Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 112 of 198
Found at i:35805286 original size:94 final size:93
Alignment explanation
Indices: 35805173--35805503 Score: 312
Period size: 94 Copynumber: 3.5 Consensus size: 93
35805163 CATAACTTAC
* *
35805173 ACAATATTAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTTTGAATTAC
1 ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAAATTTTGAATTAC
35805238 ATAACTTATATAATATTAATATTACTTTT
66 ATAACTTATATAATATTAATA-TACTTTT
* * * *
35805267 ATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATAATAAGGTAAAATTTCT-AATTA
1 ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAAATTT-TGAATTA
* * * ***
35805331 CATAACTTATACAGTATTAAGATAAAATT
65 CATAACTTATATAATATTAATATACTTTT
* * * * ** * * * * * *
35805360 CCGA-ATT-ACAT-AACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAA
1 ACAATATTAAGATAAAATT-T-CGA-ATT-ACATAACTTATACAATATTAAGATAAAATTTTGAA
**
35805422 TTACATAACTTATATAATATTACATA-ACTTAC
62 TTACATAACTTATATAATATTA-ATATACTTTT
* *
35805454 ACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGAT
1 ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGAT
35805504 TACTTTTATA
Statistics
Matches: 182, Mismatches: 45, Indels: 21
0.73 0.18 0.08
Matches are distributed among these distances:
90 4 0.02
91 4 0.02
92 4 0.02
93 28 0.15
94 127 0.70
95 7 0.04
96 4 0.02
97 4 0.02
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (93 bp):
ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAAATTTTGAATTAC
ATAACTTATATAATATTAATATACTTTT
Found at i:35805315 original size:131 final size:131
Alignment explanation
Indices: 35805130--35805440 Score: 514
Period size: 131 Copynumber: 2.4 Consensus size: 131
35805120 ATATTACATA
* * * ** * *
35805130 ACTTATATAATGTTAAGATAAAAAATCGAATTACATAACTTACACAATATTAAGGTAAAATTTCT
1 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATAATAAGGTAAAATTTCT
** *
35805195 AATTACATAACTTATACAATATTAAGATAAAATTTTGAATTACATAACTTATATAATATTAATAT
66 AATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGAT
35805260 T
131 T
35805261 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATAATAAGGTAAAATTTCT
1 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATAATAAGGTAAAATTTCT
*
35805326 AATTACATAACTTATACAGTATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGAT
66 AATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGAT
35805391 T
131 T
*
35805392 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATA
1 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATA
35805441 TTACATAACT
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 168 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (131 bp):
ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATAATAAGGTAAAATTTCT
AATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGAT
T
Found at i:35805323 original size:37 final size:37
Alignment explanation
Indices: 35805269--35805390 Score: 181
Period size: 37 Copynumber: 3.3 Consensus size: 37
35805259 TTACTTTTAT
*
35805269 AATATTAAGATCAAATTTCGAATTACATAACTTATAC
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
* * *
35805306 AATAATAAGGTAAAATTTCTAATTACATAACTTATAC
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
* * *
35805343 AGTATTAAGATAAAATTCCGAATTACATAACTTATAT
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
35805380 AATATTAAGAT
1 AATATTAAGAT
35805391 TACTTTTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.35
Consensus pattern (37 bp):
AATATTAAGATAAAATTTCGAATTACATAACTTATAC
Found at i:35805400 original size:20 final size:20
Alignment explanation
Indices: 35805372--35805410 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35805362 GAATTACATA
35805372 ACTTATATAATATTAAGATT
1 ACTTATATAATATTAAGATT
*
35805392 ACTTTTATAATATTAAGAT
1 ACTTATATAATATTAAGAT
35805411 CAAATTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ACTTATATAATATTAAGATT
Found at i:35805445 original size:19 final size:19
Alignment explanation
Indices: 35805364--35805462 Score: 69
Period size: 19 Copynumber: 5.2 Consensus size: 19
35805354 AAAATTCCGA
35805364 ATTACATAACTTATATAAT
1 ATTACATAACTTATATAAT
* * *
35805383 ATTAAGATTACTTTTATAAT
1 ATT-ACATAACTTATATAAT
* * **
35805403 ATTAAGATCAAATT-T-CGA-
1 ATT-ACAT-AACTTATATAAT
35805421 ATTACATAACTTATATAAT
1 ATTACATAACTTATATAAT
* *
35805440 ATTACATAACTTACACAAT
1 ATTACATAACTTATATAAT
35805459 ATTA
1 ATTA
35805463 AGATAAAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
16 4 0.06
17 4 0.06
18 4 0.06
19 25 0.40
20 22 0.35
21 3 0.05
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTACATAACTTATATAAT
Found at i:35805465 original size:113 final size:112
Alignment explanation
Indices: 35805327--35805968 Score: 682
Period size: 113 Copynumber: 5.5 Consensus size: 112
35805317 AAAATTTCTA
* * *
35805327 ATTACATAACTTATACAGTATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGATT
1 ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
* * *
35805392 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
66 ACTTATATAATATTAAGAT-AAATTTCGAATTACATAACTCATACAAT
* * *
35805440 ATTACATAACTTACACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATT
1 ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
* * * *
35805505 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAATCTAAAAAAAT
66 ACTTATATAATATTAAGAT-AAATTTCGAATTACATAA-CTCATACAAT
* * * *
35805554 -TTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-ACATA
1 ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
* *
35805617 ACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAAT
66 ACTTATATAATATTAAGATAA-ATTTCGAATTACATAACTCATACAAT
* * * * *
35805665 ATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAA-ATT-ATAT
1 ATT-ACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGAT
* * * *
35805728 AACTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAAT
65 TACTTATATAATATTAAGATAA-ATTTCGAATTACATAACTCATACAAT
* * *
35805777 ATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAACTCAAACAA
1 ATT-ACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTT--AT-A-T-----AA
*
35805842 TATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAACTCATACA
56 TATTAAGATTACTTATATAATATTAAGAT-AAA----T--TT-C-GAA-TTACATAACTCATACA
35805907 AT
111 AT
* * * *
35805909 ATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAA-ATTA
1 ATT-ACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTA
35805969 CATAAATTAC
Statistics
Matches: 469, Mismatches: 35, Indels: 41
0.86 0.06 0.08
Matches are distributed among these distances:
111 9 0.02
112 141 0.30
113 198 0.42
114 8 0.02
115 1 0.00
116 1 0.00
121 2 0.00
122 7 0.01
123 23 0.05
124 2 0.00
127 1 0.00
128 1 0.00
129 3 0.01
130 2 0.00
131 2 0.00
132 68 0.14
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (112 bp):
ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
ACTTATATAATATTAAGATAAATTTCGAATTACATAACTCATACAAT
Found at i:35805586 original size:31 final size:30
Alignment explanation
Indices: 35805505--35805587 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 30
35805495 TATTAAGATT
* *
35805505 ACTTTTATAATATTAAGATCAAATTT-CGA
1 ACTTATATAATATTAAGATAAAATTTCCGA
* *
35805534 A-TTACATAAT-CTAA-A-AAAATTTCCGTA
1 ACTTATATAATATTAAGATAAAATTTCCG-A
35805561 ACTTATATAATATTAAGATAAAATTTC
1 ACTTATATAATATTAAGATAAAATTTC
35805588 GAATTACATA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
27 5 0.12
28 15 0.36
29 4 0.10
30 1 0.02
31 8 0.19
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.39
Consensus pattern (30 bp):
ACTTATATAATATTAAGATAAAATTTCCGA
Found at i:35805587 original size:169 final size:168
Alignment explanation
Indices: 35805392--35805979 Score: 660
Period size: 169 Copynumber: 3.4 Consensus size: 168
35805382 TATTAAGATT
* *
35805392 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACACA
1 ACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTACACA
* *
35805457 ATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTATAATATTAAG
66 ATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATTACTTATATAATATTAAG
* *
35805522 ATCAAATTTCGAATTACATAATC-TAAAAAAATTTCCGTA
131 ATAAAATTTCTAATTACATAATCATAAAAAAATTT--GTA
*
35805561 ACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTATACA
1 ACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTACACA
* * * *
35805626 ATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTACTTATATAATATTAAG
66 ATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATTACTTATATAATATTAAG
* * * *
35805691 ATAAAATTTCTAATTACATAA-CTTACATAAATTATATA
131 ATAAAATTTCTAATTACATAATCATAAAAAAATT-TGTA
* * * * * * * * * *
35805729 ACTTATACAATATTAAGGTAAGATTTCAAATTACATAACTCATACAATATTAAGATTACTTATAT
1 ACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-ACATAACTTACAC
*
35805794 AATATTAAGATAAAATTTCTAATTACATAACTTACATAACTCAAACAATATTAAGATTACTTATA
65 AATATTAAGATAAAATTTCGAATTACATAACTT--AT-A-T-----AATATTAAGATTACTTATA
* *
35805859 TAATATTAAGATAAAATTTCTAATTACATAACTTACATAACTCATACAATATTAAGATT
121 TAATATTAAGATAAAATTTCTAATTACATAA--T-CATAA---A-A-AA-ATT-TG-TA
* * *
35805918 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAA-ATTACATAAATTACA
1 ACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTACA
35805980 TAACTTACAT
Statistics
Matches: 351, Mismatches: 45, Indels: 28
0.83 0.11 0.07
Matches are distributed among these distances:
168 48 0.14
169 187 0.53
170 1 0.00
171 2 0.01
172 1 0.00
178 50 0.14
182 3 0.01
185 1 0.00
187 10 0.03
188 7 0.02
189 41 0.12
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (168 bp):
ACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTACACA
ATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATTACTTATATAATATTAAG
ATAAAATTTCTAATTACATAATCATAAAAAAATTTGTA
Found at i:35805614 original size:19 final size:19
Alignment explanation
Indices: 35805590--35805800 Score: 86
Period size: 20 Copynumber: 11.2 Consensus size: 19
35805580 AAAATTTCGA
*
35805590 ATTACATAACTTATATAAT
1 ATTACATAACTTATACAAT
35805609 ATTACATAACTTATACAAT
1 ATTACATAACTTATACAAT
* *
35805628 ATTA-AGGTAAGATT-T-CGA-
1 ATTACA--TAA-CTTATACAAT
*
35805646 ATTACATAACTCATACAAT
1 ATTACATAACTTATACAAT
* * *
35805665 ATTAAGATTACTTATATAAT
1 ATT-ACATAACTTATACAAT
* * *
35805685 ATTAAGATAAAATT-T-CTA-
1 ATT-ACAT-AACTTATACAAT
* *
35805703 ATTACATAACTTACATAA-
1 ATTACATAACTTATACAAT
*
35805721 ATTATATAACTTATACAAT
1 ATTACATAACTTATACAAT
*
35805740 ATTA-AGGTAAGATT-T-CAA-
1 ATTACA--TAA-CTTATACAAT
*
35805758 ATTACATAACTCATACAAT
1 ATTACATAACTTATACAAT
* * *
35805777 ATTAAGATTACTTATATAAT
