Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 12 of 22
Found at i:4872940 original size:55 final size:55
Alignment explanation
Indices: 4872881--4873171 Score: 240
Period size: 55 Copynumber: 5.3 Consensus size: 55
4872871 TGTGACATGC
* * * *
4872881 AACAATTACATTTTTCAACATAGTGTATAATAATTAAATCTTTAACATGATGTAT
1 AACAACTATATTTTTCAACATAGTGTATAACAATTAAATCTTTAACATGATGTGT
* ** * * *
4872936 AACAACTAAATTTTT-AACATTA-CATATAACAACTACATCTTTAACATGGTGTGT
1 AACAACTATATTTTTCAACA-TAGTGTATAACAATTAAATCTTTAACATGATGTGT
** * **
4872990 AACAGTTATA-TTTTCAACAT-GATGTATAACCATTAAAT-TTTCAACATGACATGT
1 AACAACTATATTTTTCAACATAG-TGTATAACAATTAAATCTTT-AACATGATGTGT
* * ** *
4873044 AACAACTATATTTTTTAACATGGCATATAACAATTAAATCTTCAACATGATGTGT
1 AACAACTATATTTTTCAACATAGTGTATAACAATTAAATCTTTAACATGATGTGT
* *
4873099 AACAACTATATTTTTCAACATGACATGTAATAAC---TAAAT-TTTCAACATGATGTCT
1 AACAACTATATTTTTCAACAT-A-GTGT-ATAACAATTAAATCTTT-AACATGATGTGT
**
4873154 AACAACTCCATTTTTCAA
1 AACAACTATATTTTTCAA
4873172 TATGATGTGC
Statistics
Matches: 186, Mismatches: 38, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
53 8 0.04
54 70 0.38
55 99 0.53
56 3 0.02
57 1 0.01
58 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (55 bp):
AACAACTATATTTTTCAACATAGTGTATAACAATTAAATCTTTAACATGATGTGT
Found at i:4872977 original size:54 final size:54
Alignment explanation
Indices: 4872906--4873160 Score: 244
Period size: 55 Copynumber: 4.7 Consensus size: 54
4872896 CAACATAGTG
* * * *
4872906 TATAATAATTAAATCTTTAACATGATGTATAACAACTAAATTTTTAACATTACA
1 TATAACAACTAAATCTTTAACATGATGTGTAACAACTAAATTTTTAACATGACA
* * ** * * **
4872960 TATAACAACTACATCTTTAACATGGTGTGTAACAGTTATATTTTCAACATGATG
1 TATAACAACTAAATCTTTAACATGATGTGTAACAACTAAATTTTTAACATGACA
* * ** * *
4873014 TATAACCATTAAAT-TTTCAACATGACATGTAACAACTATATTTTTTAACATGGCA
1 TATAACAACTAAATCTTT-AACATGATGTGTAACAACTA-AATTTTTAACATGACA
* * *
4873069 TATAACAATTAAATCTTCAACATGATGTGTAACAACTATATTTTTCAACATGACA
1 TATAACAACTAAATCTTTAACATGATGTGTAACAACTAAATTTTT-AACATGACA
* * *
4873124 TGTAATAACTAAAT-TTTCAACATGATGTCTAACAACT
1 TATAACAACTAAATCTTT-AACATGATGTGTAACAACT
4873161 CCATTTTTCA
Statistics
Matches: 158, Mismatches: 38, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
53 3 0.02
54 75 0.47
55 78 0.49
56 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (54 bp):
TATAACAACTAAATCTTTAACATGATGTGTAACAACTAAATTTTTAACATGACA
Found at i:4873157 original size:82 final size:82
Alignment explanation
Indices: 4872873--4873274 Score: 289
Period size: 82 Copynumber: 4.9 Consensus size: 82
4872863 ATCTTCAATG
* * * * * *
4872873 TGACATGCAACAATTACATTTTTCAACAT-AGTGTATAATAATTAAATCTTTAACATGATGTATA
1 TGACATGTAACAACTA-AATTTTCAACATGA-TGTATAACAATTAAATCTTCAACATGATGTGTA
*
4872937 ACAACTAAATTTTT-AACA
64 ACAACTATATTTTTCAACA
* * * * * * * * *
4872955 TTACATATAACAACTACATCTTT-AACATGGTGTGTAACAGTTATATTTTCAACATGATGTATAA
1 TGACATGTAACAACTAAAT-TTTCAACATGATGTATAACAATTAAATCTTCAACATGATGTGTAA
* * *
4873019 CCATTA-AATTTTCAACA
65 CAACTATATTTTTCAACA
* * ***
4873036 TGACATGTAACAACTATATTTTTTAACATGGCATATAACAATTAAATCTTCAACATGATGTGTAA
1 TGACATGTAACAACTA-AATTTTCAACATGATGTATAACAATTAAATCTTCAACATGATGTGTAA
4873101 CAACTATATTTTTCAACA
65 CAACTATATTTTTCAACA
* * ** * * * *
4873119 TGACATGTAATAACTAAATTTTCAACATGATGTCTAACAACTCCATTTTTCAATATGATGTGCAA
1 TGACATGTAACAACTAAATTTTCAACATGATGTATAACAA-TTAAATCTTCAACATGATGTGTAA
* *
4873184 -TACT-TAAATTTTCAACA
65 CAACTAT-ATTTTTCAACA
* * * * * * * ***
4873201 TGGCATGTAACACCTACATTATCAACATGACGTGTAACAATT-AAT-TCCAACATGGCATGTAAC
1 TGACATGTAACAACTAAATTTTCAACATGATGTATAACAATTAAATCTTCAACATGATGTGTAAC
*
4873264 AACTACATTTT
66 AACTATATTTT
4873275 AGAACAAGAT
Statistics
Matches: 247, Mismatches: 63, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
79 11 0.04
80 14 0.06
81 61 0.25
82 118 0.48
83 43 0.17
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (82 bp):
TGACATGTAACAACTAAATTTTCAACATGATGTATAACAATTAAATCTTCAACATGATGTGTAAC
AACTATATTTTTCAACA
Found at i:4873166 original size:27 final size:28
Alignment explanation
Indices: 4872881--4873240 Score: 202
Period size: 27 Copynumber: 13.2 Consensus size: 28
4872871 TGTGACATGC
* * *
4872881 AACAATTACATTTTTCAACAT-AGTGTAT
1 AACAACTAAATTTTTCAACATGA-TGTGT
* * * *
4872909 AATAATTAAATCTTT-AACATGATGTAT
1 AACAACTAAATTTTTCAACATGATGTGT
* ** *
4872936 AACAACTAAATTTTT-AACATTACATAT
1 AACAACTAAATTTTTCAACATGATGTGT
* * *
4872963 AACAACTACATCTTT-AACATGGTGTGT
1 AACAACTAAATTTTTCAACATGATGTGT
** * *
4872990 AACAGTTATA-TTTTCAACATGATGTAT
1 AACAACTAAATTTTTCAACATGATGTGT
* * **
4873017 AACCATTAAA-TTTTCAACATGACATGT
1 AACAACTAAATTTTTCAACATGATGTGT
* * *** *
4873044 AACAACTATATTTTTTAACATGGCATAT
1 AACAACTAAATTTTTCAACATGATGTGT
* *
4873072 AACAATTAAA-TCTTCAACATGATGTGT
1 AACAACTAAATTTTTCAACATGATGTGT
* **
4873099 AACAACTATATTTTTCAACATGACATGT
1 AACAACTAAATTTTTCAACATGATGTGT
* *
4873127 AATAACTAAA-TTTTCAACATGATGTCT
1 AACAACTAAATTTTTCAACATGATGTGT
** * *
4873154 AACAACTCCATTTTTCAATATGATGTGC
1 AACAACTAAATTTTTCAACATGATGTGT
* ***
4873182 AA-TACTTAAA-TTTTCAACATGGCATGT
1 AACAAC-TAAATTTTTCAACATGATGTGT
* * * *
4873209 AACACCTACA-TTATCAACATGACGTGT
1 AACAACTAAATTTTTCAACATGATGTGT
4873236 AACAA
1 AACAA
4873241 TTAATTCCAA
Statistics
Matches: 252, Mismatches: 73, Indels: 15
0.74 0.21 0.04
Matches are distributed among these distances:
26 3 0.01
27 173 0.69
28 76 0.30
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (28 bp):
AACAACTAAATTTTTCAACATGATGTGT
Found at i:4873192 original size:55 final size:56
Alignment explanation
Indices: 4872909--4873231 Score: 199
Period size: 55 Copynumber: 5.9 Consensus size: 56
4872899 CATAGTGTAT
* * * **
4872909 AATAA-TTAAATCTTT-AACATGATGTATAACAACTAAATTTTT-AACATTACATAT
1 AATAACTTAAAT-TTTCAACATGATGTCTAACAACTACATTTTTCAACATGACATGC
* * * * ** *
4872963 AACAAC-TACATCTTT-AACATGGTGTGTAACAGTTATA-TTTTCAACATG--ATG-
1 AATAACTTAAAT-TTTCAACATGATGTCTAACAACTACATTTTTCAACATGACATGC
* ** * * * * **
4873014 TATAACCATTAAATTTTCAACATGACATGTAACAACTATATTTTTTAACATGGCATAT
1 AATAA-C-TTAAATTTTCAACATGATGTCTAACAACTACATTTTTCAACATGACATGC
* * * * *
4873072 AACAA-TTAAATCTTCAACATGATGTGTAACAACTATATTTTTCAACATGACATGT
1 AATAACTTAAATTTTCAACATGATGTCTAACAACTACATTTTTCAACATGACATGC
* * **
4873127 AATAAC-TAAATTTTCAACATGATGTCTAACAACTCCATTTTTCAATATGATGTGC
1 AATAACTTAAATTTTCAACATGATGTCTAACAACTACATTTTTCAACATGACATGC
* *
4873182 AAT-ACTTAAATTTTCAACATGGCATG--TAACACCTACA-TTATCAACATGAC
1 AATAACTTAAATTTTCAACAT-G-ATGTCTAACAACTACATTTTTCAACATGAC
4873232 GTGTAACAAT
Statistics
Matches: 214, Mismatches: 41, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
51 3 0.01
52 3 0.01
53 7 0.03
54 67 0.31
55 125 0.58
56 1 0.00
57 5 0.02
58 3 0.01
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (56 bp):
AATAACTTAAATTTTCAACATGATGTCTAACAACTACATTTTTCAACATGACATGC
Found at i:4873261 original size:25 final size:27
Alignment explanation
Indices: 4873196--4873272 Score: 95
Period size: 25 Copynumber: 2.9 Consensus size: 27
4873186 CTTAAATTTT
* *
4873196 CAACATGGCATGTAACACCTACATTAT
1 CAACATGGCATGTAACAACTACATTAC
* * *
4873223 CAACATGACGTGTAACAATTA-ATT-C
1 CAACATGGCATGTAACAACTACATTAC
4873248 CAACATGGCATGTAACAACTACATT
1 CAACATGGCATGTAACAACTACATT
4873273 TTAGAACAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 18 0.44
26 6 0.15
27 17 0.41
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (27 bp):
CAACATGGCATGTAACAACTACATTAC
Found at i:4875465 original size:59 final size:58
Alignment explanation
Indices: 4875373--4875487 Score: 205
Period size: 59 Copynumber: 2.0 Consensus size: 58
4875363 AAGAGGAGAA
4875373 AGATAGAGAAATAATAACATGGAAGTGATACGAAATTTAAAAAATAAA-AAACCTTTGTC
1 AGATAGAGAAATAATAACATGGAAGTGATACGAAATTT-AAAAATAAAGAAA-CTTTGTC
4875432 AGATAGAGAAATAATAACATGGAAGTGATACGAAATTTAAAAATAAAGAAACTTTG
1 AGATAGAGAAATAATAACATGGAAGTGATACGAAATTTAAAAATAAAGAAACTTTG
4875488 CCATCAATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 14 0.25
59 41 0.75
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.23
Consensus pattern (58 bp):
AGATAGAGAAATAATAACATGGAAGTGATACGAAATTTAAAAATAAAGAAACTTTGTC
Found at i:4877591 original size:33 final size:33
Alignment explanation
Indices: 4877507--4877610 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 33
4877497 CGCTGACGTA
* *
4877507 ACATGTTAATATATCATAATTAATAATGATGTG
1 ACATGCTAATATATCATAATTAATAATAATGTG
* *
4877540 ACATACTGAA-ATATCATAATTGATAATAATGTG
1 ACATGCT-AATATATCATAATTAATAATAATGTG
* * *
4877573 ACATGCTAATGTAGCATAA-TAATATGATTATGTG
1 ACATGCTAATATATCATAATTAATA--ATAATGTG
4877607 ACAT
1 ACAT
4877611 TTTTTACCCT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
32 6 0.10
33 39 0.67
34 13 0.22
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (33 bp):
