Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 18 of 186
Found at i:5495012 original size:79 final size:80
Alignment explanation
Indices: 5494915--5495180 Score: 374
Period size: 79 Copynumber: 3.2 Consensus size: 80
5494905 AAATTACAAA
* *
5494915 ATTAAAATATTCATACAAAATACTAATCCAGAACTATAAATACAAAATTAATTATAAAATAATTA
1 ATTAAAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATTA
5494980 CAATATTCAT-AAAC
66 CAATATTCATAAAAC
* *
5494994 ATTATAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATCAATTATAAAATAATTA
1 ATTAAAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATTA
5495059 CAATATTCATACAAAATTAC
66 CAATATTCAT---AAA--AC
* *
5495079 AAAATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAATAA
1 ---ATTAAAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAA
* *
5495144 -TACATTATTCATAAAAA
63 TTACAATATTCATAAAAC
5495161 ATTAAAATATTCATACAAAA
1 ATTAAAATATTCATACAAAA
5495181 AATTACACTA
Statistics
Matches: 168, Mismatches: 10, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
79 90 0.54
82 1 0.01
83 2 0.01
84 3 0.02
85 2 0.01
87 11 0.07
88 59 0.35
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (80 bp):
ATTAAAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAATTA
CAATATTCATAAAAC
Found at i:5495064 original size:61 final size:60
Alignment explanation
Indices: 5494994--5495263 Score: 188
Period size: 61 Copynumber: 4.3 Consensus size: 60
5494984 ATTCATAAAC
*
5494994 ATTATAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATCAATTATAAAATA
1 ATTACAATATTCATACAAAATACTAATCAAAAA-TATAAATACAAAATCAATTATAAAATA
* * * ** * *
5495055 ATTACAATATTCATACAAAATTACAAAAT-TACAATATTCATACAAAATACTAATCAAAAACAAT
1 ATTACAATATTCATACAAAA-TAC-TAATCAAAAATATAAATACAAAAT-C-AAT-TATAA-AAT
5495119 A
60 A
* * * * * * *** * * *
5495120 AATACAAAATTAATTATAAAATAATACATTATTCATA-AAAAATTAAAAT--ATTCATACAAAAA
1 ATTACAATATTCA-TACAAAATACTA-ATCAAAAATATAAATA-CAAAATCAATT-ATA-AAATA
* * *
5495182 ATTACACTATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATA
1 ATTACAATATTCATACAAAATACTAAT-CAAAAATATAAATACAAAATCAATTATAAAATA
5495243 ATTACAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
5495264 TATAATATTC
Statistics
Matches: 153, Mismatches: 40, Indels: 32
0.68 0.18 0.14
Matches are distributed among these distances:
60 2 0.01
61 73 0.48
62 30 0.20
63 10 0.07
64 4 0.03
65 20 0.13
66 14 0.09
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.30
Consensus pattern (60 bp):
ATTACAATATTCATACAAAATACTAATCAAAAATATAAATACAAAATCAATTATAAAATA
Found at i:5495097 original size:88 final size:87
Alignment explanation
Indices: 5494994--5495164 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 87
5494984 ATTCATAAAC
* *
5494994 ATTATAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATCAATTATAAAATAATTA
1 ATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATCAATTATAAAATAA-TA
*
5495059 CAATATTCATACAAAATTACAAA
65 CAATATTCATAAAAAATTACAAA
*
5495082 ATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAATAATAC
1 ATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATCAATTATAAAATAATAC
*
5495147 ATTATTCATAAAAAATTA
66 AATATTCATAAAAAATTA
5495165 AAATATTCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 19 0.24
88 59 0.76
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (87 bp):
ATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATCAATTATAAAATAATAC
AATATTCATAAAAAATTACAAA
Found at i:5495180 original size:21 final size:21
Alignment explanation
Indices: 5495149--5495201 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5495139 AATAATACAT
5495149 TATTCAT--AAAAAATTAAAA
1 TATTCATACAAAAAATTAAAA
* *
5495168 TATTCATACAAAAAATTACAC
1 TATTCATACAAAAAATTAAAA
5495189 TATTCATACAAAA
1 TATTCATACAAAA
5495202 TACTAATCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 7 0.23
21 23 0.77
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
TATTCATACAAAAAATTAAAA
Found at i:5495202 original size:100 final size:101
Alignment explanation
Indices: 5495079--5495303 Score: 371
Period size: 100 Copynumber: 2.2 Consensus size: 101
5495069 ACAAAATTAC
5495079 AAAATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAATAA
*
5495144 -TACATTATTCATAAAAAATTAAAATATTCATACAA
66 TTACAATATTCATAAAAAATTAAAATATTCATACAA
* * *
5495179 AAAATTACACTATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAATAA
* *
5495244 TTACAATATTCATACAAAATTATAATATTCATACAA
66 TTACAATATTCATAAAAAATTAAAATATTCATACAA
* *
5495280 AAAGTTACAATATACATACAAAAT
1 AAAATTACAATATTCATACAAAAT
5495304 TACCCATTGA
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
100 62 0.54
101 53 0.46
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (101 bp):
AAAATTACAATATTCATACAAAATACTAATCAAAAACAATAAATACAAAATTAATTATAAAATAA
TTACAATATTCATAAAAAATTAAAATATTCATACAA
Found at i:5495356 original size:27 final size:27
Alignment explanation
Indices: 5495314--5495383 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
5495304 TACCCATTGA
*
5495314 CGCCTCCCTATAAGGCACTTTTAATGG
1 CGCCTCCCTATGAGGCACTTTTAATGG
*
5495341 CGCCTCCTTATGAGGCACTTTTAATGG
1 CGCCTCCCTATGAGGCACTTTTAATGG
*
5495368 TGCCTCCCTATGAGGC
1 CGCCTCCCTATGAGGC
5495384 GCCACCTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (27 bp):
CGCCTCCCTATGAGGCACTTTTAATGG
Found at i:5495638 original size:173 final size:174
Alignment explanation
Indices: 5495342--5495671 Score: 572
Period size: 173 Copynumber: 1.9 Consensus size: 174
5495332 TTTTAATGGC
* * **
5495342 GCCTCCTTATGAGGCACTTTTAATGGTGCCTCCCTATGAGGCGCCACCTGACCCATTTTTCCCTT
1 GCCTCCCTATGAGGCACTTTTAATGGTGCCTCCCTATGAGGCGCCACCCGACCCATTTTAACCTT
