Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 15 of 132
Found at i:4238143 original size:19 final size:19
Alignment explanation
Indices: 4238115--4238154 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4238105 TTTATATATT
* *
4238115 TTGTTTATAATTTTTATAA
1 TTGTTAATAATTTTTAAAA
4238134 TTGTTAATAATTTTTAAAA
1 TTGTTAATAATTTTTAAAA
4238153 TT
1 TT
4238155 TAAAATGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTGTTAATAATTTTTAAAA
Found at i:4239739 original size:31 final size:31
Alignment explanation
Indices: 4239704--4239771 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
4239694 TTACAAAATG
*
4239704 GTCACTGAACTATTCAAAAG-TTTTCATTTGA
1 GTCACTGAACTATTCAAAAGATTTT-ATTTAA
**
4239735 GTCACTGAACTATTTGAAAGATTTTATTTAA
1 GTCACTGAACTATTCAAAAGATTTTATTTAA
4239766 GTCACT
1 GTCACT
4239772 AAGTCGTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGATTTTATTTAA
Found at i:4255547 original size:6 final size:6
Alignment explanation
Indices: 4255536--4255565 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4255526 CCTCAACCTG
4255536 GCCCTA GCCCTA GCCCTA GCCCTA GCCCTA
1 GCCCTA GCCCTA GCCCTA GCCCTA GCCCTA
4255566 ATGTAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (6 bp):
GCCCTA
Found at i:4274682 original size:19 final size:19
Alignment explanation
Indices: 4274650--4274691 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4274640 TAAAAAATCC
*
4274650 AAATTTTATATTTTTTAAA
1 AAATTATATATTTTTTAAA
* *
4274669 AAATTATATTTTTTTTTAA
1 AAATTATATATTTTTTAAA
4274688 AAAT
1 AAAT
4274692 CTAAAGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATTATATATTTTTTAAA
Found at i:4282924 original size:15 final size:15
Alignment explanation
Indices: 4282886--4282930 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4282876 CGTCTTATAT
* *
4282886 ATTTTTTTCAACGGTA
1 ATTTTTTT-AATGATA
*
4282902 ATTGTTTTAATGATA
1 ATTTTTTTAATGATA
4282917 ATTTTTTTAATGAT
1 ATTTTTTTAATGAT
4282931 TAATAGTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (15 bp):
ATTTTTTTAATGATA
Found at i:4286009 original size:19 final size:18
Alignment explanation
Indices: 4285970--4286010 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
4285960 AAAATCAAAG
*
4285970 AATATATTTAGATATGCA
1 AATATATTTAAATATGCA
*
4285988 AATATATGTTAAATATGTA
1 AATATAT-TTAAATATGCA
4286007 AATA
1 AATA
4286011 ATATATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (18 bp):
AATATATTTAAATATGCA
Found at i:4288611 original size:20 final size:20
Alignment explanation
Indices: 4288569--4288611 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
4288559 AAGGTTTTAT
*
4288569 AAATTTATAAAATATTATTA
1 AAATTTATAAAATAATATTA
4288589 AAATTTATAAAA-AATATTCA
1 AAATTTATAAAATAATATT-A
4288609 AAA
1 AAA
4288612 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTTATAAAATAATATTA
Found at i:4297891 original size:92 final size:90
Alignment explanation
Indices: 4297707--4297924 Score: 203
Period size: 92 Copynumber: 2.4 Consensus size: 90
4297697 AGCTCTTTTA
* * * * *
4297707 TTTTTTTCATTCAATTAGGTACTTGAACTTTCAAAATGTATCAAAAAGATCTTCAAGCTCTTTTA
1 TTTTTTTCATTCAATTAAGTACTTGAACTTTCAAAATGTATAAAAAAAATCCTCAAACTCTTTTA
** * * * *
4297772 GTAAAAGTATTTAAGCCATTAGTTTT
66 AAAAAAGCAATTAAACCACTAG-TTT
* *
4297798 TTTTTTTGCATTCAATTAAGTACTTGAACTTTCAAAATGTATAAAAAAAAGTCCTCAAATTTTTT
1 TTTTTTT-CATTCAATTAAGTACTTGAACTTTCAAAATGTATAAAAAAAA-TCCTCAAACTCTTT
*
4297863 TAAAATAAAGCAATTAAACCCCTA----
64 TAAAA-AAAGCAATTAAACCACTAGTTT
** *
4297887 TTTTTTAAATTCAATTGAGTACTTGAA-TTGTCAAAATG
1 TTTTTTTCATTCAATTAAGTACTTGAACTT-TCAAAATG
4297925 CATCGAAAAG
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
87 2 0.02
88 26 0.25
89 6 0.06
91 7 0.07
92 39 0.37
93 13 0.12
94 13 0.12
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (90 bp):
TTTTTTTCATTCAATTAAGTACTTGAACTTTCAAAATGTATAAAAAAAATCCTCAAACTCTTTTA
AAAAAAGCAATTAAACCACTAGTTT
Found at i:4298018 original size:10 final size:10
Alignment explanation
Indices: 4298005--4298120 Score: 61
Period size: 10 Copynumber: 12.2 Consensus size: 10
4297995 ATAAAAATCG
4298005 TAAAAAATTA
1 TAAAAAATTA
*
4298015 TAAAATA-TA
1 TAAAAAATTA
* *
4298024 T-AGAAA-TG
1 TAAAAAATTA
*
4298032 TAAAAAAGTA
1 TAAAAAATTA
**
4298042 TAAAATTTTA
1 TAAAAAATTA
**
4298052 TAAAATTTTA
1 TAAAAAATTA
4298062 -AAAAAATTA
1 TAAAAAATTA
4298071 TAAAAAATGTA
1 TAAAAAAT-TA
*
4298082 -AAGAAA-TA
1 TAAAAAATTA
4298090 T--AAAATTCA
1 TAAAAAATT-A
4298099 TAAAAATATTA
1 TAAAAA-ATTA
4298110 T-AAAAATTA
1 TAAAAAATTA
4298119 TA
1 TA
4298121 TGCCAAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
7 3 0.04
8 8 0.10
9 21 0.26
10 40 0.49
11 7 0.09
12 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:4298019 original size:9 final size:9
Alignment explanation
Indices: 4298007--4298120 Score: 63
Period size: 9 Copynumber: 12.1 Consensus size: 9
4297997 AAAAATCGTA
4298007 AAAAATTAT
1 AAAAATTAT
4298016 -AAAATATAT
1 AAAAAT-TAT
*
4298025 AGAAATGTA-
1 AAAAAT-TAT
*
4298034 AAAAAGTAT
1 AAAAATTAT
*
4298043 AAAATTTTAT
1 AAAA-ATTAT
* *
4298053 AAAATTTTAA
1 AAAA-ATTAT
4298063 AAAAATTAT
1 AAAAATTAT
* *
4298072 AAAAAATGT
1 AAAAATTAT
*
4298081 AAAGAAATAT
1 AAA-AATTAT
4298091 -AAAATTCAT
1 AAAAATT-AT
4298100 AAAAATATTAT
1 -AAAA-ATTAT
4298111 AAAAATTAT
1 AAAAATTAT
4298120 A
1 A
4298121 TGCCAAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.12
9 34 0.41
10 31 0.37
11 5 0.06
12 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4298034 original size:27 final size:27
Alignment explanation
Indices: 4297998--4298075 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
4297988 AAATTTCATA
4297998 AAAATCGTAAAAAATTATAAAA-TATAT
1 AAAAT-GTAAAAAATTATAAAATTATAT
* *
4298025 AGAAATGTAAAAAAGTATAAAATTTTAT
1 A-AAATGTAAAAAATTATAAAATTATAT
*
4298053 AAAATTTTAAAAAAATTATAAAA
1 AAAA-TGT-AAAAAATTATAAAA
4298076 AATGTAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.44
28 11 0.26
29 13 0.30
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (27 bp):
AAAATGTAAAAAATTATAAAATTATAT
Found at i:4298092 original size:48 final size:48
Alignment explanation
Indices: 4298027--4298120 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
4298017 AAATATATAG
* *
4298027 AAATGTAAAAAAGTATAAAATT-TTATAAAATTTTAAAAAAATTATAAA
1 AAATGTAAAAAAGTATAAAATTCATA-AAAATATTAAAAAAATTATAAA
*
4298075 AAATGTAAAGAAA-TATAAAATTCATAAAAATATTATAAAAATTATA
1 AAATGTAAA-AAAGTATAAAATTCATAAAAATATTAAAAAAATTATA
4298121 TGCCAAAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
48 36 0.88
49 5 0.12
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (48 bp):
AAATGTAAAAAAGTATAAAATTCATAAAAATATTAAAAAAATTATAAA
Found at i:4301640 original size:17 final size:17
Alignment explanation
Indices: 4301601--4301663 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
4301591 AACTGTGAAT
4301601 TGCGAGCTCACCAA-ACC
1 TGCGAGCTCACCAAGA-C
*
4301618 TACGAGCTCACCAAGAC
1 TGCGAGCTCACCAAGAC
* * **
4301635 TGCGAGATCATCAAGTG
1 TGCGAGCTCACCAAGAC
*
4301652 TGCTAGCTCACC
1 TGCGAGCTCACC
4301664 TTAATATATT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
17 35 0.97
18 1 0.03
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (17 bp):
TGCGAGCTCACCAAGAC
Found at i:4308266 original size:12 final size:11
Alignment explanation
Indices: 4308227--4308268 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4308217 TTTTTTATTA
*
4308227 TTTAAATAT-T
1 TTTAAATTTAT
*
4308237 TTTAAAATTAT
1 TTTAAATTTAT
4308248 TTTAAATTTAT
1 TTTAAATTTAT
4308259 TTTGAAATTT
1 TTT-AAATTT
4308269 TTGTTGAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 7 0.26
11 14 0.52
12 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:4312616 original size:23 final size:23
Alignment explanation
Indices: 4312546--4312739 Score: 189
Period size: 23 Copynumber: 8.3 Consensus size: 23
4312536 ACGGAACAAG
* *
4312546 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
4312567 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
4312592 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
4312615 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
4312638 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
4312661 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
4312684 CAGAGAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
4312709 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
4312732 CAGAGAGC
1 CAGAGAGC
4312740 GCGCTAGTGT
Statistics
Matches: 147, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.10
23 94 0.64
24 2 0.01
25 29 0.20
26 7 0.05
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:4312665 original size:69 final size:68
Alignment explanation
Indices: 4312546--4312739 Score: 214
Period size: 69 Copynumber: 2.8 Consensus size: 68
4312536 ACGGAACAAG
* *
4312546 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGT
4312609 GCTAAA
63 GCTAAA
4312615 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
4312679 CTAAT
64 CTAAA
* * * * * *
4312684 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAACAGAGAGC
4312740 GCGCTAGTGT
Statistics
Matches: 109, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.02
69 51 0.47
70 11 0.10
71 35 0.32
72 10 0.09
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.12
Consensus pattern (68 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCT
AAA
Found at i:4320001 original size:23 final size:23
Alignment explanation
Indices: 4319931--4320124 Score: 189
Period size: 23 Copynumber: 8.3 Consensus size: 23
4319921 ACGGAACAAG
* *
4319931 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
4319952 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
4319977 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
4320000 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
4320023 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
4320046 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
4320069 CAGAGAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
4320094 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
4320117 CAGAGAGC
1 CAGAGAGC
4320125 GCGCTAGTGT
Statistics
Matches: 147, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.10
23 94 0.64
24 2 0.01
25 29 0.20
26 7 0.05
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:4320050 original size:69 final size:68
Alignment explanation
Indices: 4319931--4320124 Score: 214
Period size: 69 Copynumber: 2.8 Consensus size: 68
4319921 ACGGAACAAG
* *
4319931 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGT
4319994 GCTAAA
63 GCTAAA
4320000 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
4320064 CTAAT
64 CTAAA
* * * * * *
4320069 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAACAGAGAGC
4320125 GCGCTAGTGT
Statistics
Matches: 109, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.02
69 51 0.47
70 11 0.10
71 35 0.32
72 10 0.09
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.12
Consensus pattern (68 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCT
AAA
Found at i:4326457 original size:30 final size:30
Alignment explanation
Indices: 4326415--4326706 Score: 207
Period size: 30 Copynumber: 9.8 Consensus size: 30
4326405 AAGGTCCTCG
*
4326415 AACTTCTCAAAAATTACATTTTAACCCCTA
1 AACTTTTCAAAAATTACATTTTAACCCCTA
* *
4326445 AACTTTTTAAAAATTATATTTTAACCCCTA
1 AACTTTTCAAAAATTACATTTTAACCCCTA
* * *
4326475 AACTTCTCAAACATTACATTTTGACTCCC-A
1 AACTTTTCAAAAATTACATTTTAAC-CCCTA
*
4326505 AACTTTCCAAAAATTACATTTTAACCCCTA
1 AACTTTTCAAAAATTACATTTTAACCCCTA
** * * *
4326535 AA-TTTTTTAAAATTATATTTTAGCCCTTA
1 AACTTTTCAAAAATTACATTTTAACCCCTA
* * * ** *
4326564 AACTTTGCAAAAGTTATATTTTGGCCCTTA
1 AACTTTTCAAAAATTACATTTTAACCCCTA
* * * * * *
4326594 TACTTCAT-AAAAAATACGTTTTGACTCC-A
1 AACTT-TTCAAAAATTACATTTTAACCCCTA
* * * * * *
