Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 71 of 132
Found at i:20576646 original size:17 final size:16
Alignment explanation
Indices: 20576616--20576729 Score: 66
Period size: 17 Copynumber: 6.7 Consensus size: 16
20576606 TGTTAGTAAG
* *
20576616 CATTGCCATCACATTCT
1 CATTGTCATTACATT-T
20576633 CATTGTCATTACATTT
1 CATTGTCATTACATTT
* * **
20576649 TAGTTGTCATTGCATAAG
1 CA-TTGTCATTACAT-TT
* *
20576667 CATTGTCATCACATTCC
1 CATTGTCATTACATT-T
*
20576684 CGTTGTCATTACATTTT
1 CATTGTCATTACA-TTT
* *
20576701 AATTGTCATTGCATTT
1 CATTGTCATTACATTT
20576717 CCATTTGTCATTA
1 -CA-TTGTCATTA
20576730 GAATTTAGTG
Statistics
Matches: 72, Mismatches: 19, Indels: 11
0.71 0.19 0.11
Matches are distributed among these distances:
16 5 0.07
17 56 0.78
18 11 0.15
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (16 bp):
CATTGTCATTACATTT
Found at i:20576690 original size:51 final size:51
Alignment explanation
Indices: 20576612--20576714 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
20576602 AGTCTGTTAG
* *
20576612 TAAGCATTGCCATCACATTCTCATTGTCATTACATTTTAGTTGTCATTGCA
1 TAAGCATTGCCATCACATTCCCATTGTCATTACATTTTAATTGTCATTGCA
* *
20576663 TAAGCATTGTCATCACATTCCCGTTGTCATTACATTTTAATTGTCATTGCA
1 TAAGCATTGCCATCACATTCCCATTGTCATTACATTTTAATTGTCATTGCA
20576714 T
1 T
20576715 TTCCATTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (51 bp):
TAAGCATTGCCATCACATTCCCATTGTCATTACATTTTAATTGTCATTGCA
Found at i:20581480 original size:24 final size:23
Alignment explanation
Indices: 20581449--20581514 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
20581439 CGAAAAAAAT
**
20581449 TTCTTCCTTCTCTCCTTCTTTTCC
1 TTCTTCCTTCTCTCC-TCTTTGAC
*
20581473 TTCTTCCTTTTCCTCCTCTTTGAC
1 TTCTTCCTTCT-CTCCTCTTTGAC
*
20581497 TTCTTCTTTCTCTTCCTC
1 TTCTTCCTTCTC-TCCTC
20581515 AATACCCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 30 0.86
25 4 0.11
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.58
Consensus pattern (23 bp):
TTCTTCCTTCTCTCCTCTTTGAC
Found at i:20603517 original size:16 final size:16
Alignment explanation
Indices: 20603496--20603526 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20603486 GTTCTATATA
20603496 TATATATATTTCTTTT
1 TATATATATTTCTTTT
*
20603512 TATATATTTTTCTTT
1 TATATATATTTCTTT
20603527 CTTTCTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TATATATATTTCTTTT
Found at i:20608342 original size:33 final size:33
Alignment explanation
Indices: 20608286--20608350 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
20608276 ATATATATGG
*
20608286 AAATGCAATGACAATGTAGATGCAGCGACAATA
1 AAATGCAATGACAATGTAAATGCAGCGACAATA
* *
20608319 AAATGCAATGAC-ATTTATAATGCAGGGACAAT
1 AAATGCAATGACAATGTA-AATGCAGCGACAAT
20608351 TATACTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.22
Consensus pattern (33 bp):
AAATGCAATGACAATGTAAATGCAGCGACAATA
Found at i:20617288 original size:22 final size:21
Alignment explanation
Indices: 20617241--20617288 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
20617231 GACTTTCATC
* *
20617241 ATTAACTTAATTAATCATCCT
1 ATTAACTTAATCAATCATACT
* *
20617262 TTTAACCTTAATCAATCCTACT
1 ATTAA-CTTAATCAATCATACT
20617284 ATTAA
1 ATTAA
20617289 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAACTTAATCAATCATACT
Found at i:20618376 original size:16 final size:16
Alignment explanation
Indices: 20618355--20618387 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20618345 CAGATTTCCT
20618355 CCATTCTCAGATCCAA
1 CCATTCTCAGATCCAA
20618371 CCATTCTCAGATCCAA
1 CCATTCTCAGATCCAA
20618387 C
1 C
20618388 TACTTTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.39, G:0.06, T:0.24
Consensus pattern (16 bp):
CCATTCTCAGATCCAA
Found at i:20619623 original size:29 final size:28
Alignment explanation
Indices: 20619585--20619952 Score: 119
Period size: 29 Copynumber: 12.8 Consensus size: 28
20619575 TTTGAAAATG
20619585 AAAATGTAATTTTTGGAAATTTGAGGGC
1 AAAATGTAATTTTTGGAAATTTGAGGGC
* *
20619613 AAAATGATAATTTTTGG--ATGTTCAGGGGT
1 AAAATG-TAATTTTTGGAAAT-TTGA-GGGC
* ** * *
20619642 AAAATGGTATTTTTTGGATGTTCGGGGGC
1 AAAAT-GTAATTTTTGGAAATTTGAGGGC
** *
20619671 AAAATGGTAATTTTTGGATGTTT-AAGGC
1 AAAAT-GTAATTTTTGGAAATTTGAGGGC
* * *
20619699 AAAAATGCAA-TTTTGGAAAAGTTG-GGGTT
1 -AAAATGTAATTTTTGG-AAATTTGAGGG-C
* * ** *
20619728 AAAATGGTAATTTTTAGATATTCAATGGC
1 AAAAT-GTAATTTTTGGAAATTTGAGGGC
* ** *
20619757 AAGATGGTAATTTTTGGATGTTCGA-GGC
1 AAAAT-GTAATTTTTGGAAATTTGAGGGC
* *
20619785 AAAAATGCAA-TTTTGGAAAAGTTCG-GGGTC
1 -AAAATGTAATTTTTGG-AAA-TTTGAGGG-C
** * * *
20619815 AAAACATGATTTTTGAAAAGTTTGAGGGT
1 AAAATGTAATTTTTGGAAA-TTTGAGGGC
* * *
20619844 AAAATGTAA-TTTTGTAAAGTTTAAGGTC
1 AAAATGTAATTTTTGGAAA-TTTGAGGGC
* * *
20619872 AAAATGGTAATTTTTGGATATTTGGGGGT
1 AAAAT-GTAATTTTTGGAAATTTGAGGGC
* *
20619901 GAAAT-TAA-TTTTGGAAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGAAA-TTTGAGGG-C
* * *
20619929 AAAATATGATTTTTGTGAAGTTTG
1 AAAATGTAATTTTTG-GAAATTTG
20619953 GAGGTTAAAA
Statistics
Matches: 250, Mismatches: 63, Indels: 52
0.68 0.17 0.14
Matches are distributed among these distances:
26 8 0.03
27 23 0.09
28 56 0.22
29 126 0.50
30 33 0.13
31 4 0.02
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAATTTGAGGGC
Found at i:20619704 original size:58 final size:56
Alignment explanation
Indices: 20619609--20619788 Score: 159
Period size: 57 Copynumber: 3.1 Consensus size: 56
20619599 GGAAATTTGA
* * *
20619609 GGGCAAAATGATAATTTTTGGATGTTCAGGGGTAAAATGGTATTTTTTGGATGTTCGG
1 GGGCAAAATGGTAATTTTTGGATGTTCA-AGGCAAAATGGTA-TTTTTGGATGTTCGG
* * * *
20619667 GGGCAAAATGGTAATTTTTGGATGTTTAAGGCAAAAAT-GCAATTTTGGAAAAGTT-GG
1 GGGCAAAATGGTAATTTTTGGATGTTCAAGGC-AAAATGGTATTTTTGG--ATGTTCGG
** * * *
20619724 GGTTAAAATGGTAATTTTTAGATATTCAATGGCAAGATGGTAATTTTTGGATGTTC-G
1 GGGCAAAATGGTAATTTTTGGATGTTCAA-GGCAAAATGGT-ATTTTTGGATGTTCGG
*
20619781 AGGCAAAA
1 GGGCAAAA
20619789 ATGCAATTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 15
0.74 0.15 0.12
Matches are distributed among these distances:
56 6 0.06
57 44 0.46
58 39 0.41
59 7 0.07
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.35
Consensus pattern (56 bp):
GGGCAAAATGGTAATTTTTGGATGTTCAAGGCAAAATGGTATTTTTGGATGTTCGG
Found at i:20619731 original size:86 final size:87
Alignment explanation
Indices: 20619632--20619818 Score: 261
Period size: 86 Copynumber: 2.2 Consensus size: 87
20619622 ATTTTTGGAT
* * * ** *
20619632 GTTCAGGGG-TAAAATGGTATTTTTTGGATGTTCGGGGGCAAAATGGTAATTTTTGGATGTTTAA
1 GTTC-GGGGTTAAAATGGTAATTTTTAGATATTCAAGGGCAAAATGGTAATTTTTGGATGTTCAA
20619696 GGCAAAAATGCAATTTTGGAAAA
65 GGCAAAAATGCAATTTTGGAAAA
* * *
20619719 GTT-GGGGTTAAAATGGTAATTTTTAGATATTCAATGGCAAGATGGTAATTTTTGGATGTTCGAG
1 GTTCGGGGTTAAAATGGTAATTTTTAGATATTCAAGGGCAAAATGGTAATTTTTGGATGTTCAAG
20619783 GCAAAAATGCAATTTTGGAAAA
66 GCAAAAATGCAATTTTGGAAAA
*
20619805 GTTCGGGGTCAAAA
1 GTTCGGGGTTAAAA
20619819 CATGATTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
85 4 0.05
86 72 0.82
87 12 0.14
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (87 bp):
GTTCGGGGTTAAAATGGTAATTTTTAGATATTCAAGGGCAAAATGGTAATTTTTGGATGTTCAAG
GCAAAAATGCAATTTTGGAAAA
Found at i:20619791 original size:58 final size:56
Alignment explanation
Indices: 20619585--20619788 Score: 164
Period size: 58 Copynumber: 3.6 Consensus size: 56
20619575 TTTGAAAATG
* * * * *
20619585 AAAAT-GTAATTTTTGGAAATTTGAGGGCAAAATGATAATTTTTGGATGTTCAGGGGT
1 AAAATGGTAATTTTTGGAAGTTCGA-GGCAAAATGGTAATTTTTGGATGTTCA-AGGC
* * * *
20619642 AAAATGGTATTTTTTGGATGTTCGGGGGCAAAATGGTAATTTTTGGATGTTTAAGGC
1 AAAATGGTAATTTTTGGAAGTTC-GAGGCAAAATGGTAATTTTTGGATGTTCAAGGC
* * * * *
20619699 AAAAAT-GCAA-TTTTGGAAAAGTT-GGGGTTAAAATGGTAATTTTTAGATATTCAATGGC
1 -AAAATGGTAATTTTTGG--AAGTTCGAGG-CAAAATGGTAATTTTTGGATGTTCAA-GGC
* *
20619757 AAGATGGTAATTTTTGGATGTTCGAGGCAAAA
1 AAAATGGTAATTTTTGGAAGTTCGAGGCAAAA
20619789 ATGCAATTTT
Statistics
Matches: 116, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
56 10 0.09
57 43 0.37
58 56 0.48
59 7 0.06
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (56 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGCAAAATGGTAATTTTTGGATGTTCAAGGC
Found at i:20619827 original size:115 final size:115
Alignment explanation
Indices: 20619708--20619964 Score: 285
Period size: 115 Copynumber: 2.2 Consensus size: 115
20619698 CAAAAATGCA
* *
20619708 ATTTTGGAAAAG-TTGGGGTTAAAATGGTAATTTT-TAGATA-TTCAATGG-CAAGATGGTAATT
1 ATTTTTGAAAAGTTTGGGGTTAAAATGGTAATTTTGTA-A-AGTTCAA-GGTCAAAATGGTAATT
*
20619769 TTTGGATGTTCGAGGCAAAAATGCAATTTTGGAAAAGTTCG-GGGTCAAAACATG
63 TTTGGATATTCGAGGCAAAAAT-CAATTTTGG-AAAGTTCGAGGGTCAAAACATG
*
20619823 ATTTTTGAAAAGTTTGAGGG-TAAAAT-GTAATTTTGTAAAGTTTAAGGTCAAAATGGTAATTTT
1 ATTTTTGAAAAGTTTG-GGGTTAAAATGGTAATTTTGTAAAGTTCAAGGTCAAAATGGTAATTTT
* * *** * *
20619886 TGGATATTTGGGGGTGAAATTAATTTTGGAAAGTTCGAGGGTCAAAATATG
65 TGGATATTCGAGGCAAAAATCAATTTTGGAAAGTTCGAGGGTCAAAACATG
**
20619937 ATTTTTGTGAAGTTTGGAGGTTAAAATG
1 ATTTTTGAAAAGTTTGG-GGTTAAAATG
20619965 TGTTTTTTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
113 9 0.08
114 39 0.32
115 58 0.48
116 11 0.09
117 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.36
Consensus pattern (115 bp):
ATTTTTGAAAAGTTTGGGGTTAAAATGGTAATTTTGTAAAGTTCAAGGTCAAAATGGTAATTTTT
GGATATTCGAGGCAAAAATCAATTTTGGAAAGTTCGAGGGTCAAAACATG
Found at i:20619864 original size:57 final size:57
Alignment explanation
Indices: 20619786--20619965 Score: 157
Period size: 57 Copynumber: 3.1 Consensus size: 57
20619776 GTTCGAGGCA
*
20619786 AAAATGCAATTTTGGAAAAGTTCGGGGTCAAAACATGATTTTTGAAAAGTTTGAGGGT
1 AAAATGTAATTTT-GAAAAGTTCGGGGTCAAAACATGATTTTTGAAAAGTTTGAGGGT
* *** ** * * * *
20619844 AAAATGTAATTTTGTAAAGTTTAAGGTCAAAATGGTAATTTTTGGATA-TTTGGGGGT
1 AAAATGTAATTTTGAAAAGTTCGGGGTCAAAA-CATGATTTTTGAAAAGTTTGAGGGT
* * * ** *
20619901 GAAAT-TAATTTTGGAAAGTTCGAGGGTCAAAATATGATTTTTGTGAAGTTTGGAGGTT
1 AAAATGTAATTTTGAAAAGTTCG-GGGTCAAAACATGATTTTTGAAAAGTTT-GAGGGT
20619959 AAAATGT
1 AAAATGT
20619966 GTTTTTTAAA
Statistics
Matches: 92, Mismatches: 25, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
56 23 0.25
57 38 0.41
58 30 0.33
59 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTGAAAAGTTCGGGGTCAAAACATGATTTTTGAAAAGTTTGAGGGT
Found at i:20619865 original size:28 final size:28
Alignment explanation
Indices: 20619786--20619965 Score: 102
Period size: 30 Copynumber: 6.2 Consensus size: 28
20619776 GTTCGAGGCA
* *
20619786 AAAATGCAATTTTGGAAAAGTTCG-GGGT
1 AAAATGTAATTTTGG-AAAGTTTGAGGGT
* *
20619814 CAAAACATG-ATTTTTGAAAAGTTTGAGGGT
1 --AAA-ATGTAATTTTGGAAAGTTTGAGGGT
* *
20619844 AAAATGTAATTTTGTAAAGTTT-AAGGT
1 AAAATGTAATTTTGGAAAGTTTGAGGGT
* *
20619871 CAAAATGGTAATTTTTGGATA-TTTGGGGGT
1 -AAAAT-GTAA-TTTTGGAAAGTTTGAGGGT
* *
20619901 GAAAT-TAATTTTGGAAAGTTCGAGGGT
1 AAAATGTAATTTTGGAAAGTTTGAGGGT
* * *
20619928 CAAAATATGATTTTTGTG-AAGTTTGGAGGTT
1 -AAAATGT-AATTTTG-GAAAGTTT-GAGGGT
20619959 AAAATGT
1 AAAATGT
20619966 GTTTTTTAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
26 8 0.07
27 17 0.14
28 25 0.21
29 19 0.16
30 40 0.34
31 9 0.08
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTTGAGGGT
Found at i:20620974 original size:28 final size:27
Alignment explanation
Indices: 20620922--20620977 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
20620912 TTTTTATTCA
*
20620922 TTATTTATTTAATATTATTTAATATGT
1 TTATTTATTTAATACTATTTAATATGT
*
20620949 TTATTATATTTATTACTATATTATATATG
1 TTATT-TATTTAATACTAT-TTA-ATATG
20620978 ACTTAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 11 0.46
29 3 0.12
30 5 0.21
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (27 bp):
TTATTTATTTAATACTATTTAATATGT
Found at i:20621587 original size:16 final size:16
Alignment explanation
Indices: 20621566--20621623 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
20621556 ATTCAAATTT
20621566 TAAATTTAATTTAAAA
1 TAAATTTAATTTAAAA
* *
20621582 TAAATTTAAACTCAAAA
1 TAAATTT-AATTTAAAA
*
20621599 TAAGTTTAATTTAAAA
1 TAAATTTAATTTAAAA
20621615 TAAATTTAA
1 TAAATTTAA
20621624 ACTTAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 22 0.63
17 13 0.37
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:20621607 original size:33 final size:33
Alignment explanation
Indices: 20621569--20621648 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
20621559 CAAATTTTAA
20621569 ATTTAATTTAAAATAAATTTAAACTCAAAATAAG
1 ATTTAATTTAAAATAAATTTAAACT-AAAATAAG
*
20621603 -TTTAATTTAAAATAAATTTAAACTTAAATAAG
1 ATTTAATTTAAAATAAATTTAAACTAAAATAAG
**
20621635 ATAAAATTTAAAAT
1 ATTTAATTTAAAAT
20621649 TGGGTTCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.17
33 35 0.83
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (33 bp):
ATTTAATTTAAAATAAATTTAAACTAAAATAAG
Found at i:20621633 original size:16 final size:16
Alignment explanation
Indices: 20621566--20621630 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
