Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 102 of 130
Found at i:19979417 original size:36 final size:36
Alignment explanation
Indices: 19979176--19979462 Score: 148
Period size: 36 Copynumber: 8.1 Consensus size: 36
19979166 ATAAATATTT
* *
19979176 TCATT-CTTGTTTTACTATTTTTTAA-GAAAGTA-T-
1 TCATTACTTGTTTTTCTATTTTTTAAGGAAA-CACTC
* * * *
19979209 TCATCACTTATTCTTCTA-TTTTTAAGGGAAACATTC
1 TCATTACTTGTTTTTCTATTTTTTAA-GGAAACACTC
* * ** * *
19979245 TTATTAATTGTTTTT-TATTTTTTTTGAAAATA-TC
1 TCATTACTTGTTTTTCTATTTTTTAAGGAAACACTC
* * *
19979279 TTCATTACTTATTCTACTA-TTTTT-AGGAAA-ACATC
1 -TCATTACTTGTTTTTCTATTTTTTAAGGAAACAC-TC
* * * * * * *
19979314 TTCATTACTTATTGTACT-CTTTTTAAAGAAAAACTT
1 -TCATTACTTGTTTTTCTATTTTTTAAGGAAACACTC
* * *
19979350 TCATTACTTATTCTCCTATTTTTTAAGGAAACACTC
1 TCATTACTTGTTTTTCTATTTTTTAAGGAAACACTC
*
19979386 TCATTATTTGTTTTTCTATTTTTTAAGGAAACACTC
1 TCATTACTTGTTTTTCTATTTTTTAAGGAAACACTC
* * * * *
19979422 ACATTACTCGTTCTCTTATTTTTTTTGAGGAAA-ACTC
1 TCATTACTTGTT-T-TTCTATTTTTTAAGGAAACACTC
19979459 TCAT
1 TCAT
19979463 ATCTTTTTCT
Statistics
Matches: 197, Mismatches: 41, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
33 12 0.06
34 16 0.08
35 66 0.34
36 78 0.40
37 10 0.05
38 15 0.08
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (36 bp):
TCATTACTTGTTTTTCTATTTTTTAAGGAAACACTC
Found at i:19979592 original size:34 final size:36
Alignment explanation
Indices: 19979554--19979646 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
19979544 TCATTACTTG
*
19979554 TGTTC-CT-ATTTTTTCA-AGAAATATTTATATTACT
1 TGTTCTCTAATTTTTT-AGAGAAACATTTATATTACT
*
19979588 TGTTCTCTAATTTTTTAGAGAAACATTTTTATTACT
1 TGTTCTCTAATTTTTTAGAGAAACATTTATATTACT
*
19979624 TGTTCTTCT-ATATTTTAGAGAAA
1 TGTTC-TCTAATTTTTTAGAGAAA
19979647 TACTCGCATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 5 0.10
35 3 0.06
36 41 0.79
37 3 0.06
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.52
Consensus pattern (36 bp):
TGTTCTCTAATTTTTTAGAGAAACATTTATATTACT
Found at i:19979658 original size:36 final size:37
Alignment explanation
Indices: 19979582--19979665 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
19979572 AAATATTTAT
* * ***
19979582 ATTACTTGTTC-TCTAATTTTTTAGAGAAACATTTTT
1 ATTACTTGTTCTTCTAATATTTTAGAGAAACACTCGC
*
19979618 ATTACTTGTTCTTCT-ATATTTTAGAGAAATACTCGC
1 ATTACTTGTTCTTCTAATATTTTAGAGAAACACTCGC
19979654 ATTACTTGTTCT
1 ATTACTTGTTCT
19979666 CCTAGTTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 38 0.93
37 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (37 bp):
ATTACTTGTTCTTCTAATATTTTAGAGAAACACTCGC
Found at i:19979762 original size:48 final size:47
Alignment explanation
Indices: 19979702--19979902 Score: 191
Period size: 48 Copynumber: 4.3 Consensus size: 47
19979692 TATTACTAAT
* *
19979702 TTTTTTATTTTTTAAGGAAACATTCACTTGCCTATTCCTTTTAATAA
1 TTTTTTATTTTTTAAGGAAACACTCACTTACCTATTCCTTTTAATAA
* *
19979749 TTCTTTTATTTTTTAA-GAAATACTC-CATTACCTATTCCTTTCAATAA
1 TT-TTTTATTTTTTAAGGAAACACTCAC-TTACCTATTCCTTTTAATAA
* * *
19979796 TTTTCCTA-TTTTTAAGTGAAACACTCATTTACCTATTCCTTTTAATAG
1 TTTT-TTATTTTTTAAG-GAAACACTCACTTACCTATTCCTTTTAATAA
* * * * *
19979844 TTTTCCTACTTTTT-AGGAAAACACTCCCATAACTATTCCTTTTAAT--
1 TTTT-TTATTTTTTAAGG-AAACACTCACTTACCTATTCCTTTTAATAA
19979890 TTTTTT-TTTTTTA
1 TTTTTTATTTTTTA
19979903 TAAATTTTAG
Statistics
Matches: 130, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
44 5 0.04
45 1 0.01
46 14 0.11
47 32 0.25
48 73 0.56
49 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (47 bp):
TTTTTTATTTTTTAAGGAAACACTCACTTACCTATTCCTTTTAATAA
Found at i:19983876 original size:42 final size:42
Alignment explanation
Indices: 19983830--19984142 Score: 314
Period size: 42 Copynumber: 7.5 Consensus size: 42
19983820 AGGTTTAACG
*
19983830 ACTTTGAGAAAAAT-AAATGCTCCTCTAAATAGAGGCAACACA
1 ACTTT-AGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
* * * * * * *
19983872 ACTTTTGAAAAATAAAATGTTCATTTAAACAGAGGGAGCACA
1 ACTTTAGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
* * *
19983914 ACTTTTA-AAAAATAAAATGCTCCTCTAACTAGA-GTACCATA
1 AC-TTTAGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
* *
19983955 ACTTTTGAAAAAATAAAATGCTCCTCTAAATAAAGGCACCACA
1 ACTTTAG-AAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
* * * * *
19983998 ACTTT-GAAAAATAAAA-GTTTCTCTAAATAGAGGTAACATA
1 ACTTTAGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
* * * * **
19984038 ACTTTTGAAAAATAAAATACTCTTCTAAACAGAGGCACCGTA
1 ACTTTAGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
* * *
19984080 ACTTTTGAAAAATAAAATACTCCTATAAATAGAGGCACCACA
1 ACTTTAGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
19984122 ACTTTA-AAAAATAAAATGCTC
1 ACTTTAGAAAAATAAAATGCTC
19984143 ATTGACAATC
Statistics
Matches: 222, Mismatches: 42, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
40 26 0.12
41 49 0.22
42 133 0.60
43 14 0.06
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (42 bp):
ACTTTAGAAAAATAAAATGCTCCTCTAAATAGAGGCACCACA
Found at i:19984093 original size:166 final size:165
Alignment explanation
Indices: 19983837--19984142 Score: 418
Period size: 166 Copynumber: 1.8 Consensus size: 165
19983827 ACGACTTTGA
* **
19983837 GAAAAATAAATGCTCCTCTAAATAGAGGCAACACAACTTTTGAAAAATAAAATGTTCATTTAAAC
1 GAAAAATAAAAGCTCCTCTAAATAGAGGCAACACAACTTTTGAAAAATAAAATACTCATTTAAAC
* * * * * * *
19983902 AGAGGGAGCACAACTTTTAAAAAATAAAATGCTCCTCTAACTAGA-GTACCATAACTTTTGAAAA
66 AGAGGCACCACAACTTTTAAAAAATAAAATACTCCTATAAATAGAGGCACCACAAC-TTT-AAAA
19983966 AATAAAATGCTCCTCTAAATAAAGGCACCACAACTTT
129 AATAAAATGCTCCTCTAAATAAAGGCACCACAACTTT
* * * *
19984003 GAAAAATAAAAGTTTCTCTAAATAGAGGTAACATAACTTTTGAAAAATAAAATACTC-TTCTAAA
1 GAAAAATAAAAGCTCCTCTAAATAGAGGCAACACAACTTTTGAAAAATAAAATACTCATT-TAAA
** *
19984067 CAGAGGCACCGTAACTTTTGAAAAATAAAATACTCCTATAAATAGAGGCACCACAACTTTAAAAA
65 CAGAGGCACCACAACTTTTAAAAAATAAAATACTCCTATAAATAGAGGCACCACAACTTTAAAAA
19984132 ATAAAATGCTC
130 ATAAAATGCTC
19984143 ATTGACAATC
Statistics
Matches: 121, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
165 18 0.15
166 95 0.79
167 8 0.07
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.25
Consensus pattern (165 bp):
GAAAAATAAAAGCTCCTCTAAATAGAGGCAACACAACTTTTGAAAAATAAAATACTCATTTAAAC
AGAGGCACCACAACTTTTAAAAAATAAAATACTCCTATAAATAGAGGCACCACAACTTTAAAAAA
TAAAATGCTCCTCTAAATAAAGGCACCACAACTTT
Found at i:19984096 original size:124 final size:124
Alignment explanation
Indices: 19983837--19984144 Score: 399
Period size: 124 Copynumber: 2.5 Consensus size: 124
19983827 ACGACTTTGA
* *
19983837 GAAAAAT-AAATGCTCCTCTAAATAGAGGCAACACAACTTTTGAAAAATAAAATGTTCATTTAAA
1 GAAAAATAAAATGCTCCTCTAAATAGAGGCACCACAAC-TTTGAAAAATAAAATGTTCATCTAAA
* * *
19983901 CAGAGGGAGCACAACTTTTAAAAAATAAAATGCTCCTCTAACTAGAGTACCATAACTTTT
65 CAGAGGGAACACAACTTTTAAAAAATAAAATACTCCTCTAACTAGAGCACCATAACTTTT
*
19983961 GAAAAAATAAAATGCTCCTCTAAATAAAGGCACCACAACTTTGAAAAATAAAA-GTTTC-TCTAA
1 G-AAAAATAAAATGCTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAAATG-TTCATCTAA
* * * * * *
19984024 ATAGAGGTAACATAACTTTTGAAAAATAAAATACTCTTCTAAAC-AGAGGCACCGTAACTTTT
64 ACAGAGGGAACACAACTTTTAAAAAATAAAATACTCCTCT-AACTAGA-GCACCATAACTTTT
* * * *
19984086 GAAAAATAAAATACTCCTATAAATAGAGGCACCACAACTTTAAAAAATAAAATGCTCAT
1 GAAAAATAAAATGCTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAAATGTTCAT
19984145 TGACAATCAT
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
124 91 0.57
125 41 0.26
126 28 0.17
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (124 bp):
GAAAAATAAAATGCTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAAATGTTCATCTAAAC
AGAGGGAACACAACTTTTAAAAAATAAAATACTCCTCTAACTAGAGCACCATAACTTTT
Found at i:19984562 original size:25 final size:23
Alignment explanation
Indices: 19984508--19984932 Score: 305
Period size: 25 Copynumber: 18.6 Consensus size: 23
19984498 AAAAATTATC
*
19984508 AAAGATTCTCATTTAAGA--CTT
1 AAAGATTCTCATTTAAAACTCTT
* *
19984529 AAAGGTTTTCATTTGAAAACATCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
* *
19984554 AAAGATTTTCATTTAAGACTC--
1 AAAGATTCTCATTTAAAACTCTT
* *
19984575 AAAGGTTCTCATTTGAAAATGTCTT
1 AAAGATTCTCATTT-AAAA-CTCTT
19984600 AAAGATTCTCATTTGAAAACATCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
**
19984625 AAAGATTCTCATTTATGACTC--
1 AAAGATTCTCATTTAAAACTCTT
* **
19984646 AAAGCTTCTCATTTAAGGCTC--
1 AAAGATTCTCATTTAAAACTCTT
**
19984667 AAAGATTCTCATTTGAGGACTTCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
*
19984692 AAAGATTCTCATTTAAGACTC--
1 AAAGATTCTCATTTAAAACTCTT
19984713 AAAGATTCTCATTTGAAAACATCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
* *
19984738 AAAGATTCTTATTTAAGACTC--
1 AAAGATTCTCATTTAAAACTCTT
*
19984759 AAAGCTTCTCATTTGAAAACATCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
*
19984784 AAAGATTTTCATTTGAAAACATCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
*
19984809 AAA-ATTCTCATTTAAGACTC--
1 AAAGATTCTCATTTAAAACTCTT
19984829 AAAGATTCTCATTTAAAAACATCTT
1 AAAGATTCTCATTT-AAAAC-TCTT
* * *
19984854 AAAGATTTTTATTTAAGACTC--
1 AAAGATTCTCATTTAAAACTCTT
* * *
19984875 AAAGCTTTTCATTTCAAACGTCTT
1 AAAGATTCTCATTTAAAAC-TCTT
* *
19984899 AAGGATTCTCATTTAAGA--C-T
1 AAAGATTCTCATTTAAAACTCTT
19984919 AAAGATTCTCATTT
1 AAAGATTCTCATTT
19984933 GAAGATTCAT
Statistics
Matches: 331, Mismatches: 44, Indels: 59
0.76 0.10 0.14
Matches are distributed among these distances:
20 17 0.05
21 107 0.32
22 25 0.08
23 24 0.07
24 41 0.12
25 117 0.35
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
AAAGATTCTCATTTAAAACTCTT
Found at i:19984579 original size:46 final size:46
Alignment explanation
Indices: 19984508--19984844 Score: 359
Period size: 46 Copynumber: 7.3 Consensus size: 46
19984498 AAAAATTATC
* * *
19984508 AAAGATTCTCATTTAAGACTTAAAGGTTTTCATTTGAAAACATCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
* * **
19984554 AAAGATTTTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
* **
19984600 AAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT-ATGAC-TC--
1 AAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGAAAACATCTT
* * ** *
19984646 AAAGCTTCTCATTTAAGGCTCAAAGATTCTCATTTGAGGACTTCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
19984692 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
* *
19984738 AAAGATTCTTATTTAAGACTCAAAGCTTCTCATTTGAAAACATCTT
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
* * *
19984784 AAAGATTTTCATTTGAAAACATCTTAAA-ATTCTCATTT-AAGAC-TC--
1 AAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGAAAACATCTT
19984829 AAAGATTCTCATTTAA
1 AAAGATTCTCATTTAA
19984845 AAACATCTTA
Statistics
Matches: 251, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
42 14 0.06
43 4 0.02
44 6 0.02
45 16 0.06
46 164 0.65
47 10 0.04
48 10 0.04
49 11 0.04
50 16 0.06
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (46 bp):
AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAACATCTT
Found at i:19984585 original size:67 final size:67
Alignment explanation
Indices: 19984506--19984937 Score: 337
Period size: 71 Copynumber: 6.3 Consensus size: 67
19984496 TTAAAAATTA
* * *
19984506 TCAAAGATTCTCATTTAAGACTTAAAGGTTTTCATTTGAAAACATCTTAAAGATTTTCATTTAAG
1 TCAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAG
19984571 AC
66 AC
* *
19984573 TCAAAGGTTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATT
1 TCAAAGATTCTCATTT---AA-GACTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATT
*
19984638 TATGAC
62 TAAGAC
* * * ** *
19984644 TCAAAGCTTCTCATTTAAGGCTCAAAGATTCTCATTTGAGGACTTCTTAAAGATTCTCATTTAAG
1 TCAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAG
19984709 AC
66 AC
* * * *
19984711 TCAAAGATTCTCATTTGAAAACATCTTAAAGATTCTTATTT-AAGAC-TC--AAAGCTTCTCATT
1 TCAAAGATTCTCATTT---AAGA-CTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATT
*
19984772 TGAAAAC
62 T-AAGAC
* * *
19984779 ATCTTAAAGATTTTCATTTGAAAACATCTTAAA-ATTCTCATTT-AAGAC-TC--AAAGATTCTC
1 -TC--AAAGATTCTCATTT---AAGA-CTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTC
*
19984839 ATTTAAAAAC
59 ATTT-AAGAC
* * * * * * * *
19984849 ATCTTAAAGATTTTTATTTAAGACTCAAAGCTTTTCATTT-CAAACGTCTTAAGGATTCTCATTT
1 -TC--AAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTT
19984913 AAGAC
63 AAGAC
19984918 T-AAAGATTCTCATTTGAAGA
1 TCAAAGATTCTCATTT-AAGA
19984938 TTCATAATTT
Statistics
Matches: 312, Mismatches: 36, Indels: 35
0.81 0.09 0.09
Matches are distributed among these distances:
65 12 0.04
66 9 0.03
67 100 0.32
68 9 0.03
69 8 0.03
70 73 0.23
71 101 0.32
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (67 bp):
TCAAAGATTCTCATTTAAGACTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAG
AC
Found at i:19984668 original size:92 final size:91
Alignment explanation
Indices: 19984554--19984937 Score: 383
Period size: 92 Copynumber: 4.2 Consensus size: 91
19984544 AAAACATCTT
* *
19984554 AAAGATTTTCATTTAAGACTCAAAGGTTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAAT-TCTTAAAGATTCTCATTTGAAAA
*
19984619 CATCTTAAAGATTCTCATTTATGACTC
65 CATCTTAAAGATTCTCATTTAAGACTC
* * * * *
19984646 AAAGCTTCTCATTTAAGGCTCAAAGATTCTCATTTGAGGACTTCTTAAAGATTCTCATTT-AAGA
1 AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGA-AAATTCTTAAAGATTCTCATTTGAAAA
*
19984710 C-TC--AAAGATTCTCATTTGAAAACATC
65 CATCTTAAAGATTCTCATTT-AAGAC-TC
* * * *
19984736 TTAAAGATTCTTATTTAAGACTCAAAGCTTCTCATTTGAAAACATCTTAAAGATTTTCATTTGAA
1 --AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAA-TTCTTAAAGATTCTCATTTGAA
19984801 AACATCTTAAA-ATTCTCATTTAAGACTC
63 AACATCTTAAAGATTCTCATTTAAGACTC
* * * * * * * *
19984829 AAAGATTCTCATTTAAAAACATCTTAAAGATTTTTATTT-AAGA--CTCAAAGCTTTTCATTT-C
1 AAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGAAAATTCTTAAAGATTCTCATTTGA
* *
19984890 AAACGTCTTAAGGATTCTCATTTAAGACT-
62 AAACATCTTAAAGATTCTCATTTAAGACTC
19984919 AAAGATTCTCATTTGAAGA
1 AAAGATTCTCATTT-AAGA
19984938 TTCATAATTT
Statistics
Matches: 245, Mismatches: 32, Indels: 32
0.79 0.10 0.10
Matches are distributed among these distances:
88 14 0.06
89 3 0.01
90 31 0.13
91 49 0.20
92 105 0.43
93 10 0.04
94 9 0.04
95 21 0.09
96 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (91 bp):
AAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATTCTTAAAGATTCTCATTTGAAAAC
ATCTTAAAGATTCTCATTTAAGACTC
Found at i:19984914 original size:70 final size:69
Alignment explanation
Indices: 19984692--19984867 Score: 243
Period size: 70 Copynumber: 2.6 Consensus size: 69
19984682 AGGACTTCTT
* * *
19984692 AAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGAAAACATCTTAAAGATTCTTATTTA
1 AAAGATTCTCATTTAAAAACATCTTAAAGATTTTCATTTGAAAACATC-TAAA-ATTCTCATTTA
19984753 AGACTC
64 AGACTC
* *
19984759 AAAGCTTCTCATTTGAAAACATCTTAAAGATTTTCATTTGAAAACATCTTAAAATTCTCATTTAA
1 AAAGATTCTCATTTAAAAACATCTTAAAGATTTTCATTTGAAAACATC-TAAAATTCTCATTTAA
19984824 GACTC
65 GACTC
*
19984829 AAAGATTCTCATTTAAAAACATCTTAAAGATTTTTATTT
1 AAAGATTCTCATTTAAAAACATCTTAAAGATTTTCATTT
19984868 AAGACTCAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
67 13 0.13
68 4 0.04
69 2 0.02
70 52 0.53
71 27 0.28
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (69 bp):
AAAGATTCTCATTTAAAAACATCTTAAAGATTTTCATTTGAAAACATCTAAAATTCTCATTTAAG
ACTC
Found at i:19986274 original size:13 final size:13
Alignment explanation
Indices: 19986256--19986281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19986246 TTTCCCATTC
19986256 TTTCATTTTTTTA
1 TTTCATTTTTTTA
19986269 TTTCATTTTTTTA
1 TTTCATTTTTTTA
19986282 ATTTTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCATTTTTTTA
Found at i:19991069 original size:15 final size:16
Alignment explanation
Indices: 19991031--19991075 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
19991021 AAAAATACTT
*
19991031 AAAAAAATAAACACAT
1 AAAAAAATAAACACAC
*
19991047 AAAAAAATAAATAC-C
1 AAAAAAATAAACACAC
19991062 AAAAAAATGAAACA
1 AAAAAAAT-AAACA
19991076 GTTCGGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.76, C:0.11, G:0.02, T:0.11
Consensus pattern (16 bp):
AAAAAAATAAACACAC
Found at i:20000820 original size:8 final size:8
Alignment explanation
Indices: 20000809--20000834 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20000799 TATATATATA
20000809 TATATTAC
1 TATATTAC
20000817 TATATTAC
1 TATATTAC
20000825 TATATTAC
1 TATATTAC
20000833 TA
1 TA
20000835 CAAAACTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATTAC
Found at i:20000820 original size:16 final size:16
Alignment explanation
Indices: 20000792--20000834 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
20000782 CCTTTATCCA
20000792 ATATATA-TA-TATAT
1 ATATATATTACTATAT
20000806 ATATATATTACTATAT
1 ATATATATTACTATAT
20000822 -TACTATATTACTA
1 ATA-TATATTACTA
20000835 CAAAACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.27
15 4 0.15
16 15 0.58
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATTACTATAT
Found at i:20001123 original size:7 final size:7
Alignment explanation
Indices: 20001111--20001151 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
20001101 GCATTTGCCA
20001111 AAAGAAG
1 AAAGAAG
20001118 AAAGAAG
1 AAAGAAG
*
20001125 AGAGAAG
1 AAAGAAG
20001132 AAAGAAG
1 AAAGAAG
*
20001139 AGAGAAG
1 AAAGAAG
*
20001146 AGAGAA
1 AAAGAA
20001152 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:20001132 original size:14 final size:14
Alignment explanation
Indices: 20001113--20001151 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
20001103 ATTTGCCAAA
20001113 AGAAGAAAGAAGAG
1 AGAAGAAAGAAGAG
20001127 AGAAGAAAGAAGAG
1 AGAAGAAAGAAGAG
*
20001141 AGAAGAGAGAA
1 AGAAGAAAGAA
20001152 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AGAAGAAAGAAGAG
Found at i:20001137 original size:21 final size:21
Alignment explanation
Indices: 20001111--20001151 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20001101 GCATTTGCCA
20001111 AAAGAAGAAAGAAGAGAGAAG
1 AAAGAAGAAAGAAGAGAGAAG
*
20001132 AAAGAAGAGAGAAGAGAGAA
1 AAAGAAGAAAGAAGAGAGAA
20001152 AAAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAGAAGAGAGAAG
Found at i:20001604 original size:21 final size:22
Alignment explanation
Indices: 20001562--20001614 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
20001552 TTCGAAATTA
20001562 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
20001584 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
20001605 ATAAATATAT
1 ATAAA-ATAT
20001615 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:20001979 original size:14 final size:14
Alignment explanation
Indices: 20001960--20001988 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20001950 ACCTTCACCC
20001960 CACTAAGGGTTCCT
1 CACTAAGGGTTCCT
20001974 CACTAAGGGTTCCT
1 CACTAAGGGTTCCT
20001988 C
1 C
20001989 TATCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (14 bp):
CACTAAGGGTTCCT
Found at i:20003170 original size:5 final size:5
Alignment explanation
Indices: 20003160--20003188 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
20003150 GGGAAGCTAG
20003160 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
20003189 ATTTCCCCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20003402 original size:19 final size:19
Alignment explanation
Indices: 20003364--20003403 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
20003354 AAAAATGCAA
*
20003364 AAATAAATTCAAATACCAG
1 AAATAAATTCAAATAACAG
20003383 AAATAAATT-AAATAGACAG
1 AAATAAATTCAAATA-ACAG
20003402 AA
1 AA
20003404 TGTAAGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAATTCAAATAACAG
Found at i:20003624 original size:11 final size:11
Alignment explanation
Indices: 20003605--20003647 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
20003595 TACAACCCAG
20003605 AAAGAAAAAAA
1 AAAGAAAAAAA
20003616 AAAGGAAAAAAA
1 AAA-GAAAAAAA
20003628 AAA-AAAAAAGA
1 AAAGAAAAAA-A
20003639 AAAGCAAAA
1 AAAG-AAAA
20003648 GAACAACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.21
11 7 0.25
12 11 0.39
13 4 0.14
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:20003628 original size:16 final size:16
Alignment explanation
Indices: 20003604--20003634 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20003594 CTACAACCCA
*
20003604 GAAAGAAAAAAAAAAG
1 GAAAAAAAAAAAAAAG
20003620 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAA
20003635 AAGAAAAGCA
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:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAAAAAG
Found at i:20003647 original size:18 final size:17
Alignment explanation
Indices: 20003605--20003647 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
20003595 TACAACCCAG
*
20003605 AAAGAAAAAAAAAAGGA
1 AAAGAAAAAAAAAAAGA
*
20003622 AAAAAAAAAAAAAAAGA
1 AAAGAAAAAAAAAAAGA
*
20003639 AAAGCAAAA
1 AAAGAAAAA
20003648 GAACAACTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAAAGA
Found at i:20008611 original size:3 final size:3
Alignment explanation
Indices: 20008603--20008634 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20008593 CTCAAACTCT
20008603 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20008635 CATAAGAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20008959 original size:25 final size:25
Alignment explanation
Indices: 20008915--20008977 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
20008905 TGATAGAACA
*
20008915 ATTAAAATAT-TAAAATTATTTATT
1 ATTAAAATATATTAAATTATTTATT
*
20008939 ATTAAAGTATATTAAATTATTTATT
1 ATTAAAATATATTAAATTATTTATT
20008964 ATTAAAAT-TATTAA
1 ATTAAAATATATTAA
20008978 TGTTCAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTAAAATATATTAAATTATTTATT
Found at i:20009179 original size:17 final size:16
Alignment explanation
Indices: 20009145--20009187 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
20009135 ATAAAATAGT
