Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 52 of 141
Found at i:16792613 original size:12 final size:12
Alignment explanation
Indices: 16792558--16792613 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 12
16792548 GAAGAAGAGG
16792558 AAATTCAAAAAA
1 AAATTCAAAAAA
16792570 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
*
16792582 AAATTGATTGAAAAA
1 AAATTCA---AAAAA
16792597 AAATTCAAAAAA
1 AAATTCAAAAAA
16792609 AAATT
1 AAATT
16792614 TCGAAGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 2 0.05
12 23 0.62
13 1 0.03
15 11 0.30
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:16796348 original size:31 final size:33
Alignment explanation
Indices: 16796287--16796355 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
16796277 AAGCCTATTT
16796287 AATGTGTCTGGCCGAATTAATTGTGTGTGTCTA
1 AATGTGTCTGGCCGAATTAATTGTGTGTGTCTA
16796320 AATGTGTCTGGCCGAATTAA-T-TGTGTGTCTA
1 AATGTGTCTGGCCGAATTAATTGTGTGTGTCTA
16796351 AATGT
1 AATGT
16796356 TAAATTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 15 0.42
32 1 0.03
33 20 0.56
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (33 bp):
AATGTGTCTGGCCGAATTAATTGTGTGTGTCTA
Found at i:16800380 original size:44 final size:44
Alignment explanation
Indices: 16800317--16800451 Score: 270
Period size: 44 Copynumber: 3.1 Consensus size: 44
16800307 GATCTAAACA
16800317 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
1 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
16800361 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
1 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
16800405 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
1 ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
16800449 ATA
1 ATA
16800452 GAGTTTAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (44 bp):
ATATAAACTTAATGAAAAGAATGAACATAAAGAACAATTCAAGG
Found at i:16806114 original size:27 final size:27
Alignment explanation
Indices: 16806078--16806215 Score: 177
Period size: 27 Copynumber: 5.1 Consensus size: 27
16806068 AGAGGTCAAT
* * *
16806078 AAATGATCGAAATACCCCCACACGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
16806105 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
16806132 AATTGACCAAAATACCCTCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
16806159 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
16806186 GAATGACCGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
16806213 AAA
1 AAA
16806216 AGATTGTTAT
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 96 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:16808259 original size:14 final size:13
Alignment explanation
Indices: 16808211--16808260 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
16808201 ACTGGTCATA
16808211 GAGAGA-ATTGAG
1 GAGAGATATTGAG
* *
16808223 GAGGGATATT-TG
1 GAGAGATATTGAG
16808235 GAGAGAT-TTGAG
1 GAGAGATATTGAG
16808247 GAGAGAATATTGAG
1 GAGAG-ATATTGAG
16808261 ATTTGGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.07
12 18 0.60
13 5 0.17
14 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (13 bp):
GAGAGATATTGAG
Found at i:16808900 original size:81 final size:82
Alignment explanation
Indices: 16808761--16808918 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 82
16808751 ATAAATGATA
* *
16808761 GAAATACCCCTATACGATAAAATAACCGAAATACCCCTATAGGGTAAATTGATCGAAATACCCCC
1 GAAATACCCCCATACGATAAAATAACCGAAATACCCCCATAGGGTAAATTGATCGAAATACCCCC
16808826 ATAGGG-AAAATTAACC
66 ATAGGGTAAAATTAACC
* * * * *
16808842 GAAATACCCCCATATGGTAAAATGATCGAAATACCCCCATAGGGTAGAA-TGA-CTGAAATACTC
1 GAAATACCCCCATACGATAAAATAACCGAAATACCCCCATAGGGTA-AATTGATC-GAAATACCC
16808905 CCATAGGGTAAAAT
64 CCATAGGGTAAAAT
16808919 GAATGTTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
80 1 0.01
81 59 0.88
82 7 0.10
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (82 bp):
GAAATACCCCCATACGATAAAATAACCGAAATACCCCCATAGGGTAAATTGATCGAAATACCCCC
ATAGGGTAAAATTAACC
Found at i:16808917 original size:54 final size:53
Alignment explanation
Indices: 16808753--16808920 Score: 212
Period size: 54 Copynumber: 3.1 Consensus size: 53
16808743 AGAGGTCGAT
* * * *
16808753 AAATGATAGAAATACCCCTATACGATAAAATAACCGAAATACCCCTATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAATAACCGAAATACCCC-ATAGGGTA
* *
16808807 AATTGATCGAAATACCCCCATAGGG-AAAATTAACCGAAATACCCCCATATGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAA-TAACCGAAATA-CCCCATAGGGTA
* * *
16808861 AAATGATCGAAATACCCCCATAGGGTAGAATGACTGAAATACTCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTAAAATAACCGAAATAC-CCCATAGGGTA
16808915 AAATGA
1 AAATGA
16808921 ATGTTATACC
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
53 5 0.05
54 87 0.88
55 7 0.07
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (53 bp):
AAATGATCGAAATACCCCCATAGGGTAAAATAACCGAAATACCCCATAGGGTA
Found at i:16808919 original size:27 final size:27
Alignment explanation
Indices: 16808753--16808920 Score: 187
Period size: 27 Copynumber: 6.2 Consensus size: 27
16808743 AGAGGTCGAT
* * * *
16808753 AAATGATAGAAATACCCCTATACGATA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
16808780 AAATAACCGAAATACCCCTATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
16808807 AATTGATCGAAATACCCCCATAGGG-A
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
16808833 AAATTAACCGAAATACCCCCATATGGTA
1 AAA-TGATCGAAATACCCCCATAGGGTA
16808861 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
16808888 GAATGA-CTGAAATACTCCCATAGGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
16808915 AAATGA
1 AAATGA
16808921 ATGTTATACC
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.03
27 111 0.93
28 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:16816876 original size:5 final size:5
Alignment explanation
Indices: 16816868--16816907 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
16816858 GTACAAAGTA
* * *
16816868 AAATA AAATC AAATC AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
16816908 CTAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (5 bp):
AAATT
Found at i:16818049 original size:18 final size:18
Alignment explanation
Indices: 16818026--16818061 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16818016 TGGCATTAAA
16818026 GCATTAAAGGAACAAATG
1 GCATTAAAGGAACAAATG
16818044 GCATTAAAGGAACAAATG
1 GCATTAAAGGAACAAATG
16818062 AAAATGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (18 bp):
GCATTAAAGGAACAAATG
Found at i:16819092 original size:7 final size:7
Alignment explanation
Indices: 16819080--16819108 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
16819070 TAGTCGATTG
16819080 GTATTTA
1 GTATTTA
16819087 GTATTTA
1 GTATTTA
16819094 GTATTTA
1 GTATTTA
16819101 GTATTTA
1 GTATTTA
16819108 G
1 G
16819109 AATTATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (7 bp):
GTATTTA
Found at i:16819118 original size:14 final size:14
Alignment explanation
Indices: 16819082--16819112 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16819072 GTCGATTGGT
*
16819082 ATTTAGTATTTAGT
1 ATTTAGTATTTAGA
16819096 ATTTAGTATTTAGA
1 ATTTAGTATTTAGA
16819110 ATT
1 ATT
16819113 ATGTATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (14 bp):
ATTTAGTATTTAGA
Found at i:16819790 original size:18 final size:18
Alignment explanation
Indices: 16819763--16819802 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16819753 TAGGTGCGTT
* *
16819763 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
16819781 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
16819799 TCCT
1 TCCT
16819803 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:16820362 original size:14 final size:14
Alignment explanation
Indices: 16820343--16820385 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
16820333 AATTTAATTG
16820343 ACCCTTAACCTTAA
1 ACCCTTAACCTTAA
*
16820357 ACCCTTAACCTAAAA
1 ACCCTTAACCT-TAA
16820372 ACCC-TAACCCTTAA
1 ACCCTTAA-CCTTAA
16820386 TTCTTAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (14 bp):
ACCCTTAACCTTAA
Found at i:16820380 original size:21 final size:21
Alignment explanation
Indices: 16820356--16820472 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 21
16820346 CTTAACCTTA
16820356 AACCCTTAACCTAAAAACCCT
1 AACCCTTAACCTAAAAACCCT
16820377 AACCCTTAATTCTTAACCTAAAAACCCT
1 AA-CC------CTTAACCTAAAAACCCT
* *
16820405 AACCCTCAACTTAAAAACCCT
1 AACCCTTAACCTAAAAACCCT
* *
16820426 AAACCC--AACTTAAAAACCAT
1 -AACCCTTAACCTAAAAACCCT
16820446 AAACCCTTAACCTAAAAACCCT
1 -AACCCTTAACCTAAAAACCCT
16820468 AACCC
1 AACCC
16820473 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
20 19 0.23
21 22 0.27
22 19 0.23
27 2 0.02
28 19 0.23
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTTAACCTAAAAACCCT
Found at i:16820380 original size:28 final size:27
Alignment explanation
Indices: 16820343--16820408 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
16820333 AATTTAATTG
16820343 ACCCTTAACCTTAAACCCTTAACCTAAAA
1 ACCC-TAACCTT-AACCCTTAACCTAAAA
**
16820372 ACCCTAACCCTTAATTCTTAACCTAAAA
1 ACCCTAA-CCTTAACCCTTAACCTAAAA
16820400 ACCCTAACC
1 ACCCTAACC
16820409 CTCAACTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 24 0.71
29 8 0.24
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.24
Consensus pattern (27 bp):
ACCCTAACCTTAACCCTTAACCTAAAA
Found at i:16820410 original size:49 final size:41
Alignment explanation
Indices: 16820349--16820472 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 41
16820339 ATTGACCCTT
*
16820349 AACCTTAAACCCTTAACCTAAAAACCCTAACCCTTAATTCTTAACCTAAA
1 AACCATAAACCCTTAACCTAAAAACCCTAACCC--AA--C-T----TAAA
* * *
16820399 AACCCT-AACCCTCAACTTAAAAACCCTAAACCCAACTTAAA
1 AACCATAAACCCTTAACCTAAAAACCCT-AACCCAACTTAAA
16820440 AACCATAAACCCTTAACCTAAAAACCCTAACCC
1 AACCATAAACCCTTAACCTAAAAACCCTAACCC
