Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 20 of 214
Found at i:5562513 original size:25 final size:25
Alignment explanation
Indices: 5562485--5562534 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5562475 CAGGTAAGGC
5562485 TCCTTCTCCTTCTTCCATTATTCAT
1 TCCTTCTCCTTCTTCCATTATTCAT
* * *
5562510 TCCTTTTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCATTATTCAT
5562535 CTTCTCTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.36, G:0.02, T:0.54
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCATTATTCAT
Found at i:5563958 original size:13 final size:13
Alignment explanation
Indices: 5563940--5563964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5563930 TATTTTAATA
5563940 TTATTTTGTGTGT
1 TTATTTTGTGTGT
5563953 TTATTTTGTGTG
1 TTATTTTGTGTG
5563965 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:5566017 original size:41 final size:41
Alignment explanation
Indices: 5565972--5566146 Score: 207
Period size: 41 Copynumber: 4.3 Consensus size: 41
5565962 TAGCAGATGT
*
5565972 AGTGCCGGTGAAT-T-AATTCAGACTT-TAAGTCTAGCAGGCTA
1 AGTGCCGGTG-ATCTGAA-TCAG-CTTATAAGCCTAGCAGGCTA
* *
5566013 AGTGCCGGTGATCTGAACCAGGTTATGAA-CCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCAGCTTAT-AAGCCTAGCAGGCTA
* *
5566054 AGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCAGCTTATAAGCCTAGCAGGCTA
* *
5566095 CGTGCCGGTGATCTGAATTAGGC-TATAAGCCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCA-GCTTATAAGCCTAGCAGGCTA
5566136 AGTGCCGGTGA
1 AGTGCCGGTGA
5566147 ATATGTTAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
40 6 0.05
41 108 0.91
42 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (41 bp):
AGTGCCGGTGATCTGAATCAGCTTATAAGCCTAGCAGGCTA
Found at i:5573888 original size:41 final size:40
Alignment explanation
Indices: 5573843--5573987 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 40
5573833 GACTTTAAGT
* *
5573843 CTAGCAGGCTAAGTACCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
5573884 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
* * *
5573925 CTAGCAAGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-C
5573966 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
5573988 ATATGTTAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 2 0.02
41 93 0.98
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
Found at i:5580044 original size:49 final size:48
Alignment explanation
Indices: 5579914--5580046 Score: 128
Period size: 49 Copynumber: 2.7 Consensus size: 48
5579904 AAAATTAGTT
* * * *
5579914 AATTTATATTTTATGTATCATTATATTAAATTATTTAAACATTTTATG
1 AATTTATATTTTATATATCATTATATTAAATTATTGAAAAATTTTATA
* * * *
5579962 TATCATTA-ATTTTACAAATAATTTATATT-AATTACTTGAAAAATATTTA-A
1 AAT--TTATATTTTATATATCA-TTATATTAAATTA-TTGAAAAAT-TTTATA
5580012 AATTTATATTTTATATATCATTATATTAAATTATT
1 AATTTATATTTTATATATCATTATATTAAATTATT
5580047 TAAATATCGT
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
48 14 0.21
49 29 0.44
50 19 0.29
51 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (48 bp):
AATTTATATTTTATATATCATTATATTAAATTATTGAAAAATTTTATA
Found at i:5584958 original size:36 final size:36
Alignment explanation
Indices: 5584902--5584975 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
5584892 TTATTTGTGA
* * * *
5584902 TTGTTTTTTCCAACATTCAAAGATTGAAACCTGCAT
1 TTGTTCTTTCCAACAATCAAAGATTCAAACATGCAT
* *
5584938 TTGTTCTTTCCGACAATCAAAGGTTCAAACATGCAT
1 TTGTTCTTTCCAACAATCAAAGATTCAAACATGCAT
5584974 TT
1 TT
5584976 TTTTTGTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
TTGTTCTTTCCAACAATCAAAGATTCAAACATGCAT
Found at i:5585646 original size:120 final size:120
Alignment explanation
Indices: 5585496--5586069 Score: 1049
Period size: 120 Copynumber: 4.8 Consensus size: 120
5585486 ATTTAATCAT
*
5585496 ATTTAAACATAATTTTTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * * *
5585561 ATCAATATTCTTATATAAATTTACTCAAATCATAATATACGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
5585617 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* * *
5585682 TCAATATTCTTATATGAATTTACTCAAATCATAATATAGGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
5585737 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5585802 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
5585857 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5585922 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
5585977 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5586042 TTAATATTCTTATATGAATTTACTCAAA
66 TTAATATTCTTATATGAATTTACTCAAA
5586070 AATTGTTAGC
Statistics
Matches: 444, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
120 440 0.99
121 4 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:5585657 original size:16 final size:16
Alignment explanation
Indices: 5585613--5585659 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5585603 TACTATAAAA
*
5585613 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
5585629 TATTATT-AAATATAT
1 TATAATTAAAATATAT
5585644 TATAATTAAAATATAT
1 TATAATTAAAATATAT
5585660 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:5585777 original size:16 final size:16
Alignment explanation
Indices: 5585733--5585779 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5585723 TACTATAAAA
*
5585733 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
5585749 TATTATT-AAATATAT
1 TATAATTAAAATATAT
5585764 TATAATTAAAATATAT
1 TATAATTAAAATATAT
5585780 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:5585897 original size:16 final size:16
Alignment explanation
Indices: 5585854--5585925 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
5585844 ACTATAAAAG
*
5585854 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
5585870 ATTATT-AAATATATT
1 ATAATTAAAATATATT
5585885 ATAATTAAAATATATAAT
1 ATAATTAAAATATAT--T
*
5585903 TTAA-TAAAAT-TATT
1 ATAATTAAAATATATT
5585917 AATAATTAA
1 -ATAATTAA
5585926 TATTCTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 5 0.11
15 13 0.29
16 17 0.38
17 6 0.13
18 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:5585899 original size:18 final size:18
Alignment explanation
Indices: 5585878--5585925 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5585868 TTATTATTAA
5585878 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
5585896 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
5585913 -TAT-TAATAATTAA
1 ATATATTATAATTAA
5585926 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:5585906 original size:14 final size:15
Alignment explanation
Indices: 5585854--5585908 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5585844 ACTATAAAAG
5585854 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
5585870 ATTATTAAATATATT
1 ATAATTAAATATATT
5585885 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
5585898 ATAATTTAATA
1 ATAATTAAATA
5585909 AAATTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:5586017 original size:16 final size:16
Alignment explanation
Indices: 5585974--5586019 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5585964 ACTATAAAAG
*
5585974 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
5585990 ATTATT-AAATATATT
1 ATAATTAAAATATATT
5586005 ATAATTAAAATATAT
1 ATAATTAAAATATAT
5586020 GATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:5588048 original size:33 final size:36
Alignment explanation
Indices: 5588008--5588102 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 36
5587998 AGAAAAGGGG
5588008 AAACAGAGGGAGCAAATCGGCAGAAAAG-AAA-AT-
1 AAACAGAGGGAGCAAATCGGCAGAAAAGAAAAGATA
* *
5588041 AAACAGAGAGAACAAATCGGCAGAAAAGAAAAGATAA
1 AAACAGAGGGAGCAAATCGGCAGAAAAGAAAAGAT-A
*
5588078 GAAACAGAGGGAGAAAATCGGCAGA
1 -AAACAGAGGGAGCAAATCGGCAGA
5588103 GGCTAGAAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 26 0.50
34 3 0.06
35 2 0.04
38 21 0.40
ACGTcount: A:0.56, C:0.12, G:0.27, T:0.05
Consensus pattern (36 bp):
AAACAGAGGGAGCAAATCGGCAGAAAAGAAAAGATA
Found at i:5588072 original size:38 final size:38
Alignment explanation
Indices: 5588029--5588102 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
5588019 GCAAATCGGC
*
5588029 AGAAAAGAAAATAAACAGAGAGA-ACAAATCGGCAGAAA
1 AGAAAAGAAAAGAAACAGAGAGAGA-AAATCGGCAGAAA
* *
5588067 AGAAAAGATAAGAAACAGAGGGAGAAAATCGGCAGA
1 AGAAAAGAAAAGAAACAGAGAGAGAAAATCGGCAGA
5588103 GGCTAGAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.59, C:0.09, G:0.26, T:0.05
Consensus pattern (38 bp):
AGAAAAGAAAAGAAACAGAGAGAGAAAATCGGCAGAAA
