Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 52 of 54
Found at i:20558772 original size:57 final size:58
Alignment explanation
Indices: 20558700--20558819 Score: 197
Period size: 57 Copynumber: 2.1 Consensus size: 58
20558690 TTCCCATTCA
**
20558700 TTGGTGTCTAATTATATTATTTAAGTGTGCAAGAGAAAGCTTAAA-TTGTTAATACAT
1 TTGGTGTCTAATTATATTATTTAAGTGTGCAAGAGAAAGCTTAAACTCATTAATACAT
* *
20558757 TTGGTGTCTAGTTATATTATTTAAGTGTGCAAGAGAAAGCTTAAACTCATTAATACTT
1 TTGGTGTCTAATTATATTATTTAAGTGTGCAAGAGAAAGCTTAAACTCATTAATACAT
20558815 TTGGT
1 TTGGT
20558820 ATTTGAAAGC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 44 0.76
58 14 0.24
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (58 bp):
TTGGTGTCTAATTATATTATTTAAGTGTGCAAGAGAAAGCTTAAACTCATTAATACAT
Found at i:20559973 original size:21 final size:21
Alignment explanation
Indices: 20559942--20560000 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
20559932 TTGTGAGCTT
20559942 AATT-CAT-ATGCTTTTGATG
1 AATTGCATGATGCTTTTGATG
20559961 AATTGCATGATGCTTTTGATG
1 AATTGCATGATGCTTTTGATG
*
20559982 AATTGCATGATGTTTTTGA
1 AATTGCATGATGCTTTTGA
20560001 GGATTTAGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 30 0.81
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (21 bp):
AATTGCATGATGCTTTTGATG
Found at i:20561598 original size:19 final size:20
Alignment explanation
Indices: 20561571--20561616 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
20561561 AGGAGACAAG
*
20561571 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
20561590 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
20561609 ATAATATT
1 ATAATATT
20561617 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:20563449 original size:13 final size:13
Alignment explanation
Indices: 20563431--20563455 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20563421 AGAGAAATTG
20563431 TGATTTTATAAAA
1 TGATTTTATAAAA
20563444 TGATTTTATAAA
1 TGATTTTATAAA
20563456 TTTTCTGAAA
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:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20567484 original size:14 final size:13
Alignment explanation
Indices: 20567461--20567511 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
20567451 TTTTGAAAGC
20567461 AAAAAGAAAGAAG
1 AAAAAGAAAGAAG
20567474 AAAAGAGAAAGAAGG
1 AAAA-AGAAAGAA-G
*
20567489 AAAGAA-AAATAAG
1 AAA-AAGAAAGAAG
20567502 AGAAAAGAAA
1 A-AAAAGAAA
20567512 ATATAGAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 8 0.25
14 18 0.56
15 5 0.16
16 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAGAAG
Found at i:20570433 original size:19 final size:19
Alignment explanation
Indices: 20570407--20570451 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
20570397 ATAAATAATA
20570407 ACTAAAA-TAAAAGAAATC
1 ACTAAAATTAAAAGAAATC
* *
20570425 ACATAAAATTAAAATAACTC
1 AC-TAAAATTAAAAGAAATC
20570445 ACTAAAA
1 ACTAAAA
20570452 AGTAACCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 11 0.48
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.20
Consensus pattern (19 bp):
ACTAAAATTAAAAGAAATC
Found at i:20576865 original size:14 final size:14
Alignment explanation
Indices: 20576846--20576878 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
20576836 ATCAAAATTT
20576846 ATTAATTAACTAAA
1 ATTAATTAACTAAA
20576860 ATTAATTAACTAAA
1 ATTAATTAACTAAA
20576874 ATTAA
1 ATTAA
20576879 AACCAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTAATTAACTAAA
Found at i:20577981 original size:21 final size:20
Alignment explanation
Indices: 20577957--20577996 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20577947 AAAAACTAAT
*
20577957 AAATAATAAACAAATTAAAAG
1 AAATAACAAA-AAATTAAAAG
*
20577978 AAATAACATAAAATTAAAA
1 AAATAACAAAAAATTAAAA
20577997 TAACTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAACAAAAAATTAAAAG
Found at i:20577993 original size:20 final size:20
Alignment explanation
Indices: 20577968--20578010 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20577958 AATAATAAAC
20577968 AAATTAAAAGAAATAACATA
1 AAATTAAAAGAAATAACATA
* * *
20577988 AAATTAAAATAACTAACTTA
1 AAATTAAAAGAAATAACATA
20578008 AAA
1 AAA
20578011 GTAACCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATTAAAAGAAATAACATA
Found at i:20580282 original size:13 final size:13
Alignment explanation
Indices: 20580264--20580288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20580254 GGAAAATGGG
20580264 ATTTTATAAAATA
1 ATTTTATAAAATA
20580277 ATTTTATAAAAT
1 ATTTTATAAAAT
20580289 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:20581509 original size:15 final size:14
Alignment explanation
Indices: 20581460--20581510 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
20581450 TTTAAAGATC
20581460 AAAGATTTTGATTTT
1 AAAG-TTTTGATTTT
*
20581475 AAAGCTTTGGATTTT
1 AAAG-TTTTGATTTT
20581490 AAAGTTTTCGATTTT
1 AAAGTTTT-GATTTT
20581505 AAAGTT
1 AAAGTT
20581511 GTTTTAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 3 0.09
15 29 0.91
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (14 bp):
AAAGTTTTGATTTT
Found at i:20584630 original size:13 final size:13
Alignment explanation
Indices: 20584612--20584636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20584602 GGAAAATAGG
20584612 ATTTTATAAAATA
1 ATTTTATAAAATA
20584625 ATTTTATAAAAT
1 ATTTTATAAAAT
20584637 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:20588521 original size:53 final size:53
Alignment explanation
Indices: 20588458--20588563 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
20588448 TTCACTCGCA
20588458 TCTTGTCCTCAGCCACTCAAGTCACCTCCTCACTAGAGTGATTGTGCCAAAAG
1 TCTTGTCCTCAGCCACTCAAGTCACCTCCTCACTAGAGTGATTGTGCCAAAAG
* * *
20588511 TCTTGTCCTCAGCCACTTATGTCACCTCCTCGCTAGAGTGATTGTGCCAAAAG
1 TCTTGTCCTCAGCCACTCAAGTCACCTCCTCACTAGAGTGATTGTGCCAAAAG
20588564 GCTTTCATAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (53 bp):
TCTTGTCCTCAGCCACTCAAGTCACCTCCTCACTAGAGTGATTGTGCCAAAAG
Found at i:20605912 original size:2 final size:2
Alignment explanation
Indices: 20605894--20605929 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
20605884 TCTTTTTCTG
*
20605894 TC TC T- TC TC TT 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 TC TC TC T
20605930 AAACACTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:20612423 original size:56 final size:57
Alignment explanation
Indices: 20612210--20612432 Score: 281
Period size: 57 Copynumber: 3.9 Consensus size: 57
20612200 ACACATCACA
* * *
20612210 ACATATATATATATATCA-TTCGCTAGCCTAGGCATACTCATCTAGGCAATCATATTA-
1 ACATATATACATACAT-AGTTCTCTAGCCTAGGCATACTCATCTAGGCAATCAT-TTAC
* * *
20612267 ACATATATACAGACATTGTTCTCTAGCCTAGGCATACTCATCTAGGCAATCATTTTC
1 ACATATATACATACATAGTTCTCTAGCCTAGGCATACTCATCTAGGCAATCATTTAC
* * * *
20612324 ACATATGTATATACATAGTTCTCTAGCCTAGGCATACTTATCTAGGCAA-CATGTAC
1 ACATATATACATACATAGTTCTCTAGCCTAGGCATACTCATCTAGGCAATCATTTAC
* * * *
20612380 AAATATATACATACATAGTTCTCTAGCATAAGCATACTCATCTAGGCATTCAT
1 ACATATATACATACATAGTTCTCTAGCCTAGGCATACTCATCTAGGCAATCAT
20612433 ATAACATTTA
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
56 49 0.34
57 94 0.66
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (57 bp):
ACATATATACATACATAGTTCTCTAGCCTAGGCATACTCATCTAGGCAATCATTTAC
Found at i:20613741 original size:548 final size:548
Alignment explanation
Indices: 20612688--20613755 Score: 1442
Period size: 548 Copynumber: 1.9 Consensus size: 548
20612678 AACTCCTTAA
* * *
20612688 CAATCCAACATATGAGCTCAAATCCTTCAATAATGAGCTAAACCCATACCTTAGAGGCTAGATTG
1 CAATCAAACATATGAGCTCAAATCCTTCAATAATGAGCTAAAACCATACCTTAGAGGCTAGATTA
* *
20612753 CACGATTTTGACCTCCAAATTCACTCTAAATAGCTCAAAGAATCCATTTGTGGCTTAAGTTTTAA
66 CACGATTTTGACCTCCAAATTCACTCCAAATAGCTCAAAGAATCCATTTGTGGCTTAAGTTTCAA
**
20612818 ATGGGTAAAGAAAGAAAATAAAAACCATCAAAATCAAGCTTATGAGAGTGAAAACTTTTACCTTT
131 ATGGGTAAAGAAAGAAAATAAAAACCATCAAAATCAAGCTTATGAGAGTGAAAACCCTTACCTTT
* * *
20612883 AACACTTAGAATCCAAGATTTGTTGTTAGAGTTTGAAGGTTTTGAAGGGTATGAAATTTGAGAGA
196 AACACTTAGAATCCAAGACTTGTTG-T-GAGTTTGAAGGTTTTGAAGGGTATGAAATTTGAAAAA
* * * * *
20612948 AAAGGGTGGAAGAATGAGAAGTTAGGAGAAAAATGAAGAAAATTTTGGTTTTAAGGCTTTTAAGT
259 AAAGGGTGAAAGAATGAGAAGTTAGGACAAAAAGGAAGAAAATTTTAGTTTTAAGGCTTTTAAGC
* * * * * *
20613013 TCGTTTTAGGTTGATTAGGTAGCCTAAGATTGACTATGGAAGGTTTGTAGTCAATCCTGGACCAA
324 CCGTTTTAGGTTGACTAGGCAACCTAAGATCGACTATGGAAGGTATGTAGTCAATCCTGGACCAA
* * * * *
20613078 ATGATTTCACCCATTTTTCCTTTATAGGATCGACTATGGAGGGTCTATAATTGATCTTGAACTAG
389 AAGATTTCACCCATTTTTCCTTCACAAGATCGACTATGGAGGGTCTAGAATTGATCTTGAACTAG
* *
20613143 TATGTTCATTTTTACTCAAGTTTGCTTCACAAGATCGACTATGAAGGGTCTATAGTCGATCTTGG
454 AATGTTCATTTTCACTCAAGTTTGCTTCACAAGATCGACTATGAAGGGTCTATAGTCGATCTTGG
20613208 ACCAGAATGTTATTAAGCTCATATCTTTAG
519 ACCAGAATGTTATTAAGCTCATATCTTTAG
* *
20613238 CAATCAAACATATGAGCTCAAATCCTTCAATAATGAGCTAAAACCATACCTTAGAGGTTGGATTA
1 CAATCAAACATATGAGCTCAAATCCTTCAATAATGAGCTAAAACCATACCTTAGAGGCTAGATTA
* * * * * **
20613303 TATGATTCTT-AGCTCCAAATTCACTCCACATAGCTCCAAGAATCTGTTTGTGGCTTAGAGTTTC
66 CACGATT-TTGACCTCCAAATTCACTCCAAATAGCTCAAAGAATCCATTTGTGGCTTA-AGTTTC
* ** * * * * * * *
20613367 AAATGGTTGGAGAGAGAAAATAAAAACTATCAAAATGAAGCTTTTGGGAGTGGAAACCCTTACTT
129 AAATGGGTAAAGAAAGAAAATAAAAACCATCAAAATCAAGCTTATGAGAGTGAAAACCCTTACCT
*
20613432 TTAACACTTTGAATCCAAGACTTGTTG-GAGTTTGAAGGTTTTGAAGGGTATGAAATTTGAAAAA
194 TTAACACTTAGAATCCAAGACTTGTTGTGAGTTTGAAGGTTTTGAAGGGTATGAAATTTGAAAAA
