Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 66 of 117
Found at i:12199086 original size:33 final size:33
Alignment explanation
Indices: 12199049--12199112 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
12199039 ACATTAGAGG
*
12199049 ATAAAAATGATCAGACTAAATTGCAAGTCAAGA
1 ATAAAAATGATCAAACTAAATTGCAAGTCAAGA
* * *
12199082 ATAAAGATGATCAAATTGAATTGCAAGTCAA
1 ATAAAAATGATCAAACTAAATTGCAAGTCAA
12199113 AAAATAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (33 bp):
ATAAAAATGATCAAACTAAATTGCAAGTCAAGA
Found at i:12199131 original size:34 final size:33
Alignment explanation
Indices: 12199067--12199155 Score: 115
Period size: 34 Copynumber: 2.7 Consensus size: 33
12199057 GATCAGACTA
* *
12199067 AATTGCAAGTCAAGAATAAAGATGATCAAATTG
1 AATTGCAAGTCAAAAATAAAGATGACCAAATTG
* *
12199100 AATTGCAAGTCAAAAAATAAAGGTTACCAAATTG
1 AATTGCAAGTC-AAAAATAAAGATGACCAAATTG
* *
12199134 AACTGCAAGTTAAAAATAAAGA
1 AATTGCAAGTCAAAAATAAAGA
12199156 ACGACCAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 21 0.44
34 27 0.56
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (33 bp):
AATTGCAAGTCAAAAATAAAGATGACCAAATTG
Found at i:12199211 original size:36 final size:37
Alignment explanation
Indices: 12199171--12199246 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 37
12199161 CAGGAAGTCG
* *
12199171 ATAAAAAAATGATCGAGATTAAACCATAAGTC-AAAA
1 ATAAAAAAATAATCGAGACTAAACCATAAGTCTAAAA
** * *
12199207 AT-AAATGATAATCGAGACTGAATCATAAGTCTAAAA
1 ATAAAAAAATAATCGAGACTAAACCATAAGTCTAAAA
12199243 ATAA
1 ATAA
12199247 GGATTACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
35 23 0.72
36 8 0.25
37 1 0.03
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.22
Consensus pattern (37 bp):
ATAAAAAAATAATCGAGACTAAACCATAAGTCTAAAA
Found at i:12199467 original size:36 final size:36
Alignment explanation
Indices: 12199413--12199626 Score: 126
Period size: 34 Copynumber: 6.2 Consensus size: 36
12199403 GCAAGTCGGG
* *
12199413 AATAAACATGA-TTGGATTGAACTACAAGTCAGAAA
1 AATAAAGATGACTAGGATTGAACTACAAGTCAGAAA
* * **
12199448 AATAAAGATGACCAGGATTGAACTGCAAGTTTG-AA
1 AATAAAGATGACTAGGATTGAACTACAAGTCAGAAA
* * * * *
12199483 AAT-AAGATGACTAGGACTAAACTATAAGT--TAAG
1 AATAAAGATGACTAGGATTGAACTACAAGTCAGAAA
* * ** *
12199516 GATAAAAATGACTA-GATTGAACTTTAAGTCAAAAA
1 AATAAAGATGACTAGGATTGAACTACAAGTCAGAAA
** * ***
12199551 AATAAAGATGGTTGGGATTGAACCGTAAGTC--AAA
1 AATAAAGATGACTAGGATTGAACTACAAGTCAGAAA
* *
12199585 AATAAAGATGACTAGGACT-AAATCACAAGT-A-AAA
1 AATAAAGATGACTAGGATTGAACT-ACAAGTCAGAAA
12199619 AATAAAGA
1 AATAAAGA
12199627 ACAAACAAAA
Statistics
Matches: 136, Mismatches: 35, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
33 17 0.12
34 63 0.46
35 26 0.19
36 30 0.22
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (36 bp):
AATAAAGATGACTAGGATTGAACTACAAGTCAGAAA
Found at i:12199624 original size:103 final size:103
Alignment explanation
Indices: 12199413--12199624 Score: 230
Period size: 103 Copynumber: 2.1 Consensus size: 103
12199403 GCAAGTCGGG
* * * * *
12199413 AATAAACATGATTGGATTGAACTACAAGTCAGAAAAATAAAGATGACCAGGATTGAACTGCAAGT
1 AATAAAAATGACTAGATTGAACTACAAGTCAAAAAAATAAAGATGACCAGGATTGAACCGCAAGT
** * * *
12199478 TTGAAAATAAGATGACTAGGACTAAACTATAAGTTAAG
66 TCAAAAATAAGATGACTAGGACTAAACTACAAGTAAAA
* ** **** *
12199516 GATAAAAATGACTAGATTGAACTTTAAGTCAAAAAAATAAAGATGGTTGGGATTGAACCGTAAG-
1 AATAAAAATGACTAGATTGAACTACAAGTCAAAAAAATAAAGATGACCAGGATTGAACCGCAAGT
12199580 TCAAAAATAAAGATGACTAGGACTAAA-TCACAAGTAAAA
66 TCAAAAAT-AAGATGACTAGGACTAAACT-ACAAGTAAAA
12199619 AATAAA
1 AATAAA
12199625 GAACAAACAA
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
102 7 0.08
103 81 0.92
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (103 bp):
AATAAAAATGACTAGATTGAACTACAAGTCAAAAAAATAAAGATGACCAGGATTGAACCGCAAGT
TCAAAAATAAGATGACTAGGACTAAACTACAAGTAAAA
Found at i:12199778 original size:28 final size:28
Alignment explanation
Indices: 12199738--12199791 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
12199728 GTTCTTTTAG
12199738 ATCCCTTATTTATTTGGAAGCTTCCTCT
1 ATCCCTTATTTATTTGGAAGCTTCCTCT
12199766 ATCCCTTATTTATTTGGAAGCTTCCT
1 ATCCCTTATTTATTTGGAAGCTTCCT
12199792 TCAAATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (28 bp):
ATCCCTTATTTATTTGGAAGCTTCCTCT
Found at i:12205104 original size:20 final size:20
Alignment explanation
Indices: 12205069--12205119 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
12205059 TTAAAAAACT
*
12205069 CACAAGC-TTCTTTCTCAAA
1 CACAAGCTTTTTTTCTCAAA
12205088 CACAAGCTTTTTTTCTCAAA
1 CACAAGCTTTTTTTCTCAAA
12205108 CACAAGCTTTTT
1 CACAAGCTTTTT
12205120 ATACTAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.37
Consensus pattern (20 bp):
CACAAGCTTTTTTTCTCAAA
Found at i:12205128 original size:20 final size:20
Alignment explanation
Indices: 12205069--12205128 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
12205059 TTAAAAAACT
*
12205069 CACAAGCTTCTTT-CTCAAA
1 CACAAGCTTTTTTACTCAAA
*
12205088 CACAAGCTTTTTTTCTCAAA
1 CACAAGCTTTTTTACTCAAA
12205108 CACAAGCTTTTTATACT-AAA
1 CACAAGCTTTTT-TACTCAAA
12205128 C
1 C
12205129 TTCTAGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 12 0.32
20 22 0.59
21 3 0.08
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (20 bp):
CACAAGCTTTTTTACTCAAA
Found at i:12210967 original size:17 final size:18
Alignment explanation
Indices: 12210932--12210974 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
12210922 AAGGCAGAAT
*
12210932 TCAAATATAGTCTTTTCA
1 TCAAAGATAGTCTTTTCA
*
12210950 TCTAAGATAGTC-TTTCA
1 TCAAAGATAGTCTTTTCA
12210967 TCAAAGAT
1 TCAAAGAT
12210975 TTATTACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (18 bp):
TCAAAGATAGTCTTTTCA
Found at i:12213298 original size:11 final size:11
Alignment explanation
Indices: 12213282--12213313 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
12213272 ATAATCAGCT
12213282 AATCAATATCA
1 AATCAATATCA
12213293 AATCAATATCA
1 AATCAATATCA
12213304 AATCAATATC
1 AATCAATATC
12213314 TATCAATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (11 bp):
AATCAATATCA
Found at i:12217814 original size:11 final size:12
Alignment explanation
Indices: 12217790--12217852 Score: 80
Period size: 11 Copynumber: 5.6 Consensus size: 12
12217780 ATAACCACCT
12217790 AATCAATATCTA
1 AATCAATATCTA
12217802 AATCAATAT-TA
1 AATCAATATCTA
12217813 AATCAATATCT-
1 AATCAATATCTA
* *
12217824 AAT-ATTCTCTA
1 AATCAATATCTA
12217835 AATCAATATC-A
1 AATCAATATCTA
12217846 AATCAAT
1 AATCAAT
12217853 CTAGAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 5 0.11
11 25 0.57
12 14 0.32
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (12 bp):
AATCAATATCTA
Found at i:12217861 original size:33 final size:33
Alignment explanation
Indices: 12217798--12217862 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
12217788 CTAATCAATA
* **
12217798 TCTAAATCAATATTAAATCAATATCTAATATTC
1 TCTAAATCAATATCAAATCAATATAGAATATTC
*
12217831 TCTAAATCAATATCAAATCAATCTAGAATATT
1 TCTAAATCAATATCAAATCAATATAGAATATT
12217863 ACTAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (33 bp):
TCTAAATCAATATCAAATCAATATAGAATATTC
Found at i:12217870 original size:22 final size:22
Alignment explanation
Indices: 12217845--12217907 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
12217835 AATCAATATC
12217845 AAATCAATCTAGAATATTACTA
1 AAATCAATCTAGAATATTACTA
*
12217867 AAAT-ATTACTAGAATA--A-TA
1 AAATCAAT-CTAGAATATTACTA
**
12217886 TCATCAATCTAGAATATTACTA
1 AAATCAATCTAGAATATTACTA
12217908 GAATATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
19 12 0.38
20 3 0.09
21 3 0.09
22 14 0.44
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (22 bp):
AAATCAATCTAGAATATTACTA
Found at i:12217910 original size:11 final size:11
Alignment explanation
Indices: 12217894--12217924 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12217884 TATCATCAAT
12217894 CTAGAATATTA
1 CTAGAATATTA
12217905 CTAGAATATTA
1 CTAGAATATTA
*
12217916 TTAGAATAT
1 CTAGAATAT
12217925 CATTGATAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (11 bp):
CTAGAATATTA
Found at i:12222626 original size:19 final size:19
Alignment explanation
Indices: 12222604--12222650 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
12222594 AAAATGATCT
12222604 AGAATAGCTAAAA-ATCCAA
1 AGAATAGCTAAAACAT-CAA
*
12222623 AGAATACCTAAAACATCAA
1 AGAATAGCTAAAACATCAA
12222642 AGAATAGCT
1 AGAATAGCT
12222651 TAAATCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (19 bp):
AGAATAGCTAAAACATCAA
Found at i:12224267 original size:17 final size:20
Alignment explanation
Indices: 12224229--12224264 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
12224219 AACTATTGTT
12224229 TTATAATTTTTATAATTTTA
1 TTATAATTTTTATAATTTTA
12224249 TTAT-ATTTTTA-AATTT
1 TTATAATTTTTATAATTT
12224265 ATTTTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.31
19 7 0.44
20 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATAATTTTTATAATTTTA
Found at i:12225664 original size:15 final size:15
Alignment explanation
Indices: 12225644--12225675 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12225634 CAACAAAGCT
12225644 CAAGATAATTTGCTA
1 CAAGATAATTTGCTA
12225659 CAAGATAATTTGCTA
1 CAAGATAATTTGCTA
12225674 CA
1 CA
12225676 TCTTTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (15 bp):
CAAGATAATTTGCTA
Found at i:12229194 original size:42 final size:42
Alignment explanation
Indices: 12229147--12229241 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 42
12229137 AAACATGAGG
* *
12229147 CATTTAACAATAAATCATATATACTACTAATAATAATACTAA
1 CATTTAACAATAAATCACATATACTAATAATAATAATACTAA
* * * * * *
12229189 CATTTATCAATTACTCACATATATTAATTATTATAATACTAA
1 CATTTAACAATAAATCACATATACTAATAATAATAATACTAA
* *
12229231 TATTTACCAAT
1 CATTTAACAAT
12229242 TAAGTTTGTG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (42 bp):
CATTTAACAATAAATCACATATACTAATAATAATAATACTAA
Found at i:12231281 original size:17 final size:18
Alignment explanation
Indices: 12231259--12231292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12231249 AAAGATTTAC
