Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004920.1 Hibiscus syriacus cultivar Beakdansim tig00011079_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: 1590857
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 7 of 7
Found at i:1398640 original size:33 final size:33
Alignment explanation
Indices: 1398553--1398843 Score: 242
Period size: 33 Copynumber: 8.5 Consensus size: 33
1398543 CGGAAATTAC
* *
1398553 AATCGCAACGCGAAATGAAAATCACAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
1398586 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
1398620 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
1398658 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
1398691 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* *
1398724 AATCGCAATGCGAAATGAAAATCGCAATGCG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
1398756 AAT-GAAAAT-CGCAAA-GAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCG-AAATGA-A-AATCGCAA--CG--A-GAA
*
1398795 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
1398828 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1398844 TATAAACGCA
Statistics
Matches: 218, Mismatches: 15, Indels: 50
0.77 0.05 0.18
Matches are distributed among these distances:
31 5 0.02
32 10 0.05
33 112 0.51
34 32 0.15
35 6 0.03
36 6 0.03
37 2 0.01
38 29 0.13
39 11 0.05
40 5 0.02
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:1398859 original size:52 final size:52
Alignment explanation
Indices: 1398581--1398843 Score: 508
Period size: 52 Copynumber: 5.0 Consensus size: 52
1398571 AAATCACAAC
1398581 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1398634 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1398686 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1398738 ATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1398790 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1398842 AT
1 AT
1398844 TATAAACGCA
Statistics
Matches: 208, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
52 192 0.92
53 16 0.08
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1398892 original size:19 final size:19
Alignment explanation
Indices: 1398868--1398912 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1398858 GATTCTCTCG
1398868 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1398887 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1398906 TTGCGAT
1 TTGCGAT
1398913 AGTCATTTTT
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:1398918 original size:19 final size:19
Alignment explanation
Indices: 1398877--1398920 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1398867 GTTGCGATTT
**
1398877 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
1398896 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
1398915 TCATTT
1 TCATTT
1398921 TTGCCTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1399038 original size:14 final size:14
Alignment explanation
Indices: 1399019--1399055 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1399009 CATCAATTAC
1399019 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1399033 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1399047 ACAAATCAA
1 ACAAATCAA
1399056 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:1401057 original size:14 final size:14
Alignment explanation
Indices: 1401038--1401094 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1401028 GCGAAATGAA
*
1401038 AATCGCAACGACAG
1 AATCGCAACGAAAG
1401052 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1401069 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1401085 AATCGCAACG
1 AATCGCAACG
1401095 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:1401065 original size:33 final size:33
Alignment explanation
Indices: 1401019--1401111 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1401009 GCGAAACCAA
*
1401019 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1401052 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1401085 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1401112 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:1401076 original size:19 final size:19
Alignment explanation
Indices: 1400982--1401116 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1400972 TAGTTTACTT
* *
1400982 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1401002 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1401021 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1401040 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1401054 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1401073 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1401087 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1401106 TCGCAATGCGA
1 TCGCAACGCGA
1401117 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:1401154 original size:33 final size:33
Alignment explanation
Indices: 1401112--1401203 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1401102 AAAATCGCAA
*
1401112 TGCGATTTTGGTTTCGCGTTGTGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1401145 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1401178 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1401204 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1401166 original size:19 final size:19
Alignment explanation
Indices: 1401112--1401240 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1401102 AAAATCGCAA
1401112 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1401131 TGTGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1401145 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1401164 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1401178 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1401197 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1401216 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1401236 TGCGA
1 TGCGA
1401241 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1401404 original size:93 final size:93
Alignment explanation
Indices: 1401288--1401756 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
1401278 ATGGATTGCA
1401288 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1401352 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1401380 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1401445 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1401473 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1401538 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1401566 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1401631 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1401659 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1401724 TAGCAGAATTGGCAGCAACCAAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1401752 TTACT
1 TTACT
1401757 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 371 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1403481 original size:14 final size:14
Alignment explanation
Indices: 1403462--1403551 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1403452 TTGAAATGAA
1403462 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1403476 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1403495 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1403509 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1403528 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1403542 AATCGCAACG
1 AATCGCAACG
1403552 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1403499 original size:33 final size:33
Alignment explanation
Indices: 1403454--1403568 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1403444 TCTTTTGGTT
1403454 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1403487 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1403520 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1403553 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1403569 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1403500 original size:19 final size:19
