Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 102 of 213
Found at i:28782801 original size:268 final size:267
Alignment explanation
Indices: 28782309--28782846 Score: 835
Period size: 268 Copynumber: 2.0 Consensus size: 267
28782299 GTGTTTATTT
* * * * * * *
28782309 GTAATGTAGGTTCTTGAGTTGAACCAGTTCGCCAGAAGGGACCAAGTCAGGAATGCGCAAGGGTG
1 GTAATGCAGCTTCTTGAGTTAAACCAGTTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGTG
* *
28782374 GTTGATTATAGTGCGATGTTATGCATAAAGAGGGACACTTTGGGGAATATGTTTTCAAATGATGA
66 GTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATGA
* * ** *
28782439 ATAGTATAATACGCCATGAATATGCCTATCTTATTAAAGATTTAAGTTGTAATGCTTTATACTAC
131 ATAGTATAAGACGCAACAAATATGCCTATCTTATCAAAGATTTAAGTTGTAATGCTTTATACTAC
* * *
28782504 TTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATTTTTTGACTTAGAAAACATTTTAA
196 TTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATCTTCTGACTCAGAAAACATTTTAA
28782569 ATAAATAA
261 A-AAATAA
28782577 GTAATGCAGCTTCTTGAGTTAAACCTA-TTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGT
1 GTAATGCAGCTTCTTGAGTTAAACC-AGTTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGT
28782641 GGTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATG
65 GGTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATG
* * * *
28782706 AATAGTATAAGACGCAACAAATATGCCTATTTTATCAAAGATTTAAGTTTTAATGCTTTATATTG
130 AATAGTATAAGACGCAACAAATATGCCTATCTTATCAAAGATTTAAGTTGTAATGCTTTATACTA
* * *
28782771 CTTTTAAGAGTCTGTTATAAATGCTAAACGTTTCATTCAAATCTTCTGACTCAGAAAAGATTTTA
195 CTTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATCTTCTGACTCAGAAAACATTTTA
28782836 AAAAATAA
260 AAAAATAA
28782844 GTA
1 GTA
28782847 CATCTTGTAT
Statistics
Matches: 245, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
267 9 0.04
268 235 0.96
269 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (267 bp):
GTAATGCAGCTTCTTGAGTTAAACCAGTTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGTG
GTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATGA
ATAGTATAAGACGCAACAAATATGCCTATCTTATCAAAGATTTAAGTTGTAATGCTTTATACTAC
TTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATCTTCTGACTCAGAAAACATTTTAA
AAAATAA
Found at i:28783434 original size:19 final size:19
Alignment explanation
Indices: 28783411--28783462 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28783401 AAAAATATTC
28783411 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
28783430 TAAAATTAAAAATATTTAT
1 AAAAATTCAAAATATTTAT
28783449 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
28783463 TTATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 16 0.59
20 7 0.26
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:28783434 original size:20 final size:20
Alignment explanation
Indices: 28783390--28783462 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
28783380 CTCTCACAAC
* * *
28783390 AAAAATTACAAAAAAATATTC
1 AAAAATT-CAAAATAATTTTT
28783411 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
* *
28783431 -AAAATTAAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTTT
28783449 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
28783463 TTATATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 5 0.11
19 15 0.34
20 17 0.39
21 7 0.16
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:28783512 original size:19 final size:19
Alignment explanation
Indices: 28783474--28783516 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28783464 TATATTTTAC
*
28783474 AAAAATATAAAAATTCTAA
1 AAAAATATAAAAAGTCTAA
28783493 AAAAATATAAAAAAGT-TAA
1 AAAAATAT-AAAAAGTCTAA
28783512 AAAAA
1 AAAAA
28783517 GTTACAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATATAAAAAGTCTAA
Found at i:28784371 original size:11 final size:11
Alignment explanation
Indices: 28784357--28784416 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
28784347 AGATAAATAT
28784357 TATTTTATTAA
1 TATTTTATTAA
*
28784368 TATTTTAGTAA
1 TATTTTATTAA
* *
28784379 TATTTAATGAGA
1 TATTTTATTA-A
*
28784391 TATTTTATTAT
1 TATTTTATTAA
*
28784402 TA-TTTATTAT
1 TATTTTATTAA
28784412 TATTT
1 TATTT
28784417 ATTTAGTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 10 0.25
11 21 0.52
12 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28784409 original size:10 final size:10
Alignment explanation
Indices: 28784394--28784419 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28784384 AATGAGATAT
28784394 TTTATTATTA
1 TTTATTATTA
28784404 TTTATTATTA
1 TTTATTATTA
28784414 TTTATT
1 TTTATT
28784420 TAGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTATTA
Found at i:28790684 original size:19 final size:19
Alignment explanation
Indices: 28790648--28790685 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28790638 TATATATATT
*
28790648 TAATTTTTGAATATTTTTA
1 TAATTTTTAAATATTTTTA
28790667 TAATTTTTAAAGTATTTTT
1 TAATTTTTAAA-TATTTTT
28790686 TTGACATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TAATTTTTAAATATTTTTA
Found at i:28791049 original size:13 final size:13
Alignment explanation
Indices: 28791033--28791063 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28791023 ATCAAGAAAC
28791033 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
28791046 AAAAGAAAAAAAG
1 AAAAAAAAAAAAG
28791059 AAAAA
1 AAAAA
28791064 GAAATGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:28791727 original size:22 final size:22
Alignment explanation
Indices: 28791677--28791728 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28791667 TCAAAACTCA
28791677 AAGTATCAAAACTAGAGGGTTT
1 AAGTATCAAAACTAGAGGGTTT
*
28791699 GAGTATCAAAACTAGAGGGTTT
1 AAGTATCAAAACTAGAGGGTTT
*
28791721 AATTATCA
1 AAGTATCA
28791729 GTACTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (22 bp):
AAGTATCAAAACTAGAGGGTTT
Found at i:28795082 original size:43 final size:43
Alignment explanation
Indices: 28794989--28795075 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
28794979 TCAGAAAACA
28794989 AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
1 AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
*
28795032 AGATAAATATTTAAAAGAAAACAAGGTAAGTGACCAATGAAAT
1 AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
28795075 A
1 A
28795076 AGTAAATTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (43 bp):
AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
Found at i:28795250 original size:23 final size:24
Alignment explanation
Indices: 28795206--28795251 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28795196 GATTGGTTAG
* **
28795206 AATATTTTAGTAATATTTTATTTT
1 AATATTTTAATAATATGATATTTT
28795230 AATATTTTAAT-ATATGATATTT
1 AATATTTTAATAATATGATATTT
28795252 GTATGGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AATATTTTAATAATATGATATTTT
Found at i:28795865 original size:34 final size:34
Alignment explanation
Indices: 28795827--28795897 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
28795817 ATAGTAATCA
*
28795827 AAAGTATAATTATTATATACCTCCAATTGAAAGT
1 AAAGTATAATTATTATATACATCCAATTGAAAGT
*
28795861 AAAGTATAATTGTTATATACATCCAATTGAAAGT
1 AAAGTATAATTATTATATACATCCAATTGAAAGT
28795895 AAA
1 AAA
28795898 TACAAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (34 bp):
AAAGTATAATTATTATATACATCCAATTGAAAGT
Found at i:28800310 original size:15 final size:17
Alignment explanation
Indices: 28800279--28800310 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28800269 AACATATTCT
28800279 ATAATGTTTACATTATA
1 ATAATGTTTACATTATA
28800296 ATAA-GTTTA-ATTATA
1 ATAATGTTTACATTATA
28800311 GTTTTTGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAATGTTTACATTATA
Found at i:28813298 original size:17 final size:17
Alignment explanation
Indices: 28813276--28813330 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
28813266 ATTGGGATAA
28813276 AAATAAATAATGAAAAT
1 AAATAAATAATGAAAAT
28813293 AAATAAATAA-GAAAAAT
1 AAATAAATAATG-AAAAT
* *
28813310 AAACAATAGAAT-AAAAT
1 AAATAA-ATAATGAAAAT
28813327 AAAT
1 AAAT
28813331 GAACCAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.03
17 28 0.88
18 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (17 bp):
AAATAAATAATGAAAAT
Found at i:28813310 original size:30 final size:30
Alignment explanation
Indices: 28813274--28813330 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28813264 TAATTGGGAT
*
28813274 AAAAATAAATAATGAAAAT-AAATAAATAAG
1 AAAAATAAACAAT-AAAATAAAATAAATAAG
*
28813304 AAAAATAAACAATAGAATAAAATAAAT
1 AAAAATAAACAATAAAATAAAATAAAT
28813331 GAACCAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (30 bp):
AAAAATAAACAATAAAATAAAATAAATAAG
Found at i:28813456 original size:16 final size:16
Alignment explanation
Indices: 28813435--28813468 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28813425 CTCTCAACCT
28813435 TTAACTAACTAGTCGA
1 TTAACTAACTAGTCGA
28813451 TTAACTAACTAGTCGA
1 TTAACTAACTAGTCGA
28813467 TT
1 TT
28813469 GTTTGATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (16 bp):
TTAACTAACTAGTCGA
Found at i:28814419 original size:8 final size:8
Alignment explanation
Indices: 28814406--28814436 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
28814396 TAATCTTAAG
28814406 ACCTAAAT
1 ACCTAAAT
28814414 ACCTAAAT
1 ACCTAAAT
28814422 ACCTAAAT
1 ACCTAAAT
28814430 ACCTAAA
1 ACCTAAA
28814437 ATGTAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (8 bp):
ACCTAAAT
Found at i:28816662 original size:13 final size:13
Alignment explanation
Indices: 28816644--28816701 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
28816634 TAGTTGGGAT
28816644 AAAAATAAATAAC
1 AAAAATAAATAAC
28816657 AAAAATAAAT-A-
1 AAAAATAAATAAC
* * *
28816668 AATAACAAA-AAT
1 AAAAATAAATAAC
*
28816680 AAATATAAATAAC
1 AAAAATAAATAAC
28816693 AAAAATAAA
1 AAAAATAAA
28816702 ACATGAAGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 8 0.23
12 7 0.20
13 20 0.57
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAATAAC
Found at i:28816664 original size:19 final size:19
Alignment explanation
Indices: 28816642--28816702 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
28816632 GATAGTTGGG
28816642 ATAAAAATAAATAACAAAA
1 ATAAAAATAAATAACAAAA
28816661 AT--AAATAAATAACAAAA
1 ATAAAAATAAATAACAAAA
*
28816678 ATAAATATAAATAACAAAA
1 ATAAAAATAAATAACAAAA
28816697 ATAAAA
1 ATAAAA
28816703 CATGAAGGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.45
19 21 0.55
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
ATAAAAATAAATAACAAAA
Found at i:28816668 original size:17 final size:17
Alignment explanation
Indices: 28816646--28816701 Score: 94
Period size: 17 Copynumber: 3.2 Consensus size: 17
28816636 GTTGGGATAA
28816646 AAATAAATAACAAAAAT
1 AAATAAATAACAAAAAT
28816663 AAATAAATAACAAAAAT
1 AAATAAATAACAAAAAT
28816680 AAATATAAATAACAAAAAT
1 -AA-ATAAATAACAAAAAT
28816699 AAA
1 AAA
28816702 ACATGAAGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.49
18 4 0.11
19 15 0.41
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAATAACAAAAAT
Found at i:28818781 original size:30 final size:30
Alignment explanation
Indices: 28818728--28818817 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
28818718 GTAAACTCAG
* * **
28818728 GCCACTCGGCATCGCGACATGACTCACTAA
1 GCCACTCGACGTCGCGATGTGACTCACTAA
* * *
28818758 GCCACTCGACGTCGCGATGTGACTTAGTAC
1 GCCACTCGACGTCGCGATGTGACTCACTAA
*
28818788 GACCACTCAACGTCGCGATGTGACTCACTA
1 G-CCACTCGACGTCGCGATGTGACTCACTA
28818818 TTTTGGTCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
