Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 55 of 199
Found at i:16002845 original size:14 final size:15
Alignment explanation
Indices: 16002796--16002847 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
16002786 ATTTAATCAT
* *
16002796 ATTAAACATAATTATT
1 ATTAAATAT-ATTATA
16002812 ATTAAATATATTATA
1 ATTAAATATATTATA
16002827 ATTAAA-ATA-TATA
1 ATTAAATATATTATA
*
16002840 ATTTAATA
1 ATTAAATA
16002848 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 11 0.34
16 8 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATATATTATA
Found at i:16002899 original size:61 final size:61
Alignment explanation
Indices: 16002832--16003019 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
16002822 TTATAATTAA
16002832 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
16002893 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
16002952 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
16003013 AATATAT
1 AATATAT
16003020 GATACTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 23 0.24
61 37 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:16002936 original size:120 final size:121
Alignment explanation
Indices: 16002800--16003091 Score: 518
Period size: 120 Copynumber: 2.4 Consensus size: 121
16002790 AATCATATTA
16002800 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
16002865 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
*
16002920 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
16002985 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
16003041 AA-ATAATTAATATTAAATATATT-TAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
16003092 TAAAATAATT
Statistics
Matches: 166, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
119 27 0.16
120 137 0.83
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:16002965 original size:14 final size:15
Alignment explanation
Indices: 16002916--16002967 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
16002906 ATAAAATATA
16002916 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
16002931 TATTAAATATATTAT
1 AATTAAATATATTAT
16002946 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
16002959 AATTTAATA
1 AATTAAATA
16002968 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:16003088 original size:17 final size:17
Alignment explanation
Indices: 16003057--16003090 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16003047 TTAATATTAA
16003057 ATATATTTAATTAAAAT
1 ATATATTTAATTAAAAT
16003074 ATATGATTTAA-TAAAAT
1 ATAT-ATTTAATTAAAAT
16003091 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATTTAATTAAAAT
Found at i:16003183 original size:91 final size:91
Alignment explanation
Indices: 16003088--16003314 Score: 280
Period size: 91 Copynumber: 2.5 Consensus size: 91
16003078 GATTTAATAA
* * *
16003088 AATTT-AAAATAATT-ATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTAT
1 AATTTCAAAA-AATTCATAA-TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAA
*
16003151 TATTACATATAATTTAATAATAATATAT
64 TATTAAATATAATTTAATAATAATATAT
* * * * *
16003179 AATTTCACAAAATTCTTGATAATAGATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTCATAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATA
*
16003244 TTAAATATAATTTAATAATGATATAT
66 TTAAATATAATTTAATAATAATATAT
* * *
16003270 AATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATTAATTTA
1 AATTTCAAAAAATTCATAATAAT-AAAT-TATCTTATATGAATTTA
16003315 CTAAAATCAA
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
91 95 0.81
92 22 0.19
93 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (91 bp):
AATTTCAAAAAATTCATAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATA
TTAAATATAATTTAATAATAATATAT
Found at i:16003274 original size:44 final size:43
Alignment explanation
Indices: 16003132--16003274 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
16003122 TATGAATTTG
*
16003132 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
* * * ** *
16003176 TATAATTTCACAA-AATTCTTGA-TAATAGATTTTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAA-ATATAAT-TTA-AT-AATATA
* *
16003223 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAAT-ATA
16003267 TATAATTT
1 TATAATTT
16003275 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 27 0.36
45 11 0.15
46 11 0.15
47 19 0.26
48 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (43 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATATA
Found at i:16006679 original size:6 final size:6
Alignment explanation
Indices: 16006668--16006693 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16006658 TAGTTTGAAC
16006668 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
16006694 ATAATTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:16009445 original size:12 final size:12
Alignment explanation
Indices: 16009428--16009454 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16009418 CAGGACGAAA
16009428 CAATTGCTCAAC
1 CAATTGCTCAAC
16009440 CAATTGCTCAAC
1 CAATTGCTCAAC
16009452 CAA
1 CAA
16009455 AATCAGCAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (12 bp):
CAATTGCTCAAC
Found at i:16022122 original size:23 final size:24
Alignment explanation
Indices: 16022083--16022131 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
16022073 ATTTCGTTGT
16022083 TTTCTCTTTTTTGTATTTGATTCC
1 TTTCTCTTTTTTGTATTTGATTCC
*
16022107 TTTCT-TTTTTTTTATTTGATTCC
1 TTTCTCTTTTTTGTATTTGATTCC
16022130 TT
1 TT
16022132 GTAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.71
Consensus pattern (24 bp):
TTTCTCTTTTTTGTATTTGATTCC
Found at i:16023558 original size:17 final size:17
Alignment explanation
Indices: 16023517--16023564 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
16023507 TACATCTAGG
16023517 CTTTATTATTTATTTCAT
1 CTTT-TTATTTATTTCAT
** *
16023535 CAATTTATTTATTTTAT
1 CTTTTTATTTATTTCAT
16023552 CTTTTTACTTTAT
1 CTTTTTA-TTTAT
16023565 AACCCATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTTTATTTATTTCAT
Found at i:16023631 original size:3 final size:3
Alignment explanation
Indices: 16023625--16023650 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16023615 TATTATTATT
16023625 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
16023651 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:16023846 original size:40 final size:41
Alignment explanation
Indices: 16023712--16023845 Score: 150
Period size: 40 Copynumber: 3.3 Consensus size: 41
16023702 AGCGGCATTT
** **
16023712 TTAGCGGCGTTTGGACAAAAAACGCCGCTAAAAATAGAGCA
1 TTAGCGGCGTTTTTACGTAAAACGCCGCTAAAAATAGAGCA
* *
16023753 TTAGCGGCG-CTTTACGTAAAACGCCGCTAAAGATCA-AGCA
1 TTAGCGGCGTTTTTACGTAAAACGCCGCTAAAAAT-AGAGCA
* * *
16023793 TTAGCGGCATTTTTA-TTAAAGCGCCGCTAAAAAT-GAGCA
1 TTAGCGGCGTTTTTACGTAAAACGCCGCTAAAAATAGAGCA
16023832 TTAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
16023846 TGAAAAAACG
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 17 0.22
40 47 0.60
41 14 0.18
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
TTAGCGGCGTTTTTACGTAAAACGCCGCTAAAAATAGAGCA
Found at i:16023978 original size:41 final size:41
Alignment explanation
Indices: 16023903--16024054 Score: 207
Period size: 41 Copynumber: 3.7 Consensus size: 41
16023893 CCTTTCGGGG
* *
16023903 CTTTAGCGGCGTTTTTAAAAAAAGCGCCGGTAATGCTCAGAT
1 CTTTAGCGGCGTTTTT-GAAAAAGCGCCGCTAATGCTCAGAT
* * **
16023945 CTTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTC-GGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* **
16023985 CTTTAGCGACGTTTTCCAAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
16024026 CTTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGC
16024055 AAAAACATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.35
41 45 0.48
42 15 0.16
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:16024038 original size:81 final size:82
Alignment explanation
Indices: 16023900--16024054 Score: 249
Period size: 81 Copynumber: 1.9 Consensus size: 82
16023890 ATACCTTTCG
* * * *
16023900 GGGCTTTAGCGGCGTTTTTAAAAAAAGCGCCGGTAATGCTCAGATCTTTAGCTGCGTTTTTGGAA
1 GGGCTTTAGCGACGTTTTTAAAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAA
16023965 AAGCGCCGCTAATGCTC
66 AAGCGCCGCTAATGCTC
**
16023982 GGGCTTTAGCGACG-TTTTCCAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAA
1 GGGCTTTAGCGACGTTTTTAAAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAA
16024046 AAGCGCCGC
66 AAGCGCCGC
16024055 AAAAACATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 54 0.81
82 13 0.19
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (82 bp):
GGGCTTTAGCGACGTTTTTAAAAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGAAA
AAGCGCCGCTAATGCTC
Found at i:16024491 original size:14 final size:15
Alignment explanation
Indices: 16024462--16024495 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
16024452 TAAGGTTTAT
16024462 AGATTATGGAATTAG
1 AGATTATGGAATTAG
16024477 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
16024491 AGATT
1 AGATT
16024496 CTGATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:16024720 original size:89 final size:89
Alignment explanation
Indices: 16024582--16024758 Score: 255
Period size: 89 Copynumber: 2.0 Consensus size: 89
16024572 TTTGGTGTCA
* * *
16024582 GGTTAGGGGTTAGGGTTTAGATTAATTAGTCTGTTTTAATTTATATATTAAATAATATTTAGGGG
1 GGTTAGGGGTTAGGATTTAGATTAATTAGTCTGTTTTAATTTATATATTAAATAAGATTCAGGGG
16024647 TTAGGGGTTAGGGATTTGGGGTTG
66 TTAGGGGTTAGGGATTTGGGGTTG
* * * * *
16024671 GGTTAGGGTTTATGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTTCAGGGG
1 GGTTAGGGGTTAGGATTTAGATTAATTAGTCTGTTTTAATTTATATATTAAATAAGATTCAGGGG
** *
16024736 TTATTGGTTAGGGGTTTGGGGTT
66 TTAGGGGTTAGGGATTTGGGGTT
16024759 AAGAGTTAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 77 1.00
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (89 bp):
GGTTAGGGGTTAGGATTTAGATTAATTAGTCTGTTTTAATTTATATATTAAATAAGATTCAGGGG
TTAGGGGTTAGGGATTTGGGGTTG
Found at i:16029779 original size:43 final size:43
Alignment explanation
Indices: 16029731--16029918 Score: 218
Period size: 43 Copynumber: 4.3 Consensus size: 43
16029721 AGATTATATT
** *
16029731 TTTAGCGGCGTTTGTGATAAAGGCGCCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAGGCGCCGCTAAAGGTCTTGGTC
* * *
16029774 TTTAGCGGCGTTTGTGGGGAAAGCGTCGTCGTTAAAGCTCTTGGTC
1 TTTAGCGGCGTTTGT-GGGAAAG-G-CGCCGCTAAAGGTCTTGGTC
*
16029820 TTTAGCGGCGTTTGGGGGGAAA-GCGCCGCTAAAGGT-TATGGTC
1 TTTAGCGGCGTTT-GTGGGAAAGGCGCCGCTAAAGGTCT-TGGTC
* * * *
16029863 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAATGTCTTGATC
1 TTTAGCGGCGTTTGTGGGAAAGGCGCCGCTAAAGGTCTTGGTC
16029906 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
16029919 TTTCTAAAGT
Statistics
Matches: 124, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
42 8 0.06
43 72 0.58
44 7 0.06
45 1 0.01
46 35 0.28
47 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAGGCGCCGCTAAAGGTCTTGGTC
Found at i:16032147 original size:20 final size:19
Alignment explanation
Indices: 16032119--16032175 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
16032109 CATTGCTATT
*
16032119 AATATATTATATATATTTAA
1 AATAAATTATAT-TATTTAA
*
16032139 AATAAATTATATTATTTGAG
1 AATAAATTATATTATTT-AA
*
16032159 AATAAAATATTATTATT
1 AATAAATTA-TATTATT
16032176 AATTAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 20 0.62
21 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
AATAAATTATATTATTTAA
Found at i:16033806 original size:31 final size:33
Alignment explanation
Indices: 16033760--16033822 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
16033750 ATTTCTACTA
* **
16033760 TATTCTTAGGTTAGAATAGTTTA-CTCCTAATG
1 TATTCTTAGGATAGAATAAATTAGCTCCTAATG
16033792 TATT-TTAGGATAGAATAAATTAGCTCCTAAT
1 TATTCTTAGGATAGAATAAATTAGCTCCTAAT
16033823 TTTTTGAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (33 bp):
TATTCTTAGGATAGAATAAATTAGCTCCTAATG
Found at i:16042340 original size:6 final size:6
Alignment explanation
Indices: 16042329--16042362 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
16042319 ATGCTAGCAG
*
16042329 TGAACC TGAACC TGAACC TGAACC TGAACT TGAA
1 TGAACC TGAACC TGAACC TGAACC TGAACC TGAA
16042363 ATTGAAAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (6 bp):
TGAACC
Found at i:16042368 original size:18 final size:18
Alignment explanation
Indices: 16042329--16042368 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16042319 ATGCTAGCAG
*
16042329 TGAACCTGAACCTGAACC
1 TGAACCTGAACCTGAAAC
* *
16042347 TGAACCTGAACTTGAAAT
1 TGAACCTGAACCTGAAAC
16042365 TGAA
1 TGAA
16042369 AGTGAACATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACCTGAACCTGAAAC
Found at i:16047692 original size:2 final size:2
Alignment explanation
Indices: 16047685--16047732 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
16047675 TCATATAATG
*
16047685 CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16047727 CT CT CT
1 CT CT CT
16047733 ATGAAGAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:16054930 original size:4 final size:4
Alignment explanation
Indices: 16054921--16054962 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
16054911 TTTACAAGCC
*
16054921 TTAT TTAT TTAT TTAT TCAT TTAT TTA- TTACT TT-T TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTA
16054963 CACTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.18
4 25 0.76
5 2 0.06
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:16058427 original size:21 final size:21
Alignment explanation
Indices: 16058388--16058427 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16058378 AAGCCTAAAT
* *
16058388 AATATTGAAGAGTTAAAGGGA
1 AATATAGAAGAGCTAAAGGGA
*
16058409 AATATAGAAGAGCTCAAGG
1 AATATAGAAGAGCTAAAGG
16058428 CCACACTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (21 bp):
AATATAGAAGAGCTAAAGGGA
Found at i:16058833 original size:19 final size:19
Alignment explanation
Indices: 16058792--16058846 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
16058782 TGCCTCTTTT
* *
16058792 TGCATT-CATTTCATTCATT
1 TGCATTACATTTCA-TAATA
16058811 TGCATTACATTTCATAATA
1 TGCATTACATTTCATAATA
16058830 TGCATTA-ATTTTCATAA
1 TGCATTACA-TTTCATAA
16058847 ACAGTTGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 24 0.75
20 7 0.22
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.47
Consensus pattern (19 bp):
TGCATTACATTTCATAATA
Found at i:16066740 original size:51 final size:51
Alignment explanation
Indices: 16066676--16066958 Score: 209
Period size: 51 Copynumber: 5.8 Consensus size: 51
16066666 CATTCTAGTG
*
16066676 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACA
* * * * *
16066727 AATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTGAAG--AT--G---CG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACA
* * * *
16066771 AATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAAACTATAAGTTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACA
* ** ** * *
16066822 AATCTTATCTCCCTGAAGTTGTAACGGAGTAGATTGAAG--AT--G---CG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACA
* * * *
16066866 AATCTTATTTCCCTGAAGTT-CTAGTAGAACAGACTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGC-AGTGGAACAGATTAAAGCTATAAGTTACA
* * * * * *
16066917 AATCTTATCCCCCTAAAGTAGCAGTGGAGCAAATTGAAGCTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTA
16066959 CTAATCTTAT
Statistics
Matches: 170, Mismatches: 46, Indels: 32
0.69 0.19 0.13
Matches are distributed among these distances:
44 62 0.36
46 3 0.02
47 2 0.01
48 2 0.01
49 4 0.02
51 96 0.56
52 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACA
Found at i:16066795 original size:95 final size:95
Alignment explanation
Indices: 16066675--16066995 Score: 405
Period size: 95 Copynumber: 3.4 Consensus size: 95
16066665 TCATTCTAGT
* *
16066675 GAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAGTTACAAATCTTATCTCCC
1 GAATCTTATTTCCCTAAAGTTGCAGTAGAACAGATTAAAGCTATAAGTTACAAATCTTATCTCCC
16066740 TGAAGTTACAGTGGAGCAAATTGAAGATGC
66 TGAAGTTACAGTGGAGCAAATTGAAGATGC
* * *
16066770 GAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAAACTATAAGTTAAAAATCTTATCTCCC
1 GAATCTTATTTCCCTAAAGTTGCAGTAGAACAGATTAAAGCTATAAGTTACAAATCTTATCTCCC
** ** * *
16066835 TGAAGTTGTAACGGAGTAGATTGAAGATGC
66 TGAAGTTACAGTGGAGCAAATTGAAGATGC
* * * *
16066865 GAATCTTATTTCCCTGAAGTT-CTAGTAGAACAGACTAAAGCTACAAGTTACAAATCTTATCCCC
1 GAATCTTATTTCCCTAAAGTTGC-AGTAGAACAGATTAAAGCTATAAGTTACAAATCTTATCTCC
* * *
16066929 CTAAAG-TAGCAGTGGAGCAAATTGAAGCTAC
65 CTGAAGTTA-CAGTGGAGCAAATTGAAGATGC
* * *
16066960 TAATCTTATCTT-CCTAAAGTTACAGTAGAGCAGATT
1 GAATCTTAT-TTCCCTAAAGTTGCAGTAGAACAGATT
16066996 GTAGCGACAA
Statistics
Matches: 193, Mismatches: 29, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
94 2 0.01
95 188 0.97
96 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (95 bp):
GAATCTTATTTCCCTAAAGTTGCAGTAGAACAGATTAAAGCTATAAGTTACAAATCTTATCTCCC
TGAAGTTACAGTGGAGCAAATTGAAGATGC
Found at i:16072628 original size:34 final size:34
Alignment explanation
Indices: 16072585--16072652 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
16072575 ATTAACGATT
16072585 GCCAAATTAAGGCTCACTGGAGTTTAAGTGGCAG
1 GCCAAATTAAGGCTCACTGGAGTTTAAGTGGCAG
16072619 GCCAAATTAAGGCTCACTGGAGTTTAAGTGGCAG
1 GCCAAATTAAGGCTCACTGGAGTTTAAGTGGCAG
16072653 ATCTTTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (34 bp):
GCCAAATTAAGGCTCACTGGAGTTTAAGTGGCAG
Found at i:16079476 original size:49 final size:49
Alignment explanation
Indices: 16079416--16079525 Score: 202
Period size: 49 Copynumber: 2.2 Consensus size: 49
16079406 CCCGAATAAG
16079416 AAAAGGAAAAACTACGTCGTTTTGATAAATGATTACCTTTTCTAAAGTT
1 AAAAGGAAAAACTACGTCGTTTTGATAAATGATTACCTTTTCTAAAGTT
* *
16079465 AAAAGGCAAAACTACGTCGTTTTGATAAATGTTTACCTTTTCTAAAGTT
1 AAAAGGAAAAACTACGTCGTTTTGATAAATGATTACCTTTTCTAAAGTT
16079514 AAAAGGAAAAAC
1 AAAAGGAAAAAC
16079526 CATTATACTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (49 bp):
AAAAGGAAAAACTACGTCGTTTTGATAAATGATTACCTTTTCTAAAGTT
Found at i:16084596 original size:19 final size:20
Alignment explanation
Indices: 16084573--16084612 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16084563 GTATCAGTAT
* *
16084573 TTTTTTAAGGTATCGATATA
1 TTTTCTAAGGGATCGATATA
16084593 TTTTCCTAAGGGATCGATAT
1 TTTT-CTAAGGGATCGATAT
16084613 TCCTACTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTTCTAAGGGATCGATATA
Found at i:16085647 original size:107 final size:107
Alignment explanation
Indices: 16085461--16085764 Score: 468
Period size: 107 Copynumber: 2.9 Consensus size: 107
16085451 AAGATGTAAG
* * * *
16085461 AGGATATTTAGCTATTCGGTCCG-ATGAG-AAATTGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGT-CGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
16085524 AAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
65 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
* *
16085567 AGGATATTTGGCTATTTGGTCGAACGAGAAAATCAAAACCCAGCACATTAGGGCACATTTTCTCG
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
*
16085632 AATTTCCAAATGCAAAACATTGCCTTATTTTAAAATTTTAAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
* * * *
16085674 AGGATATTTGGTTATTTAGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
*
16085739 AATTTCCAAACACAAAACATTGCCTT
66 AATTTCCAAACGCAAAACATTGCCTT
16085765 GAAAAAAAAA
Statistics
Matches: 180, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
105 2 0.01
106 22 0.12
107 156 0.87
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (107 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCG
AATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTAAA
Found at i:16086017 original size:8 final size:8
Alignment explanation
Indices: 16086004--16086075 Score: 68
Period size: 8 Copynumber: 9.6 Consensus size: 8
16085994 AGAATAAATA
16086004 AAAATAAT
1 AAAATAAT
16086012 AAAATAAT
1 AAAATAAT
16086020 AAAAT-AT
1 AAAATAAT
*
16086027 -ATATAAT
1 AAAATAAT
16086034 AAAAT-A-
1 AAAATAAT
16086040 AAAATAAT
1 AAAATAAT
16086048 --AATAAT
1 AAAATAAT
16086054 AGAAA-ACAT
1 A-AAATA-AT
16086063 AAAATAAT
1 AAAATAAT
16086071 AAAAT
1 AAAAT
16086076 CTATGTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
6 14 0.26
7 6 0.11
8 27 0.51
9 6 0.11
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:16086018 original size:14 final size:14
Alignment explanation
Indices: 16085999--16086069 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 14
16085989 TAATGAGAAT
*
16085999 AAATAAAAATAAT-A
1 AAATAATAA-AATAA
*
16086013 AAATAATAAAATAT
1 AAATAATAAAATAA
*
16086027 ATATAATAAAATAA
1 AAATAATAAAATAA
16086041 AAATAATAATAATAGA
1 AAATAATAA-AATA-A
*
16086057 AAA-CATAAAATAA
1 AAATAATAAAATAA
16086070 TAAAATCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
13 4 0.08
14 32 0.67
15 8 0.17
16 4 0.08
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (14 bp):
AAATAATAAAATAA
Found at i:16086022 original size:17 final size:17
Alignment explanation
Indices: 16086000--16086074 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
16085990 AATGAGAATA
16086000 AATAAAAATAATAAAAT
1 AATAAAAATAATAAAAT
16086017 AATAAAATATATATAATAA-
1 AATAAAA-ATA-ATAA-AAT
16086036 AATAAAAATAAT--AAT
1 AATAAAAATAATAAAAT
*
16086051 AATAGAAAA-CATAAAAT
1 AATA-AAAATAATAAAAT
16086068 AATAAAA
1 AATAAAA
16086075 TCTATGTATA
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
14 2 0.04
15 6 0.12
16 7 0.14
17 16 0.32
18 6 0.12
19 11 0.22
20 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (17 bp):
AATAAAAATAATAAAAT
Found at i:16086072 original size:3 final size:3
Alignment explanation
Indices: 16086000--16086054 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
16085990 AATGAGAATA
* *
16086000 AAT AAA AAT AAT AA- AAT AAT AA- AAT -AT ATAT AAT AA- AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
16086042 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
16086055 GAAAACATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 8 0.19
3 32 0.74
4 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:16088056 original size:132 final size:132
Alignment explanation
Indices: 16087905--16088326 Score: 702
Period size: 132 Copynumber: 3.2 Consensus size: 132
16087895 TTACTTCCCT
* *
16087905 ACTACCTTGAGAAGATAAGATTCACCATCTAT-GATCTGTTCCACTACTGCTTAGGGTGACAGAA
1 ACTATCTTGAGAAGATAAGATTCACCATCT-TCGATCTGCTCCACTACTGCTTAGGGTGACAGAA
* *
16087969 TCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAACGGCTTAAATCTGCTTT
65 TCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTC
16088034 TCC
130 TCC
* * *
16088037 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCTACTACTGCTTAGGGTGACAAAAT
1 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
*
16088102 CTGCAATCTTCAACCTACTCCACTACTCCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
*
16088167 CT
131 CC
* *
16088169 ACTATCTTGAGAAGATAAGATTCACTATCTTCGATCTGCTCCATTACTGCTTAGGGTGACAGAAT
1 ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
* *
16088234 CTGCAGTCTTCAACCTACTCCACTACTGCTTAGGGATATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
16088299 CC
131 CC
*
16088301 ACTATCTTGGGAAGATAAGATTCACC
1 ACTATCTTGAGAAGATAAGATTCACC
16088327 GTCAGTACAG
Statistics
Matches: 269, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 268 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (132 bp):
ACTATCTTGAGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
CC
Found at i:16088378 original size:45 final size:46
Alignment explanation
Indices: 16088327--16088537 Score: 229
Period size: 44 Copynumber: 4.7 Consensus size: 46
16088317 AAGATTCACC
*
16088327 GTCAGTACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTCCACT
1 GTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGATCTGCTCCGCT
* * * * * **
16088372 GTCAGTACAAGAAGGCAAG-GCTGGTGTCTT-TGATCTGCTTTGCT
1 GTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGATCTGCTCCGCT
16088416 G-CTAGTACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTCCGCT
1 GTC-AGTACAGGAAGGCAAGATCTGCTATCTTCAGATCTGCTCCGCT
* * * * *
16088461 GTCAATACAGGAAGGCAAG-GCTGATGTCTTC-GATCTGCTTCGCT
1 GTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGATCTGCTCCGCT
* *
16088505 GACAGTACAGGAAGGCATGATCTGCTATCTTCA
1 GTCAGTACAGGAAGGCAAGATCTGCTATCTTCA
16088538 CCGATCTGTT
Statistics
Matches: 132, Mismatches: 26, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
43 3 0.02
44 67 0.51
45 60 0.45
46 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (46 bp):
GTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGATCTGCTCCGCT
Found at i:16088481 original size:89 final size:89
Alignment explanation
Indices: 16088329--16088537 Score: 339
Period size: 89 Copynumber: 2.3 Consensus size: 89
16088319 GATTCACCGT
*
16088329 CAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTCAGTACAAGAAGGCAAGGCT
1 CAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTCAATACAAGAAGGCAAGGCT
* * *
16088394 GGTGTCTTTGATCTGCTTTGCTG-
66 GATGTCTTCGATCTGCTTCGCTGA
* *
16088417 CTAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTCAATACAGGAAGGCAAGGC
1 C-AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTCAATACAAGAAGGCAAGGC
16088482 TGATGTCTTCGATCTGCTTCGCTGA
65 TGATGTCTTCGATCTGCTTCGCTGA
*
16088507 CAGTACAGGAAGGCATGATCTGCTATCTTCA
1 CAGTACAGGAAGGCAAGATCTGCTATCTTCA
16088538 CCGATCTGTT
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
88 1 0.01
89 110 0.98
90 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (89 bp):
CAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGTCAATACAAGAAGGCAAGGCT
GATGTCTTCGATCTGCTTCGCTGA
Found at i:16088833 original size:24 final size:24
Alignment explanation
Indices: 16088806--16088858 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
16088796 CCAGATTGCC
*
16088806 CCACTATAATCTTTAAGGTTCAAT
1 CCACTATAACCTTTAAGGTTCAAT
**
16088830 CCACCGTAACCTTTAAGGTTCAAT
1 CCACTATAACCTTTAAGGTTCAAT
16088854 CCACT
1 CCACT
16088859 GCACCTTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.32
Consensus pattern (24 bp):
CCACTATAACCTTTAAGGTTCAAT
Found at i:16089841 original size:28 final size:28
Alignment explanation
Indices: 16089804--16089860 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
16089794 TGGCCTCTCC
16089804 TTTTCGTTTT-CTTTTCTTCTTCTTTTTT
1 TTTTCGTTTTCCTTTT-TTCTTCTTTTTT
* *
16089832 TTTTCTTTTTCCTTTTTTTTTCTTTTTT
1 TTTTCGTTTTCCTTTTTTCTTCTTTTTT
16089860 T
1 T
16089861 CTTCCTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (28 bp):
TTTTCGTTTTCCTTTTTTCTTCTTTTTT
Found at i:16089856 original size:17 final size:17
Alignment explanation
Indices: 16089804--16089858 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
16089794 TGGCCTCTCC
* *
16089804 TTTTCGTTTTCTTTTCT
1 TTTTCCTTTTTTTTTCT
* *
16089821 TCTTCTTTTTTTTTTCT
1 TTTTCCTTTTTTTTTCT
16089838 TTTTCCTTTTTTTTTCT
1 TTTTCCTTTTTTTTTCT
16089855 TTTT
1 TTTT
16089859 TTCTTCCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTCCTTTTTTTTTCT
Found at i:16089858 original size:11 final size:11
Alignment explanation
Indices: 16089810--16089863 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
16089800 CTCCTTTTCG
*
16089810 TTTTCTTTTCT
1 TTTTCTTTTTT
*
16089821 TCTTCTTTTTT
1 TTTTCTTTTTT
16089832 TTTTCTTTTTCCT
1 TTTTCTTTTT--T
*
16089845 TTTTTTTTCTTT
1 TTTTCTTT-TTT
16089857 TTTTCTT
1 TTTTCTT
16089864 CCTTGTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 18 0.51
12 7 0.20
13 8 0.23
14 2 0.06
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:16094994 original size:16 final size:16
Alignment explanation
Indices: 16094973--16095007 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16094963 TTCCAAAATG
16094973 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
16094989 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
16095005 AAA
1 AAA
16095008 CAAAATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGTCA
Found at i:16096257 original size:107 final size:107
Alignment explanation
Indices: 16095952--16096233 Score: 494
Period size: 107 Copynumber: 2.6 Consensus size: 107
16095942 TATTCGGTCC
* *
16095952 AACGAG-AAACCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACGTAAAACATTG
1 AACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACGCAAAACATTG
16096016 CCTTATTTTAAAATTTTAAAAGGATATTTGGCTATTTTGTCG
66 CCTTATTTTAAAATTTTAAAAGGATATTTGGCTATTTTGTCG
* *
16096058 AACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTTAAATTTCCAAATGCAAAACATTG
1 AACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACGCAAAACATTG
16096123 CCTTATTTTAAAATTTTAAAAGGATATTTGGCTATTTTGTCG
66 CCTTATTTTAAAATTTTAAAAGGATATTTGGCTATTTTGTCG
* * *
16096165 AACGAGAAAATCGAAACCCAGCACATTAGGGCATGTTTCCTCGAATTTCCAAACGCAAAACATTG
1 AACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACGCAAAACATTG
16096230 CCTT
66 CCTT
16096234 GAAAAAAAAA
Statistics
Matches: 166, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 6 0.04
107 160 0.96
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (107 bp):
AACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACGCAAAACATTG
CCTTATTTTAAAATTTTAAAAGGATATTTGGCTATTTTGTCG
Found at i:16096505 original size:7 final size:8
Alignment explanation
Indices: 16096470--16096556 Score: 90
Period size: 8 Copynumber: 10.6 Consensus size: 8
16096460 AGAATAAATA
16096470 AAAATAAT
1 AAAATAAT
16096478 AAAATAAT
1 AAAATAAT
16096486 AAAATATAT
1 AAAATA-AT
16096495 AAAA-AAT
1 AAAATAAT
16096502 AAAATAA-
1 AAAATAAT
16096509 AAAATAA-
1 AAAATAAT
*
16096516 AAAATAAA
1 AAAATAAT
16096524 AAAATAAT
1 AAAATAAT
*
16096532 CATAGAAAACAT
1 -A-A-AATA-AT
16096544 AAAATAAT
1 AAAATAAT
16096552 AAAAT
1 AAAAT
16096557 CTATGTATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
7 20 0.29
8 31 0.45
9 10 0.14
10 2 0.03
11 4 0.06
12 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.01, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:16096515 original size:28 final size:29
Alignment explanation
Indices: 16096463--16096555 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 29
16096453 AATAATGAGA
16096463 ATAAATAAA-AATAATAAAATAATAAAATAT
1 ATAAA-AAATAATAATAAAA-AATAAAATAT
*
16096493 ATAAAAAATAA-AATAAAAAATAAAAAAT
1 ATAAAAAATAATAATAAAAAATAAAATAT
*
16096521 A-AAAAAATAATCATAGAAAACATAAAATA-
1 ATAAAAAATAATAATA-AAAA-ATAAAATAT
16096550 ATAAAA
1 ATAAAA
16096556 TCTATGTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.16
28 13 0.24
29 15 0.27
30 18 0.33
ACGTcount: A:0.76, C:0.02, G:0.01, T:0.20
Consensus pattern (29 bp):
ATAAAAAATAATAATAAAAAATAAAATAT
Found at i:16102706 original size:12 final size:12
Alignment explanation
Indices: 16102691--16102732 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16102681 ATTCAAATAT
*
16102691 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
16102703 ATGTTCGTTTA-
1 ATGTTCGTGAAC
16102714 ATGTTCGTGAAC
1 ATGTTCGTGAAC
16102726 ATGTTCG
1 ATGTTCG
16102733 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:16102724 original size:23 final size:23
Alignment explanation
Indices: 16102691--16102756 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
16102681 ATTCAAATAT
16102691 ATGTTCATGAACATGTTCGTTTA
1 ATGTTCATGAACATGTTCGTTTA
* *
16102714 ATGTTCGTGAACATGTTCGATTA
1 ATGTTCATGAACATGTTCGTTTA
*
16102737 A-GTTAATTGAACATGTTCGT
1 ATGTTCA-TGAACATGTTCGT
16102757 GAAAATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.08
23 34 0.92
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (23 bp):
ATGTTCATGAACATGTTCGTTTA
Found at i:16102765 original size:23 final size:23
Alignment explanation
Indices: 16102721--16102765 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16102711 TTAATGTTCG
* *
16102721 TGAACATGTTCGATTAAGTTAAT
1 TGAACATGTTCGATAAAATTAAT
16102744 TGAACATGTTCG-TGAAAATTAA
1 TGAACATGTTCGAT-AAAATTAA
16102766 ACAAACGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (23 bp):
TGAACATGTTCGATAAAATTAAT
Found at i:16105586 original size:47 final size:47
Alignment explanation
Indices: 16105529--16105623 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
16105519 CATTCACCTA
16105529 TTACTTACTTTTATTGATATTTTTATATTTCAAACCTTTGCGTATTT
1 TTACTTACTTTTATTGATATTTTTATATTTCAAACCTTTGCGTATTT
16105576 TTACTTACTTTTATTGATATTTTTATATTTCAAACCTTTGCGTATTT
1 TTACTTACTTTTATTGATATTTTTATATTTCAAACCTTTGCGTATTT
16105623 T
1 T
16105624 ATTTAAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (47 bp):
TTACTTACTTTTATTGATATTTTTATATTTCAAACCTTTGCGTATTT
Found at i:16106911 original size:24 final size:24
Alignment explanation
Indices: 16106848--16106899 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16106838 TTTCTAGATG
* * *
16106848 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16106872 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16106896 ATTT
1 ATTT
16106900 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:16110787 original size:18 final size:18
Alignment explanation
Indices: 16110764--16110802 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16110754 ACCACTGAAG
*
16110764 CTGAGTACATGGTGATTA
1 CTGAGTACATGGCGATTA
16110782 CTGAGTACATGGCGATTA
1 CTGAGTACATGGCGATTA
16110800 CTG
1 CTG
16110803 CTCTTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (18 bp):
CTGAGTACATGGCGATTA
Found at i:16111127 original size:24 final size:24
Alignment explanation
Indices: 16111064--16111115 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16111054 TTTCTAGAAG
* * *
16111064 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16111088 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16111112 ATTT
1 ATTT
16111116 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:16111753 original size:13 final size:13
Alignment explanation
Indices: 16111718--16111763 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
16111708 GGTAAAATTT
*
16111718 TATACTTAATT-A
1 TATAATTAATTAA
*
16111730 TATATTTAATTAGA
1 TATAATTAATTA-A
16111744 -ATAATTAATTAA
1 TATAATTAATTAA
16111756 TATAATTA
1 TATAATTA
16111764 TTGATTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 11 0.38
13 17 0.59
14 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:16112179 original size:16 final size:18
Alignment explanation
Indices: 16112144--16112198 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
16112134 TATATAAAAA
16112144 TTATAATTTTTAATAATT
1 TTATAATTTTTAATAATT
*
16112162 TTATAA-TTTT-ATATTT
1 TTATAATTTTTAATAATT
**
16112178 TTATTAAAATTTAATAATT
1 TTA-TAATTTTTAATAATT
16112197 TT
1 TT
16112199 CTCAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 9 0.29
19 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATAATTTTTAATAATT
Found at i:16112207 original size:45 final size:45
Alignment explanation
Indices: 16112129--16112225 Score: 110
Period size: 45 Copynumber: 2.1 Consensus size: 45
16112119 TTTTTTTACG
16112129 ATTTTTATATAAAAATTATAATTTTTAATAATTT-TATAATTTTAT
1 ATTTTTATATAAAAATTATAATTTTTAATAATTTAT-TAATTTTAT
* * *
16112174 ATTTTTAT-TAAAATTTAATAATTTTCTCA-AATTTATTATTTTTAT
1 ATTTTTATATAAAAATT-ATAATTTT-TAATAATTTATTAATTTTAT
16112219 AGTTTTT
1 A-TTTTT
16112226 TCTAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 7 0.16
45 30 0.67
46 8 0.18
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (45 bp):
ATTTTTATATAAAAATTATAATTTTTAATAATTTATTAATTTTAT
Found at i:16112445 original size:93 final size:90
Alignment explanation
Indices: 16112249--16112460 Score: 211
Period size: 93 Copynumber: 2.3 Consensus size: 90
16112239 AAAAGTTTGG
* * * *
16112249 GCTTAATTAC--TTTTTTGAAAAATTTTGAAGG--TCTTTTTGATTCATTTTGAAAGTTCTAGTA
1 GCTTAATTACTTTTTTTTGAAAAAGTTTGAGGGCAT-TTTTTGATGCATTTTGAAAGTTCAAGTA
**
16112310 CCCAATTGAGTGAAAAAAAAGGCAAGA
65 CCCAATTGAGT-AAAAAAAAGAAAAGA
* * * *
16112337 GTTTAATTGCTTTTTTTTTTGAAGAAGTTTGAGGGCATTTTTTTATGCATTTTGAAAGTTCAAGT
1 GCTTAATTAC--TTTTTTTTGAAAAAGTTTGAGGGCATTTTTTGATGCATTTTGAAAGTTCAAGT
* *
16112402 GCTCAATTGAGT-AAAAAAAGAAAAGA
64 ACCCAATTGAGTAAAAAAAAGAAAAGA
16112428 GGGGCTTAATTAC-TTTTTTTGAAAAAGTTTGAG
1 ---GCTTAATTACTTTTTTTTGAAAAAGTTTGAG
16112461 AATTTTTAAC
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
88 8 0.08
91 31 0.31
92 18 0.18
93 34 0.34
94 9 0.09
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (90 bp):
GCTTAATTACTTTTTTTTGAAAAAGTTTGAGGGCATTTTTTGATGCATTTTGAAAGTTCAAGTAC
CCAATTGAGTAAAAAAAAGAAAAGA
Found at i:16115341 original size:25 final size:25
Alignment explanation
Indices: 16115313--16115362 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
16115303 ATTACATGAT
16115313 TGATGAAAAGTAAACGTTGCCACGG
1 TGATGAAAAGTAAACGTTGCCACGG
16115338 TGATGAAAAGTAAACGTTGCCACGG
1 TGATGAAAAGTAAACGTTGCCACGG
16115363 GTCGTCCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (25 bp):
TGATGAAAAGTAAACGTTGCCACGG
Found at i:16116095 original size:25 final size:25
Alignment explanation
Indices: 16116047--16116100 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
16116037 TATGATGGGC
*
16116047 AAAATCGTCAAAATTTTACCAAGGT
1 AAAATCGTCAAAATTTTACCAAGGG
* *
16116072 AAAATCGTCAAAATTTTGCTAAGGG
1 AAAATCGTCAAAATTTTACCAAGGG
16116097 AAAA
1 AAAA
16116101 ATAAAGCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (25 bp):
AAAATCGTCAAAATTTTACCAAGGG
Found at i:16116311 original size:23 final size:23
Alignment explanation
Indices: 16116281--16116327 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16116271 TCCATTCTAG
16116281 TCCTATTCTAAGTAGGATGTTAT
1 TCCTATTCTAAGTAGGATGTTAT
16116304 TCCTATTCTAAGTAGGATGTTAT
1 TCCTATTCTAAGTAGGATGTTAT
16116327 T
1 T
16116328 TTTCTATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (23 bp):
TCCTATTCTAAGTAGGATGTTAT
Found at i:16122083 original size:29 final size:30
Alignment explanation
Indices: 16122050--16122107 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
16122040 ACGACGTGAC
16122050 AAATTGTTATA-TCAAATATAATT-TATTTT
1 AAATT-TTATATTCAAATATAATTATATTTT
* *
16122079 AAATTTTATATTTACATATAATTATATTT
1 AAATTTTATATTCAAATATAATTATATTT
16122108 ATATATATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 15 0.60
30 5 0.20
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (30 bp):
AAATTTTATATTCAAATATAATTATATTTT
Found at i:16122105 original size:16 final size:16
Alignment explanation
Indices: 16122084--16122114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16122074 ATTTTAAATT
16122084 TTATATTTACATATAA
1 TTATATTTACATATAA
