Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 20 of 213
Found at i:5361524 original size:22 final size:22
Alignment explanation
Indices: 5361486--5361551 Score: 91
Period size: 21 Copynumber: 3.0 Consensus size: 22
5361476 AACACGAAAA
5361486 TTTTTAAAACACGGAAATATTTT
1 TTTTTAAAACAC-GAAATATTTT
5361509 TTTTTAAAACACGAAAT-TTTT
1 TTTTTAAAACACGAAATATTTT
* *
5361530 TTTTGAAAACAAGAAA-ATTTT
1 TTTTTAAAACACGAAATATTTT
5361551 T
1 T
5361552 GAAACACTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 23 0.57
22 5 0.12
23 12 0.30
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (22 bp):
TTTTTAAAACACGAAATATTTT
Found at i:5361698 original size:19 final size:19
Alignment explanation
Indices: 5361667--5361705 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5361657 ATACGAGAAA
*
5361667 TTTTAAACGCGAAAA-TTT
1 TTTTAAACACGAAAACTTT
5361685 TTTTCAAACACGAAAACTTT
1 TTTT-AAACACGAAAACTTT
5361705 T
1 T
5361706 GAAAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTTAAACACGAAAACTTT
Found at i:5361764 original size:18 final size:17
Alignment explanation
Indices: 5361715--5361765 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
5361705 TGAAAACGCG
5361715 AAAATTCGAAAATTTCT
1 AAAATTCGAAAATTTCT
* * *
5361732 AAAATACGAGTAATTTTT
1 AAAATTCGA-AAATTTCT
5361750 AAAGATTCGAAAATTT
1 AAA-ATTCGAAAATTT
5361766 GAAACAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAATTCGAAAATTTCT
Found at i:5362281 original size:8 final size:8
Alignment explanation
Indices: 5362260--5362321 Score: 85
Period size: 8 Copynumber: 8.0 Consensus size: 8
5362250 ATTGAACCCC
5362260 CTTTTTCTT
1 CTTTTT-TT
5362269 C-TTTTTT
1 CTTTTTTT
5362276 C-TTTTTT
1 CTTTTTTT
5362283 C-TTTTTT
1 CTTTTTTT
*
5362290 CCTTTTTT
1 CTTTTTTT
5362298 CTTTTTTT
1 CTTTTTTT
5362306 CTTTTTTT
1 CTTTTTTT
5362314 CTTTTTTT
1 CTTTTTTT
5362322 TTCTGCTGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
7 17 0.33
8 33 0.65
9 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
CTTTTTTT
Found at i:5362321 original size:16 final size:15
Alignment explanation
Indices: 5362260--5362320 Score: 88
Period size: 15 Copynumber: 4.0 Consensus size: 15
5362250 ATTGAACCCC
5362260 CTTTTTCTTCTTTTTT
1 CTTTTT-TTCTTTTTT
5362276 C-TTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
*
5362290 CCTTTTTTCTTTTTTT
1 CTTTTTTTC-TTTTTT
5362306 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
5362321 TTTCTGCTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
14 10 0.24
15 17 0.40
16 15 0.36
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
CTTTTTTTCTTTTTT
Found at i:5362474 original size:12 final size:12
Alignment explanation
Indices: 5362457--5362482 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5362447 CTTTCCCTTC
5362457 TTTTTTTTTGCT
1 TTTTTTTTTGCT
5362469 TTTTTTTTTGCT
1 TTTTTTTTTGCT
5362481 TT
1 TT
5362483 GATTTTTTTT
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:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGCT
Found at i:5362619 original size:3 final size:3
Alignment explanation
Indices: 5362613--5362658 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
5362603 TTTTTTTTCT
5362613 TTC TTC TTCC TT- TT- TTC TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TTC TT-C TTC TTC TTC TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
5362659 AAAGTCTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
3 26 0.67
4 9 0.23
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:5362625 original size:21 final size:21
Alignment explanation
Indices: 5362601--5362655 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
5362591 TATTATTTTT
* *
5362601 CTTTTTTTTTCTTTCTTCTTC
1 CTTTTTTCTTCTTCCTTCTTC
5362622 CTTTTTTCTTCTTCCTTCTT-
1 CTTTTTTCTTCTTCCTTCTTC
**
5362642 CTTCCTTCTTCTTC
1 CTTTTTTCTTCTTC
5362656 TTCAAAGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
CTTTTTTCTTCTTCCTTCTTC
Found at i:5362642 original size:10 final size:10
Alignment explanation
Indices: 5362627--5362655 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5362617 TCTTCCTTTT
5362627 TTCTTCTTCC
1 TTCTTCTTCC
5362637 TTCTTCTTCC
1 TTCTTCTTCC
5362647 TTCTTCTTC
1 TTCTTCTTC
5362656 TTCAAAGTCT
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:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:5362749 original size:10 final size:10
Alignment explanation
Indices: 5362714--5362763 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
5362704 ACGCCGGTAC
5362714 TCTT-TCTTT
1 TCTTCTCTTT
* *
5362723 TCTTCTCCTC
1 TCTTCTCTTT
5362733 T-TTCTCTTT
1 TCTTCTCTTT
5362742 TCTTCTCTTT
1 TCTTCTCTTT
*
5362752 TCTTCTTTTT
1 TCTTCTCTTT
5362762 TC
1 TC
5362764 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:5362761 original size:19 final size:19
Alignment explanation
Indices: 5362718--5362760 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5362708 CGGTACTCTT
5362718 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
5362737 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
5362754 TTCTTTT
1 -TCTTTT
5362761 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:5363040 original size:29 final size:29
Alignment explanation
Indices: 5363007--5363121 Score: 110
Period size: 30 Copynumber: 3.9 Consensus size: 29
5362997 TGTAATTTTT
* *
5363007 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAGTTTAGGGTTAAAATGAAATTTAA
* *
5363036 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAGTTTA-GGGT-TAAAATGAAATTTAA
*
5363066 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAGTTT-AGGGTTAAAATGAAATTTAA
* *
5363095 GGAAAGTTTA-GGTTCAAAATGCAATTT
1 AGAAAGTTTAGGGTT-AAAATGAAATTT
5363122 TTATTTTAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
27 3 0.04
28 12 0.17
29 17 0.24
30 37 0.52
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
AGAAAGTTTAGGGTTAAAATGAAATTTAA
Found at i:5363062 original size:30 final size:30
Alignment explanation
Indices: 5363022--5363121 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
5363012 ATTTAGGATT
*
5363022 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
5363052 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
5363082 AAAATGAAATTT-AGGAAAGTTTA-GGTTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
5363110 AAAATGCAATTT
1 AAAATGAAATTT
5363122 TTATTTTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.25
29 10 0.16
30 36 0.59
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:5363145 original size:17 final size:18
Alignment explanation
Indices: 5363119--5363153 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5363109 CAAAATGCAA
5363119 TTTTTATTTT-AAATTTT
1 TTTTTATTTTGAAATTTT
*
5363136 TTTTTTTTTTGAAATTTT
1 TTTTTATTTTGAAATTTT
5363154 GAAATTAAAC
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:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTATTTTGAAATTTT
Found at i:5363469 original size:54 final size:52
Alignment explanation
Indices: 5363387--5363950 Score: 835
Period size: 54 Copynumber: 10.8 Consensus size: 52
5363377 CACGTGAGCC
* *
5363387 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATT--AA
* *
5363441 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAA-A-ATA-GAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAACAGAAATTAA
* *
5363490 AAGGCTCAACTCACCTCTCGC-ATATGAGTTGGTTTTGAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAA
5363541 AAGGCTCAACTCACCTCTCGCAATAT-AGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAGAAATTAA
*
5363594 AAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTGAAAAACAG-AA-TAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAGAAATTAA
5363645 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAGAAATTAA
*
5363699 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAG-AA--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAACAGAAATTAA
* *
5363749 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTT-GATTTTG-AAAACAGAAATTAA
*
5363803 AAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAGAAATTAA
5363857 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAA
5363909 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA
5363951 ACAAAAGAAA
Statistics
Matches: 476, Mismatches: 16, Indels: 38
0.90 0.03 0.07
Matches are distributed among these distances:
47 5 0.01
48 13 0.03
49 24 0.05
50 40 0.08
51 71 0.15
52 85 0.18
53 67 0.14
54 166 0.35
55 5 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (52 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAA
Found at i:5363646 original size:104 final size:105
Alignment explanation
Indices: 5363387--5363950 Score: 882
Period size: 104 Copynumber: 5.4 Consensus size: 105
5363377 CACGTGAGCC
*
5363387 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAGAATTTGCAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAA-TT--AAAAGGCTCAACT
*
5363452 CACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG-----AA
63 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
5363490 AAGGCTCAACTCACCTCTCGC-ATATGAGTTGGTTTTGAAAATAGAAATTAAAAGGCTCAACTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAG-AATTAAAAGGCTCAACTCA
5363554 CCTCTCGCAATAT-AGTTGATTTTTGAAAAACAGAAATTAA
65 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
5363594 AAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTGAAAAACAGAA-TAAAAGGCTCAACTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAGAATTAAAAGGCTCAACTCA
5363658 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
65 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
5363699 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAGAA--AAAAGGCTCAACTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAACAGAATTAAAAGGCTCAACTCA
* *
5363762 CCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
65 CCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
5363803 AAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAG-AATTAAAAGGCTCAACT
5363868 CACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAGAAATTAA
63 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
5363909 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAA
5363951 ACAAAAGAAA
Statistics
Matches: 431, Mismatches: 16, Indels: 27
