Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 37
Found at i:5223422 original size:19 final size:19
Alignment explanation
Indices: 5223398--5223442 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5223388 GATTCTCTCG
5223398 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5223417 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5223436 TTGCGAT
1 TTGCGAT
5223443 AGTCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5223538 original size:14 final size:14
Alignment explanation
Indices: 5223519--5223573 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5223509 CGGAAATGAA
5223519 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5223533 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5223552 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5223566 AATCGCAA
1 AATCGCAA
5223574 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:5223553 original size:33 final size:33
Alignment explanation
Indices: 5223501--5223592 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
5223491 CCATTACATT
5223501 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
5223535 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
5223568 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
5223593 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 49 0.84
34 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:5223592 original size:52 final size:52
Alignment explanation
Indices: 5223533--5223649 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
5223523 GCAACGAGAG
5223533 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
5223585 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
5223637 AATCGCATTGCGA
1 AATCGCAATGCGA
5223650 TTCTCCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:5223698 original size:19 final size:19
Alignment explanation
Indices: 5223656--5223755 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
5223646 GCGATTCTCC
5223656 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
5223676 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
5223695 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
5223711 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
5223728 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
5223747 CATTGCGAT
1 CATTGCGAT
5223756 AGTCAATTTT
Statistics
Matches: 73, 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 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:5223752 original size:52 final size:53
Alignment explanation
Indices: 5223639--5223755 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
5223629 GAAATTAAAA
5223639 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
5223692 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
5223744 TCGCATTGCGAT
1 TCGCATTGCGAT
5223756 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:5223881 original size:14 final size:14
Alignment explanation
Indices: 5223862--5223898 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5223852 CATCAATTAC
5223862 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5223876 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5223890 ACAAATCAA
1 ACAAATCAA
5223899 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:5225900 original size:14 final size:14
Alignment explanation
Indices: 5225881--5225937 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5225871 GCGAAATGAA
*
5225881 AATCGCAACGACAG
1 AATCGCAACGAAAG
5225895 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5225912 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5225928 AATCGCAACG
1 AATCGCAACG
5225938 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:5225908 original size:33 final size:33
Alignment explanation
Indices: 5225862--5225954 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5225852 GCGAAACCAA
*
5225862 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5225895 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5225928 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5225955 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:5225919 original size:19 final size:19
Alignment explanation
Indices: 5225825--5225959 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5225815 TAGTTTACTT
* *
5225825 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5225845 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5225864 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5225883 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5225897 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5225916 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5225930 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5225949 TCGCAATGCGA
1 TCGCAACGCGA
5225960 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:5225977 original size:19 final size:19
Alignment explanation
Indices: 5225955--5226083 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5225945 AAAATCGCAA
5225955 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5225974 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5225988 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5226007 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5226021 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5226040 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5226059 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5226079 TGCGA
1 TGCGA
5226084 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:5225997 original size:33 final size:33
Alignment explanation
Indices: 5225955--5226046 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5225945 AAAATCGCAA
5225955 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5225988 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5226021 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5226047 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:5226286 original size:93 final size:93
Alignment explanation
Indices: 5226127--5226599 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
5226117 TTGAATGGAT
5226127 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5226192 AGTTTAGCAGAATTGGCAGTAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5226220 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5226285 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5226313 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5226377 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5226405 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5226470 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5226498 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5226563 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5226591 AAATTTACT
1 AAATTTACT
5226600 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 284 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5226440 original size:185 final size:186
Alignment explanation
Indices: 5226127--5226599 Score: 912
Period size: 185 Copynumber: 2.5 Consensus size: 186
5226117 TTGAATGGAT
5226127 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5226192 AGTTTAGCAGAATTGGCAGTAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
5226257 TACTATTTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5226313 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5226377 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
5226442 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5226498 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5226563 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
5226600 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 183 0.65
186 100 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5228324 original size:14 final size:14
Alignment explanation
Indices: 5228305--5228394 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
5228295 TTGAAATGAA
5228305 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5228319 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5228336 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5228352 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
5228371 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5228385 ATTCGCAACG
1 AATCGCAACG
5228395 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
14 27 0.43
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.40, C:0.24, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5228342 original size:33 final size:33
Alignment explanation
Indices: 5228297--5228411 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
5228287 TCTTTTGGTT
5228297 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5228330 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5228363 GAAATGACAATCGCAACGAGAGATTCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5228396 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5228412 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5228343 original size:19 final size:19
Alignment explanation
Indices: 5228319--5228386 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
5228309 GCAACGAGAG
5228319 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAGATGAC
5228338 AATCGCAA--CGAGA-G--
1 AATCGCAACGCGAGATGAC
*
5228352 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAGATGAC
*
5228371 AATCGCAACGAGAGAT
1 AATCGCAACGCGAGAT