12231259 AGAAG-AAGAATTTTAAG
1 AGAAGAAAGAATTTTAAG
*
12231276 AGAAGAAAGATTTTTAA
1 AGAAGAAAGAATTTTAA
12231293 TAGGTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (18 bp):
AGAAGAAAGAATTTTAAG
Found at i:12231345 original size:52 final size:52
Alignment explanation
Indices: 12231255--12231356 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
12231245 ATAAAAAGAT
* * * *
12231255 TTACAGAAGAAGAATTTTAAGAGAAGAAAGATTTTTAATAGGTAAGTTTGAC
1 TTACAGAAAAAGAATTCTAAGAGAAGAAAGATTCTTAATAGGCAAGTTTGAC
**
12231307 TTACAGAAAAAGAATTCTAAGAGTAA-AGGGATTCTTAATAGGCAAGTTTG
1 TTACAGAAAAAGAATTCTAAGAG-AAGAAAGATTCTTAATAGGCAAGTTTG
12231357 TATGCTTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 41 0.95
53 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (52 bp):
TTACAGAAAAAGAATTCTAAGAGAAGAAAGATTCTTAATAGGCAAGTTTGAC
Found at i:12233076 original size:19 final size:20
Alignment explanation
Indices: 12233042--12233079 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12233032 TTTTTTGTTG
12233042 ATAAAAAAATTTTATTTTTT
1 ATAAAAAAATTTTATTTTTT
*
12233062 ATAAATAAA-TTTATTTTT
1 ATAAAAAAATTTTATTTTT
12233080 GAAATACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAAAAAATTTTATTTTTT
Found at i:12237695 original size:26 final size:27
Alignment explanation
Indices: 12237634--12237697 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 27
12237624 TATTTTATTT
*
12237634 AAATTATTTATTAATATATTACATAATA
1 AAATTATTTATT-ATATATTAAATAATA
*
12237662 AATTTTATTTA-T-TATATTAAATTAATA
1 AA-ATTATTTATTATATATTAAA-TAATA
12237689 AAATTATTT
1 AAATTATTT
12237698 CACAATAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 14 0.45
27 7 0.23
28 3 0.10
29 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATTATTTATTATATATTAAATAATA
Found at i:12238085 original size:23 final size:23
Alignment explanation
Indices: 12238053--12238116 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
12238043 ATTTAATAAT
*
12238053 TAAATAATATTTACAAACGCATA
1 TAAATTATATTTACAAACGCATA
* * * *
12238076 TAAATTATATTTGCAAATGTATT
1 TAAATTATATTTACAAACGCATA
*
12238099 TATATTATATATTACAAA
1 TAAATTATAT-TTACAAA
12238117 TAATTAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 27 0.82
24 6 0.18
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (23 bp):
TAAATTATATTTACAAACGCATA
Found at i:12238842 original size:19 final size:19
Alignment explanation
Indices: 12238814--12238857 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
12238804 AACCAAAAAA
12238814 CTTTTT-TTTTTAAAGTCC
1 CTTTTTATTTTTAAAGTCC
12238832 CTTTTTATTTTTAAAGTCC
1 CTTTTTATTTTTAAAGTCC
12238851 CTTTTTA
1 CTTTTTA
12238858 AAGAAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.61
Consensus pattern (19 bp):
CTTTTTATTTTTAAAGTCC
Found at i:12239019 original size:196 final size:196
Alignment explanation
Indices: 12238661--12239041 Score: 611
Period size: 196 Copynumber: 1.9 Consensus size: 196
12238651 TAGTCGGCCC
*
12238661 AAAGAAATTTGGAATAAAACACAAAGGCCATGTGACCATTGGCTACCAAATTTGTAACCTTCTTT
1 AAAGAAATTTGGAATAAAACACAAAGGCCATGTGACCATTGGCTACCAAATTTGTAACCTTCCTT
*
12238726 TTGCACTTAGTTGCCTTTATTTTTCTCTTTTTCTCTCACTTTTTGCAACCAATAATATTTAAGGA
66 TTGCACTTACTTGCCTTTATTTTTCTCTTTTTCTCTCACTTTTTGCAACCAATAATATTTAAGGA
*
12238791 AAGCTAAAAGCTTAACCAAAAAACTTTTTTTTTTAAAGTCCCTTTTTATTTTTAAAGTCCCTTTT
131 AAGCTAAAAGCTTAACCAAAAAACTCTTTTTTTTAAAGTCCCTTTTTATTTTTAAAGTCCCTTTT
12238856 T
196 T
* * * *
12238857 AAAGAAATTTGGAATAAAACACAAAGGCCATGTGACTATTGGTTACCAAATTTTTAACTTTCCTT
1 AAAGAAATTTGGAATAAAACACAAAGGCCATGTGACCATTGGCTACCAAATTTGTAACCTTCCTT
*
12238922 TTGCACTTAACTT-CCTTTATTTTTCTCTTTCTTCTCTCACTTTTTGCGACCAATAATATTTAAG
66 TTGCACTT-ACTTGCCTTTATTTTTCTCTTT-TTCTCTCACTTTTTGCAACCAATAATATTTAAG
* * * *
12238986 GAAAGCTAAAGGCTTAACCAAAAAACCTTTTTTTTTTTAAGTCCCCTTTCTATTTT
129 GAAAGCTAAAAGCTTAACCAAAAAA-CTCTTTTTTTTAAAGT-CCCTTTTTATTTT
12239042 ACACTCCTGT
Statistics
Matches: 171, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
196 85 0.50
197 59 0.35
198 15 0.09
199 12 0.07
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (196 bp):
AAAGAAATTTGGAATAAAACACAAAGGCCATGTGACCATTGGCTACCAAATTTGTAACCTTCCTT
TTGCACTTACTTGCCTTTATTTTTCTCTTTTTCTCTCACTTTTTGCAACCAATAATATTTAAGGA
AAGCTAAAAGCTTAACCAAAAAACTCTTTTTTTTAAAGTCCCTTTTTATTTTTAAAGTCCCTTTT
T
Found at i:12242539 original size:25 final size:25
Alignment explanation
Indices: 12242511--12242558 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12242501 GTTCATCCAT
12242511 ATTCACCTAAAAAAAACTATACCAC
1 ATTCACCTAAAAAAAACTATACCAC
*
12242536 ATTCACCTAAAAATAACTATACC
1 ATTCACCTAAAAAAAACTATACC
12242559 CTAAACTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (25 bp):
ATTCACCTAAAAAAAACTATACCAC
Found at i:12243624 original size:21 final size:21
Alignment explanation
Indices: 12243577--12243617 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
12243567 AAATAATGCG
*
12243577 AATAAAAATCATGTAAAAATA
1 AATAAAAATCATGCAAAAATA
12243598 AATAAAAAT-ATGCAAAAATA
1 AATAAAAATCATGCAAAAATA
12243618 TCATAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (21 bp):
AATAAAAATCATGCAAAAATA
Found at i:12245449 original size:19 final size:19
Alignment explanation
Indices: 12245425--12245644 Score: 120
Period size: 19 Copynumber: 12.1 Consensus size: 19
12245415 AACTTTCAGG
12245425 TTCGCAAGAAATTCAAAGA
1 TTCGCAAGAAATTCAAAGA
* * *
12245444 TTCGCAAGCAATTAAAAGG
1 TTCGCAAGAAATTCAAAGA
* *
12245463 TTCACAAGAACTTCAAAGA
1 TTCGCAAGAAATTCAAAGA
* *
12245482 TTCACAAGTAATTCAAAGA
1 TTCGCAAGAAATTCAAAGA
* ** *
12245501 TTTGCAAG-AATT-TTAGT
1 TTCGCAAGAAATTCAAAGA
** *
12245518 TTCGCAAGAGTTTC--AGT
1 TTCGCAAGAAATTCAAAGA
* *
12245535 TTTGC-AGAAAATT--TAGA
1 TTCGCAAG-AAATTCAAAGA
**
12245552 TTCGTGAGAAATTCAAAGA
1 TTCGCAAGAAATTCAAAGA
*
12245571 TTCGCAAGAACTTCAAAGA
1 TTCGCAAGAAATTCAAAGA
* * *
12245590 TTCACAAGAGATTC--AGG
1 TTCGCAAGAAATTCAAAGA
* * *
12245607 TTTGCAAAAAATT-TAAG-
1 TTCGCAAGAAATTCAAAGA
*
12245624 TTCGTAAGAAATTCAAAGA
1 TTCGCAAGAAATTCAAAGA
12245643 TT
1 TT
12245645 TGCATTCAAA
Statistics
Matches: 150, Mismatches: 40, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
16 2 0.01
17 50 0.33
18 13 0.09
19 85 0.57
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (19 bp):
TTCGCAAGAAATTCAAAGA
Found at i:12245621 original size:72 final size:70
Alignment explanation
Indices: 12245491--12245644 Score: 193
Period size: 72 Copynumber: 2.2 Consensus size: 70
12245481 ATTCACAAGT
* ** * * * * *
12245491 AATTCAAAGATTTGCAAGAATTTTAGTTTCGCAAGAGTTTCAGTTTTGCAGAAAATTT-AGATTC
1 AATTCAAAGATTCGCAAGAATTAAAGATTCACAAGAGATTCAGGTTTGCAAAAAATTTAAG-TTC
*
12245555 GTGAGA
65 GTAAGA
12245561 AATTCAAAGATTCGCAAGAACTTCAAAGATTCACAAGAGATTCAGGTTTGCAAAAAATTTAAGTT
1 AATTCAAAGATTCGCAAGAA-TT-AAAGATTCACAAGAGATTCAGGTTTGCAAAAAATTTAAGTT
12245626 CGTAAGA
64 CGTAAGA
12245633 AATTCAAAGATT
1 AATTCAAAGATT
12245645 TGCATTCAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
70 19 0.26
71 2 0.03
72 49 0.68
73 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (70 bp):
AATTCAAAGATTCGCAAGAATTAAAGATTCACAAGAGATTCAGGTTTGCAAAAAATTTAAGTTCG
TAAGA
Found at i:12246812 original size:9 final size:9
Alignment explanation
Indices: 12246798--12246835 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
12246788 TTAAATTTCC
12246798 TTTTTTCTT
1 TTTTTTCTT
*
12246807 TTTTTTCTC
1 TTTTTTCTT
12246816 TTTTTT-TT
1 TTTTTTCTT
*
12246824 TTTTTGCTT
1 TTTTTTCTT
12246833 TTT
1 TTT
12246836 GTTTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:12246819 original size:17 final size:16
Alignment explanation
Indices: 12246799--12246869 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
12246789 TAAATTTCCT
12246799 TTTTTCTTTTTTTTCTC
1 TTTTTCTTTTTTTT-TC
*
12246816 TTTTT-TTTTTTTTGC
1 TTTTTCTTTTTTTTTC
* *
12246831 TTTTTGTTTATTTTATC
1 TTTTTCTTT-TTTTTTC
12246848 TTTTTCATTTTTTGTTT-
1 TTTTTC-TTTTTT-TTTC
12246865 TTTTT
1 TTTTT
12246870 ACACGCCTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
15 6 0.13
16 11 0.24
17 23 0.51
18 5 0.11
ACGTcount: A:0.04, C:0.08, G:0.04, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:12246835 original size:32 final size:32
Alignment explanation
Indices: 12246799--12246870 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
12246789 TAAATTTCCT
* * **
12246799 TTTTTCTTTTTTTTCTCTTTTTTTTTTTTTGC
1 TTTTTCTTTATTTTATCTTTTTCATTTTTTGC
*
12246831 TTTTTGTTTATTTTATCTTTTTCATTTTTTG-
1 TTTTTCTTTATTTTATCTTTTTCATTTTTTGC
12246862 TTTTT-TTTA
1 TTTTTCTTTA
12246871 CACGCCTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.11
31 5 0.14
32 26 0.74
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (32 bp):
TTTTTCTTTATTTTATCTTTTTCATTTTTTGC
Found at i:12248154 original size:51 final size:50
Alignment explanation
Indices: 12248076--12248181 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
12248066 ATTTGATTTA
* *
12248076 ATTTTAATATGAATTGATTCTAGAATTATATCCCAAAAATCTTTCAAAATT
1 ATTTTAATATGAATTGATTCTAGAATTA-AACCCAAAAATCTATCAAAATT
* *
12248127 ATTTTAATGTGAATTGATTCT-GAAATTAAACCCAAAAATCTATCAACATT
1 ATTTTAATATGAATTGATTCTAG-AATTAAACCCAAAAATCTATCAAAATT
12248177 ATTTT
1 ATTTT
12248182 TGCTAGATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
50 25 0.50
51 25 0.50
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (50 bp):
ATTTTAATATGAATTGATTCTAGAATTAAACCCAAAAATCTATCAAAATT
Found at i:12248583 original size:30 final size:30
Alignment explanation
Indices: 12248517--12248585 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
12248507 TCCCTTTCGC
* * * **
12248517 ACCAACATTGGCATTAGTTTTTCTTTTTGT
1 ACCAACATTGGCAATAGTTTTTCCTCTCAT
*
12248547 AACAACATTGGCAATAGTTTTTCCTCTCAT
1 ACCAACATTGGCAATAGTTTTTCCTCTCAT
12248577 ACCAACATT
1 ACCAACATT
12248586 ACCATCATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.41
Consensus pattern (30 bp):
ACCAACATTGGCAATAGTTTTTCCTCTCAT
Found at i:12253544 original size:18 final size:17
Alignment explanation
Indices: 12253517--12253550 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12253507 TTATTTTTAA
12253517 TTTGTATTAAAATAAATT
1 TTTGTATTAAAA-AAATT
