Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 41 of 113
Found at i:11714248 original size:71 final size:71
Alignment explanation
Indices: 11714173--11714312 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 71
11714163 TTTACAAATT
* * * * *
11714173 TTAGAATTTTTGCAAAACTTAGAATTTTTCCTAATCTT-GAA-ACTTTACGAATTTTGAAACCTT
1 TTAGAATTTTTGCAAAACTTAAAATTCTTACAAATCTTAGAATA-TTTACGAATCTTG-AACCTT
11714236 TGTGAATC
64 TGTGAATC
* * *
11714244 TTAGAATTTTTGCAAATCTTAAAATTCTTACAAATCTTAGAATATTTATGAATCTTGAACTTTTG
1 TTAGAATTTTTGCAAAACTTAAAATTCTTACAAATCTTAGAATATTTACGAATCTTGAACCTTTG
11714309 TGAA
66 TGAA
11714313 ATTTGAAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 44 0.75
72 14 0.24
73 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (71 bp):
TTAGAATTTTTGCAAAACTTAAAATTCTTACAAATCTTAGAATATTTACGAATCTTGAACCTTTG
TGAATC
Found at i:11714282 original size:18 final size:18
Alignment explanation
Indices: 11714240--11714282 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
11714230 AACCTTTGTG
* * *
11714240 AATCTTAGAATTTTTGCA
1 AATCTTAAAATTCTTACA
11714258 AATCTTAAAATTCTTACA
1 AATCTTAAAATTCTTACA
11714276 AATCTTA
1 AATCTTA
11714283 GAATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (18 bp):
AATCTTAAAATTCTTACA
Found at i:11714297 original size:18 final size:17
Alignment explanation
Indices: 11714238--11714312 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
11714228 GAAACCTTTG
11714238 TGAATCTTAGAATTTT-
1 TGAATCTTAGAATTTTA
*
11714254 TGCAAATCTTAAAATTCTTA
1 TG--AATCTTAGAATT-TTA
**
11714274 CAAATCTTAGAATATTTA
1 TGAATCTTAGAAT-TTTA
*
11714292 TGAATCTT-GAACTTTTG
1 TGAATCTTAGAA-TTTTA
11714309 TGAA
1 TGAA
11714313 ATTTGAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.04
17 10 0.22
18 31 0.67
19 3 0.07
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (17 bp):
TGAATCTTAGAATTTTA
Found at i:11714351 original size:71 final size:71
Alignment explanation
Indices: 11714216--11714406 Score: 174
Period size: 71 Copynumber: 2.7 Consensus size: 71
11714206 ATCTTGAAAC
* * * * * **
11714216 TTTACGAATTTTGAAACCTTTGTGAATCTTAGAAT-TTTTGCAAATCTTAAAATTCTTACAAATC
1 TTTACGAATCTTG-AACTTTTGTAAATCTT-GAATCTTTTGCGAATTTTTGAATTCTTACAAATC
11714280 TTAGAA-T
64 TTAGAACT
* * * *
11714287 ATTTATGAATCTTGAACTTTTGTGAAAT-TTGAAATC-TTTGTGAATTTTTGAATTTTTACGAAT
1 -TTTACGAATCTTGAACTTTTGT-AAATCTTG-AATCTTTTGCGAATTTTTGAATTCTTACAAAT
*
11714350 CTTGGAACT
63 CTTAGAACT
* **
11714359 TTTGCGAATCTTGAGGTTTTGTAAATCTTGAATCTTTTGCGAATTTTT
1 TTTACGAATCTTGAACTTTTGTAAATCTTGAATCTTTTGCGAATTTTT
11714407 ACAAAACTTG
Statistics
Matches: 96, Mismatches: 17, Indels: 13
0.76 0.13 0.10
Matches are distributed among these distances:
70 9 0.09
71 72 0.75
72 15 0.16
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (71 bp):
TTTACGAATCTTGAACTTTTGTAAATCTTGAATCTTTTGCGAATTTTTGAATTCTTACAAATCTT
AGAACT
Found at i:11715750 original size:21 final size:21
Alignment explanation
Indices: 11715704--11715744 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11715694 CTTTTTATTC
*
11715704 CTCAAATTGGTGATGTTGATA
1 CTCAAATTGGTAATGTTGATA
*
11715725 CTCAAGTTGGTAATGTTGAT
1 CTCAAATTGGTAATGTTGAT
11715745 GTTCAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (21 bp):
CTCAAATTGGTAATGTTGATA
Found at i:11718023 original size:3 final size:3
Alignment explanation
Indices: 11718015--11718043 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11718005 TAGTTTCAAC
11718015 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
11718044 TTAAACTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11721020 original size:29 final size:29
Alignment explanation
Indices: 11720978--11721039 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
11720968 ATATTATATT
*
11720978 ATTTAACATATTTATAA-TTCAAATATTAC
1 ATTTAAAATATTTA-AAGTTCAAATATTAC
* * *
11721007 ATTTAAAATGTTTAAAGTTTAAATATTAT
1 ATTTAAAATATTTAAAGTTCAAATATTAC
11721036 ATTT
1 ATTT
11721040 TTTACTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTTAAAATATTTAAAGTTCAAATATTAC
Found at i:11725521 original size:24 final size:23
Alignment explanation
Indices: 11725488--11725539 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
11725478 AAGCAAAAAT
* *
11725488 AATCATACAAAAATATTATAATA
1 AATCAAACAAAAATATCATAATA
11725511 ATATCAAACAAAAATATCATAATA
1 A-ATCAAACAAAAATATCATAATA
11725535 AATCA
1 AATCA
11725540 TGCAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (23 bp):
AATCAAACAAAAATATCATAATA
Found at i:11725558 original size:22 final size:22
Alignment explanation
Indices: 11725529--11725608 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
11725519 CAAAAATATC
11725529 ATAATAAATCATGCAAATAAAT
1 ATAATAAATCATGCAAATAAAT
*
11725551 ATAATAAAAAT-ATGCAAGTAATCAT
1 ATAAT--AAATCATGCAAATAA--AT
* *
11725576 ACAAAAATATCATGCAAATAAAT
1 ATAATAA-ATCATGCAAATAAAT
11725599 ATAATAAATC
1 ATAATAAATC
11725609 TTCCTTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
22 8 0.17
23 18 0.39
24 6 0.13
25 14 0.30
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (22 bp):
ATAATAAATCATGCAAATAAAT
Found at i:11725686 original size:10 final size:10
Alignment explanation
Indices: 11725660--11725742 Score: 60
Period size: 10 Copynumber: 7.7 Consensus size: 10
11725650 AATCACAATT
*
11725660 TAAAAAAATAC
1 TAAAAAAA-AA
*
11725671 TAAGAAAAAA
1 TAAAAAAAAA
*
11725681 TAAGAAAAAA
1 TAAAAAAAAA
11725691 TAAAATAATAAA
1 TAAAA-AA-AAA
11725703 TCAAAATAAAAA
1 T-AAAA-AAAAA
11725715 TAAAAAAAATCA
1 TAAAAAAAA--A
*
11725727 TAAAATAAAA
1 TAAAAAAAAA
11725737 -AAAAAA
1 TAAAAAA
11725743 CTTACGACCG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
9 5 0.08
10 20 0.32
11 13 0.21
12 17 0.27
13 7 0.11
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:11725708 original size:28 final size:28
Alignment explanation
Indices: 11725677--11725730 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
11725667 ATACTAAGAA
*
11725677 AAAATAAGAAA-AAATAAAATAATAAATC
1 AAAATAA-AAATAAAAAAAATAATAAATC
*
11725705 AAAATAAAAATAAAAAAAATCATAAA
1 AAAATAAAAATAAAAAAAATAATAAA
11725731 ATAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.17
Consensus pattern (28 bp):
AAAATAAAAATAAAAAAAATAATAAATC
Found at i:11725741 original size:18 final size:16
Alignment explanation
Indices: 11725676--11725741 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 16
11725666 AATACTAAGA
*
11725676 AAAAATAAGAAAAAAT
1 AAAAATAAAAAAAAAT
11725692 -AAAATAATAAATCAAAAT
1 AAAAATAA-AAA--AAAAT
11725710 AAAAAT-AAAAAAAAT
1 AAAAATAAAAAAAAAT
11725725 CATAAAATAAAAAAAAA
1 -A-AAAATAAAAAAAAA
11725742 ACTTACGACC
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 12 0.29
16 3 0.07
17 8 0.19
18 14 0.33
19 5 0.12
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAAATAAAAAAAAAT
Found at i:11725741 original size:28 final size:29
Alignment explanation
Indices: 11725687--11725742 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
11725677 AAAATAAGAA
*
11725687 AAAATAAAATAATAAATCAAAATAAAAAT
1 AAAATAAAATAATAAATCAAAAAAAAAAT
*
11725716 AAAA-AAAATCATAAAAT-AAAAAAAAAA
1 AAAATAAAATAAT-AAATCAAAAAAAAAA
11725743 CTTACGACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (29 bp):
AAAATAAAATAATAAATCAAAAAAAAAAT
Found at i:11732051 original size:2 final size:2
Alignment explanation
Indices: 11732044--11732069 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11732034 CTCAGTTAGA
11732044 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11732070 GTTGCTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11733171 original size:29 final size:28
Alignment explanation
Indices: 11733120--11733181 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
11733110 TTATAGTAAA
11733120 AAATATAATATTTAAACTTTAAACATTTT
1 AAATATAATATTTAAACTTTAAACA-TTT
* * *
11733149 AAATGTAATATTTGAA-TTATAAATATTT
1 AAATATAATATTTAAACTT-TAAACATTT
11733177 AAATA
1 AAATA
11733182 ATATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (28 bp):
AAATATAATATTTAAACTTTAAACATTT
Found at i:11733175 original size:15 final size:16
Alignment explanation
Indices: 11733154--11733193 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
11733144 ATTTTAAATG
*
11733154 TAATATTTGAATTATA
1 TAATATTTGAATAATA
*
11733170 -AATATTTAAATAATA
1 TAATATTTGAATAATA
11733185 TAATATTTG
1 TAATATTTG
11733194 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
TAATATTTGAATAATA
Found at i:11733273 original size:18 final size:19
Alignment explanation
Indices: 11733252--11733289 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
11733242 ATGATGAATA
*
11733252 TTATCTTAATTTAT-ATAT
1 TTATATTAATTTATCATAT
*
11733270 TTATATTCATTTATCATAT
1 TTATATTAATTTATCATAT
11733289 T
1 T
11733290 AAATATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATTAATTTATCATAT
Found at i:11736067 original size:3 final size:3
Alignment explanation
Indices: 11736059--11736099 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
11736049 GTAAGTTTAA
11736059 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11736100 GTTGAAACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11738388 original size:21 final size:21
Alignment explanation
Indices: 11738364--11738409 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11738354 TCTCGTCATT
*
11738364 TTGAACATCAACATTACCAAC
1 TTGAACATCAACATCACCAAC
** *
11738385 TTGAGTATCAACATCACCAAT
1 TTGAACATCAACATCACCAAC
11738406 TTGA
1 TTGA
11738410 GGAATAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (21 bp):
TTGAACATCAACATCACCAAC
Found at i:11738410 original size:21 final size:21
Alignment explanation
Indices: 11738370--11738410 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11738360 CATTTTGAAC
*
11738370 ATCAACATTACCAACTTGAGT
1 ATCAACATCACCAACTTGAGT
*
11738391 ATCAACATCACCAATTTGAG
1 ATCAACATCACCAACTTGAG
11738411 GAATAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (21 bp):
