Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 24
Found at i:3844752 original size:14 final size:14
Alignment explanation
Indices: 3844733--3844787 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3844723 GTGAAATGAA
3844733 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3844747 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3844766 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3844780 AATCGCAA
1 AATCGCAA
3844788 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3844901 original size:52 final size:55
Alignment explanation
Indices: 3844628--3844885 Score: 252
Period size: 52 Copynumber: 4.9 Consensus size: 55
3844618 GCAACGAGAG
*
3844628 AATCGCAATGCGAAATGAAAATCCCAA-C--ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGC-GAAATGAA
* *
3844681 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
* *
3844733 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
3844780 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAA
*
3844837 AATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAAT
3844886 TATAAACGCA
Statistics
Matches: 182, Mismatches: 8, Indels: 31
0.82 0.04 0.14
Matches are distributed among these distances:
47 10 0.05
48 10 0.05
49 3 0.02
50 2 0.01
51 3 0.02
52 96 0.53
53 24 0.13
54 2 0.01
55 2 0.01
56 1 0.01
57 29 0.16
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATGAA
Found at i:3845004 original size:52 final size:53
Alignment explanation
Indices: 3844892--3845007 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
3844882 AAATTATAAA
3844892 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
3844945 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
3844997 CGCATTGCGAT
1 CGCATTGCGAT
3845008 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:3845015 original size:19 final size:19
Alignment explanation
Indices: 3844910--3845007 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3844900 GATTCTCTCG
3844910 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3844930 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3844949 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3844963 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3844982 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3845001 TTGCGAT
1 TTGCGAT
3845008 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3845112 original size:14 final size:14
Alignment explanation
Indices: 3845093--3845129 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3845083 CATCAATTAC
3845093 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3845107 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3845121 ACAAATCAA
1 ACAAATCAA
3845130 TTAAACAATT
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:3846480 original size:14 final size:14
Alignment explanation
Indices: 3846461--3846517 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3846451 GCGAAATGAA
*
3846461 AATCGCAACGACAG
1 AATCGCAACGAAAG
3846475 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3846492 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3846508 AATCGCAACG
1 AATCGCAACG
3846518 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3846488 original size:33 final size:33
Alignment explanation
Indices: 3846442--3846534 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3846432 GCGAAACCAA
*
3846442 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3846475 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3846508 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3846535 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3846499 original size:19 final size:19
Alignment explanation
Indices: 3846405--3846539 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3846395 TAGTTTACTT
* *
3846405 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3846425 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3846444 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3846463 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3846477 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3846496 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3846510 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3846529 TCGCAATGCGA
1 TCGCAACGCGA
3846540 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3846557 original size:19 final size:19
Alignment explanation
Indices: 3846535--3846663 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3846525 AAAATCGCAA
3846535 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3846554 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3846568 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3846587 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3846601 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3846620 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3846639 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3846659 TGCGA
1 TGCGA
3846664 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3846577 original size:33 final size:33
Alignment explanation
Indices: 3846535--3846626 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3846525 AAAATCGCAA
3846535 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3846568 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3846601 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3846627 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3846827 original size:93 final size:93
Alignment explanation
Indices: 3846711--3847179 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
3846701 ATGGATTGCA
3846711 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3846775 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3846803 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3846868 TAGCAGAATTGGCAGCAACCTAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3846896 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3846961 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3846989 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3847054 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3847082 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3847147 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3847175 TTACT
1 TTACT
3847180 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3848905 original size:14 final size:14
Alignment explanation
Indices: 3848886--3848974 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
3848876 TTGAAATGAA
3848886 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3848900 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
3848919 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3848933 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3848952 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3848966 AATCGCAAC
1 AATCGCAAC
3848975 TCGAAATGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3848923 original size:33 final size:33
Alignment explanation
Indices: 3848878--3848992 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3848868 TCTTTTGGTT
3848878 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3848911 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3848944 GAAATGAAAATCGCAACGAGAGAATCGCAACTC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3848977 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3848993 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3848924 original size:19 final size:19
Alignment explanation
Indices: 3848900--3848997 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3848890 GCAACGAGAG
*
3848900 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
3848919 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3848933 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3848952 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
3848966 AATCGCAACTCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3848985 AATCGCAATGCGA
1 AATCGCAACGCGA
3848998 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3849028 original size:14 final size:14
Alignment explanation
Indices: 3849009--3849065 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3848999 TTTGGTTTCG
3849009 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3849023 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3849042 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3849056 CGTTGCGATT
1 CGTTGCGATT
3849066 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3849041 original size:33 final size:33
Alignment explanation
Indices: 3848993--3849073 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3848983 AAAATCGCAA
**
3848993 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3849026 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3849059 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3849074 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3849076 original size:21 final size:21
Alignment explanation
Indices: 3849050--3849125 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3849040 CGCGTTGCGA
3849050 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3849071 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3849091 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3849112 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3849126 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3849106 original size:41 final size:41
Alignment explanation
Indices: 3849049--3849126 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
3849039 TCGCGTTGCG
