Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008136.1 Hibiscus syriacus cultivar Beakdansim tig00110691_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1585607
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:387860 original size:16 final size:17
Alignment explanation
Indices: 387841--387873 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
387831 ATTTTCAATT
387841 TCTA-TTACAATTTCAG
1 TCTACTTACAATTTCAG
387857 TCTATCTTACAATTTCA
1 TCTA-CTTACAATTTCA
387874 TGCTCAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.45
Consensus pattern (17 bp):
TCTACTTACAATTTCAG
Found at i:397881 original size:226 final size:225
Alignment explanation
Indices: 397480--397916 Score: 569
Period size: 226 Copynumber: 1.9 Consensus size: 225
397470 CAAAAAATCG
* * * **
397480 ATTATATTTAATAGTAAAATAAAATATTAAAAATATACTAATTACCTGGATATTGAAATTGATGA
1 ATTATATTTAATAGTAAAATAAAAAATTAAAAATAAACTAATTACCTGAATATTGAAATTGACAA
* * * *
397545 ACCGCTTCTAGTACTATAATCTGGTGCAAAATAAAAAAAATTGCAAAATAATATAACTCTAAAAC
66 ACCGCTTC-A-TACAATAATCTGGAGCAAAAAAAAAAAAATTGCAAAATAATAGAACTCTAAAAC
* * * * * * *
397610 AAGATTATTTCAAAAGTAAAATACATAGAAGAATATTTCTATTTCACTTTCTTGATAATCTTTTT
129 AAGATCATCTCAAAAGTAAAATAAAGAGAAGAATATTTCTATTTCAATTACTTGATAATCTTATT
*
397675 AACCCTAAATCAAATCTTTTATAAAATATTCA
194 AAACCTAAATCAAATCTTTTATAAAATATTCA
397707 ATTATATTT-ATCAGTAAAATAAAAAAAATTAAAAA-AAACTTAATTACCTGAATATTGAAATTG
1 ATTATATTTAAT-AGTAAAAT--AAAAAATTAAAAATAAAC-TAATTACCTGAATATTGAAATTG
* * *
397770 GCAAACCGCTTC-TACAATAATCTGGAGCAAAACAAAAAAATAATTGTAAAA-AATAGAATTCTA
62 ACAAACCGCTTCATACAATAATCTGGAGCAAAA-AAAAAAA-AATTGCAAAATAATAGAACTCTA
* *
397833 AAACAAGATCA-CTCAAAAGTAAAATAAAGAGAATAATATTTTTATTTCAATTACTTGATAATCT
125 AAACAAGATCATCTCAAAAGTAAAATAAAGAGAAGAATATTTCTATTTCAATTACTTGATAATCT
397897 TATTAAACCTAAATCAAATC
190 TATTAAACCTAAATCAAATC
397917 AAATATGCAG
Statistics
Matches: 182, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
226 84 0.46
227 43 0.24
228 12 0.07
229 43 0.24
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (225 bp):
ATTATATTTAATAGTAAAATAAAAAATTAAAAATAAACTAATTACCTGAATATTGAAATTGACAA
ACCGCTTCATACAATAATCTGGAGCAAAAAAAAAAAAATTGCAAAATAATAGAACTCTAAAACAA
GATCATCTCAAAAGTAAAATAAAGAGAAGAATATTTCTATTTCAATTACTTGATAATCTTATTAA
ACCTAAATCAAATCTTTTATAAAATATTCA
Found at i:404488 original size:21 final size:22
Alignment explanation
Indices: 404464--404508 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
404454 ATAAAAGAAT
404464 AATTAAAATAA-AAATATAA-AA
1 AATTAAAATAATAAA-ATAATAA
*
404485 AATTAGAATAATAAAATAATAA
1 AATTAAAATAATAAAATAATAA
404507 AA
1 AA
404509 GGCAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AATTAAAATAATAAAATAATAA
Found at i:412783 original size:27 final size:27
Alignment explanation
Indices: 412753--412818 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
412743 TGTATCAGAC
412753 ATTATTTTAAAATTTAAAATTAGTATT
1 ATTATTTTAAAATTTAAAATTAGTATT
* *
412780 ATTATTTTAAAAATTAAAATTATTATT
1 ATTATTTTAAAATTTAAAATTAGTATT
412807 ATTA-TTTAAAAT
1 ATTATTTTAAAAT
412819 AACTCTACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 7 0.19
27 29 0.81
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
ATTATTTTAAAATTTAAAATTAGTATT
Found at i:418411 original size:2 final size:2
Alignment explanation
Indices: 418404--418429 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
418394 TATGTTTTGG
418404 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
418430 TATGTATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:419134 original size:18 final size:19
Alignment explanation
Indices: 419094--419145 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
419084 GTGTTGCTGA
* *
419094 TGGTGTGGGTTTTGGTGAC
1 TGGTGTCGGTATTGGTGAC
*
419113 -GGTGTTGGTATTGGTG-C
1 TGGTGTCGGTATTGGTGAC
*
419130 TGGTGTCGGTGTTGGT
1 TGGTGTCGGTATTGGT
419146 TTCGGTGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.04, C:0.06, G:0.48, T:0.42
Consensus pattern (19 bp):
TGGTGTCGGTATTGGTGAC
Found at i:419150 original size:12 final size:13
Alignment explanation
Indices: 419112--419170 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 13
419102 GTTTTGGTGA
419112 CGGTGTTGGTATT
1 CGGTGTTGGTATT
* *
419125 -GGTGCTGGT-GT
1 CGGTGTTGGTATT
419136 CGGTGTTGGT-TT
1 CGGTGTTGGTATT
* *
419148 CGGTGTTAGTGTT
1 CGGTGTTGGTATT
*
419161 CGGTTTTGGT
1 CGGTGTTGGT
419171 GCAGCTGGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 1 0.03
12 26 0.70
13 10 0.27
ACGTcount: A:0.03, C:0.08, G:0.42, T:0.46
Consensus pattern (13 bp):
CGGTGTTGGTATT
Found at i:422095 original size:45 final size:45
Alignment explanation
Indices: 422042--422133 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
422032 GAAATTACTT
422042 ACTTGCAAAACTAGAACTTCAATGCGAATTTATGAATTATCTATC
1 ACTTGCAAAACTAGAACTTCAATGCGAATTTATGAATTATCTATC
422087 ACTTGCAAAACTAGAACTTCAATGCGAATTTATGAATTATCTATC
1 ACTTGCAAAACTAGAACTTCAATGCGAATTTATGAATTATCTATC
422132 AC
1 AC
422134 AGCATTGTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (45 bp):
ACTTGCAAAACTAGAACTTCAATGCGAATTTATGAATTATCTATC
Found at i:423960 original size:19 final size:19
Alignment explanation
Indices: 423936--423972 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
423926 ATGACCAACA
*
423936 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
423955 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
423973 CATTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:424083 original size:20 final size:20
Alignment explanation
Indices: 424058--424130 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
424048 GATTTTACAT
*
424058 AATCGCAAAGCGAATATGTA
1 AATCGCAATGCGAATATGTA
424078 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
424098 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
424118 AATCGCAACGCGA
1 AATCGCAATGCGA
424131 TAACACGTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:424164 original size:41 final size:39
Alignment explanation
Indices: 424119--424204 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 39
424109 GAATATGTAA
*
424119 ATCGCAACGCGATAAC-ACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAT-ACGAC-T-ATCGCAACGAGATTCTGACT
*
424160 ATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAC-GACTATCGCAACGAGATTCTGACT
424200 ATCGC
1 ATCGC
424205 GTTGCGATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
40 25 0.61
41 14 0.34
42 2 0.05
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (39 bp):
ATCGCAACGCGATACGACTATCGCAACGAGATTCTGACT
Found at i:424165 original size:20 final size:20
Alignment explanation
Indices: 424140--424204 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
424130 ATAACACGTG
424140 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
424160 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
424180 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
424200 ATCGC
1 ATCGC
424205 GTTGCGATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:424812 original size:20 final size:20
Alignment explanation
Indices: 424787--424835 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
424777 GCGATTATCT
*
424787 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAATTAAATTCG
**
424807 CGTTGCGATAATTATTTTCG
1 CGTTGCGATAATTAAATTCG
*
424827 TGTTGCGAT
1 CGTTGCGAT
424836 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAATTAAATTCG
Found at i:424843 original size:20 final size:20
Alignment explanation
Indices: 424820--424858 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
424810 TGCGATAATT
*
424820 ATTTTCGTGTTGCGATTTTC
1 ATTTTCATGTTGCGATTTTC
424840 ATTTTCATGTTGCGATTTT
1 ATTTTCATGTTGCGATTTT
424859 AAGTTTCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (20 bp):
ATTTTCATGTTGCGATTTTC
Found at i:424865 original size:20 final size:20
Alignment explanation
Indices: 424822--424866 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
424812 CGATAATTAT
* * *
424822 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTTAAG
424842 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
424862 TTTCA
1 TTTCA
424867 GAAACTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:426926 original size:34 final size:34
Alignment explanation
Indices: 426880--427016 Score: 157
Period size: 34 Copynumber: 3.9 Consensus size: 34
426870 GAAAATGATT
**
426880 ATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACGGGATA
*
426914 ATCGCAATGCGAAAATGACTATCGCAACGGGGAAATGA
1 ATCGCAACGCGAAAATGACTATCGCAAC-GGG--AT-A
**
426952 CTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 --ATCGCAACGCGAAAATGACTATCGCAACGGGATA
* *
426988 ATCGCAATGCAAAAATGACTATCGCAACG
1 ATCGCAACGCGAAAATGACTATCGCAACG
427017 CAAATTTAGT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
34 50 0.57
35 3 0.03
36 1 0.01
37 4 0.05
