Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 20 of 24
Found at i:3833269 original size:13 final size:12
Alignment explanation
Indices: 3833224--3833257 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3833214 TTTTTATGTC
*
3833224 ATATTATATTTT
1 ATATTATTTTTT
3833236 A-ATTATTTTTT
1 ATATTATTTTTT
3833247 ATATTATTTTT
1 ATATTATTTTT
3833258 GTATCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:3833585 original size:11 final size:11
Alignment explanation
Indices: 3833564--3833592 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3833554 TCAAGTCATA
3833564 TTTTA-ATTAT
1 TTTTATATTAT
3833574 TTTTATATTAT
1 TTTTATATTAT
3833585 TTTTATAT
1 TTTTATAT
3833593 CATATCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:3834395 original size:22 final size:23
Alignment explanation
Indices: 3834370--3834418 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 23
3834360 ATTTTATTAA
3834370 TATTTAAATAATTTTTTAA-C-AT
1 TATTT-AATAATTTTTTAATCTAT
3834392 TA-TTAATAATTTTTTAATCTAT
1 TATTTAATAATTTTTTAATCTAT
3834414 TATTT
1 TATTT
3834419 TTAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 13 0.54
21 3 0.12
22 6 0.25
23 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTAATAATTTTTTAATCTAT
Found at i:3839689 original size:24 final size:24
Alignment explanation
Indices: 3839641--3839692 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3839631 AATAAAATTA
* *
3839641 TTTTATTATTTTATATCTTCAAAT
1 TTTTATTATTTTAAATATTCAAAT
**
3839665 TTTTATTATTTTAAATATTTTAAT
1 TTTTATTATTTTAAATATTCAAAT
3839689 TTTT
1 TTTT
3839693 CGATTTTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTATTATTTTAAATATTCAAAT
Found at i:3841052 original size:2 final size:2
Alignment explanation
Indices: 3841045--3841076 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3841035 TTTAGTAATG
3841045 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
3841077 AGCATTATGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3841448 original size:20 final size:20
Alignment explanation
Indices: 3841425--3841478 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
3841415 AAATTATATT
3841425 TAAAATATTTTATAT-TT-A
1 TAAAATATTTTATATATTAA
*
3841443 TATAAAT-TTTAATATATTAA
1 TA-AAATATTTTATATATTAA
**
3841463 TAATTTATTTTATATA
1 TAAAATATTTTATATA
3841479 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAAATATTTTATATATTAA
Found at i:3841465 original size:18 final size:17
Alignment explanation
Indices: 3841418--3841483 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 17
3841408 TATATTAAAA
3841418 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
3841434 TTATATTTATATAAATT
1 TTATATTTATATAAATT
3841451 TTAATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
3841467 TTAT-TTTATATAAATT
1 TTATATTTATATAAATT
3841483 T
1 T
3841484 AAAAATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 4 0.09
16 14 0.33
17 8 0.19
18 8 0.19
19 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:3844164 original size:2 final size:2
Alignment explanation
Indices: 3844157--3844183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3844147 AAGCATCCTT
3844157 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3844184 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3844241 original size:16 final size:16
Alignment explanation
Indices: 3844210--3844257 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3844200 ATGATTATTT
*
3844210 TAAATATAATATTAAAA
1 TAAATAAAATA-TAAAA
3844227 -AAATTAAAATATAAAA
1 TAAA-TAAAATATAAAA
*
3844243 TAAATATAATATAAA
1 TAAATAAAATATAAA
3844258 CATATGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAAAATATAAAA
Found at i:3844362 original size:27 final size:27
Alignment explanation
Indices: 3844279--3844362 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
3844269 ATTAAAATTT
* *
3844279 ATATAATATAAAT-TTTTAATATATCAAA
1 ATATAATATAAATATATAAAT-TATC-AA
* * * **
3844307 ATTTATTTTAAATATATAACA-TAAAAA
1 ATATAATATAAATATATAA-ATTATCAA
3844334 ATATAATATAAATATATAAATTATCAA
1 ATATAATATAAATATATAAATTATCAA
3844361 AT
1 AT
3844363 CTATTCCTTG
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
26 1 0.02
27 24 0.59
28 12 0.29
29 3 0.07
30 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATAATATAAATATATAAATTATCAA
Found at i:3845861 original size:34 final size:38
Alignment explanation
Indices: 3845776--3845871 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 38
3845766 AACTAAAAAA
3845776 AAATTTAAATTATTCTTAATTAATTTTAGTAAACTCTTTG
1 AAATTTAAATTATTCTTAATTAA-TTTAGTAAACTC-TTG
* *
3845816 TAATTCTAAATTATTCTTAATTAA-TT-GTCAACTC-T-
1 AAATT-TAAATTATTCTTAATTAATTTAGTAAACTCTTG
*
3845851 AAATTTAAATTATTCTAAATT
1 AAATTTAAATTATTCTTAATT
3845872 TTTGTTATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
34 15 0.29
35 4 0.08
36 1 0.02
38 7 0.14
39 2 0.04
40 4 0.08
41 18 0.35
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (38 bp):
AAATTTAAATTATTCTTAATTAATTTAGTAAACTCTTG
Found at i:3847397 original size:14 final size:15
Alignment explanation
Indices: 3847380--3847424 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
3847370 TATTATCACG
3847380 TTATAATT-ATTATT
1 TTATAATTAATTATT
*
3847394 TTATAATTTTAATTTTT
1 TTATAA--TTAATTATT
3847411 TTATAATTAATTAT
1 TTATAATTAATTAT
3847425 AATAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.23
15 7 0.27
16 2 0.08
17 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATAATTAATTATT
Found at i:3854968 original size:2 final size:2
Alignment explanation
Indices: 3854961--3855000 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3854951 TGTAAAAGAT
3854961 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3855001 GAAGGAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3857285 original size:13 final size:13
Alignment explanation
Indices: 3857267--3857291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3857257 TATATTTTTT
3857267 TTATTAATATTTG
1 TTATTAATATTTG
3857280 TTATTAATATTT
1 TTATTAATATTT
3857292 ATAATCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTATTAATATTTG
Found at i:3859982 original size:2 final size:2
Alignment explanation
Indices: 3859975--3860002 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3859965 CGCGTGTATC
3859975 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
3860003 TTTGTCTGTT
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:3861039 original size:2 final size:2
Alignment explanation
Indices: 3861034--3861067 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3861024 GTGTGTGTGC
*
3861034 AT AT AT AT AT AT AT GT 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
3861068 TCTCAATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3861471 original size:2 final size:2
Alignment explanation
Indices: 3861464--3861498 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3861454 TTTACTACAA
