Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold95
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: 582947
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Warning! 25 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:306368 original size:11 final size:10
Alignment explanation
Indices: 306321--306397 Score: 51
Period size: 8 Copynumber: 8.2 Consensus size: 10
306311 TTAATAATTT
306321 ATATTTTATA
1 ATATTTTATA
*
306331 AAATTTT-TA
1 ATATTTTATA
306340 ATA-TTTAT-
1 ATATTTTATA
*
306348 ATATTCATATA
1 ATATT-TTATA
*
306359 ATATTTATATT
1 ATATTT-TATA
306370 ATATTTTAT-
1 ATATTTTATA
306379 -TATTTT-TA
1 ATATTTTATA
*
306387 A-ATTATATA
1 ATATTTTATA
306396 AT
1 AT
306398 TTTATCGTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
7 1 0.02
8 16 0.31
9 9 0.17
10 12 0.23
11 14 0.27
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATTTTATA
Found at i:306642 original size:27 final size:27
Alignment explanation
Indices: 306610--306672 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
306600 TAATTTGATT
306610 TTAAAATTTAAAAATTAAATAAATTAA
1 TTAAAATTTAAAAATTAAATAAATTAA
* *
306637 TTAAAA-TTAAAGATTAATTAAATTAA
1 TTAAAATTTAAAAATTAAATAAATTAA
*
306663 TCAAAATTTA
1 TTAAAATTTA
306673 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
TTAAAATTTAAAAATTAAATAAATTAA
Found at i:315677 original size:4 final size:4
Alignment explanation
Indices: 315668--315693 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
315658 ATAGTCTAGA
315668 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
315694 TAAAGTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:316039 original size:25 final size:23
Alignment explanation
Indices: 316011--316059 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
316001 ATAATATTTT
316011 TATTTAAATTTAATTATAA-AAATAA
1 TATTTAAA--TAA-TATAATAAATAA
316036 TATTTAAATAATATAATAAATAA
1 TATTTAAATAATATAATAAATAA
316059 T
1 T
316060 GTAACACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
25 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTAAATAATATAATAAATAA
Found at i:316259 original size:19 final size:19
Alignment explanation
Indices: 316235--316274 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
316225 CAGATCAGAC
316235 AAAAGATAAGATTGTAAGG
1 AAAAGATAAGATTGTAAGG
316254 AAAAGATAAGATTGTAAGG
1 AAAAGATAAGATTGTAAGG
316273 AA
1 AA
316275 CTATGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (19 bp):
AAAAGATAAGATTGTAAGG
Found at i:316363 original size:19 final size:18
Alignment explanation
Indices: 316326--316365 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
316316 CAAATATATA
**
316326 TTATTTTTTAAAATTTTT
1 TTATTTTTTAAAAGATTT
316344 TTATTTATTTAAAAGATTT
1 TTATTT-TTTAAAAGATTT
316363 TTA
1 TTA
316366 AAAAGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTATTTTTTAAAAGATTT
Found at i:317357 original size:6 final size:6
Alignment explanation
Indices: 317342--317371 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
317332 AGTCCTTGGG
*
317342 GAAGAA GAAGAT GAAGAT GAAGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
317372 CGTTTGTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (6 bp):
GAAGAT
Found at i:319867 original size:15 final size:15
Alignment explanation
Indices: 319847--319875 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
319837 TTTGACAGTA
319847 TCACTTAATCAATCC
1 TCACTTAATCAATCC
319862 TCACTTAATCAATC
1 TCACTTAATCAATC
319876 TGATTAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (15 bp):
TCACTTAATCAATCC
Found at i:320748 original size:19 final size:19
Alignment explanation
Indices: 320700--320748 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
320690 TTTTATTTAA
320700 ATTTAATATAAAAAAATAT
1 ATTTAATATAAAAAAATAT
*
320719 AATATTGATATAAAAATAATAT
1 -AT-TTAATATAAAAA-AATAT
320741 -TTTAATAT
1 ATTTAATAT
320749 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 11 0.44
22 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTAATATAAAAAAATAT
Found at i:321198 original size:2 final size:2
Alignment explanation
Indices: 321191--321250 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
321181 CTAGGTGTTT
321191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
321233 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
321251 CAGGTTTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:321294 original size:23 final size:24
Alignment explanation
Indices: 321259--321317 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
321249 TACAGGTTTA
*
321259 AAAATTATAATATGATA-AAAAATT
1 AAAA-TATAATATGATATAAAAAAT
321283 AAAATATAATATGATATAAAAAAT
1 AAAATATAATATGATATAAAAAAT
*
321307 AATATA-AATAT
1 AAAATATAATAT
321318 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (24 bp):
AAAATATAATATGATATAAAAAAT
Found at i:321361 original size:18 final size:18
Alignment explanation
Indices: 321319--321374 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
321309 TATAAATATT
321319 TTAAAATTT-TTATAATA
1 TTAAAATTTATTATAATA
*
321336 TT--AA-TTATTATTATA
1 TTAAAATTTATTATAATA
321351 TTAAAATTTATT-TAA-A
1 TTAAAATTTATTATAATA
321367 TATAAAAT
1 T-TAAAAT
321375 ATATAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 11 0.34
16 2 0.06
17 12 0.38
18 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAAATTTATTATAATA
Found at i:321688 original size:27 final size:26
Alignment explanation
Indices: 321655--321716 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
321645 CTAAATAAGA
321655 TAAAATAATAAATTT-ATTTAAGAGTT
1 TAAAATAATAAATTTAATTTAA-AGTT
** *
321681 TAACAATAATTTATTTAATTTAAATTT
1 TAA-AATAATAAATTTAATTTAAAGTT
321708 TAAAATAAT
1 TAAAATAAT
321717 TTTTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 9 0.29
27 16 0.52
28 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
TAAAATAATAAATTTAATTTAAAGTT
Found at i:321726 original size:25 final size:28
Alignment explanation
Indices: 321666--321727 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
321656 AAAATAATAA
321666 ATTT-ATTTAAGAGTTTAACAATAATTT
1 ATTTAATTTAAGAGTTTAACAATAATTT
*
321693 ATTTAATTTAA-ATTTTAA-AATAATTT
1 ATTTAATTTAAGAGTTTAACAATAATTT
321719 -TTTAATTTA
1 ATTTAATTTA
321728 GATAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
26 8 0.24
27 10 0.30
28 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTTAATTTAAGAGTTTAACAATAATTT
Found at i:321732 original size:17 final size:17
Alignment explanation
Indices: 321710--321780 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
321700 TTAAATTTTA
*
321710 AAATAATTTTTTAATTT
1 AAATAATTATTTAATTT
*
321727 AGATAA--ATTTAATTT
1 AAATAATTATTTAATTT
*
321742 AAATAATTATTTAATTAA
1 AAATAATTATTTAATT-T
*
321760 AAATATATAATTT-ATTT
1 AAATA-ATTATTTAATTT
321777 AAAT
1 AAAT
321781 TTAATTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.30
17 17 0.39
18 8 0.18
19 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (17 bp):
AAATAATTATTTAATTT
Found at i:321789 original size:23 final size:23
Alignment explanation
Indices: 321721--321795 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
321711 AATAATTTTT
** *
321721 TAATTTAGATAAATTTAATTTAAA
1 TAATTTATTTAAATTTAA-TTATA
* *
321745 TAA-TTATTT-AATTAAAAATATA
1 TAATTTATTTAAATT-TAATTATA
321767 TAATTTATTTAAATTTAATTATA
1 TAATTTATTTAAATTTAATTATA
*
321790 AAATTT
1 TAATTT
321796 TTTTTAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
22 10 0.25
23 23 0.57
24 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
TAATTTATTTAAATTTAATTATA
Found at i:321934 original size:15 final size:15
