Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 119 of 121
Found at i:20554192 original size:2 final size:2
Alignment explanation
Indices: 20554187--20554212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20554177 CAAAATGGTT
20554187 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
20554213 ATTAAGCAAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20562586 original size:14 final size:14
Alignment explanation
Indices: 20562567--20562593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20562557 TGATTATTGC
20562567 ATTAATTAATATAG
1 ATTAATTAATATAG
20562581 ATTAATTAATATA
1 ATTAATTAATATA
20562594 TTATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTAATTAATATAG
Found at i:20562727 original size:32 final size:32
Alignment explanation
Indices: 20562685--20562748 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
20562675 AGAATAAATT
20562685 AAAAACTTAAAAATTAAC-CTTGAAAAATTAAA
1 AAAAACTTAAAAATTAACAC-TGAAAAATTAAA
* * *
20562717 AAAAATTTAAAAATTTACACTGAAAAGTTAAA
1 AAAAACTTAAAAATTAACACTGAAAAATTAAA
20562749 TAGGGTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAAACTTAAAAATTAACACTGAAAAATTAAA
Found at i:20565135 original size:2 final size:2
Alignment explanation
Indices: 20565128--20565164 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
20565118 AATAAGTTAT
*
20565128 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
20565165 ATTGTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:20573760 original size:48 final size:47
Alignment explanation
Indices: 20573670--20573763 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 47
20573660 AAAATATAAT
*
20573670 ATATTTAAAATAATTTTTTATATCAAATTTGGCATCGAATAATATCG
1 ATATTTAAAATAATTTTTTATATCAAATTTAGCATCGAATAATATCG
* * * *
20573717 ATATTTAAAAATAATTTTTTGTATCAAATTTAGTATTGGATAATATC
1 ATATTT-AAAATAATTTTTTATATCAAATTTAGCATCGAATAATATC
20573764 AATTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 6 0.15
48 35 0.85
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (47 bp):
ATATTTAAAATAATTTTTTATATCAAATTTAGCATCGAATAATATCG
Found at i:20573869 original size:18 final size:18
Alignment explanation
Indices: 20573846--20573890 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
20573836 GTGAAATGTA
20573846 ATTTTTAATT-TTTAATTT
1 ATTTTTAATTATTTAA-TT
**
20573864 ATTTTTTGTTATTTAATT
1 ATTTTTAATTATTTAATT
20573882 ATTTTTAAT
1 ATTTTTAAT
20573891 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTAATTATTTAATT
Found at i:20573976 original size:20 final size:20
Alignment explanation
Indices: 20573937--20573979 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
20573927 AAAAATTAAG
*
20573937 TTTGTTATTTTTTATTTTTA
1 TTTGTTATTTTTTATCTTTA
20573957 TTTGTT-TTTTTTATACTTTA
1 TTTGTTATTTTTTAT-CTTTA
20573977 TTT
1 TTT
20573980 TTTCAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTGTTATTTTTTATCTTTA
Found at i:20574200 original size:19 final size:17
Alignment explanation
Indices: 20574165--20574206 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
20574155 TTATGATATT
20574165 ATTT-TTTATTTTTTAA
1 ATTTATTTATTTTTTAA
20574181 ATTTATTTATTTGATTTAA
1 ATTTATTTATTT--TTTAA
*
20574200 ATATATT
1 ATTTATT
20574207 ACATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
19 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTATTTATTTTTTAA
Found at i:20579310 original size:4 final size:4
Alignment explanation
Indices: 20579280--20579341 Score: 61
Period size: 4 Copynumber: 15.5 Consensus size: 4
20579270 TTCTCTTTCA
* * * * *
20579280 CTCT CTTT CTGT CTGT CTGT CTGT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* *
20579328 CTCT TTAT CTCT CT
1 CTCT CTCT CTCT CT
20579342 TGGAGAGAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.02, C:0.39, G:0.06, T:0.53
Consensus pattern (4 bp):
CTCT
Found at i:20579342 original size:10 final size:10
Alignment explanation
Indices: 20579280--20579341 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 10
20579270 TTCTCTTTCA
*
20579280 CTCTCTTTCT
1 CTCTCTCTCT
* * *
20579290 GTCTGTCTGT
1 CTCTCTCTCT
*
20579300 CTGTCTCTCT
1 CTCTCTCTCT
20579310 CTCTCTCTCT
1 CTCTCTCTCT
20579320 CTCTCTCTCT
1 CTCTCTCTCT
* *
20579330 CTTTATCTCT
1 CTCTCTCTCT
20579340 CT
1 CT
20579342 TGGAGAGAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.02, C:0.39, G:0.06, T:0.53
Consensus pattern (10 bp):
CTCTCTCTCT
Found at i:20581140 original size:18 final size:19
Alignment explanation
Indices: 20581103--20581140 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
20581093 CTAAAATACA
*
20581103 TTTCTAAGAATTAGAACTTG
1 TTTCCAAGAATTA-AACTTG
20581123 TTTCCAAGAATT-AACTTG
1 TTTCCAAGAATTAAACTTG
20581141 AATTAATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (19 bp):
TTTCCAAGAATTAAACTTG
Found at i:20582658 original size:2 final size:2
Alignment explanation
Indices: 20582653--20582683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20582643 TAATGGTGTG
20582653 TA TA TA 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 T
20582684 TATTAGCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20585917 original size:3 final size:3
Alignment explanation
Indices: 20585911--20585949 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20585901 TCTTTTGTCC
20585911 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20585950 CAAGTATCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20589005 original size:31 final size:30
Alignment explanation
Indices: 20588970--20589040 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
20588960 ATTTAATTTG
*
20588970 TATTTAATAA-AAAAAATTTATTAGTTCAATT
1 TATTTAATAATAAAAAATTTA-TA-TTAAATT
*
20589001 TATTTAAGTAATAAAATATTTATATTAAATT
1 TATTTAA-TAATAAAAAATTTATATTAAATT
20589032 TAATTTAAT
1 T-ATTTAAT
20589041 TAAATAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 15 0.43
32 11 0.31
33 9 0.26
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (30 bp):
TATTTAATAATAAAAAATTTATATTAAATT
Found at i:20591274 original size:2 final size:2
Alignment explanation
Indices: 20591267--20591296 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20591257 CCTTATTTTA
20591267 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20591297 TTTGAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20592832 original size:22 final size:22
Alignment explanation
Indices: 20592804--20592847 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20592794 CTAAATCTTC
* *
20592804 CTTAATTCTAGGGATATAAATA
1 CTTAATTCTAGAGATACAAATA
20592826 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20592848 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20596703 original size:22 final size:22
Alignment explanation
Indices: 20596675--20596717 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20596665 TAAATCTTCT
*
20596675 TTAATTCTAGGGATACAAATAC
1 TTAATTCTAGAGATACAAATAC
20596697 TTAATTCTAGAGATACAAATA
1 TTAATTCTAGAGATACAAATA
20596718 TAAATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:20602956 original size:6 final size:6
Alignment explanation
Indices: 20602945--20602984 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
20602935 AAAACCCCTT
20602945 TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCT
1 TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCTGC TTCT
20602985 TTAGGCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.53
Consensus pattern (6 bp):
TTCTGC
Found at i:20621445 original size:2 final size:2
Alignment explanation
Indices: 20621438--20621465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20621428 AAATATGTTA
20621438 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20621466 CAGATCTTGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20622913 original size:36 final size:34
Alignment explanation
Indices: 20622844--20622929 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 34
20622834 AAAGGATCAG
20622844 AGTTCACAGTTTTAAAAGAGGGGCAAGGGAAAGTAA
1 AGTTCACAGTTTTAAAAGAGGGG--AGGGAAAGTAA
* *
20622880 AGTTCACAGTTTTAAAAGAGTGG-GGG--TGTAA
1 AGTTCACAGTTTTAAAAGAGGGGAGGGAAAGTAA
*
20622911 AGTTCATAGTTTTAAAAGA
1 AGTTCACAGTTTTAAAAGA
20622930 AAGGCAGGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
31 22 0.47
33 3 0.06
36 22 0.47
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.27
Consensus pattern (34 bp):
AGTTCACAGTTTTAAAAGAGGGGAGGGAAAGTAA
