Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 61 of 109
Found at i:12143509 original size:20 final size:20
Alignment explanation
Indices: 12143487--12143551 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
12143477 TTACCCATTT
* *
12143487 GGGCCAGGCCCAAATGATCT
1 GGGCCAGGCCCAATTGATCC
* *
12143507 GGGTCAAGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
*
12143527 GGGTCAGGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
12143547 GGGCC
1 GGGCC
12143552 CGGACCTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (20 bp):
GGGCCAGGCCCAATTGATCC
Found at i:12143668 original size:12 final size:11
Alignment explanation
Indices: 12143653--12143766 Score: 84
Period size: 11 Copynumber: 10.9 Consensus size: 11
12143643 AACTCAACAT
12143653 TTTTATTTTTGA
1 TTTT-TTTTTGA
12143665 -TTTTTTTT-A
1 TTTTTTTTTGA
*
12143674 TTTTTGTTTTTA
1 TTTTT-TTTTGA
12143686 -TTTTTTTTGA
1 TTTTTTTTTGA
12143696 --TTTTTTTGA
1 TTTTTTTTTGA
12143705 TTTTTTTTTTGA
1 -TTTTTTTTTGA
*
12143717 TTTTTTGTT--
1 TTTTTTTTTGA
*
12143726 TTTGTTTTT--
1 TTTTTTTTTGA
*
12143735 TTTTTTTTTGT
1 TTTTTTTTTGA
**
12143746 TTTTTTTTTTT
1 TTTTTTTTTGA
12143757 TTTTTTTTTG
1 TTTTTTTTTG
12143767 GCCGAAGCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
9 25 0.29
10 14 0.16
11 38 0.44
12 10 0.11
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:12143669 original size:1 final size:1
Alignment explanation
Indices: 12143665--12143765 Score: 94
Period size: 1 Copynumber: 101.0 Consensus size: 1
12143655 TTATTTTTGA
* * * ** ** ** * *
12143665 TTTTTTTTATTTTTGTTTTTATTTTTTTTGATTTTTTTGATTTTTTTTTTGATTTTTTGTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
12143730 TTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12143766 GGCCGAAGCT
Statistics
Matches: 79, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.05, C:0.00, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:12143908 original size:81 final size:81
Alignment explanation
Indices: 12143773--12144136 Score: 556
Period size: 81 Copynumber: 4.5 Consensus size: 81
12143763 TTTGGCCGAA
* * * *
12143773 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
*
12143837 ACTTTGGAAAGTAAATT
65 ACTTTGAAAAGTAAATT
* * *
12143854 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAACTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
*
12143919 CTTGGAAAAGTAAATT
66 CTTTGAAAAGTAAATT
*
12143935 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
*
12143998 ACTTTGAAAAAATAAATT
65 ACTTTG-AAAAGTAAATT
*
12144016 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
12144081 CTTTGAAAAGTAAATT
66 CTTTGAAAAGTAAATT
12144097 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA-TAAAT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAAT
12144137 ACTCCTAGAC
Statistics
Matches: 258, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
79 3 0.01
80 46 0.18
81 158 0.61
82 48 0.19
83 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (81 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
CTTTGAAAAGTAAATT
Found at i:12144142 original size:40 final size:39
Alignment explanation
Indices: 12143773--12144136 Score: 464
Period size: 40 Copynumber: 9.0 Consensus size: 39
12143763 TTTGGCCGAA
* * *
12143773 GCTCCTCTAAACAGAGACTCAACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAG--GCAACGACTTTGGAAAATAAATT
*
12143814 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAAC-GACTTTGGAAAATAAATT
* * *
12143854 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAACT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAATAAATT
12143895 GCTCCTCTAAACAGAGGCAACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAA-TAAATT
12143935 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAA-TAAATT
* *
12143975 GCTCCTCTAAATAGAGGCAACGAACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTG-GAAAATAAATT
*
12144016 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAATAAATT
12144057 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAA-TAAATT
12144097 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAAT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAATAAAT
12144137 ACTCCTAGAC
Statistics
Matches: 293, Mismatches: 15, Indels: 30
0.87 0.04 0.09
Matches are distributed among these distances:
39 21 0.07
40 136 0.46
41 113 0.39
42 20 0.07
43 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (39 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGGAAAATAAATT
Found at i:12147802 original size:17 final size:17
Alignment explanation
Indices: 12147782--12147842 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 17
12147772 GTAAAAAAAA
12147782 TAAAAAATGAAAAATGT
1 TAAAAAATGAAAAATGT
12147799 TAAAAAAT--AAAATGT
1 TAAAAAATGAAAAATGT
* *
12147814 GAAAAAATGAGAAATGT
1 TAAAAAATGAAAAATGT
*
12147831 GAAAAAAATGAA
1 -TAAAAAATGAA
12147843 GAAAAATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.38
17 14 0.38
18 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (17 bp):
TAAAAAATGAAAAATGT
Found at i:12147810 original size:15 final size:16
Alignment explanation
Indices: 12147783--12147842 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 16
12147773 TAAAAAAAAT
*
12147783 AAAAAATGAAAAATGTT
1 AAAAAATG-AAAATGTG
12147800 AAAAAAT-AAAATGTG
1 AAAAAATGAAAATGTG
12147815 AAAAAATGAGAAATGTG
1 AAAAAATGA-AAATGTG
12147832 AAAAAAATGAA
1 -AAAAAATGAA
12147843 GAAAAATGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
15 14 0.36
16 1 0.03
17 15 0.38
18 9 0.23
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (16 bp):
AAAAAATGAAAATGTG
Found at i:12147856 original size:19 final size:18
Alignment explanation
Indices: 12147815--12147858 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
12147805 ATAAAATGTG
**
12147815 AAAAAATGAGAAATGTGA
1 AAAAAATGAGAAAAATGA
12147833 AAAAAATGAAGAAAAATGA
1 AAAAAATG-AGAAAAATGA
12147852 GAAAAAA
1 -AAAAAA
12147859 GTAATACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11
Consensus pattern (18 bp):
AAAAAATGAGAAAAATGA
Found at i:12149024 original size:24 final size:24
Alignment explanation
Indices: 12148995--12149126 Score: 194
Period size: 24 Copynumber: 5.5 Consensus size: 24
12148985 GTTAAAAATG
12148995 ATGAGAATCTTTAAAGAGTTTTAA
1 ATGAGAATCTTTAAAGAGTTTTAA
12149019 ATGAGAATCTTTAAAGAGTTTTAA
1 ATGAGAATCTTTAAAGAGTTTTAA
* * *
12149043 ATAAGAATTTTTAAAGATTTTTAA
1 ATGAGAATCTTTAAAGAGTTTTAA
*
12149067 ATGAGAATCTTTAAGGAGTTTTAA
1 ATGAGAATCTTTAAAGAGTTTTAA
*
12149091 ATTAGAATCTTT-AAGAAGTTTTAA
1 ATGAGAATCTTTAAAG-AGTTTTAA
*
12149115 ATGAAAATCTTT
1 ATGAGAATCTTT
12149127 GAATGAGAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 2 0.02
24 94 0.98
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (24 bp):
ATGAGAATCTTTAAAGAGTTTTAA
Found at i:12149605 original size:15 final size:15
Alignment explanation
Indices: 12149585--12149624 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
12149575 TGAACTTTAG
*
12149585 ATGTGAATCTCTTAA
1 ATGTGAATCTCTCAA
12149600 ATGTGAATCTCTCAA
1 ATGTGAATCTCTCAA
*
12149615 ATATGAATCT
1 ATGTGAATCT
12149625 TAAAATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (15 bp):
ATGTGAATCTCTCAA
Found at i:12149839 original size:17 final size:17
Alignment explanation
Indices: 12149787--12149862 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
12149777 CTTACAAACT
*
12149787 TGAAATCCTTG-ATA-A
1 TGAAATCCTTGCAAATA
* * **
12149802 TCAAATTCTTGCAAACC
1 TGAAATCCTTGCAAATA
12149819 TGAAATCCTTGCAAATA
1 TGAAATCCTTGCAAATA
*
12149836 TGAAAT-TTTGCAAATA
1 TGAAATCCTTGCAAATA
*
12149852 TGAAATTCTTG
1 TGAAATCCTTG
12149863 TGAAATTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
15 9 0.19
16 17 0.35
17 22 0.46
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (17 bp):
TGAAATCCTTGCAAATA
Found at i:12149848 original size:16 final size:16
Alignment explanation
Indices: 12149804--12149883 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 16
12149794 CTTGATAATC
**
12149804 AAATTCTTGCAAACCTG
1 AAATT-TTGCAAATATG
*
12149821 AAATCCTTGCAAATATG
1 AAAT-TTTGCAAATATG
12149838 AAATTTTGCAAATATG
1 AAATTTTGCAAATATG
*
12149854 AAATTCTTGTGAAAT-TG
1 AAATT-TTG-CAAATATG
*
12149871 AAATTTTGAAAAT
1 AAATTTTGCAAAT
12149884 TCTTGTGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
15 4 0.07
16 19 0.35
17 27 0.50
18 4 0.07
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (16 bp):
AAATTTTGCAAATATG
Found at i:12149856 original size:33 final size:32
Alignment explanation
Indices: 12149787--12149883 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 32
12149777 CTTACAAACT
* * **
12149787 TGAAATCCTTGATA-ATCAAATTCTTGCAAACC
1 TGAAATCCTTGAAATATGAAATT-TTGCAAATA
12149819 TGAAATCCTTGCAAATATGAAATTTTGCAAATA
1 TGAAATCCTTG-AAATATGAAATTTTGCAAATA
* *
12149852 TGAAATTCTTGTGAAAT-TGAAATTTTGAAAAT
1 TGAAA-TCCT-TGAAATATGAAATTTTGCAAAT
