Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168385.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_602, 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: 21714
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Found at i:2031 original size:12 final size:12
Alignment explanation
Indices: 1992--2033 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1982 GAAAATTTAT
1992 AAAATAGA-ACAA
1 AAAATAGACA-AA
2004 AAAATAG-CAAGA
1 AAAATAGACAA-A
2016 AAAATAGACAAA
1 AAAATAGACAAA
2028 AAAATA
1 AAAATA
2034 AAAAATTTAA
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:2063 original size:12 final size:12
Alignment explanation
Indices: 2048--2077 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2038 ATTTAAATAT
2048 ATAAATAAAAAA
1 ATAAATAAAAAA
*
2060 ATAAATGAAAAA
1 ATAAATAAAAAA
2072 ATAAAT
1 ATAAAT
2078 TAAGAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
ATAAATAAAAAA
Found at i:2102 original size:17 final size:16
Alignment explanation
Indices: 2068--2114 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2058 AAATAAATGA
*
2068 AAAAATAAAT-TAAGAG
1 AAAAATTAATATAA-AG
2084 AAAATATTAATATAAAG
1 AAAA-ATTAATATAAAG
2101 AAAAATTAA-ATAAA
1 AAAAATTAATATAAA
2115 ATACGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 9 0.32
17 11 0.39
18 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAAATTAATATAAAG
Found at i:2473 original size:22 final size:21
Alignment explanation
Indices: 2439--2479 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2429 AAAAGCAAGA
2439 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
2461 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
2480 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:2517 original size:19 final size:18
Alignment explanation
Indices: 2475--2517 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2465 TATATAAAAT
* *
2475 AAAATTTGAGAAAAATAT
1 AAAAGTTGAGAAAAATAG
2493 ATAAAGTTGAGAAAAATGAG
1 A-AAAGTTGAGAAAAAT-AG
2513 AAAAG
1 AAAAG
2518 AGAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (18 bp):
AAAAGTTGAGAAAAATAG
Found at i:2856 original size:26 final size:26
Alignment explanation
Indices: 2801--2855 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
2791 AAATTAAAGC
*
2801 AAAAGAAAAAAGATAAATAAAGCACA
1 AAAAGAAAAAAGACAAATAAAGCACA
*
2827 AAAAGAAAAAATACAAA-AATA-CACA
1 AAAAGAAAAAAGACAAATAA-AGCACA
2852 AAAA
1 AAAA
2856 ATATAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.76, C:0.09, G:0.07, T:0.07
Consensus pattern (26 bp):
AAAAGAAAAAAGACAAATAAAGCACA
Found at i:4297 original size:26 final size:27
Alignment explanation
Indices: 4236--4297 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
4226 AAGGGATTAC
* * * *
4236 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
4263 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
4289 AAAATGAAA
1 AAAATGAAA
4298 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:5041 original size:23 final size:25
Alignment explanation
Indices: 5007--5060 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
4997 GAAAATTTAT
* *
5007 AAAATAGAACAAAAAATAGCAA-GA
1 AAAATAGAACAAAAAAAAGAAATGA
5031 AAAATAG-ACAAAAAAAAGAAATGA
1 AAAATAGAACAAAAAAAAGAAATGA
5055 AAAATA
1 AAAATA
5061 AAAATTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (25 bp):
AAAATAGAACAAAAAAAAGAAATGA
Found at i:5046 original size:13 final size:13
Alignment explanation
Indices: 5007--5047 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
4997 GAAAATTTAT
*
5007 AAAATAGA-ACAA
1 AAAATAGACAAAA
*
5019 AAAATAG-CAAGA
1 AAAATAGACAAAA
5031 AAAATAGACAAAA
1 AAAATAGACAAAA
5044 AAAA
1 AAAA
5048 GAAATGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAATAGACAAAA
Found at i:5117 original size:17 final size:18
Alignment explanation
Indices: 5087--5156 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
5077 TAAAAATTTA
*
5087 AAATAT-AAATAAAAAAT
1 AAATATAAAAGAAAAAAT
* *
5104 AAAT-TAAGAGAAAATAT
1 AAATATAAAAGAAAAAAT
* *
5121 TAATATAAAAGAAAAATT
1 AAATATAAAAGAAAAAAT
5139 AAATA-AAATACGAAAAAA
1 AAATATAAA-A-GAAAAAA
5157 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:5119 original size:28 final size:29
Alignment explanation
Indices: 5086--5148 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