Alignment explanation
Indices: 321892--321976 Score: 53
Period size: 15 Copynumber: 6.1 Consensus size: 15
321882 TAAAAAACAA
* * *
321892 TAAATATTTTAAATA
1 TAAATATATTATATT
321907 TAAATATTAATTATATT
1 TAAATA-T-ATTATATT
321924 TAAATATATTAT-TT
1 TAAATATATTATATT
*
321938 T--TTATATTAT-TT
1 TAAATATATTATATT
321950 T---TATATT-TA-T
1 TAAATATATTATATT
321960 TAAATATATTATATT
1 TAAATATATTATATT
321975 TA
1 TA
321977 TATTTTATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.05
11 6 0.10
12 11 0.19
13 6 0.10
14 5 0.09
15 14 0.24
16 2 0.03
17 11 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAAATATATTATATT
Found at i:321958 original size:6 final size:6
Alignment explanation
Indices: 321938--322007 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
321928 TATATTATTT
* **
321938 TTTATA -TTATT TTTATA TTTAT- TAAATA TATTATA TTTATA TTT-TA
1 TTTATA TTTATA TTTATA TTTATA TTTATA T-TTATA TTTATA TTTATA
* *
321984 TTTTTA TATTATA TTTATA ATTAT
1 TTTATA T-TTATA TTTATA TTTAT
322008 TAAAAAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.24
6 30 0.59
7 9 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:321967 original size:24 final size:24
Alignment explanation
Indices: 321940--322011 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
321930 TATTATTTTT
*
321940 TATATTATTTTTATATTTATTAAA
1 TATATTATATTTATATTTATTAAA
**
321964 TATATTATATTTATATTTTATT-TT
1 TATATTATATTTATA-TTTATTAAA
*
321988 TATATTATATTTATAATTATTAAA
1 TATATTATATTTATATTTATTAAA
322012 AAATTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 5 0.12
24 29 0.73
25 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTATATTTATATTTATTAAA
Found at i:321967 original size:36 final size:38
Alignment explanation
Indices: 321916--321998 Score: 125
Period size: 37 Copynumber: 2.2 Consensus size: 38
321906 ATAAATATTA
*
321916 ATTATATTTAAATATATTAT-TTTTTATATTATTTTTAT
1 ATTATA-TTAAATATATTATATTTATATATTATTTTTAT
*
321954 ATT-TATTAAATATATTATATTTATATTTTATTTTTAT
1 ATTATATTAAATATATTATATTTATATATTATTTTTAT
321991 ATTATATT
1 ATTATATT
321999 TATAATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 13 0.32
37 21 0.51
38 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (38 bp):
ATTATATTAAATATATTATATTTATATATTATTTTTAT
Found at i:321979 original size:13 final size:13
Alignment explanation
Indices: 321916--322007 Score: 81
Period size: 12 Copynumber: 7.4 Consensus size: 13
321906 ATAAATATTA
321916 ATTATATTTAAATAT
1 ATTATATTT--ATAT
*
321931 ATTAT-TTTTTAT
1 ATTATATTTATAT
321943 ATTAT-TTT-TAT
1 ATTATATTTATAT
*
321954 ATT-TATTAAATAT
1 ATTATATT-TATAT
321967 ATTATATTTATAT
1 ATTATATTTATAT
*
321980 -TT-TATTTTTAT
1 ATTATATTTATAT
321991 ATTATATTTATA-
1 ATTATATTTATAT
322003 ATTAT
1 ATTAT
322008 TAAAAAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.02
11 16 0.24
12 20 0.30
13 17 0.26
14 7 0.11
15 5 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTATATTTATAT
Found at i:322001 original size:48 final size:46
Alignment explanation
Indices: 321905--322011 Score: 133
Period size: 48 Copynumber: 2.3 Consensus size: 46
321895 ATATTTTAAA
* * *
321905 TATAAATATTAATTATATTTAAATATATTATTTTTTATATTATTTT
1 TATAATTATTAAATATATTTAAATATATTATTTTTTATATTATATT
* ** *
321951 TATATTTATTAAATATATTATATTTATATTTTATTTTTATATTATATT
1 TATAATTATTAAATATATT-TAAATATATTAT-TTTTTATATTATATT
321999 TATAATTATTAAA
1 TATAATTATTAAA
322012 AAATTTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
46 16 0.31
47 9 0.18
48 26 0.51
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (46 bp):
TATAATTATTAAATATATTTAAATATATTATTTTTTATATTATATT
Found at i:322456 original size:11 final size:11
Alignment explanation
Indices: 322441--322479 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
322431 AACTCATACT
*
322441 TATTTATTTTT
1 TATTTATTTTA
*
322452 TATTTATTTGA
1 TATTTATTTTA
322463 TATTT-TTTTA
1 TATTTATTTTA
322473 TATTTAT
1 TATTTAT
322480 ATTGATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:322484 original size:22 final size:22
Alignment explanation
Indices: 322441--322485 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
322431 AACTCATACT
*
322441 TATTTATTTTTTATTTATTTGA
1 TATTTATTTTATATTTATTTGA
322463 TATTT-TTTTATATTTATATTGA
1 TATTTATTTTATATTTAT-TTGA
322485 T
1 T
322486 TTAAATACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
TATTTATTTTATATTTATTTGA
Found at i:322899 original size:32 final size:30
Alignment explanation
Indices: 322863--322939 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
322853 CTAAATTAAA
*
322863 TTTATATAAATTTTAAAGTATTAATAATTTAT
1 TTTATATAAATTTTAAAATATTAAT-A-TTAT
*
322895 TTTATATAAA-TTTAAAATATTTATATTAT
1 TTTATATAAATTTTAAAATATTAATATTAT
*
322924 TTTATAATATATTTTA
1 TTTAT-ATAAATTTTA
322940 TATTATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 9 0.22
30 5 0.12
31 16 0.40
32 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
TTTATATAAATTTTAAAATATTAATATTAT
Found at i:322927 original size:19 final size:19
Alignment explanation
Indices: 322895--322964 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
322885 AATAATTTAT
* *
322895 TTTATATAAATTTAAAATA
1 TTTATATTATTTTAAAATA
322914 TTTATATTATTTTATAATATA
1 TTTATATTATTTTA-AA-ATA
* *
322935 TTTTATATTATATTT-TAATT
1 -TTTATATTAT-TTTAAAATA
322955 TTTATATTAT
1 TTTATATTAT
322965 ATTATTATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 22 0.51
20 4 0.09
21 4 0.09
22 10 0.23
23 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTATTTTAAAATA
Found at i:322937 original size:41 final size:41
Alignment explanation
Indices: 322881--322974 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
322871 AATTTTAAAG
*
322881 TATTAATAATTTATTTTATA-TAAATTTAAAATATTTATATTA
1 TATT-ATAATATATTTTATATTAAATTT-AAATATTTATATTA
* * * *
322923 TTTTATAATATATTTTATATTATATTTTAATTTTTATATTA
1 TATTATAATATATTTTATATTAAATTTAAATATTTATATTA
*
322964 TATTATTATAT
1 TATTATAATAT
322975 TAAATTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 35 0.80
42 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
TATTATAATATATTTTATATTAAATTTAAATATTTATATTA
Found at i:322990 original size:20 final size:20
Alignment explanation
Indices: 322965--323002 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
322955 TTTATATTAT
*
322965 ATTATTATATTAAATTTAAA
1 ATTATTAAATTAAATTTAAA
*
322985 ATTATTAAATTTAATTTA
1 ATTATTAAATTAAATTTA
323003 GACAACTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTAAATTAAATTTAAA
Found at i:323077 original size:2 final size:2
Alignment explanation
Indices: 323070--323108 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
323060 TACTTAATTC
323070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
323109 AAGGATGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:326398 original size:21 final size:22
Alignment explanation
Indices: 326360--326404 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
326350 GATATATGAG
326360 TAATTTAAAAAAATAAAAAAAA
1 TAATTTAAAAAAATAAAAAAAA
326382 TAATTT--AAAAATAAAAATAAA
1 TAATTTAAAAAAATAAAAA-AAA
326403 TA
1 TA
326405 CGTATTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
TAATTTAAAAAAATAAAAAAAA
Found at i:328014 original size:32 final size:34
Alignment explanation
Indices: 327955--328018 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
327945 ATAATTGTGT
* *
327955 TTAATGATCATATATTTTTATAAATTTTGGTAGG
1 TTAATAATCATATATTTATATAAATTTTGGTAGG
*
327989 TTAATAATCA-ATA-TTATATAGATTTTGGTA
1 TTAATAATCATATATTTATATAAATTTTGGTA
