Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 7 of 74
Found at i:1852533 original size:19 final size:19
Alignment explanation
Indices: 1852497--1852533 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1852487 ATAATGTCGC
* *
1852497 AAAAAAAAGTCAAAAAAAT
1 AAAAAAAAATAAAAAAAAT
1852516 AAAAAAAAATAAAAAAAA
1 AAAAAAAAATAAAAAAAA
1852534 AGTTGATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAAAAAAATAAAAAAAAT
Found at i:1855100 original size:9 final size:10
Alignment explanation
Indices: 1855077--1855105 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1855067 GTCCAATGAA
1855077 AAAAAATAGT
1 AAAAAATAGT
1855087 AAAAAATAGT
1 AAAAAATAGT
1855097 AAAAAATAG
1 AAAAAATAG
1855106 AGATATGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAAAATAGT
Found at i:1864924 original size:21 final size:20
Alignment explanation
Indices: 1864895--1864940 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1864885 GTTTTATTAA
*
1864895 AAATAAATAAATAAAAAATTT
1 AAATTAATAAATAAAAAA-TT
*
1864916 AAATTAATAAATTAATAAATT
1 AAATTAATAAA-TAAAAAATT
1864937 AAAT
1 AAAT
1864941 ATAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTAATAAATAAAAAATT
Found at i:1864934 original size:29 final size:29
Alignment explanation
Indices: 1864890--1864975 Score: 79
Period size: 29 Copynumber: 3.1 Consensus size: 29
1864880 TAAAAGTTTT
**
1864890 ATTAA-AAATAAATAAATAAAAAATTTAA
1 ATTAATAAATAAATAAATAAAAAATAAAA
* * *
1864918 ATTAATAAATTAATAAATTAAATATAAAA
1 ATTAATAAATAAATAAATAAAAAATAAAA
* * *
1864947 ATTAAT-AATATATAAA-AAATATTAAAA
1 ATTAATAAATAAATAAATAAAAAATAAAA
1864974 AT
1 AT
1864976 ATTATTTATA
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
27 9 0.20
28 13 0.28
29 24 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
ATTAATAAATAAATAAATAAAAAATAAAA
Found at i:1865064 original size:17 final size:18
Alignment explanation
Indices: 1865031--1865065 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1865021 ATTTTATAAA
1865031 TATTTAACTAAAAATATT
1 TATTTAACTAAAAATATT
*
1865049 TATTTAA-TAAATATATT
1 TATTTAACTAAAAATATT
1865066 ACATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAACTAAAAATATT
Found at i:1875672 original size:31 final size:31
Alignment explanation
Indices: 1875634--1875697 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1875624 TTTACTATTA
*
1875634 CTATTATTATTTTTCATTTTCCCCTTAATTT
1 CTATTATTATTTGTCATTTTCCCCTTAATTT
* *
1875665 CTATTATTATTTGTCATTTTTCCGTTAATTT
1 CTATTATTATTTGTCATTTTCCCCTTAATTT
1875696 CT
1 CT
1875698 GACTTCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.61
Consensus pattern (31 bp):
CTATTATTATTTGTCATTTTCCCCTTAATTT
Found at i:1883884 original size:15 final size:15
Alignment explanation
Indices: 1883864--1883898 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1883854 TTTTTTTTAC
*
1883864 ATTTAAAAATATTAA
1 ATTTAAAAATACTAA
*
1883879 ATTTAAAAATCCTAA
1 ATTTAAAAATACTAA
1883894 ATTTA
1 ATTTA
1883899 CTCATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAAAATACTAA
Found at i:1889785 original size:17 final size:17
Alignment explanation
Indices: 1889763--1889795 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1889753 TTTTTTAAAA
*
1889763 AACTTTTTTCAAAATTT
1 AACTTTTGTCAAAATTT
1889780 AACTTTTGTCAAAATT
1 AACTTTTGTCAAAATT
1889796 ATTTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
AACTTTTGTCAAAATTT
Found at i:1889944 original size:13 final size:13
Alignment explanation
Indices: 1889926--1889950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1889916 TTGAATTTTT
1889926 TTAAAAATATATA
1 TTAAAAATATATA
1889939 TTAAAAATATAT
1 TTAAAAATATAT
1889951 TTTTATCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAAAATATATA
Found at i:1890059 original size:24 final size:24
Alignment explanation
Indices: 1890031--1890090 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1890021 TTTGTTTTCT
*
1890031 AAAAAGAAAAAAGGAAAAACAAGA
1 AAAAAGAAAAAAGGAAAAACAAAA
* * * **
1890055 GAAAACAAAAATGGAAAATGAAAA
1 AAAAAGAAAAAAGGAAAAACAAAA
1890079 AAAAAGAAAAAA
1 AAAAAGAAAAAA
1890091 AATACTGTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (24 bp):
AAAAAGAAAAAAGGAAAAACAAAA
Found at i:1890362 original size:15 final size:16
Alignment explanation
Indices: 1890342--1890400 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1890332 ATGGAAAAAC
1890342 AAAAAG-AAAAATAAG
1 AAAAAGTAAAAATAAG
*
1890357 AAAAAGTAAAACAGGAA-
1 AAAAAGTAAAA-A-TAAG
1890374 AAAAAG-AAAAATAAG
1 AAAAAGTAAAAATAAG
*
1890389 AGAAAGTAAAAA
1 AAAAAGTAAAAA
1890401 ATAATTTGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.06
15 12 0.33
16 13 0.36
17 7 0.19
18 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (16 bp):
AAAAAGTAAAAATAAG
Found at i:1891687 original size:8 final size:8
Alignment explanation
Indices: 1891674--1891755 Score: 60
Period size: 8 Copynumber: 9.9 Consensus size: 8
1891664 TTATTTTTAA
1891674 ATAATATT
1 ATAATATT
1891682 ATAATATATT
1 AT-A-ATATT
*
1891692 AATAAATAAT
1 -AT-AATATT
*
1891702 ATAATTTT
1 ATAATATT
* *
1891710 ATATTAAT
1 ATAATATT
1891718 ATAATA-T
1 ATAATATT
*
1891725 ATTAATA-A
1 A-TAATATT
1891733 ATAATATT
1 ATAATATT
1891741 ATAATATT
1 ATAATATT
1891749 ATAATAT
1 ATAATAT
1891756 ATTAATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
7 7 0.12
8 37 0.62
9 3 0.05
10 9 0.15
11 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
ATAATATT
Found at i:1891697 original size:23 final size:23
Alignment explanation
Indices: 1891671--1891938 Score: 153
Period size: 23 Copynumber: 11.4 Consensus size: 23
1891661 ATTTTATTTT
1891671 TAAATAATATTATAATATATTAA
1 TAAATAATATTATAATATATTAA
* **
1891694 TAAATAATATAATTTTATATTAA
1 TAAATAATATTATAATATATTAA
*
1891717 T--ATAATA-TATTAATA-AATAA
1 TAAATAATATTA-TAATATATTAA
*
1891737 TATTATAATATTATAATATATTAA
1 TA-AATAATATTATAATATATTAA
*
1891761 TAAATATTATTATAAATAAATATTAA
1 TAAATAATATTAT-AAT--ATATTAA
* * *
1891787 TTTAAAAAATATTATATTA-ATAAA
1 --TAAATAATATTATAATATATTAA
* *
1891811 TAATATAATAATATTAT-TAATTTAA
1 TAA-ATAATATTATAATAT-A-TTAA
*
1891836 TTAATAAATATTATAATA-A-TACA
1 TAAAT-AATATTATAATATATTA-A
* *
1891859 TTAATAA-ATAAT-ATACTATTAA
1 TAAATAATATTATAATA-TATTAA
* *
1891881 TTAAT-ATATTAATAAATATTATAAA
1 TAAATAATATT-AT-AATA-TATTAA
* *
1891906 TAAATAATATTATAATGTCTTAA
1 TAAATAATATTATAATATATTAA
1891929 TAAATAATAT
1 TAAATAATAT
1891939 AAAGAATAAT
Statistics
Matches: 189, Mismatches: 30, Indels: 52
0.70 0.11 0.19
Matches are distributed among these distances:
20 9 0.05
21 14 0.07
22 16 0.08
23 74 0.39
24 22 0.12
25 29 0.15
26 12 0.06
27 2 0.01
28 11 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATAATATTATAATATATTAA
Found at i:1891702 original size:15 final size:15
Alignment explanation
Indices: 1891682--1891915 Score: 171
Period size: 15 Copynumber: 15.5 Consensus size: 15
1891672 AAATAATATT
1891682 ATAATATATTAATAA
1 ATAATATATTAATAA
1891697 ATAATATAATTTTATATTAA
1 ATAATAT-A--TTA-A-TAA
1891717 TATAATATATTAATAA
1 -ATAATATATTAATAA
*
1891733 ATAATAT-TATAATATT
1 ATAATATAT-TAATA-A
1891749 ATAATATATTAATAA
1 ATAATATATTAATAA
* *
1891764 ATATTATTATAAATAA
1 ATAATA-TATTAATAA
* *
1891780 ATATTA-ATTTAAAAA
1 ATAATATA-TTAATAA
*
1891795 ATATTATATTAATAA
1 ATAATATATTAATAA
*
1891810 ATAATATAATAAT-A
1 ATAATATATTAATAA
* * *
1891824 TTATTA-ATTTAATTA
1 ATAATATA-TTAATAA
1891839 ATAA-ATATT-AT-A
1 ATAATATATTAATAA
*
1891851 ATAATACATTAATAA
1 ATAATATATTAATAA
* *
1891866 ATAATATACTATTAA
1 ATAATATATTAATAA
*
1891881 TTAATATATTAATAA
1 ATAATATATTAATAA
*
1891896 AT-AT-TATAAATAA
1 ATAATATATTAATAA
1891909 ATAATAT
1 ATAATAT
1891916 TATAATGTCT
Statistics
Matches: 176, Mismatches: 23, Indels: 40
0.74 0.10 0.17
Matches are distributed among these distances:
12 5 0.03
13 17 0.10
14 20 0.11
15 83 0.47
16 31 0.18
17 2 0.01
18 6 0.03
19 1 0.01
20 4 0.02
21 7 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATATATTAATAA
Found at i:1891728 original size:36 final size:32
Alignment explanation
Indices: 1891674--1891898 Score: 142
Period size: 31 Copynumber: 6.8 Consensus size: 32
1891664 TTATTTTTAA
*
1891674 ATAATATTATAATATATTAATAAATAATATAATTTT
1 ATAATAATATAATATATTAATAAATAA-AT-A--TT
*
1891710 ATATTAATATAATATATTAATAAAT-AATATT
1 ATAATAATATAATATATTAATAAATAAATATT
* *
1891741 ATAATATTATAATATATTAATAAAT-ATTATT
1 ATAATAATATAATATATTAATAAATAAATATT
* * *
1891772 ATAAATAA-ATATTA-ATTTAAAAAATATTATATT
1 AT-AATAATATAATATA-TTAATAAATA-AATATT
* * * *
1891805 AATAAATAATATAATAATATTATTAATTTAAT-TA
1 -AT-AATAATATAAT-ATATTAATAAATAAATATT
*
1891839 ATAAATATTATAATAATACATTAATAAAT-AATA-T
1 AT-AATAATATAAT-AT--ATTAATAAATAAATATT
*
1891873 ACTATTAAT-TAATATATTAATAAATA
1 A-TAATAATATAATATATTAATAAATA
1891899 TTATAAATAA
Statistics
Matches: 153, Mismatches: 23, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
30 11 0.07
31 45 0.29
32 6 0.04
33 25 0.16
34 19 0.12
35 16 0.10
36 30 0.20
37 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
ATAATAATATAATATATTAATAAATAAATATT
Found at i:1891731 original size:44 final size:44
Alignment explanation
Indices: 1891658--1891921 Score: 144
