Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 124 of 222
Found at i:40255483 original size:30 final size:30
Alignment explanation
Indices: 40255440--40255507 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
40255430 TATTTTTACA
40255440 ATTTTTA-TAAAATTTTAAAAATTTTAATAT
1 ATTTTTATTAAAA-TTTAAAAATTTTAATAT
* * *
40255470 -TTTTTATTAAAATTTAATAATTTTTATTT
1 ATTTTTATTAAAATTTAAAAATTTTAATAT
40255499 ATTTTTATT
1 ATTTTTATT
40255508 TTTATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTTATTAAAATTTAAAAATTTTAATAT
Found at i:40258636 original size:50 final size:50
Alignment explanation
Indices: 40258523--40258768 Score: 267
Period size: 50 Copynumber: 4.8 Consensus size: 50
40258513 ATTTTGGTAA
* *
40258523 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* * *
40258579 AGAGGTCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
40258629 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * * * * *
40258679 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGAACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
** * * *
40258729 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
40258769 TAGTATATAA
Statistics
Matches: 164, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 120 0.73
52 1 0.01
53 4 0.02
55 1 0.01
56 38 0.23
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:40260673 original size:30 final size:30
Alignment explanation
Indices: 40260639--40260701 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
40260629 ACTTATTTTA
40260639 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
40260669 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
40260699 TTG
1 TTG
40260702 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:40268921 original size:27 final size:26
Alignment explanation
Indices: 40268889--40268948 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
40268879 TATACTGGTG
*
40268889 GCTTTGCCACATACACTGTTACTGGCA
1 GCTTTGCCACAT-CACTATTACTGGCA
* **
40268916 GTTTTGATACATCACTATTACTGGCA
1 GCTTTGCCACATCACTATTACTGGCA
40268942 GCTTTGC
1 GCTTTGC
40268949 TGCGATATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (26 bp):
GCTTTGCCACATCACTATTACTGGCA
Found at i:40268938 original size:26 final size:27
Alignment explanation
Indices: 40268897--40268947 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
40268887 TGGCTTTGCC
* *
40268897 ACATACACTGTTACTGGCAGTTTTGAT
1 ACATACACTATTACTGGCAGCTTTGAT
40268924 ACAT-CACTATTACTGGCAGCTTTG
1 ACATACACTATTACTGGCAGCTTTG
40268948 CTGCGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
ACATACACTATTACTGGCAGCTTTGAT
Found at i:40269115 original size:28 final size:28
Alignment explanation
Indices: 40269062--40269115 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
40269052 CATTGTATTG
* **
40269062 ATTACTGTATTGGGCTAAGGTTCACATT
1 ATTACTGTAATGGGCTAAGGCCCACATT
40269090 ATTACTGTAATGGGCTAAGGCCCACA
1 ATTACTGTAATGGGCTAAGGCCCACA
40269116 CTGTACTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (28 bp):
ATTACTGTAATGGGCTAAGGCCCACATT
Found at i:40273867 original size:9 final size:9
Alignment explanation
Indices: 40273853--40273879 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40273843 ACCTTGTGTG
40273853 GGTGTCGTA
1 GGTGTCGTA
40273862 GGTGTCGTA
1 GGTGTCGTA
40273871 GGTGTCGTA
1 GGTGTCGTA
40273880 CTCCTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.44, T:0.33
Consensus pattern (9 bp):
GGTGTCGTA
Found at i:40274700 original size:27 final size:26
Alignment explanation
Indices: 40274669--40274856 Score: 198
Period size: 27 Copynumber: 7.0 Consensus size: 26
40274659 GGCAAATAAC
**
40274669 CGAATTACCCTCGAAGGGTAAAATGTT
1 CGAATTACCC-CGAAGGGTAAAATGAA
*
40274696 CGAATTACCCCTGAAGGGTAAAATGAC
1 CGAATTACCCC-GAAGGGTAAAATGAA
*
40274723 CGAATTACTCCTGAAGGGTAAAATGAA
1 CGAATTAC-CCCGAAGGGTAAAATGAA
*
40274750 CGAATTAACCCCGAAGGGTAAAATGAT
1 CGAATT-ACCCCGAAGGGTAAAATGAA
*
40274777 TGAATTACCCCTGAAGGGTAAAAT-AA
1 CGAATTACCCC-GAAGGGTAAAATGAA
*
40274803 CTGAATTACCCTCGAAGGGTAAAATGAC
1 C-GAATTACCC-CGAAGGGTAAAATGAA
* * * *
40274831 CAAAATACCCCCATTGGGTAAAATGA
1 CGAATTACCCCGA-AGGGTAAAATGA
40274857 CTGTTATACC
Statistics
Matches: 139, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
26 9 0.06
27 123 0.88
28 7 0.05
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (26 bp):
CGAATTACCCCGAAGGGTAAAATGAA
Found at i:40274809 original size:81 final size:81
Alignment explanation
Indices: 40274669--40274829 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 81
40274659 GGCAAATAAC
*
40274669 CGAATTACCCTCGAAGGGTAAAATGTTCGAATTACCCCTGAAGGGTAAAATGACCGAATTACTCC
1 CGAATTACCCTCGAAGGGTAAAATGTTCGAATTACCCCTGAAGGGTAAAATAACCGAATTAC-CC
40274734 T-GAAGGGTAAAATGAA
65 TCGAAGGGTAAAATGAA
*
40274750 CGAATTAACCC-CGAAGGGTAAAATGATT-GAATTACCCCTGAAGGGTAAAATAACTGAATTACC
1 CGAATT-ACCCTCGAAGGGTAAAATG-TTCGAATTACCCCTGAAGGGTAAAATAACCGAATTACC
40274813 CTCGAAGGGTAAAATGA
64 CTCGAAGGGTAAAATGA
40274830 CCAAAATACC
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
80 3 0.04
81 66 0.88
82 6 0.08
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (81 bp):
CGAATTACCCTCGAAGGGTAAAATGTTCGAATTACCCCTGAAGGGTAAAATAACCGAATTACCCT
CGAAGGGTAAAATGAA
Found at i:40274841 original size:54 final size:53
Alignment explanation
Indices: 40274662--40274841 Score: 229
Period size: 54 Copynumber: 3.3 Consensus size: 53
40274652 AATCATAGGC
* **
40274662 AAATAACCGAATTA-CCCTCGAAGGGTAAAATGTTCGAATTACCCCTGAAGGGTA
1 AAATGACCGAATTACCCCT-GAAGGGTAAAATGAACGAATTACCCC-GAAGGGTA
*
40274716 AAATGACCGAATTACTCCTGAAGGGTAAAATGAACGAATTAACCCCGAAGGGTA
1 AAATGACCGAATTACCCCTGAAGGGTAAAATGAACGAATT-ACCCCGAAGGGTA
**
40274770 AAATGATTGAATTACCCCTGAAGGGTAAAAT-AACTGAATTACCCTCGAAGGGTA
1 AAATGACCGAATTACCCCTGAAGGGTAAAATGAAC-GAATTACCC-CGAAGGGTA
* *
40274824 AAATGACCAAAATACCCC
1 AAATGACCGAATTACCCC
40274842 CATTGGGTAA
Statistics
Matches: 111, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
53 7 0.06
54 96 0.86
55 8 0.07
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (53 bp):
AAATGACCGAATTACCCCTGAAGGGTAAAATGAACGAATTACCCCGAAGGGTA
Found at i:40274850 original size:81 final size:82
Alignment explanation
Indices: 40274682--40274856 Score: 241
Period size: 81 Copynumber: 2.2 Consensus size: 82
40274672 ATTACCCTCG
*
40274682 AAGGGTAAAATG-TTCGAATTACCCCTGAAGGGTAAAATGACCGAATTACTCCTGAAGGGTAAAA
1 AAGGGTAAAATGATTCGAATTACCCCTGAAGGGTAAAATAACCGAATTACTCCTGAAGGGTAAAA
* * *
40274746 TGAACGAATTAACCCCG
66 TGAACAAAATAACCCCC
*
40274763 AAGGGTAAAATGATT-GAATTACCCCTGAAGGGTAAAATAACTGAATTAC-CCTCGAAGGGTAAA
1 AAGGGTAAAATGATTCGAATTACCCCTGAAGGGTAAAATAACCGAATTACTCCT-GAAGGGTAAA
*
40274826 ATGACCAAAAT-ACCCCC
65 ATGAACAAAATAACCCCC
*
40274843 ATTGGGTAAAATGA
1 A-AGGGTAAAATGA
40274857 CTGTTATACC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
80 9 0.11
81 73 0.87
82 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (82 bp):
AAGGGTAAAATGATTCGAATTACCCCTGAAGGGTAAAATAACCGAATTACTCCTGAAGGGTAAAA
TGAACAAAATAACCCCC
Found at i:40275062 original size:26 final size:26
Alignment explanation
Indices: 40275007--40275108 Score: 98
Period size: 26 Copynumber: 3.9 Consensus size: 26
40274997 AGGGGAAGTA
** **
40275007 TACTG-TACTGGTGGCTTTGCCACAT
1 TACTGTTACTGGCAGCTTTGCTGCAT
*
40275032 ATACTGTTACTGGCAGGTTTGCTGCAT
1 -TACTGTTACTGGCAGCTTTGCTGCAT
*
40275059 TACTGTTACTGGCAGCTTTGCTACAT
1 TACTGTTACTGGCAGCTTTGCTGCAT
* * * *
40275085 CACTATTACTTGTAGCTTTGCTGC
1 TACTGTTACTGGCAGCTTTGCTGC
40275109 GATATTAGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
26 48 0.76
27 15 0.24
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCAT
Found at i:40275286 original size:28 final size:28
Alignment explanation
Indices: 40275221--40275286 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
40275211 ATTGTATTGA
* *
40275221 TTACTGTATTGGGCTGAGACCCACACTG
1 TTACTGTACTGGGCTAAGACCCACACTG
* *
40275249 TTACTCTACTGGGCTAAGGCCCACACTG
1 TTACTGTACTGGGCTAAGACCCACACTG
40275277 -TACTGATACT
1 TTACTG-TACT
40275287 AATTGGGCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (28 bp):
TTACTGTACTGGGCTAAGACCCACACTG
Found at i:40288576 original size:39 final size:39
Alignment explanation
Indices: 40288518--40288643 Score: 209
Period size: 39 Copynumber: 3.3 Consensus size: 39
40288508 AGTTTGAGTC
*
40288518 TTAATTATGTCTTAGTTTGAACATCATTAATATGTGACT
1 TTAATTATGTCTTATTTTGAACATCATTAATATGTGACT
40288557 TTAATTATGTCTTATTTTGAACATCATTAATATGTGACT
1 TTAATTATGTCTTATTTTGAACATCATTAATATGTGACT
* * *
40288596 TTGATTATGTCTTATTTTGAACACCATTAATATGTG-TT
1 TTAATTATGTCTTATTTTGAACATCATTAATATGTGACT
40288634 TTAATTATGT
1 TTAATTATGT
40288644 GTCTTAATTC
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 10 0.12
39 72 0.88
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (39 bp):
TTAATTATGTCTTATTTTGAACATCATTAATATGTGACT
Found at i:40307740 original size:24 final size:24
Alignment explanation
Indices: 40307710--40307767 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
40307700 TGATGTTGCC
40307710 GAAGAGCCCACTCAA-ACTGCTATT
1 GAAGAGCCCACTCAACA-TGCTATT
* * *
40307734 GAGGAGCCTACTCAACATGCTGTT
1 GAAGAGCCCACTCAACATGCTATT
40307758 GAAGAGCCCA
1 GAAGAGCCCA
40307768 AAAAGATGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (24 bp):
GAAGAGCCCACTCAACATGCTATT
Found at i:40320397 original size:33 final size:33
