Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 2 of 187
Found at i:294395 original size:15 final size:16
Alignment explanation
Indices: 294357--294393 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
294347 GGATATGGAT
294357 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
294373 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
294389 ATTTT
1 ATTTT
294394 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTTTTATATAATGTA
Found at i:300361 original size:22 final size:20
Alignment explanation
Indices: 300326--300374 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
300316 TAGCAGCATT
*
300326 CAGCCTCCAGCGCTGCA-GC
1 CAGCCTCCAGCGCTCCACGC
300345 CACGCCTCCGAGCCGCTCCACGC
1 CA-GCCTCC-AG-CGCTCCACGC
300368 CAGCCTC
1 CAGCCTC
300375 TGCCTCCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 2 0.08
22 11 0.44
23 4 0.16
ACGTcount: A:0.14, C:0.53, G:0.22, T:0.10
Consensus pattern (20 bp):
CAGCCTCCAGCGCTCCACGC
Found at i:302992 original size:15 final size:15
Alignment explanation
Indices: 302962--302990 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
302952 TCATCTTACG
302962 TGAAATAATTTAAAA
1 TGAAATAATTTAAAA
302977 TGAAA-AATTTAAAA
1 TGAAATAATTTAAAA
302991 ATAGATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
TGAAATAATTTAAAA
Found at i:303411 original size:20 final size:20
Alignment explanation
Indices: 303386--303428 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
303376 TTGCTGCACC
* *
303386 ATGCTGTTGTTGTCCCTTCA
1 ATGCTGCTGCTGTCCCTTCA
303406 ATGCTGCTGCTGTCCCTTCA
1 ATGCTGCTGCTGTCCCTTCA
303426 ATG
1 ATG
303429 GGAAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.40
Consensus pattern (20 bp):
ATGCTGCTGCTGTCCCTTCA
Found at i:303525 original size:3 final size:3
Alignment explanation
Indices: 303512--303544 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
303502 AAGAGAAAGG
*
303512 AGA AG- AGA AGA AGA AGA AGA AGA AAA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
303545 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:303852 original size:15 final size:16
Alignment explanation
Indices: 303814--303850 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
303804 GGATATGGAT
303814 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
303830 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
303846 ATTTT
1 ATTTT
303851 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTTTTATATAATGTA
Found at i:305849 original size:11 final size:11
Alignment explanation
Indices: 305835--305904 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
305825 TTTTTTTAAA
305835 TTTTAAAATAC
1 TTTTAAAATAC
305846 TTTTAAAATAC
1 TTTTAAAATAC
*
305857 TTTTTTTAAAT--
1 --TTTTAAAATAC
*
305868 TTTT-TAA-A-
1 TTTTAAAATAC
*
305876 TTTTAAAATAT
1 TTTTAAAATAC
305887 TTTTAAAATAC
1 TTTTAAAATAC
305898 TTTTAAA
1 TTTTAAA
305905 TTTGTTTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
8 6 0.12
9 6 0.12
10 1 0.02
11 28 0.57
13 8 0.16
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:305861 original size:41 final size:41
Alignment explanation
Indices: 305816--305966 Score: 175
Period size: 41 Copynumber: 3.7 Consensus size: 41
305806 ATATAATAAT
* *
305816 TTTTTTATTTTTTTTTAAATTTTAAAATACTTTTAAAATAC
1 TTTTTTATATTTTTTTAAATTTTAAAATATTTTTAAAATAC
*
305857 TTTTTT-TAAATTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAT-ATTTTTTTAAATTTTAAAATATTTTTAAAATAC
* * *
305898 --TTTTAAATTTGTTT-AATTTTAAAATATTTTTAAAATATT
1 TTTTTTATATTTTTTTAAATTTTAAAATATTTTTAAAATA-C
* *
305937 TTTTTTATTTTTGTTTTAATTTTTAAAATA
1 TTTTTTATATTT-TTTTAAATTTTAAAATA
305967 AATTTTGGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
38 23 0.25
39 10 0.11
40 1 0.01
41 44 0.48
42 3 0.03
43 11 0.12
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (41 bp):
TTTTTTATATTTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:305901 original size:29 final size:29
Alignment explanation
Indices: 305846--305907 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
305836 TTTAAAATAC
* *
305846 TTTTAAAATACTTTTTTTAAATTTTTTAAA
1 TTTTAAAATAC-TTTTTAAAATCTTTTAAA
305876 TTTTAAAATA-TTTTTAAAATACTTTTAAA
1 TTTTAAAATACTTTTTAAAAT-CTTTTAAA
305905 TTT
1 TTT
305908 GTTTAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.31
29 10 0.34
30 10 0.34
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAAATCTTTTAAA
Found at i:305916 original size:38 final size:38
Alignment explanation
Indices: 305826--305939 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 38
305816 TTTTTTATTT
*
305826 TTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC---TTTTAAA
305867 TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTAAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTAAA
*
305905 TTTGTTT-AATTTTAAAATATTTTTAAAATATTTTT
1 TTT-TTTAAATTTTAAAATATTTTTAAAATACTTTT
305940 TTTATTTTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
38 37 0.53
39 3 0.04
41 30 0.43
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (38 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTAAA
Found at i:305930 original size:11 final size:11
Alignment explanation
Indices: 305914--305939 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
305904 ATTTGTTTAA
305914 TTTTAAAATAT
1 TTTTAAAATAT
305925 TTTTAAAATAT
1 TTTTAAAATAT
305936 TTTT
1 TTTT
305940 TTTATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:306393 original size:33 final size:33
Alignment explanation
Indices: 306356--306457 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 33
306346 AGTCATCCTA
*
306356 GCTCGTATCCACCTCAGTACTCTGCTCCTTCCG
1 GCTCGTATCCACCTCAGTACTCCGCTCCTTCCG
* *
306389 GCTCGTATCCACCTCAGTACTCCACTCCTTTCG
1 GCTCGTATCCACCTCAGTACTCCGCTCCTTCCG
* * * * * *
306422 GCCCGTCTCCACCGCCGTACTCCGTTCCTCCCG
1 GCTCGTATCCACCTCAGTACTCCGCTCCTTCCG
306455 GCT
1 GCT
306458 TCATCGATGA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.46, G:0.16, T:0.27
Consensus pattern (33 bp):
GCTCGTATCCACCTCAGTACTCCGCTCCTTCCG
Found at i:307888 original size:35 final size:35
Alignment explanation
Indices: 307849--307933 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 35
307839 CAATTTAATT
307849 ATATTTT-ATTATTTGATTCA-AATATAATCTGTAAA
1 ATATTTTGA-TATTTGATT-AGAATATAATCTGTAAA
*
307884 ATATTTTGATATTTTATTATGAATATAATCTGTAAA
1 ATATTTTGATATTTGATTA-GAATATAATCTGTAAA
307920 ATATTTTGATATTT
1 ATATTTTGATATTT
307934 TTGAATTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 1 0.02
35 15 0.33
36 30 0.65
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (35 bp):
ATATTTTGATATTTGATTAGAATATAATCTGTAAA
Found at i:308039 original size:19 final size:18
Alignment explanation
Indices: 307997--308042 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
307987 ATATAATTGT
*
307997 AATAATTTTTAATTATTT
1 AATAATTTTTAATTATTA
* *
308015 ATTAATTTTGTAATTGTTA
1 AATAATTTT-TAATTATTA
308034 AATAATTTT
1 AATAATTTT
308043 AAAAACTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
AATAATTTTTAATTATTA
Found at i:308187 original size:21 final size:21
Alignment explanation
Indices: 308155--308209 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
308145 ACCGCTATTT
308155 CTAATCTCACCGCTACAGTATC
1 CTAATCTCACCGCTACAGTA-C
*
308177 C-AATCTTACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
308197 CTAATCTCACCGC
1 CTAATCTCACCGC
308210 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.38, G:0.09, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:315218 original size:30 final size:32
Alignment explanation
Indices: 315169--315228 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
315159 ATTATTATTA
* *
315169 TTTTTTGAATCAATGCATACTTTAATCTTTGT
1 TTTTTTGAATCAATACATACTTCAATCTTTGT
315201 TTTTTTGAA-CAA-ACATACTTCAATCTTT
1 TTTTTTGAATCAATACATACTTCAATCTTT
315229 TATTTGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 3 0.12
32 9 0.35
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (32 bp):
TTTTTTGAATCAATACATACTTCAATCTTTGT
Found at i:325139 original size:23 final size:22
Alignment explanation
Indices: 325087--325139 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
325077 TCCACGTCTT
*
325087 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
325109 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
325132 TTTCTTTT
1 TTTCTTTT
325140 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:332619 original size:52 final size:48