*
16122100 TTATATTTATATATA
1 TTATATTTACATATA
16122115 TCCAAAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATTTACATATAA
Found at i:16134936 original size:55 final size:54
Alignment explanation
Indices: 16134841--16134990 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
16134831 CTACTTTGTT
* ** * *
16134841 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
16134895 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
16134950 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
16134991 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:16134953 original size:27 final size:27
Alignment explanation
Indices: 16134813--16134990 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
16134803 TAAATTGTAC
16134813 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
16134840 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
16134866 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
16134894 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
16134922 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
16134949 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
16134976 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16134991 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:16134954 original size:82 final size:81
Alignment explanation
Indices: 16134814--16134969 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
16134804 AAATTGTACA
* * * *
16134814 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
16134879 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
16134895 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
16134958 TGTGCGAGTTGA
63 TGTGCGAATTGA
16134970 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:16149211 original size:55 final size:54
Alignment explanation
Indices: 16149116--16149265 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
16149106 CTACTTTGTT
* ** * *
16149116 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
16149170 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
16149225 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
16149266 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:16149228 original size:27 final size:27
Alignment explanation
Indices: 16149088--16149265 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
16149078 TAAATTGTAC
16149088 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
16149115 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
16149141 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
16149169 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
16149197 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
16149224 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
16149251 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16149266 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:16149229 original size:82 final size:81
Alignment explanation
Indices: 16149089--16149244 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
16149079 AAATTGTACA
* * * *
16149089 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
16149154 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
16149170 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
16149233 TGTGCGAGTTGA
63 TGTGCGAATTGA
16149245 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:16157213 original size:55 final size:54
Alignment explanation
Indices: 16157118--16157267 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
16157108 CTACTTTGTT
* ** * *
16157118 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
16157172 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
16157227 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
16157268 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:16157230 original size:27 final size:27
Alignment explanation
Indices: 16157090--16157267 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
16157080 TAAATTGTAC
16157090 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
16157117 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
16157143 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
16157171 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
16157199 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
16157226 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
16157253 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16157268 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:16157231 original size:82 final size:81
Alignment explanation
Indices: 16157091--16157246 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
16157081 AAATTGTACA
* * * *
16157091 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
16157156 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
16157172 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
16157235 TGTGCGAGTTGA
63 TGTGCGAATTGA
16157247 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:16163050 original size:27 final size:28
Alignment explanation
Indices: 16163011--16163068 Score: 109
Period size: 27 Copynumber: 2.1 Consensus size: 28
16163001 GCAAAGTATG
16163011 AAATCTTTTGGTATTGATTTGGTTATAT
1 AAATCTTTTGGTATTGATTTGGTTATAT
16163039 AAAT-TTTTGGTATTGATTTGGTTATAT
1 AAATCTTTTGGTATTGATTTGGTTATAT
16163066 AAA
1 AAA
16163069 ACAATTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (28 bp):
AAATCTTTTGGTATTGATTTGGTTATAT
Found at i:16163078 original size:27 final size:27
Alignment explanation
Indices: 16163018--16163075 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
16163008 ATGAAATCTT
***
16163018 TTGGTATTGATTTGGTTATATAAATTT
1 TTGGTATTGATTTGGTTATATAAACAA
16163045 TTGGTATTGATTTGGTTATATAAAACAA
1 TTGGTATTGATTTGGTTATAT-AAACAA
16163073 TTG
1 TTG
16163076 TATAGATCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (27 bp):
TTGGTATTGATTTGGTTATATAAACAA
Found at i:16163965 original size:19 final size:21
Alignment explanation
Indices: 16163941--16163981 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16163931 TTATATATTA
16163941 AAAATGAA-T-TGTGAAATTG
1 AAAATGAATTATGTGAAATTG
16163960 AAAATGAATTATGTGAAATTG
1 AAAATGAATTATGTGAAATTG
16163981 A
1 A
16163982 TATGTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
AAAATGAATTATGTGAAATTG
Found at i:16175681 original size:21 final size:21
Alignment explanation
Indices: 16175635--16175681 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
16175625 CAACTCCACT
*
16175635 TCAATCCTATTATTGATCTAA
1 TCAATCCTATTATTCATCTAA
* *
16175656 ACAATCCTTTTATATCATC-AA
1 TCAATCCTATTAT-TCATCTAA
16175677 TCAAT
1 TCAAT
16175682 ACCAAATACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (21 bp):
TCAATCCTATTATTCATCTAA
Found at i:16177904 original size:16 final size:17
Alignment explanation
Indices: 16177883--16177914 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16177873 AAATATGCAA
16177883 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
16177899 TCACATAACTTCATAT
1 TCACATAACTTCATAT
16177915 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:16178173 original size:41 final size:41
Alignment explanation
Indices: 16178075--16178229 Score: 152
Period size: 43 Copynumber: 3.7 Consensus size: 41
16178065 GGCTCGTACA
* ** *
16178075 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACA-CAAATCAAATA-CG
* *
16178118 ATGCCACTATCCCAGACAG-GGTCTTACACAAATCAAATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACAAATCAAATACG
* * *
16178159 ATGTCAATGTCCCAGACATGGTCTTACACATATACACAAGT-CG
1 ATGCCAATGTCCCAGACGTGGTCTTACACAAAT-CA-AA-TACG
*
16178202 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
16178230 TGAAAATACA
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
41 29 0.31
42 10 0.11
43 52 0.56
44 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACAAATCAAATACG
Found at i:16180581 original size:23 final size:25
Alignment explanation
Indices: 16180545--16180592 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
16180535 ATTGGTTATA
16180545 CTCTAATTGTTTT-CTCTTCTCATCT
1 CTCTAATTGTTTTCCT-TTCTCATCT
16180570 CTCT-ATTG-TTTCCTTTCTCATCT
1 CTCTAATTGTTTTCCTTTCTCATCT
16180593 ACCTTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.55
24 6 0.27
25 4 0.18
ACGTcount: A:0.10, C:0.29, G:0.04, T:0.56
Consensus pattern (25 bp):
CTCTAATTGTTTTCCTTTCTCATCT
Found at i:16189482 original size:7 final size:7
Alignment explanation
Indices: 16189472--16189510 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
16189462 AACTTAAAAA
16189472 TTAATTT
1 TTAATTT
16189479 TTAATTTGT
1 TTAA-TT-T
*
16189488 TTTATTT
1 TTAATTT
16189495 TTAATTT
1 TTAATTT
16189502 TTAATTT
1 TTAATTT
16189509 TT
1 TT
16189511 TTCTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 20 0.71
8 4 0.14
9 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (7 bp):
TTAATTT
Found at i:16189502 original size:23 final size:22
Alignment explanation
Indices: 16189472--16189517 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
16189462 AACTTAAAAA
16189472 TTAATTTTTAATTTGTTTTATTT
1 TTAATTTTTAATTT-TTTTATTT
*
16189495 TTAATTTTTAATTTTTTTCTTT
1 TTAATTTTTAATTTTTTTATTT
16189517 T
1 T
16189518 ATATTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
TTAATTTTTAATTTTTTTATTT
Found at i:16194254 original size:23 final size:23
Alignment explanation
Indices: 16194224--16194445 Score: 356
Period size: 23 Copynumber: 9.7 Consensus size: 23
16194214 TTAAGTTTAG
16194224 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
16194247 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
