Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 37
Found at i:5482763 original size:29 final size:29
Alignment explanation
Indices: 5482721--5482795 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
5482711 AACCCAACCA
**
5482721 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
5482750 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
5482779 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
5482796 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:5482801 original size:29 final size:29
Alignment explanation
Indices: 5482722--5482809 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
5482712 ACCCAACCAT
* * ****
5482722 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
5482751 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
5482780 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
5482809 A
1 A
5482810 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:5483057 original size:29 final size:29
Alignment explanation
Indices: 5483024--5483108 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
5483014 AACAGGGGAT
* * **
5483024 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
5483053 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
5483082 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
5483109 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:5495439 original size:18 final size:17
Alignment explanation
Indices: 5495416--5495491 Score: 50
Period size: 18 Copynumber: 4.4 Consensus size: 17
5495406 TTAAAAAGAT
5495416 TATGATATGTGAATGATA
1 TATGATAT-TGAATGATA
*
5495434 TATGATACTTGATTG-TA
1 TATGATA-TTGAATGATA
*
5495451 -ATGATATTTGAAAAGAT-
1 TATGATA-TTG-AATGATA
* *
5495468 TCTGATAAATGAATGATA
1 TATGAT-ATTGAATGATA
5495486 TATGAT
1 TATGAT
5495492 TTAGTGAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
16 9 0.20
17 9 0.20
18 24 0.55
19 2 0.05
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (17 bp):
TATGATATTGAATGATA
Found at i:5495700 original size:48 final size:48
Alignment explanation
Indices: 5495632--5495740 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
5495622 ATACTTATAA
** * ** *
5495632 CACGTGTCTGACATCTGTGTGGTGATGGTGCTACTAAATGAAACTTAG
1 CACGTGTCTGACGCCCGTGTGACGATGGTGATACTAAATGAAACTTAG
* * **
5495680 CACGTGTCTGACGCCCGTGTGACGGTGGTGATACTATATGGTACTTAG
1 CACGTGTCTGACGCCCGTGTGACGATGGTGATACTAAATGAAACTTAG
*
5495728 CACATGTCTGACG
1 CACGTGTCTGACG
5495741 TGTAACACCC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (48 bp):
CACGTGTCTGACGCCCGTGTGACGATGGTGATACTAAATGAAACTTAG
Found at i:5504456 original size:31 final size:31
Alignment explanation
Indices: 5504432--5504604 Score: 319
Period size: 31 Copynumber: 5.6 Consensus size: 31
5504422 CCATAGATTT
* *
5504432 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
5504463 CGAAGAATATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
5504494 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
5504525 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
5504556 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
5504587 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
5504605 CCTCGACCCT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:5507691 original size:22 final size:22
Alignment explanation
Indices: 5507656--5507709 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5507646 TTTGCATGTG
* *
5507656 ATTTTCCTATTATGTATTCTCA
1 ATTTTCATACTATGTATTCTCA
5507678 ATTTTCATACTATGTATTCTCA
1 ATTTTCATACTATGTATTCTCA
5507700 ATTTTCATAC
1 ATTTTCATAC
5507710 AACGGATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTTCATACTATGTATTCTCA
Found at i:5515761 original size:20 final size:20
Alignment explanation
Indices: 5515738--5515776 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5515728 GATAATTATT
5515738 TAATTA-TGACACTTTTAATC
1 TAATTACTGA-ACTTTTAATC
*
5515758 TAATTACTGATCTTTTAAT
1 TAATTACTGAACTTTTAAT
5515777 TTTATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (20 bp):
TAATTACTGAACTTTTAATC
Found at i:5517684 original size:16 final size:16
Alignment explanation
Indices: 5517659--5517697 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5517649 TAAAAATTCT
*
5517659 AATGAACTTAACGAGC
1 AATGAGCTTAACGAGC
5517675 AATGAGCTTAACGAGC
1 AATGAGCTTAACGAGC
*
5517691 AACGAGC
1 AATGAGC
5517698 ACGATTCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (16 bp):
AATGAGCTTAACGAGC
Found at i:5521190 original size:20 final size:20
Alignment explanation
Indices: 5521165--5521202 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5521155 ATCCTATTCC
5521165 CTGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
5521185 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
5521203 GTGAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:5521295 original size:2 final size:2
Alignment explanation
Indices: 5521288--5521343 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
5521278 TTAAACTATG
5521288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5521330 TA TA TA TA TCA TA T
1 TA TA TA TA T-A TA T
5521344 TTTATTATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5521483 original size:2 final size:2
Alignment explanation
Indices: 5521476--5521503 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5521466 AGGAATATCG
5521476 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
5521504 CGATTCTATA
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:5521582 original size:22 final size:23
Alignment explanation
Indices: 5521551--5521600 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5521541 AATTTCATTA
* *
5521551 AAATTGAAATATA-GACTTATAT
1 AAATTAAAATATATAACTTATAT
*
5521573 AAATTAAAATATATAATTTATAT
1 AAATTAAAATATATAACTTATAT
5521596 AAATT
1 AAATT
5521601 TATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
AAATTAAAATATATAACTTATAT
Found at i:5521602 original size:10 final size:10
Alignment explanation
Indices: 5521567--5521610 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
5521557 AAATATAGAC
5521567 TTATATAAAT
1 TTATATAAAT
*
5521577 TAAAATATATAAT
1 T--TATATA-AAT
5521590 TTATATAAAT
1 TTATATAAAT
5521600 TTATATAAAT
1 TTATATAAAT
5521610 T
1 T
5521611 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 15 0.52
11 5 0.17
12 5 0.17
13 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TTATATAAAT
Found at i:5521917 original size:31 final size:32
Alignment explanation
Indices: 5521852--5521918 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
5521842 AACTTTTACT
* *
5521852 AAATTCAAAAGATTAAATTGATATTTTACCTA
1 AAATTCAAAAGATTAAATTAATAGTTTACCTA
* * *
5521884 AAATTC-AAGGATTAAATTAATAGTTTGCTTA
1 AAATTCAAAAGATTAAATTAATAGTTTACCTA
5521915 AAAT
1 AAAT
5521919 CTAATGTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (32 bp):
AAATTCAAAAGATTAAATTAATAGTTTACCTA
Found at i:5526160 original size:31 final size:31
Alignment explanation
Indices: 5526087--5526164 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
5526077 CAGTTACGTC
*
5526087 AGAGACCATATTACAAACGGACTAAATGTTG
1 AGAGACCATATTGCAAACGGACTAAATGTTG
5526118 AGAGACCATATTGCAAACGGACTAAATGTTG
1 AGAGACCATATTGCAAACGGACTAAATGTTG
* **
5526149 GGAGATTATATTGCAA
1 AGAGACCATATTGCAA
5526165 TTTTTAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (31 bp):
AGAGACCATATTGCAAACGGACTAAATGTTG
Found at i:5527001 original size:31 final size:31
Alignment explanation
Indices: 5526961--5527037 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
5526951 AGTTACGTCG
5526961 GGGATCATATTGCAAACAGACTAAATGTTGA
1 GGGATCATATTGCAAACAGACTAAATGTTGA
* * *
5526992 GGGACCATATTGCAAATAGATTAAATGTTGA
1 GGGATCATATTGCAAACAGACTAAATGTTGA
*
5527023 GGGATTATATTGCAA
1 GGGATCATATTGCAA
5527038 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (31 bp):
GGGATCATATTGCAAACAGACTAAATGTTGA
Found at i:5527397 original size:46 final size:46
Alignment explanation
Indices: 5527346--5527456 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 46
5527336 AAATCACTAT
* * *
5527346 CTAAAACATTATTTTTTATATAAAAAATGTTACTATT-AAACGCTAC
1 CTAAAATATTATTTTTTATATAAAAAATATTAATATTGAAA-GCTAC
* *
5527392 CTAAAATATTA--TTTTCTATCAAAAATATTAATATTGAAAGCTAC
1 CTAAAATATTATTTTTTATATAAAAAATATTAATATTGAAAGCTAC
* *
5527436 TTAAAATGTTATTTTTTATAT
1 CTAAAATATTATTTTTTATAT
5527457 CAAATTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
44 34 0.63
45 3 0.06
46 17 0.31
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (46 bp):
CTAAAATATTATTTTTTATATAAAAAATATTAATATTGAAAGCTAC
Found at i:5528595 original size:15 final size:15
Alignment explanation
Indices: 5528575--5528603 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5528565 TCAAGTGTTG
5528575 GAAAGAGATGCAAAT
1 GAAAGAGATGCAAAT
5528590 GAAAGAGATGCAAA
1 GAAAGAGATGCAAA
5528604 GAGGAAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.28, T:0.10
Consensus pattern (15 bp):
GAAAGAGATGCAAAT
Found at i:5533269 original size:33 final size:33
Alignment explanation
Indices: 5533227--5533294 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
5533217 ACACTAATCT
5533227 TTAATCAATATACAGTACACTATAATGCTTGAA
1 TTAATCAATATACAGTACACTATAATGCTTGAA
