Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 163 of 226
Found at i:52068910 original size:15 final size:15
Alignment explanation
Indices: 52068888--52068920 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
52068878 CTTTTTCCCC
52068888 TTTTTCTT-TTCTTT
1 TTTTTCTTCTTCTTT
52068902 TTTTGTCTTCTTCTTT
1 TTTT-TCTTCTTCTTT
52068918 TTT
1 TTT
52068921 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 4 0.24
16 9 0.53
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTCTTCTTCTTT
Found at i:52068996 original size:17 final size:17
Alignment explanation
Indices: 52068955--52069002 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
52068945 GCTTTCGTGG
*
52068955 GCTGGCCTGCTCGCTGCT
1 GCTGGGCTGCT-GCTGCT
* *
52068973 GCAGGGCTGCTGCTGGT
1 GCTGGGCTGCTGCTGCT
52068990 GCTGGGCTGCTGC
1 GCTGGGCTGCTGC
52069003 AACCGGGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.02, C:0.31, G:0.42, T:0.25
Consensus pattern (17 bp):
GCTGGGCTGCTGCTGCT
Found at i:52069259 original size:4 final size:4
Alignment explanation
Indices: 52069252--52069307 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
52069242 TTCTTTCCCT
*
52069252 TTTC TTTC TTTT TTTC TTTC TTT- TTTC -TTC TTTC TTTC -TTC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC
52069298 -TTC -TTC TTTC
1 TTTC TTTC TTTC
52069308 CCTTCGACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 15 0.33
4 27 0.60
5 3 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:52069265 original size:11 final size:11
Alignment explanation
Indices: 52069235--52069307 Score: 69
Period size: 11 Copynumber: 6.4 Consensus size: 11
52069225 TTTTCTATTT
52069235 TTTC-TTTTTC
1 TTTCTTTTTTC
**
52069245 TTTCCCTTTTC
1 TTTCTTTTTTC
52069256 TTTCTTTTTTTC
1 TTTC-TTTTTTC
52069268 TTTCTTTTTTC
1 TTTCTTTTTTC
52069279 -TTCTTTCTTTC
1 TTTCTTT-TTTC
52069290 TTCTCTTCTTCTTC
1 TT-TCTT-TT-TTC
52069304 TTTC
1 TTTC
52069308 CCTTCGACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
10 10 0.19
11 20 0.38
12 10 0.19
13 7 0.13
14 6 0.11
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:52069266 original size:30 final size:29
Alignment explanation
Indices: 52069226--52069311 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
52069216 TCAACCGCCT
52069226 TTTCTATTTTTTCTTTTTCTTTCCCTTTTC
1 TTTCT-TTTTTTCTTTTTCTTTCCCTTTTC
* *
52069256 TTTCTTTTTTTCTTTCTT-TTTTCTTCTTTC
1 TTTCTTTTTTTCTTT-TTCTTTCCCT-TTTC
* * *
52069286 TTTCTTCTCTTCTTCTTCTTTCCCTT
1 TTTCTTTTTTTCTTTTTCTTTCCCTT
52069312 CGACCTTGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
29 18 0.39
30 28 0.61
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTCTTTTTTTCTTTTTCTTTCCCTTTTC
Found at i:52069271 original size:27 final size:26
Alignment explanation
Indices: 52069223--52069274 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52069213 GGGTCAACCG
52069223 CCTTTTCTATTTTTTCTTTTTCTTTC
1 CCTTTTCTATTTTTTCTTTTTCTTTC
*
52069249 CCTTTTCT-TTCTTTTTTTCTTTCTTT
1 CCTTTTCTATT-TTTTCTT-TTTCTTT
52069275 TTTCTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 14 0.61
27 7 0.30
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (26 bp):
CCTTTTCTATTTTTTCTTTTTCTTTC
Found at i:52069703 original size:13 final size:13
Alignment explanation
Indices: 52069685--52069709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52069675 CAATCTAACC
52069685 CAATTACCCAACT
1 CAATTACCCAACT
52069698 CAATTACCCAAC
1 CAATTACCCAAC
52069710 CCAACCCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACT
Found at i:52069832 original size:9 final size:9
Alignment explanation
Indices: 52069815--52069908 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
52069805 TGTTTGATTC
*
52069815 AATTAGGTT
1 AATTCGGTT
52069824 AATTCGGTT
1 AATTCGGTT
52069833 AATTCGGTT
1 AATTCGGTT
*
52069842 AATTCGGGT
1 AATTCGGTT
*
52069851 AATTCGGGT
1 AATTCGGTT
52069860 AATTCGGTT
1 AATTCGGTT
* *
52069869 AAGTCGGGT
1 AATTCGGTT
52069878 AATTCGGTT
1 AATTCGGTT
* *
52069887 AATTTGGCT
1 AATTCGGTT
52069896 AATTCGGTT
1 AATTCGGTT
52069905 AATT
1 AATT
52069909 TTTAACCAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:52070355 original size:29 final size:29
Alignment explanation
Indices: 52070231--52070347 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 29
52070221 GGGGATAAAG
** * *
52070231 TGTAAATTTTGGAAAATTTGGGGTCAAAA
1 TGTAAATTTAAGAAAGTTAGGGGTCAAAA
* * *
52070260 TGTAATTTTAAGAAAGTTAAGGGTTAAAA
1 TGTAAATTTAAGAAAGTTAGGGGTCAAAA
*
52070289 TGTAATTTTAAGAAAGTTTAGGGGTCAAAA
1 TGTAAATTTAAGAAAG-TTAGGGGTCAAAA
*
52070319 TG-AAATTTAAAAAAGTTAGGGGTCAAAA
1 TGTAAATTTAAGAAAGTTAGGGGTCAAAA
52070347 T
1 T
52070348 ACAAATTTCT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
28 14 0.18
29 49 0.64
30 13 0.17
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (29 bp):
TGTAAATTTAAGAAAGTTAGGGGTCAAAA
Found at i:52070519 original size:7 final size:6
Alignment explanation
Indices: 52070499--52070528 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
52070489 CAAAAACTAC
*
52070499 AAATAA AATTAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
52070529 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:52070553 original size:25 final size:24
Alignment explanation
Indices: 52070525--52070585 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
52070515 AAAAATAAAA
52070525 ATAATTTTTAAATATTT-AAATATTT
1 ATAATTTTTAAAT-TTTCAAAT-TTT
*
52070550 ATAAATTTATAAATTTTCAAATTTT
1 AT-AATTTTTAAATTTTCAAATTTT
52070575 AT-ATTTTTAAA
1 ATAATTTTTAAA
52070586 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 8 0.25
25 10 0.31
26 14 0.44
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAATTTTTAAATTTTCAAATTTT
Found at i:52070562 original size:26 final size:26
Alignment explanation
Indices: 52070527--52070603 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 26
52070517 AAATAAAAAT
*
52070527 AATTTTTAAATATTTAAATATTTATA
1 AATTTATAAATATTTAAATATTTATA
52070553 AATTTATAAAT-TTTCAAAT-TTTATA
1 AATTTATAAATATTT-AAATATTTATA
** * *
52070578 TTTTTAAAAAAATTTAAA-ATTT-TA
1 AATTTATAAATATTTAAATATTTATA
52070602 AA
1 AA
52070604 AAAAATCTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
24 2 0.05
25 22 0.54
26 17 0.41
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTTATAAATATTTAAATATTTATA
Found at i:52070592 original size:19 final size:19
Alignment explanation
Indices: 52070577--52070641 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
52070567 CAAATTTTAT
*
52070577 ATTTTTAAAAAAATTTAAA
1 ATTTTAAAAAAAATTTAAA
*
52070596 ATTTTAAAAAAAATCTAAAGA
1 ATTTTAAAAAAAAT-TTAA-A
* *
52070617 ATATATAAAGAAAATTTAAA
1 AT-TTTAAAAAAAATTTAAA
52070637 ATTTT
1 ATTTT
52070642 CTAACATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.41
20 6 0.16
21 6 0.16
22 10 0.27
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTTTAAAAAAAATTTAAA
Found at i:52070888 original size:26 final size:23
Alignment explanation
Indices: 52070851--52070905 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
52070841 GTATATCACA
*
52070851 ATTAT-AACATTACATAATATAAAT
1 ATTATAAACATT--ATAAAATAAAT
52070875 ATTATAAACAATTATAAAATAAAT
1 ATTATAAAC-ATTATAAAATAAAT
52070899 A-TATAAA
1 ATTATAAA
52070906 GAGATGAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.21
24 16 0.57
25 3 0.11
26 3 0.11
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTATAAACATTATAAAATAAAT
Found at i:52071586 original size:20 final size:22
Alignment explanation
Indices: 52071551--52071595 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
52071541 CTTGAAAATA
52071551 TTTAAAATATATTTTAATTATT
1 TTTAAAATATATTTTAATTATT
52071573 TTTAAAA-ATA-TTTAATTATT
1 TTTAAAATATATTTTAATTATT
52071593 TTT
1 TTT
52071596 GGAAGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 3 0.13
22 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAAATATATTTTAATTATT
Found at i:52072280 original size:30 final size:30
Alignment explanation
Indices: 52072230--52072318 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
52072220 CTTATTTTTT
*
52072230 TTGCATTTTGACCCCTAAACTTTTCTAAAA
1 TTGCATTTTAACCCCTAAACTTTTCTAAAA
* *
52072260 TTGCCTTTTAACCCCCAAAC-TTTCTTAAAA
1 TTGCATTTTAACCCCTAAACTTTTC-TAAAA
* * *
52072290 TTACAGTTCAACCCCTAAACTTTTCTAAA
1 TTGCATTTTAACCCCTAAACTTTTCTAAA
52072319 TTAAAATTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 4 0.08
30 41 0.84
31 4 0.08
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
TTGCATTTTAACCCCTAAACTTTTCTAAAA
Found at i:52072356 original size:45 final size:46
Alignment explanation
Indices: 52072280--52072367 Score: 108
Period size: 45 Copynumber: 1.9 Consensus size: 46
52072270 ACCCCCAAAC
*
52072280 TTTCTTAAAATTACAGTTCAACCCCTAAACTTT-TCTAAATTAAAA
1 TTTCTTAAAATTACAGTTCAACCCCTAAACTTTCTCAAAATTAAAA
* * * *
52072325 TTTCTTGAAATTACA-TTTAGACCCTTGAACTTTCTCAAAATTA
1 TTTCTTAAAATTACAGTTCA-ACCCCTAAACTTTCTCAAAATTA
52072368 CGTTTCGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 3 0.08
45 25 0.69
46 8 0.22
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (46 bp):
TTTCTTAAAATTACAGTTCAACCCCTAAACTTTCTCAAAATTAAAA
Found at i:52072732 original size:17 final size:15
Alignment explanation
