Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 172 of 207
Found at i:53131343 original size:69 final size:69
Alignment explanation
Indices: 53131228--53131383 Score: 278
Period size: 69 Copynumber: 2.3 Consensus size: 69
53131218 CTGCAACCAG
* *
53131228 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTTTATGAAGAAGAAGCAAGCAATAA
1 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
53131293 TTAA
66 TTAA
53131297 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
1 AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
53131362 TTAA
66 TTAA
53131366 AATTCAGAG-CAATTTCCG
1 AATTCAGAGTC-ATTTCCG
53131384 ACTGCAAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
68 1 0.01
69 83 0.99
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (69 bp):
AATTCAGAGTCATTTCCGTGGTTGGCAGTTAAGAAGGAATTGTATGAAGAAAAAGCAAGCAATAA
TTAA
Found at i:53134793 original size:18 final size:20
Alignment explanation
Indices: 53134760--53134797 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
53134750 GACGGGATGC
53134760 AGGGAAAGCATCAACTTTGA
1 AGGGAAAGCATCAACTTTGA
53134780 AGGG-AAGC-TCAACTTTGA
1 AGGGAAAGCATCAACTTTGA
53134798 GTAGGGAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 4 0.22
20 4 0.22
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGGGAAAGCATCAACTTTGA
Found at i:53137735 original size:22 final size:22
Alignment explanation
Indices: 53137707--53137751 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53137697 ACTTGAGAGA
53137707 ACAACAATGTTGTCATATATTT
1 ACAACAATGTTGTCATATATTT
53137729 ACAACAATGTTGTCATATATTT
1 ACAACAATGTTGTCATATATTT
53137751 A
1 A
53137752 AGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
ACAACAATGTTGTCATATATTT
Found at i:53138972 original size:11 final size:11
Alignment explanation
Indices: 53138956--53138992 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
53138946 TTTTTTAAAA
53138956 TTTTAAAATAC
1 TTTTAAAATAC
53138967 TTTTAAAATAC
1 TTTTAAAATAC
53138978 TTTTAAAATAC
1 TTTTAAAATAC
53138989 TTTT
1 TTTT
53138993 TTATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:53139015 original size:29 final size:30
Alignment explanation
Indices: 53138978--53139046 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
53138968 TTTAAAATAC
*
53138978 TTTTAAAATACTTTTT-TATTATTTTTTAA-
1 TTTTAAAATA-TTTTTAAATTATTTTTTAAT
*
53139007 TTTTAAAATATTTTTAAATTTTTTTTTAAT
1 TTTTAAAATATTTTTAAATTATTTTTTAAT
53139037 TTTTAAAATA
1 TTTTAAAATA
53139047 AATTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 10 0.28
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTAAAATATTTTTAAATTATTTTTTAAT
Found at i:53139031 original size:10 final size:10
Alignment explanation
Indices: 53138947--53139030 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 10
53138937 ATATATTTAT
53138947 TTTTTAAA-A
1 TTTTTAAATA
*
53138956 TTTTAAAATA
1 TTTTTAAATA
*
53138966 CTTTTAAAATA
1 -TTTTTAAATA
*
53138977 CTTTTAAAATA
1 -TTTTTAAATA
* *
53138988 CTTTTTTATTA
1 -TTTTTAAATA
*
53138999 TTTTT-TA-A
1 TTTTTAAATA
*
53139007 TTTTAAAATA
1 TTTTTAAATA
53139017 TTTTTAAAT-
1 TTTTTAAATA
53139026 TTTTT
1 TTTTT
53139031 TTTAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
8 5 0.08
9 13 0.21
10 15 0.24
11 29 0.47
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:53139583 original size:40 final size:38
Alignment explanation
Indices: 53139529--53139663 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 38
53139519 CGTTTAGACA
*
53139529 AAAAACGCCACTAAAAATCAAGCATTAGCGTCGCTTTTAT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCG-CGCTTTT-T
** * *
53139569 AAAAACGCCGCTAAAGGTCGAGCAATAGCGGCGCTTTTT
1 AAAAACGCCGCTAAAAATCAAGCATTAGC-GCGCTTTTT
* * *
53139608 GGAAAGCGCCGCTAAAAAT-AAGCATTAGCAGCGTTTTTT
1 -AAAAACGCCGCTAAAAATCAAGCATTAGC-GCGCTTTTT
53139647 AAAAAGCGCCGC-AAAAA
1 AAAAA-CGCCGCTAAAAA
53139664 GCCTAAGCCC
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 8 0.10
39 23 0.30
40 45 0.58
41 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGCGCTTTTT
Found at i:53139653 original size:39 final size:39
Alignment explanation
Indices: 53139528--53139663 Score: 125
Period size: 39 Copynumber: 3.5 Consensus size: 39
53139518 GCGTTTAGAC
* * *
53139528 AAAAAACGCCACTAAAAATCAAGCATTAGCGTCGCTTTTAT
1 AAAAAGCGCCGCTAAAAATCAAGCATTAGCG-CG-TTTTTT
** * * *
53139569 AAAAA-CGCCGCTAAAGGTCGAGCAATAGCGGCGCTTTTT
1 AAAAAGCGCCGCTAAAAATCAAGCATTAGC-GCGTTTTTT
**
53139608 GGAAAGCGCCGCTAAAAAT-AAGCATTAGCAGCGTTTTTT
1 AAAAAGCGCCGCTAAAAATCAAGCATTAGC-GCGTTTTTT
53139647 AAAAAGCGCCGC-AAAAA
1 AAAAAGCGCCGCTAAAAA
53139664 GCCTAAGCCC
Statistics
Matches: 76, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
38 5 0.07
39 33 0.43
40 32 0.42
41 6 0.08
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (39 bp):
AAAAAGCGCCGCTAAAAATCAAGCATTAGCGCGTTTTTT
Found at i:53140719 original size:7 final size:7
Alignment explanation
Indices: 53140713--53140746 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
53140703 TAAGGTTTAT
*
53140713 GGGTTAT
1 GGGTTAG
53140720 GGGTTAG
1 GGGTTAG
53140727 GGGTTAG
1 GGGTTAG
53140734 GGGTTAG
1 GGGTTAG
*
53140741 AGGTTA
1 GGGTTA
53140747 AAGGTTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (7 bp):
GGGTTAG
Found at i:53141036 original size:110 final size:111
Alignment explanation
Indices: 53140799--53141066 Score: 319
Period size: 110 Copynumber: 2.4 Consensus size: 111
53140789 GTCAGATTAT
* *
53140799 GGTTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATATTTAGGGGTTAGAGATTTAAG
1 GGTTTAGATTAATTAGTGT-TTTTAATTTATATATTAAATAAGATTTAGGGGTTAGAGAGTTAA-
* *
53140864 GTCAGGTTAAAGTTCAGGGTTAAAGATTTAGGGTCAGGTTAGGGTTTA
64 GTCAGGTTAAAGTTCAGGGTTAAAGATTCAGGGTCAGGTTAGGATTTA
* * * *
53140912 GGATTTAGACTAATTAGTGTTTTTAATTTATATATTAAATAAGGTTTAGGGGTTTG-GGGTTAA-
1 GG-TTTAGATTAATTAGTGTTTTTAATTTATATATTAAATAAGATTTAGGGGTTAGAGAGTTAAG
** *
53140975 T-A-GTTAGTGATTTAGGGTTTAAAGATTCAGGGTCAGGTTAGGATTTAA
65 TCAGGTTAAAG-TTCAGGG-TTAAAGATTCAGGGTCAGGTTAGGATTT-A
* *
53141023 GGTTTAGATTAATTAGTATTTTTTTAATTTATATACTAAATAAG
1 GGTTTAGATTAATTAG--TGTTTTTAATTTATATATTAAATAAG
53141067 TTCTTATATA
Statistics
Matches: 135, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
108 5 0.04
109 7 0.05
110 40 0.30
111 3 0.02
112 29 0.21
113 35 0.26
114 16 0.12
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.43
Consensus pattern (111 bp):
GGTTTAGATTAATTAGTGTTTTTAATTTATATATTAAATAAGATTTAGGGGTTAGAGAGTTAAGT
CAGGTTAAAGTTCAGGGTTAAAGATTCAGGGTCAGGTTAGGATTTA
Found at i:53141644 original size:16 final size:15
Alignment explanation
Indices: 53141619--53141653 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
53141609 CGCCATTTAT
*
53141619 AAATTTTCCCCCCTG
1 AAATTTTCCCCCCTA
53141634 AAATATTTCCCCCCTA
1 AAAT-TTTCCCCCCTA
53141650 AAAT
1 AAAT
53141654 CCCTAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATTTTCCCCCCTA
Found at i:53144866 original size:21 final size:21
Alignment explanation
Indices: 53144851--53144905 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
53144841 CAGATGCTAC
53144851 TGTAGTTACTCAAGATTGCCA
1 TGTAGTTACTCAAGATTGCCA
53144872 TGTAGTTACTCAAGATTGCCA
1 TGTAGTTACTCAAGATTGCCA
53144893 TGTAGTTACTCAA
1 TGTAGTTACTCAA
53144906 AGAAGGCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (21 bp):
TGTAGTTACTCAAGATTGCCA
Found at i:53145312 original size:13 final size:13
Alignment explanation
Indices: 53145294--53145340 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
53145284 TGAATGTTGA
53145294 AATTTATTACTAT
1 AATTTATTACTAT
* **
53145307 AATTTAATGTTGA-
1 AATTTATTACT-AT
53145320 AATTTATTACTAT
1 AATTTATTACTAT
53145333 AATTTATT
1 AATTTATT
53145341 TTACTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (13 bp):
AATTTATTACTAT
Found at i:53145315 original size:26 final size:26
Alignment explanation
Indices: 53145286--53145338 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53145276 ATTATAGGTG
53145286 AATGTTGAAATTTATTACTATAATTT
1 AATGTTGAAATTTATTACTATAATTT
53145312 AATGTTGAAATTTATTACTATAATTT
1 AATGTTGAAATTTATTACTATAATTT
53145338 A
1 A
53145339 TTTTACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (26 bp):
AATGTTGAAATTTATTACTATAATTT
Found at i:53145505 original size:43 final size:42
Alignment explanation
Indices: 53145442--53145599 Score: 228
Period size: 43 Copynumber: 3.7 Consensus size: 42
53145432 ATGGCACTTT
**
53145442 TAGCGGCGTTTATGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
* *
53145485 TAGCGGCGTTTATGGGAAAAGTGCCGCTAAAGGTCCGATCTA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* *
53145527 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGT-CTGATCTA
*
53145570 TAGCGGCGTTTTTGGG-AAAGCGCCGCTAAA
1 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAA
53145600 ATTAGCAACA
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
42 51 0.49
43 53 0.51
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (42 bp):
TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCTGATCTA
Found at i:53145545 original size:42 final size:41
Alignment explanation
Indices: 53145458--53145599 Score: 203
Period size: 42 Copynumber: 3.4 Consensus size: 41
53145448 CGTTTATGAA
* *
53145458 AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTATGGG
1 AAAAGCGCCGCTAAAGGTC-CGATCTATAGCGGCGTTT-TAGG
*
53145501 AAAAGTGCCGCTAAAGGTCCGATCTATAGCGGCGTTTGTAGG
1 AAAAGCGCCGCTAAAGGTCCGATCTATAGCGGCGTTT-TAGG
*
53145543 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTTTGG
1 AAAAGCGCCGCTAAAGGTCC-GATCTATAGCGGCGTTTTAGG
*
53145585 GAAAGCGCCGCTAAA
1 AAAAGCGCCGCTAAA
53145600 ATTAGCAACA
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
42 56 0.62
43 35 0.38
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (41 bp):
AAAAGCGCCGCTAAAGGTCCGATCTATAGCGGCGTTTTAGG
Found at i:53154180 original size:39 final size:40
Alignment explanation
Indices: 53154137--53154221 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
53154127 CCACATCAAG
* * *
53154137 AAAAAAAT-CACATAAAAATGTTTAAAAATATAAAAATAT
