Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 21
Found at i:3737984 original size:12 final size:12
Alignment explanation
Indices: 3737967--3737991 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3737957 ATATAATCCT
3737967 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3737979 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3737991 G
1 G
3737992 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3740324 original size:33 final size:34
Alignment explanation
Indices: 3740273--3740508 Score: 209
Period size: 33 Copynumber: 6.8 Consensus size: 34
3740263 CGGAAATTAC
*
3740273 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
3740306 AATCCCAAC-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* * * *
3740339 AATCGCAACGCGAAATGAAAATCACAACGAGAGAATCG-C
1 AATCGCAA--CG--ATGAAAATCGCAATGCGA-AAT-GAA
*
3740378 AATGCGGAA--ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACGATGAAAATCGCAATGCGAAATGAA
*
3740411 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
3740444 AATCGCAACGA-GAGAATCGCAACGCGGAAATG-A
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
3740477 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGA
3740509 TTCTCTCGTT
Statistics
Matches: 167, Mismatches: 18, Indels: 32
0.77 0.08 0.15
Matches are distributed among these distances:
32 6 0.04
33 96 0.57
34 22 0.13
35 3 0.02
37 3 0.02
38 26 0.16
39 6 0.04
40 5 0.03
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:3740337 original size:19 final size:19
Alignment explanation
Indices: 3740287--3740508 Score: 207
Period size: 19 Copynumber: 12.7 Consensus size: 19
3740277 GCAACGAGAG
3740287 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3740306 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3740320 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3740339 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3740358 AATCACAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3740372 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
3740392 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3740411 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3740425 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3740444 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
3740458 AATCGCAACGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
3740477 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3740496 AATCGCATTGCGA
1 AATCGCAATGCGA
3740509 TTCTCTCGTT
Statistics
Matches: 167, Mismatches: 13, Indels: 46
0.74 0.06 0.20
Matches are distributed among these distances:
14 41 0.25
15 3 0.02
16 5 0.03
17 9 0.05
18 7 0.04
19 88 0.53
20 14 0.08
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3740346 original size:52 final size:52
Alignment explanation
Indices: 3740287--3740508 Score: 267
Period size: 52 Copynumber: 4.2 Consensus size: 52
3740277 GCAACGAGAG
*
3740287 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAAAATCGCAATGCGAAATGAA
* * *
3740339 AATCGCAACGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGC-GAAATGAA
*
3740392 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
* *
3740444 AATCGCAA--CG--A-GAGAATCGCAACGCGGAAATGAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-GAGA--AAATCGCAATGCGAAATGAA
*
3740496 AATCGCATTGCGA
1 AATCGCAATGCGA
3740509 TTCTCTCGTT
Statistics
Matches: 151, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
47 10 0.07
48 1 0.01
49 1 0.01
50 5 0.03
52 81 0.54
53 51 0.34
54 2 0.01
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:3740430 original size:14 final size:14
Alignment explanation
Indices: 3740411--3740467 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3740401 GCGAAATGAA
3740411 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3740425 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3740444 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3740458 AATCGCAACG
1 AATCGCAACG
3740468 CGGAAATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3740566 original size:54 final size:52
Alignment explanation
Indices: 3740498--3740615 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 52
3740488 GAAATGAAAA
3740498 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
3740551 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
3740604 TCGCATTGCGAT
1 TCGCATTGCGAT
3740616 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
52 11 0.17
53 20 0.31
54 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:3740623 original size:19 final size:19
Alignment explanation
Indices: 3740517--3740615 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
3740507 GATTCTCTCG
3740517 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3740537 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
3740557 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3740571 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3740590 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3740609 TTGCGAT
1 TTGCGAT
3740616 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 6 0.08
18 3 0.04
19 26 0.36
20 26 0.36
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3740741 original size:14 final size:14
Alignment explanation
Indices: 3740722--3740758 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3740712 CATCAATTAC
3740722 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3740736 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3740750 ACAAATCAA
1 ACAAATCAA
3740759 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:3742722 original size:19 final size:19
Alignment explanation
Indices: 3742680--3742783 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
3742670 TAGTTTACTT
* *
3742680 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
** *
3742700 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAACCAAAA
*
3742719 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3742738 TCGCAACACGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3742757 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3742776 TCGCAACG
1 TCGCAACG
3742784 ACAGAATCGC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 61 0.84
20 12 0.16
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3742793 original size:14 final size:14
Alignment explanation
Indices: 3742774--3742830 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3742764 GCGAAACCAA
*
3742774 AATCGCAACGACAG
1 AATCGCAACGAAAG
3742788 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
3742805 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
3742821 AATCGCAACG
1 AATCGCAACG
3742831 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3742801 original size:33 final size:33
Alignment explanation
Indices: 3742715--3742847 Score: 149
Period size: 33 Copynumber: 3.9 Consensus size: 33
3742705 ACGCGAAATG
*
3742715 AGAATCGCAACGAGAAACCAAAATCGCAACACGAAACC
1 AGAATCGCAACGCGAAACCAAAATCGC-A-ACG--A-C
*
3742753 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
* ** *
3742786 AGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
**
3742819 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AGAATCGCAACGCGAAACCAAAATCGCAA
3742848 TGCGATTTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
33 57 0.66
34 1 0.01
36 3 0.03
37 1 0.01
38 25 0.29
ACGTcount: A:0.48, C:0.25, G:0.19, T:0.08
Consensus pattern (33 bp):
AGAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3742812 original size:19 final size:19
Alignment explanation
Indices: 3742788--3742852 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 19
3742778 GCAACGACAG
* *
3742788 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAACGAA
*
3742807 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAACGAA
*
3742821 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACGAA
*
3742840 AATCGCAATGCGA
1 AATCGCAACGCGA
3742853 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAACGAA
Found at i:3742864 original size:19 final size:19
Alignment explanation
Indices: 3742848--3742925 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
3742838 AAAATCGCAA
3742848 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3742867 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3742881 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
3742900 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3742919 TGCGATT
1 TGCGATT
3742926 CTCTCGTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.23
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 36 0.69
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3742909 original size:14 final size:14
Alignment explanation
Indices: 3742864--3742890 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3742854 TTTGGTTTCG
3742864 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
3742878 CGTTGCGATTTTG
1 CGTTGCGATTTTG
3742891 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3742933 original size:52 final size:53
Alignment explanation
Indices: 3742848--3742955 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 53
3742838 AAAATCGCAA
** * * *
3742848 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCGATTTT-GGTTTCGCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGCGT
*
3742900 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGTGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGCGT
3742953 TGC
1 TGC
3742956 AAAAGTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 38 0.78
53 11 0.22
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAAGTTTCGCGT
Found at i:3743214 original size:93 final size:93
Alignment explanation
Indices: 3743055--3743370 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
3743045 TCAGGGTATT
3743055 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3743120 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
3743148 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3743213 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
3743241 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3743306 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
3743334 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
3743371 AAGCAATCCA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:3745087 original size:20 final size:20
Alignment explanation
Indices: 3745056--3745162 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
3745046 TTTTGGTTGA
3745056 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
3745076 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3745096 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