5076 ATAAAAATTT
5086 AAAATA-TAA-ATAAAA-AATAAATTAAGAG
1 AAAATATTAATATAAAAGAA-AAATTAA-AG
*
5114 AAAATATTAATATAAAAGAAAAATTAAAT
1 AAAATATTAATATAAAAGAAAAATTAAAG
5143 AAAATA
1 AAAATA
5149 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:5135 original size:18 final size:16
Alignment explanation
Indices: 5087--5146 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
5077 TAAAAATTTA
* *
5087 AAATATAAATAAAAAAT
1 AAATA-AAAGAAAAATT
*
5104 AAATTAAGAGAAAATATT
1 AAA-TAAAAGAAAA-ATT
5122 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
5139 AAATAAAA
1 AAATAAAA
5147 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:5510 original size:22 final size:21
Alignment explanation
Indices: 5476--5516 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5466 AAAAGCAAGA
5476 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
5498 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
5517 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:5645 original size:17 final size:17
Alignment explanation
Indices: 5594--5645 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
5584 AAAATTTTAA
*
5594 AACAAAAAAAAAAGAGC
1 AACAAAAAAAAAAAAGC
*
5611 GAACAAAAAAAATGAAAGC
1 -AACAAAAAAAA-AAAAGC
5630 -ACATAAAAAAAAAAAG
1 AACA-AAAAAAAAAAAG
5646 AAGAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.24
18 18 0.62
19 4 0.14
ACGTcount: A:0.75, C:0.10, G:0.12, T:0.04
Consensus pattern (17 bp):
AACAAAAAAAAAAAAGC
Found at i:5889 original size:15 final size:16
Alignment explanation
Indices: 5853--5890 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5843 AAAATACAAC
*
5853 AAAAATATAAAAAGTA
1 AAAAATATAAAAAGGA
5869 AGAAAATA-AAAAAGGA
1 A-AAAATATAAAAAGGA
5885 AAAAAT
1 AAAAAT
5891 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 9 0.45
17 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAATATAAAAAGGA
Found at i:6316 original size:17 final size:18
Alignment explanation
Indices: 6294--6333 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6284 CAAAAATAGC
6294 AAAAAAGA-T-AATAAAAT
1 AAAAAAGATTCAA-AAAAT
6311 AAAAAAGATTCAAAAAAT
1 AAAAAAGATTCAAAAAAT
6329 AAAAA
1 AAAAA
6334 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 11 0.52
19 2 0.10
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAAAGATTCAAAAAAT
Found at i:7344 original size:26 final size:27
Alignment explanation
Indices: 7283--7344 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
7273 AAGGGATTAC
* * * *
7283 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
7310 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
7336 AAAATGAAA
1 AAAATGAAA
7345 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:8091 original size:13 final size:13
Alignment explanation
Indices: 8052--8092 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
8042 GAAAATTTAT
*
8052 AAAATAGA-ACAA
1 AAAATAGACAAAA
*
8064 AAAATAG-CAAGA
1 AAAATAGACAAAA
8076 AAAATAGACAAAA
1 AAAATAGACAAAA
8089 AAAA
1 AAAA
8093 AAATGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAATAGACAAAA
Found at i:8100 original size:23 final size:24
Alignment explanation
Indices: 8052--8102 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
8042 GAAAATTTAT
**
8052 AAAATAGAACAAAAAATAGCAAGA
1 AAAATAGAACAAAAAATAAAAAGA
8076 AAAATAG-ACAAAAAA-AAAAATGA
1 AAAATAGAACAAAAAATAAAAA-GA
8099 AAAA
1 AAAA
8103 AAAATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 7 0.29
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.08
Consensus pattern (24 bp):
AAAATAGAACAAAAAATAAAAAGA
Found at i:8223 original size:26 final size:26
Alignment explanation
Indices: 8170--8223 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
8160 ATATTAATAT
* *
8170 AAAAGAAAAATTAAATAAAATACGAAA
1 AAAAGAAAAAATAAACAAAATAC-AAA
*
8197 AAAGGAAAAAATAAACAAAA-ACAAA
1 AAAAGAAAAAATAAACAAAATACAAA
8222 AA
1 AA
8224 GTAACAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 2 0.08
27 17 0.71
ACGTcount: A:0.78, C:0.06, G:0.07, T:0.09
Consensus pattern (26 bp):
AAAAGAAAAAATAAACAAAATACAAA
Found at i:8547 original size:22 final size:21
Alignment explanation
Indices: 8513--8553 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
8503 AAAAGCAAGA
8513 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