Alignment explanation
Indices: 332600--332802 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
332590 TGACAAGTGG
* *
332600 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
332646 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
332698 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
332744 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
332790 AAAGTGATAAGTG
1 AAAGTGATAAGTG
332803 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:332654 original size:98 final size:98
Alignment explanation
Indices: 332534--332802 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
332524 TTTGAGTACT
*
332534 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
332599 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
332632 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
332697 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
332730 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
332795 GATAAGTG
65 GAAAAGTG
332803 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:332810 original size:37 final size:37
Alignment explanation
Indices: 332766--332911 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
332756 GATAGCTTTA
*
332766 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
332803 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
332840 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
332877 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
332912 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:335668 original size:31 final size:31
Alignment explanation
Indices: 335630--335697 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
335620 TTACAAAATT
335630 ATCACTGAACTATTCAAAAGTTTTCATTTAA
1 ATCACTGAACTATTCAAAAGTTTTCATTTAA
* * *
335661 CTCACTGAATTATTCAAAAGTTTTTATTTAA
1 ATCACTGAACTATTCAAAAGTTTTCATTTAA
335692 ATCACT
1 ATCACT
335698 TAAGTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (31 bp):
ATCACTGAACTATTCAAAAGTTTTCATTTAA
Found at i:336741 original size:31 final size:31
Alignment explanation
Indices: 336703--336770 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
336693 TTACAAAATT
336703 ATCACTGAACTATTCAAAAGTTTTTATTTAA
1 ATCACTGAACTATTCAAAAGTTTTTATTTAA
* *
336734 CTCACTGAATTATTCAAAAGTTTTTATTTAA
1 ATCACTGAACTATTCAAAAGTTTTTATTTAA
336765 ATCACT
1 ATCACT
336771 AGGCTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (31 bp):
ATCACTGAACTATTCAAAAGTTTTTATTTAA
Found at i:339029 original size:26 final size:27
Alignment explanation
Indices: 338978--339035 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
338968 TATTATTTCC
*
338978 AATA-AAAATAATAAATATATTGAAAT
1 AATATAAAATAATAAATATATCGAAAT
339004 AATATAAAATAATAAA-ATA-CGAAAAT
1 AATATAAAATAATAAATATATCG-AAAT
339030 AATATA
1 AATATA
339036 TTTTTATTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.03
26 17 0.59
27 11 0.38
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (27 bp):
AATATAAAATAATAAATATATCGAAAT
Found at i:348903 original size:3 final size:3
Alignment explanation
Indices: 348895--348926 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
348885 ATACCTTTAA
348895 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
348927 AAACTTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:349789 original size:32 final size:32
Alignment explanation
Indices: 349752--349823 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
349742 CAAAATTTCA
349752 AAATTAAAAAAGTATAA-AGACTAAAATTGACC
1 AAATTAAAAAAGTATAAGA-ACTAAAATTGACC
* *
349784 AAATT-AAAGAGTATAAGAACTAAAATTGATC
1 AAATTAAAAAAGTATAAGAACTAAAATTGACC
*
349815 AAAATAAAA
1 AAATTAAAA
349824 TATAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 26 0.74
32 9 0.26
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (32 bp):
AAATTAAAAAAGTATAAGAACTAAAATTGACC
Found at i:352991 original size:19 final size:19
Alignment explanation
Indices: 352967--353064 Score: 106
Period size: 19 Copynumber: 4.8 Consensus size: 19
352957 AATCTTCGAG
352967 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
352986 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
* *
353005 GATATATGCAATCTTAAATAT
1 G--ATATGTAATCTTAGATAT
353026 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
353048 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
353065 GATTTAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 30 0.44
20 3 0.04
21 18 0.26
22 7 0.10
23 10 0.15
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:353013 original size:21 final size:21
Alignment explanation
Indices: 352968--353030 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
352958 ATCTTCGAGG
*
352968 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
352987 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
353008 ATATGCAATCTTAAATATGAT
1 ATATGCAATCTTAGATATGAT
353029 AT
1 AT
353031 GTAATCTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.45
21 22 0.55
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:353074 original size:22 final size:23
Alignment explanation
Indices: 353030--353074 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
353020 AAATATGATA
*
353030 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
353053 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
353075 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:353765 original size:22 final size:22
Alignment explanation
Indices: 353702--353760 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
353692 TAATATAATT
*
353702 ATTATTTTTATTTATTTATATGTA
1 ATTA-TTTT-TTTATCTATATGTA
353726 ATTATTTTTTTATCTATATGT-
1 ATTATTTTTTTATCTATATGTA
353747 ATATATTTATTTTA
1 AT-TATTT-TTTTA
353761 GTATACATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.06
22 17 0.53
23 9 0.28
24 4 0.12
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTATTTTTTTATCTATATGTA
Found at i:353876 original size:15 final size:17
Alignment explanation
Indices: 353844--353881 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
353834 AATGCAAATA
353844 TATTTTTTTATATACTT
1 TATTTTTTTATATACTT
*
353861 TATTTTTTT-T-TCCTT
1 TATTTTTTTATATACTT
353876 TATTTT
1 TATTTT
353882 CATAAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTTTATATACTT
Found at i:357027 original size:2 final size:2
Alignment explanation
Indices: 357022--357067 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
357012 CCAAATACTT
357022 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
357064 GA GA
1 GA GA
357068 TTACCTTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:361291 original size:32 final size:34
Alignment explanation
Indices: 361235--361302 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 34
361225 GAATTATACT
361235 AGGTTATAACCTTTTTTTTATAATATGTAAATTA
1 AGGTTATAACCTTTTTTTTATAATATGTAAATTA
*
361269 AGGTTATAGCC-TTTTTTT-TAATATGTAAATTA
1 AGGTTATAACCTTTTTTTTATAATATGTAAATTA
361301 AG
1 AG
361303 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 16 0.48
33 7 0.21
34 10 0.30
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.49
Consensus pattern (34 bp):
AGGTTATAACCTTTTTTTTATAATATGTAAATTA
Found at i:362118 original size:35 final size:34
Alignment explanation
Indices: 362054--362119 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
362044 ACAAATTATT
* * *
362054 TGTTACTGATATTGAGATGGGCTAAGGCCCAAAC
1 TGTTACTGATACTGAAAAGGGCTAAGGCCCAAAC
*
362088 TGTTACTGATACTGAAAAAGGGCTTAGGCCCA
1 TGTTACTGATACTG-AAAAGGGCTAAGGCCCA
362120 GGACTACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 13 0.48
35 14 0.52
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (34 bp):
TGTTACTGATACTGAAAAGGGCTAAGGCCCAAAC
Found at i:370169 original size:27 final size:27
Alignment explanation
Indices: 369813--370158 Score: 374
Period size: 27 Copynumber: 12.9 Consensus size: 27
369803 AAAATAACTA
* *
369813 AAATACCCCCATAGGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
** * *
369840 AAATACCCTTAGAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGATCG
* * * *
369867 AAATACCCTCATAGTGTAAAATAACCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
369894 AAATACCCCCATAGGGTAGAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
369921 AAATACCCCCATAAGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
369948 AAATACCCCCATAGGGTAAATTGACTC-
1 AAATACCCCCATAGGGTAAAATGA-TCG
* * *
369975 AAATA-CCCCTTAAGGT-AAATGACCG