*
20613496 AAAGGGTGAAAGAATGAGAAGTTAGGACAAAAAGGAAGAAAATTTTAGTTTTAGGGCTTTTAAGC
259 AAAGGGTGAAAGAATGAGAAGTTAGGACAAAAAGGAAGAAAATTTTAGTTTTAAGGCTTTTAAGC
* * * * *** * *
20613561 CCTTTTTAGGCTT-ACTGGGCAACTTAGGATCGACTATGGAAGGTATGTAGTTGGTCTTGGACTA
324 CCGTTTTAGG-TTGACTAGGCAACCTAAGATCGACTATGGAAGGTATGTAGTCAATCCTGGACCA
** * *
20613625 AAAGATTTCACTTATTTTTCCTTCACAAGATCGACTATGGAGGGTCTAGAGTTGATCTTGGACTA
388 AAAGATTTCACCCATTTTTCCTTCACAAGATCGACTATGGAGGGTCTAGAATTGATCTTGAACTA
** * * * *
20613690 GAATGTTTGTTTTCACTCAAGTTTGCTTCATAGGAT-GAACTATGGAGGGTCTATAGTTGATCTT
453 GAATGTTCATTTTCACTCAAGTTTGCTTCACAAGATCG-ACTATGAAGGGTCTATAGTCGATCTT
20613754 GG
517 GG
20613756 TCTAAAATGT
Statistics
Matches: 446, Mismatches: 68, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
547 1 0.00
548 252 0.57
549 2 0.00
550 106 0.24
551 85 0.19
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (548 bp):
CAATCAAACATATGAGCTCAAATCCTTCAATAATGAGCTAAAACCATACCTTAGAGGCTAGATTA
CACGATTTTGACCTCCAAATTCACTCCAAATAGCTCAAAGAATCCATTTGTGGCTTAAGTTTCAA
ATGGGTAAAGAAAGAAAATAAAAACCATCAAAATCAAGCTTATGAGAGTGAAAACCCTTACCTTT
AACACTTAGAATCCAAGACTTGTTGTGAGTTTGAAGGTTTTGAAGGGTATGAAATTTGAAAAAAA
AGGGTGAAAGAATGAGAAGTTAGGACAAAAAGGAAGAAAATTTTAGTTTTAAGGCTTTTAAGCCC
GTTTTAGGTTGACTAGGCAACCTAAGATCGACTATGGAAGGTATGTAGTCAATCCTGGACCAAAA
GATTTCACCCATTTTTCCTTCACAAGATCGACTATGGAGGGTCTAGAATTGATCTTGAACTAGAA
TGTTCATTTTCACTCAAGTTTGCTTCACAAGATCGACTATGAAGGGTCTATAGTCGATCTTGGAC
CAGAATGTTATTAAGCTCATATCTTTAG
Found at i:20620488 original size:30 final size:30
Alignment explanation
Indices: 20620447--20620515 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
20620437 AGACAACAAA
*
20620447 AAAGCAATTGGGTGGACCATTGCA-ATCATC
1 AAAGGAATTGGGTGGACCATTGCAGA-CATC
* *
20620477 GAAGGAATTGGGTGGGCCATTGCAGACATC
1 AAAGGAATTGGGTGGACCATTGCAGACATC
20620507 AAAGGAATT
1 AAAGGAATT
20620516 AGTCCATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (30 bp):
AAAGGAATTGGGTGGACCATTGCAGACATC
Found at i:20623055 original size:2 final size:2
Alignment explanation
Indices: 20623050--20623076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20623040 AAATAAATAA
20623050 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
20623077 AACCATTGAC
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:20623318 original size:34 final size:34
Alignment explanation
Indices: 20623279--20623372 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 34
20623269 GGGAAAGAGA
* *
20623279 GCCATTTGAGGGTTGATTTTGGAGGCTGGAAAGT
1 GCCATTTGACGGCTGATTTTGGAGGCTGGAAAGT
** * * *
20623313 GCCATTTTTCTGCTGGTTTTGGAGGTTGGAAAGT
1 GCCATTTGACGGCTGATTTTGGAGGCTGGAAAGT
** *
20623347 GCCATTTTTCTGCTGATTTTGGAGGC
1 GCCATTTGACGGCTGATTTTGGAGGC
20623373 CAAAAAGTGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.16, C:0.13, G:0.33, T:0.38
Consensus pattern (34 bp):
GCCATTTGACGGCTGATTTTGGAGGCTGGAAAGT
Found at i:20623382 original size:34 final size:34
Alignment explanation
Indices: 20623292--20623372 Score: 144
Period size: 34 Copynumber: 2.4 Consensus size: 34
20623282 ATTTGAGGGT
20623292 TGATTTTGGAGGCTGGAAAGTGCCATTTTTCTGC
1 TGATTTTGGAGGCTGGAAAGTGCCATTTTTCTGC
* *
20623326 TGGTTTTGGAGGTTGGAAAGTGCCATTTTTCTGC
1 TGATTTTGGAGGCTGGAAAGTGCCATTTTTCTGC
20623360 TGATTTTGGAGGC
1 TGATTTTGGAGGC
20623373 CAAAAAGTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (34 bp):
TGATTTTGGAGGCTGGAAAGTGCCATTTTTCTGC
Found at i:20623707 original size:17 final size:16
Alignment explanation
Indices: 20623685--20623718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20623675 GGACGGTGGG
*
20623685 AGAGAAAGAAAGAAAGA
1 AGAGAAA-AAAAAAAGA
20623702 AGAGAAAAAAAAAAGA
1 AGAGAAAAAAAAAAGA
20623718 A
1 A
20623719 AAAGAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AGAGAAAAAAAAAAGA
Found at i:20623718 original size:11 final size:11
Alignment explanation
Indices: 20623689--20623736 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
20623679 GGTGGGAGAG
20623689 AAAGAAAGAAAGA
1 AAAGAAA-AAA-A
*
20623702 AGAGAAAAAAA
1 AAAGAAAAAAA
*
20623713 AAAGAAAAAGA
1 AAAGAAAAAAA
20623724 AAAGAAAAGAAA
1 AAAGAAAA-AAA
20623736 A
1 A
20623737 TAACAAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 18 0.60
12 6 0.20
13 6 0.20
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:20627588 original size:20 final size:20
Alignment explanation
Indices: 20627560--20627608 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
20627550 TTATAATTAG
*
20627560 TTTATTTTTAAGTGAGTTAT
1 TTTAATTTTAAGTGAGTTAT
* * * *
20627580 TTTAATTTTATGTTATTTCT
1 TTTAATTTTAAGTGAGTTAT
20627600 TTTAATTTT
1 TTTAATTTT
20627609 GTTATTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTTAAGTGAGTTAT
Found at i:20627618 original size:21 final size:20
Alignment explanation
Indices: 20627579--20627618 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20627569 AAGTGAGTTA
*
20627579 TTTTAATTTTATGTTATTTC
1 TTTTAATTTTATATTATTTC
*
20627599 TTTTAATTTTGTTATTATTT
1 TTTTAATTTT-ATATTATTT
20627619 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTAATTTTATATTATTTC
Found at i:20631097 original size:24 final size:24
Alignment explanation
Indices: 20631069--20631120 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
20631059 GGAAGAAGAT
20631069 AGGCAAATTCCAATCATCCTTGGG
1 AGGCAAATTCCAATCATCCTTGGG
20631093 AGGCAAATTCCAATCATCCTTGGG
1 AGGCAAATTCCAATCATCCTTGGG
20631117 AGGC
1 AGGC
20631121 CATTCTTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (24 bp):
AGGCAAATTCCAATCATCCTTGGG
Found at i:20637414 original size:11 final size:11
Alignment explanation
Indices: 20637398--20637423 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20637388 TTAAAAAAAT
20637398 AAAAAATTCAA
1 AAAAAATTCAA
20637409 AAAAAATTCAA
1 AAAAAATTCAA
20637420 AAAA
1 AAAA
20637424 TTAAAGTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTCAA
Found at i:20642815 original size:2 final size:2
Alignment explanation
Indices: 20642803--20642840 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
20642793 ACCATATACC
* *
20642803 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20642841 CAATCATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20650384 original size:39 final size:39
Alignment explanation
Indices: 20650330--20650408 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
20650320 AGATAGGTGC
*
20650330 ACCTCATTCATGATTGTCCCAATCCTAGGATGATATTTT
1 ACCTCACTCATGATTGTCCCAATCCTAGGATGATATTTT
20650369 ACCTCACTCATGATTGTCCCAATCCTAGGATGATATTTT
1 ACCTCACTCATGATTGTCCCAATCCTAGGATGATATTTT
20650408 A
1 A
20650409 ATTATCTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (39 bp):
ACCTCACTCATGATTGTCCCAATCCTAGGATGATATTTT
Found at i:20651677 original size:15 final size:16
Alignment explanation
Indices: 20651657--20651686 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20651647 TTCTTTTAAT
20651657 TTAGTTTTT-TATTTA
1 TTAGTTTTTATATTTA
20651672 TTAGTTTTTATATTT
1 TTAGTTTTTATATTT
20651687 TTCATAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (16 bp):
TTAGTTTTTATATTTA
Found at i:20653174 original size:15 final size:14
Alignment explanation
Indices: 20653151--20653193 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
20653141 TCCTTTTTTT
20653151 TCTCTTTTTTCTTC
1 TCTCTTTTTTCTTC
* *
20653165 TTTACTTTTTTTTTC
1 TCT-CTTTTTTCTTC
20653180 TCT-TTTTTTCTTC
1 TCTCTTTTTTCTTC
20653193 T
1 T
20653194 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTCTTTTTTCTTC
Found at i:20653185 original size:25 final size:27
Alignment explanation
Indices: 20653143--20653199 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
20653133 ATTTTTATTC
*
20653143 CTTTTTTTTCTCTTTTTTCTTCTT-TA
1 CTTTTTTTTCTCTCTTTTCTTCTTCTA
*
20653169 CTTTTTTTT-TCTCTTTTTTTCTTCTA
1 CTTTTTTTTCTCTCTTTTCTTCTTCTA
20653195 -TTTTT
1 CTTTTT
20653200 ATTATTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (27 bp):
CTTTTTTTTCTCTCTTTTCTTCTTCTA
Found at i:20654529 original size:24 final size:22
Alignment explanation
Indices: 20654488--20654560 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 22
20654478 AAGCCGACAA
*
20654488 AAAAAAAAGGGAAGGAAAATGAGAG
1 AAAAAAAA--GAA-GAAAAAGAGAG
*
20654513 AAAAGACAAGAAAGAAAAAGAAAGAG
1 AAAA-AAAAG-AAGAAAAAG--AGAG
*
20654539 AAAAAAAAGAAGAAAAGGAGAG
1 AAAAAAAAGAAGAAAAAGAGAG
20654561 GGAGCATCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 4 0.10
24 15 0.38
25 10 0.25
26 11 0.28
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.01
Consensus pattern (22 bp):
AAAAAAAAGAAGAAAAAGAGAG
Found at i:20654537 original size:14 final size:14
Alignment explanation
Indices: 20654513--20654554 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
20654503 AAAATGAGAG
*
20654513 AAAAGACAAGAAAGA
1 AAAAGA-AAGAAAAA
20654528 AAAAGAAAGAGAAAA
1 AAAAGAAAGA-AAAA
20654543 AAAAG-AAGAAAA
1 AAAAGAAAGAAAA
20654555 GGAGAGGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 14 0.56
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:20654547 original size:11 final size:13
Alignment explanation
Indices: 20654513--20654554 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
20654503 AAAATGAGAG
20654513 AAAAGACAAGAAAGA
1 AAAAGA-AAG-AAGA
20654528 AAAAGAAAG-AGA
1 AAAAGAAAGAAGA
20654540 AAAA-AAAGAAGA
1 AAAAGAAAGAAGA
20654552 AAA
1 AAA
20654555 GGAGAGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.15
12 13 0.50
14 3 0.12
15 6 0.23
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAGA
Found at i:20654697 original size:70 final size:69
Alignment explanation
Indices: 20654524--20654775 Score: 303
Period size: 70 Copynumber: 3.6 Consensus size: 69
20654514 AAAGACAAGA
* * *
20654524 AAGAAAAAGAAAGAGAAAAAAAAGAAGAAA-AGGAGAGGGAGCATCGGCGTCGAGGAGAAGAAGG
1 AAGAAAAAGAAAAAGAAAAAGAAGAAGAAAGA-GAGAGGGAGCAGC-GCGTCGAGGAGAAGAAGG
* * *
20654588 TGAAGA
64 AGAGGG
*
20654594 AAGAAAAGAAAAAAAAGAAAAAGAAGAAGAAAGAGAGAGGGAGCAGCGACGTCGAGGAGAAGAAG
1 AAG-AAA-AAGAAAAAGAAAAAGAAGAAGAAAGAGAGAGGGAGCAGCG-CGTCGAGGAGAAGAAG
20654659 GAGAGGG
63 GAGAGGG
* * * * *
20654666 AAGAAAAAGAAAGAGAAAAAGAAGAAGAAAGAGAGAGGGGGCAGCTGTGTCGAAGAGAAGAAGAA
1 AAGAAAAAGAAAAAGAAAAAGAAGAAGAAAGAGAGAGGGAGCAGC-GCGTCGAGGAGAAGAAGGA
20654731 GAGGG
65 GAGGG
*
20654736 -AG-AAAAGAAGAAAGAAAAAGAATAAGAAAGAGAGAGGGAG
1 AAGAAAAAGAA-AAAGAAAAAGAAGAAGAAAGAGAGAGGGAG
20654776 TAACGACGGT
Statistics
Matches: 160, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
68 7 0.04
69 29 0.18
70 59 0.37
71 8 0.05
72 56 0.35
73 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.37, T:0.03
Consensus pattern (69 bp):
AAGAAAAAGAAAAAGAAAAAGAAGAAGAAAGAGAGAGGGAGCAGCGCGTCGAGGAGAAGAAGGAG
AGGG
Found at i:20655112 original size:2 final size:2
Alignment explanation
Indices: 20655101--20655134 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20655091 TGTTTTTCTT
*
20655101 TA TA -A TA TA TA TA AA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20655135 CTACATGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20655596 original size:60 final size:60
Alignment explanation
Indices: 20655501--20655739 Score: 302
Period size: 60 Copynumber: 4.0 Consensus size: 60
20655491 TTTGATTTAA
* *** * * *
20655501 AAAGGGGGACTTGAAGCCTTGATTTATAT-TGGGTGGCATGGGTAATTTCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCAATTTATATAT-GGTGGCATGGGCAGTTCCCACGAGTAGGT
* * * *
20655561 AAAGGGGGACCTAAAGCCCCCATTTATATATGGTGGCGTGCGCAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCAATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
* * * * *
20655621 AAAGGAGGACTTGAAGCCCCAATTTATATATGATGGCATGGGTAGTTCCCACAAGTAGGT
1 AAAGGGGGACCTGAAGCCCCAATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
*
20655681 AAAGGGGGACCTGAAGCCTCAATTTATATATGGTGGCAT-GGCAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCAATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
20655740 GATGATGTCT
Statistics
Matches: 153, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
59 18 0.12
60 134 0.88
61 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (60 bp):
AAAGGGGGACCTGAAGCCCCAATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
Found at i:20655714 original size:120 final size:119
Alignment explanation
Indices: 20655501--20655739 Score: 345
Period size: 120 Copynumber: 2.0 Consensus size: 119
20655491 TTTGATTTAA
* *** * * *
20655501 AAAGGGGGACTTGAAGCCTTGATTTATATTGGGTGGCATGGGTAATTTCCACGAGTAGGTAAAGG
1 AAAGGAGGACTTGAAGCCCCAATTTATATTGGATGGCATGGGTAATTCCCACAAGTAGGTAAAGG
* *
20655566 GGGACCTAAAGCCCCCATTTATATATGGTGGCGTGCGCAGTTCCCACGAGTAGGT
66 GGGACCTAAAGCCCCAATTTATATATGGTGGCATG-GCAGTTCCCACGAGTAGGT
*
20655621 AAAGGAGGACTTGAAGCCCCAATTTATATAT-GATGGCATGGGTAGTTCCCACAAGTAGGTAAAG
1 AAAGGAGGACTTGAAGCCCCAATTTATAT-TGGATGGCATGGGTAATTCCCACAAGTAGGTAAAG
* *
20655685 GGGGACCTGAAGCCTCAATTTATATATGGTGGCATGGCAGTTCCCACGAGTAGGT
65 GGGGACCTAAAGCCCCAATTTATATATGGTGGCATGGCAGTTCCCACGAGTAGGT
20655740 GATGATGTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
119 19 0.18
120 86 0.81
121 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (119 bp):
AAAGGAGGACTTGAAGCCCCAATTTATATTGGATGGCATGGGTAATTCCCACAAGTAGGTAAAGG
GGGACCTAAAGCCCCAATTTATATATGGTGGCATGGCAGTTCCCACGAGTAGGT
Found at i:20661778 original size:20 final size:20
Alignment explanation
Indices: 20661753--20661798 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
20661743 CTTATAAACC
20661753 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
20661773 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
20661793 TCAAAT
1 TCAAAT
20661799 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:20667683 original size:23 final size:23
Alignment explanation
Indices: 20667639--20667683 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
20667629 TGACATGGGA
* *
20667639 AGTAAAATAATATTTAATAATAT
1 AGTAAAAAAATAATTAATAATAT
20667662 AGTAACAAAAATAATTAA-AATA
1 AGTAA-AAAAATAATTAATAATA
20667684 AAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
AGTAAAAAAATAATTAATAATAT
Found at i:20667814 original size:19 final size:18
Alignment explanation
Indices: 20667768--20667814 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
20667758 GCATGTGAAG
20667768 AGAAA-AAGAGAAGGAAA
1 AGAAAGAAGAGAAGGAAA
20667785 A-AAACGAAAGAGAAGAGAAA
1 AGAAA-G-AAGAGAAG-GAAA
20667805 AGAAAGAAGA
1 AGAAAGAAGA
20667815 AAAAGCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
19 12 0.48
20 6 0.24
21 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAGAAGAGAAGGAAA
Found at i:20667951 original size:12 final size:12
Alignment explanation
Indices: 20667907--20667962 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
20667897 CAAAAAAAGG
20667907 GAAG-AAAA-AA
1 GAAGAAAAAGAA
*
20667917 GAGAGAAAAGACAA
1 GA-AGAAAA-AGAA
20667931 GAAAGAAAAAGAA
1 G-AAGAAAAAGAA
*
20667944 GGAGAAAAAGAA
1 GAAGAAAAAGAA
20667956 GAAGAAA
1 GAAGAAA
20667963 GGGAGAGGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 2 0.05
11 2 0.05
12 19 0.50
13 5 0.13
14 9 0.24
15 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:20668000 original size:8 final size:7
Alignment explanation
Indices: 20667988--20668043 Score: 51
Period size: 8 Copynumber: 7.7 Consensus size: 7
20667978 GGCGTTAAGG
20667988 AGAAGAA
1 AGAAGAA
20667995 GAGAAGAA
1 -AGAAGAA
20668003 AGAAAGAA
1 AG-AAGAA
20668011 A-AAGAA
1 AGAAGAA
*
20668017 AGAAAAAA
1 AG-AAGAA
20668025 AGAAGAA
1 AGAAGAA
* *
20668032 AAAAGAG
1 AGAAGAA
20668039 AGAAG
1 AGAAG
20668044 GAACAGAGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
6 6 0.15
7 15 0.38
8 19 0.47
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:20668035 original size:10 final size:11
Alignment explanation
Indices: 20667990--20668042 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 11
20667980 CGTTAAGGAG
20667990 AAGAAGAGAAGA
1 AAGAA-AGAAGA
20668002 AAGAAAGAA-A
1 AAGAAAGAAGA
20668012 AAGAAAG-A-A
1 AAGAAAGAAGA
20668021 AA-AAAGAAGA
1 AAGAAAGAAGA
20668031 AA-AAAGAGAGA
1 AAGAAAGA-AGA
20668042 A
1 A
20668043 GGAACAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.11
9 5 0.13
10 16 0.42
11 8 0.21
12 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:20668157 original size:20 final size:19
Alignment explanation
Indices: 20668131--20668181 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 19
20668121 GGCGTCGAGG
20668131 AGAAGAAAGAGAGAGAAGA
1 AGAAGAAAGAGAGAGAAGA
20668150 AGGAAGAAAGA-A-A-AAGA
1 A-GAAGAAAGAGAGAGAAGA
20668167 AGAAGAAAGAGAGAG
1 AGAAGAAAGAGAGAG
20668182 GGAGCAGCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 2 0.07
19 2 0.07
20 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AGAAGAAAGAGAGAGAAGA
Found at i:20668539 original size:2 final size:2
Alignment explanation
Indices: 20668520--20668559 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
20668510 CGTTTTTCTT
* *
20668520 TA TA -A TA TA TC TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20668560 CTACATGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20669141 original size:59 final size:59
Alignment explanation
Indices: 20668927--20669164 Score: 300
Period size: 60 Copynumber: 4.0 Consensus size: 59
20668917 TTGATTTAAA
* * * * *
20668927 AAAGGGGACCTGAAGCCTCGACTTATAT-TAAGTGGTATGGGTAGTTCCCATGAGTAGGT
1 AAAGGGGACCTGAAGCCTCGATTTATATAT-GGTGGCATGGGCAGTTCCCACGAGTAGGT
* *** *
20668986 AAAGGGGGATCTGAAGCC-CTGATTTATATATGGTGATGTGGGCAATTCCCACGAGTAGGT
1 AAA-GGGGACCTGAAGCCTC-GATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
* *
20669046 AAAGGAGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGTTCCCACGAGTAGGT
1 AAAGG-GGACCTGAAGCCTCGATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
* *
20669106 AAAGGGGACCTAAAGCCTCAATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
1 AAAGGGGACCTGAAGCCTCGATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
20669165 GATGATGTCT
Statistics
Matches: 158, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
59 56 0.35
60 100 0.63
61 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (59 bp):
AAAGGGGACCTGAAGCCTCGATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
Found at i:20669155 original size:119 final size:119
Alignment explanation
Indices: 20668927--20669164 Score: 302
Period size: 119 Copynumber: 2.0 Consensus size: 119
20668917 TTGATTTAAA
* * * *
20668927 AAAGGGGACCTGAAGCCTCGACTTATATTAAGTGGTATGGGTAGTTCCCATGAGTAGGTAAAGGG
1 AAAGGGGACCTGAAGCCCCGACTTATATTAAGTGGCATGGGCAGTTCCCACGAGTAGGTAAAGGG
* * * **
20668992 GGATCTGAAGCCCTGATTTATATATGGTGATGTGGGCAATTCCCACGAGTAGGT
66 GGACCTAAAGCCCTAATTTATATATGGTGACATGGGCAATTCCCACGAGTAGGT
* * *
20669046 AAAGGAGGACCTGAAGCCCCGATTTATA-TATGGTGGCGTGGGCAGTTCCCACGAGTAGGTAAA-
1 AAAGG-GGACCTGAAGCCCCGACTTATATTA-AGTGGCATGGGCAGTTCCCACGAGTAGGTAAAG
* *
20669109 GGGGACCTAAAG-CCTCAATTTATATATGGTGGCATGGGCAGTTCCCACGAGTAGGT
64 GGGGACCTAAAGCCCT-AATTTATATATGGTGACATGGGCAATTCCCACGAGTAGGT