20621556 ATTCAAATTT
*
20621566 TAAATTTAATTTAAAA
1 TAAATTTAACTTAAAA
*
20621582 TAAATTTAAACTCAAAA
1 TAAATTT-AACTTAAAA
* *
20621599 TAAGTTTAATTTAAAA
1 TAAATTTAACTTAAAA
20621615 TAAATTTAAACTTAAA
1 TAAATTT-AACTTAAA
20621631 TAAGATAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
16 20 0.50
17 20 0.50
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTTAACTTAAAA
Found at i:20621648 original size:17 final size:17
Alignment explanation
Indices: 20621573--20621648 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 17
20621563 TTTTAAATTT
*
20621573 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTAA
* * * *
20621590 AACTCAAAATAAGTT-T
1 AATTTAAAATAAATTAA
*
20621606 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTAA
*
20621623 AACTT-AAATAAGA-TAA
1 AATTTAAAATAA-ATTAA
20621639 AATTTAAAAT
1 AATTTAAAAT
20621649 TGGGTTCCAT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
16 24 0.53
17 21 0.47
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTAA
Found at i:20627088 original size:30 final size:30
Alignment explanation
Indices: 20627042--20627106 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
20627032 AATTTTGAGG
*
20627042 AATTTGGGGATCAAAATTGAAAATTTTGGAA
1 AATTTGGGGATCAAAA-TCAAAATTTTGGAA
* * *
20627073 GATTT-GGGATTAAAATCAAACTTTTGGAA
1 AATTTGGGGATCAAAATCAAAATTTTGGAA
20627102 AATTT
1 AATTT
20627107 AAGGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 16 0.55
30 9 0.31
31 4 0.14
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (30 bp):
AATTTGGGGATCAAAATCAAAATTTTGGAA
Found at i:20627155 original size:28 final size:28
Alignment explanation
Indices: 20627124--20627183 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
20627114 AAAATGTGAT
* *
20627124 TTTTGGAAATTTGAGGGCAAAATAGTAA
1 TTTTAGAAATTCGAGGGCAAAATAGTAA
** *
20627152 TTTTAGATGTTCGAGGGCAAAATGGTAA
1 TTTTAGAAATTCGAGGGCAAAATAGTAA
20627180 TTTT
1 TTTT
20627184 TGGATGTTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (28 bp):
TTTTAGAAATTCGAGGGCAAAATAGTAA
Found at i:20627301 original size:30 final size:30
Alignment explanation
Indices: 20627114--20627449 Score: 184
Period size: 30 Copynumber: 11.4 Consensus size: 30
20627104 TTTAAGGTTG
* * *
20627114 AAAATGTGATTTTT-GGAAATTTGAGGG-C
1 AAAATGTAATTTTTAGGAAGTTCGAGGGTC
*
20627142 AAAATAGTAA-TTTTA-GATGTTCGAGGG-C
1 AAAAT-GTAATTTTTAGGAAGTTCGAGGGTC
* *
20627170 AAAATGGTAATTTTT-GGATGTTCGA-GGAC
1 AAAAT-GTAATTTTTAGGAAGTTCGAGGGTC
* * *
20627199 AAAAATGGTAATTTTT-GGATGCTCGAGGCT-
1 -AAAAT-GTAATTTTTAGGAAGTTCGAGGGTC
* *
20627229 AAAATGGT-ATTTTT-GTGGAGTTTGAGGGTC
1 AAAAT-GTAATTTTTAG-GAAGTTCGAGGGTC
** *
20627259 AAAATAAAATTTTTATGAAGTTCGAGGGTC
1 AAAATGTAATTTTTAGGAAGTTCGAGGGTC
* * *
20627289 AAAATGTGA-TTTT-GGAAAAGTT-TAGGGGTT
1 AAAATGTAATTTTTAGG--AAGTTCGA-GGGTC
* ** *
20627319 AAAATGT-ATTTTTATGAAGTTTTAGGGTT
1 AAAATGTAATTTTTAGGAAGTTCGAGGGTC
* *
20627348 AAAATGTAATTTTTACGAAGCTT-GAGGGTT
1 AAAATGTAATTTTTAGGAAG-TTCGAGGGTC
* *
20627378 AAAATGTAATTTTTTGAAAGTTCG-GGGTC
1 AAAATGTAATTTTTAGGAAGTTCGAGGGTC
** * * * *
20627407 AAAACATGATTTATGGGAAGTTCGAGGGTT
1 AAAATGTAATTTTTAGGAAGTTCGAGGGTC
20627437 AAAATGTAATTTT
1 AAAATGTAATTTT
20627450 GGAAAAGTTT
Statistics
Matches: 245, Mismatches: 42, Indels: 40
0.75 0.13 0.12
Matches are distributed among these distances:
28 38 0.16
29 80 0.33
30 123 0.50
31 4 0.02
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTAGGAAGTTCGAGGGTC
Found at i:20627302 original size:59 final size:58
Alignment explanation
Indices: 20627114--20627449 Score: 176
Period size: 59 Copynumber: 5.7 Consensus size: 58
20627104 TTTAAGGTTG
* *
20627114 AAAATGTGATTTTTGGAAATTTGAGGG-CAAAATAGTAA-TTTTA-GATGTTCGAGGG-C
1 AAAATGTGATTTTTGG-AGTTTGAGGGTCAAAATA-TAATTTTTATGAAGTTCGAGGGTC
* * * * * * * *
20627170 AAAATGGTAATTTTTGGATGTTCGA-GGACAAAAATGGTAATTTTT-GGATGCTCGAGGCT-
1 AAAAT-GTGATTTTTGGA-GTTTGAGGGTC-AAAAT-ATAATTTTTATGAAGTTCGAGGGTC
*
20627229 AAAATG-GTATTTTTGTGGAGTTTGAGGGTCAAAATAAAATTTTTATGAAGTTCGAGGGTC
1 AAAATGTG-A-TTTT-TGGAGTTTGAGGGTCAAAATATAATTTTTATGAAGTTCGAGGGTC
* * ** *
20627289 AAAATGTGA-TTTTGGAAAAGTTT-AGGGGTTAAAATGT-ATTTTTATGAAGTTTTAGGGTT
1 AAAATGTGATTTTTGG---AGTTTGA-GGGTCAAAATATAATTTTTATGAAGTTCGAGGGTC
* * * * *
20627348 AAAATGTAATTTTTACGAAGCTTGAGGGTTAAAATGTAATTTTT-TGAAAGTTCG-GGGTC
1 AAAATGTGATTTTT--GGAGTTTGAGGGTCAAAATATAATTTTTATG-AAGTTCGAGGGTC
** * * * *
20627407 AAAACATGATTTATGGGAAGTTCGAGGGTTAAAATGTAATTTT
1 AAAATGTGATTT-TTGG-AGTTTGAGGGTCAAAATATAATTTT
20627450 GGAAAAGTTT
Statistics
Matches: 219, Mismatches: 34, Indels: 51
0.72 0.11 0.17
Matches are distributed among these distances:
56 8 0.04
57 18 0.08
58 21 0.10
59 125 0.57
60 45 0.21
61 1 0.00
62 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAATGTGATTTTTGGAGTTTGAGGGTCAAAATATAATTTTTATGAAGTTCGAGGGTC
Found at i:20627328 original size:89 final size:87
Alignment explanation
Indices: 20627228--20627511 Score: 261
Period size: 89 Copynumber: 3.2 Consensus size: 87
20627218 TGCTCGAGGC
* ** *
20627228 TAAAATGGTATTTTTGTGGAGTTTGAGGGTCAAAATAAAATTTTTATGAAGTTCGAGGGTCAAAA
1 TAAAAT-GTATTTTTGTGGAGTTTGAGGGTTAAAATGTAATTTTTA-GAAGTT-GAGGGTTAAAA
20627293 TGTGATTTTGGAAAAGTTTAGGGGT
63 TGTGATTTTGGAAAAGTTTAGGGGT
* * *
20627318 TAAAATGTATTTTTATGAAGTTTTAGGGTTAAAATGTAATTTTTACGAAGCTTGAGGGTTAAAAT
1 TAAAATGTATTTTTGTGGAGTTTGAGGGTTAAAATGTAATTTTTA-GAAG-TTGAGGGTTAAAAT
* * *
20627383 GTAATTTTTTG-AAAG-TTCGGGGT
64 GTGA-TTTTGGAAAAGTTTAGGGGT
* * * * * *
20627406 CAAAACATG-ATTTATG-GGAAGTTCGAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAA
1 -TAAA-ATGTATTTTTGTGG-AGTTTGAGGGTTAAAATGTAATTTT-TAGAAG-TTGAGGGTTAA
* *
20627469 AATATGATTTTGGAAAATTTTAGGGGT
61 AATGTGATTTTGGAAAAGTTTAGGGGT
*
20627496 TAAAATATAATTTTTG
1 TAAAATGT-ATTTTTG
20627512 GAAAGTTTAG
Statistics
Matches: 155, Mismatches: 29, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
88 15 0.10
89 110 0.71
90 30 0.19
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (87 bp):
TAAAATGTATTTTTGTGGAGTTTGAGGGTTAAAATGTAATTTTTAGAAGTTGAGGGTTAAAATGT
GATTTTGGAAAAGTTTAGGGGT
Found at i:20627521 original size:30 final size:30
Alignment explanation
Indices: 20627284--20627521 Score: 163
Period size: 30 Copynumber: 8.0 Consensus size: 30
20627274 TGAAGTTCGA
* *
20627284 GGGTCAAAATGTGA-TTTTGGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTTGG-AAAGTTTAG
*
20627314 GGGTTAAAATGT-ATTTTTATG-AAGTTTTA-
1 GGGTTAAAATGTAATTTTT-GGAAAG-TTTAG
* *
20627343 GGGTTAAAATGTAATTTTTACG-AAGCTT-G
1 GGGTTAAAATGTAATTTTT-GGAAAGTTTAG
* *
20627372 AGGGTTAAAATGTAATTTTTTGAAAG-TTCG
1 -GGGTTAAAATGTAATTTTTGGAAAGTTTAG
* ** * * * *
20627402 GGGTCAAAACATGATTTATGGGAAG-TTCG
1 GGGTTAAAATGTAATTTTTGGAAAGTTTAG
*
20627431 AGGGTTAAAATGTAA-TTTTGGAAAAGTTTAA
1 -GGGTTAAAATGTAATTTTTGG-AAAGTTTAG
* * *
20627462 GGGTTAAAATATGA-TTTTGGAAAATTTTAG
1 GGGTTAAAATGTAATTTTTGG-AAAGTTTAG
*
20627492 GGGTTAAAATATAATTTTTGGAAAGTTTAG
1 GGGTTAAAATGTAATTTTTGGAAAGTTTAG
20627522 AGACCTTTTG
Statistics
Matches: 170, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
29 48 0.28
30 113 0.66
31 9 0.05
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTTGGAAAGTTTAG
Found at i:20628349 original size:17 final size:17
Alignment explanation
Indices: 20628327--20628360 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20628317 TCTAAAAGAG
*
20628327 TTTTTCTTTTCTTTTTC
1 TTTTTCTTTTCTCTTTC
20628344 TTTTTCTTTTCTCTTTC
1 TTTTTCTTTTCTCTTTC
20628361 AAATTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTCTCTTTC
Found at i:20628377 original size:6 final size:6
Alignment explanation
Indices: 20628327--20628359 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
20628317 TCTAAAAGAG
20628327 TTTTTC -TTTTC TTTTTC TTTTTC TTTTCTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTT
20628360 CAAATTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:20629180 original size:17 final size:16
Alignment explanation
Indices: 20629160--20629236 Score: 66
Period size: 17 Copynumber: 4.6 Consensus size: 16
20629150 AATTAAACTT
20629160 TAAATTTAAATTCAATA
1 TAAATTTAAATTCAA-A
*
20629177 TAAATTTAAACTCAGAA
1 TAAATTTAAATTCA-AA
* *
20629194 TAAGTTTAAATTTAAAA
1 TAAATTTAAA-TTCAAA
* *
20629211 GAAATTTAAACTTAAAA
1 TAAATTTAAA-TTCAAA
20629228 T-AATTTAAA
1 TAAATTTAAA
20629237 ATTAAAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 8 0.16
17 39 0.78
18 3 0.06
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (16 bp):
TAAATTTAAATTCAAA
Found at i:20629202 original size:34 final size:33
Alignment explanation
Indices: 20629162--20629236 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
20629152 TTAAACTTTA
* * *
20629162 AATTTAAATTCAATATAAATTTAAACTCAGAAT
1 AATTTAAATTCAAAAGAAATTTAAACTCAAAAT
* *
20629195 AAGTTTAAATTTAAAAGAAATTTAAACTTAAAAT
1 AA-TTTAAATTCAAAAGAAATTTAAACTCAAAAT
20629229 AATTTAAA
1 AATTTAAA
20629237 ATTAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (33 bp):
AATTTAAATTCAAAAGAAATTTAAACTCAAAAT
Found at i:20630543 original size:39 final size:39
Alignment explanation
Indices: 20629674--20630541 Score: 704
Period size: 39 Copynumber: 22.3 Consensus size: 39
20629664 CCCCATGATT
* * * *
20629674 GGGGTAAGAGATTAGCTGATGATGATTTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
20629713 GGGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCCAGGCTC
* *
20629752 GGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* ** *
20629791 -GGGTAAAAGA-T--CAAATGGCTGCAATCTGCCCTAGGCTC
1 GGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGGCTC
* * *
20629829 GGGGTAAGGGATTGGCTGATGGTGATCTTCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
** * *
20629868 GGCATAAAAGA-T--CAGATGGCTGCAATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGGCTC
* * *
20629907 GGGGTAAGAGATTGGCTGATGGTGATTTGCCTCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* *
20629946 -GGGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTT
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* ** * * * * *** *
20629984 GGGGTAAAAGATCAGATGGTTGTAATCTGCTTGAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * *
20630023 GGGGTAAAAGA-T--CAGATGGCTGCAATTTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAGGCTC
* * * * * *
20630062 GAGGTAAGAGATTGGTTAATGGTGAAT-TACCCTAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTG-ATCTGCCCCAGGCTC
* * ** * *
20630101 GGGGTAAAAGATCGAAT--TGCTACAATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGT--GATCTGCCCCAGGCTC
* * * * *
20630140 GAGGTAAGAGATCGGAT-A-GCTGCAATCTAG-CCCAGGCTT
1 GGGGTAAGAGATTGGCTGATGGTG--ATCT-GCCCCAGGCTC
20630179 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
20630218 GGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* *
20630257 GGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
20630296 GGGGTAAGAGATTGGCTGATTGTGATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
20630335 GGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* *
20630374 GGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* **
20630413 GGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAACTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
* * * *
20630452 GAGGTAAGAGATT-G--AATGGCTACAATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGG-T--GATCTGCCCCAGGCTC
* * * *
20630491 AGGGTAAGAGATCGGCTAATGGTGATCTGCCCTAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
*
20630530 GGGGTAAAAGAT
1 GGGGTAAGAGAT
20630542 CGAATCTTCA
Statistics
Matches: 671, Mismatches: 114, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
35 5 0.01
36 19 0.03
37 10 0.01
38 61 0.09
39 529 0.79
40 10 0.01
41 12 0.02
42 24 0.04
43 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.23
Consensus pattern (39 bp):
GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTC
Found at i:20646189 original size:29 final size:29
Alignment explanation
Indices: 20646123--20646292 Score: 155
Period size: 29 Copynumber: 5.8 Consensus size: 29
20646113 TTTCGAAGAG
* * *
20646123 TTTGGGGTTAAAATGT-AATTTTGGAAAGT
1 TTTGGGGTAAAAATGTGATTTTTGGAAA-C
* * * *
20646152 TTTACGGGTAAAAATGTCATTTTAGGAAAA
1 TTT-GGGGTAAAAATGTGATTTTTGGAAAC
** *
20646182 TTTGGGGTAAAAACATGATTTTTGG-AAG
1 TTTGGGGTAAAAATGTGATTTTTGGAAAC
20646210 TTTGGGGATAAAAATGTGATTTTTGGAAAC
1 TTTGGGG-TAAAAATGTGATTTTTGGAAAC
** * *
20646240 TTAAGGGCAAAAATATGATTTTTGGAAAC
1 TTTGGGGTAAAAATGTGATTTTTGGAAAC
* *
20646269 TTAGGGGCAAAAATGTGATTTTTG
1 TTTGGGGTAAAAATGTGATTTTTG
20646293 AAAGTTCAAG
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
28 9 0.08
29 78 0.67
30 21 0.18
31 9 0.08
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTGGGGTAAAAATGTGATTTTTGGAAAC
Found at i:20646252 original size:87 final size:86
Alignment explanation
Indices: 20646121--20646298 Score: 196
Period size: 87 Copynumber: 2.0 Consensus size: 86
20646111 AGTTTCGAAG
* * * * * *
