Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 100 of 133
Found at i:19457606 original size:21 final size:21
Alignment explanation
Indices: 19457576--19457626 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
19457566 GATATTTTTA
19457576 AATA-TTTATATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
*
19457596 AATATTTTATATTTTAAAAAT
1 AATATTTTATATTTAAAAAAT
19457617 AATATTTTAT
1 AATATTTTAT
19457627 TAATTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:19458509 original size:23 final size:23
Alignment explanation
Indices: 19458474--19458517 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
19458464 TTTGATTCGA
*
19458474 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
19458497 TTTAATATAAATATAAAATTA
1 TTTAAAATAAATATAAAATTA
19458518 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:19458521 original size:18 final size:18
Alignment explanation
Indices: 19458500--19458555 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
19458490 TATTATTTTT
19458500 AATATAAATATAAAATTA
1 AATATAAATATAAAATTA
*
19458518 AATAT--ATATAAAAATA
1 AATATAAATATAAAATTA
* *
19458534 TATATAATTATAAAATTA
1 AATATAAATATAAAATTA
19458552 AATA
1 AATA
19458556 AATAATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 14 0.45
18 17 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAAATATAAAATTA
Found at i:19458566 original size:18 final size:16
Alignment explanation
Indices: 19458498--19458559 Score: 70
Period size: 16 Copynumber: 3.7 Consensus size: 16
19458488 AATATTATTT
19458498 TTAATATAAATATAAAA
1 TTAA-ATAAATATAAAA
*
19458515 TTAAATATATATAAAAA
1 TTAAATAAATAT-AAAA
* *
19458532 TATATATAATTATAAAA
1 T-TAAATAAATATAAAA
19458549 TTAAATAAATA
1 TTAAATAAATA
19458560 ATTAAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 15 0.41
17 14 0.38
18 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAATAAATATAAAA
Found at i:19459069 original size:17 final size:17
Alignment explanation
Indices: 19459047--19459084 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19459037 AAAATTTTAA
* *
19459047 TAAATTTTTTATAATTT
1 TAAATTTATAATAATTT
19459064 TAAA-TTATAATAATTT
1 TAAATTTATAATAATTT
19459080 TAAAT
1 TAAAT
19459085 GCCTAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTTATAATAATTT
Found at i:19460726 original size:23 final size:21
Alignment explanation
Indices: 19460676--19460726 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
19460666 TTTAAATTAC
*
19460676 TATTAAATAAAATGATGTAAT
1 TATTAAATAAAATGATATAAT
*
19460697 TACTAAATACAAATGACTATAAT
1 TATTAAATA-AAATGA-TATAAT
*
19460720 TTTTAAA
1 TATTAAA
19460727 CAAGTTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 10 0.42
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (21 bp):
TATTAAATAAAATGATATAAT
Found at i:19462867 original size:15 final size:17
Alignment explanation
Indices: 19462836--19462867 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19462826 AACAGCTAAT
19462836 AAGAAGTATGCCCATTA
1 AAGAAGTATGCCCATTA
19462853 AAGAAG-ATG-CCATTA
1 AAGAAGTATGCCCATTA
19462868 TATGGGGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.22
Consensus pattern (17 bp):
AAGAAGTATGCCCATTA
Found at i:19468033 original size:2 final size:2
Alignment explanation
Indices: 19468026--19468062 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19468016 ATACAGAAGA
19468026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19468063 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19468067 original size:2 final size:2
Alignment explanation
Indices: 19468062--19468087 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19468052 ATATATATAT
19468062 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
19468088 GTGTTGCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19468528 original size:3 final size:3
Alignment explanation
Indices: 19468520--19468548 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19468510 GATTAAATTT
19468520 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19468549 CCACCAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19472342 original size:72 final size:72
Alignment explanation
Indices: 19472260--19472435 Score: 230
Period size: 72 Copynumber: 2.5 Consensus size: 72
19472250 CACTACAATT
* * *
19472260 TTTTATCTTAAAAACGTAATCTTTATTAATATTTTATAATTTTGAAAATAAAATTTTAACATCCA
1 TTTTATCTTAAAAACGTAATCTTTATTAAAATTTTATAATTTTGAAAATAAAATTTCAACATACA
19472325 CAATATG
66 CAATATG
* * * *
19472332 TTTTATCTTAAAAACGTGATTTTTATTAAAATTTTATAATTTTGAAAATATAATTTCAATATACA
1 TTTTATCTTAAAAACGTAATCTTTATTAAAATTTTATAATTTTGAAAATAAAATTTCAACATACA
* *
19472397 CTATATT
66 CAATATG
* *
19472404 TTTTATATT-AAAACATAATACTTT-TTAAAATT
1 TTTTATCTTAAAAACGTAAT-CTTTATTAAAATT
19472436 ATAAATAACA
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
71 16 0.18
72 74 0.82
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.47
Consensus pattern (72 bp):
TTTTATCTTAAAAACGTAATCTTTATTAAAATTTTATAATTTTGAAAATAAAATTTCAACATACA
CAATATG
Found at i:19475941 original size:29 final size:29
Alignment explanation
Indices: 19475898--19475957 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
19475888 TTTAAATTGT
* *
19475898 TGCTTTATATGTTTTTTGTAT-AGTTTTGA
1 TGCTTCATATATTTTTTGTATCA-TTTTGA
19475927 TGCTTCATATATTTTTTGTATCATTTTGA
1 TGCTTCATATATTTTTTGTATCATTTTGA
19475956 TG
1 TG
19475958 TCATTAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.18, C:0.07, G:0.15, T:0.60
Consensus pattern (29 bp):
TGCTTCATATATTTTTTGTATCATTTTGA
Found at i:19476169 original size:9 final size:9
Alignment explanation
Indices: 19476151--19476208 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
19476141 ACCGATTCTG
19476151 TAACAGAAA
1 TAACAGAAA
*
19476160 TAACAAAAA
1 TAACAGAAA
*
19476169 TAGCAGAAA
1 TAACAGAAA
* *
19476178 TAACCGACTA
1 TAACAGA-AA
*
19476188 TAATAGAAA
1 TAACAGAAA
*
19476197 TAACAAAAA
1 TAACAGAAA
19476206 TAA
1 TAA
19476209 GAATAATTAA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
9 31 0.84
10 6 0.16
ACGTcount: A:0.64, C:0.12, G:0.09, T:0.16
Consensus pattern (9 bp):
TAACAGAAA
Found at i:19482672 original size:43 final size:42
Alignment explanation
Indices: 19482625--19482901 Score: 152
Period size: 43 Copynumber: 6.5 Consensus size: 42
19482615 CTAAACAGAA
*
19482625 GCTAAACAACTTTAAAATAGGAAAT-GA-CCTTATATATTTAGAG
1 GCTAAACAACTTTAAAATAAGAAATGGATCC-TATATA--TAGAG
* *
19482668 GCTAAACGACTTTAAAATAAGAAATGGATTCCTCTATATAGAG
1 GCTAAACAACTTTAAAATAAGAAATGGA-TCCTATATATAGAG
* * * ** * *
19482711 GCTAAACAACATTAAAATAAAAAATGAGCTATTTTAAATAGAG
1 GCTAAACAACTTTAAAATAAGAAATG-GATCCTATATATAGAG
* * * *
19482754 G-TAAA-ATGACTTTAAAATAATAAATGGGCTCATCTATATAGAG
1 GCTAAACA--ACTTTAAAATAAGAAAT-GGATCCTATATATAGAG
* ** * * * * *
19482797 AC--AATGATTTTAAAATAGGAAATGGACTTCTCTAAATAGAG
1 GCTAAACAACTTTAAAATAAGAAATGGA-TCCTATATATAGAG
* * ** * * * *
19482838 ACAAAATGACTTTAAAATAAGAAATGAGCTCTTCTATTTAGAG
1 GCTAAACAACTTTAAAATAAGAAATG-GATCCTATATATAGAG
19482881 GCTAAACAACTTTAAAATAAG
1 GCTAAACAACTTTAAAATAAG
19482902 TGACTAGGAC
Statistics
Matches: 184, Mismatches: 37, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.01
41 28 0.15
42 6 0.03
43 136 0.74
44 5 0.03
45 5 0.03
46 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (42 bp):
GCTAAACAACTTTAAAATAAGAAATGGATCCTATATATAGAG
Found at i:19482718 original size:86 final size:85
Alignment explanation
Indices: 19482625--19482899 Score: 272
Period size: 86 Copynumber: 3.2 Consensus size: 85
19482615 CTAAACAGAA
** *
19482625 GCTAAACAACTTTAAAATAGGAAATGACCTTATATATTTAGAGGCTAAACGACTTTAAAATAAGA
1 GCTAAACAACTTTAAAATAGGAAATGA-CTTATATAAATAGAGGCTAAATGACTTTAAAATAAGA
* *
19482690 AATGGATTCCTCTATATAGAG
65 AATGGACTCATCTATATAGAG
* ** *
19482711 GCTAAACAACATTAAAATAAAAAATGAGC-TATTTTAAATAGAGG-TAAAATGACTTTAAAATAA
1 GCTAAACAACTTTAAAATAGGAAATGA-CTTA-TATAAATAGAGGCT-AAATGACTTTAAAATAA
* *
19482774 TAAATGGGCTCATCTATATAGAG
63 GAAATGGACTCATCTATATAGAG
* ** * * * * *
19482797 AC--AATGATTTTAAAATAGGAAATGGACTTCTCTAAATAGAGACAAAATGACTTTAAAATAAGA
1 GCTAAACAACTTTAAAATAGGAAAT-GACTTATATAAATAGAGGCTAAATGACTTTAAAATAAGA
* *
19482860 AAT-GAGCTCTTCTATTTAGAG
65 AATGGA-CTCATCTATATAGAG
19482881 GCTAAACAACTTTAAAATA
1 GCTAAACAACTTTAAAATA
19482900 AGTGACTAGG
Statistics
Matches: 150, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
83 1 0.01
84 61 0.41
85 6 0.04
86 82 0.55
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (85 bp):
GCTAAACAACTTTAAAATAGGAAATGACTTATATAAATAGAGGCTAAATGACTTTAAAATAAGAA
ATGGACTCATCTATATAGAG
Found at i:19482820 original size:41 final size:41
Alignment explanation
Indices: 19482675--19482901 Score: 161
Period size: 43 Copynumber: 5.3 Consensus size: 41
19482665 GAGGCTAAAC
** * *
19482675 GACTTTAAAATAAGAAATGGATTCCTCTATATAGAGGCTAAAC
1 GACTTTAAAATAAGAAATGGGCT-CTCTATATAGAGAC-AAAT
* * * * * * *
19482718 AACATTAAAATAAAAAATGAGCTATTTTAAATAGAGGTA-AAAT
1 GACTTTAAAATAAGAAATGGGCT-CTCTATATAGA-G-ACAAAT
*
19482761 GACTTTAAAATAATAAATGGGCTCATCTATATAGAGAC-AAT
1 GACTTTAAAATAAGAAATGGGCTC-TCTATATAGAGACAAAT
* * * *
19482802 GATTTTAAAATAGGAAATGGACTTCTCTAAATAGAGACAAAAT
1 GACTTTAAAATAAGAAATGGGC-TCTCTATATAGAGAC-AAAT
* * * *
19482845 GACTTTAAAATAAGAAATGAGCTCTTCTATTTAGAGGCTAAAC
1 GACTTTAAAATAAGAAATGGGCTC-TCTATATAGAGAC-AAAT
*
19482888 AACTTTAAAATAAG
1 GACTTTAAAATAAG
19482902 TGACTAGGAC
Statistics
Matches: 142, Mismatches: 34, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
