Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 33 of 39
Found at i:6567393 original size:19 final size:18
Alignment explanation
Indices: 6567353--6567435 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 18
6567343 TAGTTTACTT
*
6567353 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
6567373 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
6567392 TCGCAA--CG-AA-AGAA
1 TCGCAACGCGAAACAAAA
*
6567406 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
6567425 TCGCAATGCGA
1 TCGCAACGCGA
6567436 TTTTGGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
14 9 0.17
16 4 0.08
17 4 0.08
19 23 0.43
20 12 0.23
21 1 0.02
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:6567453 original size:19 final size:19
Alignment explanation
Indices: 6567431--6567559 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
6567421 AAAATCGCAA
6567431 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
6567450 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
6567464 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
6567483 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
6567497 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
6567516 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
6567535 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
6567555 TGCGA
1 TGCGA
6567560 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:6567473 original size:33 final size:33
Alignment explanation
Indices: 6567431--6567522 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
6567421 AAAATCGCAA
6567431 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
6567464 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
6567497 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
6567523 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:6567795 original size:93 final size:94
Alignment explanation
Indices: 6567601--6567799 Score: 364
Period size: 93 Copynumber: 2.1 Consensus size: 94
6567591 ACTTGAATGG
6567601 ATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACACAGTGTTAAAGAAT
1 ATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-ACACAGTGTTAAAGAAT
6567666 ACACAGTTTAGCAGAATTGGCAGCAACCGA
65 ACACAGTTTAGCAGAATTGGCAGCAACCGA
* *
6567696 ACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-CACAGTGTTATAGAATA
1 ATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACACAGTGTTAAAGAATA
6567760 CACAGTTTAGCAGAATTGGCAGCAACCGA
66 CACAGTTTAGCAGAATTGGCAGCAACCGA
6567789 ATAAATTTACT
1 ATAAATTTACT
6567800 AAGCAATCTA
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 55 0.54
95 46 0.46
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24
Consensus pattern (94 bp):
ATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACACAGTGTTAAAGAATA
CACAGTTTAGCAGAATTGGCAGCAACCGA
Found at i:6569511 original size:14 final size:14
Alignment explanation
Indices: 6569492--6569614 Score: 93
Period size: 14 Copynumber: 7.7 Consensus size: 14
6569482 TTGAAATGAA
6569492 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6569506 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
6569523 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
6569539 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6569558 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
6569572 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6569591 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6569605 AATCGCAACG
1 AATCGCAACG
6569615 CGAAATGAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
14 38 0.42
15 2 0.02
16 10 0.11
17 10 0.11
18 2 0.02
19 28 0.31
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6569529 original size:33 final size:33
Alignment explanation
Indices: 6569484--6569631 Score: 278
Period size: 33 Copynumber: 4.5 Consensus size: 33
6569474 GTCTTTGGTT
6569484 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
6569517 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6569550 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6569583 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6569616 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6569632 TGCGATTTTG
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 111 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:6569530 original size:19 final size:18
Alignment explanation
Indices: 6569491--6569636 Score: 108
Period size: 19 Copynumber: 8.8 Consensus size: 18
6569481 GTTGAAATGA
6569491 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
6569506 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
6569523 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
6569539 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
6569556 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
6569572 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
6569589 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
6569605 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
6569622 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
6569637 TTTTGGTTTC
Statistics
Matches: 105, Mismatches: 6, Indels: 36
0.71 0.04 0.24
Matches are distributed among these distances:
14 32 0.30
16 20 0.19
17 17 0.16
19 36 0.34
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:6569707 original size:19 final size:19
Alignment explanation
Indices: 6569683--6569747 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
6569673 TCATTTCGCG
6569683 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
6569702 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
6569716 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
6569735 AATCGCAATGCGA
1 AATCGCAACGCGA
6569748 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:6569707 original size:111 final size:111
Alignment explanation
Indices: 6569571--6569793 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
6569561 CGCAACGAGA
6569571 GAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGCG
1 GAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGCG
6569636 ATTTTGGTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGC
66 ATTTTGGTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGC
6569682 GAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGCG
1 GAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGCG
6569747 ATTTTGGTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGC
66 ATTTTGGTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGC
6569793 G
1 G
6569794 TTGCGATTCT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (111 bp):
GAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGCG
ATTTTGGTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGC
Found at i:6569778 original size:14 final size:14
Alignment explanation
Indices: 6569759--6569815 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6569749 TTTGGTTTCG
6569759 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6569773 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6569792 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6569806 CGTTGCGATT
1 CGTTGCGATT
6569816 GTCCTTCTCT
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:6569791 original size:33 final size:33
Alignment explanation
Indices: 6569743--6569862 Score: 132
Period size: 33 Copynumber: 3.4 Consensus size: 33
6569733 AAAATCGCAA
**
6569743 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
6569776 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* * *
6569809 TGCGATTGTCCTTCTCTCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCGCGTT--G-C-G--ATTCTCTCGT
6569849 TGCGATTTTCATTT
1 TGCGATTTTCATTT
6569863 ATCTCGTTGC
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 42 0.58
34 6 0.08
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 21 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:6569825 original size:20 final size:20
Alignment explanation
Indices: 6569799--6569874 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
6569789 TCGCGTTGCG
6569799 ATTCTCTCGTTGCGATTGTC
1 ATTCTCTCGTTGCGATTGTC
* **
6569819 CTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTC
*
6569839 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTGTC
*
6569859 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
6569875 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 34 0.72
21 13 0.28
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTGTC
Found at i:6569854 original size:40 final size:41
Alignment explanation
Indices: 6569799--6569875 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
6569789 TCGCGTTGCG
*
6569799 ATTCTCTCGTTGCGATTGTC-CTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCACTTATCTCGTTGCGACAGTC
* *
6569839 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCACTTATCTCGTTGCGAC
6569876 TCTTCTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 19 0.58
41 14 0.42
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCACTTATCTCGTTGCGACAGTC
Found at i:6569899 original size:15 final size:15
Alignment explanation
Indices: 6569879--6569909 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6569869 TTGCGACTCT
6569879 TCTGCAAATTGAAAC
1 TCTGCAAATTGAAAC
6569894 TCTGCAAATTGAAAC
1 TCTGCAAATTGAAAC
6569909 T
1 T
6569910 TGAATGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (15 bp):
TCTGCAAATTGAAAC
Found at i:6570016 original size:33 final size:33
