Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:2024890 original size:37 final size:37
Alignment explanation
Indices: 2024846--2024931 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
2024836 ATTTTGTTCG
2024846 GGTCGGGTCGGGTGTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTGTTTTAAGTGTGATATTCGGGTCA
* *
2024882 GAGTCGGGTCAGGTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTCGGGTGTTTTAAGTGTGATATTCGGGTCA
2024920 GGTC-GGTCGGGT
1 GGTCGGGTCGGGT
2024932 TCGGGTTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
36 8 0.18
37 36 0.80
38 1 0.02
ACGTcount: A:0.13, C:0.12, G:0.41, T:0.35
Consensus pattern (37 bp):
GGTCGGGTCGGGTGTTTTAAGTGTGATATTCGGGTCA
Found at i:2025537 original size:16 final size:18
Alignment explanation
Indices: 2025512--2025557 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2025502 TATGGAATTT
2025512 GATTCCAATT-CTT-ACA
1 GATTCCAATTCCTTCACA
*
2025528 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
2025546 GATTTCAATTCC
1 GATTCCAATTCC
2025558 CTCGTAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 13 0.52
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:2029632 original size:41 final size:41
Alignment explanation
Indices: 2029603--2029680 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
2029593 GCGAATTTGG
*
2029603 AAAATCGCAATGCGATACTGACTAACGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTAACGCAACGCGATAATAC
**
2029644 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTAACGCAACGCGATA
2029681 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTAACGCAACGCGATAATAC
Found at i:2029637 original size:20 final size:20
Alignment explanation
Indices: 2029608--2029700 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
2029598 TTTGGAAAAT
*
2029608 CGCAATGCGATACTGACTAA
1 CGCAACGCGATACTGACTAA
* *
2029628 CGCAACGCGATAAT-ACAAAA
1 CGCAACGCGATACTGAC-TAA
**
2029648 TCGCAACGCGATACTGACTTT
1 -CGCAACGCGATACTGACTAA
**
2029669 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTGACTAA
*
2029689 CGCAACGAGATA
1 CGCAACGCGATA
2029701 ATACATAATC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
CGCAACGCGATACTGACTAA
Found at i:2029654 original size:21 final size:22
Alignment explanation
Indices: 2029603--2029720 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 22
2029593 GCGAATTTGG
* *
2029603 AAAATCGCAATGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
*
2029625 -TAA-CGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATAATGAC
*
2029644 AAAATCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
** *
2029666 --TTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
** *
2029686 --TTTCGCAACGAGATAAT-AC
1 AAAATCGCAACGCGATAATGAC
* *
2029705 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
2029721 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 4 0.05
20 47 0.60
21 25 0.32
22 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
AAAATCGCAACGCGATAATGAC
Found at i:2030369 original size:25 final size:24
Alignment explanation
Indices: 2030315--2030369 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2030305 TGTTTATTAT
* *
2030315 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2030339 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2030365 TGTTT
1 TGTTT
2030370 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2031529 original size:18 final size:18
Alignment explanation
Indices: 2031499--2031545 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2031489 CCACTTCGGA
*
2031499 AGCCATCATCTCACCCAG
1 AGCCATCACCTCACCCAG
*
2031517 AGCTATCACCTCACCCAG
1 AGCCATCACCTCACCCAG
2031535 AGCCATCACCT
1 AGCCATCACCT
2031546 GATCGACCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.45, G:0.11, T:0.17
Consensus pattern (18 bp):
AGCCATCACCTCACCCAG
Found at i:2043300 original size:20 final size:21
Alignment explanation
Indices: 2043258--2043314 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
2043248 TCTGTCCAAC
* * *
2043258 AAAGGATCGATCTCTTATC-A
1 AAAGGATCGATCCCTCAGCAA
*
2043278 AAAGGATCGATCCCTCAGGAA
1 AAAGGATCGATCCCTCAGCAA
*
2043299 AAATGATCGATCCCTC
1 AAAGGATCGATCCCTC
2043315 GACCAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
AAAGGATCGATCCCTCAGCAA
Found at i:2043322 original size:21 final size:21
Alignment explanation
Indices: 2043258--2043323 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2043248 TCTGTCCAAC
* * *
2043258 AAAGGATCGATCTCTTA-TCA
1 AAAGGATCGATCCCTCAGACA
2043278 AAAGGATCGATCCCTCAGGA-A
1 AAAGGATCGATCCCTCA-GACA
*
2043299 AAATGATCGATCCCTC-GACCA
1 AAAGGATCGATCCCTCAGA-CA
2043320 AAAG
1 AAAG
2043324 AATTGATCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.05
20 15 0.41
21 20 0.54
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (21 bp):
AAAGGATCGATCCCTCAGACA
Found at i:2044996 original size:28 final size:28
Alignment explanation
Indices: 2044947--2045013 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
2044937 ATGATATTCA
* *
2044947 TCATTGGGATCGACACCATTTTCAT-TTT
1 TCATTGGCATCCACACCATTTT-ATCTTT
2044975 TCATTGGCATCCACATCC-TTTTATCTTT
1 TCATTGGCATCCACA-CCATTTTATCTTT
* *
2045003 GCATTTGCATC
1 TCATTGGCATC
2045014 TCTACATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.43
Consensus pattern (28 bp):
TCATTGGCATCCACACCATTTTATCTTT
Found at i:2047906 original size:21 final size:23
Alignment explanation
Indices: 2047867--2047908 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2047857 ATGCTAAATG
2047867 GTTTACATATAACTATTCAAAAC
1 GTTTACATATAACTATTCAAAAC
*
2047890 GTTTACA-A-AACTGTTCAAA
1 GTTTACATATAACTATTCAAA
2047909 GCTTATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (23 bp):
GTTTACATATAACTATTCAAAAC
Found at i:2048359 original size:19 final size:20
Alignment explanation
Indices: 2048315--2048361 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
2048305 TGGTCTTGTC
2048315 CATCATATTCATACACACCAT
1 CATCATA-TCATACACACCAT
* *
2048336 -GTCATATCATACA-TCCAT
1 CATCATATCATACACACCAT
2048354 CATCATAT
1 CATCATAT
2048362 AAATCATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 5 0.23
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (20 bp):
CATCATATCATACACACCAT
Found at i:2048845 original size:32 final size:30
Alignment explanation
Indices: 2048775--2048892 Score: 132
Period size: 32 Copynumber: 3.8 Consensus size: 30
2048765 AAAGGACCTA
* * *
2048775 TCCATATGTTCCAAAGAACATAGGTAAAAG
1 TCCATATGTTCCGAAGGACATAGGTAAATG
2048805 TCCATATG-TCCTGAAGGACATAGGTAATCATG
1 TCCATATGTTCC-GAAGGACATAGGTAA--ATG
*
2048837 TCCATATGTTCCGAAGGACATAGGTAAAGTA
1 TCCATATGTTCCGAAGGACATAGGTAAA-TG
*
2048868 TCCATATG-TCTCGAAAGACATAGGT
1 TCCATATGTTC-CGAAGGACATAGGT
2048893 CACCCTCGAC
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.04
30 24 0.31
31 22 0.29
32 25 0.32
33 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (30 bp):
TCCATATGTTCCGAAGGACATAGGTAAATG
Found at i:2048858 original size:62 final size:62
Alignment explanation
Indices: 2048775--2048892 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
2048765 AAAGGACCTA
*
2048775 TCCATATGTTCCAAAGAACATAGGTAAA-AGTCCATATGTC-CTGAAGGACATAGGTAATCATG
1 TCCATATGTTCCAAAGAACATAGGTAAAGA-TCCATATGTCTC-GAAAGACATAGGTAATCATG
* *
2048837 TCCATATGTTCCGAAGGACATAGGTAAAGTATCCATATGTCTCGAAAGACATAGGT
1 TCCATATGTTCCAAAGAACATAGGTAAAG-ATCCATATGTCTCGAAAGACATAGGT
2048893 CACCCTCGAC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
62 26 0.52
63 22 0.44
64 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (62 bp):
TCCATATGTTCCAAAGAACATAGGTAAAGATCCATATGTCTCGAAAGACATAGGTAATCATG
Found at i:2053348 original size:19 final size:19
Alignment explanation
Indices: 2053301--2053350 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
2053291 ACGTGGTCTT
2053301 ATCCATCAT-AT-TCATAC
1 ATCCATCATCATATCATAC
* *
2053318 ACACCAT-GTCATATCATAC
1 A-TCCATCATCATATCATAC
2053337 ATCCATCATCATAT
1 ATCCATCATCATAT
2053351 AAATCATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 2 0.08
18 10 0.40
19 13 0.52
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (19 bp):
ATCCATCATCATATCATAC
Found at i:2053833 original size:32 final size:30
Alignment explanation
Indices: 2053781--2053883 Score: 118
Period size: 32 Copynumber: 3.3 Consensus size: 30
2053771 GTTCCGAAGA
2053781 ACATAGGTAAT-TGTCCATATGTCCAAAATG
1 ACATAGGTAATCTGTCCATATGTCCAAAA-G
**
2053811 ACATAGGTAATCCTGTCCATATGTCCCGAAG
1 ACATAGGTAAT-CTGTCCATATGTCCAAAAG
* * *
2053842 AACATAGGTAAACTATCCATATGTCTCGAAAG
1 -ACATAGGTAATCTGTCCATATGTC-CAAAAG
2053874 ACATAGGTAA
1 ACATAGGTAA
2053884 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
