Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 15 of 189
Found at i:4899263 original size:16 final size:16
Alignment explanation
Indices: 4899244--4899295 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
4899234 GATTTGCTAT
* *
4899244 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
4899260 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
4899276 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
4899292 TACA
1 TACA
4899296 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:4903364 original size:43 final size:43
Alignment explanation
Indices: 4903316--4903397 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
4903306 TTAATGAAAA
4903316 TTCATTAGAATTCTTCATCTAATGCTCTATTAATTCTTTGGTT
1 TTCATTAGAATTCTTCATCTAATGCTCTATTAATTCTTTGGTT
4903359 TTCATTAGAATTCTTCATCTAATGCTCTATTAATTCTTT
1 TTCATTAGAATTCTTCATCTAATGCTCTATTAATTCTTT
4903398 ACTTTCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.51
Consensus pattern (43 bp):
TTCATTAGAATTCTTCATCTAATGCTCTATTAATTCTTTGGTT
Found at i:4909009 original size:33 final size:35
Alignment explanation
Indices: 4908936--4909009 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
4908926 GGAGAAATAA
**
4908936 AACTATTCACAAGTGTTCATATATAAGTAAATTTT
1 AACTATTCACAAGTGTTCATATATAAGTAAATAGT
*
4908971 AACTATTCACAAGTGTTGATATATAAGTAAA-AGT
1 AACTATTCACAAGTGTTCATATATAAGTAAATAGT
4909005 -ACTAT
1 AACTAT
4909010 GGAGCCTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 5 0.14
34 1 0.03
35 30 0.83
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (35 bp):
AACTATTCACAAGTGTTCATATATAAGTAAATAGT
Found at i:4911561 original size:43 final size:42
Alignment explanation
Indices: 4911478--4911668 Score: 188
Period size: 43 Copynumber: 4.5 Consensus size: 42
4911468 TTTTAGCGAT
* * *
4911478 CAAGACCTTTAGCG-TGCTTTTTCCACAAACGCCACTAAAGAC
1 CAAGACCTTTAGCGACGC-TTTCCCACAAACGCCGCTAAAGAC
* * * *
4911520 CACGACTTTTAACGACGCTTCTCCCACAAACGCCTCTAAAGAC
1 CAAGACCTTTAGCGACGCTT-TCCCACAAACGCCGCTAAAGAC
* * *
4911563 CAAGACCTTTAGCGGCGCTATTTCCACAAACGCCGCTATAGAC
1 CAAGACCTTTAGCGACGCT-TTCCCACAAACGCCGCTAAAGAC
* ** *
4911606 CATGACCTTTAGCAGCACTTTTTCCCACAAACGCCGCTAAAGAA
1 CAAGACCTTTAGC-G-ACGCTTTCCCACAAACGCCGCTAAAGAC
*
4911650 CAA-ACCTTTAGCGGCGCTT
1 CAAGACCTTTAGCGACGCTT
4911669 CTAGCAAAAA
Statistics
Matches: 120, Mismatches: 24, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
41 3 0.03
42 14 0.12
43 77 0.64
44 24 0.20
45 2 0.02
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (42 bp):
CAAGACCTTTAGCGACGCTTTCCCACAAACGCCGCTAAAGAC
Found at i:4911657 original size:86 final size:86
Alignment explanation
Indices: 4911478--4911667 Score: 242
Period size: 86 Copynumber: 2.2 Consensus size: 86
4911468 TTTTAGCGAT
* * *
4911478 CAAGACCTTTAGC-GTGCTTTTTCCACAAACGCCACTAAAGACCACGACTTTTAACGACGCTTCT
1 CAAGACCTTTAGCGGCGCTATTTCCACAAACGCCACTAAAGACCACGACCTTTAACGACGCTTCT
* *
4911542 CCCACAAACGCCTCTAAAGAC
66 CCCACAAACGCCGCTAAAGAA
* * * * *
4911563 CAAGACCTTTAGCGGCGCTATTTCCACAAACGCCGCTATAGACCATGACCTTTAGCAGCAC-TTT
1 CAAGACCTTTAGCGGCGCTATTTCCACAAACGCCACTAAAGACCACGACCTTTAAC-G-ACGCTT
*
4911627 TTCCCACAAACGCCGCTAAAGAA
64 CTCCCACAAACGCCGCTAAAGAA
4911650 CAA-ACCTTTAGCGGCGCT
1 CAAGACCTTTAGCGGCGCT
4911668 TCTAGCAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
85 13 0.14
86 50 0.55
87 26 0.29
88 2 0.02
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.22
Consensus pattern (86 bp):
CAAGACCTTTAGCGGCGCTATTTCCACAAACGCCACTAAAGACCACGACCTTTAACGACGCTTCT
CCCACAAACGCCGCTAAAGAA
Found at i:4913270 original size:14 final size:14
Alignment explanation
Indices: 4913251--4913279 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4913241 AATAAAGCAC
4913251 GTTACTACAAATAA
1 GTTACTACAAATAA
4913265 GTTACTACAAATAA
1 GTTACTACAAATAA
4913279 G
1 G
4913280 CTGTACGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (14 bp):
GTTACTACAAATAA
Found at i:4915861 original size:20 final size:21
Alignment explanation
Indices: 4915833--4915872 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4915823 CTAGTTAATC
*
4915833 TAAATCCT-AAACCATAAACT
1 TAAACCCTAAAACCATAAACT
4915853 TAAACCCTAAAACCATAAAC
1 TAAACCCTAAAACCATAAAC
4915873 CATTAACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAAACCATAAACT
Found at i:4915871 original size:8 final size:7
Alignment explanation
Indices: 4915840--4915978 Score: 68
Period size: 7 Copynumber: 19.6 Consensus size: 7
4915830 ATCTAAATCC
4915840 TAAACCA
1 TAAACCA
*
4915847 TAAA-CT
1 TAAACCA
*
4915853 TAAACCC
1 TAAACCA
4915860 TAAAACCA
1 T-AAACCA
4915868 TAAACCA
1 TAAACCA
*
4915875 TTAACACA
1 TAAAC-CA
*
4915883 T-AACCTC
1 TAAACC-A
*
4915890 TAAACCT
1 TAAACCA
4915897 TAAACC-
1 TAAACCA
** *
4915903 CCAACCTT
1 TAAACC-A
4915911 TAAACCA
1 TAAACCA
*
4915918 TAAACCG
1 TAAACCA
**
4915925 TAAACTG
1 TAAACCA
4915932 TAAACCA
1 TAAACCA
4915939 TAAACCA
1 TAAACCA
* *
4915946 TAACCCT
1 TAAACCA
4915953 TAAACCCA
1 TAAA-CCA
*
4915961 TAATCCA
1 TAAACCA
* *
4915968 CAAACCT
1 TAAACCA
4915975 TAAA
1 TAAA
4915979 TGGTAACACC
Statistics
Matches: 100, Mismatches: 24, Indels: 16
0.71 0.17 0.11
Matches are distributed among these distances:
6 10 0.10
7 68 0.68
8 22 0.22
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:4915956 original size:21 final size:20
Alignment explanation
Indices: 4915863--4915978 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 20
4915853 TAAACCCTAA
* *
4915863 AACCATAAACCATTAACACAT
1 AACCTTAAACCATAAAC-CAT
* **
4915884 AACCTCTAAACCTTAAACCCC
1 AACCT-TAAACCATAAACCAT
*
4915905 AACCTTTAAACCATAAACCGT
1 AACC-TTAAACCATAAACCAT
*
4915926 AAACTGTAAACCATAAACCAT
1 AACCT-TAAACCATAAACCAT
* *
4915947 AACCCTTAAACCCATAATCCACA
1 AA-CCTTAAA-CCATAAACCA-T
4915970 AACCTTAAA
1 AACCTTAAA
4915979 TGGTAACACC
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.01
21 44 0.58
22 29 0.38
23 2 0.03
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.20
Consensus pattern (20 bp):
AACCTTAAACCATAAACCAT
Found at i:4916236 original size:40 final size:40
Alignment explanation
Indices: 4916190--4916266 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
4916180 TTAAATCCCT
*
4916190 GAGCATTAACGGCGCTTTTTAAAAAACACCGCTAAAAATA
1 GAGCATTAACGGCGCTTTATAAAAAACACCGCTAAAAATA
** * *
4916230 GAGCATTCGCGGCGCTTTATCAAAAACGCCGCTAAAA
1 GAGCATTAACGGCGCTTTATAAAAAACACCGCTAAAA
4916267 GCCCTGAGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (40 bp):
GAGCATTAACGGCGCTTTATAAAAAACACCGCTAAAAATA
Found at i:4916321 original size:41 final size:41
Alignment explanation
Indices: 4916230--4916516 Score: 378
Period size: 41 Copynumber: 7.0 Consensus size: 41
4916220 GCTAAAAATA
* ***
4916230 GAGCATTCGCGGCGCTTTATCAAAAACGCCGCTAAAAGCCCT
1 GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCT-AAAGCCCT
*
4916272 GAGCATTAGCAGCGCTAT-CCCAAAAACGCCGCTAAAGCCCT
1 GAGCATTAGCGGCGCT-TCCCCAAAAACGCCGCTAAAGCCCT
* * * *
4916313 AAGCATTAGCGACGCTTTCCCAAAAACGCTGCTAAAGCCCT
1 GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCT
* * *
4916354 GAACATTAGCGGTGCTTCCCCAAAAATGCCGCTAAAGCCCT
1 GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCT
* * *
4916395 GAGCATTAGCGGCGCTTCCCCAAAAACACCACTAAAGACCT
1 GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCT
* *
4916436 GAGCATTAGCGGCGCTTACTCAAAAACGCCGCTAAAGCCCT
1 GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCT
* *
4916477 GAGCATTAGCGGCGCTTCCCCGAAAATGCCGCTAAAGCCC
1 GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCC
4916517 CAAAAGCTCA
Statistics
Matches: 213, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
40 1 0.00
41 184 0.86
42 27 0.13
43 1 0.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCT
Found at i:4926310 original size:22 final size:22
Alignment explanation
Indices: 4926285--4926332 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4926275 TTTAAATCTA
*
4926285 ACTTAAGTCTT-GAGACAATGTG
1 ACTTAAGT-TTCGAGACAATGTC
**
4926307 ACTTTTGTTTCGAGACAATGTC
1 ACTTAAGTTTCGAGACAATGTC
4926329 ACTT
1 ACTT
4926333 CGAAGCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (22 bp):
ACTTAAGTTTCGAGACAATGTC
Found at i:4930446 original size:94 final size:94
Alignment explanation
Indices: 4930285--4930475 Score: 319
Period size: 94 Copynumber: 2.0 Consensus size: 94
4930275 CGCAATAAAC
* * *
4930285 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGTATAAATTGTATACACTAGAATACGATCAT
1 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
*
4930350 GTTTAACGATAAATCAATTATGTTTAGCA
66 GTTTAACGATAAATCAACTATGTTTAGCA
*
4930379 CTTGTTACAATTATGCTTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
1 CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
**
4930444 GTTTAACGATAAATCGGCTATGTTTAGCA
66 GTTTAACGATAAATCAACTATGTTTAGCA
4930473 CTT
1 CTT
4930476 AGTATGAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (94 bp):