1 ATT-ACATAACTTATACAAT
35805797 ATTA
1 ATTA
35805801 AGATAAAATT
Statistics
Matches: 143, Mismatches: 29, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
16 6 0.04
17 11 0.08
18 34 0.24
19 41 0.29
20 44 0.31
21 7 0.05
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTACATAACTTATACAAT
Found at i:35805842 original size:66 final size:66
Alignment explanation
Indices: 35805759--35805964 Score: 403
Period size: 66 Copynumber: 3.1 Consensus size: 66
35805749 AGATTTCAAA
35805759 TTACATAACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
1 TTACATAACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
35805824 C
66 C
*
35805825 TTACATAACTCAAACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
1 TTACATAACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
35805890 C
66 C
35805891 TTACATAACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
1 TTACATAACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
35805956 C
66 C
35805957 TTACATAA
1 TTACATAA
35805965 ATTACATAAA
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 138 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (66 bp):
TTACATAACTCATACAATATTAAGATTACTTATATAATATTAAGATAAAATTTCTAATTACATAA
C
Found at i:35805962 original size:9 final size:9
Alignment explanation
Indices: 35805948--35806028 Score: 108
Period size: 9 Copynumber: 9.0 Consensus size: 9
35805938 AAATTTCTAA
35805948 TTACATAAC
1 TTACATAAC
*
35805957 TTACATAAA
1 TTACATAAC
*
35805966 TTACATAAA
1 TTACATAAC
35805975 TTACATAAC
1 TTACATAAC
*
35805984 TTACATAAA
1 TTACATAAC
*
35805993 TTAAATAAC
1 TTACATAAC
*
35806002 TTGCATAAC
1 TTACATAAC
*
35806011 TTAAATAAC
1 TTACATAAC
35806020 TTACATAAC
1 TTACATAAC
35806029 ACATAACCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (9 bp):
TTACATAAC
Found at i:35805977 original size:27 final size:27
Alignment explanation
Indices: 35805946--35806027 Score: 119
Period size: 27 Copynumber: 3.0 Consensus size: 27
35805936 TAAAATTTCT
35805946 AATTACATAACTTACATAAATTACATA
1 AATTACATAACTTACATAAATTACATA
*
35805973 AATTACATAACTTACATAAATTAAATA
1 AATTACATAACTTACATAAATTACATA
* * * *
35806000 ACTTGCATAACTTAAATAACTTACATA
1 AATTACATAACTTACATAAATTACATA
35806027 A
1 A
35806028 CACATAACCT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (27 bp):
AATTACATAACTTACATAAATTACATA
Found at i:35808471 original size:21 final size:21
Alignment explanation
Indices: 35808439--35808505 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
35808429 NNNNNNNNNN
*
35808439 AGAGGCGGCAGCGAGGGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
*
35808460 AGCGGCTGCAGCGAGGGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
*
35808481 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGGGAAGC
35808502 AGAG
1 AGAG
35808506 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.30, C:0.19, G:0.48, T:0.03
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGGGAAGC
Found at i:35808878 original size:44 final size:43
Alignment explanation
Indices: 35808814--35808923 Score: 166
Period size: 44 Copynumber: 2.5 Consensus size: 43
35808804 CGTTTTTGTG
* *
35808814 AAAAAGCGCCACTAAAGACCATGTTCTTTAGCGGCGCTTACAA
1 AAAAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTACAA
* *
35808857 ACAAAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTAGAA
1 A-AAAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTACAA
*
35808901 AAAAAGCGCCACTAAAGACCATG
1 AAAAAACGCCACTAAAGACCATG
35808924 CGTCGTTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 21 0.35
44 39 0.65
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (43 bp):
AAAAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTACAA
Found at i:35810791 original size:6 final size:6
Alignment explanation
Indices: 35810780--35810809 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35810770 TTCAACCTTT
35810780 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
35810810 TAGTTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:35810964 original size:23 final size:22
Alignment explanation
Indices: 35810929--35810977 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
35810919 TGTTTATCCC
35810929 AACA-TTTTTAAGGTTACCTTA
1 AACATTTTTTAAGGTTACCTTA
*
35810950 AACATTTTTTAAAGGTTTCCTTA
1 AACATTTTTT-AAGGTTACCTTA
*
35810973 GACAT
1 AACAT
35810978 GGTCTACCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 5 0.21
23 15 0.62
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
AACATTTTTTAAGGTTACCTTA
Found at i:35811031 original size:35 final size:36
Alignment explanation
Indices: 35810955--35811033 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
35810945 CCTTAAACAT
* *
35810955 TTTTTAAAGGTTTCCTTAGACATGGTCTACCCCAACC
1 TTTTT-AAGGTTGCCTTAGACAGGGTCTACCCCAACC
* *
35810992 TTTTTAAGGTTGCCTTAGAC-GGGTGTATCCCAACC
1 TTTTTAAGGTTGCCTTAGACAGGGTCTACCCCAACC
35811027 TTTTTAA
1 TTTTTAA
35811034 AAGTTTAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 19 0.50
36 14 0.37
37 5 0.13
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (36 bp):
TTTTTAAGGTTGCCTTAGACAGGGTCTACCCCAACC
Found at i:35813264 original size:131 final size:131
Alignment explanation
Indices: 35813030--35813286 Score: 478
Period size: 131 Copynumber: 2.0 Consensus size: 131
35813020 AACATTACTC
35813030 TTAAATTAGTCATATGCTTCTTACTTAGAGCGTCTATCACTACATTGGCTTTTCCGGAGTAGTAT
1 TTAAATTAGTCATATGCTTCTTACTTAGAGCGTCTATCACTACATTGGCTTTTCCGGAGTAGTAT
35813095 TCAATTACACAATCATAATCCTTTAATAGTTCTATCCACCTCCGTTGCCTCAGGTTCAATTTGCT
66 TCAATTACACAATCATAATCCTTTAATAGTTCTATCCACCTCCGTTGCCTCAGGTTCAATTTGCT
35813160 T
131 T
* * *
35813161 TTAAATTAGTCATATGCTTCTTACTTAGAGCGTCTGTCACTACATTGGGTTTTCCGGGGTAGTAT
1 TTAAATTAGTCATATGCTTCTTACTTAGAGCGTCTATCACTACATTGGCTTTTCCGGAGTAGTAT
*
35813226 TCAATTACACAATCATAATCCTTTAATAGTTCTATCCACCTTCGTTGCCTCAGGTTCAATT
66 TCAATTACACAATCATAATCCTTTAATAGTTCTATCCACCTCCGTTGCCTCAGGTTCAATT
35813287 CTTTTTAGTT
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 122 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (131 bp):
TTAAATTAGTCATATGCTTCTTACTTAGAGCGTCTATCACTACATTGGCTTTTCCGGAGTAGTAT
TCAATTACACAATCATAATCCTTTAATAGTTCTATCCACCTCCGTTGCCTCAGGTTCAATTTGCT
T
Found at i:35817418 original size:64 final size:65
Alignment explanation
Indices: 35817309--35817430 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 65
35817299 ATTGTGAATG
* * * * *
35817309 CACAATGTGTTTGCAAATAAAAGCTACTAGTAAGTATGTGGATGAACCACTAGTGTTTATGGATA
1 CACAACGTGGTTGCAAAGAAAAGCTACCAGTAAGTATATGGATGAACCACTAGTGTTTATGGATA
* *
35817374 CACAACGTGGTTGCAGAGAAAAG-TACCAGTAAGTTTATGGATGAACCACTAGTGTTT
1 CACAACGTGGTTGCAAAGAAAAGCTACCAGTAAGTATATGGATGAACCACTAGTGTTT
35817431 GCACATTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 31 0.62
65 19 0.38
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (65 bp):
CACAACGTGGTTGCAAAGAAAAGCTACCAGTAAGTATATGGATGAACCACTAGTGTTTATGGATA
Found at i:35817618 original size:38 final size:38
Alignment explanation
Indices: 35817526--35817631 Score: 124
Period size: 38 Copynumber: 2.8 Consensus size: 38
35817516 TAGAAATAGT
* * *
35817526 AGACATGTTTAACATGTATTCAAATT-AACAGTAGCAGA
1 AGACATGTTTAACATGTATTC-AGTTCAACAATAACAGA
* * *
35817564 AGACATGCTTATCATGTATTCAGTTCAACAATAACAGT
1 AGACATGTTTAACATGTATTCAGTTCAACAATAACAGA
* *
35817602 TGGCATGTTTAACATGTATTCAGTTCAACA
1 AGACATGTTTAACATGTATTCAGTTCAACA
35817632 GTGATAGTAG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 3 0.05
38 54 0.95
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (38 bp):
AGACATGTTTAACATGTATTCAGTTCAACAATAACAGA
Found at i:35818346 original size:22 final size:21
Alignment explanation
Indices: 35818305--35818352 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
35818295 TCGTAGCAGT
* *
35818305 TCAGATAAGATGCAACACAGA
1 TCAGATAAGATACAAAACAGA
35818326 TCAGATACAGATACAAAACAGA
1 TCAGATA-AGATACAAAACAGA
35818348 TCAGA
1 TCAGA
35818353 ATCACATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.15
Consensus pattern (21 bp):
TCAGATAAGATACAAAACAGA
Found at i:35822683 original size:31 final size:29
Alignment explanation
Indices: 35822646--35822707 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
35822636 ATCTCAAAAT
* *
35822646 TATACATGAACTTTACTTTAATGTGCAATTA
1 TATACATGAACTTTAATTT--GGTGCAATTA
*
35822677 TATACATGAATTTTAATTTGGTGCAATTA
1 TATACATGAACTTTAATTTGGTGCAATTA
35822706 TA
1 TA
35822708 CACGTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
31 17 0.61
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (29 bp):
TATACATGAACTTTAATTTGGTGCAATTA
Found at i:35824079 original size:31 final size:31
Alignment explanation
Indices: 35824044--35824113 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
35824034 ATTATAAAAT
* *
35824044 AGTCACTTAATTATTTGAAAGTTTTCATTTA
1 AGTCACTGAACTATTTGAAAGTTTTCATTTA
*
35824075 AGTCACTGAACTATTTGAAAGTTTTTATTTA
1 AGTCACTGAACTATTTGAAAGTTTTCATTTA
35824106 AGTCACTG
1 AGTCACTG
35824114 GTTATTAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (31 bp):
AGTCACTGAACTATTTGAAAGTTTTCATTTA
Found at i:35834407 original size:11 final size:13
Alignment explanation
Indices: 35834383--35834414 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
35834373 TAGTTTATTA
35834383 ATATTTTAATATG
1 ATATTTTAATATG
35834396 AT-TTTTAA-ATG
1 ATATTTTAATATG
35834407 ATATTTTA
1 ATATTTTA
35834415 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:35840630 original size:132 final size:131
Alignment explanation
Indices: 35840209--35840641 Score: 560
Period size: 132 Copynumber: 3.4 Consensus size: 131
35840199 GAATAGACCA
* * * *
35840209 TTGAAGATTGCAGATCCTGTCTCACTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATC
1 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGCGGAGCAGATCG-AGACGGCAAATCTTATC
* **
35840274 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTGGTCCTATCTCCCTGAGCAGCAGTAGGAGT
65 TTCCCAAGATAGTAGAGAAGCAGATTTAAGCCACCGGTCCTATCTCCCTGAGCAGCAGT-GGAGT
35840339 AGG
129 AGG
* *
35840342 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGAGCAGATC---ATGG---ATCTTATCT
1 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAGACGGCAAATCTTATCT
* * * * *
35840401 TCCCAAGGTAGTAGGGAAGCAAATTTAAGCC-CC--TCCTATTTCCCTGAGCAGTAGTGGAGTAG
66 TCCCAAGATAGTAGAGAAGCAGATTTAAGCCACCGGTCCTATCTCCCTGAGCAGCAGTGGAGTAG
35840463 G
131 G
* * * *
35840464 TTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGCGGAGCAGGTCGAGGACGGCAAATCTTATC
1 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGCGGAGCAGATCGA-GACGGCAAATCTTATC
* * * *
35840529 TTTCTAAGATAGTAGTGAAGCAGATTTAAGCCACCGGTCCTATCGCCCTGAGCAGCAGTGGAGTA