Indices: 52072716--52072769 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
52072706 AAAAGAAAGA
52072716 AAGAAAAAACAACAAG
1 AAGAAAAAA-AACAAG
52072732 AAGCAAGAAAAAACAAGG
1 AAG-AA-AAAAAACAA-G
*
52072750 AAGAAAAAAAGAAAAG
1 AAGAAAAAAA-ACAAG
52072766 AAGA
1 AAGA
52072770 GAAAGAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 13 0.39
17 12 0.36
18 8 0.24
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAACAAG
Found at i:52072732 original size:21 final size:22
Alignment explanation
Indices: 52072708--52072764 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
52072698 AAAAATAAAA
52072708 AAGAAAGAAAGAAAAAACAA-C
1 AAGAAAGAAAGAAAAAACAAGC
* *
52072729 AAG-AAGCAAGAAAAAACAAGG
1 AAGAAAGAAAGAAAAAACAAGC
*
52072750 AAGAAAAAAAGAAAA
1 AAGAAAGAAAGAAAA
52072765 GAAGAGAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.50
21 6 0.20
22 9 0.30
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (22 bp):
AAGAAAGAAAGAAAAAACAAGC
Found at i:52072877 original size:7 final size:7
Alignment explanation
Indices: 52072865--52072956 Score: 73
Period size: 7 Copynumber: 13.0 Consensus size: 7
52072855 AACGGGGAAG
52072865 AAAGAAA
1 AAAGAAA
52072872 AAAG-AA
1 AAAGAAA
*
52072878 GAAG-AA
1 AAAGAAA
52072884 AAAGAAGA
1 AAAGAA-A
*
52072892 AAGAAAAA
1 AA-AGAAA
52072900 AAAGAAA
1 AAAGAAA
52072907 AAGAGAAA
1 AA-AGAAA
*
52072915 GAAAGAAG
1 -AAAGAAA
* *
52072923 GAAGAAG
1 AAAGAAA
*
52072930 AAA-AAG
1 AAAGAAA
52072936 AAAGAAA
1 AAAGAAA
52072943 AAAGAAA
1 AAAGAAA
52072950 AAAGAAA
1 AAAGAAA
52072957 TAAAAAAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
6 16 0.23
7 35 0.49
8 15 0.21
9 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:52072888 original size:6 final size:6
Alignment explanation
Indices: 52072865--52072956 Score: 75
Period size: 6 Copynumber: 15.2 Consensus size: 6
52072855 AACGGGGAAG
* *
52072865 AAAGAAA AAAGAA GAAGAA AAAGAA GAAAG-- AAA-AA AAAGAA AAAGAG
1 AAAG-AA AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA AAAGAA AAAGAA
* *
52072912 AAAGAA AGAAGGAA GAAGAA AAAGAA AGA-AA AAAGAAA AAAGAA A
1 AAAGAA A-AA-GAA AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA A
52072957 TAAAAAAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 38 0.55
7 18 0.26
8 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:52072904 original size:35 final size:38
Alignment explanation
Indices: 52072862--52072956 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 38
52072852 CTGAACGGGG
52072862 AAGAAAGAAAAAAGAAG-AAGAAA-AA-GAAGAAAGAAA
1 AAGAAAGAAAAAAGAAGAAAGAAAGAAGGAAG-AAGAAA
52072898 AA-AAAG-AAAAAG-AGAAAGAAAGAAGGAAGAAGAAA
1 AAGAAAGAAAAAAGAAGAAAGAAAGAAGGAAGAAGAAA
*
52072933 AAGAAAGAAAAAAGAAAAAAGAAA
1 AAGAAAGAAAAAAGAAGAAAGAAA
52072957 TAAAAAAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
33 2 0.04
34 12 0.23
35 14 0.27
36 10 0.19
37 6 0.12
38 8 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (38 bp):
AAGAAAGAAAAAAGAAGAAAGAAAGAAGGAAGAAGAAA
Found at i:52072942 original size:45 final size:42
Alignment explanation
Indices: 52072867--52072954 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 42
52072857 CGGGGAAGAA
52072867 AGAAAAAAGAAGAAGAAAAAGAAGAAAGAAAAAAAAGAAAAAG
1 AGAAAAAAGAAGAAGAAAAAGAAGAAAGAAAAAAAA-AAAAAG
*
52072910 AGAAAGAAAGAAGGAAGAAGAAA-AAGAAAGAAAAAAGAAAAAAG
1 AGAAA-AAAGAA-GAAGAA-AAAGAAGAAAGAAAAAAAAAAAAAG
52072954 A
1 A
52072955 AATAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
43 5 0.12
44 13 0.32
45 20 0.49
46 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (42 bp):
AGAAAAAAGAAGAAGAAAAAGAAGAAAGAAAAAAAAAAAAAG
Found at i:52073589 original size:17 final size:17
Alignment explanation
Indices: 52073569--52073709 Score: 113
Period size: 18 Copynumber: 7.8 Consensus size: 17
52073559 TTAAAAAAAA
52073569 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
52073586 TCGTGTTTTCAAAAAAAATTT
1 TCGTG-TTTC---AAAAATTT
* *
52073607 CTTGTGTTTCAAAAACTT
1 -TCGTGTTTCAAAAATTT
* * *
52073625 CCGTGTTTTAAAAAAAATT
1 TCGTG-TTT-CAAAAATTT
*
52073644 TCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTT
* *
52073662 TCATGTTTCAAAAATCT
1 TCGTGTTTCAAAAATTT
52073679 TCGTGTCTTC-AAAATTT
1 TCGTGT-TTCAAAAATTT
52073696 CTCGTGTTTCAAAA
1 -TCGTGTTTCAAAA
52073710 TAATAATAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
17 32 0.32
18 36 0.36
19 15 0.15
21 12 0.12
22 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:52073595 original size:18 final size:18
Alignment explanation
Indices: 52073569--52073709 Score: 119
Period size: 17 Copynumber: 7.8 Consensus size: 18
52073559 TTAAAAAAAA
52073569 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
52073586 TCGTGTTTTCAAAAAAAATT
1 TCGTGTTTTC--AAAAATTT
* *
52073606 TCTTGTGTTTCAAAAACTT
1 TCGTGT-TTTCAAAAATTT
* * *
52073625 CCGTGTTTTAAAAAAAATT
1 TCGTGTTTT-CAAAAATTT
*
52073644 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
52073662 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
52073679 TCGTGTCTTC-AAAATTT
1 TCGTGTTTTCAAAAATTT
52073696 CTCGTG-TTTCAAAA
1 -TCGTGTTTTCAAAA
52073710 TAATAATAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
17 28 0.29
18 28 0.29
19 26 0.27
20 12 0.12
21 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:52073602 original size:35 final size:35
Alignment explanation
Indices: 52073561--52073709 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 35
52073551 GGTACTTCTT
52073561 AAAAAAAA-TCGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAAAAAATTCGTGTTTCAAAAATTTTCGTG-TTTC
* * *
52073596 AAAAAAAATTTCTTGTGTTTCAAAAACTTCCGTGTTTT
1 AAAAAAAA-TTC--GTGTTTCAAAAATTTTCGTGTTTC
* *
52073634 AAAAAAAATTTCGTGTTTTCAAAAATTCTCATGTTTC
1 AAAAAAAA-TTCGTG-TTTCAAAAATTTTCGTGTTTC
**
52073671 -AAAAATCTTCGTGTCTTC-AAAATTTCTCGTGTTTC
1 AAAAAAAATTCGTGT-TTCAAAAATTT-TCGTGTTTC
52073706 AAAA
1 AAAA
52073710 TAATAATAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
34 7 0.07
35 25 0.27
36 11 0.12
37 18 0.19
38 15 0.16
39 18 0.19
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (35 bp):
AAAAAAAATTCGTGTTTCAAAAATTTTCGTGTTTC
Found at i:52073618 original size:39 final size:39
Alignment explanation
Indices: 52073571--52073675 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 39
52073561 AAAAAAAATC
*
52073571 GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCTT
1 GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCGT
* *
52073610 GTGTTTCAAAAACTTCCGTGTTTT-AAAAAAAATTTCGT
1 GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCGT
* *
52073648 GT-TTTCAAAAATTCTCATG-TTTCAAAAA
1 GTGTTTCAAAAATTTTCGTGTTTTCAAAAA
52073676 TCTTCGTGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 3 0.05
37 18 0.31
38 15 0.26
39 22 0.38
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (39 bp):
GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCGT
Found at i:52073620 original size:19 final size:19
Alignment explanation
Indices: 52073571--52073709 Score: 73
Period size: 19 Copynumber: 7.6 Consensus size: 19
52073561 AAAAAAAATC
* *
52073571 GTGTTTCAAAAATTTTCGT
1 GTGTTTCAAAAAATTTCTT
52073590 GT-TTTCAAAAAAAATTTCTT
1 GTGTTTC--AAAAAATTTCTT
* * *
52073610 GTGTTTCAAAAACTTCCGT
1 GTGTTTCAAAAAATTTCTT
* *
52073629 GT-TTTAAAAAAAATTTCGT
1 GTGTTT-CAAAAAATTTCTT
*
52073648 GT-TTTC-AAAAA-TTCTC
1 GTGTTTCAAAAAATTTCTT
*
52073664 ATGTTTC-AAAAA--TCTT
1 GTGTTTCAAAAAATTTCTT
*
52073680 CGTGTCTTC--AAAATTTCTC
1 -GTGT-TTCAAAAAATTTCTT
52073699 GTGTTTCAAAA
1 GTGTTTCAAAA
52073710 TAATAATAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.07
17 24 0.26
18 14 0.15
19 33 0.35
20 12 0.13
21 4 0.04
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (19 bp):
GTGTTTCAAAAAATTTCTT
Found at i:52073721 original size:28 final size:28
Alignment explanation
Indices: 52073689--52073742 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
52073679 TCGTGTCTTC
* *
52073689 AAAATTTCTCGTGTTTCAAAATAATAAT
1 AAAATTTCCCGTGTTTCAAAAAAATAAT
52073717 AAAATTTCCCGTGTTTCAAAAAAATA
1 AAAATTTCCCGTGTTTCAAAAAAATA
52073743 TATTCCTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATTTCCCGTGTTTCAAAAAAATAAT
Found at i:52073856 original size:17 final size:17
Alignment explanation
Indices: 52073802--52073857 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
52073792 TGAATTAAAA
52073802 AAAAAGTTCGTGTTTTC
1 AAAAAGTTCGTGTTTTC
**
52073819 -AAAA-TTCCAGTGTTTGA
1 AAAAAGTT-C-GTGTTTTC
52073836 AAAAAGTTCGTGTTTTC
1 AAAAAGTTCGTGTTTTC
52073853 AAAAA
1 AAAAA
52073858 AAAATTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 2 0.06
16 5 0.16
17 17 0.55
18 5 0.16
19 2 0.06
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (17 bp):
AAAAAGTTCGTGTTTTC
Found at i:52073934 original size:36 final size:37
Alignment explanation
Indices: 52073891--52073994 Score: 126
Period size: 36 Copynumber: 2.9 Consensus size: 37
52073881 TTTGATGTTA
* *
52073891 TCGTGTTTTCAAAAAACTCCCGTG-TTTGACAA-ATTT
1 TCGTGTTTTCAAAAAA-TCCCGTGTTTTCAAAATATTT
*
52073927 TCGTGTTTTCAAAAAATTCCGTGTTTTCAAAATATTT
1 TCGTGTTTTCAAAAAATCCCGTGTTTTCAAAATATTT
*
52073964 TCGTG-TTTCAAAAATAT-TCGTGTTTTCAAAA
1 TCGTGTTTTCAAAAA-ATCCCGTGTTTTCAAAA
52073995 ATTATTATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