CTTGTTACAATTATGATTTTAATGCTTTGTTATTGCATAAATTGTATACACGAGAATACAATCAT
GTTTAACGATAAATCAACTATGTTTAGCA
Found at i:4930528 original size:40 final size:41
Alignment explanation
Indices: 4930470--4930645 Score: 123
Period size: 41 Copynumber: 4.3 Consensus size: 41
4930460 GCTATGTTTA
* ** *
4930470 GCACTTAGTATGAAATTTGAGATAGCTTCGACTAAT-TATG
1 GCACTTAGTGTGCGATTTGAGATAGCTTCGGCTAATATATG
* *
4930510 ACACTTAGTGTGCGATTTG-GAATAGCTTCGGTTATATATATG
1 GCACTTAGTGTGCGATTTGAG-ATAGCTTCGGCTA-ATATATG
* * * *
4930552 GCACTTAGTGTGTG-TGACTGAGATAGCTTCGGCT-ATGTAAG
1 GCACTTAGTGTGCGAT--TTGAGATAGCTTCGGCTAATATATG
*
4930593 GCACTTAGTGTGCGGGATTAT-A-ATAGCTTCGGCT-ATACGATG
1 GCACTTAGTGTGC--GATT-TGAGATAGCTTCGGCTAATA-TATG
*
4930635 GCAATTAGTGT
1 GCACTTAGTGT
4930646 ACAAAACATT
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
39 1 0.01
40 26 0.24
41 34 0.32
42 29 0.27
43 15 0.14
44 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (41 bp):
GCACTTAGTGTGCGATTTGAGATAGCTTCGGCTAATATATG
Found at i:4930636 original size:83 final size:82
Alignment explanation
Indices: 4930487--4930645 Score: 189
Period size: 83 Copynumber: 1.9 Consensus size: 82
4930477 GTATGAAATT
* * *
4930487 TGAGATAGCTTCGACTAATTATGACACTTAGTGTGCGATTTGGAATAGCTTCGGTTATATATATG
1 TGAGATAGCTTCGACTAATTAAGACACTTAGTGTGCGATTT-GAATAGCTTCGGCTATATAGATG
*
4930552 GCACTTAGTGTGTGTGAC
65 GCAATTAGTGTGTGTGAC
* * *
4930570 TGAGATAGCTTCGGCT-ATGTAAGGCACTTAGTGTGCGGGATTAT-AATAGCTTCGGCTATA-CG
1 TGAGATAGCTTCGACTAAT-TAAGACACTTAGTGTGC--GATT-TGAATAGCTTCGGCTATATAG
4930632 ATGGCAATTAGTGT
62 ATGGCAATTAGTGT
4930646 ACAAAACATT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
82 2 0.03
83 43 0.66
84 15 0.23
85 4 0.06
86 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (82 bp):
TGAGATAGCTTCGACTAATTAAGACACTTAGTGTGCGATTTGAATAGCTTCGGCTATATAGATGG
CAATTAGTGTGTGTGAC
Found at i:4931323 original size:46 final size:46
Alignment explanation
Indices: 4931270--4931380 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
4931260 GTTGTTTTTA
*
4931270 GATGTATAATGCTGTCCATTTTGAGCATATTG-ATGTTGTCCAATTT
1 GATGTATAATGCTGTCCATTTTGAGCATA-TGAATGCTGTCCAATTT
* *
4931316 GATGTATAATGCTGTCAATTTTGAGTATATGAATGCTGTCCAATTT
1 GATGTATAATGCTGTCCATTTTGAGCATATGAATGCTGTCCAATTT
*
4931362 GATGTATAAATGTTGTCCA
1 GATGTAT-AATGCTGTCCA
4931381 AAACAGGGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
45 2 0.03
46 47 0.81
47 9 0.16
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (46 bp):
GATGTATAATGCTGTCCATTTTGAGCATATGAATGCTGTCCAATTT
Found at i:4931381 original size:23 final size:23
Alignment explanation
Indices: 4931270--4931381 Score: 99
Period size: 24 Copynumber: 4.9 Consensus size: 23
4931260 GTTGTTTTTA
*
4931270 GATGTAT-AATGCTGTCCATTTT
1 GATGTATAAATGCTGTCCAATTT
** *
4931292 GA-GCATATTGATGTTGTCCAATTT
1 GATG--TATAAATGCTGTCCAATTT
4931316 GATGTAT-AATGCTGT-CAATTTT
1 GATGTATAAATGCTGTCCAA-TTT
4931338 GA-GTATATGAATGCTGTCCAATTT
1 GATGTATA--AATGCTGTCCAATTT
*
4931362 GATGTATAAATGTTGTCCAA
1 GATGTATAAATGCTGTCCAA
4931382 AACAGGGTAG
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
21 8 0.11
22 13 0.18
23 17 0.23
24 27 0.36
25 9 0.12
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (23 bp):
GATGTATAAATGCTGTCCAATTT
Found at i:4932171 original size:13 final size:13
Alignment explanation
Indices: 4932150--4932198 Score: 89
Period size: 13 Copynumber: 3.8 Consensus size: 13
4932140 ATGCAGGGGA
4932150 CACACGCCCAGGT
1 CACACGCCCAGGT
*
4932163 CATACGCCCAGGT
1 CACACGCCCAGGT
4932176 CACACGCCCAGGT
1 CACACGCCCAGGT
4932189 CACACGCCCA
1 CACACGCCCA
4932199 TGTGCTAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.24, C:0.47, G:0.20, T:0.08
Consensus pattern (13 bp):
CACACGCCCAGGT
Found at i:4935606 original size:21 final size:21
Alignment explanation
Indices: 4935582--4935627 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4935572 AAAATCTTAT
*
4935582 AATATA-ATTATTTAATTAATA
1 AATATATATTACTTAA-TAATA
*
4935603 AATATATTTTACTTAATAATA
1 AATATATATTACTTAATAATA
4935624 AATA
1 AATA
4935628 ATAGATATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATATTACTTAATAATA
Found at i:4935669 original size:29 final size:27
Alignment explanation
Indices: 4935594--4935669 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 27
4935584 TATAATTATT
*
4935594 TAATTAATAAATATATTTTACTTAATAA
1 TAATTAATAAATATA-TTTACTTAAAAA
* *
4935622 TAAATAATAGATATCTATTTACTTAAAAA
1 TAATTAATA-A-ATATATTTACTTAAAAA
4935651 GTAATTAAATAAATATATT
1 -TAATT-AATAAATATATT
4935670 ACAAATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 8 0.21
29 18 0.46
30 9 0.23
31 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (27 bp):
TAATTAATAAATATATTTACTTAAAAA
Found at i:4937011 original size:123 final size:123
Alignment explanation
Indices: 4936791--4937061 Score: 406
Period size: 123 Copynumber: 2.2 Consensus size: 123
4936781 TTTAAACAGA
** * *
4936791 TTCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAGA
1 TTCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGAATCAGTACACCGGCACTTAGCCTGCTAGA
*
4936856 CATATAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATA-
66 CATAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATAC
*
4936913 TATCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT-A-TATCACCGGCA-TTAAGCCTGC
1 T-TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTG-AATCAGTA-CACCGGCACTT-AGCCTGC
* *
4936975 TAGACTTAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
62 TAGACATAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATAC
4937037 TTCACCGGCATTAAGCCTGCTAGAC
1 TTCACCGGCATTAAGCCTGCTAGAC
4937062 GTAACGTCCG
Statistics
Matches: 136, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
122 5 0.04
123 128 0.94
124 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (123 bp):
TTCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGAATCAGTACACCGGCACTTAGCCTGCTAGA
CATAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATAC
Found at i:4937077 original size:41 final size:41
Alignment explanation
Indices: 4936792--4937061 Score: 368
Period size: 41 Copynumber: 6.6 Consensus size: 41
4936782 TTAAACAGAT
** * *
4936792 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATT-A-TA
* * * *
4936834 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAATTATA
*
4936874 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATATA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTATA
*
4936915 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATATA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTATA
* *
4936956 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTATA
4936997 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTACT-
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTA-TA
4937038 TCACCGGCATTAAGCCTGCTAGAC
1 TCACCGGCATTAAGCCTGCTAGAC
4937062 GTAACGTCCG
Statistics
Matches: 210, Mismatches: 13, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
40 4 0.02
41 201 0.96
42 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTATA
Found at i:4938649 original size:13 final size:13
Alignment explanation
Indices: 4938631--4938655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4938621 CAATCAAATG
4938631 CACACAAAATAAA
1 CACACAAAATAAA
4938644 CACACAAAATAA
1 CACACAAAATAA
4938656 TATTAAAATA
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:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:4939234 original size:25 final size:25
Alignment explanation
Indices: 4939200--4939257 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
4939190 AGCTTCGGAT
4939200 AGCCATATATCGGGAAGTTCAAGCG
1 AGCCATATATCGGGAAGTTCAAGCG
*
4939225 AGCCATATATTGGGAAGTTCAAGCG
1 AGCCATATATCGGGAAGTTCAAGCG
*
4939250 AGTCATAT
1 AGCCATAT
4939258 CAAGACGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (25 bp):
AGCCATATATCGGGAAGTTCAAGCG
Found at i:4945118 original size:27 final size:26
Alignment explanation
Indices: 4945088--4945151 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
4945078 GACTCACATT
4945088 CCCAAATCTCAAATTAAAAAAAAAAAC
1 CCCAAATCTCAAA-TAAAAAAAAAAAC
* * *
4945115 CCCAAATCTTTAAATAATAAAAAAATC
1 CCCAAATC-TCAAATAAAAAAAAAAAC
4945142 CCCAAATCTC
1 CCCAAATCTC
4945152 GTCTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 27 0.84
28 4 0.12
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (26 bp):
CCCAAATCTCAAATAAAAAAAAAAAC
Found at i:4951724 original size:40 final size:39
Alignment explanation
Indices: 4951657--4951798 Score: 128
Period size: 41 Copynumber: 3.5 Consensus size: 39
4951647 CCGAATATAA
* *
4951657 TAAATATTTTT-ATTTTTTTAA-TTTTAAAATACTTTTTT
1 TAAAT-TTTTTAAATTTTTAAATTTTTAAAATACTTTTTT
4951695 TAAATTTTTTAAAGTTTTTAAATTTTTAAAAAATAC-TTTTT
1 TAAATTTTTTAAA-TTTTTAAATTTTT--AAAATACTTTTTT
* * * *
4951736 TAATTTTTTTTAATTTTAAAATATTTCAAAATACTTTTTT
1 TAAATTTTTTAAATTTTTAAAT-TTTTAAAATACTTTTTT
* *