Found at i:20627451 original size:61 final size:61
Alignment explanation
Indices: 20627365--20627481 Score: 198
Period size: 62 Copynumber: 1.9 Consensus size: 61
20627355 TGAATTTGAA
* *
20627365 CTGGAAAAAGGGAAAATGTGAAAAAAGAAAACATGCATACAATCAAAATTAATTTAAATGC
1 CTGGAAAAAGGAAAAATGTGAAAAAAGAAAACATGCATACAATCAAAAGTAATTTAAATGC
*
20627426 CTGGAAAAAGGAAAAAATGTGAAAAAAGAAAGCATGCATACAATCAAAAGTAATTT
1 CTGGAAAAAGG-AAAAATGTGAAAAAAGAAAACATGCATACAATCAAAAGTAATTT
20627482 GAATACCTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 11 0.21
62 41 0.79
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (61 bp):
CTGGAAAAAGGAAAAATGTGAAAAAAGAAAACATGCATACAATCAAAAGTAATTTAAATGC
Found at i:20642289 original size:3 final size:3
Alignment explanation
Indices: 20642281--20642307 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20642271 CTCAGGCAAA
20642281 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
20642308 TAAATGAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:20647140 original size:2 final size:2
Alignment explanation
Indices: 20647133--20647169 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20647123 GAGACAGAAT
20647133 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
20647170 TGTTCCAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20648463 original size:42 final size:42
Alignment explanation
Indices: 20648412--20648491 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
20648402 TATTTATGCT
* **
20648412 CCTGATCCTCAAGGCCATGTTCCATCTTCCCCTGTTGATGTC
1 CCTGATCCTCAAGACCATGTTCCATCAACCCCTGTTGATGTC
* * *
20648454 CCTGCTCCTCAAGACCCTGTTCCTTCAACCCCTGTTGA
1 CCTGATCCTCAAGACCATGTTCCATCAACCCCTGTTGA
20648492 CCCTCCTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.15, C:0.39, G:0.15, T:0.31
Consensus pattern (42 bp):
CCTGATCCTCAAGACCATGTTCCATCAACCCCTGTTGATGTC
Found at i:20651494 original size:29 final size:29
Alignment explanation
Indices: 20651438--20651534 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
20651428 CAATTGAGGG
* *
20651438 TTTAATT-GAATGAAAATAAATGTATAAAA
1 TTTAATTAG-ATGAAAATAAATATTTAAAA
20651467 TTTAATTAGATGAAAATAAATATTT-AAA
1 TTTAATTAGATGAAAATAAATATTTAAAA
* *
20651495 TGTTCAATTA-ATTCAAAATAAAAGATTTAAAA
1 T-TT-AATTAGA-TGAAAAT-AAATATTTAAAA
*
20651527 CTTAATTA
1 TTTAATTA
20651535 ATTGTAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
28 4 0.07
29 24 0.42
30 17 0.30
31 9 0.16
32 3 0.05
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (29 bp):
TTTAATTAGATGAAAATAAATATTTAAAA
Found at i:20651534 original size:30 final size:29
Alignment explanation
Indices: 20651500--20651559 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
20651490 TTAAATGTTC
*
20651500 AATTAATTCAAAATAAAAGATTTAAAACTT
1 AATTAATT-AAAATAAAAGATTAAAAACTT
** *
20651530 AATTAATTGTAATAAAATATTAAAAACTT
1 AATTAATTAAAATAAAAGATTAAAAACTT
20651559 A
1 A
20651560 TATGATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (29 bp):
AATTAATTAAAATAAAAGATTAAAAACTT
Found at i:20662576 original size:3 final size:3
Alignment explanation
Indices: 20662568--20662602 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20662558 CTCTTGTTGG
20662568 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20662603 AAGGAGCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20670644 original size:31 final size:30
Alignment explanation
Indices: 20670606--20670671 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
20670596 ATATAAATAT
20670606 AATATATATTATAAAA-TATATTTAAATTTTA
1 AATATATATTATAAAATTATA-TT-AATTTTA
*
20670637 AATATATATTATATAATTATATTAATTTTA
1 AATATATATTATAAAATTATATTAATTTTA
20670667 AATAT
1 AATAT
20670672 CAAATTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 12 0.36
31 17 0.52
32 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
AATATATATTATAAAATTATATTAATTTTA
Found at i:20670918 original size:17 final size:18
Alignment explanation
Indices: 20670874--20670908 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20670864 TAAATATAAA
*
20670874 AAATATGTTAAATGTGTT
1 AAATATATTAAATGTGTT
20670892 AAATATATTAAATGTGT
1 AAATATATTAAATGTGT
20670909 ATTTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (18 bp):
AAATATATTAAATGTGTT
Found at i:20673945 original size:15 final size:17
Alignment explanation
Indices: 20673925--20673961 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
20673915 ATTTCCATCA
20673925 AAATTCAA-GAAAG-TC
1 AAATTCAATGAAAGTTC
*
20673940 AAATTCAATGTAAGTTC
1 AAATTCAATGAAAGTTC
20673957 AAATT
1 AAATT
20673962 AGAAACTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 4 0.21
17 7 0.37
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (17 bp):
AAATTCAATGAAAGTTC
Found at i:20676767 original size:17 final size:18
Alignment explanation
Indices: 20676739--20676773 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20676729 GTATTTATAT
20676739 TTTTTATATTCAAATAAA
1 TTTTTATATTCAAATAAA
*
20676757 TTTTTAT-TTCAGATAAA
1 TTTTTATATTCAAATAAA
20676774 AAATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTTATATTCAAATAAA
Found at i:20677513 original size:19 final size:17
Alignment explanation
Indices: 20677489--20677533 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
20677479 AATTAATTAA
*
20677489 TAAAATTTTAACTAATTT
1 TAAAATTTTAAATAA-TT
*
20677507 TATAAATATTAAATAATT
1 TA-AAATTTTAAATAATT
20677525 TAAAATTTT
1 TAAAATTTT
20677534 TGTTAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTTTAAATAATT
Found at i:20685802 original size:7 final size:7
Alignment explanation
Indices: 20685781--20685814 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
20685771 TCTGGTAGTG
20685781 TTCTG-C
1 TTCTGCC
20685787 TTCTGCC
1 TTCTGCC
*
20685794 TTTTGCC
1 TTCTGCC
20685801 TTCTGCC
1 TTCTGCC
20685808 TTCTGCC
1 TTCTGCC
20685815 CTTGATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.00, C:0.38, G:0.15, T:0.47
Consensus pattern (7 bp):
TTCTGCC
Found at i:20688060 original size:16 final size:17
Alignment explanation
Indices: 20688041--20688073 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20688031 TAGATGAAGC
20688041 ATAA-TAAAGATGTTAT
1 ATAACTAAAGATGTTAT
20688057 ATAACTAAAGATGTTAT
1 ATAACTAAAGATGTTAT
20688074 GAAACCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (17 bp):
ATAACTAAAGATGTTAT
Found at i:20698580 original size:18 final size:19
Alignment explanation
Indices: 20698559--20698612 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
20698549 CAAAATTATT
20698559 ATTTTTAAATATT-ATATA
1 ATTTTTAAATATTAATATA
20698577 A--TTTAAATTATTAATATA
1 ATTTTTAAA-TATTAATATA
20698595 ATTTTTAAATATATAATA
1 ATTTTTAAATAT-TAATA
20698613 AGACATGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.19
17 4 0.13
18 7 0.23
19 3 0.10
20 11 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTAAATATTAATATA
Found at i:20698601 original size:20 final size:19
Alignment explanation
Indices: 20698559--20698604 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
20698549 CAAAATTATT
20698559 ATTTTTAAA-TATTATATA
1 ATTTTTAAATTATTATATA
20698577 A--TTTAAATTATTAATATA
1 ATTTTTAAATTATT-ATATA
20698595 ATTTTTAAAT
1 ATTTTTAAAT
20698605 ATATAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.25
17 4 0.17
18 7 0.29
20 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTAAATTATTATATA
Found at i:20698613 original size:18 final size:19
Alignment explanation
Indices: 20698559--20698613 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
20698549 CAAAATTATT
20698559 ATTTTTAAATAT-TATATA
1 ATTTTTAAATATATATATA
20698577 A--TTTAAAT-TATTAATATA
1 ATTTTTAAATATA-T-ATATA
20698595 ATTTTTAAATATATA-ATA
1 ATTTTTAAATATATATATA
20698613 A
1 A
20698614 GACATGTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
15 1 0.03
16 7 0.23
17 1 0.03
18 11 0.35
19 1 0.03
20 8 0.26
21 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTAAATATATATATA
Found at i:20699593 original size:17 final size:16
Alignment explanation
Indices: 20699567--20699605 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
20699557 ACAATTCACC
*
20699567 TTTTTTTTAACATATT
1 TTTTTTTTAAAATATT
20699583 TTTTCTTTTAAAATATT
1 TTTT-TTTTAAAATATT
20699600 TTTTTT
1 TTTTTT
20699606 CACCCCGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTTAAAATATT
Found at i:20720554 original size:2 final size:2
Alignment explanation
Indices: 20720549--20720584 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20720539 CAGGGGGGGG
