Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168097.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_343, 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: 32981
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1721 original size:1 final size:1
Alignment explanation
Indices: 1715--1740 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1705 ACTTTCTTAG
1715 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1741 GTCTGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4269 original size:14 final size:14
Alignment explanation
Indices: 4247--4281 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4237 GTTAATTGGT
*
4247 TATGTTTTCTCACA
1 TATGCTTTCTCACA
4261 TATGCTTTCTCACA
1 TATGCTTTCTCACA
4275 TATGCTT
1 TATGCTT
4282 CCTTGGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (14 bp):
TATGCTTTCTCACA
Found at i:6075 original size:21 final size:21
Alignment explanation
Indices: 6035--6075 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6025 TTTAGTTAAC
* *
6035 ATATACAAGGAATAGCATAAT
1 ATATACAAGGAACAACATAAT
*
6056 ATATACAAGGAACAATATAA
1 ATATACAAGGAACAACATAA
6076 AAGGTTAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (21 bp):
ATATACAAGGAACAACATAAT
Found at i:7418 original size:20 final size:20
Alignment explanation
Indices: 7393--7704 Score: 194
Period size: 20 Copynumber: 15.4 Consensus size: 20
7383 ACAAATAAAT
**
7393 ATATATAATCACACAAATAA
1 ATATATAATCATGCAAATAA
*
7413 CA-ATATAAATCATGCAATTAA
1 -ATATAT-AATCATGCAAATAA
*
7434 ATATATAATCATGCAATTAA
1 ATATATAATCATGCAAATAA
7454 CA-ATATAAATCATGCAAATAA
1 -ATATAT-AATCATGCAAATAA
*
7475 ATATATAATCATGCAATTAA
1 ATATATAATCATGCAAATAA
* * *
7495 CA-ACATAAAACATGCAATTAA
1 -ATATAT-AATCATGCAAATAA
* *
7516 ATATATAATCAAGCAATTAA
1 ATATATAATCATGCAAATAA
* *
7536 CA-ATATAAAGCATGCAATTAA
1 -ATATAT-AATCATGCAAATAA
* **
7557 ATATATTATCATGCAGTTAA
1 ATATATAATCATGCAAATAA
* *
7577 CGATATA-AAACATACAAATAA
1 --ATATATAATCATGCAAATAA
*
7598 ATATAT--T-ATGC-AATTA
1 ATATATAATCATGCAAATAA
*
7614 ATGATATAAAACATGCAAATAA
1 AT-ATAT-AATCATGCAAATAA
* *
7636 ATATATTATCATGCAATTAA
1 ATATATAATCATGCAAATAA
* * *
7656 GTATATAATAATACAAAT-A
1 ATATATAATCATGCAAATAA
* *
7675 ATAATATAAATCATACAATTAA
1 AT-ATAT-AATCATGCAAATAA
7697 ATATATAA
1 ATATATAA
7705 AAATAATCAA
Statistics
Matches: 232, Mismatches: 36, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.03
17 7 0.03
19 7 0.03
20 99 0.43
21 99 0.43
22 14 0.06
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (20 bp):
ATATATAATCATGCAAATAA
Found at i:7455 original size:41 final size:41
Alignment explanation
Indices: 7384--7706 Score: 352
Period size: 41 Copynumber: 7.9 Consensus size: 41
7374 TACAATCACA
** * *
7384 CAAATAAATATATATAATCACACAAATAACAATATAAATCATG
1 CAAAT-AA-ATATATAATCATGCAATTAACAATATAAAACATG
* *
7427 CAATTAAATATATAATCATGCAATTAACAATATAAATCATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
*
7468 CAAATAAATATATAATCATGCAATTAACAACATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * *
7509 CAATTAAATATATAATCAAGCAATTAACAATATAAAGCATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * * * *
7550 CAATTAAATATATTATCATGCAGTTAACGATATAAAACATA
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
**
7591 CAAATAAATATAT--T-ATGCAATTAATGATATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* ** * *
7629 CAAATAAATATATTATCATGCAATTAAGTATATAATA-ATA
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
*
7669 CAAAT-AATAATATAAATCATACAATTAA-ATATATAAAA
1 CAAATAAAT-ATAT-AATCATGCAATTAACA-ATATAAAA
7707 ATAATCAAGC
Statistics
