Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_pilon, whole genome shotgun sequence
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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2513084 original size:20 final size:20
Alignment explanation
Indices: 2512914--2513104 Score: 193
Period size: 20 Copynumber: 9.8 Consensus size: 20
2512904 ATTCGCATGT
*
2512914 ATCCGTATATCGCAAGCG-T-
1 ATCCGTAAATCGCAA-CGATA
2512933 ATCCGTAAATCGCAATGCG-T-
1 ATCCGTAAATCGCAA--CGATA
* *
2512953 ATCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
2512973 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
2512993 A----TAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
2513009 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
2513029 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
2513049 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
2513069 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
2513089 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
2513105 ACTGAAATTT
Statistics
Matches: 150, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
16 15 0.10
18 2 0.01
19 15 0.10
20 118 0.79
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:2513814 original size:24 final size:23
Alignment explanation
Indices: 2513775--2513820 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2513765 GAATTTGGTC
2513775 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
2513799 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
2513821 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:2514010 original size:12 final size:12
Alignment explanation
Indices: 2513993--2514027 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2513983 CATATAATCC
2513993 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2514005 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2514017 -AACGAAGAAAA
1 GAA-GAAGAAAA
2514028 GAAAATGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.09
12 20 0.91
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2514013 original size:15 final size:16
Alignment explanation
Indices: 2513993--2514032 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2513983 CATATAATCC
2513993 GAAGAAGAAAAA-GAA
1 GAAGAAGAAAAACGAA
2514008 GAAGAA-AAAAACGAA
1 GAAGAAGAAAAACGAA
2514023 GAA-AAGAAAA
1 GAAGAAGAAAA
2514033 TGCCACGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
GAAGAAGAAAAACGAA
Found at i:2516313 original size:19 final size:19
Alignment explanation
Indices: 2516244--2516431 Score: 201
Period size: 19 Copynumber: 10.7 Consensus size: 19
2516234 GCAACGAGAG
2516244 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2516263 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2516277 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2516297 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2516316 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
* *
2516334 AATCACAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2516348 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2516367 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2516386 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2516400 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
2516419 AATCGCATTGCGA
1 AATCGCAATGCGA
2516432 TTCTCCCGTT
Statistics
Matches: 142, Mismatches: 10, Indels: 34
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.01
14 30 0.21
15 1 0.01
16 7 0.05
17 3 0.02
18 10 0.07
19 74 0.52
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2516378 original size:70 final size:72
Alignment explanation
Indices: 2516244--2516393 Score: 252
Period size: 70 Copynumber: 2.1 Consensus size: 72
2516234 GCAACGAGAG
*
2516244 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCACAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2516309 AAATGAA
66 AAATGAA
*
2516316 AATCGCAATGCGAAATG-AAATCACAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCACAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
2516378 GAAATGAA
65 GAAATGAA
2516386 AATCGCAA
1 AATCGCAA
2516394 CGAGAGAATC
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
70 35 0.47
71 22 0.29
72 18 0.24
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCACAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:2516411 original size:52 final size:52
Alignment explanation
Indices: 2516230--2516431 Score: 263
Period size: 52 Copynumber: 3.9 Consensus size: 52
2516220 CGGAAATTAC
*
2516230 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2516277 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2516334 AATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
2516386 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
2516432 TTCTCCCGTT
Statistics
Matches: 136, Mismatches: 7, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
51 38 0.28
52 46 0.34
53 28 0.21
54 1 0.01
55 2 0.01
57 8 0.06
58 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2516458 original size:52 final size:52
Alignment explanation
Indices: 2516402--2516516 Score: 167
Period size: 52 Copynumber: 2.2 Consensus size: 52
2516392 AACGAGAGAA
*
2516402 TCGCAATGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
** * ** *
2516454 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
2516506 TCGCATTGCGA
1 TCGCATTGCGA
2516517 TAGTCAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
Found at i:2516464 original size:19 final size:19
Alignment explanation
Indices: 2516440--2516517 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
2516430 GATTCTCCCG
2516440 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2516459 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2516478 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2516492 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2516511 TTGCGAT
1 TTGCGAT
2516518 AGTCAATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 32 0.62
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2516643 original size:14 final size:14
Alignment explanation
Indices: 2516624--2516660 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2516614 CATCAATTAC
2516624 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2516638 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2516652 ACAAATCAA
1 ACAAATCAA
2516661 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2518656 original size:14 final size:14
Alignment explanation
Indices: 2518637--2518691 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
2518627 GCGAAATGAA
*
2518637 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
2518651 AATCGCATGCGAAATG
1 AATCGCA-ACGAAA-G
2518667 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
2518682 AATCGCAACG
1 AATCGCAACG
2518692 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 17 0.49
15 5 0.14
16 6 0.17
17 7 0.20
ACGTcount: A:0.44, C:0.24, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2518674 original size:31 final size:33
Alignment explanation
Indices: 2518618--2518708 Score: 150
Period size: 31 Copynumber: 2.8 Consensus size: 33
2518608 GCGAAACCAA
*
2518618 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2518651 AATCGC-ATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2518682 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2518709 TGCGATTTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 20 0.38
32 18 0.34
33 15 0.28
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2518706 original size:19 final size:19
Alignment explanation
Indices: 2518581--2518713 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
2518571 TAGTTTACTT
* *
2518581 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2518601 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2518620 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2518639 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2518653 TCGC-ATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
2518670 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2518684 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2518703 TCGCAATGCGA
1 TCGCAACGCGA
2518714 TTTGGTTTCG
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.01
14 14 0.15
15 5 0.05
16 12 0.13
17 11 0.12
18 1 0.01
19 39 0.41
20 12 0.13
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2518754 original size:33 final size:33
Alignment explanation
Indices: 2518709--2518799 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
2518699 AAAATCGCAA
2518709 TGCGA-TTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2518741 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2518774 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2518800 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.09
33 48 0.87
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2518762 original size:19 final size:19
Alignment explanation
Indices: 2518709--2518836 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
2518699 AAAATCGCAA
2518709 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2518727 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2518741 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2518760 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2518774 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2518793 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2518812 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2518832 TGCGA
1 TGCGA
2518837 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 7 0.08