1 AAAAAAATCCACACAAAAATATTTAAAAATAGAAAAATAT
* * * *
53154176 AAAAAAATCCACCCCAAAATATTTAAAATTAGAAAATTAT
1 AAAAAAATCCACACAAAAATATTTAAAAATAGAAAAATAT
53154216 AAAAAA
1 AAAAAA
53154222 TAAAAAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (40 bp):
AAAAAAATCCACACAAAAATATTTAAAAATAGAAAAATAT
Found at i:53156488 original size:42 final size:42
Alignment explanation
Indices: 53156441--53156573 Score: 149
Period size: 42 Copynumber: 3.2 Consensus size: 42
53156431 CATAAGTGTT
* *
53156441 AACAGAAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTA
1 AACAGAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTA
* * *
53156483 AACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
1 AACAGAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTA
* * * * * * * *
53156525 AACGGAAGCTCATTAGGGTTAAATGGAAACTCATATGAGTTA
1 AACAGAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTA
53156567 AACAGAA
1 AACAGAA
53156574 GCTCGTAAGA
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
AACAGAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTA
Found at i:53156505 original size:21 final size:21
Alignment explanation
Indices: 53156431--53156510 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
53156421 AATTGAAGCA
*
53156431 CATAAGTGTT-AACAGAAACC
1 CATAAGGGTTAAACAGAAACC
* * * *
53156451 CATAAGGGTTGAACGGAAGCT
1 CATAAGGGTTAAACAGAAACC
* * *
53156472 CGTAAGAGCTAAACAGAAACC
1 CATAAGGGTTAAACAGAAACC
53156493 CATAAGGGTTAAACAGAA
1 CATAAGGGTTAAACAGAA
53156511 GCTCAAAAGA
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 9 0.20
21 36 0.80
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
CATAAGGGTTAAACAGAAACC
Found at i:53156529 original size:63 final size:63
Alignment explanation
Indices: 53156460--53156594 Score: 162
Period size: 63 Copynumber: 2.1 Consensus size: 63
53156450 CCATAAGGGT
* *
53156460 TGAACGGAAGCTCGTAAGAGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGC
1 TGAACGGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGC
* * * ** * * **
53156523 TGAACGGAAGCTCATTAGGGTTAAATGGAAACTCATATGAGTTAAACAGAAGCTCGTAAGAGC
1 TGAACGGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGC
*
53156586 TAAACGGAA
1 TGAACGGAA
53156595 AGTAAACACA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (63 bp):
TGAACGGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGC
Found at i:53163758 original size:19 final size:19
Alignment explanation
Indices: 53163734--53163770 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
53163724 GTATTTTTTA
53163734 CTTAAAAA-ATTCAAAATTC
1 CTTAAAAATATT-AAAATTC
53163753 CTTAAAAATATTAAAATT
1 CTTAAAAATATTAAAATT
53163771 TTCATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
CTTAAAAATATTAAAATTC
Found at i:53164446 original size:43 final size:43
Alignment explanation
Indices: 53164398--53164490 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
53164388 ATAAAATGTT
53164398 AGAATTTTATGAAAAATTTTAAAAATTTATGTATTGTTTTGAG
1 AGAATTTTATGAAAAATTTTAAAAATTTATGTATTGTTTTGAG
53164441 AGAATTTTATGAAAAATTTTAAAAATTTATGTATTGTTTTGAG
1 AGAATTTTATGAAAAATTTTAAAAATTTATGTATTGTTTTGAG
*
53164484 AAAATTT
1 AGAATTT
53164491 AGGGTTTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (43 bp):
AGAATTTTATGAAAAATTTTAAAAATTTATGTATTGTTTTGAG
Found at i:53164490 original size:22 final size:22
Alignment explanation
Indices: 53164419--53164491 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 22
53164409 AAAAATTTTA
53164419 AAAATTTATGTATTGTTTTGAG
1 AAAATTTATGTATTGTTTTGAG
* * ***
53164441 AGAATTTTATGAAAAATTTT-A-
1 A-AAATTTATGTATTGTTTTGAG
53164462 AAAATTTATGTATTGTTTTGAG
1 AAAATTTATGTATTGTTTTGAG
53164484 AAAATTTA
1 AAAATTTA
53164492 GGGTTTTTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 13 0.34
21 2 0.05
22 10 0.26
23 13 0.34
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (22 bp):
AAAATTTATGTATTGTTTTGAG
Found at i:53164582 original size:21 final size:21
Alignment explanation
Indices: 53164556--53164601 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
53164546 TTTCTTAAGT
53164556 AAAAAATACCATAAAATTCTAA
1 AAAAAAT-CCATAAAATTCTAA
* *
53164578 AAAAAATTCATAATATTCTAA
1 AAAAAATCCATAAAATTCTAA
53164599 AAA
1 AAA
53164602 CTTTAAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATCCATAAAATTCTAA
Found at i:53176030 original size:27 final size:27
Alignment explanation
Indices: 53175992--53176054 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
53175982 ATTGCAAAAC
* *
53175992 AGAAAAAGAAAGAAAAGCAATCG-GAAA
1 AGAAAAAAAAAG-AAACCAATCGAGAAA
*
53176019 AGAAAAAAAAAGAACCCAATCGAGAAA
1 AGAAAAAAAAAGAAACCAATCGAGAAA
*
53176046 AGGAAAAAA
1 AGAAAAAAA
53176055 GAAAACCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.68, C:0.10, G:0.19, T:0.03
Consensus pattern (27 bp):
AGAAAAAAAAAGAAACCAATCGAGAAA
Found at i:53176061 original size:27 final size:25
Alignment explanation
Indices: 53176000--53176061 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
53175990 ACAGAAAAAG
*
53176000 AAAGAAAA-GCAATCGGAAAAGAAA
1 AAAGAAAACCCAATCGGAAAAGAAA
*
53176024 AAAAAAGAACCCAATCGAGAAAAGGAAA
1 AAAGAA-AACCCAATCG-GAAAA-GAAA
53176052 AAAGAAAACC
1 AAAGAAAACC
53176062 TTTCTTGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 6 0.19
27 9 0.29
28 9 0.29
ACGTcount: A:0.66, C:0.13, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAAAACCCAATCGGAAAAGAAA
Found at i:53177555 original size:31 final size:31
Alignment explanation
Indices: 53177520--53177584 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
53177510 TCGAACACAT
* *
53177520 GGCTGTGTGGACGAATTGTGTAACAGGTTGA
1 GGCTGTGTGGACAAACTGTGTAACAGGTTGA
*
53177551 GGCTGTGTGGACAAACTGTGTAACTGGTTGA
1 GGCTGTGTGGACAAACTGTGTAACAGGTTGA
53177582 GGC
1 GGC
53177585 CGTGAGATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.12, G:0.38, T:0.28
Consensus pattern (31 bp):
GGCTGTGTGGACAAACTGTGTAACAGGTTGA
Found at i:53180632 original size:9 final size:9
Alignment explanation
Indices: 53180615--53180651 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53180605 TGAGTTTTCG
53180615 AATTCGAAT
1 AATTCGAAT
*
53180624 AACTCGAAT
1 AATTCGAAT
53180633 AATTCGAAT
1 AATTCGAAT
53180642 AATTCGAAT
1 AATTCGAAT
53180651 A
1 A
53180652 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53180731 original size:27 final size:27
Alignment explanation
Indices: 53180700--53180751 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
53180690 AAACCTTTTT
*
53180700 ACTTTTCCCTCAAAACTTTTACTCCTC
1 ACTTTTCCCCCAAAACTTTTACTCCTC
53180727 ACTTTTCCCCCAAAACTTTTACTCC
1 ACTTTTCCCCCAAAACTTTTACTCC
53180752 CCTCCCCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (27 bp):
ACTTTTCCCCCAAAACTTTTACTCCTC
Found at i:53180762 original size:27 final size:27
Alignment explanation
Indices: 53180705--53180763 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
53180695 TTTTTACTTT
* * ***
53180705 TCCCTCAAAACTTTTACTCCTCACTTT
1 TCCCCCAAAACTTTTACTCCCCACCCC
*
53180732 TCCCCCAAAACTTTTACTCCCCTCCCC
1 TCCCCCAAAACTTTTACTCCCCACCCC
53180759 TCCCC
1 TCCCC
53180764 TCCCAACCCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.49, G:0.00, T:0.32
Consensus pattern (27 bp):
TCCCCCAAAACTTTTACTCCCCACCCC
Found at i:53186824 original size:15 final size:14
Alignment explanation
Indices: 53186804--53186834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
53186794 AAGTACAATC
53186804 ATCCAAAAACTGAAA
1 ATCCAAAAACT-AAA
53186819 ATCCAAAAACTAAA
1 ATCCAAAAACTAAA
53186833 AT
1 AT
53186835 AATAGTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.16
Consensus pattern (14 bp):
ATCCAAAAACTAAA
Found at i:53186941 original size:33 final size:33
Alignment explanation
Indices: 53186903--53186969 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
53186893 TTACAATGTC
*
53186903 ACAAATATACTACAAATGTGACAAAAGCAACTA
1 ACAAATATACTACAAATGTGACAAAAACAACTA
53186936 ACAAATATACTACAAATGTGACAAAAACAACTA
1 ACAAATATACTACAAATGTGACAAAAACAACTA
53186969 A
1 A
53186970 GCGTCACATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.18
Consensus pattern (33 bp):
ACAAATATACTACAAATGTGACAAAAACAACTA
Found at i:53191404 original size:51 final size:50
Alignment explanation
Indices: 53191220--53191457 Score: 277
Period size: 50 Copynumber: 4.7 Consensus size: 50
53191210 TATCATTTGA
*
53191220 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
*
53191270 TTA-ACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
* * *
53191320 TTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTT-TGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGG
* * * * *
53191371 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACC--GTCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGT--TTTA-CGG
* * *
53191422 TTCACGTAGTAGCCTTCACACAGTACTACATACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
53191458 TTCATCGATA
Statistics
Matches: 163, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 4 0.02
50 81 0.50
51 72 0.44
52 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG
Found at i:53216243 original size:20 final size:20
Alignment explanation
Indices: 53216218--53216256 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53216208 TCTTGTAATG
* *
53216218 ATACTTTTTTTAAGGTATCA
1 ATACTTTTCTTAAGATATCA
53216238 ATACTTTTCTTAAGATATC
1 ATACTTTTCTTAAGATATC
53216257 GATATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (20 bp):
ATACTTTTCTTAAGATATCA
Found at i:53218290 original size:28 final size:29
Alignment explanation
Indices: 53218245--53218305 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
53218235 ATTTATTTGT
*
53218245 TTAAGGTTTAGGGATTTTAAAA-AATAAA
1 TTAAGGTTTAGGAATTTTAAAATAATAAA
*
53218273 TTAAGGTTTA-GAATTTTTAAAATAATTAA
1 TTAAGGTTTAGGAA-TTTTAAAATAATAAA
53218302 TTAA
1 TTAA
53218306 ATTAGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 18 0.62
29 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (29 bp):
TTAAGGTTTAGGAATTTTAAAATAATAAA
Found at i:53218324 original size:33 final size:32
Alignment explanation
