Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 26 of 127
Found at i:5695353 original size:77 final size:76
Alignment explanation
Indices: 5695138--5695682 Score: 463
Period size: 77 Copynumber: 7.1 Consensus size: 76
5695128 TCATGAAAAT
* * *
5695138 TTTAAATTTAAAAGACTCCTCTCACCAGAGGTAATGAACTTTAAATTCAAAAGGCTTCTTTAACC
1 TTTAAATTTAAAAG-CTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAAA-GCTTCTCTAACC
5695203 AAAGGCAACAAAC
64 AAAGGCAACAAAC
* * * * * * *
5695216 CTTAAATGTTGAAAGCTCTTTTCACCAGAGACAACGAACTTTAAATTCAAAAGCTCCTCTCACCA
1 TTTAAAT-TTAAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAAAGCTTCTCTAACCA
* *
5695281 GAGGTAACAAAC
65 AAGGCAACAAAC
* * * * ** * * **
5695293 TTTAAATTTAAAAGCTCCTTTAACCAAAGGCAACAAACTTTAAATGTTGAAAGTTTCTCTCATTA
1 TTTAAATTTAAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAAT-TCAAAAGCTTCTCTAACCA
* * *
5695358 GAGGTAACGAAC
65 AAGGCAACAAAC
* * * * * * ** * *
5695370 TTTAAATTCAAAAGCTCCTTTAACCAAAGGCAACAAAATTTAAATATTGAAAGCTCCTCTGACCA
1 TTTAAATTTAAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAAT-TCAAAAGCTTCTCTAACCA
* **
5695435 GAGGCAATGAAC
65 AAGGCAACAAAC
* * * * *
5695447 TTTAAATTCAAAAGCTCCTATCACCAGAGGTAACGAACTTTAAATTCAAAAGC-TCTTTTAACTA
1 TTTAAATTTAAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAAAGCTTC-TCTAACCA
5695511 AAGGCAACAAAC
65 AAGGCAACAAAC
* * * * *
5695523 TTTAAATGTTGAAAAGCTCCTCTGACCAAAGGCAACGAACTTTAAATCCAAAAGGCTACTTTAAC
1 TTTAAAT-TT-AAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAAA-GCTTCTCTAAC
5695588 CAAAGGCAACAAAC
63 CAAAGGCAACAAAC
* * * * * *
5695602 TTTAAATGTTGAAAGGCTCCTCTCACCAGAGGTAACAAACTTTAAA-T----GGCTTTTTTAACC
1 TTTAAAT-TT-AAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAAAGCTTCTCTAACC
5695662 AAAGGCAACAAAC
64 AAAGGCAACAAAC
5695675 TTTAAATT
1 TTTAAATT
5695683 AAAGATCTAA
Statistics
Matches: 392, Mismatches: 68, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
72 1 0.00
73 30 0.08
75 1 0.00
76 59 0.15
77 157 0.40
78 75 0.19
79 68 0.17
80 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (76 bp):
TTTAAATTTAAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAAAGCTTCTCTAACCAA
AGGCAACAAAC
Found at i:5695473 original size:192 final size:194
Alignment explanation
Indices: 5695138--5695648 Score: 742
Period size: 192 Copynumber: 2.6 Consensus size: 194
5695128 TCATGAAAAT
* *
5695138 TTTAAAT-TT-AAAAGACTCCTCTCACCAGAGGTAATGAACTTTAAATTCAAAAGGCTTCTTTAA
1 TTTAAATGTTGAAAAG-CTCCTCTCACCAGAGGTAACGAACTTTAAATTCAAAAGGCTACTTTAA
* * * *
5695201 CCAAAGGCAACAAACCTTAAATGTTGAAAGCTCTTTTCACCAGAGACAACGAACTTTAAATTCAA
65 CCAAAGGCAACAAACTTTAAATGTTGAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAA
* *
5695266 AAGCTCCTCTCACCAGAGGTAACAAACTTTAAATTTAAAAGCTCCTTTAACCAAAGGCAACAAAC
130 AAGCTCCTATCACCAGAGGTAACAAACTTTAAATTCAAAAGCTCCTTTAACCAAAGGCAACAAAC
* * ** *
5695331 TTTAAATGTTG-AAAGTTTCTCTCATTAGAGGTAACGAACTTTAAATTCAAAA-GCTCCTTTAAC
1 TTTAAATGTTGAAAAGCTCCTCTCACCAGAGGTAACGAACTTTAAATTCAAAAGGCTACTTTAAC
* * * *
5695394 CAAAGGCAACAAAATTTAAATATTGAAAGCTCCTCTGACCAGAGGCAATGAACTTTAAATTCAAA
66 CAAAGGCAACAAACTTTAAATGTTGAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAA
* * *
5695459 AGCTCCTATCACCAGAGGTAACGAACTTTAAATTCAAAAGCTCTTTTAACTAAAGGCAACAAAC
131 AGCTCCTATCACCAGAGGTAACAAACTTTAAATTCAAAAGCTCCTTTAACCAAAGGCAACAAAC
* * * *
5695523 TTTAAATGTTGAAAAGCTCCTCTGACCAAAGGCAACGAACTTTAAATCCAAAAGGCTACTTTAAC
1 TTTAAATGTTGAAAAGCTCCTCTCACCAGAGGTAACGAACTTTAAATTCAAAAGGCTACTTTAAC
* *
5695588 CAAAGGCAACAAACTTTAAATGTTGAAAGGCTCCTCTCACCAGAGGTAACAAACTTTAAAT
66 CAAAGGCAACAAACTTTAAATGTTGAAA-GCTCCTCTCACCAGAGGCAACGAACTTTAAAT
5695649 GGCTTTTTTA
Statistics
Matches: 279, Mismatches: 34, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
192 137 0.49
193 72 0.26
194 42 0.15
195 28 0.10
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (194 bp):
TTTAAATGTTGAAAAGCTCCTCTCACCAGAGGTAACGAACTTTAAATTCAAAAGGCTACTTTAAC
CAAAGGCAACAAACTTTAAATGTTGAAAGCTCCTCTCACCAGAGGCAACGAACTTTAAATTCAAA
AGCTCCTATCACCAGAGGTAACAAACTTTAAATTCAAAAGCTCCTTTAACCAAAGGCAACAAAC
Found at i:5695835 original size:39 final size:39
Alignment explanation
Indices: 5695770--5695898 Score: 136
Period size: 39 Copynumber: 3.3 Consensus size: 39
5695760 GAGACTCTTG
*
5695770 AAATT-AAAAAGCTCATTTGA-TCAGAGGCAACGAACTTT
1 AAATTCAAAAAGCTCCTTTGACT-AGAGGCAACGAACTTT
* * **
5695808 AAATTCAAAAGGCTCCTTTGACTAGAGGTAATAAACTTT
1 AAATTCAAAAAGCTCCTTTGACTAGAGGCAACGAACTTT
* * * *
5695847 AAATGTTAAAAATTCTCCTTTGACCAGAGACAACGAACTTT
1 AAAT-TCAAAAA-GCTCCTTTGACTAGAGGCAACGAACTTT
5695888 AAATTCAAAAA
1 AAATTCAAAAA
5695899 TCTGAGAGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
38 5 0.07
39 30 0.41
40 12 0.16
41 26 0.36
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (39 bp):
AAATTCAAAAAGCTCCTTTGACTAGAGGCAACGAACTTT
Found at i:5695886 original size:41 final size:40
Alignment explanation
Indices: 5695773--5695899 Score: 132
Period size: 41 Copynumber: 3.2 Consensus size: 40
5695763 ACTCTTGAAA
* *
5695773 TTAAAAA-GCTCATTTGATCAGAGGCAACGAACTTTAAA-
1 TTAAAAATGCTCCTTTGACCAGAGGCAACGAACTTTAAAT
* * * * **
5695811 TTCAAAAGGCTCCTTTGACTAGAGGTAATAAACTTTAAAT
1 TTAAAAATGCTCCTTTGACCAGAGGCAACGAACTTTAAAT
* *
5695851 GTTAAAAATTCTCCTTTGACCAGAGACAACGAACTTTAAAT
1 -TTAAAAATGCTCCTTTGACCAGAGGCAACGAACTTTAAAT
*
5695892 TCAAAAAT
1 TTAAAAAT
5695900 CTGAGAGGTA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 6 0.09
39 25 0.36
40 7 0.10
41 32 0.46
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (40 bp):
TTAAAAATGCTCCTTTGACCAGAGGCAACGAACTTTAAAT
Found at i:5700259 original size:9 final size:9
Alignment explanation
Indices: 5700247--5700273 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5700237 GAAAAATAAG
5700247 TGAAATGGA
1 TGAAATGGA
5700256 TGAAATGGA
1 TGAAATGGA
5700265 TGAAATGGA
1 TGAAATGGA
5700274 GAAGAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
TGAAATGGA
Found at i:5710155 original size:9 final size:9
Alignment explanation
Indices: 5710141--5710176 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
5710131 AGAAGATGAT
5710141 GAAAAAAAA
1 GAAAAAAAA
5710150 GAAAAAAATA
1 GAAAAAAA-A
5710160 GAAAAAAAA
1 GAAAAAAAA
5710169 GGAAAAAA
1 -GAAAAAA
5710177 TGAGAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:5710182 original size:20 final size:20
Alignment explanation
Indices: 5710115--5710184 Score: 76
Period size: 19 Copynumber: 3.6 Consensus size: 20
5710105 ACAATGGATG
*
5710115 AAAAATGAGGAAAAAAA-G-
1 AAAAATGAGAAAAAAAAGGA
* *
5710133 -AAGATGATGAAAAAAAAGAA
1 AAAAATGA-GAAAAAAAAGGA
5710153 AAAAAT-AGAAAAAAAAGGA
1 AAAAATGAGAAAAAAAAGGA
5710172 AAAAATGAGAAAA
1 AAAAATGAGAAAA
5710185 TGAAAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.14
18 8 0.19
19 17 0.40
20 7 0.17
21 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (20 bp):
AAAAATGAGAAAAAAAAGGA
Found at i:5711511 original size:41 final size:41
Alignment explanation
Indices: 5711428--5712156 Score: 1081
Period size: 41 Copynumber: 17.5 Consensus size: 41
5711418 AAAGTTCCGT
*
5711428 TGCCTCTGTTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTA-CTTTTCAAAGTCGTGG
5711470 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5711511 TACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5711552 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
5711593 TGCCTCTGTTGAGAGGAGCAATTTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAA-TTTACTTTTCAAAGTCGTGG
*
5711635 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5711676 TGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAATTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTA------C--TTTTCAAAGTCGTGG
*
5711725 TGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTA-CTTTTCAAAGTCGTGG
5711767 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
* *
5711808 TGCCTCTGTTGAGAGGAGCAATTTAATTTCCAAAGTTCCGT--
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAG-T-CGTGG
*
5711849 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
* *
5711890 TGCCTCTGTTGAGAGGAGCAATTTAATTTCCAAAGTTCCGT--
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAG-T-CGTGG
* *
5711931 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTT-CAAAGTCGTGG
*
5711973 TACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5712014 TGCCTCTGTTGAAGAGGAGCAATTTACTTTCCAAAGTCGTGG
1 TGCCTCTGTTG-AGAGGAGCAATTTACTTTTCAAAGTCGTGG
5712056 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
* *
5712097 TACCTCTGTTGAGAGGAGCAATTTAC-TTTCAAAAGTCGTTG
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTC-AAAGTCGTGG
* * *
5712138 AGTCTCTGTTTAGAGGAGC
1 TGCCTCTGTTGAGAGGAGC
5712157 TTCGGCAAAA
Statistics
Matches: 633, Mismatches: 34, Indels: 41
0.89 0.05 0.06
Matches are distributed among these distances:
39 3 0.00
40 8 0.01
41 398 0.63
42 177 0.28
43 6 0.01
44 1 0.00
47 1 0.00
49 39 0.06
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
Found at i:5711519 original size:83 final size:82
Alignment explanation
Indices: 5711428--5712156 Score: 1081
Period size: 83 Copynumber: 8.7 Consensus size: 82
5711418 AAAGTTCCGT
*
5711428 TGCCTCTGTTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
1 TGCCTCTGTTGAGAGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
5711493 TACTTTTCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGG
* *
5711511 TACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
5711576 ACTTTTCAAAGTCGTGG
66 ACTTTTCAAAGTCGTGG
*
5711593 TGCCTCTGTTGAGAGGAGCAATTTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
1 TGCCTCTGTTGAGAGGAGCAA-TTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
5711658 TACTTTTCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGG
*
5711676 TGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAATTTCAAAGTCGTGGTGCCTCTGTTGAGAGG
1 TGCCTCTGTTGAGAGGAGCAATTTA------C--TTTTCAAAGTCGTGGTGCCTCTGTTGAGAGG
*
5711741 AGCAATTTATTTTTTCAAAGTCGTGG
58 AGCAATTTA-CTTTTCAAAGTCGTGG
5711767 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
* *
5711832 AATTTCCAAAGTTCCGT--
66 ACTTTTCAAAG-T-CGTGG
*
5711849 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
* *
5711914 AATTTCCAAAGTTCCGT--
66 ACTTTTCAAAG-T-CGTGG
* * *
5711931 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
5711996 TACTTTTCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGG
*
5712014 TGCCTCTGTTGAAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
1 TGCCTCTGTTG-AGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
5712079 TACTTTTCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGG
* * * * *
5712097 TACCTCTGTTGAGAGGAGCAATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGC
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTGAGAGGAGC
5712157 TTCGGCAAAA
Statistics
Matches: 604, Mismatches: 25, Indels: 35
0.91 0.04 0.05
Matches are distributed among these distances:
81 6 0.01
82 239 0.40
83 259 0.43
84 20 0.03
85 1 0.00
88 1 0.00
90 38 0.06
91 40 0.07
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (82 bp):
TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
ACTTTTCAAAGTCGTGG
Found at i:5711573 original size:124 final size:123
Alignment explanation
Indices: 5711428--5712156 Score: 1081
Period size: 124 Copynumber: 5.8 Consensus size: 123
5711418 AAAGTTCCGT
*
5711428 TGCCTCTGTTTAGAGGAGCAATTTATCTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
1 TGCCTCTGTTGAGAGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
*
5711493 TACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5711552 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAA-TT
*
5711617 TACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5711676 TGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAATTTCAAAGTCGTGGTGCCTCTGTTGAGAGG
1 TGCCTCTGTTGAGAGGAGCAATTTA------C--TTTTCAAAGTCGTGGTGCCTCTGTTGAGAGG
*
5711741 AGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGT
58 AGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGT
5711806 GG
122 GG
* * *
5711808 TGCCTCTGTTGAGAGGAGCAATTTAATTTCCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAAT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAG-T-CGTGGTGCCTCTGTTGAGAGGAGCAAT
* *
5711871 TTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTAATTTCCAAAGTTCCGT--
64 TTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAG-T-CGTGG
* * *
5711931 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATT
*
5711996 TACTTTTCAAAGTCGTGGTGCCTCTGTTGAAGAGGAGCAATTTACTTTCCAAAGTCGTGG
65 TACTTTTCAAAGTCGTGGTGCCTCTGTTG-AGAGGAGCAATTTACTTTTCAAAGTCGTGG
*
5712056 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTT
1 TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
* * * *
5712121 AC-TTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGC
66 ACTTTTC-AAAGTCGTGGTGCCTCTGTTGAGAGGAGC
5712157 TTCGGCAAAA
Statistics
Matches: 559, Mismatches: 25, Indels: 43
0.89 0.04 0.07
Matches are distributed among these distances:
122 3 0.01
123 128 0.23
124 250 0.45
125 55 0.10
126 3 0.01
130 1 0.00
131 4 0.01
132 115 0.21
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (123 bp):
TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTT
ACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGG
Found at i:5712169 original size:1 final size:1
Alignment explanation
Indices: 5712163--5712284 Score: 100
Period size: 1 Copynumber: 122.0 Consensus size: 1
5712153 GAGCTTCGGC
* * * **
5712163 AAAAAAAAAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAAAAAAAAAAAAAAATCAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * ** * * * ** *
5712228 ATCAGAAAAAAATCAAAAAAATAAAAAACAAAAATAAAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5712285 TGTTGAGTTG
Statistics
Matches: 93, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 93 1.00
ACGTcount: A:0.87, C:0.07, G:0.01, T:0.06
Consensus pattern (1 bp):
A
Found at i:5712182 original size:10 final size:10
Alignment explanation
Indices: 5712163--5712278 Score: 128
Period size: 10 Copynumber: 11.3 Consensus size: 10
5712153 GAGCTTCGGC
5712163 AAAAAA-AAA
1 AAAAAACAAA
5712172 AAAAAACAAA
1 AAAAAACAAA
5712182 AAAAAACAAA
1 AAAAAACAAA
5712192 AAAAAACAAAA
1 AAAAAAC-AAA
*
5712203 AAAAAAAAAA
1 AAAAAACAAA
5712213 AAAAAATCAAA
1 AAAAAA-CAAA
*
5712224 AAAAATCAGAA
1 AAAAAACA-AA
*
5712235 AAAAATCAAA
1 AAAAAACAAA
5712245 AAAATAA-AAA
1 AAAA-AACAAA
*
5712255 ACAAAAATAAA
1 A-AAAAACAAA
*
5712266 AAAAATCAAA
1 AAAAAACAAA
5712276 AAA
1 AAA
5712279 TAAAAATGTT
Statistics
Matches: 94, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
9 6 0.06
10 53 0.56
11 35 0.37
ACGTcount: A:0.87, C:0.07, G:0.01, T:0.05
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:5712224 original size:42 final size:42
Alignment explanation
Indices: 5712163--5712278 Score: 173
Period size: 43 Copynumber: 2.8 Consensus size: 42
5712153 GAGCTTCGGC
*
5712163 AAAAAAAAAAAAAAA-CAAAAAAAAACAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAATCAAAAAAAATCAAAAAAAAACAAAAA
*
5712204 AAAAAAAAAAAAAAATCAAAAAAAATCAGAAAAAAATCAAAAA
1 AAAAAAAAAAAAAAATCAAAAAAAATCA-AAAAAAAACAAAAA
* *
5712247 AATAAAAAACAAAAAT-AAAAAAAATCAAAAAA
1 AAAAAAAAAAAAAAATCAAAAAAAATCAAAAAA
5712279 TAAAAATGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 20 0.29
42 22 0.32
43 27 0.39
ACGTcount: A:0.87, C:0.07, G:0.01, T:0.05
Consensus pattern (42 bp):
AAAAAAAAAAAAAAATCAAAAAAAATCAAAAAAAAACAAAAA
Found at i:5712509 original size:24 final size:23
Alignment explanation
Indices: 5712454--5712507 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 23
5712444 TTTTCTTTTG
5712454 TATTTTATGTATTCTATTATTAT
1 TATTTTATGTATTCTATTATTAT
5712477 TATTATTATGTATATCT-TTATTCATT
1 TATT-TTATGTAT-TCTATTATT-A-T
5712503 TATTT
1 TATTT
5712508 ATTTTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 5 0.19
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTTATGTATTCTATTATTAT
Found at i:5712566 original size:3 final size:3
Alignment explanation
Indices: 5712558--5712583 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5712548 AGTTATATAT
5712558 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5712584 TTTGTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5713032 original size:26 final size:25
Alignment explanation
Indices: 5713003--5713057 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
5712993 CTGGGAGTGA
5713003 GAAAAAAATTTCTAGAAATTTCTGG
1 GAAAAAAATTTCTAGAAATTTCTGG
* *
5713028 CGAAAAAATTTTCTGGAAATTTCTGG
1 -GAAAAAAATTTCTAGAAATTTCTGG
5713054 GAAA
1 GAAA
5713058 TTTCCAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (25 bp):
GAAAAAAATTTCTAGAAATTTCTGG
Found at i:5713224 original size:20 final size:20
Alignment explanation
Indices: 5713199--5713247 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5713189 TCCGGCGAAC
*
5713199 TTCCGGCGACATTTTCCAGA
1 TTCCGGCGACAATTTCCAGA
* *
5713219 TTCCGGCGAGAATTTCTAGA
1 TTCCGGCGACAATTTCCAGA
*
5713239 ATCCGGCGA
1 TTCCGGCGA
5713248 AATCTCACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (20 bp):
TTCCGGCGACAATTTCCAGA
Found at i:5713509 original size:14 final size:15
Alignment explanation
Indices: 5713490--5713531 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
5713480 CCGAGCCGAG
5713490 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
5713504 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
5713517 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
5713531 C
1 C
5713532 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:5713522 original size:13 final size:14
Alignment explanation
Indices: 5713490--5713526 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5713480 CCGAGCCGAG
5713490 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
5713504 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
5713516 TCCGAGCCGTT
1 -CCGAGCCGTT
5713527 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:5713610 original size:17 final size:16
Alignment explanation
Indices: 5713577--5713655 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
5713567 GCCGCTCCAG
5713577 TTTTTTTTTTTTT--T
1 TTTTTTTTTTTTTGAT
5713591 TTTTTTTTTTTTTGAAT
1 TTTTTTTTTTTTTG-AT
*
5713608 TTTTTTTTTATTTGACT
1 TTTTTTTTTTTTTGA-T
* ** *
5713625 TTGATTTTGATCTTGAT
1 TT-TTTTTTTTTTTGAT
5713642 TTTTTTTTCTTTTT
1 TTTTTTTT-TTTTT
5713656 TTTTTTCTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
14 13 0.27
16 5 0.10
17 23 0.47
18 8 0.16
ACGTcount: A:0.09, C:0.04, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTTTTGAT
Found at i:5713616 original size:1 final size:1
Alignment explanation
Indices: 5713577--5713603 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5713567 GCCGCTCCAG
5713577 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
5713604 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5713657 original size:11 final size:12
Alignment explanation
Indices: 5713641--5713665 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5713631 TTGATCTTGA
5713641 TTTTTTTTTCTT
1 TTTTTTTTTCTT
5713653 TTTTTTTTTCTT
1 TTTTTTTTTCTT
5713665 T
1 T
5713666 AATTAATCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:5713819 original size:158 final size:155
Alignment explanation
Indices: 5713656--5714114 Score: 717
Period size: 152 Copynumber: 2.9 Consensus size: 155
5713646 TTTTCTTTTT
* *
5713656 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATAC
1 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATAC
*
5713721 TCCTGAGGTGAGGGAATTTTTTTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTT
65 TCCTGAGGTGAGGGAA-TTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTT
* *
5713786 TCGATAATTAATTACTTGGCTGATTTTGA
129 TC-ACAA-TAATTACTTGGATGATTTTGA
*
5713815 TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGTATAC
1 -TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATAC
* *
5713880 TCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAATAA-TTT
65 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
*
5713944 C-CAATAATTAATTGGATGATTTTGA
130 CACAATAATTACTTGGATGATTTTGA
* *
5713969 -TTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
1 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
* *
5714033 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATCATTTCC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
5714098 AACAACTAATTACTTGG
131 -ACAA-TAATTACTTGG
5714115 TAAAATTTTA
Statistics
Matches: 278, Mismatches: 17, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
152 118 0.42
153 3 0.01
154 19 0.07
155 5 0.02
156 10 0.04
157 4 0.01
158 43 0.15
159 37 0.13
160 39 0.14
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (155 bp):
TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
ACAATAATTACTTGGATGATTTTGA
Found at i:5714535 original size:28 final size:28
Alignment explanation
Indices: 5714486--5714564 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
5714476 GTTTTGTTTA
* *
5714486 AATATTGTGATTTGTT-ATATGGTATTGTGT
1 AATATTGT--TTTGTTGA-ATGGTAATGTAT
*
5714516 GATATTGTTTTGTTGAATGGTAATGTAT
1 AATATTGTTTTGTTGAATGGTAATGTAT
* **
5714544 AATATTGGTTTACTGAATGGT
1 AATATTGTTTTGTTGAATGGT
5714565 GTTTCTATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 33 0.80
29 1 0.02
30 7 0.17
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.49
Consensus pattern (28 bp):
AATATTGTTTTGTTGAATGGTAATGTAT
Found at i:5718855 original size:7 final size:7
Alignment explanation
Indices: 5718839--5718900 Score: 63
Period size: 7 Copynumber: 8.6 Consensus size: 7
5718829 CATGATAAAA
5718839 AAAATA-
1 AAAATAT
5718845 AAAATAT
1 AAAATAT
*
5718852 AAAAGAT
1 AAAATAT
5718859 AAAAATAT
1 -AAAATAT
*
5718867 AAATTAT
1 AAAATAT
*
5718874 AAAAATAA
1 -AAAATAT