328019 CATTTTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
33 3 0.11
34 9 0.33
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (34 bp):
TTAATAATCATATATTTATATAAATTTTGGTAGG
Found at i:329476 original size:2 final size:2
Alignment explanation
Indices: 329469--329499 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
329459 CCATATGTTA
329469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
329500 AAAGAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:329875 original size:53 final size:54
Alignment explanation
Indices: 329805--329923 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 54
329795 ATTAAGAAAT
* *
329805 ATTTTTTTATTGTATTAATATTTTAATATGTT-TTTAGACTGAGAAAATAAAGAA
1 ATTTTTTTATTATATTAATATTTTAATAT-TTCTTCAGACTGAGAAAATAAAGAA
* *
329859 ATTTTTTTA-TATATTAATATTTTAATATTTCTTCAGATTGAGAAATTAAA-AA
1 ATTTTTTTATTATATTAATATTTTAATATTTCTTCAGACTGAGAAAATAAAGAA
* *
329911 GTATTTTTATTAT
1 ATTTTTTTATTAT
329924 CAGGACAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
52 11 0.19
53 37 0.65
54 9 0.16
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (54 bp):
ATTTTTTTATTATATTAATATTTTAATATTTCTTCAGACTGAGAAAATAAAGAA
Found at i:330120 original size:17 final size:18
Alignment explanation
Indices: 330100--330138 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
330090 ATCAAGAAAA
330100 TTTTCAG-ACAAAAAT-AT
1 TTTTCAGTA-AAAAATAAT
330117 TTTTCAGTAAAAAATAAT
1 TTTTCAGTAAAAAATAAT
330135 TTTT
1 TTTT
330139 ACCGACAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTCAGTAAAAAATAAT
Found at i:330942 original size:20 final size:20
Alignment explanation
Indices: 330891--330944 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
330881 TTTTACCTAG
* * *
330891 ATGTATCGATACATTTTTAA
1 ATGTATCGATATATGTATAA
*
330911 ATGTATCGATATATGTATGA
1 ATGTATCGATATATGTATAA
330931 ATGTATCGATATAT
1 ATGTATCGATATAT
330945 TCTGTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (20 bp):
ATGTATCGATATATGTATAA
Found at i:333300 original size:97 final size:97
Alignment explanation
Indices: 333129--333334 Score: 297
Period size: 97 Copynumber: 2.1 Consensus size: 97
333119 TTTATTTATC
333129 GGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCAC
1 GGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCAC
* *
333194 CATCAGGGACATTTCAACCCCATTCCTTCGAG
66 CATCAGGGACACTCCAACCCCATTCCTTCGAG
* * * ** * *
333226 GGGATATTTCAACTCCGCTTTTAAATGCATCAAAGTTTAAATTTTATTCTCACTTAAATTGTCAT
1 GGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCAC
* *
333291 CATCGGGGACACTCCAACCCCATTCC-TCTAAG
66 CATCAGGGACACTCCAACCCCATTCCTTC-GAG
333323 GGGATACTCCAA
1 GGGATACTCCAA
333335 TCCTGTTTTT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 2 0.02
97 93 0.98
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (97 bp):
GGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCAC
CATCAGGGACACTCCAACCCCATTCCTTCGAG
Found at i:334636 original size:22 final size:22
Alignment explanation
Indices: 334610--334651 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
334600 CTTTTTTATT
334610 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
334632 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
334652 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:347996 original size:22 final size:22
Alignment explanation
Indices: 347968--348011 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
347958 ATTTGTTGAA
*
347968 TTTTTAATAGAAT-TTTTAAATT
1 TTTTTAATA-AATATGTTAAATT
347990 TTTTTAATAAATATGTTAAATT
1 TTTTTAATAAATATGTTAAATT
348012 ACGCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTTTAATAAATATGTTAAATT
Found at i:348111 original size:21 final size:21
Alignment explanation
Indices: 348072--348114 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
348062 ATTTGTTGAA
* **
348072 TTTTTAATAGAATTTTTAAAT
1 TTTTTAATAAAATAGTTAAAT
348093 TTTTTAATAAAATAGTTAAAT
1 TTTTTAATAAAATAGTTAAAT
348114 T
1 T
348115 ACGCTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTTAATAAAATAGTTAAAT
Found at i:348231 original size:103 final size:103
Alignment explanation
Indices: 347911--348216 Score: 478
Period size: 103 Copynumber: 3.0 Consensus size: 103
347901 TTAATTGTAA
*
347911 TTTAATTTTACAAAAAAAATACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAAT
1 TTTAATTTTACCAAAAAAA-ACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAAT
347976 AGAATTTTTAAATTTTTTTAATAAATATGTTAAATTACGC
65 AGAATTTTTAAA-TTTTTTAATAAATATGTTAAATTACGC
348016 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
1 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
348081 GAATTTTTAAATTTTTTAATAAA-ATAGTTAAATTACGC
66 GAATTTTTAAATTTTTTAATAAATAT-GTTAAATTACGC
* * * *
348119 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTA-CA-CT-TTGAATTGTTGATA
1 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
*
348181 GAATTTTTGAAAATTTTT-ATGAAATATGTTAAATTA
66 GAATTTTT-AAATTTTTTAAT-AAATATGTTAAATTA
348217 TTAAAATAAA
Statistics
Matches: 191, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
100 22 0.12
101 21 0.11
102 5 0.03
103 68 0.36
104 57 0.30
105 18 0.09
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (103 bp):
TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
GAATTTTTAAATTTTTTAATAAATATGTTAAATTACGC
Found at i:354866 original size:41 final size:42
Alignment explanation
Indices: 354791--354874 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
354781 TCTCTCTCTT
*
354791 ATATATATATATTTGTCACGTTTGTAAACACCAACCATGGAA
1 ATATATATATATTTGTCAAGTTTGTAAACACCAACCATGGAA
354833 ATATATATATATTTGT-AAGTTTGTAAACACCAACCATGGAA
1 ATATATATATATTTGTCAAGTTTGTAAACACCAACCATGGAA
354874 A
1 A
354875 AGGGATGCGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 25 0.61
42 16 0.39
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
ATATATATATATTTGTCAAGTTTGTAAACACCAACCATGGAA
Found at i:358397 original size:25 final size:23
Alignment explanation
Indices: 358369--358417 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
358359 ATAATATTTT
358369 TATTTAAATTTAATTATAA-AAATAA
1 TATTTAAA--TAA-TATAATAAATAA
358394 TATTTAAATAATATAATAAATAA
1 TATTTAAATAATATAATAAATAA
358417 T
1 T
358418 GAAACACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
25 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTAAATAATATAATAAATAA
Found at i:358623 original size:18 final size:19
Alignment explanation
Indices: 358592--358630 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
358582 CAGATCAGAC
358592 AAAAGATAAGATTGTAAGG
1 AAAAGATAAGATTGTAAGG
358611 AAAAGAT-AGATTGTAAGG
1 AAAAGATAAGATTGTAAGG
358629 AA
1 AA
358631 CTATGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.21
Consensus pattern (19 bp):
AAAAGATAAGATTGTAAGG
Found at i:359719 original size:6 final size:6
Alignment explanation
Indices: 359704--359733 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
359694 AGTCCTTGGG
*
359704 GAAGAA GAAGAT GAAGAT GAAGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
359734 CGTTTGTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (6 bp):
GAAGAT
Found at i:363090 original size:19 final size:19
Alignment explanation
Indices: 363042--363090 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
363032 TTTTATTTAA
363042 ATTTAATATAAAAAAATAT
1 ATTTAATATAAAAAAATAT
*
363061 AATATTGATATAAAAATAATAT
1 -AT-TTAATATAAAAA-AATAT
363083 -TTTAATAT
1 ATTTAATAT
363091 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 11 0.44
22 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTAATATAAAAAAATAT
Found at i:363587 original size:24 final size:26
Alignment explanation
Indices: 363555--363603 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
363545 TATAGGTTTA
363555 AAAATTATAATATGATA-AAAAAATT
1 AAAATTATAATATGATATAAAAAATT
363580 AAAA-TATAATATGATATAAAAAAT
1 AAAATTATAATATGATATAAAAAAT
363604 AATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAATTATAATATGATATAAAAAATT
Found at i:363658 original size:18 final size:18
Alignment explanation
Indices: 363616--363671 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
363606 TATAAATATT
363616 TTAAAATTT-TTATAATA
1 TTAAAATTTATTATAATA
*
363633 TT--AA-TTATTATTATA
1 TTAAAATTTATTATAATA
363648 TTAAAATTTA-TATAA-A
1 TTAAAATTTATTATAATA
363664 TATAAAAT
1 T-TAAAAT
363672 ATATAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 11 0.34
16 2 0.06
17 14 0.44
18 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAATTTATTATAATA
Found at i:363989 original size:27 final size:26
Alignment explanation
Indices: 363956--364017 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
363946 CTAAATAAGA
363956 TAAAATAATAAATTT-ATTTAAGAGTT
1 TAAAATAATAAATTTAATTTAA-AGTT
** *
363982 TAACAATAATTTATTTAATTTAAATTT
1 TAA-AATAATAAATTTAATTTAAAGTT
364009 TAAAATAAT
1 TAAAATAAT
364018 TTTTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 9 0.29
27 16 0.52
28 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
TAAAATAATAAATTTAATTTAAAGTT
Found at i:364027 original size:25 final size:28
Alignment explanation
Indices: 363967--364028 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
363957 AAAATAATAA
363967 ATTT-ATTTAAGAGTTTAACAATAATTT
1 ATTTAATTTAAGAGTTTAACAATAATTT
*
363994 ATTTAATTTAA-ATTTTAA-AATAATTT
1 ATTTAATTTAAGAGTTTAACAATAATTT
364020 -TTTAATTTA
1 ATTTAATTTA
364029 GATAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
26 8 0.24
27 10 0.30
28 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTTAATTTAAGAGTTTAACAATAATTT
Found at i:364033 original size:17 final size:17
Alignment explanation
Indices: 364011--364081 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
364001 TTAAATTTTA
*
364011 AAATAATTTTTTAATTT
1 AAATAATTATTTAATTT
*
364028 AGATAA--ATTTAATTT
1 AAATAATTATTTAATTT
*
364043 AAATAATTATTTAATTAA
1 AAATAATTATTTAATT-T
*
364061 AAATATATAATTT-ATTT
1 AAATA-ATTATTTAATTT
364078 AAAT
1 AAAT
364082 TTATTATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.30
17 17 0.39
18 8 0.18
19 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (17 bp):
AAATAATTATTTAATTT
Found at i:364256 original size:24 final size:24
Alignment explanation
Indices: 364229--364307 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 24
364219 TTATATTTAA
364229 ATATATTATTTTTATATTATTTTT
1 ATATATTATTTTTATATTATTTTT
**
364253 ATAT-TTATTAAGTATATTA-TTTT
1 ATATATTATT-TTTATATTATTTTT
* *
364276 ATATTTTA-TTTTATATTATATTT
1 ATATATTATTTTTATATTATTTTT
364299 ATA-ATTATT
1 ATATATTATT
364308 AAAAAAGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
22 10 0.22
23 21 0.47
24 14 0.31
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (24 bp):
ATATATTATTTTTATATTATTTTT
Found at i:364260 original size:12 final size:11
Alignment explanation
Indices: 364230--364307 Score: 77
Period size: 12 Copynumber: 6.8 Consensus size: 11
364220 TATATTTAAA
364230 TATATTATTTT
1 TATATTATTTT
364241 TATATTATTTT
1 TATATTATTTT
**
364252 TATATTTATTAAG
1 TATA-TTATT-TT
364265 TATATTA-TTT
1 TATATTATTTT
*
364275 TATATTTTATTT
1 TATATTAT-TTT
*
364287 TATATTATATT
1 TATATTATTTT
364298 TATAATTATT
1 TAT-ATTATT
364308 AAAAAAGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
10 6 0.11
11 21 0.39
12 23 0.43
13 4 0.07
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (11 bp):
TATATTATTTT
Found at i:364273 original size:35 final size:36
Alignment explanation
Indices: 364218--364297 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 36
364208 ATAAATATTA
364218 ATTATATTTAAATATATTATTTTTATATTAT-TTTTAT
1 ATTATA-TTAAATATATTA-TTTTATATTATATTTTAT
* *
364255 ATT-TATTAAGTATATTATTTTATATTTTATTTTAT
1 ATTATATTAAATATATTATTTTATATTATATTTTAT
364290 ATTATATT
1 ATTATATT
364298 TATAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 10 0.26
35 20 0.51
36 6 0.15
37 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (36 bp):
ATTATATTAAATATATTATTTTATATTATATTTTAT
Found at i:364753 original size:11 final size:11
Alignment explanation
Indices: 364738--364776 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
364728 AACTCATACT
*
364738 TATTTATTTTT
1 TATTTATTTTA
*
364749 TATTTATTTGA
1 TATTTATTTTA
364760 TATTT-TTTTA
1 TATTTATTTTA
364770 TATTTAT
1 TATTTAT
364777 ATTGATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:364781 original size:22 final size:22
Alignment explanation
Indices: 364738--364782 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
364728 AACTCATACT
*
364738 TATTTATTTTTTATTTATTTGA
1 TATTTATTTTATATTTATTTGA
364760 TATTT-TTTTATATTTATATTGA
1 TATTTATTTTATATTTAT-TTGA
364782 T
1 T
364783 TTAAATACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (22 bp):
TATTTATTTTATATTTATTTGA
Found at i:364969 original size:23 final size:20
Alignment explanation
Indices: 364919--364972 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
364909 TTTTAATATT
*
364919 ATTAAATTATATTTATAAAA
1 ATTAAATTTTATTTATAAAA
*
364939 TTTAAAATTTTATTATATAAAAAA
1 ATT-AAATTTTATT-TAT--AAAA
364963 ATTAAATTTT
1 ATTAAATTTT
364973 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.07
21 9 0.33
22 3 0.11
23 7 0.26
24 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAAATTTTATTTATAAAA
Found at i:365196 original size:32 final size:30
Alignment explanation
Indices: 365160--365236 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
365150 CTAAATTAAA
*
365160 TTTATATAAATTTTAAAGTATTAATAATTTAT
1 TTTATATAAATTTTAAAATATTAAT-A-TTAT
*
365192 TTTATATAAA-TTTAAAATATTTATATTAT
1 TTTATATAAATTTTAAAATATTAATATTAT
*
365221 TTTATAATATATTTTA
1 TTTAT-ATAAATTTTA
365237 TATTATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 9 0.22
30 5 0.12
31 16 0.40
32 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
TTTATATAAATTTTAAAATATTAATATTAT
Found at i:365224 original size:19 final size:19
Alignment explanation
Indices: 365192--365261 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
365182 AATAATTTAT
* *
365192 TTTATATAAATTTAAAATA
1 TTTATATTATTTTAAAATA
365211 TTTATATTATTTTATAATATA
1 TTTATATTATTTTA-AA-ATA
* *
365232 TTTTATATTATATTT-TAATT
1 -TTTATATTAT-TTTAAAATA
365252 TTTATATTAT
1 TTTATATTAT
365262 ATTATTATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 22 0.51
20 4 0.09
21 4 0.09
22 10 0.23
23 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTATTTTAAAATA
Found at i:365234 original size:41 final size:41
Alignment explanation
Indices: 365178--365271 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
365168 AATTTTAAAG
*
365178 TATTAATAATTTATTTTATA-TAAATTTAAAATATTTATATTA
1 TATT-ATAATATATTTTATATTAAATTT-AAATATTTATATTA
* * * *
365220 TTTTATAATATATTTTATATTATATTTTAATTTTTATATTA
1 TATTATAATATATTTTATATTAAATTTAAATATTTATATTA
*
365261 TATTATTATAT
1 TATTATAATAT
365272 TAAATTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 35 0.80
42 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
TATTATAATATATTTTATATTAAATTTAAATATTTATATTA
Found at i:365287 original size:20 final size:20
Alignment explanation
Indices: 365262--365301 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
365252 TTTATATTAT
*
365262 ATTATTATATTAAATTTAAA
1 ATTATTAAATTAAATTTAAA
