Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 30 of 117
Found at i:4386272 original size:2 final size:2
Alignment explanation
Indices: 4386265--4386292 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4386255 AGACATGAGA
4386265 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
4386293 GTGGGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4386443 original size:19 final size:20
Alignment explanation
Indices: 4386409--4386447 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4386399 ACAAAACATG
*
4386409 CAAGGTGTGCAAGAAAGACA
1 CAAGGGGTGCAAGAAAGACA
4386429 CAAGGGGTG-AAGAAAGACA
1 CAAGGGGTGCAAGAAAGACA
4386448 AATAGACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.46, C:0.13, G:0.33, T:0.08
Consensus pattern (20 bp):
CAAGGGGTGCAAGAAAGACA
Found at i:4390685 original size:13 final size:13
Alignment explanation
Indices: 4390669--4390711 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
4390659 TTAATTTACA
4390669 TATATATAAAAAT
1 TATATATAAAAAT
4390682 TATATATGTAAAAAT
1 TATATA--TAAAAAT
* *
4390697 TAAAAATAAAAAT
1 TATATATAAAAAT
4390710 TA
1 TA
4390712 AGTTTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TATATATAAAAAT
Found at i:4390686 original size:15 final size:15
Alignment explanation
Indices: 4390668--4390711 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
4390658 TTTAATTTAC
4390668 ATATATATAAAAATT
1 ATATATATAAAAATT
*
4390683 ATATATGTAAAAATT
1 ATATATATAAAAATT
*
4390698 A-A-AAATAAAAATT
1 ATATATATAAAAATT
4390711 A
1 A
4390712 AGTTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
15 15 0.58
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
ATATATATAAAAATT
Found at i:4392347 original size:57 final size:57
Alignment explanation
Indices: 4392259--4392372 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
4392249 AATGAAATCA
* * *
4392259 TAAATTGGCAGTTGAAATTACGGATGATTGGTTTTCATTAATTTATCACACTTGAAT
1 TAAATTGGCAGTTGAAAGTACGGATGATTGGTCTTCATTAATTCATCACACTTGAAT
*
4392316 TAAATTGGCAGTTGAAAGTATGGATGATTGGTCTTCATTAATTCATCACACTTGAAT
1 TAAATTGGCAGTTGAAAGTACGGATGATTGGTCTTCATTAATTCATCACACTTGAAT
4392373 GTCAAAAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (57 bp):
TAAATTGGCAGTTGAAAGTACGGATGATTGGTCTTCATTAATTCATCACACTTGAAT
Found at i:4398612 original size:12 final size:13
Alignment explanation
Indices: 4398586--4398610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4398576 ATCTAATTTA
4398586 ATTTAATTTTTTT
1 ATTTAATTTTTTT
4398599 ATTTAATTTTTT
1 ATTTAATTTTTT
4398611 ATACAATCGA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTAATTTTTTT
Found at i:4401832 original size:2 final size:2
Alignment explanation
Indices: 4401825--4401853 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4401815 AACATAGATA
4401825 AT 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 AT A
4401854 GTCCTCAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4403898 original size:137 final size:139
Alignment explanation
Indices: 4403648--4403925 Score: 425
Period size: 137 Copynumber: 2.0 Consensus size: 139
4403638 CCGGCAGTGC
* * * *
4403648 AGCACGGTGTGATTGATTATTTTTGGTGGGTCTAATGGCAACATCTATCTGTACATCACCATCCA
1 AGCACGGTGTGACTGATTACTTTTGGTGAGTCTAATGG--ACAGCTATCTGTACATCACCATCCA
* *
4403713 ATATTACCAACGAAGAACGCTATGTTGTTACCAATGAAGACCGTCTTAATAAAGAGAACTTTTTT
64 ATATTACCAACGAAGAACGCTATGGTGTTACCAATGAAGACCGTCTTAATAAAGAGAACATTTTT
4403778 CATAAGACCAA
129 CATAAGACCAA
* * *
4403789 AGCACTGTGTGACTGATTACTTTTGGTGAGTCTAATGG-CAGC-ATCTGTATATCACCATCCACT
1 AGCACGGTGTGACTGATTACTTTTGGTGAGTCTAATGGACAGCTATCTGTACATCACCATCCAAT
* *
4403852 ATTACCAACGAAGAACGCTGTGGTGTTGCCAATGAAGACCGTCTTAATAAAGAGAACATTTTTCA
66 ATTACCAACGAAGAACGCTATGGTGTTACCAATGAAGACCGTCTTAATAAAGAGAACATTTTTCA
4403917 TAAGACCAA
131 TAAGACCAA
4403926 TATTTAGGAT
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
137 89 0.71
138 3 0.02
141 34 0.27
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (139 bp):
AGCACGGTGTGACTGATTACTTTTGGTGAGTCTAATGGACAGCTATCTGTACATCACCATCCAAT
ATTACCAACGAAGAACGCTATGGTGTTACCAATGAAGACCGTCTTAATAAAGAGAACATTTTTCA
TAAGACCAA
Found at i:4408118 original size:22 final size:23
Alignment explanation
Indices: 4408094--4408137 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4408084 AAAAAAAGTA
4408094 AAAAAT-AAAAGATA-TATTTTT
1 AAAAATAAAAAGATACTATTTTT
*
4408115 AAAATTAAAAAGATACTATTTTT
1 AAAAATAAAAAGATACTATTTTT
4408138 TTTAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AAAAATAAAAAGATACTATTTTT
Found at i:4413676 original size:63 final size:63
Alignment explanation
Indices: 4413571--4413696 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
4413561 AAGATCACTT
*
4413571 GGTGTTGTCTCTTCCTTGGATTCCTGCTTTATGATTGGAGTGGTAGATGGGTTCAAGTGATGA
1 GGTGTTGTCTCTTCCTTGGATTCCTGCTTTATGATTGCAGTGGTAGATGGGTTCAAGTGATGA
4413634 GGTGTTGTCTCTTCCTTGGATTCCTGCTTTATCG-TTGCAGTGGTAGATGGGTTCAAGTGATGA
1 GGTGTTGTCTCTTCCTTGGATTCCTGCTTTAT-GATTGCAGTGGTAGATGGGTTCAAGTGATGA
4413697 TGCTGTGGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 60 0.98
64 1 0.02
ACGTcount: A:0.15, C:0.14, G:0.31, T:0.40
Consensus pattern (63 bp):
GGTGTTGTCTCTTCCTTGGATTCCTGCTTTATGATTGCAGTGGTAGATGGGTTCAAGTGATGA
Found at i:4416387 original size:25 final size:23
Alignment explanation
Indices: 4416331--4416388 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
4416321 AAATAACTAT
*
4416331 TATATA-AAAAAATTTATTTAAA
1 TATATATAAAAAATTTATTAAAA
4416353 TATAT-T-AAAAATCTTATTAAAA
1 TATATATAAAAAAT-TTATTAAAA
4416375 TAATATATAAAAAA
1 T-ATATATAAAAAA
4416389 ATTAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.20
22 14 0.47
23 4 0.13
24 1 0.03
25 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TATATATAAAAAATTTATTAAAA
Found at i:4418067 original size:13 final size:13
Alignment explanation
Indices: 4418051--4418102 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
4418041 AAAATATTTT
4418051 TATTAAATTAATA
1 TATTAAATTAATA
*
4418064 TATTAAATTAAAA
1 TATTAAATTAATA
*
4418077 TATTATA-TAATA
1 TATTAAATTAATA
**
4418089 -ATTTTATTAATA
1 TATTAAATTAATA
4418101 TA
1 TA
4418103 ATATATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.15
12 9 0.27
13 19 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTAAATTAATA
Found at i:4418083 original size:18 final size:18
Alignment explanation
Indices: 4418028--4418084 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
4418018 TTACATCTTA
4418028 ATTATATATAAA-TAAAAT
1 ATTATAT-TAAATTAAAAT
*
4418046 ATT-T-TT--ATTAAATT
1 ATTATATTAAATTAAAAT
*
4418060 AATATATTAAATTAAAAT
1 ATTATATTAAATTAAAAT
4418078 ATTATAT
1 ATTATAT
4418085 AATAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
13 1 0.03
14 7 0.23
15 2 0.07
16 3 0.10
17 1 0.03
18 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATATTAAATTAAAAT
Found at i:4418097 original size:29 final size:28
Alignment explanation
Indices: 4418064--4418119 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
4418054 TAAATTAATA
*
4418064 TATTAA-ATTAAAATATTATATAATAATTT
1 TATTAATA-TAAAATATAATATAA-AATTT
*
4418093 TATTAATATAATATATAATATAAAATT
1 TATTAATATAAAATATAATATAAAATT
4418120 AAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 19 0.79
30 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTAATATAAAATATAATATAAAATTT
Found at i:4418124 original size:24 final size:24
Alignment explanation
Indices: 4418063--4418132 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
4418053 TTAAATTAAT
*
4418063 ATATTAAATTAAA-ATATTATATA
1 ATATTAAATTAAATATAATATATA
**
4418086 ATAATTTTATT-AATATAATATATA
1 AT-ATTAAATTAAATATAATATATA
*
4418110 ATATAAAATTAAATA-AATA-ATA
1 ATATTAAATTAAATATAATATATA
4418132 A
1 A
4418133 AAAATATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 4 0.11
23 13 0.34
24 21 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTAAATTAAATATAATATATA
Found at i:4422519 original size:11 final size:11
Alignment explanation
Indices: 4422492--4422520 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4422482 ATTTGAATTA