38 1 0.01
39 3 0.03
40 25 0.29
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACGGGATA
Found at i:426984 original size:74 final size:74
Alignment explanation
Indices: 426872--427016 Score: 272
Period size: 74 Copynumber: 2.0 Consensus size: 74
426862 AGCAACACGA
* *
426872 AAATGATTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAATGACTATC
1 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAATGACTATC
426937 GCAACGGGG
66 GCAACGGGG
426946 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAATGACTATC
1 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAATGACTATC
427011 GCAACG
66 GCAACG
427017 CAAATTTAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (74 bp):
AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCAAAAATGACTATC
GCAACGGGG
Found at i:427020 original size:20 final size:20
Alignment explanation
Indices: 426863--427017 Score: 109
Period size: 20 Copynumber: 8.3 Consensus size: 20
426853 AAGAATAATA
* *
426863 GCAACACGAAAATGATTATC
1 GCAACGCGAAAATGACTATC
**
426883 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
*
426903 GCAACG-G--GAT-A--ATC
1 GCAACGCGAAAATGACTATC
*
426917 GCAATGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* *
426937 GCAACGGGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
**
426957 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
*
426977 GCAACG-G--GAT-A--ATC
1 GCAACGCGAAAATGACTATC
* *
426991 GCAATGCAAAAATGACTATC
1 GCAACGCGAAAATGACTATC
427011 GCAACGC
1 GCAACGC
427018 AAATTTAGTT
Statistics
Matches: 102, Mismatches: 21, Indels: 24
0.69 0.14 0.16
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 2 0.02
17 6 0.06
18 2 0.02
19 2 0.02
20 73 0.72
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:427067 original size:19 final size:19
Alignment explanation
Indices: 427040--427114 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
427030 GTGTTGCAAT
*
427040 TTTCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
427059 TTTCGCGTTGCGAT--T-A
1 TTTCGCGTTGCGATAGTCA
*
427075 --TCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTC-A
* *
427093 ATTCGCGTTGCGATAATCA
1 TTTCGCGTTGCGATAGTCA
427112 TTT
1 TTT
427115 TCATGTTGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 11 0.24
16 2 0.04
17 1 0.02
18 1 0.02
19 16 0.36
20 14 0.31
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:427069 original size:33 final size:34
Alignment explanation
Indices: 427026--427103 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 34
427016 GCAAATTTAG
* *
427026 TTTCGTGTTGCAATTTTCTCGTTGCGATAGTC-A
1 TTTCGCGTTGCAATTATCTCGTTGCGATAGTCAA
*
427059 TTTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCAATTATCTCGTTGCGATAGTCAA
*
427093 ATTCGCGTTGC
1 TTTCGCGTTGC
427104 GATAATCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (34 bp):
TTTCGCGTTGCAATTATCTCGTTGCGATAGTCAA
Found at i:427136 original size:20 final size:20
Alignment explanation
Indices: 427113--427157 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
427103 CGATAATCAT
427113 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
*
427133 TTTCGTGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
427153 TTTCA
1 TTTCA
427158 AAAACTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:427696 original size:100 final size:100
Alignment explanation
Indices: 427523--427723 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 100
427513 GATGCTTTAC
* *
427523 GTCGGGTTTTTCTTGCACGACGGGGTTCACGCATCAGACGGTGTGCACGTGCCATTAAGTCTCCG
1 GTCGGATTTTTCTTGCACGACGGGGTTCACGCATCAGAAGGTGTGCACGTGCCATTAAGTCTCCG
427588 TTCACCCCAATAGTGCAAATACTCCGTAAGAAGAA
66 TTCACCCCAATAGTGCAAATACTCCGTAAGAAGAA
*
427623 GTCGGATTTTTCTTGCACGACGGGGTTCACGCATCAGAAGGTGTGCATGTGCCATTAAGTCTCCG
1 GTCGGATTTTTCTTGCACGACGGGGTTCACGCATCAGAAGGTGTGCACGTGCCATTAAGTCTCCG
427688 TTCACCCCAATAGTGCAAATACTCCGTAAGAAGAA
66 TTCACCCCAATAGTGCAAATACTCCGTAAGAAGAA
427723 G
1 G
427724 CCCGACTCAC
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (100 bp):
GTCGGATTTTTCTTGCACGACGGGGTTCACGCATCAGAAGGTGTGCACGTGCCATTAAGTCTCCG
TTCACCCCAATAGTGCAAATACTCCGTAAGAAGAA
Found at i:429149 original size:36 final size:30
Alignment explanation
Indices: 429069--429134 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
429059 GTAAGAGTTG
*
429069 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
429099 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
429129 ATTTGT
1 ATTTGT
429135 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:429309 original size:20 final size:20
Alignment explanation
Indices: 429284--429371 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
429274 GCGATTTTCT
429284 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCC
429304 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCC
* *
429324 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCC
* * *
429344 CGTTGTGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCC
429363 CGTTGCGAT
1 CGTTGCGAT
429372 TATCTCATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
19 13 0.21
20 49 0.79
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCC
Found at i:429406 original size:52 final size:54
Alignment explanation
Indices: 429321--429530 Score: 266
Period size: 52 Copynumber: 4.0 Consensus size: 54
429311 ATAGTCAAAT
* * * *
429321 TCCCGTTGCGATAATCAAATTCGCGTTGTGATAGTCA-TTTCGCGTTGCGATTA
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * *
429374 TCTCATTGCGATAGT-AAATTTGCGGTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * *
429427 TCCCATTGCGATAGACAAATTCGCGTTGTGATAGTCATTTTTGCATT--GATTA
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * * *
429479 TCCCGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCATTGCGAT
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
429531 AGTCATATTC
Statistics
Matches: 133, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
52 63 0.47
53 40 0.30
54 30 0.23
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (54 bp):
TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
Found at i:429424 original size:20 final size:19
Alignment explanation
Indices: 429377--429424 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
429367 GCGATTATCT
429377 CATTGCGATAGTAAATTTG
1 CATTGCGATAGTAAATTTG
** * *
429396 CGGTGCGATAGTCATTTTCG
1 CATTGCGATAGTAAATTT-G
429416 CATTGCGAT
1 CATTGCGAT
429425 TATCCCATTG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (19 bp):
CATTGCGATAGTAAATTTG
Found at i:429451 original size:106 final size:106
Alignment explanation
Indices: 429321--429530 Score: 282
Period size: 106 Copynumber: 2.0 Consensus size: 106
429311 ATAGTCAAAT
* * *
429321 TCCCGTTGCGATAATCAAATTCGCGTTGTGATAGTCA-TTTCGCGTTGCGATTATCTCATTGCGA
1 TCCCATTGCGATAATCAAATTCGCGTTGTGATAGTCATTTTCGCATT--GATTATCCCATTGCGA
** *
429385 TAGT-AAATTTGCGGTGCGATAGTCATTTTCGCATTGCGATTA
64 TAGTCAAATTCACGGTGCGATAGTCATATTCGCATTGCGATTA
* *
429427 TCCCATTGCGATAGA-CAAATTCGCGTTGTGATAGTCATTTTTGCATTGATTATCCCGTTGCGAT
1 TCCCATTGCGATA-ATCAAATTCGCGTTGTGATAGTCATTTTCGCATTGATTATCCCATTGCGAT
* *
429491 ATTCAAATTCACGTTGCGATAGTCATATTCGCATTGCGAT
65 AGTCAAATTCACGGTGCGATAGTCATATTCGCATTGCGAT
429531 AGTCATATTC
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 17 0.19
106 66 0.73
107 8 0.09
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (106 bp):
TCCCATTGCGATAATCAAATTCGCGTTGTGATAGTCATTTTCGCATTGATTATCCCATTGCGATA
GTCAAATTCACGGTGCGATAGTCATATTCGCATTGCGATTA
Found at i:429507 original size:20 final size:20
Alignment explanation
Indices: 429482--429550 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
429472 TTGATTATCC
* * *
429482 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCATATTCG
429502 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATATTCG
*
429522 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATATTCG
429542 CGTTGCGAT
1 CGTTGCGAT
429551 TATCAAATGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:429756 original size:18 final size:18
Alignment explanation
Indices: 429733--429767 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
429723 AAGCCGGTTG
429733 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
429751 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
429768 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:432963 original size:20 final size:20
Alignment explanation
Indices: 432829--432974 Score: 125
Period size: 20 Copynumber: 7.3 Consensus size: 20
432819 AATTCAGTGA
* **
432829 TGCGTTAGTCAGAATCGTTT
1 TGCGATAGTCAGAATCGCGT
* *
432849 TGCGATAGTCAGAATCACAT
1 TGCGATAGTCAGAATCGCGT
* *
432869 TGCGATTGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
*
432889 TGCGATAGTCAGAATCGCAT
1 TGCGATAGTCAGAATCGCGT
*
432909 TGCGATCACGT-A-TATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
* * * *
