Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 57 of 120
Found at i:16005470 original size:87 final size:87
Alignment explanation
Indices: 16005324--16005538 Score: 349
Period size: 87 Copynumber: 2.5 Consensus size: 87
16005314 TCATTGACCA
* * * *
16005324 ATGAAAAGGGATAGGTTCGACTATCGAATATGAAAAGCGATAGCTTCAGCTATCGATTATGAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCAGCTATCGATTATGAAAA
* *
16005389 GGGATTGTGACGACCATCGAGT
66 GGGATGGTGACGACCATCGAAT
* *
16005411 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCAGCTATCGATTATGAAAA
16005476 GGGATGGTGACGACCATCGAAT
66 GGGATGGTGACGACCATCGAAT
*
16005498 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGAT
16005539 GGTGACGACC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 119 1.00
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.25
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCAGCTATCGATTATGAAAA
GGGATGGTGACGACCATCGAAT
Found at i:16005539 original size:58 final size:58
Alignment explanation
Indices: 16005433--16005567 Score: 245
Period size: 58 Copynumber: 2.3 Consensus size: 58
16005423 AGCTTCGGCT
*
16005433 ATCGAATATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
16005491 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
16005549 ATC-AACTATGAAAAGGGAT
1 ATCGAA-TATGAAAAGGGAT
16005568 TGTGATGACT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
57 2 0.03
58 73 0.97
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (58 bp):
ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
Found at i:16005558 original size:29 final size:28
Alignment explanation
Indices: 16005468--16005572 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 28
16005458 GGCTATTGAT
16005468 TATGAAAAGGGATGGTGACGACCATCGAA
1 TATGAAAAGGGATGGTGACGACCATC-AA
* * * * *
16005497 TATGAAAAGGGATAGCT-TCGGCTATCGAT
1 TATGAAAAGGGAT-GGTGACGACCATC-AA
16005526 TATGAAAAGGGATGGTGACGACCATCAA
1 TATGAAAAGGGATGGTGACGACCATCAA
*
16005554 CTATGAAAAGGGATTGTGA
1 -TATGAAAAGGGATGGTGA
16005573 TGACTACTGA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.05
29 57 0.92
30 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (28 bp):
TATGAAAAGGGATGGTGACGACCATCAA
Found at i:16005559 original size:87 final size:87
Alignment explanation
Indices: 16005324--16005572 Score: 340
Period size: 87 Copynumber: 2.9 Consensus size: 87
16005314 TCATTGACCA
* * *
16005324 ATGAAAAGGGATAGGTTCGACTATCGAATATGAAAAGCGATAGCTTC-AGCTATCGATTATGAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGA-CTATCGATTATGAAA
* *
16005388 TGGGATTGTGACGACCATCGAGT
65 AGGGATTGTGACGACCATCGAAT
* *
16005411 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGACTATCGATTATGAAAA
*
16005476 GGGATGGTGACGACCATCGAAT
66 GGGATTGTGACGACCATCGAAT
* * * * * *
16005498 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGAT-GGTGACGACCATCAACTATGAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCT-TCGACTATCGATTATGAAA
16005562 AGGGATTGTGA
65 AGGGATTGTGA
16005573 TGACTACTGA
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
86 2 0.01
87 141 0.99
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTCGACTATCGATTATGAAAA
GGGATTGTGACGACCATCGAAT
Found at i:16005585 original size:58 final size:57
Alignment explanation
Indices: 16005433--16005628 Score: 227
Period size: 58 Copynumber: 3.4 Consensus size: 57
16005423 AGCTTCGGCT
*
16005433 ATCGAATATGAAAAGGGATAGCTTCGGCTATTGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATAGCTTCGACTA-TGATTATGAAAAGGGATGGTGACGACC
*
16005491 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATAGCTTCGACTAT-GATTATGAAAAGGGATGGTGACGACC
* ** **
16005549 ATC-AACTATGAAAAGGGATTG-TGAT-GACTACTGATTAATGAAAAATGATGGTTTCGACC
1 ATCGAA-TATGAAAAGGGATAGCT--TCGACTA-TGATT-ATGAAAAGGGATGGTGACGACC
* *
16005608 ATTGAATATGAAAATGGATAG
1 ATCGAATATGAAAAGGGATAG
16005629 TTACAACCAT
Statistics
Matches: 122, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
57 4 0.03
58 81 0.66
59 35 0.29
60 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.26
Consensus pattern (57 bp):
ATCGAATATGAAAAGGGATAGCTTCGACTATGATTATGAAAAGGGATGGTGACGACC
Found at i:16009919 original size:12 final size:12
Alignment explanation
Indices: 16009894--16009945 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
16009884 ATCTATAAGA
16009894 TAAATATTAAAT
1 TAAATATTAAAT
16009906 TAAAT-TTAATAT
1 TAAATATTAA-AT
* *
16009918 TAAGATAATAACT
1 TAA-ATATTAAAT
*
16009931 TTAATATTAAAT
1 TAAATATTAAAT
16009943 TAA
1 TAA
16009946 TAAAATACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
11 4 0.13
12 19 0.61
13 5 0.16
14 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:16009946 original size:20 final size:19
Alignment explanation
Indices: 16009896--16009948 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
16009886 CTATAAGATA
16009896 AATATTAAATT-A-AATTT
1 AATATTAAATTAATAATTT
16009913 AATATTAAGA-TAATAACTTT
1 AATATTAA-ATTAATAA-TTT
16009933 AATATTAAATTAATAA
1 AATATTAAATTAATAA
16009949 AATACTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.29
18 2 0.06
19 3 0.10
20 17 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATTAAATTAATAATTT
Found at i:16011258 original size:11 final size:11
Alignment explanation
Indices: 16011227--16011260 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16011217 GTCACAAGTG
16011227 AATTAATTCACA
1 AATTAATTCA-A
*
16011239 AATTGATTCAA
1 AATTAATTCAA
16011250 AATTAATTCAA
1 AATTAATTCAA
16011261 CTTGGGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (11 bp):
AATTAATTCAA
Found at i:16013368 original size:27 final size:30
Alignment explanation
Indices: 16013338--16013400 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 30
16013328 ATTCATTGTC
* *
16013338 TTTGAGATTTAG-TATGTA-TATGT-ATAA
1 TTTGAGATTGAGATATCTATTATGTAATAA
*
16013365 TTTGTGATTGAGATATCTATTATGTAATAA
1 TTTGAGATTGAGATATCTATTATGTAATAA
16013395 TCTTGA
1 T-TTGA
16013401 ATATTGATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 10 0.36
28 5 0.18
29 5 0.18
30 5 0.18
31 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (30 bp):
TTTGAGATTGAGATATCTATTATGTAATAA
Found at i:16017519 original size:52 final size:52
Alignment explanation
Indices: 16017436--16017539 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
16017426 ATTTGATTCA
** *
16017436 GAATTATGACGAATCTATTTTCAGCAAACTAGAGAACTAAAATGAAGACTTG
1 GAATTATGAAAAATCTATTTTCAACAAACTAGAGAACTAAAATGAAGACTTG
*
16017488 GAATTATGAAAAATCTATTTTCAACATACTAGAGAACTAAAATGAAGACTTG
1 GAATTATGAAAAATCTATTTTCAACAAACTAGAGAACTAAAATGAAGACTTG
16017540 TACTTCAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (52 bp):
GAATTATGAAAAATCTATTTTCAACAAACTAGAGAACTAAAATGAAGACTTG
Found at i:16026625 original size:23 final size:23
Alignment explanation
Indices: 16026579--16026625 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
16026569 TTTATATGAA
**
16026579 AAATATTAAAGTTATGGTGTTAT
1 AAATATTAAAGTTATGGAATTAT
16026602 AAATATTAAAGTT-TGGAATATAT
1 AAATATTAAAGTTATGGAAT-TAT
16026625 A
1 A
16026626 TATGATCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (23 bp):
AAATATTAAAGTTATGGAATTAT
Found at i:16029710 original size:21 final size:21
Alignment explanation
Indices: 16029672--16029724 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
16029662 GCATAATTTC
*
16029672 ATTTAAAAATTGATAAATAAT
1 ATTTAAAAAATGATAAATAAT
16029693 ATTTCAAAAAATGA-AAAT-AT
1 ATTT-AAAAAATGATAAATAAT
*
16029713 TTTTAGAAAAAT
1 ATTTA-AAAAAT
16029725 TAATTTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 11 0.39
21 8 0.29
22 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (21 bp):
ATTTAAAAAATGATAAATAAT
Found at i:16032500 original size:150 final size:150
Alignment explanation
Indices: 16032318--16032728 Score: 522
Period size: 150 Copynumber: 2.7 Consensus size: 150
16032308 CAAAATAGTT
*
16032318 AAAAATTCAAAATTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAACTTTAAAAAAACATATT
1 AAAAAATCAAAATTTT-TTTTAAAATTTTAAACTTTCCTTTAAAATAAC-TTAAAAAAACATATT
* * * * * **
16032383 TGT-TTTTTCAAAATCTAAACTCTCTCTTTTTTTAAAAACCATTATTTTTCTTAAAGATTACATT
64 TTTATTTTTCAAAATCTAAACTTTCTCTTTTTTTAAAAAACACTATTTTTCTTAAAGATTAAAGC
**
16032447 TTTTATTTTGAAATAGTTG-AA
129 TTTTACGTTGAAATAGTTGAAA
* *
16032468 AAAAAATCAAAATTTTTCTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAGAACAAATT
1 AAAAAATCAAAATTTTT-TTTAAAATTTTAAACTTTCCTTTAAAATAACTTAAAAA-AACATATT
*
16032533 TTTATTTTTTAAAATCTAAACTTTCTCTTTTTTTTAAAAAGAAAAACACTATTTTTCTTAAAGAT
64 TTTATTTTTCAAAATCTAAACTTTCTC-TTTTTTT----A-AAAAACACTATTTTTCTTAAAGAT
16032598 TAAAGCTTTTACGTTGAAATAGTTGAAA
123 TAAAGCTTTTACGTTGAAATAGTTGAAA
* * * * *
16032626 AAAAAATCAAAACTTTGTTTTACAATTTTAAATTTTCCTTTAAAATAAC-TAAAAATATATATTT
1 AAAAAATCAAAA-TTTTTTTTAAAATTTTAAACTTTCCTTTAAAATAACTTAAAAAAACATATTT
* *
16032690 TTATTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAAA
65 TTATTTTTCAAAATCTAAACTTTCTCTTTTTTTAAAAAA
16032729 ATCAAAACTT
Statistics
Matches: 227, Mismatches: 23, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
149 7 0.03
150 60 0.26
151 22 0.10
152 7 0.03
155 5 0.02
156 32 0.14
157 47 0.21
158 43 0.19
159 4 0.02
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.44
Consensus pattern (150 bp):
AAAAAATCAAAATTTTTTTTAAAATTTTAAACTTTCCTTTAAAATAACTTAAAAAAACATATTTT
TATTTTTCAAAATCTAAACTTTCTCTTTTTTTAAAAAACACTATTTTTCTTAAAGATTAAAGCTT
TTACGTTGAAATAGTTGAAA
Found at i:16033128 original size:3 final size:3
Alignment explanation
Indices: 16033122--16033172 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
16033112 AGTAGTGATG