5533260 TTAATCAATATACAGTACACTATAATGCTTGAA
1 TTAATCAATATACAGTACACTATAATGCTTGAA
5533293 TT
1 TT
5533295 GCCATACAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (33 bp):
TTAATCAATATACAGTACACTATAATGCTTGAA
Found at i:5537862 original size:2 final size:2
Alignment explanation
Indices: 5537855--5537883 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5537845 CAACCAAAGA
5537855 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5537884 TCCTTTTGTA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5548815 original size:2 final size:2
Alignment explanation
Indices: 5548808--5548833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5548798 CAGTGGACTC
5548808 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
5548834 TTCAGATATC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5552231 original size:19 final size:19
Alignment explanation
Indices: 5552207--5552248 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5552197 AGATTATCGA
5552207 TAAAAAATAAAAAAAAAAT
1 TAAAAAATAAAAAAAAAAT
* **
5552226 TAAAAATTAAAAATTAAAT
1 TAAAAAATAAAAAAAAAAT
5552245 TAAA
1 TAAA
5552249 TTATATGAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAATAAAAAAAAAAT
Found at i:5555650 original size:15 final size:17
Alignment explanation
Indices: 5555630--5555671 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
5555620 GATAAAATAA
5555630 AATGATT-AAGCG-TTG
1 AATGATTCAAGCGCTTG
*
5555645 AATGATTCAATCGCTTG
1 AATGATTCAAGCGCTTG
5555662 AATGATTCAA
1 AATGATTCAA
5555672 AGGCTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 4 0.17
17 13 0.54
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (17 bp):
AATGATTCAAGCGCTTG
Found at i:5555677 original size:17 final size:17
Alignment explanation
Indices: 5555630--5555677 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
5555620 GATAAAATAA
*
5555630 AATGATT-AAGCG-TTG
1 AATGATTCAAACGCTTG
*
5555645 AATGATTCAATCGCTTG
1 AATGATTCAAACGCTTG
*
5555662 AATGATTCAAAGGCTT
1 AATGATTCAAACGCTT
5555678 TGTATGAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.25
16 4 0.14
17 17 0.61
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (17 bp):
AATGATTCAAACGCTTG
Found at i:5559464 original size:22 final size:22
Alignment explanation
Indices: 5559439--5559490 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
5559429 TGAAACTATG
5559439 ATTTTTTTCACACAAAAAATGA
1 ATTTTTTTCACACAAAAAATGA
5559461 ATTTTTTTCACACAAAAAATGA
1 ATTTTTTTCACACAAAAAATGA
5559483 ATTTTTTT
1 ATTTTTTT
5559491 GGGTCATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTTTTTCACACAAAAAATGA
Found at i:5563722 original size:156 final size:154
Alignment explanation
Indices: 5563414--5563725 Score: 556
Period size: 154 Copynumber: 2.0 Consensus size: 154
5563404 GAGAAGAAAG
5563414 GGTTCTCCACCCGTGACCCGACCCGATCTGACAAAATTAATGTTTCACACCGACCCGACCCGACC
1 GGTTCTCCACCCGTGACCCGACCCGATCTGACAAAATTAATGTTTCACACCGACCCGACCCGACC
5563479 CATATGACTTAGAAAACCCGACCTGACCTGACCCGAAATAAAAAAAAATTTAATTCAAAAAACAG
66 CATATGACTTAGAAAACCCGACCTGACCTGACCCGAAATAAAAAAAAATTTAATTCAAAAAACAG
5563544 TGACTTAATTAAAAAAATATATAT
131 TGACTTAATTAAAAAAATATATAT
5563568 GGTTCTCCACCCGTGACCCGACCCGATCTGACAAAATTAATGTTTCAC-CCGACCCGACCCGACC
1 GGTTCTCCACCCGTGACCCGACCCGATCTGACAAAATTAATGTTTCACACCGACCCGACCCGACC
5563632 CGAATATATGACTTAG-AAACCCGACCTGACCTGACCCGAAATAAAAAAAAATTTAATTCAATAA
66 C----ATATGACTTAGAAAACCCGACCTGACCTGACCCGAAATAAAAAAAAATTTAATTC-A-AA
5563696 AAACAGTGACTTAATTAAAAAAATATATAT
125 AAACAGTGACTTAATTAAAAAAATATATAT
5563726 ATGGAGGGAT
Statistics
Matches: 152, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
153 17 0.11
154 48 0.32
156 43 0.28
157 12 0.08
158 32 0.21
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.22
Consensus pattern (154 bp):
GGTTCTCCACCCGTGACCCGACCCGATCTGACAAAATTAATGTTTCACACCGACCCGACCCGACC
CATATGACTTAGAAAACCCGACCTGACCTGACCCGAAATAAAAAAAAATTTAATTCAAAAAACAG
TGACTTAATTAAAAAAATATATAT
Found at i:5564248 original size:19 final size:19
Alignment explanation
Indices: 5564226--5564265 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5564216 CAGTATAACT
5564226 AATAAATGAACTAATTTTA
1 AATAAATGAACTAATTTTA
5564245 AATAAATGAACTAATTTTA
1 AATAAATGAACTAATTTTA
5564264 AA
1 AA
5564266 AATGGATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
AATAAATGAACTAATTTTA
Found at i:5572137 original size:2 final size:2
Alignment explanation
Indices: 5572130--5572156 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5572120 ATTCATGTTC
5572130 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5572157 CACACACGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5573909 original size:42 final size:45
Alignment explanation
Indices: 5573828--5573914 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 45
5573818 GATAGCATGT
*
5573828 ATAAAAATAATATTAAAGACATTATAAATAATAAATATAATACTA
1 ATAAAAATAATATTAAAGACATTATAAATAATAAATATAACACTA
* ** *
5573873 ATAAAAAT-ATATTAAA-ATATTATTTA-AATATATATAACACTA
1 ATAAAAATAATATTAAAGACATTATAAATAATAAATATAACACTA
5573915 TTTAAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 14 0.38
43 7 0.19
44 8 0.22
45 8 0.22
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (45 bp):
ATAAAAATAATATTAAAGACATTATAAATAATAAATATAACACTA
Found at i:5573949 original size:32 final size:32
Alignment explanation
Indices: 5573872--5573951 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
5573862 ATATAATACT
*
5573872 AATAAAAATATATTAAAATATTATTTAAATATA
1 AATAAAAATAT-TTAAAATATTAATTAAATATA
* * *
5573905 TATAACACTATTT-AAATATTTAATT-AATATAA
1 AATAAAAATATTTAAAATA-TTAATTAAATAT-A
5573937 AATAAAAATATTTAA
1 AATAAAAATATTTAA
5573952 TAAATTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
31 10 0.27
32 18 0.49
33 9 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAAAAATATTTAAAATATTAATTAAATATA
Found at i:5578635 original size:2 final size:2
Alignment explanation
Indices: 5578628--5578661 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5578618 ATCGATTTTA
5578628 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
5578662 CTTATACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5579274 original size:39 final size:39
Alignment explanation
Indices: 5579220--5579297 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
5579210 GATTTGGTTG
5579220 CCTTCTCTTCGGGTGCGGAGAAATCTTACTGTCCATTCT
1 CCTTCTCTTCGGGTGCGGAGAAATCTTACTGTCCATTCT
5579259 CCTTCTCTTCGGGTGCGGAGAAATCTTACTGTCCATTCT
1 CCTTCTCTTCGGGTGCGGAGAAATCTTACTGTCCATTCT
5579298 TTCTTCAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.15, C:0.28, G:0.21, T:0.36
Consensus pattern (39 bp):
CCTTCTCTTCGGGTGCGGAGAAATCTTACTGTCCATTCT
Found at i:5579808 original size:76 final size:76
Alignment explanation
Indices: 5579682--5579843 Score: 270
Period size: 76 Copynumber: 2.1 Consensus size: 76
5579672 TGTGTCTTCA
*
5579682 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAATTCATGGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
5579747 AAGAATAATGC
66 AAGAATAATGC
* * * * *
5579758 ACGTGGGGACCAGTTTTGTTATGTTTGGTAGCATGATGTTTGCAGGAAAATAAGGAAATCATTGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
5579823 AAGAATAATGC
66 AAGAATAATGC
5579834 ACGTGGGGAC
1 ACGTGGGGAC
5579844 GGGAATGAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (76 bp):
ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
AAGAATAATGC
Found at i:5582291 original size:8 final size:7
Alignment explanation
Indices: 5582256--5582461 Score: 62
Period size: 8 Copynumber: 29.4 Consensus size: 7
5582246 ACTCGAGTAT
5582256 ATATTTA
1 ATATTTA
*
5582263 ATA-ATA
1 ATATTTA
5582269 ATTATTTA
1 A-TATTTA
5582277 A-ATTTA
1 ATATTTA
5582283 ATCATTTA
1 AT-ATTTA
5582291 A-ATTTA
1 ATATTTA
*
5582297 ATGATTTT
1 AT-ATTTA
*
5582305 ATA-ATA
1 ATATTTA
5582311 ATTATTTA
1 A-TATTTA
*
5582319 A-CTTTA
1 ATATTTA
*
5582325 ATGATTTC
1 AT-ATTTA
*
5582333 ATA-ATA
1 ATATTTA
5582339 ATTATTTA
1 A-TATTTA
*
5582347 A-CTTTA
1 ATATTTA
5582353 ATGATTTA
1 AT-ATTTA
*
5582361 A-ATTAA
1 ATATTTA
5582367 ATACTTTA
1 ATA-TTTA
*
5582375 ATA-ATA
1 ATATTTA
5582381 ATTATTTA
1 A-TATTTA
*
5582389 A-CTTTA
1 ATATTTA
5582395 ATGATTTA
1 AT-ATTTA
*
5582403 A-ATTAA
1 ATATTTA
5582409 ATACTTTA
1 ATA-TTTA
*
5582417 ATA-ATA
1 ATATTTA
*
5582423 ATTACTTA
1 A-TATTTA
*
5582431 A-CTTTA
1 ATATTTA
5582437 ATGATTTA
1 AT-ATTTA
5582445 AT-TTTA
1 ATATTTA
5582451 ATGATTTA
1 AT-ATTTA
5582459 ATA
1 ATA
5582462 ATAATTACTT
Statistics
Matches: 144, Mismatches: 27, Indels: 56
0.63 0.12 0.25
Matches are distributed among these distances:
6 60 0.42
7 18 0.12
8 66 0.46
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (7 bp):
ATATTTA
Found at i:5582339 original size:70 final size:70
Alignment explanation
Indices: 5582258--5582403 Score: 231
Period size: 70 Copynumber: 2.1 Consensus size: 70
5582248 TCGAGTATAT
* *
5582258 ATTTAATAATAATTATTTAAATTTAATCATTTAAATTTAATGA-TTTTATAATAATTATTTAACT
1 ATTTAATAATAATTATTTAAATTTAATCATTTAAATTAAAT-ACTTTAATAATAATTATTTAACT
5582322 TTAATG
65 TTAATG
* * *
5582328 ATTTCATAATAATTATTTAACTTTAATGATTTAAATTAAATACTTTAATAATAATTATTTAACTT
1 ATTTAATAATAATTATTTAAATTTAATCATTTAAATTAAATACTTTAATAATAATTATTTAACTT