5718882 ATAAATAT
1 A-AAATAT
5718890 AAAATAT
1 AAAATAT
5718897 AAAA
1 AAAA
5718901 ATATTTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
6 6 0.13
7 23 0.50
8 17 0.37
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:5718860 original size:15 final size:14
Alignment explanation
Indices: 5718838--5718903 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 14
5718828 TCATGATAAA
5718838 AAAAATAAAAATAT
1 AAAAATAAAAATAT
5718852 AAAAGATAAAAATAT
1 AAAA-ATAAAAATAT
*
5718867 AAATTATAAAAATA-
1 AAA-AATAAAAATAT
5718881 AATAAATATAAAATAT
1 AA-AAATA-AAAATAT
5718897 AAAAATA
1 AAAAATA
5718904 TTTAATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
14 9 0.20
15 34 0.76
16 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
AAAAATAAAAATAT
Found at i:5718868 original size:23 final size:21
Alignment explanation
Indices: 5718837--5718903 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 21
5718827 ATCATGATAA
5718837 AAAAAATAAAAATATAAAAGAT
1 AAAAAATAAAAATATAAAA-AT
*
5718859 -AAAAATATAAATTATAAAAAT
1 AAAAAATA-AAAATATAAAAAT
5718880 AAATAAATATAAAATATAAAAAT
1 AAA-AAATA-AAAATATAAAAAT
5718903 A
1 A
5718904 TTTAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.22
22 12 0.30
23 19 0.47
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (21 bp):
AAAAAATAAAAATATAAAAAT
Found at i:5720432 original size:3 final size:3
Alignment explanation
Indices: 5720424--5720479 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5720414 TTTGCTTCTG
5720424 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5720472 TTA TTA TT
1 TTA TTA TT
5720480 GGCATCTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5720569 original size:21 final size:21
Alignment explanation
Indices: 5720527--5720572 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5720517 ATTTAATTAT
* *
5720527 TAAATAATAACAAGTAGTAAA
1 TAAATAATAACAAATAGAAAA
5720548 TAAATAATAACAAAATA-AAAA
1 TAAATAATAAC-AAATAGAAAA
5720569 TAAA
1 TAAA
5720573 GTGAAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAATAATAACAAATAGAAAA
Found at i:5721792 original size:20 final size:20
Alignment explanation
Indices: 5721768--5721815 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
5721758 AAAAAACCAA
*
5721768 AAAAAAAACCCAAAAAAATTT
1 AAAAAAAA-CCAAAAAAATTC
5721789 AAAAAAAACCAAAAAAATTC
1 AAAAAAAACCAAAAAAATTC
5721809 AAAAAAA
1 AAAAAAA
5721816 TTCCTAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAAAAAACCAAAAAAATTC
Found at i:5721802 original size:9 final size:10
Alignment explanation
Indices: 5721769--5721816 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
5721759 AAAAACCAAA
*
5721769 AAAAAAACCC
1 AAAAAAATCC
**
5721779 AAAAAAATTT
1 AAAAAAATCC
*
5721789 AAAAAAAACC
1 AAAAAAATCC
*
5721799 AAAAAAATTC
1 AAAAAAATCC
5721809 AAAAAAAT
1 AAAAAAAT
5721817 TCCTAAATCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAATCC
Found at i:5721804 original size:12 final size:13
Alignment explanation
Indices: 5721757--5721785 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5721747 AATGTTCTTC
5721757 AAAAAAA-CCAAA
1 AAAAAAACCCAAA
5721769 AAAAAAACCCAAA
1 AAAAAAACCCAAA
5721782 AAAA
1 AAAA
5721786 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACCCAAA
Found at i:5721816 original size:10 final size:10
Alignment explanation
Indices: 5721778--5721818 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
5721768 AAAAAAAACC
5721778 CAAAAAAATT
1 CAAAAAAATT
* **
5721788 TAAAAAAAAC
1 CAAAAAAATT
5721798 CAAAAAAATT
1 CAAAAAAATT
5721808 CAAAAAAATT
1 CAAAAAAATT
5721818 C
1 C
5721819 CTAAATCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (10 bp):
CAAAAAAATT
Found at i:5722263 original size:3 final size:3
Alignment explanation
Indices: 5722255--5722291 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5722245 AGATAAAAAT
5722255 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5722292 CAAGCTGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5722808 original size:60 final size:60
Alignment explanation
Indices: 5722743--5722869 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
5722733 ATATCACAAG
*
5722743 TCTGAAAGTGACCAAGATCGAGTCAAGGTAAAAAATAAATGATCAGACTAATGTCACAGA
1 TCTGAAAGTAACCAAGATCGAGTCAAGGTAAAAAATAAATGATCAGACTAATGTCACAGA
* * * * * * *
5722803 TCTGAAGGTAATCAAGATCGAGTCAAGGTCAAAAATAAATGGTTAGACTAATGTCGCAGG
1 TCTGAAAGTAACCAAGATCGAGTCAAGGTAAAAAATAAATGATCAGACTAATGTCACAGA
5722863 TCTGAAA
1 TCTGAAA
5722870 ATGATCTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (60 bp):
TCTGAAAGTAACCAAGATCGAGTCAAGGTAAAAAATAAATGATCAGACTAATGTCACAGA
Found at i:5722886 original size:60 final size:60
Alignment explanation
Indices: 5722755--5722895 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 60
5722745 TGAAAGTGAC
* **
5722755 CAAGATCGAGTCAAGGTAAAAAATAAATGATCAGACTAATGTCACAGATCTGAAGGTAAT
1 CAAGATCGAGTCAAGGTCAAAAATAAATGATCAGACTAATGTCACAGATCTGAAAATAAT
* * * * *
5722815 CAAGATCGAGTCAAGGTCAAAAATAAATGGTTAGACTAATGTCGCAGGTCTGAAAATGAT
1 CAAGATCGAGTCAAGGTCAAAAATAAATGATCAGACTAATGTCACAGATCTGAAAATAAT
* *
5722875 CTAATAT-GAGTCAAGATCAAA
1 C-AAGATCGAGTCAAGGTCAAA
5722896 TGACTGGGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
60 66 0.94
61 4 0.06
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (60 bp):
CAAGATCGAGTCAAGGTCAAAAATAAATGATCAGACTAATGTCACAGATCTGAAAATAAT
Found at i:5735529 original size:26 final size:27
Alignment explanation
Indices: 5735500--5735585 Score: 88
Period size: 25 Copynumber: 3.3 Consensus size: 27
5735490 AAATAAATAA
**
5735500 AAATTTATTTTTTATTTGATATAT-TT
1 AAATTTATTTTTTATTAAATATATATT
*
5735526 AAA-TAATTTTTTA-TAAATATATATT
1 AAATTTATTTTTTATTAAATATATATT
* *
5735551 AATATATATTTTTTATTAAAAATATATT
1 AA-ATTTATTTTTTATTAAATATATATT
*
5735579 AATTTTA
1 AAATTTA
5735586 ATTAATTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
24 7 0.15
25 13 0.27
26 4 0.08
27 11 0.23
28 13 0.27
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
AAATTTATTTTTTATTAAATATATATT
Found at i:5735534 original size:25 final size:28
Alignment explanation
Indices: 5735505--5735581 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
5735495 AATAAAAATT
**
5735505 TATTTTTTATTTGATATAT-TTAA-ATA
1 TATTTTTTATTAAATATATATTAATATA
5735531 -ATTTTTTA-TAAATATATATTAATATA
1 TATTTTTTATTAAATATATATTAATATA
*
5735557 TATTTTTTATTAAAAATATATTAAT
1 TATTTTTTATTAAATATATATTAAT
5735582 TTTAATTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.16
25 12 0.27
26 3 0.07
27 8 0.18
28 14 0.32
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TATTTTTTATTAAATATATATTAATATA
Found at i:5735601 original size:20 final size:21
Alignment explanation
Indices: 5735578--5735639 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
5735568 AAAAATATAT
5735578 TAATTTTA-ATTAATTTAA-AA
1 TAATTTTATATT-ATTTAATAA
5735598 TAATAATTTATATTATTTAATAA
1 TAAT--TTTATATTATTTAATAA
* *
5735621 AAATTTTAT-TTATTAAATA
1 TAATTTTATATTATTTAATA
5735640 TATATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 13 0.36
21 5 0.14
22 10 0.28
23 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTTTATATTATTTAATAA
Found at i:5736521 original size:26 final size:26
Alignment explanation
Indices: 5736489--5736541 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5736479 AGCATTTGCA
**
5736489 ATTTTTTGTTTTTTTTTTTCTTATTTC
1 ATTTTTT-TTTTTCATTTTCTTATTTC
*
5736516 ATTTTTTTTTTTCATTTTCTTCTTTC
1 ATTTTTTTTTTTCATTTTCTTATTTC
5736542 TATCCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.79
Consensus pattern (26 bp):
ATTTTTTTTTTTCATTTTCTTATTTC
Found at i:5736534 original size:19 final size:20
Alignment explanation
Indices: 5736497--5736534 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5736487 CAATTTTTTG
*
5736497 TTTTTTTTTTTCTTATTTCA
1 TTTTTTTTTTTCATATTTCA
5736517 TTTTTTTTTTTCAT-TTTC
1 TTTTTTTTTTTCATATTTC
5736535 TTCTTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTTTCATATTTCA
Found at i:5738074 original size:44 final size:45
Alignment explanation
Indices: 5738026--5738120 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 45
5738016 TAATAAAATA
* *
5738026 ATTTTATATATTT-ATATAAGATTAAAGATACATTATAATGTTAG
1 ATTTTATATATTTGATATAAAATCAAAGATACATTATAATGTTAG
* * * ** *
5738070 ATTTT-TGTTTTTGTTATAAAATCAATTATATATTATAATGTTAG
1 ATTTTATATATTTGATATAAAATCAAAGATACATTATAATGTTAG
5738114 ATTTTAT
1 ATTTTAT
5738121 GTATACCGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
43 5 0.12
44 35 0.85
45 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (45 bp):
ATTTTATATATTTGATATAAAATCAAAGATACATTATAATGTTAG
Found at i:5739905 original size:20 final size:21
Alignment explanation
Indices: 5739880--5739918 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5739870 CAAGTTTCAA
*
5739880 ATTTTAGGGTTT-AGGTTTTG
1 ATTTTAGGATTTGAGGTTTTG
5739900 ATTTTAGGATTTGAGGTTT
1 ATTTTAGGATTTGAGGTTT
5739919 AGGGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (21 bp):
ATTTTAGGATTTGAGGTTTTG
Found at i:5739911 original size:28 final size:29
Alignment explanation
Indices: 5739880--5740013 Score: 141
Period size: 28 Copynumber: 4.7 Consensus size: 29
5739870 CAAGTTTCAA
*
5739880 ATTTTAGGGTTT-AGGTTTTGATTTTAGG
1 ATTTGAGGGTTTAAGGTTTTGATTTTAGG
* * *
5739908 ATTTGA-GGTTTAGGGTTTTAACTTTAGG
1 ATTTGAGGGTTTAAGGTTTTGATTTTAGG
5739936 ATTTGA-GGTTTGAA-GTTTTGATTTTAGG
1 ATTTGAGGGTTT-AAGGTTTTGATTTTAGG
* * *
5739964 GTTTAGAAGATTTAAGGTTTTGATTTTAGG
1 ATTT-GAGGGTTTAAGGTTTTGATTTTAGG
*
5739994 GTTTAGAGGGTTTAAGGTTT
1 ATTT-GAGGGTTTAAGGTTT
5740014 CATTTTTAGG
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.06
28 44 0.49
29 5 0.06
30 36 0.40
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.49
Consensus pattern (29 bp):
ATTTGAGGGTTTAAGGTTTTGATTTTAGG
Found at i:5739921 original size:14 final size:14
Alignment explanation
Indices: 5739887--5739946 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
5739877 CAAATTTTAG
*
5739887 GGTTTAGGTTTTGA
1 GGTTTAGGATTTGA
*
5739901 -TTTTAGGATTTGA
1 GGTTTAGGATTTGA
* *
5739914 GGTTTAGGGTTTTA
1 GGTTTAGGATTTGA
**
5739928 ACTTTAGGATTTGA
1 GGTTTAGGATTTGA
5739942 GGTTT
1 GGTTT
5739947 GAAGTTTTGA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
13 11 0.32
14 23 0.68
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.50
Consensus pattern (14 bp):
GGTTTAGGATTTGA
Found at i:5739966 original size:21 final size:22
Alignment explanation
Indices: 5739916--5739977 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
5739906 GGATTTGAGG
* *
5739916 TTTAGGGTTTTAACTTTAGGAT
1 TTTAGGGTTTGAAGTTTAGGAT
* *
5739938 TTGA-GGTTTGAAGTTT-TGAT
1 TTTAGGGTTTGAAGTTTAGGAT
5739958 TTTAGGGTTTAGAAGATTTA
1 TTTAGGGTTT-GAAG-TTTA
5739978 AGGTTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 6 0.19
21 15 0.48
22 7 0.23
23 3 0.10
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (22 bp):
TTTAGGGTTTGAAGTTTAGGAT
