Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 14 of 82
Found at i:4461003 original size:2 final size:2
Alignment explanation
Indices: 4460998--4461030 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4460988 TATATACGTG
*
4460998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4461031 GTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4475572 original size:2 final size:2
Alignment explanation
Indices: 4475565--4475621 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
4475555 TATTGGTGTT
4475565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4475607 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
4475622 TTATTTATGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4479415 original size:18 final size:20
Alignment explanation
Indices: 4479392--4479442 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
4479382 ACAATTAATT
*
4479392 AAAACTAAATTCAA-TCA-A
1 AAAACTAAATTCAATTAACA
4479410 AAAACTAAATT-AATTAACA
1 AAAACTAAATTCAATTAACA
4479429 AAAACTAAAATTCA
1 AAAACT-AAATTCA
4479443 CTAGAGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 13 0.46
19 7 0.25
20 5 0.18
21 1 0.04
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAACTAAATTCAATTAACA
Found at i:4480649 original size:21 final size:22
Alignment explanation
Indices: 4480616--4480659 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4480606 TTCTTAATAT
*
4480616 AATTCAAAACAAACTAAATTAA
1 AATTCAAAACAAAATAAATTAA
* *
4480638 AATT-AAACCAAAATAACTTAA
1 AATTCAAAACAAAATAAATTAA
4480659 A
1 A
4480660 TGAAACTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (22 bp):
AATTCAAAACAAAATAAATTAA
Found at i:4486218 original size:20 final size:19
Alignment explanation
Indices: 4486195--4486235 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4486185 TAACTATTAT
*
4486195 TAAAGTAATATAAAACATAA
1 TAAAGTAAAATAAAAC-TAA
*
4486215 TAAAGTAAAATTAAACTAA
1 TAAAGTAAAATAAAACTAA
4486234 TA
1 TA
4486236 TAACTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
TAAAGTAAAATAAAACTAA
Found at i:4486947 original size:35 final size:34
Alignment explanation
Indices: 4486898--4487015 Score: 123
Period size: 35 Copynumber: 3.4 Consensus size: 34
4486888 CTTTTCATGG
* *
4486898 GAGCAAGCACAACCCTTACAAATGCATTTTACCGG
1 GAGCAAGCACAACCC-TACAAATGCCTTTTACCGA
* **
4486933 GAGCAAGCATAACCC-ACAAATGCCTTTTACTAA
1 GAGCAAGCACAACCCTACAAATGCCTTTTACCGA
* *
4486966 AAGCAAGCACAACCCATA-AATATGCCTTTTAACGA
1 GAGCAAGCACAACCC-TACAA-ATGCCTTTTACCGA
*
4487001 GAGCAAGCATAACCC
1 GAGCAAGCACAACCC
4487016 ATAACTAGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
33 27 0.40
34 2 0.03
35 39 0.57
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (34 bp):
GAGCAAGCACAACCCTACAAATGCCTTTTACCGA
Found at i:4501170 original size:21 final size:21
Alignment explanation
Indices: 4501130--4501170 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4501120 CTGTAGCTTC
**
4501130 TCGCTGCAACGAGATTCATTT
1 TCGCTGCAACGAGAAACATTT
*
4501151 TCGCTGCAGCGAGAAACATT
1 TCGCTGCAACGAGAAACATT
4501171 CTGATTTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
TCGCTGCAACGAGAAACATTT
Found at i:4505458 original size:39 final size:38
Alignment explanation
Indices: 4505410--4505485 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
4505400 TGTGCATTAA
* *
4505410 CCTTGAAAAGGTAG-TGACTTGTTGAAAGGTTTTGCTTGAT
1 CCTTGAAAAGGCAGTTG-CTTG-T-AAAGGTTATGCTTGAT
4505450 CCTT-AAAAGGCAGTTGCTTGTAAAGGTTATGCTTGA
1 CCTTGAAAAGGCAGTTGCTTGTAAAGGTTATGCTTGA
4505486 ACCTAGTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 14 0.42
38 1 0.03
39 12 0.36
40 6 0.18
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (38 bp):
CCTTGAAAAGGCAGTTGCTTGTAAAGGTTATGCTTGAT
Found at i:4509333 original size:38 final size:40
Alignment explanation
Indices: 4509246--4509352 Score: 146
Period size: 38 Copynumber: 2.7 Consensus size: 40
4509236 CACTCGGCTT
* *
4509246 ATGTACATCCCCCCACATTGTGCACATAGCCGGCGCCATC
1 ATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCATC
* * *
4509286 ATGTGCATCCCCCCACATCGTGCACA-A-TCAGTGCCATC
1 ATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCATC
*
4509324 GTGTACATCCCCCCACATCGTGCACATAG
1 ATGTACATCCCCCCACATCGTGCACATAG
4509353 GCACAATCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 32 0.55
39 2 0.03
40 24 0.41
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (40 bp):
ATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCATC
Found at i:4509891 original size:20 final size:20
Alignment explanation
Indices: 4509866--4509904 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4509856 AGAGTCAATA
4509866 CACAATCTCAA-CAATAAACC
1 CACAAT-TCAATCAATAAACC
4509886 CACAATTCAATCAATAAAC
1 CACAATTCAATCAATAAAC
4509905 ATTATCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (20 bp):
CACAATTCAATCAATAAACC
Found at i:4511987 original size:36 final size:36
Alignment explanation
Indices: 4511915--4512039 Score: 106
Period size: 36 Copynumber: 3.7 Consensus size: 36
4511905 GCTCATCAGC
* *
4511915 TCATGTGCACTTCCACACCGCACATAGCTGAAATCA
1 TCATGTGCACTCCCACACCGCACATAGCTAAAATCA
*
4511951 TCATGTGTACTCCCACACCGCACAT-G--ACAAAT-A
1 TCATGTGCACTCCCACACCGCACATAGCTA-AAATCA
* ** *
4511984 TCATGTACACTCCCACA-C-CACAT--C-ATCACCA
1 TCATGTGCACTCCCACACCGCACATAGCTAAAATCA
*
4512015 GCATGTGCACTCCCACACCGCACAT
1 TCATGTGCACTCCCACACCGCACAT
4512040 GCACGGTTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 13
0.76 0.10 0.13
Matches are distributed among these distances:
30 1 0.01
31 22 0.30
32 2 0.03
33 21 0.28
34 4 0.05
35 1 0.01
36 23 0.31
ACGTcount: A:0.30, C:0.38, G:0.11, T:0.20
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATAGCTAAAATCA
Found at i:4516374 original size:12 final size:13
Alignment explanation
Indices: 4516349--4516382 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
4516339 CTTACCCTCA
4516349 TTTCTCTCTTTTC
1 TTTCTCTCTTTTC
4516362 TTTCTCT-TTTTC
1 TTTCTCTCTTTTC
*
4516374 TTCCTCTCT
1 TTTCTCTCT
4516383 GGTGGAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTCTCTCTTTTC
Found at i:4536885 original size:42 final size:38
Alignment explanation
Indices: 4536800--4536897 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 38
4536790 TTCTTTAAAA
4536800 TTTAAAGTTGTGAAGTCTCAGAGGAATTTTTATTTCGT
1 TTTAAAGTTGTGAAGTCTCAGAGGAATTTTTATTTCGT
* * * *
4536838 CTTAAAGTTGTGAAGTCTCAATGAATGAGTTTTTTATTTCTT
1 TTTAAAGTTGTGAAGTCTC-A-G-AGGA-ATTTTTATTTCGT
*
4536880 TTTAAAGTTGTGGAGTCT
1 TTTAAAGTTGTGAAGTCT
4536898 TGTGGAGGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 18 0.36
39 1 0.02
40 1 0.02
41 3 0.06
42 27 0.54
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (38 bp):
TTTAAAGTTGTGAAGTCTCAGAGGAATTTTTATTTCGT
Found at i:4537038 original size:83 final size:84
Alignment explanation
Indices: 4536854--4537055 Score: 207
Period size: 83 Copynumber: 2.4 Consensus size: 84
4536844 GTTGTGAAGT
* * * * ** * *
4536854 CTCAAT-GAATGAGTTTTTTATTTCTTTTTAAAGTTGTGGAGTCTTGTGGAGGACCTTTTTTTTT
1 CTCAATAGAA-GATTTTTTTATTTCCTTTTAAAGTTATGGAGACTTGTGGAGGAAATCTTTTATT
*
4536918 TTCTTTTAAAATTGTGAAAC
65 TTCTTTTAAAATTATGAAAC
* *
4536938 CTCAATAGAGGA-GTTTTTATTTCCTTTTAAAGTTATGGA-ACTT-TGGAGGATGAATCTTTTAT
1 CTCAATAGAAGATTTTTTTATTTCCTTTTAAAGTTATGGAGACTTGTGGAGGA--AATCTTTTAT
4537000 TTTCTTTTAAAATTATGAAAC
64 TTTCTTTTAAAATTATGAAAC
*** *
4537021 CTTGTTAGAAGATTTTTTTATTT-CTCTTAAAGTTA
1 CTCAATAGAAGATTTTTTTATTTCCTTTTAAAGTTA
4537056 CGTAATCTCA
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
81 7 0.07
82 3 0.03
83 69 0.70
84 17 0.17
85 2 0.02
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (84 bp):
CTCAATAGAAGATTTTTTTATTTCCTTTTAAAGTTATGGAGACTTGTGGAGGAAATCTTTTATTT
TCTTTTAAAATTATGAAAC
Found at i:4537040 original size:42 final size:41
Alignment explanation
Indices: 4536909--4537048 Score: 113
Period size: 42 Copynumber: 3.4 Consensus size: 41
4536899 GTGGAGGACC
* ** *
4536909 TTTTTTT-TTTTCTTTTAAAATTGTGAAACCTCAATAGAGGA
1 TTTTTTTATTTTCTTTTAAAATTATGAAACCT-TGTAGAAGA
* * * * * * *
4536950 -GTTTTTATTTCCTTTTAAAGTTATGGAACTTTGGAGGATGA
1 TTTTTTTATTTTCTTTTAAAATTATGAAACCTTGTA-GAAGA
* *
4536991 ATCTTTTATTTTCTTTTAAAATTATGAAACCTTGTTAGAAGA
1 TTTTTTTATTTTCTTTTAAAATTATGAAACCTTG-TAGAAGA
4537033 TTTTTTTATTTCTCTT
1 TTTTTTTATTT-TCTT
4537049 AAAGTTACGT
Statistics
Matches: 74, Mismatches: 20, Indels: 8
0.73 0.20 0.08
Matches are distributed among these distances:
40 6 0.08
41 23 0.31
42 40 0.54
43 5 0.07
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (41 bp):
TTTTTTTATTTTCTTTTAAAATTATGAAACCTTGTAGAAGA
Found at i:4537663 original size:19 final size:19
Alignment explanation
Indices: 4537653--4537689 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4537643 ATCTTTTTAC