19 42 0.47
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2519184 original size:92 final size:93
Alignment explanation
Indices: 2518884--2519258 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
2518874 ATGGATTGCA
2518884 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2518948 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
2518976 TTACTTTCAACCAAAAGACAAAATAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2519041 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2519069 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2519133 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2519161 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2519226 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2519254 TTACT
1 TTACT
2519259 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 96 0.34
93 183 0.66
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2519201 original size:185 final size:186
Alignment explanation
Indices: 2518884--2519258 Score: 727
Period size: 185 Copynumber: 2.0 Consensus size: 186
2518874 ATGGATTGCA
2518884 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2518948 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAATAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
2519013 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
2519069 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2519133 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
2519198 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
2519254 TTACT
1 TTACT
2519259 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 130 0.69
186 58 0.31
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2520981 original size:14 final size:14
Alignment explanation
Indices: 2520962--2521051 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
2520952 TTGAAATGAA
2520962 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2520976 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
2520995 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2521009 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2521028 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2521042 AATCGCAACG
1 AATCGCAACG
2521052 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2520999 original size:33 final size:33
Alignment explanation
Indices: 2520954--2521067 Score: 219
Period size: 33 Copynumber: 3.5 Consensus size: 33
2520944 TCTTTTGGTT
2520954 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2520987 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2521020 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2521053 GAAATGAAAATCGCA
1 GAAATGAAAATCGCA
2521068 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2521000 original size:19 final size:19
Alignment explanation
Indices: 2520976--2521067 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
2520966 GCAACGAGAG
*
2520976 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
2520995 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2521009 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2521028 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2521042 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2521061 AATCGCA
1 AATCGCA
2521068 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.46
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2521103 original size:14 final size:14
Alignment explanation
Indices: 2521084--2521140 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2521074 TTTGGTTTCG
2521084 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2521098 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2521117 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2521131 CGTTGCGATT
1 CGTTGCGATT
2521141 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2521116 original size:33 final size:33
Alignment explanation
Indices: 2521068--2521148 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2521058 GAAAATCGCA
**
2521068 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2521101 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2521134 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2521149 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2521151 original size:21 final size:21
Alignment explanation
Indices: 2521125--2521200 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2521115 CGCGTTGCGA
2521125 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2521146 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2521166 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2521187 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2521201 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2521181 original size:41 final size:41
Alignment explanation
Indices: 2521124--2521201 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2521114 TCGCGTTGCG
*
2521124 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
2521165 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
2521202 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2521322 original size:33 final size:33
Alignment explanation
Indices: 2521280--2521350 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2521270 AATACTAACT
*
2521280 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2521313 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2521346 TGAAA
1 TGAAA
2521351 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2521583 original size:22 final size:22
Alignment explanation
Indices: 2521531--2521585 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2521521 TGGTTGTGAG
**
2521531 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
2521553 AGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2521575 GGATTTCTTCG
1 GGATTTCTTCG
2521586 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2521757 original size:20 final size:20
Alignment explanation
Indices: 2521732--2521885 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
2521722 CTTTAAATAT
2521732 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2521752 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2521774 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2521793 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
2521813 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2521833 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2521853 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2521873 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2521886 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2521859 original size:40 final size:40
Alignment explanation
Indices: 2521731--2521885 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
2521721 GCTTTAAATA
*
2521731 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
2521772 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
2521812 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
2521852 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
2521886 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:2521902 original size:21 final size:21
Alignment explanation
Indices: 2521872--2521954 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2521862 ATTTTCATAT
*
2521872 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2521893 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2521914 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2521935 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2521955 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2521945 original size:42 final size:43
Alignment explanation
Indices: 2521852--2521950 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2521842 ATTTATGTGT
* *
2521852 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2521893 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2521935 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2521951 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2522134 original size:21 final size:20
Alignment explanation
Indices: 2522097--2522136 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2522087 TCTCTAAATA
*
2522097 TAATAACGAAAAAAATAATT
1 TAATAAAGAAAAAAATAATT
*
2522117 TAATAAAGTAAAATAATAAT
1 TAATAAAG-AAAAAAATAAT
2522137 AATGTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAATAAAGAAAAAAATAATT
Found at i:2522138 original size:16 final size:16
Alignment explanation
Indices: 2522117--2522154 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2522107 AAAAATAATT
2522117 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
2522133 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
2522149 T-ATAAA
1 TAATAAA
2522155 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:2522367 original size:26 final size:24
Alignment explanation
Indices: 2522298--2522367 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
2522288 GCAAAAGAGA
* *
2522298 AAAATATATTATATACGTTAATAGT
1 AAAATATA-TATATATGATAATAGT
*
2522323 AAAATA-ATAATAAAT-ATAATAGTT
1 AAAATATAT-ATATATGATAATAG-T
2522347 ATAAATATATATATATGATAA
1 A-AAATATATATATATGATAA
2522368 CTTTAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
23 7 0.19
24 7 0.19
25 16 0.44
26 6 0.17
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (24 bp):
AAAATATATATATATGATAATAGT
Found at i:2522916 original size:36 final size:37
Alignment explanation
Indices: 2522840--2522940 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 37
2522830 GTGCTTGTGG
* * * * *