20669165 GATGATGTCT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 3 0.03
119 52 0.51
120 47 0.46
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (119 bp):
AAAGGGGACCTGAAGCCCCGACTTATATTAAGTGGCATGGGCAGTTCCCACGAGTAGGTAAAGGG
GGACCTAAAGCCCTAATTTATATATGGTGACATGGGCAATTCCCACGAGTAGGT
Found at i:20697407 original size:13 final size:13
Alignment explanation
Indices: 20697389--20697413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20697379 AGAGAAATTG
20697389 TGATTTTATAAAA
1 TGATTTTATAAAA
20697402 TGATTTTATAAA
1 TGATTTTATAAA
20697414 TTTTCTGGAA
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:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20700260 original size:1 final size:1
Alignment explanation
Indices: 20700249--20700391 Score: 250
Period size: 1 Copynumber: 143.0 Consensus size: 1
20700239 ATATAATAAG
*
20700249 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* **
20700314 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAATTA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20700379 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
20700392 GAGAAAACAA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 136 1.00
ACGTcount: A:0.97, C:0.01, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:20702060 original size:28 final size:27
Alignment explanation
Indices: 20702024--20702076 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
20702014 ATATCCTGGT
*
20702024 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
20702051 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
20702077 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:20702144 original size:20 final size:20
Alignment explanation
Indices: 20702121--20702166 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
20702111 CTTCTAAACC
20702121 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
20702141 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
20702161 TCAAAT
1 TCAAAT
20702167 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:20704022 original size:71 final size:71
Alignment explanation
Indices: 20703938--20704126 Score: 263
Period size: 71 Copynumber: 2.7 Consensus size: 71
20703928 ACTACTAGAT
* * * * *
20703938 AGGAATCATAGTCAACCTTATTCCAGAAAGATCTAGAAAATCAAGTTTAGAACGACCATAGTCAA
1 AGGAAACATAGTCAACCTTGTTCCAGAAAGATCTAGAAAATCAAGTTCAAAACAACCATAGTCAA
20704003 CTACAA
66 CTACAA
* *
20704009 AGGAAACATAGTCAACCTTGTTCCAGAAAGATCAAGAAAATCAAGTTCAAAACAACCATAGTCGA
1 AGGAAACATAGTCAACCTTGTTCCAGAAAGATCTAGAAAATCAAGTTCAAAACAACCATAGTCAA
20704074 CTACAA
66 CTACAA
* * * *
20704080 AGGAAGCATGGTCGACCTTGTTTCAGAAAGAT-TAAGAAAATCAAGTT
1 AGGAAACATAGTCAACCTTGTTCCAGAAAGATCT-AGAAAATCAAGTT
20704127 GAATAATAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 105 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (71 bp):
AGGAAACATAGTCAACCTTGTTCCAGAAAGATCTAGAAAATCAAGTTCAAAACAACCATAGTCAA
CTACAA
Found at i:20704873 original size:52 final size:52
Alignment explanation
Indices: 20704752--20704878 Score: 154
Period size: 50 Copynumber: 2.5 Consensus size: 52
20704742 CAAAAATCCT
* * ** *
20704752 TTGTGGATTGTGT--GGGTTACTACTTGATCCCATAAAAAGCAAGAATCTCA
1 TTGTGGATTGTGTAAGGGTTATTGCTTGATCCCATAAAAAAAAAGAATCCCA
*
20704802 TTGTGGA-T-TGTAAGGGTTATTGCTTGATCCCGTAAAAAAAAAGAATCCCA
1 TTGTGGATTGTGTAAGGGTTATTGCTTGATCCCATAAAAAAAAAGAATCCCA
* *
20704852 TTGTGGATTGTGTAAAGGTTATCGCTT
1 TTGTGGATTGTGTAAGGGTTATTGCTT
20704879 TCTAGTAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.05
49 1 0.02
50 45 0.69
51 1 0.02
52 15 0.23
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (52 bp):
TTGTGGATTGTGTAAGGGTTATTGCTTGATCCCATAAAAAAAAAGAATCCCA
Found at i:20704887 original size:50 final size:50
Alignment explanation
Indices: 20704792--20704898 Score: 121
Period size: 50 Copynumber: 2.1 Consensus size: 50
20704782 CATAAAAAGC
* * * *
20704792 AAGAATCTCATTGTGGATTGTAAGGGTTATTGCTTGATCCCGTAAAA-AAA
1 AAGAATCCCATTGTGGATTGTAAAGGTTATCGCTT-ATCCAGTAAAATAAA
*
20704842 AAGAATCCCATTGTGGATTGTGTAAAGGTTATCGCTT-TCTAGTAAAATAAA
1 AAGAATCCCATTGTGGA-T-TGTAAAGGTTATCGCTTATCCAGTAAAATAAA
20704893 AA-AATC
1 AAGAATC
20704899 TTAATAATGG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
50 28 0.57
51 6 0.12
52 15 0.31
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (50 bp):
AAGAATCCCATTGTGGATTGTAAAGGTTATCGCTTATCCAGTAAAATAAA
Found at i:20715379 original size:28 final size:28
Alignment explanation
Indices: 20715339--20715463 Score: 128
Period size: 28 Copynumber: 4.5 Consensus size: 28
20715329 TGATTACAAG
*
20715339 ATGTAG-TATTACACGCCATGTTGAAAA
1 ATGTAGTTATTACATGCCATGTTGAAAA
* *
20715366 ATGTAATTGTTACATGCCATGTT-AAAGA
1 ATGTAGTTATTACATGCCATGTTGAAA-A
* * ** *
20715394 TTTTAGTTATTACATATCATGTTTAAAA
1 ATGTAGTTATTACATGCCATGTTGAAAA
*
20715422 ATGTAGTTATTACATGTCATGTTGAAAA
1 ATGTAGTTATTACATGCCATGTTGAAAA
* *
20715450 ATTTAGTTGTTACA
1 ATGTAGTTATTACA
20715464 CACTTTGATG
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
27 8 0.10
28 69 0.86
29 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (28 bp):
ATGTAGTTATTACATGCCATGTTGAAAA
Found at i:20715407 original size:56 final size:56
Alignment explanation
Indices: 20715345--20715466 Score: 147
Period size: 56 Copynumber: 2.2 Consensus size: 56
20715335 CAAGATGTAG
* * *
20715345 TATTACACGCCATGTTGAAAAATGTAATTGTTACATGCCATGTT-AAAGATTTTAGT
1 TATTACACACCATGTTGAAAAATGTAATTATTACATGCCATGTTGAAA-AATTTAGT
* * * * *
20715401 TATTACATATCATGTTTAAAAATGTAGTTATTACATGTCATGTTGAAAAATTTAGT
1 TATTACACACCATGTTGAAAAATGTAATTATTACATGCCATGTTGAAAAATTTAGT
*
20715457 TGTTACACAC
1 TATTACACAC
20715467 TTTGATGAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
56 51 0.94
57 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (56 bp):
TATTACACACCATGTTGAAAAATGTAATTATTACATGCCATGTTGAAAAATTTAGT
Found at i:20715478 original size:56 final size:56
Alignment explanation
Indices: 20715345--20715492 Score: 128
Period size: 56 Copynumber: 2.7 Consensus size: 56
20715335 CAAGATGTAG
** * * *
20715345 TATTACACGCCATGTTGAAAAATGTAATTGTTACATGCCATGTTAAAGATTTTAGT
1 TATTACACATCATGATGAAAAATGTAATTATTACATGCCATGTTAAAGAATTTAGT
* * * * *
20715401 TATTACATATCATGTTTAAAAATGTAGTTATTACATGTCATGTTGAAA-AATTTAGT
1 TATTACACATCATGATGAAAAATGTAATTATTACATGCCATGTT-AAAGAATTTAGT
* *
20715457 TGTTACACA-CTTTGATGAAAAA-G---TTATTACATGCCA
1 TATTACACATC-ATGATGAAAAATGTAATTATTACATGCCA
20715493 CACCATGATT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
52 12 0.16
55 2 0.03
56 59 0.78
57 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (56 bp):
TATTACACATCATGATGAAAAATGTAATTATTACATGCCATGTTAAAGAATTTAGT
Found at i:20716105 original size:20 final size:20
Alignment explanation
Indices: 20716082--20716132 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
20716072 TAAATATGAG
*
20716082 TATTTATCAAAGATTACGAC
1 TATTAATCAAAGATTACGAC
** *
20716102 TATTAATCAACTATTACTAC
1 TATTAATCAAAGATTACGAC
*
20716122 TATTCATCAAA
1 TATTAATCAAA
20716133 AGGTTATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (20 bp):
TATTAATCAAAGATTACGAC
Found at i:20720103 original size:14 final size:14
Alignment explanation
Indices: 20720068--20720112 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
20720058 ATTCAAATTT
*
20720068 AAAATCAATAATTAC
1 AAAAT-AATAATAAC
*
20720083 AAAAATAATTATAAC
1 -AAAATAATAATAAC
20720098 AAAATAATAATAAC
1 AAAATAATAATAAC
20720112 A
1 A
20720113 TCAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 7 0.27
16 5 0.19
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATAATAATAAC
Found at i:20725512 original size:13 final size:13
Alignment explanation
Indices: 20725494--20725518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20725484 ATGTTGACTA
20725494 GATTTTTCAAAAT
1 GATTTTTCAAAAT
20725507 GATTTTTCAAAA
1 GATTTTTCAAAA
20725519 GTGCTTTCAA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
GATTTTTCAAAAT
Found at i:20740239 original size:13 final size:13
Alignment explanation
Indices: 20740221--20740245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20740211 AGAGAAATTG
20740221 TGATTTTATAAAA
1 TGATTTTATAAAA
20740234 TGATTTTATAAA
1 TGATTTTATAAA
20740246 TTTTTTGAAA
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:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20749678 original size:35 final size:35
Alignment explanation
Indices: 20749590--20749678 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
20749580 GTCTTGGTAG
* * * *
20749590 AGGTTACGTCTGATCCTACAAAAGGCAAGTTGTAG
1 AGGTTACGCCTGATCCTATAAAAGGCAAGTTCTAA
* * * *
20749625 AGGTTATGCTTGATCCTATAAGAGGCACGTTCTAA
1 AGGTTACGCCTGATCCTATAAAAGGCAAGTTCTAA
*
20749660 AGGTTACGCCTGACCCTAT
1 AGGTTACGCCTGATCCTAT
20749679 TGGAAAGGCC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (35 bp):
AGGTTACGCCTGATCCTATAAAAGGCAAGTTCTAA
Found at i:20751256 original size:76 final size:77
Alignment explanation
Indices: 20751160--20751322 Score: 229
Period size: 76 Copynumber: 2.1 Consensus size: 77
20751150 TGAATTTCAC
* * * * *
20751160 AAATTAAAATGATATTCTTAATTTTAGAAATTTCTTTTAAAGTAGGAAACAATTTCTTGTTCTTT
1 AAATTAAAATGATATCCTTAATTTTAGAAATTACATTTAAAGTAAGAAACAATTTCTTATTCTTT
20751225 ACGAATCACC-A
66 ACGAATCACCAA
** * *
20751236 AAATTAAAATTCTATCCTTAATTTTAGGAATTACATTTAAAGTAAGAAATAATTTCTTATTCTTT
1 AAATTAAAATGATATCCTTAATTTTAGAAATTACATTTAAAGTAAGAAACAATTTCTTATTCTTT
*
20751301 ATGAATCACCAA
66 ACGAATCACCAA
20751313 AAATTAAAAT
1 AAATTAAAAT
