Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 15 of 402
Found at i:3465509 original size:11 final size:12
Alignment explanation
Indices: 3465495--3465531 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
3465485 TTATTTTAAT
3465495 ATAAATATA-AA
1 ATAAATATATAA
3465506 ATAAAT-TATAA
1 ATAAATATATAA
3465517 ATAAATATATAA
1 ATAAATATATAA
3465529 ATA
1 ATA
3465532 TGAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 14 0.58
12 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATATATAA
Found at i:3465516 original size:7 final size:6
Alignment explanation
Indices: 3465492--3465560 Score: 65
Period size: 6 Copynumber: 11.5 Consensus size: 6
3465482 ATATTATTTT
3465492 AATATA AATATA AA-ATA AATTATA AATA-A ATATATA AATATGA AAT-TA
1 AATATA AATATA AATATA AA-TATA AATATA A-ATATA AATAT-A AATATA
*
3465540 AATAATT AAT-TA AATATA AAT
1 AAT-ATA AATATA AATATA AAT
3465561 TTATATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
5 15 0.28
6 23 0.43
7 15 0.28
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:3465517 original size:12 final size:12
Alignment explanation
Indices: 3465471--3465561 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 12
3465461 ATTTAATTTA
3465471 AAATTAATAAAAT
1 AAATT-ATAAAAT
* * *
3465484 ATTATTTTAATAT
1 A-AATTATAAAAT
3465497 AAA-TATAAAAT
1 AAATTATAAAAT
3465508 AAATTAT-AAAT
1 AAATTATAAAAT
3465519 AAATATATAAATAT
1 AAAT-TATAAA-AT
3465533 GAAATTA-AATAAT
1 -AAATTATAA-AAT
* *
3465546 TAATTA-AATAT
1 AAATTATAAAAT
3465557 AAATT
1 AAATT
3465562 TATATATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
11 23 0.37
12 14 0.23
13 13 0.21
14 8 0.13
15 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (12 bp):
AAATTATAAAAT
Found at i:3465558 original size:30 final size:29
Alignment explanation
Indices: 3465492--3465560 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
3465482 ATATTATTTT
*
3465492 AATATAAATATAAAATAAATTATAAATAA
1 AATATAAATATAAAATAAATAATAAATAA
* * *
3465521 ATATATAAATATGAAATTAAATAATTAATTA
1 A-ATATAAATAT-AAAATAAATAATAAATAA
3465552 AATATAAAT
1 AATATAAAT
3465561 TTATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.03
30 18 0.53
31 15 0.44
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (29 bp):
AATATAAATATAAAATAAATAATAAATAA
Found at i:3467080 original size:10 final size:10
Alignment explanation
Indices: 3467067--3467092 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3467057 TTTTTATATA
3467067 TTAATCGAGC
1 TTAATCGAGC
3467077 TTAATCGAGC
1 TTAATCGAGC
3467087 TTAATC
1 TTAATC
3467093 AAGCGAGCTC
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:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (10 bp):
TTAATCGAGC
Found at i:3467915 original size:20 final size:20
Alignment explanation
Indices: 3467878--3467950 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
3467868 TGTAGACACC
*
3467878 CAATTGGGTCTGGACCCGGAT
1 CAATTGGGCCT-GACCCGGAT
3467899 CAATTGGGCCTGACCCGGAT
1 CAATTGGGCCTGACCCGGAT
*
3467919 CAATTGGGCCTGACCCAGAT
1 CAATTGGGCCTGACCCGGAT
*
3467939 CATTTGGGCCTG
1 CAATTGGGCCTG
3467951 GCCCAAATGG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 39 0.80
21 10 0.20
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.23
Consensus pattern (20 bp):
CAATTGGGCCTGACCCGGAT
Found at i:3468011 original size:10 final size:10
Alignment explanation
Indices: 3467996--3468020 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3467986 GTATTTTTTA
3467996 TTTTTTATTT
1 TTTTTTATTT
3468006 TTTTTTATTT
1 TTTTTTATTT
3468016 TTTTT
1 TTTTT
3468021 CTCTCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:3468268 original size:11 final size:12
Alignment explanation
Indices: 3468247--3468280 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3468237 AATTATCTAG
*
3468247 ATTTTTTTTTTA
1 ATTTTTATTTTA
3468259 A-TTTTATTTTA
1 ATTTTTATTTTA
3468270 ATTTTTATTTT
1 ATTTTTATTTT
3468281 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:3468665 original size:31 final size:31
Alignment explanation
Indices: 3468596--3468668 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
3468586 AATTTCCAGA
* * *
3468596 TTCCGGCAAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
3468627 TTCCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
3468658 TTCCGGCGACA
1 TTCCGGCGACA
3468669 GACCCAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:3468762 original size:19 final size:19
Alignment explanation
Indices: 3468720--3468763 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3468710 CCGGCCAATT
* *
3468720 TCCGACGAAATTCCCAGAT
1 TCCGGCGAAATTCCCAGAA
*
3468739 TCCGGCGAAATTTCCAGAA
1 TCCGGCGAAATTCCCAGAA
3468758 TCCGGC
1 TCCGGC
3468764 ACCGACGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (19 bp):
TCCGGCGAAATTCCCAGAA
Found at i:3468993 original size:5 final size:5
Alignment explanation
Indices: 3468983--3469037 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
3468973 TTCAGCCCCT
* *
3468983 CCGAG CCGAG CTGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCGCGAG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG -C-CGAG
3469030 CCGAG CCG
1 CCGAG CCG
3469038 CTCCAGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 1 0.02
5 34 0.81
6 3 0.07
7 4 0.10
ACGTcount: A:0.20, C:0.42, G:0.36, T:0.02
Consensus pattern (5 bp):
CCGAG
Found at i:3469085 original size:17 final size:17
Alignment explanation
Indices: 3469056--3469114 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
3469046 TTTTTTTTTA
*
3469056 TTTTTTATT-TTTGAAT
1 TTTTTTTTTATTTGAAT
*
3469072 TTTTTTTTTATTTGACT
1 TTTTTTTTTATTTGAAT
** *
3469089 TTGATTTTGATCTTG-AT
1 TTTTTTTTTAT-TTGAAT
3469106 TTTTTTTTT
1 TTTTTTTTT
3469115 CCTTTTTTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
16 8 0.25
17 21 0.66
18 3 0.09
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (17 bp):
TTTTTTTTTATTTGAAT
Found at i:3469740 original size:156 final size:157
Alignment explanation
Indices: 3469118--3469722 Score: 1025
Period size: 157 Copynumber: 3.8 Consensus size: 157
3469108 TTTTTTTCCT
*
3469118 TTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
3469183 CCTGAGGTGAGGGAGTTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
3469248 GATAATTAATTAATTGGTTGATCTTGA
131 GATAATTAATTAATTGGTTGATCTTGA
*
3469275 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAATAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
3469340 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTCC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
* * *
3469405 GATAATTAATTACTTGGCTGATTTTGA
131 GATAATTAATTAATTGGTTGATCTTGA
* * *
3469432 TTTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTG
1 ------TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTG
3469496 CATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATA
60 CATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATA
3469561 ATTTTCGATAATTAATTAATTGGTTGATCTTGA
125 ATTTTCGATAATTAATTAATTGGTTGATCTTGA
* *
3469594 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
3469658 CTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
3469723 AACAACTAAC
Statistics
Matches: 425, Mismatches: 17, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
156 127 0.30
157 150 0.35
162 111 0.26
163 37 0.09
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (157 bp):
TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