Found at i:5739985 original size:30 final size:30
Alignment explanation
Indices: 5739887--5740035 Score: 152
Period size: 30 Copynumber: 5.2 Consensus size: 30
5739877 CAAATTTTAG
*
5739887 GGTTT-AGGTTTTGATTTTAGGATTT-G-A
1 GGTTTAAGGTTTTGATTTTAGGGTTTAGAA
* * * *
5739914 GGTTTAGGGTTTTAACTTTAGGATTT-G-A
1 GGTTTAAGGTTTTGATTTTAGGGTTTAGAA
5739942 GGTTTGAA-GTTTTGATTTTAGGGTTTAGAA
1 GGTTT-AAGGTTTTGATTTTAGGGTTTAGAA
* *
5739972 GATTTAAGGTTTTGATTTTAGGGTTTAGAG
1 GGTTTAAGGTTTTGATTTTAGGGTTTAGAA
*
5740002 GGTTTAAGG-TTTCATTTTTAGGGTTTAG-A
1 GGTTTAAGGTTTTGA-TTTTAGGGTTTAGAA
5740031 GGTTT
1 GGTTT
5740036 GGGGTTTAGT
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
27 5 0.05
28 39 0.38
29 13 0.12
30 47 0.45
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (30 bp):
GGTTTAAGGTTTTGATTTTAGGGTTTAGAA
Found at i:5739996 original size:14 final size:14
Alignment explanation
Indices: 5739889--5739997 Score: 55
Period size: 14 Copynumber: 7.7 Consensus size: 14
5739879 AATTTTAGGG
5739889 TTTA-GGTTTTGAT
1 TTTAGGGTTTTGAT
* *
5739902 TTTA-GGATTTGAGG
1 TTTAGGGTTTTGA-T
* *
5739916 TTTAGGGTTTTAAC
1 TTTAGGGTTTTGAT
* *
5739930 TTTA-GGATTTGAGG
1 TTTAGGGTTTTGA-T
*
5739944 TTT-GAAGTTTTGAT
1 TTTAG-GGTTTTGAT
* *
5739958 TTTAGGGTTTAGAAGA
1 TTTAGGGTTTTG-A-T
*
5739974 TTTAAGGTTTTGAT
1 TTTAGGGTTTTGAT
5739988 TTTAGGGTTT
1 TTTAGGGTTT
5739998 AGAGGGTTTA
Statistics
Matches: 70, Mismatches: 18, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
13 17 0.24
14 28 0.40
15 15 0.21
16 10 0.14
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:5740822 original size:37 final size:37
Alignment explanation
Indices: 5740781--5740890 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 37
5740771 ATTGTAAATA
5740781 AAAAAATAAAAAATTGATTGGGACAACACCACAAGTC
1 AAAAAATAAAAAATTGATTGGGACAACACCACAAGTC
* ** * ***
5740818 AAAAAATAAGAAAGCGATTAGGACAACACTGTAAGTC
1 AAAAAATAAAAAATTGATTGGGACAACACCACAAGTC
* * * * * *
5740855 TAAAAGTAAAGAATTAATCGGGACAATACCACAAGT
1 AAAAAATAAAAAATTGATTGGGACAACACCACAAGT
5740891 TGAAATTATG
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.17
Consensus pattern (37 bp):
AAAAAATAAAAAATTGATTGGGACAACACCACAAGTC
Found at i:5740920 original size:22 final size:22
Alignment explanation
Indices: 5740895--5740937 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5740885 ACAAGTTGAA
5740895 ATTATGCCCAGAAGTCTTAAAG
1 ATTATGCCCAGAAGTCTTAAAG
* * *
5740917 ATTATGCTCGGAGGTCTTAAA
1 ATTATGCCCAGAAGTCTTAAA
5740938 AATCATGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (22 bp):
ATTATGCCCAGAAGTCTTAAAG
Found at i:5741055 original size:22 final size:22
Alignment explanation
Indices: 5741024--5741089 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
5741014 ACTGCGAATC
5741024 GAAATTATGCTCGAAGGTCTTA
1 GAAATTATGCTCGAAGGTCTTA
* *
5741046 -AAGATTATGCCCAAAGGTCTTA
1 GAA-ATTATGCTCGAAGGTCTTA
*
5741068 GAAATTATGCTCGGAGGTCTTA
1 GAAATTATGCTCGAAGGTCTTA
5741090 CTGAATCAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (22 bp):
GAAATTATGCTCGAAGGTCTTA
Found at i:5741101 original size:132 final size:132
Alignment explanation
Indices: 5740856--5741186 Score: 362
Period size: 132 Copynumber: 2.5 Consensus size: 132
5740846 CTGTAAGTCT
* ** * * * *
5740856 AAAAGTAAAGAATTAATCGGGACAATACCAC-AAGTTGAAATTATGCCCAGAA-GTCTTAAAGAT
1 AAAAATAAAGAATCGATCGGAACAACACCACGAA-TCGAAATTATGCTC-GAAGGTCTTAAAGAT
* ** * * *
5740919 TATGCTCGGAGGTCTTAAAAATCATGTCTAAAGGTTTTACAAAATTAACTGGGATAACACCACGA
64 TATGCCCAAAGGTCTTAAAAATCATGTCTAAAGGTCTTACAAAATCAACTGGGATAACACCACAA
5740984 GTTA
129 GTTA
* * * **
5740988 AAAAATAAAGAATCGATTGGGATAACACTGCGAATCGAAATTATGCTCGAAGGTCTTAAAGATTA
1 AAAAATAAAGAATCGATCGGAACAACACCACGAATCGAAATTATGCTCGAAGGTCTTAAAGATTA
* * ** ** *
5741053 TGCCCAAAGGTCTTAGAAATTATG-CTCGGAGGTCTTACTGAATCAACTGGGATAACACCATAAG
66 TGCCCAAAGGTCTTAAAAATCATGTCT-AAAGGTCTTACAAAATCAACTGGGATAACACCACAAG
5741117 TTA
130 TTA
* * *
5741120 AAAAATAAAGAATCGATCGGAACAACACCACGAATCAAAATTATGCTTGAAGATCTTAAAGATTA
1 AAAAATAAAGAATCGATCGGAACAACACCACGAATCGAAATTATGCTCGAAGGTCTTAAAGATTA
5741185 TG
66 TG
5741187 TCTGGAGGTC
Statistics
Matches: 165, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
131 5 0.03
132 158 0.96
133 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (132 bp):
AAAAATAAAGAATCGATCGGAACAACACCACGAATCGAAATTATGCTCGAAGGTCTTAAAGATTA
TGCCCAAAGGTCTTAAAAATCATGTCTAAAGGTCTTACAAAATCAACTGGGATAACACCACAAGT
TA
Found at i:5741264 original size:110 final size:108
Alignment explanation
Indices: 5741062--5741404 Score: 300
Period size: 110 Copynumber: 3.1 Consensus size: 108
5741052 ATGCCCAAAG
* * * * *
5741062 GTCTTAGAAATTATGCTCGGAGGTCTTACTGAATCAACTGGGATAACACCATAAGTTAAAAAATA
1 GTCTTAGAAATTATGCTCGGAGGTCTTACAGAATCATC-GAGATAA-AACATAAGTCAAAAAATA
* * * *
5741127 AAGAATCGATCGGAACAACACCA-CGAATCAAAATTATGCTTG-AA
64 AAAAATCGATTGGGACAACA-TAGCGAATCAAAATTATGCTTGAAA
*
5741171 GATCTTA-AAGATTATG-TCTGGAGGTCTTACAGAATCGATCGAGATAATACTATAAGTCAAAAA
1 G-TCTTAGAA-ATTATGCTC-GGAGGTCTTACAGAATC-ATCGAGATAAAAC-ATAAGTCAAAAA
* * *
5741234 ATAAAAAATCGATTGGGATAACATAGCGAATCTAAATTATTCTTGAAA
61 ATAAAAAATCGATTGGGACAACATAGCGAATCAAAATTATGCTTGAAA
* * * * * **
5741282 GTCTTAGAAATCATGCTCGAAAGTTTTATAGAATCAATC-AGGATAACAACGCAAGTCAAAAAAT
1 GTCTTAGAAATTATGCTCGGAGGTCTTACAGAATC-ATCGA-GATAA-AACATAAGTCAAAAAAT
* * * * ***
5741346 AAATAATCAATTGGGACAACATTGGGAATCAAAATTATGCCAAAAA
63 AAAAAATCGATTGGGACAACATAGCGAATCAAAATTATGCTTGAAA
*
5741392 GTCTTAAAAATTA
1 GTCTTAGAAATTA
5741405 AGCCCCAATG
Statistics
Matches: 189, Mismatches: 34, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
109 8 0.04
110 170 0.90
111 11 0.06
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (108 bp):
GTCTTAGAAATTATGCTCGGAGGTCTTACAGAATCATCGAGATAAAACATAAGTCAAAAAATAAA
AAATCGATTGGGACAACATAGCGAATCAAAATTATGCTTGAAA
Found at i:5741507 original size:132 final size:132
Alignment explanation
Indices: 5741282--5741650 Score: 350
Period size: 132 Copynumber: 2.8 Consensus size: 132
5741272 ATTCTTGAAA
* * *
5741282 GTCTTAGAAATCATG-CTCGAAAGTTTTATAGAATCAATCAGGATAACAACGCAAGTCAAAAAAT
1 GTCTTAGAAATCATGTCT-GAAAGTTTTACAGAATCGATCGGGATAACAACGCAAGTCAAAAAAT
* ** * **
5741346 AAATAATCAATTGGGACAACATTGGGAATCAAAATTATGC-CAAAAAGTCTTAAAAATTA-AGCC
65 AAAAAATTGATCGGGACAACATCAGGAATCAAAATTATGCTC-AAAAGTCTTAAAAATTATA-CC
5741409 CCAAT
128 CCAAT
* * * ** *
5741414 GTTTTAGAAATCATGTCTGAATGTTTTACAGAATCGATCGGGATAACACCATAAATCAAAAAATA
1 GTCTTAGAAATCATGTCTGAAAGTTTTACAGAATCGATCGGGATAACAACGCAAGTCAAAAAATA
* * * * * ** * * **
5741479 AAGAATTGATCGGGATAATATCATGAATCAAATTTATGCTCGGAGGTCTTAAAGATTATACCCGG
66 AAAAATTGATCGGGACAACATCAGGAATCAAAATTATGCTCAAAAGTCTTAAAAATTATACCCCA
5741544 AT
131 AT
* * * * * *
5741546 GTCTTAGAAATAATATCTGAAGGTTTTACAAAATCGACCGGCGATAACATCGCAAGTCAAAAAAT
1 GTCTTAGAAATCATGTCTGAAAGTTTTACAGAATCGATCGG-GATAACAACGCAAGTCAAAAAAT
** *
5741611 AAAAAATTGATTAGGACAACA-CTGTGAATCAAAATTATGC
65 AAAAAATTGATCGGGACAACATCAG-GAATCAAAATTATGC
5741651 CTGAAGATCT
Statistics
Matches: 189, Mismatches: 43, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
132 136 0.72
133 53 0.28
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (132 bp):
GTCTTAGAAATCATGTCTGAAAGTTTTACAGAATCGATCGGGATAACAACGCAAGTCAAAAAATA
AAAAATTGATCGGGACAACATCAGGAATCAAAATTATGCTCAAAAGTCTTAAAAATTATACCCCA
AT
Found at i:5741811 original size:22 final size:21
Alignment explanation
Indices: 5741762--5741811 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
5741752 AATTATACTC
5741762 AGAGGTCTTAAAGATTATGTT
1 AGAGGTCTTAAAGATTATGTT
*
5741783 TGAAGGTCTTAGAA-ATTATGTCT
1 AG-AGGTCTTA-AAGATTATGT-T
5741806 AGAGGT
1 AGAGGT
5741812 TTTATAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (21 bp):
AGAGGTCTTAAAGATTATGTT
Found at i:5741908 original size:22 final size:22
Alignment explanation
Indices: 5741883--5741930 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
5741873 TCGCAAATCG
*
5741883 AAATTATGCCCGGAGGTCTTAA
1 AAATTATGCCCGAAGGTCTTAA
5741905 AAATTATGCCCGAAGGTCTTAA
1 AAATTATGCCCGAAGGTCTTAA
5741927 AAAT
1 AAAT
5741931 CATGTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (22 bp):
AAATTATGCCCGAAGGTCTTAA
Found at i:5741925 original size:242 final size:242
Alignment explanation
Indices: 5741439--5741925 Score: 557
Period size: 242 Copynumber: 2.0 Consensus size: 242
5741429 TCTGAATGTT
* * * * *
5741439 TTACAGAATCGATCGGGATAACACCATAAATCAAAAAATAAAGAATTGATCGGGATAATATCATG
1 TTACAGAATCGATCGGAATAACACCATAAATCAAAAAATAAAGAATCGATCGGGACAATACCACG
* * * * *
5741504 AATCAAATTTATGCTCGGAGGTCTTAAAGATTATACCCGGATGTCTTAGAAATAATATCTGAAGG
66 AATCAAAATTATACTCAGAGGTCTTAAAGATTATACCCGAAGGTCTTAGAAATAATATCTGAAGG
** * **
5741569 TTTTACAAAATCGACCGGCGATAACATCGCAAGTCAAAAAATAAAAAATTGATTAGGACAACACT
131 TTTTACAAAATCGACCGGAAATAACACCGCAAGTCAAAAAATAAAAAATTGATTAAAACAACACT
** * * * *
5741634 GTGAATCAAAATTATGCCTGAAGATCTTAGAAATCATGCTCGGGGTC
196 GCAAATCAAAATTATGCCCGAAGATCTTAAAAATCATGCCCGAGGTC
* * * *
5741681 TTACAGAATCGATTGGAATAACACCGTAAATCAAAAAATAAAGAATCGATTGGGACAATACCGCG
1 TTACAGAATCGATCGGAATAACACCATAAATCAAAAAATAAAGAATCGATCGGGACAATACCACG
**** * *
5741746 AATCAAAATTATACTCAGAGGTCTTAAAGATTATGTTTGAAGGTCTTAGAAATTATGTCT-AGAG
66 AATCAAAATTATACTCAGAGGTCTTAAAGATTATACCCGAAGGTCTTAGAAATAATATCTGA-AG
* * * * * *
5741810 GTTTTATAGAATTGATC-GAAATAACACCGCAAGTCGAAAAATAAAAAATTGATTAAAACAATA-
130 GTTTTACAAAATCGACCGGAAATAACACCGCAAGTCAAAAAATAAAAAATTGATTAAAACAACAC
* * * *
5741873 TCGCAAATCGAAATTATGCCCGGAGGTCTTAAAAATTATGCCCGAAGGTC
195 T-GCAAATCAAAATTATGCCCGAAGATCTTAAAAATCATGCCCG-AGGTC
5741923 TTA
1 TTA
5741926 AAAATCATGT
Statistics
Matches: 201, Mismatches: 41, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
240 1 0.00
241 73 0.36
242 127 0.63
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (242 bp):
TTACAGAATCGATCGGAATAACACCATAAATCAAAAAATAAAGAATCGATCGGGACAATACCACG
AATCAAAATTATACTCAGAGGTCTTAAAGATTATACCCGAAGGTCTTAGAAATAATATCTGAAGG
TTTTACAAAATCGACCGGAAATAACACCGCAAGTCAAAAAATAAAAAATTGATTAAAACAACACT
GCAAATCAAAATTATGCCCGAAGATCTTAAAAATCATGCCCGAGGTC
Found at i:5741943 original size:374 final size:374
Alignment explanation
Indices: 5741224--5742053 Score: 805
Period size: 374 Copynumber: 2.2 Consensus size: 374
5741214 ATAATACTAT
* * * * * *
5741224 AAGTCAAAAAATAAAAAATCGATTGGGATAACA-TAGCGAATCTAAATTATTCTTGAA-AGTCTT
1 AAGTCAAAAAATAAAAAATTGATTAGGACAACACT-GCGAATCAAAATTATACCTGAAGA-TCTT
* * * *
5741287 AGAAATCATGCTCGAAAGTTTTATAGAATCAATCAGGATAACAACGCAAGTCAAAAAATAAATAA
64 AGAAATCATGCTCGAAAGTCTTACAGAATCAATCAGGATAACAACGCAAATCAAAAAATAAAGAA
** * * * *
5741352 TCAATTGGGACAACATTGGGAATCAAAATTATGCCAAAAAGTCTTAAAAATTAAGCCCCAATGTT
129 TCAATTGGGACAACACCGCGAATCAAAATTATACCAAAAAGTCTTAAAAATTAAGCCCCAAGGTC
* ** * *
5741417 TTAGAAATCATGTCTGAATGTTTTACAGAATCGATCGGGATAACACCATAAATCAAAAAATAAAG
194 TTAGAAATCATGTCTGAAGGTTTTACAGAATCGATCGAAATAACACCACAAATCAAAAAATAAAA
