Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 12 of 133
Found at i:3210512 original size:17 final size:18
Alignment explanation
Indices: 3210491--3210559 Score: 70
Period size: 17 Copynumber: 3.8 Consensus size: 18
3210481 TCAAAACAGG
3210491 AAAAAATTTAAAAATCAT
1 AAAAAATTTAAAAATCAT
* *
3210509 -AAAAATTCAAAAATATAT
1 AAAAAATTTAAAAAT-CAT
*
3210527 AAAAAAATTTAAAAA-CCT
1 -AAAAAATTTAAAAATCAT
*
3210545 AAAAAATATAAAAAT
1 AAAAAATTTAAAAAT
3210560 TAAAATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
17 26 0.63
18 3 0.07
20 12 0.29
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAATTTAAAAATCAT
Found at i:3210667 original size:19 final size:18
Alignment explanation
Indices: 3210645--3210816 Score: 88
Period size: 19 Copynumber: 9.2 Consensus size: 18
3210635 TTTTTATTCC
3210645 TTTTAATTTTTAAGATTCTT
1 TTTTAATTTTTAAGA-T-TT
* *
3210665 TTTTGAACATTTTAGGATTT
1 TTTT-AA-TTTTTAAGATTT
*
3210685 TTTTAATTTTTCAGATTTT
1 TTTTAATTTTTAAGA-TTT
*
3210704 CTTTTATATTTTTTTAAAATTT
1 -TTTTA-A--TTTTTAAGATTT
* * *
3210726 GTAT-A-TTTT-ATA-TT
1 TTTTAATTTTTAAGATTT
*
3210740 TTTTACTTTTTAAGATTTT
1 TTTTAATTTTTAAGA-TTT
*
3210759 TTTTAATTTTTCAA-ATAT
1 TTTTAATTTTT-AAGATTT
3210777 TTTTAATTTTTTAAGA--T
1 TTTTAA-TTTTTAAGATTT
*
3210794 TTTTAATTTTTTAAAATTT
1 TTTTAA-TTTTTAAGATTT
3210813 TTTT
1 TTTT
3210817 GAAATTTGTT
Statistics
Matches: 118, Mismatches: 17, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
14 4 0.03
15 2 0.02
16 8 0.07
17 18 0.15
18 16 0.14
19 30 0.25
20 17 0.14
21 6 0.05
22 10 0.08
23 7 0.06
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAATTTTTAAGATTT
Found at i:3210759 original size:17 final size:17
Alignment explanation
Indices: 3210737--3210815 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 17
3210727 TATATTTTAT
*
3210737 ATTTTTTACTTTTTAAG
1 ATTTTTTATTTTTTAAG
*
3210754 ATTTTTTTTAATTTTTCAA-
1 A--TTTTTT-ATTTTTTAAG
3210773 ATATTTTTAATTTTTTAAG
1 AT-TTTTT-ATTTTTTAAG
* *
3210792 ATTTTTAATTTTTTAAA
1 ATTTTTTATTTTTTAAG
3210809 ATTTTTT
1 ATTTTTT
3210816 TGAAATTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 17 0.33
18 18 0.35
19 9 0.18
20 7 0.14
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTTATTTTTTAAG
Found at i:3210768 original size:9 final size:9
Alignment explanation
Indices: 3210756--3210854 Score: 56
Period size: 9 Copynumber: 10.7 Consensus size: 9
3210746 TTTTTAAGAT
3210756 TTTTTTTAA
1 TTTTTTTAA
**
3210765 TTTTTCAAA
1 TTTTTTTAA
*
3210774 TATTTTTAA
1 TTTTTTTAA
3210783 -TTTTTTAA
1 TTTTTTTAA
**
3210791 GATTTTTAA
1 TTTTTTTAA
*
3210800 TTTTTTAAAA
1 TTTTTT-TAA
3210810 TTTTTTTGAAA
1 TTTTTTT--AA
* ***
3210821 TTTGTTGGT
1 TTTTTTTAA
*
3210830 TTTTTATTTA
1 TTTTT-TTAA
3210840 TTTTTTTAA
1 TTTTTTTAA
3210849 TTTTTT
1 TTTTTT
3210855 AAATATTGCA
Statistics
Matches: 65, Mismatches: 20, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
8 7 0.11
9 37 0.57
10 14 0.22
11 7 0.11
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:3210796 original size:55 final size:55
Alignment explanation
Indices: 3210673--3210816 Score: 143
Period size: 55 Copynumber: 2.6 Consensus size: 55
3210663 TTTTTTGAAC
* * *
3210673 ATTTTAGGATTTTTTTAATTTTTCAGATTTTCTTTTATATTTTTTTAAAATTTGTAT
1 ATTTTAAGA-TTTTTTAATTTTTAAGATTTT-TTTTATATTTTTTCAAAATTTGTAT
* * *
3210730 ATTTT-ATATTTTTTACTTTTTAAGATTTTTTTTA-A-TTTTTCAAATATTTTTAAT
1 ATTTTAAGATTTTTTAATTTTTAAGATTTTTTTTATATTTTTTCAAA-ATTTGT-AT
* *
3210784 TTTTTAAGA-TTTTTAATTTTTTAAAATTTTTTT
1 ATTTTAAGATTTTTTAA-TTTTTAAGATTTTTTT
3210817 GAAATTTGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
52 8 0.11
53 6 0.08
54 17 0.23
55 36 0.49
56 1 0.01
57 5 0.07
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (55 bp):
ATTTTAAGATTTTTTAATTTTTAAGATTTTTTTTATATTTTTTCAAAATTTGTAT
Found at i:3210804 original size:18 final size:17
Alignment explanation
Indices: 3210758--3210814 Score: 87
Period size: 17 Copynumber: 3.3 Consensus size: 17
3210748 TTTAAGATTT
*
3210758 TTTTTAATTTTTCAAATA
1 TTTTTAATTTTTTAAA-A
*
3210776 TTTTTAATTTTTTAAGA
1 TTTTTAATTTTTTAAAA
3210793 TTTTTAATTTTTTAAAA
1 TTTTTAATTTTTTAAAA
3210810 TTTTT
1 TTTTT
3210815 TTGAAATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTAATTTTTTAAAA
Found at i:3214037 original size:23 final size:23
Alignment explanation
Indices: 3214001--3214051 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3213991 ACCTTCTTCA
* * *
3214001 TTTTTTTATTTTTTATTTATTAT
1 TTTTTTTATATTTTAATCATTAT
3214024 TATTTTTTA-ATTTTAATCATTAT
1 T-TTTTTTATATTTTAATCATTAT
3214047 TTTTT
1 TTTTT
3214052 AAAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTTATATTTTAATCATTAT
Found at i:3214047 original size:20 final size:18
Alignment explanation
Indices: 3214006--3214053 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
3213996 CTTCATTTTT
*
3214006 TTATTTTTT-ATTTATTA
1 TTATTTTTTAATTTATCA
3214023 TTATTTTTTAATTTTAATCA
1 TTATTTTTTAA-TTT-ATCA
3214043 TTATTTTTTAA
1 TTATTTTTTAA
3214054 AATAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.33
18 1 0.04
19 3 0.11
20 14 0.52
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTTAATTTATCA
Found at i:3214059 original size:19 final size:20
Alignment explanation
Indices: 3214022--3214064 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3214012 TTTATTTATT
** *
3214022 ATTATTTTTTAATTTTAATC
1 ATTATTTTTTAATAATAATA
3214042 ATTATTTTTTAA-AATAATA
1 ATTATTTTTTAATAATAATA
3214061 ATTA
1 ATTA
3214065 AAATAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTTTTTAATAATAATA
Found at i:3214101 original size:21 final size:22
Alignment explanation
Indices: 3214057--3214105 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
3214047 TTTTTAAAAT
*
3214057 AATAATTAAAATAAAAACTCAA
1 AATAATTAAAATAAAAACTAAA
3214079 AATAA-TAAAATAACAAA-TAAA
1 AATAATTAAAATAA-AAACTAAA
3214100 AA-AATT
1 AATAATT
3214106 TTGGGCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 14 0.58
22 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (22 bp):
AATAATTAAAATAAAAACTAAA
Found at i:3214819 original size:21 final size:21
Alignment explanation
Indices: 3214802--3214857 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
3214792 AAAATTCTTG
3214802 TTTGAAATTCAAAGATTCTCA
1 TTTGAAATTCAAAGATTCTCA
* *
3214823 TTTGAAATTCAAATATTCGCA
1 TTTGAAATTCAAAGATTCTCA
*
3214844 TTTGAGAACTCAAA
1 TTTGA-AATTCAAA
3214858 AAATTTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (21 bp):
TTTGAAATTCAAAGATTCTCA
Found at i:3216019 original size:26 final size:27
Alignment explanation
Indices: 3215990--3216050 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
3215980 AATTTGAGTC
3215990 TTTCTTTTCTCTCA-TTTTCATCTTTT
1 TTTCTTTTCTCTCAGTTTTCATCTTTT
* * **
3216016 TTTC-ATTCTTTCAGTTTTTTTCTTTT
1 TTTCTTTTCTCTCAGTTTTCATCTTTT
3216042 TTT-TTTTCT
1 TTTCTTTTCT
3216051 TTTCTTCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTCTTTTCTCTCAGTTTTCATCTTTT
Found at i:3218987 original size:28 final size:29
Alignment explanation
Indices: 3218956--3219013 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
3218946 AATCATGAGC
3218956 ATGAAAATGATGCATAGAATG-AAATGAT
1 ATGAAAATGATGCATAGAATGAAAATGAT
** *
3218984 ATGAAAATGATGTGTTGAATGAAAATGAT
1 ATGAAAATGATGCATAGAATGAAAATGAT
3219013 A
1 A
3219014 CAGGTGCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.48, C:0.02, G:0.22, T:0.28
Consensus pattern (29 bp):
ATGAAAATGATGCATAGAATGAAAATGAT
Found at i:3222715 original size:16 final size:16
Alignment explanation
Indices: 3222659--3222719 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
3222649 TTCGACATGA
3222659 AATTA-ATAAA-ATAT
1 AATTATATAAATATAT
* *
3222673 TATT-TTTAAATATA-
1 AATTATATAAATATAT
* *
3222687 AAATATTTAAATATAT
1 AATTATATAAATATAT
3222703 AATTATATAAATATAT
1 AATTATATAAATATAT
3222719 A
1 A
3222720 TAAATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.24
15 13 0.35
16 15 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATATAAATATAT
Found at i:3222717 original size:8 final size:8
Alignment explanation
Indices: 3222679--3222719 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3222669 ATATTATTTT
3222679 TAAATATA
1 TAAATATA
*
3222687 -AAATATT
1 TAAATATA
3222694 TAAATATA
1 TAAATATA
*
3222702 TAATTATA
1 TAAATATA
3222710 TAAATATA
1 TAAATATA
3222718 TA
1 TA
3222720 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:3222725 original size:26 final size:25
Alignment explanation
Indices: 3222682--3222734 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
3222672 TTATTTTTAA
* * *
3222682 ATATAAAATATTTAAATATATAATT
1 ATATAAAATATATAAATAAAAAATT
3222707 ATATAAATATATATAAATAAAAAATT
1 ATATAAA-ATATATAAATAAAAAATT
3222733 AT
1 AT
3222735 TTTTATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAAAATATATAAATAAAAAATT
Found at i:3224019 original size:13 final size:13
Alignment explanation
Indices: 3224001--3224030 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3223991 CTAGTGTCTG
*
3224001 TTTTATTCCATTT
1 TTTTATTCAATTT
3224014 TTTTATTCAATTT
1 TTTTATTCAATTT
3224027 TTTT
1 TTTT