35 6 0.10
36 44 0.72
37 11 0.18
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (37 bp):
TCGTGTTTTCAAAAAATCCCGTGTTTTCAAAATATTT
Found at i:52073970 original size:19 final size:19
Alignment explanation
Indices: 52073923--52074015 Score: 97
Period size: 18 Copynumber: 5.0 Consensus size: 19
52073913 TGTTTGACAA
52073923 ATTTTCGTGTTTTCAAAA-
1 ATTTTCGTGTTTTCAAAAT
* *
52073941 AATTCCGTGTTTTCAAAAT
1 ATTTTCGTGTTTTCAAAAT
52073960 ATTTTCGTG-TTTCAAAA-
1 ATTTTCGTGTTTTCAAAAT
*
52073977 ATATTCGTGTTTTCAAAAATT
1 ATTTTCGTGTTTTC-AAAA-T
52073998 ATTATT-GTG-TTTCAAAAT
1 ATT-TTCGTGTTTTCAAAAT
52074016 TCTCGTGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.13
18 29 0.46
19 15 0.24
20 4 0.06
21 5 0.08
22 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTTTCGTGTTTTCAAAAT
Found at i:52073984 original size:54 final size:54
Alignment explanation
Indices: 52073892--52073995 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
52073882 TTGATGTTAT
* * *
52073892 CGTGTTTTCAAAAAACTCCCGTGTTTGACAAATTTTCGTGTTTTCAAAAAATTC
1 CGTGTTTTCAAAAAACTCCCGTGTTTCAAAAATATTCGTGTTTTCAAAAAATTC
* * **
52073946 CGTGTTTTCAAAATATTTTCGTGTTTCAAAAATATTCGTGTTTTCAAAAA
1 CGTGTTTTCAAAAAACTCCCGTGTTTCAAAAATATTCGTGTTTTCAAAAA
52073996 TTATTATTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (54 bp):
CGTGTTTTCAAAAAACTCCCGTGTTTCAAAAATATTCGTGTTTTCAAAAAATTC
Found at i:52073996 original size:18 final size:18
Alignment explanation
Indices: 52073891--52073996 Score: 103
Period size: 18 Copynumber: 5.9 Consensus size: 18
52073881 TTTGATGTTA
52073891 TCGTGTTTTCAAAAA-ACT
1 TCGTGTTTTCAAAAATA-T
* * * *
52073909 CCCGTG-TTTGACAAATTT
1 -TCGTGTTTTCAAAAATAT
52073927 TCGTGTTTTCAAAAA-AT
1 TCGTGTTTTCAAAAATAT
*
52073944 TCCGTGTTTTCAAAATATTT
1 T-CGTGTTTTCAAAA-ATAT
52073964 TCGTG-TTTCAAAAATAT
1 TCGTGTTTTCAAAAATAT
52073981 TCGTGTTTTCAAAAAT
1 TCGTGTTTTCAAAAAT
52073997 TATTATTGTG
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
17 14 0.20
18 46 0.65
19 9 0.13
20 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATAT
Found at i:52073996 original size:37 final size:37
Alignment explanation
Indices: 52073923--52074014 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 37
52073913 TGTTTGACAA
52073923 ATTTTCGTGTTTTCAAAAAATTCCGTGTTTTCAAAA-T
1 ATTTTCGTG-TTTCAAAAAATTCCGTGTTTTCAAAATT
52073960 ATTTTCGTGTTTCAAAAATATT-CGTGTTTTCAAAAATT
1 ATTTTCGTGTTTCAAAAA-ATTCCGTGTTTTC-AAAATT
52073998 ATTATT-GTGTTTCAAAA
1 ATT-TTCGTGTTTCAAAA
52074015 TTCTCGTGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
36 18 0.35
37 16 0.31
38 15 0.29
39 2 0.04
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (37 bp):
ATTTTCGTGTTTCAAAAAATTCCGTGTTTTCAAAATT
Found at i:52074022 original size:54 final size:53
Alignment explanation
Indices: 52073892--52074030 Score: 140
Period size: 54 Copynumber: 2.6 Consensus size: 53
52073882 TTGATGTTAT
* * * * *
52073892 CGTGTTTTCAAAAAACTCCCGTGTTTGACAAATTTTCGTGTTTTCAAAAAATTC
1 CGTGTTTTCAAAATATTCTCGTGTTT-AAAAATATTCGTGTTTTCAAAAAATTC
*
52073946 CGTGTTTTCAAAATATTTTCGTGTTTCAAAAATATTCGTGTTTTCAAAAATTATT-
1 CGTGTTTTCAAAATATTCTCGTGTTT-AAAAATATTCGTGTTTTCAAAAA--ATTC
**
52074001 ATTGTGTTTC-AAA-ATTCTCGTGTTTAAAAA
1 CGTGT-TTTCAAAATATTCTCGTGTTTAAAAA
52074031 CAAAAAAAAG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
53 5 0.07
54 54 0.75
55 6 0.08
56 7 0.10
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (53 bp):
CGTGTTTTCAAAATATTCTCGTGTTTAAAAATATTCGTGTTTTCAAAAAATTC
Found at i:52075811 original size:44 final size:44
Alignment explanation
Indices: 52075761--52075881 Score: 127
Period size: 51 Copynumber: 2.6 Consensus size: 44
52075751 GGATCGTATT
*
52075761 TATCACTTTTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTTTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
* *
52075805 TATCACTTATCACTTGCCGCTTGTCACTGATCAGATAAGTGTAGCTGAAGC
1 TATCAC-T-T---TT--CACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
*
52075856 TA-CTACTTATCACTTGTCACTGATCA
1 TATC-ACTTTTCACTTGTCACTGATCA
52075882 AAAGTACTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
44 21 0.33
45 1 0.02
46 2 0.03
49 3 0.05
50 2 0.03
51 35 0.55
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (44 bp):
TATCACTTTTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGC
Found at i:52075836 original size:51 final size:51
Alignment explanation
Indices: 52075773--52075871 Score: 164
Period size: 51 Copynumber: 1.9 Consensus size: 51
52075763 TCACTTTTCA
*
52075773 CTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTA-TCACTTATCACTTGCCG
1 CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACT-ACTTATCACTTGCCG
*
52075824 CTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTG
1 CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTG
52075872 TCACTGATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (51 bp):
CTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTGCCG
Found at i:52086072 original size:19 final size:19
Alignment explanation
Indices: 52086044--52086082 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
52086034 ATTGAATTTC
*
52086044 AATTTTATAA-ATTTTTTA
1 AATTTTATAATAATTTTTA
52086062 AATTCTTATAATAATTTTTA
1 AATT-TTATAATAATTTTTA
52086082 A
1 A
52086083 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTATAATAATTTTTA
Found at i:52090547 original size:105 final size:105
Alignment explanation
Indices: 52090334--52090539 Score: 234
Period size: 105 Copynumber: 2.0 Consensus size: 105
52090324 ACTATAGGTA
*
52090334 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTCAGCTTCAGAGACCAT
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTCAGCTTCAGAAACCAT
* * ** *
52090399 CCCTTCCTTGCAATGCGCATGAACCAATGTATTATACGCG
66 CCCTTCCTTGCAAAGCGCATCAACCAATAAAGTATACGCG
* * * * * * * *
52090439 ACAACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACGATCT-CTACAGCTTTAGAAATCG
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCT-CAGCTTCAGAAACCA
* * * *
52090503 TTCCTTCCTTGCAAAGTGTATCAATCAATAAAGTATA
65 TCCCTTCCTTGCAAAGCGCATCAACCAATAAAGTATA
52090540 TGTGACAATA
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
104 2 0.02
105 80 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (105 bp):
ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTCAGCTTCAGAAACCAT
CCCTTCCTTGCAAAGCGCATCAACCAATAAAGTATACGCG
Found at i:52094055 original size:36 final size:37
Alignment explanation
Indices: 52093995--52094072 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
52093985 CGAATACATT
52093995 TATATCTATAATTATTCAAATACATATGCCAAAAGCA
1 TATATCTATAATTATTCAAATACATATGCCAAAAGCA
* * * * *
52094032 TATATTTATACTTA-TCAATTACATGTGCCAAATGCA
1 TATATCTATAATTATTCAAATACATATGCCAAAAGCA
*
52094068 CATAT
1 TATAT
52094073 ATACTTGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (37 bp):
TATATCTATAATTATTCAAATACATATGCCAAAAGCA
Found at i:52094342 original size:41 final size:41
Alignment explanation
Indices: 52094297--52094394 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
52094287 AAACAGATTT
**
52094297 ACCGGCACTTAGCCTGTTAGGCTTA-AAGCCTGATTCAGATC
1 ACCGGCACTTAGCCTGCCAGGCTTATAA-CCTGATTCAGATC
52094338 ACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATC
1 ACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATC
* *
52094379 ACTGGCATTTAGCCTG
1 ACCGGCACTTAGCCTG
52094395 ATTCAGATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 50 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (41 bp):
ACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATC
Found at i:52094400 original size:25 final size:25
Alignment explanation
Indices: 52094366--52094419 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
52094356 AGGCTTATAA
*
52094366 CCTGATTCAGATCACTGGCATTTAG
1 CCTGATTCAGATCACTGGCACTTAG
52094391 CCTGATTCAGATCACTGGCACTTAG
1 CCTGATTCAGATCACTGGCACTTAG
52094416 CCTG
1 CCTG
52094420 TTAGGCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (25 bp):
CCTGATTCAGATCACTGGCACTTAG
Found at i:52094404 original size:66 final size:66
Alignment explanation
Indices: 52094323--52094460 Score: 222
Period size: 66 Copynumber: 2.1 Consensus size: 66
52094313 TTAGGCTTAA
* *
52094323 AGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATCACTGGCATT
1 AGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATCACCGGCACT
52094388 T
66 T
* ** *
52094389 AGCCTGATTCAGATCACTGGCACTTAGCCTGTTAGGCTTATAACCTGGTTCAGATCACCGGCACT
1 AGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATCACCGGCACT
52094454 T
66 T
52094455 AGCCTG
1 AGCCTG
52094461 TTAGGCTTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (66 bp):
AGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATAACCTGATTCAGATCACCGGCACT
T
Found at i:52094453 original size:41 final size:41
Alignment explanation
Indices: 52094391--52094594 Score: 302
Period size: 41 Copynumber: 5.0 Consensus size: 41
52094381 TGGCATTTAG
*
52094391 CCTGATTCAGATCACTGGCACTTAGCCTGTTAGGCTTATAA
1 CCTGATTCAGATCACCGGCACTTAGCCTGTTAGGCTTATAA
*
52094432 CCTGGTTCAGATCACCGGCACTTAGCCTGTTAGGCTTATAA
1 CCTGATTCAGATCACCGGCACTTAGCCTGTTAGGCTTATAA
* * * *
52094473 CCTGATTCAGTTCACCGGCACTTAGCTTGCTAGGCTTATAG