4326623 AAATTTTCCAAAATTGCATTTTTGACCCTTG
1 AACTTTTCAAAAATTACA-TTTTAACCCCTA
*
4326654 AACTTCTCAAAAATTACATTTTAA-CCCTA
1 AACTTTTCAAAAATTACATTTTAACCCCTA
** *
4326683 AACTCATCTAAAATTACTATTTTA
1 AACTTTTCAAAAATTAC-ATTTTA
4326707 CCCTCGAACA
Statistics
Matches: 201, Mismatches: 53, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
28 1 0.00
29 53 0.26
30 130 0.65
31 17 0.08
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.39
Consensus pattern (30 bp):
AACTTTTCAAAAATTACATTTTAACCCCTA
Found at i:4326482 original size:60 final size:60
Alignment explanation
Indices: 4326415--4326706 Score: 236
Period size: 60 Copynumber: 4.9 Consensus size: 60
4326405 AAGGTCCTCG
*
4326415 AACTTCTCAAAAATTACATTTTAACCCCTAAACTTTTTAAAAATTATATTTTAACCCCTA
1 AACTTCTCAAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTATATTTTAACCCCTA
* * * *
4326475 AACTTCTCAAACATTACATTTTGACTCCC-AAACTTTCCAAAAATTACATTTTAACCCCTA
1 AACTTCTCAAAAATTACATTTTAAC-CCCTAAACTTTTCAAAAATTATATTTTAACCCCTA
* ** * * * * * ** *
4326535 AA-TTTTTTAAAATTATATTTTAGCCCTTAAACTTTGCAAAAGTTATATTTTGGCCCTTA
1 AACTTCTCAAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTATATTTTAACCCCTA
* * * * * * * * * *
4326594 TACTTCAT-AAAAAATACGTTTTGACTCC-AAAATTTTCCAAAATTGCAT-TTTTGACCCTTG
1 AACTTC-TCAAAAATTACATTTTAACCCCTAAACTTTTCAAAAATT--ATATTTTAACCCCTA
** *
4326654 AACTTCTCAAAAATTACATTTTAA-CCCTAAACTCATCTAAAATTACTATTTTA
1 AACTTCTCAAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTA-TATTTTA
4326707 CCCTCGAACA
Statistics
Matches: 177, Mismatches: 45, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
58 3 0.02
59 57 0.32
60 111 0.63
61 6 0.03
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.39
Consensus pattern (60 bp):
AACTTCTCAAAAATTACATTTTAACCCCTAAACTTTTCAAAAATTATATTTTAACCCCTA
Found at i:4326635 original size:119 final size:118
Alignment explanation
Indices: 4326424--4326686 Score: 278
Period size: 119 Copynumber: 2.2 Consensus size: 118
4326414 GAACTTCTCA
** * *
4326424 AAAATTACATTTTAACCCCTAAACTTTTTAAAAATTATATTTTAACCCCTAAACTTCTCAAACAT
1 AAAATTACATTTTAACCCCTAAACTTTGCAAAAATTATATTTTAACCCCTAAACTTCTCAAAAAA
*
4326489 TACATTTTGACTCCCAAACTTTCCAAAAATTACATTTTAACCCCTAAATTTTTT
66 TACATTTTGACTCCAAAACTTTCC-AAAATTACATTTTAACCCCTAAATTTTTT
* * * * ** * *
4326543 AAAATTATATTTTAGCCCTTAAACTTTGCAAAAGTTATATTTTGGCCCTTATACTTCAT-AAAAA
1 AAAATTACATTTTAACCCCTAAACTTTGCAAAAATTATATTTTAACCCCTAAACTTC-TCAAAAA
* * * * * * * **
4326607 ATACGTTTTGACTCCAAAATTTTCCAAAATTGCATTTTTGACCCTTGAACTTCTCA
65 ATACATTTTGACTCCAAAACTTTCCAAAATTACA-TTTTAACCCCT-AAATTTTTT
4326663 AAAATTACATTTTAA-CCCTAAACT
1 AAAATTACATTTTAACCCCTAAACT
4326687 CATCTAAAAT
Statistics
Matches: 116, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
118 8 0.07
119 89 0.77
120 19 0.16
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (118 bp):
AAAATTACATTTTAACCCCTAAACTTTGCAAAAATTATATTTTAACCCCTAAACTTCTCAAAAAA
TACATTTTGACTCCAAAACTTTCCAAAATTACATTTTAACCCCTAAATTTTTT
Found at i:4327764 original size:96 final size:96
Alignment explanation
Indices: 4327585--4327764 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 96
4327575 AAGAATGTTC
* ** *
4327585 GATTATCTCGATTTGAAGAAAGGTTACATCTAGTAAGTTAAGGAACAAATTTTCAAAATCGAAGA
1 GATTATCTCGATTCGAAGAAAAATTACACCTAGTAAGTTAAGGAACAAATTTTCAAAATCGAAGA
** **
4327650 TAATGAAACATTGTCTCGATTAAGGGTATTT
66 TAAAAAAACATTACCTCGATTAAGGGTATTT
* * * *
4327681 GATTATTTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAATCTCGAA-
1 GATTATCTCGATTCGAAGAAAAATTACACCTAGTAAGTTAAGGAACAAATTTTCAAA-ATCGAAG
*
4327745 ATAAAAAAATATTACCTCGA
65 ATAAAAAAACATTACCTCGA
4327765 ATTTTAAAGT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
96 65 0.93
97 5 0.07
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (96 bp):
GATTATCTCGATTCGAAGAAAAATTACACCTAGTAAGTTAAGGAACAAATTTTCAAAATCGAAGA
TAAAAAAACATTACCTCGATTAAGGGTATTT
Found at i:4328064 original size:29 final size:29
Alignment explanation
Indices: 4328032--4328111 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
4328022 CATTCAGGGG
*
4328032 TAAAATGGTAATTTTTTGAAAAATCAGGA
1 TAAAATGGTAATTTTTAGAAAAATCAGGA
* ** *
4328061 TAAAAAATGG-AA-TTTTAGAAAGATTGGGG
1 T--AAAATGGTAATTTTTAGAAAAATCAGGA
*
4328090 TAAAATGGTAATTTTTGGAAAA
1 TAAAATGGTAATTTTTAGAAAA
4328112 TCAATGTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
27 7 0.17
28 2 0.05
29 22 0.55
30 2 0.05
31 7 0.17
ACGTcount: A:0.45, C:0.01, G:0.21, T:0.33
Consensus pattern (29 bp):
TAAAATGGTAATTTTTAGAAAAATCAGGA
Found at i:4328067 original size:58 final size:58
Alignment explanation
Indices: 4327971--4328308 Score: 246
Period size: 58 Copynumber: 5.8 Consensus size: 58
4327961 GAATACCCGA
** ** ** * * *
4327971 GGGTAAAATGGTAATTTTGGGAAAGTTTGGGGTTAAAAATAAAATTTTAGGCA-TTCAG
1 GGGTAAAATGGTAATTTTTTGAAAAATCAGGATTAAAAATAGAATTTTAGGAAGTTC-G
* * *
4328029 GGGTAAAATGGTAATTTTTTGAAAAATCAGGATAAAAAATGGAATTTTAGAAAGATT-G
1 GGGTAAAATGGTAATTTTTTGAAAAATCAGGATTAAAAATAGAATTTTAGGAAG-TTCG
* * * * *
4328087 GGGTAAAATGGTAA-TTTTTGGAAAATCA--ATGTCAAAATGGAATTTTAAGAAGTTTGG
1 GGGTAAAATGGTAATTTTTTGAAAAATCAGGAT-TAAAAATAGAATTTTAGGAAG-TTCG
* * *
4328144 GGGTAAAATGGT-ATTTTTTGGAAAAATTAGGGTTAAAAATAGAATTTTTGGAAGTTCG
1 GGGTAAAATGGTAATTTTTT-GAAAAATCAGGATTAAAAATAGAATTTTAGGAAGTTCG
* * * * * * *
4328202 AGGGTAAAAAT-ATAATTTTTGGAAAAATCAGGGTCAAAAATAAAATTTTAGAAAGTTTAG
1 -GGGT-AAAATGGTAATTTTTTGAAAAATCAGGATTAAAAATAGAATTTTAGGAAG-TTCG
** *
4328262 AAGTAAAAAT-GTAATTTTTTGAAAAAT-AGGGATT-AAAATGGAATTTT
1 GGGT-AAAATGGTAATTTTTTGAAAAATCA-GGATTAAAAATAGAATTTT
4328309 GAAATGTTTA
Statistics
Matches: 225, Mismatches: 42, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
55 2 0.01
56 20 0.09
57 31 0.14
58 78 0.35
59 77 0.34
60 17 0.08
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTTGAAAAATCAGGATTAAAAATAGAATTTTAGGAAGTTCG
Found at i:4328191 original size:29 final size:30
Alignment explanation
Indices: 4328158--4328250 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
4328148 AAAATGGTAT
*
4328158 TTTTTGGAAAAATTAGGGTTAAAAATAGAA
1 TTTTTGGAAAAATTAGGGTTAAAAATAAAA
* *
4328188 TTTTTGG--AAGTTCGAGGG-TAAAAATATAA
1 TTTTTGGAAAAATT--AGGGTTAAAAATAAAA
* *
4328217 TTTTTGGAAAAATCAGGGTCAAAAATAAAA
1 TTTTTGGAAAAATTAGGGTTAAAAATAAAA
4328247 TTTT
1 TTTT
4328251 AGAAAGTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.08
29 21 0.40
30 24 0.46
31 3 0.06
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.34
Consensus pattern (30 bp):
TTTTTGGAAAAATTAGGGTTAAAAATAAAA
Found at i:4328192 original size:30 final size:30
Alignment explanation
Indices: 4328158--4328308 Score: 102
Period size: 29 Copynumber: 5.1 Consensus size: 30
4328148 AAAATGGTAT
4328158 TTTTTGGAAAAATTAGGGTTAAAAATAGAA
1 TTTTTGGAAAAATTAGGGTTAAAAATAGAA
* *
4328188 TTTTTGG--AAGTTCGAGGG-TAAAAATATAA
1 TTTTTGGAAAAATT--AGGGTTAAAAATAGAA
* *
4328217 TTTTTGGAAAAATCAGGGTCAAAAATA-AA
1 TTTTTGGAAAAATTAGGGTTAAAAATAGAA
* * ** *
4328246 ATTTTAGAAAGTTTAGAAG-TAAAAAT-GTAA
1 TTTTTGGAAAAATTAG-GGTTAAAAATAG-AA
* *
4328276 TTTTTTGAAAAA-TAGGGATT-AAAATGGAA
1 TTTTTGGAAAAATTAGGG-TTAAAAATAGAA
4328305 TTTT
1 TTTT
4328309 GAAATGTTTA
Statistics
Matches: 93, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
28 5 0.05
29 54 0.58
30 31 0.33
31 3 0.03
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.34
Consensus pattern (30 bp):
TTTTTGGAAAAATTAGGGTTAAAAATAGAA
Found at i:4328209 original size:59 final size:59
Alignment explanation
Indices: 4327968--4328308 Score: 281
Period size: 59 Copynumber: 5.9 Consensus size: 59
4327958 TTTGAATACC
* ** ** * *
4327968 CGAGGGTAAAATGGTAATTTTGGGAAAGTTTGGGGTTAAAAATAAAATTTTAGGCA-TT
1 CGAGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTAGGAAGTT
* * * * *
4328026 C-AGGGGTAAAATGGTAATTTTTTGAAAAATCAGGATAAAAAATGGAATTTTAGAAAGATT
1 CGA-GGGTAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTAGGAAG-TT
** * * *
4328086 -G-GGGTAAAATGGTAATTTTTGG-AAAATCAATG-TCAAAATGGAATTTTAAGAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTAGGAAGTT
* * * * *
4328141 TGGGGGTAAAATGGTATTTTTTGGAAAAATTAGGGTTAAAAATAGAATTTTTGGAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTAGGAAGTT
* * * *
4328200 CGAGGGTAAAAAT-ATAATTTTTGGAAAAATCAGGGTCAAAAATAAAATTTTAGAAAGTT
1 CGAGGGT-AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTAGGAAGTT
* * * *
4328259 -TAGAAGTAAAAAT-GTAATTTTTTGAAAAAT-AGGGATT-AAAATGGAATTTT
1 CGAG-GGT-AAAATGGTAATTTTTGGAAAAATCAGGG-TTAAAAATAGAATTTT
4328309 GAAATGTTTA
Statistics
Matches: 228, Mismatches: 44, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
55 2 0.01
56 18 0.08
57 28 0.12
58 86 0.38
59 87 0.38
60 7 0.03
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.33
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTAGGAAGTT
Found at i:4329334 original size:3 final size:3
Alignment explanation
Indices: 4329326--4329408 Score: 87
Period size: 3 Copynumber: 27.0 Consensus size: 3
4329316 CTTTCAACTT
* * * * *
4329326 TTA TTA TTA TTA ATA TTA TTA TCAA TTA TTA TTAA TTA ATG TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT-A TTA TTA TTA TTA
4329373 TTA TTGA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4329409 ATGATATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
2 1 0.02
3 59 0.89
4 6 0.09
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4329344 original size:12 final size:12
Alignment explanation
Indices: 4329327--4329424 Score: 78
Period size: 12 Copynumber: 8.2 Consensus size: 12
4329317 TTTCAACTTT
4329327 TATTATTATTAA
1 TATTATTATTAA
*
4329339 TATTATTATCAA
1 TATTATTATTAA
4329351 TTATTATTAATTAA
1 -TATTATT-ATTAA
* *
4329365 TGTTATTGTT-A
1 TATTATTATTAA
* *
4329376 T-TGA-TATTAT
1 TATTATTATTAA
*
4329386 TATTATTATTAT
1 TATTATTATTAA
4329398 TATTATTATTAA
1 TATTATTATTAA
4329410 TGA-TATTTATTAA
1 T-ATTA-TTATTAA
4329423 TA
1 TA
4329425 CGTTTTGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
9 3 0.04
10 3 0.04
11 4 0.06
12 34 0.49
13 22 0.31
14 4 0.06
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:4330099 original size:17 final size:17
Alignment explanation
Indices: 4330074--4330144 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
4330064 TTTTAATTTT
*
4330074 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
4330091 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * *
4330108 ATTCAAACTTAAAATGA
1 ATTTAAATTTAAAATAA
*
4330125 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
4330142 ATT
1 ATT
4330145 CAAACTTATT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:4330120 original size:34 final size:34
Alignment explanation
Indices: 4330082--4330152 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
4330072 TTATTTTAAT
*
4330082 TTAAAATAAATTTAAATTTAAAGTAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
* *
4330116 TTAAAATGAATTTGAATTTAAAATAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
4330150 TTA
1 TTA
4330153 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
Found at i:4333923 original size:18 final size:18
Alignment explanation
Indices: 4333902--4333938 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4333892 GTGGCATTTT
4333902 TAGGTACCTATGCATTGA
1 TAGGTACCTATGCATTGA
4333920 TAGGTACCTATGCATTGA
1 TAGGTACCTATGCATTGA
4333938 T
1 T
4333939 TTTTTTAAAT
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:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (18 bp):
TAGGTACCTATGCATTGA
Found at i:4334201 original size:20 final size:20
Alignment explanation
Indices: 4334178--4334217 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4334168 GTTCAAAAGT
4334178 TTATAATTAAACTCAAATGA
1 TTATAATTAAACTCAAATGA
**
4334198 TTATAATTAGGCTCAAATGA
1 TTATAATTAAACTCAAATGA
4334218 GTTTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
TTATAATTAAACTCAAATGA