Alignment explanation
Indices: 40320360--40320426 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
40320350 GAATGATTTA
40320360 TGCTATGTTTATGTTAATGTATGACATGTATGT
1 TGCTATGTTTATGTTAATGTATGACATGTATGT
*
40320393 TGCTATGTTTATGTTAATGTATGAGATGTATGT
1 TGCTATGTTTATGTTAATGTATGACATGTATGT
40320426 T
1 T
40320427 TCAAAGTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.49
Consensus pattern (33 bp):
TGCTATGTTTATGTTAATGTATGACATGTATGT
Found at i:40323808 original size:27 final size:27
Alignment explanation
Indices: 40323778--40323893 Score: 83
Period size: 27 Copynumber: 4.3 Consensus size: 27
40323768 CTTTTAAGGT
40323778 AAACTCTAAAAGAAAAGTCATTGTGGC
1 AAACTCTAAAAGAAAAGTCATTGTGGC
** **
40323805 AAACT-TTGAAGAAAGAAACATTGTGGC
1 AAACTCTAAAAGAAA-AGTCATTGTGGC
* * * * *
40323832 GAACTC-AGAAGGAAGAGCCTTTGTGGC
1 AAACTCTA-AAAGAAAAGTCATTGTGGC
* * * *
40323859 AAACTCTAAAGGAAGAGTCTTTGTGGA
1 AAACTCTAAAAGAAAAGTCATTGTGGC
40323886 AAACTCTA
1 AAACTCTA
40323894 GATGGACTGT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
26 7 0.10
27 58 0.83
28 5 0.07
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (27 bp):
AAACTCTAAAAGAAAAGTCATTGTGGC
Found at i:40326291 original size:16 final size:16
Alignment explanation
Indices: 40326270--40326301 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40326260 CATTCTTTTA
40326270 AATTTCCAAAAAGCCT
1 AATTTCCAAAAAGCCT
*
40326286 AATTTCCAAAAGGCCT
1 AATTTCCAAAAAGCCT
40326302 TTGATCAAGT
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:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (16 bp):
AATTTCCAAAAAGCCT
Found at i:40329128 original size:19 final size:19
Alignment explanation
Indices: 40329106--40329143 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40329096 TCATCGTCGC
*
40329106 CCACCGTAATCAAATTTGT
1 CCACCATAATCAAATTTGT
*
40329125 CCACTATAATCAAATTTGT
1 CCACCATAATCAAATTTGT
40329144 TATTGACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
CCACCATAATCAAATTTGT
Found at i:40329761 original size:30 final size:31
Alignment explanation
Indices: 40329708--40329770 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
40329698 GGGATGGGAG
40329708 GGGAGCAAAAGTTATGGAGGGAAAATG-AGA
1 GGGAGCAAAAGTTATGGAGGGAAAATGAAGA
* * *
40329738 GGGAGTAAAAGTTTTGG-GAGGAAAGTGAAGA
1 GGGAGCAAAAGTTATGGAG-GGAAAATGAAGA
40329769 GG
1 GG
40329771 TTTAGGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.04
30 22 0.79
31 5 0.18
ACGTcount: A:0.40, C:0.02, G:0.43, T:0.16
Consensus pattern (31 bp):
GGGAGCAAAAGTTATGGAGGGAAAATGAAGA
Found at i:40329842 original size:18 final size:18
Alignment explanation
Indices: 40329815--40329849 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40329805 TAGTTTGATA
*
40329815 TTCGATTTATTCAAATTG
1 TTCGAGTTATTCAAATTG
*
40329833 TTCGAGTTATTCGAATT
1 TTCGAGTTATTCAAATT
40329850 CGAAAACCAA
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:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTCGAGTTATTCAAATTG
Found at i:40332937 original size:48 final size:48
Alignment explanation
Indices: 40332873--40332991 Score: 211
Period size: 48 Copynumber: 2.5 Consensus size: 48
40332863 AGAAATGAAA
*
40332873 GAAAAAGAAAACAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
1 GAAAAAGAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
*
40332921 GAAAAACAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
1 GAAAAAGAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
*
40332969 GAGAAAGAAAAGAAAATTGAAAA
1 GAAAAAGAAAAGAAAATTGAAAA
40332992 GGAAATAGAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.62, C:0.02, G:0.23, T:0.13
Consensus pattern (48 bp):
GAAAAAGAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
Found at i:40339905 original size:424 final size:424
Alignment explanation
Indices: 40338547--40340234 Score: 2717
Period size: 424 Copynumber: 4.0 Consensus size: 424
40338537 TAGATCAAGA
*
40338547 TTGAATTCA-TCAAGAGAAGATCGTGGGAAAGGAAAAGTTGTTGAGTAGACTCTATTGTGGCGAA
1 TTGAA-TCATTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAA
*
40338611 TTATCATTTTGCTAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCT
65 TTATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCT
40338676 TAAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAAT
130 TAAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAAT
** * *
40338741 GTTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCTTGATAAACTTAGT
195 ACTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTAATAAACTTAGT
* *
40338806 AAAAGACTCAAACAATGGTTACATGTTATTTCCTGATGATTCTGAGATCCAACATTTGTTGCAGA
260 AAAAGACTCAAACAATGGTTACATGTTATTTCTTGATGATTCTGAGATCCAGCATTTGTTGCAGA
40338871 CTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTAG
325 CTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTAG
40338936 TCTGGACTAGTAACCTTACATGTATATATTGCCAT
390 TCTGGACTAGTAACCTTACATGTATATATTGCCAT
* *
40338971 TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCTAAT
1 TTGAATCATTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAAT
* *
40339036 TATCATTTTGCCAGGTAAGTATATACAATATAAACATTATTTAACTTTCTTTCCCTTTTGTTCTT
66 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCTT
* *
40339101 AAATTGTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATG
131 AAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATA
* *
40339166 CTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTGATAAACTGAGTA
196 CTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTAATAAACTTAGTA
40339231 AAAGACTCAAACAATGGTTACATGTTATTTTCTTGATGATTCTGAGATCCAGCATTTGTTGCAGA
261 AAAGACTCAAACAATGGTTACATGTTA-TTTCTTGATGATTCTGAGATCCAGCATTTGTTGCAGA
*
40339296 CTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTAA
325 CTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTAG
40339361 TCTGGACTAGTAACCTTACATGTATATATTGCCAT
390 TCTGGACTAGTAACCTTACATGTATATATTGCCAT
* * *
40339396 TTGAATCCTTCAAGAGAAGATCGTAGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
1 TTGAATCATTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAAT
*
40339461 TATCATTTTTCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCTT
66 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCTT
40339526 AAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATA
131 AAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATA
* * * * *
40339591 CTAAACTATATTACAAAGGAATGTGAGTAAAATTA-AAAAATGAAAGTGTCTTAATAAACTCAGT
196 CTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAA-GAAAGTGTCCTAATAAACTTAGT
* * * *
40339655 AAATGACTCAAATAATGGTTACATGTTATTTCATGATGATTCTGAGATCCAGCATTTGTTG-TGA
260 AAAAGACTCAAACAATGGTTACATGTTATTTCTTGATGATTCTGAGATCCAGCATTTGTTGCAG-
40339719 ACTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTA
324 ACTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTA
* * *
40339784 GTCTAGACTAATAACCTTACATGTATATATAGCCAT
389 GTCTGGACTAGTAACCTTACATGTATATATTGCCAT
* *
40339820 TTGAATCATTCAAGAGAAGATCGTGGAAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
1 TTGAATCATTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAAT
* * * * *
40339885 TATCATTTTGCTAAGTAAGTATATACAATATGAAAATTATTTAACTTTCTTTCCTTTATGCTCTT
66 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCTT
* * * *
40339950 AAATTGTATAATTGAAAATTTGGCAAGTTAGATTTGGGTTGTTAAATATATA-A-AAGAAAAATA
131 AAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATA
* * ** * *
40340013 CTGAACTATATTACGAAGGAATGTGACTAAAATTACAAAACTATAGTGTCCCAATAAACTTAGTA
196 CTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTAATAAACTTAGTA
* * *
40340078 AAAGACTCAAATAATGGTTACATGTTATTTCTTGATGATT-TCGAGATCCAGTATTTGTTACAGA
261 AAAGACTCAAACAATGGTTACATGTTATTTCTTGATGATTCT-GAGATCCAGCATTTGTTGCAGA
* * * * * *
40340142 CTCAAAGATACATGTTGCATAAATTTAGCCTGGACTGGTAA-TCTGATGCTATTTGAATGGTTTA
325 CTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTC-GATGCTGTTTTAAAGGTTTA
*
40340206 G-CATGGACTAGTAACCTTACATATATATA
389 GTC-TGGACTAGTAACCTTACATGTATATA
40340235 GACCTGACCA
Statistics
Matches: 1184, Mismatches: 71, Indels: 20
0.93 0.06 0.02
Matches are distributed among these distances:
421 4 0.00
422 193 0.16
423 9 0.01
424 579 0.49
425 399 0.34
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (424 bp):
TTGAATCATTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAAT
TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTTTGTTCTT
AAATTCTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATA
CTGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTAATAAACTTAGTA
AAAGACTCAAACAATGGTTACATGTTATTTCTTGATGATTCTGAGATCCAGCATTTGTTGCAGAC
TCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGGTTTAGT
CTGGACTAGTAACCTTACATGTATATATTGCCAT
Found at i:40346632 original size:20 final size:18
Alignment explanation
Indices: 40346609--40346676 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 18
40346599 TTGGTCCCTT
40346609 TGTTTGCACTTCGATGCCTC
1 TGTTTGCACTT-G-TGCCTC
*
40346629 TGTTTGTACTTTGGTGCCTC
1 TGTTTGCAC-TT-GTGCCTC
*
40346649 TGATTGCACATTGTGCCTC
1 TGTTTGCAC-TTGTGCCTC
*
40346668 TATTTGCAC
1 TGTTTGCAC
40346677 CTCAGTTCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 14 0.35
20 23 0.57
21 3 0.08
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.43
Consensus pattern (18 bp):
TGTTTGCACTTGTGCCTC