Alignment explanation
Indices: 6569969--6570039 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
6569959 AATACTAACT
* *
6569969 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
6570002 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
6570035 TGAAA
1 TGAAA
6570040 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:6570263 original size:22 final size:21
Alignment explanation
Indices: 6570214--6570265 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
6570204 TGGTTGTGAG
**
6570214 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
*
6570235 -GA-ATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
6570255 GGATTTCTTCG
1 GGATTTCTTCG
6570266 CCGTAGAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.38
20 7 0.29
21 2 0.08
22 6 0.25
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.25
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:6570436 original size:20 final size:20
Alignment explanation
Indices: 6570411--6570604 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
6570401 CTTTAAATAT
6570411 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6570431 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
6570453 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6570472 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
6570492 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
6570512 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6570532 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6570552 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
6570572 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
6570592 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6570605 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:6570598 original size:60 final size:60
Alignment explanation
Indices: 6570411--6570604 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
6570401 CTTTAAATAT
**
6570411 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
6570472 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
6570532 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
6570592 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6570605 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:6570621 original size:21 final size:21
Alignment explanation
Indices: 6570591--6570673 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
6570581 ATTTTCATAT
*
6570591 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
6570612 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
6570633 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
6570654 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
6570674 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:6570664 original size:42 final size:43
Alignment explanation
Indices: 6570571--6570669 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
6570561 ATTTATGTGT
* *
6570571 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
6570612 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
6570654 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
6570670 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:6571643 original size:15 final size:15
Alignment explanation
Indices: 6571623--6571655 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6571613 ACATTAGAAT
6571623 TTTGATAAATTAATA
1 TTTGATAAATTAATA
6571638 TTTGATAAATTAATA
1 TTTGATAAATTAATA
6571653 TTT
1 TTT
6571656 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
TTTGATAAATTAATA
Found at i:6577780 original size:21 final size:22
Alignment explanation
Indices: 6577737--6577801 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 22
6577727 TAAATTTAAA
*
6577737 TTTTAAAATATTATATAATTAT
1 TTTTAAAATATTATATAAATAT
6577759 TTTTAAAA-A-TATATTAAATAT
1 TTTTAAAATATTATA-TAAATAT
* *
6577780 TATTAGTAA-ATTATA-AAATAT
1 TTTTA-AAATATTATATAAATAT
6577801 T
1 T
6577802 AATAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.11
21 18 0.49
22 11 0.30
23 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTAAAATATTATATAAATAT
Found at i:6578063 original size:2 final size:2
Alignment explanation
Indices: 6578058--6578085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6578048 TAAATGTTTA
6578058 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
6578086 GTGTGTATGG
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:6580431 original size:18 final size:19
Alignment explanation
Indices: 6580407--6580449 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
6580397 TAAAATTATG
* *
6580407 TTATAAAGTTATCCTAATA
1 TTATAAAATTATACTAATA
6580426 -TATAAAATTATACTAATA
1 TTATAAAATTATACTAATA
6580444 TTATAA
1 TTATAA
6580450 TTAATCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (19 bp):
TTATAAAATTATACTAATA
Found at i:6581737 original size:5 final size:5
Alignment explanation
Indices: 6581727--6582562 Score: 1240
Period size: 5 Copynumber: 168.6 Consensus size: 5
6581717 AACAATAAAA
6581727 ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT AT-AT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6581774 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6581823 ATAAT AT-AT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6581871 ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
6581917 AT-AT ATATAT AATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAGT
1 ATAAT ATA-AT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * *
6581968 ATAAT ATAGT ATAAT ATAGT ATAAT ATAGT ATAAT ATAGT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6582017 ATAAT AT-AT AATATAT ATATAT ATAAT ATAAT AT-AT ATAAT AATAAT
1 ATAAT ATAAT -ATA-AT ATA-AT ATAAT ATAAT ATAAT ATAAT -ATAAT
6582064 ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6582113 ATATAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT A-ATAT ATAAT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT
6582162 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6582211 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6582261 ATAAT ATAAT ATAAT AT-AT ATAAT AT-A- ATAAT ATAAT AT-A- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
6582306 ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATATAT AATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT
6582357 ATAAT ATAAT ATAAT ATAAT ATAAAT ATAAT ATAATAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT AT-A-AT ATAAT ATAAT
6582405 ATAAT ATAAT ATAAT AATATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAATAT
1 ATAAT ATAAT ATAAT -ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT
6582459 ATAAT ATAAT ATAAT A-AAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
6582507 ATAAT ATAAT ATAAT ATAAT ATAAT AATAAC GTAATT ATAAT ATAATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAA-T ATAAT ATAA-T
6582555 ATAAT ATA
1 ATAAT ATA
6582563 GTTATATTGA
Statistics
Matches: 772, Mismatches: 14, Indels: 90
0.88 0.02 0.10
Matches are distributed among these distances:
3 10 0.01
4 73 0.09
5 616 0.80
6 55 0.07
7 18 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:6582830 original size:36 final size:36
Alignment explanation
Indices: 6582748--6582883 Score: 227
Period size: 36 Copynumber: 3.8 Consensus size: 36
6582738 TCTGATCTTG
* *
6582748 CTTCAGTACTCTTTTGTGAAGGCTTGAATTTGCATTG
1 CTTCACTACTCTTTTGTGAAGGCTTG-ATTTGCATTT
6582785 CTTCACTACTCTTTTGTGAAGGCTTGATTTGCATTT
1 CTTCACTACTCTTTTGTGAAGGCTTGATTTGCATTT
* *
6582821 CTTCGCTACTCTTTTGTGAATGCTTGATTTGCATTT
1 CTTCACTACTCTTTTGTGAAGGCTTGATTTGCATTT
6582857 CTTCACTACTCTTTTGTGAAGGCTTGA
1 CTTCACTACTCTTTTGTGAAGGCTTGA
6582884 ATTGACTTGA
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 68 0.73
37 25 0.27
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.46
Consensus pattern (36 bp):
CTTCACTACTCTTTTGTGAAGGCTTGATTTGCATTT
Found at i:6583173 original size:21 final size:21
Alignment explanation
Indices: 6583148--6583198 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
6583138 CTTTTAGGGA
*
6583148 TTTTGAGTTGATTACTCGTAT
1 TTTTGAGTTGATTACTCATAT
6583169 TTTTGAGTTGATTACTCATAT
1 TTTTGAGTTGATTACTCATAT
*
6583190 TTTAGAGTT
1 TTTTGAGTT
6583199 TCAATATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.08, G:0.18, T:0.53
Consensus pattern (21 bp):
TTTTGAGTTGATTACTCATAT
Found at i:6594202 original size:18 final size:19
Alignment explanation
Indices: 6594178--6594220 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
6594168 TAAAATTACG
*
6594178 TTATAAAGTTAT-CTTAATA
1 TTATAAAATTATAC-TAATA
6594197 -TATAAAATTATACTAATA
1 TTATAAAATTATACTAATA
6594215 TTATAA
1 TTATAA
6594221 TTAATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (19 bp):
TTATAAAATTATACTAATA
Found at i:6594401 original size:2 final size:2
Alignment explanation
Indices: 6594394--6594483 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
6594384 TTTTACCTTA
6594394 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
6594436 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
6594478 AT AT AT
1 AT AT AT
6594484 GTGGCAGTGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6595428 original size:5 final size:5
Alignment explanation
Indices: 6595405--6595464 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
6595395 TAAAATTATA
*
6595405 ATAAT -TAAT A-AAA ATAAT ATAAT ATAAT ATAAT ATAAT ATAA- ACGTAATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A--TAA-T