*
12253535 TTTGTTTTAAAAAAAT
1 TTTGTATTAAAAAAAT
12253551 GATTTATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTGTATTAAAAAAATT
Found at i:12253618 original size:23 final size:23
Alignment explanation
Indices: 12253588--12253643 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
12253578 CAAAATAAAT
12253588 ATTAAAATTTTATTTGGATACAA
1 ATTAAAATTTTATTTGGATACAA
*
12253611 ATTAAAATTTTATTTTGATACAA
1 ATTAAAATTTTATTTGGATACAA
12253634 ATTAAAATTT
1 ATTAAAATTT
12253644 AAAAATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (23 bp):
ATTAAAATTTTATTTGGATACAA
Found at i:12259713 original size:19 final size:20
Alignment explanation
Indices: 12259676--12259712 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
12259666 CAGAAAGAGG
12259676 AAAATATATTTTTATTTTTA
1 AAAATATATTTTTATTTTTA
12259696 AAAAT-TA-TTTTATTTTT
1 AAAATATATTTTTATTTTT
12259713 TTTAGTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 2 0.12
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AAAATATATTTTTATTTTTA
Found at i:12261834 original size:20 final size:20
Alignment explanation
Indices: 12261798--12261849 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
12261788 CTCCTATTGA
**
12261798 TATTTTTAATCGATTATT-T
1 TATTTTTAATATATTATTAT
12261817 TATTTTTAATATATTTATTAT
1 TATTTTTAATATA-TTATTAT
*
12261838 CA-TTTTAATATA
1 TATTTTTAATATA
12261850 AAATAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
20 15 0.54
21 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTAATATATTATTAT
Found at i:12264770 original size:3 final size:3
Alignment explanation
Indices: 12264762--12264797 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
12264752 TTTGGTCTTT
12264762 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12264798 ATTTGAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12267028 original size:15 final size:15
Alignment explanation
Indices: 12267010--12267061 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
12267000 CCATAATGGT
* *
12267010 TTTGGTCATTTTAGG
1 TTTGGCCATTTCAGG
*
12267025 TTTGGACCATTTCAGA
1 TTTGG-CCATTTCAGG
12267041 TTTGGGCCATTTCAGG
1 TTT-GGCCATTTCAGG
12267057 TTTGG
1 TTTGG
12267062 TCAATATCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.23
16 22 0.71
17 2 0.06
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.44
Consensus pattern (15 bp):
TTTGGCCATTTCAGG
Found at i:12267035 original size:16 final size:16
Alignment explanation
Indices: 12267016--12267061 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
12267006 TGGTTTTGGT
*
12267016 CATTTTAGGTTTGGAC
1 CATTTCAGGTTTGGAC
* *
12267032 CATTTCAGATTTGGGC
1 CATTTCAGGTTTGGAC
12267048 CATTTCAGGTTTGG
1 CATTTCAGGTTTGG
12267062 TCAATATCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.41
Consensus pattern (16 bp):
CATTTCAGGTTTGGAC
Found at i:12267058 original size:32 final size:31
Alignment explanation
Indices: 12266954--12267061 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 31
12266944 GATTTAGATA
* * * *
12266954 ATTTCTGGTTTGAAACATTTCAAATTTGGCC
1 ATTTCAGGTTTGGACCATTTCAGATTTGGCC
* * * * *
12266985 TATTTCAGGTTTAGACCATAAT-GGTTTTGGTC
1 -ATTTCAGGTTTGGACCAT-TTCAGATTTGGCC
*
12267017 ATTTTAGGTTTGGACCATTTCAGATTTGGGCC
1 ATTTCAGGTTTGGACCATTTCAGATTT-GGCC
12267049 ATTTCAGGTTTGG
1 ATTTCAGGTTTGG
12267062 TCAATATCGG
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
30 1 0.02
31 20 0.35
32 35 0.61
33 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.43
Consensus pattern (31 bp):
ATTTCAGGTTTGGACCATTTCAGATTTGGCC
Found at i:12270612 original size:30 final size:30
Alignment explanation
Indices: 12270578--12270637 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
12270568 TTGTATCTAT
* * *
12270578 TTAAGCCTTTAAAGTATTATTTTTGTTTAA
1 TTAAGCCTTTAAAGAACTATATTTGTTTAA
**
12270608 TTAAGTTTTTAAAGAACTATATTTGTTTAA
1 TTAAGCCTTTAAAGAACTATATTTGTTTAA
12270638 CTAAAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (30 bp):
TTAAGCCTTTAAAGAACTATATTTGTTTAA
Found at i:12270648 original size:30 final size:30
Alignment explanation
Indices: 12270585--12270648 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
12270575 TATTTAAGCC
* * * * **
12270585 TTTAAAGTATTATTTTTGTTTAATTAAGTT
1 TTTAAAGAACTATATTTGTTTAACTAAAAT
12270615 TTTAAAGAACTATATTTGTTTAACTAAAAT
1 TTTAAAGAACTATATTTGTTTAACTAAAAT
12270645 TTTA
1 TTTA
12270649 TTTTCTAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTAAAGAACTATATTTGTTTAACTAAAAT
Found at i:12271797 original size:13 final size:13
Alignment explanation
Indices: 12271779--12271803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12271769 AATATAATAC
12271779 TTTATTAAATAAA
1 TTTATTAAATAAA
12271792 TTTATTAAATAA
1 TTTATTAAATAA
12271804 TAAAGTTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTATTAAATAAA
Found at i:12271807 original size:16 final size:17
Alignment explanation
Indices: 12271786--12271822 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12271776 TACTTTATTA
*
12271786 AATAAATTTATTAA-AT
1 AATAAAGTTATTAATAT
12271802 AATAAAGTTATTAATAT
1 AATAAAGTTATTAATAT
12271819 AATA
1 AATA
12271823 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AATAAAGTTATTAATAT
Found at i:12272307 original size:2 final size:2
Alignment explanation
Indices: 12272302--12272336 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12272292 TATATATTCT
* *
12272302 TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12272337 CTCGAGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12272310 original size:14 final size:16
Alignment explanation
Indices: 12272291--12272330 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12272281 AGATAATAAA
12272291 ATATATAT-TCT-TAT
1 ATATATATATCTGTAT
*
12272305 ATATATATATGTGTAT
1 ATATATATATCTGTAT
12272321 ATATATATAT
1 ATATATATAT
12272331 ATATATCTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.35
15 2 0.09
16 13 0.57
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (16 bp):
ATATATATATCTGTAT
Found at i:12272312 original size:16 final size:18
Alignment explanation
Indices: 12272291--12272332 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12272281 AGATAATAAA
12272291 ATATATAT-TCT-TATAT
1 ATATATATGTCTATATAT
*
12272307 ATATATATGTGTATATAT
1 ATATATATGTCTATATAT
12272325 ATATATAT
1 ATATATAT
12272333 ATATCTCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
ATATATATGTCTATATAT
Found at i:12273004 original size:17 final size:17
Alignment explanation
Indices: 12272984--12273031 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
12272974 GAACTTTTTT
*
12272984 AATATAATATATGAATA
1 AATATAATATATAAATA
*
12273001 AATATAA-AAATAAATA
1 AATATAATATATAAATA
12273017 AATAATAAATATATA
1 AAT-AT-AATATATA
12273032 TTTTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 10 0.40
17 9 0.36
18 2 0.08
19 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATATAATATATAAATA
Found at i:12273590 original size:17 final size:18
Alignment explanation
Indices: 12273568--12273606 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12273558 TATATATAAT
12273568 AAAAATAAA-A-TAAAATA
1 AAAAATAAACAGT-AAATA
12273585 AAAAATAAACAGTAAATA
1 AAAAATAAACAGTAAATA
12273603 AAAA
1 AAAA
12273607 GTAGATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAATAAACAGTAAATA
Found at i:12278313 original size:15 final size:15
Alignment explanation
Indices: 12278293--12278327 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12278283 CTTATTAGTT
*
12278293 TGTAATGGATAATGA
1 TGTAATAGATAATGA
12278308 TGTAATAGATAATGA
1 TGTAATAGATAATGA
12278323 TGTAA
1 TGTAA
12278328 GAAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (15 bp):
TGTAATAGATAATGA
Found at i:12278484 original size:16 final size:16
Alignment explanation
Indices: 12278448--12278489 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
12278438 ATTTAGAATG
*
12278448 ATGTTGTTATTGTTATT
1 ATGTT-TTATTGCTATT
12278465 -TGTTTTATTGCTATT
1 ATGTTTTATTGCTATT
12278480 ATGTTTTATT
1 ATGTTTTATT
12278490 TTTTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.17, C:0.02, G:0.14, T:0.67
Consensus pattern (16 bp):
ATGTTTTATTGCTATT
Found at i:12285329 original size:18 final size:19
Alignment explanation
Indices: 12285306--12285341 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12285296 ATAACAATTT
*
12285306 TAAAATGAAAT-TTAAAAA
1 TAAAATAAAATATTAAAAA
12285324 TAAAATAAAATATTAAAA
1 TAAAATAAAATATTAAAA
12285342 CTGCTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAAATAAAATATTAAAAA
Found at i:12292652 original size:114 final size:115
Alignment explanation
Indices: 12292495--12292716 Score: 288
Period size: 114 Copynumber: 1.9 Consensus size: 115
12292485 TAAATATGAT
* * *
12292495 GTTTCTAAAATAGAAAACAAAATCTTTGTTGAAAACATGAAAAAAATATTTTTCAGAATTTAACA
1 GTTTCTAAAATAGAAAACAAAATCTTTATTGAAAACATAAAAAAAATATTTTTCAGAATTCAACA
* * *
12292560 AAA-ATG-ATGTTTCTAAGATAGAAAATATAGTCTTTGTTAAAAAAAATAAC
66 AAAGAGGCAT-TTT-TAAGATAAAAAATATAGTATTTGTTAAAAAAAATAAC
** * * * *
12292610 GTTTCTAAAATA-AAAATGAAATTTTTATTGAAAACATAAAAAATATATTTTTTAGAATTCAATA
1 GTTTCTAAAATAGAAAACAAAATCTTTATTGAAAACATAAAAAAAATATTTTTCAGAATTCAACA
*
12292674 AAAGAGGCATTTTTAAGATAAAAAATATAGTATTTGTTGAAAA
66 AAAGAGGCATTTTTAAGATAAAAAATATAGTATTTGTTAAAAA
12292717 CATGAAAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
114 73 0.79
115 17 0.18
116 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (115 bp):
GTTTCTAAAATAGAAAACAAAATCTTTATTGAAAACATAAAAAAAATATTTTTCAGAATTCAACA
AAAGAGGCATTTTTAAGATAAAAAATATAGTATTTGTTAAAAAAAATAAC
Found at i:12292744 original size:187 final size:187
Alignment explanation
Indices: 12292519--12292912 Score: 596
Period size: 187 Copynumber: 2.1 Consensus size: 187
12292509 AAACAAAATC
* * ** *
12292519 TTTGTTGAAAACATGAAAAAAATATTTTTCAGAATTTAACAAAAATGATGTTTCTAAGA-TAGAA
1 TTTGTTGAAAACATGAAAAAAATATTTTTCAAAATTTAACAAAAATAACATTTCTAA-ATTAAAA
* * * *
12292583 AATATAGTCTTTGTTAAAAAAAATAACGTTTCTAAAATAAAAATGAAATTTTTATTGAAAACAT-
65 AATACAGTCTTTGTT-AAAAAAATAACATTTCTAAAATAAAAATAAAAATTTTATTGAAAACATA
*
12292647 AAAAA-ATATATTTTTTAGAATTCAATAAAAGAGGCATTTTTAAGATAAAAAATATAGTA
