Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 13 of 117
Found at i:3766562 original size:17 final size:18
Alignment explanation
Indices: 3766528--3766569 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3766518 CTTAGTATTC
3766528 TTTATTTTATTTATTTTA
1 TTTATTTTATTTATTTTA
3766546 -TTATTTTATTT-TATTTA
1 TTTATTTTATTTAT-TTTA
3766563 TTTATTT
1 TTTATTT
3766570 AAATGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 15 0.68
18 6 0.27
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATTTTATTTATTTTA
Found at i:3766578 original size:22 final size:22
Alignment explanation
Indices: 3766531--3766584 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3766521 AGTATTCTTT
** *
3766531 ATTTTATTTATTTTATTATTTT
1 ATTTTATTTATTTTATTAAATG
3766553 ATTTTATTTA-TTTATTTAAATG
1 ATTTTATTTATTTTA-TTAAATG
*
3766575 ATTTTCTTTA
1 ATTTTATTTA
3766585 AATAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTTATTTATTTTATTAAATG
Found at i:3766659 original size:58 final size:58
Alignment explanation
Indices: 3766584--3766947 Score: 239
Period size: 58 Copynumber: 6.2 Consensus size: 58
3766574 GATTTTCTTT
** *
3766584 AAATAAAATTTCAAAAAAATATTTTTGAAGAAAAGTTGAAAATATCAATTTTCCTTGA
1 AAATAAAATTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGA
* * **
3766642 AAATAAATTTTTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTTGAA
1 AAATAAAATTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTG-A
** * *
3766701 AAATAAAAAGATTTAAAATATATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAAT-AAAATTTTTAAAA-A-ATAT-TTTTGAAG-AAAAGTTGAAAGTATCAATTTTCCTTGA
* * * * * *
3766764 AAATAAAATTTTCAAAAAAAAAACAAACATTTT-AGGGAAAGTTGAAAGTATTAA-TTTCTCTTG
1 AAATAAAATTTT-----TAAAAA-ATA-TTTTTGAAGAAAAGTTGAAAGTATCAATTTTC-CTTG
3766827 -
58 A
* ** * * *
3766827 -AA-AAAATTTTT--CAAAT-GCTTTAAAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAATAAAATTTTTAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCCTTGA
** * * * *
3766881 AAATAAAA-TTTCCAAAAACA-TTTT-AGGGAAAGTTGAAAGTATCAA-TTTCTCTAGA
1 AAATAAAATTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTC-CTTGA
3766936 AAATAAAATTTT
1 AAATAAAATTTT
3766948 CAAATGCTTT
Statistics
Matches: 238, Mismatches: 44, Indels: 50
0.72 0.13 0.15
Matches are distributed among these distances:
51 3 0.01
52 2 0.01
53 20 0.08
54 8 0.03
55 33 0.14
56 9 0.04
57 6 0.03
58 50 0.21
59 5 0.02
60 10 0.04
61 9 0.04
62 12 0.05
63 15 0.06
64 43 0.18
65 2 0.01
66 7 0.03
67 4 0.02
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (58 bp):
AAATAAAATTTTTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGA
Found at i:3766859 original size:53 final size:53
Alignment explanation
Indices: 3766801--3766988 Score: 216
Period size: 55 Copynumber: 3.5 Consensus size: 53
3766791 CATTTTAGGG
* * *
3766801 AAAGTTGAAAGTATTAATTTCTCTTGAAA-AAATTTTTCAAATGCTTTAAAGAA
1 AAAGTTGAAAGTATCAATTTCTCTTGAAATAAAATTTTCAAATGCTTT-AAGGA
* * * ** * *
3766854 AAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCCAAAAACATTTTAGGG
1 AAAGTTGAAAGTATCAATTTCTCTT-GAAATAAAATTTTCAAATGC-TTTAAGGA
*
3766909 AAAGTTGAAAGTATCAATTTCTCTAGAAAATAAAATTTTCAAATGCTTTAAGGA
1 AAAGTTGAAAGTATCAATTTCTCTTG-AAATAAAATTTTCAAATGCTTTAAGGA
* *
3766963 AAAGTTGAAAGTATCGATTTTTCTTG
1 AAAGTTGAAAGTATCAATTTCTCTTG
3766989 TATAAAAGCG
Statistics
Matches: 110, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
53 23 0.21
54 32 0.29
55 52 0.47
56 3 0.03
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (53 bp):
AAAGTTGAAAGTATCAATTTCTCTTGAAATAAAATTTTCAAATGCTTTAAGGA
Found at i:3766907 original size:108 final size:109
Alignment explanation
Indices: 3766788--3766987 Score: 332
Period size: 108 Copynumber: 1.8 Consensus size: 109
3766778 AAAAAAAAAC
* * *
3766788 AAACATTTTAGGGAAAGTTGAAAGTATTAATTTCTCTTG-AAA-AAATTTTTCAAATGCTTTAAA
1 AAACATTTTAGGGAAAGTTGAAAGTATCAATTTCTCTAGAAAATAAAATTTTCAAATGCTTT-AA
3766851 GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCCAA
65 GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCCAA
3766896 AAACATTTTAGGGAAAGTTGAAAGTATCAATTTCTCTAGAAAATAAAATTTTCAAATGCTTTAAG
1 AAACATTTTAGGGAAAGTTGAAAGTATCAATTTCTCTAGAAAATAAAATTTTCAAATGCTTTAAG
* *
3766961 GAAAAGTTGAAAGTATCGATTTTTCTT
66 AAAAAGTTGAAAGTATCAATTTTTCTT
3766988 GTATAAAAGC
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
108 37 0.44
109 31 0.36
110 17 0.20
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (109 bp):
AAACATTTTAGGGAAAGTTGAAAGTATCAATTTCTCTAGAAAATAAAATTTTCAAATGCTTTAAG
AAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCCAA
Found at i:3767181 original size:10 final size:9
Alignment explanation
Indices: 3767157--3767182 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3767147 AAGGTGAGAA
3767157 AATTTTTTC
1 AATTTTTTC
3767166 AATTTTTTC
1 AATTTTTTC
3767175 AATTTTTT
1 AATTTTTT
3767183 GCTAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (9 bp):
AATTTTTTC
Found at i:3767598 original size:30 final size:30
Alignment explanation
Indices: 3767562--3767618 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3767552 TCTTGTACTT
3767562 GGCTGCAATGCTATCTTGATTCACCTAATA
1 GGCTGCAATGCTATCTTGATTCACCTAATA
*
3767592 GGCTGCAATGCTGTCTTGATTCACCTA
1 GGCTGCAATGCTATCTTGATTCACCTA
3767619 GCCTTGACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (30 bp):
GGCTGCAATGCTATCTTGATTCACCTAATA
Found at i:3771950 original size:4 final size:4
Alignment explanation
Indices: 3771943--3771967 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3771933 TGTGTGTGTG
3771943 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
3771968 CCCACAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:3778520 original size:23 final size:25
Alignment explanation
Indices: 3778463--3778525 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
3778453 TTTTTTAAAG
*
3778463 ATATCTTAAAATTATGTTATTTTTT
1 ATATTTTAAAATTATGTTATTTTTT
* *
3778488 A-ACATCTAAAATT-T-TTATTTTTT
1 ATA-TTTTAAAATTATGTTATTTTTT
3778511 ATATTTTAAAATTAT
1 ATATTTTAAAATTAT
3778526 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
23 18 0.60
24 4 0.13
25 8 0.27
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATTTTAAAATTATGTTATTTTTT
Found at i:3778527 original size:13 final size:13
Alignment explanation
Indices: 3778509--3778536 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3778499 TTTTTATTTT
3778509 TTATATTTTAAAA
1 TTATATTTTAAAA
3778522 TTATATTTTAAAA
1 TTATATTTTAAAA
3778535 TT
1 TT
3778537 TTTTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATTTTAAAA
Found at i:3783845 original size:12 final size:12
Alignment explanation
Indices: 3783828--3783865 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
3783818 ATCTGCGTGA
3783828 TTCTATTACTGG
1 TTCTATTACTGG
3783840 TTCTATTACTGG
1 TTCTATTACTGG
*
3783852 TTCTATTCCTGG
1 TTCTATTACTGG
3783864 TT
1 TT
3783866 TTGGTCCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.13, C:0.18, G:0.16, T:0.53
Consensus pattern (12 bp):
TTCTATTACTGG
Found at i:3783896 original size:12 final size:12
Alignment explanation
Indices: 3783828--3783896 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
3783818 ATCTGCGTGA
*
3783828 TTCTATTACTGG
1 TTCTATTCCTGG
*
3783840 TTCTATTACTGG
1 TTCTATTCCTGG
3783852 TTCTATTCCTGG
1 TTCTATTCCTGG
* **
3783864 TTTTGGTCCTGG
1 TTCTATTCCTGG
* *
3783876 CTCTTTTCCTGG
1 TTCTATTCCTGG
*
3783888 TTCTGTTCC
1 TTCTATTCC
3783897 CGGCCAATAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.07, C:0.23, G:0.19, T:0.51
Consensus pattern (12 bp):
TTCTATTCCTGG
Found at i:3800233 original size:42 final size:42
Alignment explanation
Indices: 3800183--3800356 Score: 217
Period size: 42 Copynumber: 4.1 Consensus size: 42
3800173 TAGCCCATCC
*
3800183 AAGCCACAGTCAAAACCACAGGTCACAGCTCCTCCAACGCCA
1 AAGCCACAGCCAAAACCACAGGTCACAGCTCCTCCAACGCCA
* *
3800225 AAGCCACAGCCAAAACCACCGGTCACAGTTCCTCCAACGCCA
1 AAGCCACAGCCAAAACCACAGGTCACAGCTCCTCCAACGCCA
* * ** ** * *
3800267 AAGACGCAATCAAAACCACCTGTCACAGCTCCTACAACACCA
1 AAGCCACAGCCAAAACCACAGGTCACAGCTCCTCCAACGCCA
3800309 AAGCCACAGCCAAAACGTC-CA-GTCACAGCTCCTCCAACGCCA
1 AAGCCACAGCCAAAAC--CACAGGTCACAGCTCCTCCAACGCCA
3800351 AAGCCA
1 AAGCCA
3800357 ATACCATCCA
Statistics
Matches: 112, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 110 0.98
43 1 0.01
44 1 0.01
ACGTcount: A:0.36, C:0.41, G:0.13, T:0.10
Consensus pattern (42 bp):
AAGCCACAGCCAAAACCACAGGTCACAGCTCCTCCAACGCCA
Found at i:3800292 original size:84 final size:84
Alignment explanation