30 24 0.49
31 25 0.51
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (30 bp):
GCCACTCGACGTCGCGATGTGACTCACTAA
Found at i:28820198 original size:46 final size:46
Alignment explanation
Indices: 28820027--28820703 Score: 462
Period size: 46 Copynumber: 14.8 Consensus size: 46
28820017 AAAGTGCTGC
* * * **
28820027 AAATTGAAATGTTTAAA-TGATGTAAATTGAAGTG-TTAAAGTGTTAC
1 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA-TGTTGT
* * **
28820073 AAATTGAAGTGTTTAAA-TGTTGCGAATTGAAGTG-TTAAAGTGTTAC
1 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA-TGTTGT
* * **
28820119 AAATTGCAGTGTTTAAA-TGTTGTGAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * * * ** * *
28820165 AAATTGAATTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGG
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* ** * * *
28820211 AAATTG-AGATATTTTA-T-CATTG-TAATTGAGGTGTATAAATGTTGT
1 AAATTGAAG-TGTTAAAGTGC--TGCAAATTGAAGTGTTTAAATGTTGT
* * * * *
28820256 TAATTAAAATGTTAAAGTGCTGCATATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28820302 AAATTGAAGTGTTAAAGTGTTGCACATTGAAGTGTTTAAAGGTTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28820348 GAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28820394 AAATTAAAGTGTTCAAGTGTTGCAAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* *
28820440 AAATTGAAGTGATAAAGTGCTGCAAGTTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * * * ** * *
28820486 AAATTGAGGTGTTCTAAGTACTGCAAATTGAATTGTTTAGTTGCTGA
1 AAATTGAAGTGTT-AAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
** * * * *
28820533 AAATTG-AGATGTTTTAGCGTTG-TAATTGAGGTGTTTAAATGTTGT
1 AAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
** * * * * * * * *
28820578 TTATTG-GGATGTTAAAGTGTTGTAAGTTGAGGTTTTTACATGCTGT
1 AAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * * * * * * *
28820624 AAATTGAAGTGTTTAATTACTACAAATTCAGGTGCTTAAATGATGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28820670 AAATTGAAGTATTTAAGTGCTACAAATTG-AGTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGT
28820704 ACAAATGAGT
Statistics
Matches: 498, Mismatches: 120, Indels: 27
0.77 0.19 0.04
Matches are distributed among these distances:
44 1 0.00
45 66 0.13
46 389 0.78
47 42 0.08
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (46 bp):
AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
Found at i:28820423 original size:252 final size:252
Alignment explanation
Indices: 28819963--28820432 Score: 742
Period size: 252 Copynumber: 1.9 Consensus size: 252
28819953 TGTTTCTGTC
* * * *
28819963 TGAGATGTTTTATCACTGTAAATGAGTTGTATAAATGTTGTTAATTGAGATGTTAAAGTGCTGCA
1 TGAGATATTTTATCACTGTAAATGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
*
28820028 AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAATGT
66 AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAAGGT
* * * * * *
28820093 TGCGAATTGAAGTGTTAAAGTGTTACAAATTGCAGTGTTTAAATGTTGTGAATTGAAGTGTTTAA
131 TGCGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
* *
28820158 ATGTTGTAAATTGAATTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGGAAAT
196 ATGTTGCAAATTGAAGTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGGAAAT
* *
28820215 TGAGATATTTTATCATTGTAATTGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
1 TGAGATATTTTATCACTGTAAATGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
* * * * *
28820280 TATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGTTGCACATTGAAGTGTTTAAAGGT
66 AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAAGGT
*
28820345 TGTGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
131 TGCGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
*
28820410 GTGTTGCAAATTGAAGTGTTTAA
196 ATGTTGCAAATTGAAGTGTTTAA
28820433 ATGTTGTAAA
Statistics
Matches: 196, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
252 196 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (252 bp):
TGAGATATTTTATCACTGTAAATGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAAGGT
TGCGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
ATGTTGCAAATTGAAGTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGGAAAT
Found at i:28820638 original size:23 final size:23
Alignment explanation
Indices: 28819994--28820685 Score: 406
Period size: 23 Copynumber: 30.1 Consensus size: 23
28819984 ATGAGTTGTA
*
28819994 TAAATGTTGTTAATTG-AGATG-T
1 TAAATGTTGTAAATTGAAG-TGTT
* * *
28820016 TAAAGTGCTGCAAATTGAAATGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28820040 TAAATGATGTAAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
**
28820062 TAAAGTGTTACAAATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
**
28820086 TAAATGTTGCGAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
** *
28820108 TAAAGTGTTACAAATTGCAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28820132 TAAATGTTGTGAATTGAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
*
28820155 TAAATGTTGTAAATTGAATTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* ** * *
28820178 TAAGTACTGCAAATTAAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
** * * *
28820201 TAGTTGCTGGAAATTG-AGATATT
1 TAAATGTTGTAAATTGAAG-TGTT
* * * *
28820224 T-TATCATTGT-AATTGAGGTGTA
1 TAAAT-GTTGTAAATTGAAGTGTT
* * *
28820246 TAAATGTTGTTAATTAAAATG-T
1 TAAATGTTGTAAATTGAAGTGTT
* * *
28820268 TAAAGTGCTGCATATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28820292 TAAATGCTGTAAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
* *
28820314 TAAAGTGTTGCACATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
* *
28820338 TAAAGGTTGTGAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
* **
28820360 TAAAGTGCTACAAATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
* *
28820384 TAAATGCTGTAAATTAAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* * *
28820407 CAAGTGTTGCAAATTGAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
*
28820430 TAAATGTTGTAAATTGAAGTG-A
1 TAAATGTTGTAAATTGAAGTGTT
* * *
28820452 TAAAGTGCTGCAAGTTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28820476 TAAATGTTGTAAATTGAGGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* ** * *
28820499 CTAAGTACTGCAAATTGAATTGTT
1 -TAAATGTTGTAAATTGAAGTGTT
** * *
28820523 TAGTTGCTGAAAATTG-AGATGTT
1 TAAATGTTGTAAATTGAAG-TGTT
* ** *
28820546 TTAGCGTTGT-AATTGAGGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
** *
28820568 TAAATGTTGTTTATTG-GGATG-T
1 TAAATGTTGTAAATTGAAG-TGTT
* * *
28820590 TAAAGTGTTGTAAGTTGAGGTTTT
1 TAAA-TGTTGTAAATTGAAGTGTT
* *
28820614 TACATGCTGTAAATTGAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* ** ** * * *
28820637 TAATTACTACAAATTCAGGTGCT
1 TAAATGTTGTAAATTGAAGTGTT
* *
28820660 TAAATGATGTAAATTGAAGTATT
1 TAAATGTTGTAAATTGAAGTGTT
28820683 TAA
1 TAA
28820686 GTGCTACAAA
Statistics
Matches: 507, Mismatches: 135, Indels: 55
0.73 0.19 0.08
Matches are distributed among these distances:
22 71 0.14
23 378 0.75
24 58 0.11
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (23 bp):
TAAATGTTGTAAATTGAAGTGTT
Found at i:28821274 original size:17 final size:17
Alignment explanation
Indices: 28821252--28821284 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28821242 TATCAGATTT
28821252 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
28821269 TGATACCTATATCTTT
1 TGATACCCATATCTTT
28821285 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:28824839 original size:17 final size:17
Alignment explanation
Indices: 28824817--28824849 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28824807 TATCAGATTT
28824817 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
28824834 TGATACTCATATCTTT
1 TGATACCCATATCTTT
28824850 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:28827497 original size:45 final size:45
Alignment explanation
Indices: 28827441--28827784 Score: 272
Period size: 45 Copynumber: 7.6 Consensus size: 45
28827431 AGGAAATGAT
28827441 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAA
* * * *
28827486 TAAGACCATAGTTGAAAGACACTATAGCATTATACAAGAAAAAGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATA-AA
* *
28827532 TAAGACCATAGTTGAAAGACACTATGGCA-TCATACCAGAAATGAG
1 TAAGACCATAGTTGAAAGACACTATGGCACT-ATACCAGAAATAAA
* * * * * * *
28827577 TAAGACCATAGCTGAAAGACATTATGGCA-T-CACGATTCAAACAAG
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCA--GAAATAAA
* *** * ** ** *
28827622 TAAGACCATAGCTGAAAGATGTTATGGTTTCACGAT-TTAGACGT--G
1 TAAGACCATAGTTGAAAGACACTATGG---CACTATACCAGAAATAAA
* *
28827667 TAAGACCATAGTTGAAAGACACTATGGCAAC-ATGACGAGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGC-ACTAT-ACCAGAAATAAA
* * * *
28827713 TAAGACCATGGTTGAAATACACTATGGCAATATGA-CAGGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTAT-ACCA-GAAATAAA
28827759 TAAGACCATAGTTGAAAGACACTATG
1 TAAGACCATAGTTGAAAGACACTATG
28827785 ACATTATGTC
Statistics
Matches: 242, Mismatches: 41, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
42 3 0.01
43 5 0.02
44 4 0.02
45 125 0.52
46 101 0.42
47 1 0.00
48 2 0.01
49 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAA
Found at i:28827808 original size:91 final size:90
Alignment explanation
Indices: 28827441--28827808 Score: 311
Period size: 91 Copynumber: 4.1 Consensus size: 90
28827431 AGGAAATGAT
* *
28827441 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAATAAGACCATAGTTGAAAGAC
1 TAAGACCATAGTTGAAAGACACTATGGCAATATACCAGAAATGAATAAGACCATAGTTGAAAGAC
*
28827506 ACTAT-AGCATTAT-ACAAGAAAA-AGAA
66 ACTATGA-CATCATGAC--GAAAATA-AA
* *
28827532 TAAGACCATAGTTGAAAGACACTATGGC-ATCATACCAGAAATGAGTAAGACCATAGCTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCAAT-ATACCAGAAATGAATAAGACCATAGTTGAAAGA
* * * *** * *
28827596 CATTATGGCATCACGATTCAAACAAG
65 CACTATGACATCATGACGAAAATAAA
* *** ** ** **
28827622 TAAGACCATAGCTGAAAGATGTTATGGTTTCACGAT-TTAGACGTG--TAAGACCATAGTTGAAA
1 TAAGACCATAGTTGAAAGACACTATGG---CAATATACCAGAAATGAATAAGACCATAGTTGAAA
* * *
28827684 GACACTATGGCAACATGACGAGAAATGAA
63 GACACTATGACATCATGACGA-AAATAAA
* *
28827713 TAAGACCATGGTTGAAATACACTATGGCAATATGA-CAGGAAATGAATAAGACCATAGTTGAAAG
1 TAAGACCATAGTTGAAAGACACTATGGCAATAT-ACCA-GAAATGAATAAGACCATAGTTGAAAG
* *
28827777 ACACTATGACATTATGTCGAAAATAAA
64 ACACTATGACATCATGACGAAAATAAA
28827804 TAAGA
1 TAAGA
28827809 ACATGGATGG
Statistics
Matches: 215, Mismatches: 48, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
88 4 0.02
89 1 0.00
90 63 0.29
91 104 0.48
92 40 0.19
93 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (90 bp):
TAAGACCATAGTTGAAAGACACTATGGCAATATACCAGAAATGAATAAGACCATAGTTGAAAGAC
ACTATGACATCATGACGAAAATAAA
Found at i:28829483 original size:23 final size:23
Alignment explanation
Indices: 28829451--28830108 Score: 381
Period size: 23 Copynumber: 28.7 Consensus size: 23
28829441 ATGTTTTATC
*
28829451 GTTGT-AATTGAAGTGTATAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28829473 GTTGTTAATTG-AGATG-TTAAAGT
1 GTTGTAAATTGAAG-TGTTTAAA-T
* * *
28829496 GCTGCAAATTGAAATGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28829519 GCTCTAAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
**
28829542 GTTACAAATTGAAGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28829565 GTTGTGAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* * *
28829588 GCTGCAAATTGAAGTGTTTAAGT
1 GTTGTAAATTGAAGTGTTTAAAT
** ** * **
28829611 ACTACAAACTGAAGTGTTTAGTT
1 GTTGTAAATTGAAGTGTTTAAAT
** * *
28829634 GTTGGGAATT-AAGATGTTTTATT
1 GTTGTAAATTGAAG-TGTTTAAAT
* *