3224031 TTAATGTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATTCAATTT
Found at i:3224113 original size:24 final size:24
Alignment explanation
Indices: 3224060--3224113 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3224050 TTTTTTTTGT
* * *
3224060 AATTTTTGAATATTTAAAATTTTT
1 AATTTTTGAATATTAAAAATTATG
* *
3224084 ATTTTTTTAATATTAAAAATTATG
1 AATTTTTGAATATTAAAAATTATG
3224108 AATTTT
1 AATTTT
3224114 AATTTTATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
AATTTTTGAATATTAAAAATTATG
Found at i:3225677 original size:20 final size:20
Alignment explanation
Indices: 3225641--3225680 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3225631 CTATTCAATA
*
3225641 AAAATATTAATCGATAAATT
1 AAAATATTAATCAATAAATT
3225661 AAAATA-TAATCAAATAAATT
1 AAAATATTAATC-AATAAATT
3225681 TAACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATATTAATCAATAAATT
Found at i:3226649 original size:58 final size:58
Alignment explanation
Indices: 3226465--3226836 Score: 500
Period size: 57 Copynumber: 6.3 Consensus size: 58
3226455 TAGTGTAGGA
*
3226465 AAAATTGATTACTTTCAACTTTT-CTCCAAAAATA-TTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGA-TACTTTCAACTTTTCCT-CAAAAATATTTTTTTGAAAATTTATTTTTAAGG
* * *
3226523 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTTGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTT-ATTTTTAAGG
*
3226584 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
* * *
3226642 AAAATTGATACTTTCAACTTTT-CTCTAAAAATATTTTTTTGGAAATTTCGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAAATTT--ATTTTTAAGG
* * *
3226702 AAAATTGATACTTTCAACTTTTCTTCAAAAATCCTTTTTTTGAAAATTTACTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTGAAAATTTATTTTTAAGG
* * * *
3226761 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTAATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
3226818 AAAATTGATACTTTCAACT
1 AAAATTGATACTTTCAACT
3226837 AAGGGTGTAA
Statistics
Matches: 279, Mismatches: 25, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
57 62 0.22
58 61 0.22
59 52 0.19
60 48 0.17
61 56 0.20
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
Found at i:3226679 original size:119 final size:117
Alignment explanation
Indices: 3226463--3226836 Score: 542
Period size: 119 Copynumber: 3.2 Consensus size: 117
3226453 TTTAGTGTAG
*
3226463 GAAAAATTGATTACTTTCAACTTTT-CTCCAAAAATA-TTTTTTGGAAATTTATTTTTAAGGAAA
1 GAAAAATTGA-TACTTTCAACTTTTCCT-CAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAA
* *
3226526 ATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTTGAAATTTTGATTTTCAA
64 ATTGATACTTTCAACTTTTCCT-AAAAA-TATTTTTTTGGAAATTTTGATTTTCAA
* *
3226582 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAATTTATTTTTAAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAAT
*
3226647 TGATACTTTCAACTTTTCTCTAAAAATATTTTTTTGGAAATTTCGATTTTCAA
66 TGATACTTTCAACTTTTC-CTAAAAATATTTTTTTGGAAATTTTGATTTTCAA
* * *
3226700 GAAAAATTGATACTTTCAACTTTTCTTCAAAAATCCTTTTTTTGAAAATTTACTTTTAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTGAAAATTTATTTTTAAGGAAAA
* * *
3226765 TTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAA--TTAATTTTTAA
65 TTGATACTTTCAACTTTT-CCTAAAAATATTTTTTTGGAAATTTTGATTTTCAA
3226816 GAAAAATTGATACTTTCAACT
1 GAAAAATTGATACTTTCAACT
3226837 AAGGGTGTAA
Statistics
Matches: 235, Mismatches: 15, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
116 29 0.12
118 89 0.38
119 114 0.49
120 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (117 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGGAAAAT
TGATACTTTCAACTTTTCCTAAAAATATTTTTTTGGAAATTTTGATTTTCAA
Found at i:3227409 original size:59 final size:58
Alignment explanation
Indices: 3227324--3227789 Score: 590
Period size: 59 Copynumber: 7.9 Consensus size: 58
3227314 CTTTCAACTT
*
3227324 AAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTGAAATTTTGATTTTCAAGGA
1 AAATTGATACTTTCAAC-TTTTCCTAAAAATATTTTTTTGAAATTTTGATTTTTAAGGA
* *
3227383 AAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAAATTTCGATTTTCAAGGA
1 AAATTGATACTTTCAACTTTT-CCTAAAAATATTTTTTTG-AAATTTTGATTTTTAAGGA
* * * *
3227442 AAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTT-ACTTTTAAGAA
1 AAATTGATACTTTCAACTTTTCCT-AAAAAT-ATTTTTTTGAAATTTTGATTTTTAAGGA
* * **
3227501 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTTTTAAGGA
1 AAATTGATACTTTCAACTTTT-CCTAAAAATATTTTTTTGAAATTT-TGATTTTTAAGGA
**
3227561 AAATTGATACTTTCAACTTTTCCTCAAAAAT-CCTTTTTGAAA-TTT-A-TTTTAAGGAA
1 AAATTGATACTTTCAACTTTTCCT-AAAAATATTTTTTTGAAATTTTGATTTTTAAGG-A
**
3227617 AAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTAAAAATTTTGATTTTTAAGGA
1 AAATTGATACTTTCAACTTTT-CCTAAAAATAT-TTTTTTGAAATTTTGATTTTTAAGGA
*
3227677 AAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTGAAA-TTT-ATTTTTAAGGA
1 AAATTGATACTTTCAACTTTTCCT-AAAAATATTTTTTTGAAATTTTGATTTTTAAGGA
3227733 AAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTGAAATTTTTGATTTTTA
1 AAATTGATACTTTCAAC-TTTTCCTAAAAATA-TTTTTTTGAAA-TTTTGATTTTTA
3227790 TTTAAAGAAA
Statistics
Matches: 357, Mismatches: 27, Indels: 44
0.83 0.06 0.10
Matches are distributed among these distances:
55 8 0.02
56 62 0.17
57 14 0.04
58 53 0.15
59 124 0.35
60 74 0.21
61 22 0.06
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (58 bp):
AAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTGAAATTTTGATTTTTAAGGA
Found at i:3227649 original size:116 final size:115
Alignment explanation
Indices: 3227324--3227789 Score: 677
Period size: 116 Copynumber: 4.0 Consensus size: 115
3227314 CTTTCAACTT
*
3227324 AAATTGATACTTTCAACTTTTTCCT-AAAAATATTTTTTTGAAATTTTGA-TTTTCAAGGAAAAT
1 AAATTGATACTTTCAAC-TTTTCCTCAAAAAT-CTTTTTTGAAA-TTT-ACTTTT-AAGGAAAAT
* *
3227387 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTCGATTTTCAAGGA
61 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTTTAAGGA
*
3227442 AAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTACTTTTAAGAAAAATTG
1 AAATTGATACTTTCAACTTTTCCTCAAAAATC--TTTTTTG-AAATTTACTTTTAAGGAAAATTG
* * **
3227507 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTTTTAAGGA
63 ATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTT-TGATTTTTAAGGA
*
3227561 AAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTGAAATTTA-TTTTAAGGAAAAATTGAT
1 AAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAATTTACTTTTAAGG-AAAATTGAT
*
3227625 ACTTTCAACTTTTCCCTAAAAATATATTTTTAAAAATTTTGATTTTTAAGGA
65 ACTTTCAACTTTTCCCTAAAAATAT-TTTTTGAAAATTTTGATTTTTAAGGA
*
3227677 AAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAATTTATTTTTAAGGAAAATTGATA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAATTTACTTTTAAGGAAAATTGATA
* *
3227742 CTTTCAACTTTTTCCTAAAAATATTTTTTTTGAAATTTTTGATTTTTA
66 CTTTCAACTTTTCCCTAAAAATA--TTTTTTGAAAATTTTGATTTTTA
3227790 TTTAAAGAAA
Statistics
Matches: 318, Mismatches: 19, Indels: 23
0.88 0.05 0.06
Matches are distributed among these distances:
115 7 0.02
116 128 0.40
117 52 0.16
118 73 0.23
119 55 0.17
120 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (115 bp):
AAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAATTTACTTTTAAGGAAAATTGATA
CTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTTTAAGGA
Found at i:3227850 original size:11 final size:11
Alignment explanation
Indices: 3227807--3227852 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
3227797 AAAATAGAAT
3227807 AATAAAAA-AA
1 AATAAAAATAA
3227817 AAGTAAAACA-AA
1 AA-TAAAA-ATAA
3227829 AATAAAAATAA
1 AATAAAAATAA
*
3227840 AATAAAGATAA
1 AATAAAAATAA
3227851 AA
1 AA
3227853 AGAATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 3 0.09
11 24 0.75
12 5 0.16
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:3227850 original size:17 final size:18
Alignment explanation
Indices: 3227810--3227854 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
3227800 ATAGAATAAT
3227810 AAAA-AAAAAGTAAAACA
1 AAAATAAAAAGTAAAACA
*
3227827 AAAATAAAAA-TAAAATA
1 AAAATAAAAAGTAAAACA
*
3227844 AAGATAAAAAG
1 AAAATAAAAAG
3227855 AATATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (18 bp):
AAAATAAAAAGTAAAACA
Found at i:3228127 original size:33 final size:33
Alignment explanation
Indices: 3228085--3228157 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
3228075 CGGGTCTCGG
3228085 CAAAACGCGCGGATCCTCTGGGTTACTTAAGGC
1 CAAAACGCGCGGATCCTCTGGGTTACTTAAGGC
3228118 CAAAACGCGCGGATCCTCTGGGTTACTTAAGGC
1 CAAAACGCGCGGATCCTCTGGGTTACTTAAGGC
3228151 CAAAACG
1 CAAAACG
3228158 ACGTCGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (33 bp):
CAAAACGCGCGGATCCTCTGGGTTACTTAAGGC
Found at i:3228820 original size:18 final size:18
Alignment explanation
Indices: 3228793--3228850 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
3228783 TCCAAAATCA
3228793 AATAAAAAAATAATAGAT
1 AATAAAAAAATAATAGAT
* *
3228811 AATTAAAAAA-GATAGGAT
1 AATAAAAAAATAATA-GAT
3228829 AAATAAAAAAATAATA-AT
1 -AATAAAAAAATAATAGAT
3228847 AATA
1 AATA
3228851 TCAGATATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 7 0.21
18 14 0.42
19 9 0.27
20 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (18 bp):