Found at i:40346656 original size:40 final size:39
Alignment explanation
Indices: 40346596--40346673 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
40346586 ACGAGGTTTC
* * *
40346596 ACTTTGGTCCCTTTGTTTGCAC-TTCGATGCCTCTGTTTGT
1 ACTTTGGTCCCTCTGATTGCACATT-G-TGCCTCTATTTGT
*
40346636 ACTTTGGTGCCTCTGATTGCACATTGTGCCTCTATTTG
1 ACTTTGGTCCCTCTGATTGCACATTGTGCCTCTATTTG
40346674 CACCTCAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 11 0.33
40 20 0.61
41 2 0.06
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (39 bp):
ACTTTGGTCCCTCTGATTGCACATTGTGCCTCTATTTGT
Found at i:40346674 original size:19 final size:20
Alignment explanation
Indices: 40346623--40346676 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
40346613 TGCACTTCGA
* * *
40346623 TGCCTCTGTTTGTACTTTGG
1 TGCCTCTATTTGCACATTGG
40346643 TGCCTCTGA-TTGCACATT-G
1 TGCCTCT-ATTTGCACATTGG
40346662 TGCCTCTATTTGCAC
1 TGCCTCTATTTGCAC
40346677 CTCAGTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (20 bp):
TGCCTCTATTTGCACATTGG
Found at i:40354374 original size:37 final size:37
Alignment explanation
Indices: 40354324--40354402 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40354314 TTATTACGAA
* * *
40354324 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
40354361 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
40354398 GTCTT
1 GTCTT
40354403 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:40354608 original size:47 final size:47
Alignment explanation
Indices: 40354521--40354998 Score: 668
Period size: 47 Copynumber: 10.1 Consensus size: 47
40354511 CCTTTCGGGA
* * * * * * * * *
40354521 CTTATCACATTTATGCACTTCCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40354568 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40354615 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40354662 CTTATCACACACATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * *
40354709 CCTATCACACATATACACTTTCACATTCATCACGTCGGCTATTATGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
40354756 CCTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40354803 CCTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40354850 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40354897 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40354944 CCTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40354995 CTTA
1 CTTA
40354999 CTATCATTTC
Statistics
Matches: 400, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 359 0.90
51 41 0.10
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40363102 original size:43 final size:42
Alignment explanation
Indices: 40363041--40363177 Score: 148
Period size: 43 Copynumber: 3.2 Consensus size: 42
40363031 GCGTTTTCCC
* * *
40363041 ACAAACGTCGCTATAGAACATGCTCTTTAGCGGTGCTTTTACT
1 ACAAACGTCACTAAAGAACATGATCTTTAGCGGTG-TTTTACT
* * *
40363084 ACAAACGTCACTACAGAACATGATATTTAGTGGTGTCTTTACT
1 ACAAACGTCACTAAAGAACATGATCTTTAGCGGTGT-TTTACT
* * * *
40363127 ACAAACGCCACTAAAGAACATGGTCTTTTGCGGTGATTTTAGTT
1 ACAAACGTCACTAAAGAACATGATCTTTAGCGGTG-TTTTA-CT
40363171 ACAAACG
1 ACAAACG
40363178 CACAACATGC
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
42 1 0.01
43 69 0.87
44 9 0.11
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (42 bp):
ACAAACGTCACTAAAGAACATGATCTTTAGCGGTGTTTTACT
Found at i:40382712 original size:14 final size:16
Alignment explanation
Indices: 40382688--40382720 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40382678 TCCCTTGCTT
40382688 TTTTATCTTTC-TTTC
1 TTTTATCTTTCTTTTC
40382703 TTTT-TCTTTCTTTTC
1 TTTTATCTTTCTTTTC
40382718 TTT
1 TTT
40382721 GATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATCTTTCTTTTC
Found at i:40385124 original size:16 final size:16
Alignment explanation
Indices: 40385103--40385135 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40385093 TTCGTTGTAT
40385103 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
40385119 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
40385135 T
1 T
40385136 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:40385389 original size:18 final size:17
Alignment explanation
Indices: 40385368--40385402 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40385358 TTATTATTAA
*
40385368 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40385386 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40385403 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40385509 original size:18 final size:17
Alignment explanation
Indices: 40385486--40385522 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
40385476 AATTATTATT
40385486 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
40385502 AAATATATGATTTAATA
1 AAATATATGATTTAATA
40385519 AAAT
1 AAAT
40385523 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:40385511 original size:59 final size:59
Alignment explanation
Indices: 40385444--40385629 Score: 198
Period size: 59 Copynumber: 3.1 Consensus size: 59
40385434 CTAAAATCAT
40385444 AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
* * * * * * * * ** * *
40385503 AATATATGAT-TTAATAAAATTCTTAATAAT-CAAT-ATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATACT-ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTTAATTAA
40385564 AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
40385623 AATATAT
1 AATATAT
40385630 TATTTAATAA
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
58 2 0.02
59 41 0.43
60 16 0.17
61 34 0.36
62 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (59 bp):
AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
Found at i:40385581 original size:61 final size:61
Alignment explanation
Indices: 40385396--40385583 Score: 206
Period size: 61 Copynumber: 3.1 Consensus size: 61
40385386 ATATAATTTA
40385396 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * * * ** * * *
40385457 ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAATTCTTAATAAT-CAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
40385515 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
40385577 ATAAAAT
1 ATAAAAT
40385584 ATAATTTGAA
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
58 2 0.02
59 34 0.36
60 16 0.17
61 41 0.43
62 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:40385629 original size:18 final size:17
Alignment explanation
Indices: 40385606--40385642 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
40385596 AATTATTATT
40385606 AAATATA-T-TTTAATTA
1 AAATATATTATTTAA-TA
40385622 AAATATATTATTTAATA
1 AAATATATTATTTAATA
40385639 AAAT
1 AAAT
40385643 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 7 0.37
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATATATTATTTAATA
Found at i:40385652 original size:120 final size:120
Alignment explanation
Indices: 40385355--40385643 Score: 560
Period size: 120 Copynumber: 2.4 Consensus size: 120
40385345 TATTTTAACG
40385355 TAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATT
1 TAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATT
40385420 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAA
66 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAA
*
40385475 TAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATT
1 TAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATT
40385540 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAA
66 CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAA
*
40385595 TAATTATTATTAAATATATTTTAATTAAAATATATTATTTAATAAAATT
1 TAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
40385644 TAAAATAATT
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 167 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (120 bp):
TAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATT
CTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAA
Found at i:40385668 original size:24 final size:24
Alignment explanation
Indices: 40385619--40385665 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
40385609 TATATTTTAA
40385619 TTAAAATATATTATTTAATAAAAT
1 TTAAAATATATTATTTAATAAAAT
40385643 TTAAAATA-ATTATTAGTAATAAA
1 TTAAAATATATTATT--TAATAAA
40385666 TTTTCTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAAATATATTATTTAATAAAAT
Found at i:40385750 original size:75 final size:77
Alignment explanation
Indices: 40385663--40385817 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 77
40385653 TATTAGTAAT
* * *
40385663 AAATTTTCTTATATGAATTTGTATAATTTAATATAATTATTATTAAATATAATTTAATAAT-ATA
1 AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
40385727 TAT-TTTCATAA
66 TATATTTCATAA
*
40385738 AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTATATATAATTTAATAATGATA
1 AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
40385803 TATAATTTCATAA
66 TAT-ATTTCATAA
40385816 AA
1 AA
40385818 TTCTCGATAA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 57 0.78
76 6 0.08
78 10 0.14
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (77 bp):
AAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
TATATTTCATAA
Found at i:40385804 original size:91 final size:91
Alignment explanation
Indices: 40385708--40385940 Score: 339
Period size: 91 Copynumber: 2.5 Consensus size: 91
40385698 ATTATTATTA
*
40385708 AATATAATTTAATAATATATATTTTCATAA-AAATTTTCTTATATGAATTTATATAATTTAAAAT