Found at i:5594056 original size:29 final size:29
Alignment explanation
Indices: 5594036--5594096 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
5594026 AAAGTATTTT
5594036 AAAAA-TATTTTAAAATTAAAAAAATTAA
1 AAAAAGTATTTTAAAATTAAAAAAATTAA
5594064 AAAAAGTATTTTAAAATTAAAAAAAATTAA
1 AAAAAGTATTTTAAAATT-AAAAAAATTAA
5594094 AAA
1 AAA
5594097 GTATGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 5 0.16
29 12 0.39
30 14 0.45
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAAATTAA
Found at i:5594058 original size:39 final size:40
Alignment explanation
Indices: 5594002--5594079 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
5593992 GGCCCATTTT
*
5594002 TATTTTAAAATTTAAAAAA-TAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
5594041 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
5594080 TTAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 18 0.49
40 19 0.51
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:5594081 original size:68 final size:67
Alignment explanation
Indices: 5594002--5594128 Score: 202
Period size: 68 Copynumber: 1.9 Consensus size: 67
5593992 GGCCCATTTT
* *
5594002 TATTTTAAAATTTAAAAAATAA-AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAA
1 TATTTTAAAA-TTAAAAAA-AATAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATTAAAA
5594066 AAAG
64 AAAG
5594070 TATTTTAAAATTAAAAAAAATTAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAAT
1 TATTTTAAAATTAAAAAAAA-TAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAAT
5594129 AAATATATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
66 2 0.04
67 8 0.15
68 45 0.82
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (67 bp):
TATTTTAAAATTAAAAAAAATAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATTAAAAAA
AG
Found at i:5594090 original size:39 final size:39
Alignment explanation
Indices: 5594008--5594127 Score: 138
Period size: 39 Copynumber: 3.1 Consensus size: 39
5593998 TTTTTATTTT
* * ***
5594008 AAAATTTAAAAAA-TAAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAATTA-AAA
5594047 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAATTAAAA
1 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAATTAAAA
*
5594086 AAAATTAAAAAGTATGT-AAAAAA-TATTTTAAAATTAAAA
1 AAAATTAAAAA-AAT-TAAAAAAAGTATTTTAAAATTAAAA
5594125 AAA
1 AAA
5594128 TAAATATATT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
39 42 0.58
40 29 0.40
41 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (39 bp):
AAAATTAAAAAAATTAAAAAAAGTATTTTAAAATTAAAA
Found at i:5594107 original size:28 final size:27
Alignment explanation
Indices: 5594034--5594100 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 27
5594024 AAAAAGTATT
5594034 TTAAAAA-TATTTTAAAATTAAAAAAA
1 TTAAAAAGTATTTTAAAATTAAAAAAA
5594060 TTAAAAAAAGTATTTTAAAATTAAAAAAAA
1 TT--AAAAAGTATTTTAAAATT-AAAAAAA
5594090 TTAAAAAGTAT
1 TTAAAAAGTAT
5594101 GTAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.05
28 14 0.38
29 12 0.32
30 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (27 bp):
TTAAAAAGTATTTTAAAATTAAAAAAA
Found at i:5594108 original size:29 final size:28
Alignment explanation
Indices: 5594047--5594109 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
5594037 AAAATATTTT
**
5594047 AAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAATTAAAAAAATT-AAAAAAGTATTAA
5594076 AAAATTAAAAAAAATT-AAAAAGTATGTAA
1 AAAATT-AAAAAAATTAAAAAAGTAT-TAA
5594105 AAAAT
1 AAAAT
5594110 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 9 0.30
29 12 0.40
30 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAATTAAAAAAATTAAAAAAGTATTAA
Found at i:5595274 original size:18 final size:20
Alignment explanation
Indices: 5595242--5595290 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5595232 AATATAAAAT
* *
5595242 AATTCCAAATAATTT-TTAA
1 AATTCAAAATAATTTATAAA
5595261 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTTATAAA
5595280 AATTCTAAAAT
1 AATTC-AAAAT
5595291 TTATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 17 0.65
20 5 0.19
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTCAAAATAATTTATAAA
Found at i:5595292 original size:18 final size:19
Alignment explanation
Indices: 5595259--5595295 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5595249 AATAATTTTT
5595259 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
*
5595278 AAAATTCTAAA-ATTTATA
1 AAAATTCAAAATATTTATA
5595296 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:5595334 original size:18 final size:18
Alignment explanation
Indices: 5595299--5595334 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5595289 ATTTATATTT
*
5595299 TTTAAAAAATTATATAAA
1 TTTAAAAAAATATATAAA
*
5595317 TTTAAAAAAATATCTAAA
1 TTTAAAAAAATATATAAA
5595335 AAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAAAAAATATATAAA
Found at i:5595338 original size:21 final size:21
Alignment explanation
Indices: 5595314--5595367 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
5595304 AAAATTATAT
5595314 AAATTTAAAAA-AATA-TCTAAA
1 AAATTTAAAAAGAA-AGT-TAAA
5595335 AAATATATAAAAAGAAAGTTAAA
1 AAAT-T-TAAAAAGAAAGTTAAA
5595358 AAA-TTAAAAA
1 AAATTTAAAAA
5595368 TTTTCTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.21
21 5 0.17
22 1 0.03
23 14 0.48
24 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AAATTTAAAAAGAAAGTTAAA
Found at i:5597718 original size:16 final size:17
Alignment explanation
Indices: 5597689--5597720 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5597679 TATCATGGAG
5597689 TTTGTCCTAATGTGCTT
1 TTTGTCCTAATGTGCTT
5597706 TTTGTCC-AATGTGCT
1 TTTGTCCTAATGTGCT
5597721 ATGTGGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (17 bp):
TTTGTCCTAATGTGCTT
Found at i:5598885 original size:25 final size:27
Alignment explanation
Indices: 5598833--5598893 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
5598823 TATTATAAAC
* *
5598833 AAAAAATTATTAAAATTTACTATTTTTT
1 AAAAAATTATGAAAATTTAC-ATATTTT
*
5598861 TAAAAATTA-GAAAATTTA-ATATTTT
1 AAAAAATTATGAAAATTTACATATTTT
5598886 AAAAAATT
1 AAAAAATT
5598894 TATAAATCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 13 0.45
27 8 0.28
28 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAAAATTATGAAAATTTACATATTTT
Found at i:5599266 original size:18 final size:19
Alignment explanation
Indices: 5599226--5599272 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
5599216 ATTTTAGATT
* *
5599226 TTTTATATATTTTTTTGTAA
1 TTTTATA-AATTTTTTCTAA
5599246 TTTTATAAATTTTTTCT-A
1 TTTTATAAATTTTTTCTAA
5599264 TTTTA-AAAT
1 TTTTATAAAT
5599273 AAATTTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 6 0.24
19 8 0.32
20 7 0.28
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATAAATTTTTTCTAA
Found at i:5613013 original size:16 final size:15
Alignment explanation
Indices: 5612973--5613028 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
5612963 ATTTTGGATT
*
5612973 TTTATTATTTT-TAA
1 TTTATAATTTTATAA
5612987 TTTATCCAATTTTATAGA
1 TTTAT--AATTTTATA-A
5613005 TTTATAATTTTATTAA
1 TTTATAATTTTA-TAA
*
5613021 TTAATAAT
1 TTTATAAT
5613029 ATATTATGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.14
16 20 0.57
17 4 0.11
18 6 0.17
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTATAATTTTATAA
Found at i:5614679 original size:24 final size:25
Alignment explanation
Indices: 5614652--5614703 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
5614642 CATAGGACAA
5614652 ATGCAAACTAG-GGTCGCGAG-AAAG
1 ATGCAAA-TAGTGGTCGCGAGAAAAG
* *
5614676 ATGCGAATTGTGGTCGCGAGAAAAG
1 ATGCAAATAGTGGTCGCGAGAAAAG
5614701 ATG
1 ATG
5614704 TGAGCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 15 0.62
25 7 0.29
ACGTcount: A:0.35, C:0.13, G:0.35, T:0.17
Consensus pattern (25 bp):
ATGCAAATAGTGGTCGCGAGAAAAG
Found at i:5635185 original size:5 final size:5
Alignment explanation
Indices: 5635157--5635232 Score: 93
Period size: 5 Copynumber: 15.4 Consensus size: 5
5635147 AAAATATCAT
* *
5635157 ATTTA TTTTA A-TTA ATTTG A-TTA ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
* *
5635205 ATTTA ATTTA ATTTCA AATTA CTTTA AT
1 ATTTA ATTTA ATTT-A ATTTA ATTTA AT
5635233 CAAATTCTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
4 7 0.12
5 49 0.82
6 4 0.07
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:5636125 original size:9 final size:9
Alignment explanation
Indices: 5636108--5636144 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5636098 TGAGTTTTCG
5636108 AATTCGAAT
1 AATTCGAAT
*