20720549 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20720585 ATGGTACCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20726741 original size:6 final size:6
Alignment explanation
Indices: 20726730--20726758 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20726720 TTTGTTGTAA
20726730 TTGGAT TTGGAT TTGGAT TTGGAT TTGGA
1 TTGGAT TTGGAT TTGGAT TTGGAT TTGGA
20726759 GTTACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (6 bp):
TTGGAT
Found at i:20732051 original size:21 final size:21
Alignment explanation
Indices: 20732025--20732074 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
20732015 CCGGATGCTT
20732025 GGTCATGTAAAGGCCTTAGAA
1 GGTCATGTAAAGGCCTTAGAA
20732046 GGTCATGTAAAGGCCTTAGAA
1 GGTCATGTAAAGGCCTTAGAA
20732067 GGTCATGT
1 GGTCATGT
20732075 GAATAGCACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (21 bp):
GGTCATGTAAAGGCCTTAGAA
Found at i:20732838 original size:22 final size:22
Alignment explanation
Indices: 20732810--20732853 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20732800 CTAAATCTTC
20732810 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20732832 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20732854 TAAATATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20736556 original size:23 final size:25
Alignment explanation
Indices: 20736501--20736562 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
20736491 TTGAAAGGGT
* *
20736501 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAACAGAAG
20736526 TCGGCAATGAAGGCCTAAA-A-AAG
1 TCGGCAATGAAGGCCTAAACAGAAG
20736549 TCGGCAATGAAGGC
1 TCGGCAATGAAGGC
20736563 TGAAAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 15 0.43
24 1 0.03
25 19 0.54
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (25 bp):
TCGGCAATGAAGGCCTAAACAGAAG
Found at i:20736738 original size:22 final size:22
Alignment explanation
Indices: 20736710--20736753 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20736700 CTAAATCTTC
*
20736710 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20736732 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20736754 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20749663 original size:22 final size:22
Alignment explanation
Indices: 20749635--20749678 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20749625 CTAAATCTTC
20749635 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20749657 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20749679 TAAATATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20753387 original size:23 final size:25
Alignment explanation
Indices: 20753332--20753393 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
20753322 TTGAAAGGGT
* *
20753332 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAACAGAAG
20753357 TCGGCAATGAAGGCCTAAA-A-AAG
1 TCGGCAATGAAGGCCTAAACAGAAG
20753380 TCGGCAATGAAGGC
1 TCGGCAATGAAGGC
20753394 TGAAAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 15 0.43
24 1 0.03
25 19 0.54
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (25 bp):
TCGGCAATGAAGGCCTAAACAGAAG
Found at i:20753569 original size:22 final size:22
Alignment explanation
Indices: 20753541--20753584 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20753531 CTAAATCTTC
*
20753541 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20753563 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
20753585 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:20756782 original size:8 final size:8
Alignment explanation
Indices: 20756765--20756797 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
20756755 CCCATTACTA
*
20756765 TTTTTCTT
1 TTTTTGTT
20756773 TTTTTGTT
1 TTTTTGTT
20756781 TTTTT-TT
1 TTTTTGTT
20756788 TTTTTGTT
1 TTTTTGTT
20756796 TT
1 TT
20756798 AATTAACAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (8 bp):
TTTTTGTT
Found at i:20756789 original size:15 final size:15
Alignment explanation
Indices: 20756765--20756797 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
20756755 CCCATTACTA
20756765 TTTTTCTTTTTTTGT
1 TTTTTCTTTTTTTGT
*
20756780 TTTTTTTTTTTTTGT
1 TTTTTCTTTTTTTGT
20756795 TTT
1 TTT
20756798 AATTAACAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (15 bp):
TTTTTCTTTTTTTGT
Found at i:20763895 original size:2 final size:2
Alignment explanation
Indices: 20763888--20763919 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20763878 GGCTTAACAG
20763888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20763920 AGAATAGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20766970 original size:33 final size:31
Alignment explanation
Indices: 20766913--20766978 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 31
20766903 AGAAAATAGC
* *
20766913 GATATTTTATAAGAAATGCTGTTAATTTAGT
1 GATATTTTATAAAAAATACTGTTAATTTAGT
20766944 GATATTTGTATAAAAAAATACTGTTAATTTAGT
1 GATATTT-TAT-AAAAAATACTGTTAATTTAGT
20766977 GA
1 GA
20766979 CGCTTGTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 7 0.23
32 3 0.10
33 21 0.68
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (31 bp):
GATATTTTATAAAAAATACTGTTAATTTAGT
Found at i:20766986 original size:33 final size:33
Alignment explanation
Indices: 20766926--20766996 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
20766916 ATTTTATAAG
* * *
20766926 AAATGCTGTTAATTTAGTGATATTTGTATAAAA
1 AAATACTGTTAATTTAGTGACACTTGTATAAAA
* * *
20766959 AAATACTGTTAATTTAGTGACGCTTGTATCATA
1 AAATACTGTTAATTTAGTGACACTTGTATAAAA
20766992 AAATA
1 AAATA
20766997 TCGTTCTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (33 bp):
AAATACTGTTAATTTAGTGACACTTGTATAAAA
Found at i:20767682 original size:21 final size:21
Alignment explanation
Indices: 20767649--20767699 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
20767639 CAACTACTAA
*
20767649 AATTTT-GTATGTTCTTCGTC
1 AATTTTAGCATGTTCTTCGTC
* *
20767669 CATTTTAGCATGTTCTTCTTC
1 AATTTTAGCATGTTCTTCGTC
20767690 AATTTTAGCA
1 AATTTTAGCA
20767700 CGCTCATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.51
Consensus pattern (21 bp):
AATTTTAGCATGTTCTTCGTC
Found at i:20769363 original size:161 final size:161
Alignment explanation
Indices: 20768414--20769353 Score: 983
Period size: 161 Copynumber: 5.9 Consensus size: 161
20768404 GCATTTTGGC
* * **
20768414 TTTTCACACATATCAA-TCATGGAAACCAAATTCAATCATTTGAACAAGTTTAATATCATGTATT
1 TTTTCACACATATCAACT-GTGGAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATT
* * * * * * **
20768478 TAAGCTATCCAAACTGTTAAAATAGAACAATAATAGCAACTTTGTATTTTTAACTTTTAATGATA
65 GAAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCA
* * * *
20768543 AAAAAAGTCCTAAACATAGGTAAACAATAACT
130 TAAAAAGTCTTAAACAGACGTAAACAATAACT
* * * * * *
20768575 TTTTCACATATATTAACTGTGAAAATCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTG
1 TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTG
* *
20768640 AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACAGCCT
66 AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAT
* *
20768705 GAAAAA-TCTTAAACAAAGGTAAACAATAACT
131 -AAAAAGTCTTAAACAGACGTAAACAATAACT
* * * *
20768736 TTTTCACATATATCAACTATGAAAACCAAGTTCAATCATTCAGAA-AAATTTAATATCATGTATT
1 TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCA-AACAAGTTTAATATCATGTATT
* * * * * * * *
20768800 GAAACTATCCCAACTGTTAAAACAGAAAAATAATATCAAATTTGCA-TTTTACCTTTTAACGGCA
65 GAAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCA
* * * *** *
20768864 TAAAAAATCTTACACAAACGTAAATGTTAGCT
130 TAAAAAGTCTTAAACAGACGTAAACAATAACT
* * * * * * *
20768896 TTTTCATATATATCAACTGTGAAAATCAAGTTCAATTATTCCAACAAATTTAATATCATGTATTG
1 TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTG
* * * * * * * * * ** *
20768961 AAGCTATGCAAATTGTTAAGATAGAACAATAACAACAAA-TTGCATGTTTGCCTCTTAACAACAC
66 AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAT
* *
20769025 AAAAAGTCTTAAACAGACGTAAACGATAACC
131 AAAAAGTCTTAAACAGACGTAAACAATAACT
* *
20769056 TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCAGACCAGTTTAATATCATGTATTG
1 TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTG
* * * * *
20769121 GAGTTATCCAAACTATTAAAATAGAGCAATAACAGCAAATTTATATTTTTA-CTTATTAATGGCA
66 AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTT-TTAACGGCA
* * *
20769185 TAAAAAGTCCTAAATAGATGTAAACAATAACT
130 TAAAAAGTCTTAAACAGACGTAAACAATAACT