0.91 0.03 0.06
Matches are distributed among these distances:
99 19 0.04
100 28 0.06
102 23 0.05
103 22 0.05
104 148 0.34
105 94 0.22
106 58 0.13
107 5 0.01
108 34 0.08
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (105 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAATTAAAAGGCTCAACTCAC
CTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:5363747 original size:158 final size:157
Alignment explanation
Indices: 5363387--5363953 Score: 893
Period size: 158 Copynumber: 3.6 Consensus size: 157
5363377 CACGTGAGCC
* *
5363387 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAGAATTTGCAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATT--AAAAGGCTCAACT
*
5363452 CACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG---AAAAGGCTCAACTCACCTCTCGC-AT
64 CACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAATAAAAGGCTCAACTCACCTCTCGCAAT
* *
5363513 ATGAGTTG-GTTTTG-AAAATAGAAATTAA
128 ATGAGTTGATTTTTGAAAAACAGAAATTAA
5363541 AAGGCTCAACTCACCTCTCGCAATAT-AGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAACAGAAATTAAAAGGCTCAACT
*
5363605 CACCTCTCGCAATATAAGTTGATTTTGAAAAACAGAATAAAAGGCTCAACTCACCTCTCGCAATA
64 CACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAATAAAAGGCTCAACTCACCTCTCGCAATA
5363670 TGAGTTGATTTTTGAAAAACAGAAATTAA
129 TGAGTTGATTTTTGAAAAACAGAAATTAA
*
5363699 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATAG-AA--AAAAGGCTCAACTC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAACAGAAATTAAAAGGCTCAACTC
* * *
5363761 ACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTTTCGCAA
65 ACCTCTCGCAATATGAGTT-GATTTTGAAAAACAG-AA-TAAAAGGCTCAACTCACCTCTCGCAA
5363826 TATGAGTTGATTTTTGAAAAACAGAAATTAA
127 TATGAGTTGATTTTTGAAAAACAGAAATTAA
5363857 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAGGCTCAACTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAGGCTCAACTCA
5363922 CCTCTCGCAATATGAGTTGATTTTGAAAAACA
66 CCTCTCGCAATATGAGTTGATTTTGAAAAACA
5363954 AAAGAAATGT
Statistics
Matches: 384, Mismatches: 14, Indels: 25
0.91 0.03 0.06
Matches are distributed among these distances:
152 12 0.03
153 40 0.10
154 30 0.08
155 66 0.17
156 23 0.06
157 20 0.05
158 136 0.35
159 24 0.06
160 33 0.09
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (157 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTGAAAAACAGAATAAAAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGAAAAACAGAAATTAA
Found at i:5364475 original size:15 final size:17
Alignment explanation
Indices: 5364449--5364482 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5364439 ATTTAATTTC
5364449 AAAATTTCAAAAAA-AA
1 AAAATTTCAAAAAATAA
5364465 AAAATTT-AAAAAATAA
1 AAAATTTCAAAAAATAA
5364481 AA
1 AA
5364483 TTGCATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATTTCAAAAAATAA
Found at i:5364543 original size:30 final size:29
Alignment explanation
Indices: 5364480--5364596 Score: 119
Period size: 30 Copynumber: 3.9 Consensus size: 29
5364470 TTAAAAAATA
* *
5364480 AAATTGCATTTTGACACCTAAACTTT-TCCT
1 AAATTTCATTTTGAC-CCTAAACTTTCT-TT
5364510 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCTTT
* * *
5364540 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCTTT
* * *
5364570 AAATTTCATTTTAATCCTAAATTTTCT
1 AAATTTCATTTTGACCCTAAACTTTCT
5364597 AAAAATTACA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 57 0.78
31 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCTTT
Found at i:5364861 original size:10 final size:10
Alignment explanation
Indices: 5364842--5364891 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
5364832 TTTTTCGAAG
*
5364842 GAAAAAAGAA
1 GAAAAGAGAA
5364852 GAAAAGAGAA
1 GAAAAGAGAA
5364862 GAAAAGAGAA
1 GAAAAGAGAA
* *
5364872 -AGAGGAGAA
1 GAAAAGAGAA
5364881 GAAAAGA-AA
1 GAAAAGAGAA
5364890 GA
1 GA
5364892 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:5364892 original size:17 final size:19
Alignment explanation
Indices: 5364845--5364887 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5364835 TTCGAAGGAA
5364845 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
5364863 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
5364882 AAAAGA
1 AAAAGA
5364888 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:5364977 original size:14 final size:13
Alignment explanation
Indices: 5364947--5364983 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5364937 GCTAGACTTT
*
5364947 GAAGAAGAAGAAG
1 GAAGAAGAAAAAG
5364960 GAAGAAGAAAAGAG
1 GAAGAAGAAAA-AG
5364974 GAAGAAGAAA
1 GAAGAAGAAA
5364984 GAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAG
Found at i:5364977 original size:21 final size:22
Alignment explanation
Indices: 5364948--5365000 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
5364938 CTAGACTTTG
*
5364948 AAGAAGAAGAAGGAAG-AAGAA
1 AAGAAGAAGAAGAAAGAAAGAA
*
5364969 AAGAGGAAGAAGAAAGAAAGAA
1 AAGAAGAAGAAGAAAGAAAGAA
*
5364991 AA-AAAAAGAA
1 AAGAAGAAGAA
5365001 ATAATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAGAAAGAAAGAA
Found at i:5365263 original size:7 final size:7
Alignment explanation
Indices: 5365251--5365307 Score: 96
Period size: 7 Copynumber: 7.9 Consensus size: 7
5365241 CCAGCAGAAA
5365251 AAAAAAG
1 AAAAAAG
5365258 AAAAAAG
1 AAAAAAG
5365265 AAAAAAG
1 AAAAAAG
5365272 AAAAAAGG
1 AAAAAA-G
5365280 AAAAAAG
1 AAAAAAG
5365287 AAAAAAG
1 AAAAAAG
5365294 AAAAAAG
1 AAAAAAG
5365301 AAGAAAA
1 AA-AAAA
5365308 AGGGGGTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
7 37 0.77
8 11 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5365282 original size:22 final size:22
Alignment explanation
Indices: 5365250--5365309 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
5365240 CCCAGCAGAA
*
5365250 AAAAAAAGAAAAAAGAAAAAAG
1 AAAAAAGGAAAAAAGAAAAAAG
5365272 AAAAAAGGAAAAAAGAAAAAAG
1 AAAAAAGGAAAAAAGAAAAAAG
*
5365294 AAAAAAGAAGAAAAAG
1 AAAAAAGGA-AAAAAG
5365310 GGGGTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 29 0.83
23 6 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAGGAAAAAAGAAAAAAG
Found at i:5365851 original size:17 final size:16
Alignment explanation
Indices: 5365803--5365852 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
5365793 TTCTTGTTTC
5365803 AAATTTTCGAATCTTTA
1 AAATTTTCGAAT-TTTA
* *
5365820 AAATTACTCGTATTTTA
1 AAATT-TTCGAATTTTA
5365837 GAAATTTTCGAATTTT
1 -AAATTTTCGAATTTT
5365853 CGCGTTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (16 bp):
AAATTTTCGAATTTTA
Found at i:5365872 original size:18 final size:19
Alignment explanation
Indices: 5365847--5365902 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
5365837 GAAATTTTCG
**
5365847 AATTTTCGCGTTT-TCAAA
1 AATTTTCGCGTTTGAAAAA
* *
5365865 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTGAAAAA
5365884 AATTTTCGCGTTT-AAAAA
1 AATTTTCGCGTTTGAAAAA
5365902 A
1 A
5365903 TTTCTCGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (19 bp):
AATTTTCGCGTTTGAAAAA
Found at i:5365889 original size:19 final size:18
Alignment explanation
Indices: 5365847--5365920 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
5365837 GAAATTTTCG
* **
5365847 AATTTTCGCGTTTTCAAA
1 AATTTTCGTGTTTAAAAA
*
5365865 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGTGTTT-AAAAA
*
5365884 AATTTTCGCGTTT-AAAA
1 AATTTTCGTGTTTAAAAA
*
5365901 AATTTCTCGTATTTCAAAAA
1 AATTT-TCGTGTTT-AAAAA
5365921 TTGTCGTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 9 0.20
18 17 0.39
19 14 0.32
20 4 0.09
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
AATTTTCGTGTTTAAAAA
Found at i:5365920 original size:37 final size:37
Alignment explanation
Indices: 5365847--5365920 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
5365837 GAAATTTTCG
* * * *
5365847 AATTTTCGCGTTTTCAAAAGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
5365884 AATTTTCGCG-TTTAAAAAATTTCTCGTATTTCAAAAA
1 AATTTTCGCGTTTTAAAAAATTT-TCGTATTTCAAAAA
5365921 TTGTCGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
Found at i:5365962 original size:18 final size:18
Alignment explanation
Indices: 5365936--5366004 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
5365926 GTTTTTTATA
*
5365936 AATCTTCGTGCTTTCAAT
1 AATCCTCGTGCTTTCAAT
5365954 AATCCTCGTGCTTTCAAT
1 AATCCTCGTGCTTTCAAT
*
5365972 AATCCTCATG-TTTCAA-
1 AATCCTCGTGCTTTCAAT
* *
5365988 AATCTTCGTGTTTTCAA
1 AATCCTCGTGCTTTCAA
5366005 AATTCTAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
16 8 0.17
17 12 0.26
18 26 0.57
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (18 bp):
AATCCTCGTGCTTTCAAT
Found at i:5366002 original size:17 final size:16
Alignment explanation
Indices: 5365935--5366022 Score: 79
Period size: 18 Copynumber: 5.2 Consensus size: 16
5365925 CGTTTTTTAT
5365935 AAATCTTCGTGCTTTCA
1 AAATCTTCGTG-TTTCA
*
5365952 ATAATCCTCGTGCTTTCA
1 A-AATCTTCGTG-TTTCA
* *
5365970 ATAATCCTCATGTTTCA
1 A-AATCTTCGTGTTTCA
5365987 AAATCTTCGTGTTTTCA
1 AAATCTTCGTG-TTTCA
*
5366004 AAAT-TCTAGTGTTTCA
1 AAATCT-TCGTGTTTCA
5366020 AAA
1 AAA
5366023 ATTTTCTTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
16 17 0.27
17 20 0.32
18 26 0.41
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.41
Consensus pattern (16 bp):
AAATCTTCGTGTTTCA
Found at i:5366003 original size:34 final size:33
Alignment explanation
Indices: 5365947--5366040 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 33
5365937 ATCTTCGTGC
* *
5365947 TTTCAATAATCCTCGTGCTTTCAATAATCCTCA-TG
1 TTTCAA-AATCTTCGTGTTTTCAA-AATCCT-AGTG
*
5365982 TTTCAAAATCTTCGTGTTTTCAAAATTCTAGTG
1 TTTCAAAATCTTCGTGTTTTCAAAATCCTAGTG
* *
5366015 TTTCAAAAATTTTCTTGTTTTCAAAA
1 TTTC-AAAATCTTCGTGTTTTCAAAA
5366041 AAAAATTTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 11 0.21
34 34 0.65
35 6 0.12
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.45
Consensus pattern (33 bp):
TTTCAAAATCTTCGTGTTTTCAAAATCCTAGTG
Found at i:5366047 original size:22 final size:21
Alignment explanation
Indices: 5366019--5366101 Score: 95
Period size: 21 Copynumber: 4.0 Consensus size: 21
5366009 CTAGTGTTTC
*
5366019 AAAAATTTTCTTGTTTTCAAAA
1 AAAAATTTTCGTGTTTT-AAAA
5366041 AAAAA-TTTCGTGTTTTAAAA
1 AAAAATTTTCGTGTTTTAAAA
5366061 AAAAATATTTCCGTGTTTT----
1 AAAAAT-TTT-CGTGTTTTAAAA