16820473 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
41 14 0.21
42 19 0.29
45 1 0.02
46 1 0.02
48 2 0.03
49 19 0.29
50 10 0.15
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.20
Consensus pattern (41 bp):
AACCATAAACCCTTAACCTAAAAACCCTAACCCAACTTAAA
Found at i:16820434 original size:20 final size:20
Alignment explanation
Indices: 16820395--16820469 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
16820385 ATTCTTAACC
*
16820395 TAAAAACCCTAACCCTCAACT
1 TAAAAACCCTAAACC-CAACT
16820416 TAAAAACCCTAAACCCAACT
1 TAAAAACCCTAAACCCAACT
* *
16820436 TAAAAACCATAAACCCTTAACC
1 TAAAAACCCTAAACCC--AACT
16820458 TAAAAACCCTAA
1 TAAAAACCCTAA
16820470 CCCNNNNNNN
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
20 20 0.42
21 14 0.29
22 14 0.29
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAACCCTAAACCCAACT
Found at i:16820659 original size:22 final size:22
Alignment explanation
Indices: 16820632--16820861 Score: 295
Period size: 22 Copynumber: 10.6 Consensus size: 22
16820622 NNNNNNNNTA
* * *
16820632 AAAAACCCTAAACCATTAACTT
1 AAAAACCATAAACCCTTAACCT
16820654 AAAAACCATAAACCCTTAACCT
1 AAAAACCATAAACCCTTAACCT
16820676 AAAAACCAT-AACCCTTAACCT
1 AAAAACCATAAACCCTTAACCT
* * *
16820697 AAAACCCCTAAACCCTTAACTT
1 AAAAACCATAAACCCTTAACCT
16820719 AAAAACCATAAACCCTTAACCT
1 AAAAACCATAAACCCTTAACCT
16820741 AAAAACCAT-AACCCTTAACCT
1 AAAAACCATAAACCCTTAACCT
* * *
16820762 AAAACCCCTAAACCCTTAACTT
1 AAAAACCATAAACCCTTAACCT
16820784 AAAAACCATAAACCCTTAACCT
1 AAAAACCATAAACCCTTAACCT
* * * *
16820806 AAAATCCCTAGA-CCTTAACTT
1 AAAAACCATAAACCCTTAACCT
* * *
16820827 AAAAACCCTAAAACCTTAACTT
1 AAAAACCATAAACCCTTAACCT
16820849 AAAAACCATAAAC
1 AAAAACCATAAAC
16820862 TCTTTCGAGC
Statistics
Matches: 182, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
21 56 0.31
22 126 0.69
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAACCATAAACCCTTAACCT
Found at i:16820700 original size:43 final size:44
Alignment explanation
Indices: 16820632--16820861 Score: 304
Period size: 43 Copynumber: 5.3 Consensus size: 44
16820622 NNNNNNNNTA
* *
16820632 AAAAACCCTAAACCATTAACTTAAAAACCATAAACCCTTAACCT
1 AAAAACCATAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
* * * *
16820676 AAAAACCAT-AACCCTTAACCTAAAACCCCTAAACCCTTAACTT
1 AAAAACCATAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
*
16820719 AAAAACCATAAACCCTTAACCTAAAAACCAT-AACCCTTAACCT
1 AAAAACCATAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
* *
16820762 AAAACCCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
1 AAAAACCATAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
* * * * * *
16820806 AAAATCCCTAGA-CCTTAACTTAAAAACCCTAAAACCTTAACTT
1 AAAAACCATAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
16820849 AAAAACCATAAAC
1 AAAAACCATAAAC
16820862 TCTTTCGAGC
Statistics
Matches: 163, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
43 114 0.70
44 49 0.30
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (44 bp):
AAAAACCATAAACCCTTAACTTAAAAACCATAAACCCTTAACCT
Found at i:16820736 original size:65 final size:65
Alignment explanation
Indices: 16820632--16820861 Score: 381
Period size: 65 Copynumber: 3.5 Consensus size: 65
16820622 NNNNNNNNTA
*
16820632 AAAAACCCTAAACCATTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATAACCCTTAACCT
1 AAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATAACCCTTAACCT
*
16820697 AAAACCCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATAACCCTTAACCT
1 AAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATAACCCTTAACCT
* * * *
16820762 AAAACCCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAATCCCTAGA-CCTTAACT
1 AAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATA-ACCCTTAACC
16820826 T
65 T
*
16820827 AAAAACCCTAAAACCTTAACTTAAAAACCATAAAC
1 AAAAACCCTAAACCCTTAACTTAAAAACCATAAAC
16820862 TCTTTCGAGC
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
65 156 0.99
66 1 0.01
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (65 bp):
AAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCATAACCCTTAACCT
Found at i:16821725 original size:126 final size:126
Alignment explanation
Indices: 16821463--16821888 Score: 635
Period size: 126 Copynumber: 3.4 Consensus size: 126
16821453 CCCAAACATG
*
16821463 CTACTGTAGCAAAAGCGCGTCCACGTGGGTGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
* * * * *
16821527 CTAG-AA-G-TGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGAC
65 CTTGCAACGTTG-TTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
* * *
16821587 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTGCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
16821652 TTGCAACGTTGTTTTATACTATTTGCTCAGAAATGTGAACTCGAAATTATTTTTTCAGGAC
66 TTGCAACGTTGTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
*
16821713 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATACTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
16821778 TTGCAGCGTTGTTTTATACTATTTGCTCAGAAATGTCAACTTGAAATTATTTTTTCAGGAC
66 TTGCAACGTTGTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
* * * * * *
16821839 CTACTGTAGCAAAAGCGCGTACACATGGGCGCAACTTCAAAAATCCTTCT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCT
16821889 GATATTTTAT
Statistics
Matches: 275, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
123 2 0.01
124 60 0.22
125 2 0.01
126 209 0.76
127 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TTGCAACGTTGTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:16822551 original size:13 final size:13
Alignment explanation
Indices: 16822533--16822557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16822523 TTTGGACATG
16822533 AAATATAATAATA
1 AAATATAATAATA
16822546 AAATATAATAAT
1 AAATATAATAAT
16822558 TTAATTAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATAATA
Found at i:16828077 original size:98 final size:98
Alignment explanation
Indices: 16827908--16828105 Score: 324
Period size: 98 Copynumber: 2.0 Consensus size: 98
16827898 AGAGTTAGTT
*
16827908 CTTTTGTGCAAGATTGCTTTCTTATGGTTTTTAGAAGCAGTTTTCTTCTTGATTTTCTTTAAGGA
1 CTTTTGTGCAAGATTGCTTTCTTATGATTTTTAGAAGCAGTTTTCTTCTTGATTTTCTTTAAGGA
* *
16827973 GTCGTGGGAATTTATTCTTCATCCTTCAATTTG
66 GCCGTGGGAATTCATTCTTCATCCTTCAATTTG
* ** *
16828006 CTTTTGTGCAAGATTGCTTTCTTGTGATTTTTAGAATTAGTTTTCTTTTTGATTTTCTTTAAGGA
1 CTTTTGTGCAAGATTGCTTTCTTATGATTTTTAGAAGCAGTTTTCTTCTTGATTTTCTTTAAGGA
*
16828071 GCCGTGGGAATTCATTTTTCATCCTTCAATTTG
66 GCCGTGGGAATTCATTCTTCATCCTTCAATTTG
16828104 CT
1 CT
16828106 AAGGATTATT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (98 bp):
CTTTTGTGCAAGATTGCTTTCTTATGATTTTTAGAAGCAGTTTTCTTCTTGATTTTCTTTAAGGA
GCCGTGGGAATTCATTCTTCATCCTTCAATTTG
Found at i:16836103 original size:32 final size:35
Alignment explanation
Indices: 16836030--16836109 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 35
16836020 AATGGTAAGA
*
16836030 ATATTTTTTTTTATATTTTAATGTTGTATAATTTTT
1 ATATTTTTTTTTATATTTGAA-GTTGTATAATTTTT
16836066 ATATTTTTTTGTTATATTTGAA-TT-TA-AA-TTTT
1 ATATTTTTTT-TTATATTTGAAGTTGTATAATTTTT
*
16836098 GTATTTTTTTTT
1 ATATTTTTTTTT
16836110 CCTTTAATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 2 0.05
32 13 0.32
33 2 0.05
34 2 0.05
35 2 0.05
36 10 0.24
37 10 0.24
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (35 bp):
ATATTTTTTTTTATATTTGAAGTTGTATAATTTTT
Found at i:16837501 original size:25 final size:27
Alignment explanation
Indices: 16837453--16837504 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
16837443 TCTATATATA
*
16837453 TATATATATATATATGTATTATGTTAAG
1 TATATATATATATATG-ATGATGTTAAG
16837481 TATA-ATATATATATG-TGATGTTAA
1 TATATATATATATATGATGATGTTAA
16837505 TACTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
27 11 0.48
28 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (27 bp):
TATATATATATATATGATGATGTTAAG
Found at i:16837705 original size:18 final size:18
Alignment explanation
Indices: 16837682--16837737 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
16837672 TGAATGCCTT
16837682 CATTTTTAATGGATTTTA
1 CATTTTTAATGGATTTTA
16837700 CATTTTT-A--GA----A
1 CATTTTTAATGGATTTTA
16837711 CCATTTTTAATGGATTTTA
1 -CATTTTTAATGGATTTTA
16837730 CATTTTTA
1 CATTTTTA
16837738 GAACCCTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
11 1 0.03
12 7 0.23
13 1 0.03
15 4 0.13
17 1 0.03
18 15 0.50
19 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (18 bp):
CATTTTTAATGGATTTTA
Found at i:16837718 original size:30 final size:30
Alignment explanation
Indices: 16837682--16837742 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
16837672 TGAATGCCTT
16837682 CATTTTTAATGGATTTTACATTTTTAGAAC
1 CATTTTTAATGGATTTTACATTTTTAGAAC
16837712 CATTTTTAATGGATTTTACATTTTTAGAAC
1 CATTTTTAATGGATTTTACATTTTTAGAAC
16837742 C
1 C
16837743 CTTGGAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (30 bp):
CATTTTTAATGGATTTTACATTTTTAGAAC
Found at i:16838596 original size:35 final size:35
Alignment explanation
Indices: 16838550--16838667 Score: 112
Period size: 35 Copynumber: 3.4 Consensus size: 35
16838540 CGATTACTTG
* *
16838550 ACTAGTGCTGGGCACACTTATCGTTGGCTTATCCA
1 ACTAGCGCTGGGCACACATATCGTTGGCTTATCCA
* * * * * * *
16838585 ACTAGCGCTGGGCGCAAAACATCG-TCGATTATTCG
1 ACTAGCGCTGGGCAC-ACATATCGTTGGCTTATCCA
* * *
16838620 ACTAGTGCTGGGCACACCTATCGTTGCCTTATCCA
1 ACTAGCGCTGGGCACACATATCGTTGGCTTATCCA
16838655 ACTAGCGCTGGGC
1 ACTAGCGCTGGGC
16838668 GCAAAACATT
Statistics
Matches: 61, Mismatches: 20, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
34 5 0.08
35 51 0.84
36 5 0.08
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (35 bp):
ACTAGCGCTGGGCACACATATCGTTGGCTTATCCA
Found at i:16838628 original size:70 final size:70
Alignment explanation
Indices: 16838509--16838743 Score: 341
Period size: 70 Copynumber: 3.3 Consensus size: 70
16838499 TTGTCGGTTA