Period size: 44 Copynumber: 6.0 Consensus size: 44
1891648 ACTTTTGAAC
* *
1891658 ATAATTTTATTTTTAA-ATAATAT-TATAATATATTAATA-AATAAT
1 ATAATTTTA-TATTAATATAATATAT-TAATA-AATAATATAATAAT
*
1891702 ATAATTTTATATTAATATAATATATTAATAAATAATATTATAAT
1 ATAATTTTATATTAATATAATATATTAATAAATAATATAATAAT
* **
1891746 ATTATAATATATTAATA-AATATTATT-ATAAATAAATATTAATTTAA-
1 ATAATTTTATATTAATATAATA-TATTAATAAAT-AATA-TAA--TAAT
* * *
1891792 AAAATATTATATTAATA-AATA-ATATAAT-AATATTATTAATTTAAT
1 ATAATTTTATATTAATATAATATAT-TAATAAATAATA-TAA--TAAT
** * *
1891837 -TAA-TAAATATT-ATAATAATACATTAATAAATAATATACT-AT
1 ATAATTTTATATTAAT-ATAATATATTAATAAATAATATAATAAT
* * *
1891878 -TAATTAATATATTAATA-AATATTATAAATAAATAATATTATAAT
1 ATAATT-TTATATTAATATAATA-TATTAATAAATAATATAATAAT
1891922 GTCTTAATAA
Statistics
Matches: 178, Mismatches: 22, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
41 5 0.03
42 8 0.04
43 49 0.28
44 78 0.44
45 15 0.08
46 20 0.11
47 3 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (44 bp):
ATAATTTTATATTAATATAATATATTAATAAATAATATAATAAT
Found at i:1891761 original size:8 final size:8
Alignment explanation
Indices: 1891683--1891894 Score: 71
Period size: 8 Copynumber: 27.6 Consensus size: 8
1891673 AATAATATTA
1891683 TAATATAT
1 TAATATAT
*
1891691 TAATA-AA
1 TAATATAT
1891698 TAATATAAT
1 TAATAT-AT
*
1891707 T-TTATAT
1 TAATATAT
1891714 T-A-ATA-
1 TAATATAT
1891719 TAATATAT
1 TAATATAT
*
1891727 TAATA-AA
1 TAATATAT
1891734 TAATAT-T
1 TAATATAT
1891741 ATAATAT-T
1 -TAATATAT
1891749 ATAATATAT
1 -TAATATAT
1891758 TAATAAATAT
1 TAAT--ATAT
* *
1891768 TATTATAAA
1 TAATAT-AT
1891777 TAA-ATAT
1 TAATATAT
1891784 T-A-AT-T
1 TAATATAT
* *
1891789 TAA-AAAA
1 TAATATAT
*
1891796 TATTATAT
1 TAATATAT
*
1891804 TAATA-AA
1 TAATATAT
*
1891811 TAATATAA
1 TAATATAT
1891819 TAATATTAT
1 TAATA-TAT
*
1891828 TAATTTAAT
1 TAATAT-AT
*
1891837 TAATA-AA
1 TAATATAT
* *
1891844 TATTATAA
1 TAATATAT
*
1891852 TAATACAT
1 TAATATAT
*
1891860 TAATA-AA
1 TAATATAT
*
1891867 TAATATAC
1 TAATATAT
*
1891875 TATTA-AT
1 TAATATAT
1891882 TAATATAT
1 TAATATAT
1891890 TAATA
1 TAATA
1891895 AATATTATAA
Statistics
Matches: 154, Mismatches: 30, Indels: 40
0.69 0.13 0.18
Matches are distributed among these distances:
5 3 0.02
6 9 0.06
7 44 0.29
8 73 0.47
9 18 0.12
10 7 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (8 bp):
TAATATAT
Found at i:1891941 original size:36 final size:38
Alignment explanation
Indices: 1891799--1891917 Score: 54
Period size: 33 Copynumber: 3.2 Consensus size: 38
1891789 TAAAAAATAT
*
1891799 TATATTAATAAATAATAT-AAT-AATATTATTAATT--
1 TATATTAATAAATAATATAAATAAATAATATTAATTAA
* * *
1891833 TA-ATTAATAAATATTAT-AAT-AATACATTAATAAATAA
1 TATATTAATAAATAATATAAATAAATA-A-TATTAATTAA
* * * * * *
1891870 TATACTATTAATTAATATATTAATAAATATTATAAATAAA
1 TATATTAATAAATAATATA--AATAAATAATATTAATTAA
1891910 TAATATTA
1 T-ATATTA
1891918 TAATGTCTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
33 21 0.34
34 2 0.03
35 6 0.10
37 2 0.03
38 11 0.18
40 7 0.11
41 8 0.13
42 4 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (38 bp):
TATATTAATAAATAATATAAATAAATAATATTAATTAA
Found at i:1892055 original size:10 final size:9
Alignment explanation
Indices: 1892029--1892083 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
1892019 ATTATTTTTT
1892029 TAATTTTAA
1 TAATTTTAA
1892038 TAATTTTAA
1 TAATTTTAA
1892047 TATATTTTAA
1 TA-ATTTTAA
*
1892057 TAA--TAAA
1 TAATTTTAA
1892064 TAATTTTAA
1 TAATTTTAA
1892073 -ATATTTTAA
1 TA-ATTTTAA
1892082 TA
1 TA
1892084 GTTAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 6 0.15
8 1 0.03
9 22 0.56
10 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTTTAA
Found at i:1892070 original size:44 final size:44
Alignment explanation
Indices: 1891987--1892070 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 44
1891977 TTAACGTAAT
*
1891987 ATTTTAATATTAAATATTATTATTAAAATATAATTATTTTTTTA
1 ATTTTAATATTAAATATTATTATTAAAATATAATAATTTTTTTA
*
1892031 ATTTTAATAATTTTAATA-TATT-TTAATAATA-AATAATTTT
1 ATTTTAAT-A-TTAAATATTATTATTAA-AATATAATAATTTT
1892071 AAATATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
44 20 0.57
45 9 0.26
46 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (44 bp):
ATTTTAATATTAAATATTATTATTAAAATATAATAATTTTTTTA
Found at i:1892093 original size:26 final size:25
Alignment explanation
Indices: 1892026--1892089 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
1892016 ATAATTATTT
*
1892026 TTTTAATTTTAATAATTTTAATATA
1 TTTTAATATTAATAATTTTAATATA
*
1892051 TTTTAATAATAAATAATTTTAA-ATA
1 TTTTAAT-ATTAATAATTTTAATATA
1892076 TTTTAATAGTTAAT
1 TTTTAATA-TTAAT
1892090 TAATATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.03
25 21 0.62
26 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTAATATTAATAATTTTAATATA
Found at i:1894282 original size:16 final size:16
Alignment explanation
Indices: 1894263--1894295 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1894253 TAAATATTAA
*
1894263 TTTTAATAAAATTTAT
1 TTTTAAAAAAATTTAT
1894279 TTTTAAAAAAATTTAT
1 TTTTAAAAAAATTTAT
1894295 T
1 T
1894296 AATTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAAAAAAATTTAT
Found at i:1894887 original size:13 final size:13
Alignment explanation
Indices: 1894866--1894913 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1894856 ATAATTTAAA
*
1894866 ATATGATATAATT
1 ATATAATATAATT
1894879 ATATAATATAA--
1 ATATAATATAATT
*
1894890 ATATAATATATTT
1 ATATAATATAATT
*
1894903 ATAAAATATAA
1 ATATAATATAA
1894914 AAATTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:1894898 original size:24 final size:24
Alignment explanation
Indices: 1894864--1894926 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1894854 TGATAATTTA
* *
1894864 AAATATGATATAATTATATAATAT
1 AAATATAATATAATTATAAAATAT
*
1894888 AAATATAATATATTTATAAAATAT
1 AAATATAATATAATTATAAAATAT
* *
1894912 AAAAATTATATAATT
1 AAATATAATATAATT
1894927 TAAGATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AAATATAATATAATTATAAAATAT
Found at i:1894961 original size:22 final size:22
Alignment explanation
Indices: 1894919--1894971 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1894909 TATAAAAATT
1894919 ATATAATTTAAGATTTTAATAATA
1 ATAT-ATTTAAGATTTTAATAA-A
1894943 ATTATATTTAA-A-TTTAATAAA
1 A-TATATTTAAGATTTTAATAAA
1894964 ATATATTT
1 ATATATTT
1894972 TATATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.25
21 2 0.07
22 8 0.29
23 1 0.04
24 7 0.25
25 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATATTTAAGATTTTAATAAA
Found at i:1895041 original size:32 final size:32
Alignment explanation
Indices: 1895005--1895071 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1894995 TATATCACGT
*
1895005 AATTTTTATATAAAATATAATATAAATACATA
1 AATTTTAATATAAAATATAATATAAATACATA
*** * *
1895037 AATTTTAATATTTTATATGATATAAATATATA
1 AATTTTAATATAAAATATAATATAAATACATA
1895069 AAT
1 AAT
1895072 CATCCGATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (32 bp):
AATTTTAATATAAAATATAATATAAATACATA
Found at i:1912348 original size:17 final size:18
Alignment explanation
Indices: 1912316--1912353 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1912306 ATTATTTTTT
* *
1912316 TATGATATATGAATAATA
1 TATGATAGATGAATAAAA
1912334 TATGATAGA-GAATAAAA
1 TATGATAGATGAATAAAA
1912351 TAT
1 TAT
1912354 TTAATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (18 bp):
TATGATAGATGAATAAAA
Found at i:1915491 original size:24 final size:26
Alignment explanation
Indices: 1915440--1915493 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
1915430 TAGTGTCACA
*
1915440 TTTATTTGAAATATAAATTTAATAAT
1 TTTATTTGAAATATAAATATAATAAT
1915466 TTTA-TTGAAA-ATAAACTATAAT-AT
1 TTTATTTGAAATATAAA-TATAATAAT
1915490 TTTA
1 TTTA
1915494 ATTTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 11 0.42
25 11 0.42
26 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTATTTGAAATATAAATATAATAAT
Found at i:1916838 original size:14 final size:13
Alignment explanation
Indices: 1916799--1916853 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
1916789 TCTATCATAA
1916799 TTTATATTTTTAT
1 TTTATATTTTTAT
**
1916812 GATATATTATTTAT
1 TTTATATT-TTTAT
1916826 TTTAATATTTTTAAT
1 TTT-ATATTTTT-AT
*
1916841 TTTATAATTTTAT
1 TTTATATTTTTAT
1916854 CTCATAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 8 0.24
14 16 0.47
15 10 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTATATTTTTAT
Found at i:1919920 original size:30 final size:30
Alignment explanation
Indices: 1919880--1919936 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1919870 AAAGGAACTC
* * *
1919880 TCGCTTAAGGATTATCAAATGAGTCATGTG
1 TCGCTGAAGGATCATCAAATGAATCATGTG
*
1919910 TCGCTGAAGGATCATCAGATGAATCAT
1 TCGCTGAAGGATCATCAAATGAATCAT
1919937 ATACAACCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (30 bp):
TCGCTGAAGGATCATCAAATGAATCATGTG
Found at i:1920621 original size:17 final size:17
Alignment explanation
Indices: 1920599--1920634 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1920589 TCTTTTTAAC
1920599 GGGAGTTAGATAACTGT