Found at i:4341482 original size:29 final size:30
Alignment explanation
Indices: 4341430--4341487 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
4341420 AATTGGATCA
* *
4341430 AATCAAAATTTCATGTATAAAATTGCACAC
1 AATCAAAAGTTCATGTATAAAATTACACAC
*
4341460 AATC-AAAGTTCATGTATACAATTACACA
1 AATCAAAAGTTCATGTATAAAATTACACA
4341488 TTAAACCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
AATCAAAAGTTCATGTATAAAATTACACAC
Found at i:4341579 original size:23 final size:24
Alignment explanation
Indices: 4341552--4341597 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4341542 TAAATTTAAT
4341552 AAATC-TTTTATAGATTGATATAA
1 AAATCATTTTATAGATTGATATAA
**
4341575 AAATCAATTTTATTTATTGATAT
1 AAATC-ATTTTATAGATTGATAT
4341598 TTTTGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
25 14 0.74
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
AAATCATTTTATAGATTGATATAA
Found at i:4345977 original size:19 final size:19
Alignment explanation
Indices: 4345953--4346010 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
4345943 AGTGTGTGTG
*
4345953 AATTTTAGTCTAATTTATT
1 AATTTTAATCTAATTTATT
*
4345972 AATTTTAATTTGAATTATATT
1 AATTTTAATCT-AATT-TATT
4345993 AATTCTTAATCT-ATTTAT
1 AATT-TTAATCTAATTTAT
4346011 ATTATAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.36
20 7 0.21
21 8 0.24
22 6 0.18
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
AATTTTAATCTAATTTATT
Found at i:4346010 original size:21 final size:21
Alignment explanation
Indices: 4345953--4346014 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
4345943 AGTGTGTGTG
*
4345953 AATTTTAGTCT-AATT-TATT
1 AATTTTAATCTGAATTATATT
*
4345972 AATTTTAATTTGAATTATATT
1 AATTTTAATCTGAATTATATT
*
4345993 AATTCTTAATCT-ATTTATATT
1 AATT-TTAATCTGAATTATATT
4346014 A
1 A
4346015 TAATGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.25
20 4 0.11
21 17 0.47
22 6 0.17
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.56
Consensus pattern (21 bp):
AATTTTAATCTGAATTATATT
Found at i:4351578 original size:19 final size:17
Alignment explanation
Indices: 4351554--4351588 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
4351544 ATTATTTGGA
4351554 TATTGTATAATTCTTGTTT
1 TATTGT-TAATT-TTGTTT
4351573 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
4351589 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:4352113 original size:14 final size:15
Alignment explanation
Indices: 4352094--4352135 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
4352084 TCAAAAATTA
*
4352094 AATATTAAATTTT-T
1 AATATTAAATTTTGC
4352108 AATATTAAATTTTGC
1 AATATTAAATTTTGC
4352123 AAGTATTAAATTT
1 AA-TATTAAATTT
4352136 ATATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 2 0.08
16 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (15 bp):
AATATTAAATTTTGC
Found at i:4359541 original size:37 final size:37
Alignment explanation
Indices: 4359418--4359923 Score: 246
Period size: 38 Copynumber: 13.3 Consensus size: 37
4359408 CAGTTGAATG
4359418 AATTGAAGTAAGTTGGATATCAAGTCTTTATCTCTGA
1 AATTGAAGTAAGTTGGATATCAAGTCTTTATCTCTGA
* * * * ** *
4359455 AATTGAAGAAAG-AGTAAGATCATTTC-CTATCCTCTTGA
1 AATTGAAGTAAGTTG-GATATCAAGTCTTTAT-CTC-TGA
*
4359493 AATTGAAGTAAGTTGGATATCAAGTCTTTATCTCCGA
1 AATTGAAGTAAGTTGGATATCAAGTCTTTATCTCTGA
* * * * ** *
4359530 AATTGACGTAAG-AGTAAGATCATTTC-CTATCCTCTTGA
1 AATTGAAGTAAGTTG-GATATCAAGTCTTTAT-CTC-TGA
* *
4359568 AATTGAAGTAAAGCTAGATATCAAGTCTTTATCTCTGA
1 AATTGAAGT-AAGTTGGATATCAAGTCTTTATCTCTGA
* * * ** *
4359606 AATTGAAGTAAG-AGTAAGATCATTTC-CTATCCTCTTGA
1 AATTGAAGTAAGTTG-GATATCAAGTCTTTAT-CTC-TGA
*
4359644 AATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
1 AATTGAAGTA-AGTTGGATATCAAGTCTTTATCTCTGA
* * * ** *
4359682 AATTGAAGTAAG-AGCAAGATCATTTC-CTATCCTCTTGA
1 AATTGAAGTAAGTTG-GATATCAAGTCTTTAT-CTC-TGA
* *
4359720 AATTGAAGTAAAGCTGGATATCAAGTCTCTATCTCTGA
1 AATTGAAGT-AAGTTGGATATCAAGTCTTTATCTCTGA
* * * * **
4359758 AATTGAAATAAG-AGTAAGATCATTTC-TTATCCTCTTGA
1 AATTGAAGTAAGTTG-GATATCAAGTCTTTAT-CTC-TGA
** *
4359796 AATTGAAGTAAAACTGGATATCAGGTCTTTATCTCTGA
1 AATTGAAGT-AAGTTGGATATCAAGTCTTTATCTCTGA
* * * *
4359834 AATTGAAGTAAG-AGCAAGATC-A-TTTTCTATCCTCTTGA
1 AATTGAAGTAAGTTG-GATATCAAGTCTT-TAT-CTC-TGA
** **
4359872 AATTGAAGTAAAGTTGGATATCAAACCTTCGTCCCTCTGA
1 AATTGAAGT-AAGTTGGATATCAAGTCTT--TATCTCTGA
4359912 AATTGAAGTAAG
1 AATTGAAGTAAG
4359924 AGCTAGTGGA
Statistics
Matches: 346, Mismatches: 85, Indels: 74
0.69 0.17 0.15
Matches are distributed among these distances:
35 3 0.01
36 23 0.07
37 90 0.26
38 130 0.38
39 63 0.18
40 31 0.09
41 5 0.01
42 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (37 bp):
AATTGAAGTAAGTTGGATATCAAGTCTTTATCTCTGA
Found at i:4359625 original size:76 final size:76
Alignment explanation
Indices: 4359418--4359925 Score: 795
Period size: 76 Copynumber: 6.7 Consensus size: 76
4359408 CAGTTGAATG
*
4359418 AATTGAAGT-AAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGAAAGAGTAAGATCATTTCC
1 AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
4359482 TATCCTCTTGA
66 TATCCTCTTGA
* *
4359493 AATTGAAGT-AAGTTGGATATCAAGTCTTTATCTCCGAAATTGACGTAAGAGTAAGATCATTTCC
1 AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
4359557 TATCCTCTTGA
66 TATCCTCTTGA
* *
4359568 AATTGAAGTAAAGCTAGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
1 AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
4359633 TATCCTCTTGA
66 TATCCTCTTGA
* * *
4359644 AATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
1 AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
4359709 TATCCTCTTGA
66 TATCCTCTTGA
* * * *
4359720 AATTGAAGTAAAGCTGGATATCAAGTCTCTATCTCTGAAATTGAAATAAGAGTAAGATCATTTCT
1 AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
4359785 TATCCTCTTGA
66 TATCCTCTTGA
** * * *
4359796 AATTGAAGTAAAACTGGATATCAGGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTTC
1 AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
4359861 TATCCTCTTGA
66 TATCCTCTTGA
** **
4359872 AATTGAAGTAAAGTTGGATATCAAACCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 AATTGAAGTAAAGTTGGATATCAAGTCTT--TATCTCTGAAATTGAAGTAAGAG
4359926 CTAGTGGAGA
Statistics
Matches: 397, Mismatches: 33, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
75 81 0.20
76 295 0.74
78 21 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
AATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGTAAGATCATTTCC
TATCCTCTTGA
Found at i:4362359 original size:30 final size:30
Alignment explanation
Indices: 4362318--4362583 Score: 331
Period size: 30 Copynumber: 8.9 Consensus size: 30
4362308 AAGTTGTCCA
**
4362318 AAAATTACATTTTGACCCCAAAACTTTTTG
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
4362348 AAAATTTCATTTTGACCCCAAAACTTTCCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
4362378 AAAATTATATTTTGACCCCGAAAC-TTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
4362407 AAAATTACCATTTTTACCCCAAAAC-TTTCTA
1 AAAATTA-CATTTTGACCCCAAAACTTTTC-C
*
4362438 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
4362468 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
4362498 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
4362528 AAAATTATACTTTGACCCCAAAAC-TTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
4362557 AAAATTACTATTTTTACCCCCAAACTT
1 AAAATTAC-ATTTTGACCCCAAAACTT
4362584 CCCTAAATCC
Statistics
Matches: 205, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
29 21 0.10
30 171 0.83
31 13 0.06
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:4362658 original size:59 final size:56
Alignment explanation
Indices: 4362574--4362752 Score: 153
Period size: 59 Copynumber: 3.1 Consensus size: 56
4362564 CTATTTTTAC
* *
4362574 CCCCAAACTTCCCTAAA-TCCAATTTTTAACCTCGATTTCACCAAAACTTACCGTTTTG
1 CCCCAAACTTTCC-AAATTCC-ATTTTTAACCTCGATTTCACCAAAA-TTACCATTTTG
* * * * * ** *
4362632 CCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGCCAAAATATACCATTTTATT
1 CC-CCAAACTTTCC-AAATTCCATTTTTAACCTCGATTTCACCAAAAT-TACCA-TTT-TG
* * * *
4362693 CCCCAAACTTTTCAAATTCCATTTTTAGCCTCGATTTCACAAAAATTACCATTTTA
1 CCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCACCAAAATTACCATTTTG
4362749 CCCC
1 CCCC
4362753 TAAAAACCCA
Statistics
Matches: 94, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
56 5 0.05
57 3 0.03
58 8 0.09
59 61 0.65
60 14 0.15
61 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.05, T:0.37
Consensus pattern (56 bp):
CCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCACCAAAATTACCATTTTG
Found at i:4362961 original size:30 final size:30
Alignment explanation
Indices: 4362920--4363124 Score: 270
Period size: 30 Copynumber: 6.8 Consensus size: 30
4362910 TCATTATTTG
*
4362920 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
4362950 AAATTATATTTTGACCCCAAAAC-TTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTC-CA
*
4362980 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
4363010 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
4363040 AAATTACATTTTGACTCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * * *
4363070 AAATTATACTTTGACCCTAAAAC-TTTCAA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
4363099 AAATTACCATTTTTACCCCCAAACTT
1 AAATTA-CATTTTGACCCCAAAACTT
4363125 CCCTAAATCC
Statistics
Matches: 151, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
29 15 0.10
30 131 0.87
31 5 0.03
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:4363013 original size:60 final size:60
Alignment explanation
Indices: 4362920--4363124 Score: 306
Period size: 60 Copynumber: 3.4 Consensus size: 60
4362910 TCATTATTTG
*
4362920 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTAA
* *
4362980 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTT-TCCA
1 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCT-AA
* * *
4363040 AAATTACATTTTGACTCCAAAACTTTTCCAAAATTATACTTTGACCCTAAAACTTTC-AA
1 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTAA
* *
4363099 AAATTACCATTTTTACCCCCAAACTT
1 AAATTA-CATTTTAACCCCAAAACTT
4363125 CCCTAAATCC
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
59 8 0.06
60 123 0.94
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (60 bp):
AAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTAA
Found at i:4363198 original size:59 final size:57
Alignment explanation
Indices: 4363096--4363293 Score: 173
Period size: 59 Copynumber: 3.4 Consensus size: 57
4363086 CTAAAACTTT
* * *
4363096 CAAAAATTACCATTTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCA-TTTT-GCCCCAAACTTTCC-AAATTCCATTTTTAACCTCGATTTCAC
* * * * * * * *
4363156 CAAAACTTACCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTAC
1 CAAAAATTACCATTTTGCC-CCAAACTTTCC-AAATTCCATTTTTAACCTCGATTTCAC
* * * * *
4363215 CAAAATTTACCATTTTATTCCCTAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCA-TTT-TGCCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCAC
*
4363273 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTGCCCC
4363294 TAAAAACCCA
Statistics
Matches: 108, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
56 4 0.04
57 3 0.03
58 13 0.12
59 63 0.58
60 22 0.20
61 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.37
Consensus pattern (57 bp):
CAAAAATTACCATTTTGCCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCAC
Found at i:4363420 original size:541 final size:541
Alignment explanation
Indices: 4362379--4363459 Score: 1957
Period size: 541 Copynumber: 2.0 Consensus size: 541
4362369 AACTTTCCCA
* * * *
4362379 AAATTATATTTTGACCCCGAAACTTTCAAAAATTACCATTTTTACCCCAAAACTTTCTAAAAATT
1 AAATTACATTTTAACCCCAAAACTTTCAAAAATTACCATTTTGACCCCAAAACTTTCTAAAAATT
4362444 ACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATT
66 ACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATT
*