1 AATATAATTTCATAA-A-ATATTTTCATAATAAATTTTCTTATATGAATTTATATAATTTAAAAT
*
40385772 AATTAATATTATATATAATTTAATAATG
64 AATTAATATTAAATATAATTTAATAATG
*
40385800 ATATATAATTTCAT-AAA-ATTCTCGATAATAAATTTTCTTATATGAATTTATATAATTTAAAAT
1 A-ATATAATTTCATAAAATATTTTC-ATAATAAATTTTCTTATATGAATTTATATAATTTAAAAT
40385863 AATTAATATTAAATATAATTTAATAATG
64 AATTAATATTAAATATAATTTAATAATG
* * *
40385891 ATATATAATTTCATAAAAT-TCTTAATAATAAATATTCTTATATGAATTTA
1 A-ATATAATTTCATAAAATATTTTCATAATAAATTTTCTTATATGAATTTA
40385941 CTAAAATCAT
Statistics
Matches: 129, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
89 5 0.04
90 5 0.04
91 101 0.78
92 7 0.05
93 11 0.09
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
AATATAATTTCATAAAATATTTTCATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAA
TTAATATTAAATATAATTTAATAATG
Found at i:40385805 original size:18 final size:18
Alignment explanation
Indices: 40385770--40385815 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
40385760 ATAATTTAAA
*
40385770 ATAA-TTAAT-ATTATAT
1 ATAATTTAATAATGATAT
40385786 ATAATTTAATAATGATAT
1 ATAATTTAATAATGATAT
*
40385804 ATAATTTCATAA
1 ATAATTTAATAA
40385816 AATTCTCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 17 0.65
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAATTTAATAATGATAT
Found at i:40385852 original size:47 final size:46
Alignment explanation
Indices: 40385734--40385940 Score: 134
Period size: 44 Copynumber: 4.6 Consensus size: 46
40385724 ATATATTTTC
*
40385734 ATAA-AAATTTTCTTATATGAATTTATATAATTT-A-AAATAAT-TA
1 ATAATAAATTTTCTTATATGAATTTATATAATTTCATAAA-ATTCTA
* ** * *
40385777 ATATTATATATAAT-TTA-AT-AATGATATATAATTTCATAAAATTCTCG
1 ATA--ATAAATTTTCTTATATGAAT-TTATATAATTTCATAAAATTCT-A
*
40385824 ATAATAAATTTTCTTATATGAATTTATATAATTT-A-AAATAAT-TA
1 ATAATAAATTTTCTTATATGAATTTATATAATTTCATAAA-ATTCTA
* * *
40385868 ATATTAAATATAAT-TTA-AT-AATGATATATAATTTCATAAAATTCTTA
1 ATAATAAAT-T-TTCTTATATGAAT-TTATATAATTTCATAAAATTC-TA
*
40385915 ATAATAAATATTCTTATATGAATTTA
1 ATAATAAATTTTCTTATATGAATTTA
40385941 CTAAAATCAT
Statistics
Matches: 122, Mismatches: 20, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
43 9 0.07
44 32 0.26
45 25 0.20
46 21 0.17
47 29 0.24
48 6 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
ATAATAAATTTTCTTATATGAATTTATATAATTTCATAAAATTCTA
Found at i:40385896 original size:44 final size:44
Alignment explanation
Indices: 40385757--40385901 Score: 145
Period size: 44 Copynumber: 3.2 Consensus size: 44
40385747 TATATGAATT
*
40385757 TATATAATTTAAAATAATTAATATTATATATAATTTAATAATGA
1 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
* * * * *
40385801 TATATAATTTCATAAA-ATTCTCGATAATAAAT-T-TTCTTATATGAAT-T
1 TATATAATTT-A-AAATAAT-T-AATATTAAATATAAT-TTA-AT-AATGA
40385848 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
1 TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
40385892 TATATAATTT
1 TATATAATTT
40385902 CATAAAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
43 3 0.04
44 30 0.38
45 12 0.15
46 12 0.15
47 19 0.24
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (44 bp):
TATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGA
Found at i:40389988 original size:23 final size:24
Alignment explanation
Indices: 40389931--40389989 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
40389921 ACTCACTAAC
* *
40389931 AAATCAAGAACAATTTCCAGCAGA
1 AAATCAAGAACAAGTTCCAGCAAA
**
40389955 CTATCAA-AACAAGTTCCAG-AAA
1 AAATCAAGAACAAGTTCCAGCAAA
40389977 AAATCAAGAACAA
1 AAATCAAGAACAA
40389990 TATCAAAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 7 0.25
23 16 0.57
24 5 0.18
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.15
Consensus pattern (24 bp):
AAATCAAGAACAAGTTCCAGCAAA
Found at i:40390021 original size:107 final size:107
Alignment explanation
Indices: 40389900--40390129 Score: 397
Period size: 107 Copynumber: 2.1 Consensus size: 107
40389890 ACTATACTTG
40389900 CAATTTCCAATTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
1 CAATTTCCAATTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
40389965 AAGTTCCAGAAAAAATCAAGAACAATATCAAAACAAATGCAA
66 AAGTTCCAGAAAAAATCAAGAACAATATCAAAACAAATGCAA
* *
40390007 CAATTTCCATTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCTAGCAGACTATCAAAAC
1 CAATTTCCAATTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
* * *
40390072 AATTTCTAGAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AAGTTCCAGAAAAAATCAAGAACAATATCAAAACAAATGCAA
* *
40390114 CAATTCCCAGTTTCAT
1 CAATTTCCAATTTCAT
40390130 TGAAAACAAC
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 116 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.25
Consensus pattern (107 bp):
CAATTTCCAATTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
AAGTTCCAGAAAAAATCAAGAACAATATCAAAACAAATGCAA
Found at i:40390095 original size:23 final size:24
Alignment explanation
Indices: 40390035--40390097 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
40390025 TCTACTCACT
40390035 AACAAATCAAGAACAATTTCTAGC
1 AACAAATCAAGAACAATTTCTAGC
*
40390059 AGAC-TATCAA-AACAATTTCTAG-
1 A-ACAAATCAAGAACAATTTCTAGC
40390081 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
40390098 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 18 0.53
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCTAGC
Found at i:40390106 original size:22 final size:22
Alignment explanation
Indices: 40390064--40390109 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40390054 CTAGCAGACT
* *
40390064 ATCAAAACAATTTCTAGAACAA
1 ATCAAAACAATATCTAAAACAA
40390086 ATCAAGAACAATATC-AAAACAA
1 ATCAA-AACAATATCTAAAACAA
40390108 AT
1 AT
40390110 GCAACAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.17, G:0.04, T:0.20
Consensus pattern (22 bp):
ATCAAAACAATATCTAAAACAA
Found at i:40398198 original size:46 final size:46
Alignment explanation
Indices: 40398147--40398240 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
40398137 ATAGTGTAGC
40398147 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
*
40398193 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
40398239 GT
1 GT
40398241 CTTTTAAACC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
Found at i:40398646 original size:14 final size:14
Alignment explanation
Indices: 40398627--40398662 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40398617 ATCAAGTTGT
40398627 AAAAAAAATTCGTG
1 AAAAAAAATTCGTG
*
40398641 AAAAAAAATTCTTG
1 AAAAAAAATTCGTG
40398655 AAAAAAAA
1 AAAAAAAA
40398663 AGTTCGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTCGTG
Found at i:40402653 original size:46 final size:46
Alignment explanation
Indices: 40402602--40402695 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
40402592 ATAGTGTGGC
* * *
40402602 GTTCATCATATACTAAGGTTCCTATCATCCTTGATAGTGGGTTGAG
1 GTTCATCATATACCAAGGTTCATATCATCCTTGATAGTGGGTCGAG
* *
40402648 GTTCATCATATACCAATGTTCATATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCATATCATCCTTGATAGTGGGTCGAG
40402694 GT
1 GT
40402696 CTTTTAAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCATATCATCCTTGATAGTGGGTCGAG
Found at i:40407343 original size:30 final size:30
Alignment explanation
Indices: 40407307--40407363 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
40407297 GAGGCTCGAA
**
40407307 TTGGTTTACTGGTTTAACAATCATGGTGGG
1 TTGGTTTACTGGTACAACAATCATGGTGGG
40407337 TTGGTTTACTGGTACAACAATCATGGT
1 TTGGTTTACTGGTACAACAATCATGGT
40407364 TTCATTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (30 bp):
TTGGTTTACTGGTACAACAATCATGGTGGG
Found at i:40411962 original size:30 final size:30
Alignment explanation
Indices: 40411928--40411984 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40411918 GAGGCTTGGT
*
40411928 TTGGTTTGCTAGTTCAAT-GATCATGGTGGG
1 TTGGTTTCCTAGTTCAATAG-TCATGGTGGG
40411958 TTGGTTTCCTAGTTCAATAGTCATGGT
1 TTGGTTTCCTAGTTCAATAGTCATGGT
40411985 TTCATTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (30 bp):
TTGGTTTCCTAGTTCAATAGTCATGGTGGG
Found at i:40421928 original size:20 final size:21
Alignment explanation
Indices: 40421903--40421942 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40421893 TTTGAACTAC
40421903 TATAATAATAAACA-ATAATA
1 TATAATAATAAACATATAATA
*
40421923 TATAATAATTAACATATAAT
1 TATAATAATAAACATATAAT
40421943 GTACTACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TATAATAATAAACATATAATA
Found at i:40424672 original size:2 final size:2
Alignment explanation
Indices: 40424665--40424703 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40424655 CTTATCAAAG
40424665 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40424704 TATATATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40425428 original size:41 final size:41
Alignment explanation
Indices: 40425368--40425513 Score: 240
Period size: 41 Copynumber: 3.6 Consensus size: 41
40425358 TTTAAACAGA
*
40425368 TTCACTGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAG
* *
40425409 TTCACCGACACTTAGCCTGCTAGGCTTATAGCCCGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
*
40425450 TTCACCGGCACTTAGCCTGTTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
40425491 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
40425514 ACGTAAAGTC
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 96 0.99
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