28829657 GTTGT-AATTGAGGTGTATAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28829679 GTTGTTAATT-AA-TATGTTAAAGT
1 GTTGTAAATTGAAGTGT-TTAAA-T
* *
28829702 GCTGAAAATTGAAGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28829725 GTTGTGAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* *
28829748 GCTGCAAATTGAAGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28829771 GTTGTAAATTGAACTGTTTTAA-
1 GTTGTAAATTGAAGTGTTTAAAT
* **
28829793 GTACTGCAAATTGAAGTGTTTAGTT
1 GT--TGTAAATTGAAGTGTTTAAAT
* * * *
28829818 ATTGGAAATTG-AGATGTTTTATT
1 GTTGTAAATTGAAG-TGTTTAAAT
* *
28829841 GTTGT-AATTGAGGTGTATAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28829863 GTTGTTAATT-AAGATG-TTAAA-
1 GTTGTAAATTGAAG-TGTTTAAAT
*
28829884 GTTCTTCAAATTGAAGTGTTTAAAT
1 GTT-GT-AAATTGAAGTGTTTAAAT
* **
28829909 GCTACAAATTGAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* *
28829932 GTTGCAAATTGAAGTGTTTAACT
1 GTTGTAAATTGAAGTGTTTAAAT
* *
28829955 GTTGTGAATTAAAGTG-TTAAAGT
1 GTTGTAAATTGAAGTGTTTAAA-T
* *
28829978 GCTGCAAATTGAAGTGTTT---T
1 GTTGTAAATTGAAGTGTTTAAAT
* * *
28829998 GTCGCTATAATTGAGGTGTATAAAT
1 GTTG-TA-AATTGAAGTGTTTAAAT
* *
28830023 GTTGTTAATTG-GGATG-TTAAAGT
1 GTTGTAAATTGAAG-TGTTTAAA-T
* *
28830046 GTTGTAAGTTGAGGTGTTTAAAT
1 GTTGTAAATTGAAGTGTTTAAAT
*
28830069 GTTGTAAATTGAAGTGTTTAATT
1 GTTGTAAATTGAAGTGTTTAAAT
* * *
28830092 ATTGAAAATTGAGGTGT
1 GTTGTAAATTGAAGTGT
28830109 ACAAATGAGT
Statistics
Matches: 491, Mismatches: 102, Indels: 85
0.72 0.15 0.13
Matches are distributed among these distances:
20 3 0.01
21 6 0.01
22 102 0.21
23 307 0.63
24 64 0.13
25 9 0.02
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (23 bp):
GTTGTAAATTGAAGTGTTTAAAT
Found at i:28829851 original size:184 final size:183
Alignment explanation
Indices: 28829524--28829996 Score: 673
Period size: 184 Copynumber: 2.6 Consensus size: 183
28829514 TAAATGCTCT
**
28829524 AAATTGAAGTG-TTAAAGTGTTACAAATTGAAGTGTTTAAA-TGTTGTGAATTGAAGTG-TTAAA
1 AAATTGAAGTGTTTAAA-TGTTACAAATTGAAGTG-TTAAAGTGTTGCAAATTGAAGTGTTTAAA
* * * * * *
28829586 GTGCTGCAAATTGAAGTGTTTAAGTACTACAAACTGAAGTGTTTAGTTGTTGGGAATTAAGATGT
64 -TGTTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTAAGATGT
*
28829651 TTTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAATATGTTAAAGTGCTGA
128 TTTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGCTGA
*** *
28829707 AAATTGAAGTGTTTAAATGTTGTGAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
1 AAATTGAAGTGTTTAAATGTTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
* *
28829772 TTGTAAATTGAACTGTTTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTGAGATGTTT
66 TTGTAAATTGAAGTG-TTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTAAGATGTTT
* **
28829837 TATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTTCTTC
130 TATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGCTGA
* *
28829891 AAATTGAAGTGTTTAAATGCTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAACTG
1 AAATTGAAGTGTTTAAATGTTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
* * * *
28829956 TTGTGAATTAAAGTGTTAAAGTGCTGCAAATTGAAGTGTTT
66 TTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTT
28829997 TGTCGCTATA
Statistics
Matches: 257, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
182 5 0.02
183 77 0.30
184 175 0.68
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (183 bp):
AAATTGAAGTGTTTAAATGTTACAAATTGAAGTGTTAAAGTGTTGCAAATTGAAGTGTTTAAATG
TTGTAAATTGAAGTGTTTAAGTACTGCAAATTGAAGTGTTTAGTTATTGGAAATTAAGATGTTTT
ATTGTTGTAATTGAGGTGTATAAATGTTGTTAATTAAGATGTTAAAGTGCTGA
Found at i:28834869 original size:20 final size:20
Alignment explanation
Indices: 28834833--28834875 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
28834823 TAATAAGACA
*
28834833 TTATGGACTATTTAATTGGT
1 TTATGGACTATTGAATTGGT
*
28834853 TTATGGGACT-TTGAATTGTT
1 TTAT-GGACTATTGAATTGGT
28834873 TTA
1 TTA
28834876 GAATGTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (20 bp):
TTATGGACTATTGAATTGGT
Found at i:28842749 original size:15 final size:15
Alignment explanation
Indices: 28842716--28842746 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28842706 GTCCCTTGTA
28842716 GATTTGGTTAAAATG
1 GATTTGGTTAAAATG
28842731 GATTTAGGTTAAAATG
1 GATTT-GGTTAAAATG
28842747 ATTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (15 bp):
GATTTGGTTAAAATG
Found at i:28845989 original size:16 final size:16
Alignment explanation
Indices: 28845968--28846003 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28845958 AGAATAGGTC
* *
28845968 ATTTATCCATTTGTGG
1 ATTTATCCACTTGTGA
28845984 ATTTATCCACTTGTGA
1 ATTTATCCACTTGTGA
28846000 ATTT
1 ATTT
28846004 CATAGTGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (16 bp):
ATTTATCCACTTGTGA
Found at i:28846164 original size:29 final size:29
Alignment explanation
Indices: 28846113--28846178 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
28846103 TTTGGCCCTT
* * * *
28846113 AAATTTTTTGAAATTATATTTTA-CCTCA
1 AAATTTTTCGAAATTACACTTTAGCCCCA
28846141 AAATTTTCTCGAAATTACACTTTAGCCCCA
1 AAATTTT-TCGAAATTACACTTTAGCCCCA
*
28846171 AAAGTTTT
1 AAATTTTT
28846179 ACTGTGTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.23
29 14 0.45
30 10 0.32
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (29 bp):
AAATTTTTCGAAATTACACTTTAGCCCCA
Found at i:28846439 original size:20 final size:19
Alignment explanation
Indices: 28846408--28846451 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
28846398 GAAAAAAGAA
28846408 AGAGGAAAAAGAG-AGAATG
1 AGAGGAAAAAGAGAAG-ATG
28846427 AGAGGAGAAAAGAGAAGATG
1 AGAGGA-AAAAGAGAAGATG
28846447 AGAGG
1 AGAGG
28846452 GAGGAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.41, T:0.05
Consensus pattern (19 bp):
AGAGGAAAAAGAGAAGATG
Found at i:28846552 original size:13 final size:13
Alignment explanation
Indices: 28846534--28846558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28846524 CCTAGGGCTT
28846534 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
28846547 GAAGAAGAAGAA
1 GAAGAAGAAGAA
28846559 AAAATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:28846892 original size:11 final size:11
Alignment explanation
Indices: 28846876--28846907 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28846866 CAGTCCAGAA
28846876 AAAAAAGAAAG
1 AAAAAAGAAAG
*
28846887 AAAAAAAAAAG
1 AAAAAAGAAAG
28846898 AAAAAAGAAA
1 AAAAAAGAAA
28846908 AAACTGAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:28846894 original size:15 final size:14
Alignment explanation
Indices: 28846874--28846910 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
28846864 CCCAGTCCAG
28846874 AAAAAAAAGAAAGAA
1 AAAAAAAAGAAA-AA
28846889 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
28846903 AGAAAAAA
1 A-AAAAAA
28846911 CTGAGCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:28846903 original size:7 final size:7
Alignment explanation
Indices: 28846876--28846910 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
28846866 CAGTCCAGAA
28846876 AAAAAAG
1 AAAAAAG
*
28846883 AAAGAAAA
1 AAA-AAAG
28846891 AAAAAAG
1 AAAAAAG
28846898 AAAAAAG
1 AAAAAAG
28846905 AAAAAA
1 AAAAAA
28846911 CTGAGCTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28846904 original size:18 final size:17
Alignment explanation
Indices: 28846874--28846910 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
28846864 CCCAGTCCAG
*
28846874 AAAAAAAAGAAAGAAAA
1 AAAAAAAAAAAAGAAAA
28846891 AAAAAAGAAAAAAGAAAA
1 AAAAAA-AAAAAAGAAAA
28846909 AA
1 AA
28846911 CTGAGCTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAA
Found at i:28846908 original size:13 final size:12
Alignment explanation
Indices: 28846872--28846909 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
28846862 AGCCCAGTCC
28846872 AGAAAAAAAAGAA
1 AGAAAAAAAA-AA
28846885 AG-AAAAAAAAA
1 AGAAAAAAAAAA
28846896 AGAAAAAAGAAAA
1 AGAAAAAA-AAAA
28846909 A
1 A
28846910 ACTGAGCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 12 0.52
13 7 0.30
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:28859509 original size:78 final size:76
Alignment explanation
Indices: 28859146--28860089 Score: 1175
Period size: 78 Copynumber: 12.1 Consensus size: 76
28859136 AACCATTTCT
*
28859146 ATTTCTGTTTTTTCAAAAATCAACTCCTATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
1 ATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28859211 AGGTATTTTTTA
65 AGGTATTTTTTA
* * *
28859223 ATTTCTATTTTTCAAAAAAAAATTAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACG
1 ATTTCTGTTTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACG
* *
28859288 CTGAGGTATTTTTAAA
62 CCGAGGTATTTTT-TA
* * * * * *
28859304 ATTTTTGTTTTTCAAAAATTAACCCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCAA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGA
28859369 GGTA-TTTTTA
66 GGTATTTTTTA
*
28859379 ATTCCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
1 ATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28859444 AGGTA-TTTTTA
65 AGGTATTTTTTA
* * * *
28859455 ATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAACCTCGGGCCACATC-
1 ATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CG
* *
28859519 CCGAGGTACTTTTCA
62 CCGAGGTATTTTTTA
* * *
28859534 ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACATGCCG
1 ATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28859598 AGGTATTTTTTTTAA
65 AGGTA--TTTTTT-A
* * * * * *
28859613 ATTTCTATTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGAGTTACATGCCGA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGA
28859678 GGTA-TTTTTA
66 GGTATTTTTTA
*
28859688 ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACATGCCG
1 ATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28859752 AGGTATTTCTTTTAA
65 AGGTA-TT-TTTT-A
* *
28859767 ATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGA
28859832 GGTATTTTTTTA
66 GGTA-TTTTTTA
* *
28859844 ATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGTC
1 ATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCC
*
28859909 GAGGTACTTTTTA
64 GAGGTATTTTTTA
* * *
28859922 ATTTCTGTTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGTCTCGGGT--CACGCTG
1 ATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28859985 AGGTATTTTTTTA
65 AGGTA-TTTTTTA
* * **
28859998 ATTTCTATTTTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACAC
1 ATTTC---TGTTTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC
* *
28860063 GCCAAGGTATTTTTCA
61 GCCGAGGTATTTTTTA
*
28860079 ATTTATGTTTT
1 ATTTCTGTTTT
28860090 CACAAAAAAA
Statistics
Matches: 765, Mismatches: 69, Indels: 65
0.85 0.08 0.07
Matches are distributed among these distances:
75 42 0.05
76 152 0.20
77 147 0.19
78 174 0.23
79 117 0.15
80 101 0.13
81 22 0.03
82 10 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (76 bp):
ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGA
GGTATTTTTTA
Found at i:28859601 original size:154 final size:153
Alignment explanation
Indices: 28859146--28860089 Score: 1172
Period size: 154 Copynumber: 6.1 Consensus size: 153
28859136 AACCATTTCT
*
28859146 ATTTCTGTTTTTTCAAAAATCAACTCCTATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
1 ATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC-CCG
* * *
28859211 AGGTATTTTTTAATTTCT-ATTTTTCAAAAAAAAATTAACTCATATTGCGAGAAGTGAGTTGAGC
64 AGGTATTTTTTAATTTCTGTTTTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
28859275 CTCGGGTCACACGCTGAGGTATTTTTAAA