*
3861464 AT AT AT AT AT GT 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 A
3861499 ATGCAGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3862208 original size:21 final size:21
Alignment explanation
Indices: 3862184--3862223 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3862174 TAATGCATTG
3862184 TAATGTATACATTATATGATA
1 TAATGTATACATTATATGATA
3862205 TAATGTATACATTATATGA
1 TAATGTATACATTATATGA
3862224 ATTATCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (21 bp):
TAATGTATACATTATATGATA
Found at i:3864303 original size:20 final size:21
Alignment explanation
Indices: 3864240--3864303 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
3864230 ATCGATTTAA
*
3864240 AATTTATTATATA-AATATGATT
1 AATTTATTAAATATAATA--ATT
3864262 -ATATTATTAAATATAATAATT
1 AAT-TTATTAAATATAATAATT
*
3864283 AATTTATTAAA-ATATTAATT
1 AATTTATTAAATATAATAATT
3864303 A
1 A
3864304 TATAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 9 0.24
21 13 0.35
22 11 0.30
23 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTTATTAAATATAATAATT
Found at i:3868322 original size:2 final size:2
Alignment explanation
Indices: 3868315--3868372 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
3868305 TAATCGGAGA
*
3868315 AT AT AT AT AT AT AT AT AT -T AT GT -T 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
*
3868355 CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3868373 GAATCTGAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3870043 original size:5 final size:5
Alignment explanation
Indices: 3870037--3870074 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
3870027 GAGACAGAAG
* *
3870037 GGAAG GGAAG GGAAA GGAAA GGAAA GGAAA GGAAA GGA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA
3870075 GTGTAGGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:3870388 original size:17 final size:17
Alignment explanation
Indices: 3870365--3870411 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3870355 TAGTTGTGTA
3870365 ATAAATTATATATTT-AT
1 ATAAATTATA-ATTTGAT
*
3870382 TTAAATT-TAATTTGAT
1 ATAAATTATAATTTGAT
3870398 ATAAATTATAATTT
1 ATAAATTATAATTT
3870412 TAAATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 10 0.38
17 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATAAATTATAATTTGAT
Found at i:3870856 original size:18 final size:18
Alignment explanation
Indices: 3870833--3870868 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3870823 ATTCAAATTA
3870833 TTTTAAATATAAATAAAT
1 TTTTAAATATAAATAAAT
*
3870851 TTTTAAATTTAAATAAAT
1 TTTTAAATATAAATAAAT
3870869 AACTTGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTAAATATAAATAAAT
Found at i:3871000 original size:3 final size:3
Alignment explanation
Indices: 3870992--3871031 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3870982 AGTTTAGATG
3870992 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3871032 AAGAAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3872330 original size:2 final size:2
Alignment explanation
Indices: 3872323--3872348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3872313 AATAAAGTGC
3872323 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
3872349 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3877990 original size:29 final size:29
Alignment explanation
Indices: 3877958--3878041 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
3877948 ATGTTAAAGC
* *
3877958 TTTATTTAGATAAAAATTAAAAGTTAAAA
1 TTTATTTAAATAAAAATTAAAAATTAAAA
3877987 TTTATTTAAATAAAAATTAAAAATTAATATA
1 TTTATTTAAATAAAAATTAAAAATTAA-A-A
* * *
3878018 GCTAATTTAAATACAAATTAAAAA
1 -TTTATTTAAATAAAAATTAAAAA
3878042 CTTATTTAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 25 0.53
30 1 0.02
31 1 0.02
32 20 0.43
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (29 bp):
TTTATTTAAATAAAAATTAAAAATTAAAA
Found at i:3879285 original size:13 final size:14
Alignment explanation
Indices: 3879259--3879290 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3879249 TTTTAAAATT
3879259 TTTTAAAAATATAA
1 TTTTAAAAATATAA
3879273 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
3879286 TTTTA
1 TTTTA
3879291 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:3879307 original size:16 final size:16
Alignment explanation
Indices: 3879255--3879309 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 16
3879245 ATATTTTTAA
3879255 AATT-TTTT-AAAAAT
1 AATTATTTTAAAAAAT
*
3879269 -ATAATTTTAAAAAAT
1 AATTATTTTAAAAAAT
3879284 AATTTTATTTTAAAAAAT
1 AA--TTATTTTAAAAAAT
3879302 AATTATTT
1 AATTATTT
3879310 ATCATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.06
14 4 0.12
15 6 0.18
16 7 0.21
18 15 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTATTTTAAAAAAT
Found at i:3879861 original size:33 final size:34
Alignment explanation
Indices: 3879796--3879879 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 34
3879786 AATATATAAA
* * *
3879796 AATATTTTATATT-TATATAGATGTTAATATATT
1 AATAATTTATATTATATATAAATGTTAAAATATT
*
3879829 AATAATTTATATTATATA-AAATTTTAAAATATT
1 AATAATTTATATTATATATAAATGTTAAAATATT
* *
3879862 TATATACTTATATTATAT
1 AATA-ATTTATATTATAT
3879880 TTTTATATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
33 27 0.63
34 16 0.37
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (34 bp):
AATAATTTATATTATATATAAATGTTAAAATATT
Found at i:3879893 original size:13 final size:13
Alignment explanation
Indices: 3879869--3879921 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
3879859 ATTTATATAC
3879869 TTATATTATATTT
1 TTATATTATATTT
3879882 TTATATTATATTCAT
1 TTATATTATATT--T
3879897 ATTATATT-TAATTT
1 -TTATATTAT-ATTT
3879911 TT-TATTATATT
1 TTATATTATATT
3879922 CATACTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.20
13 15 0.43
14 1 0.03
15 2 0.06
16 10 0.29
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:3879900 original size:11 final size:10
Alignment explanation
Indices: 3879864--3879904 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
3879854 AAAATATTTA
3879864 TATACTTATAT
1 TATA-TTATAT
3879875 TATATT-T-T
1 TATATTATAT
3879883 TATATTATAT
1 TATATTATAT
3879893 TCATATTATAT
1 T-ATATTATAT
3879904 T
1 T
3879905 TAATTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.26
9 2 0.07
10 4 0.15
11 14 0.52
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATTATAT
Found at i:3879920 original size:28 final size:29
Alignment explanation
Indices: 3879869--3879941 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 29
3879859 ATTTATATAC
3879869 TTATATTATATTTTTATATTATATTCATA
1 TTATATTATATTTTTATATTATATTCATA
3879898 TTATATT-TAATTTTT-TATTATATTCATA
1 TTATATTAT-ATTTTTATATTATATTCATA
*
3879926 CTGTATATAATATTTT
1 -T-TATATTATATTTT
3879942 GAATTTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 14 0.36
