Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168462.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_672, 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: 17844
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Found at i:645 original size:12 final size:12
Alignment explanation
Indices: 606--647 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
596 GAAAATTTAT
606 AAAATAGA-ACAA
1 AAAATAGACA-AA
618 AAAATAG-CAAGA
1 AAAATAGACAA-A
630 AAAATAGACAAA
1 AAAATAGACAAA
642 AAAATA
1 AAAATA
648 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:683 original size:12 final size:11
Alignment explanation
Indices: 639--690 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
629 AAAAATAGAC
639 AAAA-AAATAA
1 AAAATAAATAA
**
649 AAAAT-TTTAA
1 AAAATAAATAA
*
659 AATATAAATAA
1 AAAATAAATAA
670 AAAATAAATGAA
1 AAAATAAAT-AA
682 AAAATAAAT
1 AAAATAAAT
691 TAAGAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 11 0.33
11 11 0.33
12 11 0.33
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:1134 original size:19 final size:20
Alignment explanation
Indices: 1102--1140 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1092 AAAATTTGAG
*
1102 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
1122 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
1141 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:1171 original size:64 final size:64
Alignment explanation
Indices: 1046--1172 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
1036 AAAAGATTTA
* * ****
1046 AGAAAAAGCAAGAAAAAAATAAAAAATAAAATACAAAAATATATATAAAATTTGAGAAAAAATG
1 AGAAAAAGCAAGAAAAAAATAAAAAATAAAAGACAAAAATATAAATAAAAAAAAAGAAAAAATG
* *
1110 AGAAAAAG-AAGAAAAAAATAAAAAATGAAGAGGCAAAAATATGAAATAAAAAAAAAGAAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAAT-AAAAGACAAAAATAT-AAATAAAAAAAAAGAAAAAA
1173 ATTTATAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 18 0.34
64 20 0.38
65 15 0.28
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (64 bp):
AGAAAAAGCAAGAAAAAAATAAAAAATAAAAGACAAAAATATAAATAAAAAAAAAGAAAAAATG
Found at i:2238 original size:13 final size:15
Alignment explanation
Indices: 2202--2240 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2192 CAAAATAGGA
2202 AAAGATATAAAAAATG
1 AAAGATA-AAAAAATG
2218 AAAGATAAAAAAAT-
1 AAAGATAAAAAAATG
2232 AAA-ATAAAA
1 AAAGATAAAA
2241 GTTAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 3 0.13
15 7 0.30
16 7 0.30
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (15 bp):
AAAGATAAAAAAATG
Found at i:3667 original size:12 final size:12
Alignment explanation
Indices: 3628--3669 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3618 GAAAATTTAT
3628 AAAATAGA-ACAA
1 AAAATAGACA-AA
3640 AAAATAG-CAAGA
1 AAAATAGACAA-A
3652 AAAATAGACAAA
1 AAAATAGACAAA
3664 AAAATA
1 AAAATA
3670 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:4149 original size:21 final size:21
Alignment explanation
Indices: 4111--4150 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4101 AAAAGCAAGA
4111 AAAAAATAAAAATGAAAATAC
1 AAAAAATAAAAATGAAAATAC
*
4132 AAAATATATAAAAT-AAAAT
1 AAAAAATA-AAAATGAAAAT
4151 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAATGAAAATAC
Found at i:4540 original size:17 final size:18
Alignment explanation
Indices: 4499--4541 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
4489 CAAAAATACA
*
4499 ACAAAAAATATAAAAAGT
1 ACAAAAAATATAAAAAGG
*
4517 A-AGAAAATA-AAAAAGG
1 ACAAAAAATATAAAAAGG
4533 ACAAAAAAT
1 ACAAAAAAT
4542 GAAGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 7 0.33
17 13 0.62
18 1 0.05
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (18 bp):
ACAAAAAATATAAAAAGG
Found at i:6729 original size:12 final size:12
Alignment explanation
Indices: 6690--6731 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
6680 GAAAATTTAT
6690 AAAATAGA-ACAA
1 AAAATAGACA-AA
6702 AAAATAG-CAAGA
1 AAAATAGACAA-A
6714 AAAATAGACAAA
1 AAAATAGACAAA
6726 AAAATA
1 AAAATA
6732 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:6745 original size:16 final size:15
Alignment explanation
Indices: 6724--6753 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6714 AAAATAGACA
6724 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
6740 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
6754 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:6808 original size:17 final size:18
Alignment explanation
Indices: 6778--6847 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
6768 AAAATTTTTA
*
6778 AAATAT-AAATAAAAAAT
1 AAATATAAAAGAAAAAAT
* *
6795 AAAT-TAAGAGAAAATAT
1 AAATATAAAAGAAAAAAT
* *
6812 TAATATAAAAGAAAAATT
1 AAATATAAAAGAAAAAAT
6830 AAATA-AAATACGAAAAAA
1 AAATATAAA-A-GAAAAAA
6848 GGAAAAAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 1 0.03
17 18 0.45
18 15 0.38
19 6 0.15