5636117 AACTCGAAT
1 AATTCGAAT
5636126 AATTCGAAT
1 AATTCGAAT
5636135 AATTCGAAT
1 AATTCGAAT
5636144 A
1 A
5636145 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5637070 original size:5 final size:5
Alignment explanation
Indices: 5637060--5637085 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5637050 GAACAAATAT
5637060 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
5637086 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:5637185 original size:5 final size:5
Alignment explanation
Indices: 5637175--5637207 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5637165 CTCGAAAATT
5637175 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTC
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTC
5637208 AATCGAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:5637847 original size:14 final size:14
Alignment explanation
Indices: 5637827--5637864 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5637817 AAGCAAAAAC
*
5637827 GAAAAAGAAGGAAA
1 GAAAAAGAAAGAAA
5637841 -AAGAAAGAAAGAAA
1 GAA-AAAGAAAGAAA
5637855 GAAAAAGAAA
1 GAAAAAGAAA
5637865 ATGGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAGAAA
Found at i:5637851 original size:18 final size:18
Alignment explanation
Indices: 5637808--5637864 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
5637798 AAATAATTAA
*
5637808 AAAGAAACAAAGCAAAAACG
1 AAAGAAAGAAAG-AAAAA-G
*
5637828 -AA-AAAGAAGGAAAAAG
1 AAAGAAAGAAAGAAAAAG
5637844 AAAGAAAGAAAGAAAAAG
1 AAAGAAAGAAAGAAAAAG
5637862 AAA
1 AAA
5637865 ATGGAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.03
17 7 0.22
18 22 0.69
19 2 0.06
ACGTcount: A:0.75, C:0.05, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAAAG
Found at i:5637864 original size:10 final size:10
Alignment explanation
Indices: 5637827--5637864 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5637817 AAGCAAAAAC
*
5637827 GAAAAAGAAG
1 GAAAAAGAAA
5637837 GAAAAAGAAA
1 GAAAAAGAAA
5637847 G--AAAGAAA
1 GAAAAAGAAA
5637855 GAAAAAGAAA
1 GAAAAAGAAA
5637865 ATGGAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:5638513 original size:25 final size:25
Alignment explanation
Indices: 5638442--5638513 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
5638432 ATTGGATCGT
* *
5638442 ATGAGCTTCCTGTTA-ATGGCTCTC
1 ATGAGCTTCCCGTTATATGGCTCAC
* **
5638466 -CGAAGCTTCCCGTTATACAGCTCAC
1 ATG-AGCTTCCCGTTATATGGCTCAC
5638491 ATGAGCTTCCCGTTATATGGCTC
1 ATGAGCTTCCCGTTATATGGCTC
5638514 GAAAGAGCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
23 1 0.03
24 11 0.30
25 24 0.65
26 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCAC
Found at i:5638521 original size:25 final size:25
Alignment explanation
Indices: 5638444--5638533 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 25
5638434 TGGATCGTAT
* * *
5638444 GAGCTTCCTGTTA-ATGGCTCTC-C
1 GAGCTTCCCGTTATATGGCTCACAA
** *
5638467 GAAGCTTCCCGTTATACAGCTCACAT
1 G-AGCTTCCCGTTATATGGCTCACAA
5638493 GAGCTTCCCGTTATATGGCTCGA-AA
1 GAGCTTCCCGTTATATGGCTC-ACAA
*
5638518 GAGCTTCCTGTT-TATG
1 GAGCTTCCCGTTATATG
5638534 TGCTTGTATG
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.02
24 15 0.28
25 36 0.67
26 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCACAA
Found at i:5638546 original size:25 final size:25
Alignment explanation
Indices: 5638469--5638552 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
5638459 GGCTCTCCGA
**
5638469 AGCTTCCCGTTATACAGCTC-ACATG
1 AGCTTCCCGTTATATGGCTCGA-ATG
*
5638494 AGCTTCCCGTTATATGGCTCGAAAG
1 AGCTTCCCGTTATATGGCTCGAATG
* * *
5638519 AGCTTCCTGTT-TATGTGCTTGTATG
1 AGCTTCCCGTTATATG-GCTCGAATG
5638544 AGCATTCCC
1 AGC-TTCCC
5638553 AAATATGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 4 0.08
25 39 0.81
26 5 0.10
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGAATG
Found at i:5645323 original size:25 final size:26
Alignment explanation
Indices: 5645289--5645338 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
5645279 CTTAACCTTT
* *
5645289 TTATTTTTTTTTG-TCAATTTGATTC
1 TTATTTTTTTTAGTTAAATTTGATTC
5645314 TTATTTTTTTTAGTTAAATTTGATT
1 TTATTTTTTTTAGTTAAATTTGATT
5645339 TTCAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.68
Consensus pattern (26 bp):
TTATTTTTTTTAGTTAAATTTGATTC
Found at i:5655269 original size:126 final size:125
Alignment explanation
Indices: 5655033--5655475 Score: 699
Period size: 125 Copynumber: 3.5 Consensus size: 125
5655023 GATAAAATCA
* * *
5655033 AAGCAAGATGTTTTATCAGAAGAATTTCTGAAATCGCGCCCATGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCATGTGGACGCGCTTTTGCTACAGT
* *
5655098 AGGTCTTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTACAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTA-TAAAAAACGCTTC
* * * * *
5655159 AGGCAGGATGCTTTATCAAAAAAATTTCTGATATCACGCCCATGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCATGTGGACGCGCTTTTGCTACAGT
5655224 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
* * **
5655284 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGTGCCCACGTGGACATGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCATGTGGACGCGCTTTTGCTACAGT
** *
5655349 AGGTCCTGAAAAAATAATTTCAAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
*
5655409 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCC-TCGTGGACGCGCTTTTACTACAG
1 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCAT-GTGGACGCGCTTTTGCTACAG
5655473 TAG
65 TAG
5655476 CATGTTTGGG
Statistics
Matches: 289, Mismatches: 27, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
125 186 0.64
126 103 0.36
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCATGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
Found at i:5658920 original size:7 final size:7
Alignment explanation
Indices: 5658910--5658935 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5658900 TTATATACAT
5658910 AATACTA
1 AATACTA
5658917 AATACTA
1 AATACTA
5658924 AATACTA
1 AATACTA
5658931 AATAC
1 AATAC
5658936 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:5662581 original size:10 final size:9
Alignment explanation
Indices: 5662563--5662685 Score: 81
Period size: 9 Copynumber: 13.0 Consensus size: 9
5662553 TTTTTTAAAT
5662563 TAATTTTTA
1 TAATTTTTA
5662572 TAAGTTTTTA
1 TAA-TTTTTA
*
5662582 TAAGTTTATA
1 TAA-TTTTTA
5662592 TAAATTTTGTA
1 T-AATTTT-TA
*
5662603 AATATTTTTA
1 TA-ATTTTTA
5662613 -AATATTTTA
1 TAAT-TTTTA
*
5662622 TTATTTTTA
1 TAATTTTTA
5662631 TAATTTTTA
1 TAATTTTTA
*
5662640 TAAGTTTATA
1 TAA-TTTTTA
*
5662650 TAAATTTT-
1 TAATTTTTA
5662658 TAATATTTTA
1 TAAT-TTTTA
*
5662668 -ATATTTTAA
1 TA-ATTTTTA
*
5662677 TATTTTTTA
1 TAATTTTTA
5662686 CGATTTCTAT
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
8 5 0.05
9 42 0.46
10 35 0.38
11 9 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5662615 original size:68 final size:56
Alignment explanation
Indices: 5662565--5662683 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 56
5662555 TTTTAAATTA
5662565 ATTTTTATAAGTTTTTATAAGTTTATATAAATTTTGTAAATATTTTTAAATATTTTATT
1 ATTTTTATAA-TTTTTATAAGTTTATATAAATTTT-T-AATATTTTTAAATATTTTATT
*
5662624 ATTTTTATAATTTTTATAAGTTTATATAAATTTTTAATA-TTTT-AATATTTTAAT
1 ATTTTTATAATTTTTATAAGTTTATATAAATTTTTAATATTTTTAAATATTTTATT
5662678 ATTTTT
1 ATTTTT
5662684 TACGATTTCT
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
54 16 0.27
55 4 0.07
56 4 0.07
57 1 0.02
58 24 0.41
59 10 0.17
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (56 bp):
ATTTTTATAATTTTTATAAGTTTATATAAATTTTTAATATTTTTAAATATTTTATT
Found at i:5662666 original size:8 final size:8
Alignment explanation
Indices: 5662655--5662682 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5662645 TTATATAAAT
5662655 TTTTAATA
1 TTTTAATA
5662663 TTTTAATA
1 TTTTAATA
5662671 TTTTAATA
1 TTTTAATA
5662679 TTTT
1 TTTT
5662683 TTACGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTAATA
Found at i:5664329 original size:10 final size:10
Alignment explanation
Indices: 5664292--5664322 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5664282 TAGATTACCA
5664292 ATATCAATTC
1 ATATCAATTC
5664302 ATATCAATTC
1 ATATCAATTC
*
5664312 ATACCAATTC
1 ATATCAATTC
5664322 A
1 A
5664323 AGTCAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATCAATTC
Found at i:5669520 original size:82 final size:82
Alignment explanation
Indices: 5669376--5669536 Score: 234
Period size: 82 Copynumber: 2.0 Consensus size: 82
5669366 GGGAGGTTCT
* * *
5669376 GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGTTGATGTCATAGAATACTACAGCGATG