1 GGGAGTTAGATAACTGT
1920616 GGGAGTTAGATAACTGT
1 GGGAGTTAGATAACTGT
1920633 GG
1 GG
1920635 CAATCTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.39, T:0.28
Consensus pattern (17 bp):
GGGAGTTAGATAACTGT
Found at i:1933882 original size:24 final size:23
Alignment explanation
Indices: 1933863--1933922 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 23
1933853 TCTAAAATTA
1933863 ATAAAATATTATT-TTTTAAAAT
1 ATAAAATATTATTATTTTAAAAT
1933885 ATAAAATATTATTATTTT-AAAT
1 ATAAAATATTATTATTTTAAAAT
*
1933907 ATAAATATATAATTAT
1 ATAAA-ATATTATTAT
1933923 ATAATTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 22 0.63
23 13 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATATTATTATTTTAAAAT
Found at i:1934751 original size:24 final size:24
Alignment explanation
Indices: 1934724--1934780 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1934714 AAATAGTAAT
1934724 AAAAATTATTATAATTATAATTAA
1 AAAAATTATTATAATTATAATTAA
* *
1934748 AAAAATTATTGTAATTGTAATTAA
1 AAAAATTATTATAATTATAATTAA
1934772 AAAAATTAT
1 AAAAATTAT
1934781 AAAAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAAATTATTATAATTATAATTAA
Found at i:1948112 original size:6 final size:6
Alignment explanation
Indices: 1948101--1948127 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1948091 AAGTACTATT
1948101 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
1948128 GCTATAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1953823 original size:20 final size:21
Alignment explanation
Indices: 1953786--1953824 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1953776 AATGAAACGT
*
1953786 AATTAAATTTTAATTATTATC
1 AATTAAATTTTAAATATTATC
1953807 AATTAAA-TTTAAATATTA
1 AATTAAATTTTAAATATTA
1953825 AATTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAAATTTTAAATATTATC
Found at i:1959998 original size:44 final size:44
Alignment explanation
Indices: 1959947--1960036 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
1959937 TAATCTGTCC
*
1959947 TAGCTTACTGCATACAGACAAAGGTTAATATGTTTATGCAGCTT
1 TAGCTTACTGCATACAGACAAAGATTAATATGTTTATGCAGCTT
* *
1959991 TAGCTTACTGCATACTGACAAAGATTATTATGTTTATGCAGCTT
1 TAGCTTACTGCATACAGACAAAGATTAATATGTTTATGCAGCTT
1960035 TA
1 TA
1960037 TCCTCACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (44 bp):
TAGCTTACTGCATACAGACAAAGATTAATATGTTTATGCAGCTT
Found at i:1963169 original size:9 final size:8
Alignment explanation
Indices: 1963153--1963181 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1963143 TGATGTTAAG
1963153 ATAAAAAA
1 ATAAAAAA
1963161 ATAAAAAA
1 ATAAAAAA
1963169 ATAAAAAA
1 ATAAAAAA
1963177 A-AAAA
1 ATAAAA
1963182 CCTCAAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
ATAAAAAA
Found at i:1965592 original size:2 final size:2
Alignment explanation
Indices: 1965585--1965619 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1965575 ATAGACACAT
1965585 TC TC 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 TC TC T
1965620 TTTTTTTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2004972 original size:25 final size:25
Alignment explanation
Indices: 2004938--2004987 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2004928 TATAGTAAAG
2004938 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
2004963 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTGTGTTAGTGGTTGAAGCA
2004988 ACTAAGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.36, T:0.40
Consensus pattern (25 bp):
TGTTAGTGTGTTAGTGGTTGAAGCA
Found at i:2007934 original size:2 final size:2
Alignment explanation
Indices: 2007886--2007920 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2007876 AAGGTCATTG
2007886 AT AT AT 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 AT AT AT A
2007921 AACTAGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2010056 original size:2 final size:2
Alignment explanation
Indices: 2010049--2010076 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2010039 CAAGAATGTA
2010049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2010077 TTACAGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2012417 original size:3 final size:3
Alignment explanation
Indices: 2012409--2012433 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2012399 CGAACCCACA
2012409 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
2012434 AAAGTGGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2012856 original size:22 final size:23
Alignment explanation
Indices: 2012803--2012857 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2012793 TGTATATTTA
2012803 AATAATTTTTTATAAACATATAT
1 AATAATTTTTTATAAACATATAT
2012826 AATATATTTTTTAATAAA-AT-TAT
1 AATA-ATTTTTT-ATAAACATATAT
*
2012849 ATTAATTTT
1 AATAATTTT
2012858 AATTAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 10 0.34
24 9 0.31
25 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
AATAATTTTTTATAAACATATAT
Found at i:2012898 original size:32 final size:31
Alignment explanation
Indices: 2012838--2012899 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2012828 TATATTTTTT
**
2012838 AATAAAATTATATTAATTTTAATTAATTTAA
1 AATAAAATTATATTAATTTTAAAAAATTTAA
2012869 AATAATAATTTATATT-ATTTTAAAAAATTTA
1 AATAA-AA-TTATATTAATTTTAAAAAATTTA
2012900 TTTACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 15 0.56
33 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AATAAAATTATATTAATTTTAAAAAATTTAA
Found at i:2013903 original size:25 final size:24
Alignment explanation
Indices: 2013866--2013912 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2013856 TTTTTTAATA
2013866 AAATGAAAAACAAAAAATAAAAAAT
1 AAATGAAAAACAAAAAA-AAAAAAT
* *
2013891 AAATTAAACACAAAAAAAAAAA
1 AAATGAAAAACAAAAAAAAAAA
2013913 GCTGAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (24 bp):
AAATGAAAAACAAAAAAAAAAAAT
Found at i:2024800 original size:25 final size:25
Alignment explanation
Indices: 2024772--2024823 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2024762 AGATATTAAA
2024772 TTAAAATATGTATATACTTAT-AATT
1 TTAAAATATGTA-ATACTTATAAATT
* * *
2024797 TTAAATTATTTAATATTTATAAATT
1 TTAAAATATGTAATACTTATAAATT
2024822 TT
1 TT
2024824 GTTTATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAATATGTAATACTTATAAATT
Found at i:2027643 original size:12 final size:12
Alignment explanation
Indices: 2027626--2027651 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2027616 TAATAATATG
2027626 TAAAAAATTATT
1 TAAAAAATTATT
2027638 TAAAAAATTATT
1 TAAAAAATTATT
2027650 TA
1 TA
2027652 TAATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:2027695 original size:26 final size:28
Alignment explanation
Indices: 2027665--2027726 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
2027655 TTTAATTCTG
*
2027665 TTAATATTTTTA-T-TAAAAATATTTAT
1 TTAATATTTTTACTCAAAAAATATTTAT
2027691 TTAATAAATTTTTACTCAAAAAATATTTAT
1 TTAAT--ATTTTTACTCAAAAAATATTTAT
2027721 TTAATA
1 TTAATA
2027727 AATATATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 5 0.16
28 8 0.26
29 1 0.03
30 17 0.55
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAATATTTTTACTCAAAAAATATTTAT
Found at i:2032873 original size:15 final size:15
Alignment explanation
Indices: 2032853--2032900 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2032843 TAAATCTCAT
2032853 AAAATAATATATTTA
1 AAAATAATATATTTA
*
2032868 AAAATAATA-ATATA
1 AAAATAATATATTTA
*
2032882 AAAATGAAT-TAATTA
1 AAAAT-AATATATTTA
2032897 AAAA
1 AAAA
2032901 AGATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAATAATATATTTA
Found at i:2037306 original size:117 final size:117
Alignment explanation
Indices: 2037100--2037415 Score: 470
Period size: 117 Copynumber: 2.7 Consensus size: 117
2037090 TCAAAACTCA
* * * * ** * *
2037100 CCCAGTCTGAATGCGCCCAAATCTGGTTTCAACCAGTCGCCCATCTGCCTGAAATCGATCCGTCA
1 CCCAGTCTGGATGCGCCCGAATCTGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATTCGTCG
* *
2037165 GAAGGGACTACGTCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACC
66 GAAGGAACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACC
* * * *
2037217 CCCAGTGTGGATGTGCCCGAATCTGGTTCCAACCAGTCACCCACCTGCTTGAGGTCGATTCGTCG
1 CCCAGTCTGGATGCGCCCGAATCTGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATTCGTCG
2037282 GAAGGAACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACC
66 GAAGGAACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACC
* * *
2037334 CCCAGTCTAGATGCGCTCGAATCTGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATTCATCG
1 CCCAGTCTGGATGCGCCCGAATCTGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATTCGTCG
*
2037399 GAAGGAATTACGCCCAG
66 GAAGGAACTACGCCCAG
2037416 GATGCGCCCG
Statistics
Matches: 177, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 177 1.00
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (117 bp):
CCCAGTCTGGATGCGCCCGAATCTGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATTCGTCG
GAAGGAACTACGCCCAGAACTGGATGCGCCCAAATCTGGTTCCAACAAGACC
Found at i:2037430 original size:73 final size:73
Alignment explanation
Indices: 2037343--2037488 Score: 204
