Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003101.1 Hibiscus syriacus cultivar Beakdansim tig00006474_pilon, 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: 77738
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4845 original size:10 final size:10
Alignment explanation
Indices: 4832--4873 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
4822 TTTTTTGAAA
4832 TTTTGGCTTT
1 TTTTGGCTTT
4842 TTTT-G-TTT
1 TTTTGGCTTT
*
4850 TTTTGCCTTT
1 TTTTGGCTTT
*
4860 TTTTTGCTTT
1 TTTTGGCTTT
4870 TTTT
1 TTTT
4874 TTTGAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.26
9 1 0.04
10 19 0.70
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.79
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:7509 original size:15 final size:15
Alignment explanation
Indices: 7485--7529 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
7475 ATCTTTGAGT
*
7485 ACCTACTTTGGGTAC
1 ACCTATTTTGGGTAC
7500 ACCTATTTTGGGTAC
1 ACCTATTTTGGGTAC
7515 ACCTATTTTGGGTAC
1 ACCTATTTTGGGTAC
7530 CTACTGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (15 bp):
ACCTATTTTGGGTAC
Found at i:14233 original size:45 final size:45
Alignment explanation
Indices: 14184--14308 Score: 124
Period size: 52 Copynumber: 2.6 Consensus size: 45
14174 TGATTTCGTT
14184 TATAATATCCATTCATACTAATTATGCATTATTGTACATTATATA
1 TATAATATCCATTCATACTAATTATGCATTATTGTACATTATATA
* *
14229 TATAACATTATAATATCATTCATACTAATTATGCATTGTTGTACATTATATA
1 TAT---A--AT-AT-CCATTCATACTAATTATGCATTATTGTACATTATATA
* * * * *
14281 TACAACATCCCTTCATATTACTTATGCA
1 TATAATATCCATTCATACTAATTATGCA
14309 CCATTCATAT
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
45 19 0.29
46 2 0.03
47 1 0.02
48 1 0.02
49 1 0.02
50 2 0.03
51 2 0.03
52 37 0.57
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (45 bp):
TATAATATCCATTCATACTAATTATGCATTATTGTACATTATATA
Found at i:14249 original size:52 final size:53
Alignment explanation
Indices: 14183--14288 Score: 187
Period size: 52 Copynumber: 2.0 Consensus size: 53
14173 ATGATTTCGT
*
14183 TTATAATATCCATTCATACTAATTATGCATTATTGTACATTATATATATAACA
1 TTATAATATCCATTCATACTAATTATGCATTATTGTACATTATATATACAACA
*
14236 TTATAATAT-CATTCATACTAATTATGCATTGTTGTACATTATATATACAACA
1 TTATAATATCCATTCATACTAATTATGCATTATTGTACATTATATATACAACA
14288 T
1 T
14289 CCCTTCATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 42 0.82
53 9 0.18
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (53 bp):
TTATAATATCCATTCATACTAATTATGCATTATTGTACATTATATATACAACA
Found at i:14478 original size:81 final size:81
Alignment explanation
Indices: 14349--14694 Score: 423
Period size: 81 Copynumber: 4.3 Consensus size: 81
14339 TTACCCAAAG
* * * * ** *
14349 GTATTTAGCCTTTCATCTAACTTGCATATTTGACA-CTTTTCTATCAAATGCACAGCTAGTCCAT
1 GTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTT-TGCCAAATGCACAGCTAGGCCAT
*
14413 TATTCTTTTACTCAATA
65 TATTCTTTTACTCAACA
* * * * * *
14430 GTGTTTAACCGTTCATCCAATTAGCATAATTGACACCTTTTTGCCAAATGCATATCTAGACCATT
1 GTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATT
14495 CA-TCTTTTACTCAAC-
66 -ATTCTTTTACTCAACA
*
14510 GATATTTAACTGTTCATCTAACT-GTCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCA
1 G-TATTTAACCGTTCATCTAACTAG-CATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCA
*
14574 TTATTATTTTACTCAACA
64 TTATTCTTTTACTCAACA
* ** * *
14592 GTATTTAATCGTTCATCTAACTAGCATAATTGACACCAGTCTGTCAAATGCACAGCTAGGCCATT
