Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 97 of 109
Found at i:19432975 original size:55 final size:56
Alignment explanation
Indices: 19432899--19433017 Score: 179
Period size: 55 Copynumber: 2.1 Consensus size: 56
19432889 AATATATGTA
* *
19432899 AAAATTAAATAAAATAAATTTATCATGTGACGTAAGTAATATAT-TAAAA-TAAAT
1 AAAATAAAATAAAATAAATTTATCACGTGACGTAAGTAATATATGTAAAATTAAAT
* *
19432953 AAAATAAAATAAATTAAAATTTATCACGTGATGTAAGTAATATATGTAAAATTAAAT
1 AAAATAAAATAAAAT-AAATTTATCACGTGACGTAAGTAATATATGTAAAATTAAAT
19433010 AAAATAAA
1 AAAATAAA
19433018 TTTATTTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
54 13 0.22
55 27 0.47
56 5 0.09
57 13 0.22
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (56 bp):
AAAATAAAATAAAATAAATTTATCACGTGACGTAAGTAATATATGTAAAATTAAAT
Found at i:19438418 original size:31 final size:31
Alignment explanation
Indices: 19438383--19438444 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
19438373 GAAGAATGTA
19438383 ATGTTATGACCAATTGGACATTGGAATAATT
1 ATGTTATGACCAATTGGACATTGGAATAATT
19438414 ATGTTATGACCAATTGGACATTGGAATAATT
1 ATGTTATGACCAATTGGACATTGGAATAATT
19438445 TTTTTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (31 bp):
ATGTTATGACCAATTGGACATTGGAATAATT
Found at i:19442265 original size:1 final size:1
Alignment explanation
Indices: 19442259--19442288 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
19442249 CACAATTTCG
19442259 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19442289 CAAATTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19444336 original size:40 final size:40
Alignment explanation
Indices: 19444292--19444372 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
19444282 CCTGAGATCT
* *
19444292 TTATAATACTGGGGTTTATCTGCTTTTGATGTTGATATAG
1 TTATAATACTGGGGTTTACCTGCTTTTAATGTTGATATAG
*
19444332 TTATAATTCTGGGGTTTACCTGCTTTTAATGTTGATATAG
1 TTATAATACTGGGGTTTACCTGCTTTTAATGTTGATATAG
19444372 T
1 T
19444373 CTTTGGAGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (40 bp):
TTATAATACTGGGGTTTACCTGCTTTTAATGTTGATATAG
Found at i:19453709 original size:168 final size:167
Alignment explanation
Indices: 19453398--19453709 Score: 446
Period size: 168 Copynumber: 1.9 Consensus size: 167
19453388 GAGATGCTAC
* * * * *
19453398 AATTTGATATTTTAGGCCTATAATTTAATGATTAAAGTAAGATTTGTATTTTATACTTTCAATTT
1 AATTTGATATTTTAGGCCTACAATTGAATGATTAAAGAAAGATTTATATTTTACACTTTCAATTT
* * *
19453463 TAGTTTTTATGAGAAAAACCAAAGTATTAGATTATGATTTTTAATCTTTTTAAATTTTTTGACAA
66 TAGCTTTTATGAGAAAAACCAAAGTATTAGATTAGGATTTTTAATCATTTTAAATTTTTTGACAA
* *
19453528 TCTTTTAGTGGTTTTTTGAAGGTATAAAAGATGTTGA
131 CCTTCTAGTGGTTTTTTGAAGGTATAAAAGATGTTGA
* * *
19453565 AATTTGATATTTTAGGCCTACAATTGAATGATTAAGGAAAGATTTATCTTTTACACTTTTTAATT
1 AATTTGATATTTTAGGCCTACAATTGAATGATTAAAGAAAGATTTATATTTTACAC-TTTCAATT
* * * *
19453630 TTGGCTTTTATGAGACAAACCCAAGTATTATATTAGGATTTTTAATCATTTTAAATTTTTTGACA
65 TTAGCTTTTATGAGAAAAACCAAAGTATTAGATTAGGATTTTTAATCATTTTAAATTTTTTGACA
19453695 ACCTTCCT-GTGGTTT
130 ACCTT-CTAGTGGTTT
19453710 CTGGGAGCAT
Statistics
Matches: 126, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
167 49 0.39
168 76 0.60
169 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.46
Consensus pattern (167 bp):
AATTTGATATTTTAGGCCTACAATTGAATGATTAAAGAAAGATTTATATTTTACACTTTCAATTT
TAGCTTTTATGAGAAAAACCAAAGTATTAGATTAGGATTTTTAATCATTTTAAATTTTTTGACAA
CCTTCTAGTGGTTTTTTGAAGGTATAAAAGATGTTGA
Found at i:19458480 original size:19 final size:19
Alignment explanation
Indices: 19458438--19458487 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
19458428 TTCAATTTCT
*
19458438 ATTTTTTTTTAAAAAATTA
1 ATTTTTATTTAAAAAATTA
**
19458457 A-TTTTATTTAATTAATTA
1 ATTTTTATTTAAAAAATTA
*
19458475 ATTTTTAATTAAA
1 ATTTTTATTTAAA
19458488 CTTACTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTATTTAAAAAATTA
Found at i:19460574 original size:8 final size:8
Alignment explanation
Indices: 19460561--19460862 Score: 57
Period size: 8 Copynumber: 38.8 Consensus size: 8
19460551 TTAGGATCTC
19460561 ATTTTAGG
1 ATTTTAGG
*
19460569 ATTTTAAG
1 ATTTTAGG
*
19460577 ATTTTAAG
1 ATTTTAGG
19460585 ATTTTAGG
1 ATTTTAGG
*
19460593 GTTTT-GG
1 ATTTTAGG
19460600 -TTTT--G
1 ATTTTAGG
19460605 AGTTTTAAAGG
1 A-TTTT--AGG
*
19460616 -TTTGAAGG
1 ATTT-TAGG
19460624 -TTTTAGG
1 ATTTTAGG
19460631 ATTTTAAGG
1 ATTTT-AGG
*
19460640 -GTTTAGG
1 ATTTTAGG
*
19460647 GTTTT-GAG
1 ATTTTAG-G
*
19460655 ATTTTAAG
1 ATTTTAGG
19460663 -TTTTAGG
1 ATTTTAGG
*
19460670 GTTTTGAGG
1 ATTTT-AGG
19460679 -TTTTAAGG
1 ATTTT-AGG
19460687 --TTT-GG
1 ATTTTAGG
*
19460692 AGGTTTA-G
1 A-TTTTAGG
19460700 AGTTTT--G
1 A-TTTTAGG
19460707 ATTTTAGGG
1 ATTTTA-GG
*
19460716 ATTTGA-G
1 ATTTTAGG
19460723 AGTTTTAGGG
1 A-TTTTA-GG
19460733 A--TT-GG
1 ATTTTAGG
19460738 ATTTTAGG
1 ATTTTAGG
19460746 ATTTT--G
1 ATTTTAGG
19460752 ATTTTTAGG
1 A-TTTTAGG
*
19460761 GTTTTA-G
1 ATTTTAGG
19460768 ATTTTAGG
1 ATTTTAGG
*
19460776 GTTTGTAGGG
1 ATTT-TA-GG
*
19460786 TTTTTAGG
1 ATTTTAGG
19460794 -TTTTGAAGG
1 ATTTT--AGG
19460803 ATTTTAAGG
1 ATTTT-AGG
*
19460812 --TTTCGG
1 ATTTTAGG
19460818 ATTTTAGG
1 ATTTTAGG
*
19460826 GTTTTCAGG
1 ATTTT-AGG
19460835 --TTTAGG
1 ATTTTAGG
* * *
19460841 GTTTAAAG
1 ATTTTAGG
*
19460849 ATTTTAGC
1 ATTTTAGG
19460857 ATTTTA
1 ATTTTA
19460863 AAAGTTTCGA
Statistics
Matches: 226, Mismatches: 27, Indels: 82
0.67 0.08 0.24
Matches are distributed among these distances:
5 6 0.03
6 15 0.07
7 50 0.22
8 113 0.50
9 30 0.13
10 11 0.05
11 1 0.00
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (8 bp):
ATTTTAGG
Found at i:19460582 original size:16 final size:16
Alignment explanation
Indices: 19460561--19460660 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 16
19460551 TTAGGATCTC
19460561 ATTTTAGGATTTTAAG
1 ATTTTAGGATTTTAAG
* *
19460577 ATTTTAAGATTTTAGG
1 ATTTTAGGATTTTAAG
* *
19460593 GTTTT-GG-TTTTGAG
1 ATTTTAGGATTTTAAG
*
19460607 -TTTTAAAGG-TTTGAAG
1 ATTTT--AGGATTTTAAG
*
19460623 GTTTTAGGATTTTAAG
1 ATTTTAGGATTTTAAG
** * *
19460639 GGTTTAGGGTTTTGAG
1 ATTTTAGGATTTTAAG
19460655 ATTTTA
1 ATTTTA
19460661 AGTTTTAGGG
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
13 4 0.06
14 5 0.08
15 4 0.06
16 48 0.74
17 4 0.06
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
ATTTTAGGATTTTAAG
Found at i:19460639 original size:24 final size:24
Alignment explanation
Indices: 19460607--19460697 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
19460597 TGGTTTTGAG
19460607 TTTTAAAGGTTTGAAGGTTTTAGGA
1 TTTT-AAGGTTTGAAGGTTTTAGGA
*
19460632 TTTTAAGGGTTT-AGGGTTTT-GAGA
1 TTTTAA-GGTTTGAAGGTTTTAG-GA
* *
19460656 TTTTAA-GTTTTAGGGTTTTGAGG-
1 TTTTAAGGTTTGAAGGTTTT-AGGA
*
19460679 TTTTAAGGTTTGGAGGTTT
1 TTTTAAGGTTTGAAGGTTT
19460698 AGAGTTTTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.07
23 15 0.27
24 27 0.48
25 10 0.18
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (24 bp):
TTTTAAGGTTTGAAGGTTTTAGGA
Found at i:19460652 original size:54 final size:55
Alignment explanation
Indices: 19460562--19460707 Score: 149
Period size: 54 Copynumber: 2.7 Consensus size: 55
19460552 TAGGATCTCA
* *
19460562 TTTT-AGGATTTTAAGATTTTAAGATTTTAGGGTTTTG-G-TTTTGAGTTTTAAAGG
1 TTTTGAGG-TTTTAAGATTTTAAGAGTTTAGGGTTTTGAGATTTTAAGTTTT-AAGG
* * *
19460616 -TTTGAAGGTTTTAGGATTTTAAGGGTTTAGGGTTTTGAGATTTTAAGTTTTAGGG
1 TTTTG-AGGTTTTAAGATTTTAAGAGTTTAGGGTTTTGAGATTTTAAGTTTTAAGG
* ** *
19460671 TTTTGAGGTTTTAAGGTTTGGAG-GTTTAGAGTTTTGA
1 TTTTGAGGTTTTAAGATTTTAAGAGTTTAGGGTTTTGA
19460708 TTTTAGGGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
53 3 0.04
54 39 0.51
55 21 0.27
56 14 0.18
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (55 bp):
TTTTGAGGTTTTAAGATTTTAAGAGTTTAGGGTTTTGAGATTTTAAGTTTTAAGG
Found at i:19460671 original size:23 final size:23
Alignment explanation
Indices: 19460598--19460789 Score: 110
Period size: 23 Copynumber: 8.3 Consensus size: 23
19460588 TTAGGGTTTT
* *
19460598 GGTTTTGAG-TTTTAAAGGTTTGAA
1 GGTTTTGAGATTTT-AA-GTTTTAG
*
19460622 GGTTTT-AGGATTTTAAGGGTTTAG
1 GGTTTTGA-GATTTTAA-GTTTTAG
19460646 GGTTTTGAGATTTTAAGTTTTAG
1 GGTTTTGAGATTTTAAGTTTTAG
* * *
19460669 GGTTTTGAGGTTTTAAGGTTTGG
1 GGTTTTGAGATTTTAAGTTTTAG
* *
19460692 AGGTTTAGAG-TTTTGA-TTTTAG
1 -GGTTTTGAGATTTTAAGTTTTAG
* * **
19460714 GGATTTGAGAGTTTTAGGGATT-G
1 GGTTTTGAGA-TTTTAAGTTTTAG
* * *
19460737 GATTTT-AGGATTTTGATTTTTAG
1 GGTTTTGA-GATTTTAAGTTTTAG
*
19460760 GGTTTT-AGATTTTAGGGTTTGTAG
1 GGTTTTGAGATTTTA-AGTTT-TAG
19460784 GGTTTT
1 GGTTTT
19460790 TAGGTTTTGA
Statistics
Matches: 129, Mismatches: 28, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
21 7 0.05
22 17 0.13
23 53 0.41
24 47 0.36
25 5 0.04
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (23 bp):
GGTTTTGAGATTTTAAGTTTTAG
Found at i:19460720 original size:14 final size:14
Alignment explanation
Indices: 19460703--19460780 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 14
19460693 GGTTTAGAGT
19460703 TTTGATTTTAGGGA
1 TTTGATTTTAGGGA
19460717 TTTGAGAGTTTTAGGGA
1 TTT--GA-TTTTAGGGA
*
19460734 TTGGATTTTA-GGA
1 TTTGATTTTAGGGA
*
19460747 TTTTGATTTTTAGGGT
1 -TTTGA-TTTTAGGGA
19460763 TTTAGATTTTAGGG-
1 TTT-GATTTTAGGGA
19460777 TTTG
1 TTTG
19460781 TAGGGTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
13 4 0.07
14 15 0.28
15 18 0.33
16 6 0.11
17 11 0.20
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.51
Consensus pattern (14 bp):
TTTGATTTTAGGGA
Found at i:19460807 original size:18 final size:18
Alignment explanation
Indices: 19460769--19460814 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
19460759 GGGTTTTAGA
* * *
19460769 TTTTAGGGTTTGTAGGGT
1 TTTTAGGTTTTGAAGGAT
19460787 TTTTAGGTTTTGAAGGAT
1 TTTTAGGTTTTGAAGGAT
*
19460805 TTTAAGGTTT