Indices: 3800192--3800353 Score: 252
Period size: 84 Copynumber: 1.9 Consensus size: 84
3800182 CAAGCCACAG
* * * *
3800192 TCAAAACCACAGGTCACAGCTCCTCCAACGCCAAAGCCACAGCCAAAACCACCGGTCACAGTTCC
1 TCAAAACCACAGGTCACAGCTCCTACAACACCAAAGCCACAGCCAAAACCACCAGTCACAGCTCC
3800257 TCCAACGCCAAAGACGCAA
66 TCCAACGCCAAAGACGCAA
** **
3800276 TCAAAACCACCTGTCACAGCTCCTACAACACCAAAGCCACAGCCAAAACGTCCAGTCACAGCTCC
1 TCAAAACCACAGGTCACAGCTCCTACAACACCAAAGCCACAGCCAAAACCACCAGTCACAGCTCC
3800341 TCCAACGCCAAAG
66 TCCAACGCCAAAG
3800354 CCAATACCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.36, C:0.41, G:0.13, T:0.10
Consensus pattern (84 bp):
TCAAAACCACAGGTCACAGCTCCTACAACACCAAAGCCACAGCCAAAACCACCAGTCACAGCTCC
TCCAACGCCAAAGACGCAA
Found at i:3800538 original size:42 final size:42
Alignment explanation
Indices: 3800478--3800559 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
3800468 ACTAGGCCAG
* * * **
3800478 CAGCACCTGAGAACCCAACACCGGAGCCACCAAAACCAACGC
1 CAGCAACTAAGAAACCAACACCCAAGCCACCAAAACCAACGC
* *
3800520 CAGCAACTAAGAAACCAACTCCCAAGTCACCAAAACCAAC
1 CAGCAACTAAGAAACCAACACCCAAGCCACCAAAACCAAC
3800560 AGCAGCACCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.43, C:0.40, G:0.12, T:0.05
Consensus pattern (42 bp):
CAGCAACTAAGAAACCAACACCCAAGCCACCAAAACCAACGC
Found at i:3800593 original size:42 final size:42
Alignment explanation
Indices: 3800502--3800593 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
3800492 CCAACACCGG
*
3800502 AGCCACCAAAACCAACGCCAGCAACTAAGAAACCAACTCCCA
1 AGCCACCAAAACCAACGCCAGCAACCAAGAAACCAACTCCCA
* * *
3800544 AGTCACCAAAACCAACAG-CAGC-ACCAGAGAATCCAATTTCCCA
1 AGCCACCAAAACCAAC-GCCAGCAACCA-AGAAACCAA-CTCCCA
3800587 A-CCACCA
1 AGCCACCA
3800594 GAATCAGCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
41 3 0.07
42 32 0.76
43 7 0.17
ACGTcount: A:0.43, C:0.39, G:0.10, T:0.08
Consensus pattern (42 bp):
AGCCACCAAAACCAACGCCAGCAACCAAGAAACCAACTCCCA
Found at i:3800727 original size:27 final size:27
Alignment explanation
Indices: 3800697--3800754 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3800687 CTCGTCCAGT
* *
3800697 CACCCTCGCCACCTGTCCATTCACCAC
1 CACCCCCGCCACCTGTCCACTCACCAC
* *
3800724 CACCCCCTCCACCTGTCTACTCACCAC
1 CACCCCCGCCACCTGTCCACTCACCAC
3800751 CACC
1 CACC
3800755 ACCTGTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.59, G:0.05, T:0.17
Consensus pattern (27 bp):
CACCCCCGCCACCTGTCCACTCACCAC
Found at i:3800748 original size:21 final size:21
Alignment explanation
Indices: 3800732--3801099 Score: 207
Period size: 21 Copynumber: 17.2 Consensus size: 21
3800722 ACCACCCCCT
3800732 CCACCTGTCTACTCACCACCA
1 CCACCTGTCTACTCACCACCA
* * *
3800753 CCACCTGTCAATTCACCACCT
1 CCACCTGTCTACTCACCACCA
* * *
3800774 CCCCCAGTCCACTCACCACCA
1 CCACCTGTCTACTCACCACCA
* *
3800795 CCTCCTGTCTACTCGCCACCA
1 CCACCTGTCTACTCACCACCA
* * *
3800816 CCACCAGTCTACTCCCCTCCA
1 CCACCTGTCTACTCACCACCA
* * * * *
3800837 CCACCCGTCCATTCTCCACCT
1 CCACCTGTCTACTCACCACCA
* * *
3800858 CCACCAGTTTTCTCACCACCA
1 CCACCTGTCTACTCACCACCA
* * * * *
3800879 CCACCCGTCCATTCTCCACCT
1 CCACCTGTCTACTCACCACCA
* * *
3800900 CCACCAGTTTTCTCACCACCA
1 CCACCTGTCTACTCACCACCA
* * * * *
3800921 CCACCCGTCCATTCTCCACCT
1 CCACCTGTCTACTCACCACCA
* * *
3800942 CCACCAGTTTTCTCACCACCA
1 CCACCTGTCTACTCACCACCA
* *
3800963 CCACCCGTCTACTCTCCACCTCCACCT
1 CCACCTGTCTA--CT-CA---CCACCA
* *
3800990 CCACCAGTATACTCACCACCA
1 CCACCTGTCTACTCACCACCA
** *
3801011 CCACCAATCTACTCACCACCT
1 CCACCTGTCTACTCACCACCA
* * *
3801032 CCACCAGTATATTCACCACCA
1 CCACCTGTCTACTCACCACCA
* * * *
3801053 CCACCCGTAC-AATCCCCACCT
1 CCACCTGT-CTACTCACCACCA
* *
3801074 CCACCGGTTTACTCACCACCA
1 CCACCTGTCTACTCACCACCA
3801095 CCACC
1 CCACC
3801100 ACCACGATCT
Statistics
Matches: 258, Mismatches: 81, Indels: 16
0.73 0.23 0.05
Matches are distributed among these distances:
21 236 0.91
23 2 0.01
24 4 0.02
25 2 0.01
27 14 0.05
ACGTcount: A:0.22, C:0.53, G:0.05, T:0.20
Consensus pattern (21 bp):
CCACCTGTCTACTCACCACCA
Found at i:3800788 original size:42 final size:42
Alignment explanation
Indices: 3800724--3801099 Score: 367
Period size: 42 Copynumber: 8.8 Consensus size: 42
3800714 CATTCACCAC
* * * *
3800724 CACCCCCTCCACCTGTCTACTCACCACCACCACCTGTCAATT
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
* ** * * * *
3800766 CACCACCTCCCCCAGTCCACTCACCACCACCTCCTGTCTACT
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
* * * * * *
3800808 CGCCACCACCACCAGTCTACTCCCCTCCACCACCCGTCCATT
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
* * *
3800850 CTCCACCTCCACCAGTTTTCTCACCACCACCACCCGTCCATT
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
* * *
3800892 CTCCACCTCCACCAGTTTTCTCACCACCACCACCCGTCCATT
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
* * *
3800934 CTCCACCTCCACCAGTTTTCTCACCACCACCACCCGTCTACTCT
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGTC-AAT-T
* ** * *
3800978 CCACCTCCACCTCCACCAGTATACTCACCACCACCACCAATCTACT
1 -CA---CCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
* *
3801024 CACCACCTCCACCAGTATATTCACCACCACCACCCGTACAA-T
1 CACCACCTCCACCAGTTTACTCACCACCACCACCCGT-CAATT
* *
3801066 CCCCACCTCCACCGGTTTACTCACCACCACCACC
1 CACCACCTCCACCAGTTTACTCACCACCACCACC
3801100 ACCACGATCT
Statistics
Matches: 286, Mismatches: 41, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
42 246 0.86
43 3 0.01
44 1 0.00
45 3 0.01
46 1 0.00
48 32 0.11
ACGTcount: A:0.22, C:0.53, G:0.05, T:0.20
Consensus pattern (42 bp):
CACCACCTCCACCAGTTTACTCACCACCACCACCCGTCAATT
Found at i:3801111 original size:132 final size:132
Alignment explanation
Indices: 3800850--3801123 Score: 354
Period size: 132 Copynumber: 2.1 Consensus size: 132
3800840 CCCGTCCATT
* * ** * * *
3800850 CTCCACCTCCACCAGTTTTCTCACCACCACCACCCGTCCATTCTCCACCTCCACCAGTTTTCTCA
1 CTCCACCTCCACCAGTATACTCACCACCACCACCAATCCACTCACCACCTCCACCAGTTATCTCA
* * * * ** *
3800915 CCACCACCACCCGTCCATTCTCCACCTCCACCAGTTTTCTCACCACCACCACCCGTCTACTCTCC
66 CCACCACCACCCGTACAATCCCCACCTCCACCAGTTTACTCACCACCACCACCCCACGACTCTCC
*
3800980 AC
131 AA
*
3800982 CTCCACCTCCACCAGTATACTCACCACCACCACCAATCTACTCACCACCTCCACCAGTATAT-TC
1 CTCCACCTCCACCAGTATACTCACCACCACCACCAATCCACTCACCACCTCCACCAGT-TATCTC
*
3801046 ACCACCACCACCCGTACAATCCCCACCTCCACCGGTTTACTCACCACCACCACCACCACGA-TCT
65 ACCACCACCACCCGTACAATCCCCACCTCCACCAGTTTACTCACCACCACCACC-CCACGACTCT
3801110 CCAA
129 CCAA
*
3801114 CTCCATCTCC
1 CTCCACCTCC
3801124 TCCTCCTGCT
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
132 117 0.96
133 5 0.04
ACGTcount: A:0.23, C:0.52, G:0.04, T:0.20
Consensus pattern (132 bp):
CTCCACCTCCACCAGTATACTCACCACCACCACCAATCCACTCACCACCTCCACCAGTTATCTCA
CCACCACCACCCGTACAATCCCCACCTCCACCAGTTTACTCACCACCACCACCCCACGACTCTCC
AA
Found at i:3814151 original size:2 final size:2
Alignment explanation
Indices: 3814144--3814168 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3814134 AAAATTTGAT
3814144 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
3814169 GTAGGGTGGT
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:3815285 original size:2 final size:2
Alignment explanation
Indices: 3815278--3815312 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3815268 AGTACAAATC
*
3815278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3815313 ACAATGGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3816326 original size:8 final size:8
Alignment explanation
Indices: 3816304--3816349 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
3816294 TTATACATGC
3816304 ATATATTT
1 ATATATTT
3816312 -TATTATTT
1 ATA-TATTT
3816320 ATATATTT
1 ATATATTT
3816328 ATAT-TTT
1 ATATATTT
3816335 ACT-TATTT
1 A-TATATTT
3816343 ATATATT
1 ATATATT
3816350 ACATGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
7 8 0.24
8 23 0.70
9 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
ATATATTT
Found at i:3816335 original size:15 final size:16
Alignment explanation
Indices: 3816304--3816349 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3816294 TTATACATGC
3816304 ATATATTT-TATTATTT
1 ATATATTTATA-TATTT
3816320 ATATATTTATAT-TTT
1 ATATATTTATATATTT
3816335 ACT-TATTTATATATT
1 A-TATATTTATATATT
3816350 ACATGTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.48
16 12 0.44
17 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATATTTATATATTT
Found at i:3816344 original size:23 final size:22
Alignment explanation
Indices: 3816305--3816349 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
3816295 TATACATGCA
3816305 TATATTTTATTATTTATATATT
