Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 110 of 131
Found at i:19633861 original size:39 final size:41
Alignment explanation
Indices: 19633818--19633895 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
19633808 AGTCAATTTT
19633818 AAAATATT-AATAAAGA-AAAATAT-CGAAAAAG-TAAAAATA
1 AAAATATTAAAT-AAGATAAAATATAC-AAAAAGTTAAAAATA
19633857 AAAATATTAAATAAGATAAAATATACAAAAAGTTAAAAA
1 AAAATATTAAATAAGATAAAATATACAAAAAGTTAAAAA
19633896 GACGATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
39 12 0.34
40 16 0.46
41 7 0.20
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (41 bp):
AAAATATTAAATAAGATAAAATATACAAAAAGTTAAAAATA
Found at i:19633878 original size:40 final size:40
Alignment explanation
Indices: 19633818--19633895 Score: 108
Period size: 39 Copynumber: 1.9 Consensus size: 40
19633808 AGTCAATTTT
19633818 AAAATATTAATAAAGAAAAATAT-CGAAAAAG-TAAAAATA
1 AAAATATTAATAAAGAAAAATATAC-AAAAAGTTAAAAATA
19633857 AAAATATTAA-ATAAGATAAAATATACAAAAAGTTAAAAA
1 AAAATATTAATA-AAGA-AAAATATACAAAAAGTTAAAAA
19633896 GACGATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
38 1 0.03
39 14 0.40
40 13 0.37
41 7 0.20
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (40 bp):
AAAATATTAATAAAGAAAAATATACAAAAAGTTAAAAATA
Found at i:19643584 original size:17 final size:18
Alignment explanation
Indices: 19643550--19643592 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
19643540 GATCCACCTT
*
19643550 AATGTATCCTCTACCACA
1 AATGTATCCTCCACCACA
*
19643568 TATGTATCC-CCACCACA
1 AATGTATCCTCCACCACA
19643585 AATGTATC
1 AATGTATC
19643593 ATTTTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.28
Consensus pattern (18 bp):
AATGTATCCTCCACCACA
Found at i:19644730 original size:19 final size:18
Alignment explanation
Indices: 19644699--19644734 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19644689 TTCCTGTTAA
*
19644699 TTGGGATGGCATGGCATT
1 TTGGGATGACATGGCATT
19644717 TTGGTGATGACATGGCAT
1 TTGG-GATGACATGGCAT
19644735 GTTAGGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.33
Consensus pattern (18 bp):
TTGGGATGACATGGCATT
Found at i:19649627 original size:3 final size:3
Alignment explanation
Indices: 19649621--19649653 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19649611 AATAATAATA
19649621 ATT ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19649654 CTTAAGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:19650881 original size:9 final size:9
Alignment explanation
Indices: 19650855--19650901 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
19650845 TGTCTTTCTT
19650855 TTTTTTTAA
1 TTTTTTTAA
19650864 TTTTGTTTAA
1 TTTT-TTTAA
19650874 TTTTTTTAA
1 TTTTTTTAA
**
19650883 -TTAATTAA
1 TTTTTTTAA
19650891 TTTTTTTAA
1 TTTTTTTAA
19650900 TT
1 TT
19650902 ATAAAAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 17 0.53
10 9 0.28
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:19650890 original size:17 final size:17
Alignment explanation
Indices: 19650870--19650902 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19650860 TTAATTTTGT
19650870 TTAATTTTTTTAATTAA
1 TTAATTTTTTTAATTAA
19650887 TTAATTTTTTTAATTA
1 TTAATTTTTTTAATTA
19650903 TAAAAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATTTTTTTAATTAA
Found at i:19651311 original size:37 final size:37
Alignment explanation
Indices: 19651229--19651312 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
19651219 GGGTTTAAAT
* *
19651229 CGTAAGTTAAGAAGTAAAAAATAGATCGGGACAACAC
1 CGTAAGTCAAGAAGTAAAAAATAGATCGAGACAACAC
** * *
19651266 CGCGAGTCAAGAAGTAAAGAATCGATCGAGACAACAC
1 CGTAAGTCAAGAAGTAAAAAATAGATCGAGACAACAC
19651303 CGTAAGTCAA
1 CGTAAGTCAA
19651313 AATCACGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (37 bp):
CGTAAGTCAAGAAGTAAAAAATAGATCGAGACAACAC
Found at i:19651459 original size:34 final size:34
Alignment explanation
Indices: 19651415--19651489 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
19651405 GAAATACTAA
* * * * *
19651415 AGATCAGGATTAAATCGTGAATCAGAGAATAAAT
1 AGATCGGGATTAAATCGCGAATCAAAAAATAAAG
19651449 AGATCGGGATTAAATCGCGAATCAAAAAATAAAG
1 AGATCGGGATTAAATCGCGAATCAAAAAATAAAG
19651483 AGATCGG
1 AGATCGG
19651490 AATAAACCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.20
Consensus pattern (34 bp):
AGATCGGGATTAAATCGCGAATCAAAAAATAAAG
Found at i:19651717 original size:170 final size:170
Alignment explanation
Indices: 19651516--19652981 Score: 1707
Period size: 170 Copynumber: 8.6 Consensus size: 170
19651506 AAGAATTATT
* * * * *
19651516 TTAACAACAATCGAGATTAAATTATGATTTTAAATTAAAAAGATCGAGATTGAACCATGAATTAG
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * *
19651581 AGAATAAAGAAATTGGATTAAACCGCGAATCAAAAAATGATGTTAACTTGGATTGAATCACAAGT
66 AGAATAAAGAGATAGGATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAGT
* * * * * *
19651646 CAGAAAATAAAAAAACCAAGAATAAATCATGAGTCAGAGG
131 CAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
* *** *
19651686 TTAACAACAATCGAGGTTAAACTACGATTTTAAATTAAAGAGATCAATATTGAATCGTGAATT-G
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * * *
19651750 AAGAATAAAGAGATCGGAGATT-AACCGTGAGTC--AAAATGACGTTAACTAGGATTGAATCACA
66 -AGAATAAAGAGAT-AG-GATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACA
* * * * *
19651812 AGTCAAAAAATAAAAAGACCGAAAATAAATCATGAGTCATAGG
128 AGTCAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
* * * * *
19651855 TTAACAACAATCGAGGTAAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACTGCGAATT-G
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
*** *
19651919 AAGAATAAAGAGACTAGGATTAAACTATGAGTCAAAAAATGACGTTAACTT-GATTGAATCACAA
66 -AGAATAAAGAGA-TAGGATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAA
* * *
19651983 GTCAGAAAATAAAAAGATCGAGAATAAACCATGAATCAGAGG
129 GTCAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
* * * *
19652025 TTAACAACAATCGAGACTAAATTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTCAATCAG
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* *
19652090 AGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGAT-AGGATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAG
* * * * *
19652155 TCAAAAAATAAAAAGATCGGGAATAAATCAC-AAGTAAAAGG
130 TCAAAAAATAAAAAGACCGAGAATAAACCACGAA-TCAGAGG
* *
19652196 TTAACAACAATCGAGATTAAACTACGATTTTAAATT-AAGAGATCGGGATTGAACCGTGTATTGG
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
** * *
19652260 AG-ATAAAGAGACCGAGATTAAACCACGAGTCAAAAAATGATGTTAACTTGGATTGAATTACAAG
66 AGAATAAAGAGATAG-GATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAG
* * *
19652324 TCAAAAAATAAAAAGATCAAGAATAAACCACGAATCAAAGG
130 TCAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
* * * * ** *
19652365 TTAACAACAATCGAGGTTAAACTACGATTTTAAATTAAAGAAATTGAGATTGAA-TATGAATTAA
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
** ** * *
19652429 AGAATAAAGAGACCGGGATTAAATTGCGAGTCAGAAAACGATGTTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGA-TAGGATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAG
*
19652494 TCAAAAAATAAAAAGACCGAGAATAAACCATGAATCAGAGG
130 TCAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
* * * * * * *
19652535 TTAACAACAATCGAGACTAAACTGCTATTTTAAACTAAAGAGATCGGGATTGAACAGCGAATCAG
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * **
19652600 AGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGACATTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGAT-AGGATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAG
* * **
19652665 TCAGAAAATAAAAAGA-CGGGAATAAACCACGTGTCAGAGG
130 TCAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
* ** ** *
19652705 TTAACAACAATCAAGATTAAACTGTGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAG
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
** **
19652770 AGAATAAAGAGACCGAGATTAAATTGCGAGTC-AAAAATGATGTTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGATAG-GATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAG
* * *
19652834 TTAGAAAATAAAAGGACCGAGAATAAAACCACGAATCAGAGG
130 TCAAAAAATAAAAAGACCGAGAAT-AAACCACGAATCAGAGG
** * * * *
19652876 TTAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGATTGGGATTAAACCGTGAATCAA
1 TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * * *
19652941 AGGATAAAAAGATTGGGATTAAACCATC-AGTCAAAAAATGA
66 AGAATAAAGAGA-TAGGATTAAACC-GCGAGTCAAAAAATGA
19652982 AATGATCGGG
Statistics
Matches: 1117, Mismatches: 155, Indels: 46
0.85 0.12 0.03
Matches are distributed among these distances:
168 5 0.00
169 320 0.29
170 499 0.45
171 279 0.25
172 14 0.01
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (170 bp):
TTAACAACAATCGAGATTAAACTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
AGAATAAAGAGATAGGATTAAACCGCGAGTCAAAAAATGATGTTAACTTGGATTGAATCACAAGT
CAAAAAATAAAAAGACCGAGAATAAACCACGAATCAGAGG
Found at i:19652209 original size:510 final size:511
Alignment explanation
Indices: 19651516--19652981 Score: 2016
Period size: 510 Copynumber: 2.9 Consensus size: 511
19651506 AAGAATTATT
* * * * * * *
19651516 TTAACAACAATCGAGATTAAATTATGATTTTAAATTAAAAAGATCGAGATTGAACCATGAATTAG
1 TTAACAACAATCGAGACTAAATTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTCAATCAG
* * * * *
19651581 AGAATAAAGAAAT-TGGATTAAACCGCGAATCAAAAAATGATGTTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAAG
* ** * *
19651645 TCAGAAAATAAAAAAACCAAGAATAAATCATGAGTCAGAGGTTAACAACAATCGAGGTTAAACTA
131 TCAGAAAATAAAAAGA-CGGGAATAAATCACGAGTCAGAGGTTAACAACAATCGAGATTAAACTA
* * *
19651710 CGATTTTAAATTAAAGAGATCAATATTGAATCGTGAATTGAAGAATAAAGAGATCGGAGATT-AA
195 CGATTTTAAATTAAAGAGATCAAGATTGAACCGTGAATTGAAGAATAAAGAGA-CCGAGATTAAA
* * *
19651774 CCGTGAGTC-AAAATGACGTTAACTAGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAAAAT
259 CCGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAAAAT
* * * * * *
19651838 AAATCATGAGTCATAGGTTAACAACAATCGAGGTAAAACTATGATTTTAAATTAAAGAGATCGGG
324 AAACCACGAATCAAAGGTTAACAACAATCGAGGTTAAACTATGATTTTAAATTAAAGAGATTGGG
* * *
19651903 ATTGAACTGCGAATTGAAGAATAAAGAGACTAGGATTAAACTATGAGTCAAAAAATGACGTTAAC
389 ATTGAACTGTGAATTAAAGAATAAAGAGACTGGGATTAAACTATGAGTCAAAAAATGACGTTAAC
* *
19651968 TT-GATTGAATCACAAGTCAGAAAATAAAAAGATCGAGAATAAACCATGAATCAGAGG
454 TTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGAATAAACCATGAATCAGAGG
19652025 TTAACAACAATCGAGACTAAATTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTCAATCAG
1 TTAACAACAATCGAGACTAAATTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTCAATCAG
19652090 AGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAAG
* * * *
19652155 TCAAAAAATAAAAAGATCGGGAATAAATCACAAGTAAAAGGTTAACAACAATCGAGATTAAACTA
131 TCAGAAAATAAAAAGA-CGGGAATAAATCACGAGTCAGAGGTTAACAACAATCGAGATTAAACTA
** * *
19652220 CGATTTTAAATT-AAGAGATCGGGATTGAACCGTGTATTGGAG-ATAAAGAGACCGAGATTAAAC
195 CGATTTTAAATTAAAGAGATCAAGATTGAACCGTGAATTGAAGAATAAAGAGACCGAGATTAAAC
* * *
19652283 CACGAGTCAAAAAATGATGTTAACTTGGATTGAATTACAAGTCAAAAAATAAAAAGATC-AAGAA
260 CGCGAGTC-AAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAA-AA
* * *
19652347 TAAACCACGAATCAAAGGTTAACAACAATCGAGGTTAAACTACGATTTTAAATTAAAGAAATTGA
323 TAAACCACGAATCAAAGGTTAACAACAATCGAGGTTAAACTATGATTTTAAATTAAAGAGATTGG
* * * ** * * *
19652412 GATTGAA-TATGAATTAAAGAATAAAGAGACCGGGATTAAATTGCGAGTCAGAAAACGATGTTAA
388 GATTGAACTGTGAATTAAAGAATAAAGAGACTGGGATTAAACTATGAGTCAAAAAATGACGTTAA
19652476 CTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGAATAAACCATGAATCAGAGG
453 CTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGAATAAACCATGAATCAGAGG
* * * * *
19652535 TTAACAACAATCGAGACTAAACTGCTATTTTAAACTAAAGAGATCGGGATTGAACAG-CGAATCA
1 TTAACAACAATCGAGACTAAATTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTC-AATCA
**
19652599 GAGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGACATTAACTTGGATTGAATCACAA
65 GAGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAA
* * * *
19652664 GTCAGAAAATAAAAAGACGGGAATAAACCACGTGTCAGAGGTTAACAACAATCAAGATTAAACTG
130 GTCAGAAAATAAAAAGACGGGAATAAATCACGAGTCAGAGGTTAACAACAATCGAGATTAAACTA
* *
19652729 TGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATT-AGAGAATAAAGAGACCGAGATTAAA
195 CGATTTTAAATTAAAGAGATCAAGATTGAACCGTGAATTGA-AGAATAAAGAGACCGAGATTAAA
** * * * *
19652793 TTGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTTAGAAAATAAAAGGACCGAGAAT
259 CCGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAAAAT
* * *
19652858 AAAACCACGAATCAGAGGTTAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGATTGG
324 -AAACCACGAATCAAAGGTTAACAACAATCGAGGTTAAACTATGATTTTAAATTAAAGAGATTGG
* * * * * * * *
19652923 GATTAAACCGTGAATCAAAGGATAAAAAGATTGGGATTAAACCATCAGTCAAAAAATGA
388 GATTGAACTGTGAATTAAAGAATAAAGAGACTGGGATTAAACTATGAGTCAAAAAATGA
19652982 AATGATCGGG
Statistics
Matches: 836, Mismatches: 108, Indels: 23
0.86 0.11 0.02
Matches are distributed among these distances:
507 7 0.01
508 18 0.02
509 198 0.24
510 485 0.58
511 91 0.11
512 37 0.04
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (511 bp):
TTAACAACAATCGAGACTAAATTACGATTTTAAATTAAAGAGATCGGGATTGAACCGTCAATCAG
AGAATAAAGAGATCAGGATTAAATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAAG
TCAGAAAATAAAAAGACGGGAATAAATCACGAGTCAGAGGTTAACAACAATCGAGATTAAACTAC
GATTTTAAATTAAAGAGATCAAGATTGAACCGTGAATTGAAGAATAAAGAGACCGAGATTAAACC
GCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAAAATAA
ACCACGAATCAAAGGTTAACAACAATCGAGGTTAAACTATGATTTTAAATTAAAGAGATTGGGAT
TGAACTGTGAATTAAAGAATAAAGAGACTGGGATTAAACTATGAGTCAAAAAATGACGTTAACTT
GGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGAATAAACCATGAATCAGAGG
Found at i:19652268 original size:339 final size:341
Alignment explanation
Indices: 19651516--19652981 Score: 1823
Period size: 339 Copynumber: 4.3 Consensus size: 341
19651506 AAGAATTATT
* * * *
19651516 TTAACAACAATCGAGATTAAATTATGATTTTAAATTAAAAAGATCGAGATTGAACCATGAATTAG
1 TTAACAACAATCGAGATTAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * * * *
19651581 AGAATAAAGA-AATTGGATTAAACCGCGAATCAAAAAATGATGTTAACTTGGATTGAATCACAAG
66 AGAATAAAGAGACTAGGATTAAACCACGAGTCAAAAAATGACGTTAACTTGGATTGAATCACAAG
* * * * * *
19651645 TCAGAAAATAAAAAAACCAAGAATAAATCATGAGTCAGAGGTTAACAACAATCGAGGTTAAACTA
131 TCAGAAAATAAAAAGATCAAGAATAAACCACGAATCAGAGGTTAACAACAATCGAGATTAAACTA
* * *
19651710 CGATTTTAAATTAAAGAGATCAATATTGAATCGTGAATT-GAAGAATAAAGAGATCGGAGATT-A
196 CGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAG-AGAATAAAGAGATCGGAGATTAA
* * * * *
19651773 ACCGTGAGTC-AAAATGACGTTAACTAGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAAAA
260 ATCGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGAA
* * * *
19651837 TAAATCATGAGTCATAGG
325 TAAACCA-CAATCAGAGG
* * * *
19651855 TTAACAACAATCGAGGTAAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACTGCGAATT-G
1 TTAACAACAATCGAGATTAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* *
19651919 AAGAATAAAGAGACTAGGATTAAACTATGAGTCAAAAAATGACGTTAACTT-GATTGAATCACAA
66 -AGAATAAAGAGACTAGGATTAAACCACGAGTCAAAAAATGACGTTAACTTGGATTGAATCACAA
* * * *
19651983 GTCAGAAAATAAAAAGATCGAGAATAAACCATGAATCAGAGGTTAACAACAATCGAGACTAAATT
130 GTCAGAAAATAAAAAGATCAAGAATAAACCACGAATCAGAGGTTAACAACAATCGAGATTAAACT
** * * * *
19652048 ACGATTTTAAATTAAAGAGATCGGGATTGAACCGTCAATCAGAGAATAAAGAGATCAG-GATTAA
195 ACGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAGAGAATAAAGAGATCGGAGATTAA
* *
19652112 ATCGCGAGTCAGAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGATCGGGA
260 ATCGCGAGTCA-AAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGA
* * *
19652177 ATAAATCACAAGTAAAAGG
324 ATAAACCACAA-TCAGAGG
* * *
19652196 TTAACAACAATCGAGATTAAACTACGATTTTAAATT-AAGAGATCGGGATTGAACCGTGTATTGG
1 TTAACAACAATCGAGATTAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * *
19652260 AG-ATAAAGAGAC-CGAGATTAAACCACGAGTCAAAAAATGATGTTAACTTGGATTGAATTACAA
66 AGAATAAAGAGACTAG-GATTAAACCACGAGTCAAAAAATGACGTTAACTTGGATTGAATCACAA
* * *
19652323 GTCAAAAAATAAAAAGATCAAGAATAAACCACGAATCAAAGGTTAACAACAATCGAGGTTAAACT
130 GTCAGAAAATAAAAAGATCAAGAATAAACCACGAATCAGAGGTTAACAACAATCGAGATTAAACT
* ** * * *
19652388 ACGATTTTAAATTAAAGAAATTGAGATTGAA-TATGAATTAAAGAATAAAGAGACCGG-GATTAA
195 ACGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAGAGAATAAAGAGATCGGAGATTAA
* *
19652451 ATTGCGAGTCAGAAAACGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGA
260 ATCGCGAGTCA-AAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGA
*
19652516 ATAAACCATGAATCAGAGG
324 ATAAACCA-CAATCAGAGG
* * * * * *
19652535 TTAACAACAATCGAGACTAAACTGCT-ATTTTAAACTAAAGAGATCGGGATTGAACAGCGAATCA
1 TTAACAACAATCGAGATTAAACT-ATGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTA
* * * *
19652599 GAGAATAAAGAGA-TCAGGATTAAATCGCGAGTCAGAAAATGACATTAACTTGGATTGAATCACA
65 GAGAATAAAGAGACT-AGGATTAAACCACGAGTCAAAAAATGACGTTAACTTGGATTGAATCACA
** ** *
19652663 AGTCAGAAAATAAAAAGA-CGGGAATAAACCACGTGTCAGAGGTTAACAACAATCAAGATTAAAC
129 AGTCAGAAAATAAAAAGATCAAGAATAAACCACGAATCAGAGGTTAACAACAATCGAGATTAAAC
** *
19652727 TGTGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAGAGAATAAAGAGA-CCGAGATTA
194 TACGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAGAGAATAAAGAGATCGGAGATTA
* * * *
19652791 AATTGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTTAGAAAATAAAAGGACCGAGA
259 AATCGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGA
19652856 ATAAAACCACGAATCAGAGG
324 AT-AAACCAC-AATCAGAGG
* * * * *
19652876 TTAACAACAATCGAGATTAAACTGTGATTTTAAATTAAAGAGATTGGGATTAAACCGTGAATCAA
1 TTAACAACAATCGAGATTAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
* * * *
19652941 AGGATAAAAAGATTGGGATTAAACCATC-AGTCAAAAAATGA
66 AGAATAAAGAGACTAGGATTAAACCA-CGAGTCAAAAAATGA
19652982 AATGATCGGG
Statistics
Matches: 976, Mismatches: 128, Indels: 44
0.85 0.11 0.04
Matches are distributed among these distances:
338 6 0.01
339 363 0.37
340 304 0.31
341 300 0.31
342 3 0.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (341 bp):
TTAACAACAATCGAGATTAAACTATGATTTTAAATTAAAGAGATCGGGATTGAACCGTGAATTAG
AGAATAAAGAGACTAGGATTAAACCACGAGTCAAAAAATGACGTTAACTTGGATTGAATCACAAG
TCAGAAAATAAAAAGATCAAGAATAAACCACGAATCAGAGGTTAACAACAATCGAGATTAAACTA
CGATTTTAAATTAAAGAGATCAAGATTGAACCATGAATTAGAGAATAAAGAGATCGGAGATTAAA
TCGCGAGTCAAAAATGATGTTAACTTGGATTGAATCACAAGTCAAAAAATAAAAAGACCGAGAAT
AAACCACAATCAGAGG
Found at i:19652975 original size:34 final size:34
Alignment explanation
Indices: 19652911--19653000 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
19652901 GATTTTAAAT
* * * **
19652911 TAAAGAGATTGGGATTAAACCGTGAATCAAAGGA
1 TAAAAAGATTGGGATTAAACCATCAATCAAAAAA
*
19652945 TAAAAAGATTGGGATTAAACCATCAGTCAAAAAA
1 TAAAAAGATTGGGATTAAACCATCAATCAAAAAA
* * *
19652979 TGAAATGATCGGGATTAAACCA
1 TAAAAAGATTGGGATTAAACCA
19653001 CAAGCCAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (34 bp):
TAAAAAGATTGGGATTAAACCATCAATCAAAAAA
Found at i:19654073 original size:21 final size:21
Alignment explanation
Indices: 19654049--19654091 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19654039 TTAATCTGAA
*
19654049 TCATTTTCTTT-TTTTTTTTTT
1 TCATTTT-TTTGTTTGTTTTTT
19654070 TCATTTTTTTGTTTGTTTTTT
1 TCATTTTTTTGTTTGTTTTTT
19654091 T
1 T
19654092 AAGCAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.84
Consensus pattern (21 bp):
TCATTTTTTTGTTTGTTTTTT
Found at i:19665812 original size:35 final size:34
Alignment explanation
Indices: 19665746--19665812 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
19665736 ATCATGCATA
* *
19665746 AATATATAAAAAAATACTTAAAATAACAAAATAAT
1 AATATATAAAAAAATAC-GAAAATAAAAAAATAAT
19665781 AATATATAAAAAAATTA-GAAAATTAAAAAAAT
1 AATATATAAAAAAA-TACGAAAA-TAAAAAAAT
19665813 TTTTTTACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 22 0.79
36 2 0.07
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (34 bp):
AATATATAAAAAAATACGAAAATAAAAAAATAAT
Found at i:19666839 original size:18 final size:17
Alignment explanation
Indices: 19666818--19666859 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
19666808 TTCTGTTCGG
19666818 ATTTTTTTGTTTGTCTTT
1 ATTTTTTT-TTTGTCTTT
*
19666836 ATTTATTTTTTTTTCTTT
1 ATTT-TTTTTTTGTCTTT
19666854 -TTTTTT
1 ATTTTTT
19666860 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 3 0.14
18 12 0.55
19 4 0.18
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (17 bp):
ATTTTTTTTTTGTCTTT
Found at i:19666865 original size:9 final size:9
Alignment explanation
Indices: 19666853--19666881 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
19666843 TTTTTTTCTT
19666853 TTTTTTTAA
1 TTTTTTTAA
19666862 TTTTTTTAA
1 TTTTTTTAA
19666871 TTTTTTTAA
1 TTTTTTTAA
19666880 TT
1 TT
19666882 ATAAAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:19666874 original size:20 final size:20
Alignment explanation
Indices: 19666837--19666877 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19666827 TTTGTCTTTA