Indices: 53218269--53218387 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 32
53218259 TTTTAAAAAA
**
53218269 TAAATTAAGGTTTAGAATTTTTAAAATAATTAAT
1 TAAATT-AGGTTTAG-GGTTTTAAAATAATTAAT
*
53218303 TAAATTAGGTTTTAGGGTTTT-AAGTAAATTAAT
1 TAAATTAGG-TTTAGGGTTTTAAAAT-AATTAAT
* * *
53218336 TAAATTAAAGTTTAGAGTTTTAAAAAAATTAAT
1 TAAATT-AGGTTTAGGGTTTTAAAATAATTAAT
53218369 TAAATTAGGGTTTAGGGTT
1 TAAATTA-GGTTTAGGGTT
53218388 GAGTGTTGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
32 4 0.06
33 52 0.73
34 15 0.21
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (32 bp):
TAAATTAGGTTTAGGGTTTTAAAATAATTAAT
Found at i:53218404 original size:67 final size:65
Alignment explanation
Indices: 53218263--53218387 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 65
53218253 TAGGGATTTT
* * * * * *
53218263 AAAAAATAAATTAAGGTTTAGAATTTTTAAAATAATTAATTAAATTAGGTTTTAGGGTTTTAAGT
1 AAAAATTAAATTAAAGTTTAGAAGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTTTTAAGG
53218328 AAATTAATTAAATTAAAGTTTAG-AGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTT
1 AAA--AATTAAATTAAAGTTTAGAAGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTT
53218388 GAGTGTTGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 3 0.06
66 34 0.64
67 16 0.30
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (65 bp):
AAAAATTAAATTAAAGTTTAGAAGTTTTAAAAAAATTAATTAAATTAGGGTTTAGGGTTTTAAGG
Found at i:53218733 original size:126 final size:126
Alignment explanation
Indices: 53218429--53218936 Score: 569
Period size: 117 Copynumber: 4.1 Consensus size: 126
53218419 ATTTTGTTTC
* * ** *
53218429 CTTTTTCTAGAGTAGTTTCTGAAAATTTAATTTTGAGAAGACGGTTCT-AAAAAATAGTGACAAA
1 CTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGATAAA
* * * *
53218493 AACGCTTCAAGCAAG-ATGCACTGTCAACAAAAGTACTGAAAAAAGCTCCTACGTGGACACT
66 AACGCTTCAAGC-AGTATGCACTGTCAACAAAATTACTGAAAAAAACTCCCACGTGGACGCT
* * * * *
53218554 CTTTTTCTACAGTAGTTTCT-AAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAATG-TAAA
1 CTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGATAAA
* * * * * * *
53218617 AATGCTTCAATCAGTATGCACTCTCAGCAGAATTACTGAAAAAAAAACTCCCATGTGGATGCT
66 AACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTG--AAAAAAACTCCCACGTGGACGCT
*
53218680 CTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAAAAGACGGTTCTGAAAAAATAGTG-TCAA
1 CTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGAT-AA
* * *
53218744 AAACGCTTCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAATCTCCCACATGGACGCT
65 AAACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTGAAAAAAACTCCCACGTGGACGCT
* *
53218806 C---TT-T-T--T--TTCCTGGAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGCA-AA
1 CTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTG-ATAA
* * * * *
53218861 AAATGCTTCAAGCAGTATGCACTGTCACCAAAATTACTGAAAAAAGCTCCCACATGGACTCT
65 AAACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTGAAAAAAACTCCCACGTGGACGCT
*
53218923 CTTTTTCTACAGTA
1 CTTTTTCTATAGTA
53218937 TTTCTTGCTT
Statistics
Matches: 324, Mismatches: 43, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
117 102 0.31
119 1 0.00
120 2 0.01
121 2 0.01
122 1 0.00
123 4 0.01
124 56 0.17
125 29 0.09
126 56 0.17
127 36 0.11
128 35 0.11
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
CTTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGATAAA
AACGCTTCAAGCAGTATGCACTGTCAACAAAATTACTGAAAAAAACTCCCACGTGGACGCT
Found at i:53230866 original size:40 final size:40
Alignment explanation
Indices: 53230813--53230917 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
53230803 GCGTTTGGAT
53230813 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
* * * * *
53230853 AAAAAACGCCGCTAAAGATTAAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
* **
53230893 TAAAAACGCCGAAAAAAATCTAAGC
1 AAAAAACGCCGCTAAAAATC-AAGC
53230918 CCGTCGTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
40 50 0.94
41 3 0.06
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
Found at i:53234775 original size:16 final size:16
Alignment explanation
Indices: 53234754--53234784 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53234744 TGTAACCTAT
53234754 CTGATGTTTACAATAA
1 CTGATGTTTACAATAA
53234770 CTGATGTTTACAATA
1 CTGATGTTTACAATA
53234785 GTTTGGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
CTGATGTTTACAATAA
Found at i:53235888 original size:14 final size:14
Alignment explanation
Indices: 53235869--53235900 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
53235859 TCCAATCACC
53235869 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
53235883 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
53235897 GGGC
1 GGGC
53235901 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:53241010 original size:14 final size:14
Alignment explanation
Indices: 53240991--53241022 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
53240981 TCCAATCACC
53240991 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
53241005 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
53241019 GGGC
1 GGGC
53241023 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:53241821 original size:43 final size:43
Alignment explanation
Indices: 53241687--53241913 Score: 264
Period size: 43 Copynumber: 5.3 Consensus size: 43
53241677 AGATTATGTT
* ** * *
53241687 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * * *
53241729 TTTAGTGGCATTT-TTGATAAAAGTGCTGCTAAAGGTCATGGT-
1 TTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGTCTTGGTC
*
53241771 TTATAGCGGCGTTTGTGGAAAAACCGCCGCTAAAGGTCTTGGTC
1 TT-TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
* *
53241815 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
*
53241858 TTTAGTGGCGTTTGTGTG-AAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGGTCTTGGTC
53241901 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
53241914 TTTCTAAAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 28 0.18
43 121 0.78
44 6 0.04
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:53250746 original size:16 final size:17
Alignment explanation
Indices: 53250727--53250760 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53250717 TTTGACTAAA
53250727 TTTAAATA-AAAAATAT
1 TTTAAATATAAAAATAT
*
53250743 TTTAAATATATAAATAT
1 TTTAAATATAAAAATAT
53250760 T
1 T
53250761 ATACTAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATATAAAAATAT
Found at i:53252337 original size:16 final size:18
Alignment explanation
Indices: 53252318--53252354 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
53252308 TTTATTATAA
*
53252318 AAATATTTA-TAATTT-T
1 AAATAATTATTAATTTGT
53252334 AAATAATTATTAATTTGT
1 AAATAATTATTAATTTGT
53252352 AAA
1 AAA
53252355 AATAGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATAATTATTAATTTGT
Found at i:53252709 original size:19 final size:19
Alignment explanation
Indices: 53252687--53252724 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53252677 TTTTAAATTT
*
53252687 AAATTA-GTTTTTGGAAAAA
1 AAATTATGTTATT-GAAAAA
53252706 AAATTATGTTATTGAAAAA
1 AAATTATGTTATTGAAAAA
53252725 TATTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (19 bp):
AAATTATGTTATTGAAAAA
Found at i:53253341 original size:22 final size:22
Alignment explanation
Indices: 53253316--53253407 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
53253306 AAATTCAATA
* *
53253316 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
53253338 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
53253360 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
53253382 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
53253404 TCAA
1 TCAA
53253408 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:53253423 original size:52 final size:51
Alignment explanation
Indices: 53253357--53253459 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
53253347 TTCAAAATTT
* * *
53253357 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
53253409 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
53253460 TCCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:53253448 original size:21 final size:22
Alignment explanation
Indices: 53253409--53253450 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53253399 TTCTCTCAAA
53253409 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
53253431 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
53253451 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:53253547 original size:29 final size:29
Alignment explanation
Indices: 53253492--53253547 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
53253482 ATTAAATTTC
53253492 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
53253521 ATTTTTTTAA-ATAATTTTAAAATTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTT
53253548 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:53253555 original size:29 final size:29
Alignment explanation
Indices: 53253492--53253555 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
53253482 ATTAAATTTC
*
53253492 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
53253521 ATTTTTTTAA-ATAATTTTAAAATTTTTA
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
53253549 ATATTTT
1 ATTTTTT
53253556 CAACAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTA
Found at i:53253700 original size:24 final size:23
Alignment explanation
Indices: 53253645--53253700 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
53253635 TAAATTTTAA
*
53253645 ATTTTTTTAAGATATTTTTATTT
1 ATTTTTTTAAGATATTTTTATAT
53253668 ATGTATTTTT-AGATATTTATTAATAT
1 AT-T-TTTTTAAGATATTT-TT-ATAT
53253694 ATTTTTT
1 ATTTTTT
53253701 GTTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 13 0.46
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTTTTTTAAGATATTTTTATAT
Found at i:53255852 original size:17 final size:18
Alignment explanation
Indices: 53255830--53255864 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53255820 TAAAATCCCT
53255830 AACCCT-ACTTAATTAAA
1 AACCCTAACTTAATTAAA
*