20646121 AGTTTGGGGTTAAAATGTAATTTTGGAAAGTTTTACGGGTAAAAATGTCATTTTAGGAAAATTTG
1 AGTTTGGGGTAAAAATGTAATTTTGGAAAG-CTTAAGGGCAAAAATATCATTTTAGGAAAATTAG
* *
20646186 GGGTAAAAACATGATTTTTGGA
65 GGGCAAAAACATGATTTTTGAA
* * * *
20646208 AGTTTGGGGATAAAAATGTGATTTTTGGAAA-CTTAAGGGCAAAAATATGATTTTTGGAAACTTA
1 AGTTTGGGG-TAAAAATGT-AATTTTGGAAAGCTTAAGGGCAAAAATATCATTTTAGGAAAATTA
**
20646272 GGGGCAAAAATGTGATTTTTGAA
64 GGGGCAAAAACATGATTTTTGAA
20646295 AGTT
1 AGTT
20646299 CAAGGGCAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
87 57 0.76
88 8 0.11
89 10 0.13
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (86 bp):
AGTTTGGGGTAAAAATGTAATTTTGGAAAGCTTAAGGGCAAAAATATCATTTTAGGAAAATTAGG
GGCAAAAACATGATTTTTGAA
Found at i:20646281 original size:58 final size:58
Alignment explanation
Indices: 20646161--20646309 Score: 167
Period size: 58 Copynumber: 2.6 Consensus size: 58
20646151 TTTTACGGGT
* * ** * * * *
20646161 AAAAATGTCATTTTAGGAAAATTTGGGGTAAAAACATGATTTTTGGAAGTTTGGGGAT
1 AAAAATGTGATTTTTGGAAAATTAAGGGCAAAAACATGATTTTTGGAACTTAGGGGAC
* *
20646219 AAAAATGTGATTTTTGGAAACTTAAGGGCAAAAATATGATTTTTGGAAACTTAGGGG-C
1 AAAAATGTGATTTTTGGAAAATTAAGGGCAAAAACATGATTTTTGG-AACTTAGGGGAC
*
20646277 AAAAATGTGATTTTT-GAAAGTTCAAGGGCAAAA
1 AAAAATGTGATTTTTGGAAAATT-AAGGGCAAAA
20646310 TGGAATTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 6 0.08
58 64 0.82
59 8 0.10
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (58 bp):
AAAAATGTGATTTTTGGAAAATTAAGGGCAAAAACATGATTTTTGGAACTTAGGGGAC
Found at i:20646305 original size:29 final size:29
Alignment explanation
Indices: 20646219--20646419 Score: 162
Period size: 29 Copynumber: 6.9 Consensus size: 29
20646209 GTTTGGGGAT
*
20646219 AAAAATGTGATTTTTGGAAACTT-AAGGGC
1 AAAAATGTGATTTTT-GAAAGTTCAAGGGC
* * *
20646248 AAAAATATGATTTTTGGAAACTT-AGGGGC
1 AAAAATGTGATTTTT-GAAAGTTCAAGGGC
20646277 AAAAATGTGATTTTTGAAAGTTCAAGGGC
1 AAAAATGTGATTTTTGAAAGTTCAAGGGC
* * *
20646306 -AAAATG-GAATTTTTGGAAGTTCGAGGGA
1 AAAAATGTG-ATTTTTGAAAGTTCAAGGGC
* * *
20646334 AAAAATGTAATTTTTAAAAGTTCGAGGGTC
1 AAAAATGTGATTTTTGAAAGTTCAAGGG-C
* * *
20646364 -AAAATGTAATTTTTGAAAAGTTTAA-GGT
1 AAAAATGTGATTTTTG-AAAGTTCAAGGGC
* * *
20646392 TAAAATGTGATTTCTGGATAGTTCAAGG
1 AAAAATGTGATTT-TTGAAAGTTCAAGG
20646420 ACCTTTTGGG
Statistics
Matches: 143, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
27 1 0.01
28 29 0.20
29 103 0.72
30 10 0.07
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAAATGTGATTTTTGAAAGTTCAAGGGC
Found at i:20646338 original size:57 final size:56
Alignment explanation
Indices: 20646199--20646378 Score: 193
Period size: 57 Copynumber: 3.1 Consensus size: 56
20646189 TAAAAACATG
* * *
20646199 ATTTTTGGAAGTTTGGGGATAAAAATGTGATTTTTGGAAACTT-AAGGGCAAAAATATG-
1 ATTTTTGGAAGTTAGGGGA-AAAAATGTGATTTTT-GAAAGTTCAAGGGC-AAAAT-GGA
* *
20646257 ATTTTTGGAAACTTAGGGGCAAAAATGTGATTTTTGAAAGTTCAAGGGCAAAATGGA
1 ATTTTTGG-AAGTTAGGGGAAAAAATGTGATTTTTGAAAGTTCAAGGGCAAAATGGA
* * * * *
20646314 ATTTTTGGAAGTTCGAGGGAAAAAATGTAATTTTTAAAAGTTCGAGGGTCAAAATGTA
1 ATTTTTGGAAGTTAG-GGGAAAAAATGTGATTTTTGAAAGTTCAAGGG-CAAAATGGA
20646372 ATTTTTG
1 ATTTTTG
20646379 AAAAGTTTAA
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
56 6 0.06
57 47 0.45
58 44 0.42
59 8 0.08
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (56 bp):
ATTTTTGGAAGTTAGGGGAAAAAATGTGATTTTTGAAAGTTCAAGGGCAAAATGGA
Found at i:20650750 original size:37 final size:37
Alignment explanation
Indices: 20650680--20650750 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
20650670 AAAATGGTCG
* * *
20650680 TCTTCCTGATAAGATACAAAGAAGTGGAGCAAATTCA
1 TCTTCCTGATAAGATACAAAGAAATAGACCAAATTCA
* * *
20650717 TCTTCCTGATGAGATACAGAGAAATATACCAAAT
1 TCTTCCTGATAAGATACAAAGAAATAGACCAAAT
20650751 CAATGAAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (37 bp):
TCTTCCTGATAAGATACAAAGAAATAGACCAAATTCA
Found at i:20650819 original size:160 final size:159
Alignment explanation
Indices: 20650553--20651072 Score: 693
Period size: 172 Copynumber: 3.2 Consensus size: 159
20650543 AGTGAGGCAG
* * *
20650553 TCATCTTCCTGATGAGATACTA-AGAAGTATACCAAATCAATGAAACAAAAGCTCAGTGTGAGCG
1 TCATCTTCCTGATGAGATAC-AGAGAAGTATACCAAATCAATGAAAC-AAAGCTCAATATGATCG
* *
20650617 AAACTTCGAACCCCAACTTCCTGATAAGGTACTGAGAAGCAGGTTGAAGCAATAAAATGGTCGTC
64 AAACTTCGAA-CCCAACTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAATGGTCGTC
* * *
20650682 TTCCTGATAAGATACAAAGAAGTGGAGCAAAT
128 TTCCTGATGAGATACAGAGAAGTGGAACAAAT
* *
20650714 TCATCTTCCTGATGAGATACAGAGAAATATACCAAATCAATGAAACAAAGCTCAATATGATCAAA
1 TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGATCGAA
*
20650779 ACTTCGAACCTCAACTTCCTGATGAGGTACTGAAAAGCAGGTCGAAGCAATAAAATGGTCGTCTT
66 ACTTCGAACC-CAACTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAATGGTCGTCTT
*
20650844 CCTGATGAGATACAGAGAAGTGGATTAAAACAAGTGTT
130 CCTGATGAGATACAGAGAAGTGG-----AACAA---AT
* *
20650882 GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATTAATGAAACAAGGCTCAATATGAG
1 ----TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGA-
*
20650947 T-GAAACTTCGAACCCAAACTTCCTGATGAGGTACTGAGAAGCAAGTCGAAGCAATAAAATGGTC
61 TCGAAACTTCGAACCC-AACTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAATGGTC
*
20651011 GTCTTCCTGATGAGATACAGAGAAGTGGACCAAAT
125 GTCTTCCTGATGAGATACAGAGAAGTGGAACAAAT
* * *
20651046 ACATCTTCCTAATGAGATACAAAGAAG
1 TCATCTTCCTGATGAGATACAGAGAAG
20651073 CGGATTAAAA
Statistics
Matches: 320, Mismatches: 23, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
159 2 0.01
160 120 0.38
161 43 0.13
164 1 0.00
165 4 0.01
167 4 0.01
168 1 0.00
171 1 0.00
172 143 0.45
173 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (159 bp):
TCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGATCGAA
ACTTCGAACCCAACTTCCTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAATGGTCGTCTTC
CTGATGAGATACAGAGAAGTGGAACAAAT
Found at i:20651106 original size:209 final size:209
Alignment explanation
Indices: 20650840--20651336 Score: 692
Period size: 209 Copynumber: 2.4 Consensus size: 209
20650830 AAAATGGTCG
* * *
20650840 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAAGTGTTGCGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAGATA
* * * * *
20650905 CAGAGAAGTATACCAAATTAATGAAACAAGGCTCAATATGAGTGAAACTTCGAACCCAAACTTCC
66 CAGAGAAGTAGACCAAATCAAGGAAACAAAGCTCAATATGAGCGAAACTTCGAACCCAAACTTCC
* * * *
20650970 TGATGAGGTACTGAGAAGCAAGTCGAAGCAATAAAATGGTCGTCTTCCTGATGAGATACAGAGAA
131 TGATGAGATACGGAGAAGCAAGTCGAAGCAATAAAACGGTCGTCTTCCTGATGAGATACAAAGAA
20651035 GTGGACCAAATACA
196 GTGGACCAAATACA
* *
20651049 TCTTCCTAATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAGATA
* * * * *
20651114 CTA-AGAAGTAGACCAAATCAAGGAAATAAAGCTCAATGTGAGCGAAACTTTGAACCCCAGCTTC
66 C-AGAGAAGTAGACCAAATCAAGGAAACAAAGCTCAATATGAGCGAAACTTCGAACCCAAACTTC
** * * * *
20651178 CTGATGAGATACGGAGAAGCGGGTTGAAGTAATAAAGCGGTCGTCTTCCTGATGAGGTACAAAGA
130 CTGATGAGATACGGAGAAGCAAGTCGAAGCAATAAAACGGTCGTCTTCCTGATGAGATACAAAGA
* * *
20651243 AGTGGATCGAATCCA
195 AGTGGACCAAATACA
*
20651258 TCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGC-AGTCATCCTCCTGATGAGAT
1 TCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGA-TCATCTTCCTGATGAGAT
*
20651322 ATAGAGAAGTAGACC
65 ACAGAGAAGTAGACC
20651337 GAGAGATGAA
Statistics
Matches: 253, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
208 2 0.01
209 250 0.99
210 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (209 bp):
TCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTGATGCGATCATCTTCCTGATGAGATA
CAGAGAAGTAGACCAAATCAAGGAAACAAAGCTCAATATGAGCGAAACTTCGAACCCAAACTTCC
TGATGAGATACGGAGAAGCAAGTCGAAGCAATAAAACGGTCGTCTTCCTGATGAGATACAAAGAA
GTGGACCAAATACA
Found at i:20652400 original size:27 final size:29
Alignment explanation
Indices: 20652347--20652402 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
20652337 GCATTAATTG
20652347 TTTAATAAATAAATAATAAATCTATAATATT
1 TTTAATAAATAAATAATAAA--TATAATATT
*
20652378 TTTAATAAAT-ATTAATAAA-ATAATA
1 TTTAATAAATAAATAATAAATATAATA
20652403 AGATTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
30 8 0.33
31 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTAATAAATAAATAATAAATATAATATT
Found at i:20652409 original size:30 final size:31
Alignment explanation
Indices: 20652347--20652409 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
20652337 GCATTAATTG
* *
20652347 TTTAATAAATAAATAATAAATCTATAATATT
1 TTTAATAAATAAATAATAAATCAATAAGATT
*
20652378 TTTAATAAAT-ATTAATAAAAT-AATAAGATT
1 TTTAATAAATAAATAAT-AAATCAATAAGATT
20652408 TT
1 TT
20652410 GAAAAGGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTAATAAATAAATAATAAATCAATAAGATT
Found at i:20653595 original size:29 final size:30
Alignment explanation
Indices: 20653563--20653733 Score: 140
Period size: 29 Copynumber: 5.8 Consensus size: 30
20653553 TAAACAGTTC
* *
20653563 AAAAATCACA-TTTTGACCCTAAACTTTTT
1 AAAAATCACATTTTTGCCCCTAAACTTTTA
* * * *
20653592 AAAAATTACA-TTCTGACCCCTGATCTTTTA
1 AAAAATCACATTTTTG-CCCCTAAACTTTTA
* *
20653622 AAAAATTACATTTTT--CCCTCAA-TTTTCAA
1 AAAAATCACATTTTTGCCCCTAAACTTTT--A
* * **
20653651 AAAAATTACATTTTTGCCCCCAAAC-TTCC
1 AAAAATCACATTTTTGCCCCTAAACTTTTA
* *
20653680 AAAAATCACATTTTTGCCCCTGAACTTCT-
1 AAAAATCACATTTTTGCCCCTAAACTTTTA
20653709 AAAAATCACATTTTTGCCCCTAAAC
1 AAAAATCACATTTTTGCCCCTAAAC
20653734 ATCCAAAAGT
Statistics
Matches: 115, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
27 4 0.03
28 5 0.04
29 75 0.65
30 21 0.18
31 10 0.09
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAAATCACATTTTTGCCCCTAAACTTTTA
Found at i:20653626 original size:30 final size:29
Alignment explanation
Indices: 20653563--20653633 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
20653553 TAAACAGTTC
* * *
20653563 AAAAATCACATTTTGACCCTAAACTTTTT
1 AAAAATTACATTCTGACCCTAAACTTTTA
* *
20653592 AAAAATTACATTCTGACCCCTGATCTTTTA
1 AAAAATTACATTCTGA-CCCTAAACTTTTA
20653622 AAAAATTACATT
1 AAAAATTACATT
20653634 TTTCCCTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTCTGACCCTAAACTTTTA
Found at i:20653693 original size:58 final size:57
Alignment explanation
Indices: 20653622--20653746 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 57
20653612 TGATCTTTTA
* * * *
20653622 AAAAATTACATTTTT-CCCTCAATTTTCAAAAAAATTACATTTTTGCCCCCAAACTTCC
1 AAAAATCACATTTTTCCCCTCAA-CTTC-AAAAAATCACATTTTTGCCCCCAAACATCC
* * *
20653680 AAAAATCACATTTTTGCCCCTGAACTTCTAAAAATCACATTTTTGCCCCTAAACATCC
1 AAAAATCACATTTTT-CCCCTCAACTTCAAAAAATCACATTTTTGCCCCCAAACATCC
*
20653738 AAAAGTCAC
1 AAAAATCAC
20653747 GCTTTTACCC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
58 48 0.84
59 3 0.05
60 6 0.11
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (57 bp):
AAAAATCACATTTTTCCCCTCAACTTCAAAAAATCACATTTTTGCCCCCAAACATCC
Found at i:20653741 original size:29 final size:29
Alignment explanation
Indices: 20653651--20653789 Score: 138
Period size: 29 Copynumber: 4.8 Consensus size: 29
20653641 CAATTTTCAA
* *
20653651 AAAAATTACATTTTTGCCCCCAAACTTCC
1 AAAAATCACATTTTTGCCCCTAAACTTCC
* *
20653680 AAAAATCACATTTTTGCCCCTGAACTTCT
1 AAAAATCACATTTTTGCCCCTAAACTTCC
*
20653709 AAAAATCACATTTTTGCCCCTAAACATCC
1 AAAAATCACATTTTTGCCCCTAAACTTCC
* ** * *
20653738 AAAAGTCACGCTTTTACCCC-AAATTTTCC
1 AAAAATCACATTTTTGCCCCTAAA-CTTCC
* * *
20653767 TAAAATAACA-TTTTACCCCTAAA
1 AAAAATCACATTTTTGCCCCTAAA
20653790 AATTTCTAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 12 0.13
29 79 0.87
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATCACATTTTTGCCCCTAAACTTCC
Found at i:20654199 original size:97 final size:97
Alignment explanation
Indices: 20654068--20654261 Score: 255
Period size: 97 Copynumber: 2.0 Consensus size: 97
20654058 AAAATATTTA
* * *
20654068 AAATCGAGGCAGTATTCCTTTATTTTGGGTTTTGAAAATTTATGCCTTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTCCTTTATTCTGGGTTTTGAAAATTTATGCCTTAACTTACTAGGCACGAC
* * *
20654133 TTTTCTTCAAACCGAGATAATTGAGTACCCTT
66 TGTTCTTCAAACCGAGATAATCGAATACCCTT
* * * **
20654165 AAATCGAGGCAATGTTTCTTTATCTCT-GGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGTGA
1 AAATCGAGGCAATATTCCTTTAT-TCTGGGTTTTGAAAATTTATGCCTTAACTTACTAGGCACGA
* *
20654229 CTGTTCTTCAAATCGGGATAATCGAATACCCTT
65 CTGTTCTTCAAACCGAGATAATCGAATACCCTT
20654262 TTCTAAGGTT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 81 0.98
98 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATTCTGGGTTTTGAAAATTTATGCCTTAACTTACTAGGCACGAC
TGTTCTTCAAACCGAGATAATCGAATACCCTT
Found at i:20660083 original size:28 final size:31
Alignment explanation
Indices: 20660032--20660106 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 31
20660022 AAAATTAAAA
* * *
20660032 TTTTTGGAAGATTTG-GGATTAAAATTAT-C
1 TTTTTGGAAAATTTGAGGATCAAAAATATGC
*
20660061 -TTTTGGAAAATTTGAGG-TCAAAAATGTGC
1 TTTTTGGAAAATTTGAGGATCAAAAATATGC
20660090 TTTTTGG-AAATTTGAGG
1 TTTTTGGAAAATTTGAGG