30 11 0.17
31 23 0.37
32 29 0.46
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.26
Consensus pattern (30 bp):
ACATAGGTAATCTGTCCATATGTCCAAAAG
Found at i:2054183 original size:2 final size:2
Alignment explanation
Indices: 2054176--2054206 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2054166 TTCTTATTCT
2054176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2054207 CTCATATACA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2055152 original size:37 final size:36
Alignment explanation
Indices: 2055087--2055156 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
2055077 CATTCAATAT
2055087 GGTATCGATACCTTCCTTAAGGTATCGGTACCCATG
1 GGTATCGATACCTTCCTTAAGGTATCGGTACCCATG
*
2055123 GGTATCGATA-CTGTTCTTCAAGGTATCGGTACCC
1 GGTATCGATACCT-TCCTT-AAGGTATCGGTACCC
2055157 CTTAAATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 2 0.06
36 14 0.45
37 15 0.48
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (36 bp):
GGTATCGATACCTTCCTTAAGGTATCGGTACCCATG
Found at i:2056479 original size:36 final size:36
Alignment explanation
Indices: 2056410--2056781 Score: 399
Period size: 36 Copynumber: 10.3 Consensus size: 36
2056400 GATCAGCTTC
* * * *
2056410 ATCTCACTCGAGATTCTTTGT-ATTAAAACAGATTTTT
1 ATCTCACTTGAGATTGTTT-TCCTTAAAACATA-TTTT
* * *
2056447 ATCTCACTAGAGATTG-TTTCCTTAAAATAGATTTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
* * *
2056482 ATCTCACTTTATATTATTTTCCTTAAAACATATTTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
*
2056518 ATCTCACTTGAGATCGATTTT-CTTAAAACATATTTT
1 ATCTCACTTGAGATTG-TTTTCCTTAAAACATATTTT
* * *
2056554 ATCTCACCTGAGATTGTTTTTCTTAAAACATACTTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
* *
2056590 ATCTCACTTGAGATCGTTTTTCTTAAAAACATATTTT
1 ATCTCACTTGAGATTGTTTTCCTT-AAAACATATTTT
*
2056627 ATCTCACTTGAGATTGTTTTCCTTAAAATATATTTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
* *
2056663 ATCTCACTCGAGATCGTTTTCCTTAAAACATATTTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
* * * *
2056699 ATTTCACTTGAGATTATTTTTCTTAAAACAAATTTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
* * * * ** *
2056735 ATCTCCCGTGATATCGTTTTTATTAAAACATATCTT
1 ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
* *
2056771 ATTTCAATTGA
1 ATCTCACTTGA
2056782 AATAAATTTT
Statistics
Matches: 285, Mismatches: 45, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
35 21 0.07
36 213 0.75
37 51 0.18
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (36 bp):
ATCTCACTTGAGATTGTTTTCCTTAAAACATATTTT
Found at i:2056676 original size:145 final size:144
Alignment explanation
Indices: 2056444--2056781 Score: 446
Period size: 145 Copynumber: 2.3 Consensus size: 144
2056434 AAAACAGATT
* * * * * * *
2056444 TTTATCTCACTAGAGATTG-TTTCCTTAAAATAGATTTTATCTCACTTTATATTATTTTCCTTAA
1 TTTATCTCACTTGAGATCGTTTTTCTTAAAACATATTTTATCTCACTTGAGATTATTTTCCTTAA
* *
2056508 AACATATTTTATCTCACTTGAGATCGATTTT-CTTAAAACATATTTTATCTCACCTGAGATTGTT
66 AACATATTTTATCTCACTCGAGATCG-TTTTCCTTAAAACATATTTTATCTCACCTGAGATTATT
*
2056572 TTTCTTAAAACATAC
130 TTTCTTAAAACAAAC
*
2056587 TTTATCTCACTTGAGATCGTTTTTCTTAAAAACATATTTTATCTCACTTGAGATTGTTTTCCTTA
1 TTTATCTCACTTGAGATCGTTTTTCTT-AAAACATATTTTATCTCACTTGAGATTATTTTCCTTA
* * *
2056652 AAATATATTTTATCTCACTCGAGATCGTTTTCCTTAAAACATATTTTATTTCACTTGAGATTATT
65 AAACATATTTTATCTCACTCGAGATCGTTTTCCTTAAAACATATTTTATCTCACCTGAGATTATT
*
2056717 TTTCTTAAAACAAAT
130 TTTCTTAAAACAAAC
* * * * * * *
2056732 TTTATCTCCCGTGATATCGTTTTTATTAAAACATATCTTATTTCAATTGA
1 TTTATCTCACTTGAGATCGTTTTTCTTAAAACATATTTTATCTCACTTGA
2056782 AATAAATTTT
Statistics
Matches: 170, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
143 17 0.10
144 30 0.18
145 123 0.72
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (144 bp):
TTTATCTCACTTGAGATCGTTTTTCTTAAAACATATTTTATCTCACTTGAGATTATTTTCCTTAA
AACATATTTTATCTCACTCGAGATCGTTTTCCTTAAAACATATTTTATCTCACCTGAGATTATTT
TTCTTAAAACAAAC
Found at i:2057421 original size:77 final size:77
Alignment explanation
Indices: 2057283--2057560 Score: 228
Period size: 77 Copynumber: 3.6 Consensus size: 77
2057273 GAAGGAAGAG
* * * ** * * * *
2057283 CAACATTTTCGATCGAAGAATTCATAATGAGAATAATTTATTCGACCATA-GCTCATCCATCACA
1 CAACATTTTCAATCAAAGAATTCATAATGAGAAGAATTCGTTCAATCA-AGGCTCGTTCATCACA
*
2057347 AAAGAAGATGGGT
65 AAAGAAGATGGAT
* * * **
2057360 CAACATTTTCAAACAAAGAATTTATAATGAGATGAATTCGTTTGA-CAAAGGCTCGTTCATCA-A
1 CAACATTTTCAATCAAAGAATTCATAATGAGAAGAATTCGTTCAATC-AAGGCTCGTTCATCACA
* *
2057423 AGAATG-AGGTGCAT
65 A-AA-GAAGATGGAT
* * *
2057437 -AAGAATTTTCAATCGAAGAATTCATAATGAGAAGAATTCGTTCAATCAAGGCTCGTTCTTCAC-
1 CAA-CATTTTCAATCAAAGAATTCATAATGAGAAGAATTCGTTCAATCAAGGCTCGTTCATCACA
*
2057500 -AAGAGGATGTGAAT
65 AAAGAAGATG-G-AT
* * *
2057514 CAACATTTTTAATCAAAGAATTCATAATGAAAATAATTCGTTCAATC
1 CAACATTTTCAATCAAAGAATTCATAATGAGAAGAATTCGTTCAATC
2057561 GTGGCTCATA
Statistics
Matches: 160, Mismatches: 30, Indels: 22
0.75 0.14 0.10
Matches are distributed among these distances:
74 1 0.01
75 5 0.03
76 6 0.04
77 144 0.90
78 4 0.03
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (77 bp):
CAACATTTTCAATCAAAGAATTCATAATGAGAAGAATTCGTTCAATCAAGGCTCGTTCATCACAA
AAGAAGATGGAT
Found at i:2058312 original size:2 final size:2
Alignment explanation
Indices: 2058305--2058335 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2058295 CAATAAATAA
2058305 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 A
2058336 ATTTCATTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2062166 original size:47 final size:47
Alignment explanation
Indices: 2062097--2062197 Score: 175
Period size: 47 Copynumber: 2.1 Consensus size: 47
2062087 TAAGTATATG
* *
2062097 AAAATCTTAAATGATATAAATGTAATATTGTTAATAGTTTAATTTAA
1 AAAATCTTAAACGATATAAATGTAATATTGTTAATAATTTAATTTAA
*
2062144 AAAATCTTAAACGATATAAATGTAATATTGTTTATAATTTAATTTAA
1 AAAATCTTAAACGATATAAATGTAATATTGTTAATAATTTAATTTAA
2062191 AAAATCT
1 AAAATCT
2062198 AAAATTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.42
Consensus pattern (47 bp):
AAAATCTTAAACGATATAAATGTAATATTGTTAATAATTTAATTTAA
Found at i:2071337 original size:17 final size:17
Alignment explanation
Indices: 2071315--2071381 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
2071305 TGTTAGAGGG
*
2071315 AAAAATGAATAAATAAA
1 AAAAATGAAAAAATAAA
*
2071332 AAAAAT--AAGAATAAA
1 AAAAATGAAAAAATAAA
* *
2071347 AATAAGTAAAAAAATAAA
1 AA-AAATGAAAAAATAAA
2071365 ATAAAA-GAAAAAATAAA
1 A-AAAATGAAAAAATAAA
2071382 TAAATAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 9 0.22
16 3 0.08
17 16 0.40
18 11 0.28
19 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAATGAAAAAATAAA
Found at i:2071349 original size:12 final size:12
Alignment explanation
Indices: 2071332--2071370 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2071322 AATAAATAAA
2071332 AAAAATAAGAAT
1 AAAAATAAGAAT
2071344 AAAAATAAGTAA-
1 AAAAATAAG-AAT
2071356 AAAAATAA-AAT
1 AAAAATAAGAAT
2071367 AAAA
1 AAAA
2071371 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 4 0.16
12 17 0.68
13 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAATAAGAAT
Found at i:2071350 original size:25 final size:23
Alignment explanation
Indices: 2071322--2071389 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 23
2071312 GGGAAAAATG
2071322 AATAAATAAAAAAAATAAGAATAAA
1 AATAAAT-AAAAAAATAA-AATAAA
*
2071347 AATAAGTAAAAAAATAAAATAAAA
1 AATAAATAAAAAAATAAAAT-AAA
* *
2071371 GAAAAAATAAATAAATAAA
1 -AATAAATAAAAAAATAAA
2071390 TGAAATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.08
24 13 0.35
25 21 0.57
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.16
Consensus pattern (23 bp):
AATAAATAAAAAAATAAAATAAA
Found at i:2071390 original size:29 final size:29
Alignment explanation
Indices: 2071315--2071396 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
2071305 TGTTAGAGGG
* * *
2071315 AAAAATGAATAAATAAAAAAAATAAGAAT
1 AAAAATAAATAAATAAATAAAATAAGAAA
* *
2071344 AAAAATAAGTAAAAAAATAAAATAA-AAGA
1 AAAAATAAATAAATAAATAAAATAAGAA-A
*
2071373 AAAAATAAATAAATAAATGAAATA
1 AAAAATAAATAAATAAATAAAATA
2071397 TTAAATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 2 0.05
29 42 0.95
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (29 bp):
AAAAATAAATAAATAAATAAAATAAGAAA
Found at i:2071403 original size:20 final size:20
Alignment explanation
Indices: 2071315--2071394 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
2071305 TGTTAGAGGG
*
2071315 AAAAATGAATAAATAAAA-A
1 AAAAATAAATAAATAAAAGA
*
2071334 AAATAA-GAATAAA-AATAAG-
1 AAA-AATAAATAAATAA-AAGA
*
2071353 TAAAA-AAATAAAATAAAAGA
1 AAAAATAAAT-AAATAAAAGA
*
