Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 49 of 171
Found at i:20579660 original size:117 final size:116
Alignment explanation
Indices: 20579500--20579762 Score: 345
Period size: 117 Copynumber: 2.3 Consensus size: 116
20579490 TCGAGAAAAT
* * *
20579500 TCGAGGTTAAAAAT-GGAATTTGGAAAGTTTAAGGGTAAAATGGTAATTTT-GGTGAAATCGGGG
1 TCGAGGTTAAAAATGGGATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGGTGAAATCAGGG
* * *
20579563 TTAAAAT-GAGATTTTGGAAAGTTTGAGGGTAAAAATGGTAATTTTTGGTGAA-A
66 TCAAAATGGA-ATTTTAGAAAGCTTGAGGGT-AAAATGGTAATTTTT-G-GAAGA
**
20579616 TCGAGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGGTGAAATCAGGG
1 TCGAGGTTAAAAATGGGATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGGTGAAATCAGGG
* *
20579681 TCAAAATGGAATTTTAGAAAGCTTGGGGGTAAAATGGTAATTTTTGGAAGTT
66 TCAAAATGGAATTTTAGAAAGCTTGAGGGTAAAATGGTAATTTTTGGAAG-A
* *
20579733 TCGAGGTCAAAAATGGAATTTTGGAAAGTT
1 TCGAGGTTAAAAATGGGATTTTGGAAAGTT
20579763 TAGGGACTAG
Statistics
Matches: 130, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
115 3 0.02
116 15 0.12
117 75 0.58
118 35 0.27
119 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (116 bp):
TCGAGGTTAAAAATGGGATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTGGGTGAAATCAGGG
TCAAAATGGAATTTTAGAAAGCTTGAGGGTAAAATGGTAATTTTTGGAAGA
Found at i:20579710 original size:29 final size:29
Alignment explanation
Indices: 20579678--20579760 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
20579668 GGTGAAATCA
*
20579678 GGGTCAAAATGGAATTTTAGAAAGCTTGG
1 GGGTCAAAATGGAATTTTAGAAAGCTTCG
* * *
20579707 GGGT-AAAATGGTAATTTTTGGAAGTTTCG
1 GGGTCAAAATGG-AATTTTAGAAAGCTTCG
* *
20579736 AGGTCAAAAATGGAATTTTGGAAAG
1 GGGTC-AAAATGGAATTTTAGAAAG
20579761 TTTAGGGACT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.16
29 20 0.45
30 10 0.23
31 7 0.16
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (29 bp):
GGGTCAAAATGGAATTTTAGAAAGCTTCG
Found at i:20581749 original size:17 final size:17
Alignment explanation
Indices: 20581723--20581759 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20581713 GGACATTTAT
*
20581723 TTTATTTTAAATTTAAA
1 TTTATATTAAATTTAAA
*
20581740 TTTATATTAAGTTTAAA
1 TTTATATTAAATTTAAA
20581757 TTT
1 TTT
20581760 TAAAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTAAATTTAAA
Found at i:20581874 original size:15 final size:15
Alignment explanation
Indices: 20581841--20581881 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
20581831 GCTTCAACAA
20581841 TCACATA-ATATTTC
1 TCACATATATATTTC
* *
20581855 ACACATATATTTTTC
1 TCACATATATATTTC
20581870 TCACATATATAT
1 TCACATATATAT
20581882 CATTATATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.44
Consensus pattern (15 bp):
TCACATATATATTTC
Found at i:20583585 original size:20 final size:19
Alignment explanation
Indices: 20583556--20583593 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
20583546 TAATGATTAT
20583556 ATTTAAATATTTAAAATATA
1 ATTTAAATA-TTAAAATATA
*
20583576 ATTTATATATTAAAATAT
1 ATTTAAATATTAAAATAT
20583594 TAACAACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATATTAAAATATA
Found at i:20583588 original size:19 final size:20
Alignment explanation
Indices: 20583538--20583593 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
20583528 TATCTAACTA
*
20583538 TAAATATTTAATGAT-TATATT
1 TAAATATTTAA-AATATA-ATT
20583559 TAAATATTTAAAATATAATT
1 TAAATATTTAAAATATAATT
*
20583579 TATATA-TTAAAATAT
1 TAAATATTTAAAATAT
20583594 TAACAACAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 9 0.28
20 10 0.31
21 13 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAATATTTAAAATATAATT
Found at i:20584671 original size:29 final size:29
Alignment explanation
Indices: 20584638--20584695 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
20584628 AAAGATGATT
* *
20584638 TTTAAATTAAAAAATAACAATATTAAATA
1 TTTAAACTAAAAAATAACAATATAAAATA
** *
20584667 TTTAAACTAATTAATAACATTATAAAATA
1 TTTAAACTAAAAAATAACAATATAAAATA
20584696 CAGAAATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTAAACTAAAAAATAACAATATAAAATA
Found at i:20587807 original size:41 final size:42
Alignment explanation
Indices: 20587757--20587839 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 42
20587747 CTTGTCCTAG
*
20587757 AAACAACATGGCCCTGACATTAAATTGATCATACCTAGCAAT
1 AAACAACATGGCCCAGACATTAAATTGATCATACCTAGCAAT
20587799 AAAC-ACATGGCCCAGACATTAAATTGATCATACCTAGCAAT
1 AAACAACATGGCCCAGACATTAAATTGATCATACCTAGCAAT
20587840 TCATGTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 36 0.90
42 4 0.10
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (42 bp):
AAACAACATGGCCCAGACATTAAATTGATCATACCTAGCAAT
Found at i:20592341 original size:29 final size:30
Alignment explanation
Indices: 20592308--20592395 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
20592298 TAATTTAATA
20592308 TGCAATTGTATATATG-AACTTTAATTTGG
1 TGCAATTGTATATATGAAACTTTAATTTGG
* * * *
20592337 TGCAATTATACACATGAAACTCTAATATTGG
1 TGCAATTGTATATATGAAACTTTAAT-TTGG
* *
20592368 TTCAAATGTATACT-TGAAACTTTAATTT
1 TGCAATTGTATA-TATGAAACTTTAATTT
20592396 TGATTTAATC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
29 13 0.28
30 10 0.22
31 23 0.50
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (30 bp):
TGCAATTGTATATATGAAACTTTAATTTGG
Found at i:20602515 original size:25 final size:23
Alignment explanation
Indices: 20602458--20602618 Score: 166
Period size: 23 Copynumber: 6.9 Consensus size: 23
20602448 TTACCGATCA
*
20602458 GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
20602481 GCACTTTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
*
20602504 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
* *
20602527 GCACTTCGTGTGCCTACTGATTT-
1 GCACTTTGTGTGCTTACTG-TTTC
* * * * *
20602550 GCGCTATGTGCGCCTACTGATT-
1 GCACTTTGTGTGCTTACTGTTTC
*
20602572 GCACTGTGTGTGCTTACTGTTTCCCC
1 GCACTTTGTGTGCTTACTGTTT---C
20602598 AGCAC-TTGTGTGCTTACTGTT
1 -GCACTTTGTGTGCTTACTGTT
20602619 AAGTACTTCG
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.16
23 77 0.65
24 3 0.03
26 15 0.13
27 4 0.03
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.41
Consensus pattern (23 bp):
GCACTTTGTGTGCTTACTGTTTC
Found at i:20610630 original size:309 final size:314
Alignment explanation
Indices: 20610063--20611069 Score: 1650
Period size: 315 Copynumber: 3.2 Consensus size: 314
20610053 GGATTTACAT
* *
20610063 TGATGGGAGTTTTAATCTGGTAATTACCGATGAAAACTT-A-T-TGTA-TTTTCATTTCTGATG-
1 TGATGGGA-TTTTAATCTGGTAATTACTGATGAAAACTTCATTCTGGATTTTTCATTTCTGATGA
* *
20610123 AATGCAAGGTTC-T--T--ACTAGCTATCTTTTTCATGATGAATCTGTCAAATTTTAGTATATTT
65 AATGCAAGGTTCTTCATGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTT
* *
20610183 TGCTAGGCATTTTGGCTAGTGGAAGCATTGCCATTAGGTTCATACTTTGAAGTAGATTATTCAGA
130 TGCTAGGCATTTTGGTTAGTGGAAGCATTGCCATTAGGTTCATACTTTGAAGTAGATGATTCAGA
*
20610248 AACAATGTATTATGAATGGATTTAGCGAAAGATTGTATGAACTATGCAATTTTTTGGTAATGTGT
195 AACAATGTATTATGAATGGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGTGT
20610313 TGCTTTCAGCTGATTTAGAA-CCAAAGCTCAAGTTTCTCATGGAAGGAATTAGAG
260 TGCTTTCAGCTGATTTAGAACCCAAAGCTCAAGTTTCTCATGGAAGGAATTAGAG
* *
20610367 TGATGGGATTTTGATCTGGTAATTACTGATGAAAACTT-A-T-TGTA-TTTTCATTTCTGATG-A
1 TGATGGGATTTTAATCTGGTAATTACTGATGAAAACTTCATTCTGGATTTTTCATTTCTGATGAA
*
20610427 ATTCAAGGTTCTTCCATGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTT
66 ATGCAAGGTTCTT-CATGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTT
* *
20610492 TGCTAGGCATTTTGGTTAGTCGAAGCATTGCCATTAAGTTCATACTTTGAAGTAGATGATTCAGA
130 TGCTAGGCATTTTGGTTAGTGGAAGCATTGCCATTAGGTTCATACTTTGAAGTAGATGATTCAGA
*
20610557 AACAATGTATTATGAATGCATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGTGT
195 AACAATGTATTATGAATGGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGTGT
* *
20610622 TGCTTTCAGCTGATTTAGAATCCAAAGCTCAAGTTGCTCATGGAAGGAATTAGAG
260 TGCTTTCAGCTGATTTAGAACCCAAAGCTCAAGTTTCTCATGGAAGGAATTAGAG
* * *
20610677 TGATGGGATTTTAATATAGTAATTACTGATGAAAATTTCATTCTGGATTTTTCATTTCTGATGAA
1 TGATGGGATTTTAATCTGGTAATTACTGATGAAAACTTCATTCTGGATTTTTCATTTCTGATGAA
*
20610742 ATGCAAGGTTCTTTCACGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTT
66 ATGCAAGGTTC-TTCATGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTT
* *
20610807 TGCTAGGCATTTTGGTTGGTGGAAGCATTGCCATTAGGTTCGTACTTTGAAGTAGATGATTCAGA
130 TGCTAGGCATTTTGGTTAGTGGAAGCATTGCCATTAGGTTCATACTTTGAAGTAGATGATTCAGA
* *
20610872 AACAATGTATTATGAATGGATTTAGTGAAAGATTGTATGAACTATGCAATGTTTTGGTAAAGTGT
195 AACAATGTATTATGAATGGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGTGT
20610937 TGCTTTCAGCTGATTTAGAACCCAAAGCTCAAGTTTCTCATGGAAGGAATTAGAG
260 TGCTTTCAGCTGATTTAGAACCCAAAGCTCAAGTTTCTCATGGAAGGAATTAGAG
* *
20610992 TGATGGGATTTTGATCTGGTAATTACTGATGAAAATTTCATTCTGGATTTTTCATTTCTGATGAA
1 TGATGGGATTTTAATCTGGTAATTACTGATGAAAACTTCATTCTGGATTTTTCATTTCTGATGAA
20611057 ATGCAAGGTTCTT
66 ATGCAAGGTTCTT
20611070 TCACGCATTT
Statistics
Matches: 659, Mismatches: 31, Indels: 16
0.93 0.04 0.02
Matches are distributed among these distances:
303 60 0.09