Matches: 245, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
38 34 0.14
39 4 0.02
40 12 0.05
41 189 0.77
42 2 0.01
43 4 0.02
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.29
Consensus pattern (41 bp):
CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
Found at i:7754 original size:20 final size:20
Alignment explanation
Indices: 7729--7821 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
7719 CTATACAAAT
*
7729 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
*
7749 AAATAAATTAATAATCATGT
1 AAATAAATTAATAATCATGC
** * **
7769 AAGCATATTAATAGCCATGC
1 AAATAAATTAATAATCATGC
* **
7789 AAATATATTAATAAATCACAC
1 AAATAAATTAAT-AATCATGC
*
7810 AAATATATTAAT
1 AAATAAATTAAT
7822 CATATAAATA
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
20 42 0.72
21 16 0.28
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:7861 original size:16 final size:18
Alignment explanation
Indices: 7842--7882 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
7832 AACTATTAGA
7842 CAAATAA-ATTA-TCATG
1 CAAATAATATTATTCATG
7858 CAAATATAATATTATTCATG
1 C-AA-ATAATATTATTCATG
7878 CAAAT
1 CAAAT
7883 TCATGCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.05
17 2 0.10
18 6 0.29
19 6 0.29
20 6 0.29
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (18 bp):
CAAATAATATTATTCATG
Found at i:7863 original size:32 final size:33
Alignment explanation
Indices: 7808--7871 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
7798 AATAAATCAC
* *
7808 ACAAATATATTAATCATATAAATA-AACTATTAG
1 ACAAATAAATTAATCATACAAATATAA-TATTAG
*
7841 ACAAATAAATT-ATCATGCAAATATAATATTA
1 ACAAATAAATTAATCATACAAATATAATATTA
7872 TTCATGCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (33 bp):
ACAAATAAATTAATCATACAAATATAATATTAG
Found at i:7878 original size:20 final size:18
Alignment explanation
Indices: 7845--7882 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
7835 TATTAGACAA
7845 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
7863 ATAATATTATTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
7883 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Found at i:12941 original size:20 final size:19
Alignment explanation
Indices: 12911--13073 Score: 123
Period size: 19 Copynumber: 8.3 Consensus size: 19
12901 TTTAAAAAAT
12911 TTTTTAGAAATCTTTTAGAAA
1 TTTTTA-AAAT-TTTTAGAAA
*
12932 TTTTTAAAATTTTTTGAAA
1 TTTTTAAAATTTTTAGAAA
* *
12951 TTTTTACAATTTTTTGAAA
1 TTTTTAAAATTTTTAGAAA
* *
12970 TTTTTACAATTTTTTTTGAAA
1 TTTTTA-AA-ATTTTTAGAAA
* *
12991 TTTTAAAAATTATTT--AAT
1 TTTTTAAAATT-TTTAGAAA
* *
13009 TTTTTATAATTTTTAAAAA
1 TTTTTAAAATTTTTAGAAA
* * *
13028 TTTTTAGAAACTTTCAAAAA
1 TTTTTA-AAATTTTTAGAAA
*
13048 ATTTTAAAATCTTTTAGAAA
1 TTTTTAAAAT-TTTTAGAAA
13068 CTTTTT
1 -TTTTT
13074 TTTCATATTG
Statistics
Matches: 116, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
17 3 0.03
18 11 0.09
19 45 0.39
20 32 0.28
21 25 0.22
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTTAAAATTTTTAGAAA
Found at i:12946 original size:11 final size:10
Alignment explanation
Indices: 12906--13032 Score: 86
Period size: 10 Copynumber: 12.9 Consensus size: 10
12896 TTTTTTTTAA
12906 AAAATTTTTT
1 AAAATTTTTT
*
12916 AGAAATCTTTT
1 A-AAATTTTTT
12927 AGAAA-TTTTT
1 A-AAATTTTTT
12937 AAAATTTTTT
1 AAAATTTTTT
*
12947 GAAA-TTTTT
1 AAAATTTTTT
*
12956 ACAATTTTTT
1 AAAATTTTTT
*
12966 GAAA-TTTTT
1 AAAATTTTTT
*
12975 ACAATTTTTTTT
1 A-AA-ATTTTTT
* *
12987 GAAA-TTTTA
1 AAAATTTTTT
*
12996 AAAATTATTT
1 AAAATTTTTT
13006 --AATTTTTT
1 AAAATTTTTT
* *
13014 ATAATTTTTA
1 AAAATTTTTT
13024 AAAATTTTT
