Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 100 of 141
Found at i:28512384 original size:9 final size:9
Alignment explanation
Indices: 28512329--28512387 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
28512319 CAGAAAAAAG
28512329 AAAAAGAAA
1 AAAAAGAAA
28512338 AAAGAAGAAA
1 AAA-AAGAAA
**
28512348 AGGAA-AAA
1 AAAAAGAAA
*
28512356 AGAAAGAAA
1 AAAAAGAAA
*
28512365 AAAAGGAAA
1 AAAAAGAAA
28512374 AAAAAGAAA
1 AAAAAGAAA
28512383 AAAAA
1 AAAAA
28512388 AAGAAGAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
8 7 0.17
9 28 0.67
10 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:28512928 original size:17 final size:17
Alignment explanation
Indices: 28512904--28513012 Score: 63
Period size: 17 Copynumber: 6.5 Consensus size: 17
28512894 AATTCTCATG
28512904 TTTC-AAAATTTTGTGT
1 TTTCAAAAATTTTGTGT
*
28512920 TTTCAAAAATTTT-TCAT
1 TTTCAAAAATTTTGT-GT
28512937 GTTTCAAAAAATTCTTGTG-
1 -TTTC-AAAAATT-TTGTGT
*
28512956 TTTCAAAAA-TTT-AGT
1 TTTCAAAAATTTTGTGT
* *
28512971 CTTCAAAAACTATTGTG-
1 TTTCAAAAA-TTTTGTGT
*
28512988 TTTC-AAAATTATCGTGT
1 TTTCAAAAATT-TTGTGT
28513005 TTT-AAAAA
1 TTTCAAAAA
28513013 AATTCTTGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 25
0.68 0.09 0.24
Matches are distributed among these distances:
14 1 0.01
15 11 0.15
16 14 0.20
17 26 0.37
18 9 0.13
19 7 0.10
20 2 0.03
21 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTCAAAAATTTTGTGT
Found at i:28512937 original size:34 final size:36
Alignment explanation
Indices: 28512885--28512967 Score: 109
Period size: 34 Copynumber: 2.4 Consensus size: 36
28512875 CGATACGTCC
* *
28512885 TTTTAAAAAAATTCTCATGTTTC-AAAATT-TTGTG
1 TTTTCAAAAATTTCTCATGTTTCAAAAATTCTTGTG
*
28512919 TTTTCAAAAATTTTTCATGTTTCAAAAAATTCTTGTG
1 TTTTCAAAAATTTCTCATGTTTC-AAAAATTCTTGTG
28512956 -TTTCAAAAATTT
1 TTTTCAAAAATTT
28512968 AGTCTTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 20 0.47
36 18 0.42
37 5 0.12
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (36 bp):
TTTTCAAAAATTTCTCATGTTTCAAAAATTCTTGTG
Found at i:28512941 original size:18 final size:17
Alignment explanation
Indices: 28512891--28512967 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
28512881 GTCCTTTTAA
* *
28512891 AAAAATTCTCATGTTTC
1 AAAAATTTTTATGTTTC
*
28512908 -AAAA-TTTTGTGTTTTC
1 AAAAATTTTTATG-TTTC
28512924 AAAAATTTTTCATGTTTC
1 AAAAATTTTT-ATGTTTC
* *
28512942 AAAAAATTCTTGTGTTTC
1 -AAAAATTTTTATGTTTC
28512960 AAAAATTT
1 AAAAATTT
28512968 AGTCTTCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.08
16 8 0.17
17 11 0.23
18 14 0.29
19 11 0.23
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (17 bp):
AAAAATTTTTATGTTTC
Found at i:28517276 original size:24 final size:25
Alignment explanation
Indices: 28517232--28517280 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
28517222 TTCTTAATAT
*
28517232 ATGTATACATATATATTAAATATGC
1 ATGTATACATATATATAAAATATGC
*
28517257 ATGTATA-TTATATATAAAATATGC
1 ATGTATACATATATATAAAATATGC
28517281 GTCTGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (25 bp):
ATGTATACATATATATAAAATATGC
Found at i:28517287 original size:26 final size:23
Alignment explanation
Indices: 28517240--28517303 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
28517230 ATATGTATAC
*
28517240 ATATATATTAAATATGCATGTAT
1 ATATATATAAAATATGCATGTAT
*
28517263 ATTATATATAAAATATGCGTCTGTAT
1 A-TATATATAAAATATGC--ATGTAT
* *
28517289 ATGTATAGAAAATAT
1 ATATATATAAAATAT
28517304 AATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 15 0.44
25 12 0.35
26 6 0.18
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (23 bp):
ATATATATAAAATATGCATGTAT
Found at i:28520848 original size:8 final size:8
Alignment explanation
Indices: 28520835--28520864 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28520825 AAAAACACAT
28520835 AAAAAATA
1 AAAAAATA
28520843 AAAAAATA
1 AAAAAATA
*
28520851 AAAAAACA
1 AAAAAATA
28520859 AAAAAA
1 AAAAAA
28520865 AAGAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (8 bp):
AAAAAATA
Found at i:28521861 original size:75 final size:75
Alignment explanation
Indices: 28521738--28522489 Score: 858
Period size: 75 Copynumber: 9.9 Consensus size: 75
28521728 TATATTTTTC
* * * * * *
28521738 AATTTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCTGATCACATACCG
1 AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
28521803 AGGTATCTTT
66 AGGTATCTTT
*
28521813 AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATACCG
1 AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
28521878 AGGTATCTTT
66 AGGTATCTTT
* * * *
28521888 AATTTCTATTTTTCAAAAATCAACTCATATTGCGATAGGTGAGTCGAGCCTCGGGTCACATACCG
1 AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
28521953 AGGTATCTTT
66 AGGTATCTTT
* * * * * *
28521963 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC-AGACACACGCCG
1 AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
* *
28522027 GGGTATTTTTTT
66 AGGTA--TCTTT
* * *
28522039 AATTTTTGTTTTTCAAAAAGATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAGTCAC--GC
1 AATTTTTATTTTTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGC
*
28522102 TGAGGTAT-TTT
64 CGAGGTATCTTT
*
28522113 CAATTTTT-TTTTT---AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCC
1 -AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCC
28522174 GAGGTATTTCTTTT
65 GAGGTA--TC-TTT
* * * *
28522188 AAATTTTT-GTTTACAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGGGTCACACGCC
1 -AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCC
*
28522252 GAGGTATTTTTTTT
65 GAGGTA---TCTTT
* * *
28522266 AATTTTTCTTTCTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACAT
1 AATTTTTATTTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
28522331 GCCGAGGTATCTTT
62 GCCGAGGTATCTTT
* * * * * * * * *
28522345 AATTTCTT-CTTTCCAAATATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGCCGCACGTC
1 AATTT-TTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCC
*
28522409 GAGGTATTTTT
65 GAGGTATCTTT
* *
28522420 CAATTTTTATTTTTTCAAAAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTCGGGTCACATG
1 -AATTTTTA-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
28522485 CCGAG
63 CCGAG
28522490 ATATTTTTTT
Statistics
Matches: 586, Mismatches: 65, Indels: 49
0.84 0.09 0.07
Matches are distributed among these distances:
69 38 0.06
70 2 0.00
71 8 0.01
73 1 0.00
74 20 0.03
75 265 0.45
76 22 0.04
77 22 0.04
78 133 0.23
79 20 0.03
80 2 0.00
82 53 0.09
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (75 bp):
AATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCG
AGGTATCTTT
Found at i:28522450 original size:382 final size:372
Alignment explanation
Indices: 28521754--28522481 Score: 996
Period size: 382 Copynumber: 1.9 Consensus size: 372
28521744 TATTTTTCAA
*
28521754 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCTGATCACATACCGAGGTATCTTTAATTTT
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCAGATCACATACCGAGGTATCTTTAATTTT
* * *
28521819 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTAT
66 TAGTTTACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACACCGAGGTAT
* *
28521884 CTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGATAGGTGAGTCGAGCCTCGGGTCACAT
131 CTTTAATTTCTATTTCTCAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGGGTCACAT
* *
28521949 ACCGAGGTATCTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCT
196 ACCGAGGTATCTTTAATTTCTGTTTTCCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCT
* * *
28522014 CAGACACACGCCGGGGTATTTTTTTAATTTTTGTTTTTCAAAAAGATCAACTCATAATGCGAGAG
261 CAGACACACGCCGAGGTATTTTTTCAATTTTTGTTTTTCAAAAAGATCAACTCATAATACGAGAG
28522079 GTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATTTTTTTTTT
326 GTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATTTTTTTTTT
* * * *
28522126 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCAGATCACATACCGAGGTA--TC-TTT-AA
* *
28522191 TTTTT-GTTTACAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGGGTCACACGCCGAG
62 TTTTTAGTTTACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACACCGAG
* * * *
28522255 GTATTTTTTTTAATTTTTCTTTCTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
127 GTA---TCTTTAATTTCTATTTCTC----AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCC
* * * *
28522320 TCGGTTCACATGCCGAGGTATCTTTAATTTCT-TCTTTCCAAATATCAACTCATAATGCGAGAGG
185 TCGGGTCACATACCGAGGTATCTTTAATTTCTGT-TTTCCAAAAATCAACTCATAATGCGAGAGA
** * * * *
28522384 TGAGTTGAGCCTTGGGCCGCACGTCGAGGTA-TTTTTCAATTTTTATTTTTTCAAAAA-ATCAAC
249 TGAGTTGAGCC-TCAGACACACGCCGAGGTATTTTTTCAATTTTT-GTTTTTCAAAAAGATCAAC
* * *
28522447 TCATATTACTAGAGGTGAGTTGAGCCTCGGGTCAC
312 TCATAATACGAGAGGTGAGTTGAGCCTCGAGTCAC
28522482 ATGCCGAGAT
Statistics
Matches: 308, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
372 49 0.16
374 2 0.01
375 60 0.19
376 7 0.02
378 15 0.05
381 1 0.00
382 150 0.49
383 24 0.08
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (372 bp):
AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCCCAGATCACATACCGAGGTATCTTTAATTTT
TAGTTTACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACACCGAGGTAT
CTTTAATTTCTATTTCTCAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGGGTCACAT
ACCGAGGTATCTTTAATTTCTGTTTTCCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCT
CAGACACACGCCGAGGTATTTTTTCAATTTTTGTTTTTCAAAAAGATCAACTCATAATACGAGAG
GTGAGTTGAGCCTCGAGTCACGCTGAGGTATTTTCAATTTTTTTTTT
Found at i:28522985 original size:30 final size:29
Alignment explanation
Indices: 28522919--28522986 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
28522909 CAGAAAAAAT
*
28522919 TAAAATTACATTTGGGCCTCTAATATTTC
1 TAAAATTACATTTGGGCCCCTAATATTTC
* *
28522948 TAGAAATTACATTTTGGCCCC-ATATTTTTAC
1 TA-AAATTACATTTGGGCCCCTA-ATATTT-C
28522979 TAAAATTA
1 TAAAATTA
28522987 TGCTTTTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 27 0.82
31 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (29 bp):
TAAAATTACATTTGGGCCCCTAATATTTC
Found at i:28523353 original size:14 final size:13
Alignment explanation
Indices: 28523329--28523408 Score: 61
Period size: 13 Copynumber: 5.8 Consensus size: 13
28523319 CCAAACAATC
* *
28523329 AAAGCAAAAAGCA
1 AAAGAAAAAAGAA
28523342 AAAGAGAAAAAGAA
1 AAAGA-AAAAAGAA
* *
28523356 ATAATAAAAAAGCA
1 A-AAGAAAAAAGAA
** *
28523370 ACCGAAAAAATAA