20009145 AATATTTAT-TACTAA
1 AATATTTATATACTAA
*
20009160 AATATTTATACTATTAA
1 AATATTTATA-TACTAA
20009177 AATATTTATAT
1 AATATTTATAT
20009188 TTTATATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
17 15 0.60
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTTATATACTAA
Found at i:20009419 original size:42 final size:42
Alignment explanation
Indices: 20009339--20009449 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
20009329 AAATATTCAT
*
20009339 ATAAAAAATAATATTATTATATTATTTAACATTAATTATTAAA
1 ATAATAAAT-ATATTATTATATTATTTAACATTAATTATTAAA
** *
20009382 ATAATAAATATATTATTATA-TATATTATTATTTATTATTAAA
1 ATAATAAATATATTATTATATTAT-TTAACATTAATTATTAAA
*
20009424 ATAATAATATAATACTATT-TATTATT
1 ATAATAA-AT-ATATTATTATATTATT
20009450 GAGATAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
41 3 0.05
42 33 0.56
43 13 0.22
44 10 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (42 bp):
ATAATAAATATATTATTATATTATTTAACATTAATTATTAAA
Found at i:20009420 original size:10 final size:12
Alignment explanation
Indices: 20009389--20009421 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20009379 AAAATAATAA
20009389 ATATATTATTAT
1 ATATATTATTAT
20009401 ATATATTATTAT
1 ATATATTATTAT
20009413 -T-TATTATTA
1 ATATATTATTA
20009422 AAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 1 0.05
12 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATATTATTAT
Found at i:20011522 original size:19 final size:19
Alignment explanation
Indices: 20011498--20011546 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
20011488 CTCTTATCAA
20011498 TTTAAATAAATTTAAATAT
1 TTTAAATAAATTTAAATAT
** *
20011517 TTTAAATGGATTTGAATAT
1 TTTAAATAAATTTAAATAT
20011536 TATTAAATAAA
1 T-TTAAATAAA
20011547 GTAAATAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
TTTAAATAAATTTAAATAT
Found at i:20012335 original size:265 final size:265
Alignment explanation
Indices: 20011862--20012393 Score: 1037
Period size: 265 Copynumber: 2.0 Consensus size: 265
20011852 AGTCTTTAGC
20011862 AAAATCAGGATTATCTGTGAATTGAATACTGTCATAACGTTTAAGTCTATGGACTTATCGTTAGA
1 AAAATCAGGATTATCTGTGAATTGAATACTGTCATAACGTTTAAGTCTATGGACTTATCGTTAGA
* *
20011927 CATTGATTTAAGAGTAGCCATGAATCATTTTTTTTTAAGTGCGATTGACTACCTAACTGAATCTG
66 CATTGATTTAAGAGTAGCCACGAATCATTTTTTTTTAAGTGCGATTGACTACCTAACTAAATCTG
20011992 TCACTTTTTAAAAAGAAATCCTAAATTTGACTTAGGTATCTTTAAAAAGTAGATTTAATATCTAC
131 TCACTTTTTAAAAAGAAATCCTAAATTTGACTTAGGTATCTTTAAAAAGTAGATTTAATATCTAC
20012057 AAAACAAAACTAGATTTGAAAGTACAATTACGTGTGAAGAAGGTTATGGTATCCCTACAATTCCC
196 AAAACAAAACTAGATTTGAAAGTACAATTACGTGTGAAGAAGGTTATGGTATCCCTACAATTCCC
20012122 ATCGA
261 ATCGA
20012127 AAAATCAGGATTATCTGTGAATTGAATACTGTCATAACGTTTAAGTCTATGGACTTATCGTTAGA
1 AAAATCAGGATTATCTGTGAATTGAATACTGTCATAACGTTTAAGTCTATGGACTTATCGTTAGA
*
20012192 CATTGATTTAAGAGTAGCCACGAATCATTTTTTTTTAAGTGCGATTGGCTACCTAACTAAATCTG
66 CATTGATTTAAGAGTAGCCACGAATCATTTTTTTTTAAGTGCGATTGACTACCTAACTAAATCTG
20012257 TCACTTTTTAAAAAGAAATCCTAAATTTGACTTAGGTATCTTTAAAAAGTAGATTTAATATCTAC
131 TCACTTTTTAAAAAGAAATCCTAAATTTGACTTAGGTATCTTTAAAAAGTAGATTTAATATCTAC
20012322 AAAACAAAACTAGATTTGAAAGTACAATTACGTGTGAAGAAGGTTATGGTATCCCTACAATTCCC
196 AAAACAAAACTAGATTTGAAAGTACAATTACGTGTGAAGAAGGTTATGGTATCCCTACAATTCCC
20012387 ATCGA
261 ATCGA
20012392 AA
1 AA
20012394 GATGGTACCA
Statistics
Matches: 264, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
265 264 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (265 bp):
AAAATCAGGATTATCTGTGAATTGAATACTGTCATAACGTTTAAGTCTATGGACTTATCGTTAGA
CATTGATTTAAGAGTAGCCACGAATCATTTTTTTTTAAGTGCGATTGACTACCTAACTAAATCTG
TCACTTTTTAAAAAGAAATCCTAAATTTGACTTAGGTATCTTTAAAAAGTAGATTTAATATCTAC
AAAACAAAACTAGATTTGAAAGTACAATTACGTGTGAAGAAGGTTATGGTATCCCTACAATTCCC
ATCGA
Found at i:20012663 original size:133 final size:133
Alignment explanation
Indices: 20012423--20012689 Score: 471
Period size: 133 Copynumber: 2.0 Consensus size: 133
20012413 CGCGTTATCC
20012423 ATTAAGCTTTAAAAATTTTATCAAGTAATTAATTATTGAAAACTATTTTTAATTGACTCCAATAC
1 ATTAAGCTTTAAAAATTTTATCAAGTAATTAATTATTGAAAACTATTTTTAATTGACTCCAATAC
* * *
20012488 TTTTTGGTAGAAAATTAAAAAAATTTTCTCACCTCAAAAGTATATACGAAACTACTGTTTCTTTT
66 TTTTTGGTAAAAAATTAAAAAAATTTTCTCACCTCAAAAGTATATAAGAAACTACTGCTTCTTTT
20012553 GTA
131 GTA
20012556 ATTAAGCTTTAAAAATTTTATCAAGTAATTAATTATTGAAAACTATTTTTAATTGACTCCAATAC
1 ATTAAGCTTTAAAAATTTTATCAAGTAATTAATTATTGAAAACTATTTTTAATTGACTCCAATAC
* * * *
20012621 TTTTTGGTAAAAAATTAAGAAAATTTTTTCACCTCAAGAGTATATAAGAAATTACTGCTTCTTTT
66 TTTTTGGTAAAAAATTAAAAAAATTTTCTCACCTCAAAAGTATATAAGAAACTACTGCTTCTTTT
20012686 GTA
131 GTA
20012689 A
1 A
20012690 AGGCTCTACC
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 127 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (133 bp):
ATTAAGCTTTAAAAATTTTATCAAGTAATTAATTATTGAAAACTATTTTTAATTGACTCCAATAC
TTTTTGGTAAAAAATTAAAAAAATTTTCTCACCTCAAAAGTATATAAGAAACTACTGCTTCTTTT
GTA
Found at i:20012940 original size:60 final size:59
Alignment explanation
Indices: 20012827--20013100 Score: 281
Period size: 61 Copynumber: 4.6 Consensus size: 59
20012817 CTTTATACAA
20012827 AAAAAAATTGATACTTTCAATTTTT--TTAAAAATATTTTTCTTTTGAAATTTTTATTCTTT
1 AAAAAAATTGATACTTTCAATTTTTCCTT-AAAATATTTTT-TTTTGAAATTTTTATT-TTT
* * * *
20012887 AAGAAAAATTGATAC-TTCAATTTTTCCTTAAAATGTTTTTTTCTAAAATTTTTATTTTCG
1 AA-AAAAATTGATACTTTCAATTTTTCCTTAAAATATTTTTTTTTGAAATTTTTATTTT-T
* *
20012947 AATAAAATTGATACTTTCAACTTTTT-CTCAAAAATATTTTTTTTTGAAATTTTTATTTTTT
1 AAAAAAATTGATACTTTCAA-TTTTTCCT-TAAAATATTTTTTTTTGAAATTTTTA-TTTTT
* * * * ** *
20013008 AAGAAAAATTGACAATTTTAACTTTTCCTTAAAATGCTTTTTTTT-AAATCTTTATTTTT
1 AA-AAAAATTGATACTTTCAATTTTTCCTTAAAATATTTTTTTTTGAAATTTTTATTTTT
*
20013067 GAAAAAAACTT-ATACTTTCAACTTTTCCTTAAAA
1 -AAAAAAA-TTGATACTTTCAATTTTTCCTTAAAA
20013101 ATACTTTTAA
Statistics
Matches: 180, Mismatches: 22, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
59 43 0.24
60 47 0.26
61 68 0.38
62 22 0.12
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (59 bp):
AAAAAAATTGATACTTTCAATTTTTCCTTAAAATATTTTTTTTTGAAATTTTTATTTTT
Found at i:20013049 original size:121 final size:122
Alignment explanation
Indices: 20012827--20013108 Score: 385
Period size: 121 Copynumber: 2.3 Consensus size: 122
20012817 CTTTATACAA
20012827 AAAAAAATTGATACTTTCAA-TTTTT-TTAAAAATATTTTTCTTTTGAAATTTTTATTCTTTAAG
1 AAAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTTGAAATTTTTATTCTTTAAG
* * * *
20012890 AAAAATTGATACTTCAATTTTTCCTTAAAATGTTTTTTTCTAAAATTTTTATTTTCG
66 AAAAATTGAAACTTCAACTTTTCCTTAAAATGTCTTTTTCTAAAATCTTTATTTTCG
* * *
20012947 AATAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT-TTTTGAAATTTTTATTTTTTAAG
1 AAAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTTGAAATTTTTATTCTTTAAG
* * * * *
20013011 AAAAATTGACAATTTTAACTTTTCCTTAAAATG-CTTTTTTTTAAATCTTTATTTTTG
66 AAAAATTGA-AACTTCAACTTTTCCTTAAAATGTCTTTTTCTAAAATCTTTATTTTCG
* *
20013068 AAAAAAACTT-ATACTTTCAACTTTTCCTTAAAAATACTTTT
1 AAAAAAA-TTGATACTTTCAACTTTTTCTTAAAAATATTTTT
20013109 AAAAAATTTT
Statistics
Matches: 142, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
120 19 0.13
121 89 0.63
122 34 0.24
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (122 bp):
AAAAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTCTTTTGAAATTTTTATTCTTTAAG
AAAAATTGAAACTTCAACTTTTCCTTAAAATGTCTTTTTCTAAAATCTTTATTTTCG
Found at i:20013102 original size:60 final size:61
Alignment explanation
Indices: 20012827--20013108 Score: 303
Period size: 60 Copynumber: 4.7 Consensus size: 61
20012817 CTTTATACAA
* *
20012827 AAAAAAATTGATACTTTCAA-TTTT-TTTAAAAATATTTTTCTTTTGAAATTTTTATTCTTT-
1 AAAAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTTT-TTTTGAAATTTTTATT-TTTG
* * * *
20012887 AAGAAAAATTGATAC-TTCAATTTTTCCTT-AAAAT-GTTTTTTTCTAAAATTTTTATTTTCG
1 AA-AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTTTTTT-TGAAATTTTTATTTTTG
* * * * *
20012947 AATAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTTGAAATTTTTATTTTTT
1 AAAAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTTTTTTTGAAATTTTTATTTTTG
* * * * *
20013008 AAGAAAAATTGACAATTTTAACTTTTCCTT-AAAATGCTTTTTTTT-AAATCTTTATTTTTG
1 AA-AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTTTTTTTGAAATTTTTATTTTTG
20013068 AAAAAAACTT-ATACTTTCAACTTTTCCTTAAAAATACTTTT
1 AAAAAAA-TTGATACTTTCAACTTTTCCTTAAAAATACTTTT
20013109 AAAAAATTTT
Statistics
Matches: 185, Mismatches: 26, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
59 37 0.20
60 63 0.34
61 55 0.30
62 30 0.16
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (61 bp):
AAAAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTTTTTTTGAAATTTTTATTTTTG
Found at i:20014900 original size:85 final size:83
Alignment explanation
Indices: 20014792--20015077 Score: 295
Period size: 85 Copynumber: 3.4 Consensus size: 83
20014782 CATAATGACT
* *
20014792 TGGATCGAACCAAAGTCTAAAATAAATAACTTAGACTAAGCTGAAGAAGGATTTGGCATAGGCCA
1 TGGATTGAACCGAAGTCTAAAATAAATAACTTAGACTAAGC--AAGAAGGATTTGGCATAGGCCA
20014857 AAATCCAAAATAAAATAACC
64 AAATCCAAAATAAAATAACC
* * * * * * *
20014877 TGGATAGAGCCGAAGTCTAAAATAAATAACTTGGACTGAA-CAAGGAAAGATCTGGCACAAGCCA
1 TGGATTGAACCGAAGTCTAAAATAAATAACTTAGACT-AAGCAA-GAAGGATTTGGCATAGGCCA
* *
20014941 AAATCTAAAACAAAATAACC
64 AAATCCAAAATAAAATAACC
* * * * *
20014961 TGAATTGAACCGAAGTCTGAAATAAATAACTTAGACTAAGCCAAAGAAGAATTTGACATAGGTCA
1 TGGATTGAACCGAAGTCTAAAATAAATAACTTAGACTAAG-C-AAGAAGGATTTGGCATAGGCCA
* * * *
20015026 AAATTCAAAATGAAATGACT
64 AAATCCAAAATAAAATAACC
* * * *
20015046 TAGATTGAACCAAAGTCTGAAATAAGTAACTT
1 TGGATTGAACCGAAGTCTAAAATAAATAACTT
20015078 GGATTAGATT
Statistics
Matches: 164, Mismatches: 32, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
83 4 0.02
84 66 0.40
85 90 0.55
86 4 0.02
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (83 bp):
TGGATTGAACCGAAGTCTAAAATAAATAACTTAGACTAAGCAAGAAGGATTTGGCATAGGCCAAA
ATCCAAAATAAAATAACC
Found at i:20014962 original size:84 final size:84
Alignment explanation
Indices: 20014798--20015001 Score: 259
Period size: 84 Copynumber: 2.4 Consensus size: 84
20014788 GACTTGGATC
* * * * *
20014798 GAACCAAAGTCTAAAATAAATAACTTAGACTAAGCTGAAGAAGGATTTGGCATAGGCCAAAATCC
1 GAACCGAAGTCTAAAATAAATAACTTAGACTAAGC-GAAGAAAGATCTGGCACAAGCCAAAATCC
* *
20014863 AAAATAAAATAACCTGGATA
65 AAAACAAAATAACCTGAATA
* *
20014883 GAGCCGAAGTCTAAAATAAATAACTTGGACTGAA-C-AAGGAAAGATCTGGCACAAGCCAAAATC
1 GAACCGAAGTCTAAAATAAATAACTTAGACT-AAGCGAA-GAAAGATCTGGCACAAGCCAAAATC
* *
20014946 TAAAACAAAATAACCTGAATT
64 CAAAACAAAATAACCTGAATA
*
20014967 GAACCGAAGTCTGAAATAAATAACTTAGACTAAGC
1 GAACCGAAGTCTAAAATAAATAACTTAGACTAAGC
20015002 CAAAGAAGAA
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
83 4 0.04
84 67 0.66
85 29 0.28
86 2 0.02
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (84 bp):
GAACCGAAGTCTAAAATAAATAACTTAGACTAAGCGAAGAAAGATCTGGCACAAGCCAAAATCCA
AAACAAAATAACCTGAATA