* * * *** * *
20769217 TTTTCATACATATCAACTGTGGAAACTAAGTTCAATAATTTGGATAAGTTTAATATCATCTATTG
1 TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTG
* * * * * * *
20769282 AAACTATCAAAACTATTAAAACAGAACAATAACTGTAAATTTATATTTTTACCTTGTAACGGCAT
66 AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAT
20769347 AAAAAGT
131 AAAAAGT
20769354 TGTAAATAGA
Statistics
Matches: 652, Mismatches: 118, Indels: 18
0.83 0.15 0.02
Matches are distributed among these distances:
159 12 0.02
160 249 0.38
161 380 0.58
162 11 0.02
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (161 bp):
TTTTCACACATATCAACTGTGGAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTG
AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAAATTTGTATTTTTACCTTTTAACGGCAT
AAAAAGTCTTAAACAGACGTAAACAATAACT
Found at i:20770544 original size:15 final size:13
Alignment explanation
Indices: 20770515--20770557 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
20770505 ATAAAAGCAA
* *
20770515 ATATATAAAAAAT
1 ATATATAAAGAAC
*
20770528 ATATGTAAAGAAC
1 ATATATAAAGAAC
20770541 ATATATAAAGAAC
1 ATATATAAAGAAC
20770554 ATAT
1 ATAT
20770558 TGATTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:20775864 original size:62 final size:61
Alignment explanation
Indices: 20775653--20775872 Score: 176
Period size: 62 Copynumber: 3.5 Consensus size: 61
20775643 ATTGAAGGCG
** * * *
20775653 CTCTAATTTTTTTAAAAAAATTATTGAAGGTGTTTTTTTTTTTATAGAAAATGCTTTCAATAATC
1 CTCTAATTTTTAAAAAAAAATTATTGAAGGTG------TTTTTGTAGAGAATGCCTTCAATAATC
20775718 TC
60 TC
* * * * * * *
20775720 TTC-CATTTTTTAAAAAAATTTATTGAAGGCGTTTCTTGTAGAAAATGCCTTCAATAATCCC
1 CTCTAATTTTTAAAAAAAAATTATTGAAGGTGTTT-TTGTAGAGAATGCCTTCAATAATCTC
* ** *
20775781 CT-TAAATTTTGATGAATAAATTATTGAAGGTGTTTTTGACTA-AGAATGCCTTCAATAATCTC
1 CTCT-AATTTTTAAAAAAAAATTATTGAAGGTGTTTTTG--TAGAGAATGCCTTCAATAATCTC
*
20775843 CTCTAATTTTTAAAAAAAAATTATTAAAGG
1 CTCTAATTTTTAAAAAAAAATTATTGAAGG
20775873 CTTTTTTTTT
Statistics
Matches: 123, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
60 3 0.02
61 27 0.22
62 64 0.52
63 3 0.02
66 24 0.20
67 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (61 bp):
CTCTAATTTTTAAAAAAAAATTATTGAAGGTGTTTTTGTAGAGAATGCCTTCAATAATCTC
Found at i:20775879 original size:62 final size:61
Alignment explanation
Indices: 20775690--20775879 Score: 181
Period size: 62 Copynumber: 3.1 Consensus size: 61
20775680 AGGTGTTTTT
* * * * * *
20775690 TTTTTTATAGAAAATGCTTTCAATAATCTCTTC-CATTTTTTAAAAAAATTTATTGAAGGC
1 TTTTTTGTAGAAAATGCCTTCAATAATCTCCTCTAATTTTTAAAAAAAAATTATTGAAGGC
* * * ** *
20775750 GTTTCTTGTAGAAAATGCCTTCAATAATCCCCT-TAAATTTTGATGAATAAATTATTGAAGG-
1 -TTTTTTGTAGAAAATGCCTTCAATAATCTCCTCT-AATTTTTAAAAAAAAATTATTGAAGGC
* *
20775811 TGTTTTTGACTA-AGAATGCCTTCAATAATCTCCTCTAATTTTTAAAAAAAAATTATTAAAGGC
1 T-TTTTTG--TAGAAAATGCCTTCAATAATCTCCTCTAATTTTTAAAAAAAAATTATTGAAGGC
20775874 TTTTTT
1 TTTTTT
20775880 TTTTTTTTTA
Statistics
Matches: 102, Mismatches: 20, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
60 1 0.01
61 32 0.31
62 65 0.64
63 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (61 bp):
TTTTTTGTAGAAAATGCCTTCAATAATCTCCTCTAATTTTTAAAAAAAAATTATTGAAGGC
Found at i:20780031 original size:35 final size:35
Alignment explanation
Indices: 20779961--20780032 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
20779951 ATATATAAAC
* *
20779961 CAAATGTTTTCTAGGTATAAACCTACAATTGACTT
1 CAAATGTTTTCTAGGTATAAACCTACAACTAACTT
* *
20779996 CAAATGTTTTCTA-GTCATAAACTTATAACTAACTT
1 CAAATGTTTTCTAGGT-ATAAACCTACAACTAACTT
20780031 CA
1 CA
20780033 CATATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (35 bp):
CAAATGTTTTCTAGGTATAAACCTACAACTAACTT
Found at i:20780167 original size:62 final size:62
Alignment explanation
Indices: 20780064--20780231 Score: 169
Period size: 62 Copynumber: 2.7 Consensus size: 62
20780054 TTTTTTGATG
* * * * ***
20780064 GGATTACTGAAGGGGTTTTTAGCTAGAAAATACTTTGAATAATTTCTTACAAAATGTTGAATA-
1 GGATTATTGAAGGCGTTTTTAGCTA-AAAATACCTTCAATAATCAATTACAAAAT-TTGAATAT
* * * **
20780127 GTATTATTGAAGGCGTTTCTAGCTAAAAATACCTTCAATAATCAATTTCAAAATTTTTATAT
1 GGATTATTGAAGGCGTTTTTAGCTAAAAATACCTTCAATAATCAATTACAAAATTTGAATAT
**
20780189 GGATTATTGAAGGCGTTTTTTA-CCGAAAATACCTTCAATAATC
1 GGATTATTGAAGGCG-TTTTTAGCTAAAAATACCTTCAATAATC
20780232 CACTCAATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
61 5 0.06
62 56 0.64
63 26 0.30
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (62 bp):
GGATTATTGAAGGCGTTTTTAGCTAAAAATACCTTCAATAATCAATTACAAAATTTGAATAT
Found at i:20780272 original size:64 final size:63
Alignment explanation
Indices: 20780129--20780324 Score: 211
Period size: 64 Copynumber: 3.1 Consensus size: 63
20780119 GTTGAATAGT
* * * *
20780129 ATTATTGAAGGC-GTTTCTAGCTAAAAATACCTTCAATAATCAATTTC-A-AAATTTTTATATGG
1 ATTATTGAAGGCATTTTTTA-CCAAAAATACCTTCAATAATCAA-CTCAATAAATTTTTATATGG
* * *
20780191 ATTATTGAAGGCGTTTTTTACCGAAAATACCTTCAATAATCCACTCAATAAATTTTTATGA-GAG
1 ATTATTGAAGGCATTTTTTACCAAAAATACCTTCAATAATCAACTCAATAAATTTTTAT-ATG-G
** * * *
20780255 ATTATTGAAGGCATTTTTTGTCAAAAATGCCTTCAATAATCTACTCAATAAATTTTTTGTATGG
1 ATTATTGAAGGCATTTTTTACCAAAAATACCTTCAATAATCAACTCAATAAA-TTTTTATATGG
20780319 ATTATT
1 ATTATT
20780325 AAATGTATTT
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
61 2 0.02
62 33 0.29
63 16 0.14
64 56 0.49
65 7 0.06
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (63 bp):
ATTATTGAAGGCATTTTTTACCAAAAATACCTTCAATAATCAACTCAATAAATTTTTATATGG
Found at i:20780335 original size:64 final size:62
Alignment explanation
Indices: 20780214--20780403 Score: 170
Period size: 64 Copynumber: 3.0 Consensus size: 62
20780204 TTTTTTACCG
* * * *
20780214 AAAATACCTTCAATAATCCACTCAATAAATTTTTATGA-GAGATTATTGAAGGCATTTTTTGTCA
1 AAAATGCCTTCAATAATCTACTCAATAAATTTTT-TGATG-GATTATT-AAAGTATTTTTTGTCA
* *
20780278 AAAATGCCTTCAATAATCTACTCAATAAATTTTTTGTATGGATTATTAAATGTATTTTTAGCCA
1 AAAATGCCTTCAATAATCTACTCAATAAATTTTTTG-ATGGATTATTAAA-GTATTTTTTGTCA
* * * * **
20780342 AAAACGCCTTTAATATTCT-CTTTCCA-AAATTTTTTGAATAAATTATTAAAGTCATTTTTTGT
1 AAAATGCCTTCAATAATCTAC--TCAATAAATTTTTTG-ATGGATTATTAAAGT-ATTTTTTGT
20780404 AAGAGATTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
63 7 0.07
64 94 0.90
65 4 0.04
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (62 bp):
AAAATGCCTTCAATAATCTACTCAATAAATTTTTTGATGGATTATTAAAGTATTTTTTGTCA
Found at i:20780412 original size:26 final size:25
Alignment explanation
Indices: 20780370--20780427 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
20780360 TCTTTCCAAA
*
20780370 ATTTTTTGAATAAATTATT-AAAGT
1 ATTTTTTGAAGAAATTATTCAAAGT
*
20780394 CATTTTTTGTAAGAGATTATTCAAAGT
1 -ATTTTTTG-AAGAAATTATTCAAAGT
20780421 ATTTTTT
1 ATTTTTT
20780428 AGCCAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 16 0.55
27 5 0.17
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.52
Consensus pattern (25 bp):
ATTTTTTGAAGAAATTATTCAAAGT
Found at i:20780567 original size:87 final size:89
Alignment explanation
Indices: 20780459--20780625 Score: 243
Period size: 89 Copynumber: 1.9 Consensus size: 89
20780449 TTATCTCCCA
* *
20780459 TTGTTTCAGGGGAAGTTTTAAA-G-GTGTTTT-GGCAAGAAATGCATTGAATAATCATTTACAAA
1 TTGTTTCAGGGGAAGTATTAAAGGCGTGTTTTGGGCAA-AAACGCATTGAATAATCATTTACAAA
20780521 TAATCTCTTGAAAAACTTTAAAAAT
65 TAATCTCTTGAAAAACTTTAAAAAT
* * *
20780546 TTGTTTCA-GGGAGAGTATTAAAGGCGTTTTTTGGGTAAAAACGTATTGAATAATCATTTACAAA
1 TTGTTTCAGGGGA-AGTATTAAAGGCGTGTTTTGGGCAAAAACGCATTGAATAATCATTTACAAA
20780610 TAATCTCTTGAAAAAC
65 TAATCTCTTGAAAAAC
20780626 GCTAAAGAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
86 4 0.06
87 16 0.23
88 1 0.01
89 46 0.65
90 4 0.06
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (89 bp):
TTGTTTCAGGGGAAGTATTAAAGGCGTGTTTTGGGCAAAAACGCATTGAATAATCATTTACAAAT
AATCTCTTGAAAAACTTTAAAAAT
Found at i:20780831 original size:63 final size:59
Alignment explanation
Indices: 20780753--20780893 Score: 156
Period size: 61 Copynumber: 2.3 Consensus size: 59
20780743 GTTTCAAGCC
* * *
20780753 AAATACCTTTTCAATAATCCCCTTAAATTTTGATGATGAGACTTATTGAAGGTATTTTTTACCAA
1 AAATACC--TTCAATAATCCCCTTAAATTTT--TGAGGAGAATTATTGAAGGTATTTTTGA-C-A
* * *
20780818 AAATACCTTCAATAATCCTCTTTAATTTTTTAGGAGAATTATTGAAGGTATTTTTGACA
1 AAATACCTTCAATAATCCCCTTAAATTTTTGAGGAGAATTATTGAAGGTATTTTTGACA
* *
20780877 AAACACCTTTAATAATC
1 AAATACCTTCAATAATC
20780894 GCTTTCATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 16 0.24