8535 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
8554 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:8627 original size:64 final size:66
Alignment explanation
Indices: 8503--8627 Score: 148
Period size: 64 Copynumber: 1.9 Consensus size: 66
8493 AGATTTAAGA
* *** *
8503 AAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAAAAATGA
1 AAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAGAAAAAAAATGA
8568 G
66 G
* * *
8569 AAAAG-AAGAAAAAAAT-AAAAATGAAGAGGCAAAA-ATATGAAATAAAAAAAAGAAAAAAA
1 AAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAAT-AAAAAAAGAAAAAAA
8628 TTTATAGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
63 8 0.16
64 26 0.52
65 11 0.22
66 5 0.10
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (66 bp):
AAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAGAAAAAAAATGA
G
Found at i:11135 original size:12 final size:12
Alignment explanation
Indices: 11096--11137 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
11086 GAAAATTTAT
11096 AAAATAGA-ACAA
1 AAAATAGACA-AA
11108 AAAATAG-CAAGA
1 AAAATAGACAA-A
11120 AAAATAGACAAA
1 AAAATAGACAAA
11132 AAAATA
1 AAAATA
11138 AAAAAATTTA
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:11173 original size:12 final size:11
Alignment explanation
Indices: 11129--11180 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
11119 AAAAATAGAC
11129 AAAA-AAATAA
1 AAAATAAATAA
**
11139 AAAA-ATTTAA
1 AAAATAAATAA
*
11149 AATATAAATAA
1 AAAATAAATAA
11160 AAAATAAATGAA
1 AAAATAAAT-AA
11172 AAAATAAAT
1 AAAATAAAT
11181 TAAGAGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 11 0.32
11 12 0.35
12 11 0.32
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:13755 original size:17 final size:17
Alignment explanation
Indices: 13735--13792 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 17
13725 AACCACAATG
13735 ATAAAATAAAAAATACA
1 ATAAAATAAAAAATACA
13752 ATAAAAATATAAAAAGT--A
1 AT-AAAATA-AAAAA-TACA
* *
13770 AGAAAATAAAAAAGACA
1 ATAAAATAAAAAATACA
13787 A-AAAAT
1 ATAAAAT
13793 GAAATGGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
16 10 0.29
17 10 0.29
18 8 0.24
19 5 0.15
20 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
ATAAAATAAAAAATACA
Found at i:14184 original size:23 final size:25
Alignment explanation
Indices: 14150--14203 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
14140 GAAAATTTAT
* *
14150 AAAATAGAACAAAAAATAGCAA-GA
1 AAAATAGAACAAAAAAAAGAAATGA
14174 AAAATAG-ACAAAAAAAAGAAATGA
1 AAAATAGAACAAAAAAAAGAAATGA
14198 AAAATA
1 AAAATA
14204 AAAAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (25 bp):
AAAATAGAACAAAAAAAAGAAATGA
Found at i:14189 original size:13 final size:13
Alignment explanation
Indices: 14150--14190 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
14140 GAAAATTTAT
*
14150 AAAATAGA-ACAA
1 AAAATAGACAAAA
*
14162 AAAATAG-CAAGA
1 AAAATAGACAAAA
14174 AAAATAGACAAAA
1 AAAATAGACAAAA
14187 AAAA
1 AAAA
14191 GAAATGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAATAGACAAAA
Found at i:14215 original size:17 final size:18
Alignment explanation
Indices: 14195--14241 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
14185 AAAAAAGAAA
14195 TGAAAAATA-AAAAATTT
1 TGAAAAATATAAAAATTT
***
14212 TGAACTTTATAAAAATTT
1 TGAAAAATATAAAAATTT
14230 T-AAAAATATAAA
1 TGAAAAATATAAA
14242 TGAAAAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (18 bp):
TGAAAAATATAAAAATTT
Found at i:14277 original size:29 final size:29
Alignment explanation
Indices: 14232--14295 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
14222 AAAAATTTTA
*
14232 AAAATATAAATGAAAAA-ATAAATTAAGAG
1 AAAATATAAATGAAAAAGAAAAATTAA-AG
* *
14261 AAAATATTAAT-ATAAAAGAAAAATTAAAT
1 AAAATATAAATGA-AAAAGAAAAATTAAAG
14290 AAAATA
1 AAAATA
14296 CGAAAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 21 0.70
30 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (29 bp):
AAAATATAAATGAAAAAGAAAAATTAAAG
Found at i:14282 original size:18 final size:17
Alignment explanation
Indices: 14234--14293 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
14224 AAATTTTAAA
* *
14234 AATATAAATGAAAAAAT
1 AATATAAAAGAAAAATT
*
14251 AA-ATTAAGAGAAAATATT
1 AATA-TAAAAGAAAA-ATT
14269 AATATAAAAGAAAAATT
1 AATATAAAAGAAAAATT
14286 AA-ATAAAA
1 AATATAAAA