Found at i:20015093 original size:85 final size:85
Alignment explanation
Indices: 20014798--20015151 Score: 250
Period size: 85 Copynumber: 4.2 Consensus size: 85
20014788 GACTTGGATC
* ** ** * * *
20014798 GAACCAAAGTCTAAAATAAATAACTTAGACTAAGCTGAAGAAGGATTTGGCATAGGCCAAAATCC
1 GAACCAAAGTCTGAAATAAATAACTTAGACTAAGCCAAAGAAAAATCTGACATAGGCCAAAATCA
** * * * *
20014863 AAAATAAAATAACCTGGATA
66 AAAACCAAATGACATAGATT
* * * * * * * * *
20014883 GAGCCGAAGTCTAAAATAAATAACTTGGACTGAA--CAAGGAAAGATCTGGCACAAGCCAAAATC
1 GAACCAAAGTCTGAAATAAATAACTTAGACT-AAGCCAAAGAAAAATCTGACATAGGCCAAAATC
* * * *
20014946 TAAAACAAAATAACCT-GAATT
65 AAAAACCAAATGACATAG-ATT
* * * *
20014967 GAACCGAAGTCTGAAATAAATAACTTAGACTAAGCCAAAGAAGAATTTGACATAGGTCAAAATTC
1 GAACCAAAGTCTGAAATAAATAACTTAGACTAAGCCAAAGAAAAATCTGACATAGGCCAAAA-TC
** *
20015032 -AAAATGAAATGACTTAGATT
65 AAAAACCAAATGACATAGATT
* * * *** * *
20015052 GAACCAAAGTCTGAAATAAGTAACTTGGA-TTAGATTGAAGAAAAATCTGGCATAGGCCGAAATC
1 GAACCAAAGTCTGAAATAAATAACTTAGACTAAG-CCAAAGAAAAATCTGACATAGGCCAAAATC
20015116 AAAAACCAAATGACATAGATT
65 AAAAACCAAATGACATAGATT
*
20015137 AAACCAAAGTCTGAA
1 GAACCAAAGTCTGAA
20015152 TTCACAACAA
Statistics
Matches: 217, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
83 3 0.01
84 71 0.33
85 138 0.64
86 5 0.02
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (85 bp):
GAACCAAAGTCTGAAATAAATAACTTAGACTAAGCCAAAGAAAAATCTGACATAGGCCAAAATCA
AAAACCAAATGACATAGATT
Found at i:20015306 original size:15 final size:15
Alignment explanation
Indices: 20015286--20015317 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20015276 ACAATTTAGA
*
20015286 AATTCAAAGGTTCAC
1 AATTCAAAGATTCAC
20015301 AATTCAAAGATTCAC
1 AATTCAAAGATTCAC
20015316 AA
1 AA
20015318 GAATTGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (15 bp):
AATTCAAAGATTCAC
Found at i:20015329 original size:17 final size:17
Alignment explanation
Indices: 20015307--20015355 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
20015297 TCACAATTCA
20015307 AAGATTCACAAGAATTG
1 AAGATTCACAAGAATTG
*
20015324 AAGATTCACAAAAAAATTG
1 AAGATTCAC--AAGAATTG
*
20015343 AAGATTCGCAAGA
1 AAGATTCACAAGA
20015356 TTTGGAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 12 0.44
19 15 0.56
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.20
Consensus pattern (17 bp):
AAGATTCACAAGAATTG
Found at i:20015426 original size:33 final size:33
Alignment explanation
Indices: 20015344--20015441 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
20015334 AAAAAATTGA
* *
20015344 AGATTCGCAAGATTTGGAAATTTGCAAGAATTTC
1 AGATTCGCAAGATTT-TAAATTTGCAAGAATTAC
* * * * * *
20015378 TGGTTCACAAAATTTTAGATTTGCAAGAATTAG
1 AGATTCGCAAGATTTTAAATTTGCAAGAATTAC
**
20015411 AGATTCGCAAGATTTTCAAATTCACAAGAAT
1 AGATTCGCAAGATTTT-AAATTTGCAAGAAT
20015442 AAAAAATTCA
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
33 26 0.54
34 22 0.46
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (33 bp):
AGATTCGCAAGATTTTAAATTTGCAAGAATTAC
Found at i:20020800 original size:60 final size:60
Alignment explanation
Indices: 20020697--20020983 Score: 288
Period size: 60 Copynumber: 4.8 Consensus size: 60
20020687 TCATTTATAC
* *
20020697 AAGAAAAATTGATACTTTCAATTTTTCCTCAAAA-ATAAGTTTTTGAAATTTTTATTCTTT
1 AAGAAAAATTGATACTTTCAATTTTTCCTTAAAATAT-ATTTTTTGAAATTTTTATTCTTT
* *
20020757 AAGAAAAATTGATACTCTCAATTTTTCCTTAAAATATATTTTTTAAAATTTTTATT-TTT
1 AAGAAAAATTGATACTTTCAATTTTTCCTTAAAATATATTTTTTGAAATTTTTATTCTTT
* * *
20020816 GAA-AAAAATTGATAGCTTTCAACTTTT-CTTCAAAAATATATTTTTTTGATATTTTTATTTTTT
1 -AAGAAAAATTGATA-CTTTCAATTTTTCCTT--AAAATATA-TTTTTTGAAATTTTTATTCTTT
* * * *
20020879 AAGAAAAATTGATACTTTTAATTTTTTCTTAAAATATATATTTT-AAATATTTATTC---
1 AAGAAAAATTGATACTTTCAATTTTTCCTTAAAATATATTTTTTGAAATTTTTATTCTTT
* * * *
20020935 ACAGAAAAATTAATATTTTTAATTTTT-TTTCAAAA-ATATGTTTTTGAAA
1 A-AGAAAAATTGATACTTTCAATTTTTCCTT-AAAATATAT-TTTTTGAAA
20020984 CAATATTTTT
Statistics
Matches: 196, Mismatches: 18, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
56 7 0.04
57 31 0.16
58 3 0.02
59 26 0.13
60 66 0.34
61 18 0.09
62 28 0.14
63 17 0.09
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (60 bp):
AAGAAAAATTGATACTTTCAATTTTTCCTTAAAATATATTTTTTGAAATTTTTATTCTTT
Found at i:20020997 original size:122 final size:118
Alignment explanation
Indices: 20020689--20020982 Score: 353
Period size: 122 Copynumber: 2.5 Consensus size: 118
20020679 AAAATTCATC
* * *
20020689 ATTTATACAAGAAAAATTGATACTTTCAATTTTTCCTCAAAAATAAGTTTTTGAA-ATTTTTATT
1 ATTTATTCAAGAAAAATTGATACTTTCAATTTTTCTTCAAAAATATGTTTTTGAATATTTTTATT
* *
20020753 CTTTAAGAAAAATTGATACTCTCAATTTTTCCTTAAAATATATTTTTTAAAAT
66 TTTTAAGAAAAATTGATACTCTCAATTTTTCCTTAAAATATATATTTTAAAAT
* * * *
20020806 TTTTATTTTTGAA-AAAAATTGATAGCTTTCAACTTTTCTTCAAAAATATATTTTTTTG-ATATT
1 ATTTA---TTCAAGAAAAATTGATA-CTTTCAATTTTTCTTC-AAAA-ATATGTTTTTGAATATT
* * *
20020869 TTTATTTTTTAAGAAAAATTGATACTTTTAATTTTTTCTTAAAATATATATTTT-AAAT
60 TTTATTTTTTAAGAAAAATTGATACTCTCAATTTTTCCTTAAAATATATATTTTAAAAT
* * * *
20020927 ATTTATTCACAGAAAAATTAATATTTTTAATTTTTTTTCAAAAATATGTTTTTGAA
1 ATTTATTCA-AGAAAAATTGATACTTTCAATTTTTCTTCAAAAATATGTTTTTGAA
20020983 ACAATATTTT
Statistics
Matches: 147, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
117 14 0.10
118 8 0.05
119 24 0.16
120 27 0.18
121 13 0.09
122 61 0.41
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (118 bp):
ATTTATTCAAGAAAAATTGATACTTTCAATTTTTCTTCAAAAATATGTTTTTGAATATTTTTATT
TTTTAAGAAAAATTGATACTCTCAATTTTTCCTTAAAATATATATTTTAAAAT
Found at i:20025486 original size:18 final size:19
Alignment explanation
Indices: 20025454--20025492 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20025444 TTTGTTTTCT
*
20025454 AGAGAGAGAACAGAGAAAA
1 AGAGAGAGAAAAGAGAAAA
*
20025473 AGAG-GAGAAAAGAGAGAA
1 AGAGAGAGAAAAGAGAAAA
20025491 AG
1 AG
20025493 GGAAGGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.36, T:0.00
Consensus pattern (19 bp):
AGAGAGAGAAAAGAGAAAA
Found at i:20025804 original size:20 final size:21
Alignment explanation
Indices: 20025766--20025804 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20025756 TTATTTGGAA
*
20025766 TTTTATCTTATTTATTTATGG
1 TTTTATCTTATTTAATTATGG
*
20025787 TTTTAT-TTGTTTAATTAT
1 TTTTATCTTATTTAATTAT
20025805 TTTTTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTTATCTTATTTAATTATGG
Found at i:20029773 original size:15 final size:16
Alignment explanation
Indices: 20029750--20029782 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20029740 GTATAAGATT
20029750 TAGTGAAAAG-AAAGA
1 TAGTGAAAAGCAAAGA
*
20029765 TAGTTAAAAGCAAAGA
1 TAGTGAAAAGCAAAGA
20029781 TA
1 TA
20029783 TGGTTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (16 bp):
TAGTGAAAAGCAAAGA
Found at i:20046803 original size:2 final size:2
Alignment explanation
Indices: 20046796--20046826 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20046786 TCGCCTTCGT
20046796 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20046827 TTAGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:20050948 original size:119 final size:120
Alignment explanation
Indices: 20050822--20051043 Score: 347
Period size: 119 Copynumber: 1.9 Consensus size: 120
20050812 CCAAACTCAA
*
20050822 GCCCATTTGGTCAAACTTGATCAAATATTAAAATTTTGAAAGAAATTAATTAAAAAACCAATGGG
1 GCCCATTTGGTCAAACTTGATCAAATAGTAAAATTTTGAAAGAAATTAATTAAAAAACCAATGGG
* * *
20050887 TTTGAACAAAACTTGGATTTTGACC-AAATGCCATTCAATCAAACCCAAGCCTAG
66 TTTAAACAAAACTTAGATTTTGACCAAAATACCATTCAATCAAACCCAAGCCTAG
* * * * * *
20050941 GCCCATTTGGTCAAACTTGGTCATATGGTAGAATTTTGAAAGAAATTAATTAAGAAACCTATGGG
1 GCCCATTTGGTCAAACTTGATCAAATAGTAAAATTTTGAAAGAAATTAATTAAAAAACCAATGGG
20051006 TTTAAACAAAACTTAGATTTTGACCAAAATACCATTCA
66 TTTAAACAAAACTTAGATTTTGACCAAAATACCATTCA
20051044 GTTAAACTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
119 81 0.88
120 11 0.12
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (120 bp):
GCCCATTTGGTCAAACTTGATCAAATAGTAAAATTTTGAAAGAAATTAATTAAAAAACCAATGGG
TTTAAACAAAACTTAGATTTTGACCAAAATACCATTCAATCAAACCCAAGCCTAG
Found at i:20052659 original size:18 final size:18
Alignment explanation
Indices: 20052612--20052740 Score: 83
Period size: 18 Copynumber: 7.3 Consensus size: 18
20052602 TTCTTTAAAA
20052612 TCAAACCCT-AACCCTAAG
1 TCAAACCCTAAACCC-AAG
* *
20052630 TAAAACCGTAAACCCAAG
1 TCAAACCCTAAACCCAAG
* *
20052648 TCAAACTCT-AA---AAC
1 TCAAACCCTAAACCCAAG
*
20052662 T-AAACCCTAAACCCTAG
1 TCAAACCCTAAACCCAAG
** *
20052679 -CTAAACTTTAAACCCTAGG
1 TC-AAACCCTAAACCC-AAG
20052698 TCAAACCCTAAACCCTAAG
1 TCAAACCCTAAACCC-AAG
**
20052717 TCAAACCCTAAACCTTAG
1 TCAAACCCTAAACCCAAG
20052735 TCAAAC
1 TCAAAC
20052741 TTAAACCCTA
Statistics
Matches: 84, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
13 6 0.07
14 5 0.06
17 3 0.04
18 35 0.42
19 34 0.40
20 1 0.01
ACGTcount: A:0.43, C:0.33, G:0.06, T:0.19
Consensus pattern (18 bp):
TCAAACCCTAAACCCAAG
Found at i:20052709 original size:19 final size:19
Alignment explanation
Indices: 20052663--20052750 Score: 101
Period size: 19 Copynumber: 4.8 Consensus size: 19
20052653 CTCTAAAACT
*
20052663 AAACCCTAAACCCTAGCT-
1 AAACCCTAAACCCTAGGTC
**
20052681 AAACTTTAAACCCTAGGTC
1 AAACCCTAAACCCTAGGTC
*
20052700 AAACCCTAAACCCTAAGTC
1 AAACCCTAAACCCTAGGTC
*
20052719 AAACCCTAAACCTTA-GTC
1 AAACCCTAAACCCTAGGTC
*
20052737 AAA-CTTAAACCCTA
1 AAACCCTAAACCCTA
20052751 AAAAGTCAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.15
18 21 0.35
19 30 0.50
ACGTcount: A:0.41, C:0.33, G:0.06, T:0.20
Consensus pattern (19 bp):
AAACCCTAAACCCTAGGTC
Found at i:20053082 original size:159 final size:159
Alignment explanation
Indices: 20052844--20053166 Score: 646
Period size: 159 Copynumber: 2.0 Consensus size: 159
20052834 ATTTGCATTT
20052844 TATTTATCCATTATAATCAGTTGCATACATTTACATTTTTAATTGTCTTCTATATAACATATTTT
1 TATTTATCCATTATAATCAGTTGCATACATTTACATTTTTAATTGTCTTCTATATAACATATTTT
20052909 ATTGCATTAATGCATTTTATTTTACATTCACATTATTTATTTTATTTTATTCAAAAATAAGAAAA
66 ATTGCATTAATGCATTTTATTTTACATTCACATTATTTATTTTATTTTATTCAAAAATAAGAAAA
20052974 AGAAATGTTTTAGAAATAAAATAAGATAA
131 AGAAATGTTTTAGAAATAAAATAAGATAA
20053003 TATTTATCCATTATAATCAGTTGCATACATTTACATTTTTAATTGTCTTCTATATAACATATTTT
1 TATTTATCCATTATAATCAGTTGCATACATTTACATTTTTAATTGTCTTCTATATAACATATTTT
20053068 ATTGCATTAATGCATTTTATTTTACATTCACATTATTTATTTTATTTTATTCAAAAATAAGAAAA
66 ATTGCATTAATGCATTTTATTTTACATTCACATTATTTATTTTATTTTATTCAAAAATAAGAAAA
20053133 AGAAATGTTTTAGAAATAAAATAAGATAA
131 AGAAATGTTTTAGAAATAAAATAAGATAA
20053162 TATTT
1 TATTT
20053167 CAAGTAAAAA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 164 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (159 bp):
TATTTATCCATTATAATCAGTTGCATACATTTACATTTTTAATTGTCTTCTATATAACATATTTT
ATTGCATTAATGCATTTTATTTTACATTCACATTATTTATTTTATTTTATTCAAAAATAAGAAAA
AGAAATGTTTTAGAAATAAAATAAGATAA
Found at i:20055248 original size:134 final size:131
