Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 108 of 182
Found at i:35133749 original size:55 final size:51
Alignment explanation
Indices: 35133625--35133821 Score: 171
Period size: 53 Copynumber: 3.9 Consensus size: 51
35133615 ACTGTTTTGA
* * **
35133625 GGCACACAGGCATGCGTCAGGGTTTGTGTGTATACTGTCTTGAGGCACACGGGCT
1 GGCACAC-GG-ATGTGTCAGGG--TGTGTGTATACTGTTTTGAGGCACACAAGCT
* *
35133680 GGCACACGGGTGTGTGTCAGGGTGTGTGTATACTATTTTGAGGCACACAAGCT
1 GGCACAC-GG-ATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACACAAGCT
* *
35133733 GGCACACGAGCATGTGTCAAGGTGTGTGTATATTGTTTTGAGGCACAC--G--
1 GGCACACG-G-ATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACACAAGCT
*
35133782 GG----C--ATGTGTCAGGGTGTGTGTATACTATTTTGAGGCACAC
1 GGCACACGGATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACAC
35133822 GGGCGTGTGT
Statistics
Matches: 125, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
41 34 0.27
45 1 0.01
49 2 0.02
51 1 0.01
52 1 0.01
53 68 0.54
55 18 0.14
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (51 bp):
GGCACACGGATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACACAAGCT
Found at i:35133885 original size:84 final size:82
Alignment explanation
Indices: 35133733--35133886 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 82
35133723 CACACAAGCT
** * *
35133733 GGCACACGAGCATGTGTCAAGGTGTGTGTATATTGTTTTGAGGCACACGGGCATGTGTCAGGGTG
1 GGCACACGAGCATGTGTCAAGGTGTGTGTATACAGTTTTGAGGCACACGGGCATGTGTCAGAGCG
35133798 TGTGTATACTATTTTGA
66 TGTGTATACTATTTTGA
* * * *
35133815 GGCACACGGGCGTGTGTTAAGGTGTGTGTGTATACAGTTTTGAGGCACATGGGC-TG-GTACACG
1 GGCACACGAGCATGTGTCAA-G-GTGTGTGTATACAGTTTTGAGGCACACGGGCATGTGT-CA-G
35133878 AGCGTGTGT
62 AGCGTGTGT
35133887 CAGGGGGTGC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
82 19 0.32
83 5 0.08
84 36 0.60
ACGTcount: A:0.19, C:0.14, G:0.36, T:0.31
Consensus pattern (82 bp):
GGCACACGAGCATGTGTCAAGGTGTGTGTATACAGTTTTGAGGCACACGGGCATGTGTCAGAGCG
TGTGTATACTATTTTGA
Found at i:35134647 original size:29 final size:29
Alignment explanation
Indices: 35134614--35134698 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
35134604 TGGGGTAGGA
* *
35134614 ATCTGCATTTGTAACCGTATCTCTATTAT
1 ATCTGCATTTGTAACTGTATCTGTATTAT
*
35134643 ATCTGCATTTGTAATTGTATCTGTATTAT
1 ATCTGCATTTGTAACTGTATCTGTATTAT
* * *
35134672 ATATGCATCTATAACTGTATCTGTATT
1 ATCTGCATTTGTAACTGTATCTGTATT
35134699 TGGAATTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (29 bp):
ATCTGCATTTGTAACTGTATCTGTATTAT
Found at i:35136913 original size:29 final size:30
Alignment explanation
Indices: 35136846--35136910 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
35136836 AATTTTTTAT
* * *
35136846 ATTTTTATAATTTTTAAATAATTAAATTAA
1 ATTTTTATTATTTTTAAAAAATAAAATTAA
35136876 ATTTTTATTATTTTTAAAAAATAAAATGT-A
1 ATTTTTATTATTTTTAAAAAATAAAAT-TAA
35136906 ATTTT
1 ATTTT
35136911 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAAATAAAATTAA
Found at i:35137623 original size:16 final size:16
Alignment explanation
Indices: 35137604--35137656 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
35137594 ATGTATCGTT
35137604 ATATTAAAGTATTTAA
1 ATATTAAAGTATTTAA
* *
35137620 ATATTACATGTA-TTATT
1 ATATTA-AAGTATTTA-A
*
35137637 ATATTAAATTATTTAA
1 ATATTAAAGTATTTAA
35137653 ATAT
1 ATAT
35137657 AAGTTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (16 bp):
ATATTAAAGTATTTAA
Found at i:35137631 original size:33 final size:33
Alignment explanation
Indices: 35137594--35137656 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
35137584 TTTATATTTT
*
35137594 ATGTATCGTTATATTAAAGTATTTAAATATTAC
1 ATGTATCATTATATTAAAGTATTTAAATATTAC
* *
35137627 ATGTATTATTATATTAAATTATTTAAATAT
1 ATGTATCATTATATTAAAGTATTTAAATAT
35137657 AAGTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (33 bp):
ATGTATCATTATATTAAAGTATTTAAATATTAC
Found at i:35137668 original size:31 final size:32
Alignment explanation
Indices: 35137602--35137687 Score: 106
Period size: 31 Copynumber: 2.7 Consensus size: 32
35137592 TTATGTATCG
*
35137602 TTATATTAAAGTATTTAAATATTACATGTATTA
1 TTATATTAAATTATTTAAATA-TACATGTATTA
35137635 TTATATTAAATTATTTAAATATA-A-GTTATTA
1 TTATATTAAATTATTTAAATATACATG-TATTA
*
35137666 TTATATTTATATT-TTTAAATAT
1 TTATA-TTAAATTATTTAAATAT
35137688 TTTATGCAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
30 1 0.02
31 20 0.41
32 8 0.16
33 20 0.41
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (32 bp):
TTATATTAAATTATTTAAATATACATGTATTA
Found at i:35137968 original size:6 final size:6
Alignment explanation
Indices: 35137957--35137991 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
35137947 CTTTTAAAAT
35137957 GCAATA GCAATA GCAATA GCAATA GCAATA GCAAT
1 GCAATA GCAATA GCAATA GCAATA GCAATA GCAAT
35137992 GGAGTACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GCAATA
Found at i:35138913 original size:18 final size:16
Alignment explanation
Indices: 35138884--35138920 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
35138874 ATATAATTTT
35138884 AAATTTTAAAAATTGAA
1 AAATTTTAAAAATT-AA
35138901 AAATTTATAAAAATTAA
1 AAATTT-TAAAAATTAA
35138918 AAA
1 AAA
35138921 AAATAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTTTAAAAATTAA
Found at i:35138921 original size:18 final size:17
Alignment explanation
Indices: 35138884--35138921 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
35138874 ATATAATTTT
*
35138884 AAATTTTAAAAATTGAA
1 AAATTTTAAAAATTAAA
35138901 AAATTTATAAAAATTAAA
1 AAATTT-TAAAAATTAAA
35138919 AAA
1 AAA
35138922 AATAGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATTTTAAAAATTAAA
Found at i:35138976 original size:20 final size:23
Alignment explanation
Indices: 35138953--35139008 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
35138943 TGCAAAAAAG
*
35138953 TTTTCGAAATTTA-AA-TATAT-
1 TTTTAGAAATTTAGAATTATATA
*
35138973 TTTTAGAATTTTAGAATTATATA
1 TTTTAGAAATTTAGAATTATATA
*
35138996 TTTTAGAATTTTA
1 TTTTAGAAATTTA
35139009 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 11 0.35
21 2 0.06
22 5 0.16
23 13 0.42
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTTAGAAATTTAGAATTATATA
Found at i:35139000 original size:15 final size:15
Alignment explanation
Indices: 35138980--35139010 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35138970 TATTTTTAGA
35138980 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
35138995 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
35139010 A
1 A
35139011 AAAAAAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:35139159 original size:21 final size:20
Alignment explanation
Indices: 35139135--35139182 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
35139125 TTTTTTACAA
*
35139135 TTTATATGTGTTGTT-TTATAT
1 TTTATATGTATT-TTCTTAT-T
35139156 TTTATATGTATTTTCTTATT
1 TTTATATGTATTTTCTTATT
35139176 TTTATAT
1 TTTATAT
35139183 ATTTATTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTATATGTATTTTCTTATT
Found at i:35139191 original size:20 final size:20
Alignment explanation
Indices: 35139150--35139199 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35139140 ATGTGTTGTT
*
35139150 TTATATTTTATATGTATTTTC
1 TTAT-TTTTATATATATTTTC
35139171 TTATTTTTATATAT-TTATTC
1 TTATTTTTATATATATT-TTC
*
35139191 TCATTTTTA
1 TTATTTTTA
35139200 CTTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATTTTTATATATATTTTC
Found at i:35147386 original size:24 final size:24
Alignment explanation
Indices: 35147342--35147387 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
35147332 TTAGCTTAAC
* *
35147342 ATATAGTATAGATTTATATAATAG
1 ATATAGTATAGATCTAAATAATAG
35147366 ATATAGTTATAGA-CTAAATAAT
1 ATATAG-TATAGATCTAAATAAT
35147388 GGATGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (24 bp):
ATATAGTATAGATCTAAATAATAG
Found at i:35150909 original size:85 final size:85
Alignment explanation
Indices: 35150766--35150935 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
35150756 TTATTAAACA
* *
35150766 GAGGAAGTAATAGTAGCAATATTTCATTGAAGTATAATTGCGATGACAATTCATCTATTTGTTAC
1 GAGGAAGTAATAGTAGCAAGATTTCATTGAAGTATAATTGCGATGACAATTCATCTATTTGTAAC
35150831 CTTGCAGCCACATTTAGCAT
66 CTTGCAGCCACATTTAGCAT
*
35150851 GAGGAAGTAATAGTAGCAAGATTTCATTGAAGTATAATTGCGGTGACAATTCATCTATTTGTAAC
1 GAGGAAGTAATAGTAGCAAGATTTCATTGAAGTATAATTGCGATGACAATTCATCTATTTGTAAC
35150916 CTTGCAGCCACATTTAGCAT
66 CTTGCAGCCACATTTAGCAT
35150936 TGTGACTTGT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (85 bp):
GAGGAAGTAATAGTAGCAAGATTTCATTGAAGTATAATTGCGATGACAATTCATCTATTTGTAAC
CTTGCAGCCACATTTAGCAT
Found at i:35156052 original size:14 final size:14
Alignment explanation
Indices: 35156033--35156060 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35156023 AATCCATCTA
35156033 ATTTTCTTTTATTT
1 ATTTTCTTTTATTT
35156047 ATTTTCTTTTATTT
1 ATTTTCTTTTATTT
35156061 CTTTAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTTCTTTTATTT
Found at i:35172692 original size:47 final size:46
Alignment explanation
Indices: 35172623--35172713 Score: 173
Period size: 47 Copynumber: 2.0 Consensus size: 46
35172613 AATGAACAAG
35172623 AAACGTTTTATATACCATAAATGAATTCAAAAAGTTGCTTGCTTAAA
1 AAACGTTTTATATACCATAAATGAATTCAAAAA-TTGCTTGCTTAAA
35172670 AAACGTTTTATATACCATAAATGAATTCAAAAATTGCTTGCTTA
1 AAACGTTTTATATACCATAAATGAATTCAAAAATTGCTTGCTTA
35172714 CTTACTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 11 0.25
47 33 0.75
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (46 bp):
AAACGTTTTATATACCATAAATGAATTCAAAAATTGCTTGCTTAAA
Found at i:35172936 original size:104 final size:101
Alignment explanation
Indices: 35172800--35173001 Score: 273
Period size: 101 Copynumber: 2.0 Consensus size: 101
35172790 CCAAATATCG
*
35172800 ATACAACTTCCCAAACTTGTATAAAACGAGTTTAAAAACACTTAGAAATATTTTGAATTAGCACA