5228387 TCGCAACGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 6 0.15
19 22 0.54
ACGTcount: A:0.41, C:0.24, G:0.25, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAGATGAC
Found at i:5228447 original size:14 final size:14
Alignment explanation
Indices: 5228428--5228484 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5228418 TTTGGTTTCG
5228428 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5228442 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5228461 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5228475 CGTTGCGATT
1 CGTTGCGATT
5228485 GTCATTTCTC
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:5228460 original size:33 final size:33
Alignment explanation
Indices: 5228412--5228492 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
5228402 AAAATCGCAA
**
5228412 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5228445 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
5228478 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
5228493 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5228495 original size:21 final size:21
Alignment explanation
Indices: 5228469--5228544 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5228459 CGCGTTGCGA
5228469 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
5228490 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
5228510 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
5228531 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
5228545 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:5228525 original size:41 final size:41
Alignment explanation
Indices: 5228468--5228545 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5228458 TCGCGTTGCG
*
5228468 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
5228509 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
5228546 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:5228671 original size:33 final size:33
Alignment explanation
Indices: 5228624--5228694 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
5228614 AATACTAACT
* *
5228624 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5228657 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5228690 TGAAA
1 TGAAA
5228695 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5228928 original size:22 final size:22
Alignment explanation
Indices: 5228876--5228930 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5228866 TGGTTGTGAG
**
5228876 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5228898 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5228920 GGATTTCTTCG
1 GGATTTCTTCG
5228931 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:5229096 original size:39 final size:40
Alignment explanation
Indices: 5229053--5229134 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
5229043 TACGCGTAGC
*
5229053 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTATAGAT-TCGCGTTGCGATTTACG
** * *
5229092 GATTATCGTTGCGATTTATAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTATAGATTCGCGTTGCGATTTACG
5229132 GAT
1 GAT
5229135 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (40 bp):
GATTATAATGGCGATTTATAGATTCGCGTTGCGATTTACG
Found at i:5229103 original size:20 final size:20
Alignment explanation
Indices: 5229076--5229308 Score: 263
Period size: 20 Copynumber: 11.7 Consensus size: 20
5229066 CTTTAAATAT
5229076 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* ** *
5229097 -TCGTTGCGATTTATAGATT
1 CGCGTTGCGATTTACGGATA
*
5229116 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5229136 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
5229156 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5229176 CGCATTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5229196 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5229216 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5229236 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5229256 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5229276 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5229296 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5229309 TGGAAAATCG
Statistics
Matches: 185, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 183 0.99
21 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5229325 original size:21 final size:21
Alignment explanation
Indices: 5229295--5229377 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
5229285 ATTTTCATAT
*
5229295 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
5229316 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
5229337 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
5229358 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
5229378 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:5229368 original size:42 final size:43
Alignment explanation
Indices: 5229275--5229373 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
5229265 ATTTATGTGT
* *
5229275 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
5229316 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
5229358 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5229374 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:5231386 original size:78 final size:78
Alignment explanation
Indices: 5231257--5231647 Score: 755
Period size: 78 Copynumber: 5.0 Consensus size: 78
5231247 ACTTGTTTGT
5231257 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
1 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
*
5231322 GAACTTGAATGGA
66 GAACTTGAAAGGA
* *
5231335 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGATGACCGTGCATGGCAATCTGG
1 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
5231400 GAACTTGAAAGGA
66 GAACTTGAAAGGA
5231413 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
1 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
5231478 GAACTTGAAAGGA
66 GAACTTGAAAGGA
5231491 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
1 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
5231556 GAACTTGAAAGGA
66 GAACTTGAAAGGA
5231569 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
1 AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
5231634 GAACTTGAAAGGA
66 GAACTTGAAAGGA
5231647 A
1 A
5231648 GAGTCATCAG
Statistics
Matches: 308, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 308 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (78 bp):
AACTTTGTTCTTCAATCAGAACCATCATCTCCTTGTATGTGTGAAGACCGTGCAAGGCAATCTGG
GAACTTGAAAGGA
Found at i:5232315 original size:2 final size:2
Alignment explanation
Indices: 5232308--5232342 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5232298 CAACTCAACC
5232308 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 T
5232343 TAGATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5253304 original size:2 final size:2
Alignment explanation
Indices: 5253297--5253324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5253287 TTTCGAACAC
5253297 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
5253325 GAGGAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5257032 original size:10 final size:10
Alignment explanation
Indices: 5257017--5257064 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
5257007 CATTTAAATG
5257017 ATAAACGAAC
1 ATAAACGAAC
5257027 ATAAACGAACAC
1 ATAAACG-A-AC
*
5257039 AAATGAACGAAC
1 --ATAAACGAAC
5257051 ATAAACGAAC
1 ATAAACGAAC
5257061 ATAA
1 ATAA
5257065 TAAATGAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 20 0.62
11 1 0.03
12 4 0.12
13 1 0.03
14 6 0.19
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5257049 original size:24 final size:23
Alignment explanation
Indices: 5257017--5257094 Score: 90
Period size: 24 Copynumber: 3.5 Consensus size: 23
5257007 CATTTAAATG
5257017 ATAAACGAACATAAACGAACACAA
1 ATAAACGAACATAAACGAACA-AA
* *
5257041 ATGAACGAACATAAACGAACATA
1 ATAAACGAACATAAACGAACAAA
*
5257064 ATAAATGAACATAAAC--A-AAA
1 ATAAACGAACATAAACGAACAAA
*
5257084 ATAAACAAACA
1 ATAAACGAACA
5257095 ACACAAACAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 11 0.23
21 1 0.02
23 15 0.32
24 20 0.43
ACGTcount: A:0.64, C:0.17, G:0.08, T:0.12
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACAAA
Found at i:5257642 original size:13 final size:13
Alignment explanation
Indices: 5257624--5257649 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5257614 TTATATCTTC
5257624 GAAATACGAAAGA
1 GAAATACGAAAGA
5257637 GAAATACGAAAGA
1 GAAATACGAAAGA
5257650 TATCTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (13 bp):
GAAATACGAAAGA
Found at i:5260557 original size:183 final size:181
Alignment explanation
Indices: 5260071--5260719 Score: 805
Period size: 182 Copynumber: 3.6 Consensus size: 181
5260061 ATACAAATTA
* * * * * * * *
5260071 AAAATGTATCGGTCCATAGCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTATGATA
1 AAAATGTATAGATCCATAACAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGATA
** * *
5260135 AAACCGGTAAAGTGCTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTGTCGACACTTT
65 AAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
* * *
5260200 TGTAATTTAAAAGATAAGAAGTTATAGCGCCTAAAAGGTGTAGATACTTTATA
130 TGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTATG
* * * ** *
5260253 AAAATATGTAGATCAATGGCAATATAACAGGTAATAATATGACAAAACATGTCTCGAAATGATAA
1 AAAATGTATAGATCCATAACAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAA
*
5260318 AACCGATAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
66 AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
*
5260383 GTAATTTAAAAGAGAAGAAGTTATAGCACCTGAAAAGTGTCGATACTTTATG
131 GTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTATG
* * * * * *
5260435 TAAATGTATCGATCCATAATAATATATCCGGTAATAATATGACAAAAAGAGGTCTCGAAATGATA
1 AAAATGTATAGATCCATAACAATATAACAGGTAATAATATGAC-AAAACAGGTCTCGAAATGATA
* * * *
5260500 AAATCGGTAAAAAGATACCGGATATATTTAAAGTGTCGATAAATTAGTATAAGTATCGACACTTT
65 AAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
* * * *
5260565 CGTAATTTAAAAGAGAATAAATTATAGCGCCTAAAAAGTGTCGATACTTTAAG
130 TGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTATG
* * * * * * * *
5260618 AAAATGTATAGATCCATAACAATATAATATGTAAAAATATGATAAAACCGATATCGAAATGACAA
1 AAAATGTATAGATCCATAACAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAA
** * *
5260683 AACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCG
66 AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCG
5260720 GTACTTTAAT
Statistics
Matches: 399, Mismatches: 65, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
182 234 0.59
183 165 0.41
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (181 bp):
AAAATGTATAGATCCATAACAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAA
AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
GTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTATG
Found at i:5262888 original size:15 final size:15
Alignment explanation
Indices: 5262865--5262894 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5262855 TTGGAGGGGT
5262865 GGATGACGGTCAGGG
1 GGATGACGGTCAGGG
*
5262880 GGATTACGGTCAGGG
1 GGATGACGGTCAGGG
5262895 AAAACAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.50, T:0.17
Consensus pattern (15 bp):
GGATGACGGTCAGGG
Found at i:5263271 original size:18 final size:18
Alignment explanation
Indices: 5263248--5263286 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5263238 GAGAAAATTT
*
5263248 GAAGAAGAAAAGATTGAG
1 GAAGAAGAAAAGATGGAG
5263266 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
5263284 GAA
1 GAA
5263287 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:5263610 original size:17 final size:17
Alignment explanation
Indices: 5263588--5263623 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5263578 TTTAAATATT
5263588 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
5263605 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
5263622 TC
1 TC
5263624 CTAATGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:5265573 original size:198 final size:199
Alignment explanation
Indices: 5265133--5265644 Score: 789
Period size: 198 Copynumber: 2.6 Consensus size: 199
5265123 TGTTTAATTT
* **
5265133 GTATCGATCCCAAAAACATCGAGAACCATAATTATAATGTAATAGGTCTATTATCAATCTAACCG
1 GTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
*
5265198 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTGTG
66 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTATG
** *
5265263 TCGATCCCATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGGAAATGTGTCGATACATT
131 TCG----CATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATCCAAATGTGTCGATACATG
*
5265328 TATAAAAC
192 TATAAAAA
* *
5265336 GTATCGATCCCAAAAACATCGAGACCCATAACTATAATGTAGTAGGTAAATTATCAATCTAACCG
1 GTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* *
5265401 GTCTAAATACACCGGTTTATGAGAAAACATGTGTACATGAAGTATCGACACTT-TTTAAATTTAT
66 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTT-AATTTAT
* *
5265465 GTCG-ATACTTTGTGTCCAGAATGATTTTCTTACTAAG-GTCA-CCATAATGTGTCGATACATGT
130 GTCGCATACTTTGTGTCCAGAATGATTTCCTTACCAAGTG-CATCCA-AATGTGTCGATACATGT
5265527 ATAAAAA
193 ATAAAAA
*
5265534 GTATCGATCCCAAAAACATCAAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
1 GTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
*
5265599 GTCTAAATACACCGGTTTATGAGAAAATAGGTGTACATAAAGTATC
66 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATC
5265645 TATACTTTGT
Statistics
Matches: 286, Mismatches: 20, Indels: 11
0.90 0.06 0.03
Matches are distributed among these distances:
197 2 0.01
198 160 0.56
202 3 0.01
203 121 0.42
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTATG
TCGCATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATCCAAATGTGTCGATACATGTATA
AAAA
Found at i:5266170 original size:15 final size:15
Alignment explanation
Indices: 5266150--5266185 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5266140 GACTCGGGGT
*
5266150 TCTTCTCAACCCAGC
1 TCTTCTCAACCCACC
5266165 TCTTCTCAACCCACC
1 TCTTCTCAACCCACC
5266180 TCTTCT
1 TCTTCT
5266186 GAGGATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.47, G:0.03, T:0.33
Consensus pattern (15 bp):
TCTTCTCAACCCACC
Found at i:5269203 original size:22 final size:21
Alignment explanation
Indices: 5269177--5269222 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5269167 TAAAAAAAGG
*
5269177 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
5269199 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
5269220 TAT
1 TAT
5269223 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:5269299 original size:198 final size:199
Alignment explanation
Indices: 5268842--5269372 Score: 667
Period size: 198 Copynumber: 2.7 Consensus size: 199
5268832 TTTCCAAACA
* * **
5268842 AAACAAGTTCACAAATAAGTGTCGACACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACC
1 AAACAAGTTCACAAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACC
* * *
5268907 CGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGATTTAAATTTACCGGTTTTATGAGAA
66 CGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATATACCGGTTTTATGAGAA
* * * * * **
5268972 AATAGGTCTACAATATGTGTCGACACTTTATTCATTTGTGTCGATACATGTTGTCCAGAATGTAT
131 AAAAGGTATACAATATGTATCGACACTTTATACATTTGTGTCGACACATGTTGTCCAGAATAAAT
5269037 TTCC
196 TTCC
* * * *
5269041 AAACCAAGTGCACGAACAAAGTGTCGATACATTTATAAAAAGTGTCGATCCTATAAACATCGAAA
1 AAA-CAAGTTCAC-AAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAA
* * * * * * * * *
5269106 CACATAATTATAATGTAATCGGTAACATAATAATGTAACCGGTCTAAATATACTGGTTATT-T-A
64 CCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATATACCGGTT-TTATGA
* * *
5269169 -AAAAAAGGTATAC-ATAATGTATCGATACTTTATACATTTGTGTCGACAC-TTTATGTCCATAA
128 GAAAAAAGGTATACAAT-ATGTATCGACACTTTATACATTTGTGTCGACACATGT-TGTCCAGAA
5269231 TAAATTTTCC
191 TAAA-TTTCC
* *
5269241 AAACAAGTTCACAAAAAAGTGTCGATACATTTAGAAAAAGTGTCGATCCGAAAAACATCGAAACC
1 AAACAAGTTCACAAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACC
* *
5269306 CGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCAGTTTTATGAGAA
66 CGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATATACCGGTTTTATGAGAA
5269371 AA
131 AA
5269373 TATATCTACA
Statistics
Matches: 277, Mismatches: 46, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
197 2 0.01
198 99 0.36
199 62 0.22
200 21 0.08
201 91 0.33
202 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (199 bp):
AAACAAGTTCACAAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACC
CGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATATACCGGTTTTATGAGAA
AAAAGGTATACAATATGTATCGACACTTTATACATTTGTGTCGACACATGTTGTCCAGAATAAAT
TTCC
Found at i:5272423 original size:87 final size:87
Alignment explanation
Indices: 5272319--5272481 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
5272309 AAATATGTCA
* *
5272319 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATTTGTTATTGTACTTTATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
*
5272384 TCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * * *
5272406 ATATAAGCGCTATCTATTACATTATCTAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
5272471 CCGGTTAAATG
66 CCGGTTAAATG
5272482 ATATAACATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:5272453 original size:23 final size:23
Alignment explanation
Indices: 5272403--5272447 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5272393 TGCCTATTTT
* *
5272403 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
5272426 ATTATCTAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
5272448 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:5273617 original size:2 final size:2
Alignment explanation
Indices: 5273610--5273635 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5273600 ACCCAATTTA
5273610 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
5273636 TATGTAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5274693 original size:2 final size:2
Alignment explanation
Indices: 5274688--5274730 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5274678 TCCTTAAAAA
5274688 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
5274730 A
1 A
5274731 AACATTAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5278397 original size:15 final size:15
Alignment explanation
Indices: 5278377--5278405 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5278367 CGTTGAATAT
5278377 AAATATGTATTTTAG
1 AAATATGTATTTTAG
5278392 AAATATGTATTTTA
1 AAATATGTATTTTA
5278406 AGTCCTTAAT
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:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
AAATATGTATTTTAG
Found at i:5291120 original size:61 final size:60
Alignment explanation
Indices: 5291055--5291168 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
5291045 GTCTCGCGAG