53255847 AACCCTAATTTAATTAAA
1 AACCCTAACTTAATTAAA
53255865 TTAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AACCCTAACTTAATTAAA
Found at i:53255932 original size:28 final size:28
Alignment explanation
Indices: 53255850--53256543 Score: 561
Period size: 28 Copynumber: 24.5 Consensus size: 28
53255840 AATTAAAAAC
53255850 CCTAATTTAATTAAATTAAAAACCCTAAA
1 CCTAATTTAATTAAATTAAAAACCCT-AA
* *
53255879 CCCT-ACTTAATTAAA--AACCCTAACCCTAA
1 -CCTAATTTAATTAAATTAA---AAACCCTAA
53255908 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
** *
53255936 CCTAACCTACTTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
53255964 CATTATTTAATTAAATTAAAAACCCTAAA
1 CCTAATTTAATTAAATTAAAAACCCT-AA
* *
53255993 CCCT-ACTTAATTAAA--AACCCTAACCCTAA
1 -CCTAATTTAATTAAATTAA---AAACCCTAA
** *
53256022 CCTAACCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
53256050 CCTAATTTTATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
53256078 CCTTATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
53256106 CCTAACCTAAACTAATTTAATTAAAAACCCTAA
1 CCTAA--T---TTAATTAAATTAAAAACCCTAA
** *
53256139 CCTAACCTACTTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
53256167 CCTTATTTAATTAAATTAAAAACCCTAAA
1 CCTAATTTAATTAAATTAAAAACCCT-AA
* *
53256196 CCCT-ACTTAATTAAA--AACCCTAACCCTAA
1 -CCTAATTTAATTAAATTAA---AAACCCTAA
** *
53256225 CCTAACCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
** *
53256253 CCTAACCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
53256281 CCCTAACCTAACCTAATTTAATTAAAAACCCTAA
1 -CCTAA--T---TTAATTAAATTAAAAACCCTAA
53256315 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
** * *
53256343 CCTAACCTAATTTAATTAAAAACCATAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
53256371 CCTTATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* **
53256399 CC----TGACCT-AATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* * *
53256422 CCTACTTAAATTAAA--AACCCTAA-CCTAA
1 CCTAATTTAATTAAATTAA---AAACCCTAA
*
53256450 CCTTATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
53256478 CC----CTACTT-AATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
53256501 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
53256529 CCCT-ATTTAATTAAA
1 -CCTAATTTAATTAAA
53256544 AACCCTAATT
Statistics
Matches: 548, Mismatches: 66, Indels: 102
0.77 0.09 0.14
Matches are distributed among these distances:
23 34 0.06
24 7 0.01
26 2 0.00
27 15 0.03
28 324 0.59
29 78 0.14
30 29 0.05
31 7 0.01
33 30 0.05
34 22 0.04
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.30
Consensus pattern (28 bp):
CCTAATTTAATTAAATTAAAAACCCTAA
Found at i:53256020 original size:23 final size:23
Alignment explanation
Indices: 53255818--53255906 Score: 117
Period size: 23 Copynumber: 3.8 Consensus size: 23
53255808 ACATTATTTG
*
53255818 ATTAAAATCCCTAACCCTACTTA
1 ATTAAAAACCCTAACCCTACTTA
** *
53255841 ATTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTACTT-A
53255864 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
53255888 ATTAAAAACCCTAACCCTA
1 ATTAAAAACCCTAACCCTA
53255907 ACCTAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
22 4 0.07
23 33 0.59
24 15 0.27
25 4 0.07
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
ATTAAAAACCCTAACCCTACTTA
Found at i:53256022 original size:114 final size:115
Alignment explanation
Indices: 53255854--53256543 Score: 579
Period size: 114 Copynumber: 6.1 Consensus size: 115
53255844 AAAAACCCTA
53255854 ATTTAATTAAATTAAAAACCCTAAACCCT-ACTTAATTAAAAACCCTAACCCTAACCTAATTTAA
1 ATTTAATTAAATTAAAAACCCTAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAA
* *
53255918 TTAAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACATT
66 TTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTT
**
53255968 ATTTAATTAAATTAAAAACCCTAAACCCT-ACTTAATTAAAAACCCTAACCCTAACCTAACCTAA
1 ATTTAATTAAATTAAAAACCCTAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAA
* ** *
53256032 TTTAATTAAAAACCCTAACCTAATTTTATTAAATTAAAAACCCTAACCTT
66 TTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTT
*
53256082 ATTTAATTAAATTAAAAACCCTAACCTAACCTAAACTAATTTAATTAAAAACCCTAA-CCTAACC
1 ATTTAATTAAATTAAAAACCCT-A---AACC----CTAACTTAATTAAAAACCCTAACCCTAACC
* * ** *
53256146 -----TACTTAAATTAAAAACCCTAACCTTATTTAATTAAATTAAAAACCCTAAACCCT
58 TAATTTAATTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCT-AACCTT
* * * *
53256200 ACTTAATTAAA--AACCCTAACCCTAACCTAACCTAATTTAATTAAAAACCCTAA-CCTAACCTA
1 ATTTAATTAAATTAA---AAACCCTAA---ACCCTAACTTAATTAAAAACCCTAACCCTAACCTA
* * *
53256262 ATTTAATTAAA--AACCCTAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCTA
60 ATTTAATTAAATTAA---AAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTT
* * *
53256319 ATTTAATTAAATTAAAAACCCT-AA-CCTAACCTAATTTAATTAAA----AACCATAACCTTATT
1 ATTTAATTAAATTAAAAACCCTAAACCCTAACTTAA-TTAA--AAACCCTAACCCTAACCTAATT
*
53256378 TAATTAAATTAAAAACCCTAACCTGACC----T-AATTAAAAACCCTAACC--
63 TAATTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTT
* * ****
53256424 ---TACTTAAATTAAAAACCCT-AA-CCTAACCTTATTTAATTAAATTAAAAACCCTAACC----
1 ATTTAATTAAATTAAAAACCCTAAACCCTAA-CTTAATTAA--AAA-CCCTAACCCTAACCTAAT
* * ** *
53256480 CTACTT-AATTAAAAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCCT
62 TTAATTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTT
53256533 ATTTAATTAAA
1 ATTTAATTAAA
53256544 AACCCTAATT
Statistics
Matches: 485, Mismatches: 43, Indels: 98
0.77 0.07 0.16
Matches are distributed among these distances:
102 53 0.11
103 7 0.01
106 1 0.00
107 43 0.09
108 1 0.00
112 23 0.05
113 26 0.05
114 162 0.33
115 4 0.01
116 5 0.01
117 46 0.09
118 28 0.06
119 27 0.06
120 30 0.06
121 2 0.00
122 9 0.02
123 18 0.04
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.30
Consensus pattern (115 bp):
ATTTAATTAAATTAAAAACCCTAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAA
TTAAATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCTT
Found at i:53256175 original size:203 final size:200
Alignment explanation
Indices: 53255850--53256530 Score: 867
Period size: 203 Copynumber: 3.4 Consensus size: 200
53255840 AATTAAAAAC
*
53255850 CCTAATTTAATTAAATTAAAAACCCTAAACC---CTACTTAATTAAAAACCCTAACCCTAACCTA
1 CCTAATTTAATTAAATTAAAAACCCT-AACCTTACTAATTAATTAAAAACCCTAA-CCTAACCTA
*
53255912 ATTTAATTAAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACATTATTTAATTA
64 A-TTAATTAAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTTAATTA
53255977 AATTAAAAACCCTAAACCCTACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAA
128 AATTAAAAACCCTAAACCCTACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAA
53256042 AACCCTAA
193 AACCCTAA
* *
53256050 CCTAATTTTATTAAATTAAAAACCCTAACCTTATTTAATTAAATTAAAAACCCTAACCTAACCTA
1 CCTAATTTAATTAAATTAAAAACCCTAACCTTA-CTAATT-AATTAAAAACCCTAACCTAACCT-
* *
53256115 AACTAATTTAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTTAATTA
63 AATTAATTAAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTTAATTA
53256180 AATTAAAAACCCTAAACCCTACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAA
128 AATTAAAAACCCTAAACCCTACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAA
53256245 AACCCTAA
193 AACCCTAA
** *
53256253 CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCT
1 CCTAATTTAATTAAATTAAAAACCCTAA-CCT----T-A-CTAA-TTAATTAAAAACCCTAACCT
* * *
53256318 AA--T--TTAATTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCATAACCTTATTT
58 AACCTAATTAATTAAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTT
*
53256379 AATTAAATTAAAAACCCT-AA-CCTGACCTAATTAAAAACCCTAA-CCT-A-CT----T-A---A
123 AATTAAATTAAAAACCCTAAACCCT-ACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTA
53256431 ATTAAAAACCCTAA
187 ATTAAAAACCCTAA
*
53256445 CCTAACCTTATTTAATTAAATTAAAAACCCTAACC---CTACTTAATTAAAAACCCTAACCTAA-
1 CCT-A----ATTTAATTAAATTAAAAACCCTAACCTTACTAATTAATTAAAAACCCTAACCTAAC
53256506 -T--TTAATTAAATTAAAAACCCTAACC
61 CTAATTAATTAAATTAAAAACCCTAACC
53256531 CTATTTAATT
Statistics
Matches: 440, Mismatches: 22, Indels: 52
0.86 0.04 0.10
Matches are distributed among these distances:
186 47 0.11
187 3 0.01
192 18 0.04
193 1 0.00
195 1 0.00
196 3 0.01
197 21 0.05
199 4 0.01
200 27 0.06
201 1 0.00
202 6 0.01
203 189 0.43
204 91 0.21
207 1 0.00
208 1 0.00
209 24 0.05
210 2 0.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (200 bp):
CCTAATTTAATTAAATTAAAAACCCTAACCTTACTAATTAATTAAAAACCCTAACCTAACCTAAT
TAATTAAATTAAAAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTTATTTAATTAAAT
TAAAAACCCTAAACCCTACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTTAATTAAAAAC
CCTAA
Found at i:53256548 original size:23 final size:23
Alignment explanation
Indices: 53256457--53256551 Score: 95
Period size: 23 Copynumber: 3.9 Consensus size: 23
53256447 TAACCTTATT
*
53256457 TAATTAAATTAAAAACCCTAACCC
1 TAATTTAATTAAAAACCCTAA-CC
*
53256481 T-ACTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
53256503 TAATTTAATTAAATTAAAAACCCTAACCC
1 TAA--T--TT-AATTAAAAACCCTAA-CC
53256532 T-ATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
53256552 TTAAATTGTA
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
22 3 0.05
23 33 0.54
24 3 0.05
26 1 0.02
27 2 0.03
28 16 0.26
29 3 0.05
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.29
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACC
Found at i:53259942 original size:124 final size:125
Alignment explanation
Indices: 53259718--53259959 Score: 373
Period size: 124 Copynumber: 1.9 Consensus size: 125
53259708 CCACGAGGGC
*
53259718 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTTATTTCCTACATGACCAACTGTAGC
1 GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAATTTATTTCCTACATGACCAACTGTAGC
* * *
53259783 GAAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCA
* *
53259843 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAA-TTATTT-CTCACATGACC-ACTGTA
1 GCGATTTGACACTATTTCCTCAG-AAACGTCAAAAAAAATTTATTTCCT-ACATGACCAACTGTA
* *
53259905 GCGAAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCT
64 GCGAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCT
53259960 AGTAGAAGCA
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
124 58 0.54
125 34 0.32
126 15 0.14
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (125 bp):
GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAATTTATTTCCTACATGACCAACTGTAGC
GAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCA
Found at i:53259981 original size:124 final size:125
Alignment explanation
Indices: 53259721--53259998 Score: 366
Period size: 124 Copynumber: 2.2 Consensus size: 125
53259711 CGAGGGCGCG
* *
53259721 ATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTTATTTCCTACATGACCAACTGTAGCGAA
1 ATTTCACACTATTTCCTCAGAAACGTCAAAAAAAATTTATTTCCTACATGACCAACTGTAGCGAA
* * * * ** *
53259786 ATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAGCG
66 ATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCA
* *
53259846 ATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAA-TTATTT-CTCACATGACC-ACTGTAGCG
1 ATTTCACACTATTTCCTCAG-AAACGTCAAAAAAAATTTATTTCCT-ACATGACCAACTGTAGCG
* *
53259908 AAATCGCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAAGCA
64 AAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCA
* *
53259970 ATTTCCCACTATTTAAC-CAGAAACGTCAA
1 ATTTCACACTATTT-CCTCAGAAACGTCAA
53259999 CTCGAAAAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
123 9 0.07
124 78 0.58
125 32 0.24
126 15 0.11
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (125 bp):
ATTTCACACTATTTCCTCAGAAACGTCAAAAAAAATTTATTTCCTACATGACCAACTGTAGCGAA
ATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCA
Found at i:53264786 original size:29 final size:28
Alignment explanation
Indices: 53264754--53264814 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
53264744 AAAGGCCGGC
53264754 TTTTTTCAA-AATTTACCGAAATGGGCCA
1 TTTTTT-AATAATTTACCGAAATGGGCCA
* *
53264782 GTTTTTTAATTATTTACCGGAATGGGCCA
1 -TTTTTTAATAATTTACCGAAATGGGCCA
53264811 TTTT
1 TTTT
53264815 CCTCGAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (28 bp):
TTTTTTAATAATTTACCGAAATGGGCCA
Found at i:53274421 original size:7 final size:7
Alignment explanation
Indices: 53274409--53274443 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
53274399 TCAGTTGTCA
53274409 ACCACCG
1 ACCACCG
53274416 ACCACCG
1 ACCACCG
53274423 ACCACCG
1 ACCACCG
53274430 ACCACCG
1 ACCACCG
53274437 ACCACCG
1 ACCACCG
53274444 GCCTCCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.57, G:0.14, T:0.00
Consensus pattern (7 bp):
ACCACCG
Found at i:53275468 original size:32 final size:32
Alignment explanation
Indices: 53275432--53275532 Score: 122
Period size: 32 Copynumber: 3.3 Consensus size: 32
53275422 TTTTATGTAT
53275432 TTAAAATTTATATTAATTACTGAAAATAGTAC
1 TTAAAATTTATATTAATTACTGAAAATAGTAC
* ** **
53275464 TTAAAATTTAT-TTTATT--T-ATTATTCTA-
1 TTAAAATTTATATTAATTACTGAAAATAGTAC
53275491 TTAAAATTTATATTAATTACTGAAAATAGTAC
1 TTAAAATTTATATTAATTACTGAAAATAGTAC
53275523 TTAAAATTTA
1 TTAAAATTTA
53275533 CTTTATTTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
27 11 0.20
28 10 0.19
29 1 0.02
30 1 0.02
31 10 0.19
32 21 0.39
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (32 bp):
TTAAAATTTATATTAATTACTGAAAATAGTAC
Found at i:53275513 original size:59 final size:59
Alignment explanation
Indices: 53275432--53275554 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
53275422 TTTTATGTAT
*
53275432 TTAAAATTTATATTAATTACTGAAAATAGTACTTAAAATTTATTTTATTTATTATTCTA
1 TTAAAATTTATATTAATTACTGAAAATAGTACTTAAAATTTACTTTATTTATTATTCTA
53275491 TTAAAATTTATATTAATTACTGAAAATAGTACTTAAAATTTACTTTATTTATTATTCTA
1 TTAAAATTTATATTAATTACTGAAAATAGTACTTAAAATTTACTTTATTTATTATTCTA
53275550 TTAAA
1 TTAAA
53275555 TTATTTAAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAAAATTTATATTAATTACTGAAAATAGTACTTAAAATTTACTTTATTTATTATTCTA
Found at i:53276937 original size:11 final size:11
Alignment explanation
Indices: 53276921--53276999 Score: 53
Period size: 11 Copynumber: 7.6 Consensus size: 11
53276911 AATTAATCAC
53276921 ATTAATATTAA
1 ATTAATATTAA
53276932 ATTAATA--AA
1 ATTAATATTAA
* *
53276941 A-TATTATCTAG
1 ATTAATAT-TAA
*
53276952 ATAAATATTAA
1 ATTAATATTAA
*
53276963 ATTAA-ATTTA
1 ATTAATATTAA
* *
53276973 A-T-ATCTTAT
1 ATTAATATTAA
53276982 ATTAATATTAA
1 ATTAATATTAA
53276993 ATTAATA
1 ATTAATA
53277000 AAATAATATC
Statistics
Matches: 49, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
8 5 0.10
9 7 0.14
10 6 0.12
11 27 0.55
12 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:53277017 original size:61 final size:62
Alignment explanation
Indices: 53276921--53277038 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 62
53276911 AATTAATCAC
* *
53276921 ATTAATATTAAATTAATAAAATATTATCTAGATAAATATTA-AATTAAATTTAATATCTTAT
1 ATTAATATTAAATTAATAAAATAATATCTACATAAATATTACAATTAAATTTAATATCTTAT
* *
53276982 ATTAATATTAAATTAATAAAATAATATCTACATAAATATTACATTTAAGTTTAATAT
1 ATTAATATTAAATTAATAAAATAATATCTACATAAATATTACAATTAAATTTAATAT
53277039 TAATTCATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 39 0.75
62 13 0.25
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (62 bp):
ATTAATATTAAATTAATAAAATAATATCTACATAAATATTACAATTAAATTTAATATCTTAT
Found at i:53283668 original size:31 final size:31
Alignment explanation
Indices: 53283630--53283696 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
53283620 ATCTTAGGAC
53283630 AGTCATCTAAAGAAAAATGAAAACCTAATGT
1 AGTCATCTAAAGAAAAATGAAAACCTAATGT
*
53283661 AGTCATCTAAAGAAAAATGAACACCTAATGT
1 AGTCATCTAAAGAAAAATGAAAACCTAATGT
53283692 AGTCA
1 AGTCA
53283697 ATTGAGTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.22
Consensus pattern (31 bp):
AGTCATCTAAAGAAAAATGAAAACCTAATGT
Found at i:53299507 original size:51 final size:50
Alignment explanation
Indices: 53299427--53299769 Score: 248
Period size: 51 Copynumber: 6.8 Consensus size: 50
53299417 TATCAATGAA
**
53299427 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAGTAATGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAGT-ATGGT
* * * * * * *
53299478 CACATGTGTGGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG-
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAG-TATG-GT
** * * * * * *
53299529 CACGTGTGTAGTACTGTGTGAATGCTACCACGTGTCTCGGTAAACTACGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGAT-AAGTATGGT
* * * * * *
53299580 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG-
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAG-TATG-GT
* * * * *
53299631 CACGTGTGTAGTACTGAGTGAAGGCTACTACGTG-AGCCATAA-AACTTGAT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAGTA--TGGT
* * * * *
53299681 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATTG-TAA-AACTGAT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAGTA-TGGT
* *
53299730 CACGTGTGTAGTACTATGTGAAGGCTAATACGTGTATCGA
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGA
53299770 ATGATAAAAA
Statistics
Matches: 225, Mismatches: 56, Indels: 23
0.74 0.18 0.08
Matches are distributed among these distances:
49 40 0.18
50 47 0.21
51 133 0.59
52 5 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAGTATGGT
Found at i:53299603 original size:102 final size:102
Alignment explanation
Indices: 53299427--53299769 Score: 405
Period size: 102 Copynumber: 3.4 Consensus size: 102
53299417 TATCAATGAA
* * *
53299427 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAGTAATGGTCACATGTGTGGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAACTAACGGTCACATGTGTAGTAC
53299492 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
66 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* * * *
53299529 CACGTGTGTAGTACTGTGTGAATGCTACCACGTGTCTCGGTAAACT-ACGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGAT-AACTAACGGTCACATGTGTAGTA
53299593 CTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* * * * *
53299631 CACGTGTGTAGTACTGAGTGAAGGCTACTACGTG-AGCCATAA--AACTTGATCACGTGTGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAACTAAC--GGTCACATGTGTAGT
* * *** *
53299693 ACTATGTGAAGGCTACTACGTGAATTGTAA-AA-C--TGAT
64 ACTAAGTGAAGGCTACTATGTG--TACCAAGAAGCTTTGAG
* *
53299730 CACGTGTGTAGTACTATGTGAAGGCTAATACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
53299770 ATGATAAAAA
Statistics
Matches: 207, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
99 36 0.17
100 5 0.02
101 36 0.17
102 124 0.60
103 6 0.03
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAACTAACGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
Found at i:53309110 original size:26 final size:25
Alignment explanation
Indices: 53309081--53309129 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
53309071 AAATTGGAAA
53309081 ATTTTACCTCC-GATAAAATTTTGATG
1 ATTTTACC-CCAG-TAAAATTTTGATG
*
53309107 ATTTTTCCCCAGTAAAATTTTGA
1 ATTTTACCCCAGTAAAATTTTGA
53309130 GAAAATCCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (25 bp):
ATTTTACCCCAGTAAAATTTTGATG
Found at i:53314285 original size:13 final size:13
Alignment explanation
Indices: 53314263--53314293 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53314253 ATTAAATAGA
53314263 TATT-TATTAAAT
1 TATTATATTAAAT
53314275 TATTATATTAAAT
1 TATTATATTAAAT
53314288 TATTAT
1 TATTAT
53314294 TGTAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTAAAT
Found at i:53314464 original size:19 final size:20
Alignment explanation
Indices: 53314440--53314483 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
53314430 AAGATATTTA
* *
53314440 TAAATATTAATT-AATTAAT
1 TAAATATAAATTAAATAAAT
53314459 TAAATATAAATTAAATAAAT
1 TAAATATAAATTAAATAAAT
53314479 TAAAT
1 TAAAT
53314484 GGTGCCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATAAATTAAATAAAT
Found at i:53314589 original size:19 final size:19
Alignment explanation
Indices: 53314549--53314603 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
53314539 CTTGTGTTAT
* * *
53314549 AATTAAAAGA-TATTTATT
1 AATTAAATGATTATTAATA
53314567 AATTAAATGATTATTAATA
1 AATTAAATGATTATTAATA
* *
53314586 AATTATATTATTA-TAATA
1 AATTAAATGATTATTAATA
