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 105 of 133
Found at i:20559417 original size:24 final size:25
Alignment explanation
Indices: 20559338--20559418 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
20559328 TATAAATATC
*
20559338 TATTAATATATATTTAATAAAAAA-
1 TATTTATATATATTTAATAAAAAAT
*
20559362 TATTTAT-TATAATTAATTTAAAATAAT
1 TATTTATATATATTTAA--TAAAA-AAT
*
20559389 AATTTATAT-TATTTAATAAAAAAT
1 TATTTATATATATTTAATAAAAAAT
20559413 TATTTA
1 TATTTA
20559419 CTAATTATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
23 8 0.17
24 14 0.30
25 10 0.21
26 2 0.04
27 12 0.26
28 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTTATATATATTTAATAAAAAAT
Found at i:20562199 original size:14 final size:13
Alignment explanation
Indices: 20562192--20562388 Score: 142
Period size: 13 Copynumber: 15.2 Consensus size: 13
20562182 AACCTAATAT
*
20562192 CCTAAACCCT-AA
1 CCTAAATCCTAAA
*
20562204 CCTAAAACCTAAAA
1 CCTAAATCCT-AAA
*
20562218 CCTAAAACCTAAA
1 CCTAAATCCTAAA
*
20562231 CCCTAAACCCTAAA
1 -CCTAAATCCTAAA
20562245 TCCTAAATCCTAAA
1 -CCTAAATCCTAAA
*
20562259 CCTAAA-CCCAAA
1 CCTAAATCCTAAA
*
20562271 CCCCAAAT-CTAAA
1 -CCTAAATCCTAAA
20562284 CTCTAAA-CCTAAA
1 C-CTAAATCCTAAA
*
20562297 CCTTAAACCCTAAA
1 CC-TAAATCCTAAA
*
20562311 -CTAAATCTTAAA
1 CCTAAATCCTAAA
*
20562323 CCCAAAT-CTAAA
1 CCTAAATCCTAAA
20562335 CCTTAAA-CCTAAA
1 CC-TAAATCCTAAA
*
20562348 CCTCAAA-CTTAAA
1 CCT-AAATCCTAAA
*
20562361 CCTAAA-CCATAAC
1 CCTAAATCC-TAAA
*
20562374 CCTAAATCTTAAA
1 CCTAAATCCTAAA
20562387 CC
1 CC
20562389 AAAACACTCA
Statistics
Matches: 152, Mismatches: 18, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
12 36 0.24
13 73 0.48
14 43 0.28
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.20
Consensus pattern (13 bp):
CCTAAATCCTAAA
Found at i:20562288 original size:7 final size:6
Alignment explanation
Indices: 20562182--20562393 Score: 149
Period size: 7 Copynumber: 32.5 Consensus size: 6
20562172 TCAAATCCTC
20562182 AACCTA ATATCCTA AACCCT- AACCTAA AACCTAA AACCTAA AACCTA
1 AACCTA A-A-CCTA AA-CCTA AACCT-A AACCT-A AACCT-A AACCTA
* * *
20562229 AACCCTA AACCCTA AATCCTA AATCCTA AACCTA AACCCA AACCCCA AATCTA
1 AA-CCTA AA-CCTA AA-CCTA AA-CCTA AACCTA AACCTA AA-CCTA AACCTA
* * *
20562282 AACTCTA AACCTA AACCTTA AACCCTA AA-CTA AATCTTA AACCCA AATCTA
1 AAC-CTA AACCTA AACC-TA AA-CCTA AACCTA AA-CCTA AACCTA AACCTA
* * *
20562333 AACCTTA AACCTA AACCTCA AACTTA AACCTA AACCATA ACCCTA AATCTTA
1 AACC-TA AACCTA AACCT-A AACCTA AACCTA AACC-TA AACCTA AA-CCTA
*
20562385 AACCAA AAC
1 AACCTA AAC
20562394 ACTCACCTTA
Statistics
Matches: 172, Mismatches: 19, Indels: 30
0.78 0.09 0.14
Matches are distributed among these distances:
5 8 0.05
6 62 0.36
7 95 0.55
8 7 0.04
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.20
Consensus pattern (6 bp):
AACCTA
Found at i:20562379 original size:19 final size:19
Alignment explanation
Indices: 20562182--20562448 Score: 156
Period size: 19 Copynumber: 13.7 Consensus size: 19
20562172 TCAAATCCTC
20562182 AACCTAATATCCTAAACCCT-
1 AACCTAA-A-CCTAAACCCTA
*
20562202 AACCTAAAACCTAAAACCTAA
1 AACCT-AAACCTAAACCCT-A
20562223 AACCTAAACCCTAAACCCTA
1 AACCTAAA-CCTAAACCCTA
20562243 AATCCTAAATCCTAAA-CCTA
1 AA-CCTAAA-CCTAAACCCTA
* * *
20562263 AACCCAAACCCCAAA-TCTA
1 AACCTAAA-CCTAAACCCTA
*
20562282 AACTCTAAACCTAAACCTTA
1 AAC-CTAAACCTAAACCCTA
* *
20562302 AACCCTAAA-CTAAATCTTA
1 AA-CCTAAACCTAAACCCTA
* * *
20562321 AACCCAAATCTAAACCTTA
1 AACCTAAACCTAAACCCTA
*
20562340 AACCTAAACCTCAAA-CTTA
1 AACCTAAACCT-AAACCCTA
20562359 AACCTAAACC-ATAACCCTA
1 AACCTAAACCTA-AACCCTA
* * *
20562378 AATCTTAAACCAAAACACT-
1 AA-CCTAAACCTAAACCCTA
* * *
20562397 CACCTTAATACATAGACCCTA
1 AACC-TAA-ACCTAAACCCTA
* *
20562418 AA-CTAACCCCAAACCCTA
1 AACCTAAACCTAAACCCTA
*
20562436 AACC-AACCCTAAA
1 AACCTAAACCTAAA
20562449 ATCCTAAAAC
Statistics
Matches: 198, Mismatches: 31, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
17 1 0.01
18 26 0.13
19 86 0.43
20 54 0.27
21 31 0.16
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (19 bp):
AACCTAAACCTAAACCCTA
Found at i:20562526 original size:20 final size:20
Alignment explanation
Indices: 20562501--20562544 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
20562491 TTTTATTTTG
*
20562501 TTGTCACATGCATTCTTTAA
1 TTGTCACATGCAATCTTTAA
20562521 TTGT--CATGCAATCTTTAA
1 TTGTCACATGCAATCTTTAA
20562539 TTGTCA
1 TTGTCA
20562545 TGCATTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 17 0.81
20 4 0.19
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (20 bp):
TTGTCACATGCAATCTTTAA
Found at i:20562530 original size:18 final size:18
Alignment explanation
Indices: 20562507--20562551 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
20562497 TTTGTTGTCA
20562507 CATGCATTCTTTAATTGT
1 CATGCATTCTTTAATTGT
*
20562525 CATGCAATCTTTAATTGT
1 CATGCATTCTTTAATTGT
20562543 CATGCATTC
1 CATGCATTC
20562552 ATACTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (18 bp):
CATGCATTCTTTAATTGT
Found at i:20567195 original size:2 final size:2
Alignment explanation
Indices: 20567188--20567220 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20567178 TTGACTACTC
*
20567188 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20567221 ATTTGTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20567227 original size:99 final size:99
Alignment explanation
Indices: 20567124--20567319 Score: 338
Period size: 99 Copynumber: 2.0 Consensus size: 99
20567114 AACAGTTTAA
*
20567124 TTGTACATAAAATTATAAAAAATTTATAACTAAATAGTTTTATATTAGTGTAACTTGACTACTCA
1 TTGTACATAAAATTATAAAAAATTTAGAACTAAATAGTTTTATATTAGTGTAACTTGACTACTCA
* *
20567189 TATATATATATATATATATATATATCTATATAAT
66 TATATATAAATATATATATATATATATATATAAT
* *
20567223 TTGTACATGAAGTTATAAAAAATTTAGAACTAAATAGTTTTATATTAGTGTAACTTGACTACTCA
1 TTGTACATAAAATTATAAAAAATTTAGAACTAAATAGTTTTATATTAGTGTAACTTGACTACTCA
*
20567288 TATGTATAAATATATATATATATATATATATA
66 TATATATAAATATATATATATATATATATATA
20567320 TATTGAAGGG
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (99 bp):
TTGTACATAAAATTATAAAAAATTTAGAACTAAATAGTTTTATATTAGTGTAACTTGACTACTCA
TATATATAAATATATATATATATATATATATAAT
Found at i:20567304 original size:2 final size:2
Alignment explanation
Indices: 20567287--20567322 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
20567277 TTGACTACTC
* *
20567287 AT AT GT AT AA 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
20567323 TGAAGGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20567762 original size:2 final size:2
Alignment explanation
Indices: 20567757--20567782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20567747 ATGAGAGATC
20567757 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
20567783 GTATTAATCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20568287 original size:2 final size:2
Alignment explanation
Indices: 20568280--20568307 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20568270 AATTTGTTGA
20568280 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
20568308 GATTAGAGAT
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:20568640 original size:26 final size:25
Alignment explanation
Indices: 20568567--20568648 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
20568557 TATAAATATC
*
20568567 TATTAATATATATTTAATAAAAAAA
1 TATTTATATATATTTAATAAAAAAA
* *
20568592 TATTTAT-TATAATTAATTTAAAATAA
1 TATTTATATATATTTAA--TAAAAAAA
*
20568618 TAATTTATAT-TATTTAATAAAAAAT
1 T-ATTTATATATATTTAATAAAAAAA
20568643 TATTTA
1 TATTTA
20568649 CTAATTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
24 13 0.28
25 13 0.28
26 8 0.17
27 12 0.26
28 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTTATATATATTTAATAAAAAAA
Found at i:20569071 original size:10 final size:9
Alignment explanation
Indices: 20569027--20569070 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
20569017 TAAACACTCT
20569027 AAAAATTAGA
1 AAAAATTA-A
*
20569037 AAATAAGTTTA
1 AAA-AA-TTAA
20569048 AAAAATTAA
1 AAAAATTAA
20569057 AAAAATTAA
1 AAAAATTAA
20569066 AAAAA
1 AAAAA
20569071 AATTCTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 17 0.57
10 5 0.17
11 6 0.20
12 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (9 bp):
AAAAATTAA
Found at i:20571496 original size:7 final size:7
Alignment explanation
Indices: 20571415--20571597 Score: 120
Period size: 7 Copynumber: 27.9 Consensus size: 7
20571405 AACCTAATAT
20571415 CCTAAAC
1 CCTAAAC
20571422 CCT-AA-
1 CCTAAAC
*
20571427 CCTAAAA
1 CCTAAAC
*
20571434 CCTAAAA
1 CCTAAAC
*
20571441 CCTAAAA
1 CCTAAAC
*
20571448 CCTAAAA
1 CCTAAAC
20571455 CCTAAAC
1 CCTAAAC
*
20571462 CCAAAAC
1 CCTAAAC
*
20571469 CCTAAAT
1 CCTAAAC
*
20571476 CCTAAAT
1 CCTAAAC
20571483 CCTAAAC
1 CCTAAAC
20571490 CCTAAA-
1 CCTAAAC
*
20571496 CGTAAAC
1 CCTAAAC
20571503 CC-AAAC
1 CCTAAAC
*
20571509 CCCAAA-
1 CCTAAAC
*
20571515 TCTAAAC
1 CCTAAAC
*
20571522 TCTAAA-
1 CCTAAAC
20571528 CCTAAAC
1 CCTAAAC
**
20571535 TTTAAAC
1 CCTAAAC
20571542 CCTAAA-
1 CCTAAAC
*
20571548 -CTAAAT
1 CCTAAAC
*
20571554 CTTAAAC
1 CCTAAAC
20571561 CC-AAA-
1 CCTAAAC
*
20571566 TCTAAAC
1 CCTAAAC
*
20571573 CTTAAA-
1 CCTAAAC
20571579 CCTAAAC
1 CCTAAAC
*
20571586 CAT-AAC
1 CCTAAAC
20571592 CCTAAA
1 CCTAAA
20571598 TCTTACACCA
Statistics
Matches: 141, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
5 9 0.06
6 40 0.28
7 92 0.65
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:20571583 original size:13 final size:13
Alignment explanation
Indices: 20571425--20571602 Score: 82
Period size: 13 Copynumber: 13.5 Consensus size: 13
20571415 CCTAAACCCT
*
20571425 AACCTAAAACCTAA
1 AACCTTAAACCT-A
*
20571439 AACCTAAAACCTAA
1 AACCTTAAACCT-A
*
20571453 AACC-TAAACCCAA
1 AACCTTAAA-CCTA
*
20571466 AACCCTAAATCCTA