1 CCTGATTCAGATCACCGGCACTTAGCCTGTTAGGCTTATAA
* *
52094514 CCTGATTCAGATAATCGGCACTTAGCCT-TCTAGGCTTATAA
1 CCTGATTCAGATCACCGGCACTTAGCCTGT-TAGGCTTATAA
* *
52094555 CCTGGTTCAGATCACCGGCACTTAGCCTGTTAGACTTATA
1 CCTGATTCAGATCACCGGCACTTAGCCTGTTAGGCTTATA
52094595 GTCCGAAATG
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
41 143 0.99
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (41 bp):
CCTGATTCAGATCACCGGCACTTAGCCTGTTAGGCTTATAA
Found at i:52094498 original size:107 final size:107
Alignment explanation
Indices: 52094300--52094498 Score: 328
Period size: 107 Copynumber: 1.9 Consensus size: 107
52094290 CAGATTTACC
52094300 GGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATA
1 GGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATA
* *
52094365 ACCTGATTCAGATCACTGGCATTTAGCCTGATTCAGATCACT
66 ACCTGATTCAGATCACCGGCACTTAGCCTGATTCAGATCACT
* **
52094407 GGCACTTAGCCTGTTAGGCTTATAA-CCTGGTTCAGATCACCGGCACTTAGCCTGTTAGGCTTAT
1 GGCACTTAGCCTGTTAGGCTTA-AAGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTAT
*
52094471 AACCTGATTCAGTTCACCGGCACTTAGC
65 AACCTGATTCAGATCACCGGCACTTAGC
52094499 TTGCTAGGCT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
107 83 0.98
108 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (107 bp):
GGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCCAGGCTTATA
ACCTGATTCAGATCACCGGCACTTAGCCTGATTCAGATCACT
Found at i:52094627 original size:123 final size:122
Alignment explanation
Indices: 52094388--52094628 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 122
52094378 CACTGGCATT
*
52094388 TAGCCTGATTCAGATCACTGGCACTTAGCCTGTTAGGCTTATAACCTGGTTCAGATCACCGGCAC
1 TAGCCTGATTCAGATAACTGGCACTTAGCCTGTTAGGCTTATAACCTGGTTCAGATCACCGGCAC
* * * *
52094453 TTAGCCTGTTAGGCTTATAACCTGATTCAGTTCACCGGCACTTAGCTTGCTAGGCTTA
66 TTAGCCTGTTAGACTTATAACCTGAAT-AGTTCACCGGCACTAAGCCTGCTAGGCTTA
52094511 TAGCCTGATTCAGATAA-TCGGCACTTAGCCT-TCTAGGCTTATAACCTGGTTCAGATCACCGGC
1 TAGCCTGATTCAGATAACT-GGCACTTAGCCTGT-TAGGCTTATAACCTGGTTCAGATCACCGGC
*
52094574 ACTTAGCCTGTTAGACTTATAGTCC-GAA-ATGTTTCACCGGCA-TCAAGCCTGCTAG
64 ACTTAGCCTGTTAGACTTATA-ACCTGAATA-G-TTCACCGGCACT-AAGCCTGCTAG
52094629 ACATAAAGTC
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
121 1 0.01
122 4 0.04
123 99 0.93
124 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (122 bp):
TAGCCTGATTCAGATAACTGGCACTTAGCCTGTTAGGCTTATAACCTGGTTCAGATCACCGGCAC
TTAGCCTGTTAGACTTATAACCTGAATAGTTCACCGGCACTAAGCCTGCTAGGCTTA
Found at i:52095022 original size:76 final size:76
Alignment explanation
Indices: 52094931--52095120 Score: 195
Period size: 78 Copynumber: 2.5 Consensus size: 76
52094921 TACATTGAAC
* * * *
52094931 ATTCGAATCTCACATATACCTATATAATTTCATAC-CCCATTTC-AATATAAAAACTTATACATG
1 ATTCGAATCTAACATATACATATATAATTTCATACTCACA-TTCGAA-ACAAAAACTTATACATG
* *
52094994 TACATATATACAT
64 TACACACATACAT
* * ** *
52095007 ATTCGAATCTAACATATATACATATATAATTTTATACTTACATTCGAAACAAGTACTTATACTTG
1 ATTCGAATCTAAC--ATATACATATATAATTTCATACTCACATTCGAAACAAAAACTTATACATG
*
52095072 TATACACATACAT
64 TACACACATACAT
* * *
52095085 TTTCGAATTTAACGTATACATATATAATTTCATACT
1 ATTCGAATCTAACATATACATATATAATTTCATACT
52095121 TATACTCAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
76 33 0.35
78 57 0.61
79 4 0.04
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (76 bp):
ATTCGAATCTAACATATACATATATAATTTCATACTCACATTCGAAACAAAAACTTATACATGTA
CACACATACAT
Found at i:52095340 original size:75 final size:78
Alignment explanation
Indices: 52095204--52095403 Score: 171
Period size: 75 Copynumber: 2.6 Consensus size: 78
52095194 TATATATATG
* * * * * * *
52095204 TAACATCCATACTTTTAA-TAAAATCCAAGAATTTATAC-T-CATATATACATACCTATTCAAAC
1 TAACATACATACTATTAACT-AAATTCAAGAACTTATACATGTATATACACATA--TATCCAAA-
*
52095266 CTCT-TGTAAACATATA
62 CTCTATGTAAACAAATA
* ** *
52095282 TAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTTATGTATATACACATATATCCAAACTTT
1 TAACATACATACTATTAACTAAATTCAAGAACTTATACATGTATATACACATATATCCAAACTCT
* * *
52095344 ATTTATATAAATA
66 ATGTAAACAAATA
*
52095357 TAACATACATACTTTTAACTAAATTCAAGAACTTATACATGTATATA
1 TAACATACATACTATTAACTAAATTCAAGAACTTATACATGTATATA
52095404 TATATTATCC
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
74 3 0.03
75 29 0.30
76 14 0.14
77 27 0.28
78 24 0.25
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (78 bp):
TAACATACATACTATTAACTAAATTCAAGAACTTATACATGTATATACACATATATCCAAACTCT
ATGTAAACAAATA
Found at i:52103867 original size:24 final size:24
Alignment explanation
Indices: 52103840--52103924 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
52103830 ATGTATTTAC
* *
52103840 ATTTGTGTCTATATTTGTATCTGT
1 ATTTGTATCTGTATTTGTATCTGT
* * *
52103864 ATTTGCATCTGTATTTGCACCTGT
1 ATTTGTATCTGTATTTGTATCTGT
* * *
52103888 ATCTGTATCTGTATATGTATATGT
1 ATTTGTATCTGTATTTGTATCTGT
**
52103912 ATTTACATCTGTA
1 ATTTGTATCTGTA
52103925 ACTGCATCTG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (24 bp):
ATTTGTATCTGTATTTGTATCTGT
Found at i:52103881 original size:12 final size:12
Alignment explanation
Indices: 52103851--52103937 Score: 84
Period size: 12 Copynumber: 7.2 Consensus size: 12
52103841 TTTGTGTCTA
*
52103851 TATTTGTATCTG
1 TATTTGCATCTG
52103863 TATTTGCATCTG
1 TATTTGCATCTG
*
52103875 TATTTGCACCTG
1 TATTTGCATCTG
* *
52103887 TATCTGTATCTG
1 TATTTGCATCTG
* * *
52103899 TATATGTATATG
1 TATTTGCATCTG
*
52103911 TATTTACATCTG
1 TATTTGCATCTG
**
52103923 TAACTGCATCTG
1 TATTTGCATCTG
52103935 TAT
1 TAT
52103938 CTAAAATTTT
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (12 bp):
TATTTGCATCTG
Found at i:52103895 original size:6 final size:6
Alignment explanation
Indices: 52103855--52103939 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
52103845 TGTCTATATT
* * * * * *
52103855 TGTATC TGTATT TGCATC TGTATT TGCACC TGTATC TGTATC TGTATA
1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC
* * ** * *
52103903 TGTATA TGTATT TACATC TGTAAC TGCATC TGTATC T
1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC T
52103940 AAAATTTTCA
Statistics
Matches: 58, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.47
Consensus pattern (6 bp):
TGTATC
Found at i:52103895 original size:36 final size:36
Alignment explanation
Indices: 52103855--52103937 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
52103845 TGTCTATATT
* * * *
52103855 TGTATCTGTATTTGCATCTGTATTTGCACCTGTATC
1 TGTATCTGTATATGCATATGTATTTACACCTGTAAC
* *
52103891 TGTATCTGTATATGTATATGTATTTACATCTGTAAC
1 TGTATCTGTATATGCATATGTATTTACACCTGTAAC
*
52103927 TGCATCTGTAT
1 TGTATCTGTAT
52103938 CTAAAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (36 bp):
TGTATCTGTATATGCATATGTATTTACACCTGTAAC
Found at i:52105755 original size:36 final size:35
Alignment explanation
Indices: 52105678--52105755 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 35
52105668 AAAGGAAACT
* *
52105678 AAAATTTTCTAATAATCATTTTCACCAAATATTTA
1 AAAAATTTCTAATAATCATTTTCACCAAATACTTA
* * *
52105713 ATAAAATTTCTAATAATTATTTTTACTAAATGACTTA
1 A-AAAATTTCTAATAATCATTTTCACCAAAT-ACTTA
52105750 AAAAAT
1 AAAAAT
52105756 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.03
36 30 0.83
37 5 0.14
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.42
Consensus pattern (35 bp):
AAAAATTTCTAATAATCATTTTCACCAAATACTTA
Found at i:52106215 original size:11 final size:12
Alignment explanation
Indices: 52106194--52106241 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
52106184 GGGCAGCAGA
52106194 AAAAAAGAAAAG
1 AAAAAAGAAAAG
52106206 AAAAAA-AAAAG
1 AAAAAAGAAAAG
*
52106217 AGAAAAGAAGAAG
1 AAAAAAGAA-AAG
52106230 AATAAGAAGAAA
1 AA-AA-AAGAAA
52106242 TGGACATACC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 10 0.33
12 8 0.27
13 4 0.13
14 3 0.10
15 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:52106230 original size:13 final size:13
Alignment explanation
Indices: 52106191--52106230 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
52106181 GCAGGGCAGC
*
52106191 AGAAAAAAAGAAA
1 AGAAAAAAAGAAG
*
52106204 AGAAAAAAAAAAG
1 AGAAAAAAAGAAG
*
52106217 AGAAAAGAAGAAG
1 AGAAAAAAAGAAG
52106230 A
1 A
52106231 ATAAGAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAG
Found at i:52112493 original size:26 final size:26
Alignment explanation
Indices: 52112464--52112517 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
52112454 AAACATTTGT
*
52112464 AAAGGGATT-TTTGTGAAAAATGACAA
1 AAAGGGATTAATTGTGAAAAATG-CAA
52112490 AAAGGGATTAAATTGTGAAAAATGCAA
1 AAAGGGATT-AATTGTGAAAAATGCAA
52112517 A
1 A
52112518 CTGAGTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 9 0.36
27 4 0.16
28 12 0.48
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.24
Consensus pattern (26 bp):
AAAGGGATTAATTGTGAAAAATGCAA
Found at i:52113141 original size:47 final size:47
Alignment explanation
Indices: 52113088--52113217 Score: 145
Period size: 47 Copynumber: 2.8 Consensus size: 47
52113078 GTGCGAATAA
* * *
52113088 TACCTTGATTTGGCTACGGGCCATGGTATAGTTATTCAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGT
* * ** * * *
52113135 TACCTTGATTTGTCTACAAGG-CATAATATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTAC-GGGCCATGGTATAGGTACTCAGAGAGAAGT