Alignment explanation
Indices: 1403476--1403573 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1403466 GCAACGAGAG
*
1403476 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
1403495 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1403509 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1403528 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1403542 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1403561 AATCGCAATGCGA
1 AATCGCAACGCGA
1403574 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1403604 original size:14 final size:14
Alignment explanation
Indices: 1403585--1403641 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1403575 TTTGGTTTCG
1403585 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1403599 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
1403618 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1403632 CGTTGCGATT
1 CGTTGCGATT
1403642 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1403619 original size:33 final size:33
Alignment explanation
Indices: 1403582--1403646 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1403572 GATTTTGGTT
1403582 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1403615 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1403647 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:1403652 original size:21 final size:21
Alignment explanation
Indices: 1403626--1403701 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1403616 CGCGTTGCGA
1403626 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1403647 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
1403667 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1403688 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1403702 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1403682 original size:41 final size:41
Alignment explanation
Indices: 1403625--1403702 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1403615 TCGCGTTGCG
* *
1403625 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
1403666 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
1403703 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:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1403823 original size:33 final size:33
Alignment explanation
Indices: 1403781--1403851 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1403771 AATACTAACT
*
1403781 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1403814 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1403847 TGAAA
1 TGAAA
1403852 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1404259 original size:20 final size:20
Alignment explanation
Indices: 1404234--1404427 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1404224 CTTTAAATAT
1404234 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1404254 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1404276 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1404295 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1404315 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1404335 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1404355 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1404375 CGAGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1404395 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1404415 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1404428 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1404421 original size:60 final size:60
Alignment explanation
Indices: 1404234--1404427 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
1404224 CTTTAAATAT
* **
1404234 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGAGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* *** *
1404295 CGCGTTGCGATATACGGATACGCA-TTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACG-AGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1404355 CACGTTGCGATTTACGGATACGAGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1404415 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1404428 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 83 0.75
61 27 0.24
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1404444 original size:21 final size:21
Alignment explanation
Indices: 1404414--1404496 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1404404 ATTTTCATAT
*
1404414 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1404435 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1404456 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1404477 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1404497 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:1404487 original size:42 final size:43
Alignment explanation
Indices: 1404394--1404492 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1404384 ATTTATGTGT
* *
1404394 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1404435 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1404477 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1404493 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:1407436 original size:37 final size:37
Alignment explanation
Indices: 1407394--1407469 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1407384 GTCCCGTACG
1407394 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
1 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
* *
1407431 TGACGGTATATGACGAGAGCCTTCTGCATTGCCTTTT
1 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
1407468 TG
1 TG
1407470 TTTTGGTTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (37 bp):
TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
Found at i:1407795 original size:22 final size:22
Alignment explanation
Indices: 1407738--1407795 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1407728 CGTTCGTGAA
**
1407738 TTTTTTTTCTAAAGTAGTTGATT
1 TTTTTTTTC-AAAAAAGTTGATT
* * *
1407761 TTTTATATAAAAAAAGTTGATT
1 TTTTTTTTCAAAAAAGTTGATT
1407783 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
1407796 TAAAATAGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTTTTTCAAAAAAGTTGATT
Found at i:1410876 original size:36 final size:36
Alignment explanation
Indices: 1410829--1410900 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1410819 CCAAGACGAC
1410829 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
1 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
1410865 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
1 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
1410901 TACTGCTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (36 bp):
ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
Found at i:1414508 original size:32 final size:32
Alignment explanation
Indices: 1414467--1414556 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
1414457 CATTATTGAT
1414467 CCATTCGATTTTAGTCCCTTAGCCATTGACTC
1 CCATTCGATTTTAGTCCCTTAGCCATTGACTC
* * *
1414499 CCATTCGATTTTAGTCCCTCAACCGTTGACTC
1 CCATTCGATTTTAGTCCCTTAGCCATTGACTC
*
1414531 CCATTCGATTTTAGTCCTTTAGCCAT
1 CCATTCGATTTTAGTCCCTTAGCCAT
1414557 GTTAGGGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (32 bp):
CCATTCGATTTTAGTCCCTTAGCCATTGACTC
Found at i:1418212 original size:29 final size:28
Alignment explanation
Indices: 1418175--1418234 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1418165 TGTGTTTTAT
* *
1418175 AATGATTGATTTTAA-TCATAATTATATA
1 AATGATTGATTGTAACT-ACAATTATATA
1418203 AATGTATTGATTGTAACTACAATTATATA
1 AATG-ATTGATTGTAACTACAATTATATA
1418232 AAT
1 AAT
1418235 TCGAATGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 23 0.82
30 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (28 bp):
AATGATTGATTGTAACTACAATTATATA
Found at i:1426458 original size:22 final size:22
Alignment explanation
Indices: 1426428--1426492 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
1426418 TAGTGCAGGA
*
1426428 GGAATCGATACCCCCTTTAAGG
1 GGAACCGATACCCCCTTTAAGG
*
1426450 GGAACCGATTCCCCCCTTTAAAGG
1 GGAACCGA-TACCCCCTTT-AAGG
* *