ATCAACATCACCAACTTGAGT
Found at i:11739732 original size:28 final size:28
Alignment explanation
Indices: 11739675--11739732 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
11739665 CAGATAAATC
* **
11739675 AAATTCACAAAAGATTCAAGTTTTGTAA
1 AAATTCACAAAAGATTCAAGATTTACAA
*
11739703 AAATTCGCAAAAGATTCAAGATTTACAA
1 AAATTCACAAAAGATTCAAGATTTACAA
11739731 AA
1 AA
11739733 CCTCAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (28 bp):
AAATTCACAAAAGATTCAAGATTTACAA
Found at i:11739815 original size:17 final size:17
Alignment explanation
Indices: 11739705--11739815 Score: 73
Period size: 17 Copynumber: 6.3 Consensus size: 17
11739695 TTTTGTAAAA
*
11739705 ATTCGCAAAAGATTCAAG
1 ATTCACAAAAG-TTCAAG
* **
11739723 ATTTACAAAACCTCAAG
1 ATTCACAAAAGTTCAAG
*
11739740 ATTCGCAAAAGTTCCAAG
1 ATTCACAAAAGTT-CAAG
** *
11739758 ATTCGTAAAA-TTCAAAA
1 ATTCACAAAAGTTC-AAG
*
11739775 ATTCACAAAGAATTTCAA-
1 ATTCAC-AA-AAGTTCAAG
11739793 ATTTCACAAAAGTTCAAG
1 A-TTCACAAAAGTTCAAG
11739811 ATTCA
1 ATTCA
11739816 TAAATATTCT
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
16 1 0.01
17 33 0.45
18 27 0.37
19 9 0.12
20 3 0.04
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (17 bp):
ATTCACAAAAGTTCAAG
Found at i:11739873 original size:18 final size:18
Alignment explanation
Indices: 11739705--11739873 Score: 71
Period size: 18 Copynumber: 9.5 Consensus size: 18
11739695 TTTTGTAAAA
*
11739705 ATTCGCAAAAGATTC-AAG
1 ATTCACAAAA-ATTCTAAG
* **
11739723 ATTTACAAAACCTC-AAG
1 ATTCACAAAAATTCTAAG
* * *
11739740 ATTCGCAAAAGTTCCAAG
1 ATTCACAAAAATTCTAAG
** * *
11739758 ATTC-GTAAAATTCAAAA
1 ATTCACAAAAATTCTAAG
11739775 ATTCACAAAGAATT-TCAA-
1 ATTCACAAA-AATTCT-AAG
*
11739793 ATTTCACAAAAGTTC-AAG
1 A-TTCACAAAAATTCTAAG
* *
11739811 ATTCATAAATATTCTAAG
1 ATTCACAAAAATTCTAAG
*** * *
11739829 ATTTGTAAGAATTTTAAG
1 ATTCACAAAAATTCTAAG
**
11739847 ATTTGCAAAAATTCTAAG
1 ATTCACAAAAATTCTAAG
11739865 ATTCACAAA
1 ATTCACAAA
11739874 GGTTTCAAAA
Statistics
Matches: 113, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
17 39 0.35
18 60 0.53
19 14 0.12
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.30
Consensus pattern (18 bp):
ATTCACAAAAATTCTAAG
Found at i:11739913 original size:52 final size:53
Alignment explanation
Indices: 11739800--11739988 Score: 152
Period size: 54 Copynumber: 3.5 Consensus size: 53
11739790 CAAATTTCAC
* * * * * * *
11739800 AAAAGTTC-AAGATTCATAAATATTCTAAGATTTGT-AAGAATTTTAAGATTTGCA
1 AAAA-TTCTAAGATTCACAAAGATTC-AAAATTCGTAAAG-ATTTCAAGATTAGCG
*
11739854 AAAATTCTAAGATTCACAAAGGTTTCAAAATTCGTAAAG-TTTCAAGATTAG-G
1 AAAATTCTAAGATTCACAAA-GATTCAAAATTCGTAAAGATTTCAAGATTAGCG
* ** * * *
11739906 AAAATTCTAAGTTTTGCAAAAATTCTAAAATTTGTAAAGATTTCAAGATTTGCG
1 AAAATTCTAAGATTCACAAAGATTC-AAAATTCGTAAAGATTTCAAGATTAGCG
**
11739960 AAGGTTCTAAGATTCACAAATGATTCAAA
1 AAAATTCTAAGATTCACAAA-GATTCAAA
11739989 TAAATTTAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
51 3 0.03
52 29 0.27
53 24 0.22
54 41 0.38
55 10 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (53 bp):
AAAATTCTAAGATTCACAAAGATTCAAAATTCGTAAAGATTTCAAGATTAGCG
Found at i:11739956 original size:18 final size:18
Alignment explanation
Indices: 11739826--11739958 Score: 53
Period size: 18 Copynumber: 7.5 Consensus size: 18
11739816 TAAATATTCT
* *
11739826 AAGATTTG-TAAGAATTTT
1 AAGATTTGCAAAG-ATTTC
*
11739844 AAGATTTGCAAA-AATTC
1 AAGATTTGCAAAGATTTC
** *
11739861 TAAGATTCACAAAGGTTTC
1 -AAGATTTGCAAAGATTTC
* * *
11739880 AAAATTCGTAAAG-TTTC
1 AAGATTTGCAAAGATTTC
* *
11739897 AAGATTAGGAAA-A-TTC
1 AAGATTTGCAAAGATTTC
* *
11739913 TAAGTTTTGCAAA-AATTC
1 -AAGATTTGCAAAGATTTC
* *
11739931 TAAAATTTGTAAAGATTTC
1 -AAGATTTGCAAAGATTTC
11739950 AAGATTTGC
1 AAGATTTGC
11739959 GAAGGTTCTA
Statistics
Matches: 86, Mismatches: 22, Indels: 14
0.70 0.18 0.11
Matches are distributed among these distances:
16 3 0.03
17 26 0.30
18 48 0.56
19 9 0.10
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (18 bp):
AAGATTTGCAAAGATTTC
Found at i:11740321 original size:24 final size:21
Alignment explanation
Indices: 11740294--11740349 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
11740284 CACATCCAGA
*
11740294 TTTAAAAATTCACATTTAAGATAT
1 TTTAAAAATTCACATCT-A-A-AT
* *
11740318 TTTAGAGATTCACATCTAAAT
1 TTTAAAAATTCACATCTAAAT
11740339 TTTAAAAATTC
1 TTTAAAAATTC
11740350 TTATTCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 11 0.41
22 1 0.04
23 1 0.04
24 14 0.52
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (21 bp):
TTTAAAAATTCACATCTAAAT
Found at i:11740460 original size:21 final size:21
Alignment explanation
Indices: 11740436--11740540 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 21
11740426 GAGATTCTCA
*
11740436 TCAAAATCCAAAGATTCATAT
1 TCAAAATTCAAAGATTCATAT
11740457 TCAAAAATTCTAGAA-ATTCATAT
1 TC-AAAATTC-A-AAGATTCATAT
*
11740480 CCAAAATTCAAAGATTTGCAT-T
1 TCAAAATTCAAAGA-TT-CATAT
*
11740502 TGAAAAGTTCAAAGATTC-TCAT
1 TCAAAA-TTCAAAGATTCAT-AT
*
11740524 TTAAAATTCAAAGATTC
1 TCAAAATTCAAAGATTC
11740541 TCATTTGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
20 3 0.04
21 16 0.23
22 28 0.40
23 21 0.30
24 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (21 bp):
TCAAAATTCAAAGATTCATAT
Found at i:11740541 original size:21 final size:22
Alignment explanation
Indices: 11740482--11740551 Score: 108
Period size: 21 Copynumber: 3.2 Consensus size: 22
11740472 ATTCATATCC
11740482 AAAATTCAAAGATT-TGCATTTG
1 AAAATTCAAAGATTCT-CATTTG
11740504 AAAAGTTCAAAGATTCTCATTT-
1 AAAA-TTCAAAGATTCTCATTTG
11740526 AAAATTCAAAGATTCTCATTTG
1 AAAATTCAAAGATTCTCATTTG
11740548 AAAA
1 AAAA
11740552 GTTTACATCC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 17 0.38
22 12 0.27
23 15 0.33
24 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (22 bp):
AAAATTCAAAGATTCTCATTTG
Found at i:11740546 original size:44 final size:43
Alignment explanation
Indices: 11740371--11740554 Score: 133
Period size: 44 Copynumber: 4.2 Consensus size: 43
11740361 TTCACATTCA
* * * * * *
11740371 AAAAGTTTAAAAATTCTCATTTGAAGATTAAAAAATTTTCATTTG
1 AAAAGTTCAAAGATTCTCA-TTCAAAATTCAAAGA-TTTCATTTG
* * * * *
11740416 AAAAATTTTAGAGATTCTCA-TCAAAATCCAAAGA-TTCATATTC
1 -AAAAGTTCAAAGATTCTCATTCAAAATTCAAAGATTTCAT-TTG
* *
11740459 AAAAATTCTAGAA-ATTCAT-ATCCAAAATTCAAAGATTTGCATTTG
1 AAAAGTTC-A-AAGATTC-TCATTCAAAATTCAAAGATTT-CATTTG
*
11740504 AAAAGTTCAAAGATTCTCATTTAAAATTCAAAGATTCTCATTTG
1 AAAAGTTCAAAGATTCTCATTCAAAATTCAAAGATT-TCATTTG
11740548 AAAAGTT
1 AAAAGTT
11740555 TACATCCAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
42 11 0.10
43 11 0.10
44 57 0.52
45 12 0.11
46 19 0.17
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (43 bp):
AAAAGTTCAAAGATTCTCATTCAAAATTCAAAGATTTCATTTG
Found at i:11741759 original size:15 final size:15
Alignment explanation
Indices: 11741733--11741771 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11741723 TTGTTTTTAG
*
11741733 TCCAAGTCATGATTT
1 TCCAATTCATGATTT
*
11741748 TTCAATTCATGATTT
1 TCCAATTCATGATTT
11741763 TCCAATTCA
1 TCCAATTCA
11741772 AACATTCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (15 bp):
TCCAATTCATGATTT
Found at i:11745520 original size:16 final size:16
Alignment explanation
Indices: 11745501--11745531 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11745491 TGATGATGGC
11745501 ATGTTATGGTGGGTTT
1 ATGTTATGGTGGGTTT
11745517 ATGTTATGGTGGGTT
1 ATGTTATGGTGGGTT
11745532 ATCTTACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (16 bp):
ATGTTATGGTGGGTTT
Found at i:11745971 original size:200 final size:199
Alignment explanation
Indices: 11745611--11746024 Score: 498
Period size: 200 Copynumber: 2.1 Consensus size: 199
11745601 TATTGTAGTG
* * *
11745611 AGTTGGAT-CTTAATATGGGTATCAGAGCCAAAATATTTTTTCTATTATCTTTCCTAATTTATCA
1 AGTTGGATGCTTAACATGGATATCAGAGCCAAAATACTTTTTCTATTATCTTTCCTAATTTATCA
* * *
11745675 CATGAAAGGCTCTTTCATGTTCGCCTACACATGATAGGGTCTGTTAAGTAGGTTATCCCACATCT
66 CATGAAAGGCTCTTTCATATTCACCTACACATGATAGGGCCTGTTAAGTAGGTTATCCCACATCT
** * * * *
11745740 AATAAATTTTTAGTATCCTATAATCTTATATTCAGGTTGGG-CT-TCTTCACTTACTGTCAATTG
131 AATAAATTTCAAATATCCTATAACCTTATATTCAGATTGGGTCTATC--CACTTACTGTCAATTA
11745803 ATTTTA
194 ATTTTA
* * * * *
11745809 GGTTGGATGCTTAACAT-GATATCAGAGTCAGAA-ACTTTTTCTATTATCTTTTCTTAATTTGTC
1 AGTTGGATGCTTAACATGGATATCAGAGCCAAAATACTTTTTCTATTATC-TTTCCTAATTTATC
* * * * *
11745872 ATATGAAAGGCTTTTTCCATATTCACCTACACGTGATGGGGACCTGTTAAAGTGGGTTAT-CCAC
65 ACATGAAAGGCTCTTT-CATATTCACCTACACATGATAGGG-CCTGTT-AAGTAGGTTATCCCAC
* * * *
11745936 ATTTAATAAATTTCAAATTTCTTATAGCCTTATATTCAGATTGGGTCTATCCACTTACTGTCAAT
127 ATCTAATAAATTTCAAATATCCTATAACCTTATATTCAGATTGGGTCTATCCACTTACTGTCAAT
11746001 TAATTTTA
192 TAATTTTA
11746009 AGTTGGATGCTTAACA
1 AGTTGGATGCTTAACA
11746025 AGAATTTTCT
Statistics
Matches: 182, Mismatches: 27, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
197 14 0.08
198 46 0.25
199 27 0.15
200 81 0.45
201 12 0.07
202 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (199 bp):
AGTTGGATGCTTAACATGGATATCAGAGCCAAAATACTTTTTCTATTATCTTTCCTAATTTATCA
CATGAAAGGCTCTTTCATATTCACCTACACATGATAGGGCCTGTTAAGTAGGTTATCCCACATCT
AATAAATTTCAAATATCCTATAACCTTATATTCAGATTGGGTCTATCCACTTACTGTCAATTAAT
TTTA
Found at i:11749274 original size:20 final size:20
Alignment explanation
Indices: 11749249--11749327 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
11749239 CAGGTCCGGG
11749249 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
11749269 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
11749289 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
11749309 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
11749328 GGATCTAGAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.19, C:0.30, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:11751629 original size:18 final size:16
Alignment explanation