4537653 TCTCTCTAAATACTTTCTT
1 TCTCTCTAAATACTTTCTT
*
4537672 TCTCTCTAAACACTTTCT
1 TCTCTCTAAATACTTTCT
4537690 CTTATATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.49
Consensus pattern (19 bp):
TCTCTCTAAATACTTTCTT
Found at i:4538349 original size:26 final size:26
Alignment explanation
Indices: 4538308--4538460 Score: 114
Period size: 26 Copynumber: 6.0 Consensus size: 26
4538298 TAATTCTACA
*
4538308 AATAATTTTACTATCAGAAGTGGATG
1 AATAATTTTACCATCAGAAGTGGATG
** * ** *
4538334 GCTAATTTTACCATCATAA-TCTAAG
1 AATAATTTTACCATCAGAAGTGGATG
** * *
4538359 AATAATTTTATTAACAGAAGTGAATG
1 AATAATTTTACCATCAGAAGTGGATG
* **
4538385 AATAATTTTATCATCAGAA-T-CTTAG
1 AATAATTTTACCATCAGAAGTGGAT-G
* *
4538410 AATAATTTTACCACCAGAAGTAGATG
1 AATAATTTTACCATCAGAAGTGGATG
* *
4538436 GATAATTTTACCACCAGAAGTGGAT
1 AATAATTTTACCATCAGAAGTGGAT
4538461 AGATGCCGTA
Statistics
Matches: 97, Mismatches: 26, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
24 1 0.01
25 35 0.36
26 60 0.62
27 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (26 bp):
AATAATTTTACCATCAGAAGTGGATG
Found at i:4538391 original size:51 final size:51
Alignment explanation
Indices: 4538308--4538454 Score: 179
Period size: 51 Copynumber: 2.9 Consensus size: 51
4538298 TAATTCTACA
* * * *
4538308 AATAATTTTACTATCAGAAGTGGATGGCTAATTTTACCATCATAATCTAAG
1 AATAATTTTACTAACAGAAGTGAATGGATAATTTTACCATCAGAATCTAAG
* * * *
4538359 AATAATTTTATTAACAGAAGTGAATGAATAATTTTATCATCAGAATCTTAG
1 AATAATTTTACTAACAGAAGTGAATGGATAATTTTACCATCAGAATCTAAG
* * *
4538410 AATAATTTTACCACCAGAAGT-AGATGGATAATTTTACCACCAGAA
1 AATAATTTTACTAACAGAAGTGA-ATGGATAATTTTACCATCAGAA
4538455 GTGGATAGAT
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 1 0.01
51 80 0.99
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (51 bp):
AATAATTTTACTAACAGAAGTGAATGGATAATTTTACCATCAGAATCTAAG
Found at i:4539233 original size:2 final size:2
Alignment explanation
Indices: 4539226--4539268 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
4539216 TGTGGCTTAT
* *
4539226 TA TA TA TA AA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4539266 TA T
1 TA T
4539269 GTATGAGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4545288 original size:29 final size:28
Alignment explanation
Indices: 4545247--4545420 Score: 177
Period size: 29 Copynumber: 5.9 Consensus size: 28
4545237 GACAGCTTTG
4545247 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
4545275 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
4545304 ATATGTTTGCCTTAATTTAAGACAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
4545334 ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* * *
4545363 ACATATTTGTCTCAATTTATACAAGATAAA
1 ACATGTTTGTCTTAATTTAGACAAG--AAA
* * *
4545393 ATATTTTTTGTCTTAATTACAGACAAGA
1 ACA-TGTTTGTCTTAATT-TAGACAAGA
4545421 GTTGTCTTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 35 0.28
29 39 0.32
30 18 0.15
31 25 0.20
32 6 0.05
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:4545360 original size:59 final size:58
Alignment explanation
Indices: 4545247--4545420 Score: 224
Period size: 59 Copynumber: 3.0 Consensus size: 58
4545237 GACAGCTTTG
* * *
4545247 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
4545304 ATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * * *
4545363 ACATATTTGTCTCAATTTATACAAGATAAAATATTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAATT-TAGACAAGA
4545421 GTTGTCTTAA
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
57 16 0.16
58 14 0.14
59 63 0.63
60 7 0.07
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (58 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:4545584 original size:17 final size:17
Alignment explanation
Indices: 4545562--4545594 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4545552 ATAATAATAA
4545562 AATAA-GAGCTTTTATTC
1 AATAAGGAG-TTTTATTC
4545579 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
4545595 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:4552564 original size:2 final size:2
Alignment explanation
Indices: 4552557--4552581 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4552547 TGGATGTTCT
4552557 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
4552582 CTTTCACATT
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:4562599 original size:15 final size:15
Alignment explanation
Indices: 4562579--4562608 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4562569 TGGTATTAAT
4562579 ATTAACAAAGAGTAG
1 ATTAACAAAGAGTAG
4562594 ATTAACAAAGAGTAG
1 ATTAACAAAGAGTAG
4562609 GAAAACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
ATTAACAAAGAGTAG
Found at i:4565850 original size:13 final size:13
Alignment explanation
Indices: 4565832--4565856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4565822 TTCTAGAAAA
4565832 TTTATAAAATCAT
1 TTTATAAAATCAT
4565845 TTTATAAAATCA
1 TTTATAAAATCA
4565857 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4570231 original size:25 final size:25
Alignment explanation
Indices: 4570202--4570252 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
4570192 TCCCACGCAT
4570202 ATTCTTATTTGGGGTTTTATATATA
1 ATTCTTATTTGGGGTTTTATATATA
*
4570227 ATTCTTATTTGGTGTTTTATATATA
1 ATTCTTATTTGGGGTTTTATATATA
4570252 A
1 A
4570253 GTGTTGTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.57
Consensus pattern (25 bp):
ATTCTTATTTGGGGTTTTATATATA
Found at i:4581367 original size:34 final size:35
Alignment explanation
Indices: 4581311--4581383 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
4581301 TTTAATAGGC
* *
4581311 TCAACCACTAACCCATACAATGGCTTTTTCCGAGA
1 TCAACCACTAACCCATACAATGGCATTTTACGAGA
* *
4581346 TCAACCA-TAACCCTTATAATGGCATTTTACGAGA
1 TCAACCACTAACCCATACAATGGCATTTTACGAGA
4581380 TCAA
1 TCAA
4581384 GCAGTAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 27 0.79
35 7 0.21
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (35 bp):
TCAACCACTAACCCATACAATGGCATTTTACGAGA
Found at i:4595615 original size:22 final size:22
Alignment explanation
Indices: 4595572--4595615 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4595562 AGAAAGATCA
*
4595572 TTGTTACAACGAAAATCCATTT
1 TTGTTACAACGAAAATCAATTT
* * *
4595594 TTGTTGCAACGCAAGTCAATTT
1 TTGTTACAACGAAAATCAATTT
4595616 GGAAGCATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
TTGTTACAACGAAAATCAATTT
Found at i:4599727 original size:17 final size:19
Alignment explanation
Indices: 4599694--4599729 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
4599684 TTTACTCTTA
4599694 CATCTTGATCATATTATTT
1 CATCTTGATCATATTATTT
4599713 CATCTTGA-C-TATTATTT
1 CATCTTGATCATATTATTT
4599730 TAGAATTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (19 bp):
CATCTTGATCATATTATTT
Found at i:4610038 original size:21 final size:21
Alignment explanation
Indices: 4610014--4610054 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4610004 TGTCTGCATG
* *
4610014 CCAATTCTGCCTTCCTGCGCT
1 CCAACTCTGCCTGCCTGCGCT
4610035 CCAACTCTGCCTGCCTGCGC
1 CCAACTCTGCCTGCCTGCGC
4610055 CCCAGAGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.46, G:0.17, T:0.27
Consensus pattern (21 bp):
CCAACTCTGCCTGCCTGCGCT
Found at i:4610629 original size:132 final size:130
Alignment explanation
Indices: 4610391--4610653 Score: 492
Period size: 132 Copynumber: 2.0 Consensus size: 130
4610381 GAATGTGGTG
4610391 GGATGGTATGCATGATAATGTATGTATATCTATATATATATATATATATGTTAATAAAAAGTTTT
1 GGATGGTATGCATGATAATGTATGTATATCTATATATATATATATATATGTTAATAAAAAGTTTT
4610456 GAAAATAATTGTGATTGTGTTGTATGTTGACATTGTTAATTGTTCCCAAATTGTCTTTTCATTTC
66 GAAAATAATTGTGATTGTGTTGTATGTTGACATTGTTAATTGTTCCCAAATTG-CTTTTCATTTC
4610521 A
130 A
4610522 GNGATGGTATGCATGATAATGTATGTATATCTATATATATATATATATATGTT-ATAAAAAGTTT
1 G-GATGGTATGCATGATAATGTATGTATATCTATATATATATATATATATGTTAATAAAAAG-TT
4610586 TTGAAAATAATTGTGATTGTGTTGTATGTTGACATTGTTAATTGTTCCCAAATTGCTTTTCATTT
64 TTGAAAATAATTGTGATTGTGTTGTATGTTGACATTGTTAATTGTTCCCAAATTGCTTTTCATTT
4610651 CA
129 CA
4610653 G
1 G
4610654 CAAGAAAATG
Statistics
Matches: 130, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
131 22 0.17
132 108 0.83
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (130 bp):
GGATGGTATGCATGATAATGTATGTATATCTATATATATATATATATATGTTAATAAAAAGTTTT
GAAAATAATTGTGATTGTGTTGTATGTTGACATTGTTAATTGTTCCCAAATTGCTTTTCATTTCA
Found at i:4616087 original size:37 final size:37
Alignment explanation
Indices: 4616037--4616149 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
4616027 CCGAGCTTGA
*
4616037 CATGTGTGCACTCCCTACTCGCACACTCTAACATCAT
1 CATGTGTGCACTCCTTACTCGCACACTCTAACATCAT
4616074 CATGTGTGCACTCCTTACTCGCACACT-TCAACATCAT
1 CATGTGTGCACTCCTTACTCGCACACTCT-AACATCAT
*
4616111 CATGTGTGCACTCCTTACTCTCACACATC-AACATCAT