1 TATATTTTATTATTTATATATT
3816327 TATATTTTACTTATTTATATATT
1 TATATTTTA-TTATTTATATATT
3816350 ACATGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATATTTTATTATTTATATATT
Found at i:3816608 original size:26 final size:26
Alignment explanation
Indices: 3816579--3816630 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3816569 TTAATGACAT
3816579 TTAATT-ATAA-ATATAATAAATGTTTA
1 TTAATTAATAATAT-TAA-AAATGTTTA
3816605 TTAATTAATAATATTAAAAATGTTTA
1 TTAATTAATAATATTAAAAATGTTTA
3816631 AATATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.62
27 7 0.29
28 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TTAATTAATAATATTAAAAATGTTTA
Found at i:3816650 original size:25 final size:25
Alignment explanation
Indices: 3816580--3816640 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
3816570 TAATGACATT
3816580 TAATT-ATAA-ATATAATAAATGTTTA
1 TAATTAATAATAT-TAA-AAATGTTTA
3816605 TTAATTAATAATATTAAAAATGTTTA
1 -TAATTAATAATATTAAAAATGTTTA
3816631 -AATATAATAA
1 TAAT-TAATAA
3816641 CTTACAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
24 3 0.09
25 6 0.19
26 14 0.44
27 7 0.22
28 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (25 bp):
TAATTAATAATATTAAAAATGTTTA
Found at i:3817176 original size:21 final size:21
Alignment explanation
Indices: 3817151--3817191 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3817141 CTTAACGCTT
*
3817151 CTTTGTCATTAAATCAAAAAG
1 CTTTGTCACTAAATCAAAAAG
*
3817172 CTTTGTCACTAGATCAAAAA
1 CTTTGTCACTAAATCAAAAA
3817192 ACGAAAGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
CTTTGTCACTAAATCAAAAAG
Found at i:3823849 original size:21 final size:20
Alignment explanation
Indices: 3823824--3823865 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3823814 AGTTATAAGC
3823824 ATAATAAA-ATATTATATTAAT
1 ATAATAAATA-ATTATA-TAAT
*
3823845 ATAATTAATAATTATATAAT
1 ATAATAAATAATTATATAAT
3823865 A
1 A
3823866 ATTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 13 0.68
22 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATAAATAATTATATAAT
Found at i:3823899 original size:22 final size:22
Alignment explanation
Indices: 3823836--3823899 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
3823826 AATAAAATAT
* *
3823836 TATATTAATATAATTAATAATTA
1 TATAATAA-ATAATTAATAATCA
*
3823859 TATAATAATTAAATT-ATAATCA
1 TATAATAAAT-AATTAATAATCA
3823881 CT-TAATAAATAATTAATAA
1 -TATAATAAATAATTAATAA
3823900 ATTAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 4 0.12
22 18 0.53
23 12 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAATAAATAATTAATAATCA
Found at i:3825502 original size:27 final size:28
Alignment explanation
Indices: 3825468--3825526 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
3825458 ATATATTTGT
3825468 TTATTAAAATCATT-TTACGTAAT-TAAA
1 TTATTAAAAT-ATTATTACGTAATATAAA
*
3825495 TTATTAAAATATTATTACGTATTATAAA
1 TTATTAAAATATTATTACGTAATATAAA
3825523 TTAT
1 TTAT
3825527 ATATAAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 3 0.10
27 18 0.62
28 8 0.28
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (28 bp):
TTATTAAAATATTATTACGTAATATAAA
Found at i:3825750 original size:231 final size:224
Alignment explanation
Indices: 3825229--3825901 Score: 1112
Period size: 224 Copynumber: 3.0 Consensus size: 224
3825219 TTTTACCCCA
* *
3825229 ACATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAGTTATTAAAATATTATTACATATT
1 ACATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAATTATTAAAATATTATTACGTATT
*
3825294 ATATATTATATATAATAATTAAATTATAAATACTTATTTTAATAGTTATATACATATGGTATATA
66 ATATATTATATATAATAATTAAATTATAAATACTTATTTCAATAGTTATATACATATGGTATATA
* *
3825359 ATAAATTATTAATATTTTTAAATAATATGATACGATTTGAATAAAAAAATATATGTTAATTTTAT
131 ATAAATGATTAATATTTTTAAATAATATGATACGATTTGAATAGAAAAATATATGTTAATTTTAT
3825424 AACGTATAGGTTTGTAAATCTATCGTTAG
196 AACGTATAGGTTTGTAAATCTATCGTTAG
3825453 ACATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAATTATTAAAATATTATTACGTATT
1 ACATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAATTATTAAAATATTATTACGTATT
* * *
3825518 ATAAATTATATATAAGAATTAAATTATAAATACTTATTTCAATAATTATATACATATGGTATATA
66 ATATATTATATATAATAATTAAATTATAAATACTTATTTCAATAGTTATATACATATGGTATATA
* * *
3825583 ATAAATGATTAATATTTTTAAATAATATGATATGATTTTAATAGAAAAATATATGTTAACTTTAT
131 ATAAATGATTAATATTTTTAAATAATATGATACGATTTGAATAGAAAAATATATGTTAATTTTAT
* *
3825648 AACGTATAGGTTTATAAACCTATCGTTAG
196 AACGTATAGGTTTGTAAATCTATCGTTAG
*
3825677 ACATTATATATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAATGATTAAAATATTATT
1 AC-------ATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAATTATTAAAATATTATT
* * *
3825742 ATGTATTATATATTATTTATAATAATTAAATTATAAATACTTATTTCAATAGCTATATACATATG
59 ACGTATTATATATTATATATAATAATTAAATTATAAATACTTATTTCAATAGTTATATACATATG
* *
3825807 ATATATAATAAATGATTAATGTTTTTAAATAATATGATACGATTTGAATAGAAAAATATATGTTA
124 GTATATAATAAATGATTAATATTTTTAAATAATATGATACGATTTGAATAGAAAAATATATGTTA
3825872 ATTTTATAACGTATAGGTTTGTAAATCTAT
189 ATTTTATAACGTATAGGTTTGTAAATCTAT
3825902 TATTAGGCAT
Statistics
Matches: 415, Mismatches: 27, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
224 213 0.51
231 202 0.49
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (224 bp):
ACATTATATATTTGTTTATTAAAATCATTTTACGTAATTAAATTATTAAAATATTATTACGTATT
ATATATTATATATAATAATTAAATTATAAATACTTATTTCAATAGTTATATACATATGGTATATA
ATAAATGATTAATATTTTTAAATAATATGATACGATTTGAATAGAAAAATATATGTTAATTTTAT
AACGTATAGGTTTGTAAATCTATCGTTAG
Found at i:3826759 original size:133 final size:134
Alignment explanation
Indices: 3826448--3826724 Score: 358
Period size: 134 Copynumber: 2.1 Consensus size: 134
3826438 TGAAAAGATG
* * * *
3826448 TTTATTTAAGAAAAATTGATACTTTCATA-TTTTCCTTAAAAAAGCTTCTTTTGAAATAT--A-T
1 TTTATTTAAGAAAAATTAATATTTTCA-ACTTTTTCTTAAAAAA--TTATTTT-AAATATAAATT
*
3826509 TTTTGAAAATTTTTTATTTTCTAAGAAAAATTGATATATTCAACTTTTTCCTTAAAACCTCATTT
62 TTTTGAAAAATTTTTATTTTCTAAGAAAAATTGATATATTCAACTTTTTCCTTAAAACCTCATTT
*
3826574 TTTATTTT
127 TTTATTGT
3826582 TTTATTTAAGAAAAATTAATATTTTCAACTTTTTCTTAAAAAATT-TTTTAAATATAAATTTTTT
1 TTTATTTAAGAAAAATTAATATTTTCAACTTTTTCTTAAAAAATTATTTTAAATATAAATTTTTT
* *
3826646 GAAAAATTTTTACTTTT-TAAGAAAATTTGAT-TCTTTCAA-TTTTTCCTTAAAA-CTC-TTTTT
66 GAAAAATTTTTA-TTTTCTAAGAAAAATTGATAT-ATTCAACTTTTTCCTTAAAACCTCATTTTT
3826706 TATTGT
129 TATTGT
3826712 TTTATTTAAGAAA
1 TTTATTTAAGAAA
3826725 TTTTGATTCT
Statistics
Matches: 130, Mismatches: 7, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
130 29 0.22
131 7 0.05
132 17 0.13
133 35 0.27
134 42 0.32
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (134 bp):
TTTATTTAAGAAAAATTAATATTTTCAACTTTTTCTTAAAAAATTATTTTAAATATAAATTTTTT
GAAAAATTTTTATTTTCTAAGAAAAATTGATATATTCAACTTTTTCCTTAAAACCTCATTTTTTA
TTGT
Found at i:3828489 original size:30 final size:28
Alignment explanation
Indices: 3828444--3828505 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
3828434 AATCAATAAA
* *
3828444 TTTATAATTTAAATATTATATTATAAAAT
1 TTTAAAATTTAAATATTACATTA-AAAAT
*
3828473 TTTAAAATTCTAAATATTACATTAAATAT
1 TTTAAAATT-TAAATATTACATTAAAAAT
3828502 TTTA
1 TTTA
3828506 TTACAATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAAAATTTAAATATTACATTAAAAAT
Found at i:3829080 original size:29 final size:29
Alignment explanation
Indices: 3829047--3829121 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
3829037 TAATTTTTTT
*
3829047 AAATAAGTTATTATATTTTTG-TTATATGC
1 AAATAAATTATTAT-TTTTTGATTATATGC
* *
3829076 AAATAAATTTTTATTTTTTGATTTATATTC
1 AAATAAATTATTATTTTTTGA-TTATATGC
*
3829106 AAATAAATCATTATTT
1 AAATAAATTATTATTT
3829122 CAAACAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.15
29 12 0.31
30 21 0.54
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.53
Consensus pattern (29 bp):
AAATAAATTATTATTTTTTGATTATATGC
Found at i:3830474 original size:2 final size:2
Alignment explanation
Indices: 3830461--3830491 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3830451 TTTCAATTTA
*
3830461 AT AT AC 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
3830492 GAAAGATGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3830695 original size:22 final size:19
Alignment explanation
Indices: 3830658--3830703 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
3830648 TTATTTAATA
*
3830658 AAAAAAATAAATTAAAAATT
1 AAAAAAATAAAATAAAAA-T
3830678 AAAAAAATGAAAAATAAAAAT
1 AAAAAAAT--AAAATAAAAAT
3830699 AAAAA
1 AAAAA
3830704 TAATTCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 9 0.39
