Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 86 of 144
Found at i:19829260 original size:14 final size:15
Alignment explanation
Indices: 19829234--19829263 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19829224 TAATCCCAAT
19829234 TATTTTTATTGTTTA
1 TATTTTTATTGTTTA
19829249 TATTTTTA-TGTTTA
1 TATTTTTATTGTTTA
19829263 T
1 T
19829264 TTTAGCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
TATTTTTATTGTTTA
Found at i:19830949 original size:17 final size:18
Alignment explanation
Indices: 19830924--19830969 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
19830914 AATTGAAGAG
19830924 ATAAAAATAAATAAAT-A
1 ATAAAAATAAATAAATAA
*
19830941 ATGAAAATAAATAAATAA
1 ATAAAAATAAATAAATAA
19830959 ATAAAAATAAA
1 ATAAAAATAAA
19830970 CAAACGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
ATAAAAATAAATAAATAA
Found at i:19833036 original size:56 final size:57
Alignment explanation
Indices: 19832930--19833043 Score: 134
Period size: 56 Copynumber: 2.1 Consensus size: 57
19832920 TTTTGTGGAA
* *
19832930 TTATTTCTTTACAATTTGGTTTTTATTTTATTTCTAACTTTACTAATTTATTCT-TT
1 TTATTTCTTTACAATTTGGTTTTCATTTTATTTCTAACTTAACTAATTTATTCTATT
* *
19832986 TTATTTCTTTGCAAATTT-GTTTTCATTTTATTT-T-AC-TAACTAA-TTCTT-TATT
1 TTATTTCTTTAC-AATTTGGTTTTCATTTTATTTCTAACTTAACTAATTTATTCTATT
19833038 TTATTT
1 TTATTT
19833044 TATTTTATTG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
51 1 0.02
52 12 0.23
53 6 0.12
54 2 0.04
55 1 0.02
56 25 0.48
57 5 0.10
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.64
Consensus pattern (57 bp):
TTATTTCTTTACAATTTGGTTTTCATTTTATTTCTAACTTAACTAATTTATTCTATT
Found at i:19836651 original size:25 final size:26
Alignment explanation
Indices: 19836567--19836752 Score: 153
Period size: 26 Copynumber: 7.3 Consensus size: 26
19836557 TGCTAGACAT
* *
19836567 TCACCGGCTTGAAACCTACTAATTAA
1 TCACCGGCTCGAAGCCTACTAATTAA
**
19836593 TCACCAACTCGAAGCCTACTAATTAA
1 TCACCGGCTCGAAGCCTACTAATTAA
* *
19836619 TCACCGGCTCGAAGTCTACTAA-AAA
1 TCACCGGCTCGAAGCCTACTAATTAA
* *
19836644 TCACCGGCTCGAAGCTTGCTAATTAA
1 TCACCGGCTCGAAGCCTACTAATTAA
** * * * *
19836670 TCATTGGCTTGAATCTTGCTAATTAA
1 TCACCGGCTCGAAGCCTACTAATTAA
* * ** *
19836696 TCACAGGCTTGAAGCCTGTTAA-AAA
1 TCACCGGCTCGAAGCCTACTAATTAA
* * *
19836721 TCACTGGCTCAAAGCCTGCTAA-TAA
1 TCACCGGCTCGAAGCCTACTAATTAA
19836746 TCACCGG
1 TCACCGG
19836753 ACATTTCTAT
Statistics
Matches: 131, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
25 49 0.37
26 82 0.63
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
TCACCGGCTCGAAGCCTACTAATTAA
Found at i:19836666 original size:51 final size:52
Alignment explanation
Indices: 19836567--19836672 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 52
19836557 TGCTAGACAT
* *
19836567 TCACCGGCTTGAAACCTACTAATTAATCACCAACTCGAAGCCTACTAATTAA
1 TCACCGGCTCGAAACCTACTAATAAATCACCAACTCGAAGCCTACTAATTAA
** ** * *
19836619 TCACCGGCTCGAAGTCTACTAA-AAATCACCGGCTCGAAGCTTGCTAATTAA
1 TCACCGGCTCGAAACCTACTAATAAATCACCAACTCGAAGCCTACTAATTAA
19836670 TCA
1 TCA
19836673 TTGGCTTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
51 27 0.59
52 19 0.41
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (52 bp):
TCACCGGCTCGAAACCTACTAATAAATCACCAACTCGAAGCCTACTAATTAA
Found at i:19837596 original size:33 final size:33
Alignment explanation
Indices: 19837557--19837622 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
19837547 GAGCTTAAAA
19837557 ATATAAAAACATTAAAAACGGGGTTAAAAAACC
1 ATATAAAAACATTAAAAACGGGGTTAAAAAACC
19837590 ATATAAAAACATTAAAAACGGGGTTAAAAAACC
1 ATATAAAAACATTAAAAACGGGGTTAAAAAACC
19837623 TTACCATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (33 bp):
ATATAAAAACATTAAAAACGGGGTTAAAAAACC
Found at i:19845667 original size:41 final size:42
Alignment explanation
Indices: 19845511--19845737 Score: 253
Period size: 42 Copynumber: 5.4 Consensus size: 42
19845501 GAATCACTTG
* * * *
19845511 ATGTATAAATGGAAGACTCATGTCTCGGTATGACCATGAGATT
1 ATGTTTAAA-GGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * *
19845554 ATGTTTAAAGGAATACTCATGTCTTGGGATAAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
19845596 ATGTTTAAAGGAAGACTCGTGACTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* *
19845638 ATGTTTAAA-GAAGACTTGTGTCTCGGGATGAGCATAAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
* * * * *
19845679 ATGTTTAATGGAAGACTTGTGTCTCAGTA-GAGCATAAGATT
1 ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
19845720 -TGTTTAAAAAGGAAGACT
1 ATGTTT--AAAGGAAGACT
19845738 TATGACTCGG
Statistics
Matches: 161, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
40 5 0.03
41 48 0.30
42 100 0.62
43 8 0.05
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
Found at i:19845686 original size:83 final size:84
Alignment explanation
Indices: 19845511--19845747 Score: 266
Period size: 83 Copynumber: 2.8 Consensus size: 84
19845501 GAATCACTTG
* * * *
19845511 ATGTATAAATGGAAGACTCATGTCTC-GGTATGACCATGAGATTATGTTTAAAGGAATACTCATG
1 ATGTTTAAA-GGAAGACTCGTGTCTCAGG-ATGAGCATGAGATTATGTTTAAAGGAAGACTCATG
* *
19845575 TCTTGGGATAAGCATGAGATT
64 TCTCGGGATAAGCATAAGATT
* **
19845596 ATGTTTAAAGGAAGACTCGTGACTCAGGATGAGCATGAGATTATGTTTAAA-GAAGACTTGTGTC
1 ATGTTTAAAGGAAGACTCGTGTCTCAGGATGAGCATGAGATTATGTTTAAAGGAAGACTCATGTC
*
19845660 TCGGGATGAGCATAAGATT
66 TCGGGATAAGCATAAGATT
* * * * *
19845679 ATGTTTAATGGAAGACTTGTGTCTCAGTA-GAGCATAAGATT-TGTTTAAAAAGGAAGACTTATG
1 ATGTTTAAAGGAAGACTCGTGTCTCAGGATGAGCATGAGATTATGTTT--AAAGGAAGACTCATG
*
19845742 ACTCGG
64 TCTCGG
19845748 TTGGAGCATA
Statistics
Matches: 131, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
81 5 0.04
82 11 0.08
83 54 0.41
84 51 0.39
85 10 0.08
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (84 bp):
ATGTTTAAAGGAAGACTCGTGTCTCAGGATGAGCATGAGATTATGTTTAAAGGAAGACTCATGTC
TCGGGATAAGCATAAGATT
Found at i:19853490 original size:22 final size:22
Alignment explanation
Indices: 19853448--19853490 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
19853438 TAAAGTGGGT
*
19853448 CATGCAAATTAATTTAATTAAG
1 CATGCAAATTAATTCAATTAAG
*
19853470 CATG-AAATTATATTCATTTAA
1 CATGCAAATTA-ATTCAATTAA
19853491 TGAACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
CATGCAAATTAATTCAATTAAG
Found at i:19860778 original size:44 final size:45
Alignment explanation
Indices: 19860727--19860844 Score: 161
Period size: 44 Copynumber: 2.6 Consensus size: 45
19860717 TGAAAGATGC
19860727 TATGACATCATGATAAAAATGAGTAAGACAATA-CTTAAAAAAT-A
1 TATGACATCATGATAAAAATGAGTAAGACAATAGC-TAAAAAATGA
* * * *
19860771 TATGACATCATGATAAAAATGCGTAAGACAATAGCTGAAAGATGC
1 TATGACATCATGATAAAAATGAGTAAGACAATAGCTAAAAAATGA
19860816 TAT-AGCATCATGATAAAAATGAGTAAGAC
1 TATGA-CATCATGATAAAAATGAGTAAGAC
19860845 CATAACTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
44 39 0.59
45 27 0.41
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (45 bp):
TATGACATCATGATAAAAATGAGTAAGACAATAGCTAAAAAATGA
Found at i:19860788 original size:21 final size:23
Alignment explanation
Indices: 19860727--19860800 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
19860717 TGAAAGATGC
19860727 TATGACATCATGATAAAAATGAG
1 TATGACATCATGATAAAAATGAG
* *
19860750 TAAGACAAT-ACTTA-AAAAAT-A-
1 TATGAC-ATCA-TGATAAAAATGAG
*
19860771 TATGACATCATGATAAAAATGCG
1 TATGACATCATGATAAAAATGAG
*
19860794 TAAGACA
1 TATGACA
19860801 ATAGCTGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 4 0.10
21 12 0.31
22 1 0.03
23 18 0.46
24 4 0.10
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (23 bp):
TATGACATCATGATAAAAATGAG
Found at i:19860871 original size:45 final size:45
Alignment explanation
Indices: 19860703--19860892 Score: 199
Period size: 45 Copynumber: 4.2 Consensus size: 45
19860693 CGCCAATATA
* *
19860703 AGTAAGACCATTATTGAAAGATGCTATGACATCATGATAAAAATG
1 AGTAAGACCATAACTGAAAGATGCTATGACATCATGATAAAAATG
* * * *
19860748 AGTAAGACAAT-ACTTAAAAAAT-ATATGACATCATGATAAAAATG
1 AGTAAGACCATAAC-TGAAAGATGCTATGACATCATGATAAAAATG
* * *
19860792 CGTAAGACAATAGCTGAAAGATGCTAT-AGCATCATGATAAAAATG
1 AGTAAGACCATAACTGAAAGATGCTATGA-CATCATGATAAAAATG
* * * *
19860837 AGTAAGACCATAACTGAAAGATGTTTTGGA-ATCATGTTACAAATG
1 AGTAAGACCATAACTGAAAGATGCTAT-GACATCATGATAAAAATG
*
19860882 TGTAAGACCAT
1 AGTAAGACCAT
19860893 GGTTGAAAGA
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
44 39 0.32
45 81 0.67
47 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (45 bp):
AGTAAGACCATAACTGAAAGATGCTATGACATCATGATAAAAATG
Found at i:19861076 original size:27 final size:27
Alignment explanation
Indices: 19861043--19861127 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
19861033 ACAATATCAT
*
19861043 GGATAGTTCAACGGGACATTAAACACG
1 GGATAGTTCGACGGGACATTAAACACG
* * * ** *
19861070 GTATAGTTTGACGAGATGTTAAACATG
1 GGATAGTTCGACGGGACATTAAACACG
* *
19861097 GGATAATTCGACGGGACATTAAACATG
1 GGATAGTTCGACGGGACATTAAACACG
19861124 GGAT
1 GGAT
19861128 GGTCCGTTAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (27 bp):
GGATAGTTCGACGGGACATTAAACACG
Found at i:19867233 original size:23 final size:23
Alignment explanation
Indices: 19867162--19867235 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
19867152 AGACCATAGC
19867162 TAAAAAATGTTATGGCATCATGA
1 TAAAAAATGTTATGGCATCATGA
* * * *
19867185 T-AACAATGAGTA-AG-ATCATAA
1 TAAAAAATG-TTATGGCATCATGA
19867206 CTAAAAAATGTTATGGCATCATGA
1 -TAAAAAATGTTATGGCATCATGA
19867230 TAAAAA
1 TAAAAA
19867236 TAAGAAAGAC
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 6 0.16
22 10 0.26
23 16 0.42
24 6 0.16
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (23 bp):
TAAAAAATGTTATGGCATCATGA
Found at i:19867345 original size:45 final size:45
Alignment explanation
Indices: 19867100--19867360 Score: 261
Period size: 45 Copynumber: 5.8 Consensus size: 45
19867090 ATACACCAAG
* * * *
19867100 ATGAGTAGGACCATAGCTGAAAATTGCTATGGCATCATGATAACA
1 ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATCATGATAAAA
* * *
19867145 ATAAGTAAGACCATAGCTAAAAAATGTTATGGCATCATGATAACA
1 ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATCATGATAAAA
* * *
19867190 ATGAGTAAGATCATAACTAAAAAATGTTATGGCATCATGATAAAA
1 ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATCATGATAAAA
* * * * * * * * *
19867235 ATAAGAAAGACCATGGTTTAAAGATGCTATTGCATCATTATAAAA
1 ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATCATGATAAAA
** * * * *
19867280 ATGAACAAGATCATAGCTGAAAAATGTTATGACATTATGTTAAAA
1 ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATCATGATAAAA
* * * *
19867325 ATGAGTAAGACCATAACTGAAAGATGATATGACATC
1 ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATC
19867361 TTGTGAAAAC
Statistics
Matches: 175, Mismatches: 41, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 175 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (45 bp):
ATGAGTAAGACCATAGCTGAAAAATGTTATGGCATCATGATAAAA
Found at i:19867575 original size:27 final size:27
Alignment explanation
Indices: 19867518--19867577 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
19867508 CCGATGACAT
* * * * * *
19867518 TAAACATGGGATAGTTCGATGGGGTGT
1 TAAACATGGAATAGTCCGACGAGGCGC
19867545 TAAACATGGAATAGTCCGACGAGGCGC
1 TAAACATGGAATAGTCCGACGAGGCGC
19867572 TAAACA
1 TAAACA
19867578 CGAGATGGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (27 bp):
TAAACATGGAATAGTCCGACGAGGCGC
Found at i:19872313 original size:51 final size:51
Alignment explanation
Indices: 19872195--19872580 Score: 474
Period size: 51 Copynumber: 7.5 Consensus size: 51
19872185 AAAGGGGTTT
* *
19872195 GATGACTAAGTGTCATCATGAGCAAAATGAATCCTTTA-TGGATTACAAGGGTCC
1 GATGACTAAGTGTCATCGTGAG-TAAATGAATCCTTTACT-GATTA-AA-GGTCC
19872249 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
* * * *
19872300 GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTTC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
*
19872351 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATT-AAGGTTCT
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGG-TCC
* * * **