29 14 0.36
30 10 0.26
31 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (29 bp):
TTATATTATATTTTTATATTATATTCATA
Found at i:3884553 original size:20 final size:20
Alignment explanation
Indices: 3884528--3884567 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3884518 TTATATAATT
3884528 AAATAATATAAATATATTAA
1 AAATAATATAAATATATTAA
*
3884548 AAATAATATTAATATATTAA
1 AAATAATATAAATATATTAA
3884568 TATATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAATATAAATATATTAA
Found at i:3884553 original size:28 final size:28
Alignment explanation
Indices: 3884522--3884602 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
3884512 TAGATATTAT
3884522 ATAAT-TAAATAATATAAATATATTAAAA
1 ATAATATAAAT-ATATAAATATATTAAAA
* *
3884550 ATAATATTAATATATTAATATATTAAAA
1 ATAATATAAATATATAAATATATTAAAA
* * *
3884578 TTTATATAAAT-TAT-AATATTTTAAA
1 ATAATATAAATATATAAATATATTAAA
3884603 TTTAATTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.22
27 3 0.07
28 29 0.63
29 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAATATAAATATATAAATATATTAAAA
Found at i:3886676 original size:21 final size:20
Alignment explanation
Indices: 3886650--3886692 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3886640 AAAAAAATAT
3886650 TTATTTAAATATAATAAAA-AA
1 TTATTTAAA-A-AATAAAACAA
3886671 TTATTTAAAAAATAAAACAA
1 TTATTTAAAAAATAAAACAA
3886691 TT
1 TT
3886693 TAAGATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTATTTAAAAAATAAAACAA
Found at i:3888471 original size:15 final size:15
Alignment explanation
Indices: 3888432--3888486 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
3888422 AATTTAGGAG
3888432 GGAAAAGAAAGGAAA
1 GGAAAAGAAAGGAAA
**
3888447 GGAAGGGAAAGGAAA
1 GGAAAAGAAAGGAAA
*
3888462 GGAAAAGAAAAGAAA
1 GGAAAAGAAAGGAAA
*
3888477 AGAAAAGAAA
1 GGAAAAGAAA
3888487 ATCATATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
GGAAAAGAAAGGAAA
Found at i:3888487 original size:5 final size:5
Alignment explanation
Indices: 3888433--3888487 Score: 56
Period size: 5 Copynumber: 11.0 Consensus size: 5
3888423 ATTTAGGAGG
* * ** * *
3888433 GAAAA GAAAG GAAAG GAAGG GAAAG GAAAG GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
3888483 GAAAA
1 GAAAA
3888488 TCATATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:3888487 original size:10 final size:10
Alignment explanation
Indices: 3888432--3888487 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
3888422 AATTTAGGAG
3888432 GGAAAAGAAA
1 GGAAAAGAAA
* *
3888442 GGAAAGGAAG
1 GGAAAAGAAA
*
3888452 GGAAAGGAAA
1 GGAAAAGAAA
3888462 GGAAAAGAAA
1 GGAAAAGAAA
*
3888472 AGAAAAGAAA
1 GGAAAAGAAA
*
3888482 AGAAAA
1 GGAAAA
3888488 TCATATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GGAAAAGAAA
Found at i:3889954 original size:6 final size:6
Alignment explanation
Indices: 3889943--3889967 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3889933 CATAGCTTCG
3889943 CCTTTC CCTTTC CCTTTC CCTTTC C
1 CCTTTC CCTTTC CCTTTC CCTTTC C
3889968 TATTATTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTTTC
Found at i:3890151 original size:21 final size:20
Alignment explanation
Indices: 3890125--3890169 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3890115 AAACAGGTCA
3890125 TTTTTTAGTCCACATTTTAAT
1 TTTTTTA-TCCACATTTTAAT
* * *
3890146 TTTTTTATTCATATTTTTAT
1 TTTTTTATCCACATTTTAAT
3890166 TTTT
1 TTTT
3890170 AAAAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTTATCCACATTTTAAT
Found at i:3892588 original size:4 final size:4
Alignment explanation
Indices: 3892581--3892632 Score: 54
Period size: 4 Copynumber: 12.5 Consensus size: 4
3892571 ATTTACATCA
3892581 TATT TATT TATT TATT ATATT ATATT ATATT TA-T TA-T TATT TAATT
1 TATT TATT TATT TATT -TATT -TATT -TATT TATT TATT TATT T-ATT
3892627 TATT TA
1 TATT TA
3892633 ACAGTGTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.13
4 21 0.47
5 18 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:3892611 original size:19 final size:17
Alignment explanation
Indices: 3892580--3892632 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 17
3892570 TATTTACATC
3892580 ATATTTATTTATTTATT
1 ATATTTATTTATTTATT
3892597 ATATTATATTATATTTATT
1 ATATT-TATT-TATTTATT
3892616 ATTATTTAATTTATTTA
1 A-TATTT-ATTTATTTA
3892633 ACAGTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.16
18 4 0.12
19 16 0.50
20 7 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTATTTATTTATT
Found at i:3894553 original size:14 final size:16
Alignment explanation
Indices: 3894530--3894566 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
3894520 GTAAGGTTTT
*
3894530 TATAACTTTT-AAATA
1 TATAAATTTTAAAATA
3894545 -ATAAATTTTAAAATA
1 TATAAATTTTAAAATA
3894560 TATAAAT
1 TATAAAT
3894567 ATTATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 5 0.26
16 6 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAAATTTTAAAATA
Found at i:3894908 original size:2 final size:2
Alignment explanation
Indices: 3894901--3894927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3894891 TCTCAAATTC
3894901 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 A
3894928 AACAAACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3896175 original size:16 final size:17
Alignment explanation
Indices: 3896154--3896186 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3896144 TATTTAAAAT
3896154 AAATATAAAAAT-TTTA
1 AAATATAAAAATATTTA
*
3896170 AAATATTAAAATATTTA
1 AAATATAAAAATATTTA
3896187 TTTGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAAAAATATTTA
Found at i:3897644 original size:16 final size:17
Alignment explanation
Indices: 3897607--3897644 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3897597 GCACATCTAA
3897607 TTCTC-TCCTTTCTCAC
1 TTCTCTTCCTTTCTCAC
3897623 TT-TCTTCCTTTCTC-C
1 TTCTCTTCCTTTCTCAC
3897638 TTCTCTT
1 TTCTCTT
3897645 TTCTTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTCTTCCTTTCTCAC
Found at i:3899775 original size:16 final size:16
Alignment explanation
Indices: 3899754--3899793 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3899744 TCTTTTGTTG
3899754 ACAAGTT-ATGAGTAGA
1 ACAAGTTGATGA-TAGA
3899770 ACAAGTTGATGATAGA
1 ACAAGTTGATGATAGA
*
3899786 AGAAGTTG
1 ACAAGTTG
3899794 CGTAAGTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (16 bp):
ACAAGTTGATGATAGA
Found at i:3906081 original size:18 final size:19
Alignment explanation
Indices: 3906050--3906087 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3906040 AATTATAAAA
3906050 AATTAAAAGTG-AAATAAT
1 AATTAAAAGTGAAAATAAT
3906068 AATTAAAA-TAGAAAATAAT
1 AATTAAAAGT-GAAAATAAT
3906087 A
1 A
3906088 TATAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 9 0.50
19 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
AATTAAAAGTGAAAATAAT
Found at i:3907175 original size:28 final size:28