16033122 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16033170 ATA
1 ATA
16033173 TGGGTCTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16036845 original size:14 final size:14
Alignment explanation
Indices: 16036826--16036865 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16036816 TTGTTTGGCA
*
16036826 GTAAAATGTTTTCC
1 GTAAAATGATTTCC
*
16036840 GTAAAATGATTTCT
1 GTAAAATGATTTCC
*
16036854 GGAAAATGATTT
1 GTAAAATGATTT
16036866 ACTTTTCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
GTAAAATGATTTCC
Found at i:16036872 original size:34 final size:33
Alignment explanation
Indices: 16036834--16036898 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
16036824 CAGTAAAATG
*
16036834 TTTTCCGTAAAATGATTT-CTGGAAAATGATTTAC
1 TTTTCCGGAAAATGATTTACT-GAAAAT-ATTTAC
*
16036868 TTTTCTGGAAAATGATTTACTGAAAATATTT
1 TTTTCCGGAAAATGATTTACTGAAAATATTT
16036899 TCTGGTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 22 0.79
35 2 0.07
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (33 bp):
TTTTCCGGAAAATGATTTACTGAAAATATTTAC
Found at i:16036874 original size:20 final size:20
Alignment explanation
Indices: 16036849--16036888 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16036839 CGTAAAATGA
16036849 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16036869 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16036889 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:16039523 original size:6 final size:6
Alignment explanation
Indices: 16039508--16039549 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
16039498 TTTGCAACCC
*
16039508 AAGGGG AAGGGA AAGGGGA AAGGG- AAGAGGA AAGGGA AAGGG
1 AAGGGA AAGGGA AA-GGGA AAGGGA AAG-GGA AAGGGA AAGGG
16039550 GAGAAGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 3 0.09
6 20 0.62
7 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:16039551 original size:19 final size:19
Alignment explanation
Indices: 16039508--16039551 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
16039498 TTTGCAACCC
16039508 AAGGGGAAGGGAAAGGGGA
1 AAGGGGAAGGGAAAGGGGA
16039527 AA-GGGAAGAGGAAA-GGGA
1 AAGGGGAAG-GGAAAGGGGA
16039545 AAGGGGA
1 AAGGGGA
16039552 GAAGAATGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (19 bp):
AAGGGGAAGGGAAAGGGGA
Found at i:16044193 original size:27 final size:27
Alignment explanation
Indices: 16044163--16044292 Score: 147
Period size: 27 Copynumber: 4.8 Consensus size: 27
16044153 AAAATAACCA
* *
16044163 AATTACCTTTGAAGGGTAAAATGACTG
1 AATTACCCTCGAAGGGTAAAATGACTG
*
16044190 AATTACCCCCGAAGGGTAAAATGA-TCG
1 AATTACCCTCGAAGGGTAAAATGACT-G
* **
16044217 AATTACCCTCGAAAGGTAAAATGACCA
1 AATTACCCTCGAAGGGTAAAATGACTG
* *
16044244 AATTACCCTTGAAGTGTAAAATGATCT-
1 AATTACCCTCGAAGGGTAAAATGA-CTG
*
16044271 AATTACCCCCGAAGGGTAAAAT
1 AATTACCCTCGAAGGGTAAAAT
16044293 AACCGAAACT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 84 0.98
28 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (27 bp):
AATTACCCTCGAAGGGTAAAATGACTG
Found at i:16044222 original size:54 final size:54
Alignment explanation
Indices: 16044163--16044292 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 54
16044153 AAAATAACCA
* * **
16044163 AATTACCTTTGAAGGGTAAAATGACTGAATTACCCCCGAAGGGTAAAATGATCG
1 AATTACCCTCGAAGGGTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCG
* ** * *
16044217 AATTACCCTCGAAAGGTAAAATGACCAAATTACCCTTGAAGTGTAAAATGATCT
1 AATTACCCTCGAAGGGTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCG
*
16044271 AATTACCCCCGAAGGGTAAAAT
1 AATTACCCTCGAAGGGTAAAAT
16044293 AACCGAAACT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (54 bp):
AATTACCCTCGAAGGGTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCG
Found at i:16044317 original size:54 final size:53
Alignment explanation
Indices: 16044201--16044321 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 53
16044191 ATTACCCCCG
* * *
16044201 AAGGGTAAAATGATCGAATTACCCTCGAAAGGTAAAATGACCAAATTACCCTT
1 AAGGGTAAAATGATCGAATTACCCCCGAAAGGTAAAATAACCAAACTACCCTT
* * * *
16044254 GAAGTGTAAAATGATCTAATTACCCCCGAAGGGTAAAATAACCGAAACT-CCCCT
1 -AAGGGTAAAATGATCGAATTACCCCCGAAAGGTAAAATAACC-AAACTACCCTT
16044308 ATAGGGTAAAATGA
1 A-AGGGTAAAATGA
16044322 CTGTTATACC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
53 1 0.02
54 52 0.91
55 4 0.07
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (53 bp):
AAGGGTAAAATGATCGAATTACCCCCGAAAGGTAAAATAACCAAACTACCCTT
Found at i:16044346 original size:81 final size:80
Alignment explanation
Indices: 16044153--16044322 Score: 218
Period size: 81 Copynumber: 2.1 Consensus size: 80
16044143 GAATCATGGG
* * * * *
16044153 AAAATAACCAAATTACCTTTGAAGGGTAAAATGACTGAATTACCCCCGAAGGGTAAAATGATCGA
1 AAAATGACCAAATTACCCTTGAAGTGTAAAATGACTGAATTACCCCCGAAGGGTAAAATAACCGA
*
16044218 ATTACCCTCGAAAGGT
66 A-TACCCCCGAAAGGT
16044234 AAAATGACCAAATTACCCTTGAAGTGTAAAATGATCT-AATTACCCCCGAAGGGTAAAATAACCG
1 AAAATGACCAAATTACCCTTGAAGTGTAAAATGA-CTGAATTACCCCCGAAGGGTAAAATAACCG
* *
16044298 AA-ACTCCCCTATAGGGT
65 AATAC-CCCCGA-AAGGT
16044315 AAAATGAC
1 AAAATGAC
16044323 TGTTATACCC
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
79 2 0.03
80 4 0.05
81 70 0.90
82 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (80 bp):
AAAATGACCAAATTACCCTTGAAGTGTAAAATGACTGAATTACCCCCGAAGGGTAAAATAACCGA
ATACCCCCGAAAGGT
Found at i:16044721 original size:28 final size:28
Alignment explanation
Indices: 16044681--16044767 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 28
16044671 TGCATTGCAT
*
16044681 TGTTACTGTATTGGGATACGGCCCACAC
1 TGTTACTGTATTGGGATAAGGCCCACAC
* *
16044709 TGTTATTGTATTGGGCTAAGGCCCACACAC
1 TGTTACTGTATTGGGATAAGG-CC-CACAC
*
16044739 TGTTACTGTAAT-GGACTAAGGCCCACAC
1 TGTTACTGTATTGGGA-TAAGGCCCACAC
16044767 T
1 T
16044768 ATACTGCTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
28 24 0.48
29 6 0.12
30 20 0.40
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (28 bp):
TGTTACTGTATTGGGATAAGGCCCACAC
Found at i:16044740 original size:30 final size:30
Alignment explanation
Indices: 16044681--16044766 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
16044671 TGCATTGCAT
* *
16044681 TGTTACTGTATTGGGATACGG-CC-CACAC
1 TGTTACTGTATTGGGCTAAGGCCCACACAC
*
16044709 TGTTATTGTATTGGGCTAAGGCCCACACAC
1 TGTTACTGTATTGGGCTAAGGCCCACACAC
* *
16044739 TGTTACTGTAATGGACTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
16044767 TATACTGCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.36
29 2 0.04
30 30 0.60
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (30 bp):
TGTTACTGTATTGGGCTAAGGCCCACACAC
Found at i:16050100 original size:27 final size:27
Alignment explanation
Indices: 16050062--16050337 Score: 322
Period size: 27 Copynumber: 10.3 Consensus size: 27
16050052 AATCATGGGC
* * *
16050062 AAATGACCGAATTACCCTTGAAAGGAA
1 AAATGACCGAATTACCCTCGAAGGGTA
*
16050089 AAATGACCGAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
* *
16050116 AAATAACCTAATTACCC-CGAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
* * *
16050142 AAATGATCGAATTACCCTCAAAAGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
*
16050169 AAATGACCGAATTACCCTCGAAAGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
* *
16050196 AAATGATCGAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
** *
16050223 AAATGATTGAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
* ** *
16050250 AAATAATTGAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
* *
16050277 AAATGATCGAATTACCCTCGAAAGGTA
1 AAATGACCGAATTACCCTCGAAGGGTA
* *
16050304 AAATGACTGAAATACCCTC-ATAGGGTA
1 AAATGACCGAATTACCCTCGA-AGGGTA
16050331 AAATGAC
1 AAATGAC
16050338 TATCATACCC
Statistics
Matches: 221, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 24 0.11
27 197 0.89
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATGACCGAATTACCCTCGAAGGGTA
Found at i:16050729 original size:30 final size:30
Alignment explanation
Indices: 16050693--16050750 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
16050683 CTTGCATTAC
* *
16050693 ACTGTTACTGTATTGGGCTAAGGCCCACCT
1 ACTGTTACTGTAATGAGCTAAGGCCCACCT
16050723 ACTGTTACTGTAATGAGCTAAGGCCCAC
1 ACTGTTACTGTAATGAGCTAAGGCCCAC
16050751 ACTATACCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (30 bp):
ACTGTTACTGTAATGAGCTAAGGCCCACCT
Found at i:16051073 original size:32 final size:32
Alignment explanation
Indices: 16051037--16051097 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
16051027 TTTTCCTTGT
*
16051037 ATATTTTAAACTGGTAGATTAGGAGATGATGA
1 ATATTTTAAACTGCTAGATTAGGAGATGATGA
16051069 ATATTTTAAACTGCTAGATTAGGAGATGA
1 ATATTTTAAACTGCTAGATTAGGAGATGA
16051098 CGACTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (32 bp):
ATATTTTAAACTGCTAGATTAGGAGATGATGA
Found at i:16055921 original size:32 final size:32
Alignment explanation
Indices: 16055859--16055936 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
16055849 GAATGGCTAC
* **
16055859 AAGCCATAAGTA-CAGTAATATGATTGGCACA
1 AAGCCATCAGTAGCAGTAATATGATCAGCACA
* *
16055890 AAGTCATCAGTAGCAGTGATATGATCAGCACA
1 AAGCCATCAGTAGCAGTAATATGATCAGCACA
*
16055922 CAGCCATCAGTAGCA
1 AAGCCATCAGTAGCA
16055937 TCGCAGAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGATCAGCACA
Found at i:16055965 original size:26 final size:26
Alignment explanation
Indices: 16055936--16055989 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
16055926 CATCAGTAGC
*
16055936 ATCGCAGAAAATCTGCCAGCAACAGT
1 ATCGCAGAAAAGCTGCCAGCAACAGT
* * *
16055962 ATCGCAGCAAAGCTGCTAGTAACAGT
1 ATCGCAGAAAAGCTGCCAGCAACAGT
16055988 AT
1 AT