* *
16838509 ATCCGACTAGCGCTAGGCGCAAAA-ATCTTGTCGATTACTT-GACTAGTGCTGGGCACACTTATC
1 ATCCAACTAGCGCTGGGCGCAAAACATC--GTCGATTA-TTCGACTAGTGCTGGGCACACTTATC
16838572 GTTGGCTT
63 GTTGGCTT
*
16838580 ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACCTATCGTT
1 ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACTTATCGTT
*
16838645 GCCTT
66 GGCTT
* *
16838650 ATCCAACTAGCGCTGGGCGCAAAACATTGTCGATTATTCGACTAGTACTGGGCACACTTATCGTT
1 ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACTTATCGTT
16838715 GG-TAT
66 GGCT-T
**
16838720 ATCCAACTAGTACTGGGCGCAAAA
1 ATCCAACTAGCGCTGGGCGCAAAA
16838744 AGATTATTTT
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
69 3 0.02
70 123 0.81
71 22 0.15
72 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (70 bp):
ATCCAACTAGCGCTGGGCGCAAAACATCGTCGATTATTCGACTAGTGCTGGGCACACTTATCGTT
GGCTT
Found at i:16838694 original size:35 final size:35
Alignment explanation
Indices: 16838585--16838694 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 35
16838575 GGCTTATCCA
16838585 ACTAGCGCTGGGCGCAAAACATCGTCGATTATTCG
1 ACTAGCGCTGGGCGCAAAACATCGTCGATTATTCG
* * * * * * *
16838620 ACTAGTGCT-GG-GCACACCTATCGTTGCCTTATCCA
1 ACTAGCGCTGGGCGCAAAAC-ATCGTCG-ATTATTCG
*
16838655 ACTAGCGCTGGGCGCAAAACATTGTCGATTATTCG
1 ACTAGCGCTGGGCGCAAAACATCGTCGATTATTCG
16838690 ACTAG
1 ACTAG
16838695 TACTGGGCAC
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
33 5 0.09
34 8 0.14
35 31 0.55
36 7 0.12
37 5 0.09
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (35 bp):
ACTAGCGCTGGGCGCAAAACATCGTCGATTATTCG
Found at i:16841340 original size:15 final size:15
Alignment explanation
Indices: 16841320--16841365 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
16841310 ACAACATGTT
16841320 AACATAAGTGACTTA
1 AACATAAGTGACTTA
*
16841335 AACATAA--CA-TTCA
1 AACATAAGTGACTT-A
16841348 AACATAAGTGACTTA
1 AACATAAGTGACTTA
16841363 AAC
1 AAC
16841366 GTAATTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
12 2 0.08
13 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATAAGTGACTTA
Found at i:16845168 original size:24 final size:24
Alignment explanation
Indices: 16845136--16845182 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
16845126 TAACAAACTG
16845136 GCACACCAAAACTAAAGTATTCAT
1 GCACACCAAAACTAAAGTATTCAT
16845160 GCACACCAAAACTAAAGTATTCA
1 GCACACCAAAACTAAAGTATTCA
16845183 CACAAGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.19
Consensus pattern (24 bp):
GCACACCAAAACTAAAGTATTCAT
Found at i:16853967 original size:23 final size:23
Alignment explanation
Indices: 16853941--16853996 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
16853931 TTCGTTTCCT
* *
16853941 ATTTAGTTTTATTTTTACTTGTA
1 ATTTAGTTTTATTTTCAATTGTA
*
16853964 ATTTAGGTTTATTTTCAATTGTA
1 ATTTAGTTTTATTTTCAATTGTA
16853987 ATTATAGTTT
1 ATT-TAGTTT
16853997 AATATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.61
Consensus pattern (23 bp):
ATTTAGTTTTATTTTCAATTGTA
Found at i:16856282 original size:20 final size:20
Alignment explanation
Indices: 16856246--16856283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16856236 TTGAGCTAAA
*
16856246 ATTGAGCTGAATTGAGCTCG
1 ATTGAGCTGAATCGAGCTCG
*
16856266 ATTGAGCTGGATCGAGCT
1 ATTGAGCTGAATCGAGCT
16856284 TTATTTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.29
Consensus pattern (20 bp):
ATTGAGCTGAATCGAGCTCG
Found at i:16857941 original size:587 final size:587
Alignment explanation
Indices: 16856829--16858003 Score: 2350
Period size: 587 Copynumber: 2.0 Consensus size: 587
16856819 TGGTGAGATC
16856829 TAGGTTCCTTTTCCTGTGAAATGGCTCCATTATTGTCACAATGAAGTTCTATAGCATTTGATATG
1 TAGGTTCCTTTTCCTGTGAAATGGCTCCATTATTGTCACAATGAAGTTCTATAGCATTTGATATG
16856894 CTAGGCACAACCCCTAGTTCAGATACGAACTTCTTGATCCAAACAGCCTCTTTTGCAGCTTCACT
66 CTAGGCACAACCCCTAGTTCAGATACGAACTTCTTGATCCAAACAGCCTCTTTTGCAGCTTCACT
16856959 AGCTACAATATACTCGGCCTCTATTGTAGAATCAACAACTGTACCTTGCTTTGAACTTTTCCATC
131 AGCTACAATATACTCGGCCTCTATTGTAGAATCAACAACTGTACCTTGCTTTGAACTTTTCCATC
16857024 TCACAGCGCCACCATTAAGGCAAAACACAAAACCCGATTACAATCATGAATCATCCTTGTCGGTT
196 TCACAGCGCCACCATTAAGGCAAAACACAAAACCCGATTACAATCATGAATCATCCTTGTCGGTT
16857089 TGGAAGCTAGCATCAGTGTAACCTTTTACATTTAGCTCTTCCTCTCCTCCATATATAAGGAATGT
261 TGGAAGCTAGCATCAGTGTAACCTTTTACATTTAGCTCTTCCTCTCCTCCATATATAAGGAATGT
16857154 ATCCTTAGTCCTTCTTAAGTACTTAAGGATATTTTTAACTACTACCGAATGACCTTCACTGGGAT
326 ATCCTTAGTCCTTCTTAAGTACTTAAGGATATTTTTAACTACTACCGAATGACCTTCACTGGGAT
16857219 CTACTTGATACCGACTCATCATGCTTAAAGCATATGAGACAACTGGATGAGTACATAGCATGACA
391 CTACTTGATACCGACTCATCATGCTTAAAGCATATGAGACAACTGGATGAGTACATAGCATGACA
16857284 TACATGATAGACCTAATAGCTGAAGCATATGGAATCTTACTCATTCGCTCTCTTTCTTGTGGAGT
456 TACATGATAGACCTAATAGCTGAAGCATATGGAATCTTACTCATTCGCTCTCTTTCTTGTGGAGT
16857349 TGAAAGACACATTTCCTTCGAAACTGATATACCATGTCTCATAGGTAAAAATCCTTTTTTAGATT
521 TGAAAGACACATTTCCTTCGAAACTGATATACCATGTCTCATAGGTAAAAATCCTTTTTTAGATT
16857414 CT
586 CT
16857416 TAGGTTCCTTTTCCTGTGAAATGGCTCCATTATTGTCACAATGAAGTTCTATAGCATTTGATATG
1 TAGGTTCCTTTTCCTGTGAAATGGCTCCATTATTGTCACAATGAAGTTCTATAGCATTTGATATG
16857481 CTAGGCACAACCCCTAGTTCAGATACGAACTTCTTGATCCAAACAGCCTCTTTTGCAGCTTCACT
66 CTAGGCACAACCCCTAGTTCAGATACGAACTTCTTGATCCAAACAGCCTCTTTTGCAGCTTCACT
16857546 AGCTACAATATACTCGGCCTCTATTGTAGAATCAACAACTGTACCTTGCTTTGAACTTTTCCATC
131 AGCTACAATATACTCGGCCTCTATTGTAGAATCAACAACTGTACCTTGCTTTGAACTTTTCCATC
16857611 TCACAGCGCCACCATTAAGGCAAAACACAAAACCCGATTACAATCATGAATCATCCTTGTCGGTT
196 TCACAGCGCCACCATTAAGGCAAAACACAAAACCCGATTACAATCATGAATCATCCTTGTCGGTT
16857676 TGGAAGCTAGCATCAGTGTAACCTTTTACATTTAGCTCTTCCTCTCCTCCATATATAAGGAATGT
261 TGGAAGCTAGCATCAGTGTAACCTTTTACATTTAGCTCTTCCTCTCCTCCATATATAAGGAATGT
16857741 ATCCTTAGTCCTTCTTAAGTACTTAAGGATATTTTTAACTACTACCGAATGACCTTCACTGGGAT
326 ATCCTTAGTCCTTCTTAAGTACTTAAGGATATTTTTAACTACTACCGAATGACCTTCACTGGGAT
16857806 CTACTTGATACCGACTCATCATGCTTAAAGCATATGAGACAACTGGATGAGTACATAGCATGACA
391 CTACTTGATACCGACTCATCATGCTTAAAGCATATGAGACAACTGGATGAGTACATAGCATGACA
16857871 TACATGATAGACCTAATAGCTGAAGCATATGGAATCTTACTCATTCGCTCTCTTTCTTGTGGAGT
456 TACATGATAGACCTAATAGCTGAAGCATATGGAATCTTACTCATTCGCTCTCTTTCTTGTGGAGT
16857936 TGAAAGACACATTTCCTTCGAAACTGATATACCATGTCTCATAGGTAAAAATCCTTTTTTAGATT
521 TGAAAGACACATTTCCTTCGAAACTGATATACCATGTCTCATAGGTAAAAATCCTTTTTTAGATT
16858001 CT
586 CT
16858003 T
1 T
16858004 CTATACTAAA
Statistics
Matches: 588, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
587 588 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (587 bp):
TAGGTTCCTTTTCCTGTGAAATGGCTCCATTATTGTCACAATGAAGTTCTATAGCATTTGATATG
CTAGGCACAACCCCTAGTTCAGATACGAACTTCTTGATCCAAACAGCCTCTTTTGCAGCTTCACT
AGCTACAATATACTCGGCCTCTATTGTAGAATCAACAACTGTACCTTGCTTTGAACTTTTCCATC
TCACAGCGCCACCATTAAGGCAAAACACAAAACCCGATTACAATCATGAATCATCCTTGTCGGTT
TGGAAGCTAGCATCAGTGTAACCTTTTACATTTAGCTCTTCCTCTCCTCCATATATAAGGAATGT
ATCCTTAGTCCTTCTTAAGTACTTAAGGATATTTTTAACTACTACCGAATGACCTTCACTGGGAT
CTACTTGATACCGACTCATCATGCTTAAAGCATATGAGACAACTGGATGAGTACATAGCATGACA
TACATGATAGACCTAATAGCTGAAGCATATGGAATCTTACTCATTCGCTCTCTTTCTTGTGGAGT
TGAAAGACACATTTCCTTCGAAACTGATATACCATGTCTCATAGGTAAAAATCCTTTTTTAGATT
CT
Found at i:16868990 original size:17 final size:17
Alignment explanation
Indices: 16868948--16868991 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
16868938 TACGATATTG
*
16868948 TAAAAAAAATTCAAAAAA
1 TAAAAAAAA-TAAAAAAA
16868966 T-AAAAAAATAAAAAAA
1 TAAAAAAAATAAAAAAA
16868982 TAAAAAAAAT
1 TAAAAAAAAT
16868992 CATAGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 15 0.62
18 1 0.04
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:16868991 original size:9 final size:8
Alignment explanation
Indices: 16868950--16868989 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
16868940 CGATATTGTA
16868950 AAAAAAATT
1 AAAAAAA-T
*
16868959 CAAAAAAT
1 AAAAAAAT
16868967 AAAAAAAT
1 AAAAAAAT
16868975 AAAAAAAT
1 AAAAAAAT
16868983 AAAAAAA
1 AAAAAAA
16868990 ATCATAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:16870146 original size:13 final size:12
Alignment explanation
Indices: 16870128--16870161 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16870118 GACGAGAAGA
16870128 GAAAAATGAAAGT
1 GAAAAA-GAAAGT
*
16870141 GAAAAAGAAATT
1 GAAAAAGAAAGT
16870153 GAAAAAGAA
1 GAAAAAGAA
16870162 GAAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (12 bp):
GAAAAAGAAAGT
Found at i:16870165 original size:15 final size:15
Alignment explanation
Indices: 16870145--16870202 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
16870135 GAAAGTGAAA
16870145 AAGAAATTGAAAAAG
1 AAGAAATTGAAAAAG
**
16870160 AAGAAAAAGAAAAAG
1 AAGAAATTGAAAAAG
16870175 AAG-AA---AAAAAG
1 AAGAAATTGAAAAAG
16870186 AAAGAAATTGAAAAAG
1 -AAGAAATTGAAAAAG
16870202 A
1 A
16870203 GAGTGAGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 6 0.17
12 3 0.08
13 2 0.06
14 2 0.06
15 17 0.47
16 6 0.17
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (15 bp):
AAGAAATTGAAAAAG
Found at i:16870190 original size:12 final size:12
Alignment explanation
Indices: 16870142--16870192 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
16870132 AATGAAAGTG
16870142 AAAAAGAAATTGAA
1 AAAAAGAAA--GAA
16870156 AAAGAAGAAA-AA
1 AAA-AAGAAAGAA
16870168 GAAAAAG-AAGAA
1 -AAAAAGAAAGAA
16870180 AAAAAGAAAGAA
1 AAAAAGAAAGAA
16870192 A
1 A
16870193 TTGAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 8 0.24
12 13 0.39
13 3 0.09
14 3 0.09
15 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:16872070 original size:22 final size:21
Alignment explanation
Indices: 16872045--16872086 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
16872035 TTAAATAAAT
*
16872045 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
16872067 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
16872087 GTTAAATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:16875346 original size:20 final size:20