Alignment explanation
Indices: 20054704--20055317 Score: 582
Period size: 134 Copynumber: 4.7 Consensus size: 131
20054694 AACAAAAAGC
* ** * * *
20054704 TGTTGTGAAAACTTATTTTATTTGTAATGATTTATT-GATGTAGTTGCTCAATTTATTT-TTTAA
1 TGTTGTAAAAACTT-TTTTATTTGTAACAATTT-TTCAATTTAGTTGCTTAATTTATTTGTTTAA
* * * ** * *
20054767 CA-TTTACACAACAAC-AAAAAAAGTTATTATGAAAATTTTTATCATATTTGTAAAGATTAAAAA
64 TATTTTATACAA-AACAAAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAA
20054830 TTAT
128 TTAT
* * *
20054834 TGTTGTGAAAAC-TTTTTA-TT-T-ACAATTTTT-AATGTCA-TTGCTTAATTTATTTGTTTATT
1 TGTTGTAAAAACTTTTTTATTTGTAACAATTTTTCAAT-TTAGTTGCTTAATTTATTTGTTTAAT
* *
20054893 ATTTTATACAATGACAAAAAAAAGTTGTTACAAAAATTTATATCATATTTGTAACGATAAAAAAT
65 ATTTTATACAA-AACAAAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAAT
*
20054958 TAA
129 TAT
* * ** * *
20054961 TATAGCT-AAAACTTTTTTATTTGTAATGATTTTTCAATATT-TTTACTTAATTTATTTGTTTAA
1 TGTTG-TAAAAACTTTTTTATTTGTAACAATTTTTCAAT-TTAGTTGCTTAATTTATTTGTTTAA
* * ** * * *
20055024 TATTTTATGCAATAAC--ATAAAAGTTGTTATGAAATTTTTTATTATATTTGTAA-TAGTAAAAA
64 TATTTTATACAA-AACAAAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGA-TAAAAA
20055086 ATTAT
127 ATTAT
* *
20055091 TGTTG-CAAAATTTTGCTTTATTTGTAACAATTTTTCAATTTAGTTGCTTAATTTATTTGTTTAA
1 TGTTGTAAAAACTTT--TTTATTTGTAACAATTTTTCAATTTAGTTGCTTAATTTATTTGTTTAA
* *
20055155 TATTTTATACAAAGACAAAAAAAAAATTGTTACAAAAACTTTTATCATATTTGTAACGATAAAAA
64 TATTTTATACAAA-AC-AAAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAA
20055220 ATTAT
127 ATTAT
* * * *
20055225 TGTTGTAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTCGTTACTTAATTTATTT-TTTAAA
1 TGTTGTAAAAACTT-TTTTATTTGTAACAATTTTTCAATTTAGTTGCTTAATTTATTTGTTT-AA
*
20055289 AATTTTATAC--AACAATAAAAAAGTTGTTA
64 TATTTTATACAAAACAA-AAAAAAGTTGTTA
20055318 TTTGTAATGA
Statistics
Matches: 399, Mismatches: 60, Indels: 49
0.79 0.12 0.10
Matches are distributed among these distances:
124 18 0.05
125 11 0.03
126 11 0.03
127 55 0.14
128 12 0.03
129 11 0.03
130 62 0.16
131 75 0.19
132 38 0.10
133 3 0.01
134 95 0.24
135 7 0.02
136 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (131 bp):
TGTTGTAAAAACTTTTTTATTTGTAACAATTTTTCAATTTAGTTGCTTAATTTATTTGTTTAATA
TTTTATACAAAACAAAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAATTA
T
Found at i:20055450 original size:114 final size:113
Alignment explanation
Indices: 20055212--20055435 Score: 299
Period size: 114 Copynumber: 2.0 Consensus size: 113
20055202 TATTTGTAAC
* * *
20055212 GATAAAAAATTATTGTTGTAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTCGTTACTTAAT
1 GATAAAATATTATTATTGTAAAAACTTGTTTTATTTGCAACAATTTTTCAATATCGTTACTTAAT
* * *
20055277 TTATTTTTTAAAAATTTTATACAACAATAAAAAAGTTGTTATTTGTAAT
66 TTATTTTTTAAAAATTTTATACAACAACAAAAAAGTTGTTA-TCGAAAT
* *
20055326 GATAAAATATTATTATTGTAAAAACTTGTTTTATTTGTAACAATTTTTCATTATCGTTACTTAAT
1 GATAAAATATTATTATTGTAAAAACTTGTTTTATTTGCAACAATTTTTCAATATCGTTACTTAAT
** * ** *
20055391 TTATTTTTT-TTAATTTTATATAATGACAAAAATGTTGTTA-CGAAA
66 TTATTTTTTAAAAATTTTATACAACAACAAAAAAGTTGTTATCGAAA
20055436 ATGTTTTATC
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
111 3 0.03
113 24 0.25
114 69 0.72
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (113 bp):
GATAAAATATTATTATTGTAAAAACTTGTTTTATTTGCAACAATTTTTCAATATCGTTACTTAAT
TTATTTTTTAAAAATTTTATACAACAACAAAAAAGTTGTTATCGAAAT
Found at i:20055451 original size:131 final size:131
Alignment explanation
Indices: 20055316--20055577 Score: 323
Period size: 131 Copynumber: 2.0 Consensus size: 131
20055306 AAAAAGTTGT
* * * * *
20055316 TATTTGTAATGATAAAATATTA-TTATTGTAAAAACTTGTTTTATTTGTAACAATTTTTCATTAT
1 TATTTGTAAGGATAAAATATTAGTT-TTGCAAAAACTTGTATTATTTGCAACAATTTTTCAATAT
* ** * * *
20055380 CGTTACTTAATTTATTTTTT-TTAATTTTATATAATGACAAA-AATGTTGTTACGAAAATGTTTT
65 CATTACTTAATTTATTTTTTAAAAATTTTATACAAGGACAAAGAA-GTTGTTACGAAAAT-TATT
20055443 ATCA
128 ATCA
* **
20055447 TATTTGTAAGGATAAAATATTAGTTTTGCAAAAATTTGTATTATTTGCAATGATTTTTCAATATC
1 TATTTGTAAGGATAAAATATTAGTTTTGCAAAAACTTGTATTATTTGCAACAATTTTTCAATATC
** *
20055512 ATTGTTTAATTTATTTTTTAAAAATTTTATACAAGGACAAAGAAGTTGTTATGAAAATTATTATC
66 ATTACTTAATTTATTTTTTAAAAATTTTATACAAGGACAAAGAAGTTGTTACGAAAATTATTATC
20055577 A
131 A
20055578 CATTGTTGTA
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
131 77 0.69
132 32 0.29
133 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (131 bp):
TATTTGTAAGGATAAAATATTAGTTTTGCAAAAACTTGTATTATTTGCAACAATTTTTCAATATC
ATTACTTAATTTATTTTTTAAAAATTTTATACAAGGACAAAGAAGTTGTTACGAAAATTATTATC
A
Found at i:20055507 original size:245 final size:246
Alignment explanation
Indices: 20055068--20055563 Score: 624
Period size: 245 Copynumber: 2.0 Consensus size: 246
20055058 TTTTTTATTA
* **
20055068 TATTTGTAATAGTAAAAAATTATTGTTGCAAAATTTTGCTTTATTTGTAACAATTTTTCAATTTA
1 TATTTGTAATAGTAAAAAATTATTATTGCAAAAACTTGCTTTATTTGTAACAATTTTTCAATTTA
*
20055133 GTTGCTTAATTTATTTGTTTAATATTTTATACAAAGACAAAAAAAAAATTGTTACAAAAACTTTT
66 GTTACTTAATTTATTTGTTTAATATTTTATACAAAGAC--AAAAAAAATTGTTACAAAAACTTTT
* *
20055198 ATCATATTTGTAACGATAAAAAATTATTGTTGTAAAAACTTGTTTTATTTGCAACAATTTTTCAA
129 ATCATATTTGTAACGATAAAAAATTATTGTTGCAAAAACTTGTATTATTTGCAACAATTTTTCAA
* * *
20055263 TGTCGTTACTTAATTTATTTTTTAAAAATTTTATACAACAATAAAAAAGTTGT
194 TATCATTACTTAATTTATTTTTTAAAAATTTTATACAACAACAAAAAAGTTGT
* * *
20055316 TATTTGTAAT-GATAAAATATTATTATTGTAAAAACTTGTTTTATTTGTAACAATTTTTC-ATTA
1 TATTTGTAATAG-TAAAAAATTATTATTGCAAAAACTTGCTTTATTTGTAACAATTTTTCAATT-
* * * * * ** **
20055379 TCGTTACTTAATTTATTTTTTTTA-ATTTTATATAATGAC-AAAAATGTTGTTACGAAAATGTTT
64 TAGTTACTTAATTTATTTGTTTAATATTTTATACAAAGACAAAAAAAATTGTTAC-AAAAACTTT
* * * **
20055442 TATCATATTTGTAAGGATAAAATATTAGTT-TTGCAAAAATTTGTATTATTTGCAATGATTTTTC
128 TATCATATTTGTAACGATAAAAAATTA-TTGTTGCAAAAACTTGTATTATTTGCAACAATTTTTC
** ** *
20055506 AATATCATTGTTTAATTTATTTTTTAAAAATTTTATACAAGGACAAAGAAGTTGT
192 AATATCATTACTTAATTTATTTTTTAAAAATTTTATACAACAACAAAAAAGTTGT
20055561 TAT
1 TAT
20055564 GAAAATTATT
Statistics
Matches: 213, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
244 12 0.06
245 111 0.52
246 2 0.01
247 17 0.08
248 71 0.33
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (246 bp):
TATTTGTAATAGTAAAAAATTATTATTGCAAAAACTTGCTTTATTTGTAACAATTTTTCAATTTA
GTTACTTAATTTATTTGTTTAATATTTTATACAAAGACAAAAAAAATTGTTACAAAAACTTTTAT
CATATTTGTAACGATAAAAAATTATTGTTGCAAAAACTTGTATTATTTGCAACAATTTTTCAATA
TCATTACTTAATTTATTTTTTAAAAATTTTATACAACAACAAAAAAGTTGT
Found at i:20056150 original size:145 final size:142
Alignment explanation
Indices: 20055985--20056444 Score: 466
Period size: 144 Copynumber: 3.2 Consensus size: 142
20055975 CTAAATCTTA
* * * *
20055985 TTCATGATTTTTGGTACATTTAAAATCACAGTAGTACCCTTGAGAAG-GTAAAATTATCAAAATA
1 TTCATGATTTTTGGTGCATTTAAAATCACAGCAGTACCC-AGA-AAGTGTGAAATTATCAAAATA
*
20056049 CTCTTCTAGAGGTATTTTTGTAATTTAGTTTTTTCGAGCTCAAATTTTAGTGAAACTTTTCAAAT
64 CTCTTATAGAGGTATTTTTGTAATTTAGTTTTTTC-AGCTCAAATTTTA-TGAAACTTTTCAAAT
*
20056114 TTTAATTTTATAATAT
127 CTTAATTTTATAATAT
* * * *
20056130 TTCATGATTTTTTGTGCATTTAAAATCACTGCAGTCCCCAAGAAAGTGTGAAATTATCAAAATAA
1 TTCATGATTTTTGGTGCATTTAAAATCACAGCAGTACCC-AGAAAGTGTGAAATTATCAAAATAC
* * * * * * *
20056195 T-TTTTAAAAGTTATTTTTGTAATTTAGCCTTTTTT-AGTTCAAAATTTTACGAAACTTTTTAGA
65 TCTTAT-AGAGGTATTTTTGTAATTTAG--TTTTTTCAGCTC-AAATTTTATGAAACTTTTCAAA
20056258 TCTTAATTTTATAATA-
126 TCTTAATTTTATAATAT
* * * *
20056274 TTCATGATTTTTAGTGCATTTAAAATCATAACAGTACCCAAAAAAGTGTGAAATTATCAAAATAC
1 TTCATGATTTTTGGTGCATTTAAAATCACAGCAGTACCC-AGAAAGTGTGAAATTATCAAAATAC
* * ** * * *
20056339 CCTTATAGGGGTATTTTCATAATTTA--TCTTTCAAAAGCTCGAATTTTCATGAAACTTTTCACA
65 TCTTATAGAGGTATTTTTGTAATTTAGTTTTTTC---AGCTCAAATTTT-ATGAAACTTTTCAAA
*
20056402 CCTTAATTTTATAATAT
126 TCTTAATTTTATAATAT
* *
20056419 TTAATGATTTTTGGTG-TTTTAAAATC
1 TTCATGATTTTTGGTGCATTTAAAATC
20056445 TCAAAAATGA
Statistics
Matches: 262, Mismatches: 41, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
140 4 0.02
143 6 0.02
144 119 0.45
145 119 0.45
146 8 0.03
147 6 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (142 bp):
TTCATGATTTTTGGTGCATTTAAAATCACAGCAGTACCCAGAAAGTGTGAAATTATCAAAATACT
CTTATAGAGGTATTTTTGTAATTTAGTTTTTTCAGCTCAAATTTTATGAAACTTTTCAAATCTTA
ATTTTATAATAT
Found at i:20056895 original size:13 final size:13
Alignment explanation
Indices: 20056861--20056895 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20056851 ATACACACAC
20056861 ACAAAAAAAA-AG
1 ACAAAAAAAATAG
20056873 -CAAAAAAAATAG
1 ACAAAAAAAATAG
20056885 ACAAAAAAAAT
1 ACAAAAAAAAT
20056896 CAAAGGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.80, C:0.09, G:0.06, T:0.06
Consensus pattern (13 bp):
ACAAAAAAAATAG
Found at i:20058044 original size:16 final size:17
Alignment explanation
Indices: 20058025--20058062 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
20058015 ATTATGTAGG
20058025 TTTTGAATGTATTAGCT
1 TTTTGAATGTATTAGCT
*
20058042 TTTGTGCATGTATTAGCT
1 TTT-TGAATGTATTAGCT
20058060 TTT
1 TTT
20058063 AAATTGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.55
Consensus pattern (17 bp):
TTTTGAATGTATTAGCT
Found at i:20060660 original size:25 final size:25
Alignment explanation
Indices: 20060613--20060660 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20060603 ATATTTTATG
* *
20060613 ATATATATTGTTATTTTTTAAAATA
1 ATATATATTGTTATTCTTAAAAATA
* *
20060638 ATATATTTTGTTCTTCTTAAAAA
1 ATATATATTGTTATTCTTAAAAA
20060661 ACAATTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
ATATATATTGTTATTCTTAAAAATA
Found at i:20064639 original size:13 final size:12
Alignment explanation
Indices: 20064604--20064663 Score: 66
Period size: 13 Copynumber: 4.7 Consensus size: 12
20064594 AAATTGTGTT
20064604 TTTACTTTTGTTTA
1 TTTA-TTTT-TTTA
*
20064618 TATATTTTTTTA
1 TTTATTTTTTTA
20064630 TTTATCTTTTTTA
1 TTTAT-TTTTTTA
*
20064643 TTTTATTTTGTTA
1 -TTTATTTTTTTA
20064656 TTTATTTT
1 TTTATTTT
20064664 ATCTTACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.39
13 17 0.41
14 8 0.20
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:20064674 original size:26 final size:27
Alignment explanation
Indices: 20064620--20064690 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
20064610 TTTGTTTATA
* *
20064620 TATTTTTTTATTTATCTTT-TTTATTT
1 TATTTTGTTATTTATCTTTATTTATCT
20064646 TATTTTGTTATTTAT-TTTATCTTA-CT
1 TATTTTGTTATTTATCTTTAT-TTATCT
*
20064672 TA-TTTGTTGTTTATCTTTA
1 TATTTTGTTATTTATCTTTA
20064691 ATTGTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 14 0.36
26 22 0.56
27 3 0.08
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (27 bp):
TATTTTGTTATTTATCTTTATTTATCT
Found at i:20065242 original size:25 final size:24
Alignment explanation
Indices: 20065187--20065247 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
20065177 TTTTCTCCAT
*
20065187 TTTATTTATTTATTTTTTTATGAG
1 TTTATTTATTTATTTTATTATGAG
*