3745115 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
3745130 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
3745149 AATGAAAATCGCAA
1 AATGAAAATCGCAA
3745163 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 30 0.41
20 17 0.23
21 12 0.16
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3745108 original size:21 final size:21
Alignment explanation
Indices: 3745054--3745118 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3745044 TCTTTTGGTT
3745054 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
3745075 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3745095 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
3745116 GAA
1 GAA
3745119 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:3745203 original size:21 final size:20
Alignment explanation
Indices: 3745174--3745249 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
3745164 GCGATTTTGG
*
3745174 TTTCGCGTTGCGATTTTCAGT
1 TTTCTCGTTGCGATTTTCA-T
**
3745195 TTTCTCGTTGCAGATAGTCAT
1 TTTCTCGTTGC-GATTTTCAT
*
3745216 TTTCACGTTGCGATTTTCAT
1 TTTCTCGTTGCGATTTTCAT
3745236 TTATCTCGTTGCGA
1 TT-TCTCGTTGCGA
3745250 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.20
21 31 0.67
22 6 0.13
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (20 bp):
TTTCTCGTTGCGATTTTCAT
Found at i:3745371 original size:33 final size:33
Alignment explanation
Indices: 3745329--3745399 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3745319 AATACTAACT
3745329 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3745362 TGAAAATCGCAACGAGAGAATTGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3745395 TGAAA
1 TGAAA
3745400 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3745804 original size:20 final size:20
Alignment explanation
Indices: 3745779--3745951 Score: 179
Period size: 20 Copynumber: 8.6 Consensus size: 20
3745769 CTTTAAAAAT
3745779 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3745799 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3745819 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3745840 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
**
3745860 CGTATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3745880 CGCGTTGCTATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * * *
3745900 CACGTTGCAATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3745920 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3745940 CGCGTTGCGATT
1 CGCGTTGCGATT
3745952 CTTGAAAATC
Statistics
Matches: 127, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
20 109 0.86
21 18 0.14
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3746394 original size:12 final size:12
Alignment explanation
Indices: 3746377--3746405 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3746367 GATTTATCCA
3746377 AAAAAAATTATT
1 AAAAAAATTATT
3746389 AAAAAAATTATT
1 AAAAAAATTATT
3746401 AAAAA
1 AAAAA
3746406 TATGAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAAAATTATT
Found at i:3746758 original size:24 final size:24
Alignment explanation
Indices: 3746731--3746785 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3746721 ATATATATAT
* * *
3746731 ATACCCGGCCCGATTCTCGGCCCA
1 ATACCCGACCCAATACTCGGCCCA
*
3746755 ATACCAGACCCAATACTCGGCCCA
1 ATACCCGACCCAATACTCGGCCCA
3746779 ATACCCG
1 ATACCCG
3746786 TTTAAATAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.44, G:0.16, T:0.15
Consensus pattern (24 bp):
ATACCCGACCCAATACTCGGCCCA
Found at i:3752867 original size:13 final size:13
Alignment explanation
Indices: 3752849--3752882 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3752839 CTATTCCATC
3752849 AAAATCATTAAAA
1 AAAATCATTAAAA
*
3752862 AAAATCATTAGAA
1 AAAATCATTAAAA
*
3752875 AATATCAT
1 AAAATCAT
3752883 CGAATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAATCATTAAAA
Found at i:3758415 original size:23 final size:21
Alignment explanation
Indices: 3758387--3758429 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
3758377 GATATAAAAA
3758387 TTAT-TTTTTATTAAATGTTTT
1 TTATATTTTTATTAAAT-TTTT
*
3758408 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
3758429 T
1 T
3758430 AAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:3758535 original size:17 final size:17
Alignment explanation
Indices: 3758513--3758557 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
3758503 ACCGATAAAT
3758513 CGATCCGGTTCACTGAC
1 CGATCCGGTTCACTGAC
*
3758530 CGATCCGATTCACTGAC
1 CGATCCGGTTCACTGAC
3758547 CGATCCGGTTC
1 CGATCCGGTTC
3758558 GCTCTGACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.18, C:0.36, G:0.22, T:0.24
Consensus pattern (17 bp):
CGATCCGGTTCACTGAC
Found at i:3759011 original size:26 final size:24
Alignment explanation
Indices: 3758959--3759011 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3758949 AATTGTTAAT
* *
3758959 TTAAAAATAAATATCATGTCAATA
1 TTAAAAATAAATATCATATCAACA
*
3758983 TTAAAAATTAAAATATCATATTAACA
1 TTAAAAA-T-AAATATCATATCAACA
3759009 TTA
1 TTA
3759012 TGTTAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 1 0.04
26 16 0.67
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (24 bp):
TTAAAAATAAATATCATATCAACA
Found at i:3761782 original size:28 final size:28
Alignment explanation
Indices: 3761751--3761804 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3761741 TATTAACTCC
3761751 TTTTTTTTAG-AACAAAAAGATCCTCTT
1 TTTTTTTTAGAAACAAAAAGATCCTCTT
* *
3761778 TTTTTTTTCGAAACAAAAATATCCTCT
1 TTTTTTTTAGAAACAAAAAGATCCTCT
3761805 GTAGATAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTTTTTTAGAAACAAAAAGATCCTCTT
Found at i:3762590 original size:14 final size:14
Alignment explanation
Indices: 3762571--3762601 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3762561 CAATTCTTAT
*
3762571 AAAAAAGAAGAAGA
1 AAAAAAGAAAAAGA
3762585 AAAAAAGAAAAAGA
1 AAAAAAGAAAAAGA
3762599 AAA
1 AAA
3762602 TAAGGAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:3764188 original size:30 final size:30
Alignment explanation
Indices: 3764152--3764212 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
3764142 ATATCAGATG
*
3764152 TGCATGGAAGCG-TGGATCTCTCGGCGTCTT
1 TGCATGGAAG-GTTGGATATCTCGGCGTCTT
3764182 TGCATGGAAGGTTGGATATCTCGGCGTCTT
1 TGCATGGAAGGTTGGATATCTCGGCGTCTT
3764212 T
1 T
3764213 AACGCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (30 bp):
TGCATGGAAGGTTGGATATCTCGGCGTCTT
Found at i:3764308 original size:34 final size:34
Alignment explanation
Indices: 3764265--3764349 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
3764255 TATGATTGAT
3764265 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
3764299 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
3764333 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
3764350 GCTGTGCATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:3764452 original size:23 final size:23
Alignment explanation
Indices: 3764426--3764469 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3764416 TGAGCAGGGG
3764426 CTGCACGTCTGCATATGGGGGTC
1 CTGCACGTCTGCATATGGGGGTC
*
3764449 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATATGGGGG
3764470 GCATGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.25, G:0.39, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATATGGGGGTC
Found at i:3764476 original size:23 final size:22
Alignment explanation
Indices: 3764422--3764476 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
3764412 GGGTTGAGCA
3764422 GGGGCTGCACGTCTGCATATGG
1 GGGGCTGCACGTCTGCATATGG
* *
3764444 GGGTCCTGCACGTCTGCATGTGG
1 GGG-GCTGCACGTCTGCATATGG
3764467 GGGGCATGCA
1 GGGGC-TGCA
3764477 ATTGTTGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.13, C:0.24, G:0.42, T:0.22
Consensus pattern (22 bp):
GGGGCTGCACGTCTGCATATGG
Found at i:3765220 original size:162 final size:161
Alignment explanation
Indices: 3764895--3765235 Score: 460
Period size: 162 Copynumber: 2.1 Consensus size: 161
3764885 TTGTAAAGTT
* *
3764895 TTAGGGACCGTTTTGTAAATTTAAGGAATTTAAGGAATAAGAGTAATTATTAAAAGTGCTATACT
1 TTAGGGATCGTTTTGTAAATTTAAGGAATTTAAGGAATAAGAGTAATTATAAAAAGTGCTATACT
3764960 ATGCGGAATTAGTATTAGTATGCTTAATTGGTTAAATTTGAAAGAATTTAAAATTAGGATTAAAT
66 ATGCGGAATTAGTATTAG-A---TTAATTGGTTAAATTTGAAAGAATTTAAAATTAGGATTAAAT
*
3765025 TGCTAAGTTTGAAAATGTTGAGAAACAAATAGTAA
127 TGCAAAGTTTGAAAATGTTGAGAAACAAATAGTAA
* * *
3765060 TTAGGGATCG-TTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGT-AAATTTAAGGAATTTAAGGAATAAGAGT-AATTATAAAAAG-TGCTAT
*
3765124 ACTATGCTTGAATTAGTATTA-A-T-ATTGGTTAAATTTGAAAGAATTTATAAATTTAGTGATTA
63 ACTATGC-GGAATTAGTATTAGATTAATTGGTTAAATTTGAAAGAATTTA-AAA-TTAG-GATTA
*
3765186 AATTGCAAAG-TTG-AAATGTTGAGAAGCAAATAGTAA
124 AATTGCAAAGTTTGAAAATGTTGAGAAACAAATAGTAA
*
3765222 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
3765236 ATATTTGATG
Statistics
Matches: 159, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
161 24 0.15
162 35 0.22
163 10 0.06
164 19 0.12
165 35 0.22
166 12 0.08
167 12 0.08
168 12 0.08
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (161 bp):
TTAGGGATCGTTTTGTAAATTTAAGGAATTTAAGGAATAAGAGTAATTATAAAAAGTGCTATACT
ATGCGGAATTAGTATTAGATTAATTGGTTAAATTTGAAAGAATTTAAAATTAGGATTAAATTGCA
AAGTTTGAAAATGTTGAGAAACAAATAGTAA
Found at i:3766908 original size:25 final size:25
Alignment explanation
Indices: 3766874--3766923 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3766864 ACGAAAAAAT
3766874 TTGGTAAACCCGAGAAACCAGAAGG
1 TTGGTAAACCCGAGAAACCAGAAGG
3766899 TTGGTAAACCCGAGAAACCAGAAGG
1 TTGGTAAACCCGAGAAACCAGAAGG
3766924 ACTGGGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.28, T:0.12
Consensus pattern (25 bp):
TTGGTAAACCCGAGAAACCAGAAGG
Found at i:3766961 original size:18 final size:18
Alignment explanation
Indices: 3766921--3766962 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3766911 AGAAACCAGA
*
3766921 AGGACTGGGAGGGGAGTG
1 AGGAGTGGGAGGGGAGTG
*
3766939 GGGAGTGGGAGTGGGAGT-
1 AGGAGTGGGAG-GGGAGTG
3766957 AGGAGT
1 AGGAGT
3766963 TCTTCTCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.21, C:0.02, G:0.62, T:0.14
Consensus pattern (18 bp):
AGGAGTGGGAGGGGAGTG
Found at i:3767452 original size:41 final size:38
Alignment explanation
Indices: 3767404--3767493 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
3767394 ATATATTTAC
* *
3767404 TATTATTATATCAGTAAATATAAATC-TTAAAGTCAAGTGAT
1 TATTATTAAATCA--AAA-ATAAATCATTAAA-TCAAGTAAT
* *
3767445 TATTATTAAATCAAAAATTAATCATTAAATTAAGTAAT
1 TATTATTAAATCAAAAATAAATCATTAAATCAAGTAAT
3767483 TATTATTAAAT
1 TATTATTAAAT