4422492 TATATTTTTAT
1 TATATTTTTAT
4422503 TA-ATTTTTAT
1 TATATTTTTAT
4422513 TATATTTT
1 TATATTTT
4422521 AAATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:4422592 original size:22 final size:22
Alignment explanation
Indices: 4422549--4422592 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4422539 AATAATTATT
* *
4422549 TTATACTTAAATTTATTAAAAA
1 TTATACTTAAAATAATTAAAAA
4422571 TTATA-TTAAAATAATTATAAAA
1 TTATACTTAAAATAATTA-AAAA
4422593 ACTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATACTTAAAATAATTAAAAA
Found at i:4422718 original size:2 final size:2
Alignment explanation
Indices: 4422711--4422748 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4422701 TATAATTTAA
*
4422711 AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
4422749 CGTTTTGGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4432325 original size:14 final size:13
Alignment explanation
Indices: 4432306--4432336 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
4432296 ATTAATATAT
4432306 ATATATATGTATGG
1 ATATATATGT-TGG
4432320 ATATATATGTTGG
1 ATATATATGTTGG
4432333 ATAT
1 ATAT
4432337 CTCTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (13 bp):
ATATATATGTTGG
Found at i:4445979 original size:170 final size:169
Alignment explanation
Indices: 4445693--4446006 Score: 477
Period size: 170 Copynumber: 1.9 Consensus size: 169
4445683 CAAACATGCT
* *
4445693 TTGTATTATTAGGTTAAATTATAGCATTTGTTGACACGTAGTTTGTAATTGTGATTTTTTTTATT
1 TTGTATTATTAGATTAAATTATAGCATTTGTTGACACGCAGTTTGTAATTGTGATTTTTTTTATT
* * **
4445758 TTTAAATAAATTTAAGGTTTTTTATGTCACGATAATATGTCTAATATTTGATAATTTAAAATAGG
66 TTTAAATAAATTTAAGGTTTTTCATGTCACGATAATATGTCTAATATTTGATAATTTAAAACAAA
4445823 TGATTACAAGTTATGTAACATGTAATTGTGGTATGTAAC
131 TGATTACAAGTTATGTAACATGTAATTGTGGTATGTAAC
* * * *
4445862 TTGTAATTATTAGATTAAATTATAGCATTTGTTGATATGCAGTTTGTAATTTTGGTTTTTTTTAT
1 TTGT-ATTATTAGATTAAATTATAGCATTTGTTGACACGCAGTTTGTAATTGTGATTTTTTTTAT
* * *
4445927 TTTTAAATAAATTTGAGGTTTTTCATGTCATGATAATATGTAC-AATATTTGATAGTTTAAAACA
65 TTTTAAATAAATTTAAGGTTTTTCATGTCACGATAATATGT-CTAATATTTGATAATTTAAAACA
*
4445991 AATGATTATAAGTTAT
129 AATGATTACAAGTTAT
4446007 ATATTCGAGA
Statistics
Matches: 129, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
169 4 0.03
170 124 0.96
171 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.48
Consensus pattern (169 bp):
TTGTATTATTAGATTAAATTATAGCATTTGTTGACACGCAGTTTGTAATTGTGATTTTTTTTATT
TTTAAATAAATTTAAGGTTTTTCATGTCACGATAATATGTCTAATATTTGATAATTTAAAACAAA
TGATTACAAGTTATGTAACATGTAATTGTGGTATGTAAC
Found at i:4447356 original size:13 final size:13
Alignment explanation
Indices: 4447316--4447372 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
4447306 TATCAAAATA
4447316 ATTAATAAATTTAT
1 ATTAA-AAATTTAT
*
4447330 AATT-TAAATATTAT
1 -ATTAAAAAT-TTAT
4447344 ATTAAAAATTTAT
1 ATTAAAAATTTAT
*
4447357 ATTAAATATTT-T
1 ATTAAAAATTTAT
4447369 ATTA
1 ATTA
4447373 TAATTAAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.14
13 21 0.57
14 8 0.22
15 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTAAAAATTTAT
Found at i:4447361 original size:25 final size:28
Alignment explanation
Indices: 4447316--4447372 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 28
4447306 TATCAAAATA
4447316 ATTAATAAATTTATAATTTAAATATTAT
1 ATTAATAAATTTATAATTTAAATATTAT
*
4447344 ATTAA-AAATTTAT-A-TTAAATATTTT
1 ATTAATAAATTTATAATTTAAATATTAT
4447369 ATTA
1 ATTA
4447373 TAATTAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 14 0.50
26 1 0.04
27 8 0.29
28 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTAATAAATTTATAATTTAAATATTAT
Found at i:4447849 original size:21 final size:22
Alignment explanation
Indices: 4447825--4447869 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4447815 CTTTTATATA
*
4447825 AATTT-AATTTTAAAATTAATT
1 AATTTAAATTTAAAAATTAATT
*
4447846 AATTTAAATTTAAAAATTATTT
1 AATTTAAATTTAAAAATTAATT
4447868 AA
1 AA
4447870 ATTTGAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTAAATTTAAAAATTAATT
Found at i:4449695 original size:1 final size:1
Alignment explanation
Indices: 4449689--4449713 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4449679 GTGAATGGAG
4449689 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
4449714 GGACTGCAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4451868 original size:2 final size:2
Alignment explanation
Indices: 4451861--4451891 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4451851 ACAGGGTTCT
4451861 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4451892 CAAACAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4455658 original size:18 final size:19
Alignment explanation
Indices: 4455628--4455665 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4455618 AAATAAAAAA
4455628 ATTAAATTATATAT-TTTT
1 ATTAAATTATATATATTTT
4455646 ATTAATATT-TATATATTTT
1 ATTAA-ATTATATATATTTT
4455665 A
1 A
4455666 AATTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTAAATTATATATATTTT
Found at i:4455731 original size:22 final size:20
Alignment explanation
Indices: 4455691--4455741 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
4455681 AAATAATTAT
4455691 TATATATAATTATTTAAAT-A
1 TATATA-AATTATTTAAATAA
4455711 TATTATAAATTATATTAAAATAA
1 TA-TATAAATTAT-TT-AAATAA
4455734 TATATAAA
1 TATATAAA
4455742 AGATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.30
21 6 0.22
22 10 0.37
23 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATAAATTATTTAAATAA
Found at i:4455737 original size:20 final size:21
Alignment explanation
Indices: 4455692--4455740 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4455682 AATAATTATT
4455692 ATATATAATTATTTAAATATA
1 ATATATAATTATTTAAATATA
*
4455713 TTATA-AATTATATTAAA-ATA
1 ATATATAATTAT-TTAAATATA
4455733 ATATATAA
1 ATATATAA
4455741 AAGATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATATAATTATTTAAATATA
Found at i:4463721 original size:2 final size:2
Alignment explanation
Indices: 4463703--4463747 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
4463693 ATGCAGGTTC
*
4463703 CT CT CC CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4463744 CT CT
1 CT CT
4463748 GCATGAATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:4485042 original size:14 final size:13
Alignment explanation
Indices: 4485018--4485051 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4485008 ATAGTATTAC
4485018 AATTATTCGAAAAT
1 AATT-TTCGAAAAT
4485032 ATATTTTCGAAAAT
1 A-ATTTTCGAAAAT
4485046 AATTTT
1 AATTTT
4485052 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (13 bp):
AATTTTCGAAAAT
Found at i:4485881 original size:53 final size:53
Alignment explanation
Indices: 4485818--4485923 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
4485808 TATTTTTAAA
4485818 CTTAAATCTTAAATCTTTTGAAATTAAACATAAAATCACACGAAAAAAAAATT
1 CTTAAATCTTAAATCTTTTGAAATTAAACATAAAATCACACGAAAAAAAAATT
4485871 CTTAAATCTTAAATCTTTTGAAATTAAACATAAAATCACACGAAAAAAAAATT
1 CTTAAATCTTAAATCTTTTGAAATTAAACATAAAATCACACGAAAAAAAAATT
4485924 ATCTTTGATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (53 bp):
CTTAAATCTTAAATCTTTTGAAATTAAACATAAAATCACACGAAAAAAAAATT
Found at i:4488846 original size:17 final size:18
Alignment explanation
Indices: 4488818--4488851 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4488808 TTCCGCCGAA
4488818 TGTTTCTTGTTTTTTTTT
1 TGTTTCTTGTTTTTTTTT
4488836 TGTTT-TTGTTTTTTTT
1 TGTTTCTTGTTTTTTTT
4488852 CCTTTCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (18 bp):
TGTTTCTTGTTTTTTTTT
Found at i:4489001 original size:30 final size:30
Alignment explanation
Indices: 4488943--4489023 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
4488933 TCTTTCAAAT
* * * * *
4488943 ATTTATTTTCATTCTATTTAACTCTTAAAC
1 ATTTATTTTCACTCAATTAAATTTTTAAAC
* *
4488973 ATTTATTTTCACTTAATTAAATTTTTAAAT
1 ATTTATTTTCACTCAATTAAATTTTTAAAC
4489003 ATTTATTTTCACTCAATTAAA