1 ATACAACTTCCCAAACTTGTATAAAACGAGTTT-AAAACACTTAAAAATATTTTGAATT-G-ACA
*
35172865 AAAA-ATTTTAGATAAATTAAAATACATTTAAAATATGTT
63 AAAATA-TTTAGATAAATTAAAATACAATTAAAATATGTT
* * * * *
35172904 ATACAACTTCCTAGACTTGTATAAAATC-AGTTTAAAACAGTTAAAAATATTTTGGATTGACTAA
1 ATACAACTTCCCAAACTTGTATAAAA-CGAGTTTAAAACACTTAAAAATATTTTGAATTGACAAA
*
35172968 AATATTTAGATAAATTAAAATATAATTAAAATAT
65 AATATTTAGATAAATTAAAATACAATTAAAATAT
35173002 ATTTTTGAGT
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
101 34 0.39
102 2 0.02
103 22 0.25
104 29 0.33
105 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (101 bp):
ATACAACTTCCCAAACTTGTATAAAACGAGTTTAAAACACTTAAAAATATTTTGAATTGACAAAA
ATATTTAGATAAATTAAAATACAATTAAAATATGTT
Found at i:35177188 original size:97 final size:98
Alignment explanation
Indices: 35177003--35177196 Score: 250
Period size: 97 Copynumber: 2.0 Consensus size: 98
35176993 TGGAAAAGGA
* * * *
35177003 TATTTGATTATCTCGATTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAACC
1 TATTCGATTATCTCGATTTGAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACC
* *
35177068 AGAGATAAAGAAACATTGACTCGA-TTTAAAGT
66 AGAAACAAAGAAACATTGACTCGATTTTAAAGT
* *
35177100 TATTCGATTAT-TCCGATTTGAAAAAAAATCGCGCCTAGTAAGTTAAGGCATAAATTTTCAAATC
1 TATTCGATTATCT-CGATTTGAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
* * *
35177164 TC-GAAACAAAGGAATATTGCCTCGATTTTAAAG
65 -CAGAAACAAAGAAACATTGACTCGATTTTAAAG
35177197 GTTTATGAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
96 1 0.01
97 74 0.89
98 8 0.10
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (98 bp):
TATTCGATTATCTCGATTTGAAAAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACC
AGAAACAAAGAAACATTGACTCGATTTTAAAGT
Found at i:35177464 original size:29 final size:28
Alignment explanation
Indices: 35177432--35177592 Score: 94
Period size: 29 Copynumber: 5.5 Consensus size: 28
35177422 GCTCAGAGGC
* *
35177432 AAAATGATCATTTTTGGATGTTCGGGAAT
1 AAAATGGTAATTTTTGGATGTTCGGG-AT
* *** **
35177461 AAAATGGTAATTTTTAGACACTCAGGGGC
1 AAAATGGTAATTTTTGGATGTTC-GGGAT
35177490 AAAATGGTAATTTTTGGATGTTCGAGGGAT
1 AAAATGGTAATTTTTGGATGTTC--GGGAT
* * *
35177520 AAAA-GGTCATTTTTGGAAAAT-TTGGGGTT
1 AAAATGGTAATTTTTGG---ATGTTCGGGAT
** *
35177549 AAAAAT-GTAATTTTTGGAAATTCGAGGGT
1 -AAAATGGTAATTTTTGGATGTTCG-GGAT
35177578 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
35177593 AGAAGCTCGA
Statistics
Matches: 101, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.01
28 8 0.08
29 63 0.62
30 25 0.25
31 2 0.02
32 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGATGTTCGGGAT
Found at i:35177503 original size:58 final size:58
Alignment explanation
Indices: 35177423--35177605 Score: 174
Period size: 58 Copynumber: 3.1 Consensus size: 58
35177413 TTTTCGGATG
* * * *
35177423 CTCAGAGGCAAAATGATCATTTTTGGATGTTCG-GGAATAAAATGGTAATTTTTAGACA
1 CTCAGGGGCAAAATGGTAATTTTTGGATGTTCGAGG-ATAAAATGGTAATTTTTAGAAA
* *
35177481 CTCAGGGGCAAAATGGTAATTTTTGGATGTTCGAGGGATAAAA-GGTCATTTTTGGAAA
1 CTCAGGGGCAAAATGGTAATTTTTGGATGTTCGA-GGATAAAATGGTAATTTTTAGAAA
* ** * ** * *
35177539 ATTTGGGGTTAAAAAT-GTAATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTAGAAG
1 CTCAGGGG--CAAAATGGTAATTTTTGGATGTTCGAGGATAAAATGGTAATTTTTAGAAA
35177598 CTCGAGGG
1 CTC-AGGG
35177606 TGAAAATATG
Statistics
Matches: 100, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
58 54 0.54
59 36 0.36
60 10 0.10
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (58 bp):
CTCAGGGGCAAAATGGTAATTTTTGGATGTTCGAGGATAAAATGGTAATTTTTAGAAA
Found at i:35177564 original size:30 final size:28
Alignment explanation
Indices: 35177490--35177782 Score: 191
Period size: 30 Copynumber: 9.9 Consensus size: 28
35177480 ACTCAGGGGC
* *
35177490 AAAATGGTAATTTTTGGATGTTCGAGGG-A
1 AAAAT-GTAATTTTTGGAAGTTTG-GGGTA
* * *
35177519 TAAAAGGTCATTTTTGGAAAATTTGGGGTTA
1 -AAAATGTAATTTTTGG-AAGTTTGGGG-TA
* *
35177550 AAAATGTAATTTTTGGAAATTCGAGGGT-
1 AAAATGTAATTTTTGGAAGTTTG-GGGTA
* * *
35177578 AAAATGGTAATTTTTAGAAGCTCGAGGGTGA
1 AAAAT-GTAATTTTTGGAAGTTTG-GGGT-A
* *
35177609 AAATATG-ATTTTTTGGAGGTTTAGGGGT-
1 AAA-ATGTAATTTTTGGAAGTTT-GGGGTA
*
35177637 AAAATGGTAA-TTTTGGAAGTTTAAGGGTA
1 AAAAT-GTAATTTTTGGAAGTTT-GGGGTA
* *
35177666 AAAATGTAATTTTTTTGAAGTTTGGAGGCA
1 AAAATGTAA-TTTTTGGAAGTTTGG-GGTA
*
35177696 AAAATGTAATTTTTGTGAAGTTTGAGGGTC
1 AAAATGTAATTTTTG-GAAGTTTG-GGGTA
** *
35177726 AAAATGTAATTTTTAAAGAGTTTAGGGGTT
1 AAAATGTAATTTTTGGA-AGTTT-GGGGTA
*
35177756 AAAATGTAATTTTTGAAGAGTTTGGGG
1 AAAATGTAATTTTTGGA-AGTTTGGGG
35177783 GTCAAAATAT
Statistics
Matches: 215, Mismatches: 29, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.01
28 29 0.13
29 57 0.27
30 117 0.54
31 8 0.04
32 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTGGGGTA
Found at i:35177602 original size:29 final size:29
Alignment explanation
Indices: 35177460--35177739 Score: 139
Period size: 29 Copynumber: 9.6 Consensus size: 29
35177450 TGTTCGGGAA
* * *
35177460 TAAAATGGTAATTTTTAGACACTC-AGGGG
1 TAAAATGGTAATTTTTGGAAATTCGA-GGG
* **
35177489 CAAAATGGTAATTTTTGGATGTTCGAGGG
1 TAAAATGGTAATTTTTGGAAATTCGAGGG
* *
35177518 ATAAAA-GGTCATTTTTGGAAAATTTG-GGG
1 -TAAAATGGTAATTTTTGG-AAATTCGAGGG
35177547 TTAAAAAT-GTAATTTTTGGAAATTCGAGGG
1 -T-AAAATGGTAATTTTTGGAAATTCGAGGG
* **
35177577 TAAAATGGTAATTTTTAGAAGCTCGAGGG
1 TAAAATGGTAATTTTTGGAAATTCGAGGG
* * ** *
35177606 TGAAAAT-ATGATTTTTTGGAGGTT-TAGGGG
1 T-AAAATGGT-AATTTTTGGAAATTCGA-GGG
* **
35177636 TAAAATGGTAA-TTTTGGAAGTTTAAGGG
1 TAAAATGGTAATTTTTGGAAATTCGAGGG
* * * *
35177664 TAAAAAT-GTAATTTTTTTGAAGTTTGGAGGC
1 T-AAAATGGTAA-TTTTTGGAA-ATTCGAGGG
* * *
35177695 AAAAAT-GTAATTTTTGTGAAGTTTGAGGG
1 TAAAATGGTAATTTTTG-GAAATTCGAGGG
35177724 TCAAAAT-GTAATTTTT
1 T-AAAATGGTAATTTTT
35177740 AAAGAGTTTA
Statistics
Matches: 196, Mismatches: 37, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
28 23 0.12
29 89 0.45
30 79 0.40
31 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGGAAATTCGAGGG
Found at i:35177620 original size:88 final size:88
Alignment explanation
Indices: 35177490--35177679 Score: 194
Period size: 88 Copynumber: 2.2 Consensus size: 88
35177480 ACTCAGGGGC
* * * *
35177490 AAAATGGTAATTTTTGGATGTTCGAGGGATAAAAGGTCA-TTTTTGGAAAATTT-GGGGTTAAAA
1 AAAATGGTAATTTTTAGAAGCTCGAGGGATAAAAGATCATTTTTTGG-AAATTTAGGGG-T-AAA
*
35177553 AT-GTAATTTTTGGAAATTCGAGGGT-
63 ATGGTAA-TTTTGGAAATTCAAGGGTA
* * **
35177578 AAAATGGTAATTTTTAGAAGCTCGAGGG-TGAAAATATGATTTTTTGGAGGTTTAGGGGTAAAAT
1 AAAATGGTAATTTTTAGAAGCTCGAGGGAT-AAAAGATCATTTTTTGGAAATTTAGGGGTAAAAT
* *
35177642 GGTAATTTTGGAAGTTTAAGGGTA
65 GGTAATTTTGGAAATTCAAGGGTA
35177666 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
35177680 TTGAAGTTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
87 30 0.35
88 45 0.52
89 11 0.13
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (88 bp):
AAAATGGTAATTTTTAGAAGCTCGAGGGATAAAAGATCATTTTTTGGAAATTTAGGGGTAAAATG
GTAATTTTGGAAATTCAAGGGTA
Found at i:35177730 original size:60 final size:59
Alignment explanation
Indices: 35177578--35177814 Score: 180
Period size: 60 Copynumber: 4.0 Consensus size: 59
35177568 ATTCGAGGGT
* * * * * * ** *
35177578 AAAATGGTAATTTTTAGAAGCTCGAGGGTGAAAATATGATTTTT-TGGAGGTTTAGGGG-T
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGTCAAAATGTAATTTTTAAAGA-GTTTAGGGGCA
* * **
35177637 AAAATGGTAA-TTTTGGAAGTTTAAGGGTAAAAATGTAATTTTT-TTGAAGTTT-GGAGGCA
1 AAAAT-GTAATTTTTGGAAGTTTGAGGGTCAAAATGTAATTTTTAAAG-AGTTTAGG-GGCA
**
35177696 AAAATGTAATTTTTGTGAAGTTTGAGGGTCAAAATGTAATTTTTAAAGAGTTTAGGGGTT
1 AAAATGTAATTTTTG-GAAGTTTGAGGGTCAAAATGTAATTTTTAAAGAGTTTAGGGGCA
* * * **
35177756 AAAATGTAATTTTTGAAGAGTTTGGGGGTCAAAATATGGTTTTTAGAA-AGTTTAGGGGC
1 AAAATGTAATTTTTGGA-AGTTTGAGGGTCAAAATGTAATTTTTA-AAGAGTTTAGGGGC
35177815 CTTCTAGGTA
Statistics
Matches: 148, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.01
58 38 0.26
59 22 0.15
60 81 0.55
61 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGTCAAAATGTAATTTTTAAAGAGTTTAGGGGCA
Found at i:35177784 original size:30 final size:29
Alignment explanation
Indices: 35177618--35177813 Score: 143
Period size: 30 Copynumber: 6.6 Consensus size: 29
35177608 AAAATATGAT
35177618 TTTTTG-GAGGTTTAGGGGT-AAAATGGTAA
1 TTTTTGAGA-GTTTAGGGGTAAAAAT-GTAA
* *
35177647 TTTTGGA-AGTTTAAGGGTAAAAATGTAA
1 TTTTTGAGAGTTTAGGGGTAAAAATGTAA
*
35177675 TTTTTTTGA-AGTTT-GGAGGCAAAAATGTAA
1 --TTTTTGAGAGTTTAGG-GGTAAAAATGTAA
* *
35177705 TTTTTGTGAAGTTT-GAGGGTCAAAATGTAA
1 TTTTTGAG-AGTTTAG-GGGTAAAAATGTAA
* *
35177735 TTTTTAAAGAGTTTAGGGGTTAAAATGTAA
1 TTTTT-GAGAGTTTAGGGGTAAAAATGTAA
* * * **
35177765 TTTTTGAAGAGTTTGGGGGTCAAAATATGG
1 TTTTTG-AGAGTTTAGGGGTAAAAATGTAA
*
35177795 TTTTTAGAAAGTTTAGGGG
1 TTTTT-GAGAGTTTAGGGG
35177814 CCTTCTAGGT
Statistics
Matches: 136, Mismatches: 19, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
28 19 0.14
29 12 0.09
30 101 0.74
31 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.39
Consensus pattern (29 bp):
TTTTTGAGAGTTTAGGGGTAAAAATGTAA
Found at i:35178552 original size:27 final size:27
Alignment explanation
Indices: 35178521--35178610 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
35178511 TCCTTTCTTC
35178521 TTTTAAAAAACATTTTTGATTTTCCTT
1 TTTTAAAAAACATTTTTGATTTTCCTT
** * *
35178548 TTTTAAAATCCCTTTATT--TTTTCATT
1 TTTTAAAAAACATTT-TTGATTTTCCTT
*
35178574 TATTT-AAAAA-TTGTTTTGATTTTTCCTT
1 T-TTTAAAAAACAT-TTTTGA-TTTTCCTT
35178602 TTTTAAAAA
1 TTTTAAAAA
35178611 CCTCTTTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
25 3 0.06
26 13 0.27
27 18 0.38
28 14 0.29
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTTAAAAAACATTTTTGATTTTCCTT
Found at i:35178623 original size:27 final size:26
Alignment explanation
Indices: 35178540--35178624 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
35178530 ACATTTTTGA
*
35178540 TTTTCCTTTTTTAAAATCC-CTTTATT