*
16194270 GGTTAGGGTTTTCAACTTAAATA
1 GGTTAGGGTTTTCAACTTAATTA
*
16194293 GGTTAGGGTTCTT-AATTTAATTA
1 GGTTAGGGTT-TTCAACTTAATTA
16194316 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
*
16194339 GGTTAGGGTTTTCAACTTAAATA
1 GGTTAGGGTTTTCAACTTAATTA
* * *
16194362 GGTTAGGGTTTTTAATTTAAATA
1 GGTTAGGGTTTTCAACTTAATTA
16194385 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
* *
16194408 GGTTATGGTTTCCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
16194431 GGTTAGGGTTTTCAA
1 GGTTAGGGTTTTCAA
16194446 TTTTTATCAC
Statistics
Matches: 183, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
22 2 0.01
23 179 0.98
24 2 0.01
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
GGTTAGGGTTTTCAACTTAATTA
Found at i:16194482 original size:25 final size:25
Alignment explanation
Indices: 16194447--16194610 Score: 178
Period size: 25 Copynumber: 6.7 Consensus size: 25
16194437 GGTTTTCAAT
*
16194447 TTTTATCACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
16194472 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
16194497 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
16194522 TTTTATTACATCAAGT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * * **
16194545 --AAATAAC-TCAAAAAAATTTAAA
1 TTTTATTACATCAAATAAACTTCTA
16194567 TTTTTATTACATCAAATAAACTTCTA
1 -TTTTATTACATCAAATAAACTTCTA
16194593 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
16194611 TATCAAAATA
Statistics
Matches: 114, Mismatches: 17, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
20 4 0.04
21 7 0.06
22 2 0.02
23 2 0.02
24 4 0.04
25 84 0.74
26 11 0.10
ACGTcount: A:0.43, C:0.15, G:0.01, T:0.41
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:16194580 original size:71 final size:71
Alignment explanation
Indices: 16194497--16194678 Score: 321
Period size: 71 Copynumber: 2.6 Consensus size: 71
16194487 TAAACTTCTA
*
16194497 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAGTAATATCAAAATAACTCAAAAAAAT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
16194562 TTAAAT
66 TTAAAT
*
16194568 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
16194633 TTAAAT
66 TTAAAT
*
16194639 TTTTTTTACATC-AATAAAACTTCTATTTTATTACATCAAA
1 TTTTATTACATCAAAT-AAACTTCTATTTTATTACATCAAA
16194679 CAAACTTCAA
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
70 3 0.03
71 104 0.97
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (71 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
TTAAAT
Found at i:16194673 original size:25 final size:25
Alignment explanation
Indices: 16194639--16194686 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
16194629 AATTTTAAAT
*
16194639 TTTTTTTACATCAATA-AAACTTCTA
1 TTTTATTACATCAA-ACAAACTTCTA
16194664 TTTTATTACATCAAACAAACTTC
1 TTTTATTACATCAAACAAACTTC
16194687 AAAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTATTACATCAAACAAACTTCTA
Found at i:16195157 original size:18 final size:18
Alignment explanation
Indices: 16195119--16195158 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
16195109 GACTCGGAAA
*
16195119 AGGATACATATAAAGGTT
1 AGGATACATATAAAGGAT
*
16195137 AGGATACATATAAGGGAT
1 AGGATACATATAAAGGAT
16195155 AGGA
1 AGGA
16195159 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAAGGAT
Found at i:16196405 original size:27 final size:27
Alignment explanation
Indices: 16196356--16196631 Score: 263
Period size: 27 Copynumber: 10.2 Consensus size: 27
16196346 AGGTCAATAG
*
16196356 AATGACCGAAATACGCCC-GTAGGGTAA
1 AATGACCGAAATAC-CCCTATAGGGTAA
*
16196383 AATAACCGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCCCTATAGGGTAA
* * ** *
16196410 AATTACCAAAATACCCCCGTAAGGTAA
1 AATGACCGAAATACCCCTATAGGGTAA
* * *
16196437 AATAACTGAAATA-CCCTCATAGGATAA
1 AATGACCGAAATACCCCT-ATAGGGTAA
*** * * *
16196464 AATGATTAAAATACCTCTGTAGAGTAA
1 AATGACCGAAATACCCCTATAGGGTAA
**
16196491 AATGATTGAAATA-CCCTCATAGGGTAA
1 AATGACCGAAATACCCCT-ATAGGGTAA
*
16196518 AATGACCGAAATA-CCCTCGTAGGGTAA
1 AATGACCGAAATACCCCT-ATAGGGTAA
*
16196545 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCTATAGGGTAA
* * *
16196572 AATGATCGAAATACCCTTATAGGATAA
1 AATGACCGAAATACCCCTATAGGGTAA
* *
16196599 AATGACCGAAATACCCCCATTGGGTAA
1 AATGACCGAAATACCCCTATAGGGTAA
16196626 AATGAC
1 AATGAC
16196632 TATTATACCC
Statistics
Matches: 205, Mismatches: 39, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
26 9 0.04
27 190 0.93
28 6 0.03
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (27 bp):
AATGACCGAAATACCCCTATAGGGTAA
Found at i:16196642 original size:81 final size:80
Alignment explanation
Indices: 16196356--16196631 Score: 302
Period size: 81 Copynumber: 3.4 Consensus size: 80
16196346 AGGTCAATAG
* * * * * *
16196356 AATGACCGAAATACGCCCGTAGGGTAAAATAACCGAAATACCCCTATAGGGTAAAATTACCAAAA
1 AATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAA
*
16196421 TACCCCCGTA-AGGTAA
66 TA--CCCTTATAGGTAA
* * * * *** * * * *
16196437 AATAACTGAAATACCCTCATAGGATAAAATGATTAAAATACCTCTGTAGAGTAAAATGATTGAAA
1 AATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAA
*
16196502 TACCCTCATAGGGTAA
66 TACCCTTATA-GGTAA
* * *
16196518 AATGACCGAAATACCCTCGTAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAA
1 AATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAA
16196583 TACCCTTATAGGATAA
66 TACCCTTATAGG-TAA
*
16196599 AATGACCGAAATACCCCCATTGGGTAAAATGAC
1 AATGACCGAAATACCCCCATAGGGTAAAATGAC
16196632 TATTATACCC
Statistics
Matches: 157, Mismatches: 35, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
79 4 0.03
80 3 0.02
81 150 0.96
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (80 bp):
AATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCGAAA
TACCCTTATAGGTAA
Found at i:16198293 original size:17 final size:18
Alignment explanation
Indices: 16198261--16198294 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16198251 AAATGTGGTT
16198261 TTAAATATTCAATTGTGC
1 TTAAATATTCAATTGTGC
*
16198279 TTAAA-ATTTAATTGTG
1 TTAAATATTCAATTGTG
16198295 TCTATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (18 bp):
TTAAATATTCAATTGTGC
Found at i:16204334 original size:19 final size:20
Alignment explanation
Indices: 16204312--16204350 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
16204302 TATTAGTGAT
16204312 TACATATGTAAAT-TTAATA
1 TACATATGTAAATATTAATA
*
16204331 TACATATGTATATATTAATA
1 TACATATGTAAATATTAATA
16204351 AATATGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
TACATATGTAAATATTAATA
Found at i:16205479 original size:40 final size:41
Alignment explanation
Indices: 16205383--16205481 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
16205373 TTCAGTTTAA
* * ** *
16205383 CCGATGAGACATTTGGTGCCAATTTACTACTTTGGATATAT
1 CCGATGAGACACTGGGTGAAAATTTACTACTTTGAATATAT
*
16205424 TCGATGAGACACTGGGTGAAAATTTACTACTTTGAAT-TAT
1 CCGATGAGACACTGGGTGAAAATTTACTACTTTGAATATAT
*
16205464 CCGATGAGGCACTGGGTG
1 CCGATGAGACACTGGGTG
16205482 CCAAACTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
40 19 0.38
41 31 0.62
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (41 bp):
CCGATGAGACACTGGGTGAAAATTTACTACTTTGAATATAT
Found at i:16205835 original size:17 final size:18
Alignment explanation
Indices: 16205803--16205840 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
16205793 AAATGTGGTT
16205803 TTAAATATTGAATTGTGC
1 TTAAATATTGAATTGTGC
*
16205821 TTAAA-ATTTAATTGTGC
1 TTAAATATTGAATTGTGC
16205838 TTA
1 TTA
16205841 TTATATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (18 bp):
TTAAATATTGAATTGTGC
Found at i:16212142 original size:20 final size:21
Alignment explanation
Indices: 16212119--16212164 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16212109 CCCAGGCCAC
16212119 GTGGCTT-CACACATGGCC-GT
1 GTGGCTTCCACACA-GGCCTGT
*
16212139 GTGGCTTCCCCACAGGCCTGT
1 GTGGCTTCCACACAGGCCTGT
16212160 GTGGC
1 GTGGC
16212165 AAAACCGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.11, C:0.33, G:0.33, T:0.24
Consensus pattern (21 bp):
GTGGCTTCCACACAGGCCTGT
Found at i:16219550 original size:18 final size:18
Alignment explanation
Indices: 16219508--16219562 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
16219498 ATGTAAGTCA
* *
16219508 TGTTAATAATTAATTAAAT
1 TGTTAAAAATTAA-AAAAT
*
16219527 TTTTAAAAATTAAAAAAT
1 TGTTAAAAATTAAAAAAT
* *
16219545 TGTTAACAATTTAAAAAT
1 TGTTAAAAATTAAAAAAT
16219563 ATAAATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
TGTTAAAAATTAAAAAAT
Found at i:16219603 original size:16 final size:16
Alignment explanation
Indices: 16219582--16219616 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
16219572 TTTAATTATA
16219582 TAAAAATAATAAAAAT
1 TAAAAATAATAAAAAT
*
16219598 TAAAAATGATAAAAAT
1 TAAAAATAATAAAAAT
16219614 TAA
1 TAA
16219617 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAAATAATAAAAAT
Found at i:16226826 original size:67 final size:69
Alignment explanation
Indices: 16226743--16226875 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 69
16226733 ATAAACAATA
* * *
16226743 TAATGGTTTTGCCTTTTAAC-TT-AATAAGTAAACATTTATCAAAACAACGTAATTTTGCCTTTT
1 TAATGGTTTTGACTTTTAACTTTAAAAAAGTAAACATTTATCAAAACAACGTAACTTTGCCTTTT
16226806 AACT
66 AACT
***
16226810 TAATGGTTTTGACTTTTAACTTTACAAAAAGTAAACATTTATCAAAATGGCGTAACTTTGCCTTT
1 TAATGGTTTTGACTTTTAACTTTA-AAAAAGTAAACATTTATCAAAACAACGTAACTTTGCCTTT
16226875 T
65 T
16226876 CTTATTTAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 2 0.04
70 36 0.63
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (69 bp):
TAATGGTTTTGACTTTTAACTTTAAAAAAGTAAACATTTATCAAAACAACGTAACTTTGCCTTTT