1 AAATACCCCCATAGGGTAAAATGATCG
* *
370000 AAATACCCCCATAGGGTAGAATAATCG
1 AAATACCCCCATAGGGTAAAATGATCG
* * *
370027 AAATACCCTCATAGGGTAAAATGAACA
1 AAATACCCCCATAGGGTAAAATGATCG
* * * ** *
370054 AAATACTCCAATAGGGTAGAATGGCCA
1 AAATACCCCCATAGGGTAAAATGATCG
* *
370081 AAATACCCCCATAGGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
* *
370108 AAATACCCTCTTAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
370135 AAATACCCTCATAGGGTAAAATGA
1 AAATACCCCCATAGGGTAAAATGA
370159 CTATTATACC
Statistics
Matches: 269, Mismatches: 46, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
24 1 0.00
25 10 0.04
26 18 0.07
27 238 0.88
28 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATCG
Found at i:370240 original size:72 final size:71
Alignment explanation
Indices: 370127--370263 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
370117 CTTAGGGTAA
* * *
370127 AATGATCGAAATACCCTCATAGGGTAAAATGACTATTATACCCC-TAGGAGATGAAATAACTGTT
1 AATGATCGAAATACCCTCATAGGGTAAAATGACGATAATACCCCATAGG-G-TAAAATAACTGTT
370191 ATGGCTAG
64 ATGGCTAG
* * * *
370199 AATGATTGGAATACCTTCATAGGGTAAAATGACCGA-AATACCCCATAGGGTAAAATGACTGTTA
1 AATGATCGAAATACCCTCATAGGGTAAAATGA-CGATAATACCCCATAGGGTAAAATAACTGTTA
370263 T
65 T
370264 ACCCCTAGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
71 13 0.23
72 37 0.66
73 6 0.11
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (71 bp):
AATGATCGAAATACCCTCATAGGGTAAAATGACGATAATACCCCATAGGGTAAAATAACTGTTAT
GGCTAG
Found at i:370265 original size:26 final size:26
Alignment explanation
Indices: 370216--370290 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
370206 GGAATACCTT
* **
370216 CATAGGGTAAAATGACCGAAATACCC
1 CATAGGGTAAAATGACTGTTATACCC
370242 CATAGGGTAAAATGACTGTTATACCC
1 CATAGGGTAAAATGACTGTTATACCC
*
370268 C-TAGGAGATGAAATGACTGTTAT
1 CATAGG-G-TAAAATGACTGTTAT
370291 GACTTTATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 4 0.09
26 25 0.58
27 14 0.33
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (26 bp):
CATAGGGTAAAATGACTGTTATACCC
Found at i:370281 original size:98 final size:99
Alignment explanation
Indices: 370109--370291 Score: 314
Period size: 98 Copynumber: 1.9 Consensus size: 99
370099 AAATGACCAA
* *
370109 AATACCCTCTTAGGGTAAAATGATCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
1 AATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
370174 GAGATGAAATAACTGTTATGGCTAGAATGATTGG
66 GAGATGAAATAACTGTTATGGCTAGAATGATTGG
* *
370208 AATACCTTCATAGGGTAAAATGACCGAAATACCC-CATAGGGTAAAATGACTGTTATACCCCTAG
1 AATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
*
370272 GAGATGAAATGACTGTTATG
66 GAGATGAAATAACTGTTATG
370292 ACTTTATGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 48 0.61
99 31 0.39
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (99 bp):
AATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACTATTATACCCCTAG
GAGATGAAATAACTGTTATGGCTAGAATGATTGG
Found at i:374294 original size:107 final size:107
Alignment explanation
Indices: 374108--374304 Score: 304
Period size: 107 Copynumber: 1.8 Consensus size: 107
374098 CAAAAAATTA
* * *
374108 AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGTTTGGGTTGTCATCCCACTTCGCGTTAAAAGGG
1 AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGCCATCCCACTTCGCGTCAAAAGGG
374173 CCAAAACATTCTTAACCAAAAAAAATATAATAGTAAATTAGG
66 CCAAAACATTCTTAACCAAAAAAAATATAATAGTAAATTAGG
* * * *
374215 AGTGTGTTGGGCTTAGTAACCGGGGTGGGGTGCTTGGGTTGCCATTCCACTTTGCGTCAAAAGGG
1 AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGCCATCCCACTTCGCGTCAAAAGGG
* **
374280 CCAATACATTCTTAAGTAAAAAAAA
66 CCAAAACATTCTTAACCAAAAAAAA
374305 AATGAAGGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 80 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (107 bp):
AGTGTGTTAGGCTGAGTAACCGGGGTGGGGTGCTTGGGTTGCCATCCCACTTCGCGTCAAAAGGG
CCAAAACATTCTTAACCAAAAAAAATATAATAGTAAATTAGG
Found at i:374897 original size:11 final size:12
Alignment explanation
Indices: 374879--374907 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
374869 AATTTGAATT
374879 TTATTTTTAGGA
1 TTATTTTTAGGA
374891 TTATTTTTAGGA
1 TTATTTTTAGGA
374903 TTATT
1 TTATT
374908 ATATTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (12 bp):
TTATTTTTAGGA
Found at i:381997 original size:123 final size:122
Alignment explanation
Indices: 381830--382081 Score: 366
Period size: 123 Copynumber: 2.1 Consensus size: 122
381820 CTCAAAAACC
* *
381830 GAAGTCAACCGAAATCGCACCCTCAATTCCCTGAAGGCGCACCAACCAACCCTTGGTCTCCACCC
1 GAAGTCAACCAAAATCGCACCCTCAATTCCCTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
*
381895 AACTA-ACGAAAGAACATAGTGCAGTTTGGCAACACAAGAGAGAAC-GAATCGAAAAGAG
66 AAC-AGACGAAAGAACATAGTGCAATTTGGCAACACAAGAGAGAACAG-ATCGAAAAG-G
* * *
381953 GAAGTCAACCAAAATCGTACCCTCAATTCCTTGAAGATGCACCAACCAACCCTTGGTCTCCACCC
1 GAAGTCAACCAAAATCGCACCCTCAATTCCCTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
* * **
382018 AACAGATGAAAGAACGTAGTGCAATTTGGCAATGCAAGAGAGAACAGATCGAAAAGG
66 AACAGACGAAAGAACATAGTGCAATTTGGCAACACAAGAGAGAACAGATCGAAAAGG
382075 GAA-TCAA
1 GAAGTCAA
382082 AGACTAGCAG
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
121 4 0.03
122 5 0.04
123 107 0.91
124 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (122 bp):
GAAGTCAACCAAAATCGCACCCTCAATTCCCTGAAGACGCACCAACCAACCCTTGGTCTCCACCC
AACAGACGAAAGAACATAGTGCAATTTGGCAACACAAGAGAGAACAGATCGAAAAGG
Found at i:382609 original size:3 final size:3
Alignment explanation
Indices: 382601--382636 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
382591 TGTACTGTAC
382601 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
382637 TATAATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:383334 original size:15 final size:16
Alignment explanation
Indices: 383302--383336 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
383292 ACTTATACCG
383302 AAAATGAAATATTAAA
1 AAAATGAAATATTAAA
383318 AAAATGAAATATTAAA
1 AAAATGAAATATTAAA
383334 AAA
1 AAA
383337 GGCAAGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAATGAAATATTAAA
Found at i:385790 original size:26 final size:26
Alignment explanation
Indices: 385727--385801 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
385717 AACACACCAA
* * *
385727 TATCACAGCAAAACTGCCAGCAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
*
385753 TATCGCAACAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* * *
385779 TATCGTAGCAAAGTTACCAGTAA
1 TATCGCAGCAAAGCTGCCAGTAA
385802 CAATATACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:387409 original size:17 final size:17
Alignment explanation
Indices: 387387--387419 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
387377 CCCAAAACCG
387387 AAATGAGAAGTATACCA
1 AAATGAGAAGTATACCA
*
387404 AAATGAGCAGTATACC
1 AAATGAGAAGTATACC
387420 CCTTTGGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGAGAAGTATACCA
Found at i:389670 original size:50 final size:50
Alignment explanation
Indices: 389595--389788 Score: 298
Period size: 50 Copynumber: 3.9 Consensus size: 50
389585 ATATGGGTAA
389595 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
389645 AGAGGTCACATGTAAGACCATGTCTGGGACATGGCGTTGGCATCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
389695 AAAGGTCCCATGTAAGACCATGTGTGGGACATAGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
389745 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACC
389789 AATATTTGAA
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 128 1.00
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:393082 original size:3 final size:3
Alignment explanation
Indices: 393074--393100 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
393064 TGTACTGCAC
393074 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
393101 AATATTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:395529 original size:18 final size:17
Alignment explanation
Indices: 395487--395534 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
395477 TGTCGTTCGT
395487 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
395504 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
395523 TTTCAAAACATT
1 TTTCAAAACATT
395535 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:400807 original size:34 final size:36
Alignment explanation
Indices: 400753--400822 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
400743 CCTCATTTTA
* *