GATAATTAATTAATTGGTTGATCTTGA
Found at i:3472973 original size:1 final size:1
Alignment explanation
Indices: 3472969--3472998 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3472959 GTAATTTTTG
3472969 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3472999 CCACAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3473428 original size:8 final size:7
Alignment explanation
Indices: 3473405--3473455 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 7
3473395 AAAGATGATG
3473405 AAAA-AA
1 AAAAGAA
3473411 AAAAGAAA
1 AAAAG-AA
3473419 AGAAAGAA
1 A-AAAGAA
*
3473427 AGAAGAA
1 AAAAGAA
3473434 AAAATGAA
1 AAAA-GAA
3473442 AAAATGAA
1 AAAA-GAA
3473450 AAAAGA
1 AAAAGA
3473456 GATCCAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
6 4 0.10
7 10 0.26
8 21 0.54
9 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:3473450 original size:23 final size:24
Alignment explanation
Indices: 3473408--3473455 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3473398 GATGATGAAA
*
3473408 AAAAAAAGAAAAGAAAGAAAGAAG
1 AAAAAAAGAAAAGAAAGAAAAAAG
* *
3473432 AAAAAATGAAAA-AATGAAAAAAG
1 AAAAAAAGAAAAGAAAGAAAAAAG
3473455 A
1 A
3473456 GATCCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAAAAGAAAAGAAAGAAAAAAG
Found at i:3474816 original size:40 final size:40
Alignment explanation
Indices: 3474653--3474975 Score: 392
Period size: 40 Copynumber: 7.9 Consensus size: 40
3474643 GTCTAGGAGT
3474653 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA-GAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
3474692 ATTTACTTTCCAAAG-TCGTTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCG-T--TGCCTCTGTTTAGAGGAGCA
* *
3474734 TATTTATTTTTTCAAAGTTCGTTTTGCCTCTATTTAGA-GAGCA
1 -ATTTA-CTTTTCAAAGTTCG--TTGCCTCTGTTTAGAGGAGCA
3474777 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
3474817 ATTTACTTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* * *
3474857 GTTTATTTTTCCAAAG-TCGTGGTGCCTCTG-TGAGAGGAGCA
1 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
3474898 ATTTACTTTTCAAAGTCCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
3474938 A-TTAC-TTTCAAAAG-TCGTTGCAGTCTCTGTTTAGAGGA
1 ATTTACTTTTC-AAAGTTCGTTGC---CTCTGTTTAGAGGA
3474976 CTTCGGCCAA
Statistics
Matches: 250, Mismatches: 16, Indels: 34
0.83 0.05 0.11
Matches are distributed among these distances:
38 13 0.05
39 45 0.18
40 72 0.29
41 66 0.26
42 18 0.07
43 10 0.04
44 21 0.08
45 3 0.01
46 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (40 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:3474873 original size:81 final size:79
Alignment explanation
Indices: 3474653--3474975 Score: 411
Period size: 81 Copynumber: 4.0 Consensus size: 79
3474643 GTCTAGGAGT
3474653 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGAGCAATTTACTTTCCAAAGTCGTTGGTGCC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGAGCAATTTACTTTCCAAAGTCG-T-GTGCC
3474718 TCTGTTTAGAGGAGCA
64 TCTGTTTAGAGGAGCA
* * *
3474734 TATTTATTTTTTCAAAGTTCGTTTTGCCTCTATTTAGAGAGCAATTTACTTTTCAAAGTTCGT-T
1 -ATTTA-CTTTTCAAAGTTCG--TTGCCTCTGTTTAGAGAGCAATTTACTTTCCAAAG-TCGTGT
3474798 GCCTCTGTTTAGAGGAGCA
61 GCCTCTGTTTAGAGGAGCA
* * *
3474817 ATTTACTTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAGTTTATTTTTCCAAAGTCGTGGTGC
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA-GAGCAATTTA-CTTTCCAAAGTCGT-GTGC
*
3474882 CTCTG-TGAGAGGAGCA
63 CTCTGTTTAGAGGAGCA
* *
3474898 ATTTACTTTTCAAAGTCCGTTGCCTCTGTTTAGAGGAGCAA-TTACTTTCAAAAGTCGT-TGCAG
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA-GAGCAATTTACTTTCCAAAGTCGTGTGC--
3474961 TCTCTGTTTAGAGGA
63 -CTCTGTTTAGAGGA
3474976 CTTCGGCCAA
Statistics
Matches: 213, Mismatches: 16, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
77 3 0.01
79 26 0.12
80 21 0.10
81 75 0.35
82 18 0.08
83 33 0.15
85 34 0.16
86 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (79 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGAGCAATTTACTTTCCAAAGTCGTGTGCCTC
TGTTTAGAGGAGCA
Found at i:3474990 original size:1 final size:1
Alignment explanation
Indices: 3474984--3475047 Score: 83
Period size: 1 Copynumber: 64.0 Consensus size: 1
3474974 GACTTCGGCC
* * ** *
3474984 AAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAACAAAAAATCAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3475048 NNNNNNNNNN
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.92, C:0.06, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:3475011 original size:19 final size:19
Alignment explanation
Indices: 3474983--3475047 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
3474973 GGACTTCGGC
3474983 CAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAA
*
3475002 AAACAAAAAAAAAAAAAAAA
1 CAA-AAAAAAAAAAAAAAAA
**
3475022 CAAAAAATCAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAA
3475041 CAAAAAA
1 CAAAAAA
3475048 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 23 0.56
20 18 0.44
ACGTcount: A:0.91, C:0.08, G:0.00, T:0.02
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAAAA
Found at i:3475018 original size:25 final size:25
Alignment explanation
Indices: 3474984--3475047 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
3474974 GACTTCGGCC
3474984 AAAAAAAAAAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAACAAA
* *
3475009 AAAAAAAAAAAAACAAAAAATCAAA
1 AAAAAAAAAAAAAAAAAAAAACAAA
*
3475034 AAAAAAACAAAAAA
1 AAAAAAAAAAAAAA
3475048 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.92, C:0.06, G:0.00, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAAAAACAAA
Found at i:3481889 original size:2 final size:2
Alignment explanation
Indices: 3481882--3481910 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3481872 ATCACATGTT
3481882 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3481911 GTTTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3484645 original size:13 final size:13
Alignment explanation
Indices: 3484627--3484652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3484617 TTAGTTAAAG
3484627 AAAAATCAAAATA
1 AAAAATCAAAATA
3484640 AAAAATCAAAATA
1 AAAAATCAAAATA
3484653 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:3484882 original size:61 final size:61
Alignment explanation
Indices: 3484689--3484913 Score: 307
Period size: 61 Copynumber: 3.7 Consensus size: 61
3484679 TTTTGCGTAG
* * * *
3484689 GGAAAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCT-CAAAAATCTTTTTTTTTTGAAAATTT-ATTTTTAA
*
3484751 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTT--TAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTTTTTGAAAATTTATTTTTAA
3484811 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
**
3484872 AAAAAATTGATACTTTCAACTTTTCC-CTAAAAGAT-TTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATCTTTTTTT
3484914 GGAAATTTTG
Statistics
Matches: 149, Mismatches: 8, Indels: 13
0.88 0.05 0.08
Matches are distributed among these distances:
59 11 0.07
60 42 0.28
61 52 0.35
62 33 0.22
63 11 0.07
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.48
Consensus pattern (61 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
Found at i:3484995 original size:16 final size:16
Alignment explanation
Indices: 3484976--3485017 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3484966 AAGTGAAAAT
3484976 AAATAAAAAAAAAACA
1 AAATAAAAAAAAAACA