* **
19666837 TTTATTTTTTTTTCTTTTTT
1 TTTAATTTTTTTAATTTTTT
19666857 TTTAATTTTTTTAATTTTTT
1 TTTAATTTTTTTAATTTTTT
19666877 T
1 T
19666878 AATTATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTAATTTTTTTAATTTTTT
Found at i:19667151 original size:23 final size:24
Alignment explanation
Indices: 19667125--19667170 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19667115 TGTACTTTCT
19667125 GTTAACA-ATTTTATTAACTTTAC
1 GTTAACAGATTTTATTAACTTTAC
*
19667148 GTTAACAGTTTTTATTAACTTTA
1 GTTAACAGATTTTATTAACTTTA
19667171 AATATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (24 bp):
GTTAACAGATTTTATTAACTTTAC
Found at i:19670853 original size:17 final size:17
Alignment explanation
Indices: 19670833--19670901 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
19670823 ATTTTCAGAG
*
19670833 ATTTTATATTCACAAAA
1 ATTTTAGATTCACAAAA
*
19670850 ATTTTAGATTCACAAAG
1 ATTTTAGATTCACAAAA
* * *
19670867 ATTCTAAATTTCACAAAG
1 ATTTTAGA-TTCACAAAA
* *
19670885 GTTCTAGATTCA-AAAA
1 ATTTTAGATTCACAAAA
19670901 A
1 A
19670902 ACTCAAATGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
16 3 0.07
17 25 0.58
18 15 0.35
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (17 bp):
ATTTTAGATTCACAAAA
Found at i:19671238 original size:45 final size:45
Alignment explanation
Indices: 19671150--19671513 Score: 280
Period size: 45 Copynumber: 8.1 Consensus size: 45
19671140 GTTCTTGTTC
* * * *
19671150 GAAAAATTTCAAGGTTTCACATCCAAAAATT-AAAGATTTTCATTT
1 GAAAAATTTTAA-GATTCACATCCAAAATTTCAAAGATTCTCATTT
* ** *
19671195 AAAAAATTTTGGGATTCACATCCAAAATTTCAAAAATTCTCATTT
1 GAAAAATTTTAAGATTCACATCCAAAATTTCAAAGATTCTCATTT
* * * * * *
19671240 GAAAAATTTTAGGATTCACAACCAAAGTTT-AAAAAGTTCACATTC
1 GAAAAATTTTAAGATTCACATCCAAAATTTCAAAGA-TTCTCATTT
* * **
19671285 GAAAAATTTTAAAGATTTACATTCAATGTTTCAAAGATTCAT-ATTT
1 GAAAAATTTT-AAGATTCACATCCAAAATTTCAAAGATTC-TCATTT
* *
19671331 GAAAAA--TTAGAGATTCACATCCAAAGTTTCAAAGATTCACATTT
1 GAAAAATTTTA-AGATTCACATCCAAAATTTCAAAGATTCTCATTT
* * * *
19671375 GAAAATTTTTAAAAATTCACATCC-AAAGTTCAAAGATTCAT-ATTC
1 GAAAAATTTT-AAGATTCACATCCAAAATTTCAAAGATTC-TCATTT
* *** * *
19671420 GAAAAA-TTAAAGATTCACATTTGAAGTTTCAAAGATTCACATTT
1 GAAAAATTTTAAGATTCACATCCAAAATTTCAAAGATTCTCATTT
** *
19671464 GAAAAATTTT-AGCATTTTGCATCCAAAATTT-AAAAATTCTCATTT
1 GAAAAATTTTAAG-A-TTCACATCCAAAATTTCAAAGATTCTCATTT
19671509 GAAAA
1 GAAAA
19671514 GCTCCTTTAA
Statistics
Matches: 253, Mismatches: 50, Indels: 32
0.76 0.15 0.10
Matches are distributed among these distances:
43 11 0.04
44 83 0.33
45 104 0.41
46 50 0.20
47 5 0.02
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (45 bp):
GAAAAATTTTAAGATTCACATCCAAAATTTCAAAGATTCTCATTT
Found at i:19671272 original size:89 final size:90
Alignment explanation
Indices: 19671150--19671513 Score: 325
Period size: 89 Copynumber: 4.1 Consensus size: 90
19671140 GTTCTTGTTC
* ** ** * **
19671150 GAAAAATTTCAAGGTTTCACATCCAAAAATT-AAAGATTTTCATTTAAAAAATTTT-GGGATTCA
1 GAAAAA-TT-AAGGATTCACATCCAAAGTTTCAAAGATTCACATTTGAAAAATTTTAAAGATTCA
19671213 CATCCAAAATTTCAAAAATTC-TCATTT
64 CATCCAAAATTTCAAAAATTCAT-ATTT
* * * * *
19671240 GAAAAATTTTAGGATTCACAACCAAAGTTT-AAAAAGTTCACATTCGAAAAATTTTAAAGATTTA
1 GAAAAA-TTAAGGATTCACATCCAAAGTTTCAAAGA-TTCACATTTGAAAAATTTTAAAGATTCA
* ** *
19671304 CATTCAATGTTTCAAAGATTCATATTT
64 CATCCAAAATTTCAAAAATTCATATTT
* *
19671331 GAAAAATT-AGAGATTCACATCCAAAGTTTCAAAGATTCACATTTGAAAATTTTTAAAAATTCAC
1 GAAAAATTAAG-GATTCACATCCAAAGTTTCAAAGATTCACATTTGAAAAATTTTAAAGATTCAC
* * *
19671395 ATCC-AAAGTTCAAAGATTCATATTC
65 ATCCAAAATTTCAAAAATTCATATTT
* *** **
19671420 GAAAAATTAAAGATTCACATTTGAAGTTTCAAAGATTCACATTTGAAAAATTTT--AGCATTTTG
1 GAAAAATTAAGGATTCACATCCAAAGTTTCAAAGATTCACATTTGAAAAATTTTAAAG-A-TTCA
19671483 CATCCAAAATTT-AAAAATTC-TCATTT
64 CATCCAAAATTTCAAAAATTCAT-ATTT
19671509 GAAAA
1 GAAAA
19671514 GCTCCTTTAA
Statistics
Matches: 225, Mismatches: 39, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
87 1 0.00
88 2 0.01
89 108 0.48
90 77 0.34
91 36 0.16
92 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (90 bp):
GAAAAATTAAGGATTCACATCCAAAGTTTCAAAGATTCACATTTGAAAAATTTTAAAGATTCACA
TCCAAAATTTCAAAAATTCATATTT
Found at i:19671366 original size:22 final size:22
Alignment explanation
Indices: 19671252--19671461 Score: 95
Period size: 22 Copynumber: 9.4 Consensus size: 22
19671242 AAAATTTTAG
*
19671252 GATTCACAACCAAAGTTT-AAA
1 GATTCACATCCAAAGTTTCAAA
* * * *
19671273 AAGTTCACATTCGAAAAATTTTAAA
1 GA-TTCACA-TC-CAAAGTTTCAAA
* * *
19671298 GATTTACATTCAATGTTTCAAA
1 GATTCACATCCAAAGTTTCAAA
* ** ** *
19671320 GATTCATATTTGAAAAATT-AGA
1 GATTCACA-TCCAAAGTTTCAAA
19671342 GATTCACATCCAAAGTTTCAAA
1 GATTCACATCCAAAGTTTCAAA
** * *
19671364 GATTCACATTTGAAAATTTTTAAA
1 GATTCACA--TCCAAAGTTTCAAA
*
19671388 AATTCACATCCAAAG-TTCAAA
1 GATTCACATCCAAAGTTTCAAA
* * **
19671409 GATTCATATTCGAAAAATT-AAA
1 GATTCACA-TCCAAAGTTTCAAA
***
19671431 GATTCACATTTGAAGTTTCAAA
1 GATTCACATCCAAAGTTTCAAA
19671453 GATTCACAT
1 GATTCACAT
19671462 TTGAAAAATT
Statistics
Matches: 135, Mismatches: 43, Indels: 21
0.68 0.22 0.11
Matches are distributed among these distances:
21 23 0.17
22 70 0.52
23 10 0.07
24 28 0.21
25 4 0.03
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (22 bp):
GATTCACATCCAAAGTTTCAAA
Found at i:19671462 original size:22 final size:22
Alignment explanation
Indices: 19671295--19671466 Score: 100
Period size: 22 Copynumber: 7.8 Consensus size: 22
19671285 GAAAAATTTT
* *
19671295 AAAGATTTACA-TTCAATGTTTC
1 AAAGATTCACATTTGAA-GTTTC
* **
19671317 AAAGATTCATATTTGAAAAATT-
1 AAAGATTCACATTTG-AAGTTTC
* ***
19671339 AGAGATTCACATCCAAAGTTTC
1 AAAGATTCACATTTGAAGTTTC
* *
19671361 AAAGATTCACATTTGAAAATTTTT
1 AAAGATTCACATTTG--AAGTTTC
* ***
19671385 AAAAATTCACATCCAAAG-TTC
1 AAAGATTCACATTTGAAGTTTC
* * **
19671406 AAAGATTCATATTCGAAAAATT-
1 AAAGATTCACATTTG-AAGTTTC
19671428 AAAGATTCACATTTGAAGTTTC
1 AAAGATTCACATTTGAAGTTTC
19671450 AAAGATTCACATTTGAA
1 AAAGATTCACATTTGAA
19671467 AAATTTTAGC
Statistics
Matches: 109, Mismatches: 33, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
21 21 0.19
22 64 0.59
23 6 0.06
24 18 0.17
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (22 bp):
AAAGATTCACATTTGAAGTTTC
Found at i:19672539 original size:12 final size:12
Alignment explanation
Indices: 19672505--19672549 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
19672495 TTAAGTCTTT
19672505 TTTTATTTTTTAA
1 TTTT-TTTTTTAA
**
19672518 TTTTAATTTTAA
1 TTTTTTTTTTAA
*
19672530 TTTTTTTTTTAC
1 TTTTTTTTTTAA
19672542 TTTTTTTT
1 TTTTTTTT
19672550 ACACATCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:19672846 original size:7 final size:7
Alignment explanation
Indices: 19672830--19672868 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
19672820 TGACCTACAA
19672830 TTTC-TT
1 TTTCTTT
19672836 TTTCTTT
1 TTTCTTT
19672843 TTTCTTT
1 TTTCTTT
19672850 TTTCTTCT
1 TTTCTT-T
19672858 TTCTCTTT
1 TT-TCTTT
19672866 TTT
1 TTT
19672869 TTTCCATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 4 0.13
7 16 0.53
8 6 0.20
9 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTCTTT
Found at i:19673431 original size:11 final size:11
Alignment explanation
Indices: 19673415--19673442 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
19673405 ACACGAAACA
19673415 GAAAATGTCAT
1 GAAAATGTCAT
19673426 GAAAATGTCAT
1 GAAAATGTCAT
19673437 GAAAAT
1 GAAAAT
19673443 ACATCATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (11 bp):
GAAAATGTCAT
Found at i:19679448 original size:18 final size:18
Alignment explanation
Indices: 19679425--19679460 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19679415 TTTTGAGTTT
*
19679425 AATATAAATATATTTATA
1 AATATAAATAGATTTATA
*
19679443 AATATATATAGATTTATA
1 AATATAAATAGATTTATA
19679461 CATAGTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATAAATAGATTTATA
Found at i:19682017 original size:30 final size:30
Alignment explanation
Indices: 19681965--19682037 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
19681955 TAATTAAGTA
* * **
19681965 AAAATAAATGTTTAAAAGTTCAATTGGGTG
1 AAAATAAATATTTAAAAGTTCAATCGAATG
*
19681995 AAAATAAATATTT-AATGATTCAATCGAATG
1 AAAATAAATATTTAAAAG-TTCAATCGAATG
19682025 AAAATAAATATTT
1 AAAATAAATATTT
19682038 GATAATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.08
30 34 0.92
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.34
Consensus pattern (30 bp):
AAAATAAATATTTAAAAGTTCAATCGAATG
Found at i:19682616 original size:108 final size:108
Alignment explanation
Indices: 19682422--19682640 Score: 384
Period size: 108 Copynumber: 2.0 Consensus size: 108
19682412 TTTAATAACG
* * * *
19682422 ATGAATAGAACTAATGAATTTGAAATATTTATAAAAGATTACGGATTTAAAAGTTAAATTTTAAA
1 ATGAATAGAACTAATGAAATTGAAATATTTATAAAAAATTACGGATTTAAAAATTAAAGTTTAAA
*
19682487 TAATGTGAATAAAAATAAAATATTGTAAAAAGATTACAAATGC
66 TAATATGAATAAAAATAAAATATTGTAAAAAGATTACAAATGC
*
19682530 ATGAGTAGAACTAATGAAATTGAAATATTTATAAAAAATTACGGATTTAAAAATTAAAGTTTAAA
1 ATGAATAGAACTAATGAAATTGAAATATTTATAAAAAATTACGGATTTAAAAATTAAAGTTTAAA
19682595 TAATATGAATAAAAATAAAATATTGTAAAAAGATTACAAATGC
66 TAATATGAATAAAAATAAAATATTGTAAAAAGATTACAAATGC
19682638 ATG
1 ATG
19682641 GTACAATTGC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.32
Consensus pattern (108 bp):
ATGAATAGAACTAATGAAATTGAAATATTTATAAAAAATTACGGATTTAAAAATTAAAGTTTAAA
TAATATGAATAAAAATAAAATATTGTAAAAAGATTACAAATGC
Found at i:19682814 original size:18 final size:17
Alignment explanation
Indices: 19682791--19682824 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19682781 TTTTGTTTTT
19682791 TTATTAGTATCAAATAAC
1 TTATTA-TATCAAATAAC
*
19682809 TTATTATTTCAAATAA
1 TTATTATATCAAATAA
19682825 AATATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (17 bp):
TTATTATATCAAATAAC
Found at i:19684045 original size:60 final size:60
Alignment explanation
Indices: 19683973--19684091 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
19683963 TTTTATATAG
* *
19683973 AAAATGCCTTAAACAATATTTTTATAAAA-ATAAAA-AGATTATTTAAGGTATTTTTTGTAC
1 AAAATGCCTTAAACAATATATTTATAAAATATAAAAGA-ATTATTTAAGG-ATTTTCTGTAC
* * *
19684033 AAAATGCTTTAAATAATCTATTTATAAAATATAAAAGAATTATTTAAGGATTTTCTGTA
1 AAAATGCCTTAAACAATATATTTATAAAATATAAAAGAATTATTTAAGGATTTTCTGTA
19684092 TATAATCCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 34 0.65
61 17 0.33