400753 CTTTCTTTTCCTTTTCTTTTTTCTTC-TGGCCGAAC
1 CTTTCTTCTCCTTCTCTTTTTTCTTCTTGGCCGAAC
400788 CTTTCTTCT-CTTCTCTTTTTTCTTCTTTGGCCGAA
1 CTTTCTTCTCCTTCTCTTTTTTCTTC-TTGGCCGAA
400823 TAATCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 15 0.48
35 8 0.26
36 8 0.26
ACGTcount: A:0.06, C:0.29, G:0.09, T:0.57
Consensus pattern (36 bp):
CTTTCTTCTCCTTCTCTTTTTTCTTCTTGGCCGAAC
Found at i:401505 original size:27 final size:27
Alignment explanation
Indices: 401475--401716 Score: 250
Period size: 27 Copynumber: 9.0 Consensus size: 27
401465 CCGTAATGGG
*
401475 ACCGAAATACCCTCGAAGGGTAAAATT
1 ACCGAAATACCCTCGAAAGGTAAAATT
* * *
401502 ACCGAAATACCTTCGAATGGTAGAATT
1 ACCGAAATACCCTCGAAAGGTAAAATT
* * *
401529 ACTGAAATACCCTTGAAAGTTAAAATT
1 ACCGAAATACCCTCGAAAGGTAAAATT
** *
401556 AGTGAAATACCCTTGAAAGGTAAAATT
1 ACCGAAATACCCTCGAAAGGTAAAATT
* * *
401583 ACCAAAATACTCTCGAAGGGTAAAATT
1 ACCGAAATACCCTCGAAAGGTAAAATT
* * *
401610 ATCGAAATACCCCCGAAAGGTAAAATG
1 ACCGAAATACCCTCGAAAGGTAAAATT
* **
401637 ATCGAAATACCCTTAAAAGGTAAAATT
1 ACCGAAATACCCTCGAAAGGTAAAATT
** * * *
401664 ACAAAAATACCCCCGAAGGGTAAAATG
1 ACCGAAATACCCTCGAAAGGTAAAATT
* *
401691 ACCGAAATACCCTTGTAAGGTAAAAT
1 ACCGAAATACCCTCGAAAGGTAAAAT
401717 GATCGTTATA
Statistics
Matches: 174, Mismatches: 41, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 174 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (27 bp):
ACCGAAATACCCTCGAAAGGTAAAATT
Found at i:401617 original size:81 final size:79
Alignment explanation
Indices: 401477--401730 Score: 294
Period size: 81 Copynumber: 3.1 Consensus size: 79
401467 GTAATGGGAC
* * * * *
401477 CGAAATACCCTCGAAGGGTAAAATTACCGAAATACCTTCGAATGGTAGAATTACTGAAATACCCT
1 CGAAATACCCTTGAAAGGTAAAATTACCAAAATACC-TCGAAGGGTAAAATTAC-GAAATACCCT
* *
401542 TGAAAGTTAAAATTAGT
64 TGAAAGGTAAAATGA-T
*
401559 -GAAATACCCTTGAAAGGTAAAATTACCAAAATACTCTCGAAGGGTAAAATTATCGAAATACCCC
1 CGAAATACCCTTGAAAGGTAAAATTACCAAAATAC-CTCGAAGGGTAAAATTA-CGAAATACCCT
*
401623 CGAAAGGTAAAATGAT
64 TGAAAGGTAAAATGAT
* * * *
401639 CGAAATACCCTTAAAAGGTAAAATTACAAAAATACCCCCGAAGGGTAAAATGACCGAAATACCCT
1 CGAAATACCCTTGAAAGGTAAAATTACCAAAATA-CCTCGAAGGGTAAAATTA-CGAAATACCCT
*
401704 TGTAAGGTAAAATGAT
64 TGAAAGGTAAAATGAT
**
401720 CGTTATACCCT
1 CGAAATACCCT
401731 AGGAGATGAA
Statistics
Matches: 149, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.01
81 145 0.97
82 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (79 bp):
CGAAATACCCTTGAAAGGTAAAATTACCAAAATACCTCGAAGGGTAAAATTACGAAATACCCTTG
AAAGGTAAAATGAT
Found at i:402140 original size:28 final size:28
Alignment explanation
Indices: 402091--402178 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
402081 ACTGCATTTT
* *
402091 ACTGATTATTGTATTGGGCTAAAGCTCAC
1 ACTG-TTACTGTATTGGGCTAAAGCCCAC
* *
402120 ATTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAAGCCCAC
* *
402148 ACTGTTACTGTAATGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAAGCCCAC
402176 ACT
1 ACT
402179 ATACTGATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 50 0.94
29 3 0.06
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAAGCCCAC
Found at i:402199 original size:33 final size:28
Alignment explanation
Indices: 402095--402212 Score: 85
Period size: 28 Copynumber: 4.0 Consensus size: 28
402085 CATTTTACTG
* * * * *
402095 ATTATTGTATTGGGCTAAAGCTCACATT
1 ATTACTGTATAGGGCTAAGGCCCACACT
* *
402123 GTTACTGTATTGGGCTAAGGCCCACACT
1 ATTACTGTATAGGGCTAAGGCCCACACT
*
402151 GTTACTGTA-ATGGGCTAAGGCCCACACT
1 ATTACTGTATA-GGGCTAAGGCCCACACT
* *
402179 ATACTGATTCTGTATAGGGCTCAGGCCCAGACT
1 AT--T-A--CTGTATAGGGCTAAGGCCCACACT
402212 A
1 A
402213 ATTCTGCATG
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
28 50 0.68
30 1 0.01
31 1 0.01
33 21 0.28
34 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (28 bp):
ATTACTGTATAGGGCTAAGGCCCACACT
Found at i:402268 original size:40 final size:40
Alignment explanation
Indices: 402213--402289 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
402203 GCCCAGACTA
*
402213 ATTCTGCATGTTGCATAGTGAATAGCTAGTAGGGGATCTG
1 ATTCTGCATGATGCATAGTGAATAGCTAGTAGGGGATCTG
* *
402253 ATTCTGCATGATGCATAGTGATTGGCTAGTAGGGGAT
1 ATTCTGCATGATGCATAGTGAATAGCTAGTAGGGGAT
402290 TACACATTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.32
Consensus pattern (40 bp):
ATTCTGCATGATGCATAGTGAATAGCTAGTAGGGGATCTG
Found at i:404634 original size:18 final size:16
Alignment explanation
Indices: 404611--404644 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
404601 TGAGTGTTGC
404611 ATTTTAATCCTTCATTTT
1 ATTTTAAT--TTCATTTT
404629 ATTTTAATTTCATTTT
1 ATTTTAATTTCATTTT
404645 TTCCCGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTAATTTCATTTT
Found at i:404726 original size:3 final size:3
Alignment explanation
Indices: 404718--404800 Score: 94
Period size: 3 Copynumber: 27.0 Consensus size: 3
404708 TTAGTTTAAG
* * *
404718 ATT ATT ATT GATTT AGT ATC ATT ATT ATT ATT ATT ATT ATT ATT AGT
1 ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** *
404765 ATT ATT ATT ATT ATT ATT GGT ATT ATT ATT CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
404801 TTTTTATTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
3 62 0.94
4 2 0.03
5 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:405106 original size:4 final size:4
Alignment explanation
Indices: 405097--405168 Score: 144
Period size: 4 Copynumber: 18.0 Consensus size: 4
405087 ATATTAAATT
405097 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
405145 ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC
405169 TCTATTGTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:405250 original size:29 final size:28
Alignment explanation
Indices: 405217--405291 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
405207 CTTTTTTAAA
*
405217 TATTTTAATATCTTTAATCTATTTCAACT
1 TATTTTAATAT-TTTAATCTATTTAAACT
* * *
405246 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTTAATATT-TTAATCTATTTAAACT
*
405275 TATTTTAACATTTTAAT
1 TATTTTAATATTTTAAT
405292 TTATATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.57
Consensus pattern (28 bp):
TATTTTAATATTTTAATCTATTTAAACT
Found at i:409783 original size:21 final size:20
Alignment explanation
Indices: 409757--409800 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
409747 TTAACTGGAC
*
409757 TGATAAGCAGCAAGAAAGTTT
1 TGATAAACAG-AAGAAAGTTT
**
409778 TGATAAATTGAAGAAAGTTT
1 TGATAAACAGAAGAAAGTTT
409798 TGA
1 TGA
409801 CTGAGGCCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (20 bp):
TGATAAACAGAAGAAAGTTT
Found at i:412955 original size:71 final size:71
Alignment explanation
Indices: 412839--412977 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
412829 TTCGTGGAAA
*
412839 TAGAACTTTTCTTGTAAACATGTGTGTAATCACACCCTTTCTCAACTGCAAATCGGTAAAAGCCG
1 TAGAACTCTTCTTGTAAACATGTGTGTAATCACACCCTTTCTCAACTGCAAATCGGTAAAAGCCG
412904 AAAAAC
66 AAAAAC
412910 TAGAACTCTTCTTGTAAACATGTGTGTAATCACACCCTTTCTCAACTGCAAATCGGTAAAAGCCG
1 TAGAACTCTTCTTGTAAACATGTGTGTAATCACACCCTTTCTCAACTGCAAATCGGTAAAAGCCG
412975 AAA
66 AAA
412978 GCTAGAAAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (71 bp):
TAGAACTCTTCTTGTAAACATGTGTGTAATCACACCCTTTCTCAACTGCAAATCGGTAAAAGCCG
AAAAAC
Found at i:413264 original size:54 final size:54
Alignment explanation
Indices: 413108--413334 Score: 253
Period size: 54 Copynumber: 4.2 Consensus size: 54
413098 TAATGGGACC
* *
413108 GAAATA-CCTTGAAAGGTAAAATTATCGAAATACCCTCAAAGGGTAAAAGTACT
1 GAAATACCCTCGAAAGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACT
* * * * **
413161 TAAATGCCCTCGAAGGGTACTTAAATTATCGAAATTCCCTTGAAGGGTAAAATTACT
1 GAAATACCCTCGAAAGGTA---AAATTATCGAAATACCCTCAAAGGGTAAAATTACT
*
413218 GAAATACCTTCGAAAGGTAAAATTATCGAAATACCCTCGAAA-GGTAAAATTACT
1 GAAATACCCTCGAAAGGTAAAATTATCGAAATACCCTC-AAAGGGTAAAATTACT
* * * * *
413272 AAAATACCCTCGAAGGGTAAAATGACCGAAATACCC-CAAAGGGTAAAATGACT
1 GAAATACCCTCGAAAGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACT
**
413325 GTTATACCCT
1 GAAATACCCT
413335 AGGAGATGAA
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
52 3 0.02
53 23 0.16
54 70 0.49
55 2 0.01
57 46 0.32
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (54 bp):
GAAATACCCTCGAAAGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACT
Found at i:413323 original size:26 final size:27
Alignment explanation
Indices: 413105--413320 Score: 188