1 AAAGAAAAAAGAA
28523383 AAAGAAAAAAGAAA
1 AAAGAAAAAAG-AA
28523397 AGAAGAAAAAAG
1 A-AAGAAAAAAG
28523409 GAGGGGAAGA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
13 19 0.37
14 19 0.37
15 13 0.25
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:28523396 original size:20 final size:21
Alignment explanation
Indices: 28523341--28523406 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
28523331 AGCAAAAAGC
*
28523341 AAAAGAGAAAAAGAAATAATA
1 AAAAGAGAAAAAGAAAAAATA
* **
28523362 AAAA-AGCAACCGAAAAAATA
1 AAAAGAGAAAAAGAAAAAATA
*
28523382 AAAAGA-AAAAAGAAAAGAAGA
1 AAAAGAGAAAAAGAAAA-AATA
28523403 AAAA
1 AAAA
28523407 AGGAGGGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAGAGAAAAAGAAAAAATA
Found at i:28523880 original size:17 final size:16
Alignment explanation
Indices: 28523840--28523906 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
28523830 AGCCCAACAG
28523840 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
* *
28523856 AAAGAAGAAAAGGAAA
1 AAAAAAGAAAAAGAAA
*
28523872 AAATAAAGAAAAAAGGGAA
1 AAA-AAAG-AAAAA-GAAA
*
28523891 GAAAAAGAAAAA-AAA
1 AAAAAAGAAAAAGAAA
28523906 A
1 A
28523907 GAAGGGGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
15 2 0.05
16 17 0.43
17 8 0.20
18 8 0.20
19 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:28523885 original size:29 final size:29
Alignment explanation
Indices: 28523838--28523910 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
28523828 ACAGCCCAAC
28523838 AGAAAAAAGAAA-AAGAAAAAAGAAGAAAA
1 AGAAAAAA-AAAGAAGAAAAAAGAAGAAAA
* **
28523867 GGAAAAAATAAAGAA-AAAAGGGAAGAAAA
1 AGAAAAAA-AAAGAAGAAAAAAGAAGAAAA
28523896 AGAAAAAAAAAGAAG
1 AGAAAAAAAAAGAAG
28523911 GGGCCCAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.16
29 29 0.78
30 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (29 bp):
AGAAAAAAAAAGAAGAAAAAAGAAGAAAA
Found at i:28523903 original size:7 final size:7
Alignment explanation
Indices: 28523838--28523886 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
28523828 ACAGCCCAAC
28523838 AGAAAAA
1 AGAAAAA
28523845 AG-AAAA
1 AGAAAAA
28523851 AGAAAAA
1 AGAAAAA
28523858 AGAAGAAA
1 AGAA-AAA
*
28523866 AG-GAAA
1 AGAAAAA
*
28523872 A-AATAA
1 AGAAAAA
28523878 AGAAAAA
1 AGAAAAA
28523885 AG
1 AG
28523887 GGAAGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 13 0.38
7 16 0.47
8 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
AGAAAAA
Found at i:28524442 original size:18 final size:18
Alignment explanation
Indices: 28524404--28524529 Score: 86
Period size: 18 Copynumber: 7.3 Consensus size: 18
28524394 TCCTTTTAAA
* *
28524404 AAAAATTCTCGTG-TTTC
1 AAAAATTTTTGTGTTTTC
*
28524421 -AAAATTTTTGTGTTTTT
1 AAAAATTTTTGTGTTTTC
28524438 AAAAATTTTTCGTG-TTTC
1 AAAAATTTTT-GTGTTTTC
**
28524456 AAAAAATTCCTGTG-TTTC
1 -AAAAATTTTTGTGTTTTC
* *
28524474 AAAAATTTCTGTGTCTTC
1 AAAAATTTTTGTGTTTTC
* *
28524492 AAAAAATATTGTG-TTTC
1 AAAAATTTTTGTGTTTTC
* *
28524509 -AAAATTATCGTGTTTT-
1 AAAAATTTTTGTGTTTTC
28524525 AAAAA
1 AAAAA
28524530 AAAGTTCTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
16 20 0.23
17 25 0.28
18 32 0.36
19 11 0.12
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (18 bp):
AAAAATTTTTGTGTTTTC
Found at i:28524460 original size:53 final size:52
Alignment explanation
Indices: 28524403--28524528 Score: 141
Period size: 53 Copynumber: 2.4 Consensus size: 52
28524393 GTCCTTTTAA
* * * * *
28524403 AAAAAATTCTCGTGTTTCAAAATTTTTGTGTTTTTAAAAATTTTTCGTGTTTC
1 AAAAAATTCTCGTGTTTCAAAATTTCTGTGTCTTCAAAAAATATT-GTGTTTC
28524456 AAAAAATTC-CTGTGTTTCAAAAATTTCTGTGTCTTCAAAAAATATTGTGTTTC
1 AAAAAATTCTC-GTGTTTC-AAAATTTCTGTGTCTTCAAAAAATATTGTGTTTC
* *
28524509 --AAAATTATCGTGTTTTAAAA
1 AAAAAATTCTCGTGTTTCAAAA
28524529 AAAAGTTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
50 4 0.06
51 12 0.19
52 2 0.03
53 23 0.37
54 22 0.35
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (52 bp):
AAAAAATTCTCGTGTTTCAAAATTTCTGTGTCTTCAAAAAATATTGTGTTTC
Found at i:28524505 original size:35 final size:34
Alignment explanation
Indices: 28524403--28524530 Score: 127
Period size: 35 Copynumber: 3.7 Consensus size: 34
28524393 GTCCTTTTAA
* ** *
28524403 AAAAAATTCTCGTGTTTCAAAATTTTTGTGTTTTT
1 AAAAATTTCTCGTGTTTCAAAAAATTTGTG-TTTC
*
28524438 AAAAATTTTTCGTGTTTCAAAAAATTCCTGTGTTTC
1 AAAAATTTCTCGTGTTTCAAAAAATT--TGTGTTTC
28524474 AAAAATTTCT-GTGTCTTCAAAAAATATTGTGTTTC
1 AAAAATTTCTCGTGT-TTCAAAAAAT-TTGTGTTTC
* *
28524509 -AAAA-TTATCGTGTTTTAAAAAA
1 AAAAATTTCTCGTGTTTCAAAAAA
28524531 AAGTTCTTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
33 11 0.14
34 8 0.10
35 34 0.43
36 22 0.28
37 5 0.06
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (34 bp):
AAAAATTTCTCGTGTTTCAAAAAATTTGTGTTTC
Found at i:28524529 original size:17 final size:16
Alignment explanation
Indices: 28524404--28524529 Score: 67
Period size: 17 Copynumber: 7.3 Consensus size: 16
28524394 TCCTTTTAAA
*
28524404 AAAAATTCTCGTGTTTC
1 AAAAATT-TCGTGTTTT
* *
28524421 AAAATTTTTGTGTTTTT
1 AAAAATTTCGTG-TTTT
*
28524438 AAAAATTTTTCGTGTTTCA
1 AAAAA--TTTCGTGTTT-T
* *
28524457 AAAAATTCCTGTGTTTC
1 AAAAATTTC-GTGTTTT
*
28524474 AAAAATTTCTGTGTCTTCA
1 AAAAATTTC-GTGT-TT-T
28524493 AAAAATATT-GTG-TTT
1 AAAAAT-TTCGTGTTTT
*
28524508 CAAAATTATCGTGTTTT
1 AAAAATT-TCGTGTTTT
28524525 AAAAA
1 AAAAA
28524530 AAAGTTCTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
14 1 0.01
15 6 0.07
16 9 0.11
17 36 0.42
18 14 0.16
19 17 0.20
20 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (16 bp):
AAAAATTTCGTGTTTT
Found at i:28524532 original size:35 final size:35
Alignment explanation
Indices: 28524466--28524531 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
28524456 AAAAAATTCC
*
28524466 TGTGTTTCAAAAATTTCTGTGTCTTCAAAAAATAT
1 TGTGTTTCAAAAATTTCTGTGTCTTAAAAAAATAT
*
28524501 TGTGTTTC-AAAATTATC-GTGTTTTAAAAAAA
1 TGTGTTTCAAAAATT-TCTGTGTCTTAAAAAAA
28524532 AGTTCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (35 bp):
TGTGTTTCAAAAATTTCTGTGTCTTAAAAAAATAT
Found at i:28528795 original size:24 final size:25
Alignment explanation
Indices: 28528751--28528799 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
28528741 TTCTTAATAT
*
28528751 ATGTATACATATATATTAAATATGC
1 ATGTATACATATATATAAAATATGC
*
28528776 ATGTATA-TTATATATAAAATATGC
1 ATGTATACATATATATAAAATATGC
28528800 GTCTGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (25 bp):
ATGTATACATATATATAAAATATGC
Found at i:28528806 original size:26 final size:23
Alignment explanation
Indices: 28528759--28528822 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
28528749 ATATGTATAC
*
28528759 ATATATATTAAATATGCATGTAT
1 ATATATATAAAATATGCATGTAT
*
28528782 ATTATATATAAAATATGCGTCTGTAT
1 A-TATATATAAAATATGC--ATGTAT
* *
28528808 ATGTATAGAAAATAT
1 ATATATATAAAATAT
28528823 AATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 15 0.44
25 12 0.35
26 6 0.18
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (23 bp):
ATATATATAAAATATGCATGTAT
Found at i:28532367 original size:8 final size:8
Alignment explanation
Indices: 28532354--28532383 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28532344 AAAAACACAT
28532354 AAAAAATA
1 AAAAAATA
28532362 AAAAAATA
1 AAAAAATA
*
28532370 AAAAAACA
1 AAAAAATA
28532378 AAAAAA
1 AAAAAA
28532384 AAGAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (8 bp):
AAAAAATA
Found at i:28533709 original size:29 final size:29
Alignment explanation
Indices: 28533658--28533752 Score: 111
Period size: 29 Copynumber: 3.2 Consensus size: 29
28533648 TATTTTTTAC
28533658 AAAATTATATTTTGACCTCTAAATTTTCTT
1 AAAATTATATTTTGACC-CTAAATTTTCTT
* *
28533688 AAAATTATATTATGACCCTAAACTTTCTT
1 AAAATTATATTTTGACCCTAAATTTTCTT
* ** *
28533717 GAAATTACCTTTTGACCCCTAAATTTTC-C
1 AAAATTATATTTTGA-CCCTAAATTTTCTT
28533746 AAAATTA
1 AAAATTA
28533753 CACTTCGACA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
29 28 0.51
30 27 0.49
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (29 bp):
AAAATTATATTTTGACCCTAAATTTTCTT
Found at i:28534280 original size:19 final size:19
Alignment explanation
Indices: 28534251--28534311 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
28534241 GCTGATCGGG
28534251 AAAGA-AAGAAAGAAAGAA
1 AAAGAGAAGAAAGAAAGAA
28534269 AAAGAGAAGAAAGAAAGAA
1 AAAGAGAAGAAAGAAAGAA
28534288 AGAA-AGAAGAAAGGGAAAGAA
1 A-AAGAGAAGAAA--GAAAGAA
28534309 AAA
1 AAA
28534312 AAATTTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.13
19 22 0.56
20 4 0.10
21 8 0.21
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAGAGAAGAAAGAAAGAA
Found at i:28534309 original size:4 final size:4
Alignment explanation
Indices: 28534250--28534300 Score: 72
Period size: 4 Copynumber: 13.2 Consensus size: 4
28534240 GGCTGATCGG
28534250 GAAA GAAA GAAA GAAA G-AA -AAA GAGAA GAAA GAAA GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
28534296 GAAA G
1 GAAA G
28534301 GGAAAGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 7 0.16
4 32 0.74
5 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:28534614 original size:23 final size:23
Alignment explanation
Indices: 28534573--28534616 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28534563 AGTCCAGAAA
**
28534573 AAAAAAAGAGGAAGAAAAAAAAG
1 AAAAAAAGAAAAAGAAAAAAAAG
*
28534596 AAAAAAAGAAAAAGGAAAAAA
1 AAAAAAAGAAAAAGAAAAAAA
28534617 CCAAACTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAAGAAAAAAAAG
Found at i:28535114 original size:18 final size:18
Alignment explanation
Indices: 28535076--28535201 Score: 86
Period size: 18 Copynumber: 7.3 Consensus size: 18
28535066 TCCTTTTAAA
* *
28535076 AAAAATTCTCGTG-TTTC
1 AAAAATTTTTGTGTTTTC
*
28535093 -AAAATTTTTGTGTTTTT
1 AAAAATTTTTGTGTTTTC
28535110 AAAAATTTTTCGTG-TTTC
1 AAAAATTTTT-GTGTTTTC
**
28535128 AAAAAATTCCTGTG-TTTC
1 -AAAAATTTTTGTGTTTTC
* *
28535146 AAAAATTTCTGTGTCTTC
1 AAAAATTTTTGTGTTTTC
* *
28535164 AAAAAATATTGTG-TTTC
1 AAAAATTTTTGTGTTTTC
* *
28535181 -AAAATTATCGTGTTTT-
1 AAAAATTTTTGTGTTTTC
28535197 AAAAA
1 AAAAA
28535202 AAAGTTCTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
16 20 0.23
17 25 0.28
18 32 0.36
19 11 0.12
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (18 bp):
AAAAATTTTTGTGTTTTC
Found at i:28535132 original size:53 final size:52
Alignment explanation
Indices: 28535075--28535200 Score: 141
Period size: 53 Copynumber: 2.4 Consensus size: 52