3767494 TATTAAATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 24 0.55
39 8 0.18
41 12 0.27
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (38 bp):
TATTATTAAATCAAAAATAAATCATTAAATCAAGTAAT
Found at i:3767490 original size:19 final size:19
Alignment explanation
Indices: 3767438--3767495 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
3767428 TCTTAAAGTC
* *
3767438 AAGTGATTATTATTAAATC
1 AAGTAATTATTATTAAATT
* *
3767457 AA-AAATTAATCATTAAATT
1 AAGTAATT-ATTATTAAATT
3767476 AAGTAATTATTATTAAATT
1 AAGTAATTATTATTAAATT
3767495 A
1 A
3767496 TTAAATCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 3 0.10
19 24 0.77
20 4 0.13
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AAGTAATTATTATTAAATT
Found at i:3767506 original size:22 final size:21
Alignment explanation
Indices: 3767487--3767843 Score: 96
Period size: 23 Copynumber: 16.8 Consensus size: 21
3767477 AGTAATTATT
3767487 ATTAA-ATTATTAAATCATTA
1 ATTAATATTATTAAATCATTA
3767507 ATTAATTATTATTAAATCATTA
1 ATTAA-TATTATTAAATCATTA
* * *
3767529 AATCATA--ATCAAATCATTA
1 ATTAATATTATTAAATCATTA
* * * * *
3767548 AATCAT-TAAAGT-AATTATT-
1 ATTAATAT-TATTAAATCATTA
*
3767567 ATTAAAGCATTAAAGTTAAATCATTAA
1 ATT-AA-TATT--A-TTAAATCATT-A
*
3767594 AGTAATTATTATTAAATCATTAA
1 ATTAA-TATTATTAAATCATT-A
* *
3767617 AGTAATTATTATTAAAGCATTAA
1 ATTAA-TATTATTAAATCATT-A
* *
3767640 AGTAATTATTATTAAAGCATTAA
1 ATTAA-TATTATTAAATCATT-A
*
3767663 AGTTAA-ATCATTAAATC----
1 A-TTAATATTATTAAATCATTA
3767680 ATTAA-A--ATTAAATCATTAA
1 ATTAATATTATTAAATCATT-A
*
3767699 AGTAATTATTATTAAATCAT--
1 ATTAA-TATTATTAAATCATTA
3767719 --TAA-A--ATTAAATCATTAA
1 ATTAATATTATTAAATCATT-A
* *
3767736 AGTAATTATTATTAAATTATTAA
1 ATTAA-TATTATTAAATCATT-A
*
3767759 AATAATCATTATTAAATCATTAA
1 ATTAAT-ATTATTAAATCATT-A
3767782 AGTTAAATTTATTATTAAATCATTAA
1 A-TT-AA--TATTATTAAATCATT-A
*
3767808 AGTTAA-ATAATTAAAT--TTA
1 A-TTAATATTATTAAATCATTA
*
3767827 AATAATTATTATTAAAT
1 ATTAA-TATTATTAAAT
3767844 ATGTACTCGA
Statistics
Matches: 270, Mismatches: 27, Indels: 80
0.72 0.07 0.21
Matches are distributed among these distances:
14 18 0.07
16 6 0.02
17 1 0.00
18 6 0.02
19 28 0.10
20 23 0.09
21 5 0.02
22 38 0.14
23 101 0.37
24 6 0.02
25 10 0.04
26 25 0.09
27 3 0.01
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (21 bp):
ATTAATATTATTAAATCATTA
Found at i:3767513 original size:30 final size:30
Alignment explanation
Indices: 3767473--3767617 Score: 124
Period size: 30 Copynumber: 4.9 Consensus size: 30
3767463 TAATCATTAA
* *
3767473 ATTAAGTAATTATTATTAAATTATTAAATC
1 ATTAATTAATTATTATTAAATCATTAAATC
3767503 ATTAATTAATTATTATTAAATCATTAAATC
1 ATTAATTAATTATTATTAAATCATTAAATC
* * *
3767533 A-TAATCAA--ATCATTAAATCATTAAAGTA
1 ATTAATTAATTATTATTAAATCATTAAA-TC
** *
3767561 ATT-ATT-ATTAAAGCATTAAA--GTTAAATC
1 ATTAATTAATT--ATTATTAAATCATTAAATC
*
3767589 ATTAAAGTAATTATTATTAAATCATTAAA
1 ATT-AATTAATTATTATTAAATCATTAAA
3767618 GTAATTATTA
Statistics
Matches: 91, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
27 17 0.19
28 8 0.09
29 19 0.21
30 31 0.34
31 16 0.18
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
ATTAATTAATTATTATTAAATCATTAAATC
Found at i:3767601 original size:23 final size:23
Alignment explanation
Indices: 3767582--3767685 Score: 158
Period size: 23 Copynumber: 4.6 Consensus size: 23
3767572 AGCATTAAAG
3767582 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
3767605 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
*
3767628 TTAAAGCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
* *
3767651 TTAAAGCATTAAAGTTAA--ATCA
1 TTAAATCATTAAAG-TAATTATTA
3767673 TTAAATCATTAAA
1 TTAAATCATTAAA
3767686 ATTAAATCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
22 15 0.19
23 59 0.77
24 3 0.04
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (23 bp):
TTAAATCATTAAAGTAATTATTA
Found at i:3767712 original size:23 final size:22
Alignment explanation
Indices: 3767658--3767722 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
3767648 TTATTAAAGC
* *
3767658 ATTAAAGTTAAATCATTAAATC
1 ATTAAAATTAAATCATTAAATA
3767680 ATTAAAATTAAATCATTAAAGTA
1 ATTAAAATTAAATCATTAAA-TA
**
3767703 ATTATTATTAAATCATTAAA
1 ATTAAAATTAAATCATTAAA
3767723 ATTAAATCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
22 19 0.50
23 19 0.50
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (22 bp):
ATTAAAATTAAATCATTAAATA
Found at i:3767714 original size:142 final size:148
Alignment explanation
Indices: 3767518--3767823 Score: 480
Period size: 142 Copynumber: 2.1 Consensus size: 148
3767508 TTAATTATTA
*
3767518 TTAAATCATTAAATCATAATCAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGT
1 TTAAATCATTAAATCAT-ATCAAA-CATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAAT
* *
3767583 TAAATCATTAAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAG-T-AA-
64 TAAATCATTAAAGTAATTATTATTAAATCATTAAAATAATCATTATTAAAGCATTAAAGTTAAAT
3767645 TTATTATTAAAGCATTAAAG
129 TTATTATTAAAGCATTAAAG
*
3767665 TTAAATCATTAAATCAT-T-AAA-ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTA
1 TTAAATCATTAAATCATATCAAACATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTA
* *
3767727 AATCATTAAAGTAATTATTATTAAATTATTAAAATAATCATTATTAAATCATTAAAGTTAAATTT
66 AATCATTAAAGTAATTATTATTAAATCATTAAAATAATCATTATTAAAGCATTAAAGTTAAATTT
*
3767792 ATTATTAAATCATTAAAG
131 ATTATTAAAGCATTAAAG
*
3767810 TTAAATAATTAAAT
1 TTAAATCATTAAAT
3767824 TTAAATAATT
Statistics
Matches: 148, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
142 92 0.62
143 1 0.01
144 5 0.03
145 33 0.22
147 17 0.11
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (148 bp):
TTAAATCATTAAATCATATCAAACATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTA
AATCATTAAAGTAATTATTATTAAATCATTAAAATAATCATTATTAAAGCATTAAAGTTAAATTT
ATTATTAAAGCATTAAAG
Found at i:3767734 original size:119 final size:125
Alignment explanation
Indices: 3767544--3767789 Score: 144
Period size: 119 Copynumber: 2.1 Consensus size: 125
3767534 TAATCAAATC
* ** *
3767544 ATTAAATCATTAAAGTAATTATTATTAAAGCATT-AAAGTTAAATCATTAAAGTAA-T-T-AT-T
1 ATTAAATAATTAAAGTAATTAAAATTAAATCATTAAAAG-TAAATCATTAAAGTAATTATAATAT
* * * * * *
3767604 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAG-TAATTATTATTAAAGCATTAAA
65 ATTAAAGCATTAAAATAATCATTATTAAAGCATTAAAGTTAAATATCATTAAATCATTAAA
* * * * *
3767664 GTTAAATCATTAAA-TCATTAAAATTAAATCATT-AAAGTAATTATTATTAAA-TCA-T-TAA-A
1 ATTAAATAATTAAAGTAATTAAAATTAAATCATTAAAAGTAA--ATCATTAAAGTAATTATAATA
* * * ** * *
3767723 -ATTAAATCATTAAAGTAATTATTATTAAATTATTAAA-AT-AATCATTATTAAATCATTAAA
64 TATTAAAGCATTAAAATAATCATTATTAAAGCATTAAAGTTAAAT-ATCATTAAATCATTAAA
*
3767783 GTTAAAT
1 ATTAAAT
3767790 TTATTATTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
118 5 0.05
119 82 0.75
120 22 0.20
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (125 bp):
ATTAAATAATTAAAGTAATTAAAATTAAATCATTAAAAGTAAATCATTAAAGTAATTATAATATA
TTAAAGCATTAAAATAATCATTATTAAAGCATTAAAGTTAAATATCATTAAATCATTAAA
Found at i:3767743 original size:23 final size:23
Alignment explanation
Indices: 3767723--3767843 Score: 135
Period size: 23 Copynumber: 5.3 Consensus size: 23
3767713 AATCATTAAA
3767723 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* * *
3767746 ATTAAATTATTAAAATAATCATT
1 ATTAAATCATTAAAGTAATTATT
3767769 ATTAAATCATTAAAGTTAAATTTATT
1 ATTAAATCATTAAAG-T-AA-TTATT
*
3767795 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAAG-TAATTATT
3767817 ATTAAAT--TTAAA-TAATTATT
1 ATTAAATCATTAAAGTAATTATT
3767837 ATTAAAT
1 ATTAAAT
3767844 ATGTACTCGA
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.04
20 14 0.16
22 9 0.11
23 33 0.39
24 1 0.01
25 4 0.05
26 21 0.25
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTAAATCATTAAAGTAATTATT
Found at i:3767761 original size:37 final size:37
Alignment explanation
Indices: 3767548--3767699 Score: 144
Period size: 37 Copynumber: 3.9 Consensus size: 37
3767538 CAAATCATTA
* *
3767548 AATCATTAAAGTAATTATTATTAAAGCATTAAAGTTA
1 AATCATTAAAGTAATTATTATTAAATCATTAAAATTA
3767585 AATCATTAAAGTAATTATTATTAAATCATTAAAGTAATTATTATTA
1 AATCATTAAAGTAATTATTATTAAATCA-T----TAA--A--ATTA
* * *
3767631 AAGCATTAAAGTAATTATTATTAAAGCATTAAAGTTA
1 AATCATTAAAGTAATTATTATTAAATCATTAAAATTA
* **
3767668 AATCATTAAA-TCATTAAAATTAAATCATTAAA
1 AATCATTAAAGTAATTATTATTAAATCATTAAA
3767700 GTAATTATTA
Statistics
Matches: 96, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
36 18 0.19
37 39 0.41
38 1 0.01
39 1 0.01
41 3 0.03
42 3 0.03
44 1 0.01
45 1 0.01
46 29 0.30
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (37 bp):
AATCATTAAAGTAATTATTATTAAATCATTAAAATTA
Found at i:3767841 original size:14 final size:14
Alignment explanation
Indices: 3767731--3767844 Score: 68
Period size: 14 Copynumber: 8.6 Consensus size: 14
3767721 AAATTAAATC
3767731 ATTAAAGTAATTATT
1 ATTAAA-TAATTATT
3767746 ATT--A-AATTATT
1 ATTAAATAATTATT
*
3767757 A--AAATAATCATT
1 ATTAAATAATTATT
* *
3767769 ATTAAATCATTA-A
1 ATTAAATAATTATT
3767782 AGTTAAAT--TTATT
1 A-TTAAATAATTATT
* *
3767795 ATTAAATCATTA-A
1 ATTAAATAATTATT
*
3767808 AGTTAAATAATTA-A
1 A-TTAAATAATTATT
3767822 ATTTAAATAATTATT
1 A-TTAAATAATTATT
3767837 ATTAAATA
1 ATTAAATA
3767845 TGTACTCGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
11 9 0.11
12 16 0.20
13 4 0.05
14 46 0.58
15 4 0.05
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTAAATAATTATT
Found at i:3771128 original size:14 final size:14
Alignment explanation
Indices: 3771109--3771136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3771099 GCATGCAATA
3771109 AATCTCACGCTTCG
1 AATCTCACGCTTCG
3771123 AATCTCACGCTTCG
1 AATCTCACGCTTCG
3771137 GCCCCAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (14 bp):
AATCTCACGCTTCG
Found at i:3773485 original size:2 final size:2
Alignment explanation
Indices: 3773480--3773552 Score: 91
Period size: 2 Copynumber: 37.5 Consensus size: 2
3773470 ATATTACGTT
3773480 TA 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 TA TA
*
3773521 TA TCA T- TA GTA T- TA T- TA TA TA TA TA TT TA TA T
1 TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
3773553 TTCCTATTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
1 4 0.06
2 55 0.87
3 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3773723 original size:38 final size:40
Alignment explanation
Indices: 3773657--3773744 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 40
3773647 TATATATATA
*
3773657 CTTTTACTTTTTATATTCTACTTATTTAT-TTATCTAT-TTT
1 CTTTTA-TTTTTATATTCTACTTATTTATCTT-TCTATCTTC
3773697 CTTTCTATTTTTAT-TCTCTA-TT-TTTATCTTTCTATCTTC
1 CTTT-TATTTTTATAT-TCTACTTATTTATCTTTCTATCTTC