1 TTTTAGGTTT
19460815 CGGATTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.52
Consensus pattern (18 bp):
TTTTAGGTTTTGAAGGAT
Found at i:19461612 original size:18 final size:18
Alignment explanation
Indices: 19461589--19461634 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
19461579 CAAAAATGCT
19461589 AATAAAAATATGAAA-AAA
1 AATAAAAATAT-AAATAAA
*
19461607 AATAAAAAAATAAATAAA
1 AATAAAAATATAAATAAA
19461625 AATAATAAAT
1 AATAA-AAAT
19461635 TTATGCCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAAAATATAAATAAA
Found at i:19461626 original size:13 final size:12
Alignment explanation
Indices: 19461601--19461634 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
19461591 TAAAAATATG
19461601 AAAAA-AAATAA
1 AAAAATAAATAA
19461612 AAAAATAAATAA
1 AAAAATAAATAA
19461624 AAATAATAAAT
1 AAA-AATAAAT
19461635 TTATGCCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 9 0.43
13 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:19463261 original size:36 final size:36
Alignment explanation
Indices: 19463198--19463349 Score: 144
Period size: 36 Copynumber: 4.2 Consensus size: 36
19463188 TGTAAGAAGG
* *
19463198 AAAATAAAAAGTTGATCAAGATAACACCGCAAGTCAA
1 AAAATAAAAA-ATAATCAAGATAACACCGCAAGTCAA
* * * * *
19463235 AAAATAAAAAACAATTAAGATAACACCGTAATTCCA
1 AAAATAAAAAATAATCAAGATAACACCGCAAGTCAA
* * * * *
19463271 AAAATAAAGAGTGACCAA-ATAACACCGTAAGTCAA
1 AAAATAAAAAATAATCAAGATAACACCGCAAGTCAA
* * **
19463306 AAAATAAAAAATAATCAGGATAATACCGCAAGTTGA
1 AAAATAAAAAATAATCAAGATAACACCGCAAGTCAA
19463342 AAAATAAA
1 AAAATAAA
19463350 GAATGATCGA
Statistics
Matches: 90, Mismatches: 24, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
35 28 0.31
36 52 0.58
37 10 0.11
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.17
Consensus pattern (36 bp):
AAAATAAAAAATAATCAAGATAACACCGCAAGTCAA
Found at i:19463315 original size:71 final size:73
Alignment explanation
Indices: 19463198--19463351 Score: 197
Period size: 71 Copynumber: 2.1 Consensus size: 73
19463188 TGTAAGAAGG
* * *
19463198 AAAATAAAAAGTTGATCAAGATAACACCGCAAGTCAAAAAATAAAAAACAATTAAGATAACACCG
1 AAAATAAAGAGTTGACCAAGATAACACCGCAAGTCAAAAAATAAAAAACAATCAAGATAACACCG
*
19463263 TAA-TTCCA
66 CAAGTT-CA
* * * *
19463271 AAAATAAAGAG-TGACCAA-ATAACACCGTAAGTCAAAAAATAAAAAATAATCAGGATAATACCG
1 AAAATAAAGAGTTGACCAAGATAACACCGCAAGTCAAAAAATAAAAAACAATCAAGATAACACCG
*
19463334 CAAGTTGA
66 CAAGTTCA
19463342 AAAATAAAGA
1 AAAATAAAGA
19463352 ATGATCGAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
71 53 0.75
72 8 0.11
73 10 0.14
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (73 bp):
AAAATAAAGAGTTGACCAAGATAACACCGCAAGTCAAAAAATAAAAAACAATCAAGATAACACCG
CAAGTTCA
Found at i:19463418 original size:73 final size:71
Alignment explanation
Indices: 19463220--19463418 Score: 184
Period size: 71 Copynumber: 2.8 Consensus size: 71
19463210 TGATCAAGAT
* * * * * * * *
19463220 AACACCGCAAGTCAAAAAATAAAAAACAATTA-AGATAACACCGTAATTCCAAAAATAAAGAGTG
1 AACACCGTAAGTCAAAAAATAAAAAATAATCAGA-ATAATACCGCAAGTCAAAAAATAAAGAATG
*
19463284 ACCAAAT
65 ACCAAAC
* **
19463291 AACACCGTAAGTCAAAAAATAAAAAATAATCAGGATAATACCGCAAGTTGAAAAATAAAGAATGA
1 AACACCGTAAGTCAAAAAATAAAAAATAATCAGAATAATACCGCAAGTCAAAAAATAAAGAATGA
*
19463356 TCGAAAC
66 -CCAAAC
* * * * * * *
19463363 AATACTGTAAGTCAAGTAATTAAAGAATGATCAGAATAATACTGCAAGTCAAAAAA
1 AACACCGTAAGTCAA-AAAATAAAAAATAATCAGAATAATACCGCAAGTCAAAAAA
19463419 AGTAAAGACG
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
71 54 0.52
72 17 0.17
73 32 0.31
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.18
Consensus pattern (71 bp):
AACACCGTAAGTCAAAAAATAAAAAATAATCAGAATAATACCGCAAGTCAAAAAATAAAGAATGA
CCAAAC
Found at i:19476821 original size:10 final size:10
Alignment explanation
Indices: 19476806--19476834 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
19476796 AGGCAAAGCA
19476806 AAGGGAAAAG
1 AAGGGAAAAG
19476816 AAGGG-AAAG
1 AAGGGAAAAG
19476825 AAGGGAAAAG
1 AAGGGAAAAG
19476835 CAAAGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (10 bp):
AAGGGAAAAG
Found at i:19480429 original size:2 final size:2
Alignment explanation
Indices: 19480424--19480484 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
19480414 ATATATATAT
19480424 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
19480466 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
19480485 TTCTATAGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19480552 original size:21 final size:21
Alignment explanation
Indices: 19480526--19480569 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19480516 GCAGAAGCAC
19480526 TACTGGCAGAAGTGGTATTAG
1 TACTGGCAGAAGTGGTATTAG
19480547 TACTGGCAGAAGTGGTATTAG
1 TACTGGCAGAAGTGGTATTAG
19480568 TA
1 TA
19480570 GAGCTGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.30
Consensus pattern (21 bp):
TACTGGCAGAAGTGGTATTAG
Found at i:19481459 original size:222 final size:219
Alignment explanation
Indices: 19481003--19481460 Score: 578
Period size: 219 Copynumber: 2.1 Consensus size: 219
19480993 CTTCAAGCTC
* * * * *
19481003 GAATTTAATATATATTATATTATAACATATAAGATTATATGATAAAAATTATTTATGTGGATATC
1 GAATTTAA-ATATATTATATTACAACATAAAAGATTACATGATAAAAATTACTTACGTGGATATC
* * * * * * * *
19481068 TAAATAGATAGTCTTTTTTATTGATATATAAGATAATGCTTATATTATGTTATTTATTAAATAAT
65 TAAATAGATAATCTCTTTTAATGACACATAAAATAATACTTATATTATGTTATTTACTAAATAAT
* * **
19481133 TTTTTCATAAATTAGTTAAATTTAATATTTGAATAATTATTTAAATTTAAATTTAAATCTATCTA
130 TTTTTAATAAATTAGTTAAATTTAATATTTGAATAATTATTTAAATTCAAATCAAAATCTATCTA
* *
19481198 GGATTAAAAATTTTGCATAAGTTTT
195 GAATTAAAAATTTTGCATAAATTTT
* * *
19481223 GAATTCAAATATATTATATTACAACATAAAAGATTACATGATAAAAATTGCTTACGTGGATATGT
1 GAATTTAAATATATTATATTACAACATAAAAGATTACATGATAAAAATTACTTACGTGGATATCT
* * * *
19481288 AAGTGGATAATCTCTTTTAATGACACATAAAATAATATTTATATTATTTTATTTACCT-AATAAA
66 AAATAGATAATCTCTTTTAATGACACATAAAATAATACTTATATTATGTTATTTA-CTAAAT-AA
*
19481352 TTTCTTTAATAAATTATTTAAATTTAATATTTTGAATAATTATTTAAATTCAAATCAAAATCTA-
129 TTT-TTTAATAAATTAGTTAAATTTAATA-TTTGAATAATTATTTAAATTCAAATCAAAATCTAT
* *
19481416 CTTGAAATTGAAAATTTTGCATAAATTTT
192 CTAG-AATTAAAAATTTTGCATAAATTTT
*
19481445 GAATTTACATATATTA
1 GAATTTAAATATATTA
19481461 AATCGTAATT
Statistics
Matches: 202, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
219 97 0.48
220 13 0.06
221 26 0.13
222 66 0.33
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (219 bp):
GAATTTAAATATATTATATTACAACATAAAAGATTACATGATAAAAATTACTTACGTGGATATCT
AAATAGATAATCTCTTTTAATGACACATAAAATAATACTTATATTATGTTATTTACTAAATAATT
TTTTAATAAATTAGTTAAATTTAATATTTGAATAATTATTTAAATTCAAATCAAAATCTATCTAG
AATTAAAAATTTTGCATAAATTTT
Found at i:19484663 original size:19 final size:19
Alignment explanation
Indices: 19484639--19484675 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19484629 AAATGAATTG
19484639 AAGAAAA-ATTTTTCATAAA
1 AAGAAAAGATTTTT-ATAAA
19484658 AAGAAAAGATTTTTATAA
1 AAGAAAAGATTTTTATAA
19484676 TTCTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
AAGAAAAGATTTTTATAAA
Found at i:19488076 original size:24 final size:24
Alignment explanation
Indices: 19488022--19488083 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
19488012 TTATTAAACA
19488022 TATTTATATT-TTTTTAAAAATTT
1 TATTTATATTATTTTTAAAAATTT
* ** **
19488045 AAAATATATTATTTTTAAATTTTT
1 TATTTATATTATTTTTAAAAATTT
19488069 TATTTATATTATTTT
1 TATTTATATTATTTT
19488084 AATATTATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTATATTATTTTTAAAAATTT
Found at i:19490044 original size:14 final size:15
Alignment explanation
Indices: 19490018--19490046 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19490008 ATAATTCGGT
19490018 TAATTCGATTTTGAA
1 TAATTCGATTTTGAA
19490033 TAATTC-ATTTTGAA
1 TAATTCGATTTTGAA
19490047 ATTAACCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (15 bp):
TAATTCGATTTTGAA
Found at i:19490975 original size:16 final size:16
Alignment explanation
Indices: 19490954--19490984 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19490944 GAGTGGTGCA
19490954 AGAAGATTTAAACTAT
1 AGAAGATTTAAACTAT
19490970 AGAAGATTTAAACTA
1 AGAAGATTTAAACTA
19490985 ACTTGATTAT
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:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (16 bp):
AGAAGATTTAAACTAT
Found at i:19491952 original size:9 final size:9
Alignment explanation
Indices: 19491938--19491963 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19491928 TCTGAAGAAA
19491938 GTATGTCTG
1 GTATGTCTG
19491947 GTATGTCTG
1 GTATGTCTG
19491956 GTATGTCT
1 GTATGTCT
19491964 ATGCCTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.46
Consensus pattern (9 bp):
GTATGTCTG
Found at i:19494518 original size:2 final size:2
Alignment explanation
Indices: 19494511--19494540 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19494501 CTATTGATCC
19494511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19494541 GACAAGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19494846 original size:19 final size:22
Alignment explanation
Indices: 19494824--19494869 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 22
19494814 CATATTTAGT
19494824 ATATAAA-ATT-TTTTAAA-TA
1 ATATAAATATTATTTTAAATTA
19494843 ATATAAATTATTATTTTAAATTA
1 ATATAAA-TATTATTTTAAATTA
19494866 ATAT
1 ATAT
19494870 TATTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.30
21 3 0.13
22 7 0.30
23 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAAATATTATTTTAAATTA
Found at i:19494881 original size:22 final size:21
Alignment explanation
Indices: 19494824--19494882 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
19494814 CATATTTAGT
19494824 ATATAAA--ATTTTTTAAATA
1 ATATAAATTATTTTTTAAATA
