Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 61 of 240
Found at i:20023054 original size:18 final size:18
Alignment explanation
Indices: 20023028--20023074 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
20023018 GGTTAAAAAA
* *
20023028 TAACTGAATTACCCTAAT
1 TAACCGAATTACCCGAAT
20023046 TAACCGAATTACCCGAAT
1 TAACCGAATTACCCGAAT
*
20023064 TACCCGAATTA
1 TAACCGAATTA
20023075 TATGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.28
Consensus pattern (18 bp):
TAACCGAATTACCCGAAT
Found at i:20023055 original size:9 final size:9
Alignment explanation
Indices: 20023033--20023074 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
20023023 AAAAATAACT
20023033 GAATTACCC
1 GAATTACCC
* *
20023042 TAATTAACC
1 GAATTACCC
20023051 GAATTACCC
1 GAATTACCC
20023060 GAATTACCC
1 GAATTACCC
20023069 GAATTA
1 GAATTA
20023075 TATGTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (9 bp):
GAATTACCC
Found at i:20023104 original size:13 final size:13
Alignment explanation
Indices: 20023087--20023136 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
20023077 TGTTTTTTAT
*
20023087 TTTTATTTTTAGA
1 TTTTAGTTTTAGA
*
20023100 CTTTAGTTTTAG-
1 TTTTAGTTTTAGA
20023112 TTTTAGTTTTAGAA
1 TTTTAGTTTTAG-A
*
20023126 TTTTATTTTTA
1 TTTTAGTTTTA
20023137 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 11 0.35
13 10 0.32
14 10 0.32
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (13 bp):
TTTTAGTTTTAGA
Found at i:20023109 original size:19 final size:18
Alignment explanation
Indices: 20023082--20023136 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
20023072 TTATATGTTT
*
20023082 TTTATTTTTATTTTTAGAC
1 TTTAGTTTTATTTTTAG-C
* *
20023101 TTTAGTTTTAGTTTTAGT
1 TTTAGTTTTATTTTTAGC
20023119 TTTAGAATTTTATTTTTA
1 TTTAG--TTTTATTTTTA
20023137 TTTATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 15 0.50
20 10 0.33
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTAGTTTTATTTTTAGC
Found at i:20023187 original size:18 final size:18
Alignment explanation
Indices: 20023164--20023207 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20023154 AATTTTTCTG
*
20023164 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
*
20023182 ATTGGGTCGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
20023200 CTTGGGTT
1 ATTGGGTT
20023208 TGGATTGAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.11, C:0.05, G:0.45, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:20024991 original size:199 final size:200
Alignment explanation
Indices: 20024650--20025050 Score: 741
Period size: 199 Copynumber: 2.0 Consensus size: 200
20024640 ATAAAAAATA
*
20024650 AGCTGGATAGTGTGGCTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
1 AGCTGGATAGTGTGACTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
20024715 AGATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATA
66 AGATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATA
*
20024780 CTCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGTTAGTCCCTTATAAACACAC
131 CTCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACAC
20024845 CAAAC
196 CAAAC
* *
20024850 AGCTGGATAGTGTGACTTGAGTGCCGACCTGATCATCCAACCTTCCAAGTATCTACAAAAAAAAT
1 AGCTGGATAGTGTGACTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
*
20024915 A-ATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGTCAGTCTAACCAAAACACACCAGATA
66 AGATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATA
*
20024979 CTCACACGAGCCAATCCAACTGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACAC
131 CTCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACAC
20025044 CAAAC
196 CAAAC
20025049 AG
1 AG
20025051 AGTATAACAT
Statistics
Matches: 195, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
199 132 0.68
200 63 0.32
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.21
Consensus pattern (200 bp):
AGCTGGATAGTGTGACTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
AGATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATA
CTCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACAC
CAAAC
Found at i:20032916 original size:14 final size:14
Alignment explanation
Indices: 20032875--20032917 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
20032865 TAGCTAAGTA
*
20032875 AATTAATTGATTTTT
1 AATTAATTGA-ATTT
* *
20032890 AATTAAATAAATTT
1 AATTAATTGAATTT
20032904 AATTAATTGAATTT
1 AATTAATTGAATTT
20032918 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AATTAATTGAATTT
Found at i:20033693 original size:43 final size:43
Alignment explanation
Indices: 20033645--20033929 Score: 389
Period size: 43 Copynumber: 6.7 Consensus size: 43
20033635 AAAACAGGCT
*** * *
20033645 TTTAGCGGCGCTTTTTTTACAAACGCCACTATAGATCAAGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
* *
20033688 TTTAGCGGCGC-TTTCCCAAAAACGACGCTATAGATCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
*
20033730 TTTAGCGGCGCTTTTCCCACAAATGCCGCTATAGATCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
* *
20033773 TTTAGCGGCGC-TTTCCCAAAAACACCGCTATAGATC--GACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
**
20033813 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAAACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
* * *
20033856 TTTAGCTGCGCTTTTCCTACAAACGCCACTATAGATCAGGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
**
20033899 TTTAGCGGCGCTTTTTTCACAAACGCCGCTA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTA
20033930 AAAGTGCCAT
Statistics
Matches: 212, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
40 15 0.07
41 23 0.11
42 57 0.27
43 117 0.55
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACC
Found at i:20033788 original size:85 final size:85
Alignment explanation
Indices: 20033645--20033929 Score: 405
Period size: 85 Copynumber: 3.4 Consensus size: 85
20033635 AAAACAGGCT
*** *
20033645 TTTAGCGGCGCTTTTTTTACAAACGCCACTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAA
20033710 CGACGCTATAGATCAGGACC
66 CGACGCTATAGATCAGGACC
* *
20033730 TTTAGCGGCGCTTTTCCCACAAATGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCAAAAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAA
20033795 C-ACCGCTATAGATC--GACC
66 CGA-CGCTATAGATCAGGACC
* * * *
20033813 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAAACCTTTAGCTGCGCTTTTCCTACAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTCCCAAAA
* *
20033878 ACGCCACTATAGATCAGGACC
65 ACGACGCTATAGATCAGGACC
**
20033899 TTTAGCGGCGCTTTTTTCACAAACGCCGCTA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTA
20033930 AAAGTGCCAT
Statistics
Matches: 179, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
83 54 0.30
84 21 0.12
85 71 0.40
86 33 0.18
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (85 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAA
CGACGCTATAGATCAGGACC
Found at i:20033908 original size:126 final size:126
Alignment explanation
Indices: 20033673--20033912 Score: 383
Period size: 126 Copynumber: 1.9 Consensus size: 126
20033663 ACAAACGCCA
**
20033673 CTATAGATCAAGACCTTTAGCGGCGCTTTCCCAAAAACGACGCTATAGATCAGGACCTTTAGCGG
1 CTATAGATC-AGACCTTTAGCGGCGCTTTCCCAAAAACGACGCTATAGATCAAAACCTTTAGCGG
* *
20033738 CGCTTTTCCCACAAATGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCAAAAACACCG
65 CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTCCCAAAAACACCG
* * *
20033800 CTATAGATC-GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAAACCTTTAGCTG
1 CTATAGATCAGACCTTTAGCGGCGC-TTTCCCAAAAACGACGCTATAGATCAAAACCTTTAGCGG
*
20033864 CGCTTTTCCTACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTT
65 CGCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTT
20033913 TTTCACAAAC
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
125 15 0.14
126 80 0.77
127 9 0.09
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (126 bp):
CTATAGATCAGACCTTTAGCGGCGCTTTCCCAAAAACGACGCTATAGATCAAAACCTTTAGCGGC
GCTTTTCCCACAAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTCCCAAAAACACCG
Found at i:20034049 original size:13 final size:13
Alignment explanation
Indices: 20034031--20034077 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
20034021 ATAAAAGTAA
20034031 AATAAATTATAGT
1 AATAAATTATAGT
**
20034044 AATAAATT-TCAAC
1 AATAAATTAT-AGT
*
20034057 ATTAAATTATAGT
1 AATAAATTATAGT
20034070 AATAAATT
1 AATAAATT
20034078 TCAACATTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
AATAAATTATAGT
Found at i:20034064 original size:26 final size:26
Alignment explanation
Indices: 20034033--20034085 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20034023 AAAAGTAAAA
20034033 TAAATTATAGTAATAAATTTCAACAT
1 TAAATTATAGTAATAAATTTCAACAT
20034059 TAAATTATAGTAATAAATTTCAACAT
1 TAAATTATAGTAATAAATTTCAACAT
20034085 T
1 T
20034086 CACCTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAATTATAGTAATAAATTTCAACAT
Found at i:20034093 original size:26 final size:26
Alignment explanation
Indices: 20034033--20034104 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
20034023 AAAAGTAAAA
*
20034033 TAAATTATAGTAATAAATTTCAACAT
1 TAAACTATAGTAATAAATTTCAACAT
*
20034059 TAAATTATAGTAATAAATTTCAACAT
1 TAAACTATAGTAATAAATTTCAACAT
* * *
20034085 TCACCTATAATAAATAAATT
1 TAAACTATAGT-AATAAATT
20034105 AACATAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 33 0.80
27 8 0.20
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (26 bp):
TAAACTATAGTAATAAATTTCAACAT
Found at i:20034522 original size:21 final size:21
Alignment explanation
Indices: 20034459--20034513 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
20034449 TCTGCCTTCT
20034459 TTGAGTAACTACATGGCAATC
1 TTGAGTAACTACATGGCAATC
20034480 TTGAGTAACTACATGGCAATC
1 TTGAGTAACTACATGGCAATC
20034501 TTGAGTAACTACA
1 TTGAGTAACTACA
20034514 GTAGCATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (21 bp):
TTGAGTAACTACATGGCAATC
Found at i:20037050 original size:57 final size:57