28535065 GTCCTTTTAA
* * * * *
28535075 AAAAAATTCTCGTGTTTCAAAATTTTTGTGTTTTTAAAAATTTTTCGTGTTTC
1 AAAAAATTCTCGTGTTTCAAAATTTCTGTGTCTTCAAAAAATATT-GTGTTTC
28535128 AAAAAATTC-CTGTGTTTCAAAAATTTCTGTGTCTTCAAAAAATATTGTGTTTC
1 AAAAAATTCTC-GTGTTTC-AAAATTTCTGTGTCTTCAAAAAATATTGTGTTTC
* *
28535181 --AAAATTATCGTGTTTTAAAA
1 AAAAAATTCTCGTGTTTCAAAA
28535201 AAAAGTTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
50 4 0.06
51 12 0.19
52 2 0.03
53 23 0.37
54 22 0.35
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (52 bp):
AAAAAATTCTCGTGTTTCAAAATTTCTGTGTCTTCAAAAAATATTGTGTTTC
Found at i:28535177 original size:35 final size:34
Alignment explanation
Indices: 28535075--28535202 Score: 127
Period size: 35 Copynumber: 3.7 Consensus size: 34
28535065 GTCCTTTTAA
* ** *
28535075 AAAAAATTCTCGTGTTTCAAAATTTTTGTGTTTTT
1 AAAAATTTCTCGTGTTTCAAAAAATTTGTG-TTTC
*
28535110 AAAAATTTTTCGTGTTTCAAAAAATTCCTGTGTTTC
1 AAAAATTTCTCGTGTTTCAAAAAATT--TGTGTTTC
28535146 AAAAATTTCT-GTGTCTTCAAAAAATATTGTGTTTC
1 AAAAATTTCTCGTGT-TTCAAAAAAT-TTGTGTTTC
* *
28535181 -AAAA-TTATCGTGTTTTAAAAAA
1 AAAAATTTCTCGTGTTTCAAAAAA
28535203 AAGTTCTTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
33 11 0.14
34 8 0.10
35 34 0.43
36 22 0.28
37 5 0.06
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (34 bp):
AAAAATTTCTCGTGTTTCAAAAAATTTGTGTTTC
Found at i:28535201 original size:17 final size:16
Alignment explanation
Indices: 28535076--28535201 Score: 67
Period size: 17 Copynumber: 7.3 Consensus size: 16
28535066 TCCTTTTAAA
*
28535076 AAAAATTCTCGTGTTTC
1 AAAAATT-TCGTGTTTT
* *
28535093 AAAATTTTTGTGTTTTT
1 AAAAATTTCGTG-TTTT
*
28535110 AAAAATTTTTCGTGTTTCA
1 AAAAA--TTTCGTGTTT-T
* *
28535129 AAAAATTCCTGTGTTTC
1 AAAAATTTC-GTGTTTT
*
28535146 AAAAATTTCTGTGTCTTCA
1 AAAAATTTC-GTGT-TT-T
28535165 AAAAATATT-GTG-TTT
1 AAAAAT-TTCGTGTTTT
*
28535180 CAAAATTATCGTGTTTT
1 AAAAATT-TCGTGTTTT
28535197 AAAAA
1 AAAAA
28535202 AAAGTTCTTG
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
14 1 0.01
15 6 0.07
16 9 0.11
17 36 0.42
18 14 0.16
19 17 0.20
20 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.45
Consensus pattern (16 bp):
AAAAATTTCGTGTTTT
Found at i:28535204 original size:35 final size:35
Alignment explanation
Indices: 28535138--28535203 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
28535128 AAAAAATTCC
*
28535138 TGTGTTTCAAAAATTTCTGTGTCTTCAAAAAATAT
1 TGTGTTTCAAAAATTTCTGTGTCTTAAAAAAATAT
*
28535173 TGTGTTTC-AAAATTATC-GTGTTTTAAAAAAA
1 TGTGTTTCAAAAATT-TCTGTGTCTTAAAAAAA
28535204 AGTTCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (35 bp):
TGTGTTTCAAAAATTTCTGTGTCTTAAAAAAATAT
Found at i:28536553 original size:19 final size:20
Alignment explanation
Indices: 28536522--28536561 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
28536512 ATTAAAGGAC
*
28536522 TTTAAATTTAATTAATTAAT
1 TTTAAATTTAATTAACTAAT
28536542 TTTAAA-TTAATTAACTAAT
1 TTTAAATTTAATTAACTAAT
28536561 T
1 T
28536562 AATCAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATTTAATTAACTAAT
Found at i:28540586 original size:22 final size:22
Alignment explanation
Indices: 28540561--28540602 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28540551 TTTAACAGAA
*
28540561 TAACT-ACTAACCGCCTGACTGC
1 TAACTAACTAA-CACCTGACTGC
28540583 TAACTAACTAACACCTGACT
1 TAACTAACTAACACCTGACT
28540603 ATCTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (22 bp):
TAACTAACTAACACCTGACTGC
Found at i:28544618 original size:30 final size:30
Alignment explanation
Indices: 28544582--28544645 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
28544572 AAAGTTTGTA
28544582 ATTTAGATATCATCGTTACATATTTTTATC
1 ATTTAGATATCATCGTTACATATTTTTATC
28544612 ATTTAGATATCATCGTTACATATTTTTATC
1 ATTTAGATATCATCGTTACATATTTTTATC
28544642 ATTT
1 ATTT
28544646 TAGCCACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (30 bp):
ATTTAGATATCATCGTTACATATTTTTATC
Found at i:28545845 original size:97 final size:96
Alignment explanation
Indices: 28545674--28546068 Score: 605
Period size: 97 Copynumber: 4.1 Consensus size: 96
28545664 AAATAAGGGT
* * * * *
28545674 TTAGGGTTTAGGGTTTCTTAATTAAATTATTTATCAATTTTAAAAAATTAGATTAGGGTTTAGTG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
* *
28545739 TTTATGGTTTTTAAGGAAAAAATTAAATAAA
66 TTTAGGGTTTTTAAGAAAAAAATTAAATAAA
* *
28545770 TTAGAGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTACT
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTT-AAAAAATTAGATTAGGGTTTAGT
* *
28545835 GTTTAGGGTTTTAAAGAAAAAAATCAAATAAA
65 GTTTAGGGTTTTTAAGAAAAAAATTAAATAAA
*
28545867 TTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
*
28545932 TTTAGGGGTTTTAAGAAAAAAAATTAAATAAA
66 TTTAGGGTTTTTAAG-AAAAAAATTAAATAAA
28545964 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAAATTAGATTAGGGTTTAG
1 TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTT--AAAAAATTAGATTAGGGTTTAG
* *
28546029 TATTTAGGG-TTTTAAG-GAAAAATTAAATAAA
64 TGTTTAGGGTTTTTAAGAAAAAAATTAAATAAA
28546060 TTAGGGTTT
1 TTAGGGTTT
28546069 GAGGTTTAGG
Statistics
Matches: 275, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
96 94 0.34
97 144 0.52
98 7 0.03
99 30 0.11
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.40
Consensus pattern (96 bp):
TTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
TTTAGGGTTTTTAAGAAAAAAATTAAATAAA
Found at i:28546059 original size:193 final size:193
Alignment explanation
Indices: 28545674--28546074 Score: 635
Period size: 193 Copynumber: 2.1 Consensus size: 193
28545664 AAATAAGGGT
* * * * *
28545674 TTAGGGTTTAGGGTTTCTTAATTAAATTATTTATCAATTTTAAAAAATTAGATTAGGGTTTAGTG
1 TTAGGGTTTAAGGTTACTTAAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
* * *
28545739 TTTATGGTTTTTAAGGAAAAAATTAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAT
66 TTTAGGGGTTTTAAGAAAAAAATTAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAT
*
28545804 AAATTTTAAAAAAATTAGATTAGGGTTTACTGTTTAGGGTTTTAAAGAAAAAAATCAAATAAA
131 AAATTTTAAAAAAATTAGATTAGGGTTTACTATTTAGGGTTTTAAAGAAAAAAATCAAATAAA
*
28545867 TTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
1 TTAGGGTTTAAGGTTACTTAAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
*
28545932 TTTAGGGGTTTTAAGAAAAAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
66 TTTAGGGGTTTTAAG-AAAAAAATTAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTA
* * *
28545997 TAAATTTTAAAAAAAATTAGATTAGGGTTTAGTATTTAGGGTTTT-AAG-GAAAAATTAAATAAA
130 TAAATTTT-AAAAAAATTAGATTAGGGTTTACTATTTAGGGTTTTAAAGAAAAAAATCAAATAAA
*
28546060 TTAGGGTTTGAGGTT
1 TTAGGGTTTAAGGTT
28546075 TAGGGTTACT
Statistics
Matches: 191, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
193 99 0.52
194 58 0.30
195 34 0.18
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (193 bp):
TTAGGGTTTAAGGTTACTTAAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTG
TTTAGGGGTTTTAAGAAAAAAATTAAATAAATTAGAGTTTAGGGTTACTTGAGTAAATTAATTAT
AAATTTTAAAAAAATTAGATTAGGGTTTACTATTTAGGGTTTTAAAGAAAAAAATCAAATAAA
Found at i:28547573 original size:30 final size:30
Alignment explanation
Indices: 28547537--28547604 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
28547527 GTTGAAGTGT
* **
28547537 TGGGCCTGGTGATTATGTAGGTGCTGTTGC
1 TGGGCCTGGTGATTATATAGGTGCTGTTAA
* *
28547567 TGGGCCTGGTGATTGTATGGGTGCTGTTAA
1 TGGGCCTGGTGATTATATAGGTGCTGTTAA
28547597 TGGGCCTG
1 TGGGCCTG
28547605 CATCGTCGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.10, C:0.13, G:0.41, T:0.35
Consensus pattern (30 bp):
TGGGCCTGGTGATTATATAGGTGCTGTTAA
Found at i:28548154 original size:7 final size:7
Alignment explanation
Indices: 28548144--28548176 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28548134 TTATATACAT
28548144 AATACTA
1 AATACTA
28548151 AATACTA
1 AATACTA
28548158 AATACTA
1 AATACTA
28548165 AATACTA
1 AATACTA
28548172 AATAC
1 AATAC
28548177 GAATCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:28549345 original size:11 final size:11
Alignment explanation
Indices: 28549331--28549362 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28549321 TAAAGAGAGC
*
28549331 TTTGAGAGGAA
1 TTTGAGAGAAA
28549342 TTTGAGAGAAA
1 TTTGAGAGAAA
28549353 TTTGAGAGAA
1 TTTGAGAGAA
28549363 TACTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:28549776 original size:18 final size:16
Alignment explanation
Indices: 28549743--28549774 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28549733 TGATGTATTA
28549743 TTTTTAATTTATATAT
1 TTTTTAATTTATATAT
28549759 TTTTTAATTTATATAT
1 TTTTTAATTTATATAT
28549775 ATAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTAATTTATATAT
Found at i:28552417 original size:12 final size:13
Alignment explanation
Indices: 28552389--28552421 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28552379 AAAAATGTAT
*
28552389 TTTTATATAACTA
1 TTTTAAATAACTA
28552402 TTTTAAATAA-TA
1 TTTTAAATAACTA
28552414 TTTTAAAT
1 TTTTAAAT
28552422 TCTTCTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTAAATAACTA
Found at i:28571519 original size:29 final size:29
Alignment explanation
Indices: 28571487--28571551 Score: 98
Period size: 27 Copynumber: 2.3 Consensus size: 29
28571477 GAATCTAATT
28571487 AATAATTTTAAAATTTATATTTACATATA
1 AATAATTTTAAAATTTATATTTACATATA
*
28571516 AAT-A-TTTAAAATTTATATTTACGTATA
1 AATAATTTTAAAATTTATATTTACATATA
28571543 AATATATTT
1 AATA-ATTT
28571552 ATAATAACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 25 0.78
28 1 0.03
29 4 0.12
30 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (29 bp):
AATAATTTTAAAATTTATATTTACATATA
Found at i:28571528 original size:27 final size:27
Alignment explanation
Indices: 28571493--28571547 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
28571483 AATTAATAAT
28571493 TTTAAAATTTATATTTACATATAAATA
1 TTTAAAATTTATATTTACATATAAATA
*
28571520 TTTAAAATTTATATTTACGTATAAATA
1 TTTAAAATTTATATTTACATATAAATA
28571547 T
1 T
28571548 ATTTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTAAAATTTATATTTACATATAAATA
Found at i:28571535 original size:13 final size:13
Alignment explanation
Indices: 28571493--28571536 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
28571483 AATTAATAAT
28571493 TTTAAAATTTATA
1 TTTAAAATTTATA
* **
28571506 TTTACATATAAATA
1 TTTA-AAATTTATA
28571520 TTTAAAATTTATA
1 TTTAAAATTTATA
28571533 TTTA
1 TTTA