1 ATTTATTTTCACTCAATTAAA
4489024 CCATCAATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (30 bp):
ATTTATTTTCACTCAATTAAATTTTTAAAC
Found at i:4495353 original size:13 final size:13
Alignment explanation
Indices: 4495322--4495372 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
4495312 ATTTATTTTA
4495322 ATAAATTTCAATT
1 ATAAATTTCAATT
4495335 AT-AATTT-AATT
1 ATAAATTTCAATT
*
4495346 ATAAAATTTCAATC
1 AT-AAATTTCAATT
4495360 ATAAATTT-AATT
1 ATAAATTTCAATT
4495372 A
1 A
4495373 AAAAGTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 6 0.18
12 9 0.27
13 13 0.39
14 5 0.15
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAAATTTCAATT
Found at i:4495354 original size:25 final size:25
Alignment explanation
Indices: 4495319--4495381 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
4495309 AATATTTATT
*
4495319 TTAATAAATTTCAATTAT-AATTTAA
1 TTAA-AAATTTCAATCATAAATTTAA
4495344 TTATAAAATTTCAATCATAAATTTAA
1 TTA-AAAATTTCAATCATAAATTTAA
*
4495370 TTAAAAAGTTCA
1 TTAAAAATTTCA
4495382 TTTGTTACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 23 0.68
26 11 0.32
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAAAAATTTCAATCATAAATTTAA
Found at i:4501846 original size:4 final size:4
Alignment explanation
Indices: 4501837--4501861 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4501827 GTGGATCTCT
4501837 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
4501862 ATACATCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4506640 original size:3 final size:3
Alignment explanation
Indices: 4506632--4506657 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4506622 TGGAGTTGAA
4506632 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
4506658 TCCTCTGACC
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:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4507524 original size:2 final size:2
Alignment explanation
Indices: 4507517--4507560 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4507507 AATAAGAAAA
4507517 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
4507559 AG
1 AG
4507561 GTTTGGGGTA
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:4510711 original size:18 final size:19
Alignment explanation
Indices: 4510678--4510713 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4510668 TGTATAATAG
4510678 TGTATAAATATTTTATTTC
1 TGTATAAATATTTTATTTC
*
4510697 TGTATAAA-GTTTTATTT
1 TGTATAAATATTTTATTT
4510714 TTTATTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (19 bp):
TGTATAAATATTTTATTTC
Found at i:4513293 original size:21 final size:21
Alignment explanation
Indices: 4513267--4513308 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4513257 AAATAGGACT
4513267 AGCAAGAGTGGTCTCCACAAG
1 AGCAAGAGTGGTCTCCACAAG
4513288 AGCAAGAGTGGTCTCCACAAG
1 AGCAAGAGTGGTCTCCACAAG
4513309 GGCTCTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (21 bp):
AGCAAGAGTGGTCTCCACAAG
Found at i:4514355 original size:4 final size:4
Alignment explanation
Indices: 4514340--4514387 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
4514330 AAGATGGGAG
*
4514340 GGAA GGAG GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA
1 GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA GGAA
4514388 ATAGTGCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (4 bp):
GGAA
Found at i:4518609 original size:2 final size:2
Alignment explanation
Indices: 4518598--4518628 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4518588 CCCATGCATG
4518598 TA TA -A 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
4518629 GAAGGAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4524680 original size:24 final size:25
Alignment explanation
Indices: 4524628--4524683 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
4524618 CACAAGCGAG
4524628 GTGGTCAGTGGACCATGAGCTGCGT
1 GTGGTCAGTGGACCATGAGCTGCGT
* * *
4524653 -TGGTCAGTGGACCGTGAG-TTCTT
1 GTGGTCAGTGGACCATGAGCTGCGT
4524676 GTGGTCAG
1 GTGGTCAG
4524684 AGGATCACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.14, C:0.18, G:0.39, T:0.29
Consensus pattern (25 bp):
GTGGTCAGTGGACCATGAGCTGCGT
Found at i:4526904 original size:7 final size:7
Alignment explanation
Indices: 4526892--4526929 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
4526882 ACCTGGCCAC
*
4526892 GGCTGTA
1 GGCTGTT
4526899 GGCTGTT
1 GGCTGTT
4526906 GGCTGTT
1 GGCTGTT
4526913 GGCTGTT
1 GGCTGTT
*
4526920 GGCCGTT
1 GGCTGTT
4526927 GGC
1 GGC
4526930 ATAACCGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.03, C:0.18, G:0.45, T:0.34
Consensus pattern (7 bp):
GGCTGTT
Found at i:4527413 original size:14 final size:15
Alignment explanation
Indices: 4527394--4527423 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4527384 AAATTCATAA
4527394 ATTTTAAT-ATAATT
1 ATTTTAATAATAATT
4527408 ATTTTAATAATAATT
1 ATTTTAATAATAATT
4527423 A
1 A
4527424 ATTAACTCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATAATT
Found at i:4535589 original size:2 final size:2
Alignment explanation
Indices: 4535582--4535628 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4535572 TTAATTCTAC
*
4535582 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4535624 CA CA C
1 CA CA C
4535629 GTAAAGGGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4546556 original size:24 final size:24
Alignment explanation
Indices: 4546528--4546631 Score: 70
Period size: 32 Copynumber: 4.1 Consensus size: 24
4546518 TTTCAACAGT
4546528 ATAAATATTTTTAATATTTTATTA
1 ATAAATATTTTTAATATTTTATTA
*
4546552 ATAAATAATATTATTTTAACATTATTATATTA
1 AT--A-AATA-T-TTTT-A-A-TATTTTATTA
**
4546584 ATAAA-ATTAATAAT-TTTTA-TA
1 ATAAATATTTTTAATATTTTATTA
*
4546605 ATAAATAATTTTTAATATTTTAATA
1 ATAAAT-ATTTTTAATATTTTATTA
4546630 AT
1 AT
4546632 TATATCAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
21 7 0.11
22 4 0.06
23 8 0.13
24 8 0.13
25 5 0.08
26 3 0.05
27 5 0.08
28 2 0.03
29 6 0.10
30 2 0.03
31 1 0.02
32 11 0.18
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAAATATTTTTAATATTTTATTA
Found at i:4546671 original size:16 final size:17
Alignment explanation
Indices: 4546645--4546677 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4546635 ATCAATATCA
4546645 TTTAAATAAAAAATAAT
1 TTTAAATAAAAAATAAT
4546662 TTTAAA-AAAAAATAAT
1 TTTAAATAAAAAATAAT
4546678 CAAACAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTAAATAAAAAATAAT
Found at i:4563283 original size:234 final size:234
Alignment explanation
Indices: 4562874--4563348 Score: 941
Period size: 234 Copynumber: 2.0 Consensus size: 234
4562864 GTGAATCAAA
4562874 TAAGCTTTAACATAATATGAAAGTAAACAAAAATGGATTAACTATAGCCATCTCAAACAAACATA
1 TAAGCTTTAACATAATATGAAAGTAAACAAAAATGGATTAACTATAGCCATCTCAAACAAACATA
4562939 GAAATATACGATATAATTAAACTAGTGTTATCAACTTATTCATATATTTGGATAAGAAAACCAAC
66 GAAATATACGATATAATTAAACTAGTGTTATCAACTTATTCATATATTTGGATAAGAAAACCAAC
4563004 TTTGGCAAGCTCCTGCTTTTCATAGACTTTTAGCATATTTTCTATTGAAAAGGTACCACGTTAAA
131 TTTGGCAAGCTCCTGCTTTTCATAGACTTTTAGCATATTTTCTATTGAAAAGGTACCACGTTAAA
4563069 CACCTTCATTTTCCAGAAAAAGACAGCCTCTGTTGATAC
196 CACCTTCATTTTCCAGAAAAAGACAGCCTCTGTTGATAC
4563108 TAAGCTTTAACATAATATGAAAGTAAACAAAAATGGATTAACTATAGCCATCTCAAACAAACATA
1 TAAGCTTTAACATAATATGAAAGTAAACAAAAATGGATTAACTATAGCCATCTCAAACAAACATA
4563173 GAAATATACGATATAATTAAACTAGTGTTATCAACTTATTCATATATTTGGATAAGAAAACCAAC
66 GAAATATACGATATAATTAAACTAGTGTTATCAACTTATTCATATATTTGGATAAGAAAACCAAC
4563238 TTTGGCAAGCTCCTGCTTTTCATAGACTTTTAGCATATTTTCTATTGAAAAGGTACCACGTTAAA
131 TTTGGCAAGCTCCTGCTTTTCATAGACTTTTAGCATATTTTCTATTGAAAAGGTACCACGTTAAA
4563303 CACCTTCATTTTCCAGAAAAAGACAGCCTCTGTTGATAC
196 CACCTTCATTTTCCAGAAAAAGACAGCCTCTGTTGATAC
4563342 TCAAGCT
1 T-AAGCT
4563349 AGAGGAATAT
Statistics
Matches: 240, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
234 235 0.98
235 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (234 bp):
TAAGCTTTAACATAATATGAAAGTAAACAAAAATGGATTAACTATAGCCATCTCAAACAAACATA
GAAATATACGATATAATTAAACTAGTGTTATCAACTTATTCATATATTTGGATAAGAAAACCAAC
