Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 72 of 150
Found at i:21442276 original size:75 final size:73
Alignment explanation
Indices: 21442086--21442275 Score: 219
Period size: 75 Copynumber: 2.6 Consensus size: 73
21442076 TCGTGTTCTC
* *
21442086 AAAAAA-TTCTCGTGCTTAAAAATTTTCGTGTTTTCAAAAATTTTTCGTATTTCAAAAAATTTTC
1 AAAAAATTTCTCGTGTTTAAAAATTTTCGTGTTTTCAAAAAATTTTCGTATTT-AAAAAATTTTC
*
21442150 GCGTTTTCA
65 GCATTTTCA
* *
21442159 AAAATATCTT-TCGTGTTTCAAAGAA-TTTCGTGTTTTCAAAAAATTTTC-TCATGCTT-AAAAT
1 AAAAAAT-TTCTCGTGTTT-AAA-AATTTTCGTGTTTTCAAAAAATTTTCGT-AT--TTAAAAAA
* *
21442220 TTTTTGTATTTTCA
60 TTTTCGCATTTTCA
21442234 AAAAAATTTCTCGTGTTTAAAAATTTTCGTGTTTTCAAAAAA
1 AAAAAATTTCTCGTGTTTAAAAATTTTCGTGTTTTCAAAAAA
21442276 AAAATGTTCT
Statistics
Matches: 100, Mismatches: 8, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
73 7 0.07
74 31 0.31
75 58 0.58
76 2 0.02
77 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (73 bp):
AAAAAATTTCTCGTGTTTAAAAATTTTCGTGTTTTCAAAAAATTTTCGTATTTAAAAAATTTTCG
CATTTTCA
Found at i:21442315 original size:39 final size:39
Alignment explanation
Indices: 21442050--21442318 Score: 164
Period size: 37 Copynumber: 7.2 Consensus size: 39
21442040 AAAAAGGAAG
* * *
21442050 AAAAAAATTTC-GTGTTACAAAGAA-TTTCGTGTTCTC--
1 AAAAAAATTTCTCTGTTTCAAA-AATTTTCGTGTTTTCAA
*
21442086 -AAAAAA-TTCTCGTGCTT-AAAAATTTTCGTGTTTTC--
1 AAAAAAATTTCTC-TGTTTCAAAAATTTTCGTGTTTTCAA
* * *
21442121 --AAAAATTTTTCGTATTTCAAAAAATTTTCGCGTTTTCAA
1 AAAAAAATTTCTC-TGTTTC-AAAAATTTTCGTGTTTTCAA
* ** *
21442160 AAATATCTTTC-GTGTTTCAAAGAA-TTTCGTGTTTTC--
1 AAAAAAATTTCTCTGTTTCAAA-AATTTTCGTGTTTTCAA
* * * * *
21442196 AAAAAATTTTCTCATGCTT-AAAATTTTTTGTATTTTC--
1 AAAAAAATTTCTC-TGTTTCAAAAATTTTCGTGTTTTCAA
21442233 AAAAAAATTTCTCGTGTTT-AAAAATTTTCGTGTTTTCAAA
1 AAAAAAATTTCTC-TGTTTCAAAAATTTTCGTGTTTTC-AA
*
21442273 AAAAAAATGTTCT-TGTTTCAAAAATTTTTGTGTTTTCAA
1 AAAAAAAT-TTCTCTGTTTCAAAAATTTTCGTGTTTTCAA
21442312 AAAAAAA
1 AAAAAAA
21442319 AAATGTGTTT
Statistics
Matches: 184, Mismatches: 30, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
34 10 0.05
35 28 0.15
36 12 0.07
37 61 0.33
38 18 0.10
39 21 0.11
40 25 0.14
41 9 0.05
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (39 bp):
AAAAAAATTTCTCTGTTTCAAAAATTTTCGTGTTTTCAA
Found at i:21443323 original size:9 final size:9
Alignment explanation
Indices: 21443309--21443348 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
21443299 TGGAAACAAG
21443309 AAAAAAGAA
1 AAAAAAGAA
21443318 AAAAAAGAA
1 AAAAAAGAA
21443327 AAAAAAGGAA
1 AAAAAA-GAA
* *
21443337 AGAAAACAA
1 AAAAAAGAA
21443346 AAA
1 AAA
21443349 GAAACAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:21443337 original size:19 final size:18
Alignment explanation
Indices: 21443302--21443348 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
21443292 TCAATTATGG
21443302 AAACAAGAAAAAAGAAAAA
1 AAACAA-AAAAAAGAAAAA
* *
21443321 AAAGAAAAAAAAGGAAAGA
1 AAACAAAAAAAA-GAAAAA
21443340 AAACAAAAA
1 AAACAAAAA
21443349 GAAACAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (18 bp):
AAACAAAAAAAAGAAAAA
Found at i:21448950 original size:13 final size:14
Alignment explanation
Indices: 21448932--21448960 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21448922 TTTGGATGCA
21448932 TTGTTGTG-TGAAT
1 TTGTTGTGTTGAAT
21448945 TTGTTGTGTTGAAT
1 TTGTTGTGTTGAAT
21448959 TT
1 TT
21448961 CCGAATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TTGTTGTGTTGAAT
Found at i:21450098 original size:7 final size:7
Alignment explanation
Indices: 21450082--21450145 Score: 51
Period size: 7 Copynumber: 8.7 Consensus size: 7
21450072 TATCAATTAT
*
21450082 AGAAACA
1 AGAAAAA
21450089 AGAAAAAA
1 AG-AAAAA
21450097 GAGAAAAA
1 -AGAAAAA
21450105 AGAAAAA
1 AGAAAAA
21450112 AGAAAAGA
1 AGAAAA-A
21450120 A-AAAAA
1 AGAAAAA
*
21450126 GGAAAGAA
1 AGAAA-AA
21450134 A-ACAAAA
1 AGA-AAAA
21450141 AGAAA
1 AGAAA
21450146 CAATGGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
6 1 0.02
7 28 0.60
8 16 0.34
9 2 0.04
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:21450107 original size:16 final size:16
Alignment explanation
Indices: 21450082--21450114 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21450072 TATCAATTAT
*
21450082 AGAAACAAGAAAAAAG
1 AGAAAAAAGAAAAAAG
21450098 AGAAAAAAGAAAAAAG
1 AGAAAAAAGAAAAAAG
21450114 A
1 A
21450115 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAG
Found at i:21450123 original size:13 final size:13
Alignment explanation
Indices: 21450088--21450135 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
21450078 TTATAGAAAC
21450088 AAGAAAAAAGAGAA
1 AAGAAAAAA-AGAA
*
21450102 AAAAGAAAAAAGAA
1 AAGA-AAAAAAGAA
*
21450116 AAGAAAAAAAGGA
1 AAGAAAAAAAGAA
21450129 AAGAAAA
1 AAGAAAA
21450136 CAAAAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 15 0.50
14 10 0.33
15 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:21454959 original size:27 final size:27
Alignment explanation
Indices: 21454929--21454982 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21454919 TAAAAGAGAA
* *
21454929 TTGTAATTCCAAAAGAGTGTAATTACT
1 TTGTAATTACAAAAGAATGTAATTACT
* *
21454956 TTGTAGTTACAAGAGAATGTAATTACT
1 TTGTAATTACAAAAGAATGTAATTACT
21454983 ATCCCAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (27 bp):
TTGTAATTACAAAAGAATGTAATTACT
Found at i:21460472 original size:27 final size:27
Alignment explanation
Indices: 21460442--21460494 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
21460432 ATTTAAAATA
21460442 ATTAATAAACATAAAAACCCTAATATC
1 ATTAATAAACATAAAAACCCTAATATC
* *
21460469 ATTAATAAAGATAATAACCCTAATAT
1 ATTAATAAACATAAAAACCCTAATAT
21460495 GAACTTACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (27 bp):
ATTAATAAACATAAAAACCCTAATATC
Found at i:21465812 original size:45 final size:45
Alignment explanation
Indices: 21465762--21465912 Score: 187
Period size: 45 Copynumber: 3.4 Consensus size: 45
21465752 AAGCCTAAAC
21465762 ATGAGTAAGACCATGGCAGAAAGACACCATGGCATCACACTATCG
1 ATGAGTAAGACCATGGCAGAAAGACACCATGGCATCACACTATCG
* * *
21465807 ATGAGTAAGACTATGGCAGAATGACAGCATGGCATCACACTATCG
1 ATGAGTAAGACCATGGCAGAAAGACACCATGGCATCACACTATCG
** * * * * *
21465852 ATGAGTAAGACCATAACAAAAAGATACTATGGCATCATGA-TATAG
1 ATGAGTAAGACCATGGCAGAAAGACACCATGGCATCA-CACTATCG
*
21465897 ATGAGTAAGGCCATGG
1 ATGAGTAAGACCATGG
21465913 TTGGAAGATA
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 88 0.99
46 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (45 bp):
ATGAGTAAGACCATGGCAGAAAGACACCATGGCATCACACTATCG
Found at i:21471229 original size:290 final size:291
Alignment explanation
Indices: 21470708--21471292 Score: 1091
Period size: 290 Copynumber: 2.0 Consensus size: 291
21470698 TCCAATAGTG
* *
21470708 TGTTTGAAAAATAGACGAAGACATAATGCATCAAATGTGCCAACATGAAAGAAAAAAAATGCTTA
1 TGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAAAAAAAATGCTTA
21470773 ACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTATGTATTA
66 ACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTATGTATTA
21470838 GCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTATTACATTT
131 GCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTATTACATTT
21470903 ATTTAAGACATATGTGACAAACGTGATGAAATTTTAGTTCCTTCAAATTCTATTCCTAAACATGT
196 ATTTAAGACATATGTGACAAACGTGATGAAATTTTAGTTCCTTCAAATTCTATTCCTAAACATGT
*
21470968 GGATGGGAATGATTTGCAAGCTAAAATAATT
261 GGATGAGAATGATTTGCAAGCTAAAATAATT
21470999 TGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAG-AAAAAAATGCTTA
1 TGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAAAAAAAATGCTTA
* *
21471063 ACGCTAACTTGTCGCTCAGGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTATGTATTA
66 ACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTATGTATTA
* *
21471128 GCCAAAACTAGAAATCATATACCTTTAACCTATTGATGCCTAATAATGTTATGTTTATTACATTT
131 GCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTATTACATTT
*
21471193 ATTTAAGACATATGTGACAAACGTGATGGAATTTTAGTTCCTTCAAATTCTATTCCTAAACATGT
196 ATTTAAGACATATGTGACAAACGTGATGAAATTTTAGTTCCTTCAAATTCTATTCCTAAACATGT
21471258 GGATGAGAATGATTTGCAAGCTAAAATAATT
261 GGATGAGAATGATTTGCAAGCTAAAATAATT
21471289 TGTT
1 TGTT
21471293 AATAATCTCT
Statistics
Matches: 286, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
290 237 0.83
291 49 0.17
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (291 bp):
TGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAAAAAAAATGCTTA
ACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTATGTATTA
GCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTATTACATTT
ATTTAAGACATATGTGACAAACGTGATGAAATTTTAGTTCCTTCAAATTCTATTCCTAAACATGT
GGATGAGAATGATTTGCAAGCTAAAATAATT
Found at i:21471595 original size:23 final size:23
Alignment explanation
Indices: 21471533--21471588 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
21471523 GCTCACTCAA
*
21471533 TTATATGTTAAATTATTATAATT
1 TTATAAGTTAAATTATTATAATT
21471556 TTATAAGTTAAATTATTATAATT
1 TTATAAGTTAAATTATTATAATT
21471579 TTATAAGTTA
1 TTATAAGTTA
21471589 CTTTATTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (23 bp):
TTATAAGTTAAATTATTATAATT