Found at i:40425536 original size:82 final size:82
Alignment explanation
Indices: 40425361--40425541 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 82
40425351 CACTTAATTT
*
40425361 AAACAGATTCACTGGCACTTCACCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGCC
1 AAACAG-TTCACCGGCACTTCACCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGCC
* * * *
40425426 TGCTAGGCTTATAGCCCG
65 TGCTAGACGTAAAGCCCA
** * *
40425444 ATTCAGTTCACCGGCACTT-AGCCTGTTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCC
1 AAACAGTTCACCGGCACTTCA-CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGCC
*
40425508 TGCTAGACGTAAAGTCCA
65 TGCTAGACGTAAAGCCCA
*
40425526 AAACATTTCACCGGCA
1 AAACAGTTCACCGGCA
40425542 ATTAATCTGA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.01
82 79 0.94
83 4 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (82 bp):
AAACAGTTCACCGGCACTTCACCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAGCCT
GCTAGACGTAAAGCCCA
Found at i:40429425 original size:18 final size:18
Alignment explanation
Indices: 40429383--40429442 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
40429373 ATATATCACA
*
40429383 AATTCTTAATAAA-TTTA-
1 AATTTTTAA-AAATTTTAT
40429400 AATTTTTAAAAATTTTAT
1 AATTTTTAAAAATTTTAT
* *
40429418 AGTTTTTAATAATTTTAT
1 AATTTTTAAAAATTTTAT
40429436 AATTTTT
1 AATTTTT
40429443 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 3 0.08
17 12 0.32
18 22 0.59
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTTAAAAATTTTAT
Found at i:40429442 original size:9 final size:9
Alignment explanation
Indices: 40429396--40429451 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
40429386 TCTTAATAAA
40429396 TTTA-AATT
1 TTTATAATT
* *
40429404 TTTAAAAAT
1 TTTATAATT
*
40429413 TTTATAGTT
1 TTTATAATT
40429422 TTTAATAA-T
1 TTT-ATAATT
40429431 TTTATAATT
1 TTTATAATT
*
40429440 TTTTTAATT
1 TTTATAATT
40429449 TTT
1 TTT
40429452 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 8 0.21
9 28 0.72
10 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:40431452 original size:29 final size:31
Alignment explanation
Indices: 40431393--40431461 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
40431383 ATTTTTATTA
*
40431393 TGGTACTTGTATTTTTATAAAATGTCCAATG
1 TGGTACTTGTATCTTTATAAAATGTCCAATG
* *
40431424 TGGTACTTGTA-CTTT-TAAATTGTTCAATG
1 TGGTACTTGTATCTTTATAAAATGTCCAATG
40431453 TGGTACTTG
1 TGGTACTTG
40431462 AACTATCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 21 0.60
30 3 0.09
31 11 0.31
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
TGGTACTTGTATCTTTATAAAATGTCCAATG
Found at i:40432303 original size:20 final size:19
Alignment explanation
Indices: 40432278--40432332 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
40432268 TTAACAATAT
40432278 ATTTAGTTAATTTATTTTTA
1 ATTTAGTTAATTT-TTTTTA
*
40432298 ATTTAGTTTAATTTTTTTTG
1 ATTTAG-TTAATTTTTTTTA
* *
40432318 TTTTATTTAATTTTT
1 ATTTAGTTAATTTTT
40432333 CACATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.29
20 15 0.48
21 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
ATTTAGTTAATTTTTTTTA
Found at i:40433179 original size:25 final size:25
Alignment explanation
Indices: 40433122--40433173 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40433112 CTCAAGTAAG
40433122 TTCATATGAAACTTACTATATTCTA
1 TTCATATGAAACTTACTATATTCTA
40433147 TTCATATGAAACTTACTATATTCTA
1 TTCATATGAAACTTACTATATTCTA
40433172 TT
1 TT
40433174 ATTATGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (25 bp):
TTCATATGAAACTTACTATATTCTA
Found at i:40437627 original size:33 final size:33
Alignment explanation
Indices: 40437579--40437692 Score: 131
Period size: 33 Copynumber: 3.5 Consensus size: 33
40437569 GATACATGTG
* *
40437579 TAAGATCATAGCTGGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGGGCTATGGCATTCTGATGA
* * **
40437612 TAAGACCATAACTGGGTTATGGCACTACAAATG-
1 TAAGACCATAACTGGGCTATGGCA-TTCTGATGA
* **
40437645 TAAGATCATGGCTGGGCTATGGCATTCTGATGA
1 TAAGACCATAACTGGGCTATGGCATTCTGATGA
40437678 TAAGACCATAACTGG
1 TAAGACCATAACTGG
40437693 TTTACGACAC
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
32 5 0.08
33 53 0.84
34 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCATTCTGATGA
Found at i:40437659 original size:66 final size:66
Alignment explanation
Indices: 40437577--40437734 Score: 246
Period size: 66 Copynumber: 2.4 Consensus size: 66
40437567 TAGATACATG
* * *
40437577 TGTAAGATCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTACAA
1 TGTAAGATCATGGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTACGACACTACAA
40437642 A
66 A
*
40437643 TGTAAGATCATGGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGTTTACGACACTACAA
1 TGTAAGATCATGGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTACGACACTACAA
40437708 A
66 A
* *
40437709 TGTAAGACCATGG-TAGGGCCATGGCA
1 TGTAAGATCATGGCT-GGGCTATGGCA
40437735 ATGCATGTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
65 1 0.01
66 84 0.99
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (66 bp):
TGTAAGATCATGGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTACGACACTACAA
A
Found at i:40437667 original size:105 final size:105
Alignment explanation
Indices: 40437472--40437668 Score: 236
Period size: 105 Copynumber: 1.9 Consensus size: 105
40437462 AATTTTTAAA
* * **
40437472 TGTAAGACCATAGCTAGGCTATGGCATTTTAATGAAAAGACCATAATTGGATTATGACACATTGA
1 TGTAAGACCATAGCTAGGCTATGGCATTCTAATGAAAAGACCATAACTGGATTATGACACATACA
*
40437537 ACATAAGACCATGGTTGGACCATGGCAGTATAGATACATG
66 ACATAAGACCATGGCTGGACCATGGCAGTATAGATACATG
* * * * * *
40437577 TGTAAGATCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCAC-TACA
1 TGTAAGACCATAGCTAGGCTATGGCATTCTAATGAAAAGACCATAACTGGATTATGACACATACA
* * *
40437641 A-ATGTAAGATCATGGCTGGGCTATGGCA
66 ACA--TAAGACCATGGCTGGACCATGGCA
40437669 TTCTGATGAT
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
103 1 0.01
104 3 0.04
105 72 0.95
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAGCTAGGCTATGGCATTCTAATGAAAAGACCATAACTGGATTATGACACATACA
ACATAAGACCATGGCTGGACCATGGCAGTATAGATACATG
Found at i:40440853 original size:26 final size:27
Alignment explanation
Indices: 40440803--40440854 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
40440793 AAAGTTGAAG
* *
40440803 GCCAAAGTAATAAAAAATAAAATTAGA
1 GCCAAAATAACAAAAAATAAAATTAGA
*
40440830 GCCAAAATAACAAAAAA-AACATTAG
1 GCCAAAATAACAAAAAATAAAATTAG
40440855 GGGCTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (27 bp):
GCCAAAATAACAAAAAATAAAATTAGA
Found at i:40441600 original size:51 final size:51
Alignment explanation
Indices: 40441498--40441600 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
40441488 AAATTCCAAA
*
40441498 TATAGGAAGAATAAAAGGACTTGAAATATTTGTAATTTTTAAAATTCTACT
1 TATAGGAAGAAGAAAAGGACTTGAAATATTTGTAATTTTTAAAATTCTACT
* *
40441549 TATAGGAAGAAGACAAGGACTTGAAATATTTGTAATTTTTAAAATTGTACT
1 TATAGGAAGAAGAAAAGGACTTGAAATATTTGTAATTTTTAAAATTCTACT
40441600 T
1 T
40441601 TATAATTTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.37
Consensus pattern (51 bp):
TATAGGAAGAAGAAAAGGACTTGAAATATTTGTAATTTTTAAAATTCTACT
Found at i:40445121 original size:40 final size:39
Alignment explanation
Indices: 40445060--40445177 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
40445050 GCGTTTGGAA
* * *
40445060 CAAAAGTGCCACTAAAAATCGAGAATTAGCAGCGTTTTT
1 CAAAAGCGCCGCTAAAAATCGAGAATTAGCGGCGTTTTT
* * * * * *
40445099 GCCAAAGCGCTGCTAAAGATCGAGCATCAGCGGCGTAATTT
1 -CAAAAGCGCCGCTAAAAATCGAGAATTAGCGGCGT-TTTT
*
40445140 CAAAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTT
1 CAAAAGCGCCGCTAAAAATCGAGAATTAGCGGCGTTTTT
40445178 TATAAAGTGC
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
38 3 0.05
39 11 0.18
40 44 0.72
41 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (39 bp):
CAAAAGCGCCGCTAAAAATCGAGAATTAGCGGCGTTTTT
Found at i:40445307 original size:41 final size:39
Alignment explanation
Indices: 40445236--40445364 Score: 105
Period size: 41 Copynumber: 3.2 Consensus size: 39
40445226 TTTTTGGAGC
* ** *
40445236 CTTTAGCGGCGTTTTTTACTAAGCATCGCTAAAGCTTGGAA
1 CTTTAGCGGCGTTTTTT-TTAAGCGCCGCTAAAGCTCGG-A
* *
40445277 CTTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGCTCGGG
1 CTTTAGCGGCGTTTTT-TTTAAGCGCCGCTAAAGCTCGGA
* * * * *
40445317 CATTTAGTGGCATTTTTGGTTAAGCGCCGCTAATGCTCTGGC
1 C-TTTAGCGGCGTTTTT-TTTAAGCGCCGCTAAAGCTC-GGA
40445359 CTTTAG
1 CTTTAG
40445365 AGGTGCTTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.01
41 69 0.93
42 4 0.05
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (39 bp):
CTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGCTCGGA
Found at i:40445382 original size:41 final size:41
Alignment explanation
Indices: 40445295--40445432 Score: 118
Period size: 41 Copynumber: 3.4 Consensus size: 41
40445285 GCGTTTTTAT
* * * **
40445295 TTAAGCGCCGCTAATGCTCGGGCATTTAGTGGCATTTTTGG
1 TTAAGCGCCGCTAATGCTCTGGCCTTTAGGGGCATTTCAGG
40445336 TTAAGCGCCGCTAATGCTCTGGCCTTTAGAGGTGC-TTTCAGG
1 TTAAGCGCCGCTAATGCTCTGGCCTTTAG-GG-GCATTTCAGG
* ** * * ** *
40445378 -TAAGCACCGCTAATGCTCTTACCTTTAGCGGCGTTTTTGA
1 TTAAGCGCCGCTAATGCTCTGGCCTTTAGGGGCATTTCAGG
*
40445418 CTAAGCGCCGCTAAT
1 TTAAGCGCCGCTAAT
40445433 AGTAACAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.03