2522840 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
*
2522877 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
2522913 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
2522941 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.02
36 29 0.52
37 26 0.46
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
Found at i:2523486 original size:7 final size:7
Alignment explanation
Indices: 2523474--2523570 Score: 99
Period size: 7 Copynumber: 13.9 Consensus size: 7
2523464 AATCAAATTA
2523474 AGGGTTT
1 AGGGTTT
2523481 AGGGTTT
1 AGGGTTT
**
2523488 AAAGTTT
1 AGGGTTT
2523495 AGGGTTT
1 AGGGTTT
2523502 AGGGTTT
1 AGGGTTT
2523509 AGGGTTT
1 AGGGTTT
* *
2523516 ATGGCTT
1 AGGGTTT
*
2523523 AGGGCTT
1 AGGGTTT
2523530 -GAGGTTT
1 AG-GGTTT
*
2523537 AGAGTTT
1 AGGGTTT
2523544 -GTGGTTT
1 AG-GGTTT
2523551 AGGGTTT
1 AGGGTTT
2523558 AGGGTTT
1 AGGGTTT
*
2523565 AAGGTT
1 AGGGTT
2523571 CATTGCAAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
6 2 0.03
7 71 0.95
8 2 0.03
ACGTcount: A:0.18, C:0.02, G:0.38, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:2530522 original size:20 final size:20
Alignment explanation
Indices: 2530498--2530576 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
2530488 TTGGTGCAGA
*
2530498 GGGAATCGATACCCCCATTA-
1 GGGAACCGATACCCCC-TTAG
*
2530518 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TT--AG
*
2530541 GGGAACCGATTCCCCC-TAG
1 GGGAACCGATACCCCCTTAG
*
2530560 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
2530577 GGGGTTCTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.32
20 16 0.32
21 1 0.02
22 1 0.02
23 16 0.32
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (20 bp):
GGGAACCGATACCCCCTTAG
Found at i:2540465 original size:15 final size:16
Alignment explanation
Indices: 2540440--2540469 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2540430 AATATAATGA
2540440 ATTATTTATATTTTGG
1 ATTATTTATATTTTGG
2540456 ATTA-TTATATTTTG
1 ATTATTTATATTTTG
2540470 TATTTTGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
ATTATTTATATTTTGG
Found at i:2545708 original size:30 final size:30
Alignment explanation
Indices: 2545664--2545836 Score: 181
Period size: 30 Copynumber: 5.7 Consensus size: 30
2545654 CATATTCGAT
*
2545664 TTAAAGGACCAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAATAGAAAC
* * * * *
2545694 ATAAAGAACTAAAATAGAAAAAATAGGAAT
1 TTAAAGGACTAAAATAGCAAAAATAGAAAC
* *
2545724 TTAAATGACTAAAATATCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAATAGAAAC
*
2545754 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAATAGAAAC
* * *
2545784 TTAAGGGAGTAAAATAGAAAAAAAAATAGAAAC
1 TTAAAGGACTAAAATAG---CAAAAATAGAAAC
2545817 TT-AAGAGACT-AAATAG-AAAA
1 TTAAAG-GACTAAAATAGCAAAA
2545837 TAAAATAATC
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.03
30 90 0.76
32 8 0.07
33 17 0.14
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAATAGAAAC
Found at i:2545838 original size:90 final size:89
Alignment explanation
Indices: 2545664--2545829 Score: 208
Period size: 90 Copynumber: 1.8 Consensus size: 89
2545654 CATATTCGAT
* *
2545664 TTAAAGGACCAAAATAGCAAAAATAGAAACATAAAGAACTAAAATAGAAAAAATAGGAATTTAAA
1 TTAAAGGACCAAAATAGCAAAAATAGAAACATAAAGAACTAAAATAGAAAAAATAGAAACTTAAA
2545729 TGACTAAAATATCAAAAATAGAAAC
66 TGACTAAAATA-CAAAAATAGAAAC
* * * * * *
2545754 TTAAGGGACTAAAATAGCAAAAATAGAAACTTAAGGGAGTAAAATAGAAAAAAAAATAGAAACTT
1 TTAAAGGACCAAAATAGCAAAAATAGAAACATAAAGAACTAAAATAG---AAAAAATAGAAACTT
2545819 AAGA-GACTAAA
63 AA-ATGACTAAA
2545830 TAGAAAATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
90 41 0.64
93 22 0.34
94 1 0.02
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.17
Consensus pattern (89 bp):
TTAAAGGACCAAAATAGCAAAAATAGAAACATAAAGAACTAAAATAGAAAAAATAGAAACTTAAA
TGACTAAAATACAAAAATAGAAAC
Found at i:2547309 original size:3 final size:3
Alignment explanation
Indices: 2547295--2547336 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2547285 AAATTTGTAT
2547295 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2547337 TTTTTGTGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2547747 original size:134 final size:131
Alignment explanation
Indices: 2547524--2547819 Score: 333
Period size: 134 Copynumber: 2.2 Consensus size: 131
2547514 GTTCTGGTCG
* * * * * *
2547524 TCTAAGGGTGACACGACTCCTATGTGATGAGGAGATCTGGTTGGTGGATGACACAGTTCCTACGC
1 TCTAGGGGTGACACGGCTTCTACGTGATGAGAAGATCTGGTCGGTGGATGACACAGTTCCTACGC
* *
2547589 GATGAGGACGACATACCATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGATGACTG
66 GATGAGGACGACAGACCATCTTTAGGGA---TGATAACACGGTTCCTACGCGATGAGGACGACTG
2547654 GTTA
128 GTTA
* * * *
2547658 TCTAGGGGTGACACGGCTTCTACGTGATGAGAAGGTCTGGTCGGTGGATGACACGGTTCTTACGT
1 TCTAGGGGTGACACGGCTTCTACGTGATGAGAAGATCTGGTCGGTGGATGACACAGTTCCTACGC
* ** * * * * * *
2547723 GATGAGGATGGTAGGCCATTTTTAGGGATGATAACATGGTTCTTACGTGATGAGGACGGCTGGTT
66 GATGAGGACGACAGACCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACGACTGGTT
2547788 A
131 A
* * *
2547789 TCTAGGGATGACTCGG-TTCTTACGCGATGAG
1 TCTAGGGGTGACACGGCTTC-TACGTGATGAG
2547820 GATGGCAGAC
Statistics
Matches: 137, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
130 3 0.02
131 57 0.42
134 77 0.56
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (131 bp):
TCTAGGGGTGACACGGCTTCTACGTGATGAGAAGATCTGGTCGGTGGATGACACAGTTCCTACGC
GATGAGGACGACAGACCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACGACTGGTT
A
Found at i:2547811 original size:43 final size:42
Alignment explanation
Indices: 2547625--2547825 Score: 153
Period size: 43 Copynumber: 4.6 Consensus size: 42
2547615 GAGGGTGATA
* * * *
2547625 ACACGGTTCCTACGCGATGAGGATGACTGGTTATCTAGGGGTG
1 ACACGGTTCTTACGTGATGAGGATGGCTGGTT-TCTAGGGATG
* *
2547668 ACACGGCTTC-TACGTGATGA-GAAGGTCTGG--TC-GGTGGATG
1 ACACGG-TTCTTACGTGATGAGGATGG-CTGGTTTCTAG-GGATG
*
2547708 ACACGGTTCTTACGTGATGAGGATGG-TAGGCCATTTTTAGGGATG
1 ACACGGTTCTTACGTGATGAGGATGGCT-GG---TTTCTAGGGATG
* *
2547753 ATAACATGGTTCTTACGTGATGAGGACGGCTGGTTATCTAGGGATG
1 ---ACACGGTTCTTACGTGATGAGGATGGCTGGTT-TCTAGGGATG
* *
2547799 ACTCGGTTCTTACGCGATGAGGATGGC
1 ACACGGTTCTTACGTGATGAGGATGGC
2547826 AGACCATCTT
Statistics
Matches: 126, Mismatches: 15, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
39 5 0.04
40 24 0.19
41 4 0.03
42 3 0.02
43 42 0.33
44 3 0.02
45 8 0.06
46 10 0.08
48 26 0.21
49 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.28
Consensus pattern (42 bp):
ACACGGTTCTTACGTGATGAGGATGGCTGGTTTCTAGGGATG
Found at i:2547991 original size:66 final size:67
Alignment explanation
Indices: 2547878--2548069 Score: 218
Period size: 66 Copynumber: 2.9 Consensus size: 67
2547868 AAGATGATGC
* * *
2547878 TTCAAGAG-AAGTTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGATGGTT
1 TTCAAGAGAAAG-TGTCTCAAG-G-GAGAAAATTTGTTTCAAGAGAAACAAACTCAAAGATGGTT
2547942 -TTGT
63 GTTGT
2547946 TTCAAGAGAAAGTGTCTCAAGGGAGAAAATTTGTTTCAA-AGGAAACAAACTC-AA-A-GGTTGT
1 TTCAAGAGAAAGTGTCTCAAGGGAGAAAATTTGTTTCAAGA-GAAACAAACTCAAAGATGGTTGT
2548007 TGT
65 TGT
* * *
2548010 TTTATGAGAAACG-GTCTCAAGGAAGATAATATTTGTTTCAAGAGAAACAAACTCAAAGAT
1 TTCAAGAGAAA-GTGTCTCAAGGGAGA-AA-ATTTGTTTCAAGAGAAACAAACTCAAAGAT
2548070 TATAAATTTT
Statistics
Matches: 108, Mismatches: 6, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
63 4 0.04
64 26 0.24
65 6 0.06
66 47 0.44
67 4 0.04
68 18 0.17
69 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (67 bp):
TTCAAGAGAAAGTGTCTCAAGGGAGAAAATTTGTTTCAAGAGAAACAAACTCAAAGATGGTTGTT
GT
Found at i:2548212 original size:37 final size:37
Alignment explanation
Indices: 2548122--2548239 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
2548112 TTAAAGAAAC
* * * *
2548122 AATTGTCTCAAGCGAGATAAAATCTGTTTTGATAG-A
1 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAA
* *
2548158 AATTTTCTCAAGTGAGACAAAATTTGTTTTTAGAGAA
1 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAA
2548195 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAG-GAAA
1 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAG-AA
2548232 AATTGTCT
1 AATTGTCT
2548240 TTAGCAAGAC
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
36 30 0.42
37 42 0.58
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (37 bp):
AATTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAA
Found at i:2549486 original size:27 final size:27
Alignment explanation
Indices: 2549399--2549488 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
2549389 TTTTTGCATG
*
2549399 TGCTTTTTGTCCATTTTTCTTTGTTTT-TT
1 TGCTTTTT-TCC-TTTTGC-TTGTTTTCTT
*
2549428 TG-TTTTTT-CTCTTTGC-T-TCTTCTT
1 TGCTTTTTTCCT-TTTGCTTGTTTTCTT
2549452 TGCTCTTTTTTCCTTTTGCTTGTTTTCTT
1 TG--CTTTTTTCCTTTTGCTTGTTTTCTT
2549481 TGCTTTTT
1 TGCTTTTT
2549489 CTTTGTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
23 3 0.06
24 5 0.10
25 1 0.02
26 5 0.10
27 18 0.36
28 8 0.16
29 10 0.20
ACGTcount: A:0.01, C:0.18, G:0.10, T:0.71
Consensus pattern (27 bp):
TGCTTTTTTCCTTTTGCTTGTTTTCTT
Found at i:2550632 original size:17 final size:19
Alignment explanation
Indices: 2550610--2550646 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
2550600 TTCATGAATG
*
2550610 ATGCATGTG-AAAAT-AAA
1 ATGCATATGCAAAATGAAA
2550627 ATGCATATGCAAAATGAAA
1 ATGCATATGCAAAATGAAA
2550646 A
1 A
2550647 GATACAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (19 bp):
ATGCATATGCAAAATGAAA
Found at i:2553047 original size:30 final size:30
Alignment explanation
Indices: 2553011--2553245 Score: 316
Period size: 30 Copynumber: 7.8 Consensus size: 30