2071373 AAAAATAAATAAATAAATGA
1 AAAAATAAATAAATAAAAGA
2071393 AA
1 AA
2071395 TATTAAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
18 7 0.14
19 20 0.40
20 19 0.38
21 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (20 bp):
AAAAATAAATAAATAAAAGA
Found at i:2071408 original size:2 final size:2
Alignment explanation
Indices: 2071401--2071433 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2071391 GAAATATTAA
2071401 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 A
2071434 AATGAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2071566 original size:27 final size:29
Alignment explanation
Indices: 2071498--2071555 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2071488 ATAATATAAT
* * *
2071498 ATAAACAAATAAAAAAACCAAAAATAAAA
1 ATAAATAAATATATAAACCAAAAATAAAA
*
2071527 ATAAATAAATATATAAACCAAATATAAAA
1 ATAAATAAATATATAAACCAAAAATAAAA
2071556 TTATACATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (29 bp):
ATAAATAAATATATAAACCAAAAATAAAA
Found at i:2071706 original size:2 final size:2
Alignment explanation
Indices: 2071699--2071731 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2071689 TATAAGTAAA
2071699 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 A
2071732 AATAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2072365 original size:37 final size:37
Alignment explanation
Indices: 2072284--2072385 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
2072274 GTGCTTGTGG
* * * * * *
2072284 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
2072321 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
* *
2072358 ATTCTATTTTTATGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
2072386 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:2073426 original size:106 final size:106
Alignment explanation
Indices: 2073119--2074584 Score: 2203
Period size: 106 Copynumber: 13.9 Consensus size: 106
2073109 GCATTGTTCC
* * ** * *
2073119 GAGTCCAATATCCTCCG-TCGTG-AGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
2073182 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2073224 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
2073283 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
2073325 G-GTCTAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
2073389 CCAGCGGTCCCTTCGTCGTGATGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2073430 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2073495 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
2073536 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
2073601 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
2073642 GAGTCCAATATATTTCACTCTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2073707 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2073748 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2073813 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2073854 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
2073919 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2073960 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
2074025 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTACATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2074066 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2074131 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2074172 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** *
2074237 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2074278 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTACTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
2074343 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
2074384 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
2074449 CCAGCAGTCTCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2074490 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
2074555 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT
2074585 CTACTCTCGA
Statistics
Matches: 1236, Mismatches: 115, Indels: 19
0.90 0.08 0.01
Matches are distributed among these distances:
100 79 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 24 0.02
106 1121 0.91
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2075354 original size:22 final size:22
Alignment explanation
Indices: 2075329--2075405 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
2075319 TTATGTTTGG
*
2075329 TCAAAAGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2075351 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2075373 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2075395 TCAACGGTTTG
1 TCAAAGGTTTG
2075406 ATGGGGTAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2076038 original size:13 final size:13
Alignment explanation
Indices: 2076022--2076067 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2076012 TTCTTTTTGA
2076022 TTTTTGTTCTTTC
1 TTTTTGTTCTTTC
* *
2076035 TTTTTTTTCTTTT
1 TTTTTGTTCTTTC
2076048 TTTTTGCTTCTTTTC
1 TTTTTG-TTC-TTTC
2076063 TTTTT
1 TTTTT
2076068 TGTTTTTGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 3 0.11
15 8 0.30
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (13 bp):
TTTTTGTTCTTTC
Found at i:2076048 original size:23 final size:25
Alignment explanation
Indices: 2076010--2076075 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 25
2076000 TTTTGTCCCT
2076010 TTTTCTTTT-TGATTTTTGTT-CTTTC
1 TTTTCTTTTCTG-TTTTTGTTGC-TTC
*
2076035 TTTT-TTTTCT-TTTTTTTTGCTTC
1 TTTTCTTTTCTGTTTTTGTTGCTTC
*
2076058 TTTTCTTTTTTGTTTTTG
1 TTTTCTTTTCTGTTTTTG
2076076 CCCTTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 14 0.41
24 10 0.29
25 10 0.29
ACGTcount: A:0.02, C:0.11, G:0.08, T:0.80
Consensus pattern (25 bp):
TTTTCTTTTCTGTTTTTGTTGCTTC
Found at i:2076052 original size:27 final size:29
Alignment explanation
Indices: 2076009--2076068 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
2075999 TTTTTGTCCC
2076009 TTTTTCTTTTTGATTTTTG-TTC-TTTCTTT
1 TTTTTC-TTTT-ATTTTTGCTTCTTTTCTTT
2076038 TTTTTCTTTT-TTTTTGCTTCTTTTCTTT
1 TTTTTCTTTTATTTTTGCTTCTTTTCTTT
2076066 TTT
1 TTT
2076069 GTTTTTGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.21
27 3 0.10
28 14 0.48
29 6 0.21
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.82
Consensus pattern (29 bp):
TTTTTCTTTTATTTTTGCTTCTTTTCTTT
Found at i:2076074 original size:13 final size:14
Alignment explanation
Indices: 2076022--2076071 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
2076012 TTCTTTTTGA
2076022 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
2076036 TTTTT-TTCTTT-T
1 TTTTTGTTCTTTCT
2076048 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
2076064 TTTTTGTT
1 TTTTTGTT
2076072 TTTGCCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 8 0.25
15 5 0.16
16 7 0.22
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:2080769 original size:2 final size:2
Alignment explanation
Indices: 2080764--2080805 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2080754 TAAAAAAAAG
* *
2080764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2080806 GTATTAAAAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2080853 original size:21 final size:24
Alignment explanation
Indices: 2080829--2080875 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
2080819 ACCAAATGAA
2080829 TATAAATAA-AA-AATATATA-TG
1 TATAAATAATAATAATATATAGTG
*
2080850 TATATATAATAATAATATATAGTG
1 TATAAATAATAATAATATATAGTG
2080874 TA
1 TA
2080876 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 8 0.36
24 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
TATAAATAATAATAATATATAGTG
Found at i:2080854 original size:23 final size:24
Alignment explanation
Indices: 2080828--2080875 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
2080818 AACCAAATGA
2080828 ATATA-AATAAAAAATATATA-TGT
1 ATATATAAT-AAAAATATATAGTGT
*
2080851 ATATATAATAATAATATATAGTGT
1 ATATATAATAAAAATATATAGTGT
2080875 A
1 A
2080876 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
ATATATAATAAAAATATATAGTGT
Found at i:2083115 original size:2 final size:2
Alignment explanation
Indices: 2083108--2083153 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2083098 TATTTTTAAA
2083108 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
2083150 AT AT
1 AT AT
2083154 CACAAGGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2083781 original size:2 final size:2
Alignment explanation
Indices: 2083774--2083817 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2083764 AATAATCCTT
2083774 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
2083816 TA
1 TA