* **
5495407 TGACCCGTTGACCGTATTTTGACCCGTATTTTTATTTAATTTTTTTTAAAAATAATATTTTATTC
66 TGACCCGTTGACCGTATTTTGACCCGTATTTTTATTTAAATTTTTAAAAAAATAATATTTTATTC
5495472 AAAAAAAG-AAAAAAATTAATAGTTTTCAAAATTACCTATTGGT
131 AAAAAAAGAAAAAAAATTAATAGTTTTCAAAATTACCTATTGGT
5495515 GCCTCCCTATGAGGCACTTTTAATGGTGCCTCCCTATGAGGCGCCACCCGACCCATTTTAACCTT
1 GCCTCCCTATGAGGCACTTTTAATGGTGCCTCCCTATGAGGCGCCACCCGACCCATTTTAACCTT
* *
5495580 TGACCCGTTGACCGTATTTTGACCCGTTTTTTTATTTAAATTTTTAAAAAAATAATATTTTATTT
66 TGACCCGTTGACCGTATTTTGACCCGTATTTTTATTTAAATTTTTAAAAAAATAATATTTTATTC
5495645 AAAAAAAGAAAAAAAATTAATAGTTTT
131 AAAAAAAGAAAAAAAATTAATAGTTTT
5495672 TTATTCATTG
Statistics
Matches: 147, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 129 0.88
174 18 0.12
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (174 bp):
GCCTCCCTATGAGGCACTTTTAATGGTGCCTCCCTATGAGGCGCCACCCGACCCATTTTAACCTT
TGACCCGTTGACCGTATTTTGACCCGTATTTTTATTTAAATTTTTAAAAAAATAATATTTTATTC
AAAAAAAGAAAAAAAATTAATAGTTTTCAAAATTACCTATTGGT
Found at i:5496744 original size:15 final size:16
Alignment explanation
Indices: 5496712--5496750 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
5496702 CAGCAGCAGC
5496712 AGAAGAAAAAGATGAAGA
1 AGAAG-AAAAGA-GAAGA
5496730 AGAAGAAAAGA-AAGA
1 AGAAGAAAAGAGAAGA
5496745 AGAAGA
1 AGAAGA
5496751 TCTGATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
17 6 0.29
18 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (16 bp):
AGAAGAAAAGAGAAGA
Found at i:5497493 original size:30 final size:32
Alignment explanation
Indices: 5497459--5497543 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 32
5497449 AGATTCGCCC
5497459 ATATTATTT-TTAAAATTTTTAAAAAA-ATTT
1 ATATTATTTATTAAAATTTTTAAAAAATATTT
**
5497489 ATATTATATTATTTTAATATTTTAAAAAATATTT
1 ATATTAT-TTATTAAAAT-TTTTAAAAAATATTT
*
5497523 -T-TTATTTATTGAAAGTTTTTA
1 ATATTATTTATT-AAAATTTTTA
5497544 TATAGTCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
30 7 0.16
31 12 0.27
32 11 0.24
33 11 0.24
34 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
ATATTATTTATTAAAATTTTTAAAAAATATTT
Found at i:5499152 original size:20 final size:20
Alignment explanation
Indices: 5499129--5499232 Score: 54
Period size: 20 Copynumber: 5.0 Consensus size: 20
5499119 TTTAGGGTTT
5499129 TTTTTAATATATATTTTTAA
1 TTTTTAATATATATTTTTAA
* *
5499149 TTTTTTATATA-ATCTTTAGA
1 TTTTTAATATATATTTTTA-A
*
5499169 CTTTTT-TTATA-ATTTTTTAGTTA
1 -TTTTTAATATATA-TTTTTA---A
* *
5499192 TTTTAAAATATATATTTTAAAA
1 TTTT-TAATATATATTTT-TAA
*
5499214 TTTCTAATAT-TATTTTTAA
1 TTTTTAATATATATTTTTAA
5499233 ACTATATATT
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
19 8 0.12
20 22 0.34
21 15 0.23
22 8 0.12
23 1 0.02
24 8 0.12
25 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTAATATATATTTTTAA
Found at i:5499154 original size:21 final size:21
Alignment explanation
Indices: 5499128--5499232 Score: 76
Period size: 21 Copynumber: 5.0 Consensus size: 21
5499118 GTTTAGGGTT
5499128 TTTTTTAATATATATTTTTAA
1 TTTTTTAATATATATTTTTAA
*
5499149 TTTTTT-ATATA-ATCTTTAGA
1 TTTTTTAATATATATTTTTA-A
* *
5499169 CTTTTTTTATA-AT-TTTTTAG
1 -TTTTTTAATATATATTTTTAA
*
5499189 TTATTTTAAAATATATATTTTAAA
1 TT-TTTT--AATATATATTTTTAA
* *
5499213 ATTTCTAATAT-TATTTTTAA
1 TTTTTTAATATATATTTTTAA
5499233 ACTATATATT
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
19 8 0.12
20 18 0.27
21 23 0.35
22 6 0.09
23 5 0.08
24 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTTAATATATATTTTTAA
Found at i:5499233 original size:21 final size:20
Alignment explanation
Indices: 5499198--5499272 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 20
5499188 GTTATTTTAA
5499198 AATATATATTTTAAAATTTCT
1 AATATAT-TTTTAAAATTTCT
5499219 AATATTATTTTT-AAA---CT
1 AATA-TATTTTTAAAATTTCT
5499236 -ATATA-TTTTAAAATTTCT
1 AATATATTTTTAAAATTTCT
5499254 AATATTATTTTTAAAATTT
1 AATA-TATTTTTAAAATTT
5499273 TGAAGTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
14 4 0.09
15 5 0.11
16 3 0.07
17 2 0.04
18 2 0.04
19 3 0.07
20 5 0.11
21 19 0.41
22 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATATTTTTAAAATTTCT
Found at i:5499239 original size:35 final size:35
Alignment explanation
Indices: 5499192--5499270 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
5499182 TTTTTAGTTA
5499192 TTTTAAAATATATATTTTAAAATTTCTAATATTAT
1 TTTTAAAATATATATTTTAAAATTTCTAATATTAT
*
5499227 TTTTAAACTATATATTTTAAAATTTCTAATATTAT
1 TTTTAAAATATATATTTTAAAATTTCTAATATTAT
5499262 TTTTAAAAT
1 TTTTAAAAT
5499271 TTTGAAGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (35 bp):
TTTTAAAATATATATTTTAAAATTTCTAATATTAT
Found at i:5505066 original size:22 final size:21
Alignment explanation
Indices: 5505024--5505068 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5505014 AAAATTGAGT
*
5505024 GAGAAATTAAGAGGGAATTGA
1 GAGAAATTAAGAGAGAATTGA
* *
5505045 GAGAAATTTGAGAGAGATTTGA
1 GAGAAA-TTAAGAGAGAATTGA
5505067 GA
1 GA
5505069 ATGAGAGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (21 bp):
GAGAAATTAAGAGAGAATTGA
Found at i:5505764 original size:18 final size:18
Alignment explanation
Indices: 5505743--5505778 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5505733 AAATCAACTT
*
5505743 AATTCGATTAATCGGTCG
1 AATTCGATTAATCAGTCG
5505761 AATTCGATTAATCAGTCG
1 AATTCGATTAATCAGTCG
5505779 GCTAATCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (18 bp):
AATTCGATTAATCAGTCG
Found at i:5507634 original size:11 final size:11
Alignment explanation
Indices: 5507620--5507667 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
5507610 ATATTCAAAT