1 TTTTCCTTTTTTAAAAACCTCTTT-TT
* * *
35178566 TTTTCATTTATTTAAAAA-TTGTTTTGAT
1 TTTTCCTTT-TTTAAAAACCTCTTTT--T
*
35178594 TTTTCCTTTTTTAAAAACCTCTTTCT
1 TTTTCCTTTTTTAAAAACCTCTTTTT
35178620 TTTTC
1 TTTTC
35178625 AGATCTGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
26 15 0.33
27 18 0.39
28 13 0.28
ACGTcount: A:0.21, C:0.15, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTCCTTTTTTAAAAACCTCTTTTT
Found at i:35178849 original size:26 final size:26
Alignment explanation
Indices: 35178800--35178854 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
35178790 TTCAACTTTT
*
35178800 TTATTTTATTATTAATAATGTATTTA
1 TTATTTTATTATTAATAATATATTTA
35178826 TTATTATTATTATTAAT-ATATATTTA
1 TTATT-TTATTATTAATAATATATTTA
35178852 TTA
1 TTA
35178855 CCATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTATTTTATTATTAATAATATATTTA
Found at i:35178864 original size:26 final size:27
Alignment explanation
Indices: 35178805--35178866 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
35178795 CTTTTTTATT
* **
35178805 TTATTATTAATAATGTATTTATTATTA
1 TTATTATTAATAATATATTTATTACCA
35178832 TTATTATTAAT-ATATATTTATTACCA
1 TTATTATTAATAATATATTTATTACCA
35178858 -TATTTATTA
1 TTA-TTATTA
35178867 GATGCGTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.06
26 18 0.58
27 11 0.35
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (27 bp):
TTATTATTAATAATATATTTATTACCA
Found at i:35179396 original size:23 final size:26
Alignment explanation
Indices: 35179353--35179401 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
35179343 GTTTGGGTCA
35179353 TTTAGGTGTGGATCTTTGTAATTGGG
1 TTTAGGTGTGGATCTTTGTAATTGGG
35179379 TTTAGGT-T-GAT-TTTGTAATTGGG
1 TTTAGGTGTGGATCTTTGTAATTGGG
35179402 CTTGGGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.52
24 3 0.13
25 1 0.04
26 7 0.30
ACGTcount: A:0.16, C:0.02, G:0.33, T:0.49
Consensus pattern (26 bp):
TTTAGGTGTGGATCTTTGTAATTGGG
Found at i:35179490 original size:17 final size:18
Alignment explanation
Indices: 35179468--35179530 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 18
35179458 TTTTATTTAT
* *
35179468 TTAAATTT-AGAATAATC
1 TTAAATTTAAAAATAAAC
35179485 TTAAATTTAAAAATAAAC
1 TTAAATTTAAAAATAAAC
* ** *
35179503 TTAAACTT-AATTTAAAT
1 TTAAATTTAAAAATAAAC
35179520 TTAAATTTAAA
1 TTAAATTTAAA
35179531 TTTAAAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 21 0.57
18 16 0.43
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAATTTAAAAATAAAC
Found at i:35179524 original size:23 final size:22
Alignment explanation
Indices: 35179466--35179544 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
35179456 GCTTTTATTT
*
35179466 ATTTAAATTTAGAA-TAATCTTAA
1 ATTTAAATTTA-AATTAAACTT-A
**
35179489 ATTTAAAAATAAACTTAAACTTA
1 ATTTAAATTTAAA-TTAAACTTA
*
35179512 ATTTAAATTTAAATTTAAATTTA
1 ATTTAAATTTAAA-TTAAACTTA
**
35179535 AAATAAATTT
1 ATTTAAATTT
35179545 TAAAAAATGG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 2 0.04
23 37 0.82
24 6 0.13
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTTAAATTTAAATTAAACTTA
Found at i:35179548 original size:7 final size:6
Alignment explanation
Indices: 35179485--35179536 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
35179475 TAGAATAATC
* * * *
35179485 TTAAAT TTAAAA ATAAAC TTAAAC TT-AAT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
35179532 TTAAA
1 TTAAA
35179537 ATAAATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:35191520 original size:3 final size:3
Alignment explanation
Indices: 35191489--35191546 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
35191479 TTGGGCCCAA
* * * * * *
35191489 ATT ATT GTT ATC ATT ACT ATT ACT ATT ATT ATT ATT GTT ATT AAAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
35191535 ATT ATT ATT ATT
1 ATT ATT ATT ATT
35191547 TTTTAAGGTT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:35192409 original size:145 final size:145
Alignment explanation
Indices: 35191952--35192455 Score: 576
Period size: 145 Copynumber: 3.4 Consensus size: 145
35191942 TTTTTTCATT
**
35191952 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTTAAGAAAAGTAGTGAGGTTTTTTTT-TTA
1 TTTTTTAACTATTTCGAAATAAAAGTTTTGA-TTTTTAAGAAAAGTAGTGA-GTTTTTTTTAAAA
* *** * *
35192016 AAATGAAATTTTAGATTTTTTTTTAA-AAAAATATGTTTTTAGGCATTTTAAAAGAAAAAAATTA
64 AAAT-AAAGTTTAGA-TTTTTAAAAATAAAAATCTGTTTTTAGGCATTTT-AAAGAGAAAAATTA
* *
35192080 ACTTTTTAAACAAAATTTGA
126 AATTTTTAAACAAAGTTTGA
* * * ***
35192100 TTTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTTTTTTTTTTTT
1 -TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGA--GTTTTTTTTAAA
* * *
35192165 AAAAGAAAGTTTAGA-TTTTAAAAAGAAAAATCTGTTTTTAGGCATTTTAAA-AGAAAATGTTTT
63 AAAATAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTAGGCATTTTAAAGAGAAAA---ATT
35192228 AAA-TTTTAAACAAAGTTT-A
125 AAATTTTTAAACAAAGTTTGA
35192247 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAA-TAGTGA-TTTTTTTTAGAAA
1 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAG-AAAAGTAGTGAGTTTTTTTTA-AAA
* *** *
35192310 AAATAAAGTTTAGATTTTTAAAAATAAAAATCTGGTTTTAATTATTTTAAAGAGAAAACTTAAAT
64 AAATAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTAGGCATTTTAAAGAGAAAAATTAAAT
35192375 TTTTAAACAAAGTTTGA
129 TTTTAAACAAAGTTTGA
* * *
35192392 TTTTTTAACTATTTCGAAATAAAAATTTTAATTTTTAAGAAAAGTAGT-AATTTTGTTTTAAAAA
1 TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGAGTTTT-TTTTAAAAA
35192456 GAAAAAAACT
Statistics
Matches: 312, Mismatches: 28, Indels: 34
0.83 0.07 0.09
Matches are distributed among these distances:
143 13 0.04
144 34 0.11
145 81 0.26
146 60 0.19
147 13 0.04
148 54 0.17
149 51 0.16
150 6 0.02
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (145 bp):
TTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGAGTTTTTTTTAAAAAA
ATAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTAGGCATTTTAAAGAGAAAAATTAAATTT
TTAAACAAAGTTTGA
Found at i:35199707 original size:9 final size:9
Alignment explanation
Indices: 35199693--35199723 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
35199683 TACGTTTGGA
35199693 GAAGATGAT
1 GAAGATGAT
35199702 GAAGATGAT
1 GAAGATGAT
35199711 GAAGATGAT
1 GAAGATGAT
35199720 GAAG
1 GAAG
35199724 TTTTTGGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.19
Consensus pattern (9 bp):
GAAGATGAT
Found at i:35203935 original size:20 final size:20
Alignment explanation
Indices: 35203910--35203954 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35203900 TATTAAAACG
* *
35203910 ATTTTGACTTGGTTGAAATT
1 ATTTTGACTTGGTTAAAATA
*
35203930 ATTTTGACTTGTTTAAAATA
1 ATTTTGACTTGGTTAAAATA
35203950 ATTTT
1 ATTTT
35203955 AGCTTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATA
Found at i:35220373 original size:49 final size:49
Alignment explanation
Indices: 35220206--35220678 Score: 277
Period size: 49 Copynumber: 9.6 Consensus size: 49
35220196 TACCATGAAG
* * * * * *
35220206 GCATGAAGGGAAAGATTTAAGTCGCAACAGTGAATCTAGTACCA-TGAG
1 GCATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
* * * * * *
35220254 GACATAAAAGGAAAGATTTAAGCCGCAACGGCAAATCC-AGTAACACA-AA
1 G-CATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCACAGAA
* * * * * *
35220303 GATAATGGAGGGAAAGGTTTAAGTTGTAACGGCGAACCTTGTACCTCAGAA
1 G--CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
* * *
35220354 GCATGAAGGGAAAGATTTAAGCCGCAACGG-TAA-ATTCAGTACCAC-GAA
1 GCATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTT--GTACCACAGAA
* * * * * *
35220402 G-ATAATAGAGGGAAAGGTTTAAGTCGTAATGGTGAACCTTGTACCTCAGAA
1 GCAT--GA-AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
* * * * *
35220453 GCGTGAAGGGAAAAATTTAAG-CTGCAATGGTGAA-TTTAGTACCAC-GAA
1 GCATGAAGGGAAAGATTTAAGTC-GCAACGGCGAACCTT-GTACCACAGAA
* * * * *
35220501 GACAAAGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
1 G-C-ATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
* * * * * *
35220552 GCATGAAGGGAAAGATTTAAGCCACAATGGCAAATCTAGTACCAC-GAA
1 GCATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
* * * * *
35220600 G-ATACAAAGGGAAAGATTTAAGTTGCAACGGCAAACCTTGTACCCCAAAA
1 GCAT--GAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
* *
35220650 GCACGAAGGGAAAGATTTAAGCCGCAACG
1 GCATGAAGGGAAAGATTTAAGTCGCAACG
35220679 ATAAATCTAG
Statistics
Matches: 320, Mismatches: 79, Indels: 51
0.71 0.18 0.11
Matches are distributed among these distances:
47 6 0.02
48 18 0.06
49 184 0.57
50 92 0.29
51 17 0.05
52 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.19
Consensus pattern (49 bp):
GCATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACAGAA
Found at i:35220383 original size:99 final size:99
Alignment explanation
Indices: 35220212--35220699 Score: 541
Period size: 99 Copynumber: 4.9 Consensus size: 99
35220202 GAAGGCATGA
* * * * * * * * *
35220212 AGGGAAAGATTTAAGTCGCAACAGTGAATCTAGTACCATGAGGA-CATAAAAGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACC-TCAGAAGCATGAAGGGAAAGATTTAAG
* *
35220276 CCGCAACGGCAAATCCAGTAACACAAAGATAATGG
65 CCGCAACGGCAAATCCAGTACCACGAAGATAATGG
* *
35220311 AGGGAAAGGTTTAAGTTGTAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * *
35220376 CGCAACGGTAAATTCAGTACCACGAAGATAATAG
66 CGCAACGGCAAATCCAGTACCACGAAGATAATGG
* * * * *
35220410 AGGGAAAGGTTTAAGTCGTAATGGTGAACCTTGTACCTCAGAAGCGTGAAGGGAAAAATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * ** ** * *
35220475 TGCAATGGTGAATTTAGTACCACGAAGACAAAGG
66 CGCAACGGCAAATCCAGTACCACGAAGATAATGG
*
35220509 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * *
35220574 CACAATGGCAAATCTAGTACCACGAAGATACA--A
66 CGCAACGGCAAATCCAGTACCACGAAGATA-ATGG
* * * * * *
35220607 AGGGAAAGATTTAAGTTGCAACGGCAAACCTTGTACCCCAAAAGCACGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
** * *
35220672 CGCAACGATAAATCTAGTACCGCGAAGA
66 CGCAACGGCAAATCCAGTACCACGAAGA