1 AACCTTAAA-CCTA
20571480 AATCC-TAAACCCTA
1 AA-CCTTAAA-CCTA
* *
20571494 AA-CGTAAACCCA
1 AACCTTAAACCTA
** *
20571506 AACCCCAAATCTA
1 AACCTTAAACCTA
20571519 AA-CTCTAAACCTA
1 AACCT-TAAACCTA
*
20571532 AACTTTAAACCCTA
1 AACCTTAAA-CCTA
*
20571546 AA-C-TAAATCTTA
1 AACCTTAAA-CCTA
* *
20571558 AACC-CAAATCTA
1 AACCTTAAACCTA
20571570 AACCTTAAACCTA
1 AACCTTAAACCTA
* *
20571583 AACCATAACCCTA
1 AACCTTAAACCTA
*
20571596 AATCTTA
1 AACCTTA
20571603 CACCAAAACA
Statistics
Matches: 128, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
12 22 0.17
13 58 0.45
14 46 0.36
15 2 0.02
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (13 bp):
AACCTTAAACCTA
Found at i:20571592 original size:19 final size:19
Alignment explanation
Indices: 20571415--20571597 Score: 52
Period size: 20 Copynumber: 9.0 Consensus size: 19
20571405 AACCTAATAT
* *
20571415 CCTAAACCCTAACCTAAAA
1 CCTAAACCATAACCTTAAA
* *
20571434 CCTAAAACCTAAAACCTAAAA
1 CCT-AAACC-ATAACCTTAAA
* *
20571455 CCTAAACCCAAAACCCTAAA
1 CCTAAA-CCATAACCTTAAA
*
20571475 TCCTAAATCC-TAAACCCTAAA
1 -CCTAAA-CCAT-AACCTTAAA
*
20571496 CGTAAACCCA-AACCCCAAATCTAAA
1 CCTAAA-CCATAA--CC---T-TAAA
*
20571521 CTCTAAACC-TAAACTTTAAA
1 C-CTAAACCAT-AACCTTAAA
* *
20571541 CCCTAAACTA-AATCTTAAA
1 -CCTAAACCATAACCTTAAA
* *
20571560 CCCAAATC-TAAACCTTAAA
1 CCTAAACCAT-AACCTTAAA
*
20571579 CCTAAACCATAACCCTAAA
1 CCTAAACCATAACCTTAAA
20571598 TCTTACACCA
Statistics
Matches: 123, Mismatches: 21, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
18 5 0.04
19 34 0.28
20 35 0.28
21 35 0.28
24 1 0.01
25 7 0.06
26 6 0.05
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.19
Consensus pattern (19 bp):
CCTAAACCATAACCTTAAA
Found at i:20571637 original size:27 final size:26
Alignment explanation
Indices: 20571606--20571656 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
20571596 AATCTTACAC
20571606 CAAAACACTCACGTTAAACCCTAAAAT
1 CAAAACACTCA-GTTAAACCCTAAAAT
* * *
20571633 CAAAACGCTTAGTTAGACCCTAAA
1 CAAAACACTCAGTTAAACCCTAAA
20571657 CTAACCCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.20
Consensus pattern (26 bp):
CAAAACACTCAGTTAAACCCTAAAAT
Found at i:20571763 original size:20 final size:20
Alignment explanation
Indices: 20571738--20571781 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
20571728 TTTTATTTTG
*
20571738 TTGTCACATGCATTCTTTAA
1 TTGTCACATGCAATCTTTAA
*
20571758 TTGT--CATGCAATCTTTAG
1 TTGTCACATGCAATCTTTAA
20571776 TTGTCA
1 TTGTCA
20571782 TGCATTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
18 16 0.80
20 4 0.20
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (20 bp):
TTGTCACATGCAATCTTTAA
Found at i:20571767 original size:18 final size:18
Alignment explanation
Indices: 20571744--20571788 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20571734 TTTGTTGTCA
20571744 CATGCATTCTTTAATTGT
1 CATGCATTCTTTAATTGT
* *
20571762 CATGCAATCTTTAGTTGT
1 CATGCATTCTTTAATTGT
20571780 CATGCATTC
1 CATGCATTC
20571789 ATACTTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (18 bp):
CATGCATTCTTTAATTGT
Found at i:20576165 original size:20 final size:18
Alignment explanation
Indices: 20576074--20576166 Score: 73
Period size: 18 Copynumber: 4.9 Consensus size: 18
20576064 TGAAAACTAG
*
20576074 TAAAATTAAATAAAAAAAT
1 TAAAATAAAAT-AAAAAAT
* *
20576093 CAAAAATAAAATAAAAACT
1 -TAAAATAAAATAAAAAAT
*
20576112 TAAGAA-AATAA-AAAAAAA
1 TAA-AATAA-AATAAAAAAT
*
20576130 TAAAATAAAATCAAAAAT
1 TAAAATAAAATAAAAAAT
20576148 TAAAATTAAAATGAAAAAA
1 TAAAA-TAAAAT-AAAAAA
20576167 GAAAACTTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
17 4 0.07
18 24 0.41
19 16 0.28
20 14 0.24
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.19
Consensus pattern (18 bp):
TAAAATAAAATAAAAAAT
Found at i:20576165 original size:36 final size:36
Alignment explanation
Indices: 20576081--20576150 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
20576071 TAGTAAAATT
*
20576081 AAATAAAAAAATCA-AAAATAAAATAAAAACTTAAGA
1 AAATAAAAAAA-AATAAAATAAAATAAAAACTTAAGA
20576117 AAATAAAAAAAAATAAAATAAAATCAAAAA-TTAA
1 AAATAAAAAAAAATAAAATAAAAT-AAAAACTTAA
20576151 AATTAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 1 0.03
36 25 0.81
37 5 0.16
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.17
Consensus pattern (36 bp):
AAATAAAAAAAAATAAAATAAAATAAAAACTTAAGA
Found at i:20576171 original size:19 final size:18
Alignment explanation
Indices: 20576124--20576171 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
20576114 AGAAAATAAA
20576124 AAAAAATAAAATAAAATC
1 AAAAAATAAAATAAAATC
* *
20576142 AAAAATTAAAATTAAAATG
1 AAAAAATAAAA-TAAAATC
*
20576161 AAAAAAGAAAA
1 AAAAAATAAAA
20576172 CTTGCGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (18 bp):
AAAAAATAAAATAAAATC
Found at i:20576577 original size:21 final size:21
Alignment explanation
Indices: 20576553--20576593 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20576543 AATCCTAATT
*
20576553 CCCATAAACCTAAAACTAAAC
1 CCCAAAAACCTAAAACTAAAC
* *
20576574 CCCAAAAATCTAAATCTAAA
1 CCCAAAAACCTAAAACTAAA
20576594 TCCAAAATCT
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:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (21 bp):
CCCAAAAACCTAAAACTAAAC
Found at i:20577021 original size:3 final size:3
Alignment explanation
Indices: 20577013--20577161 Score: 77
Period size: 3 Copynumber: 51.0 Consensus size: 3
20577003 TATTGTAAGG
* * *
20577013 ATA ATA ATA ATA ATA ATG ATA AT- CTA ATA ATA ATA GTA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
20577058 ATA AT- ATA CCATA GT- ATA ATA ATA ATA ATA ATA AT- ATG AT- ATA
1 ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
20577101 ACA TTA TATA ATA CACTA ATA ATA GTA ATA CGAT- ATA ATA ATA CT-
1 ATA ATA -ATA ATA -A-TA ATA ATA ATA ATA --ATA ATA ATA ATA ATA
20577146 ATA ATA A-A AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA
20577162 CAATGTAACA
Statistics
Matches: 112, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
2 19 0.17
3 82 0.73
4 4 0.04
5 7 0.06
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20577052 original size:17 final size:18
Alignment explanation
Indices: 20577012--20577090 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 18
20577002 ATATTGTAAG
20577012 GATAATAATAATAATAAT-
1 GATAAT-ATAATAATAATA
*
20577030 GATAATCTAATAATAATA
1 GATAATATAATAATAATA
20577048 G-TAATATAAT-ATAATATA
1 GATAATATAATAAT-A-ATA
* *
20577066 CCATAGTATAATAATAATA
1 -GATAATATAATAATAATA
20577085 -ATAATA
1 GATAATA
20577091 ATATGATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.04
17 24 0.48
18 10 0.20
19 3 0.06
20 9 0.18
21 2 0.04
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (18 bp):
GATAATATAATAATAATA
Found at i:20577121 original size:37 final size:34
Alignment explanation
Indices: 20577013--20577161 Score: 130
Period size: 35 Copynumber: 4.4 Consensus size: 34
20577003 TATTGTAAGG
*
20577013 ATAATAATAATAATAATGATA-ATC-TA-ATAATA
1 ATAATAATAATAAT-ATGATATAACATATATAATA
* * *
20577045 ATAGTAAT-ATAATATAATATACCATAGTATAATA
1 ATAATAATAATAATATGATATAACATA-TATAATA
20577079 ATAATAATAATAATATGATATAACATTATATAATA
1 ATAATAATAATAATATGATATAACA-TATATAATA
* * *
20577114 CACTAATAATAGTAATACGATATAATAATACTATAATA
1 -A-TAATAATAATAATATGATATAA-CATA-TATAATA
20577152 A-AAT-ATAATA
1 ATAATAATAATA
20577162 CAATGTAACA
Statistics
Matches: 97, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
30 5 0.05
31 7 0.07
32 9 0.09
34 18 0.19
35 24 0.25
36 3 0.03
37 23 0.24
38 8 0.08
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.34
Consensus pattern (34 bp):
ATAATAATAATAATATGATATAACATATATAATA
Found at i:20577161 original size:40 final size:40
Alignment explanation
Indices: 20577039--20577161 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 40
20577029 TGATAATCTA
* * * *
20577039 ATAATAATAGTAATATAATATAAT-ATACCATAGTATAAT
1 ATAATAATAGTAATATGATATAATAATACTATAATAAAAT
* * * *
20577078 AATAATAATAATAATATGATATAACATTA-TATAAT-ACA-
1 -ATAATAATAGTAATATGATATAATAATACTATAATAAAAT
* *
20577116 CTAATAATAGTAATACGATATAATAATACTATAATAAAAT
1 ATAATAATAGTAATATGATATAATAATACTATAATAAAAT
20577156 ATAATA
1 ATAATA
20577162 CAATGTAACA
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
37 23 0.36
38 6 0.09
39 3 0.05
40 30 0.47
41 2 0.03
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (40 bp):
ATAATAATAGTAATATGATATAATAATACTATAATAAAAT
Found at i:20577781 original size:120 final size:120
Alignment explanation
Indices: 20577672--20577919 Score: 277
Period size: 120 Copynumber: 2.1 Consensus size: 120
20577662 GAGGTTGAAT
* * * * * **
20577672 ATGGCTGATTGAAATTGAACCACCAA-TCAAGAAATGATTTAGACTAAGCTGAGATCAAATGATT
1 ATGGCTAACTGAAATAGAA-CACCAAGTCAAGAAATGATTTAGACTAAGCTGAAATCAAATAACC
* * *
20577736 AAGATGAAACCACCAGTCAAAAAGATAAAACAATCAAGACTGAGTCAAGGTCAAAG
65 AACATGAAACCACAAATCAAAAAGATAAAACAATCAAGACTGAGTCAAGGTCAAAG
* ** *
20577792 ATGGCTAACTGAGATAGAACTGCAAGTCAAGAAATGATTTGGACTAAGCTGAAATCAAATAACCA
1 ATGGCTAACTGAAATAGAACACCAAGTCAAGAAATGATTTAGACTAAGCTGAAATCAAATAACCA
* * * * *
20577857 ACATGAAACCACAAATTAGAAAGATAAAACAA-CTAAGAAC-GATTCGAGGTCGAAG
66 ACATGAAACCACAAATCAAAAAGATAAAACAATC-AAG-ACTGAGTCAAGGTCAAAG
20577912 ATGGCTAA
1 ATGGCTAA
20577920 TCAGGATGAA
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
119 5 0.05
120 99 0.93
121 2 0.02
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (120 bp):
ATGGCTAACTGAAATAGAACACCAAGTCAAGAAATGATTTAGACTAAGCTGAAATCAAATAACCA
ACATGAAACCACAAATCAAAAAGATAAAACAATCAAGACTGAGTCAAGGTCAAAG
Found at i:20577933 original size:120 final size:120
Alignment explanation
Indices: 20577698--20577954 Score: 306
Period size: 120 Copynumber: 2.1 Consensus size: 120
20577688 GAACCACCAA
* * ** * * *
20577698 TCAAGAAATGATTTAGACTAAGCTGAGATCAAATGATTAAGATGAAACCACCAGTCAAAAAGATA