ACATGCTAATATATCATAATTAATAATAATGTG
Found at i:4883812 original size:2 final size:2
Alignment explanation
Indices: 4883801--4883836 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4883791 CACTGTAGAA
4883801 AG AG AG -G 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 AG AG AG AG A
4883837 AATAGGTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4887286 original size:2 final size:2
Alignment explanation
Indices: 4887275--4887305 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4887265 GTTAAGTGAG
4887275 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4887306 TATGAAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4900285 original size:18 final size:20
Alignment explanation
Indices: 4900259--4900296 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
4900249 GTTTTACTTG
*
4900259 TTGATGGAT-AGA-ATTTTA
1 TTGAAGGATGAGATATTTTA
4900277 TTGAAGGATGAGATATTTTA
1 TTGAAGGATGAGATATTTTA
4900297 GGAGGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGAAGGATGAGATATTTTA
Found at i:4901500 original size:17 final size:18
Alignment explanation
Indices: 4901478--4901512 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4901468 TTCAATACTG
4901478 ATCAAAAATATT-ATTTA
1 ATCAAAAATATTAATTTA
*
4901495 ATCAAAATTATTAATTTA
1 ATCAAAAATATTAATTTA
4901513 TTAAGTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
ATCAAAAATATTAATTTA
Found at i:4901734 original size:13 final size:13
Alignment explanation
Indices: 4901702--4901740 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4901692 AATATATTAC
*
4901702 TAAACTATACATA
1 TAAACTATAAATA
4901715 T-AACTATAAATA
1 TAAACTATAAATA
*
4901727 TAAACTATTAATA
1 TAAACTATAAATA
4901740 T
1 T
4901741 TTTTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAACTATAAATA
Found at i:4902115 original size:29 final size:29
Alignment explanation
Indices: 4902073--4902144 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
4902063 ATATATATAG
4902073 AATAGTTTAAAACTAGTAAGAAGGGATCA
1 AATAGTTTAAAACTAGTAAGAAGGGATCA
4902102 AATAGTTTAAAACTAGTAAGAAGGGATCA
1 AATAGTTTAAAACTAGTAAGAAGGGATCA
4902131 AATAGTTTAAAACT
1 AATAGTTTAAAACT
4902145 TGCTTACCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (29 bp):
AATAGTTTAAAACTAGTAAGAAGGGATCA
Found at i:4903996 original size:13 final size:13
Alignment explanation
Indices: 4903980--4904004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4903970 TATAGTGATT
4903980 TATTTATTTTCTA
1 TATTTATTTTCTA
4903993 TATTTATTTTCT
1 TATTTATTTTCT
4904005 TTCTTTTTAT
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTATTTTCTA
Found at i:4904497 original size:96 final size:97
Alignment explanation
Indices: 4904336--4904515 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 97
4904326 TTCTCCAAGC
* * * ** *
4904336 CGCGTAGGACTCCATTAATCTCCGAGAATCCCTCAGCAACGTGTTCAAGAATCAAGCAGACCATT
1 CGCGTAAGACTCCATCAATCTCCGAGAATCCCTCAGCAACATGGCCAAGAATCAAGCAAACCATT
* *
4904401 CCGCCAACTTATGACCAGATTACCTTCCAACT
66 CAGCCAACTCATGACCAGATTACCTTCCAACT
* *
4904433 CGCGTAAGACTCCATCAAT-TACC-AGAATCCCTCATCAACATGGCCAAGAATCAAGCAAATCAT
1 CGCGTAAGACTCCATCAATCT-CCGAGAATCCCTCAGCAACATGGCCAAGAATCAAGCAAACCAT
*
4904496 TCAGCCAACTCATGTCCAGA
65 TCAGCCAACTCATGACCAGA
4904516 ATCAGACATG
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
96 52 0.73
97 19 0.27
ACGTcount: A:0.33, C:0.32, G:0.14, T:0.21
Consensus pattern (97 bp):
CGCGTAAGACTCCATCAATCTCCGAGAATCCCTCAGCAACATGGCCAAGAATCAAGCAAACCATT
CAGCCAACTCATGACCAGATTACCTTCCAACT
Found at i:4908909 original size:15 final size:16
Alignment explanation
Indices: 4908869--4908914 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
4908859 GACCGACCAA
4908869 AGATATT-ATTTAATCG
1 AGATATTAATTT-ATCG
4908885 AGATTATTAATTTATCG
1 AGA-TATTAATTTATCG
4908902 A-ATATTAATTTAT
1 AGATATTAATTTAT
4908915 AAAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 9 0.32
18 4 0.14
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (16 bp):
AGATATTAATTTATCG
Found at i:4913175 original size:2 final size:2
Alignment explanation
Indices: 4913168--4913192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4913158 TCTTCTGTTT
4913168 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
4913193 GATTTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4914265 original size:45 final size:45
Alignment explanation
Indices: 4914214--4914305 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
4914204 ATGAACAGAA
*
4914214 AAGATGCTTTCTTTATTTTTGTCATAAATTATTCAAGATTCTGTT
1 AAGATGCTTTCTTTATGTTTGTCATAAATTATTCAAGATTCTGTT
4914259 AAGATGCTTTCTTTATGTTTGTCATAAATTATTCAAGATTCTGTT
1 AAGATGCTTTCTTTATGTTTGTCATAAATTATTCAAGATTCTGTT
4914304 AA
1 AA
4914306 TTCTCATGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (45 bp):
AAGATGCTTTCTTTATGTTTGTCATAAATTATTCAAGATTCTGTT
Found at i:4918596 original size:5 final size:5
Alignment explanation
Indices: 4918586--4918616 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4918576 CCGATGCCTT
4918586 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC T
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC T
4918617 AGGTTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
TTCCC
Found at i:4924833 original size:6 final size:6
Alignment explanation
Indices: 4924822--4924849 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4924812 TATGACTTTA
4924822 TAAAAT TAAAAT TAAAAT TAAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAA
4924850 TAAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAAAT
Found at i:4924858 original size:18 final size:18
Alignment explanation
Indices: 4924822--4924860 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4924812 TATGACTTTA
*
4924822 TAAAATTAAAATTAAAAT
1 TAAAATTAAAATAAAAAT
4924840 TAAAATT-AAATAAATAAT
1 TAAAATTAAAATAAA-AAT
4924858 TAA
1 TAA
4924861 TGTAGGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTAAAATAAAAAT
Found at i:4926944 original size:74 final size:74
Alignment explanation
Indices: 4926806--4926944 Score: 217
Period size: 74 Copynumber: 1.9 Consensus size: 74
4926796 ATAATTGAAA
* *
4926806 TAAATCTTACTAATAATTATAATAAAAAATATTCCAATGATCATCTTTTGATAAGTACACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTCCAATGATCATCATTTAATAAGTACACATTTA
4926871 GAATAAGTT
66 GAATAAGTT
* * *
4926880 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATTATCATTTAATGAA-TACATATTT
1 TAAATCTTACTAATAATTATAATAAAAAATATTCCAATGATCATCATTTAAT-AAGTACACATTT
4926944 A
65 A
4926945 TAAGTATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 57 0.97
75 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTCCAATGATCATCATTTAATAAGTACACATTTA
GAATAAGTT
Found at i:4933698 original size:22 final size:22
Alignment explanation
Indices: 4933673--4933715 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4933663 ATTAAATAAG
4933673 ATTTAAGATACT-ATATAATTAA
1 ATTTAA-ATACTAATATAATTAA
*
4933695 ATTTAAATACTAATATTATTA
1 ATTTAAATACTAATATAATTA
4933716 TTTGGTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTAAATACTAATATAATTAA
Found at i:4937922 original size:3 final size:3
Alignment explanation
Indices: 4937914--4937960 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
4937904 CATTACCTAC
4937914 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4937961 CATTCATTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4938885 original size:2 final size:2
Alignment explanation
Indices: 4938880--4938906 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4938870 TGGTACTTGT
4938880 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4938907 TTGAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4940413 original size:60 final size:60
Alignment explanation
Indices: 4940346--4940540 Score: 208
Period size: 60 Copynumber: 3.4 Consensus size: 60
4940336 AAAACACAAA
* *
4940346 TTTAATATATTTATATTTGTTATTATTAATTTTTATATAATATCATTTCTTAAATATATT
1 TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATATCTTAAATATATT
* * * * * * *
4940406 TTTAATATCATATGT-TTTATTTTTATTTA-TTTT-TATAATTTTATATATT---T-TATT
1 TTTAATAT-ATTTATATTTATTATTATTAATTTTTATATAATATCATATCTTAAATATATT
* *
4940460 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATT
1 TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATATCTTAAATATATT
*
4940520 TTTAATATCATATAT-TTTATT
1 TTTAATAT-ATTTATATTTATT
4940541 TTCATTTATT
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
53 4 0.04
54 23 0.22
55 5 0.05
56 12 0.11
58 12 0.11
59 5 0.05
60 36 0.34
61 9 0.08
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (60 bp):
TTTAATATATTTATATTTATTATTATTAATTTTTATATAATATCATATCTTAAATATATT
Found at i:4940435 original size:54 final size:54