AATAAAAAAATAATAGAT
Found at i:3228923 original size:5 final size:4
Alignment explanation
Indices: 3228909--3229063 Score: 53
Period size: 4 Copynumber: 38.5 Consensus size: 4
3228899 ATTAACAGAT
* * *
3228909 AATA CAATA AGATA AATA AA-A AA-A AAT- ATTA CAAGA AA-A AAAA AATA
1 AATA -AATA A-ATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA
* * *
3228956 AATA AAT- TATA ATATA TAATA AATA TAA-A ACTA TATA AATAA AATA
1 AATA AATA AATA A-ATA -AATA AATA -AATA AATA AATA AAT-A AATA
* *
3229002 CATATA AAT- ATTA ACA-A AATA AATA AATA AATA AA-A ATATA CATA
1 -A-ATA AATA AATA A-ATA AATA AATA AATA AATA AATA A-ATA AATA
3229047 TAAT- AATA AAT- AATA AA
1 -AATA AATA AATA AATA AA
3229064 ATACAAAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 43
0.67 0.08 0.25
Matches are distributed among these distances:
3 25 0.22
4 59 0.51
5 27 0.23
6 4 0.03
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:3228978 original size:17 final size:20
Alignment explanation
Indices: 3228953--3228998 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
3228943 GAAAAAAAAA
*
3228953 ATAAATAAAT-TATAA-TAT
1 ATAAATAAATATAAAACTAT
3228971 AT-AATAAATATAAAACTAT
1 ATAAATAAATATAAAACTAT
3228990 ATAAATAAA
1 ATAAATAAA
3228999 ATACATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 6 0.25
19 5 0.21
20 6 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATAAATATAAAACTAT
Found at i:3228983 original size:9 final size:9
Alignment explanation
Indices: 3228951--3229098 Score: 59
Period size: 8 Copynumber: 17.2 Consensus size: 9
3228941 AAGAAAAAAA
3228951 AAATA-AAT
1 AAATATAAT
3228959 AAAT-T-AT
1 AAATATAAT
3228966 AATATATAAT
1 AA-ATATAAT
3228976 AAATATAA-
1 AAATATAAT
*
3228984 AACTAT-AT
1 AAATATAAT
*
3228992 AAATAAAAT
1 AAATATAAT
*
3229001 ACATATAA-
1 AAATATAAT
* *
3229009 ATAT-TAAC
1 AAATATAAT
3229017 AAA-ATAAAT
1 AAATAT-AAT
3229026 AAATA-AAT
1 AAATATAAT
*
3229034 AAAAAT-AT
1 AAATATAAT
*
3229042 ACATATAAT
1 AAATATAAT
*
3229051 AATAAATAAT
1 AA-ATATAAT
* *
3229061 AAAATACAAA
1 -AAATATAAT
*
3229071 AAATACAA-
1 AAATATAAT
*
3229079 AAAAATAAT
1 AAATATAAT
3229088 -AATAATAAT
1 AAAT-ATAAT
3229097 AA
1 AA
3229099 TACAAAGTAA
Statistics
Matches: 104, Mismatches: 19, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
7 8 0.08
8 42 0.40
9 36 0.35
10 16 0.15
11 2 0.02
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATATAAT
Found at i:3229008 original size:15 final size:16
Alignment explanation
Indices: 3228974--3229012 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3228964 ATAATATATA
3228974 ATAAATATAAAACTAT
1 ATAAATATAAAACTAT
3228990 ATAAATA-AAATAC-AT
1 ATAAATATAAA-ACTAT
3229005 ATAAATAT
1 ATAAATAT
3229013 TAACAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATATAAAACTAT
Found at i:3229008 original size:41 final size:37
Alignment explanation
Indices: 3228946--3229095 Score: 112
Period size: 37 Copynumber: 3.9 Consensus size: 37
3228936 ATTACAAGAA
* *
3228946 AAAAAAAATAAAT-AAATTATAATATATAATAAATAT
1 AAAATAAATAAATAAAAATATAATATATAATAAATAT
* *
3228982 AAAACTATATAAATAAAATACATATAA-ATATTAACAAA-AT
1 AAAA-TAAATAAAT-AAA-A-ATATAATATA-TAATAAATAT
3229022 -AAATAAATAAATAAAAATATACATATAATAATAAATAAT
1 AAAATAAATAAATAAAAATATA-ATAT-ATAATAAAT-AT
* *
3229061 AAAATACAAAAAATACAAAAAAATAATA-ATAATAA
1 AAAATA-AATAAAT--AAAAATATAATATATAATAA
3229096 TAATACAAAG
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
35 5 0.05
36 6 0.07
37 18 0.20
38 9 0.10
39 7 0.08
40 18 0.20
41 17 0.19
42 3 0.03
43 8 0.09
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (37 bp):
AAAATAAATAAATAAAAATATAATATATAATAAATAT
Found at i:3231664 original size:11 final size:11
Alignment explanation
Indices: 3231648--3231697 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 11
3231638 TAATGATTTT
*
3231648 TTTATATTTAA
1 TTTATATTAAA
3231659 TTTATATTAAA
1 TTTATATTAAA
3231670 TTTAGATATTAAA
1 TTT--ATATTAAA
3231683 TGTATATATTAAA
1 T-T-TATATTAAA
3231696 TT
1 TT
3231698 CAAATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
11 13 0.38
12 1 0.03
13 18 0.53
14 1 0.03
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:3231792 original size:18 final size:20
Alignment explanation
Indices: 3231757--3231795 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3231747 AATTGAATTA
*
3231757 ATATTTTTATCAACTTTTAT
1 ATATTTTTATCAAATTTTAT
3231777 ATATTTTT-T-AAATTTTAT
1 ATATTTTTATCAAATTTTAT
3231795 A
1 A
3231796 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTTTATCAAATTTTAT
Found at i:3231824 original size:11 final size:11
Alignment explanation
Indices: 3231810--3231866 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
3231800 AAAAATAATT
3231810 AATTATATTAA
1 AATTATATTAA
*
3231821 AATT-TATTTA
1 AATTATATTAA
3231831 AA-TATATTAAA
1 AATTATATT-AA
3231842 AATTATATTAA
1 AATTATATTAA
*
3231853 AATAATATATAA
1 AATTATAT-TAA
3231865 AA
1 AA
3231867 GATAAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 1 0.03
10 11 0.28
11 16 0.41
12 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTATATTAA
Found at i:3231847 original size:20 final size:20
Alignment explanation
Indices: 3231799--3231853 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3231789 TTTTATAAAA
* *
3231799 TAAAAA-TAATTAATTATAT
1 TAAAAATTATTTAAATATAT
*
3231818 TAAAATTTATTTAAATATAT
1 TAAAAATTATTTAAATATAT
3231838 TAAAAATTATATTAAA
1 TAAAAATTAT-TTAAA
3231854 ATAATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.17
20 20 0.67
21 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAATTATTTAAATATAT
Found at i:3231865 original size:12 final size:12
Alignment explanation
Indices: 3231830--3231882 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
3231820 AAATTTATTT
3231830 AAATATATTAAA
1 AAATATATTAAA
*
3231842 AATTATATTAAA
1 AAATATATTAAA
3231854 ATAATATA-TAAA
1 A-AATATATTAAA
* *
3231866 AGATAAATTTAAA
1 AAATATA-TTAAA
3231879 AAAT
1 AAAT
3231883 TGATGAACTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
11 4 0.12
12 17 0.52
13 12 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AAATATATTAAA
Found at i:3232535 original size:2 final size:2
Alignment explanation
Indices: 3232528--3232560 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3232518 TGTAAAATTC
3232528 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 A
3232561 ACTTAATAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3232680 original size:24 final size:24
Alignment explanation
Indices: 3232648--3232696 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3232638 CACAAATGTA
3232648 AATTTTTCACAACTTATAATCACT
1 AATTTTTCACAACTTATAATCACT
3232672 AATTTTTCACAACTTATAATCACT
1 AATTTTTCACAACTTATAATCACT
3232696 A
1 A
3232697 CTTGTTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (24 bp):
AATTTTTCACAACTTATAATCACT
Found at i:3235579 original size:21 final size:20
Alignment explanation
Indices: 3235535--3235579 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3235525 ACCCAGAAAT
* *
3235535 AAAATAAGATTAAAACTTAC
1 AAAATAAGATCAAAACTTAA
*
3235555 AAAATAAGTATCAAAATTTAA
1 AAAATAAG-ATCAAAACTTAA
3235576 AAAA
1 AAAA
3235580 AAAAAAAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAATAAGATCAAAACTTAA
Found at i:3235681 original size:15 final size:15
Alignment explanation
Indices: 3235661--3235693 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3235651 TAAGAGGAGA
*
3235661 AGAAAGAACTGAAGG
1 AGAAAGAACAGAAGG
3235676 AGAAAGAACAGAAGG
1 AGAAAGAACAGAAGG
3235691 AGA
1 AGA
3235694 GGTGGAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.33, T:0.03
Consensus pattern (15 bp):
AGAAAGAACAGAAGG
Found at i:3240418 original size:97 final size:90
Alignment explanation
Indices: 3240267--3240448 Score: 231
Period size: 89 Copynumber: 1.9 Consensus size: 90
3240257 CATCAAATTT
**
3240267 CAAACCACCCGCCTTTCAACAATAAAAAGTAATAATTAAAAAAAAAAACTTGAGAAGGAGAAAC-
1 CAAACCACCCGCCTTTCAACAATAAAAAGTAATAAAAAAAAAAAAAAACTTGAGAAGGAGAAACG
* * *
3240331 TATAGCATGAGATTAAATTGACATC
66 CATAACATGAGATGAAATTGACATC
3240356 CAAACCACCCGCCTTTCAACAATGAAAAGTAGTAATTTAGGAAAAAAAAAAAAACACTTGAGAAG
1 CAAACCACCCGCCTTTCAACAAT-AAAA--AGTAA--TA--AAAAAAAAAAAAA-ACTTGAGAAG
*
3240421 GAGAAGCGCATAACATGAGATGAAATTG
58 GAGAAACGCATAACATGAGATGAAATTG
3240449 CCTCTTATAT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
89 23 0.29
90 4 0.05
92 5 0.06
94 2 0.03
96 11 0.14
97 16 0.21
98 17 0.22
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (90 bp):
CAAACCACCCGCCTTTCAACAATAAAAAGTAATAAAAAAAAAAAAAAACTTGAGAAGGAGAAACG
CATAACATGAGATGAAATTGACATC
Found at i:3241076 original size:18 final size:20
Alignment explanation
Indices: 3241053--3241093 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
3241043 AGATCTAAGC
*
3241053 ATTAAAAAA-AAAGAGAT-A
1 ATTAAAAAATAAACAGATGA
3241071 ATTAAAAAATAAACAGATGA
1 ATTAAAAAATAAACAGATGA
3241091 ATT
1 ATT
3241094 TCCATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (20 bp):
ATTAAAAAATAAACAGATGA
Found at i:3241649 original size:28 final size:27
Alignment explanation