Indices: 11751606--11751677 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 16
11751596 CGGTCTTAAG
11751606 TTTTTTTTTA-TTTTA
1 TTTTTTTTTATTTTTA
11751621 TGATTTTTTTTATTTTTA
1 T--TTTTTTTTATTTTTA
11751639 TTTTGATTTATTA-TTTTA
1 TTTT--TTT-TTATTTTTA
*
11751657 TTTTTTCTTATTTTTTA
1 TTTTTTTTTA-TTTTTA
11751674 TTTT
1 TTTT
11751678 AATATTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
15 4 0.08
16 5 0.10
17 18 0.38
18 18 0.38
19 3 0.06
ACGTcount: A:0.15, C:0.01, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTATTTTTA
Found at i:11751648 original size:28 final size:28
Alignment explanation
Indices: 11751617--11751670 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
11751607 TTTTTTTTAT
*
11751617 TTTATGATTTT-TTTTATTTTTATTTTGA
1 TTTATGATTTTATTTT-TTCTTATTTTGA
*
11751645 TTTATTATTTTATTTTTTCTTATTTT
1 TTTATGATTTTATTTTTTCTTATTTT
11751671 TTATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (28 bp):
TTTATGATTTTATTTTTTCTTATTTTGA
Found at i:11751820 original size:22 final size:22
Alignment explanation
Indices: 11751743--11751822 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
11751733 AAAAGGGAAG
11751743 GATTTATTATATTTATTTGCAT
1 GATTTATTATATTTATTTGCAT
* * *
11751765 GATATTTTTGTATGATTACTTGCAT
1 GAT-TTATTATAT--TTATTTGCAT
11751790 -ATTTTTATTATATTTATTTGCAT
1 GA--TTTATTATATTTATTTGCAT
11751813 GATTTATTAT
1 GATTTATTAT
11751823 GATATTTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
22 11 0.24
23 16 0.35
24 2 0.04
25 16 0.35
26 1 0.02
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (22 bp):
GATTTATTATATTTATTTGCAT
Found at i:11751827 original size:25 final size:24
Alignment explanation
Indices: 11751745--11751829 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
11751735 AAGGGAAGGA
*
11751745 TTTATTATATTTATTTGCATGATAT
1 TTTATGATATTTATTTGCATGAT-T
*
11751770 TTT-TG-TATGATTACTTGCAT-ATT
1 TTTATGATAT--TTATTTGCATGATT
*
11751793 TTTATTATATTTATTTGCATGATT
1 TTTATGATATTTATTTGCATGATT
11751817 TATTATGATATTT
1 T-TTATGATATTT
11751830 TTGTTTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
23 16 0.33
24 8 0.16
25 25 0.51
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTATGATATTTATTTGCATGATT
Found at i:11751852 original size:24 final size:23
Alignment explanation
Indices: 11751793--11751863 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
11751783 CTTGCATATT
*
11751793 TTTATTAT-AT-TTATTTGCATGA
1 TTTATTATGATATT-TTTGTATGA
*
11751815 TTTATTATGATATTTTTGTTTGA
1 TTTATTATGATATTTTTGTATGA
11751838 TATTATTAT-ACTATTTTTGTATGA
1 T-TTATTATGA-TATTTTTGTATGA
11751862 TT
1 TT
11751864 ATTTTTGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.19
23 12 0.29
24 22 0.52
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (23 bp):
TTTATTATGATATTTTTGTATGA
Found at i:11751920 original size:11 final size:12
Alignment explanation
Indices: 11751894--11751927 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
11751884 TGTTTTAATT
11751894 ATGATATTATTAC
1 ATGATATT-TTAC
11751907 ATGATATTTT-C
1 ATGATATTTTAC
11751918 ATGATATTTT
1 ATGATATTTT
11751928 TTTATAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 2 0.10
13 8 0.38
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (12 bp):
ATGATATTTTAC
Found at i:11753461 original size:25 final size:26
Alignment explanation
Indices: 11753410--11753461 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
11753400 TTTTTTTCAT
*
11753410 TTTTTGATTTGATTTTAATTTTTTTG
1 TTTTTGATTTGATTTTAATTTTCTTG
*
11753436 TTTTTG-TTTTATTTTAGA-TTTCTTG
1 TTTTTGATTTGATTTTA-ATTTTCTTG
11753461 T
1 T
11753462 ATATTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.13, C:0.02, G:0.12, T:0.73
Consensus pattern (26 bp):
TTTTTGATTTGATTTTAATTTTCTTG
Found at i:11755137 original size:201 final size:201
Alignment explanation
Indices: 11754755--11755257 Score: 542
Period size: 201 Copynumber: 2.5 Consensus size: 201
11754745 AAAATTCTTG
* * * * * **
11754755 TTAAACATCCAACTTAAAATTAATTGGCAATAAGTGGATA-GA-CCCAATCTGAATATAAGGCTA
1 TTAAGCATCCAACCTAAAATCAATTGACAATAAGT-GA-AGGAGCCCAACCTGAATATAAGATTA
* * ** * * *
11754818 CAAGAAATTTGAAATTTATTAGATGTGAGATAATCCACTTTAATAAGTCCTCATCACGTGTAGGC
64 CAGGATATTAAAAATTTATTAGATGTGAGATAACCCACTTTAATAAGCCCTCACCACGTGTAGGC
*
11754883 GAAGATGAAAAAAGCTTTTCATGTGACAAATTAAAAAAAGATAATAG-AAAAAAATTCTGA-CTC
129 GAAGATGAAAAAAGCCTTTCATGTGACAAATTAAAAAAAGATAATAGAAAAAAAATT-T-ATCTC
11754946 TGATACCATA
192 TGATACCATA
*
11754956 TTAAGCATCCAACCTAAAATCAATTGACAGTAAGTGAAGGAGCCCAACCTGAATATAAGATTACA
1 TTAAGCATCCAACCTAAAATCAATTGACAATAAGTGAAGGAGCCCAACCTGAATATAAGATTACA
*
11755021 GGATATTAAAAATTTATTAGATGTG-GAATAACCCATTTTAAT-AGACCCT-ACCATC-TGTAGG
66 GGATATTAAAAATTTATTAGATGTGAG-ATAACCCACTTTAATAAG-CCCTCACCA-CGTGTAGG
* * *
11755082 CGAACG-TGAAAGAAGCCTTTCATGTGATAAATTAAGAAAAGATAATAGAAAAAAAAATTTATCT
128 CGAA-GATGAAAAAAGCCTTTCATGTGACAAATTAAAAAAAGATAATAG-AAAAAAAATTTATCT
*
11755146 TTGATACCATA
191 CTGATACCATA
** * * * * * *
11755157 TTAAGCATCCAA-CTCACTACCAATAGACAATAAGTGGAGTG-GCTCAACTTGAATTTAAGATTA
1 TTAAGCATCCAACCT-AAAATCAATTGACAATAAGTGAAG-GAGCCCAACCTGAATATAAGATTA
* * *
11755220 TAGGATATTGAAAATTTATTAGATGTAAGATAACCCAC
64 CAGGATATTAAAAATTTATTAGATGTGAGATAACCCAC
11755258 CATAAAATGC
Statistics
Matches: 256, Mismatches: 34, Indels: 24
0.82 0.11 0.08
Matches are distributed among these distances:
199 1 0.00
200 61 0.24
201 183 0.71
202 11 0.04
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (201 bp):
TTAAGCATCCAACCTAAAATCAATTGACAATAAGTGAAGGAGCCCAACCTGAATATAAGATTACA
GGATATTAAAAATTTATTAGATGTGAGATAACCCACTTTAATAAGCCCTCACCACGTGTAGGCGA
AGATGAAAAAAGCCTTTCATGTGACAAATTAAAAAAAGATAATAGAAAAAAAATTTATCTCTGAT
ACCATA
Found at i:11758806 original size:24 final size:24
Alignment explanation
Indices: 11758762--11758813 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11758752 ATCTTACTTG
* *
11758762 AAAATAATGAAAAAACCAAAAATA
1 AAAATAATGAAAAAACAAAAAAAA
*
11758786 AAAAT-ATGAATAAAAGAAAAAAAA
1 AAAATAATGAA-AAAACAAAAAAAA
11758810 AAAA
1 AAAA
11758814 AGAAAGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAATAATGAAAAAACAAAAAAAA
Found at i:11759018 original size:15 final size:15
Alignment explanation
Indices: 11758998--11759036 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11758988 TGTGAATGTT
11758998 TGAATTGGAAAATCA
1 TGAATTGGAAAATCA
*
11759013 TGAATTGAAAAATCA
1 TGAATTGGAAAATCA
*
11759028 TGACTTGGA
1 TGAATTGGA
11759037 CTAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (15 bp):
TGAATTGGAAAATCA
Found at i:11760272 original size:23 final size:22
Alignment explanation
Indices: 11760222--11760333 Score: 104
Period size: 21 Copynumber: 5.1 Consensus size: 22
11760212 ATGTAAACTG
11760222 TTCAAATGAGAATCTTTGAA-T
1 TTCAAATGAGAATCTTTGAATT
11760243 TTCAAATGAGAATCTTTGAACTT
1 TTCAAATGAGAATCTTTGAA-TT
11760266 TTCAAATGCA-AATCTTTGAATT
1 TTCAAATG-AGAATCTTTGAATT
** * * ** *
11760288 TT-GGATGGGAACCTCTAAAACT
1 TTCAAATGAGAATCT-TTGAATT
*
11760310 TTCAAATGTGAATCTTTGAATT
1 TTCAAATGAGAATCTTTGAATT
11760332 TT
1 TT
11760334 GGATATGAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
21 27 0.38
22 16 0.23
23 27 0.38
24 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAATGAGAATCTTTGAATT
Found at i:11760440 original size:22 final size:23
Alignment explanation
Indices: 11760398--11760445 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
11760388 CTCTAAAATT
*
11760398 TTTCAAATGAAAATTTTTTAATC
1 TTTCAAATGAAAATTTTTTAAAC
11760421 TTTCAAAT-AAGAA-TTTTTAAAC
1 TTTCAAATGAA-AATTTTTTAAAC
11760443 TTT
1 TTT
11760446 TTGAATGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTCAAATGAAAATTTTTTAAAC
Found at i:11760474 original size:13 final size:14
Alignment explanation
Indices: 11760443--11760475 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
11760433 ATTTTTAAAC
*
11760443 TTTTTGAATGTGAA
1 TTTTTGAATGAGAA
11760457 TTTTTGAATGAGAA
1 TTTTTGAATGAGAA
11760471 TTTTT
1 TTTTT
11760476 AAAATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (14 bp):
TTTTTGAATGAGAA
Found at i:11760524 original size:24 final size:22
Alignment explanation
Indices: 11760469--11760524 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 22
11760459 TTTGAATGAG
* *
11760469 AATTTTTAAAATTTTAGATGTG
1 AATTTTTAAAATTTTAAATGTA
* *
11760491 AATCTCTAAAATATCTTAAATGTA
1 AATTTTTAAAAT-T-TTAAATGTA
11760515 AATTTTTAAA
1 AATTTTTAAA
11760525 TCTTGGATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 10 0.38
23 1 0.04
24 15 0.58
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
AATTTTTAAAATTTTAAATGTA
Found at i:11760831 original size:22 final size:19
Alignment explanation
Indices: 11760806--11760849 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
11760796 TAAATTTTAA
11760806 AATTTTAGAAATTTCATTTATG
1 AATTTT-GAAATTT-ATTT-TG
*
11760828 AATTTTTAAATTTATTTTG
1 AATTTTGAAATTTATTTTG
11760847 AAT
1 AAT
11760850 CATTTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 6 0.29
22 6 0.29
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTTGAAATTTATTTTG
Found at i:11760883 original size:18 final size:18
Alignment explanation
Indices: 11760858--11760971 Score: 79
Period size: 18 Copynumber: 6.4 Consensus size: 18
11760848 ATCATTTGTG
*
11760858 AATCTTAGAACCTTTGCA
1 AATCTTAGAATCTTTGCA
* *
11760876 AATTTTAGAATTTTTGCA
1 AATCTTAGAATCTTTGCA
* *
11760894 AAACTTAGAATCTTTGCT
1 AATCTTAGAATCTTTGCA
* * *
11760912 AATCTT-GAAACTTTACG
1 AATCTTAGAATCTTTGCA
* * **
11760929 AAT-TTTGAAACCTTTGTG
1 AATCTTAG-AATCTTTGCA
* *
11760947 AATATTGGAATCTTTGCA
1 AATCTTAGAATCTTTGCA
11760965 AATCTTA
1 AATCTTA
11760972 AAATTGCTAC
Statistics
Matches: 73, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
16 2 0.03
17 12 0.16
18 56 0.77
19 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (18 bp):
AATCTTAGAATCTTTGCA
Found at i:11761003 original size:54 final size:53
Alignment explanation