Alignment explanation
Indices: 4940377--4940549 Score: 163
Period size: 54 Copynumber: 3.1 Consensus size: 54
4940367 ATTATTAATT
*
4940377 TTTATATAATATCATTTCTTAAATATATTTTTAATATCATATGTTTTATTTTTA
1 TTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTTA
** * * * *
4940431 TTTAT-TTTTATAATTT-TATATATTTTATTTTTAATAT-ATTTATATTTTTTATTATTAATT
1 TTTATATAATATCATTTCT-TA-AATATATTTTTAATATCA--TATA--TTTTATT-TT--TA
* *
4940491 TTTATATAATATCATCTCTTAAATATATTTTTAATATCATATATTTTATTTTCA
1 TTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTTA
4940545 TTTAT
1 TTTAT
4940550 TATTATAATT
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
52 1 0.01
53 11 0.12
54 24 0.26
55 3 0.03
56 2 0.02
57 14 0.15
58 2 0.02
59 4 0.04
60 20 0.22
61 10 0.11
62 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (54 bp):
TTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTTA
Found at i:4940439 original size:16 final size:16
Alignment explanation
Indices: 4940415--4940578 Score: 86
Period size: 15 Copynumber: 10.0 Consensus size: 16
4940405 TTTTAATATC
4940415 ATATGTTTTATTTTTAT
1 ATAT-TTTTATTTTTAT
*
4940432 TTATTTTTATAATTTTAT
1 ATATTTTTAT--TTTTAT
4940450 ATA-TTTTATTTTTAAT
1 ATATTTTTATTTTT-AT
*
4940466 ATATTTATATTTTT-T
1 ATATTTTTATTTTTAT
* *
4940481 AT-TATTAATTTTTAT
1 ATATTTTTATTTTTAT
* * * *
4940496 ATAATATCATCTCTTAAAT
1 ATATTTTTAT-T-TT-TAT
* * *
4940515 ATATTTTTAATATCAT
1 ATATTTTTATTTTTAT
*
4940531 ATA-TTTTATTTTCAT
1 ATATTTTTATTTTTAT
* *
4940546 TTATTATTATAATTTTAT
1 ATATT-TT-TATTTTTAT
4940564 ATA-TTTTATTTTTAT
1 ATATTTTTATTTTTAT
4940579 TTTTTAATAT
Statistics
Matches: 111, Mismatches: 24, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
14 8 0.07
15 30 0.27
16 22 0.20
17 23 0.21
18 20 0.18
19 8 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (16 bp):
ATATTTTTATTTTTAT
Found at i:4940452 original size:49 final size:49
Alignment explanation
Indices: 4940399--4940570 Score: 123
Period size: 57 Copynumber: 3.2 Consensus size: 49
4940389 CATTTCTTAA
* *
4940399 ATATATTTTTAATATCATATGTTTTATTTTTATTTATTTTTATAATTTTAT
1 ATATATTTTTAATATCATATATTTTATTTTAATTTATTTTTATAA-TTT-T
*
4940450 ATATTTTATTTTTAATAT-ATTTATATTTTTTATTATTAATTT-TTATATAATATCATCTCTT
1 ATA---TATTTTTAATATCA--TATA--TTTTATT-TTAATTTATT-T-T--TATAAT-T-TT
* *
4940511 AAATATATTTTTAATATCATATATTTTATTTTCATTTATTATTATAATTTT
1 --ATATATTTTTAATATCATATATTTTATTTTAATTTATTTTTATAATTTT
4940562 ATATATTTT
1 ATATATTTT
4940571 ATTTTTATTT
Statistics
Matches: 97, Mismatches: 6, Indels: 38
0.69 0.04 0.27
Matches are distributed among these distances:
49 9 0.09
51 5 0.05
52 1 0.01
53 6 0.06
54 12 0.12
55 4 0.04
56 6 0.06
57 18 0.19
58 7 0.07
59 5 0.05
60 13 0.13
61 7 0.07
62 1 0.01
63 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (49 bp):
ATATATTTTTAATATCATATATTTTATTTTAATTTATTTTTATAATTTT
Found at i:4940457 original size:9 final size:9
Alignment explanation
Indices: 4940426--4940486 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
4940416 TATGTTTTAT
*
4940426 TTTTATTTA
1 TTTTATATA
4940435 TTTT-TATAA
1 TTTTATAT-A
4940444 TTTTATATA
1 TTTTATATA
4940453 TTTTAT-T-
1 TTTTATATA
*
4940460 TTTAATATA
1 TTTTATATA
*
4940469 -TTTATATT
1 TTTTATATA
4940477 TTTTAT-TA
1 TTTTATATA
4940485 TT
1 TT
4940487 AATTTTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
7 5 0.12
8 13 0.31
9 21 0.50
10 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATATA
Found at i:4940460 original size:33 final size:32
Alignment explanation
Indices: 4940345--4940615 Score: 110
Period size: 33 Copynumber: 8.6 Consensus size: 32
4940335 TAAAACACAA
* * *
4940345 ATTTAATATATTTATATTTGT-TAT-TATTAAT
1 ATTTTATATATTT-TATTTTTATATATATTTAT
* * * *
4940376 -TTTTATATAATATCATTTCTTAAATATATTTTT
1 ATTTTATAT-ATTTTATTT-TTATATATATTTAT
* * * * *
4940409 AATATCATATGTTTTATTTTTATTTATTTTTAT
1 -ATTTTATATATTTTATTTTTATATATATTTAT
4940442 AATTTTATATATTTTATTTTTA-ATATATTTAT
1 -ATTTTATATATTTTATTTTTATATATATTTAT
*
4940474 ATTTT-T-TATTATTAATTTTTATATA-ATATCAT
1 ATTTTATATATT-TT-ATTTTTATATATAT-TTAT
* * *
4940506 CTCTTA-A-A-TATATTTTTA-ATATCA--TAT
1 ATTTTATATATTTTATTTTTATATAT-ATTTAT
* *
4940533 ATTTTAT-TTTCATTTATTATTATA-AT-TTTAT
1 ATTTTATATAT--TTTATTTTTATATATATTTAT
*
4940564 ATATTT-TAT-TTTTATTTTTTAATATATATTTTT
1 AT-TTTATATATTTTA-TTTTT-ATATATATTTAT
*
4940597 ATATTATATATTTTATTTT
1 ATTTTATATATTTTATTTT
4940616 AATTTGTTTT
Statistics
Matches: 176, Mismatches: 34, Indels: 58
0.66 0.13 0.22
Matches are distributed among these distances:
27 6 0.03
28 3 0.02
29 15 0.09
30 20 0.11
31 39 0.22
32 29 0.16
33 47 0.27
34 11 0.06
35 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (32 bp):
ATTTTATATATTTTATTTTTATATATATTTAT
Found at i:4940462 original size:24 final size:24
Alignment explanation
Indices: 4940431--4940590 Score: 84
Period size: 24 Copynumber: 6.7 Consensus size: 24
4940421 TTTATTTTTA
4940431 TTTATTTTT-ATA-ATTTTATATAT
1 TTTATTTTTAATATA-TTTATATAT
*
4940454 TTTATTTTTAATATATTTATATTT
1 TTTATTTTTAATATATTTATATAT
*
4940478 TTTATTATTAAT-T-TTTATATAAT
1 TTTATTTTTAATATATTTATAT-AT
* * * *
4940501 ATCATCTCTTAAATATATTTTTAATAT
1 TTTAT-T-TTTAATATATTTAT-ATAT
** * *
4940528 CATATATTTTATTTTCATTTAT-TAT
1 TTTAT-TTTTAATAT-ATTTATATAT
* *
4940553 TATAATTTT-ATATATTT-TAT-T
1 TTTATTTTTAATATATTTATATAT
4940574 TTTATTTTTTAATATAT
1 TTTA-TTTTTAATATAT
4940591 ATTTTTATAT
Statistics
Matches: 103, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
21 5 0.05
22 16 0.16
23 22 0.21
24 27 0.26
25 11 0.11
26 6 0.06
27 14 0.14
28 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATTTTTAATATATTTATATAT
Found at i:4940548 original size:114 final size:114
Alignment explanation
Indices: 4940346--4940577 Score: 419
Period size: 114 Copynumber: 2.0 Consensus size: 114
4940336 AAAACACAAA
*
4940346 TTTAATATATTTATATTTGTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTGTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
* * *
4940411 TATCATATGTTTTATTTTTATTTATTTTTATAATTTTATATATTTTATT
66 TATCATATATTTTATTTTCATTTATTATTATAATTTTATATATTTTATT
*
4940460 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTGTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
4940525 TATCATATATTTTATTTTCATTTATTATTATAATTTTATATATTTTATT
66 TATCATATATTTTATTTTCATTTATTATTATAATTTTATATATTTTATT
4940574 TTTA
1 TTTA
4940578 TTTTTTAATA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (114 bp):
TTTAATATATTTATATTTGTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TATCATATATTTTATTTTCATTTATTATTATAATTTTATATATTTTATT
Found at i:4940574 original size:54 final size:54
Alignment explanation
Indices: 4940402--4940577 Score: 178
Period size: 54 Copynumber: 3.1 Consensus size: 54
4940392 TTCTTAAATA
* * *
4940402 TATTTTTAATATCATATGTTTTATTTTTATTTATTTTTATAATTTTATATATTT
1 TATTTTTAATATCATATATTTTATTTTAATTTATTATTATAATTTTATATATTT
* * * *
4940456 TATTTTTAATAT-ATTTATATTTTTTATTATTAATTT-TTA-TATAATATCATCTCTTAAAT
1 TATTTTTAATATCA--TATA--TTTTATT-TTAATTTATTATTATAATTTTATATATT---T
*
4940515 ATATTTTTAATATCATATATTTTATTTTCATTTATTATTATAATTTTATATATTT
1 -TATTTTTAATATCATATATTTTATTTTAATTTATTATTATAATTTTATATATTT
4940570 TATTTTTA
1 TATTTTTA
4940578 TTTTTTAATA
Statistics
Matches: 98, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
53 1 0.01
54 20 0.20
55 4 0.04
56 18 0.18
57 19 0.19
58 18 0.18
59 5 0.05
60 12 0.12
61 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (54 bp):
TATTTTTAATATCATATATTTTATTTTAATTTATTATTATAATTTTATATATTT
Found at i:4940580 original size:20 final size:20
Alignment explanation
Indices: 4940557--4940620 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
4940547 TATTATTATA
4940557 ATTTTATATATTTTATTTTT
1 ATTTTATATATTTTATTTTT
* *
4940577 ATTTTTTA-ATATATATTTTT
1 ATTTTATATAT-TTTATTTTT
* *
4940597 ATATTATATATTTTATTTTA
1 ATTTTATATATTTTATTTTT
4940617 ATTT
1 ATTT
4940621 GTTTTACCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTATATATTTTATTTTT
Found at i:4940595 original size:13 final size:15
Alignment explanation
Indices: 4940351--4940610 Score: 95
Period size: 14 Copynumber: 18.0 Consensus size: 15
4940341 ACAAATTTAA
*
4940351 TATATT-TATATTTG
1 TATATTATATATTTT
4940365 T-TATTAT-TAATTTT
1 TATATTATAT-ATTTT
*
4940379 TATATAATATCATTTCT
1 TATATTATAT-ATTT-T
4940396 TA-A--ATATATTTT
1 TATATTATATATTTT
4940408 TA-A-TATCATATGTTT
1 TATATTAT-ATAT-TTT
4940423 TAT-TT-T-TATTTAT
1 TATATTATATATTT-T
4940436 T-T-TTATA-ATTTT
1 TATATTATATATTTT
4940448 ATATATT-T-TATTTT
1 -TATATTATATATTTT
*
4940462 TAATATATTTATATTTT
1 T-ATAT-TATATATTTT
4940479 T-TATTAT-TAATTTT
1 TATATTATAT-ATTTT
* *
4940493 TATATAATATCATCTCT
1 TATATTATAT-AT-TTT
4940510 TA-A--ATATATTTT
1 TATATTATATATTTT
*
4940522 TAATATCATATA-TTT
1 T-ATATTATATATTTT