1 CATGTGTGCACTCCTTACTCGCACAC-TCTAACATCAT
4616148 CA
1 CA
4616150 CTCAACATTA
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
36 1 0.01
37 69 0.97
38 1 0.01
ACGTcount: A:0.26, C:0.36, G:0.10, T:0.28
Consensus pattern (37 bp):
CATGTGTGCACTCCTTACTCGCACACTCTAACATCAT
Found at i:4620252 original size:23 final size:23
Alignment explanation
Indices: 4620226--4620269 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4620216 TTTCTTCTTT
* *
4620226 CTTTTTTTTCTTTCTCTTTCTCC
1 CTTTTATTTCTCTCTCTTTCTCC
*
4620249 CTTTTATTTCTCTCTTTTTCT
1 CTTTTATTTCTCTCTCTTTCT
4620270 TGCTCTCGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (23 bp):
CTTTTATTTCTCTCTCTTTCTCC
Found at i:4623442 original size:28 final size:28
Alignment explanation
Indices: 4623408--4623462 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4623398 ATATTGCAAA
*
4623408 CAAATAAATTACACCAAACATAAATAAG
1 CAAATAAACTACACCAAACATAAATAAG
*
4623436 CAAATAAACTACATCAAACATAAATAA
1 CAAATAAACTACACCAAACATAAATAA
4623463 AATTTCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.18, G:0.02, T:0.18
Consensus pattern (28 bp):
CAAATAAACTACACCAAACATAAATAAG
Found at i:4624993 original size:19 final size:20
Alignment explanation
Indices: 4624955--4624997 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4624945 GAGCGAGAGA
4624955 GAAGAAAAGAGGTTAAAAAGT
1 GAAGAAAAGAGG-TAAAAAGT
*
4624976 GAAGACAAGAGG-AAAAAGT
1 GAAGAAAAGAGGTAAAAAGT
4624995 GAA
1 GAA
4624998 AATGAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.30, T:0.09
Consensus pattern (20 bp):
GAAGAAAAGAGGTAAAAAGT
Found at i:4631281 original size:18 final size:19
Alignment explanation
Indices: 4631258--4631299 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
4631248 ACAGAAAACA
4631258 AAGAC-AACTTAGTCGACT
1 AAGACAAACTTAGTCGACT
*
4631276 AAGACATAAGTTAGTCGACT
1 AAGACA-AACTTAGTCGACT
4631296 AAGA
1 AAGA
4631300 GCATTCTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
20 16 0.76
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (19 bp):
AAGACAAACTTAGTCGACT
Found at i:4631775 original size:35 final size:35
Alignment explanation
Indices: 4631709--4631780 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
4631699 GTTAGGTGTT
* * * *
4631709 AGGTTTTAGTTGATCTTGGTAAAAACTATTGTGAA
1 AGGTTTTAGTTGAGCCTGGTAAAAACCATTGTAAA
* *
4631744 AGGTTTTGGTTGAGCCTGGTAAAAGCCATTGTAAA
1 AGGTTTTAGTTGAGCCTGGTAAAAACCATTGTAAA
4631779 AG
1 AG
4631781 CTTGGTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (35 bp):
AGGTTTTAGTTGAGCCTGGTAAAAACCATTGTAAA
Found at i:4636061 original size:24 final size:24
Alignment explanation
Indices: 4636029--4636077 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4636019 TCAAATATTA
4636029 TGGATTAAACAACAACTAAAAGAC
1 TGGATTAAACAACAACTAAAAGAC
4636053 TGGATTAAACAACAACTAAAAGAC
1 TGGATTAAACAACAACTAAAAGAC
4636077 T
1 T
4636078 ATGGAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.18
Consensus pattern (24 bp):
TGGATTAAACAACAACTAAAAGAC
Found at i:4640829 original size:17 final size:17
Alignment explanation
Indices: 4640809--4640841 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4640799 TTCTTGATAA
4640809 AATAA-AACTTCTTATTG
1 AATAATAAC-TCTTATTG
4640826 AATAATAACTCTTATT
1 AATAATAACTCTTATT
4640842 TTATCATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:4641069 original size:29 final size:28
Alignment explanation
Indices: 4640992--4641440 Score: 418
Period size: 29 Copynumber: 15.6 Consensus size: 28
4640982 TCTTATCATT
* *
4640992 AATTAAGGTAAAACATGTTGTCTTGTCTA
1 AATTAA-GAAAAACATGTTTTCTTGTCTA
* *
4641021 AATTGAGATAAACATGTTTTCTTGTCTA
1 AATTAAGAAAAACATGTTTTCTTGTCTA
* * *
4641049 GATTAAGAGAAAACATATTTTTCTTGTCTGT
1 AATTAAGA-AAAACAT-GTTTTCTTGTCT-A
* *
4641080 AATTAAGACAAACATGTTTTTCTTGTCTTC
1 AATTAAGAAAAACATG-TTTTCTTGTC-TA
* * *
4641110 AATTAAGACAAACATG-TTTCTTATATA
1 AATTAAGAAAAACATGTTTTCTTGTCTA
* *
4641137 AATTAAGACAAGCATGTTTTCTTGTCTA
1 AATTAAGAAAAACATGTTTTCTTGTCTA
* *
4641165 AATTAAAACAAAATATG-TTTCATTGTCTA
1 AATTAAGA-AAAACATGTTTTC-TTGTCTA
* * * *
4641194 AATTAAAACAAAACATATTATTCTTGCCCA
1 AATTAAGA-AAAACATGTT-TTCTTGTCTA
*
4641224 AATTAAGACAAAACATGTTTTATTGTCTA
1 AATTAAGA-AAAACATGTTTTCTTGTCTA
*
4641253 AATTAAGAAAAAACATGTTTTCTTGTTTA
1 AATTAAG-AAAAACATGTTTTCTTGTCTA
* * *
4641282 AATTGAGAGAAACATGTTTTTTTGTCTA
1 AATTAAGAAAAACATGTTTTCTTGTCTA
* *
4641310 AATTAAGACAAAATATATTTTCTTGTCTA
1 AATTAAGA-AAAACATGTTTTCTTGTCTA
* *
4641339 AATTAAAAAAAACATGTCTTCTTGTCTA
1 AATTAAGAAAAACATGTTTTCTTGTCTA
* * * *
4641367 AGTTAAGACAAAACATATTTTTTTATCTA
1 AATTAAGA-AAAACATGTTTTCTTGTCTA
*
4641396 AATTAAGATAAAA-ATGTTTTCTTGTCCA
1 AATTAAGA-AAAACATGTTTTCTTGTCTA
* *
4641424 AATTAACACAAACATGT
1 AATTAAGAAAAACATGT
4641441 AAAAGTTGTC
Statistics
Matches: 345, Mismatches: 61, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
27 19 0.06
28 122 0.35
29 126 0.37
30 67 0.19
31 11 0.03
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
AATTAAGAAAAACATGTTTTCTTGTCTA
Found at i:4641152 original size:27 final size:28
Alignment explanation
Indices: 4641002--4641440 Score: 216
Period size: 28 Copynumber: 15.3 Consensus size: 28
4640992 AATTAAGGTA
* * * * *
4641002 AAACATGTTGTCTTGTCTAAATTGAGAT
1 AAACATGTTTTCTTATATAAATTAAGAC
* * * *
4641030 AAACATGTTTTCTTGTCTAGATTAAGAGA
1 AAACATGTTTTCTTATATAAATTAAGA-C
* * * *
4641059 AAACATATTTTTCTTGTCTGTAATTAAGAC
1 AAACAT-GTTTTCTTATAT-AAATTAAGAC
* * *
4641089 AAACATGTTTTTCTTGTCTTCAATTAAGAC
1 AAACATG-TTTTCTTAT-ATAAATTAAGAC
4641119 AAACATG-TTTCTTATATAAATTAAGAC
1 AAACATGTTTTCTTATATAAATTAAGAC
* * * *
4641146 AAGCATGTTTTCTTGTCTAAATTAAAAC
1 AAACATGTTTTCTTATATAAATTAAGAC
* * * *
4641174 AAA-ATATGTTTCATTGTCTAAATTAAAAC
1 AAACATGT-TTTC-TTATATAAATTAAGAC
* ****
4641203 AAAACATATTATTCTTGCCCAAATTAAGAC
1 -AAACATGTT-TTCTTATATAAATTAAGAC
* * * *
4641233 AAAACATGTTTTATTGTCTAAATTAAGAAA
1 -AAACATGTTTTCTTATATAAATTAAG-AC
* * * *
4641263 AAACATGTTTTCTTGTTTAAATTGAGAG
1 AAACATGTTTTCTTATATAAATTAAGAC
* * *
4641291 AAACATGTTTTTTTGTCTAAATTAAGAC
1 AAACATGTTTTCTTATATAAATTAAGAC
* * * * * *
4641319 AAAATATATTTTCTTGTCTAAATTAAAAA
1 -AAACATGTTTTCTTATATAAATTAAGAC
* * * *
4641348 AAACATGTCTTCTTGTCTAAGTTAAGAC
1 AAACATGTTTTCTTATATAAATTAAGAC
* * * *
4641376 AAAACATATTTTTTTATCTAAATTAAGAT
1 -AAACATGTTTTCTTATATAAATTAAGAC
* * ** *
4641405 AAAAATGTTTTCTTGTCCAAATTAACAC
1 AAACATGTTTTCTTATATAAATTAAGAC
4641433 AAACATGT
1 AAACATGT
4641441 AAAAGTTGTC
Statistics
Matches: 336, Mismatches: 61, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
27 19 0.06
28 129 0.38
29 104 0.31
30 69 0.21
31 15 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
AAACATGTTTTCTTATATAAATTAAGAC
Found at i:4641154 original size:57 final size:56
Alignment explanation
Indices: 4641002--4641440 Score: 393
Period size: 57 Copynumber: 7.6 Consensus size: 56
4640992 AATTAAGGTA
* * * *
4641002 AAACATGTTGTCTTGTCTAAATTGAGATAAACATG-TTTTCTTGTCTAGATTAAGAGA
1 AAACATGTT-TCTTGTCTAAATTAAGACAAACATGTTTTTCTTGTCTAAATTAAGA-C
* * *
4641059 AAACATATTTTTCTTGTCTGTAATTAAGACAAACATGTTTTTCTTGTCTTCAATTAAGAC
1 AAAC--ATGTTTCTTGTCT-AAATTAAGACAAACATGTTTTTCTTGTC-TAAATTAAGAC
* * * *
4641119 AAACATGTTTCTTATATAAATTAAGACAAGCATG-TTTTCTTGTCTAAATTAAAAC
1 AAACATGTTTCTTGTCTAAATTAAGACAAACATGTTTTTCTTGTCTAAATTAAGAC
* * * * * *
4641174 AAAATATGTTTCATTGTCTAAATTAAAACAAAACATATTATTCTTGCCCAAATTAAGAC
1 -AAACATGTTTC-TTGTCTAAATTAAGAC-AAACATGTTTTTCTTGTCTAAATTAAGAC
* * * * *
4641233 AAAACATGTTTTATTGTCTAAATTAAGAAAAAACATG-TTTTCTTGTTTAAATTGAGAG
1 -AAACATG-TTTCTTGTCTAAATTAAG-ACAAACATGTTTTTCTTGTCTAAATTAAGAC
* * * *
4641291 AAACATGTTTTTTTGTCTAAATTAAGACAAA-ATATATTTTCTTGTCTAAATTAAAAA
1 AAACATG-TTTCTTGTCTAAATTAAGACAAACATGT-TTTTCTTGTCTAAATTAAGAC
* * * *
4641348 AAACATGTCTTCTTGTCTAAGTTAAGACAAAACATATTTTT-TTATCTAAATTAAGAT
1 AAACATGT-TTCTTGTCTAAATTAAGAC-AAACATGTTTTTCTTGTCTAAATTAAGAC
* * *
4641405 AAAAATGTTTTCTTGTCCAAATTAACACAAACATGT
1 AAACATG-TTTCTTGTCTAAATTAAGACAAACATGT
4641441 AAAAGTTGTC
Statistics
Matches: 313, Mismatches: 52, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
55 11 0.04
56 32 0.10
57 133 0.42
58 46 0.15
59 65 0.21
60 18 0.06
61 8 0.03
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (56 bp):
AAACATGTTTCTTGTCTAAATTAAGACAAACATGTTTTTCTTGTCTAAATTAAGAC
Found at i:4642902 original size:36 final size:37
Alignment explanation
Indices: 4642854--4642967 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
4642844 TATATGCATT
*
4642854 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCTCTACTCGCACACTTCAA
* *
4642891 CATCAT-ATGTGTGCACTCTTTACTCGTACAC-TCTAA
1 CATCATCATGTGTGCACTCTCTACTCGCACACTTC-AA
* *
4642927 TATCATCATGTGTGCACTCTCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCTCTACTCGCACACTTCAA
4642964 CATC
1 CATC
4642968 CTCACACAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.03
36 29 0.44
37 33 0.50
38 2 0.03
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.32
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCTCTACTCGCACACTTCAA
Found at i:4643791 original size:25 final size:25
Alignment explanation
Indices: 4643761--4643835 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
4643751 CATGAAGATA
4643761 AAGAAACGTGAGAGGGGAAAGGAAG
1 AAGAAACGTGAGAGGGGAAAGGAAG
**
4643786 AAGAAA--TG-G-CTGG-AA-GATA-
1 AAGAAACGTGAGAGGGGAAAGGA-AG
4643805 AAGAAACGTGAGAGGGGAAAGGAAG
1 AAGAAACGTGAGAGGGGAAAGGAAG
4643830 AAGAAA
1 AAGAAA
4643836 TGGCTGGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
19 8 0.21
20 3 0.08
21 4 0.11
22 2 0.05
23 4 0.11
24 3 0.08
25 14 0.37
ACGTcount: A:0.51, C:0.04, G:0.39, T:0.07
Consensus pattern (25 bp):
AAGAAACGTGAGAGGGGAAAGGAAG
Found at i:4643803 original size:44 final size:44
Alignment explanation
Indices: 4643754--4643845 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
4643744 AGGCTCCCAT
4643754 GAAGATAAAGAAACGTGAGAGGGGAAAGGAAGAAGAAATGGCTG
1 GAAGATAAAGAAACGTGAGAGGGGAAAGGAAGAAGAAATGGCTG
4643798 GAAGATAAAGAAACGTGAGAGGGGAAAGGAAGAAGAAATGGCTG
1 GAAGATAAAGAAACGTGAGAGGGGAAAGGAAGAAGAAATGGCTG
4643842 GAAG
1 GAAG
4643846 CTACTGGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (44 bp):
GAAGATAAAGAAACGTGAGAGGGGAAAGGAAGAAGAAATGGCTG
Found at i:4660309 original size:18 final size:17
Alignment explanation
Indices: 4660283--4660316 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4660273 TTAAACAAAA
*
4660283 ATGACAACAATGTAAATG
1 ATGAAAACAAT-TAAATG
4660301 ATGAAAACAATTAAAT
1 ATGAAAACAATTAAAT
4660317 AAAGATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
ATGAAAACAATTAAATG
Found at i:4661558 original size:22 final size:22
Alignment explanation
Indices: 4661517--4661558 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4661507 AAAAAGTAAC
*
4661517 TAAATAAACTTAAAATATAAAA
1 TAAATAAACTTAAAACATAAAA
* *
4661539 TAAATAAATTTAAAGCATAA
1 TAAATAAACTTAAAACATAA
4661559 CTAAAAACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATAAACTTAAAACATAAAA
Found at i:4661970 original size:23 final size:23
Alignment explanation
Indices: 4661944--4661989 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
4661934 AAGATAGACT
*
4661944 TTAACCACCTTGAAGGGACTAGA
1 TTAACCACCTTGAAAGGACTAGA
4661967 TTAACCACCTTGAAAGGACTAGA
1 TTAACCACCTTGAAAGGACTAGA
4661990 CCATCTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
TTAACCACCTTGAAAGGACTAGA
Found at i:4663052 original size:16 final size:16
Alignment explanation
Indices: 4663031--4663062 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4663021 TTACCATTCC
*
4663031 TTAAAGTAATTTCCTT
1 TTAAAGTAATTGCCTT
4663047 TTAAAGTAATTGCCTT
1 TTAAAGTAATTGCCTT
4663063 ACATTGTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (16 bp):
TTAAAGTAATTGCCTT
Found at i:4670506 original size:19 final size:20
Alignment explanation
Indices: 4670484--4670524 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4670474 ATAAGAGAAA
4670484 ATTTTTA-GAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
*
4670503 A-TTTTATTAATAAAATAAT
1 ATTTTTATGAATAAAATAAT
4670522 ATT
1 ATT
4670525 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 5 0.26
19 13 0.68
20 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTTTATGAATAAAATAAT
Found at i:4672272 original size:42 final size:42
Alignment explanation
Indices: 4672213--4672315 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
4672203 GTGATAATTA
*
4672213 TGACCCAGCCATATGCGGTGTAACAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGTAACAGTGCACATGAGCTGTGC
*
4672255 TGACCCAGCCATGTGCGGTGTAGCAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGTAACAGTGCACATGAGCTGTGC
* *
4672297 TAACCC-GACTATGTGCGGT
1 TGACCCAG-CCATGTGCGGT
4672316 ATGGTAGTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
41 1 0.02
42 55 0.98
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.22
Consensus pattern (42 bp):
TGACCCAGCCATGTGCGGTGTAACAGTGCACATGAGCTGTGC
Found at i:4672325 original size:42 final size:42
Alignment explanation
Indices: 4672215--4672334 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 42
4672205 GATAATTATG
* * * *
4672215 ACCCAGCCATATGCGGTGTAACAGTGCACATGAGCTGTGCTG
1 ACCCAGCCATGTGCGGTATAGCAGTGCACATGAGCTGTGCTA
*
4672257 ACCCAGCCATGTGCGGTGTAGCAGTGCACATGAGCTGTGCTA
1 ACCCAGCCATGTGCGGTATAGCAGTGCACATGAGCTGTGCTA
* * * *
4672299 ACCC-GACTATGTGCGGTATGGTAGTGCACATAAGCT
1 ACCCAG-CCATGTGCGGTATAGCAGTGCACATGAGCT
4672335 TAGACAGAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.01
42 68 0.99
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (42 bp):
ACCCAGCCATGTGCGGTATAGCAGTGCACATGAGCTGTGCTA
Found at i:4672381 original size:2 final size:2
Alignment explanation
Indices: 4672376--4672422 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
4672366 TATATGTGTT
4672376 TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4672419 TA TA
1 TA TA
4672423 GGTTTTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4674042 original size:61 final size:61
Alignment explanation
Indices: 4673939--4674054 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
4673929 GCTGCAACTT
* * * * *
4673939 TGTCATGACCCAAATTCCGGGCCATGACCGGTGCATGGGCCCAATGGACATAGTCCACTAA
1 TGTCACGACCCAAATTCCGGGCCATGACCGATGCAAGAGCCCAATAGACATAGTCCACTAA
* * * *
4674000 TGTCACGACCCAATTTTCGGGTCATGACCGATGCAAGAGCCCAATAGACGTAGTC
1 TGTCACGACCCAAATTCCGGGCCATGACCGATGCAAGAGCCCAATAGACATAGTC
4674055 TATTAAGCCC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (61 bp):
TGTCACGACCCAAATTCCGGGCCATGACCGATGCAAGAGCCCAATAGACATAGTCCACTAA
Found at i:4675385 original size:43 final size:43
Alignment explanation
Indices: 4675334--4675452 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 43
4675324 TCACCAGCTC
** *
4675334 ATGCGCACTCCCTACTCGCACATGGCTAGGTCATCAC-CGGGC-T
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATC-CTC-GGCTT
*
4675377 ATGTGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
* *
4675420 ATGCGCACTCCCTACTCGCACATAGCCAAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCA
4675453 ATGTCATTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 4 0.06
43 63 0.94
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
Found at i:4680465 original size:20 final size:20
Alignment explanation
Indices: 4680436--4680478 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4680426 ATTAGGTTAC
4680436 TTTTAAGTTAGTTATTTTAA
1 TTTTAAGTTAGTTATTTTAA
* * *
4680456 TTTTATGTTATTTCTTTTAA
1 TTTTAAGTTAGTTATTTTAA
4680476 TTT
1 TTT
4680479 GTTTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTAAGTTAGTTATTTTAA
Found at i:4683226 original size:26 final size:26
Alignment explanation
Indices: 4683197--4683249 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4683187 GACCAGCCTG
4683197 AGCCTAACCCGTAAGAGCAGCGAGAA
1 AGCCTAACCCGTAAGAGCAGCGAGAA
**
4683223 AGCCTGGCCCGTAAGAGCAGCGAGAA
1 AGCCTAACCCGTAAGAGCAGCGAGAA
4683249 A
1 A
4683250 AGCCGCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.30, T:0.08
Consensus pattern (26 bp):
AGCCTAACCCGTAAGAGCAGCGAGAA
Found at i:4692022 original size:12 final size:13
Alignment explanation
Indices: 4692002--4692040 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
4691992 TTATTATTTT
*
4692002 TAAAAAATAA-AA
1 TAAATAATAATAA
4692014 TAAATAATAATAA
1 TAAATAATAATAA
4692027 -AAATAATAATAA
1 TAAATAATAATAA
4692039 TA
1 TA
4692041 GTAAATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAATAATAA
Found at i:4692027 original size:15 final size:15
Alignment explanation
Indices: 4692010--4692040 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
4692000 TTTAAAAAAT
4692010 AAAATAAATAATAATA
1 AAAAT-AATAATAATA
4692026 AAAATAATAATAATA
1 AAAATAATAATAATA
4692041 GTAAATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:4693054 original size:2 final size:2
Alignment explanation
Indices: 4693047--4693081 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4693037 ATCATCTCGA
*
4693047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4693082 AATTATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4694951 original size:18 final size:18
Alignment explanation
Indices: 4694920--4694956 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4694910 TAAACTCTAG
*
4694920 GAGAAGAAGAAAGAAAAA
1 GAGAAAAAGAAAGAAAAA
*
4694938 GAGAAAAAGGAAGAAAAA
1 GAGAAAAAGAAAGAAAAA
4694956 G
1 G
4694957 CTTGGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
GAGAAAAAGAAAGAAAAA
Found at i:4697840 original size:9 final size:9
Alignment explanation
Indices: 4697826--4697919 Score: 143