1 GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGCTGATGTCATAGAAGACTACAGCGATA
*
5669441 GTGAACTTCTAGTCTGC
66 GTAAACTTCTAGTCTGC
* * * *
5669458 GAATCAAAAGGGAAAACAACCAGAAAATTTTGGTGAAGCTGATG-CTGTAGAAGACTATAGCGAT
1 GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGCTGATGTC-ATAGAAGACTACAGCGAT
5669522 AGTAAACTTCTAGTC
65 AGTAAACTTCTAGTC
5669537 GCTTCTGTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 1 0.01
82 69 0.99
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (82 bp):
GAATCAAAAGGGAAAACAACCAAAAAATTTCGGTGAAGCTGATGTCATAGAAGACTACAGCGATA
GTAAACTTCTAGTCTGC
Found at i:5682265 original size:23 final size:23
Alignment explanation
Indices: 5682239--5682291 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
5682229 ATAAGTGCCA
5682239 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5682262 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5682285 CACTGAT
1 CACTGAT
5682292 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5689454 original size:6 final size:6
Alignment explanation
Indices: 5689443--5689471 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5689433 TTGTTGTTAC
5689443 CAATGG CAATGG CAATGG CAATGG CAATG
1 CAATGG CAATGG CAATGG CAATGG CAATG
5689472 AATGATGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
CAATGG
Found at i:5694080 original size:14 final size:15
Alignment explanation
Indices: 5694044--5694080 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5694034 CTTAAATTCA
5694044 TAATTTTTCAACACT
1 TAATTTTTCAACACT
* *
5694059 TAATTTTTCAATATT
1 TAATTTTTCAACACT
5694074 TAATTTT
1 TAATTTT
5694081 ACAGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTTTTCAACACT
Found at i:5695632 original size:6 final size:6
Alignment explanation
Indices: 5695623--5695650 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5695613 ATGATTAGGA
5695623 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
5695651 CTTAATGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:5697357 original size:33 final size:33
Alignment explanation
Indices: 5697314--5697377 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
5697304 GTACACAAAA
5697314 TAAAAATTCATGA-ATCAAAATATACATTAAAGC
1 TAAAAATTCAT-ATATCAAAATATACATTAAAGC
* *
5697347 TAAAAGTTCATATATCAAATTATACATTAAA
1 TAAAAATTCATATATCAAAATATACATTAAA
5697378 ATAAAGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (33 bp):
TAAAAATTCATATATCAAAATATACATTAAAGC
Found at i:5700658 original size:30 final size:28
Alignment explanation
Indices: 5700622--5700686 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
5700612 AACTCTAAAC
**
5700622 TAAAAAAACTAATTTTATTTGCTTCAAAA
1 TAAAAAAACT-ATCCTATTTGCTTCAAAA
**
5700651 TTAAAAAATGTATCCTATTTGCTTCAAAA
1 -TAAAAAAACTATCCTATTTGCTTCAAAA
5700680 TAAAAAA
1 TAAAAAA
5700687 TAAAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 16 0.52
30 8 0.26
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (28 bp):
TAAAAAAACTATCCTATTTGCTTCAAAA
Found at i:5708043 original size:18 final size:18
Alignment explanation
Indices: 5708022--5708056 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5708012 AAAAGAAGGA
5708022 AATTAAAGAAAATTAAAG
1 AATTAAAGAAAATTAAAG
**
5708040 AATTAAATTAAATTAAA
1 AATTAAAGAAAATTAAA
5708057 TTGTTGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATTAAAGAAAATTAAAG
Found at i:5709551 original size:142 final size:142
Alignment explanation
Indices: 5709351--5709629 Score: 425
Period size: 142 Copynumber: 2.0 Consensus size: 142
5709341 AAAACAGATT
* *
5709351 ATTTTTTAAGTTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACGTTCGTAAAAAAAAACA
1 ATTTTTTAAATTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACGTTCGGAAAAAAAAACA
* * *
5709416 CTTTT-GGAGTCCAAGGATATTTTTAACTCTTATTTATAATCTAATGTATTTTATATAATATTTA
66 -TTTTCGGAGTCAAAGAATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATTTA
5709480 TATTGGACCGGCC
130 TATTGGACCGGCC
* * * * *
5709493 ATTTTTTAAATTAAATTTGTTTTTCAATCCAAACCCAAAAGCTATTGCGTTTGGAAAAAAAAATA
1 ATTTTTTAAATTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACGTTCGGAAAAAAAAACA
* * *
5709558 TTTTCGGAGTCAAAGAATCTTTTTAACTCTTATTTATAATTTAATATATTTTATATAATATTTGT
66 TTTTCGGAGTCAAAGAATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATTTAT
5709623 ATTGGAC
131 ATTGGAC
5709630 TTAAATTTAT
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
141 4 0.03
142 119 0.97
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (142 bp):
ATTTTTTAAATTAAAATTGATTTTCAATCCAAACCCAAAAGCTATTACGTTCGGAAAAAAAAACA
TTTTCGGAGTCAAAGAATATTTTTAACTCTTATTTATAATCTAATATATTTTATATAATATTTAT
ATTGGACCGGCC
Found at i:5723324 original size:29 final size:29
Alignment explanation
Indices: 5723272--5723329 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5723262 AGGGAAATTT
5723272 TTTAATTTTTTGGGGCCATCACAT-TAAA
1 TTTAATTTTTTGGGGCCATCACATATAAA
*
5723300 TTTACATTTTTTGGGGGCC-TTACATATAAA
1 TTTA-ATTTTTT-GGGGCCATCACATATAAA
5723330 GAGAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 12 0.46
30 10 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (29 bp):
TTTAATTTTTTGGGGCCATCACATATAAA
Found at i:5732464 original size:18 final size:18
Alignment explanation
Indices: 5732443--5732477 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5732433 CAAGTATTCA
*
5732443 ACCCAACCCAATCCAATT
1 ACCCAACCCAACCCAATT
5732461 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
5732478 CATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.49, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:5732753 original size:12 final size:12
Alignment explanation
Indices: 5732736--5732760 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5732726 TGTTATTTCG
5732736 GGTCGGTTAACC
1 GGTCGGTTAACC
5732748 GGTCGGTTAACC
1 GGTCGGTTAACC
5732760 G
1 G
5732761 AATGAAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:5736462 original size:57 final size:57
Alignment explanation
Indices: 5736374--5736491 Score: 227
Period size: 57 Copynumber: 2.1 Consensus size: 57
5736364 TAATCTGTTT
*
5736374 TTGTTTTGAGAGTATTTTAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
1 TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
5736431 TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
1 TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
5736488 TTGT
1 TTGT
5736492 CTTAAGTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (57 bp):
TTGTTTTGAGAGTATTTCAAAATAATAAATGGTTTCACGAGTTAGTTTGGACCCGTG
Found at i:5738308 original size:92 final size:92
Alignment explanation
Indices: 5738151--5738335 Score: 325
Period size: 92 Copynumber: 2.0 Consensus size: 92
5738141 CAAGAGGACT
* * * *
5738151 TTTCCTATAAATATCTTGGAAAACTATGAACAGGGGATTGCCTTTTTAGCACCCTGAAGTCACTC
1 TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
5738216 TCAACATTTATCCTTTTAATCAGCCTG
66 TCAACATTTATCCTTTTAATCAGCCTG
5738243 TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
1 TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
*
5738308 TCAACATTTATCCTTTTAATTAGCCTG
66 TCAACATTTATCCTTTTAATCAGCCTG
5738335 T
1 T
5738336 CCTCTTGTCC
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (92 bp):
TTTCCTATAAATATCTTAGAAAACTATGAACAAGGGATCGCCTTTTTAGCACCCTAAAGTCACTC
TCAACATTTATCCTTTTAATCAGCCTG
Found at i:5740474 original size:25 final size:24
Alignment explanation
Indices: 5740423--5740479 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
5740413 ATGTGGACAA
* *
5740423 AATAAAACACGAAATTTTGGATAG
1 AATAAAACACGAAATTGTAGATAG
* *
5740447 AATAAAACCATGAAATTGTAGATTG
1 AATAAAA-CACGAAATTGTAGATAG
5740472 AATTAAAA
1 AA-TAAAA
5740480 ATAAAGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 7 0.26
25 15 0.56
26 5 0.19
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (24 bp):
AATAAAACACGAAATTGTAGATAG
Found at i:5753057 original size:7 final size:7
Alignment explanation
Indices: 5753045--5753070 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5753035 TTAATAAACA
5753045 TATTAAT
1 TATTAAT
5753052 TATTAAT
1 TATTAAT
5753059 TATTAAT
1 TATTAAT
5753066 TATTA
1 TATTA
5753071 CAAAATAATT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTAAT
Found at i:5753805 original size:28 final size:28
Alignment explanation
Indices: 5753753--5753809 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
5753743 ATAAAAATCG
*
5753753 TAAAAAAATATTTAAAATATTAAAATTA
1 TAAAAAAATATTTAAAATATGAAAATTA
5753781 TAAAAAAAT-TATTAGAAAT-TGAAAATTA
1 TAAAAAAATAT-TTA-AAATATGAAAATTA