65 TTCCCAAGATAGTAGAGAAGCAGATTTAAGCCACCGGTCCTATCTCCCTGAGCAGCAGTGGAGTA
35840594 GG
130 GG
* *
35840596 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGTGGACCAGATC
1 TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGCGGAGCAGATC
35840642 ATGGATCTTG
Statistics
Matches: 256, Mismatches: 34, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
122 49 0.19
123 20 0.08
126 39 0.15
129 38 0.15
130 2 0.01
132 67 0.26
133 41 0.16
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (131 bp):
TTGAAGAATGTAGATACTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAGACGGCAAATCTTATCT
TCCCAAGATAGTAGAGAAGCAGATTTAAGCCACCGGTCCTATCTCCCTGAGCAGCAGTGGAGTAG
G
Found at i:35846047 original size:18 final size:18
Alignment explanation
Indices: 35846014--35846048 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35846004 GCAAAAGCGG
* *
35846014 GAAGAAGAATAGTAACAA
1 GAAGAAGAACAATAACAA
35846032 GAAGAAGAACAATAACA
1 GAAGAAGAACAATAACA
35846049 GCGACAATAA
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:0.63, C:0.09, G:0.20, T:0.09
Consensus pattern (18 bp):
GAAGAAGAACAATAACAA
Found at i:35851079 original size:217 final size:217
Alignment explanation
Indices: 35850704--35851131 Score: 748
Period size: 217 Copynumber: 2.0 Consensus size: 217
35850694 CGATGCAAAG
* * *
35850704 GGAATCTTTTGTATTTCTTGAATTTTAAGGTTACTTTTAGGTCATTCAGTAAGACTAAATTTATC
1 GGAATCTTTTGCATTTCTTGAATTTCAAGGTTACTTTTAGGTCATTCAGTAAGACTAAAATTATC
*
35850769 TCCTTTAGCAATAGGGGTGTCGCCTAGTCTACAACCTTGTATGTCAAACCTTTTGAGTACTTTGC
66 TCCTTTAGCAATAAGGGTGTCGCCTAGTCTACAACCTTGTATGTCAAACCTTTTGAGTACTTTGC
**
35850834 CGATATAGCTCTTTTGCAACAATCCAAGAATACCCTGAGATTGGTCTCGATGTATCTGAATTCCT
131 CGATATAGCTCTTTTGCAACAATCCAAGAATACCCTGAGATCAGTCTCGATGTATCTGAATTCCT
35850899 AAAACAAAGGAGGCGTGCATAA
196 AAAACAAAGGAGGCGTGCATAA
*
35850921 GGAATCTTTTGCATTTCTTGAATTTCAGGGTTACTTTTAGGTCATTCAGTAAGACTAAAATTATC
1 GGAATCTTTTGCATTTCTTGAATTTCAAGGTTACTTTTAGGTCATTCAGTAAGACTAAAATTATC
* * *
35850986 TCCTTTAGCAATAAGGGTGTCGCCTGGTCTACAACCTTGTATGTTAAACCTTTTGAGTACTTTGT
66 TCCTTTAGCAATAAGGGTGTCGCCTAGTCTACAACCTTGTATGTCAAACCTTTTGAGTACTTTGC
* *
35851051 CGATATAGCTCTTTTGCGACAATCCAAGAATACCTTGAGATCAGTCTCGATGTATCTGAATTCCT
131 CGATATAGCTCTTTTGCAACAATCCAAGAATACCCTGAGATCAGTCTCGATGTATCTGAATTCCT
35851116 AAAACAAAGGAGGCGT
196 AAAACAAAGGAGGCGT
35851132 CCTCAAGGTC
Statistics
Matches: 199, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 199 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (217 bp):
GGAATCTTTTGCATTTCTTGAATTTCAAGGTTACTTTTAGGTCATTCAGTAAGACTAAAATTATC
TCCTTTAGCAATAAGGGTGTCGCCTAGTCTACAACCTTGTATGTCAAACCTTTTGAGTACTTTGC
CGATATAGCTCTTTTGCAACAATCCAAGAATACCCTGAGATCAGTCTCGATGTATCTGAATTCCT
AAAACAAAGGAGGCGTGCATAA
Found at i:35852909 original size:17 final size:17
Alignment explanation
Indices: 35852868--35852909 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
35852858 TTTTATTTTG
35852868 ATTATTAAATATTATATA
1 ATTATT-AATATTATATA
*
35852886 ATAATTAATATTATA-A
1 ATTATTAATATTATATA
35852902 ATTTATTA
1 A-TTATTA
35852910 TTTTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 14 0.67
18 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTAATATTATATA
Found at i:35854297 original size:42 final size:43
Alignment explanation
Indices: 35854227--35854329 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 43
35854217 ATTGACTTGA
* *
35854227 GATTTACGTGTAAGACCATGTTCGGGACATTGGCATC-GTATAT
1 GATTT-CGTGTAAGACCATGTTCAGGACAGTGGCATCAGTATAT
* * *
35854270 GATTTCGTGTAAGACCCTG-TCTAGGACAGTGGCATCATTATTT
1 GATTTCGTGTAAGACCATGTTC-AGGACAGTGGCATCAGTATAT
* *
35854313 GATTACATGTAAGACCA
1 GATTTCGTGTAAGACCA
35854330 CGTCTGGGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.04
42 25 0.50
43 23 0.46
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTTCAGGACAGTGGCATCAGTATAT
Found at i:35854346 original size:43 final size:42
Alignment explanation
Indices: 35854189--35854347 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 42
35854179 TATGTGATAT
* *
35854189 CGTGTAAGACCACGTCTGGGACGTTGGCAT-TGACTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCTTA-TT-TGA-TTA
* * * * *
35854233 CGTGTAAGACCATGT-TCGGGACATTGGCATCGTATATGATTT
1 CGTGTAAGACCACGTCT-GGGACGTTGGCATCTTATTTGATTA
*
35854275 CGTGTAAGACC-CTGTCTAGGACAG-TGGCATCATTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATC-TTATTTGATTA
* *
35854318 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
35854348 TGTACGAGCT
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
42 27 0.30
43 35 0.38
44 28 0.31
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCTTATTTGATTA
Found at i:35860793 original size:23 final size:23
Alignment explanation
Indices: 35860758--35860802 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35860748 TGGAGTATAA
* *
35860758 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
35860781 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
35860803 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:35861453 original size:42 final size:41
Alignment explanation
Indices: 35861380--35861551 Score: 200
Period size: 42 Copynumber: 4.1 Consensus size: 41
35861370 CAGTGCCTAA
* * * * *
35861380 CAGGTTTATTGCCAGTGAAACATTTTAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAAAATTTCAGACTTTACGTCTAG
*
35861421 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACATCTAG
1 CAGGCTTAATGCCGGTGAAA-AATTTCAGACTTTACGTCTAG
* * * *
35861463 CAGGCTTAATTCTGGTGAAACAATATCAAACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAA-AATTTCAGACTTTACGTCTAG
* * * *
35861505 CGGGCTTAATGCCGGTGAAACATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAAAATTTCAGACTTTACGTCTAG
35861546 CAGGCT
1 CAGGCT
35861552 AAGTGCTGGT
Statistics
Matches: 109, Mismatches: 21, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
41 38 0.35
42 71 0.65
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
CAGGCTTAATGCCGGTGAAAAATTTCAGACTTTACGTCTAG
Found at i:35861561 original size:83 final size:84
Alignment explanation
Indices: 35861408--35861562 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
35861398 AACATTTTAG
*
35861408 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACATCTAGCAGGCTTAAT
1 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTTCAGACTATACATCTAGCAGGCTTAAT
*
35861473 TCTGGTGAAACAATATCAA
66 GCTGGTGAAACAATATCAA
* * **
35861492 ACTTTACGTCTAGCGGGCTTAATGCCGGTGAAA-CATTTCAGACTATATGTCTAGCAGGC-TAAG
1 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTTCAGACTATACATCTAGCAGGCTTAA-
35861555 TGCTGGTG
65 TGCTGGTG
35861563 TACTGAATCA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 3 0.05
83 29 0.45
84 32 0.50
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (84 bp):
ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTTCAGACTATACATCTAGCAGGCTTAAT
GCTGGTGAAACAATATCAA
Found at i:35865324 original size:43 final size:43
Alignment explanation
Indices: 35865177--35865326 Score: 130
Period size: 42 Copynumber: 3.5 Consensus size: 43
35865167 TATGTGTTAT
* *
35865177 CGTGTAAGACCACGTCTGGGAC-GTTGGCAT--TGACTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACAG-TGGCATCGTTA-TT-TGA-TTA
* * * * *
35865221 CGTGTAAGACCATGTCCGGGACATTGGCATCG-TATATGATTT
1 CGTGTAAGACCACGTCTGGGACAGTGGCATCGTTATTTGATTA
* *
35865263 CGTATAAGACC-CTATCTGGGACAGTGGCATCGTTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGACAGTGGCATCGTTATTTGATTA
*
35865306 CATGTAAGACCACGTCTGGGA
1 CGTGTAAGACCACGTCTGGGA
35865327 TGTTGGCATT
Statistics
Matches: 83, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
42 28 0.34
43 26 0.31
44 28 0.34
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACAGTGGCATCGTTATTTGATTA
Found at i:35865334 original size:43 final size:43
Alignment explanation
Indices: 35865177--35865335 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
35865167 TATGTGTTAT
* *
35865177 CGTGTAAGACCACGTCTGGGACGTTGGCAT--TGACTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGTTA-TT-TGA-TTA
* * * * *
35865221 CGTGTAAGACCATGTCCGGGACATTGGCATCG-TATATGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGTTATTTGATTA
* *
35865263 CGTATAAGACC-CTATCTGGGACAG-TGGCATCGTTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGTTATTTGATTA
* *
35865306 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
35865336 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
42 28 0.31
43 32 0.36
44 29 0.32
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGTTATTTGATTA
Found at i:35867351 original size:18 final size:19
Alignment explanation
Indices: 35867319--35867354 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
35867309 AATTTGTTCA
35867319 TTTTGATACTTATATTTTC
1 TTTTGATACTTATATTTTC
35867338 TTTTGATA-TTATATTTT
1 TTTTGATACTTATATTTT
35867355 GATATTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTTGATACTTATATTTTC
Found at i:35868756 original size:41 final size:41
Alignment explanation
Indices: 35868694--35868920 Score: 303
Period size: 41 Copynumber: 5.5 Consensus size: 41
35868684 TTTCTACCTT
* *
35868694 TCGGCGCTTTAGCGGCGTTTTTTATA-AAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTCA-AGAAGCGCCGCTAATGC
** *
35868735 TCGGGGCTTTAGCGGCGTTTTTCAAGAAGCATCGCCAATGC
1 TCGGGGCTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGC
* * *
35868776 TCGGGTCTTTAGCGGCGTTTTTAAATAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGC
* *
35868817 TCGGGGCTTTAGCGGCGTTTTCCAAGAAGCGCCACTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGC
* * * *
35868858 TCAGGGCATTAGCAGCGTTTTCCAAGAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGC
*
35868899 TCAGGGCTTTAGCGGCGTTTTT
1 TCGGGGCTTTAGCGGCGTTTTT
35868921 GAAAAAGCAC
Statistics
Matches: 162, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 1 0.01
41 161 0.99
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGC
Found at i:35869078 original size:26 final size:26
Alignment explanation
Indices: 35869030--35869080 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
35869020 AAAATGGATA
** * *
35869030 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
35869056 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
35869081 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:35869368 original size:14 final size:15
Alignment explanation
Indices: 35869340--35869372 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
35869330 AAGGTTTATA
35869340 GATTATGGAATTAGG
1 GATTATGGAATTAGG
35869355 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
35869369 GATT
1 GATT