3773736 CTTTTATTT
1 CTTTTATTT
3773745 GCTTATTCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
38 15 0.35
39 11 0.26
40 15 0.35
41 2 0.05
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (40 bp):
CTTTTATTTTTATATTCTACTTATTTATCTTTCTATCTTC
Found at i:3773774 original size:17 final size:17
Alignment explanation
Indices: 3773737--3773776 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3773727 TCTATCTTCC
3773737 TTTTATTTGCTTATTCA
1 TTTTATTTGCTTATTCA
3773754 -TTTATTTGCATTA-TCA
1 TTTTATTTGC-TTATTCA
3773770 TTTTATT
1 TTTTATT
3773777 CTTATTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTATTTGCTTATTCA
Found at i:3773844 original size:26 final size:26
Alignment explanation
Indices: 3773815--3773870 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3773805 GTGTTATTAT
* * *
3773815 TTTTCTTCATTTTATTTATTTA-TGTA
1 TTTTATTCATTTT-TATATTTACTCTA
3773841 TTTTATTCATTTTTATATTTACTCTA
1 TTTTATTCATTTTTATATTTACTCTA
3773867 TTTT
1 TTTT
3773871 TTATCACTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTATTCATTTTTATATTTACTCTA
Found at i:3777172 original size:24 final size:24
Alignment explanation
Indices: 3777120--3777172 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
3777110 GCATTTCTTG
*
3777120 CATTTTATATTTCATGTTTGTTTT
1 CATTTTATATTTCATGTTTGTTTA
*
3777144 TATTTTATATTTTCCATG-TT-TTTA
1 CATTTTATA-TTT-CATGTTTGTTTA
3777168 CATTT
1 CATTT
3777173 GTATTAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
24 15 0.62
25 5 0.21
26 4 0.17
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (24 bp):
CATTTTATATTTCATGTTTGTTTA
Found at i:3784086 original size:17 final size:17
Alignment explanation
Indices: 3784064--3784104 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
3784054 AAGAAAAAGA
3784064 AAAAAACAAAAATGAGG
1 AAAAAACAAAAATGAGG
3784081 AAAAAACAAAAATGAGG
1 AAAAAACAAAAATGAGG
3784098 AAAAAAC
1 AAAAAAC
3784105 GTTTAGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAACAAAAATGAGG
Found at i:3785367 original size:106 final size:106
Alignment explanation
Indices: 3785180--3785547 Score: 596
Period size: 106 Copynumber: 3.5 Consensus size: 106
3785170 ACGAAGGGGC
*
3785180 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGC-AAAGGATATTGGACTCAAGACAGCACAATC
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAA-GATATTGGACTCAAGACAGCACAAGC
*
3785244 TCAACTTCACGGCGAAGGGGAGGCTGACTGTCAACAAATAAT
65 TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAAT
* * *
3785286 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTGGACTCAATACAACACAAGCT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAGCACAAGCT
*
3785351 CAACTTCACGGTGAAGGGGCGGCTGACTGTCAACAAATAAT
66 CAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAAT
* *
3785392 TTCCCGACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAGCACAAGCT
3785457 CAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAAT
66 CAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAAT
* * * *
3785498 TTCCC-AGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 TTCCCAACTT-CAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTC
3785548 GGAGCAATAC
Statistics
Matches: 245, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
105 3 0.01
106 239 0.98
107 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (106 bp):
TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAGCACAAGCT
CAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAAT
Found at i:3787771 original size:38 final size:39
Alignment explanation
Indices: 3787724--3787803 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
3787714 TACTTTTACT
* *
3787724 TTTTATATTCTACT-TATTTATATATCTATTTTCTTTTTA
1 TTTTATATTCT-CTATATTTATATATCTATCTTCCTTTTA
* * *
3787763 TTTT-TATTCTCTATTTTTATCTTTCTATCTTCCTTTTA
1 TTTTATATTCTCTATATTTATATATCTATCTTCCTTTTA
3787801 TTT
1 TTT
3787804 GCTTTATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 2 0.06
38 29 0.83
39 4 0.11
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (39 bp):
TTTTATATTCTCTATATTTATATATCTATCTTCCTTTTA
Found at i:3787834 original size:17 final size:18
Alignment explanation
Indices: 3787796--3787836 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3787786 TCTATCTTCC
*
3787796 TTTTATTTGCTTTATTCA
1 TTTTATTTGCATTATTCA
3787814 -TTTATTTGCATTA-TCA
1 TTTTATTTGCATTATTCA
3787830 TTTTATT
1 TTTTATT
3787837 ATTATTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTATTTGCATTATTCA
Found at i:3787904 original size:26 final size:26
Alignment explanation
Indices: 3787875--3787930 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3787865 GTGTTATTAT
* * *
3787875 TTTTCTTCATTTTATTTATTTA-TGTA
1 TTTTATTCATTTT-TATATTTACTCTA
3787901 TTTTATTCATTTTTATATTTACTCTA
1 TTTTATTCATTTTTATATTTACTCTA
3787927 TTTT
1 TTTT
3787931 TTATCACTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTATTCATTTTTATATTTACTCTA
Found at i:3794624 original size:17 final size:16
Alignment explanation
Indices: 3794596--3794650 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
3794586 CTGGAATGTT
*
3794596 TCTGAGGGAATTGGAA
1 TCTGAAGGAATTGGAA
*
3794612 TCTGTAAGGAATTGAAA
1 TCTG-AAGGAATTGGAA
*
3794629 TCTGAAGGAATTAGAA
1 TCTGAAGGAATTGGAA
3794645 TCTGAA
1 TCTGAA
3794651 TCTGAATCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 20 0.59
17 14 0.41
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
TCTGAAGGAATTGGAA
Found at i:3797717 original size:17 final size:17
Alignment explanation
Indices: 3797695--3797728 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3797685 TCCAACCACA
3797695 GAAAGAACTCCACTTCG
1 GAAAGAACTCCACTTCG
3797712 GAAAGAACTCCACTTCG
1 GAAAGAACTCCACTTCG
3797729 ATGAACATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAGAACTCCACTTCG
Found at i:3798940 original size:20 final size:21
Alignment explanation
Indices: 3798905--3798963 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
3798895 TTAAATTAAA
3798905 ATTATTAAA-ATAATTATTATT
1 ATTATTAAATAT-ATTATTATT
*
3798926 A-TATTATATATATTA-TATT
1 ATTATTAAATATATTATTATT
3798945 ATTATTAAATATATTATTA
1 ATTATTAAATATATTATTA
3798964 CAAGGCCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTAAATATATTATTATT
Found at i:3799414 original size:14 final size:14
Alignment explanation
Indices: 3799373--3799416 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
3799363 GAAAGAGGGG
*
3799373 ACGGACGACAACAG
1 ACGGACGACAACAA
3799387 ACGGACGACAACAA
1 ACGGACGACAACAA
*
3799401 ACGGACAACAACAA
1 ACGGACGACAACAA
3799415 AC
1 AC
3799417 AGAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.50, C:0.30, G:0.20, T:0.00
Consensus pattern (14 bp):
ACGGACGACAACAA
Found at i:3807631 original size:19 final size:19
Alignment explanation
Indices: 3807595--3807634 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3807585 ATATAATATT
*
3807595 TATTTTATAATTATTTTTA
1 TATTTTATAATTAATTTTA
3807614 TATTTTA-AATTAAATTTTA
1 TATTTTATAATT-AATTTTA
3807633 TA
1 TA
3807635 ATAACTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATAATTAATTTTA
Found at i:3807873 original size:124 final size:124
Alignment explanation
Indices: 3807640--3807876 Score: 359
Period size: 124 Copynumber: 1.9 Consensus size: 124
3807630 TTATAATAAC
*
3807640 TATAAATTTTAAAATAAAAAATAACATAAATAATTAAACAAATTTAATATTTTAAATTGTAATTG
1 TATAAATTTTAAAATAAAAAATAACATAAATAATTAAACAAATCTAATATTTTAAATTGTAATTG
* * * *
3807705 ATTAAAGATTTACAATAAAAATAAATTAAAATTTCTAAATTTTAAAATATAAAAATTAT
66 ATGAAAAATTTACAATAAAAATAAATTAAAAATTCTAAAGTTTAAAATATAAAAATTAT
* * * *
3807764 TATAAATTTTCAAATAAAATATCACATAAATAATTAAATAAATCTAATATTTTAAATTGTAATTG
1 TATAAATTTTAAAATAAAAAATAACATAAATAATTAAACAAATCTAATATTTTAAATTGTAATTG
* *
3807829 ATGAAAAATTTACAATAAAAATAATTTAAAAAATTGT-AAGTTTAAAAT
66 ATGAAAAATTTACAATAAAAATAAATT-AAAAATTCTAAAGTTTAAAAT
3807877 TTAATTTAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
124 94 0.93
125 7 0.07
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (124 bp):
TATAAATTTTAAAATAAAAAATAACATAAATAATTAAACAAATCTAATATTTTAAATTGTAATTG
ATGAAAAATTTACAATAAAAATAAATTAAAAATTCTAAAGTTTAAAATATAAAAATTAT
Found at i:3807905 original size:124 final size:122
Alignment explanation
Indices: 3807652--3807911 Score: 310
Period size: 124 Copynumber: 2.1 Consensus size: 122
3807642 TAAATTTTAA
* * *
3807652 AATAAAAAATAACATAAATAATTAAACAAATTTAATATTTTAAATTGTAATTGATTAAAGATTTA
1 AATAAAAAATAACATAAATAATTAAACAAATCTAATATTTTAAATTGTAATTGATGAAAAATTTA
* * * * *
3807717 CAATAAAAATAAATTAAAATTTCTAAATTTTAAAATATAAAAATTATTATAAATTTT
66 CAATAAAAATAAATTAAAAATTCTAAAGTTTAAAATATAAAAAATATTAAAAATATT
* * *
3807774 CAAATAAAATATCACATAAATAATTAAATAAATCTAATATTTTAAATTGTAATTGATGAAAAATT
1 --AATAAAAAATAACATAAATAATTAAACAAATCTAATATTTTAAATTGTAATTGATGAAAAATT
* * *
3807839 TACAATAAAAATAATTTAAAAAATTGT-AAGTTTAAAATTTAATTTAAAATA-TAAAAATAATT
64 TACAATAAAAATAAATT-AAAAATTCTAAAGTTTAAAATATAA---AAAATATTAAAAAT-ATT
3807901 -ATAAAAAATAA
1 AATAAAAAATAA
3807912 ATATTATATT
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
124 95 0.83
125 7 0.06
126 6 0.05
127 7 0.06
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (122 bp):
AATAAAAAATAACATAAATAATTAAACAAATCTAATATTTTAAATTGTAATTGATGAAAAATTTA
CAATAAAAATAAATTAAAAATTCTAAAGTTTAAAATATAAAAAATATTAAAAATATT
Found at i:3809226 original size:30 final size:30
Alignment explanation
Indices: 3809192--3809276 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
3809182 TTGTAACCTG
* * * *
3809192 AAAATATATTTTATTCTTATTTTAATTTTT
1 AAAATATAATTTATTCTTATCTTAAATTTA
* * * *
3809222 AAAATACAGTTTAATATTATCTTAAATTTA
1 AAAATATAATTTATTCTTATCTTAAATTTA
*
3809252 AAAATATAATTTATTCTTAACTTAA
1 AAAATATAATTTATTCTTATCTTAA
3809277 CTTAAATATT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (30 bp):
AAAATATAATTTATTCTTATCTTAAATTTA
Found at i:3809374 original size:30 final size:29
Alignment explanation
Indices: 3809304--3809685 Score: 238
Period size: 30 Copynumber: 12.8 Consensus size: 29
3809294 TATTATGACA
* * *
3809304 ATATTTTAAATTTAAGATAAAAATATAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
*
3809333 ATAGTTTTTTGTAGTTAAGATAAAAATAAAAT
1 ATA--TTTTT-AAGTTAAGATAAAAATAAAAT
*
3809365 ATATTTTT--G-T-AG-TTAAAATAAAA-
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* *
3809388 ATATATTTTAAGTTAAGATAAGAATAAAAG
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
* * * *
3809418 ATATGTTTTAAGTTAAAATAAGAATTAATT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
* * * ** *
3809448 ATATTTAATAATTTAAGATAAGAATTGAGT
1 ATATTT-TTAAGTTAAGATAAAAATAAAAT
* * * * *
3809478 ATATTTAATAATTTAAGTTAATAATATAAT
1 ATATTT-TTAAGTTAAGATAAAAATAAAAT
* * * *