16055990 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (26 bp):
ATCGCAGAAAAGCTGCCAGCAACAGT
Found at i:16056146 original size:13 final size:14
Alignment explanation
Indices: 16056125--16056163 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
16056115 ACAAATCACA
16056125 AACAAATCAGTCAT
1 AACAAATCAGTCAT
16056139 AA-AAATCA-T-A-
1 AACAAATCAGTCAT
16056149 AACAAATCAGTCAT
1 AACAAATCAGTCAT
16056163 A
1 A
16056164 CATAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
10 2 0.10
11 7 0.33
12 2 0.10
13 7 0.33
14 3 0.14
ACGTcount: A:0.56, C:0.18, G:0.05, T:0.21
Consensus pattern (14 bp):
AACAAATCAGTCAT
Found at i:16056173 original size:24 final size:24
Alignment explanation
Indices: 16056112--16056163 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
16056102 CAGAATTGGC
* *
16056112 CATACAAATCACAAACAAATCAGT
1 CATAAAAATCATAAACAAATCAGT
16056136 CATAAAAATCATAAACAAATCAGT
1 CATAAAAATCATAAACAAATCAGT
16056160 CATA
1 CATA
16056164 CATAACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.21, G:0.04, T:0.19
Consensus pattern (24 bp):
CATAAAAATCATAAACAAATCAGT
Found at i:16056330 original size:26 final size:27
Alignment explanation
Indices: 16056288--16056364 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
16056278 GGATATATTG
*
16056288 GTCAATTTA-CCTAACAGAGGTATTACA
1 GTCATTTTATCCT-ACAGAGGTATTACA
* * * *
16056315 GTCATTTT-TCCTACAGGGGCATCACG
1 GTCATTTTATCCTACAGAGGTATTACA
16056341 GTCATTTTATCCTACA-AGGGTATT
1 GTCATTTTATCCTACAGA-GGTATT
16056365 TTGGTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 18 0.46
27 21 0.54
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
GTCATTTTATCCTACAGAGGTATTACA
Found at i:16056374 original size:27 final size:27
Alignment explanation
Indices: 16056344--16056581 Score: 162
Period size: 27 Copynumber: 8.8 Consensus size: 27
16056334 CATCACGGTC
16056344 ATTTTATCCTA-CAAGGGTATTTTGGTA
1 ATTTTA-CCTATCAAGGGTATTTTGGTA
* * * *
16056371 ATTTCACCCATCGAGGGTATTTTTGTA
1 ATTTTACCTATCAAGGGTATTTTGGTA
*
16056398 ATTTTACCTATCAGGGGTATTTTGGTA
1 ATTTTACCTATCAAGGGTATTTTGGTA
* **
16056425 ATTTTACCCA--AAGGGGGTATTTCAGTA
1 ATTTTACCTATCAA--GGGTATTTTGGTA
* * ** * *
16056452 ATTTAACCCAAT-GGGGGCATTTCGGTA
1 ATTTTA-CCTATCAAGGGTATTTTGGTA
* **
16056479 ATTTTACATATTGAGGGTATTTTGGTA
1 ATTTTACCTATCAAGGGTATTTTGGTA
* * *
16056506 ATTTTACCCATTAGGGGTATTTTGGTA
1 ATTTTACCTATCAAGGGTATTTTGGTA
* * ***
16056533 AATTTACCTATCGAGGGTATTTCAATA
1 ATTTTACCTATCAAGGGTATTTTGGTA
*
16056560 ATTTTACCCT-GCAAGGGTATTT
1 ATTTTA-CCTATCAAGGGTATTT
16056582 CGATATTTGC
Statistics
Matches: 164, Mismatches: 40, Indels: 14
0.75 0.18 0.06
Matches are distributed among these distances:
25 1 0.01
26 6 0.04
27 151 0.92
28 6 0.04
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCTATCAAGGGTATTTTGGTA
Found at i:16056416 original size:54 final size:55
Alignment explanation
Indices: 16056344--16056569 Score: 226
Period size: 54 Copynumber: 4.2 Consensus size: 55
16056334 CATCACGGTC
* * * *
16056344 ATTTTATCCTA-CAAGGGTATTTTGGTAATTTCACCCATCGAGGGTATTTTTGTA
1 ATTTTACCCTATCAGGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTTAGTA
** * *
16056398 ATTTTA-CCTATCAGGGGTATTTTGGTAATTTTACCCAAAGGGGGTATTTCAGTA
1 ATTTTACCCTATCAGGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTTAGTA
* * * * * ** * *
16056452 ATTTAACCCAAT-GGGGGCATTTCGGTAATTTTACATATTGAGGGTATTTTGGTA
1 ATTTTACCCTATCAGGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTTAGTA
* * * * *
16056506 ATTTTACCC-ATTAGGGGTATTTTGGTAAATTTACCTATCGAGGGTATTTCAATA
1 ATTTTACCCTATCAGGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTTAGTA
16056560 ATTTTACCCT
1 ATTTTACCCT
16056570 GCAAGGGTAT
Statistics
Matches: 139, Mismatches: 29, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
53 6 0.04
54 129 0.93
55 4 0.03
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (55 bp):
ATTTTACCCTATCAGGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTTAGTA
Found at i:16056443 original size:81 final size:80
Alignment explanation
Indices: 16056358--16056566 Score: 235
Period size: 81 Copynumber: 2.6 Consensus size: 80
16056348 TATCCTACAA
** *
16056358 GGGTATTTTGGTAATTTCACCCATCGAGGGTATTTTTGTAATTTTACCTATCAG-GGGTATTTTG
1 GGGTATTTTGGTAATTT-ACCCATCGAGGGTATTTCGGTAATTTTACATAT-AGAGGGTATTTTG
16056422 GTAATTTTACCCA-AAGG
64 GTAATTTTACCCATAA-G
** * * *
16056439 GGGTATTTCAGTAATTTAACCCAAT-GGGGGCATTTCGGTAATTTTACATATTGAGGGTATTTTG
1 GGGTATTTTGGTAATTT-ACCC-ATCGAGGGTATTTCGGTAATTTTACATATAGAGGGTATTTTG
*
16056503 GTAATTTTACCCATTAG
64 GTAATTTTACCCATAAG
* **
16056520 GGGTATTTTGGTAAATTTACCTATCGAGGGTATTTCAATAATTTTAC
1 GGGTATTTTGGT-AATTTACCCATCGAGGGTATTTCGGTAATTTTAC
16056567 CCTGCAAGGG
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
80 3 0.03
81 95 0.90
82 8 0.08
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTACCCATCGAGGGTATTTCGGTAATTTTACATATAGAGGGTATTTTGGT
AATTTTACCCATAAG
Found at i:16058796 original size:9 final size:9
Alignment explanation
Indices: 16058782--16058806 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16058772 GGTGAAATTG
16058782 TGAAATAAA
1 TGAAATAAA
16058791 TGAAATAAA
1 TGAAATAAA
16058800 TGAAATA
1 TGAAATA
16058807 TAGGGCTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
TGAAATAAA
Found at i:16063181 original size:44 final size:43
Alignment explanation
Indices: 16063091--16063196 Score: 119
Period size: 44 Copynumber: 2.4 Consensus size: 43
16063081 AACGCCATCA
* *
16063091 TCCCAGACGTGGTCTTACATGTAATCACATATTGATGCCACTG
1 TCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCACTG
16063134 TCCCAGACAG-GGTCTTACACGTAAATCACA-AGTCGATGCCAAC-G
1 TCCCAGAC-GTGGTCTTACACGT-AATCACATA-TCGATGCC-ACTG
* *
16063178 TCCCAAATGTGGTCTTACA
1 TCCCAGACGTGGTCTTACA
16063197 TGACAACACA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 21 0.39
44 31 0.57
45 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
TCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCACTG
Found at i:16068584 original size:12 final size:12
Alignment explanation
Indices: 16068559--16068597 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16068549 ACTCACTTCT
* *
16068559 TTACTTACTCAC
1 TTACTTGCTTAC
*
16068571 TTACTTGTTTAC
1 TTACTTGCTTAC
16068583 TTACTTGCTTAC
1 TTACTTGCTTAC
16068595 TTA
1 TTA
16068598 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:16068940 original size:50 final size:50
Alignment explanation
Indices: 16068847--16069041 Score: 194
Period size: 50 Copynumber: 3.9 Consensus size: 50
16068837 TTTTCTGTAC
* * * * * * ** * *
16068847 TGCCAATGTCATATCCCAGATATGGTCGTACACGGGAGTTCTCATGTTGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
16068897 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
16068947 TGCCAACGCCATGTCCCAGGCATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
16068997 TGTCAATGCCATGT-CTCAAACATGGTTTTACATGGGACCTCTCAT
1 TGCCAATGCCATGTCCT-AGACATGGTCTTACATGGGACCTCTCAT
16069042 AATCTCAATG
Statistics
Matches: 118, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
49 1 0.01
50 117 0.99
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:16073675 original size:44 final size:43
Alignment explanation
Indices: 16073576--16073692 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 43
16073566 GTTTCATACA
* *
16073576 ATGCCATCGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
16073619 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAATCACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGT-AATCACATA-TCG
16073663 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
16073693 ACAACACATA
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
42 1 0.02
43 27 0.41
44 36 0.55
45 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:16074523 original size:5 final size:6
Alignment explanation
Indices: 16074504--16074533 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
16074494 CGAATATGGC
16074504 TTTCTT TTTCTT TTTCTT TTTC-T TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
16074534 AACTAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:16079084 original size:42 final size:42
Alignment explanation
Indices: 16078996--16079234 Score: 219
Period size: 42 Copynumber: 5.6 Consensus size: 42
16078986 AATAAAAGCT
*** * * **
16078996 GCTAAAGGTCATGTTCTTTAGCGGCGCTTCAAAAAAAATGTT
1 GCTAAAGGTCATGTTCTTTAGCGGCGCTTCCTCACAAACGCC
*
16079038 GCTAAAGGTCATGTTCTTTAGCGGCGCTTCCTCAGAAACGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGCTTCCTCACAAACGCC
* * * *
16079080 GCTAAAGGTAATGTTCTTTAGCAGCGCATACC-AACAAACGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGC-TTCCTCACAAACGCC
** ** * *
16079122 GCTAAAGAACATGACCTTTAGCGGTGCTTTCTCCACAAACGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGCTTCCT-CACAAACGCC
* * ** **
16079165 GCTAAAAGTAATGTTCTTTAGCGGCATTTTTTTCCACAAACGCC
1 GCTAAAGGTCATGTTCTTTAGCGGC-GCTTCCT-CACAAACGCC
16079209 GCTAAAGGTCATGTTCTTTAGCGGCG
1 GCTAAAGGTCATGTTCTTTAGCGGCG
16079235 ATTTTTTTCA
Statistics
Matches: 158, Mismatches: 35, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
41 2 0.01
42 88 0.56
43 30 0.19
44 38 0.24
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (42 bp):
GCTAAAGGTCATGTTCTTTAGCGGCGCTTCCTCACAAACGCC
Found at i:16079170 original size:43 final size:42
Alignment explanation
Indices: 16079113--16079215 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
16079103 GCGCATACCA
16079113 ACAAACGCCGCTAAAGAACATGACCTTTAGCGG-TGCTTTCTCC
1 ACAAACGCCGCTAAAGAA-ATGACCTTTAGCGGAT-CTTTCTCC
* ** * *
16079156 ACAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCATTTTTTTCC
1 ACAAACGCCGCT-AAAGAAATGACCTTTAGCGG-ATCTTTCTCC
16079200 ACAAACGCCGCTAAAG
1 ACAAACGCCGCTAAAG
16079216 GTCATGTTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
43 28 0.54
44 23 0.44
45 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGAAATGACCTTTAGCGGATCTTTCTCC
Found at i:16079213 original size:44 final size:45
Alignment explanation
Indices: 16079153--16079252 Score: 168
Period size: 44 Copynumber: 2.3 Consensus size: 45
16079143 CGGTGCTTTC
16079153 TCCACAAACGCCGCTAAAAGTAATGTTCTTTAGCGGC-ATTTTTT
1 TCCACAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGATTTTTT
* *
16079197 TCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGATTTTTT
1 TCCACAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGATTTTTT
16079242 T-CACAAACGCC
1 TCCACAAACGCC
16079253 TCCATAGAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
44 45 0.85
45 8 0.15
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (45 bp):
TCCACAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGATTTTTT
Found at i:16081243 original size:9 final size:9
Alignment explanation
Indices: 16081226--16081639 Score: 183
Period size: 9 Copynumber: 48.4 Consensus size: 9
16081216 TAAGTATAAT
*
16081226 TAAGCTATG
1 TAAGTTATG
16081235 TAAGTTATG
1 TAAGTTATG
16081244 TAAGTTATG
1 TAAGTTATG
16081253 T-A-TTATG
1 TAAGTTATG
16081260 TAAGTTAT-
1 TAAGTTATG
*
16081268 TTA-TTATG
1 TAAGTTATG
* *
16081276 AAAATTATG
1 TAAGTTATG
16081285 TAAGTTATG
1 TAAGTTATG
16081294 T-A-TTATG
1 TAAGTTATG
*
16081301 -AATATTATG
1 TAA-GTTATG
*
16081310 TAAGTTGTG
1 TAAGTTATG
16081319 -AA-TTATG
1 TAAGTTATG
16081326 TAAGTGT-TG
1 TAAGT-TATG
16081335 T-A-TTATG
1 TAAGTTATG
16081342 ATCAA-TTATG
1 -T-AAGTTATG
16081352 TAAGTTATG
1 TAAGTTATG
16081361 T-A-TTATG
1 TAAGTTATG
* *
16081368 AAAATTATG
1 TAAGTTATG
*
16081377 TAAGTTGTG
1 TAAGTTATG
*
16081386 T-ACTGTA--
1 TAAGT-TATG
16081393 TAAGTTATG
1 TAAGTTATG
16081402 TAAGTTATG
1 TAAGTTATG
* *
16081411 AAAATTATG
1 TAAGTTATG
16081420 TAAGTTATG
1 TAAGTTATG
*
16081429 TAAGTT-TT
1 TAAGTTATG
*
16081437 TTA-TTATG
1 TAAGTTATG
* * *
16081445 AAAATTAAG
1 TAAGTTATG
*
16081454 TAACTTATG
1 TAAGTTATG
16081463 T-A-TTATG
1 TAAGTTATG
* *
16081470 AAAATTATG
1 TAAGTTATG
*
16081479 TAAGTTCA-A
1 TAAGTT-ATG
16081488 T-A-TTATG
1 TAAGTTATG
16081495 TAAGTTATG
1 TAAGTTATG
*
16081504 T-A-CTATG
1 TAAGTTATG
* *
16081511 AAAATTATG
1 TAAGTTATG
16081520 TAAGTTATG
1 TAAGTTATG
* **
16081529 TATGTTGGG
1 TAAGTTATG
*
16081538 T-ATTATATG
1 TAAGT-TATG
16081547 TAAGTTATG
1 TAAGTTATG
*
16081556 TATGTGTATAATG
1 TA--AGT-T-ATG
*
16081569 AAAGTTATG
1 TAAGTTATG
*
16081578 TAAGTTGTG
1 TAAGTTATG
*
16081587 T-A-TAATG
1 TAAGTTATG
16081594 TAAGTTATG
1 TAAGTTATG
*
16081603 TAAGTTAAG
1 TAAGTTATG
*
16081612 T-A-TAAT-
1 TAAGTTATG
*
16081618 TAAGCTATG
1 TAAGTTATG
16081627 TAAGTTATG
1 TAAGTTATG
16081636 TAAG
1 TAAG
16081640 ATGTGATAGT
Statistics
Matches: 301, Mismatches: 61, Indels: 86
0.67 0.14 0.19
Matches are distributed among these distances:
6 3 0.01
7 52 0.17
8 37 0.12
9 187 0.62
10 13 0.04
11 4 0.01
12 1 0.00
13 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:16081259 original size:25 final size:25
Alignment explanation
Indices: 16081231--16081484 Score: 130
Period size: 25 Copynumber: 10.4 Consensus size: 25
16081221 ATAATTAAGC
16081231 TATGTAAGTTATGTAAGTTATG-TAT
1 TATGTAAGTTATGTAA-TTATGATAT
* *
16081256 TATGTAAGTTAT-TTATTATGAAAAT
1 TATGTAAGTTATGTAATTATG-ATAT
16081281 TATGTAAGTTATGT-ATTATGAATAT
1 TATGTAAGTTATGTAATTATG-ATAT
*
16081306 TATGTAAGTTGTG-AATTATG-TA-
1 TATGTAAGTTATGTAATTATGATAT
* * *
16081328 -AGTGT-TG-TAT-T-ATGATCA-AT
1 TA-TGTAAGTTATGTAATTATGATAT
*
16081348 TATGTAAGTTATGT-ATTATGAAAAT
1 TATGTAAGTTATGTAATTATG-ATAT
* *
16081373 TATGTAAGTTGTGTACTGTAT-A-AGT
1 TATGTAAGTTATGTAAT-TATGATA-T
*
16081398 TATGTAAGTTATGAAAATTATG-TAAGT
1 TATGTAAGTTATG-TAATTATGAT-A-T
* * *
16081425 TATGTAAGTT-TTTTATTATGAAAAT
1 TATGTAAGTTATGTAATTATG-ATAT
* * *
16081450 TAAGTAACTTATGT-ATTATGAAAAT
1 TATGTAAGTTATGTAATTATG-ATAT
16081475 TATGTAAGTT
1 TATGTAAGTT
16081485 CAATATTATG
Statistics
Matches: 180, Mismatches: 25, Indels: 48
0.71 0.10 0.19
Matches are distributed among these distances:
19 5 0.03
20 5 0.03
21 4 0.02
22 6 0.03
23 12 0.07
24 4 0.02
25 120 0.67
26 8 0.04
27 16 0.09
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (25 bp):
TATGTAAGTTATGTAATTATGATAT
Found at i:16081260 original size:16 final size:16
Alignment explanation
Indices: 16081239--16081604 Score: 144
Period size: 16 Copynumber: 22.0 Consensus size: 16
16081229 GCTATGTAAG
16081239 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
16081255 TTATGTAAGTTATTTA
1 TTATGTAAGTTATGTA
* *
16081271 TTATGAAAATTATGTAA
1 TTATGTAAGTTATGT-A
16081288 GTTATGT-A-TTATGAATA
1 -TTATGTAAGTTATG--TA
* *
16081305 TTATGTAAGTTGTGAA
1 TTATGTAAGTTATGTA
16081321 TTATGTAAGTGT-TGTA
1 TTATGTAAGT-TATGTA
16081337 TTATGATCAA-TTATGTAA
1 TTATG-T-AAGTTATGT-A
*
16081355 GTTATGT-A-TTATGAAAA
1 -TTATGTAAGTTATG--TA
*
16081372 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* * *
16081388 CTGTATAAGTTATGTAA
1 TTATGTAAGTTATGT-A
* *
16081405 GTTATGAAAATTATGTAA
1 -TTATGTAAGTTATGT-A
* *
16081423 GTTATGTAAGTTTTTTA
1 -TTATGTAAGTTATGTA
* * *
16081440 TTATGAAAATTAAGTAA
1 TTATGTAAGTTATGT-A
*
16081457 CTTATGT-A-TTATGAAAA
1 -TTATGTAAGTTATG--TA
*
16081474 TTATGTAAGTTCA-ATA
1 TTATGTAAGTT-ATGTA
16081490 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* * *
16081506 CTATGAAAATTATGTAA
1 TTATGTAAGTTATGT-A
* **
16081523 GTTATGTATGTTGGGTA
1 -TTATGTAAGTTATGTA
16081540 TTATATGTAAGTTATGTA
1 -T-TATGTAAGTTATGTA
* * *
16081558 -TGTGT-A-TAATGAAA
1 TTATGTAAGTTATG-TA
*
16081572 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
*
16081589 TAATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
16081605 AGTTAAGTAT
Statistics
Matches: 259, Mismatches: 57, Indels: 68
0.67 0.15 0.18
Matches are distributed among these distances:
13 4 0.02
14 2 0.01
15 5 0.02
16 146 0.56
17 23 0.09
18 73 0.28
19 6 0.02
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:16081354 original size:92 final size:93
Alignment explanation
Indices: 16081254--16081424 Score: 258
Period size: 92 Copynumber: 1.8 Consensus size: 93
16081244 TAAGTTATGT
* *
16081254 ATTATGTAAGTTATTTATTATGAAAATTATGTAAGTTATGTA-T-TATGAATATTATGTAAGTTG
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTACTGTAT-AA-ATTATGTAAGTTA
16081317 TG-AATTATGTAAGTGTTGTATTATGATCA
64 TGAAATTATGTAAGTGTTGTATTATGATCA
* *
16081346 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTGTGTACTGTATAAGTTATGTAAGTTATG
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTACTGTATAAATTATGTAAGTTATG
16081411 AAAATTATGTAAGT
66 -AAATTATGTAAGT
16081425 TATGTAAGTT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
92 53 0.75
93 3 0.04
94 15 0.21
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (93 bp):
ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTATGTACTGTATAAATTATGTAAGTTATG
AAATTATGTAAGTGTTGTATTATGATCA
Found at i:16081511 original size:41 final size:41
Alignment explanation
Indices: 16081448--16081525 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
16081438 TATTATGAAA
*
16081448 ATTAAGTAACTTATGTATTATGAAAATTATGTAAGTTCAAT
1 ATTAAGTAACTTATGTACTATGAAAATTATGTAAGTTCAAT
* *
16081489 ATTATGTAAGTTATGTACTATGAAAATTATGTAAGTT
1 ATTAAGTAACTTATGTACTATGAAAATTATGTAAGTT
16081526 ATGTATGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (41 bp):
ATTAAGTAACTTATGTACTATGAAAATTATGTAAGTTCAAT
Found at i:16081605 original size:25 final size:25
Alignment explanation
Indices: 16081321--16081637 Score: 207
Period size: 25 Copynumber: 12.6 Consensus size: 25
16081311 AAGTTGTGAA
16081321 TTATGTAAG-TGTTGTATTATGATCAA-
1 TTATGTAAGTTG-TGTATTATG-T-AAG
* * *
16081347 TTATGTAAGTTATGTATTATGAAAA
1 TTATGTAAGTTGTGTATTATGTAAG
* * *
16081372 TTATGTAAGTTGTGTACTGTATAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* *
16081397 TTATGTAAGTTATGAAAATTATGTAAG
1 TTATGTAAGTTGTG--TATTATGTAAG
* * * *
16081424 TTATGTAAGTTTTTTATTATGAAAA
1 TTATGTAAGTTGTGTATTATGTAAG
* * * * *
16081449 TTAAGTAACTTATGTATTATGAAAA
1 TTATGTAAGTTGTGTATTATGTAAG
***
16081474 TTATGTAAGTTCAATATTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* ***
16081499 TTATGT-ACTATGAAAATTATGTAAG
1 TTATGTAAGT-TGTGTATTATGTAAG
* *
16081524 TTATGTATGTTGGGTATTATATGTAAG
1 TTATGTAAGTTGTGTA-T-TATGTAAG
* *
16081551 TTATGT-A--TGTGTATAATGAAAG
1 TTATGTAAGTTGTGTATTATGTAAG
*
16081573 TTATGTAAGTTGTGTATAATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
** *
16081598 TTATGTAAGTTAAGTATAAT-TAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* *
16081622 CTATGTAAGTTATGTA
1 TTATGTAAGTTGTGTA
16081638 AGATGTGATA
Statistics
Matches: 234, Mismatches: 46, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
22 12 0.05
23 2 0.01
24 27 0.12
25 139 0.59
26 20 0.09
27 34 0.15
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.44
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATTATGTAAG
Found at i:16082474 original size:14 final size:13
Alignment explanation
Indices: 16082441--16082482 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
16082431 ATAAATACGC
16082441 TAAA-AATATAAA
1 TAAATAATATAAA
16082453 TAAATAATATAATA
1 TAAATAATATAA-A
*
16082467 TCAATAATATTAAA
1 TAAATAATA-TAAA
16082481 TA
1 TA
16082483 TGCTGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 11 0.44
15 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAATATAAA
Found at i:16082893 original size:16 final size:16
Alignment explanation
Indices: 16082872--16082929 Score: 80