*** * ** * * * *
5741482 AATTGATCGGGATAATATCATGAATCAAATTTATGCTCGGAGGTCTTAAAGATTATACCCGGATG
259 AATTGATCAAAACAATATCACAAATCAAATTTATGCCCGGAGGTCTTAAAAATTATACCCGAAGG
* * * ** *
5741547 TCTTAGAAATAATATCTGAAGGTTTTACAAAATCGACCGGCGATAACATCGC
324 TCTTAAAAATAATATCTGAAGGTCTTACAAAATCAACC-GAAATAACATCAC
* *
5741599 AAGTCAAAAAATAAAAAATTGATTAGGACAACACTGTGAATCAAAATTATGCCTGAAGATCTTAG
1 AAGTCAAAAAATAAAAAATTGATTAGGACAACACTGCGAATCAAAATTATACCTGAAGATCTTAG
** * * * *
5741664 AAATCATGCTCG-GGGTCTTACAGAATCGAT-TGGAATAACACCGTAAATCAAAAAATAAAGAAT
66 AAATCATGCTCGAAAGTCTTACAGAATCAATCAGG-ATAACAACGCAAATCAAAAAATAAAGAAT
* * * * * * ****
5741727 CGATTGGGACAATACCGCGAATCAAAATTATACTC-AGAGGTCTTAAAGATTATGTTTGAAGGTC
130 CAATTGGGACAACACCGCGAATCAAAATTATAC-CAAAAAGTCTTAAAAATTAAGCCCCAAGGTC
* * * * * *
5741791 TTAGAAATTATGTCT-AGAGGTTTTATAGAATTGATCGAAATAACACCGCAAGTCGAAAAATAAA
194 TTAGAAATCATGTCTGA-AGGTTTTACAGAATCGATCGAAATAACACCACAAATCAAAAAATAAA
* * *
5741855 AAATTGATTAAAACAATATCGCAAATCGAAA-TTATGCCCGGAGGTCTTAAAAATTATGCCCGAA
258 AAATTGATCAAAACAATATCACAAATC-AAATTTATGCCCGGAGGTCTTAAAAATTATACCCGAA
* * * * * *
5741919 GGTCTTAAAAATCATGTTTGAAGGTCTTACAGAATTAACCGAAATAACATCAT
322 GGTCTTAAAAATAATATCTGAAGGTCTTACAAAATCAACCGAAATAACATCAC
* * * ** * *
5741972 AAGTTAAAAAATAAAGAATTGA-TCGAGACAACACCACGAATCGAAATTATACCTGAAGGTCTTA
1 AAGTCAAAAAATAAAAAATTGATTAG-GACAACACTGCGAATCAAAATTATACCTGAAGATCTTA
* *
5742036 -AAGATTATGCTTGAAAGT
65 GAA-ATCATGCTCGAAAGT
5742054 TTTAGAAATC
Statistics
Matches: 364, Mismatches: 82, Indels: 19
0.78 0.18 0.04
Matches are distributed among these distances:
372 4 0.01
373 72 0.20
374 216 0.59
375 70 0.19
376 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (374 bp):
AAGTCAAAAAATAAAAAATTGATTAGGACAACACTGCGAATCAAAATTATACCTGAAGATCTTAG
AAATCATGCTCGAAAGTCTTACAGAATCAATCAGGATAACAACGCAAATCAAAAAATAAAGAATC
AATTGGGACAACACCGCGAATCAAAATTATACCAAAAAGTCTTAAAAATTAAGCCCCAAGGTCTT
AGAAATCATGTCTGAAGGTTTTACAGAATCGATCGAAATAACACCACAAATCAAAAAATAAAAAA
TTGATCAAAACAATATCACAAATCAAATTTATGCCCGGAGGTCTTAAAAATTATACCCGAAGGTC
TTAAAAATAATATCTGAAGGTCTTACAAAATCAACCGAAATAACATCAC
Found at i:5742039 original size:264 final size:263
Alignment explanation
Indices: 5741641--5742153 Score: 598
Period size: 264 Copynumber: 1.9 Consensus size: 263
5741631 ACTGTGAATC
* * * * ** *
5741641 AAAATTATGCCTGAAGATCTTAGAAATCATGCTCGGGGTCTTACAGAATCGATTGGAATAACACC
1 AAAATTATGCCCGAAGATCTTAAAAATCATGCTCGAGGTCTTACAGAATCAACCGAAATAACACC
* * * * *
5741706 GTAAATCAAAAAATAAAGAATCGATTGGGACAATACCGCGAATCAAAATTATACTCAGAGGTCTT
66 ATAAATCAAAAAATAAAGAATCGATCGAGACAACACCACGAATCAAAATTATACTCAGAGGTCTT
* * * ** * * *
5741771 AAAGATTATGTTTGAAGGTCTTAGAAATTATGTCTAGAGGTTTTATAGAATTGA-TCGAAATAAC
131 AAAGATTATGCTTGAAAGTCTTAGAAATCATACCTAGAGATCTTATAAAATTGACT-GAAATAAC
* * * *
5741835 ACCGCAAGTCGAAAAATAAAAAATTGATTAAAACAATATCGCAAATCGAAATTATGCCCGGAGGT
195 ACCGCAAGTCAAAAAATAAAAAATCGATTAAAACAACATCGCAAATCAAAATTATGCCCGGAGGT
5741900 CTTA
260 CTTA
* * * * *
5741904 AAAATTATGCCCGAAGGTCTTAAAAATCATGTTTGAAGGTCTTACAGAATTAACCGAAATAACAT
1 AAAATTATGCCCGAAGATCTTAAAAATCATGCTCG-AGGTCTTACAGAATCAACCGAAATAACAC
* * * * *
5741969 CATAAGTTAAAAAATAAAGAATTGATCGAGACAACACCACGAATCGAAATTATAC-CTGAAGGTC
65 CATAAATCAAAAAATAAAGAATCGATCGAGACAACACCACGAATCAAAATTATACTCAG-AGGTC
* * **
5742033 TTAAAGATTATGCTTGAAAGTTTTAGAAATCATACCTGGAGATCTTATAAAATTGACTGGGATAA
129 TTAAAGATTATGCTTGAAAGTCTTAGAAATCATACCTAGAGATCTTATAAAATTGACTGAAATAA
* * ** *
5742098 CACCGTAAGTCAAAAAATAAAGAATCGATTAGGATAACATCGCAAATCAAAATTAT
194 CACCGCAAGTCAAAAAATAAAAAATCGATTAAAACAACATCGCAAATCAAAATTAT
5742154 ATCCGAAAAT
Statistics
Matches: 204, Mismatches: 43, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
263 32 0.16
264 171 0.84
265 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (263 bp):
AAAATTATGCCCGAAGATCTTAAAAATCATGCTCGAGGTCTTACAGAATCAACCGAAATAACACC
ATAAATCAAAAAATAAAGAATCGATCGAGACAACACCACGAATCAAAATTATACTCAGAGGTCTT
AAAGATTATGCTTGAAAGTCTTAGAAATCATACCTAGAGATCTTATAAAATTGACTGAAATAACA
CCGCAAGTCAAAAAATAAAAAATCGATTAAAACAACATCGCAAATCAAAATTATGCCCGGAGGTC
TTA
Found at i:5742167 original size:132 final size:132
Alignment explanation
Indices: 5741644--5742160 Score: 461
Period size: 132 Copynumber: 3.9 Consensus size: 132
5741634 GTGAATCAAA
* * * * * *
5741644 ATTATGCCTGAAGATCTTAGAAATCATG-CTCGG-GGTCTTACAGAATCGATTGGAATAACACCG
1 ATTATGCTTGAAGGTCTTAGAAATCATGTCT-GGAGGTCTTATAGAATTGACTGAAATAACACCG
* * * * *
5741707 TAAATCAAAAAATAAAGAATCGATTGGGACAATACCGCGAATCAAAATTATACTCAG-AGGTCTT
65 TAAGTCAAAAAATAAAGAATCGATTAGGACAACACCGCAAATCAAAATTATA-TCCGAAGGTCTT
5741771 AAAG
129 AAAG
* * * *
5741775 ATTATGTTTGAAGGTCTTAGAAATTATGTCTAGAGGTTTTATAGAATTGA-TCGAAATAACACCG
1 ATTATGCTTGAAGGTCTTAGAAATCATGTCTGGAGGTCTTATAGAATTGACT-GAAATAACACCG
* * * * ** * * * ** *
5741839 CAAGTCGAAAAATAAAAAATTGATTAAAACAATATCGCAAATCGAAATTATGCCCGGAGGTCTTA
65 TAAGTCAAAAAATAAAGAATCGATTAGGACAACACCGCAAATCAAAATTATATCCGAAGGTCTTA
*
5741904 AAA
130 AAG
** * * * * * * * *
5741907 ATTATGCCCGAAGGTCTTAAAAATCATGTTTGAAGGTCTTACAGAATTAACCGAAATAACATCAT
1 ATTATGCTTGAAGGTCTTAGAAATCATGTCTGGAGGTCTTATAGAATTGACTGAAATAACACCGT
* * * * * *
5741972 AAGTTAAAAAATAAAGAATTGA-TCGAGACAACACCACGAATCGAAATTATA-CCTGAAGGTCTT
66 AAGTCAAAAAATAAAGAATCGATTAG-GACAACACCGCAAATCAAAATTATATCC-GAAGGTCTT
5742035 AAAG
129 AAAG
* * ** * * **
5742039 ATTATGCTTGAAAGTTTTAGAAATCATACCTGGAGATCTTATAAAATTGACTGGGATAACACCGT
1 ATTATGCTTGAAGGTCTTAGAAATCATGTCTGGAGGTCTTATAGAATTGACTGAAATAACACCGT
* *
5742104 AAGTCAAAAAATAAAGAATCGATTAGGATAACATCGCAAATCAAAATTATATCCGAA
66 AAGTCAAAAAATAAAGAATCGATTAGGACAACACCGCAAATCAAAATTATATCCGAA
5742161 AATCTTACAG
Statistics
Matches: 299, Mismatches: 78, Indels: 17
0.76 0.20 0.04
Matches are distributed among these distances:
131 31 0.10
132 264 0.88
133 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (132 bp):
ATTATGCTTGAAGGTCTTAGAAATCATGTCTGGAGGTCTTATAGAATTGACTGAAATAACACCGT
AAGTCAAAAAATAAAGAATCGATTAGGACAACACCGCAAATCAAAATTATATCCGAAGGTCTTAA
AG
Found at i:5742527 original size:106 final size:105
Alignment explanation
Indices: 5742297--5742556 Score: 271
Period size: 106 Copynumber: 2.5 Consensus size: 105
5742287 CTTGGAGGTC
* * * * *
5742297 TTAAAGATTATGCTCAGAGGTCTTATAAATCTCAAAATCTTTGAATGCT-C-TTAATCAGAGGCA
1 TTAAAGATTATGTTCAGAGGTCTTAAAAATCTTAAAATCTTTGAATGCTCCTTTAATCAAAGACA
* * ** * *
5742360 ATGAAACTTTAAAATTTTAAAAAATTTTTGTTATGAGGTC
66 ATAAAACTTTAAAAATTTAAAAAATTTTTGCCATGAAGTA
* * * * *
5742400 TTAGAGATCATGTCCAAAGGTCTTACAAATCTTAAAATCTTTGAATGCTCCTATTAATCAAAGAC
1 TTAAAGATTATGTTCAGAGGTCTTAAAAATCTTAAAATCTTTGAATGCTCCT-TTAATCAAAGAC
*
5742465 AATAAAACTTTAAAAATTT-AAAATTCTTTTGCCCA-GAAGTA
65 AATAAAACTTTAAAAATTTAAAAAAT-TTTTG-CCATGAAGTA
* *
5742506 TTGAAAG-TTATGTTCAGAGGTCTTAAAAATTTTAAAATCTTTAAATG-TCCT
1 TT-AAAGATTATGTTCAGAGGTCTTAAAAATCTTAAAATCTTTGAATGCTCCT
5742557 CCCAATCAAA
Statistics
Matches: 128, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
103 42 0.33
104 1 0.01
105 9 0.07
106 72 0.56
107 4 0.03
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (105 bp):
TTAAAGATTATGTTCAGAGGTCTTAAAAATCTTAAAATCTTTGAATGCTCCTTTAATCAAAGACA
ATAAAACTTTAAAAATTTAAAAAATTTTTGCCATGAAGTA
Found at i:5747665 original size:13 final size:13
Alignment explanation
Indices: 5747647--5747676 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5747637 ATAGGGGCAA
5747647 TAAGGTAGTTTTC
1 TAAGGTAGTTTTC
*
5747660 TAAGGTAGTTTTT
1 TAAGGTAGTTTTC
5747673 TAAG
1 TAAG
5747677 AACAATGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (13 bp):
TAAGGTAGTTTTC
Found at i:5751069 original size:15 final size:15
Alignment explanation
Indices: 5751051--5751091 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
5751041 GTTTTTAGAA
5751051 TTTTGGATTTTAAGG
1 TTTTGGATTTTAAGG
5751066 TTTTGGATTTTAAGG
1 TTTTGGATTTTAAGG
*
5751081 TTTGGGATTTT
1 TTTTGGATTTT
5751092 GAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (15 bp):
TTTTGGATTTTAAGG
Found at i:5751236 original size:14 final size:14
Alignment explanation
Indices: 5751194--5751243 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
5751184 AGGTTTGAAA
5751194 TTTTGATTTTAGGG
1 TTTTGATTTTAGGG
*
5751208 TTTAAAAGA-TTTAGGG
1 TTT---TGATTTTAGGG
5751224 TTTTGATTTTAGGG
1 TTTTGATTTTAGGG
5751238 TTTTGA
1 TTTTGA
5751244 GGGTGTATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.07
14 16 0.53
16 10 0.33
17 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTTGATTTTAGGG
Found at i:5751256 original size:30 final size:30
Alignment explanation
Indices: 5751194--5751275 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
5751184 AGGTTTGAAA
* * *
5751194 TTTTGATTTTAGGGTTTAAAAGATTTAGGG
1 TTTTGATTTTAGGGTTTAGAGGATGTAGGG
* * *
5751224 TTTTGATTTTAGGGTTTTGAGGGTGTATGG
1 TTTTGATTTTAGGGTTTAGAGGATGTAGGG
*
5751254 -TTTCATTTTTAGGGTTTAGAGG
1 TTTTGA-TTTTAGGGTTTAGAGG
5751276 TTTGGGGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 4 0.09
30 39 0.91
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (30 bp):
TTTTGATTTTAGGGTTTAGAGGATGTAGGG
Found at i:5751671 original size:14 final size:12
Alignment explanation
Indices: 5751647--5751698 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
5751637 CGGTCTTCTG
*
5751647 TTTTTTCTGTTT
1 TTTTTTTTGTTT
5751659 CTATTTTTTTGTTT
1 -T-TTTTTTTGTTT
5751673 TTTTTTTT-TGTT
1 TTTTTTTTGT-TT
5751685 TTTTTTTTGTTT
1 TTTTTTTTGTTT
5751697 TT
1 TT
5751699 CTAATTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 1 0.03
12 21 0.60
13 3 0.09
14 10 0.29
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:5751678 original size:11 final size:11
Alignment explanation
Indices: 5751662--5751698 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
5751652 TCTGTTTCTA
*
5751662 TTTTTTTGTT-
1 TTTTTTTTTTG
5751672 TTTTTTTTTTG
1 TTTTTTTTTTG
5751683 TTTTTTTTTTG
1 TTTTTTTTTTG
5751694 TTTTT
1 TTTTT
5751699 CTAATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:5751678 original size:13 final size:13
Alignment explanation
Indices: 5751647--5751692 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5751637 CGGTCTTCTG
*
5751647 TTTTTTCTGTTTCT
1 TTTTTTTTGTTT-T
*
5751661 ATTTTTTTGTTTT
1 TTTTTTTTGTTTT
5751674 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
5751687 TTTTTT
1 TTTTTT
5751693 GTTTTTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.02, C:0.04, G:0.07, T:0.87
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:5757075 original size:16 final size:15
Alignment explanation
Indices: 5757047--5757091 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5757037 AAAATTAGTT
5757047 ATTATTGATTAAAATG
1 ATTATT-ATTAAAATG
*
5757063 ATTTATTATTAAAATT
1 A-TTATTATTAAAATG
*
5757079 ATTAATATTAAAA
1 ATTATTATTAAAA
5757092 AATAGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
ATTATTATTAAAATG
Found at i:5757087 original size:52 final size:49
Alignment explanation