20660107 GCACAATAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 20 0.51
29 13 0.33
30 6 0.15
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (31 bp):
TTTTTGGAAAATTTGAGGATCAAAAATATGC
Found at i:20660132 original size:29 final size:29
Alignment explanation
Indices: 20660100--20660164 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
20660090 TTTTTGGAAA
* *
20660100 TTTGAGGGCACAATAGTAAATTTTAGATG
1 TTTGAGGGCAAAATAGTAAATTTTAAATG
* * *
20660129 TTTGAGGGTAAAATGGTAATTTTTAAATG
1 TTTGAGGGCAAAATAGTAAATTTTAAATG
*
20660158 TTAGAGG
1 TTTGAGG
20660165 ATAAAAATGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
TTTGAGGGCAAAATAGTAAATTTTAAATG
Found at i:20660169 original size:29 final size:29
Alignment explanation
Indices: 20660115--20660267 Score: 157
Period size: 29 Copynumber: 5.3 Consensus size: 29
20660105 GGGCACAATA
* * *
20660115 GTAAATTTTAGATGTTTGAGGGTAAAATG
1 GTAATTTTTAGATGTTCGAGGATAAAATG
* *
20660144 GTAATTTTTAAATGTTAGAGGATAAAAATG
1 GTAATTTTTAGATGTTCGAGGAT-AAAATG
* *
20660174 GTAATTTTTAGATGCTCGAGGGTAAAATG
1 GTAATTTTTAGATGTTCGAGGATAAAATG
* * *
20660203 GT-ATTTTTGGATGTTCGAGGACAGAATG
1 GTAATTTTTAGATGTTCGAGGATAAAATG
* * *
20660231 GTAATTTTTGGATGATCAAGGGA-AAAATG
1 GTAATTTTTAGATGTTCGA-GGATAAAATG
20660260 GTAATTTT
1 GTAATTTT
20660268 ACGAAGTTTG
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
28 23 0.22
29 54 0.51
30 28 0.27
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GTAATTTTTAGATGTTCGAGGATAAAATG
Found at i:20660258 original size:57 final size:58
Alignment explanation
Indices: 20660115--20660268 Score: 166
Period size: 57 Copynumber: 2.7 Consensus size: 58
20660105 GGGCACAATA
* * **
20660115 GTAAATTTTAGATGTTTGAGGGTAAAATGGTAATTTTTAAATGTTAGAGGATAAAAATG
1 GTAATTTTTAGATGATCAAGGGTAAAATGGT-ATTTTTAAATGTTAGAGGATAAAAATG
* * ** * * *
20660174 GTAATTTTTAGATGCTCGAGGGTAAAATGGTATTTTTGGATGTTCGAGGA-CAGAATG
1 GTAATTTTTAGATGATCAAGGGTAAAATGGTATTTTTAAATGTTAGAGGATAAAAATG
* * *
20660231 GTAATTTTTGGATGATCAAGGGAAAAATGGTAATTTTA
1 GTAATTTTTAGATGATCAAGGGTAAAATGGTATTTTTA
20660269 CGAAGTTTGG
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
57 37 0.46
58 16 0.20
59 28 0.35
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
GTAATTTTTAGATGATCAAGGGTAAAATGGTATTTTTAAATGTTAGAGGATAAAAATG
Found at i:20660327 original size:29 final size:29
Alignment explanation
Indices: 20660254--20660567 Score: 164
Period size: 30 Copynumber: 10.6 Consensus size: 29
20660244 GATCAAGGGA
** **
20660254 AAAATGGTAATTTTACGAAGTTTGGGGGTC
1 AAAAT-GTAATTTTGTGAAGTTTAAGGGTC
* * **
20660284 AAAATATATTTTTTGTGAAGTTTGGGGGTC
1 AAAATGTA-ATTTTGTGAAGTTTAAGGGTC
* * *
20660314 AAAATGTGATTTTG-GAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGTG--AAGTTTAAGGGTC
* * *
20660344 AAAATATTATTTT-TAAGAAGCTTT-AGGGTT
1 AAAATGTAATTTTGT--GAAG-TTTAAGGGTC
* *
20660374 AAAATGTAATTTT-TAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGT-GAAGTTTAAGGGTC
20660403 AAAATGTAATTTT-TAGAAGTTTAAGGGT-
1 AAAATGTAATTTTGT-GAAGTTTAAGGGTC
*
20660431 TAAATGTAATTTT-TGGAGAGTTTAAGGGTC
1 AAAATGTAATTTTGT-GA-AGTTTAAGGGTC
* * *
20660461 AAAACATG-ATTTTTGGGAAGTTTGAGGGTC
1 -AAA-ATGTAATTTTGTGAAGTTTAAGGGTC
* *
20660491 AAAATGTAATTTTG-GAAAAATTTAAGGGTT
1 AAAATGTAATTTTGTG--AAGTTTAAGGGTC
* **
20660521 AAAATGTGATTTTG-GAAAAGTTTGGGGGTC
1 AAAATGTAATTTTGTG--AAGTTTAAGGGTC
*
20660551 AAAATATAATTTT-TGAA
1 AAAATGTAATTTTGTGAA
20660568 AAGTTTAGTG
Statistics
Matches: 234, Mismatches: 33, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
28 25 0.11
29 64 0.27
30 129 0.55
31 12 0.05
32 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTGTGAAGTTTAAGGGTC
Found at i:20660335 original size:30 final size:30
Alignment explanation
Indices: 20660309--20660574 Score: 224
Period size: 30 Copynumber: 9.0 Consensus size: 30
20660299 TGAAGTTTGG
* *
20660309 GGGTCAAAATGTGATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * *
20660339 GGGTTAAAATATTATTTT-TAAGAAGCTTT-A
1 GGGTCAAAATGTAATTTTGGAA-AAG-TTTAA
* *
20660369 GGGTTAAAATGTAATTTT-TAAAAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * *
20660398 GGGTTAAAATGTAATTTT-TAGAAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
20660427 GGGT-TAAATGTAATTTTTGG-AGAGTTTAA
1 GGGTCAAAATGTAA-TTTTGGAAAAGTTTAA
* * *
20660456 GGGTCAAAACATG-ATTTTTGG-GAAGTTTGA
1 GGGTC-AAA-ATGTAATTTTGGAAAAGTTTAA
*
20660486 GGGTCAAAATGTAATTTTGGAAAAATTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * **
20660516 GGGTTAAAATGTGATTTTGGAAAAGTTTGG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
20660546 GGGTCAAAATATAATTTTTGAAAAGTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTA
20660575 GTGACCTTCT
Statistics
Matches: 195, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
28 14 0.07
29 63 0.32
30 109 0.56
31 6 0.03
32 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAA
Found at i:20660335 original size:60 final size:59
Alignment explanation
Indices: 20660279--20660574 Score: 296
Period size: 60 Copynumber: 5.0 Consensus size: 59
20660269 CGAAGTTTGG
* * * * *
20660279 GGGTCAAAATATATTTTTTGTGAAGTTTGGGGGTCAAAATGTGATTTTGGAAAAGTTTAG
1 GGGTTAAAATATA-TTTTTGAGAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * *
20660339 GGGTTAAAATATTATTTTTAAGAAGCTTT-AGGGTTAAAATGTAATTTT-TAAAAGTTTAA
1 GGGTTAAAATA-TATTTTTGAGAAG-TTTGAGGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * *
20660398 GGGTTAAAATGTAATTTTT-AGAAGTTTAAGGGT-TAAATGTAATTTTTGG-AGAGTTTAA
1 GGGTTAAAATAT-ATTTTTGAGAAGTTTGAGGGTCAAAATGTAA-TTTTGGAAAAGTTTAA
* * * *
20660456 GGGTCAAAACATGATTTTTGGGAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAATTTAA
1 GGGTTAAAATAT-ATTTTTGAGAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * * * *
20660516 GGGTTAAAATGTGATTTTGGAAAAGTTTGGGGGTCAAAATATAATTTTTGAAAAGTTTA
1 GGGTTAAAATAT-ATTTTTGAGAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAGTTTA
20660575 GTGACCTTCT
Statistics
Matches: 196, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
57 11 0.06
58 38 0.19
59 43 0.22
60 99 0.51
61 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (59 bp):
GGGTTAAAATATATTTTTGAGAAGTTTGAGGGTCAAAATGTAATTTTGGAAAAGTTTAA
Found at i:20662279 original size:14 final size:14
Alignment explanation
Indices: 20662262--20662297 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20662252 AAATTTGGGT
*
20662262 TTGTGATTTTGGAC
1 TTGTAATTTTGGAC
20662276 TTGTAATTTTGGAC
1 TTGTAATTTTGGAC
*
20662290 TTTTAATT
1 TTGTAATT
20662298 AAACTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (14 bp):
TTGTAATTTTGGAC
Found at i:20665444 original size:16 final size:17
Alignment explanation
Indices: 20665408--20665446 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20665398 TATGAAAATG
20665408 AATGCAGTGACAATAAA
1 AATGCAGTGACAATAAA
20665425 AATGCAG-GCACAAT-AA
1 AATGCAGTG-ACAATAAA
20665441 AATGCA
1 AATGCA
20665447 AGAATGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AATGCAGTGACAATAAA
Found at i:20665913 original size:24 final size:26
Alignment explanation
Indices: 20665881--20665929 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
20665871 AGGTGATCGT
20665881 CATCCTTT-G-CTTCATCCTTCTCTC
1 CATCCTTTGGTCTTCATCCTTCTCTC
20665905 CATCCTTTGGTTCTTCATCCTTCTC
1 CATCCTTTGG-TCTTCATCCTTCTC
20665930 GACATGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
27 13 0.59
ACGTcount: A:0.08, C:0.39, G:0.06, T:0.47
Consensus pattern (26 bp):
CATCCTTTGGTCTTCATCCTTCTCTC
Found at i:20670231 original size:34 final size:34
Alignment explanation
Indices: 20670185--20670303 Score: 157
Period size: 34 Copynumber: 3.5 Consensus size: 34
20670175 ACACGATTAA
* * *
20670185 CCATCCAACACACCAGATGCTCGTATGAGCCAAT
1 CCATCCAACACACCAAATGCTCGTATGAGCTAGT
* *
20670219 CCATCCAGCACACCAAATGCTTGTATGAGCTAGT
1 CCATCCAACACACCAAATGCTCGTATGAGCTAGT
* * * *
20670253 CCAACCAACACACCAAATGCTCTTAAGAGATAGT
1 CCATCCAACACACCAAATGCTCGTATGAGCTAGT
20670287 CCATCCAACACACCAAA
1 CCATCCAACACACCAAA
20670304 ATACTACAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 73 1.00
ACGTcount: A:0.36, C:0.34, G:0.13, T:0.18
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTCGTATGAGCTAGT
Found at i:20673808 original size:36 final size:37
Alignment explanation
Indices: 20673737--20673809 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
20673727 CATGTCACTT
* *
20673737 CATGAGCACTTCAAGATTGCGCCCAAAACTGTCGTCG
1 CATGAGCACTTCAAGATTGCGACCAAAACTATCGTCG
* *
20673774 CATGAGCACTTCTAGATTTC-ACCAAAACTATCGTCG
1 CATGAGCACTTCAAGATTGCGACCAAAACTATCGTCG
20673810 TAGGAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 14 0.44
37 18 0.56
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (37 bp):
CATGAGCACTTCAAGATTGCGACCAAAACTATCGTCG
Found at i:20674726 original size:16 final size:16
Alignment explanation
Indices: 20674705--20674735 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20674695 TTGTGGATAC
20674705 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
20674721 CATTTTATCTTTATT
1 CATTTTACCTTTATT
20674736 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:20701163 original size:34 final size:34
Alignment explanation
Indices: 20701124--20701189 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
20701114 CAACAGAAAG
20701124 TAAATCAATTGTTATGGAAGTTTTGAGAATGTGT
1 TAAATCAATTGTTATGGAAGTTTTGAGAATGTGT
20701158 TAAATCAATTGTTATGGAAGTTTTGAGAATGT
1 TAAATCAATTGTTATGGAAGTTTTGAGAATGT
20701190 AAATGTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.41
Consensus pattern (34 bp):
TAAATCAATTGTTATGGAAGTTTTGAGAATGTGT
Found at i:20707292 original size:13 final size:13
Alignment explanation
Indices: 20707274--20707300 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20707264 GCTGTTGTTG
20707274 GTAAGAACTCAAA
1 GTAAGAACTCAAA
20707287 GTAAGAACTCAAA
1 GTAAGAACTCAAA
20707300 G
1 G
20707301 GACTTCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (13 bp):
GTAAGAACTCAAA
Found at i:20711459 original size:34 final size:34
Alignment explanation
Indices: 20711421--20711486 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
20711411 CTATAGTATA
*
20711421 ATTGTCCCTACAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTACATCTA-CAATGTCATTGCATTTTT
* *
20711455 ATTGTCGCTACATCTACATTGTCATTGCATTT
1 ATTGTCCCTACATCTACAATGTCATTGCATTT
20711487 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTACATCTACAATGTCATTGCATTTTT
Found at i:20717227 original size:60 final size:60
Alignment explanation
Indices: 20717130--20717257 Score: 240
Period size: 60 Copynumber: 2.1 Consensus size: 60
20717120 TTTTTTGAAG
20717130 TTTT-CATATAACGATAGAAAAATCTTTCTACCCGAACCTACTCCCATCCATCTATCCAA
1 TTTTACATATAACGATAGAAAAATCTTTCTACCCGAACCTACTCCCATCCATCTATCCAA
*
20717189 TTTTACATATAACGATAGAAAAATCTTTCTACCCGAACCTACTCCCATCTATCTATCCAA
1 TTTTACATATAACGATAGAAAAATCTTTCTACCCGAACCTACTCCCATCCATCTATCCAA
20717249 TTTTACATA
1 TTTTACATA
20717258 ACCAAGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 4 0.06
60 63 0.94
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (60 bp):
TTTTACATATAACGATAGAAAAATCTTTCTACCCGAACCTACTCCCATCCATCTATCCAA
Found at i:20728365 original size:36 final size:38
Alignment explanation
Indices: 20728282--20728365 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 38
20728272 AAGAAAATAA
20728282 TCACTATCACATGGGCATGAAAAACATACCCACATACT
1 TCACTATCACATGGGCATGAAAAACATACCCACATACT
* * * *
20728320 T-ACTGTCACAT-GGCATGAACAACATACGCTCAT-CT
1 TCACTATCACATGGGCATGAAAAACATACCCACATACT
*
20728355 TCACTTTCACA
1 TCACTATCACA
20728366 ACAGTCATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 3 0.08
36 27 0.68
37 9 0.22
38 1 0.03
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.25
Consensus pattern (38 bp):
TCACTATCACATGGGCATGAAAAACATACCCACATACT
Found at i:20729437 original size:24 final size:24
Alignment explanation
Indices: 20729407--20729483 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
20729397 ACACCACATT
*
20729407 ATAACTACAATATTTTCCAAGTAC
1 ATAACTACAATATTCTCCAAGTAC
* * *
20729431 ATAACT--AGTATTACACCACA-T-G
1 ATAACTACAATATT-CTCCA-AGTAC
*
20729453 ATAACTACAATATTGTCCAAGTAC
1 ATAACTACAATATTCTCCAAGTAC
20729477 ATAACTA
1 ATAACTA
20729484 ATATTACACC
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 12 0.31
23 8 0.21
24 19 0.49
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (24 bp):
ATAACTACAATATTCTCCAAGTAC
Found at i:20729457 original size:46 final size:46
Alignment explanation
Indices: 20729390--20729494 Score: 174
Period size: 46 Copynumber: 2.3 Consensus size: 46
20729380 TATTACAATT
* * *
20729390 TAGTAGTACACCACATTATAACTACAATATTTTCCAAGTACATAAC
1 TAGTATTACACCACATGATAACTACAATATTGTCCAAGTACATAAC
20729436 TAGTATTACACCACATGATAACTACAATATTGTCCAAGTACATAAC
1 TAGTATTACACCACATGATAACTACAATATTGTCCAAGTACATAAC
*
20729482 TAATATTACACCA
1 TAGTATTACACCA
20729495 TATAATTAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.30