53314604 TAAAGCAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
AATTAAATGATTATTAATA
Found at i:53314662 original size:30 final size:30
Alignment explanation
Indices: 53314605--53314666 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
53314595 ATTATAATAT
*
53314605 AAAGCAAAGAAATAAAAATAAAAGAAAAGA
1 AAAGCAAAGAAACAAAAATAAAAGAAAAGA
53314635 AAAG-AAAGAAACAAAACA-AAGAAGAAAAGA
1 AAAGCAAAGAAACAAAA-ATAA-AAGAAAAGA
53314665 AA
1 AA
53314667 CAGAGAGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (30 bp):
AAAGCAAAGAAACAAAAATAAAAGAAAAGA
Found at i:53316683 original size:220 final size:220
Alignment explanation
Indices: 53316301--53316739 Score: 869
Period size: 220 Copynumber: 2.0 Consensus size: 220
53316291 AAATTTTAGT
53316301 GATGTATTTCTTCCTTTTGTTTAAGTGGCATGTACTAGGTGATTGTACATGAGTCGTATATATAT
1 GATGTATTTCTTCCTTTTGTTTAAGTGGCATGTACTAGGTGATTGTACATGAGTCGTATATATAT
53316366 ATACTAAATGATCTTAGTTGTAAGTAATGGTTATAATCTTTTGAATGATAAATAAAGTAGTGAAT
66 ATACTAAATGATCTTAGTTGTAAGTAATGGTTATAATCTTTTGAATGATAAATAAAGTAGTGAAT
*
53316431 CAATTTATTAAGCATGATTTAGTAGCGTTTTAAAGTATAAAATTATTGATTGAAATATTGGTATT
131 CAATTTATTAAGCATGATTAAGTAGCGTTTTAAAGTATAAAATTATTGATTGAAATATTGGTATT
53316496 GGGTTGTTTTTGGTTTTAAGTTTGC
196 GGGTTGTTTTTGGTTTTAAGTTTGC
53316521 GATGTATTTCTTCCTTTTGTTTAAGTGGCATGTACTAGGTGATTGTACATGAGTCGTATATATAT
1 GATGTATTTCTTCCTTTTGTTTAAGTGGCATGTACTAGGTGATTGTACATGAGTCGTATATATAT
53316586 ATACTAAATGATCTTAGTTGTAAGTAATGGTTATAATCTTTTGAATGATAAATAAAGTAGTGAAT
66 ATACTAAATGATCTTAGTTGTAAGTAATGGTTATAATCTTTTGAATGATAAATAAAGTAGTGAAT
53316651 CAATTTATTAAGCATGATTAAGTAGCGTTTTAAAGTATAAAATTATTGATTGAAATATTGGTATT
131 CAATTTATTAAGCATGATTAAGTAGCGTTTTAAAGTATAAAATTATTGATTGAAATATTGGTATT
53316716 GGGTTGTTTTTGGTTTTAAGTTTG
196 GGGTTGTTTTTGGTTTTAAGTTTG
53316740 TAGGGGGTTT
Statistics
Matches: 218, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 218 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.44
Consensus pattern (220 bp):
GATGTATTTCTTCCTTTTGTTTAAGTGGCATGTACTAGGTGATTGTACATGAGTCGTATATATAT
ATACTAAATGATCTTAGTTGTAAGTAATGGTTATAATCTTTTGAATGATAAATAAAGTAGTGAAT
CAATTTATTAAGCATGATTAAGTAGCGTTTTAAAGTATAAAATTATTGATTGAAATATTGGTATT
GGGTTGTTTTTGGTTTTAAGTTTGC
Found at i:53322876 original size:12 final size:12
Alignment explanation
Indices: 53322859--53322883 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53322849 GGATAAACTA
53322859 ATATTTAGTTTT
1 ATATTTAGTTTT
53322871 ATATTTAGTTTT
1 ATATTTAGTTTT
53322883 A
1 A
53322884 AAGTTAAAAT
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATATTTAGTTTT
Found at i:53323440 original size:13 final size:13
Alignment explanation
Indices: 53323424--53323448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53323414 TAATTAAAGG
53323424 GTTAAAATTTAAT
1 GTTAAAATTTAAT
53323437 GTTAAAATTTAA
1 GTTAAAATTTAA
53323449 AGATGATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
GTTAAAATTTAAT
Found at i:53323517 original size:9 final size:9
Alignment explanation
Indices: 53323503--53323602 Score: 50
Period size: 9 Copynumber: 11.6 Consensus size: 9
53323493 AACTTTGGAT
53323503 CATAACTTA
1 CATAACTTA
53323512 CATAACTTA
1 CATAACTTA
53323521 CATAA--TA
1 CATAACTTA
*
53323528 CATAA-ATA
1 CATAACTTA
* * *
53323536 TATATCATA
1 CATAACTTA
*
53323545 TCATAACTTG
1 -CATAACTTA
53323555 CATAACTTA
1 CATAACTTA
*
53323564 TATAA--TA
1 CATAACTTA
*
53323571 CATAA-ATA
1 CATAACTTA
* * *
53323579 TATATCATA
1 CATAACTTA
53323588 TCATAACTTA
1 -CATAACTTA
53323598 CATAA
1 CATAA
53323603 ATATATAAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
7 13 0.18
8 10 0.14
9 37 0.52
10 11 0.15
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:53323560 original size:43 final size:43
Alignment explanation
Indices: 53323501--53323602 Score: 186
Period size: 43 Copynumber: 2.4 Consensus size: 43
53323491 AAAACTTTGG
53323501 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
* *
53323544 ATCATAACTTGCATAACTTATATAATACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
53323587 ATCATAACTTACATAA
1 ATCATAACTTACATAA
53323603 ATATATAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (43 bp):
ATCATAACTTACATAACTTACATAATACATAAATATATATCAT
Found at i:53328689 original size:22 final size:22
Alignment explanation
Indices: 53328661--53328702 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
53328651 TTCCAAACAA
53328661 TAATAACAAAATAGTAGCAATG
1 TAATAACAAAATAGTAGCAATG
53328683 TAATAACAAAATAGTAGCAA
1 TAATAACAAAATAGTAGCAA
53328703 AACAAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (22 bp):
TAATAACAAAATAGTAGCAATG
Found at i:53338505 original size:6 final size:6
Alignment explanation
Indices: 53338457--53338494 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
53338447 AGAGAGAAAT
53338457 AGAGTG AGAGTG AGAGTG AGAGTG AGAGTG AGAGTG AG
1 AGAGTG AGAGTG AGAGTG AGAGTG AGAGTG AGAGTG AG
53338495 TGAAAGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
AGAGTG
Found at i:53339672 original size:24 final size:24
Alignment explanation
Indices: 53339656--53339705 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
53339646 TAATCAATGT
*
53339656 TAAATATATTATGCTAATAAATAC
1 TAAATATATTATACTAATAAATAC
53339680 TAAATATATTATACTAATAAATAC
1 TAAATATATTATACTAATAAATAC
53339704 TA
1 TA
53339706 CATCTTCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATAC
Found at i:53342551 original size:57 final size:58
Alignment explanation
Indices: 53342445--53342560 Score: 164
Period size: 57 Copynumber: 2.0 Consensus size: 58
53342435 CGGTAAAAGG
* *
53342445 ATCTAGCCCGGACGGGTGATCTTATCCTGATATAGCCTTCCCGAAGAATATGTGTGAAAAAA
1 ATCTAACCCGGACGGGTGATC-T-T-CTGATATAGCCCTCCCGAAGAATATGTG-GAAAAAA
53342507 ATCTAACCCGGACGGGTGATC-T-TGATATAGCCCTCCCGAAGAATATGTGGAAAA
1 ATCTAACCCGGACGGGTGATCTTCTGATATAGCCCTCCCGAAGAATATGTGGAAAA
53342561 TGGATTTAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
56 5 0.10
57 26 0.50
59 1 0.02
62 20 0.38
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (58 bp):
ATCTAACCCGGACGGGTGATCTTCTGATATAGCCCTCCCGAAGAATATGTGGAAAAAA
Found at i:53347453 original size:24 final size:24
Alignment explanation
Indices: 53347438--53347489 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
53347428 AATCAATGTC
*
53347438 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
53347462 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
53347486 AAAT
1 AAAT
53347490 CTATCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:53349065 original size:45 final size:45
Alignment explanation
Indices: 53349001--53349197 Score: 297
Period size: 45 Copynumber: 4.4 Consensus size: 45
53348991 ATGTGCCAAC
53349001 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTAT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTAT
53349046 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTAT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTAT
* * * *
53349091 AACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTAT
* * * *
53349136 TACCGTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACTGATTCGA-CACTTTGTGTGTCGAATACTAT
*
53349181 TACTGTTAATGTTACTG
1 TACTGTTACTGTTACTG
53349198 CTACCGTTAC
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 139 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTAT
Found at i:53349186 original size:6 final size:6
Alignment explanation
Indices: 53349175--53349223 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
53349165 GTGTGTTGAA
* * *
53349175 TACTGT TACTGT TAATGT TACTGC TACCGT TACTGAT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG-T TACTG
53349224 GTGCGTTTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
6 23 0.66
7 12 0.34
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:53351788 original size:17 final size:17
Alignment explanation
Indices: 53351766--53351798 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53351756 ATCTGTTGTT
*
53351766 TTAATTTTTTTATATTA
1 TTAATTTTATTATATTA
53351783 TTAATTTTATTATATT
1 TTAATTTTATTATATT
53351799 GTATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTAATTTTATTATATTA
Found at i:53352056 original size:14 final size:13
Alignment explanation
Indices: 53352032--53352087 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
53352022 ATTTTCATAA
53352032 TTTATTAATATATT
1 TTTATT-ATATATT
*
53352046 TTTACT-TATATT
1 TTTATTATATATT
53352058 TTT-TTATATATT
1 TTTATTATATATT
53352070 TTTATT-TAT-TT
1 TTTATTATATATT
53352081 ATTTATT
1 -TTTATT
53352088 GATACCTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 3 0.08
12 27 0.73
13 2 0.05
14 5 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTATATATT
Found at i:53352066 original size:24 final size:22
Alignment explanation
Indices: 53352031--53352086 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
53352021 TATTTTCATA
*
53352031 ATTTATTAATATATTTTTACTTAT
1 ATTTATTTATATATTTTTA-TT-T
*
53352055 ATTTTTTTATATATTTTTATTT
1 ATTTATTTATATATTTTTATTT
53352077 ATTTATTTAT
1 ATTTATTTAT
53352087 TGATACCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 10 0.34
23 2 0.07
24 17 0.59
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTATTTATATATTTTTATTT
Found at i:53355556 original size:15 final size:15
Alignment explanation
Indices: 53355536--53355610 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 15
53355526 AGGAAGGTCT
53355536 TCAGAATGAGCAACG
1 TCAGAATGAGCAACG
*
53355551 TCAGAATGAGCATC-
1 TCAGAATGAGCAACG
* * *
53355565 T-AGAGATAAAGGAAGGTCT
1 TCAGA-AT-GAGCAA---CG
53355584 TCAGAATGAGCAACG
1 TCAGAATGAGCAACG
53355599 TCAGAATGAGCA
1 TCAGAATGAGCA
53355611 TCTAGAGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 29 0.63
18 5 0.11
19 3 0.07
20 3 0.07
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.17
Consensus pattern (15 bp):
TCAGAATGAGCAACG
Found at i:53355565 original size:48 final size:48
Alignment explanation
Indices: 53355509--53355630 Score: 244
Period size: 48 Copynumber: 2.5 Consensus size: 48
53355499 AGGTTCGGAT
53355509 TGAGCATCTAGAGATAAAGGAAGGTCTTCAGAATGAGCAACGTCAGAA