28571537 CGTATAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAAATTTATA
Found at i:28572950 original size:226 final size:217
Alignment explanation
Indices: 28572557--28572998 Score: 512
Period size: 226 Copynumber: 2.0 Consensus size: 217
28572547 TGGACCAAAT
* * *
28572557 TGTGCATTTGCACTTAAGTTTGCAAGTAACACTCTCCTTACTAAAATGAGTTACTCGAGTGTAAC
1 TGTGCACTTGCACTTAAGTTTGCAAGTAACACTCTCCTTACTAAAATAAATTACTCGAGTGTAAC
* *
28572622 TTCCATAAACTATCATTCATCCATTATTTTCATAATTCTCCCCCATTACCCACTACAAAAAATAT
66 TTCCATAAACTATCATTCATCCACTATTTTCATAATTCTCCCCCATTACCCACTACAAAAAACAT
* * * * *
28572687 GAATGTGATTTTATTCATTCTCATGACCCATTAATTCATAACACGTTCTTTTGAATTAATCCATA
131 GAATGTGATATCATTCATTCTCATGACCCAATAATTCATAACACGTTCTTATGAATTAATCCACA
*
28572752 T-TTTTCCCACGTTTCATAAAAC
196 TCTTTT-CCACGTTCCATAAAAC
* * * * * *
28572774 TGTGCACTTGCACTTAAGTTTGTAAGTAGCACTCTTCTTGCTAAAGTAAATTACAT-GAGTGTAT
1 TGTGCACTTGCACTTAAGTTTGCAAGTAACACTCTCCTTACTAAAATAAATTAC-TCGAGTGTAA
* * *
28572838 CTTTCACTAAACTA-CTATTATATCCACTATTTTCATAACTTCTCTCCCATTACCATTGCCCACT
65 CTTCCA-TAAACTATC-ATT-CATCCACTATTTTCATAA--T-TCTCCC----CCATTACCCACT
** * * *
28572902 ACAAGTAACATGAATGTGATATCATTTATTCTCATTATCCAATAATTCATAACACGTTCTTATGA
120 ACAAAAAACATGAATGTGATATCATTCATTCTCATGACCCAATAATTCATAACACGTTCTTATGA
* *
28572967 ATTACTCCACATCTTTTCTACGTTCCATAAAA
185 ATTAATCCACATCTTTTCCACGTTCCATAAAA
28572999 AATGTCACTT
Statistics
Matches: 186, Mismatches: 27, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
217 59 0.32
218 11 0.06
219 16 0.09
221 1 0.01
222 6 0.03
226 89 0.48
227 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.38
Consensus pattern (217 bp):
TGTGCACTTGCACTTAAGTTTGCAAGTAACACTCTCCTTACTAAAATAAATTACTCGAGTGTAAC
TTCCATAAACTATCATTCATCCACTATTTTCATAATTCTCCCCCATTACCCACTACAAAAAACAT
GAATGTGATATCATTCATTCTCATGACCCAATAATTCATAACACGTTCTTATGAATTAATCCACA
TCTTTTCCACGTTCCATAAAAC
Found at i:28578838 original size:49 final size:49
Alignment explanation
Indices: 28578766--28578869 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
28578756 GAAAAAAAAC
* * * *
28578766 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTATA
28578815 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTATA
1 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTATA
28578864 AAATTA
1 AAATTA
28578870 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTATA
Found at i:28579479 original size:71 final size:71
Alignment explanation
Indices: 28579363--28579575 Score: 417
Period size: 71 Copynumber: 3.0 Consensus size: 71
28579353 ATTCTTGCAG
*
28579363 AGTACTTGGTTGATAACCCTGATGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
1 AGTACTTGGTTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
28579428 GAAATC
66 GAAATC
28579434 AGTACTTGGTTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
1 AGTACTTGGTTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
28579499 GAAATC
66 GAAATC
28579505 AGTACTTGGTTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
1 AGTACTTGGTTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
28579570 GAAATC
66 GAAATC
28579576 CCTCACAATT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 141 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (71 bp):
AGTACTTGGTTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGGCCTCTAAAAGGTGCAA
GAAATC
Found at i:28581938 original size:12 final size:12
Alignment explanation
Indices: 28581923--28581956 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
28581913 ACTTAACAGA
28581923 AACCAAAACATG
1 AACCAAAACATG
28581935 AACCAAAACATG
1 AACCAAAACATG
28581947 AACCAAAACA
1 AACCAAAACA
28581957 ATAGAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.26, G:0.06, T:0.06
Consensus pattern (12 bp):
AACCAAAACATG
Found at i:28582022 original size:12 final size:12
Alignment explanation
Indices: 28582005--28582063 Score: 100
Period size: 12 Copynumber: 4.9 Consensus size: 12
28581995 TTAATACAGA
28582005 AAAACATGAACC
1 AAAACATGAACC
*
28582017 AAAACATAAACC
1 AAAACATGAACC
28582029 AAAACATGAACC
1 AAAACATGAACC
*
28582041 AAAACATAAACC
1 AAAACATGAACC
28582053 AAAACATGAAC
1 AAAACATGAAC
28582064 TTAATAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.63, C:0.24, G:0.05, T:0.08
Consensus pattern (12 bp):
AAAACATGAACC
Found at i:28582032 original size:24 final size:24
Alignment explanation
Indices: 28582005--28582063 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
28581995 TTAATACAGA
28582005 AAAACATGAACCAAAACATAAACC
1 AAAACATGAACCAAAACATAAACC
28582029 AAAACATGAACCAAAACATAAACC
1 AAAACATGAACCAAAACATAAACC
28582053 AAAACATGAAC
1 AAAACATGAAC
28582064 TTAATAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.63, C:0.24, G:0.05, T:0.08
Consensus pattern (24 bp):
AAAACATGAACCAAAACATAAACC
Found at i:28582124 original size:23 final size:23
Alignment explanation
Indices: 28582005--28582154 Score: 135
Period size: 23 Copynumber: 6.5 Consensus size: 23
28581995 TTAATACAGA
* *
28582005 AAAACATGAACCAAAACATAAACC
1 AAAACATGAA-CTAAACAGAAACC
* *
28582029 AAAACATGAACCAAAACATAAACC
1 AAAACATGAA-CTAAACAGAAACC
* *
28582053 AAAACATGAACTTAATAGAAA-C
1 AAAACATGAACTAAACAGAAACC
* * *
28582075 ATGAACAT-TA-TAACACATAAACC
1 A-AAACATGAACTAA-ACAGAAACC
* *
28582098 AAAACATGAACTTAACAGAAACT
1 AAAACATGAACTAAACAGAAACC
*
28582121 AAAACATGAACTTAACAGAAACC
1 AAAACATGAACTAAACAGAAACC
28582144 AAAACATGAAC
1 AAAACATGAAC
28582155 ATTATAACAC
Statistics
Matches: 106, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
21 2 0.02
22 13 0.12
23 55 0.52
24 36 0.34
ACGTcount: A:0.59, C:0.21, G:0.07, T:0.14
Consensus pattern (23 bp):
AAAACATGAACTAAACAGAAACC
Found at i:28582127 original size:45 final size:46
Alignment explanation
Indices: 28582030--28582154 Score: 148
Period size: 45 Copynumber: 2.7 Consensus size: 46
28582020 ACATAAACCA
* *
28582030 AAACATGAACCAAAACATAAACCAAAACATGAACTTAATAGAAACAT
1 AAACATGAA-CTAAACATAAACCAAAACATGAACTTAACAGAAACAT
* *
28582077 GAACAT-TA-TAACACATAAACCAAAACATGAACTTAACAGAAAC-T
1 AAACATGAACTAA-ACATAAACCAAAACATGAACTTAACAGAAACAT
* *
28582121 AAAACATGAACTTAACAGAAACCAAAACATGAAC
1 -AAACATGAACTAAACATAAACCAAAACATGAAC
28582155 ATTATAACAC
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 3 0.05
45 35 0.53
46 21 0.32
47 7 0.11
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.15
Consensus pattern (46 bp):
AAACATGAACTAAACATAAACCAAAACATGAACTTAACAGAAACAT
Found at i:28583280 original size:16 final size:18
Alignment explanation
Indices: 28583235--28583283 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 18
28583225 AGCCATTCGG
28583235 AAAATAATAGAATCAAAC
1 AAAATAATAGAATCAAAC
28583253 AAACATGCAATAGAAT-AAAC
1 AAA-AT--AATAGAATCAAAC
28583273 -AAATAATAGAA
1 AAAATAATAGAA
28583284 CCACATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.25
18 5 0.18
19 4 0.14
20 4 0.14
21 8 0.29
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.16
Consensus pattern (18 bp):
AAAATAATAGAATCAAAC
Found at i:28585724 original size:14 final size:14
Alignment explanation
Indices: 28585705--28585739 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28585695 TGACATTTTT
* *
28585705 TTCTAATGATATTA
1 TTCTAACGATACTA
28585719 TTCTAACGATACTA
1 TTCTAACGATACTA
28585733 TTCTAAC
1 TTCTAAC
28585740 ATGGAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:28586449 original size:6 final size:6
Alignment explanation
Indices: 28586376--28586448 Score: 110
Period size: 6 Copynumber: 12.2 Consensus size: 6
28586366 AATATAGAGG
* *
28586376 CCGAGC CAGAGC CAGAGC CCGAGC CCGAGC CCGAGC CCGAGC CCGAGC
1 CCGAGC CCGAGC CCGAGC CCGAGC CCGAGC CCGAGC CCGAGC CCGAGC
* *
28586424 CCGAGC TCGAGC CCGAGC CTGAGC C
1 CCGAGC CCGAGC CCGAGC CCGAGC C
28586449 TAAGCGATCG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.19, C:0.45, G:0.33, T:0.03
Consensus pattern (6 bp):
CCGAGC
Found at i:28587063 original size:62 final size:62
Alignment explanation
Indices: 28586985--28587150 Score: 269
Period size: 62 Copynumber: 2.7 Consensus size: 62
28586975 CAACATTACA
* * * *
28586985 ACATTAAAACACTAAAACTTGTAACAAACTTTGTAATATAAATTTTATTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTATTATATAAATTAAAT
*
28587047 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTATTATATAAATTAAAT
* *
28587109 ACATTACAATATTAAAAATTGGAACAAAATTTGTAATATAAA
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAA
28587151 GTAGGTACAT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 97 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTATTATATAAATTAAAT
Found at i:28591143 original size:43 final size:43
Alignment explanation
Indices: 28591072--28591242 Score: 138
Period size: 43 Copynumber: 4.0 Consensus size: 43
28591062 GACTCGTACA
* *
28591072 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAAACAG-GGTCTTACATGTAATCACATATCG
* * * * * *
28591115 ATGCCACTGTCTCAGACAGGGTCATACAT-CAATCAAATA-CG
1 ATGCCAATGTCCCAAACAGGGTCTTACATGTAATCACATATCG
*
28591156 ATGCCAATGTCCCAAACATGGTCTTACATGTAAAT-ACA-AGTCG
1 ATGCCAATGTCCCAAACAGGGTCTTACATGT-AATCACATA-TCG
* * * * *
28591199 ATGCCAACGTCCCAGAC-GTGGTCTTACACGAAAACACATATCG
1 ATGCCAATGTCCCAAACAG-GGTCTTACATGTAATCACATATCG
28591242 A
1 A
28591243 AATCCTATGT
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
41 27 0.27
42 12 0.12
43 60 0.59
44 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACAGGGTCTTACATGTAATCACATATCG
Found at i:28607872 original size:25 final size:25
Alignment explanation
Indices: 28607827--28607874 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28607817 ACATACCGCA
*
28607827 GCTCTTTATAAGTGTCTTGATATAT
1 GCTCTTTATAAGTGTCCTGATATAT
*
28607852 GCTCTTTATGAGCT-TCCTGATAT
1 GCTCTTTATAAG-TGTCCTGATAT
28607875 GGATCGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (25 bp):
GCTCTTTATAAGTGTCCTGATATAT
Found at i:28608266 original size:17 final size:16
Alignment explanation
Indices: 28608239--28608273 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28608229 TTAAATAGAA
28608239 ATATGATATGAAAATT
1 ATATGATATGAAAATT
*
28608255 ATATGTATATGAAAGTT
1 ATATG-ATATGAAAATT
28608272 AT
1 AT
28608274 TACATGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (16 bp):
ATATGATATGAAAATT
Found at i:28616007 original size:16 final size:16
Alignment explanation
Indices: 28615986--28616018 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28615976 CAGCCCACAT