*
365282 ATTATTAAATTTAATTTAAA
1 ATTATTAAATTAAATTTAAA
365302 CAACTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTAAATTAAATTTAAA
Found at i:366694 original size:28 final size:28
Alignment explanation
Indices: 366634--366711 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
366624 AAATGCCACA
*
366634 TTTTGTATTTGTCAAATATGATGGTTTC
1 TTTTGTATTTGTCAAATATGGTGGTTTC
*
366662 CTTTGTATTTGTCAAATATGGTGGTTAT-
1 TTTTGTATTTGTCAAATATGGTGGTT-TC
* *
366690 TTTTG--TTTGTAAAAAATGGTGG
1 TTTTGTATTTGTCAAATATGGTGG
366712 CTTGTTGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
26 15 0.34
28 28 0.64
29 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.22, T:0.50
Consensus pattern (28 bp):
TTTTGTATTTGTCAAATATGGTGGTTTC
Found at i:366728 original size:24 final size:24
Alignment explanation
Indices: 366669--366737 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
366659 TTCCTTTGTA
* * *
366669 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
*
366695 TTTGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
366719 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
366738 AATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 22 0.59
26 15 0.41
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:369290 original size:21 final size:22
Alignment explanation
Indices: 369261--369306 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
369251 TGTTCAGACA
** *
369261 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
369283 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
369304 AGT
1 AGT
369307 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:371245 original size:26 final size:27
Alignment explanation
Indices: 371210--371260 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
371200 CAAATGCCAC
* *
371210 ATTTTGTATTTGTCAAATATGGTGGTT
1 ATTTTGTATTTGTAAAAAATGGTGGTT
371237 ATTTT-TATTTGTAAAAAATGGTGG
1 ATTTTGTATTTGTAAAAAATGGTGG
371261 CTTGTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (27 bp):
ATTTTGTATTTGTAAAAAATGGTGGTT
Found at i:375229 original size:32 final size:34
Alignment explanation
Indices: 375170--375233 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
375160 ATAATTGTGT
* *
375170 TTAATGATCATATATTTTTATAAATTTTGGTAGG
1 TTAATAATCATATATTTATATAAATTTTGGTAGG
*
375204 TTAATAATCA-ATA-TTATATAGATTTTGGTA
1 TTAATAATCATATATTTATATAAATTTTGGTA
375234 CATTTTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
33 3 0.11
34 9 0.33
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (34 bp):
TTAATAATCATATATTTATATAAATTTTGGTAGG
Found at i:376391 original size:2 final size:2
Alignment explanation
Indices: 376384--376417 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
376374 TTCTTTTACA
376384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
376418 GTATGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376753 original size:2 final size:2
Alignment explanation
Indices: 376746--376776 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
376736 CCATATGTTA
376746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
376777 AAAGAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:377152 original size:53 final size:54
Alignment explanation
Indices: 377082--377200 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 54
377072 ATTAAGAAAT
* *
377082 ATTTTTTTATTGTATTAATATTTTAATATGTT-TTTAGACTGAGAAAATAAAGAA
1 ATTTTTTTATTATATTAATATTTTAATAT-TTCTTCAGACTGAGAAAATAAAGAA
* *
377136 ATTTTTTTA-TATATTAATATTTTAATATTTCTTCAGATTGAGAAATTAAA-AA
1 ATTTTTTTATTATATTAATATTTTAATATTTCTTCAGACTGAGAAAATAAAGAA
* *
377188 GTATTTTTATTAT
1 ATTTTTTTATTAT
377201 CAGGACAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
52 11 0.19
53 37 0.65
54 9 0.16
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (54 bp):
ATTTTTTTATTATATTAATATTTTAATATTTCTTCAGACTGAGAAAATAAAGAA
Found at i:377401 original size:17 final size:18
Alignment explanation
Indices: 377381--377419 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
377371 ATCAAGAAAA
377381 TTTTCAG-ACAAAAAT-AT
1 TTTTCAGTA-AAAAATAAT
377398 TTTTCAGTAAAAAATAAT
1 TTTTCAGTAAAAAATAAT
377416 TTTT
1 TTTT
377420 ACCGACAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTCAGTAAAAAATAAT
Found at i:378224 original size:20 final size:20
Alignment explanation
Indices: 378173--378226 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
378163 TTTTACCTAG
* * *
378173 ATGTATCGATACATTTTTGA
1 ATGTATCGATATATGTATGA
378193 ATGTATCGATATATGTATGA
1 ATGTATCGATATATGTATGA
378213 ATGTATCGATATAT
1 ATGTATCGATATAT
378227 TCTGTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (20 bp):
ATGTATCGATATATGTATGA
Found at i:380589 original size:97 final size:97
Alignment explanation
Indices: 380417--380623 Score: 292
Period size: 97 Copynumber: 2.1 Consensus size: 97
380407 TTTATTTATC
* *
380417 GGGGATACTCCAAC-CCTGCTTTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTC
1 GGGGATACTCCAACTTC-GCTCTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTC
* * *
380481 ACCATCAGGGACATTTCAACCCCATTCCT-TCGA
65 ACCATCAGGGACACTCCAACCCCATTCCTCT-AA
* * *
380514 GGGGATATTCCAACTTCGCTCTTAAACGCATCAAAGTTTAAATTTTATTCTCACTTAAATTGTCA
1 GGGGATACTCCAACTTCGCTCTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCA
* *
380579 TCATCGGGGACACTCCAACCCCATTCCTCTAA
66 CCATCAGGGACACTCCAACCCCATTCCTCTAA
380611 GGGGATACTCCAA
1 GGGGATACTCCAA
380624 TCCCGTTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
97 95 0.98
98 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (97 bp):
GGGGATACTCCAACTTCGCTCTTAAACACATCAAAGTTTAAATCTTATTCTCACTTAAATTGTCA
CCATCAGGGACACTCCAACCCCATTCCTCTAA
Found at i:381916 original size:22 final size:22
Alignment explanation
Indices: 381890--381931 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
381880 CTTTTTTATT
381890 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
381912 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
381932 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:389411 original size:2 final size:2
Alignment explanation
Indices: 389406--389437 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
389396 ACACACACAC
389406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
389438 GCATATAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:394177 original size:2 final size:2
Alignment explanation
Indices: 394172--394199 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
394162 CAAACATACA
394172 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
394200 GAACATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395245 original size:22 final size:23
Alignment explanation
Indices: 395217--395261 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
395207 ATTTGTTGAA
* *
395217 TTTTTAATAGAAT-TTTTAAATT
1 TTTTTAATAAAATATGTTAAATT
395239 TTTTTAATAAAATATGTTAAATT
1 TTTTTAATAAAATATGTTAAATT
395262 ACGCTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTAATAAAATATGTTAAATT
Found at i:395282 original size:105 final size:105
Alignment explanation
Indices: 395160--395471 Score: 590
Period size: 104 Copynumber: 3.0 Consensus size: 105
395150 TTAATTGTAA
*
395160 TTTAATTTTACAAAAAAAATACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAAT
1 TTTAATTTTACCAAAAAAA-ACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAAT
395225 AGAATTTTTAAATTTTTTTAATAAAATATGTTAAATTACGC
65 AGAATTTTTAAATTTTTTTAATAAAATATGTTAAATTACGC
395266 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTA-TTTATAATTTGTTGAATTTTTAATA