Period size: 27 Copynumber: 8.0 Consensus size: 27
413095 TCGTAATGGG
* *
413105 ACCGAAATACCTTGAAA-GGTAAAATT
1 ACCGAAATACCCTCAAAGGGTAAAATT
* *
413131 ATCGAAATACCCTCAAAGGGTAAAAGT
1 ACCGAAATACCCTCAAAGGGTAAAATT
** * *
413158 ACTTAAATGCCCTCGAAGGGTACTTAAATT
1 ACCGAAATACCCTCAAAGGGTA---AAATT
* * **
413188 ATCGAAATTCCCTTGAAGGGTAAAATT
1 ACCGAAATACCCTCAAAGGGTAAAATT
* *
413215 ACTGAAATACCTTCGAAA-GGTAAAATT
1 ACCGAAATACCCTC-AAAGGGTAAAATT
*
413242 ATCGAAATACCCTCGAAA-GGTAAAATT
1 ACCGAAATACCCTC-AAAGGGTAAAATT
** * *
413269 ACTAAAATACCCTCGAAGGGTAAAATG
1 ACCGAAATACCCTCAAAGGGTAAAATT
413296 ACCGAAATACCC-CAAAGGGTAAAAT
1 ACCGAAATACCCTCAAAGGGTAAAAT
413321 GACTGTTATA
Statistics
Matches: 152, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
26 28 0.18
27 101 0.66
28 2 0.01
30 21 0.14
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.23
Consensus pattern (27 bp):
ACCGAAATACCCTCAAAGGGTAAAATT
Found at i:413542 original size:26 final size:26
Alignment explanation
Indices: 413513--413588 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
413503 ATGCCACATA
*
413513 TACTGTTACTGGTAGCTTTGCTGCGT
1 TACTGTTACTGGAAGCTTTGCTGCGT
*
413539 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGAAGCTTTGCTGCGT
* * *
413565 TATTATTACTGGAAGCTTTACTGC
1 TACTGTTACTGGAAGCTTTGCTGC
413589 AATATTGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (26 bp):
TACTGTTACTGGAAGCTTTGCTGCGT
Found at i:413594 original size:26 final size:26
Alignment explanation
Indices: 413544--413594 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
413534 TGCGTTACTG
* * **
413544 TTACTGGCAGCTTTGCTGCGTTATTA
1 TTACTGGAAGCTTTACTGCAATATTA
413570 TTACTGGAAGCTTTACTGCAATATT
1 TTACTGGAAGCTTTACTGCAATATT
413595 GGTGTGTTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (26 bp):
TTACTGGAAGCTTTACTGCAATATTA
Found at i:413725 original size:28 final size:28
Alignment explanation
Indices: 413676--413768 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 28
413666 ACTGCATTGT
*
413676 ACTGATTACTGTATT-AGGCTAAAGCCCAC
1 ACTG-TTATTGTATTGA-GCTAAAGCCCAC
* * *
413705 ATTGTTATTGTATTGAGCTAATG-CCAT
1 ACTGTTATTGTATTGAGCTAAAGCCCAC
* * * *
413732 ACTGTTACTGTAATGGGCTAAGGCCCAC
1 ACTGTTATTGTATTGAGCTAAAGCCCAC
413760 ACTG-TATTG
1 ACTGTTATTG
413769 ATACTATATA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
27 25 0.49
28 22 0.43
29 4 0.08
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (28 bp):
ACTGTTATTGTATTGAGCTAAAGCCCAC
Found at i:413751 original size:27 final size:28
Alignment explanation
Indices: 413675--413764 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
413665 CACTGCATTG
*
413675 TACTGATTACTGTATTAGGCTAAAGCCCA
1 TACTG-TTACTGTATTGGGCTAAAGCCCA
* * * * *
413704 CATTGTTATTGTATTGAGCTAATG-CCA
1 TACTGTTACTGTATTGGGCTAAAGCCCA
* *
413731 TACTGTTACTGTAATGGGCTAAGGCCCA
1 TACTGTTACTGTATTGGGCTAAAGCCCA
*
413759 CACTGT
1 TACTGT
413765 ATTGATACTA
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
27 21 0.45
28 23 0.49
29 3 0.06
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (28 bp):
TACTGTTACTGTATTGGGCTAAAGCCCA
Found at i:429337 original size:17 final size:18
Alignment explanation
Indices: 429315--429349 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
429305 ATTTGGGTCA
429315 TGTGGG-CCAAACGGGCG
1 TGTGGGCCCAAACGGGCG
*
429332 TGTGGGCCCACACGGGCG
1 TGTGGGCCCAAACGGGCG
429350 AACATCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.29, G:0.46, T:0.11
Consensus pattern (18 bp):
TGTGGGCCCAAACGGGCG
Found at i:431310 original size:24 final size:23
Alignment explanation
Indices: 431270--431316 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
431260 CCATGACAAA
*
431270 TTTATTTCAGATGCAGAAAAAAT
1 TTTATTTCAGATACAGAAAAAAT
* *
431293 TTTAGTTTCATATACAGAACAAAT
1 TTTA-TTTCAGATACAGAAAAAAT
431317 CATAGTCAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (23 bp):
TTTATTTCAGATACAGAAAAAAT
Found at i:432723 original size:27 final size:27
Alignment explanation
Indices: 432693--432744 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
432683 AATGAAGAAG
* *
432693 AGAATTAAAGAATCAAAAAA-AAAAGGA
1 AGAATGAAAAAAT-AAAAAATAAAAGGA
432720 AGAATGAAAAAATAAAAAATAAAAG
1 AGAATGAAAAAATAAAAAATAAAAG
432745 ACAGTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.12
Consensus pattern (27 bp):
AGAATGAAAAAATAAAAAATAAAAGGA
Found at i:435387 original size:6 final size:6
Alignment explanation
Indices: 435376--435401 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
435366 TTTTTCTTAA
435376 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
435402 CCCAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:436296 original size:66 final size:66
Alignment explanation
Indices: 436218--436350 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
436208 CAAACCCCAC
436218 CCCAACCAGATATATATTCAAAATTACCATGCTTACATGCTCATATACATATATCAAGTAAATAT
1 CCCAACCAGATATATATTCAAAATTACCATGCTTACATGCTCATATACATATATCAAGTAAATAT
436283 A
66 A
* * * *
436284 CCCAATCAGATATATATTCAAAATTATCATGCTTACATGCTCATTTACATATATCAAGTAAGTAT
1 CCCAACCAGATATATATTCAAAATTACCATGCTTACATGCTCATATACATATATCAAGTAAATAT
436349 A
66 A
436350 C
1 C
436351 ACGGACATGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (66 bp):
CCCAACCAGATATATATTCAAAATTACCATGCTTACATGCTCATATACATATATCAAGTAAATAT
A
Found at i:438934 original size:19 final size:20
Alignment explanation
Indices: 438910--438956 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
438900 ATAATAAATA
* *
438910 TTTATTTTTTTATAT-TTTT
1 TTTATTTTTTGAAATATTTT
438929 TTTA-TTTTTGAAATATTTT
1 TTTATTTTTTGAAATATTTT
438948 TTTATTTTT
1 TTTATTTTT
438957 AAAATGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTATTTTTTGAAATATTTT
Found at i:438961 original size:19 final size:19
Alignment explanation
Indices: 438925--438961 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
438915 TTTTTTATAT
*
438925 TTTTTTTATTTTTGAAATA
1 TTTTTTTATTTTTAAAATA
438944 TTTTTTTATTTTTAAAAT
1 TTTTTTTATTTTTAAAAT
438962 GAATTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTTTATTTTTAAAATA
Found at i:446599 original size:16 final size:16
Alignment explanation
Indices: 446578--446609 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
446568 TCACACATGC
446578 CTGTGTGGCCCACACG
1 CTGTGTGGCCCACACG
*
446594 CTGTGTGGTCCACACG
1 CTGTGTGGCCCACACG
446610 GCCCAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.34, G:0.31, T:0.22
Consensus pattern (16 bp):
CTGTGTGGCCCACACG
Found at i:448396 original size:5 final size:5
Alignment explanation
Indices: 448345--448435 Score: 78
Period size: 5 Copynumber: 17.4 Consensus size: 5
448335 TTAGTTTTAT
* * * *
448345 TTTTC CTTTC TTTT- TTTATC GTTTC TCTTTC GTTCC TTTTTC TTTTTC
1 TTTTC TTTTC TTTTC TTT-TC TTTTC T-TTTC TTTTC -TTTTC -TTTTC
448393 TTTTC TTTTC TTCATT- TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TT--TTC TTTTC TTTTC TTTTC TTTTC TTTTC TT
448436 CCTTGGATTG
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 5 0.07
5 47 0.66
6 17 0.24
7 2 0.03
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:448432 original size:21 final size:21
Alignment explanation
Indices: 448345--448435 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
448335 TTAGTTTTAT
* *
448345 TTTTCCTTTCTTTT-TTTATC
1 TTTTCTTTTCTTTTCTTTTTC
* * *
448365 GTTTCTCTTTCGTTCCTTTTTC
1 TTTTCT-TTTCTTTTCTTTTTC
*
448387 TTTTTCTTTTCTTTTCTTCATT-
1 -TTTTCTTTTCTTTTCTT-TTTC
448409 TTTTCTTTTCTTTTC-TTTTC
1 TTTTCTTTTCTTTTCTTTTTC
448429 TTTTCTT
1 TTTTCTT
448436 CCTTGGATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.04
20 12 0.21
21 21 0.38
22 14 0.25
23 7 0.12
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTTTTCTTTTCTTTTTC
Found at i:450298 original size:27 final size:28
Alignment explanation
Indices: 450249--450313 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
450239 TTTTTTATTT
*
450249 CTTTTT-TTTATCGTTTCTCTTTCGTTC-
1 CTTTTTCTTTTTCGTTTCTCTTTC-TTCA
*
450276 CTTTTTCTTTTTCTTTTCT-TTTCTTCA
1 CTTTTTCTTTTTCGTTTCTCTTTCTTCA
*
450303 TTTTTTCTTTT
1 CTTTTTCTTTT
450314 CTTCCTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 20 0.61
28 10 0.30
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.74
Consensus pattern (28 bp):
CTTTTTCTTTTTCGTTTCTCTTTCTTCA
Found at i:450299 original size:16 final size:15
Alignment explanation
Indices: 450246--450316 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 15