* *
3484992 AAATAAAAATAAAATA
1 AAATAAAAAAAAAACA
3485008 AAGATAAAAA
1 AA-ATAAAAA
3485018 GAATGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (16 bp):
AAATAAAAAAAAAACA
Found at i:3485006 original size:11 final size:11
Alignment explanation
Indices: 3484976--3485016 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3484966 AAGTGAAAAT
*
3484976 AAATAAAAAAA
1 AAATAAAATAA
*
3484987 AAACAAAATAA
1 AAATAAAATAA
3484998 AAATAAAATAA
1 AAATAAAATAA
*
3485009 AGATAAAA
1 AAATAAAA
3485017 AGAATGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:3485069 original size:21 final size:22
Alignment explanation
Indices: 3485043--3485085 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3485033 CTAATCTAAT
* *
3485043 AAATAAAT-AAAATAAATAAAC
1 AAATAAATGAAAAAAAAAAAAC
3485064 AAATAAATGAAAAAAAAAAAAC
1 AAATAAATGAAAAAAAAAAAAC
3485086 CTGGAGCGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (22 bp):
AAATAAATGAAAAAAAAAAAAC
Found at i:3485908 original size:17 final size:17
Alignment explanation
Indices: 3485888--3485979 Score: 64
Period size: 17 Copynumber: 5.3 Consensus size: 17
3485878 CCAAAATCAA
3485888 ATAAATAAAAAAAATAG
1 ATAAATAAAAAAAATAG
* * *
3485905 ATAATTTAGAAAAGATAGG
1 ATAA-ATAAAAAAAATA-G
*
3485924 ATAAACAAAAAATAATA-
1 ATAAATAAAAAA-AATAG
* *
3485941 AT-AATAATAATAATCAG
1 ATAAATAAAAAAAAT-AG
3485958 AT-AATAAAAAAAATCAG
1 ATAAATAAAAAAAAT-AG
3485975 ATAAA
1 ATAAA
3485980 ATTAACAGAT
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
15 3 0.05
16 7 0.12
17 23 0.40
18 16 0.28
19 8 0.14
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (17 bp):
ATAAATAAAAAAAATAG
Found at i:3486038 original size:3 final size:3
Alignment explanation
Indices: 3486030--3486077 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
3486020 ATATTTAAAA
3486030 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT -AT AAT AAT ATAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
3486076 AA
1 AA
3486078 CTATATACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3486048 original size:16 final size:16
Alignment explanation
Indices: 3486029--3486077 Score: 80
Period size: 16 Copynumber: 2.9 Consensus size: 16
3486019 TATATTTAAA
3486029 AAATAATAATAATAAT
1 AAATAATAATAATAAT
3486045 AAATAATAATAATAAT
1 AAATAATAATAATAAT
3486061 AATATAATAATATATAA
1 AA-ATAATAATA-ATAA
3486078 CTATATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 18 0.58
17 9 0.29
18 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:3486097 original size:24 final size:22
Alignment explanation
Indices: 3486030--3486097 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
3486020 ATATTTAAAA
3486030 AATAATAATAATAATAAATA-AT
1 AATAATAATAAT-ATAAATATAT
3486052 AATAATAATAATAT-AATA-AT
1 AATAATAATAATATAAATATAT
3486072 ATATAACTATATACATATAAATATAT
1 A-ATAA-TA-ATA-ATATAAATATAT
3486098 TCTAAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.17
21 6 0.15
22 14 0.35
23 3 0.08
24 4 0.10
25 4 0.10
26 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAATAATAATATAAATATAT
Found at i:3486145 original size:12 final size:12
Alignment explanation
Indices: 3486128--3486160 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3486118 TATACAAACA
3486128 AGAAAAAAAAAG
1 AGAAAAAAAAAG
3486140 AG-AAAAAAAAG
1 AGAAAAAAAAAG
3486151 -GAAAAAAAAA
1 AGAAAAAAAAA
3486161 ACATACAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 17 0.85
12 2 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:3486159 original size:10 final size:11
Alignment explanation
Indices: 3486127--3486159 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
3486117 ATATACAAAC
3486127 AAGA-AAAAAA
1 AAGAGAAAAAA
3486137 AAGAGAAAAAA
1 AAGAGAAAAAA
3486148 AAG-GAAAAAA
1 AAGAGAAAAAA
3486158 AA
1 AA
3486160 AACATACAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAGAGAAAAAA
Found at i:3487689 original size:21 final size:21
Alignment explanation
Indices: 3487664--3487704 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3487654 AATCATAATA
*
3487664 ATTTAAAATTATGTAAAATCC
1 ATTTAAAATTATATAAAATCC
*
3487685 ATTTAAATTTATATAAAATC
1 ATTTAAAATTATATAAAATC
3487705 TCACGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAAAATTATATAAAATCC
Found at i:3488554 original size:4 final size:4
Alignment explanation
Indices: 3488542--3488586 Score: 72
Period size: 4 Copynumber: 11.2 Consensus size: 4
3488532 ACACACACAG
* *
3488542 ACAT TCAT ACAT ACAT ACAT ACAT ACAT ACAT AAAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3488587 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:3495526 original size:12 final size:11
Alignment explanation
Indices: 3495506--3495555 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
3495496 TTTTTAATAT
3495506 AAAAAATAAAA
1 AAAAAATAAAA
3495517 AAAAACATAAAA
1 AAAAA-ATAAAA
*
3495529 AAATAA-AAAA
1 AAAAAATAAAA
**
3495539 AAAATGTAAAA
1 AAAAAATAAAA
3495550 AAAAAA
1 AAAAAA
3495556 AATTTCAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 7 0.23
11 14 0.45
12 10 0.32
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.10
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:3495528 original size:11 final size:10
Alignment explanation
Indices: 3495506--3495541 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3495496 TTTTTAATAT
3495506 AAAAAATAAA
1 AAAAAATAAA
* *
3495516 AAAAAACATA
1 AAAAAATAAA
3495526 AAAAAATAAA
1 AAAAAATAAA
3495536 AAAAAA
1 AAAAAA
3495542 ATGTAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:3495537 original size:21 final size:21
Alignment explanation
Indices: 3495506--3495557 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3495496 TTTTTAATAT
3495506 AAAAAAT-AAAAAAAAACATA
1 AAAAAATAAAAAAAAAACATA
**
3495526 AAAAAATAAAAAAAAAATGTA
1 AAAAAATAAAAAAAAAACATA
3495547 AAAAAA-AAAAA
1 AAAAAATAAAAA
3495558 TTTCAAGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.87, C:0.02, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAAATAAAAAAAAAACATA
Found at i:3495549 original size:20 final size:20
Alignment explanation
Indices: 3495505--3495557 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3495495 ATTTTTAATA
3495505 TAAAAAATAAAAAAAAACAT
1 TAAAAAATAAAAAAAAACAT
*
3495525 AAAAAAATAAAAAAAAA-AT
1 TAAAAAATAAAAAAAAACAT
3495544 GTAAAAAA-AAAAAA
1 -TAAAAAATAAAAAA
3495558 TTTCAAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (20 bp):
TAAAAAATAAAAAAAAACAT
Found at i:3496279 original size:27 final size:27
Alignment explanation
Indices: 3496248--3496300 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3496238 ATCAAATTTA
*
3496248 ATTTGATTTGATATT-ATATAAAATTAT
1 ATTTGATATGAT-TTAATATAAAATTAT
*
3496275 ATTTGATATGATTTAATTTAAAATTA
1 ATTTGATATGATTTAATATAAAATTA
3496301 ATAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (27 bp):
ATTTGATATGATTTAATATAAAATTAT
Found at i:3496336 original size:11 final size:12
Alignment explanation
Indices: 3496320--3496356 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
3496310 TATTTTTAAT
3496320 ATAAATATA-AA
1 ATAAATATATAA
3496331 ATAAAT-TATAA
1 ATAAATATATAA
3496342 ATAAATATATAA
1 ATAAATATATAA
3496354 ATA
1 ATA
3496357 TGAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 14 0.58
12 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATATATAA
Found at i:3496340 original size:12 final size:12
Alignment explanation