2083818 ATCACACAAG
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2084969 original size:12 final size:13
Alignment explanation
Indices: 2084946--2084978 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2084936 ATAGAAAATT
*
2084946 ATATTTTCTATGA
1 ATATTTTGTATGA
2084959 AT-TTTTGTATGA
1 ATATTTTGTATGA
2084971 ATATTTTG
1 ATATTTTG
2084979 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (13 bp):
ATATTTTGTATGA
Found at i:2085144 original size:8 final size:9
Alignment explanation
Indices: 2085131--2085184 Score: 55
Period size: 8 Copynumber: 6.4 Consensus size: 9
2085121 ACAACATTCT
2085131 TATTA-ATA
1 TATTATATA
2085139 TATTA-A-A
1 TATTATATA
*
2085146 TAATATATA
1 TATTATATA
2085155 TA-TATATA
1 TATTATATA
2085163 TA-TATATA
1 TATTATATA
2085171 TATATATATA
1 TAT-TATATA
2085181 TATT
1 TATT
2085185 TAGTTATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
7 5 0.12
8 23 0.56
9 4 0.10
10 9 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TATTATATA
Found at i:2085153 original size:2 final size:2
Alignment explanation
Indices: 2085136--2085183 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2085126 ATTCTTATTA
*
2085136 AT AT AT -T AA AT A- 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
2085176 AT AT AT AT
1 AT AT AT AT
2085184 TTAGTTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2086424 original size:2 final size:2
Alignment explanation
Indices: 2086417--2086456 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2086407 GAAAAGAATA
2086417 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
2086457 GGTTAGAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2095666 original size:24 final size:23
Alignment explanation
Indices: 2095631--2095683 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
2095621 AGGAAAAAAT
2095631 AAAATAAATAAGTAAG--ATAAGA-
1 AAAA-AAAT-AGTAAGAAATAAGAC
2095653 AAAAAAATAGTAAGAAATAAGAC
1 AAAAAAATAGTAAGAAATAAGAC
2095676 AAAAAAAT
1 AAAAAAAT
2095684 GGGCTCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.21
21 4 0.14
22 10 0.36
23 8 0.29
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAAAAATAGTAAGAAATAAGAC
Found at i:2095672 original size:22 final size:21
Alignment explanation
Indices: 2095631--2095683 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
2095621 AGGAAAAAAT
*
2095631 AAAATAAATAAGTAAGATAAG
1 AAAAAAAATAAGTAAGATAAG
2095652 AAAAAAAAT-AGTAAGAAATAAG
1 AAAAAAAATAAGTAAG--ATAAG
2095674 ACAAAAAAAT
1 A-AAAAAAAT
2095684 GGGCTCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.21
21 8 0.29
22 6 0.21
23 8 0.29
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (21 bp):
AAAAAAAATAAGTAAGATAAG
Found at i:2096098 original size:18 final size:17
Alignment explanation
Indices: 2096075--2096117 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2096065 ATATATACAT
2096075 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2096093 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2096110 ATAA-AATA
1 ATAATAATA
2096118 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2096118 original size:54 final size:57
Alignment explanation
Indices: 2096003--2096118 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 57
2095993 TATTAAAGAA
*
2096003 ATATATATATATATAATAATAATAAAATATAGTAAAAAAAATAAATGAAAATAATTTAAT
1 ATATATATACATATAATAATAATAAAATATAGTAAAAAAAATAAATG-AAATAA--TAAT
* *
2096063 ATATATATACATATAATAATAATAACATGA-A-TAATAAAAATAAATG-AATAA-AAT
1 ATATATATACATATAATAATAATAAAAT-ATAGTAAAAAAAATAAATGAAATAATAAT
2096117 AT
1 AT
2096119 CCATATAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
54 5 0.10
57 5 0.10
59 14 0.27
60 27 0.52
61 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (57 bp):
ATATATATACATATAATAATAATAAAATATAGTAAAAAAAATAAATGAAATAATAAT
Found at i:2096125 original size:54 final size:56
Alignment explanation
Indices: 2096002--2096133 Score: 132
Period size: 60 Copynumber: 2.4 Consensus size: 56
2095992 ATATTAAAGA
*
2096002 AATATATATAT-ATATAATAATAATAAAATATAGTAAAAAAAATAAATGAAAATAATTT
1 AATATACATATAATATAATAATAATAAAATATAGTAAAAAAAATAAATG-AAATAA--T
* * *
2096060 AATATATATATACATATAATAATAATAACATGA-A-TAATAAAAATAAATG-AATAA-
1 AATATACATATA-ATATAATAATAATAAAAT-ATAGTAAAAAAAATAAATGAAATAAT
*
2096114 AATATCCATATAATA-AATAA
1 AATATACATATAATATAATAA
2096134 AGGGACTAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
52 5 0.07
53 3 0.04
54 10 0.15
57 5 0.07
58 11 0.16
59 14 0.21
60 18 0.27
61 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (56 bp):
AATATACATATAATATAATAATAATAAAATATAGTAAAAAAAATAAATGAAATAAT
Found at i:2097426 original size:105 final size:105
Alignment explanation
Indices: 2097120--2097855 Score: 1115
Period size: 105 Copynumber: 7.0 Consensus size: 105
2097110 GCATTGTTCC
* * ** *
2097120 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
2097184 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2097226 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
2097286 CAGCGGTCCCTTCGTCATGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2097326 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
2097391 CAGTGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2097431 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
2097496 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2097536 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
2097601 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2097641 AAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
2097706 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2097746 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
2097811 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2097852 GAGT
1 GAGT
2097856 GTCACGATAT
Statistics
Matches: 585, Mismatches: 38, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
100 83 0.14
101 1 0.00
102 7 0.01
104 5 0.01
105 403 0.69
106 86 0.15
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2098102 original size:36 final size:36
Alignment explanation
Indices: 2098062--2098131 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2098052 AGAGAAACTG
* **
2098062 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTA
1 TCTCAAGCGAGACAAAATTCATTTCAAGGGAAATTA
*
2098098 TCTCAAGCGAGATAAAATTCATTTCAAGGGAAAT
1 TCTCAAGCGAGACAAAATTCATTTCAAGGGAAAT
2098132 GTTTTCAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTCATTTCAAGGGAAATTA
Found at i:2098363 original size:104 final size:104
Alignment explanation
Indices: 2098030--2098347 Score: 464
Period size: 104 Copynumber: 3.1 Consensus size: 104
2098020 TTCGTTAAAT
* ** *
2098030 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TT-TGTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
2098092 AAATTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
2098131 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
2098196 AAACTATCTCAAGAGAGAAAAAAAATCATTTTAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
* * *
2098236 TGTTTTGAATGTTTATGTTTCAAGAGAAACTATCTCAA-GGAGACAAAATTTTCTGTTTTGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
** *
2098300 AAACTATCTCGGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
2098339 TGTTTTCAA
1 TGTTTTCAA
2098348 GAGAAACTGT
Statistics
Matches: 195, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
101 46 0.24
103 29 0.15
104 65 0.33
105 55 0.28
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:2098524 original size:36 final size:36
Alignment explanation
Indices: 2098482--2098586 Score: 99
Period size: 36 Copynumber: 2.9 Consensus size: 36
2098472 CTCAAGCGAG
2098482 ACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
1 ACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
* * * ** *
2098518 ATAAATCTT-TTTTCGAGAAAAACAGTCTCAAGTGAG
1 ACAAATCTTGTTTT-AAGAAAAACAATCTTGAGTGAA
*
2098554 ACAAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGT
1 ACAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
2098587 CTGATAATCA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
35 4 0.08
36 42 0.79
37 7 0.13
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.30
Consensus pattern (36 bp):
ACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
Found at i:2098566 original size:72 final size:75
Alignment explanation
Indices: 2098418--2098586 Score: 195
Period size: 72 Copynumber: 2.3 Consensus size: 75
2098408 TAAAATCTTC
* ** * **
2098418 TTAAAAAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAATGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
2098483 CAAATCTTGTT
65 CAAATCATGTT
* *