Found at i:21473681 original size:25 final size:26
Alignment explanation
Indices: 21473635--21473691 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
21473625 GCTCAATCAT
* * *
21473635 AGTCATACATATCATAGAGCCA-ATC
1 AGTCATACATAACAAAGAGCCATAAC
21473660 AGTCATACATAACACAAG-GCCATAAC
1 AGTCATACATAACA-AAGAGCCATAAC
21473686 AGTCAT
1 AGTCAT
21473692 TTCATCTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (26 bp):
AGTCATACATAACAAAGAGCCATAAC
Found at i:21473731 original size:27 final size:27
Alignment explanation
Indices: 21473701--21473817 Score: 141
Period size: 27 Copynumber: 4.3 Consensus size: 27
21473691 TTTCATCTCT
**
21473701 TAGGGGTATAAAAGTCATTTTACCCTA
1 TAGGGGTATATCAGTCATTTTACCCTA
*
21473728 TAGGGGTATTTC-GATCATTTTACCCTA
1 TAGGGGTATATCAG-TCATTTTACCCTA
* *
21473755 T-GAGGGTATTTCGGTCATTTTACCCTA
1 TAG-GGGTATATCAGTCATTTTACCCTA
21473782 T-GAGGGTATATCAGTCATTTTACCCTA
1 TAG-GGGTATATCAGTCATTTTACCCTA
21473809 TAGGGGTAT
1 TAGGGGTAT
21473818 TTTGATCATT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
26 2 0.02
27 77 0.95
28 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (27 bp):
TAGGGGTATATCAGTCATTTTACCCTA
Found at i:21473826 original size:27 final size:27
Alignment explanation
Indices: 21473715--21473832 Score: 161
Period size: 27 Copynumber: 4.4 Consensus size: 27
21473705 GGTATAAAAG
21473715 TCATTTTACCCTAT-AGGGGTATTTCGA
1 TCATTTTACCCTATGA-GGGTATTTCGA
*
21473742 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGA
*
21473769 TCATTTTACCCTATGAGGGTATATC-A
1 TCATTTTACCCTATGAGGGTATTTCGA
*
21473795 GTCATTTTACCCTAT-AGGGGTATTTTGA
1 -TCATTTTACCCTATGA-GGGTATTTCGA
21473823 TCATTTTACC
1 TCATTTTACC
21473833 TATTTTAGGG
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
26 1 0.01
27 79 0.96
28 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGAGGGTATTTCGA
Found at i:21474102 original size:19 final size:19
Alignment explanation
Indices: 21474067--21474104 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21474057 GTGTGGGGCC
*
21474067 CACGAGCCCATTGAGCCCA
1 CACGAGCCCATTCAGCCCA
21474086 CACG-GCCCATTTCAGCCCA
1 CACGAGCCCA-TTCAGCCCA
21474105 ACGTGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (19 bp):
CACGAGCCCATTCAGCCCA
Found at i:21481460 original size:22 final size:22
Alignment explanation
Indices: 21481435--21481488 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
21481425 TAAATTATCC
*
21481435 TAATAAACTAGGACAATTACTT
1 TAATAAACTAGGAAAATTACTT
21481457 TAATAAACTAGGAAAATTACTT
1 TAATAAACTAGGAAAATTACTT
21481479 TAATTAAACT
1 TAA-TAAACT
21481489 TAATTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (22 bp):
TAATAAACTAGGAAAATTACTT
Found at i:21482735 original size:13 final size:14
Alignment explanation
Indices: 21482707--21482736 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21482697 CAATTTTATT
21482707 AATGAAATATTTAA
1 AATGAAATATTTAA
21482721 AATGAAATA-TTAA
1 AATGAAATATTTAA
21482734 AAT
1 AAT
21482737 ATAACATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AATGAAATATTTAA
Found at i:21489262 original size:26 final size:26
Alignment explanation
Indices: 21489233--21489292 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
21489223 AACTTGCCAA
*
21489233 GCCCACTAGAGACCACAGTTCACTAG
1 GCCCACTAGAGACCACAGCTCACTAG
* **
21489259 GCCCATTAGAGACCATGGCTCACTAG
1 GCCCACTAGAGACCACAGCTCACTAG
21489285 GCCCACTA
1 GCCCACTA
21489293 ATGATCCCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (26 bp):
GCCCACTAGAGACCACAGCTCACTAG
Found at i:21493090 original size:9 final size:9
Alignment explanation
Indices: 21493076--21493151 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
21493066 TTTGGTTAAA
21493076 AATTAACCG
1 AATTAACCG
*
21493085 AATTAACTG
1 AATTAACCG
*
21493094 AATTAACCA
1 AATTAACCG
21493103 AATTAACCG
1 AATTAACCG
*
21493112 AATTAACTG
1 AATTAACCG
* *
21493121 AATTACCCA
1 AATTAACCG
21493130 AATT-ACCTG
1 AATTAACC-G
*
21493139 AATTACCCG
1 AATTAACCG
21493148 AATT
1 AATT
21493152 GAATCACTAC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
8 2 0.04
9 50 0.93
10 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:21493107 original size:27 final size:27
Alignment explanation
Indices: 21493075--21493143 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
21493065 TTTTGGTTAA
21493075 AAATTAACCGAATTAACTGAATTAACC
1 AAATTAACCGAATTAACTGAATTAACC
*
21493102 AAATTAACCGAATTAACTGAATTACCC
1 AAATTAACCGAATTAACTGAATTAACC
21493129 AAATT-ACCTGAATTA
1 AAATTAACC-GAATTA
21493144 CCCGAATTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 3 0.08
27 37 0.93
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (27 bp):
AAATTAACCGAATTAACTGAATTAACC
Found at i:21493196 original size:37 final size:37
Alignment explanation
Indices: 21493150--21493224 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
21493140 ATTACCCGAA
* * *
21493150 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATCACATAACTCT
21493187 TTGAATCACTACATAATTAAAAACATCACATAACTCT
1 TTGAATCACTACATAATTAAAAACATCACATAACTCT
21493224 T
1 T
21493225 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.33
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATCACATAACTCT
Found at i:21493399 original size:38 final size:39
Alignment explanation
Indices: 21493355--21493471 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
21493345 ACTTAAGGGT
*
21493355 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
*
21493393 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
21493432 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
21493471 T
1 T
21493472 TGGGTAATTG
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 27 0.36
39 49 0.64
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTAGGTAATTGGG
Found at i:21493486 original size:13 final size:13
Alignment explanation
Indices: 21493452--21493489 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
21493442 TTTTAGTTTT
*
21493452 ATTGGGTTAGGTA
1 ATTGGGTTGGGTA
21493465 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
21493478 ATTGGGTTGGGT
1 ATTGGGTTGGGT
21493490 TGGATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:21497351 original size:16 final size:17
Alignment explanation
Indices: 21497330--21497363 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21497320 ACTATTAAAA
21497330 AACTTAA-ATATCATTT
1 AACTTAATATATCATTT
*
21497346 AACTTAATTTATCATTT
1 AACTTAATATATCATTT
21497363 A
1 A
21497364 GTTTACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
AACTTAATATATCATTT
Found at i:21503172 original size:22 final size:22
Alignment explanation
Indices: 21503147--21503207 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
21503137 AGCTTGCTAG
*
21503147 GCACTAAGCCTAAATAACACAA
1 GCACTAAGCCTGAATAACACAA
* *
21503169 GCACTAAGCCTGAATAACCCCA
1 GCACTAAGCCTGAATAACACAA
21503191 GCACTAAGCCTGAATAA
1 GCACTAAGCCTGAATAA
21503208 TACCTCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.15
Consensus pattern (22 bp):
GCACTAAGCCTGAATAACACAA
Found at i:21506849 original size:25 final size:25
Alignment explanation
Indices: 21506797--21506882 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
21506787 TCATGTACAT
* * * * *
21506797 GTATGCTCATACGAGCTGTGAATTG
1 GTATGCTCACACAAGCTATAAATCG
* * * *
21506822 GTATGCTCACTCAAGTTGTAGATCG
1 GTATGCTCACACAAGCTATAAATCG
* *
21506847 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACAAGCTATAAATCG
21506872 GTATGCTCACA
1 GTATGCTCACA
21506883 TGAGTTGTGG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACAAGCTATAAATCG
Found at i:21507296 original size:16 final size:17
Alignment explanation
Indices: 21507265--21507297 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21507255 ATACGGATAA
21507265 ATTTATCTCAATTCAAT
1 ATTTATCTCAATTCAAT
*
21507282 ATTTATTTC-ATTCAAT
1 ATTTATCTCAATTCAAT
21507298 TTACCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTATCTCAATTCAAT
Found at i:21512470 original size:40 final size:36
Alignment explanation
Indices: 21512397--21512470 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
21512387 TGGAGTAGAT
*
21512397 TAGTATATCATTAACAAACACAACCACAAATCTATC
1 TAGTATATCATTAACAAACAAAACCACAAATCTATC
* *
21512433 TAGTATATTATTAATAAACAAAACCACAAATCTATC
1 TAGTATATCATTAACAAACAAAACCACAAATCTATC
21512469 TA
1 TA
21512471 ATTGAGGCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (36 bp):
TAGTATATCATTAACAAACAAAACCACAAATCTATC
Found at i:21515918 original size:24 final size:24
Alignment explanation
Indices: 21515805--21515931 Score: 91
Period size: 24 Copynumber: 5.2 Consensus size: 24
21515795 TCCAAATAAT
*
21515805 TGGCTCT-TATGAGCTACCTGATTAA
1 TGGCTCTCTA-GAGCTTCCTG-TTAA
* *
21515830 TGGCTCTCTAGAGCTTCCTGATAT
1 TGGCTCTCTAGAGCTTCCTGTTAA
* * * *
21515854 TGGCT-TACTTGAACTTCTTGTTAT
1 TGGCTCT-CTAGAGCTTCCTGTTAA
* * *
21515878 TGGCTC-GTATGATCTTCCCGTTAA
1 TGGCTCTCTA-GAGCTTCCTGTTAA
21515902 TGGCTCTCTAGAGCTT-CTGTTACA
1 TGGCTCTCTAGAGCTTCCTGTTA-A
21515926 TGGCTC
1 TGGCTC
21515932 ACATGAGCTT
Statistics
Matches: 80, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
23 7 0.09
24 53 0.66
25 18 0.22