Indices: 3496320--3496386 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 12
3496310 TATTTTTAAT
3496320 ATAAA-TATAAA
1 ATAAATTATAAA
3496331 ATAAATTAT-AA
1 ATAAATTATAAA
3496342 ATAAATATATAAA
1 ATAAAT-TATAAA
3496355 TATGAAATTA-AATA
1 -AT-AAATTATAA-A
* *
3496369 ATTAATTA-AAT
1 ATAAATTATAAA
3496380 ATAAATT
1 ATAAATT
3496387 TATATATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
11 19 0.40
12 13 0.28
13 6 0.13
14 5 0.11
15 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (12 bp):
ATAAATTATAAA
Found at i:3496341 original size:7 final size:6
Alignment explanation
Indices: 3496317--3496385 Score: 65
Period size: 6 Copynumber: 11.5 Consensus size: 6
3496307 TATTATTTTT
3496317 AATATA AATATA AA-ATA AATTATA AATA-A ATATATA AATATGA AAT-TA
1 AATATA AATATA AATATA AA-TATA AATATA A-ATATA AATAT-A AATATA
*
3496365 AATAATT AAT-TA AATATA AAT
1 AAT-ATA AATATA AATATA AAT
3496386 TTATATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
5 15 0.28
6 23 0.43
7 15 0.28
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:3496383 original size:30 final size:29
Alignment explanation
Indices: 3496317--3496385 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
3496307 TATTATTTTT
*
3496317 AATATAAATATAAAATAAATTATAAATAA
1 AATATAAATATAAAATAAATAATAAATAA
* * *
3496346 ATATATAAATATGAAATTAAATAATTAATTA
1 A-ATATAAATAT-AAAATAAATAATAAATAA
3496377 AATATAAAT
1 AATATAAAT
3496386 TTATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.03
30 18 0.53
31 15 0.44
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (29 bp):
AATATAAATATAAAATAAATAATAAATAA
Found at i:3496816 original size:15 final size:15
Alignment explanation
Indices: 3496798--3496828 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3496788 AATAAAAAAT
*
3496798 TTTATTTATATTCAA
1 TTTATTTATAATCAA
3496813 TTTATTTATAATCAA
1 TTTATTTATAATCAA
3496828 T
1 T
3496829 AACGTAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATTTATAATCAA
Found at i:3500982 original size:2 final size:2
Alignment explanation
Indices: 3500975--3501012 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3500965 TTAATCACTC
3500975 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
3501013 TAGTCGCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3503288 original size:20 final size:21
Alignment explanation
Indices: 3503250--3503292 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3503240 TGTATTTTGA
3503250 AAATTTATTTTTAAAATATAT
1 AAATTTATTTTTAAAATATAT
3503271 AAATTT-TTGTTTAAATATATAT
1 AAATTTATT-TTTAAA-ATATAT
3503293 TTAATTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 12 0.60
22 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AAATTTATTTTTAAAATATAT
Found at i:3504096 original size:7 final size:7
Alignment explanation
Indices: 3504079--3504110 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
3504069 GAAAAGGAAT
3504079 AAAAT-A
1 AAAATAA
3504085 AAAATAA
1 AAAATAA
3504092 AAAATAA
1 AAAATAA
3504099 AAAATAA
1 AAAATAA
3504106 AAAAT
1 AAAAT
3504111 GAAGGATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:3509004 original size:24 final size:22
Alignment explanation
Indices: 3508964--3509015 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
3508954 TTAATAAAAA
*
3508964 ATATTAAATATTTTTTAAATTT
1 ATATTAAAAATTTTTTAAATTT
* *
3508986 TTATTAAAAATTTAATTTATATTT
1 ATATTAAAAATTT--TTTAAATTT
3509010 ATATTA
1 ATATTA
3509016 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 11 0.46
24 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTAAAAATTTTTTAAATTT
Found at i:3512315 original size:20 final size:20
Alignment explanation
Indices: 3512279--3512316 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3512269 GTATTTGTAA
*
3512279 ATTTAATAATTTAAAATATG
1 ATTTAATAATATAAAATATG
*
3512299 ATTTAATAATATGAAATA
1 ATTTAATAATATAAAATA
3512317 AAAAGATACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTTAATAATATAAAATATG
Found at i:3521965 original size:25 final size:26
Alignment explanation
Indices: 3521937--3521989 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3521927 AATTTATATT
3521937 TATTTAATAATAAAAA-ATTTA-TTAA
1 TATTT-ATAATAAAAATATTTATTTAA
* *
3521962 TATTTTTATTAAAAATATTTATTTAA
1 TATTTATAATAAAAATATTTATTTAA
3521988 TA
1 TA
3521990 AATATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTTATAATAAAAATATTTATTTAA
Found at i:3522271 original size:17 final size:16
Alignment explanation
Indices: 3522227--3522278 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3522217 ATTTCAAATT
**
3522227 TTGATATGAATTTAAA
1 TTGATATGCTTTTAAA
* *
3522243 TTGATTTTCTTTTGAAA
1 TTGATATGCTTTT-AAA
3522260 TTGATATGC-TTTAAA
1 TTGATATGCTTTTAAA
3522275 TTGA
1 TTGA
3522279 ATTTTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 7 0.24
16 12 0.41
17 10 0.34
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (16 bp):
TTGATATGCTTTTAAA
Found at i:3522804 original size:2 final size:2
Alignment explanation
Indices: 3522797--3522835 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3522787 TCTTTAACGT
3522797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3522836 TTGACAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3527259 original size:17 final size:17
Alignment explanation
Indices: 3527239--3527271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3527229 CTTTCTCAGC
*
3527239 TTTTTTTTTTTTTCTTA
1 TTTTTTTTATTTTCTTA
3527256 TTTTTTTTATTTTCTT
1 TTTTTTTTATTTTCTT
3527272 CTTTGGGGAG
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:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTTATTTTCTTA
Found at i:3528729 original size:16 final size:17
Alignment explanation
Indices: 3528703--3528739 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3528693 ATTATTATAA
3528703 TTATAATTAAAAAAATT
1 TTATAATTAAAAAAATT
*
3528720 TTAT-ATTAAATAAATT
1 TTATAATTAAAAAAATT
3528736 TTAT
1 TTAT
3528740 TAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATAATTAAAAAAATT
Found at i:3528735 original size:25 final size:24
Alignment explanation
Indices: 3528664--3528724 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
3528654 GATAAATGAT
* **
3528664 AAAATTTATTATAATTACGATTGAA
1 AAAAATTATTATAATTATAATT-AA
3528689 AAAAATTATTATAATTATAATTAA
1 AAAAATTATTATAATTATAATTAA
3528713 AAAAATT-TTATA
1 AAAAATTATTATA
3528725 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 5 0.15
24 9 0.27
25 19 0.58
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
AAAAATTATTATAATTATAATTAA
Found at i:3543875 original size:78 final size:77
Alignment explanation
Indices: 3543744--3543901 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 77
3543734 TTTTAAACCT
3543744 TAAATTCTAAACTTCTATCTTGTCCTAAAAAGTTAGGTGCTTGACACTCAACTTCATGGCTAAGG
1 TAAATTCTAAACTTCTATCTTGTCCTAAAAAGTTAGGTGCTTGACACTCAACTTCATGGCTAAGG
3543809 TTGGAGGGTTGG
66 TTGGAGGGTTGG
* * *
3543821 TAAATTCTAAACTTTTTATCTTGTCCTAAAAAGTTAGGTGCTTGACATTTAACTTCATGGCTAAG
1 TAAATTCTAAAC-TTCTATCTTGTCCTAAAAAGTTAGGTGCTTGACACTCAACTTCATGGCTAAG
3543886 GTTGGAGGGTTGG
65 GTTGGAGGGTTGG
3543899 TAA
1 TAA
3543902 GGAAAGGAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 12 0.16
78 65 0.84
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (77 bp):
TAAATTCTAAACTTCTATCTTGTCCTAAAAAGTTAGGTGCTTGACACTCAACTTCATGGCTAAGG
TTGGAGGGTTGG
Found at i:3547238 original size:15 final size:15
Alignment explanation