Alignment explanation
Indices: 3907116--3907180 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
3907106 TTTAAGTAAA
* *
3907116 TTTTATATTTTATTTTATCAAATTAATTT
1 TTTTATTTTTTATTTTATCAAA-TAATAT
*
3907145 TTTTATTTTTTATTTATATCTAA-AATAT
1 TTTTATTTTTTATTT-TATCAAATAATAT
*
3907173 TTTGATTT
1 TTTTATTT
3907181 GTAAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 11 0.35
29 14 0.45
30 6 0.19
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTATTTTTTATTTTATCAAATAATAT
Found at i:3907675 original size:17 final size:18
Alignment explanation
Indices: 3907645--3907680 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3907635 ATTTCTTTTT
*
3907645 ATTTAATTTATTTTTTAA
1 ATTTAATATATTTTTTAA
3907663 ATTTAATAT-TTTTTTAA
1 ATTTAATATATTTTTTAA
3907680 A
1 A
3907681 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTAATATATTTTTTAA
Found at i:3908733 original size:13 final size:12
Alignment explanation
Indices: 3908682--3908741 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
3908672 ATTAAATATG
3908682 AATAATATTTAAA
1 AATAAT-TTTAAA
*
3908695 AAT-TTTTTAGAA
1 AATAATTTTA-AA
*
3908707 TCATAATTTTAAA
1 -AATAATTTTAAA
3908720 AATAATTATTAAA
1 AATAATT-TTAAA
3908733 AATAATTTT
1 AATAATTTT
3908742 TTATTTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 4 0.10
12 11 0.28
13 19 0.49
14 5 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
AATAATTTTAAA
Found at i:3909491 original size:4 final size:4
Alignment explanation
Indices: 3909482--3909507 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3909472 AAAATATGGG
3909482 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3909508 GTGATTTGTT
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:3911419 original size:18 final size:17
Alignment explanation
Indices: 3911364--3911420 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
3911354 TATTTAAATT
*
3911364 TAAATAATTATAAA-ATA
1 TAAATAATTTTAAATA-A
**
3911381 TAAATAATTTTTTATATA
1 TAAATAATTTTAAATA-A
3911399 TAAATATATTTTAAATAA
1 TAAATA-ATTTTAAATAA
3911417 TAAA
1 TAAA
3911421 AAAATTAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 11 0.33
18 14 0.42
19 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATAATTTTAAATAA
Found at i:3915471 original size:27 final size:25
Alignment explanation
Indices: 3915423--3915501 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
3915413 ATTATAATAA
3915423 ATAAATATATTAAA-ATTTATATAAAT
1 ATAAAT-TATTAAATA-TTATATAAAT
**
3915449 ATAAATTATTAATATATTAATATTTAT
1 ATAAATTATTAA-ATATT-ATATAAAT
*
3915476 ATAAA-TATAAAATATTATA-AAAT
1 ATAAATTATTAAATATTATATAAAT
3915499 ATA
1 ATA
3915502 TAAATATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
23 5 0.11
24 3 0.07
25 11 0.24
26 14 0.31
27 12 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAAATTATTAAATATTATATAAAT
Found at i:3915484 original size:8 final size:8
Alignment explanation
Indices: 3915418--3915509 Score: 55
Period size: 8 Copynumber: 10.8 Consensus size: 8
3915408 ACACGATTAT
*
3915418 AATAAATA
1 AATATATA
3915426 AATATATTAA
1 AATATA-T-A
*
3915436 AATTTATA
1 AATATATA
3915444 TAA-ATATA
1 -AATATATA
*
3915452 AAT-TATT
1 AATATATA
3915459 AATATATTA
1 AATATA-TA
3915468 ATATTTATATA
1 A-A--TATATA
3915479 AATATA-A
1 AATATATA
3915486 AATATTATAA
1 AATA-TAT-A
3915496 AATATATA
1 AATATATA
3915504 AATATA
1 AATATA
3915510 ATACGAATAC
Statistics
Matches: 67, Mismatches: 5, Indels: 24
0.70 0.05 0.25
Matches are distributed among these distances:
7 13 0.19
8 25 0.37
9 9 0.13
10 13 0.19
11 3 0.04
12 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATATATA
Found at i:3915492 original size:33 final size:33
Alignment explanation
Indices: 3915426--3915492 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3915416 ATAATAAATA
*
3915426 AATATATTAAAATTTATATAAATATAAATTATT
1 AATATATTAAAATTTATATAAATATAAAATATT
*
3915459 AATATATTAATATTTATATAAATATAAAATATT
1 AATATATTAAAATTTATATAAATATAAAATATT
3915492 A
1 A
3915493 TAAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AATATATTAAAATTTATATAAATATAAAATATT
Found at i:3915503 original size:27 final size:27
Alignment explanation
Indices: 3915425--3915510 Score: 70
Period size: 33 Copynumber: 3.0 Consensus size: 27
3915415 TATAATAAAT
*
3915425 AAATA-TATTAAAATTTATATAAATATA
1 AAATATTA-TAAAATATATATAAATATA
*
3915452 AATTATTAATATATTAATATTTATATAAATATA
1 AAATATT-ATA-A--AATA--TATATAAATATA
3915485 AAATATTAT-AAA-ATATATAAATATA
1 AAATATTATAAAATATATATAAATATA
3915510 A
1 A
3915511 TACGAATACA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
25 13 0.27
27 5 0.10
28 5 0.10
29 2 0.04
30 1 0.02
31 3 0.06
32 2 0.04
33 18 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATATTATAAAATATATATAAATATA
Found at i:3915518 original size:19 final size:17
Alignment explanation
Indices: 3915478--3915512 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3915468 ATATTTATAT
*
3915478 AAATATAAAATATTATA
1 AAATATAAAATATAATA
3915495 AAATATATAAATATAATA
1 AAATATA-AAATATAATA
3915513 CGAATACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAAAATATAATA
Found at i:3916322 original size:2 final size:2
Alignment explanation
Indices: 3916315--3916343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3916305 TTTATGAATC
3916315 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3916344 CCCCTTGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3923460 original size:14 final size:14
Alignment explanation
Indices: 3923439--3923476 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3923429 TATAAAATTA
3923439 AAAATATT-TCACGT
1 AAAATATTAT-ACGT
*
3923453 ATAATATTATACGT
1 AAAATATTATACGT
3923467 AAAATATTAT
1 AAAATATTAT
3923477 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 20 0.95
15 1 0.05
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (14 bp):
AAAATATTATACGT
Found at i:3924901 original size:19 final size:20
Alignment explanation
Indices: 3924875--3924923 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3924865 TAATTTTATG
*
3924875 ATATAAATATGATATAAAAAT
1 ATATAAATATAATA-AAAAAT
3924896 -TA-AAATATAATAAAAAAT
1 ATATAAATATAATAAAAAAT
3924914 ATATAAATAT
1 ATATAAATAT
3924924 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 11 0.44
20 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATAAATATAATAAAAAAT
Found at i:3924951 original size:36 final size:37
Alignment explanation
Indices: 3924862--3925013 Score: 102
Period size: 38 Copynumber: 4.1 Consensus size: 37
3924852 GTTAGATATA
*
3924862 ATATAATT-TT-ATGATATAAATATGATATAAAA-ATTAAA
1 ATATAATTATTAAT-ATATAAATAT--TATAAAATA-TAAT
* ** *
3924900 ATATAATAAAAAATATATAAATATTTTAAAATATAAT
1 ATATAATTATTAATATATAAATATTATAAAATATAAT
*
3924937 AT-TAATTATTAATATATTTAAAT-TTATATAAATATAAA
1 ATATAATTATTAATATA--TAAATATTATA-AAATATAAT
* *
3924975 ATATATTTATT-ATATAATAAA-ATATATAAATTATAAT