Alignment explanation
Indices: 16875321--16875374 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
16875311 CTCTACTTCA
16875321 AGCTCATTCAGCTCAACCAT
1 AGCTCATTCAGCTCAACCAT
* * *
16875341 AGCTCATTGAGCTCATCCTT
1 AGCTCATTCAGCTCAACCAT
*
16875361 AGCTCACTCAGCTC
1 AGCTCATTCAGCTC
16875375 GTTCTTAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (20 bp):
AGCTCATTCAGCTCAACCAT
Found at i:16879200 original size:10 final size:10
Alignment explanation
Indices: 16879186--16879243 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
16879176 CAGCTCCGAC
16879186 CAGCTCAATT
1 CAGCTCAATT
* *
16879196 GAGCTCATTT
1 CAGCTCAATT
16879206 CAGCTCAA-T
1 CAGCTCAATT
16879215 CGAGCTCAATT
1 C-AGCTCAATT
*
16879226 TAGCTACAATT
1 CAGCT-CAATT
16879237 CAGCTCA
1 CAGCTCA
16879244 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:16879209 original size:20 final size:20
Alignment explanation
Indices: 16879186--16879246 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
16879176 CAGCTCCGAC
16879186 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
16879206 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
16879227 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
16879247 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:16914987 original size:13 final size:13
Alignment explanation
Indices: 16914969--16914995 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16914959 TCGTGAGAAA
16914969 GCGAGCTCGACTT
1 GCGAGCTCGACTT
16914982 GCGAGCTCGACTT
1 GCGAGCTCGACTT
16914995 G
1 G
16914996 TGAACCGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GCGAGCTCGACTT
Found at i:16918789 original size:1 final size:1
Alignment explanation
Indices: 16918783--16918812 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16918773 CTTTTAAGAG
16918783 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16918813 GAGTATCCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16920665 original size:31 final size:30
Alignment explanation
Indices: 16920608--16920667 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
16920598 ACATGCACTA
*
16920608 TTTTTTATCAGTTTGGTCATTGTACTTTAC
1 TTTTTTATCAGTTTGGTCATTATACTTTAC
*
16920638 TTTTGTTATCAGTTTGG-CCTCTATACTTTA
1 TTTT-TTATCAGTTTGGTCAT-TATACTTTA
16920668 ATTATGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (30 bp):
TTTTTTATCAGTTTGGTCATTATACTTTAC
Found at i:16925243 original size:20 final size:20
Alignment explanation
Indices: 16925205--16925258 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
16925195 AAAATTGATC
*
16925205 TTTTGATAAAAATTCT-AAAA
1 TTTT-ATAAAAATACTAAAAA
16925225 TTTTATAAAAATACATAAAAA
1 TTTTATAAAAATAC-TAAAAA
*
16925246 TTATTAAAAAAAT
1 TT-TTATAAAAAT
16925259 GGTGTTGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 6 0.21
22 9 0.31
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TTTTATAAAAATACTAAAAA
Found at i:16927516 original size:58 final size:57
Alignment explanation
Indices: 16927389--16927527 Score: 163
Period size: 57 Copynumber: 2.4 Consensus size: 57
16927379 TGGTACATAG
* * * * * *
16927389 CGTAAGACCATGGATGAAAGACGTCATGACAACATGGTATAAGGTAAAGGTATATGG
1 CGTAAGACCATAGATGAAAGACGCCATGACAACATGGTATAAAGTAAAGGTAAACGA
* * **
16927446 CATAAGACCATAGATGAAAGACGCCATGGCGGCAAT-GTATAAAGTATAAGGTAAACGA
1 CGTAAGACCATAGATGAAAGACGCCATGACAAC-ATGGTATAAAGTA-AAGGTAAACGA
16927504 CGTAAGACCATAGATGAAAGACGC
1 CGTAAGACCATAGATGAAAGACGC
16927528 TTTGACAGCT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 36 0.52
58 33 0.48
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (57 bp):
CGTAAGACCATAGATGAAAGACGCCATGACAACATGGTATAAAGTAAAGGTAAACGA
Found at i:16927753 original size:29 final size:29
Alignment explanation
Indices: 16927695--16927753 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
16927685 AAGTCTGTTT
* * *
16927695 GGACATTAAACACAAGGTAAGTTTGCTGG
1 GGACAGTAAACACAAGGTAAGTCTGATGG
*
16927724 GGACAGTAAACACGAGGTAAGTCTGATGG
1 GGACAGTAAACACAAGGTAAGTCTGATGG
16927753 G
1 G
16927754 ATGCAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (29 bp):
GGACAGTAAACACAAGGTAAGTCTGATGG
Found at i:16931992 original size:9 final size:9
Alignment explanation
Indices: 16931977--16932007 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16931967 TCAGTACATG
16931977 CATTATTAT
1 CATTATTAT
*
16931986 TATTATTAT
1 CATTATTAT
16931995 CATTATTAT
1 CATTATTAT
16932004 CATT
1 CATT
16932008 TTTTCAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (9 bp):
CATTATTAT
Found at i:16950243 original size:45 final size:45
Alignment explanation
Indices: 16950160--16950259 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
16950150 TAACTGTAGC
* *
16950160 AGTAACAGTAACAGTATTCAACACATAAAGTGCTGAATCTGTAAT
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAAT
* * * *
16950205 AGTAACGGTAACAGTTTTTAACACACAAAGTG-TCGAATCGGTAAC
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCT-GAATCGGTAAT
*
16950250 AATAACAGTA
1 AGTAACAGTA
16950260 GTCGGCATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCGGTAAT
Found at i:16951651 original size:25 final size:23
Alignment explanation
Indices: 16951607--16951667 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
16951597 ATTTTGATTT
*
16951607 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
16951631 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
16951655 ATATAAATTATAT
1 AT-TTAATTATAT
16951668 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:16951670 original size:35 final size:35
Alignment explanation
Indices: 16951615--16951694 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
16951605 TTATTTAATA
* *
16951615 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
16951649 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
16951684 ATATAAT-TAAA
1 ATATAATATAAA
16951695 ACAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:16953500 original size:27 final size:26
Alignment explanation
Indices: 16953476--16953564 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
16953466 GATTACCCTG
16953476 TGTTTACTGTCCCTGTAGACTACCCCA
1 TGTTTACTGTCCC-GTAGACTACCCCA
* *
16953503 TGTTTGCTGTCCCGATGGACTACCCCA
1 TGTTTACTGTCCCG-TAGACTACCCCA
* * **
16953530 TGTTTATTGTCCCAGCAGACTATTCCA
1 TGTTTACTGTCCC-GTAGACTACCCCA
16953557 TGTTTACT
1 TGTTTACT
16953565 ATCTTGACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.02
27 49 0.96
28 1 0.02
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (26 bp):
TGTTTACTGTCCCGTAGACTACCCCA
Found at i:16960134 original size:105 final size:105
Alignment explanation
Indices: 16959952--16960159 Score: 373
Period size: 105 Copynumber: 2.0 Consensus size: 105
16959942 ACATTACCCG
16959952 GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACTTGAATTAAACAATTTATTCACCTAAT
1 GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACTTGAATTAAACAATTTATTCACCTAAT
*
16960017 ATCTTGATCCGTAGAAATCCTTAAATTATGCTAATATCCA
66 ATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCCA
* *
16960057 GGAAAGAATCTGCCTAGACTGCATCTTTCATTATCAA-TCTGAATTAAACAATTTATTCACCTAA
1 GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACT-TGAATTAAACAATTTATTCACCTAA
16960121 TATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATC
65 TATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATC
16960160 TCTCTTCAAG
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 1 0.01
105 98 0.99
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (105 bp):
GGAAAGAATCCGCCTAGACTGCATCTGTCATTATCAACTTGAATTAAACAATTTATTCACCTAAT
ATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCCA
Found at i:16964368 original size:163 final size:162
Alignment explanation
Indices: 16964091--16964426 Score: 656
Period size: 163 Copynumber: 2.1 Consensus size: 162
16964081 TATTCAGGCT
16964091 ATTAC-AAAATTAGTCATTTTTCATATCTAAGTTTAAAATCTAACCATTTAACACCAATTTCATT
1 ATTACAAAAATTAGTCATTTTTCATATCTAAGTTTAAAATCTAACCATTTAACACCAATTTCATT
16964155 AAGAAATCATCAATGGAAACTTTTAGAAACTTTAACAGTTTTAAAATTGGTTCACGGGGTAGTTA
66 AAGAAATCATCAATGGAAACTTTTAGAAACTTTAACAGTTTTAAAATTGGTTCACGGGGTAGTTA
16964220 AATCAAGCTTTCACAACCTCAAAAACATAAAA
131 AATCAAGCTTTCACAACCTCAAAAACATAAAA
16964252 ATTACAAACAATTAGTCATTTTTCATATCTAAGTTTAAAATCTAACCATTTAACACCAATTTCAT
1 ATTACAAA-AATTAGTCATTTTTCATATCTAAGTTTAAAATCTAACCATTTAACACCAATTTCAT
16964317 TAAGAAATCATCAATGGAAACTTTTAGAAACTTTAACAGTTTTAAAATTGGTTCACGGGGTAGTT
65 TAAGAAATCATCAATGGAAACTTTTAGAAACTTTAACAGTTTTAAAATTGGTTCACGGGGTAGTT
16964382 AAATCAAGCTTTCACAACCTCAAAAACATAAAA
130 AAATCAAGCTTTCACAACCTCAAAAACATAAAA
16964415 ATTACAAAAATT
1 ATTACAAAAATT
16964427 GACTAAATCA
Statistics
Matches: 173, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
161 5 0.03
162 6 0.03
163 162 0.94
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (162 bp):
ATTACAAAAATTAGTCATTTTTCATATCTAAGTTTAAAATCTAACCATTTAACACCAATTTCATT
AAGAAATCATCAATGGAAACTTTTAGAAACTTTAACAGTTTTAAAATTGGTTCACGGGGTAGTTA
AATCAAGCTTTCACAACCTCAAAAACATAAAA
Found at i:16964583 original size:21 final size:21
Alignment explanation
Indices: 16964559--16964606 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
16964549 GTCTTATATG
*
16964559 CTTAATGAATATTTAATTAAT
1 CTTAATGAATATTTAATTAAA
* ** *
16964580 CTTATTTTATTTTTAATTAAA
1 CTTAATGAATATTTAATTAAA
16964601 CTTAAT
1 CTTAAT
16964607 TAGATTAATG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (21 bp):
CTTAATGAATATTTAATTAAA
Found at i:16969799 original size:25 final size:25
Alignment explanation
Indices: 16969732--16969811 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
16969722 AGCTGTAAAT
*
16969732 GGTAAGCTCATACAAGCTGAATATC
1 GGTAAGCTCATGCAAGCTGAATATC
* *
16969757 AGTAAGCTCATGCGAGCTGAATATC
1 GGTAAGCTCATGCAAGCTGAATATC
*
16969782 GGTAAGCTC-TCTCAAGCTGAGA-ATC
1 GGTAAGCTCAT-GCAAGCTGA-ATATC