6595455 ATAAT ATAAT
1 ATAAT ATAAT
6595465 TATATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
4 8 0.17
5 32 0.68
6 6 0.13
8 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:6595481 original size:27 final size:27
Alignment explanation
Indices: 6595427--6595481 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
6595417 AATAATATAA
**
6595427 TATAATATAATATAATATAAACGTAAT
1 TATAATATAATATAATATAAACCAAAT
*
6595454 TATAATATAATTATATTA-AAACCAAAT
1 TATAATATAA-TATAATATAAACCAAAT
6595481 T
1 T
6595482 CGGACAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (27 bp):
TATAATATAATATAATATAAACCAAAT
Found at i:6596359 original size:23 final size:23
Alignment explanation
Indices: 6596318--6596411 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
6596308 TTTTCTATAC
* * *
6596318 GGTCATTCAGGATAATTCTACGT
1 GGTCCTTCAGGACAATTCTATGT
*
6596341 GGTCCTTCAGGACATTTCTATGT
1 GGTCCTTCAGGACAATTCTATGT
* * *
6596364 AGTCCTTCGGGACAATACTATGT
1 GGTCCTTCAGGACAATTCTATGT
* *
6596387 GGTCCTTC-GAGACATTTTTATGT
1 GGTCCTTCAG-GACAATTCTATGT
6596410 GG
1 GG
6596412 CACTTTGGTG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
22 1 0.02
23 57 0.98
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (23 bp):
GGTCCTTCAGGACAATTCTATGT
Found at i:6596450 original size:24 final size:24
Alignment explanation
Indices: 6596400--6596451 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6596390 CCTTCGAGAC
* * * * *
6596400 ATTTTTATGTGGCACTTTGGTGTA
1 ATTTCTATGTGACACTTCGATGCA
6596424 ATTTCTATGTGACACTTCGATGCA
1 ATTTCTATGTGACACTTCGATGCA
6596448 ATTT
1 ATTT
6596452 ATACGAGCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (24 bp):
ATTTCTATGTGACACTTCGATGCA
Found at i:6597185 original size:16 final size:16
Alignment explanation
Indices: 6597160--6597193 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6597150 TTATTAACCA
*
6597160 GTTTTTAAAAGTCAAT
1 GTTTTGAAAAGTCAAT
6597176 GTTTTGAAAAGTCAAT
1 GTTTTGAAAAGTCAAT
6597192 GT
1 GT
6597194 GACACCTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (16 bp):
GTTTTGAAAAGTCAAT
Found at i:6600289 original size:15 final size:15
Alignment explanation
Indices: 6600257--6600298 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6600247 GAACTTGAAC
*
6600257 ATTTTGTATTTGTCT
1 ATTTTGTATTTGTAT
6600272 ATTTTGTATTT-TAAT
1 ATTTTGTATTTGT-AT
6600287 ATTTTG-ATTTGT
1 ATTTTGTATTTGT
6600299 GACTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (15 bp):
ATTTTGTATTTGTAT
Found at i:6602505 original size:54 final size:54
Alignment explanation
Indices: 6602423--6602751 Score: 389
Period size: 54 Copynumber: 6.1 Consensus size: 54
6602413 CTATGTGTAC
* *
6602423 TATCGGAACTAAGTGTGTAACCCACGAAATTCATAATATGTTTATGAACGA-CTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATC-G
*
6602477 TATCGGCACTAAGTATGCAACCCACGAAATTCATAATATGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATCG
* *
6602531 TATCGGCACTAAGTGTGCAGCCCACTG-AATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCAC-GAAATTCATAATATGTTTATGAACGATCG
* *
6602585 TATCGGCACTAAGTGTGCTACCCAC-ATAATTCATAATATGTTTATGAACGATCA
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATATGTTTATGAACGATCG
* * ***
6602639 TATTGGCACTAAGTGTGCAACCCACGAACTTCATAATGA-GTTTATGAATTTTCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAAT-ATGTTTATGAACGATCG
* * * * * * * * *
6602693 TATTGACACTATGTGTGCAACCTACAAAATTCACAATGA-GTTTGTGAATGACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAAT-ATGTTTATGAACGATCG
6602747 TATCG
1 TATCG
6602752 ATACTATATG
Statistics
Matches: 241, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
54 237 0.98
55 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATCG
Found at i:6602758 original size:54 final size:53
Alignment explanation
Indices: 6602430--6602795 Score: 157
Period size: 54 Copynumber: 6.8 Consensus size: 53
6602420 TACTATCGGA
* * * * * * * *
6602430 ACTAAGTGTGTAACCCACGAAATTCATAAT-ATGTTTATGAACGACTGTATCGGC
1 ACTATGTGTGCAA-CCACAAAATTCAAAATGA-GTTTGTGAATGACCGTATCGAC
* * * * * * * *
6602484 ACTAAGTATGCAACCCACGAAATTCATAAT-ATGTTTATGAACGATCGTATCGGC
1 ACTATGTGTGCAA-CCACAAAATTCAAAATGA-GTTTGTGAATGACCGTATCGAC
* * ** * * * *
6602538 ACTAAGTGTGCAGCCCACTGAATTCATAAT-ATGTTTATGAACGACCGTATCGGC
1 ACTATGTGTGCA-ACCACAAAATTCAAAATGA-GTTTGTGAATGACCGTATCGAC
* * * * * * * * * *
6602592 ACTAAGTGTGCTACCCACATAATTCATAAT-ATGTTTATGAACGATCATATTGGC
1 ACTATGTGTGC-AACCACAAAATTCAAAATGA-GTTTGTGAATGACCGTATCGAC
* * * * * *** *
6602646 ACTAAGTGTGCAACCCACGAACTTCATAATGAGTTTATGAATTTTCGTATTGAC
1 ACTATGTGTGCAA-CCACAAAATTCAAAATGAGTTTGTGAATGACCGTATCGAC
* *
6602700 ACTATGTGTGCAACCTACAAAATTCACAATGAGTTTGTGAATGACCGTATCGAT
1 ACTATGTGTGCAACC-ACAAAATTCAAAATGAGTTTGTGAATGACCGTATCGAC
* * *
6602754 ACTATATGTGC-ACCCCAAGGATTTCAAAATGAGTTTGTGAAT
1 ACTATGTGTGCAACCACAA--AATTCAAAATGAGTTTGTGAAT
6602796 TTCTATATTG
Statistics
Matches: 268, Mismatches: 37, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
52 3 0.01
53 6 0.02
54 257 0.96
55 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (53 bp):
ACTATGTGTGCAACCACAAAATTCAAAATGAGTTTGTGAATGACCGTATCGAC
Found at i:6603734 original size:21 final size:21
Alignment explanation
Indices: 6603710--6603749 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6603700 CAGATTGCTC
6603710 AGAGGGAACCGATTCCCCCCA
1 AGAGGGAACCGATTCCCCCCA
*
6603731 AGAGGGTACCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
6603750 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCA
Found at i:6611811 original size:25 final size:25
Alignment explanation
Indices: 6611777--6611826 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
6611767 AAAGTGTTTT
*
6611777 TAAAGGGGAGAAGTGTTAGAGTAAG
1 TAAAGGGGAGAAGTGTCAGAGTAAG
6611802 TAAAGGGGAGAAGTGTCAGAGTAAG
1 TAAAGGGGAGAAGTGTCAGAGTAAG
6611827 GGGGAGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.40, T:0.18
Consensus pattern (25 bp):
TAAAGGGGAGAAGTGTCAGAGTAAG
Found at i:6611830 original size:21 final size:22
Alignment explanation
Indices: 6611780--6611832 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 22
6611770 GTGTTTTTAA
*
6611780 AGGGGAGAAGTGTTAGAGTAAG
1 AGGGGAGAAGTGTCAGAGTAAG
6611802 TAAAGGGGAGAAGTGTCAGAGTAAG
1 ---AGGGGAGAAGTGTCAGAGTAAG
6611827 -GGGGAG
1 AGGGGAG
6611833 TAATTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
25 21 0.78
ACGTcount: A:0.36, C:0.02, G:0.47, T:0.15
Consensus pattern (22 bp):
AGGGGAGAAGTGTCAGAGTAAG
Found at i:6614488 original size:20 final size:20
Alignment explanation
Indices: 6614463--6614504 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6614453 ATATTTTTAT
*
6614463 AAAATA-TTAGTAATAATTAA
1 AAAATATTTA-TAATAATCAA
6614483 AAAATATTTATAATAATCAA
1 AAAATATTTATAATAATCAA
6614503 AA
1 AA
6614505 TAAAAAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATATTTATAATAATCAA
Found at i:6614696 original size:18 final size:18
Alignment explanation
Indices: 6614659--6614697 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6614649 TCTAAATTAT
*
6614659 ATTAATTAATCATCATTA
1 ATTAATTAATCATCAATA
6614677 ATTAATTAATCA-CTAATA
1 ATTAATTAATCATC-AATA
6614695 ATT
1 ATT
6614698 TTAAACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAATTAATCATCAATA
Found at i:6616585 original size:29 final size:30
Alignment explanation
Indices: 6616535--6616614 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 30
6616525 AAATATTTTA
6616535 AAAAT-ATTTTAGTAAT-TATTTAAT-ATTCT
1 AAAATAATTTTA-TAATAT-TTTAATAATTCT
* *
6616564 AGAATAATTTTATAATATTTT-ATAATTTT
1 AAAATAATTTTATAATATTTTAATAATTCT
6616593 AAAATAATTCTT-TAATATTTTA
1 AAAATAATT-TTATAATATTTTA
6616615 GAATTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
28 2 0.05
29 32 0.74
30 9 0.21
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
AAAATAATTTTATAATATTTTAATAATTCT
Found at i:6616606 original size:21 final size:18
Alignment explanation
Indices: 6616483--6616598 Score: 58
Period size: 21 Copynumber: 6.0 Consensus size: 18
6616473 CTTATATATT
6616483 TTTTATAATTATTAATAATTA
1 TTTTATAATT-TTAA-AA-TA
*
6616504 TTTT-TATATTTTAGAAT-
1 TTTTATA-ATTTTAAAATA
* *
6616521 TTTAAAATATTTTAAAAATA
1 TTTTATA-ATTTT-AAAATA
*
6616541 TTTTAGTAATTATT-TAATA
1 TTTTA-TAATT-TTAAAATA
* *
6616560 TTCTAGAATAATTTTATAATA
1 TT-T--TATAATTTTAAAATA
6616581 TTTTATAATTTTAAAATA
1 TTTTATAATTTTAAAATA
6616599 ATTCTTTAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
17 3 0.04
18 21 0.28
19 12 0.16
20 16 0.21
21 22 0.29
22 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTATAATTTTAAAATA
Found at i:6616745 original size:34 final size:34
Alignment explanation
Indices: 6616707--6616787 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 34
6616697 AAAAATAAAA
* *
6616707 AAAAATCCATATTTTATAAG-TTTGAAATATTTTT
1 AAAAATACA-ATTTTATAAGATTTAAAATATTTTT
* *
6616741 AAAAATAGAATTTTTTAAGATTTTAAAATATTTTT
1 AAAAATACAATTTTATAAGA-TTTAAAATATTTTT
* *
6616776 TAAAATAAAATT
1 AAAAATACAATT
6616788 AAAATTTCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
33 9 0.23
34 7 0.18
35 23 0.59
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (34 bp):
AAAAATACAATTTTATAAGATTTAAAATATTTTT
Found at i:6618114 original size:23 final size:23
Alignment explanation
Indices: 6618049--6618111 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
6618039 CATGAGAATG
6618049 TGGATTCCATTCCTATGGAAATA
