGG-TTAACAACTTTGAAAAATAAATAAGG
* * * * * ** *
17394 CTCTTTTAAACAAAGACTCAATGACTTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAGAG-GTTAACAAC-TTTGAAAAATAAATAAGG
* * * * *
17438 CTCCTATAAATAGAGGCTTAATAATTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAGAGG-TTAACAACTTTGAAAAATAAATAAGG
* * * * *
17481 -TCTTCTAAACAGATGCTCAACTACCTTTGAAAAATAAATAAAG
1 CTCCTCTAAACAGA-GGTTAAC-AACTTTGAAAAATAAATAAGG
* *
17524 CTCCTCTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAGAGG-TTAACAACTTTGAAAAATAAATAAGG
17567 CTCCTC
1 CTCCTC
17573 GACAATCATA
Statistics
Matches: 265, Mismatches: 53, Indels: 43
0.73 0.15 0.12
Matches are distributed among these distances:
32 22 0.08
33 2 0.01
34 3 0.01
35 1 0.00
40 1 0.00
41 5 0.02
42 49 0.18
43 118 0.45
44 64 0.24
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (42 bp):
CTCCTCTAAACAGAGGTTAACAACTTTGAAAAATAAATAAGG
Found at i:17334 original size:32 final size:30
Alignment explanation
Indices: 17297--17359 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 30
17287 TAGAGGTTCA
*
17297 ACAACTTTGAAAAATAAATAAGGCCTCTATTT
1 ACAACTTTAAAAAATAAATAAGG-CTC-ATTT
17329 ACAACTTTAAAAAATAAATAAGGCTCATTT
1 ACAACTTTAAAAAATAAATAAGGCTCATTT
17359 A
1 A
17360 AACAAAGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 5 0.17
31 3 0.10
32 22 0.73
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (30 bp):
ACAACTTTAAAAAATAAATAAGGCTCATTT
Found at i:17455 original size:86 final size:87
Alignment explanation
Indices: 17333--17569 Score: 293
Period size: 86 Copynumber: 2.7 Consensus size: 87
17323 CTATTTACAA
* * * * *
17333 CTTTAAAAAATAAATAAGGCTCATTTAAACAAAGGCTT-ACGACTTTGAAAAATAAATAAGGCTC
1 CTTTGAAAAATAAATAAGGCTCCTATAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
*
17397 TTTTAAACA-AAGACTCAA-TGAC
66 TTCTAAACAGAAG-CTCAACT-AC
* * * * * *
17419 TTTTGAAAAGTAAATAAGGCTCCTATAAATAGAGGCTTAATAATTTTGAAAAGTAAATAAGG-TC
1 CTTTGAAAAATAAATAAGGCTCCTATAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
*
17483 TTCTAAACAGATGCTCAACTAC
66 TTCTAAACAGAAGCTCAACTAC
* *
17505 CTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
1 CTTTGAAAAATAAATAAGGCTCCTATAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
17570 CTCGACAATC
Statistics
Matches: 126, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
86 102 0.81
87 24 0.19
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (87 bp):
CTTTGAAAAATAAATAAGGCTCCTATAAACAAAGGCTTAACAACTTTGAAAAGTAAATAAGGCTC
TTCTAAACAGAAGCTCAACTAC
Found at i:20421 original size:58 final size:57
Alignment explanation
Indices: 20200--20478 Score: 294
Period size: 58 Copynumber: 4.8 Consensus size: 57
20190 TGCTTTTGTA
* * * *
20200 CAAGGAAAATTGATACTTTCAACTTTTCCCCAAAATGTTTTTTTG-AAACTTTAATTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTAGAAAAC-TTATTTT
* * * *
20257 CGAA-GAAAATTGATACTTTCAACTTTTCCTAAAAAAAAAAAACCCTTTTCAGAAAA-TTATTTT
1 C-AAGGAAAATTGATACTTTCAACTTTTCCT-----CAAAATA--TTTTTTAGAAAACTTATTTT
* * * * * *
20320 CAAAGAAAATTAACACTTTCAATTTTTCCCCAAAATGTTTTTTAGAAAACTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTAGAAAACTTATTTT
*
20377 CAAGGAAAATTAATACTTTCAACTTTTCCTCAGAAATATTTTTTAGAAAACTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCA-AAATATTTTTTAGAAAACTTATTTT
*
20435 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAATATTTTTT
20479 TTGGAATTTT
Statistics
Matches: 185, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
56 10 0.05
57 61 0.33
58 70 0.38
59 1 0.01
62 6 0.03
63 29 0.16
64 5 0.03
65 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (57 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTAGAAAACTTATTTT
Found at i:20515 original size:5 final size:5
Alignment explanation
Indices: 20505--20573 Score: 79
Period size: 5 Copynumber: 13.8 Consensus size: 5
20495 AGAAAATCAA
* **
20505 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAA AAAAT AAAAT AAGGT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT -AAAAT
20557 AAAAT -AAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
20574 GAATACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 8 0.15
5 40 0.73
6 7 0.13
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20539 original size:16 final size:16
Alignment explanation
Indices: 20498--20568 Score: 92
Period size: 16 Copynumber: 4.4 Consensus size: 16
20488 TATTTAAAGA
20498 AAATCAAAAAATAAAAT
1 AAAT-AAAAAATAAAAT
*
20515 AAA-ATAAAATAAAAT
1 AAATAAAAAATAAAAT
20530 AAATAAAAAATAAAAT
1 AAATAAAAAATAAAAT
*
20546 AAGGT-AAAAATAAAAT
1 AA-ATAAAAAATAAAAT
20562 AAATAAA
1 AAATAAA
20569 TAAAAGAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
15 15 0.32
16 28 0.60
17 4 0.09
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.18
Consensus pattern (16 bp):
AAATAAAAAATAAAAT
Found at i:20556 original size:32 final size:31
Alignment explanation
Indices: 20498--20568 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 31
20488 TATTTAAAGA
20498 AAATCAAAAAATAAAATAAAATAAAATAAAAT
1 AAAT-AAAAAATAAAATAAAATAAAATAAAAT
**
20530 AAATAAAAAATAAAATAAGGTAAAAATAAAAT
1 AAATAAAAAATAAAATAAAAT-AAAATAAAAT
20562 AAATAAA
1 AAATAAA
20569 TAAAAGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 15 0.42
32 21 0.58
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.18
Consensus pattern (31 bp):
AAATAAAAAATAAAATAAAATAAAATAAAAT
Found at i:20578 original size:21 final size:20
Alignment explanation
Indices: 20497--20572 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 20
20487 TTATTTAAAG
* *
20497 AAAATCAAA-AAATAAA-AT
1 AAAATAAAATAAATAAATAA
20515 AAAATAAAATAAAATAAATAA
1 AAAATAAAAT-AAATAAATAA
*
20536 AAAATAAAATAAGGTAAA-AA
1 AAAATAAAATAA-ATAAATAA
20556 TAAAAT-AAATAAATAAA
1 -AAAATAAAATAAATAAA
20573 AGAATACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.16
19 4 0.08
20 17 0.35
21 20 0.41
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAATAAATAA
Found at i:20612 original size:3 final size:3
Alignment explanation
Indices: 20604--20637 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20594 CTAATCAATA
20604 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20638 ATAGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:21409 original size:21 final size:20