5366080 AAAAATTTTCGTGTTTTAAAA
1 AAAAATTTTCGTGTTTTAAAA
5366101 A
1 A
5366102 TTCTCGTATT
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
17 8 0.15
18 3 0.06
19 6 0.11
20 9 0.17
21 11 0.21
22 8 0.15
23 8 0.15
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (21 bp):
AAAAATTTTCGTGTTTTAAAA
Found at i:5366062 original size:17 final size:17
Alignment explanation
Indices: 5365986--5366292 Score: 93
Period size: 17 Copynumber: 17.2 Consensus size: 17
5365976 CTCATGTTTC
*
5365986 AAAATCTTCGTGTTTT-C
1 AAAAT-TTCGTGTTTTAA
* *
5366003 AAAATTCTAGTGTTTCAA
1 AAAATT-TCGTGTTTTAA
* *
5366021 AAATTTTCTTGTTTTCAAAAA
1 AAAATTTCGTGTTTT----AA
5366042 AAAATTTCGTGTTTTAAAAAA
1 AAAATTTCGTGTTTT----AA
5366063 AAATATTTCCGTGTTTTAA
1 AAA-ATTT-CGTGTTTTAA
*
5366082 AAATTTTCGTGTTTT-A
1 AAAATTTCGTGTTTTAA
*
5366098 AAAATTCTCGT-ATTT--
1 AAAATT-TCGTGTTTTAA
5366113 AAAATTT--T-TTTTAAGAA
1 AAAATTTCGTGTTTT---AA
*
5366130 AAAATTT--TGTTTCAA
1 AAAATTTCGTGTTTTAA
* *
5366145 AAAATGTCTTGTTTT-A
1 AAAATTTCGTGTTTTAA
* *
5366161 AAAATTCCCGTGTTTCAAAA
1 AAAATT-TCGTGTTT--TAA
*
5366181 AAAATGTCGTGTTTTAA
1 AAAATTTCGTGTTTTAA
*
5366198 GAAAATTTCGTTTTTTTTTCCAA
1 -AAAATTTCG---TGTTTT--AA
*
5366221 AAATTTTCGTGTTTCTAA
1 AAAATTTCGTGTTT-TAA
*
5366239 AATA-TTCGTG-TTT-A
1 AAAATTTCGTGTTTTAA
* *
5366253 CAAATTCTCGTGTTTTCA
1 AAAATT-TCGTGTTTTAA
*
5366271 AAAATTCTCGTATTTTAA
1 AAAATT-TCGTGTTTTAA
5366289 AAAA
1 AAAA
5366293 AAAAACTTTC
Statistics
Matches: 223, Mismatches: 35, Indels: 63
0.69 0.11 0.20
Matches are distributed among these distances:
12 4 0.02
14 4 0.02
15 16 0.07
16 23 0.10
17 60 0.27
18 43 0.19
19 16 0.07
20 7 0.03
21 28 0.13
22 12 0.05
23 10 0.04
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (17 bp):
AAAATTTCGTGTTTTAA
Found at i:5366063 original size:23 final size:23
Alignment explanation
Indices: 5366019--5366084 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
5366009 CTAGTGTTTC
* * *
5366019 AAAAATTTTCTTGTTTT-CAAAA
1 AAAAATTTCCGTGTTTTAAAAAA
5366041 AAAAATTT-CGTGTTTTAAAAAA
1 AAAAATTTCCGTGTTTTAAAAAA
*
5366063 AAATATTTCCGTGTTTTAAAAA
1 AAAAATTTCCGTGTTTTAAAAA
5366085 TTTTCGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.18
22 19 0.49
23 13 0.33
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (23 bp):
AAAAATTTCCGTGTTTTAAAAAA
Found at i:5374681 original size:123 final size:123
Alignment explanation
Indices: 5374455--5374697 Score: 337
Period size: 122 Copynumber: 2.0 Consensus size: 123
5374445 AAGAAAATCA
* *
5374455 ACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATCACGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGC
*
5374520 GAGAAGTGAGTTGAGCCTAGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTAGGGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
** *
5374578 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTC-AAAATCAATTCATATTGC
1 ACTCATATCACGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGC
* * ** * * *
5374642 TAGAGGTGAGTTGAGCCTCA-GGACACGCTGAGGTAATTTTAATTTCTGTTGTTAAA
66 GAGAAGTGAGTTGAGCCT-AGGGACACGCCAAGGTATTTTTAGTTTATGTT-TTAAA
5374698 AAAATCAACT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
122 57 0.54
123 48 0.46
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (123 bp):
ACTCATATCACGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGC
GAGAAGTGAGTTGAGCCTAGGGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
Found at i:5374919 original size:72 final size:72
Alignment explanation
Indices: 5374610--5375400 Score: 961
Period size: 72 Copynumber: 11.1 Consensus size: 72
5374600 TAAGCCTTTT
* * * ** * *
5374610 AATTTATGTTTTTCAAAA-TCAATTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
*
5374674 GTAATTTT
65 GTAATTTC
* * * *
5374682 AATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 AATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
5374747 GGTAATTTC
64 GGTAATTTC
* *
5374756 AATTTCTATTTTCAAAATTCAACTTATATTGCGAGAAA-GAGTT--G----AAGACAC-TTGA-G
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
5374812 T--TTTC
66 TAATTTC
5374817 AATTTCTG-TTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
5374880 TAATTTC
66 TAATTTC
*
5374887 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT-ATT
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA-G
* ** *
5374951 TTTTTTTA
65 GTAATTTC
* * *
5374959 ATTCATTTCGAGTATTGGCCTC-AGATGCCAAACTC-TA-TGC--GAAATGAGTTGAGCCTC-AG
1 A---ATTTC-TGT-TT----TCAAAAT-TC-AACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
5375018 ACACGTT-AGGT-ATTTC
55 ACACGTTGAGGTAATTTC
5375034 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
5375099 T-ATTTC
66 TAATTTC
5375105 AATTTCTGTTTT--AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
5375168 TATTTTC
66 TAATTTC
*
5375175 AATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
5375240 GTAATTTC
65 GTAATTTC
*
5375248 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
5375313 TATTTTC
66 TAATTTC
* * *
5375320 AATTTCTGCTTTTCAAAACTT-AACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGCACGCTGA
1 AATTTCTG-TTTTCAAAA-TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
*
5375384 GGTATTTTC
64 GGTAATTTC
5375393 AATTTCTG
1 AATTTCTG
5375401 CTTTACTAAT
Statistics
Matches: 638, Mismatches: 40, Indels: 81
0.84 0.05 0.11
Matches are distributed among these distances:
59 19 0.03
60 13 0.02
61 11 0.02
62 1 0.00
63 2 0.00
64 3 0.00
65 11 0.02
66 12 0.02
67 10 0.02
68 2 0.00
69 70 0.11
70 35 0.05
71 42 0.07
72 154 0.24
73 136 0.21
74 60 0.09
75 9 0.01
76 3 0.00
77 12 0.02
78 17 0.03
80 6 0.01
81 5 0.01
82 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTC
Found at i:5375404 original size:73 final size:72
Alignment explanation
Indices: 5374999--5375400 Score: 674
Period size: 73 Copynumber: 5.6 Consensus size: 72
5374989 AACTCTATGC
5374999 GAAATGAGTTGAGCCTC-AGACACGTT-AGGTA-TTTCAATTTCTGTTTTCAAAATTCAACTCAT
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAATTCAACTCAT
5375061 ATTGCGA
66 ATTGCGA
5375068 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTCAATTTCTGTTTT--AAATTCAACTCAT
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAATTCAACTCAT
5375130 ATTGCGA
66 ATTGCGA
*
5375137 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTTCTCAAAATTCAACTCA
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG-TTTTCAAAATTCAACTCA
5375202 TATTGCGA
65 TATTGCGA
*
5375210 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCAT
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAATTCAACTCAT
5375275 ATTGCGA
66 ATTGCGA
*
5375282 GAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGCTTTTCAAAACTT-AACTC
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG-TTTTCAAAA-TTCAACTC
5375346 ATATTGCGA
64 ATATTGCGA
* * *
5375355 GAGATGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTG
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG
5375401 CTTTACTAAT
Statistics
Matches: 316, Mismatches: 9, Indels: 12
0.94 0.03 0.04
Matches are distributed among these distances:
69 70 0.22
70 21 0.07
71 24 0.08
72 69 0.22
73 130 0.41
74 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (72 bp):
GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAATTCAACTCAT
ATTGCGA
Found at i:5375412 original size:145 final size:143
Alignment explanation
Indices: 5374999--5375412 Score: 660
Period size: 145 Copynumber: 2.9 Consensus size: 143
5374989 AACTCTATGC
5374999 GAAATGAGTTGAGCCTC-AGACACGTT-AGGTA-TTTCAATTTCTGTTTTCAAAATTCAACTCAT
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAATTCAACTCAT
*
5375061 ATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTCAATTTCTGTTT-TAAATTCA
66 ATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTACAAATTCA
5375124 ACTCATATTGCGA
131 ACTCATATTGCGA
*
5375137 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTTCTCAAAATTCAACTCA
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG-TTTTCAAAATTCAACTCA
* *
5375202 TATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATT
65 TATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTAC-AAATT
5375267 CAACTCATATTGCGA
129 CAACTCATATTGCGA
*
5375282 GAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGCTTTTCAAAACTT-AACTC
1 GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG-TTTTCAAAA-TTCAACTC
* * * *
5375346 ATATTGCGAGAGATGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTGCTTTACTAAT
64 ATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG-TTTACAAAT
5375411 TC
128 TC
5375413 TACTTTTTCA
Statistics
Matches: 257, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
138 17 0.07
139 9 0.04
140 5 0.02
141 12 0.05
142 58 0.23
143 15 0.06
145 135 0.53
146 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (143 bp):
GAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAATTCAACTCAT
ATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTACAAATTCA
ACTCATATTGCGA
Found at i:5375506 original size:14 final size:14
Alignment explanation
Indices: 5375484--5375516 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5375474 TCTTTTCAAA
5375484 TTCTG-TTTTTAAT
1 TTCTGTTTTTTAAT
5375497 TTCTGTTTTTTAAT
1 TTCTGTTTTTTAAT
5375511 TTCTGT
1 TTCTGT
5375517 GTTTCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (14 bp):
TTCTGTTTTTTAAT
Found at i:5375506 original size:86 final size:87
Alignment explanation
Indices: 5375315--5375506 Score: 214
Period size: 86 Copynumber: 2.2 Consensus size: 87
5375305 CATTGAGGTA
* * * *
5375315 TTTTCAATTTCTGCTTTTCAAAACTTAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGCACG
1 TTTTTAATTTCTGTTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGGCACG
*
5375380 CTGAGGTATTTTCAATTTCTGC
66 CTGAGGTATTTTCAAATTCTGC
* * * *
5375402 TTTACTAA-TTCTACTTTTTC-AAA-TCAACTCATATTGCAAGAGGTGAGTTGAGTCTC-AGGCC
1 TTT-TTAATTTCT-GTTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGG--
*
5375463 ACACGCTGAGGTCTTTTCAAATTCTG-
62 -CACGCTGAGGTATTTTCAAATTCTGC
5375489 TTTTTAATTTCTGTTTTT
1 TTTTTAATTTCTGTTTTT
5375507 TAATTTCTGT
Statistics
Matches: 87, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
85 3 0.03
86 37 0.43
87 17 0.20
88 30 0.34
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (87 bp):
TTTTTAATTTCTGTTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGGCACG
CTGAGGTATTTTCAAATTCTGC
Found at i:5375614 original size:52 final size:54
Alignment explanation
Indices: 5375528--5375773 Score: 344
Period size: 52 Copynumber: 4.6 Consensus size: 54
5375518 TTTCAAAAGA
* *
5375528 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
*
5375582 -AAAACCAA-TCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
* **
5375634 AAAAACCAACTCATATTGCGAGAAATGAGTTGAGCC--TT--TTTCTATTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
* *
5375684 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCT-GTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--AATTTCTATTTTTC
*
5375739 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
5375774 ATTGGCTCAC
Statistics
Matches: 173, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
50 45 0.26
52 46 0.27
53 15 0.09
54 24 0.14
55 39 0.23
56 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (54 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
Found at i:5376055 original size:30 final size:29
Alignment explanation
Indices: 5376021--5376115 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 29
5376011 AATTTTCAAA
*
5376021 ATTTTGACACCTAAACTTTTC-CTAAATTTC
1 ATTTTGAC-CCTAAAC-TTTCATTAAATTTC
*
5376051 ATTTTGACCCTTAAACTTTCTTTAAATTTC
1 ATTTTGACCC-TAAACTTTCATTAAATTTC
* *
5376081 ACTTAGACCCCTAAACTTTCATTAAATTTC
1 ATTTTGA-CCCTAAACTTTCATTAAATTTC
5376111 ATTTT
1 ATTTT
5376116 AATCCTAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.11
30 47 0.84
31 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.45
Consensus pattern (29 bp):
ATTTTGACCCTAAACTTTCATTAAATTTC
Found at i:5376414 original size:18 final size:17
Alignment explanation
Indices: 5376391--5376425 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
5376381 AAGAAGAAAA
5376391 GAGAAGAAAGAGAAAGAG
1 GAGAAGAAA-AGAAAGAG
5376409 GAGAAGAAAAGAAAGAG
1 GAGAAGAAAAGAAAGAG
5376426 TACCGGCGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
GAGAAGAAAAGAAAGAG
Found at i:5376415 original size:23 final size:23
Alignment explanation
Indices: 5376380--5376425 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5376370 TCGAAGGAAA
*
5376380 AAAGAAGAAAAGAGAAGAAAGAG
1 AAAGAAGAAAAGAAAAGAAAGAG
* *
5376403 AAAGAGGAGAAGAAAAGAAAGAG
1 AAAGAAGAAAAGAAAAGAAAGAG
5376426 TACCGGCGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAAGAAGAAAAGAAAAGAAAGAG
Found at i:5376486 original size:3 final size:3
Alignment explanation
Indices: 5376480--5376525 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
5376470 GCTAGACTTT
*
5376480 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
5376526 AGAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5376498 original size:10 final size:10
Alignment explanation
Indices: 5376483--5376511 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5376473 AGACTTTGAA
5376483 GAAGAAGAAG
1 GAAGAAGAAG
5376493 GAAGAAGAAG
1 GAAGAAGAAG
5376503 GAAGAAGAA
1 GAAGAAGAA
5376512 AAGAGGAAGA
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:5376498 original size:13 final size:13
Alignment explanation
Indices: 5376480--5376525 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
5376470 GCTAGACTTT
5376480 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
5376493 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
5376506 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
5376517 GAAGAAGAA
1 GAAGAAGAA
5376526 AGAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:5376826 original size:23 final size:23
Alignment explanation
Indices: 5376800--5376877 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 23
5376790 GCAGCCCAGC
*
5376800 AGAAAAAAAAAGGAAGAAAAAGA
1 AGAAAAAAAAAAGAAGAAAAAGA
*
5376823 AGAAAAAAGAAAAAAAGAAAAAAGGA
1 AGAAAAAA-AAAAGAAG-AAAAA-GA
5376849 A-AAAAGAAAAAAGAA-AAAAAGA
1 AGAAAA-AAAAAAGAAGAAAAAGA
5376871 AGAAAAA
1 AGAAAAA
5376878 TGGGGTTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.09
23 17 0.36
24 6 0.13
25 15 0.32
26 5 0.11
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAAAGAAGAAAAAGA
Found at i:5376834 original size:7 final size:7
Alignment explanation
Indices: 5376817--5376867 Score: 75
Period size: 7 Copynumber: 6.9 Consensus size: 7
5376807 AAAAGGAAGA
5376817 AAAAGAAG
1 AAAA-AAG
5376825 AAAAAAG
1 AAAAAAG
5376832 AAAAAAAG
1 -AAAAAAG
5376840 AAAAAAGG
1 AAAAAA-G
5376848 AAAAAAG
1 AAAAAAG
5376855 AAAAAAG
1 AAAAAAG
5376862 AAAAAA
1 AAAAAA
5376868 AGAAGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
7 23 0.56
8 18 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5376835 original size:15 final size:15
Alignment explanation
Indices: 5376800--5376876 Score: 102
Period size: 15 Copynumber: 5.1 Consensus size: 15
5376790 GCAGCCCAGC
**
5376800 AGAAAAAAA-AAGGA
1 AGAAAAAAAGAAAAA
5376814 AGAAAAAGAAGAAAAA
1 AGAAAAA-AAGAAAAA
5376830 AGAAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
*
5376845 AGGAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
5376860 AGAAAAAAAGAAGAAA
1 AGAAAAAAAGAA-AAA
5376876 A
1 A
5376877 ATGGGGTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
14 7 0.12
15 35 0.62
16 14 0.25
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:5376836 original size:8 final size:8
Alignment explanation
Indices: 5376813--5376877 Score: 82
Period size: 8 Copynumber: 8.2 Consensus size: 8
5376803 AAAAAAAAGG
5376813 AAGAAAAA
1 AAGAAAAA
5376821 GAAG-AAAA
1 -AAGAAAAA
5376829 AAGAAAAA
1 AAGAAAAA
5376837 AAG-AAAA
1 AAGAAAAA
*
5376844 AAGGAAAA
1 AAGAAAAA
5376852 AAG-AAAA
1 AAGAAAAA
5376859 AAGAAAAA
1 AAGAAAAA
5376867 AAGAAGAAA
1 AAGAA-AAA
5376876 AA
1 AA
5376878 TGGGGTTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
7 17 0.33
8 27 0.52
9 8 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:5377442 original size:18 final size:19
Alignment explanation
Indices: 5377417--5377472 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
5377407 GAAATTTTCG
**
5377417 AATTTTCGCGTTT-TCAAA
1 AATTTTCGCGTTTGAAAAA
* *
5377435 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTGAAAAA
5377454 AATTTTCGCGTTT-AAAAA
1 AATTTTCGCGTTTGAAAAA
5377472 A
1 A
5377473 TTTCTCGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (19 bp):
AATTTTCGCGTTTGAAAAA
Found at i:5377459 original size:19 final size:18
Alignment explanation
Indices: 5377417--5377866 Score: 80
Period size: 17 Copynumber: 25.1 Consensus size: 18
5377407 GAAATTTTCG
* **
5377417 AATTTTCGCGTTTTCAAA
1 AATTTTCGTGTTTAAAAA
*
5377435 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGTGTTT-AAAAA
*
5377454 AATTTTCGCGTTT-AAAA
1 AATTTTCGTGTTTAAAAA
* *
5377471 AATTTCTCGTATTT-CAAA
1 AATTT-TCGTGTTTAAAAA
* ** *
5377489 AATTATCGT-TTTTTACA
1 AATTTTCGTGTTTAAAAA
* *
5377506 AATTTTCGTGCTTT-CAAT
1 AATTTTCGTG-TTTAAAAA
** *
5377524 AATCCTCGTGCTTT-TAAA
1 AATTTTCGTG-TTTAAAAA
* * *
5377542 AATTCTCATGTTT-CAAA
1 AATTTTCGTGTTTAAAAA
* **
5377559 AATCTTCGTGTTT-TCAA
1 AATTTTCGTGTTTAAAAA
* * *
5377576 AATTCTAGTGTTT-CAAA
1 AATTTTCGTGTTTAAAAA
*
5377593 AATTTTCTTGTTTTCAAAAAAA
1 AATTTTCGTG-TTT---AAAAA
*
5377615 AAATTTCGTGTTTTAAAAAAA
1 AATTTTCGTG-TTT--AAAAA
*
5377636 AATATTTCCGTGTTT-TAAA
1 AAT-TTT-CGTGTTTAAAAA
*
5377655 AATTTTCGTGTTT-TAAA
1 AATTTTCGTGTTTAAAAA
* *
5377672 AATTCTCGTATTT---AA
1 AATTTTCGTGTTTAAAAA
* *
5377687 AATTTT-TTTTTTAAGAAAA
1 AATTTTCGTGTTT-A-AAAA
*
5377706 AATTTT-GT-TTCAAAAA
1 AATTTTCGTGTTTAAAAA
* * *
5377722 AA-TGTCTTGTTT-TAAA
1 AATTTTCGTGTTTAAAAA
**
5377738 AATTCCCGTGTTTCAAAAAA
1 AATTTTCGTGTTT--AAAAA
* * *
5377758 AAATGTCGTGTTTTAAGAA
1 AATTTTCGTG-TTTAAAAA
* **
5377777 AA-TTTCGTTTTTTTTCAAA
1 AATTTTCG--TGTTTAAAAA
**
5377796 AATTTTCGTGTTT-CTAA
1 AATTTTCGTGTTTAAAAA
* *
5377813 AATATTCGTGTTT--ACA
1 AATTTTCGTGTTTAAAAA
* **
5377829 AATTCTCGTGTTTTCAAA
1 AATTTTCGTGTTTAAAAA
* *
5377847 AATTCTCGTATTTAAAAA
1 AATTTTCGTGTTTAAAAA
5377865 AA
1 AA
5377867 AAACTTTCGT
Statistics
Matches: 327, Mismatches: 76, Indels: 58
0.71 0.16 0.13
Matches are distributed among these distances:
14 4 0.01
15 9 0.03
16 27 0.08
17 107 0.33
18 82 0.25
19 45 0.14
20 16 0.05
21 12 0.04
22 21 0.06
23 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTTTCGTGTTTAAAAA
Found at i:5377490 original size:37 final size:37
Alignment explanation
Indices: 5377417--5377490 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
5377407 GAAATTTTCG
* * * *
5377417 AATTTTCGCGTTTTCAAAAGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
5377454 AATTTTCGCG-TTTAAAAAATTTCTCGTATTTCAAAAA
1 AATTTTCGCGTTTTAAAAAATTT-TCGTATTTCAAAAA
5377491 TTATCGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
Found at i:5377509 original size:35 final size:34
Alignment explanation
Indices: 5377451--5377597 Score: 113
Period size: 35 Copynumber: 4.2 Consensus size: 34
5377441 CGTGTTTGAA
* * *
5377451 AAAAATTTTCG-CGTTTAAAAAATTTCTCGTATTTC
1 AAAAA-TTTCGTCTTTTACAAAA-TTCTCGTGTTTC
* *
5377486 AAAAATTATCGTTTTTTAC-AAATTTTCGTGCTTTC
1 AAAAATT-TCGTCTTTTACAAAATTCTCGTG-TTTC
* * *
5377521 AATAATCCTCGTGCTTTTA-AAAATTCTCATGTTTC
1 AAAAAT-TTCGT-CTTTTACAAAATTCTCGTGTTTC
* *
5377556 AAAAATCTTCGTGTTTT-CAAAATTCTAGTGTTTC
1 AAAAAT-TTCGTCTTTTACAAAATTCTCGTGTTTC
5377590 AAAAATTT
1 AAAAATTT
5377598 TCTTGTTTTC
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
33 2 0.02
34 32 0.36
35 38 0.42
36 18 0.20
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (34 bp):
AAAAATTTCGTCTTTTACAAAATTCTCGTGTTTC
Found at i:5377588 original size:34 final size:34
Alignment explanation
Indices: 5377482--5377611 Score: 122
Period size: 34 Copynumber: 3.8 Consensus size: 34
5377472 ATTTCTCGTA
* * *
5377482 TTTCAAAAAT-TATCGT-TTTTTACAAATTTTCGTG
1 TTTCAAAAATCT-TCGTGTTTTCA-AAATTCTAGTG
* * *
5377516 CTTTCAATAATCCTCGTGCTTTTAAAAATTCTCA-TG
1 -TTTCAAAAATCTTCGTG-TTTTCAAAATTCT-AGTG
5377552 TTTCAAAAATCTTCGTGTTTTCAAAATTCTAGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAATTCTAGTG
* *
5377586 TTTCAAAAATTTTCTTGTTTTCAAAA
1 TTTCAAAAATCTTCGTGTTTTCAAAA
5377612 AAAAAATTTC
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
33 1 0.01
34 38 0.47
35 28 0.35
36 8 0.10
37 5 0.06
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.46