129 AAAAATATATATTTTTTAGAATTCAATAAAAG-GACATTTTTAAGATAAAAAATATAGTA
*
12292706 TTTGTTGAAAACATGAAAAAAATATTTTTCAAAATTTAAGAAAAATAACATTTCTAAATTAAAAA
1 TTTGTTGAAAACATGAAAAAAATATTTTTCAAAATTTAACAAAAATAACATTTCTAAATTAAAAA
* * *
12292771 ATACAGTCTTTGTTAAAAAGATGACATTTCTAAAATAAAAATAAAAATTTTGTTGAAAACATAAA
66 ATACAGTCTTTGTTAAAAAAATAACATTTCTAAAATAAAAATAAAAATTTTATTGAAAACATAAA
*
12292836 AAATATATATTTTTTAGAATTCAATAAAAGGACATTTTTAAGATAAAAAATATAGTT
131 AAATATATATTTTTTAGAATTCAATAAAAGGACATTTTTAAGATAAAAAATATAGTA
*
12292893 TTTGTTGAAAATATGAAAAA
1 TTTGTTGAAAACATGAAAAA
12292913 TATGTTATTC
Statistics
Matches: 188, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
186 43 0.23
187 119 0.63
188 26 0.14
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (187 bp):
TTTGTTGAAAACATGAAAAAAATATTTTTCAAAATTTAACAAAAATAACATTTCTAAATTAAAAA
ATACAGTCTTTGTTAAAAAAATAACATTTCTAAAATAAAAATAAAAATTTTATTGAAAACATAAA
AAATATATATTTTTTAGAATTCAATAAAAGGACATTTTTAAGATAAAAAATATAGTA
Found at i:12292758 original size:73 final size:74
Alignment explanation
Indices: 12292637--12292794 Score: 171
Period size: 73 Copynumber: 2.2 Consensus size: 74
12292627 GAAATTTTTA
* * * ** *
12292637 TTGAAAACAT-AAAAAATATATTTTTTAGAATTCAATAAAAGAGGCATTTTTAAGA-TAAAAAAT
1 TTGAAAACATGAAAAAATATATTTTTCAAAATTCAAGAAAAGAAACATTTCTAA-ATTAAAAAAT
*
12292700 ATAGTATTTG
65 ACAGTATTTG
*
12292710 TTGAAAACATGAAAAAA-ATATTTTTCAAAATTTAAGAAAA-ATAACATTTCTAAATTAAAAAAT
1 TTGAAAACATGAAAAAATATATTTTTCAAAATTCAAGAAAAGA-AACATTTCTAAATTAAAAAAT
*
12292773 ACAGTCTTTG
65 ACAGTATTTG
* *
12292783 TTAAAAAGATGA
1 TTGAAAACATGA
12292795 CATTTCTAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
72 2 0.03
73 63 0.89
74 6 0.08
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (74 bp):
TTGAAAACATGAAAAAATATATTTTTCAAAATTCAAGAAAAGAAACATTTCTAAATTAAAAAATA
CAGTATTTG
Found at i:12292823 original size:40 final size:41
Alignment explanation
Indices: 12292753--12292829 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
12292743 AAGAAAAATA
* * *
12292753 ACATTTCTAAATTAAAAAATACAGTCTTTGTTAAAAAGATG
1 ACATTTCTAAAATAAAAAATAAAATCTTTGTTAAAAAGATG
*
12292794 ACATTTCTAAAAT-AAAAATAAAAAT-TTTGTTGAAAA
1 ACATTTCTAAAATAAAAAAT-AAAATCTTTGTTAAAAA
12292830 CATAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
40 16 0.52
41 15 0.48
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (41 bp):
ACATTTCTAAAATAAAAAATAAAATCTTTGTTAAAAAGATG
Found at i:12294354 original size:16 final size:17
Alignment explanation
Indices: 12294328--12294360 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12294318 TTTAAAAGAT
12294328 TAAATTTAATTTCTTAA
1 TAAATTTAATTTCTTAA
12294345 TAAA-TTAATTTCTTAA
1 TAAATTTAATTTCTTAA
12294361 ATTTTCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTTAATTTCTTAA
Found at i:12298496 original size:14 final size:14
Alignment explanation
Indices: 12298477--12298510 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12298467 GTTACTTCTT
12298477 GTTTTTTTTCTTTA
1 GTTTTTTTTCTTTA
*
12298491 GTTTTTTTTTTTTA
1 GTTTTTTTTCTTTA
*
12298505 ATTTTT
1 GTTTTT
12298511 ACTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (14 bp):
GTTTTTTTTCTTTA
Found at i:12298516 original size:19 final size:19
Alignment explanation
Indices: 12298494--12298539 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
12298484 TTCTTTAGTT
12298494 TTTTTTTTTTAATTTTT-A
1 TTTTTTTTTTAATTTTTGA
* *
12298512 CTTTTTTTTTCATTTTTGA
1 TTTTTTTTTTAATTTTTGA
12298531 TTTTTTTTT
1 TTTTTTTTT
12298540 GTCAAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTTTTTTAATTTTTGA
Found at i:12298733 original size:15 final size:15
Alignment explanation
Indices: 12298711--12298748 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12298701 CAAAACTTTC
*
12298711 TTTTTTTA-TTTTTT
1 TTTTTTTACCTTTTT
12298725 TTCTTTTTACCTTTTT
1 TT-TTTTTACCTTTTT
12298741 TTTTTTTA
1 TTTTTTTA
12298749 AAAGTGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 12 0.57
16 7 0.33
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTACCTTTTT
Found at i:12298947 original size:24 final size:24
Alignment explanation
Indices: 12298920--12298972 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12298910 TGTTTTATCA
12298920 TTTTT-CTATTTACTTCCTTTTTCT
1 TTTTTACT-TTTACTTCCTTTTTCT
** *
12298944 TTTTTACTTTTTTTTCTTTTTTCT
1 TTTTTACTTTTACTTCCTTTTTCT
12298968 TTTTT
1 TTTTT
12298973 TTTGTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTACTTTTACTTCCTTTTTCT
Found at i:12298949 original size:18 final size:17
Alignment explanation
Indices: 12298928--12298973 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
12298918 CATTTTTCTA
12298928 TTTACTTCCTTTTTCTTT
1 TTTACTT-CTTTTTCTTT
*
12298946 TTTACTTTTTTTTCTTT
1 TTTACTTCTTTTTCTTT
12298963 TTT-CTT-TTTTT
1 TTTACTTCTTTTT
12298974 TTGTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 3 0.11
17 12 0.44
18 7 0.26
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTACTTCTTTTTCTTT
Found at i:12298963 original size:7 final size:7
Alignment explanation
Indices: 12298898--12298972 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 7
12298888 TTTAATCTCT
*
12298898 TTTTTTT
1 TTTTTTC
*
12298905 TTTTTTG
1 TTTTTTC
*
12298912 TTTTATC
1 TTTTTTC
*
12298919 ATTTTTC
1 TTTTTTC
12298926 TATTTACTTC
1 T-TTT--TTC
*
12298936 CTTTTTC
1 TTTTTTC
12298943 TTTTTTAC
1 TTTTTT-C
12298951 TTTTTTTTC
1 --TTTTTTC
12298960 TTTTTTC
1 TTTTTTC
12298967 TTTTTT
1 TTTTTT
12298973 TTTGTATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 37 0.69
8 4 0.07
9 4 0.07
10 9 0.17
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:12298975 original size:17 final size:17
Alignment explanation
Indices: 12298937--12298974 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12298927 ATTTACTTCC
12298937 TTTTTCTTTTTTACTTT
1 TTTTTCTTTTTTACTTT
12298954 TTTTTCTTTTTT-CTTT
1 TTTTTCTTTTTTACTTT
12298970 TTTTT
1 TTTTT
12298975 TGTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTCTTTTTTACTTT
Found at i:12302582 original size:83 final size:83
Alignment explanation
Indices: 12302428--12302582 Score: 179
Period size: 83 Copynumber: 1.9 Consensus size: 83
12302418 TTACTATATT
* * * *
12302428 TTTAGATAAGAATTACATCTTGATAATTAAAGTGTGACTAGGTCAATCAATTGGTTTAGTTGAAA
1 TTTAGATAAGAATTACATCCTAAAAATTAAAGTGTGACTAGGTCAATCAATTGGTTTAGCTGAAA
*
12302493 TGCTACTAGTGCTATCTC
66 TACTACTAGTGCTATCTC
* * * * * *
12302511 TTTATATAAGAATTACATCCTAAAAATTCAAGTTTGAGTAGGTCAGTCATTTGGCTTT-GCT-AA
1 TTTAGATAAGAATTACATCCTAAAAATTAAAGTGTGACTAGGTCAATCAATTGG-TTTAGCTGAA
12302574 GATACTACT
65 -ATACTACT
12302583 GGTGTTGTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
82 2 0.03
83 54 0.92
84 3 0.05
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (83 bp):
TTTAGATAAGAATTACATCCTAAAAATTAAAGTGTGACTAGGTCAATCAATTGGTTTAGCTGAAA
TACTACTAGTGCTATCTC
Found at i:12303350 original size:23 final size:23
Alignment explanation
Indices: 12303307--12303350 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12303297 AAAAATGTAA
*
12303307 ATTTATTTCATTTAGATTATTGT
1 ATTTATTTCATTTAGAATATTGT
*
12303330 ATTTATGTTCTTTTA-AATATT
1 ATTTAT-TTCATTTAGAATATT
12303351 CATAATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (23 bp):
ATTTATTTCATTTAGAATATTGT
Found at i:12304558 original size:21 final size:21
Alignment explanation
Indices: 12304528--12304571 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12304518 ATAAAGAATA
*
12304528 TAAGGACTTTTTGGAGTGCTC
1 TAAGGACTTTTTAGAGTGCTC
* *
12304549 TAAGGGCTTTTTAGAGTGGTC
1 TAAGGACTTTTTAGAGTGCTC
12304570 TA
1 TA
12304572 GAAGGTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.30, T:0.39
Consensus pattern (21 bp):
TAAGGACTTTTTAGAGTGCTC
Found at i:12304628 original size:18 final size:18
Alignment explanation
Indices: 12304605--12304659 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
12304595 GTTTTTTTTT
12304605 AAATAAAAAAAGAAGAAA
1 AAATAAAAAAAGAAGAAA
* *
12304623 AAAT-AAAAAAGCTATAAA
1 AAATAAAAAAAG-AAGAAA
*
12304641 AAATGAAAAAAAAAAGAAA
1 AAAT-AAAAAAAGAAGAAA
12304660 GAGGTCTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 7 0.24
18 12 0.41
19 4 0.14
20 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (18 bp):
AAATAAAAAAAGAAGAAA
Found at i:12308741 original size:9 final size:8
Alignment explanation
Indices: 12308713--12308744 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
12308703 TTGGCATTTG
12308713 TATTTAAA
1 TATTTAAA
12308721 TATTTAAA
1 TATTTAAA
12308729 TATTTATAA
1 TATTTA-AA
12308738 TATTTAA
1 TATTTAA
12308745 TTTATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TATTTAAA
Found at i:12308741 original size:17 final size:16
Alignment explanation
Indices: 12308713--12308744 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12308703 TTGGCATTTG
12308713 TATTTAAATATTTAAA
1 TATTTAAATATTTAAA
12308729 TATTTATAATATTTAA
1 TATTTA-AATATTTAA
12308745 TTTATGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTAAATATTTAAA
Found at i:12309516 original size:17 final size:18
Alignment explanation
Indices: 12309496--12309542 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12309486 GCAATACATT
12309496 AACTAAAAGAAA-TTA-A
1 AACTAAAAGAAACTTATA
*
12309512 GAACTTAAAGAAACTTATA
1 -AACTAAAAGAAACTTATA
*
12309531 AATTAAAAGAAA
1 AACTAAAAGAAA
12309543 GAAGAGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 11 0.44
18 13 0.52
19 1 0.04
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (18 bp):
AACTAAAAGAAACTTATA
Found at i:12311150 original size:12 final size:12
Alignment explanation
Indices: 12311128--12311159 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12311118 ATCATTATTT
12311128 TTTCC-TTTCCC
1 TTTCCTTTTCCC
12311139 TTTCCTTTTCCC
1 TTTCCTTTTCCC
12311151 TTT-CTTTTC
1 TTTCCTTTTC
12311160 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTCCTTTTCCC
Found at i:12311781 original size:10 final size:10
Alignment explanation
Indices: 12311766--12311790 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12311756 TCTGTTTTGC
12311766 TTTTTTCTTT
1 TTTTTTCTTT