Indices: 3241617--3241670 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
3241607 TTTGAATTGA
* *
3241617 ATTAATTAAATTATTTTATTTTATTTTT
1 ATTAATTAAATTAATTT-TTTAATTTTT
3241645 ATTAATTAAATTAATTTTTTAATTTT
1 ATTAATTAAATTAATTTTTTAATTTT
3241671 AAAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
ATTAATTAAATTAATTTTTTAATTTTT
Found at i:3241912 original size:11 final size:13
Alignment explanation
Indices: 3241872--3241912 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
3241862 AAATAGATAA
3241872 TTTTATATAT-TT
1 TTTTATATATATT
3241884 TTAGTTATATATATT
1 TT--TTATATATATT
3241899 TTTTATA-ATATT
1 TTTTATATATATT
3241911 TT
1 TT
3241913 GATTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.35
13 5 0.19
14 8 0.31
15 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTTATATATATT
Found at i:3243763 original size:42 final size:42
Alignment explanation
Indices: 3243711--3243802 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
3243701 CAATAAAAAT
* *
3243711 AACCACAAAATGATTAAATGAACTGTAAGGGATAAAATTCAA
1 AACCACAAAATGATTAAATGAACTGCAAAGGATAAAATTCAA
* * * *
3243753 AACCATAAAATGATTAAATGCACTGCAAATGATAAGATTCAA
1 AACCACAAAATGATTAAATGAACTGCAAAGGATAAAATTCAA
*
3243795 AATCACAA
1 AACCACAA
3243803 CTCTCTCCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (42 bp):
AACCACAAAATGATTAAATGAACTGCAAAGGATAAAATTCAA
Found at i:3249409 original size:18 final size:17
Alignment explanation
Indices: 3249388--3249425 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3249378 GAATTTAAGT
3249388 TTTAAATTTTAAATTAAA
1 TTTAAA-TTTAAATTAAA
*
3249406 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTAAA
3249423 TTT
1 TTT
3249426 TATATCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:3249412 original size:6 final size:6
Alignment explanation
Indices: 3249388--3249427 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
3249378 GAATTTAAGT
*
3249388 TTTAAA TTTTAAA -TTAAA TTTAAA TTTAAA TTTAAT TTTA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
3249428 TATCGATTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:3249427 original size:18 final size:19
Alignment explanation
Indices: 3249379--3249427 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
3249369 AATTTAATTG
3249379 AATTTAAGTTTTAAATTTTA
1 AATTTAA-TTTTAAATTTTA
*
3249399 AA-TTAAATTTAAA-TTTA
1 AATTTAATTTTAAATTTTA
3249416 AATTTAATTTTA
1 AATTTAATTTTA
3249428 TATCGATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 14 0.54
19 4 0.15
20 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTAATTTTAAATTTTA
Found at i:3249804 original size:35 final size:35
Alignment explanation
Indices: 3249764--3249849 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
3249754 GATATAAATA
3249764 TTATATTAATATAATTAAAAACTT-TAAAA-ATATT
1 TTATATTAATATAATTAAAAA-TTATAAAATATATT
* *
3249798 TATATATAAATTTAA-T-AAAATTAATAAAATATATT
1 T-TATATTAATATAATTAAAAATT-ATAAAATATATT
3249833 TTATATTAATATAATTA
1 TTATATTAATATAATTA
3249850 TAATATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
32 2 0.05
33 4 0.10
34 18 0.43
35 18 0.43
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (35 bp):
TTATATTAATATAATTAAAAATTATAAAATATATT
Found at i:3249841 original size:29 final size:29
Alignment explanation
Indices: 3249809--3249888 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
3249799 ATATATAAAT
3249809 TTAATAAAATTAATAAAATATATTTTATA
1 TTAATAAAATTAATAAAATATATTTTATA
* * * *
3249838 TTAATATAATT-ATAATATATAATTTGTA
1 TTAATAAAATTAATAAAATATATTTTATA
3249866 -T-ATAAAATATAATATAAATATAT
1 TTAATAAAAT-TAATA-AAATATAT
3249889 AAATTTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 6 0.15
27 2 0.05
28 17 0.41
29 16 0.39
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
TTAATAAAATTAATAAAATATATTTTATA
Found at i:3249887 original size:11 final size:11
Alignment explanation
Indices: 3249801--3249887 Score: 56
Period size: 11 Copynumber: 8.0 Consensus size: 11
3249791 AAATATTTAT
*
3249801 ATATAAATTTA
1 ATATAAATATA
3249812 ATA-AAAT-TA
1 ATATAAATATA
3249821 ATA-AAATATA
1 ATATAAATATA
* * *
3249831 TTTTATAT-TA
1 ATATAAATATA
*
3249841 ATATAATTATA
1 ATATAAATATA
* *
3249852 ATATATAATTTGT
1 ATATA-AATAT-A
3249865 ATATAAAATATA
1 ATAT-AAATATA
3249877 ATATAAATATA
1 ATATAAATATA
3249888 TAAATTTTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
9 9 0.16
10 13 0.22
11 20 0.34
12 7 0.12
13 8 0.14
14 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
ATATAAATATA
Found at i:3249887 original size:20 final size:20
Alignment explanation
Indices: 3249801--3249891 Score: 59
Period size: 18 Copynumber: 4.8 Consensus size: 20
3249791 AAATATTTAT
*
3249801 ATATAAATTTAATAAAAT-TA
1 ATATAAATAT-ATAAAATATA
***
3249821 ATA-AAATATATTTTATATTA
1 ATATAAATATATAAAATA-TA
*
3249841 ATAT-AAT-TATAATATATA
1 ATATAAATATATAAAATATA
**
3249859 AT-T-TGTATATAAAATATA
1 ATATAAATATATAAAATATA
3249877 ATATAAATATATAAA
1 ATATAAATATATAAA
3249892 TTTTTATATT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
17 2 0.04
18 20 0.37
19 13 0.24
20 19 0.35
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
ATATAAATATATAAAATATA
Found at i:3249900 original size:32 final size:32
Alignment explanation
Indices: 3249791--3249925 Score: 98
Period size: 32 Copynumber: 4.2 Consensus size: 32
3249781 AAAACTTTAA
* * *
3249791 AAATATTTATATATAAATTTAATA-AAATTAATAA
1 AAATTTTTATATA-AAATATAATATAAA-T-ATAT
*
3249825 AATATATTTTATAT-TAATATAAT-TATAATATAT
1 AA-AT-TTTTATATAAAATATAATATA-AATATAT
*
3249858 -AATTTGTATATAAAATATAATATAAATATAT
1 AAATTTTTATATAAAATATAATATAAATATAT
*** * *
3249889 AAATTTTTATATTTTATATAAAATAAATACAT
1 AAATTTTTATATAAAATATAATATAAATATAT
3249921 AAATT
1 AAATT
3249926 GGCAGATTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
30 7 0.09
31 17 0.21
32 33 0.40
33 3 0.04
34 11 0.13
35 4 0.05
36 7 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (32 bp):
AAATTTTTATATAAAATATAATATAAATATAT
Found at i:3263295 original size:15 final size:16
Alignment explanation
Indices: 3263263--3263300 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3263253 TTAATAAATT
3263263 ATATATAATTAAAAAA
1 ATATATAATTAAAAAA
* *
3263279 AT-TATAATTATATAA
1 ATATATAATTAAAAAA
3263294 ATATATA
1 ATATATA
3263301 TGAACATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATAATTAAAAAA
Found at i:3272068 original size:2 final size:2
Alignment explanation
Indices: 3272061--3272090 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3272051 TGCATGTTCC
3272061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3272091 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3274093 original size:22 final size:22
Alignment explanation
Indices: 3274050--3274093 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3274040 TTTTAACACC
* *
3274050 TATAATTTTTTTATATATAAAT
1 TATAATTTTTTTATAAAAAAAT
3274072 TATAATTTTTTCT-TAAAAAAAT
1 TATAATTTTTT-TATAAAAAAAT
3274094 AAATACAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATAATTTTTTTATAAAAAAAT
Found at i:3286709 original size:30 final size:29
Alignment explanation
Indices: 3286651--3286743 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 29
3286641 TTAAGGCTTG
* * *
3286651 GATTTTAAAGTATGAAAAATTTAAGGTTTT
1 GATTTTAAAGTTTG-AAGATTTTAGGTTTT
* *
3286681 GATTTTAGAGTTTGAAGATTTTAGGGTTTC
1 GATTTTAAAGTTTGAAGATTTTA-GGTTTT
* * * *
3286711 GGTTTTAAATTTTG-AGGTTTGAGGTTTT
1 GATTTTAAAGTTTGAAGATTTTAGGTTTT
3286739 GATTT
1 GATTT
3286744 ACGGGTTTGG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
28 9 0.18
29 13 0.26
30 28 0.56
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (29 bp):
GATTTTAAAGTTTGAAGATTTTAGGTTTT
Found at i:3286828 original size:8 final size:8
Alignment explanation
Indices: 3286795--3286871 Score: 63
Period size: 8 Copynumber: 9.9 Consensus size: 8
3286785 TTTTTGAGGG
3286795 TTTT-GGA
1 TTTTAGGA
*
3286802 TTTTAGGG
1 TTTTAGGA
* *
3286810 GTTTCGGA
1 TTTTAGGA
3286818 TTTTAGGA
1 TTTTAGGA
3286826 TTTT-GGA
1 TTTTAGGA
**
3286833 TTTTAAAA
1 TTTTAGGA
3286841 TTTT-GGA
1 TTTTAGGA
3286848 TTTTAGGGGA
1 TTTTA--GGA
3286858 TTTT-GGA
1 TTTTAGGA
3286865 TTTTAGG
1 TTTTAGG
3286872 GGTTTTAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
7 23 0.43
8 24 0.44
10 7 0.13
ACGTcount: A:0.19, C:0.01, G:0.29, T:0.51
Consensus pattern (8 bp):
TTTTAGGA
Found at i:3286835 original size:15 final size:15
Alignment explanation
Indices: 3286776--3286871 Score: 93
Period size: 15 Copynumber: 6.1 Consensus size: 15
3286766 AAAGGTTTGA
*
3286776 GATTTCGGATTTTTGAG
1 GATTTTGGA-TTTT-AG
*
3286793 GGTTTTGGATTTTAGG
1 GATTTTGGATTTTA-G
* *
3286809 GGTTTCGGATTTTAG
1 GATTTTGGATTTTAG
*
3286824 GATTTTGGATTTTAA
1 GATTTTGGATTTTAG
*
3286839 AATTTTGGATTTTAGGG
1 GATTTTGGATTTTA--G
3286856 GATTTTGGATTTTAG
1 GATTTTGGATTTTAG
3286871 G
1 G
3286872 GGTTTTAGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
15 29 0.43
16 18 0.27
17 20 0.30
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (15 bp):
GATTTTGGATTTTAG
Found at i:3288365 original size:22 final size:21
Alignment explanation
Indices: 3288323--3288367 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