*
52113182 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
52113218 TATCGATTGA
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
46 2 0.03
47 62 0.94
48 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGT
Found at i:52114473 original size:59 final size:55
Alignment explanation
Indices: 52114375--52114488 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 55
52114365 GCAGTTTCTT
* *
52114375 TGCCCCAAAAATGCCTAAGCCTAACTTGCAACGATAAAGGATTCAATAGAATTCC
1 TGCCCCAAAAACGCCTAAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
52114430 TGCCCCAAAAACGCCTAAGTCAGTCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
1 TGCCCCAAAAACGCCTAAG-C---CTAACTTGCAACGACAAAGGATTCAATAGAATTCC
52114489 CTCAAGTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 18 0.34
56 1 0.02
59 34 0.64
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (55 bp):
TGCCCCAAAAACGCCTAAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTCC
Found at i:52117204 original size:24 final size:23
Alignment explanation
Indices: 52117161--52117206 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
52117151 AGCGACTTGT
*
52117161 TATACACCACAATATCATCAAGG
1 TATACACCACAATAACATCAAGG
52117184 TATACAACCACAA-AACGATCAAG
1 TATAC-ACCACAATAAC-ATCAAG
52117207 AAAAGGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (23 bp):
TATACACCACAATAACATCAAGG
Found at i:52119580 original size:59 final size:59
Alignment explanation
Indices: 52119488--52119606 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 59
52119478 GGCAGTTTCT
* ** *
52119488 TTGCCCCAAACATGCCTAAGTCAGCCTAACTTGCAACGATAAAGGATTCAATAGAATTC
1 TTGCCCCAAAAACCCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTC
52119547 TTGCCCCAAAAACCCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTC
1 TTGCCCCAAAAACCCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTC
52119606 T
1 T
52119607 CTCAAGGCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (59 bp):
TTGCCCCAAAAACCCCTAAGTCAGCCTAACTTGCAACGACAAAGGATTCAATAGAATTC
Found at i:52125362 original size:16 final size:16
Alignment explanation
Indices: 52125313--52125362 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
52125303 ATGTATATAA
52125313 AAATTGTA-GAAAAAT
1 AAATTGTATGAAAAAT
* * *
52125328 AAAATCT-TGAATAACT
1 AAATTGTATGAA-AAAT
52125344 AAATTGTATGAAAAAT
1 AAATTGTATGAAAAAT
52125360 AAA
1 AAA
52125363 GAAAATTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 8 0.31
16 14 0.54
17 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.28
Consensus pattern (16 bp):
AAATTGTATGAAAAAT
Found at i:52132917 original size:32 final size:32
Alignment explanation
Indices: 52132862--52132922 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
52132852 TTGATTACAA
* * *
52132862 TTTTTAAAAATATGTGAGATTAATGAAAATTT
1 TTTTTAAAAAAAGGAGAGATTAATGAAAATTT
* *
52132894 TTTTTAAAAAAAGGAGAGTTTAATTAAAA
1 TTTTTAAAAAAAGGAGAGATTAATGAAAA
52132923 CTTTCAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (32 bp):
TTTTTAAAAAAAGGAGAGATTAATGAAAATTT
Found at i:52134531 original size:105 final size:105
Alignment explanation
Indices: 52134379--52134605 Score: 262
Period size: 105 Copynumber: 2.2 Consensus size: 105
52134369 ACTAATGTAT
* *
52134379 TATACGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTTCGTCAACAATACCCT-CAGCTTC
1 TATACGTGACAACATCAGGCTCAATGCCTCGCTTTATCATGTCGTCAACAAT-CCCTACAGCTTC
* * *
52134443 AGAGACCATCCCTTCCTTGCAATGCGCATCAACCAATATAC-
65 AGAAACCATCCCTTCCTTGCAAAGAGCATCAACCAATA-ACG
* * * * *
52134484 TATACGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATCGT-GTCAACGATCTCTACAGCTTT
1 TATACGTGACAACATCAGGCTCAATGCCTCGCTTTATCAT-GTCGTCAACAATCCCTACAGCTTC
* * * *
52134548 AGAAATCGTTCCTTCCTTGCAAAGAGCATCAATCAATAACG
65 AGAAACCATCCCTTCCTTGCAAAGAGCATCAACCAATAACG
* *
52134589 TATATGTGACAATATCA
1 TATACGTGACAACATCA
52134606 AGTGAAATAT
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
104 5 0.05
105 97 0.94
106 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (105 bp):
TATACGTGACAACATCAGGCTCAATGCCTCGCTTTATCATGTCGTCAACAATCCCTACAGCTTCA
GAAACCATCCCTTCCTTGCAAAGAGCATCAACCAATAACG
Found at i:52136454 original size:13 final size:13
Alignment explanation
Indices: 52136436--52136460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52136426 GAAAGGGTCT
52136436 AGTCTTCTAGCTC
1 AGTCTTCTAGCTC
52136449 AGTCTTCTAGCT
1 AGTCTTCTAGCT
52136461 ATGACTTCTC
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:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (13 bp):
AGTCTTCTAGCTC
Found at i:52137187 original size:20 final size:19
Alignment explanation
Indices: 52137143--52137188 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
52137133 CATCCAAACA
52137143 CTAGAAAAGCAAATCATTT
1 CTAGAAAAGCAAATCATTT
* *
52137162 CCAGAAAAGTAAATCATTTT
1 CTAGAAAAGCAAATCA-TTT
52137182 CTAGAAA
1 CTAGAAA
52137189 TCATTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (19 bp):
CTAGAAAAGCAAATCATTT
Found at i:52137209 original size:14 final size:14
Alignment explanation
Indices: 52137172--52137202 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52137162 CCAGAAAAGT
*
52137172 AAATCATTTTCTAG
1 AAATCATTTTCCAG
52137186 AAATCATTTTCCAG
1 AAATCATTTTCCAG
52137200 AAA
1 AAA
52137203 ATATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:52139145 original size:48 final size:47
Alignment explanation
Indices: 52139049--52139179 Score: 174
Period size: 48 Copynumber: 2.8 Consensus size: 47
52139039 GTGTGAATAA
* *
52139049 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTCAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGT
* * *
52139096 TACCTTGATTTGTCTACGGGGCCATGGTATAAGTACTCTAG-GATAAGT
1 TACCTTGATTTGGCTAC-GGGCCATGGTATAGGTACTC-AGAGAGAAGT
**
52139144 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
52139180 TATCGATTGA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 33 0.45
48 38 0.52
49 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGAGAGAAGT
Found at i:52141279 original size:5 final size:6
Alignment explanation
Indices: 52141263--52141288 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52141253 TAAAGTATTT
52141263 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
52141289 TATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:52148435 original size:13 final size:14
Alignment explanation
Indices: 52148417--52148449 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52148407 TATAATTTAA
52148417 TTTAATTTTCT-TT
1 TTTAATTTTCTATT
*
52148430 TTTAATTTTTTATT
1 TTTAATTTTCTATT
52148444 TTTAAT
1 TTTAAT
52148450 GGCTTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTAATTTTCTATT
Found at i:52150470 original size:23 final size:23
Alignment explanation
Indices: 52150444--52150497 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
52150434 ATAAATACTC
52150444 ATATTTATATTATTAAAAT-TAAA
1 ATATTTATATT-TTAAAATATAAA
* *
52150467 ATATTCATATTTTAAACTATAAA
1 ATATTTATATTTTAAAATATAAA
52150490 ATATTTAT
1 ATATTTAT
52150498 TAATAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTTATATTTTAAAATATAAA
Found at i:52154660 original size:2 final size:2
Alignment explanation
Indices: 52154653--52154689 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
52154643 AACAACTCAT
52154653 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52154690 TTGTAAGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:52156919 original size:5 final size:5
Alignment explanation
Indices: 52156909--52156939 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
52156899 TGACCTAGGA
52156909 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
52156940 GGATGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:52163530 original size:71 final size:71
Alignment explanation
Indices: 52163449--52163586 Score: 276
Period size: 71 Copynumber: 1.9 Consensus size: 71
52163439 TAAAGTACAA
52163449 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
52163514 AAAAGG
66 AAAAGG
52163520 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
1 TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
52163585 AA
66 AA
52163587 GAGGAAATTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (71 bp):
TAATGAAATAAAAGTTAAAAAAGGATCTAGTAAAATTTCAATTGCTCAATGATTCACATGATTAC
AAAAGG
Found at i:52171688 original size:30 final size:31
Alignment explanation
Indices: 52171652--52171719 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
52171642 GTTTCATTTC
*
52171652 AGTCACTCAAC-TTTTAAAAAA-TAACAAAAT
1 AGTCACT-AACGTTATAAAAAAGTAACAAAAT
*
52171682 AGTCACTAACGTTATAAAAAAGTGACAAAAT
1 AGTCACTAACGTTATAAAAAAGTAACAAAAT
52171713 AGTCACT
1 AGTCACT
52171720 GATTAACAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 15 0.44
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (31 bp):
AGTCACTAACGTTATAAAAAAGTAACAAAAT
Found at i:52171984 original size:3 final size:3
Alignment explanation
Indices: 52171976--52172001 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52171966 ACGTCTTTGC
52171976 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
52172002 ATGGCTCTCT
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:52172567 original size:14 final size:14