Indices: 3547222--3547261 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
3547212 ATTATTATAA
3547222 TTATGATTAAAAAAAT
1 TTAT-ATTAAAAAAAT
3547238 TTATATT-AAAAAAT
1 TTATATTAAAAAAAT
3547252 TT-TATTAAAA
1 TTATATTAAAA
3547262 TTAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 12 0.52
15 3 0.13
16 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTATATTAAAAAAAT
Found at i:3553764 original size:31 final size:31
Alignment explanation
Indices: 3553726--3553836 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
3553716 TGCTATATGC
3553726 AAGAATAACCAGGAAAACAAGCGCAAGACAT
1 AAGAATAACCAGGAAAACAAGCGCAAGACAT
3553757 AAGAATAACCAGGAAAACAAGCGCAAGACAT
1 AAGAATAACCAGGAAAACAAGCGCAAGACAT
*
3553788 AAGAATAACCAGGAAAACAAGTGCAAGACAT
1 AAGAATAACCAGGAAAACAAGCGCAAGACAT
**
3553819 AAGCTTAACCAGGAAAAC
1 AAGAATAACCAGGAAAAC
3553837 TAGTAGCAGG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.54, C:0.19, G:0.19, T:0.08
Consensus pattern (31 bp):
AAGAATAACCAGGAAAACAAGCGCAAGACAT
Found at i:3555262 original size:3 final size:3
Alignment explanation
Indices: 3555206--3555245 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
3555196 ATCATCGCAT
* * *
3555206 TCA TCA TCT TCA TAA TCT TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
3555246 AGGACTCATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:3561231 original size:69 final size:69
Alignment explanation
Indices: 3561132--3561260 Score: 213
Period size: 69 Copynumber: 1.9 Consensus size: 69
3561122 ATGTAAGTAT
* * * *
3561132 AGGTTGTGCTTCACAAATAGTAAGGTGAAAGGCAAATGAGTAACTGAATTACATTGCAAATGCAA
1 AGGTTGTGCTTCACAAAAAGTAAGGTGAAAGGCAAATAACTAACTGAATTAAATTGCAAATGCAA
3561197 TTGG
66 TTGG
*
3561201 AGGTTGTGCTTCACAAAAAGTAAGGTGAAAGTCAAATAACTAACTGAATTAAATTGCAAA
1 AGGTTGTGCTTCACAAAAAGTAAGGTGAAAGGCAAATAACTAACTGAATTAAATTGCAAA
3561261 GGGTGATAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (69 bp):
AGGTTGTGCTTCACAAAAAGTAAGGTGAAAGGCAAATAACTAACTGAATTAAATTGCAAATGCAA
TTGG
Found at i:3562195 original size:51 final size:52
Alignment explanation
Indices: 3562132--3562231 Score: 175
Period size: 51 Copynumber: 1.9 Consensus size: 52
3562122 ATCTTCCGTG
*
3562132 CAAATTTTCTATAAAAACTATAACG-AAAAAAAGTTAAAAGAAAAATAAGTA
1 CAAATTTTCTATAAAAACTATAACGTAAAAAAAATTAAAAGAAAAATAAGTA
*
3562183 CAAATTTTCTATAAAAACTATAATGTAAAAAAAATTAAAAGAAAAATAA
1 CAAATTTTCTATAAAAACTATAACGTAAAAAAAATTAAAAGAAAAATAA
3562232 CCTGTTGTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 24 0.52
52 22 0.48
ACGTcount: A:0.62, C:0.07, G:0.06, T:0.25
Consensus pattern (52 bp):
CAAATTTTCTATAAAAACTATAACGTAAAAAAAATTAAAAGAAAAATAAGTA
Found at i:3562342 original size:43 final size:43
Alignment explanation
Indices: 3562281--3562365 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
3562271 TTTTCTAATC
3562281 AATAAAATTAAAAAGAATTAACGTAAATAACA-ATGTAGGTTTT
1 AATAAAATTAAAAAGAATTAACGTAAA-AACACATGTAGGTTTT
*
3562324 AATAAAATTAAAAAGAATTAACGTAAAATCACATGTAGGTTT
1 AATAAAATTAAAAAGAATTAACGTAAAAACACATGTAGGTTT
3562366 CTTTTTTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 3 0.08
43 37 0.93
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (43 bp):
AATAAAATTAAAAAGAATTAACGTAAAAACACATGTAGGTTTT
Found at i:3562979 original size:23 final size:25
Alignment explanation
Indices: 3562932--3562982 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
3562922 CTTACCGGTG
**
3562932 GAAAAGAAGAAAGGAAAATGTAGAA
1 GAAAAGAAGAAAGGAAAATAAAGAA
3562957 GAAAAGAA-AAAGG-AAATAAAGAA
1 GAAAAGAAGAAAGGAAAATAAAGAA
3562980 GAA
1 GAA
3562983 GCGTCAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 5 0.21
25 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (25 bp):
GAAAAGAAGAAAGGAAAATAAAGAA
Found at i:3565005 original size:33 final size:33
Alignment explanation
Indices: 3564968--3565049 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
3564958 TCTACATTGG
3564968 TTTAAAATATTAAATTAAAAAAAATCATATAAT
1 TTTAAAATATTAAATTAAAAAAAATCATATAAT
* ****
3565001 TTTAAAATATT-AAGTAAAATTTTTCATATAAT
1 TTTAAAATATTAAATTAAAAAAAATCATATAAT
* *
3565033 TTTAAAAAATCAAATTA
1 TTTAAAATATTAAATTA
3565050 TTAGTCTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 25 0.62
33 15 0.38
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (33 bp):
TTTAAAATATTAAATTAAAAAAAATCATATAAT
Found at i:3565468 original size:17 final size:18
Alignment explanation
Indices: 3565446--3565488 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3565436 TAATATATTT
3565446 TATATTTTTAATA-AAAA
1 TATATTTTTAATAGAAAA
*
3565463 TATATTTTTGATAGAAAA
1 TATATTTTTAATAGAAAA
3565481 TAATATTT
1 T-ATATTT
3565489 CATACTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TATATTTTTAATAGAAAA
Found at i:3565647 original size:24 final size:23
Alignment explanation
Indices: 3565614--3565671 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
3565604 AAAACAAAAA
3565614 AAAAATTATATTAAGTCAAAAATAT
1 AAAAA-TATATT-AGTCAAAAATAT
** *
3565639 AAAAATATATTTTTTAAAAATAT
1 AAAAATATATTAGTCAAAAATAT
3565662 ATAAAATATA
1 A-AAAATATA
3565672 AAAAATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 14 0.48
25 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAATATATTAGTCAAAAATAT
Found at i:3567669 original size:10 final size:10
Alignment explanation
Indices: 3567654--3567679 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3567644 TAATTTAAAT
3567654 TTTTTATTTA
1 TTTTTATTTA
3567664 TTTTTATTTA
1 TTTTTATTTA
3567674 TTTTTA
1 TTTTTA
3567680 CCTCAAATTT
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):
TTTTTATTTA
Found at i:3575357 original size:10 final size:10
Alignment explanation
Indices: 3575342--3575374 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3575332 GAGATTTCTC
3575342 TTTTTTTTTA
1 TTTTTTTTTA
*
3575352 -TTTTTTTAA
1 TTTTTTTTTA
3575361 TTTTTTTTTA
1 TTTTTTTTTA
3575371 TTTT
1 TTTT
3575375 GAATGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:3592502 original size:71 final size:71
Alignment explanation
Indices: 3592350--3592493 Score: 270
Period size: 71 Copynumber: 2.0 Consensus size: 71
3592340 TTTTAATTAT
*
3592350 ATAAAATTATTATATATTTAAGCTGCCTTGGATCCAAGCTGGATAATTTTGTTTTGGTATTGATT
1 ATAAAAATATTATATATTTAAGCTGCCTTGGATCCAAGCTGGATAATTTTGTTTTGGTATTGATT
3592415 GTATTG
66 GTATTG
*
3592421 ATAAAAATATTATATATTTAAGCTGCCTTGGATCCAAGTTGGATAATTTTGTTTTGGTATTGATT
1 ATAAAAATATTATATATTTAAGCTGCCTTGGATCCAAGCTGGATAATTTTGTTTTGGTATTGATT
3592486 GTATTG
66 GTATTG
3592492 AT
1 AT
3592494 TTATATATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (71 bp):
ATAAAAATATTATATATTTAAGCTGCCTTGGATCCAAGCTGGATAATTTTGTTTTGGTATTGATT
GTATTG
Found at i:3592954 original size:27 final size:25
Alignment explanation
Indices: 3592924--3592977 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 25
3592914 AAAAATATTC
3592924 ATTT-AAATATCACGTAATTAAATTAAT
1 ATTTAAAATATCA--TAA-TAAATTAAT
3592951 ATTTAAAAATATCATAATAAATTAAT
1 ATTT-AAAATATCATAATAAATTAAT
3592977 A
1 A
3592978 ATATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 10 0.40
27 7 0.28
29 8 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATTTAAAATATCATAATAAATTAAT
Found at i:3599957 original size:22 final size:22
Alignment explanation
Indices: 3599932--3599973 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3599922 TTTTTTAATT
*
3599932 TTTTAT-ATATTATTTTAATAAG
1 TTTTATAATA-TATTTAAATAAG
3599954 TTTTATAATATATTTAAATA