19872402 GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTTA
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
* *
19872453 GATGACTAAGTGTCATCGTGAGTAAATGAATCCATGA-TGGATTAAAGGTCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACT-GATTAAAGGTCC
* ** * * * *
19872504 GATGACTTAGTGTCATCGTGAGTGTATGAATTCCTATACGGAATAAGAGATCC
1 GATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACTGATTAA-AGGTCC
19872557 GATGACTATA-TGTCATCGTGAGTA
1 GATGACTA-AGTGTCATCGTGAGTA
19872581 TTAAATGAAA
Statistics
Matches: 290, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
50 4 0.01
51 204 0.70
52 15 0.05
53 44 0.15
54 23 0.08
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (51 bp):
GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
Found at i:19872374 original size:102 final size:102
Alignment explanation
Indices: 19872195--19872580 Score: 526
Period size: 102 Copynumber: 3.7 Consensus size: 102
19872185 AAAGGGGTTT
* * *
19872195 GATGACTAAGTGTCATCATGAGCAAAATGAATCCTTTATGGATTACAAGGGTCCGATGACTAAGT
1 GATGACTAAGTGTCATCATGAG-TAAACGAATCCTTTACGGATTA-AA-GGTCCGATGACTAAGT
19872260 GTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
63 GTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
*
19872300 GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTTCGATGACTAAGTGTC
1 GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGTC
*
19872365 ATCGTGAGTAAATGAATCCTTTACTGATT-AAGGTTCT
66 ATCGTGAGTAAATGAATCCTTTACTGATTAAAGG-TCC
**
19872402 GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTTAGATGACTAAGTGTC
1 GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGTC
* *
19872467 ATCGTGAGTAAATGAATCCATGA-TGGATTAAAGGTCC
66 ATCGTGAGTAAATGAATCCTTTACT-GATTAAAGGTCC
* * ** * * * *
19872504 GATGACTTAGTGTCATCGTGAGTGTATGAATTCCTATACGGAATAAGAGATCCGATGACTATA-T
1 GATGACTAAGTGTCATCATGAGTAAACGAA-TCCTTTACGGATTAA-AGGTCCGATGACTA-AGT
19872568 GTCATCGTGAGTA
63 GTCATCGTGAGTA
19872581 TTAAATGAAA
Statistics
Matches: 256, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
101 5 0.02
102 165 0.64
103 19 0.07
104 44 0.17
105 23 0.09
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (102 bp):
GATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGTC
ATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTCC
Found at i:19875983 original size:17 final size:18
Alignment explanation
Indices: 19875940--19875985 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
19875930 ATTAAATAAT
*
19875940 CAAA-ATTTAAATTTGAA
1 CAAATATTTAAATGTGAA
*
19875957 TAAATA-TTAAATGT-AA
1 CAAATATTTAAATGTGAA
19875973 CAAATATTTAAAT
1 CAAATATTTAAAT
19875986 AAAAATATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.29
17 16 0.67
18 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (18 bp):
CAAATATTTAAATGTGAA
Found at i:19882857 original size:19 final size:19
Alignment explanation
Indices: 19882833--19882873 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
19882823 CTACTAAGGA
*
19882833 AATAATATCTCTTAATTAG
1 AATAATATCTCCTAATTAG
*
19882852 AATAATATCTCCTAGTTAG
1 AATAATATCTCCTAATTAG
19882871 AAT
1 AAT
19882874 CTCAAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (19 bp):
AATAATATCTCCTAATTAG
Found at i:19900758 original size:28 final size:28
Alignment explanation
Indices: 19900705--19900797 Score: 118
Period size: 27 Copynumber: 3.4 Consensus size: 28
19900695 TAAGCATGTG
**
19900705 TTTAAATTTT-CAAGTGTTATCCTTTAT
1 TTTAAATTTTGCTGGTGTTATCCTTTAT
*
19900732 TTTAAATTTTGCTGGTGTTATCATTTAT
1 TTTAAATTTTGCTGGTGTTATCCTTTAT
* * *
19900760 TTTGAA-TTTGCTGTTGTTATCCTTTGT
1 TTTAAATTTTGCTGGTGTTATCCTTTAT
19900787 TTTAAATTTTG
1 TTTAAATTTTG
19900798 TTGTTTGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 33 0.59
28 23 0.41
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.58
Consensus pattern (28 bp):
TTTAAATTTTGCTGGTGTTATCCTTTAT
Found at i:19903820 original size:2 final size:2
Alignment explanation
Indices: 19903813--19903837 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19903803 CAAATGTATG
19903813 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 T
19903838 TAATATCACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19908977 original size:40 final size:40
Alignment explanation
Indices: 19908916--19909015 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
19908906 GAATTAGCAA
* * * * *
19908916 TGATACTGTAAACATTTCAAGATTACAACTAAATTTATAG
1 TGATACTGTAAACACTGCAAGAATACAACTAAACTGATAG
* * *
19908956 TGATACTGTAAACACTGCAAGAATACCACTGAACTGGTAG
1 TGATACTGTAAACACTGCAAGAATACAACTAAACTGATAG
* *
19908996 TGAAACTGTAAATACTGCAA
1 TGATACTGTAAACACTGCAA
19909016 TGTGTCAGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (40 bp):
TGATACTGTAAACACTGCAAGAATACAACTAAACTGATAG
Found at i:19914638 original size:54 final size:54
Alignment explanation
Indices: 19914556--19914664 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
19914546 GGCGCAGGTT
* *
19914556 TCACACGGTCTGGCACATGATCTGAGACACGACCGTG-AGTACCAAGTCAGTGAG
1 TCACACGGTCTGACACACGATCTGAGACACGACCGTGCA-TACCAAGTCAGTGAG
* **
19914610 TCACACTGTCTGACACACGA-CTTGAGACACGGTCGTGCATACCAAGTCAGTGAG
1 TCACACGGTCTGACACACGATC-TGAGACACGACCGTGCATACCAAGTCAGTGAG
19914664 T
1 T
19914665 TATACGGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.02
54 46 0.96
55 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.20
Consensus pattern (54 bp):
TCACACGGTCTGACACACGATCTGAGACACGACCGTGCATACCAAGTCAGTGAG
Found at i:19915680 original size:35 final size:35
Alignment explanation
Indices: 19915626--19915694 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
19915616 TTCAATCAAA
* *
19915626 TAAGAGATAGCTTATAAGTCAGGTTAAACAAAATC
1 TAAGAGATAGCTTACAAGTCAAGTTAAACAAAATC
* *
19915661 TAAGAGATTGCTTGCAAGTCAAGTTAAACAAAAT
1 TAAGAGATAGCTTACAAGTCAAGTTAAACAAAAT
19915695 ATATTACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (35 bp):
TAAGAGATAGCTTACAAGTCAAGTTAAACAAAATC
Found at i:19915740 original size:24 final size:23
Alignment explanation
Indices: 19915713--19915763 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
19915703 TTTATAGAAA
*
19915713 ATTTAATATTTATTAGTATAATAT
1 ATTTAACATTTATTA-TATAATAT
** *
19915737 ATTTTGCATTTATTATATAATTT
1 ATTTAACATTTATTATATAATAT
19915760 ATTT
1 ATTT
19915764 GGCTTACGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
ATTTAACATTTATTATATAATAT
Found at i:19917601 original size:35 final size:35
Alignment explanation
Indices: 19917562--19917630 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
19917552 TTCAGTCAAA
*
19917562 TAAGAAATTGCTTGCAAGTTAAGTTAAACAAAATC
1 TAAGAAATTGCTTGCAAGTCAAGTTAAACAAAATC
* *
19917597 TAAGAGATTTCTTGCAAGTCAAGTTAAACAAAAT
1 TAAGAAATTGCTTGCAAGTCAAGTTAAACAAAAT
19917631 ATATTATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (35 bp):
TAAGAAATTGCTTGCAAGTCAAGTTAAACAAAATC
Found at i:19925774 original size:98 final size:97
Alignment explanation
Indices: 19925601--19925782 Score: 222
Period size: 98 Copynumber: 1.9 Consensus size: 97
19925591 TTAAAAAATC
* * * *
19925601 TTATTTATACTATATATAAAATAATTGATTAAATTAGTGTCACGAGTCAATTCAACATCAATTCA
1 TTATTTATACTATATATAAAATAATTGATTAAATTAGTATCACGAGTCAAATCAACACCAATTAA
* *
19925666 GCTATAAAATTATTAAAATGCTTTTACTTTAT
66 ACTACAAAATTATTAAAATGCTTTTACTTTAT
* * * * *
19925698 TTATATTATACTATATATAAAATGATTGATTGAATTCA-TATCACGAGTTAAATCGATACCAATT
1 TTAT-TTATACTATATATAAAATAATTGATTAAATT-AGTATCACGAGTCAAATCAACACCAATT
* *
19925762 AAATTACGAAATTATTAAAAT
64 AAACTACAAAATTATTAAAAT
19925783 ACTCTTAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
97 4 0.06
98 65 0.93
99 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (97 bp):
TTATTTATACTATATATAAAATAATTGATTAAATTAGTATCACGAGTCAAATCAACACCAATTAA
ACTACAAAATTATTAAAATGCTTTTACTTTAT
Found at i:19926189 original size:21 final size:20
Alignment explanation
Indices: 19926141--19926191 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
19926131 TTACTGTTGT
* *
19926141 TATTAATTTCATTGTTACAA
1 TATTAATCTCATCGTTACAA
*
19926161 TATCTAATCTCATCGTTACAG
1 TAT-TAATCTCATCGTTACAA
19926182 TAATTAATCT
1 T-ATTAATCT
19926192 TAACGCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (20 bp):
TATTAATCTCATCGTTACAA
Found at i:19927607 original size:8 final size:8
Alignment explanation
Indices: 19927596--19927631 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
19927586 TTTATTAATA
19927596 TTTTTTTC
1 TTTTTTTC
19927604 -TTTTTTC
1 TTTTTTTC
19927611 TTTTTTTC
1 TTTTTTTC
*
19927619 TTTTTGTC
1 TTTTTTTC
19927627 TTTTT
1 TTTTT
19927632 ATGAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (8 bp):
TTTTTTTC
Found at i:19927616 original size:15 final size:16
Alignment explanation
Indices: 19927596--19927631 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
19927586 TTTATTAATA
19927596 TTTTTTTCTTTTT-TC
1 TTTTTTTCTTTTTGTC
19927611 TTTTTTTCTTTTTGTC
1 TTTTTTTCTTTTTGTC
19927627 TTTTT
1 TTTTT
19927632 ATGAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTCTTTTTGTC
Found at i:19929747 original size:230 final size:230
Alignment explanation
Indices: 19929344--19929786 Score: 859
Period size: 230 Copynumber: 1.9 Consensus size: 230
19929334 TATATATTAT
*
19929344 ATGAAAGAACAGAAAATGGGGAGAAAATTTTGCAGGAGGTAGGACAAGGACAGCAATATGCAGGA
1 ATGAAAGAACAGAAAATGGGGAGAAAATTCTGCAGGAGGTAGGACAAGGACAGCAATATGCAGGA
19929409 TGAAACTACAACAGGCAAGCATTGCATTCACACTACGGTGATCATTATCTATATTGCTTGGGCAC
66 TGAAACTACAACAGGCAAGCATTGCATTCACACTACGGTGATCATTATCTATATTGCTTGGGCAC
*
19929474 TTTATTTTCCTTTAAGTACTCATGTCCAGTGACCGTGTTCAATGTATATTTGGATACGAGTATGA
131 TTTATTTTCCTTCAAGTACTCATGTCCAGTGACCGTGTTCAATGTATATTTGGATACGAGTATGA
19929539 ATATATGATCCCCCAAGAGGCAAGCAATATGCAGG
196 ATATATGATCCCCCAAGAGGCAAGCAATATGCAGG
19929574 ATGAAAGAACAGAAAATGGGGAGAAAATTCTGCAGGAGGTAGGACAAGGACAGCAATATGCAGGA
1 ATGAAAGAACAGAAAATGGGGAGAAAATTCTGCAGGAGGTAGGACAAGGACAGCAATATGCAGGA
19929639 TGAAACTACAACAGGCAAGCATTGCATTCACACTACGGTGATCATTATCTATATTGCTTGGGCAC
66 TGAAACTACAACAGGCAAGCATTGCATTCACACTACGGTGATCATTATCTATATTGCTTGGGCAC
*
19929704 TTTATTTTCCTTCAAGTACTCATGTCCAGTGACCGTGTTCAATGTATATTTGGATACTAGTATGA
131 TTTATTTTCCTTCAAGTACTCATGTCCAGTGACCGTGTTCAATGTATATTTGGATACGAGTATGA
19929769 ATATATGATCCCCCAAGA
196 ATATATGATCCCCCAAGA
19929787 ACCCTCTAAA
Statistics
Matches: 210, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
230 210 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (230 bp):
ATGAAAGAACAGAAAATGGGGAGAAAATTCTGCAGGAGGTAGGACAAGGACAGCAATATGCAGGA
TGAAACTACAACAGGCAAGCATTGCATTCACACTACGGTGATCATTATCTATATTGCTTGGGCAC
TTTATTTTCCTTCAAGTACTCATGTCCAGTGACCGTGTTCAATGTATATTTGGATACGAGTATGA
ATATATGATCCCCCAAGAGGCAAGCAATATGCAGG
Found at i:19938755 original size:181 final size:181
Alignment explanation
Indices: 19938451--19938814 Score: 683
Period size: 181 Copynumber: 2.0 Consensus size: 181
19938441 CCTATATTAT
*
19938451 TCGAATATTTATTTTATTTTTATGAAATATTTATTTTTAATACATATTGAATAATGTTCGTATTT
1 TCGAATATTTATTTTATTTTTATGAAATATTTATATTTAATACATATTGAATAATGTTCGTATTT
19938516 AGTACACTGTTAATAAAATATTTTAACTCTACTGACACATGCTCTCTTATTTAATTCTTGAATTA
66 AGTACACTGTTAATAAAATATTTTAACTCTACTGACACATGCTCTCTTATTTAATTCTTGAATTA
* *
19938581 GTAGCTTTTGCAAGAATAATTATTTTATACACAATCATTAAAATAAAAAAC
131 GTAACTTTTACAAGAATAATTATTTTATACACAATCATTAAAATAAAAAAC
19938632 TCGAATATTTATTTTATTTTTATGAAATATTTATATTTAATACATATTGAATAATGTTCGTATTT
1 TCGAATATTTATTTTATTTTTATGAAATATTTATATTTAATACATATTGAATAATGTTCGTATTT
19938697 AGTACACTGTTAATAAAATATTTTAACTCTACTGACACATGCTCTCTTATTTAATTCTTGAATTA
66 AGTACACTGTTAATAAAATATTTTAACTCTACTGACACATGCTCTCTTATTTAATTCTTGAATTA
* *
19938762 GTAACTTTTACAAGAATAATTATTTTATACACTATTATTAAAATAAAAAAC
131 GTAACTTTTACAAGAATAATTATTTTATACACAATCATTAAAATAAAAAAC
19938813 TC
1 TC
19938815 TACAAACAAA
Statistics
Matches: 178, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
181 178 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (181 bp):
TCGAATATTTATTTTATTTTTATGAAATATTTATATTTAATACATATTGAATAATGTTCGTATTT
AGTACACTGTTAATAAAATATTTTAACTCTACTGACACATGCTCTCTTATTTAATTCTTGAATTA