28615986 GCTTTTCTAAGTATAC
1 GCTTTTCTAAGTATAC
28616002 GCTTTTCTAAGTATAC
1 GCTTTTCTAAGTATAC
28616018 G
1 G
28616019 AAGGTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (16 bp):
GCTTTTCTAAGTATAC
Found at i:28619491 original size:11 final size:11
Alignment explanation
Indices: 28619475--28619499 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28619465 TTGTGCATTG
28619475 ATACTTTCTTT
1 ATACTTTCTTT
28619486 ATACTTTCTTT
1 ATACTTTCTTT
28619497 ATA
1 ATA
28619500 ATATAGGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (11 bp):
ATACTTTCTTT
Found at i:28626320 original size:17 final size:16
Alignment explanation
Indices: 28626298--28626334 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
28626288 AAAATTATTC
28626298 TAAAAAAATATCTTTAA
1 TAAAAAAATAT-TTTAA
*
28626315 TAAAAACATATTTTAA
1 TAAAAAAATATTTTAA
28626331 TAAA
1 TAAA
28626335 TGGTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAAAAATATTTTAA
Found at i:28631761 original size:32 final size:32
Alignment explanation
Indices: 28631725--28631828 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
28631715 GGGTTAGGGA
28631725 TTTCAAATAAAATGATAAATCAGGGTAAGAGT
1 TTTCAAATAAAATGATAAATCAGGGTAAGAGT
* ** * * * *
28631757 TTTC-AATTAAAT--TAGGTTAGGGTTAGGGA
1 TTTCAAATAAAATGATAAATCAGGGTAAGAGT
28631786 TTTCAAATAAAATGATAAATCAGGGTAAGAGT
1 TTTCAAATAAAATGATAAATCAGGGTAAGAGT
*
28631818 TTTCAATTAAA
1 TTTCAAATAAA
28631829 TTAGGTTAGG
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 15 0.28
30 7 0.13
31 7 0.13
32 25 0.46
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (32 bp):
TTTCAAATAAAATGATAAATCAGGGTAAGAGT
Found at i:28631766 original size:61 final size:61
Alignment explanation
Indices: 28631700--28631849 Score: 300
Period size: 61 Copynumber: 2.5 Consensus size: 61
28631690 TTTTTACATT
28631700 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATAAATCAGGGTAAGAGTTTTC
1 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATAAATCAGGGTAAGAGTTTTC
28631761 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATAAATCAGGGTAAGAGTTTTC
1 AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATAAATCAGGGTAAGAGTTTTC
28631822 AATTAAATTAGGTTAGGGTTAGGGATTT
1 AATTAAATTAGGTTAGGGTTAGGGATTT
28631850 TAATTAAGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (61 bp):
AATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAATGATAAATCAGGGTAAGAGTTTTC
Found at i:28631923 original size:23 final size:23
Alignment explanation
Indices: 28631896--28631951 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
28631886 AATAGGTTAG
28631896 GGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
* *
28631919 GGTTAGTGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
28631942 GGTTAGGGTT
1 GGTTAGGGTT
28631952 AGAGATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAACTAAATTA
Found at i:28632204 original size:23 final size:23
Alignment explanation
Indices: 28632139--28632206 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 23
28632129 TTTTTAATTA
* *
28632139 AATTAAATTAGGTTAGAGTTTTT
1 AATTAAAATAGGTTAGAGATTTT
28632162 AATTAAATTAGGTTAGGGTTAGAGATTTT
1 AATTAAA--A---TA-GGTTAGAGATTTT
28632191 AATTAAAATAGGTTAG
1 AATTAAAATAGGTTAG
28632207 GGTTAGGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
23 13 0.35
24 2 0.05
27 1 0.03
28 2 0.05
29 19 0.51
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (23 bp):
AATTAAAATAGGTTAGAGATTTT
Found at i:28632435 original size:80 final size:80
Alignment explanation
Indices: 28631839--28633199 Score: 1999
Period size: 80 Copynumber: 16.6 Consensus size: 80
28631829 TTAGGTTAGG
* * * * *
28631839 GTTAGGGATTTTAATTAAGA-TAGGTTAGGGTTAGGG-TTTTCATGTAAAATAGGTTAGGGTTAG
1 GTTAGGGTTTTTAATTAA-ATTAGGTTAGGGTAAGGGTTTTTAAT-TAAATTAAGTTA-GGTTAG
* * *
28631902 GGTTTTTAACTAAATTAG
63 GGTTTTTAATTAAGTTAA
* * * * * *
28631920 GTTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGAGATTTTAATTAAAATAGGTTAGGGTTAGGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTA-GGTTAGGG
*
28631985 TTTTTAATTAAATTAAATTA
65 TTTTTAATTAAGTT--A--A
* * * * *
28632005 GGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGG
1 -GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTA-GGTTAGG
* *
28632070 GTTTTCATGTAAAATAGGTTAA
64 G-TTT--T-T-AATTAAGTTAA
*** * *
28632092 GGTTAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAATTAGGTTAGAG
1 -GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGG
* *
28632157 TTTTTAATTAAATTAG
65 TTTTTAATTAAGTTAA
* * * * *
28632173 GTTAGGGTTAGAGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAAGTAAAATAGGTTAAGG
1 GTTAGGG-T-----TTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTT-AGG
*
28632238 TTAGGGTTTTTAATTAAATTAAAATA
59 TTAGGGTTTTTAATTAAGTT---A-A
* * * * *
28632264 GGGTAAGGGTTTTTAATTAAATTAAGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAG
1 --GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTA-GGTTAG
*
28632328 GGTTTTTAATTAAATTAAGTTAG
63 GG--TTT--TT-AATTAAGTTAA
28632351 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632416 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632431 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632496 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632511 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632576 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632591 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632656 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632671 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632736 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632751 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632816 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632831 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632896 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632911 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28632976 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28632991 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28633056 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
28633071 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
28633136 TTTTAATTAAGTTAA
66 TTTTAATTAAGTTAA
* *
28633151 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATCAAAT
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAAT
28633200 AATGTCAAAA
Statistics
Matches: 1196, Mismatches: 52, Indels: 65
0.91 0.04 0.05
Matches are distributed among these distances:
80 785 0.66
81 75 0.06
82 7 0.01
83 5 0.00
85 36 0.03
86 166 0.14
87 91 0.08
88 4 0.00
89 2 0.00
90 4 0.00
91 14 0.01
92 1 0.00
93 6 0.01
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (80 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAAGTTAGGTTAGGGT
TTTTAATTAAGTTAA
Found at i:28635349 original size:12 final size:15
Alignment explanation
Indices: 28635308--28635341 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28635298 AATAAATATC
*
28635308 TAAAAATA-CATAAA
1 TAAAAATATCTTAAA
28635322 TAAAAATATCTTAAA
1 TAAAAATATCTTAAA
28635337 TAAAA
1 TAAAA
28635342 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCTTAAA
Found at i:28635506 original size:26 final size:29
Alignment explanation
Indices: 28635442--28635504 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
28635432 AAAATATTAA
*
28635442 AAATTTTAAAATTATTTTTAAAAAAATAGG
1 AAATTTTAAAATTATTCTTAAAAAAATA-G
*
28635472 AAATTTTAAAATT-TTCTTAAAATAAT-G
1 AAATTTTAAAATTATTCTTAAAAAAATAG
28635499 AAATTT
1 AAATTT
28635505 AATGGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 7 0.23
29 11 0.35
30 13 0.42
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATTTTAAAATTATTCTTAAAAAAATAG
Found at i:28635569 original size:22 final size:22
Alignment explanation
Indices: 28635539--28635580 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28635529 ATTTGGAGAT
*
28635539 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
28635561 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
28635581 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:28635588 original size:30 final size:30
Alignment explanation
Indices: 28635552--28635610 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
28635542 TTGAAGGAAA
*
28635552 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAATTTGAGAGT
28635582 TTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTGAGAGAATTTTGGAAGGAATTTGAGAG
28635611 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAATTTGAGAGT
Found at i:28635606 original size:22 final size:22
Alignment explanation
Indices: 28635581--28635651 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
28635571 AATTTGAGAG
*
28635581 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
28635603 TTTGAGAGAATTTTTGAACGGGA
1 TTTGAGAGAATTTTTGAA-GGAA
28635626 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
28635647 ATTGA
1 TTTGA
28635652 TATTGAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 3 0.07
22 38 0.86
23 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.30, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:28638743 original size:23 final size:20
Alignment explanation
Indices: 28638699--28638747 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28638689 TTCAAAAAAC
*
28638699 AAAAAAGAAAAAAAAGAGGA
1 AAAAAAGAAAAAAAAGAAGA
*
28638719 AAAAAAGAAGAAAAAAGAAAA
1 AAAAAAGAA-AAAAAAGAAGA
28638740 GAAAAAAG
1 -AAAAAAG
28638748 GAATGAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAAGA
Found at i:28638744 original size:11 final size:10
Alignment explanation
Indices: 28638699--28638745 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
28638689 TTCAAAAAAC
28638699 AAAAAAG-AA
1 AAAAAAGAAA
*
28638708 AAAAAAGAGGA
1 AAAAAAGA-AA
*
28638719 AAAAAAGAAG
1 AAAAAAGAAA
28638729 AAAAAAGAAA
1 AAAAAAGAAA
28638739 AGAAAAA
1 A-AAAAA
28638746 AGGAATGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 14 0.45
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:28638747 original size:12 final size:11
Alignment explanation
Indices: 28638694--28638746 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
28638684 CCAGATTCAA
28638694 AAAACAAAAAAG
1 AAAA-AAAAAAG
*
28638706 AAAAAAAAGAGG
1 AAAAAAAA-AAG
*
28638718 AAAAAAAGAAG
1 AAAAAAAAAAG
28638729 AAAAAAGAAAAG
1 AAAAAA-AAAAG
28638741 AAAAAA