19494843 ATATAAATTATTATTTTAAATTA
1 ATATAAATTATT-TTTTAAA-TA
*
19494866 ATAT-TATTATATTTTTA
1 ATATAAATTAT-TTTTTA
19494883 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 7 0.21
21 3 0.09
22 17 0.50
23 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATAAATTATTTTTTAAATA
Found at i:19495479 original size:16 final size:16
Alignment explanation
Indices: 19495458--19495488 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19495448 GGACGTCCTA
19495458 AATATACGATAACTAC
1 AATATACGATAACTAC
*
19495474 AATATATGATAACTA
1 AATATACGATAACTA
19495489 ATTAATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
AATATACGATAACTAC
Found at i:19495691 original size:21 final size:20
Alignment explanation
Indices: 19495653--19495693 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19495643 ATAAAAAATT
19495653 ATTTTTTAATTAATTATTTA
1 ATTTTTTAATTAATTATTTA
19495673 ATTTTTT-ATTATATATATTTA
1 ATTTTTTAATTA-AT-TATTTA
19495694 TATAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTAATTAATTATTTA
Found at i:19495707 original size:30 final size:30
Alignment explanation
Indices: 19495673--19495742 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
19495663 TAATTATTTA
* * *
19495673 ATTTTTTATTATATATATTTATATAATGAT
1 ATTTTTTATTATATATATTTAAAAAATAAT
* * *
19495703 ATTTTTAAATATTTATATTTAAAAAATAAT
1 ATTTTTTATTATATATATTTAAAAAATAAT
19495733 A-TTTTTATTA
1 ATTTTTTATTA
19495743 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTTTTTATTATATATATTTAAAAAATAAT
Found at i:19495735 original size:20 final size:19
Alignment explanation
Indices: 19495710--19495762 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
19495700 GATATTTTTA
*
19495710 AATATTTATATTTAAAAAAT
1 AATATTT-TATTAAAAAAAT
19495730 AATATTTTTATTAAAAAAAT
1 AATA-TTTTATTAAAAAAAT
19495750 AATATTTTATTAA
1 AATATTTTATTAA
19495763 TTTCGGATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 9 0.29
20 19 0.61
21 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTTTATTAAAAAAAT
Found at i:19496844 original size:18 final size:19
Alignment explanation
Indices: 19496796--19496844 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
19496786 TTAAAAATAA
19496796 TTTAAAATTTGTTAGAATTC
1 TTTAAAATTT-TTAGAATTC
* * *
19496816 TTT-AATTTTTTTGAATTT
1 TTTAAAATTTTTAGAATTC
19496834 TTTAAAATTTT
1 TTTAAAATTTT
19496845 ATAATTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 10 0.42
19 11 0.46
20 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTAAAATTTTTAGAATTC
Found at i:19496970 original size:18 final size:19
Alignment explanation
Indices: 19496939--19496983 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
19496929 CAAATTTTTT
*
19496939 AATTTTTTATATTTT-TAA
1 AATTTTTTAGATTTTCTAA
*
19496957 AATTTTTTGGATTTTCTAA
1 AATTTTTTAGATTTTCTAA
19496976 AATTTTTT
1 AATTTTTT
19496984 CAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
AATTTTTTAGATTTTCTAA
Found at i:19497008 original size:55 final size:54
Alignment explanation
Indices: 19496832--19497019 Score: 139
Period size: 55 Copynumber: 3.2 Consensus size: 54
19496822 TTTTTTGAAT
* *
19496832 TTTTTAAAATTTTAT-AATTTATAAAAAATTTCTTAAATTAAAATTTTTTTTGGACATTTTAAA
1 TTTTTAAAATTTTTTGAATTT-TAAAAAA--TCTT---TTCAAA-TTTTTTT-GA-ATTTT-AA
* *
19496895 ATTTTAAATTTTTTTGAATTTTAAAAAATCTTTTCAAA-TTTTTT-AATTTTTTATA
1 TTTTTAAAATTTTTTGAATTTTAAAAAATCTTTTCAAATTTTTTTGAA--TTTTA-A
* ** *
19496950 TTTTTAAAATTTTTTGGATTTTCTAAAATTTTTTCAAATTATTTTTGAATTTTAA
1 TTTTTAAAATTTTTTGAATTTTAAAAAATCTTTTCAAATT-TTTTTGAATTTTAA
19497005 TTTTTTTAAAATTTT
1 --TTTTTAAAATTTT
19497020 AGAATTTCTT
Statistics
Matches: 106, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
53 1 0.01
54 2 0.02
55 38 0.36
56 12 0.11
57 18 0.17
58 7 0.07
61 4 0.04
63 19 0.18
64 5 0.05
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (54 bp):
TTTTTAAAATTTTTTGAATTTTAAAAAATCTTTTCAAATTTTTTTGAATTTTAA
Found at i:19497033 original size:18 final size:17
Alignment explanation
Indices: 19496997--19497036 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
19496987 ATTATTTTTG
* *
19496997 AATTTTAATTTTTTTAA
1 AATTTTAAATTTCTTAA
19497014 AATTTTAGAATTTCTTAA
1 AATTTTA-AATTTCTTAA
19497032 AATTT
1 AATTT
19497037 CTTTGAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTTAAATTTCTTAA
Found at i:19497035 original size:29 final size:28
Alignment explanation
Indices: 19497003--19497066 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
19496993 TTTGAATTTT
19497003 AATTTTTTTAAAATTTTAGAATTTCTTAA
1 AATTTTTTTAAAATTTTAG-ATTTCTTAA
* * *
19497032 AATTTCTTTGAAATTTTAGATTTTTTAA
1 AATTTTTTTAAAATTTTAGATTTCTTAA
*
19497060 ACTTTTT
1 AATTTTT
19497067 ATTTTTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (28 bp):
AATTTTTTTAAAATTTTAGATTTCTTAA
Found at i:19497046 original size:57 final size:58
Alignment explanation
Indices: 19496888--19497046 Score: 152
Period size: 55 Copynumber: 2.8 Consensus size: 58
19496878 TTTTTGGACA
* * * ** *
19496888 TTTTAA-AATTTTAAATTTTTTTGAATTTTAAAAAATCTTTTCAAA-T-TTTTT-AAT
1 TTTTAATATTTTTAAAATTTTTAGAATTTTCTAAAATTTTTTCAAATTATTTTTGAAT
* * *
19496942 TTTTTATATTTTTAAAATTTTTTGGATTTTCTAAAATTTTTTCAAATTATTTTTGAA-
1 TTTTAATATTTTTAAAATTTTTAGAATTTTCTAAAATTTTTTCAAATTATTTTTGAAT
* *
19496999 TTTTAATTTTTTTAAAA-TTTTAGAA-TTTCTTAAAATTTCTTTGAAATT
1 TTTTAATATTTTTAAAATTTTTAGAATTTTC-TAAAATTT-TTTCAAATT
19497047 TTAGATTTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
54 5 0.06
55 37 0.43
56 15 0.17
57 28 0.32
58 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (58 bp):
TTTTAATATTTTTAAAATTTTTAGAATTTTCTAAAATTTTTTCAAATTATTTTTGAAT
Found at i:19497072 original size:17 final size:16
Alignment explanation
Indices: 19497032--19497092 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
19497022 AATTTCTTAA
19497032 AATTTCTTTGAAA-TTTT
1 AATTT-TTT-AAATTTTT
19497049 AGATTTTTTAAACTTTTT
1 A-ATTTTTTAAA-TTTTT
* *
19497067 ATTTTTTTGAATTTTT
1 AATTTTTTAAATTTTT
19497083 AATTTTTTAA
1 AATTTTTTAA
19497093 GAATTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
16 16 0.43
17 12 0.32
18 9 0.24
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (16 bp):
AATTTTTTAAATTTTT
Found at i:19497099 original size:17 final size:17
Alignment explanation
Indices: 19497043--19497099 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
19497033 ATTTCTTTGA
19497043 AATTTTAGATTTTTTAA-
1 AATTTTA-ATTTTTTAAG
* * *
19497060 ACTTTTTATTTTTT-TG
1 AATTTTAATTTTTTAAG
19497076 AATTTTTAATTTTTTAAG
1 AA-TTTTAATTTTTTAAG
19497094 AATTTT
1 AATTTT
19497100 TTAGAAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 8 0.26
17 20 0.65
18 3 0.10
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (17 bp):
AATTTTAATTTTTTAAG
Found at i:19497100 original size:34 final size:34
Alignment explanation
Indices: 19497033--19497100 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
19497023 ATTTCTTAAA
*
19497033 ATTTCTTTGAAATTTTAGATTTTTTAAACTTTTT
1 ATTTCTTTGAAATTTTAGATTTTTTAAAATTTTT
* *
19497067 ATTTTTTTGAATTTTTA-ATTTTTTAAGAATTTTT
1 ATTTCTTTGAAATTTTAGATTTTTTAA-AATTTTT
19497101 TAGAAAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 9 0.30
34 21 0.70
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (34 bp):
ATTTCTTTGAAATTTTAGATTTTTTAAAATTTTT
Found at i:19498151 original size:16 final size:16
Alignment explanation
Indices: 19498132--19498168 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19498122 TGGATTATTC
*
19498132 AAATTTGAATTAATTT
1 AAATTTAAATTAATTT
19498148 AAATTTAAATTAATTT
1 AAATTTAAATTAATTT
*
19498164 TAATT
1 AAATT
19498169 CCAACAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AAATTTAAATTAATTT
Found at i:19498499 original size:2 final size:2
Alignment explanation
Indices: 19498492--19498519 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19498482 GTCCTGCATT
19498492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19498520 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19498524 original size:2 final size:2
Alignment explanation
Indices: 19498519--19498552 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19498509 ATATATATAT
19498519 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
19498553 GTTAATATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19499434 original size:61 final size:61
Alignment explanation
Indices: 19499335--19499457 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
19499325 ACTTGTCTTG
* * *
19499335 TTTAGTCTTGAAATCGGACTTAATTTGTAAAGGTTAATGTTTTTGATGTTTTATGCTTACC
1 TTTAGGCTCGAAATCGGACTTAATTTGTAAAGGCTAATGTTTTTGATGTTTTATGCTTACC
*
19499396 TTTAGGCTCGAAATCTGACTTAATTTGTAAAGGCTAATGTTTTTGATGTTTTATGCTTACC
1 TTTAGGCTCGAAATCGGACTTAATTTGTAAAGGCTAATGTTTTTGATGTTTTATGCTTACC
19499457 T
1 T
19499458 ACGATGAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.46
Consensus pattern (61 bp):
TTTAGGCTCGAAATCGGACTTAATTTGTAAAGGCTAATGTTTTTGATGTTTTATGCTTACC
Found at i:19508794 original size:22 final size:22
Alignment explanation
Indices: 19508769--19508812 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19508759 TGTATATTTA
*
19508769 TATTTGTATATCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
*
19508791 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
19508813 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATACCTAGAATTAAG
Found at i:19511099 original size:2 final size:2
Alignment explanation
Indices: 19511092--19511125 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19511082 TTTTCACAAA
19511092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19511126 TAAACTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19513165 original size:18 final size:18
Alignment explanation
Indices: 19513142--19513190 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 18