12311776 TTTTTTCTTT
1 TTTTTTCTTT
12311786 TTTTT
1 TTTTT
12311791 GCTTACCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:12317971 original size:82 final size:81
Alignment explanation
Indices: 12317855--12318061 Score: 195
Period size: 81 Copynumber: 2.5 Consensus size: 81
12317845 GTTTATAGGA
* * * * * * *
12317855 TTTACCCATCTCTTGTATCGATTCTTAAGTGATGTGTGATTCATGAAGTCTAAGCAAAGGAAGAG
1 TTTACCCATCCCTTGTTTTGGTTGTTAAGCGATGTGTGATTCATGAAGTCT-AGCAAAGGAAGAA
12317920 GAAAGGAATTTAT-AAG
65 GAAAGGAATTTATAAAG
* * * * * * * *
12317936 CTTTACCTATCCTTTTTTTTTGTTGTTAAGCGATGTAG-GATTCAAGATGTGTAGCCAAGGAAGA
1 -TTTACCCATCCCTTGTTTTGGTTGTTAAGCGATGT-GTGATTCATGAAGTCTAGCAAAGGAAGA
**
12318000 AGATGGGAATTTATAAAG
64 AGAAAGGAATTTATAAAG
*
12318018 TTTACCCATCCCTTGTTTTGGTTGTTCAA-CAATGTGTGATTCAT
1 TTTACCCATCCCTTGTTTTGGTTGTT-AAGCGATGTGTGATTCAT
12318062 TGTGTAGGCA
Statistics
Matches: 98, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
80 1 0.01
81 55 0.56
82 41 0.42
83 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (81 bp):
TTTACCCATCCCTTGTTTTGGTTGTTAAGCGATGTGTGATTCATGAAGTCTAGCAAAGGAAGAAG
AAAGGAATTTATAAAG
Found at i:12318297 original size:15 final size:16
Alignment explanation
Indices: 12318277--12318310 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12318267 TTTATGTCAT
*
12318277 ATATAATTTTTA-ATG
1 ATATAAATTTTATATG
12318292 ATATAAATTTTATATG
1 ATATAAATTTTATATG
12318308 ATA
1 ATA
12318311 ATTTGTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATATAAATTTTATATG
Found at i:12328286 original size:48 final size:48
Alignment explanation
Indices: 12328231--12328327 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
12328221 ATTATGGTAA
** *
12328231 GAAAGGTTATTGGAAGAGGAATTACAAGGTCTACTTAGCAAGCTTGAT
1 GAAAGGTTATTAAAAGAGGAATTACAAAGTCTACTTAGCAAGCTTGAT
* * *
12328279 GAAAGGTTATTAAAATAGGACTTGCAAAGTCTACTTAGCAAGCTTGAT
1 GAAAGGTTATTAAAAGAGGAATTACAAAGTCTACTTAGCAAGCTTGAT
12328327 G
1 G
12328328 GAGAAAAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (48 bp):
GAAAGGTTATTAAAAGAGGAATTACAAAGTCTACTTAGCAAGCTTGAT
Found at i:12335141 original size:11 final size:13
Alignment explanation
Indices: 12335101--12335142 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
12335091 ATTAAAATAA
*
12335101 TTTAAAAATAATT
1 TTTAATAATAATT
12335114 TTTAATAATTAATT
1 TTTAATAA-TAATT
12335128 TTTAATAA-AATT
1 TTTAATAATAATT
12335140 TTT
1 TTT
12335143 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 7 0.26
13 7 0.26
14 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTAATAATAATT
Found at i:12339643 original size:19 final size:19
Alignment explanation
Indices: 12339612--12339668 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
12339602 TTATTTTTAT
12339612 TATA-AAATAAAATTAAAAA
1 TATATAAAT-AAATTAAAAA
*
12339631 TATATAAATAAATATAAAAT
1 TATATAAATAAAT-TAAAAA
* *
12339651 TAAAT-AATTAATTAAAAA
1 TATATAAATAAATTAAAAA
12339669 ATAATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 14 0.44
20 13 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TATATAAATAAATTAAAAA
Found at i:12339648 original size:20 final size:20
Alignment explanation
Indices: 12339612--12339671 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
12339602 TTATTTTTAT
12339612 TATA-AAATAAA-ATTAAAAA
1 TATATAAATAAATA-TAAAAA
*
12339631 TATATAAATAAATATAAAAT
1 TATATAAATAAATATAAAAA
* * *
12339651 TAAATAATTAATTA-AAAAA
1 TATATAAATAAATATAAAAA
12339670 TA
1 TA
12339672 ATTTTTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.29
20 23 0.68
21 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TATATAAATAAATATAAAAA
Found at i:12340775 original size:21 final size:22
Alignment explanation
Indices: 12340735--12340783 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12340725 ATAAAAATAA
* *
12340735 AATAATAATTTTTAATTAAAAT
1 AATAAAAATATTTAATTAAAAT
12340757 AATAAAAATATTT-ATTAAAAT
1 AATAAAAATATTTAATTAAAAT
12340778 -ATAAAA
1 AATAAAA
12340784 CTTAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAAAATATTTAATTAAAAT
Found at i:12345546 original size:94 final size:95
Alignment explanation
Indices: 12345366--12345555 Score: 292
Period size: 94 Copynumber: 2.0 Consensus size: 95
12345356 CAAGAAAAGC
* * * *
12345366 TTTAGCGAGGTCCTTCCAAGAATGTATATGACTCCTATCCAATTGAATGTATCACCTAGTTGTAG
1 TTTAGCGAGGTCCTTCCAAGAATGTATACGACTCCTATCCAATTGAATATACCACCCAGTTGTAG
* *
12345431 ACCCAATGAGACTATGTTAGAAATAGTGGA
66 ACCAAATGAAACTATGTTAGAAATAGTGGA
*
12345461 TTTAGCGAGGTCCTTCCAAGAATGTATACGACTTCTAT-CAATTGAATATACCACCCAGTTGTAG
1 TTTAGCGAGGTCCTTCCAAGAATGTATACGACTCCTATCCAATTGAATATACCACCCAGTTGTAG
* *
12345525 ACCAAATGAAATTGTGTTAGAAATAGTGGA
66 ACCAAATGAAACTATGTTAGAAATAGTGGA
12345555 T
1 T
12345556 CAAAAGCTTA
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 50 0.58
95 36 0.42
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
TTTAGCGAGGTCCTTCCAAGAATGTATACGACTCCTATCCAATTGAATATACCACCCAGTTGTAG
ACCAAATGAAACTATGTTAGAAATAGTGGA
Found at i:12350510 original size:23 final size:23
Alignment explanation
Indices: 12350480--12350526 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12350470 TAAACGGTTA
12350480 AAGTGTAGAAAAACCTATGGGTG
1 AAGTGTAGAAAAACCTATGGGTG
12350503 AAGTGTAGAAAAACCTATGGGTG
1 AAGTGTAGAAAAACCTATGGGTG
12350526 A
1 A
12350527 CGAGAATGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (23 bp):
AAGTGTAGAAAAACCTATGGGTG
Found at i:12351144 original size:14 final size:14
Alignment explanation
Indices: 12351122--12351167 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
12351112 TATTATTTTT
*
12351122 ATTATAAATATAAA
1 ATTAAAAATATAAA
12351136 ATTAAAAATATATAA
1 ATTAAAAATATA-AA
12351151 A-T--AAATATAAA
1 ATTAAAAATATAAA
12351162 ATTAAA
1 ATTAAA
12351168 TAATTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
14 13 0.48
15 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAAAATATAAA
Found at i:12351156 original size:12 final size:12
Alignment explanation
Indices: 12351126--12351169 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
12351116 ATTTTTATTA
12351126 TAAATATAAAAT
1 TAAATATAAAAT
12351138 TAAAAATATATAAA-
1 T--AAATATA-AAAT
12351152 TAAATATAAAAT
1 TAAATATAAAAT
12351164 TAAATA
1 TAAATA
12351170 ATTAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.11
12 14 0.50
14 8 0.29
15 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:12351161 original size:20 final size:20
Alignment explanation
Indices: 12351124--12351184 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
12351114 TTATTTTTAT
*
12351124 TATAAATATAAAATTAAAAATA
1 TATAAATA-AATA-TAAAAATA
*
12351146 TATAAATAAATATAAAATTA
1 TATAAATAAATATAAAAATA
* * *
12351166 AATAATTAATTA-AAAAATA
1 TATAAATAAATATAAAAATA
12351185 ATTTTTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.18
20 16 0.48
21 3 0.09
22 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAATAAATATAAAAATA
Found at i:12352289 original size:21 final size:22
Alignment explanation
Indices: 12352249--12352298 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
12352239 ATAAAAATAA
* *
12352249 AATAATAATTTTTAATTAAAAT
1 AATAAAAATATTTAATTAAAAT
12352271 AATAAAAATATTT-ATTAAAAT
1 AATAAAAATATTTAATTAAAAT
12352292 -ATAAAAA
1 AATAAAAA
12352299 CTTAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAAAATATTTAATTAAAAT
Found at i:12352309 original size:18 final size:21
Alignment explanation
Indices: 12352260--12352308 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
12352250 ATAATAATTT
12352260 TTAATTAAAATAATAAAAATA
1 TTAATTAAAATAATAAAAATA
* *
12352281 TTTATTAAAAT-ATAAAAA-C
1 TTAATTAAAATAATAAAAATA
12352300 TTAATTAAA
1 TTAATTAAA
12352309 TTTATGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 7 0.28
21 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAATTAAAATAATAAAAATA
Found at i:12357058 original size:94 final size:95
Alignment explanation
Indices: 12356881--12357070 Score: 283
Period size: 94 Copynumber: 2.0 Consensus size: 95
12356871 CAAGAAAAGC
* * * *
12356881 TTTAGCGAGGTCCTTCCAAGAATATATATGACTCCTATCCAATTGAATGTATCACCTAGTTGTAG
1 TTTAGCGAGGTCCTTCCAAGAATATATACGACTCCTATCCAATTGAATATACCACCCAGTTGTAG
*
12356946 ACCCAATGAGACTATGTTAGAAATAGTGGA
66 ACCCAATGAAACTATGTTAGAAATAGTGGA
* * *
12356976 TTTAGCGAGGTCTTTCCAAGAATGTATACGACTTCTAT-CAATTGAATATACCACCCAGTTGTAG
1 TTTAGCGAGGTCCTTCCAAGAATATATACGACTCCTATCCAATTGAATATACCACCCAGTTGTAG
* *
12357040 ACCCAATGAAATTGTGTTAGAAATAGTGGA
66 ACCCAATGAAACTATGTTAGAAATAGTGGA
12357070 T
1 T
12357071 CAAAAGCTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 51 0.60
95 34 0.40
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
TTTAGCGAGGTCCTTCCAAGAATATATACGACTCCTATCCAATTGAATATACCACCCAGTTGTAG
ACCCAATGAAACTATGTTAGAAATAGTGGA
Found at i:12361969 original size:36 final size:37
Alignment explanation
Indices: 12361919--12361989 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
12361909 CACTTTTATT
*
12361919 TTATAAAAAAAAAATTGTTCAAATTTAAAA-AAATGA
1 TTATAAAAAAAAAATTGTTCAAATTGAAAAGAAATGA
** * *
12361955 TTATAAAATGAAAATTTTTCATATTGAAAAGAAAT
1 TTATAAAAAAAAAATTGTTCAAATTGAAAAGAAAT
12361990 TTCTAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (37 bp):
TTATAAAAAAAAAATTGTTCAAATTGAAAAGAAATGA
Found at i:12364581 original size:148 final size:143
Alignment explanation
Indices: 12364227--12364573 Score: 356
Period size: 148 Copynumber: 2.4 Consensus size: 143
12364217 GATTTTAAAA
* * * ** *
12364227 CACCAAAAATCATGAAATATTTTAAAATTGGGATCTAAAAAGTTTTATGAAAATTCAAGCTTGGA
1 CACCAAAAATCATGAAACATTATGAAATTAAGATCTAAAAAGTTTTATGAAAATT-AAGC-TCGA
* * * * * *
12364292 AAGTTCAAATTATGAAAATACTTTTATAGGGGTATTTTGATAATTTCATATTTTTCGGGGTACTG
64 AAGGTCAAATCATAAAAATACTTTTATAGGGGTATTTTGATAATTTCACATTTTTCAGGATACTG
12364357 CTATGATTTCAAATG
129 CTATGATTTCAAATG
* * * * * * * *
12364372 CACCAAAAATCATGAAATATTATGACATTAAAAGCTGAAAGGTTTTATGAAATTTTTAGCTCGAT
1 CACCAAAAATCATGAAACATTATGAAATTAAGATCTAAAAAGTTTTATGAAA-ATTAAGCTCGA-
*
12364437 AAGGTCAAATCATAAAAATACCCTTTTTATAGGGGTATTTTGATAATTTTACACTTTTT-AGGAT
64 AAGGTCAAATCATAAAAATA--C-TTTTATAGGGGTATTTTGATAATTTCACA-TTTTTCAGGAT
* *