5582393 TAATG
66 TAATG
5582398 ATTTAA
1 ATTTAA
5582404 ATTAAATACT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
69 1 0.01
70 68 0.99
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (70 bp):
ATTTAATAATAATTATTTAAATTTAATCATTTAAATTAAATACTTTAATAATAATTATTTAACTT
TAATG
Found at i:5582360 original size:42 final size:42
Alignment explanation
Indices: 5582309--5582529 Score: 302
Period size: 42 Copynumber: 5.3 Consensus size: 42
5582299 GATTTTATAA
* * *
5582309 TAATTATTTAACTTTAATGATTTCATAATAATTATTTAACTT
1 TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
*
5582351 TAATGATTTAAATTAAAT-ACTTTAATAATAATTATTTAACTT
1 TAATGATTTAAATTTAATGA-TTTAATAATAATTATTTAACTT
* *
5582393 TAATGATTTAAATTAAAT-ACTTTAATAATAATTACTTAACTT
1 TAATGATTTAAATTTAATGA-TTTAATAATAATTATTTAACTT
* * *
5582435 TAATGATTTAATTTTAATGATTTAATAATAATTACTTCACTT
1 TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
* * *
5582477 TAATAATTTAACTTTAATGATTTATTAATAATTATTTAACTT
1 TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
5582519 TAATGATTTAA
1 TAATGATTTAA
5582530 TAATAATTAA
Statistics
Matches: 163, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
41 1 0.01
42 161 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (42 bp):
TAATGATTTAAATTTAATGATTTAATAATAATTATTTAACTT
Found at i:5582533 original size:28 final size:28
Alignment explanation
Indices: 5582281--5582550 Score: 219
Period size: 28 Copynumber: 9.6 Consensus size: 28
5582271 TATTTAAATT
* * *
5582281 TAATCATTTAAATTTAATGATTTTATAA
1 TAATTATTTAACTTTAATGATTTAATAA
*
5582309 TAATTATTTAACTTTAATGATTTCATAA
1 TAATTATTTAACTTTAATGATTTAATAA
*
5582337 TAATTATTTAACTTTAATGATTTAA-AT
1 TAATTATTTAACTTTAATGATTTAATAA
* * * *
5582364 TAAATACTTTAA-TAATAATTATTTAACT-T
1 TAATTA-TTTAACT-TTAATGATTTAA-TAA
* * *
5582393 TAATGATTTAAATTAAAT-ACTTTAATAA
1 TAATTATTTAACTTTAATGA-TTTAATAA
* **
5582421 TAATTACTTAACTTTAATGATTTAATTT
1 TAATTATTTAACTTTAATGATTTAATAA
* * * * * *
5582449 TAATGATTTAA-TAATAATTACTTCACT-T
1 TAATTATTTAACT-TTAATGA-TTTAATAA
* *
5582477 TAATAATTTAACTTTAATGATTTATTAA
1 TAATTATTTAACTTTAATGATTTAATAA
5582505 TAATTATTTAACTTTAATGATTTAATAA
1 TAATTATTTAACTTTAATGATTTAATAA
* *
5582533 TAATTAATTCACTTTAAT
1 TAATTATTTAACTTTAAT
5582551 AATTAAACTT
Statistics
Matches: 195, Mismatches: 35, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
27 14 0.07
28 169 0.87
29 12 0.06
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATTATTTAACTTTAATGATTTAATAA
Found at i:5582560 original size:42 final size:42
Alignment explanation
Indices: 5582505--5582618 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
5582495 GATTTATTAA
* * *
5582505 TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTT
1 TAATAATTAAACTTTAATGATTTAATAATAATTAATTAACTT
* *
5582547 TAATAATTAAACTTTAATGATTTATTAATAATTATTTAACTT
1 TAATAATTAAACTTTAATGATTTAATAATAATTAATTAACTT
* * *
5582589 TAATGATTAAAGTTTAATAATTTAATAATA
1 TAATAATTAAACTTTAATGATTTAATAATA
5582619 GTAATGATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (42 bp):
TAATAATTAAACTTTAATGATTTAATAATAATTAATTAACTT
Found at i:5582560 original size:70 final size:70
Alignment explanation
Indices: 5582435--5582596 Score: 288
Period size: 70 Copynumber: 2.3 Consensus size: 70
5582425 TACTTAACTT
* * * *
5582435 TAATGATTTAATTTTAATGATTTAATAATAATTACTTCACTTTAATAATTTAACTTTAATGATTT
1 TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGATTT
5582500 ATTAA
66 ATTAA
5582505 TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGATTT
1 TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGATTT
5582570 ATTAA
66 ATTAA
5582575 TAATTATTTAACTTTAATGATT
1 TAATTATTTAACTTTAATGATT
5582597 AAAGTTTAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 88 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (70 bp):
TAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGATTT
ATTAA
Found at i:5582584 original size:84 final size:82
Alignment explanation
Indices: 5582334--5582623 Score: 220
Period size: 84 Copynumber: 3.5 Consensus size: 82
5582324 AATGATTTCA
* *
5582334 TAATAATTATTTAACTTTAATGATTTAA-ATTAAATACTTTA-ATAATAATTATTTAACTTTAAT
1 TAATAATTATTTAACTTTAATGATTTAATAAT-AATAATTTATATAATAATTA---AACTTTAAT
* *
5582397 GATTTA--AATTAAATACTTTAA
62 GATTTATTAA-TAATTA-TTTAT
* ** * * *
5582418 TAATAATTACTTAACTTTAATGATTTAATTTTAATGATTTA-ATAATAATTACTTCACTTTAATA
1 TAATAATTATTTAACTTTAATGATTTAATAATAATAATTTATATAATAATTA---AACTTTAATG
*
5582482 ATTTAACTT--TAATGATTTAT
63 ATTT-A-TTAATAATTATTTAT
* *
5582502 TAATAATTATTTAACTTTAATGATTTAATAATAATTAATTCACTTTAATAATTAAACTTTAATGA
1 TAATAATTATTTAACTTTAATGATTTAATAATAA-TAATTTA-TATAATAATTAAACTTTAATGA
5582567 TTTATTAATAATTATTTAACT
64 TTTATTAATAATTATTT-A-T
* * * * *
5582588 T--TAATGATTAAAGTTTAATAATTTAATAATAGTAAT
1 TAATAATTATTTAACTTTAATGATTTAATAATAATAAT
5582624 GATATTCGAT
Statistics
Matches: 170, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
82 2 0.01
83 5 0.03
84 139 0.82
85 13 0.08
86 2 0.01
87 9 0.05
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (82 bp):
TAATAATTATTTAACTTTAATGATTTAATAATAATAATTTATATAATAATTAAACTTTAATGATT
TATTAATAATTATTTAT
Found at i:5583538 original size:16 final size:16
Alignment explanation
Indices: 5583482--5583539 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
5583472 AAATAATTAT
* *
5583482 AAAAATCAACAAAATA
1 AAAAATAAACATAATA
* *
5583498 AATAAATAAAAATATTA
1 AA-AAATAAACATAATA
* *
5583515 TAATATAAACATAATA
1 AAAAATAAACATAATA
5583531 AAAAATAAA
1 AAAAATAAA
5583540 TTCGCTTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAACATAATA
Found at i:5585518 original size:76 final size:76
Alignment explanation
Indices: 5585385--5585546 Score: 270
Period size: 76 Copynumber: 2.1 Consensus size: 76
5585375 TCTTATTCCC
*
5585385 GTCCCCACGTGCATTATTCTTCCCATGATTTCCTTATTTTCCTGCAAACATCATGCTACCAAACA
1 GTCCCCACGTGCATTATTCTTCCCATGAATTCCTTATTTTCCTGCAAACATCATGCTACCAAACA
*
5585450 TAACAAAGCTG
66 TAACAAAGCTA
* * * *
5585461 GTCCCCACGTGCATTATTCTTCTCATGAATTCCTTATTTTGCTGCAAACTTCCTGCTACCAAACA
1 GTCCCCACGTGCATTATTCTTCCCATGAATTCCTTATTTTCCTGCAAACATCATGCTACCAAACA
5585526 TAACAAAGCTA
66 TAACAAAGCTA
5585537 GTCCCCACGT
1 GTCCCCACGT
5585547 TGAAGACACA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (76 bp):
GTCCCCACGTGCATTATTCTTCCCATGAATTCCTTATTTTCCTGCAAACATCATGCTACCAAACA
TAACAAAGCTA
Found at i:5587539 original size:72 final size:72
Alignment explanation
Indices: 5587435--5587858 Score: 381
Period size: 72 Copynumber: 5.8 Consensus size: 72
5587425 AGATTGTTCT
* *
5587435 TGCAACTGTTGATCAAATTGGGTTTGCGGCAATATATAACCAGAATCCTGAACTAGCTGCTT-C-
1 TGCAACTGTTGATCAAATTGGG-TTGCTGCAATATATAACCAGAATCCTGAACTAGTTG-TTGCT
5587498 CGCTGCTGC
64 CGCTGCTGC
* * * * * ** *
5587507 AGAAACTGTTGATCAAATTGGGCTTGCCGCAATATATAACCAGGATCCTGAAGTAGTACTT-CTT
1 TGCAACTGTTGATCAAATTGGG-TTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCTC
* *
5587571 GTTGTTGC
65 GCTGCTGC
** * * * *
5587579 TGC-TGTTTTAGTTCAAATTGGAGTTGCTGCAATAAATAACCAGAATCCGGAACTAGTTGTTGCT
1 TGCAACTGTT-GATCAAATTGG-GTTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCT
*
5587643 -TCTGCTGC
64 CGCTGCTGC
* * * *
5587651 TGCAACTGTTGATCGACTTGGGGTTGCTACAATATATAACTAGAATCCTGAACTAGTTGTTGCTG
1 TGCAACTGTTGATCAAATT-GGGTTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCT-
* *
5587716 CTGTTGCTTC
64 C-GCTGCTGC
* * * * *
5587726 TGCAACTATTGATCAAATTGGGATTACTGCAATATATAACAAGAATCCTGAACTTGTTGTTGTTG
1 TGCAACTGTTGATCAAATTGGG-TTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCT-
*
5587791 CTGCTGTTGC
64 C-GCTGCTGC
* * ** *
5587801 TGCAACTGTTGATCAAATTAGGGTTGCTGTAACATATAACCAGGTTCCTGAACAAGTT
1 TGCAACTGTTGATCAAATT-GGGTTGCTGCAATATATAACCAGAATCCTGAACTAGTT
5587859 CTTGTACTGG
Statistics
Matches: 280, Mismatches: 61, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
71 6 0.02
72 150 0.54
73 8 0.03
74 3 0.01
75 110 0.39
76 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (72 bp):
TGCAACTGTTGATCAAATTGGGTTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCTCG
CTGCTGC
Found at i:5587661 original size:144 final size:145
Alignment explanation
Indices: 5587435--5587862 Score: 420
Period size: 144 Copynumber: 2.9 Consensus size: 145
5587425 AGATTGTTCT
* * * * *
5587435 TGCAACTGTTGATCAAATTGGGTTTGCGGCAATATATAACCAGAATCCTGAACTAGCTGCTT-CC
1 TGCAACTATTGATCAAATTGGGATTGCTGCAATATATAACCAGAATCCTGAACTAGTTG-TTGCT
* * * * *
5587499 GCTGCTGCAGAAACTGTTGATCAAATTGGGCTTGCCGCAATATATAACCAGGATCCTGAAGTAGT
65 TCTGCTGCTGCAACTGTTGATCAAATTGGG-TTGCTGCAATATATAACCAGGATCCTGAACTAGT
5587564 ACTT-CT-TGTTG-TTGC
129 ACTTGCTCTGTTGCTT-C
** * * * *
5587579 TGC-TGTTTTAGTTCAAATT-GGAGTTGCTGCAATAAATAACCAGAATCCGGAACTAGTTGTTGC
1 TGCAACTATT-GATCAAATTGGGA-TTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGC
* * * * *
5587642 TTCTGCTGCTGCAACTGTTGATCGACTTGGGGTTGCTACAATATATAACTAGAATCCTGAACTAG
64 TTCTGCTGCTGCAACTGTTGATCAAATT-GGGTTGCTGCAATATATAACCAGGATCCTGAACTAG
**
5587707 TTGTTGCTGCTGTTGCTTC
128 TACTTGCT-CTGTTGCTTC
* * *
5587726 TGCAACTATTGATCAAATTGGGATTACTGCAATATATAACAAGAATCCTGAACTTGTTGTTG-TT
1 TGCAACTATTGATCAAATTGGGATTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCTT
* * * *