26 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (24 bp):
TGGCTCTCTAGAGCTTCCTGTTAA
Found at i:21521401 original size:24 final size:24
Alignment explanation
Indices: 21521373--21521420 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21521363 TGCCATATAA
21521373 ACCAGAATATACGCTGCAAAAGTT
1 ACCAGAATATACGCTGCAAAAGTT
21521397 ACCAGAATATACGCTGCAAAAGTT
1 ACCAGAATATACGCTGCAAAAGTT
21521421 GGATAGTATG
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:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ACCAGAATATACGCTGCAAAAGTT
Found at i:21522906 original size:20 final size:20
Alignment explanation
Indices: 21522871--21522919 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
21522861 ATCATGGTCT
*
21522871 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
21522890 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
21522910 TTGCTTACTT
1 TTGCTTACTT
21522920 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:21523182 original size:49 final size:50
Alignment explanation
Indices: 21523122--21523258 Score: 154
Period size: 49 Copynumber: 2.8 Consensus size: 50
21523112 GATAATAGCA
* * * *
21523122 TGCCAAAGCCATGTCCTATACATGGTCTTACATGGGATGTT-TCATGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCAT-AACG
* *
21523171 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATAACGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATAAC-G
* * *
21523221 TGCCCATGCCATGTCCCAGACATGATCTTATATGGGAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
21523259 CTCATTCCCC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
48 5 0.07
49 36 0.49
50 32 0.44
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATAACG
Found at i:21524595 original size:21 final size:21
Alignment explanation
Indices: 21524569--21524609 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21524559 AAGCTCGAAG
*
21524569 GCTAAACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
* *
21524590 GCTAAATAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
21524610 GGTTGAACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:21528213 original size:68 final size:68
Alignment explanation
Indices: 21528138--21528274 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
21528128 ATCATACCTT
*
21528138 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACCACACATCGTAGC
1 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTAGC
21528203 ACC
66 ACC
*
21528206 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTATC
1 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTAGC
21528271 ACC
66 ACC
21528274 T
1 T
21528275 TTCAGTTGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (68 bp):
TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTAGC
ACC
Found at i:21533288 original size:5 final size:5
Alignment explanation
Indices: 21533250--21533285 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
21533240 TACTGAACCT
*
21533250 AACAC AACAC AACAC AACAC AACAC AACAC ATCAC A
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC A
21533286 TCAAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.58, C:0.39, G:0.00, T:0.03
Consensus pattern (5 bp):
AACAC
Found at i:21537334 original size:49 final size:48
Alignment explanation
Indices: 21537261--21537385 Score: 126
Period size: 49 Copynumber: 2.5 Consensus size: 48
21537251 CTTATAAGCG
*
21537261 TCCCGATAATTGGCTCTTCAGAGCTTCTCGATAAC-TGGCTCGTATGAGCT
1 TCCCGATAA-TGGCTCTT-AGAGCTTCCCG-TAACATGGCTCGTATGAGCT
* * *
21537311 TCCCGTTAATGGCTCTCTAGAGCTTCCCGTTACATGGTTCGTATGAGCT
1 TCCCGATAATGGCTCT-TAGAGCTTCCCGTAACATGGCTCGTATGAGCT
* * *
21537360 TCTCGGTATATGGCTCTGAAGAGCTT
1 TCCCGATA-ATGGCTCT-TAGAGCTT
21537386 TCTATTTACA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.05
49 37 0.58
50 24 0.38
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (48 bp):
TCCCGATAATGGCTCTTAGAGCTTCCCGTAACATGGCTCGTATGAGCT
Found at i:21537342 original size:24 final size:24
Alignment explanation
Indices: 21537261--21537339 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
21537251 CTTATAAGCG
*
21537261 TCCCGATAATTGGCTCTTCAGAGCT
1 TCCCGATAACTGGCTCTT-AGAGCT
* *
21537286 TCTCGATAACTGGCTCGTATGAGCT
1 TCCCGATAACTGGCTCTTA-GAGCT
*
21537311 TCCCGTTAA-TGGCTCTCTAGAGCT
1 TCCCGATAACTGGCTCT-TAGAGCT
21537335 TCCCG
1 TCCCG
21537340 TTACATGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
24 17 0.37
25 29 0.63
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.32
Consensus pattern (24 bp):
TCCCGATAACTGGCTCTTAGAGCT
Found at i:21537358 original size:25 final size:26
Alignment explanation
Indices: 21537299--21537376 Score: 92
Period size: 25 Copynumber: 3.1 Consensus size: 26
21537289 CGATAACTGG
21537299 CTCGTATGAGCTTCCCGTTAATGGCT
1 CTCGTATGAGCTTCCCGTTAATGGCT
21537325 CTC-TA-GAGCTTCCCGTTACATGG-T
1 CTCGTATGAGCTTCCCGTTA-ATGGCT
* *
21537349 -TCGTATGAGCTTCTCGGTATATGGCT
1 CTCGTATGAGCTTCCCGTTA-ATGGCT
21537375 CT
1 CT
21537377 GAAGAGCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.05
24 16 0.36
25 21 0.48
26 4 0.09
27 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (26 bp):
CTCGTATGAGCTTCCCGTTAATGGCT
Found at i:21547637 original size:45 final size:44
Alignment explanation
Indices: 21547568--21547743 Score: 198
Period size: 45 Copynumber: 4.0 Consensus size: 44
21547558 ACGTGTACTG
* *
21547568 GGTACCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACC
1 GGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
*
21547612 AGGTATCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCCACC
1 -GGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
* *
21547657 GGGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCACC
1 -GGTATC-ATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
* * * *
21547702 GATTATCATTGACTAT-AAGGTTGG-TGCTATGTGTTGA-TCCAC
1 G-GTATCATTGATTATAAAGG-TGGTTGCTGTGTGCTGATTCCAC
21547744 TGTGTATCTG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
43 5 0.04
44 18 0.15
45 93 0.79
46 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.37
Consensus pattern (44 bp):
GGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
Found at i:21549679 original size:841 final size:841
Alignment explanation
Indices: 21548058--21549741 Score: 3359
Period size: 841 Copynumber: 2.0 Consensus size: 841
21548048 ATTAAATTTG
21548058 AATGAGTCTATTTTAACATAAGAGAGACGGGGCAAGAAAATGATTTTTATATTATGAGATATTTG
1 AATGAGTCTATTTTAACATAAGAGAGACGGGGCAAGAAAATGATTTTTATATTATGAGATATTTG
21548123 AATTTTAGTGAGACAGGGCTAGAATGATTTCAGAATCCCCTGTTCTGACTTTGGAAAATCATTAA
66 AATTTTAGTGAGACAGGGCTAGAATGATTTCAGAATCCCCTGTTCTGACTTTGGAAAATCATTAA
21548188 AAATTGTTCAAAAATAATTATGGGATAAAATTTATATGTTTAGAACCCTGAATGAGTCTATTTTC
131 AAATTGTTCAAAAATAATTATGGGATAAAATTTATATGTTTAGAACCCTGAATGAGTCTATTTTC
21548253 AAAATAAATAAACGAGAACATTATCCAAATTTTGTACTATGAAATAATTAATTTTAGTGAAGGAA
196 AAAATAAATAAACGAGAACATTATCCAAATTTTGTACTATGAAATAATTAATTTTAGTGAAGGAA
21548318 GGTCAGAACTATCGAGCAGTGAAATAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGATAAG
261 GGTCAGAACTATCGAGCAGTGAAATAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGATAAG
21548383 AAAAAAATTCTAAAAGTTTTATGGTAAGAAGATATATGAGTCTAGTTTCGAGAAAAATTAACGAA
326 AAAAAAATTCTAAAAGTTTTATGGTAAGAAGATATATGAGTCTAGTTTCGAGAAAAATTAACGAA
21548448 TCTTAATTTGGAGCTCGGTAGTTCGAGATATAAATAAATTAGTGACTCTAACTCAGACAGATAGT
391 TCTTAATTTGGAGCTCGGTAGTTCGAGATATAAATAAATTAGTGACTCTAACTCAGACAGATAGT
21548513 TTGAATTTACATGCAGGAAAATAGTGAAAGTATGGATAATGTTGTTTAAGTGTGTTATACACATT
456 TTGAATTTACATGCAGGAAAATAGTGAAAGTATGGATAATGTTGTTTAAGTGTGTTATACACATT
21548578 AAGGATGTGGAAGGGAGAAGAGGATGAGGAAAATTGGGAAATATATGAATGATTTGTGTTTAATT
521 AAGGATGTGGAAGGGAGAAGAGGATGAGGAAAATTGGGAAATATATGAATGATTTGTGTTTAATT
21548643 GGTAATATGCTCGATTATAATTGATAAACGATGAAATAGAAATGATGCTTATATTTGCGCATTAT
586 GGTAATATGCTCGATTATAATTGATAAACGATGAAATAGAAATGATGCTTATATTTGCGCATTAT
21548708 TGGTCATGATTTAAGCTCATGTGGGAAAATAAAGTTTCATAGTATGTGTGTATGGTATATTTGGA
651 TGGTCATGATTTAAGCTCATGTGGGAAAATAAAGTTTCATAGTATGTGTGTATGGTATATTTGGA
21548773 ATATGATTTAGCTTGAAGTAATGTCATGAATGGTTTATGAATTAACACATGTTGGTAAGTTTGAT
716 ATATGATTTAGCTTGAAGTAATGTCATGAATGGTTTATGAATTAACACATGTTGGTAAGTTTGAT
21548838 ACATTAATAAATGTTGTGCTCATCCATGCTCATAATGCTTATGATATATGTTTATTTGGTT
781 ACATTAATAAATGTTGTGCTCATCCATGCTCATAATGCTTATGATATATGTTTATTTGGTT
21548899 AATGAGTCTATTTTAACATAAGAGAGACGGGGCAAGAAAATGATTTTTATATTATGAGATATTTG
1 AATGAGTCTATTTTAACATAAGAGAGACGGGGCAAGAAAATGATTTTTATATTATGAGATATTTG
21548964 AATTTTAGTGAGACAGGGCTAGAATGATTTCAGAATCCCCTGTTCTGACTTTGGAAAATCATTAA
66 AATTTTAGTGAGACAGGGCTAGAATGATTTCAGAATCCCCTGTTCTGACTTTGGAAAATCATTAA
21549029 AAATTGTTCAAAAATAATTATGGGATAAAATTTATATGTTTAGAACCCTGAATGAGTCTATTTTC
131 AAATTGTTCAAAAATAATTATGGGATAAAATTTATATGTTTAGAACCCTGAATGAGTCTATTTTC
21549094 AAAATAAATAAACGAGAACATTATCCAAATTTTGTACTATGAAATAATTAATTTTAGTGAAGGAA
196 AAAATAAATAAACGAGAACATTATCCAAATTTTGTACTATGAAATAATTAATTTTAGTGAAGGAA
21549159 GGTCAGAACTATCGAGCAGTGAAATAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGATAAG
261 GGTCAGAACTATCGAGCAGTGAAATAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGATAAG
21549224 AAAAAAATTCTAAAAGTTTTATGGTAAGAAGATATATGAGTCTAGTTTCGAGAAAAATTAACGAA