2098494 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CTTTTTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
2098556 AAAGT-ATGTT
66 AAA-TCATGTT
2098566 TTAAGAAAAACAAAT-TTGAGT
1 TTAAGAAAAAC-AATCTTGAGT
2098587 CTGATAATCA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
72 41 0.50
73 14 0.17
75 4 0.05
76 23 0.28
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
AAATCATGTT
Found at i:2100013 original size:183 final size:183
Alignment explanation
Indices: 2099705--2100241 Score: 977
Period size: 183 Copynumber: 2.9 Consensus size: 183
2099695 ATCAGGTTTA
*
2099705 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGATCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGTCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
2099770 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
2099834 TTTCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
**
2099888 ACTGAAGGGTTTGTCTCATCACAAAGTCTTTGGTCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGTCTGACAAAAGCAGTGGAGCAAACACCGAATT
2099953 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
2100018 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
2100071 ACTGAAGGGTTCATCTCATCACAAAGTCTTCGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGTCTGACAAAAGCAGTGGAGCAAACACCGAATT
2100136 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
2100201 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
2100242 CGGATTTAAT
Statistics
Matches: 342, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 341 1.00
184 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGTCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:2104259 original size:20 final size:22
Alignment explanation
Indices: 2104234--2104275 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2104224 AAAATAAATA
2104234 AGTAAG-ATAAGA-AAAAAAAC
1 AGTAAGAATAAGACAAAAAAAC
2104254 AGTAAGAAATAAGACAAAAAAA
1 AGTAAG-AATAAGACAAAAAAA
2104276 TGGGCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.71, C:0.05, G:0.14, T:0.10
Consensus pattern (22 bp):
AGTAAGAATAAGACAAAAAAAC
Found at i:2104698 original size:17 final size:18
Alignment explanation
Indices: 2104665--2104700 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2104655 ATATATATAT
*
2104665 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
2104683 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
2104700 A
1 A
2104701 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:2104705 original size:53 final size:53
Alignment explanation
Indices: 2104590--2104705 Score: 139
Period size: 58 Copynumber: 2.1 Consensus size: 53
2104580 AATATTAAAG
2104590 AAATATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATGAAAATA
1 AAATATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATG-AAATA
*
2104644 ATTTAATATATATATATATATATAATAATAACATGA-A-TAATAAAAATAAATG-AATA
1 A---AATATATATATATATA-ATAATAATAAAAT-ATAGTAA-AAAAATAAATGAAATA
2104700 AAATAT
1 AAATAT
2104706 CCATATAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
53 5 0.09
54 1 0.02
56 5 0.09
57 19 0.35
58 24 0.44
59 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (53 bp):
AAATATATATATATATAATAATAATAAAATATAGTAAAAAAATAAATGAAATA
Found at i:2105127 original size:37 final size:37
Alignment explanation
Indices: 2105061--2105167 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 37
2105051 GTGCTTGTGG
*
2105061 ATCCTATCTTTAGGAA-TTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTA-GAAGTTTAAATCTTAGTAGAACTCT
* * * * *
2105098 ATCCTATTTTTAGAAGTTTGAATCATAGTAAAATTTT
1 ATCCTATTTTTAGAAGTTTAAATCTTAGTAGAACTCT
* * *
2105135 ATCTTATTTTTAGGAGTTTAAATCTTATTAGAA
1 ATCCTATTTTTAGAAGTTTAAATCTTAGTAGAA
2105168 AGAAAATGTG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 3 0.05
37 54 0.95
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (37 bp):
ATCCTATTTTTAGAAGTTTAAATCTTAGTAGAACTCT
Found at i:2111941 original size:11 final size:11
Alignment explanation
Indices: 2111927--2111978 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2111917 TTATTTCCTT
*
2111927 TTTCTTTTCTC
1 TTTCTTCTCTC
2111938 TTTCTTCTCTTC
1 TTTCTTCTC-TC
2111950 TTTGCTTCTCTC
1 TTT-CTTCTCTC
* *
2111962 TTTGTTTTCTC
1 TTTCTTCTCTC
2111973 TCTTCT
1 T-TTCT
2111979 CCCCTATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 15 0.44
12 13 0.38
13 6 0.18
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (11 bp):
TTTCTTCTCTC
Found at i:2111965 original size:12 final size:12
Alignment explanation
Indices: 2111934--2111976 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2111924 CTTTTTCTTT
2111934 TCTCTTT-CTTC
1 TCTCTTTGCTTC
2111945 TCTTCTTTGCTTC
1 TC-TCTTTGCTTC
*
2111958 TCTCTTTGTTTTC
1 TCTCTTTG-CTTC
2111971 TCTCTT
1 TCTCTT
2111977 CTCCCCTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 2 0.07
12 11 0.39
13 15 0.54
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65
Consensus pattern (12 bp):
TCTCTTTGCTTC
Found at i:2113694 original size:16 final size:17
Alignment explanation
Indices: 2113670--2113710 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2113660 GTTGTTTTTG
*
2113670 AATTAAAATTA-TTGTA
1 AATTTAAATTATTTGTA
*
2113686 AATTTAAA-TATTTTTA
1 AATTTAAATTATTTGTA
2113702 AATTTAAAT
1 AATTTAAAT
2113711 CATCTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTAAATTATTTGTA
Found at i:2117445 original size:49 final size:49
Alignment explanation
Indices: 2117373--2117563 Score: 325
Period size: 49 Copynumber: 3.9 Consensus size: 49
2117363 TCCAACACTA
2117373 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATG
1 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATG
2117422 ATGCTTGTCCTATATGTAGACACCGATATAGAG--ATGATCCTACAATG
1 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATG
2117469 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATG
1 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATG
* * *
2117518 ATGTTTGTCCTATATGTAGAC-GCGTATATAGAGAGATGATCCTACA
1 ATGCTTGTCCTATATGTAGACACCG-ATATAGAGATATGATCCTACA
2117564 CTGCCTGCAC
Statistics
Matches: 136, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
47 47 0.35
48 2 0.01
49 87 0.64
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (49 bp):
ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATG
Found at i:2117537 original size:96 final size:97
Alignment explanation
Indices: 2117373--2117563 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 97
2117363 TCCAACACTA
2117373 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATGATGCTTGTCCTATATG
1 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATGATGCTTGTCCTATATG
2117438 TAGACACCG-ATAT-AGAGATGATCCTACAATG
66 TAGAC-CCGTATATAAGAGATGATCCTACAATG
*
2117469 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATGATGTTTGTCCTATATG
1 ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATGATGCTTGTCCTATATG
*
2117534 TAGACGCGTATATAGAGAGATGATCCTACA
66 TAGACCCGTATATA-AGAGATGATCCTACA
2117564 CTGCCTGCAC
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
95 2 0.02
96 73 0.81
98 15 0.17
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (97 bp):
ATGCTTGTCCTATATGTAGACACCGATATAGAGATATGATCCTACAATGATGCTTGTCCTATATG
TAGACCCGTATATAAGAGATGATCCTACAATG
Found at i:2121376 original size:20 final size:20
Alignment explanation
Indices: 2121351--2121408 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2121341 CCGTTAGACA
*
2121351 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
* *
2121371 GGGGGGAATCTATACCCCTT
1 GGGGGGAATCTGTACCCCCT
2121391 GGGGGGAATCTGTACCCC
1 GGGGGGAATCTGTACCCC
2121409 ATAGGCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.28, G:0.36, T:0.19
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:2123733 original size:23 final size:23
Alignment explanation
Indices: 2123707--2123762 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
2123697 ACATATTTAT
* * *
2123707 TAAATAATATTATTTTTATTCAA
1 TAAATAATATAAATTTAATTCAA
*
2123730 TAAA-AATATAAATTTAATTGAA
1 TAAATAATATAAATTTAATTCAA
*
2123752 AAAATAATATA
1 TAAATAATATA
2123763 TAAAAGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATAATATAAATTTAATTCAA
Found at i:2124739 original size:19 final size:20
Alignment explanation
Indices: 2124697--2124739 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2124687 AAAAAACAAC
2124697 TTATTATAATAAAATATCTTA
1 TTATTATAATAAAATATC-TA
2124718 TTATTATTAA-AAAATATC-A
1 TTATTA-TAATAAAATATCTA
2124737 TTA
1 TTA
2124740 ATTTAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
21 14 0.67
22 3 0.14
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTATAATAAAATATCTA
Found at i:2125998 original size:18 final size:18