1 TCAAGAAATGATTTAGACTAAGCTGAAATCAAATAACCAACATGAAACCACAAATCAAAAAGATA
*
20577763 AAACAATCAAGACTGAGTCAAGGTCAAAGATGGCTAACTGAGATAGAACTGCAAG
66 AAACAATCAAGACTGAGTCAAGGTCAAAGATGGCTAACAGAGATAGAACTGCAAG
* * *
20577818 TCAAGAAATGATTTGGACTAAGCTGAAATCAAATAACCAACATGAAACCACAAATTAGAAAGATA
1 TCAAGAAATGATTTAGACTAAGCTGAAATCAAATAACCAACATGAAACCACAAATCAAAAAGATA
* * *
20577883 AAACAA-CTAAGAAC-GATTCGAGGTCGAAGATGGCTAATCAG-GAT-GAAACTGCAAG
66 AAACAATC-AAG-ACTGAGTCAAGGTCAAAGATGGCTAA-CAGAGATAG-AACTGCAAG
* *
20577938 TCAGGAAATGATCTAGA
1 TCAAGAAATGATTTAGA
20577955 TTGAGCCAAT
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
119 2 0.02
120 110 0.95
121 4 0.03
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (120 bp):
TCAAGAAATGATTTAGACTAAGCTGAAATCAAATAACCAACATGAAACCACAAATCAAAAAGATA
AAACAATCAAGACTGAGTCAAGGTCAAAGATGGCTAACAGAGATAGAACTGCAAG
Found at i:20578338 original size:51 final size:51
Alignment explanation
Indices: 20578241--20578364 Score: 126
Period size: 51 Copynumber: 2.4 Consensus size: 51
20578231 CAAAGGTTCT
* * * **
20578241 AGATTCACAAAGATTTTAGGTTCGCAAGGATTTTAAAATTTGTAAGAATA-AA
1 AGATTCGC-AAGATTTTAAGTTCGCAAGGACTTTAAAATTCATAAGAA-AGAA
* *
20578293 A-ATTCGCAAGGATTTTAAGTTCGCAAGGACTTTCAGATTCATAAGAAAGAA
1 AGATTCGCAA-GATTTTAAGTTCGCAAGGACTTTAAAATTCATAAGAAAGAA
* *
20578344 AGATTAGCAAGATTTCAAGTT
1 AGATTCGCAAGATTTTAAGTT
20578365 TCACAAAGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
50 3 0.05
51 49 0.82
52 8 0.13
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (51 bp):
AGATTCGCAAGATTTTAAGTTCGCAAGGACTTTAAAATTCATAAGAAAGAA
Found at i:20578391 original size:35 final size:33
Alignment explanation
Indices: 20578352--20578416 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
20578342 AAAGATTAGC
* *
20578352 AAGATTTCAAGTTTCACAAAGGTTCTAAATTTGCA
1 AAGATTTC-AGGTTCACAAA-ATTCTAAATTTGCA
20578387 AAGATTTCAGGTTCACAAAATTCTAAATTT
1 AAGATTTCAGGTTCACAAAATTCTAAATTT
20578417 CACAAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 10 0.36
34 10 0.36
35 8 0.29
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
AAGATTTCAGGTTCACAAAATTCTAAATTTGCA
Found at i:20579646 original size:20 final size:20
Alignment explanation
Indices: 20579621--20579676 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
20579611 ACCTAAACAA
20579621 TTTCTCTTTATTTTTT-ACTT
1 TTTCTCTTT-TTTTTTCACTT
*
20579641 TTTCTCTTTTTTTTTTCCCTT
1 TTTCTC-TTTTTTTTTCACTT
20579662 TTTCTCTTTTTTTTT
1 TTTCTCTTTTTTTTT
20579677 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTCTTTTTTTTTCACTT
Found at i:20579684 original size:20 final size:20
Alignment explanation
Indices: 20579621--20579677 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
20579611 ACCTAAACAA
*
20579621 TTTCTCTTTATTTTTTACTT
1 TTTCTCTTTTTTTTTTACTT
*
20579641 TTTCTCTTTTTTTTTTCCCTT
1 TTTCTCTTTTTTTTTT-ACTT
20579662 TTTCTCTTTTTTTTTT
1 TTTCTCTTTTTTTTTT
20579678 TTTTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTCTTTTTTTTTTACTT
Found at i:20584048 original size:49 final size:49
Alignment explanation
Indices: 20583992--20584085 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
20583982 TCCATAAACC
* * *
20583992 TATTTGAAAAGATTTTTTCTTTTTTTTTTGTTTCTT-TATTTTTCAAAGT
1 TATTTGAAAAGATTTTTT-TTTATTCTTTGCTTCTTCTATTTTTCAAAGT
20584041 TATTTGAAAAGATTTTTTTTTATTCTTTGCTTCTTCTATTTTTCA
1 TATTTGAAAAGATTTTTTTTTATTCTTTGCTTCTTCTATTTTTCA
20584086 GAAAAGTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 14 0.34
49 27 0.66
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (49 bp):
TATTTGAAAAGATTTTTTTTTATTCTTTGCTTCTTCTATTTTTCAAAGT
Found at i:20584136 original size:24 final size:23
Alignment explanation
Indices: 20584109--20584179 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
20584099 TCTGAAAACC
20584109 AATAAAATAAAATAAAAAATTGAA
1 AATAAAATAAAATAAAAAATT-AA
20584133 AATAAAATAAAA-ATAAAAA-TAA
1 AATAAAATAAAATA-AAAAATTAA
* *
20584155 AAGAAAATAGAATCAAAAAA-TAA
1 AATAAAATAAAAT-AAAAAATTAA
20584178 AA
1 AA
20584180 GGAAAATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 18 0.43
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (23 bp):
AATAAAATAAAATAAAAAATTAA
Found at i:20584179 original size:5 final size:5
Alignment explanation
Indices: 20584109--20584163 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
20584099 TCTGAAAACC
*
20584109 AATAA AATAA AAT-A AA-AA ATTGAA AATAA AATAAA AATAAA AATAA
1 AATAA AATAA AATAA AATAA AAT-AA AATAA AAT-AA AAT-AA AATAA
*
20584155 AAGAA AATA
1 AATAA AATA
20584164 GAATCAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 5 0.12
5 22 0.52
6 15 0.36
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:20584578 original size:22 final size:20
Alignment explanation
Indices: 20584538--20584580 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
20584528 AATCCCAAAA
20584538 CTTCCAAAATTTCCAAATTT
1 CTTCCAAAATTTCCAAATTT
*
20584558 CTTCCAAACATTTTCAGAATTT
1 CTTCCAAA-ATTTCCA-AATTT
20584580 C
1 C
20584581 AATCCCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (20 bp):
CTTCCAAAATTTCCAAATTT
Found at i:20585037 original size:3 final size:3
Alignment explanation
Indices: 20585000--20585128 Score: 96
Period size: 3 Copynumber: 45.3 Consensus size: 3
20584990 AAGAAAGAAA
* * ** *
20585000 AAT AAT AAA AAT AA- AAT AAA AAT CGT AAA AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
20585047 ACT AAT -CT AAT AAT AAT AGT AAT -AT AAT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
20585090 -AT ACCAT AGT -AT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20585129 GTCTTCGGCT
Statistics
Matches: 97, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
2 16 0.16
3 78 0.80
5 3 0.03
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20585059 original size:17 final size:16
Alignment explanation
Indices: 20585030--20585128 Score: 96
Period size: 17 Copynumber: 6.1 Consensus size: 16
20585020 AATCGTAAAA
20585030 ATAATAATAATAATAAT
1 ATAAT-ATAATAATAAT
*
20585047 ACTAATCTAATAATAAT
1 A-TAATATAATAATAAT
20585064 AGTAATATAAT-ATAAT
1 A-TAATATAATAATAAT
**
20585080 ATAATATAAT-ATACC
1 ATAATATAATAATAAT
*
20585095 ATAGTATAATAATAAT
1 ATAATATAATAATAAT
20585111 AATAATAATAAT-ATAAT
1 -ATAAT-ATAATAATAAT
20585128 A
1 A
20585129 GTCTTCGGCT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
15 21 0.30
16 10 0.14
17 29 0.42
18 9 0.13
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
ATAATATAATAATAAT
Found at i:20589631 original size:16 final size:16
Alignment explanation
Indices: 20589607--20589644 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
20589597 TGTTTTTTTA
20589607 TTATTTTTTTAC-TTT
1 TTATTTTTTTACATTT
*
20589622 TTAGTTTTTTACATTT
1 TTATTTTTTTACATTT
20589638 TTATTTT
1 TTATTTT
20589645 CCAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (16 bp):
TTATTTTTTTACATTT
Found at i:20590801 original size:14 final size:13
Alignment explanation
Indices: 20590777--20590817 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
20590767 AGATTGTATT
20590777 TTTTAAAATAATA
1 TTTTAAAATAATA
*
20590790 TTTTAAACATAATT
1 TTTTAAA-ATAATA
20590804 TTTTAAAA-AATA
1 TTTTAAAATAATA
20590816 TT
1 TT
20590818 AATAAAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.20
13 8 0.32
14 12 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTTAAAATAATA
Found at i:20591583 original size:29 final size:30
Alignment explanation
Indices: 20591529--20591606 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
20591519 AGTCTTAAAT
*
20591529 TATTTAAATAAATTTTTATATTTTTA-CTA
1 TATTCAAATAAATTTTTATATTTTTATCTA
* *
20591558 TATTCAAATAAATTTTTATCA-TTTTATTTG
1 TATTCAAATAAATTTTTAT-ATTTTTATCTA
*
20591588 TATTCGAATAAATTTTTAT
1 TATTCAAATAAATTTTTAT
20591607 TTTAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (30 bp):
TATTCAAATAAATTTTTATATTTTTATCTA
Found at i:20591815 original size:30 final size:30
Alignment explanation
Indices: 20591750--20591839 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 30
20591740 TGTTAATAGC
*
20591750 TTATTTAAATATAAATTAAAAGTTAAGGGT
1 TTATTTAAATATAAATTAAAAGTTAAGGAT
* * * * *
20591780 ATATTTTAATATAATTTAAAATTTAAGTAT
1 TTATTTAAATATAAATTAAAAGTTAAGGAT
* * * * *
20591810 TTATTTGAGTGTAAATTAAAGGCTAAGGAT
1 TTATTTAAATATAAATTAAAAGTTAAGGAT
20591840 CCATTTAGGT
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.42
Consensus pattern (30 bp):
TTATTTAAATATAAATTAAAAGTTAAGGAT
Found at i:20592853 original size:3 final size:3
Alignment explanation
Indices: 20592847--20592871 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20592837 CAACAACAAC
20592847 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
20592872 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20594128 original size:18 final size:16
Alignment explanation
Indices: 20594097--20594130 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
20594087 ATCATTTATG
20594097 TTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTCAA
20594113 TTTTTGTTTCTTTTTCAA
1 TTTTT-TTT-TTTTTCAA
20594131 GAAAGTGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTTTTTCAA
Found at i:20595538 original size:24 final size:25
Alignment explanation
Indices: 20595506--20595553 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
20595496 TCATCAATGA
20595506 TTATCATTTACAAA-GAATGTTATT
1 TTATCATTTACAAATGAATGTTATT
* **
20595530 TTATTATTTTTAAATGAATGTTAT
1 TTATCATTTACAAATGAATGTTAT
20595554 AATAAATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (25 bp):
TTATCATTTACAAATGAATGTTATT
Found at i:20597007 original size:16 final size:16
Alignment explanation
Indices: 20596988--20597030 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
20596978 TATTTATTTG
*
20596988 TTAAAATTATTATTAT
1 TTAAAATTATTATAAT
20597004 TTAAAATT-TATATAAT