GTAACTTTTACAAGAATAATTATTTTATACACAATCATTAAAATAAAAAAC
Found at i:19945559 original size:56 final size:56
Alignment explanation
Indices: 19945465--19945699 Score: 290
Period size: 56 Copynumber: 4.2 Consensus size: 56
19945455 AATGGTTTGC
**
19945465 AGCGTCGTTTGGACGCTTTGTCACTTGAGATTATCATATAAACTGCGATAATTTAT
1 AGCGTCGTTTGGACGCTTTGTCACTTGAGATTGCCATATAAACTGCGATAATTTAT
** * * * * * * *
19945521 AATGTCGTTTAGACGCTTTGTCACTTAATATTGCCATATAAGCTACGATAGTTTGT
1 AGCGTCGTTTGGACGCTTTGTCACTTGAGATTGCCATATAAACTGCGATAATTTAT
* * *
19945577 AGCGTTGTTTGGACGATTTGTCACTTGAGATTGCCATATAAACTGCGTTAATTTAT
1 AGCGTCGTTTGGACGCTTTGTCACTTGAGATTGCCATATAAACTGCGATAATTTAT
* * * * *
19945633 AGCGTCGTTTGGATGCTTTGTCACTTGAGATTGCCATATAAGCTGCAATAGTTTGT
1 AGCGTCGTTTGGACGCTTTGTCACTTGAGATTGCCATATAAACTGCGATAATTTAT
*
19945689 AGCGTCATTTG
1 AGCGTCGTTTG
19945700 AACACTTTTT
Statistics
Matches: 147, Mismatches: 32, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
56 147 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (56 bp):
AGCGTCGTTTGGACGCTTTGTCACTTGAGATTGCCATATAAACTGCGATAATTTAT
Found at i:19945598 original size:112 final size:112
Alignment explanation
Indices: 19945453--19945699 Score: 350
Period size: 112 Copynumber: 2.2 Consensus size: 112
19945443 CAAATAGACC
* * * *
19945453 ACAATGGTTTGCAGCGTCGTTTGGACGCTTTGTCACTTGAGATTATCATATAAACTGCGATAATT
1 ACAATAGTTTGTAGCGTCGTTTGGACGATTTGTCACTTGAGATTACCATATAAACTGCGATAATT
* *
19945518 TATAATGTCGTTTAGACGCTTTGTCACTTAATATTGCCATATAAGCT
66 TATAACGTCGTTTAGACGCTTTGTCACTTAAGATTGCCATATAAGCT
* * * *
19945565 ACGATAGTTTGTAGCGTTGTTTGGACGATTTGTCACTTGAGATTGCCATATAAACTGCGTTAATT
1 ACAATAGTTTGTAGCGTCGTTTGGACGATTTGTCACTTGAGATTACCATATAAACTGCGATAATT
* * * *
19945630 TATAGCGTCGTTTGGATGCTTTGTCACTTGAGATTGCCATATAAGCT
66 TATAACGTCGTTTAGACGCTTTGTCACTTAAGATTGCCATATAAGCT
* *
19945677 GCAATAGTTTGTAGCGTCATTTG
1 ACAATAGTTTGTAGCGTCGTTTG
19945700 AACACTTTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
112 117 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (112 bp):
ACAATAGTTTGTAGCGTCGTTTGGACGATTTGTCACTTGAGATTACCATATAAACTGCGATAATT
TATAACGTCGTTTAGACGCTTTGTCACTTAAGATTGCCATATAAGCT
Found at i:19945956 original size:31 final size:32
Alignment explanation
Indices: 19945877--19946001 Score: 106
Period size: 31 Copynumber: 4.2 Consensus size: 32
19945867 TCGGTACTTG
19945877 AACTTGACACTTTTTT-CTAATTTGGTACCT-
1 AACTTGACACTTTTTTCCTAATTTGGTACCTA
* *
19945907 AA-TT----TTTTTTGTCC-AATTTGGTACTTA
1 AACTTGACACTTTTT-TCCTAATTTGGTACCTA
* *
19945934 AACTTGACA-TTTTTTCCTAATTTAGTAACTA
1 AACTTGACACTTTTTTCCTAATTTGGTACCTA
* ** *
19945965 AACTTGAAACTTTTTTTTTAAGTTGGTACCTA
1 AACTTGACACTTTTTTCCTAATTTGGTACCTA
19945997 AACTT
1 AACTT
19946002 TTTGGGATCC
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
25 5 0.07
26 12 0.16
27 3 0.04
28 2 0.03
29 2 0.03
30 5 0.07
31 23 0.31
32 22 0.30
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (32 bp):
AACTTGACACTTTTTTCCTAATTTGGTACCTA
Found at i:19945998 original size:32 final size:31
Alignment explanation
Indices: 19945924--19946001 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
19945914 TTTGTCCAAT
* * *
19945924 TTGGTACTTAAACTTGACATTTTTTCCTAAT
1 TTGGTACCTAAACTTGAAATTTTTTCCTAAG
* * **
19945955 TTAGTAACTAAACTTGAAACTTTTTTTTTAAG
1 TTGGTACCTAAACTTGAAA-TTTTTTCCTAAG
19945987 TTGGTACCTAAACTT
1 TTGGTACCTAAACTT
19946002 TTTGGGATCC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 15 0.41
32 22 0.59
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.46
Consensus pattern (31 bp):
TTGGTACCTAAACTTGAAATTTTTTCCTAAG
Found at i:19946029 original size:91 final size:89
Alignment explanation
Indices: 19945877--19946057 Score: 220
Period size: 91 Copynumber: 2.0 Consensus size: 89
19945867 TCGGTACTTG
* * * ** *
19945877 AACTTGACACTTTTTTCTAATTTGGTACCTAATTTTTTTTGTCCAATTTGGTACTTAAACTTGAC
1 AACTTGAAACTTTTTTCTAAGTTGGTACCTAACTTTTTGGGTCCAATTTGGTACTTAAACTTAAC
19945942 -ATTTTTTCCTAATTTAGTAACTA
66 TATTTTTTCCTAATTTAGTAACTA
* *
19945965 AACTTGAAACTTTTTTTTTAAGTTGGTACCTAAACTTTTTGGGATCCAATTTGGTACTTGAACTT
1 AACTTGAAAC-TTTTTTCTAAGTTGGTACCT-AACTTTTTGGG-TCCAATTTGGTACTTAAACTT
* * * *
19946030 AACTTTTTTTTTCTAATTTGGTACCTA
63 AACTATTTTTTCCTAATTTAGTAACTA
19946057 A
1 A
19946058 CCTTTTTTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
88 9 0.12
89 18 0.23
90 8 0.10
91 22 0.29
92 20 0.26
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (89 bp):
AACTTGAAACTTTTTTCTAAGTTGGTACCTAACTTTTTGGGTCCAATTTGGTACTTAAACTTAAC
TATTTTTTCCTAATTTAGTAACTA
Found at i:19948873 original size:32 final size:31
Alignment explanation
Indices: 19948823--19948883 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
19948813 CCCTATTCTT
* *
19948823 AAAATCAATGTACGAACCCAGTTCTTAAAAAA
1 AAAATCAATGTACAAACCCA-TTCTGAAAAAA
19948855 AAAATCAATAG-ACAAACCCATTCTGAAAA
1 AAAATCAAT-GTACAAACCCATTCTGAAAA
19948884 GATCAATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 8 0.31
32 17 0.65
33 1 0.04
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (31 bp):
AAAATCAATGTACAAACCCATTCTGAAAAAA
Found at i:19950802 original size:29 final size:28
Alignment explanation
Indices: 19950438--19950799 Score: 251
Period size: 29 Copynumber: 12.5 Consensus size: 28
19950428 CAGAAATCAT
* * **
19950438 ATTTTGACCCCAAACTTCTCTAAAATTAT
1 ATTTTTACCCCAAACTTC-CAAAAATTCC
* * * *
19950467 ATTTTGACCCTAAAACTTTCAAAAATTAC
1 ATTTTTACCC-CAAACTTCCAAAAATTCC
* *
19950496 ATTTTTAGCCCTAAAACTTCCAAAAATTGC
1 ATTTTTA-CCC-CAAACTTCCAAAAATTCC
* * *
19950526 ATTTTTACCCCTGAACTTTCAAAAATTAC
1 ATTTTTACCCC-AAACTTCCAAAAATTCC
* * * *
19950555 ATTTTCACCCTCGAACTTCTAAAAATTCA
1 ATTTTTACCC-CAAACTTCCAAAAATTCC
* *
19950584 ATTTTTACCCTGAAACTTCCAAAAATTAC
1 ATTTTTACCC-CAAACTTCCAAAAATTCC
* **
19950613 ATTTTT-CCCTCGAACTTTTAAAAATTCC
1 ATTTTTACCC-CAAACTTCCAAAAATTCC
* * * *
19950641 ATTTTT-TCCCGAATTTCCAAAAATTCA
1 ATTTTTACCCCAAACTTCCAAAAATTCC
* *
19950668 ATTTTTGCCCCCGAACTTCCAAAAATTCC
1 ATTTTT-ACCCCAAACTTCCAAAAATTCC
* * *
19950697 ATTTTTGCCCTCGAATTTCCAAAAATTCC
1 ATTTTTACCC-CAAACTTCCAAAAATTCC
** * *
19950726 ATTTTTAATCCTAAAAATTCCTAAAATTCC
1 ATTTTT-A-CCCCAAACTTCCAAAAATTCC
*
19950756 ATTTTGGACCCCGAAACTTCCAAAAATTCC
1 ATTTT-TACCCC-AAACTTCCAAAAATTCC
*
19950786 ATTTTAACCCCAAA
1 ATTTTTACCCCAAA
19950800 ACTCTTAAAA
Statistics
Matches: 273, Mismatches: 49, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
27 20 0.07
28 31 0.11
29 146 0.53
30 74 0.27
31 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (28 bp):
ATTTTTACCCCAAACTTCCAAAAATTCC
Found at i:19950809 original size:29 final size:28
Alignment explanation
Indices: 19950718--19950817 Score: 83
Period size: 30 Copynumber: 3.4 Consensus size: 28
19950708 CGAATTTCCA
** * *
19950718 AAAATTCCATTTTTAATCCTAAAAATTCCT
1 AAAATTCCA-TTTTAA-CCCCAAAACTCTT
* * **
19950748 AAAATTCCATTTTGGACCCCGAAACTTCCA
1 AAAATTCCATTTT-AACCCCAAAAC-TCTT
19950778 AAAATTCCATTTTAACCCCAAAACTCTT
1 AAAATTCCATTTTAACCCCAAAACTCTT
19950806 AAAATTACCATT
1 AAAATT-CCATT
19950818 CTACCCTCGG
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
28 8 0.14
29 23 0.40
30 26 0.46
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCAAAACTCTT
Found at i:19951745 original size:11 final size:11
Alignment explanation
Indices: 19951708--19951744 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
19951698 GAAGATCAAC
19951708 ATTTTAAACGT
1 ATTTTAAACGT
19951719 ATTTTAAACGT
1 ATTTTAAACGT
19951730 ATTTTAAACGT
1 ATTTTAAACGT
19951741 -TTTT
1 ATTTT
19951745 TGGTGATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (11 bp):
ATTTTAAACGT
Found at i:19963293 original size:206 final size:206
Alignment explanation
Indices: 19962931--19963337 Score: 552
Period size: 206 Copynumber: 2.0 Consensus size: 206
19962921 AAGTATGCCA
* * * **
19962931 ACTCGAGGCTCAATGCGAGCAAATCCTTGAATCCTAGCTTCCTGATGAGATACTGAGAAGCGGGT
1 ACTCGAGGCTCAATGCGAGCAAATCCTTGAACCCCAACTTCCTGATGAGATACTGAGAAGCAAGT
* * *
19962996 CGAAGCAATAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAG
66 CGAAGCAATAAATGGTTAGCTTCCTGATGAGACACAGAGAAGTGAACCAAATCCGTCTTCCTGAG
* * * * * * *
19963061 GAGATCTAGAGAAGCGAATTAAAACAAGT-GGTGCGGTCATCTTCCTGATGAGACACTGAGAAGA
131 GAGAACCAGAGAAGCGAATCAAAACAAATAAG-GCGGTCATCTTCCTGATAAAACACTGAGAAGA
19963125 AGACCAAATCAT
195 AGACCAAATCAT
*
19963137 ACTCG-GGCTCAATGCGAGCAAAT-CTTCGAACCCCAACTTCCTGATGAGTTACTGAGAAGCAAG
1 ACTCGAGGCTCAATGCGAGCAAATCCTT-GAACCCCAACTTCCTGATGAGATACTGAGAAGCAAG
*
19963200 TCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTG
65 TCGAAGCAAT-AAATGGTTAGCTTCCTGATGAGACACAGAGAAGTGAACCAAATCCGTCTTCCTG
* * * *
19963265 ATGA-AACACAGAGAAGTGGATCAAAACAAATAAGGCGGTCATCTTCCTGATAAAATACTGAGAA
129 AGGAGAAC-CAGAGAAGCGAATCAAAACAAATAAGGCGGTCATCTTCCTGATAAAACACTGAGAA
*
19963329 GAAGGCCAA
193 GAAGACCAA
19963338 GCCAATGAAA
Statistics
Matches: 175, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
204 3 0.02
205 60 0.34
206 111 0.63
207 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (206 bp):
ACTCGAGGCTCAATGCGAGCAAATCCTTGAACCCCAACTTCCTGATGAGATACTGAGAAGCAAGT
CGAAGCAATAAATGGTTAGCTTCCTGATGAGACACAGAGAAGTGAACCAAATCCGTCTTCCTGAG
GAGAACCAGAGAAGCGAATCAAAACAAATAAGGCGGTCATCTTCCTGATAAAACACTGAGAAGAA
GACCAAATCAT
Found at i:19963698 original size:6 final size:6
Alignment explanation
Indices: 19963689--19963765 Score: 72
Period size: 6 Copynumber: 13.3 Consensus size: 6
19963679 GTTTAAATAG
* * *
19963689 ATTTAA ATTT-A TTGTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTT-G
1 ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
19963735 CTTTAA ATTTAA ATTT-A ATTAAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
19963766 CAATATTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 13 0.23
6 41 0.73
7 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:19963725 original size:17 final size:17
Alignment explanation
Indices: 19963689--19963765 Score: 109
Period size: 17 Copynumber: 4.5 Consensus size: 17
19963679 GTTTAAATAG
19963689 ATTTAAATTTATTGTTAA
1 ATTTAAATTTATT-TTAA
19963707 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
**
19963724 ATTTAAATTTGCTTTAA
1 ATTTAAATTTATTTTAA
* *
19963741 ATTTAAATTTAATTAAA
1 ATTTAAATTTATTTTAA
19963758 ATTTAAAT
1 ATTTAAAT
19963766 CAATATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 41 0.76
18 13 0.24
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:19963754 original size:11 final size:11
Alignment explanation
Indices: 19963706--19963763 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
19963696 TTTATTGTTA
19963706 AATTTAAATTT
1 AATTTAAATTT
*
19963717 ATTTTAAATTT
1 AATTTAAATTT
**
19963728 AAATTT-GCTTT
1 -AATTTAAATTT
19963739 AAATTTAAATTT
1 -AATTTAAATTT
*
19963751 AATTAAAATTT
1 AATTTAAATTT
19963762 AA
1 AA
19963764 ATCAATATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 31 0.82
12 7 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:19964707 original size:13 final size:13
Alignment explanation
Indices: 19964691--19964734 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
19964681 TGAAATATTA
19964691 AATATTAATAAAT
1 AATATTAATAAAT
**
19964704 AATATTAATATTT
1 AATATTAATAAAT
*
19964717 AATAATAATAAAAT
1 AATATTAAT-AAAT
19964731 AATA
1 AATA
19964735 AAAAGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATATTAATAAAT
Found at i:19964720 original size:26 final size:27
Alignment explanation
Indices: 19964684--19964734 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
19964674 GTTTTCATGA
*
19964684 AATATTAAATATTAAT-AAATAATATT
1 AATATTAAATAATAATAAAATAATATT
*
19964710 AATATTTAATAATAATAAAATAATA
1 AATATTAAATAATAATAAAATAATA
19964735 AAAAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATATTAAATAATAATAAAATAATATT
Found at i:19965793 original size:29 final size:28
Alignment explanation
Indices: 19965739--19966063 Score: 151
Period size: 29 Copynumber: 11.1 Consensus size: 28
19965729 CCCTGGAGGT
* * * *
19965739 CCCTAAACTATCCAAAAATCATATTTTGA
1 CCCTAAACT-TTCAAAAATTACATTTTTA
*