19513132 TCTGTAAACA
19513142 AAAATCTGTTTTATATTT
1 AAAATCTGTTTTATATTT
*
19513160 AAAATC--TATTATA---
1 AAAATCTGTTTTATATTT
19513173 AAAATCTGTTTTATATTT
1 AAAATCTGTTTTATATTT
19513191 GATATATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
13 6 0.25
15 6 0.25
16 6 0.25
18 6 0.25
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (18 bp):
AAAATCTGTTTTATATTT
Found at i:19517999 original size:113 final size:113
Alignment explanation
Indices: 19517792--19518017 Score: 328
Period size: 113 Copynumber: 2.0 Consensus size: 113
19517782 AAATCTGAAA
* * * * * *
19517792 TCATTTAGATCATTGCTTGGAAGTTGTGAGTGAATTATAGCATTATAAGTTTTATTAAGCAGCAT
1 TCATTTAGATCATTGCTTGAAAGTTGTAAGTGAATTATAGAATCATAAGTTTGATCAAGCAGCAT
* * * *
19517857 GTATGACCAAATATTTTTTTTACGAGTGGAATTCTTGAAGCCATTGTG
66 ATATGACCAAATATTTATCTGACGAGTGGAATTCTTGAAGCCATTGTG
19517905 TCATTTAGATCATTGCTTGAAAGTTGTAAGTGAATTATAGAATCATAAGTTTGATCAAGCAGCAT
1 TCATTTAGATCATTGCTTGAAAGTTGTAAGTGAATTATAGAATCATAAGTTTGATCAAGCAGCAT
* *
19517970 ATATGACCTAGTATTTATCTGACTG-GTGGAATTCTTGAAGCCATTGTG
66 ATATGACCAAATATTTATCTGAC-GAGTGGAATTCTTGAAGCCATTGTG
19518018 AAGAAGAGGT
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
113 99 0.99
114 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (113 bp):
TCATTTAGATCATTGCTTGAAAGTTGTAAGTGAATTATAGAATCATAAGTTTGATCAAGCAGCAT
ATATGACCAAATATTTATCTGACGAGTGGAATTCTTGAAGCCATTGTG
Found at i:19518234 original size:17 final size:18
Alignment explanation
Indices: 19518207--19518240 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19518197 ACATTTTTTA
19518207 TAATCTAAAAAAATTAAT
1 TAATCTAAAAAAATTAAT
19518225 TAAT-TAAAAAAATTAA
1 TAATCTAAAAAAATTAA
19518241 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATCTAAAAAAATTAAT
Found at i:19518263 original size:21 final size:22
Alignment explanation
Indices: 19518215--19518263 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
19518205 TATAATCTAA
* *
19518215 AAAAATTAATTAATTAAAAAAAT
1 AAAAATT-ATTAAATAAAAAAAG
*
19518238 TAAAATT-TTAAATAAAAAAAG
1 AAAAATTATTAAATAAAAAAAG
19518259 AAAAA
1 AAAAA
19518264 GAAAAGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.73
23 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATTATTAAATAAAAAAAG
Found at i:19519795 original size:24 final size:25
Alignment explanation
Indices: 19519764--19519833 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 25
19519754 TCTAGAACCC
19519764 CTAAAATCCAAAATCCCCTAAAATT
1 CTAAAATCCAAAATCCCCTAAAATT
* *
19519789 C-AAAATCCTAAAAT--CCGAAACTT
1 CTAAAATCC-AAAATCCCCTAAAATT
*
19519812 CTAAAATCCAAAATCCCTTAAA
1 CTAAAATCCAAAATCCCCTAAA
19519834 TCCAAACCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 13 0.35
24 14 0.38
25 10 0.27
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (25 bp):
CTAAAATCCAAAATCCCCTAAAATT
Found at i:19519824 original size:31 final size:31
Alignment explanation
Indices: 19519762--19519867 Score: 124
Period size: 31 Copynumber: 3.3 Consensus size: 31
19519752 TTTCTAGAAC
* *
19519762 CCCTAAAATCCAAAATCCCCTAAAATTCAAAAT
1 CCCTAAAATCC-AAA-CCTCTAAAATCCAAAAT
*
19519795 -CCTAAAATCCGAAACTTCTAAAATCCAAAAT
1 CCCTAAAATCC-AAACCTCTAAAATCCAAAAT
* *
19519826 CCCTTAAATCCAAACCTCTAAAATCCAAAAC
1 CCCTAAAATCCAAACCTCTAAAATCCAAAAT
19519857 CCCATAAAATC
1 CCC-TAAAATC
19519868 TGAAATCCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
31 35 0.56
32 28 0.44
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (31 bp):
CCCTAAAATCCAAACCTCTAAAATCCAAAAT
Found at i:19519856 original size:16 final size:16
Alignment explanation
Indices: 19519759--19519867 Score: 114
Period size: 16 Copynumber: 6.8 Consensus size: 16
19519749 AGGTTTCTAG
19519759 AACCCCTAAAATCCAA
1 AACCCCTAAAATCCAA
*
19519775 AATCCCCTAAAATTCAA
1 AA-CCCCTAAAATCCAA
* *
19519792 AA-TCCTAAAATCCGA
1 AACCCCTAAAATCCAA
**
19519807 AACTTCTAAAATCCAA
1 AACCCCTAAAATCCAA
* *
19519823 AATCCCTTAAATCC-A
1 AACCCCTAAAATCCAA
*
19519838 AACCTCTAAAATCCAA
1 AACCCCTAAAATCCAA
19519854 AACCCCATAAAATC
1 AACCCC-TAAAATC
19519868 TGAAATCCCA
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
15 24 0.32
16 29 0.39
17 22 0.29
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (16 bp):
AACCCCTAAAATCCAA
Found at i:19519865 original size:48 final size:47
Alignment explanation
Indices: 19519759--19519876 Score: 130
Period size: 48 Copynumber: 2.5 Consensus size: 47
19519749 AGGTTTCTAG
* *
19519759 AACCCCTAAAATCCAAAATCCCCTAAAATTCAAAATCCTAAAATCCGA
1 AACCCCTAAAATCCAAAAT-CCCTAAAATCCAAAATCCTAAAATCCAA
** * *
19519807 AACTTCTAAAATCCAAAATCCCTTAAATCC-AAACCTCTAAAATCCAA
1 AACCCCTAAAATCCAAAATCCCTAAAATCCAAAATC-CTAAAATCCAA
**
19519854 AACCCCATAAAATCTGAAATCCC
1 AACCCC-TAAAATCCAAAATCCC
19519877 AAACCTTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
46 4 0.07
47 23 0.40
48 31 0.53
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (47 bp):
AACCCCTAAAATCCAAAATCCCTAAAATCCAAAATCCTAAAATCCAA
Found at i:19519915 original size:15 final size:15
Alignment explanation
Indices: 19519892--19519933 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
19519882 TTTAACTCTT
19519892 AAATCCAAACTCCTA
1 AAATCCAAACTCCTA
* *
19519907 AAATTCAAAC-CCTT
1 AAATCCAAACTCCTA
*
19519921 AAATCAAAACTCC
1 AAATCCAAACTCC
19519934 AAACCTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATCCAAACTCCTA
Found at i:19520064 original size:23 final size:23
Alignment explanation
Indices: 19520036--19520083 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
19520026 ATCCAAACCC
* * *
19520036 CTTAAAATCCGAATCTTTAAAAT
1 CTTAAAACCCGAACCTTGAAAAT
*
19520059 CTTAAAACCCTAACCTTGAAAAT
1 CTTAAAACCCGAACCTTGAAAAT
19520082 CT
1 CT
19520084 CTACCCAAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (23 bp):
CTTAAAACCCGAACCTTGAAAAT
Found at i:19522427 original size:15 final size:15
Alignment explanation
Indices: 19522404--19522443 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
19522394 TGATCAGGGA
*
19522404 TTGGATGTGTTTGCT
1 TTGGCTGTGTTTGCT
19522419 TTGGCTGTGTTTGCT
1 TTGGCTGTGTTTGCT
19522434 TTGGCTGTGT
1 TTGGCTGTGT
19522444 ATGGATTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.03, C:0.10, G:0.35, T:0.53
Consensus pattern (15 bp):
TTGGCTGTGTTTGCT
Found at i:19532701 original size:34 final size:34
Alignment explanation
Indices: 19532636--19532701 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
19532626 GTCATCAATA
* *
19532636 TTTGGCTCGTGGCTTAATCCCGATTATTTTATTT
1 TTTGACTCGTGGCTTAATCCCGATTACTTTATTT
19532670 TTTGACTCGTGG-TTAAATCCCGATCT-CTTTAT
1 TTTGACTCGTGGCTT-AATCCCGAT-TACTTTAT
19532702 CTTTCGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 2 0.07
34 25 0.89
35 1 0.04
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (34 bp):
TTTGACTCGTGGCTTAATCCCGATTACTTTATTT
Found at i:19532951 original size:171 final size:170
Alignment explanation
Indices: 19532666--19533219 Score: 677
Period size: 171 Copynumber: 3.2 Consensus size: 170
19532656 CGATTATTTT
* * * * * * *
19532666 ATTTTTTGACTCGTGGTTAAATCCC-GATCTCTTTATCTTTCGATTAGC-AGTTCAATCTCGATC
1 ATTTTTTGACTTGCGGTTTAATCCCAG-TCTCTTTATCCTTCGATTCGCGA-TTCAATCCCGCTC
* *
19532729 TCTTTAATTTAAAATCGTTGTTTAATCTTGATTGTTGTTATCCTTTGACTCGTGGTTTAATCCCG
64 TCTTTAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTATCCTTTGACTCGTGGTTTAATCCCG
* *
19532794 GTTTTCTTATTTTCGAACTTGTGATTCAATCCAAGTTAATGTC
129 GTATTCTTATTTTCG-ACTTGTGATTCAATCCAAGTTAACGTC
*
19532837 ATTTTTTGACTTACGGTTTAATCCCAGTCTCTTTATCC-TCTGATTCGCGATTCAATCCCGCTCT
1 ATTTTTTGACTTGCGGTTTAATCCCAGTCTCTTTATCCTTC-GATTCGCGATTCAATCCCGCTCT
* * * *
19532901 CTTTAATTCAAAATCGTAGTTTAATCTCGATTGTTGTTATCTTTTGACTCGTGGTCTAATCTCGG
65 CTTTAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTATCCTTTGACTCGTGGTTTAATCCCGG
*
19532966 TCTTCTTATTTTCGGACTTGTGATTCAATCCAAGTTAACGTC
130 TATTCTTATTTTC-GACTTGTGATTCAATCCAAGTTAACGTC
* * * * *
19533008 ATTTTTTGACTTGCGATTTAATCTCAGTCTCTTTATCCTTCGATTCGTGGTTCAATCCCACTCTC
1 ATTTTTTGACTTGCGGTTTAATCCCAGTCTCTTTATCCTTCGATTCGCGATTCAATCCCGCTCTC
** * ** * ** * * *
19533073 TTTAATTTAAAATCACAGTTTAATCTCAATTGTCATTAACCTCCGACTCATGGTTTATTCCTGGT
66 TTTAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTATCCTTTGACTCGTGGTTTAATCCCGGT
19533138 CATT-TTATTTTCTGACTTGTGATTCAATCCAAGTTAACGTC
131 -ATTCTTATTTTC-GACTTGTGATTCAATCCAAGTTAACGTC
** *
19533179 ATTTTTTGA-TTCGCGGTTTAATCCTGGTCTCTTTATTCTTC
1 ATTTTTTGACTT-GCGGTTTAATCCCAGTCTCTTTATCCTTC
19533220 AATTTATGGT
Statistics
Matches: 332, Mismatches: 44, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
170 4 0.01
171 321 0.97
172 7 0.02
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (170 bp):
ATTTTTTGACTTGCGGTTTAATCCCAGTCTCTTTATCCTTCGATTCGCGATTCAATCCCGCTCTC
TTTAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTATCCTTTGACTCGTGGTTTAATCCCGGT
ATTCTTATTTTCGACTTGTGATTCAATCCAAGTTAACGTC
Found at i:19533538 original size:36 final size:36
Alignment explanation
Indices: 19533414--19533555 Score: 130
Period size: 36 Copynumber: 3.9 Consensus size: 36
19533404 TGACTTACAA
* **
19533414 TTTAATCCCGATCGCTTTTACTTT-TT-GACTTGCGG
1 TTTAATCCCAATCATTTTTA-TTTCTTCGACTTGCGG
* *
19533449 TTTAATCCCAATCATTCCTATAGTTTC-TCAACTTGCGG
1 TTTAATCCCAATCATT--TTTA-TTTCTTCGACTTGCGG
* * *
19533487 ATTAATCACAATCATTTTTATTTCTTCGACTTACGG
1 TTTAATCCCAATCATTTTTATTTCTTCGACTTGCGG
*
19533523 TTTAATCCCAGTCATTTTTATTTC-TCTGACTTG
1 TTTAATCCCAATCATTTTTATTTCTTC-GACTTG
19533556 TGATTCAATC
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
35 19 0.22
36 38 0.44
37 7 0.08
38 22 0.26
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (36 bp):
TTTAATCCCAATCATTTTTATTTCTTCGACTTGCGG
Found at i:19533566 original size:36 final size:36
Alignment explanation