35220700 CATAAAGGGA
Statistics
Matches: 336, Mismatches: 51, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
98 85 0.25
99 250 0.74
100 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (99 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
CGCAACGGCAAATCCAGTACCACGAAGATAATGG
Found at i:35224019 original size:20 final size:22
Alignment explanation
Indices: 35223989--35224031 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
35223979 TAAAATTTGC
*
35223989 AAATGTAATTTTCTTT-ATTAA
1 AAATGTAATTTTATTTAATTAA
35224010 AAAT-TAATTTTATTTAATTAA
1 AAATGTAATTTTATTTAATTAA
35224031 A
1 A
35224032 TGATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATGTAATTTTATTTAATTAA
Found at i:35224256 original size:17 final size:18
Alignment explanation
Indices: 35224234--35224273 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
35224224 ATGGGGGTAA
*
35224234 AAAATTGGTT-CTATAAT
1 AAAATTGATTGCTATAAT
*
35224251 AAAATTGATTGTTATAAT
1 AAAATTGATTGCTATAAT
35224269 AAAAT
1 AAAAT
35224274 ACTCTTACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (18 bp):
AAAATTGATTGCTATAAT
Found at i:35224982 original size:31 final size:30
Alignment explanation
Indices: 35224950--35225043 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
35224940 GCAAATGATT
35224950 TTAAAATTATTTTGTTAAAATATAAAAAATT-
1 TTAAAATTATTTT-TTAAAATAT-AAAAATTA
35224981 TT-AAATTA-TTTTTAAAATAT-AAAATTA
1 TTAAAATTATTTTTTAAAATATAAAAATTA
*
35225008 TTAAAATTATTTTTTTGAAATA-ATAAAATTA
1 TTAAAATTA-TTTTTTAAAATATA-AAAATTA
35225039 TTAAA
1 TTAAA
35225044 TAATTTTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
26 6 0.11
27 2 0.04
28 15 0.27
29 3 0.05
30 16 0.29
31 14 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TTAAAATTATTTTTTAAAATATAAAAATTA
Found at i:35225001 original size:28 final size:27
Alignment explanation
Indices: 35224947--35225021 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 27
35224937 TTAGCAAATG
35224947 ATTTTAAAATTATTTTGTTAAAATATAAAAA
1 ATTTTAAAATTA-TTT-TTAAAATAT--AAA
35224978 ATTTT-AAATTATTTTTAAAATATAAA
1 ATTTTAAAATTATTTTTAAAATATAAA
35225004 ATTATTAAAATTATTTTT
1 ATT-TTAAAATTATTTTT
35225022 TTGAAATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.14
27 2 0.05
28 20 0.48
29 3 0.07
30 6 0.14
31 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTTTAAAATTATTTTTAAAATATAAA
Found at i:35225038 original size:28 final size:28
Alignment explanation
Indices: 35224950--35225038 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
35224940 GCAAATGATT
* *
35224950 TTAAAATTATTTTGTTAAAATATAAAAAA
1 TTAAAATTATTTTTTTAAAATA-ATAAAA
*
35224979 TTTTAAATTA--TTTTTAAAAT-ATAAAATTA
1 -TTAAAATTATTTTTTTAAAATAAT-AAA--A
*
35225008 TTAAAATTATTTTTTTGAAATAATAAAA
1 TTAAAATTATTTTTTTAAAATAATAAAA
35225036 TTA
1 TTA
35225039 TTAAATAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 21 0.44
29 1 0.02
30 20 0.42
31 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAAAATTATTTTTTTAAAATAATAAAA
Found at i:35225050 original size:28 final size:28
Alignment explanation
Indices: 35224964--35225050 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
35224954 AATTATTTTG
* *
35224964 TTAAAATATAAAAAATT-TTAAATTATTT
1 TTAAAATA-ATAAAATTATTAAATAATTT
*
35224992 TTAAAAT-ATAAAATTATTAAAATTATTTTT
1 TTAAAATAATAAAATTATT-AAA-TA-ATTT
*
35225022 TTGAAATAATAAAATTATTAAATAATTT
1 TTAAAATAATAAAATTATTAAATAATTT
35225050 T
1 T
35225051 AATTTCCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
26 7 0.14
27 2 0.04
28 14 0.29
29 3 0.06
30 12 0.24
31 11 0.22
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TTAAAATAATAAAATTATTAAATAATTT
Found at i:35226664 original size:24 final size:24
Alignment explanation
Indices: 35226637--35226692 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
35226627 AGCCTAATTT
*
35226637 TAATCAATGCAAAATATATTATGC
1 TAATAAATGCAAAATATATTATGC
* *
35226661 TAATAAATGCTAAATATATTATAC
1 TAATAAATGCAAAATATATTATGC
*
35226685 TACTAAAT
1 TAATAAAT
35226693 CTTCTAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (24 bp):
TAATAAATGCAAAATATATTATGC
Found at i:35226758 original size:36 final size:35
Alignment explanation
Indices: 35226711--35226782 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
35226701 AAGATAATAT
* **
35226711 ATTTTGTTTAACTTTACTTGCAAGCAATTCTCTTAG
1 ATTTTGTTTAACTTGAAGTGCAAGCAA-TCTCTTAG
35226747 ATTTTGTTTAACTTGAAGTGCAAGCAATCTCTTAG
1 ATTTTGTTTAACTTGAAGTGCAAGCAATCTCTTAG
35226782 A
1 A
35226783 ATTTAGGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (35 bp):
ATTTTGTTTAACTTGAAGTGCAAGCAATCTCTTAG
Found at i:35226858 original size:29 final size:29
Alignment explanation
Indices: 35226819--35226877 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
35226809 ACCATCTTGA
* *
35226819 CACGAATTCTCAAC-AAACAAGTTCTTCAC
1 CACGAACTCTCAACGAAA-AAGTTCTCCAC
35226848 CACGAACTCTCAACGAAAAAGTTCTCCAC
1 CACGAACTCTCAACGAAAAAGTTCTCCAC
35226877 C
1 C
35226878 TCTTCCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.37, C:0.34, G:0.08, T:0.20
Consensus pattern (29 bp):
CACGAACTCTCAACGAAAAAGTTCTCCAC
Found at i:35231592 original size:6 final size:6
Alignment explanation
Indices: 35231578--35231607 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35231568 CAAAATCTTA
*
35231578 TACTTC TACTGC TACTGC TACTGC TACTGC
1 TACTGC TACTGC TACTGC TACTGC TACTGC
35231608 ATTCCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.33, G:0.13, T:0.37
Consensus pattern (6 bp):
TACTGC
Found at i:35234746 original size:3 final size:3
Alignment explanation
Indices: 35234738--35234768 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35234728 AAGGGTCCAA
35234738 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35234769 GGGTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35235378 original size:146 final size:146
Alignment explanation
Indices: 35235187--35235835 Score: 866
Period size: 146 Copynumber: 4.4 Consensus size: 146
35235177 GATCTTGGAA
** *
35235187 AAAGTTTTGATTTATTTTAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAATGATTT
1 AAAGTTTTGATTT-TTTTAATTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTT
* *
35235252 TCTTTAAAAAGGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCATTTTAAA-AA
65 TCTTTAAAAA--AGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAA
*
35235316 A-AATTAAAATTTTTAAAC
128 ACAATTTAAATTTTTAAAC
* * * *
35235334 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGCTTAGATTTTTAAGTAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTT
* *
35235399 CTTTAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGACCTTTTAAAGAAA
66 CTTT--AAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAAA
*** * *
35235464 TTTTTTAAATTTTAAAAT
129 CAATTTAAATTTTTAAAC
35235482 AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAG-TTTGAATTTTTAAGTAAAATAATGATTT
1 AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTTG-ATTTTTAAGTAAAATAATGATTT
*
35235546 T-TTTAAAAAAGAAAATTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAA-AAAC
65 TCTTTAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAAAC
*
35235609 AATTTAAATTTTTAAAT
130 AATTTAAATTTTTAAAC
* * * * * *
35235626 AAAGTTTTGATTTTTTTAATTGTTTCAAAATAAAAGTTTCGATTTTTAAGTAAAGTAGTAATTTT
1 AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTT
* *
35235691 CATTAAAAAA-AAA-TTTAGATTTTTAAAATATAAAAATCTATTTTTTTTAGTCATTTTAAAGAA
66 CTTTAAAAAAGAAAGTTTAGATTTTTAAAA-ATAAAAA--TATATTTTTTAGTCATTTTAAAGAA
*
35235754 A-AGTTTAAATTTTTAAAC
128 ACAATTTAAATTTTTAAAC
* * * *
35235772 AAAATTTTGA-TTTTTTAATTATTTCGAAATAAAAATTTTGATTTTGAAGTAAAGTAATGATTTT
1 AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTT
35235836 ATTTTAATAA
Statistics
Matches: 449, Mismatches: 42, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
143 15 0.03
144 82 0.18
145 110 0.24
146 142 0.32
147 25 0.06
148 75 0.17
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (146 bp):
AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTT
CTTTAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAAACA
ATTTAAATTTTTAAAC
Found at i:35235526 original size:51 final size:50
Alignment explanation
Indices: 35235266--35235674 Score: 123
Period size: 51 Copynumber: 8.3 Consensus size: 50
35235256 TAAAAAGGAG
* * * * *
35235266 AAAGTTTAGATTTTTAAAAATAAAAATCTG--TTTTTTAGTCATTTTAAA-A
1 AAAGTTTAGAATTTT-AAAATAAAATTATGATTTTTTTAATTA-TTTAAATA
* * * * * * *
35235315 AAA-ATTAAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATA
1 AAAGTTTAGAATTTTAAAATAAAATTATGATTTTTTTAATTATTT--AAATA
* * * *
35235366 AAAGCTTAG-ATTTTTAAGTAAAA-TAGTGATTTTCTTTAA--A---AAAAA
1 AAAGTTTAGAATTTTAAAATAAAATTA-TGATTTT-TTTAATTATTTAAATA
* * * *
35235411 GAAAGTTTAGATTTTTAAAAATAAAAATAT-A-TTTTTTAGACCT-TTTAAAGA
1 -AAAGTTTAGAATTTT-AAAATAAAATTATGATTTTTTTA-A-TTATTTAAATA
** * *
35235462 AATTTTTTA-AATTTTAAAATAAAGTTTTGATTTTTTTAATTATTTCGAAATA
1 AA-AGTTTAGAATTTTAAAATAAAATTATGATTTTTTTAATTATTT--AAATA
* * * *
35235514 AAAGTTT-GAATTTTTAAGTAAAATAATGATTTTTTTAA--A---AAAGA
1 AAAGTTTAGAATTTTAAAATAAAATTATGATTTTTTTAATTATTTAAATA
* * * *
35235558 AAA-TTTAGATTTTTAAAAATAAAAATAT-A-TTTTTTAGTCATTTTAAA-A
1 AAAGTTTAGAATTTT-AAAATAAAATTATGATTTTTTTAATTA-TTTAAATA
* * * * *
35235606 AACAATTTA-AATTTTTAAATAAAGTTTTGATTTTTTTAATTGTTTCAAAATA
1 AA-AGTTTAGAATTTTAAAATAAAATTATGATTTTTTTAATTATTT--AAATA
* *
35235658 AAAGTTTCGATTTTTAA
1 AAAGTTTAGAATTTTAA
35235675 GTAAAGTAGT
Statistics
Matches: 261, Mismatches: 57, Indels: 81
0.65 0.14 0.20
Matches are distributed among these distances:
43 10 0.04
44 14 0.05
45 18 0.07
46 12 0.05
47 14 0.05
48 31 0.12
49 38 0.15
50 29 0.11
51 72 0.28
52 23 0.09
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (50 bp):
AAAGTTTAGAATTTTAAAATAAAATTATGATTTTTTTAATTATTTAAATA
Found at i:35235592 original size:22 final size:22