12149884 TCTTGTGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
32 11 0.20
33 28 0.51
34 14 0.25
35 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (32 bp):
TGAAATCCTTGAAATATGAAATTTTGCAAATA
Found at i:12149898 original size:26 final size:27
Alignment explanation
Indices: 12149854--12149904 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
12149844 TGCAAATATG
12149854 AAATTCTTGTGAAATTG-AAATTTTGA
1 AAATTCTTGTGAAATTGAAAATTTTGA
12149880 AAATTCTTGTG-AATCTGAAAATTTT
1 AAATTCTTGTGAAAT-TGAAAATTTT
12149905 TGCAAGCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 13 0.57
27 7 0.30
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (27 bp):
AAATTCTTGTGAAATTGAAAATTTTGA
Found at i:12150485 original size:16 final size:16
Alignment explanation
Indices: 12150460--12150495 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
12150450 GAAATAAAGC
12150460 AAAG-TCAAAAACAAA
1 AAAGATCAAAAACAAA
12150475 AAAGATCAAAAACAAA
1 AAAGATCAAAAACAAA
12150491 AAAGA
1 AAAGA
12150496 AAGGAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.75, C:0.11, G:0.08, T:0.06
Consensus pattern (16 bp):
AAAGATCAAAAACAAA
Found at i:12152640 original size:39 final size:39
Alignment explanation
Indices: 12152597--12152684 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
12152587 CCCTTCAAGT
**
12152597 ATTCAAAATAATTTAATTAAACTTTTATACTACTATTTC
1 ATTCAAAATAATTTAATTAAACCCTTATACTACTATTTC
12152636 ATTCAAAATAATTTAATTAAACCCTTATACTACTATTTC
1 ATTCAAAATAATTTAATTAAACCCTTATACTACTATTTC
*
12152675 A-TCTAAATAA
1 ATTCAAAATAA
12152685 GGCCCTCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 8 0.17
39 38 0.83
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (39 bp):
ATTCAAAATAATTTAATTAAACCCTTATACTACTATTTC
Found at i:12154437 original size:14 final size:15
Alignment explanation
Indices: 12154418--12154446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12154408 TTGTATTTAA
12154418 TATAAA-AATAATTT
1 TATAAATAATAATTT
12154432 TATAAATAATAATTT
1 TATAAATAATAATTT
12154447 AAAAAGTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAAATAATAATTT
Found at i:12154868 original size:2 final size:2
Alignment explanation
Indices: 12154861--12154885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12154851 TCAATAAATC
12154861 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
12154886 ATGCACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:12159667 original size:24 final size:24
Alignment explanation
Indices: 12159635--12159685 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
12159625 TGTCTTCAAC
*
12159635 TTTTTGACCTAGTGA-TTAAGAAAA
1 TTTTTGACCTAAT-ATTTAAGAAAA
12159659 TTTTTGACCTAATATTTAAGAAAA
1 TTTTTGACCTAATATTTAAGAAAA
12159683 TTT
1 TTT
12159686 AAAAAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (24 bp):
TTTTTGACCTAATATTTAAGAAAA
Found at i:12170614 original size:8 final size:8
Alignment explanation
Indices: 12170596--12170634 Score: 60
Period size: 8 Copynumber: 4.6 Consensus size: 8
12170586 TTCTGTAAAC
12170596 AATATAAAT
1 AATA-AAAT
12170605 AATAAAAT
1 AATAAAAT
12170613 AATAAAAT
1 AATAAAAT
12170621 AATAATAAT
1 AATAA-AAT
12170630 AATAA
1 AATAA
12170635 TTGATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 17 0.59
9 12 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:12170616 original size:3 final size:3
Alignment explanation
Indices: 12170602--12170635 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
12170592 AAACAATATA
12170602 AAT AAT AA- AAT AAT AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12170636 TGATATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:12170624 original size:11 final size:12
Alignment explanation
Indices: 12170602--12170635 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
12170592 AAACAATATA
12170602 AATAATAA-AAT
1 AATAATAATAAT
12170613 AATAA-AATAAT
1 AATAATAATAAT
12170624 AATAATAATAAT
1 AATAATAATAAT
12170636 TGATATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 13 0.62
12 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:12170781 original size:19 final size:21
Alignment explanation
Indices: 12170759--12170812 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
12170749 AATTTTTTTT
12170759 ATAATA-AAAAAATAAAAA-A
1 ATAATACAAAAAATAAAAATA
*
12170778 ATAA-ACAATAAATAAAAATA
1 ATAATACAAAAAATAAAAATA
12170798 ATAATCACAATAAAA
1 ATAAT-ACAA-AAAA
12170813 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 5 0.18
22 4 0.14
23 3 0.11
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAATACAAAAAATAAAAATA
Found at i:12170810 original size:22 final size:19
Alignment explanation
Indices: 12170768--12170811 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
12170758 TATAATAAAA
12170768 AAATAAAAAAATAAACAAT
1 AAATAAAAAAATAAACAAT
12170787 AAATAAAAATAATAATCACAAT
1 AAATAAAAA-AATAA--ACAAT
12170809 AAA
1 AAA
12170812 AATTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 5 0.23
22 8 0.36
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATAAAAAAATAAACAAT
Found at i:12173392 original size:22 final size:22
Alignment explanation
Indices: 12173350--12173439 Score: 71
Period size: 21 Copynumber: 4.1 Consensus size: 22
12173340 CCCAAAGATT
*
12173350 TTCAC-TCAAAAAATTT-TAAGA
1 TTCACATC-AAAAATTTCAAAGA
12173371 TTCACATCAAAAATTTCAAAGA
1 TTCACATCAAAAATTTCAAAGA
* *
12173393 TTCTTA-ATCGAAAATTTC-ATGA
1 TTC--ACATCAAAAATTTCAAAGA
* * *
12173415 TTCACATCTAAATTTTCAAAAA
1 TTCACATCAAAAATTTCAAAGA
12173437 TTC
1 TTC
12173440 TCATTCGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 23 0.41
22 20 0.36
23 11 0.20
24 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (22 bp):
TTCACATCAAAAATTTCAAAGA
Found at i:12173417 original size:44 final size:44
Alignment explanation
Indices: 12173359--12173449 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
12173349 TTTCACTCAA
* * *
12173359 AAAATTTTAAGATTCACATCAAAAATTTCAAAGATTCTTAATCG
1 AAAATTTCAAGATTCACATCAAAAATTTCAAAAATTCTCAATCG
* * * *
12173403 AAAATTTCATGATTCACATCTAAATTTTCAAAAATTCTCATTCG
1 AAAATTTCAAGATTCACATCAAAAATTTCAAAAATTCTCAATCG
12173447 AAA
1 AAA
12173450 GACCCCTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.35
Consensus pattern (44 bp):
AAAATTTCAAGATTCACATCAAAAATTTCAAAAATTCTCAATCG
Found at i:12174765 original size:24 final size:24
Alignment explanation
Indices: 12174736--12174787 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12174726 GTCCTATCAA
*
12174736 TTTCTTCTTCATT-TTTTTTCTCTC
1 TTTCTTCTT-ATTCTTTTTTCTCCC
*
12174760 TTTCTTCTTATTCTTTTTTTTCCC
1 TTTCTTCTTATTCTTTTTTCTCCC
12174784 TTTC
1 TTTC
12174788 ATCATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTCTTCTTATTCTTTTTTCTCCC
Found at i:12177706 original size:18 final size:17
Alignment explanation
Indices: 12177683--12177720 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
12177673 ATGCATGTGT
*
12177683 AAATGAATAACATACATA
1 AAATGAATAA-ATAAATA
12177701 AAATGAATAAATAAATA
1 AAATGAATAAATAAATA
12177718 AAA
1 AAA
12177721 CAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATGAATAAATAAATA
Found at i:12178514 original size:39 final size:37
Alignment explanation
Indices: 12178464--12178536 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 37
12178454 TAATTTATTT
12178464 TCAAAAATATC-TTCTAA-TATGTTGGTAAGATTTTCTA
1 TCAAAAATATCTTTC-AAGT-TGTTGGTAAGATTTTCTA
*
12178501 TCAAGAAATTATCTTTCAAGTTGTTGGTAGGATTTT
1 TCAA-AAA-TATCTTTCAAGTTGTTGGTAAGATTTT
12178537 TTTAAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
37 4 0.13
38 3 0.10
39 20 0.65
40 4 0.13
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (37 bp):
TCAAAAATATCTTTCAAGTTGTTGGTAAGATTTTCTA
Found at i:12179118 original size:28 final size:28
Alignment explanation
Indices: 12179087--12179147 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
12179077 AAATTTCAAA
*
12179087 GAAATAATCTAACCAATTCCTAAACCTT
1 GAAATAATCTAACCAATTCCTAAAACTT
*
12179115 GAAACAATCTAACCAATTCCTAAAACTT
1 GAAATAATCTAACCAATTCCTAAAACTT
12179143 GAAAT
1 GAAAT
12179148 TTAAGGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (28 bp):
GAAATAATCTAACCAATTCCTAAAACTT
Found at i:12179579 original size:4 final size:4
Alignment explanation
Indices: 12179570--12179595 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12179560 GAATTAAACA
12179570 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
12179596 GTCAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:12181049 original size:22 final size:22
Alignment explanation
Indices: 12181024--12181067 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12181014 TTTTTAAATC
12181024 TATTCAAAT-ATATTAAAAATTA
1 TATTCAAATAATA-TAAAAATTA
*
12181046 TATTTAAATAATATAAAAATTA
1 TATTCAAATAATATAAAAATTA
12181068 AAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTCAAATAATATAAAAATTA
Found at i:12182087 original size:7 final size:7