41 34 0.24
42 5 0.04
43 102 0.72
44 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.29
Consensus pattern (41 bp):
GACTTTAAAATAAGAAATGGGCTCTCTATATAGAGACAAAT
Found at i:19482999 original size:22 final size:22
Alignment explanation
Indices: 19482974--19483016 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19482964 GTGACTGAGA
*
19482974 CTAAACCACAAGTCAGAAAAAG
1 CTAAACCACAAGTCAAAAAAAG
**
19482996 CTAAACTGCAAGTCAAAAAAA
1 CTAAACCACAAGTCAAAAAAA
19483017 TAAATAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (22 bp):
CTAAACCACAAGTCAAAAAAAG
Found at i:19483131 original size:65 final size:65
Alignment explanation
Indices: 19482999--19483149 Score: 180
Period size: 65 Copynumber: 2.3 Consensus size: 65
19482989 GAAAAAGCTA
* ** * *
19482999 AACTGCAAGTCAAAAAAATAAATAACCTAAACTGAGTCGAGATTGAAAATAAATGATCGAGATTG
1 AACTGCAAGTCAAAAAAATAAATAACCTAAACTGAGTCAAGATAAAAAATAAATGATCAAGACTG
* * *
19483064 AACTGTAAGTCAAAAAAATAAATAACCTAGACTGAG-CTAAGATAAAAAATAAGTGA-CAAAGAC
1 AACTGCAAGTCAAAAAAATAAATAACCTAAACTGAGTC-AAGATAAAAAATAAATGATC-AAGAC
19483127 TG
64 TG
* *
19483129 AACTACAAGTAAAAAAAATAA
1 AACTGCAAGTCAAAAAAATAA
19483150 CCTGGACTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 2 0.03
65 71 0.97
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (65 bp):
AACTGCAAGTCAAAAAAATAAATAACCTAAACTGAGTCAAGATAAAAAATAAATGATCAAGACTG
Found at i:19483523 original size:18 final size:18
Alignment explanation
Indices: 19483490--19483536 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
19483480 AGATTCGTAA
19483490 AAAATTCA-AAATGATTTC
1 AAAATTCACAAATGA-TTC
19483508 AAAATTCACAAA-GATTC
1 AAAATTCACAAATGATTC
* *
19483525 AAGATTCGCAAA
1 AAAATTCACAAA
19483537 AGTTTTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 10 0.38
19 3 0.12
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAATTCACAAATGATTC
Found at i:19483673 original size:17 final size:17
Alignment explanation
Indices: 19483648--19483705 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
19483638 CGTAAAATTC
19483648 CAAAGTTCGCAAAGGTTT
1 CAAA-TTCGCAAAGGTTT
19483666 CAAATTCGCAAAGGTTT
1 CAAATTCGCAAAGGTTT
* *
19483683 -AAGATTCACAAAGATTT
1 CAA-ATTCGCAAAGGTTT
19483700 CAAATT
1 CAAATT
19483706 TCACTGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 2 0.06
17 28 0.78
18 6 0.17
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (17 bp):
CAAATTCGCAAAGGTTT
Found at i:19484321 original size:46 final size:46
Alignment explanation
Indices: 19484267--19484373 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
19484257 ATTCGCATTG
* * *
19484267 AAAATTTTAAAGATTCTCATCCAAAAAAA-TTTAGTATTTTACATCC
1 AAAATTTTAAAGATTCACAT-CAAAAAAATTTTAGGAATTTACATCC
* * * *
19484313 AAAATTTTAAAAATTCACATTAAAAAAATTTTAGGAATTTCCATCT
1 AAAATTTTAAAGATTCACATCAAAAAAATTTTAGGAATTTACATCC
*
19484359 AAAATTTCAAAGATT
1 AAAATTTTAAAGATT
19484374 TACTTTCAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 7 0.14
46 44 0.86
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (46 bp):
AAAATTTTAAAGATTCACATCAAAAAAATTTTAGGAATTTACATCC
Found at i:19484338 original size:22 final size:22
Alignment explanation
Indices: 19484313--19484544 Score: 102
Period size: 22 Copynumber: 10.4 Consensus size: 22
19484303 TTTTACATCC
*
19484313 AAAATTTTAAAAATTCACATTAAA
1 AAAATTTTAAAGATTCACATT--A
*
19484337 AAAATTTTAGGAA-TTTC-CATCT-
1 AAAATTTTA--AAGATTCACAT-TA
* * *
19484359 AAAATTTCAAAGATTTACTTTCA
1 AAAATTTTAAAGATTCACATT-A
* * *
19484382 AAAATTTTTAGAGATTCATATTC
1 AAAA-TTTTAAAGATTCACATTA
* *
19484405 AAAACTTCAAAGACTT-ACATTCA
1 AAAATTTTAAAGA-TTCACATT-A
* * *
19484428 AAAA-ATTAGAGATTCACATTT
1 AAAATTTTAAAGATTCACATTA
*
19484449 AAAATTTCAAAGATTCACATTTGA
1 AAAATTTTAAAGATTCACA-TT-A
* *
19484473 AAAA--TTAGAA-ATGCACATTC
1 AAAATTTTA-AAGATTCACATTA
* *
19484493 AAAGTTTCAAAGATTCACATTA
1 AAAATTTTAAAGATTCACATTA
* * *
19484515 AAAAATTTAGAGATTCACATTC
1 AAAATTTTAAAGATTCACATTA
*
19484537 AAAGTTTT
1 AAAATTTT
19484545 GAAGGTTTTT
Statistics
Matches: 152, Mismatches: 38, Indels: 38
0.67 0.17 0.17
Matches are distributed among these distances:
20 5 0.03
21 13 0.09
22 82 0.54
23 18 0.12
24 28 0.18
25 4 0.03
26 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAATTTTAAAGATTCACATTA
Found at i:19484543 original size:44 final size:45
Alignment explanation
Indices: 19484196--19484539 Score: 274
Period size: 44 Copynumber: 7.7 Consensus size: 45
19484186 CCAAATTTAT
* * ***
19484196 ATTCAAAAATTTTAGAGATTCACATTCAAAAGTT-AAAGATTTTT
1 ATTCAAAAAATTTAGAGATTCACATTCAAAATTTCAAAGATTCAC
* * * * * * * *
19484240 ATTCGAACAACTTAGAAATTCGCATTGAAAATTTTAAAGATTCTC
1 ATTCAAAAAATTTAGAGATTCACATTCAAAATTTCAAAGATTCAC
* * * * * *
19484285 ATCCAAAAAAATTTAGTA-TTTTACATCCAAAATTTTAAAAATTCAC
1 ATTC-AAAAAATTTAG-AGATTCACATTCAAAATTTCAAAGATTCAC
* *
19484331 ATTAAAAAAATTTTAG-GAATTTC-CA-TCTAAAATTTCAAAGATTTAC
1 ATTCAAAAAA-TTTAGAG-A-TTCACATTC-AAAATTTCAAAGATTCAC
* * * *
19484377 TTTCAAAAATTTTTAGAGATTCATATTCAAAACTTCAAAGACTT-AC
1 ATTCAAAAA-ATTTAGAGATTCACATTCAAAATTTCAAAGA-TTCAC
*
19484423 ATTCAAAAAA-TTAGAGATTCACATTTAAAATTTCAAAGATTCAC
1 ATTCAAAAAATTTAGAGATTCACATTCAAAATTTCAAAGATTCAC
** * * *
19484467 ATTTGAAAAA-TTAGAAATGCACATTCAAAGTTTCAAAGATTCAC
1 ATTCAAAAAATTTAGAGATTCACATTCAAAATTTCAAAGATTCAC
19484511 ATT-AAAAAATTTAGAGATTCACATTCAAA
1 ATTCAAAAAATTTAGAGATTCACATTCAAA
19484540 GTTTTGAAGG
Statistics
Matches: 237, Mismatches: 48, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
43 7 0.03
44 112 0.47
45 21 0.09
46 89 0.38
47 8 0.03
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (45 bp):
ATTCAAAAAATTTAGAGATTCACATTCAAAATTTCAAAGATTCAC
Found at i:19486140 original size:14 final size:14
Alignment explanation
Indices: 19486121--19486153 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19486111 AGAACATACA
19486121 TTTTCATCTTT-TTT
1 TTTTCAT-TTTATTT
19486135 TTTTCATTTTATTT
1 TTTTCATTTTATTT
19486149 TTTTC
1 TTTTC
19486154 TTCATGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCATTTTATTT
Found at i:19487526 original size:134 final size:131
Alignment explanation
Indices: 19487353--19487600 Score: 322
Period size: 134 Copynumber: 1.9 Consensus size: 131
19487343 ACATGTATGT
* * * *
19487353 AATACATAGTAACAACAAGAATTCATATTCAAAATTATGTACAAAATTGAAATGGCAAAGATTTT
1 AATACATAGTAACAACAAAAATTCATATCCAAAACTATGTACAAAATTGAAAAGGC--A-ATTTT
* * * *
19487418 TTT-C-AGACAAACGAAATAACGTACATACAAAGATGTTTACATGGATTTATACGCAAATACATG
63 TTTCCTAAAC-AACGAAATAACGCACATACAAAAATGTTTACATGGATGTATACGCAAATACATG
19487481 CAAAC
127 CAAAC
19487486 AATACATAGATGAA-AACAAAAATTCATATCCAAAACTATGTACAAAATTGAAAAGGCAATTTTT
1 AATACATAG-T-AACAACAAAAATTCATATCCAAAACTATGTACAAAATTGAAAAGGCAATTTTT
* * *
19487550 TTCCTAAACAATGAAATAATGCACATATAAAAATGTTTACATGGATGTATA
64 TTCCTAAACAACGAAATAACGCACATACAAAAATGTTTACATGGATGTATA
19487601 TATATGCAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
131 8 0.08
132 38 0.38
133 12 0.12
134 40 0.40
135 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (131 bp):
AATACATAGTAACAACAAAAATTCATATCCAAAACTATGTACAAAATTGAAAAGGCAATTTTTTT
CCTAAACAACGAAATAACGCACATACAAAAATGTTTACATGGATGTATACGCAAATACATGCAAA
C
Found at i:19505159 original size:2 final size:2
Alignment explanation
Indices: 19505152--19505190 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19505142 TTTCCAATAA
19505152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19505191 GAATCTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19506194 original size:47 final size:47
Alignment explanation
Indices: 19506135--19506229 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
19506125 ATTTCAAATA
19506135 ATAATATGTGAAATATAAATAATTTTTTAAATTTCACATTAATTAAT
1 ATAATATGTGAAATATAAATAATTTTTTAAATTTCACATTAATTAAT
*
19506182 ATAATACT-TGAAATATAAATAATTTTTTAAATTTCATATTAATTAAT
1 ATAATA-TGTGAAATATAAATAATTTTTTAAATTTCACATTAATTAAT
19506229 A
1 A
19506230 AGTTTTTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 45 0.98
48 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (47 bp):
ATAATATGTGAAATATAAATAATTTTTTAAATTTCACATTAATTAAT
Found at i:19509767 original size:19 final size:18
Alignment explanation
Indices: 19509728--19509764 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19509718 AAATTTTAAT
*
19509728 ATAAAAAAAGTAATAAAA
1 ATAAAAAAAATAATAAAA
*
19509746 ATAAAAAAAATTATAAAA
1 ATAAAAAAAATAATAAAA
19509764 A
1 A
19509765 ATATATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
ATAAAAAAAATAATAAAA
Found at i:19509912 original size:22 final size:24
Alignment explanation
Indices: 19509887--19509939 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
19509877 TAAAATTATA
19509887 TATTTAATATTTTT-A-TGGAAAT
1 TATTTAATATTTTTGATTGGAAAT
* **
19509909 TATTT-TTATTTTTGATTTTAAAT
1 TATTTAATATTTTTGATTGGAAAT
19509932 TATTTAAT
1 TATTTAAT
19509940 TACTTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 10 0.42
24 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
TATTTAATATTTTTGATTGGAAAT
Found at i:19515024 original size:2 final size:2
Alignment explanation
Indices: 19515017--19515061 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19515007 CCATTGAAGC
19515017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19515059 AT A
1 AT A
19515062 AAAGAAGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19523252 original size:25 final size:24
Alignment explanation
Indices: 19523223--19523280 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 24