1 AAAATTTTT
13033 AGAAACTTTC
Statistics
Matches: 90, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
8 7 0.08
9 22 0.24
10 41 0.46
11 15 0.17
12 5 0.06
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:13033 original size:10 final size:10
Alignment explanation
Indices: 12899--13056 Score: 76
Period size: 10 Copynumber: 15.9 Consensus size: 10
12889 ATTTAAATTT
12899 TTTTTAAAAAA
1 TTTTT-AAAAA
*
12910 TTTTTTAGAAA
1 -TTTTTAAAAA
*
12921 TCTTTTAGAAA
1 T-TTTTAAAAA
12932 TTTTT-AAAA
1 TTTTTAAAAA
**
12941 TTTTTTGAAA
1 TTTTTAAAAA
*
12951 TTTTT-ACAA
1 TTTTTAAAAA
**
12960 TTTTTTGAAA
1 TTTTTAAAAA
**
12970 TTTTTACAATT
1 TTTTTA-AAAA
**
12981 TTTTTTGAAA
1 TTTTTAAAAA
12991 -TTTTAAAAA
1 TTTTTAAAAA
13000 TTATTT---AA
1 TT-TTTAAAAA
* *
13008 TTTTTTATAA
1 TTTTTAAAAA
13018 TTTTTAAAAA
1 TTTTTAAAAA
*
13028 TTTTTAGAAA
1 TTTTTAAAAA
* *
13038 CTTTCAAAAA
1 TTTTTAAAAA
*
13048 ATTTTAAAA
1 TTTTTAAAA
13057 TCTTTTAGAA
Statistics
Matches: 112, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
7 3 0.03
8 4 0.04
9 22 0.20
10 55 0.49
11 23 0.21
12 5 0.04
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:15153 original size:29 final size:27
Alignment explanation
Indices: 15114--15171 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
15104 GAGATTTTTT
*
15114 TAAAAAATTTAATTTAATAAAAATTTTAA
1 TAAAAAATTTAAATTAAT-AAAA-TTTAA
* *
15143 TAAAAACTTTAAATTGATAAAATTTAA
1 TAAAAAATTTAAATTAATAAAATTTAA
15170 TA
1 TA
15172 TGAAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAAAAATTTAAATTAATAAAATTTAA
Found at i:15271 original size:13 final size:13
Alignment explanation
Indices: 15234--15294 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
15224 TTTTCAATGA
15234 TAAAAAT-TTTAT
1 TAAAAATATTTAT
* *
15246 TAATAGT-TTTAT
1 TAAAAATATTTAT
15258 TAAAAATATTTATT
1 TAAAAATATTTA-T
*
15272 TAAAAA-ATATAT
1 TAAAAATATTTAT
15284 TAAAATATATT
1 TAAAA-ATATT
15295 AAAATTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 21 0.54
13 9 0.23
14 9 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAAAAATATTTAT
Found at i:15290 original size:10 final size:10
Alignment explanation
Indices: 15275--15299 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15265 ATTTATTTAA
15275 AAAATATATT
1 AAAATATATT
15285 AAAATATATT
1 AAAATATATT
15295 AAAAT
1 AAAAT
15300 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATATT
Found at i:18759 original size:34 final size:34
Alignment explanation
Indices: 18720--18787 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
18710 TTTCTAGAAC
* * * * *
18720 AAAATATAATTTTTGAAAATCTTTTTCTCAAAAT
1 AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
18754 AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
1 AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
18788 TATAATGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAAAACTTTCGAAAATCTATTTCTAAAAAT
Found at i:25007 original size:52 final size:52
Alignment explanation
Indices: 24920--25076 Score: 219
Period size: 52 Copynumber: 3.0 Consensus size: 52
24910 TGGACAAGAA
* *
24920 GACTTGCAAAAGAAGAATATC-AAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAAT-TCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
*
24972 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * * *
25024 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
25076 G
1 G
25077 TATGGTTATA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.93
53 5 0.05
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:26431 original size:14 final size:14
Alignment explanation