1 GTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATT
14657 -TATCTTTTACTCAACA
66 AT-TCTTTTACTCAACA
14673 GTATTTAACCGTTCATCTAACT
1 GTATTTAACCGTTCATCTAACT
14695 GACACCTTTC
Statistics
Matches: 228, Mismatches: 29, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
80 4 0.02
81 216 0.95
82 8 0.04
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (81 bp):
GTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATT
ATTCTTTTACTCAACA
Found at i:14783 original size:68 final size:68
Alignment explanation
Indices: 14694--14997 Score: 493
Period size: 68 Copynumber: 4.5 Consensus size: 68
14684 TTCATCTAAC
*
14694 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCAT
1 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACAT
14759 AAA
66 AAA
* *
14762 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCGAAGGCATTTAGCCTTTCATCTAACTGACAT
1 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACAT
14827 AAA
66 AAA
* * * *
14830 TGACACCTTTTTGTCAAATGCATAGTTAGGCCTCAATGGCACTTAGCCTTTCATCTAACTGGCAT
1 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACAT
*
14895 ATA
66 AAA
* *
14898 TGAAACTTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACAT
1 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACAT
14962 AAA
66 AAA
**
14965 TGACATATTTCTGTCAAATGCACAGTTAGGCCT
1 TGACACCTTTCTGTCAAATGCACAGTTAGGCCT
14998 ACTAATCTTT
Statistics
Matches: 215, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
67 60 0.28
68 155 0.72
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGACAT
AAA
Found at i:14983 original size:135 final size:136
Alignment explanation
Indices: 14694--14997 Score: 502
Period size: 135 Copynumber: 2.2 Consensus size: 136
14684 TTCATCTAAC
*
14694 TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCAT
1 TGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCAT
* * *
14759 AAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCGAAGGCATTTAGCCTTTCATCTAACTGA
66 AAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGA
14824 CATAAA
131 CATAAA
* * * *
14830 TGACACCTTTTTGTCAAATGCATAGTTAGGCCTCAATGGCACTTAGCCTTTCATCTAACTGGCAT
1 TGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCAT
* *
14895 ATATGAAACTTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGA
66 AAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGA
14959 CATAAA
131 CATAAA
*
14965 TGACATATTTCTGTCAAATGCACAGTTAGGCCT
1 TGACACATTTCTGTCAAATGCACAGTTAGGCCT
14998 ACTAATCTTT
Statistics
Matches: 156, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
135 79 0.51
136 77 0.49
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (136 bp):
TGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCAT
AAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGA
CATAAA
Found at i:15330 original size:55 final size:55
Alignment explanation
Indices: 15217--15360 Score: 191
Period size: 55 Copynumber: 2.6 Consensus size: 55
15207 TCCTATATGT
* * * * *
15217 AAATTCATACACTTAGTATGGATTTCTAAG-TTCGCACATATAGTGCCCATACGG
1 AAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* * **
15271 AAATTCATATATTTAGTATAAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
1 AAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
15326 AAATTCATACACTTAGTATGGATTTCTTAAGTTTT
1 AAATTCATACACTTAGTATGGATTTCTT-AGTTTT
15361 TTCACACTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
54 25 0.33
55 44 0.59
56 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