19965768 CCCTAAACTTCTCCAAAATTACATTTTTAA
1 CCCTAAACTT-TCAAAAATTACATTTTT-A
* *
19965798 CCACAAAACTTTCAAAAATTACATTTTCA
1 CC-CTAAACTTTCAAAAATTACATTTTTA
*
19965827 CCATTAAAACTTTCAAAAATT-CTATTTTTTA
1 CC-CT-AAACTTTCAAAAATTAC-A-TTTTTA
*
19965858 CCCCAAAACTTTCAAAAATTACATTTTTA
1 -CCCTAAACTTTCAAAAATTACATTTTTA
** * * *
19965887 CCCCCGAATTTTCAAAAATTCCATTTTTG
1 -CCCTAAACTTTCAAAAATTACATTTTTA
* * *
19965916 CCCTGAA-TTACCAAAAATTTCATTTTTGCA
1 CCCTAAACTT-TCAAAAATTACATTTTT--A
* *
19965946 CCC-AAA-TTTCCAAAAATTCCATTTTAAA
1 CCCTAAACTTT-CAAAAATTACATTTT-TA
** * * *
19965974 CCCTAAAAATTCTAACAATTCCACTTTTGA
1 CCCTAAACTTTC-AAAAATTACA-TTTTTA
* * * *
19966004 TCCCGAAACTTCCAAAAATTCCA-TTTAA
1 -CCCTAAACTTTCAAAAATTACATTTTTA
* *
19966032 CCCCGAAACTCTC-AAAATTACCA-TTTTA
1 -CCCTAAACTTTCAAAAATTA-CATTTTTA
19966060 CCCT
1 CCCT
19966064 CGGATGTCCA
Statistics
Matches: 236, Mismatches: 41, Indels: 40
0.74 0.13 0.13
Matches are distributed among these distances:
27 11 0.05
28 46 0.19
29 78 0.33
30 74 0.31
31 25 0.11
32 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (28 bp):
CCCTAAACTTTCAAAAATTACATTTTTA
Found at i:19965818 original size:30 final size:29
Alignment explanation
Indices: 19965772--19965914 Score: 153
Period size: 30 Copynumber: 4.8 Consensus size: 29
19965762 TTTTGACCCT
*
19965772 AAACTTCTCCAAAATTACATTTTTAACCACA
1 AAACTT-TCAAAAATTACATTTTT-ACCACA
* *
19965803 AAACTTTCAAAAATTACATTTTCACCATTA
1 AAACTTTCAAAAATTACATTTTTACCA-CA
*
19965833 AAACTTTCAAAAATT-CTATTTTTTACCCCA
1 AAACTTTCAAAAATTAC-A-TTTTTACCACA
* *
19965863 AAACTTTCAAAAATTACATTTTTACCCCC
1 AAACTTTCAAAAATTACATTTTTACCACA
* * *
19965892 GAATTTTCAAAAATTCCATTTTT
1 AAACTTTCAAAAATTACATTTTT
19965915 GCCCTGAATT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
29 35 0.36
30 49 0.50
31 14 0.14
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (29 bp):
AAACTTTCAAAAATTACATTTTTACCACA
Found at i:19966024 original size:30 final size:29
Alignment explanation
Indices: 19965743--19966029 Score: 142
Period size: 30 Copynumber: 9.7 Consensus size: 29
19965733 GGAGGTCCCT
*
19965743 AAACTATCCAAAAA-T-CATATTTTGACCCT
1 AAACT-TCCAAAAATTCCAT-TTTTGACCCG
* * * *
19965772 AAACTTCTCCAAAATTACATTTTTAACCACA
1 AAACTTC-CAAAAATTCCATTTTTGACC-CG
* * * **
19965803 AAACTTTCAAAAATTACA-TTTTCACCATTA
1 AAACTTCCAAAAATTCCATTTTTGACC--CG
* * * *
19965833 AAACTTTCAAAAATTCTATTTTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTGA-CCCG
* *
19965863 AAACTTTCAAAAATTACATTTTT-ACCCCCG
1 AAACTTCCAAAAATTCCATTTTTGA--CCCG
* *
19965893 -AATTTTCAAAAATTCCATTTTTG-CCCTG
1 AAACTTCCAAAAATTCCATTTTTGACCC-G
*
19965921 -AA-TTACCAAAAATTTCATTTTTGCACCC-
1 AAACTT-CCAAAAATTCCATTTTTG-ACCCG
* ** *
19965949 AAATTTCCAAAAATTCCATTTTAAACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCC-G
* * * *
19965979 AAAATTCTAACAATTCCACTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTTGA-CCCG
19966009 AAACTTCCAAAAATTCCATTT
1 AAACTTCCAAAAATTCCATTT
19966030 AACCCCGAAA
Statistics
Matches: 207, Mismatches: 33, Indels: 35
0.75 0.12 0.13
Matches are distributed among these distances:
27 5 0.02
28 25 0.12
29 55 0.27
30 102 0.49
31 18 0.09
32 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCG
Found at i:19966039 original size:28 final size:29
Alignment explanation
Indices: 19965772--19966059 Score: 131
Period size: 30 Copynumber: 9.8 Consensus size: 29
19965762 TTTTGACCCT
* * * *
19965772 AAACTTCTCCAAAATTACATTTTTAACCACA
1 AAACTTC-CAAAAATTCCA-TTTTAACCCCG
* * * ***
19965803 AAACTTTCAAAAATTACATTTTCACCATTA
1 AAACTTCCAAAAATTCCATTTTAACC-CCG
* * * *
19965833 AAACTTTCAAAAATTCTATTTTTTACCCCA
1 AAACTTCCAAAAATTCCA-TTTTAACCCCG
* * *
19965863 AAACTTTCAAAAATTACATTTTTACCCCCG
1 AAACTTCCAAAAATTCCA-TTTTAACCCCG
* * ** *
19965893 -AATTTTCAAAAATTCCATTTTTGCCCTG
1 AAACTTCCAAAAATTCCATTTTAACCCCG
* **
19965921 -AA-TTACCAAAAATTTCATTTTTGCACCC-
1 AAACTT-CCAAAAATTCCATTTTAAC-CCCG
* **
19965949 AAATTTCCAAAAATTCCATTTTAAACCCTA
1 AAACTTCCAAAAATTCCATTTT-AACCCCG
* * * * *
19965979 AAAATTCTAACAATTCCACTTTTGATCCCG
1 AAACTTCCAAAAATTCCA-TTTTAACCCCG
19966009 AAACTTCCAAAAATTCCA-TTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTAACCCCG
19966037 AAAC-TCTC-AAAATTACCATTTTA
1 AAACTTC-CAAAAATT-CCATTTTA
19966060 CCCTCGGATG
Statistics
Matches: 206, Mismatches: 39, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
27 10 0.05
28 43 0.21
29 47 0.23
30 89 0.43
31 17 0.08
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTAACCCCG
Found at i:19970030 original size:25 final size:25
Alignment explanation
Indices: 19969996--19970071 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
19969986 ATACATTAAG
19969996 AATGTACATTTTTTATTCCACAAAT
1 AATGTACATTTTTTATTCCACAAAT
19970021 AATGTACATTTTTTATTCCACAAAT
1 AATGTACATTTTTTATTCCACAAAT
19970046 AATGTACATTTTTTATTCCACAAAT
1 AATGTACATTTTTTATTCCACAAAT
19970071 A
1 A
19970072 TTTTAAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (25 bp):
AATGTACATTTTTTATTCCACAAAT
Found at i:19975822 original size:18 final size:18
Alignment explanation
Indices: 19975799--19975834 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19975789 TTTAGGGTTT
*
19975799 GGTTAATATTAAGGTTAG
1 GGTTAAGATTAAGGTTAG
*
19975817 GGTTAAGATTAATGTTAG
1 GGTTAAGATTAAGGTTAG
19975835 AGTTTAAGGT
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:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (18 bp):
GGTTAAGATTAAGGTTAG
Found at i:19977626 original size:11 final size:11
Alignment explanation
Indices: 19977610--19977635 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19977600 TTAGAATTAG
19977610 TATTATATATT
1 TATTATATATT
19977621 TATTATATATT
1 TATTATATATT
19977632 TATT
1 TATT
19977636 TTTTAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATATATT
Found at i:19978300 original size:22 final size:21
Alignment explanation
Indices: 19978275--19978315 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19978265 ATATAAAAAT
*
19978275 TGATTCAATTAGTTTTATATCG
1 TGATTCAATT-GATTTATATCG
*
19978297 TGATTTAATTGATTTATAT
1 TGATTCAATTGATTTATAT
19978316 TGACTCTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (21 bp):
TGATTCAATTGATTTATATCG
Found at i:19978958 original size:43 final size:43
Alignment explanation
Indices: 19978813--19978983 Score: 123
Period size: 43 Copynumber: 4.0 Consensus size: 43
19978803 GTGGAAAAAT
* * *
19978813 GCCGCTATAGAACATGGTCTTTAGCTG-CGCTTTTCCCACAAAC
1 GCCGCTAAAGAACATGTTCTTTAAC-GACGCTTTTCCCACAAAC
* * * * * *
19978856 GCTGTTAAAGACCATGATT-TTTAGC-AGCGCTTTTTCCATAAAC
1 GCCGCTAAAGAACATG-TTCTTTAACGA-CGCTTTTCCCACAAAC
** ** *
19978899 ATCAATAAAGACCATGTTCTTTAACGACGCTTTTCCCACAAAC
1 GCCGCTAAAGAACATGTTCTTTAACGACGCTTTTCCCACAAAC
* * * * *
19978942 GCCGCTATAGAACATGTTATTTAACAACGTTTTTCCTACAAA
1 GCCGCTAAAGAACATGTTCTTTAACGACGCTTTTCCCACAAA
19978984 TCTTATCAAC
Statistics
Matches: 98, Mismatches: 25, Indels: 10
0.74 0.19 0.08
Matches are distributed among these distances:
42 2 0.02
43 94 0.96
44 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (43 bp):
GCCGCTAAAGAACATGTTCTTTAACGACGCTTTTCCCACAAAC
Found at i:19979245 original size:25 final size:25
Alignment explanation
Indices: 19979217--19979269 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
19979207 AACAATCAAA
* *
19979217 ATAC-ACTAACATTTAACCGTAATGT
1 ATACAACTAACATTCAACC-CAATGT
*
19979242 ATACAACTAGCATTCAACCCAATGT
1 ATACAACTAACATTCAACCCAATGT
19979267 ATA
1 ATA
19979270 GAAGTAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.28
Consensus pattern (25 bp):
ATACAACTAACATTCAACCCAATGT
Found at i:19982087 original size:41 final size:41
Alignment explanation
Indices: 19982049--19982189 Score: 158
Period size: 41 Copynumber: 3.4 Consensus size: 41
19982039 CGTTTTTCCT
*
19982049 ATAAACGCCGCTAATGTTCTTACCTTTTGCGGCATTTTCTC
1 ATAAACGCCGCTAATGCTCTTACCTTTTGCGGCATTTTCTC
* * * * *
19982090 CTGAACGCCACTAATGCTCTTACTTTTTGTGGCATTTTCTC
1 ATAAACGCCGCTAATGCTCTTACCTTTTGCGGCATTTTCTC
** * *
19982131 ATAAATACCGCTAATGCT-TTACCTTTTACGGCGTTTTCCTC
1 ATAAACGCCGCTAATGCTCTTACCTTTTGCGGCATTTT-CTC
* *
19982172 ATAAATGCCGCTATTGCT
1 ATAAACGCCGCTAATGCT
19982190 TAACCTCTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 15 0.18
41 67 0.82
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (41 bp):
ATAAACGCCGCTAATGCTCTTACCTTTTGCGGCATTTTCTC
Found at i:19985916 original size:17 final size:18
Alignment explanation
Indices: 19985896--19985943 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
19985886 AGAATAAAGT
*
19985896 TTTAAATTAAAAT-TCTA
1 TTTAAATTAAAATGTCCA
*
19985913 TTTAATTTAAAATGTCCA
1 TTTAAATTAAAATGTCCA
*
19985931 TTTACATTAAAAT
1 TTTAAATTAAAAT
19985944 ATAAAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTAAATTAAAATGTCCA
Found at i:19986236 original size:20 final size:21
Alignment explanation
Indices: 19986203--19986256 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
19986193 ATCATCACCT
*
19986203 GCAAAA-ACATAA-AACACAGA
1 GCAAAAGACAAAACAACA-AGA
*
19986223 GACAAAAGGCAAAACAACAAGA
1 G-CAAAAGACAAAACAACAAGA
19986245 GCAAAAGACAAA
1 GCAAAAGACAAA
19986257 TGCAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.04
21 15 0.54
22 8 0.29
23 4 0.14
ACGTcount: A:0.65, C:0.19, G:0.15, T:0.02
Consensus pattern (21 bp):
GCAAAAGACAAAACAACAAGA
Found at i:19986249 original size:21 final size:23
Alignment explanation
Indices: 19986215--19986256 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
19986205 AAAAACATAA
*
19986215 AACACAGAGACAAAAGGCAAAAC
1 AACACAGAGACAAAAGACAAAAC
19986238 AACA-AGAG-CAAAAGACAAA
1 AACACAGAGACAAAAGACAAA
19986257 TGCAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.64, C:0.19, G:0.17, T:0.00
Consensus pattern (23 bp):
AACACAGAGACAAAAGACAAAAC
Found at i:19989308 original size:26 final size:26
Alignment explanation
Indices: 19989243--19989309 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 26
19989233 ACATAGTATT
19989243 TGCTAAACATTCACCGACTCAAAACC
1 TGCTAAACATTCACCGACTCAAAACC
** ** * * *
19989269 TATTAATTAATCACCGGCTCAAAGCC
1 TGCTAAACATTCACCGACTCAAAACC
19989295 TGCTAAACATTCACC
1 TGCTAAACATTCACC
19989310 TCACATTTCT
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.31, G:0.09, T:0.24
Consensus pattern (26 bp):
TGCTAAACATTCACCGACTCAAAACC
Found at i:19997114 original size:23 final size:22
Alignment explanation
Indices: 19997070--19997130 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
19997060 GAAAGGAAAA
*
19997070 AAACA-AGAGAAAACATGTTAAG
1 AAACAGAGA-AAAACATGCTAAG
*
19997092 AAACAGAGGAAAAACGTGCTAAG
1 AAACAGA-GAAAAACATGCTAAG
*
19997115 AAGCAGAGAAAAACAT
1 AAACAGAGAAAAACAT
19997131 TGTATACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 13 0.39
23 18 0.55
24 2 0.06
ACGTcount: A:0.57, C:0.11, G:0.21, T:0.10
Consensus pattern (22 bp):
AAACAGAGAAAAACATGCTAAG
Found at i:20001368 original size:8 final size:8
Alignment explanation
Indices: 20001357--20001384 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
20001347 ATTTTTATTT
20001357 TTTTATAA
1 TTTTATAA
20001365 TTTTATAA
1 TTTTATAA
20001373 TTTTATAA
1 TTTTATAA
20001381 TTTT
1 TTTT
20001385 GACTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTATAA
Found at i:20001559 original size:16 final size:15
Alignment explanation
Indices: 20001519--20001551 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20001509 ATTTAAAAAT
20001519 TTAAAAATATA-TAAA
1 TTAAAAATA-ACTAAA
20001534 TTAAAAATAACTAAA
1 TTAAAAATAACTAAA
20001549 TTA
1 TTA
20001552 GAATATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATAACTAAA
Found at i:20006150 original size:24 final size:23
Alignment explanation
Indices: 20006090--20006159 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
20006080 TTCATTTAAT
*
20006090 TTAATTGAACATGTTTACGAACA
1 TTAATTGAACATGTTCACGAACA
** *
20006113 TTAAACGAACATGTTCATGAACA
1 TTAATTGAACATGTTCACGAACA
20006136 TATAATTGAACATGTTCACGAACA
1 T-TAATTGAACATGTTCACGAACA
20006160 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:20010685 original size:28 final size:29