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATATAAAAGAAAAAAT
Found at i:6808 original size:28 final size:29
Alignment explanation
Indices: 6777--6839 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
6767 AAAAATTTTT
6777 AAAATA-TAA-ATAAAA-AATAAATTAAGAG
1 AAAATATTAATATAAAAGAA-AAATTAA-AG
*
6805 AAAATATTAATATAAAAGAAAAATTAAAT
1 AAAATATTAATATAAAAGAAAAATTAAAG
6834 AAAATA
1 AAAATA
6840 CGAAAAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 10 0.32
30 13 0.42
31 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (29 bp):
AAAATATTAATATAAAAGAAAAATTAAAG
Found at i:6826 original size:18 final size:16
Alignment explanation
Indices: 6778--6837 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
6768 AAAATTTTTA
* *
6778 AAATATAAATAAAAAAT
1 AAATA-AAAGAAAAATT
*
6795 AAATTAAGAGAAAATATT
1 AAA-TAAAAGAAAA-ATT
6813 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
6830 AAATAAAA
1 AAATAAAA
6838 TACGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 14 0.39
18 15 0.42
19 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAGAAAAATT
Found at i:7199 original size:22 final size:21
Alignment explanation
Indices: 7165--7205 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
7155 AAAAGCAAGA
7165 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
7187 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
7206 TTGAGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:7268 original size:55 final size:55
Alignment explanation
Indices: 7164--7268 Score: 122
Period size: 55 Copynumber: 1.9 Consensus size: 55
7154 AAAAAGCAAG
* ****
7164 AAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAATAAGA
1 AAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAATAAGA
* * *
7219 AAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAATAAAACAAAAAGAAA
1 AAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAA-AAAAAGAAA
7269 AAAATTTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 12 0.29
55 29 0.71
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (55 bp):
AAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAATAAGA
Found at i:9759 original size:12 final size:12
Alignment explanation
Indices: 9742--9782 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
9732 GAAAATTTAT
9742 AAAATAGAACAA
1 AAAATAGAACAA
*
9754 AAAATAGCAA-GA
1 AAAATAG-AACAA
9766 AAAATAG-ACAA
1 AAAATAGAACAA
9777 AAAATA
1 AAAATA
9783 AGAAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 1 0.04
11 7 0.28
12 15 0.60
13 2 0.08
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGAACAA
Found at i:9796 original size:16 final size:15
Alignment explanation
Indices: 9775--9804 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9765 AAAAATAGAC
9775 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
9791 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
9805 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:9846 original size:11 final size:11
Alignment explanation
Indices: 9826--9859 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
9816 TAAAAATTTT
*
9826 TAAAATATAAA
1 TAAAAAATAAA
9837 TAAAAAATAAA
1 TAAAAAATAAA
*
9848 TGAAAAATAAA
1 TAAAAAATAAA
9859 T
1 T
9860 TAAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:10261 original size:22 final size:21
Alignment explanation
Indices: 10227--10267 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
10217 AAAAGCAAGA
10227 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
10249 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
10268 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:10305 original size:19 final size:20
Alignment explanation
Indices: 10273--10311 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
10263 AAAATTTGAG
*
10273 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
10293 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
10312 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:10343 original size:66 final size:67
Alignment explanation
Indices: 10214--10344 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 67
10204 AAAAGATTTA
* ****
10214 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
10279 TG
66 TG
* * *
10281 AGAAAAAG-AAGAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAATAAAAAAAAAGAAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
10344 T
66 T
10345 TTATAGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 21 0.38
66 27 0.48
67 8 0.14
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (67 bp):
AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
TG
Found at i:10619 original size:23 final size:22
Alignment explanation
Indices: 10556--10620 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 22
10546 ATGAAACTAT
10556 AAAAAAAGAAAAAAAATTAAAGCA
1 AAAAAAAG-AAAAAAA-TAAAGCA
*
10580 AAAGAAAA-AAGATAAATAAAGCA
1 AAA-AAAAGAA-AAAAATAAAGCA