1426474 GGAACCAATTCCCCCTTTA
1 GGAACCGATACCCCCTTTA
1426493 GGGAATAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.22
23 18 0.49
24 11 0.30
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (22 bp):
GGAACCGATACCCCCTTTAAGG
Found at i:1426473 original size:24 final size:23
Alignment explanation
Indices: 1426438--1426492 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1426428 GGAATCGATA
*
1426438 CCCCCTTT-AAGGGGAACCGATT
1 CCCCCTTTAAAGGGGAACCAATT
1426460 CCCCCCTTTAAAGGGGAACCAATT
1 -CCCCCTTTAAAGGGGAACCAATT
1426484 CCCCCTTTA
1 CCCCCTTTA
1426493 GGGAATAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (23 bp):
CCCCCTTTAAAGGGGAACCAATT
Found at i:1430110 original size:23 final size:23
Alignment explanation
Indices: 1430080--1430138 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1430070 CTCGTATAAA
1430080 TGCACCGAAGTGCCAAGTAGAAT
1 TGCACCGAAGTGCCAAGTAGAAT
* **
1430103 TGCACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTGCCAAGTAGAAT
* *
1430126 TGAACCGTAGTGC
1 TGCACCGAAGTGC
1430139 TATATAAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCAAGTAGAAT
Found at i:1435631 original size:2 final size:2
Alignment explanation
Indices: 1435626--1435698 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1435616 TAAATGTGTG
1435626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1435668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1435699 TCATTTTATG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1436966 original size:12 final size:12
Alignment explanation
Indices: 1436949--1436974 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1436939 ATCAAACATC
1436949 ATTTTAAATATA
1 ATTTTAAATATA
1436961 ATTTTAAATATA
1 ATTTTAAATATA
1436973 AT
1 AT
1436975 ATTGAAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAATATA
Found at i:1437379 original size:19 final size:19
Alignment explanation
Indices: 1437332--1437379 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1437322 TAAAATATTC
1437332 ATAAAGTTATAATTTTAAAA
1 ATAAA-TTATAATTTTAAAA
* **
1437352 TTATTTTATAATTTTAAAA
1 ATAAATTATAATTTTAAAA
1437371 ATAAATTAT
1 ATAAATTAT
1437380 GAACATTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAAATTATAATTTTAAAA
Found at i:1438624 original size:19 final size:18
Alignment explanation
Indices: 1438591--1438628 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1438581 AAAATAAAAA
1438591 AAATATTTAAATTATAAT
1 AAATATTTAAATTATAAT
*
1438609 AAATGTTTATAATTATAAT
1 AAATATTTA-AATTATAAT
1438628 A
1 A
1438629 GTAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AAATATTTAAATTATAAT
Found at i:1441988 original size:20 final size:20
Alignment explanation
Indices: 1441965--1442016 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1441955 AACGCGATCC
1441965 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1441985 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1442005 CCAAAATCGCAA
1 CCAGAATCGCAA
1442017 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1442097 original size:20 final size:20
Alignment explanation
Indices: 1442072--1442265 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1442062 GATTTTCCAT
* *
1442072 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1442092 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1442112 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1442132 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1442152 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1442172 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1442192 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1442212 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1442233 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1442253 AATCGCAACGCGA
1 AATCGCAACGCGA
1442266 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1442117 original size:40 final size:39
Alignment explanation
Indices: 1442068--1442265 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
1442058 TTGCGATTTT
* ** *
1442068 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1442106 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
1442147 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1442187 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1442226 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1442266 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1442155 original size:60 final size:60
Alignment explanation
Indices: 1442072--1442264 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1442062 GATTTTCCAT
* ** * *
1442072 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1442132 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1442192 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1442253 AATCGCAACGCG
1 AATCGCAACGCG
1442265 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1442682 original size:33 final size:33
Alignment explanation
Indices: 1442643--1442713 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1442633 TTCACTTAGA
*
1442643 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1442676 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1442709 TTTCA
1 TTTCA
1442714 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1442852 original size:14 final size:14
Alignment explanation
Indices: 1442833--1442887 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1442823 AGAATGACTG
1442833 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1442847 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
1442866 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1442880 TCGCAACG
1 TCGCAACG
1442888 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1442900 original size:33 final size:33
Alignment explanation
Indices: 1442833--1442903 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1442823 AGAATGACTG
***
1442833 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1442866 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1442899 TCGCA
1 TCGCA
1442904 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1442940 original size:14 final size:14
Alignment explanation
Indices: 1442921--1442977 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1442911 TTTCATTTCG
1442921 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1442935 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1442952 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1442968 CGTTGCGATT
1 CGTTGCGATT
1442978 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1442955 original size:33 final size:33
Alignment explanation
Indices: 1442904--1442982 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
1442894 CAAAATCGCA
*
1442904 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATCTCGCGTTGCGATTCTCTCG
*
1442937 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATCTCGCGTTGCGATTCTCTCG
1442970 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1442983 TTCAACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATCTCGCGTTGCGATTCTCTCG
Found at i:1442957 original size:19 final size:18
Alignment explanation
Indices: 1442899--1442978 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 18
1442889 GAAACCAAAA
* *
1442899 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
1442918 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
1442934 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
1442951 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
1442967 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
1442979 TCATTTCAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
14 16 0.30
15 3 0.06
16 7 0.13
17 8 0.15
18 1 0.02
19 18 0.34
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:1444987 original size:93 final size:93
Alignment explanation
Indices: 1444674--1445052 Score: 744
Period size: 92 Copynumber: 4.1 Consensus size: 93
1444664 TAGATTGCTT