Alignment explanation
Indices: 12182050--12182077 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12182040 TTACATGTGC
12182050 TAAATTT
1 TAAATTT
12182057 TAAATTT
1 TAAATTT
12182064 TAAATTT
1 TAAATTT
12182071 TAAATTT
1 TAAATTT
12182078 ATTAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAAATTT
Found at i:12185454 original size:61 final size:61
Alignment explanation
Indices: 12185291--12185456 Score: 183
Period size: 61 Copynumber: 2.7 Consensus size: 61
12185281 ACTAATAATT
* * * * *
12185291 TAATTATGGTAGAAAAAG-CATTATAGTAATTTTAGTTAATGATAGTAGGAGAGTATTTTCA
1 TAATTATGATA-AAAAAGACATTATAATAATTTTAATTAATTATAGTAGGAGAGTATTTTAA
* ** * * ** *
12185352 TAATTATGACT-ATAGGGACATTATAATAACTTTGACCAATTATAGTAGGAGGGTATTTTAA
1 TAATTATGA-TAAAAAAGACATTATAATAATTTTAATTAATTATAGTAGGAGAGTATTTTAA
12185413 TAATTATGATAAAAAAGACATTATAATAATTTTAATTAATTATA
1 TAATTATGATAAAAAAGACATTATAATAATTTTAATTAATTATA
12185457 AAAGAAGTGG
Statistics
Matches: 82, Mismatches: 20, Indels: 6
0.76 0.19 0.06
Matches are distributed among these distances:
60 4 0.05
61 77 0.94
62 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (61 bp):
TAATTATGATAAAAAAGACATTATAATAATTTTAATTAATTATAGTAGGAGAGTATTTTAA
Found at i:12185822 original size:26 final size:26
Alignment explanation
Indices: 12185793--12185842 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12185783 GGGCATTATC
12185793 GTAAT-TTATTTTAATTTATGATAAGA
1 GTAATATTATTTTAA-TTATGATAAGA
*
12185819 GTAATATTTTTTTAATTATGATAA
1 GTAATATTATTTTAATTATGATAA
12185843 AAAATATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (26 bp):
GTAATATTATTTTAATTATGATAAGA
Found at i:12185848 original size:24 final size:28
Alignment explanation
Indices: 12185796--12185850 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
12185786 CATTATCGTA
*
12185796 ATTTATTTTAATTTATGATAAGAGTAAT
1 ATTTATTTTAATTTATGATAAGAGAAAT
12185824 ATTT-TTTTAA-TTATGATAA-A-AAAT
1 ATTTATTTTAATTTATGATAAGAGAAAT
12185848 ATT
1 ATT
12185851 GTAGACATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 1 0.04
26 9 0.35
27 6 0.23
28 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (28 bp):
ATTTATTTTAATTTATGATAAGAGAAAT
Found at i:12186082 original size:14 final size:14
Alignment explanation
Indices: 12186063--12186113 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
12186053 CCCAAGCCAC
12186063 CTTACCTTGCACCT
1 CTTACCTTGCACCT
* *
12186077 CTTACCCTTACAACCC
1 CTTA-CCTTGC-ACCT
12186093 CTCTACCTTGCACCT
1 CT-TACCTTGCACCT
12186108 CTTACC
1 CTTACC
12186114 ATGGCAGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 8 0.27
15 10 0.33
16 10 0.33
17 2 0.07
ACGTcount: A:0.18, C:0.47, G:0.04, T:0.31
Consensus pattern (14 bp):
CTTACCTTGCACCT
Found at i:12188523 original size:62 final size:61
Alignment explanation
Indices: 12188398--12188557 Score: 162
Period size: 62 Copynumber: 2.6 Consensus size: 61
12188388 TTTGTAAGAC
* * * *
12188398 ATTTTTGTAATTATGATAGGAGAATATTATAATAATTTTAATCAATCATGGTAGTAGAGAT
1 ATTTTTGTAATTATAATAGAAGAATATTATAATAATTTTAATAAATCATCGTAGTAGAGAT
* * *
12188459 ATTTTTGTAATTATAATAGAACGAATATTATAATAATTTTAGTAAATTATACG-ATTAG-GAAT
1 ATTTTTGTAATTATAATAGAA-GAATATTATAATAATTTTAATAAATCAT-CGTAGTAGAG-AT
** * ** *
12188521 ATTTTCATAATTATAATATAAGGGTATTATAGTAATT
1 ATTTTTGTAATTATAATAGAAGAATATTATAATAATT
12188558 CATCATTTAT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
61 33 0.40
62 49 0.59
63 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.42
Consensus pattern (61 bp):
ATTTTTGTAATTATAATAGAAGAATATTATAATAATTTTAATAAATCATCGTAGTAGAGAT
Found at i:12188702 original size:31 final size:34
Alignment explanation
Indices: 12188637--12188705 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 34
12188627 TAAGGGTATT
*
12188637 TTTATCATTTAAGAAAGAAGGGATGTTATAATAA
1 TTTATCATTTAAGAAAGAAGGGATATTATAATAA
* *
12188671 TTTATCA-TTAA-AAAG-AGGGATATTTTTATAA
1 TTTATCATTTAAGAAAGAAGGGATATTATAATAA
12188702 TTTA
1 TTTA
12188706 ATATAGGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 17 0.53
32 4 0.12
33 4 0.12
34 7 0.22
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (34 bp):
TTTATCATTTAAGAAAGAAGGGATATTATAATAA
Found at i:12198611 original size:356 final size:353
Alignment explanation
Indices: 12197624--12198735 Score: 1392
Period size: 355 Copynumber: 3.1 Consensus size: 353
12197614 TTACCAAAAG
* ** * * *
12197624 TTTTTCGGATTATTAAAGGTGTCTTTTATTATGAAACGCCTTCAATAAACCATGATGGTTATAGA
1 TTTTTTGGATTATTAAAGGCATATTTTATTATGAAATGCCTTCAATATACCATGATGGTTAT-GA
* * * ***
12197689 AGGCATTTATTCGAAAAGATGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGAAAT
65 AAGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGT
* * * *
12197754 TTGTTAATAATAGATGCCTTCAAAATTTTTTCACTAAAAATTTTGGGAATCATTAAAGG-CATCT
130 TTGTTAATAACAGACGCCTTCAAAAATTTTTCACTAAAAATTTT-GGAATCATTAAAGGACTTCT
* *** * *
12197818 ACGGTAAAATGTATTAC-ATATACTGTCATATAAATTTTAACACAGTTATTGAAGGCGTATATCC
194 ACTGTAAAATACCTT-CTATATACCGTCACATAAATTTTAACACAGTTATTGAAGGCGTATATCC
* * *
12197882 AAGAAAGATGCATTTAATAA-TTTTATCATAGTTTGTAGATAATTAGTGAAGGCGATTACAGATA
258 AAGAAAGAAGCATTTAATAATTTTTATCATAGTTTGTAAATAATTAGTGAAGGCGATTGCAGATA
* *
12197946 ACAGTACCTTCAATAATTTTTCTAAAAAAAT
323 ACAATACCTTCAATAATTTTTCTAAAAAATT
* * * *
12197977 TTTTTTGGATTATTAAAGGCGTCTTTTATTATGAAATGCCTTCAATATACTATAATGGTTATGAA
1 TTTTTTGGATTATTAAAGGCATATTTTATTATGAAATGCCTTCAATATACCATGATGGTTATGAA
* * * *
12198042 AGACGTTTATTCGAAAAAACGTCTTTAATATACCTTTAAACTTAGTAATCCATTACTTAAGGCGT
66 AG-CGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGT
* * * *
12198107 TTATTAATAACAAACGCCTTC-AAAATTTTCCCATTAAAAATTTTGAGAATCATTAAAAGCGACT
130 TTGTTAATAACAGACGCCTTCAAAAATTTT-TCACTAAAAATTTTG-GAATCATT-AAAG-GACT
* * *
12198171 TCTACTATAAAATACCTT-TATATACCGTCACATAAATTTTAATATAGTTATTGAAGGCGTATAT
191 TCTACTGTAAAATACCTTCTATATACCGTCACATAAATTTTAACACAGTTATTGAAGGCGTATAT
* * * *
12198235 CCAAGAAAGATA-AATTTAATAATTTTTATCACAGTTTGTATATAATTAGTGAAGGCGATTGTAG
256 CCAAGAAAGA-AGCATTTAATAATTTTTATCATAGTTTGTAAATAATTAGTGAAGGCGATTGCAG
*
12198299 ATAACAATACCTTTAATAATTTTTCT-AAAAATT
320 ATAACAATACCTTCAATAATTTTTCTAAAAAATT
* * * * * *
12198332 TTTTTTAGATCATTAAAGGCATTTTTTATTATGACATGCCTTTAATATACCACGATGGTTATGGA
1 TTTTTTGGATTATTAAAGGCATATTTTATTATGAAATGCCTTCAATATACCATGATGGTTAT-GA
* * * * *
12198397 ATGTGTTTATTCGAAAAGGCACCTTCAATATATCTTTAAACTTAGTAATCCATTACTGAAGGCGT
65 AAGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGT
* *
12198462 TTGTTAATAACAGACGCTTTCAAAAATTTTTCACTAAAAATTTTAGGAATTATTAAAGGTATCTT
130 TTGTTAATAACAGACGCCTTCAAAAATTTTTCACTAAAAATTTT-GGAATCATTAAAGG-A-CTT
* * * *
12198527 CTATTGTAAAATACCTTCTATATACCATCACATAAATTCTAACACGGTTATTGAAGGCGTATATC
192 CTACTGTAAAATACCTTCTATATACCGTCACATAAATTTTAACACAGTTATTGAAGGCGTATATC
* * ***
12198592 CAAGAAAGAAGCTTTTAATAATTTCTATCATAGTTTGTAAATAATTAGTGAAAATGATTGCAGAT
257 CAAGAAAGAAGCATTTAATAATTTTTATCATAGTTTGTAAATAATTAGTGAAGGCGATTGCAGAT
*
12198657 AACAATACCTTCAATAATTTTTTTAAAAAATT
322 AACAATACCTTCAATAATTTTTCTAAAAAATT
* * * *
12198689 CTTTTTGGATTATTAAAAGCATATTTTATTATAAAACGCCTTCAATA
1 TTTTTTGGATTATTAAAGGCATATTTTATTATGAAATGCCTTCAATA
12198736 ATTTGTTATA
Statistics
Matches: 649, Mismatches: 93, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
352 12 0.02
353 147 0.23
354 9 0.01
355 230 0.35
356 206 0.32
357 45 0.07
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (353 bp):
TTTTTTGGATTATTAAAGGCATATTTTATTATGAAATGCCTTCAATATACCATGATGGTTATGAA
AGCGTTTATTCGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTT
TGTTAATAACAGACGCCTTCAAAAATTTTTCACTAAAAATTTTGGAATCATTAAAGGACTTCTAC
TGTAAAATACCTTCTATATACCGTCACATAAATTTTAACACAGTTATTGAAGGCGTATATCCAAG
AAAGAAGCATTTAATAATTTTTATCATAGTTTGTAAATAATTAGTGAAGGCGATTGCAGATAACA
ATACCTTCAATAATTTTTCTAAAAAATT
Found at i:12200404 original size:63 final size:63
Alignment explanation
Indices: 12200305--12200426 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
12200295 AAAATAGTTC
12200305 AAGTTTATAAGTCTTTATGCAATATAGCCTCTGATCTATATATGTGATTGACGTAATTTCTTG
1 AAGTTTATAAGTCTTTATGCAATATAGCCTCTGATCTATATATGTGATTGACGTAATTTCTTG
* *
12200368 AAGTTTATAAGTCTTTATGCAATATAGCCTTTGATCTTTATATGTGATTGACGTAATTT
1 AAGTTTATAAGTCTTTATGCAATATAGCCTCTGATCTATATATGTGATTGACGTAATTT
12200427 TTTTTATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (63 bp):
AAGTTTATAAGTCTTTATGCAATATAGCCTCTGATCTATATATGTGATTGACGTAATTTCTTG
Found at i:12205129 original size:22 final size:24
Alignment explanation
Indices: 12205075--12205132 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
12205065 TTTGGAAAGG
*
12205075 TATTACAAAAATTTTAATCCATTAT
1 TATTA-AAAAATTTTAATCAATTAT
12205100 TA-TAAAAATATTTTAAT-AATTA-
1 TATTAAAAA-ATTTTAATCAATTAT
12205122 TATTAAAAAAT
1 TATTAAAAAAT
12205133 ATATTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.13
23 14 0.47
24 10 0.33
25 2 0.07
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTAAAAAATTTTAATCAATTAT
Found at i:12205143 original size:26 final size:25
Alignment explanation
Indices: 12205097--12205146 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
12205087 TTTAATCCAT
12205097 TATTATAAAAATATTTTAATAATTA
1 TATTATAAAAATATTTTAATAATTA
12205122 TATTA-AAAAATATATTATAATAATT
1 TATTATAAAAATAT-TT-TAATAATT
12205147 TTAATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTATAAAAATATTTTAATAATTA
Found at i:12205150 original size:23 final size:24
Alignment explanation
Indices: 12205097--12205150 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
12205087 TTTAATCCAT
* *
12205097 TATTATAAAAATATTTTAATAATTA
1 TATTA-AAAAATATATTAATAATAA
12205122 TATTAAAAAATATATT-ATAATAA
1 TATTAAAAAATATATTAATAATAA
*
12205145 TTTTAA
1 TATTAA
12205151 TTAATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 10 0.38
25 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTAAAAAATATATTAATAATAA
Found at i:12206738 original size:24 final size:24
Alignment explanation
Indices: 12206698--12206744 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12206688 CTTAAATTCA
12206698 AGTTTTCACATAAAAAAGTTTATT
1 AGTTTTCACATAAAAAAGTTTATT
*
12206722 AGTTTTTACA-AAGAAAAGTTTAT
1 AGTTTTCACATAA-AAAAGTTTAT
12206745 CTCATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (24 bp):
AGTTTTCACATAAAAAAGTTTATT
Found at i:12208733 original size:2 final size:2
Alignment explanation
Indices: 12208722--12208756 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12208712 AAGTCGCAGA
12208722 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12208757 CTGACACGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12213239 original size:13 final size:13
Alignment explanation
Indices: 12213221--12213248 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12213211 AACAAGCTCA
12213221 AGGAGGGAAATTC
1 AGGAGGGAAATTC
12213234 AGGAGGGAAATTC
1 AGGAGGGAAATTC
12213247 AG
1 AG
12213249 TATCTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.39, T:0.14
Consensus pattern (13 bp):
AGGAGGGAAATTC
Found at i:12217376 original size:22 final size:23
Alignment explanation
Indices: 12217345--12217418 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 23
12217335 TGATTTAAAG
* *
12217345 TTTTAGTAAAAAT-TATATATGA
1 TTTTAATAAAAATATAAATATGA
12217367 TTTTAATAAAAATAAATAAATATGA
1 TTTTAATAAAAAT--ATAAATATGA
12217392 TTTTAATAAAAATAAATAAATAT-A
1 TTTTAATAAAAAT--ATAAATATGA
12217416 TTT
1 TTT
12217419 CGTATTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
22 12 0.26
24 4 0.09
25 31 0.66
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTTAATAAAAATATAAATATGA
Found at i:12217426 original size:31 final size:25
Alignment explanation
Indices: 12217361--12217418 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
12217351 TAAAAATTAT
12217361 ATATGATTTTAATAAAAATAAATAA
1 ATATGATTTTAATAAAAATAAATAA
12217386 ATATGATTTTAATAAAAATAAATAA
1 ATATGATTTTAATAAAAATAAATAA
12217411 ATAT-ATTT
1 ATATGATTT
12217419 CGTATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (25 bp):
ATATGATTTTAATAAAAATAAATAA
Found at i:12227660 original size:69 final size:69
Alignment explanation
Indices: 12227544--12227681 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
12227534 CTTATATCTC
* *
12227544 ATGATTAACTTCTCCTTAGGACCATGACATCGAGGAAAGACCATGACATCCTCCTCCACTCCAAC
1 ATGATTAACTTCTCCTTAGGACCATGACACCGAGGAAAGACCATGACATACTCCTCCACTCCAAC
12227609 ACAA
66 ACAA
* * *
12227613 ATGATTAACTTCTCTTTAGGACCATGACACCGAGGAAGGACCGTGACATACTCCTCCACTCCAAC
1 ATGATTAACTTCTCCTTAGGACCATGACACCGAGGAAAGACCATGACATACTCCTCCACTCCAAC
12227678 ACAA
66 ACAA
12227682 GCCCACTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (69 bp):
ATGATTAACTTCTCCTTAGGACCATGACACCGAGGAAAGACCATGACATACTCCTCCACTCCAAC
ACAA
Found at i:12228102 original size:243 final size:243
Alignment explanation
Indices: 12227652--12228123 Score: 624
Period size: 243 Copynumber: 1.9 Consensus size: 243
12227642 CCGAGGAAGG
* *
12227652 ACCGTGACATACTCCTCCACTCCAACACAAGCCCACTATCTTCGGTGGCATATCACTAGTACCTC
1 ACCGTGACATACTCCTCCACTCCAACACAAGCCCACTATCTTCGATGGCACATCACTAGTACCTC
* * * **
12227717 TAGAGTTGACTCTGATACCAAGGACTCTTCTACGTCTCATGACCAACTTCTCTCTAGGACCGTGA
66 TAGAGTTGACTCCGATACCAAGGACTCTTCTACATCTCATGACCAACTTCTCTCTAAGACAATGA
* * * * * * *
12227782 CATACTCTCCCCTTGCAACGAAAGTCTATAGAGAAAAGATCGGGTTGAGATTTAAGCTCTAGGCT
131 CATACTCTCCCCTTCCAACGAAAGCCTACAGAGAAAAGATCAGGTCGAGACTTAAACTCTAGGCT
* *
12227847 CGTGCTGCTTCAAGACACGAAGATGGACTTTTTCGTGTCCTAGATTAA
196 CGTGCCGCTTCAAGACACGAAGATAGACTTTTTCGTGTCCTAGATTAA
* * * * * *
12227895 ACCGTGACATCCTCTTCCACTCCAACAGAGGCCCACTGTCTTCGATGGCACATCACTAGTACTTC
1 ACCGTGACATACTCCTCCACTCCAACACAAGCCCACTATCTTCGATGGCACATCACTAGTACCTC
* * * * *
12227960 TAGAGTTGACTCCGATACCATGGACTCTTCTACATCTCATGATCAATTTCTTTTTAAGACAATGA
66 TAGAGTTGACTCCGATACCAAGGACTCTTCTACATCTCATGACCAACTTCTCTCTAAGACAATGA
* *
12228025 CAT-C-CTCCCTTACTCCAACGAAAGCCTACAGAGAAAAGATCAGGTCGAGACTTAAACTCTATG
131 CATACTCTCCCCT--TCCAACGAAAGCCTACAGAGAAAAGATCAGGTCGAGACTTAAACTCTAGG
* * *
12228088 TTCGTGCCGCTTCAAGACATGGAGATAGACTTTTTC
194 CTCGTGCCGCTTCAAGACACGAAGATAGACTTTTTC
12228124 ACATTCTAAA
Statistics
Matches: 195, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
241 6 0.03
242 1 0.01
243 188 0.96
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (243 bp):
ACCGTGACATACTCCTCCACTCCAACACAAGCCCACTATCTTCGATGGCACATCACTAGTACCTC
TAGAGTTGACTCCGATACCAAGGACTCTTCTACATCTCATGACCAACTTCTCTCTAAGACAATGA
CATACTCTCCCCTTCCAACGAAAGCCTACAGAGAAAAGATCAGGTCGAGACTTAAACTCTAGGCT
CGTGCCGCTTCAAGACACGAAGATAGACTTTTTCGTGTCCTAGATTAA
Found at i:12230791 original size:16 final size:16
Alignment explanation
Indices: 12230772--12230802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12230762 AATGATAAGG
*
12230772 ATGATTTATGATGATA
1 ATGATTTACGATGATA
12230788 ATGATTTACGATGAT
1 ATGATTTACGATGAT
12230803 TTTTAATGAT
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:0.35, C:0.03, G:0.19, T:0.42
Consensus pattern (16 bp):
ATGATTTACGATGATA
Found at i:12250438 original size:59 final size:58
Alignment explanation
Indices: 12250372--12250518 Score: 158
Period size: 58 Copynumber: 2.5 Consensus size: 58
12250362 TAATTTATGT
*
12250372 TAAAAATTTTATTTGG-TATAAATTAAAATTTTAAAAATTTATTAGAAACA-AATTAAAA-A
1 TAAAAA-TTTATTTGGATATAAATTAAAA-ATTAAAAATTTATT-GAAACATAA-TAAAATA
* * * *
12250431 TAAAAATTTATTTGGATTTAAATTAAAAATTAAGAATTTATTTAAATATAATAAAATA
1 TAAAAATTTATTTGGATATAAATTAAAAATTAAAAATTTATTGAAACATAATAAAATA
** *
12250489 TAAAAATTTATTTAAATA-AAATTATAAATT
1 TAAAAATTTATTTGGATATAAATTAAAAATT
12250519 TTATATATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
57 20 0.26
58 39 0.51
59 17 0.22
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (58 bp):
TAAAAATTTATTTGGATATAAATTAAAAATTAAAAATTTATTGAAACATAATAAAATA
Found at i:12250502 original size:28 final size:28
Alignment explanation
Indices: 12250403--12250517 Score: 108
Period size: 28 Copynumber: 4.0 Consensus size: 28
12250393 ATTAAAATTT
* *
12250403 TAAAAATTTATTAGAAACA-AATTAAAAA
1 TAAAAATTTATT-TAAATATAATTAAAAA
** *
12250431 TAAAAATTTATTTGGATTTAAATTAAAAA
1 TAAAAATTTATTTAAATAT-AATTAAAAA
*
12250460 TTAAGAATTTATTTAAATATAA-TAAAATA
1 -TAAAAATTTATTTAAATATAATTAAAA-A
* *
12250489 TAAAAATTTATTTAAATAAAATTATAAA
1 TAAAAATTTATTTAAATATAATTAAAAA
12250517 T
1 T
12250518 TTTATATATT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 38 0.54
29 16 0.23
30 15 0.21
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (28 bp):
TAAAAATTTATTTAAATATAATTAAAAA
Found at i:12251946 original size:10 final size:12
Alignment explanation
Indices: 12251917--12251941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12251907 AAAATGAAAT
12251917 AGAAAATATATA
1 AGAAAATATATA
12251929 AGAAAATATATA
1 AGAAAATATATA
12251941 A
1 A
12251942 AAATAAAATA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AGAAAATATATA
Found at i:12251951 original size:15 final size:15
Alignment explanation
Indices: 12251931--12251960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12251921 AATATATAAG
*
12251931 AAAATATATAAAAAT
1 AAAATAAATAAAAAT
12251946 AAAATAAATAAAAAT
1 AAAATAAATAAAAAT
12251961 GTAATTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAAATAAAAAT
Found at i:12252327 original size:20 final size:19
Alignment explanation
Indices: 12252302--12252339 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
12252292 CTTAAAACTC
12252302 AGATTTTTCTAGAAGTTTTT
1 AGATTTTTCTAGAA-TTTTT
12252322 AGATTTTTCTAGAATTTT
1 AGATTTTTCTAGAATTTT
12252340 CTCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (19 bp):
AGATTTTTCTAGAATTTTT
Found at i:12252334 original size:10 final size:10
Alignment explanation
Indices: 12252306--12252356 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
12252296 AAACTCAGAT
12252306 TTTTCTAGAA
1 TTTTCTAGAA
*
12252316 GTTTT-TAGAT
1 -TTTTCTAGAA