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAAAATAAAATAAAAAT
Found at i:3831011 original size:16 final size:17
Alignment explanation
Indices: 3830988--3831030 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3830978 TGAGTCTGAC
3830988 ATTAAAAAAAT-TAAA-
1 ATTAAAAAAATATAAAT
3831003 ATATAAAAAAATATAAAT
1 AT-TAAAAAAATATAAAT
3831021 ATTAAAAAAA
1 ATTAAAAAAA
3831031 GAGAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 12 0.48
18 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTAAAAAAATATAAAT
Found at i:3831013 original size:17 final size:16
Alignment explanation
Indices: 3830990--3831030 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
3830980 AGTCTGACAT
3830990 TAAAAAAAT-TAAAATA
1 TAAAAAAATAT-AAATA
3831006 TAAAAAAATATAAATA
1 TAAAAAAATATAAATA
3831022 TTAAAAAAA
1 -TAAAAAAA
3831031 GAGAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAAAATATAAATA
Found at i:3849787 original size:29 final size:29
Alignment explanation
Indices: 3849754--3849815 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
3849744 ATGATTTCCC
3849754 TTATAGCTCATGAGATTTAGATATAAATA
1 TTATAGCTCATGAGATTTAGATATAAATA
*
3849783 TTATAGCTCGTGAGATTTAGATATAAATA
1 TTATAGCTCATGAGATTTAGATATAAATA
3849812 TTAT
1 TTAT
3849816 TCAATCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (29 bp):
TTATAGCTCATGAGATTTAGATATAAATA
Found at i:3860693 original size:31 final size:31
Alignment explanation
Indices: 3860641--3860709 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
3860631 TTGAGATAAA
* * *
3860641 ATCAAATAAATTTAATGATTTATGTATTTAT
1 ATCATATAAATTTAATAATTTATATATTTAT
3860672 ATCATATAAATATTAA-AATTTATATATTTAT
1 ATCATATAAAT-TTAATAATTTATATATTTAT
*
3860703 ATTATAT
1 ATCATAT
3860710 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
ATCATATAAATTTAATAATTTATATATTTAT
Found at i:3860709 original size:13 final size:13
Alignment explanation
Indices: 3860691--3860748 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
3860681 ATATTAAAAT
3860691 TTATATATTTATA
1 TTATATATTTATA
3860704 TTATAT-TTTA-A
1 TTATATATTTATA
* * *
3860715 ATAAAAATTATATA
1 TTATATATT-TATA
3860729 TTATA-ATTTATGA
1 TTATATATTTAT-A
3860742 TTATATA
1 TTATATA
3860749 AAAATATACA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
11 4 0.11
12 9 0.26
13 17 0.49
14 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:3860713 original size:20 final size:19
Alignment explanation
Indices: 3860690--3860747 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
3860680 AATATTAAAA
3860690 TTTATATATTTATATTATAT
1 TTTATA-ATTTATATTATAT
** *
3860710 TTTA-AATAAAAATTATAT
1 TTTATAATTTATATTATAT
*
3860728 ATTATAATTTATGATTATAT
1 TTTATAATTTAT-ATTATAT
3860748 AAAAATATAC
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 13 0.45
19 5 0.17
20 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTATAATTTATATTATAT
Found at i:3860720 original size:31 final size:30
Alignment explanation
Indices: 3860685--3860827 Score: 89
Period size: 30 Copynumber: 4.7 Consensus size: 30
3860675 ATATAAATAT
3860685 TAAAATTTATATATTTATATTATATTTTAAA
1 TAAAA-TTATATATTTATATTATATTTTAAA
* *
3860716 TAAAAATTATATA-TTATAATT-TATGATTATA
1 T-AAAATTATATATTTAT-ATTATAT-TTTAAA
* * * * *
3860747 TAAAAATATACATTATATTTTTTATTTT-AT
1 TAAAATTATATATT-TATATTATATTTTAAA
* * *
3860777 TAAAATCATATAATTATTATTATTTTTTAAA
1 TAAAATTATATATTTA-TATTATATTTTAAA
* *
3860808 TTATATT-TATA-TTATATTAT
1 TAAAATTATATATTTATATTAT
3860828 TATATCATAT
Statistics
Matches: 85, Mismatches: 19, Indels: 19
0.69 0.15 0.15
Matches are distributed among these distances:
28 6 0.07
29 5 0.06
30 38 0.45
31 26 0.31
32 10 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TAAAATTATATATTTATATTATATTTTAAA
Found at i:3861341 original size:33 final size:32
Alignment explanation
Indices: 3861282--3861373 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 32
3861272 TCAATGAATG
* *
3861282 ATAAAATTAATTGTAGTAAAATTAAAAATATT
1 ATAAAATTAATTATAGTAAAATTAAAAAAATT
* *
3861314 ATAAAATTTATTATAGTTATAATTAAAAAAATT
1 ATAAAATTAATTATAG-TAAAATTAAAAAAATT
* *
3861347 ATTAAAGTTGATTA-A--AAAATTAAAAAA
1 A-TAAAATTAATTATAGTAAAATTAAAAAA
3861374 TTTTAATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.22
32 14 0.27
33 16 0.31
34 10 0.20
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (32 bp):
ATAAAATTAATTATAGTAAAATTAAAAAAATT
Found at i:3862499 original size:28 final size:27
Alignment explanation
Indices: 3862468--3862526 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
3862458 TGAATTATAA
*
3862468 TAATGTTTAAATTAAAAAATTT-TTAAT
1 TAATATTTAAATT-AAAAATTTATTAAT
* *
3862495 GTAATATTTGAATTATAAATTTATTAAT
1 -TAATATTTAAATTAAAAATTTATTAAT
3862523 TAAT
1 TAAT
3862527 TAACGTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
TAATATTTAAATTAAAAATTTATTAAT
Found at i:3862611 original size:27 final size:29
Alignment explanation
Indices: 3862581--3862634 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
3862571 TAAATATTAA
* *
3862581 ATTAGA-TAATAA-ATTTATAATTCAAGT
1 ATTAGATTAAAAATATTTAAAATTCAAGT
*
3862608 ATTATATTAAAAATATTTAAAATTCAA
1 ATTAGATTAAAAATATTTAAAATTCAA
3862635 ATACTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 5 0.23
29 12 0.55
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (29 bp):
ATTAGATTAAAAATATTTAAAATTCAAGT
Found at i:3862682 original size:18 final size:18
Alignment explanation
Indices: 3862616--3862682 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
3862606 GTATTATATT
*
3862616 AAAAA-TATTTAAAATTC
1 AAAAATTATTTATAATTC
* * *
3862633 AAATACTATATAT-ATT-
1 AAAAATTATTTATAATTC
* *
3862649 AAACATTTTATTATAATTC
1 AAAAATTAT-TTATAATTC
3862668 AAAAATTATTTATAA
1 AAAAATTATTTATAA
3862683 CATTAATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
16 6 0.16
17 10 0.27
18 14 0.38
19 7 0.19
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATTATTTATAATTC
Found at i:3863964 original size:4 final size:4
Alignment explanation
Indices: 3863957--3863994 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
3863947 TACATTATTT
**
3863957 ATAA ATAA ATAA ATAA ATAA ATAA ATTG ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
3863995 CCCTTTACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:3869764 original size:25 final size:25
Alignment explanation
Indices: 3869717--3869764 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3869707 CACAGAGAGG
* *
3869717 GAGAACAAAACAAACAGAGAACAAA
1 GAGAACAAAACAAACAAAAAACAAA
* *
3869742 GAGATCAAAAGAAACAAAAAACA
1 GAGAACAAAACAAACAAAAAACA
3869765 TGGCACAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.02
Consensus pattern (25 bp):
GAGAACAAAACAAACAAAAAACAAA
Found at i:3879390 original size:12 final size:12
Alignment explanation
Indices: 3879365--3879430 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
3879355 TATATATAAA
3879365 AATTATTT-TTT
1 AATTATTTATTT
3879376 AATTATTTATTT
1 AATTATTTATTT
*
3879388 AATT-TTGTATAT
1 AATTATT-TATTT
*
3879400 ATATTATATATTT
1 A-ATTATTTATTT
3879413 AATT-TTATATTT
1 AATTATT-TATTT
3879425 ATATTA
1 A-ATTA
3879431 AAAATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
11 11 0.25
12 21 0.48
13 11 0.25
14 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:3879405 original size:25 final size:25
Alignment explanation
Indices: 3879377--3879430 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
3879367 TTATTTTTTA
* *
3879377 ATTATTTATTTAATTTTGTATATAT
1 ATTATATATTTAATTTTATATATAT
*
3879402 ATTATATATTTAATTTTATATTTAT
1 ATTATATATTTAATTTTATATATAT
3879427 ATTA
1 ATTA
3879431 AAAATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTATATATTTAATTTTATATATAT
Found at i:3879440 original size:18 final size:17
Alignment explanation
Indices: 3879419--3879462 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
3879409 ATTTAATTTT
3879419 ATATTTATATTAAAAATA
1 ATATTTATATTAAAAA-A
3879437 ATATTTTATATTAAAAAA
1 ATA-TTTATATTAAAAAA
3879455 ATATTTAT
1 ATATTTAT
3879463 TATTTTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.20
18 7 0.28
19 13 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTTATATTAAAAAA
Found at i:3879466 original size:18 final size:19
Alignment explanation
Indices: 3879419--3879466 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
3879409 ATTTAATTTT
3879419 ATATTTA-TATTAAAAATA
1 ATATTTATTATTAAAAATA
3879437 ATATTT-TATATTAAAAA-A
1 ATATTTAT-TATTAAAAATA
3879455 ATATTTATTATT
1 ATATTTATTATT
3879467 TTGAGATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTTATTATTAAAAATA
Found at i:3883267 original size:20 final size:20
Alignment explanation
Indices: 3883227--3883268 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3883217 TTAAATTATT
* * *
3883227 ATAAATTAGTAATTTACATA
1 ATAAATTAGTAAGTCAAATA
3883247 ATAAATTAGTAAGTCAAATA
1 ATAAATTAGTAAGTCAAATA
3883267 AT
1 AT
3883269 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
ATAAATTAGTAAGTCAAATA
Found at i:3883599 original size:16 final size:15
Alignment explanation
Indices: 3883574--3883622 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3883564 AAAATAATTT
* *
3883574 TAAAAATAATAATATA
1 TAAAATTAATAA-AAA
3883590 TAAAATTAATAAAAA
1 TAAAATTAATAAAAA
3883605 TAAAATATTAATAAAAA
1 T-AAA-ATTAATAAAAA
3883622 T
1 T
3883623 GATTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 14 0.48
17 12 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATTAATAAAAA
Found at i:3883631 original size:17 final size:16
Alignment explanation
Indices: 3883574--3883622 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
3883564 AAAATAATTT
*
3883574 TAAAAA-TAAT-AATA
1 TAAAAATTAATAAAAA
3883588 TATAAAATTAATAAAAA
1 TA-AAAATTAATAAAAA
3883605 TAAAATATTAATAAAAA
1 TAAAA-ATTAATAAAAA
3883622 T
1 T
3883623 GATTAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 4 0.13
16 7 0.23
17 17 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATTAATAAAAA
Found at i:3884706 original size:11 final size:11
Alignment explanation
Indices: 3884689--3884727 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3884679 TATTATAAAC
3884689 AAATAACAAAT
1 AAATAACAAAT
*
3884700 GAATAACAAAT
1 AAATAACAAAT
* *
3884711 AAATAATAAAC
1 AAATAACAAAT
3884722 AAATAA
1 AAATAA
3884728 AATTTAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAACAAAT
Found at i:3887047 original size:2 final size:2
Alignment explanation
Indices: 3887040--3887075 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3887030 AAGTCATGGG
* *
3887040 AT AT AT AT AT AT AT AT AT CT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3887076 TCTTTGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3889064 original size:23 final size:23
Alignment explanation
Indices: 3889034--3889080 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3889024 GTCAACTTGT
3889034 TGTTTGGACTAATCTTAGTTATC
1 TGTTTGGACTAATCTTAGTTATC
3889057 TGTTTGGACTAATCTTAGTTATC
1 TGTTTGGACTAATCTTAGTTATC
3889080 T
1 T
3889081 TACATAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (23 bp):
TGTTTGGACTAATCTTAGTTATC
Found at i:3896376 original size:2 final size:2
Alignment explanation
Indices: 3896365--3896396 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3896355 TAAAAGCCTG
3896365 AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3896397 GCATAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3898262 original size:16 final size:16
Alignment explanation
Indices: 3898243--3898276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3898233 CAAAATAAAT
3898243 AAATAATAAAAAATTA
1 AAATAATAAAAAATTA
* *
3898259 AAATATTTAAAAATTA
1 AAATAATAAAAAATTA
3898275 AA
1 AA
3898277 TCAATTTGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAAAAATTA
Found at i:3900386 original size:25 final size:26
Alignment explanation
Indices: 3900358--3900423 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
3900348 ATTAATTATC
3900358 TAATGATGAAATTTTTA-AAAATTTT
1 TAATGATGAAATTTTTATAAAATTTT
* *
3900383 TAATGGT-AAATTTCTATAAAATTTT
1 TAATGATGAAATTTTTATAAAATTTT
*
3900408 TAGGTGA-GAAATTTTT
1 TA-ATGATGAAATTTTT
3900424 GTTTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 8 0.24
25 16 0.48
26 9 0.27
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (26 bp):
TAATGATGAAATTTTTATAAAATTTT
Found at i:3905891 original size:3 final size:3
Alignment explanation
Indices: 3905885--3905941 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
3905875 ATCATTCCCC
3905885 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3905933 ATT ATT ATT
1 ATT ATT ATT
3905942 TGTGGATTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3908064 original size:22 final size:22
Alignment explanation
Indices: 3908039--3908089 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3908029 GTTAATTTTT
*
3908039 ATTTTATTATTTTATAGCAAAA-
1 ATTTTATTATTGTATAG-AAAAC
* *
3908061 ATTTTTTTATTGTATTGAAAAC
1 ATTTTATTATTGTATAGAAAAC
3908083 ATTTTAT
1 ATTTTAT
3908090 AAATACTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (22 bp):
ATTTTATTATTGTATAGAAAAC
Found at i:3912445 original size:24 final size:24
Alignment explanation
Indices: 3912414--3912466 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3912404 GCTGGATCCT
3912414 AAAA-CATACACCTTCAATAGAGA
1 AAAAGCATACACCTTCAATAGAGA
* *
3912437 AAAAGCATACATCTTCAATAGAGT
1 AAAAGCATACACCTTCAATAGAGA
3912461 AAAAGC
1 AAAAGC
3912467 TTCCATGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (24 bp):
AAAAGCATACACCTTCAATAGAGA
Found at i:3916015 original size:24 final size:25
Alignment explanation
Indices: 3915971--3916021 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
3915961 TTTTTTAAAT
*
3915971 AATTACAAAAATAAAC-TAAAATAA
1 AATTACAAAAATAAACAAAAAATAA
*
3915995 AATTA-AAAAATCAACAAAAAAATAA
1 AATTACAAAAATAAAC-AAAAAATAA
3916020 AA
1 AA
3916022 AAAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.18
Consensus pattern (25 bp):
AATTACAAAAATAAACAAAAAATAA
Found at i:3916932 original size:18 final size:19
Alignment explanation
Indices: 3916909--3916953 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3916899 AAATACATTT
3916909 TAAAATTAAATTTA-AAAA
1 TAAAATTAAATTTATAAAA
**
3916927 TAAAATTTTATTTATAAAA
1 TAAAATTAAATTTATAAAA
3916946 TAATAATT
1 TAA-AATT
3916954 CAAGACATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 7 0.30
20 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATTAAATTTATAAAA
Found at i:3917954 original size:16 final size:16
Alignment explanation
Indices: 3917930--3917960 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3917920 ATTCAATAAA
*
3917930 AATATAAAATAAAAAG
1 AATACAAAATAAAAAG
3917946 AATACAAAATAAAAA
1 AATACAAAATAAAAA
3917961 ACGTTAATAT
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:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
AATACAAAATAAAAAG
Found at i:3925400 original size:15 final size:16
Alignment explanation
Indices: 3925370--3925411 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3925360 TTGATAATTT
3925370 GAAAAAATTAAAAATA
1 GAAAAAATTAAAAATA
*
3925386 GAAAAAA-TAAGAATA
1 GAAAAAATTAAAAATA
3925401 -AAAATAATTAA
1 GAAAA-AATTAA
3925412 TAAAAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
GAAAAAATTAAAAATA
Found at i:3925413 original size:13 final size:12
Alignment explanation
Indices: 3925388--3925423 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
3925378 TAAAAATAGA
3925388 AAAAATAAGAAT
1 AAAAATAAGAAT
*
3925400 AAAAATAATTAAT
1 AAAAATAA-GAAT
3925413 AAAAATAAGAA
1 AAAAATAAGAA
3925424 AAGAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
AAAAATAAGAAT
Found at i:3926070 original size:3 final size:3
Alignment explanation
Indices: 3926064--3926089 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3926054 CAACAACAAC
3926064 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3926090 AAGAAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3926612 original size:18 final size:18
Alignment explanation
Indices: 3926591--3926625 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3926581 AAAAAAATCA
* *
3926591 AAAATAAAAAATAAATTG
1 AAAACAAAAAAGAAATTG
3926609 AAAACAAAAAAGAAATT
1 AAAACAAAAAAGAAATT
3926626 TCATATGTAT
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:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAACAAAAAAGAAATTG
Found at i:3933575 original size:19 final size:19
Alignment explanation
Indices: 3933551--3933587 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3933541 TTTTATTTAA
3933551 TTTTAAT-TTTATAAAATAT
1 TTTTAATATTT-TAAAATAT
3933570 TTTTAATATTTTAAAATA
1 TTTTAATATTTTAAAATA
3933588 AATAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATATTTTAAAATAT
Found at i:3951109 original size:4 final size:4
Alignment explanation
Indices: 3951094--3951157 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
3951084 TACAATGTCC
* * * * * * * *
3951094 ATAT ACAT ATAT ATAT ATAT GTAT GTAT ACAT ACAT ATAC GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
3951142 ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT
3951158 TAAATCTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:3951111 original size:6 final size:6
Alignment explanation
Indices: 3951094--3951157 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
3951084 TACAATGTCC
* * * * * ** *
3951094 ATATAC ATATAT ATATAT ATGTAT GTATAC ATACAT ATACGT ATGTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
3951142 ATATAT ATATAT ATAT
1 ATATAT ATATAT ATAT
3951158 TAAATCTATG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:3951113 original size:10 final size:10
Alignment explanation
Indices: 3951094--3951157 Score: 56
Period size: 10 Copynumber: 6.4 Consensus size: 10
3951084 TACAATGTCC
*
3951094 ATATACATAT
1 ATATATATAT
3951104 ATATATATAT
1 ATATATATAT
* * *
3951114 GTATGTATAC
1 ATATATATAT
* *
3951124 ATACATATAC
1 ATATATATAT
* *
3951134 GTATGTATAT
1 ATATATATAT
3951144 ATATATATAT
1 ATATATATAT
3951154 ATAT
1 ATAT
3951158 TAAATCTATG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:3951115 original size:24 final size:22
Alignment explanation
Indices: 3951094--3951157 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
3951084 TACAATGTCC
3951094 ATATACATATATATATATATGT
1 ATATACATATATATATATATGT
* **
3951116 ATGTATACATACATATACGTATGT
1 A--TATACATATATATATATATGT
*
3951140 ATATATATATATATATAT
1 ATATACATATATATATAT
3951158 TAAATCTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 14 0.42
24 19 0.58
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (22 bp):
ATATACATATATATATATATGT
Found at i:3951137 original size:20 final size:20
Alignment explanation
Indices: 3951108--3951152 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3951098 ACATATATAT
*
3951108 ATATATGTATGTATACATAC
1 ATATACGTATGTATACATAC
* *
3951128 ATATACGTATGTATATATAT
1 ATATACGTATGTATACATAC
3951148 ATATA
1 ATATA
3951153 TATATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (20 bp):
ATATACGTATGTATACATAC
Found at i:3956858 original size:24 final size:25
Alignment explanation
Indices: 3956803--3956852 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
3956793 AATAATAATT
3956803 TAAAATTTTATTATTTTATTATAAA
1 TAAAATTTTATTATTTTATTATAAA
3956828 TAAAATTTTAATT-TTTTATT-TAAA
1 TAAAATTTT-ATTATTTTATTATAAA
3956852 T
1 T
3956853 TGAATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.21
25 16 0.67
26 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAAAATTTTATTATTTTATTATAAA
Found at i:3963549 original size:14 final size:15
Alignment explanation
Indices: 3963522--3963550 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3963512 GAAGTGAGAG
3963522 GGAGAAGAGGGAGGA
1 GGAGAAGAGGGAGGA
3963537 GGAGAAG-GGGAGGA
1 GGAGAAGAGGGAGGA
3963551 ATTGGGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (15 bp):
GGAGAAGAGGGAGGA
Found at i:3963688 original size:15 final size:14
Alignment explanation
Indices: 3963665--3963735 Score: 70
Period size: 15 Copynumber: 4.8 Consensus size: 14
3963655 GAGGGGCAGG
3963665 GGAAGAGGAGGAGA
1 GGAAGAGGAGGAGA
3963679 GGAGAGAGGAAGGAGA
1 GGA-AGAGG-AGGAGA
* *
3963695 GGAAGGGGAAGGGGA
1 GGAAGAGG-AGGAGA
* *
3963710 GGAAGTGGGAGGAGG
1 GGAAG-AGGAGGAGA
3963725 GGAAGAGGAGG
1 GGAAGAGGAGG
3963736 CAGGGGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
14 8 0.16
15 29 0.59
16 12 0.24
ACGTcount: A:0.37, C:0.00, G:0.62, T:0.01
Consensus pattern (14 bp):
GGAAGAGGAGGAGA
Found at i:3963708 original size:42 final size:42
Alignment explanation
Indices: 3963623--3963709 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 42
3963613 TGGCGAGGAA
* *
3963623 GGAAAGGAGGGAGGCGAGAGTGAAGAAGAGGAGAGGGGCAGG
1 GGAAAGGAGGGAGGAGAGAGTGAAGAAGAGGAGAGGGGAAGG
*
3963665 GGAAGAGGAGGAGAGGAGAGAG-GAAGGAGAGGA-AGGGGAAGG
1 GGAA-AGGAGG-GAGGAGAGAGTGAAGAAGAGGAGAGGGGAAGG
3963707 GGA
1 GGA
3963710 GGAAGTGGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 15 0.38
43 16 0.40
44 9 0.22
ACGTcount: A:0.38, C:0.02, G:0.59, T:0.01
Consensus pattern (42 bp):
GGAAAGGAGGGAGGAGAGAGTGAAGAAGAGGAGAGGGGAAGG
Found at i:3963711 original size:24 final size:24
Alignment explanation
Indices: 3963668--3963735 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
3963658 GGGCAGGGGA
* *
3963668 AGAGGAGGAGAGGAGAGAGGAAG-G
1 AGAGGAGGGGAAGAG-GAGGAAGTG
*
3963692 AGAGGAAGGGGAAGGGGAGGAAGTG
1 AGAGG-AGGGGAAGAGGAGGAAGTG
*
3963717 GGAGGAGGGGAAGAGGAGG
1 AGAGGAGGGGAAGAGGAGG
3963736 CAGGGGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 25 0.68
25 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.62, T:0.01
Consensus pattern (24 bp):
AGAGGAGGGGAAGAGGAGGAAGTG
Found at i:3963740 original size:15 final size:14
Alignment explanation
Indices: 3963662--3963743 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 14
3963652 GGAGAGGGGC
3963662 AGGGGAAGAGGAGG
1 AGGGGAAGAGGAGG
*
3963676 AGAGGAGAGAGGAAGG
1 AGGGGA-AGAGG-AGG
* *
3963692 AGAGGAAGGGGAAGG
1 AGGGGAAGAGG-AGG
*
3963707 -GGAGGAAGTGGGAGG
1 AGG-GGAAG-AGGAGG
3963722 AGGGGAAGAGGAGG
1 AGGGGAAGAGGAGG
3963736 CAGGGGAA
1 -AGGGGAA
3963744 AAGAGGGAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
14 11 0.19
15 33 0.57
16 14 0.24
ACGTcount: A:0.37, C:0.01, G:0.61, T:0.01
Consensus pattern (14 bp):
AGGGGAAGAGGAGG
Found at i:3969505 original size:16 final size:16
Alignment explanation
Indices: 3969476--3969514 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3969466 TAATTTTTAG
* *
3969476 TATTTTATTTAATTAA
1 TATTTAATTGAATTAA
3969492 TATTTAATTGAATTAA
1 TATTTAATTGAATTAA
*
3969508 AATTTAA
1 TATTTAA
3969515 AATAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TATTTAATTGAATTAA
Found at i:3971308 original size:14 final size:15
Alignment explanation
Indices: 3971294--3971349 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
3971284 AAATGCCATT
3971294 AATTTTAAAATATTA
1 AATTTTAAAATATTA
* *
3971309 AAATTT-AAATTTTA
1 AATTTTAAAATATTA
* *
3971323 AATTTATTAAATATCA
1 AATTT-TAAAATATTA
*
3971339 TATTTTAAAAT
1 AATTTTAAAAT
3971350 TACCTAACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 11 0.34
15 11 0.34
16 10 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTAAAATATTA
Found at i:3984747 original size:11 final size:11
Alignment explanation
Indices: 3984731--3984756 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3984721 ATACTATAAT
3984731 ATAATATAAAA
1 ATAATATAAAA
3984742 ATAATATAAAA
1 ATAATATAAAA
3984753 ATAA
1 ATAA
3984757 ATGATACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:3989399 original size:3 final size:3
Alignment explanation
Indices: 3989391--3989430 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3989381 TGACACAAAC
3989391 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3989431 TTTGATGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3993243 original size:22 final size:22
Alignment explanation
Indices: 3993218--3993261 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3993208 TGTATATTTA
*
3993218 TATTTGTATCTCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
3993240 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
3993262 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:3997177 original size:22 final size:22
Alignment explanation
Indices: 3997151--3997194 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3997141 TGTATATTTA
*
3997151 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3997173 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3997195 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:4003632 original size:14 final size:14
Alignment explanation
Indices: 4003610--4003648 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4003600 TACAACAAAG
4003610 ACAAGCATAATGAA
1 ACAAGCATAATGAA
* * *
4003624 ACAATCATAGTGAG
1 ACAAGCATAATGAA
4003638 ACAAGCATAAT
1 ACAAGCATAAT
4003649 CAAATTCATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (14 bp):
ACAAGCATAATGAA
Found at i:4008714 original size:63 final size:62
Alignment explanation
Indices: 4008621--4008811 Score: 172
Period size: 63 Copynumber: 3.0 Consensus size: 62
4008611 AAAATATAAG
* * * ** *
4008621 AAGATTATTTAAGATGTTTTTTATCTAAAAATACATTAAATAATCTTTAATTTTATTTTAAAT
1 AAGATTATTTAAGGTATTTTTGATAAAAAAATACATTAAATAATCTTTAATTTT-TTTTAAAA
* *
4008684 GAGATTATTTAAGGTATTTTTGATAAAAAAAATATCA-TAAATAATGCTCTTCAA-TTTTTTGAA
1 AAGATTATTTAAGGTATTTTTGAT-AAAAAAATA-CATTAAATAAT-CT-TT-AATTTTTTTTAA
4008747 AA
61 AA
* * * * * * *
4008749 AATATTATTTAATGAATTTTTGA-AAAAAAATACCTTAAATAATATCTAATATTTTTTAAAA
1 AAGATTATTTAAGGTATTTTTGATAAAAAAATACATTAAATAATCTTTAATTTTTTTTAAAA