19523213 TTGGATAAGA
19523223 TTAGGAGTAAAAGTGCTTGGAATTG
1 TTAGGAGTAAAAGT-CTTGGAATTG
19523248 TTAGGAGT---A--CTTGGAATTG
1 TTAGGAGTAAAAGTCTTGGAATTG
19523267 TTAGGAGTAAAAGT
1 TTAGGAGTAAAAGT
19523281 ACACATGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
19 18 0.64
22 2 0.07
25 8 0.29
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (24 bp):
TTAGGAGTAAAAGTCTTGGAATTG
Found at i:19523262 original size:19 final size:19
Alignment explanation
Indices: 19523238--19523275 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19523228 AGTAAAAGTG
19523238 CTTGGAATTGTTAGGAGTA
1 CTTGGAATTGTTAGGAGTA
19523257 CTTGGAATTGTTAGGAGTA
1 CTTGGAATTGTTAGGAGTA
19523276 AAAGTACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.32, T:0.37
Consensus pattern (19 bp):
CTTGGAATTGTTAGGAGTA
Found at i:19523935 original size:13 final size:12
Alignment explanation
Indices: 19523913--19523955 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
19523903 TATTATACTG
19523913 TTTTAATTATAT
1 TTTTAATTATAT
19523925 TTTTAAATTATAT
1 TTTT-AATTATAT
19523938 TTTTAATTA-AT
1 TTTTAATTATAT
19523949 TTATTAA
1 TT-TTAA
19523956 GTGAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.14
12 13 0.45
13 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTAATTATAT
Found at i:19523955 original size:25 final size:28
Alignment explanation
Indices: 19523898--19523955 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 28
19523888 AGAATGAATA
*
19523898 TATTATATTATACTGTTTTAATTATATT
1 TATTAAATTATACTGTTTTAATTATATT
19523926 T-TTAAATTATA-T-TTTTAATTA-ATT
1 TATTAAATTATACTGTTTTAATTATATT
19523950 TATTAA
1 TATTAA
19523956 GTGAATAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.14
25 13 0.46
26 1 0.04
27 9 0.32
28 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTAAATTATACTGTTTTAATTATATT
Found at i:19524544 original size:49 final size:50
Alignment explanation
Indices: 19524487--19524587 Score: 168
Period size: 49 Copynumber: 2.0 Consensus size: 50
19524477 TCATAATAAC
* * *
19524487 TTGCTATCGATAGGATAATTATATTATATTATG-TTTTGATCAATATTCT
1 TTGCTATCGATAGGATAATTAAATTATATTATGTTTTTGACCAAAATTCT
19524536 TTGCTATCGATAGGATAATTAAATTATATTATGTTTTTGACCAAAATTCT
1 TTGCTATCGATAGGATAATTAAATTATATTATGTTTTTGACCAAAATTCT
19524586 TT
1 TT
19524588 CTTTTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 32 0.67
50 16 0.33
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.48
Consensus pattern (50 bp):
TTGCTATCGATAGGATAATTAAATTATATTATGTTTTTGACCAAAATTCT
Found at i:19524874 original size:2 final size:2
Alignment explanation
Indices: 19524867--19524900 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19524857 AATTAAAATG
19524867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19524901 TGAGTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19526412 original size:34 final size:34
Alignment explanation
Indices: 19526341--19526413 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
19526331 TGCAAATAAG
* * * *
19526341 TAAGCCTTTAAAAGCTTATGCAAATTCATGTCTA
1 TAAGCCTTTAAAAGCTTACGAAAATCCATGTCCA
*
19526375 TAAGCCTTTAAAAGCTTACGAAAATCCATTTCCA
1 TAAGCCTTTAAAAGCTTACGAAAATCCATGTCCA
19526409 TAAGC
1 TAAGC
19526414 TAAGAATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (34 bp):
TAAGCCTTTAAAAGCTTACGAAAATCCATGTCCA
Found at i:19528324 original size:30 final size:30
Alignment explanation
Indices: 19528286--19528373 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 30
19528276 TTTTTAATAC
19528286 ATCCATTTAAGAAACTGCTTAATATAACAT
1 ATCCATTTAAGAAACTGCTTAATATAACAT
** * * * *
19528316 ATTTATTTAATAACCTAC-TAACATAACAT
1 ATCCATTTAAGAAACTGCTTAATATAACAT
** *
19528345 ATCCATTTAAGAATTTGCTAAATATAACA
1 ATCCATTTAAGAAACTGCTTAATATAACA
19528374 CATTAATATA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (30 bp):
ATCCATTTAAGAAACTGCTTAATATAACAT
Found at i:19531773 original size:33 final size:33
Alignment explanation
Indices: 19531719--19531782 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
19531709 AGGGATAAAT
* * * *
19531719 TTAGCGACGTTTGTGTGAAAAACATCACTAATA
1 TTAGCGACGTTTGTATAAAAAAAACCACTAATA
19531752 TTAGCGAC-TGTTGTATAAAAAAAACCACTAA
1 TTAGCGACGT-TTGTATAAAAAAAACCACTAA
19531783 ATGTATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TTAGCGACGTTTGTATAAAAAAAACCACTAATA
Found at i:19535369 original size:2 final size:2
Alignment explanation
Indices: 19535362--19535392 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19535352 GTTTATGCAC
19535362 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19535393 TTGTGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19539144 original size:27 final size:28
Alignment explanation
Indices: 19539114--19539166 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
19539104 ATTTGGTTTG
*
19539114 AGAAAAT-ATTTTTAGTTTT-TATTTTCT
1 AGAAAATAATTTATA-TTTTCTATTTTCT
19539141 AGAAAATAATTTATATTTTCTATTTT
1 AGAAAATAATTTATATTTTCTATTTT
19539167 TTGTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (28 bp):
AGAAAATAATTTATATTTTCTATTTTCT
Found at i:19539175 original size:35 final size:34
Alignment explanation
Indices: 19539119--19539187 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
19539109 GTTTGAGAAA
19539119 ATATTTTTAGTTTTTATTTTCTAGAAAATA-ATTT
1 ATATTTTTAGTTTTTATTTTCTA-AAAATATATTT
* *
19539153 ATATTTTCTATTTTTTGTTTTCTAAAAATATATTT
1 ATATTTT-TAGTTTTTATTTTCTAAAAATATATTT
19539188 GGTAAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (34 bp):
ATATTTTTAGTTTTTATTTTCTAAAAATATATTT
Found at i:19539904 original size:49 final size:49
Alignment explanation
Indices: 19539845--19539950 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 49
19539835 GAGCTATGTT
* *
19539845 GATGACGTGTCCTTTTTGGGTGATG-GACGATGTCTTAACAAGCCATGCA
1 GATGACGTGTCCTTTTTGGG-CAAGAGACGATGTCTTAACAAGCCATGCA
* * * *
19539894 GATGATGTGTCCTTTTTGGGCAAGAGATGATGTCTTAACGAGCCATGCT
1 GATGACGTGTCCTTTTTGGGCAAGAGACGATGTCTTAACAAGCCATGCA
19539943 GATGACGT
1 GATGACGT
19539951 ATCCCTTTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
48 2 0.04
49 47 0.96
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (49 bp):
GATGACGTGTCCTTTTTGGGCAAGAGACGATGTCTTAACAAGCCATGCA
Found at i:19540892 original size:24 final size:26
Alignment explanation
Indices: 19540865--19540914 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
19540855 CGATATAGCA
* *
19540865 TTAAGTTCGA-GCTT-AAGCTTGATT
1 TTAAATTCGAGGCTTGAAACTTGATT
19540889 TTAAATTCGAGGCTTGAAACTTGATT
1 TTAAATTCGAGGCTTGAAACTTGATT
19540915 CAAGCTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 4 0.18
26 9 0.41
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (26 bp):
TTAAATTCGAGGCTTGAAACTTGATT
Found at i:19550742 original size:18 final size:18
Alignment explanation
Indices: 19550716--19550751 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19550706 AAGTTGCATT
19550716 TATTGGTTGTGAAGATTG
1 TATTGGTTGTGAAGATTG
* *
19550734 TATTTGTTGTGAGGATTG
1 TATTGGTTGTGAAGATTG
19550752 CTGTGAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47
Consensus pattern (18 bp):
TATTGGTTGTGAAGATTG
Found at i:19552968 original size:2 final size:2
Alignment explanation
Indices: 19552961--19552987 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19552951 CTTGATACTA
19552961 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19552988 CTGGTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19555361 original size:2 final size:2
Alignment explanation
Indices: 19555349--19555378 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19555339 CAATATTAAT
19555349 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19555379 TTTTATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:19560236 original size:203 final size:203
Alignment explanation
Indices: 19559848--19560243 Score: 487
Period size: 203 Copynumber: 2.0 Consensus size: 203
19559838 TTTCGATCAC
** * * * **
19559848 AAATCTCAATATTGAGTGACCTCATCTTAATCCTTTATTAAGGTAATTTCATTTTAAGTTTGGAC
1 AAATCTCAATATCAAGTGACCTCATCTTAATCCTTTATCAAAGTAATTTCATTATAAACTTGGAC
* * *
19559913 TCTCGATCCATAACTTTAACTAGTCTCATCTCTATGGTACCAAACCATTGAGGCAATTGCTTATG
66 TCTCGATCCATAACTTTAACTAGTCTCATATCTATGATACCAAACCATTGAGGCAATTGCTTATA
* * * * * * * *
19559978 TGAGAAGGCCAATCGAATGTTTGACATATTTTTAAATCATATTGTATAGGTACATATATATATTT
131 CGAGAAAGCCAATCGAATGTCTAACATACTTTCAAATCATATAGTATAGGTACATATACATATTT
19560043 TCAGTCAT
196 TCAGTCAT
* *
19560051 AAATCTCAATATCAAGTGACCTTATCTTAAT-CTCTTATCAAAGTGA-TTCGATTATAAACTTGG
1 AAATCTCAATATCAAGTGACCTCATCTTAATCCT-TTATCAAAGTAATTTC-ATTATAAACTTGG
* **
19560114 GCTCTCGATCCATAACTTTAACTAGTCTCATATCTATGATACCAAACCATTGAGGTGATTG-TCT
64 ACTCTCGATCCATAACTTTAACTAGTCTCATATCTATGATACCAAACCATTGAGGCAATTGCT-T
* *
19560178 ATACGAGAAAGCCAATC-ATTTGTCTAACATACCTTTCAAATC-TATAGTATATGTACATATACA
128 ATACGAGAAAGCCAATCGA-ATGTCTAACATA-CTTTCAAATCATATAGTATAGGTACATATACA
19560241 TAT
191 TAT
19560244 ACATGTATGC
Statistics
Matches: 163, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
202 7 0.04
203 148 0.91
204 8 0.05
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (203 bp):
AAATCTCAATATCAAGTGACCTCATCTTAATCCTTTATCAAAGTAATTTCATTATAAACTTGGAC
TCTCGATCCATAACTTTAACTAGTCTCATATCTATGATACCAAACCATTGAGGCAATTGCTTATA
CGAGAAAGCCAATCGAATGTCTAACATACTTTCAAATCATATAGTATAGGTACATATACATATTT
TCAGTCAT
Found at i:19564321 original size:3 final size:3
Alignment explanation