10603 CAAAAAAAGAAAAAAATA
1 -AAAAAAAGAAAAAAATA
10621 TAAAAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 19 0.54
24 12 0.34
25 4 0.11
ACGTcount: A:0.78, C:0.05, G:0.09, T:0.08
Consensus pattern (22 bp):
AAAAAAAGAAAAAAATAAAGCA
Found at i:10627 original size:16 final size:16
Alignment explanation
Indices: 10605--10643 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
10595 ATAAAGCACA
10605 AAAAAAG-AAAAAAAT
1 AAAAAAGTAAAAAAAT
*
10620 ATAAAAAGTAAGAAAAT
1 A-AAAAAGTAAAAAAAT
10637 AAAAAAG
1 AAAAAAG
10644 GACAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 12 0.57
17 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAGTAAAAAAAT
Found at i:10651 original size:16 final size:15
Alignment explanation
Indices: 10605--10652 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
10595 ATAAAGCACA
*
10605 AAAAAAGAAAAAAAT
1 AAAAAAGGAAAAAAT
*
10620 ATAAAAAGTAAGAAAAT
1 A-AAAAAGGAA-AAAAT
10637 AAAAAAGGACAAAAAT
1 AAAAAAGGA-AAAAAT
10653 TGAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 1 0.04
16 20 0.71
17 7 0.25
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.10
Consensus pattern (15 bp):
AAAAAAGGAAAAAAT
Found at i:12100 original size:26 final size:27
Alignment explanation
Indices: 12039--12100 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
12029 AAGGGATTAC
* * * *
12039 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
12066 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
12092 AAAATGAAA
1 AAAATGAAA
12101 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:12438 original size:15 final size:14
Alignment explanation
Indices: 12402--12454 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 14
12392 AAAATACAAT
12402 AAAAATATAAAAAGTA
1 AAAAATA-AAAAAG-A
12418 AGAAAATAAAAAAGA
1 A-AAAATAAAAAAGA
12433 CAAAAATGAAAAAA-A
1 -AAAAAT-AAAAAAGA
12448 AAAAATA
1 AAAAATA
12455 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 6 0.18
15 7 0.21
16 14 0.41
17 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (14 bp):
AAAAATAAAAAAGA
Found at i:12819 original size:11 final size:11
Alignment explanation
Indices: 12782--12819 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
12772 GAAAATTTAT
12782 AAAATAGAACAA
1 AAAATAG-ACAA
12794 AAAATAG-CAAA
1 AAAATAGAC-AA
12805 AAAATAGACAA
1 AAAATAGACAA
12816 AAAA
1 AAAA
12820 ATAAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 15 0.62
12 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAATAGACAA
Found at i:12820 original size:12 final size:12
Alignment explanation
Indices: 12782--12822 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
12772 GAAAATTTAT
12782 AAAATAGA-ACAA
1 AAAATAGACA-AA
12794 AAAATAG-CAAA
1 AAAATAGACAAA
12805 AAAATAGACAAA
1 AAAATAGACAAA
12817 AAAATA
1 AAAATA
12823 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:12836 original size:16 final size:15
Alignment explanation
Indices: 12815--12844 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12805 AAAATAGACA
12815 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
12831 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
12845 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:12894 original size:12 final size:11
Alignment explanation
Indices: 12867--12901 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
12857 AAAAAATTTT
*
12867 TAAAATATAAA
1 TAAAAAATAAA
12878 TAAAAAATAAA
1 TAAAAAATAAA
12889 TGAAAAAATAAA
1 T-AAAAAATAAA
12901 T
1 T
12902 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:13568 original size:12 final size:13
Alignment explanation
Indices: 13537--13577 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
13527 CGAGAATGAT
*
13537 AAAATAAAAAAAG
1 AAAAGAAAAAAAG
13550 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
*
13563 -ATAGAAAAAAA-
1 AAAAGAAAAAAAG
13574 AAAA
1 AAAA
13578 TTTCAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:14425 original size:22 final size:21
Alignment explanation
Indices: 14378--14435 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
14368 AAGAAAACAA
*
14378 AAAAAAATATAACAAATATAGG
1 AAAAAAATATAA-AAATAAAGG
* *
14400 AAAAAGATATAAAAATCAAAGT
1 AAAAAAATATAAAAAT-AAAGG
14422 AAAAATAA-ATAAAA
1 AAAAA-AATATAAAA
14436 GTTAATGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.13
22 25 0.83
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAAAATATAAAAATAAAGG
Found at i:14435 original size:21 final size:21
Alignment explanation
Indices: 14411--14461 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
14401 AAAAGATATA
14411 AAAATCAAAGTAAAAAT-AAAT
1 AAAATCAAAG-AAAAATAAAAT
* *
14432 AAAAGTTAATGAAAAATAAAAT
1 AAAA-TCAAAGAAAAATAAAAT
14454 AAAA-CAAA
1 AAAATCAAA
14462 AGAAGTGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 12 0.50
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAATCAAAGAAAAATAAAAT
Found at i:14551 original size:22 final size:22
Alignment explanation
Indices: 14526--14569 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14516 GGAATTTGTG
14526 AAAAATAGAAAAG-CAAGAAAGAA
1 AAAAAT-GAAAAGACAA-AAAGAA
14549 AAAAATGAAAAGACAAAAAGA
1 AAAAATGAAAAGACAAAAAGA
14570 TTGGAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.05
Consensus pattern (22 bp):
AAAAATGAAAAGACAAAAAGAA
Found at i:15157 original size:26 final size:27
Alignment explanation
Indices: 15096--15157 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
15086 AAGGGATTAC
* * * *
15096 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
15123 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
15149 AAAATGAAA
1 AAAATGAAA
15158 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:15512 original size:15 final size:15
Alignment explanation
Indices: 15462--15512 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
15452 AAAATACAAT
15462 AAAAATATAAAAAGTAA
1 AAAAATA-AAAAAG-AA
* *
15479 GAAAATAAAAAAGAC
1 AAAAATAAAAAAGAA
*
15494 AAAAATGAAAAA-AA
1 AAAAATAAAAAAGAA
15508 AAAAA
1 AAAAA
15513 GTTCAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 6 0.21
15 11 0.38
16 6 0.21
17 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAAAGAA
Found at i:15882 original size:12 final size:12
Alignment explanation
Indices: 15843--15884 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
15833 GAAAATTTAT
15843 AAAATAGA-ACAA
1 AAAATAGACA-AA
15855 AAAATAG-CAAGA
1 AAAATAGACAA-A
15867 AAAATAGACAAA
1 AAAATAGACAAA
15879 AAAATA
1 AAAATA
15885 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:15898 original size:16 final size:15
Alignment explanation
Indices: 15877--15906 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
15867 AAAATAGACA
15877 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
15893 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
15907 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:16358 original size:21 final size:20
Alignment explanation
Indices: 16334--16372 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16324 AAGCAAGAGA
16334 AAAAATAAAAAATGAAAATAC
1 AAAAATAAAAAAT-AAAATAC
* *
16355 AAAATTATAAAATAAAAT
1 AAAAATAAAAAATAAAAT
16373 TTGAGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAAATAAAAAATAAAATAC
Found at i:16405 original size:20 final size:21
Alignment explanation
Indices: 16365--16404 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16355 AAAATTATAA
16365 AATAAAATTTGAGAAAAAAAT
1 AATAAAATTTGAGAAAAAAAT
*
16386 AATAAAGTTTGAGAAAAAA
1 AATAAAATTTGAGAAAAAA
16405 TGAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (21 bp):
AATAAAATTTGAGAAAAAAAT
Found at i:16431 original size:19 final size:20
Alignment explanation
Indices: 16399--16437 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
16389 AAAGTTTGAG
*
16399 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
16419 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
16438 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:16682 original size:20 final size:20
Alignment explanation
Indices: 16646--16692 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
16636 AAGATAGAAA
16646 AATAAAAATTTCAAAACT-T
1 AATAAAAATTTCAAAACTAT
16665 AATAAAAATTT-ATGAAACTAT
1 AATAAAAATTTCA--AAACTAT
16686 AA-AAAAA
1 AATAAAAA
16693 GAAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 10 0.40
21 3 0.12
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (20 bp):
AATAAAAATTTCAAAACTAT
Found at i:16741 original size:24 final size:24
Alignment explanation
Indices: 16686--16748 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
16676 ATGAAACTAT
16686 AAAAAAAGAAAAAAAATTAAAGCA
1 AAAAAAAGAAAAAAAATTAAAGCA
*
16710 AAAGAAAA-AAAGATAAA-TAAAGCA
1 AAA-AAAAGAAA-AAAAATTAAAGCA
16734 CAAAAAAAGAAAAAA
1 -AAAAAAAGAAAAAA
16749 TACAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.06
Consensus pattern (24 bp):
AAAAAAAGAAAAAAAATTAAAGCA
Found at i:16800 original size:15 final size:15
Alignment explanation
Indices: 16763--16801 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
16753 AAAATACAAC
*
16763 AAAAAATATAAAAAGT
1 AAAAAA-ATAAAAAGG
*
16779 AAGAAAATAAAAAGG
1 AAAAAAATAAAAAGG
16794 AAAAAAAT
1 AAAAAAAT
16802 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAAAAATAAAAAGG
Found at i:17504 original size:19 final size:19
Alignment explanation
Indices: 17468--17531 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
17458 AAATATAGGA
*
17468 AAAAGAATAATAAAAAAAT
1 AAAAGAATAAAAAAAAAAT
*
17487 CAAAG-ATAAAAAATAAAAT
1 AAAAGAATAAAAAA-AAAAT
*
17506 AAAAGTAATGAAAAATATAAAT
1 AAAAG-AAT-AAAAA-AAAAAT
17528 AAAA
1 AAAA
17532 ACAAAAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 7 0.19
19 13 0.36
21 2 0.06
22 13 0.36
23 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAAGAATAAAAAAAAAAT
Done.