Indices: 11760901--11761003 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 53
11760891 GCAAAACTTA
* * * * *
11760901 GAATCTTTGCTAATCTTGAAACTTTACGAATTTTGAAACCTTTGTGAATATTG
1 GAATCTTTGCAAATCTTGAAAATTTACGAATCTTAAAACATTTGTGAATATTG
*
11760954 GAATCTTTGCAAATCTT-AAAATTGCTACGAATCTTAAAATATTTGTGAAT
1 GAATCTTTGCAAATCTTGAAAATT--TACGAATCTTAAAACATTTGTGAAT
11761004 TTTGAACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 5 0.12
53 16 0.38
54 21 0.50
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (53 bp):
GAATCTTTGCAAATCTTGAAAATTTACGAATCTTAAAACATTTGTGAATATTG
Found at i:11761017 original size:17 final size:18
Alignment explanation
Indices: 11760990--11761041 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
11760980 ACGAATCTTA
*
11760990 AAATATTTGTGAATTTTG
1 AAATCTTTGTGAATTTTG
* *
11761008 AACT-TTTGTGAAATTTG
1 AAATCTTTGTGAATTTTG
11761025 AAATCTTTGTGAATTTT
1 AAATCTTTGTGAATTTT
11761042 TTAATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (18 bp):
AAATCTTTGTGAATTTTG
Found at i:11761076 original size:89 final size:89
Alignment explanation
Indices: 11760932--11761103 Score: 195
Period size: 89 Copynumber: 1.9 Consensus size: 89
11760922 CTTTACGAAT
* *
11760932 TTTGAAACCTTTGTGAATATTGGAATCTTTGCAAATCTTAAAATTGCTACGAATCTTAAAATATT
1 TTTGAAACCTTTGTGAATATTGGAATCTTTACAAATCTTAAAATTGCTACAAATCTTAAAAT-TT
* *
11760997 TGTGAATTTTGAA-CTTTTGTGAAA
65 TGTAAATCTTGAATCTTTTGTGAAA
* * ** * * * * *
11761021 TTTGAAATCTTTGTGAATTTTTTAATTTTTACAAATCTTAGAACTT-TTACAAATCTTGAACTTT
1 TTTGAAACCTTTGTGAATATTGGAATCTTTACAAATCTTA-AAATTGCTACAAATCTTAAAATTT
11761085 TGTAAATCTTGAATCTTTT
65 TGTAAATCTTGAATCTTTT
11761104 ACGAATTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
88 13 0.19
89 51 0.75
90 4 0.06
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (89 bp):
TTTGAAACCTTTGTGAATATTGGAATCTTTACAAATCTTAAAATTGCTACAAATCTTAAAATTTT
GTAAATCTTGAATCTTTTGTGAAA
Found at i:11761083 original size:17 final size:17
Alignment explanation
Indices: 11761047--11761105 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
11761037 ATTTTTTAAT
11761047 TTTTACAAATCTTAGAAC
1 TTTTACAAATCTT-GAAC
11761065 TTTTACAAATCTTGAAC
1 TTTTACAAATCTTGAAC
**
11761082 TTTTGTAAATCTTGAATC
1 TTTTACAAATCTTGAA-C
11761100 TTTTAC
1 TTTTAC
11761106 GAATTTTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 18 0.50
18 18 0.50
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (17 bp):
TTTTACAAATCTTGAAC
Found at i:11761137 original size:28 final size:28
Alignment explanation
Indices: 11761077--11761137 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
11761067 TTACAAATCT
* *
11761077 TGAACTTTTGTAAATCTTGAATCTTTTA
1 TGAATTTTTGCAAATCTTGAATCTTTTA
* *
11761105 CGAATTTTTGCAAATCTTGAATCTTTTG
1 TGAATTTTTGCAAATCTTGAATCTTTTA
11761133 TGAAT
1 TGAAT
11761138 CTTGAATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (28 bp):
TGAATTTTTGCAAATCTTGAATCTTTTA
Found at i:11761138 original size:18 final size:18
Alignment explanation
Indices: 11760995--11761189 Score: 78
Period size: 18 Copynumber: 11.3 Consensus size: 18
11760985 TCTTAAAATA
*
11760995 TTTGTGAATTTTGAA-CT
1 TTTGTGAATCTTGAATCT
11761012 TTTGTGAAAT-TTGAAATC-
1 TTTGTG-AATCTTG-AATCT
* *
11761030 TTTGTGAATTTTTTAAT-T
1 TTTGTGAA-TCTTGAATCT
***
11761048 TTTACAAATCTTAGAA-CT
1 TTTGTGAATCTT-GAATCT
***
11761066 TTTACAAATCTTGAA-CT
1 TTTGTGAATCTTGAATCT
*
11761083 TTTGTAAATCTTGAATC-
1 TTTGTGAATCTTGAATCT
11761100 TTT-T--A-C--GAAT-T
1 TTTGTGAATCTTGAATCT
**
11761111 TTTGCAAATCTTGAATCT
1 TTTGTGAATCTTGAATCT
11761129 TTTGTGAATCTTGAATCT
1 TTTGTGAATCTTGAATCT
* *
11761147 TTTATGAATTTTTGAAATC-
1 TTTGTGAA-TCTTG-AATCT
** *
11761166 TTTAAGAATCTTAAATCT
1 TTTGTGAATCTTGAATCT
11761184 TTTGTG
1 TTTGTG
11761190 GATTTTTGAG
Statistics
Matches: 140, Mismatches: 18, Indels: 39
0.71 0.09 0.20
Matches are distributed among these distances:
11 7 0.05
13 1 0.01
14 2 0.01
15 1 0.01
16 1 0.01
17 43 0.31
18 67 0.48
19 14 0.10
20 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (18 bp):
TTTGTGAATCTTGAATCT
Found at i:11761139 original size:46 final size:45
Alignment explanation
Indices: 11761065--11761167 Score: 163
Period size: 46 Copynumber: 2.3 Consensus size: 45
11761055 ATCTTAGAAC
*
11761065 TTTTACAAATCTTGAACTTTTGTAAATCTTGAATCTTTTACGAAT
1 TTTTGCAAATCTTGAACTTTTGTAAATCTTGAATCTTTTACGAAT
* *
11761110 TTTTGCAAATCTTGAATCTTTTGTGAATCTTGAATCTTTTATGAAT
1 TTTTGCAAATCTTGAA-CTTTTGTAAATCTTGAATCTTTTACGAAT
11761156 TTTTG-AAATCTT
1 TTTTGCAAATCTT
11761168 TAAGAATCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 22 0.41
46 32 0.59
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.50
Consensus pattern (45 bp):
TTTTGCAAATCTTGAACTTTTGTAAATCTTGAATCTTTTACGAAT
Found at i:11762222 original size:13 final size:14
Alignment explanation
Indices: 11762206--11762279 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 14
11762196 TTTATTATAT
11762206 TTATTTGCATGAT-
1 TTATTTGCATGATA
11762219 TTA-TT--ATGATA
1 TTATTTGCATGATA
11762230 TT-TTTGCATGATA
1 TTATTTGCATGATA
*
11762243 TTA-TT--ATTATA
1 TTATTTGCATGATA
*
11762254 TT-TTTGCATGATT
1 TTATTTGCATGATA
*
11762267 TTTTTTGCATGAT
1 TTATTTGCATGAT
11762280 CTTTGCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
10 5 0.10
11 13 0.27
12 2 0.04
13 19 0.39
14 10 0.20
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.58
Consensus pattern (14 bp):
TTATTTGCATGATA
Found at i:11762250 original size:49 final size:50
Alignment explanation
Indices: 11762197--11762314 Score: 138
Period size: 49 Copynumber: 2.4 Consensus size: 50
11762187 TACTTGGTTT
*
11762197 TTATTATATTTATTTGCATGATTTATTATG-AT-ATTTTTGCATGATATT-A
1 TTATTATA-TTATTTGCATGATTTATTATGCATGATCTTTGCAT-ATATTAA
* * *
11762246 TTATTATATT-TTTGCATGATTTTTTTTGCATGATCTTTGCATATTTTAA
1 TTATTATATTATTTGCATGATTTATTATGCATGATCTTTGCATATATTAA
*
11762295 TTATGATATTA-TTGCATGAT
1 TTATTATATTATTTGCATGAT
11762315 ATTTTCTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
47 16 0.27
48 8 0.13
49 36 0.60
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (50 bp):
TTATTATATTATTTGCATGATTTATTATGCATGATCTTTGCATATATTAA
Found at i:11762309 original size:24 final size:24
Alignment explanation
Indices: 11762195--11762314 Score: 124
Period size: 24 Copynumber: 5.0 Consensus size: 24
11762185 CTTACTTGGT
11762195 TTTTATTAT-AT-TTATTTGCATGA
1 TTTTATTATGATATT-TTTGCATGA
11762218 -TTTATTATGATATTTTTGCATGA
1 TTTTATTATGATATTTTTGCATGA
* *
11762241 TATTATTATTATATTTTTGCATGA
1 TTTTATTATGATATTTTTGCATGA
* *
11762265 TTTT-TTTTGCATGATCTTTGCAT-A
1 TTTTATTATG-AT-ATTTTTGCATGA
*
11762289 TTTTAATTATGATATTATTGCATGA
1 TTTT-ATTATGATATTTTTGCATGA
11762314 T
1 T
11762315 ATTTTCTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
22 8 0.10
23 14 0.17
24 41 0.51
25 13 0.16
26 4 0.05
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTTATTATGATATTTTTGCATGA
Found at i:11762474 original size:21 final size:21
Alignment explanation
Indices: 11762450--11762492 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11762440 AACATGTAAT
11762450 TAACTTGATATCAAATTTGGG
1 TAACTTGATATCAAATTTGGG
*
11762471 TAACTTGATATCAATTTTGGG
1 TAACTTGATATCAAATTTGGG
11762492 T
1 T
11762493 GTAATGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (21 bp):
TAACTTGATATCAAATTTGGG
Found at i:11763925 original size:15 final size:16
Alignment explanation
Indices: 11763895--11763928 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
11763885 TTCTCTTAAA
11763895 ATTATAATTATTTTAT
1 ATTATAATTATTTTAT
11763911 ATTATAATT-TTTTAT
1 ATTATAATTATTTTAT
11763926 ATT
1 ATT
11763929 TTCAAACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATAATTATTTTAT
Found at i:11767216 original size:42 final size:42
Alignment explanation
Indices: 11767170--11767420 Score: 254
Period size: 42 Copynumber: 6.0 Consensus size: 42
11767160 TTTGATTTAT
*
11767170 GATTTTTTGTTGTTGTTCATAATTACTCAAATTTATAGTTAA
1 GATTTTTTGTTGTTGTTCTTAATTACTCAAATTTATAGTTAA
* * * *
11767212 GATTTTTTGTTGTTCTTCTTAATTGCTCAAATTTATATTTGA
1 GATTTTTTGTTGTTGTTCTTAATTACTCAAATTTATAGTTAA
* * *
11767254 GATTTTTTGTTGTTGTTCTTAATTACTCAAAATAATAGTTAG
1 GATTTTTTGTTGTTGTTCTTAATTACTCAAATTTATAGTTAA
* * * ** * *
11767296 GGTTTTCTATTGTTGTTCTTAATTGGTCGAAA-TCATAGTTAT
1 GATTTTTTGTTGTTGTTCTTAATTACTC-AAATTTATAGTTAA
* * *
11767338 GATTTTTTGCTATTGTTCTTAATTGCTCGAAA-TTATAGTTAA
1 GATTTTTTGTTGTTGTTCTTAATTACTC-AAATTTATAGTTAA
* * * * **
11767380 GGTTTTCTATTGTTATTCTTAATTACTTGAATTTATAGTTA
1 GATTTTTTGTTGTTGTTCTTAATTACTCAAATTTATAGTTA
11767421 GAGTTTTCTA
Statistics
Matches: 171, Mismatches: 36, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 2 0.01
42 166 0.97
43 3 0.02
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (42 bp):
GATTTTTTGTTGTTGTTCTTAATTACTCAAATTTATAGTTAA
Found at i:11767263 original size:84 final size:83
Alignment explanation
Indices: 11767166--11767403 Score: 291
Period size: 84 Copynumber: 2.8 Consensus size: 83
11767156 ATATTTTGAT
* * * * *
11767166 TTATGATTTTTTGTTGTTGTTCATAATTACTCAAATTTATAGTTAAGATTTTTTGTTGTTCTTCT
1 TTATGATTTTTTGTTGTTGTTCTTAATTACTCAAA-TTATAGTTAAGGTTTTCTATTGTTATTCT
* *
11767231 TAATTGCTC-AAATTTATAT
65 TAATTGCTCGAAA-TCATAG
* * *
11767250 TTGA-GATTTTTTGTTGTTGTTCTTAATTACTCAAAATAATAGTTAGGGTTTTCTATTGTTGTTC
1 TT-ATGATTTTTTGTTGTTGTTCTTAATTACTC-AAATTATAGTTAAGGTTTTCTATTGTTATTC
*
11767314 TTAATTGGTCGAAATCATAG
64 TTAATTGCTCGAAATCATAG
* * *
11767334 TTATGATTTTTTGCTATTGTTCTTAATTGCTCGAAATTATAGTTAAGGTTTTCTATTGTTATTCT
1 TTATGATTTTTTGTTGTTGTTCTTAATTACTC-AAATTATAGTTAAGGTTTTCTATTGTTATTCT
11767399 TAATT
65 TAATT
11767404 ACTTGAATTT
Statistics
Matches: 133, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.01
84 125 0.94
85 7 0.05
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.53
Consensus pattern (83 bp):
TTATGATTTTTTGTTGTTGTTCTTAATTACTCAAATTATAGTTAAGGTTTTCTATTGTTATTCTT
AATTGCTCGAAATCATAG
Found at i:11767319 original size:126 final size:126
Alignment explanation