Alignment explanation
Indices: 20036937--20037050 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
20036927 CTCCACTCCA
* **
20036937 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
20036994 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
20037051 TCTTCAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 48 0.94
58 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Found at i:20038692 original size:14 final size:14
Alignment explanation
Indices: 20038673--20038699 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20038663 TAACTGATCT
20038673 TAACCTCTAACCCC
1 TAACCTCTAACCCC
20038687 TAACCTCTAACCC
1 TAACCTCTAACCC
20038700 ATAAACCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.48, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCTCTAACCCC
Found at i:20039674 original size:40 final size:41
Alignment explanation
Indices: 20039603--20039718 Score: 173
Period size: 41 Copynumber: 2.8 Consensus size: 41
20039593 TTTTATTATT
* **
20039603 ATTAGCGGCACTTTTTCAAAAAACGCCGCTAAAGG-TCGAGC
1 ATTAGCGGCGCTTTTTC-AAAAACGCCGCTAAAGGAAAGAGC
20039644 ATTAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGGAAAGAGC
1 ATTAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGGAAAGAGC
20039685 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGG
20039719 CCCCCAAAAC
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
40 20 0.29
41 46 0.67
42 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGAAAGAGC
Found at i:20039804 original size:39 final size:39
Alignment explanation
Indices: 20039756--20039881 Score: 137
Period size: 39 Copynumber: 3.2 Consensus size: 39
20039746 GGGCTTAGGC
* *
20039756 TTTTT-GCGGCGCTTTTTAAAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCACTTTTTAAAAAGCGCCGCTAATGCTTA
** * *
20039794 TTTTTAGCGGCACTTTCCAAAAAGTGCCGCTAATGCTCGA
1 TTTTTAGCGGCACTTTTTAAAAAGCGCCGCTAATGCT-TA
** *
20039834 CCTTTAGCGGCATTTTTTATAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCACTTTTTA-AAAAGCGCCGCTAATGCTT-A
20039875 TTTTTAG
1 TTTTTAG
20039882 TGGCGTTTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
38 5 0.07
39 26 0.38
40 15 0.22
41 23 0.33
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (39 bp):
TTTTTAGCGGCACTTTTTAAAAAGCGCCGCTAATGCTTA
Found at i:20039881 original size:41 final size:40
Alignment explanation
Indices: 20039768--20039892 Score: 144
Period size: 41 Copynumber: 3.1 Consensus size: 40
20039758 TTTGCGGCGC
* *
20039768 TTTTTAAAAAACGCCGCTAATGCTT-ATTTTTAGCGGCAC
1 TTTTTAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCAT
** * * **
20039807 TTTCCAAAAAGTGCCGCTAATGCTCGACCTTTAGCGGCAT
1 TTTTTAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCAT
* *
20039847 TTTTTATAAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGT
1 TTTTTA-AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCAT
20039888 TTTTT
1 TTTTT
20039893 GTCTAAACGC
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 20 0.29
40 15 0.22
41 33 0.49
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (40 bp):
TTTTTAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCAT
Found at i:20039914 original size:12 final size:12
Alignment explanation
Indices: 20039897--20039922 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20039887 TTTTTTGTCT
20039897 AAACGCCGCTAA
1 AAACGCCGCTAA
20039909 AAACGCCGCTAA
1 AAACGCCGCTAA
20039921 AA
1 AA
20039923 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:20040742 original size:21 final size:20
Alignment explanation
Indices: 20040698--20040742 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
20040688 GTATATTTAT
20040698 TTTTATTTTTAATAT-TATA
1 TTTTATTTTTAATATATATA
*
20040717 -ATTATTATTTAATATATATA
1 TTTTATT-TTTAATATATATA
20040737 TTTTAT
1 TTTTAT
20040743 GTACATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 4 0.19
21 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTTTTAATATATATA
Found at i:20041239 original size:16 final size:16
Alignment explanation
Indices: 20041218--20041248 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20041208 CTTTTTACTC
20041218 AATTTTAAAAATAGAA
1 AATTTTAAAAATAGAA
*
20041234 AATTTTCAAAATAGA
1 AATTTTAAAAATAGA
20041249 GATAATACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
AATTTTAAAAATAGAA
Found at i:20042639 original size:22 final size:22
Alignment explanation
Indices: 20042609--20042651 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20042599 ACAGCAGAAC
* *
20042609 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
20042631 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
20042652 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:20042798 original size:42 final size:42
Alignment explanation
Indices: 20042723--20042990 Score: 276
Period size: 42 Copynumber: 6.4 Consensus size: 42
20042713 ACGTCACTAA
* *
20042723 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
* *
20042767 CTTTAGCGGCGCTTAGAAAAAAATGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * *
20042809 CTTTAGCGACGCTT--AAAAAAACGCCCCTAAAGATCATATT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * *
20042849 CTTTAGCGGCGCTTAGAAACAACCGCCGCTAAAGAACATGAT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * *
20042891 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* ***
20042934 CTATAGCGGCGCTTATTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGA-TCA-TGTT
20042976 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
20042991 TTTCACAAAC
Statistics
Matches: 187, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
40 35 0.19
41 1 0.01
42 107 0.57
43 31 0.17
44 13 0.07
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:20042877 original size:82 final size:83
Alignment explanation
Indices: 20042740--20042966 Score: 278
Period size: 82 Copynumber: 2.7 Consensus size: 83
20042730 GGCGCTTACA
* * *
20042740 TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCGCTAAAGATCA
1 TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACA
*
20042805 TGCTCTTTAGCGACGC-T
66 TGATCTTTAGCGACGCTT
* * *
20042822 TAAAAAAACGCCCCTAAAGATCATATTCTTTAGCGGCGCTTAGAAACAACCGCCGCTAAAGAACA
1 TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACA
*
20042887 TGATCTTTAGCGGCGCTT
66 TGATCTTTAGCGACGCTT
* * * * ***
20042905 TGGAAGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTATTCAAAAACGCCGCTAAA
1 T--AAAAAAACGCCCCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAA
20042967 AGTAGTGTTC
Statistics
Matches: 123, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
82 73 0.59
83 2 0.02
84 1 0.01
85 47 0.38
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (83 bp):
TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACA
TGATCTTTAGCGACGCTT
Found at i:20043429 original size:12 final size:12
Alignment explanation
Indices: 20043412--20043451 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
20043402 TTTTGAACCT
*
20043412 CTGCTTCTATTG
1 CTGCTTCTATCG
*
20043424 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
20043436 CTGCTTCTCTCG
1 CTGCTTCTATCG
20043448 CTGC
1 CTGC
20043452 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:20043462 original size:21 final size:21
Alignment explanation
Indices: 20043436--20043504 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
20043426 GCTTCTCTCG
*
20043436 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
20043457 CTGCTTCTCTCGTTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
20043478 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
20043499 CTGCTT
1 CTGCTT
20043505 TAGGTTGCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.01, C:0.42, G:0.20, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:20048985 original size:9 final size:9
Alignment explanation
Indices: 20048971--20049206 Score: 108
Period size: 9 Copynumber: 27.9 Consensus size: 9
20048961 AAGATATACA
20048971 TTATGTAAG
1 TTATGTAAG
20048980 TTATGTAAG
1 TTATGTAAG
20048989 TTATGTAAG
1 TTATGTAAG
* *
20048998 CTGTGTAAG
1 TTATGTAAG
**
20049007 TTGCGTAAG
1 TTATGTAAG
* *
20049016 ATGTGT-A-
1 TTATGTAAG
* *
20049023 TTATGAAAC
1 TTATGTAAG
20049032 TTATGTAAG
1 TTATGTAAG
20049041 TTATGTAAG
1 TTATGTAAG
*
20049050 TTGTGTAAG
1 TTATGTAAG
**
20049059 TTGCGTAAG
1 TTATGTAAG
* *
20049068 ATGTGT-A-
1 TTATGTAAG
* *
20049075 TTATGAAAC
1 TTATGTAAG
20049084 TTATGTAAG
1 TTATGTAAG
*
20049093 TTATGT--C
1 TTATGTAAG
*
20049100 TTATGTTAG
1 TTATGTAAG
*
20049109 TTATGTAAT
1 TTATGTAAG
*
20049118 TTTTGT-A-
1 TTATGTAAG
*
20049125 TTATTTACA-
1 TTATGTA-AG
*
20049134 -CATGTAAG
1 TTATGTAAG
*
20049142 TTATGT--C
1 TTATGTAAG
20049149 TTATGTAAG
1 TTATGTAAG
* **
20049158 ATGCGTAAG
1 TTATGTAAG
*
20049167 TTGTGT-A-
1 TTATGTAAG
*
20049174 TTATGAAAG
1 TTATGTAAG
20049183 TTATGTAAG
1 TTATGTAAG
20049192 TTATGT--G
1 TTATGTAAG
20049199 TTATGTAA
1 TTATGTAA
20049207 ATGAATATAT
Statistics
Matches: 171, Mismatches: 40, Indels: 32
0.70 0.16 0.13
Matches are distributed among these distances:
7 34 0.20
8 11 0.06
9 126 0.74
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20049039 original size:52 final size:52
Alignment explanation
Indices: 20048970--20049098 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
20048960 CAAGATATAC
* *
20048970 ATTATGTAAGTTATGTAAGTTATGTAAGCTGTGTAAGTTGCGTAAGATGTGT
1 ATTATGAAACTTATGTAAGTTATGTAAGCTGTGTAAGTTGCGTAAGATGTGT
*
20049022 ATTATGAAACTTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGATGTGT
1 ATTATGAAACTTATGTAAGTTATGTAAGCTGTGTAAGTTGCGTAAGATGTGT
20049074 ATTATGAAACTTATGTAAGTTATGT
1 ATTATGAAACTTATGTAAGTTATGT
20049099 CTTATGTTAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (52 bp):
ATTATGAAACTTATGTAAGTTATGTAAGCTGTGTAAGTTGCGTAAGATGTGT
Found at i:20049102 original size:16 final size:16
Alignment explanation
Indices: 20049083--20049114 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20049073 TATTATGAAA