326 AAAAAAATTCTAAAAGTTTTATGGTAAGAAGATATATGAGTCTAGTTTCGAGAAAAATTAACGAA
21549289 TCTTAATTTGGAGCTCGGTAGTTCGAGATATAAATAAATTAGTGACTCTAACTCAGACAGATAGT
391 TCTTAATTTGGAGCTCGGTAGTTCGAGATATAAATAAATTAGTGACTCTAACTCAGACAGATAGT
21549354 TTGAATTTACATGCAGGAAAATAGTGAAAGTATGGATAATGTTGTTTAAGTGTGTTATACACATT
456 TTGAATTTACATGCAGGAAAATAGTGAAAGTATGGATAATGTTGTTTAAGTGTGTTATACACATT
*
21549419 AAGGATGTGGAAGGGAGAGGAGGATGAGGAAAATTGGGAAATATATGAATGATTTGTGTTTAATT
521 AAGGATGTGGAAGGGAGAAGAGGATGAGGAAAATTGGGAAATATATGAATGATTTGTGTTTAATT
21549484 GGTAATATGCTCGATTATAATTGATAAACGATGAAATAGAAATGATGCTTATATTTGCGCATTAT
586 GGTAATATGCTCGATTATAATTGATAAACGATGAAATAGAAATGATGCTTATATTTGCGCATTAT
21549549 TGGTCATGATTTAAGCTCATGTGGGAAAATAAAGTTTCATAGTATGTGTGTATGGTATATTTGGA
651 TGGTCATGATTTAAGCTCATGTGGGAAAATAAAGTTTCATAGTATGTGTGTATGGTATATTTGGA
21549614 ATATGATTTAGCTTGAAGTAATGTCATGAATGGTTTATGAATTAACACATGTTGGTAAGTTTGAT
716 ATATGATTTAGCTTGAAGTAATGTCATGAATGGTTTATGAATTAACACATGTTGGTAAGTTTGAT
21549679 ACATTAATAAATGTTGTGCTCATCCATGCTCATAATGCTTATGATATATGTTTATTTGGTT
781 ACATTAATAAATGTTGTGCTCATCCATGCTCATAATGCTTATGATATATGTTTATTTGGTT
21549740 AA
1 AA
21549742 CATATTTGAT
Statistics
Matches: 842, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
841 842 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (841 bp):
AATGAGTCTATTTTAACATAAGAGAGACGGGGCAAGAAAATGATTTTTATATTATGAGATATTTG
AATTTTAGTGAGACAGGGCTAGAATGATTTCAGAATCCCCTGTTCTGACTTTGGAAAATCATTAA
AAATTGTTCAAAAATAATTATGGGATAAAATTTATATGTTTAGAACCCTGAATGAGTCTATTTTC
AAAATAAATAAACGAGAACATTATCCAAATTTTGTACTATGAAATAATTAATTTTAGTGAAGGAA
GGTCAGAACTATCGAGCAGTGAAATAGGGGAAACTTTAAAGAATAAACTGTACTTATTGGATAAG
AAAAAAATTCTAAAAGTTTTATGGTAAGAAGATATATGAGTCTAGTTTCGAGAAAAATTAACGAA
TCTTAATTTGGAGCTCGGTAGTTCGAGATATAAATAAATTAGTGACTCTAACTCAGACAGATAGT
TTGAATTTACATGCAGGAAAATAGTGAAAGTATGGATAATGTTGTTTAAGTGTGTTATACACATT
AAGGATGTGGAAGGGAGAAGAGGATGAGGAAAATTGGGAAATATATGAATGATTTGTGTTTAATT
GGTAATATGCTCGATTATAATTGATAAACGATGAAATAGAAATGATGCTTATATTTGCGCATTAT
TGGTCATGATTTAAGCTCATGTGGGAAAATAAAGTTTCATAGTATGTGTGTATGGTATATTTGGA
ATATGATTTAGCTTGAAGTAATGTCATGAATGGTTTATGAATTAACACATGTTGGTAAGTTTGAT
ACATTAATAAATGTTGTGCTCATCCATGCTCATAATGCTTATGATATATGTTTATTTGGTT
Found at i:21560632 original size:25 final size:25
Alignment explanation
Indices: 21560571--21560758 Score: 90
Period size: 25 Copynumber: 7.6 Consensus size: 25
21560561 ACACATAGAA
* * *
21560571 GCTCTTATAAGCGTCCCGATAATTG
1 GCTCTTATGAGCTTCCCGATAACTG
21560596 GCTCTTCA-GAGCTTCCCGATAACTG
1 GCTCTT-ATGAGCTTCCCGATAACTG
* **
21560621 GCTCTTATGAGCTACTTGATTAA-TG
1 GCTCTTATGAGCTTCCCGA-TAACTG
*
21560646 GCT-TTCTGGAGCTTCCCGAT-ACTG
1 GCTCTTAT-GAGCTTCCCGATAACTG
* * * * *
21560670 CCTCACT-TGAACTTCCC-ATTATTG
1 GCTC-TTATGAGCTTCCCGATAACTG
*
21560694 GCTCGTATGAGCTTCCC-ATTAA-TG
1 GCTCTTATGAGCTTCCCGA-TAACTG
* *
21560718 GCTCTCTA-GAGCTTCTCG-TTACATG
1 GCTCT-TATGAGCTTCCCGATAAC-TG
**
21560743 GCTCACATGAGCTTCC
1 GCTCTTATGAGCTTCC
21560759 TGTTACATGG
Statistics
Matches: 124, Mismatches: 24, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
23 6 0.05
24 48 0.39
25 65 0.52
26 5 0.04
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.34
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATAACTG
Found at i:21560729 original size:24 final size:24
Alignment explanation
Indices: 21560639--21560746 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
21560629 GAGCTACTTG
* *
21560639 ATTAATGGCTTTCTGGAGCTTCCC
1 ATTAATGGCTCTCTAGAGCTTCCC
* * * * *
21560663 GA-TACTGCCTCACTTGAACTTCCC
1 -ATTAATGGCTCTCTAGAGCTTCCC
* *
21560687 ATTATTGGCTC-GTATGAGCTTCCC
1 ATTAATGGCTCTCTA-GAGCTTCCC
*
21560711 ATTAATGGCTCTCTAGAGCTTCTC
1 ATTAATGGCTCTCTAGAGCTTCCC
*
21560735 GTTACATGGCTC
1 ATTA-ATGGCTC
21560747 ACATGAGCTT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.03
24 52 0.81
25 10 0.16
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (24 bp):
ATTAATGGCTCTCTAGAGCTTCCC
Found at i:21560763 original size:25 final size:25
Alignment explanation
Indices: 21560700--21560783 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
21560690 ATTGGCTCGT
** *
21560700 ATGAGCTTCCCATTA-ATGGCTCTC
1 ATGAGCTTCCTGTTACATGGCTCAC
21560724 -TAGAGCTT-CTCGTTACATGGCTCAC
1 AT-GAGCTTCCT-GTTACATGGCTCAC
21560749 ATGAGCTTCCTGTTACATGGCTCAC
1 ATGAGCTTCCTGTTACATGGCTCAC
*
21560774 ATAAGCTTCC
1 ATGAGCTTCC
21560784 CGGTTTATGG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.04
24 9 0.18
25 37 0.73
26 3 0.06
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCTGTTACATGGCTCAC
Found at i:21560793 original size:25 final size:24
Alignment explanation
Indices: 21560703--21560814 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
21560693 GGCTCGTATG
* * *
21560703 AGCTTCCCATTAATGGCTCTC-TA
1 AGCTTCCCGTTTATGGCTCACATA
* * *
21560726 GAGCTTCTCGTTACATGGCTCACATG
1 -AGCTTCCCGTT-TATGGCTCACATA
* *
21560752 AGCTTCCTGTTACATGGCTCACATA
1 AGCTTCCCGTT-TATGGCTCACATA
*
21560777 AGCTTCCCGGTTTATGGCTCA-AAA
1 AGCTTCCC-GTTTATGGCTCACATA
21560801 GAGCTTCCCGTTTA
1 -AGCTTCCCGTTTA
21560815 CAAGTCTGCA
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
24 16 0.22
25 53 0.73
26 4 0.05
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (24 bp):
AGCTTCCCGTTTATGGCTCACATA
Found at i:21565782 original size:22 final size:23
Alignment explanation
Indices: 21565754--21565799 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
21565744 GGATACACGG
21565754 ATCCAACCAAACACA-CCAGAAT
1 ATCCAACCAAACACACCCAGAAT
*
21565776 ATCCAACCTAACACACCCAGAAT
1 ATCCAACCAAACACACCCAGAAT
21565799 A
1 A
21565800 ATATAAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.48, C:0.37, G:0.04, T:0.11
Consensus pattern (23 bp):
ATCCAACCAAACACACCCAGAAT
Found at i:21567026 original size:24 final size:21
Alignment explanation
Indices: 21566995--21567042 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
21566985 AATAATAAGT
*
21566995 AAAT-TATACATA-TTATTAC
1 AAATGTATATATATTTATTAC
21567014 AAATGTATATATATTTATTAC
1 AAATGTATATATATTTATTAC
*
21567035 ACATGTAT
1 AAATGTAT
21567043 TTTATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 14 0.56
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (21 bp):
AAATGTATATATATTTATTAC
Found at i:21569785 original size:48 final size:48
Alignment explanation
Indices: 21569649--21569822 Score: 217
Period size: 48 Copynumber: 3.6 Consensus size: 48
21569639 ATAGTATAAC
*** * * * **
21569649 TATGGTCTTACAC-ATCGTCACATATCACACACTGAAGCCATAGCTCAGC
1 TATGGTCTTACACGAAAATCACATATCACAC-C-GATGCCATATCCCATA
*
21569698 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCCATA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCATA
* *
21569745 TATGGTCTTACATGAAAATCACGTATCACACCGATGCCATATCCCATA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCATA
21569793 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
21569823 TCACACTGAT
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
47 28 0.26
48 55 0.50
49 25 0.23
50 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCATA
Found at i:21575748 original size:7 final size:7
Alignment explanation
Indices: 21575736--21575778 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
21575726 CTAATTAGAT
21575736 ATTTTTA
1 ATTTTTA
21575743 ATTTTTA
1 ATTTTTA
21575750 TATTTTTTAA
1 -A-TTTTT-A
21575760 ATTTTTA
1 ATTTTTA
*
21575767 AATTTTA
1 ATTTTTA
21575774 ATTTT
1 ATTTT
21575779 AACATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 18 0.58
8 6 0.19
9 6 0.19
10 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:21575754 original size:15 final size:15
Alignment explanation
Indices: 21575734--21575778 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
21575724 CTCTAATTAG
21575734 ATATTTTTAATTTTT
1 ATATTTTTAATTTTT
21575749 ATATTTTTTAAATTTTT
1 ATA-TTTTT-AATTTTT
*
21575766 A-AATTTTAATTTT
1 ATATTTTTAATTTT
21575779 AACATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 6 0.22
17 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTTTTAATTTTT
Found at i:21580367 original size:56 final size:55
Alignment explanation
Indices: 21580300--21580453 Score: 186
Period size: 53 Copynumber: 2.8 Consensus size: 55
21580290 AGTAGTTACG
* * * *
21580300 TAAGAATCAAATTGCTAAAAGATAACATTCCATAATAATATCCTATAATATCTCAT
1 TAAGAATCAAATTGCTAAAAGATAA-ATTCCATAATAATATCCTACAAAATCCCAC
* ** *
21580356 TAAGAATCAAATTGTTAAGGGAT-AATT-CATAATAATATCTTACAAAATCCCAC
1 TAAGAATCAAATTGCTAAAAGATAAATTCCATAATAATATCCTACAAAATCCCAC
* *
21580409 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTA
1 TAAGAATCAAATTGCTAAAAGATAA-ATTCCATAATAATATCCTA
21580454 ACACCCCCTT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
53 40 0.49
54 4 0.05
55 3 0.04
56 34 0.42
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.31
Consensus pattern (55 bp):
TAAGAATCAAATTGCTAAAAGATAAATTCCATAATAATATCCTACAAAATCCCAC
Found at i:21581822 original size:16 final size:16
Alignment explanation
Indices: 21581798--21581839 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
21581788 TGATTCACTA
* *
21581798 TAATGGAATAGGGTTG
1 TAATGGAATAGAGCTG
*
21581814 TAATTGAATAGAGCTG
1 TAATGGAATAGAGCTG
21581830 TAATGGAATA