Indices: 11767179--11767435 Score: 311
Period size: 126 Copynumber: 2.0 Consensus size: 126
11767169 TGATTTTTTG
* * *
11767179 TTGTTGTTCATAATTACTC-AAATTTATAGTTAAGATTTTTTGTTGTTCTTCTTAATTGCTC-AA
1 TTGTTGTTCATAATTACTCGAAA-TCATAGTTAAGATTTTTTGCTATTCTTCTTAATTGCTCGAA
* * * * * *
11767242 ATTTATATTTGAGATTTTTTGTTGTTGTTCTTAATTACTCAAAATAATAGTTAGGGTTTTCTA
65 A-TTATAGTTAAGATTTTCTATTGTTATTCTTAATTACTCAAAATAATAGTTAGAGTTTTCTA
* ** * *
11767305 TTGTTGTTCTTAATTGGTCGAAATCATAGTTATGATTTTTTGCTATTGTTCTTAATTGCTCGAAA
1 TTGTTGTTCATAATTACTCGAAATCATAGTTAAGATTTTTTGCTATTCTTCTTAATTGCTCGAAA
* ** * *
11767370 TTATAGTTAAGGTTTTCTATTGTTATTCTTAATTACTTGAATTTATAGTTAGAGTTTTCTA
66 TTATAGTTAAGATTTTCTATTGTTATTCTTAATTACTCAAAATAATAGTTAGAGTTTTCTA
11767431 TTGTT
1 TTGTT
11767436 TAGGCATATT
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
126 104 0.95
127 6 0.05
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.53
Consensus pattern (126 bp):
TTGTTGTTCATAATTACTCGAAATCATAGTTAAGATTTTTTGCTATTCTTCTTAATTGCTCGAAA
TTATAGTTAAGATTTTCTATTGTTATTCTTAATTACTCAAAATAATAGTTAGAGTTTTCTA
Found at i:11767418 original size:84 final size:82
Alignment explanation
Indices: 11767170--11767435 Score: 284
Period size: 84 Copynumber: 3.2 Consensus size: 82
11767160 TTTGATTTAT
* * * * * * *
11767170 GATTTTTTGTTGTTGTTCATAATTACTCAAATTTATAGTTAAGATTTTTTGTTGTTCTTCTTAAT
1 GATTTTTTGCTATTGTTCTTAATTACTCAAA-TTATAGTTAAGGTTTTCTATTGTTATTCTTAAT
* *
11767235 TGCTCAAATTTATATTTGA
65 TGCTCGAATTTATAGTT-A
* * * * *
11767254 GATTTTTTGTTGTTGTTCTTAATTACTCAAAATAATAGTTAGGGTTTTCTATTGTTGTTCTTAAT
1 GATTTTTTGCTATTGTTCTTAATTACTC-AAATTATAGTTAAGGTTTTCTATTGTTATTCTTAAT
* * *
11767319 TGGTCGAAATCATAGTTA
65 TGCTCGAATTTATAGTTA
*
11767337 TGATTTTTTGCTATTGTTCTTAATTGCTCGAAATTATAGTTAAGGTTTTCTATTGTTATTCTTAA
1 -GATTTTTTGCTATTGTTCTTAATTACTC-AAATTATAGTTAAGGTTTTCTATTGTTATTCTTAA
* *
11767402 TTACTTGAATTTATAGTTA
64 TTGCTCGAATTTATAGTTA
*
11767421 GA-GTTTT-CTATTGTT
1 GATTTTTTGCTATTGTT
11767436 TAGGCATATT
Statistics
Matches: 155, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
81 8 0.05
82 4 0.03
83 3 0.02
84 137 0.88
85 3 0.02
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.53
Consensus pattern (82 bp):
GATTTTTTGCTATTGTTCTTAATTACTCAAATTATAGTTAAGGTTTTCTATTGTTATTCTTAATT
GCTCGAATTTATAGTTA
Found at i:11768149 original size:32 final size:32
Alignment explanation
Indices: 11768108--11768185 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
11768098 AGACCTTTGG
11768108 TTATAACAAAGTAAAA-ACTTATAACAAAAATT
1 TTATAACAAAGTAAAAGA-TTATAACAAAAATT
*
11768140 TTATAACAAAGCAAAAGATTATAACAAAAATT
1 TTATAACAAAGTAAAAGATTATAACAAAAATT
** *
11768172 AGATAACAATGTAA
1 TTATAACAAAGTAA
11768186 GGGACATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 39 0.98
33 1 0.03
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (32 bp):
TTATAACAAAGTAAAAGATTATAACAAAAATT
Found at i:11772937 original size:23 final size:23
Alignment explanation
Indices: 11772907--11772957 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
11772897 ATCATGAAAC
* *
11772907 AAATACCAGCAAAAACACTAAAG
1 AAATACCAACAAAAAAACTAAAG
11772930 AAATACCAACAAAAAAACTAAAG
1 AAATACCAACAAAAAAACTAAAG
11772953 AAATA
1 AAATA
11772958 TCAGTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.10
Consensus pattern (23 bp):
AAATACCAACAAAAAAACTAAAG
Found at i:11774078 original size:17 final size:17
Alignment explanation
Indices: 11774056--11774089 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11774046 CCTTGCATCT
11774056 TCAAATAACTCGATAGA
1 TCAAATAACTCGATAGA
11774073 TCAAATAACTCGATAGA
1 TCAAATAACTCGATAGA
11774090 ATAGATTCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (17 bp):
TCAAATAACTCGATAGA
Found at i:11780232 original size:34 final size:34
Alignment explanation
Indices: 11780194--11780262 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
11780184 ATGTTTGACC
*
11780194 TTGGATTTGTCATCTTTCTCCTGGATTATACTGT
1 TTGGATTTGTCATCTTTCTCCTAGATTATACTGT
*
11780228 TTGGATTTGTCATCTTTCTCCTAGATTATATTGT
1 TTGGATTTGTCATCTTTCTCCTAGATTATACTGT
11780262 T
1 T
11780263 CTGGGAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (34 bp):
TTGGATTTGTCATCTTTCTCCTAGATTATACTGT
Found at i:11781549 original size:53 final size:54
Alignment explanation
Indices: 11781456--11781561 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 54
11781446 GTCGCAAGTT
* * * *
11781456 TTAATAATGATTTGGATTTATAAATTATAATAATGGGAATCGAGTTTAAATTTA
1 TTAATAATAATTTGAATTTATAAATTATAATAATGGGAATCAAATTTAAATTTA
* *
11781510 TTAA-AATAATTTGAATTTATAAATTATAATAGTGTGAATCAAATTTAAATTT
1 TTAATAATAATTTGAATTTATAAATTATAATAATGGGAATCAAATTTAAATTT
11781562 TATAAGTAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 42 0.91
54 4 0.09
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (54 bp):
TTAATAATAATTTGAATTTATAAATTATAATAATGGGAATCAAATTTAAATTTA
Found at i:11783552 original size:29 final size:30
Alignment explanation
Indices: 11783520--11783593 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
11783510 AATTTACATA
*
11783520 TAAATTAG-TTTTAATCGTTAATTTG-TATT
1 TAAATAAGTTTTTAA-CGTTAATTTGATATT
* *
11783549 TAAATAAGTTTTTAACTTTTATTTGATATT
1 TAAATAAGTTTTTAACGTTAATTTGATATT
*
11783579 TAAATAAATTTTTAA
1 TAAATAAGTTTTTAA
11783594 TATAAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (30 bp):
TAAATAAGTTTTTAACGTTAATTTGATATT
Found at i:11783944 original size:30 final size:31
Alignment explanation
Indices: 11783870--11783947 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
11783860 AAAATTATTT
11783870 ATGTTAA-GAGTTTATTTAGATATAAATTAAA
1 ATGTTAAGGA-TTTATTTAGATATAAATTAAA
* * *
11783901 ATTTTAAGTATTTATTTGGATATAAATT-AA
1 ATGTTAAGGATTTATTTAGATATAAATTAAA
11783931 ATGTTAAGGATTTATTT
1 ATGTTAAGGATTTATTT
11783948 TTATGCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 17 0.41
31 23 0.56
32 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (31 bp):
ATGTTAAGGATTTATTTAGATATAAATTAAA
Found at i:11787901 original size:5 final size:5
Alignment explanation
Indices: 11787893--11787917 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11787883 AAAAATAAAA
11787893 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
11787918 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:11787940 original size:19 final size:20
Alignment explanation
Indices: 11787906--11787946 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
11787896 TTATATTATA
*
11787906 TTATATTATATTTTTAAAAT
1 TTATATTATATATTTAAAAT
11787926 TTATA-TATATATTTAAAAT
1 TTATATTATATATTTAAAAT
11787945 TT
1 TT
11787947 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATTATATATTTAAAAT
Found at i:11787948 original size:29 final size:31
Alignment explanation
Indices: 11787890--11787953 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
11787880 ATAAAAAATA
**
11787890 AAAATATTATATTATATTATATTATATTTTT
1 AAAATATTATATTATATTATAAAATATTTTT
11787921 AAAAT-TTATATATATATT-TAAAAT-TTTTT
1 AAAATATTATAT-TATATTATAAAATATTTTT
11787950 AAAA
1 AAAA
11787954 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.30
30 10 0.33
31 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
AAAATATTATATTATATTATAAAATATTTTT
Found at i:11787955 original size:30 final size:32
Alignment explanation
Indices: 11787888--11787956 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
11787878 GAATAAAAAA
**
11787888 TAAAAATATTATATTATATTATATTATATTTT
1 TAAAAATATTATATTATATTATAAAATATTTT
11787920 T-AAAAT-TTATATATATATT-TAAAAT-TTTT
1 TAAAAATATTATAT-TATATTATAAAATATTTT
11787949 TAAAAATA
1 TAAAAATA
11787957 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
29 5 0.16
30 15 0.47
31 11 0.34
32 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TAAAAATATTATATTATATTATAAAATATTTT
Found at i:11788015 original size:56 final size:55
Alignment explanation
Indices: 11787919--11788024 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 55
11787909 TATTATATTT
* *
11787919 TTAAAATTTATATATATATTTAAAATTTTTTAAAAATAAAAATAAAAATTTTATA
1 TTAAAATTTATATAAATATTTAAAATTTTATAAAAATAAAAATAAAAATTTTATA
* **
11787974 TTAAAATTTATTTAAATATATTAAAATTTTATAAACTTAAAAATAAAAATT
1 TTAAAATTTATATAAATAT-TTAAAATTTTATAAAAATAAAAATAAAAATT
11788025 AATAAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 17 0.38
56 28 0.62
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (55 bp):
TTAAAATTTATATAAATATTTAAAATTTTATAAAAATAAAAATAAAAATTTTATA
Found at i:11792310 original size:1 final size:1
Alignment explanation
Indices: 11792304--11792337 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
11792294 CCAGGAAGAG
11792304 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11792338 GAAAGAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11796730 original size:49 final size:49
Alignment explanation
Indices: 11796645--11796764 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 49
11796635 TTATCTCAGA
* * * * *
11796645 AGAGGCTCAACAATTTTAAAATTTCTATCTTGAAAAAGTTCTTCT-AAGC
1 AGAGGCTCAACAACTTTAAAATCTCTATCTTAAAAAAGCTCCTCTCAA-C
* *
11796694 AGAGGTTCAATAACTTTAAAATCTC-ATCTTAAAAAAAGCTCCTCTCAAC
1 AGAGGCTCAACAACTTTAAAATCTCTATCTT-AAAAAAGCTCCTCTCAAC
*
11796743 AGAGGCTCAACGACTTTAAAAT
1 AGAGGCTCAACAACTTTAAAAT
11796765 AAATCATCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 5 0.08
49 52 0.88
50 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (49 bp):
AGAGGCTCAACAACTTTAAAATCTCTATCTTAAAAAAGCTCCTCTCAAC
Found at i:11797172 original size:204 final size:204
Alignment explanation
Indices: 11796911--11797351 Score: 591
Period size: 204 Copynumber: 2.2 Consensus size: 204
11796901 AAGCTTTAAT
* *
11796911 ACTCAAATATCACCATCGAAAAAAATGTAAATACAAATTCAAACTTTAAACTCGGATATCACCAC
1 ACTCGAATATCACCATCG-AGAAAATGTAAATACAAATTCAAACTTTAAACTCGGATATCACCAC
* *
11796976 CAAGAATATGCAAATGACTTCGGATATCGCCATCGAAA-AAAACTCAAATATCACCATCAAAAAA
65 CAAGAATATGCAAATGACTTCAGATATCACCATC-AAAGAAAACTCAAATATCACCATCAAAAAA