16969807 GGTAA
1 GGTAA
16969812 CCCTAATAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.02
25 45 0.96
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCATGCAAGCTGAATATC
Found at i:16976486 original size:17 final size:18
Alignment explanation
Indices: 16976466--16976503 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
16976456 TGGCATGCCA
16976466 ATTGTATTAAAAT-ATTT
1 ATTGTATTAAAATAATTT
*
16976483 ATTGTATTAAATTAATTT
1 ATTGTATTAAAATAATTT
16976501 ATT
1 ATT
16976504 AATAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTGTATTAAAATAATTT
Found at i:16984432 original size:28 final size:29
Alignment explanation
Indices: 16984377--16984432 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
16984367 TGACTGAACT
16984377 GAATTAATTCAATTAACCGGTCGGTTAACC
1 GAATTAATTCAATTAA-CGGTCGGTTAACC
* *
16984407 GAATTAATTCGATTGA-GGTCGGTTAA
1 GAATTAATTCAATTAACGGTCGGTTAA
16984433 TAATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
30 14 0.58
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (29 bp):
GAATTAATTCAATTAACGGTCGGTTAACC
Found at i:16990135 original size:4 final size:4
Alignment explanation
Indices: 16990126--16990164 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
16990116 ATAACTTGAG
*
16990126 TATT TATT TATT TATT TATT T-TT CATTT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TAT
16990165 GTACAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 26 0.84
5 3 0.10
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:16991710 original size:17 final size:17
Alignment explanation
Indices: 16991688--16991741 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
16991678 TAGATACCCC
16991688 ATATATCGATGCCCCAT
1 ATATATCGATGCCCCAT
** * *
16991705 ATATATAAAGGTCCCAT
1 ATATATCGATGCCCCAT
*
16991722 A-AAATCGATGCCCCAT
1 ATATATCGATGCCCCAT
16991738 ATAT
1 ATAT
16991742 CAAATATTTC
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (17 bp):
ATATATCGATGCCCCAT
Found at i:16996437 original size:16 final size:17
Alignment explanation
Indices: 16996413--16996451 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
16996403 AATAAACAAT
*
16996413 TAAAATAAATT-GGAAA
1 TAAATTAAATTGGGAAA
16996429 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
16996446 TAAATT
1 TAAATT
16996452 TAGATTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:16996846 original size:201 final size:201
Alignment explanation
Indices: 16996501--16996904 Score: 763
Period size: 201 Copynumber: 2.0 Consensus size: 201
16996491 CTCGGTGGAT
*
16996501 CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTGTAACAG
1 CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
16996566 TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
66 TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
*
16996631 CCTTATCGATTATCTAATTGAGATACACACGTTCTCGATTCAAGATTCCAGCAGTCTTGCGCTCT
131 CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTCAAGATTCCAGCAGTCTTGCGCTCT
16996696 AAAGAA
196 AAAGAA
*
16996702 CCCAGATTTAGAATCAATCCTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
1 CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
*
16996767 TTAAGAACGTCTTAACCGCCCATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
66 TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
*
16996832 CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTTAAGATTCCAGCAGTCTTGCGCTCT
131 CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTCAAGATTCCAGCAGTCTTGCGCTCT
16996897 AAAGAA
196 AAAGAA
16996903 CC
1 CC
16996905 GAACTCGAAT
Statistics
Matches: 198, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 198 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (201 bp):
CCCAGATTTAGAATCAATACTCAAAAATTAATTTTCTCCTCGAAACAATAAGCTGGTTATAACAG
TTAAGAACGTCTTAACCGCCAATTTTTCCTCTCGTAGCTAGTCCCGATAAGACCTGCAAACCAAT
CCTTATCGATTATCTAATTGAGATACACACGTTCCCGATTCAAGATTCCAGCAGTCTTGCGCTCT
AAAGAA
Found at i:17003344 original size:16 final size:17
Alignment explanation
Indices: 17003323--17003360 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17003313 ATAATTTTTT
*
17003323 AAAAAATAATTT-TACA
1 AAAAAATAATTTGAACA
*
17003339 AAAAAATTATTTGAACA
1 AAAAAATAATTTGAACA
17003356 AAAAA
1 AAAAA
17003361 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAAATAATTTGAACA
Found at i:17005610 original size:21 final size:19
Alignment explanation
Indices: 17005563--17005613 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
17005553 AAAAAAATTA
*
17005563 TTTACTTTTAAAGGATTTT
1 TTTATTTTTAAAGGATTTT
*
17005582 TTTAATTTTTGAAATGATATTT
1 TTT-ATTTTT-AAAGGAT-TTT
17005604 TTTATTTTTA
1 TTTATTTTTA
17005614 TGACACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.11
20 6 0.22
21 12 0.44
22 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTATTTTTAAAGGATTTT
Found at i:17005914 original size:16 final size:16
Alignment explanation
Indices: 17005893--17005923 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17005883 CATGTTAAAG
17005893 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
17005909 CATATATATTTGAAA
1 CATATAAATTTGAAA
17005924 ACTTTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:17006074 original size:10 final size:9
Alignment explanation
Indices: 17006043--17006084 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
17006033 TTTAACTTTC
17006043 TTTATATATT
1 TTTATA-ATT
17006053 CTTTATAATT
1 -TTTATAATT
17006063 TTT-TAAATT
1 TTTAT-AATT
17006072 TTTATAATT
1 TTTATAATT
17006081 TTTA
1 TTTA
17006085 AAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 18 0.62
10 4 0.14
11 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:17006077 original size:18 final size:18
Alignment explanation
Indices: 17006054--17006176 Score: 61
Period size: 17 Copynumber: 6.6 Consensus size: 18
17006044 TTATATATTC
17006054 TTTATAATTTTTTAAATT
1 TTTATAATTTTTTAAATT
**
17006072 TTTATAA-TTTTTAAAAA
1 TTTATAATTTTTTAAATT
* * **
17006089 TATATAA-ATTTGGAATT
1 TTTATAATTTTTTAAATT
* *
17006106 TTTATAAATATTTTGAATT
1 TTTAT-AATTTTTTAAATT
* *
17006125 TTAAAAATTATTTTGAAATT
1 TTTATAATT-TTTT-AAATT
* * *
17006145 TTGAAAATTATTTTGAATTTT
1 TTTATAATT-TTTT-AA-ATT
17006166 TTTATAATTTT
1 TTTATAATTTT
17006177 GGTTGAGAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
17 23 0.28
18 12 0.15
19 16 0.20
20 22 0.27
21 9 0.11
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTATAATTTTTTAAATT
Found at i:17006146 original size:20 final size:19
Alignment explanation
Indices: 17006105--17006165 Score: 88
Period size: 20 Copynumber: 3.2 Consensus size: 19
17006095 AATTTGGAAT
*
17006105 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
17006123 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTG-AA
*
17006143 TTTTGAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
17006162 TTTT
1 TTTT
17006166 TTTATAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
18 8 0.21
19 13 0.33
20 18 0.46
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:17006166 original size:20 final size:19
Alignment explanation
Indices: 17006096--17006166 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
17006086 AAATATATAA
*
17006096 ATTTGGAATTTTTATAAA-T
1 ATTTTGAATTTTTA-AAATT
*
17006115 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
*
17006134 ATTTTGAAATTTTGAAAATT
1 ATTTTG-AATTTTTAAAATT
17006154 ATTTTGAATTTTT
1 ATTTTGAATTTTT
17006167 TTATAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.07
19 25 0.54
20 18 0.39
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:17006351 original size:20 final size:19
Alignment explanation
Indices: 17006302--17006350 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
17006292 TTTATAAATA
17006302 TTTGAATTTTAAAAATTAT
1 TTTGAATTTTAAAAATTAT
*
17006321 TTTGAAATTTTGAAAATTAT
1 TTTG-AATTTTAAAAATTAT
17006341 TTTGAATTTT
1 TTTGAATTTT
17006351 TTTATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTGAATTTTAAAAATTAT
Found at i:17006429 original size:185 final size:186
Alignment explanation
Indices: 17006106--17006476 Score: 735
Period size: 185 Copynumber: 2.0 Consensus size: 186
17006096 ATTTGGAATT
17006106 TTTATAAATATTTTGAATTTTAAAAATTATTTTGAAATTTTGAAAATTATTTTGAATTTTTTTAT
1 TTTATAAATATTTTGAATTTTAAAAATTATTTTGAAATTTTGAAAATTATTTTGAATTTTTTTAT
17006171 AATTTTGGTTGAGAAAGAGACCAATTTGCTCATTTTTAAAATTTACTAGGGCCAAAGGGGTATTT
66 AATTTTGGTTGAGAAAGAGACCAATTTGCTCATTTTTAAAATTTACTAGGGCCAAAGGGGTATTT
17006236 ATACCAATTTTTTATTCAAAATGTAAAATTCAACTCGAATTGAACTCGAAACTCGA
131 ATACCAATTTTTTATTCAAAATGTAAAATTCAACTCGAATTGAACTCGAAACTCGA
17006292 TTTATAAATA-TTTGAATTTTAAAAATTATTTTGAAATTTTGAAAATTATTTTGAATTTTTTTAT
1 TTTATAAATATTTTGAATTTTAAAAATTATTTTGAAATTTTGAAAATTATTTTGAATTTTTTTAT
17006356 AATTTTGGTTGAGAAAGAGACCAATTTGCTCATTTTTAAAATTTACTAGGGCCAAAGGGGTATTT
66 AATTTTGGTTGAGAAAGAGACCAATTTGCTCATTTTTAAAATTTACTAGGGCCAAAGGGGTATTT
17006421 ATACCAATTTTTTATTCAAAATGTAAAATTCAACTCGAATTGAACTCGAAACTCGA
131 ATACCAATTTTTTATTCAAAATGTAAAATTCAACTCGAATTGAACTCGAAACTCGA
17006477 ACTACTTATT
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 175 0.95
186 10 0.05
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (186 bp):
TTTATAAATATTTTGAATTTTAAAAATTATTTTGAAATTTTGAAAATTATTTTGAATTTTTTTAT
AATTTTGGTTGAGAAAGAGACCAATTTGCTCATTTTTAAAATTTACTAGGGCCAAAGGGGTATTT
ATACCAATTTTTTATTCAAAATGTAAAATTCAACTCGAATTGAACTCGAAACTCGA
Found at i:17012774 original size:21 final size:21
Alignment explanation
Indices: 17012744--17012788 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
17012734 TACACCAAAA
*
17012744 TAGGCTTTTAACGGCGTTTTT
1 TAGGCCTTTAACGGCGTTTTT
*
17012765 TAGGCCTTTAGCGGCGTTTTT
1 TAGGCCTTTAACGGCGTTTTT
17012786 TAG
1 TAG
17012789 TGCCGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (21 bp):
TAGGCCTTTAACGGCGTTTTT
Found at i:17012936 original size:43 final size:43
Alignment explanation