Alignment explanation
Indices: 35235533--35235592 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
35235523 ATTTTTAAGT
35235533 AAAATAATGATTTTTTTAAAAAAG
1 AAAAT-AT-ATTTTTTTAAAAAAG
* **
35235557 AAAATTTAGATTTTTAAAAATA-
1 AAAATATATTTTTTTAAAAA-AG
35235579 AAAATATATTTTTT
1 AAAATATATTTTTT
35235593 AGTCATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 22 0.76
23 2 0.07
24 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
AAAATATATTTTTTTAAAAAAG
Found at i:35235769 original size:20 final size:20
Alignment explanation
Indices: 35235744--35235789 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
35235734 TTTTTAGTCA
*
35235744 TTTTAAAGAAAAGTTTAAAT
1 TTTTAAACAAAAGTTTAAAT
* * *
35235764 TTTTAAACAAAATTTTGATT
1 TTTTAAACAAAAGTTTAAAT
35235784 TTTTAA
1 TTTTAA
35235790 TTATTTCGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTTAAACAAAAGTTTAAAT
Found at i:35245033 original size:10 final size:10
Alignment explanation
Indices: 35245018--35245046 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
35245008 GAAAAAGATT
35245018 CTTGCATTGA
1 CTTGCATTGA
35245028 CTTGCATTGA
1 CTTGCATTGA
35245038 CTTGCATTG
1 CTTGCATTG
35245047 CAAGAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (10 bp):
CTTGCATTGA
Found at i:35249789 original size:22 final size:22
Alignment explanation
Indices: 35249764--35249812 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
35249754 TTTGTCTAAA
35249764 CCCAAACCACAAGCCAATCAAG
1 CCCAAACCACAAGCCAATCAAG
* *
35249786 CCCAAACCCCAAGCCAATTAAG
1 CCCAAACCACAAGCCAATCAAG
35249808 CCCAA
1 CCCAA
35249813 TTTTTAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.43, G:0.08, T:0.06
Consensus pattern (22 bp):
CCCAAACCACAAGCCAATCAAG
Found at i:35250064 original size:28 final size:28
Alignment explanation
Indices: 35249994--35250057 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
35249984 CCGACTGTTA
*
35249994 ACCATTGACCGTTGACAGTTGATCGTTG
1 ACCATTGACCGTTGACAGTTGATCATTG
*
35250022 ACCATTAACCGTTGACAGTTGA-CTATTG
1 ACCATTGACCGTTGACAGTTGATC-ATTG
35250050 ACCATTGA
1 ACCATTGA
35250058 TAGTTGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (28 bp):
ACCATTGACCGTTGACAGTTGATCATTG
Found at i:35250092 original size:20 final size:20
Alignment explanation
Indices: 35250067--35250104 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
35250057 ATAGTTGATT
35250067 GTTGACCGTTGACTTTTTGG
1 GTTGACCGTTGACTTTTTGG
35250087 GTTGACCGTTGACTTTTT
1 GTTGACCGTTGACTTTTT
35250105 TTGAGAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
GTTGACCGTTGACTTTTTGG
Found at i:35250099 original size:7 final size:7
Alignment explanation
Indices: 35249998--35250079 Score: 56
Period size: 7 Copynumber: 11.7 Consensus size: 7
35249988 CTGTTAACCA
35249998 TTGACCG
1 TTGACCG
*
35250005 TTGACAG
1 TTGACCG
*
35250012 TTGATCG
1 TTGACCG
*
35250019 TTGACCA
1 TTGACCG
*
35250026 TTAACCG
1 TTGACCG
*
35250033 TTGACAG
1 TTGACCG
**
35250040 TTGACTA
1 TTGACCG
*
35250047 TTGACCA
1 TTGACCG
**
35250054 TTGATAG
1 TTGACCG
**
35250061 TTGATTG
1 TTGACCG
35250068 TTGACCG
1 TTGACCG
35250075 TTGAC
1 TTGAC
35250080 TTTTTGGGTT
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (7 bp):
TTGACCG
Found at i:35251530 original size:19 final size:19
Alignment explanation
Indices: 35251491--35251532 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35251481 ATGAGGATTT
*
35251491 TAAATAAATTAATATGCTA
1 TAAATAAATTAATATGATA
35251510 TAAATAAATTATATAT-ATA
1 TAAATAAATTA-ATATGATA
35251529 TAAA
1 TAAA
35251533 ATTATGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAATAAATTAATATGATA
Found at i:35257207 original size:28 final size:28
Alignment explanation
Indices: 35257175--35257252 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
35257165 CCGACCGTTG
*
35257175 ACCATTGACCGTTGACAGTTGACCATTA
1 ACCATTGACCGTTGACAGTTGACAATTA
*
35257203 ACCATTGACCGTTGATC-GTTGACAATTG
1 ACCATTGACCGTTGA-CAGTTGACAATTA
* *
35257231 ATCATTGACCATTGACAGTTGA
1 ACCATTGACCGTTGACAGTTGA
35257253 TTGTTGACCG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 42 0.95
29 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (28 bp):
ACCATTGACCGTTGACAGTTGACAATTA
Found at i:35257280 original size:20 final size:20
Alignment explanation
Indices: 35257255--35257292 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35257245 ACAGTTGATT
35257255 GTTGACCGTTGAATTTTTGG
1 GTTGACCGTTGAATTTTTGG
*
35257275 GTTGACCGTTGACTTTTT
1 GTTGACCGTTGAATTTTT
35257293 TCGAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.47
Consensus pattern (20 bp):
GTTGACCGTTGAATTTTTGG
Found at i:35257285 original size:7 final size:7
Alignment explanation
Indices: 35257147--35257266 Score: 75
Period size: 7 Copynumber: 17.6 Consensus size: 7
35257137 TGATAATTGA
*
35257147 TTGATCG
1 TTGACCG
*
35257154 TTGACCT
1 TTGACCG
35257161 TTGACC-
1 TTGACCG
35257167 --GACCG
1 TTGACCG
*
35257172 TTGACCA
1 TTGACCG
35257179 TTGACCG
1 TTGACCG
*
35257186 TTGACAG
1 TTGACCG
*
35257193 TTGACCA
1 TTGACCG
* *
35257200 TTAACCA
1 TTGACCG
35257207 TTGACCG
1 TTGACCG
*
35257214 TTGATCG
1 TTGACCG
**
35257221 TTGACAA
1 TTGACCG
* *
35257228 TTGATCA
1 TTGACCG
*
35257235 TTGACCA
1 TTGACCG
*
35257242 TTGACAG
1 TTGACCG
**
35257249 TTGATTG
1 TTGACCG
35257256 TTGACCG
1 TTGACCG
35257263 TTGA
1 TTGA
35257267 ATTTTTGGGT
Statistics
Matches: 87, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
4 4 0.05
7 83 0.95
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (7 bp):
TTGACCG
Found at i:35264091 original size:58 final size:58
Alignment explanation
Indices: 35264018--35264157 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 58
35264008 CATTCTTTTA
*
35264018 CACA-TTAATCGCATTAATCACATGAGTACTTAAGCATTTAA-CACAACACATATTAAT
1 CACATTTAATCGCATTAATCACATGAATACTTAAGCA-TTAATCACAACACATATTAAT
* * * * * *
35264075 TACATTTAATCACATTAGTCACATGAATATTTCAGCATTAATCACATCACATATTAAT
1 CACATTTAATCGCATTAATCACATGAATACTTAAGCATTAATCACAACACATATTAAT
*
35264133 CACATTTAGTCGCATTTAATCACAT
1 CACATTTAATCGCA-TTAATCACAT
35264158 TAGTCATATG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 7 0.10
58 53 0.77
59 9 0.13
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (58 bp):
CACATTTAATCGCATTAATCACATGAATACTTAAGCATTAATCACAACACATATTAAT
Found at i:35264116 original size:32 final size:32
Alignment explanation
Indices: 35264080--35264189 Score: 100
Period size: 32 Copynumber: 3.3 Consensus size: 32
35264070 TTAATTACAT
*
35264080 TTAATCACATTAGTCACATGAATATTTCAGCA
1 TTAATCACATTAGTCATATGAATATTTCAGCA
* *
35264112 TTAATCACATCA--CATATTAATCACATTT-AGTCGCA
1 TTAATCACATTAGTCATATGAAT---ATTTCA---GCA
35264147 TTTAATCACATTAGTCATATGAATATTTCAGCA
1 -TTAATCACATTAGTCATATGAATATTTCAGCA
*
35264180 TTTATCACAT
1 TTAATCACAT
35264190 CACATATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
30 7 0.11
32 21 0.34
33 7 0.11
35 7 0.11
36 12 0.19
38 8 0.13
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.37
Consensus pattern (32 bp):
TTAATCACATTAGTCATATGAATATTTCAGCA
Found at i:35264154 original size:36 final size:36
Alignment explanation
Indices: 35264112--35264225 Score: 116
Period size: 36 Copynumber: 3.3 Consensus size: 36
35264102 TATTTCAGCA
35264112 TTAATCACATCACATATTAATCACATTTAGTCGCAT
1 TTAATCACATCACATATTAATCACATTTAGTCGCAT
* *
35264148 TTAATCACATTAGTCATATGAAT---A-TT--TCAGCAT
1 TTAATCACATCA--CATATTAATCACATTTAGTC-GCAT
*
35264181 TT-ATCACATCACATATTAATCACATTTAGTCACAT
1 TTAATCACATCACATATTAATCACATTTAGTCGCAT
*
35264216 TTAATTACAT
1 TTAATCACAT
35264226 GAATATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
30 8 0.13
32 10 0.16
33 7 0.11
34 4 0.06
35 6 0.10
36 19 0.31
38 8 0.13
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (36 bp):
TTAATCACATCACATATTAATCACATTTAGTCGCAT
Found at i:35264155 original size:68 final size:68
Alignment explanation
Indices: 35264076--35264225 Score: 264
Period size: 68 Copynumber: 2.2 Consensus size: 68
35264066 CATATTAATT
35264076 ACATTTAATCACATTAGTCACATGAATATTTCAGCATTAATCACATCACATATTAATCACATTTA
1 ACATTTAATCACATTAGTCACATGAATATTTCAGCATTAATCACATCACATATTAATCACATTTA
35264141 GTC
66 GTC
* * *
35264144 GCATTTAATCACATTAGTCATATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTA
1 ACATTTAATCACATTAGTCACATGAATATTTCAGCATTAATCACATCACATATTAATCACATTTA
35264209 GTC
66 GTC
*
35264212 ACATTTAATTACAT
1 ACATTTAATCACAT
35264226 GAATATTTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (68 bp):
ACATTTAATCACATTAGTCACATGAATATTTCAGCATTAATCACATCACATATTAATCACATTTA
GTC
Found at i:35264158 original size:10 final size:10
Alignment explanation
Indices: 35264120--35264158 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
35264110 CATTAATCAC
35264120 ATCACATATTA
1 ATCACAT-TTA
35264131 ATCACATTTA
1 ATCACATTTA
* *
35264141 GTCGCATTTA
1 ATCACATTTA
35264151 ATCACATT
1 ATCACATT
35264159 AGTCATATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (10 bp):
ATCACATTTA
Found at i:35264253 original size:23 final size:23
Alignment explanation
Indices: 35264222--35264308 Score: 122
Period size: 23 Copynumber: 3.8 Consensus size: 23
35264212 ACATTTAATT
* *
35264222 ACATGAATATTTAAGAACAAATC
1 ACATTAATATTTAAGCACAAATC
*
35264245 ACATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
35264268 ATATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
35264291 ACATTAATGTTTAA-CACA
1 ACATTAATATTTAAGCACA
35264309 TTTAATGATA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 4 0.07
23 53 0.93
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (23 bp):
ACATTAATATTTAAGCACAAATC
Found at i:35264749 original size:36 final size:36
Alignment explanation
Indices: 35264702--35264788 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
35264692 TCAGCACAAT
** * *
35264702 ATATTTACTGTCACATGTTATGAATAACGTATCCAC