4951776 TAATTTTTGTTTTAATTTTTAAA
1 TAA-ATTT-TTTAAATTTTTAAA
4951799 ATAAATTTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
37 5 0.06
38 6 0.07
39 14 0.16
40 20 0.23
41 23 0.26
42 20 0.23
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (39 bp):
TAAATTTTTTAAATTTTTAAATTTTTAAAATACTTTTTT
Found at i:4951743 original size:8 final size:9
Alignment explanation
Indices: 4951690--4951721 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
4951680 TTAAAATACT
4951690 TTTTTTAAA
1 TTTTTTAAA
4951699 TTTTTTAAA
1 TTTTTTAAA
*
4951708 GTTTTTAAA
1 TTTTTTAAA
4951717 TTTTT
1 TTTTT
4951722 AAAAAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:4951745 original size:42 final size:40
Alignment explanation
Indices: 4951663--4951798 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 40
4951653 ATAATAAATA
* * *
4951663 TTTTTATTTTTTTAAT-TTT-AAAATACTTTTTTTAAATT
1 TTTTTAATTTTTAAATATTTAAAAATACTTTTTTTAATTT
* *
4951701 TTTTAAAGTTTTTAAATTTTTAAAAAATAC-TTTTTTAATTT
1 TTTTTAA-TTTTTAAATATTT-AAAAATACTTTTTTTAATTT
* *
4951742 TTTTTAATTTTAAAATATTTCAAAATACTTTTTTTAATTTT
1 TTTTTAATTTTTAAATATTTAAAAATACTTTTTTTAA-TTT
4951783 TGTTTTAATTTTTAAA
1 T-TTTTAATTTTTAAA
4951799 ATAAATTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
38 5 0.06
39 15 0.18
40 22 0.27
41 20 0.24
42 20 0.24
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (40 bp):
TTTTTAATTTTTAAATATTTAAAAATACTTTTTTTAATTT
Found at i:4954552 original size:20 final size:20
Alignment explanation
Indices: 4954527--4954624 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 20
4954517 ATTATAAAAA
*
4954527 ATAAAAATTAATAAAAAGTT
1 ATAAAAATTAATAAAAATTT
* *
4954547 AT-AAAATTTATAAAATTTT
1 ATAAAAATTAATAAAAATTT
* * **
4954566 AATAAAAAATATTTTAAATTT
1 -ATAAAAATTAATAAAAATTT
* *
4954587 ATTAAAAATTAGAAAAAAAATT
1 A-TAAAAATTA-ATAAAAATTT
*
4954609 AT-AAAATTCATAAAAA
1 ATAAAAATTAATAAAAA
4954625 ATATAAAATG
Statistics
Matches: 57, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
19 20 0.35
20 11 0.19
21 20 0.35
22 6 0.11
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAAATTAATAAAAATTT
Found at i:4954570 original size:30 final size:29
Alignment explanation
Indices: 4954512--4954632 Score: 113
Period size: 31 Copynumber: 4.1 Consensus size: 29
4954502 ACATGTGGCA
*
4954512 AAAAAATTATAAAA--AATAAAAATTAAT
1 AAAAAATTATAAAATTTATAAAAATTAAT
* *
4954539 AAAAAGTTATAAAATTTATAAAATTTTAAT
1 AAAAAATTATAAAATTTATAAAA-ATTAAT
* * *
4954569 AAAAAATATTTTAAATTTATTAAAAATTAGAA
1 AAAAAAT-TATAAAATTTA-TAAAAATTA-AT
* *
4954601 AAAAAATTATAAAATTCATAAAAAAT-AT
1 AAAAAATTATAAAATTTATAAAAATTAAT
4954629 AAAA
1 AAAA
4954633 TGCATAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
27 13 0.17
28 5 0.07
29 6 0.08
30 18 0.24
31 20 0.27
32 13 0.17
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAATTATAAAATTTATAAAAATTAAT
Found at i:4954596 original size:11 final size:10
Alignment explanation
Indices: 4954527--4954573 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
4954517 ATTATAAAAA
*
4954527 ATAAAAATTA
1 ATAAAAATTT
*
4954537 ATAAAAAGTT
1 ATAAAAATTT
4954547 AT-AAAATTT
1 ATAAAAATTT
*
4954556 ATAAAATTTT
1 ATAAAAATTT
4954566 AATAAAAA
1 -ATAAAAA
4954574 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.27
10 16 0.53
11 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:4954629 original size:18 final size:19
Alignment explanation
Indices: 4954601--4954642 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
4954591 AAAATTAGAA
*
4954601 AAAAAATTATAAAATTCAT
1 AAAAAATTATAAAATGCAT
4954620 AAAAAA-TATAAAATGCAT
1 AAAAAATTATAAAATGCAT
4954638 AAAAA
1 AAAAA
4954643 GGACATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAAATTATAAAATGCAT
Found at i:4954864 original size:10 final size:9
Alignment explanation
Indices: 4954819--4954952 Score: 53
Period size: 9 Copynumber: 14.0 Consensus size: 9
4954809 CTTTGGTAAG
4954819 ATAATTTTT
1 ATAATTTTT
4954828 ATAATTCTTTTT
1 ATAA---TTTTT
* *
4954840 ACAAATTTT
1 ATAATTTTT
4954849 AT-ATTTTT
1 ATAATTTTT
4954857 ATACATTTTT
1 ATA-ATTTTT
4954867 ATAATTTTCT
1 ATAATTTT-T
*
4954877 -TACGA-CTTT
1 ATA--ATTTTT
*
4954886 ATAAAATTTT
1 AT-AATTTTT
4954896 ATAATTTTTT
1 ATAA-TTTTT
* *
4954906 CTATATTTCT
1 ATA-ATTTTT
4954916 AT-ATATTTT
1 ATAAT-TTTT
*
4954925 ATACTTTTT
1 ATAATTTTT
4954934 -TACGATTTTT
1 ATA--ATTTTT
4954944 ATAATTTTT
1 ATAATTTTT
4954953 TTTTCTAATA
Statistics
Matches: 94, Mismatches: 13, Indels: 36
0.66 0.09 0.25
Matches are distributed among these distances:
8 11 0.12
9 35 0.37
10 35 0.37
11 5 0.05
12 8 0.09
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:4954905 original size:39 final size:38
Alignment explanation
Indices: 4954819--4954904 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
4954809 CTTTGGTAAG
* * *
4954819 ATAATTTTTATAATTCTTTTTACAAATTTTATATTTTT
1 ATAATTTTTATAATTCTTCTTACAAATTTTAAAATTTT
* *
4954857 ATACATTTTTATAATT-TTCTTACGACTTTATAAAATTTT
1 ATA-ATTTTTATAATTCTTCTTACAAATTT-TAAAATTTT
4954896 ATAATTTTT
1 ATAATTTTT
4954905 TCTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 19 0.46
39 22 0.54
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (38 bp):
ATAATTTTTATAATTCTTCTTACAAATTTTAAAATTTT
Found at i:4954953 original size:29 final size:29
Alignment explanation
Indices: 4954851--4954953 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
4954841 CAAATTTTAT
4954851 ATTTTTATACAT-TTTTATAATTTTCTTACG
1 ATTTTTATA-ATATTTTATAATTTT-TTACG
* * *
4954881 A-CTTTATAAAATTTTATAATTTTTT-CT
1 ATTTTTATAATATTTTATAATTTTTTACG
*
4954908 ATATTTCTAT-ATATTTTATACTTTTTTACG
1 AT-TTT-TATAATATTTTATAATTTTTTACG
*
4954938 ATTTTTATAATTTTTT
1 ATTTTTATAATATTTT
4954954 TTTCTAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 44 0.75
30 7 0.12
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTTTATAATATTTTATAATTTTTTACG
Found at i:4966901 original size:46 final size:46
Alignment explanation
Indices: 4966831--4967015 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
4966821 CATGGCAAAG
* *
4966831 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
4966877 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
4966923 TGTGAAAAGTAGGTATGGTGTTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
4966969 TGTGAAAAGTAGGTACGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
4967015 T
1 T
4967016 ATAGCAATGT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:4981616 original size:33 final size:34
Alignment explanation
Indices: 4981520--4981645 Score: 130
Period size: 34 Copynumber: 3.6 Consensus size: 34
4981510 TTTTAAAAAA
* *
4981520 TAAATTAGGG-TTATGTGTTTTTAAAAAAATAATAAT
1 TAAATTAGGGTTTA-GAGTTTTTAATAAAAT--TAAT
** * *
4981556 TAAATTAGATTTTAGGGGTTTTAA-ATAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAATA-AAATTAAT
*
4981590 TAACTTAGGGTTTAGAGTTTTTAATAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTAATAAAATTAAT
*
4981624 TAAATTAGGGTTTAGATTTTTT
1 TAAATTAGGGTTTAGAGTTTTT
4981646 TAAATAAGTT
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
34 51 0.67
35 2 0.03
36 20 0.26
37 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.45
Consensus pattern (34 bp):
TAAATTAGGGTTTAGAGTTTTTAATAAAATTAAT
Found at i:4981836 original size:126 final size:125
Alignment explanation
Indices: 4981702--4981970 Score: 459
Period size: 126 Copynumber: 2.1 Consensus size: 125
4981692 ACAATAAGGA
*
4981702 TTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGCCGGTTCTGAACAAATAGTGTCAAA
1 TTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAA
* *
4981767 AACGCTTCAAGCAGGATGCATTGTCAGCAAAATTGATGAAAAAAGCT-TCTACGTGGACGC
66 AACGCTACAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCTC-ACGTGGACGC
4981827 TATTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
1 T-TTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAA
*
4981892 AAACGCTACAAGCATGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCTCACGTGGACGC
65 AAACGCTACAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCTCACGTGGACGC
*
4981953 TTTTTTTCTACATTAGTT
1 TTTTTTT-TACAGTAGTT
4981971 TTTGTTTGGC
Statistics
Matches: 136, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
125 7 0.05
126 127 0.93
127 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (125 bp):
TTTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAA
AACGCTACAAGCAGGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCTCACGTGGACGC
Found at i:4983713 original size:7 final size:7
Alignment explanation
Indices: 4983703--4983731 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4983693 TTATATACAT
4983703 AATACTA
1 AATACTA
4983710 AATACTA
1 AATACTA
4983717 AATACTA
1 AATACTA
4983724 AATA-TA
1 AATACTA
4983730 AA
1 AA
4983732 ACGACTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:4986079 original size:28 final size:28
Alignment explanation
Indices: 4986048--4986103 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