304 9 0.01
307 1 0.00
309 188 0.29
310 67 0.10
311 1 0.00
312 1 0.00
313 3 0.00
314 17 0.03
315 310 0.47
316 2 0.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.39
Consensus pattern (314 bp):
TGATGGGATTTTAATCTGGTAATTACTGATGAAAACTTCATTCTGGATTTTTCATTTCTGATGAA
ATGCAAGGTTCTTCATGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTTT
GCTAGGCATTTTGGTTAGTGGAAGCATTGCCATTAGGTTCATACTTTGAAGTAGATGATTCAGAA
ACAATGTATTATGAATGGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGTGTT
GCTTTCAGCTGATTTAGAACCCAAAGCTCAAGTTTCTCATGGAAGGAATTAGAG
Found at i:20612155 original size:39 final size:39
Alignment explanation
Indices: 20612090--20612165 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
20612080 CAAATCAAGC
* *
20612090 AAATTAATAAAAATAAACAAATTTAATATCTTATATAGA
1 AAATTAACAAAAATAAACAAAATTAATATCTTATATAGA
20612129 AAATTGAACAAAAATAAA-AAAATTAATATCTTATATA
1 AAATT-AACAAAAATAAACAAAATTAATATCTTATATA
20612166 AAACATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 23 0.68
40 11 0.32
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (39 bp):
AAATTAACAAAAATAAACAAAATTAATATCTTATATAGA
Found at i:20618253 original size:21 final size:21
Alignment explanation
Indices: 20618227--20618279 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
20618217 TTTATCATTG
20618227 CATTGTTTTCACTTAGCTCAA
1 CATTGTTTTCACTTAGCTCAA
20618248 CATTGTTTTCACTTAGCTCAA
1 CATTGTTTTCACTTAGCTCAA
*
20618269 CAGTTCTTTTC
1 CA-TTGTTTTC
20618280 TAGGTACCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.21, C:0.25, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTGTTTTCACTTAGCTCAA
Found at i:20620264 original size:16 final size:17
Alignment explanation
Indices: 20620240--20620280 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20620230 ATATTATGTG
* *
20620240 AATTAAAAATGATTTGA
1 AATTAAAATTGACTTGA
20620257 AATTAAAATTGACTTGA
1 AATTAAAATTGACTTGA
*
20620274 ATTTAAA
1 AATTAAA
20620281 TATATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (17 bp):
AATTAAAATTGACTTGA
Found at i:20620859 original size:29 final size:30
Alignment explanation
Indices: 20620822--20620885 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
20620812 TAATAAATTG
* *
20620822 ATTTAAATT-TTGAAATATGAAAGTA-AAAA
1 ATTTAAATTATT-AAAAATAAAAGTATAAAA
*
20620851 ATTTAAATTATTAAAAATAAAAGTATAAAG
1 ATTTAAATTATTAAAAATAAAAGTATAAAA
20620881 ATTTA
1 ATTTA
20620886 TGATGTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (30 bp):
ATTTAAATTATTAAAAATAAAAGTATAAAA
Found at i:20621225 original size:32 final size:33
Alignment explanation
Indices: 20621184--20621254 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
20621174 ATGTAATTTA
20621184 GTAAATAATTTTGGATCTTGATACTTCCATC-T
1 GTAAATAATTTTGGATCTTGATACTTCCATCAT
20621216 GTAAATAATTTTGGATCTTGATACTTCCATCAT
1 GTAAATAATTTTGGATCTTGATACTTCCATCAT
20621249 -TAAATA
1 GTAAATA
20621255 TTAAGTTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (33 bp):
GTAAATAATTTTGGATCTTGATACTTCCATCAT
Found at i:20622251 original size:22 final size:22
Alignment explanation
Indices: 20622223--20622282 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
20622213 TGGGTCTAAA
* *
20622223 AAGGTTTATGGTTTGTAGT-TTT
1 AAGGTTTAAGGTTT-TAGTCTCT
*
20622245 AAGGTTTAGGGTTTTAGTCTCT
1 AAGGTTTAAGGTTTTAGTCTCT
*
20622267 AAAGTTTAAGGTTTTA
1 AAGGTTTAAGGTTTTA
20622283 AAATTTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.48
Consensus pattern (22 bp):
AAGGTTTAAGGTTTTAGTCTCT
Found at i:20623022 original size:23 final size:22
Alignment explanation
Indices: 20622972--20623033 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
20622962 TTTATTTGCT
* *
20622972 TTTGTGGCACGCTTTTCCTTTA
1 TTTGTGGCACGTTTTTCCTTGA
*
20622994 TCTTGTGGCACGTTTTTCCTCTGC
1 T-TTGTGGCACGTTTTTCCT-TGA
* *
20623018 TTTGTGACAAGTTTTT
1 TTTGTGGCACGTTTTT
20623034 GCTTTATTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 1 0.03
23 30 0.91
24 2 0.06
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (22 bp):
TTTGTGGCACGTTTTTCCTTGA
Found at i:20624965 original size:6 final size:6
Alignment explanation
Indices: 20624954--20624980 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20624944 ATTCAATAGT
20624954 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
20624981 GATATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:20633130 original size:26 final size:24
Alignment explanation
Indices: 20633101--20633183 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 24
20633091 AATAAAAAAT
20633101 TAAAATAAATAAGTGAAAAATTCAAG
1 TAAAA-AAATAAGT-AAAAATTCAAG
** *
20633127 TAAACAAAATAACACAAAAATT-ATAA
1 TAAA-AAAATAA-GTAAAAATTCA-AG
*
20633153 TAATAAAAATAAGTAAAAGTTCAAG
1 TAA-AAAAATAAGTAAAAATTCAAG
20633178 TAAAAA
1 TAAAAA
20633184 CATATCGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
24 3 0.07
25 11 0.24
26 29 0.64
27 2 0.04
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.22
Consensus pattern (24 bp):
TAAAAAAATAAGTAAAAATTCAAG
Found at i:20633591 original size:57 final size:57
Alignment explanation
Indices: 20633518--20633635 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 57
20633508 AAAAAGAATT
20633518 GTTTTGAGTTTATTT-AAGAATAAAATTATATTTTA-GTTTAAAAATATTTAGGTTTA
1 GTTTTGAGTTTATTTAAAGAATAAAATTATA-TTTAGGTTTAAAAATATTTAGGTTTA
* * *
20633574 GTTTATGAGTGTT-TTTAAATAATGAAATTATATTTAGGTTTAAAAATATTTGGGTTTA
1 GTTT-TGAGT-TTATTTAAAGAATAAAATTATATTTAGGTTTAAAAATATTTAGGTTTA
20633632 GTTT
1 GTTT
20633636 GTTGATGAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
56 4 0.07
57 12 0.22
58 39 0.71
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (57 bp):
GTTTTGAGTTTATTTAAAGAATAAAATTATATTTAGGTTTAAAAATATTTAGGTTTA
Found at i:20633842 original size:13 final size:13
Alignment explanation
Indices: 20633801--20633845 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
20633791 TTATTCGAAT
*
20633801 AATTCGAATTCGAA
1 AATTCGAACTCG-A
20633815 AATTC-AACTCG-
1 AATTCGAACTCGA
20633826 -ATTCGAACTCGA
1 AATTCGAACTCGA
20633838 AATTCGAA
1 AATTCGAA
20633846 AAAAAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.15
11 6 0.22
13 12 0.44
14 5 0.19
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (13 bp):
AATTCGAACTCGA
Found at i:20637082 original size:27 final size:28
Alignment explanation
Indices: 20637010--20637084 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
20637000 AGATAAAAAT
20637010 AATTTTTTG-GGCCCCTTAAAAGTTGGTA
1 AATTTTTTGTGGCCCCTTAAAAGTT-GTA
* *
20637038 AATTTTTT-TGG-TCTTTAAAAG-T-TA
1 AATTTTTTGTGGCCCCTTAAAAGTTGTA
20637062 ATATTTTTTGTGGCCCCTTAAAA
1 A-ATTTTTTGTGGCCCCTTAAAA
20637085 ATTGGAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 3 0.08
25 7 0.18
26 4 0.10
27 15 0.38
28 10 0.26
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (28 bp):
AATTTTTTGTGGCCCCTTAAAAGTTGTA
Found at i:20637971 original size:29 final size:29
Alignment explanation
Indices: 20637918--20637980 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
20637908 AAATTATGCT
*
20637918 CGTAATCTAAAATAATCTAATGAATTG-AC
1 CGTAATCTAAAATAATCTAAGGAA-TGAAC
20637947 CGTAATCTAAAATAA-CTTAAGGAATGAAC
1 CGTAATCTAAAATAATC-TAAGGAATGAAC
20637976 CGTAA
1 CGTAA
20637981 ATTGGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (29 bp):
CGTAATCTAAAATAATCTAAGGAATGAAC
Found at i:20639482 original size:24 final size:24
Alignment explanation
Indices: 20639454--20639500 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20639444 TAGAGTAATA
*
20639454 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
20639478 AGAGTTTAATTGAAACAAATAAA
1 AGAGTTTAACTCAAACAAATAAA
20639501 CAAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:20643774 original size:60 final size:59
Alignment explanation
Indices: 20643675--20643867 Score: 250
Period size: 59 Copynumber: 3.3 Consensus size: 59
20643665 ATTTTTGACT
* * * *
20643675 TTCGGGGGTAAAA-ATGTAATTTTTGGTGAAATCGAGGTTAAAATTAGG-ATTTTGGAAAG
1 TTCGAGGGTAAAATA-GTGATTTTTGGTGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAG
*
20643734 TTCGAGGGTAAAATGGT-ATTTTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAATAGTGA--TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
*
20643794 TTCGAGGGTAAAATAGTGATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAATAGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
*
20643853 TT-TAGGGTCAAAATA
1 TTCGAGGGT-AAAATA
20643868 TAATTGTTGA
Statistics
Matches: 121, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
58 6 0.05
59 63 0.52
60 51 0.42
61 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (59 bp):
TTCGAGGGTAAAATAGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
Found at i:20643847 original size:29 final size:28
Alignment explanation
Indices: 20643679--20643848 Score: 102
Period size: 29 Copynumber: 5.8 Consensus size: 28
20643669 TTGACTTTCG
*
20643679 GGGGTAAAAATGTAATTTTTGGTGAAATC
1 GGGGTAAAAATGGAA-TTTTGGTGAAATC
* *
20643708 GAGGTTAAAATTAGG-ATTTT-G-GAAAGTTC
1 G-GGGTAAAAAT-GGAATTTTGGTGAAA--TC
*
20643737 GAGGGT-AAAATGGTATTTTTTTGGTGAAATC