4362509 TTAACCCCAAAACTTTTCCAAAATTATACTTTGACCCCAAAACTTTCAAAAATTACTATTTTTAC
131 TTAACCCCAAAACTTTTCCAAAATTATACTTTGACCCCAAAACTTTCAAAAATTACCATTTTTAC
4362574 CCCCAAACTTCCCTAAATCCAATTTTTAACCTCGATTTCACCAAAACTTACCGTTTTGCCTCCGA
196 CCCCAAACTTCCCTAAATCCAATTTTTAACCTCGATTTCACCAAAACTTACCGTTTTGCCTCCGA
*
4362639 ACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGCCAAAATATACCATTTTATTCCCCAAACTTT
261 ACTTTCCAAAATTTCATTTTTGACCTTGTTTTTACCAAAATATACCATTTTATTCCCCAAACTTT
* *
4362704 TCAAATTCCATTTTTAGCCTCGATTTCACAAAAATTACCATTTTACCCCTAAAAACCCAAATTAC
326 CCAAATTCCATTTTTAGCCCCGATTTCACAAAAATTACCATTTTACCCCTAAAAACCCAAATTAC
* *
4362769 CATTTTGCCCCCGGGTATCCAAAAAGTCTTGTTTTAATCCTAATTGCATCATTTCTTTAATAATA
391 CATTTTGCCCCCAGGTATCCAAAAAGTCTTGTTTTAATCCCAATTGCATCATTTCTTTAATAATA
4362834 TTTACATTTAATCTTATTTGTTATGCCCCGTACTTTGTATTCATGTTCACTTCGTGTAATTTATG
456 TTTACATTTAATCTTATTTGTTATGCCCCGTACTTTGTATTCATGTTCACTTCGTGTAATTTATG
4362899 AAATTGCTCATTCATTATTTG
521 AAATTGCTCATTCATTATTTG
* *
4362920 AAATTACATTTTAACCCCAAAACTTTTCCAAAATTA-TATTTTGACCCCAAAACTTTCTAAAAAT
1 AAATTACATTTTAACCCCAAAAC-TTTCAAAAATTACCATTTTGACCCCAAAACTTTCTAAAAAT
4362984 TACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACAT
65 TACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACAT
* * *
4363049 TTTGACTCCAAAACTTTTCCAAAATTATACTTTGACCCTAAAACTTTCAAAAATTACCATTTTTA
130 TTTAACCCCAAAACTTTTCCAAAATTATACTTTGACCCCAAAACTTTCAAAAATTACCATTTTTA
*
4363114 CCCCCAAACTTCCCTAAATCCCATTTTTAACCTCGATTTCACCAAAACTTACCGTTTTGCCTCCG
195 CCCCCAAACTTCCCTAAATCCAATTTTTAACCTCGATTTCACCAAAACTTACCGTTTTGCCTCCG
* *
4363179 AACTTTCCAAAATTTCATTTTTGACCTTGTTTTTACCAAAATTTACCATTTTATTCCCTAAACTT
260 AACTTTCCAAAATTTCATTTTTGACCTTGTTTTTACCAAAATATACCATTTTATTCCCCAAACTT
4363244 TCCAAATTCCATTTTTAGCCCCGATTTCACAAAAATTACCATTTTACCCCTAAAAACCCAAATTA
325 TCCAAATTCCATTTTTAGCCCCGATTTCACAAAAATTACCATTTTACCCCTAAAAACCCAAATTA
*
4363309 CCATTTTGCCCCCAGGTATCCAAAAAGTCTTGTTTTAATCCCGATTGCATCATTTCTTTAATAAT
390 CCATTTTGCCCCCAGGTATCCAAAAAGTCTTGTTTTAATCCCAATTGCATCATTTCTTTAATAAT
* *
4363374 ATTTACATTTAATTTTATTTGTTATGCCCTGTACTTTGTATTCATGTTCACTTCGTGTAATTTAT
455 ATTTACATTTAATCTTATTTGTTATGCCCCGTACTTTGTATTCATGTTCACTTCGTGTAATTTAT
4363439 GAAATTGCTCATTCATTATTT
520 GAAATTGCTCATTCATTATTT
4363460 ATTTAAAAAA
Statistics
Matches: 518, Mismatches: 21, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
541 507 0.98
542 11 0.02
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (541 bp):
AAATTACATTTTAACCCCAAAACTTTCAAAAATTACCATTTTGACCCCAAAACTTTCTAAAAATT
ACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATT
TTAACCCCAAAACTTTTCCAAAATTATACTTTGACCCCAAAACTTTCAAAAATTACCATTTTTAC
CCCCAAACTTCCCTAAATCCAATTTTTAACCTCGATTTCACCAAAACTTACCGTTTTGCCTCCGA
ACTTTCCAAAATTTCATTTTTGACCTTGTTTTTACCAAAATATACCATTTTATTCCCCAAACTTT
CCAAATTCCATTTTTAGCCCCGATTTCACAAAAATTACCATTTTACCCCTAAAAACCCAAATTAC
CATTTTGCCCCCAGGTATCCAAAAAGTCTTGTTTTAATCCCAATTGCATCATTTCTTTAATAATA
TTTACATTTAATCTTATTTGTTATGCCCCGTACTTTGTATTCATGTTCACTTCGTGTAATTTATG
AAATTGCTCATTCATTATTTG
Found at i:4364885 original size:17 final size:17
Alignment explanation
Indices: 4364863--4364895 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4364853 GCTTGAGATT
*
4364863 CAAAACAATCTTAAAAC
1 CAAAACAACCTTAAAAC
4364880 CAAAACAACCTTAAAA
1 CAAAACAACCTTAAAA
4364896 AAAAGATCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAACAACCTTAAAAC
Found at i:4365951 original size:13 final size:13
Alignment explanation
Indices: 4365933--4365959 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4365923 CCAAGATCAT
4365933 CGGAAGTTATCTG
1 CGGAAGTTATCTG
4365946 CGGAAGTTATCTG
1 CGGAAGTTATCTG
4365959 C
1 C
4365960 AAAGTTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (13 bp):
CGGAAGTTATCTG
Found at i:4366108 original size:24 final size:23
Alignment explanation
Indices: 4366081--4366137 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
4366071 TATGTGAAAT
*
4366081 ATTAATTTTAAATACTTTTAATTA
1 ATTAATTTTAAATACTTTTAA-AA
* * *
4366105 ATTAATATTAATTATTTTTAAAA
1 ATTAATTTTAAATACTTTTAAAA
4366128 ATTAATTTTA
1 ATTAATTTTA
4366138 TTATATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTAATTTTAAATACTTTTAAAA
Found at i:4368898 original size:4 final size:4
Alignment explanation
Indices: 4368889--4368915 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4368879 ACCAAAATTA
4368889 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
4368916 TTTTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:4371509 original size:19 final size:18
Alignment explanation
Indices: 4371487--4371550 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
4371477 AAATTACAAA
4371487 AAAAATTAAAATAAATTTT
1 AAAAATTAAAAT-AATTTT
*
4371506 AAAATTTAAAAT-ATTTAT
1 AAAAATTAAAATAATTT-T
4371524 AAAAATTCAAAATTTATATTTT
1 AAAAATT-AAAA--TA-ATTTT
4371546 AAAAA
1 AAAAA
4371551 CATTATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 4 0.11
18 7 0.19
19 15 0.41
21 1 0.03
22 6 0.16
23 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTAAAATAATTTT
Found at i:4371526 original size:18 final size:18
Alignment explanation
Indices: 4371487--4371541 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
4371477 AAATTACAAA
4371487 AAAAATTAAAATAAATTT-T
1 AAAAATTAAAAT--ATTTAT
*
4371506 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
*
4371524 AAAAATTCAAA-ATTTAT
1 AAAAATTAAAATATTTAT
4371541 A
1 A
4371542 TTTTAAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.34
18 10 0.31
19 11 0.34
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:4371566 original size:21 final size:23
Alignment explanation
Indices: 4371542--4371584 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
4371532 AAAATTTATA
4371542 TTTTAAAA-ACAT-TATAAAAAT
1 TTTTAAAATACATATATAAAAAT
*
4371563 TTTTAAAATATATATATAAAAA
1 TTTTAAAATACATATATAAAAA
4371585 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTAAAATACATATATAAAAAT
Found at i:4371585 original size:35 final size:33
Alignment explanation
Indices: 4371520--4371585 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
4371510 TTTAAAATAT
* * *
4371520 TTATAAAAATTCAAAATTTATATTTTAAAAACA
1 TTATAAAAATTCAAAATATATATATAAAAAACA
*
4371553 TTATAAAAATTTTTAAAATATATATATAAAAAA
1 TTATAAAAA--TTCAAAATATATATATAAAAAA
4371586 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 9 0.33
35 18 0.67
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (33 bp):
TTATAAAAATTCAAAATATATATATAAAAAACA
Found at i:4379868 original size:58 final size:58
Alignment explanation
Indices: 4379796--4379915 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
4379786 ACCCATCAAC
* *
4379796 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCAT
1 AAACTAAACACAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCAT
* *
4379854 AAACTAAACACAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACACAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
4379912 AAAC
1 AAAC
4379916 AACTCCTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 3 0.05
58 54 0.95
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACACAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:4388474 original size:72 final size:73
Alignment explanation
Indices: 4388356--4388498 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 73
4388346 TCTCAAGGAA
* *
4388356 TAAAAGTTTTTATTAATTATAAAAAAAATAAAGGAAAAACTAACTTAACGAGTAAGTAGTTACTT
1 TAAAAGTTTTTATTAACTATAAAAAAAATAAAGGAAAAACTAACTTAACGAGTAAGGAGTTACTT
4388421 GGGTACCT
66 GGGTACCT
4388429 TAAAAGTTTTTATTAACTAT-AAAAAAATAAAGGAAAAACTAACTTAACGAGTAAGGAGTTACTT
1 TAAAAGTTTTTATTAACTATAAAAAAAATAAAGGAAAAACTAACTTAACGAGTAAGGAGTTACTT
4388493 GGGTAC
66 GGGTAC
4388499 GTTAGTAGTA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 49 0.72
73 19 0.28
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (73 bp):
TAAAAGTTTTTATTAACTATAAAAAAAATAAAGGAAAAACTAACTTAACGAGTAAGGAGTTACTT
GGGTACCT
Found at i:4391188 original size:21 final size:24
Alignment explanation
Indices: 4391164--4391206 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
4391154 ACATCATTCC
4391164 AAACAACA-AA-ACAA-AAAATAA
1 AAACAACACAACACAACAAAATAA
4391185 AAACAACACAACACAACAAAAT
1 AAACAACACAACACAACAAAAT
4391207 TCAAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 4 0.21
24 5 0.26
ACGTcount: A:0.74, C:0.21, G:0.00, T:0.05
Consensus pattern (24 bp):
AAACAACACAACACAACAAAATAA
Found at i:4391568 original size:42 final size:42
Alignment explanation
Indices: 4391473--4391570 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
4391463 GGGTTTAAAA
* *
4391473 ATATTTGGGTTAAATTTATGAGTGTTTTTGAAGAATGGAATT
1 ATATTTGGGTTTAATTTATGAGTGTTTTTGAAGAATGAAATT
*
4391515 ATATTTGGGTTTAGTTTATGAGTGTTTTTGAAGAATGAAATT
1 ATATTTGGGTTTAATTTATGAGTGTTTTTGAAGAATGAAATT
*
4391557 ATATGTGGGTTTAA
1 ATATTTGGGTTTAA
4391571 AAATATTTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (42 bp):
ATATTTGGGTTTAATTTATGAGTGTTTTTGAAGAATGAAATT
Found at i:4391839 original size:23 final size:23
Alignment explanation
Indices: 4391796--4391840 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4391786 AAAAAAATTC
**
4391796 AACTCGATTTGTTTAACTCGAAT
1 AACTCGATTTGAATAACTCGAAT
*
4391819 AACTCGATTTGAATAATTCGAA
1 AACTCGATTTGAATAACTCGAA
4391841 ATTCGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (23 bp):
AACTCGATTTGAATAACTCGAAT
Found at i:4393145 original size:15 final size:15
Alignment explanation
Indices: 4393125--4393155 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4393115 CGATTATACA
4393125 GCACAGAAAGTGTAG
1 GCACAGAAAGTGTAG
4393140 GCACAGAAAGTGTAG
1 GCACAGAAAGTGTAG
4393155 G
1 G
4393156 GACCATAATT
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:0.13, G:0.35, T:0.13
Consensus pattern (15 bp):
GCACAGAAAGTGTAG
Found at i:4405667 original size:21 final size:23
Alignment explanation
Indices: 4405642--4405690 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
4405632 TTACTAGTAA
*
4405642 AAAAATCAT-TAAAA-ATTATTT
1 AAAAATAATGTAAAACATTATTT
*
4405663 TAAAA-AATGTAAAACATTATTT
1 AAAAATAATGTAAAACATTATTT
4405685 AAAAAT
1 AAAAAT
4405691 GAAAAAGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.09
21 9 0.41
22 11 0.50
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAATAATGTAAAACATTATTT
Found at i:4405667 original size:22 final size:22
Alignment explanation
Indices: 4405642--4405690 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
4405632 TTACTAGTAA
4405642 AAAAATCAT-TAAAA-ATTATTTT
1 AAAAAT-ATGTAAAACATTA-TTT
4405664 AAAAA-ATGTAAAACATTATTT
1 AAAAATATGTAAAACATTATTT
4405685 AAAAAT
1 AAAAAT
4405691 GAAAAAGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 2 0.08
21 13 0.54
22 9 0.38
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAATATGTAAAACATTATTT
Found at i:4405688 original size:20 final size:21
Alignment explanation
Indices: 4405651--4405696 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4405641 AAAAAATCAT
4405651 TAAAAATTATTTTAAAAAATG
1 TAAAAATTATTTTAAAAAATG
4405672 TAAAACATTA-TTT-AAAAATG
1 TAAAA-ATTATTTTAAAAAATG
4405692 -AAAAA
1 TAAAAA
4405697 GAACTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 4 0.17
20 7 0.29
21 8 0.33
22 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TAAAAATTATTTTAAAAAATG
Found at i:4405838 original size:19 final size:19
Alignment explanation
Indices: 4405814--4405868 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
4405804 TTAAATGTAT
*
4405814 AAAATTGTGAAAACCATTA
1 AAAATTTTGAAAACCATTA
* ** *
4405833 AAAATTTTGAAGAGTATTT
1 AAAATTTTGAAAACCATTA
4405852 AAAATTTTGAAAACCAT
1 AAAATTTTGAAAACCAT
4405869 GAAATTTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (19 bp):
AAAATTTTGAAAACCATTA
Found at i:4406827 original size:10 final size:10
Alignment explanation
Indices: 4406812--4406837 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4406802 TCTGACACGA