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAATTCTAGTG
Found at i:5377591 original size:16 final size:16
Alignment explanation
Indices: 5377540--5377593 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5377530 CGTGCTTTTA
5377540 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
5377556 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
5377574 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
5377590 AAAA
1 AAAA
5377594 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:5377617 original size:23 final size:22
Alignment explanation
Indices: 5377590--5377656 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
5377580 CTAGTGTTTC
*
5377590 AAAAATTTTCTTGTTTTCAAAAA
1 AAAAATTTTCGTGTTTT-AAAAA
5377613 AAAAA-TTTCGTGTTTTAAAAA
1 AAAAATTTTCGTGTTTTAAAAA
*
5377634 AAAATATTTCCGTGTTTTAAAAA
1 AAAA-ATTTTCGTGTTTTAAAAA
5377657 TTTTCGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.22
22 11 0.28
23 20 0.50
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
AAAAATTTTCGTGTTTTAAAAA
Found at i:5377621 original size:22 final size:21
Alignment explanation
Indices: 5377590--5377656 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 21
5377580 CTAGTGTTTC
* *
5377590 AAAAATTTTCTTGTTTTCAAAA
1 AAAAAATTTCGTGTTTT-AAAA
5377612 AAAAAATTTCGTGTTTTAAAA
1 AAAAAATTTCGTGTTTTAAAA
5377633 AAAAATATTTCCGTGTTTTAAAA
1 AAAAA-ATTT-CGTGTTTTAAAA
5377656 A
1 A
5377657 TTTTCGTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.22
22 19 0.46
23 13 0.32
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAAATTTCGTGTTTTAAAA
Found at i:5377634 original size:18 final size:17
Alignment explanation
Indices: 5377438--5377865 Score: 107
Period size: 18 Copynumber: 24.0 Consensus size: 17
5377428 TTTCAAAAGT
*
5377438 TTTCGTGTTTGAAAAAAA
1 TTTCGTGTTT-TAAAAAA
*
5377456 TTTTCGCG-TTTAAAAAA
1 -TTTCGTGTTTTAAAAAA
*
5377473 TTTC-TCGTATTTCAAAAA
1 TTTCGT-GT-TTTAAAAAA
* * *
5377491 TTATCGTTTTTTACAAAT
1 TT-TCGTGTTTTAAAAAA
* * *
5377509 TTTCGTGCTTTCAATAA
1 TTTCGTGTTTTAAAAAA
*
5377526 TCCTCGTGCTTTT-AAAAA
1 T-TTCGTG-TTTTAAAAAA
* *
5377544 TTCTCATG-TTTCAAAAA
1 TT-TCGTGTTTTAAAAAA
*
5377561 TCTTCGTGTTTT-CAAAA
1 T-TTCGTGTTTTAAAAAA
* * *
5377578 TTCTAGTGTTTCAAAAAT
1 TT-TCGTGTTTTAAAAAA
*
5377596 TTTCTTGTTTTCAAAAAAAAAA
1 TTTCGTGTTTT-----AAAAAA
5377618 TTTCGTGTTTTAAAAAAAAATA
1 TTTCGTGTTTT----AAAAA-A
*
5377640 TTTCCGTGTTTTAAAAAT
1 TTT-CGTGTTTTAAAAAA
5377658 TTTCGTGTTTT-AAAAA
1 TTTCGTGTTTTAAAAAA
*
5377674 TTCTCGT-ATTT--AAAA
1 TT-TCGTGTTTTAAAAAA
* *
5377689 TTT-TTTTTTTAAGAAAAAA
1 TTTCGTGTTTT---AAAAAA
*
5377708 TTT--TGTTTCAAAAAAA
1 TTTCGTGTTT-TAAAAAA
* *
5377724 TGTCTTGTTTT-AAAAA
1 TTTCGTGTTTTAAAAAA
* *
5377740 TTCCCGTGTTTCAAAAAAAAA
1 TT-TCGTGTTT---TAAAAAA
*
5377761 TGTCGTGTTTTAAGAAAA
1 TTTCGTGTTTTAA-AAAA
* *
5377779 TTTCGTTTTTTTTCAAAAAT
1 TTTCG--TGTTTT-AAAAAA
*
5377799 TTTCGTGTTTCTAAAATA
1 TTTCGTGTTT-TAAAAAA
*
5377817 -TTCGTG-TTT-ACAAA
1 TTTCGTGTTTTAAAAAA
*
5377831 TTCTCGTGTTTTCAAAAA
1 TT-TCGTGTTTTAAAAAA
*
5377849 TTCTCGT-ATTTAAAAAA
1 TT-TCGTGTTTTAAAAAA
5377866 AAAACTTTCG
Statistics
Matches: 308, Mismatches: 57, Indels: 90
0.68 0.13 0.20
Matches are distributed among these distances:
13 1 0.00
14 7 0.02
15 8 0.03
16 39 0.13
17 81 0.26
18 82 0.27
19 25 0.08
20 21 0.07
21 17 0.06
22 19 0.06
23 8 0.03
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (17 bp):
TTTCGTGTTTTAAAAAA
Found at i:5377876 original size:21 final size:20
Alignment explanation
Indices: 5377844--5377890 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
5377834 TCGTGTTTTC
5377844 AAAAATTCTCGTATTTAAAAA
1 AAAAATTCTCGT-TTTAAAAA
5377865 AAAAACTT-TCGTTTTAAAAA
1 AAAAA-TTCTCGTTTTAAAAA
*
5377885 AGAAAT
1 AAAAAT
5377891 ACTGCGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 9 0.38
22 2 0.08
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (20 bp):
AAAAATTCTCGTTTTAAAAA
Found at i:5380810 original size:21 final size:21
Alignment explanation
Indices: 5380784--5380833 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5380774 CTACAACTTA
* *
5380784 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
5380805 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
5380826 AAGCAGAG
1 AAGCAGAG
5380834 CAGAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:5383641 original size:11 final size:12
Alignment explanation
Indices: 5383593--5383641 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
5383583 TTATTAATTC
5383593 ATTATTTTTAAT
1 ATTATTTTTAAT
5383605 ATTA-TTTTAAT
1 ATTATTTTTAAT
*
5383616 ATTGA--CTTAAT
1 ATT-ATTTTTAAT
5383627 ATTATTTTTAA-
1 ATTATTTTTAAT
5383638 ATTA
1 ATTA
5383642 ATTATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 1 0.03
11 22 0.69
12 9 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTATTTTTAAT
Found at i:5386935 original size:16 final size:17
Alignment explanation
Indices: 5386910--5386943 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5386900 GCACAAGCAT
5386910 TCATGAAACA-ATATGG
1 TCATGAAACAGATATGG
*
5386926 TCATGTAACAGATATGG
1 TCATGAAACAGATATGG
5386943 T
1 T
5386944 TTCCGATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (17 bp):
TCATGAAACAGATATGG
Found at i:5389171 original size:124 final size:124
Alignment explanation
Indices: 5388929--5389216 Score: 470
Period size: 125 Copynumber: 2.3 Consensus size: 124
5388919 CCCAAACATG
** * * *
5388929 CTACTATAGCAAAAAATGCGTCCACATGGGAGTGATTTCAAAACTTCTTTTGATAAAGCATCCTG
1 CTACTATAGC-AAAAGCGCGTCCACGTGGGAGCGATTTCAAAACTTCTTCTGATAAAGCATCCTG
*
5388994 CTTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
65 CTTCAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* *
5389054 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAA-TTCTTCTGATAAAGCATCTTG
1 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTCA-AAACTTCTTCTGATAAAGCATCCTG
5389118 CTTCAAGCGGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
65 CTTCAAGC-GTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
5389179 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
1 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
5389217 CTTAATAAAT
Statistics
Matches: 152, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
124 51 0.34
125 101 0.66
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (124 bp):
CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAACTTCTTCTGATAAAGCATCCTGC
TTCAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:5389956 original size:3 final size:3
Alignment explanation
Indices: 5389950--5389983 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5389940 AAAAATTTTA
5389950 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5389984 GAACGAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5399495 original size:14 final size:13
Alignment explanation
Indices: 5399472--5399502 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
5399462 TCGATTAAAC
5399472 TAAATAAATCGAA
1 TAAATAAATCGAA
5399485 TAAATTAAATCGAA
1 TAAA-TAAATCGAA
5399499 TAAA
1 TAAA
5399503 CTGGTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (13 bp):
TAAATAAATCGAA
Found at i:5415179 original size:18 final size:18
Alignment explanation
Indices: 5415156--5415192 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5415146 CTCTAAAATC
5415156 ACATGCA-AAAGCAAGACT
1 ACATGCATAAA-CAAGACT
5415174 ACATGCATAAACAAGACT
1 ACATGCATAAACAAGACT
5415192 A
1 A
5415193 AAAAATGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (18 bp):
ACATGCATAAACAAGACT
Found at i:5424264 original size:24 final size:24
Alignment explanation
Indices: 5424195--5424264 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
5424185 ATTTCCCCTC
5424195 TTTTCCTTCTTTCTCCTT-TGTTTA
1 TTTTCCTTCTTTCT-CTTCTGTTTA
* * *
5424219 -TTTCCTTTTTTTTCTAAC-GTTTA
1 TTTTCCTTCTTTCTCT-TCTGTTTA
*
5424242 TTTTCCTTCTTTGTCTTCTGTTT
1 TTTTCCTTCTTTCTCTTCTGTTT
5424265 TCTCTCGTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
22 2 0.06
23 17 0.47
24 17 0.47
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTTCCTTCTTTCTCTTCTGTTTA
Found at i:5428012 original size:24 final size:24
Alignment explanation
Indices: 5427980--5428027 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5427970 ATAGCCGACA
5427980 AGAAATTAATCTTTGTTATGAACT
1 AGAAATTAATCTTTGTTATGAACT
5428004 AGAAATTAATCTTTGTTATGAACT
1 AGAAATTAATCTTTGTTATGAACT
5428028 TTCTCTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (24 bp):
AGAAATTAATCTTTGTTATGAACT
Found at i:5430939 original size:6 final size:6
Alignment explanation
Indices: 5430930--5430963 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5430920 CCAAGACATA
* *
5430930 ACTTTG ACTTTG ACTTTG ACTTGG ACTTGG ACTT
1 ACTTTG ACTTTG ACTTTG ACTTTG ACTTTG ACTT
5430964 GTTCAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (6 bp):
ACTTTG
Found at i:5432043 original size:277 final size:281
Alignment explanation
Indices: 5431527--5432043 Score: 620
Period size: 277 Copynumber: 1.8 Consensus size: 281
5431517 TTTTTGTTTA
* *
5431527 TTGTGATTTTGGAAATCCCTTGCTTCATCCGAAATTGATTTCAGGTATGAATCATTACTTAAACT
1 TTGTGATTTTGGAAATCCCTTGCTTCATCCGAAACTAATTTCAGGTATGAATCATTACTTAAACT
* *
5431592 TTGTCTTTGCCTTTTCATTTCTGTTTTTAGTTTCAAATATATGCTTTTTGACTTGTATTTCAGTG
66 TTGTCTTTGCCTTTTCATCTCTGTTTTTAGTTTCAAATATATGC--TTT-ACTTGTACTT-AGTG
* * * * * * *
5431657 GGTTTATTTTATGGTTTTTGGTTTTCAGGTTTAGAAATCATTGTTTCATTTTGTGTTTCTAATCT
127 GGTTTATTCTAAGGTTTTTGGTTTTCAGCTTTAGAAATCACTGTTTCATTCTGTCTTTCAAATCT
* * ** *
5431722 GTGGATCTCAGTTTGGTTGTGATTTTTGTTTGTTTGTGGTTTACTTTCGTGAGAGAGAAACCTTA
192 ATGGATCTCAGTTCGGTTGTGATTTTTGTTTGAGTGTCGTTTACTTTCGTGAGAGAGAAACCTTA
5431787 AGTTTTTATCTGTCGTTTGTGATGT
257 AGTTTTTATCTGTCGTTTGTGATGT
* ** * * *
5431812 TTGTGATTTTTGAAA-CCCTTGCTTCATTGGAGACTAATTTTAGGTATGAATCATTACTTGAACT
1 TTGTGATTTTGGAAATCCCTTGCTTCATCCGAAACTAATTTCAGGTATGAATCATTACTTAAAC-
* *
5431876 TTTTTCTTTTCCTTTTTCATCTCTG-TTTTAGTTTCAAATCAT-TGC-TT-CTT-TACTT-GTGG
65 TTTGTCTTTGCC-TTTTCATCTCTGTTTTTAGTTTCAAAT-ATATGCTTTACTTGTACTTAGTGG
** *
5431935 GTTT-TTGCTAAGGTTTTTTTTTTTCAGCTTTAGAAATCACTGTTTCGTTCCT-TCTTTCAAATC
128 GTTTATT-CTAAGGTTTTTGGTTTTCAGCTTTAGAAATCACTGTTTCATT-CTGTCTTTCAAATC
* **
5431998 TATGGATCTCGGTTCGGTTGTTCTTTTTGTTTGAGTGTCGTTTACT