60 1 0.01
61 24 0.35
63 20 0.29
65 7 0.10
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (59 bp):
AAATACCTTCAATAATCCCCTTAAATTTTTGAGGAGAATTATTGAAGGTATTTTTGACA
Found at i:20780906 original size:59 final size:63
Alignment explanation
Indices: 20780762--20780983 Score: 174
Period size: 63 Copynumber: 3.6 Consensus size: 63
20780752 CAAATACCTT
* * * * * * * *
20780762 TTCAATAATCCCCTTAAATTTTGATGATGAGACTTATTGAAGGTATTTTTTACCAAAAATACC
1 TTCAATAATCCTCTTCAATTTTTATAAGGAGAATTATTGAAGGTATTTTTGACCAAAAACACC
*
20780825 TTCAATAATCCTCTTTAATTTTT-T-AGGAGAATTATTGAAGGTATTTTTGA-C-AAAACACC
1 TTCAATAATCCTCTTCAATTTTTATAAGGAGAATTATTGAAGGTATTTTTGACCAAAAACACC
* * * ** * **
20780884 TTTAATAATCGCT-TTCATTTTTTATAAGGAG-ATTATTTAAGGCGTTGTTTG-TCAAAAACAAA
1 TTCAATAATC-CTCTTCAATTTTTATAAGGAGAATTATTGAAGGTATT-TTTGACCAAAAACACC
* *
20780946 TT-AATAATCCCCTATCCATTTTTTATAAGGAG-ATTATT
1 TTCAATAATCCTCT-T-CAATTTTTATAAGGAGAATTATT
20780984 TCAAAACGTT
Statistics
Matches: 134, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
59 24 0.18
60 17 0.13
61 41 0.31
62 10 0.07
63 42 0.31
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (63 bp):
TTCAATAATCCTCTTCAATTTTTATAAGGAGAATTATTGAAGGTATTTTTGACCAAAAACACC
Found at i:20780914 original size:61 final size:59
Alignment explanation
Indices: 20780790--20780983 Score: 160
Period size: 61 Copynumber: 3.2 Consensus size: 59
20780780 TTTTGATGAT
* * * * *
20780790 GAGACTTATTGAAGGTATTTTTTACCAAAAATACCTTCAATAATCCTCTTTAATTTTT-T-AG
1 GAGA-TTATTGAAGGTATTTTTGA-C-AAAA-ACCTTTAATAATCCTATTCATTTTTTATAAG
20780851 GAGAATTATTGAAGGTATTTTTGACAAAACACCTTTAATAATCGCT-TTCATTTTTTATAAG
1 GAG-ATTATTGAAGGTATTTTTGACAAAA-ACCTTTAATAATC-CTATTCATTTTTTATAAG
* ** * ** *
20780912 GAGATTATTTAAGGCGTTGTTTGTCAAAAACAAATTAATAATCCCCTATCCATTTTTTATAAG
1 GAGATTATTGAAGGTATT-TTTGACAAAAAC-CTTTAATAAT--CCTATTCATTTTTTATAAG
20780975 GAGATTATT
1 GAGATTATT
20780984 TCAAAACGTT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
59 24 0.21
60 18 0.16
61 43 0.38
62 3 0.03
63 24 0.21
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (59 bp):
GAGATTATTGAAGGTATTTTTGACAAAAACCTTTAATAATCCTATTCATTTTTTATAAG
Found at i:20781030 original size:63 final size:58
Alignment explanation
Indices: 20780868--20781056 Score: 184
Period size: 63 Copynumber: 3.1 Consensus size: 58
20780858 ATTGAAGGTA
* * *
20780868 TTTTTGACAAAACACCTTTAATAATCGCTTTCATTTTTTATAAGGAGATTATTTAAGGCG
1 TTTTTGTCAAAA-ACCTTTAATAATCAC-TTCATTTTTTATAAGGAGATTATTTAAGACG
** * *
20780928 TTGTTTGTCAAAAACAAATTAATAATCCCCTATCCATTTTTTATAAGGAGATTATTTCAAAACG
1 TT-TTTGTCAAAAAC-CTTTAATAAT-CACT-T-CATTTTTTATAAGGAGATTATTT-AAGACG
20780992 TTTTCTGTCAAAAATCCTTTCAATAATCACTTCAATTTTTTA-AA-GAGGATTATTTAAGACG
1 TTTT-TGTCAAAAA-CCTTT-AATAATCACTTC-ATTTTTTATAAGGA-GATTATTTAAGACG
20781053 TTTT
1 TTTT
20781057 AATCGATAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
60 4 0.04
61 29 0.27
62 14 0.13
63 34 0.31
64 20 0.19
65 7 0.06
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTTTGTCAAAAACCTTTAATAATCACTTCATTTTTTATAAGGAGATTATTTAAGACG
Found at i:20781137 original size:20 final size:19
Alignment explanation
Indices: 20781113--20781158 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
20781103 ACAAAAGTCT
20781113 CTTTTTGAATATTTAGCAG
1 CTTTTTGAATATTTAGCAG
20781132 CTTTTTGAATATTTAGCAG
1 CTTTTTGAATATTTAGCAG
20781151 CTTTTTGA
1 CTTTTTGA
20781159 TAAAAAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (19 bp):
CTTTTTGAATATTTAGCAG
Found at i:20786341 original size:25 final size:25
Alignment explanation
Indices: 20786295--20786342 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20786285 ATGTATAATA
* * *
20786295 AATAATATAAATTATACTATACATT
1 AATAATATAAACTAAACCATACATT
*
20786320 AATAATATATACTAAACCATACA
1 AATAATATAAACTAAACCATACA
20786343 ATATTGCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (25 bp):
AATAATATAAACTAAACCATACATT
Found at i:20787729 original size:13 final size:13
Alignment explanation
Indices: 20787708--20787738 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20787698 TGATAATCAT
*
20787708 AATATAAAATAAA
1 AATAAAAAATAAA
20787721 AATAAAAAATAAA
1 AATAAAAAATAAA
20787734 AATAA
1 AATAA
20787739 TATGATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:20787880 original size:32 final size:32
Alignment explanation
Indices: 20787844--20787919 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
20787834 TTTATATAAA
20787844 ATATTATATAAATATCTAAATTTTAATATTTT
1 ATATTATATAAATATCTAAATTTTAATATTTT
20787876 ATATTATATAAATATCTAAATTTTAATATTTT
1 ATATTATATAAATATCTAAATTTTAATATTTT
20787908 ATATTATATAAA
1 ATATTATATAAA
20787920 CACAAACTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATTATATAAATATCTAAATTTTAATATTTT
Found at i:20789895 original size:53 final size:50
Alignment explanation
Indices: 20789815--20789915 Score: 166
Period size: 53 Copynumber: 2.0 Consensus size: 50
20789805 TTGGCTGGTG
20789815 CTCTCTACCATACGACTCTGCCTATTGGCTTTTCTTACAATTTCCTTCATTAC
1 CTCTCTACCATACGACTCTGCCTATTGGC---TCTTACAATTTCCTTCATTAC
*
20789868 CTCTCTACCATACGAGTCTGCCTATTGGCTCTTACAATTTCCTTCATT
1 CTCTCTACCATACGACTCTGCCTATTGGCTCTTACAATTTCCTTCATT
20789916 TTTGTTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 19 0.40
53 28 0.60
ACGTcount: A:0.19, C:0.32, G:0.09, T:0.41
Consensus pattern (50 bp):
CTCTCTACCATACGACTCTGCCTATTGGCTCTTACAATTTCCTTCATTAC
Found at i:20792285 original size:50 final size:50
Alignment explanation
Indices: 20792231--20792330 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
20792221 TGCTATCGAA
*
20792231 GATAGTAGGCCTTTGTTAAGGTAAAAGAGAATGTCACGATCTTAGAGAGG
1 GATAGTAGGCCTTTGTTAAGGTAAAAGAGAATATCACGATCTTAGAGAGG
20792281 GATAGTAGGCCTTTGTTAAGGTAAAAGAGAATATCACGATCTTAGAGAGG
1 GATAGTAGGCCTTTGTTAAGGTAAAAGAGAATATCACGATCTTAGAGAGG
20792331 AGTCATAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.26
Consensus pattern (50 bp):
GATAGTAGGCCTTTGTTAAGGTAAAAGAGAATATCACGATCTTAGAGAGG
Found at i:20796423 original size:2 final size:2
Alignment explanation
Indices: 20796416--20796441 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20796406 AGCTTCTTGC
20796416 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
20796442 TTCAAGGAAT
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:20804487 original size:30 final size:30
Alignment explanation
Indices: 20804428--20804487 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20804418 ATATAATAGG
*
20804428 AGTGAGGAAGATGTCATGATCCTAGTGGGA
1 AGTGAGGAAGATGTCATGATCCTAATGGGA
* *
20804458 AGTGA-GAAGGATGTCATGCTCTTAATGGGA
1 AGTGAGGAA-GATGTCATGATCCTAATGGGA
20804488 GCCATGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.30, C:0.10, G:0.35, T:0.25
Consensus pattern (30 bp):
AGTGAGGAAGATGTCATGATCCTAATGGGA
Found at i:20804861 original size:142 final size:143
Alignment explanation
Indices: 20804599--20804880 Score: 415
Period size: 142 Copynumber: 2.0 Consensus size: 143
20804589 GAGCCATGAG
* *
20804599 TCACATGTCGATTGTGTACTAGAGTTGATTTTGAGATATAAGTAGCCCTTTGTTGAAATGAGGAG
1 TCACACGTCGATTGTGTACTAGAGTTGATCTTGAGATATAAGTAGCCCTTTGTTGAAATGAGGAG
* * * * *
20804664 GATGTGTTGGTCTTGGGATATAAATAGGCTCCGTTGAAGTGAGGAGGATAGCATGGTCCTAGTGG
66 GATGTATTGGTCTTGGGATATAAATAGGCTCCATTGAAATGAAGAAGATAGCATGGTCCTAGTGG
*
20804729 G-GGCTTTTGGAA
131 GAGGCCTTTGGAA
* * * *
20804741 TCACACGTTGATTGTGTACTAGAGTTGGTCTTGGGATATAAGTAGCCCTTTGTTGAAATGAGGGG
1 TCACACGTCGATTGTGTACTAGAGTTGATCTTGAGATATAAGTAGCCCTTTGTTGAAATGAGGAG
* *
20804806 GATGTATTGGTCTTGGGATATAAGTAGGCTCTATTGAAATGAAGAAGAT-GTCATGGTCCTAGTG
66 GATGTATTGGTCTTGGGATATAAATAGGCTCCATTGAAATGAAGAAGATAG-CATGGTCCTAGTG
20804870 GGAGGCCTTTG
130 GGAGGCCTTTG
20804881 TTGGTTGTGT
Statistics
Matches: 124, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
141 1 0.01
142 116 0.94
143 7 0.06
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (143 bp):
TCACACGTCGATTGTGTACTAGAGTTGATCTTGAGATATAAGTAGCCCTTTGTTGAAATGAGGAG
GATGTATTGGTCTTGGGATATAAATAGGCTCCATTGAAATGAAGAAGATAGCATGGTCCTAGTGG
GAGGCCTTTGGAA
Found at i:20804863 original size:46 final size:47
Alignment explanation
Indices: 20804765--20804856 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
20804755 TGTACTAGAG
* * * **
20804765 TTGGTCTTGGGATATAAGTAGCCCTTTGTTGAAATGAGGGGGATGTA
1 TTGGTCTTGGGATATAAGTAGCCCTCTATTGAAATGAAGAAGATGTA
*
20804812 TTGGTCTTGGGATATAAGTAG-GCTCTATTGAAATGAAGAAGATGT