* ** * *
5291055 TATAAGATATAATTTTATTTGAG-TCATTTGACTTTTAAAAGTTATAAAATGATCTTACGGT
1 TATAAGATATAATTTTA-TTAAGTTC-TCCGACTATTAAAAGTTAAAAAATGATCTTACGGT
* *
5291116 TATAAGATGTTATTTTATTAAGTTCTCCGACTATTAAAAGTTAAAAAATGATC
1 TATAAGATATAATTTTATTAAGTTCTCCGACTATTAAAAGTTAAAAAATGATC
5291169 ATTCAACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
60 28 0.62
61 17 0.38
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (60 bp):
TATAAGATATAATTTTATTAAGTTCTCCGACTATTAAAAGTTAAAAAATGATCTTACGGT
Found at i:5291742 original size:20 final size:20
Alignment explanation
Indices: 5291709--5291748 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5291699 TGTGTGGTAT
* *
5291709 TAAATTTGATATTTTTTAAA
1 TAAATTTGAAATTTTATAAA
*
5291729 TAAATTTTAAATTTTATAAA
1 TAAATTTGAAATTTTATAAA
5291749 AAGAAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TAAATTTGAAATTTTATAAA
Found at i:5292579 original size:35 final size:35
Alignment explanation
Indices: 5292530--5292600 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
5292520 GTTAAAAATT
*
5292530 ATATTAATATACTAAATTAAAAGCAGAGCCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGAGCCCATAA
*
5292565 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGAGCCCATAA
5292600 A
1 A
5292601 CTTATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGAGCCCATAA
Found at i:5292984 original size:218 final size:219
Alignment explanation
Indices: 5292596--5293034 Score: 819
Period size: 218 Copynumber: 2.0 Consensus size: 219
5292586 AGCAGGGCCC
5292596 ATAAACTTATTTCTTATTGACTTATTAAAAAAATGTTGTAATAATTTTAAGATTATTTTTTTCAT
1 ATAAACTTATTTCTTATTGACTTATTAAAAAAATGTTGTAATAATTTTAAGATTATTTTTTTCAT
*
5292661 AATAATTTATCGGATGTTGATGCGAATGAATTTTTTTTGAAAATAAAGTGTTGCAATTGACTTTT
66 AATAATTTATCGGATGTTGATGCGAATGAATTTTTTTTGAAAATAAAGTGTTGCAATTGACTTTG
*
5292726 CCAAATATATTCATGTCAGCGCTTGAAGTTCTTGAGTTTGTTAAAGCTGTAGATTGTTATCCTAA
131 CCAAATATATTCATGTCAGCGCTTGAAGTTCTTGAGTTTGTTAAAGCTGGAGATTGTTATCCTAA
5292791 TGTTTCAATTGTTTATCGAATTTT
196 TGTTTCAATTGTTTATCGAATTTT
5292815 ATAAACTTATTTCTTATTGACTTATTAAAAAAATGTTGTAATAATTTTAAGATTATTATTTTTCA
1 ATAAACTTATTTCTTATTGACTTATTAAAAAAATGTTGTAATAATTTTAAGATTATT-TTTTTCA
*
5292880 TAATAATTTGTCGGATGTTGATGCGAATG-ATTTTTTTT-AAAATAAAGTGTTGCAATTGACTTT
65 TAATAATTTATCGGATGTTGATGCGAATGAATTTTTTTTGAAAATAAAGTGTTGCAATTGACTTT
*
5292943 GCCAAATGTATTCATGTCAGCGCTTGAAGTTCTTGAGTTTGTTAAAGCTGGAGATTGTTATCCTA
130 GCCAAATATATTCATGTCAGCGCTTGAAGTTCTTGAGTTTGTTAAAGCTGGAGATTGTTATCCTA
5293008 ATGTTTCAATTGTTTATCGAATTTT
195 ATGTTTCAATTGTTTATCGAATTTT
5293033 AT
1 AT
5293035 TAACAATGCT
Statistics
Matches: 215, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
218 114 0.53
219 66 0.31
220 35 0.16
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (219 bp):
ATAAACTTATTTCTTATTGACTTATTAAAAAAATGTTGTAATAATTTTAAGATTATTTTTTTCAT
AATAATTTATCGGATGTTGATGCGAATGAATTTTTTTTGAAAATAAAGTGTTGCAATTGACTTTG
CCAAATATATTCATGTCAGCGCTTGAAGTTCTTGAGTTTGTTAAAGCTGGAGATTGTTATCCTAA
TGTTTCAATTGTTTATCGAATTTT
Found at i:5296476 original size:26 final size:26
Alignment explanation
Indices: 5296447--5296497 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5296437 TATTTTCTTG
* *
5296447 TATTTCTAAAATTTTATATATTTATT
1 TATTTCTAAAATTTTAAAAATTTATT
*
5296473 TATTTTTAAAATTTTAAAAATTTAT
1 TATTTCTAAAATTTTAAAAATTTAT
5296498 CTCTCAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TATTTCTAAAATTTTAAAAATTTATT
Found at i:5298485 original size:18 final size:18
Alignment explanation
Indices: 5298439--5298486 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
5298429 GAAGGGCCGG
* *
5298439 CTTCATCGCCAATGAATC
1 CTTCATCGCCGATGAACC
*
5298457 CGTCATCGCCGATGAACC
1 CTTCATCGCCGATGAACC
5298475 CTTCATCGCCGA
1 CTTCATCGCCGA
5298487 GGAGTAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (18 bp):
CTTCATCGCCGATGAACC
Found at i:5303993 original size:21 final size:21
Alignment explanation
Indices: 5303964--5304010 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5303954 ATTCTGACTA
*
5303964 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCAATTTTCCAAAT
* *
5303985 TCGCGTTGCAATTTTCCGAAT
1 TCGCATTGCAATTTTCCAAAT
5304006 TCGCA
1 TCGCA
5304011 ATGCGAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCAAAT
Found at i:5304031 original size:20 final size:20
Alignment explanation
Indices: 5304006--5304178 Score: 150
Period size: 20 Copynumber: 8.7 Consensus size: 20
5303996 TTTTCCGAAT
*
5304006 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACAA
*
5304026 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACAA
*
5304046 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACAA
* * *
5304066 TCGCAACGAGATTATGACTA
1 TCGCAATGCGATTATGACAA
* * *
5304086 TCGCAACGAGATTATGACTA
1 TCGCAATGCGATTATGACAA
* * *
5304106 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACAA
* * *
5304126 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACAA
* ** *
5304146 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTATGACAA
*
5304166 TAGCAATGCGATT
1 TCGCAATGCGATT
5304179 TTCAAAGTGC
Statistics
Matches: 142, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
19 1 0.01
20 141 0.99
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGATTATGACAA
Found at i:5304052 original size:40 final size:40
Alignment explanation
Indices: 5304006--5304178 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
5303996 TTTTCCGAAT
* * *
5304006 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATG-ACTATCGCAACGCGATTATGACTA
*
5304046 TCGCAATGCGATTATGACTATCGCAACGAGATTATGACTA
1 TCGCAATGCGATTATGACTATCGCAACGCGATTATGACTA
* * *
5304086 TCGCAACGAGATTATGACTATCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTATCGCAACGCGATTATGACTA
* * **
5304126 TCGCAACGCGATTCTGACTATCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTATGACTATCGCAACGCGATTATGACTA
*
5304166 TAGCAATGCGATT
1 TCGCAATGCGATT
5304179 TTCAAAGTGC
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 1 0.01
40 118 0.99
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGATTATGACTATCGCAACGCGATTATGACTA
Found at i:5304091 original size:60 final size:60
Alignment explanation
Indices: 5304025--5304178 Score: 227
Period size: 60 Copynumber: 2.6 Consensus size: 60
5304015 GAATATGTAA
*
5304025 ATCGCAATGCGATTATGACTATCGCAATGCGATTATGACTATCGCAACGAGATTATGACT
1 ATCGCAACGCGATTATGACTATCGCAATGCGATTATGACTATCGCAACGAGATTATGACT
* * * * *
5304085 ATCGCAACGAGATTATGACTATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACTATCGCAATGCGATTATGACTATCGCAACGAGATTATGACT
** *
5304145 ATCGCAACGCGATGCTGACTATAGCAATGCGATT
1 ATCGCAACGCGATTATGACTATCGCAATGCGATT
5304179 TTCAAAGTGC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (60 bp):
ATCGCAACGCGATTATGACTATCGCAATGCGATTATGACTATCGCAACGAGATTATGACT
Found at i:5304379 original size:22 final size:22
Alignment explanation
Indices: 5304354--5304396 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5304344 GGCGACATCC
*
5304354 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTACGACGAAATCA
* *
5304376 GTCCTCATCTACGGCGAAATC
1 GTCCCCATCTACGACGAAATC
5304397 CGTCTATCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTACGACGAAATCA
Found at i:5304838 original size:20 final size:20
Alignment explanation
Indices: 5304773--5304840 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
5304763 AGAATCGCAA
* *
5304773 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
5304792 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
5304812 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
5304832 TGCGATTTT
1 TGCGATTTT
5304841 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.17
20 35 0.83
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:5306580 original size:18 final size:18
Alignment explanation
Indices: 5306557--5306606 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
5306547 TTTACTCGTA
5306557 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
5306575 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
5306593 ATTTCACTTAGATT
1 ATTTCACTTAGATT
5306607 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:5306779 original size:20 final size:20
Alignment explanation
Indices: 5306754--5306800 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
5306744 TAGTTTACTT
5306754 TCGCAACGCAAAAATGACTA
1 TCGCAACGCAAAAATGACTA
*
5306774 TCGCAACGCGAAAATGACTA
1 TCGCAACGCAAAAATGACTA
5306794 TCGCAAC
1 TCGCAAC
5306801 TAAAGAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACGCAAAAATGACTA
Found at i:5307477 original size:42 final size:41
Alignment explanation
Indices: 5307377--5307482 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 41
5307367 CCCGACTCAC
* *
5307377 CTGTCATCGTTCAAGA-TGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGT-CC-CCCCTACCGTTCAAGAGGCCA
* ** *
5307419 CTATCATCCCTCAAGAGTCCCCTCCTACCGTTCAAGAGGTCA
1 CTGTCATCGTTCAAGAGTCCCC-CCTACCGTTCAAGAGGCCA
*
5307461 CTGTCATCGTTGAAGAGGTCCC
1 CTGTCATCGTTCAAGA-GTCCC
5307483 TCGCAACATT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.04
42 43 0.84
43 6 0.12
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCCCCTACCGTTCAAGAGGCCA
Found at i:5308886 original size:14 final size:14
Alignment explanation
Indices: 5308867--5308928 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
5308857 TTTCTTGTTT
5308867 AATTGATTTGTAAA
1 AATTGATTTGTAAA
5308881 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