20751323 AGATGGCATT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
76 65 0.86
77 11 0.14
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (77 bp):
AAATTAAAATGATATCCTTAATTTTAGAAATTACATTTAAAGTAAGAAACAATTTCTTATTCTTT
ACGAATCACCAA
Found at i:20757069 original size:19 final size:19
Alignment explanation
Indices: 20757045--20757081 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20757035 GGTGGTAAGG
20757045 TGAAAATGGCATGGAAGCT
1 TGAAAATGGCATGGAAGCT
*
20757064 TGAAAATGGCGTGGAAGC
1 TGAAAATGGCATGGAAGC
20757082 ATGGAGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.35, T:0.19
Consensus pattern (19 bp):
TGAAAATGGCATGGAAGCT
Found at i:20761902 original size:77 final size:77
Alignment explanation
Indices: 20761796--20761959 Score: 238
Period size: 77 Copynumber: 2.1 Consensus size: 77
20761786 TGAATTTCAC
* * * *
20761796 AAATTAAAATGCTATACTTAATTTTAGGAATTTCTTTTAAAGTAATAAACAATTTCCTATTCTTT
1 AAATTAAAATGCTATACTAAATTTTAGGAATTGCTTTTAAAGTAAGAAACAATTTCCTATTCTTA
*
20761861 ATGAATCACGCA
66 ATGAATCACCCA
* * * * *
20761873 AAATTAAAATTCTATCCTAAATTTTAGGAATTGCTTTTCAAGTGAGAAACAATTTCTTATTCTTA
1 AAATTAAAATGCTATACTAAATTTTAGGAATTGCTTTTAAAGTAAGAAACAATTTCCTATTCTTA
20761938 ATGAATCACCCA
66 ATGAATCACCCA
20761950 AAATTAAAAT
1 AAATTAAAAT
20761960 AAATGGCATT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (77 bp):
AAATTAAAATGCTATACTAAATTTTAGGAATTGCTTTTAAAGTAAGAAACAATTTCCTATTCTTA
ATGAATCACCCA
Found at i:20765480 original size:14 final size:13
Alignment explanation
Indices: 20765461--20765496 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
20765451 GGTCGACAAG
*
20765461 AGAAGAGAAAAGAA
1 AGAAGAAAAAAG-A
20765475 AGAAGAAAAAAGA
1 AGAAGAAAAAAGA
20765488 AGAAGAAAA
1 AGAAGAAAA
20765497 TGGGGGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAGA
Found at i:20765883 original size:20 final size:21
Alignment explanation
Indices: 20765853--20765899 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
20765843 GGTGCCAGAG
*
20765853 GAGAAAGAGGAAGAAGAGAAA
1 GAGAAAAAGGAAGAAGAGAAA
20765874 G-GAAAAAGGAAGAAGAGAAA
1 GAGAAAAAGGAAGAAGAGAAA
20765894 GAGAAA
1 GAGAAA
20765900 CGTCGACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (21 bp):
GAGAAAAAGGAAGAAGAGAAA
Found at i:20766000 original size:8 final size:8
Alignment explanation
Indices: 20765983--20766012 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
20765973 CACGAAACAA
*
20765983 TAGCGAAG
1 TAGCGTAG
20765991 TAGCGTAG
1 TAGCGTAG
20765999 TAGCGTAG
1 TAGCGTAG
20766007 TAGCGT
1 TAGCGT
20766013 TCTGTTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (8 bp):
TAGCGTAG
Found at i:20766674 original size:60 final size:60
Alignment explanation
Indices: 20766570--20766866 Score: 346
Period size: 60 Copynumber: 5.0 Consensus size: 60
20766560 TTGATTATAA
* * * *
20766570 AAAGGGGGACCTTAAGCCCCAATTTATATTTAGTGACATAGGTAGTTCCCACAAGTAGGC
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAGTTCCCACAAGTAGGC
* * * *
20766630 AAAGGGGGACCTGAAGCCCTGATTTATATTTGGTGATGTGGGTAGTTCCCACGAGTAGGC
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAGTTCCCACAAGTAGGC
* * * * * *
20766690 AAAGAGGGACTTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTTCCACGAGTAGGC
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAGTTCCCACAAGTAGGC
* * *
20766750 AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAATTTCCACAAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAGTTCCCACAAGTAGGC
* * * * * * * * *
20766810 AAAAGGGGACTTGAAGTCCCAATTCATA--TGGTGGCGTGGGCAGTTCCCACGAGTAGG
1 AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAGTTCCCACAAGTAGG
20766867 TGATGATGTC
Statistics
Matches: 207, Mismatches: 30, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
58 23 0.11
60 184 0.89
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (60 bp):
AAAGGGGGACCTGAAGCCCCGATTTATATTTAGTGACGTGGGTAGTTCCCACAAGTAGGC
Found at i:20769834 original size:18 final size:18
Alignment explanation
Indices: 20769811--20769847 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20769801 ATAGTGAAGA
20769811 AGGAAATTTAGAAGCTAC
1 AGGAAATTTAGAAGCTAC
20769829 AGGAAATTTAGAAGCTAC
1 AGGAAATTTAGAAGCTAC
20769847 A
1 A
20769848 CTTGTAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
AGGAAATTTAGAAGCTAC
Found at i:20782986 original size:2 final size:2
Alignment explanation
Indices: 20782970--20783012 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
20782960 AAACTATCCC
20782970 TA TA -A TA TA -A 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
20783010 TA T
1 TA T
20783013 GTCATTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20783859 original size:59 final size:60
Alignment explanation
Indices: 20783674--20783904 Score: 272
Period size: 60 Copynumber: 3.9 Consensus size: 60
20783664 ATTGTAAAAG
* *
20783674 GGGGGACTTTAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAGGCAAA
1 GGGGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAGGCAAA
* * *
20783734 GGGGGACTTGAAGCCTCGATTTATATTTGGTGACATGGGTAGTTTCCACGAGTAGGCAAA
1 GGGGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAGGCAAA
** * * * *
20783794 AAGGGACCTGAAGCCCCGATTTATATTT-GTGACGTGGGTAATTCCCATGAGTAGGTAAA
1 GGGGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAGGCAAA
* * * * * *
20783853 GGGGGACCTAAAGTCTCGATTCATATGGTGGTG---TGGGTAGTTCCCATGAGTA
1 GGGGGACCTGAAGCCCCGATTTATAT-TTGGTGACATGGGTAGTTCCCACGAGTA
20783905 CGTGATGATG
Statistics
Matches: 149, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
58 18 0.12
59 46 0.31
60 82 0.55
61 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (60 bp):
GGGGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAGGCAAA
Found at i:20786314 original size:178 final size:177
Alignment explanation
Indices: 20786015--20786369 Score: 674
Period size: 178 Copynumber: 2.0 Consensus size: 177
20786005 AATCCATTAA
20786015 TTTCGATTGTTTTTCACTTTTGAAGTAGAAAATTTTTTAAGTTTAGAAGGTGTCAAAATATGTGA
1 TTTCGATTGTTTTTCACTTTTGAAGTAGAAAATTTTTTAAGTTTAGAAGGTGTCAAAATATGTGA
20786080 TTTTATAGGACAATCTTTTGGAAATAAAAATTAGTGGTAATGATTTTCTTGATTTTTAAATGATC
66 TTTTATAGGACAATCTTTTGGAAATAAAAATTAGTGGTAATGATTTTCTTGATTTTTAAATGATC
20786145 AAAAATGATTTTTTCATAATTTTTGAAGCACATTGGCTATGGTAAAT
131 AAAAATGATTTTTTCATAATTTTTGAAGCACATTGGCTATGGTAAAT
20786192 NTTTCGATTGTTTTTCACTTTTGAAGTAGAAAATTTTTTAAGTTTAGAAGGTGTCAAAATATGTG
1 -TTTCGATTGTTTTTCACTTTTGAAGTAGAAAATTTTTTAAGTTTAGAAGGTGTCAAAATATGTG
20786257 ATTTTATAGGACAATCTTTTGGAAATAAAAATTAGTGGTAATGATTTTCTTGATTTTTAAATGAT
65 ATTTTATAGGACAATCTTTTGGAAATAAAAATTAGTGGTAATGATTTTCTTGATTTTTAAATGAT
* * *
20786322 CAAAAATGATTTTTTCATAATTTTTGGAGTACATTTGCTATGGTAAAT
130 CAAAAATGATTTTTTCATAATTTTTGAAGCACATTGGCTATGGTAAAT
20786370 GGGAACTGCA
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 174 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.44
Consensus pattern (177 bp):
TTTCGATTGTTTTTCACTTTTGAAGTAGAAAATTTTTTAAGTTTAGAAGGTGTCAAAATATGTGA
TTTTATAGGACAATCTTTTGGAAATAAAAATTAGTGGTAATGATTTTCTTGATTTTTAAATGATC
AAAAATGATTTTTTCATAATTTTTGAAGCACATTGGCTATGGTAAAT
Found at i:20787873 original size:68 final size:68
Alignment explanation
Indices: 20787694--20787953 Score: 240
Period size: 68 Copynumber: 3.8 Consensus size: 68
20787684 ATGTTTGTTG
* * * * * *
20787694 TGATGAATGCCAT-ACGATTATGCATATAATGCAAATTCCATATACCGTATGAGATGATTAAGTA
1 TGATGAATGCCATGA-GATGATGTATATGATGTATATTCCATATACCATATGAGATGATTAAGTA
20787758 TGCA
65 TGCA
* *** * *
20787762 T-ATGCATATTAT-AGGATTG-TGTATATGATGTAAATTCCATATACCATATGAGGTGATTAAGT
1 TGATGAATGCCATGA-GA-TGATGTATATGATGTATATTCCATATACCATATGAGATGATTAAGT
20787824 ATGCA
64 ATGCA
* * * * * * *
20787829 TGATAAATGCCATGAGATGATGTATATGATGTATATTCCATATACTACATCAGATGAGTAAGAAA
1 TGATGAATGCCATGAGATGATGTATATGATGTATATTCCATATACCATATGAGATGATTAAGTAT
20787894 GCA
66 GCA
* * * * * *
20787897 TGATGAATGCCATGAGATTATGTATATGATTTATTTTTCATATACCTTACGAGATGA
1 TGATGAATGCCATGAGATGATGTATATGATGTATATTCCATATACCATATGAGATGA
20787954 GTAATCTAGT
Statistics
Matches: 154, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
67 56 0.36
68 97 0.63
69 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (68 bp):
TGATGAATGCCATGAGATGATGTATATGATGTATATTCCATATACCATATGAGATGATTAAGTAT
GCA
Found at i:20798360 original size:28 final size:30
Alignment explanation
Indices: 20798302--20798361 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
20798292 TTTTTGAAAT
* *
20798302 TTATACTTTTGCCCCCATAAAAGTTAAAAA
1 TTATACTTTTGCCCCCATAAAACTGAAAAA
*
20798332 TTATATTTTTG-CCCCA-AAAACTGAAAAA
1 TTATACTTTTGCCCCCATAAAACTGAAAAA
20798360 TT
1 TT
20798362 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 5 0.19
30 10 0.37
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (30 bp):
TTATACTTTTGCCCCCATAAAACTGAAAAA
Found at i:20800688 original size:16 final size:16
Alignment explanation
Indices: 20800669--20800703 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20800659 GTATAAATCT
*
20800669 CATTTTTATTAAAAAA
1 CATTTTAATTAAAAAA
*
20800685 CATTTTAATTAGAAAA
1 CATTTTAATTAAAAAA
20800701 CAT
1 CAT
20800704 AATATTTTAT
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:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (16 bp):
CATTTTAATTAAAAAA
Found at i:20812688 original size:28 final size:29
Alignment explanation
Indices: 20812640--20812705 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
20812630 GTAAATTTTT
**
20812640 AAAAATTACACTTTTGCCCCCGTAAAGTG