5753809 T
1 T
5753810 TGTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 21 0.81
29 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAAAAATATTTAAAATATGAAAATTA
Found at i:5755098 original size:19 final size:20
Alignment explanation
Indices: 5755076--5755117 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5755066 TATAATTTTA
*
5755076 TAATTTTTT-TTTCTATTTG
1 TAATTTTTTATATCTATTTG
*
5755095 TAATTTTTTATATCTTTTTG
1 TAATTTTTTATATCTATTTG
5755115 TAA
1 TAA
5755118 ATCTTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TAATTTTTTATATCTATTTG
Found at i:5755114 original size:20 final size:19
Alignment explanation
Indices: 5755071--5755117 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5755061 TATTTTATAA
* *
5755071 TTTTATAATTTTTTTTTCT
1 TTTTGTAATTTTTTTATCT
*
5755090 ATTTGTAATTTTTTATATCT
1 TTTTGTAATTTTTT-TATCT
5755110 TTTTGTAA
1 TTTTGTAA
5755118 ATCTTTTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTGTAATTTTTTTATCT
Found at i:5755720 original size:40 final size:40
Alignment explanation
Indices: 5755637--5755732 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 40
5755627 AAAAAAGCAA
*
5755637 AAAAGCGCGTTGACG-GGGATTCGCTTTACCCGTGTCAGC
1 AAAAGCACGTTGACGTGGGATTCGCTTTACCCGTGTCAGC
*
5755676 AAAAGCACGTTGACGTGGGCA-T-GCTTTGCCACGTGTCAGC
1 AAAAGCACGTTGACGTGGG-ATTCGCTTTACC-CGTGTCAGC
*
5755716 AAAAGCACGTTAACGTG
1 AAAAGCACGTTGACGTG
5755733 AACGCGCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
39 21 0.41
40 29 0.57
41 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
AAAAGCACGTTGACGTGGGATTCGCTTTACCCGTGTCAGC
Found at i:5755742 original size:40 final size:39
Alignment explanation
Indices: 5755658--5755746 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 39
5755648 GACGGGGATT
* **
5755658 CGCTTTACCCGTGTCAGCAAAAGCACGTTGACGTGGGCA
1 CGCTTTACCCGTGTCAGCAAAAGCACGTTAACGTGAACA
* * *
5755697 TGCTTTGCCACGTGTCAGCAAAAGCACGTTAACGTGAACG
1 CGCTTTACC-CGTGTCAGCAAAAGCACGTTAACGTGAACA
5755737 CGCTTTACCC
1 CGCTTTACCC
5755747 CGTATTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 8 0.20
40 33 0.80
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (39 bp):
CGCTTTACCCGTGTCAGCAAAAGCACGTTAACGTGAACA
Found at i:5768251 original size:114 final size:112
Alignment explanation
Indices: 5767943--5768252 Score: 309
Period size: 114 Copynumber: 2.7 Consensus size: 112
5767933 TGGTCATAAA
* * * *
5767943 CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTCAGTTTAGGTTTTGGGGACTTTAGTGGCGCT
1 CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTTAATTTAGGTTTTAGAGACTTTAGTGGCGCT
* * *
5768008 TACTGAAAAAAGCCGCTATAGTCAAGAATTAGCAGCGCTTTATTATAAG
66 TTCT-AAAAAAGCCGC-ATAGTCAAGAATTAGCAGCGCTTTATCACAAG
* * * * ** * * *
5768057 CGCCGCAAAACTGTTAAGAAAATGTTGCCGTTTTTCATTTATCTTTTCGAGACGTTAGTGGCGAT
1 CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTTAATTTAGGTTTTAGAGACTTTAGTGGCGCT
* ** **
5768122 TT-TCAGAAAACGCCGCAGTAG-CGAAGCTTTAGTGGCGCTTTATCACAAG
66 TTCT-A-AAAAAGCCGCA-TAGTC-AAGAATTAGCAGCGCTTTATCACAAG
* * * *
5768171 TGCCGCAAAACTGTTAAGAAAGCGATGTTGTTTTTAATTTAGGTTTTAGAGTCTTTAGTGGCGCT
1 CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTTAATTTAGGTTTTAGAGACTTTAGTGGCGCT
*
5768236 TGTCTAAAAATGCCGCA
66 T-TCTAAAAAAGCCGCA
5768253 AAATATAGGA
Statistics
Matches: 156, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
113 4 0.03
114 149 0.96
115 2 0.01
116 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (112 bp):
CGCCGCAAAACTGTTAAGAAAACGATGTCGTTTTTAATTTAGGTTTTAGAGACTTTAGTGGCGCT
TTCTAAAAAAGCCGCATAGTCAAGAATTAGCAGCGCTTTATCACAAG
Found at i:5768554 original size:73 final size:73
Alignment explanation
Indices: 5768409--5768554 Score: 172
Period size: 73 Copynumber: 2.0 Consensus size: 73
5768399 AAGCGCCACA
* * *
5768409 AAACTATTAAGCAAATGATGTCGTTTATTATTTAGCATTTAAGGCCTTTAGTGGCGCTCGTTTAA
1 AAACTATTAAGCAAAAGATGTCGTTTATTATATAGCATTTAAGGACTTTAGTGGCGC-CGTTTAA
5768474 AAACGCCAT
65 AAACGCCAT
* * **
5768483 AAACTGTTAAGGAAAAGATGTCGTTT-TTATATAGC-TTTTTGAGACTTTAGTGGCG-CGTATTA
1 AAACTATTAAGCAAAAGATGTCGTTTATTATATAGCATTTAAG-GACTTTAGTGGCGCCGT-TTA
5768545 ATAAACGCCA
64 A-AAACGCCA
5768555 CAATAGTCAG
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
71 3 0.05
72 8 0.13
73 28 0.45
74 23 0.37
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (73 bp):
AAACTATTAAGCAAAAGATGTCGTTTATTATATAGCATTTAAGGACTTTAGTGGCGCCGTTTAAA
AACGCCAT
Found at i:5768862 original size:21 final size:21
Alignment explanation
Indices: 5768840--5768912 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
5768830 TCAGGGTTTA
5768840 GGGTTTAAGGGATATGGGTTAG
1 GGGTTT-AGGGATATGGGTTAG
* *
5768862 GGGTTTATGGATATGGTTTA-
1 GGGTTTAGGGATATGGGTTAG
* * * * * *
5768882 AGGATTGGGGTTAAGGGTTAA
1 GGGTTTAGGGATATGGGTTAG
5768903 GGGTTTAGGG
1 GGGTTTAGGG
5768913 GTGAAGGGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
20 13 0.34
21 19 0.50
22 6 0.16
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (21 bp):
GGGTTTAGGGATATGGGTTAG
Found at i:5768966 original size:8 final size:7
Alignment explanation
Indices: 5768888--5768964 Score: 66
Period size: 7 Copynumber: 10.9 Consensus size: 7
5768878 TTTAAGGATT
5768888 GGGGTTA
1 GGGGTTA
*
5768895 AGGGTTAA
1 GGGGTT-A
*
5768903 GGGTTTA
1 GGGGTTA
*
5768910 GGGGTGA
1 GGGGTTA
*
5768917 AGGGTTA
1 GGGGTTA
* *
5768924 AGGGCT-
1 GGGGTTA
5768930 GGGGTTA
1 GGGGTTA
5768937 GGGGTTA
1 GGGGTTA
*
5768944 GGAGTTA
1 GGGGTTA
5768951 GGGGTTTA
1 GGGG-TTA
5768959 GGGGTT
1 GGGGTT
5768965 TATAGTTAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
6 4 0.07
7 39 0.71
8 12 0.22
ACGTcount: A:0.18, C:0.01, G:0.52, T:0.29
Consensus pattern (7 bp):
GGGGTTA
Found at i:5768972 original size:22 final size:21
Alignment explanation
Indices: 5768888--5768964 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
5768878 TTTAAGGATT
*
5768888 GGGGTTAAGGGTTAAGG-GTTTA
1 GGGGTTAGGGGTT-AGGAG-TTA
* * *
5768910 GGGGTGAAGGGTTAAGG-GCT-
1 GGGGTTAGGGGTT-AGGAGTTA
5768930 GGGGTTAGGGGTTAGGAGTTA
1 GGGGTTAGGGGTTAGGAGTTA
5768951 GGGGTTTAGGGGTT
1 GGGG-TTAGGGGTT
5768965 TATAGTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 3 0.06
20 13 0.28
21 5 0.11
22 26 0.55
ACGTcount: A:0.18, C:0.01, G:0.52, T:0.29
Consensus pattern (21 bp):
GGGGTTAGGGGTTAGGAGTTA
Found at i:5770891 original size:27 final size:29
Alignment explanation
Indices: 5770837--5770892 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
5770827 ATTTAATTTA
* *
5770837 TATTAAGTTGATTGTTACTTTATCAATTAT
1 TATTAAGTTGATTGTTA-GTGATCAATTAT
5770867 TATTAAGTTGATTGTT-GTGAT-AATTA
1 TATTAAGTTGATTGTTAGTGATCAATTA
5770893 AAATTGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (29 bp):
TATTAAGTTGATTGTTAGTGATCAATTAT
Found at i:5771808 original size:21 final size:22
Alignment explanation
Indices: 5771784--5771825 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5771774 AAATTTAAAA
* *
5771784 ATTTATTTTTTTTAAA-ATATG
1 ATTTATATATTTTAAATATATG
5771805 ATTTATATATTTTAAATATAT
1 ATTTATATATTTTAAATATAT
5771826 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTATATATTTTAAATATATG
Found at i:5772077 original size:40 final size:40
Alignment explanation
Indices: 5772020--5772096 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
5772010 TATATTTTTA
5772020 AAAATTGATACAATACATAACTTGCATAACCTACATACAT
1 AAAATTGATACAATACATAACTTGCATAACCTACATACAT
*
5772060 AAAATTGATACATTACATAACTTGCATAACCTACATA
1 AAAATTGATACAATACATAACTTGCATAACCTACATA
5772097 AAATTAAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (40 bp):
AAAATTGATACAATACATAACTTGCATAACCTACATACAT
Found at i:5772117 original size:20 final size:20
Alignment explanation
Indices: 5772094--5772132 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5772084 CATAACCTAC
5772094 ATAAAATTAAGATAACTTAT
1 ATAAAATTAAGATAACTTAT
*
5772114 ATAATATTAAGATAACTTA
1 ATAAAATTAAGATAACTTA
5772133 CATTCTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
ATAAAATTAAGATAACTTAT
Found at i:5772159 original size:25 final size:25
Alignment explanation
Indices: 5772138--5772203 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
5772128 ACTTACATTC
5772138 TACAGAACTTACATAACATACATAA
1 TACAGAACTTACATAACATACATAA
*
5772163 TACATAACTTACATAAC-TAACATAA
1 TACAGAACTTACATAACAT-ACATAA
* *
5772188 TACATAGCTTACATAA
1 TACAGAACTTACATAA
5772204 TACTCAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (25 bp):
TACAGAACTTACATAACATACATAA
Found at i:5772176 original size:41 final size:41
Alignment explanation