1 TGGATTCCATTCCTATGGAAATA
6618072 TGGATTCCATTCCTATGGAAATA
1 TGGATTCCATTCCTATGGAAATA
*
6618095 TGGATT-CATTCCCATGG
1 TGGATTCCATTCCTATGG
6618112 GAATCTCACA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 10 0.26
23 29 0.74
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (23 bp):
TGGATTCCATTCCTATGGAAATA
Found at i:6623691 original size:29 final size:29
Alignment explanation
Indices: 6623652--6623720 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
6623642 ATAAAAGAAA
*
6623652 TTTATTTTAAACAAAGTATT-GAATTTATT
1 TTTATTTTAAACAAAGTATTAG-ATCTATT
*
6623681 TTTATTTTAAACGAAGTATTAGATCTATT
1 TTTATTTTAAACAAAGTATTAGATCTATT
6623710 TTTATTTTAAA
1 TTTATTTTAAA
6623721 TTTAACGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (29 bp):
TTTATTTTAAACAAAGTATTAGATCTATT
Found at i:6624603 original size:4 final size:4
Alignment explanation
Indices: 6624594--6624625 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
6624584 TCATTTACCA
*
6624594 GTAT GTAT GTAT ATAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
6624626 CATGTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:6627711 original size:2 final size:2
Alignment explanation
Indices: 6627704--6627732 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6627694 TAATTGAAAA
6627704 AT 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 AT A
6627733 GGGGTATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6629286 original size:13 final size:13
Alignment explanation
Indices: 6629268--6629296 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6629258 GGAAGGGAAC
6629268 CAAGATTCTAATT
1 CAAGATTCTAATT
6629281 CAAGATTCTAATT
1 CAAGATTCTAATT
6629294 CAA
1 CAA
6629297 AGGATTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (13 bp):
CAAGATTCTAATT
Found at i:6635145 original size:21 final size:21
Alignment explanation
Indices: 6635113--6635205 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
6635103 CCAAGGACGA
* *
6635113 GAAGACCGTTCATAAAGATAT
1 GAAGACCATTCATAAAGACAT
* * *
6635134 GAAGGCCATTCACCAAGGACAT
1 GAAGACCATTCA-TAAAGACAT
*
6635156 GAAGACCATTCATAAAGATAT
1 GAAGACCATTCATAAAGACAT
*
6635177 GAAGACCCTTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
6635198 GAAGACCA
1 GAAGACCA
6635206 CTTCGCATGG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 42 0.71
22 17 0.29
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:6635168 original size:43 final size:43
Alignment explanation
Indices: 6635102--6635205 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
6635092 ATACAGTCAT
* *
6635102 ACCAAGGACGA-GAAGACCGTTCATAAAGATATGAAGGCCATTC
1 ACCAAGGAC-ATGAAGACCATTCATAAAGATATGAAGACCATTC
*
6635145 ACCAAGGACATGAAGACCATTCATAAAGATATGAAGACCCTTC
1 ACCAAGGACATGAAGACCATTCATAAAGATATGAAGACCATTC
* *
6635188 A-TAAAGACATGAAGACCA
1 ACCAAGGACATGAAGACCA
6635206 CTTCGCATGG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 16 0.29
43 39 0.71
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.16
Consensus pattern (43 bp):
ACCAAGGACATGAAGACCATTCATAAAGATATGAAGACCATTC
Found at i:6635371 original size:6 final size:6
Alignment explanation
Indices: 6635360--6635393 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
6635350 TAGCACCTCG
6635360 TGCATT TGCATT TGCATT TGCATT TGCA-T TGCAT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCAT
6635394 GTATTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (6 bp):
TGCATT
Found at i:6639022 original size:124 final size:123
Alignment explanation
Indices: 6638793--6639056 Score: 348
Period size: 124 Copynumber: 2.1 Consensus size: 123
6638783 AGAACATTTA
* * * * * *
6638793 AGTTATGATATGTTGGGGCACGATTGTACCCACATCATGTTGAGATGAAAAAATTCAGACCAAGG
1 AGTTAAGATATGTTGGGACACGACTGAACCCACATCATGTTGAGATGAAAAAATACAGACCAAGA
*
6638858 AGGCATAAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCACGTACC
66 AGGCATAAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCACATACC
* * * *
6638916 AGTTAAGATAATGTTGGGACATGACTGAACCCACATCATGTTGAGATGACAAGATACATACCAAG
1 AGTTAAGAT-ATGTTGGGACACGACTGAACCCACATCATGTTGAGATGAAAAAATACAGACCAAG
* ** * * *
6638981 AAGGCCTTGAGAATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCCATACT
65 AAGGCATAAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCACATACC
6639040 AGTATAAGATGATGTTG
1 AGT-TAAGAT-ATGTTG
6639057 CGGCACTAGT
Statistics
Matches: 121, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
123 8 0.07
124 101 0.83
125 12 0.10
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (123 bp):
AGTTAAGATATGTTGGGACACGACTGAACCCACATCATGTTGAGATGAAAAAATACAGACCAAGA
AGGCATAAAGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCACATACC
Found at i:6640237 original size:37 final size:37
Alignment explanation
Indices: 6640186--6640354 Score: 214
Period size: 37 Copynumber: 4.6 Consensus size: 37
6640176 GGAGATTAGG
*
6640186 GCAAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAA-TCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
6640224 GCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
** * * *
6640261 GC-GGTCTATCCTAAGCCTTCACTGAAGAGTAGTGAA
1 GCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
** **
6640297 ATAAATCCATCTTAAGCCTTCACTAAAGAGTAGTGAA
1 GCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
* *
6640334 GCAAATCCATTTTAAGTCTTC
1 GCAAATCCATCTTAAGCCTTC
6640355 TTGGAATAGT
Statistics
Matches: 113, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
36 29 0.26
37 79 0.70
38 5 0.04
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (37 bp):
GCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
Found at i:6640318 original size:73 final size:73
Alignment explanation
Indices: 6640199--6640335 Score: 229
Period size: 73 Copynumber: 1.9 Consensus size: 73
6640189 AAGTCAATCT
* *
6640199 TAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCG
1 TAAGCCTTCACCGAAGAGTAGTGAAACAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCG
6640264 GTCTATCC
66 GTCTATCC
* * *
6640272 TAAGCCTTCACTGAAGAGTAGTGAAATAAATCCATCTTAAGCCTTCACTAAAGAGTAGTGAAGC
1 TAAGCCTTCACCGAAGAGTAGTGAAACAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
6640336 AAATCCATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (73 bp):
TAAGCCTTCACCGAAGAGTAGTGAAACAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCG
GTCTATCC
Found at i:6640759 original size:56 final size:55
Alignment explanation
Indices: 6640563--6640886 Score: 327
Period size: 56 Copynumber: 5.9 Consensus size: 55
6640553 AGTGAAGCAA
** * *
6640563 AGAAGATTG-TTCGAGTTCTATACTCCCTGAAA-AATAG-GGAGCGGCCCCGTTTAC
1 AGAAGA-TGATTCGAGTTCTATACTCCCTGAAAGAA-AGAGGAGCGAACCCATTTGC
* * * * ** *
6640617 AGAAGATTATTCGAGTTCTATACTCCCT-AGAGAAAGAGTGAGTGAACCCGTAAGA
1 AGAAGATGATTCGAGTTCTATACTCCCTGAAAGAAAGAG-GAGCGAACCCATTTGC
* *
6640672 AGAAGATG-TTCGAGTTCCATACTTCCTGAAAGAAAGAGGAAGCGAACCCATTTGC
1 AGAAGATGATTCGAGTTCTATACTCCCTGAAAGAAAGAGG-AGCGAACCCATTTGC
* *
6640727 AGAAGATGATTCGAGTTTTATACTTCCTGAAAGAAAGAGGGAGCGAACCCATTTGC
1 AGAAGATGATTCGAGTTCTATACTCCCTGAAAGAAAGA-GGAGCGAACCCATTTGC
* * * * *
6640783 AGAAGATTATTCGAGTTATATACTACCTGAAAGAAAGAGGAAGCGAACCCATTCGT
1 AGAAGATGATTCGAGTTCTATACTCCCTGAAAGAAAGAGG-AGCGAACCCATTTGC
* * * *
6640839 AGAAGATTATTCGAGTTCCATACTCCC-AAAAGAAAGAAGGAGTGAACC
1 AGAAGATGATTCGAGTTCTATACTCCCTGAAAGAAAG-AGGAGCGAACC
6640887 TGTAGGAAGA
Statistics
Matches: 230, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
53 5 0.02
54 46 0.20
55 60 0.26
56 117 0.51
57 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (55 bp):
AGAAGATGATTCGAGTTCTATACTCCCTGAAAGAAAGAGGAGCGAACCCATTTGC
Found at i:6640817 original size:112 final size:111
Alignment explanation
Indices: 6640562--6640904 Score: 388
Period size: 112 Copynumber: 3.1 Consensus size: 111
6640552 TAGTGAAGCA
* ** * *
6640562 AAGAAGATTGTTCGAGTTCTATACTCCCTGAAA-AATAG-GG-AGCGGCCCCGTTTACAGAAGAT
1 AAGAAGATTGTTCGAGTTCTATACTACCTGAAAGAA-AGAGGAAGCGAACCCATTTGCAGAAGAT
* * * *
6640624 TATTCGAGTTCTATACTCCCTAGAGAAAGAGTGAGTGAACCCGTAAG
65 TATTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGTGAACCCATAAG
* * *
6640671 AAGAAGA-TGTTCGAGTTCCATACTTCCTGAAAGAAAGAGGAAGCGAACCCATTTGCAGAAGATG
1 AAGAAGATTGTTCGAGTTCTATACTACCTGAAAGAAAGAGGAAGCGAACCCATTTGCAGAAGATT
* * **
6640735 ATTCGAGTTTTATACTTCCTGAAAGAAAGAGGGAGCGAACCCATTTG
66 ATTCGAGTTCTATACTTCCT-AAAGAAAGAGGGAGTGAACCCATAAG
* * * * *
6640782 CAGAAGATTATTCGAGTTATATACTACCTGAAAGAAAGAGGAAGCGAACCCATTCGTAGAAGATT
1 AAGAAGATTGTTCGAGTTCTATACTACCTGAAAGAAAGAGGAAGCGAACCCATTTGCAGAAGATT
* * * * ** *
6640847 ATTCGAGTTCCATACTCCCAAAAGAAAGAAGGAGTGAACCTGTAGG
66 ATTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGTGAACCCATAAG
6640893 AAGAAGATTGTT
1 AAGAAGATTGTT
6640905 TTAGTCTTAT
Statistics
Matches: 194, Mismatches: 35, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
108 25 0.13
109 11 0.06
110 36 0.19
111 56 0.29
112 66 0.34
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (111 bp):
AAGAAGATTGTTCGAGTTCTATACTACCTGAAAGAAAGAGGAAGCGAACCCATTTGCAGAAGATT
ATTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGTGAACCCATAAG
Found at i:6640954 original size:55 final size:55
Alignment explanation
Indices: 6640895--6641374 Score: 630
Period size: 55 Copynumber: 8.7 Consensus size: 55
6640885 CCTGTAGGAA
** * *
6640895 GAAGATTGTTTTAGTCTTATACTCTCTGAACG-AATAGAGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGCAGACACGATTGTT
* * *
6640950 GAAGATTGTTCGAGTCTTATAC-CATCTGAAGGAATAGGGAGTAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTC-TCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
6641005 GAAGATTATTCGAGTCTTATACTCTCTGAACG-AATAGAGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGCAGACACGATTGTT
* * * * *
6641060 GAAGATTGTTTGAGTCTTATACTCTCTAAAGAAATAGAGAGCAGACACGGTTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
6641115 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
6641170 GAAGAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACATGATTGTT
1 GAAG-ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
6641226 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * * *
6641281 GAAGAATTGTTCGAGTCTTATACTCTAT-AAAAAATAAGGAGCAAACATGATTGTT
1 GAAG-ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
6641336 GAAGATTTTTCGAG--TTCTACTCTCTGAAGGAATAGGGAG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAG
6641375 TTAACGCGGC
Statistics
Matches: 382, Mismatches: 35, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
52 9 0.02
53 10 0.03
54 12 0.03
55 274 0.72
56 77 0.20
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
Found at i:6641231 original size:221 final size:219
Alignment explanation
Indices: 6640895--6641374 Score: 666
Period size: 221 Copynumber: 2.2 Consensus size: 219
6640885 CCTGTAGGAA
** * *
6640895 GAAGATTGTTTTAGTCTTATACTCTCTGAACGAATAGAGAGCAGACACGATTATTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAATAGGGAGCAAACACGATTATTGAAGATTGTT
* * *
6640960 CGAGTCTTATACCATCTGAAGGAATAGGGAGTAGACACGATTATTGAAGATTATTCGAGTCTTAT
65 CGAGTCTTATACCATCTGAAGAAATAGGGAGCAAACACGATTATTGAAGATTATTCGAGTCTTAT
* *
6641025 ACTCTCTGAACG-AATAGAGAGCAGACACGATTGTTGAAG-ATTGTTTGAGTCTTATACTCTCTA
130 ACTCTCTGAA-GAAATAGAGAGCAGACACGATTGTTGAAGAATTGTTCGAGTCTTATACTCTATA
* *
6641088 AAGAAAT-AGAGAGCAGACACGGTTATT
194 AA-AAATAAG-GAGCAAACACGATTATT
*
6641115 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGAATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAG-AATAGGGAGCAAACACGATTATTGAAG-ATTGT
* *
6641180 TCGAGTCTTATACTC-TCTGAAGAAATAGGGAGCAAACATGATTGTTGAAGATTATTCGAGTCTT
64 TCGAGTCTTATAC-CATCTGAAGAAATAGGGAGCAAACACGATTATTGAAGATTATTCGAGTCTT
* *
6641244 ATACTCTCTGAAGAAATAGGGAGCATACACGATTGTTGAAGAATTGTTCGAGTCTTATACTCTAT
128 ATACTCTCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGAATTGTTCGAGTCTTATACTCTAT
* *
6641309 AAAAAATAAGGAGCAAACATGATTGTT
193 AAAAAATAAGGAGCAAACACGATTATT
* *
6641336 GAAGATTTTTCGAG--TTCTACTCTCTGAAGGAATAGGGAG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAATAGGGAG
6641375 TTAACGCGGC
Statistics
Matches: 233, Mismatches: 20, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
219 23 0.10
220 54 0.23
221 129 0.55
222 27 0.12
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (219 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAATAGGGAGCAAACACGATTATTGAAGATTGTTC
GAGTCTTATACCATCTGAAGAAATAGGGAGCAAACACGATTATTGAAGATTATTCGAGTCTTATA
CTCTCTGAAGAAATAGAGAGCAGACACGATTGTTGAAGAATTGTTCGAGTCTTATACTCTATAAA
AAATAAGGAGCAAACACGATTATT
Found at i:6654740 original size:3 final size:3
Alignment explanation
Indices: 6654732--6654787 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
6654722 TGGGCTTTAA
6654732 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6654780 ATTT ATT A
1 A-TT ATT A
6654788 ATAATAAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6656246 original size:29 final size:30
Alignment explanation
Indices: 6656181--6656300 Score: 86
Period size: 30 Copynumber: 4.1 Consensus size: 30
6656171 TTTATTTATA
* * *
6656181 TTTG-TATTTTTGTCCCTAAAGTTTCTGTT
1 TTTGCTATTTTAGTCCCTAAAATTTCTATT
* *
6656210 TTAT-CTATTTTAGTCCCTGAATTTTCT-TT
1 TT-TGCTATTTTAGTCCCTAAAATTTCTATT
** * *
6656239 TTTGCTATTTTAAACCTTTAAATTTCTATT
1 TTTGCTATTTTAGTCCCTAAAATTTCTATT
* **
6656269 TTTGCTGTTTTAG-CCCTTTTAATTTCTATT
1 TTTGCTATTTTAGTCCC-TAAAATTTCTATT
6656299 TT
1 TT
6656301 ATCCATTAAG
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.01
29 26 0.35
30 47 0.64
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.59
Consensus pattern (30 bp):
TTTGCTATTTTAGTCCCTAAAATTTCTATT
Found at i:6656287 original size:30 final size:30
Alignment explanation
Indices: 6656232--6656300 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
6656222 GTCCCTGAAT
6656232 TTTCT-TTTTTGCTATTTTAAACCTTTAAA
1 TTTCTATTTTTGCTATTTTAAACCTTTAAA
* ** *
6656261 TTTCTATTTTTGCTGTTTTAGCCCTTTTAA
1 TTTCTATTTTTGCTATTTTAAACCTTTAAA
6656291 TTTCTATTTT
1 TTTCTATTTT
6656301 ATCCATTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.62
Consensus pattern (30 bp):
TTTCTATTTTTGCTATTTTAAACCTTTAAA
Found at i:6657568 original size:24 final size:26
Alignment explanation
Indices: 6657522--6657575 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
6657512 AATCATCTAA
*
6657522 TTTTTTCAAATAAAAGTTATAATTAT
1 TTTTTTAAAATAAAAGTTATAATTAT
*
6657548 TTTTTTAAAATAATA-TT-TAATTAT
1 TTTTTTAAAATAAAAGTTATAATTAT
6657572 TTTT
1 TTTT
6657576 ATGAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 11 0.42
25 2 0.08
26 13 0.50
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTTTTAAAATAAAAGTTATAATTAT
Found at i:6657779 original size:3 final size:3
Alignment explanation
Indices: 6657771--6657808 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
6657761 TAATTTTAAT
*
6657771 TTA TTA TTA TTA TTA TTA TTA TT- TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6657809 CACTTTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6663498 original size:36 final size:34
Alignment explanation
Indices: 6663441--6663646 Score: 139
Period size: 35 Copynumber: 5.9 Consensus size: 34
6663431 GTTTCACATT
*
6663441 AAACAAAG-TTGATCTCACTTGAGATCATTTTCTCAA
1 AAACAAAGTTTG-TCTCGCTTGAGA-CATTTTCTC-A
* * *
6663477 AAATAAAGTTTGTCTTGCTTGAGACAAATTTCTCA
1 AAACAAAGTTTGTCTCGCTTGAGAC-ATTTTCTCA
* * **
6663512 AAACACATTTTGTCTCGCTTGAGACAGTTTTCTTG
1 AAACAAAGTTTGTCTCGCTTGAGACA-TTTTCTCA
* * **
6663547 AAA-AAATTTTGTCTCGTTTGAGACAGTTCTT-GAA
1 AAACAAAGTTTGTCTCGCTTGAGACA-TT-TTCTCA
* * * *
6663581 AAACAAATTTTGTCTCACTTAAGACAATTTATCTTA
1 AAACAAAGTTTGTCTCGCTTGAGAC-ATTT-TCTCA
* **
6663617 AAACAAACTTCATCTCGCTTGAGACATTTT
1 AAACAAAGTTTGTCTCGCTTGAGACATTTT
6663647 TTTCCTTTGA
Statistics
Matches: 136, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
34 29 0.21
35 58 0.43
36 46 0.34
37 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (34 bp):
AAACAAAGTTTGTCTCGCTTGAGACATTTTCTCA
Found at i:6663896 original size:94 final size:94
Alignment explanation
Indices: 6663735--6663941 Score: 360
Period size: 94 Copynumber: 2.2 Consensus size: 94
6663725 AACAAATTTT
* *
6663735 GTCTCACTTGAGACATTTTCCCTCATAATACAAATTTCAAAGTTGTTTTACTTGAAACAAAATTA
1 GTCTCACTTGAGACATTTTCCCTCATAATACAAATTTCAAAGTTGTTGTACTTAAAACAAAATTA
*
6663800 ATATCATTTGAGATTTTCAAAGCTGATTC
66 ATATCACTTGAGATTTTCAAAGCTGATTC
6663829 GTCTCACTTGAGACATTTTCCCTCATAATACAAATTTCAAAGTTGTTGTACTTAAAACAAAATTA
1 GTCTCACTTGAGACATTTTCCCTCATAATACAAATTTCAAAGTTGTTGTACTTAAAACAAAATTA
6663894 ATATCACTTGAGATTTTCAAAGCTGATTC
66 ATATCACTTGAGATTTTCAAAGCTGATTC
* *
6663923 GTCTCGCGTGAGACCATTT
1 GTCTCACTTGAGA-CATTT
6663942 CCCATTTAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 102 0.95
95 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (94 bp):
GTCTCACTTGAGACATTTTCCCTCATAATACAAATTTCAAAGTTGTTGTACTTAAAACAAAATTA
ATATCACTTGAGATTTTCAAAGCTGATTC
Found at i:6664230 original size:66 final size:65
Alignment explanation
Indices: 6664160--6664316 Score: 253
Period size: 66 Copynumber: 2.4 Consensus size: 65
6664150 TTCGAGTCTA
*
6664160 TTTCTTTAAAAACAAATTTTGTCTCTCTTGAGAC-ATTTTCTAATGAAAAATCAACCTTTGAGAT
1 TTTCTTT-AAAACAAATTTTGTCTCTCTTGAGACAATTTT-TAATGAAAAACCAACCTTTGAGAT
6664224 TG
64 TG
6664226 TTTCTTTGAAAACAAATTTTGTCTCTCTTGAGACAATTTTTAATGAAAAACCAACCTTTGAGATT
1 TTTCTTT-AAAACAAATTTTGTCTCTCTTGAGACAATTTTTAATGAAAAACCAACCTTTGAGATT
6664291 G
65 G
*
6664292 TTTCATTTGAAACAAATTTTGTCTC
1 TTTC-TTTAAAACAAATTTTGTCTC
6664317 ACTTAAAACG
Statistics
Matches: 86, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
66 78 0.91
67 8 0.09
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (65 bp):
TTTCTTTAAAACAAATTTTGTCTCTCTTGAGACAATTTTTAATGAAAAACCAACCTTTGAGATTG
Found at i:6664378 original size:37 final size:33
Alignment explanation
Indices: 6664334--6664463 Score: 101
Period size: 36 Copynumber: 3.9 Consensus size: 33
6664324 ACGTAACCTA
6664334 TCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGT
1 TCTTTGAGTCTGTTTCTTTGGAAACAAAA-TTT-T
* * * *
6664369 CTCTCTTGAGACAGTTTCTTTTGAGA-AAAA---T
1 -TCT-TTGAGTCTGTTTCTTTGGAAACAAAATTTT
*
6664400 T-TTTGAGTCTGTTTCTTTGGAAATAAAATTTACT
1 TCTTTGAGTCTGTTTCTTTGGAAACAAAATTT--T
6664434 ATCTTTGAGTCTGTTTCATTT-GAAACAAAA
1 -TCTTTGAGTCTGTTTC-TTTGGAAACAAAA
6664464 CAAACATCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
28 17 0.23
29 5 0.07
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 29 0.39
37 20 0.27
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TCTTTGAGTCTGTTTCTTTGGAAACAAAATTTT
Found at i:6664650 original size:64 final size:64
Alignment explanation
Indices: 6664468--6664660 Score: 217
Period size: 64 Copynumber: 3.0 Consensus size: 64
6664458 ACAAAACAAA
* *
6664468 CATCTTTGAGATCGTTTCTCTTGAAACAAATTTTGTCTCATTTGAGACAGTTTCCTATGAAACAC
1 CATCTTTGAG-TCGTTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAGTTTCCTTTGAAACAC
* * ** * *
6664533 CGATCTTTGAG-AGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCCTTTAAAACG
1 C-ATCTTTGAGTCGTTTCCCTT-GAAACAAATTTTGTCTCATTTGAGACAGTTTCCTTTGAAACA
*
6664597 T
64 C
* * * * * *
6664598 CATCTATGAGTCGCTTCCCTTGAAACGAGTTTTGTCTCTTTTGAGACAGTTTCTTTTGAAACA
1 CATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAGTTTCCTTTGAAACA
6664661 AATTATCTTT
Statistics
Matches: 105, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
64 50 0.48
65 46 0.44
66 9 0.09
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (64 bp):
CATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCATTTGAGACAGTTTCCTTTGAAACAC
Found at i:6664955 original size:134 final size:134
Alignment explanation
Indices: 6664715--6665140 Score: 557
Period size: 134 Copynumber: 3.2 Consensus size: 134
6664705 ATGGTCGTCC
* ** * *
6664715 TCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACGTAGGAGCCGCGTCAACT
1 TCATCACGTATGAGTCGTGTCATCCCTCGACCATACCTCCTCATCACGTAGGAGCCGCGTCAACC
* *
6664780 TTAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAAAA
66 TTAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGATGGCCAGAA
6664845 CTCT
131 CTCT
* * *
6664849 TCATCGCGTATGAGTAGTGTCATCCCTTGACCATACCTCCTCATCACGTAGGAGCCGCGTCAACC
1 TCATCACGTATGAGTCGTGTCATCCCTCGACCATACCTCCTCATCACGTAGGAGCCGCGTCAACC
* * * * * **
6664914 GTAGATAACCAGTCGTTCTCATCGCGTAGGAACCGAGTTATCACCACTCCTAAATATGGCCAGTT
66 TTAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGATGGCCAGAA
* *
6664979 GTCC
131 CTCT
* * * * ** *
6664983 GCATCACGTAGGAATCGTGTCATCCC-CGACCATATCTCCTCATCACGTAGGAGCCGTATCACCC
1 TCATCACGTATGAGTCGTGTCATCCCTCGACCATACCTCCTCATCACGTAGGAGCCGCGTCAACC
* * * *
6665047 TTAGATAACCAGTTGTCCTCATCACGTAGGAATCGAGTTATCACCCTTCCTAAAGATGACCAGAA
66 TTAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGATGGCCAGAA
6665112 CTCT
131 CTCT
* *
6665116 TTATCACGTATGAGCCGTGTCATCC
1 TCATCACGTATGAGTCGTGTCATCC
6665141 ACCCTTGGAC
Statistics
Matches: 245, Mismatches: 47, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
133 109 0.44
134 136 0.56
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (134 bp):
TCATCACGTATGAGTCGTGTCATCCCTCGACCATACCTCCTCATCACGTAGGAGCCGCGTCAACC
TTAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGATGGCCAGAA
CTCT
Found at i:6665363 original size:23 final size:26
Alignment explanation
Indices: 6665337--6665392 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
6665327 GGGTCTTTTC
6665337 TATTTA-ATT-TTATTTTAAT-TTAT
1 TATTTATATTATTATTTTAATATTAT
6665360 TATTATTATTATTATTATTTTAATATTAT
1 TA-T-TTA-TATTATTATTTTAATATTAT
6665389 TATT
1 TATT
6665393 ACACTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
23 2 0.07
24 1 0.04
25 3 0.11
27 4 0.15
28 11 0.41
29 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TATTTATATTATTATTTTAATATTAT
Found at i:6665364 original size:3 final size:3
Alignment explanation
Indices: 6665356--6665393 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
6665346 TTATTTTAAT
*
6665356 TTA TTA TTA TTA TTA TTA TTA TT- TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6665394 CACTTTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6674425 original size:2 final size:2
Alignment explanation
Indices: 6674418--6674443 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6674408 AGAAATACGA
6674418 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
6674444 GTGTGTGTGT
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:6675951 original size:6 final size:6
Alignment explanation
Indices: 6675940--6676643 Score: 1326
Period size: 6 Copynumber: 117.3 Consensus size: 6
6675930 TAAAATGTTG
6675940 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6675988 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676036 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676084 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676132 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG- -TATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
* *
6676178 ATATGT ATATGT ATATGT ATGTAT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676226 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676274 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676322 ATATGT ATATGTAT ATATGT ATATGT ATATGT ATATGT ATATGT ATATG-
1 ATATGT ATATG--T ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676371 -TATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676418 ATATGT ATATGT ATATGT ATATGT ATATGT ATGTATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT A--TATGT ATATGT ATATGT
6676468 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676516 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676564 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6676612 ATATGT ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT ATATGT AT
6676644 GATTGTGTAG
Statistics
Matches: 686, Mismatches: 4, Indels: 16
0.97 0.01 0.02
Matches are distributed among these distances:
4 8 0.01
6 666 0.97
8 12 0.02
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:6676972 original size:2 final size:2
Alignment explanation
Indices: 6676882--6676957 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
6676872 TATGCATAAG
6676882 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
6676924 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
6676958 GTACATGTGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6677159 original size:20 final size:20
Alignment explanation
Indices: 6677134--6677176 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
6677124 TCTAAAAGCC
*
6677134 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
6677154 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
6677174 CAT
1 CAT
6677177 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:6682374 original size:20 final size:20
Alignment explanation
Indices: 6682349--6682390 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6682339 TCTAAAACCT
*
6682349 ATTTAGGATCATATAGATGC
1 ATTTAGGAGCATATAGATGC
*
6682369 ATTTAGGAGCATATAGTTGC
1 ATTTAGGAGCATATAGATGC
6682389 AT
1 AT
6682391 GTGGTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTAGGAGCATATAGATGC
Found at i:6684063 original size:22 final size:22
Alignment explanation
Indices: 6684002--6684055 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
6683992 AGTCGAGGGT
*
6684002 TTCATATGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
*
6684024 TTCACAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
6684046 TTCATAGGTC
1 TTCATAGGTC
6684056 ATTTGGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACATA
Found at i:6688451 original size:18 final size:18
Alignment explanation
Indices: 6688428--6688463 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6688418 TAGTGGATAG
6688428 ATTGACTAAATCAACCCA
1 ATTGACTAAATCAACCCA
6688446 ATTGACTAAATCAACCCA
1 ATTGACTAAATCAACCCA
6688464 TTTCATTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (18 bp):
ATTGACTAAATCAACCCA
Found at i:6690808 original size:2 final size:2
Alignment explanation
Indices: 6690801--6690854 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
6690791 TATGCATAAG
6690801 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
*
6690843 AT AT AT AC AT AT
1 AT AT AT AT AT AT
6690855 GGTTGTATGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6691056 original size:22 final size:22
Alignment explanation
Indices: 6691028--6691089 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
6691018 AGTCGAGGAT
6691028 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
*
6691050 TTCATAGGTCCTTCGAGACATA
1 TTCATAGGTCCTTCGGGACATA
* *
6691072 TTCATAGGTTCTTTGGGA
1 TTCATAGGTCCTTCGGGA
6691090 TAAATTTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACATA
Found at i:6692615 original size:14 final size:16
Alignment explanation
Indices: 6692596--6692636 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6692586 TTTATTTACT
6692596 TATA-TTAAAT-AAAA
1 TATATTTAAATGAAAA
6692610 TATATTTAAATGAAAA
1 TATATTTAAATGAAAA
*
6692626 GATACTTTAAA
1 TATA-TTTAAA
6692637 CAACTAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 7 0.30
17 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
TATATTTAAATGAAAA
Found at i:6710529 original size:36 final size:37
Alignment explanation
Indices: 6710484--6710594 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 37
6710474 AAACTCACAA
6710484 TAAGTATTAAATGGTAAATAAAAAAAATTACAATAAC
1 TAAGTATTAAATGGTAAATAAAAAAAATTACAATAAC
* * * *
6710521 T-GGTATTAAATGGT-GATAAACAAAATTAACAAAATAAAT
1 TAAGTATTAAATGGTAAATAAAAAAAATT-AC--AAT-AAC
*
6710560 TAAGTATTAAATGATAAAT-AAAAAAATTACAATAA
1 TAAGTATTAAATGGTAAATAAAAAAAATTACAATAA
6710595 AGAAAGTCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
35 11 0.18
36 16 0.27
37 4 0.07
38 3 0.05
39 5 0.08
40 19 0.32
41 2 0.03
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.28
Consensus pattern (37 bp):
TAAGTATTAAATGGTAAATAAAAAAAATTACAATAAC
Found at i:6713212 original size:24 final size:25
Alignment explanation
Indices: 6713171--6713221 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
6713161 CACTGAAGTG
6713171 CCGCGTAGAAATTTGTCCCGAAAGA
1 CCGCGTAGAAATTTGTCCCGAAAGA
*
6713196 CCGCGTAG-AATTTGTCCCGAAGGA
1 CCGCGTAGAAATTTGTCCCGAAAGA
6713220 CC
1 CC