3809508 TTA-TGTAATAGATTAAGATAAGAATAAAAT
1 ATATTTTTA-AG-TTAAGATAAAAATAAAAT
* * *
3809538 ATCTTTTTTTAAAATTAAGATAAAGATTAAAAT
1 A--TATTTTT-AAGTTAAGATAAA-AATAAAAT
*
3809571 ATATTTTTAAGTTAAAATAAAAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* * *
3809600 ATATTTTTAGGTTAAGACAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* *
3809629 ATATTTAATAAGTTAATATAAAAAATAAAAT
1 ATATTT-TTAAGTTAAGAT-AAAAATAAAAT
3809660 ATATTTTTTAATGTTAAGATATAAAA
1 ATA-TTTTTAA-GTTAAGATA-AAAA
3809686 ACTAATTTAA
Statistics
Matches: 278, Mismatches: 52, Indels: 43
0.75 0.14 0.12
Matches are distributed among these distances:
23 4 0.01
24 14 0.05
25 2 0.01
26 2 0.01
27 2 0.01
28 3 0.01
29 54 0.19
30 113 0.41
31 27 0.10
32 45 0.16
33 11 0.04
34 1 0.00
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.40
Consensus pattern (29 bp):
ATATTTTTAAGTTAAGATAAAAATAAAAT
Found at i:3809401 original size:23 final size:25
Alignment explanation
Indices: 3809355--3809413 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
3809345 AGTTAAGATA
*
3809355 AAAAT-AAAATATATTTTTGTAGTT
1 AAAATAAAAATATATTTTTGAAGTT
3809379 AAAATAAAAATATA-TTTT-AAGTT
1 AAAATAAAAATATATTTTTGAAGTT
* *
3809402 AAGATAAGAATA
1 AAAATAAAAATA
3809414 AAAGATATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.45
24 9 0.29
25 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.37
Consensus pattern (25 bp):
AAAATAAAAATATATTTTTGAAGTT
Found at i:3809630 original size:27 final size:29
Alignment explanation
Indices: 3809565--3809676 Score: 127
Period size: 29 Copynumber: 3.7 Consensus size: 29
3809555 AGATAAAGAT
*
3809565 TAAAATATATTTTTAAGTTAAAATAAAAA
1 TAAAATATATTTTTAAGTTAAAACAAAAA
* * *
3809594 TAAAATATATTTTTAGGTTAAGACAAGAA
1 TAAAATATATTTTTAAGTTAAAACAAAAA
*
3809623 TAAAATATATTTAATAAGTTAATATA-AAAAA
1 TAAAATATATTT-TTAAGTTAA-A-ACAAAAA
3809654 TAAAATATATTTTTTAATGTTAA
1 TAAAATATA-TTTTTAA-GTTAA
3809677 GATATAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 37 0.54
30 7 0.10
31 16 0.23
32 9 0.13
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (29 bp):
TAAAATATATTTTTAAGTTAAAACAAAAA
Found at i:3809684 original size:58 final size:54
Alignment explanation
Indices: 3809560--3809685 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 54
3809550 AATTAAGATA
*
3809560 AAGAT-TAAAATATATTTTTAAGTTAAAATAAAAATAAAATATATTTTTAGGTT
1 AAGATATAAAATATATTTATAAGTTAAAATAAAAATAAAATATATTTTTAGGTT
* * *
3809613 AAGACAAGAATAAAATATATTTAATAAGTTAATATAAAAAATAAAATATATTTTTTAATGTT
1 AAG---A-TATAAAATATATTT-ATAAGTTAAAAT-AAAAATAAAATATA-TTTTT-AGGTT
3809675 AAGATATAAAA
1 AAGATATAAAA
3809686 ACTAATTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
53 3 0.05
56 1 0.02
58 18 0.31
59 11 0.19
60 14 0.24
61 5 0.08
62 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (54 bp):
AAGATATAAAATATATTTATAAGTTAAAATAAAAATAAAATATATTTTTAGGTT
Found at i:3809728 original size:20 final size:20
Alignment explanation
Indices: 3809667--3809729 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
3809657 AATATATTTT
3809667 TTAATGTTAAGATATAAAA-A
1 TTAA-GTTAAGATATAAAATA
* * * *
3809687 CTAATTTAATATAT-GAAT-
1 TTAAGTTAAGATATAAAATA
3809705 TTAAGTTAAGATATAAAATA
1 TTAAGTTAAGATATAAAATA
3809725 TTAAG
1 TTAAG
3809730 AATTTAAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 13 0.41
19 11 0.34
20 8 0.25
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (20 bp):
TTAAGTTAAGATATAAAATA
Found at i:3823290 original size:15 final size:15
Alignment explanation
Indices: 3823270--3823298 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3823260 TATTTACACT
3823270 GGTGTAAGTTAGTTC
1 GGTGTAAGTTAGTTC
3823285 GGTGTAAGTTAGTT
1 GGTGTAAGTTAGTT
3823299 GGGAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.34, T:0.41
Consensus pattern (15 bp):
GGTGTAAGTTAGTTC
Found at i:3823847 original size:15 final size:15
Alignment explanation
Indices: 3823827--3823856 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3823817 TTATTTACAC
3823827 CGGTGTAAGTTAGTT
1 CGGTGTAAGTTAGTT
3823842 CGGTGTAAGTTAGTT
1 CGGTGTAAGTTAGTT
3823857 GGGAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (15 bp):
CGGTGTAAGTTAGTT
Found at i:3824230 original size:557 final size:558
Alignment explanation
Indices: 3823174--3824291 Score: 2130
Period size: 557 Copynumber: 2.0 Consensus size: 558
3823164 TTAACGTATT
*
3823174 AACATGGGTGTAAGTTAGTTATTTTTCCCTCAAGCTTTCCTGTTTAACGTGTCAAATACTTGAAA
1 AACATGGGTGTAAGTTAGTTATTTTTCCCTCAAGCTTTCCTATTTAACGTGTCAAATACTTGAAA
*
3823239 TAAAAAAATATTATTAGAACTTATTTACACTGGTGTAAGTTAGTTCGGTGTAAGTTAGTTGGGAA
66 TAAAAAAATATTATTAGAACTTATTTACACCGGTGTAAGTTAGTTCGGTGTAAGTTAGTTGGGAA
3823304 AACAAAATAAACCCTTATTTCATCAAGAAATTGTCTTAATGTGACAATAAGGTTTGTGATGTTAT
131 AACAAAATAAACCCTTATTTCATCAAGAAATTGTCTTAATGTGACAATAAGGTTTGTGATGTTAT
* *
3823369 CCAAACTTCATATGGTCTATCATGTTTTTCAGTGGCTTTTTTTTCTTTTCGATTTCGTTCATGAT
196 CCAAACTTCATATGGTCTATCATGTCTTTCAGTGGCTTTTTTTTCTTTTCGATTGCGTTCATGAT
*
3823434 ATGTTGAAAATGATTTTTTATGATTCTTCTACATGAGTCTGATACCTCTCATGAAGATAAACACA
261 ATGTTGAAAATGATTTTTTATGATTCTTCTACAGGAGTCTGATACCTCTCATGAAGATAAACACA
*
3823499 AATGCTCTCCACAAGCTTGGCAGACTAATGGAACCCAGCATACAGCTGAGGAGATGTTGGATGTT
326 AATGCTCCCCACAAGCTTGGCAGACTAATGGAACCCAGCATACAGCTGAGGAGATGTTGGATGTT
3823564 ATATCTAATGGATCTTGTAAGGAATCAAATACTGAAACAACTACTGAGATGTGTCACCGTGTTTT
391 ATATCTAATGGATCTTGTAAGGAATCAAATACTGAAACAACTACTGAGATGTGTCACCGTGTTTT
*
3823629 CTTTGATGTTTTAATTTCTGAAAAGTTCATGTATCTGTATAAGCTTCTAATTGACAATTTCCAAG
456 CTTTGATGTTTTAATTTCTGAAAAGTTCACGTATCTGTATAAGCTTCTAATTGACAATTTCCAAG
3823694 GGATTAAGCTTGACAGCCTTTTGCACTTAAGCCTAATA
521 GGATTAAGCTTGACAGCCTTTTGCACTTAAGCCTAATA
3823732 AACATGGGTGTAAGTTAGTTATTTTTCCCTCAAGCTTTCCTATTTAACGTGTCAAATACTTGAAA
1 AACATGGGTGTAAGTTAGTTATTTTTCCCTCAAGCTTTCCTATTTAACGTGTCAAATACTTGAAA
3823797 TAAAAAAATATTATTAGAACTTATTTACACCGGTGTAAGTTAGTTCGGTGTAAGTTAGTTGGGAA
66 TAAAAAAATATTATTAGAACTTATTTACACCGGTGTAAGTTAGTTCGGTGTAAGTTAGTTGGGAA
* *
3823862 AACAAAATAAACCCTTATTTCATCAAGAAATTGTCTTAATGTGATAATAAGGTTTGTGTTGTTAT
131 AACAAAATAAACCCTTATTTCATCAAGAAATTGTCTTAATGTGACAATAAGGTTTGTGATGTTAT
3823927 CCAAACTTCATATGGTCTATCATGTCTTTCAGTGGC-TTTTTTTCTTTTCGATTGCGTTCATGAT
196 CCAAACTTCATATGGTCTATCATGTCTTTCAGTGGCTTTTTTTTCTTTTCGATTGCGTTCATGAT
3823991 ATGTTGAAAATGATTTTTTATGATTCTTCTACAGGAGTCTGATACCTCTCATGAAGATAAACACA
261 ATGTTGAAAATGATTTTTTATGATTCTTCTACAGGAGTCTGATACCTCTCATGAAGATAAACACA
* *
3824056 AATGCTCCCCACAAGCTTGGTAGACTAATGGAACCCAGCATACAGCTGAGGGGATGTTGGATGTT
326 AATGCTCCCCACAAGCTTGGCAGACTAATGGAACCCAGCATACAGCTGAGGAGATGTTGGATGTT
3824121 ATATCTAATGGATCTTGTAAGGAATCAAATACTGAAACAACTACTGAGATGTGTCACCGTGTTTT
391 ATATCTAATGGATCTTGTAAGGAATCAAATACTGAAACAACTACTGAGATGTGTCACCGTGTTTT
3824186 CTTTGATGTTTTAATTTCTGAAAAGTTCACGTATCTGTATAAGCTTCTAATTGACAATTTCCAAG
456 CTTTGATGTTTTAATTTCTGAAAAGTTCACGTATCTGTATAAGCTTCTAATTGACAATTTCCAAG
3824251 GGATTAAGCTTGACAGCCTTTTGCACTTAAGCCTAATA
521 GGATTAAGCTTGACAGCCTTTTGCACTTAAGCCTAATA
3824289 AAC
1 AAC
3824292 TCAAGGATGA
Statistics
Matches: 549, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
557 323 0.59
558 226 0.41
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (558 bp):
AACATGGGTGTAAGTTAGTTATTTTTCCCTCAAGCTTTCCTATTTAACGTGTCAAATACTTGAAA
TAAAAAAATATTATTAGAACTTATTTACACCGGTGTAAGTTAGTTCGGTGTAAGTTAGTTGGGAA
AACAAAATAAACCCTTATTTCATCAAGAAATTGTCTTAATGTGACAATAAGGTTTGTGATGTTAT
CCAAACTTCATATGGTCTATCATGTCTTTCAGTGGCTTTTTTTTCTTTTCGATTGCGTTCATGAT
ATGTTGAAAATGATTTTTTATGATTCTTCTACAGGAGTCTGATACCTCTCATGAAGATAAACACA
AATGCTCCCCACAAGCTTGGCAGACTAATGGAACCCAGCATACAGCTGAGGAGATGTTGGATGTT
ATATCTAATGGATCTTGTAAGGAATCAAATACTGAAACAACTACTGAGATGTGTCACCGTGTTTT
CTTTGATGTTTTAATTTCTGAAAAGTTCACGTATCTGTATAAGCTTCTAATTGACAATTTCCAAG
GGATTAAGCTTGACAGCCTTTTGCACTTAAGCCTAATA
Found at i:3826306 original size:3 final size:3
Alignment explanation
Indices: 3826298--3826383 Score: 91
Period size: 3 Copynumber: 27.7 Consensus size: 3
3826288 ATTTTATTTA
* * *
3826298 TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3826346 AAT TAT TAT TAA TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
3826384 CAAAACCCGG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
3 59 0.86
4 10 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3826753 original size:20 final size:20
Alignment explanation
Indices: 3826727--3826771 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3826717 GAGCAAAAAC
3826727 AGAGAGACAGAGAACAACAG
1 AGAGAGACAGAGAACAACAG
*
3826747 GGAGAGACAGAGAACAACAG
1 AGAGAGACAGAGAACAACAG
3826767 AGAGA
1 AGAGA
3826772 AACGGAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAGAGACAGAGAACAACAG
Found at i:3826867 original size:15 final size:15
Alignment explanation
Indices: 3826847--3826888 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3826837 ACAACACAGC
3826847 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
3826862 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
3826877 AAAGAAGAGAAA
1 AAAGAAAAGAAA
3826889 CTTACTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:3826872 original size:20 final size:20
Alignment explanation
Indices: 3826847--3826888 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3826837 ACAACACAGC
*
3826847 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
3826867 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
3826887 AA
1 AA
3826889 CTTACTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:3827777 original size:15 final size:14
Alignment explanation
Indices: 3827758--3827804 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3827748 ATATAATAAA
3827758 TAATAATTTATTTT
1 TAATAATTTATTTT
*
3827772 TAAATAAATTA-TTT
1 T-AATAATTTATTTT
3827786 TAAT-ATTTATTTT
1 TAATAATTTATTTT
3827799 TCAATA
1 T-AATA
3827805 TCGAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 8 0.30
15 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATAATTTATTTT
Found at i:3830157 original size:14 final size:14
Alignment explanation
Indices: 3830119--3830172 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
3830109 ATTTTAAATA
*
3830119 ATTTACATTTACA-
1 ATTTACATTTGCAT
3830132 ATTTTACATTTGCAT
1 A-TTTACATTTGCAT
3830147 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
3830162 CTTTGCATTTG
1 ATTTACATTTG
3830173 TATTGCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 1 0.03
14 21 0.60
15 13 0.37
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:3830161 original size:15 final size:15
Alignment explanation
Indices: 3830134--3830172 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3830124 CATTTACAAT
3830134 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