1 G-GGGTAAAAATGG-A--ATTTTGGTGAAATC
20643768 GGGGTTAAAAATGGAATTTT-G-GAAAGTTC
1 GGGG-TAAAAATGGAATTTTGGTGAAA--TC
*
20643797 GAGGGT-AAAATAGTGATTTTTGGTGAAATC
1 G-GGGTAAAAAT-G-GAATTTTGGTGAAATC
20643827 GGGGTCAAAAATGGAATTTTGG
1 GGGGT-AAAAATGGAATTTTGG
20643849 AAAGTTTAGG
Statistics
Matches: 111, Mismatches: 9, Indels: 42
0.69 0.06 0.26
Matches are distributed among these distances:
27 10 0.09
28 11 0.10
29 33 0.30
30 25 0.23
31 16 0.14
32 12 0.11
33 4 0.04
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTGGTGAAATC
Found at i:20643860 original size:29 final size:29
Alignment explanation
Indices: 20643769--20643865 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
20643759 GGTGAAATCG
*
20643769 GGGTTAAAAATGGAATTTTGGAAAGTTCGA
1 GGGTCAAAAATGGAATTTTGGAAAGTTC-A
* *
20643799 GGGT--AAAATAGTGATTTTTGGTGAAA--TCG
1 GGGTCAAAAAT-G-GAATTTT-G-GAAAGTTCA
*
20643828 GGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGTCAAAAATGGAATTTTGGAAAGTTCA
20643857 GGGTCAAAA
1 GGGTCAAAA
20643866 TATAATTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
27 4 0.07
28 6 0.11
29 21 0.39
30 13 0.24
31 6 0.11
32 4 0.07
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTGGAAAGTTCA
Found at i:20644674 original size:6 final size:6
Alignment explanation
Indices: 20644659--20644705 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
20644649 TTATTTGGAC
* *
20644659 ATTT-A ATTTAA ATTTAA ATTTAA ATTTAT A-TTAA GTTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
20644705 A
1 A
20644706 AAAAAAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 7 0.19
6 29 0.81
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:20644681 original size:17 final size:17
Alignment explanation
Indices: 20644659--20644705 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
20644649 TTATTTGGAC
20644659 ATTT-AATTTAAATTTAA
1 ATTTAAATTTAAA-TTAA
*
20644676 ATTTAAATTTATATTAA
1 ATTTAAATTTAAATTAA
*
20644693 GTTTAAATTTAAA
1 ATTTAAATTTAAA
20644706 AAAAAAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTAAATTAA
Found at i:20645497 original size:7 final size:7
Alignment explanation
Indices: 20645485--20645514 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
20645475 TGTTAAAGTC
20645485 AGACAAA
1 AGACAAA
20645492 AGACAAA
1 AGACAAA
20645499 AGACAAA
1 AGACAAA
20645506 AGACAAA
1 AGACAAA
20645513 AG
1 AG
20645515 GGTAAACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (7 bp):
AGACAAA
Found at i:20647205 original size:14 final size:16
Alignment explanation
Indices: 20647178--20647217 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 16
20647168 AAAATAGTAA
20647178 TTTTATTTTAATAATT
1 TTTTATTTTAATAATT
20647194 TTTTATTTATAATTAATT
1 TTTTATTT-TAA-TAATT
20647212 TGTTTA
1 T-TTTA
20647218 AAGCGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 3 0.14
18 6 0.29
19 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTATTTTAATAATT
Found at i:20648075 original size:24 final size:24
Alignment explanation
Indices: 20648047--20648105 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
20648037 TAGACTAATA
*
20648047 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
20648071 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* *
20648095 AAAATTTAACT
1 AGAGTTTAACT
20648106 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:20648108 original size:24 final size:24
Alignment explanation
Indices: 20648059--20648109 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
20648049 AGTTTGACTC
* * *
20648059 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAAAATTTAACTG
20648083 AAACAAATAAATAAAATTTAACTG
1 AAACAAATAAATAAAATTTAACTG
20648107 AAA
1 AAA
20648110 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (24 bp):
AAACAAATAAATAAAATTTAACTG
Found at i:20650568 original size:155 final size:152
Alignment explanation
Indices: 20650326--20650606 Score: 420
Period size: 155 Copynumber: 1.8 Consensus size: 152
20650316 ATAATTTACT
* * *
20650326 CCCTGTTCGTCTACAAAGAAAACTGTTCAAAAAACACCTCACAGCTGAAAAAGATTCAGAAATAT
1 CCCTGTTCGTCTACAAAGAAAACTGTTCAAAAAACACCTCACAACTGAAAAAAATTCAAAAATAT
*
20650391 AACAATTAATTGACCACTTCATCGTTGTAATTAAAA-TTCCACCTTTGAACCACTTATTGGAAAA
66 AACAATTAATTGACCACTTCATCGTTGTAACTAAAATTTCCACCTTTGAACCACTTATTGGAAAA
20650455 TTTTCCATCGTTGTAATGAACC
131 TTTTCCATCGTTGTAATGAACC
* * * *
20650477 CCCTGTTCGTGTACTAAGAAAAACTGTTCAAAAAAACATCTCACAATTGGGAAAAAAATTCAAAA
1 CCCTGTTCGTCTACAAAG-AAAACTGTTC-AAAAAACACCTCACAACT--GAAAAAAATTCAAAA
* * *
20650542 ATATAACAATTAATTGACTATTTCATCTTTGTAACTAAAATTTCCACCTTTGAACCACTTATTGG
62 ATATAACAATTAATTGACCACTTCATCGTTGTAACTAAAATTTCCACCTTTGAACCACTTATTGG
20650607 GGCAGTGTCG
Statistics
Matches: 114, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
151 16 0.14
152 10 0.09
153 15 0.13
155 49 0.43
156 24 0.21
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (152 bp):
CCCTGTTCGTCTACAAAGAAAACTGTTCAAAAAACACCTCACAACTGAAAAAAATTCAAAAATAT
AACAATTAATTGACCACTTCATCGTTGTAACTAAAATTTCCACCTTTGAACCACTTATTGGAAAA
TTTTCCATCGTTGTAATGAACC
Found at i:20654642 original size:18 final size:18
Alignment explanation
Indices: 20654608--20654653 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
20654598 CAGCAAATGA
*
20654608 TTTTAAAATTATTAATTT
1 TTTTAAAATTATAAATTT
*
20654626 TTTTAAAA-TATAAA-AT
1 TTTTAAAATTATAAATTT
*
20654642 TATTAAAATTAT
1 TTTTAAAATTAT
20654654 TTTAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTAAAATTATAAATTT
Found at i:20654645 original size:25 final size:26
Alignment explanation
Indices: 20654611--20654663 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
20654601 CAAATGATTT
*
20654611 TAAAATTATT-AATTTTTTTAAAATA
1 TAAAATTATTAAATTATTTTAAAATA
20654636 TAAAATTATTAAAATTATTTTAAAATA
1 TAAAATTATT-AAATTATTTTAAAATA
20654663 T
1 T
20654664 CATCAGCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.40
27 15 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAAATTATTAAATTATTTTAAAATA
Found at i:20658766 original size:57 final size:57
Alignment explanation
Indices: 20658709--20658819 Score: 129
Period size: 57 Copynumber: 2.0 Consensus size: 57
20658699 ACAGAGTGAT
* **
20658709 TTAAATAAT-TTTTTTAAAT-AATACACTTAAATAAAAATTT-TCGAATAATTTAATGA
1 TTAAATAATAATTTTTAAATAAATA-ACCAAAATAAAAATTTATC-AATAATTTAATGA
* * *
20658765 TTAAATTATAATTTTTAATTAAATAACCAAAATAAAAATTTATCCATAATTTAAT
1 TTAAATAATAATTTTTAAATAAATAACCAAAATAAAAATTTATCAATAATTTAAT
20658820 AACAAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
56 8 0.17
57 32 0.70
58 6 0.13
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (57 bp):
TTAAATAATAATTTTTAAATAAATAACCAAAATAAAAATTTATCAATAATTTAATGA
Found at i:20665363 original size:23 final size:23
Alignment explanation
Indices: 20665328--20665448 Score: 118
Period size: 23 Copynumber: 5.2 Consensus size: 23
20665318 GCTGGGCAAT
20665328 AGAGAGCACACAAAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAAAC
* * * * *
20665351 AGAGAGTATACAAAGTACTGATC
1 AGAGAGCACACAAAGTGCTAAAC
*
20665374 AGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACAAAGTGCT-A-AAC
* *
20665399 AGAGAGCACGA-GACGTGCTAAAC
1 AGAGAGCAC-ACAAAGTGCTAAAC
* *
20665422 AGAGAGCACACACAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAAAC
20665445 AGAG
1 AGAG
20665449 CGCGCGCTAG
Statistics
Matches: 76, Mismatches: 18, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
22 1 0.01
23 57 0.75
24 1 0.01
25 16 0.21
26 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAAAC
Found at i:20665403 original size:71 final size:70
Alignment explanation
Indices: 20665277--20665427 Score: 171
Period size: 71 Copynumber: 2.1 Consensus size: 70
20665267 TAAACGAAAC
* * * ** *
20665277 AAACAGAGAGTACCGAAGTACTGAACAGAGAGCACATAAGTGCTGGGCAATAGAGAGCAC-ACAA
1 AAACAGAGAGTAACAAAGTACTGAACAGAGAGCACACAAGTGCTGAACAACAGAGAGCACGA-AA
20665341 AGTGCT
65 AGTGCT
* * *
20665347 AAACAGAGAGTATACAAAGTACTGATCAGAGAGCACACACAGTGCT-AATAACAGAGAGCACGAG
1 AAACAGAGAGTA-ACAAAGTACTGAACAGAGAGCACACA-AGTGCTGAACAACAGAGAGCACGAA
*
20665411 ACGTGCT
64 AAGTGCT
20665418 AAACAGAGAG
1 AAACAGAGAG
20665428 CACACACAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
70 12 0.18
71 49 0.72
72 7 0.10
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.13
Consensus pattern (70 bp):
AAACAGAGAGTAACAAAGTACTGAACAGAGAGCACACAAGTGCTGAACAACAGAGAGCACGAAAA
GTGCT
Found at i:20681265 original size:3 final size:3
Alignment explanation
Indices: 20681259--20681301 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
20681249 GATGATGATG
20681259 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20681302 CTAATTGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:20682365 original size:57 final size:57
Alignment explanation
Indices: 20682299--20682538 Score: 259
Period size: 57 Copynumber: 4.2 Consensus size: 57
20682289 AAAGGTTTTA
* * * * *
20682299 AATGTAAAGGTTATATCCGAAAGGAT-ATTTTCAAAAAGGGATGTCTGAAAGGATATC
1 AATGAAAAGGTTATATCCGAAAGGATAATTAT-GAAAAGGGATATCCGAAAGGATATC
* *** *
20682356 GATGAAAAGGACCTATCC-ATAAGGATAATTATGAAAAGGGATATCCGAAAGGATATT