4406812 ATTTTTTATT
1 ATTTTTTATT
4406822 ATTTTTTATT
1 ATTTTTTATT
4406832 ATTTTT
1 ATTTTT
4406838 ATATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:4410193 original size:7 final size:7
Alignment explanation
Indices: 4410183--4410221 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
4410173 ATGTATAGGA
*
4410183 TTTAGGG
1 TTTAAGG
4410190 TTTAAGG
1 TTTAAGG
4410197 TTTCAA-G
1 TTT-AAGG
4410204 TTTAAGG
1 TTTAAGG
4410211 TTTAAGG
1 TTTAAGG
4410218 TTTA
1 TTTA
4410222 CGATTTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 25 0.86
8 2 0.07
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (7 bp):
TTTAAGG
Found at i:4410268 original size:28 final size:29
Alignment explanation
Indices: 4410183--4410268 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 29
4410173 ATGTATAGGA
* * * *
4410183 TTTAGGGTTTAAGGTTTCAAGTTTAAGG-
1 TTTAAGGTTTACGATTTTAAGTTTAAGGT
* * *
4410211 TTTAAGGTTTACGATTTTTAGTCTAGGGT
1 TTTAAGGTTTACGATTTTAAGTTTAAGGT
*
4410240 TTTAA-GTTTATGA-TTTAAGGTTTAAGGT
1 TTTAAGGTTTACGATTTTAA-GTTTAAGGT
4410268 T
1 T
4410269 ATGAAATTTA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 4 0.09
28 36 0.80
29 5 0.11
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (29 bp):
TTTAAGGTTTACGATTTTAAGTTTAAGGT
Found at i:4410585 original size:45 final size:45
Alignment explanation
Indices: 4410534--4410657 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
4410524 TATTATGGTG
* ** *
4410534 GCTCGTCAAACTCAACCTGATATCCTTCGCTTGAGTATTACAGT-
1 GCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTACAGTA
* * *
4410578 GATTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGGTA
1 G-CTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTACAGTA
4410624 GCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
1 GCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
4410658 TGAGTTAGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 1 0.01
45 68 0.97
46 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (45 bp):
GCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAGTATTACAGTA
Found at i:4413378 original size:20 final size:21
Alignment explanation
Indices: 4413353--4413395 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4413343 TACTTACTAC
*
4413353 TACTAAC-AACAAAATAAAAT
1 TACTAACTAAAAAAATAAAAT
*
4413373 TACTAACTAAAAAAATTAAAT
1 TACTAACTAAAAAAATAAAAT
4413394 TA
1 TA
4413396 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAAAAAAATAAAAT
Found at i:4413588 original size:18 final size:18
Alignment explanation
Indices: 4413567--4413601 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4413557 AATTAAACTT
4413567 AAAATTAA-CTAAACTTAA
1 AAAATTAATC-AAACTTAA
4413585 AAAATTAATCAAACTTA
1 AAAATTAATCAAACTTA
4413602 CCTTTCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTAATCAAACTTAA
Found at i:4413767 original size:27 final size:26
Alignment explanation
Indices: 4413737--4413787 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
4413727 CATTATCTTT
4413737 TTCTCCTCTCTTTCTTCTCATTCTTCC
1 TTCTCCTCTCTTTCTT-TCATTCTTCC
* * *
4413764 TTCTTCTTTCTTTCTTTCTTTCTT
1 TTCTCCTCTCTTTCTTTCATTCTT
4413788 TCTTTCTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (26 bp):
TTCTCCTCTCTTTCTTTCATTCTTCC
Found at i:4413774 original size:4 final size:4
Alignment explanation
Indices: 4413745--4413804 Score: 72
Period size: 4 Copynumber: 15.5 Consensus size: 4
4413735 TTTTCTCCTC
* *
4413745 TCTT TCTT CTCAT TC-T TCCT TC-T TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT -TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
4413792 TCTT TCTT T-TT TC
1 TCTT TCTT TCTT TC
4413805 CTTCAAATCA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
3 9 0.18
4 39 0.76
5 3 0.06
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TCTT
Found at i:4416283 original size:15 final size:16
Alignment explanation
Indices: 4416263--4416293 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4416253 ATAAACTCAA
4416263 AATTTTAAAA-AAATT
1 AATTTTAAAATAAATT
4416278 AATTTTAAAATAAATT
1 AATTTTAAAATAAATT
4416294 GAAAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTTAAAATAAATT
Found at i:4416398 original size:21 final size:21
Alignment explanation
Indices: 4416369--4416409 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4416359 AGTTTAACTA
*
4416369 AAATCAATTTTAGATATTAAAC
1 AAATCAATTGTA-ATATTAAAC
4416391 AAAT-AATTGTAATATTAAA
1 AAATCAATTGTAATATTAAA
4416410 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
AAATCAATTGTAATATTAAAC
Found at i:4418576 original size:29 final size:29
Alignment explanation
Indices: 4418535--4419043 Score: 252
Period size: 29 Copynumber: 17.6 Consensus size: 29
4418525 AATGGAGTCA
4418535 AAAAT-GTAATTTTTGGATTTCGAGGGGT
1 AAAATGGTAATTTTTGGATTTCGAGGGGT
* *** *
4418563 AAAACGGTAATTTTTGGACACCCGA-GGAT
1 AAAATGGTAATTTTTGGA-TTTCGAGGGGT
*
4418592 AAAATGGTTATTTTTGGATGTT--AGGGGT
1 AAAATGGTAATTTTTGGAT-TTCGAGGGGT
*
4418620 -AAATGGTAATTTTTGGAAAGTTC-A-GGGT
1 AAAATGGTAATTTTTGG--ATTTCGAGGGGT
4418648 CAAAAAT-GTAATTTTTGGATATTCGA-GGGT
1 --AAAATGGTAATTTTTGGAT-TTCGAGGGGT
* *
4418678 AAAATGATAATTTTTGGATGTCTG-GGGGT
1 AAAATGGTAATTTTTGGATTTC-GAGGGGT
* ** *
4418707 AAAATGGTAATTTTTGAACATC-AGGGAT
1 AAAATGGTAATTTTTGGATTTCGAGGGGT
4418735 AAAATGGTAATTTTTGGATGTTCG-GGGG-
1 AAAATGGTAATTTTTGGAT-TTCGAGGGGT
4418763 -AAATGGTAATTTTTGAAGAGTTT---GGGGT
1 AAAATGGTAATTTTTG--GA-TTTCGAGGGGT
*
4418791 CAAAAAT-GTAATTTTTGGATATCTGA-GGGT
1 --AAAATGGTAATTTTTGGATTTC-GAGGGGT
* * *
4418821 AAAATGATAATTTTTGGATGTTCG-GAGAT
1 AAAATGGTAATTTTTGGAT-TTCGAGGGGT
**
4418850 AAAATGGTAATTTTCAGATAGTTC--GGGGT
1 AAAATGGTAATTTTTGGAT--TTCGAGGGGT
* **
4418879 CAAAAAT-GTGATTTTTGGACATTT-GA-TAGT
1 --AAAATGGTAATTTTTGG--ATTTCGAGGGGT
* *
4418909 AAAATAGTAATTTTTGGATGTTTGA-GGGT
1 AAAATGGTAATTTTTGGAT-TTCGAGGGGT
* *
4418938 AAAATGATAATTTTTGGAAAGTTC--GGGGT
1 AAAATGGTAATTTTTGG--ATTTCGAGGGGT
* * * *
4418967 AAAAAAT-GTGATTTTTGGACATCCGA-TGGT
1 --AAAATGGTAATTTTTGGA-TTTCGAGGGGT
* *
4418997 AAAATGGTAATTTTTGAATGTTCG-GGAGT
1 AAAATGGTAATTTTTGGAT-TTCGAGGGGT
4419026 AAAATGGTAATTTTTGGA
1 AAAATGGTAATTTTTGGA
4419044 AAGTTTGGGG
Statistics
Matches: 369, Mismatches: 59, Indels: 105
0.69 0.11 0.20
Matches are distributed among these distances:
27 39 0.11
28 62 0.17
29 181 0.49
30 66 0.18
31 19 0.05
32 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.37
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATTTCGAGGGGT
Found at i:4418721 original size:58 final size:56
Alignment explanation
Indices: 4418535--4419069 Score: 347
Period size: 59 Copynumber: 9.2 Consensus size: 56
4418525 AATGGAGTCA
* **** *
4418535 AAAAT-GTAATTTTTGGAT-TTCGAGGGGTAAAACGGTAATTTTTGGACACCCGAGGAT
1 AAAATGGTAATTTTTGGATATTC--GGGGTAAAATGGTAATTTTTGGA-TGTTGAGGGT
* * * * *
4418592 AAAATGGTTATTTTTGGATGTTAGGGGT-AAATGGTAATTTTTGGAAAGTTCAGGGT
1 AAAATGGTAATTTTTGGATATTCGGGGTAAAATGGTAATTTTTGG-ATGTTGAGGGT
* *
4418648 CAAAAAT-GTAATTTTTGGATATTCGAGGGTAAAATGATAATTTTTGGATGTCTGGGGGT
1 --AAAATGGTAATTTTTGGATATTCG-GGGTAAAATGGTAATTTTTGGATGT-TGAGGGT
* * *
4418707 AAAATGGTAATTTTTGAACA-TCAGGGATAAAATGGTAATTTTTGGATGTTCG-GGG-
1 AAAATGGTAATTTTTGGATATTC-GGGGTAAAATGGTAATTTTTGGATGTT-GAGGGT
* * * * *
4418762 GAAATGGTAATTTTTGAAGAGTTTGGGGTCAAAAAT-GTAATTTTTGGATATCTGAGGGT
1 AAAATGGTAATTTTTGGATA-TTCGGGGT--AAAATGGTAATTTTTGGATGT-TGAGGGT
* * * **
4418821 AAAATGATAATTTTTGGATGTTCGGAGATAAAATGGTAATTTTCAGATAGTTCG-GGGT
1 AAAATGGTAATTTTTGGATATTCGG-GGTAAAATGGTAATTTTTGGAT-GTT-GAGGGT
* * * ** *
4418879 CAAAAAT-GTGATTTTTGGACATTTGATAGTAAAATAGTAATTTTTGGATGTTTGAGGGT
1 --AAAATGGTAATTTTTGGATATTCG-GGGTAAAATGGTAATTTTTGGATG-TTGAGGGT
* * * ** * *
4418938 AAAATGATAATTTTTGGAAAGTTCGGGGTAAAAAAT-GTGATTTTTGGACATCCGATGGT
1 AAAATGGTAATTTTTGGATA-TTCGGGGT--AAAATGGTAATTTTTGGATGT-TGAGGGT
* * *
4418997 AAAATGGTAATTTTTGAATGTTCGGGAGTAAAATGGTAATTTTTGGAAAGTTTG-GGGT
1 AAAATGGTAATTTTTGGATATTCGGG-GTAAAATGGTAATTTTTGG-ATG-TTGAGGGT
4419055 CAAAATGGTAATTTT
1 -AAAATGGTAATTTT
4419070 GGAAGTTCAA
Statistics
Matches: 376, Mismatches: 65, Indels: 72
0.73 0.13 0.14
Matches are distributed among these distances:
55 18 0.05
56 28 0.07
57 88 0.23
58 101 0.27
59 130 0.35
60 11 0.03
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.37
Consensus pattern (56 bp):
AAAATGGTAATTTTTGGATATTCGGGGTAAAATGGTAATTTTTGGATGTTGAGGGT
Found at i:4418793 original size:143 final size:144
Alignment explanation
Indices: 4418535--4418863 Score: 472
Period size: 143 Copynumber: 2.3 Consensus size: 144
4418525 AATGGAGTCA
* * * *
4418535 AAAATG-TAATTTTTGGATTTC-GAGGGGTAAAACGGTAATTTTTGGACACCCGAGGATAAAATG
1 AAAATGATAATTTTTGGATGTCTG-GGGGTAAAATGGTAATTTTTGAACACCAGAGGATAAAATG
* *
4418598 GTTATTTTTGGATGTTAGGGGTAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAAATGTAATTTT
65 GTAATTTTTGGATGTTAGGGGGAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAAATGTAATTTT
4418663 TGGATAT-TCGAGGGT
130 TGGATATCT-GAGGGT
*
4418678 AAAATGATAATTTTTGGATGTCTGGGGGTAAAATGGTAATTTTTGAACATCAG-GGATAAAATGG
1 AAAATGATAATTTTTGGATGTCTGGGGGTAAAATGGTAATTTTTGAACACCAGAGGATAAAATGG
* **
4418742 TAATTTTTGGATGTTCGGGGGAAATGGTAATTTTT-GAAGAGTTTGGGGTCAAAAATGTAATTTT
66 TAATTTTTGGATGTTAGGGGGAAATGGTAATTTTTGGAA-AGTTCAGGGTCAAAAATGTAATTTT
4418806 TGGATATCTGAGGGT
130 TGGATATCTGAGGGT
* *
4418821 AAAATGATAATTTTTGGATGT-TCGGAGATAAAATGGTAATTTT
1 AAAATGATAATTTTTGGATGTCT-GGGGGTAAAATGGTAATTTT
4418864 CAGATAGTTC
Statistics
Matches: 169, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
142 4 0.02
143 124 0.73
144 40 0.24
145 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (144 bp):
AAAATGATAATTTTTGGATGTCTGGGGGTAAAATGGTAATTTTTGAACACCAGAGGATAAAATGG
TAATTTTTGGATGTTAGGGGGAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAAATGTAATTTTT
GGATATCTGAGGGT
Found at i:4418885 original size:88 final size:89
Alignment explanation
Indices: 4418531--4419069 Score: 474
Period size: 88 Copynumber: 6.2 Consensus size: 89
4418521 AACAAATGGA
** * *** *
4418531 GTCAAAAATGTAATTTTTGGATTTC-GAGGGGTAAAACGGTAATTTTTGGA-CACCCGAGGATAA
1 GTCAAAAATGTAATTTTTGGACATCTGA-GGGTAAAATGGTAATTTTTGGATGTTCGGAGGATAA
* *
4418594 AATGGTTATTTTTGGAT-GTTAGGG
65 AATGGTAATTTTTGGATAGTTCGGG
* * * *
4418618 GT---AAATGGTAATTTTTGGAAAGT-TCAGGGTCAAAAAT-GTAATTTTTGGATATTC-GAGGG
1 GTCAAAAAT-GTAATTTTTGGACA-TCTGAGGGT--AAAATGGTAATTTTTGGATGTTCGGAGGA
* *
4418677 TAAAATGATAATTTTTGGAT-GTCTGGGG
62 TAAAATGGTAATTTTTGGATAGT-TCGGG
* *
4418705 GT--AAAATGGTAATTTTTGAACATC--AGGGATAAAATGGTAATTTTTGGATGTTCGG-GG--G
1 GTCAAAAAT-GTAATTTTTGGACATCTGAGGG-TAAAATGGTAATTTTTGGATGTTCGGAGGATA
* * *
4418763 AAATGGTAATTTTTGAAGAGTTTGGG
64 AAATGGTAATTTTTGGATAGTTCGGG
* *
4418789 GTCAAAAATGTAATTTTTGGATATCTGAGGGTAAAATGATAATTTTTGGATGTTCGGA-GATAAA
1 GTCAAAAATGTAATTTTTGGACATCTGAGGGTAAAATGGTAATTTTTGGATGTTCGGAGGATAAA
**
4418853 ATGGTAATTTTCAGATAGTTCGGG
66 ATGGTAATTTTTGGATAGTTCGGG
* * ** * * *
4418877 GTCAAAAATGTGATTTTTGGACATTTGATAGTAAAATAGTAATTTTTGGATGTT-TGAGGGTAAA
1 GTCAAAAATGTAATTTTTGGACATCTGAGGGTAAAATGGTAATTTTTGGATGTTCGGAGGATAAA
* *
4418941 ATGATAATTTTTGGAAAGTTCGGG
66 ATGGTAATTTTTGGATAGTTCGGG
* * * * *
4418965 GTAAAAAATGTGATTTTTGGACATCCGATGGTAAAATGGTAATTTTTGAATGTTC-G-GGAGTAA
1 GTCAAAAATGTAATTTTTGGACATCTGAGGGTAAAATGGTAATTTTTGGATGTTCGGAGGA-TAA
* *
4419028 AATGGTAATTTTTGGAAAGTTTGGG
65 AATGGTAATTTTTGGATAGTTCGGG
4419053 GTC-AAAATGGTAATTTT
1 GTCAAAAAT-GTAATTTT
4419070 GGAAGTTCAA
Statistics
Matches: 376, Mismatches: 52, Indels: 47
0.79 0.11 0.10
Matches are distributed among these distances:
84 25 0.07
85 37 0.10
86 91 0.24
87 29 0.08
88 194 0.52
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.37
Consensus pattern (89 bp):
GTCAAAAATGTAATTTTTGGACATCTGAGGGTAAAATGGTAATTTTTGGATGTTCGGAGGATAAA
ATGGTAATTTTTGGATAGTTCGGG