Period size: 16 Copynumber: 3.4 Consensus size: 16
16082862 ACTCATCTGC
16082872 TTAACATTCAAAATGT
1 TTAACATTCAAAATGT
*
16082888 TTAACATTCAAAACATAGC
1 TTAACATTC-AAA-AT-GT
16082907 TTAACATTCAAAATGT
1 TTAACATTCAAAATGT
16082923 TTAACAT
1 TTAACAT
16082930 AGCTTAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 17 0.46
17 5 0.14
18 5 0.14
19 10 0.27
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (16 bp):
TTAACATTCAAAATGT
Found at i:16084967 original size:14 final size:14
Alignment explanation
Indices: 16084950--16084982 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16084940 CCTTAAATTA
*
16084950 TAAACTGCAAAGCG
1 TAAACTGCAAACCG
16084964 TAAACTGCAAACCG
1 TAAACTGCAAACCG
16084978 TAAAC
1 TAAAC
16084983 CACAAGCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.24, G:0.15, T:0.15
Consensus pattern (14 bp):
TAAACTGCAAACCG
Found at i:16085107 original size:7 final size:7
Alignment explanation
Indices: 16085056--16085139 Score: 55
Period size: 7 Copynumber: 12.0 Consensus size: 7
16085046 ACTAAAGTGG
16085056 CCTAAATC
1 CCTAAA-C
16085064 CC-AAAC
1 CCTAAAC
*
16085070 CCCAAAC
1 CCTAAAC
*
16085077 CTTAAAC
1 CCTAAAC
*
16085084 CTTAAAC
1 CCTAAAC
*
16085091 TCTCAAAC
1 CCT-AAAC
16085099 CCTAAAC
1 CCTAAAC
*
16085106 CCAAAAC
1 CCTAAAC
*
16085113 ACTAAA-
1 CCTAAAC
* *
16085119 CCTACAT
1 CCTAAAC
*
16085126 CATAAAC
1 CCTAAAC
16085133 CCTAAAC
1 CCTAAAC
16085140 TCAAAACTCT
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
6 7 0.12
7 44 0.75
8 8 0.14
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:16085146 original size:27 final size:27
Alignment explanation
Indices: 16085101--16085154 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
16085091 TCTCAAACCC
*
16085101 TAAACCCAAAACACTAAAC-CTACATCA
1 TAAACCCAAAACACAAAACTCTA-ATCA
* *
16085128 TAAACCCTAAACTCAAAACTCTAATCA
1 TAAACCCAAAACACAAAACTCTAATCA
16085155 GAAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (27 bp):
TAAACCCAAAACACAAAACTCTAATCA
Found at i:16085795 original size:113 final size:114
Alignment explanation
Indices: 16085597--16085847 Score: 258
Period size: 113 Copynumber: 2.2 Consensus size: 114
16085587 GTTTGTTAGT
* * * * * * *
16085597 AAGCGCCACAAAAGAAATCAAATGGAAATAAAACGAAGTCGTATTACTGAAATTATTTTGCGGCG
1 AAGCGCCACTAAAGAAAT-AAAAGGAAAAAAAACAAAGTCGTATTACTCAAATTATTTTACAGCG
*
16085662 TTTCTACATAAGCGCTGCTAAAGGC-CCATCTATTGCAGCGATTTTATT-A
65 TTTCTACATAAGCGCCGCTAAA-GCACCATCTATTGCAGCGATTTTATTAA
*
16085711 AAGCGCCACTAAAGAAATAAAAGGAAAAAAAACAAAGTCGT-TTAGCTCAAATTCTTTTACAGCG
1 AAGCGCCACTAAAGAAATAAAAGGAAAAAAAACAAAGTCGTATTA-CTCAAATTATTTTACAGCG
** * * *** * * *
16085775 TTTTCTATGT-TGCGCCGCTAAATCATGTTCTATTGCGGCGTTTTTTTTAA
65 -TTTCTACATAAGCGCCGCTAAAGCACCATCTATTGCAGCGATTTTATTAA
*
16085825 AAGCGCCACTAAAGAAATGAAAG
1 AAGCGCCACTAAAGAAATAAAAG
16085848 AAGCATAGAA
Statistics
Matches: 113, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
112 4 0.04
113 62 0.55
114 47 0.42
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (114 bp):
AAGCGCCACTAAAGAAATAAAAGGAAAAAAAACAAAGTCGTATTACTCAAATTATTTTACAGCGT
TTCTACATAAGCGCCGCTAAAGCACCATCTATTGCAGCGATTTTATTAA
Found at i:16089245 original size:20 final size:21
Alignment explanation
Indices: 16089186--16089245 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 21
16089176 CTTCTAAAGT
16089186 TACCAAA-TTTGAAGCTAAGCATA
1 TACCAAACTTT-AAGCTAAGC--A
* * *
16089209 TACCAAGCATTATGCTAAGC-
1 TACCAAACTTTAAGCTAAGCA
16089229 TACCAAACTTTAAGCTA
1 TACCAAACTTTAAGCTA
16089246 TCACATACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 14 0.47
23 14 0.47
24 2 0.07
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.27
Consensus pattern (21 bp):
TACCAAACTTTAAGCTAAGCA
Found at i:16089783 original size:19 final size:19
Alignment explanation
Indices: 16089732--16089796 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 19
16089722 CACTTCTTGA
*
16089732 ATTCATTTCA--AGTTCAC
1 ATTCATTTCATCATTTCAC
*
16089749 ATCTCATTTCATCATTTCAT
1 AT-TCATTTCATCATTTCAC
16089769 ATTTCATTT-ATCATTTCAC
1 A-TTCATTTCATCATTTCAC
16089788 ATTCATTTC
1 ATTCATTTC
16089797 TCTTCTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 2 0.05
18 15 0.38
19 10 0.25
20 12 0.30
21 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTCATTTCATCATTTCAC
Found at i:16089828 original size:25 final size:25
Alignment explanation
Indices: 16089793--16089864 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
16089783 TTCACATTCA
*
16089793 TTTCTCTTCTTTGTCATTTCAATAT
1 TTTCTCATCTTTGTCATTTCAATAT
16089818 TTTCTCATCTTT-TCCATTTCAATAT
1 TTTCTCATCTTTGT-CATTTCAATAT
* *
16089843 TTTCTCATCTTAGCCATTTCAA
1 TTTCTCATCTTTGTCATTTCAA
16089865 AATCAATCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (25 bp):
TTTCTCATCTTTGTCATTTCAATAT
Found at i:16090993 original size:9 final size:9
Alignment explanation
Indices: 16090979--16091014 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
16090969 CGTTCTCTCC
16090979 TTCTTTTCT
1 TTCTTTTCT
16090988 TTC-TTTCT
1 TTCTTTTCT
16090996 TTCCTTTTCT
1 TT-CTTTTCT
16091006 TTCTTTTCT
1 TTCTTTTCT
16091015 AATTTGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:16092875 original size:24 final size:24
Alignment explanation
Indices: 16092825--16092876 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16092815 TTCGTAACTC
* *
16092825 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
* *
16092849 AAATATATTATACTAATAAATATT
1 AAATAAATTATACTAATAAATACT
16092873 AAAT
1 AAAT
16092877 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:16093850 original size:46 final size:46
Alignment explanation
Indices: 16093797--16093894 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
16093787 TATAATCTAC
*
16093797 GTAGGGGCAAGCTAAAATGTAATGTCGATG-TAGCGATTTCAAATAT
1 GTAGGGGCAAGCTAAAATGTAATATCGATGCT-GCGATTTCAAATAT
* **
16093843 GTAGGGGCAAGCTGAAATGTAATATCGATGCTGTTATTTCAAATAT
1 GTAGGGGCAAGCTAAAATGTAATATCGATGCTGCGATTTCAAATAT
*
16093889 GAAGGG
1 GTAGGG
16093895 TTGACGAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.29
Consensus pattern (46 bp):
GTAGGGGCAAGCTAAAATGTAATATCGATGCTGCGATTTCAAATAT
Found at i:16096771 original size:23 final size:23
Alignment explanation
Indices: 16096741--16096790 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
16096731 AATTGTTAGT
16096741 AGAGATGTTACGTTTGATGAATC
1 AGAGATGTTACGTTTGATGAATC
16096764 AGAGATGTTACGTTTGATGAATC
1 AGAGATGTTACGTTTGATGAATC
16096787 AGAG
1 AGAG
16096791 TGGCATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (23 bp):
AGAGATGTTACGTTTGATGAATC
Found at i:16099610 original size:52 final size:52
Alignment explanation
Indices: 16099553--16099691 Score: 128
Period size: 50 Copynumber: 2.7 Consensus size: 52
16099543 TATTGTGTCA
* * *
16099553 TAATTATTATTAATTTAATTAAGAGATAAATATTAATTTTTTATATTT-TCAC
1 TAATTATTATTAAATTAATTAAGAGATAAATATTAAATTATTAT-TTTATCAC
** * * *
16099605 TAATTAAAAATAAAATAATTAA-ATGAT-AATATTAAATTATTATTTTATCTC
1 TAATTATTATTAAATTAATTAAGA-GATAAATATTAAATTATTATTTTATCAC
*
16099656 TAA--ATTAATTAAATTAA-TAAGAGATAAATAATAAAT
1 TAATTATT-ATTAAATTAATTAAGAGATAAATATTAAAT
16099692 AAATAATAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
49 7 0.10
50 21 0.30
51 21 0.30
52 20 0.29
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (52 bp):
TAATTATTATTAAATTAATTAAGAGATAAATATTAAATTATTATTTTATCAC
Found at i:16099693 original size:11 final size:11
Alignment explanation
Indices: 16099665--16099705 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
16099655 CTAAATTAAT
*
16099665 TAAATTAATAA
1 TAAATAAATAA
* *
16099676 GAGATAAATAA
1 TAAATAAATAA
16099687 TAAATAAATAA
1 TAAATAAATAA
16099698 TAAATAAA
1 TAAATAAA
16099706 AGGGTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:16101169 original size:12 final size:12
Alignment explanation
Indices: 16101152--16101182 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16101142 CCTCACACAC
16101152 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
16101164 CCGTGTGCTAGG
1 CCGTGTGCCAGG
16101176 CCGTGTG
1 CCGTGTG
16101183 AAGCTACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.29, G:0.42, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:16110677 original size:22 final size:22
Alignment explanation
Indices: 16110638--16110680 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16110628 CCTTTATGTT
*
16110638 GGTCACTTGTCTTCGAGGACAA
1 GGTCACGTGTCTTCGAGGACAA
16110660 GGTCACGTGATCTT-GAGGACA
1 GGTCACGTG-TCTTCGAGGACA
16110681 TGTTTAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (22 bp):
GGTCACGTGTCTTCGAGGACAA
Found at i:16113954 original size:11 final size:11
Alignment explanation
Indices: 16113938--16113971 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
16113928 TTATTTAGAA
16113938 AACTTCGATTG
1 AACTTCGATTG
16113949 AACTTCGATTG
1 AACTTCGATTG
16113960 AACTTCGATTG
1 AACTTCGATTG
16113971 A
1 A
16113972 TTACAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (11 bp):
AACTTCGATTG
Found at i:16114164 original size:14 final size:14
Alignment explanation
Indices: 16114118--16114166 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
16114108 AAAAAATTAA
16114118 TATAC-TTTTGACT
1 TATACTTTTTGACT
*
16114131 CATACTTTTAT-AC-
1 TATACTTTT-TGACT
16114144 T-TACTTTTTGACT
1 TATACTTTTTGACT
16114157 TATACTTTTT
1 TATACTTTTT
16114167 TGTAAGAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
11 1 0.03
12 9 0.31
13 5 0.17
14 13 0.45
15 1 0.03
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (14 bp):
TATACTTTTTGACT
Found at i:16114247 original size:40 final size:41