20065211 TTCTATTTATTTAATTATTATTATTA-
1 TT-TATTTATTT-ATT-TTATTATGAG
20065237 TTTATTTATTT
1 TTTATTTATTT
20065248 GTGATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 2 0.06
25 18 0.56
26 5 0.16
27 7 0.22
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (24 bp):
TTTATTTATTTATTTTATTATGAG
Found at i:20070077 original size:2 final size:2
Alignment explanation
Indices: 20070072--20070105 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20070062 CTCTGCTCCC
20070072 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20070106 TTTATTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20071823 original size:24 final size:25
Alignment explanation
Indices: 20071787--20071843 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
20071777 TTATATAATG
* **
20071787 ATATATTATATTTAATATATTATTA
1 ATATATTAAATTTAATATAAAATTA
*
20071812 ATATA-TAAATTTTATATAAAATTA
1 ATATATTAAATTTAATATAAAATTA
*
20071836 ATAAATTA
1 ATATATTA
20071844 TACGATAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATATTAAATTTAATATAAAATTA
Found at i:20071874 original size:64 final size:65
Alignment explanation
Indices: 20071746--20071905 Score: 157
Period size: 64 Copynumber: 2.4 Consensus size: 65
20071736 GATGCACTCG
* * * *
20071746 TAATATA-AAAGTTTTATACAAGATTAATAAATTATATAATGATATATTATATTTAATATATTA-
1 TAATATATAAA-TTTTATACAAAATTAATAAATTATACAATAATATATCATA-TTAATATATTAT
20071809 T-
64 TA
* * *
20071810 TAATATATAAATTTTATATAAAATTAATAAATTATACGATAATATCTCATA-TAATATAATTTAT
1 TAATATATAAATTTTATACAAAATTAATAAATTATACAATAATATATCATATTAATAT-A-TTAT
20071874 TGA
64 T-A
* **
20071877 TAATATATAAAATTTATACATTATTAATA
1 TAATATATAAATTTTATACAAAATTAATA
20071906 TATCAAATAT
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
62 6 0.08
63 1 0.01
64 43 0.54
65 4 0.05
67 25 0.32
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (65 bp):
TAATATATAAATTTTATACAAAATTAATAAATTATACAATAATATATCATATTAATATATTATTA
Found at i:20076011 original size:19 final size:20
Alignment explanation
Indices: 20075983--20076025 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
20075973 ATTATTTAAA
20075983 ATTTATAAAATTAATAAATT
1 ATTTATAAAATTAATAAATT
**
20076003 ATTTA-AAAATTGTTAAATT
1 ATTTATAAAATTAATAAATT
20076022 ATTT
1 ATTT
20076026 TATATCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTATAAAATTAATAAATT
Found at i:20078973 original size:2 final size:2
Alignment explanation
Indices: 20078966--20079012 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
20078956 GATCATTCGT
* * * *
20078966 AC AC AC AC AT AC AC AC AC AT AC AC AC AC AT AC AC AC AC AT AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
20079008 AC AC A
1 AC AC A
20079013 TATATAAAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (2 bp):
AC
Found at i:20078980 original size:10 final size:10
Alignment explanation
Indices: 20078965--20079012 Score: 96
Period size: 10 Copynumber: 4.8 Consensus size: 10
20078955 TGATCATTCG
20078965 TACACACACA
1 TACACACACA
20078975 TACACACACA
1 TACACACACA
20078985 TACACACACA
1 TACACACACA
20078995 TACACACACA
1 TACACACACA
20079005 TACACACA
1 TACACACA
20079013 TATATAAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (10 bp):
TACACACACA
Found at i:20081351 original size:82 final size:82
Alignment explanation
Indices: 20081214--20081366 Score: 261
Period size: 82 Copynumber: 1.9 Consensus size: 82
20081204 AGGGCAATGG
* * *
20081214 TTAGTACACAAGTATCTATGTAGTAAGACATTTACATGATGAATACCACACTAAAAAATATGGCT
1 TTAGTACACAAGTATCTATGTAATAAGACATTTACATGATAAATACCACACTAAAAAATATAGCT
20081279 TTCGACCAATATGGGTT
66 TTCGACCAATATGGGTT
* *
20081296 TTAGTAGACAAGTATCTATGTAATAAGACATTTACATGATAAATACCACACTAAAAAATGTAGCT
1 TTAGTACACAAGTATCTATGTAATAAGACATTTACATGATAAATACCACACTAAAAAATATAGCT
20081361 TTCGAC
66 TTCGAC
20081367 TAAGATGGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (82 bp):
TTAGTACACAAGTATCTATGTAATAAGACATTTACATGATAAATACCACACTAAAAAATATAGCT
TTCGACCAATATGGGTT
Found at i:20093953 original size:123 final size:125
Alignment explanation
Indices: 20093816--20094069 Score: 431
Period size: 123 Copynumber: 2.0 Consensus size: 125
20093806 TGACGAGTTT
*
20093816 TAAACAATCCTTAAATGAGCTTATTCGTGAACATAAATAAATCAAATAGATTTTTGTTCATGTTT
1 TAAACAATCCTTAAATGAGCTTATTCGTGAACATAAATAAATCAAATAGATTTTTGTTCATATTT
* * *
20093881 GGTTCATTTAATAAACAAAGAT-AAAAAGTTGTTGAAGATTGTTTATTAAGTTTAAT-GA
66 GGTTCATTTAATAAACAAACATAAAAAAGTTGTCGAAGATTGTTTATTAAGTTTAATAAA
* *
20093939 TAAACAATCCTTAAATGAGTTTATTCGTGAACATAAATGAATCAAATAGATTTTTGTTCATATTT
1 TAAACAATCCTTAAATGAGCTTATTCGTGAACATAAATAAATCAAATAGATTTTTGTTCATATTT
*
20094004 GGTTCATTTAATAAACAAACATAAAAAAGTTGTCGAAGATTGTTTGTTAAGTTTAATAAA
66 GGTTCATTTAATAAACAAACATAAAAAAGTTGTCGAAGATTGTTTATTAAGTTTAATAAA
20094064 TAAACA
1 TAAACA
20094070 TAAATGAATA
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
123 83 0.68
124 32 0.26
125 7 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (125 bp):
TAAACAATCCTTAAATGAGCTTATTCGTGAACATAAATAAATCAAATAGATTTTTGTTCATATTT
GGTTCATTTAATAAACAAACATAAAAAAGTTGTCGAAGATTGTTTATTAAGTTTAATAAA
Found at i:20097040 original size:30 final size:30
Alignment explanation
Indices: 20097006--20097065 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
20096996 TTGCTTTAAA
*
20097006 TTGTTTTGATCTTTTTTTGTTTGTATGTGT
1 TTGTTTTGATCTTTTTTTATTTGTATGTGT
20097036 TTGTTTTGATCTTTTTTTATTTGTATGTGT
1 TTGTTTTGATCTTTTTTTATTTGTATGTGT
20097066 AGATCTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.70
Consensus pattern (30 bp):
TTGTTTTGATCTTTTTTTATTTGTATGTGT
Found at i:20102505 original size:17 final size:18
Alignment explanation
Indices: 20102480--20102513 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20102470 TGAAACAAGT
20102480 TCTTAAATATG-TTTTTC
1 TCTTAAATATGATTTTTC
*
20102497 TCTTGAATATGATTTTT
1 TCTTAAATATGATTTTT
20102514 ATGTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (18 bp):
TCTTAAATATGATTTTTC
Found at i:20102667 original size:50 final size:50
Alignment explanation
Indices: 20102600--20102699 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
20102590 GAAATTTAAA
20102600 GTAAGAGTATGACTTTAGAATTTACATACTTAACTTTTGAAGGAAATTTT
1 GTAAGAGTATGACTTTAGAATTTACATACTTAACTTTTGAAGGAAATTTT
20102650 GTAAGAGTATGACTTTAGAATTTACATACTTAACTTTTGAAGGAAATTTT
1 GTAAGAGTATGACTTTAGAATTTACATACTTAACTTTTGAAGGAAATTTT
20102700 AGACTGTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (50 bp):
GTAAGAGTATGACTTTAGAATTTACATACTTAACTTTTGAAGGAAATTTT
Found at i:20106795 original size:7 final size:7
Alignment explanation
Indices: 20106783--20106812 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
20106773 TGACTTTGTT
20106783 AAGAGAA
1 AAGAGAA
20106790 AAGAGAA
1 AAGAGAA
20106797 AAGAGAA
1 AAGAGAA
20106804 AAGAAGAA
1 AAG-AGAA
20106812 A
1 A
20106813 GGGTAATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAGAGAA
Found at i:20109921 original size:30 final size:31
Alignment explanation
Indices: 20109877--20109962 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 31
20109867 TAATTGAAAT
20109877 AAAAATATAAATTTAAAGATTTAATTTAAT-
1 AAAAATATAAATTTAAAGATTTAATTTAATC
*
20109907 GAAAAT-TAATATTTAAA-AGTTTAA-TTAATC
1 AAAAATATAA-ATTTAAAGA-TTTAATTTAATC
*
20109937 AAAAATAGAAAATTT-AAGATTTAATT
1 AAAAATA-TAAATTTAAAGATTTAATT
20109963 GATTAAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
29 9 0.20
30 29 0.63
31 6 0.13
32 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (31 bp):
AAAAATATAAATTTAAAGATTTAATTTAATC
Found at i:20111254 original size:27 final size:26
Alignment explanation
Indices: 20111191--20111257 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
20111181 ACTTGAACAT
*
20111191 AAAAATTAAAAAATAAAACTTATTTA
1 AAAAATTAAAATATAAAACTTATTTA
* *
20111217 AATACAA-TAAAATATAATGATTTATTTA
1 AA-A-AATTAAAATATAA-AACTTATTTA
20111245 AAAAATTAAAATA
1 AAAAATTAAAATA
20111258 ATTCAGGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 4 0.12
27 18 0.53
28 12 0.35
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (26 bp):
AAAAATTAAAATATAAAACTTATTTA
Found at i:20111903 original size:18 final size:18
Alignment explanation
Indices: 20111880--20111949 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
20111870 ATAATATTTC
20111880 TATTATTTTAATAATAAA
1 TATTATTTTAATAATAAA
*
20111898 TATTATTTTATACAATAATA
1 TATTATTTTA-ATAATAA-A
* *
20111918 TTACTATTTTAATAATAAC
1 -TATTATTTTAATAATAAA
*
20111937 TTTTAGTTTTAAT
1 TATTA-TTTTAAT
20111950 GTGAATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 13 0.31
19 13 0.31
20 7 0.17
21 9 0.21
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (18 bp):
TATTATTTTAATAATAAA
Found at i:20111905 original size:27 final size:28
Alignment explanation
Indices: 20111840--20111905 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
20111830 AATAGTATAT
*
20111840 AATATTATATTACTATTATTTTAATAGTA
1 AATATTAT-TTACTATTATTTTAATAATA
*
20111869 AATAATATTT-CTATTATTTTAATAATA
1 AATATTATTTACTATTATTTTAATAATA
20111896 AATATTATTT
1 AATATTATTT
20111906 TATACAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 25 0.74
28 2 0.06
29 7 0.21
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (28 bp):
AATATTATTTACTATTATTTTAATAATA
Found at i:20113872 original size:34 final size:34
Alignment explanation
Indices: 20113820--20113904 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
20113810 AAATTACTTC
* * * *
20113820 CGAAAATGTATTTATGGATAATTGCAATGCTTTT
1 CGAAAATGAATTTTTGGATAATTACAATGATTTT
* * *
20113854 TGAAAATGCATTTTTGGATAATTATAATGATTTT
1 CGAAAATGAATTTTTGGATAATTACAATGATTTT
20113888 CGAAAATGAATTTTTGG
1 CGAAAATGAATTTTTGG
20113905 TATAGTTAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (34 bp):
CGAAAATGAATTTTTGGATAATTACAATGATTTT
Found at i:20113922 original size:34 final size:34
Alignment explanation
Indices: 20113820--20113937 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 34
20113810 AAATTACTTC
* * ** * *
20113820 CGAAAATGTATTTATGGATAATTGCAATGCTTTT
1 CGAAAATGCATTTTTGGATAATTATAAAGATTTT
* *
20113854 TGAAAATGCATTTTTGGATAATTATAATGATTTT
1 CGAAAATGCATTTTTGGATAATTATAAAGATTTT
* *
20113888 CGAAAATGAATTTTTGGTATAGTTA-AGAAG-TTTT
1 CGAAAATGCATTTTTGG-ATAATTATA-AAGATTTT
*
20113922 CCAAAATGCATTTTTG
1 CGAAAATGCATTTTTG
20113938 ATACACTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 62 0.89
35 8 0.11
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (34 bp):
CGAAAATGCATTTTTGGATAATTATAAAGATTTT
Found at i:20115634 original size:8 final size:8
Alignment explanation
Indices: 20115617--20115661 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
20115607 ATATTTTTCT
*
20115617 AATAAATA
1 AATAAGTA
20115625 AATAAGTA
1 AATAAGTA
20115633 AATAAGTA
1 AATAAGTA
20115641 AATAA-TA
1 AATAAGTA
* *
20115648 AAAAATTA
1 AATAAGTA
20115656 AATAAG
1 AATAAG
20115662 AAAACAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (8 bp):
AATAAGTA