* *
11797040 ATGTAATTCAAACTTTAATACTCAAATATCACGGCCGAGAG-A-ATGCAAATGACTTCAGATATC
129 ATGTAATTCAAACTTTAACACTCAAATATCAC--CAGAGAGAATATGCAAATGACTTCAGATATC
** * *
11797103 GTCATCGAAGGAA
192 ACCACCAAAGGAA
* *
11797116 ACTCGAATATCACCATCGAGAAAATGTAAATGCAAATTCAAACTTTAAACTCGGATATCATCACC
1 ACTCGAATATCACCATCGAGAAAATGTAAATACAAATTCAAACTTTAAACTCGGATATCACCACC
* * * * * * *
11797181 GAGAATATGCAAATGACTTCAGATATCATCGTCAAAGGAAACTCGAATATCACCATCGAGAAAAT
66 AAGAATATGCAAATGACTTCAGATATCACCATCAAAGAAAACTCAAATATCACCATCAAAAAAAT
* * ** *
11797246 GTAATTCGAGCTTTAACACTCGGATATCACCATAGAGAATATGCAAATGACTTCAGATATCACCA
131 GTAATTCAAACTTTAACACTCAAATATCACCAGAGAGAATATGCAAATGACTTCAGATATCACCA
11797311 CCAAAGGAA
196 CCAAAGGAA
* *
11797320 ACTTGAATATCACCATCGAGAAAATGCAAATA
1 ACTCGAATATCACCATCGAGAAAATGTAAATA
11797352 ATTTTTTAAT
Statistics
Matches: 206, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
202 5 0.02
203 4 0.02
204 180 0.87
205 17 0.08
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (204 bp):
ACTCGAATATCACCATCGAGAAAATGTAAATACAAATTCAAACTTTAAACTCGGATATCACCACC
AAGAATATGCAAATGACTTCAGATATCACCATCAAAGAAAACTCAAATATCACCATCAAAAAAAT
GTAATTCAAACTTTAACACTCAAATATCACCAGAGAGAATATGCAAATGACTTCAGATATCACCA
CCAAAGGAA
Found at i:11797203 original size:105 final size:104
Alignment explanation
Indices: 11796911--11797350 Score: 476
Period size: 99 Copynumber: 4.3 Consensus size: 104
11796901 AAGCTTTAAT
* * *
11796911 ACTCAAATATCACCATCGAAAAAAATGTAAATACAAATTCAAACTTTAA-ACTCGGATATCACCA
1 ACTCGAATATCACCATCG-AGAAAATG-AAAT-GAAATTCAAACTTTAACACTCGGATATCACCA
* * * *
11796975 CCAAGAATATGCAAATGACTTCGGATATCGCCATCGAAA-AAA
63 CCGAGAATATGCAAATGACTTCAGATATCACCATC-AAAGGAA
* * * ** **
11797017 ACTCAAATATCACCATC---AAAA--AAATGTAATTCAAACTTTAATACTCAAATATCACGGCCG
1 ACTCGAATATCACCATCGAGAAAATGAAATGAAATTCAAACTTTAACACTCGGATATCACCACCG
** *
11797077 AGAGA-ATGCAAATGACTTCAGATATCGTCATCGAAGGAA
66 AGA-ATATGCAAATGACTTCAGATATCACCATCAAAGGAA
*
11797116 ACTCGAATATCACCATCGAGAAAATGTAAATGCAAATTCAAACTTTAA-ACTCGGATATCATCAC
1 ACTCGAATATCACCATCGAGAAAATG-AAATG-AAATTCAAACTTTAACACTCGGATATCACCAC
* *
11797180 CGAGAATATGCAAATGACTTCAGATATCATCGTCAAAGGAA
64 CGAGAATATGCAAATGACTTCAGATATCACCATCAAAGGAA
* * **
11797221 ACTCGAATATCACCATCGAGAAAATG---T--AATTCGAGCTTTAACACTCGGATATCACCATAG
1 ACTCGAATATCACCATCGAGAAAATGAAATGAAATTCAAACTTTAACACTCGGATATCACCACCG
*
11797281 AGAATATGCAAATGACTTCAGATATCACCACCAAAGGAA
66 AGAATATGCAAATGACTTCAGATATCACCATCAAAGGAA
*
11797320 ACTTGAATATCACCATCGAGAAAATGCAAAT
1 ACTCGAATATCACCATCGAGAAAATG-AAAT
11797351 AATTTTTTAA
Statistics
Matches: 288, Mismatches: 30, Indels: 35
0.82 0.08 0.10
Matches are distributed among these distances:
98 28 0.10
99 139 0.48
100 1 0.00
101 1 0.00
102 8 0.03
103 1 0.00
104 1 0.00
105 78 0.27
106 31 0.11
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (104 bp):
ACTCGAATATCACCATCGAGAAAATGAAATGAAATTCAAACTTTAACACTCGGATATCACCACCG
AGAATATGCAAATGACTTCAGATATCACCATCAAAGGAA
Found at i:11797489 original size:75 final size:75
Alignment explanation
Indices: 11797366--11797735 Score: 551
Period size: 75 Copynumber: 4.9 Consensus size: 75
11797356 TTTAATGCTC
* * * * * * *
11797366 GGATATCGCCATCGAGAATATGAAATTCACACTTTAATACTCAGATATCACCACCGAAAACTTTA
1 GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
11797431 AAAATGTCTT
66 AAAATGTCTT
* *
11797441 GGATATCACCACAAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCATCGAGAACTTTG
1 GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
11797506 AAAATGTCTT
66 AAAATGTCTT
* * * * * * *
11797516 GGATATCACCACTAAGAATATGAAATTCGTAATTTAATACTCGGATATCACCACCAAGAACTTTA
1 GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
*
11797581 AAAATATCTT
66 AAAATGTCTT
* *
11797591 GGATATCACTACCAAGAAAATTAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
1 GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
11797656 AAAATGTCTT
66 AAAATGTCTT
* *
11797666 GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCGGATATCACCATCGAGAACTTTG
1 GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
11797731 AAAAT
66 AAAAT
11797736 AATTCATCAC
Statistics
Matches: 263, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 263 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (75 bp):
GGATATCACCACCAAGAAAATGAAATTCATACTTTAATACTCAGATATCACCACCGAGAACTTTG
AAAATGTCTT
Found at i:11797595 original size:33 final size:33
Alignment explanation
Indices: 11797558--11797683 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 33
11797548 TTTAATACTC
11797558 GGATATCACCACCAAGAACTTTAAAAATATCTT
1 GGATATCACCACCAAGAACTTTAAAAATATCTT
* ** *
11797591 GGATATCACTACCAAGAAAATTAAATTCATACTTTAATACTC
1 GGATATCACCACCAAGAACTTTAAA---A-A---T-AT-CTT
* * * *
11797633 AGATATCACCACCGAGAACTTTGAAAATGTCTT
1 GGATATCACCACCAAGAACTTTAAAAATATCTT
11797666 GGATATCACCACCAAGAA
1 GGATATCACCACCAAGAA
11797684 AATGAAATTC
Statistics
Matches: 70, Mismatches: 14, Indels: 18
0.69 0.14 0.18
Matches are distributed among these distances:
33 40 0.57
34 1 0.01
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 2 0.03
42 21 0.30
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (33 bp):
GGATATCACCACCAAGAACTTTAAAAATATCTT
Found at i:11797996 original size:35 final size:37
Alignment explanation
Indices: 11797918--11797999 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 37
11797908 ATATCATTAT
11797918 GATGCAAATGTCTTTTCTTAAAATGATGATGCAAATGA
1 GATGCAAATGTCTTTTCTTAAAA-GATGATGCAAATGA
* * *
11797956 AATGCAAATGTCTTTT-TTTAAA-ATGATGCACATGA
1 GATGCAAATGTCTTTTCTTAAAAGATGATGCAAATGA
11797991 GATGCAAAT
1 GATGCAAAT
11798000 AAAATACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 20 0.50
37 5 0.12
38 15 0.38
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (37 bp):
GATGCAAATGTCTTTTCTTAAAAGATGATGCAAATGA
Found at i:11798016 original size:46 final size:46
Alignment explanation
Indices: 11797940--11798046 Score: 151
Period size: 46 Copynumber: 2.3 Consensus size: 46
11797930 TTTTCTTAAA
* * * *
11797940 ATGATGATGCAAATGAAATGCAAATGTCTTTTTTTAAAATGATGCAC
1 ATGA-GATGCAAATAAAATACAAATATCTTTTCTTAAAATGATGCAC
*
11797987 ATGAGATGCAAATAAAATACAAATATCTTTTCTTAAAATGATGCAT
1 ATGAGATGCAAATAAAATACAAATATCTTTTCTTAAAATGATGCAC
*
11798033 ATGAAATGCAAATA
1 ATGAGATGCAAATA
11798047 TCTCTTCCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
46 50 0.93
47 4 0.07
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (46 bp):
ATGAGATGCAAATAAAATACAAATATCTTTTCTTAAAATGATGCAC
Found at i:11798282 original size:21 final size:22
Alignment explanation
Indices: 11798251--11798291 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11798241 ACTTTTTATT
* *
11798251 TTCATCAATTTTGCTTTCTTTC
1 TTCATCAATTTGGATTTCTTTC
11798273 TTCA-CAATTTGGATTTCTT
1 TTCATCAATTTGGATTTCTT
11798292 GACTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (22 bp):
TTCATCAATTTGGATTTCTTTC
Found at i:11803392 original size:10 final size:10
Alignment explanation
Indices: 11803365--11803402 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
11803355 AACTTATCAT
*
11803365 TTTAATAAAA
1 TTTATTAAAA
11803375 -TT-TTAAAA
1 TTTATTAAAA
11803383 TTTATTAAAA
1 TTTATTAAAA
11803393 TTTATTAAAA
1 TTTATTAAAA
11803403 AGATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 5 0.20
9 4 0.16
10 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTATTAAAA
Found at i:11804294 original size:15 final size:15
Alignment explanation
Indices: 11804274--11804331 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
11804264 CATACATTTT
11804274 TTATTAA-TTGTATTA
1 TTATTAAGTT-TATTA
11804289 TTATTAAGTTTATTA
1 TTATTAAGTTTATTA
**
11804304 TTATTATTTTTATT-
1 TTATTAAGTTTATTA
11804318 TT-TTAAAGTTTATT
1 TTATT-AAGTTTATT
11804332 TTAAAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 24 0.65
16 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
TTATTAAGTTTATTA
Found at i:11804487 original size:14 final size:15
Alignment explanation
Indices: 11804468--11804496 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11804458 CTAAATCAGA
11804468 CAGGTG-GTCCAATC
1 CAGGTGAGTCCAATC
11804482 CAGGTGAGTCCAATC
1 CAGGTGAGTCCAATC
11804497 GGTTCGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Consensus pattern (15 bp):
CAGGTGAGTCCAATC
Found at i:11817148 original size:18 final size:16
Alignment explanation
Indices: 11817117--11817159 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
11817107 TGCTGAAGCC
11817117 AAGTAATATCAATAAA
1 AAGTAATATCAATAAA
*
11817133 AAGTCAATAGTCAATAAT
1 AAGT-AATA-TCAATAAA
11817151 AAGATAATA
1 AAG-TAATA
11817160 CTATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 14 0.61
19 1 0.04
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (16 bp):
AAGTAATATCAATAAA
Found at i:11817191 original size:51 final size:51
Alignment explanation
Indices: 11817125--11817238 Score: 210
Period size: 51 Copynumber: 2.2 Consensus size: 51
11817115 CCAAGTAATA
*
11817125 TCAATAAAAAGTCAATAGTCAATAATAAGATAATACTATAATAATATAAAT
1 TCAATAATAAGTCAATAGTCAATAATAAGATAATACTATAATAATATAAAT
*
11817176 TCAATAATAAGTCAATAGTCAGTAATAAGATAATACTATAATAATATAAAT
1 TCAATAATAAGTCAATAGTCAATAATAAGATAATACTATAATAATATAAAT
11817227 TCAATAATAAGT
1 TCAATAATAAGT
11817239 ATTCTTAGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (51 bp):
TCAATAATAAGTCAATAGTCAATAATAAGATAATACTATAATAATATAAAT
Found at i:11818022 original size:10 final size:10
Alignment explanation
Indices: 11818008--11818041 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
11817998 AAAAGGACAT
11818008 GAAAGTAAAG
1 GAAAGTAAAG
*
11818018 TAAAGTAAAG
1 GAAAGTAAAG
*
11818028 GAAAGTAAAT
1 GAAAGTAAAG
11818038 GAAA
1 GAAA
11818042 CAAAACTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (10 bp):
GAAAGTAAAG
Found at i:11820405 original size:18 final size:18
Alignment explanation
Indices: 11820382--11820420 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11820372 AAAATTAGTC