Found at i:4419225 original size:29 final size:27
Alignment explanation
Indices: 4418591--4419222 Score: 215
Period size: 29 Copynumber: 21.9 Consensus size: 27
4418581 CACCCGAGGA
* * * *
4418591 TAAAATGGTTATTTTTGGATGTTAGGGG
1 TAAAAT-GTAATTTTTGAAAGTTTGGGG
**
4418619 T-AAATGGTAATTTTTGGAAAGTTCAGGG
1 TAAAAT-GTAATTTTT-GAAAGTTTGGGG
* *
4418647 TCAAAAATGTAATTTTTGGATA-TTCGAGGG
1 T--AAAATGTAATTTTT-GAAAGTTTG-GGG
* * *
4418677 TAAAATGATAATTTTTGGATGTCTGGGGG
1 TAAAATG-TAATTTTTGAAAGT-TTGGGG
** *
4418706 TAAAATGGTAATTTTTGAACA-TCAGGGA
1 TAAAAT-GTAATTTTTGAA-AGTTTGGGG
* * *
4418734 TAAAATGGTAATTTTTGGATGTTCGGGG
1 TAAAAT-GTAATTTTTGAAAGTTTGGGG
*
4418762 -GAAATGGTAATTTTTGAAGAGTTTGGGG
1 TAAAAT-GTAATTTTTGAA-AGTTTGGGG
* *
4418790 TCAAAAATGTAATTTTTGGATA-TCTGAGGG
1 T--AAAATGTAATTTTT-GAAAGTTTG-GGG
* * * *
4418820 TAAAATGATAATTTTTGGATGTTCGGAGA
1 TAAAATG-TAATTTTTGAAAGTTTGG-GG
* * *
4418849 TAAAATGGTAATTTTCAGATAGTTCGGGG
1 TAAAAT-GTAATTTT-TGAAAGTTTGGGG
* * **
4418878 TCAAAAATGTGATTTTTGGACA-TTTGATAG
1 T--AAAATGTAATTTTT-GAAAGTTTG-GGG
* *
4418908 TAAAATAGTAATTTTTGGATGTTTGAGGG
1 TAAAAT-GTAATTTTTGAAAGTTTG-GGG
*
4418937 TAAAATGATAATTTTTGGAAAGTTCGGGG
1 TAAAATG-TAATTTTT-GAAAGTTTGGGG
* * ** *
4418966 TAAAAAATGTGATTTTTGGACA-TCCGATGG
1 T--AAAATGTAATTTTT-GAAAGTTTG-GGG
* *
4418996 TAAAATGGTAATTTTTGAATGTTCGGGAG
1 TAAAAT-GTAATTTTTGAAAGTTTGGG-G
4419025 TAAAATGGTAATTTTTGGAAAGTTTGGGG
1 TAAAAT-GTAATTTTT-GAAAGTTTGGGG
* **
4419054 TCAAAATGGTAA-TTTTGGAAGTTCAAGGG
1 T-AAAAT-GTAATTTTTGAAAGTT-TGGGG
* * * *
4419083 CAAAAGTGTGATTTTGGAAAGGTTTGAGGT
1 TAAAA-TGTAATTTTTGAAA-GTTTG-GGG
** * * *
4419113 TAAAATAAAAATTTTGGAAGTTCAGGGG
1 TAAAATGTAATTTTTGAAAGTT-TGGGG
*
4419141 CAAAA-GT-ATGATTTTGAAAAGGTTTGGGG
1 TAAAATGTAAT--TTTTG-AAA-GTTTGGGG
*
4419170 TTAAAATGATAA-TTTTGGAAGTTTAGGGG
1 -TAAAATG-TAATTTTTGAAAGTTT-GGGG
4419199 TAAAATGTAATTTTTAGAAAGTTT
1 TAAAATGTAATTTTT-GAAAGTTT
4419223 AGGCTCAAAA
Statistics
Matches: 456, Mismatches: 93, Indels: 109
0.69 0.14 0.17
Matches are distributed among these distances:
26 1 0.00
27 32 0.07
28 114 0.25
29 171 0.38
30 114 0.25
31 22 0.05
32 1 0.00
33 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (27 bp):
TAAAATGTAATTTTTGAAAGTTTGGGG
Found at i:4421161 original size:35 final size:35
Alignment explanation
Indices: 4421117--4421191 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
4421107 ATTTTAATTC
4421117 AAAATAAATTTAAA-CTCAAAAATAAGTTT-AAATAT
1 AAAATAAATTTAAATCTC-AAAATAA-TTTAAAATAT
* *
4421152 AAAATAAATTTAAATTTCAAAATAATTTAAAATTT
1 AAAATAAATTTAAATCTCAAAATAATTTAAAATAT
4421187 AAAAT
1 AAAAT
4421192 TTAAAGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 3 0.08
35 31 0.86
36 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAATAAATTTAAATCTCAAAATAATTTAAAATAT
Found at i:4421173 original size:18 final size:18
Alignment explanation
Indices: 4421114--4421191 Score: 83
Period size: 17 Copynumber: 4.4 Consensus size: 18
4421104 TAGATTTTAA
4421114 TTCAAAATAAATTTAAA-
1 TTCAAAATAAATTTAAAT
* *
4421131 CTCAAAAATAAGTTTAAAT
1 TTC-AAAATAAATTTAAAT
*
4421150 AT-AAAATAAATTTAAAT
1 TTCAAAATAAATTTAAAT
4421167 TTCAAAAT-AATTTAAAAT
1 TTCAAAATAAATTT-AAAT
4421185 TT-AAAAT
1 TTCAAAAT
4421192 TTAAAGATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 27 0.52
18 24 0.46
19 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (18 bp):
TTCAAAATAAATTTAAAT
Found at i:4422086 original size:208 final size:208
Alignment explanation
Indices: 4421579--4422257 Score: 828
Period size: 208 Copynumber: 3.3 Consensus size: 208
4421569 TCCACTTTTC
* *
4421579 TGTATCTTATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAATCACTTT
1 TGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAATCGCTTT
* * * * *
4421644 ATTGCTTCGACCTGCTTCACAAG-ATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACGTTG
66 ATTGCTTCGACCTGCTTC-TAAGTATCTCATCAGGAAGCAGAGGTTCGAAGATTTGCTCACATTG
* * * *
4421708 AGCCTGGTTTCATTGATTTGGTCTACTTCTTAGTATCTTATCAAGAAGATGATCACCTCGTTGTT
130 AGCCTGGTTTCATTGATTTGGTCTATTTCTTAGTATCTCATCAGGAAGATGATCGCCTCGTTGTT
* *
4421773 ATGATCCACTTCTT
195 TTGATCCATTTCTT
* * *
4421787 TGTATCTCATTAGGAAGACGGATCTAGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTT
1 TGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAATCGCTTT
* * * *
4421852 ATTGCTTCAACCTGCTTCTAAGTATCTCGTTAGGAAGCAGAGGTTCGAAGATTTGCTCACTTTGA
66 ATTGCTTCGACCTGCTTCTAAGTATCTCATCAGGAAGCAGAGGTTCGAAGATTTGCTCACATTGA
* *
4421917 GCCTGGTTTCGTTGATTTGGTCTATTTCTTAGTATCTCATCAGGAAGATGACCGCCTCGTTGTTT
131 GCCTGGTTTCATTGATTTGGTCTATTTCTTAGTATCTCATCAGGAAGATGATCGCCTCGTTGTTT
4421982 TGATCCATTTCTT
196 TGATCCATTTCTT
* *
4421995 TGTATCTCATCAGGAAGATGGATCTGGTTCACTTCTTTGTATCTCATCAGGAAGGTAATCGCTTT
1 TGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAATCGCTTT
** ** * * * * * *
4422060 ATTATTTCGACCCACTTCTTAGTATCTCATCAGGAAG-ATAGGTTTGAAG-TTTCACTCTCACTG
66 ATTGCTTCGACCTGCTTCTAAGTATCTCATCAGGAAGCAGAGGTTCGAAGATTT-GCTCACATTG
* * * * * * **
4422123 AGCTTTGCTTT-ATTGATGTGGTCTTTTTCTCT-GTATCTCATCAGAAAGATGATCGCATCACTG
130 AGC-CTGGTTTCATTGATTTGGTCTATTTCT-TAGTATCTCATCAGGAAGATGATCGCCTCGTTG
** *
4422186 TTTCAATCCATTTCTC
193 TTTTGATCCATTTCTT
* * * * * *
4422202 TGTATCTCATCAGAAAGACGAATTTGATCCACTTCTCTGTATCTTATCAGGAAGGT
1 TGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGT
4422258 GACCATTTTA
Statistics
Matches: 406, Mismatches: 61, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
206 3 0.01
207 125 0.31
208 278 0.68
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (208 bp):
TGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAATCGCTTT
ATTGCTTCGACCTGCTTCTAAGTATCTCATCAGGAAGCAGAGGTTCGAAGATTTGCTCACATTGA
GCCTGGTTTCATTGATTTGGTCTATTTCTTAGTATCTCATCAGGAAGATGATCGCCTCGTTGTTT
TGATCCATTTCTT
Found at i:4422730 original size:50 final size:50
Alignment explanation
Indices: 4422667--4423032 Score: 233
Period size: 50 Copynumber: 7.3 Consensus size: 50
4422657 TTGTCTTCAT
* * * * * * *
4422667 GGTATAGGATTCACCGTTATGACCTTAATCC-TTCTCATCGTATCTTTTTA
1 GGTATCGGGTTCACCGTTACGACCTCAA-CCTTTCCCATCATATCTTCTTA
* * *
4422717 GGTATCGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTTA
1 GGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCATCATATCTTCTTA
** * * * * * *
4422767 GGTATCGGGTTCGTCATTGCGGCCTCAATCC--TCCCTTGTCATCTCTTCAT-
1 GGTATCGGGTTCACCGTTACGACCTCAA-CCTTTCCC--ATCATATCTTCTTA
* * * * *
4422817 GGTA-CTAGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTTTTA
1 GGTATC-GGGTTCACCGTTACGACCTCAACCTTTCCCATCATATCTTCTTA
* * * * * * *
4422867 GGTACCGGATTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTTA
1 GGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCATCATATCTTCTTA
* * * * * *
4422917 GGTACCGGGTTTAACGTTACGGCCTCAACCTTTCCCATCACATCTTATTA
1 GGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCATCATATCTTCTTA
* * * * * *
4422967 GGAATTGGGTTCACCGTTGCGGCCTTAACCTTTCCCTTCA-ATCTT-TTAA
1 GGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCATCATATCTTCTT-A
* *
4423016 GGTACCGGATTCACCGT
1 GGTATCGGGTTCACCGT
4423033 CGTGGCCTCA
Statistics
Matches: 257, Mismatches: 49, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
48 2 0.01
49 36 0.14
50 202 0.79
51 17 0.07
ACGTcount: A:0.17, C:0.30, G:0.18, T:0.35
Consensus pattern (50 bp):
GGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCATCATATCTTCTTA
Found at i:4422921 original size:100 final size:101
Alignment explanation
Indices: 4422724--4423048 Score: 349
Period size: 100 Copynumber: 3.2 Consensus size: 101
4422714 TTAGGTATCG
* * * * *
4422724 GGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTTAGGTATCGGGTTCGTCATTGCGG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTATTAGGTATCGGGTTCGCCGTTGCGG
** * *
4422789 CCTCAATCC--TCCCTTGTCATC-TCTTCATGGTACTA
66 CCTCAA-CCTTTCCCTTCACATCTTCTT-AAGGTACCA
* * * * *
4422824 GGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGATTCGCCGTTGCGG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTATTAGGTATCGGGTTCGCCGTTGCGG
*
4422889 CCTCAACCTTTCCCTTCACATCTTCTT-AGGTACCG
66 CCTCAACCTTTCCCTTCACATCTTCTTAAGGTACCA
* * * * * *
4422924 GGTTTAACGTTACGGCCTCAACCTTTCCCATCACATCTTATTAGGAATTGGGTTCACCGTTGCGG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTATTAGGTATCGGGTTCGCCGTTGCGG
*
4422989 CCTTAACCTTTCCCTTCA-ATCTT-TTAAGGTACC-
66 CCTCAACCTTTCCCTTCACATCTTCTTAAGGTACCA
* *
4423022 GGATTCACCGTCGTGGCCTCAATCCTT
1 GG-TTCACCGTTGCGGCCTCAA-CCTT
4423049 CCATGTCAAA
Statistics
Matches: 188, Mismatches: 31, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
98 4 0.02
99 28 0.15
100 142 0.76
101 10 0.05
102 4 0.02
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (101 bp):
GGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTATTAGGTATCGGGTTCGCCGTTGCGG
CCTCAACCTTTCCCTTCACATCTTCTTAAGGTACCA
Found at i:4422940 original size:150 final size:148
Alignment explanation
Indices: 4422660--4423048 Score: 417
Period size: 150 Copynumber: 2.6 Consensus size: 148
4422650 TTCCATTTTG
** * * *
4422660 TCTTCATGGTATAGGATTCACCGTTATGACCTTAATCC-TTCTCATCGTATCTTTTTAGGTATCG
1 TCTTCATGGTATAGG-TTCACCGTTGCGACCTTAA-CCTTTCCCATC-AATCTTTTTAGGTACCG
* * * ** *
4422724 GGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTTAGGTATCGGGTTCGTCATTGCGG
63 GATTCACCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCAACATTACGG
* **
4422789 CCTCAATCC-TCCCTTGTCATC
128 CCTCAA-CCTTCCCATCACATC
* *
4422810 TCTTCATGGTACTAGGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTTTTAGGTACCGG
1 TCTTCATGGTA-TAGGTTCACCGTTGCGACCTTAACCTTTCCCATCA-ATCTTTTTAGGTACCGG
* * *
4422875 ATTCGCCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGGGTTTAACGTTACGGC
64 ATTCACCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCAACATTACGGC
4422940 CTCAACCTTTCCCATCACATC
129 CTCAACC-TTCCCATCACATC
* * * * * *
4422961 T-TATTA-GGAATTGGGTTCACCGTTGCGGCCTTAACCTTTCCCTTCAATCTTTTAAGGTACCGG
1 TCT-TCATGGTA-TAGGTTCACCGTTGCGACCTTAACCTTTCCCATCAATCTTTTTAGGTACCGG
* *
4423024 ATTCACCGTCGTGGCCTCAATCCTT
64 ATTCACCGTTGCGGCCTCAA-CCTT
4423049 CCATGTCAAA
Statistics
Matches: 201, Mismatches: 31, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
149 37 0.18
150 148 0.74
151 16 0.08
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.35
Consensus pattern (148 bp):
TCTTCATGGTATAGGTTCACCGTTGCGACCTTAACCTTTCCCATCAATCTTTTTAGGTACCGGAT
TCACCGTTGCGGCCTCAACCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCAACATTACGGCCT
CAACCTTCCCATCACATC
Found at i:4423985 original size:21 final size:20
Alignment explanation
Indices: 4423960--4424011 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
4423950 CAACCTCTCC
4423960 TTTTCTTTTTTTCAT-TTTTT
1 TTTTCTTTTTTTC-TCTTTTT
*
4423980 TATTTCCTTTTTTCTCTTTTT
1 T-TTTCTTTTTTTCTCTTTTT
4424001 TTTTCTTTTTT
1 TTTTCTTTTTT
4424012 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTCTTTTTTTCTCTTTTT
Found at i:4423990 original size:12 final size:10
Alignment explanation
Indices: 4423960--4424022 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
4423950 CAACCTCTCC
4423960 TTTTCTTTTT
1 TTTTCTTTTT
4423970 TTCATT-TTTTT
1 TT--TTCTTTTT
* *
4423981 ATTTCCTTTT
1 TTTTCTTTTT
*
4423991 TTCTCTTTTT
1 TTTTCTTTTT
4424001 TTTTCTTTTT
1 TTTTCTTTTT
*
4424011 TATTTATTTTT
1 T-TTTCTTTTT
4424022 T
1 T
4424023 CTTCATTGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 23 0.55
11 15 0.36
12 2 0.05
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:4424001 original size:31 final size:30
Alignment explanation
Indices: 4423963--4424024 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
4423953 CCTCTCCTTT
*
4423963 TCTTTTTTTCAT-TTTTTTATTTCCTTTTTTC
1 TCTTTTTTT-ATCTTTTTTATTT-ATTTTTTC
*
4423994 TCTTTTTTTTTCTTTTTTATTTATTTTTTC
1 TCTTTTTTTATCTTTTTTATTTATTTTTTC
4424024 T
1 T
4424025 TCATTGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (30 bp):