Indices: 17012892--17013127 Score: 312
Period size: 43 Copynumber: 5.5 Consensus size: 43
17012882 GCGACACTAT
* *
17012892 AGAACATGACCTTTAGCGGCGC-TTTACCCACAAACGCCGCTAT
1 AGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACGCCGCTAA
* * **** * *
17012935 AGAACATGATCTTTAGCGGTGCTTCGCCCAAAAACGCAGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* *
17012978 AGATCACGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
* * *
17013021 AGATCACGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
17013064 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
*
17013107 AGATCATGACCTTTAGCGGCG
1 AGAACATGACCTTTAGCGGCG
17013128 TTTATGAAAA
Statistics
Matches: 169, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 168 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
Found at i:17014336 original size:191 final size:192
Alignment explanation
Indices: 17014117--17014539 Score: 487
Period size: 192 Copynumber: 2.2 Consensus size: 192
17014107 AAAGGTCCCA
* * * * *
17014117 AACTTGGTCTATTATGTTCATTAACATCATCA-AAAATCATCAATTACATCCTAATAACAATTTC
1 AACTTAGTCTATTATATTCATTAACATCAACATAAAAACATCAATTACATCCTAATAACAATTCC
* * * * *
17014181 AACTCCAAAGTT-GACTAAAGAAGCTTTGCAGGATATGA-AAACACAAGTGCATTTCCATTCAAG
66 AACCCCAAAGTTCAACTAAA-AAGCATTGCAGGATA-CACAAACACAAATGCATTTCCATTCAAG
** * * * *
17014244 TAAATTGTTGTGTTGTAATCACGAAG-TTCAAATGAAAACCATGACTTGAACCCATAAAAAATTC
129 T-AATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATTC
* *
17014308 AACTTAGTCTATTGTATTCATTAACATCAACATAAAAACATCAATTACTTCCTAATAACAATTCC
1 AACTTAGTCTATTATATTCATTAACATCAACATAAAAACATCAATTACATCCTAATAACAATTCC
* * **
17014373 AACCCCAAATTTCAATTAAAAAGCATTGCAGGATACACAAATGCAAATGCATTTCCATTCAAGTA
66 AACCCCAAAGTTCAACTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTCAAGTA
* * * *
17014438 ATAATAGTGTTTTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATTATAGATTAC
131 ATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATT-C
* ** *
17014501 AAACTTAGTCCA-TATGCTCATTAACATGAACATTAAAAA
1 -AACTTAGTCTATTATATTCATTAACATCAACA-TAAAAA
17014540 AACAATTCTA
Statistics
Matches: 194, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
191 48 0.25
192 108 0.56
193 22 0.11
194 16 0.08
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (192 bp):
AACTTAGTCTATTATATTCATTAACATCAACATAAAAACATCAATTACATCCTAATAACAATTCC
AACCCCAAAGTTCAACTAAAAAGCATTGCAGGATACACAAACACAAATGCATTTCCATTCAAGTA
ATAATAGTGTTGTAATCACAAAGCTCCAAATGAAAACCATGACTTAAACCCATAAAAAATTC
Found at i:17016927 original size:7 final size:7
Alignment explanation
Indices: 17016917--17016963 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
17016907 CTCTTAACAT
17016917 CTAACCC
1 CTAACCC
17016924 CTAA--C
1 CTAACCC
17016929 CTAACCC
1 CTAACCC
17016936 CTAACCC
1 CTAACCC
17016943 CTAACCC
1 CTAACCC
*
17016950 TTAACCC
1 CTAACCC
*
17016957 TTAACCC
1 CTAACCC
17016964 ATAAACCTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 5 0.14
7 32 0.86
ACGTcount: A:0.30, C:0.51, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAACCC
Found at i:17016934 original size:12 final size:12
Alignment explanation
Indices: 17016917--17016955 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
17016907 CTCTTAACAT
17016917 CTAACCCCTAAC
1 CTAACCCCTAAC
17016929 CTAACCCCTAACCC
1 CTAACCCCTAA--C
*
17016943 CTAACCCTTAAC
1 CTAACCCCTAAC
17016955 C
1 C
17016956 CTTAACCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:17016940 original size:26 final size:26
Alignment explanation
Indices: 17016902--17016955 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
17016892 ACCCTAAATC
* * *
17016902 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
* *
17016928 CCTAACCCCTAACCCCTAACCCTTAA
1 CCTAACCCCTAACACCTAACCCCTAA
17016954 CC
1 CC
17016956 CTTAACCCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.22
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:17016956 original size:14 final size:14
Alignment explanation
Indices: 17016918--17016974 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
17016908 TCTTAACATC
17016918 TAACCCCTAA-CC-
1 TAACCCCTAACCCT
*
17016930 TAACCCCTAACCCC
1 TAACCCCTAACCCT
*
17016944 TAACCCTTAACCCT
1 TAACCCCTAACCCT
* *
17016958 TAACCCATAAACCT
1 TAACCCCTAACCCT
17016972 TAA
1 TAA
17016975 ATCACATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 27 0.69
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:17016956 original size:21 final size:21
Alignment explanation
Indices: 17016901--17016974 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
17016891 AACCCTAAAT
* **
17016901 CCCTAACTCTTAACATCTAAC
1 CCCTAACCCTTAACCCCTAAC
17016922 CCCTAA-CC-TAACCCCTAAC
1 CCCTAACCCTTAACCCCTAAC
*
17016941 CCCTAACCCTTAACCCTTAAC
1 CCCTAACCCTTAACCCCTAAC
* *
17016962 CCATAAACCTTAA
1 CCCTAACCCTTAA
17016975 ATCACATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.33
20 3 0.07
21 27 0.60
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCTAACCCTTAACCCCTAAC
Found at i:17020306 original size:21 final size:21
Alignment explanation
Indices: 17020289--17020329 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17020279 TCACTAACTC
17020289 TTAACCTCTAACCCCTAACCT
1 TTAACCTCTAACCCCTAACCT
*
17020310 TTAACCTCTAACCCTTAACC
1 TTAACCTCTAACCCCTAACC
17020330 CCAAACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAACCTCTAACCCCTAACCT
Found at i:17020307 original size:14 final size:14
Alignment explanation
Indices: 17020290--17020362 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
17020280 CACTAACTCT
17020290 TAACCTCTAACCCC
1 TAACCTCTAACCCC
* *
17020304 TAACCTTTAACCTC
1 TAACCTCTAACCCC
17020318 TAACC-CTTAACCCC
1 TAACCTC-TAACCCC
* * *
17020332 AAACCCCTAACCCA
1 TAACCTCTAACCCC
*
17020346 TAA-CTACTAGCCCC
1 TAACCT-CTAACCCC
17020360 TAA
1 TAA
17020363 ACCTTATTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
13 1 0.02
14 44 0.96
15 1 0.02
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (14 bp):
TAACCTCTAACCCC
Found at i:17020336 original size:21 final size:21
Alignment explanation
Indices: 17020291--17020349 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
17020281 ACTAACTCTT
* ***
17020291 AACCTCTAACCCCTAACCTTT
1 AACCTCTAACCCATAACCCCA
*
17020312 AACCTCTAACCCTTAACCCCA
1 AACCTCTAACCCATAACCCCA
*
17020333 AACCCCTAACCCATAAC
1 AACCTCTAACCCATAAC
17020350 TACTAGCCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCTCTAACCCATAACCCCA
Found at i:17020520 original size:81 final size:81
Alignment explanation
Indices: 17020356--17020524 Score: 220
Period size: 80 Copynumber: 2.1 Consensus size: 81
17020346 TAACTACTAG
* *
17020356 CCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACTTAACCCG
1 CCCCTAAACCTTATTTAATATATAAATTAAAAACAATAATTAATCTAAACCCTAAACCTAACCCG
*
17020421 AACCCCTAACCCATAA
66 AACCACTAACCCATAA
*
17020437 CCCCTAAACCTTATTT-A-ATATAGATTAAAACACAATAATTAATCTAAACCCTAAACCCTAA-C
1 CCCCTAAACCTTATTTAATATATAAATTAAAA-ACAATAATTAATCTAAACCCTAAA-CCTAACC
* *
17020499 CTAA-CACTAAATCCATAA
64 CGAACCACT-AACCCATAA
*
17020517 ACCCTAAA
1 CCCCTAAA
17020525 TCCCTAACTC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
79 15 0.19
80 43 0.55
81 20 0.26
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (81 bp):
CCCCTAAACCTTATTTAATATATAAATTAAAAACAATAATTAATCTAAACCCTAAACCTAACCCG
AACCACTAACCCATAA
Found at i:17020959 original size:41 final size:40
Alignment explanation
Indices: 17020897--17021256 Score: 363
Period size: 41 Copynumber: 8.8 Consensus size: 40
17020887 AAATATTTTT
*
17020897 GCGGCGCTT-TTATAAAAACGCCGCTAAAAGCCCGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCT-AAAGCCCGAGCATTA
* * **** ** *
17020938 GCGGTGCTT-TCTCAAAAACGCCGCT-CAGATAAAATATTTTT
1 GCGGCGCTTCT-TCAAAAACGCCGCTAAAGCCCGAGCA--TTA
*
17020979 GCGGCGCTT-TTATAAAAACGCCGCTAAAAGCCCGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCT-AAAGCCCGAGCATTA
* *
17021020 GCGGTGCTT-TCTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTCT-TCAAAAACGCCGCTAAAGC-CCGAGCATTA
* *
17021061 GCGACGCTT-TTATAAAAACGCCGCTAAAAGCCCGAGCATTA
1 GCGGCGCTTCTT-CAAAAACGCCGCT-AAAGCCCGAGCATTA
*
17021102 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGC-CCGAGCATTA
* *
17021143 GCGGCGCTTCTTCAAAAACGCCACTAAAGCTCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGC-CCGAGCATTA
* *
17021184 GCGGCGCTTCATCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGC-CCGAGCATTA
*
17021225 GCGGCGCTTCTTCAAAAGCGCCGCTAAAGCCC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCC
17021257 CGAAAGGTAC
Statistics
Matches: 271, Mismatches: 36, Indels: 25
0.82 0.11 0.08
Matches are distributed among these distances:
39 4 0.01
40 13 0.05
41 241 0.89
42 9 0.03
43 4 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (40 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCGAGCATTA
Found at i:17021121 original size:123 final size:122
Alignment explanation
Indices: 17020979--17021256 Score: 402
Period size: 123 Copynumber: 2.3 Consensus size: 122
17020969 AAATATTTTT
* *
17020979 GCGGCGCTT-TTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGTGCTT-TCTCAAAAACGCC
1 GCGGCGCTTCTT-CAAAAACGCCGCT-AAAGCCCGAGCATTAGCGGCGCTTCT-TCAAAAACGCC
* *
17021042 GCTAAAGCTCTGAGCATTAGCGACGCTTTTAT-AAAAACGCCGCTAAAAGC-CCGAGCATTA
63 ACTAAAGCTCTGAGCATTAGCGACGC-TTCATCAAAAACGCCGCT-AAAGCTCCGAGCATTA
*
17021102 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCAC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGC-CCGAGCATTAGCGGCGCTTCTTCAAAAACGCCAC
* *
17021167 TAAAGCTCTGAGCATTAGCGGCGCTTCATCAAAAACGCCGCTAAAGCTCTGAGCATTA
65 TAAAGCTCTGAGCATTAGCGACGCTTCATCAAAAACGCCGCTAAAGCTCCGAGCATTA
*
17021225 GCGGCGCTTCTTCAAAAGCGCCGCTAAAGCCC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCC
17021257 CGAAAGGTAC
Statistics
Matches: 141, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
122 15 0.11
123 123 0.87