1 AAAAATTACACTTTTGCCCCCAAAAAGTG
* *
20812669 AAAAATTACATTTTTG-CCCCAAAAATTG
1 AAAAATTACACTTTTGCCCCCAAAAAGTG
20812697 AAAAATTAC
1 AAAAATTAC
20812706 CAAAATGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (29 bp):
AAAAATTACACTTTTGCCCCCAAAAAGTG
Found at i:20821494 original size:26 final size:26
Alignment explanation
Indices: 20821458--20821519 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
20821448 TTGCATATGA
*
20821458 GATGATGATGATGGGATGATGTGTAT
1 GATGATGATGATGGGATGATGTGCAT
*
20821484 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
20821510 GTTGATGATG
1 GATGATGATG
20821520 GGTATATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.24, C:0.02, G:0.40, T:0.34
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:20821528 original size:26 final size:24
Alignment explanation
Indices: 20821458--20821529 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 24
20821448 TTGCATATGA
20821458 GATGATGATGATGGGATGATGTGTAT
1 GATGATGATGATGGGAT-ATG-GTAT
*
20821484 GATGATGATGATGGG--ATGGTGT
1 GATGATGATGATGGGATATGGTAT
*
20821506 GCATGTTGATGATGGGTATATGGT
1 G-ATGATGATGATGGG-ATATGGT
20821530 TGTAAATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 4 0.10
23 16 0.40
26 20 0.50
ACGTcount: A:0.24, C:0.01, G:0.40, T:0.35
Consensus pattern (24 bp):
GATGATGATGATGGGATATGGTAT
Found at i:20824916 original size:22 final size:22
Alignment explanation
Indices: 20824888--20824938 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
20824878 AAGCTTTGTA
*
20824888 CTCTGATCTTTAAAACCAAAGG
1 CTCTGATCTTTAAAACCAAAAG
*
20824910 CTTTGATCTTTAAAACCAAAAG
1 CTCTGATCTTTAAAACCAAAAG
20824932 CTCTGAT
1 CTCTGAT
20824939 ACCAATCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (22 bp):
CTCTGATCTTTAAAACCAAAAG
Found at i:20830829 original size:25 final size:25
Alignment explanation
Indices: 20830795--20830842 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
20830785 TTAATCCAGA
20830795 AGTGCATCAACCTAATGAGATAAGG
1 AGTGCATCAACCTAATGAGATAAGG
*
20830820 AGTGCATCAACCTGATGAGATAA
1 AGTGCATCAACCTAATGAGATAA
20830843 TGGGCCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (25 bp):
AGTGCATCAACCTAATGAGATAAGG
Found at i:20834313 original size:14 final size:15
Alignment explanation
Indices: 20834296--20834325 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20834286 CCAAAGCAGC
20834296 AGCAGAAAC-TCAAT
1 AGCAGAAACTTCAAT
20834310 AGCAGAAACTTCAAT
1 AGCAGAAACTTCAAT
20834325 A
1 A
20834326 ACATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (15 bp):
AGCAGAAACTTCAAT
Found at i:20845075 original size:61 final size:61
Alignment explanation
Indices: 20844974--20845100 Score: 211
Period size: 61 Copynumber: 2.1 Consensus size: 61
20844964 AAAACCTTTA
* * *
20844974 AGCA-TTTTAAGCATTTTGGAGTGGTTTTTGATATACGAAGAAAAACTTTTAAGCATTTTG
1 AGCATTTTTAAGCATTTTGGAGTGATTTTTGATACACGAAGAAAAACCTTTAAGCATTTTG
*
20845034 AGCATTTTTAAGCATTTTGGAGTGATTTTTGATACATGAAGAAAAACCTTTAAGCATTTTG
1 AGCATTTTTAAGCATTTTGGAGTGATTTTTGATACACGAAGAAAAACCTTTAAGCATTTTG
20845095 AGCATT
1 AGCATT
20845101 CTTCGCCAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 4 0.06
61 58 0.94
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (61 bp):
AGCATTTTTAAGCATTTTGGAGTGATTTTTGATACACGAAGAAAAACCTTTAAGCATTTTG
Found at i:20845271 original size:22 final size:22
Alignment explanation
Indices: 20845238--20845364 Score: 148
Period size: 22 Copynumber: 5.8 Consensus size: 22
20845228 TGGGGTATTA
* *
20845238 CGTGACTCATTTTCAAGCATTG
1 CGTGACTAATTTTTAAGCATTG
*
20845260 CGTTACTAATTTTT-AGACATTG
1 CGTGACTAATTTTTAAG-CATTG
* **
20845282 CGTGAGTAATTTTTGGGCATTG
1 CGTGACTAATTTTTAAGCATTG
*
20845304 CGTGACTAATTTTTAGGCATTG
1 CGTGACTAATTTTTAAGCATTG
* *
20845326 TGTTACTAATTTTTAAGCATTG
1 CGTGACTAATTTTTAAGCATTG
*
20845348 TGTGACTAATTTTTAAG
1 CGTGACTAATTTTTAAG
20845365 TTTTGCATGA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
21 2 0.02
22 88 0.97
23 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (22 bp):
CGTGACTAATTTTTAAGCATTG
Found at i:20845310 original size:66 final size:66
Alignment explanation
Indices: 20845202--20845361 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 66
20845192 AGTTTTTGTG
* * * * * * * * *
20845202 ATTTTTAGGCATTACGTAACCAGTTTTGGGGTATTACGTGACTCATTTTCAAGCATTGCGTTACT
1 ATTTTTAAGCATTGCGTGACTAATTTTTGGGCATTGCGTGACTAATTTTCAAGCATTGCGTTACT
20845267 A
66 A
* * * *
20845268 ATTTTT-AGACATTGCGTGAGTAATTTTTGGGCATTGCGTGACTAATTTTTAGGCATTGTGTTAC
1 ATTTTTAAG-CATTGCGTGACTAATTTTTGGGCATTGCGTGACTAATTTTCAAGCATTGCGTTAC
20845332 TA
65 TA
*
20845334 ATTTTTAAGCATTGTGTGACTAATTTTT
1 ATTTTTAAGCATTGCGTGACTAATTTTT
20845362 AAGTTTTGCA
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 1 0.01
66 74 0.96
67 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (66 bp):
ATTTTTAAGCATTGCGTGACTAATTTTTGGGCATTGCGTGACTAATTTTCAAGCATTGCGTTACT
A
Found at i:20845418 original size:22 final size:23
Alignment explanation
Indices: 20845372--20845425 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
20845362 AAGTTTTGCA
* *
20845372 TGACTAGTTGATATGGCATTGCG
1 TGACTGGTTGATATGGCATTACG
*
20845395 TGATTGGTTGATA-GGCATTACG
1 TGACTGGTTGATATGGCATTACG
20845417 TGACTGGTT
1 TGACTGGTT
20845426 AGTGAGGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (23 bp):
TGACTGGTTGATATGGCATTACG
Found at i:20845600 original size:22 final size:22
Alignment explanation
Indices: 20845531--20845615 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
20845521 TTGAGTCATA
* *
20845531 CAATGCCTAAAAACCAATCT-CG
1 CAATACCTAAAAACTAAT-TACG
* * * *
20845553 CAATACTTAAAAACTAGTGACA
1 CAATACCTAAAAACTAATTACG
*
20845575 CAATACCTAAAAACTAATTATG
1 CAATACCTAAAAACTAATTACG
*
20845597 CAATACCTAATAACTAATT
1 CAATACCTAAAAACTAATT
20845616 GATTTGCTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (22 bp):
CAATACCTAAAAACTAATTACG
Found at i:20865706 original size:29 final size:30
Alignment explanation
Indices: 20865647--20865708 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
20865637 ACAACATGAT
***
20865647 AATTTTTTATTCTTTAGTCTTTTCTAAATA
1 AATTTTTTATTCTTTAGTCTTAGATAAATA
20865677 AATTTTTTATTCTTTA-T-TTAGATAACATA
1 AATTTTTTATTCTTTAGTCTTAGATAA-ATA
20865706 AAT
1 AAT
20865709 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.18
29 7 0.25
30 16 0.57
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.56
Consensus pattern (30 bp):
AATTTTTTATTCTTTAGTCTTAGATAAATA
Found at i:20866242 original size:29 final size:27
Alignment explanation
Indices: 20866189--20866244 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
20866179 GTAAATCAAA
*
20866189 AGACAAAATTATTTTAAAAAGATTTAT
1 AGACAAAATTATATTAAAAAGATTTAT
* *
20866216 AGACAAATATTACTATTCAAAATATTTAT
1 AGACAAA-ATTA-TATTAAAAAGATTTAT
20866245 TAAAATATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
28 4 0.17
29 13 0.54
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (27 bp):
AGACAAAATTATATTAAAAAGATTTAT
Found at i:20877932 original size:60 final size:59
Alignment explanation
Indices: 20877859--20878155 Score: 321
Period size: 60 Copynumber: 4.9 Consensus size: 59
20877849 CATCATCACT
* * * * * *
20877859 TACTCGTGGGAACTGCCCACGCCACC-AGATGAATCGAGGCTACAGGTCCCCCTTTTTACC
1 TACTCGTGGGAACTACCCACGTCACCAATATAAATCGAGGCTTCAAGTCCCCC--TTTACC
* *
20877919 TACTCGTGGGAACTACCCACGTCACCAAATATAAATCGGGGCTTCAAGTTCCCCTTTACC
1 TACTCGTGGGAACTACCCACGTCACC-AATATAAATCGAGGCTTCAAGTCCCCCTTTACC
* ** * * * *
20877979 TACTCATGGGAACTACTTATGCCACCAAATATAAAT-AAGGGCTTCAAGTCCCCTTTTACC
1 TACTCGTGGGAACTACCCACGTCACC-AATATAAATCGA-GGCTTCAAGTCCCCCTTTACC
* * * *
20878039 TACTCGTGGGAGCTACCAACGTCACCAATTATAAATCGGGGCTTCAGGTCCCCCTTTACC
1 TACTCGTGGGAACTACCCACGTCACCAA-TATAAATCGAGGCTTCAAGTCCCCCTTTACC
*
20878099 TATTCGTGGGAACTACCCACGTCACCAATTATAAATCG-GGCCTTCAAGTCCCCCTTT
1 TACTCGTGGGAACTACCCACGTCACCAA-TATAAATCGAGG-CTTCAAGTCCCCCTTT
20878156 TACAAACAAA
Statistics
Matches: 200, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
59 4 0.02
60 176 0.88
62 20 0.10
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (59 bp):
TACTCGTGGGAACTACCCACGTCACCAATATAAATCGAGGCTTCAAGTCCCCCTTTACC
Found at i:20878072 original size:120 final size:121
Alignment explanation
Indices: 20877904--20878158 Score: 361
Period size: 120 Copynumber: 2.1 Consensus size: 121
20877894 GAGGCTACAG
* *
20877904 GTCCCCCTTTTTACCTACTCGTGGGAACTACCCACGTCACCAAATATAAATCGGGGCTTCAAGTT
1 GTCCCCC-TTTTACCTACTCGTGGGAACTACCAACGTCACCAAATATAAATCGGGGCTTCAAGTC
** *
20877969 CCCCTTTACCTACTCATGGGAACTACTTATGCCACCAAATATAAATAAGGG-CTTCAA
65 CCCCTTTACCTACTCATGGGAACTACCCACGCCACCAAATATAAAT-AGGGCCTTCAA
* * *
20878026 GT-CCCCTTTTACCTACTCGTGGGAGCTACCAACGTCACCAATTATAAATCGGGGCTTCAGGTCC
1 GTCCCCCTTTTACCTACTCGTGGGAACTACCAACGTCACCAAATATAAATCGGGGCTTCAAGTCC
* * * * *
20878090 CCCTTTACCTATTCGTGGGAACTACCCACGTCACCAATTATAAATCGGGCCTTCAA
66 CCCTTTACCTACTCATGGGAACTACCCACGCCACCAAATATAAATAGGGCCTTCAA
20878146 GTCCCCCTTTTAC
1 GTCCCCCTTTTAC
20878159 AAACAAATAT
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
119 3 0.03
120 99 0.84
121 14 0.12
122 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (121 bp):
GTCCCCCTTTTACCTACTCGTGGGAACTACCAACGTCACCAAATATAAATCGGGGCTTCAAGTCC
CCCTTTACCTACTCATGGGAACTACCCACGCCACCAAATATAAATAGGGCCTTCAA
Found at i:20878613 original size:2 final size:2
Alignment explanation
Indices: 20878606--20878647 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