TTTGGCAAGCTCCTGCTTTTCATAGACTTTTAGCATATTTTCTATTGAAAAGGTACCACGTTAAA
CACCTTCATTTTCCAGAAAAAGACAGCCTCTGTTGATAC
Found at i:4567856 original size:18 final size:18
Alignment explanation
Indices: 4567835--4567918 Score: 75
Period size: 18 Copynumber: 4.7 Consensus size: 18
4567825 TAAATATTTT
*
4567835 TAATATTTTATTAATAAA
1 TAATATTTTAATAATAAA
** *
4567853 TAATATTATTTTTAAT-AT
1 TAATATT-TTAATAATAAA
* *
4567871 TATTATTTTAATAA-AAT
1 TAATATTTTAATAATAAA
4567888 TAATAATTTTAATAATAAA
1 TAAT-ATTTTAATAATAAA
4567907 TAAT-TTTTAATA
1 TAATATTTTAATA
4567919 TTTTAATAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
17 18 0.33
18 24 0.44
19 13 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATTTTAATAATAAA
Found at i:4567889 original size:14 final size:15
Alignment explanation
Indices: 4567829--4567918 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 15
4567819 ATAGTATAAA
*
4567829 TATTTTTAAT-ATTT
1 TATTTTTAATAATAT
* *
4567843 TATTAATAAATAATAT
1 TATT-TTTAATAATAT
*
4567859 TATTTTTAATATTAT
1 TATTTTTAATAATAT
*
4567874 TA-TTTTAATAAAAT
1 TATTTTTAATAATAT
4567888 TAATAATTTTAATAATAAAT
1 T-AT--TTTTAATAAT--AT
*
4567908 AATTTTTAATA
1 TATTTTTAATA
4567919 TTTTAATAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
14 15 0.26
15 15 0.26
16 7 0.12
17 8 0.14
18 9 0.16
19 2 0.03
20 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTTTAATAATAT
Found at i:4567899 original size:9 final size:9
Alignment explanation
Indices: 4567875--4567929 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
4567865 TAATATTATT
4567875 ATTTTAATA
1 ATTTTAATA
**
4567884 AAATTAATA
1 ATTTTAATA
4567893 ATTTTAATA
1 ATTTTAATA
*
4567902 A--TAAATA
1 ATTTTAATA
4567909 ATTTTTAAT-
1 A-TTTTAATA
4567918 ATTTTAATA
1 ATTTTAATA
4567927 ATT
1 ATT
4567930 ATATCAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
7 6 0.17
8 7 0.19
9 19 0.53
10 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTTTAATA
Found at i:4567962 original size:16 final size:16
Alignment explanation
Indices: 4567941--4567971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4567931 TATCAATATC
*
4567941 ATTTAAATAAAAAATA
1 ATTTAAAAAAAAAATA
4567957 ATTTAAAAAAAAAAT
1 ATTTAAAAAAAAAAT
4567972 CAAACAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTTAAAAAAAAAATA
Found at i:4577818 original size:30 final size:30
Alignment explanation
Indices: 4577725--4577820 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
4577715 TGTTAAGGAT
*
4577725 TTATTTAAGTACAAATTAAA-GATTAAAAGT
1 TTATTTAAGTACAAATTAAATG-TTAAAAGC
* **
4577755 TTATTT-GGTTACAAATTAAATGTTAATGGC
1 TTATTTAAG-TACAAATTAAATGTTAAAAGC
*
4577785 TTATTTAAGTACAAATTAAATGTTAAAAAC
1 TTATTTAAGTACAAATTAAATGTTAAAAGC
4577815 TTATTT
1 TTATTT
4577821 GAATGAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
29 1 0.02
30 52 0.95
31 2 0.04
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (30 bp):
TTATTTAAGTACAAATTAAATGTTAAAAGC
Found at i:4585293 original size:4 final size:4
Alignment explanation
Indices: 4585286--4585410 Score: 74
Period size: 4 Copynumber: 30.8 Consensus size: 4
4585276 TTAAAGAAAG
* * * *
4585286 AAAT AAAT AAAT AAAT AAAC AAAT AAAC ATAT AAAT GCAAGAC AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AA-AT AAAT AAAT
* * * * * *
4585337 AAAT -AAC AAAT AAAC ACAT AAA- AAAT CACAT AAAG AAAT AAAG AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT
** * *
4585384 AACC AAAC AAAC AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
4585411 CAAAAAAAAC
Statistics
Matches: 91, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
3 5 0.05
4 78 0.86
5 5 0.05
6 2 0.02
7 1 0.01
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.16
Consensus pattern (4 bp):
AAAT
Found at i:4585309 original size:20 final size:20
Alignment explanation
Indices: 4585286--4585414 Score: 107
Period size: 20 Copynumber: 6.2 Consensus size: 20
4585276 TTAAAGAAAG
4585286 AAATAAATAAATAAATAAAC
1 AAATAAATAAATAAATAAAC
* *
4585306 AAATAAACATATAAATGCAAGAC
1 AAATAAATAAATAAAT--AA-AC
4585329 AAATAAATAAATAACAAATAAAC
1 AAATAAATAAAT---AAATAAAC
* * *
4585352 ACATAAA-AAATCACATAAAG
1 AAATAAATAAAT-AAATAAAC
* **
4585372 AAATAAAGAAATAACCAAAC
1 AAATAAATAAATAAATAAAC
*
4585392 AAACAAATAAATAAATAAAC
1 AAATAAATAAATAAATAAAC
4585412 AAA
1 AAA
4585415 AAAAACTATC
Statistics
Matches: 86, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
20 50 0.58
21 4 0.05
22 6 0.07
23 20 0.23
24 2 0.02
26 4 0.05
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.16
Consensus pattern (20 bp):
AAATAAATAAATAAATAAAC
Found at i:4585357 original size:15 final size:15
Alignment explanation
Indices: 4585327--4585414 Score: 63
Period size: 15 Copynumber: 5.9 Consensus size: 15
4585317 TAAATGCAAG
*
4585327 ACAAATAAATAAATA
1 ACAAATAAACAAATA
*
4585342 ACAAATAAACACATA
1 ACAAATAAACAAATA
* * *
4585357 AAAAAT-CACATA-A
1 ACAAATAAACAAATA
* *
4585370 AGAAATAAAGAAATA
1 ACAAATAAACAAATA
*
4585385 ACCAAACAAACAAATAA
1 A-CAAATAAACAAAT-A
*
4585402 ATAAATAAACAAA
1 ACAAATAAACAAA
4585415 AAAAACTATC
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
13 6 0.11
14 7 0.13
15 20 0.36
16 20 0.36
17 2 0.04
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (15 bp):
ACAAATAAACAAATA
Found at i:4585851 original size:14 final size:14
Alignment explanation
Indices: 4585832--4585859 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4585822 ACAAAATATG
4585832 AAAATTTCTAGAAA
1 AAAATTTCTAGAAA
4585846 AAAATTTCTAGAAA
1 AAAATTTCTAGAAA
4585860 TTCAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAATTTCTAGAAA
Found at i:4586378 original size:17 final size:18
Alignment explanation
Indices: 4586349--4586395 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
4586339 AATTTAATAC
*
4586349 AGATAAAGA-ATAAAAAA
1 AGATAAATATATAAAAAA
* *
4586366 ATATAAA-ATATAAAATA
1 AGATAAATATATAAAAAA
4586383 AGATAAATATATA
1 AGATAAATATATA
4586396 CATGGACAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 19 0.76
18 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (18 bp):
AGATAAATATATAAAAAA
Found at i:4586433 original size:11 final size:10
Alignment explanation
Indices: 4586409--4586463 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
4586399 GGACAGATAC
*
4586409 AATAAAAGTAA
1 AATAAAAAT-A
4586420 AATATAAAATA
1 AATA-AAAATA
*
4586431 AATAAAAATG
1 AATAAAAATA
4586441 AATAAATAATA
1 AATAAA-AATA
*
4586452 AATAAAAGTA
1 AATAAAAATA
4586462 AA
1 AA
4586464 GAAATTCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
10 16 0.42
11 18 0.47
12 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (10 bp):
AATAAAAATA
Found at i:4586468 original size:21 final size:20
Alignment explanation
Indices: 4586409--4586468 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
4586399 GGACAGATAC
*
4586409 AATAAAAGTAAAATATAAAATA
1 AATAAAAGTAAAA-A-ATAATA
* *
4586431 AATAAAAATGAATAAATAATA
1 AATAAAAGT-AAAAAATAATA
4586452 AATAAAAGTAAAGAAAT
1 AATAAAAGTAAA-AAAT
4586469 TCAACATGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 17 0.55
22 9 0.29
23 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (20 bp):
AATAAAAGTAAAAAATAATA
Found at i:4592827 original size:11 final size:11
Alignment explanation
Indices: 4592811--4592839 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4592801 TTTTTACTTT
4592811 AAATAAAAGAA
1 AAATAAAAGAA
4592822 AAATAAAAGAA
1 AAATAAAAGAA
4592833 AAA-AAAA
1 AAATAAAA
4592840 TCTTTATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAATAAAAGAA
Found at i:4596858 original size:198 final size:198
Alignment explanation
Indices: 4596520--4596916 Score: 767
Period size: 198 Copynumber: 2.0 Consensus size: 198
4596510 AATCATTTGA
4596520 ATCAATACTTTTGTATGGGTCGTAACTAGAATAAATAGCTGAAAAGCAACCACAATTCAATTTAA
1 ATCAATACTTTTGTATGGGTCGTAACTAGAATAAATAGCTGAAAAGCAACCACAATTCAATTTAA
4596585 ATAGTATAGGCTATAGCGTTTTTGTCAATTTGAAAATTTGATCTGGATTCAGATTTAGCTTGTCG
66 ATAGTATAGGCTATAGCGTTTTTGTCAATTTGAAAATTTGATCTGGATTCAGATTTAGCTTGTCG