1 ATATAATTATTAATAT-ATAAATAT-TATAAAATATAAT
3925012 AT
1 AT
3925014 CTACTCGAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
36 11 0.12
37 29 0.32
38 31 0.34
39 18 0.20
40 2 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (37 bp):
ATATAATTATTAATATATAAATATTATAAAATATAAT
Found at i:3924978 original size:7 final size:8
Alignment explanation
Indices: 3924886--3925010 Score: 51
Period size: 7 Copynumber: 16.8 Consensus size: 8
3924876 TATAAATATG
*
3924886 ATATAAAA
1 ATATAAAT
3924894 AT-TAAA-
1 ATATAAAT
3924900 ATAT-AAT
1 ATATAAAT
*
3924907 A-AAAAAT
1 ATATAAAT
3924914 ATATAAAT
1 ATATAAAT
*
3924922 ATTTTAAA-
1 A-TATAAAT
3924930 ATAT-AAT
1 ATATAAAT
*
3924937 AT-TAATT
1 ATATAAAT
3924944 AT-TAATAT
1 ATATAA-AT
*
3924952 ATTTAAATTT
1 ATATAAA--T
3924962 ATATAAAT
1 ATATAAAT
3924970 ATA-AAAT
1 ATATAAAT
**
3924977 ATATTTAT
1 ATATAAAT
*
3924985 -TATATA-
1 ATATAAAT
3924991 ATA-AAAT
1 ATATAAAT
3924998 ATATAAAT
1 ATATAAAT
3925006 -TATAA
1 ATATAA
3925011 TATCTACTCG
Statistics
Matches: 91, Mismatches: 11, Indels: 31
0.68 0.08 0.23
Matches are distributed among these distances:
6 10 0.11
7 43 0.47
8 23 0.25
9 8 0.09
10 7 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:3924984 original size:21 final size:21
Alignment explanation
Indices: 3924958--3925001 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3924948 ATATATTTAA
3924958 ATTTATATAAAT-ATAAAATAT
1 ATTTAT-TAAATAATAAAATAT
*
3924979 ATTTATTATATAATAAAATAT
1 ATTTATTAAATAATAAAATAT
3925000 AT
1 AT
3925002 AAATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTATTAAATAATAAAATAT
Found at i:3924994 original size:27 final size:28
Alignment explanation
Indices: 3924909--3925005 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 28
3924899 AATATAATAA
**
3924909 AAAATATATAAATAT-TTTAAAATATAAT
1 AAAATATATAAATATATTTAATTTAT-AT
* *
3924937 ATTAAT-TATTAATATATTTAAATTTATAT
1 A-AAATATATAAATATATTT-AATTTATAT
3924966 -AAATATA-AAATATATTT-ATTATATAAT
1 AAAATATATAAATATATTTAATT-TAT-AT
3924993 AAAATATATAAAT
1 AAAATATATAAAT
3925006 TATAATATCT
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
25 3 0.05
26 3 0.05
27 14 0.25
28 18 0.33
29 12 0.22
30 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATATATAAATATATTTAATTTATAT
Found at i:3925004 original size:30 final size:29
Alignment explanation
Indices: 3924898--3925009 Score: 90
Period size: 30 Copynumber: 3.9 Consensus size: 29
3924888 ATAAAAATTA
*
3924898 AAATATAATAAAAAATATATAAATAT-TTT
1 AAATATAATAAAATATATA-AAATATATTT
* *
3924927 AAAATATAATATTAAT-TAT-TAATATATTT
1 -AAATATAATA-AAATATATAAAATATATTT
* *
3924956 AAAT-TTATATAA-ATATAAAATATATTT
1 AAATATAATAAAATATATAAAATATATTT
* *
3924983 ATTATATAATAAAATATATAAATTATA
1 A-AATATAATAAAATATATAAAATATA
3925010 ATATCTACTC
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
26 6 0.09
27 14 0.21
28 11 0.17
29 9 0.14
30 24 0.36
31 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATATAATAAAATATATAAAATATATTT
Found at i:3925007 original size:21 final size:21
Alignment explanation
Indices: 3924970--3925009 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3924960 TTATATAAAT
**
3924970 ATAAAATATATTTATTATATA
1 ATAAAATATATAAATTATATA
3924991 ATAAAATATATAAATTATA
1 ATAAAATATATAAATTATA
3925010 ATATCTACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAATATATAAATTATATA
Found at i:3925008 original size:24 final size:24
Alignment explanation
Indices: 3924960--3925013 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
3924950 ATATTTAAAT
*
3924960 TTATATAAATATAAAATATATTTA
1 TTATATAAATATAAAATATAATTA
3924984 TTATAT-AATA-AAATATATAAATTA
1 TTATATAAATATAAA-ATAT-AATTA
*
3925008 TAATAT
1 TTATAT
3925014 CTACTCGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 15 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTATATAAATATAAAATATAATTA
Found at i:3925313 original size:3 final size:3
Alignment explanation
Indices: 3925305--3925356 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
3925295 GGTTTACTAG
3925305 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3925353 TAT T
1 TAT T
3925357 CTAATCATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3925617 original size:27 final size:29
Alignment explanation
Indices: 3925564--3925630 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
3925554 CGTGATAATT
3925564 TTAT-ATTATATCTATAAAATTTATTATA
1 TTATAATTATATCTATAAAATTTATTATA
3925592 TTATAATTATAT-T-TAAAATATT-TTATA
1 TTATAATTATATCTATAAAAT-TTATTATA
3925619 TT-TATATTATAT
1 TTATA-ATTATAT
3925631 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 7 0.19
29 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATAATTATATCTATAAAATTTATTATA
Found at i:3925631 original size:29 final size:29
Alignment explanation
Indices: 3925563--3925678 Score: 82
Period size: 29 Copynumber: 4.0 Consensus size: 29
3925553 ACGTGATAAT
* *
3925563 TTTATATTATATCTATAAAAT-TTATTATA
1 TTTATATTATATATTTAAAATATT-TTATA
*
3925592 -TTATAAT-TATATTTAAAATATTTTATA
1 TTTATATTATATATTTAAAATATTTTATA
3925619 TTTATATTATATAAATTTTAAAATA---TATA
1 TTTATATTATAT--A-TTTAAAATATTTTATA
* *
3925648 TTTATATCATATCATATTTTAATTATTTTAT
1 TTTATAT--TAT-ATATTTAAAATATTTTAT
3925679 TACATTCATA
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
27 15 0.22
28 14 0.20
29 21 0.30
30 1 0.01
31 4 0.06
32 14 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTATATTATATATTTAAAATATTTTATA
Found at i:3925636 original size:22 final size:22
Alignment explanation
Indices: 3925592--3925651 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3925582 ATTTATTATA
3925592 TTATAATTATATTTAAAATATT
1 TTATAATTATATTTAAAATATT
* *
3925614 TTATATTTATATTATATAA-ATT
1 TTATAATTATATT-TAAAATATT
*
3925636 TTAAAATATATATTTA
1 TTATAAT-TATATTTA
3925652 TATCATATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAATTATATTTAAAATATT
Found at i:3927812 original size:28 final size:25
Alignment explanation
Indices: 3927761--3927812 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
3927751 TATTATTTAA
**
3927761 TAATTAAAATATTTATATTTAAATT
1 TAATTAAAATATTTATATAAAAATT
3927786 TAATTATAAATATATTAATATAAAAAT
1 TAATTA-AAATAT-TT-ATATAAAAAT
3927813 ACGTTTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 6 0.27
27 2 0.09
28 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTAAAATATTTATATAAAAATT
Found at i:3928765 original size:20 final size:20
Alignment explanation
Indices: 3928728--3928765 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3928718 ATTAGCTTAA
*
3928728 ATTTTATATTAATATATAAT
1 ATTTTAAATTAATATATAAT
3928748 ATTTTAAATATAAT-TATA
1 ATTTTAAAT-TAATATATA
3928766 TTACATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTAAATTAATATATAAT
Found at i:3931242 original size:18 final size:18
Alignment explanation
Indices: 3931219--3931254 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3931209 GCAATGGTGA