Alignment explanation
Indices: 20010653--20010713 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
20010643 AAAACGGAAC
*
20010653 TTTTGGATACCCG-GGGGCAAAATAGTAA
1 TTTTGGACACCCGAGGGGCAAAATAGTAA
* * *
20010681 TTTTGGACGCGCGAGGGGCAAAATGGTAA
1 TTTTGGACACCCGAGGGGCAAAATAGTAA
20010710 TTTT
1 TTTT
20010714 TGGTGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (29 bp):
TTTTGGACACCCGAGGGGCAAAATAGTAA
Found at i:20010742 original size:59 final size:60
Alignment explanation
Indices: 20010692--20010952 Score: 388
Period size: 59 Copynumber: 4.4 Consensus size: 60
20010682 TTTGGACGCG
* * *
20010692 CGAGGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATTGGAATTTTGGAAAGTT
1 CGAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* * *
20010752 TG-GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTT
1 CGAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
20010811 CGA-GGGTAAAATGGTAATTTTTGGTGAAACCGTGGTTAAAAATGGAATTTTGGAAAGTT
1 CGAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
20010870 C-AGGGGTAAAATGGTAATTTTTGATGAAA-CTGGGGCTAAAAATGGAATTTTGGAAAGTT
1 CGAGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTT
20010929 CG-GGGGTAAAATGGTAATTTTTGG
1 CGAGGGGTAAAATGGTAATTTTTGG
20010953 ACAATTTAGG
Statistics
Matches: 182, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
58 2 0.01
59 179 0.98
60 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (60 bp):
CGAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:20010761 original size:29 final size:29
Alignment explanation
Indices: 20010664--20010949 Score: 166
Period size: 29 Copynumber: 9.7 Consensus size: 29
20010654 TTTGGATACC
* * * **
20010664 CGGGGGCAAAATAGTAATTTTGG-ACGCG
1 CGGGGGTAAAATGGTAATTTTGGAAAGTT
*
20010692 CGAGGGGCAAAATGGTAATTTTTGGTGAAA--T
1 CG-GGGGTAAAATGGTAA-TTTT-G-GAAAGTT
* *
20010723 CGAGGTTAAAATTGG-AATTTTGGAAAGTT
1 CGGGGGTAAAA-TGGTAATTTTGGAAAGTT
*
20010752 TGGGGGTAAAATGGTAATTTTTGATGAAA--T
1 CGGGGGTAAAATGGTAA-TTTTG--GAAAGTT
* *
20010782 CGGGGTTAAAAATAG-AATTTTGGAAAGTT
1 CGGGGGT-AAAATGGTAATTTTGGAAAGTT
* *
20010811 CGAGGGTAAAATGGTAATTTTTGGTGAAA--C
1 CGGGGGTAAAATGGTAA-TTTT-G-GAAAGTT
* *
20010841 CGTGGTTAAAAATGG-AATTTTGGAAAGTT
1 CGGGGGT-AAAATGGTAATTTTGGAAAGTT
* *
20010870 CAGGGGTAAAATGGTAATTTTTGATGAAA-CT
1 CGGGGGTAAAATGGTAA-TTTTG--GAAAGTT
*
20010901 -GGGGCTAAAAATGG-AATTTTGGAAAGTT
1 CGGGGGT-AAAATGGTAATTTTGGAAAGTT
20010929 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
20010950 TGGACAATTT
Statistics
Matches: 201, Mismatches: 27, Indels: 59
0.70 0.09 0.21
Matches are distributed among these distances:
27 16 0.08
28 28 0.14
29 68 0.34
30 47 0.23
31 28 0.14
32 13 0.06
33 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTGGAAAGTT
Found at i:20010953 original size:30 final size:29
Alignment explanation
Indices: 20010695--20010958 Score: 174
Period size: 30 Copynumber: 8.9 Consensus size: 29
20010685 GGACGCGCGA
*
20010695 GGGGCAAAATGGTAATTTTTGGTGAAA-TCG
1 GGGGTAAAATGGTAATTTTT-G-GAAATTCG
* * *
20010725 AGGTTAAAATTGG-AA-TTTTGGAAAGTTTG
1 GGGGTAAAA-TGGTAATTTTTGGAAA-TTCG
20010754 GGGGTAAAATGGTAATTTTTGATGAAA-TCG
1 GGGGTAAAATGGTAATTTTTG--GAAATTCG
* *
20010784 GGGTTAAAAATAG-AA-TTTTGGAAAGTTCG
1 GGGGT-AAAATGGTAATTTTTGGAAA-TTCG
* *
20010813 AGGGTAAAATGGTAATTTTTGGTGAAA-CCG
1 GGGGTAAAATGGTAATTTTT-G-GAAATTCG
* * *
20010843 TGGTTAAAAATGG-AA-TTTTGGAAAGTTCA
1 GGGGT-AAAATGGTAATTTTTGGAAA-TTCG
*
20010872 GGGGTAAAATGGTAATTTTTGATGAAACT-G
1 GGGGTAAAATGGTAATTTTTG--GAAATTCG
*
20010902 GGGCTAAAAATGG-AA-TTTTGGAAAGTTCG
1 GGGGT-AAAATGGTAATTTTTGGAAA-TTCG
20010931 GGGGTAAAATGGTAATTTTTGGACAATT
1 GGGGTAAAATGGTAATTTTTGGA-AATT
20010959 TAGGGACCTA
Statistics
Matches: 183, Mismatches: 24, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
27 16 0.09
28 26 0.14
29 50 0.27
30 52 0.28
31 27 0.15
32 12 0.07
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAATTCG
Found at i:20012686 original size:18 final size:18
Alignment explanation
Indices: 20012663--20012698 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20012653 TTTGGATTGT
*
20012663 AATTGGGCCTTAATTTGG
1 AATTGGGCCCTAATTTGG
20012681 AATTGGGCCCTAATTTGG
1 AATTGGGCCCTAATTTGG
20012699 GCCTTCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (18 bp):
AATTGGGCCCTAATTTGG
Found at i:20012765 original size:6 final size:6
Alignment explanation
Indices: 20012749--20012831 Score: 64
Period size: 6 Copynumber: 14.0 Consensus size: 6
20012739 TTAATATTAT
* ** *
20012749 TTTAAA CTTAAA TTT-AA GGTAAA TTTAAA TAAGTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAAA
* * *
20012798 -ATAAA TTTAAA TTTAAA -ATGAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
20012832 ACCCATTTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
5 10 0.17
6 43 0.74
8 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:20012791 original size:31 final size:31
Alignment explanation
Indices: 20012751--20012809 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
20012741 AATATTATTT
**
20012751 TAAACTTAAATTTAAGGTAAATTTAAATAAG
1 TAAACTTAAATTTAAAATAAATTTAAATAAG
*
20012782 TAAATTTAAATTTAAAATAAATTTAAAT
1 TAAACTTAAATTTAAAATAAATTTAAAT
20012810 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (31 bp):
TAAACTTAAATTTAAAATAAATTTAAATAAG
Found at i:20012842 original size:17 final size:17
Alignment explanation
Indices: 20012751--20012832 Score: 98
Period size: 17 Copynumber: 5.0 Consensus size: 17
20012741 AATATTATTT
* **
20012751 TAAACTTAAATTTAAGG
1 TAAATTTAAATTTAAAA
*
20012768 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
20012782 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
20012799 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
20012816 TGAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
20012833 CCCATTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 1 0.02
17 44 0.76
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:20022948 original size:43 final size:43
Alignment explanation
Indices: 20022897--20022996 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 43
20022887 TGTTATTCTT
*
20022897 TGACATGTTATTAAATTATATTACTTGACTCGTGTTAATATCG
1 TGACATGTTATTAAATTATATTACTTAACTCGTGTTAATATCG
* * *
20022940 TGGCATGTTATTAAATTATATTACTTAACTCTTGTTAATATTG
1 TGACATGTTATTAAATTATATTACTTAACTCGTGTTAATATCG
20022983 TGACATGTTATTAA
1 TGACATGTTATTAA
20022997 TTGTGTTGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATTACTTAACTCGTGTTAATATCG
Found at i:20023461 original size:6 final size:6
Alignment explanation
Indices: 20023450--20023483 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
20023440 CTCCTACACT
20023450 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAG
1 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAG
20023484 GAAGAGGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAGCC
Found at i:20023489 original size:18 final size:18
Alignment explanation
Indices: 20023450--20023489 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
20023440 CTCCTACACT
*
20023450 AGAGCCAGAGCCAGAGCC
1 AGAGCCAGAGCCAGAGCA
*
20023468 AGAGCCAGAGCCAGAGGA
1 AGAGCCAGAGCCAGAGCA
20023486 AGAG
1 AGAG
20023490 GCAGTGGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (18 bp):
AGAGCCAGAGCCAGAGCA
Found at i:20029061 original size:28 final size:29
Alignment explanation
Indices: 20029018--20029088 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
20029008 TTAATATAAT
*
20029018 ATTTGGTACTTGAATTTGA-ATTTTTTTA
1 ATTTGGTACTTAAATTTGACATTTTTTTA
20029046 ATTTGGTACTTAAATTTGACATTTTTTTA
1 ATTTGGTACTTAAATTTGACATTTTTTTA
*
20029075 AATTGGTACTTAAA
1 ATTTGGTACTTAAA
20029089 CTTTTTGGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 18 0.45
29 22 0.55
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.52
Consensus pattern (29 bp):
ATTTGGTACTTAAATTTGACATTTTTTTA
Found at i:20029362 original size:31 final size:31
Alignment explanation
Indices: 20029317--20029423 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 31
20029307 TTAAAAAAAA
* *
20029317 GTTTAGGTAACAAATTAGGAAAAAATGTCAT
1 GTTTAAGTACCAAATTAGGAAAAAATGTCAT
* *
20029348 GTTCAAGTACCAAATTAAGTCCAAAAAA----AT
1 GTTTAAGTACCAAATT-AG--GAAAAAATGTCAT
* * *
20029378 -TTTAGGTACCAAATTAGGAAAAAGTGTCAA
1 GTTTAAGTACCAAATTAGGAAAAAATGTCAT
20029408 GTTTAAGTACCAAATT
1 GTTTAAGTACCAAATT
20029424 GGGTCAAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
26 5 0.09
28 2 0.03
29 13 0.22
30 3 0.05
31 27 0.47
32 2 0.03
34 6 0.10
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (31 bp):
GTTTAAGTACCAAATTAGGAAAAAATGTCAT
Found at i:20029375 original size:60 final size:59
Alignment explanation
Indices: 20029310--20029481 Score: 218
Period size: 60 Copynumber: 2.9 Consensus size: 59
20029300 TTGAATCTTA
*
20029310 AAAAAAAGTTTAGGTAACAAATTAGGAAAAAATGTCATGTTCAAGTACCAAATTAAGTCC
1 AAAAAAAGTTTAGGTAACAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTAAGT-C
* * * * **
20029370 AAAAAAATTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTAAGTACCAAATTGGGTC
1 AAAAAAAGTTTAGGTAACAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTAAGTC
* * * * * *
20029429 AAAAAAAGTTTAGGTATCAAATTAAGAAAAAGTATCAAGTTCATGTACTAAAT
1 AAAAAAAGTTTAGGTAACAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAAT
20029482 ATTATATTAA
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 47 0.48
60 51 0.52
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.27
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTAACAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTAAGTC
Found at i:20031688 original size:58 final size:60
Alignment explanation
Indices: 20031545--20031736 Score: 192
Period size: 58 Copynumber: 3.2 Consensus size: 60
20031535 TTAATATAAC
** * * *
20031545 ATTTGGTATTTAAACTTGACACTTTTTCCTAATTTGGTACCTAAAC-TTTTTTGGACCTA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGGACCCA
* * * * * *
20031604 ATTTGGTGCCTGAATTTGACA-CTTTTTCTGATTTGATACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGGACCCA
* * * * **
20031663 A-TTGGTACCTAAACTTGGCATTTTTTTTCTAATTTGGTACTTAAGCTTTTTTTAGATTCA
1 ATTTGGTACCTAAACTTGACA-TTTTTTTCTAATTTGGTACCTAAACTTTTTTTGGACCCA
*
20031723 ATTTAGTACCTAAA
1 ATTTGGTACCTAAA
20031737 TTTATTAAAT
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
58 35 0.33
59 29 0.27
60 31 0.29
61 11 0.10
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTTGGACCCA
Found at i:20031887 original size:32 final size:31
Alignment explanation
Indices: 20031850--20031930 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
20031840 GGACCCCAAA
* *
20031850 AAGTTTAAGTACCAACTTAATAAAAAAATGTC
1 AAGTTTAAGTACCAAATT-AGAAAAAAATGTC
* * * *
20031882 AAGTTTAGGTATCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATGTC
*
20031913 AAGTTTGAGTACCAAATT
1 AAGTTTAAGTACCAAATT
20031931 GGATCAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:20036629 original size:25 final size:25
Alignment explanation
Indices: 20036601--20036650 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
20036591 GAGTTAATTG
* *
20036601 ATTCAGTGCTGATAGGCGTACTATT
1 ATTCAGTGCTGATACGCGAACTATT
20036626 ATTCAGTGCTGATACGCGAACTATT
1 ATTCAGTGCTGATACGCGAACTATT
20036651 GGAAGTATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (25 bp):
ATTCAGTGCTGATACGCGAACTATT
Found at i:20040722 original size:26 final size:26
Alignment explanation
Indices: 20040693--20040746 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
20040683 TCCATTTTAC
20040693 TTAGTTTTTCAATAAAAATTATTATT
1 TTAGTTTTTCAATAAAAATTATTATT
20040719 TTAGTTTTTCAATAAAAATTATTATT
1 TTAGTTTTTCAATAAAAATTATTATT
20040745 TT
1 TT
20040747 TTGTACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TTAGTTTTTCAATAAAAATTATTATT
Found at i:20043652 original size:25 final size:25
Alignment explanation
Indices: 20043617--20043677 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
20043607 AAATAGTACT
20043617 AAAAATGAAATTA-AAATTTTTTAAA