Consensus pattern (46 bp):
TAGTATTACACCACATGATAACTACAATATTGTCCAAGTACATAAC
Found at i:20731721 original size:32 final size:32
Alignment explanation
Indices: 20731685--20731759 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 32
20731675 AATAATTTTT
20731685 ATATCCAACAAGC-TTAAAACATAATAAATTCA
1 ATATCCAACAA-CTTTAAAACATAATAAATTCA
*
20731717 ATATCCAACAACTTTAAAACATAATAATTTCA
1 ATATCCAACAACTTTAAAACATAATAAATTCA
*
20731749 AAATCCAACAA
1 ATATCCAACAA
20731760 ACTAATTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.53, C:0.20, G:0.01, T:0.25
Consensus pattern (32 bp):
ATATCCAACAACTTTAAAACATAATAAATTCA
Found at i:20731957 original size:12 final size:12
Alignment explanation
Indices: 20731926--20731960 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
20731916 TAGTAGACCA
*
20731926 TTCTCTTGCTTC
1 TTCTCTTTCTTC
20731938 TTCTCTTTCTTC
1 TTCTCTTTCTTC
20731950 TTCTCTTTCTT
1 TTCTCTTTCTT
20731961 GTCGCTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (12 bp):
TTCTCTTTCTTC
Found at i:20739769 original size:38 final size:39
Alignment explanation
Indices: 20739722--20740361 Score: 373
Period size: 38 Copynumber: 16.6 Consensus size: 39
20739712 GTAAAATGTC
20739722 GGATG-CTTCAATCTGCTCCATGATTGGAGTAAAAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
* *
20739760 -GATGTCTTCAATCTGCCTTC-TGATT-AAGGTAAAAGATT
1 GGATGTCTTCAATCTG-CTCCATGATTGGA-GTAAAAGATT
* *
20739798 GGATGTCTTCAATCTGC-CCTCTGATTAGAGTAAAAGATT
1 GGATGTCTTCAATCTGCTCC-ATGATTGGAGTAAAAGATT
* * * * *
20739837 GTAT-TCTTCAATCTGCCCCATTATCAGG-GTAAGAGATT
1 GGATGTCTTCAATCTGCTCCATGAT-TGGAGTAAAAGATT
* * * *
20739875 GG-TGTTTCTTCAATCTGCCTTC-TGATT-AAGGTAAGAGTTT
1 GGATG--TCTTCAATCTG-CTCCATGATTGGA-GTAAAAGATT
* * * *
20739915 GGCTGTCTTCAACCTGC-CCTCTGGTTAGG-GTAAAAGATT
1 GGATGTCTTCAATCTGCTCC-ATGATT-GGAGTAAAAGATT
* * * *
20739954 GGATG-CCTCAATCTGCTCCATGGTTAGAGTAAGAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
** * * * * *
20739992 GCTTGTCTTTAATCTACCTTC-TGATT-AAGGTAAGAGATT
1 GGATGTCTTCAATCT-GCTCCATGATTGGA-GTAAAAGATT
* * * * *
20740031 GGAT-TTTTCAATTTGCCCCATGATCGGGGTAAAAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
* *
20740069 GGATG-CTTCAATCTGCTCCATGATCGGAGTAAGAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
* *
20740107 GGAT-TCTTCAATCTGAC-CCATGATCGGGGTAAAAGATT
1 GGATGTCTTCAATCTG-CTCCATGATTGGAGTAAAAGATT
* * *
20740145 AGATGT-TTCAATCTGCTCCATGATCGGAGTAAGAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
** * * * *
20740183 GTCTGTCTTCAATCTACCTTC-TGATT-AAGGTAAGAGATT
1 GGATGTCTTCAATCT-GCTCCATGATTGGA-GTAAAAGATT
* * * * *
20740222 GGAT-TCTTCTATTTGCCCCATGATCGGGGTAAAAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
* * * * *
20740260 GTATG-CTTCAATCTACTCCATGATCGGGGTAAGAGATT
1 GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
* *
20740298 -GATGTGTCTTTAATCTGC-CCTTTGATTAGG-GTAAAAGATT
1 GGA--TGTCTTCAATCTGCTCC-ATGATT-GGAGTAAAAGATT
* *
20740338 GGATG-CTTCAATTTGCCCCATGAT
1 GGATGTCTTCAATCTGCTCCATGAT
20740362 AGGGGTAAGA
Statistics
Matches: 465, Mismatches: 92, Indels: 90
0.72 0.14 0.14
Matches are distributed among these distances:
37 15 0.03
38 264 0.57
39 124 0.27
40 54 0.12
41 8 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (39 bp):
GGATGTCTTCAATCTGCTCCATGATTGGAGTAAAAGATT
Found at i:20739814 original size:77 final size:78
Alignment explanation
Indices: 20739687--20740361 Score: 432
Period size: 77 Copynumber: 8.8 Consensus size: 78
20739677 TCGCTATCTA
* * *
20739687 TCTTCAATCTGCCTTGTGGTTTAGGGTAAAATG-TCGGATG-CTTCAATCTGCTCCATGATTGGA
1 TCTTCAATCTGCCTTCT-GATTAGGGTAAAA-GATTGGATGTCTTCAATCTGCTCCATGATTGGA
20739750 GTAAAAGATT-GATG
64 GTAAAAGATTGGATG
* * *
20739764 TCTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGTCTTCAATCTGC-CCTCTGATTAGAG
1 TCTTCAATCTGCCTTCTGATTAGGGTAAAAGATTGGATGTCTTCAATCTGCTCC-ATGATTGGAG
*
20739828 TAAAAGATTGTAT-
65 TAAAAGATTGGATG
* * * * *
20739841 TCTTCAATCTGCC-CCATTATCAGGGTAAGAGATTGG-TGTTTCTTCAATCTGCCTTC-TGATT-
1 TCTTCAATCTGCCTTC-TGATTAGGGTAAAAGATTGGATG--TCTTCAATCTG-CTCCATGATTG
* * * *
20739902 AAGGTAAGAGTTTGGCTG
62 GA-GTAAAAGATTGGATG
* * * * * *
20739920 TCTTCAACCTGCCCTCTGGTTAGGGTAAAAGATTGGATG-CCTCAATCTGCTCCATGGTTAGAGT
1 TCTTCAATCTGCCTTCTGATTAGGGTAAAAGATTGGATGTCTTCAATCTGCTCCATGATTGGAGT
* **
20739984 AAGAGATTGCTTG
66 AAAAGATTGGATG
* * * * * * * * *
20739997 TCTTTAATCTACCTTCTGATTAAGGTAAGAGATTGGAT-TTTTCAATTTGCCCCATGATCGGGGT
1 TCTTCAATCTGCCTTCTGATTAGGGTAAAAGATTGGATGTCTTCAATCTGCTCCATGATTGGAGT
20740061 AAAAGATTGGATG
66 AAAAGATTGGATG
* * * *
20740074 -CTTCAATCTG-CTCCATGA-TCGGAGTAAGAGATTGGAT-TCTTCAATCTGAC-CCATGATCGG
1 TCTTCAATCTGCCTTC-TGATTAGG-GTAAAAGATTGGATGTCTTCAATCTG-CTCCATGATTGG
* *
20740134 GGTAAAAGATTAGATG
63 AGTAAAAGATTGGATG
* * * ** * * *
20740150 T-TTCAATCTG-CTCCATGA-TCGGAGTAAGAGATTGTCTGTCTTCAATCTACCTTC-TGATT-A
1 TCTTCAATCTGCCTTC-TGATTAGG-GTAAAAGATTGGATGTCTTCAATCT-GCTCCATGATTGG
*
20740210 AGGTAAGAGATTGGAT-
63 A-GTAAAAGATTGGATG
* * * ** * * * *
20740226 TCTTCTATTTGCC-CCATGATCGGGGTAAAAGATTGTATG-CTTCAATCTACTCCATGATCGGGG
1 TCTTCAATCTGCCTTC-TGATTAGGGTAAAAGATTGGATGTCTTCAATCTGCTCCATGATTGGAG
*
20740289 TAAGAGATT-GATGTG
65 TAAAAGATTGGA--TG
* * *
20740304 TCTTTAATCTGCCCTT-TGATTAGGGTAAAAGATTGGATG-CTTCAATTTGCCCCATGAT
1 TCTTCAATCTG-CCTTCTGATTAGGGTAAAAGATTGGATGTCTTCAATCTGCTCCATGAT
20740362 AGGGGTAAGA
Statistics
Matches: 477, Mismatches: 87, Indels: 67
0.76 0.14 0.11
Matches are distributed among these distances:
75 11 0.02
76 142 0.30
77 212 0.44
78 77 0.16
79 31 0.06
80 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (78 bp):
TCTTCAATCTGCCTTCTGATTAGGGTAAAAGATTGGATGTCTTCAATCTGCTCCATGATTGGAGT
AAAAGATTGGATG
Found at i:20740242 original size:115 final size:116
Alignment explanation
Indices: 20740097--20740369 Score: 390
Period size: 115 Copynumber: 2.4 Consensus size: 116
20740087 CATGATCGGA
* * * *
20740097 GTAAGAGATTGGATTCTTCAATCTGACCCATGATCGGGGTAAAAGATTAG-ATGTTTCAATCTGC
1 GTAAGAGATTGGATTCTTCAATTTGCCCCATGATCGGGGTAAAAGATT-GTATGCTTCAATCTAC
20740161 TCCATGATCGGAGTAAGAGATTG-TCTGTCTTCAATCT-ACCTTCTGATTAAG
65 TCCATGATCGGAGTAAGAGATTGATCTGTCTTCAATCTGACCTT-TGATTAAG
*
20740212 GTAAGAGATTGGATTCTTCTATTTGCCCCATGATCGGGGTAAAAGATTGTATGCTTCAATCTACT
1 GTAAGAGATTGGATTCTTCAATTTGCCCCATGATCGGGGTAAAAGATTGTATGCTTCAATCTACT
* * * * *
20740277 CCATGATCGGGGTAAGAGATTGATGTGTCTTTAATCTGCCCTTTGATTAGG
66 CCATGATCGGAGTAAGAGATTGATCTGTCTTCAATCTGACCTTTGATTAAG
* * *
20740328 GTAAAAGATTGGATGCTTCAATTTGCCCCATGATAGGGGTAA
1 GTAAGAGATTGGATTCTTCAATTTGCCCCATGATCGGGGTAA
20740370 GAGACCTGTA
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
114 1 0.01
115 79 0.56
116 57 0.40
117 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (116 bp):
GTAAGAGATTGGATTCTTCAATTTGCCCCATGATCGGGGTAAAAGATTGTATGCTTCAATCTACT
CCATGATCGGAGTAAGAGATTGATCTGTCTTCAATCTGACCTTTGATTAAG
Found at i:20744939 original size:13 final size:14
Alignment explanation
Indices: 20744910--20744940 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20744900 GGCTCAAACG
20744910 AAAAAGGGAAAGAA
1 AAAAAGGGAAAGAA
*
20744924 AAAAAGGGAAGGAA
1 AAAAAGGGAAAGAA
20744938 AAA
1 AAA
20744941 GAAAAAGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAAAAGGGAAAGAA
Found at i:20756767 original size:14 final size:15
Alignment explanation
Indices: 20756748--20756776 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20756738 TAAATAATAA
20756748 TTTATTTTT-TATTT
1 TTTATTTTTATATTT
20756762 TTTATTTTTATATTT
1 TTTATTTTTATATTT
20756777 ATTTGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTTTATATTT
Found at i:20759270 original size:19 final size:19
Alignment explanation
Indices: 20759230--20759270 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20759220 TTTAGTAATG
* *
20759230 TTTTTATCTCAAAAATATT
1 TTTTTATCCCAAAAATACT
*
20759249 TTTTTATCCCAAAAGTACT
1 TTTTTATCCCAAAAATACT
20759268 TTT
1 TTT
20759271 GAGAAGCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTTATCCCAAAAATACT
Found at i:20760568 original size:26 final size:27
Alignment explanation
Indices: 20760539--20760598 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
20760529 CAAGATGACT
20760539 ATATAAAAAAT-TTAAATAAATAAAA-A
1 ATATAAAAAATATTAAAT-AATAAAATA
* *
20760565 ATATATAAAATTATTAAATATTAAAATA
1 ATATA-AAAAATATTAAATAATAAAATA
20760593 ATATAA
1 ATATAA
20760599 TATTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATAAAAAATATTAAATAATAAAATA
Found at i:20760603 original size:26 final size:26
Alignment explanation
Indices: 20760561--20760622 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
20760551 TAAATAAATA
**
20760561 AAAAAT-ATATAAAATTATTAAATATT
1 AAAAATAATATAAAATTAAAAAAT-TT
*
20760587 -AAAATAATATAATATTAAAAAATTT
1 AAAAATAATATAAAATTAAAAAATTT
20760612 AAAAATAATAT
1 AAAAATAATAT
20760623 GGACGGAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATAATATAAAATTAAAAAATTT
Found at i:20761830 original size:20 final size:21
Alignment explanation
Indices: 20761789--20761830 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20761779 TATAATATTT
* *
20761789 TGATGCCAAACTTAATTTTAA
1 TGATGCCAAACTAAATTCTAA
20761810 TGATGCCAAA-TAAATTCTAA
1 TGATGCCAAACTAAATTCTAA
20761830 T
1 T
20761831 ACTAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (21 bp):
TGATGCCAAACTAAATTCTAA
Found at i:20762032 original size:5 final size:5
Alignment explanation
Indices: 20762024--20762057 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
20762014 GTAAACTAAA
*
20762024 CGCAT CGCAT CGCAT CGCAT CGCAT CGCAC CGCA
1 CGCAT CGCAT CGCAT CGCAT CGCAT CGCAT CGCA
20762058 GTTCACCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.15
Consensus pattern (5 bp):
CGCAT
Found at i:20762899 original size:21 final size:20
Alignment explanation
Indices: 20762875--20762926 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
20762865 TTTTTTAAAT
*
20762875 ATTTATGAAAAAATATTGAAA
1 ATTTAT-AAAAAATATTCAAA
* *
20762896 ATTTGTCAAATAATATTCAAA
1 ATTTAT-AAAAAATATTCAAA
*
20762917 AGTTATAAAA
1 ATTTATAAAA
20762927 CAAAATTCAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (20 bp):
ATTTATAAAAAATATTCAAA
Found at i:20762998 original size:26 final size:26
Alignment explanation
Indices: 20762940--20762998 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
20762930 AATTCATTTT
*
20762940 ATCAAAATAAATTTAAAAATATAAAA
1 ATCAAAATAAATATAAAAATATAAAA
* * *
20762966 TTAAAAATTAATATAAAAA-ATCAAAA
1 ATCAAAATAAATATAAAAATAT-AAAA
20762992 ATCAAAA
1 ATCAAAA
20762999 CAAACTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (26 bp):
ATCAAAATAAATATAAAAATATAAAA
Found at i:20769836 original size:92 final size:92
Alignment explanation
Indices: 20769672--20769856 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 92
20769662 ATAGTCATAA
*
20769672 AAATTAAGAAGGGGTGAAGTAACATGCCAATGTCATCAAGGAGTGATGTCAACATTAGGTGTCGA
1 AAATTAAGAAGGGGTGAAGTAACATACCAATGTCATCAAGGAGTGATGTCAACATTAGGTGTCGA
* *
20769737 TTCTTCATGCAACAGGGGTTCCTTAAC
66 TTATTCATGCAACAGGGATTCCTTAAC
*
20769764 AAATTAAGAAGGGGTGAAGTAACATACCAATGTCATCAAGGAGTGATGTCAACATTAGGTGTCGG
1 AAATTAAGAAGGGGTGAAGTAACATACCAATGTCATCAAGGAGTGATGTCAACATTAGGTGTCGA
20769829 TTATTCATGCAACAGGGATTCCTTAAC
66 TTATTCATGCAACAGGGATTCCTTAAC
20769856 A
1 A
20769857 TTAGCAAGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (92 bp):
AAATTAAGAAGGGGTGAAGTAACATACCAATGTCATCAAGGAGTGATGTCAACATTAGGTGTCGA
TTATTCATGCAACAGGGATTCCTTAAC
Found at i:20772913 original size:16 final size:16
Alignment explanation
Indices: 20772892--20772926 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20772882 AATAAAATAT
* *
20772892 ATATAATAAGATTAAA
1 ATATAAAAAAATTAAA
20772908 ATATAAAAAAATTAAA
1 ATATAAAAAAATTAAA
20772924 ATA
1 ATA
20772927 AGTGGATGCC
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:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
ATATAAAAAAATTAAA
Found at i:20773239 original size:85 final size:85
Alignment explanation
Indices: 20773139--20773312 Score: 303
Period size: 85 Copynumber: 2.0 Consensus size: 85
20773129 CAAAAATACC
* * *
20773139 AGCACAAGTGCGAGTGACAACAACAAGAGAGCCAACCGCACCGTTTGTGTTTGGAAAAAGACTAT
1 AGCACAAGTGCGAGTGACAACAACAAGAGAACCAACCACACCGTTTGTGTTTGGAAAAAGACTAA
20773204 AAAAGAGGAAATTATATTTA
66 AAAAGAGGAAATTATATTTA
* *
20773224 AGCACAAGTGGGAGTGACAACAACAAGAGAACCCACCACACCGTTTGTGTTTGGAAAAAGACTAA
1 AGCACAAGTGCGAGTGACAACAACAAGAGAACCAACCACACCGTTTGTGTTTGGAAAAAGACTAA
20773289 AAAAGAGGAAATTATATTTA
66 AAAAGAGGAAATTATATTTA
20773309 AGCA
1 AGCA
20773313 AAAACACAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.19
Consensus pattern (85 bp):
AGCACAAGTGCGAGTGACAACAACAAGAGAACCAACCACACCGTTTGTGTTTGGAAAAAGACTAA
AAAAGAGGAAATTATATTTA
Found at i:20773694 original size:27 final size:27
Alignment explanation
Indices: 20773664--20773717 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