191 TATGGATCTCAGTTCGGTTGTGATTTTTGTTTGAGTGTCGTTTACT
5432044 ATATGATGTT
Statistics
Matches: 197, Mismatches: 30, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
276 2 0.01
277 90 0.46
278 1 0.01
279 4 0.02
280 3 0.02
282 2 0.01
284 41 0.21
285 41 0.21
286 13 0.07
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.51
Consensus pattern (281 bp):
TTGTGATTTTGGAAATCCCTTGCTTCATCCGAAACTAATTTCAGGTATGAATCATTACTTAAACT
TTGTCTTTGCCTTTTCATCTCTGTTTTTAGTTTCAAATATATGCTTTACTTGTACTTAGTGGGTT
TATTCTAAGGTTTTTGGTTTTCAGCTTTAGAAATCACTGTTTCATTCTGTCTTTCAAATCTATGG
ATCTCAGTTCGGTTGTGATTTTTGTTTGAGTGTCGTTTACTTTCGTGAGAGAGAAACCTTAAGTT
TTTATCTGTCGTTTGTGATGT
Found at i:5441490 original size:42 final size:42
Alignment explanation
Indices: 5441431--5441571 Score: 183
Period size: 42 Copynumber: 3.6 Consensus size: 42
5441421 TGATTCCTCC
5441431 AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGA
* *
5441473 AAGGGGTTGCTAAGTGCTGATTCC-CCG-A--CT-CAT-TG-
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGA
*
5441508 --GTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGA
*
5441548 AGGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCC
5441572 CCCAAGGGGT
Statistics
Matches: 84, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
33 21 0.25
34 3 0.04
35 1 0.01
36 2 0.02
37 3 0.04
38 3 0.04
39 2 0.02
40 1 0.01
41 3 0.04
42 45 0.54
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGA
Found at i:5441519 original size:33 final size:33
Alignment explanation
Indices: 5441475--5441703 Score: 146
Period size: 33 Copynumber: 6.5 Consensus size: 33
5441465 AAATGTGAAA
5441475 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTG
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTG
* * *
5441508 GTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAG
1 GGGGTTGCTAAGTGCTGATTCC-CCG-A--CT-CAT-T---G
*
5441550 GGGGTTGCTAAGTGCTGATT-CCC--C-CA--A
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTG
* *
5441577 GGGGTTGCTAAGTGTTGATTCCCCGAATCATTG
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTG
* * *
5441610 GTGGTTGCTAAGTGCTGATTCCACCATATCTTTGAATATG
1 GGGGTTGCTAAGTGCTGATTCC-CC-GA-C--T-CAT-TG
* *
5441650 AAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTG
1 ---GGGGTTGCTAAGTGCTGATTCCCCGACTCATTG
5441686 GGGGTTGCTAAGTGCTGA
1 GGGGTTGCTAAGTGCTGA
5441704 ACCCACCGAT
Statistics
Matches: 151, Mismatches: 20, Indels: 50
0.68 0.09 0.23
Matches are distributed among these distances:
27 19 0.13
28 3 0.02
31 2 0.01
33 60 0.40
34 5 0.03
35 2 0.01
36 2 0.01
37 2 0.01
38 4 0.03
39 3 0.02
40 4 0.03
41 2 0.01
42 22 0.15
43 21 0.14
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (33 bp):
GGGGTTGCTAAGTGCTGATTCCCCGACTCATTG
Found at i:5441531 original size:75 final size:75
Alignment explanation
Indices: 5441435--5441573 Score: 269
Period size: 75 Copynumber: 1.9 Consensus size: 75
5441425 TCCTCCAAGG
5441435 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
5441500 ACTCATTGGT
66 ACTCATTGGT
*
5441510 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
5441574 CAAGGGGTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (75 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
ACTCATTGGT
Found at i:5441596 original size:102 final size:103
Alignment explanation
Indices: 5441473--5441676 Score: 347
Period size: 102 Copynumber: 2.0 Consensus size: 103
5441463 TTAAATGTGA
* *
5441473 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT-
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
* *
5441537 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCC
*
5441575 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
*
5441640 TTTGAATATGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TTTAAATATGAAAGGGGTTGCTAAGTGCTGATTCCCC
5441677 GAATCACTGG
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 61 0.64
103 34 0.36
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
TTTAAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:5443755 original size:41 final size:40
Alignment explanation
Indices: 5443666--5443773 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 40
5443656 ATACAGACTT
* *
5443666 TACGTCTAGCAGGCTTGATGCCGGTGAAATGATTCAAACTT
1 TACGTCTAGCAGGCTTAATGCCGGTGAAAT-ATTCAAACTA
*
5443707 TACGTCTAGCAGGCTTAATGCCGGTGATACAT-TTCATACTA
1 TACGTCTAGCAGGCTTAATGCCGGTGA-A-ATATTCAAACTA
* * *
5443748 TAGGTCTAGCAGGCTAAAAGCCGGTG
1 TACGTCTAGCAGGCTTAATGCCGGTG
5443774 TACCGAATCA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
41 56 0.95
42 1 0.02
43 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (40 bp):
TACGTCTAGCAGGCTTAATGCCGGTGAAATATTCAAACTA
Found at i:5444878 original size:9 final size:9
Alignment explanation
Indices: 5444864--5444892 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5444854 TTTCAAATCA
5444864 CAACCAATT
1 CAACCAATT
5444873 CAACCAATT
1 CAACCAATT
5444882 CAACCAATT
1 CAACCAATT
5444891 CA
1 CA
5444893 TTTCACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (9 bp):
CAACCAATT
Found at i:5445506 original size:6 final size:6
Alignment explanation
Indices: 5445481--5445523 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
5445471 CCAAACACAC
5445481 CAGTATA CAGTAA TCAGTAA CAGTAA CAGTAA CAGTAA CAGTA
1 CAGTA-A CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
5445524 TTCAACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (6 bp):
CAGTAA
Found at i:5445567 original size:45 final size:45
Alignment explanation
Indices: 5445503--5445652 Score: 210
Period size: 45 Copynumber: 3.3 Consensus size: 45
5445493 ATCAGTAACA
* * *
5445503 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAACCT
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCG
* **
5445548 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAGTCG
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCG
* *
5445593 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCA
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCG
* *
5445638 ATAACAATAACAGTA
1 GTAACAGTAACAGTA
5445653 GTCGGCACAT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 94 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCG
Found at i:5445643 original size:39 final size:39
Alignment explanation
Indices: 5445510--5445669 Score: 124
Period size: 45 Copynumber: 3.8 Consensus size: 39
5445500 ACAGTAACAG
* * *
5445510 TAACAGTAACAGTATTCAACACACAAAGTGCTGAACCTGTAACAG
1 TAACAGTAACAGTATTCGACACACAAAGTGCCGAA----T--CAA
* *
5445555 TAACGGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACA
1 TAACAGTAACAGTATTCGACACACAAAGTGCCGAATC----A-A
5445599 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAA
1 -TAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAA
* * * *
5445639 TAACAATAACAGTAGTCGGCACA-TAAGTGCC
1 TAACAGTAACAGTATTCGACACACAAAGTGCC
5445670 TGATCAGTAA
Statistics
Matches: 98, Mismatches: 11, Indels: 19
0.77 0.09 0.15
Matches are distributed among these distances:
38 7 0.07
39 21 0.21
40 1 0.01
41 2 0.02
43 1 0.01
45 66 0.67
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (39 bp):
TAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAA
Found at i:5446890 original size:17 final size:17
Alignment explanation
Indices: 5446857--5446896 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5446847 TTTCCTATTC
*
5446857 TGTTTCTTTTCTCCTTT
1 TGTTTCTTTTATCCTTT
*
5446874 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATCCTTT
5446891 TAGTTT
1 T-GTTT
5446897 ATGTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (17 bp):
TGTTTCTTTTATCCTTT
Found at i:5446940 original size:16 final size:17
Alignment explanation
Indices: 5446912--5446943 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5446902 TTGTTTATTA
5446912 TTTAATAAATATAATAC
1 TTTAATAAATATAATAC
5446929 TTTAAT-AATATAATA
1 TTTAATAAATATAATA
5446944 TAATACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAATAAATATAATAC
Found at i:5447078 original size:19 final size:19
Alignment explanation
Indices: 5447056--5447108 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
5447046 CATCTTATTT
*
5447056 ATTTTATAATATAATAATA
1 ATTTAATAATATAATAATA
5447075 ATTTAATAATTTAATAATAATA
1 ATTTAATAA--T-ATAATAATA
5447097 ATTTAATAATAT
1 ATTTAATAATAT
5447109 TTTTTTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.33
20 1 0.03
21 1 0.03
22 18 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAATAATATAATAATA
Found at i:5447081 original size:11 final size:11
Alignment explanation
Indices: 5447061--5447107 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
5447051 TATTTATTTT
*
5447061 ATAATATAATA
1 ATAATTTAATA
5447072 ATAATTTAATA
1 ATAATTTAATA
5447083 AT--TTAATAATA
1 ATAATT--TAATA
5447094 ATAATTTAATA
1 ATAATTTAATA
5447105 ATA
1 ATA
5447108 TTTTTTTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
9 2 0.06
11 27 0.87
13 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:5447116 original size:14 final size:14
Alignment explanation
Indices: 5447078--5447107 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5447068 AATAATAATT
5447078 TAATAATTTAATAA
1 TAATAATTTAATAA
5447092 TAATAATTTAATAA
1 TAATAATTTAATAA
5447106 TA
1 TA
5447108 TTTTTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATAATTTAATAA
Found at i:5449615 original size:16 final size:16
Alignment explanation
Indices: 5449594--5449662 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
5449584 TTTGGTTCGC
5449594 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5449610 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5449626 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
5449643 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5449659 TGTA
1 TGTA
5449663 ATAGCTAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5449640 original size:33 final size:32
Alignment explanation
Indices: 5449594--5449662 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
5449584 TTTGGTTCGC
5449594 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
5449626 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
5449659 TGTA
1 TGTA
5449663 ATAGCTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:5449907 original size:15 final size:15