* * *
4940537 TATTTTCATTTATTAT
1 TATATT-ATATATTTT
*
4940553 TATAATTTTATATATTT
1 TAT-ATTATATAT-TTT
4940570 TAT-TT-T-TATTTT
1 TATATTATATATTTT
*
4940582 T-TAATATATATTTT
1 TATATTATATATTTT
4940596 TATATTATATATTTT
1 TATATTATATATTTT
4940611 ATTTTAATTT
Statistics
Matches: 191, Mismatches: 18, Indels: 73
0.68 0.06 0.26
Matches are distributed among these distances:
11 1 0.01
12 18 0.09
13 31 0.16
14 50 0.26
15 44 0.23
16 26 0.14
17 21 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (15 bp):
TATATTATATATTTT
Found at i:4941364 original size:33 final size:33
Alignment explanation
Indices: 4941316--4941390 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 33
4941306 AAATTTTAAT
*
4941316 TTCTTATATT-T-TATTTTATTTTA-ATTTTTTA
1 TTCTTATATTATATATTTT-TTTAATATTTTTTA
4941347 TTCTTATATTATATATTTTTTTAATATTTTTTA
1 TTCTTATATTATATATTTTTTTAATATTTTTTA
4941380 TT-TTA-ATTATA
1 TTCTTATATTATA
4941391 ACATTAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 16 0.40
32 8 0.20
33 16 0.40
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (33 bp):
TTCTTATATTATATATTTTTTTAATATTTTTTA
Found at i:4941544 original size:13 final size:13
Alignment explanation
Indices: 4941526--4941550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4941516 TATAATATAA
4941526 TTACATTACAATC
1 TTACATTACAATC
4941539 TTACATTACAAT
1 TTACATTACAAT
4941551 AGTCTGTTAC
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
TTACATTACAATC
Found at i:4945210 original size:151 final size:152
Alignment explanation
Indices: 4944913--4945217 Score: 513
Period size: 151 Copynumber: 2.0 Consensus size: 152
4944903 CTTGTATTCT
*
4944913 CATCATTACCAGTACTGAAATCACAACATAACAAGATGATCATAAACAAAATTAACAGTAAGTGA
1 CATCATTACCAGTACTGAAATCACAACATAACAAGATGATCATAAACAAAATTAACAGCAAGTGA
*
4944978 AAAGGCAAAATTCAACTTATTGTGTACTTTCAAACACATTTCGCAAAACATGTTAACCAAAACAA
66 AAAGGCAAAATTCAACTTATTGTGTACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
**
4945043 GCATATACTATGATAACAAGCA
131 GCATATACTACAATAACAAGCA
** * * *
4945065 CATCATTATTAGTAGTGAAATCATAACATAACAAGATGATCATAAACAATATTAACAGCAAGTGA
1 CATCATTACCAGTACTGAAATCACAACATAACAAGATGATCATAAACAAAATTAACAGCAAGTGA
*
4945130 AAAGGCAAAA-TCAACTTGTTGTGTACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
66 AAAGGCAAAATTCAACTTATTGTGTACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
4945194 GCATATACTACAATAACAAGCA
131 GCATATACTACAATAACAAGCA
4945216 CA
1 CA
4945218 CGAGCATGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
151 74 0.52
152 69 0.48
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.24
Consensus pattern (152 bp):
CATCATTACCAGTACTGAAATCACAACATAACAAGATGATCATAAACAAAATTAACAGCAAGTGA
AAAGGCAAAATTCAACTTATTGTGTACTTTCAAACACACTTCGCAAAACATGTTAACCAAAACAA
GCATATACTACAATAACAAGCA
Found at i:4953944 original size:25 final size:25
Alignment explanation
Indices: 4953914--4953962 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4953904 TTTTATTTTG
4953914 AATTAAATTAAGTT-TTA-TAATTAAT
1 AATTAAA-TAA-TTATTATTAATTAAT
4953939 AATTAAATAATTATTATTAATTAA
1 AATTAAATAATTATTATTAATTAA
4953963 AATATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.09
24 6 0.27
25 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
AATTAAATAATTATTATTAATTAAT
Found at i:4953969 original size:18 final size:18
Alignment explanation
Indices: 4953933--4953976 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4953923 AAGTTTTATA
*
4953933 ATTAATAATTAAATAATT
1 ATTATTAATTAAATAATT
4953951 ATTATTAATTAAA-ATATT
1 ATTATTAATTAAATA-ATT
4953969 ATTTATTA
1 A-TTATTA
4953977 TTTTATATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTAATTAAATAATT
Found at i:4956672 original size:18 final size:16
Alignment explanation
Indices: 4956637--4956702 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 16
4956627 TGCAACATGT
*
4956637 ATTATAATTTTTATAA
1 ATTATAATTTTGATAA
4956653 ATTATTAATATTTGATAA
1 ATTA-TAAT-TTTGATAA
* *
4956671 ATTAATAATCTCGATTAA
1 ATT-ATAATTTTGA-TAA
* *
4956689 ATAATATTTTTGAT
1 ATTATAATTTTGAT
4956703 CTGTATCGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 5 0.13
17 14 0.36
18 19 0.49
19 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
ATTATAATTTTGATAA
Found at i:4957126 original size:23 final size:19
Alignment explanation
Indices: 4957074--4957128 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 19
4957064 TTGACGTATA
4957074 AATTAATAAATTATTAATT
1 AATTAATAAATTATTAATT
*
4957093 TATTAACTAAATAATATTTAAATT
1 AATTAA-TAAAT--TA-TT-AATT
4957117 AATTAATAAATT
1 AATTAATAAATT
4957129 GTCATGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.17
20 5 0.17
21 1 0.03
22 2 0.07
23 7 0.24
24 9 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTAATAAATTATTAATT
Found at i:4967324 original size:16 final size:16
Alignment explanation
Indices: 4967303--4967351 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
4967293 GAGTATGATT
4967303 CAATCAAAGCTGAAAA
1 CAATCAAAGCTGAAAA
4967319 CAATCAAAGCTGAAAA
1 CAATCAAAGCTGAAAA
*
4967335 CAATCAAGGCTGAAAA
1 CAATCAAAGCTGAAAA
4967351 C
1 C
4967352 TGAAAACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.53, C:0.20, G:0.14, T:0.12
Consensus pattern (16 bp):
CAATCAAAGCTGAAAA
Found at i:4968551 original size:2 final size:2
Alignment explanation
Indices: 4968544--4968568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4968534 GGAAAAAGGG
4968544 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 A
4968569 AACATCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4971163 original size:16 final size:15
Alignment explanation
Indices: 4971135--4971177 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
4971125 ATAATAATAT
4971135 ATAAATATTATCAAAA
1 ATAAAT-TTATCAAAA
4971151 AGTAAATTTATCAAAA
1 A-TAAATTTATCAAAA
4971167 ATATAATTTAT
1 ATA-AATTTAT
4971178 ATATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 18 0.72
17 5 0.20
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAAATTTATCAAAA
Found at i:4971731 original size:36 final size:36
Alignment explanation
Indices: 4971689--4971762 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 36
4971679 GATAACTTTT
*
4971689 ATGAAATTTATAAAGCATAGGCTA-CAAAAATTATGA
1 ATGAAATTTATAAAGCACAGGCTACCAAAAA-TATGA
4971725 ATGAAATTTATAAAGCACAGGCTACGCAAAAATATGA
1 ATGAAATTTATAAAGCACAGGCTAC-CAAAAATATGA
4971762 A
1 A
4971763 AAATTATTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 23 0.66
37 6 0.17
38 6 0.17
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (36 bp):
ATGAAATTTATAAAGCACAGGCTACCAAAAATATGA
Found at i:4971911 original size:35 final size:35
Alignment explanation
Indices: 4971869--4972010 Score: 119
Period size: 35 Copynumber: 4.0 Consensus size: 35
4971859 TAAGTTATTC
*
4971869 AATCGAATGAGTAACGAGTTGATGAATGATTGCTA
1 AATCGAATGAGTAACGAGTGGATGAATGATTGCTA
* * *
4971904 AATCGAATGAGTGACGAGTGGATGTAT-A-AGCTA
1 AATCGAATGAGTAACGAGTGGATGAATGATTGCTA
* *
4971937 CGCAATTGAATAAGTAACGAGTGGATGAATGATTAG-TA
1 ---AATCGAATGAGTAACGAGTGGATGAATGATT-GCTA
* * * * * *
4971975 AATTGAATGAGTGACAAATGGATGAATAATTACTA
1 AATCGAATGAGTAACGAGTGGATGAATGATTGCTA
4972010 A
1 A
4972011 GTGACATATG
Statistics
Matches: 85, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
33 4 0.05
34 1 0.01
35 53 0.62
36 23 0.27
37 1 0.01
38 2 0.02
39 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (35 bp):
AATCGAATGAGTAACGAGTGGATGAATGATTGCTA
Found at i:4971977 original size:71 final size:71
Alignment explanation
Indices: 4971868--4972003 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 71
4971858 ATAAGTTATT
* * * * *
4971868 CAATCGAATGAGTAACGAGTTGATGAATGATTGCTAAATCGAATGAGTGACGAGTGGATGTATAA
1 CAATCGAATAAGTAACGAGTGGATGAATGATTGCTAAATCGAATGAGTGACAAATGGATGAATAA
4971933 GCTACG
66 GCTACG
* *
4971939 CAATTGAATAAGTAACGAGTGGATGAATGATTAG-TAAATTGAATGAGTGACAAATGGATGAATA
1 CAATCGAATAAGTAACGAGTGGATGAATGATT-GCTAAATCGAATGAGTGACAAATGGATGAATA
4972003 A
65 A
4972004 TTACTAAGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 56 0.98
72 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (71 bp):
CAATCGAATAAGTAACGAGTGGATGAATGATTGCTAAATCGAATGAGTGACAAATGGATGAATAA
GCTACG
Found at i:4972241 original size:38 final size:38
Alignment explanation
Indices: 4972178--4972252 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
4972168 AAAAATATGA
* * * *
4972178 AATTTATAAAGGATAGGCTATGCAATCGACTGAGTAAT
1 AATTTATAAAGCATAAGCTACGCAATCGAATGAGTAAT
*
4972216 AATTTATAAAGCATAAGTTACGCAATCGAATGAGTAA
1 AATTTATAAAGCATAAGCTACGCAATCGAATGAGTAA
4972253 CGAGTGAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (38 bp):
AATTTATAAAGCATAAGCTACGCAATCGAATGAGTAAT
Found at i:4972529 original size:15 final size:17