Alignment explanation
Indices: 16114190--16114269 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
16114180 CCTACTTTTT
*
16114190 TGACTAATATAAAAAACATAGTG-ACATCACATCTAATCTA
1 TGACTAATATAAAAAACATAATGAACATCACATCTAATCTA
* * *
16114230 TGACTCATATAACAAACATAATGAAACATCACGTCTAATC
1 TGACTAATATAAAAAACATAATG-AACATCACATCTAATC
16114270 ACTTTCATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 20 0.59
42 14 0.41
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (41 bp):
TGACTAATATAAAAAACATAATGAACATCACATCTAATCTA
Found at i:16122124 original size:19 final size:19
Alignment explanation
Indices: 16122100--16122137 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16122090 ATCGTGAGTT
16122100 GTGTATTTTGATACAGTCA
1 GTGTATTTTGATACAGTCA
16122119 GTGTATTTTGATACAGTCA
1 GTGTATTTTGATACAGTCA
16122138 AACATACACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (19 bp):
GTGTATTTTGATACAGTCA
Found at i:16124710 original size:14 final size:14
Alignment explanation
Indices: 16124691--16124719 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16124681 GGAGTAGTGT
16124691 TTACCTTAATGACA
1 TTACCTTAATGACA
16124705 TTACCTTAATGACA
1 TTACCTTAATGACA
16124719 T
1 T
16124720 CATCCTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (14 bp):
TTACCTTAATGACA
Found at i:16127234 original size:31 final size:31
Alignment explanation
Indices: 16127196--16127256 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
16127186 GGCCCATTTT
16127196 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAG
*
16127227 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
16127257 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAG
Found at i:16127236 original size:11 final size:11
Alignment explanation
Indices: 16127196--16127286 Score: 72
Period size: 11 Copynumber: 8.9 Consensus size: 11
16127186 GGCCCATTTT
16127196 TATTTT-AAAA
1 TATTTTAAAAA
16127206 -ATTTTAAAAA
1 TATTTTAAAAA
**
16127216 -ATTAAAAAAA
1 TATTTTAAAAA
16127226 GTATTTTAAAAA
1 -TATTTTAAAAA
16127238 TATTTT--AAA
1 TATTTTAAAAA
16127247 -A--TTAAAAA
1 TATTTTAAAAA
* **
16127255 AATTAAAAAAA
1 TATTTTAAAAA
16127266 TATTTTAAAAA
1 TATTTTAAAAA
16127277 TATTTTAAAA
1 TATTTTAAAA
16127287 TTAAAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.03
8 4 0.06
9 9 0.14
10 12 0.19
11 29 0.45
12 8 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:16127261 original size:40 final size:40
Alignment explanation
Indices: 16127196--16127335 Score: 205
Period size: 39 Copynumber: 3.5 Consensus size: 40
16127186 GGCCCATTTT
*
16127196 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
16127238 TATTTTAAAATTAAAAAAATTAAAAAAA-TATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
16127277 TATTTTAAAATTAAAAAAAATT-AAAAAAGTA-TGTAAAAA
1 TATTTTAAAATT-AAAAAAATTAAAAAAAGTATTTTAAAAA
*
16127316 TATTTTAAAATTTAAAAAAT
1 TATTTTAAAATTAAAAAAAT
16127336 ATATATATTT
Statistics
Matches: 93, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
38 7 0.08
39 48 0.52
40 28 0.30
41 4 0.04
42 6 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:16127927 original size:21 final size:21
Alignment explanation
Indices: 16127903--16127942 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16127893 TCTATAAAAA
16127903 ACTTATTTAACATA-ATTATAT
1 ACTTATTTAA-ATAGATTATAT
*
16127924 ACTTGTTTAAATAGATTAT
1 ACTTATTTAAATAGATTAT
16127943 CTATCTAGTC
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:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
ACTTATTTAAATAGATTATAT
Found at i:16142724 original size:58 final size:58
Alignment explanation
Indices: 16142649--16142790 Score: 144
Period size: 58 Copynumber: 2.4 Consensus size: 58
16142639 AGAGAGTTTA
* * * *
16142649 ATTATGATTAAACTTAATCACTTTAA-TATTCAACTAATATAATACTTATC-AAGATAAAT
1 ATTA-GATTAAATTTAAT-A-TTAAACTATTAAACTAATAGAATACTTATCTAAGATAAAT
* *
16142708 ATTAGATTAAATTTAATATTAAATCTATTAAATTAATAGAATATTTATCTATAAGATAAAT
1 ATTAGATTAAATTTAATATTAAA-CTATTAAACTAATAGAATACTTATC--TAAGATAAAT
* *
16142769 ATTAAATTTAATTTAATATTAA
1 ATTAGATTAAATTTAATATTAA
16142791 GATAATAACT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
56 4 0.06
57 1 0.01
58 32 0.46
59 4 0.06
61 29 0.41
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (58 bp):
ATTAGATTAAATTTAATATTAAACTATTAAACTAATAGAATACTTATCTAAGATAAAT
Found at i:16142815 original size:61 final size:60
Alignment explanation
Indices: 16142699--16142874 Score: 149
Period size: 61 Copynumber: 2.8 Consensus size: 60
16142689 AATACTTATC
* *
16142699 AAGATAAATATTAGATTAAATTTAATATTAAATCTATTAAATTAATAGAATATTTATCTAT
1 AAGATAAATATTAAATTAAATTTAATATTAAA-CTAATAAATTAATAGAATATTTATCTAT
* * *
16142760 AAGATAAATATTAAATTTAATTTAATATTAAGA-TAATAACTTTAATATTAA-ATTTATAAAATA
1 AAGATAAATATTAAATTAAATTTAATATTAA-ACTAATAA-ATTAATA-GAATA-TT-T---AT-
16142823 CTAT
57 CTAT
* * * *
16142827 CAAGATAAGTATTAAATTAAATATAATATTAAATCTATTAAAATAATA
1 -AAGATAAATATTAAATTAAATTTAATATTAAA-CTAATAAATTAATA
16142875 TTATTTTTGG
Statistics
Matches: 92, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
60 5 0.05
61 36 0.39
62 5 0.05
63 1 0.01
66 2 0.02
67 5 0.05
68 33 0.36
69 5 0.05
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (60 bp):
AAGATAAATATTAAATTAAATTTAATATTAAACTAATAAATTAATAGAATATTTATCTAT
Found at i:16142818 original size:20 final size:18
Alignment explanation
Indices: 16142766--16142818 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
16142756 CTATAAGATA
16142766 AATATTAAATT-TAATTT
1 AATATTAAATTATAATTT
*
16142783 AATATTAAGATAATAACTTT
1 AATATTAA-ATTATAA-TTT
16142803 AATATTAAATTTATAA
1 AATATTAAA-TTATAA
16142819 AATACTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 8 0.27
18 2 0.07
19 4 0.13
20 16 0.53
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATATTAAATTATAATTT
Found at i:16144113 original size:11 final size:11
Alignment explanation
Indices: 16144083--16144116 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16144073 GTCACAAGTG
16144083 AATTAATTCATA
1 AATTAATTCA-A
*
16144095 AATGAATTCAA
1 AATTAATTCAA
16144106 AATTAATTCAA
1 AATTAATTCAA
16144117 CTTGGGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (11 bp):
AATTAATTCAA
Found at i:16146602 original size:25 final size:25
Alignment explanation
Indices: 16146574--16146623 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
16146564 GAGTAGGGCC
* **
16146574 ATATTCACAGTTTGTGTGAGCATTT
1 ATATTCACAGCTCATGTGAGCATTT
16146599 ATATTCACAGCTCATGTGAGCATTT
1 ATATTCACAGCTCATGTGAGCATTT
16146624 CTATCACGAG
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:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (25 bp):
ATATTCACAGCTCATGTGAGCATTT
Found at i:16146616 original size:27 final size:23
Alignment explanation
Indices: 16146574--16146636 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 23
16146564 GAGTAGGGCC
*
16146574 ATATTCACAGTTTGTGTGAGCATTT
1 ATATTCACAG--TATGTGAGCATTT
16146599 ATATTCACAGCTCATGTGAGCATTT
1 ATATTCACAG-T-ATGTGAGCATTT
*
16146624 CTA-TCACGAGTAT
1 ATATTCAC-AGTAT
16146637 CCAATGTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.06
24 6 0.18
25 25 0.76
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATTCACAGTATGTGAGCATTT
Found at i:16152721 original size:40 final size:42
Alignment explanation
Indices: 16152667--16152744 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
16152657 TTAAAAATTT
16152667 AAAGTT-AA-AATATATTATA-ATATTATAATAATATTACTTA
1 AAAGTTAAATAATATATTATATATATTAT-ATAATATTACTTA
* * *
16152707 AAAGTTAAGTTATATATTATATATATTATATTATATTA
1 AAAGTTAAATAATATATTATATATATTATATAATATTA
16152745 TATTATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.19
41 1 0.03
42 18 0.56
43 7 0.22
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (42 bp):
AAAGTTAAATAATATATTATATATATTATATAATATTACTTA
Found at i:16152727 original size:5 final size:5
Alignment explanation
Indices: 16152719--16152752 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
16152709 AGTTAAGTTA
16152719 TATAT TATA- TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
16152753 AATAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:16152830 original size:6 final size:6
Alignment explanation
Indices: 16152819--16152851 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
16152809 AGAAAGAAAG
16152819 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
16152852 TTTGGGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:16157087 original size:31 final size:31
Alignment explanation
Indices: 16157007--16157087 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
16156997 GTCATCCTAG
*
16157007 GTTGCCCGACAATAATGACCCGCCACCTCGG
1 GTTGCCCGACAATAATGACCCGCCACCTCGA
** * * *
16157038 GTTGTTCGGCAACAATGACCTGCCACCTCGA
1 GTTGCCCGACAATAATGACCCGCCACCTCGA
*
16157069 GTTGCCCGACAATGATGAC
1 GTTGCCCGACAATAATGAC
16157088 TTACTAATAT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.20
Consensus pattern (31 bp):
GTTGCCCGACAATAATGACCCGCCACCTCGA
Found at i:16157266 original size:35 final size:35
Alignment explanation
Indices: 16157227--16157363 Score: 157
Period size: 35 Copynumber: 3.9 Consensus size: 35
16157217 AACATAGTGA
* * *
16157227 CATGCTTTACATGCAAATCAAAATAAGTATAATGG
1 CATGCTTAACATGCAAATCAAAATAAGAATAATAG
* * *
16157262 CATGCTTAACATGCAAATCATAATCAGAAAAATAG
1 CATGCTTAACATGCAAATCAAAATAAGAATAATAG
* * * *
16157297 CATGCTTAACATGCGAATCATAATTAGAATAATAA
1 CATGCTTAACATGCAAATCAAAATAAGAATAATAG
* * *
16157332 CATGTTTAACATGCGAATCAAAATAACAATAA
1 CATGCTTAACATGCAAATCAAAATAAGAATAA