432929 TGTGATGGTCTGAATCGTGT
1 TGCGATAGTCAGAATCGCGT
* *
432949 TACGATAGTCAGAATTGCGT
1 TGCGATAGTCAGAATCGCGT
432969 TGCGAT
1 TGCGAT
432975 CACGTGTTAT
Statistics
Matches: 98, Mismatches: 24, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
18 2 0.02
20 92 0.94
21 2 0.02
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:433012 original size:20 final size:20
Alignment explanation
Indices: 432984--433036 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
432974 TCACGTGTTA
*
432984 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
433004 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
433024 TCGCATTGCGATT
1 TCGCATTGCGATT
433037 ATCTAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:433132 original size:20 final size:19
Alignment explanation
Indices: 433109--433155 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
433099 TGGAAACTGA
*
433109 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
*
433129 ATTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
433148 ATTGCGAT
1 ATTGCGAT
433156 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:433145 original size:19 final size:19
Alignment explanation
Indices: 433121--433157 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
433111 TGCGATAATG
433121 GAGATCGCATTGCGATTTA
1 GAGATCGCATTGCGATTTA
433140 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
433158 TGTTGGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:433747 original size:15 final size:15
Alignment explanation
Indices: 433709--433747 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
433699 AATGAATCAA
*
433709 TAATTTATTATTTTAT
1 TAATTT-TTATTATAT
*
433725 TAAATTTTATTATAT
1 TAATTTTTATTATAT
433740 TAATTTTT
1 TAATTTTT
433748 GTAGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTATTATAT
Found at i:434823 original size:7 final size:7
Alignment explanation
Indices: 434811--434921 Score: 52
Period size: 7 Copynumber: 15.9 Consensus size: 7
434801 TATGTGTTAA
434811 GGTTTAG
1 GGTTTAG
434818 GGTTTAG
1 GGTTTAG
434825 GGTTTA-
1 GGTTTAG
* *
434831 TGTGATA-
1 GGT-TTAG
*
434838 GGTATTAA
1 GGT-TTAG
434846 GGTTTA-
1 GGTTTAG
*
434852 GATATTAG
1 GGT-TTAG
*
434860 GGTTTAA
1 GGTTTAG
434867 GGTTTA-
1 GGTTTAG
*
434873 TGTGTTAG
1 GGT-TTAG
434881 GAG-TTAG
1 G-GTTTAG
434888 GGTTTAG
1 GGTTTAG
** *
434895 AATTTAA
1 GGTTTAG
434902 GGTTTAG
1 GGTTTAG
*
434909 AGTTTAG
1 GGTTTAG
434916 GGTTTA
1 GGTTTA
434922 AGTTATGCAC
Statistics
Matches: 78, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
6 7 0.09
7 65 0.83
8 5 0.06
9 1 0.01
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:434849 original size:21 final size:20
Alignment explanation
Indices: 434818--434881 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
434808 TAAGGTTTAG
*
434818 GGTTTAGGGTTTATGTGATA
1 GGTTTAAGGTTTATGTGATA
434838 GGTATTAAGGTTTA-GAT-ATTA
1 GGT-TTAAGGTTTATG-TGA-TA
*
434859 GGGTTTAAGGTTTATGTGTTA
1 -GGTTTAAGGTTTATGTGATA
434880 GG
1 GG
434882 AGTTAGGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
20 7 0.19
21 25 0.69
22 4 0.11
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (20 bp):
GGTTTAAGGTTTATGTGATA
Found at i:434873 original size:42 final size:42
Alignment explanation
Indices: 434814--434895 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
434804 GTGTTAAGGT
*
434814 TTAGGGTTTAGGGTTTATGTGATAGGTA-TTAAGGTTTAGATA
1 TTAGGGTTTAAGGTTTATGTGATAGG-AGTTAAGGTTTAGATA
* *
434856 TTAGGGTTTAAGGTTTATGTGTTAGGAGTTAGGGTTTAGA
1 TTAGGGTTTAAGGTTTATGTGATAGGAGTTAAGGTTTAGA
434896 ATTTAAGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (42 bp):
TTAGGGTTTAAGGTTTATGTGATAGGAGTTAAGGTTTAGATA
Found at i:434891 original size:21 final size:21
Alignment explanation
Indices: 434825--434893 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
434815 TAGGGTTTAG
*
434825 GGTTTATGTGATAGGTA-TTAA
1 GGTTTATGTGTTAGG-AGTTAA
*
434846 GGTTTA-GATATTAGG-GTTTAA
1 GGTTTATG-TGTTAGGAG-TTAA
*
434867 GGTTTATGTGTTAGGAGTTAG
1 GGTTTATGTGTTAGGAGTTAA
434888 GGTTTA
1 GGTTTA
434894 GAATTTAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (21 bp):
GGTTTATGTGTTAGGAGTTAA
Found at i:434900 original size:28 final size:28
Alignment explanation
Indices: 434842--434923 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 28
434832 GTGATAGGTA
*
434842 TTAAGGTTTAGA-TATTAGGGTTTAAGGT
1 TTAAGGTTTAGAGT-TTAGGGTTTAAGAT
*
434870 TT-ATGTGTTAGGAG-TTAGGGTTT-AGAAT
1 TTAAGGT-TTA-GAGTTTAGGGTTTAAG-AT
434898 TTAAGGTTTAGAGTTTAGGGTTTAAG
1 TTAAGGTTTAGAGTTTAGGGTTTAAG
434924 TTATGCACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
27 8 0.18
28 29 0.66
29 7 0.16
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (28 bp):
TTAAGGTTTAGAGTTTAGGGTTTAAGAT
Found at i:434906 original size:42 final size:41
Alignment explanation
Indices: 434813--434907 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
434803 TGTGTTAAGG
*
434813 TTTAGGGTTTAGGGTTTATGTGATAGGTATTAAGGTTTAGA
1 TTTAGGGTTTAAGGTTTATGTGATAGGTATTAAGGTTTAGA
* *
434854 TATTAGGGTTTAAGGTTTATGTGTTAGG-AGTTAGGGTTTAGAA
1 T-TTAGGGTTTAAGGTTTATGTGATAGGTA-TTAAGGTTTAG-A
*
434897 TTTAAGGTTTA
1 TTTAGGGTTTA
434908 GAGTTTAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (41 bp):
TTTAGGGTTTAAGGTTTATGTGATAGGTATTAAGGTTTAGA
Found at i:436187 original size:23 final size:23
Alignment explanation
Indices: 436124--436188 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
436114 CAAAACCCTT
*
436124 CGAGCTTGAATCGAGCTAAAAAA
1 CGAGCTTGAATCGAGCTCAAAAA
436147 CGAGCTTGAATCGAGCTCAAAAA
1 CGAGCTTGAATCGAGCTCAAAAA
* *
436170 CGAGCTTTAATTGAGCTCA
1 CGAGCTTGAATCGAGCTCA
436189 TGAATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (23 bp):
CGAGCTTGAATCGAGCTCAAAAA
Found at i:436828 original size:17 final size:20
Alignment explanation
Indices: 436806--436846 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
436796 TCCGTATCCG
436806 TAAAAAAATT-A-AA-AATT
1 TAAAAAAATTCACAATAATT
436823 TAAAAAAATTCACAATAATT
1 TAAAAAAATTCACAATAATT
436843 TAAA
1 TAAA
436847 TAACATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 2 0.10
20 8 0.38
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAAATTCACAATAATT
Found at i:445751 original size:15 final size:15
Alignment explanation
Indices: 445733--445763 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
445723 AAATTTTAAA
445733 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
445748 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
445763 T
1 T
445764 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:455109 original size:130 final size:130
Alignment explanation
Indices: 454876--455134 Score: 473
Period size: 130 Copynumber: 2.0 Consensus size: 130
454866 CAATAAAAAA
* *
454876 AAAAAAAATTGGCATAACATAGCATATGTGATTACATATATCCTACAGTTACCCTGTCTGGGTAA
1 AAAAAAAATTGGCATAACAAAGCATATGTGATTACATATATCCTACAGTTACCCTGTCTGGATAA
* * *
454941 CATCGTTCATGTCCAATGTTAATAAACAAGTAATCCGACTCCATGTATAAACTGGAAAAATGAAG
66 CATCGTTCATGTCCAATGTTAATAAACAAGTAATCCGACTCAATGGATAAACCGGAAAAATGAAG
455006 AAAAAAAATTGGCATAACAAAGCATATGTGATTACATATATCCTACAGTTACCCTGTCTGGATAA
1 AAAAAAAATTGGCATAACAAAGCATATGTGATTACATATATCCTACAGTTACCCTGTCTGGATAA
455071 CATCGTTCATGTCCAATGTTAATAAACAAGTAATCCGACTCAATGGATAAACCGGAAAAATGAA
66 CATCGTTCATGTCCAATGTTAATAAACAAGTAATCCGACTCAATGGATAAACCGGAAAAATGAA
455135 ATTTTTTTTG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 124 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (130 bp):
AAAAAAAATTGGCATAACAAAGCATATGTGATTACATATATCCTACAGTTACCCTGTCTGGATAA
CATCGTTCATGTCCAATGTTAATAAACAAGTAATCCGACTCAATGGATAAACCGGAAAAATGAAG
Found at i:462044 original size:18 final size:19
Alignment explanation
Indices: 462009--462045 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
461999 CACGGAATGT
462009 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
462029 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
462046 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:462451 original size:36 final size:36
Alignment explanation
Indices: 462380--462452 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
462370 GTTGAAAAAT
*
462380 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
462416 ATTTATATATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATT-AAAATCATAAA
462452 A
1 A
462453 ATGGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:463401 original size:2 final size:2
Alignment explanation
Indices: 463394--463455 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
463384 TAATTAATTG
463394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463436 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
463456 TACCCGGGGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464013 original size:16 final size:16
Alignment explanation