1 ATATTTACTGTCACATGACATGAATAACATAACCAC
* * *
35264738 ATATTTTCTGTCTCATGACATGAGTAACATAACCAC
1 ATATTTACTGTCACATGACATGAATAACATAACCAC
* *
35264774 ATATTCACTTTCACA
1 ATATTTACTGTCACA
35264789 ATAGTCATCT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (36 bp):
ATATTTACTGTCACATGACATGAATAACATAACCAC
Found at i:35275801 original size:17 final size:17
Alignment explanation
Indices: 35275781--35275822 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
35275771 CTCCCTTGAC
*
35275781 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
35275798 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
35275815 CTTGTAAC
1 CTT-TAAC
35275823 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:35275806 original size:24 final size:24
Alignment explanation
Indices: 35275761--35275808 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35275751 ATGGATGTTC
* *
35275761 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
* *
35275785 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
35275809 CATATTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.02, T:0.44
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACCTTT
Found at i:35276836 original size:31 final size:30
Alignment explanation
Indices: 35276782--35276855 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
35276772 AATAAAAAAT
*
35276782 AAAAAATATATTTTTATAATTAAAT-TTAA
1 AAAAAATATATTTTTATAATTAAATAATAA
* **
35276811 ATAAAATATATTTATTATTTTTTAAATAATAA
1 AAAAAATATATTT-TTA-TAATTAAATAATAA
35276843 AAAAAATTATATT
1 AAAAAA-TATATT
35276856 GACAAATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.33
30 3 0.08
31 7 0.19
32 8 0.22
33 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAAAATATATTTTTATAATTAAATAATAA
Found at i:35277727 original size:23 final size:24
Alignment explanation
Indices: 35277696--35277747 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
35277686 GCTTTTCTTC
*
35277696 AATCTATTGGTTTGAAGCTATCCA
1 AATCTATTGGTTTCAAGCTATCCA
35277720 AATC-ATTGGTTTCAAGCTATCCA
1 AATCTATTGGTTTCAAGCTATCCA
35277743 AATCT
1 AATCT
35277748 GATGCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (24 bp):
AATCTATTGGTTTCAAGCTATCCA
Found at i:35286865 original size:108 final size:109
Alignment explanation
Indices: 35286743--35286956 Score: 295
Period size: 108 Copynumber: 2.0 Consensus size: 109
35286733 AAGACAAAGG
* * * *
35286743 ACATTTATCGATTTTAAATAGGATATTCGATTACTTAGGTTCAAAGAGAAATCATACCCAATACG
1 ACATTTATCGATTTTAAATAAGATACTCGATTACTTAGGTTCAAAGAAAAATCATACCCAATACA
* * *
35286808 TTTGAGCATAATTTCTCGAGTTTCC-AAAATAAAAGAACATCGA
66 TTAGAGCAAAATTTCTCGAATTTCCTAAAATAAAAGAACATCGA
* * * * *
35286851 ACATTTATTGATTTTAAATAAGTTGCTCGATTATTTAGGTTCAAAGAAAAATCATACCTAATACA
1 ACATTTATCGATTTTAAATAAGATACTCGATTACTTAGGTTCAAAGAAAAATCATACCCAATACA
* *
35286916 TTAGGGCAAAATTTTTCGAATTTCCTAAAATAAAAGAACAT
66 TTAGAGCAAAATTTCTCGAATTTCCTAAAATAAAAGAACAT
35286957 TGCCTCATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
108 76 0.84
109 15 0.16
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (109 bp):
ACATTTATCGATTTTAAATAAGATACTCGATTACTTAGGTTCAAAGAAAAATCATACCCAATACA
TTAGAGCAAAATTTCTCGAATTTCCTAAAATAAAAGAACATCGA
Found at i:35287229 original size:22 final size:23
Alignment explanation
Indices: 35287203--35287247 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
35287193 TAAGAGGAAA
* *
35287203 AATATTAAATAAAT-AAATATAC
1 AATATAAAATAAATGAAAAATAC
35287225 AATATAAAATAAATGAAAAATAC
1 AATATAAAATAAATGAAAAATAC
35287248 GAGTTGACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
AATATAAAATAAATGAAAAATAC
Found at i:35287358 original size:18 final size:18
Alignment explanation
Indices: 35287289--35287360 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
35287279 AAAAGGGTTT
35287289 AAATAAATAATAAAAA-AA
1 AAATAAA-AATAAAAATAA
* *
35287307 TAATAAAAGATTAAAATTTAA
1 AAATAAAA-A-TAAAA-ATAA
* *
35287328 AAA-GAAAA-GAAAATAA
1 AAATAAAAATAAAAATAA
35287344 AAATAAAAATAAAAATA
1 AAATAAAAATAAAAATA
35287361 GAATAAAAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
16 6 0.15
17 8 0.20
18 13 0.32
19 6 0.15
20 3 0.08
21 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.19
Consensus pattern (18 bp):
AAATAAAAATAAAAATAA
Found at i:35287518 original size:81 final size:81
Alignment explanation
Indices: 35287383--35287861 Score: 735
Period size: 81 Copynumber: 5.9 Consensus size: 81
35287373 GAATGGCTTT
* * *
35287383 AATCTGCCC-CATGGTTAGGGTAAGAGATTGGATGACTTCAATCTGCCCCATGGTCGAGGTAAGA
1 AATCTGCCCTC-TAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGA
*
35287447 GATTGGATGGTGCCTTC
65 GATTGGATGGTGTCTTC
*
35287464 AATCTGCCCTCTAGTTAGGGTAAAAGATTGAATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
1 AATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
*
35287529 ATTAGATGGTGTCTTC
66 ATTGGATGGTGTCTTC
* * *
35287545 AATCTGTCCTCTAGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCGAGGTAAGAG
1 AATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
*
35287610 ATTGGATGGTATCTTC
66 ATTGGATGGTGTCTTC
* *
35287626 AATCTGCCTTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTACCCCATGGTCGGGGTAAGAG
1 AATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
*
35287691 ATTGGATGGTGTTTTC
66 ATTGGATGGTGTCTTC
* * * *
35287707 AATCTGCCCTATGGTTAGGGTAAAAGATTGGATGACTTCAATCTACCTCATGGTCGGGGTAAGAG
1 AATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
* *
35287772 AATGGATGGTGTCTTT
66 ATTGGATGGTGTCTTC
* * * *
35287788 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGACTTCAATTTGCCACATGATCGGGGTAAGAG
1 AATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
35287853 ATTGGATGG
66 ATTGGATGG
35287862 CTTCTTGCCT
Statistics
Matches: 365, Mismatches: 32, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
81 364 1.00
82 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (81 bp):
AATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAG
ATTGGATGGTGTCTTC
Found at i:35296541 original size:24 final size:24
Alignment explanation
Indices: 35296509--35296556 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35296499 TAAAACGAAT
* *
35296509 AAAGAAAAGATAAAAGGAAAATAA
1 AAAGAAAAGAAAAAAAGAAAATAA
* *
35296533 AAAGGAAAGAAAAAAATAAAATAA
1 AAAGAAAAGAAAAAAAGAAAATAA
35296557 GGGAAATCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (24 bp):
AAAGAAAAGAAAAAAAGAAAATAA
Found at i:35316858 original size:21 final size:21
Alignment explanation
Indices: 35316807--35316883 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
35316797 CTAAAAAGCC
*
35316807 ATGTATCAATACATCCCTTAGA
1 ATGTATCAATACATGCCTTA-A
*
35316829 A-GTACCAATACATGCCTTAA
1 ATGTATCAATACATGCCTTAA
* * *
35316849 ATGTATCAATATATACC-TAT
1 ATGTATCAATACATGCCTTAA
35316869 ATGTATCAATACATG
1 ATGTATCAATACATG
35316884 GTTGTGAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.37
21 28 0.61
22 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
ATGTATCAATACATGCCTTAA
Found at i:35328338 original size:17 final size:17
Alignment explanation
Indices: 35328312--35328344 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35328302 GAGGTTCCAC
35328312 AAAAGAAAGAA-AAGGG
1 AAAAGAAAGAAGAAGGG
35328328 AAAAGGAAAGAAGAAGG
1 AAAA-GAAAGAAGAAGG
35328345 CCACTCAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAGAAGGG
Found at i:35329345 original size:17 final size:17
Alignment explanation
Indices: 35329311--35329353 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
35329301 GCATGCATTT
35329311 ATTTTAATTGTCATTGC
1 ATTTTAATTGTCATTGC
*
35329328 ATTTTTATTGTC-TCTGC
1 ATTTTAATTGTCAT-TGC
*
35329345 ATGTTAATT
1 ATTTTAATT
35329354 TTTTTAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (17 bp):
ATTTTAATTGTCATTGC
Found at i:35332602 original size:35 final size:35
Alignment explanation
Indices: 35332556--35332626 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
35332546 ACTCAAAAAG
35332556 ATAAATTTTTGAAATGTGGGTGCAATTGCATTTCC
1 ATAAATTTTTGAAATGTGGGTGCAATTGCATTTCC
35332591 ATAAATTTTTGAAATGTGGGTGCAATTGCATTTCC
1 ATAAATTTTTGAAATGTGGGTGCAATTGCATTTCC
35332626 A
1 A
35332627 GCCCCATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (35 bp):
ATAAATTTTTGAAATGTGGGTGCAATTGCATTTCC
Found at i:35332725 original size:17 final size:17
Alignment explanation
Indices: 35332699--35332758 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
35332689 TACAAAGACA
35332699 AATG-AAATGCAATGAC
1 AATGAAAATGCAATGAC
* * *
35332715 TATGCAAATGCAGTGAC
1 AATGAAAATGCAATGAC
*
35332732 AATTAAAATGCAATGAC
1 AATGAAAATGCAATGAC
*
35332749 AATGAGAATG
1 AATGAAAATG
35332759 TGATGATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 3 0.09
17 32 0.91
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.22
Consensus pattern (17 bp):
AATGAAAATGCAATGAC
Found at i:35340670 original size:22 final size:23
Alignment explanation
Indices: 35340633--35340688 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
35340623 TAAAACATCT
* **
35340633 AAAAAAATATGTAAAAGTAGTCA
1 AAAAAAATAAGTAAAACAAGTCA
35340656 AAAAAAATAAG-AAAACAAGTCA
1 AAAAAAATAAGTAAAACAAGTCA
*
35340678 ATAACAAATAA
1 A-AAAAAATAA
35340689 AGATTAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.68, C:0.07, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAAAAATAAGTAAAACAAGTCA
Found at i:35341536 original size:48 final size:48
Alignment explanation
Indices: 35341465--35341557 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
35341455 CTCTCATGCT
35341465 CTCCTCTTGTGTCACACTTAGGATGCTCCTCGTCAGAAGCAGATCTAC
1 CTCCTCTTGTGTCACACTTAGGATGCTCCTCGTCAGAAGCAGATCTAC
35341513 CTCCTCTTGTGTCACACTTAGGATGCTCCTCGTCAGAAGCAGATC
1 CTCCTCTTGTGTCACACTTAGGATGCTCCTCGTCAGAAGCAGATC
35341558 ACCCTTGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.29
Consensus pattern (48 bp):
CTCCTCTTGTGTCACACTTAGGATGCTCCTCGTCAGAAGCAGATCTAC