3830148 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
3830163 TTTGCATTTG
1 TTTACATTTG
3830173 TATTGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:3835925 original size:83 final size:83
Alignment explanation
Indices: 3835794--3835947 Score: 281
Period size: 83 Copynumber: 1.9 Consensus size: 83
3835784 AGAACCAATC
* *
3835794 ATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
3835859 GGTTTGGTAAAACCAGTT
66 GGTTTGGTAAAACCAGTT
*
3835877 ATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTT
1 ATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
3835942 GGTTTG
66 GGTTTG
3835948 ATATAAAACC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (83 bp):
ATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGTAAAACCAGTT
Found at i:3837015 original size:116 final size:115
Alignment explanation
Indices: 3836675--3837700 Score: 1290
Period size: 116 Copynumber: 9.0 Consensus size: 115
3836665 CAAAAAAAAA
* * * * *
3836675 GCTCAAATCTATCACTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--CTCAT
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCTCAT
*
3836738 CTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
66 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* * * * *
3836788 GCTCAAATCTATCACTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--CTCAT
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCTCAT
* *
3836851 CTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTT
66 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* ** *
3836901 GCCCAAATCCATCACTTGATGGATCAGCTTTTTTAGGTAGAGTTCCTAATGAGAAGAACTCGTCA
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCA
*
3836966 TCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
65 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* * * * *
3837017 GCTCAAATCTATCACTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--CTCAT
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCTCAT
*
3837080 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTT
66 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* ** *
3837130 GCCCAAATCCATCACTTGATGGATCAGCTTTTTTAGGTAGAGTTCCTAATGAGAAGAACTCGTCA
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCA
* * *
3837195 TCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTATTCAATCTTTT
65 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* * * *
3837246 GCTCAAATACATCACTTGATGGATCCGCTTTTCCAGAG-AAAATTCATAATGAGAAGAA--CTCA
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAG-GTAGAGTTCATAATGAGAAGAACTCTCA
* *
3837308 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
65 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* ** * * * * * * *
3837359 GTTTGAATTCATCATTTGATGGATCAACATTGCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCA
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCA
* *
3837424 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
65 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* ** * * * * * * *
3837475 GTTTGAATTCATCATTTGATGGATCAACATTGCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCA
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCA
3837540 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
65 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
* * * *
3837591 GTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAA--CTAAT
1 GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCTCAT
** * **
3837654 CTG-A-AA--AAGAAGAAGTTCACCATGAAAAGAGCTTGTTCAACCTTTT
66 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
3837700 G
1 G
3837701 AATGACTCTA
Statistics
Matches: 820, Mismatches: 82, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
109 36 0.04
111 2 0.00
112 2 0.00
113 358 0.44
114 3 0.00
115 3 0.00
116 415 0.51
117 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (115 bp):
GCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCTCAT
CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
Found at i:3837083 original size:229 final size:229
Alignment explanation
Indices: 3836678--3837650 Score: 1353
Period size: 229 Copynumber: 4.2 Consensus size: 229
3836668 AAAAAAAGCT
* * * * * * *
3836678 CAAATCTATCACTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCT
1 CAAATCCATCACTTGATGGATCAGCTTTTCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
*
3836740 GAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTT
* * *
3836805 GATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
131 GATAGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
3836870 TTCATAATGAGAAGAATTTATTCAACCTTTTGCC
196 TTCATAATGAGAAGAATTTATTCAACCTTTTGCC
*
3836904 CAAATCCATCACTTGATGGATCAGCTTTTTTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
1 CAAATCCATCACTTGATGGATCAGCTTTTCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
*
3836969 GAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTT
* *
3837034 GATAGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
131 GATAGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
3837099 TTCATAATGAGAAGAATTTATTCAACCTTTTGCC
196 TTCATAATGAGAAGAATTTATTCAACCTTTTGCC
*
3837133 CAAATCCATCACTTGATGGATCAGCTTTTTTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
1 CAAATCCATCACTTGATGGATCAGCTTTTCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
* * *
3837198 GAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTATTCAATCTTTTGCTCAAATAC-ATCACT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT-CTATCACT
* * ** * *
3837262 TGATGGATCCGCTTTTCCAGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
130 TGATAGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* * * **
3837327 GTTCATAATGAGAAGAACTTGTTCAACTTTTTGTT
195 GTTCATAATGAGAAGAATTTATTCAACCTTTTGCC
** * * * * *
3837362 TGAATTCATCATTTGATGGATCAACATTGCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
1 CAAATCCATCACTTGATGGATCAGCTTTTCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
* * * ** *
3837427 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAAT-TCATCATT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCT-ATCACT
* * * * * * *
3837491 TGATGGATCAACATTGCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAA
130 TGATAGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAA
* **
3837556 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTT
192 GAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCC
* * * *
3837594 CAAATCCATCACTTGATGGATCAGCTTTTCCAGATAAAGTTCATAATGAGAAGAACT
1 CAAATCCATCACTTGATGGATCAGCTTTTCTAGGTAGAGTTCCTAATGAGAAGAACT
3837651 AATCTGAAAA
Statistics
Matches: 672, Mismatches: 66, Indels: 12
0.90 0.09 0.02
Matches are distributed among these distances:
226 47 0.07
228 1 0.00
229 521 0.78
230 1 0.00
231 1 0.00
232 101 0.15
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (229 bp):
CAAATCCATCACTTGATGGATCAGCTTTTCTAGGTAGAGTTCCTAATGAGAAGAACTCGTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTT
GATAGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAATTTATTCAACCTTTTGCC
Found at i:3837937 original size:3 final size:3
Alignment explanation
Indices: 3837929--3838023 Score: 109
Period size: 3 Copynumber: 30.7 Consensus size: 3
3837919 ATTTTATTTA
* * *
3837929 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT AAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3837977 TAT AAT TAT TAT TAT TAT TAA TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
3838024 CAAAACCCGG
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 72 0.88
4 10 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3838393 original size:20 final size:20
Alignment explanation
Indices: 3838367--3838411 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3838357 GAGCAAAAAC
3838367 AGAGAGACAGAGAACAACAG
1 AGAGAGACAGAGAACAACAG
*
3838387 GGAGAGACAGAGAACAACAG
1 AGAGAGACAGAGAACAACAG
3838407 AGAGA
1 AGAGA
3838412 AACGGAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAGAGACAGAGAACAACAG
Found at i:3838507 original size:15 final size:15
Alignment explanation
Indices: 3838487--3838528 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3838477 ACAACACAGC
3838487 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
3838502 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
3838517 AAAGAAGAGAAA
1 AAAGAAAAGAAA
3838529 CTTACTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:3838512 original size:20 final size:20
Alignment explanation
Indices: 3838487--3838528 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3838477 ACAACACAGC
*
3838487 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
3838507 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
3838527 AA
1 AA
3838529 CTTACTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:3839415 original size:15 final size:14
Alignment explanation
Indices: 3839396--3839442 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3839386 ATATAATAAA
3839396 TAATAATTTATTTT
1 TAATAATTTATTTT
*
3839410 TAAATAAATTA-TTT
1 T-AATAATTTATTTT
3839424 TAAT-ATTTATTTT
1 TAATAATTTATTTT
3839437 TCAATA
1 T-AATA
3839443 TCGAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 8 0.30
15 8 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATAATTTATTTT
Found at i:3847052 original size:15 final size:15
Alignment explanation
Indices: 3846963--3847054 Score: 55
Period size: 15 Copynumber: 6.0 Consensus size: 15
3846953 ATAAAAATTA
3846963 TATATATAGTAAT-TT
1 TATATATA-TAATATT
* **
3846978 TATAATATTATAAGAAG
1 TAT-ATA-TATAATATT
* *
3846995 TATATTTATATTATT
1 TATATATATAATATT
* *
3847010 TAT-TATATAGAAACT
1 TATATATATA-ATATT
3847025 TATATATATAATATT
1 TATATATATAATATT
3847040 TATAT-TATAAATATT
1 TATATATAT-AATATT
3847055 ATTTTAATTT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
14 8 0.14
15 30 0.53
16 14 0.25
17 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (15 bp):
TATATATATAATATT
Found at i:3848800 original size:22 final size:22
Alignment explanation
Indices: 3848757--3848801 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3848747 TTATTAATTA
*
3848757 TATTTATATTAAATTTTATTTT
1 TATTTATATTAAATTATATTTT
* * *
3848779 TATTTATGTTATATTATGTTTT
1 TATTTATATTAAATTATATTTT
3848801 T
1 T
3848802 TAATATATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTTATATTAAATTATATTTT
Found at i:3851320 original size:46 final size:46
Alignment explanation
Indices: 3851265--3851366 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 46
3851255 CGAGTCAAAC
*
3851265 TTTAGATTTTC-GAGTCAATTCGGGTTGGTTT-GAGTTCGGATTAACT
1 TTTAGATTTTCGGA-TCAATTCGGGTTGGTTTCG-GTTCAGATTAACT