Alignment explanation
Indices: 2125977--2126013 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2125967 GTTAAAAACA
2125977 ATATTTTAT-TATTTCTTT
1 ATATTTTATATATTT-TTT
2125995 ATATTTTATATATTTTTT
1 ATATTTTATATATTTTTT
2126013 A
1 A
2126014 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
ATATTTTATATATTTTTT
Found at i:2126007 original size:27 final size:26
Alignment explanation
Indices: 2125976--2126043 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
2125966 GGTTAAAAAC
2125976 AATATTTTATTATTTCTTTAT-ATTTTA
1 AATATTTTATTATTT-TTTATCA-TTTA
* *
2126003 TATATTTT-TTAAAATTTTTATCATTTA
1 AATATTTTATT--ATTTTTTATCATTTA
2126030 AATATTTTATTATT
1 AATATTTTATTATT
2126044 AGATAACATG
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
26 4 0.12
27 23 0.70
28 6 0.18
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (26 bp):
AATATTTTATTATTTTTTATCATTTA
Found at i:2126019 original size:19 final size:18
Alignment explanation
Indices: 2125979--2126020 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2125969 TAAAAACAAT
*
2125979 ATTTTATTATTTCTTTAT
1 ATTTTATTATTTCTTTAA
2125997 ATTTTATATATTT-TTTAAA
1 ATTTTAT-TATTTCTTT-AA
2126016 ATTTT
1 ATTTT
2126021 TATCATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATTATTTCTTTAA
Found at i:2127435 original size:18 final size:19
Alignment explanation
Indices: 2127399--2127436 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2127389 CTCTTATTAA
*
2127399 AGTATATTTTATTATATTT
1 AGTATATTTTAGTATATTT
*
2127418 AGTATTTTTTAGTA-ATTT
1 AGTATATTTTAGTATATTT
2127436 A
1 A
2127437 TTTAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AGTATATTTTAGTATATTT
Found at i:2128437 original size:21 final size:21
Alignment explanation
Indices: 2128411--2128463 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 21
2128401 TATACAGTGA
2128411 ATAAGATTAGGGTGTTAATCG
1 ATAAGATTAGGGTGTTAATCG
2128432 ATAAGAAAAAATTAGGGTGTTAATCG
1 ATAAG-----ATTAGGGTGTTAATCG
2128458 ATAAGA
1 ATAAGA
2128464 AGGCTGGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
21 6 0.22
26 21 0.78
ACGTcount: A:0.43, C:0.04, G:0.25, T:0.28
Consensus pattern (21 bp):
ATAAGATTAGGGTGTTAATCG
Found at i:2129516 original size:18 final size:18
Alignment explanation
Indices: 2129477--2129523 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2129467 ACCTACTCAG
* *
2129477 GACGACGACGACATCGAT
1 GACGACGACGACATCAAA
2129495 GACGACGACGACGA-CAAA
1 GACGACGACGAC-ATCAAA
*
2129513 GACGATGACGA
1 GACGACGACGA
2129524 TGATGATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.38, C:0.26, G:0.30, T:0.06
Consensus pattern (18 bp):
GACGACGACGACATCAAA
Found at i:2129804 original size:35 final size:33
Alignment explanation
Indices: 2129765--2129849 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
2129755 GTATTTCAGT
2129765 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
2129800 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
2129835 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
2129850 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:2133205 original size:16 final size:16
Alignment explanation
Indices: 2133184--2133214 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2133174 TTTTTTTCCA
2133184 AATAATCATAATAAAT
1 AATAATCATAATAAAT
*
2133200 AATAATTATAATAAA
1 AATAATCATAATAAA
2133215 AAAATTTATC
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:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAATCATAATAAAT
Found at i:2133695 original size:30 final size:29
Alignment explanation
Indices: 2133635--2133695 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2133625 CTGTAAAGGG
* *
2133635 TGTTAGATCGGGAAATATAGTCTGACCGA
1 TGTTAGATCGGGAAATATACTCTCACCGA
* *
2133664 TGTTAGATCGGTAAATATACTGGTCACCGA
1 TGTTAGATCGGGAAATATACT-CTCACCGA
2133694 TG
1 TG
2133696 ATTTTTTGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (29 bp):
TGTTAGATCGGGAAATATACTCTCACCGA
Found at i:2135279 original size:33 final size:33
Alignment explanation
Indices: 2135237--2135307 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2135227 AGGGAGCGTT
2135237 AAGAAGCAAGCCAGCACGACGGAGTTTGAGGAC
1 AAGAAGCAAGCCAGCACGACGGAGTTTGAGGAC
**
2135270 AAGAAGCAAGCCAGCGTGACGGAGTTTGAGGAC
1 AAGAAGCAAGCCAGCACGACGGAGTTTGAGGAC
2135303 AAGAA
1 AAGAA
2135308 ACCGGATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.34, T:0.10
Consensus pattern (33 bp):
AAGAAGCAAGCCAGCACGACGGAGTTTGAGGAC
Found at i:2136482 original size:31 final size:31
Alignment explanation
Indices: 2136444--2136506 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2136434 ACCCGCATTC
2136444 TTCGTTTTCGATAAAATACTCGTTTCTGAGA
1 TTCGTTTTCGATAAAATACTCGTTTCTGAGA
*
2136475 TTCGTTTTCGATAAAGTACTCGTTTCTGAGA
1 TTCGTTTTCGATAAAATACTCGTTTCTGAGA
2136506 T
1 T
2136507 ATTCGAACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (31 bp):
TTCGTTTTCGATAAAATACTCGTTTCTGAGA
Found at i:2144476 original size:14 final size:15
Alignment explanation
Indices: 2144457--2144490 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2144447 TTATAATTCA
2144457 TTTAAAAAT-ATTTT
1 TTTAAAAATGATTTT
2144471 TTTAAAAATGATTTT
1 TTTAAAAATGATTTT
2144486 TTTAA
1 TTTAA
2144491 TAATCTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTAAAAATGATTTT
Found at i:2145928 original size:4 final size:4
Alignment explanation
Indices: 2145903--2145950 Score: 64
Period size: 4 Copynumber: 12.0 Consensus size: 4
2145893 TTATTCTAAA
2145903 ATTT GATTT -TTT -TTT ATATT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT -ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2145951 TATTGATTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.15
4 27 0.66
5 8 0.20
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:2147655 original size:32 final size:32
Alignment explanation
Indices: 2147584--2147693 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 32
2147574 GTAACTGCTA
* * ** *
2147584 TGCATTATCTGAATGTGACCCTGATGCTATTA
1 TGCATTATCTGAATGTGACACTAACACTATTG
*
2147616 TGCATTATCTGAATGTGACACTAACACTACTG
1 TGCATTATCTGAATGTGACACTAACACTATTG
* * * * *
2147648 TGTATTATCTAAATATAACACTAACACTGTTG
1 TGCATTATCTGAATGTGACACTAACACTATTG
2147680 TGCATTATCTGAAT
1 TGCATTATCTGAAT
2147694 ACAACACTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (32 bp):
TGCATTATCTGAATGTGACACTAACACTATTG
Found at i:2147700 original size:32 final size:32
Alignment explanation
Indices: 2147616--2147703 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 32
2147606 GATGCTATTA
* *
2147616 TGCATTATCTGAATGTGACACTAACACTACTG
1 TGCATTATCTGAATATAACACTAACACTACTG
* * **
2147648 TGTATTATCTAAATATAACACTAACACTGTTG
1 TGCATTATCTGAATATAACACTAACACTACTG
*
2147680 TGCATTATCTGAATACAACACTAA
1 TGCATTATCTGAATATAACACTAA
2147704 TACATCTATC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (32 bp):
TGCATTATCTGAATATAACACTAACACTACTG
Found at i:2151866 original size:23 final size:22
Alignment explanation
Indices: 2151807--2151866 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
2151797 TAACGAGCTT
* *
2151807 ATAAATGAGTTAATAAACAACCG
1 ATAAACGAGTT-ATAAACAACCA
* *
2151830 ATAAACAAGCTTATAAATAAGCCA
1 ATAAACGAG-TTATAAACAA-CCA
2151854 ATAAACGAGTTAT
1 ATAAACGAGTTAT
2151867 TCGTGTAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAAACGAGTTATAAACAACCA
Found at i:2154168 original size:26 final size:26
Alignment explanation
Indices: 2154139--2154193 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
2154129 CCTCAATCTC
*
2154139 AAAAGAATCGAGTAGGGAATGATTAA
1 AAAAGAATCGAGCAGGGAATGATTAA
*
2154165 AAAAGAATCGAGCAGGGAATGATTCA
1 AAAAGAATCGAGCAGGGAATGATTAA
2154191 AAA
1 AAA
2154194 CTAAGTCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.25, T:0.16
Consensus pattern (26 bp):
AAAAGAATCGAGCAGGGAATGATTAA
Found at i:2167538 original size:66 final size:66
Alignment explanation
Indices: 2167432--2167566 Score: 252
Period size: 66 Copynumber: 2.0 Consensus size: 66
2167422 TTTTGCTATC
* *
2167432 TGAATTTTCTGACTAAACAGAATGTGTGTCGACTTAGCCAATGGTTTGGTCATTCCATCCGCAAC
1 TGAATTTTCTGACTAAACAGAATGTGTGCCGACTTAGCCAATGGTTTAGTCATTCCATCCGCAAC
2167497 T
66 T
2167498 TGAATTTTCTGACTAAACAGAATGTGTGCCGACTTAGCCAATGGTTTAGTCATTCCATCCGCAAC
1 TGAATTTTCTGACTAAACAGAATGTGTGCCGACTTAGCCAATGGTTTAGTCATTCCATCCGCAAC
2167563 T
66 T
2167564 TGA
1 TGA
2167567 TGCTCTGCTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (66 bp):
TGAATTTTCTGACTAAACAGAATGTGTGCCGACTTAGCCAATGGTTTAGTCATTCCATCCGCAAC
T
Found at i:2171753 original size:30 final size:29
Alignment explanation
Indices: 2171707--2171776 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