Alignment explanation
Indices: 52172550--52172587 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
52172540 CTTCTTTTTC
*
52172550 TTCTTTTCTTCCTT
1 TTCTTTTCTTCATT
52172564 TTCTTTTCTTCATT
1 TTCTTTTCTTCATT
*
52172578 TTCTCTTCTT
1 TTCTTTTCTT
52172588 AAACCCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTTTCTTCATT
Found at i:52183894 original size:25 final size:24
Alignment explanation
Indices: 52183858--52183904 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
52183848 CTCATGTTTT
52183858 AAAAAATAAATCAT-AAAATTAATA
1 AAAAAATAAATC-TCAAAATTAATA
*
52183882 AAAAAATTTAATCTCAAAATTAA
1 AAAAAA-TAAATCTCAAAATTAA
52183905 AAATAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAATAAATCTCAAAATTAATA
Found at i:52186643 original size:21 final size:21
Alignment explanation
Indices: 52186617--52186656 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
52186607 ATCGGTTGGA
52186617 TAAGCTCTTACGAGCTTCTGT
1 TAAGCTCTTACGAGCTTCTGT
52186638 TAAGCTCTTACGAGCTTCT
1 TAAGCTCTTACGAGCTTCT
52186657 ACTGGAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TAAGCTCTTACGAGCTTCTGT
Found at i:52200757 original size:24 final size:22
Alignment explanation
Indices: 52200705--52200759 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
52200695 AAAAATGTTA
* *
52200705 TCATTGTAGCTAATACTTTTAG
1 TCATTGTAGATAATACTTTTAC
* *
52200727 TCCTTGTAGATAGGATATTTTTAC
1 TCATTGTAGATA--ATACTTTTAC
52200751 TCATTGTAG
1 TCATTGTAG
52200760 CTATACTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 10 0.38
24 16 0.62
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (22 bp):
TCATTGTAGATAATACTTTTAC
Found at i:52205788 original size:24 final size:26
Alignment explanation
Indices: 52205735--52205801 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
52205725 CCAAGTCGAA
**
52205735 CCTTTGTGGTGAATTATCTATAAAGC
1 CCTTTGTGGCAAATTATCTATAAAGC
*
52205761 CC-TTGTGGCAAATTATCTA-AAAGG
1 CCTTTGTGGCAAATTATCTATAAAGC
*
52205785 CCTTTGTGGCATATTAT
1 CCTTTGTGGCAAATTAT
52205802 TTGGAAAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 6 0.17
25 28 0.78
26 2 0.06
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (26 bp):
CCTTTGTGGCAAATTATCTATAAAGC
Found at i:52206922 original size:4 final size:5
Alignment explanation
Indices: 52206909--52206937 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
52206899 TCATTAAGAT
52206909 AATAA AAT-A AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
52206938 CTAATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:52208729 original size:23 final size:24
Alignment explanation
Indices: 52208664--52208731 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
52208654 CATTTTGGCC
52208664 ATCTCACTATTAAATTTTTCAGTT
1 ATCTCACTATTAAATTTTTCAGTT
* **
52208688 AT-TCAGTTCATTCTA-TTTTC-GTT
1 ATCTCA-CT-ATTAAATTTTTCAGTT
52208711 ATCTCACTATTAAATTTTTCA
1 ATCTCACTATTAAATTTTTCA
52208732 TTTTAGTCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
22 4 0.12
23 14 0.42
24 11 0.33
25 4 0.12
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.51
Consensus pattern (24 bp):
ATCTCACTATTAAATTTTTCAGTT
Found at i:52211314 original size:2 final size:2
Alignment explanation
Indices: 52211309--52211392 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
52211299 TATATAATGC
52211309 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52211351 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52211393 CAAAACTGGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52213354 original size:2 final size:2
Alignment explanation
Indices: 52213347--52213381 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52213337 ATGATAAATT
52213347 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52213382 CATGCATGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52213716 original size:2 final size:2
Alignment explanation
Indices: 52213709--52213765 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
52213699 AACACAATAA
52213709 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
52213751 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
52213766 AGTTTAACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:52215212 original size:18 final size:20
Alignment explanation
Indices: 52215175--52215217 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
52215165 ACATGTATAA
*
52215175 GTATGTTTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
52215195 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
52215213 GTATG
1 GTATG
52215218 CATGTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:52216953 original size:34 final size:32
Alignment explanation
Indices: 52216914--52216982 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
52216904 GTGGATATCG
52216914 CGATACCAAGCTCTAGGTATCATGATATCACTAT
1 CGATACCAAGCTCT-GG-ATCATGATATCACTAT
* * *
52216948 CGATACCAGGCTCTGGGTCGTGATATCACTAT
1 CGATACCAAGCTCTGGATCATGATATCACTAT
52216980 CGA
1 CGA
52216983 AGGGAGACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 17 0.53
33 2 0.06
34 13 0.41
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (32 bp):
CGATACCAAGCTCTGGATCATGATATCACTAT
Found at i:52219390 original size:2 final size:2
Alignment explanation
Indices: 52219383--52219433 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
52219373 AATCACACCA
* * * *
52219383 AC AC AC AC AC AC AC AC AC AA AA AA AC AC AC AC AC AC AC AC TC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
52219425 AC AC AC AC A
1 AC AC AC AC A
52219434 AAAGTTTAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.55, C:0.43, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:52219916 original size:34 final size:32
Alignment explanation
Indices: 52219877--52219945 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
52219867 ATGGATATCG
* * *
52219877 CGATACTAGGCTCTAGGTATCGTGATATCACTGT
1 CGATACCAGGCTCTAGG--TCGCGATATCACTAT
52219911 CGATACCAGGCTCTAGGTCGCGATATCACTAT
1 CGATACCAGGCTCTAGGTCGCGATATCACTAT
52219943 CGA
1 CGA
52219946 AGGGAAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 16 0.50
34 16 0.50
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (32 bp):
CGATACCAGGCTCTAGGTCGCGATATCACTAT
Found at i:52220693 original size:5 final size:5
Alignment explanation
Indices: 52220693--52220725 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
52220683 ATGATAAGAT
52220693 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATA
1 ATAAG ATAAG ATAAG ATAAG ATAAG ATAAG ATA
52220726 TGAAACATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (5 bp):
ATAAG
Found at i:52237481 original size:44 final size:44
Alignment explanation
Indices: 52237428--52237662 Score: 143
Period size: 44 Copynumber: 5.1 Consensus size: 44
52237418 CCTTTATTTT
* **
52237428 AATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
** * * *
52237472 AATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTGGCTCC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
52237516 AATATAATGCGATCTACTATGCTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTT
1 -A-AT-CTGC--TC--C-A--CTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* ** *
52237570 AATCTGCTCCACTGTAATCTTAGGGAGATGGGATTACCAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
52237614 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTCC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
52237658 AATCT
1 AATCT
52237663 AATGCGATCT
Statistics
Matches: 141, Mismatches: 34, Indels: 32
0.68 0.16 0.15
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 96 0.68
45 2 0.01
46 3 0.02
47 4 0.03
49 4 0.03
51 4 0.03
52 2 0.01
53 2 0.01
54 20 0.14
55 1 0.01
56 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:52237494 original size:142 final size:142
Alignment explanation
Indices: 52237238--52237764 Score: 856
Period size: 142 Copynumber: 3.7 Consensus size: 142
52237228 ATAAGACCTG
* * *
52237238 ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCCGCTCCACCGTAA
1 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* * * * *
52237303 TCTTAGGGAGATGGGATTACTAACTTCAATCTGCTCTGCTATGATCTCAGGGAGATAAGATTTCT
66 TCTCAGGGAGATGGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
*
52237368 GGCTCTAATCTA
131 GGCTCCAATCTA
* *
52237380 ATGCGATCTACTCTGTTGTAACTTCATAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
1 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
*
52237445 TCTCAGGGAGATGGGATTACTAGCTTCAATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCT
66 TCTCAGGGAGATGGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
*
52237510 GGCTCCAATATA
131 GGCTCCAATCTA
* *
52237522 ATGCGATCTACTATGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAA
1 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* *
52237587 TCTTAGGGAGATGGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
66 TCTCAGGGAGATGGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
52237652 GGCTCCAATCTA
131 GGCTCCAATCTA
* * *
52237664 ATGCGATCTACTCTGCTGTAACTTCAGATAGATAAGATCCTTTATTTTAATCCGCTTCACTATAA
1 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
* *