4008810 AA
1 AA
4008812 TTAAAACACC
Statistics
Matches: 104, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
60 2 0.02
61 12 0.12
62 2 0.02
63 37 0.36
64 15 0.14
65 29 0.28
66 5 0.05
67 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (62 bp):
AAGATTATTTAAGGTATTTTTGATAAAAAAATACATTAAATAATCTTTAATTTTTTTTAAAA
Found at i:4010104 original size:27 final size:28
Alignment explanation
Indices: 4010039--4010108 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 28
4010029 ATGTAGACGA
*
4010039 TTTATTTAATTAAA-CCATTAAAATATT
1 TTTATTTAATTAAATTCATTAAAATATT
* *
4010066 ATT-TTTAATTAAATTCA-TAAAGTATT
1 TTTATTTAATTAAATTCATTAAAATATT
4010092 TTTATTTAATTAAATTC
1 TTTATTTAATTAAATTC
4010109 CTATTTTCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 20 0.54
27 17 0.46
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTATTTAATTAAATTCATTAAAATATT
Found at i:4023714 original size:53 final size:54
Alignment explanation
Indices: 4023643--4023748 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 54
4023633 CGATTTGTGA
*
4023643 ATTGACAAAAAACTATCTCCTGCTTGAACTTTCAATTTGATGTAGATTACAGGG
1 ATTGACAAAAAACCATCTCCTGCTTGAACTTTCAATTTGATGTAGATTACAGGG
4023697 ATTGAC-AAAAACCATCTCCTGCTTGAACTTTCAATTTGATGTAGATTACAGG
1 ATTGACAAAAAACCATCTCCTGCTTGAACTTTCAATTTGATGTAGATTACAGG
4023749 TGGTTTTGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 45 0.88
54 6 0.12
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (54 bp):
ATTGACAAAAAACCATCTCCTGCTTGAACTTTCAATTTGATGTAGATTACAGGG
Found at i:4024882 original size:56 final size:53
Alignment explanation
Indices: 4024815--4024924 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 53
4024805 GTGATTTGGT
* *
4024815 GGGGAATATAATAATATAAAATGATCACAGTAGTATTGTTGAAGCCTTTACTGCCA
1 GGGGAATATAAT-A-ATAAAATAATCA-AGAAGTATTGTTGAAGCCTTTACTGCCA
* * * *
4024871 GGGGTATATAATAATAAAGTAATCATGAAGTATTGTTGAAGCTTTTACTGCCA
1 GGGGAATATAATAATAAAATAATCAAGAAGTATTGTTGAAGCCTTTACTGCCA
4024924 G
1 G
4024925 TTTCCTGCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 26 0.54
54 10 0.21
55 1 0.02
56 11 0.23
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (53 bp):
GGGGAATATAATAATAAAATAATCAAGAAGTATTGTTGAAGCCTTTACTGCCA
Found at i:4025573 original size:13 final size:13
Alignment explanation
Indices: 4025555--4025580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4025545 TTATCATTAC
4025555 TACTGATAATTTA
1 TACTGATAATTTA
4025568 TACTGATAATTTA
1 TACTGATAATTTA
4025581 GAATGTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TACTGATAATTTA
Found at i:4025883 original size:83 final size:83
Alignment explanation
Indices: 4025793--4025957 Score: 258
Period size: 83 Copynumber: 2.0 Consensus size: 83
4025783 ATAGATTTAA
* * *
4025793 TTTTTATATCTTTTATTTTTTATTTCAAAATATTATTAAAATTTATTTTTATTCTGACTAAATAT
1 TTTTTATATCTTTTATTTTTTATTTCAAAATATTATTAAAATTTATTTTTATTCTAAATAAACAT
* *
4025858 GTTTGAATAGAGAAAAAT
66 ATTTGAATAGAAAAAAAT
***
4025876 TTTTTATATCTTTTATTTTTTATTTTGTAATATTATTAAAATTTATTTTTATTCTAAATAAACAT
1 TTTTTATATCTTTTATTTTTTATTTCAAAATATTATTAAAATTTATTTTTATTCTAAATAAACAT
4025941 ATTTGAATAGAAAAAAA
66 ATTTGAATAGAAAAAAA
4025958 ATATGATAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (83 bp):
TTTTTATATCTTTTATTTTTTATTTCAAAATATTATTAAAATTTATTTTTATTCTAAATAAACAT
ATTTGAATAGAAAAAAAT
Found at i:4025983 original size:83 final size:83
Alignment explanation
Indices: 4025821--4025983 Score: 177
Period size: 83 Copynumber: 2.0 Consensus size: 83
4025811 TTTATTTCAA
* * * * ** * *
4025821 AATATTATTAAAATTTATTTTTATTCTGACTAAATATGTTTGAATAGAGAAAAATTTTTTATATC
1 AATATTATTAAAATTTATTTTTATTCTAAATAAACATATTTGAATAGAGAAAAAAATATGATATC
** ** *
4025886 TTTTATTTTTTATTTTGT
66 TAATATAATATATTTTGT
4025904 AATATTATTAAAATTTATTTTTATTCTAAATAAACATATTTGAATAGA-AAAAAAATATGATAGT
1 AATATTATTAAAATTTATTTTTATTCTAAATAAACATATTTGAATAGAGAAAAAAATATGATA-T
4025968 CTGAATA-AATATATTT
65 CT-AATATAATATATTT
4025984 GAATAAAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
82 10 0.15
83 53 0.82
84 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (83 bp):
AATATTATTAAAATTTATTTTTATTCTAAATAAACATATTTGAATAGAGAAAAAAATATGATATC
TAATATAATATATTTTGT
Found at i:4025995 original size:18 final size:18
Alignment explanation
Indices: 4025974--4026034 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
4025964 TAGTCTGAAT
4025974 AAATATATTTGAATAAAA
1 AAATATATTTGAATAAAA
* **
4025992 AAATATGA-CTGTTTAAATA
1 AAATAT-ATTTGAATAAA-A
* *
4026011 AAATTTATTTAAATAAAA
1 AAATATATTTGAATAAAA
4026029 AAATAT
1 AAATAT
4026035 GTCTATATAA
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
18 19 0.61
19 12 0.39
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATATATTTGAATAAAA
Found at i:4025999 original size:36 final size:36
Alignment explanation
Indices: 4025928--4026035 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 36
4025918 TTATTTTTAT
*
4025928 TCTAAATAAACATATTTGAATAGAAAAAAAATATGA-TAG
1 TCTAAATAAATATATTTGAAT---AAAAAAATATGACT-G
*
4025967 TCTGAATAAATATATTTGAATAAAAAAATATGACTG
1 TCTAAATAAATATATTTGAATAAAAAAATATGACTG
* * *
4026003 TTTAAATAAAATTTATTTAAATAAAAAAATATG
1 TCTAAAT-AAATATATTTGAATAAAAAAATATG
4026036 TCTATATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
36 18 0.30
37 24 0.39
39 19 0.31
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (36 bp):
TCTAAATAAATATATTTGAATAAAAAAATATGACTG
Found at i:4026031 original size:39 final size:38
Alignment explanation
Indices: 4025928--4026031 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 38
4025918 TTATTTTTAT
*
4025928 TCTAAATAAACATATTTGAATAGAAAAAAAATATGATAG
1 TCTAAATAAATATATTTGAATA-AAAAAAAATATGATAG
*
4025967 TCTGAATAAATATATTTGAAT--AAAAAAATATGACT-G
1 TCTAAATAAATATATTTGAATAAAAAAAAATATGA-TAG
* * *
4026003 TTTAAATAAAATTTATTTAAATAAAAAAA
1 TCTAAAT-AAATATATTTGAATAAAAAAA
4026032 TATGTCTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
36 18 0.33
37 13 0.24
39 24 0.44
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (38 bp):
TCTAAATAAATATATTTGAATAAAAAAAAATATGATAG
Found at i:4026044 original size:18 final size:18
Alignment explanation
Indices: 4025986--4026046 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
4025976 ATATATTTGA
* *
4025986 ATAAAAAAATATGACTGT
1 ATAAAAAAATATGTCTAT
* * * * *
4026004 TTAAATAAAATTTATTTAA
1 ATAAA-AAAATATGTCTAT
4026023 ATAAAAAAATATGTCTAT
1 ATAAAAAAATATGTCTAT
4026041 ATAAAA
1 ATAAAA
4026047 TATAATGACT
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
ATAAAAAAATATGTCTAT
Found at i:4029632 original size:21 final size:21
Alignment explanation
Indices: 4029588--4029626 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4029578 TTATCAAAAT
*
4029588 TTAAAATTTAAAATTTAATCA
1 TTAAAATTTAAAAGTTAATCA
4029609 TTAAAA-TTAAAAGTTAAT
1 TTAAAATTTAAAAGTTAAT
4029627 ATATTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
TTAAAATTTAAAAGTTAATCA
Found at i:4043625 original size:45 final size:45
Alignment explanation
Indices: 4043574--4043664 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
4043564 TATTTAAATT
*
4043574 ATTTCATTAAAAATTAAAATTTTTGGATGTATGGAGAAAAAAGTA
1 ATTTCATTAAAAATAAAAATTTTTGGATGTATGGAGAAAAAAGTA
*
4043619 ATTTCATTAAAAATAAAAATTTTTGGATGTATTGAGAAAAAAGTA
1 ATTTCATTAAAAATAAAAATTTTTGGATGTATGGAGAAAAAAGTA
4043664 A
1 A
4043665 GGGTATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.35
Consensus pattern (45 bp):
ATTTCATTAAAAATAAAAATTTTTGGATGTATGGAGAAAAAAGTA
Found at i:4047507 original size:14 final size:14
Alignment explanation
Indices: 4047488--4047516 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4047478 GAATATTACT
4047488 TCTTAAAGTGATTA
1 TCTTAAAGTGATTA
4047502 TCTTAAAGTGATTA
1 TCTTAAAGTGATTA
4047516 T
1 T
4047517 ATGAACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TCTTAAAGTGATTA
Found at i:4050433 original size:158 final size:158
Alignment explanation
Indices: 4050145--4050463 Score: 602
Period size: 158 Copynumber: 2.0 Consensus size: 158
4050135 TTTACTTAGA
** *
4050145 TTAGGTGAGGTGCAATTCTTCAGAAATTTTTTCTTTCCATAATGTCCTAAACTCTGCAATGGAAC
1 TTAGGTGAGGTGCAATTCTTCAGAAACATGTTCTTTCCATAATGTCCTAAACTCTGCAATGGAAC
4050210 TGAATTGACTAATTTGGAAATTAATAAAGCAAACTACTCCTTCAGGGTTTTCGTGGAAGCAAAGC
66 TGAATTGACTAATTTGGAAATTAATAAAGCAAACTACTCCTTCAGGGTTTTCGTGGAAGCAAAGC
4050275 TTCCCCTCCCTCCTTTTGCACTATTTAT
131 TTCCCCTCCCTCCTTTTGCACTATTTAT
4050303 TTAGGTGAGGTGCAATTCTTCAGAAACATGTTCTTTCCATAATGTCCTAAACTCTGCAATGGAAC
1 TTAGGTGAGGTGCAATTCTTCAGAAACATGTTCTTTCCATAATGTCCTAAACTCTGCAATGGAAC