Alignment explanation
Indices: 5449887--5449928 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5449877 TTTAAACATA
5449887 ATTATAATTAAATAT
1 ATTATAATTAAATAT
5449902 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5449916 A-TATAATTTAATA
1 ATTATAATTAAATA
5449929 AAATTCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5449915 original size:16 final size:16
Alignment explanation
Indices: 5449878--5449919 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
5449868 TTAATCATAT
5449878 TTAAACATA-ATTATAA
1 TTAAA-ATATATTATAA
5449894 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5449909 TTAAAATATAT
1 TTAAAATATAT
5449920 AATTTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5449927 original size:18 final size:18
Alignment explanation
Indices: 5449884--5449932 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
5449874 ATATTTAAAC
5449884 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
*
5449902 AT--TATAATTAAAATAT
1 ATAATTTAATTAAAATAT
5449918 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
5449933 TCTTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 5 0.19
16 9 0.35
17 6 0.23
18 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:5450163 original size:14 final size:15
Alignment explanation
Indices: 5450114--5450165 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5450104 ATAAAATATA
5450114 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5450129 TATTAAATATATTAT
1 AATTAAATATATTAT
5450144 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5450157 AATTTAATA
1 AATTAAATA
5450166 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5450274 original size:16 final size:17
Alignment explanation
Indices: 5450249--5450289 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
5450239 AAATAATTAA
5450249 AATT-AAATATAT-TTT
1 AATTAAAATATATATTT
5450264 AATTAAAATATATGATTT
1 AATTAAAATATAT-ATTT
5450282 AA-TAAAAT
1 AATTAAAAT
5450290 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 6 0.26
18 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAAAATATATATTT
Found at i:5450301 original size:120 final size:120
Alignment explanation
Indices: 5449881--5450290 Score: 711
Period size: 120 Copynumber: 3.4 Consensus size: 120
5449871 ATCATATTTA
5449881 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5449946 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
5450001 AACATAA-T-T-ATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
5450063 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
5450118 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* * *
5450183 TATTCTTATATGAATTTACTCAAATCATAATATATTATACTATAAAAGATAACTTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA-ATT
* * *
5450239 AA-ATAATTAAAATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
5450291 TAAAATAATT
Statistics
Matches: 278, Mismatches: 8, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
117 115 0.41
118 2 0.01
119 2 0.01
120 155 0.56
121 4 0.01
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:5453549 original size:159 final size:159
Alignment explanation
Indices: 5453260--5453562 Score: 606
Period size: 159 Copynumber: 1.9 Consensus size: 159
5453250 AAATGTGCAG
5453260 CTATACACAATTTCCGAAACATTAATTGGCAATTTAAATGAACCTAAATCAACAATACAACAATG
1 CTATACACAATTTCCGAAACATTAATTGGCAATTTAAATGAACCTAAATCAACAATACAACAATG
5453325 ATCAACTTATTCAAGCCTAAGCTCGGCATTATCCAGAAAAAATCAATCTAAAAAAGATTGCATGA
66 ATCAACTTATTCAAGCCTAAGCTCGGCATTATCCAGAAAAAATCAATCTAAAAAAGATTGCATGA
5453390 ACAATAGGGTAAACAATACAACAATACAA
131 ACAATAGGGTAAACAATACAACAATACAA
5453419 CTATACACAATTTCCGAAACATTAATTGGCAATTTAAATGAACCTAAATCAACAATACAACAATG
1 CTATACACAATTTCCGAAACATTAATTGGCAATTTAAATGAACCTAAATCAACAATACAACAATG
5453484 ATCAACTTATTCAAGCCTAAGCTCGGCATTATCCAGAAAAAATCAATCTAAAAAAGATTGCATGA
66 ATCAACTTATTCAAGCCTAAGCTCGGCATTATCCAGAAAAAATCAATCTAAAAAAGATTGCATGA
5453549 ACAATAGGGTAAAC
131 ACAATAGGGTAAAC
5453563 CCATCCTCTA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 144 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (159 bp):
CTATACACAATTTCCGAAACATTAATTGGCAATTTAAATGAACCTAAATCAACAATACAACAATG
ATCAACTTATTCAAGCCTAAGCTCGGCATTATCCAGAAAAAATCAATCTAAAAAAGATTGCATGA
ACAATAGGGTAAACAATACAACAATACAA
Found at i:5456074 original size:35 final size:35
Alignment explanation
Indices: 5456034--5456142 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
5456024 TTAAAGCAAT
5456034 ATTTATTAAATTACAATTTAAATATATGAATAAAA
1 ATTTATTAAATTACAATTTAAATATATGAATAAAA
* * *
5456069 ATTTATAATAAA-TATAATTTAAATA-AAGAA-AGCAAT
1 ATTTAT--TAAATTACAATTTAAATATATGAATA--AAA
*
5456105 ATTTATTAAATTACAATTTAAATATATAAATAAAA
1 ATTTATTAAATTACAATTTAAATATATGAATAAAA
5456140 ATT
1 ATT
5456143 CAAATAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
34 5 0.08
35 27 0.45
36 23 0.38
37 5 0.08
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
ATTTATTAAATTACAATTTAAATATATGAATAAAA
Found at i:5456089 original size:36 final size:37
Alignment explanation
Indices: 5456040--5456150 Score: 117
Period size: 36 Copynumber: 3.1 Consensus size: 37
5456030 CAATATTTAT
5456040 TAAATTACAATTTAAATATATGAATAAAAATTTATAA
1 TAAATTACAATTTAAATATATGAATAAAAATTTATAA
* * *
5456077 TAAA-TATAATTTAAATA-AAGAA-AGCAATATTTAT--
1 TAAATTACAATTTAAATATATGAATA--AAAATTTATAA
* *
5456111 TAAATTACAATTTAAATATATAAATAAAAATTCA-AA
1 TAAATTACAATTTAAATATATGAATAAAAATTTATAA
5456147 TAAA
1 TAAA
5456151 ATTTATTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
34 5 0.08
35 22 0.37
36 27 0.46
37 5 0.08
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (37 bp):
TAAATTACAATTTAAATATATGAATAAAAATTTATAA
Found at i:5456323 original size:17 final size:16
Alignment explanation
Indices: 5456298--5456340 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5456288 AAAAAGAAAA
*
5456298 AAAAGTGAAATGAAATT
1 AAAA-TGAAATCAAATT
5456315 AAAATTGAAATCAAATT
1 AAAA-TGAAATCAAATT
*
5456332 CAAATGAAA
1 AAAATGAAA
5456341 AAAATTCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (16 bp):
AAAATGAAATCAAATT
Found at i:5459163 original size:36 final size:36
Alignment explanation
Indices: 5459080--5459184 Score: 128
Period size: 35 Copynumber: 2.9 Consensus size: 36
5459070 ATATCAATTT
*
5459080 AAAGCAATATTTATTAAATTACAATTTAAATATATG
1 AAAGCAATATTTATTAAATTACAATTTAAATATAAG
* *
5459116 AATA--AAAATTTATAATAAA-TATAATTTAAATA-AAG
1 AA-AGCAATATTTAT--TAAATTACAATTTAAATATAAG
5459151 AAAGCAATATTTATTAAATTACAATTTAAATATA
1 AAAGCAATATTTATTAAATTACAATTTAAATATA
5459185 TATATAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
34 5 0.09
35 24 0.42
36 23 0.40
37 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (36 bp):
AAAGCAATATTTATTAAATTACAATTTAAATATAAG
Found at i:5459204 original size:23 final size:23
Alignment explanation
Indices: 5459156--5459213 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
5459146 TAAAGAAAGC
* * *
5459156 AATATTTATTAAATTACAATTTA
1 AATATATATTAAATTACAAATAA
5459179 AATATATATATAAATT-CAAATAA
1 AATATATAT-TAAATTACAAATAA
*
5459202 AATTTA-ATTAAA
1 AATATATATTAAA
5459214 ATTTACATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.13
22 2 0.07
23 18 0.60
24 6 0.20
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATATTAAATTACAAATAA
Found at i:5459379 original size:17 final size:16
Alignment explanation
Indices: 5459357--5459394 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
5459347 AAAAAAAAAG
5459357 TGAAATCAAATTCAAA
1 TGAAATCAAATTCAAA
5459373 TTGAAATCAAATTCAAA
1 -TGAAATCAAATTCAAA
5459390 TGAAA
1 TGAAA
5459395 AAAAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (16 bp):
TGAAATCAAATTCAAA
Found at i:5461573 original size:3 final size:3
Alignment explanation
Indices: 5461565--5461590 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5461555 TATGGTTTTA
5461565 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
5461591 ATAAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5466677 original size:21 final size:21
Alignment explanation
Indices: 5466636--5466679 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5466626 AAACATTATA
*
5466636 AAAATTGTAAAAATGAGAAAT
1 AAAATTGTAAAAATGAAAAAT
*
5466657 AAAATTTTAAAAAAT-AAAAAT
1 AAAATTGT-AAAAATGAAAAAT
5466678 AA
1 AA
5466680 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAATTGTAAAAATGAAAAAT
Found at i:5467707 original size:13 final size:13
Alignment explanation
Indices: 5467689--5467732 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5467679 CCTTGAGGGC
5467689 AAATTCTGTTCTT
1 AAATTCTGTTCTT
* *
5467702 AAATTCTGAATGCAT
1 AAATTCTG--TTCTT
5467717 AAATTCTGTTCTT
1 AAATTCTGTTCTT
5467730 AAA
1 AAA
5467733 GGAACGCACC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 14 0.56
15 11 0.44
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (13 bp):
AAATTCTGTTCTT
Found at i:5468524 original size:10 final size:10
Alignment explanation
Indices: 5468509--5468533 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5468499 CAGATCTAAC
5468509 ATTATGTAAA
1 ATTATGTAAA
5468519 ATTATGTAAA
1 ATTATGTAAA
5468529 ATTAT
1 ATTAT
5468534 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:5468658 original size:56 final size:57
Alignment explanation
Indices: 5468516--5468659 Score: 161
Period size: 56 Copynumber: 2.5 Consensus size: 57
5468506 AACATTATGT
* * *
5468516 AAAATTATGTAAAATTATTAAGCCAAAAAATTTTTCTTAATGGTTAGTAAAATTTATC
1 AAAA-TATGTAAAATTATTAAGCCAAAAAAATTGTCTTAATGGTTAGTAAAATGTATC
* * * * *
5468574 -AAATAATCTCAAATTATTAAGTCC--AAAAATTGTGTTAATGGTTATTAAAGTGT-TC
1 AAAAT-ATGTAAAATTATTAAG-CCAAAAAAATTGTCTTAATGGTTAGTAAAATGTATC
5468629 AAAATATGTAAAATTATTAAGCCAAAAAAAT
1 AAAATATGTAAAATTATTAAGCCAAAAAAAT
5468660 ATGTAAAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
54 2 0.03
55 16 0.23
56 34 0.48
57 17 0.24
58 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.36
Consensus pattern (57 bp):
AAAATATGTAAAATTATTAAGCCAAAAAAATTGTCTTAATGGTTAGTAAAATGTATC
Found at i:5468662 original size:26 final size:26
Alignment explanation
Indices: 5468629--5468685 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
5468619 TAAAGTGTTC
5468629 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