20049083 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
*
20049099 CTTATGTTAGTTATGT
1 CTTATGTAAGTTATGT
20049115 AATTTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (16 bp):
CTTATGTAAGTTATGT
Found at i:20049103 original size:25 final size:25
Alignment explanation
Indices: 20048970--20049203 Score: 130
Period size: 25 Copynumber: 9.2 Consensus size: 25
20048960 CAAGATATAC
*
20048970 ATTATGTAAGTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
* * * ** * *
20048995 AAGCTGTGTAAGTTGCGTAAGATGTGT
1 -A-TTATGAAAGTTATGTAAGTTATGT
*
20049022 ATTATGAAACTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
* * ** * *
20049047 AAGTTGTGTAAGTTGCGTAAGATGTGT
1 -A-TTATGAAAGTTATGTAAGTTATGT
*
20049074 ATTATGAAACTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
* ** * *
20049099 CTTATGTTAGTTATGTAATTTTTGT
1 ATTATGAAAGTTATGTAAGTTATGT
* * *
20049124 ATTATTTACA--CATGTAAGTTATGT
1 ATTA-TGAAAGTTATGTAAGTTATGT
* * * ** *
20049148 CTTATGTAAGATGCGTAAGTTGTGT
1 ATTATGAAAGTTATGTAAGTTATGT
20049173 ATTATGAAAGTTATGTAAGTTATGT
1 ATTATGAAAGTTATGTAAGTTATGT
*
20049198 GTTATG
1 ATTATG
20049204 TAAATGAATA
Statistics
Matches: 146, Mismatches: 56, Indels: 13
0.68 0.26 0.06
Matches are distributed among these distances:
23 2 0.01
24 14 0.10
25 89 0.61
26 6 0.04
27 35 0.24
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (25 bp):
ATTATGAAAGTTATGTAAGTTATGT
Found at i:20050422 original size:14 final size:14
Alignment explanation
Indices: 20050403--20050432 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20050393 CACGAACAGC
20050403 AAGATGATTAACTA
1 AAGATGATTAACTA
20050417 AAGATGATTAACTA
1 AAGATGATTAACTA
20050431 AA
1 AA
20050433 AACCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:20050661 original size:36 final size:36
Alignment explanation
Indices: 20050620--20050735 Score: 116
Period size: 36 Copynumber: 3.2 Consensus size: 36
20050610 AAAAACAAAT
20050620 TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
1 TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
* ** *
20050656 TATTTCAGAACAT-AACAACA-TA-ATCAAAAACAAA--T
1 TATTTCAG-AC-TCAA-AA-ATTATTTCAAATCCAAAGCA
*
20050691 TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
1 TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
20050727 TATTTCAGA
1 TATTTCAGA
20050736 ACATAACAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
32 1 0.02
33 5 0.08
34 12 0.19
35 8 0.13
36 17 0.27
37 13 0.21
38 5 0.08
39 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (36 bp):
TATTTCAGACTCAAAAATTATTTCAAATCCAAAGCA
Found at i:20050684 original size:71 final size:71
Alignment explanation
Indices: 20050568--20050768 Score: 368
Period size: 71 Copynumber: 2.8 Consensus size: 71
20050558 CCAGATCCAG
*
20050568 ATTTCAGAA-CCAAAGCATAATTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTC
1 ATTTCA-AATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTC
20050632 AAAAATT
65 AAAAATT
20050639 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
1 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
*
20050704 GAAATT
66 AAAATT
20050710 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCA
1 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCA
20050769 AATCCACTCA
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
70 2 0.02
71 125 0.98
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (71 bp):
ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
AAAATT
Found at i:20051103 original size:22 final size:22
Alignment explanation
Indices: 20051075--20051121 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
20051065 GTGGCTGTAA
*
20051075 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
20051097 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
20051119 TAA
1 TAA
20051122 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:20052123 original size:7 final size:8
Alignment explanation
Indices: 20052113--20052144 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
20052103 TTTAGGATTT
20052113 AACC-CTA
1 AACCTCTA
20052120 AACCTCTA
1 AACCTCTA
20052128 AACCTCTA
1 AACCTCTA
20052136 AACC-CTA
1 AACCTCTA
20052143 AA
1 AA
20052145 ATTTTAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 9 0.38
8 15 0.62
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (8 bp):
AACCTCTA
Found at i:20052343 original size:23 final size:23
Alignment explanation
Indices: 20052289--20052344 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
20052279 CTAAACCTTA
*
20052289 AACCCAAAACACCCTAATACCCT
1 AACCCTAAACACCCTAATACCCT
20052312 AACCCTAAACACCCTAATACCCT
1 AACCCTAAACACCCTAATACCCT
*
20052335 AACCTTAAAC
1 AACCCTAAAC
20052345 CTACATCGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (23 bp):
AACCCTAAACACCCTAATACCCT
Found at i:20052363 original size:7 final size:7
Alignment explanation
Indices: 20052242--20052364 Score: 54
Period size: 7 Copynumber: 17.0 Consensus size: 7
20052232 ACTAAAGTAG
20052242 CCTAAAC
1 CCTAAAC
*
20052249 CCCAAAC
1 CCTAAAC
*
20052256 CTTAAAC
1 CCTAAAC
* *
20052263 CTTATAC
1 CCTAAAC
* *
20052270 CCCAGAC
1 CCTAAAC
20052277 TCCTAAAC
1 -CCTAAAC
*
20052285 CTTAAAC
1 CCTAAAC
*
20052292 CCAAAACAC
1 CC-TAA-AC
20052301 CCTAATAC
1 CCTAA-AC
20052309 CCT-AAC
1 CCTAAAC
20052315 CCTAAACAC
1 CCT-AA-AC
20052324 CCTAATAC
1 CCTAA-AC
20052332 CCT-AAC
1 CCTAAAC
*
20052338 CTTAAA-
1 CCTAAAC
* *
20052344 CCTACAT
1 CCTAAAC
*
20052351 CGTAAAC
1 CCTAAAC
20052358 CCTAAAC
1 CCTAAAC
20052365 TTTAAACTTT
Statistics
Matches: 86, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
6 13 0.15
7 42 0.49
8 22 0.26
9 9 0.10
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:20052926 original size:114 final size:114
Alignment explanation
Indices: 20052529--20053506 Score: 820
Period size: 113 Copynumber: 8.6 Consensus size: 114
20052519 ACTTTCAACA
* * * * * * * ** *
20052529 AAGCGCCACTAATTTTAGTATAAATTAAGAACAAAACGTTGCGTTTTGTTTATGGTAAGTCGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* * * * *
20052594 CGCTATC-AACAAATCGCCGCTAATACTATGATTTAGCGGCGTTTTACCGA
66 CGCT-TCTCACAAAGCGCCGCTAATACTATGCTTTAACGGCG-TTTACCGT
* * ** * * ** * *
20052644 AATCGCCACTAAATCAAGTATACATCAAGACCAAAATGATGCGTTTTGGTTCAGATGCTTGGTGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* *
20052709 CGCTT-TTATCCAAGCGCCGCTAATACTATGCTTTAACGGCGTTT-CAC-T
66 CGCTTCTCA-CAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTAC-CGT
* * * * **
20052757 AAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* * * *
20052822 CGCTTCTCACAAAGCGCCGCTACTAATATTCTTTAGCGGCGGTTTACCGT
66 CGCTTCTCACAAAGCGCCGCTAATACTATGCTTTAACGGC-GTTTACCGT
* * * *
20052872 AAGCGCCACTAATTTTA-TATACATTAAGATCAAAACGCTGCGTTTTTGTTAAGATATTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* *
20052936 CGCTAGCT-ACAAATCGCCGCTAATACTATGCTTTAACGGCGTTT-CAC-T
66 CGCT-TCTCACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTAC-CGT
* * * * ** *
20052984 AAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGATAAGATATTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* * * * * *
20053049 CGCTTCTCACAAAACGCCGCTATTAATATTCTTTAGCGGTGGTTTACCGT
66 CGCTTCTCACAAAGCGCCGCTAATACTATGCTTTAACGG-CGTTTACCGT
* * * *
20053099 AAGCGCCACTAATTTTA-TATACATTAAGATCAAAACGCTGCGTTTTTGTTAAGATATTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* * * *
20053163 CGCTAGCT-ACAAATCGCCGCTAATACTATTCTTTAGCGGCGTTTGACCGT
66 CGCT-TCTCACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTT-ACCGT
* * * * * * * *
20053213 ATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATGTGTTTCGCTTAAGATAGTTTGCGG
1 AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* * * * * * *
20053278 CGCTTC-CATAAAGCGTCGCTATTACTGTACTTTAACGGCGTTTTCCTAT
66 CGCTTCTCACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTACC-GT
* * * * ** *
20053327 AAACACCACTAATTCTAAG-ATACCTCAAGACC-AAACTCTGCGTTTTGGTTAAGCTATTTTGCG
1 AAGCGCCACTAATT-TTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCG
* * * * *
20053390 GCGTTTC-CAGAAAGCGCCGCTATTACTGTCCTTTAACGGCGTTT-CGCGT
65 GCGCTTCTCACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTAC-CGT
* * * * * * *
20053439 AAACGCCACTACTTTTAAG-ATACACCAAGACGAAAAC-ACAGCGTTTTGGTTAAGAGATTTCGC
1 AAGCGCCACTAATTTT-AGTATACATCAAGACCAAAACGA-TGCGTTTTGGTTAAGATATTTTGC
20053502 GGCGC
64 GGCGC
20053507 ATTGTGGTAA
Statistics
Matches: 696, Mismatches: 143, Indels: 50
0.78 0.16 0.06
Matches are distributed among these distances:
111 1 0.00
112 46 0.07
113 257 0.37
114 229 0.33
115 163 0.23
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (114 bp):
AAGCGCCACTAATTTTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
CGCTTCTCACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTACCGT
Found at i:20052998 original size:227 final size:228
Alignment explanation
Indices: 20052723--20053449 Score: 962
Period size: 227 Copynumber: 3.2 Consensus size: 228
20052713 TTTATCCAAG
20052723 CGCCGCTAATACTATGCTTTAACGGCGTTTCAC-TAAGCGCCACTAATTCTACTATACATCGAGG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACGTAAGCGCCACTAATTCTACTATACATCGAGG
*
20052787 CCAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTACTAATATT
66 CCAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTATTAATATT
20052852 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTT
131 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTT
20052917 TTGTTAAGATATTTTGCGGCGCTAGCTACAAAT
196 TTGTTAAGATATTTTGCGGCGCTAGCTACAAAT
20052950 CGCCGCTAATACTATGCTTTAACGGCGTTTCAC-TAAGCGCCACTAATTCTACTATACATCGAGG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACGTAAGCGCCACTAATTCTACTATACATCGAGG
* *
20053014 CCAAAATTATGCGTTTTGGATAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTATTAATATT
66 CCAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTATTAATATT
*
20053079 CTTTAGCGGTGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTT
131 CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTT
20053144 TTGTTAAGATATTTTGCGGCGCTAGCTACAAAT
196 TTGTTAAGATATTTTGCGGCGCTAGCTACAAAT
* * * * * * * *
20053177 CGCCGCTAATACTATTCTTTAGCGGCGTTTGACCGTATGCGCCACTAGTTCTAGTATAAATCAAG
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCA-CGTAAGCGCCACTAATTCTACTATACATCGAG
* ** * * * * * * * *
20053242 ACCAAAACGATGTGTTTCGCTTAAGATAGTTTGCGGCGCTTC-CATAAAGCGTCGCTATTACTGT
65 GCCAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTATTAATAT
* * * * * * * * * * * *
20053306 ACTTTAACGGC-GTTTTCCTATAAACACCACTAATTCTAAGATACCTCAAGA-CCAAACTCTGCG
130 TCTTTAGCGGCGGTTTACC-GTAAGCGCCACTAATT-TTATATACATTAAGATCAAAACGCTGCG
* * ** * * *
20053369 TTTTGGTTAAGCTATTTTGCGGCG-TTTCCAGAAAG
193 TTTTTGTTAAGATATTTTGCGGCGCTAGCTACAAAT
* * * * *
20053404 CGCCGCTATTACTGTCCTTTAACGGCGTTTCGCGTAAACGCCACTA
1 CGCCGCTAATACTATGCTTTAACGGCGTTTCACGTAAGCGCCACTA
20053450 CTTTTAAGAT
Statistics
Matches: 443, Mismatches: 53, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
226 12 0.03
227 290 0.65
228 71 0.16
229 70 0.16
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (228 bp):
CGCCGCTAATACTATGCTTTAACGGCGTTTCACGTAAGCGCCACTAATTCTACTATACATCGAGG
CCAAAATTATGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTATTAATATT
CTTTAGCGGCGGTTTACCGTAAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTT
TTGTTAAGATATTTTGCGGCGCTAGCTACAAAT
Found at i:20053313 original size:341 final size:340
Alignment explanation
Indices: 20052529--20053506 Score: 854
Period size: 341 Copynumber: 2.9 Consensus size: 340
20052519 ACTTTCAACA
* * * * * * *
20052529 AAGCGCCACTAATTTTAGTATAAATTAAGAACAAAACGTTGCGTTTT-GTTTATGGTAAG-TCGC
1 AAGCGCCACTAATTCTA-TATAAATCAAGACCAAAACGATGCGTTTTCG-TTAAGAT-AGTTTGC
* * * * * *
20052592 GGCGCTATCAACAAATCGCCGCTAATACTATGA-TTTAGCGGCGTTTTACCGA-AATCGCCACTA
63 GGCGCTAGCCACAAAGCGCCGCTAATACTAT-ACTTTAACGGCGTTTT-CC-ATAAACACCACTA
* * * * ** * * **
20052655 AATC-AAGTATACATCAAGACCAAAATGATGCGTTTTGGTTCAGATGCTTGGTGGCGCTTTTATC
125 ATTCTAAG-ATACATCAAGACCAAACT-ATGCGTTTTGGATAAGATATTTTGCGGCGCTTCCA-C
* * * * * * * * ** *
20052719 CAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCAC-TAAGCGCCACTAATTCTACTATACATC
187 AAAACGCCGCTATTAATATCCTTTAACGGCGTTTCGCGTAAACGCCACTAATTTTAAGATACACC
* * * * * *
20052783 GAGGCCAAAATTA-TGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTACTA
252 AAGACGAAAA-CACTGCGTTTTGGTTAAGATATTTTGCGGCGCTGCTCACAAAGCGCCGCTAATA
20052847 ATATTCTTTAGCGGCGGTTTACCGT
316 ATATTCTTTAGCGGCGGTTTACCGT
* * * * * * *
20052872 AAGCGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTTTTGTTAAGATATTTTGCGGC
1 AAGCGCCACTAATTCTATATAAATCAAGACCAAAACGATGCGTTTTCGTTAAGATAGTTTGCGGC
* * * * *
20052937 GCTAGCTACAAATCGCCGCTAATACTATGCTTTAACGGCG-TTT-CACTAAGCGCCACTAATTCT
66 GCTAGCCACAAAGCGCCGCTAATACTATACTTTAACGGCGTTTTCCA-TAAACACCACTAATTCT
** * * *
20053000 ACTATACATCGAGGCCAAAATTATGCGTTTTGGATAAGATATTTTGCGGCGCTTCTCACAAAACG
130 AAGATACATCAAGACC-AAACTATGCGTTTTGGATAAGATATTTTGCGGCGCTTC-CACAAAACG
* * * * * **
20053065 CCGCTATTAATATTCTTTAGCGGTGGTTTAC-CGTAAGCGCCACTAATTTT-ATATACATTAAGA
193 CCGCTATTAATATCCTTTAACGG-CGTTT-CGCGTAAACGCCACTAATTTTAAGATACACCAAGA
* * * *
20053128 TC-AAAACGCTGCGTTTTTGTTAAGATATTTTGCGGCGCTAGCT-ACAAATCGCCGCTAATACTA
256 -CGAAAACACTGCGTTTTGGTTAAGATATTTTGCGGCGCT-GCTCACAAAGCGCCGCTAATAATA
20053191 TTCTTTAGCGGC-GTTTGACCGT
319 TTCTTTAGCGGCGGTTT-ACCGT
* * *
20053213 ATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATGTG-TTTCGCTTAAGATAGTTTGCG
1 AAGCGCCACTAATTCTA-TATAAATCAAGACCAAAACGATGCGTTTTCG-TTAAGATAGTTTGCG
* * * * *
20053277 GCGCT-TCCATAAAGCGTCGCTATTACTGTACTTTAACGGCGTTTTCCTATAAACACCACTAATT
64 GCGCTAGCCACAAAGCGCCGCTAATACTATACTTTAACGGCGTTTTCC-ATAAACACCACTAATT
* * * * * * *
20053341 CTAAGATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGCTATTTTGCGGCGTTTCCAGAAAGCG
128 CTAAGATACATCAAGACCAAACTATGCGTTTTGGATAAGATATTTTGCGGCGCTTCCACAAAACG
* * *
20053406 CCGCTATTACTGTCCTTTAACGGCGTTTCGCGTAAACGCCACTACTTTTAAGATACACCAAGACG
193 CCGCTATTAATATCCTTTAACGGCGTTTCGCGTAAACGCCACTAATTTTAAGATACACCAAGACG
* * *
20053471 AAAACACAGCGTTTTGGTTAAGAGATTTCGCGGCGC
258 AAAACACTGCGTTTTGGTTAAGATATTTTGCGGCGC
20053507 ATTGTGGTAA
Statistics
Matches: 520, Mismatches: 92, Indels: 48
0.79 0.14 0.07
Matches are distributed among these distances:
338 1 0.00
339 2 0.00
340 100 0.19
341 204 0.39
342 167 0.32
343 45 0.09
344 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (340 bp):
AAGCGCCACTAATTCTATATAAATCAAGACCAAAACGATGCGTTTTCGTTAAGATAGTTTGCGGC
GCTAGCCACAAAGCGCCGCTAATACTATACTTTAACGGCGTTTTCCATAAACACCACTAATTCTA
AGATACATCAAGACCAAACTATGCGTTTTGGATAAGATATTTTGCGGCGCTTCCACAAAACGCCG
CTATTAATATCCTTTAACGGCGTTTCGCGTAAACGCCACTAATTTTAAGATACACCAAGACGAAA
ACACTGCGTTTTGGTTAAGATATTTTGCGGCGCTGCTCACAAAGCGCCGCTAATAATATTCTTTA
GCGGCGGTTTACCGT
Found at i:20055860 original size:107 final size:107
Alignment explanation
Indices: 20055674--20055884 Score: 386
Period size: 107 Copynumber: 2.0 Consensus size: 107
20055664 CCATACTTTG
** *
20055674 AAGTTTAAAGGGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACTCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
20055739 GTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTTAA
66 GTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTTAA
*
20055781 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCATGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
20055846 GTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
66 GTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
20055885 AGAAAAACTT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (107 bp):
AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
GTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTTTAA
Found at i:20060464 original size:38 final size:37
Alignment explanation
Indices: 20060409--20060486 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 37
20060399 GGTAGTAGCT
20060409 TAGATTTTTAATGTCTTTTAAGAAATTATTGGAATGG
1 TAGATTTTTAATGTCTTTTAAGAAATTATTGGAATGG
20060446 TAGAGTTTTTAATGTCTTTTAAGAAATTATTGGAATGG
1 TAGA-TTTTTAATGTCTTTTAAGAAATTATTGGAATGG
20060484 TAG
1 TAG
20060487 GGTGTTTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (37 bp):
TAGATTTTTAATGTCTTTTAAGAAATTATTGGAATGG
Found at i:20069549 original size:14 final size:15
Alignment explanation
Indices: 20069506--20069550 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
20069496 ATAACTTAAA
*
20069506 TTCAACACTTAATTT
1 TTCAACACTTATTTT
* *
20069521 TTCAATATTTATTTT
1 TTCAACACTTATTTT
20069536 TTCAACACTT-TTTT
1 TTCAACACTTATTTT
20069550 T
1 T
20069551 AGCACTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.58
Consensus pattern (15 bp):
TTCAACACTTATTTT
Found at i:20070978 original size:16 final size:15
Alignment explanation
Indices: 20070953--20070982 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20070943 ATTTTTTCCC
20070953 TTTTTTTATTTATTA
1 TTTTTTTATTTATTA
20070968 TTTTATTTATTTATT
1 TTTT-TTTATTTATT
20070983 TTTAGCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTATTTATTA
Found at i:20070985 original size:14 final size:14
Alignment explanation
Indices: 20070955--20071006 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
20070945 TTTTTCCCTT
20070955 TTTTTATTTA-TTA
1 TTTTTATTTATTTA
20070968 -TTTTATTTATTTA
1 TTTTTATTTATTTA
** *
20070981 TTTTTAGCTATTCA
1 TTTTTATTTATTTA
*
20070995 CTTTTATTTATT
1 TTTTTATTTATT
20071007 GTTTATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 9 0.29
13 3 0.10
14 19 0.61
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:20071098 original size:23 final size:24
Alignment explanation
Indices: 20071063--20071110 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
20071053 TTAGACTAGA
20071063 TTATTATATTTTT-ATTGTCCCTT
1 TTATTATATTTTTGATTGTCCCTT
*
20071086 TTATTAT-TATTTTGATTGTTCCTT
1 TTATTATAT-TTTTGATTGTCCCTT
20071110 T
1 T
20071111 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 11 0.50
24 10 0.45
ACGTcount: A:0.17, C:0.10, G:0.06, T:0.67
Consensus pattern (24 bp):
TTATTATATTTTTGATTGTCCCTT
Found at i:20071120 original size:24 final size:24
Alignment explanation
Indices: 20071063--20071110 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
20071053 TTAGACTAGA
*
20071063 TTATTA-TATTTTTATTGTCCCTT
1 TTATTATTATTTTGATTGTCCCTT
*
20071086 TTATTATTATTTTGATTGTTCCTT
1 TTATTATTATTTTGATTGTCCCTT
20071110 T
1 T
20071111 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.17, C:0.10, G:0.06, T:0.67
Consensus pattern (24 bp):
TTATTATTATTTTGATTGTCCCTT
Found at i:20072794 original size:18 final size:21
Alignment explanation
Indices: 20072762--20072807 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
20072752 ATTTATTTTC
*
20072762 ATTTTTATTACTCGT-TT-AT
1 ATTTTTTTTACTCGTATTGAT
20072781 ATTTTTTTTA-TCGTATTGAT
1 ATTTTTTTTACTCGTATTGAT
20072801 ATTTTTT
1 ATTTTTT
20072808 ATAGTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 9 0.38
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (21 bp):
ATTTTTTTTACTCGTATTGAT
Found at i:20072808 original size:18 final size:19
Alignment explanation
Indices: 20072784--20072824 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
20072774 CGTTTATATT
* *
20072784 TTTTTTATCGT-ATTGATA
1 TTTTTTATAGTAATTAATA
20072802 TTTTTTATAGTAATTAATA
1 TTTTTTATAGTAATTAATA
20072821 TTTT
1 TTTT
20072825 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTTTTATAGTAATTAATA
Found at i:20073834 original size:21 final size:22
Alignment explanation
Indices: 20073810--20073866 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
20073800 ACCATTGAAT
* *
20073810 TTAAAATTTTAAATTCA-GAAA
1 TTAAAATTATAAATTCATAAAA
**
20073831 TTAAAAGAATAAATTCATAAAA
1 TTAAAATTATAAATTCATAAAA
*
20073853 TTAAAATTAAAAAT
1 TTAAAATTATAAAT
20073867 ATGATTACTA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
TTAAAATTATAAATTCATAAAA
Found at i:20083739 original size:14 final size:14
Alignment explanation