3288313 TTTTCACTTT
*
3288323 TTTTTAAATAATTAATAATTA
1 TTTTAAAATAATTAATAATTA
* *
3288344 TTTTAAAATATATTTATTATTA
1 TTTTAAAATA-ATTAATAATTA
3288366 TT
1 TT
3288368 ATTATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAAAATAATTAATAATTA
Found at i:3289286 original size:22 final size:21
Alignment explanation
Indices: 3289256--3289304 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3289246 TTTAACTAAG
*
3289256 ATTATATTTAAGATTATCAAAA
1 ATTAAATTTAA-ATTATCAAAA
* *
3289278 ATTAAATTTTAATTATTAAAA
1 ATTAAATTTAAATTATCAAAA
3289299 ATTAAA
1 ATTAAA
3289305 ATATTTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTAAATTTAAATTATCAAAA
Found at i:3289310 original size:24 final size:23
Alignment explanation
Indices: 3289259--3289312 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
3289249 AACTAAGATT
*
3289259 ATATTTAAGATTATCAAAAATTA
1 ATATTTTAGATTATCAAAAATTA
*
3289282 A-ATTTTA-ATTATTAAAAATTAAA
1 ATATTTTAGATTATCAAAAATT--A
3289305 ATATTTTA
1 ATATTTTA
3289313 TCAACCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 12 0.46
22 5 0.19
23 3 0.12
24 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATTTTAGATTATCAAAAATTA
Found at i:3289960 original size:25 final size:27
Alignment explanation
Indices: 3289905--3289961 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
3289895 AATCAATTTA
*
3289905 AAATAATATTTATGAGATAAAAAAGTT
1 AAATAATATTTATCAGATAAAAAAGTT
*
3289932 --ATAATATTTATCA-AT-GAAAAGTT
1 AAATAATATTTATCAGATAAAAAAGTT
3289955 AAATAAT
1 AAATAAT
3289962 GCATGCAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 7 0.27
24 2 0.08
25 17 0.65
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (27 bp):
AAATAATATTTATCAGATAAAAAAGTT
Found at i:3291658 original size:14 final size:14
Alignment explanation
Indices: 3291641--3291683 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3291631 TATTATATTT
3291641 AATAATTTAAAATA
1 AATAATTTAAAATA
*
3291655 AATAATTATAAATTA
1 AATAATT-TAAAATA
*
3291670 TAT-ATTTAAAATA
1 AATAATTTAAAATA
3291683 A
1 A
3291684 TTTTAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAATTTAAAATA
Found at i:3292331 original size:19 final size:19
Alignment explanation
Indices: 3292296--3292334 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3292286 GTTAACATAA
*
3292296 TATATAAATTTTTAAAATT
1 TATATAAATTTTAAAAATT
3292315 TATAT-AATTTATAAAAATT
1 TATATAAATTT-TAAAAATT
3292334 T
1 T
3292335 TAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATAAATTTTAAAAATT
Found at i:3294048 original size:25 final size:25
Alignment explanation
Indices: 3294015--3294062 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
3294005 TTTATTAAAA
3294015 TTTTTTAATTATAATTATAATAACT
1 TTTTTTAATTATAATTATAATAACT
3294040 TTTTTTAATTATAATTATAATAA
1 TTTTTTAATTATAATTATAATAA
3294063 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTTAATTATAATTATAATAACT
Found at i:3299298 original size:15 final size:15
Alignment explanation
Indices: 3299260--3299302 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
3299250 ATTTTAATTT
3299260 AATATATATTTATAA
1 AATATATATTTATAA
* *
3299275 AATAT-TATTTTTGA
1 AATATATATTTATAA
3299289 AATATATA-TTATAA
1 AATATATATTTATAA
3299303 TTTAATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATATATTTATAA
Found at i:3299407 original size:42 final size:40
Alignment explanation
Indices: 3299330--3299415 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 40
3299320 TATTTTAAAT
* * *
3299330 ATAATATTTTTATTAAGTTAATGTCTCAAATTAAAATATTAA
1 ATAATAATTTTATTAAGTTAATATATCAAATT-AAA-ATTAA
3299372 ATAATAATTTTATTAA-TATAATATAT-AAATATAAAATTAA
1 ATAATAATTTTATTAAGT-TAATATATCAAAT-TAAAATTAA
3299412 ATAA
1 ATAA
3299416 ATATATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
40 9 0.23
41 8 0.21
42 22 0.56
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (40 bp):
ATAATAATTTTATTAAGTTAATATATCAAATTAAAATTAA
Found at i:3299712 original size:18 final size:18
Alignment explanation
Indices: 3299689--3299732 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3299679 TATTTATACA
*
3299689 ATATTATTTTTTAAATAT
1 ATATTATATTTTAAATAT
*
3299707 ATATTATATTTTAATTAT
1 ATATTATATTTTAAATAT
*
3299725 ATAATATA
1 ATATTATA
3299733 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATATTTTAAATAT
Found at i:3299736 original size:21 final size:21
Alignment explanation
Indices: 3299682--3299754 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
3299672 TAATATATAT
* * *
3299682 TTATACAATATTATTTTTTAA
1 TTATATAATATAATATTTTAA
*
3299703 --ATAT-ATATTATATTTTAA
1 TTATATAATATAATATTTTAA
*
3299721 TTATATAATATAATATTTTTA
1 TTATATAATATAATATTTTAA
*
3299742 TTAAATTAATATA
1 TTATA-TAATATA
3299755 TTAAATAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 13 0.30
19 3 0.07
20 4 0.09
21 16 0.37
22 7 0.16
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATAATATAATATTTTAA
Found at i:3299742 original size:18 final size:18
Alignment explanation
Indices: 3299675--3299742 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
3299665 ATTAATTTAA
* *
3299675 TATATATTTATACAATAT
1 TATATTTTTATATAATAT
*
3299693 TAT-TTTTTAAATATATAT
1 TATATTTTTATATA-ATAT
3299711 TATATTTTAATTATATAATAT
1 TATA-TTT--TTATATAATAT
*
3299732 AATATTTTTAT
1 TATATTTTTAT
3299743 TAAATTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 7 0.17
18 14 0.35
20 6 0.15
21 7 0.17
22 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTTTATATAATAT
Found at i:3299755 original size:29 final size:27
Alignment explanation
Indices: 3299717--3299788 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 27
3299707 ATATTATATT
*
3299717 TTAATTATATAATATAATATTTTTATTAAA
1 TTAA-TATATAA-ATAATAATTTTATT-AA
3299747 TTAATATATTAAATAATAATTTTATTAA
1 TTAATATA-TAAATAATAATTTTATTAA
3299775 TATAATATATAAAT
1 T-TAATATATAAAT
3299789 TTTAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 8 0.21
29 24 0.62
30 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATATATAAATAATAATTTTATTAA
Found at i:3299789 original size:22 final size:24
Alignment explanation
Indices: 3299746--3299808 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
3299736 TTTTTATTAA
*
3299746 ATTAATATATTAAATAATAATTTT
1 ATTAATATAATAAATAATAATTTT
*
3299770 ATTAATATAATATAT-A-AATTTT
1 ATTAATATAATAAATAATAATTTT
*
3299792 A-AAATA-AATAAATAATA
1 ATTAATATAATAAATAATA
3299809 TATATTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.18
21 5 0.15
22 8 0.24
23 1 0.03
24 13 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTAATATAATAAATAATAATTTT
Found at i:3300666 original size:18 final size:17
Alignment explanation
Indices: 3300643--3300677 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3300633 AAATTACAAC
*
3300643 AAACAAGGTTTCAGTTTT
1 AAACAAAGTTTCA-TTTT
3300661 AAACAAAGTTTCATTTT
1 AAACAAAGTTTCATTTT
3300678 CAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
AAACAAAGTTTCATTTT
Found at i:3301430 original size:13 final size:13
Alignment explanation
Indices: 3301412--3301436 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3301402 CAATTATAAG
3301412 ATTATAATAAAAA
1 ATTATAATAAAAA
3301425 ATTATAATAAAA
1 ATTATAATAAAA
3301437 TGCTCTCATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTATAATAAAAA
Found at i:3313758 original size:17 final size:18
Alignment explanation
Indices: 3313736--3313770 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3313726 GAGATCCATT
3313736 GAGAAT-AGAAAAACAAA
1 GAGAATAAGAAAAACAAA
*
3313753 GAGAATAAGATAAACAAA
1 GAGAATAAGAAAAACAAA
3313771 TAAGGGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.09
Consensus pattern (18 bp):
GAGAATAAGAAAAACAAA
Found at i:3320271 original size:23 final size:21
Alignment explanation
Indices: 3320225--3320267 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3320215 CTCAATTATG
3320225 GATAAAATTTACATAAAATTTTA
1 GATAAAATTT--ATAAAATTTTA
3320248 GATAAAATTTATAAAATTTT
1 GATAAAATTTATAAAATTTT
3320268 TTAGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (21 bp):
GATAAAATTTATAAAATTTTA
Found at i:3320279 original size:14 final size:14
Alignment explanation
Indices: 3320260--3320303 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3320250 TAAAATTTAT
*
3320260 AAAATTTTTTAGTA
1 AAAATTTTTTAATA
*
3320274 AAAATTATTTAATA
1 AAAATTTTTTAATA
3320288 AAAA--TTTTAATA
1 AAAATTTTTTAATA
3320300 AAAA
1 AAAA
3320304 ATTTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AAAATTTTTTAATA
Found at i:3320302 original size:11 final size:11
Alignment explanation
Indices: 3320226--3320302 Score: 52
Period size: 12 Copynumber: 6.5 Consensus size: 11
3320216 TCAATTATGG
3320226 ATAAAA-TTTA
1 ATAAAATTTTA
3320236 CATAAAATTTTA
1 -ATAAAATTTTA
3320248 GATAAAA-TTT-
1 -ATAAAATTTTA
3320258 ATAAAATTTTTTA
1 ATAAAA--TTTTA
*
3320271 GTAAAAATTATTTA
1 AT-AAAA-T-TTTA
3320285 ATAAAAATTTTA
1 AT-AAAATTTTA
3320297 ATAAAA
1 ATAAAA
3320303 AATTTAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
9 6 0.11
11 13 0.23
12 19 0.34
13 4 0.07
14 14 0.25
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (11 bp):