4986038 TTGTTGTTTC
*
4986048 TGATGATGGGTTAAGAGAAGTAAAATGA
1 TGATGATGGGTTAAAAGAAGTAAAATGA
4986076 TGATGATGGGTTAAAAGAAGTAAAATGA
1 TGATGATGGGTTAAAAGAAGTAAAATGA
4986104 AGATTATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (28 bp):
TGATGATGGGTTAAAAGAAGTAAAATGA
Found at i:4992816 original size:31 final size:32
Alignment explanation
Indices: 4992750--4992816 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 32
4992740 TTGAAATTGT
* * *
4992750 AAAAAAAATTTAGAAAATTTATAAAAATTTCA
1 AAAAAAAATATAGAAAACTTATAAAAATATCA
*
4992782 AAAAAAAATATA-ATAACTTATAAAAAGTAT-A
1 AAAAAAAATATAGAAAACTTATAAAAA-TATCA
4992813 AAAA
1 AAAA
4992817 CGCTAACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (32 bp):
AAAAAAAATATAGAAAACTTATAAAAATATCA
Found at i:4993188 original size:26 final size:26
Alignment explanation
Indices: 4993156--4993210 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
4993146 CGCACTTCCC
4993156 TTGTTTTCCTAATTTAGCTTCAATGT
1 TTGTTTTCCTAATTTAGCTTCAATGT
4993182 TTGTTTTCCTAATTTAGCTTCAATGT
1 TTGTTTTCCTAATTTAGCTTCAATGT
4993208 TTG
1 TTG
4993211 GATGCCCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.55
Consensus pattern (26 bp):
TTGTTTTCCTAATTTAGCTTCAATGT
Found at i:4993649 original size:15 final size:15
Alignment explanation
Indices: 4993629--4993660 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4993619 TGCCTTTGCA
4993629 CTCCTTTTAAGAGGC
1 CTCCTTTTAAGAGGC
4993644 CTCCTTTTAAGAGGC
1 CTCCTTTTAAGAGGC
4993659 CT
1 CT
4993661 ACGCCCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (15 bp):
CTCCTTTTAAGAGGC
Found at i:4997877 original size:20 final size:20
Alignment explanation
Indices: 4997852--4997891 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4997842 CTAAATGATT
4997852 GTTCAAACAGAAGGTACAAC
1 GTTCAAACAGAAGGTACAAC
4997872 GTTCAAACAGAAGGTACAAC
1 GTTCAAACAGAAGGTACAAC
4997892 ACATGGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (20 bp):
GTTCAAACAGAAGGTACAAC
Found at i:5007514 original size:32 final size:33
Alignment explanation
Indices: 5007452--5007523 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
5007442 ATTTGCATAT
5007452 AAAAATTGATAAAATTATTATTTAGACCCCC-A
1 AAAAATTGATAAAATTATTATTTAGACCCCCTA
* * *
5007484 AAAATATTGATAAAA-TGTTATTTGGTCCCCCTA
1 AAAA-ATTGATAAAATTATTATTTAGACCCCCTA
5007517 AAAAATT
1 AAAAATT
5007524 ACTTGACTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (33 bp):
AAAAATTGATAAAATTATTATTTAGACCCCCTA
Found at i:5008687 original size:10 final size:10
Alignment explanation
Indices: 5008664--5008712 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
5008654 TAACTTATTA
*
5008664 TTTTAGAATAT
1 TTTTAAAAT-T
5008675 TTTTAAAA-T
1 TTTTAAAATT
5008684 TTTTATAAATT
1 TTTTA-AAATT
*
5008695 TTTTATAATT
1 TTTTAAAATT
5008705 TTTTAAAA
1 TTTTAAAA
5008713 AAATTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 6 0.18
10 14 0.42
11 13 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:5008740 original size:19 final size:18
Alignment explanation
Indices: 5008704--5008739 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5008694 TTTTTATAAT
*
5008704 TTTTTAAAAAAATTTATA
1 TTTTTAAAAAAATATATA
5008722 TTTTT-AAAAAATATATA
1 TTTTTAAAAAAATATATA
5008739 T
1 T
5008740 AAATTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAAAAAATATATA
Found at i:5008760 original size:18 final size:17
Alignment explanation
Indices: 5008737--5008780 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5008727 AAAAAATATA
5008737 TATAAATTTTAGAATGTT
1 TATAAATTTTAGAAT-TT
*
5008755 TATAAATATTTTGAATTT
1 TATAAAT-TTTAGAATTT
5008773 TA-AAATTT
1 TATAAATTT
5008781 ATTTTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 4 0.17
18 11 0.46
19 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (17 bp):
TATAAATTTTAGAATTT
Found at i:5010554 original size:20 final size:21
Alignment explanation
Indices: 5010526--5010565 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5010516 AATAAAATAT
*
5010526 AATATTAAT-TATATATTTTA
1 AATAATAATATATATATTTTA
5010546 AATAATAATACTATATATTT
1 AATAATAATA-TATATATTT
5010566 ATATTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATAATATATATATTTTA
Found at i:5010745 original size:40 final size:40
Alignment explanation
Indices: 5010666--5010752 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
5010656 CTAAACATCA
* * *
5010666 TATT-TAATAAAATATTTATTATATCTATTTGAGTTTTTT
1 TATTATAATAAAACATTTATTATATCTATGTGAGTGTTTT
* *
5010705 TATTATAATAAAGCATTTATTATATTTATG-GTAGTGTTTT
1 TATTATAATAAAACATTTATTATATCTATGTG-AGTGTTTT
*
5010745 TAATATAA
1 TATTATAA
5010753 ATACTTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 5 0.12
40 35 0.88
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (40 bp):
TATTATAATAAAACATTTATTATATCTATGTGAGTGTTTT
Found at i:5017680 original size:8 final size:8
Alignment explanation
Indices: 5017667--5017691 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5017657 ATCATGCATG
5017667 ATTGGGGT
1 ATTGGGGT
5017675 ATTGGGGT
1 ATTGGGGT
5017683 ATTGGGGT
1 ATTGGGGT
5017691 A
1 A
5017692 CACACTTAAA
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:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (8 bp):
ATTGGGGT
Found at i:5017825 original size:36 final size:36
Alignment explanation
Indices: 5017778--5017849 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
5017768 TGTGAAAGCT
5017778 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
1 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
**
5017814 ACCATTTTTATCATTGGGAAGTGACACTAACAATTA
1 ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
5017850 TTACTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (36 bp):
ACCATTTTTATCATTGAAAAGTGACACTAACAATTA
Found at i:5021199 original size:18 final size:18
Alignment explanation
Indices: 5021160--5021201 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
5021150 TTCTAAATTT
*
5021160 TTTTATAATTATTAAGTA
1 TTTTATAATTATTAAGGA
*
5021178 TTTTA-AATTATTTAGGA
1 TTTTATAATTATTAAGGA
5021195 GTTTTAT
1 -TTTTAT
5021202 GTTAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTTATAATTATTAAGGA
Found at i:5021599 original size:18 final size:18
Alignment explanation
Indices: 5021568--5021602 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5021558 TGATTTATTG
5021568 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
5021586 TTTTAATTTT-TTTATTT
1 TTTT-ATTTTATTTATTT
5021603 GACTTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:5037802 original size:3 final size:3
Alignment explanation
Indices: 5037796--5037820 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5037786 AAGATTTCCC
5037796 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
5037821 TGATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5048480 original size:30 final size:30
Alignment explanation
Indices: 5048444--5048528 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
5048434 GGAGGGGAGG
*
5048444 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
5048474 GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
*
5048504 GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGAGTAAAAGTTTTGAGGGGAAAGT
5048529 AAAAAGGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.36, C:0.00, G:0.42, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGGAAAGTGGGAA
Found at i:5051600 original size:40 final size:38
Alignment explanation
Indices: 5051546--5051663 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 38
5051536 AAATATATTT
5051546 ATTTTTTTAATTTTAAAATATTTTTACATACTTTTTAAA
1 ATTTTTTTAATTTTAAAATATTTTTA-ATACTTTTTAAA
**
5051585 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTA
1 ATTTTTTT-AATTTTAAAATATTTTT--AATAC-TTTTTAAA
*
5051627 A-TTTTTTAATTTTAAAATATTTTTAA-AATTTTTAAA
1 ATTTTTTTAATTTTAAAATATTTTTAATACTTTTTAAA
5051663 A
1 A
5051664 AATTTTAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
36 7 0.10
37 1 0.01
38 2 0.03
39 8 0.11
40 34 0.49
41 10 0.14
42 8 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (38 bp):
ATTTTTTTAATTTTAAAATATTTTTAATACTTTTTAAA
Found at i:5057294 original size:12 final size:13
Alignment explanation
Indices: 5057275--5057328 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
5057265 GAGGATTTCA
5057275 AGGAGAGAAGGGAG
1 AGGAGAG-AGGGAG
5057289 A-G-GAGAGGGAG
1 AGGAGAGAGGGAG
5057300 AGG-GAGAGGGAG
1 AGGAGAGAGGGAG
*
5057312 AGG-GAGAGGCAG
1 AGGAGAGAGGGAG
5057324 AGGAG
1 AGGAG
5057329 GTGGTGCAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
11 7 0.19
12 27 0.73
13 2 0.05
14 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.61, T:0.00
Consensus pattern (13 bp):
AGGAGAGAGGGAG
Found at i:5057301 original size:6 final size:6
Alignment explanation
Indices: 5057283--5057326 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
5057273 CAAGGAGAGA
*