Indices: 5757030--5757138 Score: 132
Period size: 52 Copynumber: 2.2 Consensus size: 49
5757020 TAACTATTAA
* * *
5757030 AATATTAAAAATTAGTTATTATTGATTAAAATGAT-TTATTATTAAAATTATT
1 AATATTAAAAAATAGTTA-TATT--TTAAAATAATATTAATATTAAAA-TATT
5757082 AATATTAAAAAATAGTTATATTTTAAAATAATAATTAATATTAAAATATT
1 AATATTAAAAAATAGTTATATTTTAAAATAAT-ATTAATATTAAAATATT
5757132 -ATATTAA
1 AATATTAA
5757139 TATTAAACAC
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
49 16 0.31
50 4 0.08
51 15 0.29
52 17 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (49 bp):
AATATTAAAAAATAGTTATATTTTAAAATAATATTAATATTAAAATATT
Found at i:5757092 original size:16 final size:17
Alignment explanation
Indices: 5757030--5757145 Score: 74
Period size: 18 Copynumber: 6.5 Consensus size: 17
5757020 TAACTATTAA
5757030 AATATTAAAAATTAGTT
1 AATATTAAAAATTAGTT
* * *
5757047 ATTATTGATTAAAATGATTT
1 AATATT-A--AAAATTAGTT
*
5757067 ATTATT-AAAATTA-TT
1 AATATTAAAAATTAGTT
*
5757082 AATATTAAAAAATAGTT
1 AATATTAAAAATTAGTT
* * *
5757099 ATATTTTAAAATAATAATT
1 A-ATATTAAAA-ATTAGTT
*
5757118 AATATTAAAATATTATATT
1 AATATTAAAA-ATTA-GTT
5757137 AATATTAAA
1 AATATTAAA
5757146 CACTTAAAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.09
16 12 0.15
17 8 0.10
18 21 0.26
19 19 0.23
20 14 0.17
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AATATTAAAAATTAGTT
Found at i:5757107 original size:18 final size:18
Alignment explanation
Indices: 5757079--5757145 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
5757069 TATTAAAATT
5757079 ATTAATATTAAAA-AATA
1 ATTAATATTAAAATAATA
* *
5757096 GTTATATTTTAAAATAATA
1 ATTA-ATATTAAAATAATA
*
5757115 ATTAATATTAAAATATTA
1 ATTAATATTAAAATAATA
5757133 TATTAATATTAAA
1 -ATTAATATTAAA
5757146 CACTTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 3 0.07
18 20 0.48
19 19 0.45
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTAATATTAAAATAATA
Found at i:5757134 original size:33 final size:31
Alignment explanation
Indices: 5757045--5757137 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 31
5757035 TAAAAATTAG
*
5757045 TTATTATTGATTAAAATGATT-TATTATTAAAA
1 TTATTAAT-ATTAAAAT-ATTATATTATTAAAA
5757077 TTATTAATATTAAAAAATAGTTATATT-TTAAAA
1 TTATTAATATT--AAAATA-TTATATTATTAAAA
5757110 TAATAATTAATATTAAAATATTATATTA
1 T--T-ATTAATATTAAAATATTATATTA
5757138 ATATTAAACA
Statistics
Matches: 52, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
31 3 0.06
32 8 0.15
33 21 0.40
34 10 0.19
35 1 0.02
36 9 0.17
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
TTATTAATATTAAAATATTATATTATTAAAA
Found at i:5757219 original size:20 final size:20
Alignment explanation
Indices: 5757194--5757231 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5757184 TTAAACTATT
*
5757194 TAAAATAGTATTACTATTCC
1 TAAAATACTATTACTATTCC
*
5757214 TAAAATACTATTTCTATT
1 TAAAATACTATTACTATT
5757232 AATATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAAATACTATTACTATTCC
Found at i:5757443 original size:18 final size:18
Alignment explanation
Indices: 5757422--5757460 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5757412 TTAGATTGGA
* *
5757422 AAATATTTTTAAATTATT
1 AAATATATTCAAATTATT
*
5757440 AAATATATTCATATTATT
1 AAATATATTCAAATTATT
5757458 AAA
1 AAA
5757461 ATAATAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATATATTCAAATTATT
Found at i:5760867 original size:3 final size:3
Alignment explanation
Indices: 5760859--5760918 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5760849 AATCACATCT
5760859 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5760907 ATA ATA ATA ATA
1 ATA ATA ATA ATA
5760919 CTTTTAAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5761300 original size:2 final size:2
Alignment explanation
Indices: 5761293--5761359 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
5761283 TACCCATCAC
*
5761293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5761335 TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5761360 TTATCAAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5767463 original size:21 final size:23
Alignment explanation
Indices: 5767439--5767488 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
5767429 TTCATCTTTT
5767439 AACAATGAAAGAG-AAAAATT-A
1 AACAATGAAAGAGTAAAAATTCA
*
5767460 AACAA-GATAGAGTAAAAATTCCA
1 AACAATGAAAGAGTAAAAATT-CA
5767483 AACAAT
1 AACAAT
5767489 TAGTAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
23 6 0.25
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (23 bp):
AACAATGAAAGAGTAAAAATTCA
Found at i:5771167 original size:13 final size:13
Alignment explanation
Indices: 5771136--5771182 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
5771126 TAAATGATTC
*
5771136 ATAAATTCAATT-
1 ATAAATTAAATTA
5771148 A-AAATTAAATTA
1 ATAAATTAAATTA
5771160 ATAAATTAAATTA
1 ATAAATTAAATTA
*
5771173 ATAATTTAAA
1 ATAAATTAAA
5771183 AAATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 20 0.65
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAATTAAATTA
Found at i:5771291 original size:13 final size:14
Alignment explanation
Indices: 5771262--5771288 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5771252 GAATTTAAAA
5771262 AAAAAATTAAATCC
1 AAAAAATTAAATCC
5771276 AAAAAATTAAATC
1 AAAAAATTAAATC
5771289 AAATTGGGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAATTAAATCC
Found at i:5774559 original size:27 final size:27
Alignment explanation
Indices: 5774528--5774586 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
5774518 AATTGTTAAA
* * *
5774528 ATATTAAAAATTATTTATTATTAAAGT
1 ATATTAAAAATGATTTATCATTAAAAT
*
5774555 ATATT-GAAATGATTTATCATTAAAAT
1 ATATTAAAAATGATTTATCATTAAAAT
5774581 -TATTAA
1 ATATTAA
5774587 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 4 0.15
26 17 0.65
27 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (27 bp):
ATATTAAAAATGATTTATCATTAAAAT
Found at i:5774629 original size:19 final size:20
Alignment explanation
Indices: 5774607--5774649 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5774597 TAGTTATATT
5774607 TTAAAAATAATA-ATTAAAA
1 TTAAAAATAATATATTAAAA
* *
5774626 TT-AAAATATTATATTAATA
1 TTAAAAATAATATATTAAAA
5774645 TTAAA
1 TTAAA
5774650 CACTTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 10 0.50
20 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAAATAATATATTAAAA
Found at i:5774646 original size:40 final size:41
Alignment explanation
Indices: 5774606--5774699 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
5774596 ATAGTTATAT
*
5774606 TTTAAA-A-ATAATAATTAAAATTAAAA-TATTATATTAATA
1 TTTAAACACATAA-AATAAAAATTAAAATTATTATATTAATA
* *
5774645 -TTAAACACTTAAAGTAAAAATTAAAATTATTATATTAATA
1 TTTAAACACATAAAATAAAAATTAAAATTATTATATTAATA
* *
5774685 -TAAAACACTTAAAAT
1 TTTAAACACATAAAAT
5774700 TGGTAGATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 5 0.11
39 13 0.28
40 29 0.62
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (41 bp):
TTTAAACACATAAAATAAAAATTAAAATTATTATATTAATA
Found at i:5789997 original size:13 final size:12
Alignment explanation
Indices: 5789955--5789997 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
5789945 TTTATTATTA
* *
5789955 TTTTTATTTCTT
1 TTTTTCTTTTTT
5789967 TTTTTCTTTTTT
1 TTTTTCTTTTTT
5789979 TCTTTTCTTTTTAT
1 T-TTTTCTTTTT-T
5789993 TTTTT
1 TTTTT
5789998 TGGTAGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 14 0.52
14 2 0.07
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:5791801 original size:16 final size:16
Alignment explanation
Indices: 5791772--5791812 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5791762 ATGGCCCATT
5791772 TTATTTTTA-GTTTTA
1 TTATTTTTATGTTTTA
*
5791787 TTATTTTTATTTTTTA
1 TTATTTTTATGTTTTA
5791803 TTATTTTTAT
1 TTATTTTTAT
5791813 ATATTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTTTATGTTTTA
Found at i:5791806 original size:3 final size:3
Alignment explanation
Indices: 5791784--5792002 Score: 68
Period size: 3 Copynumber: 70.7 Consensus size: 3
5791774 ATTTTTAGTT
* * *
5791784 TTA TTA TTT TTA TT- TT- TTA TTA TTT TTA TATA TT- TATA TCTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA T-TA TTA
* * * *
5791829 ATA -TA TATA TTT TTA TTA GTTA TCCA TTA ATA TTA TT- TT- TTA TTA
1 TTA TTA T-TA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA
5791874 TTTA TCTA TTAA TGTA -TA TT- TT- TTA -TA CTTA TCTA TTA TTA TTA
1 -TTA T-TA TT-A T-TA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA
* * * *
5791918 TTT TTA TTTA TCTA TTA ATA TT- TTT TTA -TA TCTA TCGA TTAA TGTA
1 TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA T-TA T-TA TT-A T-TA
5791964 -TA TATA TTA TTA TCTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
5792003 TTTGGGTTGG
Statistics
Matches: 169, Mismatches: 19, Indels: 56
0.69 0.08 0.23
Matches are distributed among these distances:
2 25 0.15
3 93 0.55
4 49 0.29
5 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5791868 original size:58 final size:55
Alignment explanation
Indices: 5791801--5791937 Score: 156
Period size: 54 Copynumber: 2.5 Consensus size: 55
5791791 TTTTATTTTT
*
5791801 TATTATTTTTATA-TATTTATATCTAATAATATATATATTTTTATTAGTTATCCATTAA
1 TATTATTTTTATATTA-TT-TATCTAATAATATATAT-TTTTTA-TACTTATCCATTAA
* * * *
5791859 TATTATTTTT-TATTATTTATCTATTAATGTATATTTTTTATACTTATCTATTAT
1 TATTATTTTTATATTATTTATCTAATAATATATATTTTTTATACTTATCCATTAA
*
5791913 TATTATTTTTAT-TTATCTAT-TAATA
1 TATTATTTTTATATTATTTATCTAATA
5791938 TTTTTTTATA
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
53 4 0.06
54 28 0.40
55 7 0.10
56 15 0.21
57 4 0.06
58 12 0.17
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (55 bp):
TATTATTTTTATATTATTTATCTAATAATATATATTTTTTATACTTATCCATTAA
Found at i:5791869 original size:27 final size:25
Alignment explanation
Indices: 5791801--5791990 Score: 131
Period size: 27 Copynumber: 7.3 Consensus size: 25
5791791 TTTTATTTTT
*
5791801 TATTATTTTTATATATTTATATCTAATAA
1 TATTATTTTT-TATA--T-TATCTATTAA
*
5791830 TATATATATTTTTATTAGTTATCCATTAA
1 TAT-TAT-TTTTTA-TA-TTATCTATTAA
5791859 TATTATTTTTTATTATTTATCTATTAA
1 TATTATTTTTTA-TA-TTATCTATTAA
* *
5791886 TGTATATTTTTTATACTTATCTATTAT
1 TAT-TATTTTTTATA-TTATCTATTAA
5791913 TATTA-TTTTTAT-TTATCTATTAA
1 TATTATTTTTTATATTATCTATTAA
*
5791936 TA-T-TTTTTTATATCTATCGATTAA
1 TATTATTTTTTATAT-TATCTATTAA
* * * *
5791960 T-GTA-TATATATTATTATCTATTAT
1 TATTATTTTTTA-TATTATCTATTAA
5791984 TATTATT
1 TATTATT
5791991 ATTATTATTA
Statistics
Matches: 133, Mismatches: 16, Indels: 27
0.76 0.09 0.15
Matches are distributed among these distances:
22 8 0.06
23 13 0.10
24 24 0.18
25 12 0.09
26 3 0.02
27 35 0.26
28 12 0.09
29 14 0.11
30 6 0.05
31 6 0.05
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTATTTTTTATATTATCTATTAA
Found at i:5791939 original size:20 final size:20
Alignment explanation