20773654 AAATATATAT
20773664 TGATTAGACCTGTTTTTGATATTATTG
1 TGATTAGACCTGTTTTTGATATTATTG
20773691 TGATTAGACCTGTTTTTGATATTATTG
1 TGATTAGACCTGTTTTTGATATTATTG
20773718 AGGTTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (27 bp):
TGATTAGACCTGTTTTTGATATTATTG
Found at i:20773841 original size:26 final size:27
Alignment explanation
Indices: 20773792--20773842 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20773782 TAAAAGTTAA
* *
20773792 TAAAAAAAAATTTGAGCTCTTAAAAGT
1 TAAAAAAAAATTTGAGATCCTAAAAGT
*
20773819 TAAAAAAAATTTTG-GATCCTAAAA
1 TAAAAAAAAATTTGAGATCCTAAAA
20773843 AAGTTGGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (27 bp):
TAAAAAAAAATTTGAGATCCTAAAAGT
Found at i:20778973 original size:14 final size:14
Alignment explanation
Indices: 20778954--20778980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20778944 AAATACTCTG
20778954 ATAAGACATTTGAC
1 ATAAGACATTTGAC
20778968 ATAAGACATTTGA
1 ATAAGACATTTGA
20778981 TAAGAAAATT
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:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (14 bp):
ATAAGACATTTGAC
Found at i:20794238 original size:21 final size:21
Alignment explanation
Indices: 20794212--20794263 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
20794202 AGGAGTTTGT
20794212 TGTATCGGTAGAAGTAATAAA
1 TGTATCGGTAGAAGTAATAAA
* * * **
20794233 TGTATCAGTAGTAGTCATACT
1 TGTATCGGTAGAAGTAATAAA
20794254 TGTATCGGTA
1 TGTATCGGTA
20794264 AAACCTTCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (21 bp):
TGTATCGGTAGAAGTAATAAA
Found at i:20795700 original size:2 final size:2
Alignment explanation
Indices: 20795684--20795723 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
20795674 AAAATATTTT
* *
20795684 TA TA TA AA TA AA 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
20795724 AAATTGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:20797742 original size:18 final size:19
Alignment explanation
Indices: 20797719--20797754 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20797709 AATCTTGCCC
*
20797719 GTTTTT-AGTTCTTTTTAT
1 GTTTTTAAGTTCATTTTAT
20797737 GTTTTTAAGTTCATTTTA
1 GTTTTTAAGTTCATTTTA
20797755 GCTTGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (19 bp):
GTTTTTAAGTTCATTTTAT
Found at i:20799500 original size:21 final size:21
Alignment explanation
Indices: 20799474--20799529 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
20799464 CTGGAGTTTG
20799474 TTGTATCGATAGAAGTAATAA
1 TTGTATCGATAGAAGTAATAA
* * * *
20799495 TTGTATCGGTAGTAGTCATAC
1 TTGTATCGATAGAAGTAATAA
20799516 TTGTATCGATAGAA
1 TTGTATCGATAGAA
20799530 CCTTCCCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
TTGTATCGATAGAAGTAATAA
Found at i:20804313 original size:62 final size:59
Alignment explanation
Indices: 20804160--20804360 Score: 181
Period size: 62 Copynumber: 3.2 Consensus size: 59
20804150 TCCAAAAATA
* * * * *
20804160 ATATTATTTTAAT-A-ATTTAATATTAAATTTAATTTAATACTTATCTTAATAGTATGTT
1 ATATTAATTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTGATA-AATATT
** * *
20804218 ATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATTTAATGTTTATTTTATAGATAA
1 A-T-A-TTAAT-TT-AA-T-AAGAT-TTAATATTAAATTTAATTTAATATTTA-TCT-T-GATAA
20804283 ATATT
55 ATATT
* *
20804288 TTATTATTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTGATAAATATT
20804347 ATATTAATTTAATA
1 ATATTAATTTAATA
20804361 TTAAAGTGAT
Statistics
Matches: 114, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
58 1 0.01
59 23 0.20
60 2 0.02
61 6 0.05
62 28 0.25
63 5 0.04
64 2 0.02
65 2 0.02
66 2 0.02
67 6 0.05
68 26 0.23
69 3 0.03
70 5 0.04
71 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (59 bp):
ATATTAATTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTGATAAATATT
Found at i:20811106 original size:3 final size:3
Alignment explanation
Indices: 20811100--20811141 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
20811090 GATGATGATG
20811100 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20811142 CACCTTACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20811277 original size:10 final size:10
Alignment explanation
Indices: 20811218--20811281 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
20811208 GGAGAATGTG
20811218 TAAA-AAAACA
1 TAAATAAAA-A
*
20811228 TAAATATAAA
1 TAAATAAAAA
*
20811238 TAGACATGAAAA
1 TA-A-ATAAAAA
*
20811250 TAAATAAAGA
1 TAAATAAAAA
20811260 TGAAATAAAAA
1 T-AAATAAAAA
20811271 TAAATAAAAA
1 TAAATAAAAA
20811281 T
1 T
20811282 TATACAAGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 23 0.52
11 14 0.32
12 7 0.16
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.20
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:20812078 original size:21 final size:20
Alignment explanation
Indices: 20812032--20812069 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20812022 TTCGAAATAA
20812032 TTAAAAAATTAAAATTTTAT
1 TTAAAAAATTAAAATTTTAT
* *
20812052 TTAAAAATTTAAACTTTT
1 TTAAAAAATTAAAATTTT
20812070 TCTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAAAATTAAAATTTTAT
Found at i:20812130 original size:23 final size:25
Alignment explanation
Indices: 20812104--20812150 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
20812094 TTTTATTTTT
20812104 AAAAAT-CTAATTTTTTA-AAAAAG
1 AAAAATACTAATTTTTTACAAAAAG
* *
20812127 AAAATTACTATTTTTTTACAAAAA
1 AAAAATACTAATTTTTTACAAAAA
20812151 TCAAAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAAATACTAATTTTTTACAAAAAG
Found at i:20812154 original size:142 final size:143
Alignment explanation
Indices: 20811833--20812409 Score: 670
Period size: 141 Copynumber: 4.0 Consensus size: 143
20811823 TTTTCTTTTT
* * * * * * * ** *
20811833 TTTTTTTTAAACAAAATCACTACTTTTCTTAAAAATTAAAACTTTTATTTCGAGATGGTTAATGA
1 TTTTTTTAAAAAAAAATAACTA-TTTTTTTAAAAATCAAAACTTTTATTTTGAAATAATTAA-AA
20811898 AAATC-AAACTTTGTTT-AAAATTT-AACTTTTT-TTTAAAATGACTAAAAAACATATTTTTATT
64 AAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATT
20811959 TTTAAAAA-CTTAAAC
129 TTTAAAAATC-TAAAC
* * * * * *
20811974 TTTTTTTAAGAAAAAATAACCACTTTTCTTAATAATCAAAACTTTTAATTCGAAATAATT-AAAA
1 TTTTTTTAAAAAAAAATAACTA-TTTTTTTAAAAATCAAAACTTTTATTTTGAAATAATTAAAAA
* * * *
20812038 AATTAAAATTTTATTTAAAAATTTAAACTTTTTCTTTAAAATGA-TTAAAAACATATTTTTATTT
65 AATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTT
20812102 TTAAAAATCT-AA-
130 TTAAAAATCTAAAC
* * *
20812114 TTTTTTAAAAAAGAAAATTACTATTTTTTTACAAAAATCAAAACTTTTATTTTGAAATAGTTAAA
1 TTTTTTTAAAAA-AAAATAACTATTTTTTT--AAAAATCAAAACTTTTATTTTGAAATAATTAAA
* * *
20812179 AAAATCAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACCAAAAAAAATATTTTTAT
63 AAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTAT
20812244 TTTTAAAAATCTAAACTTTC
128 TTTTAAAAATCTAAA----C
*** * *
20812264 TTTTTTTTTTAAAAAATCACTATTTTTCTTAAAAATTAAAACTTTTATTTTGAAATAATTAAAAA
1 TTTTTTTAAAAAAAAATAACTATTTTT-TTAAAAATCAAAACTTTTATTTTGAAATAATTAAAAA
* * *
20812329 AATCAAAACTTTGTTTAAAAATTTAAA-ATTTTCTTTAAAATGACTAAAAAACAAATTTTTAGTT
65 AATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTT
20812393 TTAAAAATCTAAAC
130 TTAAAAATCTAAAC
20812407 TTT
1 TTT
20812410 CAATTTTTTT
Statistics
Matches: 374, Mismatches: 45, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
139 5 0.01
140 26 0.07
141 66 0.18
142 61 0.16
143 59 0.16
144 27 0.07
145 2 0.01
147 44 0.12
148 60 0.16
149 14 0.04
150 10 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (143 bp):
TTTTTTTAAAAAAAAATAACTATTTTTTTAAAAATCAAAACTTTTATTTTGAAATAATTAAAAAA
ATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTT
TAAAAATCTAAAC
Found at i:20812209 original size:51 final size:51
Alignment explanation
Indices: 20812154--20812360 Score: 153
Period size: 51 Copynumber: 4.2 Consensus size: 51
20812144 ACAAAAATCA
*
20812154 AAACTTTTATTTTGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTT
1 AAACTTTTATTTTGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAATTT
* * * ** *** * *
20812205 AAACTTTTACTTTAAAATGACCAAAAAAA--ATATTTTTATTTTTAAAAATCT
1 AAACTTTTATTTTGAAATAATTAAAAAAATCA-AAACTT-TGTTTAAAAATTT
* * ** * *
20812256 AAACTTTCT-TTTT----T-TTTTAAAAAATCACTA-TTTTTCTTAAAAATTA
1 AAACTTT-TATTTTGAAATAATTAAAAAAATCAAAACTTTGT-TTAAAAATTT
20812302 AAACTTTTATTTTGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAATTT
1 AAACTTTTATTTTGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAATTT
*
20812353 AAAATTTT
1 AAACTTTT
20812361 CTTTAAAATG
Statistics
Matches: 116, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
45 4 0.03
46 27 0.23
47 2 0.02
48 1 0.01
49 1 0.01
50 4 0.03
51 72 0.62
52 5 0.04
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (51 bp):
AAACTTTTATTTTGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAATTT
Found at i:20812326 original size:148 final size:147
Alignment explanation
Indices: 20811827--20812428 Score: 666
Period size: 148 Copynumber: 4.1 Consensus size: 147
20811817 CAAAGTTTTT
* * **
20811827 CTTT-TTTTTTTTTTAAACAAAATCACTACTTTTCTTAAAAATTAAAACTTTTATTTCGAGATGG
1 CTTTCTTTTTTTTTT-AA-AAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAA
* * *
20811891 TTAATGAAAATC-AAACTTTGTTT-AAAATTT-AACTTTTTTTTAAAATGACTAAAAAACATATT
64 TTAA-AAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTCTTTAAAATGACTAAAAAAAATATT
20811953 TTTATTTTTAAAAA-CTTAAA
128 TTTATTTTTAAAAATC-TAAA
*** * * * *
20811973 ----CTTTTTTTAAGAAAAAATAACCACTTTTCTTAATAATCAAAACTTTTAATTCGAAATAATT
1 CTTTCTTTTTTTTTTAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAATT
* * * * *
20812034 -AAAAAATTAAAATTTTATTTAAAAATTTAAACTTTTTCTTTAAAATGA-TTAAAAACATATTTT
66 AAAAAAATCAAAACTTTGTTTAAAAATTTAAAC-TTTTCTTTAAAATGACTAAAAAAAATATTTT
20812097 TATTTTTAAAAATCT-AA
130 TATTTTTAAAAATCTAAA
**** * * *
20812114 -----TTTTTTAAAAAAGAAAATTACTA-TTTTTTTACAAAAATCAAAACTTTTATTTTGAAATA
1 CTTTCTTTTTTTTTTAA-AAAATCACTACTTTTCTT--AAAAATCAAAACTTTTATTTCGAAATA
* *
20812173 GTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTACTTTAAAATGACCAAAAAAAATAT
63 ATTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTT-CTTTAAAATGACTAAAAAAAATAT
20812238 TTTTATTTTTAAAAATCTAAA
127 TTTTATTTTTAAAAATCTAAA
* * *
20812259 CTTTCTTTTTTTTTTAAAAAATCACTATTTTTCTTAAAAATTAAAACTTTTATTTTGAAATAATT
1 CTTTCTTTTTTTTTTAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAATT
*
20812324 AAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTCTTTAAAATGACTAAAAAACAA-ATTTT
66 AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTCTTTAAAATGACTAAAAAA-AATATTTT
*
20812388 TAGTTTTAAAAATCTAAA
130 TATTTTTAAAAATCTAAA
*
20812406 CTTTCAATTTTTTTTTAAAAAAT
1 CTTTC-TTTTTTTTTTAAAAAAT
20812429 AAAAATTTTC
Statistics
Matches: 391, Mismatches: 44, Indels: 40
0.82 0.09 0.08
Matches are distributed among these distances:
139 5 0.01
140 26 0.07
141 57 0.15
142 62 0.16
143 62 0.16
144 27 0.07
145 2 0.01
147 45 0.12
148 82 0.21
149 9 0.02
150 14 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (147 bp):
CTTTCTTTTTTTTTTAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAATT
AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTCTTTAAAATGACTAAAAAAAATATTTTT
ATTTTTAAAAATCTAAA
Found at i:20813241 original size:42 final size:42
Alignment explanation
Indices: 20813169--20813599 Score: 474
Period size: 42 Copynumber: 10.3 Consensus size: 42
20813159 TTGAAATGAG
* * * *
20813169 AATGCAGAAGAAATGTAAATAGACC-ACACACCTGGGCATCTA
1 AATGC-GATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* * * *
20813211 AATGCAATGAAAAGTAAATGGACTTCCACACTTGGGCCTCTA
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* *
20813253 AATGCGATGAAAAGTAAAT-GAAACTCTACACCTGGGCCTCTA
1 AATGCGATGAAAAGTAAATAG-ACCTCCACACCTGGGCCTCTA
* * * * *
20813295 AATACGATGAAAAGTAAATAGATCTCCATACCTTGGCCTTTA
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* * * *
20813337 AATGCAATGAAAAGTAAATGGACCTCCACACTTAGGCCTCTA
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* * *
20813379 AATGCGATGAAAGGTAAACAGACCTCTACACCTGGGCCTCTA
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* * *
20813421 AATGTGATGAAAAGTAAATAGACCTCCACACCTAGGCCTCAA
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* * * *
20813463 AATGCGATGAAAAGTAAA-CGAACCACCACACCTGGGCTTTTA
1 AATGCGATGAAAAGTAAATAG-ACCTCCACACCTGGGCCTCTA
* * *
20813505 AATGCGATGAAAAGTAAATAAACCTCCACACCTAGGTCTCTA
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
* **
20813547 AATGCAATGAAAAGTAAAT-GACCCTCCACACCTATGCCTCTA
1 AATGCGATGAAAAGTAAATAGA-CCTCCACACCTGGGCCTCTA
*
20813589 AATGCAATGAA
1 AATGCGATGAA
20813600 TGCTTTCCTT
Statistics
Matches: 325, Mismatches: 58, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
41 17 0.05
42 307 0.94
43 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (42 bp):
AATGCGATGAAAAGTAAATAGACCTCCACACCTGGGCCTCTA
Found at i:20813434 original size:126 final size:125
Alignment explanation