3931219 CGAAAGATTTAACCTCGT
1 CGAAAGATTTAACCTCGT
3931237 CGAAAGATTTAACCTCGT
1 CGAAAGATTTAACCTCGT
3931255 TGTTCTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
CGAAAGATTTAACCTCGT
Found at i:3933879 original size:30 final size:30
Alignment explanation
Indices: 3933780--3933883 Score: 109
Period size: 30 Copynumber: 3.3 Consensus size: 30
3933770 ATTTTATATT
3933780 AAATTTAAAATTATTATTTAAAAATAATAA
1 AAATTTAAAATTATTATTTAAAAATAATAA
* * * * *
3933810 AAATTAAAAAATATTTTTTATTAAAATTTATATT
1 AAATTTAAAATTATTATTTA--AAAA-TAATA-A
* *
3933844 AAATTTCAAATTACTATTTAAAAATAATAA
1 AAATTTAAAATTATTATTTAAAAATAATAA
3933874 AAATTTAAAA
1 AAATTTAAAA
3933884 AATATTTTGC
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
30 26 0.46
31 4 0.07
32 8 0.14
33 4 0.07
34 15 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATTTAAAATTATTATTTAAAAATAATAA
Found at i:3933941 original size:14 final size:15
Alignment explanation
Indices: 3933909--3933954 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3933899 ATCTTAAATA
3933909 ATTATTAAAAAATATT
1 ATTATTAAAAAAT-TT
*
3933925 TTATATTAAAAAATTT
1 AT-TATTAAAAAATTT
3933941 ATTATTAAAAAATT
1 ATTATTAAAAAATT
3933955 AATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTATTAAAAAATTT
Found at i:3935002 original size:21 final size:21
Alignment explanation
Indices: 3934977--3935032 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3934967 TATTTATGAG
3934977 ATTTAATATTTTTAAAAAATA
1 ATTTAATATTTTTAAAAAATA
* * *
3934998 ATTTAAGATTTAATATAAAATA
1 ATTTAATATTT-TTAAAAAATA
*
3935020 TTTTAAT-TTTTTA
1 ATTTAATATTTTTA
3935033 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.07
21 13 0.46
22 13 0.46
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTAATATTTTTAAAAAATA
Found at i:3935022 original size:51 final size:51
Alignment explanation
Indices: 3934967--3935123 Score: 151
Period size: 51 Copynumber: 3.1 Consensus size: 51
3934957 TAAAAAATTG
3934967 TATTTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTAATATAAAA
1 TATTTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTAATATAAAA
* ** * * * ** * **
3935018 TATTT-TAATTTTTTATTATTTTTAAATAGTAA-AAAATTATTTAA-A-AATTG
1 TATTTATGA-GATTTAATATTTTTAAAAAATAATTTAA-GATTTAATATAA-AA
*
3935068 TAATTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTAATATAAAA
1 TATTTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTAATATAAAA
3935119 TATTT
1 TATTT
3935124 TTTAATTTTT
Statistics
Matches: 75, Mismatches: 24, Indels: 14
0.66 0.21 0.12
Matches are distributed among these distances:
49 2 0.03
50 33 0.44
51 38 0.51
52 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (51 bp):
TATTTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTAATATAAAA
Found at i:3935093 original size:101 final size:106
Alignment explanation
Indices: 3934901--3935146 Score: 398
Period size: 101 Copynumber: 2.3 Consensus size: 106
3934891 TTCAATACAT
3934901 ATATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTGAAAAAATTTATTATTTTAAAAAATT
1 ATATAAAATATTTTTAATTTTTTATTATTTTTAAATAGT-AAAAAA--TATTATTTTAAAAAATT
*
3934966 GTATTTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTA
63 GTAATTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTA
3935010 ATATAAAATA-TTTTAATTTTTTATTATTTTTAAATAGT-AAAAA-ATTA-TTT-AAAAATTGTA
1 ATATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAAAAAATATTATTTTAAAAAATTGTA
3935070 ATTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTA
66 ATTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTA
3935111 ATATAAAATATTTTTTAATTTTTTA-T-TTTTTAAATA
1 ATATAAAATA-TTTTTAATTTTTTATTATTTTTAAATA
3935147 ATATTTTTAA
Statistics
Matches: 134, Mismatches: 1, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
101 70 0.52
102 4 0.03
103 17 0.13
106 5 0.04
108 28 0.21
109 10 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (106 bp):
ATATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAAAAAATATTATTTTAAAAAATTGTA
ATTATGAGATTTAATATTTTTAAAAAATAATTTAAGATTTA
Found at i:3935279 original size:2 final size:2
Alignment explanation
Indices: 3935274--3935302 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3935264 TTTCAATCCT
3935274 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3935303 ATTAGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3935414 original size:42 final size:43
Alignment explanation
Indices: 3935368--3935449 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
3935358 ATTATAAATA
* * *
3935368 ATAATTCAAGATTTAATATGAAATTTTTTTTAAT-TTTTAATT
1 ATAATTCAAGAATTAATATAAAATATTTTTTAATATTTTAATT
**
3935410 ATAATTTGAGAATTAATATAAAATATTTTTTAATATTTTA
1 ATAATTCAAGAATTAATATAAAATATTTTTTAATATTTTA
3935450 TATTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 29 0.85
43 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (43 bp):
ATAATTCAAGAATTAATATAAAATATTTTTTAATATTTTAATT
Found at i:3935561 original size:2 final size:2
Alignment explanation
Indices: 3935556--3935581 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3935546 ATATATGTTC
3935556 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
3935582 AATTATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3935723 original size:52 final size:49
Alignment explanation
Indices: 3935667--3935824 Score: 154
Period size: 53 Copynumber: 3.0 Consensus size: 49
3935657 ATATATTATT
* *
3935667 TTTTATAAATTTTTAAATAGTAATTTAAGTTTTAATATAAAATATTTTTAAA
1 TTTTAT-AATTTTTAAATA-TAATTTAA-ATTTAATATAAAATATTTTTTAA
* * * * *
3935719 TTTTATTATTTTTAAATAATTATTCAAAATCTAACATAAAATACTTTTTTAA
1 TTTTATAATTTTTAAAT-ATAATT-TAAATTTAATATAAAATA-TTTTTTAA
* *
3935771 TTTTTTTATTTTTTAAATTATAATTTATAATTTAATATAAAATATTTTTTAA
1 -TTTTATAATTTTTAAA-TATAATTTA-AATTTAATATAAAATATTTTTTAA
3935823 TT
1 TT
3935825 ATTTACATCC
Statistics
Matches: 86, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
51 28 0.33
52 25 0.29
53 32 0.37
54 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (49 bp):
TTTTATAATTTTTAAATATAATTTAAATTTAATATAAAATATTTTTTAA
Found at i:3935741 original size:17 final size:16
Alignment explanation
Indices: 3935709--3935742 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3935699 TAATATAAAA
*
3935709 TATTTTTAAATTTTAT
1 TATTTTTAAATATTAT
3935725 TATTTTTAAATAATTAT
1 TATTTTTAAAT-ATTAT
3935742 T
1 T
3935743 CAAAATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAAATATTAT
Found at i:3935811 original size:53 final size:50
Alignment explanation
Indices: 3935675--3935824 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 50
3935665 TTTTTTATAA
* *
3935675 ATTTTTAAA-TAGTAATTTAAGTTTTAATATAAAATATTTTTAAATTTTATT
1 ATTTTTAAATTA-TAATTTAA-ATTTAATATAAAATATTTTTTAATTTTATT
* * * * * *
3935726 ATTTTTAAATAATTATTCAAAATCTAACATAAAATACTTTTTTAATTTTTTT
1 ATTTTTAAATTATAATT-TAAATTTAATATAAAATA-TTTTTTAATTTTATT