*
4050368 TGAATTGACTAATTTGGAAATTAATAAAGCAAACTACTCCTTCAGGGTTTTTGTGGAAGCAAAGC
66 TGAATTGACTAATTTGGAAATTAATAAAGCAAACTACTCCTTCAGGGTTTTCGTGGAAGCAAAGC
4050433 TTCCCCTCCCTCCTTTTGCACTATTTAT
131 TTCCCCTCCCTCCTTTTGCACTATTTAT
4050461 TTA
1 TTA
4050464 TTTTTGAGTT
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
158 157 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (158 bp):
TTAGGTGAGGTGCAATTCTTCAGAAACATGTTCTTTCCATAATGTCCTAAACTCTGCAATGGAAC
TGAATTGACTAATTTGGAAATTAATAAAGCAAACTACTCCTTCAGGGTTTTCGTGGAAGCAAAGC
TTCCCCTCCCTCCTTTTGCACTATTTAT
Found at i:4056782 original size:15 final size:14
Alignment explanation
Indices: 4056762--4056796 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
4056752 TAGGACAAAG
4056762 TTATTTGAAAATATT
1 TTATTT-AAAATATT
*
4056777 TTATTTATAATATT
1 TTATTTAAAATATT
4056791 TTATTT
1 TTATTT
4056797 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTATTTAAAATATT
Found at i:4056795 original size:19 final size:17
Alignment explanation
Indices: 4056773--4056809 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
4056763 TATTTGAAAA
4056773 TATTTTATTTATAATATTT
1 TATTTTATTT-TAA-ATTT
4056792 TATTTTATTTTAAATTT
1 TATTTTATTTTAAATTT
4056809 T
1 T
4056810 GTAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTATTTTAAATTT
Found at i:4062465 original size:119 final size:120
Alignment explanation
Indices: 4062329--4062563 Score: 400
Period size: 119 Copynumber: 2.0 Consensus size: 120
4062319 TAAAAAAATT
* * *
4062329 AAATACAATATTTCAATACATTTAAAACTAAGATAAGCATGGAATAGAAGTACATTTAGATAATA
1 AAATACAATATTTCAATACATTTAAAACTAAGATAAGCATGGAATAGAAGTACACTTAAAAAATA
*
4062394 ATAAAACT-CAAAAAAATAGACTTTATTAAACAAACGATAGGGAAAAACATAATG
66 ATAAAACTAAAAAAAAATAGACTTTATTAAACAAACGATAGGGAAAAACATAATG
*
4062448 AAATACCATATTTCAATACATTTAAAACTAAGATAAGCATGGAATAGAAGTACACTTAAAAAATA
1 AAATACAATATTTCAATACATTTAAAACTAAGATAAGCATGGAATAGAAGTACACTTAAAAAATA
* *
4062513 ATAAAACTAAAAAAAAATAGACTTTATTAAACAAATGATAGGGGAAAACAT
66 ATAAAACTAAAAAAAAATAGACTTTATTAAACAAACGATAGGGAAAAACAT
4062564 GTATTCACAA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 69 0.64
120 39 0.36
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (120 bp):
AAATACAATATTTCAATACATTTAAAACTAAGATAAGCATGGAATAGAAGTACACTTAAAAAATA
ATAAAACTAAAAAAAAATAGACTTTATTAAACAAACGATAGGGAAAAACATAATG
Found at i:4067827 original size:7 final size:7
Alignment explanation
Indices: 4067815--4067865 Score: 68
Period size: 7 Copynumber: 7.0 Consensus size: 7
4067805 TTGAGCTCCA
4067815 TTTTTCT
1 TTTTTCT
4067822 TTTTTCT
1 TTTTTCT
4067829 TTTTTCT
1 TTTTTCT
4067836 TTTTT-T
1 TTTTTCT
4067842 TTTTGTCT
1 TTTT-TCT
4067850 TTTTCTCT
1 TTTT-TCT
4067858 GTTTTTCT
1 -TTTTTCT
4067866 AAATAAATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
6 5 0.12
7 20 0.50
8 11 0.28
9 4 0.10
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:4067844 original size:20 final size:22
Alignment explanation
Indices: 4067815--4067863 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
4067805 TTGAGCTCCA
*
4067815 TTTTTCTTTTT-TCTTTTT-TC
1 TTTTTTTTTTTGTCTTTTTCTC
4067835 TTTTTTTTTTTGTCTTTTTCTC
1 TTTTTTTTTTTGTCTTTTTCTC
*
4067857 TGTTTTT
1 TTTTTTT
4067864 CTAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 7 0.28
22 8 0.32
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTTTGTCTTTTTCTC
Found at i:4069701 original size:18 final size:18
Alignment explanation
Indices: 4069678--4069714 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4069668 AACTTCAGAA
4069678 AAGTTTCTCTTCTATATC
1 AAGTTTCTCTTCTATATC
*
4069696 AAGTTTCTCTTGTATATC
1 AAGTTTCTCTTCTATATC
4069714 A
1 A
4069715 CTCTATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (18 bp):
AAGTTTCTCTTCTATATC
Found at i:4069906 original size:250 final size:250
Alignment explanation
Indices: 4069474--4069924 Score: 682
Period size: 250 Copynumber: 1.8 Consensus size: 250
4069464 ACCTTATATT
4069474 AATTTAAAACTAAATTTAAAGTAATTTATCTTTTTCAATTTATCTGCAATTAACATAAATACTTA
1 AATTTAAAACTAAATTTAAAGTAATTTATCTTTTTCAATTTATCTGCAATTAACATAAATACTTA
*
4069539 AATTTATCACAACTTTTAAAAGTATTATTTAATATCTTTAATATTTTTTATAAATAATCATTACA
66 AATTTATCACAACTTTTAAAAGAATTATTTAATATCTTTAATATTTTTTATAAATAATCATTACA
* * * *
4069604 TTATCTTTAGCTTTTAAATATTATTCACAAAATAAATTTGAAAAATATATATAAATACCA-AATC
131 TTATCTTCAACTTTTAAATATTATTCACAAAATAAATGTGAAAAAAATATATAAATACCATAA-C
4069668 AACTTCAGAAAAGTTTCTCTTCTATATCAAGTTTCTCTTGTATATCACTCTATCTC
195 AACTTCAGAAAAGTTTCTCTTCTATATCAAGTTTCTCTTGTATATCACTCTATCTC
* * * * *
4069724 AATTTAAAA-TCAATTTTAAATTAATTTATTTTTTTCAATTTATCTGTAATTAACATAAATATTT
1 AATTTAAAACT-AAATTTAAAGTAATTTATCTTTTTCAATTTATCTGCAATTAACATAAATACTT
4069788 AAATTTATCACAACTTTTAAACA-AATTATTTAATATCTTT-A-ATTTTTTATAAAATAATCATT
65 AAATTTATCACAACTTTTAAA-AGAATTATTTAATATCTTTAATATTTTTTAT-AAATAATCATT
* *
4069850 ATATTATCTTCAACTTTTAAATA-TATTTCACACAGA-AAATGTGAAAAAAAATATATAAATACC
128 ACATTATCTTCAACTTTTAAATATTA-TTCACA-AAATAAATGTG-AAAAAAATATATAAATACC
4069913 ATAACAACTTCA
190 ATAACAACTTCA
4069925 ATAAAGCCCT
Statistics
Matches: 182, Mismatches: 12, Indels: 14
0.88 0.06 0.07
Matches are distributed among these distances:
248 11 0.06
249 45 0.25
250 123 0.68
251 3 0.02
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (250 bp):
AATTTAAAACTAAATTTAAAGTAATTTATCTTTTTCAATTTATCTGCAATTAACATAAATACTTA
AATTTATCACAACTTTTAAAAGAATTATTTAATATCTTTAATATTTTTTATAAATAATCATTACA
TTATCTTCAACTTTTAAATATTATTCACAAAATAAATGTGAAAAAAATATATAAATACCATAACA
ACTTCAGAAAAGTTTCTCTTCTATATCAAGTTTCTCTTGTATATCACTCTATCTC
Found at i:4072139 original size:20 final size:20
Alignment explanation
Indices: 4072116--4072154 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4072106 TAAAAAGTTC
4072116 AAAAAAAAAGAAAG-AAAAGG
1 AAAAAAAAA-AAAGTAAAAGG
*
4072136 AAAACAAAAAAAGTAAAAG
1 AAAAAAAAAAAAGTAAAAG
4072155 CTTTAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAAGTAAAAGG
Found at i:4081462 original size:2 final size:2
Alignment explanation
Indices: 4081455--4081482 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4081445 TACATTCAAC
4081455 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
4081483 CAAAGATTCA
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:4082688 original size:14 final size:14
Alignment explanation
Indices: 4082666--4082729 Score: 69
Period size: 13 Copynumber: 4.6 Consensus size: 14
4082656 AAAATATTTA
4082666 ATAATAAATAGAAAT
1 ATAA-AAATAGAAAT
*
4082681 ATAAAAATA-TAAT
1 ATAAAAATAGAAAT
* * *
4082694 ATAAAAGT-TATAT
1 ATAAAAATAGAAAT
4082707 ATAAAAATAGAAAT
1 ATAAAAATAGAAAT
4082721 ATAAAAATA
1 ATAAAAATA
4082730 TAAAAAAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
13 19 0.47
14 17 0.43
15 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (14 bp):
ATAAAAATAGAAAT
Found at i:4082693 original size:26 final size:26
Alignment explanation
Indices: 4082653--4082726 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
4082643 TTGAATTATA
4082653 ATAAAAATATTTAATAATAAATAG-AAAT
1 ATAAAAATA-TTAAT-ATAAA-AGTAAAT
*
4082681 ATAAAAATA-TAATATAAAAGTTATAT
1 ATAAAAATATTAATATAAAAG-TAAAT
**
4082707 ATAAAAATAGAAATATAAAA
1 ATAAAAATATTAATATAAAA
4082727 ATATAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 2 0.05
25 5 0.12
26 16 0.39
27 9 0.22
28 9 0.22
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
ATAAAAATATTAATATAAAAGTAAAT
Found at i:4082731 original size:26 final size:26
Alignment explanation
Indices: 4082679--4082738 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
4082669 ATAAATAGAA
* *
4082679 ATATAAAAATATAATATAAAAGTTAT
1 ATATAAAAATAAAATATAAAAGATAT
4082705 ATATAAAAATAGAAATATAAAA-ATAT
1 ATATAAAAATA-AAATATAAAAGATAT
4082731 A-A-AAAAAT
1 ATATAAAAAT
4082739 CATAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.19
25 1 0.03
26 15 0.48
27 9 0.29
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (26 bp):
ATATAAAAATAAAATATAAAAGATAT
Found at i:4087275 original size:23 final size:23
Alignment explanation
Indices: 4087248--4087322 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
4087238 AAGATAAAGA
4087248 TTATAATAACGATT-AATTTTTTT
1 TTATAA-AACGATTCAATTTTTTT
**
4087271 TTATAAAATTATTCAATTTTTTT
1 TTATAAAACGATTCAATTTTTTT
** *
4087294 AAATAAAA-AATT--ATTTTTTAT
1 TTATAAAACGATTCAATTTTTT-T
4087315 TTATAAAA
1 TTATAAAA
4087323 TTAAACTTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 7 0.16
21 7 0.16
22 8 0.19
23 21 0.49
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (23 bp):
TTATAAAACGATTCAATTTTTTT
Done.