Indices: 20813169--20813599 Score: 526
Period size: 126 Copynumber: 3.4 Consensus size: 125
20813159 TTGAAATGAG
* * * * *
20813169 AATGCAGAAGAAATGTAAATAGACC-ACACACCTGGGCATCTAAATGCAATGAAAAGTAAATGGA
1 AATGC-GATGAAAAGTAAATAGACCTCCACACCTTGGCCTCTAAATGCAATGAAAAGTAAATGGA
* * *
20813233 CTTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGAAACTCTACACCTGGGCCTCTA
65 CCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAAAG-ACCTCTACACCTGGGCCTCTA
* * * *
20813295 AATACGATGAAAAGTAAATAGATCTCCATACCTTGGCCTTTAAATGCAATGAAAAGTAAATGGAC
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTTGGCCTCTAAATGCAATGAAAAGTAAATGGAC
* *
20813360 CTCCACACTTAGGCCTCTAAATGCGATGAAAGGTAAACAGACCTCTACACCTGGGCCTCTA
66 CTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAA-AGACCTCTACACCTGGGCCTCTA
* * * * * *
20813421 AATGTGATGAAAAGTAAATAGACCTCCACACCTAGGCCTCAAAATGCGATGAAAAGTAAACGAAC
1 AATGCGATGAAAAGTAAATAGACCTCCACACCTTGGCCTCTAAATGCAATGAAAAGTAAATGGAC
* * * * * * * *
20813486 CACCACACCTGGGCTTTTAAATGCGATGAAAAGTAAATAAACCTCCACACCTAGGTCTCTA
66 CTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAA-AGACCTCTACACCTGGGCCTCTA
*
20813547 AATGCAATGAAAAGTAAAT-GACCCTCCACACCTAT-GCCTCTAAATGCAATGAA
1 AATGCGATGAAAAGTAAATAGA-CCTCCACACCT-TGGCCTCTAAATGCAATGAA
20813600 TGCTTTCCTT
Statistics
Matches: 261, Mismatches: 40, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
125 18 0.07
126 242 0.93
127 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (125 bp):
AATGCGATGAAAAGTAAATAGACCTCCACACCTTGGCCTCTAAATGCAATGAAAAGTAAATGGAC
CTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAAAGACCTCTACACCTGGGCCTCTA
Found at i:20814532 original size:109 final size:109
Alignment explanation
Indices: 20814341--20814550 Score: 312
Period size: 109 Copynumber: 1.9 Consensus size: 109
20814331 AAAACACTTA
* * * * * ** *
20814341 TCGATTTTAAATAGGATGTTCAGTTACTTAGATTCAAAGAAAAATCATGCTCAGTACGTTAGGGC
1 TCGATTTTAAATAGGATATTAAATTACTTAGATTCAAAGAAAAATCATACCCAACACATTAGGGC
*
20814406 ATAATTTCTCGAGTTCCCTAAAATAAAAGAACATTGAACATTTG
66 ACAATTTCTCGAGTTCCCTAAAATAAAAGAACATTGAACATTTG
*
20814450 TCGATTTTAAATAGGATATTAAATTACTTAGGTTCAAAGAAAAATCATACCCAACACATTAGGGC
1 TCGATTTTAAATAGGATATTAAATTACTTAGATTCAAAGAAAAATCATACCCAACACATTAGGGC
* *
20814515 ACAATTTCTTGAGTTCCCTAAAATAAAATAACATTG
66 ACAATTTCTCGAGTTCCCTAAAATAAAAGAACATTG
20814551 CCTCGATTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
109 89 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (109 bp):
TCGATTTTAAATAGGATATTAAATTACTTAGATTCAAAGAAAAATCATACCCAACACATTAGGGC
ACAATTTCTCGAGTTCCCTAAAATAAAAGAACATTGAACATTTG
Found at i:20816236 original size:15 final size:15
Alignment explanation
Indices: 20816216--20816244 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20816206 ATGCCTCACA
20816216 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
20816231 CACCGTGTTATCAA
1 CACCGTGTTATCAA
20816245 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:20826322 original size:21 final size:20
Alignment explanation
Indices: 20826276--20826323 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
20826266 GGAGTTTTTA
20826276 GTATCGGTAGAGGTAAGACTT
1 GTATCGGTAGAGG-AAGACTT
*
20826297 ATATCGGTAGAGG-AGTCACTT
1 GTATCGGTAGAGGAAG--ACTT
20826318 GTATCG
1 GTATCG
20826324 ATACAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.09
21 21 0.91
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.29
Consensus pattern (20 bp):
GTATCGGTAGAGGAAGACTT
Found at i:20838679 original size:12 final size:12
Alignment explanation
Indices: 20838662--20838686 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20838652 GATATCATCG
20838662 TCATAAATTTCA
1 TCATAAATTTCA
20838674 TCATAAATTTCA
1 TCATAAATTTCA
20838686 T
1 T
20838687 TTGCACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCATAAATTTCA
Found at i:20851817 original size:14 final size:14
Alignment explanation
Indices: 20851798--20851831 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
20851788 GGAGTTGAAG
20851798 ATTGCCTCCAAAAT
1 ATTGCCTCCAAAAT
20851812 ATTGCCTCCAAAAT
1 ATTGCCTCCAAAAT
20851826 ATTGCC
1 ATTGCC
20851832 AACCTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (14 bp):
ATTGCCTCCAAAAT
Found at i:20855305 original size:30 final size:29
Alignment explanation
Indices: 20855260--20855582 Score: 240
Period size: 30 Copynumber: 11.1 Consensus size: 29
20855250 AAAGCCCCCG
*
20855260 AACTCTTCCAAAATTACATTTTGACCCTCG
1 AACT-TTCCAAAATTACATTTTGACCCTCA
*
20855290 AACTTCTCCATAATTACATTTT-AGCCCTCGA
1 AACTT-TCCAAAATTACATTTTGA-CCCTC-A
* *
20855321 ACAC-TTCCAAAATTGCATTTTAATCCCT-A
1 A-ACTTTCCAAAATTACATTTTGA-CCCTCA
* * *
20855350 AACTTTTCCAAAAATATATTTT-AGCCCTTA
1 AAC-TTTCCAAAATTACATTTTGA-CCCTCA
* *
20855380 AACTTTTCAAAATTACATTTTAGCCCCT-A
1 AACTTTCCAAAATTACATTTT-GACCCTCA
*
20855409 AACTTTTCC-AAATTACATTTTAACCC-CTA
1 AAC-TTTCCAAAATTACATTTTGACCCTC-A
* * *
20855438 AACTTTCCCAAAATCACATCTTGATCC-CA
1 AACTTT-CCAAAATTACATTTTGACCCTCA
* *
20855467 AACTTTTCCAAAATTATATTTTGACCCCCA
1 AAC-TTTCCAAAATTACATTTTGACCCTCA
*
20855497 AACCTTTCCAAAATCACA-TTTGA-CCT-A
1 AA-CTTTCCAAAATTACATTTTGACCCTCA
* * * *
20855524 AACTTACAAAAATCACATTTTGACCC-CG
1 AACTTTCCAAAATTACATTTTGACCCTCA
20855552 AACTTTCCAAAAATTACATTTTGA-CCTCA
1 AACTTTCC-AAAATTACATTTTGACCCTCA
20855581 AA
1 AA
20855583 TTCTCTAAAA
Statistics
Matches: 236, Mismatches: 34, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
26 13 0.06
27 8 0.03
28 20 0.08
29 88 0.37
30 97 0.41
31 8 0.03
32 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTGACCCTCA
Found at i:20855408 original size:59 final size:58
Alignment explanation
Indices: 20855260--20855574 Score: 234
Period size: 59 Copynumber: 5.4 Consensus size: 58
20855250 AAAGCCCCCG
* * * * *
20855260 AACTCTTCCAAAATTACATTTTGACCCTCGAACTTCTCCATAATTACATTTTAGCCCTCGA
1 AACT-TTCCAAAATTACATTTTGTCCCT-AAACTTTTCCAAAATTACATTTTAGCCCT-TA
* * * *
20855321 ACAC-TTCCAAAATTGCATTTTAATCCCTAAACTTTTCCAAAAATATATTTTAGCCCTTA
1 A-ACTTTCCAAAATTACATTTT-GTCCCTAAACTTTTCCAAAATTACATTTTAGCCCTTA
* * * *
20855380 AACTTTTCAAAATTACATTTTAGCCCCTAAACTTTTCC-AAATTACATTTTAACCCCTA
1 AACTTTCCAAAATTACATTTT-GTCCCTAAACTTTTCCAAAATTACATTTTAGCCCTTA
* * * **
20855438 AACTTTCCCAAAATCACATCTTGATCCC-AAACTTTTCCAAAATTATATTTT-GACCCCCA
1 AACTTT-CCAAAATTACATTTTG-TCCCTAAACTTTTCCAAAATTACATTTTAG-CCCTTA
* * * * * **
20855497 AACCTTTCCAAAATCACA-TTTG-ACCTAAAC-TTACAAAAATCACATTTT-GACCC-CG
1 AA-CTTTCCAAAATTACATTTTGTCCCTAAACTTTTCCAAAATTACATTTTAG-CCCTTA
20855552 AACTTTCCAAAAATTACATTTTG
1 AACTTTCC-AAAATTACATTTTG
20855575 ACCTCAAATT
Statistics
Matches: 211, Mismatches: 32, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
54 6 0.03
55 11 0.05
56 25 0.12
57 4 0.02
58 38 0.18
59 76 0.36
60 44 0.21
61 5 0.02
62 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AACTTTCCAAAATTACATTTTGTCCCTAAACTTTTCCAAAATTACATTTTAGCCCTTA
Found at i:20855570 original size:29 final size:28
Alignment explanation
Indices: 20855255--20855582 Score: 229
Period size: 29 Copynumber: 11.2 Consensus size: 28
20855245 ATAAAAAAGC
*
20855255 CCCCGAACTCTTCCAAAATTACATTTTGA
1 CCCCAAACT-TTCCAAAATTACATTTTGA
* *
20855284 CCCTCGAACTTCTCCATAATTACATTTT-A
1 CCC-CAAACTT-TCCAAAATTACATTTTGA
* *
20855313 GCCCTCGAACAC-TTCCAAAATTGCATTTTAA
1 -CCC-C-AA-ACTTTCCAAAATTACATTTTGA
* * *
20855344 TCCCTAAACTTTTCCAAAAATATATTTT-A
1 -CCCCAAAC-TTTCCAAAATTACATTTTGA
* *
20855373 GCCCTTAAACTTTTCAAAATTACATTTT-A
1 -CCC-CAAACTTTCCAAAATTACATTTTGA
*
20855402 GCCCCTAAACTTTTCC-AAATTACATTTTAA
1 -CCCC-AAAC-TTTCCAAAATTACATTTTGA
* *
20855432 CCCCTAAACTTTCCCAAAATCACATCTTGA
1 CCCC-AAACTTT-CCAAAATTACATTTTGA
* *
20855462 TCCCAAACTTTTCCAAAATTATATTTTGA
1 CCCCAAAC-TTTCCAAAATTACATTTTGA
*
20855491 CCCCCAAACCTTTCCAAAATCACA-TTTGA
1 -CCCCAAA-CTTTCCAAAATTACATTTTGA
* * * *
20855520 -CCTAAACTTACAAAAATCACATTTTGA
1 CCCCAAACTTTCCAAAATTACATTTTGA
*
20855547 CCCCGAACTTTCCAAAAATTACATTTTGA
1 CCCCAAACTTTCC-AAAATTACATTTTGA
*
20855576 CCTCAAA
1 CCCCAAA
20855583 TTCTCTAAAA
Statistics
Matches: 244, Mismatches: 35, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
26 13 0.05
27 10 0.04
28 13 0.05
29 100 0.41
30 99 0.41
31 7 0.03
32 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
CCCCAAACTTTCCAAAATTACATTTTGA
Found at i:20857476 original size:12 final size:12
Alignment explanation
Indices: 20857459--20857493 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20857449 CAAAGAGAGA
20857459 TGCAAGAACAGT
1 TGCAAGAACAGT
* *
20857471 TGCAAGAATAAT
1 TGCAAGAACAGT
20857483 TGCAAGAACAG
1 TGCAAGAACAG
20857494 ATGAAGAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (12 bp):
TGCAAGAACAGT
Found at i:20863666 original size:50 final size:50
Alignment explanation
Indices: 20863549--20864465 Score: 517
Period size: 50 Copynumber: 18.7 Consensus size: 50
20863539 TTTGACAGGG
* ** * * *
20863549 AAGATTGAGGCCGCAACGGTGAATCTAATACCCT-GGAGATATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * *
20863598 AAGGTTGAGGTCGTAACGGTGAACCCGATACCTTAAAAGATGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * *
20863648 AAGATTGAGGCCACAACGGTGAATCCGGTACCAT-GAAGATATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * *
20863697 AAGGTTGAGGCTGTAACGGTGAACCCGGTACCTTAGCAGATATGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * ** *
20863747 AAGATTAAGGCCGCAACGGTGAA-TC--T--GGT-GAAGATATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * ** * * *
20863791 AAGGTTGAGGCCGTAATAGCGAACCCGATACCTTAGCAGATGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* ** * * *
20863841 AAGATTGAGG-C-CAATGACGAATCCG--ACATT--AAGATATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * * * *
20863885 AAGGTTGAGGCCGTAACGGCGAACTCGATACCTTAGCATATGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * * *
20863935 AAGATTGAGGCCACAACGGCGAACTCGATACCTTAGCATATGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * *
20863985 AAGATTGAGGCCGCAACGGTGAATCTGGTA-C-TATGAAGAAATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTA-GAAGATATGATGGGA
* **** *
20864034 AAGGTTGAGGCCGCAATTACGAACCC-AGTACCTTAGAAGATGTGATGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGA-TACCTTAGAAGATATGATGGGA
* * ** * * * * * *
20864084 AGGATTGAGACCATAATGGCGAATCCGATACCATAG-AGATATGAAGCGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * ** * *
20864133 AAGGTTGAGGCCGTAACGATGAACTCGGCACCTTAGAAGATGTGATAGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * * * * * * *
20864183 AATATTAAGGCTGTAACAGCGAATCCGATACCAT-GTAGATATGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * * * *
20864232 AAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTGGAAGATGTGATGAGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * * * **
20864282 AGGATTGAGGCCACAACAGTGAATCCGTTACCAT-GAAGATATGAAAGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * * *
20864331 AAGATTGAGGTCGTAACGGTGAACCCGGTACCTTGGAAGATGTGATGAGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * * * ** * * * *
20864381 AGGATTGAGGCCACAATGGCGAATTCGACACCAT-GAAGATTTGAAGGGA
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
* * ** * *
20864430 AAGGTTGAGGTCGCAACGACGAACCTGGTACCTTAG
1 AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAG
20864466 GAACATGACG
Statistics
Matches: 641, Mismatches: 204, Indels: 45
0.72 0.23 0.05
Matches are distributed among these distances:
44 50 0.08
45 3 0.00
46 13 0.02
47 2 0.00
48 16 0.02
49 242 0.38
50 312 0.49
51 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (50 bp):
AAGATTGAGGCCGCAACGGTGAACCCGATACCTTAGAAGATATGATGGGA
Found at i:20863720 original size:99 final size:97
Alignment explanation
Indices: 20863549--20863953 Score: 507
Period size: 94 Copynumber: 4.2 Consensus size: 97
20863539 TTTGACAGGG
* *** * * *
20863549 AAGATTGAGGCCGCAACGGTGAATCTAATACCCTGGAGATATGAAGGGAAAGGTTGAGGTCGTAA
1 AAGATTGAGGCCACAACGGTGAATC-CGGA-CATGAAGATATGAAGGGAAAGGTTGAGGCCGTAA
* **
20863614 CGGTGAACCCGATACCTTAAAAGATGTGATGGGA
64 CGGCGAACCCGATACCTTAGCAGATGTGATGGGA
*
20863648 AAGATTGAGGCCACAACGGTGAATCCGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCTGTAA
1 AAGATTGAGGCCACAACGGTGAATCCGG-A-CATGAAGATATGAAGGGAAAGGTTGAGGCCGTAA
* * *
20863713 CGGTGAACCCGGTACCTTAGCAGATATGATGGGA
64 CGGCGAACCCGATACCTTAGCAGATGTGATGGGA
* * * **
20863747 AAGATTAAGGCCGCAACGGTGAATCTGG---TGAAGATATGAAGGGAAAGGTTGAGGCCGTAATA
1 AAGATTGAGGCCACAACGGTGAATCCGGACATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACG
20863809 GCGAACCCGATACCTTAGCAGATGTGATGGGA
66 GCGAACCCGATACCTTAGCAGATGTGATGGGA
* ** *
20863841 AAGATTGAGG-C-CAATGACGAATCC-GACATTAAGATATGAAGGGAAAGGTTGAGGCCGTAACG
1 AAGATTGAGGCCACAACGGTGAATCCGGACATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACG
* *
20863903 GCGAACTCGATACCTTAGCATATGTGATGGGA
66 GCGAACCCGATACCTTAGCAGATGTGATGGGA
20863935 AAGATTGAGGCCACAACGG
1 AAGATTGAGGCCACAACGG
20863954 CGAACTCGAT
Statistics