1 TTAAAATTAT-TATAAT
20597020 TT-AAATTATTA
1 TTAAAATTATTA
20597031 ATGTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAATTATTATAAT
Found at i:20597014 original size:17 final size:17
Alignment explanation
Indices: 20596974--20597024 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
20596964 AAAAAATTAT
20596974 AATTTATTTATT-TGTTAA
1 AATTTA-TTATTAT-TTAA
20596992 AA-TTATTATTATTTAA
1 AATTTATTATTATTTAA
*
20597008 AATTTA-TATAATTTAA
1 AATTTATTATTATTTAA
20597024 A
1 A
20597025 TTATTAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 21 0.70
17 7 0.23
18 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTATTATTATTTAA
Found at i:20597956 original size:208 final size:207
Alignment explanation
Indices: 20597599--20598015 Score: 755
Period size: 208 Copynumber: 2.0 Consensus size: 207
20597589 TATATTGAAT
*
20597599 GAACTTTGAGCTGGAAAGCAAATGGGAATCTAAACATGACATGTGAAACATAATGGTGTATAAAG
1 GAACTTTGAGCTGGAAAGCAAATGGGAATCCAAACATGACATGTGAAACATAATGGTGTATAAAG
* *
20597664 CAGATGGGACTCTTTACATAAGTGAAATTTCAAGTTAAAAAGCAGTCTCCATTGGAATCCCAATG
66 CAAATGGGACTCTTTACATAAGTGAAATTTCAAGTCAAAAAGCAGTCTCCATTGGAATCCCAATG
*
20597729 TGAGTGGCATGCCCCAAT-GGGTCCATTGTGAGTTCAACTTTTTCTCAAACTCAGGTAATTCCAA
131 TGAGCGGCATGCCCCAATGGGGT-CATTGTGAGTTCAACTTTTTCTCAAACTCAGGTAATTCCAA
20597793 TTAACCCAACTGC
195 TTAACCCAACTGC
20597806 GAACTTTGAGCTGGAAAGCAAATGGGAATCCAAAGCATGACATGTGAAACATAATGGTGTATAAA
1 GAACTTTGAGCTGGAAAGCAAATGGGAATCCAAA-CATGACATGTGAAACATAATGGTGTATAAA
* *
20597871 GCAAATGGGACTCTTTACGTAAGTGAAATTTCAAGTCAAAAAGCAGTGTCCATTGGAATCCCAAT
65 GCAAATGGGACTCTTTACATAAGTGAAATTTCAAGTCAAAAAGCAGTCTCCATTGGAATCCCAAT
20597936 GTGAGCGGCATGCCCCAATGGGGTCATTGTGAGTTCAACTTTTTCTCAAACTCAGGTAATTCCAA
130 GTGAGCGGCATGCCCCAATGGGGTCATTGTGAGTTCAACTTTTTCTCAAACTCAGGTAATTCCAA
20598001 TTAACCCAACTGC
195 TTAACCCAACTGC
20598014 GA
1 GA
20598016 GTCCGCGACC
Statistics
Matches: 202, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
207 33 0.16
208 165 0.82
209 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (207 bp):
GAACTTTGAGCTGGAAAGCAAATGGGAATCCAAACATGACATGTGAAACATAATGGTGTATAAAG
CAAATGGGACTCTTTACATAAGTGAAATTTCAAGTCAAAAAGCAGTCTCCATTGGAATCCCAATG
TGAGCGGCATGCCCCAATGGGGTCATTGTGAGTTCAACTTTTTCTCAAACTCAGGTAATTCCAAT
TAACCCAACTGC
Found at i:20599431 original size:27 final size:27
Alignment explanation
Indices: 20599401--20599462 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
20599391 TTAAATCTGA
* *
20599401 AAAATAGAT-AAATATTAATCATTTGTC
1 AAAATA-ATAAAATATTAATCAATTGCC
*
20599428 AAAATTAATAAAATATTAGTCAATTGCC
1 AAAA-TAATAAAATATTAATCAATTGCC
20599456 AAAATAA
1 AAAATAA
20599463 ATTTAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.32
Consensus pattern (27 bp):
AAAATAATAAAATATTAATCAATTGCC
Found at i:20603374 original size:22 final size:22
Alignment explanation
Indices: 20603330--20603374 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20603320 TACTAATATA
* * *
20603330 TATTTTTTTTATTTTTATCTTT
1 TATTTTATTTATTTTCATATTT
*
20603352 TATTTTATTTATTTTCGTATTT
1 TATTTTATTTATTTTCATATTT
20603374 T
1 T
20603375 TATATATCTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (22 bp):
TATTTTATTTATTTTCATATTT
Found at i:20604306 original size:12 final size:11
Alignment explanation
Indices: 20604284--20604330 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
20604274 TCTCTTTGAA
20604284 TTTTT-TTTAT
1 TTTTTATTTAT
*
20604294 TTCTTTGTTTAT
1 TT-TTTATTTAT
20604306 TTGTTTATTTTAT
1 TT-TTTA-TTTAT
20604319 TTTTTATTTAT
1 TTTTTATTTAT
20604330 T
1 T
20604331 AGATTAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 2 0.06
11 9 0.28
12 14 0.44
13 7 0.22
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:20604614 original size:60 final size:58
Alignment explanation
Indices: 20604398--20604741 Score: 453
Period size: 60 Copynumber: 5.7 Consensus size: 58
20604388 AAAAAATTCT
20604398 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-T---AG-AAAATAAATTT-C
20604462 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TAGAAAATAAATTTC
* * *
20604520 -CAAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAG-AAATAAATTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-AGAAAATAAATTTC
*
20604577 AAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTC
1 --AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT--AAATTTC
* *
20604639 -AAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTC
1 AAAAAAAATA-TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT--AAATTTC
* *
20604699 CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
20604742 CTACAAAAAA
Statistics
Matches: 262, Mismatches: 9, Indels: 22
0.89 0.03 0.08
Matches are distributed among these distances:
56 1 0.00
57 52 0.20
58 1 0.00
59 20 0.08
60 125 0.48
61 11 0.04
62 7 0.03
64 45 0.17
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (58 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAGAAAATAAATTTC
Found at i:20608410 original size:15 final size:16
Alignment explanation
Indices: 20608387--20608426 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
20608377 AAAAGACATA
20608387 TTTT-AAAAATATAT-
1 TTTTAAAAAATATATC
20608401 TTTTAAAAAATATATC
1 TTTTAAAAAATATATC
20608417 TTTTAAAAAA
1 TTTTAAAAAA
20608427 AAAACCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 4 0.17
15 10 0.42
16 10 0.42
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTAAAAAATATATC
Found at i:20608889 original size:17 final size:18
Alignment explanation
Indices: 20608860--20608903 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
20608850 TTTTATTTTT
20608860 ATTTTT-TTGCTTTTATTC
1 ATTTTTATT-CTTTTATTC
20608878 -TTTTTATTCTTTTATTC
1 ATTTTTATTCTTTTATTC
20608895 ATTTTTATT
1 ATTTTTATT
20608904 TTTAGTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (18 bp):
ATTTTTATTCTTTTATTC
Found at i:20609613 original size:30 final size:30
Alignment explanation
Indices: 20609540--20609628 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
20609530 ATATTTTATG
20609540 TTAAGGGTTTATTTAAATATAAATTAAAAAT
1 TTAA-GGTTTATTTAAATATAAATTAAAAAT
* * * * *
20609571 TAAAGGTATATTTAGATAT-AATTTAAATT
1 TTAAGGTTTATTTAAATATAAATTAAAAAT
* * *
20609600 TTAAGTGTTTATTTGAGTGTAAATTAAAA
1 TTAAG-GTTTATTTAAATATAAATTAAAA
20609629 GTTAAAAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
29 12 0.27
30 22 0.50
31 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (30 bp):
TTAAGGTTTATTTAAATATAAATTAAAAAT
Found at i:20610451 original size:16 final size:16
Alignment explanation
Indices: 20610426--20610456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20610416 TAATGGTGTT
*
20610426 TAAATCAAATAAAAAA
1 TAAATAAAATAAAAAA
20610442 TAAATAAAATAAAAA
1 TAAATAAAATAAAAA
20610457 GGAAATGGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAATAAAATAAAAAA
Found at i:20610765 original size:3 final size:3
Alignment explanation
Indices: 20610759--20610792 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
20610749 ATAATAATAA
20610759 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20610793 TTCCCTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20611413 original size:3 final size:3
Alignment explanation
Indices: 20611407--20611452 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
20611397 CACGAAATTC
* *
20611407 ATT ATT ATT A-T ATT ATT ATT GTT ATT ATC A-T ATT ATT ATT ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
20611451 AT
1 AT
20611453 AGTAAGTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 3 0.08
3 30 0.83
4 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:20611433 original size:17 final size:16
Alignment explanation
Indices: 20611407--20611453 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
20611397 CACGAAATTC
20611407 ATTATTATTATATTATT
1 ATTATTATTATA-TATT
*
20611424 ATTGTTATTATCATATT
1 ATTATTATTAT-ATATT
20611441 ATTATTACTTATA
1 ATTATTA-TTATA
20611454 GTAAGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTATTATTATATATT
Found at i:20611433 original size:20 final size:20
Alignment explanation
Indices: 20611408--20611446 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20611398 ACGAAATTCA
*
20611408 TTATTATTATATTATTATTG
1 TTATTATCATATTATTATTG
20611428 TTATTATCATATTATTATT
1 TTATTATCATATTATTATT
20611447 ACTTATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATTATCATATTATTATTG
Found at i:20612049 original size:2 final size:2
Alignment explanation
Indices: 20612042--20612073 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20612032 ACTTAATCTC
*
20612042 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20612074 GTGAATATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20615244 original size:47 final size:47
Alignment explanation
Indices: 20615153--20615245 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
20615143 AGAGTTTCTA
* * *
20615153 TTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAACGTTTTTTT
1 TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAACATTTTTTT
* * *
20615200 TTTTAAGGAAAATTGGTACTTCCAACTTTTTCC-CAAAATATTTTTT
1 TTTTAAGAAAAATTGATACTTCCAAC-TTTTCCTCAAAACATTTTTT
20615246 CTGAAACTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 33 0.85
48 6 0.15
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (47 bp):
TTTTAAGAAAAATTGATACTTCCAACTTTTCCTCAAAACATTTTTTT
Found at i:20615278 original size:58 final size:58
Alignment explanation
Indices: 20615201--20615328 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 58
20615191 CGTTTTTTTT
*
20615201 TTTAAGGAAAATTGGTACTTCCAACTTTTTCC-C-AAAATAT-TTTTTCTGAAACTTTAA
1 TTTAAGGAAAATTGATACTTCCAAC-TTTTCCTCAAAAATATATTTTTCTGAAA-TTTAA
** * *
20615258 TTTCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATATTTTTTTGAAATTTTA
1 TTT-AAGGAAAATTGATACTTCCAACTTTTCCTCAAAAATATATTTTTCTGAAATTTAA
*
20615317 TTTAAAGAAAAT
1 TTTAAGGAAAAT
20615329 CATTTAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
57 9 0.15
58 28 0.46
59 14 0.23
60 10 0.16
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (58 bp):
TTTAAGGAAAATTGATACTTCCAACTTTTCCTCAAAAATATATTTTTCTGAAATTTAA
Found at i:20615348 original size:5 final size:5
Alignment explanation
Indices: 20615333--20615386 Score: 74
Period size: 5 Copynumber: 10.6 Consensus size: 5
20615323 GAAAATCATT
*
20615333 TAAAA -AAAA TAAAA TAAAA TAAAA TAAAA TAAAAA TAACAA TAAAA AAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAA-AA TAAAA TAAAA
20615384 TAA
1 TAA
20615387 GGAATACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
4 4 0.09
5 30 0.68
6 10 0.23
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:20615367 original size:16 final size:16
Alignment explanation
Indices: 20615334--20615386 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
20615324 AAAATCATTT
20615334 AAAA-AAAATAAAAT-
1 AAAATAAAATAAAATA
20615348 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
20615364 AAAATAACAATAAAA-A
1 AAAATAA-AATAAAATA
20615380 AAAATAA
1 AAAATAA
20615387 GGAATACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.11
15 10 0.28
16 15 0.42
17 7 0.19
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:20615426 original size:3 final size:3
Alignment explanation
Indices: 20615418--20615467 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
20615408 CTAATCAATA
*
20615418 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAGA AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
20615463 AAT AA
1 AAT AA
20615468 ATAAAGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:20615454 original size:24 final size:24
Alignment explanation
Indices: 20615424--20615476 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
20615414 AATAAATAAT
20615424 AATAATAATAATAATAATAATAAA-A
1 AATAATAATAATAAT-A-AATAAAGA
20615449 GAAATAATAATAATAATAAATAAAGA
1 -AA-TAATAATAATAATAAATAAAGA
20615475 AA
1 AA
20615477 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 8 0.32
26 4 0.16
27 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (24 bp):
AATAATAATAATAATAAATAAAGA
Found at i:20615903 original size:13 final size:13
Alignment explanation
Indices: 20615885--20615909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20615875 GGAAAACTTG
20615885 AATTTCATCGAAA
1 AATTTCATCGAAA
20615898 AATTTCATCGAA
1 AATTTCATCGAA
20615910 TTCTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
AATTTCATCGAAA
Found at i:20616262 original size:16 final size:17
Alignment explanation
Indices: 20616243--20616276 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
20616233 AATTCAGAAC
20616243 AGATAAATA-AAAAAAT
1 AGATAAATATAAAAAAT
20616259 AGATAAATATAAAAAAT
1 AGATAAATATAAAAAAT
20616276 A
1 A
20616277 TACATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AGATAAATATAAAAAAT
Found at i:20616287 original size:27 final size:28
Alignment explanation
Indices: 20616256--20616351 Score: 94
Period size: 27 Copynumber: 3.5 Consensus size: 28
20616246 TAAATAAAAA
*
20616256 AATAGATAA-ATATAAAAAATATACATT
1 AATAGATAACATATAAAAAATATATATT
*
20616283 AATAGTTAA-ATAATAAAAAATA-ATATT
1 AATAGATAACAT-ATAAAAAATATATATT
*
20616310 AATGGATAACCA-AT-AAAAATATATATT
1 AATAGATAA-CATATAAAAAATATATATT
* *
20616337 ATTAGATAATATATA
1 AATAGATAACATATA
20616352 TATAATAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
26 8 0.14
27 37 0.66
28 10 0.18
29 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (28 bp):
AATAGATAACATATAAAAAATATATATT
Found at i:20616370 original size:14 final size:15
Alignment explanation
Indices: 20616353--20616385 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20616343 TAATATATAT
20616353 ATAATAAAA-TAAAA
1 ATAATAAAACTAAAA
20616367 ATAATAAAACTAAAA
1 ATAATAAAACTAAAA
20616382 ATAA
1 ATAA
20616386 AATGGGCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAATAAAACTAAAA
Found at i:20616790 original size:44 final size:43
Alignment explanation
Indices: 20616582--20616780 Score: 281
Period size: 43 Copynumber: 4.6 Consensus size: 43
20616572 AATTTTGATC
* * *
20616582 AAAGCTACTCTAAACAAAAGCTCAACGACTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * *
20616625 AAAGCTCCTTTAAACAGAGGCTCATCAACTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* *
20616668 AAAGCTCCTTTCAACAGAGGCTCAACGACTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * *
20616711 AAAGCTCCTCTAAATAGAGGCTCAACGACTTTTAAAAGATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAA-ATAAAT
*
20616755 AAAGCTCCTATAAACAGAGGCTCAAC
1 AAAGCTCCTCTAAACAGAGGCTCAAC
20616781 AACATTTAAA
Statistics
Matches: 139, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 110 0.79
44 29 0.21
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.22
Consensus pattern (43 bp):
AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
Found at i:20616831 original size:106 final size:104
Alignment explanation
Indices: 20616685--20616893 Score: 321
Period size: 106 Copynumber: 2.0 Consensus size: 104
20616675 CTTTCAACAG
*
20616685 AGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAAATAGAGGCTCAACGACTTTT-AAAAG
1 AGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAATAGAGGCTCAACGACTTTTGAAAA-
20616749 ATAAACAAAGCTCCTATAAACAGAGGCTCAACAACATTTAA
65 ATAAACAAAGCTCCTATAAACAGAGGCTCAACAAC-TTTAA
* * * *
20616790 AGGCTTAACGACTTTGGAAAGATAAACAAAGCTTCTCTAAATAGAGGCTCAATGACTTTTGAAAA
1 AGGCTCAACGACTTT-GAAAAATAAACAAAGCTCCTCTAAATAGAGGCTCAACGACTTTTGAAAA
* *
20616855 ATAAATAAAGCTCCTCTAAACAGAGGCTCAACAACTTTA
65 ATAAACAAAGCTCCTATAAACAGAGGCTCAACAACTTTA
20616894 GAAAAGTAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
105 18 0.19
106 73 0.77
107 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (104 bp):
AGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAATAGAGGCTCAACGACTTTTGAAAAA
TAAACAAAGCTCCTATAAACAGAGGCTCAACAACTTTAA
Found at i:20616847 original size:44 final size:44
Alignment explanation
Indices: 20616790--20616923 Score: 146
Period size: 44 Copynumber: 3.1 Consensus size: 44
20616780 CAACATTTAA
* * * *
20616790 AGGCTTAACGACTTTGGAAAGATAAACAAAGCTTCTCTAAATAG
1 AGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAG
* * *
20616834 AGGCTCAATGACTTTTGAAAAATAAATAAAGCTCCTCTAAACAG
1 AGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAG
* * * **
20616878 AGGCTCAACAACTTTAGAAAAGT-AA-ATTGCTCCTCTAAACAG
1 AGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAG
20616920 AGGC
1 AGGC
20616924 ATCACAACTT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 19 0.25
43 2 0.03
44 56 0.73
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (44 bp):
AGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAG
Found at i:20616923 original size:42 final size:41
Alignment explanation
Indices: 20616824--20616948 Score: 139
Period size: 44 Copynumber: 3.0 Consensus size: 41
20616814 AACAAAGCTT
* ** * *
20616824 CTCTAAATAGAGGCTCAATGACTTTTGAAAAATAAATAAAGCTC
1 CTCTAAACAGAGGCTCAACAAC-TTTGAAAAGTAAAT--TGCTC
20616868 CTCTAAACAGAGGCTCAACAACTTTAGAAAAGTAAATTGCTC
1 CTCTAAACAGAGGCTCAACAACTTT-GAAAAGTAAATTGCTC
20616910 CTCTAAACAGAGGCATC-ACAACTTTG-AAAGTAAA-TGCTC
1 CTCTAAACAGAGGC-TCAACAACTTTGAAAAGTAAATTGCTC
20616949 ATTGACAATC
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
39 5 0.07
40 8 0.11
41 1 0.01
42 26 0.35
43 5 0.07
44 29 0.39
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (41 bp):
CTCTAAACAGAGGCTCAACAACTTTGAAAAGTAAATTGCTC
Found at i:20617985 original size:14 final size:14
Alignment explanation
Indices: 20617954--20618000 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
20617944 TAAGTCTTCA
* *
20617954 TTTTTCATTCTTTC
1 TTTTTCTTTTTTTC
20617968 TTTTTCTTTTTTT-
1 TTTTTCTTTTTTTC
20617981 TTTTTACTTTTTTTC
1 TTTTT-CTTTTTTTC
*
20617996 CTTTT
1 TTTTT
20618001 AAGCATAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 5 0.18
14 19 0.68
15 4 0.14
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:20623771 original size:60 final size:60
Alignment explanation
Indices: 20623680--20623797 Score: 134
Period size: 60 Copynumber: 2.0 Consensus size: 60
20623670 TACAGTCCTT
* * ** *
20623680 AAAATATTTTTTTTAAAGGAAAATTGGTACTTCCAATTTTTTTCC-C-AAAATATTTTTTTA
1 AAAAAATTTTTTTTAAAGAAAAATTAATACTTCCAA--CTTTTCCTCAAAAATATTTTTTTA
*
20623740 AAAAAATTTATTTTT-AAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 AAAAAATTT-TTTTTAAAGAAAAATTAATACTTCCAACTTTTCCTCAAAAATATTTTTT
20623798 AGAATTTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
58 6 0.12
59 1 0.02
60 37 0.76
61 5 0.10
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (60 bp):
AAAAAATTTTTTTTAAAGAAAAATTAATACTTCCAACTTTTCCTCAAAAATATTTTTTTA
Found at i:20623798 original size:59 final size:58
Alignment explanation
Indices: 20623690--20624019 Score: 408
Period size: 59 Copynumber: 5.7 Consensus size: 58
20623680 AAAATATTTT
* * * * * *
20623690 TTTTAAAGGAAAATTGGTACTTCCAATTTTTTTCC-C-AAAATATTTTTTTAAAAAAATTTA
1 TTTTGAAGGAAAATTGATACTTTCAA--CTTTTCCTCAAAAATA-TTTTTT-AGAAAACTTA
* * *
20623750 TTTTTAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTAG---A---A
1 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTA
* * **
20623802 -TTTCAAAGAAAATTGATACTTTCAACTTTTCCTTGAAAATATTTTTTAGAAAACTTA
1 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTA
* *
20623859 TTTTCAAGGAAAATTGATACTTTCAACTTTTCATCAAAAATATTTTGTTAGAAAACTTA
1 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT-TTAGAAAACTTA
20623918 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTGTTAGAAAACTTA
1 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT-TTAGAAAACTTA
20623977 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT
1 TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT
20624020 ATATTTTTGG
Statistics
Matches: 241, Mismatches: 19, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
51 43 0.18
52 1 0.00
54 1 0.00
55 1 0.00
57 1 0.00
58 48 0.20
59 119 0.49
60 27 0.11
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (58 bp):
TTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTA
Found at i:20624891 original size:27 final size:26
Alignment explanation
Indices: 20624861--20624974 Score: 104
Period size: 27 Copynumber: 4.3 Consensus size: 26
20624851 AATTCAAAAC
20624861 AGATAAATCAAAAAAAATATTAATAAT
1 AGATAAAT-AAAAAAAATATTAATAAT
*
20624888 AGATAAATATAAAAAATA-TACATTAAT
1 AGATAAATAAAAAAAATATTA-A-TAAT
* * *
20624915 AGATAAATAATAAAAATAATATTAAT
1 AGATAAATAAAAAAAATATTAATAAT
* * * * *
20624941 GGATAACTAATAAAAATATATATTATT
1 AGATAAATAAAAAAAATAT-TAATAAT
20624968 AGATAAA
1 AGATAAA
20624975 CTATATATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.03
26 30 0.41
27 39 0.53
28 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (26 bp):
AGATAAATAAAAAAAATATTAATAAT
Found at i:20624915 original size:30 final size:30
Alignment explanation
Indices: 20624861--20624974 Score: 85
Period size: 26 Copynumber: 4.2 Consensus size: 30
20624851 AATTCAAAAC
*
20624861 AGATAAATCA-AAAAA-AATATTA-A-TAAT
1 AGATAAATAATAAAAATAATA-TACATTAAT
20624888 AGATAAAT-AT-AAAA-AATATACATTAAT
1 AGATAAATAATAAAAATAATATACATTAAT
20624915 AGATAAATAATAAAAAT-A-AT--ATTAAT
1 AGATAAATAATAAAAATAATATACATTAAT
* * *
20624941 GGATAACTAATAAAAAT-ATAT--ATTATT
1 AGATAAATAATAAAAATAATATACATTAAT
20624968 AGATAAA
1 AGATAAA
20624975 CTATATATAT
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.03
26 32 0.43
27 32 0.43
28 4 0.05
29 5 0.07
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (30 bp):
AGATAAATAATAAAAATAATATACATTAAT
Found at i:20624929 original size:26 final size:26
Alignment explanation
Indices: 20624874--20624974 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 26
20624864 TAAATCAAAA
* *
20624874 AAAATAT-TAATAATAGATAAATATAA
1 AAAATATATATTAATAGATAAATA-AT
*
20624900 AAAATATACATTAATAGATAAATAAT
1 AAAATATATATTAATAGATAAATAAT
* *
20624926 AAAA-ATAATATTAATGGATAACTAAT
1 AAAATAT-ATATTAATAGATAAATAAT
*
20624952 AAAAATATATATTATTAGATAAA
1 -AAAATATATATTAATAGATAAA
20624975 CTATATATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.03
26 28 0.45
27 30 0.48
28 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAATATATATTAATAGATAAATAAT
Found at i:20624956 original size:53 final size:54
Alignment explanation
Indices: 20624861--20624974 Score: 142
Period size: 53 Copynumber: 2.1 Consensus size: 54
20624851 AATTCAAAAC
*
20624861 AGATAAATCAAAAAAAATATTAATAATAGATAAATATAAAAAATATACATTAAT
1 AGATAAATCAAAAAAAATAATAATAATAGATAAATATAAAAAATATACATTAAT
* * * * * *
20624915 AGATAAAT-AATAAAAATAATATTAATGGATAACTA-ATAAAAATATATATTATT
1 AGATAAATCAAAAAAAATAATAATAATAGATAAATATA-AAAAATATACATTAAT
20624968 AGATAAA
1 AGATAAA
20624975 CTATATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.02
53 43 0.83
54 8 0.15
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (54 bp):
AGATAAATCAAAAAAAATAATAATAATAGATAAATATAAAAAATATACATTAAT
Found at i:20630722 original size:41 final size:41
Alignment explanation
Indices: 20630648--20630725 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
20630638 TGATAATTTG
* *
20630648 TCAATTAAGGTGTTTCCTCCTAGAAATGCCTTAATTGATGA
1 TCAATTAAGGTGTTTACTCCTAGAAACGCCTTAATTGATGA
* * *
20630689 TCAATTAAGGTGTTTACTTCTTGAAACGTCTTAATTG
1 TCAATTAAGGTGTTTACTCCTAGAAACGCCTTAATTG
20630726 CAACATAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (41 bp):
TCAATTAAGGTGTTTACTCCTAGAAACGCCTTAATTGATGA
Found at i:20632772 original size:17 final size:17
Alignment explanation
Indices: 20632752--20632797 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
20632742 ATATATAAAA
20632752 ATATATATTTTATAATT
1 ATATATATTTTATAATT
*
20632769 ATAT-TAATTT-TAATT
1 ATATATATTTTATAATT
* *
20632784 TTATATATATTATA
1 ATATATATTTTATA
20632798 TTCATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 8 0.35
16 9 0.39
17 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATATTTTATAATT
Found at i:20632905 original size:17 final size:17
Alignment explanation
Indices: 20632883--20632929 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
20632873 TTGTATGACC
*
20632883 TTTTTTATTTTTATT-T
1 TTTTTTATTTTTATTCA
*
20632899 TTTTTTTTCTTTTATTCA
1 TTTTTTAT-TTTTATTCA
20632917 TTTTTTATTTTTA
1 TTTTTTATTTTTA
20632930 ATTAGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTATTTTTATTCA
Found at i:20633383 original size:30 final size:30
Alignment explanation
Indices: 20633310--20633398 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
20633300 ATATTTTATG
20633310 TTAAGGGTTTATTTAAATATAAATTAAAAAT
1 TTAA-GGTTTATTTAAATATAAATTAAAAAT
* * * * *
20633341 TAAAGGTATATTTAGATAT-AATTTAAATT
1 TTAAGGTTTATTTAAATATAAATTAAAAAT
* * *
20633370 TTAAGTGTTTATTTGAGTGTAAATTAAAA
1 TTAAG-GTTTATTTAAATATAAATTAAAA
20633399 GTTAAAAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
29 12 0.27
30 22 0.50
31 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (30 bp):
TTAAGGTTTATTTAAATATAAATTAAAAAT
Found at i:20633439 original size:29 final size:30
Alignment explanation
Indices: 20633360--20633440 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 30
20633350 ATTTAGATAT
* *
20633360 AATTTAAATTTTAAGTGTTTATTTGAGTGTA
1 AATTAAAATTATAAGTGTTTA-TTGAGTGTA
**
20633391 AATTAAAAGTTA-AA-AATTTATTGAG-GTGA
1 AATTAAAA-TTATAAGTGTTTATTGAGTGT-A
20633420 AA-TAAAATTATAAGTGTTTAT
1 AATTAAAATTATAAGTGTTTAT
20633441 GTAATAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
27 3 0.08
28 9 0.22
29 13 0.32
30 4 0.10
31 9 0.22
32 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (30 bp):
AATTAAAATTATAAGTGTTTATTGAGTGTA
Found at i:20637431 original size:145 final size:144
Alignment explanation
Indices: 20637166--20637719 Score: 533
Period size: 145 Copynumber: 3.8 Consensus size: 144
20637156 TATACTTGGG
* * * * * * * *
20637166 AAAGTTTGAAATTACCAAAATATCCCTATAAGGGTATTTCCAT-AATTTAGCCTCCTTGAGCTCG
1 AAAGTGTGAAATTACCAAAATACCCCTATAAAGGTATTTTCGTAAATTGA-CCTTCTTGAGCTCA
* * * * *
20637230 GATTTTCATGAAACTTTTCAAATCTCAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAAT
65 GATTTTCATGAAAC-TTTCAGATCTTAATTTCATAATATTTTATAATTTTTGGTGCATTTGAAAT
* * *
20637295 AACAGCAGTACCCCAA
129 CACAACAGTACCCCGA
* *
20637311 AAAGTATGAAATTACCAAAATACCCCTATAAAGGTATTTTTGTAAATTGACCTTCTTGAGCTCAG
1 AAAGTGTGAAATTACCAAAATACCCCTATAAAGGTATTTTCGTAAATTGACCTTCTTGAGCTCAG
* *
20637376 ATTTTTATGAAAACTTTCAGATCTTAATTTCATAATATTTTATAATTTTTGGTGCATTTTAAATC
66 ATTTTCATG-AAACTTTCAGATCTTAATTTCATAATATTTTATAATTTTTGGTGCATTTGAAATC
* **
20637441 ACAACTGTACCTTGA
130 ACAACAGTACCCCGA
* * * * * * * * **
20637456 GAAGTGTGAAATTACCAAATTACCCATATAAGGGTATTTTTGTAATTTAACCTTCTCGAGCTTGG
1 AAAGTGTGAAATTACCAAAATACCCCTATAAAGGTATTTTCGTAAATTGACCTTCTTGAGCTCAG
* * * *
20637521 ATTTCCATGAAATTTTTTAGATCTTAATTTCATAATATTTTATGATTTTTGGTGCATTTGAAATC
66 ATTTTCATGAAA-CTTTCAGATCTTAATTTCATAATATTTTATAATTTTTGGTGCATTTGAAATC
*
20637586 ATAACAGTACCCCGA
130 ACAACAGTACCCCGA
** * * * **
20637601 GGAGTGTGAAACTACTAAAATACCCCTAT-AAGGATATTTTCGTAATTTGA--TGTCACAGAGCT
1 AAAGTGTGAAATTACCAAAATACCCCTATAAAGG-TATTTTCGTAAATTGACCT-TC-TTGAGCT
* * * * * *
20637663 CAGATTTTAATGAAACTTTACATATATAAATTTTATAGTATTTTATGAA-TTTTGGTG
63 CAGATTTTCATGAAACTTT-CAGATCTTAATTTCATAATATTTTAT-AATTTTTGGTG
20637720 TTTAAAATCC
Statistics
Matches: 337, Mismatches: 64, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
143 1 0.00
144 11 0.03
145 315 0.93
146 10 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (144 bp):
AAAGTGTGAAATTACCAAAATACCCCTATAAAGGTATTTTCGTAAATTGACCTTCTTGAGCTCAG
ATTTTCATGAAACTTTCAGATCTTAATTTCATAATATTTTATAATTTTTGGTGCATTTGAAATCA
CAACAGTACCCCGA
Found at i:20637568 original size:290 final size:290
Alignment explanation
Indices: 20637167--20637719 Score: 695
Period size: 290 Copynumber: 1.9 Consensus size: 290
20637157 ATACTTGGGA
* * *
20637167 AAGTTTGAAATTACCAAAATATCCCTATAAGGGTATTTCCATAATTTAGCCTCCTTGAGCTCGGA
1 AAGTGTGAAATTACCAAAATATCCCTATAAGGGTATTTCCATAATTTAACCTCCTCGAGCTCGGA
*
20637232 TTTTCATGAAACTTTTCAAATCTCAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATAA
66 TTTCCATGAAACTTTTCAAATCTCAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATAA
* * *
20637297 CAGCAGTACCCCAAAAAGTATGAAATTACCAAAATACCCCTATAAAGG-TATTTTTGTAAATTGA
131 CAACAGTACCCCAAAAAGTATGAAACTACCAAAATACCCCTAT-AAGGATATTTTCGTAAATTGA
** * * *
20637361 CCT-TC-TTGAGCTCAGATTTTTATGAAAACTTT-CAGATCTTAATTTCATAATATTTTAT-AAT
195 --TGTCACAGAGCTCAGATTTTAATG-AAACTTTACAGATATAAATTTCATAATATTTTATGAA-
20637422 TTTTGGTGCATTTTAAATCACAACTGTACCTTGAG
256 TTTTGGTGCATTTTAAATCACAACTGTACCTTGAG
* *** * *
20637457 AAGTGTGAAATTACCAAATTA-CCCATATAAGGGTATTTTTGTAATTTAACCTTCTCGAGCTTGG
1 AAGTGTGAAATTACCAAAATATCCC-TATAAGGGTATTTCCATAATTTAACCTCCTCGAGCTCGG
* * * * * * *
20637521 ATTTCCATGAAATTTTTTAGATCTTAATTTCATAATATTTTATGATTTTTGGTGCATTTGAAATC
65 ATTTCCATGAAACTTTTCAAATCTCAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATA
* * ** * * *
20637586 ATAACAGTACCCCGAGGAGTGTGAAACTACTAAAATACCCCTATAAGGATATTTTCGTAATTTGA
130 ACAACAGTACCCCAAAAAGTATGAAACTACCAAAATACCCCTATAAGGATATTTTCGTAAATTGA
* * *
20637651 TGTCACAGAGCTCAGATTTTAATGAAACTTTACATATATAAATTTTATAGTATTTTATGAATTTT
195 TGTCACAGAGCTCAGATTTTAATGAAACTTTACAGATATAAATTTCATAATATTTTATGAATTTT
20637716 GGTG
260 GGTG
20637720 TTTAAAATCC
Statistics
Matches: 222, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
288 1 0.00
289 16 0.07
290 203 0.91
291 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (290 bp):
AAGTGTGAAATTACCAAAATATCCCTATAAGGGTATTTCCATAATTTAACCTCCTCGAGCTCGGA