*
5507620 AATAATAACAA
1 AATAATAGCAA
*
5507631 AATAATAGTAA
1 AATAATAGCAA
*
5507642 AATAATAGCGA
1 AATAATAGCAA
*
5507653 AATGATAGCAA
1 AATAATAGCAA
5507664 AATA
1 AATA
5507668 GCAACGAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:5517586 original size:31 final size:31
Alignment explanation
Indices: 5517546--5517614 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
5517536 CAAATCCAAT
* *
5517546 AATCTCAGTTGAATTATTAT-ATTGATACTAA
1 AATCCCAGTTGAATTATTATGA-TAATACTAA
*
5517577 AATCCCAGTTGAATTATTATGATAATGCTAA
1 AATCCCAGTTGAATTATTATGATAATACTAA
5517608 AATCCCA
1 AATCCCA
5517615 CCAACACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (31 bp):
AATCCCAGTTGAATTATTATGATAATACTAA
Found at i:5519698 original size:3 final size:3
Alignment explanation
Indices: 5519690--5519714 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5519680 TTATTAGTGT
5519690 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5519715 GGGGAGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5524890 original size:8 final size:9
Alignment explanation
Indices: 5524853--5524888 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
5524843 GGTGTTTCCC
5524853 TAGGGTTTT
1 TAGGGTTTT
5524862 TAGGGTTTT
1 TAGGGTTTT
* *
5524871 TCGGATTTT
1 TAGGGTTTT
5524880 TAGGGTTTT
1 TAGGGTTTT
5524889 AGAGAGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.11, C:0.03, G:0.31, T:0.56
Consensus pattern (9 bp):
TAGGGTTTT
Found at i:5529703 original size:26 final size:24
Alignment explanation
Indices: 5529672--5529721 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
5529662 CTCGATTTTT
5529672 AATAAACACAAAAAAAATATTTTAAA
1 AATAAA-A-AAAAAAAATATTTTAAA
*
5529698 AATAAAAAATAAAAATATTTTAAA
1 AATAAAAAAAAAAAATATTTTAAA
5529722 CGTATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
25 1 0.04
26 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
AATAAAAAAAAAAAATATTTTAAA
Found at i:5531070 original size:58 final size:58
Alignment explanation
Indices: 5531006--5531136 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 58
5530996 ACAAAAATGG
* *
5531006 TGAAAATGAAGAAATGAGAAACATTTGGAAATGATTATGATTTTCTCCAAAAT-AAAAA
1 TGAAAAT-AAGAAATGAGAAACATTTGGAAATGAATATGATTTTATCCAAAATGAAAAA
* * * *
5531064 TGAAAATAGAGAAATG-GAATCATTTGGAAATGAATGTGGTTTTATTCAAAATGAAAAA
1 TGAAAATA-AGAAATGAGAAACATTTGGAAATGAATATGATTTTATCCAAAATGAAAAA
*
5531122 TAAAAATAA-AAATGA
1 TGAAAATAAGAAATGA
5531137 CCTGGAAATG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
56 5 0.08
57 32 0.51
58 26 0.41
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (58 bp):
TGAAAATAAGAAATGAGAAACATTTGGAAATGAATATGATTTTATCCAAAATGAAAAA
Found at i:5532000 original size:16 final size:16
Alignment explanation
Indices: 5531979--5532011 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5531969 TCTTATAATT
5531979 GTATACATGTTTTGGG
1 GTATACATGTTTTGGG
5531995 GTATACATGTTTTGGG
1 GTATACATGTTTTGGG
5532011 G
1 G
5532012 AATATTTGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.33, T:0.42
Consensus pattern (16 bp):
GTATACATGTTTTGGG
Found at i:5535681 original size:3 final size:3
Alignment explanation
Indices: 5535673--5535723 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
5535663 TGGTTTGAAG
5535673 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5535720 GAA G
1 GAA G
5535724 GCCAATACGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5545603 original size:14 final size:15
Alignment explanation
Indices: 5545578--5545606 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5545568 ATTAATTTTG
5545578 ATCAAGTCAAATTAA
1 ATCAAGTCAAATTAA
5545593 ATCAA-TCAAATTAA
1 ATCAAGTCAAATTAA
5545607 TTAAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (15 bp):
ATCAAGTCAAATTAA
Found at i:5549009 original size:23 final size:23
Alignment explanation
Indices: 5548982--5549603 Score: 295
Period size: 23 Copynumber: 26.7 Consensus size: 23
5548972 ACTACATATT
5548982 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* * *
5549005 ACAAAATAT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
*
5549028 ACAAAATTTGG-CAGCAT-TGATTC
1 AC-AAATTTGGACAGCATGT-ATAC
* * ** *
5549051 ACCAAAATTGGGCAGCATACATAT
1 A-CAAATTTGGACAGCATGTATAC
5549075 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* *
5549098 ACAAAATAT-AACAGCATGTATGTAC
1 AC-AAATTTGGACAGCATGTA--TAC
5549123 A-AAATTT-GACAGCATTGCT-T-C
1 ACAAATTTGGACAGCA-TG-TATAC
* * **
5549144 ACCAAAATTGGGCAGCATACATAC
1 A-CAAATTTGGACAGCATGTATAC
5549168 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* *
5549191 ACAAAATTT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
* *
5549214 ACAAAATTGGACAGCAT-TGATTC
1 ACAAATTTGGACAGCATGT-ATAC
* * ** *
5549237 ACCAAAATTGGGCAGCATACATAT
1 A-CAAATTTGGACAGCATGTATAC
5549261 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* * *
5549284 ACAAAATAT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
* *
5549307 ACAAAATTGGACAGCATTTATTCAC
1 ACAAATTTGGACAGCATGTA-T-AC
* * **
5549332 CCAAAATTAGG-CAGCATACATAC
1 AC-AAATTTGGACAGCATGTATAC
*
5549355 ACAAATTTGGACAGCATTTATAC
1 ACAAATTTGGACAGCATGTATAC
* * *
5549378 ACAAAATTT-AATAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
* *
5549401 ACAAAATTGGACAGCAT-TGATTC
1 ACAAATTTGGACAGCATGT-ATAC
* * ** *
5549424 ACCAAAATTGGGCAGCATACATAT
1 A-CAAATTTGGACAGCATGTATAC
5549448 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* * *
5549471 ACAAAATAT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
*
5549494 ACAAAATTGGACAGCATTGCT-T-C
1 ACAAATTTGGACAGCA-TG-TATAC
* * **
5549517 ACCAAAATTGGGCAGCATACATAC