35869373 TTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:35869409 original size:14 final size:14
Alignment explanation
Indices: 35869392--35869444 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
35869382 GGGTTGTGAT
* *
35869392 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
35869406 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
* *
35869420 TTAGGGGTTAGAGG
1 TTAAGGGTTAGGGG
*
35869434 TTAAGAGTTAG
1 TTAAGGGTTAG
35869445 AGATTTAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.34
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:35869445 original size:14 final size:14
Alignment explanation
Indices: 35869404--35869456 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
35869394 AAGGTTTATG
*
35869404 GGTTAAGGGTTAGG
1 GGTTAAGGGTTAGA
*
35869418 GGTTAGGGGTTAGA
1 GGTTAAGGGTTAGA
*
35869432 GGTTAAGAGTTAGA
1 GGTTAAGGGTTAGA
* *
35869446 GATTTAGGGTT
1 GGTTAAGGGTT
35869457 TATAGATTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.43, T:0.32
Consensus pattern (14 bp):
GGTTAAGGGTTAGA
Found at i:35869549 original size:82 final size:82
Alignment explanation
Indices: 35869471--35869623 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 82
35869461 GATTCAGTGT
* * * *
35869471 TAGG-TTAGGGTTTAGGGTTTAAATTAATTAGTGTGTTTTATTTTATATATTAAATAATATTTAG
1 TAGGATTAGGGTTAAGGGTTTAAATTAATTAATGTGTTTTAATTTATATATTAAATAAGATTTAG
35869535 GGGTTAGGGGTTCAGGG
66 GGGTTAGGGGTTCAGGG
* * * * *
35869552 TCGGATTAGGGTTAAGGGTTTAGATTGATTAATGTTTTTTAATTTATATATTAAATAAGGTTTAG
1 TAGGATTAGGGTTAAGGGTTTAAATTAATTAATGTGTTTTAATTTATATATTAAATAAGATTTAG
35869617 GGGTTAG
66 GGGTTAG
35869624 TGGATAGGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
81 3 0.05
82 59 0.95
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (82 bp):
TAGGATTAGGGTTAAGGGTTTAAATTAATTAATGTGTTTTAATTTATATATTAAATAAGATTTAG
GGGTTAGGGGTTCAGGG
Found at i:35870752 original size:147 final size:144
Alignment explanation
Indices: 35870465--35870851 Score: 539
Period size: 147 Copynumber: 2.7 Consensus size: 144
35870455 ACACGCAAAA
* * *
35870465 TTTTATGAAAAACGTCACAAAAGGTAAGCAATAGCGGCATTTTTATAAAAAACGCCAC-AAAAA-
1 TTTTATGAAAAACG-C-CAAAAAGTAAGCAATAGCGGCGTTTTTATAAAAAAAGCCACAAAAAAT
* *
35870528 AA--TTACTTTAAAAAATAGCGCCATTTTATATAGTAAAATAGTGTCATTTTATTCCAAATGAAA
64 AATTTTACTTTAAAAAATAGCGCCATTTTATATAGCAAAACAGTGTCATTTTATTCCAAATGAAA
35870591 TAATTTTTTACGGCGT
129 TAATTTTTTACGGCGT
* * *
35870607 TTTTATGAAAGACGCCGCAAAAAGTAAGCAATAGCGGCGTTTTTATGAAAAATGCCACAAAAAAT
1 TTTTATGAAAAACG-C-CAAAAAGTAAGCAATAGCGGCGTTTTTATAAAAAAAGCCACAAAAAAT
* * *
35870672 AATTTTACTTTAAAAAAATAGCGCCATTTTATATAGCAAAACAGTTTCGTTTTATTTCAAATGAA
64 AATTTTACTTT-AAAAAATAGCGCCATTTTATATAGCAAAACAGTGTCATTTTATTCCAAATGAA
*
35870737 ATAATTTTTTGCGGCGT
128 ATAATTTTTTACGGCGT
* *
35870754 TTTTATGAAAAATGCCAGAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAAAACCACAAAAAAT
1 TTTTATGAAAAACGCCA-AAAAG-TAAGCAATAGCGGCGTTTTTATAAAAAAAGCCACAAAAAAT
*
35870819 AATTTTACTTTTAAAAAATAGCACCATTTTATA
64 AATTTTAC-TTTAAAAAATAGCGCCATTTTATA
35870852 GAATCCCCTC
Statistics
Matches: 218, Mismatches: 19, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
142 51 0.23
143 5 0.02
144 2 0.01
145 2 0.01
146 13 0.06
147 142 0.65
148 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (144 bp):
TTTTATGAAAAACGCCAAAAAGTAAGCAATAGCGGCGTTTTTATAAAAAAAGCCACAAAAAATAA
TTTTACTTTAAAAAATAGCGCCATTTTATATAGCAAAACAGTGTCATTTTATTCCAAATGAAATA
ATTTTTTACGGCGT
Found at i:35870904 original size:20 final size:21
Alignment explanation
Indices: 35870867--35870905 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35870857 CCCTCCCCCG
*
35870867 AAATCCCTAACTTTCCCCCTA
1 AAATCCCTAACTTACCCCCTA
*
35870888 AAATCCTTAA-TTACCCCC
1 AAATCCCTAACTTACCCCC
35870906 CTTGAAACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCCTAACTTACCCCCTA
Found at i:35876543 original size:43 final size:43
Alignment explanation
Indices: 35876454--35876575 Score: 138
Period size: 43 Copynumber: 2.9 Consensus size: 43
35876444 GTCATGTTTT
* * ** *
35876454 TAGCGGCGTTTGTCA-AAAAGCGCCGCTAAAGGTCTTGTTCTT
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAATCTA
* *
35876496 TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGATCATAATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAATCTA
* * * *
35876539 TAGCGCCGTCTGTGGGATAAGCGCCGCTAAAGGTCAT
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCAT
35876576 GACCTTTAGC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 14 0.21
43 53 0.79
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAATCTA
Found at i:35876586 original size:43 final size:43
Alignment explanation
Indices: 35876471--35876586 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
35876461 GTTTGTCAAA
* * * *
35876471 AAGCGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGTGAGAG
1 AAGCGCCGCTAAAGGTCATGATCTTTAGCGCCGTCTGTGAGAG
* * * * *
35876514 AAGCGCCGCTAAAGATCATAATCTATAGCGCCGTCTGTGGGAT
1 AAGCGCCGCTAAAGGTCATGATCTTTAGCGCCGTCTGTGAGAG
*
35876557 AAGCGCCGCTAAAGGTCATGACCTTTAGCG
1 AAGCGCCGCTAAAGGTCATGATCTTTAGCG
35876587 GTGTTTTTGT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGATCTTTAGCGCCGTCTGTGAGAG
Found at i:35877070 original size:17 final size:16
Alignment explanation
Indices: 35877050--35877081 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
35877040 TTAATATATA
35877050 AATTATATTATTAAATT
1 AATTATATTA-TAAATT
35877067 AATTATATTATAAAT
1 AATTATATTATAAAT
35877082 ATTATGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATATTATAAATT
Found at i:35878163 original size:23 final size:24
Alignment explanation
Indices: 35878137--35878182 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
35878127 GTGTGAATTT
* *
35878137 GTGAAATAATTATTG-ATTGAAAG
1 GTGAAAAAATGATTGAATTGAAAG
35878160 GTGAAAAAATGATTGAATTGAAA
1 GTGAAAAAATGATTGAATTGAAA
35878183 ATGTGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (24 bp):
GTGAAAAAATGATTGAATTGAAAG
Found at i:35884444 original size:20 final size:18
Alignment explanation
Indices: 35884419--35884467 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
35884409 TTATTTATTT
*
35884419 TTATTAATATATAAATTTTA
1 TTATTAATAT-T-AATTATA
35884439 TTATTAA-ATTAATTATA
1 TTATTAATATTAATTATA
*
35884456 TTATAAATATTA
1 TTATTAATATTA
35884468 TGTTAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 12 0.46
18 5 0.19
19 2 0.08
20 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATTAATATTAATTATA
Found at i:35884656 original size:17 final size:17
Alignment explanation
Indices: 35884612--35884649 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35884602 AGTTAAAATA
*
35884612 AAAAGAATAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
*
35884629 TAAAGAAGAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
35884646 AAAA
1 AAAA
35884650 TAGGAAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAC
Found at i:35885546 original size:23 final size:24
Alignment explanation
Indices: 35885520--35885565 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
35885510 GTGTGAATTT
* *
35885520 GTGAAATAATTATTG-ATTGAAAG
1 GTGAAAAAATGATTGAATTGAAAG
35885543 GTGAAAAAATGATTGAATTGAAA
1 GTGAAAAAATGATTGAATTGAAA
35885566 ATGTGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (24 bp):
GTGAAAAAATGATTGAATTGAAAG
Found at i:35885826 original size:39 final size:39
Alignment explanation
Indices: 35885687--35885827 Score: 142
Period size: 38 Copynumber: 3.6 Consensus size: 39
35885677 TACTTCGACC
* * *
35885687 TCGAGTCGATGAGACACTGGGTGTCACTATATTTCTTCAGA
1 TCGATTCGATGAGGCACTGGGTGTCAAT-TA-TTCTTCAGA
* ** *
35885728 TCGATTCGATGAGGTACTGGGTACCAACT-TTCTTCAGA
1 TCGATTCGATGAGGCACTGGGTGTCAATTATTCTTCAGA
*
35885766 TCGATTCGATGAGGTACTGGGTGTCAATTATTACTTC-GA
1 TCGATTCGATGAGGCACTGGGTGTCAATTATT-CTTCAGA
* * *
35885805 ACTATCCGATGAGGCACTGGGTG
1 TCGATTCGATGAGGCACTGGGTG
35885828 CCATACTGGT
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 35 0.42
39 23 0.27
40 5 0.06
41 21 0.25
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (39 bp):
TCGATTCGATGAGGCACTGGGTGTCAATTATTCTTCAGA
Found at i:35890857 original size:68 final size:69
Alignment explanation
Indices: 35890743--35890883 Score: 230
Period size: 68 Copynumber: 2.1 Consensus size: 69
35890733 TATTATGAAT
* *
35890743 TAACGTGTCAAATCAACTTCTCATACATCTTCAATTGAAATTTAAAGTGATTA-AATGTGATAAA
1 TAACATGTCAAATCAACTTCTCATACATCTTCAATTGAAAATTAAAGTGATTATAATGTGATAAA
*
35890807 TTGA
66 TCGA
* *
35890811 TAACATGTCAAATCAATTTCTCATATATCTTCAATTGAAAATTAAAGTGATTATAATGTGATAAA
1 TAACATGTCAAATCAACTTCTCATACATCTTCAATTGAAAATTAAAGTGATTATAATGTGATAAA
35890876 TCGA
66 TCGA
35890880 TAAC
1 TAAC
35890884 TTAATGGTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 49 0.73
69 18 0.27
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (69 bp):
TAACATGTCAAATCAACTTCTCATACATCTTCAATTGAAAATTAAAGTGATTATAATGTGATAAA
TCGA
Found at i:35893773 original size:2 final size:2
Alignment explanation
Indices: 35893766--35893804 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35893756 TTAAAAAGGA
35893766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35893805 AACAAATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35901109 original size:102 final size:101
Alignment explanation
Indices: 35900917--35901109 Score: 323
Period size: 102 Copynumber: 1.9 Consensus size: 101
35900907 GACAGTGACA
* * *
35900917 GGGCTGGTTTTGTTGATGATATGAAGAGCACTTCAGGGTATTTTTTCTCTCTAGGCTTAAGAGTG
1 GGGCTAGTTTTGTTGATGATATAAAGAGCACTTCAGGGTATTTTTTCTCTCTAGGCTCAAGAGTG
* * *
35900982 TTTTGTTGGAGCTCGAAGAAGCAAAAAACAATGGAT
66 TTTAGTTAGAGCTCAAAGAAGCAAAAAACAATGGAT
35901018 GGGCTAGTTTTGTTGATGATATAAAGAGCACTTCAGGGTATTTTTTTCTCTCTAGGCTCAAGAGT
1 GGGCTAGTTTTGTTGATGATATAAAGAGCACTTCAGGGTA-TTTTTTCTCTCTAGGCTCAAGAGT
35901083 GTTTAGTTAGAGCTCAAAGAAGCAAAA
65 GTTTAGTTAGAGCTCAAAGAAGCAAAA
35901110 GATAGTGGCA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 38 0.45
102 47 0.55
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (101 bp):
GGGCTAGTTTTGTTGATGATATAAAGAGCACTTCAGGGTATTTTTTCTCTCTAGGCTCAAGAGTG
TTTAGTTAGAGCTCAAAGAAGCAAAAAACAATGGAT
Found at i:35903187 original size:3 final size:3
Alignment explanation
Indices: 35903116--35903172 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
35903106 AATACTTTAA
*
35903116 AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35903164 AAT AAT AAT
1 AAT AAT AAT
35903173 GACGGAGTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:35908299 original size:14 final size:14
Alignment explanation