6713222 ACATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (25 bp):
CCGCGTAGAAATTTGTCCCGAAAGA
Found at i:6713465 original size:30 final size:31
Alignment explanation
Indices: 6713416--6713486 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
6713406 ACATAATTTA
* *
6713416 TATCGCATAGACATATCA-TTTACATACCTT
1 TATCACATAAACATATCATTTTACATACCTT
* * *
6713446 TATTACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTACATACCTT
6713477 TATCACATAA
1 TATCACATAA
6713487 TTCATATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTACATACCTT
Found at i:6713918 original size:21 final size:21
Alignment explanation
Indices: 6713894--6713936 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6713884 TCATATTCGT
* * *
6713894 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCAATTCCCC
*
6713915 TTGAATGGGTACCAATTCCCC
1 TTGAAGGGGTACCAATTCCCC
6713936 T
1 T
6713937 AGCCCAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCAATTCCCC
Found at i:6719429 original size:19 final size:19
Alignment explanation
Indices: 6719405--6719442 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6719395 TACCATTAAA
6719405 TGTAACACCCCCAACCCGT
1 TGTAACACCCCCAACCCGT
6719424 TGTAACACCCCCAACCCGT
1 TGTAACACCCCCAACCCGT
6719443 ACCCGACCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.47, G:0.11, T:0.16
Consensus pattern (19 bp):
TGTAACACCCCCAACCCGT
Found at i:6720090 original size:24 final size:25
Alignment explanation
Indices: 6720041--6720099 Score: 95
Period size: 24 Copynumber: 2.4 Consensus size: 25
6720031 AGTTTTTGCA
6720041 CCGAAGTG-CCGCGTAGAAATTTGTC
1 CCGAAG-GACCGCGTAGAAATTTGTC
6720066 CCGAAGGACCGCGTAG-AATTTGTC
1 CCGAAGGACCGCGTAGAAATTTGTC
6720090 CCGAAGGACC
1 CCGAAGGACC
6720100 ACATATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAAATTTGTC
Found at i:6721811 original size:17 final size:18
Alignment explanation
Indices: 6721779--6721812 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6721769 TAATTAAATA
6721779 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
6721797 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
6721813 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:6722678 original size:50 final size:50
Alignment explanation
Indices: 6722590--6722716 Score: 182
Period size: 50 Copynumber: 2.5 Consensus size: 50
6722580 GATTTAAGGC
* * *
6722590 GAAGACGCGACCCATGCACCGCGCCATTCTGACACGTGTCAGACTGTCAG
1 GAAGGCGCAACCCATGCACCGCGCTATTCTGACACGTGTCAGACTGTCAG
* * * *
6722640 GAAGGTGCAACCCATGCATCGCGCTATTTTGACGCGTGTCAGACTGTCAG
1 GAAGGCGCAACCCATGCACCGCGCTATTCTGACACGTGTCAGACTGTCAG
*
6722690 GAAGGCGCGACCCATGCACCGCGCTAT
1 GAAGGCGCAACCCATGCACCGCGCTAT
6722717 ACCCCTATGT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (50 bp):
GAAGGCGCAACCCATGCACCGCGCTATTCTGACACGTGTCAGACTGTCAG
Found at i:6723700 original size:2 final size:2
Alignment explanation
Indices: 6723695--6723729 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6723685 TGTGTGAGTA
6723695 AT AT AT AT 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 AT AT AT AT A
6723730 ATACAATAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6724269 original size:16 final size:16
Alignment explanation
Indices: 6724207--6724270 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
6724197 CCTAATTATA
6724207 ATATATTAAATAATCTT
1 ATAT-TTAAATAATCTT
*
6724224 ATATTTTAATAATCTT
1 ATATTTAAATAATCTT
* *
6724240 ATTTTTAAATATAATATT
1 ATATTT-AA-ATAATCTT
*
6724258 ACATTTAAATAAT
1 ATATTTAAATAAT
6724271 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 21 0.54
17 7 0.18
18 11 0.28
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTAAATAATCTT
Found at i:6724378 original size:20 final size:20
Alignment explanation
Indices: 6724353--6724390 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6724343 TTTGGTTCAC
*
6724353 AGAATGTAATATTACCAGTA
1 AGAATGTAAGATTACCAGTA
6724373 AGAATGTAAGATTACCAG
1 AGAATGTAAGATTACCAG
6724391 GGAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGTAAGATTACCAGTA
Found at i:6724623 original size:39 final size:40
Alignment explanation
Indices: 6724540--6724628 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 40
6724530 TAATAAGTTG
* *
6724540 AAAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
6724580 -AAAAT-TTATATATATATTT-TTTACAAAATTAAAAAT-AT
1 AAAAATATT-TATATAT-TTTCTTTAAAAAATTAAAAATCAT
*
6724618 AAAAATGTTTA
1 AAAAATATTTA
6724629 ATGAAATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
38 4 0.10
39 33 0.79
40 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (40 bp):
AAAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:6727719 original size:216 final size:219
Alignment explanation
Indices: 6727322--6727756 Score: 833
Period size: 216 Copynumber: 2.0 Consensus size: 219
6727312 GCCCTCAAAA
6727322 GAAAGACAAATTAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAACTAATGGACGTAGAC
1 GAAAGACAAATTAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAACTAATGGACGTAGAC
6727387 TTTGGTTGAGAAAGTCGAACCACTATAAATCGCTGTGCAATATATTTCAATTTTCTGCAAAAGAT
66 TTTGGTTGAGAAAGTCGAACCACTATAAATCGCTGTGCAATATATTTCAATTTTCTGCAAAAGAT
6727452 TCCACCAAAATTTTTATTGTCAATTCACCCCCTCTTGGTCGATTCCATCAATTGATTAACTCAGC
131 TCCACCAAAATTTTTATTGTCAATTCACCCCCTCTTGGTCGATTCCATCAATTGATTAACTCAGC
6727517 AATTGGTATCAGAGTCTAACTCAT
196 AATTGGTATCAGAGTCTAACTCAT
6727541 GAAAGACAAATTAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAACTAATGGACGTAGAC
1 GAAAGACAAATTAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAACTAATGGACGTAGAC
6727606 TTTGGTTGAGAAAGTCGAA-C-C-AT-AATCCGCTGTGCAATATATTTCAATTTTCTGCAAAAGA
66 TTTGGTTGAGAAAGTCGAACCACTATAAAT-CGCTGTGCAATATATTTCAATTTTCTGCAAAAGA
6727667 TTCCACCAAAATTTTTATTGTCAATTCACCCCCTCTTGGTCGATTCCATCAATTGATTAACTCAG
130 TTCCACCAAAATTTTTATTGTCAATTCACCCCCTCTTGGTCGATTCCATCAATTGATTAACTCAG
6727732 CAATTGGTATCAGAGTCTAACTCAT
195 CAATTGGTATCAGAGTCTAACTCAT
6727757 TTGAAGGTTT
Statistics
Matches: 215, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
215 3 0.01
216 126 0.59
217 1 0.00
218 1 0.00
219 84 0.39
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (219 bp):
GAAAGACAAATTAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAACTAATGGACGTAGAC
TTTGGTTGAGAAAGTCGAACCACTATAAATCGCTGTGCAATATATTTCAATTTTCTGCAAAAGAT
TCCACCAAAATTTTTATTGTCAATTCACCCCCTCTTGGTCGATTCCATCAATTGATTAACTCAGC
AATTGGTATCAGAGTCTAACTCAT
Found at i:6729096 original size:14 final size:14
Alignment explanation
Indices: 6729077--6729111 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6729067 AAATTTTGGA
6729077 TTTGCAAAATTTAC
1 TTTGCAAAATTTAC
6729091 TTTGCAAAATTTAC
1 TTTGCAAAATTTAC
6729105 TTT-CAAA
1 TTTGCAAA
6729112 GGTGAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTGCAAAATTTAC
Found at i:6732884 original size:19 final size:18
Alignment explanation
Indices: 6732830--6732891 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 18
6732820 TTTGGTACAG
*
6732830 AGGGAATCGATACCCTCAT
1 AGGGAATCGATACCC-CCT
* *
6732849 GAGGGAACCGATTCCCCCT
1 -AGGGAATCGATACCCCCT
6732868 AGGAGAATCGATACCCCCCT
1 AGG-GAATCGATA-CCCCCT
6732888 AGGG
1 AGGG
6732892 TTCTGGAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 22 0.63
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (18 bp):
AGGGAATCGATACCCCCT
Found at i:6735151 original size:9 final size:9
Alignment explanation
Indices: 6735137--6735170 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
6735127 GGGAGAAGTG
6735137 TTAAATGTT
1 TTAAATGTT
*
6735146 TTAAATGTG
1 TTAAATGTT
6735155 TTAAATGTT
1 TTAAATGTT
6735164 TTAAATG
1 TTAAATG
6735171 GGAGAAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (9 bp):
TTAAATGTT
Found at i:6735157 original size:18 final size:18
Alignment explanation
Indices: 6735134--6735170 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6735124 AGGGGGAGAA
6735134 GTGTTAAATGTTTTAAAT
1 GTGTTAAATGTTTTAAAT
6735152 GTGTTAAATGTTTTAAAT
1 GTGTTAAATGTTTTAAAT
6735170 G
1 G
6735171 GGAGAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (18 bp):
GTGTTAAATGTTTTAAAT
Found at i:6736761 original size:24 final size:24
Alignment explanation
Indices: 6736717--6736762 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6736707 AACAGTCAAC
*
6736717 GGGTCAGGTCAAACAGGGTCAAAT
1 GGGTCAGGTCAAACAGAGTCAAAT
*
6736741 GGGTCGGGTCAAACCA-AGTCAA
1 GGGTCAGGTCAAA-CAGAGTCAA
6736763 TTGCCCCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.15
Consensus pattern (24 bp):
GGGTCAGGTCAAACAGAGTCAAAT
Found at i:6739855 original size:25 final size:26
Alignment explanation
Indices: 6739818--6739866 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
6739808 TATGTGGTCC
* *
6739818 TACGCGGTCCTTCGG-GATAAATTTT
1 TACGCGGTACTTCGGTGAAAAATTTT
6739843 TACGCGGTACTTCGGTGAAAAATT
1 TACGCGGTACTTCGGTGAAAAATT
6739867 CTACGTGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (26 bp):
TACGCGGTACTTCGGTGAAAAATTTT
Found at i:6739871 original size:25 final size:25
Alignment explanation
Indices: 6739817--6739871 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
6739807 CTATGTGGTC
* *
6739817 CTACGCGGTCCTTCGGGATAAATTT
1 CTACGCGGTACTTCGGGATAAAATT
*
6739842 TTACGCGGTACTTCGGTGA-AAAATT
1 CTACGCGGTACTTCGG-GATAAAATT
6739867 CTACG
1 CTACG
6739872 TGGCACTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (25 bp):
CTACGCGGTACTTCGGGATAAAATT
Found at i:6744828 original size:25 final size:25