Period size: 9 Copynumber: 10.4 Consensus size: 9
4697816 AATAATACTT
4697826 TTAACACGA
1 TTAACACGA
*
4697835 TTAACACGT
1 TTAACACGA
*
4697844 TTAACATGA
1 TTAACACGA
4697853 TTAACACGA
1 TTAACACGA
*
4697862 TTAACACGT
1 TTAACACGA
4697871 TTAACACGA
1 TTAACACGA
*
4697880 TTAACACGT
1 TTAACACGA
4697889 TTAACACGA
1 TTAACACGA
*
4697898 TTAACACGT
1 TTAACACGA
4697907 TTAACACGA
1 TTAACACGA
4697916 TTAA
1 TTAA
4697920 ATAAAAATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 75 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (9 bp):
TTAACACGA
Found at i:4698187 original size:18 final size:18
Alignment explanation
Indices: 4698164--4698219 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
4698154 ATAAATGTGT
4698164 CATGTATACTCGTTTAAA
1 CATGTATACTCGTTTAAA
4698182 CATGTATA-TACGTTTAAA
1 CATGTATACT-CGTTTAAA
* * *
4698200 CACGTATACACATTTAAA
1 CATGTATACTCGTTTAAA
4698218 CA
1 CA
4698220 CGATAACACG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (18 bp):
CATGTATACTCGTTTAAA
Found at i:4703347 original size:245 final size:244
Alignment explanation
Indices: 4702918--4703402 Score: 790
Period size: 245 Copynumber: 2.0 Consensus size: 244
4702908 TAGTTACCTG
*
4702918 ATTGTATGTGCTGATGATACTGTTTCATATAAGATGGTAGCAAACTAGAGTGGAATGAAATTAAT
1 ATTGTATGTGCCGATGATACTGTTTCATATAAGATGGTAGCAAACTAGAGTGGAATGAAATTAAT
* *
4702983 TTCAGGTTAAAACATCAAAATACTCCAAAAATGAGATTATGCTTCAACGATAACTATGATTATGA
66 TTCAGGTTAAAACATCAAAATACTCCAAAAATGAGATTACGCTTCAACGATAACTATGATGATGA
* * *
4703048 AAATTTGACACAACAGCATTCATTTGGAAAAATGTTGAGTTGGGCATGTAAAACACAGCAATCAT
131 AAATTTGACACAACAGCATTCATTTGGAAAAATGCTGACTTGGGCATGTAAAACACAACAATCAT
* *
4703113 AGTCTGCAAAACTCCCATAATGATATTTAAAAAAATTGTATTTTTGATC
196 AGTCTGCAAAACTCCCATAACGATATTTAAAAAAAATGTATTTTTGATC
*
4703162 ATTGTATGTGCCGATGATACTGTTTCATATAAGATGGTAGCAAAACTGGAGTGGAATGAAATTAA
1 ATTGTATGTGCCGATGATACTGTTTCATATAAGATGGTAGC-AAACTAGAGTGGAATGAAATTAA
* * * * * * *
4703227 TTTCATGTTAAATCATCAAAATACTCCAAAAATGAGGTTACGCTTGAATGGTATCTATGATGATG
65 TTTCAGGTTAAAACATCAAAATACTCCAAAAATGAGATTACGCTTCAACGATAACTATGATGATG
* *
4703292 AAAATTTGACACAATAGCATTCATTTGGAAAAATGCTGACTTGGGTATGTAAAACACAACAATCA
130 AAAATTTGACACAACAGCATTCATTTGGAAAAATGCTGACTTGGGCATGTAAAACACAACAATCA
*
4703357 TAGTGTGCAAAACTCCCATAACGATATTTAAAAAAAATGTATTTTT
195 TAGTCTGCAAAACTCCCATAACGATATTTAAAAAAAATGTATTTTT
4703403 TATTTATTGT
Statistics
Matches: 221, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
244 40 0.18
245 181 0.82
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (244 bp):
ATTGTATGTGCCGATGATACTGTTTCATATAAGATGGTAGCAAACTAGAGTGGAATGAAATTAAT
TTCAGGTTAAAACATCAAAATACTCCAAAAATGAGATTACGCTTCAACGATAACTATGATGATGA
AAATTTGACACAACAGCATTCATTTGGAAAAATGCTGACTTGGGCATGTAAAACACAACAATCAT
AGTCTGCAAAACTCCCATAACGATATTTAAAAAAAATGTATTTTTGATC
Found at i:4709620 original size:29 final size:30
Alignment explanation
Indices: 4709584--4709656 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
4709574 AAATATTTAT
4709584 AATATCCATAATAGCTAAACAAG-ATATAC
1 AATATCCATAATAGCTAAACAAGCATATAC
* * **
4709613 AATATCCATAGTAGCTAAGCAAGCTATATTG
1 AATATCCATAATAGCTAAACAAGC-ATATAC
4709644 AATATCCATAATA
1 AATATCCATAATA
4709657 ACTAGCACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (30 bp):
AATATCCATAATAGCTAAACAAGCATATAC
Found at i:4710137 original size:45 final size:45
Alignment explanation
Indices: 4709993--4710139 Score: 215
Period size: 45 Copynumber: 3.2 Consensus size: 45
4709983 AGATCACTCA
* * * *
4709993 AATAATGTTCAAGCAAGTCTGATCATTTTATCATAATCAAAATTAT
1 AATAAT-TTTAAGCAAATTTGATCATTTTGTCATAATCAAAATTAT
*
4710039 AATAATTTAAAGCAAATTTGATCATTTTGTCATAATC-AAATCTAT
1 AATAATTTTAAGCAAATTTGATCATTTTGTCATAATCAAAAT-TAT
*
4710084 AATAATTTTAAGCAAATTTGATCATTTTGTCATAATCAAAATTGT
1 AATAATTTTAAGCAAATTTGATCATTTTGTCATAATCAAAATTAT
4710129 AATAATTTTAA
1 AATAATTTTAA
4710140 TGTCAAGCCC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
44 4 0.04
45 79 0.85
46 10 0.11
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (45 bp):
AATAATTTTAAGCAAATTTGATCATTTTGTCATAATCAAAATTAT
Found at i:4713885 original size:20 final size:20
Alignment explanation
Indices: 4713860--4713899 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4713850 GCATAAATAT
4713860 CTCATTCCTCCAACAGCTTC
1 CTCATTCCTCCAACAGCTTC
** *
4713880 CTCATTTTTCCAGCAGCTTC
1 CTCATTCCTCCAACAGCTTC
4713900 TTCTTCTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.07, T:0.35
Consensus pattern (20 bp):
CTCATTCCTCCAACAGCTTC
Found at i:4714763 original size:43 final size:43
Alignment explanation
Indices: 4714704--4714796 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
4714694 TTGTGTGATA
*
4714704 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATAAGTTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATAAGCTG
*
4714747 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATAAGCTG
4714790 ATGATGA
1 ATGATGA
4714797 TGATATTGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATAAGCTG
Found at i:4714812 original size:46 final size:46
Alignment explanation
Indices: 4714699--4714836 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 46
4714689 TCCTTTTGTG
* * *
4714699 TGATAATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATAAG-
1 TGATGATGATGACACAGCTATGTGCGGTGTGGGAGTGCACATGAGC
*
4714744 T--TGATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGC
1 TGATGATGATGACACAGCTATGTGCGGTGTGGGAGTGCACATGAGC
* ** *
4714788 TGATGATGATGATATTGC-ATTGTGC-GTGTAGGGAGTGCACATGATC
1 TGATGATGATGACACAGCTA-TGTGCGGTGT-GGGAGTGCACATGAGC
4714834 TGA
1 TGA
4714837 GTGTGGCAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
43 40 0.49
44 1 0.01
45 6 0.07
46 34 0.42
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (46 bp):
TGATGATGATGACACAGCTATGTGCGGTGTGGGAGTGCACATGAGC
Found at i:4721137 original size:2 final size:2
Alignment explanation
Indices: 4721130--4721173 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4721120 CTAAACGTGT
4721130 AG AG AG AG AG AG 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 AG AG AG AG AG AG
4721172 AG
1 AG
4721174 TGTGTGTGNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4721988 original size:43 final size:43
Alignment explanation
Indices: 4721928--4722020 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
4721918 TTGTGTGATA
* *
4721928 ATGATGACCCATCTATGTGCGGTGTGGGAGTGCACATAAGTTG
1 ATGATGACCCATCTATGTGCGATGTGGGAGTGCACATAAGCTG
* *
4721971 ATGATGACCCAGT-TATGTGCGATGTGGGAGTGGACATGAGCTG
1 ATGATGACCCA-TCTATGTGCGATGTGGGAGTGCACATAAGCTG
4722014 ATGATGA
1 ATGATGA
4722021 TGATATTGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 44 0.98
44 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (43 bp):
ATGATGACCCATCTATGTGCGATGTGGGAGTGCACATAAGCTG
Found at i:4728592 original size:19 final size:20
Alignment explanation
Indices: 4728568--4728605 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4728558 CTATAAATAC
4728568 CTTGAA-TTTCCAGTAGCTT
1 CTTGAATTTTCCAGTAGCTT
4728587 CTTGAATTTTCCAGTAGCT
1 CTTGAATTTTCCAGTAGCT
4728606 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (20 bp):
CTTGAATTTTCCAGTAGCTT
Found at i:4729469 original size:43 final size:43
Alignment explanation
Indices: 4729399--4729510 Score: 161
Period size: 43 Copynumber: 2.6 Consensus size: 43
4729389 TATTGACTCG
* * *
4729399 GCTATGTGCGAGTAGGGAGTGCACATAAGCCGATGATGACCTG
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCTA
* * *
4729442 GTTATGGGCGAGTACGGAGTGCGCATAACCCGATGATGACCTA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCTA
*
4729485 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
4729511 GAGCTGGTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCTA
Found at i:4729888 original size:21 final size:21
Alignment explanation
Indices: 4729845--4729890 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4729835 ACACTGTAGC
* *
4729845 TTCTCGCTGCAGTGAAATGCA
1 TTCTCGCTGCAGCGAAATACA
4729866 TTCTCGCTGCAGCGAGAA-ACA
1 TTCTCGCTGCAGCGA-AATACA
4729887 TTCT
1 TTCT
4729891 GTTTTCTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (21 bp):
TTCTCGCTGCAGCGAAATACA
Found at i:4729990 original size:60 final size:61
Alignment explanation
Indices: 4729867--4730016 Score: 221
Period size: 60 Copynumber: 2.5 Consensus size: 61
4729857 TGAAATGCAT
* * *
4729867 TCTCGCTGCAGCGAGAAACATTCTGTTTTCTGGGTTGCAATTTCACTGCAGCGAGATTGAA
1 TCTCGCTGCAGCGAGAAACATTCTGTTTTCTGGGTAGAAATTTCACTACAGCGAGATTGAA
*
4729928 TCTCGCTGCAGCGAGAAACATTCTGTTTT-TGGGTAGAAATTTCACTACATCGAGATTGAA
1 TCTCGCTGCAGCGAGAAACATTCTGTTTTCTGGGTAGAAATTTCACTACAGCGAGATTGAA
* * * *
4729988 TCTTGTTGCAGCGAAAAACTTTCTGTTTT
1 TCTCGCTGCAGCGAGAAACATTCTGTTTT
4730017 GGTCTCTTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 52 0.64