5308895 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
5308910 TATTGATGTGTAAA
1 AATTGATTTGTAAA
5308924 TAATT
1 -AATT
5308929 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:5308900 original size:28 final size:29
Alignment explanation
Indices: 5308869--5308923 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5308859 TCTTGTTTAA
*
5308869 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
5308897 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
5308924 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:5309052 original size:20 final size:20
Alignment explanation
Indices: 5309027--5309080 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
5309017 AGGTACACTT
5309027 TCGTAATGCGAAAGCCAAAA
1 TCGTAATGCGAAAGCCAAAA
5309047 TCGTAATGCGAAAGCCAAAA
1 TCGTAATGCGAAAGCCAAAA
* *
5309067 TCGCAACGCGAAAG
1 TCGTAATGCGAAAG
5309081 TAAATTCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGTAATGCGAAAGCCAAAA
Found at i:5309148 original size:20 final size:20
Alignment explanation
Indices: 5309123--5309273 Score: 170
Period size: 20 Copynumber: 7.8 Consensus size: 20
5309113 GCGATTTTCT
* * *
5309123 CGTTGCGATAGTCGAATACC
1 CGTTGCGATAGTCAAATTCA
5309143 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
5309163 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
5309183 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCA
* *
5309203 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
**
5309223 CGTTGCGA-A-T----TTTT
1 CGTTGCGATAGTCAAATTCA
*
5309237 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
5309257 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
5309274 GAATGTGTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
18 1 0.01
19 1 0.01
20 99 0.88
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:5309187 original size:40 final size:40
Alignment explanation
Indices: 5309119--5309273 Score: 196
Period size: 40 Copynumber: 4.0 Consensus size: 40
5309109 CTTTGCGATT
* * *
5309119 TTCTCGTTGCGATAGTCGAATACCCGTTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
* *
5309159 TTCACGTTGCGATAGTCAAATTCACGTTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
*
5309199 TTCTCATTGCGATAGTCAAATTCGCGTTGCGA-A-T----
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
* *
5309233 TTTTCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAA
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
5309273 T
1 T
5309274 GAATGTGTAA
Statistics
Matches: 100, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
34 30 0.30
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 66 0.66
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (40 bp):
TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
Found at i:5309248 original size:34 final size:37
Alignment explanation
Indices: 5309091--5309266 Score: 166
Period size: 40 Copynumber: 4.8 Consensus size: 37
5309081 TAAATTCGCA
* * *
5309091 TTGCGATAGTCTAATACGCTTTGCGAT--T-TTCTCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTATTCTCG
* * * *
5309125 TTGCGATAGTCGAATACCCGTTGCGATAGTCAAATTCACG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGT---ATTCTCG
* *
5309165 TTGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCTCA
1 TTGCGATAGTCAAATTCGCGTTGCGATAGT---ATTCTCG
*
5309205 TTGCGATAGTCAAATTCGCGTTGCGA-A-T-TTTTCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTATTCTCG
5309239 TTGCGATAGTCAAATTCGCGTTGCGATA
1 TTGCGATAGTCAAATTCGCGTTGCGATA
5309267 TTCAAATGAA
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
34 54 0.44
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 65 0.53
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (37 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTATTCTCG
Found at i:5312627 original size:20 final size:20
Alignment explanation
Indices: 5312595--5312740 Score: 186
Period size: 20 Copynumber: 7.3 Consensus size: 20
5312585 AAATTCAGTG
* * *
5312595 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
* * * *
5312615 TTACGATAGTCAGAATCTCG
1 TTGCGATAGTCATAATCGCA
*
5312635 TTGCGATAATCATAATCGCA
1 TTGCGATAGTCATAATCGCA
5312655 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
5312675 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
5312695 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
5312715 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
5312735 TTGCGA
1 TTGCGA
5312741 ATTCGGAAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
19 1 0.01
20 113 0.99
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:5312761 original size:21 final size:21
Alignment explanation
Indices: 5312737--5312782 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5312727 TATTCGCATT
*
5312737 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGAAAAATCGCAAC
* *
5312758 GCGAATTCGAAAAATTGCAAT
1 GCGAATTCGAAAAATCGCAAC
5312779 GCGA
1 GCGA
5312783 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTCGAAAAATCGCAAC
Found at i:5319285 original size:26 final size:27
Alignment explanation
Indices: 5319235--5319315 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 27
5319225 AATATTTTAA
*
5319235 ATTAAAATATTATTTTTTTCAAATATAAAT
1 ATTAAAATA--ATTTTTAT-AAATATAAAT
*
5319265 AATTAAAAT-ATTTTTAT-AATAAAAAT
1 -ATTAAAATAATTTTTATAAATATAAAT
*
5319291 ATTAAAATAATTTTTTTAAATATAA
1 ATTAAAATAATTTTTATAAATATAA
5319316 TAAAAGAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 8 0.18
26 15 0.34
27 6 0.14
28 7 0.16
31 8 0.18
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAAAATAATTTTTATAAATATAAAT
Found at i:5319294 original size:25 final size:25
Alignment explanation
Indices: 5319256--5319359 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
5319246 ATTTTTTTCA
*
5319256 AATATAAATAATTAAAATATTTTTAT
1 AATAAAAAT-ATTAAAATATTTTTAT
*
5319282 AATAAAAATATTAAAATAATTTTTTTAA
1 AATAAAAATATTAAAAT-A--TTTTTAT
* *
5319310 ATATAATAAAAGAGTTATAATATTTTTAT
1 A-AT-A-AAAATA-TTAAAATATTTTTAT
*
5319339 AATAAAAATACTAAAATATTT
1 AATAAAAATATTAAAATATTT
5319360 CAGTTTGACA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
25 17 0.27
26 14 0.22
27 1 0.02
28 9 0.14
29 9 0.14
30 1 0.02
31 6 0.10
32 6 0.10
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (25 bp):
AATAAAAATATTAAAATATTTTTAT
Found at i:5319295 original size:56 final size:59
Alignment explanation
Indices: 5319235--5319358 Score: 170
Period size: 57 Copynumber: 2.2 Consensus size: 59
5319225 AATATTTTAA
*
5319235 ATTAAAATATTATTTTTTTCAAATAT-A-AATA-A-TTAAAATATTTTTATAATAAAAAT
1 ATTAAAATATTATTTTTTT-AAATATAATAAAAGAGTTAAAATATTTTTATAATAAAAAT
*
5319291 ATTAAAATA--ATTTTTTTAAATATAATAAAAGAGTTATAATATTTTTATAATAAAAAT
1 ATTAAAATATTATTTTTTTAAATATAATAAAAGAGTTAAAATATTTTTATAATAAAAAT
*
5319348 ACTAAAATATT
1 ATTAAAATATT
5319359 TCAGTTTGAC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
53 6 0.10
54 9 0.15
55 3 0.05
56 10 0.17
57 31 0.53
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (59 bp):
ATTAAAATATTATTTTTTTAAATATAATAAAAGAGTTAAAATATTTTTATAATAAAAAT
Found at i:5320607 original size:25 final size:26
Alignment explanation
Indices: 5320576--5320626 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
5320566 TTAATTTAAA
*
5320576 ATAATTGATTAATAAAT-TATAAAAT
1 ATAATTGATAAATAAATATATAAAAT
*
5320601 ATAATTGATAAATAAATATTTAAAAT
1 ATAATTGATAAATAAATATATAAAAT
5320627 TTAGAAGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAATTGATAAATAAATATATAAAAT
Found at i:5322552 original size:11 final size:11
Alignment explanation
Indices: 5322536--5322560 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5322526 TCTTGAATAT
5322536 CCAGTAGTGAG
1 CCAGTAGTGAG
5322547 CCAGTAGTGAG
1 CCAGTAGTGAG
5322558 CCA
1 CCA
5322561 AATTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.32, T:0.16
Consensus pattern (11 bp):
CCAGTAGTGAG
Found at i:5323402 original size:20 final size:22
Alignment explanation
Indices: 5323363--5323403 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
5323353 AGAGATTTAT
5323363 AAAGTTAGAAAGGATTAATAAC
1 AAAGTTAGAAAGGATTAATAAC
*
5323385 AAAGTT-GAAA-GTTTAATAA
1 AAAGTTAGAAAGGATTAATAA
5323404 GATTCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (22 bp):
AAAGTTAGAAAGGATTAATAAC
Found at i:5323752 original size:24 final size:24
Alignment explanation
Indices: 5323724--5323780 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
5323714 GCATGGGTAG
5323724 TGCATCGATGCACATATTAACGGA
1 TGCATCGATGCACATATTAACGGA
*
5323748 TGCATCGATGCACATGTTAACGGA
1 TGCATCGATGCACATATTAACGGA
*
5323772 TACATCGAT
1 TGCATCGAT
5323781 ACACTATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACATATTAACGGA
Found at i:5331236 original size:19 final size:19
Alignment explanation
Indices: 5331208--5331247 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5331198 AAACTTGATA
*
5331208 CAAATTAAATTTAT-CAAAT
1 CAAATGAAA-TTATCCAAAT
5331227 CAAATGAAATTATCCAAAT
1 CAAATGAAATTATCCAAAT
5331246 CA
1 CA
5331248 TAAATAAATC
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:0.53, C:0.15, G:0.03, T:0.30
Consensus pattern (19 bp):
CAAATGAAATTATCCAAAT
Found at i:5338215 original size:23 final size:23
Alignment explanation
Indices: 5338171--5338217 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5338161 TAAATTAATC
*
5338171 ATATAAATTAAAATTATTAAAAT
1 ATATAAATTAAAATTATAAAAAT
*
5338194 ATATAAATTAGACA-TATAAAAAT
1 ATATAAATTA-AAATTATAAAAAT
5338217 A
1 A