*
3849049 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
3849090 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
3849127 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:3849247 original size:33 final size:33
Alignment explanation
Indices: 3849205--3849275 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
3849195 AATACTAACT
*
3849205 TGAAAATCGCAACGAGAGAAT-AGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATCA-CAACGCGAAA
*
3849238 TGAAAATCGCAACGACAGAATCATAACGCGAAA
1 TGAAAATCGCAACGACAGAATCACAACGCGAAA
3849271 TGAAA
1 TGAAA
3849276 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATCACAACGCGAAA
Found at i:3849509 original size:22 final size:22
Alignment explanation
Indices: 3849457--3849511 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3849447 TGGTTGTGAG
**
3849457 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3849479 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3849501 GGATTTCTTCG
1 GGATTTCTTCG
3849512 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3849843 original size:60 final size:60
Alignment explanation
Indices: 3849657--3849871 Score: 295
Period size: 60 Copynumber: 3.6 Consensus size: 60
3849647 GCTTTAAATA
3849657 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTAT
** * * ***
3849718 TATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCCAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
* * *
3849778 ACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
* ** *
3849838 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
3849872 TGGAAAATCG
Statistics
Matches: 131, Mismatches: 23, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
60 84 0.64
61 47 0.36
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
Found at i:3849872 original size:20 final size:20
Alignment explanation
Indices: 3849658--3849871 Score: 261
Period size: 20 Copynumber: 10.7 Consensus size: 20
3849648 CTTTAAATAT
3849658 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
3849678 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3849698 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3849720 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3849739 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3849759 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3849779 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3849799 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3849819 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3849839 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3849859 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3849872 TGGAAAATCG
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 148 0.89
21 15 0.09
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3849888 original size:21 final size:21
Alignment explanation
Indices: 3849858--3849940 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3849848 ATTTTCATAT
*
3849858 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3849879 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3849900 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3849921 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3849941 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3849931 original size:42 final size:43
Alignment explanation
Indices: 3849838--3849936 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3849828 ATTTATGTGT
* *
3849838 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3849879 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3849921 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3849937 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3851413 original size:21 final size:23
Alignment explanation
Indices: 3851369--3851416 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
3851359 CGTATAATTA
*
3851369 TAAATTAGTTAAAAATTTAAAGG
1 TAAATTAGTTAAAAATTAAAAGG
*
3851392 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTAAAAATTAAAAGG
3851413 TAAA
1 TAAA
3851417 CTATACTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTAAAAATTAAAAGG
Found at i:3857780 original size:56 final size:56
Alignment explanation
Indices: 3857711--3857843 Score: 203
Period size: 56 Copynumber: 2.4 Consensus size: 56
3857701 AGATTCTGAC
* * * *
3857711 TGAAACACAGAGGTGCTCAATCATTTTTAACTGTACAGAGGTTTAAGTTTTTTGAT
1 TGAACCACAGAGGTGCTCAATCATTTTTAACTGCACAAAGGTGTAAGTTTTTTGAT
* *
3857767 TGAACCACAGAGGTGCTCAATCATTTTTAACTGCACAAAGGTGTCAGTTTTTTTAT
1 TGAACCACAGAGGTGCTCAATCATTTTTAACTGCACAAAGGTGTAAGTTTTTTGAT
*
3857823 TGAACCACAGAGGTGTTCAAT
1 TGAACCACAGAGGTGCTCAAT
3857844 AGTTAATTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (56 bp):
TGAACCACAGAGGTGCTCAATCATTTTTAACTGCACAAAGGTGTAAGTTTTTTGAT
Found at i:3857803 original size:28 final size:28
Alignment explanation
Indices: 3857716--3857809 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
3857706 CTGACTGAAA
3857716 CACAGAGGTGCTCAATCATTTTTAACTG
1 CACAGAGGTGCTCAATCATTTTTAACTG
* * * *
3857744 TACAGAGGT--TTAAGT--TTTTTGATTG
1 CACAGAGGTGCTCAA-TCATTTTTAACTG
3857769 AACCACAGAGGTGCTCAATCATTTTTAACTG
1 ---CACAGAGGTGCTCAATCATTTTTAACTG
*
3857800 CACAAAGGTG
1 CACAGAGGTG
3857810 TCAGTTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
25 8 0.16
26 3 0.06
27 1 0.02
28 25 0.51
29 1 0.02
30 3 0.06
31 8 0.16
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (28 bp):
CACAGAGGTGCTCAATCATTTTTAACTG
Found at i:3862796 original size:18 final size:18
Alignment explanation
Indices: 3862775--3862809 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3862765 GTCGTTATTC
*
3862775 ATTTAATCTCTTTTTACT
1 ATTTAATCTCATTTTACT
3862793 ATTTAATCTCATTTTAC
1 ATTTAATCTCATTTTAC
3862810 CAAAATTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAATCTCATTTTACT
Found at i:3866342 original size:18 final size:18
Alignment explanation
Indices: 3866319--3866354 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3866309 TGTCGTTATT
*
3866319 TATTTAATCTCTTTTTAC
1 TATTTAATCTCATTTTAC
3866337 TATTTAATCTCATTTTAC
1 TATTTAATCTCATTTTAC
3866355 CAAAATCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTAATCTCATTTTAC
Found at i:3866894 original size:2 final size:2
Alignment explanation
Indices: 3866882--3866914 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3866872 ATCTCCCTCG
3866882 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3866915 ATCTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3867493 original size:2 final size:2
Alignment explanation
Indices: 3867486--3867511 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3867476 ATAATTCTTT
3867486 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3867512 AGATTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3869750 original size:35 final size:35
Alignment explanation
Indices: 3869677--3869751 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
3869667 CATCACGTCC
**
3869677 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
* *
3869712 AGTAAGGCCCTGAGCACACAGCCGATGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
3869747 AGTAA
1 AGTAA
3869752 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:3869855 original size:24 final size:24
Alignment explanation
Indices: 3869828--3869911 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
3869818 CATAATTCAA
3869828 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
3869852 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
*
3869876 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
*
3869899 GTCAGGTATCATA
1 GTCAAGTATCATA
3869912 AAATAATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 20 0.38
24 32 0.62
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:3876245 original size:2 final size:2
Alignment explanation
Indices: 3876238--3876268 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3876228 ACTTAAGAAT
3876238 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 T
3876269 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3889003 original size:17 final size:18
Alignment explanation
Indices: 3888981--3889029 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3888971 TTTCTCACAT
3888981 TATTTTATTTTATT-TTA
1 TATTTTATTTTATTCTTA
*
3888998 TATTTTAATTTAATTCTTA
1 TATTTT-ATTTTATTCTTA
* *
3889017 TAATATATTTTAT
1 TATTTTATTTTAT
3889030 CTCATCATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.23
18 13 0.50
19 7 0.27
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTATTTTATTCTTA
Found at i:3889497 original size:25 final size:24
Alignment explanation
Indices: 3889452--3889510 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
3889442 CACATAATAC
* *
3889452 CAGGAGTACACGAATGTACTAGAAT
1 CAGGAGTGCACCAATGTACTA-AAT
*
3889477 CAGGAGTGCACCAAT-TCACTAATT
1 CAGGAGTGCACCAATGT-ACTAAAT
*
3889501 CAGAAGTGCA
1 CAGGAGTGCA
3889511 AAATTGCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (24 bp):
CAGGAGTGCACCAATGTACTAAAT
Found at i:3889520 original size:24 final size:25
Alignment explanation
Indices: 3889480--3889555 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
3889470 CTAGAATCAG
* *
3889480 GAGTGCACCAATT-CACTAATTC-A
1 GAGTGCACAAATTGCACTAATACAA
*
3889503 GAAGTGCA-AAATTGCACTGATACAA
1 G-AGTGCACAAATTGCACTAATACAA
*
3889528 GAGTGCACAAA-TGCACTAATACAG
1 GAGTGCACAAATTGCACTAATACAA
3889552 GAGT
1 GAGT
3889556 ACCCATTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.11
24 34 0.77
25 5 0.11
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (25 bp):
GAGTGCACAAATTGCACTAATACAA