1 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
*
395330 GAATTTTTAAAATTTTTTAATAAAATATGTTAAATTACGC
66 GAATTTTTAAATTTTTTTAATAAAATATGTTAAATTACGC
395370 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
1 TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
395435 GAATTTTTAAATTTTTTTAATAAAATATGTTAAATTA
66 GAATTTTTAAATTTTTTTAATAAAATATGTTAAATTA
395472 TTAAAATAAA
Statistics
Matches: 202, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
104 103 0.51
105 81 0.40
106 18 0.09
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (105 bp):
TTTAATTTTACCAAAAAAAACTATGAAACTCAAATTTTATTTTATAATTTGTTGAATTTTTAATA
GAATTTTTAAATTTTTTTAATAAAATATGTTAAATTACGC
Found at i:395365 original size:22 final size:22
Alignment explanation
Indices: 395321--395363 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
395311 ATTTGTTGAA
* *
395321 TTTTTAATAGAATTTTTAAAAT
1 TTTTTAATAAAATTGTTAAAAT
395343 TTTTTAATAAAATATGTTAAA
1 TTTTTAATAAAAT-TGTTAAA
395364 TTACGCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTAATAAAATTGTTAAAAT
Found at i:395454 original size:22 final size:23
Alignment explanation
Indices: 395426--395470 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
395416 ATTTGTTGAA
* *
395426 TTTTTAATAGAAT-TTTTAAATT
1 TTTTTAATAAAATATGTTAAATT
395448 TTTTTAATAAAATATGTTAAATT
1 TTTTTAATAAAATATGTTAAATT
395471 ATTAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTAATAAAATATGTTAAATT
Found at i:395662 original size:19 final size:18
Alignment explanation
Indices: 395634--395670 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
395624 GAAATCAAGA
*
395634 ATTTATTTTTTTTATTTT
1 ATTTATTTTTATTATTTT
395652 ATTTAATTTTTATTATTTT
1 ATTT-ATTTTTATTATTTT
395671 TAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTATTTTTATTATTTT
Found at i:395663 original size:16 final size:16
Alignment explanation
Indices: 395642--395675 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
395632 GAATTTATTT
395642 TTTTTATT-TTATTTAA
1 TTTTTATTATT-TTTAA
395658 TTTTTATTATTTTTAA
1 TTTTTATTATTTTTAA
395674 TT
1 TT
395676 AAATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTATTATTTTTAA
Found at i:395682 original size:25 final size:25
Alignment explanation
Indices: 395635--395683 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
395625 AAATCAAGAA
* * * *
395635 TTTATTTTTTTTATTTTATTTAATT
1 TTTATTATTTTTAATTAAATTAATT
395660 TTTATTATTTTTAATTAAATTAAT
1 TTTATTATTTTTAATTAAATTAAT
395684 ATTATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATTATTTTTAATTAAATTAATT
Found at i:397223 original size:21 final size:21
Alignment explanation
Indices: 397197--397236 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
397187 ATTAAAAAAT
397197 TATTTT-TAATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
397218 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
397237 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:397245 original size:49 final size:46
Alignment explanation
Indices: 397191--397290 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 46
397181 TAAAATATTA
* *
397191 AAAAATTATT-TTTAATTAAT-ATTTATATATTTTATAATTAAATTTAAAT
1 AAAAA-TATTATTTAATTAATAAATAAT-TA-TTTA-AATT-AATTTAAAT
397240 AAAAATATTATTTAATTAATAAATAATTATTTAAATTAATTTAAAT
1 AAAAATATTATTTAATTAATAAATAATTATTTAAATTAATTTAAAT
397286 AAAAA
1 AAAAA
397291 AATTTAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
46 14 0.30
47 4 0.09
48 8 0.17
49 17 0.36
50 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (46 bp):
AAAAATATTATTTAATTAATAAATAATTATTTAAATTAATTTAAAT
Found at i:397262 original size:20 final size:20
Alignment explanation
Indices: 397237--397279 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
397227 ATTAAATTTA
397237 AATAAAAATATTATTT-AATT
1 AATAAAAA-ATTATTTAAATT
*
397257 AATAAATAATTATTTAAATT
1 AATAAAAAATTATTTAAATT
397277 AAT
1 AAT
397280 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAAAAAATTATTTAAATT
Found at i:397278 original size:24 final size:24
Alignment explanation
Indices: 397249--397310 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
397239 TAAAAATATT
*
397249 ATTTAATT-AATAAATAATTATTTAA
1 ATTTAATTAAATAAA-AA-AATTTAA
397274 A-TTAATTTAAATAAAAAAATTTAA
1 ATTTAA-TTAAATAAAAAAATTTAA
397298 ATTTAATTTAAAT
1 ATTTAA-TTAAAT
397311 TAAATGGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 11 0.33
25 16 0.48
26 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTAATTAAATAAAAAAATTTAA
Found at i:401289 original size:34 final size:33
Alignment explanation
Indices: 401229--401294 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
401219 TGTTTAAAGT
401229 ATTCAATATTTATATAAATTTTGATATGATAATA
1 ATTCAATATTTATATAAATTTTGATATG-TAATA
*
401263 ATTC-ATA-TTATATAGATTTTAAGATATGTAAT
1 ATTCAATATTTATATAAATTTT--GATATGTAAT
401295 CGTATCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 12 0.41
33 7 0.24
34 10 0.34
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (33 bp):
ATTCAATATTTATATAAATTTTGATATGTAATA
Found at i:406642 original size:2 final size:2
Alignment explanation
Indices: 406635--406668 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
406625 TCATAACTAT
406635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
406669 AAGACAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:412051 original size:16 final size:15
Alignment explanation
Indices: 412032--412072 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
412022 GATCCTGTCT
412032 ATCCACCACCCTGTGC
1 ATCCACCACCCT-TGC
*
412048 ATCCACAACCCTTGC
1 ATCCACCACCCTTGC
412063 ATCCACCACC
1 ATCCACCACC
412073 TATTTACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.24, C:0.51, G:0.07, T:0.17
Consensus pattern (15 bp):
ATCCACCACCCTTGC
Found at i:412065 original size:15 final size:16
Alignment explanation
Indices: 412032--412068 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
412022 GATCCTGTCT
*
412032 ATCCACCACCCTGTGC
1 ATCCACAACCCTGTGC
412048 ATCCACAACCCT-TGC
1 ATCCACAACCCTGTGC
412063 ATCCAC
1 ATCCAC
412069 CACCTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.24, C:0.49, G:0.08, T:0.19
Consensus pattern (16 bp):
ATCCACAACCCTGTGC
Found at i:412225 original size:27 final size:27
Alignment explanation
Indices: 412173--412229 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
412163 ACCATATTTC
* **
412173 CCTACTCAATCTCCATACTCGTCATAT
1 CCTACTCAATCTCCATACCCAACATAT
412200 CCTACTCAA-CTTCCATACCCAACATAT
1 CCTACTCAATC-TCCATACCCAACATAT
412227 CCT
1 CCT
412230 GCCACAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.28, C:0.40, G:0.02, T:0.30
Consensus pattern (27 bp):
CCTACTCAATCTCCATACCCAACATAT
Found at i:413482 original size:21 final size:20
Alignment explanation
Indices: 413458--413499 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
413448 TAAAATTTAT
413458 ACAAAATAAATTATAAATATA
1 ACAAAATAAA-TATAAATATA
**
413479 ACAAAATTTATATAAATATA
1 ACAAAATAAATATAAATATA
413499 A
1 A
413500 AATATCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
ACAAAATAAATATAAATATA
Found at i:414096 original size:131 final size:133
Alignment explanation
Indices: 413939--414203 Score: 333
Period size: 131 Copynumber: 2.0 Consensus size: 133
413929 TATTAGCTCT
* * * *
413939 ATTTATAAAATTTAAAAACTTTATTAATTAT-GAATAAAATAATTT-AGATGAAGGATG-A-CTT
1 ATTTATAAAATTTAAAAACTCTATTAACTATAG-ATAAAATAATTTAAGA-GAAAGATGAATATT
** * *
414000 TAGGGTTCAAAATTTATTTAAATTTGTATTCTTAGTA-TTTTCAAACAAAACTTATTTAAAATAC
64 TAGGGCACAAAATCTATTTAAATTTGTATTCATAGTATTTTTC-AACAAAACTTATTTAAAATAC
414064 TTAAAA