61 29 0.36
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (61 bp):
TCTCGCTGCAGCGAGAAACATTCTGTTTTCTGGGTAGAAATTTCACTACAGCGAGATTGAA
Found at i:4733236 original size:23 final size:22
Alignment explanation
Indices: 4733190--4733236 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4733180 AGTTTGACCC
*
4733190 TTAATCGATTAACCCTTTTTGT
1 TTAATCGATTAAACCTTTTTGT
4733212 TTAATCGATTATTAACC-TTTTGT
1 TTAATCGATTA--AACCTTTTTGT
4733235 TT
1 TT
4733237 TGTGTCTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
23 8 0.36
24 3 0.14
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.53
Consensus pattern (22 bp):
TTAATCGATTAAACCTTTTTGT
Found at i:4733631 original size:67 final size:67
Alignment explanation
Indices: 4733523--4733698 Score: 239
Period size: 67 Copynumber: 2.6 Consensus size: 67
4733513 GTTTAGCCAA
* * * *
4733523 AACCTTTCACAATAGTTTTT-ACAAGGAACAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCAC-GGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
4733587 CAC
65 CAC
*
4733590 AACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
4733655 AC
66 AC
* * * *
4733657 AACC-TACAACAGTGGTTTTTCATGGGATCAACCAAGACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
4733699 CAACTAACTT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
66 2 0.02
67 93 0.96
68 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:4733643 original size:32 final size:32
Alignment explanation
Indices: 4733551--4733698 Score: 145
Period size: 35 Copynumber: 4.4 Consensus size: 32
4733541 TTACAAGGAA
*
4733551 CAACTAAAACCCAAAGTGGTTTTTCAAAGGCT
1 CAACCAAAACCCAAAGTGGTTTTTCAAAGGCT
* **
4733583 CAACCACAACCTTTCACAA-TGGTTTTTCACGGGCT
1 CAACCAAAACC---CA-AAGTGGTTTTTCAAAGGCT
4733618 CAACCAAAACCCAAAGTGGTTTTTCAAAGGCT
1 CAACCAAAACCCAAAGTGGTTTTTCAAAGGCT
* ** *
4733650 CAACCACAACCTACAACAGTGGTTTTTCATGGGAT
1 CAACCAAAACC--CAA-AGTGGTTTTTCAAAGGCT
*
4733685 CAACCAAGACCCAA
1 CAACCAAAACCCAA
4733699 CAACTAACTT
Statistics
Matches: 95, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.02
32 35 0.37
33 3 0.03
34 3 0.03
35 50 0.53
36 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (32 bp):
CAACCAAAACCCAAAGTGGTTTTTCAAAGGCT
Found at i:4734151 original size:20 final size:20
Alignment explanation
Indices: 4734109--4734151 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4734099 GACAGAGAGC
* *
4734109 TCTTAGTCGACTAACTTCTT
1 TCTTAGTCAACTAACTTCGT
* *
4734129 TCTTAGTCAATTAACTTGGT
1 TCTTAGTCAACTAACTTCGT
4734149 TCT
1 TCT
4734152 ATCATTTGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (20 bp):
TCTTAGTCAACTAACTTCGT
Found at i:4734579 original size:17 final size:17
Alignment explanation
Indices: 4734557--4734594 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
4734547 AATGGAGGAT
4734557 TGCTCCCCCTAAGTGTG
1 TGCTCCCCCTAAGTGTG
*
4734574 TGCTCCCCCTTAGTGTG
1 TGCTCCCCCTAAGTGTG
4734591 TGCT
1 TGCT
4734595 TATTTTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.34, G:0.24, T:0.34
Consensus pattern (17 bp):
TGCTCCCCCTAAGTGTG
Found at i:4739384 original size:43 final size:43
Alignment explanation
Indices: 4739268--4739389 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
4739258 TTCATCGTCG
** *
4739268 TGTGCACTCCCTACTCGCACATAGTCAAGTCATCATCGACTTA
1 TGTGCACTCCCTACTCGCACATAGTCGGGTCATCATCGACTCA
*
4739311 TGCGCACTCCCTACTCGCACATAGTCGGGTCATCATC-AGCTCA
1 TGTGCACTCCCTACTCGCACATAGTCGGGTCATCATCGA-CTCA
* *
4739354 TGTGCACTCCC-ACATTGCACATAGTTGGGTCATCAT
1 TGTGCACTCCCTAC-TCGCACATAGTCGGGTCATCAT
4739390 TATCACACAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.04
43 67 0.96
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (43 bp):
TGTGCACTCCCTACTCGCACATAGTCGGGTCATCATCGACTCA
Found at i:4740907 original size:2 final size:2
Alignment explanation
Indices: 4740902--4740926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4740892 ACACATATTT
4740902 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4740927 TATATATACA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4741861 original size:19 final size:20
Alignment explanation
Indices: 4741827--4741864 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4741817 GAAGAAGACC
4741827 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
4741847 AGCTGCTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
4741865 GTATTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:4742845 original size:20 final size:20
Alignment explanation
Indices: 4742820--4742859 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4742810 AAAAGAACAA
*
4742820 GAAGCTGCTGGAAAAATGAG
1 GAAGCTGCTAGAAAAATGAG
*
4742840 GAAGCTGCTAGAGAAATGAG
1 GAAGCTGCTAGAAAAATGAG
4742860 ATATTTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (20 bp):
GAAGCTGCTAGAAAAATGAG
Found at i:4747954 original size:35 final size:33
Alignment explanation
Indices: 4747915--4748011 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 33
4747905 GCCAAAGCGA
4747915 TTTTTCAAAGGCTCAACCACAACCTTTCACAA-TGG
1 TTTTTCAAAGGCTCAACCACAACC--TC-CAACTGG
** *
4747950 TTTTTCATGGGCTCAACCAAAACC-CCAACTGG
1 TTTTTCAAAGGCTCAACCACAACCTCCAACTGG
*
4747982 TTTTTCAAAGGCTCAACCACAACCTACAAC
1 TTTTTCAAAGGCTCAACCACAACCTCCAAC
4748012 AGTGGTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 3 0.06
32 25 0.47
33 4 0.08
35 21 0.40
ACGTcount: A:0.32, C:0.31, G:0.11, T:0.26
Consensus pattern (33 bp):
TTTTTCAAAGGCTCAACCACAACCTCCAACTGG
Found at i:4747986 original size:67 final size:67
Alignment explanation
Indices: 4747915--4748041 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 67
4747905 GCCAAAGCGA
* * * * *
4747915 TTTTTCAAAGGCTCAACCACAACCTTTC-ACAATGGTTTTTCATGGGCTCAACCAAAACCCCAAC
1 TTTTTCAAAGGCTCAACCACAACC-TACAACAATGGTTATTCACGAGATCAACCAAAACCCCAAC
4747979 TGG
65 TGG
*
4747982 TTTTTCAAAGGCTCAACCACAACCTACAACAGTGGTTATTCACGAGATCAACCAAAACCC
1 TTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTATTCACGAGATCAACCAAAACCC
4748042 TACAACTAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 2 0.04
67 51 0.96
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (67 bp):
TTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTATTCACGAGATCAACCAAAACCCCAACT
GG
Found at i:4747988 original size:32 final size:33
Alignment explanation
Indices: 4747915--4748041 Score: 96
Period size: 35 Copynumber: 3.8 Consensus size: 33
4747905 GCCAAAGCGA
* * *
4747915 TTTTTCAAAGGCTCAACCACAACCTTTC-ACAATGG
1 TTTTTCAAGGGCTCAACCAAAACC--CCAAC-ATGG
*
4747950 TTTTTCATGGGCTCAACCAAAACCCCAAC-TGG
1 TTTTTCAAGGGCTCAACCAAAACCCCAACATGG
* * *
4747982 TTTTTCAAAGGCTCAACCACAACCTACAACAGTGG
1 TTTTTCAAGGGCTCAACCAAAACC-CCAACA-TGG
* * * *
4748017 TTATTCACGAGATCAACCAAAACCC
1 TTTTTCAAGGGCTCAACCAAAACCC
4748042 TACAACTAAC
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
32 24 0.33
33 5 0.07
34 2 0.03
35 42 0.58
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (33 bp):
TTTTTCAAGGGCTCAACCAAAACCCCAACATGG
Found at i:4754458 original size:15 final size:15
Alignment explanation
Indices: 4754433--4754473 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4754423 GATCAGAGAT
4754433 TTTGGTTTTAAAG-C
1 TTTGGTTTTAAAGTC
*
4754447 TTTGGATTTTAAAGTT
1 TTTGG-TTTTAAAGTC
4754463 TTTGGTTTTAA
1 TTTGGTTTTAA
4754474 GGTTGTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (15 bp):
TTTGGTTTTAAAGTC
Found at i:4759629 original size:29 final size:29
Alignment explanation
Indices: 4759591--4759667 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
4759581 AAATATTTAT
*
4759591 AATATCCATAATAACTAAACAAGTTATAC
1 AATATCCATAATAACTAAACAAGATATAC
* * * * *
4759620 AATATGCATATTAGCTAAGCAAGATATATTG
1 AATATCCATAATAACTAAACAAGATATA--C
*
4759651 AATATCCATTATAACTA
1 AATATCCATAATAACTA
4759668 GTAGGCAATA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 23 0.64
31 13 0.36
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (29 bp):
AATATCCATAATAACTAAACAAGATATAC
Found at i:4760064 original size:45 final size:45
Alignment explanation
Indices: 4759994--4760096 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
4759984 AAGGATCACT
*
4759994 TAATAATGTTCAAGCAAATTTGATCATTTTGTCATAATCAAAACTA
1 TAATAAT-TTTAAGCAAATTTGATCATTTTGTCATAATCAAAACTA
* *
4760040 TAATAATTTTAAGGAAATTTGATCATTTTGTCATGATCAAAACTA
1 TAATAATTTTAAGCAAATTTGATCATTTTGTCATAATCAAAACTA
*
4760085 CAATAATTTTAA
1 TAATAATTTTAA
4760097 AGTTGACAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 46 0.87
46 7 0.13
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (45 bp):
TAATAATTTTAAGCAAATTTGATCATTTTGTCATAATCAAAACTA
Found at i:4766259 original size:20 final size:20
Alignment explanation
Indices: 4766236--4766273 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4766226 TTACAAGGGA