12364501 A-TGATTGTGATTTCAAATG
125 ACTG-CTATGATTTCAAATG
* * * *
12364520 CACTAAAACTTATGAAACATTATGAAATTAAGATCTAAAAAGTTTCATGAAAAT
1 CACCAAAAATCATGAAACATTATGAAATTAAGATCTAAAAAGTTTTATGAAAAT
12364574 CTGAGCTCAG
Statistics
Matches: 163, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
144 3 0.02
145 63 0.39
146 2 0.01
147 4 0.02
148 86 0.53
149 5 0.03
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (143 bp):
CACCAAAAATCATGAAACATTATGAAATTAAGATCTAAAAAGTTTTATGAAAATTAAGCTCGAAA
GGTCAAATCATAAAAATACTTTTATAGGGGTATTTTGATAATTTCACATTTTTCAGGATACTGCT
ATGATTTCAAATG
Found at i:12369287 original size:2 final size:2
Alignment explanation
Indices: 12369280--12369314 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12369270 AACCAGGAAA
12369280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12369315 AACTAGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12370876 original size:32 final size:32
Alignment explanation
Indices: 12370840--12370904 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
12370830 TTCCCTTCAC
* *
12370840 TACACAAGATATTTTAAATGCTAACTTCAAAT
1 TACACAAGATATATTAAATGATAACTTCAAAT
*
12370872 TACACAAGATATATTAGATGATAACTTCAAAT
1 TACACAAGATATATTAAATGATAACTTCAAAT
12370904 T
1 T
12370905 TAAAGGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (32 bp):
TACACAAGATATATTAAATGATAACTTCAAAT
Found at i:12373024 original size:47 final size:47
Alignment explanation
Indices: 12372970--12373063 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
12372960 ATGAAAAGGA
* * *
12372970 GAAATAGAAGAATG-GAAAGTAGGATTTTACCGTCACATCCTATAGTC
1 GAAATAGAAGAATGAAAAAG-AGGATTTTACCCTCACATCCTACAGTC
*
12373017 GAAATAGAAGAATGAAAAAGAGGATTTTACCCTCATATCCTACAGTC
1 GAAATAGAAGAATGAAAAAGAGGATTTTACCCTCACATCCTACAGTC
12373064 TTACTTTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 38 0.90
48 4 0.10
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (47 bp):
GAAATAGAAGAATGAAAAAGAGGATTTTACCCTCACATCCTACAGTC
Found at i:12381494 original size:22 final size:23
Alignment explanation
Indices: 12381463--12381507 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
12381453 CATTTTTCTA
12381463 TCTTTGTTCTCATT-TTTTCTTTT
1 TCTTTGTTCTC-TTATTTTCTTTT
12381486 TCTTT-TTCTCTTATTTTCTTTT
1 TCTTTGTTCTCTTATTTTCTTTT
12381508 CATTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.10
22 14 0.67
23 5 0.24
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (23 bp):
TCTTTGTTCTCTTATTTTCTTTT
Found at i:12382963 original size:12 final size:13
Alignment explanation
Indices: 12382915--12382968 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
12382905 CCTGATTCTC
12382915 TAAAAATAAATAA
1 TAAAAATAAATAA
*
12382928 TAAAAA-GAA-AA
1 TAAAAATAAATAA
*
12382939 CAAAAATGAAATAA
1 TAAAAAT-AAATAA
12382953 TAAAAAT-AATAA
1 TAAAAATAAATAA
12382965 TAAA
1 TAAA
12382969 GGAAATAGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 7 0.21
12 11 0.32
13 8 0.24
14 8 0.24
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (13 bp):
TAAAAATAAATAA
Found at i:12384681 original size:18 final size:18
Alignment explanation
Indices: 12384658--12384693 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12384648 TTATTTTAAG
*
12384658 AATTTTTTACATTAATAT
1 AATTTTTAACATTAATAT
*
12384676 AATTTTTAATATTAATAT
1 AATTTTTAACATTAATAT
12384694 TATTATTAAA
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:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTTAACATTAATAT
Found at i:12384702 original size:18 final size:18
Alignment explanation
Indices: 12384668--12384702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12384658 AATTTTTTAC
*
12384668 ATTAATATAATTTTTAAT
1 ATTAATATAATTATTAAT
*
12384686 ATTAATATTATTATTAA
1 ATTAATATAATTATTAA
12384703 AATATAATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTAATATAATTATTAAT
Found at i:12387090 original size:3 final size:3
Alignment explanation
Indices: 12387082--12387122 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
12387072 TGATTTGATT
12387082 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T
12387123 TGTTAACAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12387873 original size:21 final size:20
Alignment explanation
Indices: 12387834--12387873 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12387824 TGGACAGGAA
* *
12387834 AGAAAGATGGGAGGGAAGGT
1 AGAAAGATGGAAAGGAAGGT
12387854 AGAAAGATTGGAAAGGAAGG
1 AGAAAGA-TGGAAAGGAAGG
12387874 GAATGGGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.10
Consensus pattern (20 bp):
AGAAAGATGGAAAGGAAGGT
Found at i:12389262 original size:21 final size:21
Alignment explanation
Indices: 12389236--12389276 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12389226 TCTATTCTAG
* *
12389236 CACGTTGCTCTTAAATTTTAC
1 CACGTTCCTCTTAAAATTTAC
12389257 CACGTTCCTCTTAAAATTTA
1 CACGTTCCTCTTAAAATTTA
12389277 GCACATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (21 bp):
CACGTTCCTCTTAAAATTTAC
Found at i:12390345 original size:161 final size:160
Alignment explanation
Indices: 12390005--12392641 Score: 2387
Period size: 161 Copynumber: 16.4 Consensus size: 160
12389995 CAGTTTACCC
* * *
12390005 TTTCACACATATCAATCGTGAAAACCAAGTTCAATCATT-TAGACAAGTTTAATATTATGTATTA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGA-ACAAGTTTAATATCATGTATT-
* * * * *
12390069 AAGCTATCCAAACTGTTAAAATAAAACATTAAGTTTATGCAAATTTGCATTTTTATCTTTTAATG
64 AAGCTATCCAAACTATTAAAATAGAACAATAA---TA-GCAAATTTGCATTTTTACCTTTTAACG
* * *
12390134 GCACAAAAA-TTCCTAAACAGAGGTAAATAATAACTT
125 GCACAAAAAGCT-CTAAATAGAGGTAAACAATAACTT
* * * * *
12390170 TTTCACATATATCAACCGTGAAAACTAAGTTTAATCGTTCGAACAATTTTAATATCATGTATGTA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTAT-TA
** * ** ** **
12390235 AGCTATCCAAACTATTAAAGCAGAACAATAACAATAAATTTATATTTTTACCTTTTAATAGCACA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* * *
12390300 AAAAGCTTTACATAGATGTAAACAATAACTT
130 AAAAGCTCTAAATAGAGGTAAACAATAACTT
* * * * * *
12390331 TTTCACACATATCAACCATGAAAACCAAGTTTAATTATTC-AGACAAGTTTAATATCATATGCTG
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGA-ACAAGTTTAATATCATGT-ATT
* * * * * * *
12390395 AACCTATACAAACTGTTAAAATAGAACAATAGTAGCAAATTTACATTTTTGCCTTTTAACGGCAT
64 AAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCAC
* *
12390460 AAAAAG-TCCTAAATAAAGGTAAAAAATAACTT
129 AAAAAGCT-CTAAATAGAGGTAAACAATAACTT
** * * *
12390492 TTTCACACATATCAATTGT-AGAAACTAAGTTCAATCATTCAAACAAGTTTAAAATCATGTATTT
1 TTTCACACATATCAACCGTGA-AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTA-TT
* * * * * *
12390556 AAGCTATCCAAACTGTTAAAATAGAACAATAACAGTAAATTT-CTTTTTTTACTTTTTAACAGCA
64 AAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGC-ATTTTTACCTTTTAACGGCA
* * * * **
12390620 TAAAAAGC-CTTACACAGACGTAAATGATAACTT
128 CAAAAAGCTC-TAAATAGAGGTAAACAATAACTT
* * * * * *
12390653 TTTCACACATATCGATCGTGGAAACCAAGTTCAATCTTTCGAATAAGTTTAATATCATGTGTTAA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATT-A
* * * * * * *
12390718 AACTATCCAAACTGTTAAAATAGATCAATAATAGCAAAATTGTATTTTTGCCTTTTAATGGCACA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* * * * *
12390783 AAAAG-TCCTAAACAAAAAGTAAATAGTAA-TT
130 AAAAGCT-CTAAA-TAGAGGTAAACAATAACTT
* * * * **
12390814 TTTCACACATGTCAATCGT-AGAAACTAAATTCAATC-TTTTAGACAAGTTTAATATCATGTATT
1 TTTCACACATATCAACCGTGA-AAACCAAGTTCAATCATTCGA-ACAAGTTTAATATCATGTATT
* * * * *
12390877 GAAGCTATCTAAACTATTAAAATAGAATAATAATAGCAAATTTACATTTTTACCTTTTAACAGTA
64 -AAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCA
* * **
12390942 TAAAAA-ATCCTAAATAGAGGTAAA-TGTAACTT
128 CAAAAAGCT-CTAAATAGAGGTAAACAATAACTT
* * * * * *
12390974 TTTCACATATATCAATCGT-AGAAATCAAATTCAATCATTCGAATAAGTTTAATATCATATATAT
1 TTTCACACATATCAACCGTGA-AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTAT-T
* * * * *
12391038 AAGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGTATTTTTACCTTTTAACAGCAC
64 AAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCAC
* * *
12391103 AAAAAAGCCCTAAACAGAGGTAAACAGTAACTT
129 -AAAAAGCTCTAAATAGAGGTAAACAATAACTT
* * * * * *
12391136 TTTTACAC--ATCAACCATAAAAATCAAGTTCAATTATTCAAACAAGTTTAATATCATGTATGTA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTAT-TA
* * * *
12391199 AGCTATCCAAACTATTAAAATAGAATAATAATAGCAATTTTGCATTTTTGCTTTTTAACGGCACA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* * * *
12391264 AAAAGC-CATACACAAACGTAAACAATAACTT
130 AAAAGCTC-TAAATAGAGGTAAACAATAACTT
* * * * *
12391295 TTTCACAGATATCAACCGTGGAAACCAAGTTTAATCATTCGAATAAGTTTAATATCATGTACTAA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTA-TTA
* * * * * * * * * *
12391360 AGCTATCCAAACTGTTAAAAAAGAACAGTAACATCATATTTGTATTTTTGCCTTTTAACGACATA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* *
12391425 AAAA-ATCCTAAATAGAGGTAAACAACAACTT
130 AAAAGCT-CTAAATAGAGGTAAACAATAACTT
* *
12391456 TTTCACACACATATCAACTGTGAAAACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATA
1 TTT--CACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTAT-
* * * * *
12391521 TAAGCTATCCACACTGTTAAAATAAAACAATAATAGCAATTTTGCATTTTAACCTTTTAACGGCA
63 TAAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCA
* *
12391586 TAAAAAG-TCTTAAATAGAGGTAAACAGTAACTT
128 CAAAAAGCTC-TAAATAGAGGTAAACAATAACTT
* ** * * * *
12391619 TTTTACACATATCAACTATAAAAACCCAGTTCAATCATTCAAACAAGTTTAATATGATGTATGTA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTAT-TA
* * ** * *
12391684 AGCTATCCAAACTATTAAAATAGAATAATAACAATAGATTTGCATTTTGT--CTTTTAACGGCAT
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTT-TACCTTTTAACGGCAC
** * * * ** *
12391747 TGAAAGCCCTACATAGACGTAAATGACAACTT
129 AAAAAGCTCTAAATAGAGGTAAACAATAACTT
** * * *
12391779 TTTCACACATATCAACTATGAAAATCAAGTTCAATCATTCGGATAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATT-A
* * * * * * *
12391844 AGCTATCAAAACTGTTAAAACAGAACAATAACAACAAATTTGTATTTTTACCTTTTAACGGCATA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* *
12391909 AAAAG-TCATAAACAAAGGTAAAC-ATCAACTT
130 AAAAGCTC-TAAATAGAGGTAAACAAT-AACTT
** * *
12391940 TTTCACACATATCAATTGTGAAAACCAAGTTCAATCATTCGAAAAAGTTTAATATTATGTATTTA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTA-TTA