1 AAAAAT-AAATTATAAATTTTTTAAA
**
20043642 AATAAATAAATTATATTTTTTTTAAA
1 AA-AAATAAATTATAAATTTTTTAAA
20043668 AAAAA-AAATT
1 AAAAATAAATT
20043678 GATGTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 5 0.16
25 11 0.34
26 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAAATAAATTATAAATTTTTTAAA
Found at i:20046004 original size:22 final size:22
Alignment explanation
Indices: 20045979--20046023 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
20045969 CAAAATAGAG
20045979 AAGAATCAACTAATTTTGCAGA
1 AAGAATCAACTAATTTTGCAGA
20046001 AAGAATCAACTAATTTTGCAGA
1 AAGAATCAACTAATTTTGCAGA
20046023 A
1 A
20046024 CAAGAGGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (22 bp):
AAGAATCAACTAATTTTGCAGA
Found at i:20048582 original size:17 final size:18
Alignment explanation
Indices: 20048560--20048595 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20048550 TTGTTTGGTG
20048560 TTTAAATTGATTTT-AAA
1 TTTAAATTGATTTTGAAA
*
20048577 TTTAAATTTATTTTGAAA
1 TTTAAATTGATTTTGAAA
20048595 T
1 T
20048596 AAAATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATTGATTTTGAAA
Found at i:20049921 original size:29 final size:29
Alignment explanation
Indices: 20049889--20050077 Score: 124
Period size: 29 Copynumber: 6.5 Consensus size: 29
20049879 TTCGGAGGCA
20049889 AAAAT-GTAATTTTGGGAAAATTCGGGGTT
1 AAAATGGTAATTTT-GGAAAATTCGGGGTT
* **
20049918 AAAAAT--AAGATTTTGGAAGGTTCGGGG-T
1 -AAAATGGTA-ATTTTGGAAAATTCGGGGTT
*
20049946 AAAATGGTAATTTTTGGTAAAA-TCGGGGTCA
1 AAAATGGTAA-TTTTGG-AAAATTCGGGGT-T
* * *
20049977 AAAATAG-AATTTTGGAAAGTTCGGGGAT
1 AAAATGGTAATTTTGGAAAATTCGGGGTT
* * *
20050005 AAAATGGTAATTTTTGGTGAAATT-GGTGTCA
1 AAAATGGTAA-TTTTGG-AAAATTCGGGGT-T
* * *
20050036 AAAATGG-AATTTTAGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGAAAATTCGGGGTT
20050064 AAAATGGTAATTTT
1 AAAATGGTAATTTT
20050078 TGGTGAAATC
Statistics
Matches: 122, Mismatches: 23, Indels: 29
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.04
28 22 0.18
29 53 0.43
30 25 0.20
31 17 0.14
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAATTCGGGGTT
Found at i:20049942 original size:59 final size:57
Alignment explanation
Indices: 20049879--20050137 Score: 240
Period size: 59 Copynumber: 4.4 Consensus size: 57
20049869 ACTTTTGACT
* *
20049879 TTCGGAGGCAAAAAT-GTAATTTTGGGAAAATTCGGGGTTAAAAATA-AGATTTTGGAAGG
1 TTCGG-GG-AAAAATGGTAATTTTGGGAAAA-TCGGGGTCAAAAATAGA-ATTTTGGAAAG
* *
20049938 TTCGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATAGAATTTTGGAAAG
1 TTCGGGGAAAAATGGTAA-TTTTGGGAAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * * *
20049996 TTCGGGGATAAAATGGTAATTTTTGGTG-AAATTGGTGTCAAAAATGGAATTTTAGAAAG
1 TTCGGGGA-AAAATGGTAA-TTTTGG-GAAAATCGGGGTCAAAAATAGAATTTTGGAAAG
* * * * *
20050055 TTCGGGGGTAAAATGGTAATTTTTGGTG-AAATCAGGGTCAAAAATGGGATTTTAGAAAG
1 TTC-GGGGAAAAATGGTAA-TTTTGG-GAAAATCGGGGTCAAAAATAGAATTTTGGAAAG
20050114 TTCGGGGGTAAAAAAT-GTAATTTT
1 TTC-GGGG--AAAAATGGTAATTTT
20050138 TTAAAGTTTT
Statistics
Matches: 176, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
57 5 0.03
58 37 0.21
59 121 0.69
60 8 0.05
61 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (57 bp):
TTCGGGGAAAAATGGTAATTTTGGGAAAATCGGGGTCAAAAATAGAATTTTGGAAAG
Found at i:20050092 original size:29 final size:30
Alignment explanation
Indices: 20049939--20050097 Score: 115
Period size: 29 Copynumber: 5.4 Consensus size: 30
20049929 TTTGGAAGGT
*
20049939 TCGGGGT-AAAATGGTAATTTTTGGTAAAA
1 TCGGGGTCAAAATGGTAATTTTTGGTGAAA
*
20049968 TCGGGGTCAAAAATAG-AA-TTTT-G-GAAA
1 TCGGGGTC-AAAATGGTAATTTTTGGTGAAA
20049995 GTTCGGGGAT-AAAATGGTAATTTTTGGTGAAA
1 --TCGGGG-TCAAAATGGTAATTTTTGGTGAAA
* * *
20050027 TTGGTGTCAAAAATGG-AA-TTTT--AGAAA
1 TCGGGGTC-AAAATGGTAATTTTTGGTGAAA
20050054 GTTCGGGGGT-AAAATGGTAATTTTTGGTGAAA
1 --TC-GGGGTCAAAATGGTAATTTTTGGTGAAA
*
20050086 TCAGGGTCAAAA
1 TCGGGGTCAAAA
20050098 ATGGGATTTT
Statistics
Matches: 101, Mismatches: 10, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
27 7 0.07
28 14 0.14
29 31 0.31
30 27 0.27
31 14 0.14
32 8 0.08
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.31
Consensus pattern (30 bp):
TCGGGGTCAAAATGGTAATTTTTGGTGAAA
Found at i:20050126 original size:29 final size:29
Alignment explanation
Indices: 20049879--20050137 Score: 94
Period size: 30 Copynumber: 8.8 Consensus size: 29
20049869 ACTTTTGACT
* * * * *
20049879 TTCGGAGGCAAAAATGTAATTTTGGGAAAA
1 TTCGGGGGTAAAAATGGAATTTT-AGAAAG
* * * *
20049909 TTCGGGGTTAAAAAT-AAGATTTTGGAAGG
1 TTCGGGGGTAAAAATGGA-ATTTTAGAAAG
*
20049938 TTC-GGGGT-AAAATGGTAATTTTTGGTAAA-
1 TTCGGGGGTAAAAATGG-AA-TTTTAG-AAAG
* * *
20049967 ATC-GGGGTCAAAAATAGAATTTTGGAAAG
1 TTCGGGGGT-AAAAATGGAATTTTAGAAAG
* *
20049996 TTCGGGGAT-AAAATGGTAATTTTTGGTGAAA-
1 TTCGGGGGTAAAAATGG-AA-TTTT--AGAAAG
*
20050027 TT--GGTGTCAAAAATGGAATTTTAGAAAG
1 TTCGGGGGT-AAAAATGGAATTTTAGAAAG
*
20050055 TTCGGGGGT-AAAATGGTAATTTTTGGTGAAA-
1 TTCGGGGGTAAAAATGG-AA-TTTT--AGAAAG
* *
20050086 -TC-AGGGTCAAAAATGGGATTTTAGAAAG
1 TTCGGGGGT-AAAAATGGAATTTTAGAAAG
*
20050114 TTCGGGGGTAAAAAATGTAATTTT
1 TTCGGGGGT-AAAAATGGAATTTT
20050138 TTAAAGTTTT
Statistics
Matches: 175, Mismatches: 27, Indels: 54
0.68 0.11 0.21
Matches are distributed among these distances:
27 13 0.07
28 23 0.13
29 51 0.29
30 58 0.33
31 22 0.13
32 8 0.05
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
TTCGGGGGTAAAAATGGAATTTTAGAAAG
Found at i:20051245 original size:19 final size:19
Alignment explanation
Indices: 20051200--20051261 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
20051190 TCTTTTTTTA
20051200 TATTATTATTATTAATATT
1 TATTATTATTATTAATATT
* ** *
20051219 AAACATTATTATTAATGTT
1 TATTATTATTATTAATATT
**
20051238 TATTATTATTAAAAATATT
1 TATTATTATTATTAATATT
20051257 TATTA
1 TATTA
20051262 ACGTTTATTA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTATTATTATTAATATT
Found at i:20051272 original size:29 final size:29
Alignment explanation
Indices: 20051208--20051275 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
20051198 TATATTATTA
* * *
20051208 TTATTAATATTAAACATTATTATTAATGT
1 TTATTATTATTAAAAATTATTATTAACGT
20051237 TTATTATTATTAAAAA-TATTTATTAACGT
1 TTATTATTATTAAAAATTA-TTATTAACGT
20051266 TTATTATTAT
1 TTATTATTAT
20051276 AACAGTCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 2 0.06
29 33 0.94
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
TTATTATTATTAAAAATTATTATTAACGT
Found at i:20052025 original size:23 final size:22
Alignment explanation
Indices: 20051995--20052043 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
20051985 GTATTTGGAC
* *
20051995 ATTTAATTTATATTTATTTTAA
1 ATTTAATTTATATTAAGTTTAA
20052017 ATTTCAATTTATATTAAGTTTAA
1 ATTT-AATTTATATTAAGTTTAA
20052040 ATTT
1 ATTT
20052044 TGGAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTAATTTATATTAAGTTTAA
Found at i:20052026 original size:17 final size:17
Alignment explanation
Indices: 20051999--20052043 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
20051989 TTGGACATTT
* *
20051999 AATTTATATTTATTTTA
1 AATTTAAATTTATATTA
*
20052016 AATTTCAATTTATATTA
1 AATTTAAATTTATATTA
*
20052033 AGTTTAAATTT
1 AATTTAAATTT
20052044 TGGAAAAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTAAATTTATATTA
Found at i:20053063 original size:200 final size:200
Alignment explanation
Indices: 20052420--20053063 Score: 950
Period size: 200 Copynumber: 3.2 Consensus size: 200
20052410 TTCATTGACC
* * * * * **
20052420 TGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCACTTCTCTG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCGTTTGTTTTAATTTGCTTCTCTG
* *
20052485 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTAT
65 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * *
20052550 TGCTTCAACCTGCTTCTCAGTATCTCATCAGGGAGCTGGGTTCGAAGATTTGCTCGCGTTGAGCG
130 TGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTGAGCG
*
20052615 TTGAGT
195 TTGAAT
* *
20052621 TGGTATTCTTCTCTGTATCTTATCAGGAAGATGATCGCCTC-TGTTGTTTTAATTTGCTTCTCTG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGT-TTGTTTTAATTTGCTTCTCTG
* * *
20052685 GATCTCCTCAAGAAGACAAATTTGGTCCGCTTCTCTGTATCTCATCATGAAGCTAACCATTTTAT
65 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
* *
20052750 TGTTTCGACCTGCTTCTCAGTGTCTCATTAGGAAGCTGGGTACGAAGATTTGCTCGCT-TTGAGC
130 TGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCG-TGTTGAGC
* *
20052814 ATTGATT
194 GTTGAAT
20052821 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGTTTGTTTTAATTTGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGTTTGTTTTAATTTGCTTCTCTGG
* *
20052886 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * * * *
20052951 ATTTCGACTTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTTGAAGATTGGCTTGTGTTGAGCGT
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTGAGCGT
20053016 TGAAT
196 TGAAT
* *
20053021 TGGTATTCTTCTCTGTATCTTATCAGGAAGATGACTGCCTCGT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGT
20053064 CTCTTGTTGA
Statistics
Matches: 399, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
199 2 0.01
200 362 0.91
201 35 0.09
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (200 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGTTTGTTTTAATTTGCTTCTCTGG
ATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTGAGCGT
TGAAT
Found at i:20065328 original size:59 final size:58
Alignment explanation
Indices: 20065215--20065460 Score: 316
Period size: 59 Copynumber: 4.2 Consensus size: 58
20065205 AAAAATGTAA
* * * *
20065215 TTTGGGAAAATTCGAGGTTAAAAAT-AAGATTTTGGAAGGTTTAGGGTAAAATGGTAATT
1 TTTGGTAAAA-TCGAGGTCAAAAATGAA-ATTTTGGAAAGTTTGGGGTAAAATGGTAATT
20065274 TTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTGGGGATAAAATGGTAATT
1 TTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTGGGG-TAAAATGGTAATT
* * * *
20065333 TTTGGTGAAATCGGGGTCAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATT
1 TTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTT-GGGGTAAAATGGTAATT
* * * *
20065392 TTTGGTAAAATCGGGGT-TAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATT
1 TTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTG-GGGTAAAATGGTAATT
*
20065450 TTTGGTGAAAT
1 TTTGGTAAAAT
20065461 TGGCAACACG
Statistics
Matches: 170, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
57 1 0.01
58 75 0.44
59 90 0.53
60 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
TTTGGTAAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTGGGGTAAAATGGTAATT
Found at i:20067922 original size:9 final size:10
Alignment explanation
Indices: 20067897--20067934 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
20067887 ACCCAATAAA
20067897 AAGAAAAAAG
1 AAGAAAAAAG
20067907 -A-AAAAAAG
1 AAGAAAAAAG
20067915 AGAGAAAAAAG
1 A-AGAAAAAAG
20067926 AAGAAAAAA
1 AAGAAAAAA
20067935 TCAAGATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 9 0.36
11 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:20068726 original size:7 final size:7
Alignment explanation
Indices: 20068714--20068791 Score: 66
Period size: 7 Copynumber: 10.0 Consensus size: 7
20068704 AGATGCAATG
20068714 AAGAAAA
1 AAGAAAA
20068721 AAGAAAA
1 AAGAAAA
20068728 AAGAAGAAGA
1 AAG-A-AA-A
20068738 AAGAAAA
1 AAGAAAA
20068745 AAGAAGAA
1 AAGAA-AA
*
20068753 AGAGAAGA
1 A-AGAAAA
20068761 AAGAAAA
1 AAGAAAA
20068768 TAGAGAAAA
1 -A-AGAAAA
*
20068777 ATGGAAAA
1 A-AGAAAA
20068785 AAGAAAA
1 AAGAAAA
20068792 GGAGAGGTCG
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
7 26 0.44
8 16 0.27
9 13 0.22
10 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:20068735 original size:17 final size:17
Alignment explanation
Indices: 20068713--20068791 Score: 76
Period size: 16 Copynumber: 4.9 Consensus size: 17
20068703 CAGATGCAAT
20068713 GAAGAAAAAAGAAAAAA
1 GAAGAAAAAAGAAAAAA
*
20068730 GAAGAAGAAAGAAAAAA
1 GAAGAAAAAAGAAAAAA
* *
20068747 GAAG-AAAGAGAAGAAA
1 GAAGAAAAAAGAAAAAA
* * *
20068763 GAA-AATAGAGAAAAAT
1 GAAGAAAAAAGAAAAAA
20068779 G--GAAAAAAGAAAA
1 GAAGAAAAAAGAAAA