4766236 AAATATATCGATACATTCCC
1 AAATATATCGATACATTCCC
* *
4766256 AAATGTATGGATACATTC
1 AAATATATCGATACATTC
4766274 TTGGCAGAAT
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:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
AAATATATCGATACATTCCC
Found at i:4769939 original size:2 final size:2
Alignment explanation
Indices: 4769932--4769964 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4769922 ACCCTAACTT
*
4769932 TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4769965 AACCCTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:4770554 original size:2 final size:2
Alignment explanation
Indices: 4770547--4770573 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4770537 GTATATGTAC
4770547 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4770574 ACTATATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4778105 original size:27 final size:27
Alignment explanation
Indices: 4778075--4778133 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
4778065 AGCTATGTCC
*
4778075 TTAGTT-TTAATTATAATTTAG-TTATTT
1 TTAGTTGTT-ATTATAA-TTAGTTTAATT
*
4778102 TTAGTTGTTTTTATAATTAGTTTAATT
1 TTAGTTGTTATTATAATTAGTTTAATT
4778129 TTAGT
1 TTAGT
4778134 GAGTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 22 0.79
28 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (27 bp):
TTAGTTGTTATTATAATTAGTTTAATT
Found at i:4785365 original size:35 final size:35
Alignment explanation
Indices: 4785294--4785367 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
4785284 TTGCTCTTAT
** * *
4785294 AAAAGGACATTGTATGGGTTGTGTTTGAGCCCAAA
1 AAAAGGACATTGTAAAGGTTATGCTTGAGCCCAAA
**
4785329 AAAAGG-CATTGTAAAGGTTATGCTTGAGCCTTAA
1 AAAAGGACATTGTAAAGGTTATGCTTGAGCCCAAA
4785363 AAAAG
1 AAAAG
4785368 TATTTTCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 27 0.82
35 6 0.18
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (35 bp):
AAAAGGACATTGTAAAGGTTATGCTTGAGCCCAAA
Found at i:4786947 original size:68 final size:68
Alignment explanation
Indices: 4786861--4787101 Score: 331
Period size: 68 Copynumber: 3.5 Consensus size: 68
4786851 TAAGATTATG
* **
4786861 TATATGATGAAAATTCCATATACCATATGAGATGATTAAGTATGCATAATGTATACTATATGATT
1 TATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATAATGTATACTATACAATT
4786926 GTT
66 GTT
*
4786929 TATATGATTTAAATTCCATATACCATATGAGATGATTAAGTATGCATAATGTATACTATACAATT
1 TATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATAATGTATACTATACAATT
4786994 GTT
66 GTT
* ** * *
4786997 TATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGATAAATTCCATGA-AAT
1 TATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATAATGTATACTAT-ACAAT
* *
4787061 TATG
65 TGTT
* * * *
4787065 TATATGATGTATATTCCATATACTACATAAGATGATT
1 TATATGATGTAAATTCCATATACCATATGAGATGATT
4787102 CAGAAAGCAT
Statistics
Matches: 156, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 155 0.99
69 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (68 bp):
TATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATAATGTATACTATACAATT
GTT
Found at i:4787112 original size:68 final size:68
Alignment explanation
Indices: 4786844--4787156 Score: 202
Period size: 68 Copynumber: 4.6 Consensus size: 68
4786834 TGGTATAATG
* * * * * *
4786844 AATGCCAT-AAGATTATGTATATGATGAAAATTCCATATACCATATGAGATGATTAAGTATGCAT
1 AATGCCATGAA-ATTATGTATATGATGTATATTCCATATACCACATAAGATGATTAAGAAAGCAT
* *
4786908 AATG
65 GATA
* * * * * * * * * * * *
4786912 TATACTAT-ATGATTGTTTATATGATTTAAATTCCATATACCATATGAGATGATTAAGTATGCAT
1 AATGCCATGA-AATTATGTATATGATGTATATTCCATATACCACATAAGATGATTAAGAAAGCAT
* *
4786976 AATG
65 GATA
* * * * * * * * * *
4786980 TATACTAT-ACAATTGTTTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCAT
1 AATGCCATGA-AATTATGTATATGATGTATATTCCATATACCACATAAGATGATTAAGAAAGCAT
4787044 GATA
65 GATA
* * *
4787048 AATTCCATGAAATTATGTATATGATGTATATTCCATATACTACATAAGATGATTCAGAAAGCATG
1 AATGCCATGAAATTATGTATATGATGTATATTCCATATACCACATAAGATGATTAAGAAAGCATG
*
4787113 ATG
66 ATA
* * * *
4787116 AATGCTATGACATTATG-AGTATGATGTATTTTCTATATACC
1 AATGCCATGAAATTATGTA-TATGATGTATATTCCATATACC
4787157 TTACGAGATG
Statistics
Matches: 210, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
67 1 0.00
68 208 0.99
69 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (68 bp):
AATGCCATGAAATTATGTATATGATGTATATTCCATATACCACATAAGATGATTAAGAAAGCATG
ATA
Found at i:4787139 original size:136 final size:134
Alignment explanation
Indices: 4786838--4787172 Score: 330
Period size: 136 Copynumber: 2.5 Consensus size: 134
4786828 CATGTTTGGT
* * *
4786838 ATAATGAATGCCATAAGATTATGTATATGATGAAAATTCCATATACCATATGAGATGATTAAGTA
1 ATAATGAATGCTAT-ACATTATG-ATATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
** * * * * * * *
4786903 TGCATAATGTATACTATATGATTGTTTATATGATTTAAATTCCATATACCATATGAGATGATTAA
64 TGCATAATAAATACCATATAATTATGTATATGATGTAAATTCCATATACCACATAAGATGATTAA
* *
4786968 GTATGC
129 GAAAGC
* * * *
4786974 ATAATGTATACTATACAATTGTTTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
1 ATAATGAATGCTATAC-ATT-ATGATATGATGTAAATTCCATATACCATATGAGATGATTAAGTA
* * * * *
4787039 TGCATGATAAATTCCATGA-AATTATGTATATGATGTATATTCCATATACTACATAAGATGATTC
64 TGCATAATAAATACCAT-ATAATTATGTATATGATGTAAATTCCATATACCACATAAGATGATTA
4787103 AGAAAGC
128 AGAAAGC
* ** * * * *
4787110 ATGATGAATGCTATGACATTATGAGTATGATGTATTTTCTATATACCTTACGAGATGAGTAAG
1 ATAATGAATGCTAT-ACATTATGA-TATGATGTAAATTCCATATACCATATGAGATGATTAAG
4787173 CATGTATCTG
Statistics
Matches: 160, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
135 3 0.02
136 153 0.96
137 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (134 bp):
ATAATGAATGCTATACATTATGATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATG
CATAATAAATACCATATAATTATGTATATGATGTAAATTCCATATACCACATAAGATGATTAAGA
AAGC
Found at i:4799505 original size:64 final size:63
Alignment explanation
Indices: 4799373--4799505 Score: 137
Period size: 64 Copynumber: 2.1 Consensus size: 63
4799363 AGATTATGTA
* ** *
4799373 TATG-ATGTAAATTACATATACCATATGAGATGATTAAGTACGCATGATGTATACTATACGAT
1 TATGTATGTAAATTACATATACCATATAAGATGATTAAGTACGCATGATAAATACCATACGAT
* * * * *
4799435 TGTGTATGTGAAATTCCATATACCATATAA-AGTGATTAAGTATGCATGGTAAATTCCATGA-GA
1 TATGTATGT-AAATTACATATACCATATAAGA-TGATTAAGTACGCATGATAAATACCAT-ACGA
4799498 T
63 T
4799499 TATGTAT
1 TATGTAT
4799506 ATGATGTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
62 3 0.05
63 5 0.09
64 48 0.84
65 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (63 bp):
TATGTATGTAAATTACATATACCATATAAGATGATTAAGTACGCATGATAAATACCATACGAT
Found at i:4802061 original size:24 final size:24
Alignment explanation
Indices: 4802014--4802061 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4802004 GTTAACTAAT
**
4802014 GATTGCTTGGCTTTTCCCTTACAA
1 GATTGCTTGGCTTTTCCCCAACAA
4802038 GATTGCATT-GCTTTTCCCCAACAA
1 GATTGC-TTGGCTTTTCCCCAACAA
4802062 AATCTAGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (24 bp):
GATTGCTTGGCTTTTCCCCAACAA
Found at i:4810049 original size:27 final size:27
Alignment explanation
Indices: 4810011--4810065 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4810001 GTGTAGTGAG
4810011 TTAGGCTAGAACAAATTATGTTTTTTT
1 TTAGGCTAGAACAAATTATGTTTTTTT
4810038 TTAGGCTAGAACAAATTATGTTTTTTT
1 TTAGGCTAGAACAAATTATGTTTTTTT
4810065 T
1 T
4810066 GCAGAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (27 bp):
TTAGGCTAGAACAAATTATGTTTTTTT
Found at i:4818934 original size:16 final size:17
Alignment explanation
Indices: 4818910--4818956 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
4818900 AATAGAAGGG
*
4818910 GAGGAAAGAAGGATG-A
1 GAGGGAAGAAGGATGAA
*
4818926 GAGGGAAGAAAGATGAAA
1 GAGGGAAGAAGGATG-AA
*
4818944 GAGGGAGGAAGGA
1 GAGGGAAGAAGGA
4818957 AGTGGAGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (17 bp):
GAGGGAAGAAGGATGAA
Found at i:4819289 original size:180 final size:180
Alignment explanation
Indices: 4818970--4819298 Score: 473
Period size: 180 Copynumber: 1.8 Consensus size: 180
4818960 GGAGGAAGCT
* * * **
4818970 TCGGTCAGTTTGAGGCTATTTCTGGCTCTACAAAGGCTACATCTGTCTTTGATTGGTCCGATTTG
1 TCGGTCAGTTTGAGGCTATTTCTAGCTATACAAAGGCTACATCTGTCTTTGATTAGTCAAATTTG
* * * *
4819035 GTATTATATTTTTATTTTTAAATTATTTTTTATTTTATTATGAAGTTTAAAATTCATCAAATTTG
66 GTATTACATTTTTATTTTTAAATTATTTTTTATTTCATTATAAAGTTCAAAATTCATCAAATTTG
*
4819100 ATCTATTTGAGGTCATTTTTTACCATTGAAATTAGCTTAGGTTAGCCGTA
131 ATCTATTTGAGATCATTTTTTACCATTGAAATTAGCTTAGGTTAGCCGTA
* * * * *
4819150 TCGGTTAGTTTGAGGTTATTTCTAGCTATATAAAGGCTACATTTGTCTTTGATTAGTCAAATTTT
1 TCGGTCAGTTTGAGGCTATTTCTAGCTATACAAAGGCTACATCTGTCTTTGATTAGTCAAATTTG
* *
4819215 GTATTACATTTTTATTTTTAAATTATTTTTTATTTCATT-TCAAAGTTCAAATTTCATCATATTT