12252326 TTTTCTAGAA
1 TTTTCTAGAA
*
12252336 TTTTCTCAAAA
1 TTTTCT-AGAA
12252347 TTTTCTAGAA
1 TTTTCTAGAA
12252357 AATTTTCCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.12
10 17 0.50
11 13 0.38
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (10 bp):
TTTTCTAGAA
Found at i:12252759 original size:3 final size:3
Alignment explanation
Indices: 12252751--12252850 Score: 92
Period size: 3 Copynumber: 33.3 Consensus size: 3
12252741 TAAATAAATA
** * * * * * *
12252751 AAT AAT AAT AAT AAT AAT AAT TGT AAT AGT AGT AGT AAT AGT AGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
12252799 AAT AGT AGT AGT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12252847 AAT A
1 AAT A
12252851 GTAAATACAA
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12253274 original size:64 final size:65
Alignment explanation
Indices: 12253194--12253340 Score: 161
Period size: 65 Copynumber: 2.3 Consensus size: 65
12253184 ACTGAACCGT
* * * * * * * *
12253194 AAGTTAAAAAGGTAAAATGATTTGGACCAAGCTAAAATC-AAATAGGTGATCACGATTGAACCGC
1 AAGTCAAAAAAGTAAAATGATCTGGACCAAGCCAAAATCAAAACAAGTGATCAAGATTGAACAGC
* * * * *
12253258 GAGTCAGAAAAGTAAAATGATCTGGACGAAGCCGAGATCAAAACAAGTGATCAAGATTGAACAGC
1 AAGTCAAAAAAGTAAAATGATCTGGACCAAGCCAAAATCAAAACAAGTGATCAAGATTGAACAGC
*
12253323 AAGTCAAAAAAATAAAAT
1 AAGTCAAAAAAGTAAAAT
12253341 AATCCAAACT
Statistics
Matches: 66, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
64 30 0.45
65 36 0.55
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (65 bp):
AAGTCAAAAAAGTAAAATGATCTGGACCAAGCCAAAATCAAAACAAGTGATCAAGATTGAACAGC
Found at i:12253328 original size:65 final size:64
Alignment explanation
Indices: 12253239--12253432 Score: 171
Period size: 65 Copynumber: 3.0 Consensus size: 64
12253229 AATCAAATAG
* * * *
12253239 GTGATCACGATTGAACCGCGAGTCAGAAAAGTAAAATGATCTGGACGAAGCCGAGATCAAAACAA
1 GTGATCAAGATTGAACAGCAAGTCAGAAAA-TAAAATAATCTGGACGAAGCCGAGATCAAAACAA
* *** *
12253304 GTGATCAAGATTGAACAGCAAGTCAAAAAAATAAAATAATCCAAACTG-AGCTGAGATCAAAACA
1 GTGATCAAGATTGAACAGCAAGTC-AGAAAATAAAATAATCTGGAC-GAAGCCGAGATCAAAACA
*
12253368 G
64 A
* * * *
12253369 GTGATCGAGATT--A-AGTCGAGAGTCAAGAAAATAAAATAATCTGGACTAAGCCAAGACCAAAA
1 GTGATCAAGATTGAACAG-C-A-AGTC-AGAAAATAAAATAATCTGGACGAAGCCGAGATCAAAA
12253431 CA
62 CA
12253433 TGGTAATACA
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 1 0.01
65 93 0.89
66 6 0.06
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (64 bp):
GTGATCAAGATTGAACAGCAAGTCAGAAAATAAAATAATCTGGACGAAGCCGAGATCAAAACAA
Found at i:12265474 original size:15 final size:17
Alignment explanation
Indices: 12265441--12265474 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12265431 TTAATCTTAC
12265441 TTATCTGTTCTTGGGTT
1 TTATCTGTTCTTGGGTT
12265458 TTATCTGTT-TT-GGTT
1 TTATCTGTTCTTGGGTT
12265473 TT
1 TT
12265475 CTTATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.06, C:0.09, G:0.21, T:0.65
Consensus pattern (17 bp):
TTATCTGTTCTTGGGTT
Found at i:12266355 original size:14 final size:14
Alignment explanation
Indices: 12266336--12266368 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12266326 TTTTTTAAAA
*
12266336 TTTTTTTGT-GTTT
1 TTTTTTTTTAGTTT
12266349 TTTTTTTTTAGTTT
1 TTTTTTTTTAGTTT
12266363 TTTTTT
1 TTTTTT
12266369 GCATGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTAGTTT
Found at i:12270852 original size:8 final size:8
Alignment explanation
Indices: 12270823--12270919 Score: 101
Period size: 8 Copynumber: 12.1 Consensus size: 8
12270813 CTAATGGATG
12270823 GAAAAAGAT
1 GAAAAA-AT
*
12270832 GAAAAAGAA
1 GAAAAA-AT
12270841 GAAAAAAT
1 GAAAAAAT
12270849 GAAAAAAAT
1 G-AAAAAAT
*
12270858 GAAAGAA-
1 GAAAAAAT
12270865 -AAAAAAT
1 GAAAAAAT
12270872 GAAAAAAT
1 GAAAAAAT
12270880 G-AAAAAT
1 GAAAAAAT
12270887 GAAAAAAT
1 GAAAAAAT
*
12270895 GAAACAAT
1 GAAAAAAT
*
12270903 AAAAAAAT
1 GAAAAAAT
*
12270911 GAAAGAAT
1 GAAAAAAT
12270919 G
1 G
12270920 GGAAAATGTA
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
6 5 0.07
7 7 0.09
8 41 0.55
9 22 0.29
ACGTcount: A:0.73, C:0.01, G:0.15, T:0.10
Consensus pattern (8 bp):
GAAAAAAT
Found at i:12270872 original size:23 final size:24
Alignment explanation
Indices: 12270835--12270898 Score: 98
Period size: 23 Copynumber: 2.8 Consensus size: 24
12270825 AAAAGATGAA
12270835 AAAGAAGAAAAAATGAAAAAAATG
1 AAAGAAGAAAAAATGAAAAAAATG
12270859 AAAGAA-AAAAAATG-AAAAAATG
1 AAAGAAGAAAAAATGAAAAAAATG
12270881 AAA-AATGAAAAAATGAAA
1 AAAGAA-GAAAAAATGAAA
12270899 CAATAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.05
22 11 0.30
23 16 0.43
24 8 0.22
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (24 bp):
AAAGAAGAAAAAATGAAAAAAATG
Found at i:12270876 original size:31 final size:31
Alignment explanation
Indices: 12270832--12270914 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
12270822 GGAAAAAGAT
*
12270832 GAAAAAGAA-GAAAAAATGAAAAAAATGAAA
1 GAAAAAAAATGAAAAAATGAAAAAAATGAAA
12270862 GAAAAAAAATGAAAAAATG--AAAAATGAAA
1 GAAAAAAAATGAAAAAATGAAAAAAATGAAA
*
12270891 -AAATGAAACAATAAAAAAATGAAA
1 GAAA--AAA-AATGAAAAAATGAAA
12270915 GAATGGGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 3 0.07
29 10 0.22
30 11 0.24
31 20 0.44
33 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (31 bp):
GAAAAAAAATGAAAAAATGAAAAAAATGAAA
Found at i:12270927 original size:16 final size:15
Alignment explanation
Indices: 12270841--12270919 Score: 90
Period size: 15 Copynumber: 5.1 Consensus size: 15
12270831 TGAAAAAGAA
12270841 GAAAAAATGAAAAAAAT
1 GAAAAAATG--AAAAAT
12270858 GAAAGAAA--AAAAAT
1 GAAA-AAATGAAAAAT
12270872 GAAAAAATGAAAAAT
1 GAAAAAATGAAAAAT
12270887 GAAAAAATGAAACAAT
1 GAAAAAATGAAA-AAT
*
12270903 AAAAAAATGAAAGAAT
1 GAAAAAATGAAA-AAT
12270919 G
1 G
12270920 GGAAAATGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
13 3 0.05
14 10 0.18
15 18 0.33
16 17 0.31
17 4 0.07
18 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.14, T:0.11
Consensus pattern (15 bp):
GAAAAAATGAAAAAT
Found at i:12270932 original size:24 final size:22
Alignment explanation
Indices: 12270841--12270919 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 22
12270831 TGAAAAAGAA
12270841 GAAAAAATGAAAAAAATGAAAGAA-
1 GAAAAAATG--AAAAATGAAA-AAT
12270865 -AAAAAATGAAAAAATGAAAAAT
1 GAAAAAATG-AAAAATGAAAAAT
*
12270887 GAAAAAATGAAACAATAAAAAAAT
1 GAAAAAATGAAA-AAT-GAAAAAT
*
12270911 GAAAGAATG
1 GAAAAAATG
12270920 GGAAAATGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.04
22 14 0.29
23 19 0.39
24 14 0.29
ACGTcount: A:0.73, C:0.01, G:0.14, T:0.11
Consensus pattern (22 bp):
GAAAAAATGAAAAATGAAAAAT
Found at i:12271722 original size:63 final size:63
Alignment explanation
Indices: 12271628--12271810 Score: 204
Period size: 63 Copynumber: 2.9 Consensus size: 63
12271618 GATTAGTGGG
** * * *
12271628 CAAAATTTGTTCTGAAATAATTAAGGCTGAGAAACCTATGATTGGTGACCAAGTGATGGAGGA
1 CAAAATTTGTTCTGAAATGGTTAATGCTGAGAAACCTATGAGTGGTGACCAAGTGATGAAGGA
* * * * * *
12271691 CGAAATTTGTTTTAAAATGGTTAATGCTGAGAAACCTATGAGTAGTGACCAAATGATTAAGGA
1 CAAAATTTGTTCTGAAATGGTTAATGCTGAGAAACCTATGAGTGGTGACCAAGTGATGAAGGA
* * * * ** *
12271754 TAAAATTTATTCTGAAATGGCTAGTATTAAGAAACCTATGAGTGGTGACCAAGTGAT
1 CAAAATTTGTTCTGAAATGGTTAATGCTGAGAAACCTATGAGTGGTGACCAAGTGAT
12271811 AGAAAATAGA
Statistics
Matches: 97, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 97 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (63 bp):
CAAAATTTGTTCTGAAATGGTTAATGCTGAGAAACCTATGAGTGGTGACCAAGTGATGAAGGA
Found at i:12271833 original size:63 final size:63
Alignment explanation
Indices: 12271720--12271841 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
12271710 GTTAATGCTG
** *
12271720 AGAAACCTATGAGTAGTGACCAAATGATTAAGGATAAAATTTATTCTGAAATGGCTAGTATTA
1 AGAAACCTATGAGTAGTGACCAAATGATTAAAAATAAAATTCATTCTGAAATGGCTAGTATTA
* * * *
12271783 AGAAACCTATGAGTGGTGACCAAGTGA-TAGAAAATAGAATTCATTTTGAAATGGCTAGT
1 AGAAACCTATGAGTAGTGACCAAATGATTA-AAAATAAAATTCATTCTGAAATGGCTAGT
12271842 GTTATAAAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (63 bp):
AGAAACCTATGAGTAGTGACCAAATGATTAAAAATAAAATTCATTCTGAAATGGCTAGTATTA
Found at i:12272337 original size:22 final size:21
Alignment explanation
Indices: 12272204--12272380 Score: 219
Period size: 21 Copynumber: 8.3 Consensus size: 21
12272194 ATGAATCCTT
*
12272204 AAATGAGAATCTTTGAATCTC
1 AAATGAGAATCTTTGAATTTC
12272225 AAATGAGAATCTTTGAATTTC
1 AAATGAGAATCTTTGAATTTC
* *
12272246 AATTGAGAATCTTTGAATTGC
1 AAATGAGAATCTTTGAATTTC
*
12272267 AAATGAGAATATTTGAATTTC
1 AAATGAGAATCTTTGAATTTC
* * * * *
12272288 AAATCATAATCATTAAATTTT
1 AAATGAGAATCTTTGAATTTC
*
12272309 AAATGAGAATCTTTGAGTTTTC
1 AAATGAGAATCTTTGA-ATTTC
*
12272331 AAATGAGAATCTTTGAGTTGTC
1 AAATGAGAATCTTTGAATT-TC
*
12272353 AAATGAGAATCTTTGAGTTTTC
1 AAATGAGAATCTTTGA-ATTTC
12272375 AAATGA
1 AAATGA
12272381 AAATATCTAA
Statistics