Indices: 19533498--19533570 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
19533488 TTAATCACAA
* *
19533498 TCATTTTTATTTCTTCGACTTACGGTTTAATCCCAG
1 TCATTTTTATTTCTTCGACTTACGATTCAATCCCAG
**
19533534 TCATTTTTATTTC-TCTGACTTGTGATTCAATCCCAG
1 TCATTTTTATTTCTTC-GACTTACGATTCAATCCCAG
19533570 T
1 T
19533571 TGTCGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (36 bp):
TCATTTTTATTTCTTCGACTTACGATTCAATCCCAG
Found at i:19535364 original size:17 final size:17
Alignment explanation
Indices: 19535342--19535439 Score: 123
Period size: 17 Copynumber: 6.0 Consensus size: 17
19535332 TCTAAAACCT
19535342 CTAAAATCCAAAATCCC
1 CTAAAATCCAAAATCCC
19535359 CTAAAATCCAAAAT-CC
1 CTAAAATCCAAAATCCC
19535375 CTAAAATCC-AAA-CCC
1 CTAAAATCCAAAATCCC
*
19535390 CTAAAATCCGAAA-CCC
1 CTAAAATCCAAAATCCC
*
19535406 CTAAAATCTAAAATCCC
1 CTAAAATCCAAAATCCC
* * *
19535423 ATAAAATTCGAAATCCC
1 CTAAAATCCAAAATCCC
19535440 AAACCTTTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.19
16 28 0.39
17 30 0.42
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (17 bp):
CTAAAATCCAAAATCCC
Found at i:19535378 original size:16 final size:16
Alignment explanation
Indices: 19535342--19535439 Score: 117
Period size: 16 Copynumber: 6.1 Consensus size: 16
19535332 TCTAAAACCT
19535342 CTAAAATCCAAAATCCC
1 CTAAAATCCAAAAT-CC
19535359 CTAAAATCCAAAATCC
1 CTAAAATCCAAAATCC
*
19535375 CTAAAATCC-AAACCC
1 CTAAAATCCAAAATCC
* *
19535390 CTAAAATCCGAAACCC
1 CTAAAATCCAAAATCC
*
19535406 CTAAAATCTAAAATCC
1 CTAAAATCCAAAATCC
* *
19535422 CATAAAATTCGAAATCC
1 C-TAAAATCCAAAATCC
19535439 C
1 C
19535440 AAACCTTTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
15 14 0.19
16 31 0.43
17 27 0.38
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (16 bp):
CTAAAATCCAAAATCC
Found at i:19535394 original size:31 final size:33
Alignment explanation
Indices: 19535335--19535429 Score: 131
Period size: 31 Copynumber: 2.9 Consensus size: 33
19535325 ATTCGTTTCT
*
19535335 AAAACCTCTAAAATCCAAAATCCCCTAAAATCC
1 AAAACCCCTAAAATCCAAAATCCCCTAAAATCC
*
19535368 AAAATCCCTAAAATCC-AAA-CCCCTAAAATCC
1 AAAACCCCTAAAATCCAAAATCCCCTAAAATCC
* * *
19535399 GAAACCCCTAAAATCTAAAATCCCATAAAAT
1 AAAACCCCTAAAATCCAAAATCCCCTAAAAT
19535430 TCGAAATCCC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
31 25 0.46
32 6 0.11
33 23 0.43
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (33 bp):
AAAACCCCTAAAATCCAAAATCCCCTAAAATCC
Found at i:19535459 original size:22 final size:22
Alignment explanation
Indices: 19535433--19535526 Score: 60
Period size: 22 Copynumber: 4.5 Consensus size: 22
19535423 ATAAAATTCG
19535433 AAATCCCAAACCTTTAACTCTT
1 AAATCCCAAACCTTTAACTCTT
* * * *
19535455 AAAT-CCAAACCCCTAAAATCTA
1 AAATCCCAAA-CCTTTAACTCTT
* *
19535477 AAATCCCATAA-----AATTC-G
1 AAATCCCA-AACCTTTAACTCTT
19535494 AAATCCCAAACCTTTAACTCTT
1 AAATCCCAAACCTTTAACTCTT
19535516 AAAT-CCAAACC
1 AAATCCCAAACC
19535527 CCTAAAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
16 2 0.04
17 8 0.15
18 4 0.07
21 16 0.29
22 20 0.36
23 3 0.05
24 2 0.04
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.24
Consensus pattern (22 bp):
AAATCCCAAACCTTTAACTCTT
Found at i:19535481 original size:61 final size:61
Alignment explanation
Indices: 19535393--19535534 Score: 275
Period size: 61 Copynumber: 2.3 Consensus size: 61
19535383 CAAACCCCTA
19535393 AAATCCGAAACCCCTAAAATCTAAAATCCCATAAAATTCGAAATCCCAAACCTTTAACTCTT
1 AAATCC-AAACCCCTAAAATCTAAAATCCCATAAAATTCGAAATCCCAAACCTTTAACTCTT
19535455 AAATCCAAACCCCTAAAATCTAAAATCCCATAAAATTCGAAATCCCAAACCTTTAACTCTT
1 AAATCCAAACCCCTAAAATCTAAAATCCCATAAAATTCGAAATCCCAAACCTTTAACTCTT
19535516 AAATCCAAACCCCTAAAAT
1 AAATCCAAACCCCTAAAAT
19535535 TCAAACCCTT
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
61 74 0.93
62 6 0.08
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (61 bp):
AAATCCAAACCCCTAAAATCTAAAATCCCATAAAATTCGAAATCCCAAACCTTTAACTCTT
Found at i:19535539 original size:15 final size:15
Alignment explanation
Indices: 19535516--19535557 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
19535506 TTTAACTCTT
19535516 AAATCCAAACCCCTA
1 AAATCCAAACCCCTA
* *
19535531 AAATTCAAA-CCCTT
1 AAATCCAAACCCCTA
*
19535545 AAATCAAAACCCC
1 AAATCCAAACCCC
19535558 AAACCTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:19535665 original size:58 final size:56
Alignment explanation
Indices: 19535498--19535673 Score: 135
Period size: 58 Copynumber: 3.1 Consensus size: 56
19535488 AATTCGAAAT
* * *
19535498 CCCAAACCTTTAACTCTTAAATC-CAAACCCCTAAAA--TTCAAACCCTTAAATCAAAAC
1 CCCAAACCTTAAAC-CTTAAAACTCAAA-CCCTAAAACCCTCAAA--CTTAAATCAAAAC
** * * *
19535555 CCCAAACCTTAAATTTTAAAACTGAAACCCTAAAATCTTCAAACTCTAAAATCAAAAC
1 CCCAAACCTTAAACCTTAAAACTCAAACCCTAAAACCCTCAAACT-T-AAATCAAAAC
* * * *
19535613 CCTAAACCTTCCATACCTTAAAAC-CAAACCTTAAAACCCTCAAAACTTAAATCCAAAC
1 CCCAAACCTT--AAACCTTAAAACTCAAACCCTAAAACCCTC-AAACTTAAATCAAAAC
19535671 CCC
1 CCC
19535674 TTAAAATCTG
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
56 16 0.17
57 16 0.17
58 36 0.38
59 14 0.15
60 14 0.15
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (56 bp):
CCCAAACCTTAAACCTTAAAACTCAAACCCTAAAACCCTCAAACTTAAATCAAAAC
Found at i:19539138 original size:13 final size:14
Alignment explanation
Indices: 19539122--19539150 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19539112 AAATTTACAG
19539122 AAAAAAAAAA-GAA
1 AAAAAAAAAAGGAA
19539135 AAAAAAAAAAGGAA
1 AAAAAAAAAAGGAA
19539149 AA
1 AA
19539151 GCAAAACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGGAA
Found at i:19545045 original size:42 final size:41
Alignment explanation
Indices: 19544971--19545052 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 41
19544961 GTATTAATTT
19544971 TATTTGAATACAAACAATTATTATATGGTAAATTATCATAAC
1 TATTTGAATACAAACAATTATTATATGGTAAA-TATCATAAC
* * **
19545013 TATTTGAATATAAATAGATTATTAT-TTTTAAATATCATAA
1 TATTTGAATACAAACA-ATTATTATATGGTAAATATCATAA
19545053 TTATACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 8 0.23
42 19 0.54
43 8 0.23
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (41 bp):
TATTTGAATACAAACAATTATTATATGGTAAATATCATAAC
Found at i:19552888 original size:24 final size:25
Alignment explanation
Indices: 19552835--19552899 Score: 96
Period size: 24 Copynumber: 2.6 Consensus size: 25
19552825 CATTTGCATT
19552835 TGCATCATGAAAAAGACACCCACATG
1 TGCATCATGAAAAAGACA-CCACATG
*
19552861 TGCATCATGAAAAAGACA-TACATG
1 TGCATCATGAAAAAGACACCACATG
*
19552885 TGCATCATTAAAAAG
1 TGCATCATGAAAAAG
19552900 GCATTTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 19 0.51
26 18 0.49
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (25 bp):
TGCATCATGAAAAAGACACCACATG
Found at i:19552916 original size:26 final size:26
Alignment explanation
Indices: 19552885--19552945 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
19552875 GACATACATG
19552885 TGCATCATTAAAAAGGCATTTGTATT
1 TGCATCATTAAAAAGGCATTTGTATT
19552911 TGCATCATTAAAAAGGCATTTGTATT
1 TGCATCATTAAAAAGGCATTTGTATT
19552937 TGCATCATT
1 TGCATCATT
19552946 CACATGTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (26 bp):
TGCATCATTAAAAAGGCATTTGTATT
Found at i:19553950 original size:149 final size:144
Alignment explanation
Indices: 19553627--19554033 Score: 458
Period size: 149 Copynumber: 2.8 Consensus size: 144
19553617 ACTTTTGGGT
* * *
19553627 AAAATATTTTAAAATTTCAAAGTTTCAATGCCTCTAATACGAAGAGCATTCAAAGATTTTAGATT
1 AAAATATTTTAAAATTTCAAAGTTTTAATGCCTCTAATACG-AGAGCATTCAAAGATTTTAAATC
* * * *
19553692 TTTAAGACCTCTGAACATAATTTTCAAAACCTTCTGGGCATAATTTTCAGACCTCTAGTATAATC
65 TTTAAGACCTC-GAGCATAATTTTTAAAACCTTCTAGGCATAATTTTCAGACCTCTAGCATAATC
* *
19553757 TCCAAGACCTTCAAGC
129 TCCAAGACATCCAAGC
* * * * *
19553773 AAAACATTTTAAATTTTTAAAGTTTTAATACCACTAATACGATGAGCATTCAAAGATTTTGAAAT
1 AAAATATTTTAAAATTTCAAAGTTTTAATGCCTCTAATACGA-GAGCATTCAAAGATTTT-AAAT
**
19553838 CTTTAAGACCTTCGAGCATAATTTTTAAAGATTTTC-AGGCATAATTTTCTAGACCTCTAGGCAT
64 CTTTAAGACC-TCGAGCATAATTTTTAAA-ACCTTCTAGGCATAATTTTC-AGACCTCTA-GCAT
* * * *
19553902 AATTTCTAAGATATCCGAGC
125 AATCTCCAAGACATCCAAGC
*
19553922 AAAATATTTTAAAATTTCAAAGTTTTAATGCCTCTAATACGAGAAGCATTCAAAGATTTTAAAAG
1 AAAATATTTTAAAATTTCAAAGTTTTAATGCCTCTAATACGAG-AGCATTCAAAGATTTT-AAAT
* * * * *
19553987 CTTTAAAACCTCTAGACATAATTTCTAAAAACC-TCTGGGCACAATTT
64 CTTTAAGACCTCGAG-CATAATTT-TTAAAACCTTCTAGGCATAATTT
19554034 CCAAAACCTC
Statistics
Matches: 217, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
145 1 0.00
146 52 0.24
147 38 0.18
148 22 0.10
149 100 0.46
150 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (144 bp):
AAAATATTTTAAAATTTCAAAGTTTTAATGCCTCTAATACGAGAGCATTCAAAGATTTTAAATCT
TTAAGACCTCGAGCATAATTTTTAAAACCTTCTAGGCATAATTTTCAGACCTCTAGCATAATCTC
CAAGACATCCAAGC
Found at i:19554042 original size:22 final size:23
Alignment explanation
Indices: 19553991--19554043 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
19553981 TAAAAGCTTT
*
19553991 AAAACCTCTAGACATAATTTCTA
1 AAAACCTCTAGACACAATTTCTA
* * *
19554014 AAAACCTCTGGGCACAATTTC-C
1 AAAACCTCTAGACACAATTTCTA
19554036 AAAACCTC
1 AAAACCTC
19554044 CGAACATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.25
Consensus pattern (23 bp):
AAAACCTCTAGACACAATTTCTA
Found at i:19554054 original size:22 final size:22
Alignment explanation
Indices: 19554002--19554163 Score: 101
Period size: 22 Copynumber: 7.3 Consensus size: 22
19553992 AAACCTCTAG
* * *
19554002 ACATAATTTCTAAAAACCTCTGG
1 ACATAATTTC-CAAAACCTCCGA
* *
19554025 GCACAATTTCCAAAACCTCCGA
1 ACATAATTTCCAAAACCTCCGA
* * * *
19554047 ACATAATTTTCAAGACATTCGA
1 ACATAATTTCCAAAACCTCCGA
*
19554069 ACATAATTTCCAAAACCT-CTA
1 ACATAATTTCCAAAACCTCCGA
* * * **
19554090 AGCATAATCTCTAAGACCTTTGA
1 A-CATAATTTCCAAAACCTCCGA