2553001 CATATTCGAT
*
2553011 TTAAAGGACCAAAATAGCAAAAAAAGAAAC
1 TTAAAGGACTAAAATAGCAAAAAAAGAAAC
*
2553041 TTAAAGGACTAAAATAGCAAAAACAA-AAAT
1 TTAAAGGACTAAAATAGCAAAAA-AAGAAAC
2553071 TTAAAGGACTAAAATAG-AAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAAA-AGAAAC
*
2553101 TTAAAGGACTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAAAAGAAAC
* * *
2553131 TTAAGGGATTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAAAAGAAAC
* *
2553161 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAAAAGAAAC
* *
2553191 TTAAGGGACTAAAATAACAAAAATAA-AAAC
1 TTAAAGGACTAAAATAGCAAAAA-AAGAAAC
2553221 TTAAAGGACT-AAATAGCAAATAAAA
1 TTAAAGGACTAAAATAGCAAA-AAAA
2553246 TAATCTAGAG
Statistics
Matches: 188, Mismatches: 11, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
28 1 0.01
29 17 0.09
30 162 0.86
31 8 0.04
ACGTcount: A:0.61, C:0.09, G:0.13, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAAAAGAAAC
Found at i:2554186 original size:6 final size:6
Alignment explanation
Indices: 2554177--2554229 Score: 97
Period size: 6 Copynumber: 8.7 Consensus size: 6
2554167 TTTCTCTCTA
2554177 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTCT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T
2554226 TCTT
1 TCTT
2554230 CCTCTGATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 41 0.89
7 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:2554687 original size:3 final size:3
Alignment explanation
Indices: 2554675--2554706 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2554665 AATTGTATTG
2554675 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2554707 TTTTGTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2558547 original size:11 final size:12
Alignment explanation
Indices: 2558525--2558550 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2558515 CAATTTCTTA
2558525 TTTTAGATTTTT
1 TTTTAGATTTTT
2558537 TTTTAGATTTTT
1 TTTTAGATTTTT
2558549 TT
1 TT
2558551 ATTGATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTAGATTTTT
Found at i:2561830 original size:31 final size:29
Alignment explanation
Indices: 2561762--2561831 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
2561752 AATATTATTT
*
2561762 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
2561792 TGGTATATTTTATTAAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
2561825 TTATATT
1 TTATATT
2561832 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:2561968 original size:19 final size:20
Alignment explanation
Indices: 2561900--2561968 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
2561890 TTAAATATCT
* *
2561900 TTATTAA-AATATTATTAGA
1 TTATTAATAATAATATTAAA
*
2561919 TTATT-ATATTAATATTAAA
1 TTATTAATAATAATATTAAA
* *
2561938 TATATAAATAATAATATT-CA
1 T-TATTAATAATAATATTAAA
2561958 TTATTAATAAT
1 TTATTAATAAT
2561969 TTAATAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 5 0.12
21 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (20 bp):
TTATTAATAATAATATTAAA
Found at i:2562203 original size:24 final size:25
Alignment explanation
Indices: 2562156--2562204 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2562146 TTTAATAATT
*
2562156 AATATTTTGATTAAAATGATATTCA
1 AATATTTTGATTAAAATGAAATTCA
* *
2562181 AATATTTT-ATTAATATTAAATTCA
1 AATATTTTGATTAAAATGAAATTCA
2562205 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTTTGATTAAAATGAAATTCA
Found at i:2566079 original size:2 final size:2
Alignment explanation
Indices: 2566072--2566110 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2566062 TAATTTGAAC
2566072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2566111 TAAAACTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2566927 original size:32 final size:31
Alignment explanation
Indices: 2566891--2566969 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
2566881 ATATAATTTA
2566891 AAATTAAAAAAAAATTGAAAATTAGAGTAATT
1 AAATTAAAAAAAAATTGAAAATTA-AGTAATT
** ** * *
2566923 AAATTAGGAGTAATTTGAAAGTTAAGTAATT
1 AAATTAAAAAAAAATTGAAAATTAAGTAATT
*
2566954 AAATTTAAAAAAAATT
1 AAATTAAAAAAAAATT
2566970 AAACTTTAGT
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (31 bp):
AAATTAAAAAAAAATTGAAAATTAAGTAATT
Found at i:2566935 original size:15 final size:14
Alignment explanation
Indices: 2566909--2566958 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
2566899 AAAAAATTGA
2566909 AAATTAGAGTAATT
1 AAATTAGAGTAATT
2566923 AAATTAGGAGTAATTT
1 AAATTA-GAGTAA-TT
2566939 GAAAGTTA-AGTAATT
1 -AAA-TTAGAGTAATT
2566954 AAATT
1 AAATT
2566959 TAAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 8 0.25
16 7 0.22
17 3 0.09
18 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (14 bp):
AAATTAGAGTAATT
Found at i:2567420 original size:42 final size:42
Alignment explanation
Indices: 2567346--2567465 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
2567336 GTTTAACCTA
* * *
2567346 ATAAAGGTCAGGCGCGACCCTTAACCTGCGCTATATATAATT
1 ATAAAGGTCAGACGCGGCCCTTAACCTACGCTATATATAATT
* *
2567388 ATAAAGGTCAGACGCGGCCTTTAATCTACGCTATATATAATT
1 ATAAAGGTCAGACGCGGCCCTTAACCTACGCTATATATAATT
* *
2567430 ATAAAGGTCAGACGCGGTCCC-TGACCTGCGCTATAT
1 ATAAAGGTCAGACGCGG-CCCTTAACCTACGCTATAT
2567466 CCTACGTGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 66 0.97
43 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (42 bp):
ATAAAGGTCAGACGCGGCCCTTAACCTACGCTATATATAATT
Found at i:2568705 original size:2 final size:2
Alignment explanation
Indices: 2568663--2568691 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2568653 TTAGTATTGA
2568663 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2568692 CCTACTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2573709 original size:6 final size:6
Alignment explanation
Indices: 2573698--2573736 Score: 51
Period size: 7 Copynumber: 6.0 Consensus size: 6
2573688 AATGAAGTCA
2573698 ACGGTC ACGGTC ACGGTCC ACGGTC AACGGTC AACGGTC
1 ACGGTC ACGGTC ACGGT-C ACGGTC -ACGGTC -ACGGTC
2573737 GGGTCAGTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (6 bp):
ACGGTC
Found at i:2573751 original size:5 final size:5
Alignment explanation
Indices: 2573733--2573779 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
2573723 AACGGTCAAC
* * *
2573733 GGTCG GGTC- AGTCG GGTCG GGTCG TGTC- AGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
2573780 AGTCTGGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 6 0.17
5 29 0.83
ACGTcount: A:0.04, C:0.21, G:0.51, T:0.23
Consensus pattern (5 bp):
GGTCG
Found at i:2573755 original size:19 final size:19
Alignment explanation
Indices: 2573733--2573788 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
2573723 AACGGTCAAC
2573733 GGTCGGGTCAGTCGGGTCG
1 GGTCGGGTCAGTCGGGTCG
*
2573752 GGTCGTGTCAGTCGGGTCG
1 GGTCGGGTCAGTCGGGTCG
*
2573771 GGTCGGGTCAGTCTGGTC
1 GGTCGGGTCAGTCGGGTC
2573789 AAACCGGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.05, C:0.21, G:0.48, T:0.25
Consensus pattern (19 bp):
GGTCGGGTCAGTCGGGTCG
Found at i:2582196 original size:42 final size:42
Alignment explanation
Indices: 2582047--2582189 Score: 173
Period size: 42 Copynumber: 3.4 Consensus size: 42
2582037 AGGTCTTATG
* * *
2582047 GATGGCCTGAAGGACTT-ATCATCTTGCTCGAAAGACTTA-T
1 GATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
* * **
2582087 AGAAGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTTACT
1 -GATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
* * *
2582130 GTTGGCCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
2582172 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
2582190 CTCATCAAGA
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 12 0.14
42 73 0.85
43 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
Found at i:2582390 original size:98 final size:98
Alignment explanation
Indices: 2582191--2582520 Score: 434
Period size: 98 Copynumber: 3.4 Consensus size: 98
2582181 AAGGACTTAC
* * *
2582191 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAA-TTGTCATAACAGAACTCCTAAAAAT
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTC-TAAGTTGTC--AAGA-AACACCTAAAAAT
* * ** * *
2582255 TAGGCTTAGTTTTCTTTTGCAAACTCTTTGGAAATCA
62 TAGGCTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* *
2582292 T--T-AAGAAACCCATGAAAATCAAGCTTAGTTTCTAAGTTGTCAAGAAACCCCTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTAAGTTGTCAAGAAACACCTAAAAATTAGG
2582354 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* * *
2582387 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAGTTGTCAAGGAACAACTAAAAATTAGG
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTAAGTTGTCAAGAAACACCTAAAAATTAGG
* *
2582452 CTTAGCTTCCTTTTAAAAAATCATTGAAAATCT
66 CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
* *
2582485 TCATTAAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCT
2582521 TATAAAATCT
Statistics
Matches: 208, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
95 44 0.21
96 3 0.01
97 4 0.02
98 155 0.75
99 1 0.00
101 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (98 bp):
TCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTAAGTTGTCAAGAAACACCTAAAAATTAGG
CTTAGCTTCCTTTTAAAAACTCATTGAAAATCA
Found at i:2582653 original size:21 final size:21
Alignment explanation
Indices: 2582629--2582690 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2582619 GGAAATGATC
2582629 TCAAGCGAGATAAAATCTGTT
1 TCAAGCGAGATAAAATCTGTT
*
2582650 TCAAG-G-G---AAA-CTATCT
1 TCAAGCGAGATAAAATCTGT-T
2582666 T-AAGCGAGATAAAATCTGTT
1 TCAAGCGAGATAAAATCTGTT
2582686 TCAAG
1 TCAAG