66 GTATTACATTTTTATTTTTAAATTATTTTTTATTTCATTAT-AAAGTTCAAAATTCATCAAATTT
4819279 GA-CTTATTTGAGATCATTTT
130 GATC-TATTTGAGATCATTTT
4819299 CGACCATACG
Statistics
Matches: 130, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
179 2 0.02
180 128 0.98
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (180 bp):
TCGGTCAGTTTGAGGCTATTTCTAGCTATACAAAGGCTACATCTGTCTTTGATTAGTCAAATTTG
GTATTACATTTTTATTTTTAAATTATTTTTTATTTCATTATAAAGTTCAAAATTCATCAAATTTG
ATCTATTTGAGATCATTTTTTACCATTGAAATTAGCTTAGGTTAGCCGTA
Found at i:4820208 original size:24 final size:24
Alignment explanation
Indices: 4820176--4820225 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
4820166 GAAACAACAA
4820176 ACCTTCTACAGTTAAAAGATAAAG
1 ACCTTCTACAGTTAAAAGATAAAG
4820200 ACCTTCTACAGTTAAAAGATAAAG
1 ACCTTCTACAGTTAAAAGATAAAG
4820224 AC
1 AC
4820226 ATGTTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (24 bp):
ACCTTCTACAGTTAAAAGATAAAG
Found at i:4824211 original size:9 final size:9
Alignment explanation
Indices: 4824199--4824227 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
4824189 ACTCTTGGAA
4824199 CCATTTTGG
1 CCATTTTGG
4824208 CCATTTTGG
1 CCATTTTGG
4824217 CCATTTTGG
1 CCATTTTGG
4824226 CC
1 CC
4824228 GTGGGATGTC
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:0.10, C:0.28, G:0.21, T:0.41
Consensus pattern (9 bp):
CCATTTTGG
Found at i:4832440 original size:19 final size:19
Alignment explanation
Indices: 4832412--4832449 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4832402 CCATTTGATT
*
4832412 TATTGGAGTATGATTTGAG
1 TATTGAAGTATGATTTGAG
4832431 TATTGAAGTATGATTTGAG
1 TATTGAAGTATGATTTGAG
4832450 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGAAGTATGATTTGAG
Found at i:4836727 original size:43 final size:43
Alignment explanation
Indices: 4836661--4836757 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
4836651 CTCTCAACTT
*
4836661 ATGTGCACTCCCACATCACACATAGCTGGGTCATCATCAGCTC
1 ATGTGCACTCCCACATCACACATAGCTAGGTCATCATCAGCTC
**
4836704 ATGTGCACTCCCTAC-TCGTACATAGCTAGGTCATCATCAGCTC
1 ATGTGCACTCCC-ACATCACACATAGCTAGGTCATCATCAGCTC
*
4836747 ATGTGTACTCC
1 ATGTGCACTCC
4836758 TCCATACATG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 47 0.96
44 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGTGCACTCCCACATCACACATAGCTAGGTCATCATCAGCTC
Found at i:4854954 original size:28 final size:28
Alignment explanation
Indices: 4854895--4854954 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
4854885 TGGGTGGTGT
* * * *
4854895 AAAATTACAATTTTACCCCTAGGGTGGC
1 AAAATGACAATTTTACCCCTAGGCTCGA
* *
4854923 AAAATGACTATTTTACCCCTATGCTCGA
1 AAAATGACAATTTTACCCCTAGGCTCGA
4854951 AAAA
1 AAAA
4854955 ATATCGAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (28 bp):
AAAATGACAATTTTACCCCTAGGCTCGA
Found at i:4856664 original size:43 final size:43
Alignment explanation
Indices: 4856546--4856667 Score: 165
Period size: 43 Copynumber: 2.8 Consensus size: 43
4856536 TGACTCGACT
***
4856546 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCAGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAACC
* *
4856589 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCTAACC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAACC
* *
4856632 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
4856668 TGATTATGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 69 0.99
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAACC
Found at i:4863264 original size:12 final size:12
Alignment explanation
Indices: 4863247--4863271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4863237 TCACAATGGA
4863247 AAAGAGGTAAGT
1 AAAGAGGTAAGT
4863259 AAAGAGGTAAGT
1 AAAGAGGTAAGT
4863271 A
1 A
4863272 GTAAGGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AAAGAGGTAAGT
Found at i:4863949 original size:14 final size:14
Alignment explanation
Indices: 4863932--4863970 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
4863922 AAATATCGAT
*
4863932 CATTCTTGGGAGAC
1 CATTCTTGAGAGAC
4863946 CATTCTTGAGAGAC
1 CATTCTTGAGAGAC
4863960 CATTCTTGAGA
1 CATTCTTGAGA
4863971 ACTGCTCGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (14 bp):
CATTCTTGAGAGAC
Found at i:4868103 original size:21 final size:20
Alignment explanation
Indices: 4868079--4868117 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4868069 CATTTTCGAA
4868079 TTTTTTCTTTAAGTTTTTTTT
1 TTTTTTCTTTAA-TTTTTTTT
*
4868100 TTTTTTCTTTTATTTTTT
1 TTTTTTCTTTAATTTTTT
4868118 AATATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.85
Consensus pattern (20 bp):
TTTTTTCTTTAATTTTTTTT
Found at i:4869522 original size:15 final size:15
Alignment explanation
Indices: 4869498--4869531 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4869488 TAAGGGTACT
4869498 AATGAGGCAGAGGAC
1 AATGAGGCAGAGGAC
* *
4869513 AATGATGCAGAGGAT
1 AATGAGGCAGAGGAC
4869528 AATG
1 AATG
4869532 GTGATGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.35, T:0.15
Consensus pattern (15 bp):
AATGAGGCAGAGGAC
Found at i:4870888 original size:3 final size:3
Alignment explanation
Indices: 4870880--4870920 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
4870870 ACTTTATCTC
*
4870880 TAG TAG TAG TAG TAG TAA TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
4870921 ATAACTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:4880780 original size:35 final size:34
Alignment explanation
Indices: 4880726--4880794 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
4880716 TAGTTGTTGA
* *
4880726 GTTTTGGTTGATCTCGGTAAACACCATTGTGAAAG
1 GTTTTGGCTGAGCTCGGTAAACACCATTGT-AAAG
* **
4880761 GTTTTGGCTGAGCTTGGTAAATTCCATTGTAAAG
1 GTTTTGGCTGAGCTCGGTAAACACCATTGTAAAG
4880795 CTCGGTGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (34 bp):
GTTTTGGCTGAGCTCGGTAAACACCATTGTAAAG
Found at i:4892083 original size:72 final size:72
Alignment explanation
Indices: 4891975--4892174 Score: 247
Period size: 72 Copynumber: 2.8 Consensus size: 72
4891965 GGAAAACATG
* * * * **
4891975 AAGATTACATAACCATAGTCAACTACAGAGGAAGCATAGTTGACCTTGACAAGTCAGAAGCAAGA
1 AAGATTACACAGCCATAGTCGACTATAGAGGAAGCATAGTCAACCTTGACAAGTCAGAAGCAAGA
*
4892040 AAATGTC
66 AAAAGTC
* *
4892047 AAGATTACACAGCCATAGTCGACTATAGAGGAAGCATAGTCAACCTTGATAAGTTAGAAGCAAGA
1 AAGATTACACAGCCATAGTCGACTATAGAGGAAGCATAGTCAACCTTGACAAGTCAGAAGCAAGA
*
4892112 AAAAGTT
66 AAAAGTC
* * * * * * *
4892119 AAGATTACACAGTCATAGTTGACTATAGAAGAGGTATAGTCAACCTCGACCAGTCA
1 AAGATTACACAGCCATAGTCGACTATAGAGGAAGCATAGTCAACCTTGACAAGTCA
4892175 AGGGCTAGAT
Statistics
Matches: 109, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 109 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (72 bp):
AAGATTACACAGCCATAGTCGACTATAGAGGAAGCATAGTCAACCTTGACAAGTCAGAAGCAAGA
AAAAGTC
Found at i:4917096 original size:20 final size:19
Alignment explanation
Indices: 4917071--4917111 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
4917061 GATCAATTGG
4917071 AAGAAAGAAGAAAGGAAAGA
1 AAGAAAGAAGAAAGG-AAGA
*
4917091 AAGAAAGGAGAAAGGAAGA
1 AAGAAAGAAGAAAGGAAGA
4917110 AA
1 AA
4917112 AAGCTTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAGAAAGGAAGA
Found at i:4921226 original size:68 final size:69
Alignment explanation
Indices: 4921147--4921282 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 69
4921137 ATAGCATTTA
* *
4921147 ATCATGTGCTCATACTTATCTCATATAGCATGTGAAATCATCATCACAT-ACATTGCAACATAGC
1 ATCATGTGCTCATACTTATCTCATATAGCATGTGAAATCATCATCACATAAAATAGCAACATAGC
4921211 ATAC
66 ATAC
* * * * *
4921215 ATCATGTGCTCATCCTTATCTCATATGGTATGTGAAATCATTATCACATAAAATAGCAACATCGC
1 ATCATGTGCTCATACTTATCTCATATAGCATGTGAAATCATCATCACATAAAATAGCAACATAGC
4921280 ATA
66 ATA
4921283 GAGCATTTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 45 0.75
69 15 0.25
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (69 bp):
ATCATGTGCTCATACTTATCTCATATAGCATGTGAAATCATCATCACATAAAATAGCAACATAGC
ATAC
Found at i:4923912 original size:20 final size:20
Alignment explanation
Indices: 4923888--4923934 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
4923878 ACTTATAAAC
*
4923888 CTCAAATCATACTTCAATTAA
1 CTCAAATCATACTCCAA-TAA
4923909 -TCAAATCATACTCCAATAA
1 CTCAAATCATACTCCAATAA
4923928 CTCAAAT
1 CTCAAAT
4923935 GGGACCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (20 bp):
CTCAAATCATACTCCAATAA
Found at i:4925204 original size:28 final size:29
Alignment explanation
Indices: 4925168--4925222 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
4925158 CGAAGTATAT
4925168 GGGCAAAATC-GTAAATTTTTTCGCCCCGG
1 GGGCAAAATCGGTAAATTTTTT-GCCCCGG
4925197 GGGC-AAATCGGTAAATTTTTTGCCCC
1 GGGCAAAATCGGTAAATTTTTTGCCCC
4925223 AGCACTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (29 bp):
GGGCAAAATCGGTAAATTTTTTGCCCCGG
Done.