*
4596650 TGTTGATGAACTGTTTCCTTAAAGGTATAGAAATAACAAGTAGAAACCAGCAGTTGCAAAAGATT
131 TGTTGATGAACTGTTTCCTTAAAGGTATAGAAACAACAAGTAGAAACCAGCAGTTGCAAAAGATT
4596715 ATT
196 ATT
*
4596718 ATCAATACTTTTGTATGGGTTGTAACTAGAATAAATAGCTGAAAAGCAACCACAATTCAATTTAA
1 ATCAATACTTTTGTATGGGTCGTAACTAGAATAAATAGCTGAAAAGCAACCACAATTCAATTTAA
*
4596783 ATAGTATAGGCTATAGCGTTTTTGTCAATTTGAAAATTTGATCTGGATTCAGATTTAGCTTGTTG
66 ATAGTATAGGCTATAGCGTTTTTGTCAATTTGAAAATTTGATCTGGATTCAGATTTAGCTTGTCG
4596848 TGTTGATGAACTGTTTCCTTAAAGGTATAGAAACAACAAGTAGAAACCAGCAGTTGCAAAAGATT
131 TGTTGATGAACTGTTTCCTTAAAGGTATAGAAACAACAAGTAGAAACCAGCAGTTGCAAAAGATT
4596913 ATT
196 ATT
4596916 A
1 A
4596917 CCCAGTAAAA
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 196 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (198 bp):
ATCAATACTTTTGTATGGGTCGTAACTAGAATAAATAGCTGAAAAGCAACCACAATTCAATTTAA
ATAGTATAGGCTATAGCGTTTTTGTCAATTTGAAAATTTGATCTGGATTCAGATTTAGCTTGTCG
TGTTGATGAACTGTTTCCTTAAAGGTATAGAAACAACAAGTAGAAACCAGCAGTTGCAAAAGATT
ATT
Found at i:4598333 original size:3 final size:3
Alignment explanation
Indices: 4598327--4598370 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4598317 CATCATTGTT
4598327 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4598371 GAAAAGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4611214 original size:45 final size:45
Alignment explanation
Indices: 4611161--4611248 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
4611151 TAATGATGTT
* ** *
4611161 AAAAAATAAGAGTTAATGTAATTTTGTAAATTCACTAAATTATAC
1 AAAAAATAAGACTTAAAATAATTTTATAAATTCACTAAATTATAC
* *
4611206 AAAAAATAAGACTTAAAATAATTTTATAATTTCATTAAATTAT
1 AAAAAATAAGACTTAAAATAATTTTATAAATTCACTAAATTAT
4611249 GCTTGATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (45 bp):
AAAAAATAAGACTTAAAATAATTTTATAAATTCACTAAATTATAC
Found at i:4613110 original size:20 final size:20
Alignment explanation
Indices: 4613057--4613103 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
4613047 CTCCAATGCA
* *
4613057 AAAAAAATAAGAAAAAGAAG
1 AAAAAATTAGGAAAAAGAAG
4613077 AAAAAATTAGGAAAAAGAAG
1 AAAAAATTAGGAAAAAGAAG
4613097 AAAAAAT
1 AAAAAAT
4613104 CTTGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (20 bp):
AAAAAATTAGGAAAAAGAAG
Found at i:4613168 original size:6 final size:6
Alignment explanation
Indices: 4613159--4613218 Score: 66
Period size: 6 Copynumber: 9.8 Consensus size: 6
4613149 AAAAACTCAA
* * * * *
4613159 AATTTT AATTTC AATTCT AATTTT GATTTT AACTTT AATTTT GATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
4613207 AATTTTT AATTT
1 AA-TTTT AATTT
4613219 GGATTTGGAT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:4613219 original size:18 final size:18
Alignment explanation
Indices: 4613176--4613224 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
4613166 ATTTCAATTC
4613176 TAATTTTGATTTTAACTT
1 TAATTTTGATTTTAACTT
*
4613194 TAATTTTGATTTTAATTTT
1 TAATTTTGATTTTAA-CTT
*
4613213 TAATTTGGATTT
1 TAATTTTGATTT
4613225 GGATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (18 bp):
TAATTTTGATTTTAACTT
Found at i:4613230 original size:19 final size:19
Alignment explanation
Indices: 4613192--4613232 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4613182 TGATTTTAAC
* *
4613192 TTTAATTTTGATTTTAATT
1 TTTAATTTGGATTTGAATT
*
4613211 TTTAATTTGGATTTGGATT
1 TTTAATTTGGATTTGAATT
4613230 TTT
1 TTT
4613233 TTTATTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (19 bp):
TTTAATTTGGATTTGAATT
Found at i:4614280 original size:5 final size:6
Alignment explanation
Indices: 4614263--4614297 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
4614253 CCAATCATAA
4614263 ATTTTT ATTTTT -TATTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT AT-TTTT ATTTTT ATTTTT ATTTT
4614298 CTTATTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.04
6 25 0.93
7 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:4614282 original size:12 final size:12
Alignment explanation
Indices: 4614265--4614303 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4614255 AATCATAAAT
4614265 TTTTATTTTTTA
1 TTTTATTTTTTA
4614277 TTTTA-TTTTTA
1 TTTTATTTTTTA
4614288 TTTTTATTTTCTTA
1 -TTTTATTTT-TTA
4614302 TT
1 TT
4614304 GTTTTGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.25
12 10 0.42
13 5 0.21
14 3 0.12
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:4614286 original size:18 final size:17
Alignment explanation
Indices: 4614263--4614297 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
4614253 CCAATCATAA
4614263 ATTTTTATTTTTTATTTT
1 ATTTTTA-TTTTTATTTT
4614281 ATTTTTATTTTTATTTT
1 ATTTTTATTTTTATTTT
4614298 CTTATTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
ATTTTTATTTTTATTTT
Found at i:4614844 original size:2 final size:2
Alignment explanation
Indices: 4614837--4614878 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
4614827 CGTGGCCAAT
* *
4614837 CA CA CA CA CA GA CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4614879 TATATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.45, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4618538 original size:17 final size:17
Alignment explanation
Indices: 4618516--4618552 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4618506 TTATTTAATA
*
4618516 TAATAATATTATAATTT
1 TAATAATATGATAATTT
*
4618533 TAATAATATGATATTTT
1 TAATAATATGATAATTT
4618550 TAA
1 TAA
4618553 CAATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TAATAATATGATAATTT
Found at i:4618692 original size:22 final size:23
Alignment explanation
Indices: 4618664--4618707 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
4618654 TGATTTAATA
4618664 ATAAATAATTTC-AATATAAAAT
1 ATAAATAATTTCAAATATAAAAT
*
4618686 ATAAATATTTTCATAATATAAA
1 ATAAATAATTTCA-AATATAAA
4618708 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAAATAATTTCAAATATAAAAT
Found at i:4618719 original size:15 final size:16
Alignment explanation
Indices: 4618683--4618719 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
4618673 TTCAATATAA
4618683 AATATAAATATTTTCAT
1 AATATAAATATTTT-AT
4618700 AATATAAATATTTT-T
1 AATATAAATATTTTAT
4618715 AATAT
1 AATAT
4618720 TTTACTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
17 14 0.70
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATAAATATTTTAT
Found at i:4618913 original size:17 final size:17
Alignment explanation
Indices: 4618891--4618940 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
4618881 AAATATAATT
4618891 TTTTAATAATTTAATAA
1 TTTTAATAATTTAATAA
* *
4618908 TTTTAATAA-TAAATTAT
1 TTTTAATAATTTAA-TAA
*
4618925 TTTTAATATTTTAATA
1 TTTTAATAATTTAATA
4618941 GTTATGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATAATTTAATAA
Found at i:4621235 original size:20 final size:20
Alignment explanation
Indices: 4621188--4621235 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
4621178 TACTAGAGAG
*
4621188 ATTGATCCCTTAACTGAAAGT
1 ATTGATCCCTTAAC-GAAAGA
*
4621209 ATCGATCCCTTCAAC-AAAGA
1 ATTGATCCCTT-AACGAAAGA
4621229 ATTGATC
1 ATTGATC
4621236 TTAGAATCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.43
21 10 0.43
22 3 0.13
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.29
Consensus pattern (20 bp):
ATTGATCCCTTAACGAAAGA
Found at i:4628460 original size:10 final size:10
Alignment explanation
Indices: 4628447--4628513 Score: 66
Period size: 10 Copynumber: 6.8 Consensus size: 10
4628437 GAAAAGTTTA
4628447 AAAAAATTCT
1 AAAAAATTCT
4628457 AAAAAATTCT
1 AAAAAATTCT
*
4628467 AAAAAATTTT
1 AAAAAATTCT
**
4628477 AAAATGTT-T
1 AAAAAATTCT
*
4628486 TAAAAATTC-
1 AAAAAATTCT
*
4628495 AAAATAATTTT
1 AAAA-AATTCT
4628506 AAAAAATT
1 AAAAAATT
4628514 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
9 9 0.20
10 33 0.72
11 4 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:4628490 original size:18 final size:19
Alignment explanation
Indices: 4628448--4628510 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