Indices: 19564315--19564342 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19564305 TTAAAAAAAA
19564315 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19564343 GTAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:19566321 original size:144 final size:143
Alignment explanation
Indices: 19565956--19566457 Score: 488
Period size: 144 Copynumber: 3.5 Consensus size: 143
19565946 TCATTTTTGA
* * * * * ** ***
19565956 GATTTTAAA-GCACAAAAAATCATAAAATATTATGAAATTAAGATAAAAAAAGTTTCGTAAAAAT
1 GATTTTAAATACACCAAAAATCATGAAATATTATAAAATTGAGATATGAAAAGTTTTACAAAAAT
* * * * *
19566020 CCAAACTTAGGAAGGCCAAATTATGAAAATACCCCTATAAGAGTATTTTGGTAATTTCACACTTT
66 CCAAGCTCAGGAAGGCCAAATTATGAAAATACCCCTAGAAGGGTATTTTGGTAATTTCACATTTT
* *
19566085 TGGGTACTGTTGT
131 TGGGTATTGCTGT
* * * ** *
19566098 GATTTTAAATGCACCAAAAATTATGAAACATTATAAAATTGAGATATGAAAAGTTTTGTAAAATT
1 GATTTTAAATACACCAAAAATCATGAAATATTATAAAATTGAGATATGAAAAGTTTTACAAAAAT
* ** *
19566163 CCAAGCTCAAGAAGGCCAAATTATGAAAATACCCCTTA-AAGGGTATTTTCATAATTTCATATTT
66 CCAAGCTCAGGAAGGCCAAATTATGAAAATACCCC-TAGAAGGGTATTTTGGTAATTTCACA-TT
*
19566227 TTTGGGTATTACTGT
129 TTTGGGTATTGCTGT
* * * * **
19566242 GGTTTTAAACT-CACCAAAAATCATGAAATATTTTAAAATTGAGATTTAAAAAGTTCCACAAAAA
1 GATTTTAAA-TACACCAAAAATCATGAAATATTATAAAATTGAGATATGAAAAGTTTTACAAAAA
** * * * ** * *
19566306 TCTTAGTTCGGGAAGGTCAAATTACAAAAATACCCATAGAATGGTATTTTGGTAATTTCACCATT
65 TCCAAGCTCAGGAAGGCCAAATTATGAAAATACCCCTAGAAGGGTATTTTGGTAATTTCA-CATT
* * *
19566371 GTCGGGTATTGCTAT
129 TTTGGGTATTGCTGT
* * * *
19566386 GATTTTAAATACACCAAAATTCATAAAATATTATAAAATTAAGATCTGAAAAGTTTTACAAAAAT
1 GATTTTAAATACACCAAAAATCATGAAATATTATAAAATTGAGATATGAAAAGTTTTACAAAAAT
*
19566451 TCAAGCT
66 CCAAGCT
19566458 GAAAAAGATC
Statistics
Matches: 291, Mismatches: 62, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
142 9 0.03
143 99 0.34
144 181 0.62
145 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (143 bp):
GATTTTAAATACACCAAAAATCATGAAATATTATAAAATTGAGATATGAAAAGTTTTACAAAAAT
CCAAGCTCAGGAAGGCCAAATTATGAAAATACCCCTAGAAGGGTATTTTGGTAATTTCACATTTT
TGGGTATTGCTGT
Found at i:19567910 original size:161 final size:161
Alignment explanation
Indices: 19567575--19568365 Score: 519
Period size: 161 Copynumber: 4.9 Consensus size: 161
19567565 CAATAACTTA
* * * * *
19567575 TTCATACATATCAATCGTAGAAACTAAGTTCAATCATTTGAACAAGTTTAA-TATCATGTATTTA
1 TTCACACATATCAATCGTTGAAACCAAGTTCAATCATTTGGACAAGTTTAATTA-CATGTATTAA
* * * * * * * *
19567639 AGCTATTTAAATTGTTAAAATATAAATA-AACTATAAAATTACAATTTTTTCCTTTGATA-GCAT
65 AGCTATCTAAACTGTTAAAATAGAAATATAATTGTAAAATTA-TATTTTTGCCTTTTA-ACG-AT
* * * *
19567702 A-ACAAAGTTCTAAA-AGGACATGAATGGTAACTTTT
127 ACAAAAAGTTCTAAACA-GACATAAACGATAA-TTTT
* * * *
19567737 TT-ACAAATATCAATCGTTGAAACTAAGTTCAACCATTTGGACAAGTTTAATTACATGTATTGAA
1 TTCACACATATCAATCGTTGAAACCAAGTTCAATCATTTGGACAAGTTTAATTACATGTATTAAA
* *
19567801 GCTATCTAAACTGTTAAAATATAAATATAATTGTAAAATTATATTTTTGCCTTTTAACGGTACAA
66 GCTATCTAAACTGTTAAAATAGAAATATAATTGTAAAATTATATTTTTGCCTTTTAACGATACAA
* *
19567866 AAAGTGCTAAACAGAGATAAACGATAATTTT
131 AAAGTTCTAAACAGACATAAACGATAATTTT
* * * * * * * * * *
19567897 TTCACACATATCAACCATTAAAACAAAGTTTAATCACTTGGATAGGTTCAA-TATCATGTATCAA
1 TTCACACATATCAATCGTTGAAACCAAGTTCAATCATTTGGACAAGTTTAATTA-CATGTATTAA
** * ** * **
19567961 AGCTATCTAAACTGTTAAAATAG-AATAATAAACGTAAATTTGCATTTTTGTCTTTTAACGACGC
65 AGCTATCTAAACTGTTAAAATAGAAAT-ATAATTGTAAAATTATATTTTTGCCTTTTAACGATAC
* *
19568025 AAAAAGTACTAAACAGACATAAAC-AGTAACTTT
129 AAAAAGTTCTAAACAGACATAAACGA-TAATTTT
* * ** * * * *
19568058 TTCACACATCAT-TAT-G--GAAACCAAGTTCACTCATTCAGACAAGTGTAGTAATATGTATTAA
1 TTCACACAT-ATCAATCGTTGAAACCAAGTTCAATCATTTGGACAAGTTTAATTACATGTATTAA
* * * * * * *
19568119 AGCTATCAAAACTATTAAAATAGAACA-GTAA--CTACAAATTTTATTTTTGCCTTTTAAAGGTA
65 AGCTATCTAAACTGTTAAAATAGAA-ATATAATTGTA-AAATTATATTTTTGCCTTTTAACGATA
* * * * *
19568181 TAAAAAGTTCTAAACAAACATAAACAACAA-CTT
128 CAAAAAGTTCTAAACAGACATAAACGATAATTTT
* * * * * * * *
19568214 TTCACATATAT-ATAACTATTGAAACCAAGTTAAATTA-TTCGAGCCAGTTTAATGT-CACGTAT
1 TTCACACATATCA-ATC-GTTGAAACCAAGTTCAATCATTTGGA-CAAGTTTAAT-TACATGTAT
* ** * **
19568276 TGAAA-CTATCTAAACTATTAAAATAGAACGATAATTGTAAATTTATATTTTT-CTCTTTTAATA
62 T-AAAGCTATCTAAACTGTTAAAATAGAAATATAATTGTAAAATTATATTTTTGC-CTTTTAACG
* * * *
19568339 ACATAAAAAGTTATAAAGAGACATAAA
125 ATACAAAAAGTTCTAAACAGACATAAA
19568366 TTGCAAGTTT
Statistics
Matches: 493, Mismatches: 109, Indels: 55
0.75 0.17 0.08
Matches are distributed among these distances:
155 2 0.00
156 13 0.03
157 43 0.09
158 53 0.11
159 5 0.01
160 69 0.14
161 288 0.58
162 20 0.04
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (161 bp):
TTCACACATATCAATCGTTGAAACCAAGTTCAATCATTTGGACAAGTTTAATTACATGTATTAAA
GCTATCTAAACTGTTAAAATAGAAATATAATTGTAAAATTATATTTTTGCCTTTTAACGATACAA
AAAGTTCTAAACAGACATAAACGATAATTTT
Found at i:19569477 original size:13 final size:13
Alignment explanation
Indices: 19569456--19569492 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
19569446 ATAACAAACG
19569456 ATATATAAAGAAC
1 ATATATAAAGAAC
*
19569469 ATATCTAAAGAAC
1 ATATATAAAGAAC
19569482 ATATATAAAGA
1 ATATATAAAGA
19569493 CTTTGGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:19570871 original size:29 final size:28
Alignment explanation
Indices: 19570838--19570892 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
19570828 GTGGGAAAAA
*
19570838 TGAAAAAAATAAA-GAGAGAAAAGAAAACG
1 TGAAAAAAAGAAAGGA-AG-AAAGAAAACG
*
19570867 TGAAAGAAAGAAAGGAAGAAAGAAAA
1 TGAAAAAAAGAAAGGAAGAAAGAAAA
19570893 GAGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 13 0.57
30 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (28 bp):
TGAAAAAAAGAAAGGAAGAAAGAAAACG
Found at i:19570872 original size:21 final size:21
Alignment explanation
Indices: 19570848--19570901 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
19570838 TGAAAAAAAT
* *
19570848 AAAGAGAGAAAAGAA-AACGTG
1 AAAGAGAGAAAAGAAGAAAG-A
* *
19570869 AAAGAAAGAAAGGAAGAAAGA
1 AAAGAGAGAAAAGAAGAAAGA
19570890 AAAGAGAGAAAA
1 AAAGAGAGAAAA
19570902 ATTATGAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.28, T:0.02
Consensus pattern (21 bp):
AAAGAGAGAAAAGAAGAAAGA
Found at i:19571648 original size:19 final size:19
Alignment explanation
Indices: 19571626--19571669 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
19571616 ACCACCCATG
*
19571626 AAACCTTAAATCACCTTCC
1 AAACCTTAAATCACCTTCA
*
19571645 AAACTTTAAATCACCTTCA
1 AAACCTTAAATCACCTTCA
19571664 AAACCT
1 AAACCT
19571670 AAAACCATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (19 bp):
AAACCTTAAATCACCTTCA
Found at i:19572175 original size:8 final size:8
Alignment explanation
Indices: 19572162--19572189 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
19572152 ATTTCCAAAA
19572162 AAAAAAGG
1 AAAAAAGG
19572170 AAAAAAGG
1 AAAAAAGG
19572178 AAAAAAGG
1 AAAAAAGG
19572186 AAAA
1 AAAA
19572190 GGAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:19574857 original size:19 final size:19
Alignment explanation
Indices: 19574829--19574867 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19574819 CCATGAAACT
*
19574829 CTTAAAACCCAAAACTACC
1 CTTAAAACCCAAAACCACC
* *
19574848 CTTAAGACCCCAAACCACC
1 CTTAAAACCCAAAACCACC
19574867 C
1 C
19574868 ATGAAACCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.44, G:0.03, T:0.13
Consensus pattern (19 bp):
CTTAAAACCCAAAACCACC
Found at i:19574928 original size:14 final size:13
Alignment explanation
Indices: 19574900--19574941 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
19574890 AAACCATAAA
*
19574900 CTAAACCCCAAGC
1 CTAAACCCTAAGC
*
19574913 CTAAACTCTAAAGC
1 CTAAACCCT-AAGC
19574927 CTAAACCCTAAGC
1 CTAAACCCTAAGC
19574940 CT
1 CT
19574942 TTGTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.38, C:0.38, G:0.07, T:0.17
Consensus pattern (13 bp):
CTAAACCCTAAGC
Found at i:19580468 original size:3 final size:3
Alignment explanation
Indices: 19580462--19580510 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
19580452 GTTGTTGTTG
19580462 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19580510 T
1 T
19580511 GTCTGTTCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19580595 original size:3 final size:3
Alignment explanation
Indices: 19580581--19580612 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
19580571 AAATAAGAGT
19580581 TTA TTCA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T
19580613 GTTTGTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19580629 original size:102 final size:102
Alignment explanation
Indices: 19580480--19580688 Score: 402
Period size: 102 Copynumber: 2.1 Consensus size: 102
19580470 ATTATTATTA
19580480 TTATT-ATTATTATTATTATTATTATTATTATGTCTGTTCTCTTCCCAATAACTTTTCTTCCATA
1 TTATTCATTATTATTATTATTATTATTATTATGTCTGTTCTCTTCCCAATAACTTTTCTTCCATA
19580544 TATTTACCTATAGGTTATAGTTCTTGCAAATAAGAGT
66 TATTTACCTATAGGTTATAGTTCTTGCAAATAAGAGT
*
19580581 TTATTCATTATTATTATTATTATTATTATTATGTTTGTTCTCTTCCCAATAACTTTTCTTCCATA
1 TTATTCATTATTATTATTATTATTATTATTATGTCTGTTCTCTTCCCAATAACTTTTCTTCCATA
19580646 TATTTACCTATAGGTTATAGTTCTTGCAAATAAGAGT
66 TATTTACCTATAGGTTATAGTTCTTGCAAATAAGAGT
19580683 TTATTC
1 TTATTC
19580689 CCCAACTGAA
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 5 0.05
102 101 0.95
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (102 bp):
TTATTCATTATTATTATTATTATTATTATTATGTCTGTTCTCTTCCCAATAACTTTTCTTCCATA