1444674 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1444739 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1444766 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1444830 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1444858 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1444923 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1444951 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1445016 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1445044 AGTAAATTT
1 AGTAAATTT
1445053 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 19 0.07
92 134 0.47
93 132 0.46
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1445134 original size:19 final size:19
Alignment explanation
Indices: 1445094--1445221 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1445084 TAGTTTACTT
* *
1445094 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1445114 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1445133 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1445152 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1445166 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1445185 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1445199 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
1445217 TCGCA
1 TCGCA
1445222 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 9 0.10
19 38 0.43
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1445173 original size:33 final size:32
Alignment explanation
Indices: 1445130--1445221 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1445120 CGCGAAACCA
**
1445130 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1445162 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1445195 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1445222 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1445244 original size:19 final size:19
Alignment explanation
Indices: 1445217--1445351 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1445207 CGAAACCAAA
*
1445217 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1445236 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1445252 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1445269 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1445285 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1445302 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1445321 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1445341 TCGTGTTGCGA
1 TCGCGTTGCGA
1445352 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1445258 original size:14 final size:14
Alignment explanation
Indices: 1445239--1445295 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1445229 TTTCATTTCG
1445239 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1445253 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1445270 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1445286 CGTTGCGATT
1 CGTTGCGATT
1445296 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1445264 original size:33 final size:33
Alignment explanation
Indices: 1445222--1445314 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1445212 CCAAATCGCA
*
1445222 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1445255 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1445288 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1445315 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1447196 original size:38 final size:38
Alignment explanation
Indices: 1447153--1447225 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1447143 AATTGATTGT
*
1447153 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1447191 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1447226 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:1447212 original size:19 final size:19
Alignment explanation
Indices: 1447148--1447212 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1447138 AGTTTAATTG
*
1447148 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1447167 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1447185 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1447205 ATTGATTT
1 ATTGATTT
1447213 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:1447226 original size:14 final size:14
Alignment explanation
Indices: 1447207--1447242 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1447197 ATTGTTTAAT
1447207 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1447221 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1447235 TGATTTGT
1 TGATTTGT
1447243 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1447365 original size:19 final size:19
Alignment explanation
Indices: 1447349--1447449 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
1447339 AAAAATGACT
1447349 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1447368 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1447386 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1447400 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1447419 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1447439 ATCGCAATGCG
1 ATCGCAATGCG
1447450 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
13 1 0.01
14 9 0.12
16 4 0.05
18 10 0.14
19 30 0.41
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1447498 original size:33 final size:33
Alignment explanation
Indices: 1447456--1447784 Score: 219
Period size: 33 Copynumber: 9.5 Consensus size: 33
1447446 TGCGTTTATA
1447456 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
1447489 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCT-CG--TTGCGATTTTC
*
1447526 -TTTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-ATCTCG--TTGCGATTTTC
* *
1447560 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
1447598 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
1447631 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
1447671 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
1447702 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
1447735 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
1447769 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
1447785 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 20, Indels: 54
0.77 0.06 0.17
Matches are distributed among these distances:
31 9 0.04
32 15 0.06
33 80 0.32
34 40 0.16
35 17 0.07
36 15 0.06
37 15 0.06
38 40 0.16
39 9 0.04
40 9 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:1447502 original size:19 final size:19
Alignment explanation
Indices: 1447478--1447784 Score: 342
Period size: 19 Copynumber: 17.4 Consensus size: 19
1447468 GATTATCTCG
1447478 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1447497 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1447517 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1447531 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1447549 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1447568 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1447587 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1447606 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
1447621 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1447639 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1447658 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1447672 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1447691 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1447710 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1447724 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1447744 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1447758 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1447777 TTGCGATT
1 TTGCGATT
1447785 GTATTTTCCG
Statistics
Matches: 248, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 5 0.02
16 30 0.12
17 23 0.09
18 14 0.06
19 122 0.49
20 22 0.09
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1447556 original size:71 final size:70
Alignment explanation
Indices: 1447478--1447717 Score: 344
Period size: 71 Copynumber: 3.4 Consensus size: 70
1447468 GATTATCTCG