Alignment explanation
Indices: 4972500--4972532 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4972490 AATTTATGAA
4972500 TTTTAATATATTTATTT
1 TTTTAATATATTTATTT
4972517 TTTTAAT-TA-TTATTT
1 TTTTAATATATTTATTT
4972532 T
1 T
4972533 AATTATGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATATATTTATTT
Found at i:4973600 original size:2 final size:2
Alignment explanation
Indices: 4973593--4973622 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4973583 TTGTTAACAA
4973593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4973623 TAATGGATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4976324 original size:22 final size:23
Alignment explanation
Indices: 4976294--4976336 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
4976284 AAATGTGTAA
4976294 TTAATATTAATTGATTAATTATT
1 TTAATATTAATTGATTAATTATT
*
4976317 TTAA-ATTAATTTATTAATTA
1 TTAATATTAATTGATTAATTA
4976337 ATATGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTAATATTAATTGATTAATTATT
Found at i:4976380 original size:18 final size:19
Alignment explanation
Indices: 4976343--4976380 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4976333 ATTAATATGG
* *
4976343 ATTAATTTACTTTTTAAAA
1 ATTAATTTAATTTATAAAA
4976362 ATTAA-TTAATTTATAAAA
1 ATTAATTTAATTTATAAAA
4976380 A
1 A
4976381 ATAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATTTAATTTATAAAA
Found at i:4981453 original size:19 final size:20
Alignment explanation
Indices: 4981401--4981453 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
4981391 AATTTTTATA
*
4981401 TTTT-TTAATT-ACATAAGT
1 TTTTATTAATTAAAATAAGT
4981419 TTTTA-TAA-TAATAATAA-T
1 TTTTATTAATTAA-AATAAGT
4981437 TTTTATTAATTAAAATA
1 TTTTATTAATTAAAATA
4981454 TAATTTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
17 1 0.03
18 14 0.48
19 11 0.38
20 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTATTAATTAAAATAAGT
Found at i:4983770 original size:2 final size:2
Alignment explanation
Indices: 4983763--4983794 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4983753 CTTAATTGCA
4983763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4983795 TGTGCTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4985472 original size:53 final size:53
Alignment explanation
Indices: 4985392--4985492 Score: 175
Period size: 53 Copynumber: 1.9 Consensus size: 53
4985382 AGTGCTCGAC
* *
4985392 GTTCAGATCATGATTGGTGTATGTTGTCAATTACGGACAAGTCTTGAGTGGAT
1 GTTCAGATCATGATTGGTGTATGTTGTCAATTACAGACAAGCCTTGAGTGGAT
*
4985445 GTTCATATCATGATTGGTGTATGTTGTCAATTACAGACAAGCCTTGAG
1 GTTCAGATCATGATTGGTGTATGTTGTCAATTACAGACAAGCCTTGAG
4985493 GTTTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (53 bp):
GTTCAGATCATGATTGGTGTATGTTGTCAATTACAGACAAGCCTTGAGTGGAT
Found at i:4997783 original size:39 final size:39
Alignment explanation
Indices: 4997730--4997805 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
4997720 AATTGTTTTC
4997730 TTTCACAATACAACTATTCAAAAA-TTATATTTAATAACT
1 TTTCACAATACAACTATT-AAAAAGTTATATTTAATAACT
*
4997769 TTTCATAATACAACTATTAAAAAGTTATATTTAATAA
1 TTTCACAATACAACTATTAAAAAGTTATATTTAATAA
4997806 AATAATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (39 bp):
TTTCACAATACAACTATTAAAAAGTTATATTTAATAACT
Found at i:4999419 original size:25 final size:24
Alignment explanation
Indices: 4999391--4999442 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
4999381 TTCTAAAATT
4999391 TTTAAAATATT-TTATATATTATATA
1 TTTAAAATATTATT-TATATTAT-TA
4999416 TTTAAAATATTAATTTATATTATTA
1 TTTAAAATATT-ATTTATATTATTA
4999441 TT
1 TT
4999443 ATGAGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 15 0.60
26 8 0.32
27 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAAAATATTATTTATATTATTA
Found at i:5000867 original size:12 final size:12
Alignment explanation
Indices: 5000852--5000888 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
5000842 GAAAGAAAGC
5000852 AAAGAAAAGAAA
1 AAAGAAAAGAAA
5000864 AAAGAAAA-AAA
1 AAAGAAAAGAAA
5000875 AAGAGAAAAGAAA
1 AA-AGAAAAGAAA
5000888 A
1 A
5000889 CATGGGGGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.22
12 14 0.61
13 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:5000876 original size:17 final size:17
Alignment explanation
Indices: 5000842--5000888 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
5000832 AAAGAAGCGG
* *
5000842 GAAAGAAAGCAAAGAAAA
1 GAAA-AAAGAAAAAAAAA
5000860 GAAAAAAGAAAAAAAAA
1 GAAAAAAGAAAAAAAAA
*
5000877 GAGAAAAGAAAA
1 GAAAAAAGAAAA
5000889 CATGGGGGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAAAAAAA
Found at i:5008667 original size:16 final size:17
Alignment explanation
Indices: 5008636--5008670 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5008626 CATTACAAAT
5008636 AAAATATTAATATTTTA
1 AAAATATTAATATTTTA
*
5008653 AAAATGTTAAT-TTTTA
1 AAAATATTAATATTTTA
5008669 AA
1 AA
5008671 TGTTGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAAATATTAATATTTTA
Found at i:5009214 original size:30 final size:29
Alignment explanation
Indices: 5009166--5009347 Score: 127
Period size: 31 Copynumber: 5.9 Consensus size: 29
5009156 CATTTTTTAA
*
5009166 ATTTTCTTTATTTGTCAATTTCATCCTTCAA-
1 ATTTTC-TTCTTT-TCAATTT-ATCCTTCAAT
5009197 ATTTCTCTTCTTTTCAATTTGATCCTTCAA-
1 ATTT-TCTTCTTTTCAATTT-ATCCTTCAAT
* * * *
5009227 ACTTTTTATTCTTTTCAATTTAGCCCCTCAAC
1 A--TTTTCTTCTTTTCAATTTA-TCCTTCAAT
*
5009259 ATTTTCTTCTTTTTTAATTTAGTCAC-TCAAT
1 ATTTTCTTC-TTTTCAATTTA-TC-CTTCAAT
* *
5009290 ATTTTTCTTTTTTTCAATTTTATCCCTCAAT
1 A-TTTTCTTCTTTTCAA-TTTATCCTTCAAT
*
5009321 ATTTTTTTCTTTTTCAATTTAATCCTT
1 ATTTTCTTC-TTTTCAATTT-ATCCTT
5009348 TTCTTATTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 24
0.77 0.09 0.15
Matches are distributed among these distances:
30 35 0.28
31 72 0.58
32 18 0.14
ACGTcount: A:0.21, C:0.20, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTTTCTTCTTTTCAATTTATCCTTCAAT
Found at i:5011058 original size:38 final size:38
Alignment explanation
Indices: 5011016--5011090 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
5011006 TATTGAAGTG
* * *
5011016 CACATACCATTTGAAAATAAACTCCTTGTATTCAAGCA
1 CACATACAATTTGAAAATAAACTCCTCGTACTCAAGCA
*
5011054 CACATGCAATTTGAAAATAAACTCCTCGTACTCAAGC
1 CACATACAATTTGAAAATAAACTCCTCGTACTCAAGC
5011091 TCATGGGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (38 bp):
CACATACAATTTGAAAATAAACTCCTCGTACTCAAGCA
Found at i:5011197 original size:13 final size:14
Alignment explanation
Indices: 5011172--5011202 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5011162 CATCTTTTTC
5011172 TGAGAGAGAGCATT
1 TGAGAGAGAGCATT
5011186 TGAGAG-GAGCATT
1 TGAGAGAGAGCATT
5011199 TGAG
1 TGAG
5011203 CATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.32, C:0.06, G:0.39, T:0.23
Consensus pattern (14 bp):
TGAGAGAGAGCATT
Found at i:5011329 original size:71 final size:72
Alignment explanation
Indices: 5011193--5011337 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
5011183 ATTTGAGAGG
* ** *
5011193 AGCATTTGAGCATTTATATTGTTCGATTCTACCCTAAACTCAAAAGCTAGCAAAGTGTTCAAACA
1 AGCATTTGAGCATTTACATCATTCGATTCTACCCTAAACTCAAAAGCTAGCAAAATGTTCAAACA
5011258 AGTTCAA
66 AGTTCAA
* **
5011265 AGCATTTGAGCATTTACATCATTTGATTCTA-CCTAAACTCAAAAGCTAGCAAAATGTTTGAACA
1 AGCATTTGAGCATTTACATCATTCGATTCTACCCTAAACTCAAAAGCTAGCAAAATGTTCAAACA
5011329 AGTTCAA
66 AGTTCAA
5011336 AG
1 AG
5011338 TAAAGTAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
71 39 0.59
72 27 0.41
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (72 bp):
AGCATTTGAGCATTTACATCATTCGATTCTACCCTAAACTCAAAAGCTAGCAAAATGTTCAAACA
AGTTCAA
Found at i:5014159 original size:166 final size:169
Alignment explanation
Indices: 5013876--5014180 Score: 517
Period size: 166 Copynumber: 1.8 Consensus size: 169
5013866 AGTTTGAGTC
* * * *
5013876 TTTCTCAACGTCATGAGGTGTTGTCGTTTTAGTAATGTTGGCTATGTTGTAAAACCAAAACGTCT
1 TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTGGCTATGTTGTAAAACCAAAACCTCT
* *
5013941 TTTATGTGTCATTTTGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTAG
66 TTGATGTGTCATTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTAG
5014006 TTGTCTTCTTGAAATTTCTGTTGAAGTGGCCGGTGGTGG
131 TTGTCTTCTTGAAATTTCTGTTGAAGTGGCCGGTGGTGG
*
5014045 TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTTGCT-TGTTGT-AAACCAAAACCTC-
1 TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTGGCTATGTTGTAAAACCAAAACCTCT
*
5014107 TTGATGTGTCGTTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTAG
66 TTGATGTGTCATTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTAG
5014172 TTGTCTTCT
131 TTGTCTTCT
5014181 GCCGGTGGTG
Statistics
Matches: 128, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
166 71 0.55
167 12 0.09