** *
19554113 ACATAATTTCCAAAACCTTTGG
1 ACATAATTTCCAAAACCTCCGA
** * *
19554135 ATGTAATCTCCAAAACCTCCAA
1 ACATAATTTCCAAAACCTCCGA
19554157 ACATAAT
1 ACATAAT
19554164 CTTTAAGACC
Statistics
Matches: 104, Mismatches: 33, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
21 3 0.03
22 91 0.88
23 10 0.10
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (22 bp):
ACATAATTTCCAAAACCTCCGA
Found at i:19554096 original size:44 final size:44
Alignment explanation
Indices: 19554029--19554130 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
19554019 CTCTGGGCAC
*
19554029 AATTTCCAAAACCTCCGAACATAAT-TTTCAAGACATTCGAACAT
1 AATTTCCAAAACCTCCGAACATAATCTCT-AAGACATTCGAACAT
* * *
19554073 AATTTCCAAAACCT-CTAAGCATAATCTCTAAGACCTTTGAACAT
1 AATTTCCAAAACCTCCGAA-CATAATCTCTAAGACATTCGAACAT
19554117 AATTTCCAAAACCT
1 AATTTCCAAAACCT
19554131 TTGGATGTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 3 0.06
44 47 0.90
45 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.28
Consensus pattern (44 bp):
AATTTCCAAAACCTCCGAACATAATCTCTAAGACATTCGAACAT
Found at i:19554115 original size:66 final size:66
Alignment explanation
Indices: 19554045--19554174 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
19554035 CAAAACCTCC
* * * * *
19554045 GAACATAATTTTCAAGACATTCGAACATAATTTCCAAAACCTCTAAGCATAATCTCTAAGACCTT
1 GAACATAATTTCCAAAACATTCGAACATAATCTCCAAAACCTCCAAACATAATCTCTAAGACCTT
19554110 T
66 T
* * * ** *
19554111 GAACATAATTTCCAAAACCTTTGGATGTAATCTCCAAAACCTCCAAACATAATCTTTAAGACCT
1 GAACATAATTTCCAAAACATTCGAACATAATCTCCAAAACCTCCAAACATAATCTCTAAGACCT
19554175 CCAGGCAAAG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (66 bp):
GAACATAATTTCCAAAACATTCGAACATAATCTCCAAAACCTCCAAACATAATCTCTAAGACCTT
T
Found at i:19554477 original size:6 final size:6
Alignment explanation
Indices: 19554468--19554509 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
19554458 AAAAAAAGGC
*
19554468 AAAACA AAAACA AAAACAA AAAACA AAAATA AAAACA CAAAA
1 AAAACA AAAACA AAAAC-A AAAACA AAAACA AAAACA -AAAA
19554510 AGAAATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:19554482 original size:19 final size:19
Alignment explanation
Indices: 19554454--19554510 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
19554444 TAAATTTTGT
***
19554454 AAAAAAAAAAAGGCAAAAC
1 AAAAAAAAAAACAAAAAAC
*
19554473 AAAAACAAAAACAAAAAAC
1 AAAAAAAAAAACAAAAAAC
19554492 AAAAATAAAAACACAAAAA
1 AAAAA-AAAAA-ACAAAAA
19554511 GAAATGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 20 0.65
20 4 0.13
21 7 0.23
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAACAAAAAAC
Found at i:19554483 original size:12 final size:12
Alignment explanation
Indices: 19554468--19554509 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
19554458 AAAAAAAGGC
19554468 AAAACAAAAACA
1 AAAACAAAAACA
19554480 AAAACAAAAAACA
1 AAAAC-AAAAACA
*
19554493 AAAATAAAAACA
1 AAAACAAAAACA
19554505 CAAAA
1 -AAAA
19554510 AGAAATGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (12 bp):
AAAACAAAAACA
Found at i:19555274 original size:14 final size:13
Alignment explanation
Indices: 19555235--19555278 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
19555225 GTCTATCAAG
*
19555235 AAACAAAAAAAAA
1 AAACCAAAAAAAA
*
19555248 AAACCTAGAAAAAA
1 AAACC-AAAAAAAA
19555262 AAACCAAACAAAAA
1 AAACCAAA-AAAAA
19555276 AAA
1 AAA
19555279 AATAAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.82, C:0.14, G:0.02, T:0.02
Consensus pattern (13 bp):
AAACCAAAAAAAA
Found at i:19555275 original size:16 final size:14
Alignment explanation
Indices: 19555235--19555300 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 14
19555225 GTCTATCAAG
19555235 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
*
19555249 AACCTAGAAAAAAAAA
1 AAAC-A-AAAAAAAAA
19555265 CCAAACAAAAAAAAAATA
1 --AAAC-AAAAAAAAA-A
19555283 AAACAAAACATAAAAA
1 AAACAAAA-A-AAAAA
19555299 AA
1 AA
19555301 TCAATCACAG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 17 0.40
17 12 0.29
18 5 0.12
ACGTcount: A:0.82, C:0.12, G:0.02, T:0.05
Consensus pattern (14 bp):
AAACAAAAAAAAAA
Found at i:19555280 original size:21 final size:21
Alignment explanation
Indices: 19555256--19555300 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19555246 AAAAACCTAG
*
19555256 AAAAAAAAACCAAACAAAAAA
1 AAAAAAAAACAAAACAAAAAA
* *
19555277 AAAATAAAACAAAACATAAAA
1 AAAAAAAAACAAAACAAAAAA
19555298 AAA
1 AAA
19555301 TCAATCACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.04
Consensus pattern (21 bp):
AAAAAAAAACAAAACAAAAAA
Found at i:19556320 original size:3 final size:3
Alignment explanation
Indices: 19556314--19556376 Score: 60
Period size: 3 Copynumber: 20.7 Consensus size: 3
19556304 AGAATTATTA
*
19556314 AAT AAT AAT AAT AA- AATT AA- AAGTT AAT AA- ATT AAT AATT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AA--T AAT AAT AAT AAT AA-T AAT AAT
19556360 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
19556377 GAGAAATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 5 0.10
3 39 0.76
4 5 0.10
5 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19556347 original size:15 final size:15
Alignment explanation
Indices: 19556306--19556373 Score: 63
Period size: 15 Copynumber: 4.6 Consensus size: 15
19556296 AATATTAGAG
*
19556306 AATTATTAAA-TAAT
1 AATTAATAAATTAAT
19556320 AA-TAATAAAATTAA-
1 AATTAAT-AAATTAAT
19556334 AAGTTAATAAATTAAT
1 AA-TTAATAAATTAAT
*
19556350 AATTAATAATAATAAT
1 AATTAATAA-ATTAAT
19556366 AA-TAATAA
1 AATTAATAA
19556374 TAAGAGAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
13 3 0.07
14 7 0.15
15 23 0.50
16 13 0.28
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (15 bp):
AATTAATAAATTAAT
Found at i:19556539 original size:15 final size:15
Alignment explanation
Indices: 19556501--19556568 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
19556491 TAAATCTTCG
19556501 AAACCCTAAAAT-C-
1 AAACCCTAAAATCCA
*
19556514 AAACTCC-AAAATCCT
1 AAAC-CCTAAAATCCA
*
19556529 AAACCTTAAAATCCA
1 AAACCCTAAAATCCA
*
19556544 AAACCCT-AAACCTCA
1 AAACCCTAAAATC-CA
19556559 AAACCCTAAA
1 AAACCCTAAA
19556569 TCAAAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
13 9 0.20
14 8 0.18
15 26 0.58
16 2 0.04
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACCCTAAAATCCA
Found at i:19556545 original size:22 final size:22
Alignment explanation
Indices: 19556512--19556570 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
19556502 AACCCTAAAA
*
19556512 TCAAACTCCAAAATCCTAAACC
1 TCAAAATCCAAAATCCTAAACC
* *
19556534 TTAAAATCCAAAACCCTAAACC
1 TCAAAATCCAAAATCCTAAACC
* *
19556556 TCAAAACCCTAAATC
1 TCAAAATCCAAAATC
19556571 AAAAATTCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (22 bp):
TCAAAATCCAAAATCCTAAACC
Found at i:19562346 original size:144 final size:142
Alignment explanation
Indices: 19562153--19562547 Score: 369
Period size: 139 Copynumber: 2.8 Consensus size: 142
19562143 TTTATTGAAT
* * **
19562153 CAAAAATTATGAAATAATATAAAAATATGATTTGAAAATTTTT-GTGAAAAAATTACATCGAGAA
1 CAAAAATAATGAAATAATATAAAAATATGATTTG-AAGTTTTTCACGAAAAAATTAC-TCGAGAA
* * *
19562217 GATCAAATTACAAAAATATTCTTAAAATGTATTTTAGTAATGTTATA-AC-TT-TCGATGTGTGG
64 GATCAAATTACGAAAATATTCTTAAAATGTATTTTAGTAAT-TT-TACACATTGT-G-GGTGTGA
* **
19562279 TTAGGATTTTTAATTTAC
125 TTAAGATTTTTAATACAC
* * * * *
19562297 CATAAATCATGAAATAATATGAAAATATGATTTGAAGTTTTTCACG-AAAATTTGATCTCAAGAA
1 CAAAAATAATGAAATAATATAAAAATATGATTTGAAGTTTTTCACGAAAAAATT-A-CTCGAGAA
*
19562361 GATCAAATTATGAAAATATCTCTT----T-TATTTTAGTAATTTTACACATTGTGGGTGTGATTA
64 GATCAAATTACGAAAATAT-TCTTAAAATGTATTTTAGTAATTTTACACATTGTGGGTGTGATTA
*
19562421 AGATTTTTAATACAT
128 AGATTTTTAATACAC
* * * * * * ** *
19562436 CAAAAATAATGGAATGATATCAAAATCTAATATGAAGTTTTTCACGAAAATCTAACCTCGAGAAG
1 CAAAAATAATGAAATAATATAAAAATATGATTTGAAGTTTTTCACGAAAAAATTA-CTCGAGAAG
* *
19562501 ATCAAAATTACGAAAATATTTTTAAAAAGTATTTTAGTAATTTTACA
65 ATC-AAATTACGAAAATATTCTTAAAATGTATTTTAGTAATTTTACA
19562548 TTTTTTGAGA
Statistics
Matches: 205, Mismatches: 32, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
138 2 0.01
139 76 0.37
140 33 0.16
141 2 0.01
143 13 0.06
144 74 0.36
145 5 0.02
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (142 bp):
CAAAAATAATGAAATAATATAAAAATATGATTTGAAGTTTTTCACGAAAAAATTACTCGAGAAGA
TCAAATTACGAAAATATTCTTAAAATGTATTTTAGTAATTTTACACATTGTGGGTGTGATTAAGA
TTTTTAATACAC
Found at i:19565296 original size:22 final size:23
Alignment explanation
Indices: 19565254--19565296 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
19565244 TTTTATTTTA
19565254 ATTTAATAATTATAATAATAAAT
1 ATTTAATAATTATAATAATAAAT
19565277 ATTTAA-AA-TATATATAATAA
1 ATTTAATAATTATA-ATAATAA
19565297 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAATAATTATAATAATAAAT
Found at i:19565308 original size:11 final size:11
Alignment explanation
Indices: 19565294--19565318 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19565284 ATATATATAA
19565294 TAATTAAAAAT
1 TAATTAAAAAT
19565305 TAATTAAAAAT
1 TAATTAAAAAT
19565316 TAA
1 TAA
19565319 AAAAAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATTAAAAAT
Found at i:19568863 original size:14 final size:13
Alignment explanation
Indices: 19568844--19568875 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
19568834 TTGTTCATTC
19568844 ATTTATTTATTTTT
1 ATTTATTTA-TTTT
19568858 ATTTATTTATTTT
1 ATTTATTTATTTT
19568871 ATTTA
1 ATTTA
19568876 CATTATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:19575110 original size:2 final size:2
Alignment explanation
Indices: 19575105--19575153 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
19575095 CATATATGAC
* *
19575105 AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19575147 AT AT AT A