2171697 ATTTTAAGTT
*
2171707 AGGAGGGGCAAACTTCAACTTATAAAATTTC
1 AGGA-GGGCGAACTTCAAC-TATAAAATTTC
* *
2171738 AGGAGGGCGAACTTCAACTATTAAATTTT
1 AGGAGGGCGAACTTCAACTATAAAATTTC
2171767 AGG-GGGCGAA
1 AGGAGGGCGAA
2171777 AACAGATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.19
29 12 0.33
30 13 0.36
31 4 0.11
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (29 bp):
AGGAGGGCGAACTTCAACTATAAAATTTC
Found at i:2172838 original size:20 final size:21
Alignment explanation
Indices: 2172813--2172866 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
2172803 CTGAATAGTC
*
2172813 TCGATAC-CCCTCCTATGGTA
1 TCGATACTCCCTACTATGGTA
*
2172833 TCGATACTCCTATACTATGGTA
1 TCGATACTCC-CTACTATGGTA
2172855 TCGATACTCCCT
1 TCGATACTCCCT
2172867 TCAGTATCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 19 0.66
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.33
Consensus pattern (21 bp):
TCGATACTCCCTACTATGGTA
Found at i:2186789 original size:138 final size:137
Alignment explanation
Indices: 2186541--2186821 Score: 379
Period size: 138 Copynumber: 2.0 Consensus size: 137
2186531 CCGAAGTGCT
* * * *
2186541 GAAATAGAAATTCACAAACTCATTATGAAATCCATGGATGCACATATAGTGCCAAAAGTACATAT
1 GAAATGGAAATTCACAAACTCATTACGAAATCCATGGATGCACATATAGTACCAAAAGTACACAT
* * * *
2186606 ATTATTGATACAAAAATGCACCTTTATGCATTAAACAAAATCGATCGATAACTT-TTATATATAA
66 AGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAA-TTATTATATACAA
*
2186670 TTATATTTC
130 TT-TATGTC
* * * *
2186679 GAAATGGAAATTTACAAACTCATTACG-AATACCAT-GATTGCATATCTAGTACCGAAAGTACAC
1 GAAATGGAAATTCACAAACTCATTACGAAAT-CCATGGA-TGCACATATAGTACCAAAAGTACAC
*
2186742 ATAGTACTGATACTAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAATTATTATATACA
64 ATAGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAATTATTATATACA
2186807 ATTTATGTC
129 ATTTATGTC
2186816 GAAATG
1 GAAATG
2186822 CACCTGACTC
Statistics
Matches: 126, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
137 18 0.14
138 108 0.86
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (137 bp):
GAAATGGAAATTCACAAACTCATTACGAAATCCATGGATGCACATATAGTACCAAAAGTACACAT
AGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAATTATTATATACAAT
TTATGTC
Found at i:2199802 original size:24 final size:24
Alignment explanation
Indices: 2199766--2199812 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2199756 TTACGCCCAT
*
2199766 GTTTGTTCGTTTGTGTTCATTTAC
1 GTTTGTTCATTTGTGTTCATTTAC
2199790 GTTTGTTCATTTGTGTTCATTTA
1 GTTTGTTCATTTGTGTTCATTTA
2199813 TCATTTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (24 bp):
GTTTGTTCATTTGTGTTCATTTAC
Found at i:2205411 original size:31 final size:31
Alignment explanation
Indices: 2205371--2205439 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2205361 AACAGTTACG
** *
2205371 TAGGGGACCATATTGCAAACGGACTAAATGT
1 TAGGGGACCATATTAAAAACAGACTAAATGT
* *
2205402 TGGGGGACCATATTAAAAATAGACTAAATGT
1 TAGGGGACCATATTAAAAACAGACTAAATGT
2205433 TAGGGGA
1 TAGGGGA
2205440 TTGTATTGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (31 bp):
TAGGGGACCATATTAAAAACAGACTAAATGT
Found at i:2205527 original size:3 final size:3
Alignment explanation
Indices: 2205519--2205553 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2205509 TACCTTACCC
2205519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2205554 AGCTTAGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2206226 original size:23 final size:24
Alignment explanation
Indices: 2206181--2206235 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2206171 TTATCAAATA
*
2206181 ATTTAATTATATTCAATATTCAAT
1 ATTTAATTATATTCAATAATCAAT
*
2206205 -TTTAATTATACTTTAA-AATCAAT
1 ATTTAATTATA-TTCAATAATCAAT
2206228 ATTTAATT
1 ATTTAATT
2206236 TTTTATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTAATTATATTCAATAATCAAT
Found at i:2206364 original size:24 final size:22
Alignment explanation
Indices: 2206337--2206410 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 22
2206327 ATTAAGACTT
2206337 ATAAAGAAACAATAAAAACAATAA
1 ATAAA-AAACAATAAAAAC-ATAA
*
2206361 ATAATAAAACAATAAAAACATAT
1 ATAA-AAAACAATAAAAACATAA
*
2206384 ATAAAATTAATAATAAAAA-AT-A
1 ATAAAA--AACAATAAAAACATAA
2206406 ATAAA
1 ATAAA
2206411 TAATAGGGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
22 7 0.16
23 9 0.20
24 27 0.61
25 1 0.02
ACGTcount: A:0.73, C:0.05, G:0.01, T:0.20
Consensus pattern (22 bp):
ATAAAAAACAATAAAAACATAA
Found at i:2206531 original size:31 final size:31
Alignment explanation
Indices: 2206494--2206591 Score: 142
Period size: 31 Copynumber: 3.2 Consensus size: 31
2206484 TGTAATACAA
* * *
2206494 TCCCCCAACCTTTACTCTATTTTCAATATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
2206525 TCCCCCAACATTTAGTCTATTTGCAATATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
* **
2206556 TCCCCCAAAATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
2206587 TCCCC
1 TCCCC
2206592 GACGTAACTG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.35
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCTATTTGCAATATGG
Found at i:2206978 original size:16 final size:17
Alignment explanation
Indices: 2206957--2206999 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2206947 ATGTAAAAAC
2206957 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
2206973 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
2206990 AAATATTTAA
1 AAATATTTAA
2207000 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:2215621 original size:17 final size:17
Alignment explanation
Indices: 2215584--2215621 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2215574 CATTTTGAAT
*
2215584 ATTT-TGGATTGTTTGA
1 ATTTGTGGATTGTTAGA
*
2215600 TTTTGTGGATTGTTAGA
1 ATTTGTGGATTGTTAGA
2215617 ATTTG
1 ATTTG
2215622 GATTTGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.55
Consensus pattern (17 bp):
ATTTGTGGATTGTTAGA
Found at i:2215625 original size:24 final size:24
Alignment explanation
Indices: 2215598--2215644 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2215588 TGGATTGTTT
2215598 GATTT-TGTGGATTGTTAGAATTTG
1 GATTTGTGTGGA-TGTTAGAATTTG
* *
2215622 GATTTGTTTGGATGTTTGAATTT
1 GATTTGTGTGGATGTTAGAATTT
2215645 ATATATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (24 bp):
GATTTGTGTGGATGTTAGAATTTG
Found at i:2219478 original size:22 final size:21
Alignment explanation
Indices: 2219453--2219502 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2219443 ACTTGTTTAG
2219453 TAAAGAAA-AAAATATTAAAAAA
1 TAAAGAAATAAAATA-T-AAAAA
*
2219475 TAAAAGAAATAAAGTATAAAAA
1 T-AAAGAAATAAAATATAAAAA
2219497 TAAAGA
1 TAAAGA
2219503 GGGTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 7 0.28
23 8 0.32
24 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
TAAAGAAATAAAATATAAAAA
Found at i:2219480 original size:23 final size:22
Alignment explanation
Indices: 2219454--2219500 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2219444 CTTGTTTAGT
2219454 AAAGAAA-AAAATATTAAAAAATA
1 AAAGAAATAAAATA-T-AAAAATA
*
2219477 AAAGAAATAAAGTATAAAAATA
1 AAAGAAATAAAATATAAAAATA
2219499 AA
1 AA
2219501 GAGGGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 8 0.36
24 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAGAAATAAAATATAAAAATA
Found at i:2220733 original size:3 final size:3
Alignment explanation
Indices: 2220725--2220753 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2220715 TAAATTAATG
2220725 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2220754 TGTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2226792 original size:57 final size:57
Alignment explanation
Indices: 2226724--2226838 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
2226714 CTAATGTGAC
2226724 GAGTCCTACATGTTCAAAGTGATGACGTAACATGTTTTATGTCATCACTTTAAAAAT
1 GAGTCCTACATGTTCAAAGTGATGACGTAACATGTTTTATGTCATCACTTTAAAAAT
* *
2226781 GAGTTCTACATGTTCAAAGTGATGACGTAGCATGTTTTATGTCATCACTTTAAAAAT
1 GAGTCCTACATGTTCAAAGTGATGACGTAACATGTTTTATGTCATCACTTTAAAAAT
2226838 G
1 G
2226839 TGACAATATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (57 bp):
GAGTCCTACATGTTCAAAGTGATGACGTAACATGTTTTATGTCATCACTTTAAAAAT
Found at i:2228180 original size:16 final size:17
Alignment explanation
Indices: 2228159--2228192 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2228149 TTGAATAAAT
2228159 AATTTGAA-AATTTTTA
1 AATTTGAATAATTTTTA
2228175 AATTTGAATAATTTTTA
1 AATTTGAATAATTTTTA
2228192 A
1 A
2228193 TCGAGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
AATTTGAATAATTTTTA
Found at i:2229210 original size:20 final size:20
Alignment explanation