2582691 GGAAACTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 16
0.63 0.04 0.33
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 1 0.03
19 1 0.03
20 6 0.19
21 11 0.35
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (21 bp):
TCAAGCGAGATAAAATCTGTT
Found at i:2582657 original size:36 final size:36
Alignment explanation
Indices: 2582533--2582780 Score: 277
Period size: 36 Copynumber: 6.7 Consensus size: 36
2582523 TAAAATCTTT
* * *
2582533 TGTTTCAAGCGAAACTAACTCAAGTGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA---TC
* *
2582572 TGTTT-GAGGGAAACTATCTCAAGTGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA---TC
*
2582610 TGTTTCGAGGGAAA-TGATCTCAAGCGAGATAAAATC
1 TGTTTCAAGGGAAACT-ATCTCAAGCGAGATAAAATC
*
2582646 TGTTTCAAGGGAAACTATCTTAAGCGAGATAAAATC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * *
2582682 TGTTTCAAGGGAAACTATCTCAAGTGAAATAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
2582718 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA---TC
* *
2582757 TGATTCGAGGGAAACT-TCTCAAGC
1 TGTTTCAAGGGAAACTATCTCAAGC
2582781 TTTTAAAAAC
Statistics
Matches: 188, Mismatches: 15, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
36 98 0.52
37 1 0.01
38 44 0.23
39 45 0.24
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
Found at i:2582992 original size:98 final size:98
Alignment explanation
Indices: 2582823--2583017 Score: 309
Period size: 98 Copynumber: 2.0 Consensus size: 98
2582813 AACCCCTTTC
* * * *
2582823 TAAGTTTTCAAGGAACCCCTAAAAATTAGGCTTAGCTTTCTTTTAAAAATTCATTGAAAATCATC
1 TAAGTTGTCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAACTCATTGAAAATCATA
*
2582888 ATCAAGAAACCCCTGAAAATCAGGCTTAGTTTT
66 AACAAGAAACCCCTGAAAATCAGGCTTAGTTTT
* * *
2582921 TAAGTTGTCAAGGAACCCCTAAAAATTAGGCTTATCTTCCTTTTAAAAACTCTTTGAAAATCTTA
1 TAAGTTGTCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAACTCATTGAAAATCATA
*
2582986 AACAAGAAACCCCTGAAAATCAGTCTTAGTTT
66 AACAAGAAACCCCTGAAAATCAGGCTTAGTTT
2583018 CTTATAAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (98 bp):
TAAGTTGTCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAACTCATTGAAAATCATA
AACAAGAAACCCCTGAAAATCAGGCTTAGTTTT
Found at i:2583077 original size:39 final size:39
Alignment explanation
Indices: 2583023--2583105 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
2583013 AGTTTCTTAT
*
2583023 AAAATCTTTTGTTTCGAAC-GAAACTATCTCAAGCGAGAA
1 AAAATCTTCTGTTTCG-ACTGAAACTATCTCAAGCGAGAA
* *
2583062 AAAATCTTCTGTTTCGACTGTAACTATCTCAAGCGAGAT
1 AAAATCTTCTGTTTCGACTGAAACTATCTCAAGCGAGAA
2583101 AAAAT
1 AAAAT
2583106 TCATTTCCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.05
39 38 0.95
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.30
Consensus pattern (39 bp):
AAAATCTTCTGTTTCGACTGAAACTATCTCAAGCGAGAA
Found at i:2583177 original size:36 final size:36
Alignment explanation
Indices: 2583083--2583214 Score: 140
Period size: 36 Copynumber: 3.7 Consensus size: 36
2583073 TTTCGACTGT
* * *
2583083 AACTATCTCAAGCGAGATAAAATTCATTTCCAAG-GA
1 AACTATCTCAAGGGAGACAAAATTAATTT-CAAGAGA
* * * * *
2583119 AATTATCTTAAGTGATATAAAATTAATTTCAAGAGA
1 AACTATCTCAAGGGAGACAAAATTAATTTCAAGAGA
**
2583155 AACTATCTCAAGGGAGACAAAATTTGTTTCAAGAGA
1 AACTATCTCAAGGGAGACAAAATTAATTTCAAGAGA
* *
2583191 AATTGTCTCAAGGGAGACAAAATT
1 AACTATCTCAAGGGAGACAAAATT
2583215 TTGTTTTGAG
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 4 0.05
36 77 0.95
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (36 bp):
AACTATCTCAAGGGAGACAAAATTAATTTCAAGAGA
Found at i:2583193 original size:72 final size:74
Alignment explanation
Indices: 2583083--2583257 Score: 176
Period size: 72 Copynumber: 2.4 Consensus size: 74
2583073 TTTCGACTGT
* * ** * * * *
2583083 AACTATCTCAAGCGAGATAAAATTCATTTCCAAGGAAATTATCTTAAGTGATATAAAA-TTAATT
1 AACTATCTCAAGAGAGACAAAATTTGTTTCCAAGGAAATTATCTCAAGGGAGACAAAATTTAATT
2583147 TCAAG-AGA
66 TCAAGTAGA
* * **
2583155 AACTATCTCAAGGGAGACAAAATTTGTTT-CAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGT
1 AACTATCTCAAGAGAGACAAAATTTGTTTCCAAG-GAAATTATCTCAAGGGAGACAAAATTTAAT
**
2583219 TTTGAGTAGA
65 TTCAAGTAGA
* *
2583229 AATTGTCTCAAGAGAGACAAAATTTGTTT
1 AACTATCTCAAGAGAGACAAAATTTGTTT
2583258 TGAGTAAAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
71 4 0.05
72 44 0.52
73 7 0.08
74 29 0.35
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (74 bp):
AACTATCTCAAGAGAGACAAAATTTGTTTCCAAGGAAATTATCTCAAGGGAGACAAAATTTAATT
TCAAGTAGA
Found at i:2583247 original size:74 final size:73
Alignment explanation
Indices: 2583160--2583349 Score: 229
Period size: 74 Copynumber: 2.6 Consensus size: 73
2583150 AGAGAAACTA
* * * *
2583160 TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTTGAG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTGAA
*
2583225 TAGAAATTG
65 TAAAAATTG
** *
2583234 TCTCAAGAGAGACAAAATTTGTTTTGAGTAAAAACTGTCTCAAGAGAGACAAAATTTGTTTTGAA
1 TCTCAAGAGAGACAAAATTTGTTTCAAG-AGAAACTGTCTCAAGAGAGACAAAATTTGTTTTGAA
2583299 TAAAAATTG
65 TAAAAATTG
* * ** *
2583308 TCTGAAGTGAGACAAAATTCATTTCAAGGGAAAC-GTTCTCAA
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTG-TCTCAA
2583350 AGTTTATTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
72 1 0.01
73 10 0.10
74 65 0.66
75 22 0.22
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (73 bp):
TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTGAAT
AAAAATTG
Found at i:2583255 original size:37 final size:37
Alignment explanation
Indices: 2583160--2583326 Score: 228
Period size: 37 Copynumber: 4.5 Consensus size: 37
2583150 AGAGAAACTA
* ** *
2583160 TCTCAAGGGAGACAAAATTTGTTTCAAG-AGAAATTG
1 TCTCAAGAGAGACAAAATTTGTTTTGAGTAAAAATTG
* *
2583196 TCTCAAGGGAGACAAAATTTTGTTTTGAGTAGAAATTG
1 TCTCAAGAGAGACAAAA-TTTGTTTTGAGTAAAAATTG
*
2583234 TCTCAAGAGAGACAAAATTTGTTTTGAGTAAAAACTG
1 TCTCAAGAGAGACAAAATTTGTTTTGAGTAAAAATTG
*
2583271 TCTCAAGAGAGACAAAATTTGTTTTGAATAAAAATTG
1 TCTCAAGAGAGACAAAATTTGTTTTGAGTAAAAATTG
* *
2583308 TCTGAAGTGAGACAAAATT
1 TCTCAAGAGAGACAAAATT
2583327 CATTTCAAGG
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
36 17 0.14
37 79 0.66
38 24 0.20
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.31
Consensus pattern (37 bp):
TCTCAAGAGAGACAAAATTTGTTTTGAGTAAAAATTG
Found at i:2583505 original size:37 final size:36
Alignment explanation
Indices: 2583371--2583506 Score: 114
Period size: 37 Copynumber: 3.6 Consensus size: 36
2583361 CAAGAGAAAC
2583371 TGTCTCAAGGGAGACAAAA-TTTGTTTTGAGTAAAAAT
1 TGTCTCAA-GGAGACAAAATTTTGTTTTGAG-AAAAAT
* *
2583408 TGTCTCAAAGGAGACAAAAAATTTTTTTTTAGAGAAAAAC
1 TGTCTC-AAGGAGAC--AAAATTTTGTTTT-GAGAAAAAT
** ** *
2583448 AATCTCAAGTGAGA-TTAATTTTGTTTTGAGGAAAAT
1 TGTCTCAAG-GAGACAAAATTTTGTTTTGAGAAAAAT
*
2583484 TGTCTCTAGCGAGACAAAATTTT
1 TGTCTCAAG-GAGACAAAATTTT
2583507 TTCTTAGGAA
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
36 17 0.22
37 28 0.36
38 2 0.03
39 7 0.09
40 20 0.26
41 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (36 bp):
TGTCTCAAGGAGACAAAATTTTGTTTTGAGAAAAAT
Found at i:2583532 original size:72 final size:76
Alignment explanation
Indices: 2583373--2583544 Score: 194
Period size: 72 Copynumber: 2.3 Consensus size: 76
2583363 AGAGAAACTG
* * *
2583373 TCTCAAGGGAGA-CAAAATTTGTTTTGAGTAAAAATTGTCTCAAAGGAGACAAAAAATTTTTTTT
1 TCTCAAGTGAGATC-AACTTTGTTTTGAGTAAAAATTGTCTCAAAGGAGAC-AAAAATTTTTTCT
2583437 TAGAGAAAAACAA
64 TAGAGAAAAACAA
* * * *
2583450 TCTCAAGTGAGATTAATTTTGTTTTGAG-GAAAATTGTCTC-TAGCGAGAC-AAAATTTTTTCTT
1 TCTCAAGTGAGATCAACTTTGTTTTGAGTAAAAATTGTCTCAAAG-GAGACAAAAATTTTTTCTT
*
2583512 AG-G-AAAACTA
65 AGAGAAAAACAA
*
2583522 TCTCATGTGAGATCAACTTTGTT
1 TCTCAAGTGAGATCAACTTTGTT
2583545 CTAAATATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
72 26 0.31
73 1 0.01
74 14 0.17
75 2 0.02
76 16 0.19
77 24 0.29
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (76 bp):
TCTCAAGTGAGATCAACTTTGTTTTGAGTAAAAATTGTCTCAAAGGAGACAAAAATTTTTTCTTA
GAGAAAAACAA
Found at i:2590027 original size:19 final size:17
Alignment explanation
Indices: 2589982--2590029 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
2589972 CTAACTTTAA
2589982 AGAAATTAAAATTAAAG
1 AGAAATTAAAATTAAAG
*
2589999 ACAAATTTAAAATGTAAAG
1 AGAAA-TTAAAAT-TAAAG
*
2590018 TTGAAATTAAAA
1 -AGAAATTAAAA
2590030 CATAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 4 0.16
18 7 0.28
19 11 0.44
20 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.27
Consensus pattern (17 bp):
AGAAATTAAAATTAAAG
Found at i:2591794 original size:13 final size:12
Alignment explanation
Indices: 2591777--2591819 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
2591767 AAATTAACTA
2591777 ATTAAATCAGTT
1 ATTAAATCAGTT
2591789 AGTTAAATCAGTT
1 A-TTAAATCAGTT
*
2591802 ATTAAAATCAGCT
1 ATT-AAATCAGTT
2591815 ATTAA
1 ATTAA
2591820 CTATAAGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (12 bp):
ATTAAATCAGTT
Found at i:2595493 original size:15 final size:15
Alignment explanation
Indices: 2595475--2595542 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
2595465 TCCACCACCG
2595475 GGATATCCTCCGCAA
1 GGATATCCTCCGCAA
*
2595490 GGATATCCT---CAG
1 GGATATCCTCCGCAA
* *
2595502 GGTTATCCTCCTC-A
1 GGATATCCTCCGCAA
*
2595516 GGCATATCCTCAGCAA
1 GG-ATATCCTCCGCAA
2595532 GGATATCCTCC
1 GGATATCCTCC
2595543 TCAATATGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 10 0.24
14 2 0.05
15 26 0.63
16 3 0.07
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (15 bp):
GGATATCCTCCGCAA
Found at i:2598793 original size:2 final size:2
Alignment explanation