1 A-CAAATTTGGACAGCATGTATAC
5549541 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* *
5549564 ACAAAATTT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
5549587 ACAAAATTT-GACAGCAT
1 AC-AAATTTGGACAGCAT
5549604 TGATTTATCA
Statistics
Matches: 458, Mismatches: 90, Indels: 102
0.70 0.14 0.16
Matches are distributed among these distances:
21 2 0.00
22 35 0.08
23 280 0.61
24 120 0.26
25 15 0.03
26 6 0.01
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (23 bp):
ACAAATTTGGACAGCATGTATAC
Found at i:5549085 original size:93 final size:93
Alignment explanation
Indices: 5548974--5549634 Score: 1135
Period size: 93 Copynumber: 7.1 Consensus size: 93
5548964 CTAACTATAC
5548974 TACATATTACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGG
1 TACATA-TACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAA-TTGG
5549039 -CAGCATTGATTCACCAAAATTGGGCAGCA
64 ACAGCATTGATTCACCAAAATTGGGCAGCA
* *
5549068 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATGTACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
*
5549133 AGCATTGCTTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
* *
5549161 TACATACACAAATTTGGACAGCACTTATACACAAAATTTAACAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
5549226 AGCATTGATTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
5549254 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
* *
5549319 AGCATTTATTCACCCAAAATTAGGCAGCA
66 AGCATTGATTCA-CCAAAATTGGGCAGCA
* * * *
5549348 TACATACACAAATTTGGACAGCATTTATACACAAAATTTAATAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
5549413 AGCATTGATTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
5549441 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
*
5549506 AGCATTGCTTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
* * *
5549534 TACATACACAAATTTGGACAGCACTTATACACAAAATTTAACAGCATGTATATACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
* *
5549599 AGCATTGATTTATCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
5549627 TACATATA
1 TACATATA
5549635 ACAATTGGGC
Statistics
Matches: 535, Mismatches: 30, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
92 3 0.01
93 439 0.82
94 93 0.17
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (93 bp):
TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTGGAC
AGCATTGATTCACCAAAATTGGGCAGCA
Found at i:5550003 original size:28 final size:28
Alignment explanation
Indices: 5549971--5550097 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
5549961 ATTTAATAAG
* * *
5549971 CTCGCACACTTAGTGCTCAATAATCAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
5549999 CTCGCACACTTAGTGCTTTACCATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
5550027 CTCGCACACTTAGTGCTCTACAATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
5550055 CTCGCACACTTAGTGCTTTATAATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
*
5550083 TTCGCACACTTAGTG
1 CTCGCACACTTAGTG
5550098 TCGAAAATTA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 89 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (28 bp):
CTCGCACACTTAGTGCTCTACAATTAAA
Found at i:5556394 original size:23 final size:23
Alignment explanation
Indices: 5556367--5556615 Score: 119
Period size: 23 Copynumber: 10.7 Consensus size: 23
5556357 ACTACATATT
5556367 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* * *
5556390 ACAAAATAT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
*
5556413 ACAAAATTTGG-CAGCAT-TGATTC
1 AC-AAATTTGGACAGCATGT-ATAC
* * ** *
5556436 ACCAAAATTGGGCAGCATACATAT
1 A-CAAATTTGGACAGCATGTATAC
5556460 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* *
5556483 ACAAAATAT-AACAGCATGTATGTAC
1 AC-AAATTTGGACAGCATGTA--TAC
5556508 A-AAATTT-GACAGCATTGCT-T-C
1 ACAAATTTGGACAGCA-TG-TATAC
* * **
5556529 ACCAAAATTGGGCAGCATACATAC
1 A-CAAATTTGGACAGCATGTATAC
5556553 ACAAATTTGGACAGCACT-TATAC
1 ACAAATTTGGACAGCA-TGTATAC
* *
5556576 ACAAAATTT-AACAGCATGTATAT
1 AC-AAATTTGGACAGCATGTATAC
5556599 ACAAAATTT-GACAGCAT
1 AC-AAATTTGGACAGCAT
5556616 TGATTTATCA
Statistics
Matches: 175, Mismatches: 29, Indels: 44
0.71 0.12 0.18
Matches are distributed among these distances:
21 2 0.01
22 5 0.03
23 125 0.71
24 38 0.22
25 5 0.03
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (23 bp):
ACAAATTTGGACAGCATGTATAC
Found at i:5556470 original size:93 final size:93
Alignment explanation
Indices: 5556359--5556646 Score: 504
Period size: 93 Copynumber: 3.1 Consensus size: 93
5556349 CTAACTATAC
*
5556359 TACATATTACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGG
1 TACATA-TACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGA
5556424 CAGCATTGATTCACCAAAATTGGGCAGCA
65 CAGCATTGATTCACCAAAATTGGGCAGCA
*
5556453 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATGTACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
*
5556518 AGCATTGCTTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
* *
5556546 TACATACACAAATTTGGACAGCACTTATACACAAAATTTAACAGCATGTATATACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
* *
5556611 AGCATTGATTTATCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
5556639 TACATATA
1 TACATATA
5556647 ACAATTGGGC
Statistics
Matches: 184, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 178 0.97
94 6 0.03
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (93 bp):
TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
AGCATTGATTCACCAAAATTGGGCAGCA
Found at i:5557417 original size:28 final size:28
Alignment explanation
Indices: 5557385--5557511 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
5557375 ATTTAATAAG
* * *