Found at i:35346090 original size:24 final size:24
Alignment explanation
Indices: 35346063--35346110 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35346053 TCGAGAAAGG
35346063 GCAAGGCTCTAATGGAACCACAAT
1 GCAAGGCTCTAATGGAACCACAAT
35346087 GCAAGGCTCTAATGGAACCACAAT
1 GCAAGGCTCTAATGGAACCACAAT
35346111 ATCTTTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (24 bp):
GCAAGGCTCTAATGGAACCACAAT
Found at i:35361124 original size:18 final size:18
Alignment explanation
Indices: 35361092--35361144 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
35361082 CGATTACATG
* *
35361092 ACCAGATGCGATCATAAA
1 ACCAAATGCAATCATAAA
* * *
35361110 ATCAAATGCATTCATATA
1 ACCAAATGCAATCATAAA
*
35361128 ACCAGATGCAATCATAA
1 ACCAAATGCAATCATAA
35361145 GCTCGAATGC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (18 bp):
ACCAAATGCAATCATAAA
Found at i:35367677 original size:21 final size:21
Alignment explanation
Indices: 35367639--35367678 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35367629 GGTTGACTCC
*
35367639 AAGGATAAGAAAAGAAAGAGG
1 AAGGATAAGAAAAAAAAGAGG
35367660 AAGGATAA-AAAGAAAAAGA
1 AAGGATAAGAAA-AAAAAGA
35367679 AGCATAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.05
Consensus pattern (21 bp):
AAGGATAAGAAAAAAAAGAGG
Found at i:35367680 original size:18 final size:19
Alignment explanation
Indices: 35367648--35367686 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
35367638 CAAGGATAAG
* *
35367648 AAAAGAAAGAGGAAGGATA
1 AAAAGAAAGAAGAAGCATA
35367667 AAAAGAAA-AAGAAGCATA
1 AAAAGAAAGAAGAAGCATA
35367685 AA
1 AA
35367687 GTAGAGCGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.69, C:0.03, G:0.23, T:0.05
Consensus pattern (19 bp):
AAAAGAAAGAAGAAGCATA
Found at i:35367814 original size:18 final size:18
Alignment explanation
Indices: 35367788--35367841 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
35367778 ATGCATATCA
* *
35367788 TTTAGTTGTCATTACATT
1 TTTATTTGTCACTACATT
35367806 TTTATTTGTCACTACA-T
1 TTTATTTGTCACTACATT
* *
35367823 TTTATTTGTTAGTACATT
1 TTTATTTGTCACTACATT
35367841 T
1 T
35367842 GTACTGTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCACTACATT
Found at i:35367827 original size:17 final size:17
Alignment explanation
Indices: 35367788--35367841 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
35367778 ATGCATATCA
* *
35367788 TTTAGTTGTCATTACATT
1 TTTATTTGTCACTACA-T
35367806 TTTATTTGTCACTACAT
1 TTTATTTGTCACTACAT
* *
35367823 TTTATTTGTTAGTACAT
1 TTTATTTGTCACTACAT
35367840 TT
1 TT
35367842 GTACTGTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTACAT
Found at i:35368450 original size:17 final size:17
Alignment explanation
Indices: 35368434--35368465 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35368424 GAGAAGAAGA
35368434 AAAAG-AAAGCAAAAAG
1 AAAAGAAAAGCAAAAAG
35368450 AAAAGAAAAGCAAAAA
1 AAAAGAAAAGCAAAAA
35368466 ATATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGCAAAAAG
Found at i:35368478 original size:16 final size:17
Alignment explanation
Indices: 35368459--35368492 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35368449 GAAAAGAAAA
35368459 GCAAAAAATATT-TATT
1 GCAAAAAATATTGTATT
*
35368475 GCAATAAATATTGTATT
1 GCAAAAAATATTGTATT
35368492 G
1 G
35368493 GTTAAGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
GCAAAAAATATTGTATT
Found at i:35370995 original size:19 final size:19
Alignment explanation
Indices: 35370952--35370996 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 19
35370942 ATGAAGGGCG
*
35370952 TTTTGAGGAATTAATTCCA
1 TTTTGAGGAACTAATTCCA
35370971 ---TGAGGAACTAATTCCA
1 TTTTGAGGAACTAATTCCA
35370987 TTTTGAGGAA
1 TTTTGAGGAA
35370997 TTAGGAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 15 0.68
19 7 0.32
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
TTTTGAGGAACTAATTCCA
Found at i:35390480 original size:22 final size:22
Alignment explanation
Indices: 35390455--35390500 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
35390445 AAATCAGAGC
35390455 TAAGCGTTATGAGAAAATTATT
1 TAAGCGTTATGAGAAAATTATT
35390477 TAAGCGTTATGAGAAAATTATT
1 TAAGCGTTATGAGAAAATTATT
35390499 TA
1 TA
35390501 CGAACGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (22 bp):
TAAGCGTTATGAGAAAATTATT
Found at i:35402725 original size:93 final size:93
Alignment explanation
Indices: 35402527--35402734 Score: 224
Period size: 93 Copynumber: 2.2 Consensus size: 93
35402517 AACTTTCTCT
* * ** * *
35402527 ATTTTTGGGTTTCTTAAAGCTTTCATCTTTGGGTTTTATATAGCTTTCCAAGTACATTTAATCTC
1 ATTTTT-GGTTTCTTAAAGCTTTCATCTTTGGGTTTCATATAGCTTCCCAACCAAATTTAATATC
* * * *
35402592 TATTTTTTGGGTTTATTAGAGCTTCCTCA
65 CATTTTATGAGTTTATTAGAGCATCCTCA
* *
35402621 ATTTTTTGTTTCTTAAAGTTTTCATCTTTGGGTTTCATGA-AGCTTCCCAACCAAATTTAATATC
1 ATTTTTGGTTTCTTAAAGCTTTCATCTTTGGGTTTCAT-ATAGCTTCCCAACCAAATTTAATATC
* * *
35402685 CA-TTTATGATTTTCTT-GAAGCATCCTCC
65 CATTTTATGAGTTTATTAG-AGCATCCTCA
35402713 ATTTTTAGGTTTCTTAAAGCTT
1 ATTTTT-GGTTTCTTAAAGCTT
35402735 CCTTCATATT
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
91 1 0.01
92 24 0.26
93 62 0.66
94 7 0.07
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (93 bp):
ATTTTTGGTTTCTTAAAGCTTTCATCTTTGGGTTTCATATAGCTTCCCAACCAAATTTAATATCC
ATTTTATGAGTTTATTAGAGCATCCTCA
Found at i:35402969 original size:25 final size:25
Alignment explanation
Indices: 35402935--35402984 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
35402925 TTTGTAGTCC
*
35402935 ATATTTTAAGGCCACTTTAAGGTTA
1 ATATTTTAAGGCCACTCTAAGGTTA
* *
35402960 ATATTTTAAGGGCACTCTGAGGTTA
1 ATATTTTAAGGCCACTCTAAGGTTA
35402985 CAATTCTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (25 bp):
ATATTTTAAGGCCACTCTAAGGTTA
Found at i:35406287 original size:19 final size:18
Alignment explanation
Indices: 35406245--35406280 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
35406235 TTATTTTTTT
35406245 ATTT-TTATTAATTTAAA
1 ATTTATTATTAATTTAAA
35406262 ATTTATTATTAAATTTAAA
1 ATTTATTATT-AATTTAAA
35406281 TTATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATTATTAATTTAAA
Found at i:35418663 original size:28 final size:28
Alignment explanation
Indices: 35418630--35418777 Score: 106
Period size: 28 Copynumber: 5.2 Consensus size: 28
35418620 GTAGAATAAT
* *
35418630 CTCTACTTAAGCAAGATTCAAAATATCG
1 CTCTACCTGAGCAAGATTCAAAATATCG
* * *
35418658 CTCTACCTGAGCCAAAAGT-AGAATAAT-G
1 CTCTACCTGAG-CAAGATTCAAAAT-ATCG
*
35418686 CTCTACCCGAGCAAGATTCAAAATATCG
1 CTCTACCTGAGCAAGATTCAAAATATCG
* * * *
35418714 CTCTACCCGAGCTAGAAGT-AGAATAAT-G
1 CTCTACCTGAGCAAG-ATTCAAAAT-ATCG
* *
35418742 TTCTACCTCGAGTAAGATTCAAAATATCG
1 CTCTACCT-GAGCAAGATTCAAAATATCG
*
35418771 CCCTACC
1 CTCTACC
35418778 CAAGCATTCC
Statistics
Matches: 91, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
27 7 0.08
28 58 0.64
29 26 0.29
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (28 bp):
CTCTACCTGAGCAAGATTCAAAATATCG
Found at i:35418777 original size:57 final size:57
Alignment explanation
Indices: 35418601--35418778 Score: 254
Period size: 56 Copynumber: 3.2 Consensus size: 57
35418591 AACAAATTAA
* **
35418601 CGCTCCACCCGAGCTAGAAGTAGAATAAT-CTCTA-CTTAAGCAAGATTCAAAATAT
1 CGCTCTACCCGAGCTAGAAGTAGAATAATGCTCTACCTCGAGCAAGATTCAAAATAT
* * *
35418656 CGCTCTACCTGAGCCAAAAGTAGAATAATGCTCTACC-CGAGCAAGATTCAAAATAT
1 CGCTCTACCCGAGCTAGAAGTAGAATAATGCTCTACCTCGAGCAAGATTCAAAATAT
* *
35418712 CGCTCTACCCGAGCTAGAAGTAGAATAATGTTCTACCTCGAGTAAGATTCAAAATAT
1 CGCTCTACCCGAGCTAGAAGTAGAATAATGCTCTACCTCGAGCAAGATTCAAAATAT
*
35418769 CGCCCTACCC
1 CGCTCTACCC
35418779 AAGCATTCCA
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
55 25 0.23
56 55 0.51
57 28 0.26
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (57 bp):
CGCTCTACCCGAGCTAGAAGTAGAATAATGCTCTACCTCGAGCAAGATTCAAAATAT
Found at i:35433612 original size:207 final size:207
Alignment explanation
Indices: 35433257--35433868 Score: 1134
Period size: 207 Copynumber: 3.0 Consensus size: 207
35433247 GATTTTTTTA
*
35433257 ATAGTACAATGACTAAATTGATCCATTTTGTAACATCTCGATACTCGATTTGATCACCGAATTCG
1 ATAGTACAATGACTAAATTGATCCATTTTGTAACATCTCGATACTCGATTTGATCACCAAATTCG
* * * *
35433322 AGCTACAAGTGTCACATTAATTGTTGGAGCAACTACAATCAACAATATACAATTCAATGCCATTA
66 AGCTACAAGTGTCACATTAGTTGTTAGAGAAACTACAATCAACAATATACAATTCAATGTCATTA
35433387 TACAATTAAATACAAGTAAATCATGTACTTTAAACATTGTGTTATCATTTTCGAGTCTTATACGA
131 TACAATTAAATACAAGTAAATCATGTACTTTAAACATTGTGTTATCATTTTCGAGTCTTATACGA
35433452 GCTACAAGTGTC
196 GCTACAAGTGTC
*
35433464 ATAGTACAATGACTAAATTGATTCATTTTGTAACATCTCGATACTCGATTTGATCACCAAATTCG
1 ATAGTACAATGACTAAATTGATCCATTTTGTAACATCTCGATACTCGATTTGATCACCAAATTCG
35433529 AGCTACAAGTGTCACATTAGTTGTTAGAGAAACTACAATCAACAATATACAATTCAATGTCATTA
66 AGCTACAAGTGTCACATTAGTTGTTAGAGAAACTACAATCAACAATATACAATTCAATGTCATTA
* *
35433594 TACAACTAAATACAAGTAAATCATGTACTTTAAACATTTTGTTATCATTTTCGAGTCTTATACGA
131 TACAATTAAATACAAGTAAATCATGTACTTTAAACATTGTGTTATCATTTTCGAGTCTTATACGA
35433659 GCTACAAGTGTC
196 GCTACAAGTGTC
35433671 ATAGTACAATGACTAAATTGATCCATTTTGTAACATCTCGATACTCGATTTGATCACCAAATTCG
1 ATAGTACAATGACTAAATTGATCCATTTTGTAACATCTCGATACTCGATTTGATCACCAAATTCG
* *
35433736 AGCTACAAGTGTCACATTAGTTGTTAGAGAAACTACAATCAACAATCTACAATTCAATGTCAATA
66 AGCTACAAGTGTCACATTAGTTGTTAGAGAAACTACAATCAACAATATACAATTCAATGTCATTA
35433801 TACAATTAAATACAAGTAAATCATGTACTTTAAACATTGTGTTATCATTTTCGAGTCTTATACGA
131 TACAATTAAATACAAGTAAATCATGTACTTTAAACATTGTGTTATCATTTTCGAGTCTTATACGA
35433866 GCT
196 GCT
35433869 TACGAAAGCT
Statistics
Matches: 392, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
207 392 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (207 bp):
ATAGTACAATGACTAAATTGATCCATTTTGTAACATCTCGATACTCGATTTGATCACCAAATTCG
AGCTACAAGTGTCACATTAGTTGTTAGAGAAACTACAATCAACAATATACAATTCAATGTCATTA