AACT
Found at i:16227268 original size:15 final size:15
Alignment explanation
Indices: 16227244--16227277 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
16227234 TTATCAAAAA
16227244 AAATTATAATTTTTT
1 AAATTATAATTTTTT
*
16227259 AAATTTTAATTTTTT
1 AAATTATAATTTTTT
16227274 AAAT
1 AAAT
16227278 AATTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATTATAATTTTTT
Found at i:16229439 original size:27 final size:27
Alignment explanation
Indices: 16229409--16229563 Score: 150
Period size: 27 Copynumber: 5.7 Consensus size: 27
16229399 AAGTCCTTAT
* **
16229409 TACAGAATACGCCACAAAGGTGATCCA
1 TACAGAGTACGCCACAAAGGTGATATA
* *
16229436 TACAGAGTACACCACAAAGGTTATATA
1 TACAGAGTACGCCACAAAGGTGATATA
* ** * *
16229463 TAGAGAGTATACCACAAAGGCGACATA
1 TACAGAGTACGCCACAAAGGTGATATA
* *
16229490 TACAGATTATGCCACAAAGGTGATATA
1 TACAGAGTACGCCACAAAGGTGATATA
* **
16229517 TACAGAGTATGCCACAAAGGCAAT-TCA
1 TACAGAGTACGCCACAAAGGTGATAT-A
*
16229544 TTCAGAGTACGCCACAAAGG
1 TACAGAGTACGCCACAAAGG
16229564 CTGACAGGAT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 106 0.99
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
TACAGAGTACGCCACAAAGGTGATATA
Found at i:16229551 original size:81 final size:82
Alignment explanation
Indices: 16229409--16229569 Score: 191
Period size: 81 Copynumber: 2.0 Consensus size: 82
16229399 AAGTCCTTAT
* ** * *
16229409 TACAGAATACGCCACAAAGGTGATCCATACAGAGTACACCACAAAGGTTATATATAGAGAGTATA
1 TACAGAATACGCCACAAAGGTGATACATACAGAGTACACCACAAAGGCAATATATACAGAGTACA
16229474 CCACAAAGGC-GACATA
66 CCACAAAGGCTGACATA
* * * ** *
16229490 TACAGATTATGCCACAAAGGTGATATATACAGAGTATGCCACAAAGGCAAT-TCATTCAGAGTAC
1 TACAGAATACGCCACAAAGGTGATACATACAGAGTACACCACAAAGGCAATAT-ATACAGAGTAC
*
16229554 GCCACAAAGGCTGACA
65 ACCACAAAGGCTGACA
16229570 GGATGCCACA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
80 1 0.02
81 61 0.92
82 4 0.06
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (82 bp):
TACAGAATACGCCACAAAGGTGATACATACAGAGTACACCACAAAGGCAATATATACAGAGTACA
CCACAAAGGCTGACATA
Found at i:16229558 original size:54 final size:54
Alignment explanation
Indices: 16229409--16229563 Score: 170
Period size: 54 Copynumber: 2.9 Consensus size: 54
16229399 AAGTCCTTAT
* * ** * * *
16229409 TACAGAATACGCCACAAAGGTGATCCATACAGAGTACACCACAAAGGTTATATA
1 TACAGAGTATGCCACAAAGGCAATTCATACAGAGTACGCCACAAAGGTGATATA
* * * *
16229463 TAGAGAGTATACCACAAAGGCGACA-T-ATACAGATTATGCCACAAAGGTGATATA
1 TACAGAGTATGCCACAAAGGC-A-ATTCATACAGAGTACGCCACAAAGGTGATATA
*
16229517 TACAGAGTATGCCACAAAGGCAATTCATTCAGAGTACGCCACAAAGG
1 TACAGAGTATGCCACAAAGGCAATTCATACAGAGTACGCCACAAAGG
16229564 CTGACAGGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 77 0.95
56 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (54 bp):
TACAGAGTATGCCACAAAGGCAATTCATACAGAGTACGCCACAAAGGTGATATA
Found at i:16235174 original size:38 final size:38
Alignment explanation
Indices: 16235123--16235235 Score: 118
Period size: 38 Copynumber: 3.0 Consensus size: 38
16235113 GTTATATCGT
* * *
16235123 TATTCAAGTTTTGTGCATAGTAGGCTTAGTGCTGGTGA
1 TATTCAGGATTTGTGCCTAGTAGGCTTAGTGCTGGTGA
* * ** *
16235161 TATTCAGGATTTGTGCCTAGCATGCTTAGTGCCAGTGT
1 TATTCAGGATTTGTGCCTAGTAGGCTTAGTGCTGGTGA
* * * *
16235199 TATTCAGGCTTAGTGCCTAGTAGGTTTATTGCTGGTG
1 TATTCAGGATTTGTGCCTAGTAGGCTTAGTGCTGGTG
16235236 TAATTAAAGT
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (38 bp):
TATTCAGGATTTGTGCCTAGTAGGCTTAGTGCTGGTGA
Found at i:16236839 original size:12 final size:12
Alignment explanation
Indices: 16236822--16236854 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
16236812 TGCCACGCAC
16236822 GGCCGTGTGTCA
1 GGCCGTGTGTCA
*
16236834 GGCCGTGTGTTA
1 GGCCGTGTGTCA
16236846 GGCCGTGTG
1 GGCCGTGTG
16236855 CCAAGCTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.21, G:0.45, T:0.27
Consensus pattern (12 bp):
GGCCGTGTGTCA
Found at i:16236854 original size:24 final size:24
Alignment explanation
Indices: 16236822--16236877 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
16236812 TGCCACGCAC
* * **
16236822 GGCCGTGTGTCAGGCCGTGTGTTA
1 GGCCGTGTGCCAAGCCGTGTACTA
*
16236846 GGCCGTGTGCCAAGCTGTGTACTA
1 GGCCGTGTGCCAAGCCGTGTACTA
16236870 GGCCGTGT
1 GGCCGTGT
16236878 AACTCACTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.23, G:0.39, T:0.27
Consensus pattern (24 bp):
GGCCGTGTGCCAAGCCGTGTACTA
Found at i:16239245 original size:11 final size:11
Alignment explanation
Indices: 16239229--16239262 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
16239219 AAGGTTTTTG
16239229 AATTATTAATT
1 AATTATTAATT
16239240 AATTATTAATT
1 AATTATTAATT
16239251 AATTA-TAATT
1 AATTATTAATT
16239261 AA
1 AA
16239263 ATAATTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTATTAATT
Found at i:16239849 original size:22 final size:20
Alignment explanation
Indices: 16239797--16239835 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16239787 TTTATCTTCT
16239797 TAGAATAAATTATATTTTTA
1 TAGAATAAATTATATTTTTA
16239817 TAGAATAAATTATATTTTT
1 TAGAATAAATTATATTTTT
16239836 TGGGAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TAGAATAAATTATATTTTTA
Found at i:16241463 original size:41 final size:41
Alignment explanation
Indices: 16241350--16241470 Score: 127
Period size: 41 Copynumber: 3.0 Consensus size: 41
16241340 GTGATAATCG
* * * *
16241350 GGCTTTGTGCCTAGT-AGGCTTTATGCCGGTGAATTATATCA
1 GGCTTTATGCCTA-TCAGGCTTAATGCCGGTGTATCATATCA
* * * * *
16241391 GGTTTTACGCCTAGCAGGCTTAATACCGGTGTACCATATCA
1 GGCTTTATGCCTATCAGGCTTAATGCCGGTGTATCATATCA
**
16241432 GGCTTTATGCCTATCAGGCTTCGTGCCGGTGTATCATAT
1 GGCTTTATGCCTATCAGGCTTAATGCCGGTGTATCATAT
16241471 TAAGATTTGT
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (41 bp):
GGCTTTATGCCTATCAGGCTTAATGCCGGTGTATCATATCA
Found at i:16254927 original size:37 final size:36
Alignment explanation
Indices: 16254876--16254966 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 36
16254866 ATTCCAAAAA
* *
16254876 TAATATTATTTTAATAGT-TTAATATTAATTTTA-ATT
1 TAATATTATCTTAATAGTATT--TATTAATTTAATATT
16254912 TAATACTTATCTTAATAGTATTTATTAATTTAATATT
1 TAATA-TTATCTTAATAGTATTTATTAATTTAATATT
16254949 TAAGTGATTATCTTAATA
1 TAA-T-ATTATCTTAATA
16254967 TTAAAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
36 15 0.31
37 18 0.38
38 14 0.29
39 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTTATTAATTTAATATT
Found at i:16254951 original size:25 final size:25
Alignment explanation
Indices: 16254879--16254951 Score: 58
Period size: 29 Copynumber: 2.7 Consensus size: 25
16254869 CCAAAAATAA
* *
16254879 TATTATTTTAATAGTTTAATATTAAT
1 TATTAATTTAATA-TTTAATAGTAAT
*
16254905 T-TTAATTTAATACTTATCTTAATAGTATT
1 TATTAATTT-A-A--TAT-TTAATAGTAAT
16254934 TATTAATTTAATATTTAA
1 TATTAATTTAATATTTAA
16254952 GTGATTATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
25 10 0.26
26 5 0.13
27 1 0.03
28 2 0.05
29 13 0.34
30 7 0.18
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
TATTAATTTAATATTTAATAGTAAT
Found at i:16254970 original size:67 final size:65
Alignment explanation
Indices: 16254893--16255089 Score: 179
Period size: 67 Copynumber: 3.0 Consensus size: 65
16254883 ATTTTAATAG
* *
16254893 TTTAATATTAATTTTAATTTAATACTTATCTTAATAGTATTTATTAATTTAATATTTAAGTGATT
1 TTTAATATTAAATTTAATTTAATATTTATCTT-ATAGTATTTATTAATTTAATATTTAAGTGATT
16254958 A
65 A
* * * * ** *
16254959 TCTTAATATTAAAATAAATTTAATGTTTAT-TT-T-GTATATAAACAATTTATTATTTTAA-T-A
1 T-TTAATATTAAATTTAATTTAATATTTATCTTATAGTAT-TTATTAATTTAATA-TTTAAGTGA
*
16255019 ATA
63 TTA
* * *
16255022 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATATTTATCTT-AT-AGTATT-TATTAATTTAATATTTAAGTGA
16255087 TTA
63 TTA
16255090 GGTTTAATTA
Statistics
Matches: 99, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
62 24 0.24
63 10 0.10
64 12 0.12
65 6 0.06
66 8 0.08
67 36 0.36
68 3 0.03
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (65 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTATAGTATTTATTAATTTAATATTTAAGTGATTA
Found at i:16255216 original size:25 final size:24
Alignment explanation
Indices: 16255187--16255235 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
16255177 AGTTGCAAAG
16255187 AGAAAA-TTCTTAAAGAGATTATTTC
1 AGAAAATTTC-TAAAGAGATT-TTTC
*
16255212 AGAAAATTTCTAAAGATATTTTTC
1 AGAAAATTTCTAAAGAGATTTTTC
16255236 TGATTTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 15 0.68
26 3 0.14
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (24 bp):
AGAAAATTTCTAAAGAGATTTTTC
Found at i:16270332 original size:29 final size:28
Alignment explanation
Indices: 16270300--16270360 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
16270290 AAAAGTCATT
*
16270300 TTTTTTCAAAATTTATCGAAATGGGTCGA
1 TTTTTTCAAAATTTATCGAAAT-GGTCCA
* ** *
16270329 TTTTTTGATTATTTATCGGAATGGTCCA
1 TTTTTTCAAAATTTATCGAAATGGTCCA
16270357 TTTT
1 TTTT
16270361 CCGAGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (28 bp):
TTTTTTCAAAATTTATCGAAATGGTCCA
Found at i:16270694 original size:32 final size:31
Alignment explanation
Indices: 16270656--16270721 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 31
16270646 CTCAAATCCA
*
16270656 TTTTTTAAAATAATTATAATTTTTTTTTATAT
1 TTTTTTAAAATAATTATAA-ATTTTTTTATAT
*
16270688 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
16270719 TTT
1 TTT
16270722 CATCAATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:16271813 original size:7 final size:7
Alignment explanation
Indices: 16271801--16271832 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
16271791 AGTCGATTGA
16271801 TATTTAG
1 TATTTAG