5587790 GCTGCTGTTGCTGCAACTGTTGATCAAATTAGGGTTGCTGTAACATATAACCAGGTTCCTGAACA
66 -CTGC---TGCTGCAACTGTTGATCAAATT-GGGTTGCTGCAATATATAACCAGGATCCTGAACT
*
5587855 AGTTCTTG
126 AGTACTTG
5587863 TACTGGAACT
Statistics
Matches: 228, Mismatches: 42, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
143 7 0.03
144 97 0.43
145 5 0.02
146 2 0.01
147 55 0.24
148 8 0.04
150 54 0.24
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (145 bp):
TGCAACTATTGATCAAATTGGGATTGCTGCAATATATAACCAGAATCCTGAACTAGTTGTTGCTT
CTGCTGCTGCAACTGTTGATCAAATTGGGTTGCTGCAATATATAACCAGGATCCTGAACTAGTAC
TTGCTCTGTTGCTTC
Found at i:5592336 original size:3 final size:3
Alignment explanation
Indices: 5592328--5592355 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5592318 TCTGTTGCTA
5592328 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5592356 TCTAAATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5597774 original size:6 final size:6
Alignment explanation
Indices: 5597765--5597810 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
5597755 AGATGAAGAT
5597765 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAG
5597811 TGGGTGTGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:5598704 original size:21 final size:23
Alignment explanation
Indices: 5598663--5598705 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5598653 ATGCTCCAAA
*
5598663 AACTTCACAAATATTATGAAATT
1 AACTTCACAAATATGATGAAATT
5598686 AACTTCA-AAATATGA-GAAAT
1 AACTTCACAAATATGATGAAAT
5598706 ATTGTGGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (23 bp):
AACTTCACAAATATGATGAAATT
Found at i:5600426 original size:21 final size:18
Alignment explanation
Indices: 5600405--5600445 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5600395 TTGAAGTTAT
5600405 TATTA-TTCTATTAAAAAA
1 TATTATTTCTA-TAAAAAA
5600423 TATTATTTCTATAAAAAA
1 TATTATTTCTATAAAAAA
*
5600441 AATTA
1 TATTA
5600446 AAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTATTTCTATAAAAAA
Found at i:5608163 original size:35 final size:37
Alignment explanation
Indices: 5608104--5608178 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
5608094 TTTTTATATT
5608104 TTTAATTTTGTAAAAAAATTATATAAATATTATA-AA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATACAA
* * *
5608140 TTTAATTTTTTTAAAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATACAA
5608176 TTT
1 TTT
5608179 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 14 0.40
36 21 0.60
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATACAA
Found at i:5614647 original size:74 final size:75
Alignment explanation
Indices: 5614514--5614657 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 75
5614504 TTATCTTCAT
* * *
5614514 AACATAAAAATCATGATTTCATCATTACAGTCTTCTTACAGTTGCGACGAATATTTTGTCTCTTG
1 AACATAAAAATCATGATTTCATCACTACAGTCTTATTACAGTTGCGACGAATATCTTGTCTCTTG
5614579 ATATCTTTGC
66 ATATCTTTGC
** * *
5614589 AACAT-AAAATCATGATTTCATCACTACAGTCTTATTTTAGTTTCGACAGACT-TCTTGTCTCTT
1 AACATAAAAATCATGATTTCATCACTACAGTCTTATTACAGTTGCGAC-GAATATCTTGTCTCTT
5614652 GATATC
65 GATATC
5614658 CTATAAGAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 53 0.87
75 8 0.13
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.40
Consensus pattern (75 bp):
AACATAAAAATCATGATTTCATCACTACAGTCTTATTACAGTTGCGACGAATATCTTGTCTCTTG
ATATCTTTGC
Found at i:5617536 original size:15 final size:15
Alignment explanation
Indices: 5617516--5617547 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5617506 TATTAAATAC
5617516 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
5617531 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
5617546 TT
1 TT
5617548 GGATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTCTTTTCTTTT
Found at i:5629376 original size:29 final size:29
Alignment explanation
Indices: 5629314--5629390 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
5629304 TTAAATATCG
*
5629314 ATTTTAGCATTGAAA-TTTAAAATATTTTA
1 ATTTTAGCATT-AAACTTTAAAATATTTCA
*
5629343 GTTTTAGCATTAAACTTTAAAATATTTCA
1 ATTTTAGCATTAAACTTTAAAATATTTCA
*
5629372 ATTTTAACATTAAACTTTA
1 ATTTTAGCATTAAACTTTA
5629391 GTTTATGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 3 0.07
29 40 0.93
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (29 bp):
ATTTTAGCATTAAACTTTAAAATATTTCA
Found at i:5631954 original size:2 final size:2
Alignment explanation
Indices: 5631947--5631971 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5631937 TGCCGACAGT
5631947 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
5631972 GTATGTCAAA
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:5634193 original size:128 final size:128
Alignment explanation
Indices: 5633964--5634846 Score: 1319
Period size: 128 Copynumber: 6.9 Consensus size: 128
5633954 TTTAATTTAA
* * *
5633964 TATTCACATGAAGGAGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
* *
5634029 TTGCCATATTATGTCACTCATGTCCCTCGGGAACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
5634092 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
*
5634157 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTTAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
5634220 TATTCACATGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
*
5634285 TTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
5634348 TATTCATATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
* * * *
5634413 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTA-TTCATATCAATACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCAC
*** * *
5634476 -AGGGGACTTGAAGGGGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
* * *
5634540 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTA-TTCATATCAGTACCTATTATTTC-T
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCAC
*** * *
5634603 TAGGGGACTTGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
* * * *
5634668 ATTGCCCTATTATGTCACTCATGTCCCTCAGGGACATTA-TTCATATCAGTACCTATTATTTCTC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCAC
*** * * *
5634732 -AGGGGACTTGAAGGCGCGTTCCCGGGGGGGCGCATTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
5634796 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
5634847 AATCAGGTAA
Statistics
Matches: 714, Mismatches: 36, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
127 2 0.00
128 711 1.00
129 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:5635121 original size:14 final size:14
Alignment explanation
Indices: 5635102--5635131 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5635092 CATAAGTTGA
*
5635102 TTTTAATGTATATG
1 TTTTAATATATATG
5635116 TTTTAATATATATG
1 TTTTAATATATATG
5635130 TT
1 TT
5635132 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:5635285 original size:34 final size:33
Alignment explanation
Indices: 5635247--5635341 Score: 119
Period size: 28 Copynumber: 3.0 Consensus size: 33
5635237 AAATTTAATG
5635247 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATA-TATAATTTATATTTTAAAT
*
5635281 TTAAATTTCGAATA-AT-A-TTAT-TTTT-ATT
1 TTAAATTTCGAATATATAATTTATATTTTAAAT
*
5635309 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAAT-ATATAATTTATATTTTAAA
5635342 AACATTTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
28 15 0.29
29 5 0.10
30 6 0.12
31 2 0.04
32 5 0.10
33 4 0.08
34 15 0.29
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (33 bp):
TTAAATTTCGAATATATAATTTATATTTTAAAT
Found at i:5635888 original size:21 final size:20
Alignment explanation
Indices: 5635861--5635930 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
5635851 GGTATAAAAC
*
5635861 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
5635881 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
5635902 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
5635923 CCCTGCGG
1 -CCTGCGG
5635931 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:5635960 original size:21 final size:21
Alignment explanation
Indices: 5635934--5635981 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5635924 CCTGCGGAGA
*
5635934 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
5635955 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
5635976 GGGCAT
1 TGGCAT
5635982 GTACCCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:5637748 original size:34 final size:31
Alignment explanation
Indices: 5637705--5637793 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
5637695 TAAATAATTC
*
5637705 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
5637739 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
5637770 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
5637794 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:5637770 original size:31 final size:33
Alignment explanation
Indices: 5637705--5637784 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 33
5637695 TAAATAATTC
* *
5637705 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
5637739 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
5637770 TATAAAAAATAATAA
1 TA-AAAAAATAATAA
5637785 CTATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 2 0.05
34 22 0.54