1 AATGAAAAGGTTATATCCGA-AAGGATAATTATGAAAAGGGATATCCGAAAGGATATC
* * * *
20682413 AATGAAAAGGGTACATCCGAAAGGATAATTATGAAAAGGGATATCCGTAAGAATATC
1 AATGAAAAGGTTATATCCGAAAGGATAATTATGAAAAGGGATATCCGAAAGGATATC
* * * * * *
20682470 AATGGAAAGGTTATATCCGTAAGGATAACTATGAGAAGGGATATCTGTAAGGATATC
1 AATGAAAAGGTTATATCCGAAAGGATAATTATGAAAAGGGATATCCGAAAGGATATC
*
20682527 AAAGAAAAGGTT
1 AATGAAAAGGTT
20682539 TACTCCATAA
Statistics
Matches: 152, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
56 1 0.01
57 146 0.96
58 5 0.03
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (57 bp):
AATGAAAAGGTTATATCCGAAAGGATAATTATGAAAAGGGATATCCGAAAGGATATC
Found at i:20682536 original size:28 final size:28
Alignment explanation
Indices: 20682332--20682536 Score: 164
Period size: 28 Copynumber: 7.2 Consensus size: 28
20682322 GATATTTTCA
* * * *
20682332 AAAAGGGATGTCTGAAAGGATATCGATG
1 AAAAGGGATATCCGTAAGGATATCAATG
* *
20682360 AAAA-GGACCTATCCATAAGGATAAT-TATG
1 AAAAGGGA--TATCCGTAAGGAT-ATCAATG
* *
20682389 AAAAGGGATATCCGAAAGGATATTAATG
1 AAAAGGGATATCCGTAAGGATATCAATG
* * *
20682417 AAAAGGGTACATCCGAAAGGATAAT-TATG
1 AAAAGGG-ATATCCGTAAGGAT-ATCAATG
*
20682446 AAAAGGGATATCCGTAAGAATATCAATG
1 AAAAGGGATATCCGTAAGGATATCAATG
* * * *
20682474 GAAAGGTTATATCCGTAAGGATAACTATG
1 AAAAGG-GATATCCGTAAGGATATCAATG
* * *
20682503 AGAAGGGATATCTGTAAGGATATCAAAG
1 AAAAGGGATATCCGTAAGGATATCAATG
20682531 AAAAGG
1 AAAAGG
20682537 TTTACTCCAT
Statistics
Matches: 141, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
27 7 0.05
28 66 0.47
29 61 0.43
30 7 0.05
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (28 bp):
AAAAGGGATATCCGTAAGGATATCAATG
Found at i:20683467 original size:20 final size:20
Alignment explanation
Indices: 20683442--20683479 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20683432 ACTTGACTTT
*
20683442 TACCGATACTCACTCAATTC
1 TACCGATACTCACCCAATTC
20683462 TACCGATACTCACCCAAT
1 TACCGATACTCACCCAAT
20683480 CGGGTATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (20 bp):
TACCGATACTCACCCAATTC
Found at i:20693130 original size:30 final size:29
Alignment explanation
Indices: 20693090--20693153 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
20693080 TTAATAAATA
* *
20693090 ATTATTTTGT-CATTTTTAACAATTTTAGTG
1 ATTATGTTGTACATTTTTAA-AA-TTGAGTG
20693120 ATTATGTTGTCACATTTTTAAAATTGAGTG
1 ATTATGTTGT-ACATTTTTAAAATTGAGTG
20693150 ATTA
1 ATTA
20693154 AAATGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 19 0.63
31 2 0.07
32 9 0.30
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (29 bp):
ATTATGTTGTACATTTTTAAAATTGAGTG
Found at i:20693382 original size:28 final size:29
Alignment explanation
Indices: 20693351--20693406 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
20693341 TTTTAATGGT
* *
20693351 TAAATTTTAA-TTGTTACGTTTTAGTCAC
1 TAAACTTTAATTTGTTACATTTTAGTCAC
*
20693379 TAAACTTTAATTTGTTATATTTTAGTCA
1 TAAACTTTAATTTGTTACATTTTAGTCA
20693407 TGAGATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (29 bp):
TAAACTTTAATTTGTTACATTTTAGTCAC
Found at i:20698983 original size:21 final size:20
Alignment explanation
Indices: 20698957--20699013 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
20698947 GGAAAAGTTA
*
20698957 AATATTAATTAAGTTATATAT
1 AATATTAATTAAATTA-ATAT
*
20698978 AATATTTAAATAAATTAATAT
1 AATA-TTAATTAAATTAATAT
*
20698999 AATAATACATTAAAT
1 AATATTA-ATTAAAT
20699014 ATTTAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 18 0.60
22 10 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AATATTAATTAAATTAATAT
Found at i:20698996 original size:16 final size:16
Alignment explanation
Indices: 20698977--20699031 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
20698967 AAGTTATATA
20698977 TAATATTTAAATAAAT
1 TAATATTTAAATAAAT
* *
20698993 TAATA-TAATAATACAT
1 TAATATTTA-AATAAAT
*
20699009 TAAATATTTAAATAATT
1 T-AATATTTAAATAAAT
20699026 TAATAT
1 TAATAT
20699032 AATGATACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.06
16 17 0.55
17 10 0.32
18 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATTTAAATAAAT
Found at i:20699015 original size:33 final size:33
Alignment explanation
Indices: 20698978--20699048 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
20698968 AGTTATATAT
*
20698978 AATATTTAAATAAATTAATATAATAATACATTA
1 AATATTTAAATAAATTAATATAATAATACATAA
* *
20699011 AATATTTAAATAATTTAATATAATGATACATAA
1 AATATTTAAATAAATTAATATAATAATACATAA
20699044 AATAT
1 AATAT
20699049 AAGTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (33 bp):
AATATTTAAATAAATTAATATAATAATACATAA
Found at i:20700278 original size:30 final size:31
Alignment explanation
Indices: 20700214--20700285 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
20700204 AAGCCAAGAG
*
20700214 GACTGTTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACTTTTCGATAACTTAAGT
*
20700245 GACTGTTTTGTCACATTTTC-A-AAGTTAAGT
1 GACTGTTTTGTCAC-TTTTCGATAACTTAAGT
20700275 GACTGTTTTGT
1 GACTGTTTTGT
20700286 TAAATGTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 18 0.47
31 15 0.39
32 5 0.13
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTAAGT
Found at i:20704736 original size:16 final size:17
Alignment explanation
Indices: 20704709--20704740 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20704699 TTTTTCCAAA
20704709 CATCATTCAATGAATAC
1 CATCATTCAATGAATAC
20704726 CATCA-TCAATGAATA
1 CATCATTCAATGAATA
20704741 ATTCGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (17 bp):
CATCATTCAATGAATAC
Found at i:20705045 original size:23 final size:24
Alignment explanation
Indices: 20705019--20705079 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
20705009 TTTATATTTT
20705019 TATATAAAAATAAATAT-TAAAAA
1 TATATAAAAATAAATATATAAAAA
* *
20705042 TATA-ATACATCAAATATACTAAAAA
1 TATATAAAAAT-AAATATA-TAAAAA
20705067 TAT-T-AAAATAAAT
1 TATATAAAAATAAAT
20705080 GTTTCCCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
22 4 0.13
23 14 0.47
24 3 0.10
25 9 0.30
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (24 bp):
TATATAAAAATAAATATATAAAAA
Found at i:20705290 original size:21 final size:22
Alignment explanation
Indices: 20705249--20705299 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
20705239 GTAATATTAT
20705249 AGCAAAATGACAGTAAAACAAC
1 AGCAAAATGACAGTAAAACAAC
* *
20705271 ATCAAAATGACAG-CAAACAAC
1 AGCAAAATGACAGTAAAACAAC
20705292 AGCAAAAT
1 AGCAAAAT
20705300 AGTAGCAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (22 bp):
AGCAAAATGACAGTAAAACAAC
Found at i:20706754 original size:3 final size:3
Alignment explanation
Indices: 20706748--20706779 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20706738 TTTATCATGT
20706748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20706780 GGTAACAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20707654 original size:67 final size:60
Alignment explanation
Indices: 20707513--20707706 Score: 182
Period size: 62 Copynumber: 3.1 Consensus size: 60
20707503 CTTAATTACT
*
20707513 TTAATATTAAATTAATATAATAATACTTATCAAAATAAATATTAAATTAATATTAATATTAAA
1 TTAATATTAAATT-A-ATAA-AATACTTATCAAAATAAATATTAAATTAATATTAATATCAAA
*
20707576 TCT--TATTAAATTAATAAAATATTTATCTACAAGATAAATATTAAATTTAATATTAAGATAATC
1 T-TAATATTAAATTAATAAAATACTTATC-A-AA-ATAAATATTAAA-TTAATATT-A-AT-ATC
*
20707639 ACA
58 AAA
* * * *
20707642 TTAATATTAAATTAATAAAATAC-TATTAAGATAATTATTAAATTAA-ATTATTAT-AAA
1 TTAATATTAAATTAATAAAATACTTATCAAAATAAATATTAAATTAATATTAATATCAAA
*
20707699 TTATTATT
1 TTAATATT
20707707 TTTTAAATAT
Statistics
Matches: 111, Mismatches: 10, Indels: 26
0.76 0.07 0.18
Matches are distributed among these distances:
57 9 0.08
58 2 0.02
59 10 0.09
60 6 0.05
61 6 0.05
62 25 0.23
63 20 0.18
64 3 0.03
65 4 0.04
66 8 0.07
67 18 0.16
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (60 bp):
TTAATATTAAATTAATAAAATACTTATCAAAATAAATATTAAATTAATATTAATATCAAA
Found at i:20711587 original size:7 final size:7
Alignment explanation
Indices: 20711577--20711633 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
20711567 CATCCCCAAG
20711577 CTTTTTT
1 CTTTTTT
20711584 C--TTTT
1 CTTTTTT
20711589 CTTTTTT
1 CTTTTTT
20711596 -TTTTTT
1 CTTTTTT
20711602 -TTTTTT
1 CTTTTTT
*
20711608 CCTTTTT
1 CTTTTTT
20711615 CTTTTTT
1 CTTTTTT
* *
20711622 ATATTTT
1 CTTTTTT
20711629 CTTTT
1 CTTTT
20711634 GATTAAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
5 5 0.12
6 12 0.29
7 24 0.59
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (7 bp):
CTTTTTT
Found at i:20711603 original size:20 final size:19
Alignment explanation
Indices: 20711578--20711633 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
20711568 ATCCCCAAGC
* *
20711578 TTTTTTCTTTTCTTTTTTT
1 TTTTTTTTTTTCTTTTTCT
20711597 TTTTTTTTTTTCCTTTTTCT
1 TTTTTTTTTTT-CTTTTTCT
*
20711617 TTTTTATATTTTCTTTT
1 TTTTT-TTTTTTCTTTT
20711634 GATTAAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.31
20 17 0.53
21 5 0.16
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTTTCTTTTTCT
Found at i:20718073 original size:15 final size:15
Alignment explanation