* * * * ** * * *
12392005 AGCTATCCAAACTATTAAAACAAAACAATAATAGTAAATTTGCATTTATGTCTTTTAATGACATA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* * ** ** *
12392070 AAATG-TCATAAATAAACCTAAATGATAACCT
130 AAAAGCTC-TAAATAGAGGTAAACAATAACTT
** * *
12392101 TTTCACACATATCAACAATGAAAACCAAGTTCAATCATTTGAACAAGTTTAATATCATATATTGA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATT-A
* * * * * * * * * *
12392166 AGCTATTCAAACTATTAAAACAAAATAGTAATAACAAATTCGTATTTTTTTCCTTTTAACGGCAT
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCA-TTTTTACCTTTTAACGGCAC
* * * * * ** *
12392231 AAAAAGCCCTACACAAATGTAAATGACAACTT
129 AAAAAGCTCTAAATAGAGGTAAACAATAACTT
* * **
12392263 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAAACAAGTTTAATATGC-TAAATTG
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATAT-CATGTATT-
*
12392327 AAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGTATTTTTACCTTTTAACGGCAC
64 AAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCAC
* * *
12392392 -AAAAG-TCTAACATAGACGTATATAATAACTT
129 AAAAAGCTCTAA-ATAGAGGTAAACAATAACTT
* * * * *
12392423 TTTCACACGTATCAATCGTAAAAACTAAGTTTAATCATTCGAACAAGTTTAATATCATGTATTTA
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTA-TTA
* ** * * * * *
12392488 AACTATTGAAACTGTTAAAATAAAACAATAATAGCAAATTTGCATTTTTACCGTTTAACAGCATA
65 AGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACA
* * *
12392553 AAAAG-TCATAAATAAACGTAAACGATAACTT
130 AAAAGCTC-TAAATAGAGGTAAACAATAACTT
* * * *
12392584 TTTCACACATATCAACCATGAAAATCAAGTTCAATTATTTGAACAAGTTTAATATCAT
1 TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCAT
12392642 AAACTTACTT
Statistics
Matches: 2039, Mismatches: 376, Indels: 118
0.80 0.15 0.05
Matches are distributed among these distances:
158 1 0.00
159 42 0.02
160 488 0.24
161 1118 0.55
162 172 0.08
163 137 0.07
165 79 0.04
166 2 0.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (160 bp):
TTTCACACATATCAACCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTAA
GCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGCATTTTTACCTTTTAACGGCACAA
AAAGCTCTAAATAGAGGTAAACAATAACTT
Found at i:12392484 original size:644 final size:642
Alignment explanation
Indices: 12389859--12392641 Score: 2790
Period size: 644 Copynumber: 4.3 Consensus size: 642
12389849 AAGTACGGTT
* * * ** *
12389859 ATCAAGTTCAAACATTCAGACAAGTTTAATATCATGTA-TG-AGTTATTTAAACTGTTAAAACA-
1 ATCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATAG
* * * * * * *
12389921 AAAACATAACTA-TAAAATTATATTTTTATCC-TTTAACAGCATAAAAAGTCCTAAATAAACATA
66 AACA-ATAAC-AGCAAATTTGTATTTTTA-CCTTTTAACAGCATAAAAAGTCATAAACAAACGTA
*
12389984 AACAATAACAACAGTTTACCCTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATT-TAGA
128 AACAAT---AAC---TT----TTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCGA-A
* *
12390048 CAAGTTTAATATTATGTATTAAAGCTATCCAAACTGTTAAAATAAAACATTAAGTTTATGCAAAT
182 CAAGTTTAATATCATGTATTAAAGCTATCCAAACTGTTAAAATAAAACAATAA---TA-GCAAAT
** * * * * * *
12390113 TTGCATTTTTATCTTTTAATGGCACAAAAATTCCTAAACAGAGGTAAATAATAACTTTTTCACAT
243 TTGCATTTTTGCCTTTTAATGACATAAAAAGTCCTAAATAAAGGTAAATAATAACTTTTTCACAC
* * * *
12390178 ATATCAACCGTGAAAACTAAGTTTAATCGTTCGAACAATTTTAATATCATGTA-TGTAAGCTATC
308 ATATCAA-CGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTG-AAGCTATC
* * * * * * *
12390242 CAAACTATTAAAGCAGAACAATAACAATAAATTTATATTTTTACCTTTTAATAGCACAAAAAGCT
371 CAAACTATTAAAACAAAACAATAATAACAAATTTAT-TTTTTACCTTTTAACAGCATAAAAAGCC
* * * ** * * *
12390307 TTACATAGATGTAAACAATAACTTTTTCACACATATCAACCATGAAAACCAAGTTTAATTATTCA
435 CTAAATAGAGGTAAATGATAACTTTTTCACACATATCAACTATGAAAACCAAGTTCAATCATTCA
* * * * * ** *
12390372 GACAAGTTTAATATC-ATATGCTGAACCTATACAAACTGTTAAAATAGAACAATAGTAGCAAATT
500 AACAAGTTTAATATCTATAT-ATGAAGCTATCCAAACTATTAAAATAGAACAATAACAACAAATT
* * * * * * *
12390436 TACATTTTTGCCTTTTAACGGCATAAAAAGTCCTAAATAAAGGTAAAAAATAACTTTTTCACACA
564 TGCATTTTTACCTTTTAACGGCATCAAAAGCCCTAAATAGACGTAAATAATAACTTTTTCACACA
* *
12390501 TATCAATTGTAGAA
629 TATCAATCGTAAAA
* *
12390515 A-CTAAGTTCAATCATTCAAACAAGTTTAAAATCATGTATTTAAGCTATCCAAACTGTTAAAATA
1 ATC-AAGTTCAATCATTCAAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATA
* * * * * * * *
12390579 GAACAATAACAGTAAATTTCTTTTTTTACTTTTTAACAGCATAAAAAGCCTTACACAGACGTAAA
65 GAACAATAACAGCAAATTTGTATTTTTACCTTTTAACAGCATAAAAAGTCATAAACAAACGTAAA
** * * * *
12390644 TGATAACTTTTTCACACATATCGATCGTGGAAACCAAGTTCAATCTTTCGAATAAGTTTAATATC
130 CAATAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATC
* * * * * *
12390709 ATGTGTTAAAACTATCCAAACTGTTAAAATAGATCAATAATAGCAAAATTGTATTTTTGCCTTTT
195 ATGTATTAAAGCTATCCAAACTGTTAAAATAAAACAATAATAGCAAATTTGCATTTTTGCCTTTT
* * * * * *
12390774 AATGGCACAAAAAGTCCTAAACAAAAAGTAAATAGTAA-TTTTTCACACATGTCAATCGT-AGAA
260 AATGACATAAAAAGTCCTAAA-TAAAGGTAAATAATAACTTTTTCACACATATCAA-CGTGA-AA
* * ** * *
12390837 ACTAAATTCAATC-TTTTAGACAAGTTTAATATCATGTATTGAAGCTATCTAAACTATTAAAATA
322 ACCAAGTTCAATCATTCGA-ACAAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAACA
* * * * * **
12390901 GAATAATAATAGCAAATTTACATTTTTACCTTTTAACAGTATAAAAAATCCTAAATAGAGGTAAA
386 AAACAATAATAACAAATTTA-TTTTTTACCTTTTAACAGCATAAAAAGCCCTAAATAGAGGTAAA
* * * * *
12390966 TG-TAACTTTTTCACATATATCAATCGTA-G-AAATCAAATTCAATCATTCGAATAAGTTTAATA
450 TGATAACTTTTTCACACATATCAA-C-TATGAAAACCAAGTTCAATCATTCAAACAAGTTTAATA
* *
12391028 TCATATATAT-AAGCTATCCAAACTATTAAAATAGAATAATAACAACAAATTTGTATTTTTACCT
513 TC-TATATATGAAGCTATCCAAACTATTAAAATAGAACAATAACAACAAATTTGCATTTTTACCT
* * * * * * * *
12391092 TTTAACAGCA-CAAAAAAGCCCTAAACAGAGGTAAACAGTAACTTTTTTACAC--ATCAACCATA
577 TTTAACGGCATC--AAAAGCCCTAAATAGACGTAAATAATAACTTTTTCACACATATCAATCGTA
12391154 AAA
640 AAA
* *
12391157 ATCAAGTTCAATTATTCAAACAAGTTTAATATCATGTA-TGTAAGCTATCCAAACTATTAAAATA
1 ATCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTG-AAGCTATCCAAACTGTTAAAATA
* * * * * * * * * *
12391221 GAATAATAATAGCAATTTTGCATTTTTGCTTTTTAACGGCACAAAAAGCCATACACAAACGTAAA
65 GAACAATAACAGCAAATTTGTATTTTTACCTTTTAACAGCATAAAAAGTCATAAACAAACGTAAA
* * * * *
12391286 CAATAACTTTTTCACAGATATCAACCGTGGAAACCAAGTTTAATCATTCGAATAAGTTTAATATC
130 CAATAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATC
* * * * * *
12391351 ATGTACTAAAGCTATCCAAACTGTTAAAA-AAGAACAGTAACATCATATTTGTATTTTTGCCTTT
195 ATGTATTAAAGCTATCCAAACTGTTAAAATAA-AACAATAATAGCAAATTTGCATTTTTGCCTTT
* * * * *
12391415 TAACGACATAAAAAATCCTAAATAGAGGTAAACAACAACTTTTTCACACACATATCAACTGTGAA
259 TAATGACATAAAAAGTCCTAAATAAAGGTAAATAATAACTTTTT--CACACATATCAAC-GTGAA
* * * *
12391480 AACCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATAT-AAGCTATCCACACTGTTAAAAT
321 AACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTAT-TGAAGCTATCCAAACTATTAAAAC
* * * * * *
12391544 AAAACAATAATAGCAATTTTGCA-TTTTAACCTTTTAACGGCATAAAAAGTCTTAAATAGAGGTA
385 AAAACAATAATAACAAATTT--ATTTTTTACCTTTTAACAGCATAAAAAGCCCTAAATAGAGGTA
* * * *
12391608 AA-CAGTAACTTTTTTACACATATCAACTATAAAAACCCAGTTCAATCATTCAAACAAGTTTAAT
448 AATGA-TAACTTTTTCACACATATCAACTATGAAAACCAAGTTCAATCATTCAAACAAGTTTAAT
* * * * *
12391672 AT-GATGTATGTAAGCTATCCAAACTATTAAAATAGAATAATAACAATAGATTTGCATTTTGT--
512 ATCTATATATG-AAGCTATCCAAACTATTAAAATAGAACAATAACAACAAATTTGCATTTT-TAC
** * * *
12391734 CTTTTAACGGCATTGAAAGCCCTACATAGACGTAAATGACAACTTTTTCACACATATCAA-C-TA
575 CTTTTAACGGCATCAAAAGCCCTAAATAGACGTAAATAATAACTTTTTCACACATATCAATCGTA
12391797 TGAAA
640 --AAA
** * * *
12391802 ATCAAGTTCAATCATTCGGATAAGTTTAATATCATGTATTGAAGCTATCAAAACTGTTAAAACAG
1 ATCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATAG
* * *
12391867 AACAATAACAACAAATTTGTATTTTTACCTTTTAACGGCATAAAAAGTCATAAACAAAGGTAAAC
66 AACAATAACAGCAAATTTGTATTTTTACCTTTTAACAGCATAAAAAGTCATAAACAAACGTAAAC
* * *
12391932 -ATCAACTTTTTCACACATATCAATTGTGAAAACCAAGTTCAATCATTCGAAAAAGTTTAATATT
131 AAT-AACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATC
* * * * * *
12391996 ATGTATTTAAGCTATCCAAACTATTAAAACAAAACAATAATAGTAAATTTGCATTTATGTCTTTT
195 ATGTATTAAAGCTATCCAAACTGTTAAAATAAAACAATAATAGCAAATTTGCATTTTTGCCTTTT
* * ** * * *
12392061 AATGACATAAAATGTCATAAATAAACCTAAATGATAACCTTTTCACACATATCAACAATGAAAAC
260 AATGACATAAAAAGTCCTAAATAAAGGTAAATAATAACTTTTTCACACATATCAAC-GTGAAAAC
* * *
12392126 CAAGTTCAATCATTTGAACAAGTTTAATATCATATATTGAAGCTATTCAAACTATTAAAACAAAA
324 CAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAACAAAA
* * * * * * * *
12392191 TAGTAATAACAAATTCGTATTTTTTTCCTTTTAACGGCATAAAAAGCCCTACACAAATGTAAATG
389 CAATAATAACAAATT--TATTTTTTACCTTTTAACAGCATAAAAAGCCCTAAATAGAGGTAAATG
* *
12392256 ACAACTTTTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTCAAACAAGTTTAATATGCT
452 ATAACTTTTTCACACATATCAACTATGAAAACCAAGTTCAATCATTCAAACAAGTTTAATAT-CT
* * * *
12392321 AAAT-TGAAGCTATCCAAACTATTAAAATAGAACAATAATAGCAAATTTGTATTTTTACCTTTTA
516 ATATATGAAGCTATCCAAACTATTAAAATAGAACAATAACAACAAATTTGCATTTTTACCTTTTA
* * *
12392385 ACGGCA-CAAAAG-TCTAACATAGACGTATATAATAACTTTTTCACACGTATCAATCGTAAAA
581 ACGGCATCAAAAGCCCTAA-ATAGACGTAAATAATAACTTTTTCACACATATCAATCGTAAAA
* * * * **
12392446 A-CTAAGTTTAATCATTCGAACAAGTTTAATATCATGTATTTAAACTATTGAAACTGTTAAAATA
1 ATC-AAGTTCAATCATTCAAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATA
* * * * *
12392510 AAACAATAATAGCAAATTTGCATTTTTACCGTTTAACAGCATAAAAAGTCATAAATAAACGTAAA
65 GAACAATAACAGCAAATTTGTATTTTTACCTTTTAACAGCATAAAAAGTCATAAACAAACGTAAA
* * * * * *
12392575 CGATAACTTTTTCACACATATCAACCATGAAAATCAAGTTCAATTATTTGAACAAGTTTAATATC
130 CAATAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATC
12392640 AT
195 AT
12392642 AAACTTACTT
Statistics
Matches: 1769, Mismatches: 299, Indels: 130
0.80 0.14 0.06
Matches are distributed among these distances:
641 12 0.01
642 252 0.14
643 239 0.14
644 668 0.38
645 393 0.22
646 10 0.01
648 83 0.05
649 1 0.00
652 2 0.00
655 4 0.00
656 33 0.02
657 3 0.00
658 66 0.04
659 3 0.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (642 bp):
ATCAAGTTCAATCATTCAAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAATAG
AACAATAACAGCAAATTTGTATTTTTACCTTTTAACAGCATAAAAAGTCATAAACAAACGTAAAC
AATAACTTTTTCACACATATCAATCGTGAAAACCAAGTTCAATCATTCGAACAAGTTTAATATCA