Found at i:3889718 original size:24 final size:24
Alignment explanation
Indices: 3889673--3889751 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 24
3889663 ACTGATTCAG
* * * *
3889673 GAGTGCACAAAGGCACTGATACAT
1 GAGTGCACAAAAGAACTAATACAC
*
3889697 GAGTGCATAAAAGAACTAATACAC
1 GAGTGCACAAAAGAACTAATACAC
* * * *
3889721 GAGTATC-CAAAGGTACTAATACAG
1 GAGT-GCACAAAAGAACTAATACAC
3889745 GAGTGCA
1 GAGTGCA
3889752 ATAAATGCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (24 bp):
GAGTGCACAAAAGAACTAATACAC
Found at i:3897270 original size:18 final size:18
Alignment explanation
Indices: 3897229--3897274 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3897219 TTTTTTATTT
*
3897229 TTTTTATTTTAGTCTTCA
1 TTTTTAATTTAGTCTTCA
*
3897247 TATTTAATTTAGT-TTCA
1 TTTTTAATTTAGTCTTCA
3897264 CTTTTT-ATTTA
1 -TTTTTAATTTA
3897275 ATATTTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTTAATTTAGTCTTCA
Found at i:3903623 original size:16 final size:16
Alignment explanation
Indices: 3903599--3903644 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
3903589 TGAAAAAAAT
*
3903599 ATTCCGAAGCATATCA
1 ATTCTGAAGCATATCA
3903615 ATTCTGAAGCATATCA
1 ATTCTGAAGCATATCA
3903631 ATTCTGAAGCATAT
1 ATTCTGAAGCATAT
3903645 ATTCCGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (16 bp):
ATTCTGAAGCATATCA
Found at i:3904096 original size:16 final size:16
Alignment explanation
Indices: 3904072--3904117 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
3904062 TGAAAAAAAT
*
3904072 ATTCCGAAGCATATCA
1 ATTCTGAAGCATATCA
3904088 ATTCTGAAGCATATCA
1 ATTCTGAAGCATATCA
3904104 ATTCTGAAGCATAT
1 ATTCTGAAGCATAT
3904118 ATTCCGAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (16 bp):
ATTCTGAAGCATATCA
Found at i:3904291 original size:473 final size:473
Alignment explanation
Indices: 3903406--3904355 Score: 1864
Period size: 473 Copynumber: 2.0 Consensus size: 473
3903396 CAACCCTCAC
*
3903406 ACCATATAAGTAGGGTCTACCACAAAGGCAGAGACCACTGAATCAAAAAAAGTGGCATTCATCCT
1 ACCATATAAGTAGGGTCTACCACAAAGACAGAGACCACTGAATCAAAAAAAGTGGCATTCATCCT
*
3903471 ATCGAGTGAATGTACTGAGCTTCCGCTATCAATATTAGTCCCAATATGATATGTAAAATGACAAA
66 ATCGAGTGAATGCACTGAGCTTCCGCTATCAATATTAGTCCCAATATGATATGTAAAATGACAAA
3903536 CAAATATGATTTTTGATTTGATCCGAATAAACAATATATCATCAACAAATATTTGAAAAAAATAT
131 CAAATATGATTTTTGATTTGATCCGAATAAACAATATATCATCAACAAATATTTGAAAAAAATAT
3903601 TCCGAAGCATATCAATTCTGAAGCATATCAATTCTGAAGCATATATTCCGAGAAAGCAACTCATT
196 TCCGAAGCATATCAATTCTGAAGCATATCAATTCTGAAGCATATATTCCGAGAAAGCAACTCATT
3903666 CACATGTTATGTATGCGCAATCATATTCTGATTCAAAAAGTTAAACATGCATCACATAGCAGTAT
261 CACATGTTATGTATGCGCAATCATATTCTGATTCAAAAAGTTAAACATGCATCACATAGCAGTAT
3903731 TTCCCAATTTTAATTTATATAGTCAAACTCATAGACATACATACTTTCAATCATAGTTCCAACCA
326 TTCCCAATTTTAATTTATATAGTCAAACTCATAGACATACATACTTTCAATCATAGTTCCAACCA
3903796 ATCAAGCAAATATCAACCACAAGTAATATAGCACCGAGTAAAGAGACATACCTCGACAAAAGCTA
391 ATCAAGCAAATATCAACCACAAGTAATATAGCACCGAGTAAAGAGACATACCTCGACAAAAGCTA
*
3903861 ATGTCGATAATAACCATA
456 ACGTCGATAATAACCATA
3903879 ACCATATAAGTAGGGTCTACCACAAAGACAGAGACCACTGAATCAAAAAAAGTGGCATTCATCCT
1 ACCATATAAGTAGGGTCTACCACAAAGACAGAGACCACTGAATCAAAAAAAGTGGCATTCATCCT
3903944 ATCGAGTGAATGCACTGAGCTTCCGCTATCAATATTAGTCCCAATATGATATGTAAAATGACAAA
66 ATCGAGTGAATGCACTGAGCTTCCGCTATCAATATTAGTCCCAATATGATATGTAAAATGACAAA
3904009 CAAATATGATTTTTGATTTGATCCGAATAAACAATATATCATCAACAAATATTTGAAAAAAATAT
131 CAAATATGATTTTTGATTTGATCCGAATAAACAATATATCATCAACAAATATTTGAAAAAAATAT
3904074 TCCGAAGCATATCAATTCTGAAGCATATCAATTCTGAAGCATATATTCCGAGAAAGCAACTCATT
196 TCCGAAGCATATCAATTCTGAAGCATATCAATTCTGAAGCATATATTCCGAGAAAGCAACTCATT
3904139 CACATGTTATGTATGCGCAATCATATTCTGATTCAAAAAGTTAAACATGCATCACATAGCAGTAT
261 CACATGTTATGTATGCGCAATCATATTCTGATTCAAAAAGTTAAACATGCATCACATAGCAGTAT
3904204 TTCCCAATTTTAATTTATATAGTCAAACTCATAGACATACATACTTTCAATCATAGTTCCAACCA
326 TTCCCAATTTTAATTTATATAGTCAAACTCATAGACATACATACTTTCAATCATAGTTCCAACCA
3904269 ATCAAGCAAATATCAACCACAAGTAATATAGCACCGAGTAAAGAGACATACCTCGACAAAAGCTA
391 ATCAAGCAAATATCAACCACAAGTAATATAGCACCGAGTAAAGAGACATACCTCGACAAAAGCTA
*
3904334 ACGTCGATAATAACCATT
456 ACGTCGATAATAACCATA
3904352 ACCA
1 ACCA
3904356 CGGTCAGCTC
Statistics
Matches: 473, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
473 473 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (473 bp):
ACCATATAAGTAGGGTCTACCACAAAGACAGAGACCACTGAATCAAAAAAAGTGGCATTCATCCT
ATCGAGTGAATGCACTGAGCTTCCGCTATCAATATTAGTCCCAATATGATATGTAAAATGACAAA
CAAATATGATTTTTGATTTGATCCGAATAAACAATATATCATCAACAAATATTTGAAAAAAATAT
TCCGAAGCATATCAATTCTGAAGCATATCAATTCTGAAGCATATATTCCGAGAAAGCAACTCATT
CACATGTTATGTATGCGCAATCATATTCTGATTCAAAAAGTTAAACATGCATCACATAGCAGTAT
TTCCCAATTTTAATTTATATAGTCAAACTCATAGACATACATACTTTCAATCATAGTTCCAACCA
ATCAAGCAAATATCAACCACAAGTAATATAGCACCGAGTAAAGAGACATACCTCGACAAAAGCTA
ACGTCGATAATAACCATA
Found at i:3905707 original size:20 final size:19
Alignment explanation
Indices: 3905684--3905722 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3905674 TACTAAACCT
*
3905684 TTGGTATCGATACCCGCCTG
1 TTGGCATCGATACCC-CCTG
3905704 TTGGCATCGATACCCCCTG
1 TTGGCATCGATACCCCCTG
3905723 CCTGACGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.28
Consensus pattern (19 bp):
TTGGCATCGATACCCCCTG
Found at i:3905811 original size:18 final size:21
Alignment explanation
Indices: 3905766--3905817 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
3905756 TACCCTAGAA
*
3905766 TGAGTATCGATATTATGGTAC
1 TGAGTATCGATACTATGGTAC
*
3905787 TGGGTATCGATACT-T-G-AC
1 TGAGTATCGATACTATGGTAC
3905805 TGAGTATCGATAC
1 TGAGTATCGATAC
3905818 CAAATTTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 1 0.04
21 12 0.43
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (21 bp):
TGAGTATCGATACTATGGTAC
Found at i:3905866 original size:12 final size:12
Alignment explanation
Indices: 3905851--3905877 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3905841 AAAATACCAG
3905851 TATCGATACTCC
1 TATCGATACTCC
3905863 TATCGATACTCC
1 TATCGATACTCC
3905875 TAT
1 TAT
3905878 AGGGATTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (12 bp):
TATCGATACTCC
Found at i:3918004 original size:14 final size:14
Alignment explanation
Indices: 3917957--3918005 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
3917947 TGAATAAATA
*
3917957 TCTGAAGCAAATAT
1 TCTGAAGCATATAT
*
3917971 TTTGAAGCATATCAAT
1 TCTGAAGCATAT--AT
3917987 TCTGAAGCATATAT
1 TCTGAAGCATATAT
3918001 TCTGA
1 TCTGA
3918006 GAAAGCAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 17 0.57
16 13 0.43
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (14 bp):
TCTGAAGCATATAT
Found at i:3920376 original size:4 final size:4
Alignment explanation
Indices: 3920367--3920402 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
3920357 CACTTAGTTT
3920367 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
3920403 TTAGGTACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3924559 original size:20 final size:20
Alignment explanation
Indices: 3924531--3924582 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3924521 TGGATTTCAA
3924531 TTATGGAAAATAAATTACAT
1 TTATGGAAAATAAATTACAT
* *
3924551 TTCTGGAAAATGAATTACAT
1 TTATGGAAAATAAATTACAT
3924571 TTATGGAAAATA
1 TTATGGAAAATA
3924583 TTTTCCGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (20 bp):
TTATGGAAAATAAATTACAT
Found at i:3924849 original size:31 final size:29
Alignment explanation
Indices: 3924781--3924850 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
3924771 AATATTATTT
*
3924781 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
3924811 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
3924844 TTATATT
1 TTATATT
3924851 AATTATTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:3925038 original size:23 final size:22
Alignment explanation
Indices: 3925012--3925069 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
3925002 TCTTTGAAAT
3925012 TAATAAATAATATAAGTTATTAA
1 TAATAAATAATATAA-TTATTAA
** *
3925035 TAATTTATTATAT-ATTATTAA
1 TAATAAATAATATAATTATTAA
3925056 -AATAAA-AATATAAT
1 TAATAAATAATATAAT
3925070 ATCTTATATT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
19 4 0.14
20 6 0.21
21 7 0.25
22 1 0.04
23 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATAAATAATATAATTATTAA
Found at i:3925130 original size:22 final size:22
Alignment explanation
Indices: 3925102--3925145 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3925092 TTGATTCTTT
3925102 TATTATAATATTAAAAATATTA
1 TATTATAATATTAAAAATATTA
* *
3925124 TATTATATTATTAGAAATATTA
1 TATTATAATATTAAAAATATTA
3925146 ATAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATAATATTAAAAATATTA
Found at i:3925163 original size:22 final size:22
Alignment explanation
Indices: 3925115--3925183 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 22
3925105 TATAATATTA
3925115 AAAATATT-AT-ATTATATTATT
1 AAAATATTAATAATTATATT-TT
*
3925136 AGAAATATTAATAAATATATTTT
1 A-AAATATTAATAATTATATTTT
3925159 AAAATGACTTAATAATTAATATTTT
1 AAAAT-A-TTAATAATT-ATATTTT
3925184 GATTAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 1 0.03
22 11 0.28
23 6 0.15
24 15 0.38
25 7 0.17
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (22 bp):
AAAATATTAATAATTATATTTT
Found at i:3925436 original size:42 final size:42
Alignment explanation
Indices: 3925380--3925474 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
3925370 TTCCTCCAAT
* * * **
3925380 CAAACACTGTAAAACATTTTCTGGGAAAAGAATTACGTGAAA
1 CAAACACAGGAAAACATTTTCCGAAAAAAGAATTACGTGAAA
3925422 CAAACACAGGAAAACATTTTCCGAAAAAAGAATTACGTGAAA