Indices: 5772125--5772358 Score: 119
Period size: 41 Copynumber: 5.7 Consensus size: 41
5772115 TAATATTAAG
* *
5772125 ATAACTTACATTCTACAGAACTTACATAACATACATAATAC
1 ATAACTTACATACTACATAACTTACATAACATACATAATAC
* *
5772166 ATAACTTACATAACTAACATAA--TACATAGCTTACATAATACTC
1 ATAACTTACAT-ACT-ACATAACTTACATAACATACATAATA--C
* * * * *
5772209 AACTTAGCTTACATAATAAATAACTTACATAAAATACA-ACTTAC
1 -A--TAACTTACATACTACATAACTTACATAACATACATA-ATAC
* * * * * * * *
5772253 ATAGCTTACATTCTACACAATTTACGTAGCTTACATAATAA
1 ATAACTTACATACTACATAACTTACATAACATACATAATAC
** * *
5772294 ATAACTTACATAAAATACAACTTACATAA-A-A-A-AATGA-
1 ATAACTTACATACTACATAACTTACATAACATACATAAT-AC
*
5772331 ACAACTTACATA-T-CATAACTTACATAAC
1 ATAACTTACATACTACATAACTTACATAAC
5772359 TCATTTATAC
Statistics
Matches: 145, Mismatches: 35, Indels: 31
0.69 0.17 0.15
Matches are distributed among these distances:
35 12 0.08
37 14 0.10
38 2 0.01
39 1 0.01
41 75 0.52
42 3 0.02
43 7 0.05
44 7 0.05
45 3 0.02
46 21 0.14
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (41 bp):
ATAACTTACATACTACATAACTTACATAACATACATAATAC
Found at i:5772180 original size:9 final size:9
Alignment explanation
Indices: 5772072--5772306 Score: 84
Period size: 9 Copynumber: 26.9 Consensus size: 9
5772062 AATTGATACA
5772072 TTACATAAC
1 TTACATAAC
*
5772081 TTGCATAAC
1 TTACATAAC
* *
5772090 CTACATAAAA
1 TTACAT-AAC
*
5772100 TTAAGATAAC
1 TT-ACATAAC
* *
5772110 TTATATAATA
1 TTACATAA-C
*
5772120 TTAAGATAAC
1 TT-ACATAAC
*
5772130 TTACAT-TC
1 TTACATAAC
*
5772138 -TACAGAAC
1 TTACATAAC
5772146 TTACATAAC
1 TTACATAAC
*
5772155 ATACATAA-
1 TTACATAAC
5772163 -TACATAAC
1 TTACATAAC
5772171 TTACATAAC
1 TTACATAAC
*
5772180 TAACATAA-
1 TTACATAAC
*
5772188 -TACATAGC
1 TTACATAAC
5772196 TTACATAATAC
1 TTACAT-A-AC
* * *
5772207 TCAACTTAGC
1 T-TACATAAC
5772217 TTACATAA-
1 TTACATAAC
*
5772225 -TAAATAAC
1 TTACATAAC
*
5772233 TTACATAAA
1 TTACATAAC
*
5772242 ATAC--AAC
1 TTACATAAC
*
5772249 TTACATAGC
1 TTACATAAC
*
5772258 TTACAT-TC
1 TTACATAAC
* *
5772266 -TACACAAT
1 TTACATAAC
* *
5772274 TTACGTAGC
1 TTACATAAC
5772283 TTACATAA-
1 TTACATAAC
*
5772291 -TAAATAAC
1 TTACATAAC
5772299 TTACATAA
1 TTACATAA
5772307 AATACAACTT
Statistics
Matches: 159, Mismatches: 46, Indels: 42
0.64 0.19 0.17
Matches are distributed among these distances:
7 37 0.23
8 3 0.02
9 91 0.57
10 14 0.09
11 11 0.07
12 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:5772214 original size:16 final size:16
Alignment explanation
Indices: 5772125--5772322 Score: 80
Period size: 16 Copynumber: 11.8 Consensus size: 16
5772115 TAATATTAAG
**
5772125 ATAACTTACATTCTAC
1 ATAACTTACATAATAC
*
5772141 AGAACTTACATAACATAC
1 ATAACTTACAT-A-ATAC
5772159 ATAA--TACATAACTTAC
1 ATAACTTACATAA--TAC
*
5772175 ATAACTAACATAATAC
1 ATAACTTACATAATAC
*
5772191 ATAGCTTACATAATACTC
1 ATAACTTACATAATA--C
* *
5772209 AACTTAGCTTACATAATAA
1 -A--TAACTTACATAATAC
* *
5772228 ATAACTTACATAAAAT
1 ATAACTTACATAATAC
* *
5772244 ACAACTTACATAGCTTAC
1 ATAACTTACATA--ATAC
* *
5772262 AT-TC-TACACAATTTAC
1 ATAACTTACATAA--TAC
* * *
5772278 GTAGCTTACATAATAA
1 ATAACTTACATAATAC
* *
5772294 ATAACTTACATAAAAT
1 ATAACTTACATAATAC
*
5772310 ACAACTTACATAA
1 ATAACTTACATAA
5772323 AAAAATGAAC
Statistics
Matches: 137, Mismatches: 28, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
14 1 0.01
15 1 0.01
16 96 0.70
17 2 0.01
18 22 0.16
19 1 0.01
21 14 0.10
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:5772233 original size:21 final size:21
Alignment explanation
Indices: 5772192--5772235 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5772182 ACATAATACA
*
5772192 TAGCTTACATAATACTCAACT
1 TAGCTTACATAATAATCAACT
5772213 TAGCTTACATAATAAAT-AACT
1 TAGCTTACATAAT-AATCAACT
5772234 TA
1 TA
5772236 CATAAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (21 bp):
TAGCTTACATAATAATCAACT
Found at i:5772236 original size:62 final size:64
Alignment explanation
Indices: 5772156--5772321 Score: 196
Period size: 66 Copynumber: 2.6 Consensus size: 64
5772146 TTACATAACA
* * * *
5772156 TACATAATACATAACTTACAT-AACTAACATA-ATACATAGCTTACATAATACTC-A-ACTTAGC
1 TACATAATAAATAACTTACATAAAAT-ACA-ACATACATAGCTTACATAATACACAATACGTAGC
5772217 T
64 T
* **
5772218 TACATAATAAATAACTTACATAAAATACAACTTACATAGCTTACATTCTACACAATTTACGTAGC
1 TACATAATAAATAACTTACATAAAATACAACATACATAGCTTACATAATACACAA--TACGTAGC
5772283 T
64 T
*
5772284 TACATAATAAATAACTTACATAAAATACAACTTACATA
1 TACATAATAAATAACTTACATAAAATACAACATACATA
5772322 AAAAAATGAA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
61 1 0.01
62 41 0.45
63 4 0.04
66 45 0.49
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (64 bp):
TACATAATAAATAACTTACATAAAATACAACATACATAGCTTACATAATACACAATACGTAGCT
Found at i:5772260 original size:25 final size:24
Alignment explanation
Indices: 5772232--5772305 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
5772222 TAATAAATAA
5772232 CTTACATAAAATACAACTTACATAG
1 CTTACATAAAA-ACAACTTACATAG
** * * *
5772257 CTTACATTCTACACAATTTACGTAG
1 CTTACA-TAAAAACAACTTACATAG
*
5772282 CTTACATAATAAATAACTTACATA
1 CTTACATAA-AAACAACTTACATA
5772306 AAATACAACT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
24 1 0.03
25 33 0.92
26 2 0.06
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (24 bp):
CTTACATAAAAACAACTTACATAG
Found at i:5777780 original size:21 final size:20
Alignment explanation
Indices: 5777754--5777821 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
5777744 CTACAACTTA
*
5777754 AAGCAGAGACGGCAGCGAGGG
1 AAGCAGAG-CTGCAGCGAGGG
*
5777775 AAGCAGCAGTTGCAGCGAGGG
1 AAGCAG-AGCTGCAGCGAGGG
* *
5777796 AATCAGAGGCTGCAGCGAGAG
1 AAGCAGA-GCTGCAGCGAGGG
5777817 AAGCA
1 AAGCA
5777822 AAGTAGAGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.41, T:0.06
Consensus pattern (20 bp):
AAGCAGAGCTGCAGCGAGGG
Found at i:5779795 original size:22 final size:23
Alignment explanation
Indices: 5779761--5779804 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5779751 GTGATGAGGT
**
5779761 TATCTTATGAATACGTT-AAATC
1 TATCTTAAAAATACGTTGAAATC
*
5779783 TATCTTAAAAATATGTTGAAAT
1 TATCTTAAAAATACGTTGAAAT
5779805 GGATTGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
TATCTTAAAAATACGTTGAAATC
Found at i:5780384 original size:157 final size:156
Alignment explanation
Indices: 5780089--5780384 Score: 409
Period size: 157 Copynumber: 1.9 Consensus size: 156
5780079 AGCTGGGAGG
* * * * *
5780089 TTTTTTAGTATTTTTGTTGACAATGCATCCTACTTGAAGCGTTTTTCAACCCCAACTATCAGATT
1 TTTTTTAGTACTTTTGCTGACAATACATCCTACTTGAAACATTTTTCAACCCCAACTATCAGATT
* * *
5780154 TCCCGTGAATCCCAGGATTTTTTTTTTCAAAAACATCTTCTCAAAAATATTTTTCAAAATCAACA
66 TCCCGTGAATCCCAAGA-TTATTTTTTCAAAAACATCTTCACAAAAATATTTTTCAAAATCAACA
5780219 GTACAAAAAAAACGTCTAGGTGAGAGC
130 GTACAAAAAAAACGTCTAGGTGAGAGC
* *
5780246 TTTTTTAGTACTTTTGCTGACAGTACATCCTACTTGAAACATTTTTCAACCCCAATTATCAGATT
1 TTTTTTAGTACTTTTGCTGACAATACATCCTACTTGAAACATTTTTCAACCCCAACTATCAGATT
* * * * *
5780311 TCCCAG-GAATCCCAAGA-TATTTTTTC-GAACCATCTTCACAAAATTATATTTTCAGATTCAAC
66 TCCC-GTGAATCCCAAGATTATTTTTTCAAAAACATCTTCACAAAAATAT-TTTTCAAAATCAAC
5780373 AGTACAAAAAAA
129 AGTACAAAAAAA
5780385 GTCCAATTGG
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
154 17 0.14
155 32 0.26
157 72 0.59
158 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (156 bp):
TTTTTTAGTACTTTTGCTGACAATACATCCTACTTGAAACATTTTTCAACCCCAACTATCAGATT
TCCCGTGAATCCCAAGATTATTTTTTCAAAAACATCTTCACAAAAATATTTTTCAAAATCAACAG
TACAAAAAAAACGTCTAGGTGAGAGC
Found at i:5782350 original size:31 final size:32
Alignment explanation
Indices: 5782313--5782392 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 32
5782303 TTAAATTTTG
*
5782313 AAAAAAATATAAAAACTAAAATTCAAA-AAAT
1 AAAAAAATATAAAAATTAAAATTCAAACAAAT
* *
5782344 AAAAAAATA-AAAAATTTAAATTTAAACAAAT
1 AAAAAAATATAAAAATTAAAATTCAAACAAAT
*
5782375 --TAAAATATAAAAATTAAA
1 AAAAAAATATAAAAATTAAA
5782393 TTAACAGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 6 0.14
30 23 0.55
31 13 0.31
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (32 bp):
AAAAAAATATAAAAATTAAAATTCAAACAAAT
Found at i:5782374 original size:16 final size:15
Alignment explanation
Indices: 5782316--5782392 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
5782306 AATTTTGAAA
*
5782316 AAAATAT-AAAAACT
1 AAAATATAAAAAATT
*
5782330 AAAAT-TCAAAAAATA
1 AAAATAT-AAAAAATT
*
5782345 AAAAAATAAAAAATT
1 AAAATATAAAAAATT
* *
5782360 TAAATTTAAACAAATT
1 AAAATATAAA-AAATT
5782376 AAAATAT-AAAAATT
1 AAAATATAAAAAATT
5782390 AAA
1 AAA