20878596 CAAATATGAC
20878606 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20878647 A
1 A
20878648 GGGACATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20878798 original size:18 final size:18
Alignment explanation
Indices: 20878775--20878811 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20878765 ATGCCGCTGC
20878775 TCTTTTTCTCCTTCTTAT
1 TCTTTTTCTCCTTCTTAT
**
20878793 TCTTTTTCTTTTTCTTAT
1 TCTTTTTCTCCTTCTTAT
20878811 T
1 T
20878812 TCTTCCCTCT
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:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (18 bp):
TCTTTTTCTCCTTCTTAT
Found at i:20879000 original size:20 final size:23
Alignment explanation
Indices: 20878972--20879026 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 23
20878962 CGTTGCCGTG
*
20878972 CTCCCTCTCTTT-TTTTT-C-TT
1 CTCCTTCTCTTTCTTTTTCCTTT
20878992 CTCCTTCTCTTTCTTTTTCCTTT
1 CTCCTTCTCTTTCTTTTTCCTTT
20879015 CTCCTT-TCTTTC
1 CTCCTTCTCTTTC
20879027 CCTCGAGCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.35
21 5 0.16
22 7 0.23
23 8 0.26
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (23 bp):
CTCCTTCTCTTTCTTTTTCCTTT
Found at i:20879071 original size:18 final size:18
Alignment explanation
Indices: 20879048--20879105 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
20879038 CTACTCTCTT
20879048 CCTTCTCTT-TCCTC-TTC
1 CCTT-TCTTCTCCTCTTTC
20879065 CCTTTCTTCTCCTCTTTC
1 CCTTTCTTCTCCTCTTTC
*
20879083 CCTTTCTTCTCTTCTTTC
1 CCTTTCTTCTCCTCTTTC
*
20879101 TCTTT
1 CCTTT
20879106 TTTTTTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 4 0.11
17 9 0.24
18 24 0.65
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (18 bp):
CCTTTCTTCTCCTCTTTC
Found at i:20880952 original size:18 final size:17
Alignment explanation
Indices: 20880891--20880967 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 17
20880881 GTCAAACAAG
20880891 AAGAAAGAGAAAAAAA-A
1 AAGAAAGA-AAAAAAAGA
* *
20880908 AAG--AGAGAAAAATG-
1 AAGAAAGAAAAAAAAGA
* *
20880922 AAGAAGGAGAAAAAGAGA
1 AAGAAAGA-AAAAAAAGA
*
20880940 GAGAAAAGAAAAAAAAGA
1 AAG-AAAGAAAAAAAAGA
20880958 AAGAAAGAAA
1 AAGAAAGAAA
20880968 GAGAGTAGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
14 8 0.18
15 3 0.07
16 2 0.05
17 15 0.34
18 12 0.27
19 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (17 bp):
AAGAAAGAAAAAAAAGA
Found at i:20880958 original size:26 final size:26
Alignment explanation
Indices: 20880900--20880959 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
20880890 GAAGAAAGAG
*
20880900 AAAAA-AAAAAGAGAGAAAAATGAAG
1 AAAAAGAAAAAGAGAGAAAAATGAAA
**
20880925 AAGGAGAAAAAGAGAGAGAAAA-GAAA
1 AAAAAGAAAAAGAGAGA-AAAATGAAA
20880951 AAAAAGAAA
1 AAAAAGAAA
20880960 GAAAGAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.11
26 21 0.75
27 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAAGAGAGAAAAATGAAA
Found at i:20881209 original size:69 final size:67
Alignment explanation
Indices: 20881037--20881259 Score: 286
Period size: 67 Copynumber: 3.3 Consensus size: 67
20881027 ACATCTCGGG
* * *
20881037 GAGAAGAAAGAAAAAAGAAAAAGAAGAAGAATGAGAGAAGGAGTAGTGGCAGAGGAGAAGAAAGA
1 GAGAAGAAAGAAAAAAGAAAAAGAAGAAGAAAGAGAGAAGGAGCAGCGGCAGAGGAGAAGAAAGA
20881102 GA
66 GA
* * * *
20881104 GAGAAGAAAGAAAAAAGAAAAATAAGAAGAAAGAGAGAAGGTGCAGCGGCAGAGGAAAAGAAAAA
1 GAGAAGAAAGAAAAAAGAAAAAGAAGAAGAAAGAGAGAAGGAGCAGCGGCAGAGGAGAAGAAAGA
20881169 GA
66 GA
* * * * * *
20881171 GCGAAGAAAGAAGAAAAAGAAAAAGAAGAAGAAGGAGAGAATGAGCAACGACAGAGGAGAAGAAT
1 GAGAAGAAAG-A-AAAAAGAAAAAGAAGAAGAAAGAGAGAAGGAGCAGCGGCAGAGGAGAAGAAA
20881236 GAGA
64 GAGA
* *
20881240 GGGAAGAAA-AAAAAATAAAA
1 GAGAAGAAAGAAAAAAGAAAA
20881260 TAGCTACATA
Statistics
Matches: 135, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
66 9 0.07
67 70 0.52
68 1 0.01
69 55 0.41
ACGTcount: A:0.61, C:0.04, G:0.32, T:0.04
Consensus pattern (67 bp):
GAGAAGAAAGAAAAAAGAAAAAGAAGAAGAAAGAGAGAAGGAGCAGCGGCAGAGGAGAAGAAAGA
GA
Found at i:20882012 original size:60 final size:61
Alignment explanation
Indices: 20881857--20882034 Score: 252
Period size: 61 Copynumber: 2.9 Consensus size: 61
20881847 ATTTGATTAT
* *
20881857 AAAGGGGACCTGAAGCCCCAATTTATATTGGGTGTCGTGGGCAGTTCCCACGAGTAGGAAA
1 AAAGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGAAA
** *
20881918 AAAGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAAATCCCACGAGTAGG-TA
1 AAAGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGAAA
* * * *
20881978 AAAGGGGACCTAAAGCCTCGATTTATATAT-GGTGGCATGGGTAGTTCCCACGAGTAG
1 AAAGGGGACCTGAAGCCCCGATTTATAT-TGGGTGGCGTGGGCAGTTCCCACGAGTAG
20882035 ATGATGATGT
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 50 0.48
61 55 0.52
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (61 bp):
AAAGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGCAGTTCCCACGAGTAGGAAA
Found at i:20895770 original size:60 final size:61
Alignment explanation
Indices: 20895659--20895784 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 61
20895649 AAAACTTTTA
* * *
20895659 AGCA-TTTTGAGCATTTTGGAGTGGTTTTTTATGCACGAAGAAAAACCTTTGAGCGCTTTG
1 AGCATTTTTGAGCATTTTGGAGTGGTTTTTGATACACGAAGAAAAACCTTTGAGCACTTTG
* * ** *
20895719 AGCATTTTTTAGCATTTTGGAGTGG-TTTTGATACATGAAGAAAAATTTTTGAGCATTTTG
1 AGCATTTTTGAGCATTTTGGAGTGGTTTTTGATACACGAAGAAAAACCTTTGAGCACTTTG
20895779 AGCATT
1 AGCATT
20895785 CGTCGCCAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 38 0.67
61 19 0.33
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (61 bp):
AGCATTTTTGAGCATTTTGGAGTGGTTTTTGATACACGAAGAAAAACCTTTGAGCACTTTG
Found at i:20895956 original size:22 final size:22
Alignment explanation
Indices: 20895908--20896014 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 22
20895898 TGCGTAATCG
* *
20895908 ATTTTAAGGCATTGCGTG-GCTA
1 ATTTTTAGGCATTGTGTGAG-TA
* * *
20895930 GTTTTTAAGCATTGTGTTAGTA
1 ATTTTTAGGCATTGTGTGAGTA
* * *
20895952 ATTTTTAGGCATCGTGTGATTG
1 ATTTTTAGGCATTGTGTGAGTA
** * *
20895974 ATTTTTAGGCATTGCATGATTG
1 ATTTTTAGGCATTGTGTGAGTA
* *
20895996 ATTTTTAGGTATTGCGTGA
1 ATTTTTAGGCATTGTGTGA
20896015 CTGGTTGATA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
22 67 0.99
23 1 0.01
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.45
Consensus pattern (22 bp):
ATTTTTAGGCATTGTGTGAGTA
Found at i:20896054 original size:22 final size:22
Alignment explanation
Indices: 20896001--20896054 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
20895991 GATTGATTTT
*
20896001 TAGGTATTGCGTGACTGGTTGA
1 TAGGCATTGCGTGACTGGTTGA
*
20896023 TATGGCATTGCGTTACTGGTTGA
1 TA-GGCATTGCGTGACTGGTTGA
20896046 TAGGCATTG
1 TAGGCATTG
20896055 TGTAATTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.37
Consensus pattern (22 bp):
TAGGCATTGCGTGACTGGTTGA
Found at i:20896064 original size:22 final size:23
Alignment explanation
Indices: 20896006--20896078 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
20895996 ATTTTTAGGT
*
20896006 ATTGCGTGACTGGTTGATATGGC
1 ATTGCGTAACTGGTTGATATGGC
*
20896029 ATTGCGTTACTGGTTGATA-GGC
1 ATTGCGTAACTGGTTGATATGGC
* * *
20896051 ATTGTGTAATTGGTT-AGTAAGGC
1 ATTGCGTAACTGGTTGA-TATGGC
20896074 ATTGC
1 ATTGC
20896079 ATGACTAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 25 0.58
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (23 bp):
ATTGCGTAACTGGTTGATATGGC
Found at i:20916338 original size:22 final size:21
Alignment explanation
Indices: 20916296--20916356 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
20916286 TGACTTGTGC
*
20916296 ATTACTTGACTAGGTTTTAGGA
1 ATTACTTGAGTA-GTTTTAGGA
*
20916318 ATTACTTGAGTAGTTTGTAGGC
1 ATTACTTGAGTAGTTT-TAGGA
* *
20916340 ATTGCTTAAGTAGTTTT
1 ATTACTTGAGTAGTTTT
20916357 CAATCATTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (21 bp):
ATTACTTGAGTAGTTTTAGGA
Found at i:20918992 original size:176 final size:176
Alignment explanation
Indices: 20918698--20919054 Score: 579
Period size: 176 Copynumber: 2.0 Consensus size: 176
20918688 CTTGTAGAAC
*
20918698 CACACAACACATAGTGCAATTGGTCACGATTGTTCAATGTTGTGCAATTCGCATATAACTTACAA
1 CACACAACACATAGTGCAATTGGTCAAGATTGTTCAATGTTGTGCAATTCGCATATAACTTACAA
*
20918763 GAAGGTAACCTCATAATTGTGAAGTTGCATCTCATCCTTATCGACCAAAAGCTATACAAGGGCCT
66 GAAGGCAACCTCATAATTGTGAAGTTGCATCTCATCCTTATCGACCAAAAGCTATACAAGGGCCT
* * * *
20918828 AACAAGGCTCTTTAAAGGACCATTTTGCATTTTTAAAATGATATGG
131 AACAAGACTCTATAAAGGACCATTTTGCATTTTCAAAAGGATATGG
* *
20918874 CACACAACACATAGTGCAATTGGTCAATATTGTTCAATGTTGTGCAGTTCGCATATAACTTACAA
1 CACACAACACATAGTGCAATTGGTCAAGATTGTTCAATGTTGTGCAATTCGCATATAACTTACAA
* * *
20918939 GAAGGCAACCTCGTAATTGTGAAGTTGCATCTCATCCTTATTGACCAAAAGCTATATAAGGGCCT
66 GAAGGCAACCTCATAATTGTGAAGTTGCATCTCATCCTTATCGACCAAAAGCTATACAAGGGCCT
* * * *
20919004 AATAAGACTCTATAAGGGACCATTTTGCATTTTCGAGAGGATATGG
131 AACAAGACTCTATAAAGGACCATTTTGCATTTTCAAAAGGATATGG
20919050 CACAC
1 CACAC
20919055 TGTTTACAAG
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
176 166 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (176 bp):
CACACAACACATAGTGCAATTGGTCAAGATTGTTCAATGTTGTGCAATTCGCATATAACTTACAA
GAAGGCAACCTCATAATTGTGAAGTTGCATCTCATCCTTATCGACCAAAAGCTATACAAGGGCCT
AACAAGACTCTATAAAGGACCATTTTGCATTTTCAAAAGGATATGG
Found at i:20920246 original size:21 final size:21
Alignment explanation
Indices: 20920207--20920246 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20920197 AATTAATCTT
* **
20920207 TTTTATTTTATTTCTAAATTA
1 TTTTAATTTATTTAAAAATTA
20920228 TTTTAATTTATTTAAAAAT