TCTTTTTTTATCTTTTTTATTTATTTTTTC
Found at i:4428168 original size:58 final size:58
Alignment explanation
Indices: 4428054--4428523 Score: 292
Period size: 58 Copynumber: 8.1 Consensus size: 58
4428044 TGGTTTGTTA
* * ** *
4428054 AAAAT-GTAATTTTTCGAC-TTCGATGGGTAAAACGGTAATTTTTGGACA-CACAAGGGT
1 AAAATGGTAATTTTTTGACATTCGA-GGGTAAAATGGTAATTTTTGGA-AGTTCGAGGGT
* * *
4428111 AAAATGGTAATTTTTTGACACTCGAGGGTAAAATGGTTATTTTTGGATGTTCGAGGGT
1 AAAATGGTAATTTTTTGACATTCGAGGGTAAAATGGTAATTTTTGGAAGTTCGAGGGT
* * * * * *
4428169 AAAATGATAATTTTTGGAAAGTT-TAGGGTCAAAATGGTAA-TTTTGAAAAGTT-TAGGGTT
1 AAAATGGTAATTTTTTGACA-TTCGAGGGT-AAAATGGTAATTTTTG-GAAGTTCGAGGG-T
* * * * *
4428228 AAAAAT-GTAATTTTTTGACATT-TAGGGGTAAAATGGTAATTTTTAGATGTTTGGGGGT
1 -AAAATGGTAATTTTTTGACATTCGA-GGGTAAAATGGTAATTTTTGGAAGTTCGAGGGT
* * * *
4428286 AAAATGGTAA-TTTTTG-CATGGTTCGA-GGTCAAAAAT-GTAATTTTTAGAAATCCGAAGGT
1 AAAATGGTAATTTTTTGACA---TTCGAGGGT--AAAATGGTAATTTTTGGAAGTTCGAGGGT
* ** *
4428345 AAAATGGTAA-TTTTTAATGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGA-GGT
1 AAAATGGTAATTTTTTGACATTCGAGGGTAAAATGGTAATTTTTGG-AAGTTCGAGGGT
* * * * * * *
4428402 CAAAAAT-ATAATTTTTGGACA-TCTAGTGGTAAAAAGGTAATTTTTAGATGTTCAAGGGT
1 --AAAATGGTAATTTTTTGACATTCGAG-GGTAAAATGGTAATTTTTGGAAGTTCGAGGGT
* * * *
4428461 AAAATGGTAATTTTTGGAAAGTTTG-GGGTCAAAAATGGTAA-TTTTGGAAGTTCGAGGGA
1 AAAATGGTAATTTTTTGACA-TTCGAGGGT--AAAATGGTAATTTTTGGAAGTTCGAGGGT
4428520 AAAA
1 AAAA
4428524 GTGCTATTTT
Statistics
Matches: 322, Mismatches: 59, Indels: 62
0.73 0.13 0.14
Matches are distributed among these distances:
56 7 0.02
57 38 0.12
58 131 0.41
59 125 0.39
60 21 0.07
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGGTAATTTTTTGACATTCGAGGGTAAAATGGTAATTTTTGGAAGTTCGAGGGT
Found at i:4428196 original size:29 final size:29
Alignment explanation
Indices: 4428078--4428699 Score: 263
Period size: 29 Copynumber: 21.3 Consensus size: 29
4428068 CGACTTCGAT
* * ****
4428078 GGGTAAAACGGTAATTTTTGGACACACAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
* * * **
4428107 GGGTAAAATGGTAATTTTTTGACACTCGA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
* * *
4428136 GGGTAAAATGGTTATTTTTGG-ATGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAAGTT-TA
*
4428165 GGGTAAAATGATAATTTTTGGAAAGTTTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
*
4428194 GGGTCAAAATGGTAA-TTTTGAAAAGTTTA
1 GGGT-AAAATGGTAATTTTTGGAAAGTTTA
* *
4428223 GGGTTAAAAAT-GTAATTTTTTGACA-TTTA
1 GGG-T-AAAATGGTAATTTTTGGAAAGTTTA
* * *
4428252 GGGGTAAAATGGTAATTTTTAG-ATGTTTGG
1 -GGGTAAAATGGTAATTTTTGGAAAGTTT-A
* * * *
4428282 GGGTAAAATGGTAATTTTT-GCATGGTTC
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
* **
4428310 GAGGTCAAAAAT-GTAATTTTTAGAAA-TCCGA
1 G-GGT--AAAATGGTAATTTTTGGAAAGT-TTA
* * **
4428341 AGGTAAAATGGTAATTTTT--AATGTTCGG
1 GGGTAAAATGGTAATTTTTGGAAAGTT-TA
*
4428369 GGGTAAAATGGTAATTTTTGGAAAG-TTC
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
* * *
4428397 GAGGTCAAAAAT-ATAATTTTTGGACA-TCTA
1 G-GGT--AAAATGGTAATTTTTGGAAAGTTTA
* * * *
4428427 GTGGTAAAAAGGTAATTTTTAG-ATGTTCAA
1 G-GGTAAAATGGTAATTTTTGGAAAGTT-TA
*
4428457 GGGTAAAATGGTAATTTTTGGAAAGTTTG
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
*
4428486 GGGTCAAAAATGGTAA-TTTTGG-AAGTTCGA
1 GGGT--AAAATGGTAATTTTTGGAAAGTT-TA
* * * *
4428516 GGGAAAAAGTGCT-A-TTTTGGAAAGGTCTG
1 GGGTAAAA-TGGTAATTTTTGGAAA-GTTTA
* *
4428545 GGGTTAAAACGGTAA-TTTTGG-AAGTTCA
1 GGG-TAAAATGGTAATTTTTGGAAAGTTTA
* *
4428573 GGGGCAAAA-GTGTAA-TTTTGGAAAGGTTCGA
1 -GGGTAAAATG-GTAATTTTTGGAAA-GTT-TA
* * *
4428604 GGATAAAATGATAA-TTTT-GTAAGTTTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTA
*
4428631 GGGGTAAAAAT-GTAATTTTTGTG-AAGTTTG
1 -GGGT-AAAATGGTAATTTTTG-GAAAGTTTA
* * *
4428661 GGGTCAAAAT-GTAATTTTTTGTAAGTTCA
1 GGGT-AAAATGGTAATTTTTGGAAAGTTTA
4428690 GGGTCAAAAT
1 GGGT-AAAAT
4428700 ATTTATTCTG
Statistics
Matches: 461, Mismatches: 84, Indels: 96
0.72 0.13 0.15
Matches are distributed among these distances:
27 4 0.01
28 75 0.16
29 247 0.54
30 110 0.24
31 25 0.05
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTTA
Found at i:4428348 original size:117 final size:117
Alignment explanation
Indices: 4428105--4428523 Score: 287
Period size: 117 Copynumber: 3.6 Consensus size: 117
4428095 TTGGACACAC
* * * * *
4428105 AAGGGTAAAATGGTAATTTTTTGACA-CTCGAGGGTAAAATGGTTATTTTTGGATGTTCGAGGGT
1 AAGGTTAAAATGGTAATTTTTTGACATTTAG-GGGTAAAATGGTAATTTTTAGATGTTCGAGGGT
* * **
4428169 AAAATGATAATTTTTGGAAAGTTTAGGGTCAAAATGGTAATTTTGAAAAGTTT
65 AAAATGATAATTTTTGCAAAGTTGAGGGTCAAAATGGTAATTTTGAAAAGTCG
* * *
4428222 AGGGTTAAAAAT-GTAATTTTTTGACATTTAGGGGTAAAATGGTAATTTTTAGATGTTTGGGGGT
1 AAGGTT-AAAATGGTAATTTTTTGACATTTAGGGGTAAAATGGTAATTTTTAGATGTTCGAGGGT
* ** *
4428286 AAAATGGTAATTTTTGCATGGTTCGA-GGTCAAAAAT-GTAATTTTTAGAAA-TCCG
65 AAAATGATAATTTTTGCAAAGTT-GAGGGTC-AAAATGGTAATTTTGA-AAAGT-CG
* * *
4428340 AAGG-TAAAATGGTAA-TTTTT-A-ATGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGA-G
1 AAGGTTAAAATGGTAATTTTTTGACAT-TT-AGGGGTAAAATGGTAATTTTTAG-ATGTTCGAGG
* * * * * *
4428400 GTCAAAAAT-ATAATTTTTGGACA-TCT-AGTGGT-AAAAAGGTAATTTTTAGATGTTC-
63 GT--AAAATGATAATTTTTGCAAAGT-TGAG-GGTCAAAATGGTAATTTTGAAAAG-TCG
* * * * *
4428455 AAGGGTAAAATGGTAATTTTTGGAAAGTTT-GGGGTCAAAAATGGTAA-TTTTGGAAGTTCGAGG
1 AAGGTTAAAATGGTAATTTTTTGACA-TTTAGGGGT--AAAATGGTAATTTTTAGATGTTCGAGG
*
4428518 GAAAAA
63 GTAAAA
4428524 GTGCTATTTT
Statistics
Matches: 245, Mismatches: 31, Indels: 53
0.74 0.09 0.16
Matches are distributed among these distances:
114 2 0.01
115 13 0.05
116 61 0.25
117 122 0.50
118 33 0.13
119 13 0.05
120 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (117 bp):
AAGGTTAAAATGGTAATTTTTTGACATTTAGGGGTAAAATGGTAATTTTTAGATGTTCGAGGGTA
AAATGATAATTTTTGCAAAGTTGAGGGTCAAAATGGTAATTTTGAAAAGTCG
Found at i:4428374 original size:87 final size:88
Alignment explanation
Indices: 4428194--4428505 Score: 362
Period size: 88 Copynumber: 3.5 Consensus size: 88
4428184 GGAAAGTTTA
* * * * * ** *
4428194 GGGTCAAAATGGTAA-TTTTGAAAAGTT-TAGGGTTAAAAATGTAATTTTTTGACATTTAGGGGT
1 GGGT-AAAATGGTAATTTTTGGAAAGTTCGA-GGTCAAAAATGTAATTTTTAGAAATCGAGAGGT
*
4428257 AAAATGGTAATTTTTAGATGTTTGG
64 AAAATGGTAATTTTTAGATGTTCGG
* **
4428282 GGGTAAAATGGTAATTTTTGCATGGTTCGAGGTCAAAAATGTAATTTTTAGAAATCCGA-AGGTA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTAGAAAT-CGAGAGGTA
4428346 AAATGGTAATTTTTA-ATGTTCGG
65 AAATGGTAATTTTTAGATGTTCGG
* * * * *
4428369 GGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATATAATTTTTGGACATCTAGTGGTAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTAGAAATCGAGAGGTAA
* **
4428434 AAAGGTAATTTTTAGATGTTCAA
66 AATGGTAATTTTTAGATGTTCGG
* *
4428457 GGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAAT-GTAATTTT
4428506 GGAAGTTCGA
Statistics
Matches: 193, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
86 2 0.01
87 84 0.44
88 98 0.51
89 9 0.05
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (88 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTAGAAATCGAGAGGTAA
AATGGTAATTTTTAGATGTTCGG
Found at i:4430570 original size:35 final size:35
Alignment explanation
Indices: 4430530--4430596 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
4430520 TTTTTAATTA
4430530 AAAAATAAATTTAAATTCAAAATAAATTTAAACTC
1 AAAAATAAATTTAAATTCAAAATAAATTTAAACTC
* * *
4430565 AAAAATGAGTTTAAATTTAAAATAAATTTAAA
1 AAAAATAAATTTAAATTCAAAATAAATTTAAA
4430597 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (35 bp):
AAAAATAAATTTAAATTCAAAATAAATTTAAACTC
Found at i:4430598 original size:18 final size:17
Alignment explanation
Indices: 4430531--4430605 Score: 87
Period size: 17 Copynumber: 4.3 Consensus size: 17
4430521 TTTTAATTAA
*
4430531 AAAATAAATTTAAATTC
1 AAAATAAATTTAAATTT
**
4430548 AAAATAAATTTAAACTCA
1 AAAATAAATTTAAA-TTT
* *
4430566 AAAATGAGTTTAAATTT
1 AAAATAAATTTAAATTT
4430583 AAAATAAATTTAAAATTT
1 AAAATAAATTT-AAATTT
4430601 AAAAT
1 AAAAT
4430606 TTAAAGATTG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
17 24 0.50
18 24 0.50
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATAAATTTAAATTT
Found at i:4435083 original size:23 final size:22
Alignment explanation
Indices: 4435044--4435086 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4435034 AAATTAAATA
*
4435044 AAATATAAAATATATAATTACT
1 AAATATAAAATAAATAATTACT
*
4435066 AAATATTAAATAAAATAATTA
1 AAATATAAAAT-AAATAATTA
4435087 TATCTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATAAAATAAATAATTACT
Found at i:4435422 original size:19 final size:20
Alignment explanation
Indices: 4435394--4435432 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4435384 TTTGCCACAA
*
4435394 TTTTCATTTTATGCAATTAT
1 TTTTCATTTTATACAATTAT
4435414 TTTTC-TTTTATACAATTAT
1 TTTTCATTTTATACAATTAT
4435433 AAGCAGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTCATTTTATACAATTAT
Found at i:4436444 original size:14 final size:14
Alignment explanation
Indices: 4436425--4436455 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4436415 CAAGACTGCC
4436425 TGTTTCTTCAATCG
1 TGTTTCTTCAATCG
4436439 TGTTTCTTCAATCG
1 TGTTTCTTCAATCG
4436453 TGT
1 TGT
4436456 CCTTTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (14 bp):
TGTTTCTTCAATCG
Found at i:4436878 original size:2 final size:2
Alignment explanation
Indices: 4436871--4436927 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
4436861 ATTAAATGTG
4436871 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
4436913 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
4436928 AATCTAAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4437015 original size:21 final size:22
Alignment explanation
Indices: 4436974--4437016 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4436964 ATTTTATTTA
4436974 AAACTCAATCTAAAATAAAAAT
1 AAACTCAATCTAAAATAAAAAT
* *
4436996 AAACTCATTC-AAAATTAAAAT
1 AAACTCAATCTAAAATAAAAAT
4437017 TTTATAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (22 bp):
AAACTCAATCTAAAATAAAAAT
Found at i:4443059 original size:49 final size:50
Alignment explanation
Indices: 4442976--4443109 Score: 159
Period size: 49 Copynumber: 2.7 Consensus size: 50
4442966 ATCACATTAC
* * * *
4442976 AACTCA-GACTCCTAATTCACAGTGGTTATACAGTCACAGGTTGAAGTAT
1 AACTCAGGACTCCTAGTTGACAGTGGTTATGCAGTCACAAGTTGAAGTAT
*
4443025 AACT-AGGACTCCTAGTTGACAGTGGTTATGCAGTCACAAGTTGGAGTAT
1 AACTCAGGACTCCTAGTTGACAGTGGTTATGCAGTCACAAGTTGAAGTAT
* * *
4443074 AACTCGGGAAC-CC-AGTTGACAGTAGTTATGCGGTCA
1 AACTCAGG-ACTCCTAGTTGACAGTGGTTATGCAGTCA
4443110 GGGTTCAAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
48 1 0.01
49 67 0.91
50 4 0.05
51 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (50 bp):
AACTCAGGACTCCTAGTTGACAGTGGTTATGCAGTCACAAGTTGAAGTAT
Found at i:4450743 original size:12 final size:12
Alignment explanation
Indices: 4450726--4450766 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
4450716 TCATTATTAA
4450726 ATTTATTCTAAT
1 ATTTATTCTAAT
**
4450738 ATTTATAATAA-
1 ATTTATTCTAAT
4450749 ATTTATTCTAAT
1 ATTTATTCTAAT
4450761 ATTTAT
1 ATTTAT
4450767 AATAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATTCTAAT
Found at i:4450754 original size:11 final size:11
Alignment explanation
Indices: 4450723--4450777 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
4450713 CTTTCATTAT
**
4450723 TAAATTTATTC
1 TAAATTTATAA
4450734 TAATATTTATAA
1 TAA-ATTTATAA
**
4450746 TAAATTTATTC
1 TAAATTTATAA
4450757 TAATATTTATAA
1 TAA-ATTTATAA
4450769 TAAATTTAT
1 TAAATTTAT
4450778 TAAACTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 18 0.50
12 18 0.50
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAATTTATAA
Found at i:4450791 original size:23 final size:23
Alignment explanation
Indices: 4450723--4450778 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