Indices: 35908280--35908308 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35908270 AAGGTCTTAG
35908280 TACCTTACCACCTT
1 TACCTTACCACCTT
35908294 TACCTTACCACCTT
1 TACCTTACCACCTT
35908308 T
1 T
35908309 CTAGATTTTT
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:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (14 bp):
TACCTTACCACCTT
Found at i:35910118 original size:214 final size:215
Alignment explanation
Indices: 35909740--35910177 Score: 779
Period size: 214 Copynumber: 2.0 Consensus size: 215
35909730 TTAATCTTAG
*
35909740 TAATTTTATATCATTTAAGCTCTAACATTCATAAAAAATTAGAAATACAATTTAGTTCATATTAA
1 TAATTTTATATCATTTAAGCTCTAACATTCATAAAAAATTACAAATACAATTTAGTTCATATTAA
* ** *
35909805 ATGAACTTACCTGATAAAAAAACGAAGTCAAAATTGGGAAAATGATCAATCCTTTACTTTAGCCT
66 ATGAACTTACCTGATAAAAAAACGAAGTCAAAATTGAGAAAACAATCAATCATTTACTTTAGCCT
*
35909870 TTCCGCGATTCAAACCTGATCGATTTATTTCTTGATCTAAAATAATAATTCTATTTAATTACCAA
131 TTCCGCGATTCAAACCTGATCGATTTATTTCTTGATCAAAAATAATAATTCTATTTAATTACCAA
35909935 CTTCCAGCAACATAATTAAC
196 CTTCCAGCAACATAATTAAC
*
35909955 TAATTTTA-ATCATTTAAGCTCTAACATTCATAAAAAATTACAAATATAATTTAGTTCATATTAA
1 TAATTTTATATCATTTAAGCTCTAACATTCATAAAAAATTACAAATACAATTTAGTTCATATTAA
*
35910019 ATGAACTTACCTGATAAAAAAACGAAGTCGAAATTGAGAAAACAATCAATCATTTACTTTAGCCT
66 ATGAACTTACCTGATAAAAAAACGAAGTCAAAATTGAGAAAACAATCAATCATTTACTTTAGCCT
*
35910084 TTCCGCGATTCAAACCTGATCGATTTATTTCTTGATCAAAAATAATAATTCTATTTAATTATCAA
131 TTCCGCGATTCAAACCTGATCGATTTATTTCTTGATCAAAAATAATAATTCTATTTAATTACCAA
*
35910149 CTTCCAGCAACATAATTAGC
196 CTTCCAGCAACATAATTAAC
35910169 TAATTTTAT
1 TAATTTTAT
35910178 GCAATTAAGT
Statistics
Matches: 212, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
214 204 0.96
215 8 0.04
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.35
Consensus pattern (215 bp):
TAATTTTATATCATTTAAGCTCTAACATTCATAAAAAATTACAAATACAATTTAGTTCATATTAA
ATGAACTTACCTGATAAAAAAACGAAGTCAAAATTGAGAAAACAATCAATCATTTACTTTAGCCT
TTCCGCGATTCAAACCTGATCGATTTATTTCTTGATCAAAAATAATAATTCTATTTAATTACCAA
CTTCCAGCAACATAATTAAC
Found at i:35912448 original size:17 final size:16
Alignment explanation
Indices: 35912422--35912455 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
35912412 GTAAACATAA
*
35912422 TGTAATAAATTGTTTT
1 TGTAATAAATTATTTT
35912438 TGTATATAAATTATTTT
1 TGTA-ATAAATTATTTT
35912455 T
1 T
35912456 AAATGGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TGTAATAAATTATTTT
Found at i:35918741 original size:70 final size:70
Alignment explanation
Indices: 35918621--35918754 Score: 171
Period size: 70 Copynumber: 1.9 Consensus size: 70
35918611 AACCGCATAG
* * *
35918621 ATATATTACAGAGAACTGCAAAGCAATACAACTAGAAAAAATTCCAAGCCATATTAATATTCACA
1 ATATATTACAGAGAACTGAAAAGAAATACAACTAGAAAAAATTCCAAGCCATATTAACATTCACA
35918686 TAGAT
66 TAGAT
* * * * * *
35918691 ATATATTATAGAGAACTGAAAAGAAATATAACTTGAAAAAGA-TGCGAGCCATATTGACATTCAC
1 ATATATTACAGAGAACTGAAAAGAAATACAACTAGAAAAA-ATTCCAAGCCATATTAACATTCAC
35918755 CATTTAGTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
70 53 0.98
71 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.25
Consensus pattern (70 bp):
ATATATTACAGAGAACTGAAAAGAAATACAACTAGAAAAAATTCCAAGCCATATTAACATTCACA
TAGAT
Found at i:35941885 original size:4 final size:4
Alignment explanation
Indices: 35941868--35941994 Score: 119
Period size: 4 Copynumber: 31.8 Consensus size: 4
35941858 CAAAAAACAC
* * * * * *
35941868 ATGT ATGT ACGT ATGT ATGT ATGC ATGT ATGC ATGT ATGC ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
35941916 ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGA ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * **
35941964 ATGC ATGA ATGC ATGT ACAT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
35941995 CCAGTATGAG
Statistics
Matches: 103, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 103 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (4 bp):
ATGT
Found at i:35942032 original size:17 final size:17
Alignment explanation
Indices: 35942010--35942044 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
35942000 ATGAGTTAAG
35942010 ACAATAGAGATACTGAA
1 ACAATAGAGATACTGAA
35942027 ACAATAGAGATACTGAA
1 ACAATAGAGATACTGAA
35942044 A
1 A
35942045 GAGCAACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (17 bp):
ACAATAGAGATACTGAA
Found at i:35951434 original size:17 final size:17
Alignment explanation
Indices: 35951390--35951435 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
35951380 GCTTGATATT
*
35951390 TGAAATGGAAAAGGATG
1 TGAAATGGAAATGGATG
*
35951407 AGAAATGGAAATGAGATG
1 TGAAATGGAAATG-GATG
35951425 TGAAAT-GAAAT
1 TGAAATGGAAAT
35951436 ATGAAATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (17 bp):
TGAAATGGAAATGGATG
Found at i:35958609 original size:165 final size:164
Alignment explanation
Indices: 35958337--35958660 Score: 603
Period size: 165 Copynumber: 2.0 Consensus size: 164
35958327 AAGACTAAAT
35958337 TGTGGAGTTAAATGTTAATTTTGAGCAATAGGGATTAAATTGTAAAAAAATCAAAATTAAGGGGT
1 TGTGGAGTTAAATGTTAATTTTGAGCAATAGGGATTAAATTGTAAAAAAATCAAAATTAAGGGGT
35958402 AAAATTGAAAATAGGGAGCTAAGTTTAGCTTAGAGTGAAATTAGTCTCAGTTTAGGGACTAAATT
66 AAAATTGAAAATAGGGAGCTAAGTTTAGCTTAGAGTGAAATTAGTCTCAGTTTAGGGACTAAATT
*
35958467 GAGGAATAAACAAAATATAGTAGAAAAATAAAAAC
131 GAAGAATAAA-AAAATATAGTAGAAAAATAAAAAC
*
35958502 TGTGGAGTTAAATGTTAATTTTGAGCAATAGGGATTAAATTGTAAAAAATTCAAAATTAAGGGGT
1 TGTGGAGTTAAATGTTAATTTTGAGCAATAGGGATTAAATTGTAAAAAAATCAAAATTAAGGGGT
* *
35958567 AGAATTGAAAATAGGGAGCTAAGTTTAGCTTAGAGTGAAATTAGTCTCGGTTTAGGGACTAAATT
66 AAAATTGAAAATAGGGAGCTAAGTTTAGCTTAGAGTGAAATTAGTCTCAGTTTAGGGACTAAATT
35958632 GAAGAATAAAAAAATATAGTAGAAAAATA
131 GAAGAATAAAAAAATATAGTAGAAAAATA
35958661 GAAATTCTTG
Statistics
Matches: 155, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
164 19 0.12
165 136 0.88
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (164 bp):
TGTGGAGTTAAATGTTAATTTTGAGCAATAGGGATTAAATTGTAAAAAAATCAAAATTAAGGGGT
AAAATTGAAAATAGGGAGCTAAGTTTAGCTTAGAGTGAAATTAGTCTCAGTTTAGGGACTAAATT
GAAGAATAAAAAAATATAGTAGAAAAATAAAAAC
Found at i:35959408 original size:18 final size:18
Alignment explanation
Indices: 35959367--35959413 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
35959357 GCTTGATATT
*
35959367 TGAAATGG-AATAATATG
1 TGAAATGGAAATAAGATG
* *
35959384 AGAAATGGAAATGAGATG
1 TGAAATGGAAATAAGATG
35959402 TGAAAT-GAAATA
1 TGAAATGGAAATA
35959414 TGAAATGGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (18 bp):
TGAAATGGAAATAAGATG
Found at i:35960434 original size:9 final size:9
Alignment explanation
Indices: 35960417--35960504 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
35960407 ATGATATTTT
*
35960417 AAAATTATA
1 AAAACTATA
35960426 AAAACTAT-
1 AAAACTATA
35960434 AAAA-TA-A
1 AAAACTATA
35960441 TAAAACTATA
1 -AAAACTATA
**
35960451 AAATTTATA
1 AAAACTATA
35960460 TAAAACTATA
1 -AAAACTATA
*
35960470 AAAAGTTATTTTA
1 AAAA-CTA---TA
35960483 AAAACTATA
1 AAAACTATA
*
35960492 AGAACTATA
1 AAAACTATA
35960501 AAAA
1 AAAA
35960505 AAAGTTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
7 2 0.03
8 8 0.13
9 33 0.54
10 10 0.16
12 2 0.03
13 6 0.10
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAACTATA
Found at i:35963558 original size:21 final size:22
Alignment explanation
Indices: 35963532--35963577 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35963522 TGTAACAAGA
* **
35963532 TTTTT-ATTTGACTTGTTTAAT
1 TTTTTAATTTAACTTGAATAAT
35963553 TTTTTAATTTAACTTGAATAAT
1 TTTTTAATTTAACTTGAATAAT
35963575 TTT
1 TTT
35963578 ACTCTATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTTAATTTAACTTGAATAAT
Found at i:35965451 original size:2 final size:2
Alignment explanation
Indices: 35965444--35965553 Score: 113
Period size: 2 Copynumber: 57.5 Consensus size: 2
35965434 NNNNNNNNNN
* * *
35965444 AT AT AT AT AT AT -T AT -T AT TT AT -T AT -T AT AT AT AC AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
35965482 AT AT TT TT AT A- 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
* * *
35965523 AT AT AT AT AT AT AG AT AT AG AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35965554 CACATATACC
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
1 5 0.06
2 84 0.94
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35971676 original size:45 final size:43
Alignment explanation
Indices: 35971611--35971706 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
35971601 TGAATACAAA
* * * *
35971611 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCCAAGAAAAT
1 AGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCAAAG-AAAC
**
35971656 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAC
1 AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGAAAC
35971699 AGATCTTG
1 AGATCTTG
35971707 CCCCCCTAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 11 0.24
44 15 0.33
45 19 0.42
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (43 bp):
AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGAAAC
Found at i:35971882 original size:44 final size:45
Alignment explanation
Indices: 35971826--35972183 Score: 319
Period size: 44 Copynumber: 8.0 Consensus size: 45
35971816 TCAATCGAAA
* **
35971826 AAAGCGGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
* * * *
35971870 ATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCCAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
* * ** * *
35971915 AAAGTAGATCTTATCTTCATGTATTGG-CGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
* * * * * * *
35971959 ATACCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC-AAAG
** * *
35972005 AAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTATATCAGAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
* * * * * * *
35972049 ATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
** * * * *
35972094 AAAGCAGATCTTGTCTTCATGTATTAG-CATGAAGTAGATCAGAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
* * *
35972138 AAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAG
1 AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
35972183 A
1 A
35972184 TACAAGTCTC
Statistics
Matches: 236, Mismatches: 73, Indels: 9
0.74 0.23 0.03
Matches are distributed among these distances:
44 113 0.48
45 99 0.42
46 24 0.10
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (45 bp):
AAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCAAAG
Found at i:35971983 original size:89 final size:89
Alignment explanation
Indices: 35971826--35972183 Score: 511
Period size: 89 Copynumber: 4.0 Consensus size: 89
35971816 TCAATCGAAA
* * *