1 TTTTAATTTATTTAAAAAT
20920247 AAATATATGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATTTATTTAAAAATTA
Found at i:20930726 original size:42 final size:42
Alignment explanation
Indices: 20930670--20930770 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
20930660 CTCCCCGCTA
* * **
20930670 GCACATGGCTGGGTCAACATCGGCTTATGCACACTCTTACTC
1 GCACATAGCCGGGTCAACATCGGCTTATGCACACTCCCACTC
* * *
20930712 GCACATAGTCGGGTCAACATCGGTTTATGCGCACTCCCACTC
1 GCACATAGCCGGGTCAACATCGGCTTATGCACACTCCCACTC
*
20930754 GCACATAGCCAGGTCAA
1 GCACATAGCCGGGTCAA
20930771 TATCATTACA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.23
Consensus pattern (42 bp):
GCACATAGCCGGGTCAACATCGGCTTATGCACACTCCCACTC
Found at i:20931648 original size:23 final size:23
Alignment explanation
Indices: 20931585--20931649 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
20931575 GAAGGAAGAA
*
20931585 GGAGAAGAAGCTGCTGAAAAATG
1 GGAGAAGAAGCTGCTGGAAAATG
*
20931608 GGAGAAGAAGCTGTTGGAAAATG
1 GGAGAAGAAGCTGCTGGAAAATG
*
20931631 GGAGAAGAAGCTACTGGAA
1 GGAGAAGAAGCTGCTGGAA
20931650 GAAAGAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.37, T:0.14
Consensus pattern (23 bp):
GGAGAAGAAGCTGCTGGAAAATG
Found at i:20933376 original size:38 final size:40
Alignment explanation
Indices: 20933333--20933438 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 40
20933323 ATAGTGCCCG
*
20933333 TGTGCACGATGTGGGGGAATGTACATGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGAATGTACATGATGGTGC-CGGATA
* * * *
20933371 TGTGCATGATGTGGAGGG-ATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGG-GGGAATGTACATGATGGTGCCGGATA
20933411 TGTGCACGATGT-GGGGAGATGTACATGA
1 TGTGCACGATGTGGGGGA-ATGTACATGA
20933439 CTCGGGTGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
38 25 0.46
39 8 0.15
40 21 0.39
ACGTcount: A:0.23, C:0.14, G:0.39, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGAATGTACATGATGGTGCCGGATA
Found at i:20941274 original size:19 final size:19
Alignment explanation
Indices: 20941250--20941349 Score: 58
Period size: 19 Copynumber: 5.1 Consensus size: 19
20941240 TGCTCGTGTG
20941250 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
20941269 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
20941288 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* * ** *
20941307 CATGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
20941328 CACGATGTGGGGGGGATGTA
1 CACGATGT-GGGGGGATGTA
20941348 CA
1 CA
20941350 TGAGTCGAGT
Statistics
Matches: 54, Mismatches: 22, Indels: 9
0.64 0.26 0.11
Matches are distributed among these distances:
18 3 0.06
19 24 0.44
20 16 0.30
21 11 0.20
ACGTcount: A:0.20, C:0.16, G:0.42, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:20941339 original size:40 final size:38
Alignment explanation
Indices: 20941246--20941352 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 38
20941236 ATAGTGCTCG
* *
20941246 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
* *
20941284 TGTGCACGATGTGGGGGGATGCACATGATGGTGC-CGGCT
1 TGTGCACGATGTGGGGGGATGTACATGAT-G-GCACGGAT
20941323 ATGTGCACGATGTGGGGGGGATGTACATGA
1 -TGTGCACGATGT-GGGGGGATGTACATGA
20941353 GTCGAGTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
38 27 0.45
39 4 0.07
40 14 0.23
41 15 0.25
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACGGAT
Found at i:20942039 original size:22 final size:22
Alignment explanation
Indices: 20942014--20942078 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
20942004 AATCCCAACG
*
20942014 TCGCTGCAACGAAAATTCATTC
1 TCGCTGCAGCGAAAATTCATTC
* * * *
20942036 TCGCTGCAGCGAGAATGCCTTT
1 TCGCTGCAGCGAAAATTCATTC
20942058 TCGCTGCAGC-AAAGATTCATT
1 TCGCTGCAGCGAAA-ATTCATT
20942079 GTCGTATTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 2 0.06
22 32 0.94
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (22 bp):
TCGCTGCAGCGAAAATTCATTC
Found at i:20945654 original size:72 final size:71
Alignment explanation
Indices: 20945537--20945797 Score: 328
Period size: 72 Copynumber: 3.6 Consensus size: 71
20945527 TGAGAAACAA
*
20945537 AACCAACTTAGTCAACCAAGATGAGAGTTAGTCGACTAAGGAGCTACTGCCAAAATTTGGACTTC
1 AACCAACTTAGTCAACCAAGATGAGAGTTAGTCGACTAA-GAGCTACTGCCAAAATCTGGACTTC
*
20945602 AAGATAG
65 AAGACAG
*
20945609 AACCAACTTAGTCAACCAAGATGAGAGTTAGTCGACTAAGGAGCTATTGCCAAAATCTGGACTTC
1 AACCAACTTAGTCAACCAAGATGAGAGTTAGTCGACTAA-GAGCTACTGCCAAAATCTGGACTTC
20945674 AAGACAG
65 AAGACAG
** * * *
20945681 AACCAACTTAGTTGACCAAGA-AATGAGTTAGTCGACTAA-ATGCTCTCTGCCAAAGTCTGTGAC
1 AACCAACTTAGTCAACCAAGATGA-GAGTTAGTCGACTAAGA-GCT-ACTGCCAAAATCTG-GAC
***
20945744 CAGAAGACAG
62 TTCAAGACAG
* * *
20945754 AACCAACTTAGTCGACCAAGAAGAAAGTTAGTCGACTAAGAGCT
1 AACCAACTTAGTCAACCAAGATGAGAGTTAGTCGACTAAGAGCT
20945798 CTTTGTCTGC
Statistics
Matches: 168, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
70 1 0.01
71 4 0.02
72 114 0.68
73 47 0.28
74 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (71 bp):
AACCAACTTAGTCAACCAAGATGAGAGTTAGTCGACTAAGAGCTACTGCCAAAATCTGGACTTCA
AGACAG
Found at i:20946278 original size:32 final size:32
Alignment explanation
Indices: 20946237--20946342 Score: 133
Period size: 32 Copynumber: 3.2 Consensus size: 32
20946227 TTGTAGCTTG
20946237 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
** *
20946269 TGGTTGAGCCCGTGAAAAACCA-TTGTGAAAGGTTG
1 TGGTTGAGCCTTTGAAAAACCACTT-TG---GGTTT
*
20946304 TGGTTGAGCCTTTGAAAAACCACTTTGGATTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
20946336 TGGTTGA
1 TGGTTGA
20946343 TCTTGGTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
31 2 0.03
32 32 0.52
35 26 0.42
36 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (32 bp):
TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
Found at i:20946285 original size:67 final size:67
Alignment explanation
Indices: 20946194--20946342 Score: 228
Period size: 67 Copynumber: 2.2 Consensus size: 67
20946184 AAGTTGGTTG
* *
20946194 TTGGATTTTGGTTGATCCAATGAAAAACCATTGTTG-TAGCTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGATTTTGGTTGAGCCAATGAAAAACCATTG-TGAAAGCTTGTGGTTGAGCCTTTGAAAAACC
20946258 ACT
65 ACT
* ** *
20946261 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGATTTTGGTTGAGCCAATGAAAAACCATTGTGAAAGCTTGTGGTTGAGCCTTTGAAAAACCA
20946326 CT
66 CT
20946328 TTGGATTTTGGTTGA
1 TTGGATTTTGGTTGA
20946343 TCTTGGTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 2 0.03
67 72 0.97
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (67 bp):
TTGGATTTTGGTTGAGCCAATGAAAAACCATTGTGAAAGCTTGTGGTTGAGCCTTTGAAAAACCA
CT
Found at i:20946313 original size:35 final size:33
Alignment explanation
Indices: 20946214--20946363 Score: 130
Period size: 32 Copynumber: 4.5 Consensus size: 33
20946204 GTTGATCCAA
*
20946214 TGAAAAACCATTGTTGTAGCTTGTGGTTGAGCCTT
1 TGAAAAACCATTG-TG-AGGTTGTGGTTGAGCCTT
* **
20946249 TGAAAAACCACTT-TG-GGTTTTGGTTGAGCCCG
1 TGAAAAACCA-TTGTGAGGTTGTGGTTGAGCCTT
20946281 TGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTT
1 TGAAAAACCATTGTG--AGGTTGTGGTTGAGCCTT
* * *
20946316 TGAAAAACCACTT-TG-GATTTTGGTTGA-TCTT
1 TGAAAAACCA-TTGTGAGGTTGTGGTTGAGCCTT
*
20946347 GGTAAAAACCATTGTGA
1 TG-AAAAACCATTGTGA
20946364 AAGGTTTTGG
Statistics
Matches: 95, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
31 8 0.08
32 45 0.47
34 2 0.02
35 36 0.38
36 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (33 bp):
TGAAAAACCATTGTGAGGTTGTGGTTGAGCCTT
Found at i:20946354 original size:67 final size:65
Alignment explanation
Indices: 20946194--20946369 Score: 221
Period size: 67 Copynumber: 2.6 Consensus size: 65
20946184 AAGTTGGTTG
* *
20946194 TTGGATTTTGGTTGATCCAATG-AAAAACCATTGTTG-TAGCTTGTGGTTGAGCCTTTGAAAAAC
1 TTGGATTTTGGTTGAT-C--TGTAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCTTTGAAAAAC
20946257 CACT
62 CACT
* * *
20946261 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGATTTTGGTTGA-TCTGT-AAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
20946326 CT
64 CT
20946328 TTGGATTTTGGTTGATCTTGGTAAAAACCATTGTGAAAGGTT
1 TTGGATTTTGGTTGATC-T-GTAAAAACCATTGTGAAAGGTT
20946370 TTGGCTAAGC
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
65 1 0.01
66 3 0.03
67 89 0.94
68 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (65 bp):
TTGGATTTTGGTTGATCTGTAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACT
Found at i:20948704 original size:2 final size:2
Alignment explanation
Indices: 20948697--20948744 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
20948687 TTCGATCAGA
20948697 AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT -T 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
*
20948736 AA AT AT AT A
1 AT AT AT AT A
20948745 AATACTTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20951810 original size:37 final size:37
Alignment explanation
Indices: 20951704--20951812 Score: 148
Period size: 37 Copynumber: 2.9 Consensus size: 37
20951694 TGATGTTGAG
* * *
20951704 GTGTGCAAGTAGGGAGTGCACACATGACAATGATAGA
1 GTGTGCGAGTAGGGAGTGCACACATGACGATGATGGA
20951741 GTGTGCGAGTAGGGAGTGCACACATGACGATGATGGA
1 GTGTGCGAGTAGGGAGTGCACACATGACGATGATGGA
* * *
20951778 GTGTGTGAGTAAGGTA-TGCACACATGATGATGATG
1 GTGTGCGAGT-AGGGAGTGCACACATGACGATGATG
20951813 TATGTATATG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 61 0.94
38 4 0.06
ACGTcount: A:0.30, C:0.12, G:0.36, T:0.22
Consensus pattern (37 bp):
GTGTGCGAGTAGGGAGTGCACACATGACGATGATGGA
Done.