Period size: 73 Copynumber: 2.0 Consensus size: 73
2037333 CCCCAGTCTA
* * * *
2037343 GATGCGCTCGAATCTGGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATTCATCGGAAG-GAAT
1 GATGCGCCCGAATCTAGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATCCATCGGAAGAG-AC
2037407 TACGCCCAG
65 TACGCCCAG
* * * *
2037416 GATGCGCCCGAATCTAGTTCCAACCAGTTGCCTACCTGCTTGAGGTCGATCCGTCGGAAGAGACT
1 GATGCGCCCGAATCTAGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATCCATCGGAAGAGACT
2037481 ACGCCCAG
66 ACGCCCAG
2037489 AACTGGATGC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 63 0.98
74 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.21
Consensus pattern (73 bp):
GATGCGCCCGAATCTAGTTCCAACCAGTCGCCCACCTGCCTGAGGTCGATCCATCGGAAGAGACT
ACGCCCAG
Found at i:2043288 original size:30 final size:31
Alignment explanation
Indices: 2043245--2043306 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
2043235 AAATTTAGAT
**
2043245 ATTTTATTTTTTGATAATTTAAT-TTTA-AAA
1 ATTTTATAATTTGATAA-TTAATGTTTATAAA
*
2043275 ATTTTATAATTTGATCATTAATGTTTATAAA
1 ATTTTATAATTTGATAATTAATGTTTATAAA
2043306 A
1 A
2043307 ATTATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 18 0.67
31 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (31 bp):
ATTTTATAATTTGATAATTAATGTTTATAAA
Found at i:2043733 original size:169 final size:170
Alignment explanation
Indices: 2043542--2043875 Score: 589
Period size: 171 Copynumber: 2.0 Consensus size: 170
2043532 TTGAAGTAAT
2043542 ACTATTTAGTAATTTTATAAATTGAATAATATTCAACA-ATTTTTAAAATTTAAATAGTATAATT
1 ACTATTTAGTAATTTTATAAATTGAATAATATTCAACAGATTTTTAAAATTTAAATAGTATAATT
* *
2043606 ACAATAAAATAAATAGATAATATCATTACTGATCTTTAAATTATATTGAAATATTTAATATAGTA
66 ACAATAAAATAAATAGATAATATCATTACTGATCTTTAAATTATACTGAAATATTCAATATAGTA
2043671 CTTAAAATTTTAAAATTTTACATAAATTATAAATTTGTTA
131 CTTAAAATTTTAAAATTTTACATAAATTATAAATTTGTTA
* *
2043711 ACTATTTAGTAATTTTATAAATTGAATAATATTCATCAGTTTTTTTAAAATTTAAATAGTATAAT
1 ACTATTTAGTAATTTTATAAATTGAATAATATTCAACAG-ATTTTTAAAATTTAAATAGTATAAT
* *
2043776 TACAATAAAATAAATAGATAATATCATTACTGATCTTTAAATTATACTGAAATATTCAATGTGGT
65 TACAATAAAATAAATAGATAATATCATTACTGATCTTTAAATTATACTGAAATATTCAATATAGT
*
2043841 ACTTAAAATTTTAAAATTTTACATGAATTATAAAT
130 ACTTAAAATTTTAAAATTTTACATAAATTATAAAT
2043876 CTATTAATTA
Statistics
Matches: 156, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
169 37 0.24
171 119 0.76
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (170 bp):
ACTATTTAGTAATTTTATAAATTGAATAATATTCAACAGATTTTTAAAATTTAAATAGTATAATT
ACAATAAAATAAATAGATAATATCATTACTGATCTTTAAATTATACTGAAATATTCAATATAGTA
CTTAAAATTTTAAAATTTTACATAAATTATAAATTTGTTA
Found at i:2052665 original size:13 final size:13
Alignment explanation
Indices: 2052647--2052673 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2052637 TATCAATTCA
2052647 TCAATTTTAATTT
1 TCAATTTTAATTT
2052660 TCAATTTTAATTT
1 TCAATTTTAATTT
2052673 T
1 T
2052674 TATTGAATCA
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TCAATTTTAATTT
Found at i:2052883 original size:4 final size:4
Alignment explanation
Indices: 2052874--2052898 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2052864 AGATGGATCT
2052874 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
2052899 ATAACCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2055639 original size:24 final size:24
Alignment explanation
Indices: 2055607--2055662 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
2055597 TGTTAATTTA
*
2055607 TATTTTTAA-GATACTTGTTATAGG
1 TATTATTAACGATACTTGTTA-AGG
** *
2055631 TATTATTAACGATTGTTTTTAAGG
1 TATTATTAACGATACTTGTTAAGG
2055655 TATTATTA
1 TATTATTA
2055663 TTATATTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (24 bp):
TATTATTAACGATACTTGTTAAGG
Found at i:2057612 original size:180 final size:180
Alignment explanation
Indices: 2057308--2058021 Score: 1060
Period size: 180 Copynumber: 4.0 Consensus size: 180
2057298 AATAGATTTG
* *
2057308 ACAGAAGAGGAATTAATCAGTTCCTTCTGATAGTGAT-TTCCATCAACACTTATGTTCGAATCTT
1 ACAGAAGAGGAATTAATCAGTTCCTTCTGAGAGTGATCTT-CATCAACACTTATGTTTGAATCTT
* * * * * ** **
2057372 TATAGGCTGTGAGACCAGCATTTTGCACTAGAGATGAGTTAATCTCTTCCACCAAATTGGTAGGA
65 CATAGGCTGTAACACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGA
* *
2057437 GATGAAGGGAGCTCCTCTTGCATTAGTTCTGTCCAGAATTGTTTAGATTCG
130 GATGAAGGGAGCTCCTCTTGCATTAGTTCTGTCCACAATTGTTTAGATTCA
* *
2057488 ACAGAAGAGGAATTAATCAGCTCCTTCTGAGAGTGATCTTCATCAACACTTATATTTGAATCTTC
1 ACAGAAGAGGAATTAATCAGTTCCTTCTGAGAGTGATCTTCATCAACACTTATGTTTGAATCTTC
2057553 ATAGGCTGTAACACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGAG
66 ATAGGCTGTAACACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGAG
* * **
2057618 ATGAAGGGAGCTCCTCTTGCATTAGTTCTG-CACAGAATTGTTTACAGCCA
131 ATGAAGGGAGCTCCTCTTGCATTAGTTCTGTC-CACAATTGTTTAGATTCA
* * *
2057668 ACGGAAGGGGAATTAATCAGTTCTTTCTGAGAGTGATCTTCATCAACACTTATGTTTGAATCTTC
1 ACAGAAGAGGAATTAATCAGTTCCTTCTGAGAGTGATCTTCATCAACACTTATGTTTGAATCTTC
2057733 ATAGGCTGTGAA-ACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGA
66 ATAGGCTGT-AACACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGA
*
2057797 GATGAAGGGAGCAT-CTCTTGCATTAGTTCTGTGCACAATTGTTTAGATTCA
130 GATGAAGGGAGC-TCCTCTTGCATTAGTTCTGTCCACAATTGTTTAGATTCA
* *
2057848 ACGGAAGAGGAATTAATCAGTTCCTTCTTG-GAGTGATCTTCATCAACACTTACGTTTGAATCTT
1 ACAGAAGAGGAATTAATCAGTTCCTTC-TGAGAGTGATCTTCATCAACACTTATGTTTGAATCTT
* * **
2057912 CATAGCCTGTGACACCCACATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGA
65 CATAGGCTGTAACACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGA
* * *
2057977 GATGAAGGGAGCACCTCTTGCACTAGTTCTGTGCACAATTGTTTA
130 GATGAAGGGAGCTCCTCTTGCATTAGTTCTGTCCACAATTGTTTA
2058022 ACATTGGCAC
Statistics
Matches: 490, Mismatches: 36, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
179 2 0.00
180 481 0.98
181 7 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (180 bp):
ACAGAAGAGGAATTAATCAGTTCCTTCTGAGAGTGATCTTCATCAACACTTATGTTTGAATCTTC
ATAGGCTGTAACACCGGCATTTTGCACCAGAGACAAGTTAATCTCTTCCACTGAATTGGTAGGAG
ATGAAGGGAGCTCCTCTTGCATTAGTTCTGTCCACAATTGTTTAGATTCA
Found at i:2060359 original size:17 final size:15
Alignment explanation
Indices: 2060337--2060368 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2060327 TTTATTAAAA
2060337 ATTATT-TTTATTAT
1 ATTATTATTTATTAT
2060351 ATTATTATTTATTAT
1 ATTATTATTTATTAT
2060366 ATT
1 ATT
2060369 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATTATTTATTAT
Found at i:2060595 original size:2 final size:2
Alignment explanation
Indices: 2060588--2060612 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2060578 ATAATACATG
2060588 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
2060613 CAATCATATA
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:2081351 original size:41 final size:42
Alignment explanation
Indices: 2081277--2081356 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
2081267 AATTGATGAA
**
2081277 AATTATTTTTAAAATTTTAATATTTTTTATGA-TTAAATATG
1 AATTATTTTTAAAATTTTAATATTTAATATGATTTAAATATG
*
2081318 AATTATTTTTAAAATTTTAATATTTAATGTGATTTAAAT
1 AATTATTTTTAAAATTTTAATATTTAATATGATTTAAAT
2081357 TTTATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 29 0.83
42 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (42 bp):
AATTATTTTTAAAATTTTAATATTTAATATGATTTAAATATG
Found at i:2089080 original size:30 final size:30
Alignment explanation
Indices: 2089023--2089094 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
2089013 ATCCTTAATA
*
2089023 TTTAATTTATACCCAAATAAACCTTTAACC
1 TTTAATTTATACCCAAATAAACATTTAACC
* * * * *
2089053 TTTAATTTTTATCTAAATAAATATTTAA-A
1 TTTAATTTATACCCAAATAAACATTTAACC
2089082 TTTAAATTTATAC
1 TTT-AATTTATAC
2089095 TTAAATAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTAATTTATACCCAAATAAACATTTAACC
Found at i:2092651 original size:2 final size:2
Alignment explanation
Indices: 2092644--2092669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2092634 TAAAAATCTA
2092644 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2092670 TATTATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2095273 original size:58 final size:58
Alignment explanation
Indices: 2095148--2095354 Score: 228
Period size: 58 Copynumber: 3.6 Consensus size: 58
2095138 TTGTGCAGAA
* * * * * *
2095148 AAAATTGATATTTTTAACTTTT-TTCCAAAATATTTTTTAG-AAACTTTAAT-TTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAC-TT-ATCTTCAAGG
* *
2095205 AAAATTGATACCTTT-AACTTTTCCTCAAAAATCCA-TTTTT-GAAAACTTATTTTTAAGG
1 AAAATTGATA-CTTTCAACTTTTCCTCAAAAAT--ATTTTTTAGAAAACTTATCTTCAAGG
* *
2095263 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGCTTATCTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATCTTCAAGG
*
2095321 AAATTTGATACTTTCAACTTTTCCTCAAAAATAT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATAT
2095355 ATATTTTTTG
Statistics
Matches: 129, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
56 1 0.01
57 28 0.22
58 90 0.70
59 9 0.07
60 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATCTTCAAGG
Found at i:2095387 original size:5 final size:5