5338218 CATATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
ATATAAATTAAAATTATAAAAAT
Found at i:5338976 original size:96 final size:97
Alignment explanation
Indices: 5338865--5339049 Score: 318
Period size: 96 Copynumber: 1.9 Consensus size: 97
5338855 CGACCAAATT
*
5338865 GATACACAAAACAAAAATCAACGACTAATAGGATAGTTTACCA-TTTTTTAATTAAACATATCTA
1 GATACACAAAACAAAAATCAACGACTAATAGGATAGTTTACCATTTTTTTAATTAAACATATATA
* **
5338929 ATTTACCTATTGGAACAATCAATGACTAATAG
66 ATTAACCTAGAGGAACAATCAATGACTAATAG
*
5338961 GATACACAAAACAAAAATCAATGACTAATAGGATAGTTTACCATTTTTTTAATTAAACATATATA
1 GATACACAAAACAAAAATCAACGACTAATAGGATAGTTTACCATTTTTTTAATTAAACATATATA
5339026 ATTAACCTAGAGGAACAATCAATG
66 ATTAACCTAGAGGAACAATCAATG
5339050 CACAATTGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
96 42 0.51
97 41 0.49
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.30
Consensus pattern (97 bp):
GATACACAAAACAAAAATCAACGACTAATAGGATAGTTTACCATTTTTTTAATTAAACATATATA
ATTAACCTAGAGGAACAATCAATGACTAATAG
Found at i:5345021 original size:13 final size:13
Alignment explanation
Indices: 5345003--5345032 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5344993 ATTACAACCC
5345003 GACCCGACCCGTT
1 GACCCGACCCGTT
5345016 GACCCGACCCGTT
1 GACCCGACCCGTT
5345029 GACC
1 GACC
5345033 GTTGACTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:5347565 original size:24 final size:24
Alignment explanation
Indices: 5347530--5347597 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
5347520 ATTTTCGATT
*
5347530 TGAATTCTGATATGACACTTGACA
1 TGAATTCTGATATGATACTTGACA
*
5347554 TGGATTCTGATATGATA-TCTGACA
1 TGAATTCTGATATGATACT-TGACA
*
5347578 TGAATTCTGATCTGATACTT
1 TGAATTCTGATATGATACTT
5347598 AACTTGGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:5347768 original size:2 final size:2
Alignment explanation
Indices: 5347761--5347789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5347751 CTGATGGGGG
5347761 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 T
5347790 GTTTTAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5352234 original size:24 final size:24
Alignment explanation
Indices: 5352207--5352322 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
5352197 TTCGATTTGA
5352207 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
5352231 ATTCTGATCTAATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
5352255 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
5352279 ATTTTGATCTGATACTTGATC-TGG
1 ATTCTGATCTGATACTTGA-CATGG
* * *
5352303 ATTTTGATATGAAACTTGAC
1 ATTCTGATCTGATACTTGAC
5352323 CTGATTTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:5354876 original size:16 final size:16
Alignment explanation
Indices: 5354832--5354867 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5354822 CCCATGATTC
5354832 ATATACAAATAGAATT
1 ATATACAAATAGAATT
5354848 ATATACAAATAGAATT
1 ATATACAAATAGAATT
5354864 ATAT
1 ATAT
5354868 TAAATTAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (16 bp):
ATATACAAATAGAATT
Found at i:5355422 original size:182 final size:181
Alignment explanation
Indices: 5355129--5355778 Score: 856
Period size: 182 Copynumber: 3.6 Consensus size: 181
5355119 CGATACAAAT
* * * * * *
5355129 TAAAAATGTATCGACCCATAGCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTACGA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGA-AATGA
* *** * *
5355193 TAAAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTGTCGACACT
65 TAAAACCGGTAAAAAACTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
*
5355258 TTTGTAATTTAAAATAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTA
* * * *
5355311 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAACATGTCTCTAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
*
5355376 AAAACCGGTAAAAAACTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCAACACTT
66 AAAACCGGTAAAAAACTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
*
5355441 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTGAAAAGTGCCGATACTTTA
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * * * *
5355493 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAAGAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
* *
5355558 AAAATCGGTAAAAATA-TATCGGATATATTGAAAGTGTTGATAAATTAATATAAGTATCGACACT
66 AAAACCGGTAAAAA-ACTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
** * *
5355622 TTCATAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATATTTTA
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * * *
5355675 -AGAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGATAAAACCGGTATCGAAATGA
1 TA-AAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGA
* ** * *
5355739 CAAAACCGGTAAAACGCTATCGGTTATGTTGAAAGTGTCG
65 TAAAACCGGTAAAAAACTATCGGATATATTGAAAGTGTCG
5355779 GTACTTTAAT
Statistics
Matches: 410, Mismatches: 53, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
181 1 0.00
182 403 0.98
183 6 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (181 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
AAAACCGGTAAAAAACTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTA
Found at i:5357512 original size:21 final size:21
Alignment explanation
Indices: 5357486--5357538 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
5357476 GTGCACGAAC
5357486 AAAGTGTCGATACATTTATAA
1 AAAGTGTCGATACATTTATAA
5357507 AAAGTGTCGATACATTTATAA
1 AAAGTGTCGATACATTTATAA
5357528 AAAGTGTCGAT
1 AAAGTGTCGAT
5357539 CCCAAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (21 bp):
AAAGTGTCGATACATTTATAA
Found at i:5358058 original size:22 final size:21
Alignment explanation
Indices: 5358032--5358077 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5358022 AAAAAAAAGG
*
5358032 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
5358054 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
5358075 TAT
1 TAT
5358078 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:5358072 original size:426 final size:401
Alignment explanation
Indices: 5357244--5358254 Score: 1179
Period size: 426 Copynumber: 2.5 Consensus size: 401
5357234 CAAAGGCAAA
*
5357244 AGTGTCCATAATGTGTTTTCCAAACAAAACAAATTCACAAATAAGTGTCGACACATTTATATCAA
1 AGTGTCCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATATCAA
*
5357309 GTGTCGATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCG
66 GTGTCGATCCAAAAAACATCGAAA-CCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCG
* *
5357374 GTTTAAATTTACAGGTTTTATGAGAAAATATGTCTACAATATGTGTCGACACTTTATTCATTTAT
130 GTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACAATATGTGTCGACACTTTATTCATTTAT
5357439 GTCGATACATGTTATCCAGAATGTATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTA
195 GTCGATACATGTTATCCAGAATGTATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTA
5357504 TAAAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAATTCGTAATTATAAT
260 TAAAAAGTGTCGATAC---TATAAAAA--G-CGAT-CCAAAAACATC--AA-T--TAATTATAAT
* *
5357569 GTAATAGGTAAAATAAAAATGTAACCGGTCTAAATATATCGGTTTATGAGAAAAGAGGTATTCAT
313 GTAATAGGTAAAATAAAAATGTAACCGGTCTAAATATATCGGTTTATGAAAAAAAAGGTATTCAT
5357634 AAAGTATCGACACTTTATAAATTTGTACCGAT
378 AAAGTATCGACAC-TT-T--A--TGT-CC-AT
**
5357666 ACTTTGTGTCCATAATGTGTTTTCCAAACAAAACAAGTTCATTAATAAGTGTCGACACATTTATA
1 A----GTGTCCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATA
5357731 TCAAGTGTCGATCCAAAAAACATCGAAACTCGTAACTATAATGTAATAGGTCACTTTACAATGTA
62 TCAAGTGTCGATCCAAAAAACATCGAAAC-CGTAACTATAATGTAATAGGTCACTTTACAATGTA
*
5357796 ACCAGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACAATATGTGTCGACACTTTATTCAT
126 ACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACAATATGTGTCGACACTTTATTCAT
* * *
5357861 TTGTGTCGATACATGTTGTCCAGAATGTATTTCCAAACCAAGTGCATGAACAAAGTGTCGATACA
191 TTATGTCGATACATGTTATCCAGAATGTATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACA
* * * *
5357926 TTTATAAAAAGTGTCGAT-C-CTACAAA-C-AT-C-GAAACA-C-A-TAATTATAATGTAATCGG
256 TTTATAAAAAGTGTCGATACTATAAAAAGCGATCCAAAAACATCAATTAATTATAATGTAATAGG
* * * * *
5357982 TAACATAACAATGTAACCGGTCTAAATATA-CTGG-TTATTTAAAAAAAAGGTATACATAATGTA
321 TAAAATAAAAATGTAACCGGTCTAAATATATC-GGTTTA-TGAAAAAAAAGGTATTCATAAAGTA
* *
5358045 TCGATACTTTA--TACATT
384 TCGACACTTTATGTCCA-T
* * *** *** * * * *
5358062 TGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAA-AATTATCGATACAT
1 AGTGTC--CA--TAATGTGTTTTCCAAA----CAAAACAAGTTCAC-AAATAAGTGTCGACACAT
* ** * *
5358126 TTAGAAAAAGTGTCGATCCTAAAAACATCGAAACCTGTAATTATAATGTAATAGGTCACTTTACA
57 TTATATCAAGTGTCGATCCAAAAAACATCGAAACC-GTAACTATAATGTAATAGGTCACTTTACA
* *
5358191 ATGTAACCGGTTTAAATTTATCGGTTTTATGAGAAAATAGGTCTACAGA-ATGTATCGACACTTT
121 ATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACA-ATATGTGTCGACACTTT
5358255 TTAAATTAAT
Statistics
Matches: 525, Mismatches: 45, Indels: 60
0.83 0.07 0.10
Matches are distributed among these distances:
392 5 0.01
394 2 0.00
395 1 0.00
396 11 0.02
397 1 0.00
399 1 0.00
400 140 0.27
401 4 0.01
403 1 0.00
404 6 0.01
405 73 0.14
409 1 0.00
412 1 0.00
413 5 0.01
414 1 0.00
416 2 0.00
417 1 0.00
421 5 0.01
422 1 0.00
425 2 0.00
426 261 0.50
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (401 bp):
AGTGTCCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATATCAA
GTGTCGATCCAAAAAACATCGAAACCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGG
TTTAAATTTACCGGTTTTATGAGAAAATAGGTCTACAATATGTGTCGACACTTTATTCATTTATG
TCGATACATGTTATCCAGAATGTATTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTAT
AAAAAGTGTCGATACTATAAAAAGCGATCCAAAAACATCAATTAATTATAATGTAATAGGTAAAA
TAAAAATGTAACCGGTCTAAATATATCGGTTTATGAAAAAAAAGGTATTCATAAAGTATCGACAC
TTTATGTCCAT
Found at i:5358282 original size:20 final size:19
Alignment explanation
Indices: 5358244--5358282 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5358234 TACAGAATGT
*
5358244 ATCGACACTTTTTAAATTA
1 ATCGACACTTTTAAAATTA
*
5358263 ATCGATACTTTTGAAAATTA
1 ATCGACACTTTT-AAAATTA
5358283 CGCGTGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (19 bp):
ATCGACACTTTTAAAATTA
Found at i:5361826 original size:198 final size:198
Alignment explanation
Indices: 5361383--5361826 Score: 492
Period size: 197 Copynumber: 2.2 Consensus size: 198
5361373 GATTTTGTGT
* *
5361383 CGATAAATATAATGTAATAGGTAAATTT-TCAATGTAACCGG-TAGAAATATATCGGGTTCATGA
1 CGATAATTATAATGTAATA-GTAAATTTAT-AATGTAACCGGTTA-AAATATATCGGGTTAATGA
* * *
5361446 GAGAATAGGTCAACATAAAGTATCGACACTTTATTTAATTTGTGTCGATACATTTTTTCAAAATG
63 GAGAATAGGTCAACATAAAGTATCGACACTTCATTAAATATGTGTCGATACATTTTTTCAAAATG
* * * * *
5361511 AATGGCAAACGAGGTGTACGCATAAAGTGTCGATATATTTTTAAAAAGTATCGATCCTCGAAACA
128 AAAGACAAACGAGGTGCACGCATAAAATGTCGATACA-TTTTAAAAAGTATCGATCCTCGAAACA
* *
5361576 TCGAAAT
192 TCAAAAC
* * * *
5361583 CGATAATTATTATGTAACAGATAAATTTACAATGTAACCGGTTAAAATATATC-GGTTAATTAGC
1 CGATAATTATAATGTAATAG-TAAATTTATAATGTAACCGGTTAAAATATATCGGGTTAATGAG-
* * * *
5361647 A-AATAGGTCTACATTATGTATCGACAC-TCGTTAAATATGTGTCGATAC-TTTTTTCCAAAAT-
64 AGAATAGGTCAACATAAAGTATCGACACTTCATTAAATATGTGTCGATACATTTTTT-CAAAATG
* *
5361708 AAAGCACAAACGAGTTGCACGCATAAAATGTCGATACA-TTTAAAATTGTATCGATCCT-GAAAA
128 AAAG-ACAAACGAGGTGCACGCATAAAATGTCGATACATTTTAAAA-AGTATCGATCCTCG-AAA
5361771 CATCAAAAC
190 CATCAAAAC
* * *
5361780 CGATATTTATAATGTAATATGTCAATTTATATTGTAACCGGGTTAAA
1 CGATAATTATAATGTAATA-GTAAATTTATAATGTAACC-GGTTAAA
5361827 TTTACCGTTT
Statistics
Matches: 206, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
196 8 0.04
197 61 0.30
198 59 0.29
199 32 0.16
200 44 0.21
201 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
CGATAATTATAATGTAATAGTAAATTTATAATGTAACCGGTTAAAATATATCGGGTTAATGAGAG
AATAGGTCAACATAAAGTATCGACACTTCATTAAATATGTGTCGATACATTTTTTCAAAATGAAA
GACAAACGAGGTGCACGCATAAAATGTCGATACATTTTAAAAAGTATCGATCCTCGAAACATCAA
AAC
Found at i:5361989 original size:23 final size:23
Alignment explanation
Indices: 5361939--5361983 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5361929 TGCATATTTT
*
5361939 ATTATATAAGCGCTACCTACTAC
1 ATTATATAAGCGCTACCTAATAC
*
5361962 ATTATCTAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
5361984 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:5362437 original size:23 final size:23
Alignment explanation
Indices: 5362364--5362438 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 23
5362354 TACATTTATG
* *
5362364 TTTATTTAATATTCACTAACATA
1 TTTATTTAATGTTCACAAACATA
* **
5362387 TTT-TTTAGTGTTCATGAA-ATA
1 TTTATTTAATGTTCACAAACATA
*
5362408 TTAATTTAATGTTCACAAACATA
1 TTTATTTAATGTTCACAAACATA
5362431 TTTATTTA
1 TTTATTTA
5362439 TATAACTAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 5 0.12
22 23 0.56
23 13 0.32
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (23 bp):
TTTATTTAATGTTCACAAACATA
Found at i:5372188 original size:2 final size:2
Alignment explanation
Indices: 5372183--5372216 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5372173 TTTTGAGCAA
5372183 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
5372217 GAATGTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5375662 original size:31 final size:31
Alignment explanation
Indices: 5375627--5375692 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
5375617 GTTCAATCGA
5375627 CTGTCCTTTCATTTCGACGGTTCCGGTTGAC
1 CTGTCCTTTCATTTCGACGGTTCCGGTTGAC
5375658 CTGTCCTTTCATTTCGACGGTTCCGGTTGAC
1 CTGTCCTTTCATTTCGACGGTTCCGGTTGAC
5375689 CTGT
1 CTGT
5375693 TCGCAGCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.09, C:0.29, G:0.23, T:0.39
Consensus pattern (31 bp):
CTGTCCTTTCATTTCGACGGTTCCGGTTGAC
Found at i:5391915 original size:2 final size:2
Alignment explanation
Indices: 5391908--5391946 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5391898 ATCCTTCCCC
5391908 AT AT AT AT AT -T 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
5391947 TGCTTCACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5395363 original size:210 final size:209
Alignment explanation
Indices: 5394986--5395405 Score: 723
Period size: 210 Copynumber: 2.0 Consensus size: 209
5394976 TTGGCAACTA
* * *
5394986 TTCCCCAGAATATGTGAAGATAAACCGGTTTTAGCAAATCAGTTTTCTGTAAGTTGGAATATCTT
1 TTCCCCAGAATATGTGAAGATAAACCGGTTTTACCAAAACAGTTTACTGTAAGTTGGAATATCTT
5395051 GACAGCACAGAGAAAAGAAATTTATTGTTGTTCATCGTTGCCTTTCTCAGCAGCAATAATTAAAT
66 GACAGCACAGAGAAAAGAAATTTATTGTTGTTCATCGTTGCCTTTCTCAGCAGCAATAATTAAAT
5395116 TAAACTAGATCCTTTTTATATCAAAAGTAGGCATGTTATAAAGCTGGAAACCATCCTAATTAGCA
131 TAAACTAGATCCTTTTTATATCAAAAGTAGGCATGTTATAAAGCTGGAAACCATCCTAATTAGCA
*
5395181 TATTATGCATTGCT
196 TATTATACATTGCT
* * * *
5395195 TTCCCCAGAATATGTGAAGCTAAACTGTTTTTACCAAAACAGTTTACTGTAAGTTGGAATCTCTT
1 TTCCCCAGAATATGTGAAGATAAACCGGTTTTACCAAAACAGTTTACTGTAAGTTGGAATATCTT
*
5395260 GACATCACAGAGAAAAGAAATTTATTGTTGTTCCATCGTTGCCTTTCTCAGCAGCAATAATTAAA
66 GACAGCACAGAGAAAAGAAATTTATTGTTGTT-CATCGTTGCCTTTCTCAGCAGCAATAATTAAA
* * *
5395325 TTAAACTATATCCTTTTTCTATCAAAAGTAGGCATGTTATAAAGCTGGAAATCATCCTAATTAGC
130 TTAAACTAGATCCTTTTTATATCAAAAGTAGGCATGTTATAAAGCTGGAAACCATCCTAATTAGC
5395390 ATATTATACATTGCT
195 ATATTATACATTGCT
5395405 T
1 T
5395406 CTTCGAATCC
Statistics
Matches: 198, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
209 89 0.45
210 109 0.55
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (209 bp):
TTCCCCAGAATATGTGAAGATAAACCGGTTTTACCAAAACAGTTTACTGTAAGTTGGAATATCTT
GACAGCACAGAGAAAAGAAATTTATTGTTGTTCATCGTTGCCTTTCTCAGCAGCAATAATTAAAT
TAAACTAGATCCTTTTTATATCAAAAGTAGGCATGTTATAAAGCTGGAAACCATCCTAATTAGCA
TATTATACATTGCT
Found at i:5402833 original size:15 final size:15
Alignment explanation
Indices: 5402813--5402847 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5402803 AAAGCTTTCA
5402813 TCTTCCTCTTCACT-T
1 TCTTCCTCTTC-CTCT
5402828 TCTTCCTCTTCCTCT
1 TCTTCCTCTTCCTCT
5402843 TCTTC
1 TCTTC
5402848 ATTGTCCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (15 bp):
TCTTCCTCTTCCTCT
Found at i:5405733 original size:5 final size:5
Alignment explanation
Indices: 5405723--5405748 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5405713 AGACCCCTGC
5405723 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
5405749 CAAGAGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5408513 original size:64 final size:63
Alignment explanation
Indices: 5408400--5408605 Score: 151
Period size: 63 Copynumber: 3.2 Consensus size: 63
5408390 TTGGACCCTT
* * * *
5408400 AGTGCATCGATACACTGATA-GTGCATCGATGCATAAATATGCTTCGATGTTTTGAA-AAAGCCT
1 AGTGCATCGATGCA-TGGTATGTGCATCGGTGCATAAATATGCTTCGATG-TTT-AATAAA-CAT
5408463 GG
62 GG
* * *
5408465 -GTGCATCGATGCATGGCT-TGTGCATCGGTGCATAAA-AT-CAATTTGATGTTTAATATATATG
1 AGTGCATCGATGCATGG-TATGTGCATCGGTGCATAAATATGC--TTCGATGTTTAATAAACATG
5408526 G
63 G
* * * *
5408527 AGTGCATCGATGCATGGTATGTGCATCGGTACACAAA-A-GCCATTCGATGTTCAATTAAAACAA
1 AGTGCATCGATGCATGGTATGTGCATCGGTGCATAAATATG-C-TTCGATGTTTAA-T-AAACAT
5408590 GG
62 GG
5408592 -GTGCATCGATGCAT
1 AGTGCATCGATGCAT
5408606 TGATTCATGC
Statistics
Matches: 116, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
62 7 0.06
63 53 0.46
64 51 0.44
65 5 0.04
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTATGTGCATCGGTGCATAAATATGCTTCGATGTTTAATAAACATGG
Found at i:5415422 original size:8 final size:8
Alignment explanation
Indices: 5415409--5415445 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
5415399 TCATAACTTG
5415409 TACACATA
1 TACACATA
5415417 TACACAT-
1 TACACATA
5415424 T-CACATA
1 TACACATA
5415431 TACACATA
1 TACACATA
*
5415439 GACACAT
1 TACACAT
5415446 GGTTCACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 5 0.19
7 2 0.08
8 19 0.73
ACGTcount: A:0.46, C:0.27, G:0.03, T:0.24
Consensus pattern (8 bp):
TACACATA
Found at i:5415430 original size:14 final size:14
Alignment explanation
Indices: 5415411--5415437 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5415401 ATAACTTGTA
5415411 CACATATACACATT
1 CACATATACACATT
5415425 CACATATACACAT
1 CACATATACACAT
5415438 AGACACATGG
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:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
CACATATACACATT
Found at i:5420098 original size:45 final size:45
Alignment explanation
Indices: 5420010--5420111 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 45
5420000 ACTACCAATG
* * *
5420010 CATCGATACACAAATTACATTCGATGTTTTAATCTTAAGGGGGTA
1 CATCGATGCACTAATTACATTCGATGTTTCAATCTTAAGGGGGTA
* * * * *
5420055 TATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAA-GGGGTG
1 CATCGATGCACTAATTACATTCGATGTTT-CAATCTTAAGGGGGTA
5420100 CATCGATGCACT
1 CATCGATGCACT
5420112 TCCTGTGCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 41 0.87
46 6 0.13
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (45 bp):
CATCGATGCACTAATTACATTCGATGTTTCAATCTTAAGGGGGTA
Found at i:5421978 original size:64 final size:63
Alignment explanation
Indices: 5421903--5422023 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 63