1447478 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTTTCGTTGCGATTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTTTCGTTGCGATTTCAT
1447543 TTCGCA
65 TTCGCA
* *
1447549 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA-T
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
1447613 T-ATGTCG-G
61 TCATTTCGCA
*
1447621 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGA-TTTCAT
1447685 TTCGCA
65 TTCGCA
1447691 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1447718 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 11 0.07
71 98 0.65
72 4 0.03
73 10 0.07
74 2 0.01
75 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (70 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTCATT
TCGCA
Found at i:1447642 original size:52 final size:52
Alignment explanation
Indices: 1447478--1447756 Score: 329
Period size: 52 Copynumber: 5.2 Consensus size: 52
1447468 GATTATCTCG
*
1447478 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCT-CG--TTGCGATTTTCATTTCGCA
* *
1447531 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCA
* *
1447587 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCA
*
1447639 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCA
*
1447691 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCA
1447744 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1447757 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 6, Indels: 18
0.90 0.03 0.08
Matches are distributed among these distances:
51 13 0.06
52 135 0.64
53 28 0.13
54 9 0.04
55 3 0.01
56 6 0.03
57 17 0.08
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCA
Found at i:1450105 original size:12 final size:12
Alignment explanation
Indices: 1450088--1450112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1450078 TCTTCGGGGA
1450088 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1450100 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1450112 C
1 C
1450113 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1450320 original size:24 final size:24
Alignment explanation
Indices: 1450286--1450332 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1450276 CTGAAACATC
1450286 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1450310 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1450333 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1451033 original size:20 final size:20
Alignment explanation
Indices: 1451005--1451340 Score: 445
Period size: 20 Copynumber: 17.1 Consensus size: 20
1450995 AAATTTCAGT
* * * *
1451005 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1451025 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1451045 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1451065 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1451085 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1451105 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1451125 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1451145 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1451165 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1451185 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1451205 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1451225 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1451245 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1451265 ATTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1451285 GTTGCGATTTACGGATA--C
1 GTTGCGATTTACGGATACGC
1451303 ---GCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1451320 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1451340 G
1 G
1451341 AATTTGCGAT
Statistics
Matches: 284, Mismatches: 21, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
15 14 0.05
17 1 0.00
18 1 0.00
19 5 0.02
20 259 0.91
21 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1451308 original size:15 final size:15
Alignment explanation
Indices: 1451288--1451320 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1451278 GATACACGTT
1451288 GCGATTTACGGATAC
1 GCGATTTACGGATAC
1451303 GCGATTTACGGATAC
1 GCGATTTACGGATAC
1451318 GCG
1 GCG
1451321 TTGCGATTTA
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:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (15 bp):
GCGATTTACGGATAC
Found at i:1451605 original size:13 final size:13
Alignment explanation
Indices: 1451561--1451607 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1451551 CTGTTCTTTG
*
1451561 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1451575 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1451587 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1451601 ATATTTA
1 ATATTTA
1451608 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1453047 original size:11 final size:11
Alignment explanation
Indices: 1453024--1453055 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1453014 TGTAATTAAT
1453024 TATTTATATATA
1 TATTTA-ATATA
1453036 TATTTAATATA
1 TATTTAATATA
1453047 TATTTAATA
1 TATTTAATA
1453056 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:1453059 original size:3 final size:3
Alignment explanation
Indices: 1453051--1453117 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
1453041 AATATATATT
*
1453051 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1453098 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1453118 TGGATAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1453821 original size:117 final size:114
Alignment explanation
Indices: 1453436--1454046 Score: 852
Period size: 114 Copynumber: 5.3 Consensus size: 114
1453426 TAGAATTATG
* * * *
1453436 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1453501 TTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* *
1453550 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *** * * * *
1453615 TTATGAACT-TTCTCTGGAAAAAATAATCCATCCAGTGATGAATTCAGA-
66 TTATGAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
*
1453663 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1453728 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
63 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* *
1453780 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTC
*
1453845 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
63 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
*
1453897 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** *** * * **
1453962 TTATGAACT-TTCTCTGAAAAAAATAATCCATCAATTTGATGAATTC-AGG
66 TTATGAACTCTTC-CTGGCAATGTTGATCCATCAA-ATGATGAATTCAAAC
*
1454011 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
1454047 AATAGCCCTG
Statistics
Matches: 448, Mismatches: 38, Indels: 22
0.88 0.07 0.04
Matches are distributed among these distances:
113 55 0.12
114 173 0.39
115 11 0.02
116 48 0.11
117 157 0.35
119 1 0.00
120 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (114 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:1454459 original size:83 final size:84
Alignment explanation
Indices: 1454315--1455049 Score: 1099
Period size: 83 Copynumber: 8.6 Consensus size: 84
1454305 GTAATTCCTA
* *
1454315 CCAACCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAA
1454380 ATTCAATGATTGGTTCTG-
66 ATTCAATGATTGGTTCTGT
1454398 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAA
*
1454463 ACTCAATGATTGGTTCTG-
66 ATTCAATGATTGGTTCTGT
*
1454481 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACATT-ATTCTTCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCA-TCTTCC
1454545 AAATTCAATGATTGGTTCTGT
64 AAATTCAATGATTGGTTCTGT
* * *
1454566 CC-AACCAGATCAGATAACTCAAAGAACACTTCTAAAAGATGCTATTGAGCACATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCCA
1454630 AATTCAATGATTGGTTCTGTAATT
65 AATTCAATGATTGGTTCTG----T
*
1454654 CCTACCAACCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 CC-A--AA-CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
1454719 CCAAATTCAATGATTGGTTCTG-
62 CCAAATTCAATGATTGGTTCTGT
1454741 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAA
*
1454806 ACTCAATGATTGGTTCTG-
66 ATTCAATGATTGGTTCTGT
*