Found at i:16538 original size:35 final size:35
Alignment explanation
Indices: 16465--16539 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
16455 CGTCACTAAC
**
16465 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
16500 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
16535 AGTAA
1 AGTAA
16540 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:16644 original size:24 final size:24
Alignment explanation
Indices: 16617--16691 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
16607 CATAATTCAA
*
16617 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
16641 GTCATGTATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
16665 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
16688 GTCA
1 GTCA
16692 GGATCATAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.45
24 24 0.55
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:16697 original size:23 final size:23
Alignment explanation
Indices: 16621--16697 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
16611 ATTCAAGTCA
*
16621 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* *
16644 ATGTATTAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
16668 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
16691 AGGATCA
1 AGTATCA
16698 TAACATAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
23 25 0.56
24 20 0.44
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:17870 original size:18 final size:18
Alignment explanation
Indices: 17849--17886 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17839 TCCTTCCATC
*
17849 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
17867 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
17885 CA
1 CA
17887 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:19193 original size:18 final size:18
Alignment explanation
Indices: 19172--19241 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 18
19162 GGTCAACAAT
19172 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
19190 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
* **
19203 GGTAAACGGGTTAGGTCG
1 GGTCAACGGGTCGGGTCG
*
19221 GGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
19239 GGT
1 GGT
19242 TGTGACCGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
13 12 0.30
18 28 0.70
ACGTcount: A:0.14, C:0.17, G:0.49, T:0.20
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:19199 original size:13 final size:13
Alignment explanation
Indices: 19183--19213 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19173 GTCAACGGGT
*
19183 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
19196 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
19209 CGGGT
1 CGGGT
19214 TAGGTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:19213 original size:31 final size:31
Alignment explanation
Indices: 19176--19236 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
19166 AACAATGGTC
*
19176 AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
1 AACGGGTCAGGTCGGGTCAACGGGTCGGGTA
* *
19207 AACGGGTTAGGTCGGGTCAATGGGTCGGGT
1 AACGGGTCAGGTCGGGTCAACGGGTCGGGT
19237 CGGGTTGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (31 bp):
AACGGGTCAGGTCGGGTCAACGGGTCGGGTA
Found at i:21567 original size:19 final size:19
Alignment explanation
Indices: 21527--21580 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
21517 GGCAGAAATG
*
21527 GTATCAATACCGTAATAGA
1 GTATCAATACCATAATAGA
21546 GTATCAATACCATAGTATAGTA