TATTTACCTATAGGTTATAGTTCTTGCAAATAAGAGT
Found at i:19582200 original size:42 final size:42
Alignment explanation
Indices: 19582125--19582205 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
19582115 AACGAAATGT
**
19582125 CATTAACTTATTGCCATTAGCGGCATTTCTACTTAAAAACAC
1 CATTAACTTATTGCCATTAGCAACATTTCTACTTAAAAACAC
* * * *
19582167 CATTAACTTATTGCCCTTAGTAATATTTTTACTTAAAAA
1 CATTAACTTATTGCCATTAGCAACATTTCTACTTAAAAA
19582206 TGCCACTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (42 bp):
CATTAACTTATTGCCATTAGCAACATTTCTACTTAAAAACAC
Found at i:19585371 original size:21 final size:21
Alignment explanation
Indices: 19585347--19585396 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
19585337 TGAGGAAATG
19585347 TAAAAATG-CAATCAAAATCAA
1 TAAAAA-GCCAATCAAAATCAA
19585368 TAAAAAGCCAATCAAAATCAA
1 TAAAAAGCCAATCAAAATCAA
19585389 TAAAAAGC
1 TAAAAAGC
19585397 TACGAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (21 bp):
TAAAAAGCCAATCAAAATCAA
Found at i:19585373 original size:10 final size:10
Alignment explanation
Indices: 19585347--19585394 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
19585337 TGAGGAAATG
19585347 TAAAAATGCAA
1 TAAAAAT-CAA
*
19585358 TCAAAATCAA
1 TAAAAATCAA
*
19585368 TAAAAAGCCAA
1 TAAAAA-TCAA
*
19585379 TCAAAATCAA
1 TAAAAATCAA
19585389 TAAAAA
1 TAAAAA
19585395 GCTACGAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 16 0.53
11 14 0.47
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.17
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:19586568 original size:6 final size:6
Alignment explanation
Indices: 19586546--19586601 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
19586536 CATTTTATTG
* *
19586546 CTTTTG CTTTTG C-TTTT CTTTTT CTTGTGATT -TTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-T--TT CTTTTT CTTTTT CTTTTT
19586595 CTTTTT C
1 CTTTTT C
19586602 ACAACTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
5 6 0.14
6 32 0.73
7 2 0.05
8 2 0.05
9 2 0.05
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (6 bp):
CTTTTT
Found at i:19586764 original size:19 final size:19
Alignment explanation
Indices: 19586742--19586785 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
19586732 ACAAAAGATA
19586742 AAAAAAAAAAGAAATATAC
1 AAAAAAAAAAGAAATATAC
*
19586761 AAAAAAATAAGAAATATAC
1 AAAAAAAAAAGAAATATAC
19586780 AAAAAA
1 AAAAAA
19586786 GGGTATAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAAGAAATATAC
Found at i:19591030 original size:8 final size:8
Alignment explanation
Indices: 19591008--19591045 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
19590998 ACTCAACATG
19591008 AAAAATTC
1 AAAAATTC
**
19591016 ACGAATTC
1 AAAAATTC
19591024 AAAAATTC
1 AAAAATTC
19591032 AAAAATTC
1 AAAAATTC
19591040 AAAAAT
1 AAAAAT
19591046 ATATGAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:19591360 original size:15 final size:15
Alignment explanation
Indices: 19591340--19591377 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
19591330 TTTATCTTTA
19591340 AAATTAAATATAAAT
1 AAATTAAATATAAAT
19591355 AAATTAAAATATAAAT
1 AAATT-AAATATAAAT
19591371 -AATTAAA
1 AAATTAAA
19591378 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTAAATATAAAT
Found at i:19591379 original size:16 final size:16
Alignment explanation
Indices: 19591340--19591378 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
19591330 TTTATCTTTA
19591340 AAATT-AAATATAAAT
1 AAATTAAAATATAAAT
19591355 AAATTAAAATATAAAT
1 AAATTAAAATATAAAT
19591371 -AATTAAAA
1 AAATTAAAA
19591379 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAATATAAAT
Found at i:19597204 original size:32 final size:30
Alignment explanation
Indices: 19597165--19597232 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
19597155 AATTCTAGAT
*
19597165 TTTGGTGAAATTTTCTGGCATCGGTTGAATTG
1 TTTGGTG-AATTTT-TGGCATCGATTGAATTG
* * *
19597197 TTTGGTGACTTTTTTGCATCGATTGAATTT
1 TTTGGTGAATTTTTGGCATCGATTGAATTG
19597227 TTTGGT
1 TTTGGT
19597233 AAGGTTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 20 0.62
31 5 0.16
32 7 0.22
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (30 bp):
TTTGGTGAATTTTTGGCATCGATTGAATTG
Found at i:19597395 original size:2 final size:2
Alignment explanation
Indices: 19597390--19597415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19597380 AAGGAGAAAA
19597390 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
19597416 GGGAAGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19597406 original size:20 final size:19
Alignment explanation
Indices: 19597362--19597406 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
19597352 CAACTGAGTT
*
19597362 AGAGAAAAAGGGGAGAGAA
1 AGAGAAAAAGGAGAGAGAA
*
19597381 AGGAGAAAAAGAGAGAGAGAG
1 A-GAGAAAAAG-GAGAGAGAA
19597402 AGAGA
1 AGAGA
19597407 GAGAGAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.59
21 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (19 bp):
AGAGAAAAAGGAGAGAGAA
Found at i:19597794 original size:11 final size:10
Alignment explanation
Indices: 19597748--19597797 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 10
19597738 TAAATTCTTT
19597748 AAAA-AAAAA
1 AAAATAAAAA
19597757 AAAA-AAAAA
1 AAAATAAAAA
19597766 AAAATAAAAA
1 AAAATAAAAA
**
19597776 AGGTATAAAACA
1 A-AAATAAAA-A
19597788 AAAATAAAAA
1 AAAATAAAAA
19597798 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 13 0.38
10 7 0.21
11 12 0.35
12 2 0.06
ACGTcount: A:0.86, C:0.02, G:0.04, T:0.08
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:19598213 original size:51 final size:51
Alignment explanation
Indices: 19598158--19598270 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 51
19598148 TTTTTCTTTC
19598158 GAAATAAAAAATAAAAAAATTTCTAAATAAGCCCAAATGGTGAAA-AATTTA
1 GAAATAAAAAATAAAAAAATTTCTAAATAAGCCCAAATGGTGAAATAA-TTA
* * * * * **
19598209 GAAATTAAAAA-AAAGATATTTTTAATTTGGCCCAAATGGTGAAATAATTA
1 GAAATAAAAAATAAAAAAATTTCTAAATAAGCCCAAATGGTGAAATAATTA
19598259 G--ATAAAAAATAA
1 GAAATAAAAAATAA
19598271 TTAAACATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
48 7 0.13
49 2 0.04
50 31 0.60
51 12 0.23
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.27
Consensus pattern (51 bp):
GAAATAAAAAATAAAAAAATTTCTAAATAAGCCCAAATGGTGAAATAATTA
Found at i:19602251 original size:28 final size:27
Alignment explanation
Indices: 19602210--19602293 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 27
19602200 CTAATTGATG
*
19602210 GAAAAAAAT-TACAAAAAAGGGAAAAAAA
1 GAAAAAAATGAACAAAAAA--GAAAAAAA
*
19602238 G-AAAAAATGAACAAAAAAAATGAAAAAAT
1 GAAAAAAATGAAC--AAAAAA-GAAAAAAA
19602267 GAAAAAAATGAA-AAGAAAAGAAAAAAA
1 GAAAAAAATGAACAA-AAAAGAAAAAAA
19602294 TACTCAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
27 16 0.34
28 7 0.15
29 8 0.17
30 16 0.34
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.07
Consensus pattern (27 bp):
GAAAAAAATGAACAAAAAAGAAAAAAA
Found at i:19602255 original size:21 final size:20
Alignment explanation
Indices: 19602231--19602285 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
19602221 CAAAAAAGGG
19602231 AAAAAAAGAAAAAATGAACAA
1 AAAAAAAGAAAAAATGAA-AA
*
19602252 AAAAAATGAAAAAATGAAAA
1 AAAAAAAGAAAAAATGAAAA
19602272 AAATGAAAAGAAAA
1 AAA--AAAAGAAAA
19602286 GAAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 5 0.17
21 17 0.57
22 8 0.27
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAAAGAAAAAATGAAAA
Found at i:19603391 original size:21 final size:21
Alignment explanation
Indices: 19603367--19603413 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
19603357 GAGAATCTAT
* * *
19603367 GAATTTTTTAATTTCAAATTA
1 GAATCTTTAAATTTCAAATGA
19603388 GAATCTTTAAATTTCAAATGA
1 GAATCTTTAAATTTCAAATGA
19603409 GAATC
1 GAATC
19603414 ATTGAGACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (21 bp):
GAATCTTTAAATTTCAAATGA
Found at i:19603505 original size:21 final size:21
Alignment explanation
Indices: 19603481--19603521 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19603471 ATTTTAAACT
* *
19603481 TTTGGATATGAATCTCTAAAA
1 TTTGAATAAGAATCTCTAAAA
*
19603502 TTTGAATAAGAATCTTTAAA
1 TTTGAATAAGAATCTCTAAA
19603522 TGTTGGAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (21 bp):
TTTGAATAAGAATCTCTAAAA
Found at i:19603580 original size:23 final size:23
Alignment explanation
Indices: 19603535--19603585 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
19603525 TGGAAGCGAG
*
19603535 TCTTGAAATTTGCATATGCGAA-
1 TCTTGAAATTTGCAAATGCGAAT
19603557 TCTTGAAATCTTGCAAAT-CTGAAT
1 TCTTGAAAT-TTGCAAATGC-GAAT
19603581 TCTTG
1 TCTTG
19603586 TATATCTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 10 0.40
23 10 0.40
24 5 0.20
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (23 bp):
TCTTGAAATTTGCAAATGCGAAT
Found at i:19603584 original size:16 final size:16
Alignment explanation
Indices: 19603555--19603597 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19603545 TGCATATGCG
19603555 AATCTTGAAATCTTGCA
1 AATC-TGAAATCTTGCA
* *
19603572 AATCTGAATTCTTGTA
1 AATCTGAAATCTTGCA
*
19603588 TATCTGAAAT
1 AATCTGAAAT
19603598 TTTACGAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (16 bp):
AATCTGAAATCTTGCA
Found at i:19603834 original size:41 final size:41
Alignment explanation
Indices: 19603779--19604449 Score: 503
Period size: 41 Copynumber: 16.1 Consensus size: 41
19603769 ATGATTGTCA
* * *