4450713 CTTTCATTAT
4450723 TAAATTTATTCTAATATTTATAA
1 TAAATTTATTCTAATATTTATAA
4450746 TAAATTTATTCTAATATTTATAA
1 TAAATTTATTCTAATATTTATAA
4450769 TAAATTTATT
1 TAAATTTATT
4450779 AAACTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TAAATTTATTCTAATATTTATAA
Found at i:4452764 original size:15 final size:15
Alignment explanation
Indices: 4452744--4452775 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4452734 CAATTTCCAT
4452744 ACCATCCCATTTGCA
1 ACCATCCCATTTGCA
4452759 ACCATCCCATTTGCA
1 ACCATCCCATTTGCA
4452774 AC
1 AC
4452776 TATCAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.41, G:0.06, T:0.25
Consensus pattern (15 bp):
ACCATCCCATTTGCA
Found at i:4460944 original size:16 final size:16
Alignment explanation
Indices: 4460921--4460976 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
4460911 CGTTTGGTCT
4460921 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
4460937 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
4460953 GCTGTAATGGAATAGG
1 GCTGTAATGGAATAGA
4460969 GCTGTAAT
1 GCTGTAAT
4460977 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:4461210 original size:58 final size:58
Alignment explanation
Indices: 4461148--4461292 Score: 188
Period size: 57 Copynumber: 2.5 Consensus size: 58
4461138 TTTTAATAAG
* *
4461148 ATTATTATTAAATATAATTTAATAAAAATAATA-ATTAATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATAACATTTTAACATA
* * *
4461206 ATTATTATTAAATACAATATAAT-AAAATAATATATAATTTAATAACATTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTTTAACATA
*
4461263 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
4461293 TTTAATATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
57 38 0.51
58 30 0.40
59 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTTTAACATA
Found at i:4461264 original size:57 final size:58
Alignment explanation
Indices: 4461137--4461274 Score: 192
Period size: 57 Copynumber: 2.4 Consensus size: 58
4461127 TTGTTATTAA
* * * *
4461137 ATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAATTAATTTAATTAT
1 ATTTTAATATA-ATTATTATTAAATACAATATAATAAAAATAATAATTAATTTAATAAC
*
4461195 ATTTTAACATAATTATTATTAAATACAATATAAT-AAAATAAT-ATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATACAATATAATAAAAATAATAAT-TAATTTAATAAC
4461252 ATTTTAATATAATTATTATTAAA
1 ATTTTAATATAATTATTATTAAA
4461275 ATATGAATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
56 2 0.03
57 40 0.56
58 29 0.40
59 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATACAATATAATAAAAATAATAATTAATTTAATAAC
Found at i:4461297 original size:24 final size:24
Alignment explanation
Indices: 4461270--4461316 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4461260 ATAATTATTA
*
4461270 TTAAAATATGA-ATTAGTAAAAATT
1 TTAAAATATAATATTAG-AAAAATT
*
4461294 TTAATATATAATATTAGAAAAAT
1 TTAAAATATAATATTAGAAAAAT
4461317 AATATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
TTAAAATATAATATTAGAAAAATT
Found at i:4461306 original size:57 final size:54
Alignment explanation
Indices: 4461137--4461306 Score: 155
Period size: 58 Copynumber: 3.0 Consensus size: 54
4461127 TTGTTATTAA
* * *
4461137 ATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAATTAATTTAATTAT
1 ATTTTAATATA-ATTATTATTAAATATAA-TTAATAAAAATTATAA-T-A-TTAATAAC
* *
4461195 ATTTTAACATAATTATTATTAAATACAATATAATAAAATAATATATAAT-TTAATAAC
1 ATTTTAATATAATTATTATTAAATATAAT-TAAT-AAA-AAT-TATAATATTAATAAC
* *
4461252 ATTTTAATATAATTATTATTAAAATATGAATTAGTAAAAATTTTAATATATAATA
1 ATTTTAATATAATTATTATT-AAATAT-AATTAATAAAAATTATAATAT-TAATA
4461307 TTAGAAAAAT
Statistics
Matches: 94, Mismatches: 9, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
55 5 0.05
56 4 0.04
57 34 0.36
58 36 0.38
59 7 0.07
60 4 0.04
61 4 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (54 bp):
ATTTTAATATAATTATTATTAAATATAATTAATAAAAATTATAATATTAATAAC
Found at i:4470680 original size:21 final size:19
Alignment explanation
Indices: 4470652--4470698 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 19
4470642 ATGGTCATCC
4470652 AAATTAAAAAATATTTTTAA
1 AAATT-AAAAATATTTTTAA
4470672 AAATGTAAAAATATTTTTAA
1 AAAT-TAAAAATATTTTTAA
4470692 AATATTA
1 AA-ATTA
4470699 TATAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAATTAAAAATATTTTTAA
Found at i:4488322 original size:21 final size:21
Alignment explanation
Indices: 4488298--4488352 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
4488288 TTTGCACTAG
4488298 TTCTACCGATACAAGTAAGAT
1 TTCTACCGATACAAGTAAGAT
4488319 TTCTACCGATACAAGTAAGAT
1 TTCTACCGATACAAGTAAGAT
4488340 TTCTACCGATACA
1 TTCTACCGATACA
4488353 TGTTATACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAAGTAAGAT
Found at i:4489087 original size:11 final size:11
Alignment explanation
Indices: 4489071--4489177 Score: 123
Period size: 11 Copynumber: 9.7 Consensus size: 11
4489061 TACTTTGAAA
*
4489071 TTAAATTTATT
1 TTAAATTTAAT
4489082 TTAAATTTTAAT
1 TTAAA-TTTAAT
4489094 TT-AATTTAAT
1 TTAAATTTAAT
4489104 TTAAATTT-AT
1 TTAAATTTAAT
4489114 TTAAATTTAAT
1 TTAAATTTAAT
*
4489125 TTAAGTTTGAAT
1 TTAAATTT-AAT
4489137 TT-AATTTAAAT
1 TTAAATTT-AAT
4489148 TT-AATTTAAGT
1 TTAAATTTAA-T
*
4489159 TTGAATTTAAT
1 TTAAATTTAAT
4489170 TTAAATTT
1 TTAAATTT
4489178 GATATTATTT
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
10 20 0.24
11 46 0.54
12 19 0.22
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:4489088 original size:28 final size:28
Alignment explanation
Indices: 4489085--4489177 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 28
4489075 ATTTATTTTA
* *
4489085 AATTTTAATTTAATTTAA-TTTAAATTT
1 AATTTAAATTTAATTTAAGATTAAATTT
* *
4489112 -ATTTAAATTTAATTTAAGTTTGAATTT
1 AATTTAAATTTAATTTAAGATTAAATTT
* *
4489139 AATTTAAATTTAATTTAAGTTTGAATTT
1 AATTTAAATTTAATTTAAGATTAAATTT
4489167 AATTTAAATTT
1 AATTTAAATTT
4489178 GATATTATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
26 16 0.26
27 8 0.13
28 38 0.61
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
AATTTAAATTTAATTTAAGATTAAATTT
Found at i:4489096 original size:5 final size:5
Alignment explanation
Indices: 4489069--4489173 Score: 104
Period size: 5 Copynumber: 19.4 Consensus size: 5
4489059 TTTACTTTGA
* *
4489069 AATTA AATTT ATTTT AAATTTT AATTT AATTT AATTT AAATTT -ATTT
1 AATTT AATTT AATTT -AA-TTT AATTT AATTT AATTT -AATTT AATTT
4489116 AAATTT AATTT AAGTTT GAATTT AATTT AAATTT AATTT AAGTTT GAATTT
1 -AATTT AATTT AA-TTT -AATTT AATTT -AATTT AATTT AA-TTT -AATTT
4489167 AATTT AA
1 AATTT AA
4489174 ATTTGATATT
Statistics
Matches: 87, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
4 4 0.05
5 47 0.54
6 29 0.33
7 7 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:4489430 original size:28 final size:28
Alignment explanation
Indices: 4489377--4489430 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
4489367 GCAGACCACT
* * *
4489377 ATCTCCACTTGCTTCTGCCACGGCCATC
1 ATCTCCACCTGCTGCTGCCACCGCCATC
4489405 ATCTCCACCTGCTGCT-CCAACCGCCA
1 ATCTCCACCTGCTGCTGCC-ACCGCCA
4489431 CTGTGGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.17, C:0.46, G:0.13, T:0.24
Consensus pattern (28 bp):
ATCTCCACCTGCTGCTGCCACCGCCATC
Found at i:4490000 original size:30 final size:29
Alignment explanation
Indices: 4489926--4490036 Score: 116
Period size: 29 Copynumber: 3.8 Consensus size: 29
4489916 CCCTAAACAG
* *
4489926 TCCAAAAATTACATTTTGACCTCAAAACT
1 TCCAAAAATTACATTTTAACCCCAAAACT
**
4489955 TTAAAAAATTACATTTTAACCCCAAAACT
1 TCCAAAAATTACATTTTAACCCCAAAACT
*
4489984 TCCAAAAATTACCATTTT-ACCCCTAAACT
1 TCCAAAAATTA-CATTTTAACCCCAAAACT
*** *
4490013 TTTTAAAATTCCATTTTTAACCCC
1 TCCAAAAATTACA-TTTTAACCCC
4490037 GATTTCACCA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.03
29 55 0.81
30 11 0.16
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTACATTTTAACCCCAAAACT
Found at i:4490021 original size:58 final size:57
Alignment explanation
Indices: 4489926--4490343 Score: 321
Period size: 58 Copynumber: 7.2 Consensus size: 57
4489916 CCCTAAACAG
* * ** * * *
4489926 TCCAAAAATTA-CATTTTGACCTCAAAACTTTAAAAAATTACA-TTTTAACCCCAAAACT
1 TCCAAAAATTACCATTTT-ACCCCTAAACTTTCTAAAATTCCATTTTTAACCCC--GATT
*
4489984 TCCAAAAATTACCATTTTACCCCTAAACTTTTTAAAATTCCATTTTTAACCCCGATT
1 TCCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATT
* * * * * * *
4490041 TCACCAAAAATTACCGTTTTA-CACTCGAAC-TTCCAAAATTTCATTTTTGACCTCGATT
1 T--CCAAAAATTACCATTTTACCCCT-AAACTTTCTAAAATTCCATTTTTAACCCCGATT
* * *
4490099 TCACCAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCA-TTTTAACCCCAATT
1 TC-CAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATT
* ** ** * *
4490156 TCACCTAAAATTACTGTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAATCCCGATT
1 T--CCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATT
* * * *
4490215 TCACCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGGTTT
1 T--CCAAAAATTACCATTTTACCCCT-AAACTTTCTAAAATTCCATTTTTAACC-CCGATT
* * * *
4490275 TACCAAAAATTACCATTTTACCCCGAACCATTC-AAAA-TCTCATTTTTAATCCCGAATTT
1 T-CCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTC-CATTTTTAACCCCG-A-TT
*
4490334 TCCCAAAATT
1 TCCAAAAATT
4490344 CATTTTGCCC
Statistics
Matches: 296, Mismatches: 47, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
56 1 0.00
57 37 0.12
58 130 0.44
59 120 0.41
60 8 0.03
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATT
Found at i:4490048 original size:59 final size:59
Alignment explanation
Indices: 4489985--4490329 Score: 400
Period size: 59 Copynumber: 5.9 Consensus size: 59
4489975 CCCAAAACTT
* **
4489985 CCAAAAATTACCATTTTACCCCTAAACTTTTTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
4490044 CCAAAAATTACCGTTTTA-CACTCGAAC-TTCCAAAATTTCATTTTTGACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
** * *
4490102 CC-AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCA-TTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* ** * *
4490159 CCTAAAATTACTGTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAATCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
4490218 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGGTTTTA
1 CCAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
4490277 CCAAAAATTACCATTTTACCCC-GAACCATT-CAAAA-TCTCATTTTTAATCCCGA
1 CCAAAAATTACCATTTTACCCCTGAA-CTTTCCAAAATTC-CATTTTTAACCCCGA
4490330 ATTTTCCCAA
Statistics
Matches: 242, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
57 35 0.14
58 101 0.42
59 103 0.43
60 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:4490049 original size:29 final size:28
Alignment explanation
Indices: 4490017--4490300 Score: 135
Period size: 29 Copynumber: 9.8 Consensus size: 28
4490007 TAAACTTTTT
4490017 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
* * *
4490046 AAAAATTACC-GTTTT-ACACTCGAACTT-CC
1 -AAAATT-CCATTTTTAAC-CCCG-ATTTACC
* * *
4490075 AAAATTTCATTTTTGACCTCGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
* * *
4490104 AAAATTACCA-TTTTACCCCCAAACTTT-CT
1 AAAATT-CCATTTTTAACCCC-GA-TTTACC
*
4490133 AAAATTCCA-TTTTAACCCCAATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
* *
4490161 TAAAATTAC-TGTTTTACCCCCGAACTTT-CC
1 -AAAATTCCAT-TTTTAACCCCG-A-TTTACC
*
4490191 AAAATTCCATTTTTAATCCCGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
4490220 AAAAATTACCA-TTTT-ACCCTCGAACTTT-CC
1 -AAAATT-CCATTTTTAACCC-CG-A-TTTACC
* *
4490250 AAAATTCCATTTTTAACCTCGGTTTTACC
1 AAAATTCCATTTTTAACC-CCGATTTACC
4490279 AAAAATTACCA-TTTT-ACCCCGA
1 -AAAATT-CCATTTTTAACCCCGA
4490301 ACCATTCAAA
Statistics
Matches: 198, Mismatches: 25, Indels: 64
0.69 0.09 0.22
Matches are distributed among these distances:
26 3 0.02
27 9 0.05
28 36 0.18
29 71 0.36
30 56 0.28
31 17 0.09
32 6 0.03
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTTAACCCCGATTTACC
Done.