52237729 TCTCAGGGAGATAGGATTACAAGCTTCAATCTGCTC
66 TCTCAGGGAGATGGGATTACTAGCTTCAATCTGCTC
52237765 TCTTACACTT
Statistics
Matches: 356, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 356 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA
TCTCAGGGAGATGGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCT
GGCTCCAATCTA
Found at i:52238715 original size:8 final size:8
Alignment explanation
Indices: 52238702--52238744 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
52238692 TTATCTTAGC
52238702 AAAAGAAG
1 AAAAGAAG
*
52238710 AAAAGAAA
1 AAAAGAAG
52238718 AAAAGAAGG
1 AAAAGAA-G
52238727 AAAA-AAG
1 AAAAGAAG
52238734 AAAA-AAG
1 AAAAGAAG
52238741 AAAA
1 AAAA
52238745 ATATATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 12 0.38
8 16 0.50
9 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:52244810 original size:142 final size:142
Alignment explanation
Indices: 52244554--52245058 Score: 884
Period size: 142 Copynumber: 3.6 Consensus size: 142
52244544 GGGACTAGAC
* * *
52244554 TCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACCGTAATCTCAGGGAGATGGGATTACTAG
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAG
*
52244619 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTCCAATCTAATGCGATCTAC
66 CTTCAATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTGGCTCCAATCTAATGCGATCTAC
*
52244684 TCTGTTGTAACT
131 TCTGCTGTAACT
* *
52244696 TCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTTAGGGAGATGGGATTACTAG
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAG
* *
52244761 CTTCAATCTGCTCCGTTGCAATCTCAGGGAGATAAGATTTCTAGCTCCAATCTAATGCGATCTAC
66 CTTCAATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTGGCTCCAATCTAATGCGATCTAC
52244826 TCTGCTGTAACT
131 TCTGCTGTAACT
*
52244838 TTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAG
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAG
* *
52244903 CTTCAATCTACTCCGTTGTAATCTCAGGGAGATAAGATTTTTGGCTCCAATCTAATGCGATCTAC
66 CTTCAATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTGGCTCCAATCTAATGCGATCTAC
52244968 TCTGCTGTAACT
131 TCTGCTGTAACT
* *
52244980 TCAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAG
1 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAG
52245045 CTTCAATCTGCTCC
66 CTTCAATCTGCTCC
52245059 CTTACACTTG
Statistics
Matches: 343, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 343 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (142 bp):
TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATGGGATTACTAG
CTTCAATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTGGCTCCAATCTAATGCGATCTAC
TCTGCTGTAACT
Found at i:52246314 original size:2 final size:2
Alignment explanation
Indices: 52246307--52246337 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52246297 ATGATAAATT
52246307 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52246338 AATGCATGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52249468 original size:39 final size:40
Alignment explanation
Indices: 52249388--52249471 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 40
52249378 AAGCATTTAA
52249388 TTAATATTTTAAAGTTTTAAAAAATAATAATAAATACATTT
1 TTAATATTTTAAAGTTTTAAAAAATAAT-ATAAATACATTT
* *
52249429 TTAATAATTTT-AA-TTTTAAAAAATAAGT-TACATATATTT
1 TTAAT-ATTTTAAAGTTTTAAAAAATAA-TATAAATACATTT
52249468 TTAA
1 TTAA
52249472 AACCTTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
39 13 0.33
40 13 0.33
41 8 0.21
42 5 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (40 bp):
TTAATATTTTAAAGTTTTAAAAAATAATATAAATACATTT
Found at i:52250465 original size:21 final size:21
Alignment explanation
Indices: 52250439--52250499 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
52250429 TTATGCTTTC
52250439 CACAACATTCGTCTTTTTATA
1 CACAACATTCGTCTTTTTATA
** * *
52250460 CACAACA-T--TAATTATATC
1 CACAACATTCGTCTTTTTATA
52250478 CACAACATTCGTCTTTTTATA
1 CACAACATTCGTCTTTTTATA
52250499 C
1 C
52250500 GCGTAATTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
18 13 0.45
19 1 0.03
20 1 0.03
21 14 0.48
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (21 bp):
CACAACATTCGTCTTTTTATA
Found at i:52256935 original size:28 final size:28
Alignment explanation
Indices: 52256889--52256945 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
52256879 TATAGTTTTT
52256889 ATAATATTTATAAAGGTTATAATAATAA
1 ATAATATTTATAAAGGTTATAATAATAA
*
52256917 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATAT-TTATAAAGGTTATAATAATAA
52256945 A
1 A
52256946 AACAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (28 bp):
ATAATATTTATAAAGGTTATAATAATAA
Found at i:52258185 original size:64 final size:64
Alignment explanation
Indices: 52258101--52258277 Score: 238
Period size: 64 Copynumber: 2.8 Consensus size: 64
52258091 ATATATATTT
*
52258101 AAAGTTCTTGAGTTGCATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGTTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* * * *
52258165 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAGTATAGGTTAC
1 AAAGTTCTTGAGTTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
*
52258229 AAA-TTCTTTGAGTTGAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTC-TTGAGTTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
52258278 GAATGTTTGT
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
62 15 0.15
63 4 0.04
64 73 0.72
65 10 0.10
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (64 bp):
AAAGTTCTTGAGTTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:52258420 original size:16 final size:16
Alignment explanation
Indices: 52258399--52258443 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
52258389 CTGAGATTTT
52258399 CAGGCTTAATGCCTAG
1 CAGGCTTAATGCCTAG
52258415 CAGGCTTAATGCCTAG
1 CAGGCTTAATGCCTAG
*
52258431 CAGGCTTGATGCC
1 CAGGCTTAATGCC
52258444 GGTGAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (16 bp):
CAGGCTTAATGCCTAG
Found at i:52258485 original size:41 final size:41
Alignment explanation
Indices: 52258423--52258529 Score: 121
Period size: 41 Copynumber: 2.6 Consensus size: 41
52258413 AGCAGGCTTA
52258423 ATGCCTAGCAGGC-TTGATGCCGGTG-AAT-TAATTCAGACTTT
1 ATGCCTAGCAGGCTTTG-TGCCGGTGAAATGT-A-TCAGACTTT
* * *
52258464 ATGTCTAGCAGGCTTTGTGCCGGTGAAATGTATCGGGCTTT
1 ATGCCTAGCAGGCTTTGTGCCGGTGAAATGTATCAGACTTT
* *
52258505 GTGCCTAGCAGGCTTTATGCCGGTG
1 ATGCCTAGCAGGCTTTGTGCCGGTG
52258530 TTTTATACAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
41 49 0.86
42 7 0.12
43 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.32
Consensus pattern (41 bp):
ATGCCTAGCAGGCTTTGTGCCGGTGAAATGTATCAGACTTT
Found at i:52259269 original size:14 final size:15
Alignment explanation
Indices: 52259245--52259279 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
52259235 TACTTTAATC
52259245 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
52259260 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
52259275 ATGGT
1 ATGGT
52259280 AATGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:52260996 original size:2 final size:2
Alignment explanation
Indices: 52260989--52261037 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
52260979 ATGATAAATT
52260989 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52261031 AG AG AG A
1 AG AG AG A
52261038 TGCATGGGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52261367 original size:3 final size:3
Alignment explanation
Indices: 52261355--52261392 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
52261345 TTAATCATAC
* *
52261355 CAA C-A CAA CAA CAA CAA CAA CAA TAG CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
52261393 AAAACACGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.63, C:0.32, G:0.03, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:52261916 original size:32 final size:34
Alignment explanation
Indices: 52261856--52261924 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 34
52261846 GTAGATATCA
*
52261856 CGATACCAGGCTCTAGGTATCGTGATATCAGTAT
1 CGATACCAGGCTCTAGGTATCGTGATATCACTAT
*
52261890 CGATACCAGGCTCT-GG-GTCGTGATATCACTAT
1 CGATACCAGGCTCTAGGTATCGTGATATCACTAT
52261922 CGA
1 CGA
52261925 AGTGAGACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 17 0.52
33 2 0.06
34 14 0.42
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (34 bp):
CGATACCAGGCTCTAGGTATCGTGATATCACTAT
Found at i:52262448 original size:41 final size:41
Alignment explanation
Indices: 52262403--52262485 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
52262393 AGATAAAATA
*
52262403 GGTTGTTTTTATCTTGTTACTTTTGAAATCAATTTCATTTT
1 GGTTGTTTTTATCTTGTTACTTTTGAAATAAATTTCATTTT
52262444 GGTTGTTTTTATCTTGTTACTTTTGAAATAAATTTCATTTT
1 GGTTGTTTTTATCTTGTTACTTTTGAAATAAATTTCATTTT
52262485 G
1 G
52262486 TTTCATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.08, G:0.13, T:0.58
Consensus pattern (41 bp):
GGTTGTTTTTATCTTGTTACTTTTGAAATAAATTTCATTTT
Found at i:52265737 original size:36 final size:36
Alignment explanation
Indices: 52265672--52265743 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
52265662 GCACAGCAAA
* *
52265672 AATTAAAGTTTTGAAAACTAAATCGGTTTGTAATAT
1 AATTAAAATTTTGAAAACTAAATCAGTTTGTAATAT