125 CTCGGGTCACACGCCGAGGTATTTTTTAA
* * * * * *
28859304 ATTTTTGTTTTTCAAAAATTAACCCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCAA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CCCGA
*
28859369 GGTA-TTTTTAATTCCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
65 GGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
28859433 GTCACACGCCGAGGTA-TTTTT-A
130 GTCACACGCCGAGGTATTTTTTAA
* * * *
28859455 ATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAACCTCGGGCCACATCC
1 ATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CC
* *
28859520 CGAGGTACTTTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
62 CGAGGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
28859585 C-AGACACATGCCGAGGTATTTTTTTTAA
127 CGGGTCACACGCCGAGGTA--TTTTTTAA
* * * * * *
28859613 ATTTCTATTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGAGTTACATGCCGA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CCCGA
28859678 GGTA-TTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
65 GGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
28859742 G-CACATGCCGAGGTATTTCTTTTAA
130 GTCACACGCCGAGGTA-TT-TTTTAA
* *
28859767 ATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGA
1 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC-CCGA
*
28859832 GGTATTTTTTTAATTTTTG-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
65 GGTA-TTTTTTAATTTCTGTTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
28859896 CGGGTCACACGTCGAGGTACTTTTT-A
127 CGGGTCACACGCCGAGGTATTTTTTAA
* * * *
28859922 ATTTCTGTTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGTCTCGGGTCAC-GCTGA
1 ATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACCCGA
* *
28859986 GGTATTTTTTTAATTTCTATTTTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
65 GGTA-TTTTTTAATTTC--TGTTTTTT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
** * *
28860051 CTCAAGTCACACGCCAAGGTA-TTTTTCA
125 CTCGGGTCACACGCCGAGGTATTTTTTAA
*
28860079 ATTTATGTTTT
1 ATTTCTGTTTT
28860090 CACAAAAAAA
Statistics
Matches: 697, Mismatches: 64, Indels: 51
0.86 0.08 0.06
Matches are distributed among these distances:
151 13 0.02
152 4 0.01
153 56 0.08
154 218 0.31
155 123 0.18
156 76 0.11
157 176 0.25
158 31 0.04
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (153 bp):
ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACCCGAG
GTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
TCACACGCCGAGGTATTTTTTAA
Found at i:28859612 original size:233 final size:231
Alignment explanation
Indices: 28859146--28860089 Score: 1185
Period size: 233 Copynumber: 4.0 Consensus size: 231
28859136 AACCATTTCT
*
28859146 ATTTCTGTTTTTTCAAAAATCAACTCCTATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
1 ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
* * * *
28859211 AGGTATTTTTTAATTTCTATTTTTCAAAAAAAAATTAACTCATATTGCGAGAAGTGAGTTGAGCC
66 AGGTACTTTTTAATTTCTGTTTTTC---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * * *
28859276 TCGGGTCACACGCTGAGGTAT-TTTTAAAATTTTTGTTTTTCAAAAATTAACCCATATTGCGAGA
128 TCGGGTCACAC-CCGAGGTATCTTTT-AAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGA
*** *
28859340 GGTGAGTTGAGCCTTGGGTCACATGCCAAGGTA--TTTTTA
191 GGTGAGTTGAGCCTCAAGTCACACGCCAAGGTATTTTTTTA
*
28859379 ATTCCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
1 ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
* * *
28859444 AGGTA-TTTTTAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAACCT
66 AGGTACTTTTTAATTTCTGTTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
28859508 CGGGCCACATCCCGAGGTA-CTTTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAG
129 CGGGTCACA-CCCGAGGTATCTTTTAAATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAG
* * *
28859572 GTGAGTTGAGCCTC-AGACACATGCCGAGGTATTTTTTTTAA
192 GTGAGTTGAGCCTCAAGTCACACGCCAAGGTA-TTTTTTT-A
* * * * * *
28859613 ATTTCT-ATTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGAGTTACATGCCG
1 ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
28859677 AGGTA-TTTTTAATTTCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
66 AGGTACTTTTTAATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
28859740 GGG-CACATGCCGAGGTATTTCTTTTAAATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAG
130 GGGTCACA-CCCGAGGTA--TCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAG
** **
28859804 GTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTTTA
192 GTGAGTTGAGCCTCAAGTCACACGCCAAGGTATTTTTTTA
* *
28859844 ATTTTTG-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGT
1 ATTTCTGTTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGC
* *
28859908 CGAGGTACTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGTCT
64 CGAGGTACTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * * * * *
28859973 CGGGTCAC-GCTGAGGTATTTTTTTAATTTCTATTTTTTTTAAAAAAAATCAACTCATATTGCGA
129 CGGGTCACACCCGAGGTATCTTTTAAATTTC---TGTTTTT--CAAAAATCAACTCATATTGCGA
*
28860037 GAGGTGAGTTGAGCCTCAAGTCACACGCCAAGGTA-TTTTTCA
189 GAGGTGAGTTGAGCCTCAAGTCACACGCCAAGGTATTTTTTTA
*
28860079 ATTTATGTTTT
1 ATTTCTGTTTT
28860090 CACAAAAAAA
Statistics
Matches: 631, Mismatches: 56, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
230 34 0.05
231 155 0.25
232 70 0.11
233 232 0.37
234 70 0.11
235 15 0.02
236 55 0.09
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (231 bp):
ATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCG
AGGTACTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
GGTCACACCCGAGGTATCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGA
GTTGAGCCTCAAGTCACACGCCAAGGTATTTTTTTA
Found at i:28860641 original size:93 final size:93
Alignment explanation
Indices: 28860482--28860668 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
28860472 CAAGATACCA
*
28860482 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACTGACTCCCGAACTCTAATTTT
1 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
28860547 CTCTGGATTTTAACGTGGACTTAAAATT
66 CTCTGGATTTTAACGTGGACTTAAAATT
28860575 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
1 ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
28860640 CTCTGGATTTTAACGTGGACTTAAAATT
66 CTCTGGATTTTAACGTGGACTTAAAATT
28860668 A
1 A
28860669 CCTCTTTTTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (93 bp):
ATTTTGGGCGTCACAAGGGTGCTAATACCTTCCTCGCGCGTAACCGACTCCCGAACTCTAATTTT
CTCTGGATTTTAACGTGGACTTAAAATT
Found at i:28866258 original size:13 final size:12
Alignment explanation
Indices: 28866238--28866282 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
28866228 AAAACATTTA
28866238 TTATAAATAAAT
1 TTATAAATAAAT
*
28866250 TTCATAAATAAAA
1 TT-ATAAATAAAT
*
28866263 TTAAAAATAAATT
1 TTATAAATAAA-T
28866276 TTATAAA
1 TTATAAA
28866283 CATTTTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
TTATAAATAAAT
Found at i:28866860 original size:20 final size:21
Alignment explanation
Indices: 28866835--28866873 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28866825 ATAATTTGAA
28866835 TATTTTATATTTAA-AAAATT
1 TATTTTATATTTAATAAAATT
*
28866855 TATTTTATTTTTAATAAAA
1 TATTTTATATTTAATAAAA
28866874 AAAATCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTATATTTAATAAAATT
Found at i:28867851 original size:29 final size:28
Alignment explanation
Indices: 28867811--28867884 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
28867801 TTTACCTTAG
* *
28867811 GTTACATTTTAGTCACTTATGTTTAAAAT
1 GTTACATTTTAGTCACTTACG-CTAAAAT
*
28867840 GTTACATTTTAGTCACTTACGCTAACAT
1 GTTACATTTTAGTCACTTACGCTAAAAT
* *
28867868 GTAATATTTTAGTCACT
1 GTTACATTTTAGTCACT
28867885 AAGCTATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 20 0.50
29 20 0.50
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (28 bp):
GTTACATTTTAGTCACTTACGCTAAAAT
Found at i:28869798 original size:32 final size:33
Alignment explanation
Indices: 28869729--28869800 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
28869719 GAGCTTATTC
* *
28869729 TTTATTTTGATATTTATATTTTTGGTAATTAGG
1 TTTATTTTGATATTTATATTTTTGGTAATAAGA
*
28869762 TTTATTTTGATATTTGTA-TTTTGGT-ATAAAGA
1 TTTATTTTGATATTTATATTTTTGGTAAT-AAGA
28869794 TTTATTT
1 TTTATTT
28869801 GACCTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.06
32 16 0.46
33 17 0.49
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (33 bp):
TTTATTTTGATATTTATATTTTTGGTAATAAGA
Found at i:28870030 original size:30 final size:29
Alignment explanation
Indices: 28869995--28870075 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
28869985 ATTTTTTTAA
28869995 ATTTTAAAAAATTAAAAAATATAAAAACTT
1 ATTTTAAAAAATTAAAAAATATAAAAAC-T
* * *
28870025 ATTTTAAATAATTAAAAATTATTAAAACT
1 ATTTTAAAAAATTAAAAAATATAAAAACT
*
28870054 A-ATT-AAAAATATAAAAAATATA
1 ATTTTAAAAAAT-TAAAAAATATA
28870076 TTTTTTCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 5 0.12
28 11 0.26
29 2 0.05
30 25 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
ATTTTAAAAAATTAAAAAATATAAAAACT
Found at i:28870046 original size:20 final size:19
Alignment explanation
Indices: 28870006--28870063 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
28869996 TTTTAAAAAA
*
28870006 TTAAAAAATATAAAAACTTATT
1 TTAAATAAT-TAAAAA-TTA-T
28870028 TTAAATAATTAAAAATTAT
1 TTAAATAATTAAAAATTAT
*
28870047 TAAAACTAATTAAAAAT
1 TTAAA-TAATTAAAAAT
28870064 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 6 0.18
22 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAATAATTAAAAATTAT
Found at i:28870048 original size:10 final size:10
Alignment explanation
Indices: 28869993--28870077 Score: 54
Period size: 10 Copynumber: 8.8 Consensus size: 10
28869983 TAATTTTTTT
28869993 AAATT-TTAA
1 AAATTATTAA
28870002 AAA--ATTAA
1 AAATTATTAA
*
28870010 AAAATA-TAA
1 AAATTATTAA
**
28870019 AAACTTATTTT
1 AAA-TTATTAA
*
28870030 AAATAATTAA
1 AAATTATTAA
28870040 AAATTATTAA
1 AAATTATTAA
* *
28870050 AACTAATTAA
1 AAATTATTAA
*
28870060 AAA-TATAAA
1 AAATTATTAA
28870069 AAATATATT
1 AAAT-TATT
28870078 TTTTCATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
8 7 0.12
9 16 0.29
10 26 0.46
11 7 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:28870071 original size:20 final size:20
Alignment explanation
Indices: 28870033--28870070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28870023 TTATTTTAAA
*
28870033 TAATTAAAAATTATTAAAAC
1 TAATTAAAAATTATAAAAAC
28870053 TAATTAAAAA-TATAAAAA
1 TAATTAAAAATTATAAAAA
28870071 ATATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATTAAAAATTATAAAAAC
Found at i:28872204 original size:21 final size:21
Alignment explanation
Indices: 28872179--28872222 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28872169 ATCTTCGAGG
28872179 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28872200 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
28872221 AT
1 AT
28872223 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:28872228 original size:19 final size:19
Alignment explanation
Indices: 28872178--28872233 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
28872168 AATCTTCGAG
28872178 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28872197 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
28872218 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
28872234 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28872240 original size:22 final size:23
Alignment explanation
Indices: 28872191--28872256 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
28872181 ATGCAATCTT
*