19603779 AGGAG-CTTTTATTTTTCAAAATTGTTGTGCCTCTACTTAA
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * **
19603819 AGGAGCCTTTTATTTTTCAAAGTTATTGTACCTTTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
19603860 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
** * * *
19603901 ATAAGCTTTTTATTTTTTAAAGTTGTTGTGCCTCTACTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * **
19603942 AGGAGCCTCTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* **
19603983 AGGAG-CTTTTA-TTTTCTAAAGTCATTAAGCCTCTACTTAG
1 AGGAGCCTTTTATTTTTC-AAAGTTATTGTGCCTCTACTTAG
* * * * * * *
19604023 ATGAGCTTTTTATTTTTCAAAGTCATTGAGCTTCTACGTAA
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * *
19604064 ATGAGCCTTTTATTTTTCAAAGTTATTGTGCCTTTATTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* *
19604105 AGGAGCCTTTTTTATTTTCCAAAGTTATTGTGCCTCTGCTTAG
1 AGGAGCC--TTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
** ** * * *
19604148 ATAATACTTTTATTTTTTAAAGTTGTTGTGCCTC-ATTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * * * **
19604188 AAGAG-ATTTTATTTTTCAAAGTTGTTGTACCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * **
19604228 AGGAG-CTTTTATTTTTCAAAGCTTTCAAAGTCGTTGAGCCTTTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAG--TT---A----TTGTGCCTCTACTTAG
* * * * * *
19604277 AAGAGCTTTTTATTTTTTAAAGTCATTGAGCCTCTATTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * ** * *
19604318 AGGAG-CATTTATTTTTTAAAGTCGTTGGGCCTCTGCTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * * *
19604358 -GGAAGCCTTATTTTATTTTTCGAAGTCATTGAGCCTGTACTTAG
1 AGG-AGCC---TTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* ** *
19604402 AGGAGCCTAATTTTATTTTTCAAAGTTGTTAAGCCTCTATTTAG
1 AGGAGCC---TTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
19604446 AGGA
1 AGGA
19604450 AGTCTGAGTA
Statistics
Matches: 510, Mismatches: 98, Indels: 42
0.78 0.15 0.06
Matches are distributed among these distances:
39 32 0.06
40 92 0.18
41 246 0.48
42 7 0.01
43 33 0.06
44 65 0.13
45 3 0.01
48 1 0.00
49 17 0.03
50 14 0.03
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (41 bp):
AGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
Found at i:19604215 original size:245 final size:244
Alignment explanation
Indices: 19603781--19604242 Score: 714
Period size: 245 Copynumber: 1.9 Consensus size: 244
19603771 GATTGTCAAG
** * *
19603781 GAGCTTTTATTTTTCAAAATTGTTGTGCCTCTACTTAAAGGAGCCTTTTATTTTTCAAAGTTATT
1 GAGCTTTTATTTTTCAAAATCATTGAGCCTCTACGTAAAGGAGCCTTTTATTTTTCAAAGTTATT
* * *
19603846 GTACCTTTGTTTAGAGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAGATAAGCTTTT
66 GTACCTTTATTTAGAGGAGCCTTTTATTTTCCAAAGTTATTGTGCCTCTACTTAGATAAACTTTT
* * *
19603911 TATTTTTTAAAGTTGTTGTGCCTCTACTTAGAGGAGCCTCTTATTTTTCAAAGTTGTTGTGCCTC
131 TATTTTTTAAAGTTGTTGTGCCTCTACTTAGAAGAGCATCTTATTTTTCAAAGTTGTTGTACCTC
19603976 TGTTTAGAGGAGCTTTTATTTTCTAAAGTCATTAAGCCTCTACTTAGAT
196 TGTTTAGAGGAGCTTTTATTTTCTAAAGTCATTAAGCCTCTACTTAGAT
* * *
19604025 GAGCTTTTTATTTTTCAAAGTCATTGAGCTTCTACGTAAATGAGCCTTTTATTTTTCAAAGTTAT
1 GAGC-TTTTATTTTTCAAAATCATTGAGCCTCTACGTAAAGGAGCCTTTTATTTTTCAAAGTTAT
* *
19604090 TGTGCCTTTATTTAGAGGAGCCTTTTTTATTTTCCAAAGTTATTGTGCCTCTGCTTAGATAATAC
65 TGTACCTTTATTTAGAGGAGCC--TTTTATTTTCCAAAGTTATTGTGCCTCTACTTAGATAA-AC
* *
19604155 -TTTTATTTTTTAAAGTTGTTGTGCCTC-ATTTAGAAGAG-ATTTTATTTTTCAAAGTTGTTGTA
127 TTTTTATTTTTTAAAGTTGTTGTGCCTCTACTTAGAAGAGCATCTTATTTTTCAAAGTTGTTGTA
19604217 CCTCTGTTTAGAGGAGCTTTTATTTT
192 CCTCTGTTTAGAGGAGCTTTTATTTT
19604243 TCAAAGCTTT
Statistics
Matches: 197, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
244 4 0.02
245 120 0.61
246 9 0.05
247 63 0.32
248 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (244 bp):
GAGCTTTTATTTTTCAAAATCATTGAGCCTCTACGTAAAGGAGCCTTTTATTTTTCAAAGTTATT
GTACCTTTATTTAGAGGAGCCTTTTATTTTCCAAAGTTATTGTGCCTCTACTTAGATAAACTTTT
TATTTTTTAAAGTTGTTGTGCCTCTACTTAGAAGAGCATCTTATTTTTCAAAGTTGTTGTACCTC
TGTTTAGAGGAGCTTTTATTTTCTAAAGTCATTAAGCCTCTACTTAGAT
Found at i:19604239 original size:163 final size:161
Alignment explanation
Indices: 19603779--19604248 Score: 451
Period size: 163 Copynumber: 2.9 Consensus size: 161
19603769 ATGATTGTCA
* * * * * * ** *
19603779 AGGAG-CTTTTATTTTTCAAAATTGTTGTGCCTCTACTTAAAGGAGCCTTTTATTTTTCAAAGTT
1 AGGAGCCTCTTATTTTCCAAAGTTATTGTGCCTCTGCTTAGA-GAAACTTTTATTTTTTAAAGTT
* ** * * * *
19603843 ATTGTACCTTTGTTTAGAGGAGCCTTTTATTTTTCAAAGTTATTGTGCCTCTACTTAGATAAGCT
65 ATTGTGCC-TCATTTAGAAGAGCATTTTATTTTTCAAAGTTATTGTACCTCTACTTAGATGAGC-
* *
19603908 TTTTATTTTTTAAAGTTGTTGTGCCTCTACTTAG
128 TTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* * * * * * *
19603942 AGGAGCCTCTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTTTTATTTTCTAAAGTCA
1 AGGAGCCTCTTATTTTCCAAAGTTATTGTGCCTCTGCTTAGAGAAACTTTTATTTTTTAAAGTTA
** * * * * * * *
19604007 TTAAGCCTCTACTTAGATGAGCTTTTTATTTTTCAAAGTCATTG-AGCTTCTACGTAAATGAGCC
66 TTGTGCCTC-ATTTAGAAGAGCATTTTATTTTTCAAAGTTATTGTA-CCTCTACTTAGATGAG-C
* *
19604071 TTTTATTTTTCAAAGTTATTGTGCCTTTATTTAG
128 TTTTATTTTTCAAAGTTATTGTGCCTCTACTTAG
* *
19604105 AGGAGCCTTTTTTATTTTCCAAAGTTATTGTGCCTCTGCTTAGATAATACTTTTATTTTTTAAAG
1 AGGAGCC--TCTTATTTTCCAAAGTTATTGTGCCTCTGCTTAGAGAA-ACTTTTATTTTTTAAAG
* * ** *
19604170 TTGTTGTGCCTCATTTAGAAGAG-ATTTTATTTTTCAAAGTTGTTGTACCTCTGTTTAGAGGAGC
63 TTATTGTGCCTCATTTAGAAGAGCATTTTATTTTTCAAAGTTATTGTACCTCTACTTAGATGAGC
19604234 TTTTATTTTTCAAAG
128 TTTTATTTTTCAAAG
19604249 CTTTCAAAGT
Statistics
Matches: 247, Mismatches: 52, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
162 1 0.00
163 120 0.49
164 61 0.25
165 42 0.17
166 23 0.09
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.46
Consensus pattern (161 bp):
AGGAGCCTCTTATTTTCCAAAGTTATTGTGCCTCTGCTTAGAGAAACTTTTATTTTTTAAAGTTA
TTGTGCCTCATTTAGAAGAGCATTTTATTTTTCAAAGTTATTGTACCTCTACTTAGATGAGCTTT
TATTTTTCAAAGTTATTGTGCCTCTACTTAG
Found at i:19604274 original size:49 final size:50
Alignment explanation
Indices: 19604201--19604298 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 50
19604191 AGATTTTATT
* *
19604201 TTTCAAAGTTGTTGTACCTCTGTTTAGAGGAGC-TTTTATTTTTCAAAGC
1 TTTCAAAGTCGTTGTACCTCTGTTTAGAAGAGCTTTTTATTTTTCAAAGC
* *
19604250 TTTCAAAGTCGTTG-AGCCTTTGTTTAGAAGAGCTTTTTATTTTTTAAAG
1 TTTCAAAGTCGTTGTA-CCTCTGTTTAGAAGAGCTTTTTATTTTTCAAAG
19604299 TCATTGAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 1 0.02
49 28 0.65
50 14 0.33
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (50 bp):
TTTCAAAGTCGTTGTACCTCTGTTTAGAAGAGCTTTTTATTTTTCAAAGC
Found at i:19604369 original size:39 final size:40
Alignment explanation
Indices: 19604286--19604415 Score: 113
Period size: 40 Copynumber: 3.2 Consensus size: 40
19604276 GAAGAGCTTT
* *
19604286 TTATTTTTTAAAGTCATTGAGCCTCTATTTAGAGGAGCAT
1 TTATTTTTTAAAGTCATTGAGCCTCTACTTAGAGGAGCAC
* * *
19604326 TTATTTTTTAAAGTCGTTGGGCCTCTGCTTAG-GGAAGC-C
1 TTATTTTTTAAAGTCATTGAGCCTCTACTTAGAGG-AGCAC
* *
19604365 TTATTTTATTTTTCGAAGTCATTGAGCCTGTACTTAGAGGAGC-C
1 TTA---T-TTTTT-AAAGTCATTGAGCCTCTACTTAGAGGAGCAC
*
19604409 TAATTTT
1 TTATTTT
19604416 ATTTTTCAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
39 5 0.07
40 34 0.47
41 1 0.01
42 1 0.01
43 5 0.07
44 24 0.33
45 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (40 bp):
TTATTTTTTAAAGTCATTGAGCCTCTACTTAGAGGAGCAC
Found at i:19618491 original size:2 final size:2
Alignment explanation
Indices: 19618484--19618530 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
19618474 ATCCTTCTTT
19618484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19618526 TA TA T
1 TA TA T
19618531 GCTTCAATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19623802 original size:27 final size:28
Alignment explanation
Indices: 19623772--19623832 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
19623762 ATTTTTAAAT
19623772 AAATATTTT-TTGTAAA-AAATATT-ATTC
1 AAAT-TTTTATTGTAAATAAATATTGA-TC
19623799 AAATTTTTATTGTAAATAAATATTGATC
1 AAATTTTTATTGTAAATAAATATTGATC
19623827 AAATTT
1 AAATTT
19623833 AAATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.13
27 11 0.35
28 15 0.48
29 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (28 bp):
AAATTTTTATTGTAAATAAATATTGATC
Found at i:19623842 original size:28 final size:28
Alignment explanation
Indices: 19623784--19623845 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
19623774 ATATTTTTTG
** *
19623784 TAAA-AAATATTATTCAAATTTTTATTG
1 TAAATAAATATTATTCAAATTTAAATTA
19623811 TAAATAAATATTGA-TCAAATTTAAATTA
1 TAAATAAATATT-ATTCAAATTTAAATTA
19623839 TAAATAA
1 TAAATAA
19623846 CATTTTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 25 0.83
29 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
TAAATAAATATTATTCAAATTTAAATTA
Found at i:19623936 original size:28 final size:29
Alignment explanation
Indices: 19623874--19623938 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
19623864 ATATTTTATT
*
19623874 ACTTTTTATATTAAAATTTATTAGATTTA
1 ACTTTTTATATTAAAATTTATTAGATATA
*
19623903 AATTTTT-TATTAAAAATTTTATTA-A-ATA
1 ACTTTTTATATT-AAAA-TTTATTAGATATA
19623931 ACTTTTTA
1 ACTTTTTA
19623939 AAAAATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 12 0.40
29 11 0.37
30 7 0.23
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
ACTTTTTATATTAAAATTTATTAGATATA
Found at i:19625592 original size:21 final size:23
Alignment explanation
Indices: 19625560--19625614 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
19625550 ATGATATTTT