1 TAATGGAATA
21581840 AAACTGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:21584125 original size:50 final size:49
Alignment explanation
Indices: 21584000--21584297 Score: 251
Period size: 50 Copynumber: 5.9 Consensus size: 49
21583990 TGATAATAAC
* * * *
21584000 ATGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGA--TGT-TTTCTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATT-TG
* * * **
21584047 TACTACCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-TTG
* * ** * *
21584099 ATGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATTTG
* *
21584148 AGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-TTG
* * *
21584199 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---AT-T---TG
* * *
21584255 ATGCCAATACCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21584298 TTACCCAAAT
Statistics
Matches: 204, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
48 1 0.00
49 34 0.17
50 118 0.58
51 3 0.01
52 3 0.01
53 5 0.02
56 40 0.20
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (49 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATTTG
Found at i:21584184 original size:100 final size:104
Alignment explanation
Indices: 21584052--21584297 Score: 293
Period size: 100 Copynumber: 2.4 Consensus size: 104
21584042 TTCTGTACTA
* * ** * * *
21584052 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGATGCCCATGCCATGTCCC
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAACGCCATGTCCC
*
21584117 AAACATGGTCTTACGGGGGACCTCTC-ATCTC-A-G-TG
66 AAACATGGTCTTACAGGGGACCTCTCAATCTCAATGATG
* * * *
21584152 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAACGCCATGTCCC
* *
21584217 AGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
66 AAACATGGTCTTACAGGGGACCTCTC--AATCTCAATGATG
* * *
21584258 CCAATACCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21584298 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
100 77 0.63
103 5 0.04
104 1 0.01
105 1 0.01
106 38 0.31
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (104 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGATGCCAACGCCATGTCCC
AAACATGGTCTTACAGGGGACCTCTCAATCTCAATGATG
Found at i:21597586 original size:11 final size:11
Alignment explanation
Indices: 21597570--21597594 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21597560 GGTCATGTAG
21597570 AATAGACTTGT
1 AATAGACTTGT
21597581 AATAGACTTGT
1 AATAGACTTGT
21597592 AAT
1 AAT
21597595 GGCATAGCCA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATAGACTTGT
Found at i:21597657 original size:73 final size:73
Alignment explanation
Indices: 21597535--21597694 Score: 275
Period size: 73 Copynumber: 2.2 Consensus size: 73
21597525 TAGGGTATTC
* *
21597535 CATTGAACCAAACAACTATTTGTGTGGTCATGTAGAATAGACTTGTAATAGACTTGTAATGGCAT
1 CATTGAACCAAACAACTATTTGTGTGGGCATGTAGAATAGACTTATAATAGACTTGTAATGGCAT
21597600 AGCCATTA
66 AGCCATTA
* * *
21597608 CATTGAACCAAACAACTGTTTGTGTGGGCCTGTAGAATATACTTATAATAGACTTGTAATGGCAT
1 CATTGAACCAAACAACTATTTGTGTGGGCATGTAGAATAGACTTATAATAGACTTGTAATGGCAT
21597673 AGCCATTA
66 AGCCATTA
21597681 CATTGAACCAAACA
1 CATTGAACCAAACA
21597695 TTACCTAAGT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 82 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (73 bp):
CATTGAACCAAACAACTATTTGTGTGGGCATGTAGAATAGACTTATAATAGACTTGTAATGGCAT
AGCCATTA
Found at i:21601805 original size:23 final size:22
Alignment explanation
Indices: 21601758--21601801 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
21601748 ATAAAATTAT
*
21601758 TAAATATTAAAATAATATAATA
1 TAAATATTAAAATAATATAAAA
21601780 TAAATAATTAAAATAAT-TAAAA
1 TAAAT-ATTAAAATAATATAAAA
21601802 ATAATATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATATTAAAATAATATAAAA
Found at i:21616267 original size:15 final size:15
Alignment explanation
Indices: 21616247--21616279 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
21616237 TAACTATTTT
*
21616247 TATTATTATTGTTAC
1 TATTATTAATGTTAC
21616262 TATTATTAATGTTAC
1 TATTATTAATGTTAC
21616277 TAT
1 TAT
21616280 AACTATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (15 bp):
TATTATTAATGTTAC
Found at i:21616304 original size:18 final size:18
Alignment explanation
Indices: 21616283--21616321 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21616273 TTACTATAAC
21616283 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
*
21616301 TATTAGTTTATATGTTTA
1 TATTAGTTTATATATTTA
21616319 TAT
1 TAT
21616322 ACCTATGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:21617844 original size:13 final size:13
Alignment explanation
Indices: 21617778--21617848 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
21617768 ATATCTATCT
*
21617778 ATATAAACATTTC
1 ATATAATCATTTC
*
21617791 GTATAATCACTTT-
1 ATATAATCA-TTTC
21617804 ATATAA-CTATTTCC
1 ATATAATC-ATTT-C
* **
21617818 ATTTAATCGGTTC
1 ATATAATCATTTC
21617831 ATATAATCATTTC
1 ATATAATCATTTC
21617844 ATATA
1 ATATA
21617849 CCGAATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
12 4 0.09
13 29 0.66
14 10 0.23
15 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (13 bp):
ATATAATCATTTC
Found at i:21623327 original size:28 final size:26
Alignment explanation
Indices: 21623296--21623358 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
21623286 ACAGAATTTT
* *
21623296 CCACTAAGTATTCATTTAGCAGAGATCC
1 CCACAAAGGATTCATTT--CAGAGATCC
* *
21623324 CCACAAAGGCTTCCTTTCAGAGATCC
1 CCACAAAGGATTCATTTCAGAGATCC
21623350 CCACAAAGG
1 CCACAAAGG
21623359 CTTTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 18 0.58
28 13 0.42
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (26 bp):
CCACAAAGGATTCATTTCAGAGATCC
Found at i:21623384 original size:29 final size:29
Alignment explanation
Indices: 21623316--21623444 Score: 108
Period size: 29 Copynumber: 4.7 Consensus size: 29
21623306 TTCATTTAGC
* * *
21623316 AGAGATCCCCACAAAGGCTTC-CTTT--C
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
* *
21623342 AGAGATCCCCACAAAGGCTTTTATTTAAT
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
* *
21623371 AGAGATTGTCACAAAGGCTTCTATTTAAT
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
* * * *
21623400 AGTGATCGCCATAAAGGCTTC-ACTTCAT
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
*
21623428 AGATAT--CCACAAAGGCT
1 AGAGATCGCCACAAAGGCT
21623445 CACTTATACT
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
26 30 0.36
27 3 0.04
28 9 0.11
29 42 0.50
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (29 bp):
AGAGATCGCCACAAAGGCTTCTATTTAAT
Found at i:21623700 original size:30 final size:30
Alignment explanation
Indices: 21623664--21623725 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
21623654 GAATCATACT
* *
21623664 TGATAGACTCATTCACATTTGACTTGGTCA
1 TGATAGACTCATTCACAATAGACTTGGTCA
* * *
21623694 TGATAGAGTCTTTCACAATAGACTTGTTCA
1 TGATAGACTCATTCACAATAGACTTGGTCA
21623724 TG
1 TG
21623726 TCATTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
TGATAGACTCATTCACAATAGACTTGGTCA
Found at i:21626190 original size:27 final size:27
Alignment explanation
Indices: 21626128--21626190 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
21626118 AGCATAGTTT
*
21626128 TCGCCAAATCACATCTGGAAGCACAGC
1 TCGCCAAATCACATATGGAAGCACAGC
* *
21626155 TCACTAAATCACATATGTG-AGCACAGC
1 TCGCCAAATCACATATG-GAAGCACAGC
21626182 TCGCCAAAT
1 TCGCCAAAT
21626191 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (27 bp):
TCGCCAAATCACATATGGAAGCACAGC
Found at i:21626820 original size:27 final size:28
Alignment explanation
Indices: 21626754--21626824 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
21626744 TGATTACAGA
*
21626754 TCGCCAAGCCCACTGGCGAATCCCCAGC
1 TCGCCAAGCCCACTGGCGAATCACCAGC
* *
21626782 TCGCCAGGCCCACTGGCG-ATCACTA-C
1 TCGCCAAGCCCACTGGCGAATCACCAGC
*
21626808 TTCGCCAATCCCACTGG
1 -TCGCCAAGCCCACTGG
21626825 TGATTATAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.20, C:0.44, G:0.21, T:0.15
Consensus pattern (28 bp):
TCGCCAAGCCCACTGGCGAATCACCAGC
Found at i:21630147 original size:21 final size:23
Alignment explanation
Indices: 21630122--21630166 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21630112 AACAAGGTAG
*
21630122 ATAAAAAT-A-GAACAAAATAAA
1 ATAAAAATAATGAAAAAAATAAA
21630143 ATAAAAATAATGAAAAAAATAAA
1 ATAAAAATAATGAAAAAAATAAA
21630166 A
1 A
21630167 ATTACTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 1 0.05
23 12 0.57
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
ATAAAAATAATGAAAAAAATAAA
Found at i:21630603 original size:28 final size:28
Alignment explanation
Indices: 21630538--21630591 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
21630528 TTAATTAAAC
21630538 TAATTAAATTAATTATCCTAAAATAATA
1 TAATTAAATTAATTATCCTAAAATAATA
21630566 TAATTAAATTAATTAATCC-AAAATAA
1 TAATTAAATTAATT-ATCCTAAAATAA
21630592 CTTAATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATTAAATTAATTATCCTAAAATAATA
Found at i:21645234 original size:26 final size:26
Alignment explanation
Indices: 21645205--21645257 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
21645195 CGAGAGAGAT
21645205 TGATCATGCCTTAATCTTTTAAATTA