20068792 GGAGAGGTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
15 9 0.18
16 22 0.43
17 20 0.39
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (17 bp):
GAAGAAAAAAGAAAAAA
Found at i:20068758 original size:23 final size:24
Alignment explanation
Indices: 20068714--20068775 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
20068704 AGATGCAATG
*
20068714 AAGAAAAAAGAAAAAAGAAGAAGA
1 AAGAAAAAAGAAGAAAGAAGAAGA
20068738 AAGAAAAAAGAAGAAAG-AGAAGA
1 AAGAAAAAAGAAGAAAGAAGAAGA
*
20068761 AAGAAAATAG-AGAAA
1 AAGAAAAAAGAAGAAA
20068776 AATGGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.14
23 15 0.42
24 16 0.44
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02
Consensus pattern (24 bp):
AAGAAAAAAGAAGAAAGAAGAAGA
Found at i:20070177 original size:49 final size:48
Alignment explanation
Indices: 20070116--20070597 Score: 401
Period size: 49 Copynumber: 9.9 Consensus size: 48
20070106 AGACATGACG
* *
20070116 GGGAAAGATCTAAGATCGCAACGGTGGATCCAGTACCTCGAAGACACAA
1 GGGAAAGATCTAAG-CCGCAACGGTGGATCCAGTACCACGAAGACACAA
* * * *
20070165 GGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAAACACGAC
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGAAGACAC-AA
* * * * * *
20070214 GGGAAAGATCTAAGATCGCAACGGCGAATCTAGTACCGCAAAGACACAA
1 GGGAAAGATCTAAG-CCGCAACGGTGGATCCAGTACCACGAAGACACAA
* * *
20070263 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACAAAAACACGAC
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGAAGACAC-AA
** *
20070312 GGGAAAGATCTAAGACCGCAACGGTATATCCAGTACCGCGAAGACACAA
1 GGGAAAGATCTAAG-CCGCAACGGTGGATCCAGTACCACGAAGACACAA
* * ** *
20070361 GGGAAAGATCTAAGTCGCGACGGCAGATCCAGTACCGCGAAGACACAGA
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGAAGACACA-A
* * * * ** * * ** * *
20070410 GGGAAAGGTTTAAGTCGCAATGACGAAACTTGTACCTC-AGAGACATAAA
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGA-AGACA-CAA
* * * **
20070459 GGGAAAGATTTAAGCCGTAACAGTAAATCCAGTACCACGAAGACACAAA
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGAAGACAC-AA
* * * * * * * *
20070508 GGGAAAGGTTTAAGTCGCAACGG-CGAACCATGTACCTCAAAGACATAAA
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCA-GTACCACGAAGACA-CAA
* *
20070557 GGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAA
1 GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGAA
20070598 TATTTGACGA
Statistics
Matches: 350, Mismatches: 71, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
48 87 0.25
49 203 0.58
50 60 0.17
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (48 bp):
GGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCACGAAGACACAA
Found at i:20070285 original size:98 final size:98
Alignment explanation
Indices: 20070116--20070594 Score: 518
Period size: 98 Copynumber: 4.9 Consensus size: 98
20070106 AGACATGACG
* * *
20070116 GGGAAAGATCTAAGATCGCAACGGTGGATCCAGTACCTCGAAGACACAAGGGAAAGATCTAAGCC
1 GGGAAAGATCTAAGATCGCAACGGCGAATCCAGTACCTCAAAGACACAAGGGAAAGATCTAAGCC
*
20070181 GCAACGGCGGATCCAGTACCACAAAAACACGAC
66 GCAACGGTGGATCCAGTACCACAAAAACACGAC
* *
20070214 GGGAAAGATCTAAGATCGCAACGGCGAATCTAGTACCGCAAAGACACAAGGGAAAGATCTAAGCC
1 GGGAAAGATCTAAGATCGCAACGGCGAATCCAGTACCTCAAAGACACAAGGGAAAGATCTAAGCC
20070279 GCAACGGTGGATCCAGTACCACAAAAACACGAC
66 GCAACGGTGGATCCAGTACCACAAAAACACGAC
* * * * *
20070312 GGGAAAGATCTAAGACCGCAACGG-TATATCCAGTACCGCGAAGACACAAGGGAAAGATCTAAGT
1 GGGAAAGATCTAAGATCGCAACGGCGA-ATCCAGTACCTCAAAGACACAAGGGAAAGATCTAAGC
* ** * * *
20070376 CGCGACGGCAGATCCAGTACCGCGAAGACACAGA-
65 CGCAACGGTGGATCCAGTACCACAAAAACAC-GAC
* * * * * ** * * *
20070410 GGGAAAGGTTTAAG-TCGCAATGACGAAACTTGTACCTCAGAGACATAAAGGGAAAGATTTAAGC
1 GGGAAAGATCTAAGATCGCAACGGCGAATCCAGTACCTCAAAGACA-CAAGGGAAAGATCTAAGC
* * ** * * * *
20070474 CGTAACAGTAAATCCAGTACCACGAAGACACAAA
65 CGCAACGGTGGATCCAGTACCACAAAAACACGAC
* * * *
20070508 GGGAAAGGTTTAAG-TCGCAACGGCGAA-CCATGTACCTCAAAGACATAAAGGGAAAGATTTAAG
1 GGGAAAGATCTAAGATCGCAACGGCGAATCCA-GTACCTCAAAGACA-CAAGGGAAAGATCTAAG
*
20070571 CCGCAACGGTGAATCCAGTACCAC
64 CCGCAACGGTGGATCCAGTACCAC
20070595 GAATATTTGA
Statistics
Matches: 328, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
97 22 0.07
98 304 0.93
99 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (98 bp):
GGGAAAGATCTAAGATCGCAACGGCGAATCCAGTACCTCAAAGACACAAGGGAAAGATCTAAGCC
GCAACGGTGGATCCAGTACCACAAAAACACGAC
Found at i:20070595 original size:98 final size:97
Alignment explanation
Indices: 20070101--20070642 Score: 502
Period size: 98 Copynumber: 5.5 Consensus size: 97
20070091 CTGAGAAAAA
* * * * *
20070101 CACGAAGACATGACGGGGAAAGATCTAAGATCGCAACGGTGGATCCAGTACCTCGAAGACACAAG
1 CACGAAAACACGAC-GGGAAAGATCTAAGATCGCAACGG-CGAACCAGTACCTCAAAGACACAAG
* *
20070166 GGAAAGATCTAAGCCGCAACGGCGGATCCAGTAC
64 GGAAAGATCTAAGCCGCAACGGTGAATCCAGTAC
* * *
20070200 CACAAAAACACGACGGGAAAGATCTAAGATCGCAACGGCGAATCTAGTACCGCAAAGACACAAGG
1 CACGAAAACACGACGGGAAAGATCTAAGATCGCAACGGCGAA-CCAGTACCTCAAAGACACAAGG
*
20070265 GAAAGATCTAAGCCGCAACGGTGGATCCAGTAC
65 GAAAGATCTAAGCCGCAACGGTGAATCCAGTAC
* * * * *
20070298 CACAAAAACACGACGGGAAAGATCTAAGACCGCAACGG-TATATCCAGTACCGCGAAGACACAAG
1 CACGAAAACACGACGGGAAAGATCTAAGATCGCAACGGCGA-A-CCAGTACCTCAAAGACACAAG
* * *
20070362 GGAAAGATCTAAGTCGCGACGG-CAGATCCAGTAC
64 GGAAAGATCTAAGCCGCAACGGTGA-ATCCAGTAC
* * * * * * ** * *
20070396 CGCGAAGACACAGA-GGGAAAGGTTTAAG-TCGCAATGACGAAACTTGTACCTCAGAGACATAAA
1 CACGAAAACAC-GACGGGAAAGATCTAAGATCGCAACGGCG-AACCAGTACCTCAAAGACA-CAA
* * * *
20070459 GGGAAAGATTTAAGCCGTAACAGTAAATCCAGTAC
63 GGGAAAGATCTAAGCCGCAACGGTGAATCCAGTAC
* * * * * *
20070494 CACGAAGACACAAAGGGAAAGGTTTAAG-TCGCAACGGCGAACCATGTACCTCAAAGACATAAAG
1 CACGAAAACACGACGGGAAAGATCTAAGATCGCAACGGCGAACCA-GTACCTCAAAGACA-CAAG
*
20070558 GGAAAGATTTAAGCCGCAACGGTGAATCCAGTAC
64 GGAAAGATCTAAGCCGCAACGGTGAATCCAGTAC
* *** * * * *
20070592 CACGAATATTTGACGAGAAAGGTTTAAG-TCGCAATGGCGAACCCAGTACCT
1 CACGAAAACACGACGGGAAAGATCTAAGATCGCAACGGCGAA-CCAGTACCT
20070643 TAGAAACACG
Statistics
Matches: 376, Mismatches: 56, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
97 25 0.07
98 333 0.89
99 18 0.05
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (97 bp):
CACGAAAACACGACGGGAAAGATCTAAGATCGCAACGGCGAACCAGTACCTCAAAGACACAAGGG
AAAGATCTAAGCCGCAACGGTGAATCCAGTAC
Found at i:20071102 original size:17 final size:17
Alignment explanation
Indices: 20071070--20071165 Score: 93
Period size: 17 Copynumber: 5.5 Consensus size: 17
20071060 TTGGATCAAA
* * *
20071070 ATTTTAGATTTTAATTC
1 ATTTTAAATTTAAATTT
*
20071087 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* *
20071104 ATTGTAAATTTAAGACTT
1 ATTTTAAATTTAA-ATTT
* **
20071122 GTTTGGAATTTAAATTT
1 ATTTTAAATTTAAATTT
20071139 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
20071156 ATTTTGAAAT
1 ATTTT-AAAT
20071166 AAAATTTTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
17 46 0.74
18 16 0.26
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:20073037 original size:59 final size:59
Alignment explanation
Indices: 20072964--20073299 Score: 273
Period size: 59 Copynumber: 5.7 Consensus size: 59
20072954 TTTTAAATTA
*
20072964 ACCCTCTG-ACTTTCCAAAATTCCATTTTTGA-CTCTAATTTTTCTAAAAATTA-CATTTTT
1 ACCCTC-GAACTTTCCAAAATTCCATTTTTAACCTC-AATTTTTCTAAAAATTACCA-TTTT
* *
20073023 ACCCTCGAACTTTCCAAAATTCCA-TTTTAACCTCGATTTTTCAAAAAATTA-CATTTT
1 ACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTCTAAAAATTACCATTTT
** * *
20073080 ATCCC-C-AAGCTTTCCAAAATTTAATTTTTAACCTCAATTTTTTTTCAAAATTACCATTTT
1 A-CCCTCGAA-CTTTCCAAAATTCCATTTTTAACCTCAA-TTTTTCTAAAAATTACCATTTT
* * * ** *
20073140 ACCC-CTAAAC-TTCTAAAAATTCCATTTTTAACCCCAAACTTTCTAAGAATTACCATTTT
1 ACCCTC-GAACTTTC-CAAAATTCCATTTTTAACCTCAATTTTTCTAAAAATTACCATTTT
* * * * * * *
20073199 ACCCTCGAA-TGTCCAAAAATTCCATTTTTGACCTTGAA-CTTTCCAAGAATTATCATTTT
1 ACCCTCGAACTTTCC-AAAATTCCATTTTTAACC-TCAATTTTTCTAAAAATTACCATTTT
* * *
20073258 ACCCTCGAA-TGTCTAAAAATTCCATTTTTAACCCTAAATTTT
1 ACCCTCGAACTTTC-CAAAATTCCATTTTTAA-CCTCAATTTT
20073300 CCAAAATCAC
Statistics
Matches: 230, Mismatches: 30, Indels: 33
0.78 0.10 0.11
Matches are distributed among these distances:
56 2 0.01
57 19 0.08
58 37 0.16
59 136 0.59
60 34 0.15
61 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (59 bp):
ACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTCTAAAAATTACCATTTT
Found at i:20073042 original size:29 final size:29
Alignment explanation
Indices: 20073009--20073317 Score: 137
Period size: 29 Copynumber: 10.6 Consensus size: 29
20072999 AATTTTTCTA
20073009 AAAATTACATTTTTACCCTCGAACTTTCC
1 AAAATTACATTTTTACCCTCGAACTTTCC
* * ** *
20073038 AAAATTCCA-TTTTAACCTCGATTTTTCAA
1 AAAATTACATTTTTACCCTCGAACTTTC-C
20073067 AAAATTACA-TTTTATCCC-C-AAGCTTTCC
1 AAAATTACATTTTTA-CCCTCGAA-CTTTCC
* * *
20073095 AAAATTTA-ATTTTTAACCTC-AATTTTTTTTC
1 AAAA-TTACATTTTTACCCTCGAA---CTTTCC
* *
20073126 AAAATTACCA-TTTTACCC-CTAAAC-TTCTA
1 AAAATTA-CATTTTTACCCTC-GAACTTTC-C
* * *
20073155 AAAATTCCATTTTTAACCC-CAAACTTTCT
1 AAAATTACATTTTT-ACCCTCGAACTTTCC
*
20073184 AAGAATTACCA-TTTTACCCTCGAA-TGTCC
1 AA-AATTA-CATTTTTACCCTCGAACTTTCC
* *
20073213 AAAAATTCCATTTTTGA-CCTTGAACTTTCC
1 -AAAATTACATTTTT-ACCCTCGAACTTTCC
* *
20073243 AAGAATTATCA-TTTTACCCTCGAA-TGTCTA
1 AA-AATTA-CATTTTTACCCTCGAACTTTC-C
* * *
20073273 AAAATTCCATTTTTAACCCT-AAATTTTCC
1 AAAATTACATTTTT-ACCCTCGAACTTTCC
*
20073302 AAAATCACATTTTTAC
1 AAAATTACATTTTTAC
20073318 TCCGTCTGTT
Statistics
Matches: 213, Mismatches: 37, Indels: 61
0.68 0.12 0.20
Matches are distributed among these distances:
28 33 0.15
29 102 0.48
30 56 0.26
31 19 0.09
32 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCGAACTTTCC
Found at i:20095596 original size:14 final size:14
Alignment explanation
Indices: 20095570--20095608 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
20095560 ACATTTGTTT
20095570 TTTCTTGTTGTCTTG
1 TTTCTT-TTGTCTTG
*
20095585 TTTCTTTTGTCTTT
1 TTTCTTTTGTCTTG
20095599 TTTCTTTTGT
1 TTTCTTTTGT
20095609 TTTTGTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (14 bp):
TTTCTTTTGTCTTG
Found at i:20106615 original size:13 final size:13
Alignment explanation
Indices: 20106597--20106651 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
20106587 ACACTTAACT
*
20106597 CTTTTCAAAAGTA
1 CTTTTCAAAAGCA
**
20106610 CTTTTCAAAATTA
1 CTTTTCAAAAGCA
* *
20106623 CTTTTCTAACGCA
1 CTTTTCAAAAGCA
*
20106636 CTTTTTAAAAGCA
1 CTTTTCAAAAGCA
20106649 CTT
1 CTT
20106652 CGTAAATGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:20111923 original size:2 final size:2
Alignment explanation
Indices: 20111916--20111942 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20111906 TGTTTTTATT
20111916 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
20111943 TAATACATAC
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:20114033 original size:322 final size:322
Alignment explanation
Indices: 20113441--20114034 Score: 745
Period size: 322 Copynumber: 1.8 Consensus size: 322
20113431 ATAAACCTTT
* * * *
20113441 AAAACCGAGGCAATATCCTTTTCATGTGGAAATCTCAAAAATCATGCCCTAACGTGCTGGGTGTG
1 AAAAACGAGGCAATATCCTTTTCATGTGAAAATCTCAAAAATCATGCCCTAACGTCCTGGGTATG
* * *
20113506 ATTTTTTGTATAATCTGCACAATCGAATATCCTCTTCCAAACTTTTCAAACGCCCTTTAATTTCG
66 ATTTTTCGTATAATCTGCACAATCGAATATCCTCTTCAAAACTTTTCAAACGCCCTTCAATTTCG
* * * * * *
20113571 AGATTCCGAGAACGTCTTGCCCTAACGTGTTGGACACGACTTCATTTTTTCGATAAATTTGAAAC
131 AAATTCCGAGAACGTCGTGCCCTAACGTGTTGGACACGACTTCATTCTCTCGAGAAATTCGAAAC
* * * * * *
20113636 ATACGGGCATTTTTCTTCAAATCTAATTTTTGAAAATCACGTGAAATAAGTTATGTGTTAGAGGA
196 ACACGGACATTTTTCTTCAAATATAATTTTTGAAAATCACGCGAAATAAGTTATGAGTTAAAGGA
*
20113701 TCGTATTTTAAACTTAATTCAAAATTTCAAGTTCTCAAAAAATATACAAATAATTTTAAAAC
261 TCGCATTTTAAACTTAATTCAAAATTTCAAGTTCTCAAAAAATATACAAATAATTTTAAAAC
* *
20113763 AAAAACGAGGCAATATCC-TTTCGTGTGAAAA-CTTCCAAAAATCATGCTCTAACGTCCTGGGTA
1 AAAAACGAGGCAATATCCTTTTCATGTGAAAATC-T-CAAAAATCATGCCCTAACGTCCTGGGTA
* * * * * *
20113826 TGA-TTTTCGTATAAT-TCGCGCGATCGATTATCCTCTTTAAAA-TCTTTCAAAATGTCCTTCAA