11820382 ATATTAA-GAATAAATATT
1 ATATTAATGAATAAAT-TT
*
11820400 ATATTAATTAATAAATTT
1 ATATTAATGAATAAATTT
11820418 ATA
1 ATA
11820421 ATTTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATTAATGAATAAATTT
Found at i:11820457 original size:29 final size:29
Alignment explanation
Indices: 11820415--11820474 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
11820405 AATTAATAAA
* *
11820415 TTTATAATTTAAATATCATATTAAAAATT
1 TTTAAAATTTAAATATCACATTAAAAATT
*
11820444 TTTAAAATTTAAATATCACATTAAATATT
1 TTTAAAATTTAAATATCACATTAAAAATT
11820473 TT
1 TT
11820475 ATTATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAAAATTTAAATATCACATTAAAAATT
Found at i:11820768 original size:13 final size:13
Alignment explanation
Indices: 11820752--11820785 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11820742 TTATTTAAAA
11820752 TAATTAATTAATT
1 TAATTAATTAATT
*
11820765 TAATCAATTAATT
1 TAATTAATTAATT
11820778 T-ATTAATT
1 TAATTAATT
11820786 TTGAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TAATTAATTAATT
Found at i:11827577 original size:103 final size:103
Alignment explanation
Indices: 11827398--11827604 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
11827388 TCATGAATAT
* *
11827398 TGGTTGCTTTGTGGACATTGATCCACATGTTCAAATAATTTAGGATTTAACTAGCATTTGTTATT
1 TGGTTGCTTTGTAGACATTGATCCACATGTTCAAATAATCTAGGATTTAACTAGCATTTGTTATT
*
11827463 ATTTTAAGATTATTGTGGTGATCTAATTATTAAAGTGA
66 ATTTAAAGATTATTGTGGTGATCTAATTATTAAAGTGA
11827501 TGGTTGCTTTGTAGACATTGATCCACATGTTCAAATAATCTAGGATTTAACTAGCATTTGTTATT
1 TGGTTGCTTTGTAGACATTGATCCACATGTTCAAATAATCTAGGATTTAACTAGCATTTGTTATT
11827566 ATTTAAAGATTATTGTGGTGATCTAATTATTAAAGTGA
66 ATTTAAAGATTATTGTGGTGATCTAATTATTAAAGTGA
11827604 T
1 T
11827605 TTGATATTAG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (103 bp):
TGGTTGCTTTGTAGACATTGATCCACATGTTCAAATAATCTAGGATTTAACTAGCATTTGTTATT
ATTTAAAGATTATTGTGGTGATCTAATTATTAAAGTGA
Found at i:11828701 original size:77 final size:75
Alignment explanation
Indices: 11828558--11828761 Score: 218
Period size: 78 Copynumber: 2.7 Consensus size: 75
11828548 AAAGATAACA
* * * * *
11828558 TTTTAAGAT-AAAACATGATCTTTATTGAAAATAT-GAAAAGATT-TATTTTTTAGAATTTAACC
1 TTTTAAGATAAAAACATGATCTTTGTTGAAAATATAAAAAAAATTATTTTTTTTAGAATTTAACA
*
11828620 AAAAT-AGTGT
66 AAAATGA-TAT
*
11828630 TTTTAAGATAAAAATCATGATGTTTGTTGAAAATATAAAAAAAAATTATTTTTTTTAGAATTTAA
1 TTTTAAGATAAAAA-CATGATCTTTGTTGAAAATAT-AAAAAAAATTATTTTTTTTAGAATTTAA
11828695 CAAAAATGATAT
64 CAAAAATGATAT
* ** * *
11828707 TTTTAAAGTAAAAAAACACAATTTTTGTTGAAAACATGAAAAAAAATTATTTTTT
1 TTTT-AAG-ATAAAAACATGATCTTTGTTGAAAATAT-AAAAAAAATTATTTTTT
11828762 GAAATTCTTA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
72 9 0.08
73 4 0.04
74 19 0.17
76 7 0.06
77 28 0.25
78 38 0.34
79 6 0.05
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (75 bp):
TTTTAAGATAAAAACATGATCTTTGTTGAAAATATAAAAAAAATTATTTTTTTTAGAATTTAACA
AAAATGATAT
Found at i:11829725 original size:20 final size:21
Alignment explanation
Indices: 11829702--11829746 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
11829692 TTTCCTAACA
*
11829702 TCTTGGAAGCTTTCTTTCTT-
1 TCTTCGAAGCTTTCTTTCTTC
*
11829722 TCTTCGAAGCTTTTTTTCTTC
1 TCTTCGAAGCTTTCTTTCTTC
11829743 TCTT
1 TCTT
11829747 TCCCCTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.09, C:0.22, G:0.11, T:0.58
Consensus pattern (21 bp):
TCTTCGAAGCTTTCTTTCTTC
Found at i:11834784 original size:2 final size:2
Alignment explanation
Indices: 11834777--11834806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11834767 GTAACGATTA
11834777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11834807 TATGTAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11836569 original size:57 final size:56
Alignment explanation
Indices: 11836508--11836796 Score: 416
Period size: 57 Copynumber: 4.9 Consensus size: 56
11836498 TTGTGTGGGG
*
11836508 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAAGA
* * *
11836565 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAACTTTGATTTTCAAGT
1 AAAATTGATACTTTCAACTTTTCC-CAAAAATA-TTTTTTGGAAA-TTT-ATTTTTAAGA
11836625 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTGGAAATTTATTTTTAAGA
* *
11836682 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTGTTTGGAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAAGA
11836739 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTTA
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATA--TTTTTTGGAAA-TTT-ATTTTTA
11836797 TTTAAAGAAA
Statistics
Matches: 211, Mismatches: 10, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
56 12 0.06
57 107 0.51
58 19 0.09
59 24 0.11
60 42 0.20
61 7 0.03
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAAGA
Found at i:11836655 original size:117 final size:114
Alignment explanation
Indices: 11836508--11836796 Score: 445
Period size: 117 Copynumber: 2.5 Consensus size: 114
11836498 TTGTGTGGGG
*
11836508 AAAATTGATACTTTCAACTTTTTCCC-AAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTG
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATTG
* * *
11836572 ATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAACTTTGATTTTCAAGT
65 ATACTTTCAACTTTTCCTCAAAAATA-TTGTTTGGAAA-TTT-ATTTTCAAGA
11836625 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATTGA
* *
11836690 TACTTTCAACTTTTTCTCAAAAATATTGTTTGGAAATTTATTTTTAAGA
66 TACTTTCAACTTTTCCTCAAAAATATTGTTTGGAAATTTATTTTCAAGA
11836739 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTTTA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAA-TTT-ATTTTTA
11836797 TTTAAAGAAA
Statistics
Matches: 161, Mismatches: 6, Indels: 9
0.91 0.03 0.05
Matches are distributed among these distances:
114 41 0.25
115 3 0.02
116 27 0.17
117 83 0.52
118 7 0.04
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGAAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATTGTTTGGAAATTTATTTTCAAGA
Found at i:11836831 original size:12 final size:12
Alignment explanation
Indices: 11836814--11836959 Score: 57
Period size: 12 Copynumber: 11.2 Consensus size: 12
11836804 AAAATAGAAT
11836814 AATAAAAAAATA
1 AATAAAAAAATA
*
11836826 AATAAAAATAGAAA
1 AATAAAAA-A-ATA
11836840 AATAAAGAAAAGTA
1 AATAAA-AAAA-TA
*
11836854 AA-ACAAAAATA
1 AATAAAAAAATA
*
11836865 AA-AATAAAATTA
1 AATAA-AAAAATA
11836877 AGATAAAAAGAATATTA
1 A-AT-AAAA-AA-A-TA
** *
11836894 AATAAACCTAATCT
1 AATAAA-AAAAT-A
11836908 AATAAATAAAA-A
1 AATAAA-AAAATA
*
11836920 AATAAAATAAACA
1 AATAAAA-AAATA
*
11836933 AATAAACAAATA
1 AATAAAAAAATA
11836945 AATGAAAAAAA-A
1 AAT-AAAAAAATA
11836957 AAT
1 AAT
11836960 TCAAAAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
11 6 0.06
12 39 0.38
13 19 0.19
14 23 0.23
15 10 0.10
16 2 0.02
17 3 0.03
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (12 bp):
AATAAAAAAATA
Found at i:11836837 original size:26 final size:27
Alignment explanation
Indices: 11836804--11836873 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
11836794 TTATTTAAAG
*
11836804 AAAATAGAATAATAAAAAAA-T-AAATA
1 AAAATAGAA-AATAAAAAAAGTAAAACA
11836830 AAAATAGAAAAATAAAGAAAAGTAAAACA
1 AAAATAG-AAAATAAA-AAAAGTAAAACA
11836859 AAAATA-AAAATAAAA
1 AAAATAGAAAATAAAA
11836874 TTAAGATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 14 0.36
27 14 0.36
28 1 0.03
29 10 0.26
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (27 bp):
AAAATAGAAAATAAAAAAAGTAAAACA
Found at i:11836840 original size:18 final size:17
Alignment explanation
Indices: 11836818--11836959 Score: 73
Period size: 17 Copynumber: 8.4 Consensus size: 17
11836808 TAGAATAATA
11836818 AAAAAATAAATAAAAAT
1 AAAAAATAAATAAAAAT
* *
11836835 AGAAAAATAAAGAAAAGT
1 A-AAAAATAAATAAAAAT
11836853 AAAACAA-AAATAAAAAT
1 AAAA-AATAAATAAAAAT
*
11836870 -AAAATTAAGATAAAAA-
1 AAAAAATAA-ATAAAAAT
* * * **
11836886 GAATATTAAATAAACCT
1 AAAAAATAAATAAAAAT
**
11836903 AATCTAATAAATAAAAA-
1 AA-AAAATAAATAAAAAT
*
11836920 AATAAAAT-AA-ACAAAT
1 AA-AAAATAAATAAAAAT
*
11836936 AAACAAATAAATGAAAA-
1 AAA-AAATAAATAAAAAT
11836953 AAAAAAT
1 AAAAAAT
11836960 TCAAAAAAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
15 6 0.06
16 22 0.23
17 38 0.40
18 30 0.31
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAAAATAAATAAAAAT
Found at i:11836882 original size:17 final size:16
Alignment explanation
Indices: 11836800--11836899 Score: 55
Period size: 17 Copynumber: 6.1 Consensus size: 16
11836790 ATTTTTATTT
11836800 AAAGAAAA-TAGAATAA
1 AAAGAAAATTA-AATAA
11836816 TAAA-AAAA-TAAATAAA
1 -AAAGAAAATTAAAT-AA
* *
11836832 AATAGAAAAATAAA-GA
1 AA-AGAAAATTAAATAA
**
11836848 AAAGTAAAACAAAAATAA
1 AAAG-AAAA-TTAAATAA
*
11836866 AAATAAAATTAAGATAA
1 AAAGAAAATTAA-ATAA
*
11836883 AAAGAATATTAAATAA
1 AAAGAAAATTAAATAA
11836899 A
1 A
11836900 CCTAATCTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
15 7 0.10
16 23 0.34
17 29 0.43
18 8 0.12
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAGAAAATTAAATAA
Found at i:11836930 original size:17 final size:17
Alignment explanation
Indices: 11836814--11836959 Score: 63
Period size: 18 Copynumber: 8.5 Consensus size: 17
11836804 AAAATAGAAT
11836814 AATAAAA-AAATAAATAAA
1 AATAAAATAAAT-AA-AAA
*
11836832 AATAGAA-AAATAAAGAA
1 AATAAAATAAATAAA-AA
*
11836849 AAGTAAAACAAA-AATAAA
1 AA-TAAAATAAATAA-AAA
11836867 AATAAAATTAAGATAAAAA
1 AATAAAA-TAA-ATAAAAA
* **
11836886 GAAT--ATTAAATAAACCT
1 -AATAAAATAAATAAA-AA
**
11836903 AATCTAATAAATAAAAA
1 AATAAAATAAATAAAAA
* *
11836920 AATAAAATAAACAAATA
1 AATAAAATAAATAAAAA
* *
11836937 AA-CAAATAAATGAAAA
1 AATAAAATAAATAAAAA
11836953 AA-AAAAT
1 AATAAAAT
11836960 TCAAAAAAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
16 25 0.25
17 29 0.29
18 32 0.32
19 8 0.08
20 5 0.05
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (17 bp):
AATAAAATAAATAAAAA
Found at i:11837861 original size:23 final size:22
Alignment explanation