35971826 AAAGCGGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGTCTTCCCA
* * *
35971891 TACTGGTGGTGAAGTAGATCCAAG
66 TACTGGTGGCGAAGCAGATCAAAG
* * * *
35971915 AAAGTAGATCTTATCTTCATGTATTGGCGTGAAGTAGATC-GAAGATACCAGATCTTGTCTCCCC
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAG-AGATACCAGATCTTGTCTTCCC
35971979 ATACTGGTGGCGAAGCAGATCGAAAG
65 ATACTGGTGGCGAAGCAGATC-AAAG
* *
35972005 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTATATCAGAGATACCAGATCTTGCCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGTCTTCCCA
35972070 TACTGGTGGCGAAGCAGATCAAAG
66 TACTGGTGGCGAAGCAGATCAAAG
* * * * *
35972094 AAAGCAGATCTTGTCTTCATGTATTAGCATGAAGTAGATCAGAGAAAGCAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGTCTTCCCA
* * *
35972159 TACTGGTGGTGAAGTAGATCGAAG
66 TACTGGTGGCGAAGCAGATCAAAG
35972183 A
1 A
35972184 TACAAGTCTC
Statistics
Matches: 240, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
89 159 0.66
90 80 0.33
91 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (89 bp):
AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGTCTTCCCA
TACTGGTGGCGAAGCAGATCAAAG
Found at i:35972132 original size:179 final size:178
Alignment explanation
Indices: 35971819--35972181 Score: 548
Period size: 179 Copynumber: 2.0 Consensus size: 178
35971809 AGTGGAATCA
* * *
35971819 ATCGAAAAAAGCGGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGT
1 ATCGAAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGC
* * * * * *
35971884 CTTCCCATACTGGTGGTGAAGTAGATCCAAGAAAGTAGATCTTATCTTCATGTATTGGCGTGAAG
66 CTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTATCTTCATGTATTAGCATGAAG
*
35971949 TAGATC-GAAGATACCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAG
131 TAGATCAG-AGAAACCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAG
* *
35971997 ATCGAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTATATCAGAGATACCAGATCTTG
1 ATCGAAA-AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTG
*
35972062 CCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTAGCATGAA
65 CCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTATCTTCATGTATTAGCATGAA
* * * *
35972127 GTAGATCAGAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAG
130 GTAGATCAGAGAAACCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAG
35972176 ATCGAA
1 ATCGAA
35972182 GATACAAGTC
Statistics
Matches: 166, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
178 7 0.04
179 158 0.95
180 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (178 bp):
ATCGAAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGC
CTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTATCTTCATGTATTAGCATGAAG
TAGATCAGAGAAACCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAG
Found at i:35973991 original size:13 final size:12
Alignment explanation
Indices: 35973973--35974002 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
35973963 TTCCATAGTT
35973973 TATTTATATATTA
1 TATTTATATA-TA
35973986 TATTTATATATA
1 TATTTATATATA
35973998 TATTT
1 TATTT
35974003 TGTTCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTATATATA
Found at i:35977060 original size:18 final size:18
Alignment explanation
Indices: 35977019--35977060 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
35977009 GATTTTGTTG
35977019 AGTTATCTTTTCCATTTC
1 AGTTATCTTTTCCATTTC
*
35977037 ATTTATCTTTTCCATTTC
1 AGTTATCTTTTCCATTTC
*
35977055 GGTTAT
1 AGTTAT
35977061 TTAAAGCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.57
Consensus pattern (18 bp):
AGTTATCTTTTCCATTTC
Found at i:35977810 original size:3 final size:3
Alignment explanation
Indices: 35977802--35977845 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
35977792 GTTATTTTTG
*
35977802 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35977846 GTAGTAGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:35977850 original size:3 final size:3
Alignment explanation
Indices: 35977844--35977869 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35977834 TTATTATTAT
35977844 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
35977870 TTATTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:35978030 original size:25 final size:27
Alignment explanation
Indices: 35978002--35978062 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
35977992 CTTAGTTTTT
35978002 ATATATATACATTTAT-AT-TTTTATA
1 ATATATATACATTTATCATATTTTATA
* *
35978027 ATATTTATACATTTTTCATATTTTATA
1 ATATATATACATTTATCATATTTTATA
35978054 ATATATATA
1 ATATATATA
35978063 TATATATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 14 0.45
26 2 0.06
27 15 0.48
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATATATACATTTATCATATTTTATA
Found at i:35978065 original size:6 final size:6
Alignment explanation
Indices: 35978050--35978088 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
35978040 TTTCATATTT
* *
35978050 TATA-A TATATA TATATA TATAGA TATAGA TATAGA TATA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATA
35978089 CACATATACC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (6 bp):
TATAGA
Found at i:35980950 original size:101 final size:101
Alignment explanation
Indices: 35980835--35981121 Score: 468
Period size: 101 Copynumber: 2.8 Consensus size: 101
35980825 AAAGTGATGG
35980835 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
35980900 TATGTGCAGGCTACTATGTATACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGTATACCGGATAGCTTCGA
*
35980936 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGTATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
**
35981001 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGTATACCGGATAGCTTCGA
* * * *
35981037 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
* *
35981101 ACTATGTGTATGCTACTATGT
64 ACTATGTGCAGGCTACTATGT
35981122 GAATCCACAT
Statistics
Matches: 173, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
101 137 0.79
102 32 0.18
103 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGTATACCGGATAGCTTCGA
Found at i:35980955 original size:51 final size:50
Alignment explanation
Indices: 35980835--35981118 Score: 283
Period size: 51 Copynumber: 5.6 Consensus size: 50
35980825 AAAGTGATGG
* * * * *
35980835 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GTTCGA
* * * *
35980885 TCGCATGTGTAGTACTATGTGCAGGCTACTATGTATACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TTCGA
* *
35980936 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCG-
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-G---GATAGTTCGA
* *
35980989 T-A--TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TTCGA
* *
35981037 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT--TCGA
* * *
35981088 TCACATGTGTAGTACTATGTGTATGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
35981119 TGTGAATCCA
Statistics
Matches: 195, Mismatches: 26, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
46 5 0.03
47 3 0.02
48 1 0.01
49 2 0.01
50 69 0.35
51 103 0.53
52 3 0.02
53 1 0.01
54 3 0.02
55 5 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTCGA
Found at i:35981122 original size:26 final size:25
Alignment explanation
Indices: 35981042--35981122 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
35981032 TTCGATCACG
*
35981042 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTG-ATGCTACTA
* * *
35981068 CGTGTA-T-CGGATAGTGATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGATGCT-ACTA
35981093 TGTGTAGTACTATGTGTATGCTACTA
1 TGTGTAGTACTATGTG-ATGCTACTA
35981119 TGTG
1 TGTG
35981123 AATCCACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (25 bp):
TGTGTAGTACTATGTGATGCTACTA
Found at i:35984294 original size:50 final size:50
Alignment explanation
Indices: 35984191--35984477 Score: 254
Period size: 50 Copynumber: 5.6 Consensus size: 50
35984181 TGCGAGCCAG
* * *
35984191 TGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGATAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATGAGAGGTCCCA
* * *
35984247 TGTAAGACCATGTTTGGGGCATAGCGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * *
35984297 TGTAAGACTATGTCTGGGACATGGCGTTGGCACCGGGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * * * **
35984347 CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * * * * * * * ** *
35984397 TGTAAGACCATATCTGAGATATAGCATTGGCA--GTACAGGAAACATCTCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATGAGAGGTCCCA
*
35984446 TGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TGTAAGACCATGTCTGGGACATGGCGTTGGCA
35984478 TGTTATTATC
Statistics
Matches: 192, Mismatches: 38, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
48 1 0.01
49 36 0.19
50 123 0.64
53 3 0.02
55 1 0.01
56 28 0.15
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
Found at i:35984856 original size:22 final size:22
Alignment explanation
Indices: 35984828--35984870 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35984818 CTCTCTGATA
*
35984828 TTTAGCACGTCAGTGCTCTCTT
1 TTTAGCACATCAGTGCTCTCTT
*
35984850 TTTAGCACATCTGTGCTCTCT
1 TTTAGCACATCAGTGCTCTCT
35984871 GTATAACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.16, T:0.42
Consensus pattern (22 bp):
TTTAGCACATCAGTGCTCTCTT
Found at i:35990134 original size:23 final size:23
Alignment explanation
Indices: 35990107--35990150 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35990097 ATTGGAAAAT
*
35990107 AATTTAATTGAAATAATTAATTA
1 AATTTAATTGAAATAAATAATTA
* *
35990130 AATTTATTTTAAATAAATAAT
1 AATTTAATTGAAATAAATAAT
35990151 ATTTTGGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTTAATTGAAATAAATAATTA
Found at i:35994712 original size:51 final size:51
Alignment explanation
Indices: 35994576--35995142 Score: 658
Period size: 51 Copynumber: 11.5 Consensus size: 51
35994566 TTTAATCTGT
*
35994576 TGCAATGCCAGGAAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--AC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* * *
35994622 TGCAACGCCAGGGAAA-AAGATTCGTTGCCTTCAGTTTTAATCTGTTCCAC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* *
35994672 TGCAATGCCAGGGAAATAAGATTCGCTCCCTTCAGCTTTAATTTGTTCCAC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* * *
35994723 TGCAATGCCAAGGAAATAAGATTCGTTGCCTTCAACTTTAATC---T--AC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* * *
35994769 TACAACGCCAGGGAAA-AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCAC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
*
35994819 TGCAATGCCAGGGAAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTTCAC
1 TGCAATGCCAGGG-AAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