40 5 0.06
41 65 0.81
42 6 0.08
43 2 0.03
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (41 bp):
TTAAGCGCCGCTAATGCTCTGGCCTTTAGGGGCATTTCAGG
Found at i:40446005 original size:15 final size:15
Alignment explanation
Indices: 40445984--40446021 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40445974 TTTAAGGTTA
40445984 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
40445999 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
40446014 ATTTAGGG
1 ATTTAGGG
40446022 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:40446385 original size:16 final size:16
Alignment explanation
Indices: 40446356--40446392 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40446346 TATAGGACCA
*
40446356 AAAT-AATAATAAAAT
1 AAATAAATAAAAAAAT
40446371 AAATAAATAAAAAAAT
1 AAATAAATAAAAAAAT
40446387 AAATAA
1 AAATAA
40446393 TTACGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAAATAAAAAAAT
Found at i:40446417 original size:28 final size:28
Alignment explanation
Indices: 40446386--40446440 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
40446376 AATAAAAAAA
*
40446386 TAAATAATTACG-CAATTAATTATTTAAG
1 TAAATAAATACGTC-ATTAATTATTTAAG
*
40446414 TAAATAAATAGGTCATTAATTATTTAA
1 TAAATAAATACGTCATTAATTATTTAA
40446441 ATGTAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (28 bp):
TAAATAAATACGTCATTAATTATTTAAG
Found at i:40447704 original size:10 final size:10
Alignment explanation
Indices: 40447689--40447716 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40447679 TTTTTGATAT
40447689 ATATATATGG
1 ATATATATGG
40447699 ATATATATGG
1 ATATATATGG
40447709 ATATATAT
1 ATATATAT
40447717 AGTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
ATATATATGG
Found at i:40447821 original size:27 final size:27
Alignment explanation
Indices: 40447783--40447834 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40447773 AATAAACAAA
* *
40447783 TAAATAAGTAGGTAATTATTTATTTGT
1 TAAATAAATAGGTAATTAATTATTTGT
40447810 TAAATAAATAGGTAATTAATTATTT
1 TAAATAAATAGGTAATTAATTATTT
40447835 AAATGTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (27 bp):
TAAATAAATAGGTAATTAATTATTTGT
Found at i:40452945 original size:66 final size:65
Alignment explanation
Indices: 40452825--40452989 Score: 197
Period size: 66 Copynumber: 2.5 Consensus size: 65
40452815 GAGCAAATTA
* * * * *
40452825 CACAAATTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAG
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAG
* *
40452890 TTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCC
1 -CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCC
40452954 AG
64 AG
* * * *
40452956 CAGCAGCTTAAAGTAGATGCGGCAGTGAGAGAAG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAG
40452990 TAGAGGCTGC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 80 0.94
67 4 0.05
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAG
Found at i:40452990 original size:21 final size:21
Alignment explanation
Indices: 40452966--40453036 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
40452956 CAGCAGCTTA
* *
40452966 AAGTAGATGCGGCAGTGAGAG
1 AAGTAGAGGCGGCAGCGAGAG
* *
40452987 AAGTAGAGGCTGCAGCGAGGG
1 AAGTAGAGGCGGCAGCGAGAG
* * *
40453008 AAGTAGAGGCTGCAACGAGGG
1 AAGTAGAGGCGGCAGCGAGAG
*
40453029 AAGCAGAG
1 AAGTAGAG
40453037 CAACGTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.44, T:0.10
Consensus pattern (21 bp):
AAGTAGAGGCGGCAGCGAGAG
Found at i:40453474 original size:85 final size:86
Alignment explanation
Indices: 40453374--40453585 Score: 237
Period size: 87 Copynumber: 2.5 Consensus size: 86
40453364 CGTTTTTAAA
* * * *
40453374 AAAAATGCCGCTAAAGTTCATGGTCTTTAGCAGCGTTTGT-GGAAAAAGCGCCGCTAATGATCAT
1 AAAAATGCCGCTAAAGATCATGGTATTTAGCAGCGTTTATGGGAAAAAGCGCCGCTAAAGATCAT
* *
40453438 GGTCTTTTGCGGCGTTTGTGG
66 GGTCTTTAGCAGCGTTTGTGG
* * *
40453459 AAAAATGCCGCTAAAGATCATGGTATTTAGCGGCGTTTATGGGAAAAATCGCCGCTAAAGGTCAT
1 AAAAATGCCGCTAAAGATCATGGTATTTAGCAGCGTTTATGGGAAAAAGCGCCGCTAAAGATCAT
* *
40453524 TGTCTTTAGCAGCGTTTTTTGG
66 GGTCTTTAGCAGCG-TTTGTGG
** * * *** *
40453546 GTAAGTGCCGCTAAAGACCATGACCTTTAGCGGCGTTTAT
1 AAAAATGCCGCTAAAGATCATGGTATTTAGCAGCGTTTAT
40453586 TTCTAAAAAC
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 36 0.34
86 32 0.30
87 39 0.36
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (86 bp):
AAAAATGCCGCTAAAGATCATGGTATTTAGCAGCGTTTATGGGAAAAAGCGCCGCTAAAGATCAT
GGTCTTTAGCAGCGTTTGTGG
Found at i:40453482 original size:42 final size:42
Alignment explanation
Indices: 40453374--40453583 Score: 231
Period size: 43 Copynumber: 4.9 Consensus size: 42
40453364 CGTTTTTAAA
* *
40453374 AAAAATGCCGCTAAAGTTCATGGTCTTTAGCAGCGTTTGTGG
1 AAAAATGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* * *
40453416 AAAAAGCGCCGCTAATGATCATGGTCTTTTGCGGCGTTTGTGG
1 AAAAA-TGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* *
40453459 AAAAATGCCGCTAAAGATCATGGTATTTAGCGGCGTTTATGGG
1 AAAAATGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGT-GG
* * * *
40453502 AAAAATCGCCGCTAAAGGTCATTGTCTTTAGCAGCGTTTTTTGG
1 AAAAAT-GCCGCTAAAGATCATGGTCTTTAGCGGCG-TTTGTGG
** * * **
40453546 GTAAGTGCCGCTAAAGACCATGACCTTTAGCGGCGTTT
1 AAAAATGCCGCTAAAGATCATGGTCTTTAGCGGCGTTT
40453584 ATTTCTAAAA
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
42 38 0.27
43 68 0.49
44 30 0.21
45 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
AAAAATGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
Found at i:40462052 original size:16 final size:16
Alignment explanation
Indices: 40462028--40462075 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
40462018 TAACAATTTC
40462028 TATTCAAAATAAGTAT
1 TATTCAAAATAAGTAT
* * *
40462044 TATTTAAAAAAAATAT
1 TATTCAAAATAAGTAT
*
40462060 CATTCAAGAATAAGTA
1 TATTCAA-AATAAGTA
40462076 CCACTTAAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (16 bp):
TATTCAAAATAAGTAT
Found at i:40469156 original size:16 final size:17
Alignment explanation
Indices: 40469129--40469161 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40469119 GGCACTTTTA
*
40469129 AAAACAATGCAAGTAAC
1 AAAACAATGCAAATAAC
40469146 AAAAC-ATGCAAATAAC
1 AAAACAATGCAAATAAC
40469162 TCTATGATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAACAATGCAAATAAC
Found at i:40472405 original size:15 final size:14
Alignment explanation
Indices: 40472381--40472418 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
40472371 GTTTGCCAGT
40472381 AAAATG-TTTTTCGG
1 AAAATGATTTTT-GG
40472395 AAAATGATTTTTGG
1 AAAATGATTTTTGG
40472409 AAAATGATTT
1 AAAATGATTT
40472419 ACTTTTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (14 bp):
AAAATGATTTTTGG
Found at i:40472431 original size:20 final size:19
Alignment explanation
Indices: 40472402--40472441 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
40472392 CGGAAAATGA
40472402 TTTTTGGAAAATGATTTAC
1 TTTTTGGAAAATGATTTAC
40472421 TTTTCTGGAAAATGATTTAC
1 TTTT-TGGAAAATGATTTAC
40472441 T
1 T
40472442 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (19 bp):
TTTTTGGAAAATGATTTAC
Found at i:40472446 original size:34 final size:32
Alignment explanation
Indices: 40472388--40472451 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 32
40472378 AGTAAAATGT
*
40472388 TTTTCGGAAAATGATTTTTGGAAAATGATTTAC
1 TTTTCGGAAAATGATTTCTGGAAAAT-ATTTAC
40472421 TTTTCTGGAAAATGATTTACT-GAAAATATTT
1 TTTTC-GGAAAATGATTT-CTGGAAAATATTT
40472452 TCTGGTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.32
34 18 0.64
35 1 0.04
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (32 bp):
TTTTCGGAAAATGATTTCTGGAAAATATTTAC
Found at i:40475347 original size:6 final size:6
Alignment explanation
Indices: 40475336--40475384 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
40475326 TAGCCCAAGA
* * * * *
40475336 GAAAGG GAAAGG GAAAAG GAAGGG GAAAGG GGAAGG GGAAGG GGAAGG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
40475384 G
1 G
40475385 GAGAGGGGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:40475363 original size:18 final size:18
Alignment explanation
Indices: 40475340--40475386 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
40475330 CCAAGAGAAA
40475340 GGGAAAGGGAAAAGGAAG
1 GGGAAAGGGAAAAGGAAG
**
40475358 GGGAAAGGGGAAGGGGAAG
1 GGGAAA-GGGAAAAGGAAG
*
40475377 GGGAAGGGGA
1 GGGAAAGGGA
40475387 GAGGGGAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GGGAAAGGGAAAAGGAAG
Found at i:40475374 original size:25 final size:25
Alignment explanation
Indices: 40475336--40475393 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
40475326 TAGCCCAAGA
40475336 GAAA-GGGAAAGGGAAAAGGAAGGG
1 GAAAGGGGAAAGGGAAAAGGAAGGG
* **
40475360 GAAAGGGGAAGGGGAAGGGGAAGGG
1 GAAAGGGGAAAGGGAAAAGGAAGGG
*
40475385 GAGAGGGGA
1 GAAAGGGGA
40475394 GGAGAAGGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (25 bp):
GAAAGGGGAAAGGGAAAAGGAAGGG
Found at i:40475394 original size:7 final size:6
Alignment explanation
Indices: 40475353--40475393 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
40475343 AAAGGGAAAA
40475353 GGAAGG GGAAAGG GGAAGG GGAAGG GGAAGG GGAGAGG GGA
1 GGAAGG GG-AAGG GGAAGG GGAAGG GGAAGG GGA-AGG GGA
40475394 GGAGAAGGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 21 0.64
7 12 0.36
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:40475400 original size:18 final size:18