5557385 CTCGCACACTTAGTGCTCAATAATCAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
5557413 CTCGCACACTTAGTGCTTTACCATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
5557441 CTCGCACACTTAGTGCTCTACAATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
5557469 CTCGCACACTTAGTGCTTTATAATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
*
5557497 TTCGCACACTTAGTG
1 CTCGCACACTTAGTG
5557512 TCGAAAATCA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 89 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (28 bp):
CTCGCACACTTAGTGCTCTACAATTAAA
Found at i:5558130 original size:9 final size:9
Alignment explanation
Indices: 5558116--5558183 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
5558106 TTTGATTAAA
5558116 AATTACCCG
1 AATTACCCG
5558125 AATTACCCG
1 AATTACCCG
5558134 AATTACCCG
1 AATTACCCG
*
5558143 AATTAACCG
1 AATTACCCG
5558152 AATTA-CCG
1 AATTACCCG
*
5558160 AAAAATACCCG
1 --AATTACCCG
*
5558171 AATTACCTG
1 AATTACCCG
5558180 AATT
1 AATT
5558184 TTTTTTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
8 3 0.06
9 42 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:5558343 original size:13 final size:13
Alignment explanation
Indices: 5558325--5558354 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5558315 TTTTAGTTTT
5558325 ATTGGGTTGAGTA
1 ATTGGGTTGAGTA
*
5558338 ATTGGGTTGGGTA
1 ATTGGGTTGAGTA
5558351 ATTG
1 ATTG
5558355 AGTTTGGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGAGTA
Found at i:5560556 original size:228 final size:231
Alignment explanation
Indices: 5560322--5560824 Score: 580
Period size: 230 Copynumber: 2.2 Consensus size: 231
5560312 TAATACAACG
*
5560322 CCGCTAAAT-ATCAGTATTAGCGGCGCTT-CTAGTTAAGCACCGCAAGATAT-GCACACCAAAAC
1 CCGCTAAATCAT-ATTATTAGCGGCGCTTACTAGTTAAGCACCGCAAGATATAGCA-ACCAAAAC
* * * *
5560384 G-TAGAGCTT-GGTATTGAGGTATATTAG-ATGTAGTGGCGCTTT-C-AGAAAACGCTGCAAAAG
64 GCTA-AGCTTAGATATTGACGTATACTAGAAT-TAGTGGCG-TTTACAAGAAAACGCCGCAAAA-
* * * * *
5560444 T-ATACTATTAGCGGCACTTTCTTAGAAGTGCCGCAATATATATTAACGGAAAAGCTGCGTTTAA
125 TCATACTATTAGCAGCACTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAAAGCTACGTTTAA
* *
5560508 ATCTTGATGTATACTGGAGTTAGTGGCGTTCACGAGAAATCA
190 ATCTTGATGTATACGGGAATTAGTGGCGTTCACGAGAAATCA
* * ** *
5560550 CCGCTAAATCATATTATTAGCGGCGCTTGCTAAG--AAGCGCCGCAAGATATATTAACCTAAACG
1 CCGCTAAATCATATTATTAGCGGCGCTTACT-AGTTAAGCACCGCAAGATATAGCAACCAAAACG
* * * * * *
5560613 CTACGTTTAGATCTTGACGTATACTGGAATTAGTGGCGTTTACAAGAAATCGCCGCTAAATCATA
65 CTAAGCTTAGATATTGACGTATACTAGAATTAGTGGCGTTTACAAGAAAACGCCGCAAAATCATA
* * * *
5560678 TTATTGGCAGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTACGTTTAAATCTT
130 CTATTAGCAGCACTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAAAGCTACGTTTAAATCTT
*
5560743 GATGTATACGGGAATTAGTGGCGTTCACGAGAAATCG
195 GATGTATACGGGAATTAGTGGCGTTCACGAGAAATCA
* * *
5560780 CTGCTAAATCATATTATTAGCGGCGCTTATTTGTT-AGCACCGCAA
1 CCGCTAAATCATATTATTAGCGGCGCTTACTAGTTAAGCACCGCAA
5560825 AAGATCTTTC
Statistics
Matches: 231, Mismatches: 32, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
228 53 0.23
229 31 0.13
230 147 0.64
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (231 bp):
CCGCTAAATCATATTATTAGCGGCGCTTACTAGTTAAGCACCGCAAGATATAGCAACCAAAACGC
TAAGCTTAGATATTGACGTATACTAGAATTAGTGGCGTTTACAAGAAAACGCCGCAAAATCATAC
TATTAGCAGCACTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAAAGCTACGTTTAAATCTTG
ATGTATACGGGAATTAGTGGCGTTCACGAGAAATCA
Found at i:5560603 original size:115 final size:115
Alignment explanation
Indices: 5560449--5560807 Score: 547
Period size: 115 Copynumber: 3.1 Consensus size: 115
5560439 AAAAGTATAC
* * * * * *
5560449 TATTAGCGGCACTTTCTTAGAAGTGCCGCAATATATATTAACGGAAAAGCTGCGTTTAAATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTACGTTTAAATCTTG
* *
5560514 ATGTATACTGGAGTTAGTGGCGTTCACGAGAAATCACCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
* * * *
5560564 TATTAGCGGCGCTTGCTAAGAAGCGCCGCAAGATATATTAACCTAAACGCTACGTTTAGATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTACGTTTAAATCTTG
* * *
5560629 ACGTATACTGGAATTAGTGGCGTTTACAAGAAATCGCCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
* *
5560679 TATTGGCAGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTACGTTTAAATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTACGTTTAAATCTTG
* *
5560744 ATGTATACGGGAATTAGTGGCGTTCACGAGAAATCGCTGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
5560794 TATTAGCGGCGCTT
1 TATTAGCGGCGCTT
5560808 ATTTGTTAGC
Statistics
Matches: 216, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 216 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (115 bp):
TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTACGTTTAAATCTTG
ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
Found at i:5561848 original size:71 final size:71
Alignment explanation
Indices: 5561759--5561903 Score: 263
Period size: 71 Copynumber: 2.0 Consensus size: 71
5561749 TTAATAATAT
* *
5561759 TAATAATGTCATAATTTTAATGTATGAATTAAAAATAATGTCTACAACAATGTAAATAATTTATA
1 TAATAATGGCATAATTTTAATGTATGAATCAAAAATAATGTCTACAACAATGTAAATAATTTATA
5561824 AAAAGC
66 AAAAGC
*
5561830 TAATAATGGCCTAATTTTAATGTATGAATCAAAAATAATGTCTACAACAATGTAAATAATTTATA
1 TAATAATGGCATAATTTTAATGTATGAATCAAAAATAATGTCTACAACAATGTAAATAATTTATA
5561895 AAAAGC
66 AAAAGC
5561901 TAA
1 TAA
5561904 ATATTAGCGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (71 bp):
TAATAATGGCATAATTTTAATGTATGAATCAAAAATAATGTCTACAACAATGTAAATAATTTATA
AAAAGC
Found at i:5562543 original size:45 final size:45
Alignment explanation