Indices: 20718053--20718093 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
20718043 ATATTTTCAA
20718053 TTTAAAATTATTATT
1 TTTAAAATTATTATT
20718068 TTT-AAATT-TTATT
1 TTTAAAATTATTATT
* *
20718081 ATTAAAAATATTA
1 TTTAAAATTATTA
20718094 AATAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.32
14 9 0.41
15 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAAATTATTATT
Found at i:20718729 original size:22 final size:23
Alignment explanation
Indices: 20718682--20718729 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
20718672 TTAAAATTTA
*
20718682 AAAAATAAAATAACCAAATTTTT
1 AAAAATAAAATAACCAAATTTCT
20718705 AAAAATAAAA-AGACCAAA-TTCT
1 AAAAATAAAATA-ACCAAATTTCT
20718727 AAA
1 AAA
20718730 TTACAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAATAAAATAACCAAATTTCT
Found at i:20732748 original size:60 final size:60
Alignment explanation
Indices: 20732655--20732771 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
20732645 AATTCTTGTT
**
20732655 GATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAATGAGTCTTAGCATGTC
1 GATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAAAAAGTCTTAGCATGTC
* * * * *
20732715 GATTCTGGGGTGATCAAGTATAAGGATTATGCAGCCTCATCGAAAAAGTCTTAGCAT
1 GATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAAAAAGTCTTAGCAT
20732772 TTTGGATGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (60 bp):
GATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAAAAAGTCTTAGCATGTC
Found at i:20734012 original size:31 final size:31
Alignment explanation
Indices: 20733977--20734050 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
20733967 AAAATTTGTT
*
20733977 ATTTTAGTCACTCAAGTTAGATAAGTTGTCA
1 ATTTTAGTCACTCAAGTTAAATAAGTTGTCA
*
20734008 ATTTTAGTCACTCCAGTTAAATAAGTTGTCA
1 ATTTTAGTCACTCAAGTTAAATAAGTTGTCA
*
20734039 ATTTTGGTCACT
1 ATTTTAGTCACT
20734051 AGATAAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (31 bp):
ATTTTAGTCACTCAAGTTAAATAAGTTGTCA
Found at i:20734334 original size:16 final size:15
Alignment explanation
Indices: 20734308--20734338 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
20734298 ATTTTTGTTA
20734308 TTCAATTAAATATAT
1 TTCAATTAAATATAT
20734323 TTCAAGTTAAATATAT
1 TTCAA-TTAAATATAT
20734339 ATTTTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (15 bp):
TTCAATTAAATATAT
Found at i:20734827 original size:2 final size:2
Alignment explanation
Indices: 20734820--20734847 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20734810 AAAAGAAAAC
20734820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20734848 CTTGGAGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20736048 original size:15 final size:15
Alignment explanation
Indices: 20736014--20736054 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
20736004 GTTTTTTACT
20736014 AAAATAATATA-AAA
1 AAAATAATATATAAA
**
20736028 AAAATAATATATACC
1 AAAATAATATATAAA
20736043 AAAATAATATAT
1 AAAATAATATAT
20736055 TCTCCGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAATATATAAA
Found at i:20736248 original size:27 final size:27
Alignment explanation
Indices: 20736210--20736272 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
20736200 GTATAAATGG
20736210 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
20736237 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
20736264 GTGGTGCCT
1 GTGGTGCCT
20736273 TTCTATCAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.14, C:0.32, G:0.35, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:20736281 original size:27 final size:27
Alignment explanation
Indices: 20736210--20736290 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
20736200 GTATAAATGG
20736210 GTGGTGCCTACCTGA-CAGGCGGCACCA
1 GTGGTGCCTACCT-ATCAGGCGGCACCA
*
20736237 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
** *
20736264 GTGGTGCCTTTCTATCAGGTGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
20736291 ACTCGTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.16, C:0.31, G:0.32, T:0.21
Consensus pattern (27 bp):
GTGGTGCCTACCTATCAGGCGGCACCA
Found at i:20736684 original size:27 final size:27
Alignment explanation
Indices: 20736645--20736703 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
20736635 TTACAAGAGG
20736645 TGCCTACCAGGTAGGCGGCACTAGTGC
1 TGCCTACCAGGTAGGCGGCACTAGTGC
** *
20736672 TGCCTACTGGGTAGGCGGCACTAGTGG
1 TGCCTACCAGGTAGGCGGCACTAGTGC
20736699 TGCCT
1 TGCCT
20736704 TTGTCAATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.22
Consensus pattern (27 bp):
TGCCTACCAGGTAGGCGGCACTAGTGC
Found at i:20736778 original size:28 final size:26
Alignment explanation
Indices: 20736738--20736815 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 26
20736728 CAGATCTGTT
20736738 TAACAGCAAATTTTTGAAGAAGAAGGAA
1 TAACAG-AAATTTTTGAAGAAGAAGG-A
20736766 TAACAGTAAATTTTTGAAGAAGGAAAGGA
1 TAACAG-AAATTTTTGAAGAA-G-AAGGA
*
20736795 -AACA-AAAGTTTTGAAGAAGAA
1 TAACAGAAATTTTTGAAGAAGAA
20736816 AAGGAAACAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 13 0.28
28 24 0.52
29 2 0.04
30 4 0.09
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (26 bp):
TAACAGAAATTTTTGAAGAAGAAGGA
Found at i:20736838 original size:26 final size:26
Alignment explanation
Indices: 20736781--20736838 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
20736771 GTAAATTTTT
* * *
20736781 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
20736807 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
20736833 GCAGAA
1 GAAGAA
20736839 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:20739762 original size:28 final size:28
Alignment explanation
Indices: 20739709--20739766 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
20739699 CATTTTTCTG
*
20739709 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
20739737 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
20739765 TT
1 TT
20739767 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:20739883 original size:6 final size:6
Alignment explanation
Indices: 20739872--20739936 Score: 105
Period size: 6 Copynumber: 10.8 Consensus size: 6
20739862 ATATTTGCAT
*
20739872 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
20739920 ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA
20739937 TTTAATGGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 1 0.02
6 53 0.96
7 1 0.02
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:20740378 original size:6 final size:6
Alignment explanation
Indices: 20740369--20740393 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20740359 CTGCGACTGC
20740369 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
20740394 CCGGCTGAAA
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:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:20742359 original size:17 final size:16
Alignment explanation
Indices: 20742327--20742358 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20742317 TTTTTTTTAA
20742327 AAAATATTTAATATAT
1 AAAATATTTAATATAT
20742343 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
20742358 A
1 A
20742359 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:20743358 original size:27 final size:27
Alignment explanation
Indices: 20743328--20743389 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
20743318 CTGGTAGGTT
*
20743328 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTAGTGCCGCCTACCAGACA
20743355 GGCACCACTAGTGCCGCCTACCAGACA
1 GGCACCACTAGTGCCGCCTACCAGACA
20743382 GGCACCAC
1 GGCACCAC
20743390 CCAAAAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.42, G:0.24, T:0.10
Consensus pattern (27 bp):
GGCACCACTAGTGCCGCCTACCAGACA
Found at i:20744203 original size:16 final size:18
Alignment explanation
Indices: 20744164--20744197 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20744154 TATGTTTATA
20744164 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
20744181 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
20744198 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:20744527 original size:16 final size:18
Alignment explanation
Indices: 20744488--20744521 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20744478 AAATATATTA
20744488 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
20744505 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
20744522 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:20746284 original size:96 final size:96
Alignment explanation
Indices: 20746126--20746318 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 96
20746116 TTCCTTGGGG
* *
20746126 AGAGTTGTGGTTGTATGTCCTCTTATATTATCTTTATCATTTGGATGATAATTTGTAGTCTTAAT
1 AGAGTTGTGGTTGTATGTCCTCTTATATTATCTTTATCATTTGGATGATAATATGTAATCTTAAT
*
20746191 TCTCAATCCTAAATCTGTCAGAAGGTTTTCA
66 TCTCAATCCTAAATCTGTCAGAAAGTTTTCA
20746222 AGAGTTGTGGTTGTATGTCCTCTTATATTATCTTTATCATTTGGATGATAATATGTAATCTTAAT
1 AGAGTTGTGGTTGTATGTCCTCTTATATTATCTTTATCATTTGGATGATAATATGTAATCTTAAT
* * *
20746287 TCTTAATTCTAAATCTGTCATAAAGTTTTCA
66 TCTCAATCCTAAATCTGTCAGAAAGTTTTCA
20746318 A
1 A