Indices: 26409--26443 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
26399 GTTAATTGGT
*
26409 TATGTTTTCTCACA
1 TATGCTTTCTCACA
26423 TATGCTTTCTCACA
1 TATGCTTTCTCACA
26437 TATGCTT
1 TATGCTT
26444 CCTTGGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (14 bp):
TATGCTTTCTCACA
Found at i:29566 original size:22 final size:22
Alignment explanation
Indices: 29538--29606 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
29528 TTAATCATAC
29538 AATCACACAAATAAATATATAT
1 AATCACACAAATAAATATATAT
29560 AATCACACAAATAACA-ATATA-
1 AATCACACAAATAA-ATATATAT
** *
29581 AATCATGCAATTAAATATATAAT
1 AATCACACAAATAAATATAT-AT
29604 AAT
1 AAT
29607 GCAATTAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 20 0.50
23 4 0.10
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (22 bp):
AATCACACAAATAAATATATAT
Found at i:29610 original size:20 final size:20
Alignment explanation
Indices: 29575--29850 Score: 171
Period size: 20 Copynumber: 13.9 Consensus size: 20
29565 CACAAATAAC
*
29575 AATATA-AATCATGCAATTA
1 AATATATAATAATGCAATTA
29594 AATATATAATAATGCAATTA
1 AATATATAATAATGCAATTA
* *
29614 ACA-ATATAAATCATGCAAATA
1 A-ATATAT-AATAATGCAATTA
*
29635 AATATATAATCATGCAATTA
1 AATATATAATAATGCAATTA
* *
29655 ACA-ACATAAAACATGCAATTA
1 A-ATATATAATA-ATGCAATTA
*
29676 AATATATAATCAA-GTAATTA
1 AATATATAAT-AATGCAATTA
*
29696 ACATATA-AA-ACATGTAATTA
1 A-ATATATAATA-ATGCAATTA
* * *
29716 AATATATTATCATGCAGTTA
1 AATATATAATAATGCAATTA
* * *
29736 ACA-ATATAAAACATACAAATA
1 A-ATATATAATA-ATGCAATTA
29757 AATATAT--T-ATGCAATTA
1 AATATATAATAATGCAATTA
** * *
29774 ACGATATAAAACATGCAAATA
1 AATATATAATA-ATGCAATTA
* *
29795 AATATATTATCATGCAATTA
1 AATATATAATAATGCAATTA
*
29815 AATATATAATAATACAA-TA
1 AATATATAATAATGCAATTA
* *
29834 TA-ATATAATCATGCAAT
1 AATATATAATAATGCAAT
29851 AAACATGCAA
Statistics
Matches: 197, Mismatches: 39, Indels: 42
0.71 0.14 0.15
Matches are distributed among these distances:
17 12 0.06
18 13 0.07
19 15 0.08
20 91 0.46
21 65 0.33
22 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.31
Consensus pattern (20 bp):
AATATATAATAATGCAATTA
Found at i:29616 original size:41 final size:41
Alignment explanation
Indices: 29545--29855 Score: 341
Period size: 41 Copynumber: 7.7 Consensus size: 41
29535 TACAATCACA
** * *
29545 CAAATAAATATATATAATCACACAAATAACAATATAAATCATG
1 CAAAT-AA-ATATATAATCATGCAATTAACAATATAAAACATG
* * *
29588 CAATTAAATATATAATAATGCAATTAACAATATAAATCATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
*
29629 CAAATAAATATATAATCATGCAATTAACAACATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * *
29670 CAATTAAATATATAATCAAGTAATTAAC-ATATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * * * *
29710 TAATTAAATATATTATCATGCAGTTAACAATATAAAACATA
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
*
29751 CAAATAAATATAT--T-ATGCAATTAACGATATAAAACATG
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
* * *
29789 CAAATAAATATATTATCATGCAATTAA-ATATATAATA-ATA
1 CAAATAAATATATAATCATGCAATTAACA-ATATAAAACATG
* *
29829 C-AATATA-ATATAATCATGCAATAAACA
1 CAAATAAATATATAATCATGCAATTAACA
29856 TGCAATTAAA
Statistics
Matches: 232, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
38 50 0.22
39 7 0.03
40 38 0.16
41 131 0.56
42 2 0.01
43 4 0.02
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (41 bp):
CAAATAAATATATAATCATGCAATTAACAATATAAAACATG
Found at i:29677 original size:82 final size:81
Alignment explanation
Indices: 29545--29856 Score: 343
Period size: 81 Copynumber: 3.9 Consensus size: 81
29535 TACAATCACA