* * * *
3851311 TTTAAATTTTTGGATCATTTGGGGTTGGTTTCGGTTCAGATTAACT
1 TTTAGATTTTCGGATCAATTCGGGTTGGTTTCGGTTCAGATTAACT
3851357 TTTAGATTTT
1 TTTAGATTTT
3851367 TAGGCCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
46 45 0.94
47 3 0.06
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.48
Consensus pattern (46 bp):
TTTAGATTTTCGGATCAATTCGGGTTGGTTTCGGTTCAGATTAACT
Found at i:3851618 original size:3 final size:3
Alignment explanation
Indices: 3851610--3851641 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3851600 ATCAAATTAC
3851610 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3851642 CAATTATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3851751 original size:16 final size:16
Alignment explanation
Indices: 3851726--3851767 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3851716 ACTTAAATTC
* *
3851726 GAGTTGCTTTTGATTT
1 GAGTTACTTTCGATTT
3851742 GAGTTACTTTCGATTT
1 GAGTTACTTTCGATTT
*
3851758 GGGTTA-TTTC
1 GAGTTACTTTC
3851768 AGTTCGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (16 bp):
GAGTTACTTTCGATTT
Found at i:3853194 original size:21 final size:21
Alignment explanation
Indices: 3853168--3853220 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
3853158 GTTTCCAGAT
*
3853168 TCGCAACGCGAACTTCG-ACTA
1 TCGCAATGCGAACTT-GAACTA
3853189 TCGCAATGCGAACTTGAACTA
1 TCGCAATGCGAACTTGAACTA
3853210 TCGCAATGCGA
1 TCGCAATGCGA
3853221 TTTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTGAACTA
Found at i:3853284 original size:21 final size:21
Alignment explanation
Indices: 3853229--3853287 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 21
3853219 GATTTACATA
*
3853229 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3853250 TTCGATCGAATTGCGATAGTCGAAG
1 TTCG--CG--TTGCGATAGTCCAAG
3853275 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3853288 TTATTCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 11 0.34
23 3 0.09
25 18 0.56
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:3854062 original size:21 final size:21
Alignment explanation
Indices: 3854036--3854153 Score: 127
Period size: 21 Copynumber: 5.6 Consensus size: 21
3854026 TTTGGAATAA
3854036 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
3854057 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
3854076 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
3854099 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
3854118 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
*
3854141 ATCGCAATGCGAA
1 ATCGCAACGCGAA
3854154 TATGTAAATC
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
19 20 0.25
21 40 0.50
23 20 0.25
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:3854081 original size:42 final size:42
Alignment explanation
Indices: 3854022--3854147 Score: 234
Period size: 42 Copynumber: 3.0 Consensus size: 42
3854012 ACCGTCGTTG
3854022 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
*
3854064 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
*
3854106 CGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
3854148 TGCGAATATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
Found at i:3859712 original size:3 final size:3
Alignment explanation
Indices: 3859693--3859745 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
3859683 AAAACAGACC
* *
3859693 AAG ATG AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3859741 AAG AA
1 AAG AA
3859746 AGAGATTGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:3861596 original size:13 final size:12
Alignment explanation
Indices: 3861550--3861639 Score: 66
Period size: 11 Copynumber: 7.7 Consensus size: 12
3861540 TTGGAAGGTA
*
3861550 ATTTTTTAACTTT
1 ATTTTTTAA-TAT
3861563 ACTTTTTTAACTA-
1 A-TTTTTTAA-TAT
3861576 ATTTTTTAATAT
1 ATTTTTTAATAT
*
3861588 ATTTATTTAATTT
1 ATTT-TTTAATAT
3861601 A-TTTTT-ATAT
1 ATTTTTTAATAT
* *
3861611 -CTTTTTAAT-C
1 ATTTTTTAATAT
3861621 ATTTTTT-ATAT
1 ATTTTTTAATAT
3861632 ATTTTTTA
1 ATTTTTTA
3861640 GATAGTGCCA
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
10 10 0.16
11 19 0.30
12 14 0.22
13 10 0.16
14 10 0.16
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTTTAATAT
Found at i:3861596 original size:25 final size:26
Alignment explanation
Indices: 3861548--3861606 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
3861538 GGTTGGAAGG
*
3861548 TAATTTTTTAACTTTACTTTTTTAAC
1 TAATTTTTTAACTATACTTTTTTAAC
*
3861574 TAATTTTTTAA-TATA-TTTATTTAAT
1 TAATTTTTTAACTATACTTT-TTTAAC
*
3861599 TTATTTTT
1 TAATTTTT
3861607 ATATCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 15 0.52
26 11 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (26 bp):
TAATTTTTTAACTATACTTTTTTAAC
Found at i:3861598 original size:21 final size:19
Alignment explanation
Indices: 3861574--3861639 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 19
3861564 CTTTTTTAAC
3861574 TAATTTTTTAATATATTTATT
1 TAATTTTTT-ATATATTT-TT
*
3861595 TAATTTATTTTTATATCTTTT
1 TAATTT-TTTATATAT-TTTT
3861616 TAATCATTTTTTATATATTTTT
1 T-A--ATTTTTTATATATTTTT
3861638 TA
1 TA
3861640 GATAGTGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 15 0.39
22 11 0.29
23 8 0.21
24 4 0.11
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TAATTTTTTATATATTTTT
Found at i:3862749 original size:43 final size:43
Alignment explanation
Indices: 3862648--3862750 Score: 163
Period size: 43 Copynumber: 2.4 Consensus size: 43
3862638 ATATAAAATA
*
3862648 TAAATAAATTTTATT-ATGTACATATTAGTTTGTAAACATTTTT
1 TAAATAAA-ATTATTAATGTACATATTAGTTTGTAAACATTTTT
**
3862691 TAAATAAAAAAATTAATGTACATATTAGTTTGTAAACATTTTT
1 TAAATAAAATTATTAATGTACATATTAGTTTGTAAACATTTTT
3862734 TAAATAAAATTATTAAT
1 TAAATAAAATTATTAAT
3862751 TTACTTTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 3 0.06
43 51 0.94
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (43 bp):
TAAATAAAATTATTAATGTACATATTAGTTTGTAAACATTTTT
Found at i:3868979 original size:15 final size:15
Alignment explanation
Indices: 3868935--3868983 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3868925 TTTCTGCTTT
*
3868935 TTTCTTTCTCTCCGG
1 TTTCTGTCTCTCCGG
*
3868950 -TTCTGT-T-T-TGG
1 TTTCTGTCTCTCCGG
3868961 TTTCTGTCTCTCCGG
1 TTTCTGTCTCTCCGG
3868976 TTTCTGTC
1 TTTCTGTC
3868984 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.07
12 7 0.26
13 2 0.07
14 6 0.22
15 10 0.37
ACGTcount: A:0.00, C:0.27, G:0.18, T:0.55
Consensus pattern (15 bp):
TTTCTGTCTCTCCGG
Found at i:3869452 original size:3 final size:3
Alignment explanation
Indices: 3869444--3869537 Score: 163
Period size: 3 Copynumber: 31.7 Consensus size: 3
3869434 TAATATAAAT
*
3869444 TAA TAA TAA TAA TAA TAA TGA 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
*
3869492 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3869538 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3869897 original size:115 final size:112
Alignment explanation
Indices: 3869673--3871000 Score: 1738
Period size: 115 Copynumber: 11.6 Consensus size: 112
3869663 ATTGAATAAA
* * ** *
3869673 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATGATCCATC
* * *
3869737 AAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAGTGATGAATT-AGA-AAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * * *
3869786 TTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCC
*
3869850 ATCAAGTGATGAATTAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCAAGTGATGAATTAGAAAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
3869901 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAAATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
*
3869966 AGTGATGAATTCAGAAAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AGTGATGAATT-AG--AAAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
3870016 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* * * * *
3870081 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAAC
66 AGTGATGAATTAGA-AAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
3870129 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCC
* *
3870193 ATCAAATGATGAATTTA-AACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAGTGATGAA-TTAGAA-AAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
3870245 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAAATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
*
3870310 AGTGATGAATTCAGAAAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AGTGATGAATT-AG--AAAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
3870360 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* * * * *
3870424 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAAC
66 AGTGATGAATTAGA-AAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
3870472 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCC
*
3870536 ATCAAGTGATGAATTAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCAAGTGATGAATTAGAAAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
3870587 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAAATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
*
3870652 AGTGATGAATTCAGAAAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AGTGATGAATT-AG--AAAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
3870702 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* * * * *
3870767 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAAC
66 AGTGATGAATTAGA-AAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * * *
3870815 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATAAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCC
* *
3870879 ATCAAATGATGAATTTA-AACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAGTGATGAA-TTAGAA-AAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * * *
3870931 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTATCTGGCAATGAATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG-ATGATCCATC
3870996 AAGTG
65 AAGTG
3871001 GATTTGAAAT
Statistics
Matches: 1082, Mismatches: 92, Indels: 81
0.86 0.07 0.06
Matches are distributed among these distances:
111 7 0.01
112 152 0.14
113 181 0.17
114 50 0.05
115 414 0.38
116 246 0.23
117 30 0.03
118 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (112 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
AGTGATGAATTAGAAAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:3870330 original size:343 final size:343
Alignment explanation
Indices: 3869673--3871000 Score: 2358
Period size: 343 Copynumber: 3.9 Consensus size: 343
3869663 ATTGAATAAA
* * ** * *
3869673 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGCTGATCCATC
* * ** * *
3869737 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTC
65 AAGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
*
3869802 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAGTGATGAATTAG
130 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTAG
*
3869867 AAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
195 AAAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
3869932 ATTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAACA
260 ATTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAACA
3869997 AATTCTTCTCATTATGAAC
325 AATTCTTCTCATTATGAAC
3870016 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
3870081 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
3870146 GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTTA-
131 GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAA-TTAG
*
3870210 AACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
195 AA-AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
3870275 CATTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAAC
259 CATTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAAC
3870340 AAATTCTTCTCATTATGAAC
324 AAATTCTTCTCATTATGAAC
3870360 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
3870424 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
3870489 GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAGTGATGAATTAGA
131 GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTAGA
*
3870554 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
196 AAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
3870619 TTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAACAA
261 TTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAACAA
3870684 ATTCTTCTCATTATGAAC
326 ATTCTTCTCATTATGAAC
3870702 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
3870767 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
3870832 GATGACGAGTTCTTCTCATTATAAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTTA-
131 GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAA-TTAG
* *
3870896 AACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCT
195 AA-AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* ** *
3870961 CATTATGAACCTTATCTGGCAATGAATGATCCATCAAGTG
259 CATTATGAACCTTCTCTGG-AAAAAATAATCCATCAAGTG
3871001 GATTTGAAAT
Statistics
Matches: 950, Mismatches: 27, Indels: 14
0.96 0.03 0.01
Matches are distributed among these distances:
342 197 0.21
343 423 0.45
344 313 0.33
345 17 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (343 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
AGTGATGGATTTGAGCAGAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTAGA
AAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAAAGGTTGAACAA
ATTCTTCTCATTATGAAC
Found at i:3871869 original size:82 final size:82
Alignment explanation
Indices: 3871651--3872032 Score: 640
Period size: 82 Copynumber: 4.6 Consensus size: 82
3871641 ATTCTTACCA
* * * *
3871651 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCTTCTTCCAAATT
* *
3871716 CAATGATTGGTTTTG-CTA
66 CAATGATT-GTTCTGTC-C
* *
3871734 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCTTCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCTTCTTCCAAATT
3871799 CAATGATTGTTCTGTCC
66 CAATGATTGTTCTGTCC
3871816 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCTTCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCTTCTTCCAAATT
*
3871881 CAATGATTGTTATGTCC
66 CAATGATTGTTCTGTCC
* *
3871898 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTAACATATTCTTCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCTTCTTCCAAATT
3871963 CAATGATTGTTCTGTCC
66 CAATGATTGTTCTGTCC
3871980 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTC
3872033 ATTTGTTCTA
Statistics
Matches: 285, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
82 214 0.75
83 71 0.25
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (82 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCTTCTTCCAAATT
CAATGATTGTTCTGTCC
Found at i:3873078 original size:17 final size:17
Alignment explanation
Indices: 3873053--3873091 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3873043 CACCTTGACC
3873053 CTTTT-TTTTTTCTTTT
1 CTTTTCTTTTTTCTTTT
3873069 CTTTTCTTTTTTCTTTT
1 CTTTTCTTTTTTCTTTT
3873086 CTTTTC
1 CTTTTC
3873092 AAGCATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTTCTTTTTTCTTTT
Found at i:3873080 original size:12 final size:12
Alignment explanation
Indices: 3873053--3873090 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3873043 CACCTTGACC
3873053 CTTTTTT-TTTT
1 CTTTTTTCTTTT
3873064 C--TTTTCTTTT
1 CTTTTTTCTTTT
3873074 CTTTTTTCTTTT
1 CTTTTTTCTTTT
3873086 CTTTT
1 CTTTT
3873091 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.17
10 5 0.21
11 1 0.04
12 14 0.58
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
CTTTTTTCTTTT
Found at i:3885393 original size:15 final size:15
Alignment explanation
Indices: 3885349--3885397 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3885339 TTCTTTGCTT
*
3885349 TTTCTTTCTCTCCGG
1 TTTCTGTCTCTCCGG
*
3885364 -TTCTGT-T-T-TGG
1 TTTCTGTCTCTCCGG
3885375 TTTCTGTCTCTCCGG
1 TTTCTGTCTCTCCGG
3885390 TTTCTGTC
1 TTTCTGTC
3885398 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.07
12 7 0.26
13 2 0.07
14 6 0.22
15 10 0.37
ACGTcount: A:0.00, C:0.27, G:0.18, T:0.55
Consensus pattern (15 bp):
TTTCTGTCTCTCCGG
Found at i:3885862 original size:3 final size:3
Alignment explanation
Indices: 3885854--3885936 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
3885844 TAATATAAAT
*
3885854 TAA TAA TAA TAA TAA TAA TGA 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
* *
3885902 TAA TAT TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3885937 TGGATAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3886817 original size:21 final size:21
Alignment explanation
Indices: 3886773--3886817 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3886763 CCCAAAATCT
* * **
3886773 TAAACCTCAAATCCTAAATTC
1 TAAAACTCAAATCATAAACCC
3886794 TAAAACTCAAATCATAAACCC
1 TAAAACTCAAATCATAAACCC
3886815 TAA
1 TAA
3886818 GCCCTATACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAACTCAAATCATAAACCC
Found at i:3887081 original size:27 final size:26
Alignment explanation
Indices: 3887051--3887126 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
3887041 GGTTAGGGTG
3887051 TAGGCTTTAGGGTTTAAGATTTA-AACT
1 TAGG-TTTAGGGTTTAAGATTTATAA-T
* * *
3887078 TAGGGTTTA-AGTTTAAGAATTATGAT
1 TA-GGTTTAGGGTTTAAGATTTATAAT
3887104 TGAGGTTTAGGGTTTAAGATTTA
1 T-AGGTTTAGGGTTTAAGATTTA
3887127 GAGTTTGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
26 19 0.47
27 19 0.47
28 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (26 bp):
TAGGTTTAGGGTTTAAGATTTATAAT
Found at i:3887956 original size:39 final size:39
Alignment explanation
Indices: 3887909--3888033 Score: 133
Period size: 39 Copynumber: 3.2 Consensus size: 39
3887899 CACAAAGCAT
*
3887909 AGGAGCCTACAGTAAGGACTTACCCTTAGAAAAAAACCA
1 AGGAGCCTACAGTAAGGACTTACCCTGAGAAAAAAACCA
* * * ** *
3887948 AGGAGCCTACAGTAAGGATTTACCCTGAGCACAAAGTCG
1 AGGAGCCTACAGTAAGGACTTACCCTGAGAAAAAAACCA
* * * * * *
3887987 AGGAGCCTGCAATAAGGACTTACCCTGAGCACAAAGCCG
1 AGGAGCCTACAGTAAGGACTTACCCTGAGAAAAAAACCA
3888026 AGGAGCCT
1 AGGAGCCT
3888034 TCGGAAGGCG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (39 bp):
AGGAGCCTACAGTAAGGACTTACCCTGAGAAAAAAACCA
Found at i:3888030 original size:78 final size:79
Alignment explanation
Indices: 3887840--3888033 Score: 203
Period size: 78 Copynumber: 2.5 Consensus size: 79
3887830 TTGTACACCG
** * * * ** * * *
3887840 AATAAGGGGTTACCCTGTGCACGAAGCAGAGGAGCCTGGAGTAAGGTCTTTATCCTGTGCACAAA
1 AATAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTACAGTAAGGTATTTACCCTGAGCACAAA
*
3887905 GCATAGGAGCCTAC
66 GCAGAGGAGCCTAC
* * * * * *
3887919 AGTAAGGACTTACCCTTAGAAAAAAACCAAGGAGCCTACAGTAAGG-ATTTACCCTGAGCACAAA
1 AATAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTACAGTAAGGTATTTACCCTGAGCACAAA
*
3887983 GTC-GAGGAGCCTGC
66 G-CAGAGGAGCCTAC
3887997 AATAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCT
1 AATAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCT
3888034 TCGGAAGGCG
Statistics
Matches: 90, Mismatches: 24, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
78 56 0.62
79 34 0.38
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.18
Consensus pattern (79 bp):
AATAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTACAGTAAGGTATTTACCCTGAGCACAAA
GCAGAGGAGCCTAC
Found at i:3888832 original size:18 final size:18
Alignment explanation
Indices: 3888809--3888857 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
3888799 TTTCGGTCAA
3888809 AGTCAACGGTCAACGATC
1 AGTCAACGGTCAACGATC
* *
3888827 AGTCAACAGTCAACGGTC
1 AGTCAACGGTCAACGATC
* *
3888845 GGTCAACGATCAA
1 AGTCAACGGTCAA
3888858 TGGTCACTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (18 bp):
AGTCAACGGTCAACGATC
Found at i:3894764 original size:15 final size:18
Alignment explanation
Indices: 3894746--3894787 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
3894736 TTAATAAATA
3894746 AAATAA-ATATTA-GA-T
1 AAATAATATATTATGACT
3894761 AAATATATATATTATGACT
1 AAATA-ATATATTATGACT
3894780 AAATAATA
1 AAATAATA
3894788 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.22
16 1 0.04
17 6 0.26
18 5 0.22
19 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATAATATATTATGACT
Found at i:3896182 original size:3 final size:3
Alignment explanation
Indices: 3896176--3896241 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
3896166 AATAATTATT
* **
3896176 TAA TAA TAA T-A TAC TAA TAA TAA TGTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
3896221 TAA -ATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
3896242 ATTTAAATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.06
3 46 0.90
4 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3896228 original size:24 final size:24
Alignment explanation
Indices: 3896165--3896241 Score: 102
Period size: 24 Copynumber: 3.1 Consensus size: 24
3896155 TTTGGGCTTG
*
3896165 TAATAAT-TATTTAATAATAATATA
1 TAATAATAAATTTAATAATAATA-A
*
3896189 CTAATAATAATGTTTAATAATAATAA
1 -TAATAATAA-ATTTAATAATAATAA
3896215 TAATAATAAATTTAATAATAATAA
1 TAATAATAAATTTAATAATAATAA
3896239 TAA
1 TAA
3896242 ATTTAAATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 17 0.36
25 16 0.34
26 1 0.02
27 13 0.28
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
TAATAATAAATTTAATAATAATAA
Done.