Indices: 2598786--2598825 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2598776 ATAAGTCGAC
2598786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2598826 GTAAGCAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2600045 original size:14 final size:14
Alignment explanation
Indices: 2600015--2600104 Score: 67
Period size: 14 Copynumber: 6.3 Consensus size: 14
2600005 TATTCAAAAG
**
2600015 AAAA-AAAAAGGTC
1 AAAAGAAAAAGGAA
**
2600028 AAAAGAAAATTGAA
1 AAAAGAAAAAGGAA
2600042 AAAAGAAAAAGGAA
1 AAAAGAAAAAGGAA
*
2600056 AAAGTTGAAAAAGGAA
1 AAA--AGAAAAAGGAA
*
2600072 AAAAGAAAAAATTG-A
1 AAAAG-AAAAA-GGAA
*
2600087 AAAAGAAAAAAGAA
1 AAAAGAAAAAGGAA
2600101 AAAA
1 AAAA
2600105 ATCAAATAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
13 5 0.08
14 31 0.51
15 11 0.18
16 14 0.23
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAAGAAAAAGGAA
Found at i:2600049 original size:7 final size:7
Alignment explanation
Indices: 2600028--2600104 Score: 66
Period size: 7 Copynumber: 10.6 Consensus size: 7
2600018 AAAAAAGGTC
2600028 AAAAGAA
1 AAAAGAA
**
2600035 AATTGAA
1 AAAAGAA
2600042 AAAAGAA
1 AAAAGAA
*
2600049 AAAGGAA
1 AAAAGAA
*
2600056 AAAGTTGAA
1 AAA--AGAA
*
2600065 AAAGGAA
1 AAAAGAA
2600072 AAAAGAA
1 AAAAGAA
2600079 AAAATTG-A
1 AAAA--GAA
2600087 AAAAGAA
1 AAAAGAA
2600094 AAAAGAA
1 AAAAGAA
2600101 AAAA
1 AAAA
2600105 ATCAAATAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
6 1 0.02
7 44 0.77
8 5 0.09
9 7 0.12
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (7 bp):
AAAAGAA
Found at i:2600106 original size:23 final size:22
Alignment explanation
Indices: 2600033--2600104 Score: 108
Period size: 23 Copynumber: 3.2 Consensus size: 22
2600023 AGGTCAAAAG
*
2600033 AAAATTGAAAAAAGAAAAAGGAA
1 AAAATTG-AAAAAGAAAAAAGAA
*
2600056 AAAGTTGAAAAAGGAAAAAAGAA
1 AAAATTGAAAAA-GAAAAAAGAA
2600079 AAAATTGAAAAAGAAAAAAGAA
1 AAAATTGAAAAAGAAAAAAGAA
2600101 AAAA
1 AAAA
2600105 ATCAAATAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.42
23 26 0.58
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (22 bp):
AAAATTGAAAAAGAAAAAAGAA
Found at i:2600136 original size:46 final size:44
Alignment explanation
Indices: 2600019--2600136 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 44
2600009 CAAAAGAAAA
** * ** *
2600019 AAAAAGGTCAAAAG-AAAATTGAAAAAAGAAAAAGGAAAAAGTTG
1 AAAAAGGAAAAAAGAAAAATTG-AAAAAGAAAAAAGAAAAAAATC
2600063 AAAAAGGAAAAAAGAAAAAATTGAAAAAGAAAAAAGAAAAAAATC
1 AAAAAGGAAAAAAG-AAAAATTGAAAAAGAAAAAAGAAAAAAATC
2600108 AAATAAGTTGAAAAAAGAAAAATT-AAAAA
1 AAA-AAG--GAAAAAAGAAAAATTGAAAAA
2600137 TGTTTAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
44 12 0.19
45 21 0.33
46 15 0.24
47 7 0.11
48 8 0.13
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (44 bp):
AAAAAGGAAAAAAGAAAAATTGAAAAAGAAAAAAGAAAAAAATC
Found at i:2600259 original size:29 final size:30
Alignment explanation
Indices: 2600208--2600268 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2600198 TTGAATAAAT
* *
2600208 AAAAGAAATAAATACATATATA-T-AATAA
1 AAAAGAAAAAAATACAAATATATTAAATAA
*
2600236 AAAAGTAAAAAAATATAAATATATTAAATAA
1 AAAAG-AAAAAAATACAAATATATTAAATAA
2600267 AA
1 AA
2600269 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.19
29 14 0.52
30 1 0.04
31 7 0.26
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAAGAAAAAAATACAAATATATTAAATAA
Found at i:2600272 original size:9 final size:9
Alignment explanation
Indices: 2600201--2600281 Score: 53
Period size: 9 Copynumber: 9.1 Consensus size: 9
2600191 TGTTAAATTG
2600201 AATAAATAA
1 AATAAATAA
*
2600210 AAGAAAT-A
1 AATAAATAA
*
2600218 AATACAT-A
1 AATAAATAA
*
2600226 TATATAATAA
1 AATA-AATAA
*
2600236 AA-AAGTAA
1 AATAAATAA
2600244 AA-AAATATA
1 AATAAATA-A
* *
2600253 AATATATTA
1 AATAAATAA
2600262 AATAAAATAA
1 AAT-AAATAA
2600272 AATAAATAA
1 AATAAATAA
2600281 A
1 A
2600282 GGGAAAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
8 20 0.36
9 23 0.42
10 12 0.22
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (9 bp):
AATAAATAA
Found at i:2600278 original size:29 final size:29
Alignment explanation
Indices: 2600201--2600279 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 29
2600191 TGTTAAATTG
* *
2600201 AATAAATAAAA-GAAATAAATACATATATAT
1 AATAAATAAAATAAAATAAAT--ATAAATAT
*
2600231 AATAAA-AAAGTAAAA-AAATATAAATAT
1 AATAAATAAAATAAAATAAATATAAATAT
*
2600258 ATTAAATAAAATAAAATAAATA
1 AATAAATAAAATAAAATAAATA
2600280 AAGGGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
27 12 0.29
28 8 0.20
29 12 0.29
30 9 0.22
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (29 bp):
AATAAATAAAATAAAATAAATATAAATAT
Found at i:2600280 original size:27 final size:28
Alignment explanation
Indices: 2600202--2600281 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
2600192 GTTAAATTGA
* *
2600202 ATAAATAAAA-GAAATAAATACATATAT
1 ATAAATAAAATAAAATAAATAAATATAT
* *
2600229 ATAATAAAAAAGTAAAAAAATATAAATATAT
1 ATAA-ATAAAA-TAAAATAA-ATAAATATAT
2600260 -TAAATAAAATAAAATAAATAAA
1 ATAAATAAAATAAAATAAATAAA
2600282 GGGAAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
27 9 0.21
28 12 0.28
29 5 0.12
30 8 0.19
31 9 0.21
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (28 bp):
ATAAATAAAATAAAATAAATAAATATAT
Found at i:2600372 original size:17 final size:19
Alignment explanation
Indices: 2600350--2600388 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
2600340 ATTAAATTAA
2600350 AAATATT-ATAAAAA-ATC
1 AAATATTAATAAAAATATC
2600367 AAATATTAATAAAAATATC
1 AAATATTAATAAAAATATC
2600386 AAA
1 AAA
2600389 ATATGCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATATTAATAAAAATATC
Found at i:2600681 original size:2 final size:2
Alignment explanation
Indices: 2600676--2600705 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2600666 TCTCCTGGGG
2600676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2600706 TGAAGACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2600771 original size:117 final size:116
Alignment explanation
Indices: 2600572--2600792 Score: 433
Period size: 117 Copynumber: 1.9 Consensus size: 116
2600562 TTTGCCCGGA
2600572 ATATATATATATATATATGAAGACAAAATAGTCTTATTTTCCCATTTCTCACCCTTTAGCCGAGA
1 ATATATATATATATATATGAAGACAAAATAGTCTTATTTTCCCATTTCTCACCCTTTAGCCGAGA
2600637 GAAGAGAGAGAGAGAAATTCTCTCAACTCTCTCCTGGGGATATATATATAT
66 GAAGAGAGAGAGAGAAATTCTCTCAACTCTCTCCTGGGGATATATATATAT
2600688 ATATATATATATATATATTGAAGACAAAATAGTCTTATTTTCCCATTTCTCACCCTTTAGCCGAG
1 ATATATATATATATATA-TGAAGACAAAATAGTCTTATTTTCCCATTTCTCACCCTTTAGCCGAG
2600753 AGAAGAGAGAGAGAGAAATTCTCTCAACTCTCTCCTGGGG
65 AGAAGAGAGAGAGAGAAATTCTCTCAACTCTCTCCTGGGG
2600793 GGTTCATCGG
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 17 0.16
117 87 0.84
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (116 bp):
ATATATATATATATATATGAAGACAAAATAGTCTTATTTTCCCATTTCTCACCCTTTAGCCGAGA
GAAGAGAGAGAGAGAAATTCTCTCAACTCTCTCCTGGGGATATATATATAT
Found at i:2601574 original size:3 final size:3
Alignment explanation
Indices: 2601555--2601601 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
2601545 AAACAAAAAT
*
2601555 TAA TAA TAT TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2601602 ATATATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2602476 original size:85 final size:85
Alignment explanation
Indices: 2602327--2603413 Score: 1236
Period size: 85 Copynumber: 12.8 Consensus size: 85
2602317 ATGTGTCGTC
* * * * ** * * * *
2602327 GAGCTGAATGGAATCGAACTCGACA-GTTTTTGTTGACAAATAGCTTTTCTTGACTTAAGTTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
2602391 CTGTAAATTTGACATGCCCTT
65 CTGTAAATTTGATATGCCTTT
* * * * * * * *
2602412 GAGCTAAATGGAATCGAACTTGAAGGTATTTATTGACAGATATCCCTTCTCGTCTAGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
2602477 TGTAAA-TTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
2602496 GAGCTGAATGTAATTGAACTCAAAGATCTTTTGTTGACATATAACCTTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
2602561 CTGTAAA-TTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* ** * * * *
2602581 GTGCTGAATGTAATCGATTTCGATGGTATTGGTGGACAGATAA-CCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
2602645 TGTAAGTTTGACATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
2602665 GAGCTAAATGTAATCGAACTCAAAGGTCTTTGCTGGCAGATAGA-CATTCTCACCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA-ACCCTTCTCGCCTTGAGCTATG
2602729 CTGTAAATTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * * * *
2602750 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTGGACATATAACCCTTCTCGCCTTGAGATATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
2602815 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * * * *
2602835 GATCTGAACGTAATCGAACTCGAAGGTCTTTGCTGGCAAATAACCCTTATCGCCTTGAGCTCTGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
2602900 TGCAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * ** *
2602920 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTGGATAGATAGTCCTTCTCGCCTTGAGCTATTC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
2602985 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
2603005 GAGCTGAATGTAATCGAACTCGAAGATCTTTGCTGGCAAATAACCCTTCTTGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
2603070 TGCAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* ** * * * *
2603090 GAGCT-AAGTGTAATCAAACTCGAAGGTAATAGTTGATAGATAGCCCTTCTCGCCTTGAGTTATG
1 GAGCTGAA-TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
2603154 CTGTAAATTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * **
2603175 AAGCTGACTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGTCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
2603240 TGTAAATTTGATGTGCCTTT
66 TGTAAATTTGATATGCCTTT
* * *
2603260 GAGTTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTATCACCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * **
2603325 TTGTAAATTTGATGTGTTTTT
65 CTGTAAATTTGATATGCCTTT
* *
2603346 GAGCTGAATGTAAAT-GAACTCGAAGGTCTTTTGTT-AGCAGATAACCCTTTTCACCTTGAGCTA
1 GAGCTGAATGT-AATCGAACTCGAAGGTC-TTTGTTGA-CAGATAACCCTTCTCGCCTTGAGCTA
2603409 TGCTG
63 TGCTG
2603414 CGAATTGTTC
Statistics
Matches: 843, Mismatches: 149, Indels: 19
0.83 0.15 0.02
Matches are distributed among these distances:
83 25 0.03
84 91 0.11
85 615 0.73
86 109 0.13
87 3 0.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTT
Found at i:2604743 original size:99 final size:98
Alignment explanation
Indices: 2604523--2604776 Score: 365
Period size: 99 Copynumber: 2.6 Consensus size: 98
2604513 AGCTGGATCT
* *
2604523 ATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGAACAACTCAA--TATCATTGTATAGATATT
1 ATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGTATAGATATT
* *
2604586 ATAATCACCTTTTCAGGCTAGCTGAATATTATCC
65 ATAATAACCTTTTCAGGCTAGCTGAATACTATCC
*
2604620 ATAAAG-CTGGGGCATTTAACCAATTGCCCTAGAGGGACAACTCAAGCTTTATTGTATAGATATT
1 ATAAAGTC-GGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATATT
2604684 ATAATAACCTTTATCAGGCTTAGCTGAAT-CTATCC
65 ATAATAACCTTT-TCAGGC-TAGCTGAATACTATCC
**
2604719 ATAAAGTCGGGG-AGTTTAACCAATTGCTCTAGAGGGACAGTTCAAGCTTTATTGTATA
1 ATAAAGTCGGGGCA-TTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATA
2604777 TAAAATATTA
Statistics
Matches: 142, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
96 1 0.01
97 41 0.29
98 27 0.19
99 63 0.44
100 10 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (98 bp):
ATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATATTA
TAATAACCTTTTCAGGCTAGCTGAATACTATCC
Found at i:2608985 original size:7 final size:7
Alignment explanation
Indices: 2608969--2609016 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
2608959 AAAAAAGTTG
*
2608969 AAAAGTA
1 AAAAGGA
2608976 AAAAGGA
1 AAAAGGA
2608983 AAAAGTTGA
1 AAAAG--GA
*
2608992 AAAATGA
1 AAAAGGA
*
2608999 GAAAGGA
1 AAAAGGA
2609006 AAAAGGA
1 AAAAGGA
2609013 AAAA
1 AAAA
2609017 AAGTTGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 28 0.82
9 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (7 bp):
AAAAGGA
Found at i:2608985 original size:22 final size:23
Alignment explanation
Indices: 2608960--2609010 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
2608950 AAAATGTCAA
*
2608960 AAAAAGTTGAAAAGT-AAAAAGG
1 AAAAAGTTGAAAAATGAAAAAGG
*
2608982 AAAAAGTTGAAAAATGAGAAAGG
1 AAAAAGTTGAAAAATGAAAAAGG
2609005 AAAAAG
1 AAAAAG
2609011 GAAAAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (23 bp):
AAAAAGTTGAAAAATGAAAAAGG
Found at i:2608995 original size:23 final size:22
Alignment explanation
Indices: 2608960--2609010 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
2608950 AAAATGTCAA
2608960 AAAAAGTTGAAAA-GTAAAAAGG
1 AAAAAGTTGAAAATG-AAAAAGG
*
2608982 AAAAAGTTGAAAAATGAGAAAGG
1 AAAAAGTTG-AAAATGAAAAAGG
2609005 AAAAAG
1 AAAAAG
2609011 GAAAAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 16 0.62
24 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (22 bp):
AAAAAGTTGAAAATGAAAAAGG
Found at i:2609018 original size:32 final size:30
Alignment explanation
Indices: 2608970--2609028 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
2608960 AAAAAGTTGA
*
2608970 AAAGTAAAAAGGAAAAAGTTGAAAAATGAG
1 AAAGGAAAAAGGAAAAAGTTGAAAAATGAG
2609000 AAAGGAAAAAGGAAAAAAAGTTGAAAAAT
1 AAAGGAAAAAGG--AAAAAGTTGAAAAAT
2609029 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.42
32 15 0.58
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (30 bp):
AAAGGAAAAAGGAAAAAGTTGAAAAATGAG
Found at i:2609118 original size:4 final size:4
Alignment explanation
Indices: 2609109--2609195 Score: 66
Period size: 4 Copynumber: 20.5 Consensus size: 4
2609099 TGTTGAATTG
* * * * * *
2609109 AATA AATAA AAGA AATA AATA TATA TATA TATA TATA TAATAA AATA AAAA
1 AATA AAT-A AATA AATA AATA AATA AATA AATA AATA -AAT-A AATA AATA
*
2609160 ATATA AATA TATTA AATA AATA AATA AATA AATA AA
1 A-ATA AATA -AATA AATA AATA AATA AATA AATA AA
2609196 GGAAAAAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
4 55 0.79
5 14 0.20
6 1 0.01
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (4 bp):
AATA
Found at i:2609169 original size:23 final size:23
Alignment explanation
Indices: 2609137--2609195 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
2609127 ATATATATAT
*
2609137 ATATATATATAATAAAATAAAAA
1 ATATAAATATAATAAAATAAAAA
* *
2609160 ATATAAATAT-ATTAAATAAATA
1 ATATAAATATAATAAAATAAAAA
2609182 A-ATAAATA-AATAAA
1 ATATAAATATAATAAA
2609196 GGAAAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.35
22 11 0.35
23 9 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATAAATATAATAAAATAAAAA
Found at i:2609170 original size:31 final size:33
Alignment explanation
Indices: 2609113--2609193 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 33
2609103 GAATTGAATA
* *
2609113 AATAAAAGAAATAAATATATATATATATATATAT
1 AATAAAATAAATAAATATATATATATAT-TAAAT
2609147 AATAAAATAAA-AAATATA-A-ATATATTAAAT
1 AATAAAATAAATAAATATATATATATATTAAAT
2609177 AA-ATAAATAAATAAATA
1 AATA-AAATAAATAAATA
2609194 AAGGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 13 0.30
31 11 0.26
32 1 0.02
33 7 0.16
34 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
AATAAAATAAATAAATATATATATATATTAAAT
Found at i:2609171 original size:27 final size:26
Alignment explanation
Indices: 2609121--2609193 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 26
2609111 TAAATAAAAG
* *
2609121 AAATAAATATATATATATATATATATAAT
1 AAATAAA-AAATATAAATATAT-TA-AAT
2609150 AAAATAAAAAATATAAATATATTAAAT
1 -AAATAAAAAATATAAATATATTAAAT
*
2609177 AAATAAATAA-ATAAATA
1 AAATAAAAAATATAAATA
2609194 AAGGAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 7 0.17
26 9 0.22
27 3 0.08
28 2 0.05
29 12 0.30
30 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATAAAAAATATAAATATATTAAAT
Found at i:2610350 original size:3 final size:3
Alignment explanation
Indices: 2610331--2610373 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2610321 CAAACAAAAT
*
2610331 TAA TAA TAT TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2610374 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2610378 original size:2 final size:2
Alignment explanation
Indices: 2610371--2610396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2610361 AATAATAATA
2610371 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2610397 TCTTTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2617195 original size:105 final size:106
Alignment explanation
Indices: 2616885--2617452 Score: 952
Period size: 105 Copynumber: 5.4 Consensus size: 106
2616875 TGGTGACCCA
* * * *
2616885 TTCGTCGTGAAGTTGAAATTGACTCT-AGAATTG-GAAAATTGTTTATTGACAACCAGCGGTCCC
1 TTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGAG-AAGTTGTTTGTTGACAACCAGCGGTCCC
2616948 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
64 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
2616991 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTT
* **
2617056 CGTCGTGAAGTTGAACATGCGTTGTCAAGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
2617097 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTT
2617161 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* *
2617202 TTCGCTCTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTG-TTGTTGACAACCAGCGGTCCCT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACAACCAGCGGTCCCT
2617265 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
65 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
2617307 TTCGTTGTGAAGTTGAAATTGGCTCTG-AATTAGAGAAGTTGTTTATTGACAACCAGCGGTCCCT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTTGTTGACAACCAGCGGTCCCT
2617371 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT-C
65 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
2617412 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
2617453 ATTGAGGTGT
Statistics
Matches: 439, Mismatches: 16, Indels: 15
0.93 0.03 0.03
Matches are distributed among these distances:
104 5 0.01
105 231 0.53
106 201 0.46
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTT
CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
Found at i:2622749 original size:11 final size:11
Alignment explanation
Indices: 2622723--2622758 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2622713 AATTAATAAA
2622723 TATTTA-ATAT
1 TATTTATATAT
2622733 TA--TATATAT
1 TATTTATATAT
2622742 TATTTATATAT
1 TATTTATATAT
2622753 TATTTA
1 TATTTA
2622759 GCTTTAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
8 2 0.09
9 6 0.26
10 2 0.09
11 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTATATAT
Found at i:2623358 original size:29 final size:30
Alignment explanation
Indices: 2623324--2623397 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2623314 TATGATAAAA
*
2623324 AATCAAT-ATGACCACCGAACT-TTCAATTG
1 AATCAATCA-GACCACCCAACTATTCAATTG
*
2623353 AATCAATCAGACCACCCAACTATTTAATTG
1 AATCAATCAGACCACCCAACTATTCAATTG
* *
2623383 ATTCAATCAAACCAC
1 AATCAATCAGACCAC
2623398 TGGCAGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.26
Consensus pattern (30 bp):
AATCAATCAGACCACCCAACTATTCAATTG
Found at i:2623844 original size:16 final size:17
Alignment explanation