19625560 TAAATA-TTTATA-TTTAAAAAA
1 TAAATATTTTATATTTTAAAAAA
19625581 T-AATATTTTATATTTTAAAAAA
1 TAAATATTTTATATTTTAAAAAA
19625603 TAAATATTTTAT
1 TAAATATTTTAT
19625615 TAATTTTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.13
21 7 0.23
22 10 0.32
23 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATATTTTATATTTTAAAAAA
Found at i:19627831 original size:47 final size:47
Alignment explanation
Indices: 19627780--19627872 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
19627770 ATTAAAAATT
*
19627780 TATTAATTAATATAAAATTAAAAAAATTATTTATATTTCACGTATTA
1 TATTAATTAATATAAAATTAAAAAAATTATTTATATTTCACATATTA
* *
19627827 TATTAATTAATGTGAAATTAAAAAAATTATTTATATTTCACATATT
1 TATTAATTAATATAAAATTAAAAAAATTATTTATATTTCACATATT
19627873 GTTATTTGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (47 bp):
TATTAATTAATATAAAATTAAAAAAATTATTTATATTTCACATATTA
Found at i:19628500 original size:21 final size:22
Alignment explanation
Indices: 19628462--19628502 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19628452 TAAAAAGAGT
**
19628462 ATTTACAAAAAAGTTTTTCATG
1 ATTTACAAAAAAAATTTTCATG
19628484 ATTT-CAAAAAAAATTTTCA
1 ATTTACAAAAAAAATTTTCA
19628503 ATTTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (22 bp):
ATTTACAAAAAAAATTTTCATG
Found at i:19628865 original size:2 final size:2
Alignment explanation
Indices: 19628852--19628898 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
19628842 AAATAGATTC
*
19628852 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19628894 TA TA T
1 TA TA T
19628899 TGGAAATCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19642137 original size:1 final size:1
Alignment explanation
Indices: 19642131--19642155 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
19642121 AAGCAACTTT
19642131 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
19642156 CCTCATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19647181 original size:14 final size:14
Alignment explanation
Indices: 19647162--19647196 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19647152 AATTTGATCA
19647162 AATTTTATTTATTC
1 AATTTTATTTATTC
* *
19647176 AATTTTGTTTATTG
1 AATTTTATTTATTC
19647190 AATTTTA
1 AATTTTA
19647197 AATTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (14 bp):
AATTTTATTTATTC
Found at i:19647223 original size:11 final size:11
Alignment explanation
Indices: 19647197--19647249 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
19647187 TTGAATTTTA
19647197 AATTTTAAT-T
1 AATTTTAATAT
19647207 -ATTTTAATAT
1 AATTTTAATAT
19647217 AATTTTAATAT
1 AATTTTAATAT
*
19647228 -ATTTAAAT-T
1 AATTTTAATAT
* *
19647237 AACTTAAATAT
1 AATTTTAATAT
19647248 AA
1 AA
19647250 ATAATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
9 9 0.24
10 15 0.41
11 13 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTTAATAT
Found at i:19647233 original size:9 final size:10
Alignment explanation
Indices: 19647198--19647231 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
19647188 TGAATTTTAA
19647198 ATTTTAAT-T
1 ATTTTAATAT
19647207 ATTTTAATAT
1 ATTTTAATAT
19647217 AATTTTAATAT
1 -ATTTTAATAT
19647228 ATTT
1 ATTT
19647232 AAATTAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 5 0.22
11 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:19649713 original size:61 final size:61
Alignment explanation
Indices: 19649634--19649765 Score: 165
Period size: 61 Copynumber: 2.1 Consensus size: 61
19649624 TTTTATCTAG
* * *
19649634 TAAAATCTCACAAATTCTCACCATAAATAATAAAATTATAAAATATATAAAACTTAGTAAAT
1 TAAAA-CTCACAAATTCTCACCATAAATAATAAAATTAGAAAATATATAAAACTTAATAAAC
* * * ** * *
19649696 TAAAACTCACAAATTCTCATCATATATGATGGAATTAGGAAATATATAAAATTTAATAAAC
1 TAAAACTCACAAATTCTCACCATAAATAATAAAATTAGAAAATATATAAAACTTAATAAAC
19649757 TAAAACTCA
1 TAAAACTCA
19649766 AATATTAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 55 0.92
62 5 0.08
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (61 bp):
TAAAACTCACAAATTCTCACCATAAATAATAAAATTAGAAAATATATAAAACTTAATAAAC
Found at i:19650186 original size:13 final size:15
Alignment explanation
Indices: 19650168--19650208 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
19650158 ATGAAATAAT
19650168 AAAATAT-TAA-CAA
1 AAAATATATAACCAA
*
19650181 ATAATATATAACCAA
1 AAAATATATAACCAA
19650196 AAAATATAATAAC
1 AAAATAT-ATAAC
19650209 TAACAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 6 0.26
14 3 0.13
15 9 0.39
16 5 0.22
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATATATAACCAA
Found at i:19659189 original size:2 final size:2
Alignment explanation
Indices: 19659182--19659217 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19659172 CTCCTTTCAA
19659182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19659218 TATTTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19661266 original size:21 final size:21
Alignment explanation
Indices: 19661242--19661289 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
19661232 TCTCTAATTT
*
19661242 TAATATAATAATTATAATAAC
1 TAATATAATAACTATAATAAC
* * *
19661263 TAATCTTATCACTATAATAAC
1 TAATATAATAACTATAATAAC
*
19661284 AAATAT
1 TAATAT
19661290 CACCTAGCTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATAATAACTATAATAAC
Found at i:19661434 original size:23 final size:22
Alignment explanation
Indices: 19661399--19661445 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19661389 TTTTCTCCAA
* *
19661399 AAAAAAATGTTAAACTTATATTT
1 AAAAAAATATT-AACTTACATTT
*
19661422 AAAATAATATTAACTTACATTT
1 AAAAAAATATTAACTTACATTT
19661444 AA
1 AA
19661446 TTAGAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAAATATTAACTTACATTT
Found at i:19671930 original size:13 final size:13
Alignment explanation
Indices: 19671912--19671979 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
19671902 AAAATATCAT
19671912 AATAAATCATGCA
1 AATAAATCATGCA
19671925 AATAAAT-AT--A
1 AATAAATCATGCA
*
19671935 ACAAAAATCATGCA
1 A-ATAAATCATGCA
*
19671949 AGT-AATCATGCA
1 AATAAATCATGCA
*
19671961 AA-AATATCATTCA
1 AATAA-ATCATGCA
19671974 AATAAA
1 AATAAA
19671980 CATAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 15 0.35
13 17 0.40
14 4 0.09
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (13 bp):
AATAAATCATGCA
Found at i:19671944 original size:24 final size:23
Alignment explanation
Indices: 19671915--19672008 Score: 82
Period size: 24 Copynumber: 3.9 Consensus size: 23
19671905 ATATCATAAT
19671915 AAATCATGCAAATAAATATAACAA
1 AAATCATGCAAATAAATATAA-AA
*
19671939 AAATCATGCAAGT-AATCATGCAAAA
1 AAATCATGCAAATAAAT-AT--AAAA
* * *
19671964 ATATCATTCAAATAAACATAATAA
1 AAATCATGCAAATAAATATAA-AA
* *
19671988 AAATTATGCATATAAATATAA
1 AAATCATGCAAATAAATATAA
19672009 TAATAAAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
23 5 0.09
24 32 0.58
25 14 0.25
26 4 0.07
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (23 bp):
AAATCATGCAAATAAATATAAAA
Found at i:19672129 original size:13 final size:12
Alignment explanation
Indices: 19672095--19672144 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
19672085 AAGAAATAAG
19672095 AAAAT-AAAACAA
1 AAAATCAAAA-AA
*
19672107 AAAATCAAAAAT
1 AAAATCAAAAAA
19672119 AAAATCAAAAAA
1 AAAATCAAAAAA
*
19672131 GAAAA-GAAAAAA
1 -AAAATCAAAAAA
19672143 AA
1 AA
19672145 TCTATGATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 2 0.06
12 23 0.70
13 8 0.24
ACGTcount: A:0.82, C:0.06, G:0.04, T:0.08
Consensus pattern (12 bp):
AAAATCAAAAAA
Found at i:19672580 original size:19 final size:20
Alignment explanation
Indices: 19672541--19672581 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19672531 ATTTCAAATC
* *
19672541 TAAATAAAATCACAATCTTT
1 TAAAAAAAATCAAAATCTTT
19672561 TAAAAAAAATCAAAAT-TTT
1 TAAAAAAAATCAAAATCTTT
19672580 TA
1 TA
19672582 TATATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAAATCAAAATCTTT
Found at i:19673378 original size:20 final size:20
Alignment explanation
Indices: 19673350--19673408 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
19673340 ATAAATGCAA
*
19673350 TGTTTTTAATATGATGCATG
1 TGTTCTTAATATGATGCATG
19673370 TGTTCTTAATATGATGCATG
1 TGTTCTTAATATGATGCATG
19673390 TGTTCTTAATATGATGCAT
1 TGTTCTTAATATGATGCAT
19673409 TCATGAAGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (20 bp):
TGTTCTTAATATGATGCATG
Found at i:19678503 original size:23 final size:23
Alignment explanation
Indices: 19678477--19678539 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
19678467 AATCAAAATC
19678477 TACAAAATAAATAAATAGATTAA-
1 TACAAAATAAATAAATAGA-TAAG
* * *
19678500 TAC-ACATAAAAAAAT-TATAAG
1 TACAAAATAAATAAATAGATAAG
19678521 TTACAAAATAAATAAATAG
1 -TACAAAATAAATAAATAG
19678540 GTTAGTGCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 3 0.10
21 1 0.03
22 13 0.43
23 13 0.43
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.25
Consensus pattern (23 bp):
TACAAAATAAATAAATAGATAAG
Found at i:19679363 original size:24 final size:24
Alignment explanation
Indices: 19679251--19679373 Score: 135
Period size: 24 Copynumber: 5.1 Consensus size: 24
19679241 AAATCCATGC
*
19679251 AAAACATCATGC-AA-AAATATCAT
1 AAAA-ATCATGCAAATAAATATAAT
*
19679274 AATAAATCATGTAAATAAATATAAT
1 AA-AAATCATGCAAATAAATATAAT
*
19679299 AAAAATCATGCAAGTAATCATATAA-
1 AAAAATCATGCAAATAA--ATATAAT
* *
19679324 AAATATCTTGCAAATAAATATAAT
1 AAAAATCATGCAAATAAATATAAT
*
19679348 AAAAATTATGCAAATAAATATAAT
1 AAAAATCATGCAAATAAATATAAT