64 TGATTTTTCGTATAATCT-GCACAATCGAATATCCTCTTCAAAACT-TTTC-AAACGCCCTTCAA
20113888 TTTCGAAATTCCGAGAACGTCGTGCCCTAACGTGTTGGACACGACTTCAATTCTCT-GAGAAATT
126 TTTCGAAATTCCGAGAACGTCGTGCCCTAACGTGTTGGACACGACTTC-ATTCTCTCGAGAAATT
* * * * * * *
20113952 CGAAACGCACGGACGTTTTT-TCTCAAATATGATTTTTGAAAATCATGCGAAGTTATTTATGAG-
190 CGAAACACACGGACATTTTTCT-TCAAATATAATTTTTGAAAATCACGCGAAATAAGTTATGAGT
20114015 TACAAGGATCGCATTTTAAA
254 TA-AAGGATCGCATTTTAAA
20114035 GATTCGCTCG
Statistics
Matches: 229, Mismatches: 35, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
320 3 0.01
321 50 0.22
322 171 0.75
323 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (322 bp):
AAAAACGAGGCAATATCCTTTTCATGTGAAAATCTCAAAAATCATGCCCTAACGTCCTGGGTATG
ATTTTTCGTATAATCTGCACAATCGAATATCCTCTTCAAAACTTTTCAAACGCCCTTCAATTTCG
AAATTCCGAGAACGTCGTGCCCTAACGTGTTGGACACGACTTCATTCTCTCGAGAAATTCGAAAC
ACACGGACATTTTTCTTCAAATATAATTTTTGAAAATCACGCGAAATAAGTTATGAGTTAAAGGA
TCGCATTTTAAACTTAATTCAAAATTTCAAGTTCTCAAAAAATATACAAATAATTTTAAAAC
Found at i:20125456 original size:39 final size:39
Alignment explanation
Indices: 20125356--20125873 Score: 209
Period size: 39 Copynumber: 13.3 Consensus size: 39
20125346 CTTCTTGAAG
* * * *
20125356 TTGCAGCCATTCGATCTTTTACCCCGAGCCTAGGACAGA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
** * * * * *
20125395 TCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* * *
20125434 TTGCAACCATTCGATCTTTTACCCCGAGCTTGGGGTAGA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* * *
20125473 TT---ACCATCAGTTAATCTCTTACCCCGAGCTTGGGGCAGA
1 TTGCAACCATCCG---ATCTTTTACCCCGAGCCTGGGGCAGA
* ** * ** * *
20125512 TTGTAGTCATTCGATCTTTTACCCTTAGCCTGGGGTATA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
** * * * * * * * * ** *
20125551 TCACCATCAGCCAATCTCTTACCTC-AGGCTTAGGAAAAA
1 TTGCAACCATCCGATCTTTTACCCCGA-GCCTGGGGCAGA
* * * *
20125590 TTG-AAGCCATCCGATCTCTTACCCCAAGCTTGGGGCAAA
1 TTGCAA-CCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
** * * * * * * *
20125629 TCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAAA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* * * * * *
20125668 TTGTAGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
** * * * * * * *
20125707 TCACCATCAGCCAATCTTTTACCTCAAGCCTAGGGCAGA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* * * *
20125746 TTGCAGCCATTCGATCTTTTACCCCGAGCCCGGGGTAGA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* ** * *
20125785 TTGCAGCCATCCGATCTTTTACCCTAATCATGGGGCAGA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* * * * * * *
20125824 TTGTAACCATCCAATCTCTTACCCCGATCATGAGGCAAA
1 TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
*
20125863 TTGCAGCCATC
1 TTGCAACCATC
20125874 ATCCAATCTT
Statistics
Matches: 343, Mismatches: 126, Indels: 20
0.70 0.26 0.04
Matches are distributed among these distances:
36 6 0.02
38 2 0.01
39 329 0.96
40 2 0.01
42 4 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (39 bp):
TTGCAACCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
Found at i:20125489 original size:78 final size:78
Alignment explanation
Indices: 20125356--20125785 Score: 511
Period size: 78 Copynumber: 5.5 Consensus size: 78
20125346 CTTCTTGAAG
* **
20125356 TTGCAGCCATTCGATCTTTTACCCCGAGCCTAGGACAGATCACCATCAGCCAATCTCTTACCCCG
1 TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG
20125421 AGCCTGGGGCAGA
66 AGCCTGGGGCAGA
* * * **
20125434 TTGCAACCATTCGATCTTTTACCCCGAGCTTGGGGTAGATTACCATCAGTTAATCTCTTACCCCG
1 TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG
*
20125499 AGCTTGGGGCAGA
66 AGCCTGGGGCAGA
* * ** * *
20125512 TTGTAGTCATTCGATCTTTTACCCTTAGCCTGGGGTATATCACCATCAGCCAATCTCTTACCTC-
1 TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG
* * ** *
20125576 AGGCTTAGGAAAAA
66 A-GCCTGGGGCAGA
* * * * * * *
20125590 TTGAAGCCATCCGATCTCTTACCCCAAGCTTGGGGCAAATCACCATCAGCCAATCTCTTACCCCG
1 TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG
* *
20125655 AGCCTGAGGCAAA
66 AGCCTGGGGCAGA
* * * * * *
20125668 TTGTAGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTTTTACCTCA
1 TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG
*
20125733 AGCCTAGGGCAGA
66 AGCCTGGGGCAGA
*
20125746 TTGCAGCCATTCGATCTTTTACCCCGAGCCCGGGGTAGAT
1 TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGAT
20125786 TGCAGCCATC
Statistics
Matches: 294, Mismatches: 56, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
77 1 0.00
78 292 0.99
79 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (78 bp):
TTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCG
AGCCTGGGGCAGA
Found at i:20125821 original size:78 final size:77
Alignment explanation
Indices: 20125360--20125936 Score: 221
Period size: 78 Copynumber: 7.3 Consensus size: 77
20125350 TTGAAGTTGC
* ** * **
20125360 AGCCATTCGATCTTTTACCCCGAGCCTAGGACAGA-T-CA-CCATCAGCCAATCTCTTACCCCGA
1 AGCCATTCGATCTTTTACCCCGAGCCTGGGGTA-ATTGCAGCCAT---CCAATCTTTTACCCTAA
* * *
20125422 GCCTGGGGCAGATTGC
62 TCATGGGGCAGATTGT
* * * * **
20125438 AACCATTCGATCTTTTACCCCGAGCTTGGGGTAGATT--A-CCATCAGTTAATCTCTTACCCCGA
1 AGCCATTCGATCTTTTACCCCGAGCCTGGGGTA-ATTGCAGCCATC---CAATCTTTTACCCTAA
* *
20125500 GCTTGGGGCAGATTGT
62 TCATGGGGCAGATTGT
* ** *
20125516 AGTCATTCGATCTTTTACCCTTAGCCTGGGGT-ATAT-CA-CCATCAGCCAATCTCTTA-CCTCA
1 AGCCATTCGATCTTTTACCCCGAGCCTGGGGTAAT-TGCAGCCAT---CCAATCTTTTACCCT-A
** * * ** * *
20125577 GGCTTAGGAAAAATTGA
61 ATCATGGGGCAGATTGT
* * * * * * * ** *
20125594 AGCCATCCGATCTCTTACCCCAAGCTTGGGGCAAAT-CA-CCATCAGCCAATCTCTTACCCCGAG
1 AGCCATTCGATCTTTTACCCCGAGCCTGGGGTAATTGCAGCCAT---CCAATCTTTTACCCTAAT
* * *
20125657 CCTGAGGCAAATTGT
63 CATGGGGCAGATTGT
* *
20125672 AGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAAT-CA-CCATCAGCCAATCTTTTA-CCTCAA
1 AGCCATTCGATCTTTTACCCCGAGCCTGGGGTAATTGCAGCCAT---CCAATCTTTTACCCT-AA
* * * *
20125734 GCCTAGGGCAGATTGC
62 TCATGGGGCAGATTGT
* *
20125750 AGCCATTCGATCTTTTACCCCGAGCCCGGGGTAGATTGCAGCCATCCGATCTTTTACCCTAATCA
1 AGCCATTCGATCTTTTACCCCGAGCCTGGGGTA-ATTGCAGCCATCCAATCTTTTACCCTAATCA
20125815 TGGGGCAGATTGT
65 TGGGGCAGATTGT
* * * * * * **
20125828 AACCATCCAATCTCTTACCCCGATCATGAGGCAAATTGCAGCCATCATCCAATCTTTTACCCTTA
1 AGCCATTCGATCTTTTACCCCGAGCCTG-GGGTAATTGCAG-C--CATCCAATCTTTTACCC-TA
* *
20125893 AGTCAAGAGGGGCAGATTGA
61 A-TC-A-TGGGGCAGATTGT
20125913 AGCCACATTCTGATCTTTTACCCC
1 AG-C-CATTC-GATCTTTTACCCC
20125937 TAGTCAAGAG
Statistics
Matches: 395, Mismatches: 76, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
75 1 0.00
76 2 0.01
77 5 0.01
78 317 0.80
79 13 0.03
80 2 0.01
81 21 0.05
82 3 0.01
83 2 0.01
84 1 0.00
85 12 0.03
86 1 0.00
87 4 0.01
88 11 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (77 bp):
AGCCATTCGATCTTTTACCCCGAGCCTGGGGTAATTGCAGCCATCCAATCTTTTACCCTAATCAT
GGGGCAGATTGT
Found at i:20125827 original size:156 final size:154
Alignment explanation
Indices: 20125360--20125850 Score: 536
Period size: 156 Copynumber: 3.1 Consensus size: 154
20125350 TTGAAGTTGC
** * * *
20125360 AGCCATTCGATCTTTTACCCCGAGCCTAGGACAGATCACCATCAGCCAATCTCTTACCCCGAGCC
1 AGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCTCAAGCC
* * *
20125425 TGGGGCAGATTGCAACCATTCGATCTTTTACCCCGAGCTTGGGGTAGATT-ACCATCAGTTAATC
66 TAGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGTAGATTCACCATCCG---ATC
*
20125489 TCTTACCCCGAGCTTGGGGCAGATTGT
128 TCTTACCCCGAGCATGGGGCAGATTGT
* ** * * * *
20125516 AGTCATTCGATCTTTTACCCTTAGCCTGGGGTATATCACCATCAGCCAATCTCTTACCTCAGGCT
1 AGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCTCAAGCC
** * * * * * * * *
20125581 TAGGAAAAATTGAAGCCATCCGATCTCTTACCCCAAGCTTGGGGCA-AATCACCATCAGCCAATC
66 TAGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGTAGATTCACCAT---CCGATC
* * *
20125645 TCTTACCCCGAGCCTGAGGCAAATTGT
128 TCTTACCCCGAGCATGGGGCAGATTGT
*
20125672 AGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTTTTACCTCAAGCC
1 AGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCTCAAGCC
**
20125737 TAGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCCGGGGTAGATTGCAGCCATCCGATCT
66 TAGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGTAGATT-CA-CCATCCGATCT
* ** *
20125802 TTTACCCTAATCATGGGGCAGATTGT
129 CTTACCCCGAGCATGGGGCAGATTGT
* * * *
20125828 AACCATCCAATCTCTTACCCCGA
1 AGCCATTCGATCTTTTACCCCGA
20125851 TCATGAGGCA
Statistics
Matches: 270, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
155 2 0.01
156 259 0.96
157 2 0.01
158 2 0.01
159 5 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (154 bp):
AGCCATTCGATCTTTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCTCAAGCC
TAGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGTAGATTCACCATCCGATCTCT
TACCCCGAGCATGGGGCAGATTGT
Found at i:20126660 original size:18 final size:18
Alignment explanation
Indices: 20126633--20126680 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
20126623 CAAAAACAAA
*
20126633 TAAATCAAAAATAAATTT
1 TAAATTAAAAATAAATTT
* * *
20126651 TAAATTAAAATTTATTTT
1 TAAATTAAAAATAAATTT
*
20126669 TAAATTTAAAAT
1 TAAATTAAAAAT
20126681 GTCCAAATAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTAAAAATAAATTT
Found at i:20127207 original size:15 final size:15
Alignment explanation
Indices: 20127187--20127217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20127177 TTTCAAAGTA
20127187 TAATAAATACATAAT
1 TAATAAATACATAAT
*
20127202 TAATAAATATATAAT
1 TAATAAATACATAAT
20127217 T
1 T
20127218 TTAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAATACATAAT
Found at i:20129758 original size:109 final size:109
Alignment explanation
Indices: 20129592--20130029 Score: 628
Period size: 109 Copynumber: 4.0 Consensus size: 109
20129582 ATTTGCTCAT
* * *
20129592 GCTGAATATATGATTCGATCGAATTTACCCTTATTTTT-TTTGCTTGTTTTAGGAAGTTGGTGAG
1 GCTGAATATATGATTCAATTGAATTTACCCTT-TTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAG
20129656 TTTTGATTTTCTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
65 TTTTGATTTTCTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
* *
20129701 GCTGAGTATATGATTCAATTGAATTTACCTTTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
1 GCTGAATATATGATTCAATTGAATTTACCCTTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
* * * * * *
20129766 TTTTATTTTTTAAGTTTAATTTTTCTTTGCATTTTAGCAATTAG
66 TTTGATTTTCTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
* * * * * * * *
20129810 GTTAAATATATGGTTCGATTGAATTTGCCCCTTTTTTCTTTGTTTGTTTTAGGAAGTTGGTGAGT
1 GCTGAATATATGATTCAATTGAATTTACCCTTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
* *
20129875 TTTGATTTTCTAAGTTTAGTTGTACTCTCAATTTTAGCAATTAG
66 TTTGATTTTCTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
* * *
20129919 GTTGAATATATGATTCAATTGAATTTGCCCATTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
1 GCTGAATATATGATTCAATTGAATTTACCCTTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
20129984 TTTGAATTTT-TAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
66 TTTG-ATTTTCTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
20130028 GC
1 GC
20130030 AATTTGATTT
Statistics
Matches: 289, Mismatches: 38, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
108 5 0.02
109 279 0.97
110 5 0.02
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.50
Consensus pattern (109 bp):
GCTGAATATATGATTCAATTGAATTTACCCTTTTTTTCTCTGCTTGTTTTAGGAAGTTGGTGAGT
TTTGATTTTCTAAGTTTAGTTTTACTCTCCATTTTAGCAATTAG
Found at i:20130951 original size:54 final size:54
Alignment explanation
Indices: 20130881--20130987 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
20130871 AAAAGGCAAA
* * *
20130881 AAAGAAAAAAAGAAAGGGGAAGAATGAGATCAACTAGCGGCATAAAAGGAGTTT
1 AAAGAAAAAAAGAAAGGGGAAGAAGGAGATCAACCAGCAGCATAAAAGGAGTTT
* * *
20130935 AAAGAAAAAAAGAAAGGTGAAGAAGGAGATTAACCAGCAGCATAAAATGAGTT
1 AAAGAAAAAAAGAAAGGGGAAGAAGGAGATCAACCAGCAGCATAAAAGGAGTT
20130988 GTGGGGTAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.53, C:0.07, G:0.26, T:0.13
Consensus pattern (54 bp):
AAAGAAAAAAAGAAAGGGGAAGAAGGAGATCAACCAGCAGCATAAAAGGAGTTT
Done.