1 TTGGTCTTGGGATATAAGTAGCCCTCTATTGAAATGAAGAAGATGT
20804857 CATGGTCCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 18 0.46
47 21 0.54
ACGTcount: A:0.27, C:0.08, G:0.32, T:0.34
Consensus pattern (47 bp):
TTGGTCTTGGGATATAAGTAGCCCTCTATTGAAATGAAGAAGATGTA
Found at i:20805192 original size:34 final size:34
Alignment explanation
Indices: 20805135--20805220 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
20805125 ATAAATAAGT
* *
20805135 CTTCATTGAAGTGAGGAGAATGTCATAGTTTTGC
1 CTTCATTGGAGTGAGGAGAATGTCATAGTCTTGC
* *
20805169 TTTCATTGGAGTAAGGACG-ATGTCATAGTCTTGC
1 CTTCATTGGAGTGAGGA-GAATGTCATAGTCTTGC
20805203 CTTCATTGGAGTGAGGAG
1 CTTCATTGGAGTGAGGAG
20805221 GACATCATGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 1 0.02
34 43 0.96
35 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (34 bp):
CTTCATTGGAGTGAGGAGAATGTCATAGTCTTGC
Found at i:20805348 original size:154 final size:153
Alignment explanation
Indices: 20805016--20805355 Score: 430
Period size: 154 Copynumber: 2.2 Consensus size: 153
20805006 TAAGTCAATC
* * * * *
20805016 TTCGTTGAAGTAAGGAGGATGTTATGGTCCTACCTTTATTGGAGTGAGAAGGATATCATAATCCT
1 TTCGTTGGAGTAAGGA-GATGTCATGGTCTTACCTTCATTGGAGTGAGAAGGACATCATAATCCT
* * *
20805081 AGTGGTAGCCTTTGTTGGTTGTGTACTAAATTTGATATTGAGATATAAATAAGTCTTCATTGAAG
65 AGTGGTAGCCTTTGTTAGTTGTATACTAAATTTGATATTGAGATATAAATAAGTCTTCATTAAAG
* ** * **
20805146 TGAGGAGAATGTCATAGTTTTGCT
130 CGAAAAGAATGTCATAATCCTGCT
* * * * **
20805170 TTCATTGGAGTAAGGACGATGTCATAGTCTTGCCTTCATTGGAGTGAGGAGGACATCATGGTCCT
1 TTCGTTGGAGTAAGGA-GATGTCATGGTCTTACCTTCATTGGAGTGAGAAGGACATCATAATCCT
* *
20805235 AGTGAG-AGCCTTTGTTAGTTGTATACTAAATTTGATTTTGGGATATAAATAAGTCTTCATTAAA
65 AGTG-GTAGCCTTTGTTAGTTGTATACTAAATTTGATATTGAGATATAAATAAGTCTTCATTAAA
20805299 GCGAAAAGAATGTCATAATCCTGCT
129 GCGAAAAGAATGTCATAATCCTGCT
*
20805324 TTCGTTGGAGTAAGGAGAAAGTCATGGTCTTA
1 TTCGTTGGAGTAAGGAG-ATGTCATGGTCTTA
20805356 ATGGGGGCCT
Statistics
Matches: 157, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
153 1 0.01
154 155 0.99
155 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (153 bp):
TTCGTTGGAGTAAGGAGATGTCATGGTCTTACCTTCATTGGAGTGAGAAGGACATCATAATCCTA
GTGGTAGCCTTTGTTAGTTGTATACTAAATTTGATATTGAGATATAAATAAGTCTTCATTAAAGC
GAAAAGAATGTCATAATCCTGCT
Found at i:20806842 original size:17 final size:17
Alignment explanation
Indices: 20806806--20806839 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20806796 ACCGTCGTCC
*
20806806 ATTATTATTATTATTTT
1 ATTATTATTATTATATT
20806823 ATTATTATTAATTATAT
1 ATTATTATT-ATTATAT
20806840 ATTTCATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTATTATTATTATATT
Found at i:20814249 original size:21 final size:21
Alignment explanation
Indices: 20814223--20814276 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
20814213 GAGCCTCAAT
20814223 GCTGGAAGTTGATGGTGACTG
1 GCTGGAAGTTGATGGTGACTG
20814244 GCTGGAAGTTGATGGTGACTG
1 GCTGGAAGTTGATGGTGACTG
*
20814265 GCTAGAAGTTGA
1 GCTGGAAGTTGA
20814277 ATCTGAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.41, T:0.28
Consensus pattern (21 bp):
GCTGGAAGTTGATGGTGACTG
Found at i:20815856 original size:72 final size:74
Alignment explanation
Indices: 20815737--20815882 Score: 251
Period size: 72 Copynumber: 2.0 Consensus size: 74
20815727 TAGACTCTTC
* *
20815737 CATTTGGAAATTATATCCAGTCCCAAGTTTTCAAATTGACCATTACTACCTCTAAGATTTTATTT
1 CATTTGGAAATTATATCCAGTCCCAAGTTTTCAAATTGACCATTACTACCTCTAAAATTTCATTT
20815802 TCACAATTT
66 TCACAATTT
*
20815811 CATTTGGAAATTAT-T-CAGTCCCAAGTTTTCAAATTTACCATTACTACCTCTAAAATTTCATTT
1 CATTTGGAAATTATATCCAGTCCCAAGTTTTCAAATTGACCATTACTACCTCTAAAATTTCATTT
20815874 TCACAATTT
66 TCACAATTT
20815883 AAGTTATCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 54 0.78
73 1 0.01
74 14 0.20
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.41
Consensus pattern (74 bp):
CATTTGGAAATTATATCCAGTCCCAAGTTTTCAAATTGACCATTACTACCTCTAAAATTTCATTT
TCACAATTT
Found at i:20825553 original size:14 final size:14
Alignment explanation
Indices: 20825534--20825561 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20825524 GATCTTTTGA
20825534 GAAGCTTTCACTGC
1 GAAGCTTTCACTGC
20825548 GAAGCTTTCACTGC
1 GAAGCTTTCACTGC
20825562 CCATTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
GAAGCTTTCACTGC
Found at i:20839724 original size:12 final size:11
Alignment explanation
Indices: 20839711--20839757 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
20839701 AGTTAATTTA
20839711 ATTTTTTTTTT
1 ATTTTTTTTTT
*
20839722 AATTTTTCTTTT
1 -ATTTTTTTTTT
*
20839734 A-TTCTTTTTT
1 ATTTTTTTTTT
20839744 -TTTTTTTTTT
1 ATTTTTTTTTT
20839754 ATTT
1 ATTT
20839758 CAAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 15 0.52
11 4 0.14
12 10 0.34
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:20839996 original size:18 final size:18
Alignment explanation
Indices: 20839952--20839995 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
20839942 CTCACCCACC
*
20839952 ATAAAAAAATTTTAAAAA
1 ATAAAAAAATTATAAAAA
*
20839970 ATAAAAAAATTAT-AATA
1 ATAAAAAAATTATAAAAA
20839987 ATAAAAAAA
1 ATAAAAAAA
20839996 AATTCCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAAAAATTATAAAAA
Found at i:20841234 original size:15 final size:14
Alignment explanation
Indices: 20841210--20841240 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
20841200 AATATTGATA
20841210 ATATATTTAATAAT
1 ATATATTTAATAAT
20841224 ATATAATTTAATAAT
1 ATAT-ATTTAATAAT
20841239 AT
1 AT
20841241 TTATCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATTTAATAAT
Found at i:20841349 original size:31 final size:29
Alignment explanation
Indices: 20841303--20841368 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
20841293 CTTAACATAG
* * *
20841303 TATATAATTTGAAAATTGAAGGTGTAAATTA
1 TATATTATTTAAAAATTGAA-G-ATAAATTA
*
20841334 TATATTATTTAAAAATTTAAGATAAATTA
1 TATATTATTTAAAAATTGAAGATAAATTA
20841363 TATATT
1 TATATT
20841369 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.42
30 1 0.03
31 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (29 bp):
TATATTATTTAAAAATTGAAGATAAATTA
Found at i:20841378 original size:27 final size:26
Alignment explanation
Indices: 20841348--20841401 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
20841338 TTATTTAAAA
20841348 ATTTAAGATA-AATTATATATTTTTTTT
1 ATTT-AGATATAATT-TATATTTTTTTT
20841375 ATTTAGATATTAATTTATATTTTTTTT
1 ATTTAGATA-TAATTTATATTTTTTTT
20841402 TTCGAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.20
27 16 0.64
28 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (26 bp):
ATTTAGATATAATTTATATTTTTTTT
Found at i:20842081 original size:2 final size:2
Alignment explanation
Indices: 20842074--20842101 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20842064 TTTTTGGTTT
20842074 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
20842102 CACATACATG
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):
TA
Found at i:20851128 original size:16 final size:16
Alignment explanation
Indices: 20851104--20851164 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 16
20851094 AATAAATAAA
20851104 AAAATTAATTTAAATAT
1 AAAA-TAATTTAAATAT
* *
20851121 AAAATAA-TAAAAAAT
1 AAAATAATTTAAATAT
* *
20851136 TAAATATCTATTAAATAT
1 AAAATA-AT-TTAAATAT
20851154 AAAATAATTTA
1 AAAATAATTTA
20851165 TTTTAACAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
15 11 0.33
16 6 0.18
17 5 0.15
18 11 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATAATTTAAATAT
Found at i:20852424 original size:2 final size:2
Alignment explanation
Indices: 20852417--20852445 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20852407 TGACACATTA
20852417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20852446 CACATTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20852797 original size:13 final size:13
Alignment explanation
Indices: 20852779--20852803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20852769 AAGAGTCATA
20852779 TATATATATATAT
1 TATATATATATAT
20852792 TATATATATATA
1 TATATATATATA
20852804 GAAAGCCATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:20858909 original size:21 final size:23
Alignment explanation
Indices: 20858869--20858910 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20858859 AACTAAAACA
*
20858869 CTATTAACTTTATCAACAGATTT
1 CTATTAACTCTATCAACAGATTT