Indices: 5562483--5562573 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
5562473 TTTTGCGTCC
* *
5562483 TTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCCT
* *
5562528 TTCTTGCCTAATTTCTTGAAATCCGAAATCCCTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCCT
5562573 T
1 T
5562574 CCTCTTTCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (45 bp):
TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCCT
Found at i:5563197 original size:23 final size:23
Alignment explanation
Indices: 5563170--5563228 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
5563160 ATTTTATACA
5563170 TTAAAGTATGCAAAAACATGTAC
1 TTAAAGTATGCAAAAACATGTAC
5563193 TTAAAGTATGCAAAAACATGTAC
1 TTAAAGTATGCAAAAACATGTAC
5563216 TTAAAGTATGCAA
1 TTAAAGTATGCAA
5563229 CAGAGCCTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (23 bp):
TTAAAGTATGCAAAAACATGTAC
Found at i:5564265 original size:15 final size:15
Alignment explanation
Indices: 5564245--5564279 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5564235 ATTTACCTAA
5564245 TTAAATAAATTGTAT
1 TTAAATAAATTGTAT
5564260 TTAAATAAATTGTAT
1 TTAAATAAATTGTAT
5564275 TTAAA
1 TTAAA
5564280 GTTTTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTAAATAAATTGTAT
Found at i:5564382 original size:18 final size:17
Alignment explanation
Indices: 5564354--5564403 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
5564344 TTAAAGTTCA
*
5564354 AATTTCATATCTTACGT
1 AATTTCATATCTTACAT
5564371 AATTTACATATCTTACAT
1 AATTT-CATATCTTACAT
*
5564389 AA-TTCATAACTTACA
1 AATTTCATATCTTACA
5564404 CAACTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 13 0.43
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTCATATCTTACAT
Found at i:5564479 original size:19 final size:19
Alignment explanation
Indices: 5564457--5564494 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5564447 TTATATATAG
5564457 TTTATATATATATTTAAAA
1 TTTATATATATATTTAAAA
*
5564476 TTTATATATATTTTTAAAA
1 TTTATATATATATTTAAAA
5564495 ATTGATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATATATATATTTAAAA
Found at i:5564549 original size:23 final size:22
Alignment explanation
Indices: 5564499--5564699 Score: 65
Period size: 24 Copynumber: 9.3 Consensus size: 22
5564489 TTAAAAATTG
5564499 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
5564522 CTACATACATAAGCTTACAT---
1 ATACATACATAA-CTTACATAAC
*
5564542 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
* * * *
5564563 TTAAATTTAGCA-ATCATATCATAAC
1 ATACA--TA-CATAACTTA-CATAAC
* *
5564588 TTACATACATAA-TTA-GT-A-
1 ATACATACATAACTTACATAAC
*
5564606 AT-CATATCACAACTTACATAACC
1 ATACATA-CATAACTTACATAA-C
*
5564629 A-ACATA-ATGACTTACATAATAAC
1 ATACATACATAACTTAC---ATAAC
* *
5564652 CTACATA-ATAACTTACATAATA
1 ATACATACATAACTTACATAA-C
5564674 ATACATA-ATAA--TACATAAC
1 ATACATACATAACTTACATAAC
*
5564693 ATCCATA
1 ATACATA
5564700 AATTAAATAA
Statistics
Matches: 134, Mismatches: 22, Indels: 48
0.66 0.11 0.24
Matches are distributed among these distances:
17 4 0.03
18 11 0.08
19 18 0.13
20 11 0.08
21 14 0.10
22 22 0.16
23 20 0.15
24 23 0.17
25 11 0.08
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:5564643 original size:21 final size:21
Alignment explanation
Indices: 5564616--5564692 Score: 68
Period size: 24 Copynumber: 3.6 Consensus size: 21
5564606 ATCATATCAC
5564616 AACTTACATAACCAACATAAT
1 AACTTACATAACCAACATAAT
* *
5564637 GACTTACATAATAACCTACATAAT
1 AACTTAC---ATAACCAACATAAT
**
5564661 AACTTACATAATAATACATAAT
1 AACTTACATAACCA-ACATAAT
5564683 AA--TACATAAC
1 AACTTACATAAC
5564693 ATCCATAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.16
21 10 0.22
22 9 0.20
24 19 0.42
ACGTcount: A:0.52, C:0.19, G:0.01, T:0.27
Consensus pattern (21 bp):
AACTTACATAACCAACATAAT
Found at i:5564647 original size:12 final size:12
Alignment explanation
Indices: 5564630--5564791 Score: 79
Period size: 12 Copynumber: 13.8 Consensus size: 12
5564620 TACATAACCA
*
5564630 ACATAATGACTT
1 ACATAATAACTT
*
5564642 ACATAATAACCT
1 ACATAATAACTT
5564654 ACATAATAACTT
1 ACATAATAACTT
5564666 ACATAATAA--T
1 ACATAATAACTT
5564676 ACATAATAA--T
1 ACATAATAACTT
* * *
5564686 ACATAACATCCAT
1 ACATAATA-ACTT
* *
5564699 AAATTAAATAAGTT
1 ACA-T-AATAACTT
**
5564713 ACATAATACACAA
1 ACATAATA-ACTT
* * *
5564726 AAACAAAAACTT
1 ACATAATAACTT
5564738 AC---ATAACTT
1 ACATAATAACTT
* *
5564747 ACATAATATCCT
1 ACATAATAACTT
**
5564759 ACATCCCT-ACTT
1 ACAT-AATAACTT
5564771 ACATAATAACTT
1 ACATAATAACTT
5564783 ACATAATAA
1 ACATAATAA
5564792 TACATACTCT
Statistics
Matches: 110, Mismatches: 29, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
9 8 0.07
10 18 0.16
11 1 0.01
12 65 0.59
13 11 0.10
14 4 0.04
15 3 0.03
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.28
Consensus pattern (12 bp):
ACATAATAACTT
Found at i:5564657 original size:24 final size:24
Alignment explanation
Indices: 5564623--5564691 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
5564613 CACAACTTAC
* *
5564623 ATAACCAACATAATGACTTACATA
1 ATAACCTACATAATAACTTACATA
5564647 ATAACCTACATAATAACTTACATA
1 ATAACCTACATAATAACTTACATA
5564671 ATAA--TACATAATAA--TACATA
1 ATAACCTACATAATAACTTACATA
5564691 A
1 A
5564692 CATCCATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.16
22 10 0.23
24 26 0.60
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (24 bp):
ATAACCTACATAATAACTTACATA
Found at i:5564806 original size:19 final size:19
Alignment explanation
Indices: 5564776--5564826 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
5564766 TACTTACATA
5564776 ATAACTTACATAATAATAC
1 ATAACTTACATAATAATAC