1 TGAGCATCTAGAGATAAAGGAAGGTCTTCAGAATGAGCAACGTCAGAA
53355557 TGAGCATCTAGAGATAAAGGAAGGTCTTCAGAATGAGCAACGTCAGAA
1 TGAGCATCTAGAGATAAAGGAAGGTCTTCAGAATGAGCAACGTCAGAA
53355605 TGAGCATCTAGAGATAAAGGAAGGTC
1 TGAGCATCTAGAGATAAAGGAAGGTC
53355631 ACCTACAAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.19
Consensus pattern (48 bp):
TGAGCATCTAGAGATAAAGGAAGGTCTTCAGAATGAGCAACGTCAGAA
Found at i:53364413 original size:42 final size:42
Alignment explanation
Indices: 53364188--53364522 Score: 195
Period size: 44 Copynumber: 7.9 Consensus size: 42
53364178 CGGTGAAACT
* *
53364188 TCAG-TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAAAA
1 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT----AAAA
* * *
53364233 T-A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
1 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA
* * ** ***
53364273 TCAGATCTTATCTTTCTGAAGTTGTAGAAGAGCAGA-TCGCA
1 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA
*
53364314 TCCAG-TCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAGAAAA
1 T-CAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT----AAAA
* * * * *
53364360 T-A-ATCCTATCTCTTTAAAGTTACAGTGGAGCGGATTAAAA
1 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA
* ** ***
53364400 TCAGATCTTATCTCTCTGAAGTTACAGAAGAGCAGA-TCGCA
1 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA
* * *
53364441 TCTAG-TTTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGATGA
1 TC-AGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAA-A--A
* * ** *
53364486 T-ATATCTCATCTCTCTGCGGTTGCAGTAGAGCAGATT
1 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT
53364523 GTATCAGACT
Statistics
Matches: 221, Mismatches: 51, Indels: 37
0.72 0.17 0.12
Matches are distributed among these distances:
40 10 0.05
41 63 0.29
42 57 0.26
43 1 0.00
44 85 0.38
45 3 0.01
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (42 bp):
TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAA
Found at i:53364499 original size:127 final size:127
Alignment explanation
Indices: 53364189--53364477 Score: 470
Period size: 127 Copynumber: 2.3 Consensus size: 127
53364179 GGTGAAACTT
* * *
53364189 CAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAAAATAATCCTATCTCCCTGAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAATAATCCTATCTCTCTAAAGTT
* * **
53364254 GCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTGAAGTTGTAGAAGAGCAGATCGCATC
66 ACAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTACAGAAGAGCAGATCGCATC
* * *
53364316 CAGTCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAGAAAATAATCCTATCTCTTTAAAGTT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAATAATCCTATCTCTCTAAAGTT
53364381 ACAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTACAGAAGAGCAGATCGCATC
66 ACAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTACAGAAGAGCAGATCGCATC
* *
53364443 TAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
53364478 CAAGATGATA
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
127 148 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (127 bp):
CAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAATAATCCTATCTCTCTAAAGTT
ACAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTACAGAAGAGCAGATCGCATC
Found at i:53365844 original size:17 final size:17
Alignment explanation
Indices: 53365822--53365854 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53365812 ATCTGTTGTT
*
53365822 TTAATTTTTTTATATTA
1 TTAATTTTATTATATTA
53365839 TTAATTTTATTATATT
1 TTAATTTTATTATATT
53365855 GTATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTAATTTTATTATATTA
Found at i:53365860 original size:24 final size:24
Alignment explanation
Indices: 53365832--53365879 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
53365822 TTAATTTTTT
*
53365832 TATATTATTAATTTTAT-TATATTG
1 TATATTATT-ATTATATCTATATTG
53365856 TATATTATTATTATATCTATATTG
1 TATATTATTATTATATCTATATTG
53365880 CATAGGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
TATATTATTATTATATCTATATTG
Found at i:53371884 original size:21 final size:22
Alignment explanation
Indices: 53371860--53371901 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
53371850 TATTTAAATT
53371860 AAAT-TAAATTATAAAA-TATAC
1 AAATATAAA-TATAAAAGTATAC
*
53371881 AAATATTAATATAAAAGTATA
1 AAATATAAATATAAAAGTATA
53371902 TATTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATATAAATATAAAAGTATAC
Found at i:53374913 original size:30 final size:28
Alignment explanation
Indices: 53374858--53374916 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
53374848 TAAAAGACAT
* *
53374858 ATATATGTGTATATGTATAAGTTATAAA
1 ATATATATGTATATGTATAAATTATAAA
53374886 ATATATATGTATATGTATATATATTATAAA
1 ATATATATGTATATGTATA-A-ATTATAAA
53374916 A
1 A
53374917 ACGTATGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 18 0.67
29 1 0.04
30 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (28 bp):
ATATATATGTATATGTATAAATTATAAA
Found at i:53377570 original size:3 final size:3
Alignment explanation
Indices: 53377555--53377620 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
53377545 TTTAAGATTT
* * ** * *
53377555 TTA TTA TTG TTA TTA TTA TTA TTA TTA ATA CCA TCA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
53377603 TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
53377621 AATTGTTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:53383094 original size:18 final size:16
Alignment explanation
Indices: 53383065--53383098 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
53383055 TCAAAGTAAA
53383065 TATTATTTATTAAATT
1 TATTATTTATTAAATT
53383081 TATTATATTAATTAAATT
1 TATTAT-TT-ATTAAATT
53383099 AATTTCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTATTAAATT
Found at i:53385130 original size:17 final size:19
Alignment explanation
Indices: 53385099--53385135 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53385089 GTATATTAGT
53385099 AAATTAATAAAAAA-TAAA
1 AAATTAATAAAAAATTAAA
*
53385117 AAATT-ATAATAAATTAAA
1 AAATTAATAAAAAATTAAA
53385135 A
1 A
53385136 GGTAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATTAATAAAAAATTAAA
Found at i:53385464 original size:16 final size:17
Alignment explanation
Indices: 53385443--53385482 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
53385433 TGTTAATTTT
53385443 AATGTTAAAG-GACT-AA
1 AATGTTAAAGTGA-TAAA
53385459 AATGTTAAAGTGATAAA
1 AATGTTAAAGTGATAAA
53385476 AATGTTA
1 AATGTTA
53385483 GGACTTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (17 bp):
AATGTTAAAGTGATAAA
Found at i:53386159 original size:45 final size:45
Alignment explanation
Indices: 53386060--53386182 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 45
53386050 AATGAAACGG
* * * **
53386060 ATAAGACCATAGTTGAAAGACATTATGACATTATACCGGAATTGA
1 ATAAAACCATAGTTGAAAGACATTATGACATCATACCAGAACCGA
* *
53386105 ATAAGACCATAGTTGAAAGGA-ATTATGACATCATACTAGAACCGA
1 ATAAAACCATAGTTGAAA-GACATTATGACATCATACCAGAACCGA
* * * * *
53386150 GTAAAACCATAGCTGAAAAACGTTATGGCATCA
1 ATAAAACCATAGTTGAAAGACATTATGACATCA
53386183 CGATTTTAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.02
45 62 0.95
46 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (45 bp):
ATAAAACCATAGTTGAAAGACATTATGACATCATACCAGAACCGA
Found at i:53386198 original size:45 final size:45
Alignment explanation
Indices: 53386147--53386452 Score: 375
Period size: 45 Copynumber: 6.8 Consensus size: 45
53386137 ATACTAGAAC
* *
53386147 CGAGTAAAACCATAGCTGAAAAACGTTATGGCATCACGATTTTAA
1 CGAGTAAGACCATAGCTGAAAAACGTTATGGCATCACGATTCTAA
* * * * *
53386192 CAAGTAAGATCATAGCTGAAAGACGTTATGGCATCATGATTTTAA
1 CGAGTAAGACCATAGCTGAAAAACGTTATGGCATCACGATTCTAA
* *
53386237 CGAGTAAGACCATAGCTGAAATACATTATGGCATCACGAGTT-TAA
1 CGAGTAAGACCATAGCTGAAAAACGTTATGGCATCACGA-TTCTAA
* *
53386282 TGAGTAAGACCATAGCT-AAAAGACGTTATGGAATCACGATTCTAA
1 CGAGTAAGACCATAGCTGAAAA-ACGTTATGGCATCACGATTCTAA
** *
53386327 CGAGTAAGACCATAGCT-AAAAGACACTATAGCATCACGATTCTAA
1 CGAGTAAGACCATAGCTGAAAA-ACGTTATGGCATCACGATTCTAA
* *
53386372 CGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCTAA
1 CGAGTAAGACCATAGCTGAAAAACGTTATGGCATCACGATTCTAA
* * * * *
53386417 CAAGTAAGACTATAGCTGAAAGATGCTATGGCATCA
1 CGAGTAAGACCATAGCTGAAAAACGTTATGGCATCA
53386453 TGAATCAGAC
Statistics
Matches: 232, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
44 5 0.02
45 222 0.96
46 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (45 bp):
CGAGTAAGACCATAGCTGAAAAACGTTATGGCATCACGATTCTAA
Found at i:53386221 original size:90 final size:89
Alignment explanation
Indices: 53386106--53386437 Score: 355
Period size: 90 Copynumber: 3.7 Consensus size: 89
53386096 CGGAATTGAA
* * * * *
53386106 TAAGACCATAGTTGAAAGGA-ATTATGACATCATACTAGAACCGAGTAAAACCATAGCTGAAAAA
1 TAAGACCATAGCTGAAA-GACGTTATGACATCATATTATAA-CGAGTAAGACCATAGCTGAAAAA
* *
53386170 CGTTATGGCATCACGATTTTAACAAG
64 CATTATGGCATCACGATTTTAACGAG
* * * *
53386196 TAAGATCATAGCTGAAAGACGTTATGGCATCATGATTTTAACGAGTAAGACCATAGCTGAAATAC
1 TAAGACCATAGCTGAAAGACGTTATGACATCAT-ATTATAACGAGTAAGACCATAGCTGAAAAAC
* *
53386261 ATTATGGCATCACGAGTTTAATGAG
65 ATTATGGCATCACGATTTTAACGAG
* * *
53386286 TAAGACCATAGCTAAAAGACGTTATGGA-ATCACGATTCTAACGAGTAAGACCATAGCT-AAAAG
1 TAAGACCATAGCTGAAAGACGTTAT-GACATCA-TATTATAACGAGTAAGACCATAGCTGAAAA-
* * *
53386349 ACACTATAGCATCACGATTCTAACGAG
63 ACATTATGGCATCACGATTTTAACGAG
* * * * * *
53386376 TAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCTAACAAGTAAGACTATAGCTGAAA
1 TAAGACCATAGCTGAAAGACGTTATGACATCA-TATTATAACGAGTAAGACCATAGCTGAAA
53386438 GATGCTATGG
Statistics
Matches: 206, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
89 6 0.03
90 192 0.93
91 8 0.04
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (89 bp):
TAAGACCATAGCTGAAAGACGTTATGACATCATATTATAACGAGTAAGACCATAGCTGAAAAACA
TTATGGCATCACGATTTTAACGAG
Found at i:53386439 original size:90 final size:90
Alignment explanation
Indices: 53386147--53386496 Score: 400
Period size: 90 Copynumber: 3.9 Consensus size: 90