Alignment explanation
Indices: 2095379--2095462 Score: 63
Period size: 5 Copynumber: 17.0 Consensus size: 5
2095369 TTATTTAAAG
*
2095379 AAAAT AAAAT --AAT AAAAT AAAA- AATA- AAAAT GAAAAT AAAATT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA-T -AAAAT
*
2095428 AAAGA- AAAAT AAAAT AAAAAT AAAA- ATAAT AAAAT
1 AAA-AT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
2095463 GTTAAACAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
3 3 0.05
4 10 0.15
5 35 0.54
6 13 0.20
7 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2095407 original size:6 final size:6
Alignment explanation
Indices: 2095379--2095456 Score: 74
Period size: 6 Copynumber: 13.2 Consensus size: 6
2095369 TTATTTAAAG
* *
2095379 AAAAT- AAAATAA TAAAATAA AAAATA AAAATG AAAATA AAATTA AAAAT-
1 AAAATA AAAAT-A -AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
*
2095428 -AAAGA AAAAT- AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA A
2095457 TAAAATGTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
4 3 0.05
5 10 0.16
6 36 0.59
7 5 0.08
8 7 0.11
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:2095754 original size:20 final size:21
Alignment explanation
Indices: 2095718--2095758 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2095708 ACAGACTAAG
2095718 CCTTCCTTTCTCTCTCTCTTC
1 CCTTCCTTTCTCTCTCTCTTC
*
2095739 CCTTTCTTTC-CTCTCTCTTC
1 CCTTCCTTTCTCTCTCTCTTC
2095759 TCTCTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (21 bp):
CCTTCCTTTCTCTCTCTCTTC
Found at i:2096000 original size:22 final size:22
Alignment explanation
Indices: 2095952--2096001 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2095942 TTTCAGAAAT
*
2095952 TTTCAAAAAAAATTCATCAAAA
1 TTTCTAAAAAAATTCATCAAAA
* *
2095974 ATTCTAAAAAAATTC-TCACCAA
1 TTTCTAAAAAAATTCATCA-AAA
2095996 TTTCTA
1 TTTCTA
2096002 GAGCTATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTCTAAAAAAATTCATCAAAA
Found at i:2096247 original size:30 final size:30
Alignment explanation
Indices: 2096208--2096355 Score: 54
Period size: 33 Copynumber: 4.5 Consensus size: 30
2096198 AAAATTAATC
*
2096208 AAAATAAAAAGATAAATATATTAATAGATAACA
1 AAAAT-AAAA-ATAAATATATTAATAAATAA-A
*
2096241 AAAA-AAATAGATAAATAATAATT-ATAAAAAATA
1 AAAATAAA-A-ATAAAT-AT-ATTAATAAATAA-A
*
2096274 AAAATAGATAAAT-AATA-A-AAATATTAATAGATA
1 AAAATA-A-AAATAAATATATTAATA--AATA-A-A
*
2096307 AAAAAATAAAAAAAAATATATTAATAAATAGACA
1 AA-A-ATAAAAATAAATATATTAATAAATA-A-A
2096341 AATAATAAAAATAAA
1 AA-AATAAAAATAAA
2096356 ATGAAAATAA
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
30 4 0.04
31 3 0.03
32 12 0.13
33 38 0.42
34 22 0.24
35 6 0.07
36 5 0.06
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (30 bp):
AAAATAAAAATAAATATATTAATAAATAAA
Found at i:2096259 original size:27 final size:29
Alignment explanation
Indices: 2096229--2096290 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
2096219 ATAAATATAT
*
2096229 TAATA-GATAACAAA-AAAAATAGATAAA
1 TAATATGATAAAAAATAAAAATAGATAAA
*
2096256 TAATAATTATAAAAAATAAAAATAGATAAA
1 TAAT-ATGATAAAAAATAAAAATAGATAAA
2096286 TAATA
1 TAATA
2096291 AAAATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.13
28 1 0.03
29 8 0.27
30 17 0.57
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (29 bp):
TAATATGATAAAAAATAAAAATAGATAAA
Found at i:2096269 original size:23 final size:24
Alignment explanation
Indices: 2096230--2096353 Score: 73
Period size: 24 Copynumber: 5.2 Consensus size: 24
2096220 TAAATATATT
*
2096230 AATAGAT-AACAA-AAAAAATAGATA
1 AATAGATAAATAATAAAAAATA-A-A
*
2096254 AATA-AT-AATTATAAAAAATAAA
1 AATAGATAAATAATAAAAAATAAA
**
2096276 AATAGATAAATAAT-AAAAATATT
1 AATAGATAAATAATAAAAAATAAA
*
2096299 AATAGATAAAAAAATAAAAAA-AAA
1 AATAGAT-AAATAATAAAAAATAAA
* *
2096323 TATATTA-ATAAATAGACAAATAATAAA
1 -A-A-TAGATAAATA-ATAAAAAATAAA
2096350 AATA
1 AATA
2096354 AAATGAAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
22 5 0.06
23 22 0.28
24 26 0.33
25 11 0.14
26 10 0.13
27 5 0.06
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (24 bp):
AATAGATAAATAATAAAAAATAAA
Found at i:2096367 original size:5 final size:6
Alignment explanation
Indices: 2096267--2096373 Score: 53
Period size: 6 Copynumber: 17.7 Consensus size: 6
2096257 AATAATTATA
* ** *
2096267 AAAAAT AAAAAT --AGAT AAATAAT AAAAAT ATTAAT AGATAA- AAAAAT
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT A-AAAAT AAAAAT
** * *
2096314 AAAAA- AAAATAT ATTAAT AAATAGAC AAATAAT AAAAAT -AAAAT GAAAAT
1 AAAAAT AAAA-AT AAAAAT AAA-A-AT AAA-AAT AAAAAT AAAAAT AAAAAT
2096364 AAAAAT AAAA
1 AAAAAT AAAA
2096374 GCCCATTGGG
Statistics
Matches: 78, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
4 3 0.04
5 12 0.15
6 42 0.54
7 15 0.19
8 6 0.08
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:2097210 original size:43 final size:42
Alignment explanation
Indices: 2097150--2097231 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
2097140 TTTAGCAAAC
* * *
2097150 TTGGAATTCATATCCAAAAA-TCTAAAGCTTTTTATTTGAATT
1 TTGGAATTCACATCCAAAAATTC-AAAGCTTCTCATTTGAATT
2097192 TTGGAGATTCACATCCAAAAATTCAAAGCTTCTCATTTGA
1 TTGGA-ATTCACATCCAAAAATTCAAAGCTTCTCATTTGA
2097232 GTTCAAAGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 5 0.14
43 28 0.80
44 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAGCTTCTCATTTGAATT
Found at i:2097446 original size:22 final size:21
Alignment explanation
Indices: 2097400--2097457 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
2097390 GTTTCACTCT
2097400 TCAAAGATTCTCATTTTGAAAC
1 TCAAAGATTCTCA-TTTGAAAC
**
2097422 TCAAAGATTCTCATTTGAGTTC
1 TCAAAGATTCTCATTTGA-AAC
*
2097444 TCAAAAATTCTCAT
1 TCAAAGATTCTCAT
2097458 CAAAATATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAC
Found at i:2098661 original size:31 final size:33
Alignment explanation
Indices: 2098626--2098689 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
2098616 TTTTCTCTCT
2098626 TTTTC-ATCCATTTTTTTT-TCATCTTTCATCA
1 TTTTCTATCCATTTTTTTTCTCATCTTTCATCA
* **
2098657 TTTTCTTTTCTTTTTTTTTTCTCATCTTTCATC
1 TTTTC-TATCCATTTTTTTTCTCATCTTTCATC
2098690 CATTGTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 5 0.19
33 10 0.37
34 12 0.44
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTTCTATCCATTTTTTTTCTCATCTTTCATCA
Found at i:2102707 original size:58 final size:58
Alignment explanation
Indices: 2102638--2102845 Score: 312
Period size: 58 Copynumber: 3.6 Consensus size: 58
2102628 TTGTATAGGA
* *
2102638 AAAATTGATACTTTCAACTTTTCTTCAAAAATCCA-TTTTT-GAAAACTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCTTCAAAAAT--ATTTTTTAGAAAGCTTATTTTCAAGG
* * *
2102696 AAAATTAATACTTTCAACTTTTTTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
* *
2102754 AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAGTTTATCTTCAAGG
1 AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
*
2102812 AAAATTGATACTTTCAACTTTTCCTCAAAAATAT
1 AAAATTGATACTTTCAACTTTTCTTCAAAAATAT
2102846 ATATTTTTTA
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
56 1 0.01
57 5 0.04
58 131 0.96
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTAGAAAGCTTATTTTCAAGG
Found at i:2102726 original size:27 final size:27
Alignment explanation
Indices: 2102637--2102727 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
2102627 TTTGTATAGG
* *
2102637 AAAAATTGATACTTTCAACTTTTCTTC
1 AAAAATTAATACTTTCAACTTTTTTTC
** * * *
2102664 AAAAATCCAT-TTTTGAAAACTTATTTTTA
1 AAAAATTAATACTTT--CAACTT-TTTTTC
2102693 AGGAAAATTAATACTTTCAACTTTTTTTC
1 A--AAAATTAATACTTTCAACTTTTTTTC
2102722 AAAAAT
1 AAAAAT
2102728 ATTTTTTAGA
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
26 3 0.06
27 13 0.28
28 5 0.11
29 11 0.23
30 5 0.11
31 7 0.15
32 3 0.06
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (27 bp):
AAAAATTAATACTTTCAACTTTTTTTC
Found at i:2102783 original size:27 final size:27
Alignment explanation
Indices: 2102753--2102843 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
2102743 TATTTTCAAG
2102753 AAAAATTGATACTTTCAACTTTTCTTC
1 AAAAATTGATACTTTCAACTTTTCTTC
** * *
2102780 AAAAA-T-ATTTTTTAGAAAGTTTATCTTC
1 AAAAATTGATACTTT--CAACTTT-TCTTC
*
2102808 AAGGAAAATTGATACTTTCAACTTTTCCTC
1 -A--AAAATTGATACTTTCAACTTTTCTTC
2102838 AAAAAT
1 AAAAAT
2102844 ATATATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 15 0.32
28 5 0.11
29 2 0.04
30 4 0.09
31 9 0.19
32 1 0.02
33 5 0.11
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTCTTC
Found at i:2102806 original size:28 final size:28
Alignment explanation
Indices: 2102719--2102809 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
2102709 TCAACTTTTT
* *
2102719 TTCAAAAATATTTTTTAGAAAGCTTATT
1 TTCAAAAATATTTTTTAGAAAGTTTATC
* * *
2102747 TTCAAGAAAAATTGATACTTT--CAACTTT-TC
1 TTCAA-AAATATT--T--TTTAGAAAGTTTATC
2102777 TTCAAAAATATTTTTTAGAAAGTTTATC
1 TTCAAAAATATTTTTTAGAAAGTTTATC
2102805 TTCAA
1 TTCAA
2102810 GGAAAATTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
25 3 0.06
27 6 0.13
28 12 0.26
29 12 0.26
30 6 0.13
31 5 0.11
33 3 0.06