20746319 AACTAAACTC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (96 bp):
AGAGTTGTGGTTGTATGTCCTCTTATATTATCTTTATCATTTGGATGATAATATGTAATCTTAAT
TCTCAATCCTAAATCTGTCAGAAAGTTTTCA
Found at i:20753640 original size:24 final size:22
Alignment explanation
Indices: 20753579--20753643 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
20753569 TTTCGTGCCC
*
20753579 TCTGTTCAGCACTCTGTGTGCT
1 TCTGTTCAGCACTGTGTGTGCT
20753601 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTCAGCACTGTGTGTGCT
* *
20753623 TCTGTTTAGCACTTTGTGTGC
1 TCTGTTCAGCACTGTGTGTGC
20753644 CTACTGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.43
Consensus pattern (22 bp):
TCTGTTCAGCACTGTGTGTGCT
Found at i:20758224 original size:23 final size:23
Alignment explanation
Indices: 20758198--20758330 Score: 162
Period size: 23 Copynumber: 5.7 Consensus size: 23
20758188 ACACTAGCGC
20758198 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
20758221 GCTCTCTGTTTAGCACTATGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
20758244 GCTCTCTGATTAGCATGTGTGTGT
1 GCTCTCTGATTAGCA-CTGTGTGT
* *
20758268 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
20758291 GCTCTCTGTTATTAGCACT-TCGTGT
1 GCTCTCTG--ATTAGCACTGT-GTGT
20758316 GCTCTCTGATTAGCA
1 GCTCTCTGATTAGCA
20758331 TTTTGTATGC
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
22 3 0.03
23 52 0.55
24 20 0.21
25 18 0.19
26 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:20758330 original size:72 final size:70
Alignment explanation
Indices: 20758198--20758331 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 70
20758188 ACACTAGCGC
*
20758198 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTATGTGTGCTCTCTGATTAGCATGTG
1 GCTCTCTGATTAGCACTGTCTGTGCTCTCTGTTTAGCACTATGTGTGCTCTCTGATTAGCATGTG
20758263 TGTGT
66 TGTGT
*
20758268 GCTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACT-TCGTGTGCTCTCTGATTAGCA
1 GCTCTCTGATTAGCACTGTCT-GTGCTCTCTG-T-TTAGCACTAT-GTGTGCTCTCTGATTAGCA
20758331 T
62 T
20758332 TTTGTATGCT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
69 3 0.05
70 25 0.43
71 2 0.03
72 28 0.48
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (70 bp):
GCTCTCTGATTAGCACTGTCTGTGCTCTCTGTTTAGCACTATGTGTGCTCTCTGATTAGCATGTG
TGTGT
Found at i:20758341 original size:23 final size:23
Alignment explanation
Indices: 20758198--20758420 Score: 160
Period size: 23 Copynumber: 9.8 Consensus size: 23
20758188 ACACTAGCGC
*
20758198 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
20758221 GCTCTCTGTTTAGCACTATGTGT
1 GCTCTCTGATTAGCACTTTGTGT
20758244 GCTCTCTGATTAGCA-TGTGTGTGT
1 GCTCTCTGATTAGCACT-T-TGTGT
* * *
20758268 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCAC-TTTGTGT
*
20758291 GCTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTTTGTGT
* *
20758316 GCTCTCTGATTAGCATTTTGTAT
1 GCTCTCTGATTAGCACTTTGTGT
*
20758339 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * *
20758355 ACTCCCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
20758378 GCTCTCTGTTATCCAGCAC-TTATGT
1 GCTCTCTG--AT-TAGCACTTTGTGT
*
20758403 GCTCTCTGTTTAGCACTT
1 GCTCTCTGATTAGCACTT
20758421 CGGTACTCTC
Statistics
Matches: 155, Mismatches: 27, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
16 9 0.06
18 2 0.01
21 3 0.02
22 6 0.04
23 77 0.50
24 21 0.14
25 31 0.20
26 6 0.04
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:20758381 original size:39 final size:39
Alignment explanation
Indices: 20758307--20758381 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
20758297 TGTTATTAGC
* * *
20758307 ACTTCGTGTGCTCTCTGATTAGCATTTTGTATGCTCAGT
1 ACTTCGTGTACTCCCTGATTAGCACTTTGTATGCTCAGT
* * *
20758346 ACTTTGTGTACTCCCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCCCTGATTAGCACTTTGTATGCTC
20758382 TCTGTTATCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCCCTGATTAGCACTTTGTATGCTCAGT
Found at i:20761567 original size:31 final size:31
Alignment explanation
Indices: 20761501--20761568 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
20761491 ATTTATTTAA
*
20761501 ATGTATACAATTGAATCAAAATTAAAATTTT
1 ATGTATACAATTGAATCAAAATTAAAATTTC
* * *
20761532 ATGTATACATTTGAATC-ATATTCAAAGTTTC
1 ATGTATACAATTGAATCAAAATT-AAAATTTC
20761563 ATGTAT
1 ATGTAT
20761569 TGTGCATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (31 bp):
ATGTATACAATTGAATCAAAATTAAAATTTC
Found at i:20771332 original size:15 final size:15
Alignment explanation
Indices: 20771298--20771336 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20771288 ACACAGATCA
*
20771298 AGATGATCATGAGAT
1 AGATGATGATGAGAT
*
20771313 AGATGATGATGAGTT
1 AGATGATGATGAGAT
*
20771328 TGATGATGA
1 AGATGATGA
20771337 AGTATTGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (15 bp):
AGATGATGATGAGAT
Found at i:20779796 original size:21 final size:21
Alignment explanation
Indices: 20779772--20779812 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20779762 ACATGTCATG
20779772 TTGATGAGTAGGCTAATGTAC
1 TTGATGAGTAGGCTAATGTAC
20779793 TTGATGAGTAGGCTAATGTA
1 TTGATGAGTAGGCTAATGTA
20779813 TCTAAGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (21 bp):
TTGATGAGTAGGCTAATGTAC
Found at i:20802541 original size:12 final size:12
Alignment explanation
Indices: 20802524--20802593 Score: 83
Period size: 12 Copynumber: 6.1 Consensus size: 12
20802514 ACTTTTATAT
*
20802524 TTTAATTTTGAA
1 TTTAATTTTAAA
*
20802536 TTTAATTTTGAA
1 TTTAATTTTAAA
20802548 TTT-A-TTTAAA
1 TTTAATTTTAAA
*
20802558 TTTAAATTTAAA
1 TTTAATTTTAAA
20802570 TTT-ATTTTAAA
1 TTTAATTTTAAA
*
20802581 TTTAAATTTAAA
1 TTTAATTTTAAA
20802593 T
1 T
20802594 CAAATTATGG
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
10 8 0.15
11 12 0.23
12 32 0.62
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:20802562 original size:6 final size:6
Alignment explanation
Indices: 20802524--20802593 Score: 74
Period size: 6 Copynumber: 12.2 Consensus size: 6
20802514 ACTTTTATAT
* * * *
20802524 TTTAAT TTTGAA TTTAAT TTTGAA TTT--A TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
20802570 TTT-AT TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
20802594 CAAATTATGG
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 45 0.85
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:20802562 original size:22 final size:23
Alignment explanation
Indices: 20802528--20802593 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
20802518 TTATATTTTA
* * *
20802528 ATTTTGAATTTAATTTTGAATTT
1 ATTTTAAATTTAAATTTAAATTT
20802551 A-TTTAAATTTAAATTTAAATTT
1 ATTTTAAATTTAAATTTAAATTT
20802573 ATTTTAAATTTAAATTTAAAT
1 ATTTTAAATTTAAATTTAAAT
20802594 CAAATTATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
ATTTTAAATTTAAATTTAAATTT
Found at i:20802598 original size:17 final size:17
Alignment explanation
Indices: 20802551--20802599 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
20802541 TTTTGAATTT
20802551 ATTTAAATTTAAATTTAA
1 ATTTAAA-TTAAATTTAA
**
20802569 ATTTATTTTAAATTTAA
1 ATTTAAATTAAATTTAA
*
20802586 ATTTAAATCAAATT
1 ATTTAAATTAAATT
20802600 ATGGAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATTAAATTTAA
Found at i:20804619 original size:30 final size:29
Alignment explanation
Indices: 20804581--20804749 Score: 223
Period size: 29 Copynumber: 5.7 Consensus size: 29
20804571 CCTAAACTGC
*
20804581 CCAAAATTATATTTTGATCCCAAAAC-TTT
1 CCAAAATTACATTTTGA-CCCAAAACTTTT
*
20804610 CTAAAAATTACATTTTGACCCCAAAACTTTT
1 C-CAAAATTACATTTTGA-CCCAAAACTTTT
20804641 CCAAAATTACATTTTGACCCAAAACTTTT
1 CCAAAATTACATTTTGACCCAAAACTTTT
*
20804670 CCAAAATTACATTTTGACCCTAAACTTTT
1 CCAAAATTACATTTTGACCCAAAACTTTT
* * *
20804699 CTAATATTACATTTTAACCCTAAAACTTTT
1 CCAAAATTACATTTTGACCC-AAAACTTTT
*
20804729 CCAATATTACATTTTTGACCC
1 CCAAAATTACA-TTTTGACCC
20804750 CGATTTTTCC
Statistics
Matches: 125, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
29 58 0.46
30 55 0.44
31 12 0.10
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
CCAAAATTACATTTTGACCCAAAACTTTT
Found at i:20804668 original size:59 final size:59
Alignment explanation
Indices: 20804581--20804750 Score: 227
Period size: 59 Copynumber: 2.8 Consensus size: 59
20804571 CCTAAACTGC
* *
20804581 CCAAAATTATATTTTGATCCCAAAAC-TTTCTAAAAATTACATTTTGACCCCAAAACTTTT
1 CCAAAATTACATTTTGA-CCCAAAACTTTTC-CAAAATTACATTTTGACCCCAAAACTTTT
*
20804641 CCAAAATTACATTTTGACCCAAAACTTTTCCAAAATTACATTTTGA-CCCTAAACTTTT
1 CCAAAATTACATTTTGACCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTT
* * * *
20804699 CTAATATTACATTTTAACCCTAAAACTTTTCCAATATTACATTTTTGACCCC
1 CCAAAATTACATTTTGACCC-AAAACTTTTCCAAAATTACA-TTTTGACCCC
20804751 GATTTTTCCA
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
58 28 0.28
59 42 0.42
60 26 0.26
61 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (59 bp):
CCAAAATTACATTTTGACCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTT
Found at i:20804758 original size:59 final size:58
Alignment explanation
Indices: 20804581--20804775 Score: 214
Period size: 59 Copynumber: 3.3 Consensus size: 58
20804571 CCTAAACTGC