Alignment explanation
Indices: 40475362--40475401 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40475352 AGGAAGGGGA
*
40475362 AAGGGGAAGGGGAAGGGG
1 AAGGGGAAGGGGAAGGAG
40475380 AAGGGGAGAGGGG-AGGAG
1 AAGGGGA-AGGGGAAGGAG
40475398 AAGG
1 AAGG
40475402 CGTCATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAGGAG
Found at i:40478049 original size:42 final size:41
Alignment explanation
Indices: 40477895--40478050 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
40477885 TATGTTATCG
*
40477895 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
40477937 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
40477981 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
40478023 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
40478051 TGTACGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:40481578 original size:47 final size:47
Alignment explanation
Indices: 40481524--40481617 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
40481514 TTATGTAAAT
*
40481524 GAACAAATACATAACTAAGAATGATATGATATAGATACAACGACAAA
1 GAACAAATAAATAACTAAGAATGATATGATATAGATACAACGACAAA
40481571 GAACAAATAAATAACTAAGAATGATATGATATAGATACAACGACAAA
1 GAACAAATAAATAACTAAGAATGATATGATATAGATACAACGACAAA
40481618 TAATAATGGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.56, C:0.12, G:0.13, T:0.19
Consensus pattern (47 bp):
GAACAAATAAATAACTAAGAATGATATGATATAGATACAACGACAAA
Found at i:40487817 original size:12 final size:12
Alignment explanation
Indices: 40487800--40487829 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40487790 CCTCACACGC
40487800 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
40487812 CCGTGTGCTAGG
1 CCGTGTGCCAGG
40487824 CCGTGT
1 CCGTGT
40487830 AAAACCTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:40490642 original size:39 final size:40
Alignment explanation
Indices: 40490551--40490770 Score: 258
Period size: 40 Copynumber: 5.5 Consensus size: 40
40490541 ATGCTGTCCA
*
40490551 GGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAA-ATCCG
* *
40490590 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAATCCG
*
40490630 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCG
* *
40490669 GGTTAAGTCCCGAAGGCATTTGTGCGAGGTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCG
*
40490709 GGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AATCCG
*
40490749 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
40490771 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 49 0.30
40 99 0.61
41 12 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAATCCG
Found at i:40490788 original size:80 final size:80
Alignment explanation
Indices: 40490554--40490803 Score: 255
Period size: 80 Copynumber: 3.2 Consensus size: 80
40490544 CTGTCCAGGC
* * * **
40490554 TAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCATTTGTGC
1 TAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-ATCCGGGCTAAG-TCCCGAAGGCATTTGAAC
* * *
40490615 GAGATACTAATTCCGGGC
63 GAGGTACTAAATCCGGGT
* * **
40490633 TAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG
40490697 GTACTAAATCCGGGT
66 GTACTAAATCCGGGT
*
40490712 TAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGA
1 TAAGTCCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGA
*
40490776 GG-AGCTATATCC-GGT
65 GGTA-CTAAATCCGGGT
* *
40490791 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
40490804 TACGTGATTT
Statistics
Matches: 148, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
78 10 0.07
79 67 0.45
80 69 0.47
81 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (80 bp):
TAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG
GTACTAAATCCGGGT
Found at i:40498656 original size:40 final size:40
Alignment explanation
Indices: 40498567--40498869 Score: 395
Period size: 40 Copynumber: 7.7 Consensus size: 40
40498557 TTGAATGCTG
* * *
40498567 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
** * *
40498606 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40498646 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
40498685 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40498725 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
40498765 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
40498805 TCCGGGTTAAGTCCCGAAGGTATTTGTGTGAATTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40498846 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
40498870 AACGAGGAGC
Statistics
Matches: 240, Mismatches: 17, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
39 65 0.27
40 165 0.69
41 10 0.04
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40505928 original size:43 final size:45
Alignment explanation
Indices: 40505880--40505964 Score: 129
Period size: 43 Copynumber: 1.9 Consensus size: 45
40505870 TAAATCCAAT
* *
40505880 AACCCATGTTTATCTTCTCCTCTTTTT-AAATTCTTT-TTTCAAC
1 AACCCAAGATTATCTTCTCCTCTTTTTAAAATTCTTTCTTTCAAC
*
40505923 AACCCAAGATTATCTTCTCCTTTTTTTAAAATTCTTTCTTTC
1 AACCCAAGATTATCTTCTCCTCTTTTTAAAATTCTTTCTTTC
40505965 TAGGATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 24 0.65
44 9 0.24
45 4 0.11
ACGTcount: A:0.22, C:0.25, G:0.02, T:0.51
Consensus pattern (45 bp):
AACCCAAGATTATCTTCTCCTCTTTTTAAAATTCTTTCTTTCAAC
Found at i:40507169 original size:100 final size:100
Alignment explanation
Indices: 40506996--40507200 Score: 302
Period size: 100 Copynumber: 2.0 Consensus size: 100
40506986 TGGTACCTAT
* * *
40506996 TTCAATGCTTCCGAACCAACTTGTAACATATTCACCTAATGTCAAACTCATCTAATCCAAAACAT
1 TTCAATGCTTCCAAACCAAATTGTAACATAGTCACCTAATGTCAAACTCATCTAATCCAAAACAT
* * *
40507061 GCATTAAACCATGCCAATCAAGTTTACGCACTCAA
66 GCATTAAACCATACCAATCAAATTTACGCACCCAA
* * * * * *
40507096 TTCAATGTTTCCAAACCAAATTGTGACATAGTCACCTAATGTCAAACTCATCTGATTCAAATCCT
1 TTCAATGCTTCCAAACCAAATTGTAACATAGTCACCTAATGTCAAACTCATCTAATCCAAAACAT
40507161 GCATTAAACCATACCAATCAAATTTACGCACCCAA
66 GCATTAAACCATACCAATCAAATTTACGCACCCAA
40507196 TTCAA
1 TTCAA
40507201 CTTCTTAACA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.28
Consensus pattern (100 bp):
TTCAATGCTTCCAAACCAAATTGTAACATAGTCACCTAATGTCAAACTCATCTAATCCAAAACAT
GCATTAAACCATACCAATCAAATTTACGCACCCAA
Found at i:40510326 original size:50 final size:49
Alignment explanation
Indices: 40510151--40510326 Score: 176
Period size: 50 Copynumber: 3.5 Consensus size: 49
40510141 TTAAGATAAT
* * *
40510151 GAGTTAC-TAATGGATGAC-TTCATTTAAAGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACATT-ATTT-ATGATGC-AAC-TTAACTAACATGA
* * * *
40510202 GAGTTACATAATACATAACATAATTTATGATGCAATCTTCACTAACATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCAA-CTTAACTAACATGA
** *
40510252 GAGTTACATAATGCATTTCATTATTTATGATGCATACGTAACTAACATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCA-ACTTAACTAACATGA
* *
40510302 AAGTTACATAATGCATGACTTTATT
1 GAGTTACATAATGCATGACATTATT
40510327 AAATGCAAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
50 76 0.73
51 15 0.14
52 12 0.12
53 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (49 bp):
GAGTTACATAATGCATGACATTATTTATGATGCAACTTAACTAACATGA
Found at i:40511056 original size:14 final size:14
Alignment explanation
Indices: 40511037--40511063 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40511027 ACATAGATCA
40511037 ATTCATATCATATT
1 ATTCATATCATATT
40511051 ATTCATATCATAT
1 ATTCATATCATAT
40511064 GCACGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTCATATCATATT
Found at i:40516364 original size:18 final size:18
Alignment explanation
Indices: 40516341--40516377 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
40516331 ACAAAAAGAT
40516341 AGCTTATATTTGTAGACG
1 AGCTTATATTTGTAGACG
40516359 AGCTTATATTTGTAGACG
1 AGCTTATATTTGTAGACG
40516377 A
1 A
40516378 ACCTAAACAT
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:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (18 bp):
AGCTTATATTTGTAGACG
Found at i:40519352 original size:20 final size:20
Alignment explanation
Indices: 40519327--40519364 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
40519317 GTCACTAAAT
40519327 AACAATCAGATACTAAGAAC
1 AACAATCAGATACTAAGAAC
40519347 AACAATCAGATACTAAGA
1 AACAATCAGATACTAAGA
40519365 CTTCACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (20 bp):
AACAATCAGATACTAAGAAC
Found at i:40523565 original size:18 final size:18
Alignment explanation
Indices: 40523528--40523565 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40523518 CAGTGCGGGG
*
40523528 TCATCATCTTCTATCTCT
1 TCATCATCCTCTATCTCT
40523546 TCATCATCCTC-ATCTGCT
1 TCATCATCCTCTATCT-CT
40523564 TC
1 TC
40523566 CTCTTCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.16, C:0.37, G:0.03, T:0.45
Consensus pattern (18 bp):
TCATCATCCTCTATCTCT
Found at i:40526313 original size:18 final size:18
Alignment explanation
Indices: 40526290--40526324 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40526280 CCCAATCTTC
*
40526290 TTCCTTTGAAACATAACT
1 TTCCTTAGAAACATAACT
*
40526308 TTCCTTAGAAACTTAAC
1 TTCCTTAGAAACATAAC
40526325 ATATTTCAAA
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:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (18 bp):
TTCCTTAGAAACATAACT
Found at i:40528992 original size:21 final size:22
Alignment explanation