168 6 0.05
169 39 0.30
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (169 bp):
TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTGGCTATGTTGTAAAACCAAAACCTCT
TTGATGTGTCATTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTAG
TTGTCTTCTTGAAATTTCTGTTGAAGTGGCCGGTGGTGG
Found at i:5015417 original size:19 final size:19
Alignment explanation
Indices: 5015380--5015418 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5015370 TATGCTTCAG
*
5015380 GTCATTAATTGTATAAAAT
1 GTCATTAATTGTAGAAAAT
* *
5015399 GTCATTACTTGTAGGAAAT
1 GTCATTAATTGTAGAAAAT
5015418 G
1 G
5015419 GGGATAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (19 bp):
GTCATTAATTGTAGAAAAT
Found at i:5016909 original size:28 final size:27
Alignment explanation
Indices: 5016868--5016969 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 27
5016858 TTTTATTTAG
*
5016868 ATAAGAAACTATATTTGTCTTAATCTAAA
1 ATAAGAAA-AATATTTGTCTTAATCT-AA
* *
5016897 ATAAGAAAAATATTTTTTATCTTAATCTAG
1 ATAAGAAAAATA---TTTGTCTTAATCTAA
* *
5016927 ACAAGAAAACATATTTGTCTTAAT-TTA
1 ATAAGAAAA-ATATTTGTCTTAATCTAA
*
5016954 ACAAGATAAAATATTT
1 ATAAGA-AAAATATTT
5016970 TCATCTTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
27 13 0.21
28 16 0.26
29 8 0.13
30 9 0.15
31 15 0.25
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (27 bp):
ATAAGAAAAATATTTGTCTTAATCTAA
Found at i:5016941 original size:59 final size:57
Alignment explanation
Indices: 5016865--5016979 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 57
5016855 TGATTTTATT
* * *
5016865 TAGATAAGAAACTATATTTGTCTTAATCTAAAATAAGA-AAAATATTTTTTATCTTAATC
1 TAGACAAGAAACTATATTTGTCTTAAT-T-AAACAAGATAAAATA-TTTTCATCTTAATC
*
5016924 TAGACAAGAAAAC-ATATTTGTCTTAATTTAACAAGATAAAATATTTTCATCTTAAT
1 TAGACAAG-AAACTATATTTGTCTTAATTAAACAAGATAAAATATTTTCATCTTAAT
5016980 TATGAATAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
57 18 0.36
58 7 0.14
59 21 0.42
60 4 0.08
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (57 bp):
TAGACAAGAAACTATATTTGTCTTAATTAAACAAGATAAAATATTTTCATCTTAATC
Found at i:5016977 original size:29 final size:28
Alignment explanation
Indices: 5016833--5016980 Score: 88
Period size: 27 Copynumber: 5.2 Consensus size: 28
5016823 CATGTTTGTC
* * * *
5016833 TAATTTAGATAAGAAAACTGTTTGAT-T
1 TAATTTAGACAAGAAAAATATTTTATCT
* * * *
5016860 TTATTTAGATAAG-AAACTATATTTGTCT
1 TAATTTAGACAAGAAAAATAT-TTTATCT
* * *
5016888 TAATCTAAAATAAGAAAAATATTTTTTATCT
1 TAAT-TTAGACAAGAAAAATA--TTTTATCT
* *
5016919 TAATCTAGACAAGAAAACATA-TTTGTCT
1 TAATTTAGACAAGAAAA-ATATTTTATCT
5016947 TAATTTA-ACAAGATAAAATATTTTCATCT
1 TAATTTAGACAAGA-AAAATATTTT-ATCT
5016976 TAATT
1 TAATT
5016981 ATGAATAAGA
Statistics
Matches: 95, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
26 6 0.06
27 24 0.25
28 22 0.23
29 15 0.16
30 14 0.15
31 13 0.14
32 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (28 bp):
TAATTTAGACAAGAAAAATATTTTATCT
Found at i:5018237 original size:35 final size:37
Alignment explanation
Indices: 5018160--5018243 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 37
5018150 TTTTTATGGC
* * *
5018160 CATTAATATTTTTTTTAAGAAAAGAGAGTTTTTCTTG
1 CATTAATATTTTTTTGAAGAAAAGAGAGTTTTTATTA
* **
5018197 TATTAAT-TTTTTTTGAATTAAA-AGAGTTTTTATTA
1 CATTAATATTTTTTTGAAGAAAAGAGAGTTTTTATTA
*
5018232 CATTAAAATTTT
1 CATTAATATTTT
5018244 GTTATTATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
35 16 0.42
36 16 0.42
37 6 0.16
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.52
Consensus pattern (37 bp):
CATTAATATTTTTTTGAAGAAAAGAGAGTTTTTATTA
Found at i:5018242 original size:37 final size:35
Alignment explanation
Indices: 5018201--5018293 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 35
5018191 TTCTTGTATT
5018201 AATTTTTTTTGAATTAAAAGAGT-TTTTATTAC-ATTAA
1 AATTTTTTTT--ATTAAAA-A-TATTTTATTACTATTAA
* *
5018238 AATTTTGTTATTATTAAAAATATTTTTTTTCTATTAA
1 AATTTT-TT-TTATTAAAAATATTTTATTACTATTAA
5018275 AATTTTTTTTATTACAAAA
1 AATTTTTTTTATTA-AAAA
5018294 ATGGGGAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
35 7 0.14
36 14 0.29
37 24 0.49
38 2 0.04
39 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (35 bp):
AATTTTTTTTATTAAAAATATTTTATTACTATTAA
Found at i:5018272 original size:20 final size:18
Alignment explanation
Indices: 5018233--5018284 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
5018223 TTTTTATTAC
* *
5018233 ATTAAAATTTTGTTAT-T
1 ATTAAAATTTTTTTTTCT
5018250 ATTAAAAATATTTTTTTTCT
1 ATT-AAAAT-TTTTTTTTCT
5018270 ATTAAAATTTTTTTT
1 ATTAAAATTTTTTTT
5018285 ATTACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 11 0.37
20 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTAAAATTTTTTTTTCT
Found at i:5023635 original size:3 final size:3
Alignment explanation
Indices: 5023627--5023665 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
5023617 TTATCCTCAA
*
5023627 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5023666 TTCCTTCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5028719 original size:53 final size:53
Alignment explanation
Indices: 5028639--5028744 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
5028629 GTGATTTTAA
5028639 TATGAAAAAATTCATATATGGTAGGACTCATCTACAATCATTAACTTGGGTTC
1 TATGAAAAAATTCATATATGGTAGGACTCATCTACAATCATTAACTTGGGTTC
5028692 TATGAAAAAATTCATATATGGTAGGACTCATCTACAATCATTAACTTGGGTTC
1 TATGAAAAAATTCATATATGGTAGGACTCATCTACAATCATTAACTTGGGTTC
5028745 CTGTACCTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (53 bp):
TATGAAAAAATTCATATATGGTAGGACTCATCTACAATCATTAACTTGGGTTC
Found at i:5029768 original size:72 final size:71
Alignment explanation
Indices: 5029651--5029794 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 71
5029641 TCTCAAATAT
*
5029651 AATTCCTTTGAAAAGTTTTGTTAATCTCATAACTTAGATGCATGCTATCCTCATAAAGGCAGTGA
1 AATTCCTTTGAAAAGTTTTGTTAATCTCATAACTTAGATGCATGCTATCCTCAT-AAGACAGTGA
5029716 CAGGATC
65 CAGGATC
* * **
5029723 AATTCCTTTGAATAGTTTTGTTAATTTCATCCCTTAGATGCATGCTATCCTCATAAGACAGTGAC
1 AATTCCTTTGAAAAGTTTTGTTAATCTCATAACTTAGATGCATGCTATCCTCATAAGACAGTGAC
5029788 AGGATC
66 AGGATC
5029794 A
1 A
5029795 TGGAGATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 17 0.25
72 50 0.75
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (71 bp):
AATTCCTTTGAAAAGTTTTGTTAATCTCATAACTTAGATGCATGCTATCCTCATAAGACAGTGAC
AGGATC
Found at i:5052268 original size:27 final size:27
Alignment explanation
Indices: 5052238--5052291 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5052228 GTATTATCTG
5052238 TTCTAAAAGTAGGTTGAGACAAGTTGA
1 TTCTAAAAGTAGGTTGAGACAAGTTGA
5052265 TTCTAAAAGTAGGTTGAGACAAGTTGA
1 TTCTAAAAGTAGGTTGAGACAAGTTGA
5052292 CCCACTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (27 bp):
TTCTAAAAGTAGGTTGAGACAAGTTGA
Found at i:5060768 original size:6 final size:6
Alignment explanation
Indices: 5060757--5060796 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
5060747 GAGAACCTGA
*
5060757 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGA AGAA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA
5060797 AATAAAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:5084165 original size:2 final size:2
Alignment explanation
Indices: 5084158--5084183 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5084148 CCCACCATTT
5084158 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5084184 AAGTCAGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5084395 original size:20 final size:21
Alignment explanation
Indices: 5084353--5084396 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5084343 ACATTTTATT
5084353 TTTTTATTATTTTTAATTAAA
1 TTTTTATTATTTTTAATTAAA
* *
5084374 TTTTTA-TATTTTTATTTTAA
1 TTTTTATTATTTTTAATTAAA
5084394 TTT
1 TTT
5084397 AAATAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTATTATTTTTAATTAAA
Found at i:5084398 original size:30 final size:29
Alignment explanation
Indices: 5084338--5084410 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
5084328 ACTATTATTC
*
5084338 AAAT-AACATTTTATTTTTTTATTATTTTT
1 AAATAAAC-TTTTATATTTTTATTATTTTT
* *
5084367 AATTAAATTTTTATATTTTTATT-TTAATTT
1 AAATAAACTTTTATATTTTTATTATT--TTT
5084397 AAATAAACTTTTAT
1 AAATAAACTTTTAT
5084411 GATTGACTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 17 0.47
30 17 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
AAATAAACTTTTATATTTTTATTATTTTT
Found at i:5090274 original size:28 final size:28
Alignment explanation
Indices: 5090234--5090291 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5090224 GTTCAGTATT
5090234 TCTCTGGGTTATGTCAGAAGCACTTGTG
1 TCTCTGGGTTATGTCAGAAGCACTTGTG
*
5090262 TCTCTGGGTTATGTCAGAAGCAGTTGTG
1 TCTCTGGGTTATGTCAGAAGCACTTGTG
5090290 TC
1 TC