Indices: 463982--464022 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
463972 GGTAATTTTG
463982 TTATAATT-TT-TTTA
1 TTATAATTATTGTTTA
*
463996 TTATACTTATTGTTTA
1 TTATAATTATTGTTTA
464012 TTATAATTATT
1 TTATAATTATT
464023 TGAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 14 0.61
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATAATTATTGTTTA
Found at i:467464 original size:35 final size:34
Alignment explanation
Indices: 467379--467465 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
467369 AATATAATTT
* *
467379 TAAATAAAACAAACTTACAATAAGTATTAAATGG
1 TAAATGAAACAAAATTACAATAAGTATTAAATGG
467413 TAAATGATAATC-AAATTACAATAACTGATATTAAATGG
1 TAAATGA-AA-CAAAATTACAATAA--G-TATTAAATGG
467451 T-AAT-AAACAAAATTA
1 TAAATGAAACAAAATTA
467466 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 7 0.16
35 21 0.47
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATGAAACAAAATTACAATAAGTATTAAATGG
Found at i:469859 original size:24 final size:25
Alignment explanation
Indices: 469817--469870 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
469807 ATATCTGCAA
*
469817 AAAAAATTAAATAAATAAA-ATATT
1 AAAAAATTAAATAAATAAATAAATT
* **
469841 AAAAATTTAAATACTTAAATAAATT
1 AAAAAATTAAATAAATAAATAAATT
469866 AAAAA
1 AAAAA
469871 CAAAATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAAAATTAAATAAATAAATAAATT
Found at i:471852 original size:74 final size:74
Alignment explanation
Indices: 471774--471919 Score: 283
Period size: 74 Copynumber: 2.0 Consensus size: 74
471764 AAAATCATAA
471774 ATAACTATTACTTTTTCCCTCAAAGTTGACCTTCAATCCCTCCATGCAATATATAATAATTAATT
1 ATAACTATTACTTTTTCCCTCAAAGTTGACCTTCAATCCCTCCATGCAATATATAATAATTAATT
471839 AATTGGTAG
66 AATTGGTAG
*
471848 ATAACTATTACTTTTTCCCTCAAAGTTGACCTTCAATCCCTCCATGCAATATATAGTAATTAATT
1 ATAACTATTACTTTTTCCCTCAAAGTTGACCTTCAATCCCTCCATGCAATATATAATAATTAATT
471913 AATTGGT
66 AATTGGT
471920 TAGGTTAAAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (74 bp):
ATAACTATTACTTTTTCCCTCAAAGTTGACCTTCAATCCCTCCATGCAATATATAATAATTAATT
AATTGGTAG
Found at i:472695 original size:59 final size:60
Alignment explanation
Indices: 472603--472720 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 60
472593 TACACAACTA
* * *
472603 GTCCTCTGACTATATAGTATTGCTTTATTGAGTCATCT-GGCTATTAAAAGTTA-AAAATG
1 GTCCTCTAACTATAGAGTATTGCTTTATTGAGTC-TCTCGACTATTAAAAGTTACAAAATG
*
472662 GTCCTCTAACTATAGGGTATTGCTTTATTGAGTCTCTCGACTATTAAAAGTTACAAAAT
1 GTCCTCTAACTATAGAGTATTGCTTTATTGAGTCTCTCGACTATTAAAAGTTACAAAAT
472721 AGTTACCTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 3 0.06
59 45 0.85
60 5 0.09
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (60 bp):
GTCCTCTAACTATAGAGTATTGCTTTATTGAGTCTCTCGACTATTAAAAGTTACAAAATG
Found at i:473036 original size:60 final size:60
Alignment explanation
Indices: 472943--473055 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
472933 GTCAGATGAC
*
472943 CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGTAAG-ACCCTATAATTAAAGGAT
1 CATTTTATAACTTTTAATAATCGAGGGACTCAACAAAGT-AGTACCCTATAATTAAAGGAT
* *
473003 CATTTTATAATTTTTAATAGTC-AGTGGACTCAACAAAGTAGTACCCTATAATT
1 CATTTTATAACTTTTAATAATCGAG-GGACTCAACAAAGTAGTACCCTATAATT
473056 GGGGGACCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
59 4 0.08
60 44 0.92
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAATCGAGGGACTCAACAAAGTAGTACCCTATAATTAAAGGAT
Found at i:473788 original size:22 final size:22
Alignment explanation
Indices: 473760--473813 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
473750 TATAATTAAA
*
473760 ATAATTTTTTGTGTTTTGTATT
1 ATAATTTTTTGTATTTTGTATT
473782 ATAATTTTTTGTATTTTGTATT
1 ATAATTTTTTGTATTTTGTATT
473804 ATAATTTTTT
1 ATAATTTTTT
473814 CCGATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (22 bp):
ATAATTTTTTGTATTTTGTATT
Found at i:473941 original size:2 final size:2
Alignment explanation
Indices: 473934--473959 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
473924 TCTTATCTTT
473934 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
473960 GAGTTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:478029 original size:20 final size:20
Alignment explanation
Indices: 478006--478054 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
477996 AATAACTAAT
478006 AGATTGATCTAATTTTCAAA
1 AGATTGATCTAATTTTCAAA
478026 AGATTGATCTAATTTTCAAA
1 AGATTGATCTAATTTTCAAA
*
478046 AGATCGATC
1 AGATTGATC
478055 ACTTTCTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (20 bp):
AGATTGATCTAATTTTCAAA
Found at i:478697 original size:17 final size:18
Alignment explanation
Indices: 478665--478698 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
478655 GGAAGAAAGG
*
478665 TTAATAGTAGATATTGAT
1 TTAATAGTAAATATTGAT
478683 TTAATA-TAAATATTGA
1 TTAATAGTAAATATTGA
478699 GAGTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
TTAATAGTAAATATTGAT
Found at i:482015 original size:23 final size:23
Alignment explanation
Indices: 481986--482059 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 23
481976 GCGATCGTCG
481986 AAATTCGCATTGCGATTTATTCC
1 AAATTCGCATTGCGATTTATTCC
* *
482009 AAATTCG--TTGCGA--TAGTCG
1 AAATTCGCATTGCGATTTATTCC
* *
482028 AAGTTCGCGTTGCGATTTATTCC
1 AAATTCGCATTGCGATTTATTCC
482051 AAATTCGCA
1 AAATTCGCA
482060 ACAACTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 10 0.25
21 12 0.30
23 18 0.45
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (23 bp):
AAATTCGCATTGCGATTTATTCC
Found at i:482019 original size:21 final size:20
Alignment explanation
Indices: 481953--482057 Score: 72
Period size: 19 Copynumber: 5.1 Consensus size: 20
481943 TCGAAGTTCG
481953 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* ** *
481972 TGTTGCGA-TCGTCGAAATT
1 CGTTGCGATTATTCCAAATT
481991 CGCATTGCGATTTATTCCAAATT
1 CG--TTGCGA-TTATTCCAAATT
* * *
482014 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
482033 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
482056 CG
1 CG
482058 CAACAACTGG
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.02
19 23 0.36
21 22 0.34
23 18 0.28
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:482022 original size:42 final size:42
Alignment explanation
Indices: 481934--482057 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
481924 AACGCGAACT
* *
481934 TTGCAATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTTG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
481974 TTGCGATCGTCGAAATTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
482016 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
482058 CAACAACTGG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 23 0.31
41 2 0.03
42 49 0.66
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:482153 original size:6 final size:6
Alignment explanation
Indices: 482142--482183 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
482132 GACACGTATT
482142 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
482184 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:482174 original size:5 final size:5
Alignment explanation
Indices: 482146--482186 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
482136 CGTATTACCA
482146 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
482187 GACGAGACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:482837 original size:42 final size:42
Alignment explanation
Indices: 482790--483092 Score: 470
Period size: 42 Copynumber: 7.3 Consensus size: 42
482780 TGCGATTTTG
*
482790 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
482832 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAATTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
482874 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
482916 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
482958 GACTATCGCAACGAATTTGGAATAAATCGCAACGCCAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
483000 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
483040 GACTATCGCAACACGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGC-A-ACGAATTTGGAATAAATCGCAACGCGAACTTC
483082 GACTATCGCAA
1 GACTATCGCAA
483093 TGCGAATATG
Statistics
Matches: 241, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
40 28 0.12
41 3 0.01
42 210 0.87
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:483047 original size:21 final size:21
Alignment explanation
Indices: 482787--483098 Score: 252
Period size: 21 Copynumber: 15.0 Consensus size: 21
482777 CGTTGCGATT
*
482787 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
482806 TTGGAATAAATCGCAACGCAAAC
1 TTGGACT--ATCGCAACGCGAAC
*
482829 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* * *
482848 TTGGAATAAATCGCAATGCGAAT
1 TTGGACT--ATCGCAACGCGAAC
* *
482871 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
482890 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