1 AAAAAA
28638747 GGAATGAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 12 0.34
12 23 0.66
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:28640194 original size:45 final size:45
Alignment explanation
Indices: 28640057--28640196 Score: 119
Period size: 45 Copynumber: 3.2 Consensus size: 45
28640047 CCTGAGCAGT
* * *
28640057 AGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGAC
1 AGTGGAGCAGGTTGAAGATAACAGATCTTGCCCTCCTGCATTGAC
* * * * * * * *
28640102 AGCGAAGCAGATCGAAGA-CACA-AGCCTTG-CCTCCAT-CGGTTG-T
1 AGTGGAGCAGGTTGAAGATAACAGA-TCTTGCCCTCC-TGC-ATTGAC
28640145 AGTGGAGCAGGTTGAAGATAACAGATCTTGCCCTCCTGCATTGAC
1 AGTGGAGCAGGTTGAAGATAACAGATCTTGCCCTCCTGCATTGAC
28640190 AGTGGAG
1 AGTGGAG
28640197 TAGATCGAAG
Statistics
Matches: 68, Mismatches: 19, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
43 20 0.29
44 20 0.29
45 28 0.41
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (45 bp):
AGTGGAGCAGGTTGAAGATAACAGATCTTGCCCTCCTGCATTGAC
Found at i:28640571 original size:132 final size:132
Alignment explanation
Indices: 28640190--28640801 Score: 750
Period size: 132 Copynumber: 4.6 Consensus size: 132
28640180 CTGCATTGAC
* * * *
28640190 AGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCA
* * *** * *
28640255 GTAATTCTATCTCTCTAGTTGGCAGTGGAATAGATTGAAGATTTCGGATCTTATCTCCCT----A
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
28640316 --
131 GT
* * * *
28640316 AGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTTTGATTACAGTGGAGTACATTGAAGTAC
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAG-----T--A-T--
* *** *
28640381 ATTGAAGCCAGTAATTCTATCTCCCTAGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATC
56 ATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATC
* *
28640446 TCTCTAAGCAAT
121 TCCCTAAGCAGT
* *
28640458 AGTTGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTAAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCA
** *
28640523 AAAATTCTATCTCCTTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
28640588 GT
131 GT
* *
28640590 AGTGGAGCAGATCGAAGATGGCGGATTTTACATCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCA
* * *
28640655 GTAATTCTATCTCCCTGGGTAGCAGTGGAATAGATTGAAGATCACAGATATTATCTCCCTAAGCA
66 GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
28640720 GT
131 GT
* * * ** *
28640722 AGTGGAGTAGATCGAAAATGGCGAATTTTACCTCCCTAAGGTTACAGTGGAGTATATTGAAGCTA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCA
28640787 GTAATTCTATCTCCC
66 GTAATTCTATCTCCC
28640802 CGACGTTGCG
Statistics
Matches: 429, Mismatches: 41, Indels: 26
0.86 0.08 0.05
Matches are distributed among these distances:
126 49 0.11
131 1 0.00
132 260 0.61
133 1 0.00
134 1 0.00
135 1 0.00
136 67 0.16
137 1 0.00
140 1 0.00
142 47 0.11
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTATATTGAAGCCA
GTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCA
GT
Found at i:28640594 original size:44 final size:44
Alignment explanation
Indices: 28640541--28640733 Score: 110
Period size: 44 Copynumber: 4.4 Consensus size: 44
28640531 ATCTCCTTGG
* *
28640541 GCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAA
* * ** * *
28640585 GCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA-CATCCCT--
1 GCAGTAGTGGAGTAGATTGAAGATTACAGATCTTATC-TCCCTAA
** * * * **
28640627 GTGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGG
1 GCAG-T--AGTGGAGTAGATTGAAG--ATTACAGATCTTATCTCCCTAA
* * * * *
28640673 GTAGCAGTGGAATAGATTGAAGATCACAGATATTATCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAA
28640717 GCAGTAGTGGAGTAGAT
1 GCAGTAGTGGAGTAGAT
28640734 CGAAAATGGC
Statistics
Matches: 105, Mismatches: 32, Indels: 24
0.65 0.20 0.15
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 18 0.17
44 62 0.59
45 16 0.15
46 3 0.03
47 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (44 bp):
GCAGTAGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAA
Found at i:28640801 original size:44 final size:44
Alignment explanation
Indices: 28640629--28640801 Score: 108
Period size: 44 Copynumber: 3.9 Consensus size: 44
28640619 ACATCCCTGT
* **
28640629 GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT--
1 GGTTACAGTGGAGTAGATTGAAGATAGTAATTCTATCTCCCTAA
* * *
28640671 GGGTAGCAGTGGAATAGATTGAAGATCA-CAGATAT-TATCTCCCTAA
1 GGTTA-CAGTGGAGTAGATTGAAGAT-AGTA-AT-TCTATCTCCCTAA
* * * * * *
28640717 GCAG-T--AGTGGAGTAGATCGAAAATGGCGAATTTTACCTCCCTAA
1 G--GTTACAGTGGAGTAGATTGAAGATAG-TAATTCTATCTCCCTAA
* *
28640761 GGTTACAGTGGAGTATATTGAAGCTAGTAATTCTATCTCCC
1 GGTTACAGTGGAGTAGATTGAAGATAGTAATTCTATCTCCC
28640802 CGACGTTGCG
Statistics
Matches: 97, Mismatches: 20, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
42 5 0.05
43 19 0.20
44 52 0.54
45 18 0.19
46 1 0.01
47 1 0.01
48 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
GGTTACAGTGGAGTAGATTGAAGATAGTAATTCTATCTCCCTAA
Found at i:28641059 original size:12 final size:12
Alignment explanation
Indices: 28641042--28641073 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28641032 AAGCTACTTG
*
28641042 AAGAGAAGCGTC
1 AAGAGAAGCATC
28641054 AAGAGAAGCATC
1 AAGAGAAGCATC
28641066 AAGAGAAG
1 AAGAGAAG
28641074 TCAAGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.31, T:0.06
Consensus pattern (12 bp):
AAGAGAAGCATC
Found at i:28643821 original size:41 final size:41
Alignment explanation
Indices: 28643760--28643868 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
28643750 GACTATACGT
*
28643760 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
28643801 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
28643842 CTAGCAGGCCAAGTGCTGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
28643869 TTAAATTAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 56 0.92
42 5 0.08
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:28645135 original size:9 final size:9
Alignment explanation
Indices: 28645111--28645173 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
28645101 TTAGTCCCTT
*
28645111 TTTTTAGTA
1 TTTTTATTA
28645120 TTTTTATTA
1 TTTTTATTA
28645129 --TTT-TTA
1 TTTTTATTA
28645135 TTTTTATTA
1 TTTTTATTA
**
28645144 TTACTATTA
1 TTTTTATTA
*
28645153 TTTATTATTG
1 TTT-TTATTA
*
28645163 TTTATATTA
1 TTTTTATTA
28645172 TT
1 TT
28645174 GTTGCTTATC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 3 0.07
9 26 0.62
10 7 0.17
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTTATTA
Found at i:28645884 original size:108 final size:108
Alignment explanation
Indices: 28645673--28645985 Score: 479
Period size: 108 Copynumber: 2.9 Consensus size: 108
28645663 AAGGAAAATT
* * *
28645673 TTTCTAAATGAGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTT-GCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
28645738 CGATTTTTTTCGTTCAACTAAATAGCCAAATATCATTTCAAAAA
65 CGATTTTCTTCGTTCAACTAAATAGCCAAATATCATTTCAAAAA
28645782 TTTCAAAATAAGGCAATGTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
1 TTTCAAAATAAGGCAATGTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
* *
28645847 GATTTTCTTCGTTCAGCTAAATTGCCAAATATCATTTCAAAAA
66 GATTTTCTTCGTTCAACTAAATAGCCAAATATCATTTCAAAAA
* * * *
28645890 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAG-GAACATGCCATAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATG-TTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
28645954 CGA-TTTC-TCGTTTAACCAAATAGCCAAATATC
65 CGATTTTCTTCGTTCAACTAAATAGCCAAATATC
28645986 CTCTTGAATT
Statistics
Matches: 189, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
106 21 0.11
107 4 0.02
108 127 0.67
109 37 0.20
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATGTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTC
GATTTTCTTCGTTCAACTAAATAGCCAAATATCATTTCAAAAA
Found at i:28648318 original size:20 final size:21
Alignment explanation
Indices: 28648279--28648318 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28648269 CACCAAGTGA
28648279 AAGCATTTACATGAACAACTTC
1 AAGCATTTACAT-AACAACTTC
*
28648301 AAGCATTTATAT-ACAACT
1 AAGCATTTACATAACAACT
28648319 ATGTTCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (21 bp):
AAGCATTTACATAACAACTTC
Found at i:28649842 original size:19 final size:19
Alignment explanation
Indices: 28649817--28649861 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
28649807 TATTTTATTT
28649817 ATAATAT-TT-TAATATAAC
1 ATAATATATTATAAT-TAAC
*
28649835 AT-ATATATTATAGTTAAC
1 ATAATATATTATAATTAAC
28649853 ATAATATAT
1 ATAATATAT
28649862 ATTACATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 10 0.43
19 9 0.39
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAATATATTATAATTAAC
Found at i:28656529 original size:19 final size:20
Alignment explanation
Indices: 28656481--28656531 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
28656471 CCTTGATCTG
28656481 ATACATGATGAGAAAATTTA
1 ATACATGATGAGAAAATTTA
* *
28656501 A-ACGAAGATGA-AGAATTTA
1 ATAC-ATGATGAGAAAATTTA
28656520 ATACATGATGAG
1 ATACATGATGAG
28656532 CTTAAAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (20 bp):
ATACATGATGAGAAAATTTA
Found at i:28663354 original size:17 final size:17
Alignment explanation
Indices: 28663324--28663357 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28663314 AATAATTTCT
* *
28663324 AAAAACATGTATATGTA
1 AAAAAAATGCATATGTA
28663341 AAAAAAATGCATATGTA
1 AAAAAAATGCATATGTA
28663358 TTATAAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
AAAAAAATGCATATGTA
Found at i:28665083 original size:44 final size:44
Alignment explanation
Indices: 28664956--28665485 Score: 521
Period size: 44 Copynumber: 11.9 Consensus size: 44
28664946 AAGACTTATA
* * * *
28664956 TCTTTGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTA
1 TCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGTTT
* * * * *** * *
28665001 TCTTCGACCTACTTCGCCACCAGTATGGGAATACAAGATCTGTTA
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTT
28665046 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* * *
28665090 TCTTCGATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTGTTT
* *
28665135 TCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCCGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* * * *** *
28665179 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTG
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTT
*