450236 TTATTTTTTA
*
450246 TTTCTTTTTTTTATCG
1 TTTCTTTTTTTT-TCT
** *
450262 TTTCTCTTTCGTTCCTT
1 TTTCT-TTTTTTTTC-T
450279 TTTCTTTTTCTTTTCT
1 TTTCTTTTT-TTTTCT
*
450295 TTTCTTCATTTTTTCT
1 TTTCTT-TTTTTTTCT
450311 TTTCTT
1 TTTCTT
450317 CCTTGGATTG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
16 28 0.65
17 15 0.35
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTTTTTCT
Found at i:459665 original size:5 final size:5
Alignment explanation
Indices: 459614--459705 Score: 62
Period size: 5 Copynumber: 17.4 Consensus size: 5
459604 TTAGTTTTAT
* * * *
459614 TTTTC CTTTC TTTT- TTTATC GTTTC TCTTTC GTTCC TTTTTC TTTTTC
1 TTTTC TTTTC TTTTC TTT-TC TTTTC T-TTTC TTTTC -TTTTC -TTTTC
*
459662 TTTTC TTTTC TTCATT- TTTTC TTTTC TTTTTT TTTTC TTTTC TT
1 TTTTC TTTTC TT--TTC TTTTC TTTTC -TTTTC TTTTC TTTTC TT
459706 CCTTGGATTG
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
4 5 0.07
5 41 0.59
6 21 0.30
7 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:459665 original size:11 final size:11
Alignment explanation
Indices: 459651--459702 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
459641 TTTCGTTCCT
459651 TTTTCTTTTTC
1 TTTTCTTTTTC
459662 TTTTC-TTTTC
1 TTTTCTTTTTC
*
459672 TTCAT-TTTTTC
1 TT-TTCTTTTTC
*
459683 TTTTCTTTTTT
1 TTTTCTTTTTC
459694 TTTTCTTTT
1 TTTTCTTTT
459703 CTTCCTTGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 8 0.23
11 27 0.77
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:459702 original size:21 final size:21
Alignment explanation
Indices: 459635--459705 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
459625 TTTTTTATCG
* *
459635 TTTCTCTTTCGTTCCTTTTTCTT
1 TTTCT-TTTCTTTTCTTTTT-TT
**
459658 TTTCTTTTCTTTTCTTCATTT
1 TTTCTTTTCTTTTCTTTTTTT
459679 TTTCTTTTCTTTT-TTTTTTCT
1 TTTCTTTTCTTTTCTTTTTT-T
459700 TTTCTT
1 TTTCTT
459706 CCTTGGATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 4 0.10
21 22 0.54
22 10 0.24
23 5 0.12
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCTTTTCTTTTTTT
Found at i:463431 original size:27 final size:26
Alignment explanation
Indices: 463390--463585 Score: 119
Period size: 27 Copynumber: 7.3 Consensus size: 26
463380 GAGAGGTCAA
* * *
463390 TAAAATGATCAAATTACCTCCATAGTG
1 TAAAATGACCAAATTACC-CCACAGGG
*
463417 TAAAATGACCGAATTACACCCACAGGG
1 TAAAATGACCAAATTAC-CCCACAGGG
* **
463444 TAAAATGACTAAATTACCCTCAC-GACA
1 TAAAATGACCAAATTACCC-CACAG-GG
* *
463471 TAAAATGATCAAATTACTCCTACAGGG
1 TAAAATGACCAAATTAC-CCCACAGGG
* *
463498 TAAAATGATCGAAA-TACCCCTGA-AGGA
1 TAAAATGA-CCAAATTACCCC--ACAGGG
* * * *
463525 TAAACTAACCAAAATACCCCCAAAGGG
1 TAAAATGACCAAATTA-CCCCACAGGG
* * *
463552 TAAAATGACTAAAATACCCCCATAGGG
1 TAAAATGACCAAATTA-CCCCACAGGG
463579 TAAAATG
1 TAAAATG
463586 GTTGTTATAC
Statistics
Matches: 133, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
26 10 0.08
27 111 0.83
28 12 0.09
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (26 bp):
TAAAATGACCAAATTACCCCACAGGG
Found at i:463458 original size:54 final size:53
Alignment explanation
Indices: 463390--463585 Score: 143
Period size: 54 Copynumber: 3.6 Consensus size: 53
463380 GAGAGGTCAA
*
463390 TAAAATGA-TCAAATTACCTCCATAGTGTAAAATGACCGAATTACACCCACAGGG
1 TAAAATGACT-AAATTACCTCCATAG-GTAAAATGACCAAATTACACCCACAGGG
* * * *
463444 TAAAATGACTAAATTACCCTCACGACA--TAAAATGATCAAATTACTCCTACAGGG
1 TAAAATGACTAAATTA-CCTC-C-ATAGGTAAAATGACCAAATTACACCCACAGGG
* * * * * *
463498 TAAAATGATCGAAA-TACC-CC-TGAAGGATAAACTAACCAAAATACCCCCAAAGGG
1 TAAAATGA-CTAAATTACCTCCAT--AGG-TAAAATGACCAAATTACACCCACAGGG
* *
463552 TAAAATGACTAAAATACCCCCATAGGGTAAAATG
1 TAAAATGACTAAATTACCTCCATA-GGTAAAATG
463586 GTTGTTATAC
Statistics
Matches: 111, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
51 2 0.02
52 1 0.01
53 6 0.05
54 85 0.77
55 13 0.12
56 2 0.02
57 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (53 bp):
TAAAATGACTAAATTACCTCCATAGGTAAAATGACCAAATTACACCCACAGGG
Found at i:463543 original size:81 final size:81
Alignment explanation
Indices: 463389--463543 Score: 181
Period size: 81 Copynumber: 1.9 Consensus size: 81
463379 TGAGAGGTCA
* * * * * *
463389 ATAAAATGATCAAATTACCTCCATAGTGTAAAATGACCGAATTACACCCACAGGGTAAAATGACT
1 ATAAAATGATCAAATTACCTCCACAGGGTAAAATGACCGAAATACACCCACAGGATAAAATAACC
*
463454 AAATTACCCTCACGAC
66 AAAATACCCTCACGAC
* *
463470 ATAAAATGATCAAATTA-CTCCTACAGGGTAAAATGATCGAAATAC-CCCTGA-AGGATAAACTA
1 ATAAAATGATCAAATTACCTCC-ACAGGGTAAAATGACCGAAATACACCC--ACAGGATAAAATA
463532 ACCAAAATACCC
63 ACCAAAATACCC
463544 CCAAAGGGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
80 7 0.11
81 54 0.87
82 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (81 bp):
ATAAAATGATCAAATTACCTCCACAGGGTAAAATGACCGAAATACACCCACAGGATAAAATAACC
AAAATACCCTCACGAC
Found at i:464032 original size:28 final size:28
Alignment explanation
Indices: 463992--464099 Score: 171
Period size: 28 Copynumber: 3.9 Consensus size: 28
463982 ACTGTACTGA
*
463992 TACTGTATTGGGCTAATGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
464020 TACTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
464048 TACTATTTTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
464076 TACTGTATTTGGCTAAAGCCCACA
1 TACTGTATTGGGCTAAGGCCCACA
464100 CTATACGGTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:466912 original size:8 final size:8
Alignment explanation
Indices: 466901--466929 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
466891 TATATATATA
466901 TATTCACC
1 TATTCACC
466909 TATTCACC
1 TATTCACC
466917 TATTCACC
1 TATTCACC
466925 T-TTCA
1 TATTCA
466930 AATTTTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (8 bp):
TATTCACC
Found at i:467093 original size:76 final size:75
Alignment explanation
Indices: 466967--467177 Score: 309
Period size: 74 Copynumber: 2.8 Consensus size: 75
466957 TATCCGTTAT
* * * * *
466967 CGGTGGATTCAGCACTTAGCAACCACGAGTG-ATGCGGGGGATGAGCACTTAGCAACCCCTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAAT-CGGGGAATCAGCACTTAGCAACCCCTTTCA
467031 CATTCAATGATA
65 CATTCAA-GATA
467043 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
467107 ATTTAAGATA
66 ATTCAAGATA
* * *
467117 CGGTGGGATCAACATTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
467178 GGGGGAATCA
Statistics
Matches: 124, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
74 56 0.45
75 19 0.15
76 47 0.38
77 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAAGATA
Found at i:467230 original size:102 final size:102
Alignment explanation
Indices: 467078--467321 Score: 427
Period size: 102 Copynumber: 2.4 Consensus size: 102
467068 CCAATGAATC
* * * *
467078 GGGGAATCAGCACTTAGCAA-CCCTTTCACATTTAAGATACGGTGGGATCAACATTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
467142 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
467179 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
467244 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
**
467281 GCCGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
467322 TCCGGCCTAT
Statistics
Matches: 136, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 20 0.15
102 116 0.85
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:470984 original size:6 final size:6
Alignment explanation
Indices: 470969--470997 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
470959 AGAAATTTTG
470969 TTAA-T TTAATT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT
470998 CTGTGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:471222 original size:8 final size:8
Alignment explanation
Indices: 471205--471256 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
471195 CTTTCGTTCC
471205 TTTTTC-T
1 TTTTTCTT
471212 TTTTTCTT
1 TTTTTCTT
471220 TTTTTCTT
1 TTTTTCTT
471228 CATTTTT-TT
1 --TTTTTCTT
*
471237 CTTTTCTT
1 TTTTTCTT
*
471245 TTCTTCTT
1 TTTTTCTT
471253 TTTT
1 TTTT
471257 CTTCCTTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
7 10 0.27
8 20 0.54
9 2 0.05
10 5 0.14
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:471233 original size:25 final size:25
Alignment explanation
Indices: 471196--471252 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
471186 ATCGTTTCTC
*
471196 TTTCGTTCCTTTTTCTT-TTTTCTTTT
1 TTTC-TTCATTTTT-TTCTTTTCTTTT
471222 TTTCTTCATTTTTTTCTTTTCTTTT
1 TTTCTTCATTTTTTTCTTTTCTTTT
*
471247 CTTCTT
1 TTTCTT
471253 TTTTCTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.79