62 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (60 bp):
AAAATGCCTTAAACAATATATTTATAAAATATAAAAGAATTATTTAAGGATTTTCTGTAC
Found at i:19684231 original size:63 final size:63
Alignment explanation
Indices: 19684135--19684259 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
19684125 CTTAAGATAC
** * * * *
19684135 AAAAGATTATTTAAGGTATTTTTGTATAGAAAATGCTTTAAA-AAATCTATTTATAAAAATATA
1 AAAAGATTATTTAAGACATTTCTGTACAAAAAATACTTTAAATAAATCT-TTTATAAAAATATA
* * *
19684198 AAAAGATTATTTATGACATTTCTGTACAAAAAATATTTTAAATAATTCTTTTATAAAAATAT
1 AAAAGATTATTTAAGACATTTCTGTACAAAAAATACTTTAAATAAATCTTTTATAAAAATAT
19684260 TAACCCTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 47 0.90
64 5 0.10
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (63 bp):
AAAAGATTATTTAAGACATTTCTGTACAAAAAATACTTTAAATAAATCTTTTATAAAAATATA
Found at i:19684357 original size:53 final size:53
Alignment explanation
Indices: 19684278--19684381 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
19684268 TACCCTAAAA
* *
19684278 TATAAAACGATTATTTAAGGCA-TTTTTGTATAGAAAATACCTTAAATAATCCT
1 TATAAAACGATTATTTAAGGAATTTTTTGTACA-AAAATACCTTAAATAATCCT
* * *
19684331 TATAAAAGGATTATTTAA-GAAGTTTTTTGTACATAAATGCCTTAAATAATC
1 TATAAAACGATTATTTAAGGAA-TTTTTTGTACAAAAATACCTTAAATAATC
19684382 TATTTATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
52 2 0.05
53 33 0.75
54 9 0.20
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (53 bp):
TATAAAACGATTATTTAAGGAATTTTTTGTACAAAAATACCTTAAATAATCCT
Found at i:19684410 original size:63 final size:63
Alignment explanation
Indices: 19684331--19684455 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
19684321 AAATAATCCT
* * * **
19684331 TATAAAAGGATTATTTAA-GAAGTTTTTTGTACATAAATGCCTTAAATAAT-CTATTTATAAAAG
1 TATAAAAAGATTATTTAATG-AGTTTTTTATACAAAAACACCTTAAATAATCCT-TTTATAAAAG
* *
19684394 TATAAAAAGATTATTTAATGTGTTTTTTATATAAAAACACCTTAAATAATCCTTTTATAAAA
1 TATAAAAAGATTATTTAATGAGTTTTTTATACAAAAACACCTTAAATAATCCTTTTATAAAA
19684456 ATATTAACCC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 50 0.94
64 3 0.06
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (63 bp):
TATAAAAAGATTATTTAATGAGTTTTTTATACAAAAACACCTTAAATAATCCTTTTATAAAAG
Found at i:19686493 original size:23 final size:23
Alignment explanation
Indices: 19686457--19686503 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
19686447 AAGTTGCTTT
* *
19686457 TTTTCTCCCTTTCTTTTCATAAA
1 TTTTCACCCATTCTTTTCATAAA
19686480 TTTTCACCCATTCTTTTCATAAA
1 TTTTCACCCATTCTTTTCATAAA
19686503 T
1 T
19686504 CATATGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTCACCCATTCTTTTCATAAA
Found at i:19687981 original size:18 final size:19
Alignment explanation
Indices: 19687958--19687995 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19687948 CACGCTAAAA
19687958 TTTTTTTCTTTTTTT-TTT
1 TTTTTTTCTTTTTTTCTTT
*
19687976 TTTTTTTGTTTTTTTCTTT
1 TTTTTTTCTTTTTTTCTTT
19687995 T
1 T
19687996 GCATTGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.92
Consensus pattern (19 bp):
TTTTTTTCTTTTTTTCTTT
Found at i:19687996 original size:13 final size:13
Alignment explanation
Indices: 19687958--19687996 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
19687948 CACGCTAAAA
*
19687958 TTTTTTTCTTTTT
1 TTTTTTTCTTTTG
*
19687971 TTTTTTTTTTTTG
1 TTTTTTTCTTTTG
19687984 TTTTTTTCTTTTG
1 TTTTTTTCTTTTG
19687997 CATTGCTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.90
Consensus pattern (13 bp):
TTTTTTTCTTTTG
Found at i:19689053 original size:26 final size:28
Alignment explanation
Indices: 19689024--19689086 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
19689014 TATACTTTTT
19689024 TATT-TTT-AGGAATTGAGTCTCTT-TAG
1 TATTATTTAAGGAATTGAGTC-CTTATAG
*
19689050 TATTATTTAAAGGAATTTAGTCCTTATAG
1 TATTATTT-AAGGAATTGAGTCCTTATAG
19689079 TATTATTT
1 TATTATTT
19689087 TTTAAGGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.12
27 3 0.09
28 3 0.09
29 22 0.69
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (28 bp):
TATTATTTAAGGAATTGAGTCCTTATAG
Found at i:19689063 original size:29 final size:29
Alignment explanation
Indices: 19689031--19689086 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
19689021 TTTTATTTTT
19689031 AGGAATTGAGTCTCTT-TAGTATTATTTAA
1 AGGAATTGAGTC-CTTATAGTATTATTTAA
*
19689060 AGGAATTTAGTCCTTATAGTATTATTT
1 AGGAATTGAGTCCTTATAGTATTATTT
19689087 TTTAAGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.46
Consensus pattern (29 bp):
AGGAATTGAGTCCTTATAGTATTATTTAA
Found at i:19705373 original size:54 final size:54
Alignment explanation
Indices: 19705287--19705414 Score: 130
Period size: 54 Copynumber: 2.4 Consensus size: 54
19705277 TGTATTGAGC
** * * * * * * *
19705287 GTGTTGGCATAAAGTCTTAATGCGATATATATGGCACATAAGGATGCATTTAGT
1 GTGTTGGCATAAAGTCTTAACACCATAAATATGACACACAAGAATGCATTGAAT
* **
19705341 GTGTTGGCATAAAGTTTTAACACCATAAATATGACGTACAAGAATGCATTGAAT
1 GTGTTGGCATAAAGTCTTAACACCATAAATATGACACACAAGAATGCATTGAAT
* *
19705395 GTGTTGGCATAGAGCCTTAA
1 GTGTTGGCATAAAGTCTTAA
19705415 TGCAATAAGT
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (54 bp):
GTGTTGGCATAAAGTCTTAACACCATAAATATGACACACAAGAATGCATTGAAT
Found at i:19716271 original size:19 final size:22
Alignment explanation
Indices: 19716244--19716291 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
19716234 ACTATTATGT
19716244 TATTATTATTTCTAATTCAATA
1 TATTATTATTTCTAATTCAATA
*
19716266 TATTATTATTTCTAATTTAATA
1 TATTATTATTTCTAATTCAATA
19716288 TATT
1 TATT
19716292 CAAAGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTATTATTTCTAATTCAATA
Found at i:19721075 original size:16 final size:18
Alignment explanation
Indices: 19721036--19721075 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
19721026 AAGATATGAT
*
19721036 AATTTATTTATTTATCAA
1 AATTTATTTATTTATAAA
19721054 AA-TTATTT-TTTA-AAA
1 AATTTATTTATTTATAAA
19721069 AATTTAT
1 AATTTAT
19721076 GCAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 6 0.30
18 2 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTATTTATTTATAAA
Found at i:19721530 original size:22 final size:22
Alignment explanation
Indices: 19721504--19721545 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19721494 AAGGAAAATA
19721504 AAGGAAAATAAAGTAATGGAGG
1 AAGGAAAATAAAGTAATGGAGG
*
19721526 AAGGAAAATAAAGTCATGGA
1 AAGGAAAATAAAGTAATGGA
19721546 AACAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (22 bp):
AAGGAAAATAAAGTAATGGAGG
Found at i:19721555 original size:22 final size:22
Alignment explanation
Indices: 19721503--19721555 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
19721493 GAAGGAAAAT
*
19721503 AAAGGAAAATAAAGTAATGGAG
1 AAAGAAAAATAAAGTAATGGAG
* * *
19721525 GAAGGAAAATAAAGTCATGGA-
1 AAAGAAAAATAAAGTAATGGAG
19721546 AACAGAAAAA
1 AA-AGAAAAA
19721556 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.60, C:0.04, G:0.25, T:0.11
Consensus pattern (22 bp):
AAAGAAAAATAAAGTAATGGAG
Found at i:19724522 original size:21 final size:21
Alignment explanation
Indices: 19724498--19724539 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
19724488 AAACATTATA
*
19724498 TTATAAATAAAT-TTACAAAAT
1 TTATAAA-AAATCATACAAAAT
*
19724519 TTATGAAAAATCATACAAAAT
1 TTATAAAAAATCATACAAAAT
19724540 ATTTTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTATAAAAAATCATACAAAAT
Found at i:19728962 original size:23 final size:23
Alignment explanation
Indices: 19728926--19728969 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19728916 CGTTAAAGAT
*
19728926 TGGTTTTAGGGTTTAGGGTTTTA
1 TGGTTTTAGAGTTTAGGGTTTTA
*
19728949 TGGTTTTTGAGTTTAGGGTTT
1 TGGTTTTAGAGTTTAGGGTTT
19728970 CAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (23 bp):
TGGTTTTAGAGTTTAGGGTTTTA
Found at i:19729764 original size:8 final size:8
Alignment explanation
Indices: 19729751--19729785 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
19729741 TCAATTGATA
19729751 AAAAAAAT
1 AAAAAAAT
19729759 AAAAAAAT
1 AAAAAAAT
19729767 AAATAAAAAT
1 -AA-AAAAAT
19729777 AAAAAAAT
1 AAAAAAAT
19729785 A
1 A
19729786 CTAGATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.60
9 4 0.16
10 6 0.24
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:19729776 original size:18 final size:17
Alignment explanation
Indices: 19729748--19729785 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
19729738 AAGTCAATTG
19729748 ATAAAAAAAATAAAAAA
1 ATAAAAAAAATAAAAAA
19729765 ATAAATAAAAATAAAAAA
1 ATAAA-AAAAATAAAAAA
19729783 ATA
1 ATA
19729786 CTAGATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (17 bp):
ATAAAAAAAATAAAAAA
Found at i:19730316 original size:21 final size:21
Alignment explanation
Indices: 19730288--19730522 Score: 117
Period size: 21 Copynumber: 10.9 Consensus size: 21
19730278 CAATTGCATA
19730288 TTATTTGCATGATTTATATTG
1 TTATTTGCATGATTTATATTG
* *
19730309 TTGTTTGCATGA-TCATATAT-
1 TTATTTGCATGATTTATAT-TG
*
19730329 TTAATTGCATGATTTATATTG
1 TTATTTGCATGATTTATATTG
* * **
19730350 TTAATTGTATGATCATTGCATGATCA
1 TTATTTGCATGAT--TT--AT-ATTG
19730376 TATATTTATTTGCATGATTTATATTG
1 T-TA-TT---TGCATGATTTATATTG
* *
19730402 TTAATTGCATGA-TCATATAT-
1 TTATTTGCATGATTTATAT-TG
19730422 TTATTTGCATGATTTATATTG
1 TTATTTGCATGATTTATATTG
* *
19730443 TTAATTGCATGA-TCATATAT-
1 TTATTTGCATGATTTATAT-TG
* * * **
19730463 TTAATTGCAAGATATATATCA
1 TTATTTGCATGATTTATATTG
*
19730484 TTAATTGCATGA-TTATATAT-
1 TTATTTGCATGATTTATAT-TG
* *
19730504 TTAATTGAATGATTTATAT
1 TTATTTGCATGATTTATAT
19730523 GATTATATAT
Statistics
Matches: 167, Mismatches: 26, Indels: 42
0.71 0.11 0.18
Matches are distributed among these distances:
20 65 0.39
21 75 0.45
23 2 0.01
24 1 0.01
25 4 0.02
26 6 0.04
27 4 0.02
28 1 0.01
29 2 0.01
31 7 0.04
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
TTATTTGCATGATTTATATTG
Found at i:19730338 original size:41 final size:41
Alignment explanation
Indices: 19730292--19730686 Score: 403
Period size: 41 Copynumber: 9.2 Consensus size: 41
19730282 TGCATATTAT
**
19730292 TTGCATGATTTATATTGTTGTTTGCATGATCATATATTTAA
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
*
19730333 TTGCATGATTTATATTGTTAATTGTATGATCATTGCATGATCATATATTTAT
1 TTGCATGA-TT-TA----T-ATTGT-T-A--ATTGCATGATCATATATTTAA
*
19730385 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAT
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
19730426 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