124 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (122 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCACT
AAAGCTCTGAGCATTAGCGACGCTTCATCAAAAACGCCGCTAAAGCTCCGAGCATTA
Found at i:17021128 original size:82 final size:82
Alignment explanation
Indices: 17020897--17021256 Score: 466
Period size: 82 Copynumber: 4.4 Consensus size: 82
17020887 AAATATTTTT
*
17020897 GCGGCGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
1 GCGGCGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * ** ** *
17020962 T-CAGAT-AAAATATTTTT
66 TAAAGCTCTGAGCA--TTA
*
17020979 GCGGCGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
1 GCGGCGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
17021044 TAAAGCTCTGAGCATTA
66 TAAAGCTCTGAGCATTA
*
17021061 GCGACGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGCGC-TTCTTCAAAAACGCCG
1 GCGGCGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGCGCTTTC-TCAAAAACGCCG
17021125 CTAAAGCTCTGAGCATTA
65 CTAAAGCTCTGAGCATTA
* * *
17021143 GCGGCGCTTCTT-CAAAAACGCCACT-AAAGCTCTGAGCATTAGCGGCGC-TTCATCAAAAACGC
1 GCGGCGCTT-TTATAAAAACGCCGCTAAAAGC-CCGAGCATTAGCGGCGCTTTC-TCAAAAACGC
17021205 CGCTAAAGCTCTGAGCATTA
63 CGCTAAAGCTCTGAGCATTA
* *
17021225 GCGGCGCTTCTT-CAAAAGCGCCGCT-AAAGCCC
1 GCGGCGCTT-TTATAAAAACGCCGCTAAAAGCCC
17021257 CGAAAGGTAC
Statistics
Matches: 256, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
81 9 0.04
82 240 0.94
83 5 0.02
84 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (82 bp):
GCGGCGCTTTTATAAAAACGCCGCTAAAAGCCCGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
TAAAGCTCTGAGCATTA
Found at i:17026991 original size:67 final size:67
Alignment explanation
Indices: 17026883--17027016 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
17026873 TATATGAGAT
* * *
17026883 TGGGACATTTGATGTATTGAAAATTGAAATGAGACTCTATTAACTGTTTCGAGCTAAGTCGGATA
1 TGGGACATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAACTGTTTCGAGCTAAGTCAGATA
17026948 TA
66 TA
* * *
17026950 TGGGAGATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAATTGTTTCGGGCTAAGTCAGATA
1 TGGGACATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAACTGTTTCGAGCTAAGTCAGATA
17027015 TA
66 TA
17027017 GATGGCATGC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.34
Consensus pattern (67 bp):
TGGGACATTTGATGTATTGAAAAGTGAAATGAGACCCTATTAACTGTTTCGAGCTAAGTCAGATA
TA
Found at i:17027344 original size:20 final size:19
Alignment explanation
Indices: 17027289--17027336 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
17027279 ATGGCAAAGT
* *
17027289 TGAGAAATG-ATTATGAGA
1 TGAGAAATGAAATATGAAA
17027307 TGAGAAATGAAATATGAAA
1 TGAGAAATGAAATATGAAA
17027326 TGATGAAATGA
1 TGA-GAAATGA
17027337 GATGTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 10 0.38
20 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (19 bp):
TGAGAAATGAAATATGAAA
Found at i:17033785 original size:30 final size:31
Alignment explanation
Indices: 17033749--17033811 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
17033739 TGTGGGTAGT
*
17033749 CCACACGAGCTA-TTTTTTGGGCCGTGTGGA
1 CCACACGAGCTAGCTTTTTGGGCCGTGTGGA
*
17033779 CCACACGAGCTAGCTTTTTGGGCCTTGTGGA
1 CCACACGAGCTAGCTTTTTGGGCCGTGTGGA
17033810 CC
1 CC
17033812 TTTTGGGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (31 bp):
CCACACGAGCTAGCTTTTTGGGCCGTGTGGA
Found at i:17042595 original size:21 final size:21
Alignment explanation
Indices: 17042571--17042619 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
17042561 CCAATCAAGT
* *
17042571 TACCATTTCTGATTCACTCCA
1 TACCATTTCTGACTCAATCCA
17042592 TACCATTTCTGACTCAATCCA
1 TACCATTTCTGACTCAATCCA
17042613 TACCATT
1 TACCATT
17042620 CCATATACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.37
Consensus pattern (21 bp):
TACCATTTCTGACTCAATCCA
Found at i:17048986 original size:18 final size:18
Alignment explanation
Indices: 17048949--17048995 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
17048939 TTTAAAATTT
* *
17048949 TGGGCCCATATTCTCATG
1 TGGGCCCACATGCTCATG
*
17048967 TGGGCCCACATGCTCGTG
1 TGGGCCCACATGCTCATG
17048985 T-GGCCCACATG
1 TGGGCCCACATG
17048996 GCCTGGCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.15, C:0.32, G:0.28, T:0.26
Consensus pattern (18 bp):
TGGGCCCACATGCTCATG
Found at i:17049794 original size:6 final size:6
Alignment explanation
Indices: 17049777--17049811 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
17049767 TACCCACTAA
*
17049777 CCACCT CTACCT CCACCT CCACCT CCACCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
17049812 ACCTTAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (6 bp):
CCACCT
Found at i:17051274 original size:5 final size:6
Alignment explanation
Indices: 17051251--17051308 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
17051241 AAATATTGTG
* * **
17051251 ATAATT ATAATT ATAATT -TAATTT AAAATT ATTATT -TAAAA ATAATT
1 ATAATT ATAATT ATAATT ATAA-TT ATAATT ATAATT ATAATT ATAATT
17051298 ATAATT -TAATT
1 ATAATT ATAATT
17051309 TTGAAATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
5 10 0.24
6 29 0.71
7 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:17051340 original size:35 final size:34
Alignment explanation
Indices: 17051257--17051341 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 34
17051247 TGTGATAATT
17051257 ATAATTATAATTTAATTTAAAATTATTATTTAAAA
1 ATAATTATAATTTAATTTAAAATTATTA-TTAAAA
*
17051292 ATAATTATAATTTAATTTTGAAATTATTA-TAAAA
1 ATAATTATAATTTAA-TTTAAAATTATTATTAAAA
* *
17051326 ATGATTTATTATTTAA
1 AT-AATTATAATTTAA
17051342 AAAATGGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 7 0.16
35 26 0.58
36 12 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (34 bp):
ATAATTATAATTTAATTTAAAATTATTATTAAAA
Found at i:17062034 original size:18 final size:18
Alignment explanation
Indices: 17062011--17062089 Score: 70
Period size: 18 Copynumber: 4.2 Consensus size: 18
17062001 TTAAAATTAA
17062011 ATAAAAATATTAAAAATT
1 ATAAAAATATTAAAAATT
*
17062029 ATAAAACA-ATTAGAAATTT
1 ATAAAA-ATATTA-AAAATT
* *
17062048 ATAAAAAAATAAAAAATT
1 ATAAAAATATTAAAAATT
* *
17062066 CTAAATATATTATAAAAATT
1 ATAAAAATA-T-TAAAAATT
17062086 ATAA
1 ATAA
17062090 TCAAGTATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 22 0.46
19 16 0.33
20 10 0.21
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.32
Consensus pattern (18 bp):
ATAAAAATATTAAAAATT
Found at i:17062064 original size:19 final size:19
Alignment explanation
Indices: 17062011--17062065 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
17062001 TTAAAATTAA
*
17062011 ATAAAAATATTAAAAA-TT
1 ATAAAAAAATTAAAAATTT
* *
17062029 ATAAAACAATTAGAAATTT
1 ATAAAAAAATTAAAAATTT
*
17062048 ATAAAAAAATAAAAAATT
1 ATAAAAAAATTAAAAATT
17062066 CTAAATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAAAATTAAAAATTT
Found at i:17067306 original size:25 final size:26
Alignment explanation
Indices: 17067253--17067302 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
17067243 AAACTTACAT
*
17067253 TTAATTTTATTTTATATTATAATTCA
1 TTAATTTTATTTTATATTATAAATCA
17067279 TTAA-TTTATTTT-TATTCA-AAATCA
1 TTAATTTTATTTTATATT-ATAAATCA
17067303 ATTACCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (26 bp):
TTAATTTTATTTTATATTATAAATCA
Found at i:17071559 original size:18 final size:17
Alignment explanation
Indices: 17071473--17071560 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 17
17071463 TGTTAACACT
*
17071473 TAAAATAATATTATATAA
1 TAAAATAATAATATA-AA
* *
17071491 TAAAATAATGCATATACA
1 TAAAATAAT-AATATAAA
17071509 TAAAA-AATTATATAGATAAA
1 TAAAATAA-TA-AT--ATAAA
17071529 T-AAATGAACTAATATAAA
1 TAAAAT-AA-TAATATAAA
17071547 TAATAATAATAATA
1 TAA-AATAATAATA
17071561 ATAATGGTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
17 2 0.04
18 29 0.53
19 10 0.18
20 10 0.18
21 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAAATAATAATATAAA
Found at i:17075745 original size:23 final size:23
Alignment explanation
Indices: 17075720--17075785 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
17075710 TTTTTTAAAA
17075720 TTTAAAAAATTTAAAAATAATTAT
1 TTTAAAAAATTTAAAAAT-ATTAT
*
17075744 TTTTAAAAA-TTAAAAATATTAT
1 TTTAAAAAATTTAAAAATATTAT
*
17075766 TGTTACAAAATTATAAAAAT
1 T-TTAAAAAATT-TAAAAAT
17075786 TATAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.17
23 14 0.39
24 9 0.25
25 7 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTAAAAAATTTAAAAATATTAT
Found at i:17082205 original size:15 final size:15
Alignment explanation
Indices: 17082185--17082291 Score: 58
Period size: 15 Copynumber: 7.3 Consensus size: 15
17082175 AGGTTGCACA
17082185 TAGGGGTTCACACCT
1 TAGGGGTTCACACCT
*** *
17082200 TAGGGGTTTGTA-CA
1 TAGGGGTTCACACCT
* *
17082214 TATGGGTTCACACTT
1 TAGGGGTTCACACCT
* *
17082229 TAGAGGTTCGCACCT
1 TAGGGGTTCACACCT
** * * *
17082244 TAAAGTTTCTCACAT
1 TAGGGGTTCACACCT
*
17082259 TA-GGGTTCGCACC-
1 TAGGGGTTCACACCT
*
17082272 TAGGGGTTCACACGT
1 TAGGGGTTCACACCT
17082287 TAGGG
1 TAGGG
17082292 TTTGCACCTA
Statistics
Matches: 65, Mismatches: 24, Indels: 6
0.68 0.25 0.06
Matches are distributed among these distances:
13 2 0.03
14 25 0.38
15 38 0.58
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (15 bp):
TAGGGGTTCACACCT
Found at i:17082207 original size:28 final size:28
Alignment explanation
Indices: 17082176--17082318 Score: 92
Period size: 29 Copynumber: 5.0 Consensus size: 28
17082166 ACACATATAA
*
17082176 GGTTGCACATAGGGGTTCACACCTTAGG
1 GGTTGCACATAGGGGTTCACACATTAGG
* * * *
17082204 GGTTTGTACATATGGGTTCACACTTTAGA
1 GG-TTGCACATAGGGGTTCACACATTAGG
* ** * *
17082233 GGTTCGCACCTTAAAGTTTCTCACATTA-G
1 GGTT-GCA-CATAGGGGTTCACACATTAGG
* *
17082262 GGTTCGCACCTAGGGGTTCACACGTTAGG
1 GGTT-GCACATAGGGGTTCACACATTAGG
* * **
17082291 GTTTGCACCTA-GGGTTCGTACATTAGG
1 GGTTGCACATAGGGGTTCACACATTAGG
17082318 G
1 G
17082319 TTCGCATCTA