Found at i:20115657 original size:15 final size:15
Alignment explanation
Indices: 20115623--20115665 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
20115613 TTCTAATAAA
*
20115623 TAAATAAGTAAATAAG
1 TAAATAA-TAAAAAAG
*
20115639 TAAATAATAAAAAAT
1 TAAATAATAAAAAAG
*
20115654 TAAATAAGAAAA
1 TAAATAATAAAA
20115666 CAAAATAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (15 bp):
TAAATAATAAAAAAG
Found at i:20115683 original size:13 final size:13
Alignment explanation
Indices: 20115640--20115683 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
20115630 GTAAATAAGT
*
20115640 AAATAATAAAAAA
1 AAATAAGAAAAAA
*
20115653 TTAAATAAGAAAACA
1 --AAATAAGAAAAAA
20115668 AAATAAGAAAAAA
1 AAATAAGAAAAAA
20115681 AAA
1 AAA
20115684 AAAAAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (13 bp):
AAATAAGAAAAAA
Found at i:20121823 original size:23 final size:22
Alignment explanation
Indices: 20121779--20121832 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
20121769 AAGGCTTACT
*
20121779 AATATAAAGTATATATAAAATAA
1 AATAT-AATTATATATAAAATAA
*
20121802 CAA-ATAATTATATAATATAATAA
1 -AATATAATTATAT-ATAAAATAA
20121825 AATATAAT
1 AATATAAT
20121833 CGGGTCAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.35
23 15 0.58
24 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATAATTATATATAAAATAA
Found at i:20123306 original size:17 final size:16
Alignment explanation
Indices: 20123237--20123304 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 16
20123227 TTGATATCAT
**
20123237 ATAAAATTTTAATTTA
1 ATAAAATTTTAATAAA
20123253 A-AAAA-TTTAA-AAA
1 ATAAAATTTTAATAAA
**
20123266 ATTAATTTTTTAATAAA
1 A-TAAAATTTTAATAAA
*
20123283 ATAAAATTTTAATTAA
1 ATAAAATTTTAATAAA
20123299 ATAAAA
1 ATAAAA
20123305 ATAAATACTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 6 0.15
16 24 0.59
17 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAAATTTTAATAAA
Found at i:20123755 original size:2 final size:2
Alignment explanation
Indices: 20123743--20123780 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
20123733 TAACCACACT
*
20123743 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20123781 ATTTTTAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20128289 original size:21 final size:21
Alignment explanation
Indices: 20128263--20128313 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20128253 ATAATTGTAG
* *
20128263 TGAGATTAGTTATTGTAATAA
1 TGAGATTAATTATTATAATAA
**
20128284 TGAGATTAATTATTATAATGG
1 TGAGATTAATTATTATAATAA
20128305 TGAGATTAA
1 TGAGATTAA
20128314 AATAAATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (21 bp):
TGAGATTAATTATTATAATAA
Found at i:20128518 original size:18 final size:20
Alignment explanation
Indices: 20128476--20128531 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
20128466 AATTTAATAA
*
20128476 AATTATTTTTATATAATTATAT
1 AATTA-TTTTAT-TTATTATAT
*
20128498 -ATAATTTTTATTTATTATAT
1 AATTA-TTTTATTTATTATAT
20128518 AATTATTTTATTTA
1 AATTATTTTATTTA
20128532 ATAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTATTTTATTTATTATAT
Found at i:20128525 original size:21 final size:20
Alignment explanation
Indices: 20128467--20128533 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
20128457 AATAATTGAA
*
20128467 ATTTAA-TAAAATTATTTTT
1 ATTTAATTATAATTATTTTT
* *
20128486 ATATAATTATATATAATTTTT
1 ATTTAATTATA-ATTATTTTT
*
20128507 ATTTATTATATAATTA-TTTT
1 ATTTAAT-TATAATTATTTTT
20128527 ATTTAAT
1 ATTTAAT
20128534 AAATAAGTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.13
20 13 0.34
21 16 0.42
22 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAATTATAATTATTTTT
Found at i:20129565 original size:16 final size:17
Alignment explanation
Indices: 20129546--20129578 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20129536 ATTAATCGAT
20129546 AAAATTAATA-ATTTTG
1 AAAATTAATATATTTTG
*
20129562 AAAATTTATATATTTTG
1 AAAATTAATATATTTTG
20129579 TTAGTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AAAATTAATATATTTTG
Found at i:20134727 original size:10 final size:10
Alignment explanation
Indices: 20134714--20134743 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20134704 ATCGAGTTTT
20134714 TATATTTTAA
1 TATATTTTAA
20134724 TATATTTTAA
1 TATATTTTAA
20134734 T-TATTTTAA
1 TATATTTTAA
20134743 T
1 T
20134744 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:20137587 original size:28 final size:25
Alignment explanation
Indices: 20137541--20137599 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
20137531 TTTTTAAAAA
*
20137541 TTTTTTTTTATTGATTTTTTTGGTTTT
1 TTTTTTTTTATTGA--ATTTTGGTTTT
*
20137568 TTATTTTTTTCTTGAATTTTGGTTTT
1 TT-TTTTTTTATTGAATTTTGGTTTT
20137594 TTTTTT
1 TTTTTT
20137600 CTATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 4 0.14
26 12 0.41
27 2 0.07
28 11 0.38
ACGTcount: A:0.08, C:0.02, G:0.10, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTATTGAATTTTGGTTTT
Found at i:20138039 original size:22 final size:22
Alignment explanation
Indices: 20138014--20138056 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20138004 AAGGTTTGAC
*
20138014 AGATTATGCTTGGAGGTCTTAG
1 AGATTATGCGTGGAGGTCTTAG
20138036 AGATTATGCGTGGAGGTCTTA
1 AGATTATGCGTGGAGGTCTTA
20138057 CAAACCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.33, T:0.35
Consensus pattern (22 bp):
AGATTATGCGTGGAGGTCTTAG
Found at i:20138145 original size:126 final size:125
Alignment explanation
Indices: 20137905--20138134 Score: 336
Period size: 126 Copynumber: 1.8 Consensus size: 125
20137895 TGTCTGAAGC
* * * * *
20137905 TCTTAGAGATTATGTTGGAGGTCTTACAAATCTTAATATCTTTGAATGCTCTTTATATCATAGGC
1 TCTTAGAGATTATGGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCATATCATAGGC
* * ** *
20137970 ATTGAAACTTTGAAATTTTAAAATGTTTTGCCTGAAGGTTTGACAGATTATGCTTGGAGG
66 ATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGTTTGACAGATTATGCTTGGAGG
*
20138030 TCTTAGAGATTATGCGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCGTATCAGT-G
1 TCTTAGAGATTATG-GTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCATATCA-TAG
20138094 GCATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGT
64 GCATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGT
20138135 CTTAGAGATT
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
125 14 0.15
126 77 0.84
127 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (125 bp):
TCTTAGAGATTATGGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCATATCATAGGC
ATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGTTTGACAGATTATGCTTGGAGG
Found at i:20138159 original size:126 final size:125
Alignment explanation
Indices: 20137900--20138165 Score: 329
Period size: 126 Copynumber: 2.1 Consensus size: 125
20137890 GATTATGTCT
* * * * *
20137900 GAAGCTCTTAGAGATTATGTTGGAGGTCTTACAAATCTTAATATCTTTGAATGCTCTTTATATCA
1 GAAG-TCTTAGAGATTATGGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCATATCA
* * ** * * * *
20137965 TAGGCATTGAAACTTTGAAATTTTAAAATGTTTTGCCTGAAGGTTTGACAGATTATGCTTG
65 TAGGCATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGTTTGACAGATTAGGCCTA
* *
20138026 GAGGTCTTAGAGATTATGCGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCGTATCA
1 GAAGTCTTAGAGATTATG-GTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCATATCA
*
20138091 GT-GGCATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGTCTT-AGAGATTAGGCCTA
65 -TAGGCATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGT-TTGACAGATTAGGCCTA
*
20138152 GAAGTCTTATAGAT
1 GAAGTCTTAGAGAT
20138166 CTCAACATCT
Statistics
Matches: 119, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
125 14 0.12
126 102 0.86
127 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (125 bp):
GAAGTCTTAGAGATTATGGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCATATCAT
AGGCATTAAAACTTTGAAAATTTAAAAAATTTTACCTGAAGGTTTGACAGATTAGGCCTA
Found at i:20138208 original size:104 final size:104
Alignment explanation
Indices: 20138027--20138251 Score: 299
Period size: 104 Copynumber: 2.2 Consensus size: 104
20138017 TTATGCTTGG
* * * * *
20138027 AGGTCTTAGAGATTATGCGTGGAGGTCTTACAAACCTTAACATCTTTGAATGCTCCTCGTATCAG
1 AGGTCTTAGAGATTAGGCCTAGAAGTCTTACAAACCTCAACATCTTTGAATGCTCCTCGTATCAG
* *
20138092 TGGCATTAAAACTTTGAAAA-TTTAAAAAATTTTACCTGA
66 AGGCATTAAAACTTT-AAAATTTTAAAAAATTTTACCCGA
* * * *
20138131 AGGTCTTAGAGATTAGGCCTAGAAGTCTTATAGATCTCAACATCTTTGAATGCTCTTCGTATCAG
1 AGGTCTTAGAGATTAGGCCTAGAAGTCTTACAAACCTCAACATCTTTGAATGCTCCTCGTATCAG
* **
20138196 AGGCATTGAAACTTTAAAATTTTAAAATGTTTTACCCGA
66 AGGCATTAAAACTTTAAAATTTTAAAAAATTTTACCCGA
*
20138235 AAGTCTTAGAGATTAGG
1 AGGTCTTAGAGATTAGG
20138252 GTGCTAACTT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 4 0.04
104 101 0.96
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (104 bp):
AGGTCTTAGAGATTAGGCCTAGAAGTCTTACAAACCTCAACATCTTTGAATGCTCCTCGTATCAG
AGGCATTAAAACTTTAAAATTTTAAAAAATTTTACCCGA
Found at i:20138336 original size:32 final size:32
Alignment explanation
Indices: 20138262--20138338 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
20138252 GTGCTAACTT
* * *
20138262 GACTGGGCTTAGTTTGATATGGGTGCCAATTA
1 GACTGGGCTTAATTTGATATAGGTGCCAAGTA
* * * *
20138294 AACTGAGCTTAATTTGATTTAGGTGCCAGGTA
1 GACTGGGCTTAATTTGATATAGGTGCCAAGTA
20138326 GACTGGGCTTAAT
1 GACTGGGCTTAAT
20138339 GTGCCAACTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.34
Consensus pattern (32 bp):
GACTGGGCTTAATTTGATATAGGTGCCAAGTA
Found at i:20138383 original size:23 final size:23
Alignment explanation
Indices: 20138333--20138384 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
20138323 GTAGACTGGG
* * *
20138333 CTTAATGTGCCAACTAAACTAGG
1 CTTAAAGTACCAACTAAACTAGA
*
20138356 TTTAAAGTACCAACTAAACTAGA
1 CTTAAAGTACCAACTAAACTAGA
20138379 CTTAAA
1 CTTAAA
20138385 ATCTCAATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (23 bp):
CTTAAAGTACCAACTAAACTAGA
Found at i:20138957 original size:32 final size:31
Alignment explanation
Indices: 20138860--20138959 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 31
20138850 ATACAACTGC
* *
20138860 GAATGTCTTTTCCATTATGTAGATACAAATGT
1 GAATGTCTTTT-CATGATGTAGATGCAAATGT
* * * * *
20138892 AAATGTTTTTCTCATGATGCATATGCAAGTGT
1 GAATGTCTTT-TCATGATGTAGATGCAAATGT
20138924 GAATGTCCTTTTCATGATGTAGATGCAAATGT
1 GAATGT-CTTTTCATGATGTAGATGCAAATGT
20138956 GAAT
1 GAAT
20138960 ACAAGTGATA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
32 50 0.93
33 4 0.07
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (31 bp):
GAATGTCTTTTCATGATGTAGATGCAAATGT
Found at i:20140271 original size:146 final size:147
Alignment explanation
Indices: 20139989--20140272 Score: 310
Period size: 146 Copynumber: 1.9 Consensus size: 147
20139979 AATTCCATCT
* *
20139989 TTTTTTTTTCAAGATTCTAACTAAAGCTTTATTCATTTTTTTACCCCAAATTCTCATCTCCGACG
1 TTTTTTTTT-AAGATTCTAACTAAAGCTTTATTCATTTTTTTACCACAAATCCTCATCTCCGACG
* * * **