Indices: 20083720--20083746 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20083710 CACCTATAGA
20083720 AGATGGAGACTGGT
1 AGATGGAGACTGGT
20083734 AGATGGAGACTGG
1 AGATGGAGACTGG
20083747 ACCACACGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (14 bp):
AGATGGAGACTGGT
Found at i:20086286 original size:45 final size:45
Alignment explanation
Indices: 20086236--20086480 Score: 332
Period size: 45 Copynumber: 5.5 Consensus size: 45
20086226 AACGATAGCA
* * * **
20086236 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTAAATTT
1 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCG
*
20086281 GTAACAGT-ACGGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCG
* * *
20086325 GTAACAGTAACGATAACAGTATTTGACACACAAAGTGCCGAATCG
1 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCG
* *
20086370 GTAACAGTAACGGTAATAGTATTCGACACACAAAGTG-TCGAATCA
1 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCT-GAATCG
* * *
20086415 ATAATAGTAATGGTAACAGTATTCGACACACAAAGTGCTGAATCG
1 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCG
*
20086460 GTAACAGTAACAGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
20086481 ACAGTAGTCG
Statistics
Matches: 175, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
44 38 0.22
45 136 0.78
46 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCG
Found at i:20086471 original size:6 final size:6
Alignment explanation
Indices: 20086460--20086486 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20086450 TGCTGAATCG
20086460 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
20086487 GTCGGCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:20093420 original size:13 final size:13
Alignment explanation
Indices: 20093399--20093464 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
20093389 AGTTTGGCAA
20093399 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
20093412 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
20093425 TGAC-GTGGAAAAG
1 TG-CTTTTGAAAAG
*
20093438 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
*
20093451 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
20093464 T
1 T
20093465 TTGGTTTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
12 1 0.02
13 41 0.98
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:20093461 original size:26 final size:27
Alignment explanation
Indices: 20093397--20093464 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
20093387 CTAGTTTGGC
*
20093397 AATG-CTTTTGAAAAGTGTTTTTGAAA
1 AATGACTTTTGAAAAGTGCTTTTGAAA
* * *
20093423 AGTGAC-GTGGAAAAGTGCTTTTGAAA
1 AATGACTTTTGAAAAGTGCTTTTGAAA
20093449 AAT-ACTTTTGAAAAGT
1 AATGACTTTTGAAAAGT
20093465 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
25 2 0.06
26 30 0.91
27 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (27 bp):
AATGACTTTTGAAAAGTGCTTTTGAAA
Found at i:20097207 original size:33 final size:33
Alignment explanation
Indices: 20097160--20097225 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
20097150 AATAAGTTAG
*
20097160 AAAATTATAGAGACTTAAGTGCAATTATCCTAT
1 AAAAGTATAGAGACTTAAGTGCAATTATCCTAT
20097193 AAAAGTATAGAGACTTAAGTGCAATTATCCTAT
1 AAAAGTATAGAGACTTAAGTGCAATTATCCTAT
20097226 TTTATTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (33 bp):
AAAAGTATAGAGACTTAAGTGCAATTATCCTAT
Found at i:20099416 original size:17 final size:17
Alignment explanation
Indices: 20099373--20099417 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
20099363 GCATAATGGT
20099373 CACATGTCAT-ATAAACA
1 CACAT-TCATAATAAACA
*
20099390 CACA-TCATAATACACA
1 CACATTCATAATAAACA
20099406 CACATTCATAAT
1 CACATTCATAAT
20099418 TTAAGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 11 0.44
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (17 bp):
CACATTCATAATAAACA
Found at i:20101486 original size:28 final size:28
Alignment explanation
Indices: 20101452--20101630 Score: 175
Period size: 28 Copynumber: 6.4 Consensus size: 28
20101442 TTTTTTATTG
*
20101452 TACAATTTTACCCCTATTTTGCAGATTT
1 TACAATTTTACCCCTATTTTTCAGATTT
*
20101480 TACAATTTTGCCCCT-TTTTTCTAGATTT
1 TACAATTTTACCCCTATTTTTC-AGATTT
*
20101508 TATAATTTTACCCCT-TTTTTCAGATTT
1 TACAATTTTACCCCTATTTTTCAGATTT
* * *
20101535 TACAATTTTACTCATA-TTTTCTAGATCT
1 TACAATTTTACCCCTATTTTTC-AGATTT
* * * * *
20101563 TACAGTTTTGCCCTTATTTTCCAAATTT
1 TACAATTTTACCCCTATTTTTCAGATTT
* * *
20101591 TATAGTTTTACCCCTATTTTTTAGATTT
1 TACAATTTTACCCCTATTTTTCAGATTT
* *
20101619 TATAGTTTTACC
1 TACAATTTTACC
20101631 TAGAATTATA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 28 0.22
28 94 0.75
29 4 0.03
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (28 bp):
TACAATTTTACCCCTATTTTTCAGATTT
Found at i:20101522 original size:56 final size:56
Alignment explanation
Indices: 20101455--20101630 Score: 194
Period size: 56 Copynumber: 3.2 Consensus size: 56
20101445 TTTATTGTAC
* *
20101455 AATTTTACCCCTATTTTGCAGATTTTACAATTTTGCCCCTTTTTTCTAGATTTTAT
1 AATTTTACCCCTATTTTCCAGATTTTACAATTTTACCCCTTTTTTCTAGATTTTAT
* * * * * *
20101511 AATTTTACCCCT-TTTTTCAGATTTTACAATTTTACTCATATTTTCTAGATCTTAC
1 AATTTTACCCCTATTTTCCAGATTTTACAATTTTACCCCTTTTTTCTAGATTTTAT
* * * * * *
20101566 AGTTTTGCCCTTATTTTCCAAATTTTATAGTTTTACCCCTATTTTT-TAGATTTTAT
1 AATTTTACCCCTATTTTCCAGATTTTACAATTTTACCCCT-TTTTTCTAGATTTTAT
*
20101622 AGTTTTACC
1 AATTTTACC
20101631 TAGAATTATA
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
55 45 0.46
56 49 0.50
57 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (56 bp):
AATTTTACCCCTATTTTCCAGATTTTACAATTTTACCCCTTTTTTCTAGATTTTAT
Found at i:20101566 original size:83 final size:84
Alignment explanation
Indices: 20101452--20101630 Score: 229
Period size: 83 Copynumber: 2.1 Consensus size: 84
20101442 TTTTTTATTG
* * * *
20101452 TACAATTTTACCCCTATTTTGCAGATTTTACAATTTTGCCCCTT-TTTTCTAGATTTTATAATTT
1 TACAATTTTACCCATATTTTGCAGATCTTACAATTTTG-CCCTTATTTTCCAAATTTTATAATTT
20101516 TACCCCT-TTTTTCAGATTT
65 TACCCCTATTTTTCAGATTT
* * *
20101535 TACAATTTTACTCATATTTT-CTAGATCTTACAGTTTTGCCCTTATTTTCCAAATTTTATAGTTT
1 TACAATTTTACCCATATTTTGC-AGATCTTACAATTTTGCCCTTATTTTCCAAATTTTATAATTT
*
20101599 TACCCCTATTTTTTAGATTT
65 TACCCCTATTTTTCAGATTT
* *
20101619 TATAGTTTTACC
1 TACAATTTTACC
20101631 TAGAATTATA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
82 6 0.07
83 56 0.68
84 20 0.24
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (84 bp):
TACAATTTTACCCATATTTTGCAGATCTTACAATTTTGCCCTTATTTTCCAAATTTTATAATTTT
ACCCCTATTTTTCAGATTT
Found at i:20102441 original size:23 final size:23
Alignment explanation
Indices: 20102389--20102435 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
20102379 TGCCATAGCA
*
20102389 TATTATTATAATAAGTTATATAT
1 TATTTTTATAATAAGTTATATAT
20102412 TATTTTTATAAT-A-TTATATAT
1 TATTTTTATAATAAGTTATATAT
20102433 TAT
1 TAT
20102436 GATTTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTTTTATAATAAGTTATATAT
Found at i:20102454 original size:24 final size:23
Alignment explanation
Indices: 20102405--20102454 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
20102395 TATAATAAGT
* *
20102405 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
20102428 TATATTATGATTTTTATGAAT-TCA
1 TATA-TATGATTTTTAT-AATATCA
20102452 TAT
1 TAT
20102455 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 16 0.70
25 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:20107946 original size:21 final size:21
Alignment explanation
Indices: 20107889--20107962 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
20107879 ATCTATAAAC
* *
20107889 TATATTTTAAATATTAAAATA
1 TATAATTTAAATATTTAAATA
20107910 TTATAA-TTACAA-ATTTAAATA
1 -TATAATTTA-AATATTTAAATA
*
20107931 TATAATTTATATATTTAAA-A
1 TATAATTTAAATATTTAAATA
*
20107951 TA-AATTTCAATA
1 TATAATTTAAATA
20107963 GAAATATACT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
19 8 0.18
20 9 0.20
21 21 0.48
22 6 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAATTTAAATATTTAAATA
Found at i:20108003 original size:35 final size:35
Alignment explanation
Indices: 20107925--20108003 Score: 81
Period size: 35 Copynumber: 2.2 Consensus size: 35
20107915 ATTACAAATT
*
20107925 TAAATATATAATTTATATATTTAAAATAAATTTCAA
1 TAAA-ATATAATTTATATATCTAAAATAAATTTCAA
* *
20107961 TAGAAATATACTTT-TATATCTAATATAAATATT-ACA
1 TA-AAATATAATTTATATATCTAAAATAAAT-TTCA-A
20107997 TAAAATA
1 TAAAATA
20108004 CATTGAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
35 20 0.54
36 15 0.41
37 2 0.05
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAAATATAATTTATATATCTAAAATAAATTTCAA
Found at i:20114725 original size:17 final size:18
Alignment explanation
Indices: 20114703--20114737 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20114693 ATTTGGGTCA
20114703 TGTGGG-CCACACGGGCG
1 TGTGGGCCCACACGGGCG
20114720 TGTGGGCCCACACGGGCG
1 TGTGGGCCCACACGGGCG
20114738 AACATCATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.31, G:0.46, T:0.11
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCG
Found at i:20115942 original size:45 final size:45
Alignment explanation
Indices: 20115893--20116063 Score: 177
Period size: 45 Copynumber: 3.8 Consensus size: 45
20115883 GTTTGATTCA
* *
20115893 TGATGCCATAGTA-TCTTTCAG-TGATGATCTTACTTGATAAAATCG
1 TGATGCCATA-AAGTCTTTCAGCT-ATGATCTTACTCGATAAAATCG
* *
20115938 TGATGCCATAAAGTCTTTCAGCTATGGTCTTACTCGATAGAATCG
1 TGATGCCATAAAGTCTTTCAGCTATGATCTTACTCGATAAAATCG
* * * * * *
20115983 TGATGCCATAACGTCTTTTAGCCAT-AGTTTTACTTGATAGAATCG
1 TGATGCCATAAAGTCTTTCAGCTATGA-TCTTACTCGATAAAATCG
* * *
20116028 TGATGTCATAACGTCTTTCAACTATGATCTTACTCG
1 TGATGCCATAAAGTCTTTCAGCTATGATCTTACTCG
20116064 TTTCTGGTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
44 1 0.01
45 103 0.97
46 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (45 bp):
TGATGCCATAAAGTCTTTCAGCTATGATCTTACTCGATAAAATCG
Found at i:20115963 original size:90 final size:90
Alignment explanation