28872191 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
28872212 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
28872234 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
28872257 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:28872266 original size:22 final size:23
Alignment explanation
Indices: 28872222--28872266 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28872212 AGATATGATA
*
28872222 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
28872245 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
28872267 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:28872687 original size:3 final size:3
Alignment explanation
Indices: 28872666--28872721 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
28872656 GTTTTTAGTC
28872666 TAT T-T TAT TAAT T-T TAT TAT TAT TAAT T-T TAT TAT TA- TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
28872709 ATAT TAT TAT TAT
1 -TAT TAT TAT TAT
28872722 ACCTACATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
2 8 0.17
3 29 0.63
4 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28872690 original size:15 final size:15
Alignment explanation
Indices: 28872666--28872720 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
28872656 GTTTTTAGTC
28872666 TATT-TTATTAATTT
1 TATTATTATTAATTT
28872680 TATTATTATTAATTT
1 TATTATTATTAATTT
28872695 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
28872709 ATATTATTATTA
1 -TATTATTATTA
28872721 TACCTACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.08
14 6 0.17
15 26 0.72
16 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:28872702 original size:18 final size:19
Alignment explanation
Indices: 28872679--28872721 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
28872669 TTTATTAATT
*
28872679 TTATTATTATTA-ATTTTA
1 TTATTATTATTATATATTA
28872697 TTATTA-TATTATATATTA
1 TTATTATTATTATATATTA
28872715 TTATTAT
1 TTATTAT
28872722 ACCTACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATTATTATATATTA
Found at i:28875679 original size:19 final size:20
Alignment explanation
Indices: 28875655--28875692 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28875645 GAAAAATGAA
28875655 AAATTATAAA-AAT-GAAAAC
1 AAATTA-AAATAATAGAAAAC
28875674 AAATTAAAATAATAGAAAA
1 AAATTAAAATAATAGAAAA
28875693 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 9 0.53
20 5 0.29
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATTAAAATAATAGAAAAC
Found at i:28882967 original size:20 final size:20
Alignment explanation
Indices: 28882942--28882983 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28882932 GAAGAAGTAT
28882942 GTTGGCCAGGTATACATTGA
1 GTTGGCCAGGTATACATTGA
*
28882962 GTTGGCCAGTTATACATTGA
1 GTTGGCCAGGTATACATTGA
28882982 GT
1 GT
28882984 GAAAGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (20 bp):
GTTGGCCAGGTATACATTGA
Found at i:28894541 original size:25 final size:26
Alignment explanation
Indices: 28894495--28894543 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
28894485 GCTTAATGTC
* *
28894495 AAAAATTTAAAAATCTGATCCTTAAT
1 AAAAACTTAAAAAGCTGATCCTTAAT
*
28894521 AAAAACTTAAAAAGC-GTTCCTTA
1 AAAAACTTAAAAAGCTGATCCTTA
28894544 TTAAGCCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAACTTAAAAAGCTGATCCTTAAT
Found at i:28895391 original size:2 final size:2
Alignment explanation
Indices: 28895384--28895409 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28895374 GACATGTGCG
28895384 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28895410 AAAAGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28896157 original size:19 final size:19
Alignment explanation
Indices: 28896133--28896183 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
28896123 CATATCTTCT
28896133 AAGATTGCATATCATATCC
1 AAGATTGCATATCATATCC
* *
28896152 AAGATTACATATCATATCT
1 AAGATTGCATATCATATCC
28896171 AAGATTGCATATC
1 AAGATTGCATATC
28896184 CTTGAAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (19 bp):
AAGATTGCATATCATATCC
Found at i:28899013 original size:6 final size:6
Alignment explanation
Indices: 28899002--28899052 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
28898992 TTTCCCATTC
* *
28899002 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
28899046 TATTAG T
1 TATTAG T
28899053 TAGTCATCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:28899019 original size:11 final size:12
Alignment explanation
Indices: 28899002--28899052 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
28898992 TTTCCCATTC
28899002 TATTAGTATTAG
1 TATTAGTATTAG
*
28899014 -ATTAGTATT-C
1 TATTAGTATTAG
*
28899024 TATT-CTATTAG
1 TATTAGTATTAG
28899035 TATTAG-ATTAG
1 TATTAGTATTAG
28899046 TATTAGT
1 TATTAGT
28899053 TAGTCATCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (12 bp):
TATTAGTATTAG
Found at i:28899028 original size:27 final size:27
Alignment explanation
Indices: 28898998--28899049 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
28898988 TATTTTTCCC
28898998 ATTCTATTAGTATTAGATTAGTATTCT
1 ATTCTATTAGTATTAGATTAGTATTCT
28899025 ATTCTATTAGTATTAGATTAGTATT
1 ATTCTATTAGTATTAGATTAGTATT
28899050 AGTTAGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (27 bp):
ATTCTATTAGTATTAGATTAGTATTCT
Found at i:28901423 original size:31 final size:31
Alignment explanation
Indices: 28901330--28901423 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
28901320 AGATAATTTT
* *
28901330 AAAGAGTTTTATTAGGATTCAATTAATCTTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28901361 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
28901393 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28901424 TAATTTGCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:28902348 original size:6 final size:6
Alignment explanation
Indices: 28902337--28902387 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
28902327 TTTCCCATTC
* *
28902337 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
28902381 TATTAG T
1 TATTAG T
28902388 TAGTCATCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:28902354 original size:11 final size:12
Alignment explanation
Indices: 28902337--28902387 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
28902327 TTTCCCATTC
28902337 TATTAGTATTAG
1 TATTAGTATTAG
*
28902349 -ATTAGTATT-C
1 TATTAGTATTAG
*
28902359 TATT-CTATTAG
1 TATTAGTATTAG
28902370 TATTAG-ATTAG
1 TATTAGTATTAG
28902381 TATTAGT
1 TATTAGT
28902388 TAGTCATCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (12 bp):
TATTAGTATTAG
Found at i:28902363 original size:27 final size:27
Alignment explanation
Indices: 28902333--28902384 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
28902323 TATTTTTCCC
28902333 ATTCTATTAGTATTAGATTAGTATTCT
1 ATTCTATTAGTATTAGATTAGTATTCT
28902360 ATTCTATTAGTATTAGATTAGTATT
1 ATTCTATTAGTATTAGATTAGTATT
28902385 AGTTAGTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (27 bp):
ATTCTATTAGTATTAGATTAGTATTCT
Found at i:28904759 original size:31 final size:31
Alignment explanation
Indices: 28904666--28904759 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
28904656 AGATAATTTT
* *
28904666 AAAGAGTTTTATTAGGATTCAATTAATCTTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28904697 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
28904729 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28904760 TAATTTGCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 31 0.52
32 29 0.48
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:28905318 original size:8 final size:9
Alignment explanation
Indices: 28905298--28905348 Score: 59
Period size: 10 Copynumber: 5.4 Consensus size: 9
28905288 TCTTATTAAT
28905298 AAAAGCAAAA
1 AAAAGC-AAA
28905308 AAACAGCAAA
1 AAA-AGCAAA
*
28905318 AACAGCAAA
1 AAAAGCAAA
28905327 AAAAGC-AA
1 AAAAGCAAA
28905335 AAAAGCATAA
1 AAAAGCA-AA
28905345 AAAA
1 AAAA
28905349 AGAGAGAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 8 0.22
9 11 0.31
10 14 0.39
11 3 0.08
ACGTcount: A:0.75, C:0.14, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAGCAAA
Found at i:28905318 original size:9 final size:9
Alignment explanation
Indices: 28905306--28905346 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
28905296 ATAAAAGCAA
28905306 AAAAACAGC
1 AAAAACAGC
28905315 AAAAACAGC
1 AAAAACAGC
*
28905324 AAAAAAAGC
1 AAAAACAGC
28905333 AAAAA-AGC
1 AAAAACAGC
28905341 ATAAAA
1 A-AAAA
28905347 AAAGAGAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 26 0.87
ACGTcount: A:0.73, C:0.15, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAACAGC
Found at i:28905326 original size:20 final size:18
Alignment explanation
Indices: 28905298--28905350 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
28905288 TCTTATTAAT
28905298 AAAAGCAAAAAAACAGCAA
1 AAAAGCAAAAAAA-AGCAA
28905317 AAACAGC-AAAAAAAGCAA
1 AAA-AGCAAAAAAAAGCAA
28905335 AAAAGCATAAAAAAAG
1 AAAAGCA-AAAAAAAG
28905351 AGAGAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.10
18 8 0.26
19 17 0.55
20 3 0.10
ACGTcount: A:0.74, C:0.13, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAGCAAAAAAAAGCAA
Found at i:28905327 original size:18 final size:17
Alignment explanation
Indices: 28905298--28905348 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
28905288 TCTTATTAAT
28905298 AAAAGCAAAAAAACAGCAA
1 AAAAGC-AAAAAA-AGCAA
28905317 AAACAGCAAAAAAAGCAA
1 AAA-AGCAAAAAAAGCAA
28905335 AAAAGCATAAAAAA
1 AAAAGCA-AAAAAA
28905349 AGAGAGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.13
18 14 0.47
19 9 0.30
20 3 0.10
ACGTcount: A:0.75, C:0.14, G:0.10, T:0.02
Consensus pattern (17 bp):
AAAAGCAAAAAAAGCAA
Found at i:28905370 original size:24 final size:23
Alignment explanation
Indices: 28905343--28905427 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 23
28905333 AAAAAAGCAT
*
28905343 AAAAAAAGAGAGAGTAAAAAGCGCA
1 AAAAAAAGA-AGA-AAAAAAGCGCA
28905368 AAAAAAAGAAGCAAAAAAAGCGCAA
1 AAAAAAAGAAG-AAAAAAAGCGC-A
*
28905393 AAAAAAAGCAAAAAGCAAAAAAGCGCA
1 AAAAAAAG----AAGAAAAAAAGCGCA
28905420 AAAAAAAG
1 AAAAAAAG
28905428 TTGCCTACCT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
24 11 0.21
25 19 0.37
27 9 0.17
28 10 0.19
29 3 0.06
ACGTcount: A:0.71, C:0.11, G:0.18, T:0.01
Consensus pattern (23 bp):
AAAAAAAGAAGAAAAAAAGCGCA
Found at i:28911058 original size:31 final size:31
Alignment explanation
Indices: 28910965--28911058 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
28910955 AGATAATTTT
* * *
28910965 AAAGAGTTTTATGAGGATTCAATTAATCTTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28910996 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
1 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
28911028 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
28911059 TCATTTGCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:28921557 original size:10 final size:10
Alignment explanation
Indices: 28921538--28921572 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28921528 AAATCTATTG
28921538 AAAA-TAATC
1 AAAATTAATC
28921547 AAAATTAATC
1 AAAATTAATC
*
28921557 AAAATTAATT
1 AAAATTAATC
28921567 AAAATT
1 AAAATT
28921573 CAACATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTAATC
Found at i:28934039 original size:32 final size:33
Alignment explanation
Indices: 28933993--28934058 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
28933983 ATCTTTATGC
*
28933993 CTTAAATGGAAAATGATTTTTA-TATAGGGGAG
1 CTTAAATGGAAAATGACTTTTATTATAGGGGAG