** * *
29545 CAAATAAATATATATAATCACACAAATAACAATATAAATCATGCAATTAAATATATAATAATGCA
1 CAAAT-AA-ATATATAATCATGCAATTAACAATATAAAACATGCAATTAAATATATAATAATGCA
*
29610 ATTAACAATATAAATCATG
64 ATTAAC-ATATAAAACATG
* *
29629 CAAATAAATATATAATCATGCAATTAACAACATAAAACATGCAATTAAATATATAATCAA-GTAA
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATGCAATTAAATATATAAT-AATGCAA
29693 TTAACATATAAAACATG
65 TTAACATATAAAACATG
* * * * * *
29710 TAATTAAATATATTATCATGCAGTTAACAATATAAAACATACAAATAAATATAT--T-ATGCAAT
1 CAAATAAATATATAATCATGCAATTAACAATATAAAACATGCAATTAAATATATAATAATGCAAT
29772 TAACGATATAAAACATG
66 TAAC-ATATAAAACATG
* * * * *
29789 CAAATAAATATATTATCATGCAATTAA-ATATATAATA-ATACAA-TATA-ATATAATCATGCAA
1 CAAATAAATATATAATCATGCAATTAACA-ATATAAAACATGCAATTAAATATATAATAATGCAA
*
29850 TAAACAT
65 TTAACAT
29857 GCAATTAAAT
Statistics
Matches: 200, Mismatches: 21, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
76 4 0.02
77 4 0.02
78 18 0.09
79 54 0.27
81 58 0.29
82 53 0.26
83 4 0.02
84 5 0.03
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (81 bp):
CAAATAAATATATAATCATGCAATTAACAATATAAAACATGCAATTAAATATATAATAATGCAAT
TAACATATAAAACATG
Found at i:29921 original size:20 final size:20
Alignment explanation
Indices: 29896--29988 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
29886 CTATACAAAT
*
29896 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
*
29916 AAATAAATTAATAATCATGT
1 AAATAAATTAATAATCATGC
** * *
29936 AAGCATATTAATAGTCATGC
1 AAATAAATTAATAATCATGC
* **
29956 AAATATATTAATAAATCACAC
1 AAATAAATTAAT-AATCATGC
*
29977 AAATATATTAAT
1 AAATAAATTAAT
29989 CATATAAATA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
20 43 0.72
21 17 0.28
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:30028 original size:16 final size:18
Alignment explanation
Indices: 30009--30049 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
29999 AACTATTAGA
30009 CAAATAA-ATTA-TCATG
1 CAAATAATATTAGTCATG
30025 CAAATATAATATTAGTCATG
1 C-AA-ATAATATTAGTCATG
30045 CAAAT
1 CAAAT
30050 TCATGCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.05
17 2 0.10
18 6 0.29
19 6 0.29
20 6 0.29
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (18 bp):
CAAATAATATTAGTCATG
Found at i:30030 original size:32 final size:33
Alignment explanation
Indices: 29975--30039 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
29965 AATAAATCAC
* *
29975 ACAAATATATTAATCATATAAATA-AACTATTAG
1 ACAAATAAATTAATCATACAAATATAA-TATTAG
*
30008 ACAAATAAATT-ATCATGCAAATATAATATTAG
1 ACAAATAAATTAATCATACAAATATAATATTAG
30040 TCATGCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (33 bp):
ACAAATAAATTAATCATACAAATATAATATTAG
Found at i:30045 original size:20 final size:18
Alignment explanation
Indices: 30012--30049 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
30002 TATTAGACAA
30012 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
30030 ATAATATTAGTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
30050 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Found at i:31126 original size:2 final size:2
Alignment explanation
Indices: 31121--31146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31111 GTTGTGTGCA
31121 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31147 CAAACACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32461 original size:2 final size:2
Alignment explanation
Indices: 32456--32482 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32446 ATATATATAT
32456 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
32483 AGTGGCACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.