4628438 AAAAGTTTAA
*
4628448 AAAAATTCTAAAA-AATTCTA
1 AAAAATTC-AAAATAATT-TT
* *
4628468 AAAAATTTTAAAAT-GTTTT
1 AAAAA-TTCAAAATAATTTT
4628487 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
4628506 AAAAA
1 AAAAA
4628511 ATTAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 7 0.20
19 15 0.43
20 11 0.31
21 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:4628521 original size:12 final size:12
Alignment explanation
Indices: 4628506--4628539 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4628496 AAATAATTTT
*
4628506 AAAAAATTAAAA
1 AAAAAACTAAAA
4628518 AAAAAACTAAAA
1 AAAAAACTAAAA
*
4628530 AAAATACTAA
1 AAAAAACTAA
4628540 TCTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAACTAAAA
Found at i:4628565 original size:20 final size:22
Alignment explanation
Indices: 4628542--4628584 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
4628532 AATACTAATC
4628542 TTTTT-AAAATTCT-AAATTTT
1 TTTTTAAAAATTCTAAAATTTT
4628562 TTTTTAAAAATTCTAAAATTTT
1 TTTTTAAAAATTCTAAAATTTT
4628584 T
1 T
4628585 CAAAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAAAAATTCTAAAATTTT
Found at i:4628590 original size:20 final size:21
Alignment explanation
Indices: 4628547--4628592 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
4628537 TAATCTTTTT
* **
4628547 AAAATTCTAAATTTTTTTTTA
1 AAAATTCTAAATATTTTTCAA
4628568 AAAATTCTAAA-ATTTTTCAA
1 AAAATTCTAAATATTTTTCAA
4628588 AAAAT
1 AAAAT
4628593 ACAATACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATTCTAAATATTTTTCAA
Found at i:4628591 original size:21 final size:21
Alignment explanation
Indices: 4628547--4628591 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4628537 TAATCTTTTT
* ***
4628547 AAAATTCTAAATTTTTTTTTA
1 AAAATTCTAAAATTTTTCAAA
4628568 AAAATTCTAAAATTTTTCAAA
1 AAAATTCTAAAATTTTTCAAA
4628589 AAA
1 AAA
4628592 TACAATACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATTCTAAAATTTTTCAAA
Found at i:4628646 original size:10 final size:10
Alignment explanation
Indices: 4628620--4628668 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
4628610 CATATTATAA
* *
4628620 AAATTCAAAA
1 AAATTCTAAT
4628630 AAATTCTAAT
1 AAATTCTAAT
4628640 AAATTCTAAT
1 AAATTCTAAT
*
4628650 AAATTTTGAA-
1 AAATTCT-AAT
4628660 AAATTCTAA
1 AAATTCTAA
4628669 AAGAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (10 bp):
AAATTCTAAT
Found at i:4628682 original size:18 final size:19
Alignment explanation
Indices: 4628659--4628699 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4628649 TAAATTTTGA
*
4628659 AAAATTCTA-AAAGAATTT
1 AAAATTCTATAAAAAATTT
*
4628677 AAAATTTTATAAAAAATTT
1 AAAATTCTATAAAAAATTT
4628696 AAAA
1 AAAA
4628700 ATATGAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTCTATAAAAAATTT
Found at i:4628692 original size:30 final size:30
Alignment explanation
Indices: 4628600--4628700 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
4628590 AATACAATAC
*
4628600 AATTCTAAAACATATTATAAAAATTCA-AAAA
1 AATTCTAAAA-A-ATTATAAAAATTTATAAAA
* * *
4628631 AATTCTAATAAATTCTAATAAATTT-TGAAA
1 AATTCTAAAAAATTATAA-AAATTTATAAAA
*
4628661 AATTCTAAAAGAATT-TAAAATTTTATAAAA
1 AATTCTAAAA-AATTATAAAAATTTATAAAA
4628691 AATT-TAAAAA
1 AATTCTAAAAA
4628701 TATGAAACTT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.02
29 16 0.27
30 29 0.49
31 13 0.22
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (30 bp):
AATTCTAAAAAATTATAAAAATTTATAAAA
Found at i:4628700 original size:20 final size:19
Alignment explanation
Indices: 4628600--4628701 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 19
4628590 AATACAATAC
*
4628600 AATTCTAAAACATATTATAAA
1 AATTCTAAAA-AAATT-TAAA
4628621 AATTC-AAAAAAATTCTAATA
1 AATTCTAAAAAAATT-TAA-A
* *
4628641 AATTCTAATAAATTTTGAAA
1 AATTCTAAAAAAATTT-AAA
*
4628661 AATTCTAAAAGAATTT-AA
1 AATTCTAAAAAAATTTAAA
*
4628679 AATTTTATAAAAAATTTAAA
1 AATTCTA-AAAAAATTTAAA
4628699 AAT
1 AAT
4628702 ATGAAACTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.12
19 15 0.22
20 30 0.45
21 14 0.21
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTCTAAAAAAATTTAAA
Found at i:4628775 original size:21 final size:19
Alignment explanation
Indices: 4628741--4628784 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
4628731 ATGATATTTT
*
4628741 AAAATTTTTAAAAATTCTA
1 AAAATTTTTAAAAAGTCTA
4628760 AAAATTTTAATAAAAAGTCTA
1 AAAATTTT--TAAAAAGTCTA
4628781 AAAA
1 AAAA
4628785 AATGAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTTTTAAAAAGTCTA
Found at i:4628927 original size:20 final size:21
Alignment explanation
Indices: 4628904--4628943 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4628894 TAAAAAAGTA
4628904 TAAAAATCTTT-GAAAAATTC
1 TAAAAATCTTTAGAAAAATTC
* *
4628924 TAAAAGTTTTTAGAAAAATT
1 TAAAAATCTTTAGAAAAATT
4628944 ATAAGAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
TAAAAATCTTTAGAAAAATTC
Found at i:4628956 original size:21 final size:20
Alignment explanation
Indices: 4628891--4628956 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
4628881 AGTTTTGAAA
*
4628891 ATTTA-AAAAAGTATAAAA-
1 ATTTAGAAAAATTATAAAAT
* *
4628909 ATCTTTGAAAAATTCTAAAAGT
1 AT-TTAGAAAAATTATAAAA-T
*
4628931 TTTTAGAAAAATTATAAGAAT
1 ATTTAGAAAAATTATAA-AAT
4628952 ATTTA
1 ATTTA
4628957 AAATTTTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 11 0.31
21 18 0.50
22 3 0.08
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
ATTTAGAAAAATTATAAAAT
Found at i:4629008 original size:26 final size:25
Alignment explanation
Indices: 4628931--4629010 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 25
4628921 TTCTAAAAGT
*
4628931 TTTTAGAAAAATTATAAGAATATTTAAAA
1 TTTT-GAAAAATTA-AATAA-A-TTAAAA
*
4628960 TTTTGAAAAATTAAATAATTTAAAA
1 TTTTGAAAAATTAAATAAATTAAAA
*
4628985 TTTTTGAAACATTAGAA-AAATTAAAA
1 -TTTTGAAAAATTA-AATAAATTAAAA
4629011 AAATTTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
25 6 0.13
26 20 0.44
27 6 0.13
28 9 0.20
29 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (25 bp):
TTTTGAAAAATTAAATAAATTAAAA
Found at i:4629093 original size:19 final size:19
Alignment explanation
Indices: 4629053--4629094 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4629043 TAAAAATCCA
* * *
4629053 AAAAATTTAAAAAATTTTT
1 AAAAATTCAAAAAATATGT
4629072 AAAAATTCAAAAAATATGT
1 AAAAATTCAAAAAATATGT
4629091 AAAA
1 AAAA
4629095 CATAAAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAATTCAAAAAATATGT
Found at i:4629176 original size:18 final size:17
Alignment explanation
Indices: 4629134--4629176 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
4629124 AATTTTTAGA
4629134 ATTTTTAAAAAATTTTT
1 ATTTTTAAAAAATTTTT
*
4629151 ACGGTTTTAAAAAATTTTAT
1 A--TTTTTAAAAAATTTT-T
4629171 ATTTTT
1 ATTTTT
4629177 TATTTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 14 0.67
20 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (17 bp):
ATTTTTAAAAAATTTTT
Found at i:4629270 original size:18 final size:18
Alignment explanation
Indices: 4629248--4629292 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
4629238 TAAATCTTCA
4629248 TTTTTTTAATTTTTAGAAC
1 TTTTTTTAATTTTT-GAAC
*
4629267 TTTTTTTAGTTTTTGAA-
1 TTTTTTTAATTTTTGAAC
4629284 TTTTTTTAA
1 TTTTTTTAA
4629293 AATTTAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 3 0.12
19 13 0.54
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTTTTAATTTTTGAAC
Found at i:4629379 original size:20 final size:19
Alignment explanation
Indices: 4629334--4629523 Score: 71
Period size: 20 Copynumber: 9.2 Consensus size: 19
4629324 TTCCTTTATT
*
4629334 TTTTTTAGAATTTTCAAAAA
1 TTTTTTAGAATTTT-TAAAA
**
4629354 AGTTTTAGAATTTTTAAAA
1 TTTTTTAGAATTTTTAAAA
**
4629373 CTTTTTTCA-AATTGACTAAAA
1 -TTTTTT-AGAATT-TTTAAAA
* *
4629394 TTTTTTAAATATTATTTTAGAA
1 TTTTTTAGA-A-T-TTTTAAAA
4629416 -TTTTTAGAATTTTTGAAAA
1 TTTTTTAGAATTTTT-AAAA
* *
4629435 TTTTTTTGAAATTTTT-ATA
1 TTTTTTAG-AATTTTTAAAA
* **
4629454 TTTTCTTAATAAATTTTTTTTGAA
1 TTTT-TT-A-GAA--TTTTTAAAA