1 CAAACACAGGAAAACATTTTCCGAAAAAAGAATTACGTGAAA
*
3925464 GAAACACAGGA
1 CAAACACAGGA
3925475 TTTCGGAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.18
Consensus pattern (42 bp):
CAAACACAGGAAAACATTTTCCGAAAAAAGAATTACGTGAAA
Found at i:3927546 original size:18 final size:18
Alignment explanation
Indices: 3927523--3927567 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3927513 AACATTCCCA
**
3927523 GTAATCTTATTCCCGTCG
1 GTAATCTTATTCCCACCG
*
3927541 GTAATCCTATTCCCACCG
1 GTAATCTTATTCCCACCG
3927559 GTAATCTTA
1 GTAATCTTA
3927568 CATTCCGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (18 bp):
GTAATCTTATTCCCACCG
Found at i:3927674 original size:16 final size:16
Alignment explanation
Indices: 3927653--3927780 Score: 66
Period size: 16 Copynumber: 7.4 Consensus size: 16
3927643 AGTATTCATA
3927653 ATAATAATAATAATAC
1 ATAATAATAATAATAC
* *
3927669 ATAATACTAGTGCAATA-
1 ATAATAATAAT--AATAC
3927686 AT-ATAAATAATAATAC
1 ATAAT-AATAATAATAC
*
3927702 TATAAT-ATAATTATAC
1 -ATAATAATAATAATAC
*
3927718 ATACATATATACTAACATAC
1 ATA-ATA-ATAAT-A-ATAC
*
3927738 TATAAATAATAATAATAT
1 -AT-AATAATAATAATAC
3927756 ATGATATAACTAAT-ATAC
1 AT-A-ATAA-TAATAATAC
3927774 ATAATAA
1 ATAATAA
3927781 ATAGACCTGG
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
15 7 0.08
16 26 0.30
17 12 0.14
18 22 0.26
19 5 0.06
20 8 0.09
21 5 0.06
22 1 0.01
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAATAATAATAATAC
Found at i:3927706 original size:20 final size:19
Alignment explanation
Indices: 3927683--3927783 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 19
3927673 TACTAGTGCA
3927683 ATAATATAAATAATAATACT
1 ATAATAT-AATAATAATACT
*
3927703 ATAATATAATTATACATAC-
1 ATAATATAATAATA-ATACT
* *
3927722 AT-ATATACTAA-CATACT
1 ATAATATAATAATAATACT
3927739 ATAA-ATAATAATAATA-T
1 ATAATATAATAATAATACT
*
3927756 ATGATATAACTAAT-ATAC-
1 ATAATATAA-TAATAATACT
3927774 ATAATA-AATA
1 ATAATATAATA
3927784 GACCTGGACA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
16 6 0.09
17 14 0.21
18 23 0.35
19 12 0.18
20 11 0.17
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.35
Consensus pattern (19 bp):
ATAATATAATAATAATACT
Found at i:3928619 original size:72 final size:72
Alignment explanation
Indices: 3928529--3928811 Score: 372
Period size: 72 Copynumber: 4.0 Consensus size: 72
3928519 GACAAAAACT
** * *
3928529 TTCAAGGG-AAATATCTCAAGGGAGATTCAATTTTGTTTCGAGATAAACTGTCTTGAGTGAGACA
1 TTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACA
3928593 AAAAAAA
66 AAAAAAA
* * * * *
3928600 ATCAAGGGACAATATCTCAAGGGATATAAAATTTTGTTTTGAGAGAAACTGTCTCGAGTAAGAC-
1 TTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACA
3928664 AAAAAAA
66 AAAAAAA
* * *
3928671 TTCAAGGGAAAATATCTCAATGAAGATGAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACA
1 TTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACA
* ***
3928736 GAAACCT
66 AAAAAAA
* * **
3928743 TTCAAGGGAAAATATCTCAAGGGAAATAAAATTTTGTTTCGAGAGGAACTACCTCGAGTGAGACA
1 TTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACA
3928808 AAAA
66 AAAA
3928812 TTCTCAAAGG
Statistics
Matches: 181, Mismatches: 29, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
71 70 0.39
72 111 0.61
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (72 bp):
TTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACA
AAAAAAA
Found at i:3928704 original size:143 final size:142
Alignment explanation
Indices: 3928518--3929344 Score: 746
Period size: 143 Copynumber: 5.9 Consensus size: 142
3928508 GTTTTGAGCG
** ** *
3928518 AGACAAAAACTTTCAAGGG-AAATATCTCAAGGGAGATTCAATTTTGTTTCGAGATAAACTGTCT
1 AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTTTCGAGAGAAACTGTCT
** * ** * * *
3928582 TGAGTGAGACAAAAAAAAATCAAGGGACAATATCTCAAGGGATATAAAATTTTGTTTTGAGAGAA
66 CAAGTGAGACAGAAAAATTTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAA
3928647 ACTGTCTCGAGT
131 ACTGTCTCGAGT
* *
3928659 AAGACAAAAAAATTCAAGGGAAAATATCTCAATGAAGATGAAATTTTGTTTCGAGAGAAACTGTC
1 -AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTTTCGAGAGAAACTGTC
* ** * *
3928724 TCGAGTGAGACAGAAACCTTTCAAGGGAAAATATCTCAAGGGAAATAAAATTTTGTTTCGAGAGG
65 TCAAGTGAGACAGAAAAATTTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGA
**
3928789 AACTACCTCGAGT
130 AACTGTCTCGAGT
* * * *
3928802 -G------AGA--C-A---AAAAT-TCTCAAAGGAGATTAAACTTTTGTTCCGAGAGAAACTGTC
1 AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGAAA-TTTTGTTTCGAGAGAAACTGTC
* * *
3928853 TCAAGTGAGAC-GAAAATTTTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGA
65 TCAAGTGAGACAGAAAAATTTCAAGGGAAAATATCTCAAGGGAGAT-AAA-ATTTTGTTTCGAGA
3928917 GAAACTGTCTCGAGT
128 GAAACTGTCTCGAGT
*** *** * *
3928932 GAGGTGAAAGTTTTCAAGGGAAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAGAAACTGT
1 -AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGAAA-TTTTGTTTCGAGAGAAACTGT
* * *
3928997 CTCAAGTGAGA-TGAAAAATTTCAAGGGAAAATATCTAAAGGGAGATGAAATTTTTGTTTC-ATG
64 CTCAAGTGAGACAGAAAAATTTCAAGGGAAAATATCTCAAGGGAGAT-AAAATTTTGTTTCGA-G
*
3929060 AGAAACTGTCTCAAGT
127 AGAAACTGTCTCGAGT
* *** ** * **
3929076 -GAGATGTAAATTTTAGGGAAAAAATCTCAAGGGAGATGATTTTTTTGTTTCGAGAGAAACTGTC
1 AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGA-AATTTTGTTTCGAGAGAAACTGTC
* * *
3929140 TCAAATGAGA-TGAAAATTTTCAAGGGAAAATATCTCAAGGGAGATAAAACTTTTGTTTCGAGAG
65 TCAAGTGAGACAGAAAAATTTCAAGGGAAAATATCTCAAGGGAGATAAAA-TTTTGTTTCGAGAG
*
3929204 AAACTATCTCGAGT
129 AAACTGTCTCGAGT
* *** * * * * *
3929218 GAGACGAAAGTTTTCAAGGGAAAATATCTCAAGTGAGATAAAACTTTGTTTTGA-ATTAAACTGT
1 -AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTTTCGAGA-GAAACTGT
* ** * *
3929282 CTCGAGTGAGACA-AAAATTATTTTGA-GGAAAATTATCTCCAGTGAGATAAAATTTTGTTTCGA
64 CTCAAGTGAGACAGAAAA--ATTTCAAGGGAAAA-TATCTCAAGGGAGATAAAATTTTGTTTCGA
3929345 ATGAGAGTTG
Statistics
Matches: 561, Mismatches: 93, Indels: 60
0.79 0.13 0.08
Matches are distributed among these distances:
128 45 0.08
129 39 0.07
130 24 0.04
132 2 0.00
133 1 0.00
135 2 0.00
140 1 0.00
141 5 0.01
142 131 0.23
143 136 0.24
144 74 0.13
145 101 0.18
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.29
Consensus pattern (142 bp):
AGACAAAAAAATTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTGTTTCGAGAGAAACTGTCT
CAAGTGAGACAGAAAAATTTCAAGGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCGAGAGAA
ACTGTCTCGAGT
Found at i:3928835 original size:57 final size:56
Alignment explanation
Indices: 3928751--3928881 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 56
3928741 CTTTCAAGGG
* * * *
3928751 AAAATATCTCAAGGGAAATAAAATTTTGTTTCGAGAGGAACTACCTCGAGTGAGACA
1 AAAAT-TCTCAAAGGAAATAAAATTTTGTTCCGAGAGAAACTACCTCAAGTGAGACA
* * ** *
3928808 AAAATTCTCAAAGGAGATTAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACG
1 AAAATTCTCAAAGGA-AATAAAATTTTGTTCCGAGAGAAACTACCTCAAGTGAGACA
* *
3928865 AAAATTTTCAAGGGAAA
1 AAAATTCTCAAAGGAAA
3928882 ATATCTCAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
56 10 0.16
57 51 0.84
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (56 bp):
AAAATTCTCAAAGGAAATAAAATTTTGTTCCGAGAGAAACTACCTCAAGTGAGACA
Found at i:3928860 original size:129 final size:130
Alignment explanation
Indices: 3928679--3929222 Score: 416
Period size: 142 Copynumber: 4.0 Consensus size: 130
3928669 AATTCAAGGG
* * * *
3928679 AAAATATCTCAATGAAGATGAAATTTTGTTTCGAGAGAAACTGTCTCGAGTGAGACAGAAACCTT
1 AAAATATCTCAAAGAAGATGAAATTTTGTTCCGAGAGAAACTGTCTCAAGTGAGAC-GAAAACTT
* *
3928744 TCAAGGGAAAATATCTCAAGGGAAAT-AAA-ATTTTGTTTCGAGAGGAACTACCTCGAGTGAGAC
65 TCAAGGGAAAATATCTCAAGGGAAATGAAATATTTTGTTTCAAGAGAAACTACCTCGAGTGAGAC
3928807 A
130 A
* * *
3928808 AAAAT-TCTCAAAGGAGATTAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATTT
1 AAAATATCTCAAAGAAGATGAAA-TTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAACTT
* * **
3928872 TCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCGAGTGAGGT
65 TCAAGGGAAAATATCTCAAGGGAAATGAAATATTTTGTTTCAAGAGAAACTACCTCGAGTGA---
3928937 GAAAGTTTTCAA
127 G--A-----C-A
* ** * * *
3928949 GGGAAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAA
1 ---AAAATATCTCAAAGAAGATGAAA-TTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAA
* * * * **
3929014 ATTTCAAGGGAAAATATCTAAAGGGAGATGAAAT-TTTTGTTTCATGAGAAACTGTCTCAAGTGA
62 CTTTCAAGGGAAAATATCTCAAGGGAAATGAAATATTTTGTTTCAAGAGAAACTACCTC----GA
* *
3929078 GATGTAAATTTTA
123 G-TG-AGA---CA
* * * ** * * *
3929091 GGGAAAAAATCTCAAGGGAGATGATTTTTTTGTTTCGAGAGAAACTGTCTCAAATGAGATGAAAA
1 ---AAAATATCTCAAAGAAGATGA-AATTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAA
* * * *
3929156 TTTTCAAGGGAAAATATCTCAAGGGAGAT-AAA-ACTTTTGTTTCGAGAGAAACTATCTCGAGTG
62 CTTTCAAGGGAAAATATCTCAAGGGAAATGAAATA-TTTTGTTTCAAGAGAAACTACCTCGAGTG
3929219 AGAC
126 AGAC
3929223 GAAAGTTTTC
Statistics
Matches: 350, Mismatches: 38, Indels: 50
0.80 0.09 0.11
Matches are distributed among these distances:
128 45 0.13
129 39 0.11
130 26 0.07
133 1 0.00
135 1 0.00
136 2 0.01
137 2 0.01
138 3 0.01
140 1 0.00
141 4 0.01
142 107 0.31
143 3 0.01
144 28 0.08
145 82 0.23
148 3 0.01
149 2 0.01
150 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (130 bp):
AAAATATCTCAAAGAAGATGAAATTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAACTTT
CAAGGGAAAATATCTCAAGGGAAATGAAATATTTTGTTTCAAGAGAAACTACCTCGAGTGAGACA
Found at i:3928940 original size:39 final size:38
Alignment explanation
Indices: 3928808--3929256 Score: 236
Period size: 34 Copynumber: 12.5 Consensus size: 38
3928798 GAGTGAGACA
* * * *
3928808 AAAAT-TCTCAAAG-GAGATTAAACTTTTGTTCCGAGAG
1 AAAATATCTC-AAGTGAGATGAAATTTTTGTTTCAAGAG