* * ** *
19730467 TTGCAAGATATATATCATTAATTGCATGATTATATATTTAA
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
* * *
19730508 TTGAATGATTTATATGATTATATATTTAATTGCATGATTATATATTTAA
1 TTGCATGA--T-T-T-A-TAT-T-GTTAATTGCATGATCATATATTTAA
* * * *
19730557 TTGCATGATTTATATTGTTAATTGCATAATTATATTTTTGA
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
* * *
19730598 TTGAATGATTTATATTGTTAATTGCATAATTATATATTTAA
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
* * * * *
19730639 TTGCATGTTTTACATTGTTATTTGTATGATTATATATTTAA
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
19730680 TTGCATG
1 TTGCATG
19730687 TCTATTTGCA
Statistics
Matches: 307, Mismatches: 28, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
41 212 0.69
42 3 0.01
43 7 0.02
44 2 0.01
45 7 0.02
46 3 0.01
47 5 0.02
48 5 0.02
49 32 0.10
50 2 0.01
51 2 0.01
52 27 0.09
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (41 bp):
TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAA
Found at i:19730369 original size:52 final size:52
Alignment explanation
Indices: 19730313--19730458 Score: 197
Period size: 52 Copynumber: 3.0 Consensus size: 52
19730303 ATATTGTTGT
*
19730313 TTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTGTATGATCA
1 TTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTGCATGATCA
*
19730365 TTGCATGATCATATATTTATTTGCATGATTTATATTGTTAATTGCATGATCA
1 TTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTGCATGATCA
19730417 -T--AT-AT--T-TA--T--TTGCATGATTTATATTGTTAATTGCATGATCA
1 TTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTGCATGATCA
19730458 T
1 T
19730459 ATATTTAATT
Statistics
Matches: 91, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
41 32 0.35
43 1 0.01
45 2 0.02
46 1 0.01
48 2 0.02
49 2 0.02
51 1 0.01
52 50 0.55
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.49
Consensus pattern (52 bp):
TTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTGCATGATCA
Found at i:19730402 original size:93 final size:93
Alignment explanation
Indices: 19730288--19730624 Score: 373
Period size: 93 Copynumber: 3.8 Consensus size: 93
19730278 CAATTGCATA
**
19730288 TTATTTGCATGATTTATATTGTTGTTTGCATGATCATATATTTAATTGCATGATTTATATTGTTA
1 TTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCATGATTTATATTGTTA
*
19730353 ATTGTATGATCATTGCATGATCATATAT
66 ATTGCATGATCATTGCATGATCATATAT
*
19730381 TTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTATTTGCATGATTTATATTGTTA
1 TTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCATGATTTATATTGTTA
19730446 ATTGCATGATCA-T--AT-AT--T-TA-
66 ATTGCATGATCATTGCATGATCATATAT
* * ** * *
19730466 --A-TTGCAAGATATATATCATTAATTGCATGATTATATATTTAATTGAATGATTTATA-TGATT
1 TTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCATGATTTATATTG-TT
* * *
19730527 -ATAT--AT-TTAATTGCATGATTATATAT
65 AAT-TGCATGATCATTGCATGATCATATAT
* * * * * *
19730553 TTAATTGCATGATTTATATTGTTAATTGCATAATTATATTTTTGATTGAATGATTTATATTGTTA
1 TTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCATGATTTATATTGTTA
19730618 ATTGCAT
66 ATTGCAT
19730625 AATTATATAT
Statistics
Matches: 207, Mismatches: 20, Indels: 35
0.79 0.08 0.13
Matches are distributed among these distances:
79 2 0.01
80 3 0.01
81 4 0.02
82 53 0.26
83 3 0.01
85 1 0.00
86 4 0.02
87 1 0.00
89 3 0.01
90 53 0.26
91 4 0.02
92 3 0.01
93 73 0.35
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (93 bp):
TTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCATGATTTATATTGTTA
ATTGCATGATCATTGCATGATCATATAT
Found at i:19730525 original size:29 final size:30
Alignment explanation
Indices: 19730492--19730552 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
19730482 CATTAATTGC
19730492 ATGATTATATATTTAATTGAATGATT-TAT
1 ATGATTATATATTTAATTGAATGATTATAT
*
19730521 ATGATTATATATTTAATTGCATGATTATAT
1 ATGATTATATATTTAATTGAATGATTATAT
19730551 AT
1 AT
19730553 TTAATTGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (30 bp):
ATGATTATATATTTAATTGAATGATTATAT
Found at i:19730538 original size:49 final size:50
Alignment explanation
Indices: 19730475--19730571 Score: 169
Period size: 49 Copynumber: 1.9 Consensus size: 50
19730465 AATTGCAAGA
19730475 TATATATCATTAATTGCATGATTATATATTTAATTGAATGATTTATATGAT
1 TATATAT-ATTAATTGCATGATTATATATTTAATTGAATGATTTATATGAT
*
19730526 TATATAT-TTAATTGCATGATTATATATTTAATTGCATGATTTATAT
1 TATATATATTAATTGCATGATTATATATTTAATTGAATGATTTATAT
19730572 TGTTAATTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 38 0.84
51 7 0.16
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (50 bp):
TATATATATTAATTGCATGATTATATATTTAATTGAATGATTTATATGAT
Found at i:19730542 original size:90 final size:91
Alignment explanation
Indices: 19730430--19730612 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 91
19730420 ATTTATTTGC
*
19730430 ATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATATATATCATTAATTGCATG
1 ATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATATATATCATTAATTGCATA
19730495 ATTATATATTTAATTGAATGATTTAT
66 ATTATATATTTAATTGAATGATTTAT
* * * **
19730521 ATGA-TTATATAT-TTAATTGCATGATTATATATTTAATTGCATGATTTATATTGTTAATTGCAT
1 ATGATTTATAT-TGTTAATTGCATGATCATATATTTAATTGCAAGATATATATCATTAATTGCAT
* *
19730584 AATTATATTTTTGATTGAATGATTTAT
65 AATTATATATTTAATTGAATGATTTAT
19730611 AT
1 AT
19730613 TGTTAATTGC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 78 0.94
91 5 0.06
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (91 bp):
ATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATATATATCATTAATTGCATA
ATTATATATTTAATTGAATGATTTAT
Found at i:19730578 original size:131 final size:132
Alignment explanation
Indices: 19730292--19730653 Score: 428
Period size: 131 Copynumber: 2.7 Consensus size: 132
19730282 TGCATATTAT
** *
19730292 TTGCATGATTTATATTGTTGTTTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTG
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATTTATATTGTTAATTG
* * * * * * *
19730357 TATGATCAT-TGCATGATCATAT-ATTTATTTGCATGATTTATATTGTTAATTGCATGATCATAT
66 CATGATTATAT--AT-TTAAT-TGAATGATTTACATGATTTATATTGTTAATTGCATGATCATAT
*
19730420 ATTTAT
127 ATTTAA
* **
19730426 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATATATATCATTAATTG
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATTTATATTGTTAATTG
* *
19730491 CATGATTATATATTTAATTGAATGATTTATATGA-TTATATAT-TTAATTGCATGATTATATATT
66 CATGATTATATATTTAATTGAATGATTTACATGATTTATAT-TGTTAATTGCATGATCATATATT
19730554 TAA
130 TAA
* * * *
19730557 TTGCATGATTTATATTGTTAATTGCATAATTATATTTTTGATTG-AATGATTTATATTGTTAATT
1 TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAA-GATTTATATTGTTAATT
* * *
19730621 GCATAATTATATATTTAATTGCATGTTTTACAT
65 GCATGATTATATATTTAATTGAATGATTTACAT
19730654 TGTTATTTGT
Statistics
Matches: 197, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
130 2 0.01
131 112 0.57
132 14 0.07
133 2 0.01
134 66 0.34
135 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (132 bp):
TTGCATGATTTATATTGTTAATTGCATGATCATATATTTAATTGCAAGATTTATATTGTTAATTG
CATGATTATATATTTAATTGAATGATTTACATGATTTATATTGTTAATTGCATGATCATATATTT
AA
Found at i:19730587 original size:49 final size:49
Alignment explanation
Indices: 19730485--19730628 Score: 157
Period size: 49 Copynumber: 3.1 Consensus size: 49
19730475 TATATATCAT
*
19730485 TAATTGCATGATTATATATTTAATTGAATGATTTATA-TGATTATATAT--T
1 TAATTGCATGATTATATATTTAATTGAATGATTTATATTG-TTA-AT-TGCA
*
19730534 TAATTGCATGATTATATATTTAATTGCATGATTTATATTGTTAATTGCA
1 TAATTGCATGATTATATATTTAATTGAATGATTTATATTGTTAATTGCA
*
19730583 TAA-T---T-A-TAT-T-TTTGATTGAATGATTTATATTGTTAATTGCA
1 TAATTGCATGATTATATATTTAATTGAATGATTTATATTGTTAATTGCA
19730624 TAATT
1 TAATT
19730629 ATATATTTAA
Statistics
Matches: 87, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
41 32 0.37
42 2 0.02
43 3 0.03
44 1 0.01
45 1 0.01
47 1 0.01
48 3 0.03
49 42 0.48
50 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (49 bp):
TAATTGCATGATTATATATTTAATTGAATGATTTATATTGTTAATTGCA
Found at i:19730608 original size:172 final size:175
Alignment explanation
Indices: 19730313--19730682 Score: 498
Period size: 172 Copynumber: 2.1 Consensus size: 175
19730303 ATATTGTTGT
* * * *
19730313 TTGCATGATCATATATTTAATTGCATGATTTATATTGTTAATTGTATGATCATTGCATGATCATA
1 TTGCATGATTATATATTTAATTGAATGATTTATATTGTTAATTATATGATAATTGCATGATCATA
* * *
19730378 TATTTATTTGCATGATTTATATTGTTAATTGCATGATCATATATTTATTTGCATGATTTATATTG
66 TATTTAATTGCATGATTTATATTGTTAATTGCATAATCATATATTTATTTGAATGATTTATATTG
* *
19730443 TTAATTGCATGATCATATATTTAATTGCAAGATATATATCATTAA
131 TTAATTGCATAATCATATATTTAATTGCAAGATATACATCATTAA
* *
19730488 TTGCATGATTATATATTTAATTGAATGATTTATA-TGATT-A-TATAT-TTAATTGCATGATTAT
1 TTGCATGATTATATATTTAATTGAATGATTTATATTG-TTAATTATATGATAATTGCATGATCAT
* *
19730549 ATATTTAATTGCATGATTTATATTGTTAATTGCATAATTATATTTTTGA-TTGAATGATTTATAT
65 ATATTTAATTGCATGATTTATATTGTTAATTGCATAATCATATATTT-ATTTGAATGATTTATAT
* * * * ** *
19730613 TGTTAATTGCATAATTATATATTTAATTGCATGTTTTACATTGTTAT
129 TGTTAATTGCATAATCATATATTTAATTGCAAGATATACATCATTAA
*
19730660 TTGTATGATTATATATTTAATTG
1 TTGCATGATTATATATTTAATTG
19730683 CATGTCTATT
Statistics
Matches: 172, Mismatches: 21, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
172 130 0.76
173 5 0.03
174 3 0.02
175 34 0.20
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.51
Consensus pattern (175 bp):
TTGCATGATTATATATTTAATTGAATGATTTATATTGTTAATTATATGATAATTGCATGATCATA
TATTTAATTGCATGATTTATATTGTTAATTGCATAATCATATATTTATTTGAATGATTTATATTG
TTAATTGCATAATCATATATTTAATTGCAAGATATACATCATTAA
Found at i:19730812 original size:18 final size:18
Alignment explanation
Indices: 19730771--19730812 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19730761 TATTCAGTAT
* *
19730771 TATTATTGCATGATTTTA
1 TATTATTGCATGATATGA
*
19730789 TTTTATTGCATGATATGA
1 TATTATTGCATGATATGA
19730807 TATTAT
1 TATTAT
19730813 ATTAATTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (18 bp):
TATTATTGCATGATATGA
Found at i:19730989 original size:2 final size:2
Alignment explanation
Indices: 19730984--19731014 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19730974 TGCATGACAT
*
19730984 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19731015 GATCATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:19731086 original size:26 final size:26
Alignment explanation
Indices: 19731034--19731100 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