1 GTATCAATACCATA--ATAG-A
*
21568 GTATCGATACCAT
1 GTATCAATACCAT
21581 GGTAGGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (19 bp):
GTATCAATACCATAATAGA
Found at i:22036 original size:54 final size:54
Alignment explanation
Indices: 21978--22286 Score: 392
Period size: 54 Copynumber: 5.8 Consensus size: 54
21968 CTGTATGGGT
* * *
21978 ACTATGCGTACAACTCACTGAATTCATCATATGTTGATGAACAACCATTTCAGC
1 ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCAGC
22032 ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTC-GAC
1 ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCAG-C
* * * * *
22086 ACTATTTGTGTAACTCACGGAATTCATCATATGTTGATGAACAATCGTTTCGGC
1 ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCAGC
* * * **
22140 ACTATGTGTGCAACTCAC-GAAGTTAATCATATGTTGATGAATAACCGTTTTGGC
1 ACTATGTGTGCAACTCACGGAA-TTCATCATATGTTGATGAACAACCATTTCAGC
* *
22194 AC--TGTGTGAAACTCACGGAATTCATCATATGTTGATGAACAACAATTTCAGC
1 ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCAGC
* * * * *
22246 ACTATGTGTGCAACCCACGTAACTCATAATATGTTTATGAA
1 ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAA
22287 TGATCGTATA
Statistics
Matches: 223, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
52 41 0.18
53 7 0.03
54 174 0.78
55 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (54 bp):
ACTATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCAGC
Found at i:22311 original size:160 final size:161
Alignment explanation
Indices: 21970--22311 Score: 429
Period size: 160 Copynumber: 2.1 Consensus size: 161
21960 ATGAATTTCT
* * * *
21970 GTATGGGTACTATGCGTACAACTCACTGAATTCATCATATGTTGATGAACAACCATTTCAGCACT
1 GTATAGGTACTATGTGTGCAACTCACTGAATTAATCATATGTTGATGAACAACCATTTCAGCAC-
* * * *
22035 ATGTGTGCAACTCACGGAATTCATCATATGTTGATGAACAACCATTTCGACACTATTTGTGTAAC
65 ATGTGTGAAACTCACGGAATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAAC
* * *
22100 TCACGGAATTCATCATATGTTGATGAACAATC
130 CCACGGAACTCATAATATGTTGATGAACAATC
* * * * * **
22132 GTTTCGGCACTATGTGTGCAACTCAC-GAAGTTAATCATATGTTGATGAATAACCGTTTTGGCAC
1 GTATAGGTACTATGTGTGCAACTCACTGAA-TTAATCATATGTTGATGAACAACCATTTCAGCAC
22196 -TGTGTGAAACTCACGGAATTCATCATATGTTGATGAACAACAATTTC-AGCACTATGTGTGCAA
65 ATGTGTGAAACTCACGGAATTCATCATATGTTGATGAACAACAATTTCGA-CACTATGTGTGCAA
* * **
22259 CCCACGTAACTCATAATATGTTTATGAATGATC
129 CCCACGGAACTCATAATATGTTGATGAACAATC
*
22292 GTATAGGTACTACGTGTGCA
1 GTATAGGTACTATGTGTGCA
22312 TTGCAACGAA
Statistics
Matches: 153, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
159 1 0.01
160 99 0.65
161 3 0.02
162 50 0.33
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (161 bp):
GTATAGGTACTATGTGTGCAACTCACTGAATTAATCATATGTTGATGAACAACCATTTCAGCACA
TGTGTGAAACTCACGGAATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACC
CACGGAACTCATAATATGTTGATGAACAATC
Found at i:27009 original size:25 final size:24
Alignment explanation
Indices: 26962--27011 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
26952 TCTTGGGATC
26962 TTTTCGATTAAATTTTTTGATGTA
1 TTTTCGATTAAATTTTTTGATGTA
*
26986 TTTTC-ATTACATATTTTTGTATGTA
1 TTTTCGATTAAAT-TTTTTG-ATGTA
27011 T
1 T
27012 GGTTAGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.60
Consensus pattern (24 bp):
TTTTCGATTAAATTTTTTGATGTA
Found at i:30152 original size:73 final size:73
Alignment explanation
Indices: 30033--30178 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
30023 AAGAAGAATC
30033 ACAACTTCTTCCCATGCCATCTCCTTATGCGATGCCACCTCATTTCCCCTCGAGGTTAGTAAAAC