TACAATTAAATACAAGTAAATCATGTACTTTAAACATTGTGTTATCATTTTCGAGTCTTATACGA
GCTACAAGTGTC
Found at i:35436663 original size:55 final size:54
Alignment explanation
Indices: 35436574--35436727 Score: 166
Period size: 55 Copynumber: 2.8 Consensus size: 54
35436564 AATGGTGTTT
* * * * * *
35436574 TTTGAAGGCACAAGGGCTAACACACGGGGGTGTGTCCAAGTGTGTG-TCTATACTA
1 TTTGGAGGCACACGGGCTGACACACGAGCGTGTGT-C-AGGGTGTGATCTATACTA
35436629 TTTGGAGGCACACGGGCTGACACACGAGCGTGTGTCAGGGTGTGCATCTATACTA
1 TTTGGAGGCACACGGGCTGACACACGAGCGTGTGTCAGGGTGTG-ATCTATACTA
* * * * * *
35436684 TTTGGAGGTATACGGGCTGGCACACGCGCGTGGGTCAGGATGTG
1 TTTGGAGGCACACGGGCTGACACACGAGCGTGTGTCAGGGTGTG
35436728 TGTGGCACAC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
53 7 0.08
54 1 0.01
55 77 0.91
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (54 bp):
TTTGGAGGCACACGGGCTGACACACGAGCGTGTGTCAGGGTGTGATCTATACTA
Found at i:35436799 original size:96 final size:95
Alignment explanation
Indices: 35436635--35436920 Score: 321
Period size: 96 Copynumber: 3.0 Consensus size: 95
35436625 ACTATTTGGA
* ** * *
35436635 GGCACACGGGCTGACACAC-GAGCGTGTGTCAGGGTGTGCATCTATACTATTTGGAGGTATACGG
1 GGCACACGGGCTGACACACGGA-CATGTGTCAGGGTGTGTGTCTATACTGTTTGGAGGCATACGG
*
35436699 GCTGGCACACGCGCGTGGGTCAGGATGTGTGT
65 GCTGGCACACGGGCGTGGGTCAGG-TGTGTGT
*
35436731 GGCACACGGGCTGACACACGGACTTGTGTCAGGGTGTGTGTCTATACTGTTTGGAGGCATACGGG
1 GGCACACGGGCTGACACACGGACATGTGTCAGGGTGTGTGTCTATACTGTTTGGAGGCATACGGG
*
35436796 CTGGCACACGGGCGTGGGTTAAGGTGTGTGT
66 CTGGCACACGGGCGTGGG-TCAGGTGTGTGT
* * * * * *
35436827 GGCATATGGGCTGGCACATGCG-CATGTGTTAGGGTATGTG--TATACTGTTCT-GAGGCATACG
1 GGCACACGGGCTGACACACG-GACATGTGTCAGGGTGTGTGTCTATACTGTT-TGGAGGCATACG
* * * *
35436888 AGCTGTCACATGGGCGTGTGTCAGGGTGTGTGT
64 GGCTGGCACACGGGCGTGGGTCA-GGTGTGTGT
35436921 ATATTGTTTT
Statistics
Matches: 166, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
93 2 0.01
94 44 0.27
95 1 0.01
96 112 0.67
97 7 0.04
ACGTcount: A:0.17, C:0.19, G:0.38, T:0.26
Consensus pattern (95 bp):
GGCACACGGGCTGACACACGGACATGTGTCAGGGTGTGTGTCTATACTGTTTGGAGGCATACGGG
CTGGCACACGGGCGTGGGTCAGGTGTGTGT
Found at i:35436867 original size:41 final size:41
Alignment explanation
Indices: 35436786--35436867 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
35436776 ACTGTTTGGA
* * *
35436786 GGCATACGGGCTGGCACACGGGCGTGGGTTAAGGTGTGTGT
1 GGCATACGGGCTGGCACACGCGCATGGGTTAAGGTATGTGT
* * * *
35436827 GGCATATGGGCTGGCACATGCGCATGTGTTAGGGTATGTGT
1 GGCATACGGGCTGGCACACGCGCATGGGTTAAGGTATGTGT
35436868 ATACTGTTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.26
Consensus pattern (41 bp):
GGCATACGGGCTGGCACACGCGCATGGGTTAAGGTATGTGT
Found at i:35436908 original size:53 final size:53
Alignment explanation
Indices: 35436827--35436928 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
35436817 AGGTGTGTGT
* * *
35436827 GGCATATGGGCTGGCACATGCGCATGTGTTAGGGTATGTGTATACTGTTCTGA
1 GGCATACGAGCTGGCACATGCGCATGTGTCAGGGTATGTGTATACTGTTCTGA
* * * * *
35436880 GGCATACGAGCTGTCACATGGGCGTGTGTCAGGGTGTGTGTATATTGTT
1 GGCATACGAGCTGGCACATGCGCATGTGTCAGGGTATGTGTATACTGTT
35436929 TTGGGGAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (53 bp):
GGCATACGAGCTGGCACATGCGCATGTGTCAGGGTATGTGTATACTGTTCTGA
Found at i:35436951 original size:53 final size:53
Alignment explanation
Indices: 35436832--35436954 Score: 129
Period size: 53 Copynumber: 2.3 Consensus size: 53
35436822 TGTGTGGCAT
* * * * *
35436832 ATGGGCTGGCACATGCGCATGTGTTAGGGTATGTGTATACTGTTCTGAGGCAT
1 ATGGGCTGACACATGGGCATGTGTCAGGGTATGTGTATACTGTTCTGAGGAAC
* * * * * * * *
35436885 ACGAGCTGTCACATGGGCGTGTGTCAGGGTGTGTGTATATTGTTTTGGGGAAC
1 ATGGGCTGACACATGGGCATGTGTCAGGGTATGTGTATACTGTTCTGAGGAAC
35436938 ATGGGCTGACACATGGG
1 ATGGGCTGACACATGGG
35436955 TGTGAGTACA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.19, C:0.15, G:0.37, T:0.30
Consensus pattern (53 bp):
ATGGGCTGACACATGGGCATGTGTCAGGGTATGTGTATACTGTTCTGAGGAAC
Found at i:35437572 original size:29 final size:29
Alignment explanation
Indices: 35437535--35437616 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
35437525 CGGGGGTATT
*
35437535 ATGTTTGCATCTATAACTGTATCTAT-ATC
1 ATGTCTGCATCTATAACTGTATCTATGA-C
* * *
35437564 ATGTCTGCATCCT-TAACTATATTTGTGAC
1 ATGTCTGCAT-CTATAACTGTATCTATGAC
*
35437593 ATGACTGCATCTATAACTGTATCT
1 ATGTCTGCATCTATAACTGTATCT
35437617 CTGCTTCGAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.05
29 38 0.88
30 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (29 bp):
ATGTCTGCATCTATAACTGTATCTATGAC
Found at i:35437630 original size:17 final size:17
Alignment explanation
Indices: 35437608--35437650 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
35437598 TGCATCTATA
*
35437608 ACTGTATCTCTG-CTTCG
1 ACTGTATCTCTGACAT-G
35437625 ACTGTATCTCTGACATG
1 ACTGTATCTCTGACATG
35437642 ACTGTATCT
1 ACTGTATCT
35437651 ATAACTGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (17 bp):
ACTGTATCTCTGACATG
Found at i:35439334 original size:2 final size:2
Alignment explanation
Indices: 35439329--35439357 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35439319 ATATATATAT
35439329 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 A
35439358 ACATTCAAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35440233 original size:28 final size:29
Alignment explanation
Indices: 35440199--35440259 Score: 115
Period size: 28 Copynumber: 2.1 Consensus size: 29
35440189 TATGAAATTA
35440199 AAAACATATATAAAAATCCAAAACTA-TT
1 AAAACATATATAAAAATCCAAAACTATTT
35440227 AAAACATATATAAAAATCCAAAACTATTT
1 AAAACATATATAAAAATCCAAAACTATTT
35440256 AAAA
1 AAAA
35440260 TCACATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (29 bp):
AAAACATATATAAAAATCCAAAACTATTT
Found at i:35440267 original size:28 final size:28
Alignment explanation
Indices: 35440199--35440268 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
35440189 TATGAAATTA
*
35440199 AAAACATATATAAAAATCCAAAACTATT
1 AAAACATACATAAAAATCCAAAACTATT
*
35440227 AAAACATATATAAAAATCCAAAACTATT
1 AAAACATACATAAAAATCCAAAACTATT
*
35440255 TAAA-ATCACATAAA
1 AAAACAT-ACATAAA
35440269 TTTATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 2 0.05
28 37 0.95
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.24
Consensus pattern (28 bp):
AAAACATACATAAAAATCCAAAACTATT
Found at i:35442765 original size:119 final size:119
Alignment explanation
Indices: 35442549--35442766 Score: 328
Period size: 119 Copynumber: 1.8 Consensus size: 119
35442539 GATATTTTGA
* * * *
35442549 GGTATCGCATATGTTGCGAGTTCTCGACAGCTCGTATGAGCAGCATCATTTTCTGGTAACAGAGT
1 GGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTATGAGCAGCATCATATACTGGTAACAGAGT
*
35442614 TGATACATACATGAGAATGAAATTCTAGATTATAGCATATTGTATCGATGGCTG
66 TGATACAGACATGAGAATGAAATTCTAGATTATAGCATATTGTATCGATGGCTG
* * * *
35442668 GGTACCGCATATGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTATACTGGTAACAGAGT
1 GGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTATGAGCAGCATCATATACTGGTAACAGAGT
* * *
35442733 TGATACAGACATGAGGATGAAATTTTGGATTATA
66 TGATACAGACATGAGAATGAAATTCTAGATTATA
35442767 CCTTGTGGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 87 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (119 bp):
GGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTATGAGCAGCATCATATACTGGTAACAGAGT
TGATACAGACATGAGAATGAAATTCTAGATTATAGCATATTGTATCGATGGCTG
Found at i:35444956 original size:21 final size:22
Alignment explanation
Indices: 35444932--35444972 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35444922 TATATAAATT
35444932 ATTT-AAATATTTTTATTTTAA
1 ATTTCAAATATTTTTATTTTAA
* *
35444953 ATTTCAAATCTTTTTTTTTT
1 ATTTCAAATATTTTTATTTT
35444973 TGAAAAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTCAAATATTTTTATTTTAA
Found at i:35446582 original size:25 final size:25
Alignment explanation
Indices: 35446546--35446604 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
35446536 TAGCTCATTT
* *
35446546 GAGCCTAAATAAGGTTAACTCTTAC
1 GAGCCTAGATAAAGTTAACTCTTAC
*
35446571 GAGCCTAGATAAAGTTAGCTCTTAC
1 GAGCCTAGATAAAGTTAACTCTTAC
*
35446596 AAGCCTAGA
1 GAGCCTAGA
35446605 CAGAGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (25 bp):
GAGCCTAGATAAAGTTAACTCTTAC
Found at i:35446611 original size:25 final size:25
Alignment explanation
Indices: 35446559--35446611 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
35446549 CCTAAATAAG
* *
35446559 GTTAACTCTTACGAGCCTAGATAAA
1 GTTAACTCTTACAAGCCTAGACAAA
* *
35446584 GTTAGCTCTTACAAGCCTAGACAGA
1 GTTAACTCTTACAAGCCTAGACAAA
35446609 GTT
1 GTT
35446612 TAACCAGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (25 bp):
GTTAACTCTTACAAGCCTAGACAAA
Found at i:35455924 original size:18 final size:18
Alignment explanation
Indices: 35455898--35455958 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
35455888 TGAGGTGGAT
*
35455898 GAGGGTATCCTCCATGAG
1 GAGGATATCCTCCATGAG
*
35455916 GAGGATATCCTGCA-G-G
1 GAGGATATCCTCCATGAG
*
35455932 TG-GG-TATCCGCCATGAG
1 -GAGGATATCCTCCATGAG
35455949 GAGGATATCC
1 GAGGATATCC
35455959 CGCAGGTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 5 0.15
18 17 0.50
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (18 bp):
GAGGATATCCTCCATGAG
Found at i:35455946 original size:33 final size:33
Alignment explanation
Indices: 35455900--35455967 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
35455890 AGGTGGATGA
* *
35455900 GGGTATCCTCCATGAGGAGGATATCCTGCAGGT
1 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
35455933 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
1 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
35455966 GG
1 GG
35455968 AGGATAACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.37, T:0.21
Consensus pattern (33 bp):
GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
Done.