1 TTTTATAATATATTTAAATA
3599974 GATATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATAATATATTTAAATAAG
Found at i:3599988 original size:28 final size:27
Alignment explanation
Indices: 3599954--3600008 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
3599944 TTTTAATAAG
* * *
3599954 TTTTATAATATATTTAAATAGATATATA
1 TTTTATAAAAAATTTAAA-AAATATATA
3599982 TTTTATAAAAAATTTAAAAAATATATA
1 TTTTATAAAAAATTTAAAAAATATATA
3600009 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTTATAAAAAATTTAAAAAATATATA
Found at i:3600018 original size:19 final size:20
Alignment explanation
Indices: 3599985--3600025 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3599975 ATATATATTT
*
3599985 TATAAAAAATTTAAAAAATA
1 TATAAAAAATATAAAAAATA
*
3600005 TATAAAAAA-ATAAAATATA
1 TATAAAAAATATAAAAAATA
3600024 TA
1 TA
3600026 ATTTAGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAAAAATATAAAAAATA
Found at i:3600207 original size:11 final size:12
Alignment explanation
Indices: 3600183--3600207 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3600173 AACATTACAA
3600183 TTTAAAATTTTT
1 TTTAAAATTTTT
3600195 TTTAAAATTTTT
1 TTTAAAATTTTT
3600207 T
1 T
3600208 CCTCCCCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAAATTTTT
Found at i:3607731 original size:15 final size:15
Alignment explanation
Indices: 3607700--3607733 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3607690 ATGTAATATT
3607700 TAATATTTATTTTTA
1 TAATATTTATTTTTA
3607715 TAAT-TTTATTTTATA
1 TAATATTTATTTT-TA
3607730 TAAT
1 TAAT
3607734 CAAGCTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATATTTATTTTTA
Found at i:3610785 original size:15 final size:15
Alignment explanation
Indices: 3610765--3610803 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3610755 CTCATTTTTA
3610765 TTATTATTTTTAATT
1 TTATTATTTTTAATT
***
3610780 TTATTAAAATTAATT
1 TTATTATTTTTAATT
3610795 TTATTATTT
1 TTATTATTT
3610804 ATTCAAATAA
Statistics
Matches: 18, Mismatches: 6, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATTTTTAATT
Found at i:3610796 original size:21 final size:22
Alignment explanation
Indices: 3610767--3610831 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
3610757 CATTTTTATT
*
3610767 ATTATTTTTAAT-TTTATTAAA
1 ATTAATTTTAATATTTATTAAA
* *
3610788 ATTAATTTTATTATTTATTCAA
1 ATTAATTTTAATATTTATTAAA
* *
3610810 ATAAATCTTTAATCTTT-TTAAA
1 ATTAAT-TTTAATATTTATTAAA
3610832 TTTTAAGAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 10 0.29
22 17 0.49
23 8 0.23
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTAATTTTAATATTTATTAAA
Found at i:3611292 original size:14 final size:15
Alignment explanation
Indices: 3611263--3611295 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3611253 CGAATAAAAT
*
3611263 TTTTTAAATTTATAA
1 TTTTTAAATATATAA
3611278 TTTTTAAATAT-TAA
1 TTTTTAAATATATAA
3611292 TTTT
1 TTTT
3611296 AATTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTAAATATATAA
Found at i:3611584 original size:27 final size:27
Alignment explanation
Indices: 3611546--3611599 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3611536 ATGCTTTTCC
3611546 GCTTTCTCTACATCATTGGTCGGTTCA
1 GCTTTCTCTACATCATTGGTCGGTTCA
3611573 GCTTTCTCTACATCATTGGTCGGTTCA
1 GCTTTCTCTACATCATTGGTCGGTTCA
3611600 AATCAAAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.41
Consensus pattern (27 bp):
GCTTTCTCTACATCATTGGTCGGTTCA
Found at i:3612555 original size:31 final size:30
Alignment explanation
Indices: 3612518--3612599 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
3612508 AAAAAAATAG
*
3612518 TAATTAATTTAATTAATTTTTATTTAATAAA
1 TAATTAATTTAATTAATTTTT-TTAAATAAA
* * * *
3612549 TAATTAAATTGATTAAAATTTTTTAAATAAT
1 TAATTAATTTAATT-AATTTTTTTAAATAAA
*
3612580 TAATCATAATTAAATTAATT
1 TAAT--TAATTTAATTAATT
3612600 CGATTTAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
31 23 0.59
32 9 0.23
33 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TAATTAATTTAATTAATTTTTTTAAATAAA
Found at i:3613300 original size:21 final size:21
Alignment explanation
Indices: 3613258--3613300 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3613248 TTATTGTATA
* *
3613258 AATTAATTTAATTAAATTTTT
1 AATTAATATAATTAAATATTT
3613279 AATTAATATAATTATAA-ATTT
1 AATTAATATAATTA-AATATTT
3613300 A
1 A
3613301 TATATAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTAATATAATTAAATATTT
Found at i:3618186 original size:15 final size:15
Alignment explanation
Indices: 3618166--3618195 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3618156 AATAATTTTA
3618166 AAATTTTAATATAAT
1 AAATTTTAATATAAT
*
3618181 AAATTTTAATTTAAT
1 AAATTTTAATATAAT
3618196 TATTATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATTTTAATATAAT
Found at i:3618749 original size:14 final size:15
Alignment explanation
Indices: 3618720--3618752 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3618710 CGAATAAAAT
3618720 TTTTTAAATTTATAA
1 TTTTTAAATTTATAA
3618735 TTTTTAAATTT-TAA
1 TTTTTAAATTTATAA
3618749 TTTT
1 TTTT
3618753 AATTACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTAAATTTATAA
Found at i:3619997 original size:18 final size:18
Alignment explanation
Indices: 3619976--3620028 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3619966 TTTATTTAAT
*
3619976 AAATAATTAAATTGATTA
1 AAATAATTAAATTAATTA
**
3619994 AAATTTTTAAA-TAATTA
1 AAATAATTAAATTAATTA
*
3620011 ATCATAATTAAATTAATT
1 A-AATAATTAAATTAATT
3620029 CGATTTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATAATTAAATTAATTA
Found at i:3625678 original size:31 final size:33
Alignment explanation
Indices: 3625645--3625708 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
3625635 AAAATAAAAT
* *
3625645 AAAT-TTAATAATTCATGTATTTATATCATATA
1 AAATATTAAAAATTCATATATTTATATCATATA
* *
3625677 AAATATTAAAAATTTATATATTTATATTATAT
1 AAATATTAAAAATTCATATATTTATATCATAT
3625709 TTTATATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (33 bp):
AAATATTAAAAATTCATATATTTATATCATATA
Found at i:3625809 original size:22 final size:22
Alignment explanation
Indices: 3625764--3625810 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3625754 TATTTTTTTA
* **
3625764 TTTTATTAAATTTATTTATAAT
1 TTTTATTAAAATTATAAATAAT
*
3625786 TTTTATTAAAATTATAAATCAT
1 TTTTATTAAAATTATAAATAAT
3625808 TTT
1 TTT
3625811 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTAAAATTATAAATAAT
Found at i:3627032 original size:2 final size:2
Alignment explanation
Indices: 3627025--3627050 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3627015 AGGTAGTTTG
3627025 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
3627051 TTTTTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3627097 original size:15 final size:16
Alignment explanation
Indices: 3627079--3627108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3627069 TTTTATTTTA
3627079 AAAAT-AATTTTTATC
1 AAAATCAATTTTTATC
3627094 AAAATCAATTTTTAT
1 AAAATCAATTTTTAT
3627109 TTTAATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATCAATTTTTATC
Found at i:3627846 original size:7 final size:7
Alignment explanation
Indices: 3627834--3627861 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3627824 AGCAGCCTTT
3627834 CCTTTTC
1 CCTTTTC
3627841 CCTTTTC
1 CCTTTTC
3627848 CCTTTTC
1 CCTTTTC
3627855 CCTTTTC
1 CCTTTTC
3627862 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
CCTTTTC