* * *
28934025 CTTAAATTGCAAATGACTTTTATTATGGGGGAG
1 CTTAAATGGAAAATGACTTTTATTATAGGGGAG
28934058 C
1 C
28934059 AATCTATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (33 bp):
CTTAAATGGAAAATGACTTTTATTATAGGGGAG
Found at i:28939162 original size:101 final size:100
Alignment explanation
Indices: 28939049--28939270 Score: 236
Period size: 101 Copynumber: 2.2 Consensus size: 100
28939039 TGGCACAGAT
* *
28939049 TGTGTGTAGGCTACTATGTAAAAGTGAAAGTGAT-GGTCACATGTGCAGTACTATGTGCAGGCTA
1 TGTGTGCAGGCTACTATGTAAAA--GAAAGT-ATCGATCACATGTGCAGTACTATGTGCAGGCTA
* *
28939113 CTACGTGTACCGGAAT-G-ACA-GGTCGCATGTGTAGTAC
63 CTACATGTACCGG-ATGGTA-ATGGTCACATGTGTAGTAC
** * * * *
28939150 TGTGTGCAGGCTACTATGCGTACCAGATAGTTTCGATCACGTGTGTAGTACTATGTGCAGGCTAC
1 TGTGTGCAGGCTACTAT--GTAAAAGAAAGTATCGATCACATGTGCAGTACTATGTGCAGGCTAC
*
28939215 TACATGTATCGGATGGTAATGGTCACATGTGTAGTAC
64 TACATGTACCGGATGGTAATGGTCACATGTGTAGTAC
* *
28939252 TATGTGCAGGCTACAATGT
1 TGTGTGCAGGCTACTATGT
28939271 GAACCTAACA
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
100 5 0.05
101 61 0.60
102 32 0.31
103 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (100 bp):
TGTGTGCAGGCTACTATGTAAAAGAAAGTATCGATCACATGTGCAGTACTATGTGCAGGCTACTA
CATGTACCGGATGGTAATGGTCACATGTGTAGTAC
Found at i:28939210 original size:51 final size:51
Alignment explanation
Indices: 28939085--28939265 Score: 163
Period size: 51 Copynumber: 3.6 Consensus size: 51
28939075 AAAGTGATGG
* ** * *
28939085 TCACATGTGCAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGACA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGT-A-ATGA
* * ** *
28939135 TCGCATGTGTAGTACTGTGTGCAGGCTACTATGCGTACCAGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAAT-GA
* * * * * *
28939186 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAATGA
28939237 TCACATGTGTAGTACTATGTGCAGGCTAC
1 TCACATGTGTAGTACTATGTGCAGGCTAC
28939266 AATGTGAACC
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
50 36 0.34
51 68 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACACGTACCAGATAGTAATGA
Found at i:28939329 original size:45 final size:45
Alignment explanation
Indices: 28939278--28939365 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
28939268 TGTGAACCTA
* *
28939278 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
*
28939323 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
28939366 GAGTATCTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:28954638 original size:69 final size:69
Alignment explanation
Indices: 28954517--28954711 Score: 259
Period size: 69 Copynumber: 2.8 Consensus size: 69
28954507 ACTCTAACAT
*
28954517 TAAGACCATAGTTGGGGCTATGGCAACATATGAAGTCTGC-CAA-GACAATAAACATGGGATCAT
1 TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTC--CACAAGGACAATAAACATGGGATCAT
28954580 ATTGTG
64 ATTGTG
* * * * * * *
28954586 TAAGACCACAGCTAGGGTTATGGCAACATATAAAGTCCATAAGGACAGTAAACATGGGATCTTAT
1 TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTCCACAAGGACAATAAACATGGGATCATAT
28954651 TGTG
66 TGTG
* * *
28954655 TAAGACCATAGCTGGGGCTATGGCAACATTTGAACTCCACCAGGACAATAAACATGG
1 TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTCCACAAGGACAATAAACATGG
28954712 TAGCATATGG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 1 0.01
68 2 0.02
69 104 0.97
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (69 bp):
TAAGACCATAGCTGGGGCTATGGCAACATATGAAGTCCACAAGGACAATAAACATGGGATCATAT
TGTG
Found at i:28957292 original size:14 final size:15
Alignment explanation
Indices: 28957275--28957307 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28957265 TTCTCATTTG
28957275 CTTTTTCTCTC-TTT
1 CTTTTTCTCTCTTTT
*
28957289 CTTTTTCTTTCTTTT
1 CTTTTTCTCTCTTTT
28957304 CTTT
1 CTTT
28957308 GATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTCTCTCTTTT
Found at i:28959601 original size:25 final size:25
Alignment explanation
Indices: 28959546--28959639 Score: 97
Period size: 25 Copynumber: 3.8 Consensus size: 25
28959536 GTTCATACCC
*
28959546 ACAGCTCGTG-TGAGCATATCGATTT
1 ACAGCTCGTGATGAGCATACCGA-TT
* *
28959571 ATAGCTTGTGA-GAGCATACCGATCT
1 ACAGCTCGTGATGAGCATACCGAT-T
*
28959596 ACAGCTCG-AATGAGCATACCGATT
1 ACAGCTCGTGATGAGCATACCGATT
28959620 CACAGCTCGT-ATGAGCATAC
1 -ACAGCTCGTGATGAGCATAC
28959640 ATGTATATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.05
25 55 0.95
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (25 bp):
ACAGCTCGTGATGAGCATACCGATT
Found at i:28964670 original size:18 final size:18
Alignment explanation
Indices: 28964647--28964683 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28964637 AATCAATTTA
28964647 TATTACGTAAAACTGAAT
1 TATTACGTAAAACTGAAT
28964665 TATTACGTAAAACTGAAT
1 TATTACGTAAAACTGAAT
28964683 T
1 T
28964684 TATATTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (18 bp):
TATTACGTAAAACTGAAT
Found at i:28964925 original size:20 final size:18
Alignment explanation
Indices: 28964874--28964922 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28964864 ATTTGGCATA
28964874 TAACAGAATAATTTTTTAT
1 TAACA-AATAATTTTTTAT
* *
28964893 AAACATATCAATTTTTTATT
1 TAACAAAT-AATTTTTTA-T
28964913 TAACAAATAA
1 TAACAAATAA
28964923 ATTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (18 bp):
TAACAAATAATTTTTTAT
Found at i:28972184 original size:63 final size:61
Alignment explanation
Indices: 28972085--28972206 Score: 226
Period size: 63 Copynumber: 2.0 Consensus size: 61
28972075 TGTCAAATGT
28972085 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTTTATTTAGAAATTTTGTTGC
1 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCA--TTTTTTATTTAGAAATTTTGTTGC
28972148 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTATTTAGAAATTTTGTT
1 TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTATTTAGAAATTTTGTT
28972207 TTCACCGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 22 0.37
63 37 0.63
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.56
Consensus pattern (61 bp):
TCTTATACTTTTTGAAATTTAAAATTTAATCATTCCATTTTTTATTTAGAAATTTTGTTGC
Found at i:28973228 original size:21 final size:20
Alignment explanation
Indices: 28973190--28973228 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28973180 GGTTCAACTG
*
28973190 CTAGTTCAACTGTTTGTAGC
1 CTAGTTCAACCGTTTGTAGC
28973210 CTAGTTCAACCGATTTGTA
1 CTAGTTCAACCG-TTTGTA
28973229 CTGTTCAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
CTAGTTCAACCGTTTGTAGC
Found at i:28974137 original size:6 final size:7
Alignment explanation
Indices: 28974120--28974147 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28974110 TATTATAAAT
28974120 TTTTTTA
1 TTTTTTA
28974127 TTTTTTA
1 TTTTTTA
28974134 TTTTTTA
1 TTTTTTA
28974141 TTTTTTA
1 TTTTTTA
28974148 ATAACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:28977613 original size:63 final size:63
Alignment explanation
Indices: 28977536--28977657 Score: 201
Period size: 63 Copynumber: 1.9 Consensus size: 63
28977526 AATTTATCGA
* *
28977536 TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAGAT-TTATAGTTAAAACCTTATTGC
1 TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAAATCCT-TAGTTAAAACCTTATTGC
*
28977599 TAATTTTTATTGTATGAAATATTTTATTACATAAACTTAAATCCTTAGTTAAAACCTTA
1 TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAAATCCTTAGTTAAAACCTTA
28977658 AAATATAGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 54 0.98
64 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (63 bp):
TAATTTTTATTGTATGAAATATTTTAATACATAAACTTAAATCCTTAGTTAAAACCTTATTGC
Found at i:28978466 original size:26 final size:27
Alignment explanation
Indices: 28978433--28978483 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
28978423 TAAATATATA
28978433 TTTTTA-TTTTTTAATTTTAAAATACT
1 TTTTTATTTTTTTAATTTTAAAATACT
*
28978459 TTTTTATTTTTTTATTTTTAAAATA
1 TTTTTATTTTTTTAATTTTAAAATA
28978484 AATATTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTTTTAATTTTAAAATACT
Found at i:28989185 original size:23 final size:23
Alignment explanation
Indices: 28989131--28989185 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
28989121 GATTATGCAT
* *
28989131 TTCGATGCAATTAATATTGGCAC
1 TTCGATGCAACTAATACTGGCAC
* *
28989154 TAT-GGTGCAACTGATACTGGCAC
1 T-TCGATGCAACTAATACTGGCAC
28989177 TTCGATGCA
1 TTCGATGCA
28989186 TTACTGTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (23 bp):
TTCGATGCAACTAATACTGGCAC
Found at i:29000025 original size:12 final size:12
Alignment explanation
Indices: 29000008--29000037 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28999998 AGTCACACAC
29000008 CCGTGTGCTAGG
1 CCGTGTGCTAGG
29000020 CCGTGTGCTAGG
1 CCGTGTGCTAGG
29000032 CCGTGT
1 CCGTGT
29000038 AACAGCCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.27, G:0.40, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:29001223 original size:25 final size:24
Alignment explanation
Indices: 29001184--29001270 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 24
29001174 TCATGTACAT
* *
29001184 GTATGCTTATACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGT-AATCG
* * *
29001209 ATATGCTCACTCGAGTTGTAGATCG
1 GTATGCTCACACGAGCTGTA-ATCG
* *
29001234 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGT-AATCG
29001259 GTATGCTCACAC
1 GTATGCTCACAC
29001271 AAGTTGTGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (24 bp):
GTATGCTCACACGAGCTGTAATCG
Found at i:29006723 original size:24 final size:24
Alignment explanation
Indices: 29006679--29006724 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29006669 GGACAAGCTG
* *
29006679 AAATTTCCAACAGGGAAATTAAAC
1 AAATTTCCAACAAGCAAATTAAAC
*
29006703 AAATTTCCAACAAGCATATTAA
1 AAATTTCCAACAAGCAAATTAA
29006725 TGATGATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (24 bp):
AAATTTCCAACAAGCAAATTAAAC
Found at i:29008916 original size:49 final size:49
Alignment explanation
Indices: 29008819--29008933 Score: 117
Period size: 49 Copynumber: 2.3 Consensus size: 49
29008809 GCGGTGTGGT
* * * * ** * *
29008819 AGGCTGTGCGGAGCACACGGTCGTTTGAAACATTGTAGACTGTGTGGCC
1 AGGCCGTGTGGAGCACACGATCGTGTGAAACATTACAGACCGTATGGCC
29008868 AGGCCGTGTGGAGCACACGATCGTGTGAAAC-TCTACAGACCGTATGGCC
1 AGGCCGTGTGGAGCACACGATCGTGTGAAACAT-TACAGACCGTATGGCC
*
29008917 AGACCGTGTAGG-GCACA
1 AGGCCGTGT-GGAGCACA
29008934 TGGCCATGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 1 0.02
49 52 0.95
50 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.20
Consensus pattern (49 bp):
AGGCCGTGTGGAGCACACGATCGTGTGAAACATTACAGACCGTATGGCC
Found at i:29032593 original size:53 final size:53
Alignment explanation
Indices: 29032513--29032620 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
29032503 ATTGACACGG
*
29032513 CCGTGTGACAAAGCCCAGGCCATGTGGCATAGGGACATGGCCATGTGGCCAAA
1 CCGTGTGACAAAGCCCAGGCCACGTGGCATAGGGACATGGCCATGTGGCCAAA
* * *
29032566 CCGTGTGATAAAGCCCAGGCCGCGTGGCATTGGGACATGGCCATGTGGCCAAA
1 CCGTGTGACAAAGCCCAGGCCACGTGGCATAGGGACATGGCCATGTGGCCAAA
29032619 CC
1 CC
29032621 ATGTAACTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (53 bp):
CCGTGTGACAAAGCCCAGGCCACGTGGCATAGGGACATGGCCATGTGGCCAAA
Found at i:29036071 original size:27 final size:26
Alignment explanation
Indices: 29036021--29036265 Score: 238
Period size: 27 Copynumber: 9.1 Consensus size: 26
29036011 TATAATAGTT
* *
29036021 ATTTTACCCTATAGAGGTAATTCGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* * *
29036048 ATTTTACCCTATAGGCGTATTTCGATT
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* *