19731024 TACTGCATAA
*
19731034 TTATG-TATAATTGCATGAATGACTT
1 TTATGATATAATTGCATGAATGAATT
*
19731059 TTATGATATGATTGCATGATAT-AATT
1 TTATGATATAATTGCATGA-ATGAATT
* *
19731085 TTATAATATATTTGCA
1 TTATGATATAATTGCA
19731101 CGATAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 5 0.14
26 28 0.80
27 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (26 bp):
TTATGATATAATTGCATGAATGAATT
Found at i:19731675 original size:14 final size:15
Alignment explanation
Indices: 19731646--19731677 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19731636 AAGAATAAAA
19731646 TTGGGCTTTCAAATT
1 TTGGGCTTTCAAATT
19731661 TTGGGCTTT-AAATT
1 TTGGGCTTTCAAATT
19731675 TTG
1 TTG
19731678 ATTTTGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.19, C:0.09, G:0.22, T:0.50
Consensus pattern (15 bp):
TTGGGCTTTCAAATT
Found at i:19732221 original size:17 final size:18
Alignment explanation
Indices: 19732187--19732233 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
19732177 AAAAATGAGG
*
19732187 AGAAGAAAA-GAGAATGA
1 AGAAGAAAATGAAAATGA
19732204 A-AAGAAAATGAAAATGA
1 AGAAGAAAATGAAAATGA
19732221 AGAA-AAAAT-AAAA
1 AGAAGAAAATGAAAA
19732234 AATATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 11 0.41
17 14 0.52
18 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (18 bp):
AGAAGAAAATGAAAATGA
Found at i:19733082 original size:25 final size:23
Alignment explanation
Indices: 19733053--19733101 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
19733043 TTAAAATTTA
19733053 AATTTTAATACTTGTAATTTTTTTT
1 AATTTT-AT-CTTGTAATTTTTTTT
* *
19733078 AATTTTATTTTGTGATTTTTTTT
1 AATTTTATCTTGTAATTTTTTTT
19733101 A
1 A
19733102 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 2 0.09
25 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (23 bp):
AATTTTATCTTGTAATTTTTTTT
Found at i:19737860 original size:13 final size:13
Alignment explanation
Indices: 19737842--19737866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19737832 ATTAAAAATA
19737842 TAAAATTTATATT
1 TAAAATTTATATT
19737855 TAAAATTTATAT
1 TAAAATTTATAT
19737867 ATAATTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAATTTATATT
Found at i:19737887 original size:24 final size:24
Alignment explanation
Indices: 19737839--19737885 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19737829 AAAATTAAAA
19737839 ATATAAAATTTATATTTAAAATTT
1 ATATAAAATTTATATTTAAAATTT
* *
19737863 ATATATAATTTTTA-TTAAAATTT
1 ATATAAAATTTATATTTAAAATTT
19737886 TAAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATAAAATTTATATTTAAAATTT
Found at i:19737895 original size:24 final size:24
Alignment explanation
Indices: 19737845--19737895 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
19737835 AAAAATATAA
*
19737845 AATTTATATTTAAAATTTATATAT
1 AATTTATATTTAAAATTTAAATAT
* *
19737869 AATTTTTA-TTAAAATTTTAAATTT
1 AATTTATATTTAAAA-TTTAAATAT
19737893 AAT
1 AAT
19737896 CATAGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTTATATTTAAAATTTAAATAT
Found at i:19738202 original size:15 final size:16
Alignment explanation
Indices: 19738174--19738205 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
19738164 ATTTAGTAAA
19738174 TAAATTTATTTGTATT
1 TAAATTTATTTGTATT
19738190 TAAATTT-TTTGTATT
1 TAAATTTATTTGTATT
19738205 T
1 T
19738206 TTAAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TAAATTTATTTGTATT
Found at i:19738601 original size:7 final size:7
Alignment explanation
Indices: 19738589--19738617 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
19738579 TCAATTAAGC
19738589 TTTTTTA
1 TTTTTTA
19738596 TTTTTTA
1 TTTTTTA
19738603 TTTTTTA
1 TTTTTTA
19738610 TTTTTTA
1 TTTTTTA
19738617 T
1 T
19738618 GTTTGGGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:19738943 original size:18 final size:18
Alignment explanation
Indices: 19738920--19738954 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19738910 TTTTTATTTT
19738920 AATTATTCAATTATTAAA
1 AATTATTCAATTATTAAA
* *
19738938 AATTATTTATTTATTAA
1 AATTATTCAATTATTAA
19738955 CATTTATAAA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTATTCAATTATTAAA
Found at i:19740360 original size:24 final size:23
Alignment explanation
Indices: 19740302--19740369 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
19740292 AAATTAATAA
* *
19740302 CTATGTTTTATATTTAATAAATTT
1 CTATATTTTATATATAAT-AATTT
* **
19740326 ATATAAATTATAATATAATAATTT
1 CTATATTTTAT-ATATAATAATTT
*
19740350 CTATATTTTATATAAAATAA
1 CTATATTTTATATATAATAA
19740370 ATACAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
23 8 0.24
24 20 0.59
25 6 0.18
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (23 bp):
CTATATTTTATATATAATAATTT
Found at i:19746824 original size:28 final size:28
Alignment explanation
Indices: 19746784--19746837 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
19746774 GAAACAAATA
*
19746784 GATTATAATAACAAAGAAAAAAAAAACT
1 GATTATAACAACAAAGAAAAAAAAAACT
* * *
19746812 GATTATAGCAACAATGAAACAAAAAA
1 GATTATAACAACAAAGAAAAAAAAAA
19746838 TTGTCAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (28 bp):
GATTATAACAACAAAGAAAAAAAAAACT
Found at i:19755049 original size:25 final size:25
Alignment explanation
Indices: 19755021--19755072 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
19755011 TACACACGAT
*
19755021 TTGCTAGTTGGGTTAACAACTGTCA
1 TTGCTAGTTGGGTTAACAACAGTCA
19755046 TTGCTAGTTGGGTTAACAACAGTCA
1 TTGCTAGTTGGGTTAACAACAGTCA
19755071 TT
1 TT
19755073 TCGAATCCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (25 bp):
TTGCTAGTTGGGTTAACAACAGTCA
Found at i:19757774 original size:4 final size:4
Alignment explanation
Indices: 19757765--19757802 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
19757755 AGCATTCCAC
*
19757765 AATA AATA AATG AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
19757803 AGGTTAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:19758666 original size:10 final size:10
Alignment explanation
Indices: 19758638--19758686 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
19758628 ACAAAAATTT
19758638 TTTTAAAAAA
1 TTTTAAAAAA
19758648 TTCTT--AAAA
1 TT-TTAAAAAA
19758657 TTTTAAAAAA
1 TTTTAAAAAA
19758667 TTTATAAAAAA
1 TTT-TAAAAAA
*
19758678 ATTTAAAAA
1 TTTTAAAAA
19758687 CTGAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 15 0.44
11 11 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:19759032 original size:24 final size:21
Alignment explanation
Indices: 19758999--19759046 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
19758989 ACATTTTAGA
19758999 TTTTTTAAATTCTTTTTGGATTT
1 TTTTTTAAATT-TTTTT-GATTT
*
19759022 TTTTGTTAAATTTTTTTTATTT
1 TTTT-TTAAATTTTTTTGATTT
19759044 TTT
1 TTT
19759047 ATTTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 9 0.39
24 7 0.30
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (21 bp):
TTTTTTAAATTTTTTTGATTT
Found at i:19759209 original size:23 final size:24
Alignment explanation
Indices: 19759183--19759239 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
19759173 TTTTTCAAAA
*
19759183 ATTTTT-AGATTTTTTTATT-TTTT
1 ATTTTTAAG-TTTTTTTATCTTTTT
19759206 ATTTTTAAGTTTTTTTATCTTTTT
1 ATTTTTAAGTTTTTTTATCTTTTT
*
19759230 AAATTTTAAG
1 -ATTTTTAAG
19759240 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 15 0.52
24 6 0.21
25 8 0.28
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (24 bp):
ATTTTTAAGTTTTTTTATCTTTTT
Found at i:19759221 original size:18 final size:18
Alignment explanation
Indices: 19759153--19759236 Score: 53
Period size: 23 Copynumber: 4.3 Consensus size: 18
19759143 TTTTTAAAAT
19759153 AATTTTTTTA-ATTTTTA
1 AATTTTTTTATATTTTTA
* *
19759170 AATTTTTTCAAAAATTTTTA
1 AATTTTTT--TATATTTTTA
*
19759190 GATTTTTTTATTTTTTATTTTTA
1 AATTTTTTTA-----TATTTTTA
* *
19759213 AGTTTTTTTATCTTTTTA
1 AATTTTTTTATATTTTTA
19759231 AATTTT
1 AATTTT
19759237 AAGAAAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
17 8 0.16
18 13 0.25
19 1 0.02
20 14 0.27
23 15 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
AATTTTTTTATATTTTTA
Found at i:19759253 original size:17 final size:17
Alignment explanation
Indices: 19759233--19759270 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
19759223 TCTTTTTAAA
19759233 TTTTAAGAAAATTTTAT
1 TTTTAAGAAAATTTTAT
**
19759250 TTTTATTAAAATTTTAT
1 TTTTAAGAAAATTTTAT
19759267 TTTT
1 TTTT
19759271 TTCTTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTAAGAAAATTTTAT
Found at i:19759592 original size:6 final size:6
Alignment explanation
Indices: 19759581--19759640 Score: 68
Period size: 6 Copynumber: 10.0 Consensus size: 6
19759571 TGAATGATTG
* * * *
19759581 AAAGTA AAAGTA AAAGTA AAAGTA AGAG-A TAAAGTG AAAGTG AAAGTG
1 AAAGTA AAAGTA AAAGTA AAAGTA AAAGTA -AAAGTA AAAGTA AAAGTA
19759629 AAAGTA AAAGTA
1 AAAGTA AAAGTA
19759641 TTCAGAATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.98
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (6 bp):
AAAGTA
Found at i:19761999 original size:26 final size:24
Alignment explanation
Indices: 19761949--19762000 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
19761939 GTTTGGTGAG
19761949 ATTTTATTTGAAAATCATTTATAAA
1 ATTTTATTTGAAAA-CATTTATAAA
*
19761974 ATTTTACTTTGAGAAA-ATTTATTAA
1 ATTTTA-TTTGA-AAACATTTATAAA
19761999 AT
1 AT
19762001 CTTCCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 16 0.67
26 5 0.21
27 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTTTATTTGAAAACATTTATAAA
Found at i:19762177 original size:98 final size:98
Alignment explanation
Indices: 19761987--19762177 Score: 246
Period size: 99 Copynumber: 1.9 Consensus size: 98
19761977 TTACTTTGAG
* * *
19761987 AAAATTTATTAAATCTTCCAATATTTTGGTAAGATTTAATTCAAGATTTGATTTTCAATAGTTTG
1 AAAATTTATTAAATCTTCCAATAATTTGGTAAGACTTAATTCAAGATTTAATTTTCAATAGTTTG
*
19762052 GTAAGATTAAAATGTATTATTTATTTTATTTAA
66 GTAAGATTAAAATGTATTACTTATTTTATTTAA
* *
19762085 AAAATTTATTAAATC-TCTAATAATTTGGTATGACTTAA-TCTAAGATTTAAATATTTCAATAGT
1 AAAATTTATTAAATCTTCCAATAATTTGGTAAGACTTAATTC-AAGATTT-AAT-TTTCAATAGT
* *
19762148 TTGGTAGGATTAGAAAT-TTTTACTT-TTTTA
63 TTGGTAAGATTA-AAATGTATTACTTATTTTA
19762178 AAACCCCTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
96 2 0.02
97 26 0.32
98 22 0.27
99 27 0.33
100 4 0.05
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (98 bp):