5090292 CCTTCAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.36
Consensus pattern (28 bp):
TCTCTGGGTTATGTCAGAAGCACTTGTG
Found at i:5095576 original size:27 final size:28
Alignment explanation
Indices: 5095528--5095581 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5095518 CTTTTTAATT
**
5095528 ATAAATTATTAATATTTTAAAT-AAATA
1 ATAAATTATTAATATTAAAAATGAAATA
5095555 ATAATATT-TTAATATTAAAAATGAAAT
1 ATAA-ATTATTAATATTAAAAATGAAAT
5095582 TAAGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
ATAAATTATTAATATTAAAAATGAAATA
Found at i:5116225 original size:16 final size:16
Alignment explanation
Indices: 5116204--5116235 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5116194 GACTTTGCAC
5116204 CATCTGCAAAATCCCA
1 CATCTGCAAAATCCCA
5116220 CATCTGCAAAATCCCA
1 CATCTGCAAAATCCCA
5116236 TAGGAGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.06, T:0.19
Consensus pattern (16 bp):
CATCTGCAAAATCCCA
Found at i:5122083 original size:43 final size:45
Alignment explanation
Indices: 5122032--5122136 Score: 137
Period size: 43 Copynumber: 2.4 Consensus size: 45
5122022 GGGAAAAAGG
* *
5122032 AAAA-GAAAATGAAAAATAATTGGGAAAAA-ATTGGAG-AGGGAA-
1 AAAAGGAAAAAGAAAAATAATT-GGAAAAAGATTGGAGAAAGGAAC
5122074 AAAAGGAAAAAGAAAAATAATTGGAAAAAGATTGGAGAAAGGAAC
1 AAAAGGAAAAAGAAAAATAATTGGAAAAAGATTGGAGAAAGGAAC
*
5122119 AAAAGAGAAAAAGGAAAA
1 AAAAG-GAAAAAGAAAAA
5122137 GAAAAATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
42 11 0.20
43 23 0.42
44 5 0.09
45 5 0.09
46 11 0.20
ACGTcount: A:0.64, C:0.01, G:0.25, T:0.10
Consensus pattern (45 bp):
AAAAGGAAAAAGAAAAATAATTGGAAAAAGATTGGAGAAAGGAAC
Found at i:5136412 original size:26 final size:26
Alignment explanation
Indices: 5136382--5136433 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5136372 AAATCCCAAG
*
5136382 AATTTATTAAACAGCTCATTCAACAA
1 AATTTATCAAACAGCTCATTCAACAA
* * *
5136408 AATTTATCCAACAGTTCATTCTACAA
1 AATTTATCAAACAGCTCATTCAACAA
5136434 CTTTCTTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (26 bp):
AATTTATCAAACAGCTCATTCAACAA
Found at i:5143767 original size:80 final size:80
Alignment explanation
Indices: 5143634--5143786 Score: 272
Period size: 80 Copynumber: 1.9 Consensus size: 80
5143624 CACATAAGAT
* *
5143634 TTATATACATTAATTCCCATTTATATTAGACTGACCATGTTTCCTTCTAACAGAAGCATAAACAC
1 TTATATACATTAATTCCCATTTATATTAGACTGACCATGATTCCTTCTAACAGAAGCACAAACAC
5143699 CAATTATGTGATGCA
66 CAATTATGTGATGCA
5143714 TTATATACATTAATTCCCATATT-TATTAGACTGACCATGATTCCTTCTAACAGAAGCACAAACA
1 TTATATACATTAATTCCCAT-TTATATTAGACTGACCATGATTCCTTCTAACAGAAGCACAAACA
5143778 CCAATTATG
65 CCAATTATG
5143787 CCATGCACGC
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
80 68 0.97
81 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (80 bp):
TTATATACATTAATTCCCATTTATATTAGACTGACCATGATTCCTTCTAACAGAAGCACAAACAC
CAATTATGTGATGCA
Found at i:5146106 original size:19 final size:19
Alignment explanation
Indices: 5146063--5146113 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
5146053 AAAATAGTCG
5146063 TATTTATTAATTATGAAAA
1 TATTTATTAATTATGAAAA
* *
5146082 TTTTTATTAA-TATTAATAA
1 TATTTATTAATTATGAA-AA
5146101 TATTTATTTAATT
1 TATTTA-TTAATT
5146114 TTTAGACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 4 0.15
21 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATTTATTAATTATGAAAA
Found at i:5146194 original size:16 final size:17
Alignment explanation
Indices: 5146173--5146207 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5146163 ATCTAGTGAT
5146173 TTTTATTA-AAATATTA
1 TTTTATTATAAATATTA
5146189 TTTTATTATAAATATTA
1 TTTTATTATAAATATTA
5146206 TT
1 TT
5146208 AAATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTATTATAAATATTA
Found at i:5147291 original size:18 final size:17
Alignment explanation
Indices: 5147240--5147294 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 17
5147230 CTCTCAAAGA
5147240 ATTT-ATAATTTTTATAT
1 ATTTAATAATTTTT-TAT
5147257 ATTTAATAATGTTTTTTAGT
1 ATTTAATAA--TTTTTTA-T
*
5147277 TTTTAATAATTTTTTAT
1 ATTTAATAATTTTTTAT
5147294 A
1 A
5147295 CATATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 5 0.16
18 11 0.34
19 2 0.06
20 14 0.44
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
ATTTAATAATTTTTTAT
Found at i:5165366 original size:18 final size:17
Alignment explanation
Indices: 5165339--5165372 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5165329 GGAACAACCC
*
5165339 AAATTTCCAAACAATCT
1 AAATTTCCAAAAAATCT
5165356 AAATATTCCAAAAAATC
1 AAAT-TTCCAAAAAATC
5165373 CAAACACAAT
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:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTTCCAAAAAATCT
Found at i:5167162 original size:30 final size:31
Alignment explanation
Indices: 5167128--5167213 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
5167118 GATTTACTTA
* *
5167128 AATATTTATATTTTTTAAATTTTAT-CCT-T
1 AATATATATATTTTTTAAATTTAATACCTAT
* * *
5167157 CAATATCTAAATTTTATTTAATTTAATACCTAT
1 -AATATATATATTTT-TTAAATTTAATACCTAT
*
5167190 ATTATATATATTTTTT-AATTTAAT
1 AATATATATATTTTTTAAATTTAAT
5167214 CTCTATGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 20 0.43
31 11 0.24
32 14 0.30
33 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (31 bp):
AATATATATATTTTTTAAATTTAATACCTAT
Found at i:5167816 original size:29 final size:29
Alignment explanation
Indices: 5167756--5167817 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
5167746 TAATAATTTT
* *
5167756 TTAT-TTTTTATTATATTTAAACAAAATT
1 TTATATTTTTATTATAATTAAACAAAATA
*
5167784 TTATATTTTTATTATGAATTAAA-TAAATA
1 TTATATTTTTATTAT-AATTAAACAAAATA
5167813 TTATA
1 TTATA
5167818 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 19 0.66
30 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
TTATATTTTTATTATAATTAAACAAAATA
Found at i:5183506 original size:17 final size:17
Alignment explanation
Indices: 5183486--5183518 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5183476 ATAATTATTT
5183486 ATTT-TTTAATTATAAAG
1 ATTTATTTAATT-TAAAG
5183503 ATTTATTTAATTTAAA
1 ATTTATTTAATTTAAA
5183519 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTATTTAATTTAAAG
Found at i:5203129 original size:20 final size:22
Alignment explanation
Indices: 5203085--5203129 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
5203075 TATGTGCTCC
*
5203085 TTTCAAAATTCGAGTTTGAAAT
1 TTTCAAAATTCGAGTTTCAAAT
*
5203107 TTTCAAAA-T-GAGTTTCAAGT
1 TTTCAAAATTCGAGTTTCAAAT
5203127 TTT
1 TTT
5203130 AACCTTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (22 bp):
TTTCAAAATTCGAGTTTCAAAT
Found at i:5204456 original size:3 final size:3
Alignment explanation
Indices: 5204448--5204494 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5204438 ACCATCGTTG
5204448 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5204495 TTGAGAAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5212134 original size:26 final size:25
Alignment explanation
Indices: 5212084--5212136 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
5212074 ATACATCATA
* *
5212084 ATGAATGATAATATGACATGTTGAT
1 ATGAATGATAACATAACATGTTGAT
5212109 ATGATATGATAACATAATCATG-TGAT
1 ATGA-ATGATAACATAA-CATGTTGAT
5212135 AT
1 AT
5212137 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 16 0.67
27 4 0.17
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (25 bp):
ATGAATGATAACATAACATGTTGAT
Found at i:5213245 original size:21 final size:22
Alignment explanation
Indices: 5213214--5213256 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5213204 ATTATTTATT
* *
5213214 ATTAAGTCAAATATTGAATATA
1 ATTAAGTCAAATACTCAATATA
5213236 ATTAA-TCAAATACTCAATATA
1 ATTAAGTCAAATACTCAATATA
5213257 TATACATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (22 bp):
ATTAAGTCAAATACTCAATATA
Found at i:5216139 original size:22 final size:21
Alignment explanation
Indices: 5216091--5216138 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5216081 AATAAAAAAG
*
5216091 TTAAAATATTTTTTTATTAAT
1 TTAAAATATTCTTTTATTAAT
*
5216112 TTAAAATTATTCTTTTATT-TT
1 TTAAAA-TATTCTTTTATTAAT
5216133 TTAAAA
1 TTAAAA
5216139 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAAATATTCTTTTATTAAT
Found at i:5216748 original size:39 final size:36
Alignment explanation
Indices: 5216705--5216776 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
5216695 TCTTGTACTA
5216705 TTTAATAAAATTCAAATAATATTTTTATTTTTTATTATG
1 TTTAATAAAATTC--AT-ATATTTTTATTTTTTATTATG
* *
5216744 TTTAATTAAGTTCATATATTTTTATTTTTTATT
1 TTTAATAAAATTCATATATTTTTATTTTTTATT
5216777 CAAATAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 18 0.58
37 2 0.06
39 11 0.35
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTAATAAAATTCATATATTTTTATTTTTTATTATG