* * * *
20804581 CCAAAATTATATTTTGATCCCAAAAC-TTTCTAAAAATTACATTTTGACCCCAAAACTTTT
1 CCAAAATTACATTTT-AACCCAAAACTTTTC-CAAAATTACATTTTGA-CCCTAAACTTTT
*
20804641 CCAAAATTACATTTTGACCCAAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTT
1 CCAAAATTACATTTTAACCCAAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTT
* * * ** *
20804699 CTAATATTACATTTTAACCCTAAAACTTTTCCAATATTACATTTTTGACCC-CGATTTTT
1 CCAAAATTACATTTTAACCC-AAAACTTTTCCAAAATTACA-TTTTGACCCTAAACTTTT
20804758 CCAAAATTTATCATTTTA
1 CCAAAA-TTA-CATTTTA
20804776 TCCTCCCGAA
Statistics
Matches: 116, Mismatches: 14, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
58 28 0.24
59 51 0.44
60 30 0.26
61 7 0.06
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (58 bp):
CCAAAATTACATTTTAACCCAAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTT
Found at i:20804969 original size:15 final size:16
Alignment explanation
Indices: 20804942--20804987 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
20804932 ATTTATTTGC
*
20804942 ATCTGCATCTTATATT
1 ATCTGCATATTATATT
*
20804958 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
20804972 ATCTGCTTATTATATT
1 ATCTGCATATTATATT
20804988 GCTTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:20810588 original size:67 final size:66
Alignment explanation
Indices: 20810471--20810598 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
20810461 ATTTGAGAAA
* **
20810471 GAAACTATATTGCTTCAGTAGGAATAGCAATTTCAGAAACGGAATAATTTGCTTCACTATCAAAC
1 GAAACTATATTGCTTCAGTAGGAATAGCAATTCCAGAAACCAAATAATTTGCTTCACTATCAAAC
20810536 G
66 G
** * * *
20810537 GAAACTATATTGCTTTGTGTAGGAATAGCAGTTCCAGAATCCAAATCATTTGCTTCACTATC
1 GAAACTATATTGC-TTCAGTAGGAATAGCAATTCCAGAAACCAAATAATTTGCTTCACTATC
20810599 TCTCTATATC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
66 13 0.25
67 40 0.75
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (66 bp):
GAAACTATATTGCTTCAGTAGGAATAGCAATTCCAGAAACCAAATAATTTGCTTCACTATCAAAC
G
Found at i:20811274 original size:14 final size:14
Alignment explanation
Indices: 20811242--20811280 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
20811232 ATTGTGTAAT
*
20811242 GTGCAATGTGTTCT
1 GTGCAATGTGTTCG
*
20811256 ATGCAATGTGTTCG
1 GTGCAATGTGTTCG
20811270 GTGCAA-GTGTT
1 GTGCAATGTGTT
20811281 TTTGTATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.18, C:0.13, G:0.31, T:0.38
Consensus pattern (14 bp):
GTGCAATGTGTTCG
Found at i:20814991 original size:6 final size:6
Alignment explanation
Indices: 20814942--20814989 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
20814932 ATATATATCC
*
20814942 CGGATT CGGATT CGGATT CGGATT CGGATT CGGATT CGGATT TGGATT
1 CGGATT CGGATT CGGATT CGGATT CGGATT CGGATT CGGATT CGGATT
20814990 TGAAAATCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.15, G:0.33, T:0.35
Consensus pattern (6 bp):
CGGATT
Found at i:20816207 original size:23 final size:20
Alignment explanation
Indices: 20816157--20816208 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
20816147 TAACCATGTG
20816157 TTTAGATGTGTTTAAATATGC
1 TTTA-ATGTGTTTAAATATGC
*
20816178 TTGAATGATGTTTAGAATATGC
1 TTTAATG-TGTTTA-AATATGC
20816200 TTTTAATGT
1 -TTTAATGT
20816209 TACATAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 8 0.31
23 6 0.23
ACGTcount: A:0.29, C:0.04, G:0.19, T:0.48
Consensus pattern (20 bp):
TTTAATGTGTTTAAATATGC
Found at i:20817600 original size:14 final size:15
Alignment explanation
Indices: 20817581--20817609 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20817571 ATTAGCATTA
20817581 TTCCTT-TTTTTTGT
1 TTCCTTCTTTTTTGT
20817595 TTCCTTCTTTTTTGT
1 TTCCTTCTTTTTTGT
20817610 GTCAACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (15 bp):
TTCCTTCTTTTTTGT
Found at i:20826490 original size:15 final size:15
Alignment explanation
Indices: 20826468--20826510 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20826458 AATTTTTTTT
20826468 TATTTTAGTCATTAA
1 TATTTTAGTCATTAA
* *
20826483 TTTTTTAG-AATTTAA
1 TATTTTAGTCA-TTAA
20826498 TATTTTAGTCATT
1 TATTTTAGTCATT
20826511 CGCTTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (15 bp):
TATTTTAGTCATTAA
Found at i:20831549 original size:22 final size:21
Alignment explanation
Indices: 20831511--20831558 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20831501 TACGGAATAT
* *
20831511 AATTAAAATATACTAATCTAA
1 AATTTAAATATACTAATATAA
20831532 CAATTTAAATATTA-TAATATAA
1 -AATTTAAATA-TACTAATATAA
20831554 AATTT
1 AATTT
20831559 TCAAATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 16 0.70
23 2 0.09
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAAATATACTAATATAA
Found at i:20831946 original size:24 final size:22
Alignment explanation
Indices: 20831910--20831981 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 22
20831900 TAATTAAAAA
*
20831910 TTTAAATTAAATTATAATTATT
1 TTTAAATTGAATTATAATTATT
* **
20831932 TTTAAATGTGTAATTATCACAATT
1 TTTAAAT-TG-AATTATAATTATT
20831956 TTT--ATTGAATTATAATTATT
1 TTTAAATTGAATTATAATTATT
20831976 TTTAAA
1 TTTAAA
20831982 ATCCTAAAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 13 0.33
21 2 0.05
22 10 0.26
23 1 0.03
24 13 0.33
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTAAATTGAATTATAATTATT
Found at i:20834540 original size:4 final size:4
Alignment explanation
Indices: 20834511--20834559 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
20834501 AAAGGGAAAT
* * * *
20834511 AGAG ACAG ACAG ACAG AGAG ACAG AGAG AGAG AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
20834559 A
1 A
20834560 AAAGATGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.08, G:0.41, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:20835120 original size:16 final size:17
Alignment explanation
Indices: 20835088--20835123 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20835078 ACCCTCAATC
20835088 TTTTAAAAGGAATCAAA
1 TTTTAAAAGGAATCAAA
*
20835105 TTTTAAAATG-ATCAAA
1 TTTTAAAAGGAATCAAA
20835121 TTT
1 TTT
20835124 AGTCATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (17 bp):
TTTTAAAAGGAATCAAA
Found at i:20842986 original size:20 final size:19
Alignment explanation
Indices: 20842948--20842987 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20842938 TTTGGTATAG
*
20842948 AGACTAAATCGTAAAAATT
1 AGACTAAATCGAAAAAATT
*
20842967 AGACTAAATTGAATAAAATT
1 AGACTAAATCGAA-AAAATT
20842987 A
1 A
20842988 AAATTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (19 bp):
AGACTAAATCGAAAAAATT
Found at i:20844328 original size:16 final size:17
Alignment explanation
Indices: 20844298--20844338 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
20844288 TTATGAACTT
20844298 TTTTATAATTTTTTTGAA
1 TTTTA-AATTTTTTTGAA
*
20844316 TTTTAAATTTTTTTTAA
1 TTTTAAATTTTTTTGAA
20844333 TTTTAA
1 TTTTAA
20844339 GTTATTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTAAATTTTTTTGAA
Found at i:20851951 original size:3 final size:3
Alignment explanation
Indices: 20851943--20851974 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20851933 ATATATTTTT
20851943 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20851975 GAAAATGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20858670 original size:107 final size:106
Alignment explanation
Indices: 20858547--20858763 Score: 271
Period size: 107 Copynumber: 2.0 Consensus size: 106
20858537 ACTCTCCTCC
* * *
20858547 TTTATTTTATTTTTTTAGTTGAAGGAGTAAAATTTTAACCGATC-TCAAT-AGATTCGAC-CTTA
1 TTTATTTTATTTTTTTAGTTAAAGGAATAAAATTTCAACCGATCTTC-ATGA-ATTCGACTC-TA
** *
20858609 CTTGTCGCTTCTACTAATTATTTTTCTTCAAGTA-AGTTTTATTT
63 CTCATCACTTCTACTAATTATTTTTCTTCAAGTAGA-TTTTATTT
* * *
20858653 TTTATTTTATTTATTTTAGTTAAAGGAATAAAGTTTCAACTGATCTTCGTGAATTCGACTCTACT
1 TTTATTTTATTT-TTTTAGTTAAAGGAATAAAATTTCAACCGATCTTCATGAATTCGACTCTACT
*
20858718 CATCACTTCTATTAATTATTTTTCTTCAAGTAGATTTTATTT
65 CATCACTTCTACTAATTATTTTTCTTCAAGTAGATTTTATTT
20858760 TTTA
1 TTTA
20858764 CGACTTTGAC
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
106 12 0.12
107 79 0.82
108 5 0.05
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (106 bp):
TTTATTTTATTTTTTTAGTTAAAGGAATAAAATTTCAACCGATCTTCATGAATTCGACTCTACTC
ATCACTTCTACTAATTATTTTTCTTCAAGTAGATTTTATTT
Found at i:20870718 original size:25 final size:25
Alignment explanation
Indices: 20870690--20870737 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
20870680 TCATAATTAA
20870690 AAAATGTATATTT-AATTTTAATTTT
1 AAAAT-TATATTTAAATTTTAATTTT
*
20870715 AAAATTATTTTTAAATTTTAATT
1 AAAATTATATTTAAATTTTAATT
20870738 GATAAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
AAAATTATATTTAAATTTTAATTTT
Found at i:20872366 original size:26 final size:28
Alignment explanation
Indices: 20872332--20872391 Score: 88
Period size: 26 Copynumber: 2.2 Consensus size: 28
20872322 AAAACTTTTA
* *
20872332 AATTGATTTTAAAATTCT-TTTTTG-AT
1 AATTTATTTTAAAATTCTAATTTTGAAT
20872358 AATTTATTTTAAAATTCTAATTTTGAAT
1 AATTTATTTTAAAATTCTAATTTTGAAT
20872386 AATTTA
1 AATTTA
20872392 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 17 0.57