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:5639641 original size:54 final size:54
Alignment explanation
Indices: 5639577--5639702 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 54
5639567 ATTTAAATGA
* * * *
5639577 TATATATTTTATTTATATTTTTAATTGAAAATACATTTTTATTTCTTAAAATTT
1 TATATATTTTATTTATATTTTCAATTGAAAAAACATTTTTATTCCCTAAAATTT
* *
5639631 TATATATTTTATTTATATTTTCAGTTGAAAAAATATTTTTATTCCCTAAAATTT
1 TATATATTTTATTTATATTTTCAATTGAAAAAACATTTTTATTCCCTAAAATTT
*
5639685 TATAAATTTGTATTTATA
1 TATATATTT-TATTTATA
5639703 ATATAGCATT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 56 0.88
55 8 0.12
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (54 bp):
TATATATTTTATTTATATTTTCAATTGAAAAAACATTTTTATTCCCTAAAATTT
Found at i:5642106 original size:27 final size:27
Alignment explanation
Indices: 5642028--5642107 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
5642018 ACATGCCTAA
*
5642028 ATTTCAATTTAGTTTTTAGTTTTAAATTT
1 ATTTCAATTTAGTCTTTA-TTTT-AATTT
* * *
5642057 ATTGCAATTTAG-CTCCTATTTTATTTT
1 ATTTCAATTTAGTCT-TTATTTTAATTT
*
5642084 ATTTCAATTTAGTCTTTACTTTAA
1 ATTTCAATTTAGTCTTTATTTTAA
5642108 ATCATTTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
27 21 0.51
28 7 0.17
29 13 0.32
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.57
Consensus pattern (27 bp):
ATTTCAATTTAGTCTTTATTTTAATTT
Found at i:5646103 original size:55 final size:54
Alignment explanation
Indices: 5645950--5646113 Score: 149
Period size: 55 Copynumber: 3.0 Consensus size: 54
5645940 TGATAGGATG
5645950 TTTTCAAATGAATTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGATTTCTTGATG-T
1 TTTTCAAATGAATTTTT-AAAGAAGCTAAGCCTAATTTTTA-GG-TTTCTTGATGAT
* ** * * *
5646006 TTTT-AAATGAGTTTTT--AGAAATTAAGCTTGATTTTTAGAGGTTTGTTGATGAT
1 TTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTT--AGGTTTCTTGATGAT
* * *
5646059 TATTTCCAAA-GAATTTTTAAAGAAGCTAGGCCTAATTTTTAGGTTTTTTTATGAT
1 T-TTT-CAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGTTTCTTGATGAT
5646114 AACTGTAAAC
Statistics
Matches: 86, Mismatches: 14, Indels: 17
0.74 0.12 0.15
Matches are distributed among these distances:
52 25 0.29
53 4 0.05
54 4 0.05
55 31 0.36
56 7 0.08
57 15 0.17
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (54 bp):
TTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGTTTCTTGATGAT
Found at i:5646569 original size:228 final size:228
Alignment explanation
Indices: 5646166--5646712 Score: 760
Period size: 228 Copynumber: 2.4 Consensus size: 228
5646156 AGGGTTTCTT
* * * *
5646166 AATGAGTAAGTCCTTCGGGCCATCCATAAGACATTCGGGCATGATGTTTTCAACATTTCCTTTGC
1 AATGA-TAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATATTTTCAACATTTCCTTTGC
* * *
5646231 TCGATTCACAACACTTCGAATCAGCAATGCCCCACTAGAGGGGTTAACATTTCCTATTGCCCGAT
65 TCGATTCACAACACTTCGAATCAGCAACGCCCCACTAAAGGGGTTAACAATTCCTATTGCCCGAT
* * * * *
5646296 TCACAACATTTTGAATCAGTAAAACTTCTTCGGGCCATCAGTAAGTCTTTCGAGTATGATGCTTA
130 TCACAACACTTTGAATCACTAAAACTCCATCAGGCCATCAGTAAGTCTTTCGAGTATGATGCTTA
* * ***
5646361 AATCCTTT-AGGTCATTTATAAGTTTTTTGAGCAA
195 AAT-CTTTCAGGTCATCTATAAGTCTTCCAAGCAA
* * *
5646395 AATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGAGCAGGATTTTTTCAATATTTCCTTTGCT
1 AATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATATTTTCAACATTTCCTTTGCT
* * * * **
5646460 CTATTCACAACACTTCGATTTAGGAACGCCCCACTAAAGGGGTTAACAATTCCTATTGCTTGATT
66 CGATTCACAACACTTCGAATCAGCAACGCCCCACTAAAGGGGTTAACAATTCCTATTGCCCGATT
* *
5646525 CACAACACTTTGAATCAACT-TAAGTCCATCAGGCCATCAGTAAGTCTTTCGAGTATGATGCTTA
131 CACAACACTTTGAATC-ACTAAAACTCCATCAGGCCATCAGTAAGTCTTTCGAGTATGATGCTTA
5646589 AATCTTTCAGGTCATCTATAAGTCTTCCAAGCAA
195 AATCTTTCAGGTCATCTATAAGTCTTCCAAGCAA
* *
5646623 GATGATAAGTTCTTCGGGCCATCCATAAGACCTTC-ATGCAGGATATTTTC-ACATTTCCTTTGC
1 AATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGA-GCAGGATATTTTCAACATTTCCTTTGC
5646686 TCGATTCACAACACTTCGAATCAGCAA
65 TCGATTCACAACACTTCGAATCAGCAA
5646713 TGCATCACTC
Statistics
Matches: 279, Mismatches: 36, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
227 40 0.14
228 232 0.83
229 7 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (228 bp):
AATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATATTTTCAACATTTCCTTTGCT
CGATTCACAACACTTCGAATCAGCAACGCCCCACTAAAGGGGTTAACAATTCCTATTGCCCGATT
CACAACACTTTGAATCACTAAAACTCCATCAGGCCATCAGTAAGTCTTTCGAGTATGATGCTTAA
ATCTTTCAGGTCATCTATAAGTCTTCCAAGCAA
Found at i:5650501 original size:2 final size:2
Alignment explanation
Indices: 5650496--5650529 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5650486 TAAAATAAAT
5650496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5650530 GAGAAATCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5651835 original size:12 final size:12
Alignment explanation
Indices: 5651818--5651842 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5651808 ATATAATCCT
5651818 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5651830 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5651842 G
1 G
5651843 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5654159 original size:19 final size:19
Alignment explanation
Indices: 5654137--5654267 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
5654127 GGAAATTACT
5654137 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5654156 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
5654170 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
5654189 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
5654203 TTCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
5654222 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
5654236 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5654255 ATCGCAACGCGAA
1 ATCGCAATGCGAA
5654268 TTCGAGTTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 39 0.48
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5654179 original size:33 final size:33
Alignment explanation
Indices: 5654137--5654263 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
5654127 GGAAATTACT
*
5654137 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
5654170 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
5654202 TTTCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
5654236 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5654264 CGAATTCGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5654248 original size:66 final size:66
Alignment explanation
Indices: 5654142--5654269 Score: 229
Period size: 66 Copynumber: 1.9 Consensus size: 66
5654132 TTACTATCGC
* *
5654142 AATGCGAAATGAAAATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
5654207 T
66 T
*
5654208 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
5654270 CGAGTTTCGC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:5654286 original size:20 final size:20
Alignment explanation
Indices: 5654263--5654307 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5654253 AAATCGCAAC
5654263 GCGA-ATTCGAGTTTCGCGTT
1 GCGATATTC-AGTTTCGCGTT
* *
5654283 GCGATTTTCATTTTCGCGTT
1 GCGATATTCAGTTTCGCGTT
5654303 GCGAT
1 GCGAT
5654308 TCTCTCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (20 bp):
GCGATATTCAGTTTCGCGTT
Found at i:5654466 original size:14 final size:14
Alignment explanation
Indices: 5654447--5654483 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5654437 CATCAATTAA
5654447 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5654461 ACAAATCACCTTTT
1 ACAAATCAACTTTT
5654475 ACAAATCAA
1 ACAAATCAA
5654484 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5655774 original size:21 final size:21
Alignment explanation
Indices: 5655708--5655774 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5655698 GTGAATCGGG
*
5655708 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
5655728 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
5655750 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
5655771 CTCT
1 CTCT
5655775 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:5655793 original size:42 final size:41
Alignment explanation
Indices: 5655708--5655830 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
5655698 GTGAATCGGG
* * * *
5655708 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
5655750 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
5655792 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
5655831 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:5657914 original size:33 final size:33
Alignment explanation
Indices: 5657857--5657955 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
5657847 ACGAGATAAT
*
5657857 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
5657891 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
5657924 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
5657956 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:5657949 original size:19 final size:19
Alignment explanation
Indices: 5657832--5658011 Score: 164
Period size: 19 Copynumber: 9.8 Consensus size: 19
5657822 TCTTTTGGTT
*
5657832 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