Found at i:3629780 original size:14 final size:14
Alignment explanation
Indices: 3629761--3629806 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3629751 TTGCTATTGA
*
3629761 AAAAAAATTTTAAT
1 AAAAAAATTTTATT
*
3629775 AAAAAAATTATATT
1 AAAAAAATTTTATT
**
3629789 AAATGAATTTTATT
1 AAAAAAATTTTATT
3629803 AAAA
1 AAAA
3629807 TTAATATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
AAAAAAATTTTATT
Found at i:3635585 original size:3 final size:3
Alignment explanation
Indices: 3635577--3635602 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3635567 ATTTATTTAT
3635577 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3635603 GAAATATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3643801 original size:2 final size:2
Alignment explanation
Indices: 3643794--3643823 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3643784 AGCTCAAATT
3643794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3643824 GGGTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3652569 original size:15 final size:16
Alignment explanation
Indices: 3652533--3652570 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3652523 ATTTTTTTAT
3652533 TTAAAATTTTGATGAA
1 TTAAAATTTTGATGAA
*
3652549 TT-AAATTTTGAT-CA
1 TTAAAATTTTGATGAA
3652563 TTAAAATT
1 TTAAAATT
3652571 ACTGTACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 15 0.75
16 2 0.10
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (16 bp):
TTAAAATTTTGATGAA
Found at i:3652899 original size:2 final size:2
Alignment explanation
Indices: 3652886--3652915 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3652876 TTGTGGGGGA
*
3652886 AT AT AT AC 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
3652916 GTGCATCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3662590 original size:19 final size:19
Alignment explanation
Indices: 3662527--3662597 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
3662517 ATATTAATTT
* *
3662527 TAATAAAATTTATTTAATA
1 TAATAATATTTATTTAAAA
* *
3662546 TAA-AAT-TTTAAATTATAA
1 TAATAATATTT-ATTTAAAA
*
3662564 TTATAATATTTATTTAAAA
1 TAATAATATTTATTTAAAA
*
3662583 TAATAATAATTATTT
1 TAATAATATTTATTT
3662598 TTTTAATATC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.08
18 9 0.22
19 25 0.62
20 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAATATTTATTTAAAA
Found at i:3662591 original size:22 final size:23
Alignment explanation
Indices: 3662560--3662603 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3662550 ATTTTAAATT
*
3662560 ATAATTATAA-TATTTATTTAAA
1 ATAATAATAATTATTTATTTAAA
*
3662582 ATAATAATAATTATTTTTTTAA
1 ATAATAATAATTATTTATTTAA
3662604 TATCATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATAATAATTATTTATTTAAA
Found at i:3663144 original size:18 final size:19
Alignment explanation
Indices: 3663109--3663150 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3663099 ATATTTAAAT
3663109 TATAA-ATTTATTAATTAA
1 TATAATATTTATTAATTAA
*
3663127 TATAATATTTATT-TTTAA
1 TATAATATTTATTAATTAA
3663145 TATAAT
1 TATAAT
3663151 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAATATTTATTAATTAA
Found at i:3663212 original size:28 final size:30
Alignment explanation
Indices: 3663154--3663209 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3663144 ATATAATTAA
*
3663154 TTTTAAATAAATAATAAATATTACATAATT
1 TTTTAAATAAATAATAAATATAACATAATT
*
3663184 TTTTAAAT-ATTATATAAAT-TAACATA
1 TTTTAAATAAATA-ATAAATATAACATA
3663210 TTTAAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
29 9 0.39
30 14 0.61
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTTAAATAAATAATAAATATAACATAATT
Found at i:3665811 original size:18 final size:18
Alignment explanation
Indices: 3665785--3665929 Score: 57
Period size: 18 Copynumber: 7.8 Consensus size: 18
3665775 ATAAAATATG
3665785 TAAAA-AAATTTAAATTA
1 TAAAATAAATTTAAATTA
3665802 TAAAATAAATTT-AATCTA
1 TAAAATAAATTTAAAT-TA
* * **
3665820 TTAAATTTATAA-TAAAAGAA
1 -TAAA-ATA-AATTTAAATTA
* *
3665840 AAATAAAAAATTTAAATTA
1 TAA-AATAAATTTAAATTA
3665859 TAAAATAAATTT-AATCTA
1 TAAAATAAATTTAAAT-TA
* * **
3665877 TTAAATTTATAA-TAAAAGAA
1 -TAAA-ATA-AATTTAAATTA
* *
3665897 AAATAAAAAATTTAAATTA
1 TAA-AATAAATTTAAATTA
3665916 TAAAATAAATTTAA
1 TAAAATAAATTTAA
3665930 TCTATTAAAT
Statistics
Matches: 89, Mismatches: 24, Indels: 29
0.63 0.17 0.20
Matches are distributed among these distances:
17 11 0.12
18 32 0.36
19 28 0.31
20 10 0.11
21 8 0.09
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
TAAAATAAATTTAAATTA
Found at i:3665850 original size:25 final size:25
Alignment explanation
Indices: 3665822--3665967 Score: 94
Period size: 27 Copynumber: 5.3 Consensus size: 25
3665812 TTAATCTATT
3665822 AAATTTATAATAAAAGAAAAATAAA
1 AAATTTATAATAAAAGAAAAATAAA
* * **
3665847 AAATTTAAATTATAAAATAAATTTAATCTATT
1 AAATTT--ATAATAAAAGAAA---AA--TAAA
3665879 AAATTTATAATAAAAGAAAAATAAA
1 AAATTTATAATAAAAGAAAAATAAA
* * **
3665904 AAATTTAAATTATAAAATAAATTTAATCTATT
1 AAATTT--ATAATAAAAGAAA---AA--TAAA
3665936 AAATTTATAATAAAAGAAAAATAAA
1 AAATTTATAATAAAAGAAAAATAAA
3665961 AAATTTA
1 AAATTTA
3665968 AATTATATAT
Statistics
Matches: 91, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
25 23 0.25
27 26 0.29
30 26 0.29
32 16 0.18
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATTTATAATAAAAGAAAAATAAA
Found at i:3665859 original size:57 final size:57
Alignment explanation
Indices: 3665787--3665974 Score: 376
Period size: 57 Copynumber: 3.3 Consensus size: 57
3665777 AAAATATGTA
3665787 AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
1 AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
3665844 AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
1 AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
3665901 AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
1 AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
3665958 AAAAAATTTAAATTATA
1 AAAAAATTTAAATTATA
3665975 TATAAAATAT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 131 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (57 bp):
AAAAAATTTAAATTATAAAATAAATTTAATCTATTAAATTTATAATAAAAGAAAAAT
Found at i:3665886 original size:27 final size:26
Alignment explanation
Indices: 3665794--3665949 Score: 98
Period size: 27 Copynumber: 5.7 Consensus size: 26
3665784 GTAAAAAAAT
3665794 TTAAATTATAAAATAAATTTAATCTA
1 TTAAATTATAAAATAAATTTAATCTA
* ** ***
3665820 TTAAATTTATAATAAAAGAAAAATAAAAAA
1 TTAAA--T-T-ATAAAATAAATTTAATCTA
3665850 TTTAAATTATAAAATAAATTTAATCTA
1 -TTAAATTATAAAATAAATTTAATCTA
* ** ***
3665877 TTAAATTTATAATAAAAGAAAAATAAAAAA
1 TTAAA--T-T-ATAAAATAAATTTAATCTA
3665907 TTTAAATTATAAAATAAATTTAATCTA
1 -TTAAATTATAAAATAAATTTAATCTA
*
3665934 TTAAATT-TATAATAAA
1 TTAAATTATAAAATAAA
3665950 AGAAAAATAA
Statistics
Matches: 95, Mismatches: 25, Indels: 21
0.67 0.18 0.15
Matches are distributed among these distances:
25 8 0.08
26 17 0.18
27 26 0.27
28 4 0.04
29 4 0.04
30 26 0.27
31 10 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (26 bp):
TTAAATTATAAAATAAATTTAATCTA
Found at i:3666067 original size:15 final size:16
Alignment explanation
Indices: 3666047--3666076 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3666037 TTAGTTTGAA
3666047 AATATAAAA-AATTAT
1 AATATAAAATAATTAT
3666062 AATATAAAATAATTA
1 AATATAAAATAATTA
3666077 CAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:3669770 original size:14 final size:16