** * *
35994871 TGCAATGCCAAAGAAATGAGATTCGCTGTCTTCAGCTTTAATC---T--AC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* *
35994917 TGCGATGCCAGGGAAATAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* * * * * * *
35994968 TGCAACGCCAAGGAAATTAGATTCGCTGCATTCATCTTTAATC--TACC-G
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
* *
35995016 TG--ATGCCAGGGAAATGAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
1 TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
** * *
35995065 TGCAACT-CCAAAGAAATGAGATTCGCTGCCTTCATCTTTAATCTGTTCCAC
1 TGCAA-TGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
*
35995116 TGCAATGCCAAGGAAATAAGATTCGCT
1 TGCAATGCCAGGGAAATAAGATTCGCT
35995143 ATGATAACTT
Statistics
Matches: 439, Mismatches: 57, Indels: 45
0.81 0.11 0.08
Matches are distributed among these distances:
45 47 0.11
46 101 0.23
48 9 0.02
49 6 0.01
50 31 0.07
51 201 0.46
52 44 0.10
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (51 bp):
TGCAATGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCAC
Found at i:35994861 original size:97 final size:97
Alignment explanation
Indices: 35994576--35995142 Score: 568
Period size: 97 Copynumber: 5.8 Consensus size: 97
35994566 TTTAATCTGT
* *
35994576 TGCAATGCC-AGGAAAATAAGATTCGCTGCCTTCAGCTTTAATC-T--ACTGCAACGCCAGGGAA
1 TGCAACGCCAAGG-AAATAAGATTCGCTGCCTTCAGCTTTAATCTTCCACTGCAATGCCAGGGAA
* *
35994637 A-AAGATTCGTTGCCTTCAGTTTTAATCTGTTCCAC
65 ATAAGATTCGCTGCCTTCAGCTTTAATC--TT-CAC
* * * * *
35994672 TGCAATGCCAGGGAAATAAGATTCGCTCCCTTCAGCTTTAATTTGTTCCACTGCAATGCCAAGGA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAA--TCTTCCACTGCAATGCCAGGGA
* *
35994737 AATAAGATTCGTTGCCTTCAACTTTAATC-T-AC
64 AATAAGATTCGCTGCCTTCAGCTTTAATCTTCAC
* * *
35994769 TACAACGCCAGGGAAA-AAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTGCAATGCCAGGGA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC--TTCCACTGCAATGCCAGGG-
35994833 AAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTTCAC
63 AAATAAGATTCGCTGCCTTCAGCTTTAATC---TTCAC
* * * * *
35994871 TGCAATGCCAAAGAAATGAGATTCGCTGTCTTCAGCTTTAATC-T--ACTGCGATGCCAGGGAAA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTCCACTGCAATGCCAGGGAAA
*
35994933 TAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
66 TAAGATTCGCTGCCTTCAGCTTTAATC--TT-CAC
* * * * *
35994968 TGCAACGCCAAGGAAATTAGATTCGCTGCATTCATCTTTAATCTACC-GTG--ATGCCAGGGAAA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTCCACTGCAATGCCAGGGAAA
* *
35995030 TGAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
66 TAAGATTCGCTGCCTTCAGCTTTAATC--TT-CAC
* * * * *
35995065 TGCAACTCCAAAGAAATGAGATTCGCTGCCTTCATCTTTAATCTGTTCCACTGCAATGCCAAGGA
1 TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC--TTCCACTGCAATGCCAGGGA
35995130 AATAAGATTCGCT
64 AATAAGATTCGCT
35995143 ATGATAACTT
Statistics
Matches: 402, Mismatches: 44, Indels: 44
0.82 0.09 0.09
Matches are distributed among these distances:
94 1 0.00
96 78 0.19
97 200 0.50
98 15 0.04
99 7 0.02
100 3 0.01
101 17 0.04
102 58 0.14
103 23 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (97 bp):
TGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTTCCACTGCAATGCCAGGGAAA
TAAGATTCGCTGCCTTCAGCTTTAATCTTCAC
Found at i:35994916 original size:148 final size:148
Alignment explanation
Indices: 35994576--35995142 Score: 729
Period size: 148 Copynumber: 3.8 Consensus size: 148
35994566 TTTAATCTGT
35994576 TGCAATGCC-AGGAAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAA-A
1 TGCAATGCCAAGG-AAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATA
* * * *
35994639 AGATTCGTTGCCTTCAGTTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGCTCCCTT
65 AGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCGCTGCCTT
* *
35994704 CAGCTTTAATTTGTTCCAC
130 CAGCTTTAATCTGTTACAC
* * *
35994723 TGCAATGCCAAGGAAATAAGATTCGTTGCCTTCAACTTTAATCTACTACAACGCCAGGGAAA-AA
1 TGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAA
* *
35994787 GATTCGCTGCCTTTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAAATAAGATTCGCTGCCTT
66 GATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAAGG-AAATAAGATTCGCTGCCTT
*
35994852 CAGCTTTAATCTGTTTCAC
130 CAGCTTTAATCTGTTACAC
* * * * *
35994871 TGCAATGCCAAAGAAATGAGATTCGCTGTCTTCAGCTTTAATCTACTGCGATGCCAGGGAAATAA
1 TGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAA
* * * *
35994936 GATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATTAGATTCGCTGCATTC
66 GATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCGCTGCCTTC
*
35995001 ATCTTTAATC---TAC-C
131 AGCTTTAATCTGTTACAC
* * * * **
35995015 GTG--ATGCCAGGGAAATGAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACTCCAAAG
1 -TGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--ACTGCAACGCCAGGG
* *
35995078 AAATGAGATTCGCTGCCTTCATCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCGCT
60 AAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCGCT
35995143 ATGATAACTT
Statistics
Matches: 372, Mismatches: 39, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
143 35 0.09
144 1 0.00
145 4 0.01
146 1 0.00
147 99 0.27
148 189 0.51
149 43 0.12
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (148 bp):
TGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAA
GATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCGCTGCCTTC
AGCTTTAATCTGTTACAC
Found at i:36005706 original size:16 final size:16
Alignment explanation
Indices: 36005685--36005718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36005675 TTTTATGATG
* *
36005685 AAATGCTATGCAGTCA
1 AAATGCCATGCAATCA
36005701 AAATGCCATGCAATCA
1 AAATGCCATGCAATCA
36005717 AA
1 AA
36005719 GCAAAACATA
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:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAATCA
Found at i:36007342 original size:20 final size:20
Alignment explanation
Indices: 36007300--36007342 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
36007290 TTTTTTGACA
*
36007300 AAAATAAAAAAATAGGATAT
1 AAAATAAAAAAATAGCATAT
*
36007320 AAAATAAAATAAAT-GCATTT
1 AAAATAAAA-AAATAGCATAT
36007340 AAA
1 AAA
36007343 GTGTTTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATAAAAAAATAGCATAT
Found at i:36008501 original size:13 final size:13
Alignment explanation
Indices: 36008466--36008529 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
36008456 TCCATGTAAA
*
36008466 CATTTCATATAAT
1 CATTTCATATAAC
*
36008479 TATTTCCATATAAC
1 CATTT-CATATAAC
*
36008493 CGA-TTCATATAGC
1 C-ATTTCATATAAC
*
36008506 CATTTCATATAAT
1 CATTTCATATAAC
36008519 CATTTCATATA
1 CATTTCATATA
36008530 TTCTTTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.02
13 31 0.74
14 9 0.21
15 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (13 bp):
CATTTCATATAAC
Found at i:36014384 original size:17 final size:16
Alignment explanation
Indices: 36014342--36014385 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
36014332 TCCGTGCTTA
36014342 AGAATTGAGAGAATGG
1 AGAATTGAGAGAATGG
36014358 ATGAATTGAGAGAATTAGG
1 A-GAATTGAGAGAA-T-GG
36014377 AGAA-TGAGA
1 AGAATTGAGA
36014386 TTTGAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 17 0.68
18 4 0.16
19 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.20
Consensus pattern (16 bp):
AGAATTGAGAGAATGG
Found at i:36020973 original size:8 final size:8
Alignment explanation
Indices: 36020930--36020989 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
36020920 TATTATAGGT
36020930 TTTTATAA
1 TTTTATAA
**
36020938 TAGTAT-A
1 TTTTATAA
*
36020945 TTTTGATAT
1 TTTT-ATAA
36020954 TTTTATAA
1 TTTTATAA
36020962 -TTTATAA
1 TTTTATAA
36020969 TTTTATAA
1 TTTTATAA
36020977 -TTTATATA
1 TTTTATA-A
36020985 TTTTA
1 TTTTA
36020990 AAATAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
7 16 0.39
8 17 0.41
9 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
TTTTATAA
Found at i:36020974 original size:15 final size:15
Alignment explanation
Indices: 36020931--36020989 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
36020921 ATTATAGGTT
** *
36020931 TTTATAATAGTATAT
1 TTTATAATTTTATAA
*
36020946 TTTGATATTTTTATAA
1 TTT-ATAATTTTATAA
36020962 TTTATAATTTTATAA
1 TTTATAATTTTATAA
36020977 TTTATATATTTTA
1 TTTATA-ATTTTA
36020990 AAATAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 20 0.54
16 17 0.46
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTATAATTTTATAA
Found at i:36022393 original size:12 final size:12
Alignment explanation
Indices: 36022373--36022413 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
36022363 AAAGTAAATT
*
36022373 TTCACCATTTTC
1 TTCAACATTTTC
36022385 TTCAACATTTTTTC
1 TTCAACA--TTTTC
36022399 TTCAACATTTTC
1 TTCAACATTTTC
36022411 TTC
1 TTC
36022414 TTCTCCTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 14 0.54
14 12 0.46
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (12 bp):
TTCAACATTTTC
Found at i:36022399 original size:14 final size:14
Alignment explanation
Indices: 36022380--36022416 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36022370 ATTTTCACCA
36022380 TTTTCTTCAACATT
1 TTTTCTTCAACATT
36022394 TTTTCTTCAACATT
1 TTTTCTTCAACATT
36022408 TTCTTCTTC
1 TT-TTCTTC
36022417 TCCTCCACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTCTTCAACATT
Found at i:36025815 original size:46 final size:46
Alignment explanation
Indices: 36025762--36025864 Score: 170
Period size: 46 Copynumber: 2.2 Consensus size: 46
36025752 GAGGGGGTGT
*
36025762 TAGGATATTATTATGGGATATTATATTTTAGCAATTTGATTCCTAA
1 TAGGATATTATTATGGGATATTATATCTTAGCAATTTGATTCCTAA
* *
36025808 TAGGATATTATTATGGGATATTATCTCTTAGCAATTTGGTTCCTAA
1 TAGGATATTATTATGGGATATTATATCTTAGCAATTTGATTCCTAA
*
36025854 TGGGATATTAT
1 TAGGATATTAT
36025865 AGGATATTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (46 bp):
TAGGATATTATTATGGGATATTATATCTTAGCAATTTGATTCCTAA
Found at i:36043050 original size:22 final size:23
Alignment explanation
Indices: 36043006--36043050 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
36042996 TTTTTCGTAG
** *
36043006 ATTTATATTTTTATTTTTTAAAA
1 ATTTATATTTTTAAATTTAAAAA
36043029 ATTTA-ATTTTTAAATTTAAAAA
1 ATTTATATTTTTAAATTTAAAAA
36043051 TTCAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTATATTTTTAAATTTAAAAA
Found at i:36043489 original size:5 final size:5
Alignment explanation
Indices: 36043479--36043504 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
36043469 TGAGCATTCG
36043479 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
36043505 AATTTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:36043977 original size:17 final size:18