128 TTAAAA
414070 ATTTATAAAATTTAAAAACTCTATTAACTATAGATAAAATAATTTAAAGAGAAAGATGAATTTTA
1 ATTTATAAAATTTAAAAACTCTATTAACTATAGATAAAATAATTT-AAGAGAAAGATGAA---TA
* *
414135 TTTAGGGCACAAAATCTATTTAAATTTGTATTCATAGTATTTTTTCAACTAAATTTATTTAAAAT
62 TTTAGGGCACAAAATCTATTTAAATTTGTATTCATAGTA-TTTTTCAACAAAACTTATTTAAAAT
414200 ACTT
126 ACTT
414204 GAAACTTTTA
Statistics
Matches: 114, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
131 41 0.36
132 8 0.07
133 4 0.04
137 35 0.31
138 21 0.18
139 5 0.04
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (133 bp):
ATTTATAAAATTTAAAAACTCTATTAACTATAGATAAAATAATTTAAGAGAAAGATGAATATTTA
GGGCACAAAATCTATTTAAATTTGTATTCATAGTATTTTTCAACAAAACTTATTTAAAATACTTA
AAA
Found at i:414496 original size:2 final size:2
Alignment explanation
Indices: 414491--414522 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
414481 AAAAATTATG
414491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
414523 ATGTTTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:414781 original size:2 final size:2
Alignment explanation
Indices: 414774--414825 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
414764 GCAAACATAC
* *
414774 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
414816 AT AT AT AT AT
1 AT AT AT AT AT
414826 TCTAAAACCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:414787 original size:14 final size:14
Alignment explanation
Indices: 414768--414824 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
414758 AGGGCTGCAA
414768 ACATACATATATAT
1 ACATACATATATAT
414782 ACATACATATATAT
1 ACATACATATATAT
* *
414796 ATATATATATATAT
1 ACATACATATATAT
* *
414810 ATATATATATATAT
1 ACATACATATATAT
414824 A
1 A
414825 TTCTAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (14 bp):
ACATACATATATAT
Found at i:414993 original size:16 final size:16
Alignment explanation
Indices: 414984--415032 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 16
414974 TTTTTGAATT
414984 TTTATATTTTAAAATA
1 TTTATATTTTAAAATA
*
415000 TTTATA--TT--AATT
1 TTTATATTTTAAAATA
415012 TTTATATTTTATAAATA
1 TTTATATTTTA-AAATA
415029 TTTA
1 TTTA
415033 AATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
12 9 0.35
14 4 0.15
16 6 0.23
17 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATTTTAAAATA
Found at i:417631 original size:22 final size:21
Alignment explanation
Indices: 417575--417642 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 21
417565 ATTATTTAAA
**
417575 AAATAATAATATATTAAAA--
1 AAATAATTTTATATTAAAATT
* * *
417594 AATTATTTTTATATTAATATT
1 AAATAATTTTATATTAAAATT
*
417615 ATATAATTTTATAATTAAAATT
1 AAATAATTTTAT-ATTAAAATT
417637 AAATAA
1 AAATAA
417643 AAATTATTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
19 14 0.39
21 9 0.25
22 13 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAATTTTATATTAAAATT
Found at i:419058 original size:18 final size:17
Alignment explanation
Indices: 419035--419085 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
419025 TTAAGCTTGG
419035 TTGGTTTTAAATTAAAGC
1 TTGGTTTTAAATTAAA-C
** *
419053 TTGGTTTATAGCTTAAAT
1 TTGGTTT-TAAATTAAAC
419071 TTGG-TTTAAATTAAA
1 TTGGTTTTAAATTAAA
419086 ACTTTATCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 7 0.26
17 2 0.07
18 11 0.41
19 7 0.26
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (17 bp):
TTGGTTTTAAATTAAAC
Found at i:419368 original size:21 final size:19
Alignment explanation
Indices: 419321--419376 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
419311 CGATCTGGTC
*
419321 TAATTCAAAATAATAT-TTT
1 TAATT-AAAATAATATAATT
419340 TAATTAAAATAATATAATT
1 TAATTAAAATAATATAATT
419359 TAATTGTAAAAT-ATATAA
1 TAA-T-TAAAATAATATAA
419377 ATATATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 10 0.30
19 10 0.30
20 7 0.21
21 6 0.18
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATTAAAATAATATAATT
Found at i:419399 original size:10 final size:10
Alignment explanation
Indices: 419386--419410 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
419376 AATATATAAA
419386 AATAATTTTT
1 AATAATTTTT
419396 AATAATTTTT
1 AATAATTTTT
419406 AATAA
1 AATAA
419411 AATAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATAATTTTT
Found at i:421137 original size:13 final size:13
Alignment explanation
Indices: 421119--421156 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
421109 TTTTACCAAT
* *
421119 TAAAAATATATAA
1 TAAAAATAAAAAA
421132 TAAAAATAAAAAA
1 TAAAAATAAAAAA
421145 T-AAAATAAAAAA
1 TAAAAATAAAAAA
421157 ACCTAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:421142 original size:18 final size:18
Alignment explanation
Indices: 421119--421155 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
421109 TTTTACCAAT
*
421119 TAAAAATATATAATAAAAA
1 TAAAAA-ATAAAATAAAAA
421138 TAAAAAATAAAATAAAAA
1 TAAAAAATAAAATAAAAA
421156 AACCTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAAATAAAATAAAAA
Found at i:421931 original size:72 final size:72
Alignment explanation
Indices: 421775--421938 Score: 166
Period size: 72 Copynumber: 2.3 Consensus size: 72
421765 TCTCGAGAGG
* * * * * *
421775 CAAACACAAATATCAAGCATGCAACAAAGTCGTTATTGGAATCAAAATTTCGAGATTTGATCACA
1 CAAACATAGATATCAAACATGCAACAAAGTCATTATTGAAATCAAAATCTCGAGATTTGATCACA
*
421840 TTTAAGT
66 TTCAAGT
* * * * * **
421847 TAAACATAGATATCAAACATGCGACAAGGTTATTATTGAAATCAAAATCTCGAGATTTGGTCATG
1 CAAACATAGATATCAAACATGCAACAAAGTCATTATTGAAATCAAAATCTCGAGATTTGATCACA
421912 TTCAAGT
66 TTCAAGT
* * * *
421919 CAGATATCGATATGAAACAT
1 CAAACATAGATATCAAACAT
421939 AGTTTTCATG
Statistics
Matches: 73, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (72 bp):
CAAACATAGATATCAAACATGCAACAAAGTCATTATTGAAATCAAAATCTCGAGATTTGATCACA
TTCAAGT
Found at i:422442 original size:24 final size:24
Alignment explanation
Indices: 422378--422443 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
422368 TTCAATCTTA
* * *
422378 ATTATTATTAAAATAATAAAAAAT
1 ATTAATATAAAAATAATTAAAAAT
* * ** *
422402 ATTTATTTAAATTTAATTATAAAT
1 ATTAATATAAAAATAATTAAAAAT
422426 ATTAATATAAAAATAATT
1 ATTAATATAAAAATAATT
422444 TTTTATAAGA
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTAATATAAAAATAATTAAAAAT
Found at i:423063 original size:137 final size:133
Alignment explanation
Indices: 422802--423086 Score: 331
Period size: 137 Copynumber: 2.1 Consensus size: 133
422792 TGTTAGCTTC
* *
422802 ATTTATGAAATTTAAAAACTCCACTAAGTATGCATAAAATAATTTAGACAACAGATAACTTTAGT
1 ATTTATAAAATTTAAAAACTCCACTAACTATGCATAAAATAATTTAGACAACAGATAACTTTAGT
* * * ** * *
422867 GTACGAAATTTATTTAAATTTATATTTTTATTATTTTTTCAACAAAATTTATTTAAAATACTTAA
66 GCACAAAATCTATTTAAATTTATATTCATAGTATTTCTTCAACAAAATTTATTTAAAATACTTAA
422932 -AA
131 GAA
* * * *
422934 ATTTATAAAATTTAAAAACTCTACTAACTATAG-ATAAAATAATTTAGAGAGCAGATGAATTTTA
1 ATTTATAAAATTTAAAAACTCCACTAACTAT-GCATAAAATAATTTAGACAACAGAT-AACTTTA
* * *
422998 TTTAGGACACAAAATCTATTTAAATTTATGTTCATAGTATTTCTTCAACTAAATTTATTTAAAAT
64 -GT--G-CACAAAATCTATTTAAATTTATATTCATAGTATTTCTTCAACAAAATTTATTTAAAAT
423063 ACTTAAGAA
125 ACTTAAGAA
423072 ACTTTTATATAAATT
1 A--TTTATA-AAATT
423087 AAGTCTCTTG
Statistics
Matches: 127, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
132 49 0.39
133 7 0.06
134 1 0.01
136 1 0.01
137 55 0.43
138 3 0.02
140 6 0.05
141 5 0.04
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (133 bp):
ATTTATAAAATTTAAAAACTCCACTAACTATGCATAAAATAATTTAGACAACAGATAACTTTAGT
GCACAAAATCTATTTAAATTTATATTCATAGTATTTCTTCAACAAAATTTATTTAAAATACTTAA
GAA
Found at i:423605 original size:2 final size:2