Found at i:5217102 original size:20 final size:20
Alignment explanation
Indices: 5217073--5217112 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5217063 ATATAGACTT
5217073 ATTTAAATTTTTTT-AAATA
1 ATTTAAATTTTTTTGAAATA
5217092 ATTTAAAATTTTTTTGAAATA
1 ATTT-AAATTTTTTTGAAATA
5217113 TTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTAAATTTTTTTGAAATA
Found at i:5239805 original size:22 final size:22
Alignment explanation
Indices: 5239777--5239820 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5239767 TAACTAAGCT
5239777 CAAGTTTAGTCTAGCTATTGCA
1 CAAGTTTAGTCTAGCTATTGCA
* *
5239799 CAAGTTTATTCTCGCTATTGCA
1 CAAGTTTAGTCTAGCTATTGCA
5239821 TTTTCGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (22 bp):
CAAGTTTAGTCTAGCTATTGCA
Found at i:5242737 original size:153 final size:152
Alignment explanation
Indices: 5242472--5242753 Score: 385
Period size: 153 Copynumber: 1.8 Consensus size: 152
5242462 TCTTACCAAA
* *
5242472 ATTTTACAAACATCAATTTTTACATCAAAAATTACAGAACTCAGGCACTACTGTTGCATTATATA
1 ATTTTACAAACATCAATTGTTACATCAAAAATTACAGAACTCAGGCACTACTGTTGCATTAGATA
* **
5242537 TTACATAAGAGACTGAAAATATACAGATATTATGATGCCGGAACATTCCAGA-TTTAGTCTCAAT
66 TTACATAAGAGACTGAAAATATACAGAGATTATGATGCCAAAACATTCCAGAGTTTA-TCTCAAT
5242601 AAGTAATGTCCAATAACAGCAAC
130 AAGTAATGTCCAATAACAGCAAC
* * *
5242624 ATTTTAC-AACAATCAATTGTTATATCAAAAAATTACAGAA-TATAGGCACTTCTGTTGCATTAG
1 ATTTTACAAAC-ATCAATTGTTACATC-AAAAATTACAGAACT-CAGGCACTACTGTTGCATTAG
* *
5242687 ATATTACATAAGTGACT-AAAAGTATCCAGAGATTATGATG-CAAAAGCATTCCAGAGTTTATCT
63 ATATTACATAAGAGACTGAAAA-TATACAGAGATTATGATGCCAAAA-CATTCCAGAGTTTATCT
5242750 CAAT
126 CAAT
5242754 CAGTTATCTT
Statistics
Matches: 114, Mismatches: 10, Indels: 11
0.84 0.07 0.08
Matches are distributed among these distances:
151 3 0.03
152 28 0.25
153 79 0.69
154 4 0.04
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (152 bp):
ATTTTACAAACATCAATTGTTACATCAAAAATTACAGAACTCAGGCACTACTGTTGCATTAGATA
TTACATAAGAGACTGAAAATATACAGAGATTATGATGCCAAAACATTCCAGAGTTTATCTCAATA
AGTAATGTCCAATAACAGCAAC
Found at i:5248261 original size:28 final size:29
Alignment explanation
Indices: 5248229--5248286 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
5248219 AATAAGTTAG
5248229 TTTCATACTGAAAGTC-TAAAGGTTTTAT
1 TTTCATACTGAAAGTCTTAAAGGTTTTAT
5248257 TTTCATACTGAAAGTCTTAAAGGTTTTAT
1 TTTCATACTGAAAGTCTTAAAGGTTTTAT
5248286 T
1 T
5248287 CCTAAGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTTCATACTGAAAGTCTTAAAGGTTTTAT
Found at i:5249850 original size:16 final size:16
Alignment explanation
Indices: 5249829--5249859 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5249819 ATCTTTACCT
5249829 TATTAAATTATTAATA
1 TATTAAATTATTAATA
*
5249845 TATTAAATTCTTAAT
1 TATTAAATTATTAAT
5249860 GAAAGTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAAATTATTAATA
Found at i:5250177 original size:15 final size:16
Alignment explanation
Indices: 5250151--5250181 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5250141 TTTAGTTTTT
5250151 AATTACATATTTTAAA
1 AATTACATATTTTAAA
5250167 AATTA-ATATTTTAAA
1 AATTACATATTTTAAA
5250182 TTTAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTACATATTTTAAA
Found at i:5250214 original size:17 final size:17
Alignment explanation
Indices: 5250152--5250214 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 17
5250142 TTAGTTTTTA
5250152 ATTACATATTTTAAAA--
1 ATTA-ATATTTTAAAATT
*
5250168 ATTAATATTTTAAATTT
1 ATTAATATTTTAAAATT
*
5250185 A-GAA-ATTAATTAAAATT
1 ATTAATATT--TTAAAATT
5250202 ATTAATATTTTAA
1 ATTAATATTTTAA
5250215 TCATAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 13 0.35
16 6 0.16
17 13 0.35
18 2 0.05
19 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTAATATTTTAAAATT
Found at i:5250292 original size:40 final size:41
Alignment explanation
Indices: 5250227--5250304 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
5250217 ATAACAATAT
*
5250227 TAAATTATAAATAAACTATTAATATTTAAAATATTAATGAC
1 TAAATTATAAATAAAATATTAATATTTAAAATATTAATGAC
* **
5250268 TAAATTAT-AATAAAATATTTATATTTAAGTTATTAAT
1 TAAATTATAAATAAAATATTAATATTTAAAATATTAAT
5250305 TATTAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 25 0.76
41 8 0.24
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (41 bp):
TAAATTATAAATAAAATATTAATATTTAAAATATTAATGAC
Found at i:5250331 original size:40 final size:39
Alignment explanation
Indices: 5250227--5250332 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 39
5250217 ATAACAATAT
5250227 TAAATTATAAATAAACTATTA-ATATTTAAAATATTAATGAC
1 TAAATTAT-AATAAA--ATTATATATTTAAAATATTAATGAC
* ** * *
5250268 TAAATTATAATAAAATATTTATATTTAAGTTATTAATTAT
1 TAAATTATAATAAAAT-TATATATTTAAAATATTAATGAC
* *
5250308 TAATATTTTAATTAAATTATATATT
1 TAA-ATTATAATAAAATTATATATT
5250333 ATTAATATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 32 0.59
41 19 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (39 bp):
TAAATTATAATAAAATTATATATTTAAAATATTAATGAC
Found at i:5250333 original size:27 final size:28
Alignment explanation
Indices: 5250281--5250343 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
5250271 ATTATAATAA
* *
5250281 AATATTTATATTTAAGTTATTAATTATT
1 AATATTTATAATTAAATTATTAATTATT
5250309 AATATTT-TAATTAAATTA-TATATTATT
1 AATATTTATAATTAAATTATTA-ATTATT
5250336 AATATTTA
1 AATATTTA
5250344 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
27 22 0.71
28 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
AATATTTATAATTAAATTATTAATTATT
Found at i:5253658 original size:6 final size:6
Alignment explanation
Indices: 5253649--5253683 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5253639 AAAAATTAAA
* *
5253649 AAAAAC AAAAAC AAAAAC AAAAGC AAAAGC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
5253684 GTTTTCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:5263317 original size:39 final size:39
Alignment explanation
Indices: 5263263--5263341 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
5263253 ACAGAAAGAT
5263263 CAATTATTTTCTTCAAACAAATAGAGAAAGGATAATGTA
1 CAATTATTTTCTTCAAACAAATAGAGAAAGGATAATGTA
5263302 CAATTATTTTCTTCAAACAAATAGAGAAAGGATAATGTA
1 CAATTATTTTCTTCAAACAAATAGAGAAAGGATAATGTA
5263341 C
1 C
5263342 CTCTCAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (39 bp):
CAATTATTTTCTTCAAACAAATAGAGAAAGGATAATGTA
Found at i:5268959 original size:3 final size:3
Alignment explanation
Indices: 5268953--5268978 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5268943 TCCTCTGAAC
5268953 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
5268979 CCACCACCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:5277593 original size:13 final size:13
Alignment explanation
Indices: 5277575--5277609 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5277565 CATATGCTGA
5277575 AGCAAATTTGTAT
1 AGCAAATTTGTAT
5277588 AGCAAATTTGTAT
1 AGCAAATTTGTAT
*
5277601 AGTAAATTT
1 AGCAAATTT
5277610 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (13 bp):
AGCAAATTTGTAT
Found at i:5277867 original size:14 final size:14
Alignment explanation
Indices: 5277848--5277874 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5277838 TATTTTTCAT
5277848 AATATTTTTATAAA
1 AATATTTTTATAAA
5277862 AATATTTTTATAA
1 AATATTTTTATAA
5277875 TATGATATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTTTTATAAA
Found at i:5277947 original size:33 final size:32
Alignment explanation
Indices: 5277904--5277970 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
5277894 TACTAAAGAG
*
5277904 TTTTCTATAATAAGATCCAAATAATAAAAAATA
1 TTTTCAATAAT-AGATCCAAATAATAAAAAATA
** **
5277937 TTTTCAATAATTTATTTAAATAATAAAAAATA
1 TTTTCAATAATAGATCCAAATAATAAAAAATA
5277969 TT
1 TT
5277971 AAATTCTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (32 bp):
TTTTCAATAATAGATCCAAATAATAAAAAATA
Found at i:5279541 original size:20 final size:20
Alignment explanation
Indices: 5279518--5279555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5279508 CAAAAGTTAA
*
5279518 CAAAAGCAACAAAAAAAACT
1 CAAAAACAACAAAAAAAACT
*
5279538 CAAAAACAATAAAAAAAA
1 CAAAAACAACAAAAAAAA
5279556 TAAGCAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.16, G:0.03, T:0.05
Consensus pattern (20 bp):
CAAAAACAACAAAAAAAACT
Found at i:5301435 original size:26 final size:27
Alignment explanation
Indices: 5301386--5301436 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
5301376 GGAATCTTTA
*
5301386 AGCTCTTTTTAATATAGGGATTTACTC
1 AGCTCTTTTTAATAAAGGGATTTACTC
5301413 AGCT-TTTTTAATAAAGTGG-TTTAC
1 AGCTCTTTTTAATAAAG-GGATTTAC
5301437 CTGACTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (27 bp):
AGCTCTTTTTAATAAAGGGATTTACTC
Done.