5468655 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
5468681 AAAAT
1 AAAAT
5468686 TTAGGTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (26 bp):
AAAATATGTAAAATTATTAAGCCAAA
Found at i:5468769 original size:29 final size:29
Alignment explanation
Indices: 5468683--5469271 Score: 838
Period size: 29 Copynumber: 20.7 Consensus size: 29
5468673 AAGCCAAAAA
5468683 AATTTAGGTTA-GTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* * *
5468711 AATTTAGGTTA-GATTAGGGTTTCTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
5468739 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
5468768 AATTTAGGTTA-GATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
5468796 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5468825 AATTTAGGTTA-GATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5468853 AATTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5468882 AATTTAGGTTA-GATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
5468910 AATTTAGGTTA-GATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
5468938 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* * *
5468967 AATTTAGGTTA-GATTAGAGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* * *
5468995 AATTTAGGTTAGATTTAGGGTTTCTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* * *
5469024 AATTTAGGTAAGGTTTAAGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5469053 AATTTAGGTTA-GATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* **
5469081 AATTTAGGTTAGGTTTAAGGTTTTTAGCT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
5469110 AATTTAGGTTA-GATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5469138 AATTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5469167 AATTTAGGTTA-GATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
5469195 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
5469224 AATTTAGATTAGGTTTAGTGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
5469253 AATTTAGGTTAGGGTTAGG
1 AATTTAGGTTAGGTTTAGG
5469272 TTAGGGTTTT
Statistics
Matches: 504, Mismatches: 49, Indels: 15
0.89 0.09 0.03
Matches are distributed among these distances:
28 243 0.48
29 261 0.52
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (29 bp):
AATTTAGGTTAGGTTTAGGGTTTTTAATT
Found at i:5468770 original size:57 final size:57
Alignment explanation
Indices: 5468683--5469271 Score: 932
Period size: 57 Copynumber: 10.3 Consensus size: 57
5468673 AAGCCAAAAA
* * *
5468683 AATTTAGGTTA-GTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTCTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
* *
5468739 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
*
5468796 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
5468853 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
* *
5468910 AATTTAGGTTA-GATTAGGGTTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTA-GATTAGGGTTTTTAATT
* * * *
5468967 AATTTAGGTTA-GATTAGAGTTTTTAGTTAATTTAGGTTAGATTTAGGGTTTCTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGA-TTAGGGTTTTTAATT
* *
5469024 AATTTAGGTAAGGTTTAAGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
* * *
5469081 AATTTAGGTTAGGTTTAAGGTTTTTAGCTAATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
5469138 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
* * * *
5469195 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGATTAGGTTTAGTGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTA-GATTAGGGTTTTTAATT
*
5469253 AATTTAGGTTAGGGTTAGG
1 AATTTAGGTTAGGTTTAGG
5469272 TTAGGGTTTT
Statistics
Matches: 502, Mismatches: 26, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
56 39 0.08
57 403 0.80
58 60 0.12
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (57 bp):
AATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
Found at i:5469306 original size:86 final size:81
Alignment explanation
Indices: 5468703--5469306 Score: 439
Period size: 86 Copynumber: 7.1 Consensus size: 81
5468693 AGTTTAGGGT
* * * * * *
5468703 TTTTAATTAATTTAGGTTA-GATTAGGGTTTCTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAAT
1 TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTCAAT
* *
5468767 TAATTTAGGTTAGATTAGGG
65 TAAATTAGGTT-GTTTA--G
* * *
5468787 TTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAAT
1 -TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTCAAT
*
5468852 TAATTTAGGTTAGGTTTAGGG
65 TAAATTAGGTT--GTTTA--G
* * * * *
5468873 TTTTTAGTTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGT
1 -TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTCAAT
*
5468937 TAATTTAGGTTAGGTTTAGGG
65 TAAATTAGGTT--GTTTA--G
* * * *
5468958 TTTTTAATTAATTTAGGTTA-GATTAGAGTTTTTAGTTAATTTAGGTTAGATTTAGGG-TTTCTA
1 -TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGA-TTAGGGTTTTC-A
* * *
5469021 GTTAATTTAGGTAAGGTTTAAGG
63 ATTAAATTAGGT--TGTTT-A-G
* * * * * * *
5469044 TTTTTAGTTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTTAG
1 -TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTCAA
* * *
5469108 CTAATTTAGGTTAGATTAGGG
64 TTAAATTAGGTT-GTTTA--G
* * * *
5469129 TTTTTAGTTAATTTAGGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAAT
1 -TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTCAAT
*
5469194 TAATTTAGGTTAGGTTTAGGG
65 TAAATTAGGTT--GTTTA--G
*
5469215 TTTTTAATTAATTTAGATTAGGTTTAGTGTTTTTAATTAATTTAGGTTAGGGTTAGGTTAGGGTT
1 -TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTA--G--A--TTAGGGTT
5469280 TTCAATTAAATTAGGGTT-TTTA-
59 TTCAATTAAATTA-GGTTGTTTAG
5469302 TTTTA
1 TTTTA
5469307 TTATATCAAA
Statistics
Matches: 462, Mismatches: 37, Indels: 39
0.86 0.07 0.07
Matches are distributed among these distances:
84 1 0.00
85 205 0.44
86 222 0.48
87 5 0.01
88 1 0.00
90 5 0.01
92 19 0.04
93 4 0.01
ACGTcount: A:0.25, C:0.01, G:0.23, T:0.50
Consensus pattern (81 bp):
TTTTAATTAATTTAGATTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTCAATT
AAATTAGGTTGTTTAG
Found at i:5469531 original size:24 final size:24
Alignment explanation
Indices: 5469501--5469556 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
5469491 GGCGACGGTT
*
5469501 GTTCTTCCTCCGGTGGTGATTGCG
1 GTTCTTCCTCCAGTGGTGATTGCG
* *
5469525 GTTCTTCCTCCAGTGGTGGTTGTG
1 GTTCTTCCTCCAGTGGTGATTGCG
5469549 GTTCTTCC
1 GTTCTTCC
5469557 GGTTCGGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.04, C:0.25, G:0.30, T:0.41
Consensus pattern (24 bp):
GTTCTTCCTCCAGTGGTGATTGCG
Found at i:5470511 original size:7 final size:7
Alignment explanation
Indices: 5470501--5470525 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5470491 TTATATACAT
5470501 AATACTA
1 AATACTA
5470508 AATACTA
1 AATACTA
5470515 AATACTA
1 AATACTA
5470522 AATA
1 AATA
5470526 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:5474614 original size:30 final size:31
Alignment explanation
Indices: 5474561--5474623 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
5474551 GCCATTGATG
5474561 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
*
5474592 AAAATATAAAAAAA-TTATAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
5474622 AA
1 AA
5474624 TGGAATTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:5474694 original size:22 final size:22
Alignment explanation
Indices: 5474669--5474720 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
5474659 AAATATGGGT
5474669 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
5474691 TTGAAAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
5474713 TTGAGAGA
1 TTGAGAGA
5474721 GAGGATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:5495568 original size:108 final size:110
Alignment explanation
Indices: 5495368--5495579 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 110
5495358 ATCTCCATCA
* ** * *
5495368 ATATCAATATTTTAGTTAGATTATTATTGTAGTCGAAGTGTTTTATTTGTGGTTGTTATGATTAA
1 ATATCAATATTTTAGTTAGATTATTATTATAGTCGAAGTACTTTATTTGCGGTTGTTATGACTAA
*
5495433 ATTGTAGTTCATTTCATT-TTTTCTTTTT-TGATAACGTATCTTT
66 ATTGTAGTTCATTTAATTATTTTCTTTTTGTGATAACGTATCTTT
*
5495476 ATATCAATATTTTAGTTAGGTTATTATTATAGTCGAAGTACTTTATTTGCGGTTGTTATGACTAA
1 ATATCAATATTTTAGTTAGATTATTATTATAGTCGAAGTACTTTATTTGCGGTTGTTATGACTAA
5495541 ATTGTAGTTCATTTTAATTATTTT-TTTTTGTGATAACGT
66 ATTGTAGTTCA-TTTAATTATTTTCTTTTTGTGATAACGT
5495580 GAATCAAAGC
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
108 70 0.74
109 11 0.12
110 13 0.14
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (110 bp):
ATATCAATATTTTAGTTAGATTATTATTATAGTCGAAGTACTTTATTTGCGGTTGTTATGACTAA
ATTGTAGTTCATTTAATTATTTTCTTTTTGTGATAACGTATCTTT
Found at i:5498267 original size:23 final size:23
Alignment explanation
Indices: 5498241--5498285 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5498231 AGGAGGATTA
*
5498241 AATTAAA-TTAAATAATTTAATGT
1 AATTAAACTT-AATAATTAAATGT
5498264 AATTAAACTTAATAATTAAATG
1 AATTAAACTTAATAATTAAATG
5498286 AAAAGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
AATTAAACTTAATAATTAAATGT
Found at i:5503375 original size:7 final size:7
Alignment explanation
Indices: 5503363--5503388 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5503353 ATGTTTTCCC
5503363 CTTATTT
1 CTTATTT
5503370 CTTATTT
1 CTTATTT
5503377 CTTATTT
1 CTTATTT
5503384 CTTAT
1 CTTAT
5503389 GTTTTCCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (7 bp):
CTTATTT
Found at i:5511070 original size:27 final size:28
Alignment explanation
Indices: 5511030--5511085 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
5511020 TTTGATAGGG
* *
5511030 TTTTTTACTAAAATATG-GTAAAAAAAA
1 TTTTGTACTAAAATAGGAGTAAAAAAAA
*
5511057 TTTTGTACTGAAATAGGATGTAAAAAAAA
1 TTTTGTACTAAAATAGGA-GTAAAAAAAA
5511086 ATTATTTACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
29 10 0.42
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (28 bp):
TTTTGTACTAAAATAGGAGTAAAAAAAA
Found at i:5511451 original size:15 final size:16
Alignment explanation
Indices: 5511431--5511467 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5511421 ACAAAATCAA
5511431 ATAAAA-TTACATTAT
1 ATAAAAGTTACATTAT
5511446 ATAAAAGTTACATTAT
1 ATAAAAGTTACATTAT
5511462 ATAAAA
1 ATAAAA
5511468 ATTAAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAAAAGTTACATTAT
Done.