1 AT AT AT A
19575154 GGATGAGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19575559 original size:244 final size:243
Alignment explanation
Indices: 19575153--19575618 Score: 878
Period size: 244 Copynumber: 1.9 Consensus size: 243
19575143 ATATATATAT
*
19575153 AGGATGAGTATAGAAATTTTCATCCAAGATAAGAATTGTCATGAAATCAAATATTTTCTTCCTGT
1 AGGATGAGTATAGAAATTTTCATCCAAGATAAGAATTGCCATGAAATCAAATATTTTCTTCCTGT
*
19575218 CTTCCCTGCCAAGGAAACACTTTCTTAAGGTTTAACTACTTGGCCTAGACTCATCTTATTTCCCT
66 CTTCCCTGCCAAGGAAACACTTTCTTAAGGTTTAACTACTCGGCCTAGACTCATCTTATTTCCCT
19575283 GTATAATACATTTACTTATAGAATTAACTTGAAGCATAACTTTATGGGGACAAGACAACTACTTG
131 GTATAATACATTTACTTATAGAATTAACTTGAAGCATAACTTTATGGGGACAAGACAACTACTTG
19575348 GCAATATTTTATTGTTGCTGATGAATATATATATATACAAAGTCCAAA
196 GCAATATTTTATTGTTGCTGATGAATATATATATATACAAAGTCCAAA
*
19575396 AGGATGAGTATAGAAATTTTTCATCCAAGATAAGAATTGCCGTGAAATCAAATATTTTCTTCCTG
1 AGGATGAGTATAGAAA-TTTTCATCCAAGATAAGAATTGCCATGAAATCAAATATTTTCTTCCTG
*
19575461 TCTTTCCTGCCAAGGAAACACTTTCTTAAGGTTTAACTACTCGGCCTAGACTCATCTTATTTCCC
65 TCTTCCCTGCCAAGGAAACACTTTCTTAAGGTTTAACTACTCGGCCTAGACTCATCTTATTTCCC
*
19575526 TGTATAATATATTTACTTATAGAATTAACTTGAAGCATAACTTTATGGGGACAAGACAACTACTT
130 TGTATAATACATTTACTTATAGAATTAACTTGAAGCATAACTTTATGGGGACAAGACAACTACTT
19575591 GGCAATATTTTATTGTTGCTGATGAATA
195 GGCAATATTTTATTGTTGCTGATGAATA
19575619 AGTTAATGTT
Statistics
Matches: 217, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
243 16 0.07
244 201 0.93
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (243 bp):
AGGATGAGTATAGAAATTTTCATCCAAGATAAGAATTGCCATGAAATCAAATATTTTCTTCCTGT
CTTCCCTGCCAAGGAAACACTTTCTTAAGGTTTAACTACTCGGCCTAGACTCATCTTATTTCCCT
GTATAATACATTTACTTATAGAATTAACTTGAAGCATAACTTTATGGGGACAAGACAACTACTTG
GCAATATTTTATTGTTGCTGATGAATATATATATATACAAAGTCCAAA
Found at i:19577013 original size:24 final size:25
Alignment explanation
Indices: 19576982--19577039 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
19576972 TGATTTAGCA
*
19576982 AAATCTAATA-T-AAGTTTTTCATG
1 AAATCTAATATTGAAGTTTTTCACG
*
19577005 AAATTCTAACATTGAAGTTTTTCACG
1 AAA-TCTAATATTGAAGTTTTTCACG
19577031 AAATCTAAT
1 AAATCTAAT
19577040 CTCGAGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 6 0.21
25 6 0.21
26 14 0.48
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (25 bp):
AAATCTAATATTGAAGTTTTTCACG
Found at i:19579049 original size:11 final size:11
Alignment explanation
Indices: 19579033--19579065 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19579023 TTAAATTTAA
19579033 TTTTTTTCTTC
1 TTTTTTTCTTC
19579044 TTTTTTTCTT-
1 TTTTTTTCTTC
*
19579054 TTTTTTTTTTC
1 TTTTTTTCTTC
19579065 T
1 T
19579066 GTGGGACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:19587112 original size:2 final size:2
Alignment explanation
Indices: 19587107--19587135 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19587097 ACATACATAC
19587107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19587136 CAAAGTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19592397 original size:11 final size:11
Alignment explanation
Indices: 19592381--19592443 Score: 65
Period size: 11 Copynumber: 5.4 Consensus size: 11
19592371 AGCTGAGCCG
19592381 TTTTTAGTTTT
1 TTTTTAGTTTT
19592392 TTTTTAGTATTT
1 TTTTTAGT-TTT
*
19592404 TTTTTATTTTTTT
1 TTTTTA--GTTTT
19592417 ATTTTTA-TGTTT
1 -TTTTTAGT-TTT
19592429 TTTTTAGTTTT
1 TTTTTAGTTTT
19592440 TTTT
1 TTTT
19592444 GCATGATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
11 22 0.49
12 13 0.29
13 3 0.07
14 7 0.16
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTTTAGTTTT
Found at i:19592439 original size:26 final size:25
Alignment explanation
Indices: 19592388--19592443 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
19592378 CCGTTTTTAG
19592388 TTTTTTTTTAGTATTTTTTTTATTT
1 TTTTTTTTTAGTATTTTTTTTATTT
* *
19592413 TTTTATTTTTA-TGTTTTTTTTAGTT
1 TTTT-TTTTTAGTATTTTTTTTATTT
19592438 TTTTTT
1 TTTTTT
19592444 GCATGATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 20 0.71
26 6 0.21
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (25 bp):
TTTTTTTTTAGTATTTTTTTTATTT
Found at i:19592687 original size:18 final size:18
Alignment explanation
Indices: 19592664--19592704 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
19592654 CAGAGAAAGA
19592664 AAGAGAGAAAAGAAAGGG
1 AAGAGAGAAAAGAAAGGG
* *
19592682 AAGAGA-AAGAGAACGGG
1 AAGAGAGAAAAGAAAGGG
19592699 AA-AGAG
1 AAGAGAG
19592705 GGATCTAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.15
17 11 0.55
18 6 0.30
ACGTcount: A:0.59, C:0.02, G:0.39, T:0.00
Consensus pattern (18 bp):
AAGAGAGAAAAGAAAGGG
Found at i:19592937 original size:13 final size:13
Alignment explanation
Indices: 19592919--19592985 Score: 70
Period size: 12 Copynumber: 5.3 Consensus size: 13
19592909 AGCTGAGCCA
19592919 TTTTTAGTTTTTT
1 TTTTTAGTTTTTT
*
19592932 TTTTTAG-TATTT
1 TTTTTAGTTTTTT
19592944 TTTTTA-TTTATTT
1 TTTTTAGTTT-TTT
*
19592957 ATTTTTAG-TATTT
1 -TTTTTAGTTTTTT
19592970 TTTTTA-TTTTTT
1 TTTTTAGTTTTTT
19592982 TTTT
1 TTTT
19592986 GCATGATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
12 25 0.56
13 13 0.29
14 7 0.16
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.82
Consensus pattern (13 bp):
TTTTTAGTTTTTT
Found at i:19592961 original size:26 final size:24
Alignment explanation
Indices: 19592919--19592985 Score: 107
Period size: 26 Copynumber: 2.7 Consensus size: 24
19592909 AGCTGAGCCA
19592919 TTTTTAGTTTTTTTTTTTAGTATTT
1 TTTTTA-TTTTTTTTTTTAGTATTT
19592944 TTTTTATTTATTTATTTTTAGTATTT
1 TTTTTATTT-TTT-TTTTTAGTATTT
19592970 TTTTTATTTTTTTTTT
1 TTTTTATTTTTTTTTT
19592986 GCATGATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 7 0.17
25 12 0.30
26 21 0.52
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.82
Consensus pattern (24 bp):
TTTTTATTTTTTTTTTTAGTATTT
Found at i:19592977 original size:9 final size:9
Alignment explanation
Indices: 19592926--19592983 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
19592916 CCATTTTTAG
19592926 TTTTTT-TT
1 TTTTTTATT
**
19592934 TTTAGTATT
1 TTTTTTATT
19592943 TTTTTTA-T
1 TTTTTTATT
*
19592951 TTATTTATT
1 TTTTTTATT
**
19592960 TTTAGTATT
1 TTTTTTATT
19592969 TTTTTTATT
1 TTTTTTATT
19592978 TTTTTT
1 TTTTTT
19592984 TTGCATGATT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
8 11 0.29
9 27 0.71
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTATT
Found at i:19593202 original size:541 final size:536
Alignment explanation
Indices: 19592052--19593663 Score: 2590
Period size: 538 Copynumber: 3.0 Consensus size: 536
19592042 AACTTTTGAC
* * * * * * *
19592052 GAAAAACTTAAATTTTGATCAAATTTTTTAGAATTCGATGAAATTCAACCGGTGTTCTTAAGGTG
1 GAAAAACTCAGATTTCGACCAAATTTTTCAGAATCCGATGAAATTCAACCGGTGTTCTTAGGGTG
* *
19592117 CCAAAGAAAGAAAAAGAGAAAAGAAAAGGAAGAGAGA-AAGCGGGGAGGAGGGATCTAAGGAAAA
66 CCAGAGAAAGAAAGAGAGAAAAG-AAAGGAAGAGAGAGAA-CGGGGAGGAGGGATCTAAGGAAAA
* * * *
19592181 AGAATTGAACTCAGCCTTTTATACGCCCTACAAAACAACGTCATTTTGACCTTCATAATCTCAAA
129 AGAATTGAACTCAGCCTTTTATAC-CCCTACAAAACGACGTCGTTTTGACCTTCATAATCCCAGA
* * * *
19592246 GGATCCGCGTGTTTTGTCATCGGGCGACCTGACCCGAACGTGAACCCATTTCTGACCTGGGTGCC
193 GGATCCGCGTGTTTTGTCATCAGGCGACCCGACCCGAGCGTGAACCCGTTTCTGACCTGGGTGCC
* * *
19592311 AGCCAAACCCTTCAGCCGCGCTGATCCAACCTTTTTTTGAGTCTATAGCTGAA-CCACTCCAGCT
258 AGCCAAACCCTTCAGCTGCACTGATCCAACCTCTTTTTGAGTCTATAGCT-AAGCCACTCCAGCT
* * *
19592375 GAGCCGTTTTTAG--TTTTTTTTTAGTATTTTTTTTATTTTTTTATTTTTATGTTTTTTTTAGTT
322 GAGCCATTTTTAGTTTTTTTTTTTAGTATTTTTTTTATTTATTTATTTTTATGTTTTTTTTATTT
*
19592438 TTTTTTGCATGATTAAATTTAGAAAAAAAATAAATAAAAATATTAAAAATAAAATTTTGGGAATA
387 TTTTTTGCATGATTAAATTTAGGAAAAAAATAAATAAAAATATTAAAAATAAAATTTTGGGAATA
* * * *
19592503 AATTTTATTTATCCAATAATAGAATTTATAGAAATTTTAAATAGTAAATTTCTATAAAATTCCTA
452 AATATTATTTATCCAATAATAGAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCTTA
*
19592568 GGTGAGAAATTTTGTCTAAG
517 AGTGAGAAATTTTGTCTAAG
19592588 GAAAAACTCAGATTTCGACCAAATTTTTCAGAATCCGATGAAATTCAACCGGTGTTCTTAGGGTG
1 GAAAAACTCAGATTTCGACCAAATTTTTCAGAATCCGATGAAATTCAACCGGTGTTCTTAGGGTG
* *
19592653 CCAGAGAAAGAAAGAGAGAAAAGAAAGGGAAGAGAAAGAGAACGGGAAAGAGGGATCTAAGGAAA
66 CCAGAGAAAGAAAGAGAGAAAAGAAA-GGAAGAG--AGAGAACGGGGAGGAGGGATCTAAGGAAA
*
19592718 AAGAATTGAACTCAGCCTTTTATACCCTTTACAAAACGACGTCGTTTTGACCTTCATAATCCCAG
128 AAGAATTGAACTCAGCCTTTTATACCC-CTACAAAACGACGTCGTTTTGACCTTCATAATCCCAG
* * * * * *
19592783 AGGATCCACGTGTTTTGTCATTAGGCAACCCGACCCGAGCGTAAACTCGTTTCTGATCTGGGTGC
192 AGGATCCGCGTGTTTTGTCATCAGGCGACCCGACCCGAGCGTGAACCCGTTTCTGACCTGGGTGC
*
19592848 CAGCCAAACCCTTCAGTTGCACTGATCCAACCTCTTTTTGAGTCTATAGCTAAGCCACTCCAGCT
257 CAGCCAAACCCTTCAGCTGCACTGATCCAACCTCTTTTTGAGTCTATAGCTAAGCCACTCCAGCT
*
19592913 GAGCCATTTTTAGTTTTTTTTTTTAGTATTTTTTTTATTTATTTATTTTTAGTATTTTTTTTATT
322 GAGCCATTTTTAGTTTTTTTTTTTAGTATTTTTTTTATTTATTTATTTTTA-TGTTTTTTTTA-T
*
19592978 TTTTTTTTGCATGATTAAATTTAGGAAAAAAATAAATAAAAATATTAAAAAT-AAATTTTGAGAA
385 TTTTTTTTGCATGATTAAATTTAGGAAAAAAATAAATAAAAATATTAAAAATAAAATTTTGGGAA
19593042 TAAATATTATTTATCCAATAATAGAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCT
450 TAAATATTATTTATCCAATAATAGAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCT
19593107 TAAGTGAGAAATTTTGTCTAAG
515 TAAGTGAGAAATTTTGTCTAAG
*
19593129 GAAAAACTCAGATTTCGACCAAATTTTTCAGAATCCGATGAAATTCAACTGGTGTTCTTAGGGTG
1 GAAAAACTCAGATTTCGACCAAATTTTTCAGAATCCGATGAAATTCAACCGGTGTTCTTAGGGTG
19593194 CCAGAGAAAGAAAGAGAGAAAAGAAAGGAAGAGAGAGAACGGGGAGGAGGGATCTAAGGAAAAAG
66 CCAGAGAAAGAAAGAGAGAAAAGAAAGGAAGAGAGAGAACGGGGAGGAGGGATCTAAGGAAAAAG
19593259 AATTGAACTCAGCCTTTTATACCCCCTACAAAACGACGTCGTTTTGACCTTCATAATCCCAGAGG
131 AATTGAACTCAGCCTTTTATA-CCCCTACAAAACGACGTCGTTTTGACCTTCATAATCCCAGAGG