16157364 ACTAGAGTCA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 88 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (35 bp):
CATGCTTAACATGCAAATCAAAATAAGAATAATAG
Found at i:16160158 original size:66 final size:66
Alignment explanation
Indices: 16160052--16160176 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
16160042 ATCCGAATAG
* * * * *
16160052 CTGTCAGGTGCAGCGACAATTCTGAATGAAATTTGGAATTAACCCATGCAGCGACATTACAGACA
1 CTGTCAGGTACAGCGACAATTCTGAACGAAATCTGAAATTAACCAATGCAGCGACATTACAGACA
16160117 T
66 T
* * *
16160118 CTGTCAGGTACAGCGACAATTCT-AGACGCAATCTGAAATTAACTAATGCAGCTACATTA
1 CTGTCAGGTACAGCGACAATTCTGA-ACGAAATCTGAAATTAACCAATGCAGCGACATTA
16160177 ATACAATAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
65 1 0.02
66 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (66 bp):
CTGTCAGGTACAGCGACAATTCTGAACGAAATCTGAAATTAACCAATGCAGCGACATTACAGACA
T
Found at i:16161194 original size:17 final size:17
Alignment explanation
Indices: 16161147--16161194 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
16161137 CATTGTCCCC
*
16161147 AATGCACTGAC-ATGAA
1 AATGCAATGACAATGAA
* *
16161163 AATGTAATGATAATGAA
1 AATGCAATGACAATGAA
*
16161180 AATGCAATGGCAATG
1 AATGCAATGACAATG
16161195 TATACTTATC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (17 bp):
AATGCAATGACAATGAA
Found at i:16162338 original size:17 final size:17
Alignment explanation
Indices: 16162316--16162355 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
16162306 AACTAAGATT
16162316 CCAGTCTGCCTTGCAGC
1 CCAGTCTGCCTTGCAGC
*
16162333 CCAGTCTGCCTTGTAGC
1 CCAGTCTGCCTTGCAGC
16162350 CCAGTC
1 CCAGTC
16162356 AGCTATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.40, G:0.23, T:0.25
Consensus pattern (17 bp):
CCAGTCTGCCTTGCAGC
Found at i:16169471 original size:19 final size:19
Alignment explanation
Indices: 16169447--16169493 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
16169437 TTCAAACCCT
*
16169447 AAGATTAAACAATAAAAGC
1 AAGATTAAAAAATAAAAGC
16169466 AAGATTAAAAAATAAAAGC
1 AAGATTAAAAAATAAAAGC
16169485 AAGATTAAA
1 AAGATTAAA
16169494 TAAGATAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (19 bp):
AAGATTAAAAAATAAAAGC
Found at i:16173460 original size:37 final size:37
Alignment explanation
Indices: 16173416--16173540 Score: 159
Period size: 37 Copynumber: 3.5 Consensus size: 37
16173406 GATGTTCTAG
* *
16173416 TTCGCATGTTAAACATGCTAATATTCTGATATTCTGA
1 TTCGCATGTTAAGCATGCTATTATTCTGATATTCTGA
* *
16173453 TTCGCATGTTAATCATGCTATTAATCTGAT-TT-TGA
1 TTCGCATGTTAAGCATGCTATTATTCTGATATTCTGA
* *
16173488 CTCGCATGTTAAGCATGCCATTATTTCTG--ATTCTGA
1 TTCGCATGTTAAGCATGCTATTA-TTCTGATATTCTGA
16173524 TTCGCATGTTAAGCATG
1 TTCGCATGTTAAGCATG
16173541 TCACTGTGTG
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
35 25 0.32
36 25 0.32
37 27 0.35
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (37 bp):
TTCGCATGTTAAGCATGCTATTATTCTGATATTCTGA
Found at i:16173529 original size:36 final size:35
Alignment explanation
Indices: 16173416--16173540 Score: 160
Period size: 35 Copynumber: 3.5 Consensus size: 35
16173406 GATGTTCTAG
* *
16173416 TTCGCATGTTAAACATGCTAATATTCTGATATTCTGA
1 TTCGCATGTTAAGCATGCTATTATTCTG--ATTCTGA
* * *
16173453 TTCGCATGTTAATCATGCTATTAATCTGATTTTGA
1 TTCGCATGTTAAGCATGCTATTATTCTGATTCTGA
* *
16173488 CTCGCATGTTAAGCATGCCATTATTTCTGATTCTGA
1 TTCGCATGTTAAGCATGCTATTA-TTCTGATTCTGA
16173524 TTCGCATGTTAAGCATG
1 TTCGCATGTTAAGCATG
16173541 TCACTGTGTG
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
35 26 0.34
36 26 0.34
37 25 0.32
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (35 bp):
TTCGCATGTTAAGCATGCTATTATTCTGATTCTGA
Found at i:16175837 original size:22 final size:22
Alignment explanation
Indices: 16175812--16175891 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
16175802 ACGAGATTTT
16175812 CACTACGGTGCCTATTGATTCG
1 CACTACGGTGCCTATTGATTCG
* *
16175834 CACTACGGTGCCCATTGATTTG
1 CACTACGGTGCCTATTGATTCG
* **
16175856 CACTCCGGTATCTATTGATTCG
1 CACTACGGTGCCTATTGATTCG
*
16175878 CACTCCGGTGCCTA
1 CACTACGGTGCCTA
16175892 CTGTTAAAGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.31
Consensus pattern (22 bp):
CACTACGGTGCCTATTGATTCG
Found at i:16177064 original size:23 final size:23
Alignment explanation
Indices: 16177038--16177101 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
16177028 CACACGACCA
* *
16177038 TGTGACCCTGGTTTACACGGTCG
1 TGTGACCCTGCTTTACACGGGCG
**
16177061 TGTGACCCTATTTTACACGGGCG
1 TGTGACCCTGCTTTACACGGGCG
16177084 TGTGACCCTGCTTTACAC
1 TGTGACCCTGCTTTACAC
16177102 TTTTGTCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.31
Consensus pattern (23 bp):
TGTGACCCTGCTTTACACGGGCG
Found at i:16184011 original size:20 final size:20
Alignment explanation
Indices: 16183983--16184039 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
16183973 AATATTATGA
* *
16183983 ACCACTCCATTTACTTTCTT
1 ACCATTCCATTTACTTACTT
16184003 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
16184023 TCCATTTCATTTACTTA
1 ACCATTCCATTTACTTA
16184040 GCATAATCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:16190873 original size:26 final size:26
Alignment explanation
Indices: 16190838--16190907 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
16190828 ATTAATTTTT
16190838 TTTTAAAATTTAAAAATTAT-AAATA
1 TTTTAAAATTTAAAAATTATAAAATA
* *
16190863 TTTTAAAAATTAAAAAGTATAAAATA
1 TTTTAAAATTTAAAAATTATAAAATA
* *
16190889 TTTTTAATTTTAAAAATTA
1 TTTTAAAATTTAAAAATTA
16190908 ATTAATTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
TTTTAAAATTTAAAAATTATAAAATA
Found at i:16198002 original size:35 final size:34
Alignment explanation
Indices: 16197963--16198030 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
16197953 AATTCTCTAC
16197963 AAGGAGAGAAAAT-AAG-GTAAATAGTTTGCTAAAAA
1 AAGGAGA-AAAATAAAGAGTAAA-AG-TTGCTAAAAA
*
16197998 AAGGAGAAAGATAAAGAGTAAAAGTTGCTAAAA
1 AAGGAGAAAAATAAAGAGTAAAAGTTGCTAAAA
16198031 TGTTGGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 13 0.43
35 12 0.40
36 5 0.17
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (34 bp):
AAGGAGAAAAATAAAGAGTAAAAGTTGCTAAAAA
Found at i:16201948 original size:20 final size:20
Alignment explanation
Indices: 16201923--16201964 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
16201913 ACTATTCTGA
**
16201923 ATAATATTATTTGAATAATT
1 ATAATATTAAATGAATAATT
16201943 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
16201963 AT
1 AT
16201965 GTGTCCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:16218366 original size:18 final size:17
Alignment explanation
Indices: 16218314--16218366 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
16218304 TTATTATTAA
16218314 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
16218332 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
16218349 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
16218367 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16224106 original size:6 final size:6
Alignment explanation
Indices: 16224095--16224119 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16224085 CCATTTTCTT
16224095 TCTAAA TCTAAA TCTAAA TCTAAA T
1 TCTAAA TCTAAA TCTAAA TCTAAA T
16224120 TTCATTTCAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TCTAAA
Found at i:16232739 original size:10 final size:10
Alignment explanation
Indices: 16232724--16232758 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
16232714 TAACATGTTG
*
16232724 AATTTTAATT
1 AATTTTGATT
16232734 AATTTTGATT
1 AATTTTGATT
16232744 AATTTTGATT
1 AATTTTGATT
16232754 -ATTTT
1 AATTTT
16232759 CGACAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (10 bp):
AATTTTGATT
Found at i:16237195 original size:27 final size:27
Alignment explanation
Indices: 16237154--16237567 Score: 456
Period size: 27 Copynumber: 15.4 Consensus size: 27
16237144 CCTTAAAATA
* *
16237154 GGTAAAATGATCGTAATGCCCATGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
16237181 GGTAAAATAACCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
16237208 GGTAAAATGACCCTAATGCCCCTATAA
1 GGTAAAATGACCGTAATGCCCCTGTAG
** * * *
16237235 GGTAAAATGATTGTAATACCCCTATAA
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
16237262 GGTAAAATGACCGTAATACCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * * *
16237289 GGTAAAAGGACCATAATGCCCCCGTAA
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
16237316 GGTAAAATAACCGTAATGCCTCAGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
16237343 GATAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * * * *
16237370 GGTAAAATAATCGTAATACCCTTATAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * * *
16237397 GGTAAAAAGGCCGTAATGCCTCTGTAA
1 GGTAAAATGACCGTAATGCCCCTGTAG
16237424 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
16237451 GGTAAAATAACCGTAATGCCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
16237478 GGTAAAATGATCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
16237505 GATAAAATGACCGTAATACCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
16237532 GGTAAAATGACCGTAATG-CCCTG-ATG
1 GGTAAAATGACCGTAATGCCCCTGTA-G
16237558 GGT-AAATGAC
1 GGTAAAATGAC
16237568 TATTTTTGCC
Statistics
Matches: 324, Mismatches: 62, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
25 8 0.02
26 9 0.03
27 307 0.95
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:16237288 original size:81 final size:81
Alignment explanation
Indices: 16237153--16237552 Score: 507
Period size: 81 Copynumber: 4.9 Consensus size: 81
16237143 ACCTTAAAAT
* * * *
16237153 AGGTAAAATGATCGTAATGCCCATGTAGGGTAAAATAACCGTAATACCCTTGTAGGGTAAAATGA