5564795 AT-ACTCTACATAATAATAC
1 ATAACT-TACATAATAATAC
5564814 ATAACTTACATAA
1 ATAACTTACATAA
5564827 GACATAACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.10
19 24 0.80
20 3 0.10
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATAATAC
Found at i:5564823 original size:9 final size:9
Alignment explanation
Indices: 5564776--5564914 Score: 107
Period size: 9 Copynumber: 15.9 Consensus size: 9
5564766 TACTTACATA
5564776 ATAACTTAC
1 ATAACTTAC
5564785 ATAA-TAATAC
1 ATAACT--TAC
5564795 AT-ACTCTAC
1 ATAACT-TAC
5564804 ATAA-TAATAC
1 ATAACT--TAC
5564814 ATAACTTAC
1 ATAACTTAC
*
5564823 ATAA--GAC
1 ATAACTTAC
*
5564830 ATAACGTAC
1 ATAACTTAC
* *
5564839 ATAAGTTTC
1 ATAACTTAC
5564848 ATAA--TAC
1 ATAACTTAC
*
5564855 ACAACTTAC
1 ATAACTTAC
*
5564864 ACAACTTAC
1 ATAACTTAC
*
5564873 ACAACTTAC
1 ATAACTTAC
5564882 ATAACTTAC
1 ATAACTTAC
5564891 ATAACTTAC
1 ATAACTTAC
5564900 ATAA--TAC
1 ATAACTTAC
5564907 ATAACTTA
1 ATAACTTA
5564915 TTCCTAAATC
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
7 18 0.17
8 1 0.01
9 74 0.69
10 14 0.13
11 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.29
Consensus pattern (9 bp):
ATAACTTAC
Found at i:5564864 original size:25 final size:25
Alignment explanation
Indices: 5564811--5564914 Score: 127
Period size: 25 Copynumber: 4.1 Consensus size: 25
5564801 TACATAATAA
* *
5564811 TACATAACTTACATAAGACATAACG
1 TACATAACTTACATAATACATAACT
* * *
5564836 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACATAACT
* *
5564861 TACACAACTTACACAACTTACATAACT
1 TACATAACTTACATAA--TACATAACT
5564888 TACATAACTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
5564913 TA
1 TA
5564915 TTCCTAAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 43 0.66
27 22 0.34
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:5573792 original size:21 final size:21
Alignment explanation
Indices: 5573766--5573834 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
5573756 CAACAACTTA
* *
5573766 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
**
5573787 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
5573808 AAGCAAAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
5573829 AAGCAG
1 AAGCAG
5573835 CGATAGAAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:5574301 original size:43 final size:42
Alignment explanation
Indices: 5574254--5574345 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
5574244 ATCAAACAGT
* *
5574254 GGCGTTTGTGAAATAAGCACCGCTAAAGAACA-CTACTTTTAGC
1 GGCGTTTGTG-AACAAGCACCGCTAAAGAACATC-ACTTTTAGA
* * *
5574297 GGCGTTTTTGAACAAGCGCCGCTATAGAACATCACTTTTAGA
1 GGCGTTTGTGAACAAGCACCGCTAAAGAACATCACTTTTAGA
5574339 GGCGTTT
1 GGCGTTT
5574346 TCTTCCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 33 0.77
43 10 0.23
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (42 bp):
GGCGTTTGTGAACAAGCACCGCTAAAGAACATCACTTTTAGA
Found at i:5574326 original size:42 final size:42
Alignment explanation
Indices: 5574254--5574456 Score: 148
Period size: 43 Copynumber: 4.8 Consensus size: 42
5574244 ATCAAACAGT
* * *
5574254 GGCGTTTGTGAAATAAGCACCGCTAAAGAACA-CTACTTTTAGC
1 GGCGTTTTTG-AACAAGCGCCGCTAAAGAACATC-ACTTTTAGC
* *
5574297 GGCGTTTTTGAACAAGCGCCGCTATAGAACATCACTTTTAGA
1 GGCGTTTTTGAACAAGCGCCGCTAAAGAACATCACTTTTAGC
** *
5574339 GGCGTTTTCT-TCCAAAGCGCCGCTAAAGAACATGA-TCTTTAGC
1 GGCGTTTT-TGAAC-AAGCGCCGCTAAAGAACATCACT-TTTAGC
** * *
5574382 GGCGTTTATT-TCCTTAGCGCCGCTAAAGAACATGA-TCTTTAGC
1 GGCGTTT-TTGAAC-AAGCGCCGCTAAAGAACATCACT-TTTAGC
***
5574425 GGCGTTTATT-TTTAAGCGCCGCTAAAGAACAT
1 GGCGTTT-TTGAACAAGCGCCGCTAAAGAACAT
5574457 GGTCTTTAGT
Statistics
Matches: 140, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
42 54 0.39
43 85 0.61
44 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (42 bp):
GGCGTTTTTGAACAAGCGCCGCTAAAGAACATCACTTTTAGC
Found at i:5574457 original size:42 final size:41
Alignment explanation
Indices: 5574267--5574578 Score: 317
Period size: 42 Copynumber: 7.4 Consensus size: 41
5574257 GTTTGTGAAA
* **
5574267 TAAGCACCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAA
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TT
* * * * *
5574309 CAAGCGCCGCTATAGAACATCA-CTTTTAGAGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TT-T
*
5574352 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCCT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTT--T
5574396 T-AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTT
* *
5574437 TAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTATTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTT
* * *
5574479 TTAGCGCCACTAAAGAACATGATCTTTAGCGGTGTTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
* *
5574520 CTAAGCGCCGCTAAAGAACATGATCTTTAGAGGCTTTTTTTCT
1 -TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-T
*
5574563 GTAAGCGCCGCAAAAG
1 -TAAGCGCCGCTAAAG
5574579 TTTGCGACGT
Statistics
Matches: 235, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
41 7 0.03
42 137 0.58
43 88 0.37
44 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
Found at i:5578986 original size:18 final size:18
Alignment explanation
Indices: 5578960--5578994 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5578950 GCGGAGTAAA
*
5578960 AAATACAAATTTAAATCC
1 AAATACAAATTCAAATCC
*
5578978 AAATCCAAATTCAAATC
1 AAATACAAATTCAAATC
5578995 TGAATGGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACAAATTCAAATCC
Found at i:5579121 original size:3 final size:3
Alignment explanation
Indices: 5579113--5579155 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