Indices: 11837811--11837866 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
11837801 TAATTAGAAA
*
11837811 AGATAAATAAAAAAAATATTAT
1 AGATAAATAAAAAAAATAATAT
*
11837833 AGGATAAATAAAAATAATAATAT
1 A-GATAAATAAAAAAAATAATAT
*
11837856 CAGATATATAA
1 -AGATAAATAA
11837867 TTAGATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 27 0.93
24 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (22 bp):
AGATAAATAAAAAAAATAATAT
Found at i:11837888 original size:8 final size:8
Alignment explanation
Indices: 11837877--11837924 Score: 62
Period size: 9 Copynumber: 5.9 Consensus size: 8
11837867 TTAGATAAAT
*
11837877 AAAAATAC
1 AAAAATAA
11837885 AAAAATAA
1 AAAAATAA
11837893 ATAAAATAA
1 A-AAAATAA
11837902 AAAAAT-A
1 AAAAATAA
11837909 AAAAATAA
1 AAAAATAA
11837917 TAAAAATA
1 -AAAAATA
11837925 TATATTAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.19
8 14 0.39
9 15 0.42
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:11837899 original size:23 final size:22
Alignment explanation
Indices: 11837873--11837921 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
11837863 ATAATTAGAT
11837873 AAAT-AAAAATACAAAAATAAATA
1 AAATAAAAAATA-AAAAAT-AATA
11837896 AAATAAAAAAATAAAAAATAATA
1 AAAT-AAAAAATAAAAAATAATA
11837919 AAA
1 AAA
11837922 ATATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.46
24 6 0.25
25 7 0.29
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (22 bp):
AAATAAAAAATAAAAAATAATA
Found at i:11837900 original size:17 final size:18
Alignment explanation
Indices: 11837871--11837922 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
11837861 ATATAATTAG
*
11837871 ATAAATAAAAATACAAAA
1 ATAAATAAAAATAAAAAA
11837889 ATAAAT-AAAATAAAAAA
1 ATAAATAAAAATAAAAAA
11837906 ATAAA-AAATAATAAAAA
1 ATAAATAAA-AATAAAAA
11837923 TATATATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAATAAAAATAAAAAA
Found at i:11838158 original size:10 final size:10
Alignment explanation
Indices: 11838143--11838190 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
11838133 CAATTCAACA
11838143 TGTTTTTTTT
1 TGTTTTTTTT
*
11838153 TGTTTTGTTT
1 TGTTTTTTTT
11838163 TGTTTTGTTTTT
1 TG-TTT-TTTTT
*
11838175 TGTTTTTATT
1 TGTTTTTTTT
11838185 T-TTTTT
1 TGTTTTT
11838191 ACCAAAGCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 5 0.15
10 16 0.48
11 6 0.18
12 6 0.18
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.85
Consensus pattern (10 bp):
TGTTTTTTTT
Found at i:11838163 original size:15 final size:15
Alignment explanation
Indices: 11838143--11838173 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11838133 CAATTCAACA
*
11838143 TGTTTTTTTTTGTTT
1 TGTTTTGTTTTGTTT
11838158 TGTTTTGTTTTGTTT
1 TGTTTTGTTTTGTTT
11838173 T
1 T
11838174 TTGTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
TGTTTTGTTTTGTTT
Found at i:11838188 original size:15 final size:14
Alignment explanation
Indices: 11838143--11838190 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
11838133 CAATTCAACA
11838143 TGTTTTTTTTTGTTT
1 TGTTTTTTTTT-TTT
11838158 TGTTTTGTTTTGTTTTT
1 TG-TTT-TTTT-TTTTT
11838175 TGTTTTTATTTTTTT
1 TGTTTTT-TTTTTTT
11838190 T
1 T
11838191 ACCAAAGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.34
16 8 0.28
17 9 0.31
18 2 0.07
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.85
Consensus pattern (14 bp):
TGTTTTTTTTTTTT
Found at i:11838265 original size:43 final size:42
Alignment explanation
Indices: 11838197--11838497 Score: 457
Period size: 42 Copynumber: 7.1 Consensus size: 42
11838187 TTTTACCAAA
* *
11838197 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-AGTAAATT
*
11838240 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
11838282 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAAGTAAATT
* *
11838325 GCTCTTCTAAACAGAGGCATCACGACTTTTG-AAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAAGTAAATT
*
11838367 GCTCCTCTAAATAGAGGCACCACGACTTTTG--AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAAGTAAATT
*
11838408 GCTCTTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
*
11838450 GCTCCTCTAAACAGAAGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
11838492 GCTCCT
1 GCTCCT
11838498 TGACAATCAT
Statistics
Matches: 241, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.02
41 35 0.15
42 130 0.54
43 72 0.30
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
Found at i:11838340 original size:85 final size:84
Alignment explanation
Indices: 11838197--11838495 Score: 469
Period size: 85 Copynumber: 3.5 Consensus size: 84
11838187 TTTTACCAAA
* * *
11838197 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACA-TAAATTGCTCCTCTAAACAGAGGCACC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-AGTAAATTGCTCTTCTAAACAGAGGCACC
11838261 ACGACTTTGGAAAAGTAAATT
64 ACGACTTTGGAAAAGTAAATT
*
11838282 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAAGTAAATTGCTCTTCTAAACAGAGGCATCA
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAAGTAAATTGCTCTTCTAAACAGAGGCACCA
*
11838347 CGACTTTTGAAAAGTAAATT
65 CGACTTTGGAAAAGTAAATT
*
11838367 GCTCCTCTAAATAGAGGCACCACGACTTTTG--AAAGTAAATTGCTCTTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAAGTAAATTGCTCTTCTAAACAGAGGCACCA
*
11838430 CGACTTTGAAAAAGTAAATT
65 CGACTTTGGAAAAGTAAATT
*
11838450 GCTCCTCTAAACAGAAGCACCACGACTTTGAAAAAGTAAATTGCTC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTC
11838496 CTTGACAATC
Statistics
Matches: 199, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
82 4 0.02
83 73 0.37
84 15 0.08
85 102 0.51
86 5 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (84 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCTTCTAAACAGAGGCACCAC
GACTTTGGAAAAGTAAATT
Found at i:11839105 original size:251 final size:251
Alignment explanation
Indices: 11838658--11839166 Score: 966
Period size: 251 Copynumber: 2.0 Consensus size: 251
11838648 TCTTTATATC
* *
11838658 TGTC-TTTCCATGTGGGATGTTGGAACACCCTTGCTTCTTGGATTTATATACTATACTTTCTTGA
1 TGTCTTTTCCATGTGAGATGTTGGAACACCCTTGCTTCTTGGATTTATACACTATACTTTCTTGA
11838722 AAGTAGTGTATGCTATGCAAATGTATATGAATTTCAATGCATGCTATGCAAATGTTGGCCAATTA
66 AAGTAGTGTATGCTATGCAAATGTATATGAATTTCAATGCATGCTATGCAAATGTTGGCCAATTA
11838787 ATTCCTGTTCAATGTATGGTACTCAAGTTTCTCAAGCTCTTTTCTTAGGCATCAAGCCCTTTGAT
131 ATTCCTGTTCAATGTATGGTACTCAAGTTTCTCAAGCTCTTTTCTTAGGCATCAAGCCCTTTGAT
11838852 TCTTCAGAGATCCAATTACACTACTCTTCTAAGATCGAACCAATGTAGCTCTCAAT
196 TCTTCAGAGATCCAATTACACTACTCTTCTAAGATCGAACCAATGTAGCTCTCAAT
*
11838908 TGTCTTTTCCATGTGAGATGTTGGAACACCCTTGCTTCTTGGATTTATACACTATATTTTCTTGA
1 TGTCTTTTCCATGTGAGATGTTGGAACACCCTTGCTTCTTGGATTTATACACTATACTTTCTTGA
11838973 AAGTAGTGTATGCTATGCAAATGTATATGAATTTCAATGCATGCTATGCAAATGTTGGCCAATTA
66 AAGTAGTGTATGCTATGCAAATGTATATGAATTTCAATGCATGCTATGCAAATGTTGGCCAATTA
11839038 ATTCCTGTTCAATGTATGGTACTCAAGTTTCTCAAGCTCTTTTCTTAGGCATCAAGCCCTTTGAT
131 ATTCCTGTTCAATGTATGGTACTCAAGTTTCTCAAGCTCTTTTCTTAGGCATCAAGCCCTTTGAT
*
11839103 TCTTCAGAGATCCAATTACACTGCTCTTCTAAGATCGAACCAATGTAGCTCTCAAT
196 TCTTCAGAGATCCAATTACACTACTCTTCTAAGATCGAACCAATGTAGCTCTCAAT
*
11839159 TATCTTTT
1 TGTCTTTT
11839167 TCACTCACAT
Statistics
Matches: 253, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
250 4 0.02
251 249 0.98
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (251 bp):
TGTCTTTTCCATGTGAGATGTTGGAACACCCTTGCTTCTTGGATTTATACACTATACTTTCTTGA
AAGTAGTGTATGCTATGCAAATGTATATGAATTTCAATGCATGCTATGCAAATGTTGGCCAATTA
ATTCCTGTTCAATGTATGGTACTCAAGTTTCTCAAGCTCTTTTCTTAGGCATCAAGCCCTTTGAT
TCTTCAGAGATCCAATTACACTACTCTTCTAAGATCGAACCAATGTAGCTCTCAAT
Found at i:11839934 original size:8 final size:8
Alignment explanation
Indices: 11839923--11839975 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
11839913 TCAATTTGAA
11839923 TTTCTTTT
1 TTTCTTTT
*
11839931 TTTCATTT
1 TTTCTTTT
*
11839939 TTTCATTTC
1 TTTC-TTTT
11839948 TTTCTTTT
1 TTTCTTTT
*
11839956 TCTTTTTTT
1 T-TTCTTTT
11839965 TTTCTTTT
1 TTTCTTTT
11839973 TTT
1 TTT
11839976 TTCCTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 24 0.65
9 13 0.35
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTCTTTT
Found at i:11839948 original size:21 final size:21
Alignment explanation
Indices: 11839922--11840014 Score: 91
Period size: 22 Copynumber: 4.2 Consensus size: 21
11839912 TTCAATTTGA
11839922 ATTTC-TTTTTTTCATTTTTTC
1 ATTTCTTTTTTTTC-TTTTTTC
11839943 ATTTCTTTCTTTTTCTTTTTT-
1 ATTTCTTT-TTTTTCTTTTTTC
*
11839964 TTTTCTTTTTTTTTCCTTTTTTC
1 ATTTC-TTTTTTTT-CTTTTTTC
*
11839987 ATCATCTTTTTTTTCTCTTTTCTC
1 AT-TTCTTTTTTTTCT-TTTT-TC
11840011 ATTT
1 ATTT
11840015 TTCATCCATT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
21 14 0.23
22 20 0.33
23 20 0.33
24 6 0.10
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTCTTTTTTTTCTTTTTTC
Found at i:11839957 original size:10 final size:10
Alignment explanation
Indices: 11839927--11839985 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 10
11839917 TTTGAATTTC
11839927 TTTTTTTCATT
1 TTTTTTTC-TT
11839938 TTTTCATTTCTT
1 TTTT--TTTCTT
*
11839950 TCTTTTTCTTT
1 TTTTTTTC-TT
11839961 TTTTTTTCTT
1 TTTTTTTCTT
11839971 TTTTTTTCCTT
1 TTTTTTT-CTT
11839982 TTTT
1 TTTT
11839986 CATCATCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 13 0.31
11 20 0.48
12 5 0.12
13 4 0.10
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:11839975 original size:35 final size:34
Alignment explanation
Indices: 11839927--11840007 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 34
11839917 TTTGAATTTC
* * **
11839927 TTTTTTTC-ATTTTTTCATTTCTTTCTTTTTCTTT
1 TTTTTTTCTTTTTTTTCATTT-TTTCATCATCTTT
*
11839961 TTTTTTTCTTTTTTTTTCCTTTTTTCATCATCTTT
1 TTTTTTTCTTTT-TTTTCATTTTTTCATCATCTTT
*
11839996 TTTTTCTCTTTT
1 TTTTTTTCTTTT
11840008 CTCATTTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
34 8 0.21
35 23 0.59
36 8 0.21
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTTTTCTTTTTTTTCATTTTTTCATCATCTTT
Done.