482913 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
482932 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
482955 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
482974 TTGGAATAAATCGCAACGCCAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
482997 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
483016 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
483037 TTCGACTATCGCAACACGAAC
1 TTGGACTATCGCAACGCGAAC
483058 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
483079 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
483099 TATGTAAATC
Statistics
Matches: 233, Mismatches: 38, Indels: 42
0.74 0.12 0.13
Matches are distributed among these distances:
19 59 0.25
21 129 0.55
23 45 0.19
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:484225 original size:39 final size:39
Alignment explanation
Indices: 484177--484284 Score: 180
Period size: 39 Copynumber: 2.8 Consensus size: 39
484167 AAACTTAAAT
* *
484177 ACTCTAGGAGTGCACGGCGTCTTCAGGCCAATGGATAAG
1 ACTCCAGGAGTGCACGACGTCTTCAGGCCAATGGATAAG
* *
484216 ACTCCAGGAGTGCACAACGTCTTCAGGCCAATGTATAAG
1 ACTCCAGGAGTGCACGACGTCTTCAGGCCAATGGATAAG
484255 ACTCCAGGAGTGCACGACGTCTTCAGGCCA
1 ACTCCAGGAGTGCACGACGTCTTCAGGCCA
484285 TACAGAAACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (39 bp):
ACTCCAGGAGTGCACGACGTCTTCAGGCCAATGGATAAG
Found at i:485246 original size:37 final size:38
Alignment explanation
Indices: 485196--485301 Score: 198
Period size: 37 Copynumber: 2.8 Consensus size: 38
485186 TGATCAACCT
485196 TTGATTTAGTATTTCTAGTAAAAATGTTAAAATAAT-A
1 TTGATTTAGTATTTCTAGTAAAAATGTTAAAATAATAA
485233 TTGATTTAGTATTTCTAGTAAAAATGTTAAAATAATAA
1 TTGATTTAGTATTTCTAGTAAAAATGTTAAAATAATAA
485271 TT-ATTTAGTATTTCTAGTAAAAATGTTAAAA
1 TTGATTTAGTATTTCTAGTAAAAATGTTAAAA
485302 CAATTATTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
37 65 0.96
38 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (38 bp):
TTGATTTAGTATTTCTAGTAAAAATGTTAAAATAATAA
Found at i:485366 original size:16 final size:16
Alignment explanation
Indices: 485332--485370 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
485322 ATAATAATAA
485332 TAATAGTAACTTTAATC
1 TAATA-TAACTTTAATC
* *
485349 TAATATAATTTTATTC
1 TAATATAACTTTAATC
485365 TAATAT
1 TAATAT
485371 GTCACATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (16 bp):
TAATATAACTTTAATC
Found at i:488195 original size:27 final size:27
Alignment explanation
Indices: 488144--488195 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
488134 TGTTGATGTT
*
488144 ATATTTGAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATGAATATCA
* *
488171 ATATTTGAGTGAATGTGATGGATAT
1 ATATTTGAATGAATGTGATGAATAT
488196 TTATTGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATGAATATCA
Found at i:488248 original size:24 final size:24
Alignment explanation
Indices: 488219--488264 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
488209 ATTTGAATGA
* *
488219 ATGTGATTAATCTCAATATTTTCT
1 ATGTGAATAATATCAATATTTTCT
488243 ATGTGAATAATATCAATATTTT
1 ATGTGAATAATATCAATATTTT
488265 ATTTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
ATGTGAATAATATCAATATTTTCT
Found at i:490624 original size:93 final size:92
Alignment explanation
Indices: 490439--490622 Score: 237
Period size: 93 Copynumber: 2.0 Consensus size: 92
490429 AAAACAATAA
** * * * *
490439 AATTTAAACTAAACTTATTAAACCACTCAAATACGATTTAATCTATAAAATAAAAATAATTAGTC
1 AATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATATAAAATAAAAATAAATAGTC
*
490504 TAATAATTTATATTACTCAATAAAAAAT
66 TAATAATTTATATTA-TAAATAAAAAAT
* * *
490532 AATTTAAACTAAACTTACCAAACTACTCAAATACAACTTAATATGTAAAATCAAAATAAATAGTC
1 AATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATATAAAATAAAAATAAATAGTC
490597 TAATAA-TTATAATT-TAAATTAAAAAA
66 TAATAATTTAT-ATTATAAA-TAAAAAA
490623 ATTACACTAA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
91 3 0.04
92 11 0.14
93 65 0.82
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (92 bp):
AATTTAAACTAAACTTACCAAACCACTCAAATACAACTTAATATATAAAATAAAAATAAATAGTC
TAATAATTTATATTATAAATAAAAAAT
Found at i:494395 original size:59 final size:60
Alignment explanation
Indices: 494283--494418 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 60
494273 ATAGTTGAGT
* * * * * *
494283 GACCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAATATCACCCTATAGTCGAAC
1 GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAGTCGAAA
* * * **
494343 GA-CATTTTGTAATTTTTCATAGTCGAGAGACTTAACAAAACAACGTCATATAGTCGAAA
1 GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAGTCGAAA
494402 GACCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
494419 ATCCTATCTA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
59 48 0.77
60 11 0.18
61 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCATATAGTCGAAA
Found at i:499806 original size:64 final size:64
Alignment explanation
Indices: 499660--499818 Score: 225
Period size: 64 Copynumber: 2.5 Consensus size: 64
499650 TGCACTAAGA
* *
499660 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATAGCTGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCTCAGTGCATCGATGCATGGTTG
* *
499723 GTGCATCGATGCATCAAATGCATTCGATGTTCTCATAAA-ATCTCAGTGCATCGGTGCATGG-TG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCA-AAATAGCTCAGTGCATCGATGCATGGTTG
* *
499786 TGTGTATCGATGCATGAAATGCATTCGATGTTC
1 -GTGCATCGATGCATCAAATGCATTCGATGTTC
499819 AATTTAATTC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
63 32 0.37
64 52 0.60
65 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCTCAGTGCATCGATGCATGGTTG
Found at i:499836 original size:64 final size:64
Alignment explanation
Indices: 499660--499868 Score: 221
Period size: 64 Copynumber: 3.3 Consensus size: 64
499650 TGCACTAAGA
* * * *
499660 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAA-AATAGCTGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCT-AATAAAATCTCAGTGCATCGATGCATGGTTG
* *
499723 GTGCATCGATGCATCAAATGCATTCGATGTTCTCATAAAATCTCAGTGCATCGGTGCATGG-TG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCAGTGCATCGATGCATGGTTG
* * ** *
499786 TGTGTATCGATGCATGAAATGCATTCGATGTTC-AATTTAAT-TCATGGTGCATCGATGTATGGA
1 -GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCA--GTGCATCGATGCATGG-
499849 TTG
62 TTG
* *
499852 ATGCATCGGTGCATCAA
1 GTGCATCGATGCATCAA
499869 TCTGAAAATT
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
62 3 0.02
63 38 0.31
64 66 0.54
65 13 0.11
66 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:500338 original size:3 final size:3
Alignment explanation
Indices: 500325--500358 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
500315 GAAATAAATA
500325 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
500359 AAACAGTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:500554 original size:3 final size:3
Alignment explanation
Indices: 500482--500537 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
500472 TAAATGGAAA
500482 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
500528 AAT AAT AAT A
1 AAT AAT AAT A
500538 CGTATAGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:500688 original size:9 final size:9
Alignment explanation
Indices: 500675--500764 Score: 114
Period size: 9 Copynumber: 9.8 Consensus size: 9
500665 GATAAAACAA
500675 AATAA-AAT
1 AATAATAAT
500683 ATATAAATA-T
1 A-AT-AATAAT
500693 AATAATAAT
1 AATAATAAT
500702 AATAATAAT
1 AATAATAAT
500711 AATAATAAT
1 AATAATAAT
500720 AATAATAAT
1 AATAATAAT
500729 AATAATAAT
1 AATAATAAT
500738 AATAATGAAGT
1 AATAAT-AA-T
500749 -ATATATAAT
1 AATA-ATAAT
500758 AATAATA
1 AATAATA
500765 GTAAGAAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 15
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.07
9 51 0.69
10 14 0.19
11 4 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AATAATAAT
Found at i:500699 original size:3 final size:3
Alignment explanation
Indices: 500691--500764 Score: 114
Period size: 3 Copynumber: 24.0 Consensus size: 3
500681 ATATATAAAT
500691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
500739 ATA ATGA AGT- ATA TATA ATA ATA ATA
1 ATA AT-A A-TA ATA -ATA ATA ATA ATA
500765 GTAAGAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.01
3 60 0.90
4 5 0.07
5 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:500790 original size:17 final size:20
Alignment explanation
Indices: 500691--500791 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 20
500681 ATATATAAAT
* * *
500691 ATAATAATAATAATAATAATA
1 ATAATAATAGTAAGAA-AAAA
* * *
500712 ATAATAATAATAATAATAATA
1 ATAATAATAGTAAGAA-AAAA
* * *
500733 ATAATAATAATGAAGTATATATA
1 ATAATAATAGT-AAG-A-AAAAA
500756 ATAATAATAGTAAGAAAAAA
1 ATAATAATAGTAAGAAAAAA
500776 ATAA-AATA-TAA-AAAAA