Alignment explanation
Indices: 21383--21450 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 20
21373 AGCCAAAAAA
21383 AAATAAAAATAGATAAATAAT
1 AAATAAAAATAGAT-AATAAT
* * *
21404 AAATAAATATATATACTAAT
1 AAATAAAAATAGATAATAAT
*
21424 AGATAAATAATAGATAATAAT
1 AAATAAA-AATAGATAATAAT
*
21445 TAATAA
1 AAATAA
21451 TAAAAATTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 11 0.30
21 26 0.70
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (20 bp):
AAATAAAAATAGATAATAAT
Found at i:21444 original size:10 final size:10
Alignment explanation
Indices: 21385--21525 Score: 60
Period size: 10 Copynumber: 13.9 Consensus size: 10
21375 CCAAAAAAAA
*
21385 ATAAAAATAG
1 ATAATAATAG
*
21395 ATAAATAATAA
1 AT-AATAATAG
*
21406 ATAA-ATATAT
1 ATAATA-ATAG
*
21416 ATACTAATAG
1 ATAATAATAG
21426 ATAAATAATAG
1 AT-AATAATAG
21437 ATAATAATTA-
1 ATAATAA-TAG
*
21447 ATAATAA-AA
1 ATAATAATAG
* *
21456 AT-TTATATAC
1 ATAATA-ATAG
*
21466 ATTAATAGATAA
1 A-TAATA-ATAG
*
21478 ATAATAATAT
1 ATAATAATAG
*
21488 ATATTAATAG
1 ATAATAATAG
*
21498 ATAA-AAGTAT
1 ATAATAA-TAG
*
21508 ATATTAATA-
1 ATAATAATAG
21517 ATAATAATA
1 ATAATAATA
21526 ATAGCAATAA
Statistics
Matches: 101, Mismatches: 18, Indels: 25
0.70 0.12 0.17
Matches are distributed among these distances:
8 3 0.03
9 14 0.14
10 50 0.50
11 28 0.28
12 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
ATAATAATAG
Found at i:21463 original size:48 final size:48
Alignment explanation
Indices: 21398--21529 Score: 150
Period size: 48 Copynumber: 2.8 Consensus size: 48
21388 AAAATAGATA
*
21398 AATAATAAATAA-ATATATATACTAATAGATAAATAATAGATA-ATAATT
1 AATAATAAA-AATATATATATAATAATAGATAAATAATAGATATAT-ATT
* * *
21446 AATAATAAAAATTTATATACATTAATAGATAAATAATA-ATATATATT
1 AATAATAAAAATATATATATAATAATAGATAAATAATAGATATATATT
*
21493 AATAGATAAAAGTATATAT-TAATAATA-AT-AATAATAG
1 AATA-ATAAAAATATATATATAATAATAGATAAATAATAG
21530 CAATAAATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
45 7 0.10
46 2 0.03
47 18 0.25
48 46 0.63
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (48 bp):
AATAATAAAAATATATATATAATAATAGATAAATAATAGATATATATT
Found at i:21544 original size:42 final size:44
Alignment explanation
Indices: 21383--21544 Score: 102
Period size: 48 Copynumber: 3.6 Consensus size: 44
21373 AGCCAAAAAA
* * * * *
21383 AAATAAAAATAGATAAATAATAAATAAATA-TATATACTAATAGAT
1 AAATAATAATACATATA-AATAAATAAA-AGTATACATTAATAGAT
* *
21428 AAATAATAGATA-ATAATTAAT-AATAAAAATTTATATACATTAATAGAT
1 AAATAATA-ATACAT-ATAAATAAAT-AAAA---GTATACATTAATAGAT
* * * *
21476 AAATAATAATATATATTAATAGATAAAAGTATATATTAATA-AT
1 AAATAATAATACATATAAATAAATAAAAGTATACATTAATAGAT
21519 -AATAATAATAGCA-ATAAATAAATAAA
1 AAATAATAATA-CATATAAATAAATAAA
21545 TAAGATACAA
Statistics
Matches: 96, Mismatches: 11, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
42 21 0.22
43 3 0.03
44 15 0.16
45 15 0.16
46 4 0.04
47 13 0.14
48 25 0.26
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (44 bp):
AAATAATAATACATATAAATAAATAAAAGTATACATTAATAGAT
Done.