1 AGGTAAAATGATCGTAATGCCCCTGTAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGA
*
16237218 CCCTAATGCCCCTATA
66 CCGTAATGCCCCTATA
* * * *
16237234 AGGTAAAATGATTGTAATACCCCTATAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAAGGA
1 AGGTAAAATGATCGTAATGCCCCTGTAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGA
* **
16237299 CCATAATGCCCCCGTA
66 CCGTAATGCCCCTATA
* * * * * *
16237315 AGGTAAAATAACCGTAATGCCTCAGT-AGGATAAAATGACCGTAATACCCTTGTAGGGTAAAATA
1 AGGTAAAATGATCGTAATGCCCCTGTAAGG-TAAAATGACCGTAATACCCCTGTAGGGTAAAATG
* * *
16237379 ATCGTAATACCCTTATA
65 ACCGTAATGCCCCTATA
* * ** * * *
16237396 GGGTAAAAAGGCCGTAATGCCTCTGTAAGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATAA
1 AGGTAAAATGATCGTAATGCCCCTGTAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGA
16237461 CCGTAATGCCCCTATA
66 CCGTAATGCCCCTATA
*
16237477 GGGTAAAATGATCGTAATGCCCCTGT-AGGATAAAATGACCGTAATACCCCTGTAGGGTAAAATG
1 AGGTAAAATGATCGTAATGCCCCTGTAAGG-TAAAATGACCGTAATACCCCTGTAGGGTAAAATG
16237541 ACCGTAATGCCC
65 ACCGTAATGCCC
16237553 TGATGGGTAA
Statistics
Matches: 273, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 6 0.02
81 264 0.97
82 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (81 bp):
AGGTAAAATGATCGTAATGCCCCTGTAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGA
CCGTAATGCCCCTATA
Found at i:16237643 original size:24 final size:24
Alignment explanation
Indices: 16237612--16237671 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
16237602 TCTATGGTTA
16237612 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
*
16237636 GATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
16237660 AATGACTGATTT
1 AATGACTGATTT
16237672 TGAGTATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.20, C:0.08, G:0.27, T:0.45
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:16237839 original size:26 final size:26
Alignment explanation
Indices: 16237786--16237839 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
16237776 TTGGCCACAT
*
16237786 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTACG
* *
16237812 ATACTATTACTGGTAGCTTTGTTACG
1 ATACTATTACTGGCAGCTTTGCTACG
16237838 AT
1 AT
16237840 GCTACTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTACG
Found at i:16237883 original size:32 final size:32
Alignment explanation
Indices: 16237842--16238120 Score: 269
Period size: 32 Copynumber: 8.7 Consensus size: 32
16237832 GTTACGATGC
**
16237842 TACTGATGGCTTTGTGCAAATCATAGT-ACCGT
1 TACTGATGGCTTTGTGCCGATCATA-TCACCGT
*
16237874 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * *
16237906 TA-TCGATGG-TTGTGTGCTGATCATTTCACTGT
1 TACT-GATGGCTT-TGTGCCGATCATATCACCGT
* * *
16237938 TATTGATGG-TTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATATCACCGT
* *
16237970 TACTGATGGCTTTGTGCCGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * ***
16238002 TACTGATGACTATGTGCCGATCATATCACTAC
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * * *
16238034 TACTGATAGCTTTGTGCCAATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * * *
16238066 TACTGATGGCTGTGTGCCGGTCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
*
16238098 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
16238121 CATTACTGTA
Statistics
Matches: 201, Mismatches: 41, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
31 4 0.02
32 194 0.97
33 3 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATCACCGT
Found at i:16237978 original size:64 final size:64
Alignment explanation
Indices: 16237839--16238120 Score: 347
Period size: 64 Copynumber: 4.4 Consensus size: 64
16237829 TTTGTTACGA
** * *
16237839 TGCTACTGATGGCTTTGTGCAAATCATAG-TACCGTTACTGATGGCTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCAT-GTTACCGTTACTGATGGCTGTGTGCCGATCATATCAC
* * * * * *
16237903 CGTTA-TCGATGG-TTGTGTGCTGATCAT-TTCACTGTTATTGATGGTTGTGTGCCGATCATATC
1 TGCTACT-GATGGCTT-TGTGCCGATCATGTT-ACCGTTACTGATGGCTGTGTGCCGATCATATC
16237965 AC
63 AC
* *
16237967 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGACTATGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGATCATATCAC
* * * *
16238031 TACTACTGATAGCTTTGTGCCAATCATGTTACCGTTACTGATGGCTGTGTGCCGGTCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGATCATATCAC
*
16238095 TGCTACTGATGGCTTTGTGCCAATCA
1 TGCTACTGATGGCTTTGTGCCGATCA
16238121 CATTACTGTA
Statistics
Matches: 186, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
63 4 0.02
64 177 0.95
65 5 0.03
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGATCATATCAC
Found at i:16238157 original size:22 final size:21
Alignment explanation
Indices: 16238132--16238196 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
16238122 ATTACTGTAC
*
16238132 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCTATTCTGT
* *
16238154 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGCTATTCTGT
*
16238176 TTACGGCTCTTAGCTATTCTG
1 TTATGGCT-TTAGCTATTCTG
16238197 ACTACTGGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCTATTCTGT
Found at i:16249797 original size:11 final size:10
Alignment explanation
Indices: 16249765--16249811 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
16249755 TAACATGTTG
*
16249765 AATTTTAATT
1 AATTTTGATT
*
16249775 AATTTTATATT
1 AATTTT-GATT
16249786 AAATTTTGATT
1 -AATTTTGATT
16249797 AATTTTGATT
1 AATTTTGATT
16249807 -ATTTT
1 AATTTT
16249812 CGACAGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 5 0.15
10 16 0.48
11 6 0.18
12 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTGATT
Found at i:16254513 original size:22 final size:22
Alignment explanation
Indices: 16254485--16254532 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
16254475 TATTGCATCT
16254485 CCCTTAACTCT-TAAATTCACAA
1 CCCTTAACTCTCTAAA-TCACAA
*
16254507 CCCTTAACTCTCTAAATCACCA
1 CCCTTAACTCTCTAAATCACAA
16254529 CCCT
1 CCCT
16254533 AAACACCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (22 bp):
CCCTTAACTCTCTAAATCACAA
Found at i:16258053 original size:6 final size:6
Alignment explanation
Indices: 16258039--16258073 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16258029 TAGGTTTCAA
*
16258039 AAATAG AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
16258074 ATACATTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:16264156 original size:14 final size:14
Alignment explanation
Indices: 16264133--16264162 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16264123 CGTCGGTCTC
16264133 TTCTTATTCTTTCT
1 TTCTTATTCTTTCT
*
16264147 TTCTTTTTCTTTCT
1 TTCTTATTCTTTCT
16264161 TT
1 TT
16264163 TAATTTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCTTATTCTTTCT
Found at i:16264234 original size:3 final size:3
Alignment explanation
Indices: 16264226--16264303 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
16264216 CCTTATCTAA
16264226 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16264274 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16264304 ACATACATTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16266475 original size:16 final size:16
Alignment explanation
Indices: 16266454--16266505 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
16266444 TTTGGTTCGC
16266454 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
16266470 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
16266486 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16266502 TGTA
1 TGTA
16266506 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:16266829 original size:157 final size:157
Alignment explanation
Indices: 16266635--16266929 Score: 518
Period size: 157 Copynumber: 1.9 Consensus size: 157
16266625 CCCTTAGCAT
*
16266635 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
16266700 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
16266765 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
* * *
16266792 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
16266857 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
16266922 TTTAATAA
131 TTTAATAA
16266930 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 130 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:16267841 original size:13 final size:13
Alignment explanation
Indices: 16267823--16267852 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16267813 CAATCAGCTA
16267823 AATTCAGAAAAAC
1 AATTCAGAAAAAC
16267836 AATTCAGAAAAAC
1 AATTCAGAAAAAC
16267849 AATT
1 AATT
16267853 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:16274616 original size:70 final size:70
Alignment explanation
Indices: 16274503--16274645 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
16274493 GCCGATTGAA
16274503 TGCGTGAAATGTGTTCTATCCTAATTGAAAGATTCAGCATATCAGTGGTGGAACACTCTAGTTTC
1 TGCGTGAAATGTGTTCTATCCTAATTGAAAGATTCAGCATATCAGTGGTGGAACACTCTAGTTTC
16274568 TGTTG
66 TGTTG
*
16274573 TGCGTGAAATGTGTTCTATCCTAATTGAAAGATTTAGCATATCAGTGGTGGAACACTCTAGTTTC
1 TGCGTGAAATGTGTTCTATCCTAATTGAAAGATTCAGCATATCAGTGGTGGAACACTCTAGTTTC
16274638 TGTTG
66 TGTTG
16274643 TGC
1 TGC
16274646 CGAGAGATCA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (70 bp):
TGCGTGAAATGTGTTCTATCCTAATTGAAAGATTCAGCATATCAGTGGTGGAACACTCTAGTTTC
TGTTG
Found at i:16295703 original size:15 final size:15
Alignment explanation
Indices: 16295683--16295714 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16295673 AGAAAAAGTG
16295683 ATAGATTGGTGAATT
1 ATAGATTGGTGAATT
16295698 ATAGATTGGTGAATT
1 ATAGATTGGTGAATT
16295713 AT
1 AT
16295715 CCATTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (15 bp):
ATAGATTGGTGAATT
Done.