* *
4629478 TTTTTTAATAATTTTAAAAA
1 TTTTTT-AGAATTTTTAAAA
4629498 TTCTTTTTAGAATTTTTTAAAA
1 -T-TTTTTAGAA-TTTTTAAAA
4629520 TTTT
1 TTTT
4629524 AATAAAATTT
Statistics
Matches: 127, Mismatches: 24, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
18 4 0.03
19 15 0.12
20 45 0.35
21 28 0.22
22 20 0.16
23 10 0.08
24 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTTTAGAATTTTTAAAA
Found at i:4629427 original size:31 final size:30
Alignment explanation
Indices: 4629391--4629534 Score: 121
Period size: 32 Copynumber: 4.6 Consensus size: 30
4629381 AAATTGACTA
* *
4629391 AAATTTTTTAAATATTATTTTAGAATTTTT
1 AAATTTTTTAAAAATTTTTTTAGAATTTTT
*
4629421 AGAA-TTTTTGAAAATTTTTTT-GAAATTTTT
1 A-AATTTTTTAAAAATTTTTTTAG-AATTTTT
* *
4629451 ATATTTTCTTAATAAATTTTTTTTGAATTTTT
1 AAATTTT-TTAA-AAATTTTTTTAGAATTTTT
* *
4629483 TAATAATTTTAAAAATTCTTTTTAGAATTTTTT
1 AAAT-TTTTTAAAAATT-TTTTTAGAA-TTTTT
* *
4629516 AAAATTTTAATAAAATTTT
1 AAATTTTTTA-AAAATTTT
4629535 AAAAACTACT
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
29 2 0.02
30 26 0.29
31 10 0.11
32 37 0.41
33 16 0.18
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (30 bp):
AAATTTTTTAAAAATTTTTTTAGAATTTTT
Found at i:4629502 original size:42 final size:43
Alignment explanation
Indices: 4629456--4629559 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 43
4629446 TTTTTATATT
** *
4629456 TTCTTAATAAATTTTTTTTGAATTTT-TTAATAATTTTAAAAA-
1 TTCTTAATAAATTTTTTTAAAATTTTAATAA-AATTTTAAAAAC
**
4629498 TTCTTTTTAGAA-TTTTTTAAAATTTTAATAAAATTTTAAAAAC
1 TTCTTAATA-AATTTTTTTAAAATTTTAATAAAATTTTAAAAAC
*
4629541 TACTTAA-AAATTTTTTTAA
1 TTCTTAATAAATTTTTTTAA
4629560 TGATGATATG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.04
42 39 0.78
43 9 0.18
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (43 bp):
TTCTTAATAAATTTTTTTAAAATTTTAATAAAATTTTAAAAAC
Found at i:4630399 original size:2 final size:2
Alignment explanation
Indices: 4630392--4630421 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4630382 TCACTATCTT
*
4630392 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4630422 CCTCACGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4634276 original size:29 final size:29
Alignment explanation
Indices: 4634239--4634377 Score: 118
Period size: 30 Copynumber: 4.7 Consensus size: 29
4634229 TTTATCACTT
*
4634239 TATTTAAATAAATTTTTATATTTTTA-TTA
1 TATTTAAATAAATTTTTA-ATTTTAATTTA
* * *
4634268 TATTTAAATAAGTTTTTAAACTTTAATTTG
1 TATTTAAATAAATTTTT-AATTTTAATTTA
* *
4634298 TATTCAAATAAATTATTAACTTTTAATTTA
1 TATTTAAATAAATTTTTAA-TTTTAATTTA
* * * *
4634328 TATCTAAATAAACTCTTAACTTTTAATTTG
1 TATTTAAATAAATTTTTAA-TTTTAATTTA
* * *
4634358 TACTTAAATAAGTCTTTAAT
1 TATTTAAATAAATTTTTAAT
4634378 ATAAATTAAC
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
29 24 0.28
30 63 0.72
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (29 bp):
TATTTAAATAAATTTTTAATTTTAATTTA
Found at i:4634336 original size:60 final size:58
Alignment explanation
Indices: 4634242--4634368 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 58
4634232 ATCACTTTAT
* * * ** *
4634242 TTAAATAAATTTTTATATTTTTATTATATTTAAATAAGTTTTTAAAC-TTTAATTTGTA
1 TTAAATAAATTATTATATTTTAATTATATCTAAATAAACTCTT-AACTTTTAATTTGTA
4634300 TTCAAATAAATTATTA-ACTTTTAATTTATATCTAAATAAACTCTTAACTTTTAATTTGTA
1 TT-AAATAAATTATTATA-TTTTAA-TTATATCTAAATAAACTCTTAACTTTTAATTTGTA
4634360 CTTAAATAA
1 -TTAAATAA
4634369 GTCTTTAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
58 3 0.05
59 20 0.34
60 33 0.57
61 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (58 bp):
TTAAATAAATTATTATATTTTAATTATATCTAAATAAACTCTTAACTTTTAATTTGTA
Found at i:4634463 original size:28 final size:30
Alignment explanation
Indices: 4634408--4634470 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
4634398 AAGTAAAGGC
4634408 TTATTTGAATATAAATAAACAATAAAAG-T
1 TTATTTGAATATAAATAAACAATAAAAGAT
4634437 TTATTT-AGATAT-AATAAA-AATATAAAGAT
1 TTATTTGA-ATATAAATAAACAATA-AAAGAT
4634466 TTATT
1 TTATT
4634471 AAAAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 4 0.13
28 11 0.35
29 16 0.52
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (30 bp):
TTATTTGAATATAAATAAACAATAAAAGAT
Found at i:4641703 original size:15 final size:15
Alignment explanation
Indices: 4641673--4641808 Score: 80
Period size: 15 Copynumber: 8.5 Consensus size: 15
4641663 TTTAATGATT
*
4641673 ATAATATTATTAATAA
1 ATAATA-TATTTATAA
4641689 ATAATATATTTATAA
1 ATAATATATTTATAA
* *
4641704 ATATTATATTAATAA
1 ATAATATATTTATAA
4641719 ATAATAT-TTATAAATAA
1 ATAATATATT-T--ATAA
*
4641736 ATTATATATTATTTATTA
1 A-TA-ATA-TATTTATAA
4641754 AT-ATAATATTTATAA
1 ATAAT-ATATTTATAA
**
4641769 ATAAATTATATATTATTT
1 AT-AA-TATAT-TTATAA
*
4641787 AT-ATATTATTAATAA
1 ATAATA-TATTTATAA
4641802 ATAATAT
1 ATAATAT
4641809 TTATTAATAT
Statistics
Matches: 94, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.02
15 47 0.50
16 14 0.15
17 11 0.12
18 13 0.14
19 3 0.03
20 2 0.02
21 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAATATATTTATAA
Found at i:4641716 original size:30 final size:28
Alignment explanation
Indices: 4641680--4641823 Score: 104
Period size: 28 Copynumber: 5.1 Consensus size: 28
4641670 ATTATAATAT
4641680 TATTAATAAATAATATATTTATAAATATTA
1 TATTAATAAAT-A-ATATTTATAAATATTA
4641710 TATTAATAAATAATATTTATAAATA--A
1 TATTAATAAATAATATTTATAAATATTA
* * *
4641736 -ATT-AT--ATATTATTTATTAATATAA
1 TATTAATAAATAATATTTATAAATATTA
* *
4641760 TATTTATAAATAA-ATTATATATTATTTATATA
1 TATTAATAAATAATATT-TATA--A-ATAT-TA
* *
4641792 TTATTAATAAATAATATTTATTAATATCA
1 -TATTAATAAATAATATTTATAAATATTA
4641821 TAT
1 TAT
4641824 ATTATACTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 28
0.71 0.08 0.22
Matches are distributed among these distances:
22 14 0.15
24 3 0.03
25 6 0.07
26 3 0.03
27 3 0.03
28 22 0.24
29 2 0.02
30 15 0.16
31 4 0.04
32 1 0.01
33 15 0.16
34 3 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTAATAAATAATATTTATAAATATTA
Found at i:4641763 original size:11 final size:11
Alignment explanation
Indices: 4641749--4641818 Score: 54
Period size: 11 Copynumber: 6.3 Consensus size: 11
4641739 ATATATTATT
*
4641749 TATTAATATAA
1 TATTTATATAA
4641760 TATTTATA-AA
1 TATTTATATAA
* *
4641770 TAAATTATATAT
1 T-ATTTATATAA
*
4641782 TATTTATATAT
1 TATTTATATAA
*
4641793 TATTAATAAATAA
1 TATT--TATATAA
4641806 TATTTAT-TAA
1 TATTTATATAA
4641816 TAT
1 TAT
4641819 CATATATTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 9 0.19
11 28 0.58
12 2 0.04
13 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTTATATAA
Found at i:4641785 original size:33 final size:33
Alignment explanation
Indices: 4641670--4641829 Score: 129
Period size: 33 Copynumber: 4.8 Consensus size: 33
4641660 ATTTTTAATG
* **
4641670 ATTATAATATTATTAATA-AATAATATATTTATAA
1 ATTAT-ATATTATTAATATAAT-ATTTATAAATAA
*
4641704 A-TATTATATTAATAA-ATAATATTTATAAATAA
1 ATTA-TATATTATTAATATAATATTTATAAATAA
4641736 ATTATATATTATTTATTAATATAATATTTATAAATAA
1 A-T-TATA-TA-TTATTAATATAATATTTATAAATAA
*
4641773 ATTATATATTATT--TAT-ATA-TTATTAATAA
1 ATTATATATTATTAATATAATATTTATAAATAA
* *
4641802 ATAATAT-TTATTAATATCATATATTATA
1 ATTATATATTATTAATATAATAT-TTATA
4641830 CTAATAATAT
Statistics
Matches: 105, Mismatches: 8, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
28 5 0.05
29 15 0.14
30 6 0.06
31 6 0.06
32 11 0.10
33 23 0.22
34 6 0.06
35 8 0.08
36 7 0.07
37 18 0.17
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTATATATTATTAATATAATATTTATAAATAA
Found at i:4641788 original size:37 final size:36
Alignment explanation
Indices: 4641704--4641788 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 36
4641694 ATATTTATAA
*
4641704 ATATTATATTAATAAATAATATTTATAAATAAATTAT
1 ATATTAT-TTATTAAATAATATTTATAAATAAATTAT
4641741 ATATTATTTATTAATATAATATTTATAAATAAATTAT
1 ATATTATTTATTAA-ATAATATTTATAAATAAATTAT
4641778 ATATTATTTAT
1 ATATTATTTAT
4641789 ATATTATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 6 0.13