1 ACAACTTCTTCCCATGCCATCTCCTTATGCGATGCCACCTCATTTCCCCTCGAGGTTAGTAAAAC
30098 TTGATAAA
66 TTGATAAA
30106 ACAACTTCTTCCCATGCCATCTCCTTATGCGATGCCACCTCATTTCCCCTCGAGGTTAGTAAAAC
1 ACAACTTCTTCCCATGCCATCTCCTTATGCGATGCCACCTCATTTCCCCTCGAGGTTAGTAAAAC
30171 TTGATAAA
66 TTGATAAA
30179 CAAAGGGATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (73 bp):
ACAACTTCTTCCCATGCCATCTCCTTATGCGATGCCACCTCATTTCCCCTCGAGGTTAGTAAAAC
TTGATAAA
Found at i:31505 original size:27 final size:27
Alignment explanation
Indices: 31463--31523 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
31453 CCGAGGCAAC
31463 TCAATTGTCGTGACAA-TGAAAATTGAT
1 TCAATTGTCGTGACAACTGAAAA-TGAT
*
31490 TCAATTGTCGTTACAACTGAAAATGAT
1 TCAATTGTCGTGACAACTGAAAATGAT
31517 TCAATTG
1 TCAATTG
31524 CCTTAGCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 26 0.81
28 6 0.19
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (27 bp):
TCAATTGTCGTGACAACTGAAAATGAT
Found at i:31533 original size:27 final size:28
Alignment explanation
Indices: 31463--31535 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
31453 CCGAGGCAAC
* *
31463 TCAATTGTCGTGACAA-TGAAAATTGAT
1 TCAATTGTCCTTACAACTGAAAATTGAT
*
31490 TCAATTGTCGTTACAACTGAAAA-TGAT
1 TCAATTGTCCTTACAACTGAAAATTGAT
31517 TCAATTG-CCTTAGCAACTG
1 TCAATTGTCCTTA-CAACTG
31536 GGTTCCTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.10
27 32 0.76
28 6 0.14
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (28 bp):
TCAATTGTCCTTACAACTGAAAATTGAT
Found at i:34273 original size:19 final size:20
Alignment explanation
Indices: 34239--34277 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34229 TTTTTTTTTC
*
34239 TATTTTTTTTACTTTAGTTT
1 TATTTTATTTACTTTAGTTT
34259 TATTTTATTTA-TTTAGTTT
1 TATTTTATTTACTTTAGTTT
34278 ACTTGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
TATTTTATTTACTTTAGTTT
Found at i:39730 original size:234 final size:233
Alignment explanation
Indices: 39321--39787 Score: 925
Period size: 234 Copynumber: 2.0 Consensus size: 233
39311 AAAATTTGTA
39321 AAATCAATGTATTAAAATCAATTTTGACCAAAATTCATTATGATGGACTAAAAAATTATGAAAAA
1 AAATCAATGTATTAAAATCAATTTTGACCAAAATTCATTATGATGGACTAAAAAATTATGAAAAA
39386 ACATTAAAACTTTAAAATGACTATCATAATACATTTTTCAACATACATGAGATGAAAACATAAAA
66 ACATTAAAACTTTAAAATGACTATCATAATACATTTTTCAACATACATGAGATGAAAACATAAAA
39451 TTATTTAACATCAAAACTCATGCATGCTTAAACTAAATGAGCAACCAATTATGCAAGATAATTAA
131 TTATTTAACATCAAAACTCATGCATGCTTAAACTAAATGAGCAACCAATTATGCAAGATAATTAA
39516 AATAATCTTAGAGGTTGCCTATTCCTTGTGAAGTGTGGC
196 AATAATCTTAGAGGTTGCCTATTCCTTGTGAAG-GTGGC
39555 AAATCAATGTATTAAAATCAATTTTGACCAAAATTCATTATGATGGACTAAAAAATTATGAAAAA
1 AAATCAATGTATTAAAATCAATTTTGACCAAAATTCATTATGATGGACTAAAAAATTATGAAAAA
39620 ACATTAAAACTTTAAAATGACTATCATAATACATTTTTCAACATACATGAGATGAAAACATAAAA
66 ACATTAAAACTTTAAAATGACTATCATAATACATTTTTCAACATACATGAGATGAAAACATAAAA
39685 TTATTTAACATCAAAACTCATGCATGCTTAAACTAAATGAGCAACCAATTATGCAAGATAATTAA
131 TTATTTAACATCAAAACTCATGCATGCTTAAACTAAATGAGCAACCAATTATGCAAGATAATTAA
39750 AATAATCTTAGAGGTTGCCTATTCCTTGTGAAGGTGGC
196 AATAATCTTAGAGGTTGCCTATTCCTTGTGAAGGTGGC
39788 TAGAGCATTT
Statistics
Matches: 233, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
233 5 0.02
234 228 0.98
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (233 bp):
AAATCAATGTATTAAAATCAATTTTGACCAAAATTCATTATGATGGACTAAAAAATTATGAAAAA
ACATTAAAACTTTAAAATGACTATCATAATACATTTTTCAACATACATGAGATGAAAACATAAAA