16271808 TATTTAG
1 TATTTAG
16271815 TATTTAG
1 TATTTAG
16271822 TATTTAG
1 TATTTAG
16271829 TATT
1 TATT
16271833 ATGTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:16272510 original size:18 final size:18
Alignment explanation
Indices: 16272489--16272541 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
16272479 TGTTTCCTAG
*
16272489 CCCTTATATGTACCTTAA
1 CCCTTACATGTACCTTAA
*
16272507 CCCTTACATGTACCCTAA
1 CCCTTACATGTACCTTAA
16272525 CCCTTACATGTATCCTT
1 CCCTTACATGTA-CCTT
16272542 TTCCGAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.36
Consensus pattern (18 bp):
CCCTTACATGTACCTTAA
Found at i:16272830 original size:24 final size:23
Alignment explanation
Indices: 16272795--16272851 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
16272785 ATGCCGAACC
*
16272795 GGAAGAACCACAACCACCACCGGA
1 GGAAGAA-CACAACCACCACCAGA
* *
16272819 GGAAGGAACACAATCACCACTAGA
1 GGAA-GAACACAACCACCACCAGA
16272843 GGAAGAACA
1 GGAAGAACA
16272852 ACCGCCGCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.17
24 21 0.72
25 3 0.10
ACGTcount: A:0.46, C:0.28, G:0.23, T:0.04
Consensus pattern (23 bp):
GGAAGAACACAACCACCACCAGA
Found at i:16273207 original size:28 final size:28
Alignment explanation
Indices: 16273080--16274157 Score: 1501
Period size: 28 Copynumber: 37.6 Consensus size: 28
16273070 AAAACCCTAA
*
16273080 CCTAACCCTACCCTAAATTAATTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAAC
*
16273109 CCTAAACCTAACTCAAAATTAATTAAAAAC
1 CCT-AACCTAAC-CTAAATTAATTAAAAAC
16273139 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
*
16273168 CCTAAACCTAACCTAAATTAACTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* *
16273197 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
16273225 CCTAACCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
16273253 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* *
16273282 CCTAATCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
16273310 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
16273339 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
16273368 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* *
16273397 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
16273425 CCTAATCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* * *
16273453 CCTAATCTAACATAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* *
16273481 CCTAATCTAACCTAAATTAATTAAAAAA
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
16273509 CCTAAACCTAAGCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* *
16273538 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
16273566 CCTAATCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
**
16273594 CCTAAACCTGCCCTAAAATTAATTAAAAAC
1 CCT-AACCTAACCT-AAATTAATTAAAAAC
* * *
16273624 CCTAATCAAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
16273652 CCTAACCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
16273680 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
*
16273709 CCTAAACCTAACCTAAATTAACTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
*
16273738 CCTAATCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
16273766 CCTAAACCTAAGCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* *
16273795 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* *
16273823 CCTAATCTAACATAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
16273851 CCTAAACCTAAGCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* *
16273880 CCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* *
16273908 CCTAATCTAACCTAAAATTAATTTAAAAC
1 CCTAACCTAACCT-AAATTAATTAAAAAC
16273937 CCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCT-AACCTAACCT-AAATTAATTAAAAAC
16273967 CCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCT-AACCTAACCT-AAATTAATTAAAAAC
* *
16273997 CCTAAAACTAACCTAAAATTAATTACAAAC
1 CCT-AACCTAACCT-AAATTAATTAAAAAC
* * *
16274027 CCTAATCTAATCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
16274055 CCTAACCTAACCTAAATTAACT-AAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* *
16274082 ACCTAATCTAGCCTAAATTAATTAAAAAC
1 -CCTAACCTAACCTAAATTAATTAAAAAC
16274111 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
* * *
16274140 TCTAAACTAATCTAAATT
1 CCTAACCTAACCTAAATT
16274158 TTTTTGGCTT
Statistics
Matches: 961, Mismatches: 73, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.01
28 457 0.48
29 366 0.38
30 133 0.14
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.25
Consensus pattern (28 bp):
CCTAACCTAACCTAAATTAATTAAAAAC
Found at i:16273264 original size:57 final size:57
Alignment explanation
Indices: 16273080--16274157 Score: 1553
Period size: 57 Copynumber: 18.8 Consensus size: 57
16273070 AAAACCCTAA
* * * *
16273080 CCTAACCCTACCCTAAATTAATTAAAAACCCTAAACCTAACTCAAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAAC-CTAAATTAATTAAAAAC
* *
16273139 CCTAAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAATTAAAAAC
* * *
16273197 CCT-AATCTAACCTAAATTAACTAAAAACCCTAACCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
*
16273253 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTTAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
*
16273310 CCTAAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAATTAAAAAC
*
16273368 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
* * *
16273425 CCT-AATCTAACCTAAATTAATTAAAAACCCTAATCTAACATAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
* * * *
16273481 CCT-AATCTAACCTAAATTAATTAAAAAACCTAAACCTAAGCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAATTAAAAAC
* *
16273538 CCT-AATCTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
** * *
16273594 CCTAAACCTGCCCTAAAATTAATTAAAAACCCTAATCAAACCTAAATTAACTAAAAAC
1 CCTAAACCTAACCT-AAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
*
16273652 CCT-AACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAATTAAAAAC
*
16273709 CCTAAACCTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
* *
16273766 CCTAAACCTAAGCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
* * * *
16273823 CCT-AATCTAACATAAATTAATTAAAAACCCTAAACCTAAGCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAATTAAAAAC
* * *
16273880 CCT-AATCTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAAATTAATTTAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCT-AAATTAATTAAAAAC
*
16273937 CCTAAACCTAACCTAAAATTAATTAAAAACCCTAAACCTAACCTAAAATTAATTAAAAAC
1 CCTAAACCTAACCT-AAATTAATTAAAAACCCT-AATCTAACCT-AAATTAATTAAAAAC
* * * *
16273997 CCTAAAACTAACCTAAAATTAATTACAAACCCTAATCTAATCTAAATTAACTAAAAAC
1 CCTAAACCTAACCT-AAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
* *
16274055 CCT-AACCTAACCTAAATTAACT-AAAACACCTAATCTAGCCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAAC-CCTAATCTAACCTAAATTAATTAAAAAC
* * *
16274111 CCTAAACCTAACCTAAATTAATTAAAAACTCTAAACTAATCTAAATT
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATT
16274158 TTTTTGGCTT
Statistics
Matches: 931, Mismatches: 73, Indels: 32
0.90 0.07 0.03
Matches are distributed among these distances:
55 4 0.00
56 221 0.24
57 413 0.44
58 174 0.19
59 64 0.07
60 55 0.06
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.25
Consensus pattern (57 bp):
CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAAC
Found at i:16274173 original size:23 final size:25
Alignment explanation
Indices: 16274147--16274211 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
16274137 AACTCTAAAC
16274147 TAATCTA-A-ATTTTTTTGGCTTAA
1 TAATCTACATATTTTTTTGGCTTAA
*
16274170 TAATTTTACATATTTTTTTGGCTTAA
1 TAA-TCTACATATTTTTTTGGCTTAA
*
16274196 TAATTTTACATATTTT
1 TAA-TCTACATATTTT
16274212 GAACACTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
23 3 0.08
24 3 0.08
25 1 0.03
26 31 0.82
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (25 bp):
TAATCTACATATTTTTTTGGCTTAA
Found at i:16274184 original size:26 final size:26
Alignment explanation
Indices: 16274155--16274211 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
16274145 ACTAATCTAA
16274155 ATTTTTTTGGCTTAATAATTTTACAT
1 ATTTTTTTGGCTTAATAATTTTACAT
16274181 ATTTTTTTGGCTTAATAATTTTACAT
1 ATTTTTTTGGCTTAATAATTTTACAT
16274207 ATTTT
1 ATTTT
16274212 GAACACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (26 bp):
ATTTTTTTGGCTTAATAATTTTACAT
Found at i:16275444 original size:125 final size:126
Alignment explanation
Indices: 16275139--16275476 Score: 572
Period size: 125 Copynumber: 2.7 Consensus size: 126
16275129 CCAAACTTGA
*
16275139 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATTCTCGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCGT
16275204 AGAAACGATTTTATACTATTTGCTCAAAAACATCAGAAAAAAAATTATTTCTTACATGACC
66 AGAAACGATTTTATACTATTTGCTCAAAAACATCAGAAAAAAAATTATTTCTTACATGACC
* *
16275265 TACTGTAGCAAAACCGCGTCCACGAAGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCGT
*
16275330 AGAAATGATTTTATACTATTTGCTCAGAAAA-ATCAG-AAAAAAATTATTTCTTACATGACC
66 AGAAACGATTTTATACTATTTGCTCA-AAAACATCAGAAAAAAAATTATTTCTTACATGACC
* * * *
16275390 TACTGTAGCAAAATTGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCAAATAGCATCTTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCGT
*
16275455 AGAAGCGATTTTATACTATTTG
66 AGAAACGATTTTATACTATTTG
16275477 ACCAGAGACG
Statistics
Matches: 199, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
125 103 0.52
126 92 0.46
127 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (126 bp):
TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCGT
AGAAACGATTTTATACTATTTGCTCAAAAACATCAGAAAAAAAATTATTTCTTACATGACC
Done.