14294 TACGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 7 0.19
17 15 0.42
18 13 0.36
19 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AATATAAAAGAAAAATT
Found at i:14656 original size:22 final size:21
Alignment explanation
Indices: 14622--14662 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14612 AAAAGCAAGA
14622 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
14644 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
14663 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:14710 original size:19 final size:22
Alignment explanation
Indices: 14669--14744 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
14659 AAATTTGAGA
14669 AAAAAAATGAGAAAAAAGAAAG
1 AAAAAAATGAGAAAAAAGAAAG
*
14691 AAAAAAAT-A-AAAAATGAAGAGG
1 AAAAAAATGAGAAAAAAGAA-A-G
* * *
14713 CAAAAATATGAAATAAAAAAAAAG
1 -AAAAAAATGAGA-AAAAAGAAAG
14737 AAAAAAAT
1 AAAAAAAT
14745 TTATAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
20 8 0.19
21 2 0.05
22 9 0.21
23 14 0.33
24 2 0.05
25 2 0.05
26 6 0.14
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.09
Consensus pattern (22 bp):
AAAAAAATGAGAAAAAAGAAAG
Found at i:14742 original size:70 final size:70
Alignment explanation
Indices: 14611--14743 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
14601 AAGATTTAAG
* * ****
14611 AAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAAAAAAA
1 AAAAAGAAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAAAA
14676 TGAGA
66 TGAGA
* * *
14681 AAAAAGAAAGAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAATAAAAAAAAAGAAAAAAA
1 AAAAAGAAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAAA
14744 TTTATAGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
69 21 0.39
70 33 0.61
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.12
Consensus pattern (70 bp):
AAAAAGAAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAAAA
TGAGA
Found at i:15072 original size:16 final size:17
Alignment explanation
Indices: 15033--15073 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
15023 CAAAAATACA
*
15033 ACAAAAATATAAAAAGT
1 ACAAAAATATAAAAAGG
15050 A-AGAAAATA-AAAAAGG
1 ACA-AAAATATAAAAAGG
15066 ACAAAAAT
1 ACAAAAAT
15074 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.12
Consensus pattern (17 bp):
ACAAAAATATAAAAAGG
Found at i:16540 original size:26 final size:27
Alignment explanation
Indices: 16479--16540 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
16469 AAGGGATTAC
* * * *
16479 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
16506 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
16532 AAAATGAAA
1 AAAATGAAA
16541 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:17234 original size:12 final size:12
Alignment explanation
Indices: 17217--17264 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
17207 GAAAATTTTG
17217 AAAATAGAAAAA
1 AAAATAGAAAAA
* *
17229 AAAATAGCAAGA
1 AAAATAGAAAAA
17241 AAAATAGACAAAA
1 AAAATAGA-AAAA
*
17254 AAAAAAGAAAA
1 AAAATAGAAAA
17265 TGAAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAATAGAAAAA
Found at i:17334 original size:28 final size:29
Alignment explanation
Indices: 17303--17365 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
17293 AAAAAATTTT
17303 AAAATA-TAA-ATAAAA-AATAAATTAAGAG
1 AAAATATTAATATAAAAGAA-AAATTAA-AG
*
17331 AAAATATTAATATAAAAGAAAAATTAAAT
1 AAAATATTAATATAAAAGAAAAATTAAAG
17360 AAAATA
1 AAAATA
17366 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:17352 original size:18 final size:16
Alignment explanation
Indices: 17304--17363 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
17294 AAAAATTTTA
* *
17304 AAATATAAATAAAAAAT
1 AAATA-AAAGAAAAATT
*
17321 AAATTAAGAGAAAATATT
1 AAA-TAAAAGAAAA-ATT
17339 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
17356 AAATAAAA
1 AAATAAAA
17364 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:17727 original size:22 final size:21
Alignment explanation
Indices: 17693--17733 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17683 AAAAGCAAGA
17693 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
17715 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
17734 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:17778 original size:19 final size:21
Alignment explanation