28665224 TCTTTGATCTACTTCACGCCAGTGCATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* * * * * *
28665268 TATTCGATCTACTTCGCCACCAGT--ATGGAAAAACAAGATCTGTTA
1 TCTTTGATCTACTTC-ACGCCAGTACAT-G-AAGACAAGATCTGTTT
28665313 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* * * *** *
28665357 TCTTCGAT-TACTTCGCCACCAGTATGGGAAGACAAGATATGTTT
1 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTT
* *
28665401 TCTTTGATCTACTTCACGCCAGTACATGAAGACCAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
* ***
28665445 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCT
28665486 ACTCCTACTC
Statistics
Matches: 394, Mismatches: 76, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
42 7 0.02
43 10 0.03
44 194 0.49
45 171 0.43
46 5 0.01
47 7 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTT
Found at i:28665086 original size:89 final size:89
Alignment explanation
Indices: 28664954--28665485 Score: 859
Period size: 89 Copynumber: 6.0 Consensus size: 89
28664944 ATAAGACTTA
* * * * *
28664954 TATCTTTGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCGACCTACTTCGCC
1 TATCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCC
*
28665019 ACCAGTATGGGAATACAAGATCTGT
65 ACCAGTATGGGAAGACAAGATCTGT
28665044 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
*
28665109 CTAGTATGGGAAGACAAGATCTGT
66 CCAGTATGGGAAGACAAGATCTGT
* * *
28665133 TTTCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCCGTTTTCTTCGATCTACTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
28665198 CCAGTATGGGAAGACAAGATCTGT
66 CCAGTATGGGAAGACAAGATCTGT
* * *
28665222 TGTCTTTGATCTACTTCACGCCAGTGCATGAAGACAAGATCTGTTTTATTCGATCTACTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
* *
28665287 CCAGTATGGAAAAACAAGATCTGT
66 CCAGTATGGGAAGACAAGATCTGT
28665311 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGAT-TACTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
*
28665375 CCAGTATGGGAAGACAAGATATGT
66 CCAGTATGGGAAGACAAGATCTGT
* * * * *
28665399 TTTCTTTGATCTACTTCACGCCAGTACATGAAGACCAGATCTGCTTTCTTTGATCTACTTCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
28665464 CCAGTATGGGAAGACAAGATCT
66 CCAGTATGGGAAGACAAGATCT
28665486 ACTCCTACTC
Statistics
Matches: 411, Mismatches: 30, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
88 81 0.20
89 311 0.76
90 19 0.05
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (89 bp):
TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
CCAGTATGGGAAGACAAGATCTGT
Found at i:28673590 original size:20 final size:20
Alignment explanation
Indices: 28673565--28673604 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28673555 TAAAGGTCTT
28673565 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
28673585 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
28673605 ATGAGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:28677376 original size:17 final size:17
Alignment explanation
Indices: 28677346--28677379 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28677336 AATAATTTCT
* *
28677346 AAAAACATGTATATGTA
1 AAAAAAATGCATATGTA
28677363 AAAAAAATGCATATGTA
1 AAAAAAATGCATATGTA
28677380 TTATAAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
AAAAAAATGCATATGTA
Found at i:28690758 original size:12 final size:12
Alignment explanation
Indices: 28690741--28690765 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28690731 CGTGTTCATT
28690741 CGGTTAACCGAC
1 CGGTTAACCGAC
28690753 CGGTTAACCGAC
1 CGGTTAACCGAC
28690765 C
1 C
28690766 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:28690948 original size:9 final size:9
Alignment explanation
Indices: 28690924--28690982 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
28690914 TTTGGTTAAA
*
28690924 AATTAACTG
1 AATTAACCG
*
28690933 AACTAACCG
1 AATTAACCG
*
28690942 AATTAACTG
1 AATTAACCG
*
28690951 AATT-ACCTA
1 AATTAACC-G
28690960 AATTAACCG
1 AATTAACCG
*
28690969 AATTACCCG
1 AATTAACCG
28690978 AATTA
1 AATTA
28690983 CTTAACCGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 2 0.05
9 35 0.88
10 3 0.08
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:28690954 original size:27 final size:27
Alignment explanation
Indices: 28690924--28690982 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
28690914 TTTGGTTAAA
* *
28690924 AATTAACTGAACTAACCGAATTAACTG
1 AATTAACTAAACTAACCGAATTAACCG
* * *
28690951 AATTACCTAAATTAACCGAATTACCCG
1 AATTAACTAAACTAACCGAATTAACCG
28690978 AATTA
1 AATTA
28690983 CTTAACCGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.27
Consensus pattern (27 bp):
AATTAACTAAACTAACCGAATTAACCG
Found at i:28690981 original size:18 final size:18
Alignment explanation
Indices: 28690924--28690982 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
28690914 TTTGGTTAAA
* *
28690924 AATTAACTGAACTAACCG
1 AATTAACTGAATTACCCG
**
28690942 AATTAACTGAATTACCTA
1 AATTAACTGAATTACCCG
*
28690960 AATTAACCGAATTACCCG
1 AATTAACTGAATTACCCG
28690978 AATTA
1 AATTA
28690983 CTTAACCGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTAACTGAATTACCCG
Found at i:28691120 original size:18 final size:18
Alignment explanation
Indices: 28691097--28691131 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
28691087 AATTTTTATG
28691097 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
28691115 ATTGGGTTGGGTTGGGT
1 ATTGGGTTGGGTTGGGT
28691132 TGAATACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.51, T:0.40
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:28691686 original size:20 final size:21
Alignment explanation
Indices: 28691641--28691687 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
28691631 ATGATCTACG
*
28691641 CACACAAGCGTGTGGAGTAGT
1 CACACAAGCGTGTGGAGTAAT
28691662 CACACAAGCGTGTGGA-TAAT
1 CACACAAGCGTGTGGAGTAAT
28691682 CACACA
1 CACACA
28691688 GTTTGGGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (21 bp):
CACACAAGCGTGTGGAGTAAT
Found at i:28692170 original size:24 final size:24
Alignment explanation
Indices: 28692138--28692185 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28692128 CCAGAGGAAA
28692138 GCAAATTGGTAAATCGGTTAGATT
1 GCAAATTGGTAAATCGGTTAGATT
28692162 GCAAATTGGTAAATCGGTTAGATT
1 GCAAATTGGTAAATCGGTTAGATT
28692186 ACAAGGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (24 bp):
GCAAATTGGTAAATCGGTTAGATT
Found at i:28698254 original size:27 final size:27
Alignment explanation
Indices: 28698193--28698273 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
28698183 TACTGCTGCT
* *
28698193 TCTCTCTCTCC-TCTCGCTCTCCCT-T
1 TCTCTCTCTCCTTCTCCCTCTCCCTCC
* *
28698218 TC-CT-TCTCCTTCTGCCTTTCCCTCC
1 TCTCTCTCTCCTTCTCCCTCTCCCTCC
* *
28698243 TCTCTCTCTCCTTTTCCCTCTCTCTCC
1 TCTCTCTCTCCTTCTCCCTCTCCCTCC
28698270 TCTC
1 TCTC
28698274 CTTATCTCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 5 0.11
24 12 0.27
25 4 0.09
26 2 0.05
27 21 0.48
ACGTcount: A:0.00, C:0.52, G:0.02, T:0.46
Consensus pattern (27 bp):
TCTCTCTCTCCTTCTCCCTCTCCCTCC
Found at i:28698284 original size:21 final size:20
Alignment explanation
Indices: 28698202--28698292 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 20
28698192 TTCTCTCTCT
*
28698202 CCTCTCGCTCTC-CCTT-TC
1 CCTCTCTCTCTCTCCTTATC
*
28698220 CTTCTC-CT-TCTGCCTT-TC
1 CCTCTCTCTCTCT-CCTTATC
*
28698238 CCTCCTCTCTCTCTCCTTTTC
1 CCT-CTCTCTCTCTCCTTATC
28698259 CCTCTCTCTCCTCTCCTTATC
1 CCTCTCTCT-CTCTCCTTATC
* *
28698280 TCTCTCTTTCTCT
1 CCTCTCTCTCTCT
28698293 TTCTCTTTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
16 2 0.03
17 2 0.03
18 13 0.21
19 3 0.05
20 16 0.26
21 25 0.41
ACGTcount: A:0.01, C:0.49, G:0.02, T:0.47
Consensus pattern (20 bp):
CCTCTCTCTCTCTCCTTATC
Found at i:28698328 original size:28 final size:30
Alignment explanation
Indices: 28698270--28698331 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
28698260 CTCTCTCTCC
* * *
28698270 TCTCCTTATCTCTCTCTTTCTCTTTCTCTT
1 TCTCCTTATCTCTCTCTTTCCCTATCCCTT
*
28698300 TCTCCTTATC-C-CNCTTTCCCTATCCCTT
1 TCTCCTTATCTCTCTCTTTCCCTATCCCTT
28698328 TCTC
1 TCTC
28698332 TATCTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 17 0.61
29 1 0.04
30 10 0.36
ACGTcount: A:0.05, C:0.42, G:0.00, T:0.52
Consensus pattern (30 bp):
TCTCCTTATCTCTCTCTTTCCCTATCCCTT
Found at i:28701038 original size:73 final size:70
Alignment explanation
Indices: 28700860--28701107 Score: 164
Period size: 73 Copynumber: 3.4 Consensus size: 70
28700850 TTTTTTTTAT
* * * *
28700860 CAAATTTTAGCCACCAAAATTGTAAGCAACTGTGACAAAAAATGGTCACACACATATTTAACCTT
1 CAAATTTT-GACACTAAAATTGTAAGCAATTGTGACAAAAAATGGT-ACACACATATTCAACCTT
28700925 TTGTGAC
64 TTGTGAC
* * * * * * *
28700932 CAAATTGTTTACACTAAAACTATAAGTACTTGTGACGGTAATAAATGGT-CACATATATTCAACT
1 CAAATT-TTGACACTAAAATTGTAAGCAATTGTGAC---AAAAAATGGTACACACATATTCAAC-
*
28700996 TTTTTGTGA-
61 CTTTTGTGAC
* * * *
28701005 TAAATTTTCGACACTAAAATTGTAAGCAATTGTGGCAAAATTAAATGGTTACA-A-TTATTTAA-
1 CAAATTTT-GACACTAAAATTGTAAGCAATTGTGAC-AAA--AAATGG-TACACACATATTCAAC
*
28701067 TTTTTGTGAC
61 CTTTTGTGAC
* * *
28701077 CAATTTTTTTACACTAAAATCGTAAGCAATT
1 CAA-ATTTTGACACTAAAATTGTAAGCAATT
28701108 CTGATGAACA
Statistics
Matches: 137, Mismatches: 27, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
71 11 0.08
72 49 0.36
73 56 0.41
74 10 0.07
75 11 0.08
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (70 bp):
CAAATTTTGACACTAAAATTGTAAGCAATTGTGACAAAAAATGGTACACACATATTCAACCTTTT
GTGAC
Found at i:28705429 original size:29 final size:29
Alignment explanation
Indices: 28705377--28705460 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
28705367 ATTTAACATA
* *
28705377 AGGAGTTTTTGGGCCTTTCCCGTATCATG
1 AGGAGTTTTTGGGCCTCTCACGTATCATG
*
28705406 AGGAGTTTTTGGGTCTCTCACGTATCATG
1 AGGAGTTTTTGGGCCTCTCACGTATCATG
* *
28705435 AGGAGATTTTGGGCCTCTCTCGTATC
1 AGGAGTTTTTGGGCCTCTCACGTATC
28705461 GAGTCCAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.37
Consensus pattern (29 bp):
AGGAGTTTTTGGGCCTCTCACGTATCATG
Found at i:28707781 original size:31 final size:32
Alignment explanation
Indices: 28707743--28707805 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
28707733 AGGAAATTTA
28707743 TAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 TAAGAGTAATTGAATCCTAATAAAAACTCTTT
28707774 TAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 TAAGAGTAATTGAATCCTAATAAAAACTCTTT
28707806 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.35