20858892 CTATTAACTCT-T-AACAGAT
1 CTATTAACTCTATCAACAGAT
20858911 CACACTGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (23 bp):
CTATTAACTCTATCAACAGATTT
Found at i:20859003 original size:10 final size:10
Alignment explanation
Indices: 20858988--20859030 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
20858978 GCACACATAC
20858988 ATACATACAT
1 ATACATACAT
20858998 ATACATACAT
1 ATACATACAT
* *
20859008 ATATATATAT
1 ATACATACAT
* *
20859018 ATATATATAT
1 ATACATACAT
20859028 ATA
1 ATA
20859031 TATATATGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (10 bp):
ATACATACAT
Found at i:20859003 original size:14 final size:14
Alignment explanation
Indices: 20858984--20859028 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
20858974 GAGCGCACAC
*
20858984 ATACATACATACAT
1 ATACATACATATAT
20858998 ATACATACATATAT
1 ATACATACATATAT
* *
20859012 ATATATATATATAT
1 ATACATACATATAT
20859026 ATA
1 ATA
20859029 TATATATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (14 bp):
ATACATACATATAT
Found at i:20859005 original size:18 final size:18
Alignment explanation
Indices: 20858982--20859018 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20858972 ATGAGCGCAC
20858982 ACATACATACATACATAT
1 ACATACATACATACATAT
* *
20859000 ACATACATATATATATAT
1 ACATACATACATACATAT
20859018 A
1 A
20859019 TATATATATA
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:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (18 bp):
ACATACATACATACATAT
Found at i:20859013 original size:2 final size:2
Alignment explanation
Indices: 20858996--20859037 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
20858986 ACATACATAC
* *
20858996 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20859038 GACATCGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20863430 original size:86 final size:86
Alignment explanation
Indices: 20863282--20863453 Score: 197
Period size: 86 Copynumber: 2.0 Consensus size: 86
20863272 CATTCTTATG
* *
20863282 AAGCATACCATATCTCCTAAAAGCATGTTACTACCAAATGCAGGTATCTGCTGGTGTATTGGCGC
1 AAGCATACCATATCTCCTAAAAGCATGTTACTACCAAAGGCAGGCATCTGCTGGTGTATT-G-GC
20863347 ATACA-AA-AGATGAAGGCATAC
64 ATACACAACAGATGAAGGCATAC
* * * * * * * *
20863368 AAGCATATCTTATCTCCTGAAAGCATGTTTCTAGCAAAGGCGGGCATCT-TTGAGTGTTTTGGCA
1 AAGCATACCATATCTCCTAAAAGCATGTTACTACCAAAGGCAGGCATCTGCTG-GTGTATTGGCA
*
20863432 TACACAACAGATGAAGGTATAC
65 TACACAACAGATGAAGGCATAC
20863454 TAACATTTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 7 0.10
85 5 0.07
86 60 0.83
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (86 bp):
AAGCATACCATATCTCCTAAAAGCATGTTACTACCAAAGGCAGGCATCTGCTGGTGTATTGGCAT
ACACAACAGATGAAGGCATAC
Found at i:20867664 original size:17 final size:18
Alignment explanation
Indices: 20867642--20867688 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
20867632 AATAAATATA
20867642 TAAAAAATTAATATTT-T
1 TAAAAAATTAATATTTAT
20867659 TAAAAAATT--TATTTAT
1 TAAAAAATTAATATTTAT
*
20867675 TAAAAAAATAATAT
1 TAAAAAATTAATAT
20867689 CATTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 9 0.35
18 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAAATTAATATTTAT
Found at i:20867666 original size:28 final size:27
Alignment explanation
Indices: 20867597--20867666 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
20867587 TGTATGATAT
* *
20867597 TATTTATTAATAAATAAATAAATATTAA
1 TATTT-TTAAAAAATAAATAAAAATTAA
* *
20867625 T-TTTTAAAATAAATATATAAAAAATTAA
1 TATTTTTAAA-AAATAAAT-AAAAATTAA
20867653 TATTTTTAAAAAAT
1 TATTTTTAAAAAAT
20867667 TTATTTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 3 0.09
27 10 0.29
28 14 0.41
29 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TATTTTTAAAAAATAAATAAAAATTAA
Found at i:20867677 original size:16 final size:16
Alignment explanation
Indices: 20867642--20867681 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
20867632 AATAAATATA
20867642 TAAAAAATTAATATTTT
1 TAAAAAATT-ATATTTT
20867659 TAAAAAATT-TATTTAT
1 TAAAAAATTATATTT-T
20867675 TAAAAAA
1 TAAAAAA
20867682 ATAATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAAATTATATTTT
Found at i:20868350 original size:3 final size:3
Alignment explanation
Indices: 20868342--20868372 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
20868332 GTGTAGTTGT
*
20868342 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20868373 GTTGATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20869091 original size:71 final size:70
Alignment explanation
Indices: 20869014--20869153 Score: 203
Period size: 71 Copynumber: 2.0 Consensus size: 70
20869004 ACATCAAGAT
* * *
20869014 AAATTTGATGATTTATATATATTCATGTTATA-AAA-TATTAAAATTTATATATTTATATTATAT
1 AAATTTGATGA-TT-CATACATTCATATTATATAAATTATTAAAATTTATATA-TTATATTATAT
20869077 TTTATATG
63 TTTATATG
*
20869085 AAATTTGATGATTCATGCATTCATATTATATAAATTATTAAAATTTATATATTATATTATATTTT
1 AAATTTGATGATTCATACATTCATATTATATAAATTATTAAAATTTATATATTATATTATATTTT
20869150 ATAT
66 ATAT
20869154 AAAAATTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
69 13 0.21
70 23 0.37
71 27 0.43
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (70 bp):
AAATTTGATGATTCATACATTCATATTATATAAATTATTAAAATTTATATATTATATTATATTTT
ATATG
Found at i:20869161 original size:18 final size:18
Alignment explanation
Indices: 20869140--20869187 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
20869130 TATATATTAT
* *
20869140 ATTATATTTTATATAAAA
1 ATTATATATTATAAAAAA
20869158 ATTATATATTATAAAAAA
1 ATTATATATTATAAAAAA
*
20869176 A-TATAAATTATA
1 ATTATATATTATA
20869188 TTTTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATATATTATAAAAAA
Found at i:20870004 original size:42 final size:42
Alignment explanation
Indices: 20869943--20870026 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
20869933 GGTCTCTTCA
* *
20869943 GCTTTGGTTTTGGCGGCATCATAG-CCTCCTTTAGCTTTCTCG
1 GCTTTGCTTTTGGCCGCATCAT-GCCCTCCTTTAGCTTTCTCG
*
20869985 GCTTTGCTTTTGGCCGCATCATGCCCTTCTTTAGCTTTCTCG
1 GCTTTGCTTTTGGCCGCATCATGCCCTCCTTTAGCTTTCTCG
20870027 TTAGCCCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.08, C:0.29, G:0.21, T:0.42
Consensus pattern (42 bp):
GCTTTGCTTTTGGCCGCATCATGCCCTCCTTTAGCTTTCTCG
Found at i:20873177 original size:19 final size:19
Alignment explanation
Indices: 20873145--20873182 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
20873135 GAGATGAAAG
20873145 AAAAGAAAGTAAAATAAAA
1 AAAAGAAAGTAAAATAAAA
20873164 AAAAGTAAAG-AAAATAAAA
1 AAAAG-AAAGTAAAATAAAA
20873183 TTTATTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAGAAAGTAAAATAAAA
Found at i:20873331 original size:15 final size:15
Alignment explanation
Indices: 20873311--20873340 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20873301 GGAAAGTTGA
*
20873311 AAAAAAAATTTTTAT
1 AAAAAAAATTATTAT
20873326 AAAAAAAATTATTAT
1 AAAAAAAATTATTAT
20873341 GTCCATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAAAAATTATTAT
Found at i:20876777 original size:39 final size:39
Alignment explanation
Indices: 20876723--20876798 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
20876713 GTCAGCCCTA
20876723 AGATAGAGCCATTCCTACCTATTGATAGATGTAACTCAC
1 AGATAGAGCCATTCCTACCTATTGATAGATGTAACTCAC
20876762 AGATAGAGCCATTCCTACCTATTGATAGATGTAACTC
1 AGATAGAGCCATTCCTACCTATTGATAGATGTAACTC
20876799 GTAGCCCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (39 bp):
AGATAGAGCCATTCCTACCTATTGATAGATGTAACTCAC
Found at i:20879298 original size:11 final size:10
Alignment explanation
Indices: 20879272--20879315 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
20879262 AAGATAGAAG
20879272 AAAAAAAAG-
1 AAAAAAAAGA
20879281 -AAAAAAAGTA
1 AAAAAAAAG-A
*
20879291 AAACAAAAGA
1 AAAAAAAAGA
20879301 AAAAAAAAGA
1 AAAAAAAAGA
20879311 AAAAA
1 AAAAA
20879316 GAAAAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.27
10 15 0.50
11 7 0.23
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:20879701 original size:11 final size:11
Alignment explanation
Indices: 20879685--20879760 Score: 93
Period size: 11 Copynumber: 6.6 Consensus size: 11
20879675 TAATAGATGA
20879685 AAAAAAAAAAT
1 AAAAAAAAAAT
20879696 AAAAAAAAAAT
1 AAAAAAAAAAT
20879707 -AAAAAAAAAT
1 AAAAAAAAAAT
20879717 AAAAAAAAAAT
1 AAAAAAAAAAT
20879728 GAAAAAAAGGAAA-
1 -AAAAAAA--AAAT
20879741 AAAAGAAAAAAT
1 AAAA-AAAAAAT
20879753 GAAAAAAA
1 -AAAAAAA
20879761 GAGAAATGGA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.17