3935778 ATTTTTTAAATTATAATTTATAATTTAATATAAAATATTTTTTAATT
1 A-TTTTTAAATTATAATTTA-AATTTAATATAAAATATTTTTTAATT
3935825 ATTTACATCC
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
51 25 0.31
52 28 0.35
53 28 0.35
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (50 bp):
ATTTTTAAATTATAATTTAAATTTAATATAAAATATTTTTTAATTTTATT
Found at i:3940557 original size:21 final size:21
Alignment explanation
Indices: 3940532--3940574 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3940522 CTGCCGTAAG
3940532 TTCTAAAAATTTGTAGTGTGA
1 TTCTAAAAATTTGTAGTGTGA
3940553 TTCTAAAAATTTGTAGTGTGA
1 TTCTAAAAATTTGTAGTGTGA
3940574 T
1 T
3940575 ACTTGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (21 bp):
TTCTAAAAATTTGTAGTGTGA
Found at i:3947244 original size:2 final size:2
Alignment explanation
Indices: 3947237--3947272 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3947227 CAAGGGTTTC
3947237 AT 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 AT
3947273 TAAATTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3948695 original size:2 final size:2
Alignment explanation
Indices: 3948690--3948728 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3948680 ACAACTCTGA
3948690 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3948729 TTCTTTGTCT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3949451 original size:14 final size:15
Alignment explanation
Indices: 3949421--3949453 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3949411 ATTATCAAAA
3949421 TTTTATGAGTAATTT
1 TTTTATGAGTAATTT
3949436 TTTTATGAGTAATTT
1 TTTTATGAGTAATTT
3949451 TTT
1 TTT
3949454 GTTACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
TTTTATGAGTAATTT
Found at i:3949953 original size:2 final size:2
Alignment explanation
Indices: 3949946--3949972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3949936 TGGTTTTGCT
3949946 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3949973 GTAAATGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3951454 original size:2 final size:2
Alignment explanation
Indices: 3951447--3951480 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3951437 GATTGAAAGA
3951447 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
3951481 CTCTATAAGA
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:3953077 original size:22 final size:22
Alignment explanation
Indices: 3953052--3953094 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3953042 GTTTCACTCT
3953052 TTTAATTTTG-TTAAAATAACTA
1 TTTAATTTTGTTTAAAA-AACTA
*
3953074 TTTACTTTTGTTTAAAAAACT
1 TTTAATTTTGTTTAAAAAACT
3953095 TCCTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTAATTTTGTTTAAAAAACTA
Found at i:3953916 original size:2 final size:2
Alignment explanation
Indices: 3953877--3953904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3953867 TATACTATTG
3953877 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
3953905 GTTTTATATA
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:3954769 original size:13 final size:13
Alignment explanation
Indices: 3954753--3954789 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3954743 ATTATTTTAA
3954753 AATATTTATTTTT
1 AATATTTATTTTT
*
3954766 AATATTTATATTT
1 AATATTTATTTTT
*
3954779 AATATATATTT
1 AATATTTATTT
3954790 AAATAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATTTTT
Found at i:3954863 original size:6 final size:6
Alignment explanation
Indices: 3954852--3954893 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
3954842 ATTTAAAAAA
*
3954852 TATATT TATATT TA-ATA TATATT TATATT TAATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT T-ATATT TATATT
3954894 CAAATATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
7 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:3954869 original size:13 final size:12
Alignment explanation
Indices: 3954852--3954893 Score: 59
Period size: 13 Copynumber: 3.5 Consensus size: 12
3954842 ATTTAAAAAA
3954852 TATATTTATATT
1 TATATTTATATT
*
3954864 TA-ATATATATT
1 TATATTTATATT
3954875 TATATTTAATATT
1 TATATTT-ATATT
3954888 TATATT
1 TATATT
3954894 CAAATATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 10 0.38
12 5 0.19
13 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTATATT
Found at i:3954870 original size:15 final size:16
Alignment explanation
Indices: 3954849--3954900 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 16
3954839 AAAATTTAAA
3954849 AAATATATTTATATTT
1 AAATATATTTATATTT
3954865 AATATATATTTATATTT
1 AA-ATATATTTATATTT
*
3954882 --A-ATATTTATATTC
1 AAATATATTTATATTT
3954895 AAATAT
1 AAATAT
3954901 TACAGCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
15 1 0.03
16 4 0.13
17 14 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATATTTATATTT
Found at i:3954873 original size:17 final size:17
Alignment explanation
Indices: 3954851--3954886 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3954841 AATTTAAAAA
3954851 ATATATTTATATTTAAT
1 ATATATTTATATTTAAT
3954868 ATATATTTATATTTAAT
1 ATATATTTATATTTAAT
3954885 AT
1 AT
3954887 TTATATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTATATTTAAT
Found at i:3960641 original size:31 final size:32
Alignment explanation
Indices: 3960605--3960681 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
3960595 TAAATTTATA
3960605 TTTAATTATAAATAAAGTTAT-TA-AATAATT
1 TTTAATTATAAATAAAGTTATATATAATAATT
* * *
3960635 TATTAATAATATATAAATTTATATATTAATAATT
1 T-TTAATTATAAATAAAGTTATATA-TAATAATT
3960669 TTT-ATATATAAAT
1 TTTAAT-TATAAAT
3960682 CAATATATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 1 0.03
31 17 0.46
32 4 0.11
33 7 0.19
34 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
TTTAATTATAAATAAAGTTATATATAATAATT
Found at i:3960981 original size:21 final size:21
Alignment explanation
Indices: 3960955--3961003 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3960945 AAATCGCATT
3960955 AAAAAAAAAGT-TAAAAATTA
1 AAAAAAAAAGTATAAAAATTA
* *
3960975 GAAAAAAAAAGTATAATAGTTA
1 -AAAAAAAAAGTATAAAAATTA
3960997 AAAAAAA
1 AAAAAAA
3961004 TTAAAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AAAAAAAAAGTATAAAAATTA
Found at i:3961001 original size:22 final size:21
Alignment explanation
Indices: 3960955--3961003 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
3960945 AAATCGCATT
*
3960955 AAAAAAAAAGTTAAAAATTAG
1 AAAAAAAAAGTTAAAAATTAA
* *
3960976 AAAAAAAAAGTATAATAGTTAA
1 AAAAAAAAAGT-TAAAAATTAA
3960998 AAAAAA
1 AAAAAA
3961004 TTAAAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AAAAAAAAAGTTAAAAATTAA
Found at i:3961490 original size:21 final size:20
Alignment explanation
Indices: 3961456--3961495 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3961446 ATTAATTGAA
*
3961456 AATTATTTTATATTTTATTT
1 AATTATTTTATATTATATTT
*
3961476 AATTAATTTTTTATTATATT