* * * * *
3928845 AAACTGTCTCAAGTGAGACGAAA---AT-TTTCAAGGG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
*
3928879 AAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAG
1 AAAATATCTCAAGTGAGATGAAA-TTTTTGTTTCAAGAG
* * * * * *
3928918 AAACTGTCTCGAGTGAGGTGAAA---GT-TTTCAAGGG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* *
3928952 AAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* * ** *
3928990 AAACTGTCTCAAGTGAGATGAAA----AATTTCAAGGG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* * *
3929024 AAAATATCTAAAGGGAGATGAAATTTTTGTTTCATGAG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* * *
3929062 AAACTGTCTCAAGTGAGATGTAAA----T-TTT--AGGG
1 AAAATATCTCAAGTGAGATG-AAATTTTTGTTTCAAGAG
* * ** *
3929094 AAAAAATCTCAAGGGAGATGATTTTTTTGTTTCGAGAG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* * * * *
3929132 AAACTGTCTCAAATGAGATGAAA---AT-TTTCAAGGG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* * * *
3929166 AAAATATCTCAAGGGAGATAAAACTTTTGTTTCGAGAG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
* * * * *
3929204 AAACTATCTCGAGTGAGACGAAA---GT-TTTCAAGGG
1 AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
3929238 AAAATATCTCAAGTGAGAT
1 AAAATATCTCAAGTGAGAT
3929257 AAAACTTTGT
Statistics
Matches: 300, Mismatches: 85, Indels: 57
0.68 0.19 0.13
Matches are distributed among these distances:
31 1 0.00
32 18 0.06
34 128 0.43
35 6 0.02
36 3 0.01
37 9 0.03
38 106 0.35
39 29 0.10
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (38 bp):
AAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAG
Found at i:3929019 original size:72 final size:72
Alignment explanation
Indices: 3928808--3929256 Score: 625
Period size: 72 Copynumber: 6.3 Consensus size: 72
3928798 GAGTGAGACA
* * * * * *
3928808 AAAAT-TCTCAAAGGAGATTAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATTT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3928872 TCAAGGG
66 TCAAGGG
* * *
3928879 AAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCGAGTGAGGTGAAAGTT
1 AAAATATCTCAAGGGAGATGAAA-TTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATT
3928944 TTCAAGGG
65 TTCAAGGG
* *
3928952 AAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAAATT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929017 TCAAGGG
66 TCAAGGG
* * *
3929024 AAAATATCTAAAGGGAGATGAAATTTTTGTTTCATGAGAAACTGTCTCAAGTGAGATGTAAATTT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929089 T--AGGG
66 TCAAGGG
* ** * *
3929094 AAAAAATCTCAAGGGAGATGATTTTTTTGTTTCGAGAGAAACTGTCTCAAATGAGATGAAAATTT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929159 TCAAGGG
66 TCAAGGG
* * * * * * *
3929166 AAAATATCTCAAGGGAGATAAAACTTTTGTTTCGAGAGAAACTATCTCGAGTGAGACGAAAGTTT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929231 TCAAGGG
66 TCAAGGG
*
3929238 AAAATATCTCAAGTGAGAT
1 AAAATATCTCAAGGGAGAT
3929257 AAAACTTTGT
Statistics
Matches: 336, Mismatches: 38, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
70 62 0.18
71 5 0.01
72 205 0.61
73 64 0.19
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (72 bp):
AAAATATCTCAAGGGAGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAATTT
TCAAGGG
Found at i:3929152 original size:142 final size:142
Alignment explanation
Indices: 3928808--3929292 Score: 638
Period size: 142 Copynumber: 3.4 Consensus size: 142
3928798 GAGTGAGACA
* * * * *
3928808 AAAAT-TCTCAAAGGAGATTAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATTT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
*
3928872 TCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCGAGTGAGGT
66 TCAAGGGAAAATATCTCAAGGGAGATGAAA-TTTTTGTTTC-AGAGAAACTGTCTCGAGTGAGAT
3928937 GAAAGTTTTCAAGGG
129 GAAAGTTTT-AAGGG
* * *
3928952 AAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAAATT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
* *
3929017 TCAAGGGAAAATATCTAAAGGGAGATGAAATTTTTGTTTCATGAGAAACTGTCTCAAGTGAGATG
66 TCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTGTTTCA-GAGAAACTGTCTCGAGTGAGATG
3929082 TAAA-TTTT-AGGG
130 -AAAGTTTTAAGGG
* ** *
3929094 AAAAAATCTCAAGGGAGATGATTTTTTTGTTTCGAGAGAAACTGTCTCAAATGAGATGAAAATTT
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
* * * *
3929159 TCAAGGGAAAATATCTCAAGGGAGATAAAACTTTTGTTTCGAGAGAAACTATCTCGAGTGAGACG
66 TCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTGTTTC-AGAGAAACTGTCTCGAGTGAGATG
3929224 AAAGTTTTCAAGGG
130 AAAGTTTT-AAGGG
* ** * * *
3929238 AAAATATCTCAAGTGAGAT-AAAACTTTGTTTTGA-ATTAAACTGTCTCGAGTGAGA
1 AAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGA-GAAACTGTCTCAAGTGAGA
3929293 CAAAAATTAT
Statistics
Matches: 299, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
141 3 0.01
142 124 0.41
143 28 0.09
144 61 0.20
145 83 0.28
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (142 bp):
AAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
TCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTGTTTCAGAGAAACTGTCTCGAGTGAGATGA
AAGTTTTAAGGG
Found at i:3929206 original size:214 final size:216
Alignment explanation
Indices: 3928808--3929300 Score: 640
Period size: 214 Copynumber: 2.3 Consensus size: 216
3928798 GAGTGAGACA
*
3928808 AAAAT-TCTCAAA-GGAGATTAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATT
1 AAAATATCT-AAAGGGAGATGAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATT
* * * *
3928871 TTCAAGGGAAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCGAGTGAGG
65 TT-AAGGGAAAAAATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCAAATGAGA
* * * * *
3928936 TGAAAGTTTTCAAGGGAAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAGAAACTGTCTCA
129 TGAAAATTTTCAAGGGAAAATATCTCAAGGGAGATAAAACTTTTGTTTCAAGAGAAACTATCTCA
*
3929001 AGTGAGATGAAAAATTTCAAGGG
194 AGTGAGACGAAAAATTTCAAGGG
* * * *
3929024 AAAATATCTAAAGGGAGATGAAATTTTTGTTTC-ATGAGAAACTGTCTCAAGTGAGATGTAAATT
1 AAAATATCTAAAGGGAGATGAAACTTTTGTTCCGA-GAGAAACTGTCTCAAGTGAGACGAAAATT
* *
3929088 TT-AGGGAAAAAATCTCAAGGGAGATG-ATTTTTTTGTTTCGAGAGAAACTGTCTCAAATGAGAT
65 TTAAGGGAAAAAATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCAAATGAGAT
* *
3929151 GAAAATTTTCAAGGGAAAATATCTCAAGGGAGATAAAACTTTTGTTTCGAGAGAAACTATCTCGA
130 GAAAATTTTCAAGGGAAAATATCTCAAGGGAGATAAAACTTTTGTTTCAAGAGAAACTATCTCAA
**
3929216 GTGAGACGAAAGTTTTCAAGGG
195 GTGAGACGAAAAATTTCAAGGG
* * * ** * * *
3929238 AAAATATCTCAAGTGAGATAAAAC-TTTGTTTTGA-ATTAAACTGTCTCGAGTGAGACAAAAATT
1 AAAATATCTAAAGGGAGATGAAACTTTTGTTCCGAGA-GAAACTGTCTCAAGTGAGACGAAAATT
3929301 ATTTTGAGGA
Statistics
Matches: 241, Mismatches: 31, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
212 1 0.00
213 29 0.12
214 130 0.54
215 23 0.10
216 9 0.04
217 49 0.20
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (216 bp):
AAAATATCTAAAGGGAGATGAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATTT
TAAGGGAAAAAATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCAAATGAGATG
AAAATTTTCAAGGGAAAATATCTCAAGGGAGATAAAACTTTTGTTTCAAGAGAAACTATCTCAAG
TGAGACGAAAAATTTCAAGGG
Found at i:3929257 original size:72 final size:72
Alignment explanation
Indices: 3928808--3929344 Score: 622
Period size: 72 Copynumber: 7.5 Consensus size: 72
3928798 GAGTGAGACA
* * * * *
3928808 AAAAT-TCTCAAAGGAGATTAAACTTTTGTTCCGAGAGAAACTGTCTCAAGTGAGACGAAAATTT
1 AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3928872 TCAAGGG
66 TCAAGGG
* * * * *
3928879 AAAATATCTCAAGGGAGATGAAATTTTTTGTTTCAAGAGAAACTGTCTCGAGTGAGGTGAAAGTT
1 AAAATATCTCAAGGGAGAT-AAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATT
3928944 TTCAAGGG
65 TTCAAGGG
* * * *
3928952 AAAATATCTCAAGGGGGATGAAATTTTTGTTTCAAGAGAAACTGTCTCAAGTGAGATGAAAAATT
1 AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929017 TCAAGGG
66 TCAAGGG
* * *
3929024 AAAATATCTAAAGGGAGATGAAATTTTTGTTTC-ATGAGAAACTGTCTCAAGTGAGATGTAAATT
1 AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGA-GAGAAACTGTCTCAAGTGAGATGAAAATT
3929088 TT--AGGG
65 TTCAAGGG
* * ** *
3929094 AAAAAATCTCAAGGGAGATGATTTTTTTGTTTCGAGAGAAACTGTCTCAAATGAGATGAAAATTT
1 AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929159 TCAAGGG
66 TCAAGGG
* * * * *
3929166 AAAATATCTCAAGGGAGATAAAACTTTTGTTTCGAGAGAAACTATCTCGAGTGAGACGAAAGTTT
1 AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
3929231 TCAAGGG
66 TCAAGGG
* * * * * **
3929238 AAAATATCTCAAGTGAGATAAAA-CTTTGTTTTGA-ATTAAACTGTCTCGAGTGAGACAAAAATT
1 AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGAGA-GAAACTGTCTCAAGTGAGATGAAAATT
**
3929301 ATT-TTGAGG
65 -TTCAAG-GG
* *
3929310 AAAATTATCTCCAGTGAGATAAAA-TTTTGTTTCGA
1 AAAA-TATCTCAAGGGAGATAAAATTTTTGTTTCGA
3929345 ATGAGAGTTG
Statistics
Matches: 407, Mismatches: 49, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
70 63 0.15
71 40 0.10
72 215 0.53
73 89 0.22
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.30
Consensus pattern (72 bp):
AAAATATCTCAAGGGAGATAAAATTTTTGTTTCGAGAGAAACTGTCTCAAGTGAGATGAAAATTT
TCAAGGG
Found at i:3929290 original size:37 final size:36
Alignment explanation
Indices: 3929238--3929346 Score: 94
Period size: 36 Copynumber: 3.0 Consensus size: 36
3929228 TTTTCAAGGG
3929238 AAAA-TATCTCAAGTGAGATAAAACTTTGTTTTGAAT
1 AAAACTATCTCAAGTGAGATAAAA-TTTGTTTTGAAT
* * * * * * **
3929274 TAAACTGTCTCGAGTGAGACAAAAATTATTTTGAGG
1 AAAACTATCTCAAGTGAGATAAAATTTGTTTTGAAT
* * *
3929310 AAAATTATCTCCAGTGAGATAAAATTTTGTTTCGAAT
1 AAAACTATCTCAAGTGAGATAAAA-TTTGTTTTGAAT
3929347 GAGAGTTGTC
Statistics
Matches: 53, Mismatches: 18, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
36 30 0.57
37 23 0.43