11 24 0.41
12 14 0.24
13 7 0.12
14 3 0.05
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:20879760 original size:1 final size:1
Alignment explanation
Indices: 20879684--20879751 Score: 64
Period size: 1 Copynumber: 68.0 Consensus size: 1
20879674 CTAATAGATG
* * * ** ** *
20879684 AAAAAAAAAAATAAAAAAAAAATAAAAAAAAATAAAAAAAAAATGAAAAAAAGGAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20879749 AAA
1 AAA
20879752 TGAAAAAAAG
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (1 bp):
A
Found at i:20879766 original size:10 final size:9
Alignment explanation
Indices: 20879683--20879766 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
20879673 ACTAATAGAT
20879683 GAAAAAAAA
1 GAAAAAAAA
20879692 -AAATAAAAA
1 GAAA-AAAAA
20879701 -AAAAATAAA
1 GAAAAA-AAA
20879710 -AAAAAATAA
1 GAAAAAA-AA
20879719 -AAAAAAAA
1 GAAAAAAAA
20879727 TG-AAAAAAA
1 -GAAAAAAAA
*
20879736 GGAAAAAAA
1 GAAAAAAAA
*
20879745 G-AAAAAAT
1 GAAAAAAAA
20879753 GAAAAAAAGA
1 GAAAAAAA-A
20879763 GAAA
1 GAAA
20879767 TGGAATACTT
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
8 16 0.25
9 45 0.69
10 4 0.06
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.06
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:20880404 original size:32 final size:32
Alignment explanation
Indices: 20880365--20880430 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
20880355 TGATTGAATG
*
20880365 ATGAAAATAATATGGATCAGAGGATAAAATTT
1 ATGAAAATAATATGGATCAAAGGATAAAATTT
20880397 ATGAAAATAATATGGATCAAAGGATAAAATTT
1 ATGAAAATAATATGGATCAAAGGATAAAATTT
20880429 AT
1 AT
20880431 TCTAAAGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.17, T:0.29
Consensus pattern (32 bp):
ATGAAAATAATATGGATCAAAGGATAAAATTT
Found at i:20880972 original size:21 final size:21
Alignment explanation
Indices: 20880947--20881023 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
20880937 ATGAATTCTC
20880947 AAATGAGAATTTTTTAGTCTT
1 AAATGAGAATTTTTTAGTCTT
* * *
20880968 AAATGAAAAATTTTCAGAAATCTT
1 AAATGAGAATTTTTTAG---TCTT
*
20880992 CAAATGAGAATCTTTTAGTCTT
1 -AAATGAGAATTTTTTAGTCTT
*
20881014 AAATAAGAAT
1 AAATGAGAAT
20881024 CTTTAAGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
21 23 0.52
22 4 0.09
24 4 0.09
25 13 0.30
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (21 bp):
AAATGAGAATTTTTTAGTCTT
Found at i:20881002 original size:46 final size:46
Alignment explanation
Indices: 20880945--20881034 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
20880935 TTATGAATTC
* *
20880945 TCAAATGAGAATTTTTTAGTCTTAAATGAAAAAT-TTTCAGAAATCT
1 TCAAATGAGAATCTTTTAGTCTTAAAT-AAAAATCTTTAAGAAATCT
*
20880991 TCAAATGAGAATCTTTTAGTCTTAAATAAGAATCTTTAAGAAAT
1 TCAAATGAGAATCTTTTAGTCTTAAATAAAAATCTTTAAGAAAT
20881035 AAAACTCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 5 0.12
46 35 0.88
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (46 bp):
TCAAATGAGAATCTTTTAGTCTTAAATAAAAATCTTTAAGAAATCT
Found at i:20881237 original size:31 final size:31
Alignment explanation
Indices: 20881199--20881259 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
20881189 AGTTGAAAAA
* **
20881199 TCTTGTGAATCTGAAATTTTGCTAATTAAAT
1 TCTTGTGAAACTGAAATTTTGAGAATTAAAT
20881230 TCTTGTGAAACTGAAATTTTGAGAATTAAA
1 TCTTGTGAAACTGAAATTTTGAGAATTAAA
20881260 ATTTGGTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (31 bp):
TCTTGTGAAACTGAAATTTTGAGAATTAAAT
Found at i:20881269 original size:31 final size:30
Alignment explanation
Indices: 20881195--20881269 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
20881185 GTGAAGTTGA
* **
20881195 AAAATCTTGTGAATCTGAAATTTTGCTAATT
1 AAAAT-TTGTGAAACTGAAATTTTGAGAATT
*
20881226 AAATTCTTGTGAAACTGAAATTTTGAGAATT
1 AAAAT-TTGTGAAACTGAAATTTTGAGAATT
20881257 AAAATTTGGTGAA
1 AAAATTT-GTGAA
20881270 TTCTTGTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
AAAATTTGTGAAACTGAAATTTTGAGAATT
Found at i:20881508 original size:44 final size:44
Alignment explanation
Indices: 20881432--20881829 Score: 288
Period size: 44 Copynumber: 9.3 Consensus size: 44
20881422 GTCGATGGGT
* * * *
20881432 TTTATTCATTTTTTTGAAAGTTGTTGAGCCTCTGATTAGATGAGC
1 TTTATTTA-TTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
* * * *
20881477 TTTATTTATTTTCTCAAACTCGTTGAGCCTCTGTTTAGAGAAGC
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
* * * * *
20881521 TTTATATATTTTTTAAAAATCGTTAAGCTTCTG-TTCAGAGGAGC
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGATT-AGAGGAGC
* *
20881565 TTTATTTATTTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAG-
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
* * *
20881608 --TGTTTATTTTTTCAAAGTTGTTGAGCCTCT-ATATAGATGAG-
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGAT-TAGAGGAGC
* * * * * * *
20881649 --GATTTATTTTCT-AAAGTTGTTGAACATTTGTTTAGAGGAGC
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
*** ** *
20881690 CCCA-TTATTTTTTCAAAGTTATTGAGCCT-TTATTTAGAGGAGC
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGC
* * * * *
20881733 TTTATTTAATTTTTCAAAGTTGTTGAGCTTTTGTTTAGAGGAGC
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
** *
20881777 ---ATTTA-TTTTTCAAAGTTATTGAGCCTCT-ACTTAGAGGAGT
1 TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGC
20881817 TTTATTTATTTTT
1 TTTATTTATTTTT
20881830 CTAAGTTGTG
Statistics
Matches: 283, Mismatches: 54, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
40 51 0.18
41 49 0.17
42 9 0.03
43 31 0.11
44 133 0.47
45 10 0.04
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (44 bp):
TTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
Found at i:20881650 original size:88 final size:86
Alignment explanation
Indices: 20881441--20881829 Score: 341
Period size: 88 Copynumber: 4.6 Consensus size: 86
20881431 TTTTATTCAT
* * * *
20881441 TTTTTTGAAAGTTGTTGAGCCTCTGATT-AGATGAGCTTTATTTATTTTCTCAAACTCGTTGAGC
1 TTTTTTCAAAGTTGTTGAGCCTCT-ATTGAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGAGC
* * *
20881505 CTCTGTTTAGAGAAGCTTTATATA
65 CTCTGTTTAGAGGAGC--CATTTA
* * * * * * * *
20881529 TTTTTTAAAAATCGTTAAGCTTCTGTTCAGAGGAGCTTTATTTATTTTTTCAAAGTCATTGAGCC
1 TTTTTTCAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGAGCC
**
20881594 TCTGTTTAGAGGAG-TGTTTA
66 TCTGTTTAGAGGAGCCATTTA
* * * * *
20881614 TTTTTTCAAAGTTGTTGAGCCTCTATAT-AGATGAG---GATTTATTTTCT-AAAGTTGTTGAAC
1 TTTTTTCAAAGTTGTTGAGCCTCTAT-TGAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGAGC
* *
20881674 ATTTGTTTAGAGGAGCCCCA-TTA
65 CTCTGTTTAGAGGAG--CCATTTA
* * * * * *
20881697 TTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAGCTTTATTTAATTTTTCAAAGTTGTTGAGCT
1 TTTTTTCAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGAGCC
*
20881762 TTTGTTTAGAGGAG-CATTTA
66 TCTGTTTAGAGGAGCCATTTA
* *
20881782 -TTTTTCAAAGTTATTGAGCCTCTACTT-AGAGGAGTTTTATTTATTTTT
1 TTTTTTCAAAGTTGTTGAGCCTCTA-TTGAGAGGAGCTTTATTTATTTTT
20881830 CTAAGTTGTG
Statistics
Matches: 249, Mismatches: 40, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
81 23 0.09
82 11 0.04
83 33 0.13
84 44 0.18
85 35 0.14
86 10 0.04
87 28 0.11
88 65 0.26
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (86 bp):
TTTTTTCAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGAGCC
TCTGTTTAGAGGAGCCATTTA
Found at i:20881799 original size:40 final size:41
Alignment explanation
Indices: 20881568--20881802 Score: 233
Period size: 41 Copynumber: 5.7 Consensus size: 41
20881558 GAGGAGCTTT
* * *
20881568 ATTTATTTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGT
1 ATTTATTTTTTCAAAGTTATTGAGCCTTTGTTTAGAGGAGC
* * * * * * *
20881609 GTTTATTTTTTCAAAGTTGTTGAGCCTCTATATAGATGAGG
1 ATTTATTTTTTCAAAGTTATTGAGCCTTTGTTTAGAGGAGC
* * * *
20881650 ATTTATTTTCT-AAAGTTGTTGAACATTTGTTTAGAGGAGCCCC
1 ATTTATTTTTTCAAAGTTATTGAGCCTTTGTTTAGAGGAG---C
*
20881693 A-TTATTTTTTCAAAGTTATTGAGCCTTTATTTAGAGGAGC
1 ATTTATTTTTTCAAAGTTATTGAGCCTTTGTTTAGAGGAGC
* * *
20881733 TTTATTTAATTTTTCAAAGTTGTTGAGCTTTTGTTTAGAGGAGC
1 ---ATTTATTTTTTCAAAGTTATTGAGCCTTTGTTTAGAGGAGC
20881777 ATTTA-TTTTTCAAAGTTATTGAGCCT
1 ATTTATTTTTTCAAAGTTATTGAGCCT
20881803 CTACTTAGAG
Statistics
Matches: 159, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
40 42 0.26
41 48 0.30
42 8 0.05
43 26 0.16
44 35 0.22
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.46
Consensus pattern (41 bp):
ATTTATTTTTTCAAAGTTATTGAGCCTTTGTTTAGAGGAGC
Done.