Matches: 133, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
21 86 0.65
22 45 0.34
23 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (21 bp):
AAATGAGAATCTTTGAATTTC
Found at i:12273034 original size:42 final size:41
Alignment explanation
Indices: 12272857--12273125 Score: 317
Period size: 41 Copynumber: 6.5 Consensus size: 41
12272847 GATTGTCGAT
*
12272857 GAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGC-ATTTATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAG
* * *
12272899 G-GCATTTATTTTTTCAAAGTTATGGTGTCTTTGTTTAGAG
1 GAGCATTTATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAG
** * * * *
12272939 GAGCATTTATTTTTCCAAAGTGGTAGTACCTTTATTTAGAG
1 GAGCATTTATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAG
* *
12272980 GAGCATTTATTTTTCCAAAGTTATGATGCCCTCTGTGTAGAG
1 GAGCATTTATTTTTCCAAAGTTATGGTG-CCTCTGTTTAGAG
* *
12273022 GAGTATTTATTTTT-CAAAGTTATGGTACCTCTGTTTAGAG
1 GAGCATTTATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAG
** * *
12273062 GAGCAATTTATTTTTCCAAAGTTGCGATGCCTCTATTTAGAG
1 GAGC-ATTTATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAG
*
12273104 GTGCATTTATTTTTCTCAAAGT
1 GAGCATTTATTTTTC-CAAAGT
12273126 CGTTGAGCTT
Statistics
Matches: 192, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
40 49 0.26
41 89 0.46
42 54 0.28
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (41 bp):
GAGCATTTATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAG
Found at i:12273401 original size:22 final size:23
Alignment explanation
Indices: 12273376--12273431 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 23
12273366 TTTAGCCCAA
*
12273376 CTATTTTTT-TTATTTTATTTAT
1 CTATTTTTTATTAGTTTATTTAT
12273398 CTATTTGTTATTATTAGTTTATTTAT
1 CTA-TT-TT-TTATTAGTTTATTTAT
*
12273424 TTATTTTT
1 CTATTTTT
12273432 AAGGTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 4 0.14
25 4 0.14
26 14 0.50
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (23 bp):
CTATTTTTTATTAGTTTATTTAT
Found at i:12274428 original size:24 final size:25
Alignment explanation
Indices: 12274376--12274431 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
12274366 AATAGATATT
12274376 AATTATCAAATGATGAAATTTATAGA
1 AATT-TCAAATGATGAAATTTATAGA
* * *
12274402 AATTTCAAATGGT-AAATTTTTATA
1 AATTTCAAATGATGAAATTTATAGA
12274426 AATTTC
1 AATTTC
12274432 TAGGTGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 8 0.30
26 4 0.15
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (25 bp):
AATTTCAAATGATGAAATTTATAGA
Found at i:12275540 original size:47 final size:47
Alignment explanation
Indices: 12275471--12275565 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
12275461 CTTTCCTTTT
12275471 TTCCTTATTCCTTTGTGTAATTTTTGCCTTTAATTTATAGCTTGTTC
1 TTCCTTATTCCTTTGTGTAATTTTTGCCTTTAATTTATAGCTTGTTC
12275518 TTCCTTATTCCTTTGTGTAATTTTTGCCTTTAATTTATAGCTTGTTC
1 TTCCTTATTCCTTTGTGTAATTTTTGCCTTTAATTTATAGCTTGTTC
12275565 T
1 T
12275566 AGTAGAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.58
Consensus pattern (47 bp):
TTCCTTATTCCTTTGTGTAATTTTTGCCTTTAATTTATAGCTTGTTC
Found at i:12275761 original size:3 final size:3
Alignment explanation
Indices: 12275753--12275804 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
12275743 GAAAAATGGA
12275753 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12275800 AAT AA
1 AAT AA
12275805 ATACAATGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12276517 original size:22 final size:23
Alignment explanation
Indices: 12276478--12276524 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
12276468 GGCTTTGTTT
*
12276478 TTGTGTTTTGATTTTTTTTATGCA
1 TTGTGTTTT-ATTTTTTTCATGCA
12276502 TTGTGTTTT-TTTTTTTCATGCA
1 TTGTGTTTTATTTTTTTCATGCA
12276524 T
1 T
12276525 GGTAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.68
Consensus pattern (23 bp):
TTGTGTTTTATTTTTTTCATGCA
Found at i:12276859 original size:382 final size:389
Alignment explanation
Indices: 12276139--12276897 Score: 988
Period size: 382 Copynumber: 2.0 Consensus size: 389
12276129 TAGCAACATC
* * * * * *
12276139 AAAATAATATGATTGTTCGGTTATTTTGAGATTTTAAGATGTTATTTTTAAGGTCGGTGTGTAGT
1 AAAACAATATGATTGTTCAGTTATTTTGAAAATTTAAGATGTTATTTTTAAGGTCAGCGTGTAGT
* * * *
12276204 GTGTTTCGCGCTTCTTTTTCATTTCTTGTTGCATCAAACTTTCTCTGTTTTTTTTTTCGTTTTCT
66 GTGTTTCGCACTTCTTTTTCATTTCTTATTGCATCAAACTTTCTCTGATTTTTTTTTCATTTTCT
*
12276269 TTTCAAGTTCGTTTTTTAATTTGGTCTCATGTTTCATCTATTTGTTTTTTGTTTTTTTTTTTTAT
131 TTTCAAGTTCGTTTTTTAATTTGGTCTCATGTTTCATCTATTTGTTTTTTGTTTTTTTTTGTTA-
* * *
12276334 TGATAGAGTAATTCCATATGAGTTAATTCAAAATTCAAATAATTTTAATGTTTTTTTCTATAAGT
195 T-ACAAAGTAATTCCATATGAGTTAACTCAAAATTCAAATAATTTTAATGTTTTTTTCTATAAGT
* *
12276399 ATGGGTATTTTGTGATCTACAATTTTTATTTTTCATGCATTATACAAATTATTATTTTTATGATT
259 ATGGGTATTTTGTAATCTACAATTTTTATTTTTCATGCATTACACAAATTATTATTTTTATGATT
12276464 TGTAGGCTTTGTTTTTGTGTTTTGA-TTTTTTT-TATGCATTGTGTTTTTTTTTTTCATGCATGG
324 TGTAGGCTTTGTTTTTGTGTTTTGATTTTTTTTCTATGCATTGTGTTTTTTTTTTTCATGCATGG
12276527 T
389 T
* *
12276528 AAAACAATATGATTG-TCTAGTTATTTTGAAAATTTAAGATGTTGTTTTTAAGGTTAGCGTGTAG
1 AAAACAATATGATTGTTC-AGTTATTTTGAAAATTTAAGATGTTATTTTTAAGGTCAGCGTGTAG
* * *
12276592 TGTGCTTT-GCACTT-TTTTT-ATTTCTTATTGCGTTAGACTTTCTCT-ATTTTTTTTTCATTTT
65 TGTG-TTTCGCACTTCTTTTTCATTTCTTATTGCATCAAACTTTCTCTGATTTTTTTTTCATTTT
* * *
12276653 TTCTTTCAAGTT-GATTTTTTCATTTGGTCTCATGTTTCATCTGTTTG-TTTTT-TTTTTTTTTG
129 CT-TTTCAAGTTCG-TTTTTTAATTTGGTCTCATGTTTCATCTATTTGTTTTTTGTTTTTTTTTG
** * * * *
12276715 TTA-ACAAAGTAATTTTA-AGTGGGTTAACTCATAATTCAAATAATTTTGATGTTTTTGTT-TGT
192 TTATACAAAGTAATTCCATA-TGAGTTAACTCAAAATTCAAATAATTTTAATGTTTTT-TTCTAT
* * * * * * *
12276777 -AGTTATGGGTATTTTGTAATTTACAATTTTTGTTTTTCATGTATTGCACAGATTGTTGTTTTTA
255 AAG-TATGGGTATTTTGTAATCTACAATTTTTATTTTTCATGCATTACACAAATTATTATTTTTA
* *
12276841 TGGTTTGTAGGTTTTGTTTTTGTGTTTTGATTTTTTTTCTATGCATTGTGTTTTTTT
319 TGATTTGTAGGCTTTGTTTTTGTGTTTTGATTTTTTTTCTATGCATTGTGTTTTTTT
12276898 CATGCAAGGT
Statistics
Matches: 322, Mismatches: 39, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
381 3 0.01
382 125 0.39
383 9 0.03
384 18 0.06
385 12 0.04
386 21 0.07
387 62 0.19
388 7 0.02
389 62 0.19
390 3 0.01
ACGTcount: A:0.20, C:0.08, G:0.15, T:0.56
Consensus pattern (389 bp):
AAAACAATATGATTGTTCAGTTATTTTGAAAATTTAAGATGTTATTTTTAAGGTCAGCGTGTAGT
GTGTTTCGCACTTCTTTTTCATTTCTTATTGCATCAAACTTTCTCTGATTTTTTTTTCATTTTCT
TTTCAAGTTCGTTTTTTAATTTGGTCTCATGTTTCATCTATTTGTTTTTTGTTTTTTTTTGTTAT
ACAAAGTAATTCCATATGAGTTAACTCAAAATTCAAATAATTTTAATGTTTTTTTCTATAAGTAT
GGGTATTTTGTAATCTACAATTTTTATTTTTCATGCATTACACAAATTATTATTTTTATGATTTG
TAGGCTTTGTTTTTGTGTTTTGATTTTTTTTCTATGCATTGTGTTTTTTTTTTTCATGCATGGT
Found at i:12286397 original size:49 final size:49
Alignment explanation
Indices: 12286324--12286420 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
12286314 TCCAAGAGCT
* *
12286324 AAGGTTAAAAAATGTTTTTCAATTGATGAATATGTAGTAAACTTTTTTA
1 AAGGTTAAAAAAGGTTTTTCAATTGATGAATATATAGTAAACTTTTTTA
*
12286373 AAGGTTAAAAAAGGTTTTTTAATTGATGAATATATAGTAAACTTTTTT
1 AAGGTTAAAAAAGGTTTTTCAATTGATGAATATATAGTAAACTTTTTT
12286421 CCTTCATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.43
Consensus pattern (49 bp):
AAGGTTAAAAAAGGTTTTTCAATTGATGAATATATAGTAAACTTTTTTA
Found at i:12292779 original size:28 final size:28
Alignment explanation
Indices: 12292705--12292805 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 28
12292695 GACTCATTTA
*
12292705 ATGTTATCCTTTTGTTAAACAGCTTCTG
1 ATGTTATACTTTTGTTAAACAGCTTCTG
* * * * *
12292733 ATGTTATAATGTTGCTAAATATCTAT-TG
1 ATGTTATACTTTTGTTAAACAGCT-TCTG
* *
12292761 ATGTTCTACTTTTGTTAAACAGC-TGTG
1 ATGTTATACTTTTGTTAAACAGCTTCTG
12292788 TATGTTATGA-TTTTGTTA
1 -ATGTTAT-ACTTTTGTTA
12292806 GAAAAGACTT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 51 0.91
29 2 0.04
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (28 bp):
ATGTTATACTTTTGTTAAACAGCTTCTG
Found at i:12293775 original size:68 final size:68
Alignment explanation
Indices: 12293666--12293804 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
12293656 CTCCTTGTGA
*
12293666 AAACTTAAACATAAAACCTTGTCTTTATCAAATACCAAGTAACAACAAAATGAAATACTCAATGC
1 AAACTTAAACATAAAACCTCGTCTTTATCAAATACCAAGTAACAACAAAATGAAATACTCAATGC
12293731 TTG
66 TTG
12293734 AAACTTAAACATAAAACCTCGTCTTTATCAAATACCAAGTAACAACAAAATGAAATACTCAATGC
1 AAACTTAAACATAAAACCTCGTCTTTATCAAATACCAAGTAACAACAAAATGAAATACTCAATGC
12293799 TTG
66 TTG
12293802 AAA
1 AAA
12293805 AAAAAAATGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.25
Consensus pattern (68 bp):
AAACTTAAACATAAAACCTCGTCTTTATCAAATACCAAGTAACAACAAAATGAAATACTCAATGC
TTG
Found at i:12296157 original size:2 final size:2
Alignment explanation
Indices: 12296150--12296178 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12296140 CGACCTGCAA
12296150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12296179 AAATTTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12296766 original size:30 final size:31