TTTCCATGAAACTTTTCAAATCTCAATTTCATAATATTTCATGATTTTTAGTGCATTTGAAATAA
CAACAGTACCCCAAAAAGTATGAAACTACCAAAATACCCCTATAAGGATATTTTCGTAAATTGAT
GTCACAGAGCTCAGATTTTAATGAAACTTTACAGATATAAATTTCATAATATTTTATGAATTTTG
GTGCATTTTAAATCACAACTGTACCTTGAG
Found at i:20641668 original size:16 final size:14
Alignment explanation
Indices: 20641639--20641673 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
20641629 AAACAAAATC
20641639 ACAAATAAAAACAA
1 ACAAATAAAAACAA
20641653 ACAAATAGACAAACAA
1 ACAAATA-A-AAACAA
20641669 ACAAA
1 ACAAA
20641674 AATTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 1 0.05
16 11 0.58
ACGTcount: A:0.74, C:0.17, G:0.03, T:0.06
Consensus pattern (14 bp):
ACAAATAAAAACAA
Found at i:20646406 original size:6 final size:6
Alignment explanation
Indices: 20646395--20646455 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
20646385 TGATGGTTGT
* * *
20646395 TAAAAA TAAAAA T-AAAA TAAAAAA TAAAACA AAAAAA TGAAAA TGAAAA
1 TAAAAA TAAAAA TAAAAA T-AAAAA TAAAA-A TAAAAA TAAAAA TAAAAA
* *
20646444 TGAAAA CAAAAA
1 TAAAAA TAAAAA
20646456 CAAAGAGGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
5 5 0.11
6 32 0.68
7 10 0.21
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (6 bp):
TAAAAA
Found at i:20646438 original size:26 final size:25
Alignment explanation
Indices: 20646402--20646455 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
20646392 TGTTAAAAAT
20646402 AAAAATAAAATAAAAAAT-AAAACAA
1 AAAAATAAAAT-AAAAATGAAAACAA
*
20646427 AAAAATGAAAATGAAAATGAAAACAA
1 AAAAAT-AAAATAAAAATGAAAACAA
20646453 AAA
1 AAA
20646456 CAAAGAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (25 bp):
AAAAATAAAATAAAAATGAAAACAA
Found at i:20646456 original size:32 final size:31
Alignment explanation
Indices: 20646396--20646459 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
20646386 GATGGTTGTT
20646396 AAAAATAAAAATAAAATAAAAAATAAAACAA
1 AAAAATAAAAATAAAATAAAAAATAAAACAA
* *
20646427 AAAAATGAAAATGAAAATGAAAACA-AAAACAA
1 AAAAATAAAAAT-AAAAT-AAAAAATAAAACAA
20646459 A
1 A
20646460 GAGGAGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 11 0.38
32 13 0.45
33 5 0.17
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.11
Consensus pattern (31 bp):
AAAAATAAAAATAAAATAAAAAATAAAACAA
Found at i:20647542 original size:15 final size:15
Alignment explanation
Indices: 20647516--20647556 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 15
20647506 TTGTGTTAAT
*
20647516 CAAAATAAAAAAAAA
1 CAAAACAAAAAAAAA
20647531 C--AACAAAAAAAAA
1 CAAAACAAAAAAAAA
20647544 CAAAACAAAAAAA
1 CAAAACAAAAAAA
20647557 TATAGAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 12 0.52
15 11 0.48
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.02
Consensus pattern (15 bp):
CAAAACAAAAAAAAA
Found at i:20647543 original size:18 final size:18
Alignment explanation
Indices: 20647516--20647556 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20647506 TTGTGTTAAT
*
20647516 CAAAATAAAAAAAAACAA
1 CAAAAAAAAAAAAAACAA
*
20647534 CAAAAAAAAACAAAACAA
1 CAAAAAAAAAAAAAACAA
20647552 -AAAAA
1 CAAAAA
20647557 TATAGAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.02
Consensus pattern (18 bp):
CAAAAAAAAAAAAAACAA
Found at i:20648255 original size:83 final size:83
Alignment explanation
Indices: 20648112--20648275 Score: 188
Period size: 83 Copynumber: 2.0 Consensus size: 83
20648102 TGCAACCCTC
** * *
20648112 ATCGAGCCTTCCTTGAAACATACCCATCAGTGAAAATTTTGAATTATCAATCATCCCATCCACAA
1 ATCGAGCCTTCCTTGAAACATACCCATCAGTGAAAAAATTGAATTACCAATCATCACATCCACAA
* *
20648177 ATATTCTAAATAGTAAGT
66 ACATTCCAAATAGTAAGT
* * * * *
20648195 ATCGAGCCTTCTTTG-AACAATGCCCA-CTAGTGAAAAAATTGAATTGCCAATCATGACATCCAT
1 ATCGAGCCTTCCTTGAAAC-ATACCCATC-AGTGAAAAAATTGAATTACCAATCATCACATCCAC
*
20648258 AAGCATTCCAAATAGTAA
64 AAACATTCCAAATAGTAA
20648276 TCATCAATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 4 0.06
83 63 0.94
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (83 bp):
ATCGAGCCTTCCTTGAAACATACCCATCAGTGAAAAAATTGAATTACCAATCATCACATCCACAA
ACATTCCAAATAGTAAGT
Found at i:20649046 original size:104 final size:102
Alignment explanation
Indices: 20648809--20649134 Score: 294
Period size: 104 Copynumber: 3.2 Consensus size: 102
20648799 CAAAAAAAAG
* * * * * * *** * * * *
20648809 ACATTCATATATGCATTACTTGCATCTATATCA-TAAAAAAGGACATTTGTATTTGTAGCACTCA
1 ACATTCACATTTGCATCACTTGCATCTACATCACAAAAAAAAGACATTCACAATTGCATCACTCG
* *
20648873 CATTCATACTTACATGTGCATCATGAGAAAAATATTT
66 CATTCATACTTGCATGTGCATCATGAGAAAAACATTT
* *
20648910 ACATTCACATTTGCATCACTTGCATCTACATCACAAAAAAAAAATACATTCACATTTGCATCACT
1 ACATTCACATTTGCATCACTTGCATCTACATCAC--AAAAAAAAGACATTCACAATTGCATCACT
20648975 CGCATTCATACTTGCATGTGCATCATGAGAAAAACATTT
64 CGCATTCATACTTGCATGTGCATCATGAGAAAAACATTT
* * * ** * * ** ** *
20649014 GCATTCATATTTGCATCATTTGTTTTTGCATCACAAAGGAAAGACATTTGCAATTGCATCACTTG
1 ACATTCACATTTGCATCACTTGCATCTACATCACAAAAAAAAGACATTCACAATTGCATCACTCG
*** * *
20649079 CATTTGCACTTGCATGTGCATAATGAGAAAGACATTT
66 CATTCATACTTGCATGTGCATCATGAGAAAAACATTT
* * *
20649116 TCATTCACATCTACATCAC
1 ACATTCACATTTGCATCAC
20649135 AAAAAAGACA
Statistics
Matches: 183, Mismatches: 39, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
101 29 0.16
102 70 0.38
104 84 0.46
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (102 bp):
ACATTCACATTTGCATCACTTGCATCTACATCACAAAAAAAAGACATTCACAATTGCATCACTCG
CATTCATACTTGCATGTGCATCATGAGAAAAACATTT
Found at i:20649506 original size:2 final size:2
Alignment explanation
Indices: 20649501--20649527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20649491 AAGACACCAA
20649501 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 A
20649528 AAGAACAAAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20649868 original size:96 final size:96
Alignment explanation
Indices: 20649701--20649973 Score: 377
Period size: 96 Copynumber: 2.8 Consensus size: 96
20649691 CAGATATATC
* * * * * * *
20649701 TCCAAGACCTCCGGGTAAACTAGTTTAAATTTTCAAAGTCTCAACGCTTCTATTATGAGGAACAT
1 TCCAAGACCTTCGGGTAAAATATTTTAAATTTTTAAAGTTTCAACGCCTCTATTATGAGGAGCAT
*
20649766 TTAAAGATTTCAAAGACCTCATG-GCATAATT
66 TCAAAGATTTCAAAGACCTC-TGAGCATAATT
* **
20649797 TTCAAGACCTTCGGGTAAAATATTTTAAATTTTTAAAGTTTCATTGCCTCTATTATGAGGAGCAT
1 TCCAAGACCTTCGGGTAAAATATTTTAAATTTTTAAAGTTTCAACGCCTCTATTATGAGGAGCAT
*
20649862 TCAAAGATTTCAAAGATCTCTGAGCATAATT
66 TCAAAGATTTCAAAGACCTCTGAGCATAATT
* * * * *
20649893 TCCAAAACCTTTGGGCAAAACATTTTAAATTTTTAAAGTTTCAACGCCTTTATTATGAGGAGCAT
1 TCCAAGACCTTCGGGTAAAATATTTTAAATTTTTAAAGTTTCAACGCCTCTATTATGAGGAGCAT
20649958 TCAAAGATTTCAAAGA
66 TCAAAGATTTCAAAGA
20649974 TTTCTAGGCA
Statistics
Matches: 156, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
95 2 0.01
96 154 0.99
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (96 bp):
TCCAAGACCTTCGGGTAAAATATTTTAAATTTTTAAAGTTTCAACGCCTCTATTATGAGGAGCAT
TCAAAGATTTCAAAGACCTCTGAGCATAATT
Found at i:20650892 original size:144 final size:144
Alignment explanation
Indices: 20650658--20651063 Score: 478
Period size: 145 Copynumber: 2.8 Consensus size: 144
20650648 TTGTACTAAA
* * * * *
20650658 AGAAGTATGAAATTACCAAAATACCCCTATATGGGTATTTTTGTAATTTGATCTTTCCAAGCT-T
1 AGAAGTATAAAATTA-CAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAGCTCT
* * *
20650722 AGATTTTCATGAAA-TTGTTTACATTTTAATTTCATAATATTTCATAATTTTTGGTATATCTGAA
65 A-ATTTTCATGAAACTT-TTCAGATTTTAATTTTATAATATTTCATAATTTTTGGTATATCTGAA
*
20650786 ATCATAACTGTACCACG
128 ATCATAACAGTACCACG
*
20650803 AGAAGTGTAAAATTACAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTC-AGCCTCT
1 AGAAGTATAAAATTACAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAG-CTCT
* * * * * *
20650867 AATTTTTATGAAACTTTTCAGATTTTAATTTTATAATATTTCATGATTTTTTTGTGTATTTGAGA
65 AATTTTCATGAAACTTTTCAGATTTTAATTTTATAATATTTCAT-AATTTTTGGTATATCTGAAA
* *
20650932 TCATAGCAGTACCATG
129 TCATAACAGTACCACG
* * * * * *
20650948 A-AAATATCAAATTACTAAAATACCGTTATTAGGGTATTTTTATAATTTGACCTTTTCAAGCTCG
1 AGAAGTATAAAATTAC-AAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAGCTCT
* * * *
20651012 GATTTTCATAAAACTTTTCAGATGTAAATTTTATAATATTTCATAATTTTTG
65 AATTTTCATGAAACTTTTCAGATTTTAATTTTATAATATTTCATAATTTTTG
20651064 ATGTTTTAAA
Statistics
Matches: 223, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
143 2 0.01
144 93 0.42
145 126 0.57
146 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (144 bp):
AGAAGTATAAAATTACAAAATACCCTTATAAGGGTATTTTTGTAATTTGACCTTTTCAAGCTCTA
ATTTTCATGAAACTTTTCAGATTTTAATTTTATAATATTTCATAATTTTTGGTATATCTGAAATC
ATAACAGTACCACG
Found at i:20654092 original size:11 final size:12
Alignment explanation
Indices: 20654064--20654096 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20654054 CTGTTACAAC
20654064 ATTTACTATATAT
1 ATTTA-TATATAT
20654077 ATTTATATAT-T
1 ATTTATATATAT
20654088 ATTTATATA
1 ATTTATATA
20654097 AGCATTTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 5 0.25
13 5 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:20655558 original size:21 final size:21
Alignment explanation
Indices: 20655532--20655580 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
20655522 AATATTTAAT
* * *
20655532 AAATAATAAATTACTCAAATA
1 AAATAAAAAAATACTAAAATA
*
20655553 AAATAAAAAAATAGTAAAATA
1 AAATAAAAAAATACTAAAATA
20655574 AAATAAA
1 AAATAAA
20655581 TAATAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATAAAAAAATACTAAAATA
Found at i:20655570 original size:16 final size:17
Alignment explanation
Indices: 20655549--20655664 Score: 64
Period size: 16 Copynumber: 6.8 Consensus size: 17
20655539 AAATTACTCA
20655549 AATAAAATAAAA-AAAT
1 AATAAAATAAAATAAAT
*
20655565 AGTAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
***
20655582 AAT-AAATAATGGAAAT
1 AATAAAATAAAATAAAT
*
20655598 --TAAAATAACAATATAAA