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (28 bp):
TTCAAAAATATTTTTTAGAAAGTTTATC
Found at i:2102887 original size:13 final size:13
Alignment explanation
Indices: 2102869--2102945 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 13
2102859 TTTATTTAAG
2102869 AAAATAAAATAAT
1 AAAATAAAATAAT
*
2102882 AAAAT-AAATAAAA
1 AAAATAAAAT-AAT
2102895 AAAATAAAA-AAT
1 AAAATAAAATAAT
*
2102907 ATTAAACAACAATAAT
1 A--AAATAA-AATAAT
2102923 AATAATAATAATAA-
1 AA-AATAA-AATAAT
2102937 ATAAATAAA
1 A-AAATAAA
2102946 TAAATAAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
12 7 0.14
13 13 0.25
14 15 0.29
15 12 0.24
16 4 0.08
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:2102892 original size:12 final size:11
Alignment explanation
Indices: 2102869--2102953 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 11
2102859 TTTATTTAAG
2102869 AAAATAAAATAA
1 AAAAT-AAATAA
2102881 TAAAATAAAT-A
1 -AAAATAAATAA
2102892 AAAA-AAATAA
1 AAAATAAATAA
*
2102902 AAAAT-ATTAA
1 AAAATAAATAA
* *
2102912 ACAA-CAATAA
1 AAAATAAATAA
2102922 TAATAAT-AATAA
1 -AA-AATAAATAA
*
2102934 TAAATAAATAA
1 AAAATAAATAA
2102945 ATAAATAAA
1 A-AAATAAA
2102954 CGAAAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.07
10 23 0.40
11 8 0.14
12 18 0.31
13 5 0.09
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:2102893 original size:9 final size:9
Alignment explanation
Indices: 2102870--2102953 Score: 63
Period size: 9 Copynumber: 9.3 Consensus size: 9
2102860 TTATTTAAGA
2102870 AAATAAAAT
1 AAATAAAAT
2102879 -AATAAAAT
1 AAATAAAAT
*
2102887 AAATAAAAA
1 AAATAAAAT
2102896 AAATAAAA-
1 AAATAAAAT
2102904 AATATTAAACA-
1 AA-A-TAAA-AT
2102915 ACAATAATAAT
1 A-AATAA-AAT
2102926 -AATAATAAT
1 AAATAA-AAT
2102935 AAAT-AAAT
1 AAATAAAAT
2102943 AAAT-AAAT
1 AAATAAAAT
2102951 AAA
1 AAA
2102954 CGAAAAAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 17
0.79 0.01 0.20
Matches are distributed among these distances:
8 24 0.36
9 26 0.39
10 11 0.17
11 4 0.06
12 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2103734 original size:9 final size:9
Alignment explanation
Indices: 2103720--2103865 Score: 62
Period size: 9 Copynumber: 16.4 Consensus size: 9
2103710 GATAACAAAA
*
2103720 AAAATAGAT
1 AAAATAAAT
2103729 AAAATAAAT
1 AAAATAAAT
2103738 -AAATAAAT
1 AAAATAAAT
2103746 -AAAT-AAT
1 AAAATAAAT
2103753 AATAA-AAAT
1 AA-AATAAAT
*
2103762 AAAAGCAAAT
1 AAAA-TAAAT
2103772 -AAATAATAT
1 AAAATAA-AT
2103781 AAATATAAAT
1 AAA-ATAAAT
*
2103791 -AGATAAA-
1 AAAATAAAT
*
2103798 AAATAAAAAT
1 AAA-ATAAAT
*
2103808 AAAAATATAT
1 -AAAATAAAT
*
2103818 ATTAATAAAT
1 A-AAATAAAT
* *
2103828 -AGACAAAT
1 AAAATAAAT
2103836 AATAA-AAAT
1 AA-AATAAAT
2103845 AAAAT-AAT
1 AAAATAAAT
2103853 AATAAT-AAT
1 AA-AATAAAT
2103862 AAAA
1 AAAA
2103866 ACCCATTGGA
Statistics
Matches: 107, Mismatches: 13, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
7 3 0.03
8 37 0.35
9 41 0.38
10 19 0.18
11 7 0.07
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (9 bp):
AAAATAAAT
Found at i:2103737 original size:4 final size:4
Alignment explanation
Indices: 2103685--2103847 Score: 65
Period size: 4 Copynumber: 40.8 Consensus size: 4
2103675 AAATTAATTA
* * * * *
2103685 AAAT AAA- AAGAT AAAT ATAT TAAT AGAT AACA- AAAA AAAT AGAT AAAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT -AAAT
* *
2103734 AAAT AAAT AAAT AAAT -AAT AATAA AAAT AAAAGC AAAT AAAT AATAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT -AAA-T AAAT AAAT AA-AT
* * *
2103781 AAAT --AT AAAT AGAT AAA- AAAT -AA- AAAT AAA- AATAT ATAT TAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT
* * *
2103824 AAAT AGAC AAAT AATAA AAAT AAA
1 AAAT AAAT AAAT AA-AT AAAT AAA
2103848 ATAATAATAA
Statistics
Matches: 116, Mismatches: 25, Indels: 36
0.66 0.14 0.20
Matches are distributed among these distances:
2 2 0.02
3 15 0.13
4 76 0.66
5 23 0.20
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2103744 original size:45 final size:43
Alignment explanation
Indices: 2103683--2103805 Score: 125
Period size: 45 Copynumber: 2.9 Consensus size: 43
2103673 GAAAATTAAT
2103683 TAAAATAAA-AAGATAAATATATTAATAGATAACAAAAAAAATAG
1 TAAAATAAATAAGATAAATATA-TAATAGATAA-AAAAAAAATAG
* *
2103727 ATAAAATAAATAA-ATAAATAAATAATA-AT-AAAAATAAA-AG
1 -TAAAATAAATAAGATAAATATATAATAGATAAAAAAAAAATAG
* *
2103767 -CAAATAAATAATATAAATATA-AATAGATAAAAAATAAAA
1 TAAAATAAATAAGATAAATATATAATAGATAAAAAA-AAAA
2103806 ATAAAAATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
38 14 0.21
39 10 0.15
40 7 0.10
41 10 0.15
42 1 0.01
43 2 0.03
44 5 0.07
45 17 0.25
46 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (43 bp):
TAAAATAAATAAGATAAATATATAATAGATAAAAAAAAAATAG
Found at i:2103762 original size:6 final size:6
Alignment explanation
Indices: 2103746--2103866 Score: 54
Period size: 6 Copynumber: 20.5 Consensus size: 6
2103736 ATAAATAAAT
* ** * * *
2103746 AAATAA TAATAA AAAT-A AAA-GC AAATAA ATAATAT AAATAT AAATAG
1 AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA AAATAA
* * * * * *
2103793 ATA-AA AAATAA AAATAA AAATATA TATTAA TAAATAG ACA-AA TAATAA
1 AAATAA AAATAA AAATAA AAATA-A AAATAA -AAATAA AAATAA AAATAA
* *
2103841 AAAT-A AAATAA TAATAA TAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
2103867 CCCATTGGAC
Statistics
Matches: 85, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
5 17 0.20
6 56 0.66
7 12 0.14
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (6 bp):
AAATAA
Found at i:2103784 original size:23 final size:22
Alignment explanation
Indices: 2103686--2103857 Score: 88
Period size: 23 Copynumber: 7.7 Consensus size: 22
2103676 AATTAATTAA
* * *
2103686 AATAAAAAGATAAATATATTAAT
1 AATAAAAATA-AAATAAATAAAT
* *
2103709 AGATAACAAAAAAAATAGATAAAAT
1 A-ATAA-AAATAAAATAAAT-AAAT
*
2103734 AA-ATAAAT-AAATAAAT-AAT
1 AATAAAAATAAAATAAATAAAT
*
2103753 AATAAAAATAAAAGCAAATAAAT
1 AATAAAAATAAAA-TAAATAAAT
* * *
2103776 AATATAAATATAAATAGATAAAA
1 AATAAAAATA-AAATAAATAAAT
* *
2103799 AATAAAAATAAAA-ATATATATT
1 AATAAAAATAAAATAAATA-AAT
* *
2103821 AATAAATAGACAAAT-AATAAA-
1 AATAAAAATA-AAATAAATAAAT
2103842 AAT-AAAATAATAATAA
1 AATAAAAATAA-AATAA
2103858 TAATAAAAAC
Statistics
Matches: 114, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.05
20 12 0.11
21 18 0.16
22 20 0.18
23 35 0.31
24 15 0.13
25 8 0.07
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (22 bp):
AATAAAAATAAAATAAATAAAT
Found at i:2103790 original size:29 final size:30
Alignment explanation
Indices: 2103768--2103864 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 30
2103758 AAATAAAAGC
2103768 AAATAAATAATATAAATATAAATAGATAAA
1 AAATAAATAATATAAATATAAATAGATAAA
* *
2103798 AAATAAA-AATAAAAATATATATTA-ATAAA
1 AAATAAATAATATAAATATA-AATAGATAAA
* * *
2103827 TAGACAAATAATAAAAATA-AAATA-ATAATA
1 -AAATAAATAATATAAATATAAATAGATAA-A
2103857 ATAATAAA
1 A-AATAAA
2103865 AACCCATTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 24 0.44
30 21 0.38
31 10 0.18
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (30 bp):
AAATAAATAATATAAATATAAATAGATAAA
Found at i:2103826 original size:37 final size:37
Alignment explanation
Indices: 2103768--2103860 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
2103758 AAATAAAAGC
*
2103768 AAATAAATAATATA-AAT-ATAAATAGATAAAAAATAA
1 AAATAAA-AATATATAATAATAAATAGACAAAAAATAA
* *
2103804 AAATAAAAATATATATTAATAAATAGACAAATAATAA
1 AAATAAAAATATATAATAATAAATAGACAAAAAATAA
2103841 AAAT-AAAATA-ATAATAATAA
1 AAATAAAAATATATAATAATAA
2103861 TAAAAACCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
35 15 0.29
36 15 0.29
37 21 0.41
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (37 bp):
AAATAAAAATATATAATAATAAATAGACAAAAAATAA
Found at i:2109220 original size:2 final size:2
Alignment explanation
Indices: 2109213--2109239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2109203 GTTTAATCAA
2109213 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2109240 CACACCACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2110665 original size:58 final size:58
Alignment explanation
Indices: 2110540--2110753 Score: 233
Period size: 58 Copynumber: 3.7 Consensus size: 58
2110530 TTGTGCAGAA
* * * * *
2110540 AAAATTGATATTTTCAACTTTT-TTCCAAAATATTTTTTAG-AAACTTTAAT-TTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAC-TT-ATCTTCAAGG
* *
2110597 AAAATTGATACCTTT-AACTTTTCCTCAAAAATCCA-TTTTT-GAAAACTTATTTTTAAGG
1 AAAATTGATA-CTTTCAACTTTTCCTCAAAAAT--ATTTTTTAGAAAACTTATCTTCAAGG
* *
2110655 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAGCTTATCTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATCTTCAAGG
*
2110713 AAATTTGATACTTTCAACTTTTCCTCAAAATATATATTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAA-ATAT-TTTTT
2110754 TGAATTTTAT
Statistics
Matches: 134, Mismatches: 12, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
56 1 0.01
57 28 0.21
58 86 0.64
59 13 0.10
60 6 0.04
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATCTTCAAGG
Found at i:2110774 original size:5 final size:5
Alignment explanation
Indices: 2110766--2110833 Score: 75