5782393 TTAACAGAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
13 1 0.02
14 13 0.26
15 25 0.50
16 11 0.22
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATATAAAAAATT
Found at i:5785098 original size:30 final size:31
Alignment explanation
Indices: 5785050--5785108 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
5785040 TGCTTATAAT
* *
5785050 ATAATTTTTATAACTTAAA-CTTGTATGAAA
1 ATAATTTTTATAAATTAAATCATGTATGAAA
5785080 ATAATTTTT-TAAAATTAAATCATGTATGA
1 ATAATTTTTAT-AAATTAAATCATGTATGA
5785109 GTGTCTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 16 0.64
31 8 0.32
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
ATAATTTTTATAAATTAAATCATGTATGAAA
Found at i:5787298 original size:4 final size:4
Alignment explanation
Indices: 5787289--5787319 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
5787279 AAGAAAAGAA
*
5787289 TCTT TCTT TCTT TCTT TCTT TCTT TTTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
5787320 CACACGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:5800890 original size:40 final size:40
Alignment explanation
Indices: 5800846--5800989 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 40
5800836 GATGCAGAAC
5800846 AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
* * * *
5800886 AGGGGTATGTATGTGCATTTAGGGATA-CAGAAGTACAAAT
1 AGGGGCACGTATGTGCATTCAGGGGTACCA-AAGTACAAAT
* * * * * *
5800926 AGGGGCACGCATTTGCATTTAGGGGTACCGAAGTATAAAC
1 AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
* *
5800966 AGGAGCACATATGTGCATTCAGGG
1 AGGGGCACGTATGTGCATTCAGGG
5800990 ACATTTTCCT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 2 0.02
40 82 0.96
41 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.23
Consensus pattern (40 bp):
AGGGGCACGTATGTGCATTCAGGGGTACCAAAGTACAAAT
Found at i:5810332 original size:21 final size:21
Alignment explanation
Indices: 5810308--5810361 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5810298 ACAGCTGTGG
*
5810308 CGGTGAGATTAGTTACTGTAA
1 CGGTGAGATTAGGTACTGTAA
* *
5810329 CGGTGAGATTGGGTACTGTAG
1 CGGTGAGATTAGGTACTGTAA
5810350 CGGTGAGATTAG
1 CGGTGAGATTAG
5810362 AAACAATGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.09, G:0.37, T:0.30
Consensus pattern (21 bp):
CGGTGAGATTAGGTACTGTAA
Found at i:5816938 original size:12 final size:12
Alignment explanation
Indices: 5816921--5816945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5816911 TTGCAGGAGA
5816921 TGTTTTCTTATT
1 TGTTTTCTTATT
5816933 TGTTTTCTTATT
1 TGTTTTCTTATT
5816945 T
1 T
5816946 TATCAGGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTTCTTATT
Found at i:5817289 original size:11 final size:11
Alignment explanation
Indices: 5817273--5817298 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5817263 TTCTTAGCTA
5817273 AGAACAAGATG
1 AGAACAAGATG
5817284 AGAACAAGATG
1 AGAACAAGATG
5817295 AGAA
1 AGAA
5817299 GGAAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
AGAACAAGATG
Found at i:5829695 original size:21 final size:19
Alignment explanation
Indices: 5829670--5829715 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5829660 AAAGACAAGA
5829670 TATGAAAGATAATAATTTAAC
1 TATGAAA-AT-ATAATTTAAC
*
5829691 TATG-AAATTTAATTTAAC
1 TATGAAAATATAATTTAAC
5829709 TATGAAA
1 TATGAAA
5829716 TTTTATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 2 0.09
21 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (19 bp):
TATGAAAATATAATTTAAC
Found at i:5829705 original size:18 final size:18
Alignment explanation
Indices: 5829682--5829718 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5829672 TGAAAGATAA
5829682 TAATTTAACTATGAAATT
1 TAATTTAACTATGAAATT
5829700 TAATTTAACTATGAAATT
1 TAATTTAACTATGAAATT
5829718 T
1 T
5829719 TATTAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TAATTTAACTATGAAATT
Found at i:5833909 original size:20 final size:20
Alignment explanation
Indices: 5833884--5833935 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5833874 CTAAAATCCT
5833884 AGACCTTAAACCAAGACCGA
1 AGACCTTAAACCAAGACCGA
5833904 AGACCTTAAACCAAGACCGA
1 AGACCTTAAACCAAGACCGA
5833924 AGACCTTAAACC
1 AGACCTTAAACC
5833936 TTTAAACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.31, G:0.13, T:0.12
Consensus pattern (20 bp):
AGACCTTAAACCAAGACCGA
Found at i:5834829 original size:26 final size:26
Alignment explanation
Indices: 5834761--5834817 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
5834751 CCTCAATTTT
*
5834761 TTTTAAAAATAAATTAAATTATTAATC
1 TTTTAAAAA-GAATTAAATTATTAATC
5834788 TTTTAAAAAGAATTAAATTATT-AT-
1 TTTTAAAAAGAATTAAATTATTAATC
5834812 TTTTAA
1 TTTTAA
5834818 CGAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.21
25 2 0.07
26 12 0.41
27 9 0.31
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTAAAAAGAATTAAATTATTAATC
Found at i:5837640 original size:51 final size:51
Alignment explanation
Indices: 5837576--5837915 Score: 343
Period size: 51 Copynumber: 6.7 Consensus size: 51
5837566 TATCGATGAA
* * * *
5837576 CACGTGTGTAGTACTGTGTGAAGGCTACTGCGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* ** * * * * * *
5837627 CACATGTGTAGTACTAACTGAAGGCTACTATGTATACCCAGAAGTTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* **
5837678 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGA-TGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATTGGT
* * *
5837729 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * *
5837780 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAA-ATTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
* * * *
5837830 CACGCGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
*
5837880 CACGTGTGTAGTACTATGTGAAGACTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
5837916 TCGAATGATA
Statistics
Matches: 239, Mismatches: 43, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
50 85 0.36
51 153 0.64
52 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:5837752 original size:102 final size:101
Alignment explanation
Indices: 5837576--5837915 Score: 393
Period size: 102 Copynumber: 3.4 Consensus size: 101
5837566 TATCGATGAA
* * * *
5837576 CACGTGTGTAGTACTGTGTGAAGGCTACTGCGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGATCACATGTGTAGTAC
* *
5837641 TAACTGAAGGCTACTATGTATACCCAGAAGTTTTGGT
65 TAAGTGAAGGCTACTATGTATACCCAGAAGATTTGGT
* *
5837678 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGATCACATGTGTAGTAC
* * * *
5837743 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTATACCCAGAAGATTTGGT
* * * **
5837780 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAATTTGATCACGCGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAT-AAATATGATCACATGTGTAGTAC
* * * *
5837844 TATGTGAAGGCTACTACATG-A-A-CC-GTAAAACTTGAT
65 TAAGTGAAGGCTACT--ATGTATACCCAG-AAGATTTGGT
*
5837880 CACGTGTGTAGTACTATGTGAAGACTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
5837916 TCGAATGATA
Statistics
Matches: 206, Mismatches: 28, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
100 40 0.19
101 31 0.15
102 132 0.64
103 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGATCACATGTGTAGTACT
AAGTGAAGGCTACTATGTATACCCAGAAGATTTGGT
Found at i:5841775 original size:16 final size:16
Alignment explanation
Indices: 5841734--5841781 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5841724 ATTCAATTTC
5841734 ATAATCTCAATTCA-A
1 ATAATCTCAATTCACA
5841749 ATAATCATCAATTCACA
1 ATAATC-TCAATTCACA
** *
5841766 ATCTTCTCAAATCACA
1 ATAATCTCAATTCACA
5841782 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATCTCAATTCACA
Found at i:5859998 original size:27 final size:27
Alignment explanation
Indices: 5859960--5860013 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5859950 ATTTCTAAAA
5859960 AGCCCTTATGTTATTATTGAAGGGATT
1 AGCCCTTATGTTATTATTGAAGGGATT
5859987 AGCCCTTATGTTATTATTGAAGGGATT
1 AGCCCTTATGTTATTATTGAAGGGATT
5860014 TATGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (27 bp):
AGCCCTTATGTTATTATTGAAGGGATT
Found at i:5860674 original size:30 final size:30
Alignment explanation
Indices: 5860633--5860694 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
5860623 CCGAATTAGG
* * *
5860633 TATGAGTATAAACTGTATAAGTAAGCATGT
1 TATGAGGATAAACTCTATAAATAAGCATGT
*
5860663 TATGAGGATAAACTCTATAAATAGGCATGT
1 TATGAGGATAAACTCTATAAATAAGCATGT
5860693 TA
1 TA
5860695 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (30 bp):
TATGAGGATAAACTCTATAAATAAGCATGT
Found at i:5861391 original size:16 final size:16
Alignment explanation