Indices: 20115845--20116063 Score: 233
Period size: 90 Copynumber: 2.4 Consensus size: 90
20115835 TCATTTTTCT
* ** * * * * * **
20115845 TCGTGTTGCCATAGTGTCTTTCAACTATGGTCTTATTGGTTTGATTCATGATGCCATAGTATCTT
1 TCGTGATGCCATAAAGTCTTTCAACTATGGTCTTACTCGATAGAATCATGATGCCATAACATCTT
**
20115910 TCAGTGAT-GATCTTACTTGATAAAA
66 TCAGCCATAG-TCTTACTTGATAAAA
* * *
20115935 TCGTGATGCCATAAAGTCTTTCAGCTATGGTCTTACTCGATAGAATCGTGATGCCATAACGTCTT
1 TCGTGATGCCATAAAGTCTTTCAACTATGGTCTTACTCGATAGAATCATGATGCCATAACATCTT
* * *
20116000 TTAGCCATAGTTTTACTTGATAGAA
66 TCAGCCATAGTCTTACTTGATAAAA
* * *
20116025 TCGTGATGTCATAACGTCTTTCAACTATGATCTTACTCG
1 TCGTGATGCCATAAAGTCTTTCAACTATGGTCTTACTCG
20116064 TTTCTGGTAT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
90 105 0.99
91 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (90 bp):
TCGTGATGCCATAAAGTCTTTCAACTATGGTCTTACTCGATAGAATCATGATGCCATAACATCTT
TCAGCCATAGTCTTACTTGATAAAA
Found at i:20116491 original size:16 final size:16
Alignment explanation
Indices: 20116453--20116485 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20116443 CCATTTTTCC
*
20116453 ATTAAA-ATAACATAT
1 ATTAAATATAAAATAT
20116468 ATTAAATATAAAATAT
1 ATTAAATATAAAATAT
20116484 AT
1 AT
20116486 GTAATAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATATAAAATAT
Found at i:20121434 original size:21 final size:20
Alignment explanation
Indices: 20121386--20121430 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 20
20121376 CTAAAGTATT
20121386 GATACTTTACATCAGGGTACC
1 GATACTTTACA-CAGGGTACC
20121407 GATACTTTACA-AGGGTACC
1 GATACTTTACACAGGGTACC
20121426 GATAC
1 GATAC
20121431 ACTTGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.54
21 11 0.46
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
GATACTTTACACAGGGTACC
Found at i:20122839 original size:20 final size:22
Alignment explanation
Indices: 20122807--20122856 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
20122797 CATAAATATT
20122807 ATATAATTAATT-AACT-TAT-A
1 ATAT-ATTAATTAAACTATATAA
20122827 ATATATTAGATTAAACTATATAA
1 ATATATTA-ATTAAACTATATAA
20122850 ATATATT
1 ATATATT
20122857 TGAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 4 0.15
22 3 0.12
23 8 0.31
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATATTAATTAAACTATATAA
Found at i:20130605 original size:21 final size:21
Alignment explanation
Indices: 20130579--20130619 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20130569 ATCTGCTCAA
* *
20130579 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
20130600 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
20130620 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:20138488 original size:4 final size:4
Alignment explanation
Indices: 20138479--20138509 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
20138469 CACCACCAAA
20138479 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
20138510 AACAACTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:20151029 original size:79 final size:78
Alignment explanation
Indices: 20150892--20151039 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 78
20150882 TATCGATGAA
* * * *
20150892 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAGTAATGGTCACATGTGTGGTAC
1 CACGTGTATAGTACTGTGTGAAGGCTACCACGTGTATCGATAACTAA-GGTCACATGTGTAGTAC
20150957 TAAGAAGCTTTGAG
65 TAAGAAGCTTTGAG
* * * *
20150971 CACGTGTATAGTACTGTGTGAATGCTACCACGTGTCTCGATAAACTACA-GTTATATGTGTAGTA
1 CACGTGTATAGTACTGTGTGAAGGCTACCACGTGTATCGAT-AACTA-AGGTCACATGTGTAGTA
20151035 CTAAG
64 CTAAG
20151040 TGAAGGCTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 54 0.92
80 4 0.07
81 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (78 bp):
CACGTGTATAGTACTGTGTGAAGGCTACCACGTGTATCGATAACTAAGGTCACATGTGTAGTACT
AAGAAGCTTTGAG
Found at i:20151053 original size:26 final size:26
Alignment explanation
Indices: 20151024--20151101 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
20151014 ACTACAGTTA
20151024 TATGTGTAGTACTAAGTGAAGGCTAC
1 TATGTGTAGTACTAAGTGAAGGCTAC
* * **
20151050 TATGTGAACTAAGAAGCTTG-A-GC-AC
1 TATGTGTAGTACTAAG--TGAAGGCTAC
*
20151075 -GTGTGTAGTACTAAGTGAAGGCTAC
1 TATGTGTAGTACTAAGTGAAGGCTAC
20151100 TA
1 TA
20151102 CGTGAGTCGT
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 12 0.33
25 4 0.11
26 14 0.39
27 1 0.03
28 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (26 bp):
TATGTGTAGTACTAAGTGAAGGCTAC
Found at i:20151078 original size:101 final size:101
Alignment explanation
Indices: 20150955--20151157 Score: 250
Period size: 101 Copynumber: 2.0 Consensus size: 101
20150945 CATGTGTGGT
** * *
20150955 ACTAAGAAGCTTTGAGCACGTGTATAGTACTGTGTGAATGCTACCACGTGTCTCG-ATAAACTAC
1 ACTAAGAAGCTTTGAGCACGTGTATAGTACTAAGTGAAGGCTACCACGTGACTCGTA-AAACT--
* *
20151019 AGTT-ATATGTGTAGTACTAAGTGAAGGCTACTATGTGA
63 AGTTCACATGTGTAGTACTAAGTGAAGGCTACTACGTGA
* * * *
20151057 ACTAAGAAGC-TTGAGCACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAGTCGTAAAACTTGT
1 ACTAAGAAGCTTTGAGCACGTGTATAGTACTAAGTGAAGGCTACCACGTGACTCGTAAAACTAGT
* *
20151121 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGA
66 TCACATGTGTAGTACTAAGTGAAGGCTACTACGTGA
20151157 A
1 A
20151158 TTGTAAAACT
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
99 3 0.03
100 31 0.36
101 42 0.48
102 11 0.13
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (101 bp):
ACTAAGAAGCTTTGAGCACGTGTATAGTACTAAGTGAAGGCTACCACGTGACTCGTAAAACTAGT
TCACATGTGTAGTACTAAGTGAAGGCTACTACGTGA
Found at i:20151087 original size:50 final size:48
Alignment explanation
Indices: 20151026--20151204 Score: 225
Period size: 50 Copynumber: 3.6 Consensus size: 48
20151016 TACAGTTATA
* *
20151026 TGTGTAGTACTAAGTGAAGGCTACTATGTGAACTAAGAAGCTTGAGCACG
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGAACTAA-AA-CTTGATCACG
* *
20151076 TGTGTAGTACTAAGTGAAGGCTACTACGTGAGTCGTAAAACTTGTTCACG
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGA-AC-TAAAACTTGATCACG
* *
20151126 TGTGTAGTACTATGTGAAGGCTACTACGTGAATTGTAAAAC-TGATCACG
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGAA--CTAAAACTTGATCACG
* *
20151175 TGTGTAGTACTATGTGAAGGATACTACGTG
1 TGTGTAGTACTAAGTGAAGGCTACTACGTG
20151205 TATCGAATGA
Statistics
Matches: 116, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
49 36 0.31
50 74 0.64
51 3 0.03
52 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGAAGGCTACTACGTGAACTAAAACTTGATCACG
Found at i:20153148 original size:6 final size:6
Alignment explanation
Indices: 20153134--20153168 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
20153124 TAGAGCTAAT
*
20153134 GGAGTA GGAGCA GGAGCA GGAGCA GGAGCA GGAGC
1 GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGC
20153169 TAGTGGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.51, T:0.03
Consensus pattern (6 bp):
GGAGCA
Found at i:20155537 original size:19 final size:18
Alignment explanation
Indices: 20155510--20155548 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
20155500 CAGCCCCCCA
20155510 TTAACTCTTTCATTACAAT
1 TTAACTC-TTCATTACAAT
*
20155529 TTAATTCTTCATTACAAT
1 TTAACTCTTCATTACAAT
20155547 TT
1 TT
20155549 GGTTCTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAACTCTTCATTACAAT
Found at i:20157784 original size:19 final size:19
Alignment explanation
Indices: 20157760--20157812 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
20157750 AAGCTAGTTT
20157760 TAATTCTAGTTTTAAAGGC
1 TAATTCTAGTTTTAAAGGC
* * * *
20157779 TAATTCCAATTTTATAGGT
1 TAATTCTAGTTTTAAAGGC
* *
20157798 TAATCCTAGTATTAA
1 TAATTCTAGTTTTAA
20157813 GTCTAATACT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
TAATTCTAGTTTTAAAGGC
Found at i:20163633 original size:21 final size:21
Alignment explanation
Indices: 20163594--20163636 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20163584 ATTTTATTTT
**
20163594 ATTTTTTAAAGTTTAAAAATA
1 ATTTTTTAAAAATTAAAAATA
20163615 ATTTTTTAAAAATTCAAAAATA
1 ATTTTTTAAAAATT-AAAAATA
20163637 TATCATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTTTTAAAAATTAAAAATA
Found at i:20164523 original size:18 final size:18
Alignment explanation
Indices: 20164495--20164534 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
20164485 ATTTTAAAAC
20164495 TTTTTTAAA-TTACAATT
1 TTTTTTAAATTTACAATT
20164512 TTTTTTATAATTTTACAATT
1 TTTTTTA-AA-TTTACAATT
20164532 TTT
1 TTT
20164535 ATATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
20 11 0.55
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTTAAATTTACAATT
Found at i:20164546 original size:20 final size:20
Alignment explanation
Indices: 20164504--20164543 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
20164494 CTTTTTTAAA
*
20164504 TTACAATTTTTTTTATAATT
1 TTACAATTTTTTATATAATT
20164524 TTACAA-TTTTTATAT-ATT
1 TTACAATTTTTTATATAATT
20164542 TT
1 TT
20164544 TTAATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TTACAATTTTTTATATAATT
Found at i:20167454 original size:40 final size:42
Alignment explanation
Indices: 20167366--20167455 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 42
20167356 TATTATGCTT
20167366 AGTATAACGGGAAGTTAACTTACCAATCATTTACATTTACCTTTAA
1 AGTATAACGGGAAGTTAACTTACCAATCATTTAC---TA-CTTTAA
*
20167412 AGTATAAGGGGAAGTTAACTTACCAATCATTTAC-A-TTTAA
1 AGTATAACGGGAAGTTAACTTACCAATCATTTACTACTTTAA
20167452 AGTA
1 AGTA
20167456 AGCATGCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
40 9 0.21
42 1 0.02
46 33 0.77
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (42 bp):
AGTATAACGGGAAGTTAACTTACCAATCATTTACTACTTTAA
Found at i:20170352 original size:38 final size:38
Alignment explanation
Indices: 20170301--20170390 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
20170291 TTCGGTACAG
20170301 CATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCCA
1 CATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCCA
*
20170339 CATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCTCA
1 CATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCCA
20170377 CATGGTGTGTAGGG
1 CATGGTGTGTAGGG
20170391 TTGGACGGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.18, C:0.11, G:0.39, T:0.32
Consensus pattern (38 bp):
CATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCCA
Found at i:20171935 original size:38 final size:38
Alignment explanation
Indices: 20171879--20171973 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
20171869 ACACACCAGA
*
20171879 TTGACACCCAGTGCCTCATCAG-ATAGTTCGAAGCAAAG
1 TTGACACCCAGTGTCTCATCAGCATAG-TCGAAGCAAAG
* * *
20171917 TTGACACCCAGTGTCTCATCGGCCTAGTCGAAGTAAAG
1 TTGACACCCAGTGTCTCATCAGCATAGTCGAAGCAAAG
* *
20171955 -TGATACCCAGTATCTCATC
1 TTGACACCCAGTGTCTCATC
20171974 GAATCTATCC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
37 17 0.34
38 30 0.60
39 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (38 bp):
TTGACACCCAGTGTCTCATCAGCATAGTCGAAGCAAAG
Found at i:20173988 original size:11 final size:11
Alignment explanation
Indices: 20173974--20174001 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20173964 TATACTAAAT
20173974 ATAATAAAAAA
1 ATAATAAAAAA
20173985 ATAATAAAAAA
1 ATAATAAAAAA
20173996 ATAATA
1 ATAATA
20174002 TCTCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
ATAATAAAAAA
Found at i:20174627 original size:24 final size:23
Alignment explanation
Indices: 20174596--20174682 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 23
20174586 TCTGGGCTGT
*
20174596 ATAACAGGAAGCTCATAAGAGCC
1 ATAATAGGAAGCTCATAAGAGCC
**
20174619 ATAATCAGGAAGCTCATGCGAGCC
1 ATAAT-AGGAAGCTCATAAGAGCC
* *
20174643 AATAATAGGTAGCTC-TGAAAAGCC
1 -ATAATAGGAAGCTCAT-AAGAGCC
*
20174667 ATTAATGGGAAGCTCA
1 A-TAATAGGAAGCTCA
20174683 GGATAGCCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
23 6 0.12
24 39 0.78
25 5 0.10
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (23 bp):
ATAATAGGAAGCTCATAAGAGCC
Found at i:20174776 original size:26 final size:26
Alignment explanation
Indices: 20174740--20174790 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
20174730 CGGAGGGCCA
*
20174740 TTAATCAGGAAGCTCACAAAGAGCCT
1 TTAATCAGGAAGCTCACAAAAAGCCT
*
20174766 TTAATCGGGAAGCTCACAAAAAGCC
1 TTAATCAGGAAGCTCACAAAAAGCC
20174791 ATATAACGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAAAGCCT
Found at i:20174806 original size:26 final size:26
Alignment explanation
Indices: 20174748--20174807 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
20174738 CATTAATCAG
* * *
20174748 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCACAAAAAGCCTATAATCGA
20174774 GAAGCTCACAAAAAGCCATATAA-CGA
1 GAAGCTCACAAAAAGCC-TATAATCGA
*
20174800 GACGCTCA
1 GAAGCTCA
20174808 TAAGAGCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (26 bp):
GAAGCTCACAAAAAGCCTATAATCGA
Found at i:20178586 original size:4 final size:4
Alignment explanation
Indices: 20178577--20178622 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
20178567 TTCTCCTTCT
*
20178577 TTTC TTTC TTTC TTTC TTT- TTTT TTTC TTTC TTTTC TTTC -TTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTT
20178623 TTCTATTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
3 6 0.16
4 28 0.74
5 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:20178594 original size:12 final size:12
Alignment explanation
Indices: 20178577--20178622 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
20178567 TTCTCCTTCT
20178577 TTTCTTTCTTTC
1 TTTCTTTCTTTC
*
20178589 TTTCTTT-TTTT
1 TTTCTTTCTTTC
20178600 TTTCTTTCTTTTC
1 TTTCTTTC-TTTC
20178613 TTTC-TTCTTT
1 TTTCTTTCTTT
20178623 TTCTATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 13 0.43
12 10 0.33
13 7 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTTCTTTC
Found at i:20178598 original size:19 final size:20
Alignment explanation
Indices: 20178576--20178622 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
20178566 GTTCTCCTTC
20178576 TTTTCTTTCTTTC-TTTCTT
1 TTTTCTTTCTTTCTTTTCTT
*
20178595 TTTTTTTTCTTTCTTTTCTT
1 TTTTCTTTCTTTCTTTTCTT
*
20178615 TCTTCTTT
1 TTTTCTTT
20178623 TTCTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTCTTTCTTTCTTTTCTT
Found at i:20178602 original size:23 final size:24
Alignment explanation
Indices: 20178567--20178624 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
20178557 AAATTATGTG
* *
20178567 TTCTCCTTCTTTTCTTTC-TTTCT
1 TTCTTCTTTTTTTCTTTCTTTTCT
*
20178590 TTCTTTTTTTTTTCTTTCTTTTCT
1 TTCTTCTTTTTTTCTTTCTTTTCT
20178614 TTCTTCTTTTT
1 TTCTTCTTTTT
20178625 CTATTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
TTCTTCTTTTTTTCTTTCTTTTCT
Found at i:20181543 original size:21 final size:22
Alignment explanation
Indices: 20181519--20181560 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20181509 AGGGGAATTA
* *
20181519 CTTGGATTTTTA-TAAGAAAAC
1 CTTGGAGTTTTACAAAGAAAAC
20181540 CTTGGAGTTTTACAAAGAAAA
1 CTTGGAGTTTTACAAAGAAAA
20181561 ACTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
CTTGGAGTTTTACAAAGAAAAC
Found at i:20183979 original size:63 final size:63
Alignment explanation
Indices: 20183902--20184113 Score: 246
Period size: 63 Copynumber: 3.4 Consensus size: 63
20183892 CCGTGTGCCT
* * * * * *
20183902 CAAAATAGTGAGTTACACAGTCTGGACACATATCCATGTCTTTGGCCCATGTGTCC-CTAATTC
1 CAAAACAGTGAGTTACACGGCCTGGACACATATCCGTGTCTTTAGCCCGTGTG-CCTCTAATTC
* ** * * *
20183965 CAAAACAGTGAGTTACATGGCCTGGACACGCATCTGTGTCTTTTGCTCGTGTGCCTCTAATTC
1 CAAAACAGTGAGTTACACGGCCTGGACACATATCCGTGTCTTTAGCCCGTGTGCCTCTAATTC
* ** * * *
20184028 CAAAACAGTGAGTTACACGGCCTGGACATATGCCCGTATCTCTAGCCCGTGTGCCTCTAACTC
1 CAAAACAGTGAGTTACACGGCCTGGACACATATCCGTGTCTTTAGCCCGTGTGCCTCTAATTC
20184091 CAAAACAGTGAGTTACACGGCCT
1 CAAAACAGTGAGTTACACGGCCT
20184114 ACCACACGGC
Statistics
Matches: 125, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
62 2 0.02
63 123 0.98
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (63 bp):
CAAAACAGTGAGTTACACGGCCTGGACACATATCCGTGTCTTTAGCCCGTGTGCCTCTAATTC
Found at i:20185309 original size:19 final size:19
Alignment explanation
Indices: 20185284--20185327 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
20185274 CAAAGCACGA
20185284 AGTTGCAAAAAACTTCTAC
1 AGTTGCAAAAAACTTCTAC
*
20185303 GGTTGCAAAAAACTTCTAC
1 AGTTGCAAAAAACTTCTAC
20185322 AGTTGC
1 AGTTGC
20185328 CGAGTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (19 bp):
AGTTGCAAAAAACTTCTAC
Found at i:20186014 original size:29 final size:29
Alignment explanation
Indices: 20185957--20186023 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
20185947 GGATGGAGGA
20185957 TTTTTA-TTTTATTTAATATTAATATAATT
1 TTTTTATTTTTATTTAATATTAATATAA-T
* *
20185986 TTTTTATTTTTATTTAA-ATT-TTTTGAAT
1 TTTTTATTTTTATTTAATATTAATAT-AAT
20186014 TTTTTATTTT
1 TTTTTATTTT
20186024 ATATATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 13 0.38
29 11 0.32
30 10 0.29
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (29 bp):
TTTTTATTTTTATTTAATATTAATATAAT
Found at i:20186024 original size:27 final size:28
Alignment explanation
Indices: 20185957--20186046 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 28
20185947 GGATGGAGGA
* * *
20185957 TTTTTATTTTATTTAATATTAATAT-AATT
1 TTTTTATTTTATTTAA-ATT-TTTTGAACT
20185986 TTTTTATTTTTATTTAAATTTTTTGAA-T
1 TTTTTA-TTTTATTTAAATTTTTTGAACT
*
20186014 TTTTTATTTTA--TATATTTCTTTGAACT
1 TTTTTATTTTATTTAAATTT-TTTGAACT
20186041 TTTTTA
1 TTTTTA
20186047 GAATTAGGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.11
26 6 0.11
27 12 0.22
28 9 0.17
29 11 0.20
30 10 0.19
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTTATTTTATTTAAATTTTTTGAACT
Found at i:20190833 original size:9 final size:10
Alignment explanation
Indices: 20190784--20190831 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
20190774 AAATTTTAAC
20190784 TTTTTTATATA
1 TTTTTTATA-A
20190795 TTTTTTTATAA
1 -TTTTTTATAA
20190806 TTTTTTATAA
1 TTTTTTATAA
*
20190816 TTTTATA-AA
1 TTTTTTATAA
20190825 TTTTTTA
1 TTTTTTA
20190832 AAAATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
11 1 0.03
12 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:20190892 original size:27 final size:27
Alignment explanation
Indices: 20190840--20190895 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20190830 TAAAAATATA
*
20190840 AATTTTGAATTTTTTCTAAATATTTTG
1 AATTTTAAATTTTTTCTAAATATTTTG
20190867 AATTTTAAACTTTATTT-TAAAT-TTTTG
1 AATTTTAAA-TTT-TTTCTAAATATTTTG
20190894 AA
1 AA
20190896 AATTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 15 0.58
28 8 0.31
29 3 0.12
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (27 bp):
AATTTTAAATTTTTTCTAAATATTTTG
Found at i:20191563 original size:17 final size:17
Alignment explanation
Indices: 20191543--20191579 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20191533 AATTTTTGAA
20191543 TTAGTGAATTCTATGAT
1 TTAGTGAATTCTATGAT
*
20191560 TTAGTGAATTTTATGAT
1 TTAGTGAATTCTATGAT
20191577 TTA
1 TTA
20191580 AAAAGAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTATGAT
Found at i:20192854 original size:46 final size:46
Alignment explanation
Indices: 20192801--20192986 Score: 318
Period size: 46 Copynumber: 4.0 Consensus size: 46
20192791 CCATGGAAAA
* *
20192801 TTGTGAAAAGTAGGTATGGTGTTTTAGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
20192847 TTGTGAAAAGTAGGTGTGGTGTTTCAGTGAAAAAAACCATACTAAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
20192893 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
20192939 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
20192985 TT
1 TT
20192987 ATAGCATTGT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:20199905 original size:60 final size:60
Alignment explanation
Indices: 20199836--20199955 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
20199826 AGTTATAATT
20199836 TATATGTATAGATTCCTTAGTGAGTCTATTTTCAATAGAAACAAACGAGAATGTTATCTA
1 TATATGTATAGATTCCTTAGTGAGTCTATTTTCAATAGAAACAAACGAGAATGTTATCTA