53386137 ATACTAGAAC
* * ** * * *
53386147 CGAGTAAAACCATAGCTGAAAAACGTTATGGCATCACGATTTTAACAAGTAAGATCATAGCTGAA
1 CGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAA
* * *
53386212 AGACGTTATGGCATCATGATTTTAA
66 AGACGCTATGGCATCACGATTCTAA
* * * *
53386237 CGAGTAAGACCATAGCTGAAATACATTATGGCATCACGAGTT-TAATGAGTAAGACCATAGCTAA
1 CGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGA-TTCTAACGAGTAAGACCATAGCTGA
* *
53386301 AAGACGTTATGGAATCACGATTCTAA
65 AAGACGCTATGGCATCACGATTCTAA
* *
53386327 CGAGTAAGACCATAGCTAAAAGACACTATAGCATCACGATTCTAACGAGTAAGACCATAGCTGAA
1 CGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAA
53386392 AGACGCTATGGCATCACGATTCTAA
66 AGACGCTATGGCATCACGATTCTAA
* * ** * * * * *
53386417 CAAGTAAGACTATAGCTGAAAGATGCTATGGCATCATGAATC-AGACGAATAAGATCAT-GATTG
1 CGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTCTA-ACGAGTAAGACCATAG-CTG
*
53386480 AAAGACACTATGGCATC
64 AAAGACGCTATGGCATC
53386497 CTTCAACCTT
Statistics
Matches: 226, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
89 4 0.02
90 220 0.97
91 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (90 bp):
CGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAA
AGACGCTATGGCATCACGATTCTAA
Found at i:53386470 original size:45 final size:45
Alignment explanation
Indices: 53386155--53386496 Score: 318
Period size: 45 Copynumber: 7.6 Consensus size: 45
53386145 ACCGAGTAAA
* *
53386155 ACCATAGCTGAAAA-ACGTTATGGCATCACGATTTTAAC-AAGTAAG
1 ACCATAGCT-AAAAGACGCTATGGCATCACGATTCTAACGAA-TAAG
* * * * * *
53386200 ATCATAGCTGAAAGACGTTATGGCATCATGATTTTAACGAGTAAG
1 ACCATAGCTAAAAGACGCTATGGCATCACGATTCTAACGAATAAG
* * ** * *
53386245 ACCATAGCTGAAATACATTATGGCATCACGAGTT-TAATGAGTAAG
1 ACCATAGCTAAAAGACGCTATGGCATCACGA-TTCTAACGAATAAG
* * *
53386290 ACCATAGCTAAAAGACGTTATGGAATCACGATTCTAACGAGTAAG
1 ACCATAGCTAAAAGACGCTATGGCATCACGATTCTAACGAATAAG
* * *
53386335 ACCATAGCTAAAAGACACTATAGCATCACGATTCTAACGAGTAAG
1 ACCATAGCTAAAAGACGCTATGGCATCACGATTCTAACGAATAAG
*
53386380 ACCATAGCTGAAAGACGCTATGGCATCACGATTCTAAC-AAGTAAG
1 ACCATAGCTAAAAGACGCTATGGCATCACGATTCTAACGAA-TAAG
* * * * *
53386425 ACTATAGCTGAAAGATGCTATGGCATCATGAATC-AGACGAATAAG
1 ACCATAGCTAAAAGACGCTATGGCATCACGATTCTA-ACGAATAAG
* * * *
53386470 ATCAT-GATTGAAAGACACTATGGCATC
1 ACCATAG-CTAAAAGACGCTATGGCATC
53386497 CTTCAACCTT
Statistics
Matches: 258, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
44 8 0.03
45 245 0.95
46 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (45 bp):
ACCATAGCTAAAAGACGCTATGGCATCACGATTCTAACGAATAAG
Found at i:53386470 original size:135 final size:135
Alignment explanation
Indices: 53386149--53386496 Score: 382
Period size: 135 Copynumber: 2.6 Consensus size: 135
53386139 ACTAGAACCG
* * * * *
53386149 AGTAAAACCATAGCTGAAAA-ACGTTATGGCATCACGATTTTAAC-AAGTAAGATCATAGCTGAA
1 AGTAAGACCATAGCT-AAAAGACGCTATGGAATCACGAATCTAACGAA-TAAGATCATAGCTGAA
** * * * *
53386212 AGACGTTATGGCATCATGATTTTAACGAGTAAGACCATAGCTGAAATACATTATGGCATCACGAG
64 AGACACTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGAG
**
53386277 TTTAATG
129 TTTAACA
* * * * *
53386284 AGTAAGACCATAGCTAAAAGACGTTATGGAATCACGATTCTAACGAGTAAGACCATAGCTAAAAG
1 AGTAAGACCATAGCTAAAAGACGCTATGGAATCACGAATCTAACGAATAAGATCATAGCTGAAAG
* *
53386349 ACACTATAGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGA-TT
66 ACACTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGAGTT
53386413 CTAACA
131 -TAACA
* * * * * *
53386419 AGTAAGACTATAGCTGAAAGATGCTATGGCATCATGAATC-AGACGAATAAGATCAT-GATTGAA
1 AGTAAGACCATAGCTAAAAGACGCTATGGAATCACGAATCTA-ACGAATAAGATCATAG-CTGAA
53386482 AGACACTATGGCATC
64 AGACACTATGGCATC
53386497 CTTCAACCTT
Statistics
Matches: 180, Mismatches: 28, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
134 8 0.04
135 171 0.95
136 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (135 bp):
AGTAAGACCATAGCTAAAAGACGCTATGGAATCACGAATCTAACGAATAAGATCATAGCTGAAAG
ACACTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACACTATGGCATCACGAGTT
TAACA
Found at i:53393126 original size:51 final size:52
Alignment explanation
Indices: 53393049--53393177 Score: 174
Period size: 52 Copynumber: 2.5 Consensus size: 52
53393039 CGGATACCCG
* * *
53393049 GTGGCCTGCATATAGTACCAGC-CTTGT-AGCCAAAGCTA-CCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCA-CACTTGTGA-CAAAAGCTATCCTTCTTCACAAA
* *
53393100 GTGGCCTTCACATAGTACCACACTTGTGACAAAAGCTATCTTTCTTTACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACAAAAGCTATCCTTCTTCACAAA
53393152 GTGGCCTTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
53393178 AGTCACTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
50 1 0.01
51 31 0.44
52 38 0.54
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTGACAAAAGCTATCCTTCTTCACAAA
Found at i:53400370 original size:52 final size:52
Alignment explanation
Indices: 53400262--53400439 Score: 215
Period size: 52 Copynumber: 3.5 Consensus size: 52
53400252 CGGATACCCG
* * * *
53400262 GTGGCCTGCACATAGTACCACCCTTG-AAGCCAAAGCTA-CCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCTTTCTTCACAAA
*
53400313 GTGGCCTTCACACAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
* *
53400365 GTGGCCTTCACATAGTACCACACTTGTGATC-AAGTTATCTATTC-T--CAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCT-TTCTTCACAAA
* *
53400414 GTGTCCGTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
53400440 AGTCACTAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
49 28 0.25
51 41 0.36
52 45 0.39
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
Found at i:53403040 original size:25 final size:25
Alignment explanation
Indices: 53403012--53403061 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
53403002 CTAATAGGCT
*
53403012 AAACATCCCTCCAAAAACACACTTG
1 AAACATACCTCCAAAAACACACTTG
*
53403037 AAACATACCTCCAAAAACACGCTTG
1 AAACATACCTCCAAAAACACACTTG
53403062 GGCACTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.34, G:0.06, T:0.16
Consensus pattern (25 bp):
AAACATACCTCCAAAAACACACTTG
Found at i:53404524 original size:36 final size:36
Alignment explanation
Indices: 53404484--53404555 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
53404474 GAGAAAACTA
*
53404484 GATAAAACTCTAAGCTAAAACTAATTTAGTGTGGCC
1 GATAAAACCCTAAGCTAAAACTAATTTAGTGTGGCC
53404520 GATAAAACCCTAAGCTAAAACTAATTTAGTGTGGCC
1 GATAAAACCCTAAGCTAAAACTAATTTAGTGTGGCC
53404556 TCCTTTTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (36 bp):
GATAAAACCCTAAGCTAAAACTAATTTAGTGTGGCC
Found at i:53404796 original size:21 final size:21
Alignment explanation
Indices: 53404772--53404811 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53404762 GCTTCTTGGC
*
53404772 AAGTGGATATTGCGATACCCA
1 AAGTGGATATCGCGATACCCA
*
53404793 AAGTGGTTATCGCGATACC
1 AAGTGGATATCGCGATACC
53404812 ACTGAAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGTGGATATCGCGATACCCA
Found at i:53417136 original size:4 final size:4
Alignment explanation
Indices: 53417127--53417155 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
53417117 TTTTCGAAAT
53417127 TTAA TTAA TTAA TTAA TTAA TTAA -TAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
53417156 TGAAAAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:53427550 original size:6 final size:6
Alignment explanation
Indices: 53427535--53427570 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
53427525 CAATGGTATA
* *
53427535 TATATC TATATG TATATG TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC
53427571 CAGTGTTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:53427558 original size:18 final size:18
Alignment explanation
Indices: 53427535--53427569 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53427525 CAATGGTATA
*
53427535 TATATCTATATGTATATG
1 TATATCTATATCTATATG
53427553 TATATCTATATCTATAT
1 TATATCTATATCTATAT
53427570 CCAGTGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (18 bp):
TATATCTATATCTATATG
Found at i:53429760 original size:14 final size:14
Alignment explanation
Indices: 53429741--53429780 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53429731 TTGATTGCCA
53429741 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
53429755 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
53429769 GGAAAATGTTTT
1 GTAAAATGTTTT
53429781 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:53429789 original size:20 final size:20
Alignment explanation
Indices: 53429764--53429803 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53429754 CGTAAAATGA
*
53429764 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
53429784 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53429804 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53429793 original size:34 final size:35
Alignment explanation
Indices: 53429749--53429815 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53429739 CAGTAAAATG
*
53429749 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
53429783 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
53429816 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:53429819 original size:14 final size:15
Alignment explanation
Indices: 53429743--53429819 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
53429733 GATTGCCAGT
* *
53429743 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
53429757 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
53429771 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
53429791 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
53429806 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
53429820 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:53430219 original size:21 final size:21
Alignment explanation
Indices: 53430190--53430231 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
53430180 ATGGAAATTG
*
53430190 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
*
53430211 AAAATGTAACACATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
53430232 TGTTTTGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAGGTAACACATTTTCCCT
Done.