1 TGATCATGCCTTAATCTTTTAAATTA
21645231 TGATCATGCCTTAATCTTTTAAATTA
1 TGATCATGCCTTAATCTTTTAAATTA
21645257 T
1 T
21645258 CTATGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (26 bp):
TGATCATGCCTTAATCTTTTAAATTA
Found at i:21645366 original size:6 final size:6
Alignment explanation
Indices: 21645355--21645382 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21645345 CTCTCGCAAC
21645355 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
21645383 CAAATTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:21649831 original size:2 final size:2
Alignment explanation
Indices: 21649824--21649866 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21649814 GGTTGTATGG
21649824 AT AT AT AT 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 AT AT AT AT
21649866 A
1 A
21649867 CACGTCTGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21668083 original size:25 final size:25
Alignment explanation
Indices: 21668051--21668168 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 25
21668041 CCCTCTCTTC
21668051 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGTG
* * *
21668076 AGCCATATAATGGGAAGCTTATCT-
1 AGCCATATAACGGGAAGCTCATGTG
* * **
21668100 AGGCAGTATAATGGGAAGCTCATAAG
1 AGCCA-TATAACGGGAAGCTCATGTG
* ** *
21668126 AGCCATAT-TCAAGAAGCTCATGCG
1 AGCCATATAACGGGAAGCTCATGTG
* *
21668150 AGCC-TATAACAGGTAGCTC
1 AGCCATATAACGGGAAGCTC
21668169 TGAAGAGCCA
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
23 3 0.04
24 26 0.36
25 40 0.55
26 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGTG
Found at i:21668279 original size:26 final size:26
Alignment explanation
Indices: 21668245--21668299 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
21668235 AGCTCTGGCA
*
21668245 AGCCATTAATCGGGAAGCTTACAAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
* *
21668271 AGCCTTTAATCGGGAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
21668297 AGC
1 AGC
21668300 TATATAACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
AGCCATTAATCGGGAAGCTCACAAAG
Found at i:21668310 original size:26 final size:26
Alignment explanation
Indices: 21668249--21668327 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
21668239 CTGGCAAGCC
*
21668249 ATTAATCGGGAAGCTTACAAAGAGCCT
1 ATTAATCGGGAAGCTCACAAAGAG-CT
*
21668276 -TTAATCGGGAAGCTCACGAAGAGCT
1 ATTAATCGGGAAGCTCACAAAGAGCT
*
21668301 ATATAA-CGGGACA-CTCA-TAAGAGCT
1 AT-TAATCGGGA-AGCTCACAAAGAGCT
21668326 AT
1 AT
21668328 GGTGTGTCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 11 0.24
26 31 0.67
27 4 0.09
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (26 bp):
ATTAATCGGGAAGCTCACAAAGAGCT
Found at i:21668960 original size:20 final size:20
Alignment explanation
Indices: 21668935--21668975 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
21668925 AGCCCATGTA
*
21668935 TTTCATAAATTTTATAACTT
1 TTTCATAAATTTTACAACTT
*
21668955 TTTCATGAATTTTACAACTT
1 TTTCATAAATTTTACAACTT
21668975 T
1 T
21668976 ACAATTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTCATAAATTTTACAACTT
Found at i:21670223 original size:21 final size:21
Alignment explanation
Indices: 21670199--21670241 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
21670189 ATTTTGGTTC
21670199 ATGCCAAAATAGGCTAAAACA
1 ATGCCAAAATAGGCTAAAACA
21670220 ATGCCAAAATAGGCTAAAACA
1 ATGCCAAAATAGGCTAAAACA
21670241 A
1 A
21670242 CCTATACGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (21 bp):
ATGCCAAAATAGGCTAAAACA
Found at i:21692935 original size:17 final size:17
Alignment explanation
Indices: 21692913--21692964 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
21692903 TAAAAAATTG
21692913 TTTTAAAAATATAAATA
1 TTTTAAAAATATAAATA
*
21692930 TTTTAAAAATTATAAAAA
1 TTTTAAAAA-TATAAATA
*
21692948 TTATAAATAA-ATAAATA
1 TTTTAAA-AATATAAATA
21692965 ATTAATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.50
18 13 0.43
19 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTAAAAATATAAATA
Found at i:21692938 original size:18 final size:18
Alignment explanation
Indices: 21692913--21692964 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
21692903 TAAAAAATTG
21692913 TTTT-AAAAATATAAATA
1 TTTTAAAAAATATAAATA
* *
21692930 TTTTAAAAATTATAAAAA
1 TTTTAAAAAATATAAATA
* *
21692948 TTATAAATAA-ATAAATA
1 TTTTAAAAAATATAAATA
21692965 ATTAATTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTTAAAAAATATAAATA
Found at i:21692945 original size:9 final size:9
Alignment explanation
Indices: 21692916--21692954 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
21692906 AAAATTGTTT
21692916 TAAAAA-TA
1 TAAAAATTA
* *
21692924 TAAATATTT
1 TAAAAATTA
21692933 TAAAAATTA
1 TAAAAATTA
21692942 TAAAAATTA
1 TAAAAATTA
21692951 TAAA
1 TAAA
21692955 TAAATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:21692967 original size:27 final size:26
Alignment explanation
Indices: 21692916--21692968 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
21692906 AAAATTGTTT
**
21692916 TAAAAATATAAATATTTTAAAAATTA
1 TAAAAATATAAATATAATAAAAATTA
21692942 TAAAAATTATAAATA-AATAAATAATTA
1 TAAAAA-TATAAATATAATAAA-AATTA
21692969 ATTACTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAAAATATAAATATAATAAAAATTA
Found at i:21693854 original size:20 final size:22
Alignment explanation
Indices: 21693829--21693882 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
21693819 TATTAATCTT
21693829 TTTATAATTTTTC-TCTAA-TA
1 TTTATAATTTTTCTTCTAATTA
* *
21693849 TTTAT-ATATCTCTTCTAATTTA
1 TTTATAATTTTTCTTCTAA-TTA
21693871 TTTATAATTTTT
1 TTTATAATTTTT
21693883 AAACAATCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 5 0.19
20 10 0.38
22 7 0.27
23 4 0.15
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATAATTTTTCTTCTAATTA
Found at i:21701325 original size:2 final size:2
Alignment explanation
Indices: 21701318--21701350 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21701308 NNNNNNNNNN
21701318 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
21701351 TTTGTGCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21702615 original size:12 final size:12
Alignment explanation
Indices: 21702575--21702616 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21702565 TAGTTAACAA
* *
21702575 TTTTATTATAAA
1 TTTTAATATAAT
21702587 TTTTAAT-TAATT
1 TTTTAATATAA-T
21702599 TTTTAATATAAT
1 TTTTAATATAAT
21702611 TTTTAA
1 TTTTAA
21702617 AATTACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAATATAAT
Found at i:21706918 original size:53 final size:53
Alignment explanation
Indices: 21706838--21706952 Score: 194
Period size: 53 Copynumber: 2.2 Consensus size: 53
21706828 TCAAAAAGAA
* *
21706838 ACAAAAACGAAACCCAAAAAAGCAGAGTCAACAAAGATAGTCGAAGCAAGTTC
1 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
*
21706891 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATATTCGAACCAAGTTC
1 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
21706944 ACGAAAAAC
1 AC-AAAAAC
21706953 AGAGCCCCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 52 0.90
54 6 0.10
ACGTcount: A:0.55, C:0.22, G:0.14, T:0.10
Consensus pattern (53 bp):
ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
Found at i:21709313 original size:33 final size:33
Alignment explanation
Indices: 21709249--21709323 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
21709239 GGAAGTAATC
*
21709249 TTAGGAACAACTAACCTTGGGAACGATATTATG
1 TTAGGAACAACTAACCTTGGGAACGACATTATG
* *
21709282 TTAGGAACAACTAACTTTTGGAAC-AGCATTATG
1 TTAGGAACAACTAACCTTGGGAACGA-CATTATG
* *
21709315 GTGGGAACA
1 TTAGGAACA
21709324 CTTTGGAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (33 bp):
TTAGGAACAACTAACCTTGGGAACGACATTATG
Found at i:21710111 original size:23 final size:22
Alignment explanation
Indices: 21710085--21710127 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
21710075 AGATCGAAAG
21710085 AAGAAAAGAAAAGAGAGAAAACA
1 AAGAAAAGAAAAGAG-GAAAACA
* *
21710108 AAGAAGAGAGAAGAGGAAAA
1 AAGAAAAGAAAAGAGGAAAA
21710128 TTTCATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (22 bp):
AAGAAAAGAAAAGAGGAAAACA
Found at i:21716688 original size:30 final size:30
Alignment explanation
Indices: 21716630--21716691 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
21716620 AAAACTCTTG
* * * * *
21716630 AATAAAATAAAAGTTTTTTTTTTGAAACAA
1 AATAAAATAAAAGATTTATGTATCAAACAA
21716660 AATAAAATAAAAGATTTATGTATCAAACAA
1 AATAAAATAAAAGATTTATGTATCAAACAA
21716690 AA
1 AA
21716692 GGGATGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (30 bp):
AATAAAATAAAAGATTTATGTATCAAACAA
Found at i:21720149 original size:17 final size:19
Alignment explanation
Indices: 21720129--21720169 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
21720119 ATATAATTTT
*
21720129 AAAATATA-T-AATACATC
1 AAAATATACTAAAAACATC
21720146 AAAA-ATACTAAAAACATC
1 AAAATATACTAAAAACATC
21720164 AAAATA
1 AAAATA
21720170 AATATTTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 5 0.25
18 11 0.55
19 1 0.05
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATATACTAAAAACATC
Found at i:21720294 original size:30 final size:30
Alignment explanation