Indices: 5791889--5791952 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 20
5791879 CTATTAATGT
5791889 ATATTTTTTATACTTATCTATTA
1 ATATTTTTT-TA--TATCTATTA
*
5791912 TTATTATTTTTATTTATCTATTA
1 ATATT-TTTTTA--TATCTATTA
5791935 ATATTTTTTTATATCTAT
1 ATATTTTTTTATATCTAT
5791953 CGATTAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.19
22 6 0.16
23 20 0.54
24 4 0.11
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTTTTTATATCTATTA
Found at i:5791959 original size:74 final size:74
Alignment explanation
Indices: 5791836--5791996 Score: 202
Period size: 71 Copynumber: 2.2 Consensus size: 74
5791826 ATAATATATA
* * * * * *
5791836 TATTTTTATTAGTTATCCATTAATATTATTTTTTATTATTTATCTATTAATGTATATTTTTTATA
1 TATTATTATTATTTATCCATTAATATTATTTTTTATTATCTATCGATTAATGTATA-TATAT-TA
5791901 CTTATCTATTAT
64 -TTATCTATTAT
* *
5791913 TATTATTTTTATTTATCTATTAATA-T-TTTTTTA-TATCTATCGATTAATGTATATATATTATT
1 TATTATTATTATTTATCCATTAATATTATTTTTTATTATCTATCGATTAATGTATATATATTATT
5791975 ATCTATTAT
66 ATCTATTAT
5791984 TATTATTATTATT
1 TATTATTATTATT
5791997 ATTATTTTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
71 23 0.31
72 2 0.03
73 3 0.04
74 18 0.24
75 7 0.09
76 1 0.01
77 21 0.28
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (74 bp):
TATTATTATTATTTATCCATTAATATTATTTTTTATTATCTATCGATTAATGTATATATATTATT
ATCTATTAT
Found at i:5791999 original size:74 final size:76
Alignment explanation
Indices: 5791810--5791999 Score: 212
Period size: 74 Copynumber: 2.5 Consensus size: 76
5791800 TTATTATTTT
* * *
5791810 TATATATTTA-TATCTAATAATATATATATTTTTATTAGTTATCCATTAATATTATTTTTTATTA
1 TATATATTTATTATCT-ATTAT-TAT-TATTATTATTATTTATCCATTAATATTATTTTTTATTA
* *
5791874 TTTATCTATTAATG
63 TCTATCGATTAATG
* *
5791888 TATAT-TTT-TTATACTTATCTATTATTATTATTTTTATTTATCTATTAATA-T-TTTTTTA-TA
1 TATATATTTATTAT-C-TAT-TATTATTATTATTATTATTTATCCATTAATATTATTTTTTATTA
5791948 TCTATCGATTAATG
63 TCTATCGATTAATG
5791962 TATATATATTATTATCTATTATTATTATTATTATTATT
1 TATATAT-TTATTATCTATTATTATTATTATTATTATT
5792000 ATTTTTGGGT
Statistics
Matches: 97, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
74 37 0.38
75 11 0.11
76 4 0.04
77 31 0.32
78 11 0.11
79 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (76 bp):
TATATATTTATTATCTATTATTATTATTATTATTATTTATCCATTAATATTATTTTTTATTATCT
ATCGATTAATG
Found at i:5792002 original size:77 final size:79
Alignment explanation
Indices: 5791810--5792003 Score: 217
Period size: 77 Copynumber: 2.5 Consensus size: 79
5791800 TTATTATTTT
* * * *
5791810 TATATATTTA-TATCTAATAATA-TATATATTTTTATTAGTTATCCATTAATATTATTTTTTATT
1 TATATATTTATTATCTATTATTATTAT-TATTATTATTATTTATCCATTAATATTATTTTTTATT
* *
5791873 ATTTATCTATTAATG
65 ATCTATCGATTAATG
* *
5791888 TATAT-TTT-TTA--TACTTATCTATTATTATTATTTTTATTTATCTATTAATA-T-TTTTTTA-
1 TATATATTTATTATCTA-TTAT-TATTATTATTATTATTATTTATCCATTAATATTATTTTTTAT
5791946 TATCTATCGATTAATG
64 TATCTATCGATTAATG
5791962 TATATATATTATTATCTATTATTATTATTATTATTATTATTT
1 TATATAT-TTATTATCTATTATTATTATTATTATTATTATTT
5792004 TTGGGTTGGT
Statistics
Matches: 98, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
74 19 0.19
75 10 0.10
76 5 0.05
77 50 0.51
78 12 0.12
79 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (79 bp):
TATATATTTATTATCTATTATTATTATTATTATTATTATTTATCCATTAATATTATTTTTTATTA
TCTATCGATTAATG
Found at i:5792845 original size:3 final size:3
Alignment explanation
Indices: 5792839--5792881 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
5792829 AAGTTTTTTT
*
5792839 TTA TTA TTA TTA TTA TT- TCT- TTT TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
5792882 TATTGATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:5792861 original size:26 final size:26
Alignment explanation
Indices: 5792832--5792882 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5792822 TGTTCCAAAG
*
5792832 TTTTTTTTTATTATTATTATTATTTC
1 TTTTTTATTATTATTATTATTATTTC
5792858 TTTTTTATTATTATTATTATTATTT
1 TTTTTTATTATTATTATTATTATTT
5792883 ATTGATTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTATTATTATTATTATTATTTC
Found at i:5792865 original size:23 final size:23
Alignment explanation
Indices: 5792835--5792878 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5792825 TCCAAAGTTT
5792835 TTTTTTATTATTATTATTATTTC
1 TTTTTTATTATTATTATTATTTC
5792858 TTTTTTATTATTATTATTATT
1 TTTTTTATTATTATTATTATT
5792879 ATTTATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTTATTATTATTATTATTTC
Found at i:5792890 original size:23 final size:23
Alignment explanation
Indices: 5792841--5792890 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5792831 GTTTTTTTTT
* *
5792841 ATTATTATTATTATTTCTTTTTT
1 ATTATTATTATTATTTCTTATTG
5792864 ATTATTATTATTATTAT-TTATTG
1 ATTATTATTATTATT-TCTTATTG
5792887 ATTA
1 ATTA
5792891 GATTAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
ATTATTATTATTATTTCTTATTG
Found at i:5792923 original size:5 final size:5
Alignment explanation
Indices: 5792913--5792973 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
5792903 TTAGTACTCC
*
5792913 TTATT TTA-T TT-TT TTATTT TTATTT TTATTT TTATC TTATT TTATT
1 TTATT TTATT TTATT TTA-TT TTA-TT TTA-TT TTATT TTATT TTATT
5792959 TTA-T TT-TT TTATT TT
1 TTATT TTATT TTATT TT
5792974 CTTTAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
4 12 0.24
5 20 0.41
6 17 0.35
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:5792932 original size:6 final size:6
Alignment explanation
Indices: 5792913--5792973 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
5792903 TTAGTACTCC
* *
5792913 TTATTT TATTTTT TTATTT TTATTT TTATTT TTA-TC TTA-TT TTATTT
1 TTATTT T-TATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
5792960 TATTTTT TTATTT T
1 T-TATTT TTATTT T
5792974 CTTTAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
5 8 0.17
6 28 0.61
7 10 0.22
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:5792957 original size:10 final size:9
Alignment explanation
Indices: 5792913--5792978 Score: 59
Period size: 8 Copynumber: 7.3 Consensus size: 9
5792903 TTAGTACTCC
5792913 TTATTTTAT
1 TTATTTTAT
5792922 TT-TTTTAT
1 TTATTTTAT
5792930 TT-TTATT-T
1 TTATT-TTAT
5792938 TTATTTTTAT
1 TTA-TTTTAT
5792948 CTTATTTTATT
1 -TTATTTTA-T
5792959 TTATTTT-T
1 TTATTTTAT
*
5792967 TTATTTTCT
1 TTATTTTAT
5792976 TTA
1 TTA
5792979 AATAAATTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
8 21 0.42
9 10 0.20
10 15 0.30
11 4 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTAT
Found at i:5793075 original size:59 final size:57
Alignment explanation
Indices: 5792981--5793149 Score: 182
Period size: 59 Copynumber: 2.9 Consensus size: 57
5792971 TTTCTTTAAA
* * *
5792981 TAAA-TTTCCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTTAAAA-
1 TAAAGTTT-CAAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTAAAAAT
** * *
5793038 TAATTTTTTAAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAAAAAT
1 TAAAGTTTCAAAAAAA---TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTAAAAAT
*
5793098 TAAAGTTTCAAAAAAATATTTTG-GGAAAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAGTTTCAAAAAAATTTTTTGAGG--AAAAGTTGAAAGTATCAATTTTTCT
5793150 TGTACAAAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
56 2 0.02
57 16 0.17
58 27 0.29
59 35 0.37
60 14 0.15
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.38
Consensus pattern (57 bp):
TAAAGTTTCAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTAAAAAT
Found at i:5803632 original size:11 final size:10
Alignment explanation
Indices: 5803628--5803679 Score: 61
Period size: 10 Copynumber: 4.9 Consensus size: 10
5803618 AAAAAATGAA
5803628 AAAAATAAAATG
1 AAAAA-AAAA-G
5803640 AAAATAAAAAG
1 AAAA-AAAAAG
5803651 -AAAAAAAAG
1 AAAAAAAAAG
5803660 AAAATAAAAAG
1 AAAA-AAAAAG
5803671 AAAAAAAAA
1 AAAAAAAAA
5803680 AGTGAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.16
10 11 0.30
11 11 0.30
12 8 0.22
13 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5803649 original size:20 final size:20
Alignment explanation
Indices: 5803616--5803678 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
5803606 ACTATGCTTG
*
5803616 AAAA-AAAATGAAAAA-AATA
1 AAAAGAAAAT-AAAAAGAAAA
*
5803635 AAATGAAAATAAAAAGAAAA
1 AAAAGAAAATAAAAAGAAAA
5803655 AAAAGAAAATAAAAAGAAAA
1 AAAAGAAAATAAAAAGAAAA
5803675 AAAA
1 AAAA
5803679 AAGTGAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAGAAAATAAAAAGAAAA
Found at i:5803680 original size:11 final size:11
Alignment explanation
Indices: 5803616--5803681 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
5803606 ACTATGCTTG
*
5803616 AAAAAAAATGAA
1 AAAAAAAAAG-A
5803628 AAAAATAAAATGA
1 AAAAA-AAAA-GA
*
5803641 AAATAAAAAG-
1 AAAAAAAAAGA
5803651 -AAAAAAAAGA
1 AAAAAAAAAGA
*
5803661 AAATAAAAAGA
1 AAAAAAAAAGA
5803672 AAAAAAAAAG
1 AAAAAAAAAG
5803682 TGAATGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
9 8 0.18
11 19 0.42
12 9 0.20
13 8 0.18
14 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.08
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:5804744 original size:41 final size:39
Alignment explanation
Indices: 5804699--5804995 Score: 200
Period size: 41 Copynumber: 7.1 Consensus size: 39
5804689 GATCGTCAAA
*
5804699 GAGCATTTACTTTTTCAAAGTTGTGATACCTCTATTTAGAG
1 GAGCATTTA-TTTTTCAAAGTTGTGA-ACCTCTGTTTAGAG
* * * **
5804740 GAGCAATGTACTTTTCAAAAGTCGTGGCGCCTCTGTTTAGAG
1 GAGC-ATTTATTTTTC-AAAGTTGT-GAACCTCTGTTTAGAG
* **
5804782 GAGCAATTTA-CTTTCAAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGC-ATTTATTTTTC-AAAGTTGT-GAACCTCTGTTTAGAG
* *
5804823 GAGCTTTGTTTATTTTTCAAAGTTGTTAAGCCTCTGTTTAGAG
1 GAGC---ATTTATTTTTCAAAGTTGTGAA-CCTCTGTTTAGAG
* * * *
5804866 GAGCCATTTATTTTCCAAAGTCGTTAAACCTCTGTTCAGAG
1 GAG-CATTTATTTTTCAAAGTTG-TGAACCTCTGTTTAGAG
* * **
5804907 GAGCCATTTATTTTTTTCAAAAGTCGTTGAGCCTCTAATTAGAG
1 GAG-CATTTA--TTTTTC-AAAGTTG-TGAACCTCTGTTTAGAG
* * *
5804951 GAACCATTTATTTTTCAAAGTTGTTGAGCCTCTGCTTAGAG
1 G-AGCATTTATTTTTCAAAGTTG-TGAACCTCTGTTTAGAG
5804992 GAGC
1 GAGC
5804996 TTTGATCAAA
Statistics
Matches: 211, Mismatches: 32, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
40 2 0.01
41 101 0.48
42 41 0.19
43 34 0.16
44 32 0.15
45 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (39 bp):
GAGCATTTATTTTTCAAAGTTGTGAACCTCTGTTTAGAG
Found at i:5804867 original size:84 final size:83
Alignment explanation
Indices: 5804710--5805001 Score: 277
Period size: 84 Copynumber: 3.5 Consensus size: 83
5804700 AGCATTTACT
* * ** ** ***
5804710 TTTTCAAAGTTG-TGATACCTCTATTTAGAGGAGCAATG-TACTTTTCAAAAGTCGTGGCGCCTC
1 TTTTCAAAGTTGTTGA-GCCTCTGTTTAGAGGAGCTTTGATTTTTTTCAAAAGTCGTTAAGCCTC
*
5804773 TGTTTAGAGGAGCAATTTA
65 TGTTTAGAGGAGCCATTTA
* * * * *
5804792 CTTTCAAAAGTTGTGGTGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTC-AAAGTTGTTAAGCCT
1 TTTTC-AAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTGATT-TTTTTCAAAAGTCGTTAAGCCT