27 5 0.17
28 8 0.27
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (28 bp):
AATTTATTTTAAAATTCTAATTTTGAAT
Found at i:20883836 original size:24 final size:24
Alignment explanation
Indices: 20883809--20883863 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
20883799 ATTCATTTAC
**
20883809 AAATTTGAATTTATCTTAAAATTT
1 AAATTTGAATCAATCTTAAAATTT
* * *
20883833 AAATTTAAATCAATTTTTAAATTT
1 AAATTTGAATCAATCTTAAAATTT
20883857 AAATTTG
1 AAATTTG
20883864 TGTTAAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTTGAATCAATCTTAAAATTT
Found at i:20883871 original size:17 final size:17
Alignment explanation
Indices: 20883849--20883881 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20883839 AAATCAATTT
20883849 TTAAATTTAAATTTGTG
1 TTAAATTTAAATTTGTG
20883866 TTAAATTTAAATTTGT
1 TTAAATTTAAATTTGT
20883882 TAAATTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TTAAATTTAAATTTGTG
Found at i:20883964 original size:27 final size:27
Alignment explanation
Indices: 20883933--20883989 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
20883923 TCCAAGGCCT
20883933 AATTAAAGGCCCAATTACAATGGCCCA
1 AATTAAAGGCCCAATTACAATGGCCCA
20883960 AATTAAAGGCCCAATTACAATGGCCCA
1 AATTAAAGGCCCAATTACAATGGCCCA
20883987 AAT
1 AAT
20883990 AGGCCCAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (27 bp):
AATTAAAGGCCCAATTACAATGGCCCA
Found at i:20883972 original size:13 final size:14
Alignment explanation
Indices: 20883928--20883987 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 14
20883918 TAAAGTCCAA
*
20883928 GGCCTAATTA-AA-
1 GGCCCAATTACAAT
20883940 GGCCCAATTACAAT
1 GGCCCAATTACAAT
20883954 GGCCCAAATTA-AA-
1 GGCCC-AATTACAAT
20883967 GGCCCAATTACAAT
1 GGCCCAATTACAAT
20883981 GGCCCAA
1 GGCCCAA
20883988 ATAGGCCCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
12 14 0.33
13 9 0.21
14 14 0.33
15 5 0.12
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:20884524 original size:7 final size:7
Alignment explanation
Indices: 20884512--20884572 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
20884502 TAAAAATATT
20884512 ATTAATA
1 ATTAATA
20884519 ATTAATA
1 ATTAATA
20884526 ATT-ATA
1 ATTAATA
20884532 ATTAAT-
1 ATTAATA
* *
20884538 ATTTATG
1 ATTAATA
*
20884545 ACT-ATA
1 ATTAATA
*
20884551 GTTAAT-
1 ATTAATA
20884557 ATTAATA
1 ATTAATA
20884564 ATTAATA
1 ATTAATA
20884571 AT
1 AT
20884573 ATTGAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 19 0.43
7 25 0.57
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (7 bp):
ATTAATA
Found at i:20884570 original size:13 final size:13
Alignment explanation
Indices: 20884511--20884570 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 13
20884501 ATAAAAATAT
20884511 TATTAATAATTAA
1 TATTAATAATTAA
20884524 TAATT-ATAATTAA
1 T-ATTAATAATTAA
20884537 TATTTATGACTATAGTTAA
1 TA-TTA--A-TA-A-TTAA
20884556 TATTAATAATTAA
1 TATTAATAATTAA
20884569 TA
1 TA
20884571 ATATTGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
12 1 0.03
13 18 0.46
14 4 0.10
15 2 0.05
16 2 0.05
17 2 0.05
18 4 0.10
19 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (13 bp):
TATTAATAATTAA
Found at i:20885747 original size:30 final size:30
Alignment explanation
Indices: 20885711--20885878 Score: 230
Period size: 30 Copynumber: 5.6 Consensus size: 30
20885701 AAACAATTCA
*
20885711 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* * *
20885741 AAAATTATATTTTAACCCTAAAACTTTTCT
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
20885771 AAAATTACATTTTGACCCCAAAACTTTTCA
1 AAAATTACATTTTAACCCCAAAACTTTTCC
20885801 AAAATTACATTTTAACCCCAAAAC-TTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
**
20885830 AAAATTACATTTTAACCCCAAAAAATTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* **
20885860 TAAATCCCATTTTAACCCC
1 AAAATTACATTTTAACCCC
20885879 GATTTCACTA
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
29 27 0.22
30 96 0.78
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:20885893 original size:59 final size:58
Alignment explanation
Indices: 20885830--20886021 Score: 158
Period size: 59 Copynumber: 3.2 Consensus size: 58
20885820 AAAACTTTCC
20885830 AAAATTA-CATTTTAACCCCAAAAAATTTCCTAAATCCCATTTTAACCCCGATTTCACTA
1 AAAATTACCATTTTAACCCC-AAAAATTT-CTAAATCCCATTTTAACCCCGATTTCACTA
* ** ** * *
20885889 AAAATTTACCATTTT-ACCCTC-GAAGCTTCTAAAATTCCGTTTTTAACCCTGATTTCACTG
1 AAAA-TTACCATTTTAACCC-CAAAAATTTCT-AAA-TCCCATTTTAACCCCGATTTCACTA
* ** * * * *
20885949 AAAATTACCATTTTACCCCCGAAACCTTT-AAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTAACCCC-AAAAATTTCTAAATCCCA-TTTTAACCCCGATTTCACTA
20886008 AAAATTACCATTTT
1 AAAATTACCATTTT
20886022 GCCCTCGGGT
Statistics
Matches: 104, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
58 4 0.04
59 55 0.53
60 35 0.34
61 10 0.10
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTAACCCCAAAAATTTCTAAATCCCATTTTAACCCCGATTTCACTA
Found at i:20885937 original size:60 final size:59
Alignment explanation
Indices: 20885861--20886028 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 59
20885851 AAAATTTCCT
* *
20885861 AAATCCCA-TTTTAACCCCGATTTCACTAAAAATTTACCATTTTACCCTCG-AAGCTTCTA
1 AAATTCCATTTTTAACCCCGATTTCACTAAAAA-TTACCATTTTACCCTCGAAACCTT-TA
* * * *
20885920 AAATTCCGTTTTTAACCCTGATTTCACTGAAAATTACCATTTTACCCCCGAAACCTTTA
1 AAATTCCATTTTTAACCCCGATTTCACTAAAAATTACCATTTTACCCTCGAAACCTTTA
* * *
20885979 AAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCCTCG
1 AAATTCCATTTTTAACCCCGATTTCACTAAAAATTACCATTTTACCCTCG
20886029 GGTATCCATA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
59 67 0.71
60 27 0.29
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCCGATTTCACTAAAAATTACCATTTTACCCTCGAAACCTTTA
Found at i:20885963 original size:30 final size:29
Alignment explanation
Indices: 20885866--20886021 Score: 81
Period size: 30 Copynumber: 5.2 Consensus size: 29
20885856 TTCCTAAATC
*
20885866 CCATTTTAACCCCGATTTCACTAAAAATTTA
1 CCATTTTAACCCTGATTTCACT-AAAA-TTA
*
20885897 CCATTTT-ACCCTCGAAGCTT--CTAAAATT-
1 CCATTTTAACCCT-G-A-TTTCACTAAAATTA
*
20885925 CCGTTTTTAACCCTGATTTCACTGAAAATTA
1 CC-ATTTTAACCCTGATTTCACT-AAAATTA
* * *** **
20885956 CCATTTTACCCCCGAAACCTTTAAAATT-
1 CCATTTTAACCCTGATTTCACTAAAATTA
*
20885984 CCATTTTTAA-CCTCGATTTCACCAAAAATTA
1 CCA-TTTTAACCCT-GATTTCA-CTAAAATTA
20886015 CCATTTT
1 CCATTTT
20886022 GCCCTCGGGT
Statistics
Matches: 92, Mismatches: 20, Indels: 27
0.66 0.14 0.19
Matches are distributed among these distances:
27 2 0.02
28 8 0.09
29 23 0.25
30 41 0.45
31 15 0.16
32 1 0.01
33 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (29 bp):
CCATTTTAACCCTGATTTCACTAAAATTA
Found at i:20898154 original size:68 final size:68
Alignment explanation
Indices: 20898045--20898793 Score: 1020
Period size: 68 Copynumber: 11.0 Consensus size: 68
20898035 CTGCAGGTCT
20898045 CAACGTCATCCCCTC-AGAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCGA-AATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA
20898109 AGAG
65 AGAG
* * *
20898113 CAACGTCATCCCCTCGAAATTAAAGTAGAGTGGATAACACATC-TGACCTCTGAAATTGAAGTAG
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTA-
20898177 TAGAG
65 -AGAG
* ** *
20898182 CAACGTCATCCCCTTGAAATGAAATTAGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTG
1 CAACGTCATCCCC-T----CGAAATT-GAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTG
20898247 AAGTAAGAG
60 AAGTAAGAG
*
20898256 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
20898321 GAG
66 GAG
* * *
20898324 CAACGTCATCCCGTTGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
20898389 GAG
66 GAG
* * *
20898392 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTAAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
20898457 GAG
66 GAG
20898460 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTG--A---AA-TAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
20898519 GAG
66 GAG
* * * *
20898522 CAACGTCATCCTCTCGAAATTGAAGTAGAGTGGATAATACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
20898587 GAG
66 GAG
* * *
20898590 CAATGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCCGAAATTGAAGTA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAG-TGGATAACACATCTTTATCTCTGAAATTGAAGTA
20898655 AGAG
65 AGAG
* * * *
20898659 CGACGTCATCCGCTTGAAA-TGAAGTAGAGTTGTATAACACATCTTTATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTCGAAATTGAAGTAGAG-TGGATAACACATCTTTATCTCTGAAATTGAAGTA
20898723 AGAG
65 AGAG
* * * *
20898727 CAA---CATCCTCTTGAAATTGAAGTAGAGTGGATAACA-AGCCTTTGTCTATCTGAAATTGAAG
1 CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACA-TCTTTATC--TCTGAAATTGAAG
20898788 TAAGAG
63 TAAGAG
20898794 AGTAAGATGA
Statistics
Matches: 615, Mismatches: 45, Indels: 43
0.87 0.06 0.06
Matches are distributed among these distances:
62 55 0.09
63 2 0.00
64 2 0.00
65 26 0.04
66 11 0.02
67 39 0.06
68 344 0.56
69 74 0.12
70 1 0.00
73 1 0.00
74 23 0.04
75 19 0.03
76 18 0.03
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (68 bp):
CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
GAG
Done.