Indices: 17751--17805 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 21
17741 AAAAATGTTT
17751 GAGAAAAAATGAAAAAA-GAA
1 GAGAAAAAATGAAAAAATGAA
17771 GA-AAAAAAT-AAAAAATGAA
1 GAGAAAAAATGAAAAAATGAA
17790 GAGGCAAAAAATGAAA
1 GA-G-AAAAAATGAAA
17806 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.20
19 12 0.40
20 2 0.07
22 7 0.23
23 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (21 bp):
GAGAAAAAATGAAAAAATGAA
Found at i:18151 original size:16 final size:17
Alignment explanation
Indices: 18112--18152 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
18102 CAAAAATACA
*
18112 ACAAAAATATAAAAAGT
1 ACAAAAATATAAAAAGG
18129 A-AGAAAATA-AAAAAGG
1 ACA-AAAATATAAAAAGG
18145 ACAAAAAT
1 ACAAAAAT
18153 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.12
Consensus pattern (17 bp):
ACAAAAATATAAAAAGG
Found at i:19609 original size:26 final size:27
Alignment explanation
Indices: 19548--19609 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
19538 AAGGGATTAC
* * * *
19548 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
19575 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
19601 AAAATGAAA
1 AAAATGAAA
19610 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:19913 original size:21 final size:19
Alignment explanation
Indices: 19897--19950 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 19
19887 CAACAATGAT
19897 AAAATAAAAAAATACAATA
1 AAAATAAAAAAATACAATA
* *
19916 AAAATATAAAAAGTAAGAAATA
1 AAAATA-AAAAAAT-A-CAATA
*
19938 AAAAGAAAAAAAT
1 AAAATAAAAAAAT
19951 GAAATGGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 7 0.25
22 9 0.32
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.15
Consensus pattern (19 bp):
AAAATAAAAAAATACAATA
Found at i:20344 original size:13 final size:13
Alignment explanation
Indices: 20305--20347 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
20295 GAAAATTTAT
*
20305 AAAATAGA-ACAA
1 AAAATAGACAAAA
*
20317 AAAATAG-CAAGA
1 AAAATAGACAAAA
20329 AAAATAGACAAAA
1 AAAATAGACAAAA
20342 AAAATA
1 AAAATA
20348 AGAAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAATAGACAAAA
Found at i:20361 original size:16 final size:15
Alignment explanation
Indices: 20340--20369 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20330 AAATAGACAA
20340 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
20356 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
20370 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:20888 original size:65 final size:64
Alignment explanation
Indices: 20764--20890 Score: 148
Period size: 63 Copynumber: 2.0 Consensus size: 64
20754 AAAAGATTTA
* * ****
20764 AGAAAAAGACGAAAAAAAATAAAAAATGAAAATACAAATATATAAATAAAATTTGAGAAAAATGC
1 AGAAAAAGAC-AAAAAAAATAAAAAATGAAAAGACAAAAATATAAATAAAAAAAAAGAAAAATGC
* *
20829 AGAAAAAGA-AAAAAAAATAAAAAATGAAGAGGCAAAAATATGAAATAAAAAAAAAAGAAAAA
1 AGAAAAAGACAAAAAAAATAAAAAATGAAAAGACAAAAATAT-AAAT-AAAAAAAAAGAAAAA
20891 AATTTATAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
63 28 0.54
64 4 0.08
65 20 0.38
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.13
Consensus pattern (64 bp):
AGAAAAAGACAAAAAAAATAAAAAATGAAAAGACAAAAATATAAATAAAAAAAAAGAAAAATGC
Found at i:21158 original size:24 final size:24
Alignment explanation
Indices: 21107--21159 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
21097 ATGAAACTAT
*
21107 AAAAAAAAGAAAAAAAATTAAAGC
1 AAAAAAAAGAAAAAAAATTAAAAC
*
21131 AAAAGAAAA-AAGAAAAA-TAAAAC
1 AAAA-AAAAGAAAAAAAATTAAAAC
21154 AAAAAA
1 AAAAAA
21160 TATAAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 2 0.08
23 9 0.35
24 11 0.42
25 4 0.15
ACGTcount: A:0.83, C:0.04, G:0.08, T:0.06
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAATTAAAAC
Found at i:21166 original size:19 final size:18
Alignment explanation
Indices: 21104--21167 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
21094 TTTATGAAAC
21104 TATAAAAAAAAGAAAAAA
1 TATAAAAAAAAGAAAAAA
* *
21122 AATTAAAGCAAAAGAAAAAA
1 TA-TAAA-AAAAAGAAAAAA
* *
21142 GA-AAAATAAAACAAAAAA
1 TATAAAA-AAAAGAAAAAA
21160 TATAAAAA
1 TATAAAAA
21168 GTAAGAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 16 0.44
19 8 0.22
20 12 0.33
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (18 bp):
TATAAAAAAAAGAAAAAA
Done.