5657851 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
5657871 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
5657889 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
5657905 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
5657923 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5657938 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
5657958 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5657977 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5657996 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
5658012 TGCCATTTTT
Statistics
Matches: 133, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 57 0.43
20 45 0.34
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5657970 original size:39 final size:38
Alignment explanation
Indices: 5657927--5658011 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 38
5657917 GCGACCAGAC
5657927 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
5657966 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
5658004 AATCGCAA
1 AATCGCAA
5658012 TGCCATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 19 0.41
39 27 0.59
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:5658046 original size:20 final size:20
Alignment explanation
Indices: 5658017--5658054 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5658007 CGCAATGCCA
*
5658017 TTTTTGTTTCGCGTTGCGTT
1 TTTTTATTTCGCGTTGCGTT
5658037 TTTTTATTTCGCGTTGCG
1 TTTTTATTTCGCGTTGCG
5658055 ATAGTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.24, T:0.58
Consensus pattern (20 bp):
TTTTTATTTCGCGTTGCGTT
Found at i:5658621 original size:20 final size:20
Alignment explanation
Indices: 5658596--5658648 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5658586 GCGCTATGTA
5658596 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
5658616 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
5658636 TATCTCGTTGCGA
1 AATCGCGTTGCGA
5658649 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:5658682 original size:20 final size:20
Alignment explanation
Indices: 5658657--5658706 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
5658647 GATTTTTTAT
5658657 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
5658677 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
5658697 TATCGCATTG
1 TATCGCATTG
5658707 AGTATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:5660329 original size:20 final size:19
Alignment explanation
Indices: 5660293--5660331 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5660283 AGGAAAGAAA
*
5660293 ATTTTTTATTTTAATTTAT
1 ATTTTTTATGTTAATTTAT
*
5660312 ATTTGTTTATGTTCATTTAT
1 ATTT-TTTATGTTAATTTAT
5660332 TGTGTTCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTTTTATGTTAATTTAT
Found at i:5660365 original size:10 final size:10
Alignment explanation
Indices: 5660350--5660398 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
5660340 TTTACATTTA
*
5660350 TTCGTTTGTG
1 TTCGTTTATG
*
5660360 TTCGTTTACG
1 TTCGTTTATG
5660370 TTCGTTTATTGTG
1 TTCGTTTA---TG
5660383 TTCGTTTATG
1 TTCGTTTATG
5660393 TTCGTT
1 TTCGTT
5660399 CATTTGTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 24 0.73
13 9 0.27
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.59
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:5660378 original size:47 final size:47
Alignment explanation
Indices: 5660316--5660414 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 47
5660306 ATTTATATTT
* * *
5660316 GTTTATGTTCATTTATTGTGTTCGTTTACATTTATTCGTTTGTGTTC
1 GTTTACGTTCATTTATTGTGTTCGTTTACATTCATTCATTTGTGTTC
* ** *
5660363 GTTTACGTTCGTTTATTGTGTTCGTTTATGTTCGTTCATTTGTGTTC
1 GTTTACGTTCATTTATTGTGTTCGTTTACATTCATTCATTTGTGTTC
5660410 GTTTA
1 GTTTA
5660415 TAATTTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (47 bp):
GTTTACGTTCATTTATTGTGTTCGTTTACATTCATTCATTTGTGTTC
Found at i:5660410 original size:24 final size:23
Alignment explanation
Indices: 5660316--5660415 Score: 101
Period size: 24 Copynumber: 4.3 Consensus size: 23
5660306 ATTTATATTT
*
5660316 GTTTATGTTCATTTATTGTGTTC
1 GTTTATGTTCATTCATTGTGTTC
** * *
5660339 GTTTACATTTATTCGTTTGTGTTC
1 GTTTATGTTCATTC-ATTGTGTTC
* * *
5660363 GTTTACGTTCGTTTATTGTGTTC
1 GTTTATGTTCATTCATTGTGTTC
*
5660386 GTTTATGTTCGTTCATTTGTGTTC
1 GTTTATGTTCATTCA-TTGTGTTC
5660410 GTTTAT
1 GTTTAT
5660416 AATTTAAATG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
23 31 0.49
24 32 0.51
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (23 bp):
GTTTATGTTCATTCATTGTGTTC
Found at i:5663804 original size:35 final size:34
Alignment explanation
Indices: 5663758--5663870 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
5663748 AAAACAATCC
*
5663758 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
5663793 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
5663828 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
5663863 TCAATTTC
1 TCAATTTC
5663871 TGTCTTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.90
36 6 0.08
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:5664971 original size:35 final size:34
Alignment explanation
Indices: 5664923--5665034 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
5664913 ATTCCTCCTT
* *
5664923 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
5664958 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
5664993 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
5665028 AAATTGA
1 AAATTGA
5665035 GGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:5665940 original size:42 final size:42
Alignment explanation
Indices: 5665876--5665994 Score: 220
Period size: 42 Copynumber: 2.8 Consensus size: 42
5665866 AATTCAAATA
5665876 TATTAATATTTTAAAATAGTTAAAATAATATATTTATAGTTATT
1 TATT-ATATTTT-AAATAGTTAAAATAATATATTTATAGTTATT
5665920 TATTATATTTTAAATAGTTAAAATAATATATTTATAGTTATT
1 TATTATATTTTAAATAGTTAAAATAATATATTTATAGTTATT
5665962 TATTATATTTTAAATAGTTAAAATAATATATTT
1 TATTATATTTTAAATAGTTAAAATAATATATTT
5665995 TACCTTAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
42 64 0.85
43 7 0.09
44 4 0.05
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (42 bp):
TATTATATTTTAAATAGTTAAAATAATATATTTATAGTTATT
Found at i:5669180 original size:17 final size:17
Alignment explanation
Indices: 5669158--5669190 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5669148 AGTGAATAAA
5669158 ATTTCTTACACTGAAAC
1 ATTTCTTACACTGAAAC
5669175 ATTTCTTACACTGAAA
1 ATTTCTTACACTGAAA
5669191 AAATTAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTCTTACACTGAAAC
Found at i:5673836 original size:18 final size:18
Alignment explanation
Indices: 5673810--5673844 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5673800 TCGAAAGGAC
*
5673810 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
5673828 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
5673845 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:5679644 original size:43 final size:43
Alignment explanation
Indices: 5679597--5679831 Score: 255
Period size: 43 Copynumber: 5.5 Consensus size: 43
5679587 ATATCTATTA
* **
5679597 CGGCGTTTTTTGA-ACAAACGCCGCAAAAAGTTATGATATATAG
1 CGGCGTTTTTAGACACAAACGCCGCAAAAAGTTA-GACCTATAG
* * * * *
5679640 CGGCGTTTCTAGAAAAAAACACCGCAAAAGAG-AAGACCTATA-
1 CGGCGTTTTTAGACACAAACGCCGCAAAA-AGTTAGACCTATAG
* *
5679682 CTGGCGTTTTTAGA-ACAAACGCCGCAAAAGGTTAAACCTATAG
1 C-GGCGTTTTTAGACACAAACGCCGCAAAAAGTTAGACCTATAG
* * *
5679725 CGGCGTTTTTGGACACAAACGCCGCAAAAGGTTAGACCTATAA
1 CGGCGTTTTTAGACACAAACGCCGCAAAAAGTTAGACCTATAG
*
5679768 CGGCGTTTTT-GAACACAAACGCCGCAAAAAGTCAGACCTATAG
1 CGGCGTTTTTAG-ACACAAACGCCGCAAAAAGTTAGACCTATAG
* *
5679811 CGGCGTTTTTGGATACAAACG
1 CGGCGTTTTTAGACACAAACG
5679832 TCGCTAATTA
Statistics
Matches: 164, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 34 0.21
43 112 0.68
44 15 0.09
45 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (43 bp):
CGGCGTTTTTAGACACAAACGCCGCAAAAAGTTAGACCTATAG
Found at i:5679805 original size:128 final size:129
Alignment explanation
Indices: 5679597--5679831 Score: 309
Period size: 128 Copynumber: 1.8 Consensus size: 129
5679587 ATATCTATTA
* * *
5679597 CGGCGTTTTTTGAACAAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGAAAAAAACAC
1 CGGCGTTTTTGGAACAAACGCCGCAAAAAGTTATGACATATAACGGCGTTTCTAGAAAAAAACAC
5679662 CGCAAAAGAGAAGACCTATA-CTGGCGTTTTTAGA-ACAAACGCCGCAAAAGGTTAAACCTATAG
66 CGCAAAAGAGAAGACCTATAGC-GGCGTTTTTAGATACAAACGCCGCAAAAGGTTAAACCTATAG
* * * *
5679725 CGGCGTTTTTGGACACAAACGCCGCAAAAGGTTA-GACCTATAACGGCGTTT-TTGAACACAAAC
1 CGGCGTTTTTGGA-ACAAACGCCGCAAAAAGTTATGACATATAACGGCGTTTCTAGAA-AAAAAC
* * *
5679788 GCCGCAAAA-AGTCAGACCTATAGCGGCGTTTTTGGATACAAACG
64 ACCGCAAAAGAG-AAGACCTATAGCGGCGTTTTTAGATACAAACG
5679832 TCGCTAATTA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
127 6 0.07
128 59 0.64
129 27 0.29
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (129 bp):
CGGCGTTTTTGGAACAAACGCCGCAAAAAGTTATGACATATAACGGCGTTTCTAGAAAAAAACAC
CGCAAAAGAGAAGACCTATAGCGGCGTTTTTAGATACAAACGCCGCAAAAGGTTAAACCTATAG
Found at i:5679819 original size:86 final size:84
Alignment explanation
Indices: 5679595--5679831 Score: 282