5057283 AGGGAG A-GGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGCAG AGG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGG
5057327 AGGTGGTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.34, C:0.02, G:0.64, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:5064305 original size:9 final size:9
Alignment explanation
Indices: 5064281--5064317 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5064271 TGAGTTTTCA
*
5064281 AATTCGAAG
1 AATTCGAAT
*
5064290 AACTCGAAT
1 AATTCGAAT
5064299 AATTCGAAT
1 AATTCGAAT
5064308 AATTCGAAT
1 AATTCGAAT
5064317 A
1 A
5064318 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5064427 original size:5 final size:5
Alignment explanation
Indices: 5064417--5064441 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5064407 AAAACTTTTA
5064417 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
5064442 AACCCCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:5064575 original size:30 final size:31
Alignment explanation
Indices: 5064541--5064600 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
5064531 AAACCTTTTA
*
5064541 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
5064571 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
5064601 TCCCATCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:5064870 original size:9 final size:9
Alignment explanation
Indices: 5064856--5064884 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5064846 AATTTCACAT
5064856 TTTATATTA
1 TTTATATTA
5064865 TTTATATTA
1 TTTATATTA
5064874 TTTATATTA
1 TTTATATTA
5064883 TT
1 TT
5064885 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:5065374 original size:5 final size:5
Alignment explanation
Indices: 5065364--5065389 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5065354 CTCAAAAATT
5065364 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
5065390 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:5077659 original size:15 final size:16
Alignment explanation
Indices: 5077626--5077659 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5077616 CAATCTTTCA
5077626 CTTTTCTTCCAACTTT
1 CTTTTCTTCCAACTTT
*
5077642 CTTTTCTTCTAA-TTT
1 CTTTTCTTCCAACTTT
5077657 CTT
1 CTT
5077660 ACTTCTTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTTCTTCCAACTTT
Found at i:5077943 original size:21 final size:19
Alignment explanation
Indices: 5077894--5077945 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
5077884 AATATCTCAA
5077894 CTAATTTAATAATAAAATT
1 CTAATTTAATAATAAAATT
* *
5077913 TTATTGTTTAATATATAAAATT
1 CTA--ATTTAATA-ATAAAATT
5077935 CTAACTTTAAT
1 CTAA-TTTAAT
5077946 CATTTTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (19 bp):
CTAATTTAATAATAAAATT
Found at i:5090608 original size:19 final size:20
Alignment explanation
Indices: 5090584--5090628 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5090574 TTCTAGGCAT
* *
5090584 ATTTTTTAAT-AATTTTTAA
1 ATTTTTTAATAAAATATTAA
5090603 ATTTTTTAATAAAATATTAA
1 ATTTTTTAATAAAATATTAA
5090623 ATTTTT
1 ATTTTT
5090629 ACATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTAATAAAATATTAA
Found at i:5090690 original size:19 final size:18
Alignment explanation
Indices: 5090649--5090693 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5090639 TTTAAAATTT
*
5090649 AAAATATATAAAATCTAA
1 AAAATATTTAAAATCTAA
*
5090667 AAAATATTTAAAATTTATA
1 AAAATATTTAAAATCTA-A
5090686 AAAATATT
1 AAAATATT
5090694 ATTTAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATTTAAAATCTAA
Found at i:5097984 original size:25 final size:25
Alignment explanation
Indices: 5097938--5097985 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5097928 AGCTATTTAC
**
5097938 TTTTTAAAAGTATAAATTAAAAATG
1 TTTTTAAAAGTATAAAAGAAAAATG
5097963 TTTTTAAAAAGTA-AAAAGAAAAA
1 TTTTT-AAAAGTATAAAAGAAAAA
5097986 ACACATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTTTTAAAAGTATAAAAGAAAAATG
Found at i:5097985 original size:26 final size:25
Alignment explanation
Indices: 5097938--5097986 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5097928 AGCTATTTAC
* **
5097938 TTTTTAAAAGTATAAATTAAAAATG
1 TTTTTAAAAGTAAAAAGAAAAAATG
5097963 TTTTTAAAAAGTAAAAAGAAAAAA
1 TTTTT-AAAAGTAAAAAGAAAAAA
5097987 CACATTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTTTTAAAAGTAAAAAGAAAAAATG
Found at i:5098417 original size:5 final size:5
Alignment explanation
Indices: 5098407--5098433 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5098397 ACAATAAACT
5098407 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
5098434 GAAATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:5098542 original size:18 final size:19
Alignment explanation
Indices: 5098507--5098544 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5098497 AAAATGAACA
*
5098507 TTTTATTTCTCAAAAATAC
1 TTTTATTTCACAAAAATAC
*
5098526 TTTT-TTTCACAATAATAC
1 TTTTATTTCACAAAAATAC
5098544 T
1 T
5098545 AAACTCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTATTTCACAAAAATAC
Found at i:5104026 original size:21 final size:22
Alignment explanation
Indices: 5103978--5104031 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
5103968 CCTTTTGAAC
*
5103978 TATT-TTATTTATGTTCTTAAT
1 TATTATTATTTATATTCTTAAT
*
5103999 TA-TATTATTTATATT-TTATT
1 TATTATTATTTATATTCTTAAT
5104019 TATTATTAATTTA
1 TATTATT-ATTTA
5104032 GGGAATACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 7 0.25
21 16 0.57
22 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTATTTATATTCTTAAT
Found at i:5104834 original size:36 final size:36
Alignment explanation
Indices: 5104793--5104861 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5104783 ATAAAGATTC
5104793 AATATGATAA-GCAATTCAATAATATAAATAGTACAA
1 AATATGA-AATGCAATTCAATAATATAAATAGTACAA
** *
5104829 AATATGAAATTTAATTTAATAATATAAATAGTA
1 AATATGAAATGCAATTCAATAATATAAATAGTA
5104862 GATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.33
Consensus pattern (36 bp):
AATATGAAATGCAATTCAATAATATAAATAGTACAA
Found at i:5106341 original size:31 final size:30
Alignment explanation
Indices: 5106306--5106371 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
5106296 TTGGCTTTTT
5106306 TTTTTAAAGA-TTTTTT-AAAATTTCATATAA
1 TTTTT-AAGACTTTTTTGAAAATTT-ATATAA
*
5106336 CTTTTT-AGACTTTTTTGAAAATTTATGTAA
1 -TTTTTAAGACTTTTTTGAAAATTTATATAA
5106366 TTTTTA
1 TTTTTA
5106372 TTTTTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
29 8 0.26
30 11 0.35
31 12 0.39
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTTTAAGACTTTTTTGAAAATTTATATAA
Found at i:5110911 original size:2 final size:2
Alignment explanation
Indices: 5110904--5110933 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5110894 CAGCATTTGC
5110904 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5110934 GCAATGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5115397 original size:31 final size:32
Alignment explanation
Indices: 5115341--5115402 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
5115331 CTAATTAAAA
*
5115341 TTTTAAAGAGAATTTTTGAAAATTTT-AAAGG
1 TTTTAAAGAGAATTTTTCAAAATTTTGAAAGG
5115372 TTTTAAATGA-AA-TTTTCAAACATTTTGAAAG
1 TTTTAAA-GAGAATTTTTCAAA-ATTTTGAAAG
5115403 ACTCAAGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.26
31 14 0.52
32 6 0.22
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (32 bp):
TTTTAAAGAGAATTTTTCAAAATTTTGAAAGG
Found at i:5117156 original size:46 final size:46
Alignment explanation
Indices: 5117078--5117216 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
5117068 GCAATGCTAT
* * *
5117078 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTCTCAC
* *
5117124 AACTCAGTATGATTTTCTTTACTAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTCTCAC
5117170 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACGTTC-CAC
1 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTAC-TTCTCAC
5117216 A
1 A
5117217 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
46 83 0.98
47 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTCTCAC
Found at i:5135118 original size:24 final size:24
Alignment explanation
Indices: 5135091--5135142 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5135081 AATCAAAGTC
* *
5135091 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
5135115 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
5135139 AAAT
1 AAAT
5135143 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:5139565 original size:24 final size:24
Alignment explanation
Indices: 5139523--5139574 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5139513 AATCAAAGTC
** *
5139523 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
5139547 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
5139571 AAAT
1 AAAT
5139575 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:5142607 original size:27 final size:27
Alignment explanation