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
27 14 0.16
28 24 0.27
29 38 0.43
30 13 0.15
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (28 bp):
GGTTGCACATAGGGGTTCACACATTAGG
Found at i:17082280 original size:14 final size:13
Alignment explanation
Indices: 17082259--17082331 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 13
17082249 TTTCTCACAT
17082259 TAGGGTTCGCACC
1 TAGGGTTCGCACC
* *
17082272 TAGGGGTTCACACGT
1 TA-GGGTTCGCAC-C
*
17082287 TAGGGTTTGCACC
1 TAGGGTTCGCACC
* *
17082300 TAGGGTTCGTACAT
1 TAGGGTTCGCAC-C
*
17082314 TAGGGTTCGCATC
1 TAGGGTTCGCACC
17082327 TAGGG
1 TAGGG
17082332 GGTTACACCT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 17 0.37
14 27 0.59
15 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.29
Consensus pattern (13 bp):
TAGGGTTCGCACC
Found at i:17084713 original size:18 final size:18
Alignment explanation
Indices: 17084692--17084728 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17084682 TATTGTCTGA
17084692 GGTTCGCA-TACTGTAGGG
1 GGTTCGCACTACT-TAGGG
17084710 GGTTCGCACTACTTAGGG
1 GGTTCGCACTACTTAGGG
17084728 G
1 G
17084729 TCGCAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.27
Consensus pattern (18 bp):
GGTTCGCACTACTTAGGG
Found at i:17085590 original size:43 final size:43
Alignment explanation
Indices: 17085529--17085624 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
17085519 CAGATAAAAA
** *
17085529 GTTTGCAGGCAAACTGCCAGTAAGTTATGTATGAACCACCAGT
1 GTTTGCAGATAAACTGCCAGTAAGTTATGGATGAACCACCAGT
* * * *
17085572 GTTTGCAGATAAATTGCCAGTAAGTTTTGGATGAACCTCTAGT
1 GTTTGCAGATAAACTGCCAGTAAGTTATGGATGAACCACCAGT
17085615 GTTTGCAGAT
1 GTTTGCAGAT
17085625 TATTGAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
GTTTGCAGATAAACTGCCAGTAAGTTATGGATGAACCACCAGT
Found at i:17085793 original size:38 final size:38
Alignment explanation
Indices: 17085711--17085805 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
17085701 GTACAAAAAT
* * *
17085711 AGTAGACATGCTTAACATGTATTTAGTTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTAAGCTCAACAGTAGC
* * *
17085749 AATAGACATGTTTAACATGTATTAAGCTCAACCA-TCGC
1 AGTAGACATGCTTAACATGTATTAAGCTCAA-CAGTAGC
* *
17085787 AGTAGACATTCTTCACATG
1 AGTAGACATGCTTAACATG
17085806 CCTTTAGTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
38 45 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTAAGCTCAACAGTAGC
Found at i:17086163 original size:38 final size:38
Alignment explanation
Indices: 17086112--17086213 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
17086102 AAAGAAACAG
17086112 TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
1 TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
* * *
17086150 TAGACATGCTTAACATGTATTCAGTTCAATAGTAGCAG
1 TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
* *
17086188 TAAACATGCTTCACATGCT-TTCAATT
1 TAGACATGCTTAACATG-TATTCAATT
17086214 TCAATTGTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 56 0.98
39 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (38 bp):
TAGACATGCTTAACATGTATTCAATTCAAAAGTAGCAA
Found at i:17101504 original size:38 final size:38
Alignment explanation
Indices: 17101419--17101513 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
17101409 GGACATGAAT
*
17101419 AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGT
1 AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGC
* * * *
17101457 AATAGACATGCTTAACATGTATTTAGTTTAATAGTTGC
1 AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGC
* *
17101495 AGTAAACATGCTTCACATG
1 AGTAGACATGCTTAACATG
17101514 CTTTCAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCAGTTCAATAGTAGC
Found at i:17109039 original size:36 final size:36
Alignment explanation
Indices: 17108992--17109063 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
17108982 TGTACCTTTG
17108992 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
1 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
17109028 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
1 TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
17109064 AAAAATATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.19
Consensus pattern (36 bp):
TTGAAATTAAAAATCAAAAGGTCAAAAATAGAAGAA
Found at i:17109408 original size:4 final size:4
Alignment explanation
Indices: 17109401--17109554 Score: 71
Period size: 4 Copynumber: 39.0 Consensus size: 4
17109391 GAAGGAGAGG
* *
17109401 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA
* * *
17109450 -AAA GAAT GTAAG GAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GAAA G-AA
1 GAAA GAAA G-AAA GAAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
*
17109496 G-AA G-AA G-AA GAAGA GGAAA GGAAA GGAGAG GAAA -AAA GAAA G-AA
1 GAAA GAAA GAAA GAA-A -GAAA -GAAA -GA-AA GAAA GAAA GAAA GAAA
*
17109540 -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
17109555 AGGAAAGGAG
Statistics
Matches: 123, Mismatches: 11, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
3 31 0.25
4 58 0.47
5 30 0.24
6 4 0.03
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:17109462 original size:28 final size:30
Alignment explanation
Indices: 17109405--17109561 Score: 100
Period size: 28 Copynumber: 5.3 Consensus size: 30
17109395 GAGAGGGAAA
17109405 GAAA-GAAAGAAAGAAAGAAAGAAAGGAAG
1 GAAAGGAAAGAAAGAAAGAAAGAAAGGAAG
* * *
17109434 GAGAGGAAAGAAAG-AA-AAAGAATGTAAG
1 GAAAGGAAAGAAAGAAAGAAAGAAAGGAAG
* *
17109462 GAAAGGAAAG-GAGAAGAGAAA-AAA--AAA
1 GAAAGGAAAGAAAGAA-AGAAAGAAAGGAAG
*
17109489 GAAAGAAGAAG-AAG-AAGAAGAGGAAAGGAAAG
1 GAAAGGA-AAGAAAGAAAGAA-A-GAAAGG-AAG
* *
17109521 GAGAGGAAA-AAAGAAAGAAAAAGAAGGAAAG
1 GAAAGGAAAGAAAGAAAGAAAGA-AAGG-AAG
*
17109552 AAAAGGAAAG
1 GAAAGGAAAG
17109562 GAGAAGAGAA
Statistics
Matches: 98, Mismatches: 15, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
26 4 0.04
27 12 0.12
28 25 0.26
29 11 0.11
30 13 0.13
31 21 0.21
32 12 0.12
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (30 bp):
GAAAGGAAAGAAAGAAAGAAAGAAAGGAAG
Found at i:17109469 original size:5 final size:5
Alignment explanation
Indices: 17109400--17109563 Score: 59
Period size: 5 Copynumber: 34.6 Consensus size: 5
17109390 AGAAGGAGAG
*
17109400 GGAAA -GAAA -GAAA -GAAA -GAAA -GAAA -GAAA GG-AA GGAGA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * * * ** *
17109443 -GAAA GAAAA AG-AA TGTAA GGAAA GGAAA GGAGAA GAGAAA AAAAA AGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA-AA G-GAAA GGAAA GGAAA
* * *
17109493 -GAAGA AGAAGA AGAAGA GGAAA GGAAA GGAGA GGAAA --AAA -GAAA
1 GGAA-A GGAA-A GGAA-A GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * *
17109537 GAAAA AG-AA GGAAA GAAAA GGAAA GGA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGA
17109564 GAAGAGAAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
3 3 0.02
4 44 0.34
5 60 0.47
6 19 0.15
7 2 0.02
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (5 bp):
GGAAA
Found at i:17109493 original size:46 final size:44
Alignment explanation
Indices: 17109440--17109577 Score: 172
Period size: 46 Copynumber: 3.0 Consensus size: 44
17109430 GAAGGAGAGG
17109440 AAAGAAAGAAAAAGAATGTAAGGAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAAAGAA-G-AAGGAAAGGAAAGGAGAAGAGAAAAAA
* **
17109486 AAAGAAAGAAGAAGAAGAA-GAAGAGGAAAGGA-AAGGAGAGGAAA
1 AAAGAAAGAAAAAGAAGAAGGAA-AGGAAAGGAGAA-GAGAAAAAA
*
17109530 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAAAGAA-G-AAGGAAAGGAAAGGAGAAGAGAAAAAA
17109576 AA
1 AA
17109578 GAAGAAGAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.06
44 33 0.42
45 2 0.03
46 35 0.44
47 4 0.05
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (44 bp):
AAAGAAAGAAAAAGAAGAAGGAAAGGAAAGGAGAAGAGAAAAAA
Found at i:17109531 original size:44 final size:41
Alignment explanation
Indices: 17109392--17109587 Score: 199
Period size: 41 Copynumber: 4.7 Consensus size: 41
17109382 GGGGGGGGAG
*
17109392 AAGGAGAGGGAAAGAAAGAAAG-A-AAGAAAGAAA-GAAAGG-
1 AAGGAGA-GGAAA-AAAGAAAGAAGAAGAAGGAAAGGAAAGGA
17109431 AAGGAGAGGAAAGAAAGAAA-AAGAATGTAAGGAAAGGAAAGGA
1 AAGGAGAGGAAA-AAAGAAAGAAGAA-G-AAGGAAAGGAAAGGA
**
17109474 GAA-GAGAAAAAAAAAGAAAGAAGAAGAAGAAGAAGAGGAAAGGA
1 -AAGGAGAGGAAAAAAGAAAGAAGAAGAAG--GAA-AGGAAAGGA
* *
17109518 AAGGAGAGGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
1 AAGGAGAGGAAAAAAGAAAGAAGAAGAAGGAAAGGAAAGGA
*
17109559 AAGGAGAAGAGAAAAA-AAAGAAGAAGAAG
1 AAGGAGAGGA-AAAAAGAAAGAAGAAGAAG
17109588 CGGGAAGGAA
Statistics
Matches: 135, Mismatches: 9, Indels: 24
0.80 0.05 0.14
Matches are distributed among these distances:
38 14 0.10
39 9 0.07
40 1 0.01
41 38 0.28
42 22 0.16
43 17 0.13
44 34 0.25
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (41 bp):
AAGGAGAGGAAAAAAGAAAGAAGAAGAAGGAAAGGAAAGGA
Found at i:17110269 original size:9 final size:8
Alignment explanation
Indices: 17110255--17110279 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17110245 AAAATATTAC
17110255 AAAAAAAT
1 AAAAAAAT
17110263 AAAAAAAT
1 AAAAAAAT
17110271 AAAAAAAT
1 AAAAAAAT
17110279 A
1 A
17110280 TTATAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17115352 original size:18 final size:18
Alignment explanation
Indices: 17115329--17115366 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17115319 ATCCCAATGA
17115329 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
* *
17115347 TCGCCAGCACCTTTTTCT
1 TCGCCACCACCTTCTTCT
17115365 TC
1 TC
17115367 ACTACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.45, G:0.08, T:0.37
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:17116226 original size:3 final size:3
Alignment explanation
Indices: 17116218--17116243 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17116208 TCTTAATACT
17116218 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
17116244 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Done.