1 ATAATAATAGTAAGAAAAA
500792 TTGAATTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.07
18 3 0.04
19 4 0.06
20 7 0.10
21 33 0.46
22 5 0.07
23 14 0.19
24 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
ATAATAATAGTAAGAAAAAA
Found at i:501176 original size:37 final size:37
Alignment explanation
Indices: 501126--501237 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
501116 ATGCTTATGG
*
501126 ATCATATTTTTAGGAGTTTGAATCATAGTAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
501163 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
501200 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
501237 A
1 A
501238 AAGTTATGTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:502156 original size:18 final size:20
Alignment explanation
Indices: 502121--502157 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
502111 GCTGGTTTGA
502121 TATTTTTAATATTTAAAACT
1 TATTTTTAATATTTAAAACT
502141 TATTTTT-ATA-TTAAAAC
1 TATTTTTAATATTTAAAAC
502158 AAGAGTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTAATATTTAAAACT
Found at i:502241 original size:60 final size:61
Alignment explanation
Indices: 502164--502287 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 61
502154 AAACAAGAGT
*
502164 AAAGTATATCCACCGACTAT-AGGATACTATTTT-TTCGAGTCATTCAACTATCACAAGTTAC
1 AAAGTATATCCACCGACTATAAGG-TACTATTTTATT-GAGTCATTCAACTATCAAAAGTTAC
* ** * * *
502225 AAAGTA-ATCCATCGACTATAAGGTTTTGTTTTATTGAGTCTTTCAACTATTAAAAGTTAC
1 AAAGTATATCCACCGACTATAAGGTACTATTTTATTGAGTCATTCAACTATCAAAAGTTAC
502285 AAA
1 AAA
502288 ATGGTTAACT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
60 43 0.80
61 11 0.20
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (61 bp):
AAAGTATATCCACCGACTATAAGGTACTATTTTATTGAGTCATTCAACTATCAAAAGTTAC
Found at i:503676 original size:53 final size:54
Alignment explanation
Indices: 503580--503682 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
503570 TTGACTTAAG
* *
503580 AATTTATAGAGTCGTTGAACATTTTTTTTATTTTCTAAAACTACGACTTCTAAA
1 AATTTATAAAGTCGTTGAACATTTTTTTCATTTTCTAAAACTACGACTTCTAAA
* *
503634 AATTTATAAATTCTTTGAACA-TTTTTTCATTTTCTAAAACTACGACTTC
1 AATTTATAAAGTCGTTGAACATTTTTTTCATTTTCTAAAACTACGACTTC
503683 AGAGTTCTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 27 0.60
54 18 0.40
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (54 bp):
AATTTATAAAGTCGTTGAACATTTTTTTCATTTTCTAAAACTACGACTTCTAAA
Found at i:505057 original size:19 final size:20
Alignment explanation
Indices: 505033--505080 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
505023 GGCAAAGAGC
505033 ATGTATTTTCATT-AAAATA
1 ATGTATTTTCATTAAAAATA
*
505052 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATTAAAAATA
505072 ATGTATTTT
1 ATGTATTTT
505081 TAAAGGGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATA
Found at i:505176 original size:33 final size:33
Alignment explanation
Indices: 505134--505208 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
505124 GCCTAAACCC
505134 TTTGAAAACTATAAATAGGACATTAGTTTGTCA
1 TTTGAAAACTATAAATAGGACATTAGTTTGTCA
*
505167 TTTGAAAACTATAAATAGGCCATTAGTTTGTCA
1 TTTGAAAACTATAAATAGGACATTAGTTTGTCA
505200 TTTGAAAAC
1 TTTGAAAAC
505209 AATCATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (33 bp):
TTTGAAAACTATAAATAGGACATTAGTTTGTCA
Found at i:512880 original size:2 final size:2
Alignment explanation
Indices: 512873--512910 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
512863 TCATTGCTTT
512873 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
512911 AGCCACGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:522867 original size:19 final size:20
Alignment explanation
Indices: 522843--522880 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
522833 TGAAAATGGT
522843 TTGATTTTGAAAG-CAAAAG
1 TTGATTTTGAAAGTCAAAAG
522862 TTGATTTTGAAAGTCAAAA
1 TTGATTTTGAAAGTCAAAA
522881 TGAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (20 bp):
TTGATTTTGAAAGTCAAAAG
Found at i:525380 original size:3 final size:3
Alignment explanation
Indices: 525372--525396 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
525362 TTCATCCCGC
525372 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
525397 TTTAATTTAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:528359 original size:20 final size:20
Alignment explanation
Indices: 528328--528374 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
528318 TGGTCATCCA
528328 ATTTTCTAAACCCCAGACCGG
1 ATTTT-TAAACCCCAGACCGG
*
528349 ATTTTTAAACCCTAGACCGG
1 ATTTTTAAACCCCAGACCGG
528369 ATTTTT
1 ATTTTT
528375 TTCCGGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (20 bp):
ATTTTTAAACCCCAGACCGG
Found at i:528964 original size:2 final size:2
Alignment explanation
Indices: 528957--528996 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
528947 GTTCCCATCA
528957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
528997 GACCACAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:529048 original size:21 final size:21
Alignment explanation
Indices: 529024--529068 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
529014 ATGTGTAATC
529024 ATAAGTAATTATTAATATGTA
1 ATAAGTAATTATTAATATGTA
529045 ATAAGTAATTATTAATATGTA
1 ATAAGTAATTATTAATATGTA
529066 ATA
1 ATA
529069 TATATAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (21 bp):
ATAAGTAATTATTAATATGTA
Found at i:529939 original size:21 final size:21
Alignment explanation
Indices: 529887--529945 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
529877 CATATGAAAA
* *
529887 CATCTTGCTCGAAGGTCTTAT
1 CATCTTGCTCGAAAGACTTAT
** *
529908 -AGATGGCTCGAAAGACTTAT
1 CATCTTGCTCGAAAGACTTAT
529928 CATCTTGCTCGAAAGACT
1 CATCTTGCTCGAAAGACT
529946 GACAGATGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (21 bp):
CATCTTGCTCGAAAGACTTAT
Found at i:529953 original size:41 final size:41
Alignment explanation
Indices: 529887--530012 Score: 119
Period size: 41 Copynumber: 3.0 Consensus size: 41
529877 CATATGAAAA
* * * *
529887 CATCTTGCTCGAAGGTCTTATAGATGGCTCGAAAGACTTAT
1 CATCTTGCTCGAAAGACTTACAGATGGCCCGAAAGACTTAT
* * * *
529928 CATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAAT
1 CATCTTGCTCGAAAGACTTACAGATGGCCCGAAAGACTT-AT
* ** *
529970 TAT-TATGCTTAAAAGACTTACTGATGGCCCGAAAGACTTAT
1 CATCT-TGCTCGAAAGACTTACAGATGGCCCGAAAGACTTAT
530011 CA
1 CA
530013 ATTTTGGAAA
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
41 35 0.53
42 31 0.47
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (41 bp):
CATCTTGCTCGAAAGACTTACAGATGGCCCGAAAGACTTAT
Found at i:530337 original size:257 final size:257
Alignment explanation
Indices: 529830--530478 Score: 793
Period size: 257 Copynumber: 2.5 Consensus size: 257
529820 TTAAAATATT
** * ** * *
529830 TTAAATGAGAAACTTTGAAAAT-AACTTTATCATTTTCTTACAAATACCATATGAAAACATCTTG
1 TTAAATGAGAAACTTTGAAAATCAA-TTTCCCA-TTT-TT-CAAAT-TCACGTGAAAACATCATA
* * *
529894 CTCGAAGGTCTTATAGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCG
61 CTCGAAGGTCTTACAGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGAATGACAGATGACCCA
* * *
529959 AAGGATTTAATTATTATGCTTAAAAGACTTACTGATGGCCCGAAAGACTTATCAATTTTGGAAAT
126 AAGGATTTAATTATCATGCTCAAAAGACTTACTGATGGCCCGAAAGACTTATCAATTTTAGAAAT
* *
530024 AGTCTACTGGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAAAAATTTCATTTTTTGAAAG
191 AGTCTACTGGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
530089 TA
256 TA
* * * *
530091 TTAAATGGGTAACTTTGAAAATCAATTTCCCATTTTTCAAATTCACGTGAAAACATCCTACCCGA
1 TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCACGTGAAAACATCATACTCGA
* * * * * *
530156 AGGTCATACAGATGGCCCGAAGGACTTATCATCTTGCTTGAGAGAATGATAGATGACCCAAAGGA
66 AGGTCTTACAGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGAATGACAGATGACCCAAAGGA
* *
530221 TTTAATTATCATGCTCGAAAGACTTACTGATGGCCACGAAGGACTTA-CAAATTTTAGAAATAGT
131 TTTAATTATCATGCTCAAAAGACTTACTGATGGCC-CGAAAGACTTATC-AATTTTAGAAATAGT
* * * *
530285 TTATTGTGTAAGAAACTTTGGAAATCACTTTCTTA-TTCTTC-AAAATTTCATTTTCTGAAAATA
194 CTACTGGGTAAGAAACTTTGGAAATCAATTTCTTACTT-TTCAAAAATTTCATTTTCTGAAAATA
*** * *
530348 TTAAATGAGAAACTTTGAAAATTGCTTTCCCATTTTTCAAATTCATGTGAAAACATCATACTTGA
1 TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCACGTGAAAACATCATACTCGA
* * * * * * * *
530413 AGGTTTTACGGATGGCTCGAATGACTTATCATCATGCTCAAAAGACTTACAGATGGCCCGAAAGG
66 AGGTCTTACAGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGAATGACAGATGACCC-AAAGG
530478 A
130 A
530479 CTTACTAAGT
Statistics
Matches: 331, Mismatches: 52, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
257 230 0.69
258 69 0.21
259 2 0.01
260 3 0.01
261 25 0.08
262 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (257 bp):
TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCACGTGAAAACATCATACTCGA
AGGTCTTACAGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGAATGACAGATGACCCAAAGGA
TTTAATTATCATGCTCAAAAGACTTACTGATGGCCCGAAAGACTTATCAATTTTAGAAATAGTCT
ACTGGGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATA
Found at i:530582 original size:198 final size:196
Alignment explanation
Indices: 530292--530659 Score: 499
Period size: 199 Copynumber: 1.9 Consensus size: 196
530282 AGTTTATTGT
*
530292 GTAAGAAACTTTGGAAATCACTTTCTTATTCTTCAAAATTTCATTTTCTGAAAATATTAAATGAG
1 GTAAGAAACTTTGGAAATCACTTTCTTATTCTTCAAAATTTCATTTTCAGAAAATATTAAATGAG
** * *** *
530357 AAACTTTGAAAATTGCTTTCCCA-TTTTTCAAATTCATGTGAAAACATCATACTTGAAGGTTTTA
66 AAACTTTGAAAATCACTTTCCCATTTTTTCAAAATCATGTGAAAACATCATACCCAAAGGTCTTA
*
530421 CGGATGG-CTCGAATGACTTATCATCATGCTCAAAAGACTTACAGATGGCCCGAAAGGACTTACT
131 CGGATGGCCT-GAAGGACTTATCATCATGCTCAAAAGACTTACAGATGGCCCGAAAGGACTTACT
530485 AA
195 AA
* *
530487 GTAAGAAACTTTGGAAATCATTTTTCTTACTTC-TCAAAATTTTCATTTTCAGAAAGTATTCAAA
1 GTAAGAAACTTTGGAAATCA-CTTTCTTA-TTCTTCAAAA-TTTCATTTTCAGAAAATATT-AAA
* * * * *
530551 TGAGAAACTTTGGAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTGCCCAAAGGT
62 TGAGAAACTTTGAAAATCACTTTCCCATTTTTTCAAAATCATGTGAAAACATCATACCCAAAGGT
** *
530616 CTTGTGGATGGCCTGAAGGACTTATCATCTTGCTCAAAAGACTT
127 CTTACGGATGGCCTGAAGGACTTATCATCATGCTCAAAAGACTT
530660 GATAGATGAC
Statistics
Matches: 148, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
195 20 0.14
196 13 0.09
197 21 0.14
198 26 0.18
199 66 0.45
200 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (196 bp):
GTAAGAAACTTTGGAAATCACTTTCTTATTCTTCAAAATTTCATTTTCAGAAAATATTAAATGAG
AAACTTTGAAAATCACTTTCCCATTTTTTCAAAATCATGTGAAAACATCATACCCAAAGGTCTTA
CGGATGGCCTGAAGGACTTATCATCATGCTCAAAAGACTTACAGATGGCCCGAAAGGACTTACTA
A
Found at i:530715 original size:42 final size:42
Alignment explanation
Indices: 530622--530722 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
530612 AGGTCTTGTG
* * *
530622 GATGGCCTGAAGGACTTATCATCTTGCTCAAAAGACTTGATA
1 GATGGCCCGAAGGACTTATCATCATGATCAAAAGACTTGATA
* * *
530664 GAT-GACCGAAGGATTTAATCATCATGATCGAAAGACTT-ACT-
1 GATGGCCCGAAGGACTT-ATCATCATGATCAAAAGACTTGA-TA
530705 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
530723 CTAAGTAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTATCATCATGATCAAAAGACTTGATA
Found at i:530867 original size:239 final size:239
Alignment explanation
Indices: 530440--531061 Score: 908
Period size: 239 Copynumber: 2.6 Consensus size: 239
530430 CGAATGACTT
* *
530440 ATCATCATGCTCAAAAGACTTACAGATGGCCCGAAAGGACTTACTAAGTAAGAAACTTTGGAAAT
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCG-AAGGACTTACTAAGTAAGAAACTTTGGAAAT
* * *
530505 CAT-TTTTCTTACTTCTCAAAATTTTCATTTTCAG-AAAGTATTCAAATGAGAAACTTTGGAAAT
65 --TGTTTTCTTACTTTTCAAAAATTTCATTTTCAGAAAAGT-TTTAAATGAGAAACTTTGGAAAT
* * * * *
530568 CACTTTCTCATTTTTTGAAAATCATGTGAAAACATCCTGCCCAAAGGTCTTGTGGATGGCCTGAA
127 CGCTTTCTCATTTTTTGAAAATCATGTGAAAACATCATACCCAAAGGTCTTATGGATGGCCAGAA
*
530633 GGACTTATCATCTTGCTCAAAAGACTTGATAGATGA-CCGAAGGATTTA
192 GGACTTATCATCTTGCTCAAAAGAC-TGATAGATGACCCGAAGAATTTA
*
530681 ATCATCATGATCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATT
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATT
* *
530746 GTTTTATTTCTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATGAGAAACTTTGGAAATCGCT
66 GTTTTCTTACTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATGAGAAACTTTGGAAATCGCT
* *
530811 TTCTCATTTTTTGAAAATCATGTGAAAACATCATACCCGAAGGTCTTATTGATGGCCAGAAGGAC
131 TTCTCATTTTTTGAAAATCATGTGAAAACATCATACCCAAAGGTCTTATGGATGGCCAGAAGGAC
*
530876 TTATCATCTTGCTCGAAAGACTGATAGATGACCCGAAGAATTTA
196 TTATCATCTTGCTCAAAAGACTGATAGATGACCCGAAGAATTTA
* * ** * * *
530920 ATCATCATGCTCGAAAGACTTACTAATGTCTTGAAGGACTTATTGAGTAAAAAAACTTTGGAAAT
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGT-AAGAAACTTTGGAAAT
* * * *
530985 TGTTTTCTTACTTTTCAAAAACTTCATTTTCAAAAAAGATTTAAATGAGATACTTTGGAAATCGC
65 TGTTTTCTTACTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATGAGAAACTTTGGAAATCGC
*
531050 TTTCTCAATTTT
130 TTTCTCATTTTT
531062 AAAAATAACT
Statistics
Matches: 345, Mismatches: 32, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
238 11 0.03
239 183 0.53
240 121 0.35
241 30 0.09
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (239 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATT
GTTTTCTTACTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATGAGAAACTTTGGAAATCGCT
TTCTCATTTTTTGAAAATCATGTGAAAACATCATACCCAAAGGTCTTATGGATGGCCAGAAGGAC
TTATCATCTTGCTCAAAAGACTGATAGATGACCCGAAGAATTTA
Found at i:532693 original size:2 final size:2
Alignment explanation
Indices: 532686--532714 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
532676 CTTTATTATG
532686 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
532715 ATCTCCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:540976 original size:2 final size:2
Alignment explanation
Indices: 540969--540993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
540959 TAAATTAATG
540969 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
540994 TACCACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:541102 original size:3 final size:3
Alignment explanation
Indices: 541094--541132 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
541084 AGCGTCTACA
* * *
541094 ATT ATT ATT ATT ATT TTT ATT TTT ATT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
541133 TGTAATTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:541391 original size:16 final size:16
Alignment explanation
Indices: 541370--541403 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
541360 ACACAACATC
541370 ATAATCA-TTGTATTTT
1 ATAATCATTTG-ATTTT
541386 ATAATCATTTGATTTT
1 ATAATCATTTGATTTT
541402 AT
1 AT
541404 CAGACAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
ATAATCATTTGATTTT
Found at i:548519 original size:23 final size:22
Alignment explanation
Indices: 548418--548549 Score: 237
Period size: 22 Copynumber: 5.9 Consensus size: 22
548408 AGTCGAGGGT
*
548418 TACATAGGTTCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
548440 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
548462 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
548484 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
548506 TACATGAGGTCCTTCGGGACATA
1 TACAT-AGGTCCTTCGGGACATA
548529 TACATGAGGTCCTTCGGGACA
1 TACAT-AGGTCCTTCGGGACA
548550 AATTTCATAT
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
22 70 0.65
23 38 0.35
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:552432 original size:25 final size:25
Alignment explanation
Indices: 552375--552423 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
552365 CTATAGGAAG
552375 GGGAGCCAAGGTTGGAAGAGAGCTA
1 GGGAGCCAAGGTTGGAAGAGAGCTA
552400 GGGAGCCAAGGTTGGAAGAGAGCT
1 GGGAGCCAAGGTTGGAAGAGAGCT
552424 GGAGTGCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.45, T:0.12
Consensus pattern (25 bp):
GGGAGCCAAGGTTGGAAGAGAGCTA
Found at i:556715 original size:9 final size:8
Alignment explanation
Indices: 556701--556773 Score: 69
Period size: 9 Copynumber: 8.6 Consensus size: 8
556691 ATGAAAAATG
*
556701 AAAAATGA
1 AAAAAAGA
556709 AAAAAATGA
1 AAAAAA-GA
556718 AAAAAAGGGA
1 AAAAAA--GA
556728 AAAAAGAGA
1 AAAAA-AGA
556737 AAAAAAG-
1 AAAAAAGA
556744 AAAAAAGA
1 AAAAAAGA
556752 AAGAAAA-A
1 AA-AAAAGA
556760 AGAAAAAGA
1 A-AAAAAGA
556769 AAAAA
1 AAAAA
556774 CAAAATGGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
7 7 0.12
8 19 0.34
9 22 0.39
10 7 0.12
11 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:556721 original size:7 final size:7
Alignment explanation
Indices: 556522--556708 Score: 256
Period size: 7 Copynumber: 26.9 Consensus size: 7
556512 GAAGGAAGAA
*
556522 AAATGAA
1 AAATGAG
*
556529 AAATGAA
1 AAATGAG
*
556536 AAATGAA
1 AAATGAG
556543 AAATGAG
1 AAATGAG
556550 AAATGAG
1 AAATGAG
556557 AAATGAG
1 AAATGAG
556564 AAATGAG
1 AAATGAG
556571 AAATGAG
1 AAATGAG
556578 AAATGAG
1 AAATGAG
556585 AAATGAG
1 AAATGAG
556592 AAATGAG
1 AAATGAG
556599 AAATGAG
1 AAATGAG
556606 AAATGAG
1 AAATGAG
556613 AAATGAG
1 AAATGAG
556620 AAATGAG
1 AAATGAG
556627 AAATGAG
1 AAATGAG
556634 AAATGAG
1 AAATGAG
556641 AAATGAG
1 AAATGAG
*
556648 AAATGAA
1 AAATGAG
556655 AAATGA-
1 AAATGAG
556661 AAATG-G
1 AAATGAG
556667 AAAATG-G
1 -AAATGAG
556674 AAAATG-G
1 -AAATGAG
*
556681 AAAATGAA
1 -AAATGAG
*
556689 AAATGAA
1 AAATGAG
*
556696 AAATGAA
1 AAATGAG
556703 AAATGA
1 AAATGA
556709 AAAAAATGAA
Statistics
Matches: 174, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
6 5 0.03
7 169 0.97
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.14
Consensus pattern (7 bp):
AAATGAG
Found at i:556729 original size:19 final size:19
Alignment explanation
Indices: 556707--556761 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