Indices: 21720250--21720309 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
21720240 ACTTAACAAG
21720250 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
21720280 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
21720310 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:21726426 original size:23 final size:23
Alignment explanation
Indices: 21726383--21726428 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
21726373 TCATGTGAGC
*
21726383 ATTAATGTAAAGGAAAGACTATG
1 ATTAATGTAAAGGAAACACTATG
*
21726406 ATTATATGTAAAGG-CACACTATG
1 ATTA-ATGTAAAGGAAACACTATG
21726429 TGTGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (23 bp):
ATTAATGTAAAGGAAACACTATG
Found at i:21735368 original size:22 final size:23
Alignment explanation
Indices: 21735316--21735369 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
21735306 ATTTTAATCT
*
21735316 TTTAAATATAAAAATTACAAAAA
1 TTTAAAAATAAAAATTACAAAAA
* * *
21735339 -ATATAAATAAAATTTA-AAAAA
1 TTTAAAAATAAAAATTACAAAAA
21735360 TTTAAAAATA
1 TTTAAAAATA
21735370 TGTTAAAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TTTAAAAATAAAAATTACAAAAA
Found at i:21735898 original size:19 final size:19
Alignment explanation
Indices: 21735876--21735931 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
21735866 TAAAAATTAG
*
21735876 TAATTTTGTTATATTTATA
1 TAATTTTGTAATATTTATA
* *
21735895 TAATTTTTTGTAATCTTTTTA
1 TAA--TTTTGTAATATTTATA
21735916 TAATTTTGTAATATTT
1 TAATTTTGTAATATTT
21735932 TTAGTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TAATTTTGTAATATTTATA
Found at i:21735932 original size:19 final size:19
Alignment explanation
Indices: 21735876--21735934 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
21735866 TAAAAATTAG
* *
21735876 TAATTTTGTTATATTTATA
1 TAATTTTGTAATATTTTTA
*
21735895 TAATTTTTTGTAATCTTTTTA
1 TAA--TTTTGTAATATTTTTA
21735916 TAATTTTGTAATATTTTTA
1 TAATTTTGTAATATTTTTA
21735935 GTTTATACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TAATTTTGTAATATTTTTA
Found at i:21737062 original size:25 final size:25
Alignment explanation
Indices: 21737029--21737085 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
21737019 CGTTGACATG
21737029 GTCG-TTAACAGATGCCACGCTAAT
1 GTCGATTAACAGATGCCACGCTAAT
21737053 GTCGATTAACAGATGCCACGCTAAT
1 GTCGATTAACAGATGCCACGCTAAT
*
21737078 GTTGATTA
1 GTCGATTA
21737086 CTAACATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (25 bp):
GTCGATTAACAGATGCCACGCTAAT
Found at i:21739875 original size:18 final size:18
Alignment explanation
Indices: 21739833--21739868 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21739823 TGCCAAGTGC
21739833 ATATCCTAACCCTTATAT
1 ATATCCTAACCCTTATAT
21739851 ATATCCTAACCCTTATAT
1 ATATCCTAACCCTTATAT
21739869 GTTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATCCTAACCCTTATAT
Found at i:21740383 original size:62 final size:59
Alignment explanation
Indices: 21740267--21740387 Score: 136
Period size: 62 Copynumber: 2.0 Consensus size: 59
21740257 TTGTACAAAC
* * ****
21740267 TATTTTTATATTGTTTCATTTAATAAAATAGAAGTTGTTTTAAATATTTTAATAGTAAAT
1 TATTTTTATATTGTTTCATTTAATAAAATAGAAGCTCTTTTAAATAAGGCAATAG-AAAT
*
21740327 TATTTTTATATT-TTATCCTATTTAATAAAATAGAAGCTCTTTTGAATAAGGCAATAGAAAT
1 TATTTTTATATTGTT-T-C-ATTTAATAAAATAGAAGCTCTTTTAAATAAGGCAATAGAAAT
21740388 GATGCAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 5 0.10
62 31 0.61
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (59 bp):
TATTTTTATATTGTTTCATTTAATAAAATAGAAGCTCTTTTAAATAAGGCAATAGAAAT
Found at i:21743563 original size:28 final size:27
Alignment explanation
Indices: 21743517--21743585 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
21743507 TTTTTGACAC
* *
21743517 TATTTTTTCAGAACTGTCTTCTCAAAAT
1 TATTTTTTTAGAACCGTCTTCTC-AAAT
* *
21743545 TATTTTTTTAGAGCCGTCTTTTCAAAT
1 TATTTTTTTAGAACCGTCTTCTCAAAT
*
21743572 TTTTTTTTTCAGAA
1 TATTTTTTT-AGAA
21743586 ACTACTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (27 bp):
TATTTTTTTAGAACCGTCTTCTCAAAT
Found at i:21743765 original size:125 final size:124
Alignment explanation
Indices: 21743545--21743849 Score: 407
Period size: 125 Copynumber: 2.4 Consensus size: 124
21743535 TTCTCAAAAT
* * * * *
21743545 TATTTTTTTAGAGCCGTCTTTTCAAATTTTTTTTTTCAGAAACTAC--TAAAAAAAGTGCGTCAA
1 TATTTTTTTAGAACCGTCTTTTCAAA-ATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGTCAA
* * * *
21743608 GTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCTTGCTTGAAGTGTTTTTGACAC
65 GTGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
*
21743668 TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAC
1 TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGT-CAA
*
21743733 GTGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGGCAC
65 GTGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
* * * * * *
21743793 TATTTTTTCAGAACTGTCTTCTCAAAATTAATTTTTTAGAAATTACTGGACGAAAAA
1 TATTTTTTTAGAACCGTCTTTTCAAAATT-ATTTTTCAGAAACTACTGTA-GAAAAA
21743850 AAGACAAAAT
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
122 17 0.11
123 25 0.16
124 12 0.08
125 83 0.52
126 17 0.11
127 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (124 bp):
TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGTCAAG
TGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
Found at i:21743981 original size:33 final size:32
Alignment explanation
Indices: 21743938--21744025 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 32
21743928 TACAAAATTA
*
21743938 TTTTTAAAAACCCTAAACCCTAATTTAATTTAT
1 TTTTTTAAAACCCTAAACCCT-ATTTAATTTAT
**
21743971 TTTTTTAAAACAATAAA-CC---TTAATTTAT
1 TTTTTTAAAACCCTAAACCCTATTTAATTTAT
**
21743999 TTTTTTAAATTCCTAAACCCTGATTTA
1 TTTTTTAAAACCCTAAACCCT-ATTTA
21744026 TTTTTTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
28 22 0.51
29 2 0.05
32 2 0.05
33 17 0.40
ACGTcount: A:0.38, C:0.16, G:0.01, T:0.45
Consensus pattern (32 bp):
TTTTTTAAAACCCTAAACCCTATTTAATTTAT
Found at i:21744029 original size:27 final size:28
Alignment explanation
Indices: 21743963--21744041 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
21743953 AACCCTAATT
* ** *
21743963 TAATTTATTTTTTTAAAACAATAAACCT
1 TAATTTATTTTTTTAAATCCCTAAACCC
*
21743991 TAATTTATTTTTTTAAATTCCTAAACCC
1 TAATTTATTTTTTTAAATCCCTAAACCC
*
21744019 TGATTTA-TTTTTTAAATCCCTAA
1 TAATTTATTTTTTTAAATCCCTAA
21744042 CCCATAACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 15 0.34
28 29 0.66
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATTTATTTTTTTAAATCCCTAAACCC
Found at i:21752515 original size:25 final size:25
Alignment explanation
Indices: 21752479--21752593 Score: 117
Period size: 25 Copynumber: 4.6 Consensus size: 25
21752469 CGGACACACC
*
21752479 ACAGCTCGTATGAGCTTCTTAATTT
1 ACAGCTCGTATGAGCTTCTCAATTT
* *
21752504 ACAGCTCATATGAGCTTCTCGATTT
1 ACAGCTCGTATGAGCTTCTCAATTT
* *
21752529 ACAGCTCGTATGAGCTTCCCAATTC
1 ACAGCTCGTATGAGCTTCTCAATTT
* * *
21752554 ATAGCTCGTGA-GAGCATACT-GATTT
1 ACAGCTCGT-ATGAGC-TTCTCAATTT
*
21752579 AGAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
21752594 ATGCATGAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.01
25 70 0.95
26 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCTCAATTT
Found at i:21752560 original size:50 final size:50
Alignment explanation
Indices: 21752479--21752593 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
21752469 CGGACACACC
** * *
21752479 ACAGCTCGTATGAGCTTCTTAATTTACAGCTCAT-ATGAGC-TTCTCGATTT
1 ACAGCTCGTATGAGCTTCCCAATTCACAGCTCATGA-GAGCATACT-GATTT
* *
21752529 ACAGCTCGTATGAGCTTCCCAATTCATAGCTCGTGAGAGCATACTGATTT
1 ACAGCTCGTATGAGCTTCCCAATTCACAGCTCATGAGAGCATACTGATTT
*
21752579 AGAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
21752594 ATGCATGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 52 0.93
51 4 0.07
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (50 bp):
ACAGCTCGTATGAGCTTCCCAATTCACAGCTCATGAGAGCATACTGATTT
Found at i:21755903 original size:59 final size:58
Alignment explanation
Indices: 21755817--21755930 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
21755807 ATAATCAAAG
* * * *
21755817 TTTCTTGTCATCACAGTTCATAGTAGGTGAGTCTATACTCAAACAAGAATATGATCAT
1 TTTCCTGTCATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGATCAT
* *
21755875 TTTCCTGTCAATCACAGTTCACAATAGGTAAGTTTATACTTAAACAAGAATATGAT
1 TTTCCTGTC-ATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGAT
21755931 TATTCATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 8 0.16
59 41 0.84
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (58 bp):
TTTCCTGTCATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGATCAT
Found at i:21764921 original size:7 final size:6
Alignment explanation
Indices: 21764896--21764920 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21764886 GATTAGTTAT
21764896 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
21764921 ACTAAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:21777803 original size:20 final size:20
Alignment explanation
Indices: 21777759--21777856 Score: 106
Period size: 20 Copynumber: 4.8 Consensus size: 20
21777749 CAAAACACAT
* * *