1 AATAAAATAA-AATA-AAT
*
20655615 AACTTAAACATAAAAT-GAT
1 AA--TAAA-ATAAAATAAAT
*
20655634 AA-AAAATAAAATCAAAA
1 AATAAAATAAAAT-AAAT
20655651 AATAAAAATAAAAT
1 AAT-AAAATAAAAT
20655665 GAAAATGAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 23
0.67 0.12 0.21
Matches are distributed among these distances:
14 1 0.01
15 13 0.18
16 25 0.34
17 11 0.15
19 13 0.18
21 7 0.09
22 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (17 bp):
AATAAAATAAAATAAAT
Found at i:20655577 original size:26 final size:25
Alignment explanation
Indices: 20655548--20655616 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 25
20655538 TAAATTACTC
*
20655548 AAATAAAATAAAAAAATAGTAAAATA
1 AAATAAAATAAAAAAAT-GGAAAATA
*
20655574 AAAT-AAATAATAAATAATGGAAATTA
1 AAATAAAATAA-AAA-AATGGAAAATA
*
20655600 AAATAACAATATAAAAA
1 AAATAA-AATAAAAAAA
20655617 CTTAAACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 6 0.17
26 19 0.53
27 7 0.19
28 4 0.11
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (25 bp):
AAATAAAATAAAAAAATGGAAAATA
Found at i:20655635 original size:22 final size:21
Alignment explanation
Indices: 20655597--20655638 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
20655587 ATAATGGAAA
20655597 TTAAAATAACAATATAAAAAC
1 TTAAAATAACAATATAAAAAC
20655618 TTAAACATAA-AATGATAAAAA
1 TTAAA-ATAACAAT-ATAAAAA
20655639 ATAAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TTAAAATAACAATATAAAAAC
Found at i:20655676 original size:13 final size:11
Alignment explanation
Indices: 20655548--20655680 Score: 51
Period size: 11 Copynumber: 11.3 Consensus size: 11
20655538 TAAATTACTC
20655548 AAATAAAATAA
1 AAATAAAATAA
*
20655559 AAA-AATAGT-A
1 AAATAA-AATAA
20655569 AAATAAAATAA
1 AAATAAAATAA
20655580 ATAAT-AAATAA
1 A-AATAAAATAA
20655591 TGGAAATTAAAATAA
1 ---AAA-TAAAATAA
20655606 CAATATAAAAACTTAA
1 -AA-AT-AAAA--TAA
* *
20655622 ACATAAAATGA
1 AAATAAAATAA
*
20655633 TAA-AAAATAA
1 AAATAAAATAA
*
20655643 AATCAAAAAATAA
1 AA--ATAAAATAA
*
20655656 AAATAAAATGA
1 AAATAAAATAA
20655667 AAATGAAAA-AA
1 AAAT-AAAATAA
20655678 AAA
1 AAA
20655681 CTTACAATCG
Statistics
Matches: 93, Mismatches: 12, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
10 15 0.16
11 33 0.35
12 8 0.09
13 18 0.19
14 9 0.10
15 7 0.08
16 3 0.03
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.20
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:20655677 original size:19 final size:18
Alignment explanation
Indices: 20655634--20655669 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20655624 ATAAAATGAT
20655634 AAAAAATAAAATCAAAAA
1 AAAAAATAAAATCAAAAA
*
20655652 ATAAAAATAAAATGAAAA
1 A-AAAAATAAAATCAAAA
20655670 TGAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.06
19 15 0.94
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAATAAAATCAAAAA
Found at i:20655835 original size:16 final size:16
Alignment explanation
Indices: 20655814--20655848 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20655804 TTTATAAGCA
* *
20655814 TCTAGCCCATTTTCTC
1 TCTAGCCAAATTTCTC
20655830 TCTAGCCAAATTTCTC
1 TCTAGCCAAATTTCTC
20655846 TCT
1 TCT
20655849 GCCTTCTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.34, G:0.06, T:0.43
Consensus pattern (16 bp):
TCTAGCCAAATTTCTC
Found at i:20656052 original size:21 final size:21
Alignment explanation
Indices: 20656010--20656048 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20656000 TCAAATTTTT
*
20656010 CCAAAAATTCAAACTTCAATC
1 CCAAAAATTCAAACTCCAATC
*
20656031 CCAAAACTTCAAA-TCCAA
1 CCAAAAATTCAAACTCCAA
20656049 ATCCTAGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
CCAAAAATTCAAACTCCAATC
Found at i:20656469 original size:3 final size:3
Alignment explanation
Indices: 20656463--20656600 Score: 170
Period size: 3 Copynumber: 46.3 Consensus size: 3
20656453 TGAGAAAAAA
* *
20656463 AAT AAT ACT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
20656510 AAT AAT AAT AAT AAT AGT AAT AGT AAT AAT AAT AGT AAT AAT AAG AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
20656558 AAT AAA AAT AAT AAA AAT AAT AAT AGT AAA AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20656601 GTAGCAATAA
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
2 2 0.02
3 111 0.98
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20656926 original size:57 final size:56
Alignment explanation
Indices: 20656851--20657000 Score: 144
Period size: 55 Copynumber: 2.7 Consensus size: 56
20656841 GATAAAGCCG
* ** *
20656851 AGATCGAACGACCAGGATTGAACCATAAGTCTGAAAAAATCAACCTAGATTGAGTCA
1 AGATCGAATGACTGGGATTGAACCATAAGTCTGAAAAAATCAACC-AGATCGAGTCA
* * * * * * *
20656908 AGGTCGAATGA-TGGGGATTGAATCACAAATCT-AAAAAATGATCCGGATCGAGTCA
1 AGATCGAATGACT-GGGATTGAACCATAAGTCTGAAAAAATCAACCAGATCGAGTCA
20656963 AGATCGAATGACTGGGATTGAACC-TCAAGTCTAGAAAA
1 AGATCGAATGACTGGGATTGAACCAT-AAGTCT-GAAAA
20657001 TAGACTTGGA
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
55 34 0.47
56 11 0.15
57 28 0.38
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (56 bp):
AGATCGAATGACTGGGATTGAACCATAAGTCTGAAAAAATCAACCAGATCGAGTCA
Found at i:20660346 original size:3 final size:3
Alignment explanation
Indices: 20660340--20660453 Score: 64
Period size: 3 Copynumber: 40.3 Consensus size: 3
20660330 CTATTATTTG
* * * * *
20660340 TTA TTA TT- TTA CTA TTG TTA TTA TTA CTA TTA TTA TAA TATA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * * * **
20660385 -TG TTA -CA TTA -TG TTA -TA TTA TTA TTG TTA TTA TTA TTA TTA GAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20660429 TTA TTA -TA TTA -TA TTA -TA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20660454 CATCATCATC
Statistics
Matches: 81, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
2 13 0.16
3 67 0.83
4 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:20660407 original size:45 final size:45
Alignment explanation
Indices: 20660357--20660453 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
20660347 TTTACTATTG
* * *
20660357 TTATTATTACTATTATTATAATATAGTA-TGTTACATTATGTTATA
1 TTATTATTACTATTATTATAAT-TAGAATTATTACATTATATTATA
** * *
20660402 TTATTATTGTTATTATTATTATTAGAATTATTATATTATATTATA
1 TTATTATTACTATTATTATAATTAGAATTATTACATTATATTATA
20660447 TTATTAT
1 TTATTAT
20660454 CATCATCATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 4 0.09
45 40 0.91
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (45 bp):
TTATTATTACTATTATTATAATTAGAATTATTACATTATATTATA
Found at i:20660431 original size:15 final size:15
Alignment explanation
Indices: 20660340--20660452 Score: 71
Period size: 15 Copynumber: 7.8 Consensus size: 15
20660330 CTATTATTTG
*
20660340 TTATTATT-TTACTA
1 TTATTATTATTAGTA
* *
20660354 TTGTTATTATTACTA
1 TTATTATTATTAGTA
*
20660369 TTATTATAATATAGTA
1 TTATTATTAT-TAGTA
* *
20660385 -TGTTA-CATTATGT-
1 TTATTATTATTA-GTA
20660398 TATATTATTATT-GTTA
1 T-TATTATTATTAG-TA
*
20660414 TTATTATTATTAGAA
1 TTATTATTATTAGTA
20660429 TTATTA-TATTA-TA
1 TTATTATTATTAGTA
20660442 TTA-TATTATTA
1 TTATTATTATTA
20660453 TCATCATCAT
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
12 2 0.03
13 11 0.14
14 17 0.22
15 40 0.51
16 9 0.11
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (15 bp):
TTATTATTATTAGTA
Found at i:20660953 original size:19 final size:19
Alignment explanation
Indices: 20660929--20660967 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
20660919 TTGAAGTTTA
*
20660929 GATTTTTAGAAAATTT-TG
1 GATTTTTTGAAAATTTATG
20660947 GATTTTTTGAAAATTTATG
1 GATTTTTTGAAAATTTATG
20660966 GA
1 GA
20660968 AAATTTGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (19 bp):
GATTTTTTGAAAATTTATG
Found at i:20661317 original size:13 final size:13
Alignment explanation
Indices: 20661301--20661345 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
20661291 CCTTTTTCTA
20661301 TTTTAATTTTATT
1 TTTTAATTTTATT
*
20661314 TTTTAATTTCATT
1 TTTTAATTTTATT
* *
20661327 TTTTGATTTTATA
1 TTTTAATTTTATT
20661340 TTTTAA
1 TTTTAA
20661346 GTTATTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:20661330 original size:26 final size:25
Alignment explanation
Indices: 20661301--20661353 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
20661291 CCTTTTTCTA
* *
20661301 TTTTAATTTTATTTTTTAATTTCATT
1 TTTTAATTTTATATTTTAAGTT-ATT
*
20661327 TTTTGATTTTATATTTTAAGTTATT
1 TTTTAATTTTATATTTTAAGTTATT
20661352 TT
1 TT
20661354 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTAATTTTATATTTTAAGTTATT
Found at i:20661361 original size:20 final size:19
Alignment explanation
Indices: 20661299--20661378 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 19
20661289 TTCCTTTTTC
20661299 TATTTTAA-TTTTATT-TTT
1 TATTTTAAGTTTT-TTATTT
* *
20661317 TAATTTCA-TTTTTTGATTTT
1 TATTTTAAGTTTTTT-A-TTT
20661337 ATATTTTAAGTTATTTTATTT
1 -TATTTTAAGTT-TTTTATTT
*
20661358 TATTTTGAGTTTTTTATTT
1 TATTTTAAGTTTTTTATTT
20661377 TA
1 TA
20661379 CTGATTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
17 2 0.04
18 10 0.20
19 10 0.20
20 13 0.25
21 9 0.18
22 3 0.06
23 4 0.08
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.71
Consensus pattern (19 bp):
TATTTTAAGTTTTTTATTT
Found at i:20669953 original size:5 final size:5
Alignment explanation
Indices: 20669945--20670042 Score: 107
Period size: 5 Copynumber: 20.2 Consensus size: 5
20669935 TTTTTATTTT
*
20669945 TATTA TATTA TATTA TATTA TATTA TATTA TA-T- TATTA TAGTA TA-T-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* * *
20669991 TATTA TAGTA TAGTA TATTA TATTG TATTA TATTA TTATTA T-TATA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TAT-TA TATTA
20670042 T
1 T
20670043 TTTTTTATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
3 4 0.05
4 5 0.06
5 66 0.81
6 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Done.