26 4 0.14
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTCTTCATTTTTTTCTTTTCTTTT
Found at i:471236 original size:22 final size:21
Alignment explanation
Indices: 471211--471256 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
471201 TTCCTTTTTC
471211 TTTTTTC-TTT-TTTTCTTCAT
1 TTTTTTCTTTTCTTTTCTTC-T
471231 TTTTTTCTTTTCTTTTCTTCT
1 TTTTTTCTTTTCTTTTCTTCT
471252 TTTTT
1 TTTTT
471257 CTTCCTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 9 0.38
22 8 0.33
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTCTTTTCTTTTCTTCT
Found at i:471257 original size:20 final size:19
Alignment explanation
Indices: 471208--471259 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
471198 TCGTTCCTTT
471208 TTCTTTTTTC-TTTTTTTC
1 TTCTTTTTTCTTTTTTTTC
471226 TTCATTTTTTTCTTTTCTTTTC
1 TTC--TTTTTTCTTTT-TTTTC
471248 TTCTTTTTTCTT
1 TTCTTTTTTCTT
471260 CCTTGGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
20 16 0.53
21 3 0.10
22 8 0.27
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (19 bp):
TTCTTTTTTCTTTTTTTTC
Found at i:475617 original size:16 final size:17
Alignment explanation
Indices: 475596--475629 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
475586 ACAAAATTAT
*
475596 TAGTAA-AAGGTTAATA
1 TAGTAATAAGGTAAATA
475612 TAGTAATAAGGTAAATA
1 TAGTAATAAGGTAAATA
475629 T
1 T
475630 TAACTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGTAATAAGGTAAATA
Found at i:476556 original size:42 final size:42
Alignment explanation
Indices: 476502--476601 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
476492 CTATATGAAC
* *
476502 GGCACTACGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
* *
476544 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGTATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
476586 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
476602 TACCGAGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
Found at i:483939 original size:22 final size:21
Alignment explanation
Indices: 483909--483975 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
483899 TTTTTATTTT
483909 AAAA-ATTTTAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
***
483929 AAAAGTATTTTAAAAATATTTTT
1 AAAA-TATTTTAAAAA-ATTAAA
483952 AAAATATTTT--AAAATTAAA
1 AAAATATTTTAAAAAATTAAA
483971 AAAAT
1 AAAAT
483976 TAAAAAAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 8 0.21
20 7 0.18
22 16 0.42
23 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
AAAATATTTTAAAAAATTAAA
Found at i:483980 original size:8 final size:9
Alignment explanation
Indices: 483962--484053 Score: 51
Period size: 9 Copynumber: 9.4 Consensus size: 9
483952 AAAATATTTT
483962 AAAATTAAA
1 AAAATTAAA
483971 AAAATTAAAA
1 AAAATT-AAA
***
483981 AAAAGTATTTT
1 AAAA-T-TAAA
483992 AAAATTAAA
1 AAAATTAAA
484001 AAAATTAAAA
1 AAAATT-AAA
484011 AAAGTATTTTAAA
1 AAA--A--TTAAA
* **
484024 AATATT-TT
1 AAAATTAAA
484032 AAAATTAAA
1 AAAATTAAA
484041 AAAATTAAA
1 AAAATTAAA
484050 AAAA
1 AAAA
484054 AGTATTTTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
8 5 0.08
9 28 0.45
10 14 0.23
11 6 0.10
12 2 0.03
13 5 0.08
14 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATTAAA
Found at i:483984 original size:29 final size:29
Alignment explanation
Indices: 483952--484024 Score: 128
Period size: 30 Copynumber: 2.5 Consensus size: 29
483942 AAATATTTTT
483952 AAAATATTTTAAAATTAAAAAAATTAAAA
1 AAAATATTTTAAAATTAAAAAAATTAAAA
483981 AAAAGTATTTTAAAATTAAAAAAATTAAAA
1 AAAA-TATTTTAAAATTAAAAAAATTAAAA
*
484011 AAAGTATTTTAAAA
1 AAAATATTTTAAAA
484025 ATATTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 14 0.33
30 28 0.67
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATATTTTAAAATTAAAAAAATTAAAA
Found at i:483984 original size:40 final size:40
Alignment explanation
Indices: 483904--484130 Score: 271
Period size: 40 Copynumber: 5.6 Consensus size: 40
483894 GCCCATTTTT
*
483904 ATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAAT
1 ATTTT-AAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAAT
*** ***
483946 ATTTTTAAAATATTTTAAAATTAAAAAAA-T-TAAAAAAAAGT
1 A-TTTTAAAAT-TAAAAAAATTAAAAAAAGTATTTTAAAAA-T
483987 ATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAT
1 ATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAT
484027 ATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAAT
1 ATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAAAT
* * *
484068 ATTTTAAAATTTAAAAAAATT-TAAAAAGTATGTAAAAAAT
1 ATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAAT
*
484108 ATTTTAAAATTAAAAAAAATAAA
1 ATTTTAAAATTAAAAAAATTAAA
484131 TATATTTATT
Statistics
Matches: 161, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
39 24 0.15
40 63 0.39
41 39 0.24
42 31 0.19
43 4 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
ATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAT
Found at i:484009 original size:81 final size:82
Alignment explanation
Indices: 483903--484130 Score: 286
Period size: 81 Copynumber: 2.8 Consensus size: 82
483893 GGCCCATTTT
* ***
483903 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATTTTAAAATT
1 TATTTT-AAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATA-TTTTAAAAT-TAAAAAAATT
483968 -AAAAAAA-T-TAAAAAAAA
63 AAAAAAAAGTATAAAAAAAA
483985 GTATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
1 -TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
***
484049 AAAAAAGTATTTTAAAAA
65 AAAAAAGTATAAAAAAAA
* * * *
484067 TATTTTAAAATTTAAAAAAATT-TAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAAATAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA
484131 TATATTTATT
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
79 7 0.05
80 16 0.12
81 80 0.62
82 21 0.16
83 6 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (82 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA
AAAAAGTATAAAAAAAA
Found at i:484024 original size:12 final size:11
Alignment explanation
Indices: 484009--484116 Score: 56
Period size: 12 Copynumber: 10.4 Consensus size: 11
483999 AAAAAATTAA
484009 AAAAAGTATTTT
1 AAAAA-TATTTT
484021 AAAAATATTTT
1 AAAAATATTTT
484032 --AAA-A--TT
1 AAAAATATTTT
* **
484038 AAAAAAATTAAA
1 AAAAATATT-TT
484050 AAAAAGTATTTT
1 AAAAA-TATTTT
484062 AAAAATATTTT
1 AAAAATATTTT
484073 --AAA-A-TTT
1 AAAAATATTTT
*
484080 AAAAA-AATTT
1 AAAAATATTTT
* *
484090 AAAAAGTATGTA
1 AAAAA-TATTTT
484102 AAAAATATTTT
1 AAAAATATTTT
484113 AAAA
1 AAAA
484117 TTAAAAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 5 0.07
9 11 0.15
10 8 0.11
11 20 0.27
12 22 0.30
13 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:484026 original size:30 final size:29
Alignment explanation
Indices: 483952--484024 Score: 130
Period size: 29 Copynumber: 2.5 Consensus size: 29
483942 AAATATTTTT
483952 AAAA-TATTTTAAAATTAAAAAAATTAAAA
1 AAAAGTATTTTAAAATTAAAAAAATT-AAA
483981 AAAAGTATTTTAAAATTAAAAAAATTAAA
1 AAAAGTATTTTAAAATTAAAAAAATTAAA
484010 AAAAGTATTTTAAAA
1 AAAAGTATTTTAAAA
484025 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAGTATTTTAAAATTAAAAAAATTAAA
Found at i:488357 original size:18 final size:18
Alignment explanation
Indices: 488319--488354 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
488309 TTATTATTTT
*
488319 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
488337 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
488355 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:490559 original size:18 final size:19
Alignment explanation
Indices: 490536--490587 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
490526 AGCCCGAATA
*
490536 TATTATGTT-ATTAAAATT
1 TATTATATTAATTAAAATT
*
490554 TATTATATTAATTAATATT
1 TATTATATTAATTAAAATT
490573 TA-TAT-TTATATTAAA
1 TATTATATTA-ATTAAA
490588 TTACTAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 16 0.55
19 10 0.34
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTATATTAATTAAAATT
Found at i:490573 original size:19 final size:18
Alignment explanation
Indices: 490536--490575 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
490526 AGCCCGAATA
*
490536 TATTATGTTATTAAAATT
1 TATTATATTATTAAAATT
*
490554 TATTATATTAATTAATATT
1 TATTATATT-ATTAAAATT
490573 TAT
1 TAT
490576 ATTTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTATATTATTAAAATT
Found at i:497553 original size:23 final size:22
Alignment explanation