Alignment explanation
Indices: 6744800--6744856 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
6744790 ATTCTTAAGG
* *
6744800 AATTTCTATGTGATCCTTCGGGACA
1 AATTTCTAAGCGATCCTTCGGGACA
* *
6744825 AA-TTCTAAGCGGTCCTTCGGGATA
1 AATTTCTAAGCGATCCTTCGGGACA
6744849 AATTTCTA
1 AATTTCTA
6744857 CGCGGCACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (25 bp):
AATTTCTAAGCGATCCTTCGGGACA
Found at i:6744861 original size:25 final size:24
Alignment explanation
Indices: 6744813--6744869 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
6744803 TTCTATGTGA
6744813 TCCTTCGGGACAAATTCTAAGCGG
1 TCCTTCGGGACAAATTCTAAGCGG
* *
6744837 TCCTTCGGGATAAATTTCTACGCGG
1 TCCTTCGGGACAAA-TTCTAAGCGG
6744862 -CACTTCGG
1 TC-CTTCGG
6744870 TGCAAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (24 bp):
TCCTTCGGGACAAATTCTAAGCGG
Found at i:6745872 original size:30 final size:31
Alignment explanation
Indices: 6745836--6745924 Score: 121
Period size: 30 Copynumber: 2.9 Consensus size: 31
6745826 AGATCAATTT
6745836 TTAATTTGATCTTTTAA-TTTAGATAAAATA
1 TTAATTTGATCTTTTAATTTTAGATAAAATA
6745866 TTAATTTGAT-TTTTAGATTTTAGATAAAATA
1 TTAATTTGATCTTTTA-ATTTTAGATAAAATA
* * *
6745897 TCAA-TTGATCTTTAAATTTTAAATAAAA
1 TTAATTTGATCTTTTAATTTTAGATAAAA
6745925 ATATCAGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
29 5 0.09
30 28 0.53
31 20 0.38
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (31 bp):
TTAATTTGATCTTTTAATTTTAGATAAAATA
Found at i:6747470 original size:229 final size:229
Alignment explanation
Indices: 6747064--6747526 Score: 773
Period size: 229 Copynumber: 2.0 Consensus size: 229
6747054 CTAATGTAGA
* *
6747064 GCTCATAATCCTTGTCGAAGTGAAGTGGCTCATTTGCTTGGCCTCAGCACAGTTCGTTGATCTCT
1 GCTCTTAATCCTTGTCGAAGTGAAGTGGCTCATTTGCTTGGCCTCAGCACAGTTCGTTGATCTCC
* * *
6747129 GCACTCCAGTTGATTGTCGGTTTGCTCCTTCGATTTCAGGGTACGTCTTTACGTTATGTTTCTCT
66 GCACTCCAGTTGATTGTCGATTTGCTCCTTCGATTTCAGGCTACGTCTTTACGTCATGTTTCTCT
* *
6747194 GTTACTCCTTGTTTGGCTCTTCGTTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTT
131 GCTACTCCTTGTTTGGCTCTTCGTTTTTCAAATCTGATGAGATCGCTCCTTTACTGCTCTCGGTT
*
6747259 GTTTTGGCATACTATTTTTCAATTTACGGTTACT
196 GTTTTGGCATACTATTGTTCAATTTACGGTTACT
* *
6747293 GCTCTTAATCCTTGTCGAAGTGAAGTGGCTCCTTTGTTTGGCCTCAGCACAGTTCGTTGATCTCC
1 GCTCTTAATCCTTGTCGAAGTGAAGTGGCTCATTTGCTTGGCCTCAGCACAGTTCGTTGATCTCC
* * * *
6747358 GCACTCCGGTTGATTGTCGATTTGCTCCTTCGATTTCAGGCTGCGTCTTTGCGTCCTGTTTCTCT
66 GCACTCCAGTTGATTGTCGATTTGCTCCTTCGATTTCAGGCTACGTCTTTACGTCATGTTTCTCT
6747423 GCTACTCCTTGTTTGGCTCTTCGTTTTTCAAATCTGATGAGATCGCTCCTTTACTGCTCTCGGTT
131 GCTACTCCTTGTTTGGCTCTTCGTTTTTCAAATCTGATGAGATCGCTCCTTTACTGCTCTCGGTT
* * *
6747488 GTTTTGGCATATTGTTGTTCAATTTATGGTTACT
196 GTTTTGGCATACTATTGTTCAATTTACGGTTACT
6747522 GCTCT
1 GCTCT
6747527 CCGTTAATCT
Statistics
Matches: 217, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
229 217 1.00
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (229 bp):
GCTCTTAATCCTTGTCGAAGTGAAGTGGCTCATTTGCTTGGCCTCAGCACAGTTCGTTGATCTCC
GCACTCCAGTTGATTGTCGATTTGCTCCTTCGATTTCAGGCTACGTCTTTACGTCATGTTTCTCT
GCTACTCCTTGTTTGGCTCTTCGTTTTTCAAATCTGATGAGATCGCTCCTTTACTGCTCTCGGTT
GTTTTGGCATACTATTGTTCAATTTACGGTTACT
Found at i:6748697 original size:15 final size:15
Alignment explanation
Indices: 6748674--6748754 Score: 99
Period size: 15 Copynumber: 5.4 Consensus size: 15
6748664 ACCCCAAATT
* *
6748674 CCTCGATTTTTTGCA
1 CCTCAATTTTCTGCA
6748689 CCTCAATTTTCTGCA
1 CCTCAATTTTCTGCA
**
6748704 CCTCGGTTTTCTGCA
1 CCTCAATTTTCTGCA
*
6748719 CCTCAATTTTCTACA
1 CCTCAATTTTCTGCA
* *
6748734 CCTTAACTTTCTGCA
1 CCTCAATTTTCTGCA
6748749 CCTCAA
1 CCTCAA
6748755 ATTCCCCACA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (15 bp):
CCTCAATTTTCTGCA
Found at i:6750621 original size:12 final size:12
Alignment explanation
Indices: 6750606--6750640 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
6750596 CCACCTCCTT
*
6750606 CACCATCACCAC
1 CACCTTCACCAC
6750618 CACCTTCACCAC
1 CACCTTCACCAC
6750630 CACCTTCACCA
1 CACCTTCACCA
6750641 TCATCACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (12 bp):
CACCTTCACCAC
Found at i:6750639 original size:18 final size:18
Alignment explanation
Indices: 6750595--6750633 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6750585 CTTCATTATT
* *
6750595 ACCACCTCCTTCACCATC
1 ACCACCACCTTCACCACC
6750613 ACCACCACCTTCACCACC
1 ACCACCACCTTCACCACC
6750631 ACC
1 ACC
6750634 TTCACCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.59, G:0.00, T:0.15
Consensus pattern (18 bp):
ACCACCACCTTCACCACC
Found at i:6750660 original size:30 final size:30
Alignment explanation
Indices: 6750579--6750660 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
6750569 TCATCATTAT
** *
6750579 CATCACCTTCATTAT-TACCACCTCCTTCAC
1 CATCACCACCATTATCT-CCACCACCTTCAC
* *
6750609 CATCACCACCACCT-TCACCACCACCTTCAC
1 CATCACCACCA-TTATCTCCACCACCTTCAC
*
6750639 CATCATCACCATTATCTCCACC
1 CATCACCACCATTATCTCCACC
6750661 TCGGCTAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.26, C:0.49, G:0.00, T:0.26
Consensus pattern (30 bp):
CATCACCACCATTATCTCCACCACCTTCAC
Found at i:6755317 original size:20 final size:20
Alignment explanation
Indices: 6755292--6755397 Score: 99
Period size: 20 Copynumber: 5.3 Consensus size: 20
6755282 TTGCGATTTT
*
6755292 TCAAATTCGCAACGTGAAAG
1 TCAAATTCGCAACGCGAAAG
*
6755312 TCAAATTCGCAACGCG-AAT
1 TCAAATTCGCAACGCGAAAG
* * * *
6755331 TTATAAATCACAACAC-AGAAG
1 TCA-AATTCGCAACGCGA-AAG
* *
6755352 TCAAATTCGGAACGCGATAG
1 TCAAATTCGCAACGCGAAAG
*
6755372 TCAAATTCACAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
6755392 TCAAAT
1 TCAAAT
6755398 GTTTTACACG
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.06
20 57 0.86
21 5 0.08
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
TCAAATTCGCAACGCGAAAG
Found at i:6755552 original size:22 final size:22
Alignment explanation
Indices: 6755524--6755575 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
6755514 CTACGAAGAC
6755524 ATCCGTCTCCATCTCCGACAAA
1 ATCCGTCTCCATCTCCGACAAA
* * *
6755546 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCTCCATCTCCGACAAA
6755568 ATCCGTCT
1 ATCCGTCT
6755576 ATCTCCATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.25
Consensus pattern (22 bp):
ATCCGTCTCCATCTCCGACAAA
Found at i:6757630 original size:21 final size:21
Alignment explanation
Indices: 6757606--6757647 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6757596 GAATTATGTG
* *
6757606 ATGAGGTCGGTGCTTTGCGTC
1 ATGAGGTCGGTACTTTACGTC
6757627 ATGAGGTCGGTACTTTACGTC
1 ATGAGGTCGGTACTTTACGTC
6757648 GAGAAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (21 bp):
ATGAGGTCGGTACTTTACGTC
Found at i:6758320 original size:39 final size:39
Alignment explanation
Indices: 6758266--6758354 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
6758256 ACTCAAGTTG
6758266 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
*
6758305 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
*
6758344 TGGATTTTGAT
1 TAGATTTTGAT
6758355 GAGCATCAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (39 bp):
TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
Found at i:6758688 original size:18 final size:18
Alignment explanation
Indices: 6758665--6758701 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6758655 CGAAATTTAT
6758665 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
6758683 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
6758701 A
1 A
6758702 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:6759122 original size:25 final size:25
Alignment explanation
Indices: 6759088--6759137 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
6759078 ATTATTTTTC
*
6759088 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
6759113 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
6759138 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:6759281 original size:34 final size:34
Alignment explanation
Indices: 6759243--6759307 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
6759233 AGTCAAATTT
6759243 GCAACGCTTATTTCGCGTTGTAAATTTGACTATC
1 GCAACGCTTATTTCGCGTTGTAAATTTGACTATC
* *
6759277 GCAACGCTTATTTTGCGTTGTGAATTTGACT
1 GCAACGCTTATTTCGCGTTGTAAATTTGACT
6759308 TTTGCGTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (34 bp):
GCAACGCTTATTTCGCGTTGTAAATTTGACTATC
Found at i:6759339 original size:54 final size:54
Alignment explanation
Indices: 6759253--6759370 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 54
6759243 GCAACGCTTA
** * * *
6759253 TTTCGCGTTGTAAATTTGACTATCGCAACGCTTATTTTGCGTTGTGAATTTGAC
1 TTTCGCGTTGCGAATTTAACTATCGCAACGCTTATTTCGCGTTGCGAATTTGAC
*
6759307 TTTTGCGTTGCGAATTTAACTATCGCAACGCTTATTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTAACTATCGCAACGCTTATTTCGCGTTGCGAATTTGAC
6759361 TTTCGCGTTG
1 TTTCGCGTTG
6759371 ATTGCAACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (54 bp):
TTTCGCGTTGCGAATTTAACTATCGCAACGCTTATTTCGCGTTGCGAATTTGAC
Found at i:6759679 original size:18 final size:18
Alignment explanation
Indices: 6759656--6759691 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6759646 AAGCCGGTTG
*
6759656 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
6759674 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
6759692 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Done.