Indices: 40528968--40529014 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40528958 TGTTTAGAAC
*
40528968 AATAATA-TGTTAT-AATATTAA
1 AATAATATTGTAATAAAT-TTAA
40528989 AATAATATTGTAATAAATTTAA
1 AATAATATTGTAATAAATTTAA
40529011 AATA
1 AATA
40529015 TACTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 13 0.57
23 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AATAATATTGTAATAAATTTAA
Found at i:40533829 original size:22 final size:24
Alignment explanation
Indices: 40533779--40533830 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 24
40533769 TTGCAATGCT
40533779 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
40533804 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
40533825 TTTATA
1 TTTATA
40533831 AATAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 3 0.12
22 6 0.24
23 4 0.16
24 6 0.24
25 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:40534021 original size:20 final size:20
Alignment explanation
Indices: 40533996--40534035 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40533986 AATATTTTCC
*
40533996 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40534016 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40534036 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40534041 original size:34 final size:35
Alignment explanation
Indices: 40533984--40534050 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40533974 CAAACACGAG
*
40533984 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40534019 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40534051 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40534042 original size:14 final size:14
Alignment explanation
Indices: 40534019--40534058 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40534009 ACAGAAAAGT
*
40534019 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
40534033 AAATCATTTTACGG
1 AAAACATTTTACAG
40534047 AAAACATTTTAC
1 AAAACATTTTAC
40534059 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:40535994 original size:37 final size:37
Alignment explanation
Indices: 40535944--40536022 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40535934 TTATTACGAA
* *
40535944 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
40535981 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
40536018 GTCTT
1 GTCTT
40536023 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:40536219 original size:47 final size:47
Alignment explanation
Indices: 40536141--40536456 Score: 479
Period size: 47 Copynumber: 6.6 Consensus size: 47
40536131 CCCTTCGGGA
* * * * * *
40536141 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40536188 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40536235 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40536282 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40536329 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40536376 CTTATCACATATATACACTCTCACATTCATCACGTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40536423 CTTATCACATATATATATACACTTTCACATTCAT
1 CTTATCAC----ATATATACACTTTCACATTCAT
40536457 TCAAATATAC
Statistics
Matches: 250, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 229 0.92
51 21 0.08
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40543541 original size:6 final size:6
Alignment explanation
Indices: 40543530--40543557 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40543520 GTTAGGAAGT
40543530 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
40543558 CATATGTATA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:40544170 original size:19 final size:19
Alignment explanation
Indices: 40544146--40544237 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
40544136 AATCATATCT
40544146 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40544165 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
40544184 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40544203 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
40544222 ACGAAGATTGCATATC
1 TCTAAGATTGCATATC
40544238 CTTGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 69 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40544195 original size:38 final size:38
Alignment explanation
Indices: 40544123--40544237 Score: 158
Period size: 38 Copynumber: 2.9 Consensus size: 38
40544113 AAATTAAATC
*
40544123 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
40544165 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* * *
40544203 TCTAAGATTGCATATCATAACGAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
40544238 CTTGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
38 51 0.74
41 7 0.10
42 11 0.16
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:40544844 original size:45 final size:45
Alignment explanation
Indices: 40544787--40544910 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
40544777 TTGTTTATTT
* * *
40544787 AGTCTGCCCCACTGCAATTTCAGGG-GCATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAG-ATAAGACTCGATTTCTTG
* *
40544832 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* *
40544877 GGTCTGCTCCATTGCAACTTCAGGGAGATAAGAC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
40544911 CCAATGCGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
45 69 0.99
46 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:40545475 original size:44 final size:44
Alignment explanation
Indices: 40545424--40545523 Score: 157
Period size: 44 Copynumber: 2.3 Consensus size: 44
40545414 CACTGTTGCT
40545424 CAGGGAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTGAC
1 CAGGGAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGAC
* *
40545468 CAGGGAGATAGGACTTACAATTTTCAACCTATTCCACTGCTGTC
1 CAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGAC
*
40545512 CCGGGAGATAGG
1 CAGGGAGATAGG
40545524 GCTAGGGTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 50 0.96
45 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (44 bp):
CAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGAC
Found at i:40545703 original size:88 final size:86
Alignment explanation
Indices: 40545537--40545782 Score: 384
Period size: 88 Copynumber: 2.8 Consensus size: 86
40545527 AGGGTCATTA
*
40545537 ATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTAACCTGCTCCGCTGCAAACCAG
1 ATCTGCTTCGCTGTCG-TGCAGGAAGGCAAGATCTGCTATTTTAACCTGCTCCGCTGCAACCCAG
40545602 GGAGGCAAGGCTGGTGTCTTCG
65 GGAGGCAAGGCTGGTGTCTTCG
* * * *
40545624 ATTTGCTTCGCTGTCTGTGCAGGAAGGAAACATCTGCTATTTTTAACCTGCTCCGCTACAACCCA
1 ATCTGCTTCGCTGTC-GTGCAGGAAGGCAAGATCTGCTA-TTTTAACCTGCTCCGCTGCAACCCA
*
40545689 GGGAGGCGAGGCTGGTGTCTTCG
64 GGGAGGCAAGGCTGGTGTCTTCG
* *
40545712 ATCTGCTTCGCTGTCCGTACAGGAAGGCAAGATCTGCTATTTTAACCTGCTTCGCTGCAACCCAG
1 ATCTGCTTCGCTGT-CGTGCAGGAAGGCAAGATCTGCTATTTTAACCTGCTCCGCTGCAACCCAG
40545777 GGAGGC
65 GGAGGC
40545783 NNNNNNNNNN
Statistics
Matches: 144, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
87 64 0.44
88 79 0.55
89 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.26
Consensus pattern (86 bp):
ATCTGCTTCGCTGTCGTGCAGGAAGGCAAGATCTGCTATTTTAACCTGCTCCGCTGCAACCCAGG
GAGGCAAGGCTGGTGTCTTCG
Found at i:40557367 original size:12 final size:12
Alignment explanation
Indices: 40557348--40557381 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40557338 AAATTTTAAA
40557348 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
40557360 GTGTGAAAAAGT
1 GAGTGAAAAGGT
40557372 GAGTGAAAAG
1 GAGTGAAAAG
40557382 AAATGAGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:40559924 original size:20 final size:20
Alignment explanation
Indices: 40559901--40559954 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40559891 AGTTTTTCCC
*
40559901 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40559921 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40559941 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40559955 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:40559936 original size:30 final size:30
Alignment explanation
Indices: 40559901--40559974 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40559891 AGTTTTTCCC
40559901 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40559931 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40559961 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40559975 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40559964 original size:20 final size:20
Alignment explanation
Indices: 40559901--40559965 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40559891 AGTTTTTCCC
* * * *
40559901 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40559921 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40559940 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40559961 AGCTC
1 AGCTC
40559966 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40562395 original size:18 final size:18
Alignment explanation
Indices: 40562369--40562418 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
40562359 AAATTGAAAG
*
40562369 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
40562387 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
40562405 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
40562419 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Done.