Alignment explanation
Indices: 12296699--12296767 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
12296689 ATGCATGGGT
* *
12296699 ACTAAATTTCTTAAAAAATAATACTATAGGG
1 ACTAAATTTCTTAAAAAATAATACTACAAGG
* ** *
12296730 ATTAAATTTCTT-AAAAATAATTTTACAATG
1 ACTAAATTTCTTAAAAAATAATACTACAAGG
12296760 ACTAAATT
1 ACTAAATT
12296768 GTTTTAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (31 bp):
ACTAAATTTCTTAAAAAATAATACTACAAGG
Found at i:12298950 original size:22 final size:20
Alignment explanation
Indices: 12298900--12298953 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
12298890 AAAGGGTTTG
*
12298900 TGATAAAAATTATTATATTT
1 TGATAAAAATTATTATAATT
*
12298920 TGACAAAAATTATATATAAATT
1 TGATAAAAATTAT-TAT-AATT
*
12298942 TGATGAAAATTA
1 TGATAAAAATTA
12298954 AAAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 3 0.11
22 13 0.46
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
TGATAAAAATTATTATAATT
Found at i:12305386 original size:19 final size:18
Alignment explanation
Indices: 12305361--12305408 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
12305351 ATTCTTCAAT
*
12305361 TTTATATTTGAT-TTTTTA
1 TTTATATTT-ATCTTTATA
12305379 TATTATATTTATCTTTATA
1 T-TTATATTTATCTTTATA
12305398 TTTATATTTAT
1 TTTATATTTAT
12305409 AAAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATATTTATCTTTATA
Found at i:12305395 original size:6 final size:6
Alignment explanation
Indices: 12305361--12305409 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
12305351 ATTCTTCAAT
* *
12305361 TTTATA TTTGAT- TTTTTA TATTATA TTTATC TTTATA TTTATA TTTATA
1 TTTATA TTT-ATA TTTATA T-TTATA TTTATA TTTATA TTTATA TTTATA
12305410 AAATATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 1 0.03
6 28 0.78
7 7 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:12306458 original size:2 final size:2
Alignment explanation
Indices: 12306453--12306483 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12306443 TATCTATTTA
12306453 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12306484 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12306488 original size:2 final size:2
Alignment explanation
Indices: 12306483--12306507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12306473 TCTCTCTCTC
12306483 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12306508 TCTTACAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12306939 original size:29 final size:29
Alignment explanation
Indices: 12306900--12306959 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
12306890 AATTAATAAA
* *
12306900 TTTATAATTTAAAAATTATATTAAAAATT
1 TTTAAAATTTAAAAATCATATTAAAAATT
* *
12306929 TTTAAAATTTAAATATCATATTAAATATT
1 TTTAAAATTTAAAAATCATATTAAAAATT
12306958 TT
1 TT
12306960 ATTATAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTAAAATTTAAAAATCATATTAAAAATT
Found at i:12307560 original size:15 final size:17
Alignment explanation
Indices: 12307522--12307555 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12307512 TTATTTTTAA
*
12307522 ATTTTATAAAATAATAT
1 ATTTTAAAAAATAATAT
12307539 ATTTTAAAAAATAATAT
1 ATTTTAAAAAATAATAT
12307556 TTTAACTAAC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTAAAAAATAATAT
Found at i:12312279 original size:20 final size:20
Alignment explanation
Indices: 12312243--12312281 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12312233 ATGTATAATA
12312243 CATGTGCATCTCTCTCTTGG
1 CATGTGCATCTCTCTCTTGG
*
12312263 CATGATGCATGTC-CTCTTG
1 CATG-TGCATCTCTCTCTTG
12312282 TTTGCTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (20 bp):
CATGTGCATCTCTCTCTTGG
Found at i:12314878 original size:21 final size:20
Alignment explanation
Indices: 12314845--12314883 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12314835 AATAAACTAG
12314845 AATATAATTAAAT-AAATTT
1 AATATAATTAAATCAAATTT
12314864 AATATAAAGTTAAATCAAAT
1 AATAT-AA-TTAAATCAAAT
12314884 ACACATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 6 0.35
22 4 0.24
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
AATATAATTAAATCAAATTT
Found at i:12318793 original size:29 final size:30
Alignment explanation
Indices: 12318706--12318799 Score: 104
Period size: 29 Copynumber: 3.1 Consensus size: 30
12318696 AATTGCATGA
12318706 AAAT-AAATATTTAAAAATTTAAATGATT-T
1 AAATAAAATA-TTAAAAATTTAAATGATTAT
* * *
12318735 GAAATAAAAAATAAAAAATTTAATTGATTAT
1 -AAATAAAATATTAAAAATTTAAATGATTAT
*
12318766 -AATAAAATATTAAAAATTTAAATAATTATT
1 AAATAAAATATTAAAAATTTAAATGATTA-T
12318796 AAAT
1 AAAT
12318800 TTTTATTCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
29 24 0.45
30 21 0.40
31 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATAAAATATTAAAAATTTAAATGATTAT
Found at i:12319353 original size:27 final size:27
Alignment explanation
Indices: 12319317--12319376 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
12319307 TGATATATAC
12319317 TATTA-TAATA-ATATAAAATAAAATAA
1 TATTATTAATATA-ATAAAATAAAATAA
* * *
12319343 TTTTATTAATATAATTAAATTAAATAA
1 TATTATTAATATAATAAAATAAAATAA
12319370 TATTATT
1 TATTATT
12319377 TTATTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.14
27 23 0.82
28 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTATTAATATAATAAAATAAAATAA
Found at i:12319465 original size:18 final size:18
Alignment explanation
Indices: 12319442--12319481 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12319432 CAAAAATTTT
*
12319442 TTTTAATAATTTATATAA
1 TTTTAATAATTGATATAA
*
12319460 TTTTAATTATTGATATAA
1 TTTTAATAATTGATATAA
12319478 TTTT
1 TTTT
12319482 TAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAATAATTGATATAA
Found at i:12320031 original size:27 final size:27
Alignment explanation
Indices: 12319983--12320052 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
12319973 CTATTATTTG
12319983 AAAAAATACAAAA-T-TATTATT-A-GA
1 AAAAAATA-AAAATTATATTATTAATGA
12320007 AACAAAATAAAAATTATATTAATTAATGA
1 AA-AAAATAAAAATTATATT-ATTAATGA
*
12320036 AAATAA-AAAAATTATAT
1 AAAAAATAAAAATTATAT
12320053 CAATGAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
24 6 0.15
25 7 0.18
26 4 0.10
27 14 0.36
28 4 0.10
29 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAAAATAAAAATTATATTATTAATGA
Found at i:12320044 original size:26 final size:26
Alignment explanation
Indices: 12320010--12320074 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
12320000 TATTAGAAAC
* * *
12320010 AAAAT-AAAAATTATATTAATTAATG
1 AAAATAAAAAATTATATCAATGAATA
12320035 AAAATAAAAAAATTATATCAATGAATA
1 AAAAT-AAAAAATTATATCAATGAATA
*
12320062 AAAATACAAAATT
1 AAAATAAAAAATT
12320075 TAAATTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.15
26 7 0.21
27 22 0.65
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (26 bp):
AAAATAAAAAATTATATCAATGAATA
Found at i:12320065 original size:27 final size:27
Alignment explanation
Indices: 12320015--12320072 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
12320005 GAAACAAAAT
* * *
12320015 AAAAATTATATTAATTAATGAAAATAA
1 AAAAATTATATCAATGAATAAAAATAA
*
12320042 AAAAATTATATCAATGAATAAAAATAC
1 AAAAATTATATCAATGAATAAAAATAA
12320069 AAAA
1 AAAA
12320073 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATTATATCAATGAATAAAAATAA
Found at i:12332527 original size:37 final size:36
Alignment explanation
Indices: 12332471--12332549 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
12332461 ATTTAGTAAA
12332471 AAATTTAAACTTGAATTTGATTTGAAATTT-ATTGTTT
1 AAATTTAAACTTGAATTTGA-TTGAAATTTAATT-TTT
* *
12332508 GAAATTT-AACTTGAGTTTGATTGAATTTTAATTTTT
1 -AAATTTAAACTTGAATTTGATTGAAATTTAATTTTT
12332544 AAATTT
1 AAATTT
12332550 GAGTTTGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 6 0.16
36 11 0.29
37 15 0.39
38 6 0.16
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (36 bp):
AAATTTAAACTTGAATTTGATTGAAATTTAATTTTT
Found at i:12339487 original size:16 final size:16
Alignment explanation
Indices: 12339458--12339556 Score: 85
Period size: 16 Copynumber: 6.2 Consensus size: 16
12339448 TAAAAGAATC
*
12339458 AATAATTCAAATTTAA
1 AATAATTTAAATTTAA
*
12339474 AATGATTTAAATTTAA
1 AATAATTTAAATTTAA
* * * *
12339490 TGATAATCTGAATATAA
1 -AATAATTTAAATTTAA
*
12339507 AATAATTTAAACTTAA
1 AATAATTTAAATTTAA
12339523 AATAATTTAAAATTT--
1 AATAATTT-AAATTTAA
* *
12339538 AATTATTTCAATTTAA
1 AATAATTTAAATTTAA
12339554 AAT
1 AAT
12339557 GATTCAAACT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.08
15 7 0.11
16 36 0.56
17 16 0.25
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:12341320 original size:12 final size:12
Alignment explanation
Indices: 12341295--12341347 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
12341285 TATCTATATC
12341295 TATATATATA--
1 TATATATATAGT
12341305 TATATATATAGT
1 TATATATATAGT
12341317 TATAGT-TATAGT
1 TATA-TATATAGT