5421893 TTTATTCAAG
*
5421903 GTGTATCGATGCACATGAAGTGCATCGATGCA-CTAATTTTAAATACAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCTAA--TTAAATACAAACATCGAATGCCATCA
* * *
5421967 GTGTATCGATGCACAAGTAGTGCATCGATGCACCTCATTATATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCTAATTAAATACAAACATCGAATG
5422024 GGATTTATGC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 19 0.37
64 30 0.58
65 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCTAATTAAATACAAACATCGAATGCCATCA
Found at i:5428952 original size:64 final size:63
Alignment explanation
Indices: 5428877--5428997 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 63
5428867 ATTGTTTAAG
5428877 GTGTATCGATGCACATA-AAGTGCATCGATGCA-CTAATTTAAAATACAAACATCGAATGTCATC
1 GTGTATCGATGCACA-AGAAGTGCATCGATGCACCTAA-TT-AAATACAAACATCGAATGTCATC
5428940 A
63 A
* * *
5428941 GTGTATCGATGCACAAGTAGTGCATCGATGCACCTCATTATATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCTAATTAAATACAAACATCGAATG
5428998 GGATTTATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 18 0.35
64 31 0.60
65 3 0.06
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCTAATTAAATACAAACATCGAATGTCATCA
Found at i:5429685 original size:23 final size:23
Alignment explanation
Indices: 5429658--5429749 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
5429648 CAATCTTATA
*
5429658 TGGCACTACGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTATACG
* * *
5429681 CGGCAGTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
5429704 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
5429727 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
5429750 AGCTGTGGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:5433850 original size:20 final size:20
Alignment explanation
Indices: 5433805--5433882 Score: 111
Period size: 20 Copynumber: 3.7 Consensus size: 20
5433795 GCATGGGTAG
5433805 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
5433829 TGCATCCATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
5433849 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
5433869 TGCATCGATGCACT
1 TGCATCGATGCACT
5433883 TCAAGGGGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 37 0.71
22 1 0.02
23 2 0.04
24 12 0.23
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:5437109 original size:18 final size:18
Alignment explanation
Indices: 5437086--5437245 Score: 230
Period size: 18 Copynumber: 8.9 Consensus size: 18
5437076 GAGGGTCTAC
*
5437086 GTGGTCTTTCGGGACATA
1 GTGGTCCTTCGGGACATA
5437104 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
5437122 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
5437140 GTGGTCCTTCAGGACACA
1 GTGGTCCTTCGGGACATA
*
5437158 GTGATCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
5437176 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
5437194 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
* *
5437212 ATGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
*
5437230 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
5437246 AATTCTACGC
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 126 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:5439329 original size:13 final size:13
Alignment explanation
Indices: 5439311--5439342 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5439301 AAACAAGCAC
*
5439311 ACACTCGCTCACT
1 ACACTCACTCACT
5439324 ACACTCACTCACT
1 ACACTCACTCACT
5439337 ACACTC
1 ACACTC
5439343 TGTGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.47, G:0.03, T:0.22
Consensus pattern (13 bp):
ACACTCACTCACT
Found at i:5449619 original size:227 final size:227
Alignment explanation
Indices: 5449224--5449683 Score: 920
Period size: 227 Copynumber: 2.0 Consensus size: 227
5449214 TCAATGTGAG
5449224 ATTAATGGGGCTAATGGCTCATCATATATGCCGTCAATTGATGATATTGGCTTCTTTATTTCGAT
1 ATTAATGGGGCTAATGGCTCATCATATATGCCGTCAATTGATGATATTGGCTTCTTTATTTCGAT
5449289 CTCATGCGAGCCTGTGAGAAATGATTGGGCTCGCGGTCCCATTGTTCTTTCAGAACAAATTGGGC
66 CTCATGCGAGCCTGTGAGAAATGATTGGGCTCGCGGTCCCATTGTTCTTTCAGAACAAATTGGGC
5449354 CTGTTGTAGCTGGTATAAACTTTCTATTCTAAAACCTTTTTTCCTTTTTCCTTTTTTCATTTCCT
131 CTGTTGTAGCTGGTATAAACTTTCTATTCTAAAACCTTTTTTCCTTTTTCCTTTTTTCATTTCCT
5449419 TCTTTACCTACTGGGTTACCATTGTTTCAATC
196 TCTTTACCTACTGGGTTACCATTGTTTCAATC
5449451 ATTAATGGGGCTAATGGCTCATCATATATGCCGTCAATTGATGATATTGGCTTCTTTATTTCGAT
1 ATTAATGGGGCTAATGGCTCATCATATATGCCGTCAATTGATGATATTGGCTTCTTTATTTCGAT
5449516 CTCATGCGAGCCTGTGAGAAATGATTGGGCTCGCGGTCCCATTGTTCTTTCAGAACAAATTGGGC
66 CTCATGCGAGCCTGTGAGAAATGATTGGGCTCGCGGTCCCATTGTTCTTTCAGAACAAATTGGGC
5449581 CTGTTGTAGCTGGTATAAACTTTCTATTCTAAAACCTTTTTTCCTTTTTCCTTTTTTCATTTCCT
131 CTGTTGTAGCTGGTATAAACTTTCTATTCTAAAACCTTTTTTCCTTTTTCCTTTTTTCATTTCCT
5449646 TCTTTACCTACTGGGTTACCATTGTTTCAATC
196 TCTTTACCTACTGGGTTACCATTGTTTCAATC
5449678 ATTAAT
1 ATTAAT
5449684 AATGGAGATA
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 233 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (227 bp):
ATTAATGGGGCTAATGGCTCATCATATATGCCGTCAATTGATGATATTGGCTTCTTTATTTCGAT
CTCATGCGAGCCTGTGAGAAATGATTGGGCTCGCGGTCCCATTGTTCTTTCAGAACAAATTGGGC
CTGTTGTAGCTGGTATAAACTTTCTATTCTAAAACCTTTTTTCCTTTTTCCTTTTTTCATTTCCT
TCTTTACCTACTGGGTTACCATTGTTTCAATC
Found at i:5450918 original size:22 final size:22
Alignment explanation
Indices: 5450890--5450935 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5450880 TACCGAATCC
5450890 CGATTTTGAAACGACTGGAACG
1 CGATTTTGAAACGACTGGAACG
5450912 CGATTTTGAAACGACTGGAACG
1 CGATTTTGAAACGACTGGAACG
5450934 CG
1 CG
5450936 TTTGTACCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (22 bp):
CGATTTTGAAACGACTGGAACG
Found at i:5463433 original size:19 final size:19
Alignment explanation
Indices: 5463409--5463445 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5463399 TGCTCCCTAT
5463409 ATTATATTAATTTTTTCAG
1 ATTATATTAATTTTTTCAG
*
5463428 ATTATATTTATTTTTTCA
1 ATTATATTAATTTTTTCA
5463446 ACTTGGTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTATATTAATTTTTTCAG
Found at i:5464193 original size:3 final size:3
Alignment explanation
Indices: 5464185--5464214 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
5464175 GGTGTTTCAC
5464185 TCT TCT TCT TCT TCT TCT TCT TCT CTCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT -TCT TC
5464215 GGAAAGCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:5467442 original size:20 final size:21
Alignment explanation
Indices: 5467406--5467448 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5467396 ATAAGAACAC
*
5467406 ATAATTTTTTAATGATTTTAT
1 ATAATTATTTAATGATTTTAT
5467427 ATAATTATTT-ATGATTTTAT
1 ATAATTATTTAATGATTTTAT
5467447 AT
1 AT
5467449 TTTTAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATAATTATTTAATGATTTTAT
Found at i:5467483 original size:19 final size:19
Alignment explanation
Indices: 5467440--5467475 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5467430 ATTATTTATG
*
5467440 ATTTTATATTTTTAAATAC
1 ATTTTATATTTTAAAATAC
5467459 ATTTTATA-TTTAAAATA
1 ATTTTATATTTTAAAATA
5467476 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATATTTTAAAATAC
Found at i:5479502 original size:3 final size:3
Alignment explanation
Indices: 5479494--5479520 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5479484 AGAGAGAACA
5479494 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5479521 TAATGACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5479697 original size:16 final size:16
Alignment explanation
Indices: 5479676--5479720 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
5479666 TTTTTTAAAA
5479676 ATTTTAAATTATATAT
1 ATTTTAAATTATATAT
*
5479692 ATTTTAAATTTTTTATAT
1 ATTTTAAA--TTATATAT
*
5479710 ATTTTATATTA
1 ATTTTAAATTA
5479721 AAAATTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAAATTATATAT
Found at i:5480114 original size:8 final size:8
Alignment explanation
Indices: 5480098--5480131 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5480088 ATTTTCTAAT
5480098 TTTTGAAAA
1 TTTT-AAAA
5480107 TTTTAAAA
1 TTTTAAAA
5480115 TTTTAAAA
1 TTTTAAAA
*
5480123 TTATAAAA
1 TTTTAAAA
5480131 T
1 T
5480132 AATTATGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (8 bp):
TTTTAAAA
Found at i:5480551 original size:30 final size:30
Alignment explanation
Indices: 5480515--5480571 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5480505 TTTACAATAG
* *
5480515 TTTGAAAATTTTAATAATTATT-TATAATCA
1 TTTG-AAAGTTTAATAATCATTATATAATCA
5480545 TTTGAAAGTTTAATAATCATTATATAA
1 TTTGAAAGTTTAATAATCATTATATAA
5480572 CTTCAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTGAAAGTTTAATAATCATTATATAATCA
Found at i:5481333 original size:20 final size:20
Alignment explanation
Indices: 5481308--5481347 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5481298 TATTGGAATA
*
5481308 TGCATTCTGGAATATACATT
1 TGCATTCTAGAATATACATT
*
5481328 TGCATTCTAGAATATGCATT
1 TGCATTCTAGAATATACATT
5481348 GTTAACGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGCATTCTAGAATATACATT
Found at i:5481488 original size:17 final size:17
Alignment explanation
Indices: 5481466--5481504 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
5481456 TTGTTATAGG
5481466 AAGCTAAGAGATTGAGT
1 AAGCTAAGAGATTGAGT
5481483 AAGCTAAGAGATTGAGT
1 AAGCTAAGAGATTGAGT
5481500 AAGCT
1 AAGCT
5481505 TGAAGTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (17 bp):
AAGCTAAGAGATTGAGT
Done.