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (36 bp):
AAAACTATCTCAAGTGAGATAAAATTTGTTTTGAAT
Found at i:3931459 original size:19 final size:19
Alignment explanation
Indices: 3931435--3931476 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
3931425 TAAGAGCTAA
3931435 AAAAGAAGAAAACAAAAA-G
1 AAAAGAAGAAAA-AAAAAGG
3931454 AAAAGAAGAAAAAAAAAGG
1 AAAAGAAGAAAAAAAAAGG
3931473 AAAA
1 AAAA
3931477 AATTAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAAAAAAAGG
Found at i:3935658 original size:10 final size:10
Alignment explanation
Indices: 3935643--3935667 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3935633 TACAGATTAC
3935643 ATCATTCGAG
1 ATCATTCGAG
3935653 ATCATTCGAG
1 ATCATTCGAG
3935663 ATCAT
1 ATCAT
3935668 AGGACTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (10 bp):
ATCATTCGAG
Found at i:3935873 original size:30 final size:30
Alignment explanation
Indices: 3935801--3935880 Score: 126
Period size: 29 Copynumber: 2.7 Consensus size: 30
3935791 AGTAACGTTA
3935801 ATGGGCTTATAAAAGATATCAGTATTGTAC
1 ATGGGCTTATAAAAGATATCAGTATTGTAC
*
3935831 AT-GGCTTATAAAAGATATCAGTATTGTAT
1 ATGGGCTTATAAAAGATATCAGTATTGTAC
* *
3935860 ATGGGCCTATAAAAAATATCA
1 ATGGGCTTATAAAAGATATCA
3935881 AAAGTGTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 28 0.61
30 18 0.39
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (30 bp):
ATGGGCTTATAAAAGATATCAGTATTGTAC
Found at i:3939723 original size:14 final size:14
Alignment explanation
Indices: 3939704--3939733 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3939694 AATAAAAGGG
3939704 ATCAAAAATAAATT
1 ATCAAAAATAAATT
3939718 ATCAAAAATAAATT
1 ATCAAAAATAAATT
3939732 AT
1 AT
3939734 AATTTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
ATCAAAAATAAATT
Found at i:3941650 original size:14 final size:14
Alignment explanation
Indices: 3941631--3941702 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
3941621 AATTATGTGA
3941631 TAAGGTTTAGGGTT
1 TAAGGTTTAGGGTT
*
3941645 TAAGGTTTAGAGTT
1 TAAGGTTTAGGGTT
* * *
3941659 T-ATGTGATAGGATT
1 TAAGGT-TTAGGGTT
**
3941673 TAAGGTTTAAAGTT
1 TAAGGTTTAGGGTT
3941687 T-AGAGTTTAGGGTT
1 TAAG-GTTTAGGGTT
3941701 TA
1 TA
3941703 TGTGTTAAGG
Statistics
Matches: 42, Mismatches: 12, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
13 5 0.12
14 34 0.81
15 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
TAAGGTTTAGGGTT
Found at i:3941674 original size:21 final size:21
Alignment explanation
Indices: 3941650--3941741 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 21
3941640 GGGTTTAAGG
*
3941650 TTTAGAGTTTATGTGATAGGA
1 TTTAGAGTTTATGTGTTAGGA
*
3941671 TTTA-AGGTTTAAAGT-TTA-GA
1 TTTAGA-GTTT-ATGTGTTAGGA
*
3941691 GTTTAGGGTTTATGTGTTAAGG-
1 -TTTAGAGTTTATGTGTT-AGGA
* *
3941713 TTTAGGGTTTATGTGTTAGGT
1 TTTAGAGTTTATGTGTTAGGA
3941734 TTTA-AGTT
1 TTTAGAGTT
3941742 ATGCCATGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
20 12 0.21
21 41 0.71
22 4 0.07
23 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (21 bp):
TTTAGAGTTTATGTGTTAGGA
Found at i:3941680 original size:35 final size:35
Alignment explanation
Indices: 3941623--3941695 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
3941613 TCATAACTAA
* *
3941623 TTATGTGATAAGGTTTAGGGTTTAAGGTTTAGAGT
1 TTATGTGATAAGGTTTAAGGTTTAAAGTTTAGAGT
3941658 TTATGTGAT-AGGATTTAAGGTTTAAAGTTTAGAGT
1 TTATGTGATAAGG-TTTAAGGTTTAAAGTTTAGAGT
3941693 TTA
1 TTA
3941696 GGGTTTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (35 bp):
TTATGTGATAAGGTTTAAGGTTTAAAGTTTAGAGT
Found at i:3941697 original size:28 final size:27
Alignment explanation
Indices: 3941635--3941702 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
3941625 ATGTGATAAG
* *
3941635 GTTTAGGGTTTAAGGTTTAGAGTTTAT
1 GTTTAGGGTTTAAGGTTTAAAGTTTAA
* *
3941662 GTGATAGGATTTAAGGTTTAAAGTTTAGA
1 GT-TTAGGGTTTAAGGTTTAAAGTTTA-A
3941691 GTTTAGGGTTTA
1 GTTTAGGGTTTA
3941703 TGTGTTAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (27 bp):
GTTTAGGGTTTAAGGTTTAAAGTTTAA
Found at i:3942038 original size:17 final size:17
Alignment explanation
Indices: 3942016--3942052 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3942006 ATTCGAGTTT
*
3942016 GAGTTCGAGCTTTAATC
1 GAGTTCGAGCTTGAATC
3942033 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
3942050 GAG
1 GAG
3942053 CTCAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:3942051 original size:11 final size:11
Alignment explanation
Indices: 3942037--3942101 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
3942027 TTAATCGAGT
*
3942037 TCGAGCTTGAA
1 TCGAGCTTCAA
3942048 TCGAGC-TCAAAA
1 TCGAGCTTC--AA
3942060 TCGAGCTTCAA
1 TCGAGCTTCAA
*
3942071 TCGAGC-TCGAGTC
1 TCGAGCTTC-A--A
3942084 TCGAGCTTCAA
1 TCGAGCTTCAA
3942095 TCGAGCT
1 TCGAGCT
3942102 CTTGAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.07
11 22 0.50
12 8 0.18
13 9 0.20
14 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:3942092 original size:24 final size:23
Alignment explanation
Indices: 3942031--3942102 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
3942021 CGAGCTTTAA
*
3942031 TCGAGTTCGAGCTTGAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
* **
3942054 TCAAAATCGAGCTTCAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
3942077 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGT-TCGAGCTTCAATCGAGC
3942101 TC
1 TC
3942103 TTGAATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (23 bp):
TCGAGTTCGAGCTTCAATCGAGC
Found at i:3944018 original size:14 final size:14
Alignment explanation
Indices: 3943982--3944032 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
3943972 CAAACTCTAA
*
3943982 CATTATTTACTTTCT
1 CATTATTTA-TTTTT
*
3943997 CATAATTT-TTTATT
1 CATTATTTATTT-TT
3944011 CATTATTTATTTTT
1 CATTATTTATTTTT
3944025 -ATTATTTA
1 CATTATTTA
3944033 ATACTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.35
14 10 0.32
15 10 0.32
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
CATTATTTATTTTT
Found at i:3948286 original size:20 final size:20
Alignment explanation
Indices: 3948258--3948300 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3948248 CATGGTTTCA
* *
3948258 TTTTGGTCACCTAACTATTT
1 TTTTAGTCACCCAACTATTT
*
3948278 TTTTAGTCACCCAATTATTT
1 TTTTAGTCACCCAACTATTT
3948298 TTT
1 TTT
3948301 GTTTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTAGTCACCCAACTATTT
Found at i:3949903 original size:20 final size:21
Alignment explanation
Indices: 3949873--3949927 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
3949863 ATTATTTTGA
*
3949873 AAAAAATAATAATTGGGTAAT-
1 AAAAAA-AATAATTAGGTAATC
* *
3949894 AAAAAAAATAGTTAGGTGATC
1 AAAAAAAATAATTAGGTAATC
3949915 AAAACAAAATAAT
1 AAAA-AAAATAAT
3949928 GAGAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 11 0.39
21 10 0.36
22 7 0.25
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.24
Consensus pattern (21 bp):
AAAAAAAATAATTAGGTAATC
Found at i:3952532 original size:60 final size:60
Alignment explanation
Indices: 3952359--3952538 Score: 254
Period size: 60 Copynumber: 3.0 Consensus size: 60
3952349 ATACCCCAGA
* * * * * **
3952359 ACATACATCCATAAGGACTTACCCTAGACCCCTAGGATATAGTAGTCCAATGTAAAAGAT
1 ACATACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
*
3952419 ACA-AGCATCCATAAGGACTTACCCTAGAACACTAAGATCTAGGAGTCCAATATGGAAGAT
1 ACATA-CATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
* *
3952479 ACATACATCAATAAGGACTTACCCTAGTCCACTAAGATCTAGGAGTCCAATATGGAAGAT
1 ACATACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
3952539 TAGAACAAAT
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 1 0.01
60 105 0.98
61 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (60 bp):
ACATACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
Found at i:3957535 original size:2 final size:2
Alignment explanation
Indices: 3957528--3957554 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3957518 ATTTACACCC
3957528 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3957555 GCTAAGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3958470 original size:28 final size:28
Alignment explanation
Indices: 3958425--3958478 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3958415 AAACAAAAAC
*
3958425 TTGTTGCTCGACTCGTTGTTCGTTAAGA
1 TTGTTGCTCGACTCGTTGTTCATTAAGA
*
3958453 TTGTTGCTCG-CATTGTTGTTCATTAA
1 TTGTTGCTCGAC-TCGTTGTTCATTAA
3958479 ACTCACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (28 bp):
TTGTTGCTCGACTCGTTGTTCATTAAGA
Found at i:3958727 original size:20 final size:19
Alignment explanation
Indices: 3958700--3958745 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3958690 TATTAATTAA
* *
3958700 TAATTTAATATTTATAGCAT
1 TAATTTAAAATTAATAG-AT
*
3958720 TTATTTAAAATTAATAGAT
1 TAATTTAAAATTAATAGAT
3958739 TAATTTA
1 TAATTTA
3958746 TCATCTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (19 bp):
TAATTTAAAATTAATAGAT
Found at i:3960103 original size:20 final size:21
Alignment explanation
Indices: 3960051--3960105 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3960041 ATACTCAAAG
3960051 GGGTATCGATACT-TGACCTA
1 GGGTATCGATACTATGACCTA
* **
3960071 GGAGTATCAATACTAT-ATTTA
1 GG-GTATCGATACTATGACCTA
3960092 GGGTATCGATACTA
1 GGGTATCGATACTA
3960106 CTCATTTCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.45
21 15 0.52
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (21 bp):
GGGTATCGATACTATGACCTA
Found at i:3963688 original size:35 final size:35
Alignment explanation
Indices: 3963648--3963737 Score: 139
Period size: 34 Copynumber: 2.6 Consensus size: 35