AAAATTTATTAAATCTTCCAATAATTTGGTAAGACTTAATTCAAGATTTAATTTTCAATAGTTTG
GTAAGATTAAAATGTATTACTTATTTTATTTAA
Found at i:19762265 original size:20 final size:20
Alignment explanation
Indices: 19762219--19762294 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
19762209 AACAAAAATT
19762219 ATCATGCAA-AATAATAT--
1 ATCATGCAATAATAATATAA
19762236 -T-ATGCAAATAATAATATAA
1 ATCATGC-AATAATAATATAA
19762255 TATCAT-CAATAATAATATGAA
1 -ATCATGCAATAATAATAT-AA
19762276 ATCATGCAAT--TAATATAA
1 ATCATGCAATAATAATATAA
19762294 A
1 A
19762295 CTATCATGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
15 4 0.08
16 3 0.06
17 8 0.16
18 3 0.06
19 6 0.12
20 16 0.32
21 8 0.16
22 2 0.04
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (20 bp):
ATCATGCAATAATAATATAA
Found at i:19762291 original size:19 final size:20
Alignment explanation
Indices: 19762267--19762306 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19762257 TCATCAATAA
*
19762267 TAATATGAA-ATCATGCAAT
1 TAATATAAACATCATGCAAT
19762286 TAATATAAACTATCATGCAAT
1 TAATATAAAC-ATCATGCAAT
19762307 CAAGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (20 bp):
TAATATAAACATCATGCAAT
Found at i:19762300 original size:21 final size:21
Alignment explanation
Indices: 19762276--19762323 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
19762266 ATAATATGAA
* * *
19762276 ATCATGCAATTAATATAAACT
1 ATCATGCAATCAAGATAAAAT
19762297 ATCATGCAATCAAGATAAAAT
1 ATCATGCAATCAAGATAAAAT
19762318 ATCATG
1 ATCATG
19762324 TAAATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (21 bp):
ATCATGCAATCAAGATAAAAT
Found at i:19762393 original size:24 final size:25
Alignment explanation
Indices: 19762324--19762420 Score: 63
Period size: 24 Copynumber: 3.8 Consensus size: 25
19762314 AAATATCATG
*
19762324 TAAATTTATTA-ATAATCATGCAAAAA
1 TAAATATATTACATAATCATGC--AAA
* * *
19762350 TGAATCATATAAACAAAATCATGCAAA
1 TAAAT-ATAT-TACATAATCATGCAAA
* *
19762377 TAAATATATTA-ATAATCATACAAT
1 TAAATATATTACATAATCATGCAAA
* * *
19762401 TAAATAAAATATATAATCAT
1 TAAATATATTACATAATCAT
19762421 ATAAGGAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
24 19 0.34
25 9 0.16
26 8 0.14
27 10 0.18
28 1 0.02
29 9 0.16
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (25 bp):
TAAATATATTACATAATCATGCAAA
Found at i:19763125 original size:16 final size:16
Alignment explanation
Indices: 19763090--19763124 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19763080 CTGATTTCTA
19763090 TTTT-TTTTTACTTTT
1 TTTTATTTTTACTTTT
19763105 TTTTATTTTTGACTTTT
1 TTTTATTTTT-ACTTTT
19763122 TTT
1 TTT
19763125 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTATTTTTACTTTT
Found at i:19763515 original size:18 final size:19
Alignment explanation
Indices: 19763488--19763526 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19763478 TTTTCAAAGA
*
19763488 TTCAAGATTCGCAAAAGTT
1 TTCAAGATTCGCAAAAATT
19763507 TTCAA-ATTCGCAAAAATT
1 TTCAAGATTCGCAAAAATT
19763525 TT
1 TT
19763527 GAGTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (19 bp):
TTCAAGATTCGCAAAAATT
Found at i:19763612 original size:18 final size:17
Alignment explanation
Indices: 19763589--19763644 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
19763579 TTTAGATTTA
19763589 CAAAGATTCTAAGTTTCG
1 CAAAGATT-TAAGTTTCG
*
19763607 CAAAGATTTTAGATTT-G
1 CAAAGATTTAAG-TTTCG
19763624 CAAA-ATTTCAAGTTTCG
1 CAAAGATTT-AAGTTTCG
19763641 CAAA
1 CAAA
19763645 AATTCCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 7 0.21
17 15 0.45
18 11 0.33
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (17 bp):
CAAAGATTTAAGTTTCG
Found at i:19763642 original size:34 final size:35
Alignment explanation
Indices: 19763578--19763644 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
19763568 TTTTTAGAAG
19763578 TTTTAGATTTACAAAGATTCTAAGTTTCGCAAAGA
1 TTTTAGATTTACAAAGATTCTAAGTTTCGCAAAGA
*
19763613 TTTTAGATTTGCAAA-ATT-TCAAGTTTCGCAAA
1 TTTTAGATTTACAAAGATTCT-AAGTTTCGCAAA
19763645 AATTCCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 1 0.03
34 15 0.50
35 14 0.47
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (35 bp):
TTTTAGATTTACAAAGATTCTAAGTTTCGCAAAGA
Found at i:19763648 original size:18 final size:18
Alignment explanation
Indices: 19763599--19763715 Score: 55
Period size: 17 Copynumber: 6.7 Consensus size: 18
19763589 CAAAGATTCT
*
19763599 AAGTTTCGCAAAGATTT-
1 AAGTTTCGCAAAAATTTC
*
19763616 TAGATTT-GC-AAAATTTC
1 AAG-TTTCGCAAAAATTTC
*
19763633 AAGTTTCGCAAAAATTCC
1 AAGTTTCGCAAAAATTTC
* **
19763651 AA-ATTCGCAAAGGTTTC
1 AAGTTTCGCAAAAATTTC
* ** *
19763668 AA-ATTCATAAAAATTTT
1 AAGTTTCGCAAAAATTTC
* * *
19763685 TAGATTCGCAAGAATTTTC
1 AAGTTTCGCAA-AAATTTC
*
19763704 AAGTTTTGCAAA
1 AAGTTTCGCAAA
19763716 GGTTTCATAT
Statistics
Matches: 73, Mismatches: 21, Indels: 11
0.70 0.20 0.10
Matches are distributed among these distances:
16 9 0.12
17 32 0.44
18 19 0.26
19 13 0.18
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (18 bp):
AAGTTTCGCAAAAATTTC
Found at i:19763670 original size:17 final size:17
Alignment explanation
Indices: 19763650--19763772 Score: 66
Period size: 18 Copynumber: 7.0 Consensus size: 17
19763640 GCAAAAATTC
19763650 CAAATTCGCAAAGGTTT
1 CAAATTCGCAAAGGTTT
** **
19763667 CAAATTCATAAAAATTTT
1 CAAATTC-GCAAAGGTTT
* * **
19763685 TAGATTCGCAAGAATTTT
1 CAAATTCGCAA-AGGTTT
* *
19763703 CAAGTTTTGCAAAGGTTT
1 CAA-ATTCGCAAAGGTTT
* * **
19763721 CATATTCGTAATTGTTT
1 CAAATTCGCAAAGGTTT
* *
19763738 CAAGTTTCGAAAAGGTTT
1 CAA-ATTCGCAAAGGTTT
19763756 CAAATTCGCAAAGGTTT
1 CAAATTCGCAAAGGTTT
19763773 TAGATTCGTA
Statistics
Matches: 75, Mismatches: 27, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
17 32 0.43
18 37 0.49
19 6 0.08
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (17 bp):
CAAATTCGCAAAGGTTT
Found at i:19763780 original size:17 final size:17
Alignment explanation
Indices: 19763713--19763772 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
19763703 CAAGTTTTGC
* *
19763713 AAAGGTTTCATATTCGT
1 AAAGGTTTCAAATTCGA
** *
19763730 AATTGTTTCAAGTTTCGA
1 AAAGGTTTCAA-ATTCGA
*
19763748 AAAGGTTTCAAATTCGC
1 AAAGGTTTCAAATTCGA
19763765 AAAGGTTT
1 AAAGGTTT
19763773 TAGATTCGTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (17 bp):
AAAGGTTTCAAATTCGA
Found at i:19763955 original size:33 final size:33
Alignment explanation
Indices: 19763917--19764018 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
19763907 CAAAGATTCA
*
19763917 AATTTCAAATTCACAATAACTCAAATTTGTAAG
1 AATTTCAAATTCACAACAACTCAAATTTGTAAG
* * *
19763950 AATTTCAAGTTCATAACAAATCAAATATT-T--G
1 AATTTCAAATTCACAACAACTCAAAT-TTGTAAG
* * * * * *
19763981 AATTTCATATTCGCAAGAACTTATATTTGCAAG
1 AATTTCAAATTCACAACAACTCAAATTTGTAAG
19764014 AATTT
1 AATTT
19764019 TAGTTTCGTA
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
30 2 0.04
31 19 0.37
33 29 0.56
34 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (33 bp):
AATTTCAAATTCACAACAACTCAAATTTGTAAG
Found at i:19763971 original size:64 final size:64
Alignment explanation
Indices: 19763882--19764018 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
19763872 TTTAGTTTTA
** * *
19763882 CAAGAATTTCAAGTTTGCAAGAAATCAAAGATTCAAATTTCAAATTCACAATAACTCAAATTTG
1 CAAGAATTTCAAGTTCACAACAAATCAAAGATTCAAATTTCAAATTCACAAGAACTCAAATTTG
* * * ** * * * *
19763946 TAAGAATTTCAAGTTCATAACAAATCAAATATTTGAATTTCATATTCGCAAGAACTTATATTTG
1 CAAGAATTTCAAGTTCACAACAAATCAAAGATTCAAATTTCAAATTCACAAGAACTCAAATTTG
19764010 CAAGAATTT
1 CAAGAATTT
19764019 TAGTTTCGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (64 bp):
CAAGAATTTCAAGTTCACAACAAATCAAAGATTCAAATTTCAAATTCACAAGAACTCAAATTTG
Found at i:19764130 original size:17 final size:17
Alignment explanation
Indices: 19764099--19764154 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
19764089 TTACAAGAGT
* * *
19764099 TTCAAATTCTCAAGAAT
1 TTCAAGTTCACAAGAAA
* *
19764116 TTTAAGTTCATAAGAAA
1 TTCAAGTTCACAAGAAA
*
19764133 TTCAAGTTCACAAGAAC
1 TTCAAGTTCACAAGAAA
19764150 TTCAA
1 TTCAA
19764155 ATGGAAGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (17 bp):
TTCAAGTTCACAAGAAA
Found at i:19764457 original size:22 final size:23
Alignment explanation
Indices: 19764431--19764485 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
19764421 TATTTCACAA
*
19764431 CCAAAATTTTTA-ATATTCATATT
1 CCAAAATTTTTAGAGATTCATA-T
* *
19764454 CAAAAAATTTTAGAGATTCATAT
1 CCAAAATTTTTAGAGATTCATAT
19764477 CCAAAATTT
1 CCAAAATTT
19764486 CAAAGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.40
Consensus pattern (23 bp):
CCAAAATTTTTAGAGATTCATAT
Found at i:19764761 original size:21 final size:21
Alignment explanation
Indices: 19764736--19764794 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 21
19764726 GATGCCATAT
*
19764736 CATGATTCAATATGCCCCAAC
1 CATGATGCAATATGCCCCAAC
19764757 CATGATGCGAATGTATGCCCCAAC
1 CATGATGC-AA--TATGCCCCAAC
19764781 CATGATGCAA-ATGC
1 CATGATGCAATATGC
19764795 AATGTGCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 4 0.12
21 7 0.21
22 2 0.06
23 2 0.06
24 19 0.56
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (21 bp):
CATGATGCAATATGCCCCAAC
Found at i:19764775 original size:24 final size:24
Alignment explanation
Indices: 19764746--19764793 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19764736 CATGATTCAA
*
19764746 TATGCCCCAACCATGATGCGAATG
1 TATGCCCCAACCATGATGCAAATG
19764770 TATGCCCCAACCATGATGCAAATG
1 TATGCCCCAACCATGATGCAAATG
19764794 CAATGTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (24 bp):
TATGCCCCAACCATGATGCAAATG
Found at i:19768086 original size:177 final size:177
Alignment explanation
Indices: 19767790--19768133 Score: 593
Period size: 177 Copynumber: 1.9 Consensus size: 177
19767780 TTCTAGCATA
19767790 AAGGGAAATGATGGCTCTAACTTAGGTTTGGAACCTTAAAGTTTATTTACATATTAGGTTCAAAG
1 AAGGGAAATGATGGCTCTAACTTAGGTTTGGAACCTTAAAGTTTATTTACATATTAGGTTCAAAG
* *
19767855 ATTTGACAATCTAATGGTTCTCAAATTATTCCTTATATCATTATTCATTATAAACTAATAAAGCA
66 ATTTGACAATCTAATGGTTCTCAAATAATTCCTTATATCATTATCCATTATAAACTAATAAAGCA
*
19767920 CCACAATCCTCACCAATTATAGGTTATAAGCGAAAATAGTTCAATTT
131 CCACAATCCTCACCAATTATAGGTTACAAGCGAAAATAGTTCAATTT
*
19767967 AAGGGAAATGATGGCTCTAACTTAGGTTT-GAACCCTTAAAGTTTATTTACATATTAGGTTTAAA
1 AAGGGAAATGATGGCTCTAACTTAGGTTTGGAA-CCTTAAAGTTTATTTACATATTAGGTTCAAA
*
19768031 GATTT-AGCAATCTAATGGTTCTCAAATAATTCCTTATATCATTATCCATTATAAACTAATAAGG