Alignment explanation
Indices: 423600--423638 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
423590 ACACACACAC
423600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
423639 TCTAAAACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:426943 original size:22 final size:22
Alignment explanation
Indices: 426902--426943 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
426892 AGGATTTAAA
* *
426902 TTAAAGATATTTATTTTTTATT
1 TTAAAGATATTTAATATTTATT
*
426924 TTAAATATATTTAATATTTA
1 TTAAAGATATTTAATATTTA
426944 ATCTGATTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAAAGATATTTAATATTTATT
Found at i:429241 original size:15 final size:17
Alignment explanation
Indices: 429223--429264 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
429213 AATTTTTAAG
429223 TTTTAAAAAAA-ATA-A
1 TTTTAAAAAAATATATA
429238 TTTTAAAAAAATATATA
1 TTTTAAAAAAATATATA
*
429255 TATTAAAAAA
1 TTTTAAAAAA
429265 TAAATATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTTAAAAAAATATATA
Found at i:429248 original size:16 final size:17
Alignment explanation
Indices: 429223--429271 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
429213 AATTTTTAAG
429223 TTTT-AAAAAAAATA-A
1 TTTTAAAAAAAAATATA
*
429238 TTTTAAAAAAATATATA
1 TTTTAAAAAAAAATATA
*
429255 TATTAAAAAATAAATAT
1 TTTTAAAAAA-AAATAT
429272 CACGTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 10 0.36
18 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAAAATATA
Found at i:429507 original size:24 final size:28
Alignment explanation
Indices: 429474--429535 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 28
429464 TTTTATTTTT
*
429474 AATTTTAATT-TT-ATT-ATATT-TAAA
1 AATTTAAATTATTAATTAATATTATAAA
429498 AATTTAAATTATTAATTAAATATTAATAAA
1 AATTTAAATTATTAATT-AATATT-ATAAA
429528 AATTTAAA
1 AATTTAAA
429536 ATATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 9 0.29
25 2 0.06
26 3 0.10
28 5 0.16
30 12 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTTAAATTATTAATTAATATTATAAA
Found at i:429548 original size:28 final size:30
Alignment explanation
Indices: 429487--429553 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
429477 TTTAATTTTA
*
429487 TTATATT--TAAAAATTTAAATTATTAATT
1 TTATATTAATAAAAATTTAAAATATTAATT
**
429515 AAATATTAATAAAAATTTAAAATA-T-ATT
1 TTATATTAATAAAAATTTAAAATATTAATT
429543 TTATATTAATA
1 TTATATTAATA
429554 TATATTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 17 0.53
29 1 0.03
30 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTATATTAATAAAAATTTAAAATATTAATT
Found at i:429555 original size:15 final size:16
Alignment explanation
Indices: 429535--429567 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
429525 AAAAATTTAA
*
429535 AATATATTTTA-TATT
1 AATATATATTATTATT
429550 AATATATATTATTATT
1 AATATATATTATTATT
429566 AA
1 AA
429568 ATTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATATATTATTATT
Found at i:429556 original size:17 final size:18
Alignment explanation
Indices: 429531--429564 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
429521 TAATAAAAAT
429531 TTAAAATATATT-TTATA
1 TTAAAATATATTATTATA
*
429548 TTAATATATATTATTAT
1 TTAAAATATATTATTAT
429565 TAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAAATATATTATTATA
Found at i:429880 original size:26 final size:25
Alignment explanation
Indices: 429851--429966 Score: 68
Period size: 25 Copynumber: 4.8 Consensus size: 25
429841 ACTTATTAAA
429851 ATATTATATATTTATATTTATTTAAT
1 ATATTATATATTTATATTTATTT-AT
* * *
429877 ATATT-TAAAATAATAATTTATTTAT
1 ATATTATATATTTAT-ATTTATTTAT
* * *
429902 -TA-AATAAATTTTAATATTAATTT-T
1 ATATTATATA-TTT-ATATTTATTTAT
* *
429926 ATATCATA-ATTTTTA-TTATTT-T
1 ATATTATATATTTATATTTATTTAT
429948 ATATTATATA-TTATATTTA
1 ATATTATATATTTATATTTA
429967 AAATTATAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
22 17 0.24
23 6 0.09
24 10 0.14
25 19 0.27
26 18 0.26
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTATATATTTATATTTATTTAT
Found at i:429901 original size:30 final size:32
Alignment explanation
Indices: 429829--429912 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 32
429819 TTTATTTTAG
*
429829 ATTTATTTATTTACT-TA-TTAAAATATTATAT
1 ATTTATTTATTTAATATATTTAAAATA-TATAT
429860 ATTTATATTTATTTAATATATTTAAAATA-ATA-
1 A-TT-TATTTATTTAATATATTTAAAATATATAT
* *
429892 ATTTATTTATTAAATAAATTT
1 ATTTATTTATTTAATATATTT
429913 TAATATTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
30 16 0.35
31 3 0.07
32 3 0.07
33 14 0.30
34 2 0.04
35 8 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
ATTTATTTATTTAATATATTTAAAATATATAT
Found at i:429927 original size:30 final size:31
Alignment explanation
Indices: 429846--429927 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 31
429836 TATTTACTTA
* *
429846 TTAAAATATTATATATTTATATTTATTTAATATAT
1 TTAAAATA--ATA-ATTT-TATTTATTAAATAAAT
429881 TTAAAATAATAA-TTTATTTATTAAATAAAT
1 TTAAAATAATAATTTTATTTATTAAATAAAT
* *
429911 TT-TAATATTAATTTTAT
1 TTAAAATAATAATTTTAT
429928 ATCATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.17
30 21 0.50
31 2 0.05
32 1 0.02
33 3 0.07
35 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TTAAAATAATAATTTTATTTATTAAATAAAT
Found at i:429964 original size:22 final size:23
Alignment explanation
Indices: 429915--429964 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
429905 ATAAATTTTA
429915 ATATTAATTTTATATCATAATTT
1 ATATTAATTTTATATCATAATTT
* *
429938 TTATT-ATTTTATATTAT-ATATT
1 ATATTAATTTTATATCATAAT-TT
429960 ATATT
1 ATATT
429965 TAAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 17 0.74
23 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTAATTTTATATCATAATTT
Found at i:430333 original size:32 final size:31
Alignment explanation
Indices: 430280--430386 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 31
430270 ATTAAGGTAT
430280 TTTAAATT-TTTAAAATTTTAAATTATTTTAAAA
1 TTTAAATTATTT--AATTTTAAATTATTTT-AAA
* *
430313 TTTAAATTATTTGATTTTAAATTAATTTAAA
1 TTTAAATTATTTAATTTTAAATTATTTTAAA
* * * *
430344 TTT-TATCATTTTAATTTTAAATCATTTTAAG
1 TTTAAATTA-TTTAATTTTAAATTATTTTAAA
430375 TTTAAATTATTT
1 TTTAAATTATTT
430387 TAGATCAGAG
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
30 3 0.05
31 30 0.49
32 17 0.28
33 8 0.13
34 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
TTTAAATTATTTAATTTTAAATTATTTTAAA
Found at i:430369 original size:16 final size:16
Alignment explanation
Indices: 430278--430388 Score: 104
Period size: 16 Copynumber: 7.0 Consensus size: 16
430268 AGATTAAGGT
*
430278 ATTTTAAATT-TTTAAA
1 ATTTTAAATTATTT-TA
430294 ATTTTAAATTATTTTAA
1 ATTTTAAATTATTTT-A
* *
430311 AATTTAAATTA-TTTG
1 ATTTTAAATTATTTTA
*
430326 ATTTTAAATTAATTTAA
1 ATTTTAAATT-ATTTTA
*
430343 ATTTT--ATCATTTTA
1 ATTTTAAATTATTTTA
*
430357 ATTTTAAATCATTTTA
1 ATTTTAAATTATTTTA
*
430373 AGTTTAAATTATTTTA
1 ATTTTAAATTATTTTA
430389 GATCAGAGTT
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.13
15 11 0.14
16 37 0.47
17 21 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTTAAATTATTTTA
Found at i:430592 original size:21 final size:23
Alignment explanation
Indices: 430551--430600 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
430541 AAACTCAAGT
430551 AATTATAAATTCGAATCATTTTA
1 AATTATAAATTCGAATCATTTTA
430574 AATT-TAAA-TCG-ATCAATTTTA
1 AATTATAAATTCGAATC-ATTTTA
430595 AATTAT
1 AATTAT
430601 TGACTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 5 0.20
23 4 0.16
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (23 bp):
AATTATAAATTCGAATCATTTTA
Done.