Period size: 86 Copynumber: 2.8 Consensus size: 84
5679585 CAATATCTAT
** * * *
5679595 TACGGCGTTTTTTG-AACAAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGAAAAAAA
1 TACGGCG-TTTTTGAAACAAACGCCGCAAAAAGTTA-GACCTATAGCGGCGTTTTTGGAAACAAA
*
5679659 CACCGCAAAAGAGAAGACCTA
64 CGCCGCAAAAGAGAAGACCTA
* * *
5679680 TACTGGCGTTTTT-AGAACAAACGCCGCAAAAGGTTAAACCTATAGCGGCGTTTTTGGACACAAA
1 TAC-GGCGTTTTTGA-AACAAACGCCGCAAAAAGTTAGACCTATAGCGGCGTTTTTGGAAACAAA
*
5679744 CGCCGCAAAAG-GTTAGACCTA
64 CGCCGCAAAAGAG-AAGACCTA
* *
5679765 TAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAA
1 T-ACGGCGTTTTTGAA-ACAAACGCCGCAAAAAGTTAGACCTATAGCGGCGTTTTTGGAAACAAA
5679830 CG
64 CG
5679832 TCGCTAATTA
Statistics
Matches: 131, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
84 1 0.01
85 57 0.44
86 73 0.56
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (84 bp):
TACGGCGTTTTTGAAACAAACGCCGCAAAAAGTTAGACCTATAGCGGCGTTTTTGGAAACAAACG
CCGCAAAAGAGAAGACCTA
Found at i:5683174 original size:41 final size:41
Alignment explanation
Indices: 5683107--5683628 Score: 526
Period size: 41 Copynumber: 12.6 Consensus size: 41
5683097 TTGTAAACTT
* * * * *
5683107 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* *
5683150 GCGGCGTTTGAATAAAAACGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *** *
5683191 GCGACGTTTGTATAAAAATATCAATAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
5683232 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * * *
5683273 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * * * *
5683316 ACGGCGTTTGAATAAAAATGTCACTAAAGTACGCGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
5683357 GCGGAGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
5683398 GCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
5683439 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* ** * * *
5683482 ACGGCGTTTGTATAAAAATACCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
5683523 GCAGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
5683564 GTGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
5683605 GCGGCGTTTGT-TGAAAAAACGCCA
1 GCGGCGTTTGTAT--AAAAACGCCA
5683629 TTATCAATGA
Statistics
Matches: 396, Mismatches: 75, Indels: 17
0.81 0.15 0.03
Matches are distributed among these distances:
40 1 0.00
41 305 0.77
42 17 0.04
43 73 0.18
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:5683387 original size:166 final size:165
Alignment explanation
Indices: 5683107--5683615 Score: 766
Period size: 166 Copynumber: 3.1 Consensus size: 165
5683097 TTGTAAACTT
* *
5683107 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
* ** *
5683172 ACTAAAGTATGAGTCTTTAGCGACGTTTGTATAAAAATATCAATAAAGTACGAGTCTTTAGCGGC
66 ACTAAAGTACGAGTCTTTAGCGA-GTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
*
5683237 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
130 GTTTGTATAAAAACGCCACTAAATTACGAGTCTTTA
* *
5683273 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGTC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
* *
5683338 ACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGGC
66 ACTAAAGTACGAGTCTTTAGC-GAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
*
5683403 GTTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
130 GTTTGTATAAAAACGCCACTAAATTACGAGTCTTTA
* * *
5683439 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAATACC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
* * * * * *
5683504 ACTAAAGTACAATTCTATAGCAGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGTGGC
66 ACTAAAGTACGAGTCTTTAGC-GAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
* * * *
5683569 GTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
130 GTTTGTATAAAAACGCCACTAAATTACGAGTCTTTA
5683605 GCGGCGTTTGT
1 GCGGCGTTTGT
5683616 TGAAAAAACG
Statistics
Matches: 311, Mismatches: 31, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
166 309 0.99
167 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (165 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
ACTAAAGTACGAGTCTTTAGCGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCG
TTTGTATAAAAACGCCACTAAATTACGAGTCTTTA
Found at i:5683466 original size:125 final size:123
Alignment explanation
Indices: 5683107--5683615 Score: 527
Period size: 125 Copynumber: 4.1 Consensus size: 123
5683097 TTGTAAACTT
* * * * * * *
5683107 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * * *** *
5683172 ACTAAAGTATGAGTCTTTAGCGACGTTTGTATAAAAATATCAATAAAGTACGAGTCTTTA
64 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
5683232 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGACGTTTGTAAACACAAACGCC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A-AAACGCC
* * * * * * * *
5683297 ACTATAGTACAAGTGTATAACGGCGTTTG-AATAAAAATGTCACTAAAGTACGCGTCTTTA
64 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTAA-AAAAACGCCACTAAAGTACGAGTCTTTA
* *
5683357 GCGGAGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
* * * * *
5683422 TAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
66 TAAAGTACGAGTCTTTAGCGGCGTTTGTAAA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* * * * * * *
5683482 ACGGCGTTTGTATAAAAATACCACTAAAGTACAATTCTATAGCAGCGTTTGTATAAAAATGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
* * * * * *
5683547 TAAATTACGAGTCTTTAGTGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
66 TAAAGTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTTTA
5683605 GCGGCGTTTGT
1 GCGGCGTTTGT
5683616 TGAAAAAACG
Statistics
Matches: 319, Mismatches: 57, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
123 90 0.28
124 9 0.03
125 220 0.69
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (123 bp):
GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
TAAAGTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:5684817 original size:2 final size:2
Alignment explanation
Indices: 5684810--5684857 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5684800 TATTTCTTAA
5684810 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
5684852 AT AT AT
1 AT AT AT
5684858 GTATGTATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5684862 original size:4 final size:4
Alignment explanation
Indices: 5684855--5684901 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
5684845 TATATATATA
*
5684855 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5684902 TTCATTGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5686851 original size:2 final size:2
Alignment explanation
Indices: 5686844--5686878 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
5686834 ATGGATTGCT
5686844 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
5686879 TTAGTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5687048 original size:13 final size:13
Alignment explanation
Indices: 5687030--5687059 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5687020 AATGACACAC
*
5687030 AATGTAAGTCGTA
1 AATGTAAGTCATA
5687043 AATGTAAGTCATA
1 AATGTAAGTCATA
5687056 AATG
1 AATG
5687060 CGTGTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:5687089 original size:98 final size:98
Alignment explanation
Indices: 5686978--5687221 Score: 251
Period size: 98 Copynumber: 2.5 Consensus size: 98
5686968 ATACAATCAC
* ** ** *
5686978 GACACACAAATGTGTGTCATATT-TTTTAATGACTTGTTCTTCAATGACACACAATGTAAGTCGT
1 GACACACAAATGTGTGTCATATTCATTT-ATGACGAGGGCTTCAATGACACACAATGTAAGTCAT
* *
5687042 AAATGTAAGTCATAAATGCGTGTCATAAATTTAT
65 AAATGCAAGTCATAAATGCGCGTCATAAATTTAT
* * ** **
5687076 GACACACAAATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGACGCGTAATGTGCGTCATA
1 GACACACAAATGTGTGTCATATTCATTTATGACGAGGGCTTCAATGACACACAATGTAAGTCATA
* *
5687141 AATGCATGTCATAAATGCGCGTCATAGATTTAT
66 AATGCAAGTCATAAATGCGCGTCATAAATTTAT
* * * *
5687174 GACACACAATTGCGTATCATCTGAT-ATTTATGACG-GTGGCTTCAATGA
1 GACACACAAATGTGTGTCATAT--TCATTTATGACGAG-GGCTTCAATGA
5687222 AGCGTATTTG
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
98 98 0.80
99 24 0.20
100 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (98 bp):
GACACACAAATGTGTGTCATATTCATTTATGACGAGGGCTTCAATGACACACAATGTAAGTCATA
AATGCAAGTCATAAATGCGCGTCATAAATTTAT
Found at i:5687164 original size:13 final size:13
Alignment explanation
Indices: 5687128--5687166 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5687118 AATGACGCGT
*
5687128 AATGTGCGTCATA
1 AATGCGCGTCATA
**
5687141 AATGCATGTCATA
1 AATGCGCGTCATA
5687154 AATGCGCGTCATA
1 AATGCGCGTCATA
5687167 GATTTATGAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:5687946 original size:3 final size:3
Alignment explanation
Indices: 5687933--5687966 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
5687923 GTAAATAAGA
5687933 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5687967 CTTTTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5724367 original size:60 final size:60
Alignment explanation
Indices: 5724295--5724431 Score: 149
Period size: 60 Copynumber: 2.3 Consensus size: 60
5724285 TATTTTTATT
* *
5724295 TTAAAA-ATATATTTTATTTTTATCTTAATTTA-TTAAATATATTTTATTATC-AAACTAA-A
1 TTAAAATATATATTTTATTTAT-TCTTAATTTAGTTAAAAATATTTT-TT-TCTAAACTAACA