3963638 ATTCTAAGTG
*
3963648 TTTACAGTTATCAGATGATTTTCAGTTATTAGATA
1 TTTACAGATATCAGATGATTTTCAGTTATTAGATA
*
3963683 TTTACAGATATCAGATGA-TTACAGTTATTAGATA
1 TTTACAGATATCAGATGATTTTCAGTTATTAGATA
*
3963717 TTTACAGATATAAGAT-ATTTT
1 TTTACAGATATCAGATGATTTT
3963738 ATAATTATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.02
34 32 0.64
35 17 0.34
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTACAGATATCAGATGATTTTCAGTTATTAGATA
Found at i:3963698 original size:17 final size:17
Alignment explanation
Indices: 3963648--3963736 Score: 99
Period size: 17 Copynumber: 5.2 Consensus size: 17
3963638 ATTCTAAGTG
3963648 TTTACAGTTATCAGATGA
1 TTTACAGTTATCAGAT-A
* *
3963666 TTTTCAGTTATTAGATA
1 TTTACAGTTATCAGATA
*
3963683 TTTACAGATATCAGATGA
1 TTTACAGTTATCAGAT-A
*
3963701 -TTACAGTTATTAGATA
1 TTTACAGTTATCAGATA
* *
3963717 TTTACAGATATAAGATA
1 TTTACAGTTATCAGATA
3963734 TTT
1 TTT
3963737 TATAATTATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 1 0.02
17 44 0.73
18 15 0.25
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:3966275 original size:22 final size:22
Alignment explanation
Indices: 3966247--3966297 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
3966237 ACGTTAATTA
3966247 GTGTGTGTTGCAATTGTTGACT
1 GTGTGTGTTGCAATTGTTGACT
3966269 GTGTGTGTTGCAATTGTTGACT
1 GTGTGTGTTGCAATTGTTGACT
3966291 GTGTGTG
1 GTGTGTG
3966298 ATGAGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.12, C:0.08, G:0.35, T:0.45
Consensus pattern (22 bp):
GTGTGTGTTGCAATTGTTGACT
Found at i:3969517 original size:22 final size:22
Alignment explanation
Indices: 3969487--3969539 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3969477 GCACTTCCAC
* *
3969487 ACCATTGCTGAGACGCTTTAGT
1 ACCAGTGCTGAGACGCTTTAGG
3969509 ACCAGTGCTGAGACGCTTTAGG
1 ACCAGTGCTGAGACGCTTTAGG
3969531 ACCAGTGCT
1 ACCAGTGCT
3969540 ACGACACTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (22 bp):
ACCAGTGCTGAGACGCTTTAGG
Found at i:3972368 original size:42 final size:42
Alignment explanation
Indices: 3972309--3972399 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
3972299 TCACGAGCTT
*
3972309 TTCGAGTCGAGTATCAAGTAGCTAGTTTCGGTTCGTTAAGAA
1 TTCGAGTCGAGTATCAAGTAGCTAGTTTCGGCTCGTTAAGAA
*
3972351 TTCGAGTCGGGTATCAAGTAGCTAGTTTCGGCTCGTTAAGAA
1 TTCGAGTCGAGTATCAAGTAGCTAGTTTCGGCTCGTTAAGAA
3972393 TTCGAGT
1 TTCGAGT
3972400 TGAGCTCGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
TTCGAGTCGAGTATCAAGTAGCTAGTTTCGGCTCGTTAAGAA
Found at i:3973879 original size:26 final size:28
Alignment explanation
Indices: 3973850--3973909 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
3973840 TTTATAAATT
3973850 TTATA-TT-ATAATAAGCATTAATAGTA
1 TTATATTTCATAATAAGCATTAATAGTA
*
3973876 TTATGATTTCATAATAAGCATTAATGGTA
1 TTAT-ATTTCATAATAAGCATTAATAGTA
3973905 TTATA
1 TTATA
3973910 AGGTCTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
28 3 0.10
29 22 0.73
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (28 bp):
TTATATTTCATAATAAGCATTAATAGTA
Found at i:3976147 original size:14 final size:14
Alignment explanation
Indices: 3976128--3976157 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3976118 CATTTTTGAA
3976128 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
3976142 AGGAGATCTATATG
1 AGGAGATCTAGATG
3976156 AG
1 AG
3976158 AACAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Found at i:3979308 original size:21 final size:22
Alignment explanation
Indices: 3979266--3979309 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3979256 GAGCCTTGGA
3979266 TACCAACAAGTTTACTTTCTGT
1 TACCAACAAGTTTACTTTCTGT
*
3979288 TACCAACATGTTTAC-TTCTGT
1 TACCAACAAGTTTACTTTCTGT
3979309 T
1 T
3979310 GTTGTCGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (22 bp):
TACCAACAAGTTTACTTTCTGT
Found at i:3983189 original size:22 final size:21
Alignment explanation
Indices: 3983146--3983207 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 21
3983136 TCTAGTCTTG
*
3983146 TTTATTTTATTTTTTAATTTA
1 TTTATTTTATTTTTTAAATTA
3983167 TTTATTCTT-TTTCTTTAAATTA
1 TTTATT-TTATTT-TTTAAATTA
3983189 TTTATTTTAATTATTTTAA
1 TTTATTTT-ATT-TTTTAA
3983208 TAATCATTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 11 0.31
22 16 0.46
23 7 0.20
24 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTTTATTTTTTAAATTA
Found at i:3993980 original size:3 final size:3
Alignment explanation
Indices: 3993974--3994019 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
3993964 TTCATCATAT
*
3993974 TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
3994020 AATAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3998934 original size:21 final size:22
Alignment explanation
Indices: 3998889--3998961 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
3998879 CATACATGCA
*
3998889 TTTACATTTTGTATCTGTGCAT
1 TTTACATTTTGTATCTGTACAT
*
3998911 TTT-CATTTTGTATTCT-TACTT
1 TTTACATTTTGTA-TCTGTACAT
* *
3998932 TTTACATCTTTGAAT-TGCACAT
1 TTTACAT-TTTGTATCTGTACAT
*
3998954 TTTGCATT
1 TTTACATT
3998962 CTTATTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 17 0.41
22 19 0.46
23 5 0.12
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTACATTTTGTATCTGTACAT
Found at i:4001531 original size:8 final size:8
Alignment explanation
Indices: 4001507--4001585 Score: 63
Period size: 8 Copynumber: 9.4 Consensus size: 8
4001497 CTCATCCAGC
4001507 AAAGAAAGA
1 AAAGAAA-A
4001516 ATAAGGAAAA
1 A-AA-GAAAA
*
4001526 AAGGAAAA
1 AAAGAAAA
*
4001534 AAACAAAA
1 AAAGAAAA
4001542 ATGAA-AAAA
1 A--AAGAAAA
4001551 AAAGGAAAA
1 AAA-GAAAA
*
4001560 AAA-ACAA
1 AAAGAAAA
4001567 AAAGAAAA
1 AAAGAAAA
4001575 AAAGAAAA
1 AAAGAAAA
4001583 AAA
1 AAA
4001586 AGGGAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
7 8 0.14
8 26 0.45
9 14 0.24
10 6 0.10
11 4 0.07
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:4001547 original size:15 final size:14
Alignment explanation
Indices: 4001523--4001583 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
4001513 AGAATAAGGA
4001523 AAAAAGGAAAAAAAC
1 AAAAA-GAAAAAAAC
4001538 AAAAATGAAAAAAA-
1 AAAAA-GAAAAAAAC
**
4001552 AAGGA-AAAAAAAC
1 AAAAAGAAAAAAAC
*
4001565 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAC
4001579 AAAAA
1 AAAAA
4001584 AAAGGGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 7 0.18
13 3 0.08
14 15 0.39
15 13 0.34
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAAAAC
Found at i:4001551 original size:10 final size:11
Alignment explanation
Indices: 4001533--4001593 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
4001523 AAAAAGGAAA
*
4001533 AAAACAAAAATG
1 AAAA-AAAAAGG
4001545 AAAAAAAAAGG
1 AAAAAAAAAGG
*
4001556 AAAAAAAACA-A
1 AAAAAAAA-AGG
*
4001567 AAAGAAAAAAAG
1 AAA-AAAAAAGG
*
4001579 AAAAAAAAGGG
1 AAAAAAAAAGG
4001590 AAAA
1 AAAA
4001594 TTGAATCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 28 0.68
12 13 0.32
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:4001554 original size:26 final size:26
Alignment explanation
Indices: 4001522--4001577 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
4001512 AAGAATAAGG
4001522 AAAAAAGG-AAAAAAACAAAAATGAAA
1 AAAAAAGGAAAAAAAACAAAAA-GAAA
4001548 AAAAAAGGAAAAAAAACAAAAAGAAA
1 AAAAAAGGAAAAAAAACAAAAAGAAA
4001574 AAAA
1 AAAA
4001578 GAAAAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.02
Consensus pattern (26 bp):
AAAAAAGGAAAAAAAACAAAAAGAAA
Found at i:4001561 original size:34 final size:34
Alignment explanation
Indices: 4001507--4001593 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
4001497 CTCATCCAGC
* * *
4001507 AAAGAAAGAATAAGGAAAAAAGGAA-AAAAA-CAAA
1 AAAGAAAAAAAAAGGAAAAAA--AACAAAAAGAAAA
*
4001541 AATGAAAAAAAAAGGAAAAAAAACAAAAAGAAAA
1 AAAGAAAAAAAAAGGAAAAAAAACAAAAAGAAAA
*
4001575 AAAGAAAAAAAAGGGAAAA
1 AAAGAAAAAAAAAGGAAAA
4001594 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.04
33 5 0.11
34 38 0.84
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (34 bp):
AAAGAAAAAAAAAGGAAAAAAAACAAAAAGAAAA
Found at i:4001586 original size:27 final size:27
Alignment explanation
Indices: 4001530--4001586 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
4001520 GGAAAAAAGG
**
4001530 AAAAAAACAAAAATGAAAAAAAAAGGA
1 AAAAAAACAAAAATGAAAAAAAAAAAA
*
4001557 AAAAAAACAAAAA-GAAAAAAAGAAAA
1 AAAAAAACAAAAATGAAAAAAAAAAAA
4001583 AAAA
1 AAAA
4001587 GGGAAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.86, C:0.04, G:0.09, T:0.02
Consensus pattern (27 bp):
AAAAAAACAAAAATGAAAAAAAAAAAA
Found at i:4001593 original size:24 final size:24
Alignment explanation
Indices: 4001522--4001586 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 24
4001512 AAGAATAAGG
4001522 AAAAAAGG-AAAAAAACAAAAATGAAA
1 AAAAAAGGAAAAAAAACAAAAA-G--A
4001548 AAAAAAGGAAAAAAAACAAAAAGA
1 AAAAAAGGAAAAAAAACAAAAAGA
4001572 AAAAAA-GAAAAAAAA
1 AAAAAAGGAAAAAAAA
4001587 GGGAAAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.24
24 7 0.18
26 9 0.24
27 13 0.34
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.02
Consensus pattern (24 bp):
AAAAAAGGAAAAAAAACAAAAAGA
Found at i:4006223 original size:22 final size:22
Alignment explanation
Indices: 4006197--4006295 Score: 180
Period size: 22 Copynumber: 4.5 Consensus size: 22
4006187 ATCTACACTC
4006197 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
4006219 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
4006241 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
4006263 TTTAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
4006285 TTCAAAGATGA
1 TTCAAAGATGA