Alignment explanation
Indices: 3669745--3669786 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
3669735 ATCCTAAATG
3669745 AATTAAAATTTAAT-TT
1 AATT-AAATTTAATATT
3669761 AATT-AATTT-ATATT
1 AATTAAATTTAATATT
3669775 AATTAAATTTAA
1 AATTAAATTTAA
3669787 AATTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 11 0.48
15 5 0.22
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAAATTTAATATT
Found at i:3673825 original size:12 final size:13
Alignment explanation
Indices: 3673810--3673855 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
3673800 ATATAATATT
3673810 AAATTTGAATTT-
1 AAATTTGAATTTA
*
3673822 AAA-TTCAATTTA
1 AAATTTGAATTTA
*
3673834 AAATTTGAGATTTG
1 AAATTTGA-ATTTA
3673848 AAATTTGA
1 AAATTTGA
3673856 TTCAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 7 0.25
12 6 0.21
13 3 0.11
14 12 0.43
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (13 bp):
AAATTTGAATTTA
Found at i:3684997 original size:22 final size:21
Alignment explanation
Indices: 3684949--3684999 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
3684939 ATTATTTTTA
*
3684949 AAATTTTATATTTAATAAATTT
1 AAATTTTAAATTTAAT-AATTT
3684971 AAATTTTAAATTTAAGT-ATTT
1 AAATTTTAAATTTAA-TAATTT
3684992 ATAATTTT
1 A-AATTTT
3685000 TCATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 20 0.77
23 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTTTAAATTTAATAATTT
Found at i:3689142 original size:5 final size:5
Alignment explanation
Indices: 3689134--3689186 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
3689124 TAAAATAAAA
* * *
3689134 TTATT TTATT TTATT TTATT TTATT CATAATA TTAAT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT --TTATT TTATT TTATT TTATT TTATT
3689186 T
1 T
3689187 ATAATCATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 37 0.93
7 3 0.08
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:3689174 original size:32 final size:33
Alignment explanation
Indices: 3689128--3689195 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
3689118 CAAATATAAA
* *
3689128 ATAAAATTATTTTATTTTATTTTATTT-TATTC
1 ATAAAATTAATTTATTTTATTTTATTTATAATC
*
3689160 ATAATATTAATTTATTTTATTTTATTTATAATC
1 ATAAAATTAATTTATTTTATTTTATTTATAATC
3689193 ATA
1 ATA
3689196 TACACCAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (33 bp):
ATAAAATTAATTTATTTTATTTTATTTATAATC
Found at i:3689515 original size:25 final size:25
Alignment explanation
Indices: 3689478--3689525 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3689468 TGAGTTAATG
3689478 CTGTTTTGCTTAAAATGTCACACTT
1 CTGTTTTGCTTAAAATGTCACACTT
*
3689503 CTGTTTTGTTTAAAATGTCACAC
1 CTGTTTTGCTTAAAATGTCACAC
3689526 CTCAGAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (25 bp):
CTGTTTTGCTTAAAATGTCACACTT
Found at i:3692898 original size:2 final size:2
Alignment explanation
Indices: 3692893--3692922 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3692883 CTCTCTCTCT
3692893 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3692923 TATATGACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3692971 original size:39 final size:39
Alignment explanation
Indices: 3692911--3692997 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
3692901 CACACACACA
* * *
3692911 CACACACACACATATATGACTTAACTCACATTAGATAAG
1 CACACACACACACACAGGACTTAACTCACATTAGATAAG
3692950 CACACACACACACACAGGACTTAACTCACATTAGATAAG
1 CACACACACACACACAGGACTTAACTCACATTAGATAAG
*
3692989 TA-ACACACA
1 CACACACACA
3692998 TATATATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 7 0.16
39 37 0.84
ACGTcount: A:0.45, C:0.29, G:0.08, T:0.18
Consensus pattern (39 bp):
CACACACACACACACAGGACTTAACTCACATTAGATAAG
Found at i:3693222 original size:2 final size:2
Alignment explanation
Indices: 3693215--3693250 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3693205 TAAGAAACAA
3693215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3693251 GCACCGTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3695060 original size:19 final size:20
Alignment explanation
Indices: 3695038--3695076 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3695028 ATATAAATAT
3695038 ATAAAAA-TTAAAATTTTTG
1 ATAAAAATTTAAAATTTTTG
3695057 ATAAAAATTTTAAAATTTTT
1 ATAAAAA-TTTAAAATTTTT
3695077 AATATGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATAAAAATTTAAAATTTTTG
Found at i:3697315 original size:8 final size:8
Alignment explanation
Indices: 3697299--3697360 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
3697289 TTATTTTTAA
3697299 ATATAAAT
1 ATATAAAT
*
3697307 ATTTAAAT
1 ATATAAAT
*
3697315 ATATAATT
1 ATATAAAT
3697323 ATATAAATGT
1 ATATAAA--T
3697333 ATATAAAT
1 ATATAAAT
3697341 A-A-AAA-
1 ATATAAAT
3697346 AT-TAAAT
1 ATATAAAT
*
3697353 TTATAAAT
1 ATATAAAT
3697361 TAATTTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
5 1 0.02
6 6 0.14
7 2 0.05
8 26 0.60
10 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:3698860 original size:27 final size:24
Alignment explanation
Indices: 3698818--3698866 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
3698808 GTAAGACTTT
*
3698818 TAATTTATTTATTGATTTATTTTC
1 TAATTTATTTATTGATTCATTTTC
3698842 TAATTTGATATTATATGATTCATTT
1 TAATTT-AT-TTAT-TGATTCATTT
3698867 GATCTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 2 0.10
26 4 0.19
27 9 0.43
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (24 bp):
TAATTTATTTATTGATTCATTTTC
Found at i:3707226 original size:12 final size:12
Alignment explanation
Indices: 3707206--3707275 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 12
3707196 CCATATTACT
*
3707206 CCCCGCCACCAC
1 CCCCTCCACCAC
*
3707218 CCCCTCCACCTC
1 CCCCTCCACCAC
3707230 CTTCTCCTCCACCCCCAC
1 C--C-CCTCCA---CCAC
3707248 CCCCTCCACCAC
1 CCCCTCCACCAC
*
3707260 CTCCTCCACCAC
1 CCCCTCCACCAC
3707272 CCCC
1 CCCC
3707276 ACCCGACTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
12 29 0.62
14 1 0.02
15 12 0.26
16 1 0.02
18 4 0.09
ACGTcount: A:0.13, C:0.73, G:0.01, T:0.13
Consensus pattern (12 bp):
CCCCTCCACCAC
Found at i:3707248 original size:30 final size:30
Alignment explanation
Indices: 3707214--3707279 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
3707204 CTCCCCGCCA
* * *
3707214 CCACCCCCTCCACCTCCTTCTCCTCCACCC
1 CCACCCCCTCCACCACCTCCTCCACCACCC
3707244 CCACCCCCTCCACCACCTCCTCCACCACCC
1 CCACCCCCTCCACCACCTCCTCCACCACCC
3707274 CCACCC
1 CCACCC
3707280 GACTGTAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.14, C:0.73, G:0.00, T:0.14
Consensus pattern (30 bp):
CCACCCCCTCCACCACCTCCTCCACCACCC
Found at i:3708046 original size:16 final size:17
Alignment explanation
Indices: 3708025--3708064 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3708015 ATTTTTTTTA
3708025 TTTTATTTTACCTATG-
1 TTTTATTTTACCTATGC
*
3708041 TTTTA-TTAACCTATGC
1 TTTTATTTTACCTATGC
3708057 TTTT-TTTT
1 TTTTATTTT
3708065 TTTATGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTATTTTACCTATGC
Found at i:3725175 original size:25 final size:25
Alignment explanation
Indices: 3725147--3725197 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3725137 TATTTTTATA
3725147 ATTTTTAAATAAT-AATTATAATAAT
1 ATTTTTAAAT-ATCAATTATAATAAT
* *
3725172 ATTTTTTAATCTCAATTATAATAAT
1 ATTTTTAAATATCAATTATAATAAT
3725197 A
1 A
3725198 ATTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTTTAAATATCAATTATAATAAT
Done.