Consensus pattern (32 bp):
TAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:28710169 original size:36 final size:37
Alignment explanation
Indices: 28710090--28710178 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 37
28710080 GAATATGAAA
28710090 AAAAGAGAGGAAAATAGTAAAAAAAATAAGAAAAAAAT
1 AAAAGAGAGGAAAATAG-AAAAAAAATAAGAAAAAAAT
* * * *
28710128 GAAAGAGAGTAAAA-AG-AAAAAAATATGAAAAGTAAT
1 AAAAGAGAGGAAAATAGAAAAAAAATAAGAAAA-AAAT
*
28710164 AAAAGA-AAGAAAATA
1 AAAAGAGAGGAAAATA
28710179 AATCTTAACA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
35 19 0.45
36 9 0.21
37 2 0.05
38 12 0.29
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (37 bp):
AAAAGAGAGGAAAATAGAAAAAAAATAAGAAAAAAAT
Found at i:28710728 original size:19 final size:18
Alignment explanation
Indices: 28710695--28710739 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
28710685 TGTTGCTACT
28710695 ATTTTGTTGTTATTGTATA
1 ATTTTGTTGTTATTGT-TA
28710714 ACTTTTGTT-TTATTGTTA
1 A-TTTTGTTGTTATTGTTA
28710732 ATTTTGTT
1 ATTTTGTT
28710740 ACTATTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 8 0.32
20 7 0.28
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (18 bp):
ATTTTGTTGTTATTGTTA
Found at i:28716553 original size:41 final size:41
Alignment explanation
Indices: 28716496--28716816 Score: 236
Period size: 41 Copynumber: 7.8 Consensus size: 41
28716486 ATTTTTAAAC
* * * *
28716496 CTTTAGCGGCGTTTTTATTTTAGCACCGCTAATGGTCCGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
* * * **
28716537 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
* *
28716578 CTTTAGCGGCGTTTTTCTCTAAGCGTCGCTAATGCT-CGTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCG-AT
* * * * * * **
28716619 CTTTAGTGGCATTTTTATCTGAGCGCCACTAATTCTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
* **
28716660 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAATG-TTAGTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCG-AT
* * * * *
28716701 CTTTAGTGGCGTTTTTATCTGAGCGCCCCTAATGCTCTG-G
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
* ** * ** *
28716741 CTTTTAGCGGCATTTTATAGGTAAGCGCCGCGAATGCAT-TTAC
1 C-TTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGC-TCCGAT
** *
28716784 CTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
28716817 AGTAACAAAA
Statistics
Matches: 215, Mismatches: 57, Indels: 16
0.75 0.20 0.06
Matches are distributed among these distances:
40 4 0.02
41 177 0.82
42 32 0.15
43 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCCGAT
Found at i:28716634 original size:82 final size:82
Alignment explanation
Indices: 28716495--28716799 Score: 380
Period size: 82 Copynumber: 3.7 Consensus size: 82
28716485 GATTTTTAAA
* * * * *
28716495 CCTTTAGCGGCGTTTTTATTTTAGCACCGCTAATGGTCCG-ATCTTTAGCGGCGTTTTTATCTGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
28716559 GCGCCACTAATGCTCTGG
65 GCGCCACTAATGCTCTGG
* * *
28716577 CCTTTAGCGGCGTTTTTCTCTAAGCGTCGCTAATGCTCGTATCTTTAGTGGCATTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
28716642 CGCCACTAATTCTCTGG
66 CGCCACTAATGCTCTGG
* * *
28716659 CCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAATGTTAGTATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
28716724 CGCCCCTAATGCTCTGG
66 CGCCACTAATGCTCTGG
* * ** * * * *
28716741 CTTTTAGCGGCATTTTATAGGTAAGCGCCGCGAATGCAT-TTACCTTTAGCGGCGTTTTT
1 CCTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGC-TCGTATCTTTAGTGGCGTTTTT
28716800 GCCGAAGCGC
Statistics
Matches: 194, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
81 2 0.01
82 159 0.82
83 32 0.16
84 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATGCTCTGG
Found at i:28719216 original size:8 final size:10
Alignment explanation
Indices: 28719194--28719230 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
28719184 TATTTTTACT
28719194 TATATATGGA
1 TATATATGGA
*
28719204 TATATATGAA
1 TATATATGGA
28719214 TATATATGGA
1 TATATATGGA
28719224 TATATAT
1 TATATAT
28719231 ATATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:28721073 original size:11 final size:11
Alignment explanation
Indices: 28721057--28721093 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
28721047 TTGACTTTTC
*
28721057 TAATTTGATTA
1 TAATTTCATTA
28721068 TAATTTCATTA
1 TAATTTCATTA
28721079 TAATTTCATTA
1 TAATTTCATTA
28721090 TAAT
1 TAAT
28721094 GTAGTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (11 bp):
TAATTTCATTA
Found at i:28721321 original size:34 final size:34
Alignment explanation
Indices: 28721280--28721344 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
28721270 GCATAACTTG
28721280 TTAATTAATTAATATTATACATAAATTACATAAC
1 TTAATTAATTAATATTATACATAAATTACATAAC
*
28721314 TTAATTAATTAATATTATACATAACTTACAT
1 TTAATTAATTAATATTATACATAAATTACAT
28721345 TAATATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAATTAATTAATATTATACATAAATTACATAAC
Found at i:28721335 original size:25 final size:22
Alignment explanation
Indices: 28721306--28721359 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
28721296 ATACATAAAT
28721306 TACATAACTTAATTAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
28721331 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
28721353 TACATAA
1 TACATAA
28721360 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:28721349 original size:22 final size:22
Alignment explanation
Indices: 28721316--28721366 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28721306 TACATAACTT
28721316 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
28721337 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
28721359 AATTACAT
1 AATTACAT
28721367 AACTTAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:28721354 original size:56 final size:56
Alignment explanation
Indices: 28721287--28721456 Score: 313
Period size: 56 Copynumber: 3.0 Consensus size: 56
28721277 TTGTTAATTA
28721287 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
*
28721343 ATTAATATTATACATAAATTACATAACTTAATGAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
* *
28721399 ATTAATATTATACATAAATTACATAACTTAGTTAATTAATATTGTACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
28721455 AT
1 AT
28721457 AACTTACAAC
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 110 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.41
Consensus pattern (56 bp):
ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
Found at i:28721391 original size:25 final size:22
Alignment explanation
Indices: 28721362--28721415 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
28721352 ATACATAAAT
28721362 TACATAACTTAATGAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
28721387 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
28721409 TACATAA
1 TACATAA
28721416 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:28721405 original size:22 final size:22
Alignment explanation
Indices: 28721377--28721422 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28721367 AACTTAATGA
*
28721377 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
28721399 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
28721421 AT
1 AT
28721423 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:28721457 original size:9 final size:9
Alignment explanation
Indices: 28721297--28721660 Score: 95
Period size: 9 Copynumber: 42.2 Consensus size: 9
28721287 ATTAATATTA
*
28721297 TACATAAAT
1 TACATAACT
28721306 TACATAACT
1 TACATAACT
28721315 TA-ATTAA-T
1 TACA-TAACT
*
28721323 TA-AT-ATT
1 TACATAACT
28721330 ATACATAACT
1 -TACATAACT
*
28721340 TACATTAATATT
1 TACA-T-A-ACT
*
28721352 ATACATAAAT
1 -TACATAACT
28721362 TACATAACT
1 TACATAACT
28721371 TA-ATGAA-T
1 TACAT-AACT
*
28721379 TA-AT-ATT
1 TACATAACT
28721386 ATACATAACT
1 -TACATAACT
*
28721396 TACATTAATATT
1 TACA-T-A-ACT
*
28721408 ATACATAAAT
1 -TACATAACT
28721418 TACATAACT
1 TACATAACT
**
28721427 TAGTTAA-T
1 TACATAACT
*
28721435 TA-AT-ATT
1 TACATAACT
28721442 GTACATAACT
1 -TACATAACT
28721452 TACATAACT
1 TACATAACT
28721461 TAC--AACT
1 TACATAACT
28721468 TACATAACT
1 TACATAACT
***
28721477 TACATTTTTT
1 TACA-TAACT
*
28721487 TA-ATTA-T
1 TACATAACT
* *
28721494 T-CGTAAAT
1 TACATAACT
28721502 TACATAACT
1 TACATAACT
* *
28721511 TACTTAATT
1 TACATAACT
*
28721520 TGCATAA--
1 TACATAACT
*
28721527 TAAATAACT
1 TACATAACT
28721536 TACATAACT
1 TACATAACT
*
28721545 CACATAA--
1 TACATAACT
28721552 TACATAACT
1 TACATAACT
* **
28721561 TATACGACT
1 TACATAACT
28721570 TACATAACT
1 TACATAACT
28721579 TACAT-A--
1 TACATAACT
* *
28721585 -GCATAATT
1 TACATAACT
*
28721593 TTCATAA--
1 TACATAACT
* *
28721600 TAAAAAACT
1 TACATAACT
*
28721609 TACATAATT
1 TACATAACT
*
28721618 TTCATAA--
1 TACATAACT
*
28721625 TAAATAACT
1 TACATAACT
28721634 TACATAA--
1 TACATAACT
28721641 TACATAACT
1 TACATAACT
*
28721650 TACATAGCT
1 TACATAACT
28721659 TA
1 TA
28721661 ATTATACTTA
Statistics
Matches: 264, Mismatches: 49, Indels: 84
0.66 0.12 0.21
Matches are distributed among these distances:
5 3 0.01
6 4 0.02
7 43 0.16
8 26 0.10
9 154 0.58
10 16 0.06
11 4 0.02
12 6 0.02
13 8 0.03
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:28721469 original size:16 final size:16
Alignment explanation
Indices: 28721448--28721480 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28721438 TATTGTACAT
28721448 AACTTACATAACTTAC
1 AACTTACATAACTTAC
28721464 AACTTACATAACTTAC
1 AACTTACATAACTTAC
28721480 A
1 A
28721481 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:28721481 original size:34 final size:34
Alignment explanation
Indices: 28721443--28721584 Score: 89
Period size: 34 Copynumber: 4.2 Consensus size: 34
28721433 ATTAATATTG
*
28721443 TACATAACTTACATAACT-TACAACTTACATAACT
1 TACATAATTTACATAA-TATACAACTTACATAACT
** * *
28721477 TACAT--TTT-TTTAATTATTCGTAAATTACATAACT
1 TACATAATTTACATAA-TATAC--AACTTACATAACT
* * * *
28721511 TACTTAATTTGCATAATAAATAACTTACATAACT
1 TACATAATTTACATAATATACAACTTACATAACT
* *
28721545 CACATAA--TACATAACTTATACGACTTACATAACT
1 TACATAATTTACATAA--TATACAACTTACATAACT
28721579 TACATA
1 TACATA
28721585 GCATAATTTT
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
31 4 0.05
32 10 0.12
34 58 0.73
36 5 0.06
37 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.37
Consensus pattern (34 bp):
TACATAATTTACATAATATACAACTTACATAACT
Done.