1454824 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACATT-ATTCTTCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCA-TCTTCC
1454888 AAATTCAATGATTGGTTCTGT
64 AAATTCAATGATTGGTTCTGT
* * *
1454909 CC-AACCAGATCAGATAACTCAAAGAACACTTCTAAAAGATGCTATTGAGCACATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCCA
1454973 AATTCAATGATTGGTTCTGTAATT
65 AATTCAATGATTGGTTCTG----T
1454997 CCTACCAACCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
1 CC-A--AA-CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
1455050 GCACATTATA
Statistics
Matches: 605, Mismatches: 19, Indels: 46
0.90 0.03 0.07
Matches are distributed among these distances:
83 256 0.42
84 214 0.35
85 6 0.01
86 1 0.00
87 2 0.00
88 6 0.01
92 37 0.06
93 83 0.14
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAA
ATTCAATGATTGGTTCTGT
Found at i:1454902 original size:343 final size:343
Alignment explanation
Indices: 1454276--1455048 Score: 1521
Period size: 343 Copynumber: 2.3 Consensus size: 343
1454266 AATCATGCAT
*
1454276 TTCATCTTTC-AATTACAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAG
1 TTCATCTTCCAAATT-CAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAG
1454340 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACC
65 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACC
1454405 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAAT
130 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAAT
1454470 GATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACA
195 GATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACA
1454535 TTATTCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTA
260 TTATTCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTA
1454600 AAAGATGCTATTGAGCACA
325 AAAGATGCTATTGAGCACA
1454619 TTCATCTTCCAAATTCAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAGA
1 TTCATCTTCCAAATTCAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAGA
1454684 ACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCA
66 ACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCA
1454749 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAATG
131 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAATG
1454814 ATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACAT
196 ATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACAT
1454879 TATTCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAA
261 TATTCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAA
1454944 AAGATGCTATTGAGCACA
326 AAGATGCTATTGAGCACA
1454962 TTCATCTTCCAAATTCAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAGA
1 TTCATCTTCCAAATTCAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAGA
1455027 ACACTTCCAGAAGATGCTATTG
66 ACACTTCCAGAAGATGCTATTG
1455049 AGCACATTAT
Statistics
Matches: 428, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
343 424 0.99
344 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (343 bp):
TTCATCTTCCAAATTCAATGATTGGTTCTGTAATTCCTACCAACCCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCA
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAATG
ATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACAT
TATTCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAA
AAGATGCTATTGAGCACA
Found at i:1456218 original size:11 final size:11
Alignment explanation
Indices: 1456201--1456248 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
1456191 CTTGACCCCC
1456201 CTTTTTTCTTTT
1 CTTTTTT-TTTT
*
1456213 -TTTTTTCTTT
1 CTTTTTTTTTT
1456223 CTTTTTTTTTT
1 CTTTTTTTTTT
*
1456234 CTTCATTTTTTT
1 CTT-TTTTTTTT
1456246 CTT
1 CTT
1456249 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 18 0.58
12 10 0.32
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:1456225 original size:15 final size:15
Alignment explanation
Indices: 1456205--1456245 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1456195 ACCCCCCTTT
1456205 TTTCTTTTTTTTTTC
1 TTTCTTTTTTTTTTC
1456220 TTTCTTTTTTTTTTC
1 TTTCTTTTTTTTTTC
1456235 -TTCATTTTTTT
1 TTTC-TTTTTTT
1456246 CTTCAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTTTTTTC
Found at i:1456229 original size:14 final size:14
Alignment explanation
Indices: 1456202--1456245 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1456192 TTGACCCCCC
*
1456202 TTTTTTCTTTTTTT
1 TTTTTTCATTTTTT
1456216 TTTCTTTC-TTTTTT
1 TTT-TTTCATTTTTT
1456230 TTTTCTTCATTTTTT
1 TTTT-TTCATTTTTT
1456245 T
1 T
1456246 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.04
14 15 0.56
15 11 0.41
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTCATTTTTT
Found at i:1466829 original size:13 final size:13
Alignment explanation
Indices: 1466785--1466831 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1466775 CTGTTCTTTG
*
1466785 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1466799 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1466811 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1466825 ATATTTA
1 ATATTTA
1466832 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1468268 original size:3 final size:3
Alignment explanation
Indices: 1468260--1468318 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
1468250 TAATATATTT
*
1468260 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1468308 TAA TAA TAA TA
1 TAA TAA TAA TA
1468319 TGGATAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1469150 original size:33 final size:34
Alignment explanation
Indices: 1469087--1469151 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1469077 AAAATATTTA
* *
1469087 TATATTTTCTTTAAAAATTTAAATTCATAAAATT
1 TATATTTTCTTTAAAAATTAAAAATCATAAAATT
1469121 TATATTTT-TTTATAAAATTAAAAAT-ATAAAA
1 TATATTTTCTTTA-AAAATTAAAAATCATAAAA
1469152 AGGTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (34 bp):
TATATTTTCTTTAAAAATTAAAAATCATAAAATT
Found at i:1474987 original size:2 final size:2
Alignment explanation
Indices: 1474980--1475023 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1474970 TTATTGAACC
*
1474980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1475022 AT
1 AT
1475024 TTACAGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1478272 original size:11 final size:11
Alignment explanation
Indices: 1478273--1478335 Score: 76
Period size: 11 Copynumber: 5.6 Consensus size: 11
1478263 GAGCTCAAGT
1478273 TCGAGTCGAGC
1 TCGAGTCGAGC
1478284 TCGAGTTCGAG-
1 TCGAG-TCGAGC
*
1478295 TCGAGCTCGAGT
1 TCGAG-TCGAGC
1478307 TCGAGTCGAGC
1 TCGAGTCGAGC
1478318 TCGAGTTCGAG-
1 TCGAG-TCGAGC
1478329 TCGAGTC
1 TCGAGTC
1478336 CATTCGATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
10 2 0.04
11 30 0.64
12 15 0.32
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (11 bp):
TCGAGTCGAGC
Found at i:1478281 original size:17 final size:17
Alignment explanation
Indices: 1478259--1478333 Score: 141
Period size: 17 Copynumber: 4.4 Consensus size: 17
1478249 TAAGAATTCA
*
1478259 AGTCGAGCTCAAGTTCG
1 AGTCGAGCTCGAGTTCG
1478276 AGTCGAGCTCGAGTTCG
1 AGTCGAGCTCGAGTTCG
1478293 AGTCGAGCTCGAGTTCG
1 AGTCGAGCTCGAGTTCG
1478310 AGTCGAGCTCGAGTTCG
1 AGTCGAGCTCGAGTTCG
1478327 AGTCGAG
1 AGTCGAG
1478334 TCCATTCGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.23
Consensus pattern (17 bp):
AGTCGAGCTCGAGTTCG
Found at i:1480660 original size:21 final size:21
Alignment explanation
Indices: 1480634--1480678 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1480624 GATTTCTGGG
* *
1480634 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1480655 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1480676 CAA
1 CAA
1480679 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1482515 original size:23 final size:23
Alignment explanation
Indices: 1482471--1482515 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1482461 ATCATTATAT
*
1482471 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1482494 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1482516 AGCTGTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1485674 original size:21 final size:21
Alignment explanation