TGTATTAAAGCTATCCAAACTGTTAAAATAAAACAATAATAGCAAATTTGCATTTTTGCCTTTTA
ATGACATAAAAAGTCCTAAATAAAGGTAAATAATAACTTTTTCACACATATCAACGTGAAAACCA
AGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTATTAAAACAAAACA
ATAATAACAAATTTATTTTTTACCTTTTAACAGCATAAAAAGCCCTAAATAGAGGTAAATGATAA
CTTTTTCACACATATCAACTATGAAAACCAAGTTCAATCATTCAAACAAGTTTAATATCTATATA
TGAAGCTATCCAAACTATTAAAATAGAACAATAACAACAAATTTGCATTTTTACCTTTTAACGGC
ATCAAAAGCCCTAAATAGACGTAAATAATAACTTTTTCACACATATCAATCGTAAAA
Found at i:12393787 original size:13 final size:13
Alignment explanation
Indices: 12393766--12393802 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
12393756 ATAACAAATG
*
12393766 ATATATAAAGAAT
1 ATATATAAAGAAC
*
12393779 ATATCTAAAGAAC
1 ATATATAAAGAAC
12393792 ATATATAAAGA
1 ATATATAAAGA
12393803 CATCGAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:12398759 original size:31 final size:29
Alignment explanation
Indices: 12398720--12398794 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
12398710 GATATAACAT
12398720 TATA-ATGAATATAAAAATAATATGAAAAAA
1 TATATATGAATATAAAAATAAT-T-AAAAAA
* *
12398750 TATATATGAATGA-AAAATTAATTATAAAA
1 TATATATGAAT-ATAAAAATAATTAAAAAA
12398779 TATATAT-ATATATAAA
1 TATATATGA-ATATAAA
12398795 TTTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 2 0.05
29 17 0.44
30 5 0.13
31 14 0.36
32 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (29 bp):
TATATATGAATATAAAAATAATTAAAAAA
Found at i:12398799 original size:29 final size:27
Alignment explanation
Indices: 12398745--12398807 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
12398735 AATAATATGA
12398745 AAAAATATATATGAATGAAAAATTAATT
1 AAAAATATATATGAATGAAAAATTAA-T
*
12398773 ATAAAATATATAT-ATAT-ATAAATTTAAT
1 A-AAAATATATATGA-ATGA-AAAATTAAT
12398801 AAAAATA
1 AAAAATA
12398808 AAAAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 20 0.65
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAAATATATATGAATGAAAAATTAAT
Found at i:12399144 original size:2 final size:2
Alignment explanation
Indices: 12399137--12399169 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12399127 AGGGATTGGA
12399137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12399170 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12399174 original size:2 final size:2
Alignment explanation
Indices: 12399169--12399197 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12399159 ATATATATAT
12399169 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12399198 TTCATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12400299 original size:29 final size:29
Alignment explanation
Indices: 12400257--12400316 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12400247 AAATCTGTAC
12400257 TTTCTGCTTTATTTGGGGTTTGTCGTATA
1 TTTCTGCTTTATTTGGGGTTTGTCGTATA
12400286 TTTCTGCTTTATTTGGGGTTTGTCGTATA
1 TTTCTGCTTTATTTGGGGTTTGTCGTATA
12400315 TT
1 TT
12400317 GTAAACTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (29 bp):
TTTCTGCTTTATTTGGGGTTTGTCGTATA
Found at i:12404444 original size:6 final size:6
Alignment explanation
Indices: 12404411--12404489 Score: 58
Period size: 6 Copynumber: 13.0 Consensus size: 6
12404401 TTATTCTCAA
*
12404411 ATTTTT -TTATT A-TTTT A-TTTT A-TTTT ATTTTT ATTAAATTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT---TTT ATTTTT
* *
12404458 ATTTTT ATTTTT AAATTTTA AATTTT ATTTTT
1 ATTTTT ATTTTT --ATTTTT ATTTTT ATTTTT
12404490 GTTAGATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
5 18 0.30
6 31 0.52
8 5 0.08
9 6 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:12404444 original size:21 final size:21
Alignment explanation
Indices: 12404411--12404468 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
12404401 TTATTCTCAA
*
12404411 ATTTT-TTTATTATTTTATTTT
1 ATTTTATTT-TTATTTTAATTT
*
12404432 ATTTTATTTTTA-TTAAATTT
1 ATTTTATTTTTATTTTAATTT
12404452 ATTTTTATTTTTATTTT
1 A-TTTTATTTTTATTTT
12404469 TAAATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.23
21 19 0.61
22 5 0.16
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
ATTTTATTTTTATTTTAATTT
Found at i:12404489 original size:26 final size:26
Alignment explanation
Indices: 12404414--12404489 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
12404404 TTCTCAAATT
* *
12404414 TTTTTAT-TATTTTATTTTA-TTTTA
1 TTTTTATAAATTTAATTTTATTTTTA
*
12404438 TTTTTATTAAATTTATTTTTATTTTTA
1 TTTTTA-TAAATTTAATTTTATTTTTA
*
12404465 TTTTTA-AATTTTAAATTTTATTTTT
1 TTTTTATAAATTT-AATTTTATTTTT
12404490 GTTAGATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.14
25 6 0.14
26 20 0.47
27 11 0.26
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTATAAATTTAATTTTATTTTTA
Found at i:12406080 original size:3 final size:3
Alignment explanation
Indices: 12406072--12406113 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
12406062 TAATAAAGTA
12406072 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
12406114 ATGGGGAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12406738 original size:77 final size:76
Alignment explanation
Indices: 12406624--12406769 Score: 177
Period size: 77 Copynumber: 1.9 Consensus size: 76
12406614 ACTTCAATCT
* * * * * * * *
12406624 ATTGCATTAAAGGGGAAATTTTGATTTTTTTTTTATTCAGTGTAACCATCTGGA-TACTTCTAAT
1 ATTGCATTAAAAGAGAAATTATGATTTGTGTTCTATTCAGT-CAACCATC-CGATTACTTCTAAT
12406688 ATACTTTTGTCTC
64 ATACTTTTGTCTC
* *
12406701 ATTGGATTAAAAGAGAAATTATGATTTGTGTTCTATTCAGTCAACCATCCGATTGCTTCTAATAT
1 ATTGCATTAAAAGAGAAATTATGATTTGTGTTCTATTCAGTCAACCATCCGATTACTTCTAATAT
12406766 ACTT
66 ACTT
12406770 CTACCCCATT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
75 2 0.03
76 22 0.38
77 34 0.59
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (76 bp):
ATTGCATTAAAAGAGAAATTATGATTTGTGTTCTATTCAGTCAACCATCCGATTACTTCTAATAT
ACTTTTGTCTC
Found at i:12410987 original size:125 final size:126
Alignment explanation
Indices: 12410661--12411039 Score: 530
Period size: 127 Copynumber: 3.0 Consensus size: 126
12410651 ATTCTTTGAA
* * * * * * *
12410661 ATAGGAGAGTATGTAATGCTTAATCCTGAAAAAAGCCCAATAGATGTTAAATTGAAAATGTGGTT
1 ATAGG-GAGTATGTAATACTCAATCCTAAAAAAAGCCTAATATATGTTAAATTGGACATGTGGTT
* *
12410726 ATTAGTCTATTAGTTTTATTAGAGTAAAATAAAATAAAAGGAAGAGAAAAGATAAGAAAACCT
65 ATTAGCCTATTAGTTTTATTAGAGTAAAATAAAATAAAAGGAGGAGAAAAGATAAG-AAACCT
* *
12410789 ATAAGGAGTATGTAATACTCAATCCTAAAAAAAGCCTAATCTATGTTAAATTGGACATGTGGTTA
1 ATAGGGAGTATGTAATACTCAATCCTAAAAAAAGCCTAATATATGTTAAATTGGACATGTGGTTA
*
12410854 TTAGCCTATTAGCTTTATTAGAGTAAAATAAAATAAAAGGAGGAGAAAAGATAAGAAACC-
66 TTAGCCTATTAGTTTTATTAGAGTAAAATAAAATAAAAGGAGGAGAAAAGATAAGAAACCT
* * *
12410914 CTAGGGAGTATGTAATACTCAATCTTAAAAAAAGCCTAATATATGTTAAATTGGACATGTGGTCA
1 ATAGGGAGTATGTAATACTCAATCCTAAAAAAAGCCTAATATATGTTAAATTGGACATGTGGTTA
* * * *
12410979 TTAACCTATGAGTTTTATTAAAGTAAAA-AAAATAAAATGAGGTA-AAAAGATAAGACAACCT
66 TTAGCCTATTAGTTTTATTAGAGTAAAATAAAATAAAAGGAGG-AGAAAAGATAAGA-AACCT
12411040 TGAGACATTT
Statistics
Matches: 226, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
124 24 0.11
125 89 0.39
126 5 0.02
127 104 0.46
128 4 0.02
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (126 bp):
ATAGGGAGTATGTAATACTCAATCCTAAAAAAAGCCTAATATATGTTAAATTGGACATGTGGTTA
TTAGCCTATTAGTTTTATTAGAGTAAAATAAAATAAAAGGAGGAGAAAAGATAAGAAACCT
Found at i:12414309 original size:143 final size:143
Alignment explanation
Indices: 12413986--12414309 Score: 336
Period size: 142 Copynumber: 2.3 Consensus size: 143
12413976 TTGAAGTGCG
* * * *
12413986 ATCAAAGTTTTTAATGCATCAAAAATCATATAATAATATGAAAACATGATCTAGAGCGTTTCGTG
1 ATCAAGGTTTTTAATGCATAAAAAATCATAAAATAATATGAAAACATGATCTAGAGCGTTTCATG
* * *
12414051 AAAAACGATCTCGAAATGGTTAAATTATAAAAATACCTCTTCAAAGTGTTTTAATAATTTCATAC
66 AAAAACGATCTCGAAAAGGTTAAATTATAAAAATACCTCTTCAAAGTATTTTAATAATTTCATAA
*
12414116 CTTCTAAGGTGCA
131 CTTCTAAGGTACA
* * * * *
12414129 ATCAAGG-TTTTAATGCATAAAAAAAT-ATTATATAATAT-AAAACCATGATTTGGAGCTTTTCA
1 ATCAAGGTTTTTAATGCAT-AAAAAATCATAAAATAATATGAAAA-CATGATCTAGAGCGTTTCA
* * * * * *
12414191 TGAAAAATTGATCTTGAAAAGGTTAATTTATGAAAATACCTC-T-AAGGTTATTTTGATAATTTC
64 TGAAAAA-CGATCTCGAAAAGGTTAAATTATAAAAATACCTCTTCAAAG-TATTTTAATAATTTC
* **
12414254 A-AACTTCTTGAGGTATG
127 ATAACTTC-TAAGGTACA
* * *
12414271 ATTAAGGTTTTTAATGCATAACAAATCATAAAACAATAT
1 ATCAAGGTTTTTAATGCATAAAAAATCATAAAATAATAT
12414310 TTAAATGTGA
Statistics
Matches: 147, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
141 12 0.08
142 74 0.50
143 61 0.41
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (143 bp):
ATCAAGGTTTTTAATGCATAAAAAATCATAAAATAATATGAAAACATGATCTAGAGCGTTTCATG
AAAAACGATCTCGAAAAGGTTAAATTATAAAAATACCTCTTCAAAGTATTTTAATAATTTCATAA
CTTCTAAGGTACA
Found at i:12415237 original size:12 final size:12
Alignment explanation
Indices: 12415222--12415260 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
12415212 TGCTTTTTTT
12415222 TTTTTATAACAA
1 TTTTTATAACAA
12415234 TTTTTATAA-ATA
1 TTTTTATAACA-A
12415246 TTTTTATAAC-A
1 TTTTTATAACAA
12415257 TTTT
1 TTTT
12415261 AAATTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTATAACAA
Found at i:12415721 original size:14 final size:13
Alignment explanation
Indices: 12415669--12415721 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
12415659 CAATCCAATG
*
12415669 ATTTCTCTTTTCTT
1 ATTT-TCTTTTTTT
*
12415683 -TTTTCTTTTTTC
1 ATTTTCTTTTTTT
*
12415695 ATTTTCATTTTTT
1 ATTTTCTTTTTTT
12415708 ATATTTCTTTTTTT
1 AT-TTTCTTTTTTT
12415722 TCTCTGAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 7 0.22
13 15 0.47
14 10 0.31
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTCTTTTTTT
Found at i:12419935 original size:22 final size:20
Alignment explanation
Indices: 12419910--12419954 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
12419900 GTTAGATATG
*
12419910 TTAGGAGAAGTACTTTTTTATA
1 TTAGGAGAA-TA-TTTTTAATA
*
12419932 TTAGGTGAATATTTTTAATA
1 TTAGGAGAATATTTTTAATA
12419952 TTA
1 TTA
12419955 AAAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 2 0.10
22 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (20 bp):
TTAGGAGAATATTTTTAATA
Done.