Alignment explanation
Indices: 36043941--36043980 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
36043931 GGGTGAGAAG
36043941 TAAAAATTTAGGGGGAAA
1 TAAAAATTTAGGGGGAAA
**
36043959 TAAAAATTTTTGGGG-AA
1 TAAAAATTTAGGGGGAAA
36043976 TAAAA
1 TAAAA
36043981 GTTTGAGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.28
Consensus pattern (18 bp):
TAAAAATTTAGGGGGAAA
Found at i:36044366 original size:9 final size:9
Alignment explanation
Indices: 36044352--36044388 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
36044342 TATAGTTGGA
36044352 TATTCGAAT
1 TATTCGAAT
36044361 TATTCGAAT
1 TATTCGAAT
*
36044370 TATTCGAGT
1 TATTCGAAT
36044379 TATTCGAAT
1 TATTCGAAT
36044388 T
1 T
36044389 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:36044459 original size:9 final size:9
Alignment explanation
Indices: 36044442--36044472 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
36044432 TCAAGTTGAT
36044442 TCGAATAAC
1 TCGAATAAC
*
36044451 TCGATTAAC
1 TCGAATAAC
36044460 TCGAATAAC
1 TCGAATAAC
36044469 TCGA
1 TCGA
36044473 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:36051371 original size:14 final size:15
Alignment explanation
Indices: 36051352--36051381 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36051342 ATATACTAAG
36051352 ATTAAAC-TTAATTA
1 ATTAAACTTTAATTA
36051366 ATTAAACTTTAATTA
1 ATTAAACTTTAATTA
36051381 A
1 A
36051382 CCAAACCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTAAACTTTAATTA
Found at i:36052625 original size:13 final size:13
Alignment explanation
Indices: 36052607--36052631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36052597 GCAACACGGA
36052607 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
36052620 AAAAAAGAAAAA
1 AAAAAAGAAAAA
36052632 CAGAACACGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:36052952 original size:18 final size:18
Alignment explanation
Indices: 36052892--36052952 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
36052882 AATTAATATA
* *
36052892 AAAATTAAAAATATTGTT
1 AAAATTTAAAATATTATT
36052910 AAAATTTAAAA-ATTA-T
1 AAAATTTAAAATATTATT
**
36052926 AATTTTTTAAAATATTATT
1 AA-AATTTAAAATATTATT
36052945 AAAATTTA
1 AAAATTTA
36052953 TATAAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 18 0.53
19 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATTTAAAATATTATT
Found at i:36053511 original size:20 final size:19
Alignment explanation
Indices: 36053488--36053555 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
36053478 CATTTTGGAT
36053488 TTAACTTTTAAATTTTTTTA
1 TTAA-TTTTAAATTTTTTTA
* *
36053508 TTAATTTTTAATTTTTTAAA
1 TTAATTTTAAATTTTTT-TA
* * *
36053528 TT-TTTTTTAATATTTTTA
1 TTAATTTTAAATTTTTTTA
*
36053546 TTAACTTTAA
1 TTAATTTTAA
36053556 TAATGTATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
18 3 0.08
19 28 0.74
20 7 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAATTTTAAATTTTTTTA
Found at i:36055899 original size:7 final size:7
Alignment explanation
Indices: 36055889--36055920 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
36055879 ATTCGATTGA
36055889 TATTTAG
1 TATTTAG
36055896 TATTTAG
1 TATTTAG
36055903 TATTTAG
1 TATTTAG
*
36055910 AATTTAG
1 TATTTAG
36055917 TATT
1 TATT
36055921 ATGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
TATTTAG
Found at i:36056595 original size:18 final size:18
Alignment explanation
Indices: 36056569--36056603 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36056559 AGGTGCGTTT
*
36056569 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
36056587 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
36056604 TCATTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:36057010 original size:17 final size:18
Alignment explanation
Indices: 36056969--36057010 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
36056959 TTTACTAACC
* *
36056969 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
36056987 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
36057004 ATTAATA
1 ATTAATA
36057011 ATTTCAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:36059393 original size:35 final size:35
Alignment explanation
Indices: 36059331--36059416 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
36059321 ATTTTATTTG
*
36059331 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
36059364 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
36059400 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
36059417 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:36059402 original size:25 final size:23
Alignment explanation
Indices: 36059358--36059418 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
36059348 TGATATTTAA
*
36059358 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
36059382 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
36059407 ATATTATTAAAT
1 ATATAATTAAAT
36059419 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:36060076 original size:12 final size:12
Alignment explanation
Indices: 36060059--36060083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36060049 GGTGTTCATT
36060059 CGGTTAACCGAC
1 CGGTTAACCGAC
36060071 CGGTTAACCGAC
1 CGGTTAACCGAC
36060083 C
1 C
36060084 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:36061671 original size:24 final size:27
Alignment explanation
Indices: 36061634--36061697 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
36061624 AATTGCGGAT
*
36061634 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
36061658 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
36061684 TTGTGATTGAATTG
1 TAATGATTGAATTG
36061698 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:36064195 original size:126 final size:125
Alignment explanation
Indices: 36063880--36064231 Score: 566
Period size: 126 Copynumber: 2.8 Consensus size: 125
36063870 CCCAAACATG
36063880 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
36063945 TAGAAGCGATTTTATATTATTTACTCAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * *
36064004 CTACTGTAGCAAAAGCGTG-CTGACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * * *
36064068 CTAGAAGCGATTTTATACTATTTGCTTAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
65 CTAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
* *
36064130 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
36064195 TAGAAGCGATTTTATACTATTTTA-TCAGAAACGTCAA
66 TAGAAGCGATTTTATACTA-TTTACTCAGAAACGTCAA
36064232 CTCGAAATTA
Statistics
Matches: 208, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
123 1 0.00
124 92 0.44
125 6 0.03
126 105 0.50
127 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:36065473 original size:13 final size:12
Alignment explanation
Indices: 36065457--36065494 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
36065447 TAATTTAACG
*
36065457 TTCCTATTTGTTT
1 TTCCCATTT-TTT
36065470 TTCCCA-TTTTT
1 TTCCCATTTTTT
36065481 TTCCCATTTTTT
1 TTCCCATTTTTT
36065493 TT
1 TT
36065495 TCTTTTGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 9 0.39
12 9 0.39
13 5 0.22
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (12 bp):
TTCCCATTTTTT
Found at i:36065490 original size:10 final size:11
Alignment explanation
Indices: 36065467--36065493 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
36065457 TTCCTATTTG
36065467 TTTTTCCCATT
1 TTTTTCCCATT
36065478 TTTTTCCCATT
1 TTTTTCCCATT
36065489 TTTTT
1 TTTTT
36065494 TTCTTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTCCCATT
Found at i:36066319 original size:42 final size:42
Alignment explanation
Indices: 36066204--36066323 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 42
36066194 TATTTTAGAA
* * * *
36066204 CCACACAGGCAATGGACATGGGCATGTGCCCAGG-CTGTGTAAG
1 CCACACGGGCAA-GGACATGAGCGTGTGTCCAGGTC-GTGTAAG
* * * * *
36066247 TCACGCGAGCAAAGACATGA-CGTGTGTCCAGGTCGTGTGAG
1 CCACACGGGCAAGGACATGAGCGTGTGTCCAGGTCGTGTAAG
36066288 CCACACGGGCAAGGACATGAGCGTGTGTCCAGGTCG
1 CCACACGGGCAAGGACATGAGCGTGTGTCCAGGTCG
36066324 CGTGGCATAT
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
41 32 0.52
42 22 0.35
43 8 0.13
ACGTcount: A:0.24, C:0.25, G:0.34, T:0.17
Consensus pattern (42 bp):
CCACACGGGCAAGGACATGAGCGTGTGTCCAGGTCGTGTAAG
Found at i:36069791 original size:19 final size:19
Alignment explanation
Indices: 36069767--36069829 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
36069757 AGTTTCTGGT
36069767 GATGCCTTTCGGCTTGATG
1 GATGCCTTTCGGCTTGATG
*
36069786 GATGCCTTTCGGCTTGACG
1 GATGCCTTTCGGCTTGATG
36069805 GATGCCTTTCGGCTTGATG
1 GATGCCTTTCGGCTTGATG
*
36069824 AATGCC
1 GATGCC
36069830 CCGACAGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.13, C:0.24, G:0.30, T:0.33
Consensus pattern (19 bp):
GATGCCTTTCGGCTTGATG
Found at i:36073331 original size:105 final size:104
Alignment explanation
Indices: 36073111--36073331 Score: 246
Period size: 104 Copynumber: 2.1 Consensus size: 104
36073101 TGAAGGGTTT
* * * * *
36073111 ACACGGACGTGTGTCTAGGCCGTGTAACTCACTGTTTGTGACTTAGGACCACACAGCTAGAGAAA
1 ACACGGACGTGTCTCTAGGACGTGTAACTCACCGTTTATGACTTAGAACCACACAGCTAGAGAAA
* * * *
36073176 TGGGCGTGTGCCCAAGCCTTGTGAGTCATACGGGCAAGG
66 TGGGCATGTGCCCAAGCCGTATGAGTCACACGGGCAAGG
* * * * *
36073215 GCACGGACGTGTCTCTAGGACGTGTAACTCACCGTTTAT-ATTTTAGAACCACACGGGTAGTGGA
1 ACACGGACGTGTCTCTAGGACGTGTAACTCACCGTTTATGA-CTTAGAACCACACAGCTAG-AGA
* * *
36073279 CATGGGCATGTGCCTAGGCCGTATGAGTCACACGGGCAAGG
64 AATGGGCATGTGCCCAAGCCGTATGAGTCACACGGGCAAGG
* *
36073320 ACATGGGCGTGT
1 ACACGGACGTGT
36073332 GTTCAAGCCG
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
103 1 0.01
104 49 0.52
105 45 0.47
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.23
Consensus pattern (104 bp):
ACACGGACGTGTCTCTAGGACGTGTAACTCACCGTTTATGACTTAGAACCACACAGCTAGAGAAA
TGGGCATGTGCCCAAGCCGTATGAGTCACACGGGCAAGG
Found at i:36075128 original size:19 final size:20
Alignment explanation
Indices: 36075106--36075146 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
36075096 AAAAAAAAAC
36075106 TTTATTTCTAAA-A-TTTAAA
1 TTTATTT-TAAACATTTTAAA
36075125 TTTATTTTAAACATTTTAAA
1 TTTATTTTAAACATTTTAAA
36075145 TT
1 TT
36075147 AAGTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTTTAAACATTTTAAA
Found at i:36078411 original size:3 final size:3
Alignment explanation
Indices: 36078398--36078450 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
36078388 TATAGTGGTC
36078398 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36078444 TAT TAT T
1 TAT TAT T
36078451 TTGTTACCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.