12341329 TATAGTTATATAGT
1 TATA--TATATAGT
12341343 TATAT
1 TATAT
12341348 CCACATCTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 10 0.27
12 15 0.41
13 2 0.05
14 10 0.27
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
TATATATATAGT
Found at i:12341346 original size:6 final size:6
Alignment explanation
Indices: 12341311--12341338 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12341301 TATATATATA
12341311 TATAGT TATAGT TATAGT TATAGT TATA
1 TATAGT TATAGT TATAGT TATAGT TATA
12341339 TAGTTATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
TATAGT
Found at i:12342138 original size:35 final size:36
Alignment explanation
Indices: 12342083--12342168 Score: 124
Period size: 35 Copynumber: 2.4 Consensus size: 36
12342073 CGAACTATTA
12342083 ATAA-TATCTTTTAATAATTGATTTATAAATTTAAT
1 ATAAGTATCTTTTAATAATTGATTTATAAATTTAAT
* *
12342118 GTAAGTATC-TTTAATGATTGATTTATAAATTTAAT
1 ATAAGTATCTTTTAATAATTGATTTATAAATTTAAT
12342153 ATAAGTAT-TTTCTAAT
1 ATAAGTATCTTT-TAAT
12342169 TCATACTATC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
35 37 0.82
36 8 0.18
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (36 bp):
ATAAGTATCTTTTAATAATTGATTTATAAATTTAAT
Found at i:12345613 original size:19 final size:18
Alignment explanation
Indices: 12345585--12345620 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12345575 ATATCACTAA
*
12345585 ATAATTAATTAATAAATT
1 ATAATTAATTAAAAAATT
12345603 ATAATTTAATTAAAAAAT
1 ATAA-TTAATTAAAAAAT
12345621 CAAACTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTAATTAAAAAATT
Found at i:12345989 original size:50 final size:51
Alignment explanation
Indices: 12345935--12346038 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 51
12345925 TTGAAATGGG
* *
12345935 AAGCTGTGCTCGATGCGAAACCCGTTCGTTCATTTC-TTTTTTGTCGGGTC
1 AAGCTGTGCCCGATGCGAAACCCGTTCGTTCATTTCTTTTTTTGTCGAGTC
* * * *
12345985 AAGCTGTGCCCGGTGCGAAGCTCGTTCGTTCCTTTCTTTTTTTGTCGAGTC
1 AAGCTGTGCCCGATGCGAAACCCGTTCGTTCATTTCTTTTTTTGTCGAGTC
12346036 AAG
1 AAG
12346039 GAGAATTACC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 31 0.66
51 16 0.34
ACGTcount: A:0.13, C:0.24, G:0.25, T:0.38
Consensus pattern (51 bp):
AAGCTGTGCCCGATGCGAAACCCGTTCGTTCATTTCTTTTTTTGTCGAGTC
Found at i:12356264 original size:29 final size:29
Alignment explanation
Indices: 12356213--12356278 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
12356203 ATCCTTTTTT
12356213 TTGTTTT-AATTTTTTAAAAATTTTA-AA
1 TTGTTTTAAATTTTTTAAAAATTTTATAA
**
12356240 TTGTTTTAAATTTTTTTTGAAATTTTATAA
1 TTGTTTTAAA-TTTTTTAAAAATTTTATAA
12356270 TT-TTTTAAA
1 TTGTTTTAAA
12356279 GATTTGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 7 0.21
28 2 0.06
29 21 0.62
30 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (29 bp):
TTGTTTTAAATTTTTTAAAAATTTTATAA
Found at i:12363951 original size:26 final size:26
Alignment explanation
Indices: 12363921--12363976 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
12363911 CAGCATGATG
12363921 ATTTATGCACCTATCTTGACAGTTAC
1 ATTTATGCACCTATCTTGACAGTTAC
12363947 ATTTATGCACCTATCTTGACAGTTAC
1 ATTTATGCACCTATCTTGACAGTTAC
12363973 ATTT
1 ATTT
12363977 TACTCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTTATGCACCTATCTTGACAGTTAC
Found at i:12366975 original size:19 final size:21
Alignment explanation
Indices: 12366938--12366979 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
12366928 AATTGATTAA
12366938 TTAATTCTTATTGTGATTATT
1 TTAATTCTTATTGTGATTATT
*
12366959 TTAATT-TT-TTGTTATTATT
1 TTAATTCTTATTGTGATTATT
12366978 TT
1 TT
12366980 TTGTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (21 bp):
TTAATTCTTATTGTGATTATT
Found at i:12366980 original size:13 final size:14
Alignment explanation
Indices: 12366962--12366994 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12366952 GATTATTTTA
12366962 ATTTTTTG-TTATT
1 ATTTTTTGTTTATT
12366975 ATTTTTTGTTTATT
1 ATTTTTTGTTTATT
12366989 ATTTTT
1 ATTTTT
12366995 ATCTCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (14 bp):
ATTTTTTGTTTATT
Found at i:12368167 original size:17 final size:17
Alignment explanation
Indices: 12368145--12368198 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
12368135 TCACAAGAAA
12368145 TGTTTTTGATTTTTTTT
1 TGTTTTTGATTTTTTTT
*
12368162 TGTTTTTGAAATTTTTTTG
1 TGTTTTTG--ATTTTTTTT
*
12368181 TGTTTTT-TTTTTTTTT
1 TGTTTTTGATTTTTTTT
12368197 TG
1 TG
12368199 CTACTAGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.28
17 8 0.25
19 15 0.47
ACGTcount: A:0.07, C:0.00, G:0.13, T:0.80
Consensus pattern (17 bp):
TGTTTTTGATTTTTTTT
Found at i:12368186 original size:28 final size:28
Alignment explanation
Indices: 12368141--12368198 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
12368131 TAGATCACAA
12368141 GAAATGTTTTTGATTTTTTTTTGTTTTT
1 GAAATGTTTTTGATTTTTTTTTGTTTTT
* * *
12368169 GAAATTTTTTTGTGTTTTTTTTTTTTTTT
1 GAAATGTTTTTG-ATTTTTTTTTGTTTTT
12368198 G
1 G
12368199 CTACTAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.12, C:0.00, G:0.14, T:0.74
Consensus pattern (28 bp):
GAAATGTTTTTGATTTTTTTTTGTTTTT
Found at i:12368584 original size:3 final size:3
Alignment explanation
Indices: 12368576--12368638 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
12368566 TGTCAAAAGA
12368576 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12368624 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
12368639 TAAATTATCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12370524 original size:14 final size:14
Alignment explanation
Indices: 12370505--12370542 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
12370495 ATATATTTTT
12370505 TTAAAAATTTCTTA
1 TTAAAAATTTCTTA
12370519 TTAAAAATTTCTTA
1 TTAAAAATTTCTTA
12370533 -TAATAAATTT
1 TTAA-AAATTT
12370543 TATTTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAAAATTTCTTA
Found at i:12373000 original size:3 final size:3
Alignment explanation
Indices: 12372992--12373055 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
12372982 AAAAGGAAAG
* * *
12372992 ATA ATA ATA ATA ATA ATA ATA GATT ACA ATAA ATA ACA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA AT-A ATA ATA ATA ATA ATA
12373038 A-A ATA A-A ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
12373056 TACTATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.16
3 36 0.73
4 5 0.10
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12373042 original size:20 final size:20
Alignment explanation
Indices: 12372992--12373044 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
12372982 AAAAGGAAAG
*
12372992 ATAATAATAAT-AATAATAAT
1 ATAATAA-AATAAATAACAAT
* * *
12373012 AGATTACAATAAATAACAAT
1 ATAATAAAATAAATAACAAT
12373032 ATAATAAAATAAA
1 ATAATAAAATAAA
12373045 ATAATATAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
ATAATAAAATAAATAACAAT
Found at i:12373054 original size:5 final size:5
Alignment explanation
Indices: 12373029--12373087 Score: 50
Period size: 5 Copynumber: 12.2 Consensus size: 5
12373019 AATAAATAAC
* * * * *
12373029 AATAT AATA- AA-AT AAAAT AATAT AATAT ACTAT AATAT ATTAC ACTAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
12373077 ACTAT AATAT A
1 AATAT AATAT A
12373088 GTAACAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 39 0.89
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:12373063 original size:15 final size:15
Alignment explanation
Indices: 12373045--12373087 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
12373035 ATAAAATAAA
12373045 ATAATATAATATACT
1 ATAATATAATATACT
* *
12373060 ATAATATATTACACT
1 ATAATATAATATACT
*
12373075 ATACTATAATATA
1 ATAATATAATATA
12373088 GTAACAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATATAATATACT
Found at i:12375079 original size:2 final size:2
Alignment explanation
Indices: 12375074--12375106 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12375064 GTGTCTATTT
12375074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12375107 GTCTAGTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12377610 original size:16 final size:17
Alignment explanation
Indices: 12377579--12377611 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12377569 TCAATTATCT
*
12377579 CTTTAGTTGTTTATTAG
1 CTTTAGTTGTTAATTAG
12377596 CTTTAGTT-TTAATTAG
1 CTTTAGTTGTTAATTAG
12377612 AAGAGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.58
Consensus pattern (17 bp):
CTTTAGTTGTTAATTAG
Found at i:12379718 original size:27 final size:27
Alignment explanation
Indices: 12379680--12379735 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
12379670 TAGATATATG
12379680 TTAAAGATAGTTAAATTTCCAAAGACA
1 TTAAAGATAGTTAAATTTCCAAAGACA
12379707 TTAAAGATAGTTAAATTTCCAAAGACA
1 TTAAAGATAGTTAAATTTCCAAAGACA
12379734 TT
1 TT
12379736 TTGGGGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (27 bp):
TTAAAGATAGTTAAATTTCCAAAGACA
Done.