* * *
52265708 AATTAAAATTTTGAAAACTGACTCAGTTTGTGATAT
1 AATTAAAATTTTGAAAACTAAATCAGTTTGTAATAT
52265744 TTATAGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (36 bp):
AATTAAAATTTTGAAAACTAAATCAGTTTGTAATAT
Found at i:52269355 original size:59 final size:59
Alignment explanation
Indices: 52269265--52269777 Score: 745
Period size: 59 Copynumber: 8.8 Consensus size: 59
52269255 TGTTTATGTA
* *
52269265 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATAATTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
52269324 AATTAATAAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*
52269383 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTTTTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
52269442 AATTATTCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGGTTATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* * *
52269501 AATTAGTCACAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTACTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* * * * *
52269560 AATTAATC--GAA--AACTAATTATTCATACAATTATTATGAAATAAGATTATTTAATT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
*** * * *
52269615 AATTAATTGGAAATTAATTAAGTATTCGTAAAATTATTATGAAATATGATTATTTATCT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
52269674 AACTAATC--AAA--AATTAATTATTCATAAAATTATTATGAAATATGATGATTTATTT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
* *
52269729 AATTAATAAAAAATTAATTAATTATTCGTAAAATTATTATGAAATATGA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGA
52269778 CCCAGCATTT
Statistics
Matches: 407, Mismatches: 39, Indels: 16
0.88 0.08 0.03
Matches are distributed among these distances:
55 92 0.23
57 10 0.02
59 305 0.75
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (59 bp):
AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTT
Found at i:52269609 original size:114 final size:115
Alignment explanation
Indices: 52269265--52269777 Score: 733
Period size: 114 Copynumber: 4.4 Consensus size: 115
52269255 TGTTTATGTA
* *
52269265 AATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATAATTATTTATTTAATTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
*
52269330 TAAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
66 T--CAAA-TAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
* *
52269383 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTTTTTATTTAATTAT
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
* *
52269448 TCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGGTTATTTATTT
66 TC--AAA-TAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
* * *
52269501 AATTAGTCACAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTACTTATTTAATTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
* * * *
52269566 TCGAA-AACTAATTATTCATACAATTATTATGAAATAAGATTATTTAATT
66 TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
*** * * * *
52269615 AATTAATTGGAAATTAATTAAGTATTCGTAAAATTATTATGAAATATGATTATTTATCTAACTAA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
* *
52269680 TCAAA-AATTAATTATTCATAAAATTATTATGAAATATGATGATTTATTT
66 TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
* *
52269729 AATTAATAAAAAATTAATTAATTATTCGTAAAATTATTATGAAATATGA
1 AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGA
52269778 CCCAGCATTT
Statistics
Matches: 356, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
114 183 0.51
116 2 0.01
118 171 0.48
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (115 bp):
AATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTAATTAA
TCAAATAATTAATTATTCATAAAATTATTATGAAATATGATTATTTAATT
Found at i:52280767 original size:29 final size:30
Alignment explanation
Indices: 52280720--52280779 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
52280710 ATAGAAAATT
*
52280720 AATATACAAAATTAATCAA-AGTTTAATTTA
1 AATATAAAAAATTAATCAATA-TTTAATTTA
*
52280750 AATATAAAAAATT-GTCAATATTTAATTTA
1 AATATAAAAAATTAATCAATATTTAATTTA
52280779 A
1 A
52280780 TAAAAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
AATATAAAAAATTAATCAATATTTAATTTA
Found at i:52284865 original size:40 final size:40
Alignment explanation
Indices: 52284821--52284896 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
52284811 ACAAAACACT
* *
52284821 GCTATAGATCGCGCATTAGCGGTGCTTCTTGAAAAACGTG
1 GCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGTG
* *
52284861 GCTATAGGTCGAGCATTAGCGGCGCTTTTTGAAAAA
1 GCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAA
52284897 TGCCGCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (40 bp):
GCTATAGATCGAGCATTAGCGGCGCTTCTTGAAAAACGTG
Found at i:52285168 original size:7 final size:7
Alignment explanation
Indices: 52285126--52285169 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
52285116 GGTAATTTAG
52285126 GGATTAT
1 GGATTAT
* *
52285133 GTGTTTAG
1 G-GATTAT
*
52285141 GGATTAG
1 GGATTAT
52285148 GGATTAT
1 GGATTAT
52285155 GGATTAT
1 GGATTAT
52285162 GGATTAT
1 GGATTAT
52285169 G
1 G
52285170 TGGTTTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (7 bp):
GGATTAT
Found at i:52285864 original size:15 final size:14
Alignment explanation
Indices: 52285843--52285891 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
52285833 ATGATTTTAA
52285843 GGTTTAGGGATTAT
1 GGTTTAGGGATTAT
52285857 GTGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
* *
52285872 GGATTATGGATTAT
1 GGTTTAGGGATTAT
52285886 GGTTTA
1 GGTTTA
52285892 AGGGTTTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:52285912 original size:21 final size:21
Alignment explanation
Indices: 52285886--52285955 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
52285876 TATGGATTAT
*
52285886 GGTTTAAGGGTTTGGGTTTAA
1 GGTTTAAGGGTTAGGGTTTAA
* *
52285907 GGTTTAGGGGTTAGGGGTTAA
1 GGTTTAAGGGTTAGGGTTTAA
* *
52285928 GGGTT-AGAGGTTAGGGGTTTAG
1 GGTTTAAG-GGTTA-GGGTTTAA
52285950 GGTTTA
1 GGTTTA
52285956 TGTTTTATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.71
22 10 0.26
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (21 bp):
GGTTTAAGGGTTAGGGTTTAA
Found at i:52285952 original size:7 final size:7
Alignment explanation
Indices: 52285838--52285955 Score: 62
Period size: 7 Copynumber: 16.6 Consensus size: 7
52285828 ATTAAATGAT
*
52285838 TTTAAGG
1 TTTAGGG
52285845 TTTAGGG
1 TTTAGGG
* *
52285852 ATTATGTG
1 TTTA-GGG
52285860 TTTAGGG
1 TTTAGGG
* *
52285867 ATTATGG
1 TTTAGGG
* *
52285874 ATTATGG
1 TTTAGGG
* *
52285881 ATTATGG
1 TTTAGGG
52285888 TTTAAGGG
1 TTT-AGGG
52285896 TTT-GGG
1 TTTAGGG
*
52285902 TTTAAGG
1 TTTAGGG
52285909 TTTAGGG
1 TTTAGGG
*
52285916 GTTAGGGG
1 TTTA-GGG
*
52285924 TTAAGGG
1 TTTAGGG
52285931 -TTAGAGG
1 TTTAG-GG
52285938 -TTAGGGG
1 TTTA-GGG
52285945 TTTAGGG
1 TTTAGGG
52285952 TTTA
1 TTTA
52285956 TGTTTTATGA
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
6 9 0.10
7 60 0.67
8 20 0.22
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:52288657 original size:43 final size:43
Alignment explanation
Indices: 52288308--52288642 Score: 420
Period size: 43 Copynumber: 7.8 Consensus size: 43
52288298 TGTTTTTAGT
* * * * * * *
52288308 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGTTCTATAAC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* *
52288350 GGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * *
52288393 GGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * *
52288436 GGCGTTTGTGGAAAAAGCGCTGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* * * * *
52288479 GGCATTTGTGGGAAAAACACCGCTAAAGGTCACGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
** * * *
52288522 GGCGTTTGTGAAAAAAGGGCTGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
* *
52288565 GGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
52288608 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA
52288643 CTTTTAGCAG
Statistics
Matches: 251, Mismatches: 41, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
42 25 0.10
43 226 0.90
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGC
Found at i:52296486 original size:13 final size:13
Alignment explanation
Indices: 52296448--52296486 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
52296438 TCCAAGTCAG
*
52296448 ATAAAAAAATAAA
1 ATAAAATAATAAA
52296461 AT-AAATAACTAAA
1 ATAAAATAA-TAAA
52296474 ATAAAATAATAAA
1 ATAAAATAATAAA
52296487 TCAAAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 6 0.26
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAAATAATAAA
Found at i:52302873 original size:15 final size:14
Alignment explanation
Indices: 52302853--52302882 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
52302843 ATAACCTTCT
52302853 AAATATTTACTATTA
1 AAATATTTA-TATTA
52302868 AAATATTTATATTA
1 AAATATTTATATTA
52302882 A
1 A
52302883 TCAAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:52305642 original size:13 final size:13
Alignment explanation
Indices: 52305624--52305653 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52305614 AAATTATTAA
52305624 AATTATTAGATTT
1 AATTATTAGATTT
52305637 AATTATTAGATTT
1 AATTATTAGATTT
52305650 AATT
1 AATT
52305654 TCAAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
AATTATTAGATTT
Done.