Indices: 1485648--1485692 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1485638 GATTTCTGGG
* *
1485648 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1485669 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1485690 CAA
1 CAA
1485693 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1487379 original size:25 final size:26
Alignment explanation
Indices: 1487345--1487395 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
1487335 GAGTAGAGGG
1487345 TCTACGCGGTCCTTCGGGATA-ATAT
1 TCTACGCGGTCCTTCGGGATATATAT
1487370 TCTACGCGGTCCTTCGGGATATATAT
1 TCTACGCGGTCCTTCGGGATATATAT
1487396 ATATTCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (26 bp):
TCTACGCGGTCCTTCGGGATATATAT
Found at i:1487547 original size:23 final size:23
Alignment explanation
Indices: 1487503--1487547 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1487493 ATCATTATAT
*
1487503 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1487526 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1487548 AGCTTTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1500831 original size:31 final size:31
Alignment explanation
Indices: 1500773--1500845 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
1500763 ATTGAGTGAT
* * * *
1500773 CAATTTGTTACAAATCGATAATATTAATAAT
1 CAATTTATTATAAATCGATAACATTAATAAC
* * *
1500804 TAATTTATTATAAATCGATAACGTTAATTAC
1 CAATTTATTATAAATCGATAACATTAATAAC
1500835 CAATTTATTAT
1 CAATTTATTAT
1500846 TTTAAAAACT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
CAATTTATTATAAATCGATAACATTAATAAC
Found at i:1515283 original size:22 final size:22
Alignment explanation
Indices: 1515256--1515315 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1515246 AAACAACCTA
*
1515256 AAAATGTGTCAAAAGAAATAAG
1 AAAATGTGTCAAAAGAAAGAAG
* *
1515278 AAAATGTATCATAAGAAAGAAG
1 AAAATGTGTCAAAAGAAAGAAG
*
1515300 AAAACGTGTCATAAAG
1 AAAATGTGTCA-AAAG
1515316 GTAAATTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (22 bp):
AAAATGTGTCAAAAGAAAGAAG
Found at i:1518189 original size:60 final size:60
Alignment explanation
Indices: 1518082--1518238 Score: 151
Period size: 60 Copynumber: 2.6 Consensus size: 60
1518072 GTATATATGT
* * ***
1518082 ATAGTTTGTGATGAAATT-AGAATATTCAAAAAG-TTAGGGGACCAATTTAGAATGAA-GGTC
1 ATAGTTTGGGATGAAATTGA-AATATTC-AAAAGTTTAGAGGACCAATTTAGAAT-AATAACC
*
1518142 ATAGTTTGGGGATGAAATTGAAATATTCAAAAGTTTA-AGGACTAATTTAGAATAATAACC
1 ATAGTTT-GGGATGAAATTGAAATATTCAAAAGTTTAGAGGACCAATTTAGAATAATAACC
* * * *
1518202 ATAGTTTAAGGATGAGATTGAAACATTTAAAAGTTTA
1 ATAGTTT-GGGATGAAATTGAAATATTCAAAAGTTTA
1518239 TGTGCCAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.02
60 59 0.72
61 20 0.24
62 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATATTCAAAAGTTTAGAGGACCAATTTAGAATAATAACC
Found at i:1523306 original size:12 final size:13
Alignment explanation
Indices: 1523280--1523310 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1523270 TTGTATATTG
1523280 TATTTTAATAATA
1 TATTTTAATAATA
1523293 TATTTTAA-AATA
1 TATTTTAATAATA
1523305 TATTTT
1 TATTTT
1523311 TTTAAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTTTAATAATA
Found at i:1523595 original size:27 final size:29
Alignment explanation
Indices: 1523563--1523634 Score: 112
Period size: 27 Copynumber: 2.5 Consensus size: 29
1523553 AAATATTTAT
1523563 ACACTTTAATATAATACTCTTACAACC-C
1 ACACTTTAATATAATACTCTTACAACCAC
*
1523591 -CACTTTAATATAATACTCTTATAACCAC
1 ACACTTTAATATAATACTCTTACAACCAC
1523619 ACAACTTTAATATAAT
1 AC-ACTTTAATATAAT
1523635 GGGTTAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 25 0.62
28 1 0.03
29 1 0.03
30 13 0.32
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.35
Consensus pattern (29 bp):
ACACTTTAATATAATACTCTTACAACCAC
Found at i:1523851 original size:29 final size:31
Alignment explanation
Indices: 1523818--1523889 Score: 112
Period size: 32 Copynumber: 2.4 Consensus size: 31
1523808 ACGCCGAGCG
*
1523818 TGCATGGCGACC-TA-CTTCTTCGCCCCGAC
1 TGCATGGCGACCATACCTGCTTCGCCCCGAC
1523847 TGCATGGCGACCAATACCTGCTTCGCCCCGAC
1 TGCATGGCGACC-ATACCTGCTTCGCCCCGAC
1523879 TGCATGGCGAC
1 TGCATGGCGAC
1523890 AAATCTCACC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 12 0.31
31 2 0.05
32 25 0.64
ACGTcount: A:0.17, C:0.39, G:0.24, T:0.21
Consensus pattern (31 bp):
TGCATGGCGACCATACCTGCTTCGCCCCGAC
Found at i:1524571 original size:185 final size:185
Alignment explanation
Indices: 1524196--1524572 Score: 614
Period size: 185 Copynumber: 2.0 Consensus size: 185
1524186 ATAAAATTTT
* * * ** *
1524196 AAATTTTAAATATATTTTATATAACATATGGGCTCAACCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAAAATATTATATATAACATATAAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
1524261 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAATTTA
* * *
1524326 TATTTTATAATTATATATTATTTAAATTAATTGTAAATTTTTTTTTCTGAATTAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTCTGAATTAA
*
1524381 AAATATTAAAAATATTATATATAACATATAAGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAAAATATTATATATAACATATAAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
1524446 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATAT-AAATTT
1524511 ATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-T-AATTATA
130 ATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTCTGAATTA-A
1524566 AAATATT
1 AAATATT
1524573 TATTTTTTAT
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
184 5 0.03
185 124 0.70
186 49 0.28
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (185 bp):
AAATATTAAAAATATTATATATAACATATAAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAATTTA
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTCTGAATTAA
Found at i:1529510 original size:15 final size:14
Alignment explanation
Indices: 1529492--1529529 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
1529482 ATCTTTATTT
1529492 TTTTATAATTTATAA
1 TTTTATAATTT-TAA
1529507 TTTTATAATTTTAA
1 TTTTATAATTTTAA
1529521 TTTT-TAATT
1 TTTTATAATT
1529530 AAAATAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATAATTTTAA
Found at i:1532961 original size:60 final size:60
Alignment explanation
Indices: 1532854--1533035 Score: 165
Period size: 60 Copynumber: 3.0 Consensus size: 60
1532844 GTCCTTAATA
* * * * * **
1532854 TATGATCTTCATTCTAAATTAGTCTCTAAAC-TTCTAAACATTCCAATTTTATCCTGAAAC
1 TATGA-CTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTTATCCCCAAAC
* * * * **
1532914 TATGA-TTGCCATTCTAAATTATTCCTCATAC-TTTTGAATATTTCAATTCCATCCCCAAAC
1 TATGACTT--CATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTTATCCCCAAAC
* *
1532974 TATGACCTTCATTCTACATTAGTCCCCAAACTTTTTGAACATTTTAATTTTAT-CCCAAAC
1 TATGA-CTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTTATCCCCAAAC
1533034 TA
1 TA
1533036 CATGTATATA
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
58 2 0.02
60 75 0.78
61 17 0.18
62 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (60 bp):
TATGACTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTTATCCCCAAAC
Found at i:1533155 original size:60 final size:59
Alignment explanation
Indices: 1533087--1533204 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 59
1533077 AAGTTTGGGG
* * * *
1533087 ACTAATTTAAAATGAGAGTCATAATTTGGGGATGAAATTAGAATGTTCAAAAATTTAAAA
1 ACTAATTTAAAATGAGAGTCATAATTTAGAGATGAAAATAGAATATTC-AAAATTTAAAA
* *
1533147 ACTAATTTAGAATGAGAGTCATATTTTAGAGATGAAAATAGAATATTCAAAATTTAAA
1 ACTAATTTAAAATGAGAGTCATAATTTAGAGATGAAAATAGAATATTCAAAATTTAAA
1533205 GACCGATTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 10 0.19
60 42 0.81
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.32
Consensus pattern (59 bp):
ACTAATTTAAAATGAGAGTCATAATTTAGAGATGAAAATAGAATATTCAAAATTTAAAA
Found at i:1535825 original size:27 final size:26
Alignment explanation
Indices: 1535786--1535848 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
1535776 TTTTATATTG
* *
1535786 ATAATTTGTTTACTCTTTAA-TATTTT
1 ATAATTTATTTACT-TCTAATTATTTT
*
1535812 ATAAGTTTATTTACTTCTAATTTTTTT
1 ATAA-TTTATTTACTTCTAATTATTTT
1535839 ATAAATTTAT