ATAAAATTTTA
Found at i:3320303 original size:12 final size:12
Alignment explanation
Indices: 3320239--3320309 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
3320229 AAATTTACAT
3320239 AAAATTTTAGAT-
1 AAAATTTTA-ATA
3320251 AAAA-TTT-ATA
1 AAAATTTTAATA
* *
3320261 AAATTTTTTAGTA
1 AAA-ATTTTAATA
3320274 AAAATTATTTAATA
1 AAAA-T-TTTAATA
3320288 AAAATTTTAATA
1 AAAATTTTAATA
*
3320300 AAAAATTTAA
1 AAAATTTTAA
3320310 ATTAATAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
9 2 0.04
10 3 0.06
11 3 0.06
12 23 0.48
13 7 0.15
14 10 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
AAAATTTTAATA
Found at i:3320400 original size:28 final size:29
Alignment explanation
Indices: 3320365--3320427 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
3320355 AATTATTTAA
*
3320365 AATA-TTATTT-ATAATTTAAA-TTTAATC
1 AATATTTATTTAATAA-TAAAATTTTAATC
*
3320392 GATATTTATTTAATAATAAAATTTTAATC
1 AATATTTATTTAATAATAAAATTTTAATC
3320421 AATATTT
1 AATATTT
3320428 TTATTCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 3 0.10
28 10 0.33
29 17 0.57
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (29 bp):
AATATTTATTTAATAATAAAATTTTAATC
Found at i:3324293 original size:28 final size:27
Alignment explanation
Indices: 3324236--3324295 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
3324226 TAATTTTTTT
*
3324236 TATATAATTTTATTTTTAATTTTTACA
1 TATATAATTTTATTTTTAATTTATACA
*
3324263 TATATAATTTTAATTTTTAATTTATATA
1 TATATAATTTT-ATTTTTAATTTATACA
3324291 TATAT
1 TATAT
3324296 GAGTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TATATAATTTTATTTTTAATTTATACA
Found at i:3331134 original size:6 final size:6
Alignment explanation
Indices: 3331127--3331175 Score: 80
Period size: 6 Copynumber: 8.0 Consensus size: 6
3331117 ATGATGTGAC
*
3331127 AATGAC AATGAT AATGAT AATGAT GAATGAT AATGAT AATGAT AATGAT
1 AATGAT AATGAT AATGAT AATGAT -AATGAT AATGAT AATGAT AATGAT
3331176 GGATGATGGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 35 0.85
7 6 0.15
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (6 bp):
AATGAT
Found at i:3331157 original size:19 final size:18
Alignment explanation
Indices: 3331127--3331175 Score: 80
Period size: 19 Copynumber: 2.7 Consensus size: 18
3331117 ATGATGTGAC
*
3331127 AATGACAATGATAATGAT
1 AATGATAATGATAATGAT
3331145 AATGATGAATGATAATGAT
1 AATGAT-AATGATAATGAT
3331164 AATGATAATGAT
1 AATGATAATGAT
3331176 GGATGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (18 bp):
AATGATAATGATAATGAT
Found at i:3331161 original size:25 final size:25
Alignment explanation
Indices: 3331127--3331182 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
3331117 ATGATGTGAC
*
3331127 AATGACAATGATAATGATAATGATG
1 AATGATAATGATAATGATAATGATG
3331152 AATGATAATGATAATGATAATGATG
1 AATGATAATGATAATGATAATGATG
*
3331177 GATGAT
1 AATGAT
3331183 GGAGACAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.30
Consensus pattern (25 bp):
AATGATAATGATAATGATAATGATG
Found at i:3332852 original size:33 final size:33
Alignment explanation
Indices: 3332813--3332875 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
3332803 GATAGTTGGA
3332813 AAGTAGGGTTAAGCCAAGTTGACCACCAAATGG
1 AAGTAGGGTTAAGCCAAGTTGACCACCAAATGG
3332846 AAGTAGGGTTAAGCCAAGTTGACCACCAAA
1 AAGTAGGGTTAAGCCAAGTTGACCACCAAA
3332876 CATCAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (33 bp):
AAGTAGGGTTAAGCCAAGTTGACCACCAAATGG
Found at i:3334534 original size:2 final size:2
Alignment explanation
Indices: 3334529--3334557 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3334519 AGCGTTTATT
3334529 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3334558 AAGAATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3337564 original size:32 final size:31
Alignment explanation
Indices: 3337528--3337624 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 31
3337518 ATTTTTTGGA
3337528 AACTTTGATTTTCAAGGAAAATTGATACTTTC
1 AACTTTGATTTTCAA-GAAAATTGATACTTTC
* * * *
3337560 AAC-TT--TTTCCCA-AAAA-T-ATTCTTTGGA
1 AACTTTGATTTTCAAGAAAATTGATACTTT--C
3337587 AACTTTGATTTTCAAGAAAAATTGATACTTTC
1 AACTTTGATTTTCAAG-AAAATTGATACTTTC
3337619 AACTTT
1 AACTTT
3337625 TTCTCAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 18
0.65 0.11 0.24
Matches are distributed among these distances:
25 6 0.12
26 1 0.02
27 7 0.15
28 2 0.04
29 5 0.10
30 5 0.10
31 2 0.04
32 13 0.27
33 1 0.02
34 6 0.12
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
AACTTTGATTTTCAAGAAAATTGATACTTTC
Found at i:3337572 original size:59 final size:58
Alignment explanation
Indices: 3337322--3337702 Score: 428
Period size: 58 Copynumber: 6.4 Consensus size: 58
3337312 TAATTTCGAG
* *
3337322 ACTTTTCCTCAAAACTTTTATTTTTTTGAAACTTTAATTTT-GAGAAAAATTGATACTTTCA
1 ACTTTTCCTCAAAA--ATTA-TTTTTTGAAACTTT-ATTTTCAAGAAAAATTGATACTTTCA
* * *
3337383 ACTTTTCCTCAAAAATTTTATTTTTTTGAAACTTTAATTTCGAGGAAAATTGATACTTTCA
1 ACTTTTCCTCAAAAA--TTA-TTTTTTGAAACTTTATTTTCAAGAAAAATTGATACTTTCA
*** * *
3337444 ACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTTTCA
1 ACTTTTCCTCAAAAATTATTTTTTGAAACTTTATTTTCAAGAAAAATTGATACTTTCA
* *
3337502 ACTTTTCCCCAAAAA-TATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACTTTCA
1 ACTTTTCCTCAAAAATTATTTTTT-GAAACTTT-ATTTTCAAGAAAAATTGATACTTTCA
*
3337561 ACTTTTTCC-CAAAAA-TATTCTTTGGAAACTTTGATTTTCAAGAAAAATTGATACTTTCA
1 AC-TTTTCCTCAAAAATTATT-TTTTGAAACTTT-ATTTTCAAGAAAAATTGATACTTTCA
* *** * * *
3337620 ACTTTTTCTCAAAAACCCTTTTTTGAAAATTTATTTTTAAGAAAAATTGATACTTTAA
1 ACTTTTCCTCAAAAATTATTTTTTGAAACTTTATTTTCAAGAAAAATTGATACTTTCA
*
3337678 ACTTTTCCTTAAAAATATATTTTTT
1 ACTTTTCCTCAAAAAT-TATTTTTT
3337703 TATTTTTATT
Statistics
Matches: 279, Mismatches: 31, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.02
58 98 0.35
59 94 0.34
60 15 0.05
61 66 0.24
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (58 bp):
ACTTTTCCTCAAAAATTATTTTTTGAAACTTTATTTTCAAGAAAAATTGATACTTTCA
Found at i:3337633 original size:27 final size:27
Alignment explanation
Indices: 3337545--3337634 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
3337535 ATTTTCAAGG
*
3337545 AAAATTGATACTTTCAACTTTTTCCCA
1 AAAATTGATACTTTCAACTTTTTCTCA
* * *
3337572 AAAA-T-ATTCTTTGGAAACTTTGATTTTCAAGA
1 AAAATTGATACTTT--CAACTTT--TTCTC---A
3337604 AAAATTGATACTTTCAACTTTTTCTCA
1 AAAATTGATACTTTCAACTTTTTCTCA
3337631 AAAA
1 AAAA
3337635 CCCTTTTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
25 6 0.13
26 1 0.02
27 15 0.32
29 3 0.06
30 4 0.09
32 11 0.23
33 1 0.02
34 6 0.13
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTTCTCA
Found at i:3337635 original size:176 final size:175
Alignment explanation
Indices: 3337340--3337701 Score: 539
Period size: 176 Copynumber: 2.0 Consensus size: 175
3337330 TCAAAACTTT
* *
3337340 TATTTTTTTGAAACTTTAATTTTGAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTATT
1 TATTTTTTGGAAACTTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TTATT
* * * *
3337405 TTTTTGAAACTTTAATTTCGAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGA
64 CTTTGGAAACTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGA
*
3337470 AAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAA
129 AAATTTATTTTTAAGAAAAATTGATACTTTAAACTTTTCCCCAAAAA
* *
3337517 TATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACTTTCAACTTTTTCC-CAAAAA-TATT
1 TATTTTTTGGAAACTTTAATTTT-AAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATTATT
* *
3337580 CTTTGGAAACTTTGATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTG
64 CTTTGGAAACTTT-AATTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTG
**
3337645 AAAATTTATTTTTAAGAAAAATTGATACTTTAAACTTTTCCTTAAAAA
128 AAAATTTATTTTTAAGAAAAATTGATACTTTAAACTTTTCCCCAAAAA
3337693 TATATTTTT
1 TAT-TTTTT
3337702 TTATTTTTAT
Statistics
Matches: 168, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
175 15 0.09
176 95 0.57
177 26 0.15
178 26 0.15
179 6 0.04
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (175 bp):
TATTTTTTGGAAACTTTAATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTCT
TTGGAAACTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAA
ATTTATTTTTAAGAAAAATTGATACTTTAAACTTTTCCCCAAAAA
Found at i:3337713 original size:58 final size:58
Alignment explanation
Indices: 3337364--3337702 Score: 337
Period size: 59 Copynumber: 5.7 Consensus size: 58
3337354 TTTAATTTTG
* * * * *
3337364 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTATTTTTTTGAAACTTTAATTTCG
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAA--CTA-TTTTTTAAAATTTTATTTTCA
* ** *
3337425 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAA-TTTATTTTTA
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTT-AAAATTTTATTTTCA
* * *
3337483 AGAAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGGAAACTTTGATTTTCA
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTT--AAAATTTTATTTTCA
* * * *
3337542 AGGAAAATTGATACTTTCAACTTTTTCC-CAAAAA-TATTCTTTGGAAACTTTGATTTTCA
1 AGAAAAATTGATACTTTCAAC-TTTTCCTCAAAAACTATT-TTT-TAAAATTTTATTTTCA
* ** *