29036075 ATTCTACCATATGGGGGTATTTCGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* **
29036102 ATATTACCCTATGGGGGTATTTCAATC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
29036129 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* *
29036156 ATTCTACCCTATAGGGGTATTTAGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
* * *
29036183 ATTTTACCCTATGGATGAATTTCAGTC
1 ATTTTACCCTATGG-GGTATTTCGGTC
*
29036210 ATTCTACCCTATGTGGGTATTTCGGTC
1 ATTTTACCCTATG-GGGTATTTCGGTC
* *
29036237 ATTTTACCCTATGGAGTTATTTTGGTC
1 ATTTTACCCTATGG-GGTATTTCGGTC
29036264 AT
1 AT
29036266 AACAGTGTAA
Statistics
Matches: 181, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.02
27 177 0.98
28 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:29036149 original size:81 final size:81
Alignment explanation
Indices: 29036024--29036266 Score: 281
Period size: 81 Copynumber: 3.0 Consensus size: 81
29036014 AATAGTTATT
* ** * * * *
29036024 TTACCCTATAGAGGTAA-TTCGGTCATTTTACCCTATAGGCGTATTTCGATTATTCTACCATATG
1 TTACCCTATGGAGG-AATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATG
*
29036088 GGGGTATTTCGGTCATA
65 GGGGTATTTAGGTCATA
* * *
29036105 TTACCCTATGGGGGTATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATAG
1 TTACCCTATGGAGGAATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGG
*
29036170 GGGTATTTAGGTCATT
66 GGGTATTTAGGTCATA
* * * * * *
29036186 TTACCCTATGGATGAATTTCAGTCATTCTACCCTATGTGGGTATTTCGGTCATTTTACCCTATGG
1 TTACCCTATGGAGGAATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGG
* * *
29036251 AGTTATTTTGGTCATA
66 GGGTATTTAGGTCATA
29036267 ACAGTGTAAA
Statistics
Matches: 136, Mismatches: 25, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
80 1 0.01
81 135 0.99
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (81 bp):
TTACCCTATGGAGGAATTTCAATCATTTTACCCTATGGGGGTATTTCGATCATTCTACCCTATGG
GGGTATTTAGGTCATA
Found at i:29044786 original size:36 final size:36
Alignment explanation
Indices: 29044736--29044813 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
29044726 TTTTGTTGAC
** *
29044736 ATAAAACTTTTGAATAACTTAGAATACTTAATAATT
1 ATAAAACTCATGAATAACTTAAAATACTTAATAATT
29044772 ATAAAACTCATGAATAACTTAAAATACTTAATAATT
1 ATAAAACTCATGAATAACTTAAAATACTTAATAATT
29044808 ATAAAA
1 ATAAAA
29044814 AATTCAGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (36 bp):
ATAAAACTCATGAATAACTTAAAATACTTAATAATT
Found at i:29058346 original size:51 final size:50
Alignment explanation
Indices: 29058253--29058389 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 50
29058243 CCACAGCTCA
*
29058253 TGAGAGCATACTGATTTAAAGCTTATGTGAGCATACTGATTTACAACTCG
1 TGAGAGCATACTGATTTAAAGCTTATGTGAGCATACTAATTTACAACTCG
* * * *
29058303 TGAGAGCATACTGATGTTACAGCTTGTGTGCGCATA-TCAATTTACAGCTCG
1 TGAGAGCATACTGAT-TTAAAGCTTATGTGAGCATACT-AATTTACAACTCG
* *
29058354 TGAGAGCATACTGATTTATAGCTCGA-GTGAGCATAC
1 TGAGAGCATACTGATTTAAAGCT-TATGTGAGCATAC
29058390 ATGTACATGA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
50 31 0.42
51 43 0.58
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (50 bp):
TGAGAGCATACTGATTTAAAGCTTATGTGAGCATACTAATTTACAACTCG
Found at i:29058378 original size:25 final size:25
Alignment explanation
Indices: 29058245--29058389 Score: 148
Period size: 25 Copynumber: 5.8 Consensus size: 25
29058235 GGTCTGACCC
*
29058245 ACAGCTCATGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* ** *
29058270 AAAGCTTATGTGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
*
29058295 ACAACTCGTGAGAGCATACTGATGTT
1 ACAGCTCGTGAGAGCATACTGAT-TT
* * * *
29058321 ACAGCTTGTGTGCGCATA-TCAATTT
1 ACAGCTCGTGAGAGCATACT-GATTT
29058346 ACAGCTCGTGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* * *
29058371 ATAGCTCGAGTGAGCATAC
1 ACAGCTCGTGAGAGCATAC
29058390 ATGTACATGA
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
25 78 0.80
26 19 0.20
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACTGATTT
Found at i:29082283 original size:29 final size:28
Alignment explanation
Indices: 29082261--29082354 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 28
29082251 TTTTATTATT
* *
29082261 TTTTATATTTTTTTATGATTTTTATAAAA
1 TTTTAAATTTTCTTAT-ATTTTTATAAAA
29082290 TTTTAAATTTTCTTATATTTTT-TAAAA
1 TTTTAAATTTTCTTATATTTTTATAAAA
* * * *
29082317 TTTT-TATTTT-TTCTAATTTTAATAAAT
1 TTTTAAATTTTCTTAT-ATTTTTATAAAA
29082344 TTTTAATATTT
1 TTTTAA-ATTT
29082355 GAATTTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.06
26 10 0.19
27 17 0.31
28 6 0.11
29 18 0.33
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTTAAATTTTCTTATATTTTTATAAAA
Found at i:29082300 original size:26 final size:26
Alignment explanation
Indices: 29082271--29082372 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 26
29082261 TTTTATATTT
*
29082271 TTTTATGATTTTTATAAAATTTTAAA
1 TTTTCTGATTTTTATAAAATTTTAAA
* * **
29082297 TTTTCTTATATTTTTTAAAATTTTTATT
1 TTTTCTGAT-TTTTATAAAA-TTTTAAA
* * *
29082325 TTTTCTAATTTTAAT-AAATTTTTAA
1 TTTTCTGATTTTTATAAAATTTTAAA
*
29082350 TATT-TGAATTTTTATTAAAATTT
1 TTTTCTG-ATTTTTA-TAAAATTT
29082373 AATAATATTA
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
24 1 0.02
25 13 0.23
26 11 0.19
27 19 0.33
28 13 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTCTGATTTTTATAAAATTTTAAA
Found at i:29082310 original size:27 final size:27
Alignment explanation
Indices: 29082269--29082354 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
29082259 TTTTTTATAT
*
29082269 TTTTTTATGATTTTTATAAAATTTTAAA
1 TTTTTTAT-AATTTTATAAAATTTTAAA
* *
29082297 TTTTCTTAT-ATTTTTTAAAATTTT-TA
1 TTTT-TTATAATTTTATAAAATTTTAAA
* *
29082323 TTTTTTCTAATTTTAATAAATTTTTAATA
1 TTTTTTATAATTTT-ATAAAATTTTAA-A
29082352 TTT
1 TTT
29082355 GAATTTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.07
26 10 0.22
27 21 0.46
28 4 0.09
29 8 0.17
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTTTATAATTTTATAAAATTTTAAA
Found at i:29082312 original size:19 final size:17
Alignment explanation
Indices: 29082290--29082328 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
29082280 TTTTATAAAA
*
29082290 TTTTAAATTTTCTTATATT
1 TTTTAAAATTT-TTAT-TT
29082309 TTTTAAAATTTTTATTT
1 TTTTAAAATTTTTATTT
29082326 TTT
1 TTT
29082329 CTAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTAAAATTTTTATTT
Found at i:29082650 original size:89 final size:90
Alignment explanation
Indices: 29082430--29082752 Score: 334
Period size: 89 Copynumber: 3.5 Consensus size: 90
29082420 AATTTTTAAT
* * *
29082430 AAAAGCATGGGCTTAATTGA-TTTTTTTGAAAAAG-TTCAAGGGTCTTTTTGATGCATTTTGAAA
1 AAAAGCAGGGGCTTAATT-ACTTTTTTTGAAAAAGTTTC-AGGGCCTTTTTGAAGCATTTTGAAA
* *
29082493 GTTCAAATACCCAATTGAGTGCAAAAAA
64 GTTCAAGTACCCAAATGAGTGC-AAAAA
* * * ** *
29082521 AAAAGTAGGGCCTTAGTTGTTTTTTTTTTTTTTGAAAAGGTTTCAGGGCCTTTTTGAAGCATTTT
1 AAAAGCAGGGGCTTA------ATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTTGAAGCATTTT
29082586 GAAAGTTCAAGTACCCAAATGAGTGCAAAAA
60 GAAAGTTCAAGTACCCAAATGAGTGCAAAAA
* * *
29082617 AAAAGCA-GGGCTTAATTACTTTTTTTGAAAAGGTTTGAGGGCGTTTTTGATA-CATTTTGAAAG
1 AAAAGCAGGGGCTTAATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTTGA-AGCATTTTGAAAG
*
29082680 TTCAAGTACCCAAATGAGTG-TAAAA
65 TTCAAGTACCCAAATGAGTGCAAAAA
* * * * *
29082705 ACAAGTAGGGGCTTAATTGCTTTGTTTGAAAAAGTTTTAGGG-CTTTTT
1 AAAAGCAGGGGCTTAATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTT
29082753 ACACCCTTAA
Statistics
Matches: 197, Mismatches: 25, Indels: 23
0.80 0.10 0.09
Matches are distributed among these distances:
88 14 0.07
89 92 0.47
90 1 0.01
91 12 0.06
95 6 0.03
96 11 0.06
97 58 0.29
98 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (90 bp):
AAAAGCAGGGGCTTAATTACTTTTTTTGAAAAAGTTTCAGGGCCTTTTTGAAGCATTTTGAAAGT
TCAAGTACCCAAATGAGTGCAAAAA
Found at i:29085941 original size:38 final size:38
Alignment explanation
Indices: 29085890--29085972 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
29085880 AAACGTACTA
* * *
29085890 TTATTTAGGCTTAGTGCCTAGCAGGCTTAGTGCTGGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTCAGTGCCGGTG
*
29085928 TTATTCAGGCTTAGTGCCTAGTAGGCTCAGTGCCGGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTCAGTGCCGGTG
29085966 TTATTCA
1 TTATTCA
29085973 AACTTATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36
Consensus pattern (38 bp):
TTATTCAGGCTTAGTGCCTAGCAGGCTCAGTGCCGGTG
Found at i:29100420 original size:449 final size:448
Alignment explanation
Indices: 29099578--29100474 Score: 1546
Period size: 449 Copynumber: 2.0 Consensus size: 448
29099568 TCGGAGCGGC
29099578 GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
1 GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
29099643 TAAAGCTTTATTGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGAT
66 TAAAGCTTTATTGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGAT
* *
29099708 TTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACGGGTTTTTAAAAGAATTGC
131 TTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACGGGTTTGTAAAAGAAATGC
* *
29099773 ATATGTTTTAGCAAAATACCCACAAGAACACAAACTGTTTTAAAAAGCTTCCGCAACGTATAACA
196 ATATGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTCCGCAACGTATAACA
*
29099838 TTTTGCAAACTAATGACTGAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAGATC
261 TTTTGCAAACTAATGACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAGATC
* * *
29099903 TAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACACGAGCATCGGTTTTCAAACATACT
326 TAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACAAGAGCAGCGGTTTTCAAACACACT
* * *
29099968 ATCATGTGACATCGCCAAATTCGGCCATAACGTCTAGGCCAGTTTTGCGGTGTTACAT
391 ATCATGTGACATCACCAAATTCGGCCATAACGTCCAGGCCAGGTTTGCGGTGTTACAT
*
29100026 GGAGGACTCAGCTGTGGCCACACGACTCTTTTTTACTGTTTCATATTTAATTAGGTTTA-TTTTT
1 GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
*
29100090 TAAAGCTTTATATGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTTGA
66 TAAAGCTTTAT-TGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGA
*
29100155 TTTTATACTGCTTTATGTTTTATATCTGCTGGAGGTAGATAAAACACGAGGTTTGTAAAAGAAAT
130 TTTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACG-GGTTTGTAAAAGAAAT
* *
29100220 GCATGTGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTTCGCAACGTATAA
194 GCATATGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTCCGCAACGTATAA
*
29100285 CATTTTGCAAACTAACT-ACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAATGACGAG
259 CATTTTGCAAACTAA-TGACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAG
* *
29100349 ATTTAAACGAAAAATGTTTTAAGCAAAGTTACGGTTTTTCAACAAGAGCAGCGGTTTTCAAACAC
323 ATCTAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACAAGAGCAGCGGTTTTCAAACAC
* * * *
29100414 ACTATCATGTGACATCATCAAATTCGGCCATAATGTCCAGGCCGGGTTTGGGGTGTTACAT
388 ACTATCATGTGACATCACCAAATTCGGCCATAACGTCCAGGCCAGGTTTGCGGTGTTACAT
29100475 ATGGACTCAG
Statistics
Matches: 423, Mismatches: 23, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
447 16 0.04
448 157 0.37
449 249 0.59
450 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (448 bp):
GGAGGACTCAGCTGTGGCCACACGACTCCTTTTTACTGTTTCATATTTAATTAGGTTTACTTTTT
TAAAGCTTTATTGGGGTATTTTTCTGTAATAATGGCCACTATGAGTTTTTGCTTAAAATTTGGAT
TTTATACTGCTTTATGTTTTATATCTGCTAGAGGTAGATAAAACACGGGTTTGTAAAAGAAATGC
ATATGTTTTAGCAAAATACCCACAAGAACACAAACTATTTAAAAAAGCTTCCGCAACGTATAACA
TTTTGCAAACTAATGACTAAATAAAAATCACTATTTTAGGATTAATAAAAGATAACGACGAGATC
TAAACGAAAAATGTTTTAAGCAAAGTTACGATTTTTCAACAAGAGCAGCGGTTTTCAAACACACT