Indices: 2623807--2623844 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2623797 AGGATAAAAA
*
2623807 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
2623824 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
2623840 TTAAA
1 TTAAA
2623845 TTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:2624106 original size:29 final size:29
Alignment explanation
Indices: 2624074--2624137 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2624064 AAAAAATCGG
*
2624074 TTAATTCGGTTCGATTAATAATTTTTAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
2624103 TTAATTCGGTTCTATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
2624132 TAAATT
1 TTAATT
2624138 TTGGTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:2624150 original size:30 final size:29
Alignment explanation
Indices: 2624076--2624150 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
2624066 AAAATCGGTT
* * *
2624076 AATTCGGTTCGATTAATAATTTTTAAATT
1 AATTCGGTTCAATTAATAATTTTCAAATA
*
2624105 AATTCGGTTCTATTAATAATTTTCAAATA
1 AATTCGGTTCAATTAATAATTTTCAAATA
*
2624134 AATTTTGGTTCAATTAA
1 AA-TTCGGTTCAATTAA
2624151 CCGAATCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (29 bp):
AATTCGGTTCAATTAATAATTTTCAAATA
Found at i:2624193 original size:94 final size:97
Alignment explanation
Indices: 2624083--2624277 Score: 263
Period size: 103 Copynumber: 2.0 Consensus size: 97
2624073 GTTAATTCGG
*
2624083 TTCGATTAATAA-TTTTT-AAA-TTAATTCGGTTCTA-TTAATAATTTTCAAATAAATTTTGGTT
1 TTCGATTAATAATTTTTTAAAAGTTAATTCAGTTC-AGTTAATAATTTTCAAATAAATTTTGGTT
*
2624144 CAATTAACCGAATCAAATTAACCGAATTTTTGA
65 CAATTAACCGAACCAAATTAACCGAATTTTTGA
*
2624177 TTCGGTTAATAATTTTTTAAAAAAATTGGTTAATTCAGTTCAGTTAATAATTTTCAAATAAATTT
1 TTCGATTAATAATTTTTT---AAAA---GTTAATTCAGTTCAGTTAATAATTTTCAAATAAATTT
*
2624242 TGGTTCAATTAACCGAACCGAATTAACCGAATTTTT
60 TGGTTCAATTAACCGAACCAAATTAACCGAATTTTT
2624278 TTCTTTAACT
Statistics
Matches: 87, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
94 11 0.13
95 5 0.06
99 3 0.03
102 1 0.01
103 67 0.77
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (97 bp):
TTCGATTAATAATTTTTTAAAAGTTAATTCAGTTCAGTTAATAATTTTCAAATAAATTTTGGTTC
AATTAACCGAACCAAATTAACCGAATTTTTGA
Found at i:2625033 original size:14 final size:13
Alignment explanation
Indices: 2625014--2625050 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
2625004 GAGAATGTAT
2625014 TATTATATTTATTA
1 TATTATATTTA-TA
2625028 TATTATTATTTATA
1 TATTA-TATTTATA
2625042 TATTATATT
1 TATTATATT
2625051 AATACTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 12 0.55
15 6 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTATATTTATA
Found at i:2625183 original size:31 final size:28
Alignment explanation
Indices: 2625113--2625194 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
2625103 ATGGTGATTT
2625113 ATTATTACTTTATATATATATATTATATTAC
1 ATTATTA-TTT-TATATAT-TATTATATTAC
2625144 A-TAGTTATTTTATATATTATTACTATTAC
1 ATTA-TTATTTTATATATTATTA-TATTAC
*
2625173 -TCATTATTATTATTATATTATT
1 ATTATTATT-TTA-TATATTATT
2625195 TACACAAGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
28 10 0.22
29 17 0.38
30 14 0.31
31 4 0.09
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTATTATTTTATATATTATTATATTAC
Found at i:2625214 original size:3 final size:3
Alignment explanation
Indices: 2625011--2625194 Score: 50
Period size: 3 Copynumber: 60.3 Consensus size: 3
2625001 TATGAGAATG
*
2625011 TAT TAT TA- TATT TAT TA- TAT TAT TATT TAT ATAT TA- TAT TAA TACT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TA-T
* * *
2625057 AAC TAT TACT CT-T TAT TAA TAT T-T T-T TAAT TAT TAT TAT TAAT TA-
1 TAT TAT TA-T -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT
** * * *
2625102 TAT GGT GATT TAT TAT TAC T-T TA- TAT ATAT ATAT TA- TAT TACA TAGT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TA-T TA-T
* *
2625149 TAT T-T TAT ATAT TAT TAC TAT TACT CAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
2625194 T
1 T
2625195 TACACAAGTA
Statistics
Matches: 136, Mismatches: 21, Indels: 48
0.66 0.10 0.23
Matches are distributed among these distances:
2 22 0.16
3 80 0.59
4 33 0.24
5 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:2625648 original size:26 final size:27
Alignment explanation
Indices: 2625567--2625649 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
2625557 AACCGGTTTT
2625567 TAAAAAAAAACCGGATTTTT--T-CGGA
1 TAAAAAAAAACCGG-TTTTTAATCCGGA
* *
2625592 T---AAAAAACCGGTTTTTTATCCGGT
1 TAAAAAAAAACCGGTTTTTAATCCGGA
**
2625616 TTGAAAAAAACCGGTTTTTAATCC-GA
1 TAAAAAAAAACCGGTTTTTAATCCGGA
2625642 TAAAAAAA
1 TAAAAAAA
2625650 CCGGTCGTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
21 5 0.11
22 10 0.21
23 1 0.02
24 4 0.09
25 1 0.02
26 7 0.15
27 19 0.40
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (27 bp):
TAAAAAAAAACCGGTTTTTAATCCGGA
Found at i:2625651 original size:24 final size:23
Alignment explanation
Indices: 2625570--2625654 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 23
2625560 CGGTTTTTAA
*
2625570 AAAAAAACCGGATTTTT-TCGGAT
1 AAAAAAACCGG-TTTTTATCCGAT
*
2625593 -AAAAAACCGGTTTTTTATCCGGTTT
1 AAAAAAACCGG-TTTTTATCC-G-AT
2625618 GAAAAAAACCGGTTTTTAATCCGAT
1 -AAAAAAACCGGTTTTT-ATCCGAT
2625643 AAAAAAACCGGT
1 AAAAAAACCGGT
2625655 CGTTCAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
22 15 0.29
23 2 0.04
24 13 0.25
25 2 0.04
26 6 0.12
27 14 0.27
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (23 bp):
AAAAAAACCGGTTTTTATCCGAT
Found at i:2626599 original size:185 final size:184
Alignment explanation
Indices: 2626268--2626657 Score: 561
Period size: 185 Copynumber: 2.1 Consensus size: 184
2626258 ATTTTAAATT
* * *
2626268 TATATAA-AAATTAAATATTTTTTTAATTAAAAAACAGTTTATAACTAATTTAAATAATATATAA
1 TATATAATATATTTAATA-TTTTTTAATTAAAAAACAATTTATAACTAATTTAAATAATATATAA
*
2626332 TTATAAAATAAAAAGTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAGTTTATATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTAT
* * * * * ***
2626397 AGGATTTTAAATTATTAATT-AGATTTTAAATGGTTTGGGCTTAGTTCATATATTA
130 AGAATCTTAAATTATTAATTGAG-TTTTAAATAGTTTGGACTAAACCCATATATTA
* *
2626452 TATATAATATATTTAATATTTTTTAATTCAAAAAAATAATTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATT--AAAAAACAATTTATAACTAATTTAAATAATATATA
* *
2626517 ATTATAAAATAAAAATTTTATAT-AATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAGTTA
64 ATTATAAAATAAAAAGTTTATATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTA
* *
2626581 TTGAATCTTAAGTTATTAATTGAGTTTTAAATAGTTTGGACTAAACCCATATATTA
129 TAGAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGACTAAACCCATATATTA
2626637 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
2626658 AAAATTTAAT
Statistics
Matches: 184, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
184 17 0.09
185 111 0.60
186 56 0.30
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAACAATTTATAACTAATTTAAATAATATATAAT
TATAAAATAAAAAGTTTATATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATA
GAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGACTAAACCCATATATTA
Found at i:2627503 original size:16 final size:17
Alignment explanation
Indices: 2627471--2627506 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2627461 ATGATTTGTA
2627471 TTATTTTAGTCCATGAC
1 TTATTTTAGTCCATGAC
*
2627488 TTATTTTA-TTCATGAC
1 TTATTTTAGTCCATGAC
2627504 TTA
1 TTA
2627507 CAAATTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (17 bp):
TTATTTTAGTCCATGAC
Found at i:2637522 original size:17 final size:19
Alignment explanation
Indices: 2637484--2637522 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2637474 TTTTGGTGCT
2637484 TATAGATTGTTATGAAAGA
1 TATAGATTGTTATGAAAGA
*
2637503 TATA-ATTGTTA-GAAATA
1 TATAGATTGTTATGAAAGA
2637520 TAT
1 TAT
2637523 GAAAATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (19 bp):
TATAGATTGTTATGAAAGA
Found at i:2641711 original size:22 final size:22
Alignment explanation
Indices: 2641683--2641725 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2641673 TTGAGGGTTA
2641683 CATAGGTCCTTCGGGACATATG
1 CATAGGTCCTTCGGGACATATG
2641705 CATAGGTCCTTCGGGACATAT
1 CATAGGTCCTTCGGGACATAT
2641726 TTCACATGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACATATG
Found at i:2643712 original size:18 final size:18
Alignment explanation
Indices: 2643689--2643723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2643679 ACTGAAAATT
*
2643689 TATCCCGAAGGACCACTA
1 TATCCCGAAAGACCACTA
2643707 TATCCCGAAAGACCACT
1 TATCCCGAAAGACCACT
2643724 CTTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (18 bp):
TATCCCGAAAGACCACTA
Found at i:2648711 original size:21 final size:23
Alignment explanation
Indices: 2648681--2648734 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
2648671 AAGTTCTGCG
*
2648681 GGTATTGATACCCTCCA-CATA-
1 GGTATCGATACCCTCCACCATAT
*
2648702 GGTATCGATA-CCTCTACCATAT
1 GGTATCGATACCCTCCACCATAT
2648724 GGTATCGATAC
1 GGTATCGATAC
2648735 TGTTCATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 10 0.36
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
GGTATCGATACCCTCCACCATAT
Found at i:2651952 original size:23 final size:21
Alignment explanation
Indices: 2651903--2651957 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2651893 CCGAAGTACC
*
2651903 ACATATATGTTCCACAAAATT
1 ACATATATGTCCCACAAAATT
2651924 ACATATATGTCCCACAAAATT
1 ACATATATGTCCCACAAAATT
2651945 ACATATATGTCCC
1 ACATATATGTCCC
2651958 GAAGGACCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (21 bp):
ACATATATGTCCCACAAAATT
Done.