65 GATTTGA-CAATCTAATGGTTCTCAAATAATTCCTTATATCATTATCCATTATAAACTAATAAAG
* *
19768095 CACCTCAATCCTCACCCATTATAGGTTACAAGCGAAAAT
129 CACCACAATCCTCACCAATTATAGGTTACAAGCGAAAAT
19768134 GATTTAATTT
Statistics
Matches: 158, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
176 4 0.03
177 154 0.97
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (177 bp):
AAGGGAAATGATGGCTCTAACTTAGGTTTGGAACCTTAAAGTTTATTTACATATTAGGTTCAAAG
ATTTGACAATCTAATGGTTCTCAAATAATTCCTTATATCATTATCCATTATAAACTAATAAAGCA
CCACAATCCTCACCAATTATAGGTTACAAGCGAAAATAGTTCAATTT
Found at i:19769171 original size:21 final size:21
Alignment explanation
Indices: 19769141--19769185 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
19769131 ATATTATGCA
*
19769141 AATAATAATAT-AATATCATAC
1 AATAACAATATCAA-ATCATAC
*
19769162 AATAACAATATCAAATCATGC
1 AATAACAATATCAAATCATAC
19769183 AAT
1 AAT
19769186 TAATATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAACAATATCAAATCATAC
Found at i:19769200 original size:21 final size:21
Alignment explanation
Indices: 19769176--19769226 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
19769166 ACAATATCAA
* * *
19769176 ATCATGCAATTAATATAAACT
1 ATCATGCAATCAAGATAAAAT
19769197 ATCATGCAATCAAGATAAAAT
1 ATCATGCAATCAAGATAAAAT
19769218 ATCATGCAA
1 ATCATGCAA
19769227 ATTTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (21 bp):
ATCATGCAATCAAGATAAAAT
Found at i:19770082 original size:18 final size:18
Alignment explanation
Indices: 19770049--19770083 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19770039 CGAAGCTTTC
*
19770049 CAATCAAATCTAATTTTA
1 CAATCAAAGCTAATTTTA
*
19770067 CAATCAAAGCTCATTTT
1 CAATCAAAGCTAATTTT
19770084 TAATCTCGAA
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:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (18 bp):
CAATCAAAGCTAATTTTA
Found at i:19781008 original size:15 final size:16
Alignment explanation
Indices: 19780985--19781018 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19780975 TATAAATTTC
19780985 TTTAGTTTTTTTT-TT
1 TTTAGTTTTTTTTATT
*
19781000 TTTATTTTTTTTTATT
1 TTTAGTTTTTTTTATT
19781016 TTT
1 TTT
19781019 GGGAATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (16 bp):
TTTAGTTTTTTTTATT
Found at i:19781009 original size:10 final size:10
Alignment explanation
Indices: 19780990--19781018 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
19780980 ATTTCTTTAG
19780990 TTTT-TTTTT
1 TTTTATTTTT
19780999 TTTTATTTTT
1 TTTTATTTTT
19781009 TTTTATTTTT
1 TTTTATTTTT
19781019 GGGAATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:19796546 original size:24 final size:24
Alignment explanation
Indices: 19796499--19796546 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19796489 TATTTGAAAG
* *
19796499 ATTTTAAAAAACTTTTGAACATTT
1 ATTTTAAAAAACTTTTAAAAATTT
* *
19796523 ATTTTTAAAATCTTTTAAAAATTT
1 ATTTTAAAAAACTTTTAAAAATTT
19796547 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTAAAAAACTTTTAAAAATTT
Found at i:19796552 original size:9 final size:9
Alignment explanation
Indices: 19796523--19796556 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
19796513 TTGAACATTT
19796523 ATTTTTAAA
1 ATTTTTAAA
19796532 ATCTTTTAAAA
1 AT-TTTT-AAA
19796543 ATTTTTAAA
1 ATTTTTAAA
19796552 ATTTT
1 ATTTT
19796557 ATTTTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 10 0.43
10 8 0.35
11 5 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:19797536 original size:32 final size:34
Alignment explanation
Indices: 19797453--19797536 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
19797443 ATTGTATTGC
**
19797453 ATTTTTTAAAATGGATTTCTGAAAATATAATATA
1 ATTTTTTAAAATATATTTCTGAAAATATAATATA
* * *
19797487 ATTTTTGAAAATTTATTTTTG-AAA-ATAATA-A
1 ATTTTTTAAAATATATTTCTGAAAATATAATATA
19797518 ATTTTTTAAATATATATTT
1 ATTTTTTAAA-ATATATTT
19797537 AATTATAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
31 10 0.23
32 13 0.30
33 3 0.07
34 17 0.40
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (34 bp):
ATTTTTTAAAATATATTTCTGAAAATATAATATA
Found at i:19797601 original size:21 final size:19
Alignment explanation
Indices: 19797568--19797606 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
19797558 TTTAATTTTA
19797568 ATTTAAATAAAATAAATAT
1 ATTTAAATAAAATAAATAT
19797587 ATTTAATATTAAAATAAATA
1 ATTTAA-A-TAAAATAAATA
19797607 ATACTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAAATAAAATAAATAT
Found at i:19798898 original size:58 final size:57
Alignment explanation
Indices: 19798805--19798915 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
19798795 CTTCTTTTCC
*
19798805 TAAATAACAAAAATACCCATCTTATAAATATCAAATCATTATAATACCCTTTATATCT
1 TAAATAACAAAAATACCCATCTTATAAATATCAAATCACTATAATA-CCTTTATATCT
* * * * *
19798863 TAAATGACGAAAATACCCCTCTTATAAATGA-CAAATTACTATGATACCTTTAT
1 TAAATAACAAAAATACCCATCTTATAAAT-ATCAAATCACTATAATACCTTTAT
19798916 GTCATAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 7 0.15
58 38 0.83
59 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (57 bp):
TAAATAACAAAAATACCCATCTTATAAATATCAAATCACTATAATACCTTTATATCT
Found at i:19799623 original size:62 final size:62
Alignment explanation
Indices: 19799518--19799636 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 62
19799508 ATTCTCCTCT
* **
19799518 TACCATAATTTGAAAAAATTACTATGACACATTTACTATCATAATTATGAAAATATCCCTTC
1 TACCATAATTTGAAAAAATTACTATGACACATTTACTACCATAATTACAAAAATATCCCTTC
** * *
19799580 TACCATAATTTTTAAAAATTACTAT-A-ATATCTCTCCTACCATAATTACAAAAATATC
1 TACCATAATTTGAAAAAATTACTATGACACAT-T-TACTACCATAATTACAAAAATATC
19799637 TTTCCTATCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 3 0.06
61 2 0.04
62 43 0.90
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (62 bp):
TACCATAATTTGAAAAAATTACTATGACACATTTACTACCATAATTACAAAAATATCCCTTC
Found at i:19799634 original size:26 final size:26
Alignment explanation
Indices: 19799596--19799677 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
19799586 AATTTTTAAA
* *
19799596 AATTACTATAATATCTCTCCTACCAT
1 AATTACAAAAATATCTCTCCTACCAT
* *
19799622 AATTACAAAAATATCTTTCCTATCAT
1 AATTACAAAAATATCTCTCCTACCAT
* *
19799648 AATTATAAAAATA-CTC-CC-ACCAA
1 AATTACAAAAATATCTCTCCTACCAT
19799671 AATTACA
1 AATTACA
19799678 TTAATACCCT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 9 0.19
24 2 0.04
25 2 0.04
26 34 0.72
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTACAAAAATATCTCTCCTACCAT
Found at i:19806752 original size:21 final size:21
Alignment explanation
Indices: 19806728--19806782 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 21
19806718 TACACATTTT
*
19806728 TTTTTCGTCTTCTTTTTATTC
1 TTTTTCGTCTTCTTTTTATTA
*
19806749 TTTTT-G--TTCTTATTATTA
1 TTTTTCGTCTTCTTTTTATTA
* *
19806767 TTATTCTTCTTCTTTT
1 TTTTTCGTCTTCTTTT
19806783 ATCCCTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
18 14 0.54
20 1 0.04
21 11 0.42
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTTCGTCTTCTTTTTATTA
Found at i:19809089 original size:19 final size:19
Alignment explanation
Indices: 19809065--19809113 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
19809055 AAATATTTGA
19809065 AAAGTTAACCATCCAATCC
1 AAAGTTAACCATCCAATCC
19809084 AAAGTTAACCATCCAATCC
1 AAAGTTAACCATCCAATCC
19809103 -AAGATTAACCA
1 AAAG-TTAACCA
19809114 AATCATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.20
Consensus pattern (19 bp):
AAAGTTAACCATCCAATCC
Found at i:19810171 original size:17 final size:18
Alignment explanation
Indices: 19810137--19810181 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
19810127 AATTGTTAAG
19810137 AGTTTATATTGATGTTTAT
1 AGTTTATATT-ATGTTTAT
19810156 AGTTTATATT-TGTTTAT
1 AGTTTATATTATGTTTAT
*
19810173 ACTTTATAT
1 AGTTTATAT
19810182 ACTGAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 15 0.60
19 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (18 bp):
AGTTTATATTATGTTTAT
Found at i:19810317 original size:33 final size:33
Alignment explanation
Indices: 19810280--19810344 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
19810270 TATTTTATAA
19810280 ATATAAACAAAATGAACTAAATATAAAATTAGG
1 ATATAAACAAAATGAACTAAATATAAAATTAGG
* * *
19810313 ATATAAATATAATTAACTAAATATAAAATTAG
1 ATATAAACAAAATGAACTAAATATAAAATTAG
19810345 TCTCAATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (33 bp):
ATATAAACAAAATGAACTAAATATAAAATTAGG
Found at i:19815053 original size:30 final size:30
Alignment explanation
Indices: 19815010--19815078 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
19815000 AAACCCCAAA
19815010 CCCTAAACCAATACCCAAACCAAACCTAAG
1 CCCTAAACCAATACCCAAACCAAACCTAAG
* * *
19815040 CCTTAAACTAATACCTAAACCAAACCTAAG
1 CCCTAAACCAATACCCAAACCAAACCTAAG
19815070 CCCTAAACC
1 CCCTAAACC
19815079 GACTTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.14
Consensus pattern (30 bp):
CCCTAAACCAATACCCAAACCAAACCTAAG
Found at i:19815928 original size:14 final size:14
Alignment explanation
Indices: 19815909--19815937 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19815899 CTTTGTTTTT
19815909 AACAACTTTTTTAA
1 AACAACTTTTTTAA
19815923 AACAACTTTTTTAA
1 AACAACTTTTTTAA
19815937 A
1 A
19815938 TTAATCTATT
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:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
AACAACTTTTTTAA
Found at i:19818439 original size:126 final size:124
Alignment explanation
Indices: 19818291--19818524 Score: 296
Period size: 126 Copynumber: 1.9 Consensus size: 124
19818281 GTGTTTCATA
* * *
19818291 AGAAATTGACATGTGACATTTTACTTCAAAATTA-TATGATAC-CCTTATTAAATTACGTAT-TA
1 AGAAATTGACAAGTGACATTTTACTTAAAAATTATTATAATACTCC-TATTAAATTA--TATATA
* *
19818353 AAATTTTAACATGATATAAAATT-TATCACATATTAAATTATTAAAATTTTGCCATTGCTTTAT
63 AAATTTTAACATAATATAAAATTAAAT-ACATATTAAA-TATTAAAATTTTGCCATTGCTTTAT
* * * *
19818416 AGAAATTTGACAAGTGATATTTTATTTAAAAATTATTATAATTCTCCTATTAAATTATATATGAA
1 AGAAA-TTGACAAGTGACATTTTACTTAAAAATTATTATAATACTCCTATTAAATTATATATAAA
*
19818481 ATTTTAACATAATATAAAATTAAATATATATTAAATATTAAAAT
65 ATTTTAACATAATATAAAATTAAATACATATTAAATATTAAAAT
19818525 ATCCTTACCA
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
125 17 0.18
126 57 0.61
127 18 0.19
128 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (124 bp):
AGAAATTGACAAGTGACATTTTACTTAAAAATTATTATAATACTCCTATTAAATTATATATAAAA
TTTTAACATAATATAAAATTAAATACATATTAAATATTAAAATTTTGCCATTGCTTTAT
Done.