TTATTTAACATCAAAACTCATGCATGCTTAAACTAAATGAGCAACCAATTATGCAAGATAATTAA
AATAATCTTAGAGGTTGCCTATTCCTTGTGAAGGTGGC
Found at i:42317 original size:19 final size:19
Alignment explanation
Indices: 42289--42333 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
42279 CACTTTGATA
* * *
42289 TTATTATAAAGTTTATTTT
1 TTATTTTAAAGTCTAATTT
42308 TTATTTTAAAGTCTAATTT
1 TTATTTTAAAGTCTAATTT
42327 TTATTTT
1 TTATTTT
42334 TGAAATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
TTATTTTAAAGTCTAATTT
Found at i:51651 original size:31 final size:31
Alignment explanation
Indices: 51589--51654 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
51579 TACAATACAT
*
51589 TCCCCAAACATTTAATCCATTTGCAACATGG
1 TCCCCAAACATTTAATCCATTTACAACATGG
* * ** *
51620 TCCCCCAACATTTAGTCTGTTTACAATATGG
1 TCCCCAAACATTTAATCCATTTACAACATGG
51651 TCCC
1 TCCC
51655 TGACCATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (31 bp):
TCCCCAAACATTTAATCCATTTACAACATGG
Found at i:53366 original size:12 final size:12
Alignment explanation
Indices: 53349--53376 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53339 AAATGACCAA
53349 TTTATGTAAGAT
1 TTTATGTAAGAT
53361 TTTATGTAAGAT
1 TTTATGTAAGAT
53373 TTTA
1 TTTA
53377 GCAATCGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (12 bp):
TTTATGTAAGAT
Found at i:60903 original size:19 final size:19
Alignment explanation
Indices: 60859--60904 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
60849 ACTTTTGATA
* * *
60859 TTTATTATAAAGTTTATTT
1 TTTATTTTAAAGTCTAATT
60878 TTTATTTTAAAGTCTAATT
1 TTTATTTTAAAGTCTAATT
60897 TTTATTTT
1 TTTATTTT
60905 TGAAATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTATTTTAAAGTCTAATT
Found at i:64098 original size:24 final size:24
Alignment explanation
Indices: 64071--64122 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 24
64061 CCTCAAGGGG
*
64071 CACTGAATATTTGTCCCGAAGGAC
1 CACTGAATATTTGTCCCGAAAGAC
64095 CACTG----TTTGTCCCGAAAGAC
1 CACTGAATATTTGTCCCGAAAGAC
64115 CACT-AATA
1 CACTGAATA
64123 ATCCCTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 9
0.70 0.03 0.27
Matches are distributed among these distances:
20 18 0.78
24 5 0.22
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (24 bp):
CACTGAATATTTGTCCCGAAAGAC
Found at i:64105 original size:20 final size:20
Alignment explanation
Indices: 64080--64118 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
64070 GCACTGAATA
*
64080 TTTGTCCCGAAGGACCACTG
1 TTTGTCCCGAAAGACCACTG
64100 TTTGTCCCGAAAGACCACT
1 TTTGTCCCGAAAGACCACT
64119 AATAATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (20 bp):
TTTGTCCCGAAAGACCACTG
Found at i:70237 original size:31 final size:31
Alignment explanation
Indices: 70175--70240 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
70165 TACAATACAT
*
70175 TCCCCAAACATTTAATCCATTTGCAACATGG
1 TCCCCAAACATTTAATCCATTTACAACATGG
* * ** *
70206 TCCCCCAACATTTAGTCTGTTTACAATATGG
1 TCCCCAAACATTTAATCCATTTACAACATGG
70237 TCCC
1 TCCC
70241 TGACCATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (31 bp):
TCCCCAAACATTTAATCCATTTACAACATGG
Found at i:75790 original size:18 final size:18
Alignment explanation
Indices: 75756--75790 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
75746 GTGTAAAGTA
*
75756 GTATCGGTACCCCTTTGG
1 GTATCGGTACCCATTTGG
*
75774 GTATCGGTACCTATTTG
1 GTATCGGTACCCATTTG
75791 TATTCTAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (18 bp):
GTATCGGTACCCATTTGG
Done.