20140054 TGCATGTCTTTCTTTTTTTTATTTTCTTCTTTTTTGGAAACATCTGACTTTAACTTCAGTAATTT
65 TGCATATCTTTCTTTTTTTTATTTTCTTCTTTTTTGGAAACATCTGACTTCAACTTCAGCAAACT
20140119 ACTTTCTTATATTTTATC
130 ACTTTCTTATATTTTATC
*** * *
20140137 TTTTTTTTT-AGATTCTAA-TAAAAGCTTTATTCATTTTTTTTACCATGGATCCTCATCTCTGAG
1 TTTTTTTTTAAGATTCTAACT-AAAGCTTTATTCA-TTTTTTTACCACAAATCCTCATCTCCGAC
* * * * *
20140200 GTGCATATCTTTCTTTATTTTT-TTATT-TT-TTTATTT-TAGACATTTGACTTCACCTTTAGCA
64 GTGCATATCTTTCTTT-TTTTTATT-TTCTTCTTT-TTTGGAAACATCTGACTTCAACTTCAGCA
*
20140261 AACTATTTTCTT
126 AACTACTTTCTT
20140273 GAGTTCTTGG
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
145 1 0.01
146 52 0.46
147 44 0.39
148 16 0.14
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (147 bp):
TTTTTTTTTAAGATTCTAACTAAAGCTTTATTCATTTTTTTACCACAAATCCTCATCTCCGACGT
GCATATCTTTCTTTTTTTTATTTTCTTCTTTTTTGGAAACATCTGACTTCAACTTCAGCAAACTA
CTTTCTTATATTTTATC
Found at i:20143949 original size:154 final size:152
Alignment explanation
Indices: 20143721--20144267 Score: 679
Period size: 154 Copynumber: 3.6 Consensus size: 152
20143711 GGAAAAATGA
** *
20143721 TTTTTAATTTTAGGATATTTTTAATTTTTATTATTTACATTTT-AAT-TTGTTTGATTAAAGGGT
1 TTTTTAATTTTAGGATATTTTTAATTTTTATTATTTATGTTTTAAATATTTTTTGATTAAAGGGT
* * *
20143784 AAAATGGTTATTATATAATATGAAAGGGATAAAATAATCATTGTTTAATATTGGATACATGTCAA
66 AAAATGGTCATTATATAATATGAAAGGAATAAAATAATCATTGTTTAATATTGGAAACATGTCAA
*
20143849 CAAATAAACCGCTTAAGGGATAG
131 CAAATAAACTG-TTAAGGGATAG
* * *
20143872 TTTTTAATTTTATGAATTTTTTTAATTGTTATTATTTATGTTTTAAATATTTTTTGATTAAAGGG
1 TTTTTAATTTTA-GGATATTTTTAATTTTTATTATTTATGTTTTAAATATTTTTTGATTAAAGGG
* * * *
20143937 TAAAATAGTTATTATATAATATGAAAGGAATAAAATAATCATTGTTTAATATT-GAACATATGAC
65 TAAAATGGTCATTATATAATATGAAAGGAATAAAATAATCATTGTTTAATATTGGAA-ACATGTC
20144001 AACAAATAAACTGTTTAAGGGATAG
129 AACAAATAAACTG-TTAAGGGATAG
* * * *
20144026 TTTTTAATTTTAGGATATTTTTAAATTTTATTAGTTATGTTTTGAATTATTTTTTTGATTAAGGG
1 TTTTTAATTTTAGGATATTTTTAATTTTTATTATTTATGTTTT-AAATA-TTTTTTGATTAAAGG
* * * ** * *
20144091 GTAAAATGGACATTATATAATATGAAA-AAAGTCAAATAGCCATTGTTTAATGTTAGAAACATGT
64 GTAAAATGGTCATTATATAATATGAAAGGAA-TAAAATAATCATTGTTTAATATTGGAAACATGT
** * *
20144155 CTGCAAATAAATTGTTGAGGGATAG
128 CAACAAATAAACTGTTAAGGGATAG
* * **
20144180 TTTTTAATTTTAGGATATTTATAATTTTTATTAATTATGTTTTAAATTATTTTTTGATTAAAAAG
1 TTTTTAATTTTAGGATATTTTTAATTTTTATTATTTATGTTTTAAA-TATTTTTTGATTAAAGGG
* *
20144245 TTAAATGATCATTATATAATATG
65 TAAAATGGTCATTATATAATATG
20144268 GCAAGGGTAG
Statistics
Matches: 343, Mismatches: 44, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
151 12 0.03
152 26 0.08
153 66 0.19
154 164 0.48
155 72 0.21
156 3 0.01
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (152 bp):
TTTTTAATTTTAGGATATTTTTAATTTTTATTATTTATGTTTTAAATATTTTTTGATTAAAGGGT
AAAATGGTCATTATATAATATGAAAGGAATAAAATAATCATTGTTTAATATTGGAAACATGTCAA
CAAATAAACTGTTAAGGGATAG
Found at i:20144048 original size:17 final size:19
Alignment explanation
Indices: 20144020--20144055 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20144010 ACTGTTTAAG
20144020 GGATAGTTTTT-AATTTTA
1 GGATAGTTTTTAAATTTTA
20144038 GGATA-TTTTTAAATTTTA
1 GGATAGTTTTTAAATTTTA
20144056 TTAGTTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (19 bp):
GGATAGTTTTTAAATTTTA
Found at i:20144209 original size:18 final size:18
Alignment explanation
Indices: 20144174--20144207 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20144164 AATTGTTGAG
*
20144174 GGATAGTTTTTAATTTTA
1 GGATAGTTTATAATTTTA
20144192 GGATA-TTTATAATTTT
1 GGATAGTTTATAATTTT
20144208 TATTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (18 bp):
GGATAGTTTATAATTTTA
Found at i:20144492 original size:2 final size:2
Alignment explanation
Indices: 20144470--20144511 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
20144460 ATTGCTTTCA
*
20144470 AT AT AT A- AT AT AG AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
20144512 TAATTGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20158153 original size:2 final size:2
Alignment explanation
Indices: 20158146--20158197 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
20158136 TGATCTCACC
* * *
20158146 CT CT CT CT CT CT TT CT TT CT CT CT CT CT CT CT CA CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20158188 CT CT CT CT CT
1 CT CT CT CT CT
20158198 ATATATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:20160537 original size:2 final size:2
Alignment explanation
Indices: 20160532--20160561 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20160522 AAAGAGGTTC
20160532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20160562 GATTTCAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20162467 original size:15 final size:15
Alignment explanation
Indices: 20162437--20162484 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
20162427 AGAAAAATTA
*
20162437 TATTGTTTTACATTTT
1 TATTGTATT-CATTTT
*
20162453 TATTGTGTTCATTTTT
1 TATTGTATTCA-TTTT
*
20162469 TATTGAATTCATTTT
1 TATTGTATTCATTTT
20162484 T
1 T
20162485 TTATTATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (15 bp):
TATTGTATTCATTTT
Found at i:20162495 original size:18 final size:16
Alignment explanation
Indices: 20162449--20162485 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
20162439 TTGTTTTACA
**
20162449 TTTTTATTGTGTTCAT
1 TTTTTATTGAATTCAT
20162465 TTTTTATTGAATTCAT
1 TTTTTATTGAATTCAT
20162481 TTTTT
1 TTTTT
20162486 TATTATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.70
Consensus pattern (16 bp):
TTTTTATTGAATTCAT
Found at i:20164469 original size:3 final size:3
Alignment explanation
Indices: 20164457--20164511 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
20164447 GAGCTATAAA
20164457 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20164504 ATT ATT AT
1 ATT ATT AT
20164512 ATACCTATAC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20164964 original size:11 final size:11
Alignment explanation
Indices: 20164948--20164980 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
20164938 TATTATCAAT
20164948 CTAAAATATTA
1 CTAAAATATTA
20164959 CTAAAATATTA
1 CTAAAATATTA
*
20164970 CTAGAATATTA
1 CTAAAATATTA
20164981 TTAACACCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (11 bp):
CTAAAATATTA
Found at i:20171349 original size:63 final size:63
Alignment explanation
Indices: 20171282--20171457 Score: 171
Period size: 63 Copynumber: 2.8 Consensus size: 63
20171272 TATAACATTC
* * *
20171282 CAATATATTAATAAGGTTTATTTTTATTTTTCAAAAATTAATTTTTTTAAATTTCAAAACC-CT
1 CAATATATTGATAAGGTTTTTTTTTATTTTTCAAAAATT-ATTTTTTTAAATTACAAAACCTCT
* ** * * * * *
20171345 CAATATGTTGGCAATGTTTTGTTTTTTATTTTTCAAAAA-T-TGTTTTAAAATTACCAAACCTTT
1 CAATATATTGATAA-GGTTT-TTTTTTATTTTTCAAAAATTATTTTTTTAAATTACAAAACCTCT
* *
20171408 TAATATATTGATAAAGTTTTTTTTTA-TTTTCAAAAATTATTTTTCTTAAA
1 CAATATATTGATAAGGTTTTTTTTTATTTTTCAAAAATTATTTTT-TTAAA
20171458 ACTATTTTTG
Statistics
Matches: 88, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
60 10 0.11
61 8 0.09
62 23 0.26
63 25 0.28
64 5 0.06
65 17 0.19
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.51
Consensus pattern (63 bp):
CAATATATTGATAAGGTTTTTTTTTATTTTTCAAAAATTATTTTTTTAAATTACAAAACCTCT
Found at i:20172202 original size:11 final size:10
Alignment explanation
Indices: 20172153--20172254 Score: 61
Period size: 11 Copynumber: 9.8 Consensus size: 10
20172143 AAAATAATAA
20172153 AAATAAAGAT
1 AAATAAAGAT
*
20172163 AAAGATAA-AT
1 AAATA-AAGAT
20172173 AAAATAAA-AGT
1 -AAATAAAGA-T
20172184 AAAGTAAAGAT
1 AAA-TAAAGAT
20172195 AACATAAAGAT
1 AA-ATAAAGAT
20172206 -AAT-AA-AT
1 AAATAAAGAT
*
20172213 AAATAAATAAT
1 AAATAAA-GAT
20172224 AAAAATAAAGAT
1 --AAATAAAGAT
20172236 AACATAAAGAT
1 AA-ATAAAGAT
*
20172247 ATATAAAG
1 AAATAAAG
20172255 TAGGAAAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
7 2 0.03
8 5 0.07
9 4 0.05
10 21 0.28
11 32 0.43
12 4 0.05
13 7 0.09
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.21
Consensus pattern (10 bp):
AAATAAAGAT
Found at i:20172210 original size:52 final size:43
Alignment explanation
Indices: 20172161--20172254 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 43
20172151 AAAAATAAAG
20172161 ATAAAGATAAATAAAATAA-AAGTAAAGTAAAGATAACATAAAGATA
1 ATAAAGATAAAT-AAATAATAA--AAA-TAAAGATAACATAAAGATA
20172207 AT-AA-ATAAATAAATAATAAAAATAAAGATAACATAAAGATA
1 ATAAAGATAAATAAATAATAAAAATAAAGATAACATAAAGATA
20172248 TATAAAG
1 -ATAAAG
20172255 TAGGAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
41 19 0.43
42 5 0.11
43 8 0.18
44 8 0.18
45 2 0.05
46 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.21
Consensus pattern (43 bp):
ATAAAGATAAATAAATAATAAAAATAAAGATAACATAAAGATA
Found at i:20173610 original size:12 final size:11
Alignment explanation
Indices: 20173581--20173627 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
20173571 AATTTTTATT
20173581 TTTAT-ATATTA
1 TTTATAATA-TA
20173592 TTT-TAATATGA
1 TTTATAATAT-A
20173603 TTTATAATATA
1 TTTATAATATA
20173614 TTTA-AATATA
1 TTTATAATATA
20173624 TTTA
1 TTTA
20173628 GGTATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
10 12 0.36
11 15 0.45
12 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTATAATATA
Found at i:20174024 original size:26 final size:25
Alignment explanation
Indices: 20173994--20174051 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
20173984 GGGAAAAACC
* *
20173994 AAAAAATAAGAAAGGAAGAAAAAAGAG
1 AAAAAGTAACAAA-GAA-AAAAAAGAG
*
20174021 AAAAATGTTACAAAGAAAAAAAAGAG
1 AAAAA-GTAACAAAGAAAAAAAAGAG
20174047 AAAAA
1 AAAAA
20174052 CAGTTATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.52
27 8 0.30
28 5 0.19
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (25 bp):
AAAAAGTAACAAAGAAAAAAAAGAG
Found at i:20176881 original size:1 final size:1
Alignment explanation
Indices: 20176875--20176899 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20176865 ATTATGTTTG
20176875 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
20176900 AAAATCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20182291 original size:2 final size:2
Alignment explanation
Indices: 20182276--20182315 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
20182266 TGGTATGTGA
*
20182276 AT AT AT A- AT TT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20182316 CTACAAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20182573 original size:33 final size:33
Alignment explanation
Indices: 20182523--20182588 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
20182513 TTTTGCCATG
* *
20182523 ATAGCCTAATCATTTCATATCAGTTATAATTAC
1 ATAGCCTAATCACTTCATAGCAGTTATAATTAC
*
20182556 ATAGCCTTATCACTTCATAGCAGTTATAATTAC
1 ATAGCCTAATCACTTCATAGCAGTTATAATTAC
20182589 TTAGGCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.38
Consensus pattern (33 bp):
ATAGCCTAATCACTTCATAGCAGTTATAATTAC
Done.