Indices: 5142577--5142637 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
5142567 TATACATATA
5142577 TTAAGTATGATTAGTTTAGTTTCTTGT
1 TTAAGTATGATTAGTTTAGTTTCTTGT
5142604 TTAAGTATGATTAGTTTAGTTTCTTGT
1 TTAAGTATGATTAGTTTAGTTTCTTGT
5142631 TTAAGTA
1 TTAAGTA
5142638 AAAATGGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (27 bp):
TTAAGTATGATTAGTTTAGTTTCTTGT
Found at i:5148267 original size:21 final size:22
Alignment explanation
Indices: 5148243--5148289 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
5148233 AATCATTTGG
* * *
5148243 ATTTTATTTTTTAAA-TTAAAT
1 ATTTTATTATTAAAAGTTAAAA
5148264 ATTTTATTATTAAAAGTTAAAA
1 ATTTTATTATTAAAAGTTAAAA
5148286 ATTT
1 ATTT
5148290 AACATAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTATTATTAAAAGTTAAAA
Found at i:5148599 original size:3 final size:3
Alignment explanation
Indices: 5148591--5148628 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5148581 CCCAGATTTT
5148591 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5148629 TTTTTCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5151205 original size:3 final size:3
Alignment explanation
Indices: 5151199--5151233 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5151189 GAATAAGACA
*
5151199 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5151234 ATACTAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5166493 original size:17 final size:17
Alignment explanation
Indices: 5166471--5166506 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5166461 TAAATTTTAT
5166471 TGCTTGAATTTTTAAAG
1 TGCTTGAATTTTTAAAG
5166488 TGCTTGAATTTTTAAAG
1 TGCTTGAATTTTTAAAG
5166505 TG
1 TG
5166507 GGGTGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (17 bp):
TGCTTGAATTTTTAAAG
Found at i:5182781 original size:16 final size:17
Alignment explanation
Indices: 5182751--5182785 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
5182741 TAAATTTTAT
5182751 TGCTTGAATTTTTAAAG
1 TGCTTGAATTTTTAAAG
5182768 TGCTTGAA-TTTTAAAG
1 TGCTTGAATTTTTAAAG
5182784 TG
1 TG
5182786 GGGTGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.46
Consensus pattern (17 bp):
TGCTTGAATTTTTAAAG
Found at i:5204952 original size:34 final size:33
Alignment explanation
Indices: 5204911--5204979 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
5204901 TCAACATTTA
*
5204911 AAAAACAAAACATTATCACAAAAGGTGAAAAACT
1 AAAAACAAAACATTATCACAAAAGGAG-AAAACT
*
5204945 AAAAACAAAACATTATCACAGAAGGAGAAAACT
1 AAAAACAAAACATTATCACAAAAGGAGAAAACT
5204978 AA
1 AA
5204980 TACTTACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.13
Consensus pattern (33 bp):
AAAAACAAAACATTATCACAAAAGGAGAAAACT
Found at i:5209974 original size:26 final size:26
Alignment explanation
Indices: 5209938--5209991 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5209928 GCAAGAGATG
5209938 TTGTCACCTTAAATCTCACTTTGTGA
1 TTGTCACCTTAAATCTCACTTTGTGA
5209964 TTGTCACCTTAAATCTCACTTTGTGA
1 TTGTCACCTTAAATCTCACTTTGTGA
5209990 TT
1 TT
5209992 CTTCTGACTT
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:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (26 bp):
TTGTCACCTTAAATCTCACTTTGTGA
Found at i:5222648 original size:22 final size:22
Alignment explanation
Indices: 5222623--5222671 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5222613 TGTTTTCTCC
5222623 TTATTTTGCTACCATTTTACTA
1 TTATTTTGCTACCATTTTACTA
* * * **
5222645 TTATGTTGTTACTATTTTGTTA
1 TTATTTTGCTACCATTTTACTA
5222667 TTATT
1 TTATT
5222672 GTTTGGATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (22 bp):
TTATTTTGCTACCATTTTACTA
Found at i:5222892 original size:17 final size:18
Alignment explanation
Indices: 5222860--5222896 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5222850 ATGTTTTTAG
*
5222860 TATTTTTTATATATTATA
1 TATTTTTTATAAATTATA
5222878 TATTTTTTA-AAATTATA
1 TATTTTTTATAAATTATA
5222895 TA
1 TA
5222897 AAAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTTATAAATTATA
Found at i:5229597 original size:40 final size:40
Alignment explanation
Indices: 5229544--5229683 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 40
5229534 AACACACCAG
* * *
5229544 TTTGGCACACAGTGTCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* *
5229584 TTTGACACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* * *
5229622 TTAG-CACCCAGTGCCTCATCGAATTAATCCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGA-TAATCCGAAGTAATAA
*
5229662 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGTCTCATCG
5229684 ACTCAAAGTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
37 16 0.19
38 15 0.18
39 2 0.02
40 34 0.41
41 16 0.19
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
Found at i:5229671 original size:41 final size:40
Alignment explanation
Indices: 5229553--5229684 Score: 155
Period size: 41 Copynumber: 3.4 Consensus size: 40
5229543 GTTTGGCACA
* * *
5229553 CAGTGTCTCATCGGATAATTCGAAGTAATAATTTGACACC
1 CAGTGTCTCATCGAATAATCCGAAGTAATAAATTGACACC
** *
5229593 CAGTGTCTCATCGGCTAAACCGAAG---TAAATT-AGCACC
1 CAGTGTCTCATCGAATAATCCGAAGTAATAAATTGA-CACC
*
5229630 CAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGACACC
1 CAGTGTCTCATCGAA-TAATCCGAAGTAATAAATTGACACC
5229671 CAGTGTCTCATCGA
1 CAGTGTCTCATCGA
5229685 CTCAAAGTTG
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
36 1 0.01
37 21 0.27
38 9 0.12
40 22 0.29
41 23 0.30
42 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
CAGTGTCTCATCGAATAATCCGAAGTAATAAATTGACACC
Found at i:5230686 original size:19 final size:20
Alignment explanation
Indices: 5230662--5230709 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
5230652 ATTAATAAGC
*
5230662 AATACATAT-TTTATTATTA
1 AATACACATGTTTATTATTA
5230681 AATACACATGTTTATTATT-
1 AATACACATGTTTATTATTA
*
5230700 ATTACACATG
1 AATACACATG
5230710 AATTTACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (20 bp):
AATACACATGTTTATTATTA
Found at i:5235949 original size:34 final size:34
Alignment explanation
Indices: 5235887--5235951 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
5235877 TTTGTAGTAA
5235887 TTTATTTTTTCTTTCATATTTCAATTATATATTT
1 TTTATTTTTTCTTTCATATTTCAATTATATATTT
*
5235921 TTTATTATTTTCTTCTC-TATTT-AGTTATATA
1 TTTATT-TTTTCTT-TCATATTTCAATTATATA
5235952 GATAAAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 14 0.50
35 12 0.43
36 2 0.07
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (34 bp):
TTTATTTTTTCTTTCATATTTCAATTATATATTT
Found at i:5236785 original size:2 final size:2
Alignment explanation
Indices: 5236780--5236804 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5236770 ATATATATAT
5236780 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5236805 AACCTAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5239928 original size:20 final size:22
Alignment explanation
Indices: 5239886--5239931 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5239876 GATATTTTAA
*
5239886 ATATAAATATTTATTTTATTTT
1 ATATAAATATTTAGTTTATTTT
5239908 ATATAAATATTT-GTTTA-TTT
1 ATATAAATATTTAGTTTATTTT
5239928 ATAT
1 ATAT
5239932 TTATTCGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.30
21 4 0.17
22 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATAAATATTTAGTTTATTTT
Found at i:5241631 original size:20 final size:20
Alignment explanation
Indices: 5241605--5241653 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
5241595 AACAATGAAT
5241605 CTGTTCATCAAGAGATACAA
1 CTGTTCATCAAGAGATACAA
* *
5241625 TTGTTCA--AA-AGATACGA
1 CTGTTCATCAAGAGATACAA
5241642 CTGTTCATCAAG
1 CTGTTCATCAAG
5241654 TGACAGAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 2 0.09
20 6 0.26
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
CTGTTCATCAAGAGATACAA
Found at i:5246248 original size:10 final size:11
Alignment explanation
Indices: 5246229--5246264 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
5246219 GGTGCTGCGG
5246229 AAAAGAAGAGA
1 AAAAGAAGAGA
5246240 AAAAG-AGAGA
1 AAAAGAAGAGA
5246250 AAAAGAAGAGA
1 AAAAGAAGAGA
5246261 AAAA
1 AAAA
5246265 AAAGGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:5246260 original size:13 final size:12
Alignment explanation
Indices: 5246229--5246265 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
5246219 GGTGCTGCGG
5246229 AAAAGAAGAG-A
1 AAAAGAAGAGAA
5246240 AAAAG-AGAG-A
1 AAAAGAAGAGAA
5246250 AAAAGAAGAGAA
1 AAAAGAAGAGAA
5246262 AAAA
1 AAAA
5246266 AAGGTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 9 0.38
12 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAGAA
Found at i:5246330 original size:19 final size:21
Alignment explanation
Indices: 5246292--5246330 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5246282 AATAATTGAT
*
5246292 TATATTGTTGTTATTGTTTTG
1 TATATTGTTGTTAATGTTTTG
5246313 TATATT-TTG-TAATGTTTT
1 TATATTGTTGTTAATGTTTT
5246331 TTGTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATGTTTTG
Found at i:5247244 original size:18 final size:18
Alignment explanation
Indices: 5247221--5247258 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5247211 GGTTGGTGGT
5247221 GAAGAAGAAAGTGCTGGC
1 GAAGAAGAAAGTGCTGGC
* *
5247239 GAAGAAGAATGTGGTGGC
1 GAAGAAGAAAGTGCTGGC
5247257 GA
1 GA
5247259 TCATTGGGAT
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:0.37, C:0.08, G:0.42, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAAGTGCTGGC
Found at i:5252205 original size:27 final size:27
Alignment explanation
Indices: 5252163--5252218 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
5252153 TTAGCCACAT
*
5252163 ATTGGTGCCGCCTTTTTATTCCTCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
*
5252190 ATTGGTGCCGCTTTTTTATTCCCCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
5252217 AT
1 AT
5252219 CACCCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.09, C:0.32, G:0.14, T:0.45
Consensus pattern (27 bp):
ATTGGTGCCGCCTTTTTATTCCCCTCC
Found at i:5253002 original size:14 final size:13
Alignment explanation
Indices: 5252987--5253154 Score: 50
Period size: 14 Copynumber: 11.5 Consensus size: 13
5252977 CCTCTTCTTC
5252987 TTCTTTTTTTTCT
1 TTCTTTTTTTTCT
5253000 CTTCTCCTTTCCTTTTCT
1 -TTCT--TTT--TTTTCT
*
5253018 TTCCTTCTTTTTCT
1 TT-CTTTTTTTTCT
5253032 TTCTTTTTTCTTTTCCT
1 TTC--TTTT-TTTT-CT
*
5253049 TTCCTCTTCTTCTTCT
1 TT-CT-TT-TTTTTCT
*
5253065 TCCTTTTTTTTTCT
1 TTC-TTTTTTTTCT
5253079 CTTCTCCTTTCCTTTTCT
1 -TTCT--TTT--TTTTCT
*
5253097 TTCCTTCTTTTTCT
1 TT-CTTTTTTTTCT
** * *
5253111 TTCTTTCCTCTCC
1 TTCTTTTTTTTCT
**
5253124 TTCTTTCCTTTCT
1 TTCTTTTTTTTCT
*
5253137 TTC-TTTCTTTCT
1 TTCTTTTTTTTCT
5253149 TTCTTT
1 TTCTTT
5253155 CCCTCTCCTT
Statistics
Matches: 119, Mismatches: 15, Indels: 41
0.68 0.09 0.23
Matches are distributed among these distances:
12 11 0.09
13 23 0.19
14 27 0.23
15 8 0.07
16 19 0.16
17 13 0.11
18 18 0.15
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:5253008 original size:41 final size:41
Alignment explanation
Indices: 5252949--5253133 Score: 159
Period size: 41 Copynumber: 4.6 Consensus size: 41
5252939 AAAAATTACC
* * *
5252949 TTTTTTTCTTTTTTTCC-TTCCTTCCTTCCCTCTTCTTCTTCT
1 TTTTTTTC-TCTTCTCCTTTCCTT-CTTCCTTCTTCTTCTTCT
* *
5252991 TTTTTTTCTCTTCTCCTTTCCTT-TTCTTTCCTTCTTTTTCT
1 TTTTTTTCTCTTCTCCTTTCCTTCTTCCTT-CTTCTTCTTCT
* *
5253032 TTCTTTTT-TCTTTTCCTTTCC-TCTT-CTTCTTCTTCCT-T
1 TT-TTTTTCTCTTCTCCTTTCCTTCTTCCTTCTTCTTCTTCT
* *
5253070 TTTTTTTCTCTTCTCCTTTCCTT-TTCTTTCCTTCTTTTTCT
1 TTTTTTTCTCTTCTCCTTTCCTTCTTCCTT-CTTCTTCTTCT
* * * *
5253111 TTCTTTCCTCTCCTTCTTTCCTT
1 TTTTTTTCTCTTCTCCTTTCCTT
5253134 TCTTTCTTTC
Statistics
Matches: 117, Mismatches: 17, Indels: 19
0.76 0.11 0.12
Matches are distributed among these distances:
37 5 0.04
38 17 0.15
39 10 0.09
40 14 0.12
41 52 0.44
42 19 0.16
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (41 bp):
TTTTTTTCTCTTCTCCTTTCCTTCTTCCTTCTTCTTCTTCT
Found at i:5253027 original size:13 final size:13
Alignment explanation
Indices: 5253011--5253154 Score: 58
Period size: 13 Copynumber: 11.3 Consensus size: 13
5253001 TTCTCCTTTC
5253011 CTTTTCTTTCCTT
1 CTTTTCTTTCCTT
5253024 CTTTTTCTTT-CTT
1 C-TTTTCTTTCCTT
5253037 -TTTTCTTTTCCTTT
1 CTTTTC-TTTCC-TT
*
5253051 CCTCTTC-TT-CTT
1 -CTTTTCTTTCCTT
*
5253063 C-TTCCTTT--TT
1 CTTTTCTTTCCTT
*
5253073 TTTTCTCTTCTCCTTT
1 CTTT-TCTT-TCC-TT
5253089 CCTTTTCTTTCCTT
1 -CTTTTCTTTCCTT
*
5253103 C--TT-TTTCTTT
1 CTTTTCTTTCCTT
* *
5253113 CTTTCCTCTCCTT
1 CTTTTCTTTCCTT
* *
5253126 CTTTCCTTTCTTT
1 CTTTTCTTTCCTT
*
5253139 C-TTTCTTTCTTT
1 CTTTTCTTTCCTT
5253151 CTTT
1 CTTT
5253155 CCCTCTCCTT
Statistics
Matches: 100, Mismatches: 13, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
10 11 0.11
11 12 0.12
12 20 0.20
13 27 0.27
14 14 0.14
15 3 0.03
16 10 0.10
17 3 0.03
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTTTCTTTCCTT
Found at i:5253034 original size:4 final size:4
Alignment explanation
Indices: 5253013--5253155 Score: 81
Period size: 4 Copynumber: 36.0 Consensus size: 4
5253003 CTCCTTTCCT
*
5253013 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTTTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTT-C T-TTC
* * *
5253058 -TTC -TTC TTCC TTT- TTT- TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC
* *
5253104 -TT- TTTC TTTC TTTCC TCTC CTTC TTTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC
5253152 TTTC
1 TTTC
5253156 CCTCTCCTTC
Statistics
Matches: 113, Mismatches: 10, Indels: 32
0.73 0.06 0.21
Matches are distributed among these distances:
3 25 0.22
4 60 0.53
5 22 0.19
6 6 0.05
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:5253047 original size:36 final size:36
Alignment explanation
Indices: 5252986--5253148 Score: 153
Period size: 38 Copynumber: 4.6 Consensus size: 36
5252976 CCCTCTTCTT
5252986 CTTCTTTTT-TTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTCTTCTCCTTTCCTTTTCTTTC
* * *
5253021 CTTCTTTTTCTTTCTTTTTTCTTTTCCTTTCCTCTTCTTCTT
1 CTTCTTTTTCTTTC-----TCTTCTCCTTTCCTTTTCTT-TC
*
5253063 CTTCCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTT-CTTTTTCTTTCTCTTCTCCTTTCCTTTTCTTTC
*
5253100 CTTCTTTTTC-TT-TCTT-TCCTCTCC--TTCTTTC
1 CTTCTTTTTCTTTCTCTTCTCCTTTCCTTTTCTTTC
*
5253131 CTT-TCTTTCTTTCT-TTCT
1 CTTCTTTTTCTTTCTCTTCT
5253149 TTCTTTCCCT
Statistics
Matches: 107, Mismatches: 10, Indels: 25
0.75 0.07 0.18
Matches are distributed among these distances:
30 5 0.05
31 14 0.13
32 2 0.02
33 7 0.07
34 4 0.04
35 11 0.10
36 10 0.09
37 4 0.04
38 18 0.17
41 18 0.17
42 4 0.04
43 10 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (36 bp):
CTTCTTTTTCTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:5253130 original size:79 final size:77
Alignment explanation
Indices: 5252947--5253137 Score: 268
Period size: 79 Copynumber: 2.5 Consensus size: 77
5252937 AAAAAAATTA
* *
5252947 CCTT-TTTTTCTTTTTTTCCT-TCCTTCCTTCC-C-TCTTCTTCTTCTTTTTTTTCTCTTCTCCT
1 CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCTCTTCTTCTTCTTCTTTTTTTTCTCTTCTCCT
5253008 TTCCTTTTCTTT
66 TTCCTTTTCTTT
** *
5253020 CCTTCTTTTTCTTTCTTTTTTCT-TTTCCTTTCCTCTTCTTCTTCTTCCTTTTTTTTTCTCTTCT
1 CCTTCTTTTTCTTTCTTTCCTCTCCTT-CTTTCCTCTTCTTCTTCTT-C-TTTTTTTTCTCTTCT
5253084 CCTTTCCTTTTCTTT
63 CCTTTCCTTTTCTTT
5253099 CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCT-TTCTT
1 CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCTCTTCTT
5253138 TCTTTCTTTC
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
73 4 0.04
74 15 0.15
75 6 0.06
76 1 0.01
77 10 0.10
78 6 0.06
79 58 0.57
80 2 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (77 bp):
CCTTCTTTTTCTTTCTTTCCTCTCCTTCTTTCCTCTTCTTCTTCTTCTTTTTTTTCTCTTCTCCT
TTCCTTTTCTTT
Found at i:5253313 original size:27 final size:29
Alignment explanation
Indices: 5253280--5253350 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
5253270 TTTTGTTTTT
5253280 TTATATATTTTGGTAAATAATAAAAA-TAA
1 TTATATATTTTGGTAAATAA-AAAAAGTAA
* *
5253309 TTATAATATTTTAGTAAATAAAAAAAGTTA
1 TTAT-ATATTTTGGTAAATAAAAAAAGTAA
5253339 -TA-ATATTTTGGT
1 TTATATATTTTGGT
5253351 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.24
29 11 0.30
30 17 0.46
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (29 bp):
TTATATATTTTGGTAAATAAAAAAAGTAA
Found at i:5253319 original size:30 final size:27
Alignment explanation
Indices: 5253280--5253350 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
5253270 TTTTGTTTTT
5253280 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTGGTAAAT-A-AAAAA-AA
* *
5253309 TTATAATATTTTAGTAAATAAAAAAAG
1 TTATAATATTTTGGTAAATAAAAAAAA
5253336 TTATAATATTTTGGT
1 TTATAATATTTTGGT
5253351 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 15 0.39
28 5 0.13
29 5 0.13
30 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (27 bp):
TTATAATATTTTGGTAAATAAAAAAAA
Found at i:5256816 original size:22 final size:23
Alignment explanation
Indices: 5256780--5256825 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5256770 TTATCTGTAC
* *
5256780 TTTTATTTTTAAAAATTTAGTCT
1 TTTTAATTTTAAAAATTAAGTCT
5256803 TTTTAATTTTAAAAATTAAGTCT
1 TTTTAATTTTAAAAATTAAGTCT
5256826 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTAATTTTAAAAATTAAGTCT
Found at i:5259579 original size:20 final size:21
Alignment explanation
Indices: 5259523--5259580 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
5259513 CACACCAAAA
5259523 TTTTAA-AT-TTTTATAAAATT
1 TTTTAACATATTTT-TAAAATT
*
5259543 TTTTAACATATTGTTAAAA-T
1 TTTTAACATATTTTTAAAATT
* *
5259563 TTTTGATATATTTTTAAA
1 TTTTAACATATTTTTAAA
5259581 GCATTTGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 22 0.69
21 7 0.22
22 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTAACATATTTTTAAAATT
Found at i:5263330 original size:16 final size:18
Alignment explanation
Indices: 5263309--5263349 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5263299 CAAGTTTCAC