Period size: 5 Copynumber: 12.6 Consensus size: 5
2110756 AATTTTATTT
2110766 AAATA AAATA AAATAA TAAATA AAAT- AAATGA AAATAA AAATAA AAATAA
1 AAATA AAATA AAAT-A -AAATA AAATA AAAT-A AAAT-A AAAT-A AAAT-A
2110816 AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAA
2110834 AAATGTTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
4 4 0.07
5 27 0.47
6 23 0.40
7 4 0.07
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:2110788 original size:12 final size:11
Alignment explanation
Indices: 2110766--2110833 Score: 81
Period size: 12 Copynumber: 6.3 Consensus size: 11
2110756 AATTTTATTT
2110766 AAAT-AAAATA
1 AAATAAAAATA
2110776 AAATAATAAATA
1 AAATAA-AAATA
2110788 AAAT--AAATGA
1 AAATAAAAAT-A
2110798 AAATAAAAATAA
1 AAATAAAAAT-A
2110810 AAATAAAAATA
1 AAATAAAAATA
2110821 AAAT-AAAATA
1 AAATAAAAATA
2110831 AAA
1 AAA
2110834 AAATGTTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
9 4 0.08
10 18 0.35
11 6 0.12
12 24 0.46
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:2110809 original size:38 final size:38
Alignment explanation
Indices: 2110766--2110886 Score: 113
Period size: 43 Copynumber: 3.1 Consensus size: 38
2110756 AATTTTATTT
*
2110766 AAATAAAATAAAATAATAAATAAAATAAATGAAAATAA
1 AAATAAAATAAAATAATAAATAAAATAAATGAAAAAAA
* *
2110804 AAATAAAAATAAAAATAAAATAAAATAAAA-AAATGTTAAACAA
1 AAAT-AAAAT-AAAAT--AAT-AAATAAAATAAATG-AAAAAAA
* *
2110847 ACA-ACAATAATAATAATAAAT-AAATAAATGAAAAAAA
1 AAATAAAATAA-AATAATAAATAAAATAAATGAAAAAAA
2110884 AAA
1 AAA
2110887 CTTGGGAACG
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
37 10 0.15
38 13 0.19
39 8 0.12
40 7 0.10
41 7 0.10
42 8 0.12
43 15 0.22
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (38 bp):
AAATAAAATAAAATAATAAATAAAATAAATGAAAAAAA
Found at i:2110810 original size:33 final size:32
Alignment explanation
Indices: 2110766--2110827 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
2110756 AATTTTATTT
2110766 AAATAAAAT-AAAATAATAAATAAAATAAATGA
1 AAATAAAATAAAAATAA-AAATAAAATAAATGA
2110798 AAATAAAAATAAAAATAAAAATAAAATAAA
1 AAAT-AAAATAAAAATAAAAATAAAATAAA
2110828 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (32 bp):
AAATAAAATAAAAATAAAAATAAAATAAATGA
Found at i:2110834 original size:22 final size:22
Alignment explanation
Indices: 2110767--2110834 Score: 88
Period size: 22 Copynumber: 3.1 Consensus size: 22
2110757 ATTTTATTTA
2110767 AATAAAATAAAATAATAAAT-AA
1 AATAAAATAAAATAA-AAATAAA
2110789 AAT-AAATGAAAATAAAAATAAA
1 AATAAAAT-AAAATAAAAATAAA
2110811 AATAAAAATAAAAT-AAAATAAA
1 AAT-AAAATAAAATAAAAATAAA
2110833 AA
1 AA
2110835 AATGTTAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.19
22 25 0.60
23 5 0.12
24 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.19
Consensus pattern (22 bp):
AATAAAATAAAATAAAAATAAA
Found at i:2111627 original size:16 final size:15
Alignment explanation
Indices: 2111608--2111674 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
2111598 TAAATATATT
2111608 AATAGATAACAAAAAA
1 AATAGATAA-AAAAAA
*
2111624 AATAGATAAAAAATA
1 AATAGATAAAAAAAA
* *
2111639 ATTATA-AAAAATAAA
1 AATAGATAAAAA-AAA
2111654 AATAGATAAATAATAAA
1 AATAGATAAA-AA-AAA
2111671 AATA
1 AATA
2111675 TTAATAGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
14 5 0.12
15 15 0.36
16 12 0.29
17 10 0.24
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (15 bp):
AATAGATAAAAAAAA
Found at i:2111654 original size:6 final size:6
Alignment explanation
Indices: 2111645--2111756 Score: 56
Period size: 6 Copynumber: 18.7 Consensus size: 6
2111635 AATAATTATA
* **
2111645 AAAAAT AAAAAT --AGAT AAATAAT AAAAAT ATTAAT AGATAAA- AAAAAT
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT A-A-AAAT AAAAAT
* * *
2111693 AAAAAT AAAAA- AAAATATT AATAAAT AGACA- AATAAT AAAAAT -AAAAT
1 AAAAAT AAAAAT AAAA-A-T AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
**
2111741 GGAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAA
2111757 GCCCATTGGG
Statistics
Matches: 79, Mismatches: 15, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
4 3 0.04
5 14 0.18
6 47 0.59
7 8 0.10
8 5 0.06
9 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:2111656 original size:19 final size:18
Alignment explanation
Indices: 2111632--2111677 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2111622 AAAATAGATA
2111632 AAAAATAATTATAAAAAAT
1 AAAAAT-ATTATAAAAAAT
* *
2111651 AAAAATA-GATAAATAAT
1 AAAAATATTATAAAAAAT
2111668 AAAAATATTA
1 AAAAATATTA
2111678 ATAGATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 15 0.65
18 2 0.09
19 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATATTATAAAAAAT
Found at i:2111657 original size:30 final size:29
Alignment explanation
Indices: 2111613--2111669 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2111603 ATATTAATAG
*
2111613 ATAACAAAAAAAATAGATAAAAAATAATT
1 ATAAAAAAAAAAATAGATAAAAAATAATT
*
2111642 ATAAAAAATAAAAATAGATAAATAATAA
1 ATAAAAAA-AAAAATAGATAAAAAATAA
2111670 AAATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (29 bp):
ATAAAAAAAAAAATAGATAAAAAATAATT
Found at i:2111662 original size:23 final size:21
Alignment explanation
Indices: 2111648--2111751 Score: 60
Period size: 19 Copynumber: 5.0 Consensus size: 21
2111638 AATTATAAAA
2111648 AATAAAAATAGATAAATAATAAA
1 AATAAAAATAGAT-AATAA-AAA
**
2111671 AATATTAATAGAT-A-AAAAA
1 AATAAAAATAGATAATAAAAA
2111690 AATAAAAATA-A-AA-AAAAA
1 AATAAAAATAGATAATAAAAA
* *
2111708 TATTAATAAATAGACAAATAATAAA
1 -AATAA-AAATAGA-TAATAA-AAA
*
2111733 AAT-AAAATGGA-AATAAAAA
1 AATAAAAATAGATAATAAAAA
2111752 TAAAAGCCCA
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
18 7 0.11
19 18 0.27
20 12 0.18
21 2 0.03
22 6 0.09
23 14 0.21
24 4 0.06
25 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (21 bp):
AATAAAAATAGATAATAAAAA
Found at i:2111685 original size:16 final size:16
Alignment explanation
Indices: 2111595--2111688 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 16
2111585 CAAAATAAAA
*
2111595 AGATAAATATATTAAT
1 AGATAAAAATATTAAT
**
2111611 AGATAACAAA-AAAAAT
1 AGATAA-AAATATTAAT
*
2111627 AGATAAAAAATAATTATAAA
1 AGAT-AAAAAT-A-T-TAAT
* *
2111647 AAATAAAAATAGATAAAT
1 AGATAAAAAT--ATTAAT
2111665 A-ATAAAAATATTAAT
1 AGATAAAAATATTAAT
2111680 AGATAAAAA
1 AGATAAAAA
2111689 AAATAAAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
15 6 0.10
16 24 0.41
17 12 0.20
18 4 0.07
19 7 0.12
20 6 0.10
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.24
Consensus pattern (16 bp):
AGATAAAAATATTAAT
Found at i:2111691 original size:69 final size:68
Alignment explanation
Indices: 2111587--2111739 Score: 181
Period size: 68 Copynumber: 2.2 Consensus size: 68
2111577 AAATTAATCA
* * * *
2111587 AAATAA-AAAGATAAATATATTAATAGATAACAAAAAA-AATAGATAAAAAATAAT-TATAAAAA
1 AAATAATAAAAATAAAAATATTAATAGATAA-AAAAAATAA-AAATAAAAAAAAATAT-TAAAAA
2111649 ATA-A-
63 ATAGAC
*
2111653 AAATAGATAAATAATAAAAATATTAATAGATAAAAAAAATAAAAATAAAAAAAAATATTAATAAA
1 AAATA-ATAAA-AATAAAAATATTAATAGATAAAAAAAATAAAAATAAAAAAAAATATTAAAAAA
2111718 TAGAC
64 TAGAC
2111723 AAATAATAAAAATAAAA
1 AAATAATAAAAATAAAA
2111740 TGGAAATAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
66 5 0.07
67 1 0.01
68 36 0.48
69 28 0.37
70 5 0.07
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (68 bp):
AAATAATAAAAATAAAAATATTAATAGATAAAAAAAATAAAAATAAAAAAAAATATTAAAAAATA
GAC
Found at i:2111739 original size:37 final size:35
Alignment explanation
Indices: 2111621--2111739 Score: 118
Period size: 35 Copynumber: 3.3 Consensus size: 35
2111611 AGATAACAAA
*
2111621 AAAAATAGATAAAAAATAATT-ATAAA-AAATAAAAAT
1 AAAAATA-AAAAAAAAT-ATTAATAAATAAA-AAAAAT
* *
2111657 AGATAAAT-AATAAAAATATTAATAGATAAAAAAAAT
1 A-A-AAATAAAAAAAAATATTAATAAATAAAAAAAAT
*
2111693 AAAAATAAAAAAAAATATTAATAAATAGACAAATAAT
1 AAAAATAAAAAAAAATATTAATAAATA-A-AAAAAAT
2111730 AAAAATAAAA
1 AAAAATAAAA
2111740 TGGAAATAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
34 4 0.06
35 22 0.31
36 20 0.29
37 20 0.29
38 4 0.06
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (35 bp):
AAAAATAAAAAAAAATATTAATAAATAAAAAAAAT
Found at i:2112156 original size:27 final size:25
Alignment explanation
Indices: 2112122--2112173 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
2112112 AGCTCAACGT
*
2112122 CTTTGAAAAATAAATGGCTCTTCTAA
1 CTTTG-AAAATAAATGGCTCCTCTAA
2112148 CTTTAGAAAATAAATGGCTCCTCTAA
1 CTTT-GAAAATAAATGGCTCCTCTAA
2112174 TCAGAGACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (25 bp):
CTTTGAAAATAAATGGCTCCTCTAA
Found at i:2112204 original size:41 final size:40
Alignment explanation
Indices: 2112147--2112250 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 40
2112137 GGCTCTTCTA
*
2112147 ACTTTAGAAAATAAATGGCTCCTCTAATCAG-AGACTCGACG
1 ACTTT-GAAAATAAATGGCTCCTCTAATCAGAAG-CTCAACG
* * *
2112188 ACTTTGAAAACTAAATGGCTCCTTTAATCAGAAGCTTAATG
1 ACTTTGAAAA-TAAATGGCTCCTCTAATCAGAAGCTCAACG
*
2112229 ACTTTGGAAATAAATGGCTCCT
1 ACTTTGAAAATAAATGGCTCCT
2112251 TGACGATTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
40 17 0.30
41 37 0.66