Indices: 2229162--2229213 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2229152 TCGATTTCAA
*
2229162 TTCAAGTCGACCTTTAGATT
1 TTCAAGTCAACCTTTAGATT
**
2229182 TTCGGGTCAACCTTTAGATT
1 TTCAAGTCAACCTTTAGATT
2229202 TTCAAGTCAACC
1 TTCAAGTCAACC
2229214 ATTATCGCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (20 bp):
TTCAAGTCAACCTTTAGATT
Found at i:2229972 original size:32 final size:33
Alignment explanation
Indices: 2229936--2230003 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
2229926 GAAAAGAAAG
2229936 ATAAAAGGAGACAAAAATA-TAAAAAAATATAT
1 ATAAAAGGAGACAAAAATATTAAAAAAATATAT
2229968 ATAAAAGGAGACAAAAATATTAAAAAAATATAT
1 ATAAAAGGAGACAAAAATATTAAAAAAATATAT
2230001 ATA
1 ATA
2230004 TAAATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 19 0.54
33 16 0.46
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (33 bp):
ATAAAAGGAGACAAAAATATTAAAAAAATATAT
Found at i:2247794 original size:11 final size:11
Alignment explanation
Indices: 2247778--2247826 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2247768 TTGTTATCAG
2247778 TGTTATTAATT
1 TGTTATTAATT
*
2247789 TGTTA-TGATT
1 TGTTATTAATT
**
2247799 TGTTATTAGCT
1 TGTTATTAATT
*
2247810 TGTTATTAGTT
1 TGTTATTAATT
2247821 TGTTAT
1 TGTTAT
2247827 GTTGGTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (11 bp):
TGTTATTAATT
Found at i:2247804 original size:21 final size:22
Alignment explanation
Indices: 2247778--2247826 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2247768 TTGTTATCAG
*
2247778 TGTTATTAATTTGTTATGA-TT
1 TGTTATTAACTTGTTATGAGTT
* *
2247799 TGTTATTAGCTTGTTATTAGTT
1 TGTTATTAACTTGTTATGAGTT
2247821 TGTTAT
1 TGTTAT
2247827 GTTGGTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (22 bp):
TGTTATTAACTTGTTATGAGTT
Found at i:2250460 original size:12 final size:12
Alignment explanation
Indices: 2250443--2250472 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2250433 GAGGAACGAA
*
2250443 AAAAAAAACCAG
1 AAAAAAAACAAG
2250455 AAAAAAAACAAG
1 AAAAAAAACAAG
2250467 AAAAAA
1 AAAAAA
2250473 GAGAACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAG
Found at i:2256089 original size:20 final size:20
Alignment explanation
Indices: 2256064--2256104 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2256054 ACATTCCCTC
2256064 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
2256084 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
2256104 T
1 T
2256105 GTATTTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:2256773 original size:13 final size:13
Alignment explanation
Indices: 2256755--2256788 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2256745 CAAAAAGAGG
*
2256755 ACAAAGAGCATAA
1 ACAAAGAGCACAA
*
2256768 ACAAAGAGCACAG
1 ACAAAGAGCACAA
2256781 ACAAAGAG
1 ACAAAGAG
2256789 TCTCTCGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.18, G:0.21, T:0.03
Consensus pattern (13 bp):
ACAAAGAGCACAA
Found at i:2265875 original size:13 final size:13
Alignment explanation
Indices: 2265857--2265899 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
2265847 TAAGGGGGAG
2265857 TAATTTCAAAACT
1 TAATTTCAAAACT
2265870 TAATTTCAAAACT
1 TAATTTCAAAACT
*
2265883 TGATTTCAAAATCT
1 TAATTTCAAAA-CT
2265897 TAA
1 TAA
2265900 AATTACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (13 bp):
TAATTTCAAAACT
Found at i:2267040 original size:8 final size:8
Alignment explanation
Indices: 2267029--2267391 Score: 523
Period size: 8 Copynumber: 45.6 Consensus size: 8
2267019 TTTCCTTACT
2267029 TACATACA
1 TACATACA
2267037 TACATACA
1 TACATACA
2267045 TACATACA
1 TACATACA
2267053 TACATACA
1 TACATACA
2267061 TACATACA
1 TACATACA
2267069 TACATACA
1 TACATACA
2267077 TACATACA
1 TACATACA
2267085 TACATACA
1 TACATACA
2267093 TACATACA
1 TACATACA
2267101 TACATACA
1 TACATACA
2267109 TACATACA
1 TACATACA
*
2267117 TGCATACA
1 TACATACA
*
2267125 TGCATACA
1 TACATACA
*
2267133 TGCATACA
1 TACATACA
*
2267141 TGCATACA
1 TACATACA
*
2267149 TGCATACA
1 TACATACA
*
2267157 TGCATACA
1 TACATACA
*
2267165 TGCATACA
1 TACATACA
*
2267173 TGCATACA
1 TACATACA
*
2267181 TGCATACA
1 TACATACA
*
2267189 TGCATACA
1 TACATACA
*
2267197 TGCATACA
1 TACATACA
*
2267205 TGCATACA
1 TACATACA
*
2267213 TGCATACA
1 TACATACA
*
2267221 TGCATACA
1 TACATACA
2267229 TACATACA
1 TACATACA
2267237 TACATACA
1 TACATACA
2267245 TACATACA
1 TACATACA
2267253 TACATACA
1 TACATACA
2267261 TACATACA
1 TACATACA
2267269 TACATACA
1 TACATACA
2267277 TACATACA
1 TACATACA
2267285 TACATACA
1 TACATACA
2267293 TACATACA
1 TACATACA
*
2267301 TACATGCA
1 TACATACA
2267309 TACATACA
1 TACATACA
* *
2267317 TGCATGCA
1 TACATACA
2267325 TACATACA
1 TACATACA
2267333 TACATACA
1 TACATACA
*
2267341 TACATATA
1 TACATACA
2267349 TACATACA
1 TACATACA
*
2267357 TATATACA
1 TACATACA
*
2267365 TACAAACA
1 TACATACA
*
2267373 TATATAC-
1 TACATACA
2267380 -ACATACA
1 TACATACA
2267387 TACAT
1 TACAT
2267392 TATATAAAAA
Statistics
Matches: 337, Mismatches: 16, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
6 5 0.01
8 332 0.99
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (8 bp):
TACATACA
Found at i:2267946 original size:34 final size:35
Alignment explanation
Indices: 2267876--2267959 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 35
2267866 TTGAGATCGC
*
2267876 TTTCTCAAAAACAACCTTTGTCTCGCGTGAGACAATT
1 TTTCT-AAAAACAAACTTTGTCTC-CGTGAGACAATT
* *
2267913 TTTCTAAAAACAAATTTTGTCT-CTTGAGACAATT
1 TTTCTAAAAACAAACTTTGTCTCCGTGAGACAATT
*
2267947 TCTCTAAAAACAA
1 TTTCTAAAAACAA
2267960 TGTTACAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 23 0.53
36 15 0.35
37 5 0.12
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (35 bp):
TTTCTAAAAACAAACTTTGTCTCCGTGAGACAATT
Found at i:2268054 original size:33 final size:30
Alignment explanation
Indices: 2268006--2268088 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 30
2267996 AATTATGAAT
* *
2268006 TTGTTTCATTGGAAACAAACCATCATCTTTGAG
1 TTGTTTCTTTTGAAACAAACCAT--T-TTTGAG
**
2268039 TTGTTTCTTTTGAAACAAAGGATTTTTGAG
1 TTGTTTCTTTTGAAACAAACCATTTTTGAG
*
2268069 TCTATTTCTTTTGAAACAAA
1 T-TGTTTCTTTTGAAACAAA
2268089 ACTTTGTCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
30 7 0.16
31 18 0.41
33 19 0.43
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (30 bp):
TTGTTTCTTTTGAAACAAACCATTTTTGAG
Found at i:2268707 original size:31 final size:31
Alignment explanation
Indices: 2268672--2268739 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
2268662 TTTTGTCTCC
2268672 TTGAGGCAGTTTCTCTAGAAATACAAA-ATCT
1 TTGAGGCAGTTTCTCTAGAAATA-AAACATCT
*** *
2268703 TTGAGTTTGTTTCTCTTGAAATAAAACCATCT
1 TTGAGGCAGTTTCTCTAGAAATAAAA-CATCT
2268735 TTGAG
1 TTGAG
2268740 TCATTTCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 3 0.10
31 19 0.61
32 9 0.29
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (31 bp):
TTGAGGCAGTTTCTCTAGAAATAAAACATCT
Found at i:2268740 original size:32 final size:31
Alignment explanation
Indices: 2268680--2268740 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2268670 CCTTGAGGCA
2268680 GTTTCTCTAGAAATACAAAATCTTTGAGTTT
1 GTTTCTCTAGAAATACAAAATCTTTGAGTTT
*
2268711 GTTTCTCTTGAAATA-AAACCATCTTTGAGT
1 GTTTCTCTAGAAATACAAA--ATCTTTGAGT
2268741 CATTTCCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 10 0.37
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (31 bp):
GTTTCTCTAGAAATACAAAATCTTTGAGTTT
Found at i:2268940 original size:74 final size:70
Alignment explanation
Indices: 2268857--2268992 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 70
2268847 CTTTTGAATG
* *
2268857 AAAATCTTTGAGTTTGTTTCTT-TGGAAACAAAATTTACCATCTTTGAGTTTGTTTCCCTTGAAA
1 AAAATCTTTGAGTATGTTT-TTCTGGAAACAAAA---A-CATCTTTGAGTTTGTTTCCCTCGAAA
2268921 CAAAACAAAC
61 CAAAACAAAC
* *
2268931 AAAATCTTTGAGTATGTTTTTCTTGAAACAAAAACATCTTTGAGTTTGTTTCTCTCGAAACA
1 AAAATCTTTGAGTATGTTTTTCTGGAAACAAAAACATCTTTGAGTTTGTTTCCCTCGAAACA
2268993 CTGATCTTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 26 0.46
71 1 0.02
73 2 0.04
74 28 0.49
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (70 bp):
AAAATCTTTGAGTATGTTTTTCTGGAAACAAAAACATCTTTGAGTTTGTTTCCCTCGAAACAAAA
CAAAC
Found at i:2268973 original size:32 final size:33
Alignment explanation
Indices: 2268923--2268992 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
2268913 CCTTGAAACA
* *
2268923 AAACAAACAAAATCTTTGAGTATGTTTTTCTTG
1 AAACAAACAAAATCTTTGAGTATGTTTCTCTCG
* *
2268956 AAACAAA-AACATCTTTGAGTTTGTTTCTCTCG
1 AAACAAACAAAATCTTTGAGTATGTTTCTCTCG
2268988 AAACA
1 AAACA
2268993 CTGATCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (33 bp):
AAACAAACAAAATCTTTGAGTATGTTTCTCTCG
Done.