1 AATT-ATTTTATATTATATT
3961496 CAAAATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATTATTTTATATTATATTT
Found at i:3961928 original size:24 final size:24
Alignment explanation
Indices: 3961901--3961946 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3961891 AGTAGAAAAT
3961901 TTTTAAAAAATGA-TTTATTATTTA
1 TTTT-AAAAATGATTTTATTATTTA
* *
3961925 TTTTTAAAATTATTTTATTATT
1 TTTTAAAAATGATTTTATTATT
3961947 AAAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTAAAAATGATTTTATTATTTA
Found at i:3961943 original size:17 final size:18
Alignment explanation
Indices: 3961917--3961956 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3961907 AAAATGATTT
*
3961917 ATTA-TTTATT-TTTAAA
1 ATTATTTTATTATTAAAA
3961933 ATTATTTTATTATTAAAA
1 ATTATTTTATTATTAAAA
3961951 ATTATT
1 ATTATT
3961957 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATTTTATTATTAAAA
Found at i:3962549 original size:21 final size:20
Alignment explanation
Indices: 3962525--3962563 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3962515 AAATTTTGAG
*
3962525 ATAATAAAAGTTTTATAAAGT
1 ATAATAAAAATTTT-TAAAGT
3962546 ATAATAAAAATTTTTAAA
1 ATAATAAAAATTTTTAAA
3962564 TAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATAATAAAAATTTTTAAAGT
Found at i:3966411 original size:3 final size:3
Alignment explanation
Indices: 3966403--3966441 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3966393 CGACAGCTGC
*
3966403 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3966442 AGTTGTTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:3967486 original size:2 final size:2
Alignment explanation
Indices: 3967479--3967511 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3967469 GAATACATAC
3967479 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 A
3967512 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3967516 original size:2 final size:2
Alignment explanation
Indices: 3967511--3967535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3967501 ATATATATAT
3967511 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
3967536 AACACACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3968677 original size:3 final size:3
Alignment explanation
Indices: 3968671--3968703 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3968661 CCATCATCAT
*
3968671 CTG CTG CTG CTG CTG CTG CTG CTG CTG TTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
3968704 TTGCAGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.36
Consensus pattern (3 bp):
CTG
Found at i:3975893 original size:18 final size:17
Alignment explanation
Indices: 3975870--3975916 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
3975860 AAAGCTTATT
3975870 ATTTTTTAAATAAATATC
1 ATTTTTTAAATAAAT-TC
** *
3975888 ATTTTTTATTTAAATTT
1 ATTTTTTAAATAAATTC
3975905 ATTTTTTAAATA
1 ATTTTTTAAATA
3975917 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTTAAATAAATTC
Found at i:3975912 original size:13 final size:14
Alignment explanation
Indices: 3975888--3975936 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
3975878 AATAAATATC
3975888 ATTT-TTTATTTAA
1 ATTTATTTATTTAA
3975901 ATTTATTT-TTTAA
1 ATTTATTTATTTAA
*
3975914 ATATT-TTTATTAAA
1 AT-TTATTTATTTAA
3975928 ATTTATTTA
1 ATTTATTTA
3975937 AATATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 16 0.52
14 15 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTATTTATTTAA
Found at i:3976117 original size:3 final size:3
Alignment explanation
Indices: 3976109--3976137 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3976099 AGGTGGGTTC
3976109 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3976138 GGCTAAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3976701 original size:13 final size:13
Alignment explanation
Indices: 3976669--3976694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3976659 TATAGATTTG
3976669 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3976682 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3976695 ATTAAATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:3977379 original size:21 final size:19
Alignment explanation
Indices: 3977351--3977394 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3977341 TTATTAAATT
*
3977351 AAAA-TATTTGTAAATTAATA
1 AAAATTATTT-TAAAATAA-A
3977371 AAAATTATTTTAAAATAAA
1 AAAATTATTTTAAAATAAA
3977390 AAAAT
1 AAAAT
3977395 AAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATTATTTTAAAATAAA
Found at i:3977395 original size:8 final size:8
Alignment explanation
Indices: 3977382--3977434 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
3977372 AAATTATTTT
3977382 AAAATAAA
1 AAAATAAA
3977390 AAAATAAA
1 AAAATAAA
* *
3977398 AATTATTAA
1 AA-AATAAA
*
3977407 AAAATCAA
1 AAAATAAA
3977415 AAAATCAAA
1 AAAAT-AAA
3977424 AAAATAAA
1 AAAATAAA
3977432 AAA
1 AAA
3977435 TATTTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
8 25 0.66
9 13 0.34
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:3977395 original size:25 final size:25
Alignment explanation
Indices: 3977367--3977425 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
3977357 TTTGTAAATT
**
3977367 AATAAAAATTATTTTAAAATAAAAA
1 AATAAAAATTATTAAAAAATAAAAA
*
3977392 AATAAAAATTATTAAAAAATCAAAA
1 AATAAAAATTATTAAAAAATAAAAA
3977417 AATCAAAAA
1 AAT-AAAAA
3977426 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (25 bp):
AATAAAAATTATTAAAAAATAAAAA
Found at i:3977408 original size:17 final size:16
Alignment explanation
Indices: 3977388--3977438 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
3977378 TTTTAAAATA
3977388 AAAAAATAAAAATTATT
1 AAAAAATAAAAA-TATT
*
3977405 AAAAAATCAAAAA-ATCA
1 AAAAAAT-AAAAATAT-T
3977422 AAAAAATAAAAAATATT
1 AAAAAAT-AAAAATATT
3977439 TTATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 2 0.07
17 19 0.68
18 7 0.25
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAATAAAAATATT
Found at i:3977433 original size:25 final size:25
Alignment explanation
Indices: 3977383--3977434 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
3977373 AATTATTTTA
* *
3977383 AAATAAAAAAATAAAAATTATTAAA
1 AAATAAAAAAATAAAAAATATAAAA
*
3977408 AAATCAAAAAATCAAAAAA-ATAAAA
1 AAATAAAAAAAT-AAAAAATATAAAA
3977433 AA
1 AA
3977435 TATTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (25 bp):
AAATAAAAAAATAAAAAATATAAAA
Found at i:3977483 original size:23 final size:22
Alignment explanation
Indices: 3977432--3977484 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
3977422 AAAAAATAAA
*
3977432 AAATATTTTATTAAATTATTTTT
1 AAAT-TTTTATTAAATTATTATT
3977455 ATAATTTTTA-TATAATATATTATT
1 A-AATTTTTATTA-AAT-TATTATT
3977479 AAATTT
1 AAATTT
3977485 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.08
23 14 0.54
24 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTTTTATTAAATTATTATT
Done.