*
19593324 ATCCGCGTGTTTTGTCATCAGGCGACCCGACCCGAGCGTGAACCCGTTTCTGACCTGGATGCCAG
195 ATCCGCGTGTTTTGTCATCAGGCGACCCGACCCGAGCGTGAACCCGTTTCTGACCTGGGTGCCAG
* *
19593389 CCAAACCCTTCAGCTGCATTGATCCAACCTCTTTTTGAGTCTATAGCCAAGCCACTCCAGCTGAG
260 CCAAACCCTTCAGCTGCACTGATCCAACCTCTTTTTGAGTCTATAGCTAAGCCACTCCAGCTGAG
*
19593454 CCATTTTTGGTTTTTTTTTTT-GTA-TTTTTTTATTTATTTATTTTTATGTTTTTTTTAGTTTTT
325 CCATTTTTAGTTTTTTTTTTTAGTATTTTTTTTATTTATTTATTTTTATGTTTTTTTTA-TTTTT
* * *
19593517 TTTTGTATGATTAAATTTAGGAAATAAATAAATAAATATATTAAAAATAAAATTTTGGGAATAAA
389 TTTTGCATGATTAAATTTAGGAAAAAAATAAATAAAAATATTAAAAATAAAATTTTGGGAATAAA
* * * *
19593582 TATTATTTATCCAATGATAGAATTTATAAAAATTTCAAATGGTAAATTTCTATAAAATTTTTATG
454 TATTATTTATCCAATAATAGAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCTTAAG
19593647 TGAGAAATTTTGTCTAA
519 TGAGAAATTTTGTCTAA
19593664 ATTTGACCCA
Statistics
Matches: 998, Mismatches: 66, Indels: 24
0.92 0.06 0.02
Matches are distributed among these distances:
535 63 0.06
536 201 0.20
537 7 0.01
538 436 0.44
539 5 0.01
540 42 0.04
541 193 0.19
542 51 0.05
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (536 bp):
GAAAAACTCAGATTTCGACCAAATTTTTCAGAATCCGATGAAATTCAACCGGTGTTCTTAGGGTG
CCAGAGAAAGAAAGAGAGAAAAGAAAGGAAGAGAGAGAACGGGGAGGAGGGATCTAAGGAAAAAG
AATTGAACTCAGCCTTTTATACCCCTACAAAACGACGTCGTTTTGACCTTCATAATCCCAGAGGA
TCCGCGTGTTTTGTCATCAGGCGACCCGACCCGAGCGTGAACCCGTTTCTGACCTGGGTGCCAGC
CAAACCCTTCAGCTGCACTGATCCAACCTCTTTTTGAGTCTATAGCTAAGCCACTCCAGCTGAGC
CATTTTTAGTTTTTTTTTTTAGTATTTTTTTTATTTATTTATTTTTATGTTTTTTTTATTTTTTT
TTGCATGATTAAATTTAGGAAAAAAATAAATAAAAATATTAAAAATAAAATTTTGGGAATAAATA
TTATTTATCCAATAATAGAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCTTAAGTG
AGAAATTTTGTCTAAG
Found at i:19593622 original size:25 final size:25
Alignment explanation
Indices: 19593594--19593641 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19593584 TTATTTATCC
19593594 AATGATAGAATTTATA-AAAATTTCA
1 AATGATA-AATTTATATAAAATTTCA
* *
19593619 AATGGTAAATTTCTATAAAATTT
1 AATGATAAATTTATATAAAATTT
19593642 TTATGTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
AATGATAAATTTATATAAAATTTCA
Found at i:19593753 original size:16 final size:16
Alignment explanation
Indices: 19593732--19593762 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19593722 ATTTTCAAAC
19593732 AAAAAAATAAAAAATG
1 AAAAAAATAAAAAATG
*
19593748 AAAAAAATATAAAAT
1 AAAAAAATAAAAAAT
19593763 TATGGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAAAATAAAAAATG
Found at i:19593871 original size:194 final size:189
Alignment explanation
Indices: 19593608--19594113 Score: 542
Period size: 191 Copynumber: 2.6 Consensus size: 189
19593598 ATAGAATTTA
* * * *
19593608 TAAAAATTTCAAATGGTAAATTTCTATAAAATTTTTATGTGAGAAATTTTGTCTAAATTTGACCC
1 TAAAAATTTCAAATGGTAAATTTCTA-AAAATCTCTAAGTGAGAAATTTTCTCTAAATTTGACCC
*
19593673 AAATTGTGAAATAATTTAAAT-AAAGTTTCAATAATAATAATTAATATTTATTTTCAAACAAAAA
65 AAATTGTGAAATAATTTAGATGAAAGTTTCAATAA-AATAATTAATATTTATTTTCAAAC-AAAA
*
19593737 AATAAAAAATGAAAAAAATAT-AAAATTATGGAAATTAAAT-ACA-AATTACCAAATAATAAGAT
128 AATAAAAAATG-AAAAAATATGAAAATTAT-CAAA-T-AATGACATAATTA-CAAAT-ATAAGAT
19593799 TCT
187 TCT
* *
19593802 TAAAAATTTTAAATGGTAAATTTCTAAGAAATCTCTAAGTGAGAAATTTTCTCTAAATTTGTCCC
1 TAAAAATTTCAAATGGTAAATTTCTAA-AAATCTCTAAGTGAGAAATTTTCTCTAAATTTGACCC
* *
19593867 AAATTGT-AGAATAATATAGATGAAAGTTTCAATAAAAGTAATTATATATTT-TTTCCAAACAAA
65 AAATTGTGA-AATAATTTAGATGAAAGTTTCAATAAAA-TAATTA-ATATTTATTTTCAAACAAA
****** * * * * ** * * *
19593930 AAATTTTGGTTGAAAATATATGATAATTATCCAATAATGAGATTCTTAGAAATTTACGATTCT
127 AAATAAAAAATGAAAAAATATGAAAATTATCAAATAATGACATAATTACAAATATAAGATTCT
* *
19593993 TAGAAATTTCAAATGGTAAATTTCTAATAAATCTCTAGGTGAGAAATTTTCTCTAAATTTGACCC
1 TAAAAATTTCAAATGGTAAATTTCTAA-AAATCTCTAAGTGAGAAATTTTCTCTAAATTTGACCC
* *
19594058 AGATTGTGGAATAATTTAGATGAAA-TTTCAATAAAAATAATT-ATCATATTATTTTC
65 AAATTGTGAAATAATTTAGATGAAAGTTTCAAT-AAAATAATTAAT-AT-TTATTTTC
19594114 TTTCCAAGAA
Statistics
Matches: 265, Mismatches: 34, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
188 2 0.01
189 2 0.01
190 14 0.05
191 100 0.38
192 7 0.03
193 15 0.06
194 92 0.35
195 27 0.10
196 6 0.02
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (189 bp):
TAAAAATTTCAAATGGTAAATTTCTAAAAATCTCTAAGTGAGAAATTTTCTCTAAATTTGACCCA
AATTGTGAAATAATTTAGATGAAAGTTTCAATAAAATAATTAATATTTATTTTCAAACAAAAAAT
AAAAAATGAAAAAATATGAAAATTATCAAATAATGACATAATTACAAATATAAGATTCT
Found at i:19604641 original size:11 final size:11
Alignment explanation
Indices: 19604604--19604643 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
19604594 ACTATGCTTG
*
19604604 AAAAAGAGAAA
1 AAAAAGAAAAA
**
19604615 AAAAATTAAAA
1 AAAAAGAAAAA
19604626 AAAAAGAAAAA
1 AAAAAGAAAAA
19604637 AAAAAGA
1 AAAAAGA
19604644 GGACTCAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:19605516 original size:20 final size:21
Alignment explanation
Indices: 19605493--19605536 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19605483 ATTATGAATT
*
19605493 TTTTG-ATGAAAATCTTTGAA
1 TTTTGAATGAAAACCTTTGAA
*
19605513 TTTTGAATGAAAGCCTTTGAA
1 TTTTGAATGAAAACCTTTGAA
19605534 TTT
1 TTT
19605537 CAAAGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (21 bp):
TTTTGAATGAAAACCTTTGAA
Found at i:19605516 original size:21 final size:22
Alignment explanation
Indices: 19605487--19605536 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
19605477 AAAGAAATTA
*
19605487 TGAATTTTTTG-ATGAAAATCTT
1 TGAA-TTTTTGAATGAAAACCTT
*
19605509 TGAA-TTTTGAATGAAAGCCTT
1 TGAATTTTTGAATGAAAACCTT
19605530 TGAATTT
1 TGAATTT
19605537 CAAAGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (22 bp):
TGAATTTTTGAATGAAAACCTT
Found at i:19605628 original size:20 final size:20
Alignment explanation
Indices: 19605603--19605684 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
19605593 TTGAGATTTA
19605603 TTGAATGTGAATCTTTAAAC
1 TTGAATGTGAATCTTTAAAC
* * *
19605623 TTGAATGAGAAGCTTTGAAC
1 TTGAATGTGAATCTTTAAAC
* * ** *
19605643 TTTTGGAGGTGAATCCCTAAAG
1 --TTGAATGTGAATCTTTAAAC
19605665 TTCGAATGTGAATCTTTAAA
1 TT-GAATGTGAATCTTTAAA
19605685 TGTTGGAAGT
Statistics
Matches: 44, Mismatches: 15, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
20 19 0.43
21 13 0.30
22 12 0.27
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGAATGTGAATCTTTAAAC
Found at i:19605928 original size:40 final size:40
Alignment explanation
Indices: 19605874--19605964 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
19605864 ATCATGATTA
*
19605874 TCAAA-GAGCCATTTATTTTCCAAAGTTTGTTGCCTCTAT
1 TCAAAGGAACCATTTATTTTCCAAAGTTTGTTGCCTCTAT
*
19605913 TCAAAGGAACCATTTATTTTTCAAAGTTTGTTGCCTCTAT
1 TCAAAGGAACCATTTATTTTCCAAAGTTTGTTGCCTCTAT
19605953 TCAAAGGAACCA
1 TCAAAGGAACCA
19605965 AACTCTTCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 5 0.10
40 44 0.90
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (40 bp):
TCAAAGGAACCATTTATTTTCCAAAGTTTGTTGCCTCTAT
Found at i:19606680 original size:12 final size:13
Alignment explanation
Indices: 19606665--19606722 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
19606655 TTTTGGTTTT
19606665 TTTTTTTTA-GTA
1 TTTTTTTTATGTA
* *
19606677 TTTTATTTATTTA
1 TTTTTTTTATGTA
*
19606690 TTTATTTTTATGTG
1 TTT-TTTTTATGTA
19606704 TTTTTTTTA-GT-
1 TTTTTTTTATGTA
19606715 TTTTTTTT
1 TTTTTTTT
19606723 TTTTTTGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 8 0.21
12 10 0.26
13 11 0.28
14 10 0.26
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTTATGTA
Found at i:19611673 original size:29 final size:28
Alignment explanation
Indices: 19611640--19611706 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
19611630 AATATTGTTA
*
19611640 TAAAAATATAT-TATTAATAATTAAAATAT
1 TAAAAATATATGTA-AAATAA-TAAAATAT
19611669 TAAAAATATATGTAAAATAATAAAATAT
1 TAAAAATATATGTAAAATAATAAAATAT
19611697 TAAAAATATA
1 TAAAAATATA
19611707 GGTTACTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 18 0.50
29 16 0.44
30 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
TAAAAATATATGTAAAATAATAAAATAT
Found at i:19618630 original size:30 final size:30
Alignment explanation
Indices: 19618595--19618661 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
19618585 TTCCTCCATT
*
19618595 TTTTTTTAAATTTTTTATTTTATTT-ATATA
1 TTTTTTAAAATTTTTTATTTT-TTTGATATA
*
19618625 TTTTTTAAAATTTTTTATTTTTTTGATTTA
1 TTTTTTAAAATTTTTTATTTTTTTGATATA
19618655 TTTTTTA
1 TTTTTTA
19618662 TTAGATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (30 bp):
TTTTTTAAAATTTTTTATTTTTTTGATATA
Found at i:19618899 original size:9 final size:9
Alignment explanation
Indices: 19618885--19618909 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19618875 TTTAAAGGTT
19618885 TTTTTTTAA
1 TTTTTTTAA
19618894 TTTTTTTAA
1 TTTTTTTAA
19618903 TTTTTTT
1 TTTTTTT
19618910 TTACTATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:19622585 original size:23 final size:24
Alignment explanation
Indices: 19622537--19622593 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
19622527 TCTGACGTGG
* *
19622537 ATAAATA-TATTAAAAGTAGAATA
1 ATAAATATTAATAAAAGTAGAAAA
*
19622560 ATAAATATTAATAAAA-TATAAAA
1 ATAAATATTAATAAAAGTAGAAAA
*
19622583 ATATATATTAA
1 ATAAATATTAA
19622594 AAATAAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAAATATTAATAAAAGTAGAAAA
Found at i:19622588 original size:21 final size:19
Alignment explanation
Indices: 19622556--19622602 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
19622546 TTAAAAGTAG
19622556 AATAATAAATAT-TAATAAA
1 AATAA-AAATATATAATAAA
*
19622575 ATATAAAAATATATATTAAA
1 A-ATAAAAATATATAATAAA
19622595 AATAAAAA
1 AATAAAAA
19622603 GTTTGATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAAAAATATATAATAAA
Done.