4006296 AAGCTTTATT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:4007112 original size:166 final size:164
Alignment explanation
Indices: 4006803--4007129 Score: 555
Period size: 166 Copynumber: 2.0 Consensus size: 164
4006793 CCACAAAAAT
4006803 AGCCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAAATGAGAAAAC
1 AGCCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAAATGAGAAAAC
* **
4006868 AATTTCCATAGTTTCTTATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAAGATTT
66 AATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAAGATTT
4006933 CCTTAGTTTTTTTACTTAGTAAACTATTTCCAAC
131 CCTTAGTTTTTTTACTTAGTAAACTATTTCCAAC
* * *
4006967 AGCCTTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAA
1 AGCCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTA-TTTCAAAAAAAATGAGAAAA
** *
4007032 TGATTTCCATAGTTTCTCATTCAATCTTTTCTAGAAATGAAATTGTTGAAAAGTAAGAAAACGAT
65 CAATTTCCATAGTTTCTCATTCAATCTTTTCTA-AAATGAAATTGTTGAAAAGTAAGAAAAAGAT
4007097 TTCCTTAGTTTTTTTACTTAGTAAACTATTTCC
129 TTCCTTAGTTTTTTTACTTAGTAAACTATTTCC
4007130 CACATATGTA
Statistics
Matches: 152, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
164 43 0.28
165 46 0.30
166 63 0.41
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (164 bp):
AGCCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAAATGAGAAAAC
AATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAAGATTT
CCTTAGTTTTTTTACTTAGTAAACTATTTCCAAC
Found at i:4007231 original size:76 final size:76
Alignment explanation
Indices: 4007136--4007617 Score: 885
Period size: 76 Copynumber: 6.3 Consensus size: 76
4007126 TTCCCACATA
* *
4007136 TGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
4007201 TTAGGGTCATC
66 TTAGGGTCATC
4007212 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
4007277 TTAGGGTCATC
66 TTAGGGTCATC
4007288 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
4007353 TTAGGGTCATC
66 TTAGGGTCATC
4007364 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
4007429 TTAGGGTCATC
66 TTAGGGTCATC
*
4007440 TGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
4007505 TTAGGGTCATC
66 TTAGGGTCATC
* * *
4007516 TGTAAGTCCTACAGTGCATGATGTTTCCAAAACGCCTTTGGGAGCTTTTTGATGTTTTCAAAACC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
4007581 TTAGGGTCATC
66 TTAGGGTCATC
*
4007592 TGTAAG-CCTTTCAGTGCATGATGTTT
1 TGTAAGTCC-TACAGTGCATGATGTTT
4007618 ACAATATTTC
Statistics
Matches: 397, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 2 0.01
76 395 0.99
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
TTAGGGTCATC
Found at i:4007754 original size:3 final size:3
Alignment explanation
Indices: 4007748--4007796 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
4007738 TTCATCATAT
* * *
4007748 TTA TTA TTA ATA TTA TTA ATA TTA TTA TTA TTA TATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
4007794 TTA
1 TTA
4007797 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:4007763 original size:9 final size:9
Alignment explanation
Indices: 4007749--4007793 Score: 72
Period size: 9 Copynumber: 4.9 Consensus size: 9
4007739 TCATCATATT
4007749 TATTATTAA
1 TATTATTAA
4007758 TATTATTAA
1 TATTATTAA
*
4007767 TATTATTAT
1 TATTATTAA
4007776 TATTATATAA
1 TATTAT-TAA
4007786 TATTATTA
1 TATTATTA
4007794 TTAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 25 0.76
10 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Found at i:4013404 original size:19 final size:18
Alignment explanation
Indices: 4013341--4013403 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
4013331 ATTTATAAAA
4013341 TTAAATTAATTATTT-ATT
1 TTAAA-TAATTATTTAATT
* *
4013359 TGAAATAA-TA-TTATTT
1 TTAAATAATTATTTAATT
4013375 TTAAATAATTTATTTAATT
1 TTAAATAA-TTATTTAATT
4013394 TTAAATAATT
1 TTAAATAATT
4013404 TTAAATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 3 0.08
18 8 0.22
19 13 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAAATAATTATTTAATT
Found at i:4017546 original size:6 final size:6
Alignment explanation
Indices: 4017535--4017559 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4017525 GAAGACACGT
4017535 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
4017560 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:4017565 original size:6 final size:6
Alignment explanation
Indices: 4017556--4017615 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
4017546 CATTACCATT
4017556 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4017604 ACCACG ACCACG
1 ACCACG ACCACG
4017616 TGCCGAGACG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4020039 original size:2 final size:2
Alignment explanation
Indices: 4020032--4020093 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
4020022 AGTTTTAAGG
4020032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4020074 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
4020094 TAAAGTTTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4021246 original size:13 final size:14
Alignment explanation
Indices: 4021220--4021249 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4021210 GTACATGAAG
4021220 AATAGAAGAAATGA
1 AATAGAAGAAATGA
4021234 AATAGAA-AAATGA
1 AATAGAAGAAATGA
4021247 AAT
1 AAT
4021250 CTTTGATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (14 bp):
AATAGAAGAAATGA
Found at i:4021689 original size:64 final size:63
Alignment explanation
Indices: 4021596--4021751 Score: 167
Period size: 63 Copynumber: 2.5 Consensus size: 63
4021586 ATTGTTCAAG
* * * * *
4021596 ATGTATCGATGCACATGA-AGTACAGCGATGCACTCCTTTAAAATAAAAACATCGAAT-GCCA-T
1 ATGTATCGATGCATA-GATAGTGCATCGATGCACCCCCTTAAAA-AAAAACATCGAATAG-CATT
4021658 T
63 T
* * *
4021659 AGTGTATTGATGCATA-AGTAGTGCATCGATGCACCCCCTTAAAAACAAACATCGAATAGGATTT
1 A-TGTATCGATGCATAGA-TAGTGCATCGATGCACCCCCTTAAAAAAAAACATCGAATAGCATTT
4021723 ATGTATCGATGCATAGATAGTGCATCGAT
1 ATGTATCGATGCATAGATAGTGCATCGAT
4021752 ACATGGTGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 39 0.50
64 38 0.49
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (63 bp):
ATGTATCGATGCATAGATAGTGCATCGATGCACCCCCTTAAAAAAAAACATCGAATAGCATTT
Found at i:4022408 original size:23 final size:23
Alignment explanation
Indices: 4022375--4022434 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
4022365 ATTATTATAT
4022375 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
4022398 GGCACTCCGGTGCAATTCTGCGT
1 GGCACTACGGTGCAATTCTACGC
4022421 GGCACTTA-GGTGCA
1 GGCAC-TACGGTGCA
4022435 TTTATACGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:4022879 original size:2 final size:2
Alignment explanation
Indices: 4022872--4022898 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4022862 TTGTATAAAC
4022872 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4022899 GTATTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4031059 original size:37 final size:38
Alignment explanation
Indices: 4031005--4031185 Score: 181
Period size: 37 Copynumber: 4.8 Consensus size: 38
4030995 TATAATATCT
* * *
4031005 TATTCTAATCGAATATAAATTCAT-AATAATATATTCA
1 TATTTTAATCAAATATAAATTTATAAATAATATATTCA
* **
4031042 TATTTTAATTAAATATAAATTTATAAATAATATATTTG
1 TATTTTAATCAAATATAAATTTATAAATAATATATTCA
* * * *
4031080 TA-TTTAATCAAATATAAATTTATAAACAATACATCCT
1 TATTTTAATCAAATATAAATTTATAAATAATATATTCA
* * *
4031117 TATTTTAATCGAATATAAATTTGT-AATAACATATTCA
1 TATTTTAATCAAATATAAATTTATAAATAATATATTCA
* **
4031154 AATTTTAATTGAATATAAATTCT-TAAATAATA
1 TATTTTAATCAAATATAAATT-TATAAATAATA
4031186 GAATATTATC
Statistics
Matches: 118, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
37 79 0.67
38 39 0.33
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (38 bp):
TATTTTAATCAAATATAAATTTATAAATAATATATTCA
Found at i:4031161 original size:75 final size:74
Alignment explanation
Indices: 4031010--4031175 Score: 181
Period size: 75 Copynumber: 2.2 Consensus size: 74
4031000 TATCTTATTC
* * * * *
4031010 TAATCGAATATAAATTCATAATAATATATTCATATTTTAATTAAATATAAATTTATAAATAATAT
1 TAATCGAATATAAATTCATAACAATACATCCATATTTTAATCAAATATAAATTTATAAATAACAT
***
4031075 ATTTGTATT
66 ATTCAAATT
* * * * *
4031084 TAATCAAATATAAATTTATAAACAATACATCCTTATTTTAATCGAATATAAATTTGT-AATAACA
1 TAATCGAATATAAATTCAT-AACAATACATCCATATTTTAATCAAATATAAATTTATAAATAACA
4031148 TATTCAAATTT
65 TATTCAAA-TT
*
4031159 TAATTGAATATAAATTC
1 TAATCGAATATAAATTC
4031176 TTAAATAATA
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
74 28 0.38
75 46 0.62
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (74 bp):
TAATCGAATATAAATTCATAACAATACATCCATATTTTAATCAAATATAAATTTATAAATAACAT
ATTCAAATT
Found at i:4032611 original size:29 final size:31
Alignment explanation
Indices: 4032578--4032648 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
4032568 ATTATATCTT
*
4032578 TTATACCATTGAACTTTTAATTTTA-TT-AA
1 TTATACCATTGAACTTTGAATTTTATTTCAA
* * *
4032607 TTATAGCATTAAACTTTGATTTTTATTTCAA
1 TTATACCATTGAACTTTGAATTTTATTTCAA
4032638 TTATACCATTG
1 TTATACCATTG
4032649 GGTTGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.62
30 2 0.06
31 11 0.32
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (31 bp):
TTATACCATTGAACTTTGAATTTTATTTCAA
Found at i:4032816 original size:29 final size:28
Alignment explanation
Indices: 4032771--4032829 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
4032761 ACAATTAAAC
*
4032771 TAAAATCAAAGTCCAATGTTATAATTGA
1 TAAAATCAAAGTCCAATGTTATAAATGA
*
4032799 TAAAATCGAAAGTTCAATGTTATAAATGA
1 TAAAATC-AAAGTCCAATGTTATAAATGA
4032828 TA
1 TA
4032830 CAACACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (28 bp):
TAAAATCAAAGTCCAATGTTATAAATGA
Done.