Indices: 5861372--5861403 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5861362 TATTTGGTTT
*
5861372 ATTTTTAGTTTAATTA
1 ATTTTTAGGTTAATTA
5861388 ATTTTTAGGTTAATTA
1 ATTTTTAGGTTAATTA
5861404 GGTTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATTTTTAGGTTAATTA
Found at i:5861850 original size:22 final size:22
Alignment explanation
Indices: 5861825--5861869 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5861815 TGATTCAGTG
5861825 TATGACTCGAAGTGGAATTCTT
1 TATGACTCGAAGTGGAATTCTT
*
5861847 TATGACTCGGAGTGGAATTCTT
1 TATGACTCGAAGTGGAATTCTT
5861869 T
1 T
5861870 CTATCGAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.38
Consensus pattern (22 bp):
TATGACTCGAAGTGGAATTCTT
Found at i:5865524 original size:25 final size:25
Alignment explanation
Indices: 5865490--5865542 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5865480 ACACTCCATA
*
5865490 CTATGTTTCTGATGCATTGGACGTG
1 CTATGTTTCTAATGCATTGGACGTG
5865515 CTATGTTTCTAATGCATTGGACGTG
1 CTATGTTTCTAATGCATTGGACGTG
5865540 CTA
1 CTA
5865543 GATATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (25 bp):
CTATGTTTCTAATGCATTGGACGTG
Found at i:5869401 original size:16 final size:16
Alignment explanation
Indices: 5869380--5869411 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5869370 TAATTGGTTG
*
5869380 ATTTTTAGTTTAATTA
1 ATTTTTAGATTAATTA
5869396 ATTTTTAGATTAATTA
1 ATTTTTAGATTAATTA
5869412 GATTAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTTTTAGATTAATTA
Found at i:5869715 original size:19 final size:18
Alignment explanation
Indices: 5869691--5869751 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
5869681 TAATAAACAT
5869691 TAAAAAATTATTTTAAAAA
1 TAAAAAA-TATTTTAAAAA
***
5869710 TAAAAAA-ATAAAAAAAA
1 TAAAAAATATTTTAAAAA
* *
5869727 TTTAAAAGTATTTTAAAAA
1 -TAAAAAATATTTTAAAAA
5869746 TAAAAA
1 TAAAAA
5869752 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 5
0.69 0.20 0.11
Matches are distributed among these distances:
17 7 0.23
18 10 0.32
19 14 0.45
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAAATATTTTAAAAA
Found at i:5869740 original size:36 final size:37
Alignment explanation
Indices: 5869694--5869764 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 37
5869684 TAAACATTAA
*
5869694 AAAATTATTTTAAAAATAAAAA-AATAAA-AAAAATTT
1 AAAAGTATTTTAAAAATAAAAATAA-AAATAAAAATTT
5869730 AAAAGTATTTTAAAAATAAAAATAAAAATAAAAAT
1 AAAAGTATTTTAAAAATAAAAATAAAAATAAAAAT
5869765 ATATATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (37 bp):
AAAAGTATTTTAAAAATAAAAATAAAAATAAAAATTT
Found at i:5869756 original size:5 final size:6
Alignment explanation
Indices: 5869740--5869765 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5869730 AAAAGTATTT
5869740 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
5869766 TATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:5872540 original size:15 final size:15
Alignment explanation
Indices: 5872520--5872548 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5872510 ATTTCACACC
5872520 TCTTCTGTTGCAATG
1 TCTTCTGTTGCAATG
5872535 TCTTCTGTTGCAAT
1 TCTTCTGTTGCAAT
5872549 CAAAAACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (15 bp):
TCTTCTGTTGCAATG
Found at i:5876435 original size:3 final size:3
Alignment explanation
Indices: 5876427--5876477 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
5876417 GGGTTAATCC
5876427 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5876475 ATA
1 ATA
5876478 GATTTTTGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5880505 original size:9 final size:9
Alignment explanation
Indices: 5880491--5880518 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5880481 ACGAATTTAG
5880491 AAAAATAAA
1 AAAAATAAA
5880500 AAAAATAAA
1 AAAAATAAA
5880509 AAAAATAAA
1 AAAAATAAA
5880518 A
1 A
5880519 TCAGGCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:5884350 original size:49 final size:49
Alignment explanation
Indices: 5884237--5884474 Score: 266
Period size: 49 Copynumber: 4.8 Consensus size: 49
5884227 ACCGAAAAAA
* * *
5884237 ATGAATGCAACAAAAACAAACAATGAAGCATAATTAGAAACACCACTTTATTT
1 ATGAATGCAAC-AAAACAATCAATGAAACATAAATA-AAACA--ACTTTATTT
* * *
5884290 ATGAATACAACAAAACAATGAATGAAGCATAAATAAAACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
* *
5884339 ATGAATGCAACAAAACAATCAATGAAATATAAATAAAACAATTTTATTT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
* * * *
5884388 ATGAATGCAAC-AATCAATGAA-GCATAA-GTAAAGAAAACACAACTTTATTT
1 ATGAATGCAACAAAACAATCAATG-A-AACATAAA-TAAA-ACAACTTTATTT
*
5884438 ATGAATGCAACAAAACATTCAATGAAACATAAATAAA
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAA
5884475 TAAATAAAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
47 1 0.01
48 13 0.08
49 69 0.43
50 27 0.17
51 17 0.11
52 22 0.14
53 10 0.06
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (49 bp):
ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACAACTTTATTT
Found at i:5884445 original size:99 final size:99
Alignment explanation
Indices: 5884237--5884474 Score: 293
Period size: 99 Copynumber: 2.4 Consensus size: 99
5884227 ACCGAAAAAA
* * *
5884237 ATGAATGCAACAAAAACAAACAATGAAGCATAATTAGAAACACCACTTTATTTATGAATACAACA
1 ATGAATGCAAC-AAAACAATCAATGAAACATAAATA-AAACA-CACTTTATTTATGAATACAACA
* *
5884302 AAACAATGAATGAAGCATAAATAAAACAACTTTATTT
63 AAACAATGAATGAAGAATAAAAAAAACAACTTTATTT
* * * *
5884339 ATGAATGCAACAAAACAATCAATGAAATATAAATAAAACA-ATTTTATTTATGAATGCAAC-AAT
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACACACTTTATTTATGAATACAACAAAA
* *
5884402 CAATGAA-GCATAAGTAAAGAAAACACAACTTTATTT
66 CAATGAATGAAGAA-TAAA-AAAA-ACAACTTTATTT
*
5884438 ATGAATGCAACAAAACATTCAATGAAACATAAATAAA
1 ATGAATGCAACAAAACAATCAATGAAACATAAATAAA
5884475 TAAATAAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
96 3 0.03
97 13 0.11
98 21 0.17
99 47 0.39
100 5 0.04
101 20 0.17
102 11 0.09
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (99 bp):
ATGAATGCAACAAAACAATCAATGAAACATAAATAAAACACACTTTATTTATGAATACAACAAAA
CAATGAATGAAGAATAAAAAAAACAACTTTATTT
Found at i:5884487 original size:55 final size:50
Alignment explanation
Indices: 5884367--5884502 Score: 148
Period size: 55 Copynumber: 2.6 Consensus size: 50
5884357 TCAATGAAAT
* * *
5884367 ATAAATAAAACAATTTTATTTATGAATGCAACAATCAATGAAGCATAAGTAA
1 ATAAAT-AAA-AACTTTATTTATGAATGCAACAATCAATGAAACATAAATAA
* *
5884419 AGAAA-ACACAACTTTATTTATGAATGCAACAAAACATTCAATGAAACATAAATAA
1 ATAAATA-AAAACTTTATTTATGAATGCAAC---A-A-TCAATGAAACATAAATAA
5884474 ATAAATAAAAACTTTATTTATGAATGCAA
1 ATAAATAAAAACTTTATTTATGAATGCAA
5884503 ATTTGCTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
50 21 0.30
51 1 0.01
52 4 0.06
53 1 0.01
54 1 0.01
55 41 0.59
56 1 0.01
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (50 bp):
ATAAATAAAAACTTTATTTATGAATGCAACAATCAATGAAACATAAATAA
Found at i:5886109 original size:30 final size:32
Alignment explanation
Indices: 5886040--5886111 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 32
5886030 TTGTTGTTTT
* *
5886040 TTTTACTACTTTCTTGCTTTTTTTTTATCGTT
1 TTTTGCTACTTTCTTGCTTTTTTTTTATCGTA
*
5886072 TTGTTGCTATTTTCTTG-TTTTTTTTTCA-C-TA
1 TT-TTGCTACTTTCTTGCTTTTTTTTT-ATCGTA
5886103 TTTTGCTAC
1 TTTTGCTAC
5886112 CATTTCACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 6 0.18
31 3 0.09
32 12 0.35
33 13 0.38
ACGTcount: A:0.10, C:0.15, G:0.08, T:0.67
Consensus pattern (32 bp):
TTTTGCTACTTTCTTGCTTTTTTTTTATCGTA
Found at i:5921457 original size:27 final size:28
Alignment explanation
Indices: 5921427--5921487 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
5921417 ATATATTTTT
*
5921427 ATATATTTTAA-ATAAATTTTA-ATAGAA
1 ATATATTTTAATATAAATATTACATA-AA
*
5921454 ATATA-CTTAATATAAATATTACATAAA
1 ATATATTTTAATATAAATATTACATAAA
5921481 ATATATT
1 ATATATT
5921488 AAAGTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 21 0.75
28 3 0.11
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATATTTTAATATAAATATTACATAAA
Found at i:5921498 original size:28 final size:27
Alignment explanation
Indices: 5921434--5921499 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
5921424 TTTATATATT
*
5921434 TTAA-ATAAATTTTAATAGAAATATAC
1 TTAATATAAATATTAATAGAAATATAC
5921460 TTAATATAAATATTACATA-AAATATA-
1 TTAATATAAATATTA-ATAGAAATATAC
5921486 TTAAAGTATAAATA
1 TT-AA-TATAAATA
5921500 AGGGTTAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 6 0.17
27 18 0.51
28 11 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
TTAATATAAATATTAATAGAAATATAC
Done.