5263309 GAAAAT-TAA-AAAACTA
1 GAAAATATAACAAAACTA
5263325 GAAAATATAACAAAACTA
1 GAAAATATAACAAAACTA
*
5263343 AAAAATA
1 GAAAATA
5263350 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 13 0.59
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (18 bp):
GAAAATATAACAAAACTA
Found at i:5263360 original size:26 final size:24
Alignment explanation
Indices: 5263331--5263381 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 24
5263321 ACTAGAAAAT
5263331 ATAACAAAACTAAAAAATAAT-TTAAA
1 ATAA-AAAA-TAAAAAA-AATCTTAAA
*
5263357 ATAAAGAATAAAAAAAATCTTAAA
1 ATAAAAAATAAAAAAAATCTTAAA
5263381 A
1 A
5263382 CTCAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.13
24 13 0.57
25 3 0.13
26 4 0.17
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (24 bp):
ATAAAAAATAAAAAAAATCTTAAA
Found at i:5291811 original size:150 final size:150
Alignment explanation
Indices: 5291248--5292104 Score: 1263
Period size: 150 Copynumber: 5.7 Consensus size: 150
5291238 CACATTTTGT
* *
5291248 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* * * * *
5291313 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * *
5291377 CAGCTTTTCATAGCTTATAA
131 TAGCTTCTCATACCTTATAA
* * **
5291397 AATCATAAATTCTTAAGATTTTGAAATTTATGTTTTTCTTAATACATTTCAAATACATAATCAGC
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTT-TT-ATACATTTCAAATACATAATCAAA
* * * *
5291462 GTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATAAAAGAAATGAAAAATCCAAA
64 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAA
* * *
5291527 TTCAGCTTTTCATAGCTTATAA
129 TTTAGCTTCTCATACCTTATAA
* * *
5291549 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATACATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
* *
5291614 TCAACCTTAACCAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAATATCCAAATT
66 TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
*
5291678 TAACTTCTCATACCTTATAA
131 TAGCTTCTCATACCTTATAA
* *
5291698 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATATATTTCAAATACATAGTCAAAG
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTT-ATACATTTCAAATACATAATCAAAG
* * *
5291763 TTCAACCTTGACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAGTGAAATATCCAAAT
65 TTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
5291827 TTAGCTTCTCATACCTTATAA
130 TTAGCTTCTCATACCTTATAA
* *
5291848 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTTAATATATTTCAAATACATAGTCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTTT-ATACATTTCAAATACATAATCAAA
*
5291913 GTTCAACCTTAACTAATTTGGCTTTTTCA-AGCTCAAAATCAGTATAACAAATGAAAAATCCAAA
64 GTTCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAA
5291977 TTTAGCTTCTCATACCTTATAA
129 TTTAGCTTCTCATACCTTATAA
* * * * *
5291999 AATCCTAAATTCCTAAGATTTTGACATTCATGTTTTCTTATACAATTCAAATACAGAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
*
5292064 TCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCA
66 TCAACCTTAACT-AATTTGGCTTTTTCATAGCTCAAAATCA
5292105 TAAATTTCAA
Statistics
Matches: 652, Mismatches: 49, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
149 154 0.24
150 205 0.31
151 201 0.31
152 92 0.14
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (150 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATAATCAAAGT
TCAACCTTAACTAATTTGGCTTTTTCATAGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
TAGCTTCTCATACCTTATAA
Found at i:5291899 original size:301 final size:299
Alignment explanation
Indices: 5291248--5292108 Score: 1271
Period size: 301 Copynumber: 2.9 Consensus size: 299
5291238 CACATTTTGT
* *
5291248 AATCATAAATTCCCAAGATTTTGAAATTCATGTTTTTCTATACATTTCAAATACATAATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACAT-ATCAAAGT
* * * * *
5291313 TCAACCTTAACTAATTTGTC-TTTTCATAGCTCATAGTTAATATAACAAATAAAAAATCCAAATT
65 TCAACCTTAACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATAACAAATGAAAAATCCAAATT
* * * * *
5291377 CAGCTTTTCATAGCTTATAAAATCATAAATTCTTAAGATTTTGAAATTTATGTTTTTCTTAATAC
129 TAGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTT-TTAATAC
** * * *
5291442 ATTTCAAATACATAATCAGCGTTCAACCTTAACTAATTTGGCCTTTTCATAGCTCAAAATTAATA
193 ATTTCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATA
* * *
5291507 AAAGAAATGAAAAATCCAAATTCAGCTTTTCATAGCTTATAA
258 AAACAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
* *
5291549 AATCATAAATTCCTAAGATTTTGAAATTCTTGTTTTCTTATACATTTCAAATACATGATCAAAGT
1 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACAT-ATCAAAGT
* *
5291614 TCAACCTTAACCAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAATATCCAAATTT
65 TCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAATTT
* *
5291679 AACTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATATAT
130 AGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATACAT
* * *
5291744 TTCAAATACATAGTCAAAGTTCAACCTTGACTAATTTGGCTTTTTCA-AGCTCAAAATCAATATA
195 TTCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATAAA
* * *
5291808 ACAAGTGAAATATCCAAATTTAGCTTCTCATACCTTATAA
260 ACAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
*
5291848 AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTTAATATATTTCAAATACATAGTCAAA
1 AATCATAAATTCCTAAGATTTTGAAATTCATG-TTTTTTT-ATACATTTCAAATACATA-TCAAA
*
5291913 GTTCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAGTATAACAAATGAAAAATCCAAAT
63 GTTCAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAAT
* * *
5291978 TTAGCTTCTCATACCTTATAAAATCCTAAATTCCTAAGATTTTGACATTCATGTTTTCTT-ATAC
128 TTAGCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATAC
* *
5292042 AATTCAAATACAGAATCAAAGTTCAACCTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATC-AT
193 ATTTCAAATACATAATCAAAGTTCAACCTTAACT-AATTTGGCTTTTTCAGAGCTCAAAATCAAT
5292106 AAA
257 AAA
5292109 TTTCAAAATT
Statistics
Matches: 506, Mismatches: 48, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
299 80 0.16
300 90 0.18
301 319 0.63
302 17 0.03
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (299 bp):
AATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTATACATTTCAAATACATATCAAAGTT
CAACCTTAACTAATTTGGCTTTTTCAAGCTCAAAATCAATATAACAAATGAAAAATCCAAATTTA
GCTTCTCATACCTTATAAAATCATAAATTCCTAAGATTTTGAAATTCATGTTTTTTTAATACATT
TCAAATACATAATCAAAGTTCAACCTTAACTAATTTGGCTTTTTCAGAGCTCAAAATCAATAAAA
CAAATGAAAAATCCAAATTCAGCTTCTCATACCTTATAA
Found at i:5292151 original size:109 final size:107
Alignment explanation
Indices: 5292005--5292209 Score: 286
Period size: 109 Copynumber: 1.9 Consensus size: 107
5291995 ATAAAATCCT
* * *
5292005 AAATTCCTAAGATTTTGACATTCATGTTTTCTTATACAATTC-AAATACAGAATCAAAGTTCAAC
1 AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
5292069 CTTAACTAAATTTGGCTTTTTCAGAGCTCAAAATCATAAATTTCA
66 CTTAAC-AAATTT-GC-TTTTCAGAGCTCAAAATCATAAATTTCA
* ** * * *
5292114 AAATTCCTAAGCTTTCGAAATTTGTGTTTTCTAATACATTTCAAAATTCATAATCAAAGTTCAAC
1 AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
*
5292179 CTTAACAAATTTGCTTTTCATAGCTCAAAAT
66 CTTAACAAATTTGCTTTTCAGAGCTCAAAAT
5292210 TAATATAACA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 16 0.19
108 2 0.02
109 41 0.48
110 26 0.31
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (107 bp):
AAATTCCTAAGATTTCGAAATTCATGTTTTCTAATACAATTCAAAATACAGAATCAAAGTTCAAC
CTTAACAAATTTGCTTTTCAGAGCTCAAAATCATAAATTTCA
Found at i:5293054 original size:14 final size:14
Alignment explanation
Indices: 5293037--5293084 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
5293027 CATAGTAATA
5293037 TTTTATAAAATTAT
1 TTTTATAAAATTAT
* * *
5293051 TTTTTTGAAACT-T
1 TTTTATAAAATTAT
*
5293064 TTTTATAAATTTAT
1 TTTTATAAAATTAT
5293078 TTTTATA
1 TTTTATA
5293085 TACAACTATA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTTATAAAATTAT
Found at i:5296828 original size:42 final size:42
Alignment explanation
Indices: 5296782--5296935 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 42
5296772 TGCTACACAA
* * * *
5296782 AAACCCGTAAGGGTTAAACGGAAGCTCATAAGAGCTAAACGG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
* **
5296824 AAACCCATAAAGGTTAATTTGAAGCTCAAAAGAGCTAAACTG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
* * * * *
5296866 AAACCCATTAGGGTAAAACTAAAGCTCAAAATAGCTGAACTG
1 AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
* *
5296908 AAACCCAGAAGGGTTAAACTGAAACTCA
1 AAACCCATAAGGGTTAAACTGAAGCTCA
5296936 TATGAGTTGA
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAACTG
Found at i:5296832 original size:21 final size:21
Alignment explanation
Indices: 5296782--5296833 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
5296772 TGCTACACAA
* * *
5296782 AAACCCGTAAGGGTTAAACGG
1 AAACCCATAAGAGCTAAACGG
* *
5296803 AAGCTCATAAGAGCTAAACGG
1 AAACCCATAAGAGCTAAACGG
5296824 AAACCCATAA
1 AAACCCATAA
5296834 AGGTTAATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (21 bp):
AAACCCATAAGAGCTAAACGG
Done.