21777759 CAGAGAGCATCGAAATGCTAA
1 CAGAG-GCACCGAAGTGCAAA
*
21777780 CAGAGGCACCGTAGTGCAAA
1 CAGAGGCACCGAAGTGCAAA
21777800 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCGAAGTGCAAA
* * * *
21777820 CAGATGCATCAAAATGCAAA
1 CAGAGGCACCGAAGTGCAAA
*
21777840 CAAAGGCACCGAAGTGC
1 CAGAGGCACCGAAGTGC
21777857 GATCCCATAC
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
20 58 0.92
21 5 0.08
ACGTcount: A:0.41, C:0.23, G:0.26, T:0.10
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAA
Found at i:21785638 original size:40 final size:40
Alignment explanation
Indices: 21785542--21785645 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
21785532 ACCAAAATCC
* *
21785542 TTATTATAATTATTGTAATTATAA--TTTACGATCGAATA
1 TTATTATAATTATTGTAATTATAATTTTTACGATCAAACA
* * *
21785580 TTATTATAATTATTGTAATTGTAATTTTTTCGGTCAAACA
1 TTATTATAATTATTGTAATTATAATTTTTACGATCAAACA
*
21785620 TTATTATAATTATGGTAATTATAATT
1 TTATTATAATTATTGTAATTATAATT
21785646 ATAATATTCG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 23 0.40
40 34 0.60
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.50
Consensus pattern (40 bp):
TTATTATAATTATTGTAATTATAATTTTTACGATCAAACA
Found at i:21796465 original size:28 final size:29
Alignment explanation
Indices: 21796433--21796492 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
21796423 GATTTAATAT
21796433 TTATAAAAATATTCA-AAAAA-TAAAAAAA
1 TTATAAAAA-ATTCATAAAAATTAAAAAAA
* *
21796461 TTATAAAAAGTTCATAAAAATTCAAAAAA
1 TTATAAAAAATTCATAAAAATTAAAAAAA
21796490 TTA
1 TTA
21796493 GTATGAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.14
28 14 0.50
29 10 0.36
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (29 bp):
TTATAAAAAATTCATAAAAATTAAAAAAA
Found at i:21796468 original size:17 final size:17
Alignment explanation
Indices: 21796435--21796490 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
21796425 TTTAATATTT
*
21796435 ATAAAAATATTCAAAAA
1 ATAAAAAAATTCAAAAA
21796452 ATAAAAAAATT-ATAAAA
1 ATAAAAAAATTCA-AAAA
*
21796469 AGTTCATAAAAATTCAAAAA
1 A--T-AAAAAAATTCAAAAA
21796489 AT
1 AT
21796491 TAGTATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 15 0.47
18 1 0.03
19 1 0.03
20 13 0.41
21 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (17 bp):
ATAAAAAAATTCAAAAA
Found at i:21805414 original size:73 final size:73
Alignment explanation
Indices: 21805276--21805431 Score: 253
Period size: 73 Copynumber: 2.2 Consensus size: 73
21805266 GAAGAAAAGG
21805276 AAAATA-AATAAGTAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTTA
1 AAAATATAATAAGTAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTTA
*
21805340 ACAAATGA
66 ACAAATAA
* * *
21805348 AAAATATAATACGTTAAAAAGAAAAAAATTTAAATTGTT-TAAAAAAAGTATAATGATTAGTTTT
1 AAAATATAATAAG-TAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTT
21805412 AACAAATAA
65 AACAAATAA
21805421 AAAATATAATA
1 AAAATATAATA
21805432 TATTAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
72 6 0.08
73 47 0.60
74 25 0.32
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (73 bp):
AAAATATAATAAGTAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTTA
ACAAATAA
Found at i:21806706 original size:13 final size:13
Alignment explanation
Indices: 21806659--21806716 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
21806649 AAATCCAAAA
21806659 TATAAAAAA-AAT
1 TATAAAAAATAAT
21806671 TAT-AAAAATAA-
1 TATAAAAAATAAT
**
21806682 TATGAAGCAATAAT
1 TAT-AAAAAATAAT
*
21806696 TATAAAAAATATT
1 TATAAAAAATAAT
*
21806709 TTTAAAAA
1 TATAAAAA
21806717 TTATAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 8 0.22
12 5 0.14
13 20 0.56
14 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (13 bp):
TATAAAAAATAAT
Found at i:21809351 original size:23 final size:23
Alignment explanation
Indices: 21809324--21809367 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21809314 CTGAAAATTA
21809324 TAGATATGACTTTTATTTTTAAT
1 TAGATATGACTTTTATTTTTAAT
* *
21809347 TAGATTTGATTTTTATTTTTA
1 TAGATATGACTTTTATTTTTA
21809368 TTTACCTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (23 bp):
TAGATATGACTTTTATTTTTAAT
Found at i:21811004 original size:22 final size:22
Alignment explanation
Indices: 21810975--21811027 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
21810965 CCAAACCTCA
*
21810975 TTTT-TTTGTTG-GTAAGTTTG
1 TTTTCTTTGTTGTGTAAGTTCG
*
21810995 CTTTTCTTTG-TGTGTTAGTTCG
1 -TTTTCTTTGTTGTGTAAGTTCG
21811017 TTTTCTTTGTT
1 TTTTCTTTGTT
21811028 ATTTATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.06, C:0.08, G:0.21, T:0.66
Consensus pattern (22 bp):
TTTTCTTTGTTGTGTAAGTTCG
Found at i:21816194 original size:15 final size:16
Alignment explanation
Indices: 21816162--21816194 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21816152 AGAGAATACT
*
21816162 GAATTTGATCATGAAA
1 GAATTTGATCAAGAAA
21816178 GAATTTG-TCAAGAAA
1 GAATTTGATCAAGAAA
21816193 GA
1 GA
21816195 GGTTATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (16 bp):
GAATTTGATCAAGAAA
Found at i:21823903 original size:18 final size:18
Alignment explanation
Indices: 21823871--21823906 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21823861 TTAAGTTAGT
*
21823871 GGAAACAAATAAAACAAA
1 GGAAACAAAGAAAACAAA
*
21823889 GGAAACAAAGGAAACAAA
1 GGAAACAAAGAAAACAAA
21823907 TAGCTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.11, G:0.17, T:0.03
Consensus pattern (18 bp):
GGAAACAAAGAAAACAAA
Found at i:21824833 original size:74 final size:75
Alignment explanation
Indices: 21824740--21824998 Score: 310
Period size: 74 Copynumber: 3.5 Consensus size: 75
21824730 AAAATAAATA
* * * * * *
21824740 ACTATTTATTTGTCGGTTTATTCGACTAGTGCTGGGCG-TAATTCTCATTGGTAAATCCAACTAG
1 ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTAG
*
21824804 AGTTTGGCTC
66 AGTTAGGCTC
* * * * *
21824814 ACTATTTATTCGTTGGTTTA-ACGGACTAGCGCTGGGTGCAAATAC-CGTTGGTATATCCAACTA
1 ACTAATTATTTGTCGGTTTATTC-GACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTA
*
21824877 GAGCTAGGCTC
65 GAGTTAGGCTC
* * *
21824888 ACTAATTATTTGTCGATTTATTCGACTAGCGCTGGACGCAAATACT-GTTGGTATATCCAACTTG
1 ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTAG
*
21824952 AGTTGGGCTC
66 AGTTAGGCTC
* *
21824962 CCTAATTATTTGTCGGTTTATTCGACTAGCGTTGGGC
1 ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGC
21824999 ACAACTTTCG
Statistics
Matches: 156, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
73 1 0.01
74 150 0.96
75 5 0.03
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (75 bp):
ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTAG
AGTTAGGCTC
Found at i:21826070 original size:25 final size:25
Alignment explanation
Indices: 21826038--21826117 Score: 126
Period size: 25 Copynumber: 3.2 Consensus size: 25
21826028 TCAGTGAGTT
*
21826038 ACACGGCTTGGCACAC-GGACGTGTG
1 ACACGGCTTTGCACACGGGA-GTGTG
*
21826063 ACATGGCTTTGCACACGGGAGTGTG
1 ACACGGCTTTGCACACGGGAGTGTG
21826088 ACACGGCTTTGCACACGGGAGTGTG
1 ACACGGCTTTGCACACGGGAGTGTG
21826113 ACACG
1 ACACG
21826118 ACTGCGTGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
25 48 0.94
26 3 0.06
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (25 bp):
ACACGGCTTTGCACACGGGAGTGTG
Found at i:21836469 original size:21 final size:21
Alignment explanation
Indices: 21836443--21836505 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
21836433 TTGGTATTTG
21836443 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
21836464 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21836485 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
21836506 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:21837402 original size:31 final size:32
Alignment explanation
Indices: 21837357--21837423 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
21837347 ACATGCATGC
*
21837357 ACCTTGCTAAAATGAATCTTCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-TCACACATTCGGCCA
*
21837389 ACCTTG-TTAAATGATCTCACACATTCGGCCA
1 ACCTTGCTAAAATGATCTCACACATTCGGCCA
21837420 ACCT
1 ACCT
21837424 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCTCACACATTCGGCCA
Found at i:21841893 original size:22 final size:22
Alignment explanation
Indices: 21841868--21841957 Score: 135
Period size: 22 Copynumber: 4.0 Consensus size: 22
21841858 ATGTGCCAGT
*
21841868 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
21841890 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
21841912 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * *
21841934 ACGAACTAAACCCTCATGATTTA
1 ACGTACTAAGCTCTCATG-TTTA
21841957 A
1 A
21841958 AAAGTTTGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
22 58 0.92
23 5 0.08
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:21860408 original size:21 final size:21
Alignment explanation
Indices: 21860362--21860412 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
21860352 ATGAAACTAT
* *
21860362 TTACTATGTCGTGACACGCCC
1 TTACTATGTCGCGACACGCAC
*
21860383 CTACTATGTCGCGACAC-CAAC
1 TTACTATGTCGCGACACGC-AC
21860404 TTACTATGT
1 TTACTATGT
21860413 TGCAACATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (21 bp):
TTACTATGTCGCGACACGCAC
Done.