3337601 AGAAAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTGAAAA-TTTATTTTTA
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTT-AAAATTTTATTTTCA
* * *
3337659 AGAAAAATTGATACTTTAAACTTTTCCTTAAAAATATATTTTTT
1 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-CTATTTTTT
3337703 TATTTTTATT
Statistics
Matches: 237, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
57 6 0.03
58 93 0.39
59 94 0.40
60 11 0.05
61 33 0.14
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (58 bp):
AGAAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTTAAAATTTTATTTTCA
Found at i:3337764 original size:6 final size:6
Alignment explanation
Indices: 3337736--3337819 Score: 72
Period size: 6 Copynumber: 14.7 Consensus size: 6
3337726 ATAATGAAAC
* *
3337736 AAAATA AAAGTG AAAAT- -AAATA AAAATA AAAA-A ATAAA-A AAAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A-AAATA AAAA-TA
* *
3337781 AAAACA AAAATA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
3337820 AATATTAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
4 4 0.06
5 10 0.16
6 50 0.78
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:3337764 original size:35 final size:34
Alignment explanation
Indices: 3337736--3337811 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
3337726 ATAATGAAAC
* *
3337736 AAAATAAAAGTGAAA-ATAAATAAAAATAAAAAAAT
1 AAAATAAAAGTAAAACAAAAATAAAAAT--AAAAAT
3337771 AAAA-AAAAGTAAAACAAAAATAAAAATAAAAAT
1 AAAATAAAAGTAAAACAAAAATAAAAATAAAAAT
3337804 AAAATAAA
1 AAAATAAA
3337812 GATAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 10 0.27
34 12 0.32
35 15 0.41
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.14
Consensus pattern (34 bp):
AAAATAAAAGTAAAACAAAAATAAAAATAAAAAT
Found at i:3337768 original size:17 final size:17
Alignment explanation
Indices: 3337748--3337820 Score: 80
Period size: 17 Copynumber: 4.2 Consensus size: 17
3337738 AATAAAAGTG
3337748 AAAATAAATAAAAATAAA
1 AAAATAAATAAAAAT-AA
3337766 AAAATAAA-AAAAAGTAA
1 AAAATAAATAAAAA-TAA
3337783 AACAA-AAATAAAAAT-A
1 AA-AATAAATAAAAATAA
*
3337799 AAAATAAAATAAAGATAA
1 AAAAT-AAATAAAAATAA
3337817 AAAA
1 AAAA
3337821 ATATTAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
15 2 0.04
16 3 0.06
17 22 0.46
18 21 0.44
ACGTcount: A:0.82, C:0.01, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATAAATAAAAATAA
Found at i:3337801 original size:11 final size:11
Alignment explanation
Indices: 3337736--3337831 Score: 78
Period size: 10 Copynumber: 9.1 Consensus size: 11
3337726 ATAATGAAAC
*
3337736 AAAATAAAAGTG
1 AAAATAAAA-TA
3337748 AAAAT-AAATA
1 AAAATAAAATA
3337758 AAAAT--AA-A
1 AAAATAAAATA
3337766 AAAATAAAA-A
1 AAAATAAAATA
* *
3337776 AAAGTAAAACA
1 AAAATAAAATA
3337787 AAAATAAAAATA
1 AAAAT-AAAATA
3337799 AAAATAAAATA
1 AAAATAAAATA
*
3337810 AAGATAAAA-A
1 AAAATAAAATA
* *
3337820 AATATTAAATA
1 AAAATAAAATA
3337831 A
1 A
3337832 CCCTAATCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
8 6 0.08
9 2 0.03
10 25 0.35
11 24 0.33
12 15 0.21
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:3338776 original size:19 final size:19
Alignment explanation
Indices: 3338733--3338776 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3338723 AAAAGGAAAA
* *
3338733 AAAAAAAATCCGATAAATG
1 AAAAAAAATCAGATAAACG
*
3338752 AGAAAAAATCAGATAAACG
1 AAAAAAAATCAGATAAACG
3338771 AAAAAA
1 AAAAAA
3338777 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAAAAATCAGATAAACG
Found at i:3338814 original size:21 final size:21
Alignment explanation
Indices: 3338785--3338870 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 21
3338775 AAGAAAGAAA
3338785 AAAATAGATAATTAAAAATAAT
1 AAAA-AGATAATTAAAAATAAT
* * *
3338807 AATAAGATAAATAAAAAATACT
1 AAAAAGAT-AATTAAAAATAAT
* *
3338829 -ACAAGATAAATAAAAA-AAT
1 AAAAAGATAATTAAAAATAAT
* *
3338848 AAAAAAATAA-TAATAATAAT
1 AAAAAGATAATTAAAAATAAT
3338868 AAA
1 AAA
3338871 TATATAACTA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 7 0.14
20 20 0.39
21 10 0.20
22 14 0.27
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (21 bp):
AAAAAGATAATTAAAAATAAT
Found at i:3338826 original size:22 final size:21
Alignment explanation
Indices: 3338790--3338845 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3338780 AGAAAAAAAT
* *
3338790 AGAT-AATTAAAAATAATAATA
1 AGATAAATAAAAAATAAT-ACA
*
3338811 AGATAAATAAAAAATACTACA
1 AGATAAATAAAAAATAATACA
3338832 AGATAAATAAAAAA
1 AGATAAATAAAAAA
3338846 ATAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (21 bp):
AGATAAATAAAAAATAATACA
Found at i:3338840 original size:36 final size:36
Alignment explanation
Indices: 3338782--3338889 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 36
3338772 AAAAAGAAAG
*
3338782 AAAAAAATAGATAATTAA-AAATAATAATAAGATAAAT
1 AAAATAATA-ATAA-TAATAAATAATAATAAGATAAAT
*
3338819 AAAA-AATACTACA-AGATAAATAA-AA-AA-ATAAA-
1 AAAATAATAATA-ATA-ATAAATAATAATAAGATAAAT
3338851 AAAATAATAATAATAATAAATATATAACT-AGATAAAT
1 AAAATAATAATAATAATAAATA-ATAA-TAAGATAAAT
3338888 AA
1 AA
3338890 CATACATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
32 12 0.21
33 13 0.22
34 5 0.09
35 6 0.10
36 16 0.28
37 6 0.10
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (36 bp):
AAAATAATAATAATAATAAATAATAATAAGATAAAT
Found at i:3338888 original size:20 final size:17
Alignment explanation
Indices: 3338787--3338889 Score: 61
Period size: 17 Copynumber: 5.9 Consensus size: 17
3338777 GAAAGAAAAA
*
3338787 AATAGATAATTAA-AAAT
1 AATA-ATAATAAATAAAT
*
3338804 AATAATAAGATAAATAAAA
1 AATAAT-A-ATAAATAAAT
* *
3338823 AATACTACA-AGATAAAT
1 AATAATA-ATAAATAAAT
* *
3338840 AA-AAAAATAAAAAAAT
1 AATAATAATAAATAAAT
3338856 AATAATAAT-AATAAAT
1 AATAATAATAAATAAAT
3338872 ATATAACTAGATAAATAA
1 A-ATAA-TA-ATAAATAA
3338890 CATACATATA
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
15 1 0.02
16 19 0.29
17 22 0.34
18 8 0.12
19 10 0.15
20 5 0.08
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (17 bp):
AATAATAATAAATAAAT
Found at i:3339000 original size:21 final size:20
Alignment explanation
Indices: 3338976--3339014 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3338966 ACATAAATAC
3338976 ATAAAATACAAAAGAAAAAAA
1 ATAAAATA-AAAAGAAAAAAA
*
3338997 ATAAAATAAAAATAAAAA
1 ATAAAATAAAAAGAAAAA
3339015 TACACACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (20 bp):
ATAAAATAAAAAGAAAAAAA
Found at i:3339312 original size:42 final size:42
Alignment explanation
Indices: 3339213--3339343 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 42
3339203 TTGATCAAAA
** * * *
3339213 CTCCTCTAGGCAGAGGCTCAATGACTTTGAGAAACATAAATGG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGA-AAAAATAAATTG
* *
3339256 CTCCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAATTG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAATTG
* * * * *
3339298 CTTCTTTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAATTG
3339339 CTCCT
1 CTCCT
3339344 TGACAATCAT
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 15 0.20
42 33 0.45
43 26 0.35
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (42 bp):
CTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAATTG
Found at i:3340367 original size:14 final size:14
Alignment explanation
Indices: 3340350--3340429 Score: 101
Period size: 14 Copynumber: 5.6 Consensus size: 14
3340340 TGAGTCTTTC
3340350 TTTTTCATTTTTTA
1 TTTTTCATTTTTTA
3340364 TTTTT-ATTTTTTTA
1 TTTTTCA-TTTTTTA
3340378 TTTTTCATTTTTT-
1 TTTTTCATTTTTTA
3340391 TTTTTCATTTTTTA
1 TTTTTCATTTTTTA
* *
3340405 TTTTTTTATTTTTTT
1 -TTTTTCATTTTTTA
3340420 TATTTTCATT
1 T-TTTTCATT
3340430 CATTTTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
13 14 0.24
14 24 0.41
15 20 0.34
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCATTTTTTA
Found at i:3340368 original size:8 final size:8
Alignment explanation
Indices: 3340364--3340425 Score: 63
Period size: 8 Copynumber: 7.2 Consensus size: 8
3340354 TCATTTTTTA
3340364 TTTTTATT
1 TTTTTATT
3340372 TTTTTATT
1 TTTTTATT
3340380 TTTCATT-TT
1 TTT--TTATT
*
3340389 TTTTTTTCAT
1 TTTTTAT--T
3340399 TTTTTATT
1 TTTTTATT
3340407 TTTTTATTT
1 TTTTTA-TT
3340416 TTTTTATT
1 TTTTTATT
3340424 TT
1 TT
3340426 CATTCATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
7 2 0.04
8 23 0.49
9 13 0.28
10 9 0.19
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:3340381 original size:28 final size:27
Alignment explanation
Indices: 3340350--3340425 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
3340340 TGAGTCTTTC
3340350 TTTTTCATTTTTTATTTTTATTTTTTTA
1 TTTTTCATTTTTT-TTTTTATTTTTTTA
3340378 TTTTTCATTTTTTTTTTTCA-TTTTTTA
1 TTTTTCATTTTTTTTTTT-ATTTTTTTA
*
3340405 TTTTT--TTATTTTTTTTATTTT
1 TTTTTCATTTTTTTTTTTATTTT
3340426 CATTCATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
24 1 0.02
25 13 0.29
27 17 0.38
28 14 0.31
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTCATTTTTTTTTTTATTTTTTTA
Found at i:3340425 original size:7 final size:7
Alignment explanation
Indices: 3340350--3340418 Score: 79
Period size: 7 Copynumber: 9.9 Consensus size: 7
3340340 TGAGTCTTTC
*
3340350 TTTTTCA