5804856 CTGTTTAGAGGAGCCATTTA
64 CTGTTTAGAGGAGCCATTTA
* * * * *
5804876 TTTTCCAAAGTCGTTAAACCTCTGTTCAGAGGAGCCATTT-ATTTTTTTCAAAAGTCGTTGAGCC
1 TTTT-CAAAGTTGTTGAGCCTCTGTTTAGAGGAG-C-TTTGATTTTTTTCAAAAGTCGTTAAGCC
** *
5804940 TCTAATTAGAGGAACCATTTA
63 TCTGTTTAGAGGAGCCATTTA
*
5804961 TTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCTTTGAT
1 -TTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTGAT
5805002 CAAAATTTTA
Statistics
Matches: 168, Mismatches: 32, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
82 4 0.02
83 28 0.17
84 66 0.39
85 63 0.38
86 7 0.04
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (83 bp):
TTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTGATTTTTTTCAAAAGTCGTTAAGCCTCT
GTTTAGAGGAGCCATTTA
Found at i:5804961 original size:126 final size:125
Alignment explanation
Indices: 5804702--5804995 Score: 315
Period size: 126 Copynumber: 2.3 Consensus size: 125
5804692 CGTCAAAGAG
* *
5804702 CATTTACTTTTTCAAAGTTGTGATA-CCTCTATTTAGAGGAGCAATGTACTTTTCAAAAGTCGTG
1 CATTTA-TTTTTCAAAGTTGTTA-AGCCTCTGTTTAGAGGAGCAATGTACTTTTCAAAAGTCGTG
*** * * * ** *
5804766 GCGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTGTTTAGAGGAGCTT
64 AAACCTCTGTTCAGAGGAGCAATTTACTTTCAAAAGTCGTGGAGCCTCTAATTAGAGGAAC-T
** * * * *
5804829 TGTTTATTTTTCAAAGTTGTTAAGCCTCTGTTTAGAGGAGCCATTTA-TTTTCCAAAGTCGTTAA
1 CATTTATTTTTCAAAGTTGTTAAGCCTCTGTTTAGAGGAGCAATGTACTTTTCAAAAGTCGTGAA
* * *
5804893 ACCTCTGTTCAGAGGAGCCATTTATTTTTTTCAAAAGTCGTTGAGCCTCTAATTAGAGGAAC-
66 ACCTCTGTTCAGAGGAGCAATTTA---CTTTCAAAAGTCGTGGAGCCTCTAATTAGAGGAACT
* *
5804955 CATTTATTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGC
1 CATTTATTTTTCAAAGTTGTTAAGCCTCTGTTTAGAGGAGC
5804996 TTTGATCAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
125 35 0.25
126 72 0.52
127 4 0.03
128 28 0.20
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (125 bp):
CATTTATTTTTCAAAGTTGTTAAGCCTCTGTTTAGAGGAGCAATGTACTTTTCAAAAGTCGTGAA
ACCTCTGTTCAGAGGAGCAATTTACTTTCAAAAGTCGTGGAGCCTCTAATTAGAGGAACT
Found at i:5804963 original size:85 final size:85
Alignment explanation
Indices: 5804751--5805001 Score: 278
Period size: 85 Copynumber: 3.0 Consensus size: 85
5804741 AGCAATGTAC
* * * * * * *
5804751 TTTTCAAAAGTCGTGGCGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTG
1 TTTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCATTTATTTTCCAAAGTTGTTGAGCCTCTG
*
5804816 TTTAGAGGAG-CTTTGTTTAT
66 -TTAGAGGAGCCTTTGATTAT
* * * * *
5804836 TTTTC-AAAGTTGTTAAGCCTCTGTTTAGAGGAGCCATTTATTTTCCAAAGTCGTTAAACCTCTG
1 TTTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCATTTATTTTCCAAAGTTGTTGAGCCTCTG
5804900 TTCAGAGGAGCCATTT-ATT-T
66 TT-AGAGGAGCC-TTTGATTAT
** * *
5804920 TTTTCAAAAGTCGTTGAGCCTCTAATTAGAGGAACCATTTATTTTTCAAAGTTGTTGAGCCTCTG
1 TTTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCATTTATTTTCCAAAGTTGTTGAGCCTCTG
5804985 CTTAGAGGAG-CTTTGAT
66 -TTAGAGGAGCCTTTGAT
5805002 CAAAATTTTA
Statistics
Matches: 138, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
83 5 0.04
84 63 0.46
85 65 0.47
86 5 0.04
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (85 bp):
TTTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCCATTTATTTTCCAAAGTTGTTGAGCCTCTG
TTAGAGGAGCCTTTGATTAT
Found at i:5805193 original size:18 final size:17
Alignment explanation
Indices: 5805166--5805209 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5805156 AAAATGACCC
*
5805166 ATTTTATTTTTAGTTTT-
1 ATTTTTTTTTTA-TTTTA
5805183 ATTTTTTTTTTATTTTA
1 ATTTTTTTTTTATTTTA
5805200 TATTTTTTTT
1 -ATTTTTTTT
5805210 ATATCTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 11 0.46
18 9 0.38
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (17 bp):
ATTTTTTTTTTATTTTA
Found at i:5805198 original size:16 final size:16
Alignment explanation
Indices: 5805166--5805211 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
5805156 AAAATGACCC
*
5805166 ATTTTATTTTTAGTTTT
1 ATTTTTTTTTTA-TTTT
5805183 ATTTTTTTTTTATTTT
1 ATTTTTTTTTTATTTT
*
5805199 ATATTTTTTTTAT
1 ATTTTTTTTTTAT
5805212 ATCTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (16 bp):
ATTTTTTTTTTATTTT
Found at i:5805209 original size:11 final size:12
Alignment explanation
Indices: 5805166--5805213 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
5805156 AAAATGACCC
5805166 ATTTTATTTT-T
1 ATTTTATTTTAT
5805177 AGTTTTATTTT-T
1 A-TTTTATTTTAT
*
5805189 TTTTTATTTTAT
1 ATTTTATTTTAT
5805201 ATTTT-TTTTAT
1 ATTTTATTTTAT
5805212 AT
1 AT
5805214 CTAATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:5805224 original size:23 final size:23
Alignment explanation
Indices: 5805198--5805312 Score: 72
Period size: 27 Copynumber: 4.6 Consensus size: 23
5805188 TTTTTTATTT
5805198 TATATTTTTTTTATATCTAATAA
1 TATATTTTTTTTATATCTAATAA
* *
5805221 TATATATTTTTATTAGTTATCCATTAA
1 TATAT-TTTTT-TTA--TATCTAATAA
*
5805248 TATTATTTTTTATTATTTATCTATTAA
1 TA-TATTTTTT-TTA--TATCTAATAA
* *
5805275 TGTA-TTTTTTTATA-CTTATATAT
1 TATATTTTTTTTATATC-TA-ATAA
5805298 TATTATTTTTTTTAT
1 TA-TATTTTTTTTAT
5805313 TTATCTATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.01
22 4 0.05
23 8 0.11
24 10 0.13
25 17 0.23
26 2 0.03
27 30 0.40
28 3 0.04
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TATATTTTTTTTATATCTAATAA
Found at i:5805249 original size:27 final size:27
Alignment explanation
Indices: 5805218--5805287 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
5805208 TTATATCTAA
5805218 TAATATATATTTTTATTAGTTATCCAT
1 TAATATATATTTTTATTAGTTATCCAT
* *
5805245 TAATAT-TATTTTTTATTATTTATCTAT
1 TAATATATA-TTTTTATTAGTTATCCAT
* *
5805272 TAATGTATTTTTTTAT
1 TAATATATATTTTTAT
5805288 ACTTATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 34 0.92
28 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (27 bp):
TAATATATATTTTTATTAGTTATCCAT
Found at i:5805263 original size:3 final size:3
Alignment explanation
Indices: 5805243--5805382 Score: 51
Period size: 3 Copynumber: 44.0 Consensus size: 3
5805233 TTAGTTATCC
* *
5805243 ATT AAT ATT ATT -TT -TT ATT ATTT ATCT ATT AATGT ATT -TT TTT A-T
1 ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT -AT-T ATT ATT ATT ATT
* *
5805288 ACTT ATAT ATT ATT ATT TTT TTT ATTT ATCT ATT ATT ATT -TT -TT A-T
1 A-TT AT-T ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT ATT
*
5805334 ATTT ATCG ATT AATGT ATAT ATAT ATT ATT ATAT ATT ATT ATT ATT ATT
1 A-TT AT-T ATT -AT-T AT-T AT-T ATT ATT AT-T ATT ATT ATT ATT ATT
5805383 TTTGGTTGGT
Statistics
Matches: 111, Mismatches: 8, Indels: 36
0.72 0.05 0.23
Matches are distributed among these distances:
2 14 0.13
3 56 0.50
4 39 0.35
5 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5805316 original size:23 final size:23
Alignment explanation
Indices: 5805184--5805339 Score: 115
Period size: 23 Copynumber: 6.6 Consensus size: 23
5805174 TTTAGTTTTA
5805184 TTTTTTT-TTTAT-T-TTA-TAT
1 TTTTTTTATTTATATATTATTAT
*
5805203 TTTTTTTATATCTA-ATAATATATAT
1 TTTTTTTAT-T-TATATATTAT-TAT
* * *
5805228 TTTTATTAGTTATCCATTAATATTAT
1 TTTTTTTATTTAT--A-TATTATTAT
*
5805254 TTTTTATTATTTATCTATTAATGTAT
1 TTTTT-TTATTTATATATT-AT-TAT
*
5805280 TTTTTTATACTTATATATTATTAT
1 TTTTTT-TATTTATATATTATTAT
*
5805304 TTTTTTTATTTATCTATTATTAT
1 TTTTTTTATTTATATATTATTAT
*
5805327 TTTTTATATTTAT
1 TTTTTTTATTTAT
5805340 CGATTAATGT
Statistics
Matches: 110, Mismatches: 12, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
19 7 0.06
20 1 0.01
21 1 0.01
22 3 0.03
23 31 0.28
24 13 0.12
25 15 0.14
26 26 0.24
27 13 0.12
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTTTTTATTTATATATTATTAT
Found at i:5805340 original size:23 final size:23
Alignment explanation
Indices: 5805248--5805345 Score: 124
Period size: 23 Copynumber: 4.1 Consensus size: 23
5805238 TATCCATTAA
5805248 TATTATTTTTTATTATTTATCTAT
1 TATTATTTTTTA-TATTTATCTAT
* *
5805272 TAATGTATTTTTTTATACTTATATAT
1 T-AT-TA-TTTTTTATATTTATCTAT
*
5805298 TATTATTTTTTTTATTTATCTAT
1 TATTATTTTTTATATTTATCTAT
*
5805321 TATTATTTTTTATATTTATCGAT
1 TATTATTTTTTATATTTATCTAT
5805344 TA
1 TA
5805346 ATGTATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
23 38 0.59
24 3 0.05
25 4 0.06
26 12 0.19
27 7 0.11
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATTTTTTATATTTATCTAT
Found at i:5805368 original size:10 final size:10
Alignment explanation
Indices: 5805353--5805382 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5805343 TTAATGTATA
5805353 TATATATTAT
1 TATATATTAT
5805363 TATATATTAT
1 TATATATTAT
5805373 TAT-TATTAT
1 TATATATTAT
5805382 T
1 T
5805383 TTTGGTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATATTAT
Found at i:5805368 original size:16 final size:16
Alignment explanation
Indices: 5805221--5805381 Score: 58
Period size: 16 Copynumber: 10.2 Consensus size: 16
5805211 TATCTAATAA
*
5805221 TATATATTTTTATTAGT
1 TATATATTATTATTA-T
** *
5805238 TATCCATTAATATTAT
1 TATATATTATTATTAT
5805254 T-T-T-TTATTA-T-T
1 TATATATTATTATTAT
* *
5805265 TATCTATTAATGTATTTT
1 TATATATT-AT-TATTAT
*
5805283 TTTATACTTATATATTAT
1 TATATA-TTAT-TATTAT
5805301 TAT-T-TT-TT-TTATT
1 TATATATTATTATTA-T
*
5805314 TATCTATTATTATT-T
1 TATATATTATTATTAT
* *
5805329 TTTATATTTATCGATTAAT
1 TATATA-TTAT-TATT-AT
5805348 GTATATA-TA-TATTAT
1 -TATATATTATTATTAT
5805363 TATATATTATTATTAT
1 TATATATTATTATTAT
5805379 TAT
1 TAT
5805382 TTTTGGTTGG
Statistics
Matches: 108, Mismatches: 16, Indels: 41
0.65 0.10 0.25
Matches are distributed among these distances:
11 2 0.02
12 5 0.05
13 11 0.10
14 10 0.09
15 16 0.15
16 22 0.20
17 18 0.17
18 16 0.15
19 3 0.03
20 5 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
TATATATTATTATTAT
Found at i:5805734 original size:19 final size:19
Alignment explanation
Indices: 5805712--5805761 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
5805702 CAGATTCCAG
5805712 TGAATTTTTCGACAAAATT
1 TGAATTTTTCGACAAAATT
5805731 TGAATTTTTCGACAAAATT
1 TGAATTTTTCGACAAAATT
5805750 TGAATTTTTCGA
1 TGAATTTTTCGA
5805762 TGACTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (19 bp):
TGAATTTTTCGACAAAATT
Found at i:5806331 original size:5 final size:5
Alignment explanation
Indices: 5806302--5806339 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
5806292 TTAGTACTCC
5806302 TTATT TT-TT TTATCT TTATTT TTATT TTATT TTATT TT
1 TTATT TTATT TTAT-T TTA-TT TTATT TTATT TTATT TT
5806340 TTGATTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.13
5 17 0.57
6 8 0.27
7 1 0.03
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:5806341 original size:17 final size:17
Alignment explanation
Indices: 5806305--5806340 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5806295 GTACTCCTTA
5806305 TTTT-TTTTATCTTTAT
1 TTTTATTTTATCTTTAT
5806321 TTTTATTTTAT-TTTAT
1 TTTTATTTTATCTTTAT
5806337 TTTT
1 TTTT
5806341 TGATTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTATTTTATCTTTAT
Done.