20199896 TATATGTATAGATTCCTTAGTGAGTCTATTTTCAATAGAAACAAACGAGAATGTTATCTA
1 TATATGTATAGATTCCTTAGTGAGTCTATTTTCAATAGAAACAAACGAGAATGTTATCTA
20199956 AATTTTTTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (60 bp):
TATATGTATAGATTCCTTAGTGAGTCTATTTTCAATAGAAACAAACGAGAATGTTATCTA
Found at i:20202107 original size:29 final size:29
Alignment explanation
Indices: 20202063--20202119 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
20202053 CTGTCTTCTC
*
20202063 CCCCAAACGTTTTTTCCCCTCTGCTGGTT
1 CCCCAAACGTTCTTTCCCCTCTGCTGGTT
*
20202092 CCCCAAACGTTCTTTCCCCTCTGTTGGT
1 CCCCAAACGTTCTTTCCCCTCTGCTGGT
20202120 GAAATTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.11, C:0.39, G:0.14, T:0.37
Consensus pattern (29 bp):
CCCCAAACGTTCTTTCCCCTCTGCTGGTT
Found at i:20205622 original size:18 final size:18
Alignment explanation
Indices: 20205599--20205678 Score: 142
Period size: 18 Copynumber: 4.4 Consensus size: 18
20205589 TATGAGAAAC
*
20205599 GATGTTCACATTTTAAAT
1 GATGTTCACATTTCAAAT
*
20205617 GATGTTCACATTTTAAAT
1 GATGTTCACATTTCAAAT
20205635 GATGTTCACATTTCAAAT
1 GATGTTCACATTTCAAAT
20205653 GATGTTCACATTTCAAAT
1 GATGTTCACATTTCAAAT
20205671 GATGTTCA
1 GATGTTCA
20205679 AATTGATGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (18 bp):
GATGTTCACATTTCAAAT
Found at i:20206220 original size:72 final size:73
Alignment explanation
Indices: 20206103--20206275 Score: 271
Period size: 72 Copynumber: 2.4 Consensus size: 73
20206093 AAAAAACAAT
* * *
20206103 TGTAAACTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTT
1 TGTAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTT
*
20206168 ATTTAT-G
66 ATTTATAC
*
20206175 TGTAATCTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTT
1 TGTAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTT
20206240 ATTTATAC
66 ATTTATAC
*
20206248 T-AAAT-TAGTTTTATCAATAGTTGTTTAT
1 TGTAATCTAGTTTTATCAATAGTTGTTTAT
20206276 AAATGATTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
71 22 0.24
72 70 0.75
73 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.54
Consensus pattern (73 bp):
TGTAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTT
ATTTATAC
Found at i:20208961 original size:47 final size:47
Alignment explanation
Indices: 20208900--20209200 Score: 467
Period size: 47 Copynumber: 6.4 Consensus size: 47
20208890 CAGCCAAGAC
20208900 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20208947 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAG
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
20208994 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20209041 AGTGTATATATGTAATAAGGCCTAATAGCCGATGTAATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
20209088 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * *
20209135 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
20209182 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
20209201 TCCCGAAGGG
Statistics
Matches: 234, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 234 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:20209375 original size:37 final size:37
Alignment explanation
Indices: 20209319--20209397 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
20209309 CCGAGCTCTA
* *
20209319 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
20209356 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
20209393 AAGAC
1 AAGAC
20209398 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:20211965 original size:3 final size:3
Alignment explanation
Indices: 20211957--20212004 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
20211947 GTCGAGAAAG
* * * * *
20211957 TGA TGA TGA CGA TGA CGA TGA TGA TGG TGA TGA TGA CGG TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
20212005 CGGTGAATCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.38, T:0.27
Consensus pattern (3 bp):
TGA
Found at i:20212007 original size:12 final size:12
Alignment explanation
Indices: 20211973--20212010 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
20211963 TGACGATGAC
*
20211973 GATGATGATGGT
1 GATGATGACGGT
20211985 GATGATGACGGT
1 GATGATGACGGT
20211997 GATGATGACGGT
1 GATGATGACGGT
20212009 GA
1 GA
20212011 ATCAAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.42, T:0.26
Consensus pattern (12 bp):
GATGATGACGGT
Found at i:20212644 original size:13 final size:13
Alignment explanation
Indices: 20212626--20212650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20212616 ACACTCAAAT
20212626 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
20212639 TTCTCAAAAGCA
1 TTCTCAAAAGCA
20212651 ATAAAGAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:20214237 original size:25 final size:25
Alignment explanation
Indices: 20214186--20214243 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
20214176 ACAATCCATG
** * * *
20214186 TAAATCATGTATTTCATGTAGCTTT
1 TAAATCATGTAAATCATATAACATT
20214211 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
20214236 TATATCAT
1 TAAATCAT
20214244 TTTTTTTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:20214535 original size:23 final size:23
Alignment explanation
Indices: 20214505--20214563 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
20214495 CGAGCTGAAT
* *
20214505 AAACGGTAAGCTCTATTGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
*
20214528 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
20214551 AAACGGTAAGCTC
1 AAACGGTAAGCTC
20214564 ATACAAGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:20219541 original size:21 final size:21
Alignment explanation
Indices: 20219491--20219557 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
20219481 GACTGCGGGT
*
20219491 TGTAACTTGGAGAGGTAGGG-C
1 TGTAACTTGGTGAGGT-GGGAC
* * *
20219512 TATAGCTTGGTGATGTGGGAC
1 TGTAACTTGGTGAGGTGGGAC
*
20219533 TGTAACTTGGTGAGGTTGGAC
1 TGTAACTTGGTGAGGTGGGAC
20219554 TGTA
1 TGTA
20219558 CCCAGGAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 3 0.08
21 34 0.92
ACGTcount: A:0.21, C:0.09, G:0.39, T:0.31
Consensus pattern (21 bp):
TGTAACTTGGTGAGGTGGGAC
Found at i:20219587 original size:21 final size:21
Alignment explanation
Indices: 20219561--20219743 Score: 170
Period size: 21 Copynumber: 8.7 Consensus size: 21
20219551 GACTGTACCC
*
20219561 AGGAGAAGTGGGGCTATAGGA
1 AGGAGAAGTGGGGCTATATGA
* *
20219582 AGGAGATGTGGGGCTATAGGA
1 AGGAGAAGTGGGGCTATATGA
* * *
20219603 AGGAGATGTGGGGCTGTACGA
1 AGGAGAAGTGGGGCTATATGA
* * *
20219624 AGGAGATGTAGGGCTGTATGA
1 AGGAGAAGTGGGGCTATATGA
* * * *
20219645 TGGAGATGTCGGGCTGTATGA
1 AGGAGAAGTGGGGCTATATGA
* *
20219666 TGGAGAAGTGGGGCTATATGC
1 AGGAGAAGTGGGGCTATATGA
* *
20219687 AGGAGAAGTGGGGGTATATGC
1 AGGAGAAGTGGGGCTATATGA
*
20219708 AGGTGAAGTGGGGCTATAT-A
1 AGGAGAAGTGGGGCTATATGA
* *
20219728 CGGGTGAAGTGGGGCT
1 -AGGAGAAGTGGGGCT
20219744 GTAGCTAGGT
Statistics
Matches: 144, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
21 144 1.00
ACGTcount: A:0.26, C:0.07, G:0.46, T:0.21
Consensus pattern (21 bp):
AGGAGAAGTGGGGCTATATGA
Found at i:20219620 original size:63 final size:63
Alignment explanation
Indices: 20219553--20219761 Score: 188
Period size: 63 Copynumber: 3.3 Consensus size: 63
20219543 TGAGGTTGGA
* * *
20219553 CTGTACCCAGGAGAAGTGGGGCTATAGGAAGGAGATGTGGGGCTATAGGAAGGAGATGTGGGG
1 CTGTACGCAGGAGAAGTGGGGCTATATGAAGGAGATGTGGGGCTATAGGAAGGAGAAGTGGGG
* * * * * * * * *
20219616 CTGTACGAAGGAGATGTAGGGCTGTATGATGGAGATGTCGGGCTGTATGATGGAGAAGTGGGG
1 CTGTACGCAGGAGAAGTGGGGCTATATGAAGGAGATGTGGGGCTATAGGAAGGAGAAGTGGGG
* * * * * * * * *
20219679 CTATATGCAGGAGAAGTGGGGGTATATGCAGGTGAAGTGGGGCTATA-TACGGGTGAAGTGGGG
1 CTGTACGCAGGAGAAGTGGGGCTATATGAAGGAGATGTGGGGCTATAGGA-AGGAGAAGTGGGG
*
20219742 CTGTA-GCTAGGTGAAGTGGG
1 CTGTACGC-AGGAGAAGTGGG
20219762 ACTGTAACTG
Statistics
Matches: 114, Mismatches: 30, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
62 3 0.03
63 111 0.97
ACGTcount: A:0.25, C:0.09, G:0.45, T:0.22
Consensus pattern (63 bp):
CTGTACGCAGGAGAAGTGGGGCTATATGAAGGAGATGTGGGGCTATAGGAAGGAGAAGTGGGG
Found at i:20219754 original size:21 final size:21
Alignment explanation
Indices: 20219670--20219761 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
20219660 GTATGATGGA
*
20219670 GAAGTGGGGCTATATGCAGGA
1 GAAGTGGGGCTATATGCAGGT
*
20219691 GAAGTGGGGGTATATGCAGGT
1 GAAGTGGGGCTATATGCAGGT
* *
20219712 GAAGTGGGGCTATATACGGGT
1 GAAGTGGGGCTATATGCAGGT
*
20219733 GAAGTGGGGCTGTA-GCTAGGT
1 GAAGTGGGGCTATATGC-AGGT
20219754 GAAGTGGG
1 GAAGTGGG
20219762 ACTGTAACTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 1 0.02
21 61 0.98
ACGTcount: A:0.24, C:0.08, G:0.47, T:0.22
Consensus pattern (21 bp):
GAAGTGGGGCTATATGCAGGT
Found at i:20219766 original size:21 final size:21
Alignment explanation
Indices: 20219708--20219791 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
20219698 GGGTATATGC
* *
20219708 AGGTGAAGTGGGGCTATATAC-
1 AGGTGAAGTGGGACTGTA-ACT
* * *
20219729 GGGTGAAGTGGGGCTGTAGCT
1 AGGTGAAGTGGGACTGTAACT
20219750 AGGTGAAGTGGGACTGTAACT
1 AGGTGAAGTGGGACTGTAACT
* * *
20219771 GGGGGATGTGGGACTGTAACT
1 AGGTGAAGTGGGACTGTAACT
20219792 TGGAGATGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 1 0.02
21 52 0.98
ACGTcount: A:0.23, C:0.10, G:0.44, T:0.24
Consensus pattern (21 bp):
AGGTGAAGTGGGACTGTAACT
Found at i:20219782 original size:42 final size:42
Alignment explanation
Indices: 20219708--20219788 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
20219698 GGGTATATGC
* * *
20219708 AGGTGAAGTGGGGCTATATACGGGTGAAGTGGGGCTGTAGCT
1 AGGTGAAGTGGGACTATATACGGGGGAAGTGGGACTGTAGCT
* *
20219750 AGGTGAAGTGGGACTGTA-ACTGGGGGATGTGGGACTGTA
1 AGGTGAAGTGGGACTATATAC-GGGGGAAGTGGGACTGTA
20219789 ACTTGGAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 31 0.94
ACGTcount: A:0.22, C:0.09, G:0.46, T:0.23
Consensus pattern (42 bp):
AGGTGAAGTGGGACTATATACGGGGGAAGTGGGACTGTAGCT
Done.