ATCATGTGACATCACCAAATTCGGCCATAACGTCCAGGCCAGGTTTGCGGTGTTACAT
Found at i:29101998 original size:108 final size:108
Alignment explanation
Indices: 29101801--29102014 Score: 306
Period size: 108 Copynumber: 2.0 Consensus size: 108
29101791 TTGTGCAGGT
*
29101801 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGAATTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGAATTTTTTTATAAACAATAGTCCATT
* * * * *
29101866 CACTAATTATTTCTAGAGGTTTTTTACCTCTTTCCATAAGGCC
66 CACCAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
* *
29101909 ACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTG-GTTTTTTTATAAACAATAGTCCAT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTG-TTGAATTTTTTTATAAACAATAGTCCAT
* *
29101973 TCACCAACTGTTTTTAGA-ATCTTTTTACCTATATCCATAAGG
65 TCACCAACTATTTCTAGAGAT-TTTTTACCTATATCCATAAGG
29102015 TTTGCTAAGA
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 90 0.96
109 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (108 bp):
ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGAATTTTTTTATAAACAATAGTCCATT
CACCAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
Found at i:29102727 original size:107 final size:108
Alignment explanation
Indices: 29102514--29102727 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 108
29102504 TTGTGCAGGT
*
29102514 ACAAATCCTTGTTTGGAATTTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
29102579 CACTAACTATTTCTAGAGATTTTTTACCTCTTTCCATAAGGCC
66 CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
* *
29102622 ACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG-TTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
29102686 CTAC-AACTGTTTTTAGA-ATCTTTTTACCTATATCCATAAGGC
66 C-ACTAACTATTTCTAGAGAT-TTTTTACCTATATCCATAAGGC
29102728 TTGCTAAGAT
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
106 2 0.02
107 55 0.57
108 40 0.41
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (108 bp):
ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
Found at i:29103049 original size:712 final size:713
Alignment explanation
Indices: 29101365--29104214 Score: 5474
Period size: 712 Copynumber: 4.0 Consensus size: 713
29101355 CTAGGAAATA
29101365 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
* * * *
29101430 AGATACTGGAGCTACAATTAGTAGTTGTAGAAAGAATGTCATTCCGGTAGAAAAATGGGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
29101495 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
*
29101560 AATATTCCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
*
29101625 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACTATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
29101690 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
29101755 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
* ** * *
29101820 TTATTGCTTTCCCTTTGTTGAATTTTTTTATAAACAGTAGTCCATTCACTAATTATTTCTAGAGG
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
29101885 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
521 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
*
29101950 TTTTTTTATAAACAATAGTCCATTCACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGG
586 TTTTTTTATAAACAGTAGTCCATTCACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGG
*
29102015 TTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
651 CTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
29102078 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
29102143 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
29102208 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
29102273 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
29102338 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
29102403 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
29102468 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
29102533 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
29102598 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
521 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
29102663 -TTTTTTATAAACAGTAGTCCATTCTA-CAACTGTTTTTAGAATCTTTTTACCTATATCCATAAG
586 TTTTTTTATAAACAGTAGTCCATTC-ACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAG
29102726 GCTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
650 GCTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
29102790 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
29102855 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
29102920 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
29102985 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
29103050 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
29103115 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
29103180 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
29103245 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
29103310 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
521 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
29103375 -TTTTTTATAAACAGTAGTCCATTCTA-CAACTGTTTTTAGAATCTTTTTACCTATATCCATAAG
586 TTTTTTTATAAACAGTAGTCCATTC-ACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAG
29103438 GCTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
650 GCTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
29103502 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
1 TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
29103567 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
66 AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
29103632 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
131 TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
29103697 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
196 AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
29103762 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
261 GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
29103827 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
326 AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
*
29103892 GTGTGTAATAAAACTTTTACACCGTTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
391 GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
* * *
29103957 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCATTAACTATTTTTAGAGG
456 TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
*
29104022 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTGGG
521 TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
29104087 TTTTTTTATAAACAGTAGTCCATTCACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGG
586 TTTTTTTATAAACAGTAGTCCATTCACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGG
* *
29104152 CTTGCTAAGATAATCAGCAATAATTTATTAGTACATAAAAGCACATAATTTATTCTTTTAATG
651 CTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
29104215 GTGTAAAAGT
Statistics
Matches: 2114, Mismatches: 20, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
712 1416 0.67
713 698 0.33
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (713 bp):
TAATACATATATTGAAATTACATTTCAATTTAAAGAATATAAAAATATTCTTTACATGCTTTATT
AGATACTGGAGCTACAATTAGTAGTTGCAGAAAGAATGCCATTCCTGTAGAAAAATGAGAAATTA
TTAAAAATCCTATAAAAGCAATAGGTATAGATGGTAATAAAACCATAATTCCATATAAAGATAAA
AATATTTCAATCTACATAAATAATGTAAGATTTGTAATTCTTAAAATTTTATATTTTCCTGAAAT
GCATGGAGATATATTATTAGGAAACAATTTTATATGTCAATATTTACCATTTTCTATTAATAAAA
AGTCAATTAGTTTATCTATAAAAAATTCTTATATAGAAATACCATTAGTTAATAATAATAAATTT
GTGTGTAATAAAACTTTTACACCATTAAAATGGTACTTGTGCAGGTACAAATCCTTGTTTGGAAT
TTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATTCACTAACTATTTCTAGAGA
TTTTTTACCTCTTTCCATAAGGCCACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG
TTTTTTTATAAACAGTAGTCCATTCACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGG
CTTGCTAAGATAATCAGAAATAATTTATTAGTACATAAAAGTACATAATTTATTCTTTTAATG
Found at i:29103439 original size:107 final size:108
Alignment explanation
Indices: 29103226--29103439 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 108
29103216 TTGTGCAGGT
*
29103226 ACAAATCCTTGTTTGGAATTTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
29103291 CACTAACTATTTCTAGAGATTTTTTACCTCTTTCCATAAGGCC
66 CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
* *
29103334 ACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTTGG-TTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
* *
29103398 CTAC-AACTGTTTTTAGA-ATCTTTTTACCTATATCCATAAGGC
66 C-ACTAACTATTTCTAGAGAT-TTTTTACCTATATCCATAAGGC
29103440 TTGCTAAGAT
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
106 2 0.02
107 55 0.57
108 40 0.41
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (108 bp):
ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
CACTAACTATTTCTAGAGATTTTTTACCTATATCCATAAGGCC
Found at i:29104094 original size:108 final size:108
Alignment explanation
Indices: 29103938--29104152 Score: 342
Period size: 108 Copynumber: 2.0 Consensus size: 108
29103928 TTGTGCAGGT
*
29103938 ACAAATCCTTGTTTGGAATTTATTGCTTTTCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
** * * *
29104003 CATTAACTATTTTTAGAGGT-TTTTTACCTCTTTCCATAAGGCC
66 CACCAACTATTTTTAGA-ATCTTTTTACCTATATCCATAAGGCC
*
29104046 ACAAATCCTTGTTTGGAATTTGTTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
1 ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
*
29104111 CACCAACTGTTTTTAGAATCTTTTTACCTATATCCATAAGGC
66 CACCAACTATTTTTAGAATCTTTTTACCTATATCCATAAGGC
29104153 TTGCTAAGAT
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 1 0.01
108 97 0.99
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (108 bp):
ACAAATCCTTGTTTGGAATTTATTGCTTTCCCTTTGTTGGGTTTTTTTATAAACAGTAGTCCATT
CACCAACTATTTTTAGAATCTTTTTACCTATATCCATAAGGCC
Found at i:29106248 original size:24 final size:24
Alignment explanation
Indices: 29106221--29106269 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29106211 AATAAGATAC
29106221 ATACTTTTTTATACATATCTTGTA
1 ATACTTTTTTATACATATCTTGTA
29106245 ATACTTTTTTATACATATCTTGTA
1 ATACTTTTTTATACATATCTTGTA
29106269 A
1 A
29106270 CACCCCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (24 bp):
ATACTTTTTTATACATATCTTGTA
Found at i:29110966 original size:42 final size:44
Alignment explanation
Indices: 29110886--29111004 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 44
29110876 CGTTTTCTCT
* * **
29110886 ATGCCATAGTCCAAATATGGTCTTACACA-TATTTACATAT-TG
1 ATGCCATAGCCCAGATATGGTCTTACACAGTATGCACATATCTG
*
29110928 ATGCCATAGCCCAGCTATGGTCTTACACAGTA-GCACATATCACACTG
1 ATGCCATAGCCCAGATATGGTCTTACACAGTATGCACATAT----CTG
* *
29110975 ATGCCATATCCCAGATATGGTCTTATACAG
1 ATGCCATAGCCCAGATATGGTCTTACACAG
29111005 AAATCACATA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 32 0.51
43 2 0.03
47 29 0.46
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (44 bp):
ATGCCATAGCCCAGATATGGTCTTACACAGTATGCACATATCTG
Found at i:29110988 original size:47 final size:47
Alignment explanation
Indices: 29110926--29111028 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 47
29110916 ATTTACATAT
* *
29110926 TGATGCCATAGCCCAGCTATGGTCTTACACAG-TAGCACATATCACA
1 TGATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
* * *
29110972 CTGATGCCATATCCCAGATATGGTCTTATACAGAAATCACATATCACA
1 -TGATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
*
29111020 TGTTGCCAT
1 TGATGCCAT
29111029 GGTCCTGCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 37 0.76
48 12 0.24
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (47 bp):
TGATGCCATAGCCCAGATATGGTCTTACACAGAAAGCACATATCACA
Done.