Matches: 267, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
91 1 0.00
92 9 0.03
93 1 0.00
94 140 0.52
95 1 0.00
96 4 0.01
99 111 0.42
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (97 bp):
AAGATTGAGGCCACAACGGTGAATCCGGACATGAAGATATGAAGGGAAAGGTTGAGGCCGTAACG
GCGAACCCGATACCTTAGCAGATGTGATGGGA
Found at i:20864066 original size:99 final size:99
Alignment explanation
Indices: 20863931--20864465 Score: 559
Period size: 99 Copynumber: 5.4 Consensus size: 99
20863921 CATATGTGAT
* * * * * * * *
20863931 GGGAAAGATTGAGGCCACAACGGCGAACTCGATACCTTAGCATATGTGATGGGAAAGATTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC
* * * * * *
20863996 CGCAACGGTGAATCTGGTACTATGAAGAAATGAA
66 CACAACGGCGAATCCGATACCATGAAGATATGAA
** * *
20864030 GGGAAAGGTTGAGGCCGCAATTACGAACCCAGTACCTTAGAAGATGTGATGGGAAGGATTGAGAC
1 GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC
* *
20864095 CATAATGGCGAATCCGATACCAT-AGAGATATGAA
66 CACAACGGCGAATCCGATACCATGA-AGATATGAA
* * * * * * ** *
20864129 GCGAAAGGTTGAGGCCGTAACGATGAACTCGGCACCTTAGAAGATGTGATAGGAAATATTAAGGC
1 GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC
*** * *
20864194 TGTAACAGCGAATCCGATACCATGTAGATATGAA
66 CACAACGGCGAATCCGATACCATGAAGATATGAA
* * * *
20864228 GGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTGGAAGATGTGATGAGAAGGATTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC
* * *
20864293 CACAACAGTGAATCCGTTACCATGAAGATATGAA
66 CACAACGGCGAATCCGATACCATGAAGATATGAA
* * * * ** * *
20864327 AGGAAAGATTGAGGTCGTAACGGTGAACCCGGTACCTTGGAAGATGTGATGAGAAGGATTGAGGC
1 GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC
* * * *
20864392 CACAATGGCGAATTCGACACCATGAAGATTTGAA
66 CACAACGGCGAATCCGATACCATGAAGATATGAA
* *
20864426 GGGAAAGGTTGAGGTCGCAACGACGAACCTGGTACCTTAG
1 GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAG
20864466 GAACATGACG
Statistics
Matches: 357, Mismatches: 77, Indels: 4
0.82 0.18 0.01
Matches are distributed among these distances:
98 1 0.00
99 356 1.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.19
Consensus pattern (99 bp):
GGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC
CACAACGGCGAATCCGATACCATGAAGATATGAA
Found at i:20864168 original size:198 final size:198
Alignment explanation
Indices: 20863932--20864465 Score: 615
Period size: 198 Copynumber: 2.7 Consensus size: 198
20863922 ATATGTGATG
** ** * * *
20863932 GGAAAGATTGAGGCCACAACGGCGAACTCGATACCTTAGCATATGTGATGGGAAAGATTGAGGCC
1 GGAAAGATTGAGGCCGTAACGATGAACTCGGTACCTTAGAAGATGTGATGGGAAAGATTGAGGCC
* * * * * *
20863997 GCAACGGTGAATCTGGTACTATGAAGAAATGAAGGGAAAGGTTGAGGCCGCAATTACGAACCCAG
66 GCAACGGCGAATCTGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGACGAACCCGG
* * **
20864062 TACCTTAGAAGATGTGATGGGAAGGATTGAGACCATAATGGCGAATCCGATACCAT-AGAGATAT
131 TACCTTAGAAGATGTGATGAGAAGGATTGAGACCACAACAGCGAATCCGATACCATGA-AGATAT
20864126 G-AA
195 GAAA
* * * * *
20864129 GCGAAAGGTTGAGGCCGTAACGATGAACTCGGCACCTTAGAAGATGTGATAGGAAATATTAAGGC
1 G-GAAAGATTGAGGCCGTAACGATGAACTCGGTACCTTAGAAGATGTGATGGGAAAGATTGAGGC
* * * * * *
20864194 TGTAACAGCGAATCCGATACCATGTAGATATGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCG
65 CGCAACGGCGAATCTGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGACGAACCCG
* * * *
20864259 GTACCTTGGAAGATGTGATGAGAAGGATTGAGGCCACAACAGTGAATCCGTTACCATGAAGATAT
130 GTACCTTAGAAGATGTGATGAGAAGGATTGAGACCACAACAGCGAATCCGATACCATGAAGATAT
20864324 GAAA
195 GAAA
* * * * * *
20864328 GGAAAGATTGAGGTCGTAACGGTGAACCCGGTACCTTGGAAGATGTGATGAGAAGGATTGAGGCC
1 GGAAAGATTGAGGCCGTAACGATGAACTCGGTACCTTAGAAGATGTGATGGGAAAGATTGAGGCC
* * * * * * *
20864393 ACAATGGCGAAT-TCGACACCATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGACGAACCTG
66 GCAACGGCGAATCT-GATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGACGAACCCG
20864457 GTACCTTAG
130 GTACCTTAG
20864466 GAACATGACG
Statistics
Matches: 276, Mismatches: 57, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
197 1 0.00
198 271 0.98
199 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.19
Consensus pattern (198 bp):
GGAAAGATTGAGGCCGTAACGATGAACTCGGTACCTTAGAAGATGTGATGGGAAAGATTGAGGCC
GCAACGGCGAATCTGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGACGAACCCGG
TACCTTAGAAGATGTGATGAGAAGGATTGAGACCACAACAGCGAATCCGATACCATGAAGATATG
AAA
Found at i:20866569 original size:30 final size:29
Alignment explanation
Indices: 20866519--20866844 Score: 213
Period size: 30 Copynumber: 11.0 Consensus size: 29
20866509 AAAAAGCCTC
20866519 CAAACTTTTCCAGAAA-TACATTTTGACCCT
1 CAAAC-TTTCCA-AAATTACATTTTGACCCT
* *
20866549 CGAACTTATCTAAAATTACATTTT-AGCCC-
1 CAAACTT-TCCAAAATTACATTTTGA-CCCT
* * * *
20866578 CCAACTACTTCTAAAATTATATTTTAACCC-
1 CAAACT--TTCCAAAATTACATTTTGACCCT
*
20866608 CTAAACTTTTCCAAAATTATATTTT-AGCCCT
1 C-AAAC-TTTCCAAAATTACATTTTGA-CCCT
** * *
20866639 TGAACATTTTCACAATTACATTTT-AGCCCT
1 CAAAC-TTTCCAAAATTACATTTTGA-CCCT
*
20866669 TAAACTTTTCC-AAATTACATTTTGACCCT
1 CAAAC-TTTCCAAAATTACATTTTGACCCT
** * *
20866698 TGAACTTTCCTAAAATCACATCTTGATCCCT
1 CAAACTTTCC-AAAATTACATTTTGA-CCCT
* *
20866729 -AAACTTGTCCAAAATTATATTTTAACCCT
1 CAAACTT-TCCAAAATTACATTTTGACCCT
* *
20866758 TAAACCTTTCCAAAATCACATTTTGACCC-
1 CAAA-CTTTCCAAAATTACATTTTGACCCT
* *
20866787 CGAACTTTCCAAAATCACATTTTGA-CCT
1 CAAACTTTCCAAAATTACATTTTGACCCT
* *
20866815 CAAACTTTCCAAAAATTGCATTTTAACCCT
1 CAAACTTTCC-AAAATTACATTTTGACCCT
20866845 AAATTCTTCG
Statistics
Matches: 243, Mismatches: 33, Indels: 40
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.01
28 35 0.14
29 49 0.20
30 141 0.58
31 15 0.06
32 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (29 bp):
CAAACTTTCCAAAATTACATTTTGACCCT
Found at i:20866713 original size:89 final size:88
Alignment explanation
Indices: 20866652--20866844 Score: 250
Period size: 89 Copynumber: 2.2 Consensus size: 88
20866642 ACATTTTCAC
* *
20866652 AATTACATTTTAGCCCTTAAACTTTTCC-AAATTACATTTTGACCCTTGAACTTTCCTAAAATCA
1 AATTACATTTTAACCCTTAAACCTTTCCAAAATTACATTTTGACCC-TGAACTTTCC-AAAATCA
*
20866716 CATCTTGATCCCTAAACTTGTCCAA
64 CATCTTGAGCCCTAAACTTGTCCAA
* * *
20866741 AATTATATTTTAACCCTTAAACCTTTCCAAAATCACATTTTGACCCCGAACTTTCCAAAATCACA
1 AATTACATTTTAACCCTTAAACCTTTCCAAAATTACATTTTGACCCTGAACTTTCCAAAATCACA
*
20866806 TTTTGA--CCTCAAACTT-TCCAAA
66 TCTTGAGCCCT-AAACTTGTCC-AA
*
20866828 AATTGCATTTTAACCCT
1 AATTACATTTTAACCCT
20866845 AAATTCTTCG
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
86 6 0.06
87 23 0.25
88 14 0.15
89 34 0.37
90 16 0.17
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (88 bp):
AATTACATTTTAACCCTTAAACCTTTCCAAAATTACATTTTGACCCTGAACTTTCCAAAATCACA
TCTTGAGCCCTAAACTTGTCCAA
Found at i:20871934 original size:22 final size:22
Alignment explanation
Indices: 20871906--20871949 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20871896 TAAAATAATA
20871906 TATCTTAGATGACTTTTATTAG
1 TATCTTAGATGACTTTTATTAG
20871928 TATCTTAGATGACTTTTATTAG
1 TATCTTAGATGACTTTTATTAG
20871950 CTTTCTTAAA
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:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (22 bp):
TATCTTAGATGACTTTTATTAG
Found at i:20873206 original size:51 final size:50
Alignment explanation
Indices: 20873151--20873385 Score: 123
Period size: 51 Copynumber: 4.7 Consensus size: 50
20873141 CAAAGTTACT
20873151 ACTTTTCTTAAAAATCAAAACTTTTATTTTAAAATGGTTAAAAAAAATCAA
1 ACTTTT-TTAAAAATCAAAACTTTTATTTTAAAATGGTTAAAAAAAATCAA
** *** * *
20873202 ACTTTGTTTAAAAATTTAAACTTTT-TCTTTAAAATAACTAAAAAACAT-ATT
1 ACTTT-TTTAAAAATCAAAACTTTTAT-TTTAAAATGGTTAAAAAAAATCA-A
** * * * *
20873253 TTTATTTTTAAAAATCTAAA-TTTTCTTTCT----T--TTTAAAAAAATCACT
1 ACT-TTTTTAAAAATCAAAACTTTTATTT-TAAAATGGTTAAAAAAAATCA-A
* ** *
20873299 ACTTTTCTTAAAAATCAAAATTTTTATTTCGAAATTGTT-AAAAAAATCAAA
1 ACTTTT-TTAAAAATCAAAACTTTTATTTTAAAATGGTTAAAAAAAATC-AA
* *
20873350 ACTTTGTTTAAAAATTTAAAATTTTTA-TTTAAAATG
1 ACTTT-TTTAAAAA-TCAAAACTTTTATTTTAAAATG
20873386 ACTAGAAAAC
Statistics
Matches: 142, Mismatches: 24, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
45 11 0.08
46 15 0.11
47 8 0.06
50 9 0.06
51 81 0.57
52 18 0.13
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (50 bp):
ACTTTTTTAAAAATCAAAACTTTTATTTTAAAATGGTTAAAAAAAATCAA
Found at i:20873493 original size:150 final size:148
Alignment explanation
Indices: 20873116--20873569 Score: 642
Period size: 148 Copynumber: 3.1 Consensus size: 148
20873106 TTTTTTTTGC
* * ** * * *
20873116 AAAATCAAAATTTTCCTT-TTTTTATCAAAGTTACTACTTTTCTTAAAAATCAAAACTTTTATTT
1 AAAATCTAAATTTTCTTTCTTTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAATTTTTATTT
** * * *
20873180 TAAAATGGTTAAAAAAAATC-AAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAA
66 CGAAATAGTT-AAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACTAAA
20873244 AAACATATTTTTATTTTTA
130 AAACATATTTTTATTTTTA
20873263 AAAATCTAAATTTTCTTTCTTTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAATTTTTATTT
1 AAAATCTAAATTTTCTTTCTTTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAATTTTTATTT
* * *
20873328 CGAAATTGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTATTTAAAATGACTAGAA
66 CGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACTAAAA
*
20873393 AACATATTTTTATTTTTT
131 AACATATTTTTATTTTTA
* * * *
20873411 AAAATCTAAACTTTCTTTTTTTTTTTAAGAAAATCACTATTTTTCTTAAAAATCAAAATTTTTAT
1 AAAATCTAAA-TTT-TCTTTCTTTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAATTTTTAT
* *
20873476 TTCGAAATAGTTAAAAAAATCAAAACTTTATTTAAAAATTTAAATTTTTTCTTTAAAATGACTAA
64 TTCGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACT-A
* *
20873541 AAAAACATATTTTAAATTTTA
128 AAAAACATATTTTTATTTTTA
20873562 AAAATCTA
1 AAAATCTA
20873570 TTTTTTTTAA
Statistics
Matches: 275, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
147 25 0.09
148 116 0.42
149 3 0.01
150 105 0.38
151 26 0.09
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (148 bp):
AAAATCTAAATTTTCTTTCTTTTTAAAAAAATCACTACTTTTCTTAAAAATCAAAATTTTTATTT
CGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACTAAAA
AACATATTTTTATTTTTA
Found at i:20873495 original size:51 final size:50
Alignment explanation
Indices: 20873285--20873497 Score: 145
Period size: 51 Copynumber: 4.2 Consensus size: 50
20873275 TTCTTTCTTT
*
20873285 TTAAAAAAATCACTACTTTTCTTAAAAATCAAAATTTTTATTTCGAAATTG
1 TTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTT-GAAATTG
** * * *
20873336 TTAAAAAAATCAAAACTTTGT-TTAAAAATTTAAAATTTTTATTT-AAAATG
1 TTAAAAAAATCACTA-TTTTTCTTAAAAA-TCAAAATTTTTATTTGAAATTG
* * * * * * * *
20873386 ACTAGAAAACAT-A-TTTTTATTTTTTAAAATCTAAACTTTCTT-TTT---TTTT
1 -TTA-AAAAAATCACTATTT-TTCTTAAAAATC-AAAATTT-TTATTTGAAATTG
* *
20873435 TTAAGAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAG
1 TTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTT-GAAATTG
20873486 TTAAAAAAATCA
1 TTAAAAAAATCA
20873498 AAACTTTATT
Statistics
Matches: 119, Mismatches: 28, Indels: 30
0.67 0.16 0.17
Matches are distributed among these distances:
46 2 0.02
47 14 0.12
48 13 0.11
49 8 0.07
50 7 0.06
51 50 0.42
52 25 0.21
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (50 bp):
TTAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTGAAATTG
Found at i:20873511 original size:51 final size:50
Alignment explanation
Indices: 20873285--20873524 Score: 138
Period size: 51 Copynumber: 4.8 Consensus size: 50
20873275 TTCTTTCTTT
**
20873285 TTAAAAAAATCACTACTTT-TCTTAAAAATCAAAATTTTTATTTCGAAATTG
1 TTAAAAAAATCAAAACTTTAT-TTAAAAATCAAAATTTTTATTT-GAAATTG
* * *
20873336 TTAAAAAAATCAAAACTTTGTTTAAAAATTTAAAATTTTTATTT-AAAATG
1 TTAAAAAAATCAAAACTTTATTTAAAAA-TCAAAATTTTTATTTGAAATTG
* * * ** * * * *
20873386 ACT-AGAAAA-CATATTTTTATTTTTTAAAATCTAAACTTTCTT-TTT---TTTT
1 -TTAAAAAAATCAAAACTTTA--TTTAAAAATC-AAAATTT-TTATTTGAAATTG
* ** * *
20873435 TTAAGAAAATCACTA-TTTTTCTTAAAAATCAAAATTTTTATTTCGAAATAG
1 TTAAAAAAATCAAAACTTTAT-TTAAAAATCAAAATTTTTATTT-GAAATTG
**
20873486 TTAAAAAAATCAAAACTTTATTTAAAAATTTAAATTTTT
1 TTAAAAAAATCAAAACTTTATTTAAAAATCAAAATTTTT
20873525 TCTTTAAAAT
Statistics
Matches: 141, Mismatches: 32, Indels: 32
0.69 0.16 0.16
Matches are distributed among these distances:
46 2 0.01
47 10 0.07
48 9 0.06
49 16 0.11
50 13 0.09
51 70 0.50
52 21 0.15
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (50 bp):
TTAAAAAAATCAAAACTTTATTTAAAAATCAAAATTTTTATTTGAAATTG
Found at i:20878303 original size:33 final size:33
Alignment explanation
Indices: 20878206--20878304 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
20878196 GCAGAATGCC
**
20878206 TTAATTCATCATGATGCCACCTCATAGACTCAA
1 TTAATTCATCATGATGCCACCTCATAGACTCGG
*
20878239 TTAATTCATCATGAGGCCACCTCATAGACTCGG
1 TTAATTCATCATGATGCCACCTCATAGACTCGG
*
20878272 TTAATTCATCATGATGCCACCTTATAGACTCGG
1 TTAATTCATCATGATGCCACCTCATAGACTCGG
20878305 CTGCCTTCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (33 bp):
TTAATTCATCATGATGCCACCTCATAGACTCGG
Done.