Indices: 497522--497567 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
497512 TGTATGATTT
*
497522 ATGTGAAAAATATATGAAATATA
1 ATGTGAAAAATAAAT-AAATATA
* *
497545 ATGTTAAAATTAAATAAATATA
1 ATGTGAAAAATAAATAAATATA
497567 A
1 A
497568 GGGAGTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (22 bp):
ATGTGAAAAATAAATAAATATA
Found at i:502080 original size:18 final size:17
Alignment explanation
Indices: 502047--502080 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
502037 AAAAATTCTA
*
502047 TTAAATTATGATTATTT
1 TTAAATTATAATTATTT
502064 TTAAATGTATAATTATT
1 TTAAAT-TATAATTATT
502081 AAAACTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTAAATTATAATTATTT
Found at i:502660 original size:36 final size:36
Alignment explanation
Indices: 502608--502734 Score: 114
Period size: 36 Copynumber: 3.5 Consensus size: 36
502598 TTTAGAGTTC
*
502608 TAATAATTCTATTTTAAAATTAGCATAATTTTTAAT
1 TAATAATTCTAATTTAAAATTAGCATAATTTTTAAT
* * * * *
502644 TAATAATTGTAATTTAAATTCTA--ATTATTTTGAGTT
1 TAATAATTCTAATTTAAAAT-TAGCATAATTTTTA-AT
* * **
502680 CTAAAAATTCTATTTTAAAATTAGCATAACATTTAAT
1 -TAATAATTCTAATTTAAAATTAGCATAATTTTTAAT
*
502717 TAATAATTGTAATTTAAA
1 TAATAATTCTAATTTAAA
502735 TTCTTATATT
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
35 8 0.12
36 35 0.51
37 19 0.28
38 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.47
Consensus pattern (36 bp):
TAATAATTCTAATTTAAAATTAGCATAATTTTTAAT
Found at i:502689 original size:73 final size:75
Alignment explanation
Indices: 502593--502738 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 75
502583 TCCCTATATT
* **
502593 TTATGTTTAGAGTTCTAATAATTCTATTTTAAAATTAGCATAATTTTTAATTAATAATTGTAATT
1 TTATGTTTAGAGTTCTAAAAATTCTATTTTAAAATTAGCATAACATTTAATTAATAATTGTAATT
502658 TAAATTCTAA
66 TAAATTCTAA
502668 TTAT-TTT-GAGTTCTAAAAATTCTATTTTAAAATTAGCATAACATTTAATTAATAATTGTAATT
1 TTATGTTTAGAGTTCTAAAAATTCTATTTTAAAATTAGCATAACATTTAATTAATAATTGTAATT
502731 TAAATTCT
66 TAAATTCT
502739 TATATTGGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 61 0.90
74 3 0.04
75 4 0.06
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (75 bp):
TTATGTTTAGAGTTCTAAAAATTCTATTTTAAAATTAGCATAACATTTAATTAATAATTGTAATT
TAAATTCTAA
Found at i:503642 original size:21 final size:21
Alignment explanation
Indices: 503609--503648 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
503599 TGTCTCTTTA
*
503609 TTTAAATTTATTAAAATATGT
1 TTTAAATTAATTAAAATATGT
* *
503630 TTTAAGTTAATTAATATAT
1 TTTAAATTAATTAAAATAT
503649 TACTTATGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTAAATTAATTAAAATATGT
Found at i:513842 original size:142 final size:141
Alignment explanation
Indices: 513586--513870 Score: 489
Period size: 142 Copynumber: 2.0 Consensus size: 141
513576 CCGTGCTGCC
*
513586 TGACCTGTCTACGTGAGAGGTGCCTCCGACAACTTTCGAGCTTGTCCCAAACAAAGGGTTGCGTA
1 TGACCTGTCTACGTGAGAGGTGCCTCCGACAACTTTCGAGCTTGTCCCAAACAAAGGGTTGCATA
513651 GGAATCCGAAAGGTCATCCGCAATCATCCAGAATTCGTAATGAAATGGACATTAGGGAGAAATCT
66 GGAATCCGAAAGGTCATCCGCAATCATCCAGAATTCGTAATGAAATGGACATTAGGGAGAAATCT
513716 GACAGTAAGCGT
131 GA-AGTAAGCGT
* * * *
513728 TGACCTGTCTACGTGGGAGGTGCCTCCGACAACTTTTGAGCTTGTTCCAGACAAAGGGTTGCATA
1 TGACCTGTCTACGTGAGAGGTGCCTCCGACAACTTTCGAGCTTGTCCCAAACAAAGGGTTGCATA
* *
513793 GGAATCCGAAAGGTTATCCGCAATCATCCAGAATTCGTAATGAAATGGACATTAGGGAGAAATTT
66 GGAATCCGAAAGGTCATCCGCAATCATCCAGAATTCGTAATGAAATGGACATTAGGGAGAAATCT
*
513858 GAGGTAAGCGT
131 GAAGTAAGCGT
513869 TG
1 TG
513871 TGGATTATAC
Statistics
Matches: 135, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
141 10 0.07
142 125 0.93
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (141 bp):
TGACCTGTCTACGTGAGAGGTGCCTCCGACAACTTTCGAGCTTGTCCCAAACAAAGGGTTGCATA
GGAATCCGAAAGGTCATCCGCAATCATCCAGAATTCGTAATGAAATGGACATTAGGGAGAAATCT
GAAGTAAGCGT
Found at i:514051 original size:14 final size:14
Alignment explanation
Indices: 514032--514060 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
514022 TAATGTATTT
514032 AATTTATATTACAA
1 AATTTATATTACAA
514046 AATTTATATTACAA
1 AATTTATATTACAA
514060 A
1 A
514061 GTTTGTTCCA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:514081 original size:62 final size:62
Alignment explanation
Indices: 513984--514137 Score: 265
Period size: 62 Copynumber: 2.5 Consensus size: 62
513974 CAAAGTACCT
513984 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
*
514046 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTGTATTACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
* *
514108 AATTTATAGTACAAAGCTTT-TTCTAATTTT
1 AATTTATATTACAAAG-TTTGTTCCAATTTT
514138 AGTGTTTTAA
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
62 85 0.97
63 3 0.03
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.50
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATTACAA
Found at i:515489 original size:17 final size:17
Alignment explanation
Indices: 515456--515489 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
515446 TTGTGTTTTG
*
515456 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
515473 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
515490 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:515747 original size:21 final size:21
Alignment explanation
Indices: 515707--515748 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
515697 AGAATATATA
*
515707 TATGTTCTATAAGCCGAATTT
1 TATGTTCTATAAGCCAAATTT
*
515728 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCCAAATTT
515749 GATTTTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGTTCTATAAGCCAAATTT
Found at i:516702 original size:54 final size:54
Alignment explanation
Indices: 516604--516709 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
516594 GTTTTTATAT
*
516604 GCTTAGTGAGTATACATCTACATTCCGGTTTTGCATTTGATTAAACATAGTTTC
1 GCTTAGTGAGTATACATCTACATTCCGGTTTTGCATGTGATTAAACATAGTTTC
* * *
516658 GCTTGGTGAGTATACATCTACATTTCGGTTTATGC-TGTGGTTAAACATAGTT
1 GCTTAGTGAGTATACATCTACATTCCGGTTT-TGCATGTGATTAAACATAGTT
516710 GTATGCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
54 44 0.94
55 3 0.06
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
GCTTAGTGAGTATACATCTACATTCCGGTTTTGCATGTGATTAAACATAGTTTC
Found at i:524832 original size:17 final size:17
Alignment explanation
Indices: 524799--524832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
524789 TTGTGTTTTG
*
524799 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
524816 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
524833 GTGAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:525090 original size:21 final size:21
Alignment explanation
Indices: 525050--525091 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
525040 AGAATATATA
*
525050 TATGTTCTATAAGCCGAATTT
1 TATGTTCTATAAGCCAAATTT
*
525071 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCCAAATTT
525092 GATTTTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGTTCTATAAGCCAAATTT
Found at i:525790 original size:41 final size:41
Alignment explanation
Indices: 525705--525807 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
525695 AGCTATGTGC
* * *
525705 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACAT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACAT
* * * **
525746 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACAT
* *
525787 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
525808 TACTGAATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACAT
Found at i:527482 original size:14 final size:14
Alignment explanation
Indices: 527463--527493 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
527453 TTACATGTTT
*
527463 GAATAGTATCGTTA
1 GAATAGTATCATTA
527477 GAATAGTATCATTA
1 GAATAGTATCATTA
527491 GAA
1 GAA
527494 AAAAATGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (14 bp):
GAATAGTATCATTA
Found at i:528740 original size:26 final size:26
Alignment explanation
Indices: 528686--528741 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
528676 AAGTTCATAT
**
528686 TAAAAAAATAAAAAATAACATGCCAA
1 TAAAAAAATAAAAAATAACATAACAA
528712 TAAAAAAATATAACAAA-AACATAAC-A
1 TAAAAAAATA-AA-AAATAACATAACAA
528738 TAAA
1 TAAA
528742 CGATACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 15 0.58
27 8 0.31
28 3 0.12
ACGTcount: A:0.71, C:0.11, G:0.02, T:0.16
Consensus pattern (26 bp):
TAAAAAAATAAAAAATAACATAACAA
Done.