1 TTTTTTA
3340357 TTTTTTA
1 TTTTTTA
3340364 -TTTTTA
1 TTTTTTA
3340370 TTTTTTTA
1 -TTTTTTA
*
3340378 TTTTTCA
1 TTTTTTA
3340385 TTTTTT-
1 TTTTTTA
*
3340391 TTTTTCA
1 TTTTTTA
3340398 TTTTTTA
1 TTTTTTA
3340405 TTTTTTTA
1 -TTTTTTA
3340413 TTTTTT
1 TTTTTT
3340419 TTATTTTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 11 0.21
7 29 0.55
8 13 0.25
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:3340426 original size:43 final size:42
Alignment explanation
Indices: 3340350--3340441 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 42
3340340 TGAGTCTTTC
*
3340350 TTTTTCATTTTTTATTTTTATTTTTTTATTTTTCATT-TTTT
1 TTTTTCATTTTTTATTTTTATTTTTTTATTTTTCATTCATTT
3340391 TTTTTCATTTTTTATTTTTTTATTTTTTT-TATTTTCATTCATTT
1 TTTTTCATTTTTTA--TTTTTATTTTTTTAT-TTTTCATTCATTT
3340435 TTTTTCA
1 TTTTTCA
3340442 AGCATAGTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
41 14 0.30
42 1 0.02
43 21 0.46
44 10 0.22
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (42 bp):
TTTTTCATTTTTTATTTTTATTTTTTTATTTTTCATTCATTT
Found at i:3340436 original size:28 final size:28
Alignment explanation
Indices: 3340350--3340441 Score: 107
Period size: 28 Copynumber: 3.2 Consensus size: 28
3340340 TGAGTCTTTC
*
3340350 TTTTTCA-TTTTTTATTTTTATTTTTTT
1 TTTTTCATTTTTTTATTTTCATTTTTTT
3340377 ATTTTTCATTTTTTT-TTTTCATTTTTTAT
1 -TTTTTCATTTTTTTATTTTCATTTTTT-T
* **
3340406 TTTTTTATTTTTTTTATTTTCATTCATTT
1 TTTTTCA-TTTTTTTATTTTCATTTTTTT
3340435 TTTTTCA
1 TTTTTCA
3340442 AGCATAGTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 24 0.44
29 21 0.38
30 10 0.18
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTTCATTTTTTTATTTTCATTTTTTT
Found at i:3340438 original size:35 final size:34
Alignment explanation
Indices: 3340364--3340437 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 34
3340354 TCATTTTTTA
**
3340364 TTTTTATTTTTTTATTTTTCATTTTTTTTTTTCAT
1 TTTTTATTTTTTTATTTTT-ATTTTTTTCATTCAT
3340399 TTTTTATTTTTTTATTTTT-TTTATTTTCATTCAT
1 TTTTTATTTTTTTATTTTTATTT-TTTTCATTCAT
3340433 TTTTT
1 TTTTT
3340438 TTCAAGCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 3 0.08
34 14 0.39
35 19 0.53
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (34 bp):
TTTTTATTTTTTTATTTTTATTTTTTTCATTCAT
Found at i:3350962 original size:118 final size:116
Alignment explanation
Indices: 3350824--3351159 Score: 381
Period size: 118 Copynumber: 2.8 Consensus size: 116
3350814 TTTATGCAGA
* *
3350824 AAAAATTGATACTCTCAACTTTTCCCCAAAATATTCTTTTGAAACTTTAATTTCGAGAAAAATTG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAATATT-TTTTGAAACTTTAATTTCAAGAAAAATTG
* * *
3350889 ATACTTTCAACTTTTCCCTAAAAACCTTTTTTTTTTAAAAATTT-ATTTTTAAG
65 ATACTTTCAACTTTTTCCTAAAAA--TTTTTTTTTGAAAAATTTGATTTTCAAG
* * * *
3350942 AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTGTGGAAACTTTGATTATCAAGGAAAAT
1 AAAAATTGATACTTTCAACTTTTC-CCCAAAATATTTT-TTGAAACTTTAATT-TCAAGAAAAAT
* * * *
3351007 TGATACTTTCAA-TTTTTTCTCAAAAA-TATTTTTTGGAAACTTTGATTTTCAAG
63 TGATACTTTCAACTTTTTCCT-AAAAATTTTTTTTTGAAAAATTTGATTTTCAAG
* * * * * *
3351060 AAAAATTGATACTTTCAACTTTTCCTCAAAAACTCTTTTTTAAAAATTTATTTTTAAGAAAAATT
1 AAAAATTGATACTTTCAACTTTTCC-CCAAAA-TATTTTTTGAAACTTTAATTTCAAGAAAAATT
*
3351125 GATACTTTCAACTTTTTCTTAAAAATATTTTTTTT
64 GATACTTTCAACTTTTTCCTAAAAAT-TTTTTTTT
3351160 ATTTTTATTT
Statistics
Matches: 184, Mismatches: 24, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
117 40 0.22
118 78 0.42
119 40 0.22
120 26 0.14
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.44
Consensus pattern (116 bp):
AAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTGAAACTTTAATTTCAAGAAAAATTGA
TACTTTCAACTTTTTCCTAAAAATTTTTTTTTGAAAAATTTGATTTTCAAG
Found at i:3351149 original size:58 final size:58
Alignment explanation
Indices: 3350824--3351157 Score: 338
Period size: 59 Copynumber: 5.7 Consensus size: 58
3350814 TTTATGCAGA
* * * * * * *
3350824 AAAAATTGATACTCTCAAC-TTTTCCCCAAAATATTCTTTTGAAACTTT-AATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATT-TTTTAAAAATTTGATTTTCAAG
* * *
3350881 AAAAATTGATACTTTCAAC-TTTTCCCTAAAAACCTTTTTTTTTTAAAAATTT-ATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCTC-AAAAA----TATTTTTTAAAAATTTGATTTTCAAG
** * *
3350942 AAAAATTGATACTTTCAAC-TTTTCTCCAAAAATATTTTGTGGAAACTTTGATTATCAAG
1 AAAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTT-TTAAAAATTTGATTTTCAAG
* * * *
3351001 GAAAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTTGGAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT-AAAAATTTGATTTTCAAG
* * *
3351060 AAAAATTGATACTTTCAACTTTTCCTCAAAAACTCTTTTTTAAAAATTT-ATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAA-TATTTTTTAAAAATTTGATTTTCAAG
*
3351118 AAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT
3351158 TTATTTTTAT
Statistics
Matches: 237, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
57 37 0.16
58 50 0.21
59 88 0.37
60 13 0.05
61 45 0.19
62 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.44
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAATTTGATTTTCAAG
Found at i:3351220 original size:6 final size:6
Alignment explanation
Indices: 3351192--3351269 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
3351182 ATAATGAAAC
* * * *
3351192 AAAATA AAAGTG AAAAT- -AAATA AAAATA AAAA-A ATAAAGA AAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA
* *
3351237 AAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
3351270 GGATATTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
4 4 0.07
5 10 0.18
6 40 0.71
7 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:3351224 original size:29 final size:28
Alignment explanation
Indices: 3351192--3351257 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
3351182 ATAATGAAAC
*
3351192 AAAATAAAAGTGAAAA-T-AAATAAAAATA
1 AAAATAAAA--GAAAAGTAAAACAAAAATA
*
3351220 AAAAAATAAAGAAAAGTAAAACAAAAATA
1 AAAATA-AAAGAAAAGTAAAACAAAAATA
3351249 AAAATAAAA
1 AAAATAAAA
3351258 TAAAGATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.16
28 9 0.28
29 18 0.56
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.14
Consensus pattern (28 bp):
AAAATAAAAGAAAAGTAAAACAAAAATA
Found at i:3351226 original size:8 final size:8
Alignment explanation
Indices: 3351213--3351351 Score: 57
Period size: 8 Copynumber: 15.8 Consensus size: 8
3351203 GAAAATAAAT
3351213 AAAAATAA
1 AAAAATAA
3351221 AAAAATAA
1 AAAAATAA
3351229 AGAAAAGTAA
1 A-AAAA-TAA
3351239 AACAAA-AA
1 AA-AAATAA
3351247 TAAAAATAAA
1 -AAAAAT-AA
3351257 ATAAAGATAA
1 A-AAA-ATAA
3351267 AAAGGATATTAA
1 AAA--A-A-TAA
*
3351279 ATAAACCTAA
1 A-AAA-ATAA
**
3351289 ACTAATAA
1 AAAAATAA
3351297 ATAAAA-AA
1 A-AAAATAA
3351305 AACAAATAA
1 AA-AAATAA
*
3351314 ACAAATAA
1 AAAAATAA
*
3351322 ATAAATAA
1 AAAAATAA
*
3351330 ATAAATAA
1 AAAAATAA
*
3351338 ATAAATAA
1 AAAAATAA
*
3351346 ATAAAT
1 AAAAAT
3351352 TTTTTTTAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 30
0.73 0.07 0.21
Matches are distributed among these distances:
7 1 0.01
8 59 0.56
9 16 0.15
10 19 0.18
11 5 0.05
12 4 0.04
13 2 0.02
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (8 bp):
AAAAATAA
Found at i:3351299 original size:4 final size:4
Alignment explanation
Indices: 3351292--3351351 Score: 84
Period size: 4 Copynumber: 14.8 Consensus size: 4
3351282 AACCTAAACT
* * *
3351292 AATA AATAA AAAA AACA AATA AACA AATA AATA AATA AATA AATA AATA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
3351341 AATA AATA AAT
1 AATA AATA AAT
3351352 TTTTTTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
4 47 0.94
5 3 0.06
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:3352204 original size:20 final size:19
Alignment explanation
Indices: 3352169--3352214 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
3352159 AAAGAAAAAA
*
3352169 AAAAAGAAATCCGATAAACG
1 AAAAA-AAATCAGATAAACG
3352189 AGAAAAAAATCAGATAAACG
1 A-AAAAAAATCAGATAAACG
3352209 AAAAAA
1 AAAAAA
3352215 GAAAGAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.67, C:0.11, G:0.13, T:0.09
Consensus pattern (19 bp):
AAAAAAAATCAGATAAACG
Found at i:3352259 original size:21 final size:21
Alignment explanation
Indices: 3352234--3352313 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 21
3352224 AAAAAATAAC
3352234 AGATAATTAAAAATAATAATA
1 AGATAATTAAAAATAATAATA
* * *
3352255 AGATAAATAAAAAATACT-ACA
1 AGAT-AATTAAAAATAATAATA
*
3352276 AGATAAATAAAAA-AATAATA
1 AGATAATTAAAAATAATAATA
* * *
3352296 AAAAAATT-ATAATAATAA
1 AGATAATTAAAAATAATAA
3352314 ATATATAACT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
19 5 0.11
20 19 0.42
21 10 0.22
22 11 0.24
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.24
Consensus pattern (21 bp):
AGATAATTAAAAATAATAATA
Found at i:3352555 original size:13 final size:13
Alignment explanation
Indices: 3352537--3352566 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3352527 GGGTGTCTAC
3352537 ATATATATATATT
1 ATATATATATATT
3352550 ATATATATATATT
1 ATATATATATATT
3352563 -TATA
1 ATATA
3352567 AAGGGACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Done.