556697 AATGAAAAAT
556707 GAAAAAA-ATGAAAAAAAGG
1 GAAAAAAGA-GAAAAAAAGG
556726 GAAAAAAGAGAAAAAAA--
1 GAAAAAAGAGAAAAAAAGG
*
556743 GAAAAAAGAAAGAAAAAAG
1 GAAAAAAGAGA-AAAAAAG
556762 AAAAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 10 0.31
18 6 0.19
19 15 0.47
20 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (19 bp):
GAAAAAAGAGAAAAAAAGG
Found at i:556741 original size:11 final size:10
Alignment explanation
Indices: 556727--556778 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
556717 AAAAAAAGGG
*
556727 AAAAAAGAGA
1 AAAAAAGAAA
556737 AAAAAAGAAA
1 AAAAAAGAAA
556747 AAAGAAAGAAA
1 AAA-AAAGAAA
*
556758 AAAGAAA-AAG
1 AAA-AAAGAAA
*
556768 AAAAAACAAA
1 AAAAAAGAAA
556778 A
1 A
556779 TGGGAGTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 3 0.08
10 20 0.54
11 14 0.38
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:556757 original size:28 final size:28
Alignment explanation
Indices: 556707--556766 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
556697 AATGAAAAAT
**
556707 GAAAAAAATGAAAAAAAGGGAAAAAAGA
1 GAAAAAAATGAAAAAAAAAGAAAAAAGA
556735 GAAAAAAA-GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAATGAAAAAA-AAAGAAAAAAGA
556763 -AAAA
1 GAAAA
556767 GAAAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (28 bp):
GAAAAAAATGAAAAAAAAAGAAAAAAGA
Found at i:556767 original size:17 final size:17
Alignment explanation
Indices: 556687--556773 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
556677 ATGGAAAATG
* *
556687 AAAAATGAAAAATGAAA
1 AAAAAAGAAAAAAGAAA
** *
556704 AATGAA-AAAAATGAAA
1 AAAAAAGAAAAAAGAAA
** *
556720 AAAAGGGAAAAAAGAGA
1 AAAAAAGAAAAAAGAAA
556737 AAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAGAAA
556754 GAAAAAAG-AAAAAGAAA
1 -AAAAAAGAAAAAAGAAA
556771 AAA
1 AAA
556774 CAAAATGGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
16 15 0.27
17 34 0.61
18 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAA
Found at i:556773 original size:7 final size:7
Alignment explanation
Indices: 556681--556778 Score: 58
Period size: 7 Copynumber: 13.4 Consensus size: 7
556671 TGGAAAATGG
*
556681 AAAATGA
1 AAAAAGA
*
556688 AAAATGA
1 AAAAAGA
*
556695 AAAATGA
1 AAAAAGA
*
556702 AAAATGAA
1 AAAAAG-A
556710 AAAAATGAA
1 AAAAA-G-A
556719 AAAAAGGGA
1 AAAAA--GA
556728 AAAAAGA
1 AAAAAGA
556735 GAAAAA-A
1 -AAAAAGA
556742 AGAAAA-A
1 A-AAAAGA
*
556749 AGAAAGA
1 AAAAAGA
556756 AAAAAG-
1 AAAAAGA
556762 AAAAAGA
1 AAAAAGA
*
556769 AAAAACA
1 AAAAAGA
556776 AAA
1 AAA
556779 TGGGAGTTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
6 10 0.13
7 44 0.56
8 10 0.13
9 14 0.18
10 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (7 bp):
AAAAAGA
Found at i:558434 original size:136 final size:135
Alignment explanation
Indices: 558021--558598 Score: 635
Period size: 135 Copynumber: 4.3 Consensus size: 135
558011 AACTCAATTT
* * * ** * * **
558021 AATCTTCCTTGAAGAA-TAGTGGAATAAATCAACGTCCCCATATCTAATTTTCCTTGAAGAAAAA
1 AATCTTCCCTGAAGAACT-GTGGAATGAATCAACATTTCCATATCTAATTTTCCCTCAAGAAGCA
* * * * *
558085 GTGGAACAGATCCCCTCTCTTTTCAAATTTGATCTTCCCTGTGTAGCATTGGAACAAGTCTGCCT
65 GCGGAACATATCCCCTCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCT
558150 CGATTC
130 CGATTC
* * * * * *
558156 AATTTTCCCTGAAGAACAGTGGAATGAGTCAACATTTCTAGATCTAATTTTCCCTCAAGAAGTAG
1 AATCTTCCCTGAAGAACTGTGGAATGAATCAACATTTCCATATCTAATTTTCCCTCAAGAAGCAG
* * * * * * ** * *
558221 CGAAACAAAT-CACTCTTTTTTCCAAATTTGATTTTCCCTGAGGAATAGTGAAACAAATCTGCCT
66 CGGAACATATCCCCTC-TCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCT
*
558285 TGATTC
130 CGATTC
* *
558291 AATCTTCCCTGAAGAACTGTGGAATGAATCAACATTTCCATATTTGATTTTCCCTCAAGAAGCAG
1 AATCTTCCCTGAAGAACTGTGGAATGAATCAACATTTCCATATCTAATTTTCCCTCAAGAAGCAG
* * *
558356 CGGAACATATCCCTCTCTCTTTCCATATTTGATCTTCCCTGAGTAGTAGTGGAACAAGTCTGCTT
66 CGGAACATATCCC-CTCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCT
*
558421 CGGTTC
130 CGATTC
* * * *
558427 AATCTTCCCTGAAGAA-TAGTGTAATGAATCAACATTTCCATATCTGATTTTCCCTAAAAAAGCA
1 AATCTTCCCTGAAGAACT-GTGGAATGAATCAACATTTCCATATCTAATTTTCCCTCAAGAAGCA
* * * * *
558491 TG-GGAACATAT-CCCTCTCTTTCCAGATTTGTTCTTCCCTGGGTAGCAGTGGAACTAGTCTACC
65 -GCGGAACATATCCCCTCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCC
558554 TCGATTC
129 TCGATTC
* * *
558561 AATATTCCCTGAATAACAGTGGAATGAATCAACATTTC
1 AATCTTCCCTGAAGAACTGTGGAATGAATCAACATTTC
558599 TCGATCTGAT
Statistics
Matches: 370, Mismatches: 66, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
134 86 0.23
135 168 0.45
136 112 0.30
137 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (135 bp):
AATCTTCCCTGAAGAACTGTGGAATGAATCAACATTTCCATATCTAATTTTCCCTCAAGAAGCAG
CGGAACATATCCCCTCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCTC
GATTC
Found at i:558771 original size:3 final size:3
Alignment explanation
Indices: 558763--558788 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
558753 TTTATCCCGC
558763 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
558789 ATTTATGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:560926 original size:7 final size:8
Alignment explanation
Indices: 560899--560933 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
560889 CTATATTTAT
560899 TTAAAATA
1 TTAAAATA
560907 TTAAAATA
1 TTAAAATA
560915 TTAAAA-A
1 TTAAAATA
560922 TT-AAATA
1 TTAAAATA
560929 TTAAA
1 TTAAA
560934 TTACAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 6 0.24
8 16 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TTAAAATA
Found at i:562131 original size:25 final size:26
Alignment explanation
Indices: 562089--562145 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
562079 TGTGATAATT
562089 TAATAATAATATTATATAATAAT-AA
1 TAATAATAATATTATATAATAATAAA
* *
562114 TAATAATAATA-TATTATATTATTAAA
1 TAATAATAATATTA-TATAATAATAAA
562140 TAATAA
1 TAATAA
562146 AAACAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 18 0.64
26 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAATAATAATATTATATAATAATAAA
Found at i:562144 original size:3 final size:3
Alignment explanation
Indices: 562089--562124 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
562079 TGTGATAATT
*
562089 TAA TAA TAA TAT TATA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
562125 TATTATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 28 0.93
4 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:563477 original size:2 final size:2
Alignment explanation
Indices: 563470--563498 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
563460 CCGATCCGAT
563470 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
563499 TTTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:569045 original size:13 final size:13
Alignment explanation
Indices: 569027--569052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
569017 GCGGACTATT
569027 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
569040 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
569053 GACATCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:584431 original size:12 final size:12
Alignment explanation
Indices: 584396--584424 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
584386 AGAAAAACCT
584396 GAAAAAGATAAG
1 GAAAAAGATAAG
584408 GAAAAAGATAAG
1 GAAAAAGATAAG
584420 GAAAA
1 GAAAA
584425 TAATAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (12 bp):
GAAAAAGATAAG
Found at i:585050 original size:17 final size:17
Alignment explanation
Indices: 585028--585062 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
585018 CTAAAGGTGC
*
585028 CCTATGTTATCTCTAGT
1 CCTATGATATCTCTAGT
585045 CCTATGATATCTCTAGT
1 CCTATGATATCTCTAGT
585062 C
1 C
585063 AATGGACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.43
Consensus pattern (17 bp):
CCTATGATATCTCTAGT
Found at i:589797 original size:19 final size:20
Alignment explanation
Indices: 589755--589798 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
589745 AATTTGAATT
*
589755 TTTTATAATAATTAACTTTA
1 TTTTATAATAATTAACTGTA
*
589775 TTTTATAATAATTTA-TGTA
1 TTTTATAATAATTAACTGTA
589794 TTTTA
1 TTTTA
589799 AGTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATAATAATTAACTGTA
Found at i:589903 original size:29 final size:30
Alignment explanation
Indices: 589858--589935 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 30
589848 TATAAAATTA
*
589858 AATTAAAAATAT-A--TTTTATTGTTAT-T
1 AATTAAAAATATAATTTTTTATTCTTATCT
*
589884 TATTAAAAATATAATTTTTTATTCTTATCT
1 AATTAAAAATATAATTTTTTATTCTTATCT
*
589914 AACATAAAAATATATATTTTTT
1 AA-TTAAAAATATA-ATTTTTT
589936 CTCATCTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 11 0.26
27 1 0.02
29 11 0.26
30 2 0.05
31 10 0.24
32 7 0.17
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (30 bp):
AATTAAAAATATAATTTTTTATTCTTATCT
Done.