19679372 AA
1 AA
19679374 TAAAAATCCT
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
23 14 0.17
24 40 0.48
25 24 0.29
26 6 0.07
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.28
Consensus pattern (24 bp):
AAAAATCATGCAAATAAATATAAT
Found at i:19679479 original size:17 final size:19
Alignment explanation
Indices: 19679440--19679481 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
19679430 CAATCACAAT
*
19679440 TAAAAAATACTAAAATAGA
1 TAAAAAAAACTAAAATAGA
19679459 -AAAAAAAAC-AAAATA-A
1 TAAAAAAAACTAAAATAGA
19679475 TAAAAAA
1 TAAAAAA
19679482 TAAGAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 12 0.57
18 8 0.38
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (19 bp):
TAAAAAAAACTAAAATAGA
Found at i:19679483 original size:7 final size:7
Alignment explanation
Indices: 19679440--19679580 Score: 99
Period size: 7 Copynumber: 20.1 Consensus size: 7
19679430 CAATCACAAT
19679440 TAAAAAA
1 TAAAAAA
*
19679447 TACTAAAA
1 TA-AAAAA
19679455 TAGAAAAA
1 TA-AAAAA
*
19679463 -AAAACA
1 TAAAAAA
*
19679469 -AAATAA
1 TAAAAAA
19679475 TAAAAAA
1 TAAAAAA
*
19679482 TAAGAAA
1 TAAAAAA
*
19679489 T-CAAAA
1 TAAAAAA
*
19679495 TCAAAAA
1 TAAAAAA
*
19679502 TCAAAAA
1 TAAAAAA
*
19679509 TCAAAAA
1 TAAAAAA
*
19679516 TCAAAAA
1 TAAAAAA
*
19679523 TCAAAAA
1 TAAAAAA
* *
19679530 TCAAAGA
1 TAAAAAA
* *
19679537 TCAAAGA
1 TAAAAAA
*
19679544 TCAAAAA
1 TAAAAAA
19679551 TCAAAAAA
1 T-AAAAAA
19679559 TAAAAAA
1 TAAAAAA
19679566 TAAAAAA
1 TAAAAAA
19679573 TAAAAAA
1 TAAAAAA
19679580 T
1 T
19679581 GAGAACTTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
6 12 0.10
7 88 0.76
8 16 0.14
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:19679494 original size:14 final size:14
Alignment explanation
Indices: 19679477--19679580 Score: 131
Period size: 14 Copynumber: 7.4 Consensus size: 14
19679467 CAAAATAATA
19679477 AAAAAT-AAGAAATC
1 AAAAATCAA-AAATC
19679491 -AAAATCAAAAATC
1 AAAAATCAAAAATC
19679504 AAAAATCAAAAATC
1 AAAAATCAAAAATC
19679518 AAAAATCAAAAATC
1 AAAAATCAAAAATC
* *
19679532 AAAGATCAAAGATC
1 AAAAATCAAAAATC
*
19679546 AAAAATCAAAAAATA
1 AAAAATC-AAAAATC
* *
19679561 AAAAATAAAAAATA
1 AAAAATCAAAAATC
19679575 AAAAAT
1 AAAAAT
19679581 GAGAACTTGT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
13 10 0.12
14 60 0.74
15 11 0.14
ACGTcount: A:0.73, C:0.10, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAATCAAAAATC
Found at i:19679515 original size:21 final size:21
Alignment explanation
Indices: 19679477--19679580 Score: 131
Period size: 21 Copynumber: 5.0 Consensus size: 21
19679467 CAAAATAATA
19679477 AAAAAT-AAGAAATC-AAAATC
1 AAAAATCAA-AAATCAAAAATC
19679497 AAAAATCAAAAATCAAAAATC
1 AAAAATCAAAAATCAAAAATC
*
19679518 AAAAATCAAAAATCAAAGATC
1 AAAAATCAAAAATCAAAAATC
* *
19679539 AAAGATCAAAAATCAAAAAATA
1 AAAAATCAAAAATC-AAAAATC
* *
19679561 AAAAATAAAAAATAAAAAAT
1 AAAAATCAAAAATCAAAAAT
19679581 GAGAACTTGT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
20 11 0.15
21 47 0.64
22 16 0.22
ACGTcount: A:0.73, C:0.10, G:0.03, T:0.14
Consensus pattern (21 bp):
AAAAATCAAAAATCAAAAATC
Found at i:19680741 original size:12 final size:12
Alignment explanation
Indices: 19680726--19680750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19680716 TTTGATATTA
19680726 TTTTAATATAAT
1 TTTTAATATAAT
19680738 TTTTAATATAAT
1 TTTTAATATAAT
19680750 T
1 T
19680751 AAATAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTAATATAAT
Found at i:19683455 original size:233 final size:230
Alignment explanation
Indices: 19682889--19683615 Score: 650
Period size: 233 Copynumber: 3.1 Consensus size: 230
19682879 TATTGGTAAC
* * * * **
19682889 ATAAAATTTTAATTAATTATT-ATTTTGTA-AATACTAAGAAAAATAGCTAAAACTTAAAAAAAA
1 ATAAAATTTTAACTAATTATTGTTTTTGTACTATA-TAAAAAAAATAGCTAAAA---ATGAAAAA
* * *
19682952 ATTAAATTGATAACATAAACAAG-CACAAACATAAAATTAGTATCATTTGAC-TAAAAT-AAGTA
62 A-TAAATTGATAACATAAACAAGTTAGAAACATAAAATTAATAT-ATTTGACGT-AAATGAA-TA
* * * * * * * *
19683014 AAAAATATCGTAACATATTAAAAAAGAGTTATGACAATTTTAAACGTAATGAAAAA-TAAAAATA
123 AAAAGTGTCATAACACACTAAAAAAGAGCTATGACAATTCTAAACGTAAT-AAAAAGTAAGAATA
* * *
19683078 ATCATAAAAAGATAATATTGTAAAGCAAATAATTATGTTGAC-AT
187 ATCATAAAAATATATTATTGTAAA-TAAATAATTATGTTGACAAT
* *
19683122 CGTAAAATTTTAACTAATTATTGTTCTTGTACCTATATAAAAAAAATAGCTAAAAATGAAAAAAT
1 -ATAAAATTTTAACTAATTATTGTTTTTGTA-CTATATAAAAAAAATAGCTAAAAATGAAAAAAT
* * * * * *
19683187 AAATTGATAATATAAACCAGTTAGAAATATAAAATTAGTAT-TGTT-ATTGTAAAATGAATAAGA
64 AAATTGATAACATAAACAAGTTAGAAACATAAAATTAATATAT-TTGA-CGT-AAATGAATAAAA
* * * * * * * * *
19683250 AGTGTCATAATATATTGAGAAAGGGCTATGACAATTCTAATCGTAATAAAAAGTAAGAACAATTA
126 AGTGTCATAACACACTAAAAAAGAGCTATGACAATTCTAAACGTAATAAAAAGTAAGAATAATCA
* *
19683315 TAAAAATATATTATTATAATATAAATAATTATGATGACAAT
191 TAAAAATATATTATTGTAA-ATAAATAATTATGTTGACAAT
* * * * * *
19683356 ATAGAATTTTAAGTAATTATTGTTTTTGTA-TGTAT-AAGAAAATAGCTAGAAATTAAAAAATAA
1 ATAAAATTTTAACTAATTATTGTTTTTGTACTATATAAAAAAAATAGCTAAAAATGAAAAAATAA
* * *
19683419 ATTAGA-ACCATAAACAAGTTATAAGAAACGTAAAATTAATATCATTTGACGTAAATGAGTAAAA
66 ATT-GATAACATAAACAAG-T-T-AGAAACATAAAATTAATAT-ATTTGACGTAAATGAATAAAA
* * * * * *
19683483 AGTTTCATAACACGCTAAAAAAGAGTTATGACAATTCTAAACGTAATATAAGGTAAGAATAACCA
126 AGTGTCATAACACACTAAAAAAGAGCTATGACAATTCTAAACGTAATAAAAAGTAAGAATAATCA
* * *
19683548 TAACAATATATTATTGTAACATAAATAATTATGTTGGCAAC
191 TAAAAATATATTATTGTAA-ATAAATAATTATGTTGACAAT
*
19683589 ATAAAATTTTAACTAATTATTATTTTT
1 ATAAAATTTTAACTAATTATTGTTTTT
19683616 AAATATATAA
Statistics
Matches: 401, Mismatches: 74, Indels: 37
0.78 0.14 0.07
Matches are distributed among these distances:
230 37 0.09
231 9 0.02
232 27 0.07
233 272 0.68
234 28 0.07
235 8 0.02
236 17 0.04
237 3 0.01
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.32
Consensus pattern (230 bp):
ATAAAATTTTAACTAATTATTGTTTTTGTACTATATAAAAAAAATAGCTAAAAATGAAAAAATAA
ATTGATAACATAAACAAGTTAGAAACATAAAATTAATATATTTGACGTAAATGAATAAAAAGTGT
CATAACACACTAAAAAAGAGCTATGACAATTCTAAACGTAATAAAAAGTAAGAATAATCATAAAA
ATATATTATTGTAAATAAATAATTATGTTGACAAT
Found at i:19684907 original size:234 final size:230
Alignment explanation
Indices: 19684519--19684936 Score: 522
Period size: 234 Copynumber: 1.8 Consensus size: 230
19684509 TATTTTTATA
* * ** * * *
19684519 AAATATATAAGAAAATAGCTAAAATTTAAAGAACAAATAGGTAATATAAACAAGTGAAAAATTTA
1 AAATATATAACAAAATAACTAAAAGCTAAAAAACAAATAGGTAATATAAACAAGTGAAAAAATCA
* * * * *
19684584 TAAAATTTTATGCATTTGTTGTAAATAGATAAGAAGTGTTGTAAAACATTATAAAATAGTTATAA
66 TAAAATTGTATGCATTTGTTGTAAATAAATAAAAAGTGTCGTAAAACATTATAAAAAAGTTATAA
* * *
19684649 CAATTCTAAACGTAATGAAAAGTAA-AACCATTATAAGAATATATTATTATAACAAAAATAATTA
131 CAATTCTAAACGTAATGAAAAGTAAGAACAATAATAAGAAAATATTATTATAACAAAAATAATTA
19684713 AGTAACACAAATTTTTAATTAATAATTGTTTTCGT
196 AGTAACACAAATTTTTAATTAATAATTGTTTTCGT
* *
19684748 AAATATATAAACAAAATAACTAAAAGCTAAAAAACTAAT-GGTAATGTAAACAAGTGAAAAAGAA
1 AAATATAT-AACAAAATAACTAAAAGCTAAAAAACAAATAGGTAATATAAACAAGTG-AAAA-AA
**
19684812 TCATAAAATTCGTAT-CATTT-TATGTGAAATAAATAAAAAGTGTCGTAACGCA-TATTAAGAAA
63 TCATAAAATT-GTATGCATTTGT-TGT-AAATAAATAAAAAGTGTCGTAAAACATTA-T-A-AAA
* * *
19684874 AAGTTATAATAATTCTAAACGTAATGGAAAGTAAGAATAATAATAAGAAAATATTATTATAAC
122 AAGTTATAACAATTCTAAACGTAATGAAAAGTAAGAACAATAATAAGAAAATATTATTATAAC
19684937 GTAAATAAAT
Statistics
Matches: 157, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
229 24 0.15
230 29 0.18
231 20 0.13
232 25 0.16
233 1 0.01
234 34 0.22
235 24 0.15
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (230 bp):
AAATATATAACAAAATAACTAAAAGCTAAAAAACAAATAGGTAATATAAACAAGTGAAAAAATCA
TAAAATTGTATGCATTTGTTGTAAATAAATAAAAAGTGTCGTAAAACATTATAAAAAAGTTATAA
CAATTCTAAACGTAATGAAAAGTAAGAACAATAATAAGAAAATATTATTATAACAAAAATAATTA
AGTAACACAAATTTTTAATTAATAATTGTTTTCGT
Found at i:19690777 original size:38 final size:38
Alignment explanation
Indices: 19690735--19690814 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
19690725 ATATAAACTT
*
19690735 ATTCTTAATCCTT-ATCTATGCACACTTTTCTAATGATA
1 ATTCTT-ATCCTTAATCTATGCACACTTTTATAATGATA
* * *
19690773 ATTCTTATTCTTAATCTCTGCACACTTTTATAGTGATA
1 ATTCTTATCCTTAATCTATGCACACTTTTATAATGATA
19690811 ATTC
1 ATTC
19690815 ACATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (38 bp):
ATTCTTATCCTTAATCTATGCACACTTTTATAATGATA
Found at i:19691965 original size:2 final size:2
Alignment explanation
Indices: 19691958--19691997 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19691948 GTTCATCAAA
19691958 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19691998 ACACACACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19700384 original size:2 final size:2
Alignment explanation
Indices: 19700377--19700427 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19700367 AAGTTGTATG
19700377 CT CT CT CT CT CT CT CT CT 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
19700419 CT CT CT CT C
1 CT CT CT CT C
19700428 CCTCATTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:19708391 original size:6 final size:6
Alignment explanation
Indices: 19708380--19708422 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
19708370 TGAAGGGTGG
** *
19708380 GGCAAA GGCAAA GAAAAA GGCAAA GGTAAA GGCAAA GGCAAA G
1 GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA G
19708423 AAGTTGCCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.33, T:0.02
Consensus pattern (6 bp):
GGCAAA
Done.