* * *
5724354 TTAAAATATATATTTTA-TTATTCTTATTTTAGTTTAAAAATATTTTTTTCTTATCTAACA
1 TTAAAATATATATTTTATTTATTCTTAATTTAG-TTAAAAATATTTTTTTCTAAACTAACA
*
5724414 TAAAAATATATATTTTAT
1 TTAAAATATATATTTTAT
5724432 CTCATCTTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
58 11 0.17
59 16 0.24
60 39 0.59
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (60 bp):
TTAAAATATATATTTTATTTATTCTTAATTTAGTTAAAAATATTTTTTTCTAAACTAACA
Found at i:5726132 original size:14 final size:14
Alignment explanation
Indices: 5726115--5726154 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
5726105 ATAAAATTAT
5726115 AATTTAAATAAATA
1 AATTTAAATAAATA
*
5726129 AATTTAAATAAATG
1 AATTTAAATAAATA
5726143 AATTTAAATAAA
1 AATTTAAATAAA
5726155 ATTAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
AATTTAAATAAATA
Found at i:5727159 original size:23 final size:22
Alignment explanation
Indices: 5727134--5727184 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 22
5727124 AATTAATCAT
5727134 AAAATAAACTTCTACCATTTAATA
1 AAAAT-AA-TTCTACCATTTAATA
*
5727158 AAAATTATTCTACCATTTAATA
1 AAAATAATTCTACCATTTAATA
5727180 AAAAT
1 AAAAT
5727185 TATTTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 20 0.77
23 1 0.04
24 5 0.19
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATAATTCTACCATTTAATA
Found at i:5727170 original size:22 final size:22
Alignment explanation
Indices: 5727143--5727188 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5727133 TAAAATAAAC
5727143 TTCTACCATTTAATAAAAATTA
1 TTCTACCATTTAATAAAAATTA
5727165 TTCTACCATTTAATAAAAATTA
1 TTCTACCATTTAATAAAAATTA
5727187 TT
1 TT
5727189 TTTTCTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (22 bp):
TTCTACCATTTAATAAAAATTA
Found at i:5727819 original size:18 final size:18
Alignment explanation
Indices: 5727796--5727856 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 18
5727786 TCGACTTTAA
5727796 CTTTCTT-CTCTTATTCTT
1 CTTTCTTCCTCTT-TTCTT
5727814 CTTTCTTCCTCTTTTTTTCTT
1 CTTTCTTCCTC---TTTTCTT
*
5727835 CTTTCTTCCTCTTTTTTT
1 CTTTCTTCCTCTTTTCTT
5727853 CTTT
1 CTTT
5727857 TTTCTTCTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 17 0.45
19 3 0.08
21 16 0.42
22 2 0.05
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTCTTCCTCTTTTCTT
Found at i:5727835 original size:21 final size:21
Alignment explanation
Indices: 5727809--5727874 Score: 105
Period size: 21 Copynumber: 3.0 Consensus size: 21
5727799 TCTTCTCTTA
5727809 TTCTTCTTTCTTCCTCTTTTT
1 TTCTTCTTTCTTCCTCTTTTT
5727830 TTCTTCTTTCTTCCTCTTTTT
1 TTCTTCTTTCTTCCTCTTTTT
*
5727851 TTCTTTTTTCTTCTCCTCTTTTT
1 TTCTTCTTTC-T-TCCTCTTTTT
5727874 T
1 T
5727875 CTTTCACTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
21 30 0.71
22 1 0.02
23 11 0.26
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTTCTTTCTTCCTCTTTTT
Found at i:5731745 original size:2 final size:2
Alignment explanation
Indices: 5731738--5731767 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5731728 TGTAAAGTTC
5731738 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
5731768 TACTAACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5732138 original size:2 final size:2
Alignment explanation
Indices: 5732131--5732165 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5732121 ATAACACATG
5732131 AT AT AT 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 AT AT AT A
5732166 AAGTATGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5740767 original size:20 final size:20
Alignment explanation
Indices: 5740738--5740778 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5740728 TTTTCTTTTA
*
5740738 GGGGGTATCGATACCCCTAT
1 GGGGGAATCGATACCCCTAT
*
5740758 GGGGGAATCGGTACCCCTAT
1 GGGGGAATCGATACCCCTAT
5740778 G
1 G
5740779 ATATTCTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGATACCCCTAT
Found at i:5740874 original size:65 final size:64
Alignment explanation
Indices: 5740738--5740882 Score: 159
Period size: 65 Copynumber: 2.2 Consensus size: 64
5740728 TTTTCTTTTA
* * * * * * *
5740738 GGGGGTATCGATACCCCTATGGGGGAATCGGTACCCCTATGATATTCTGTAATTTTTTCGTCAAT
1 GGGGGTATCGGTACCCCTATGGGGGAATCGATACCCCCATAACATTCTGGAATTTTCTCGT-AAT
* *
5740803 GGGGGTATCGGTACCCCTCTGGGGGGAATCGATACCCCCATAACATTCTGGAA-TTTCTCGT-TT
1 GGGGGTATCGGTACCCCTAT-GGGGGAATCGATACCCCCATAACATTCTGGAATTTTCTCGTAAT
5740866 GAGAGGGTATCGGTACC
1 G-G-GGGTATCGGTACC
5740883 TATTGAATGG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.03
64 1 0.01
65 38 0.56
66 27 0.40
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (64 bp):
GGGGGTATCGGTACCCCTATGGGGGAATCGATACCCCCATAACATTCTGGAATTTTCTCGTAAT
Found at i:5741989 original size:34 final size:33
Alignment explanation
Indices: 5741947--5742034 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
5741937 AATGGTAATA
*
5741947 AACAAAATTAACAAAAATATATTAACAAAAAATCC
1 AACAAAATTAAC-AAAATAAATTAA-AAAAAATCC
* *
5741982 AACAAATTTAACAAAATAAATTAAAATAAATCC
1 AACAAAATTAACAAAATAAATTAAAAAAAATCC
**
5742015 AACAAAATTAATGAAATAAA
1 AACAAAATTAACAAAATAAA
5742035 GTATGTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 25 0.53
34 11 0.23
35 11 0.23
ACGTcount: A:0.66, C:0.11, G:0.01, T:0.22
Consensus pattern (33 bp):
AACAAAATTAACAAAATAAATTAAAAAAAATCC
Found at i:5744354 original size:28 final size:29
Alignment explanation
Indices: 5744322--5744392 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
5744312 AAAAAAATTA
5744322 ATTAAATAAAATATAA-AAAA-ATTAAAT
1 ATTAAATAAAATATAACAAAATATTAAAT
* *
5744349 ACTTAAATAAATTAAAAACAAAATATTAAAT
1 A-TTAAATAAAAT-ATAACAAAATATTAAAT
5744380 A-T-AATAAAATATA
1 ATTAAATAAAATATA
5744393 CCTTAAACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.08
28 17 0.47
29 4 0.11
30 4 0.11
31 8 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (29 bp):
ATTAAATAAAATATAACAAAATATTAAAT
Found at i:5744356 original size:23 final size:22
Alignment explanation
Indices: 5744321--5744389 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
5744311 CAAAAAAATT
5744321 AATTAAATA--AAATATAAAAA
1 AATTAAATATTAAATATAAAAA
5744341 AATTAAATACTTAAATA-AATTAAA
1 AATTAAATA-TTAAATATAA--AAA
** *
5744365 AACAAAATATTAAATATAATAA
1 AATTAAATATTAAATATAAAAA
5744387 AAT
1 AAT
5744390 ATACCTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 9 0.23
22 6 0.15
23 12 0.31
24 12 0.31
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
AATTAAATATTAAATATAAAAA
Found at i:5744365 original size:24 final size:23
Alignment explanation
Indices: 5744330--5744388 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
5744320 TAATTAAATA
**
5744330 AAATATAA-AAAAATTAAATACTT
1 AAATATAATAAAAACAAAATA-TT
5744353 AAATA-AATTAAAAACAAAATATT
1 AAATATAA-TAAAAACAAAATATT
5744376 AAATATAATAAAA
1 AAATATAATAAAA
5744389 TATACCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 17 0.55
24 12 0.39
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATATAATAAAAACAAAATATT
Found at i:5748172 original size:29 final size:29
Alignment explanation
Indices: 5748098--5748172 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
5748088 TAAAATTATC
5748098 TTTTATTTTTGTTTTAACTTATTAAATATA
1 TTTTATTTTT-TTTTAACTTATTAAATATA
* *
5748128 TTTTATTTTTTCTTAACTTATTATATAT-
1 TTTTATTTTTTTTTAACTTATTAAATATA
5748156 TTTTATTTTTATTTTAA
1 TTTTATTTTT-TTTTAA
5748173 TGTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 10 0.24
29 21 0.51
30 10 0.24
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTTATTTTTTTTTAACTTATTAAATATA
Found at i:5748739 original size:50 final size:50
Alignment explanation
Indices: 5748624--5748739 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 50
5748614 AGTGCGCCTT
* * * *
5748624 CTGAACCGCGTTATATGCTGATTTGGTGCCACGTGAGTATAGCGCGCCCC
1 CTGAACCGCGATATACGCTGATTTGGCGCAACGTGAGTATAGCGCGCCCC
** * * * *
5748674 CTGCCCCACGATATACGGTGATTTGGCGCAACGTGGGTATAGCGTGCCCC
1 CTGAACCGCGATATACGCTGATTTGGCGCAACGTGAGTATAGCGCGCCCC
* *
5748724 CTGATCCGCGCTATAC
1 CTGAACCGCGATATAC
5748740 ATGTGTATCT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (50 bp):
CTGAACCGCGATATACGCTGATTTGGCGCAACGTGAGTATAGCGCGCCCC
Found at i:5748944 original size:16 final size:16
Alignment explanation
Indices: 5748931--5748968 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
5748921 TTACTATTAT
5748931 ATATTTACTTTATTTA
1 ATATTTACTTTATTTA
5748947 ATATTTACTTTATTTA
1 ATATTTACTTTATTTA
5748963 ATATTT
1 ATATTT
5748969 TACTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTACTTTATTTA
Found at i:5749225 original size:109 final size:109
Alignment explanation
Indices: 5749034--5749238 Score: 365
Period size: 109 Copynumber: 1.9 Consensus size: 109
5749024 TGGAAATCAT
* *
5749034 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
5749099 TATTTAGTTGATTTATTTAATGCATGATTTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTTAGATTAAGAATTAA
*
5749143 ATATCTCGACATTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
5749208 TAATTAGTTGATTTATTTAATGCATTATTTA
66 TAATTAGTTGATTTATTTAATGCATGATTTA
5749239 TTTAAGCTCA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (109 bp):
ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTTAGATTAAGAATTAA
Done.