37 40 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
ATATTATTTATTAAATAATATTTATAAATAAATTAT
Found at i:4641797 original size:83 final size:82
Alignment explanation
Indices: 4641672--4641843 Score: 215
Period size: 83 Copynumber: 2.1 Consensus size: 82
4641662 TTTTAATGAT
*
4641672 TATAATATTATTAATAAATAATATATTTATAAATATTATATTAATAAATAATATTTATAAATAAA
1 TATAATATTATAAATAAATAATATATTTATAAATATTATATTAATAAATAATATTTATAAAT--A
* * *
4641737 TTATATATTAT-TTATTAA
64 TCATATATTATACTAATAA
* ** *
4641755 TATAATATTTATAAATAAATTATATA-TTATTTATA-TATTATTAATAAATAATATTTATTAATA
1 TATAATA-TTATAAATAAATAATATATTTATAAATATTA-TATTAATAAATAATATTTATAAATA
4641818 TCATATATTATACTAATAA
64 TCATATATTATACTAATAA
4641837 TATAATA
1 TATAATA
4641844 CATTATTTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
81 11 0.14
82 14 0.18
83 37 0.47
84 16 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (82 bp):
TATAATATTATAAATAAATAATATATTTATAAATATTATATTAATAAATAATATTTATAAATATC
ATATATTATACTAATAA
Found at i:4642069 original size:10 final size:10
Alignment explanation
Indices: 4642009--4642069 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
4641999 AACTCAAATC
*
4642009 TAATTTTGTT
1 TAATTTTATT
* *
4642019 TATTTTTGTT
1 TAATTTTATT
*
4642029 T-ATTTGATTT
1 TAATTTTA-TT
*
4642039 TAATTTTAGT
1 TAATTTTATT
*
4642049 TAATTTAATT
1 TAATTTTATT
4642059 TAATTTTATT
1 TAATTTTATT
4642069 T
1 T
4642070 TCCTATTAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 3 0.08
10 32 0.80
11 5 0.12
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.69
Consensus pattern (10 bp):
TAATTTTATT
Found at i:4643001 original size:17 final size:16
Alignment explanation
Indices: 4642970--4643009 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4642960 GTTTTTCTTT
4642970 TTCTTTTTCCTTTTTA
1 TTCTTTTTCCTTTTTA
*
4642986 TTCTTTTATTCTTTTTA
1 TTCTTTT-TCCTTTTTA
4643003 TT-TTTTT
1 TTCTTTTT
4643010 GTTTTGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.50
17 10 0.45
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTTCCTTTTTA
Found at i:4643082 original size:17 final size:15
Alignment explanation
Indices: 4643046--4643093 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
4643036 TGTGTTGATT
4643046 TTAT-TTATTTTTTA
1 TTATATTATTTTTTA
*
4643060 TGATATTATTGTTATTA
1 TTATATTATT-TT-TTA
4643077 TTATATTATTATTTTA
1 TTATATTATT-TTTTA
4643093 T
1 T
4643094 GTTATTATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 6 0.21
17 14 0.50
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (15 bp):
TTATATTATTTTTTA
Found at i:4643100 original size:33 final size:33
Alignment explanation
Indices: 4643023--4643101 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 33
4643013 TTGATTTTTG
*
4643023 ATTTTAT-TTATTTTGTGTTGATTTTATTTATT
1 ATTTTATGTTATTATGTGTTGATTTTATTTATT
*
4643055 -TTTTATGATATTAT-TGTT-ATTATTATATTATT
1 ATTTTATGTTATTATGTGTTGATT-TTAT-TTATT
4643087 ATTTTATGTTATTAT
1 ATTTTATGTTATTAT
4643102 CATTATTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 3 0.08
31 14 0.35
32 10 0.25
33 13 0.32
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (33 bp):
ATTTTATGTTATTATGTGTTGATTTTATTTATT
Found at i:4643108 original size:33 final size:31
Alignment explanation
Indices: 4643046--4643108 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
4643036 TGTGTTGATT
**
4643046 TTATTTATTTTTTATGATATTATTGTTATTA
1 TTATTTATTTTTTATGATATTATCATTATTA
*
4643077 TTATATTATTATTTTATGTTATTATCATTATT
1 TTAT-TTATT-TTTTATGATATTATCATTATT
4643109 CATTCTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 4 0.15
32 5 0.19
33 18 0.67
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (31 bp):
TTATTTATTTTTTATGATATTATCATTATTA
Found at i:4643663 original size:21 final size:22
Alignment explanation
Indices: 4643637--4643690 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
4643627 AGAATTATTT
*
4643637 AAATAATAA-GAAAAATAATGA
1 AAATAATAATAAAAAATAATGA
*
4643658 AAATAAAAAATAAAAAATAATGA
1 AAAT-AATAATAAAAAATAATGA
*
4643681 ATAAAAATAA
1 A-AATAATAA
4643691 ATGTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 16 0.62
24 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (22 bp):
AAATAATAATAAAAAATAATGA
Found at i:4643693 original size:14 final size:13
Alignment explanation
Indices: 4643636--4643692 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
4643626 AAGAATTATT
*
4643636 TAAATAATAAGAA
1 TAAATAATAAAAA
*
4643649 -AAATAATGAAAA
1 TAAATAATAAAAA
*
4643661 TAAAAAATAAAAA
1 TAAATAATAAAAA
4643674 -ATAATGAATAAAAA
1 TA-AAT-AATAAAAA
4643688 TAAAT
1 TAAAT
4643693 GTTTAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 11 0.31
13 12 0.34
14 11 0.31
15 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:4661192 original size:33 final size:33
Alignment explanation
Indices: 4661147--4661243 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
4661137 AGATGTAAGC
*
4661147 CCTCTATTTAAAGAAATCATTCAAATTTCATGG
1 CCTCTATCTAAAGAAATCATTCAAATTTCATGG
*
4661180 CCTC-AGTCTAAAGGAATCATTCAAATTTCATGG
1 CCTCTA-TCTAAAGAAATCATTCAAATTTCATGG
* * * *
4661213 CCTCTATTTAGAGAGATCATTCAAGTTTCAT
1 CCTCTATCTAAAGAAATCATTCAAATTTCAT
4661244 AATGTCTGCT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 53 0.96
34 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (33 bp):
CCTCTATCTAAAGAAATCATTCAAATTTCATGG
Found at i:4661529 original size:36 final size:35
Alignment explanation
Indices: 4661484--4661560 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
4661474 ATAGTCATTG
*
4661484 GTTATAGGAGCTGCCTTTAAAATGTCATAGCCTCTA
1 GTTAGAGGAG-TGCCTTTAAAATGTCATAGCCTCTA
** * * *
4661520 GTTAGAGGAGTTTCTTTAAAGTGTCATAGTCTCTG
1 GTTAGAGGAGTGCCTTTAAAATGTCATAGCCTCTA
4661555 GTTAGA
1 GTTAGA
4661561 AAAAGGTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 26 0.74
36 9 0.26
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (35 bp):
GTTAGAGGAGTGCCTTTAAAATGTCATAGCCTCTA
Found at i:4661545 original size:35 final size:35
Alignment explanation
Indices: 4661498--4661676 Score: 128
Period size: 36 Copynumber: 5.0 Consensus size: 35
4661488 TAGGAGCTGC
* *
4661498 CTTTAAAATGTCATAGCCTCTAGTTAGAGGAGTTT
1 CTTTAAAGTGTCATAGCCTCTAGTTAAAGGAGTTT
* * **
4661533 CTTTAAAGTGTCATAGTCTCTGGTTAGAAAAAGGTTT
1 CTTTAAAGTGTCATAGCCTCTAGTTA-AAGGA-GTTT
* * * * *
4661570 ATTTAAAGTGTTATAACCTCAAGTTAAAAGAGCCTTT
1 CTTTAAAGTGTCATAGCCTCTAGTTAAAGGAG--TTT
* * * * *
4661607 -TTTAAAGT-CCTAAAGTCTCTAGTTAAAAGAACTTT
1 CTTTAAAGTGTC-ATAGCCTCTAGTT-AAAGGAGTTT
* *
4661642 CTTTAAAGTGCCATAGCCTTTAGTTAAAGGAGTTT
1 CTTTAAAGTGTCATAGCCTCTAGTTAAAGGAGTTT
4661677 TTCAAGATTA
Statistics
Matches: 109, Mismatches: 27, Indels: 16
0.72 0.18 0.11
Matches are distributed among these distances:
35 35 0.32
36 41 0.38
37 33 0.30
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (35 bp):
CTTTAAAGTGTCATAGCCTCTAGTTAAAGGAGTTT
Found at i:4663695 original size:21 final size:21
Alignment explanation
Indices: 4663649--4663719 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
4663639 AAAATTAAAC
*
4663649 TAAAAATTATTCTCAAT-A-AA
1 TAAAAATTATT-TAAATAATAA
4663669 TAAAAAATTATTTAAATAATAA
1 T-AAAAATTATTTAAATAATAA
* **
4663691 TAAAAATGATGAAAATAATAAA
1 TAAAAATTATTTAAATAAT-AA
4663713 TAAAAAT
1 TAAAAAT
4663720 AATGAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.12
21 26 0.60
22 12 0.28
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
TAAAAATTATTTAAATAATAA
Found at i:4663719 original size:22 final size:22
Alignment explanation
Indices: 4663663--4663737 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
4663653 AATTATTCTC
* **
4663663 AATAAATAAAAAATTATTTAAAT
1 AATAAAT-AAAAATAATGAAAAT
*
4663686 AAT-AATAAAAATGATGAAAAT
1 AATAAATAAAAATAATGAAAAT
*
4663707 AATAAATAAAAATAATGAATAAA
1 AATAAATAAAAATAATGAA-AAT
4663730 AATAAATA
1 AATAAATA
4663738 TTTAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
21 15 0.33
22 17 0.38
23 13 0.29
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
AATAAATAAAAATAATGAAAAT
Done.