1 AT-AATTTAT
1535849 CATCTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 8 0.26
27 21 0.68
28 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.60
Consensus pattern (26 bp):
ATAATTTATTTACTTCTAATTATTTT
Found at i:1543558 original size:12 final size:12
Alignment explanation
Indices: 1543522--1543559 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1543512 GTGAACAGTA
*
1543522 ATGAACAGCGTC
1 ATGAACAGCGTT
1543534 ATGAACAGCGTT
1 ATGAACAGCGTT
*
1543546 ATGAACAGTGTT
1 ATGAACAGCGTT
1543558 AT
1 AT
1543560 AGTGCATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (12 bp):
ATGAACAGCGTT
Found at i:1544556 original size:14 final size:14
Alignment explanation
Indices: 1544537--1544579 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1544527 TTTACTGCAT
1544537 ATTCATGTCATATA
1 ATTCATGTCATATA
* *
1544551 ATTCATATAATATGA
1 ATTCATGTCATAT-A
*
1544566 ATCCATGTCATATA
1 ATTCATGTCATATA
1544580 TCATAATATG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (14 bp):
ATTCATGTCATATA
Found at i:1545481 original size:12 final size:12
Alignment explanation
Indices: 1545454--1545486 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1545444 CACATTTGGG
1545454 AGAAGA-GAAGA
1 AGAAGATGAAGA
1545465 AGAAGATGAAGA
1 AGAAGATGAAGA
*
1545477 TGAAGATGAA
1 AGAAGATGAA
1545487 TAAATTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (12 bp):
AGAAGATGAAGA
Found at i:1547334 original size:22 final size:22
Alignment explanation
Indices: 1547285--1547363 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
1547275 TTTTGGGCAA
*
1547285 GGGGAATCAGTACCCATTCAA-
1 GGGGAATCGGTACCCATTCAAT
1547306 -GGGAATCGGTACCCATTCAAT
1 GGGGAATCGGTACCCATTCAAT
1547327 GGGGAATCGGTACCCATTCAAT
1 GGGGAATCGGTACCCATTCAAT
*
1547349 GGGGAATCGATACCC
1 GGGGAATCGGTACCC
1547364 CCCTCAAACG
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 19 0.35
22 35 0.65
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGGAATCGGTACCCATTCAAT
Found at i:1548910 original size:103 final size:103
Alignment explanation
Indices: 1548731--1548943 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
1548721 GGGTCTACGC
1548731 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
1548796 CCTTGGCATATGTATATTATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
1548834 GGTCCTTCGTGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
1548899 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
1548937 GGTCCTT
1 GGTCCTT
1548944 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1548999 original size:23 final size:23
Alignment explanation
Indices: 1548973--1549027 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1548963 ACTACGGTGT
1548973 AATTCTACGCGGCACTCCAGTGC
1 AATTCTACGCGGCACTCCAGTGC
* * *
1548996 AATTCTACGTGGCACTTCGGTGC
1 AATTCTACGCGGCACTCCAGTGC
*
1549019 AATTATACG
1 AATTCTACG
1549028 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (23 bp):
AATTCTACGCGGCACTCCAGTGC
Found at i:1552417 original size:23 final size:22
Alignment explanation
Indices: 1552373--1552417 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1552363 AATCTCATAG
*
1552373 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
1552395 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1552418 AAATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1552879 original size:20 final size:20
Alignment explanation
Indices: 1552851--1552894 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1552841 ATAAGTCGAG
*
1552851 AGATGTAGGGAAATAGAAAT
1 AGATATAGGGAAATAGAAAT
1552871 AGATATAGGGAAATAGAAAT
1 AGATATAGGGAAATAGAAAT
1552891 AGAT
1 AGAT
1552895 GTTTATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.20
Consensus pattern (20 bp):
AGATATAGGGAAATAGAAAT
Found at i:1553896 original size:103 final size:103
Alignment explanation
Indices: 1553712--1553924 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
1553702 GGGTCTACGC
* *
1553712 GGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
1553777 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
1553815 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
1553880 CCCTAGTATATGTATATGATTCTTAAGGAATGATATAT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
1553918 GGTCCTT
1 GGTCCTT
1553925 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
Found at i:1553974 original size:23 final size:23
Alignment explanation
Indices: 1553941--1554008 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1553931 ATTATTATAT
1553941 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* **
1553964 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACGC
* * *
1553987 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTCTACG
1554009 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1560016 original size:17 final size:17
Alignment explanation
Indices: 1559991--1560033 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1559981 TAATCATTAC
* *
1559991 AAAATTAAAATAATAAT
1 AAAAATAAAAGAATAAT
*
1560008 AAAAATAAAAGAATAGT
1 AAAAATAAAAGAATAAT
1560025 -AAAATAAAA
1 AAAAATAAAA
1560034 ATTATTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAGAATAAT
Found at i:1563540 original size:15 final size:15
Alignment explanation
Indices: 1563520--1563550 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1563510 ATATTGACTT
1563520 AGGCATCAAGTTCAC
1 AGGCATCAAGTTCAC
1563535 AGGCATCAAGTTCAC
1 AGGCATCAAGTTCAC
1563550 A
1 A
1563551 CTTGAACCAA
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:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (15 bp):
AGGCATCAAGTTCAC
Found at i:1570952 original size:21 final size:20
Alignment explanation
Indices: 1570928--1570971 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1570918 TAAAAAGGGT
1570928 AATTTCTAATTTTTTATACTA
1 AATTTCTAATTTTTTATA-TA
* * *
1570949 AATTTTTATTTTTTTTTATA
1 AATTTCTAATTTTTTATATA
1570969 AAT
1 AAT
1570972 GAGCGTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTCTAATTTTTTATATA
Found at i:1571358 original size:3 final size:3
Alignment explanation
Indices: 1571332--1571373 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1571322 ACCTGAAAAG
* * *
1571332 GAA GAG GAA GAG GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1571374 AGAGCCCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1571667 original size:21 final size:21
Alignment explanation
Indices: 1571643--1571691 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1571633 TCAATGGTGA
1571643 AGATTCCCAACCTTTGGTTTC
1 AGATTCCCAACCTTTGGTTTC
*
1571664 AGATTCCCAGCCTTTGGTTTC
1 AGATTCCCAACCTTTGGTTTC
1571685 AGATTCC
1 AGATTCC
1571692 GATGTCGTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (21 bp):
AGATTCCCAACCTTTGGTTTC
Found at i:1580194 original size:32 final size:30
Alignment explanation
Indices: 1580157--1580223 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1580147 GTTTTCGTTT
*
1580157 TCACTACTGATGTTTCAAAAGTTATAAATTGG
1 TCACTACT-AT-TATCAAAAGTTATAAATTGG
***
1580189 TCACTACTATTATCATTTGTTATAAATTGG
1 TCACTACTATTATCAAAAGTTATAAATTGG
1580219 TCACT
1 TCACT
1580224 CTCCGTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 21 0.68
31 2 0.06
32 8 0.26
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (30 bp):
TCACTACTATTATCAAAAGTTATAAATTGG
Found at i:1580561 original size:21 final size:21
Alignment explanation
Indices: 1580535--1580575 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1580525 CATGAACAGA
1580535 GCTACAGTGCACCGATGCACT
1 GCTACAGTGCACCGATGCACT
*
1580556 GCTACAGTGTACCGATGCAC
1 GCTACAGTGCACCGATGCAC
1580576 AAAAACATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (21 bp):
GCTACAGTGCACCGATGCACT
Found at i:1580621 original size:21 final size:21
Alignment explanation
Indices: 1580596--1580639 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1580586 AATATAAATT
*
1580596 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
* *
1580617 GTGTACCGATGTACTGCTGCA
1 GTGTACCGATGCACTGCTACA
1580638 GT
1 GT
1580640 AGCTTCAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Done.