42 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (40 bp):
ACTTTGAAAATAAATGGCTCCTCTAATCAGAAGCTCAACG
Found at i:2112608 original size:43 final size:42
Alignment explanation
Indices: 2112548--2112629 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
2112538 TTTAGCAAAC
* * *
2112548 TTGGAATTCATATCCAAAAA-TCTAAAGCTTTTTATTTGAATT
1 TTGGAATTCACATCCAAAAATTC-AAAGCTTCTCATTTGAATT
2112590 TTGGAGATTCACATCCAAAAATTCAAAGCTTCTCATTTGA
1 TTGGA-ATTCACATCCAAAAATTCAAAGCTTCTCATTTGA
2112630 GTTCAAAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 5 0.14
43 28 0.80
44 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAGCTTCTCATTTGAATT
Found at i:2112844 original size:22 final size:22
Alignment explanation
Indices: 2112798--2112855 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2112788 GTTTCACTCT
*
2112798 TCAAAGATTCTCATTTTAAAAC
1 TCAAAGATTCTCATTTGAAAAC
***
2112820 TCAAAGATTCTCATTTGAGTTC
1 TCAAAGATTCTCATTTGAAAAC
*
2112842 TCAAAAATTCTCAT
1 TCAAAGATTCTCAT
2112856 CAAAATATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (22 bp):
TCAAAGATTCTCATTTGAAAAC
Found at i:2118194 original size:61 final size:58
Alignment explanation
Indices: 2118122--2118260 Score: 183
Period size: 61 Copynumber: 2.4 Consensus size: 58
2118112 TAAAAATAAC
* * *
2118122 CTTTCAACTTTTTTTCAAAAATATTTTTTATAAAGCCTTAT-TTCAAGGAAAAATTGAATA
1 CTTTCAACTTTTCTTCAAAAAAATTTTTTAGAAAG-CTTATCTTCAAGG-AAAATTG-ATA
*
2118182 CTTTCCAACTTTTCTTCAAAAAAATTTTTTAGAAAGTTTATCTTCAAGGAAAATTGATA
1 CTTT-CAACTTTTCTTCAAAAAAATTTTTTAGAAAGCTTATCTTCAAGGAAAATTGATA
*
2118241 CTTTCAAC-TTTCCTCAAAAA
1 CTTTCAACTTTTCTTCAAAAA
2118261 TATATATTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
57 11 0.15
58 4 0.06
59 7 0.10
60 15 0.21
61 35 0.49
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.41
Consensus pattern (58 bp):
CTTTCAACTTTTCTTCAAAAAAATTTTTTAGAAAGCTTATCTTCAAGGAAAATTGATA
Found at i:2118300 original size:9 final size:9
Alignment explanation
Indices: 2118286--2118311 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2118276 TTTATTTAGA
2118286 AAATAAAAT
1 AAATAAAAT
2118295 AAATAAAAT
1 AAATAAAAT
2118304 AAATAAAA
1 AAATAAAA
2118312 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2118602 original size:15 final size:16
Alignment explanation
Indices: 2118581--2118625 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
2118571 GCAGATCGAG
2118581 CCTTCCCTCTCTCTTT
1 CCTTCCCTCTCTCTTT
2118597 -CTTCCCT-TC-CTTT
1 CCTTCCCTCTCTCTTT
2118610 CCTCTCCCTTCTCTCT
1 CCT-TCCC-TCTCTCT
2118626 AAACTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 11 0.46
16 1 0.04
17 2 0.08
18 2 0.08
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (16 bp):
CCTTCCCTCTCTCTTT
Found at i:2119152 original size:4 final size:4
Alignment explanation
Indices: 2119103--2119246 Score: 68
Period size: 4 Copynumber: 36.2 Consensus size: 4
2119093 AAATTAATTA
* * * * *
2119103 AAAT AAA- AAGAT AAAT ATAT TAAT AGAT AACA- AAAA AAAT AGAT AAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
* * *
2119151 AAAAG AAAT AAAT AAAT -AAT AAAA AAAT AAAAGC AAAT AAAT -AAT AAA-
1 -AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT AAAT AAAT AAAT
* * * * *
2119199 AATAT AAAT AGAT AAAA AAAT -AA- AAAT AAAT ATAT ATAT TAAT AAAT
1 AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2119246 A
1 A
2119247 GACAAATAAT
Statistics
Matches: 104, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
3 15 0.14
4 75 0.72
5 14 0.13
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2119230 original size:41 final size:41
Alignment explanation
Indices: 2119103--2119230 Score: 129
Period size: 41 Copynumber: 3.1 Consensus size: 41
2119093 AAATTAATTA
* * * *
2119103 AAATAAAAAGATAAATATATTAATAGAT-AACAAA-AAAAAT
1 AAATAAATA-ATAAAAATATAAATAGATAAAAAAATAAAAAT
* **
2119143 AGATAAATAA-AAGAAATAAATAAATA-ATAAAAAAATAAAAGC
1 AAATAAATAATAA-AAAT--ATAAATAGATAAAAAAATAAAAAT
2119185 AAATAAATAATAAAAATATAAATAGATAAAAAAATAAAAAT
1 AAATAAATAATAAAAATATAAATAGATAAAAAAATAAAAAT
2119226 AAATA
1 AAATA
2119231 TATATATTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
38 2 0.03
39 4 0.06
40 16 0.23
41 30 0.42
42 17 0.24
43 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (41 bp):
AAATAAATAATAAAAATATAAATAGATAAAAAAATAAAAAT
Found at i:2119244 original size:30 final size:31
Alignment explanation
Indices: 2119148--2119272 Score: 93
Period size: 31 Copynumber: 4.2 Consensus size: 31
2119138 AAAATAGATA
* * *
2119148 AATAAAAGAAATAAAT-A-AATAATA-AAAA
1 AATAAAACAAATAAATAATAAAAATATAAAT
2119176 AATAAAAGCAAATAAATAATAAAAATATAAAT
1 AATAAAA-CAAATAAATAATAAAAATATAAAT
* *
2119208 AGATAAAA-AAATAAA-AATAAATATATATATT
1 A-ATAAAACAAATAAATAATAAAAATATA-AAT
* * * *
2119239 AAT-AAATAGACAAATAATAATAATA-AAAT
1 AATAAAACAAATAAATAATAAAAATATAAAT
2119268 AATAA
1 AATAA
2119273 TAATAATAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
28 7 0.09
29 16 0.21
30 21 0.27
31 24 0.31
32 4 0.05
33 6 0.08
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (31 bp):
AATAAAACAAATAAATAATAAAAATATAAAT
Found at i:2119259 original size:3 final size:3
Alignment explanation
Indices: 2119251--2119281 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2119241 TAAATAGACA
2119251 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2119282 AAACCCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2119268 original size:8 final size:8
Alignment explanation
Indices: 2119138--2119283 Score: 56
Period size: 8 Copynumber: 17.5 Consensus size: 8
2119128 GATAACAAAA
2119138 AAAATAGAT
1 AAAATA-AT
*
2119147 -AAATAAA
1 AAAATAAT
2119154 AGAAATAA-
1 A-AAATAAT
2119162 ATAAATAAT
1 A-AAATAAT
*
2119171 AAAAAAAT
1 AAAATAAT
*
2119179 AAAAGCAA-
1 AAAA-TAAT
2119187 ATAAATAAT
1 A-AAATAAT
2119196 -AAA-AAT
1 AAAATAAT
2119202 ATAAATAGAT
1 A-AAATA-AT
*
2119212 AAAAAAAT
1 AAAATAAT
2119220 -AAA-AAT
1 AAAATAAT
2119226 AAATATATAT
1 AAA-ATA-AT
*
2119236 ATTAATAAAT
1 A-AAAT-AAT
*
2119246 AGACA-AAT
1 A-AAATAAT
2119254 AATAATAAT
1 AA-AATAAT
2119263 AAAATAAT
1 AAAATAAT
2119271 AATAATAAT
1 AA-AATAAT
2119280 AAAA
1 AAAA
2119284 ACCCATTGGA
Statistics
Matches: 107, Mismatches: 11, Indels: 39
0.68 0.07 0.25
Matches are distributed among these distances:
6 6 0.06
7 10 0.09
8 46 0.43
9 31 0.29
10 12 0.11
11 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:2119268 original size:38 final size:38
Alignment explanation
Indices: 2119124--2119282 Score: 123
Period size: 38 Copynumber: 4.1 Consensus size: 38
2119114 TAAATATATT
*
2119124 AATAGATAACAAAAA-AAATAGATAAATAA-AAGAAATAAATA
1 AATAGATAA-AAAAATAAA-A-ATAAATAATAA-TAAT-AATA
*
2119165 AATA-ATAAAAAAATAAAAGCAAATAAATAATAAAAAT-ATA
1 AATAGATAAAAAAAT--AA--AAATAAATAATAATAATAATA
*
2119205 AATAGATAAAAAAATAAAAATAAAT-ATATATATTAATA
1 AATAGATAAAAAAATAAAAATAAATAATA-ATAATAATA
* * *
2119243 AATAGA-CAAATAATAATAATAAAATAATAATAATAATA
1 AATAGATAAAAAAATAAAAAT-AAATAATAATAATAATA
2119281 AA
1 AA
2119283 AACCCATTGG
Statistics
Matches: 101, Mismatches: 6, Indels: 25
0.77 0.05 0.19
Matches are distributed among these distances:
36 3 0.03
37 22 0.22
38 23 0.23
39 10 0.10
40 11 0.11
41 14 0.14
42 14 0.14
43 3 0.03
44 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (38 bp):
AATAGATAAAAAAATAAAAATAAATAATAATAATAATA
Found at i:2119271 original size:17 final size:17
Alignment explanation
Indices: 2119251--2119283 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2119241 TAAATAGACA
2119251 AATAATAATAATAAAAT
1 AATAATAATAATAAAAT
2119268 AATAATAATAATAAAA
1 AATAATAATAATAAAA
2119284 ACCCATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAATAATAAAAT
Found at i:2127222 original size:11 final size:11
Alignment explanation
Indices: 2127208--2127246 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2127198 TAAATAATAA
2127208 TTAAATTTAAT
1 TTAAATTTAAT
*
2127219 TTAAATTTTAT
1 TTAAATTTAAT
* *
2127230 TTAAATTAAAC
1 TTAAATTTAAT
2127241 TTAAAT
1 TTAAAT
2127247 AATTTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2136314 original size:23 final size:22
Alignment explanation
Indices: 2136290--2136349 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
2136280 GAAATTCGTA
2136290 TTTAATTTATAAAATATTATTTAT
1 TTTAATTTATAAAAT-TTA-TTAT
* * *
2136314 TTTGATTTAAAAAATTTATAAT
1 TTTAATTTATAAAATTTATTAT
*
2136336 TTTATTTTATAAAA
1 TTTAATTTATAAAA
2136350 AATATTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 14 0.47
23 3 0.10
24 13 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAATTTATAAAATTTATTAT
Found at i:2136337 original size:22 final size:23
Alignment explanation
Indices: 2136289--2136359 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 23
2136279 AGAAATTCGT
* * *
2136289 ATTTAATTTATAAAATATTATTT
1 ATTTTATTTAAAAAATATTATTA
2136312 ATTTTGATTTAAAAAAT-TTA-TA
1 ATTTT-ATTTAAAAAATATTATTA
2136334 ATTTTATTTTATAAAAAATATT-TTA
1 ATTTTA--TT-TAAAAAATATTATTA
2136359 A
1 A
2136360 AATTTTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.03
22 6 0.15
23 9 0.23
24 18 0.46
25 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
ATTTTATTTAAAAAATATTATTA
Done.