5579103 GAGTACCAAT
* * *
5579113 TCA TCA TCA TCA ACA TTA TCA TCA TCT TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5579156 TAAGGACATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:5583868 original size:43 final size:42
Alignment explanation
Indices: 5583802--5583971 Score: 177
Period size: 43 Copynumber: 4.0 Consensus size: 42
5583792 ATAGGATTTC
*
5583802 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACATTGGCAT
* *
5583845 CGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TTGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
* * **
5583888 CGTATT-TGATT-CGTGTAAGACTC-TGTTTGGGACAACGGCAT
1 CG-ATTGTGATTACGTGTAAGAC-CACGTCTGGGACATTGGCAT
* *
5583929 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
5583972 TGTACGAGTC
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
40 2 0.02
41 28 0.26
42 11 0.10
43 61 0.57
44 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
CGATTGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
Found at i:5584161 original size:16 final size:17
Alignment explanation
Indices: 5584132--5584163 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5584122 TGAATTGATG
5584132 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
5584149 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
5584164 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:5593272 original size:14 final size:12
Alignment explanation
Indices: 5593241--5593269 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5593231 TTGTTTCTAT
5593241 TATATGTACATG
1 TATATGTACATG
5593253 TATATGTACATG
1 TATATGTACATG
5593265 TATAT
1 TATAT
5593270 ATGACTGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (12 bp):
TATATGTACATG
Found at i:5601341 original size:6 final size:6
Alignment explanation
Indices: 5601330--5601355 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5601320 TCTAAATTCA
5601330 CATTGC CATTGC CATTGC CATTGC CA
1 CATTGC CATTGC CATTGC CATTGC CA
5601356 AATACATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (6 bp):
CATTGC
Found at i:5607426 original size:126 final size:123
Alignment explanation
Indices: 5607241--5607591 Score: 560
Period size: 126 Copynumber: 2.8 Consensus size: 123
5607231 TAATTTTGAG
**
5607241 TTGACGTTTCTGATAAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
5607306 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAAT-A--ATTTTT
* *
5607367 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * *
5607432 AAATCGCGGCCTCGT-CAGCGTGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
66 AAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTTTT
*
5607490 TTGACGTTTCTGAGCAAATAATATAAAATTGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
5607555 AAATCGCGCCCTCGTGGACGCGTTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
5607592 CATGTTTGGG
Statistics
Matches: 207, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
123 99 0.48
124 1 0.00
125 2 0.01
126 105 0.51
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTTTT
Found at i:5610834 original size:115 final size:115
Alignment explanation
Indices: 5610622--5611138 Score: 1016
Period size: 115 Copynumber: 4.5 Consensus size: 115
5610612 TGATAAATTG
*
5610622 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTC-AAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
5610687 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
65 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
5610738 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
1 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
5610803 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
5610853 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
1 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
5610918 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
5610968 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
1 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
5611033 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
5611083 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTA
1 TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTA
5611139 AGTTAAGGGT
Statistics
Matches: 400, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
115 391 0.98
116 9 0.02
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (115 bp):
TATTAAGTCAAAAATAGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTT
AGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:5611186 original size:29 final size:29
Alignment explanation
Indices: 5611133--5611247 Score: 134
Period size: 29 Copynumber: 4.1 Consensus size: 29
5611123 AAATTATATA
* *
5611133 AAATTAAGTTAAGGGTTTAGTGTTTTTAATT
1 AAATTAGGTT-AGGG-TTAGGGTTTTTAATT
5611164 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
5611193 -AA--A--TTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5611216 AAATTAGGTTAAGGTTAGGGTTTTTAAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTAA-TT
5611246 AA
1 AA
5611248 GGGTTTAGGG
Statistics
Matches: 75, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
23 17 0.23
24 5 0.07
26 2 0.03
28 5 0.07
29 29 0.39
30 8 0.11
31 9 0.12
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.45
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:5611223 original size:18 final size:21
Alignment explanation
Indices: 5611177--5611219 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
5611167 TTAGGTTAGG
5611177 GTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATTAAA-TA
5611199 GGTTAGGGTTTTTAATTAAAT
1 -GTTAGGGTTTTTAATTAAAT
5611220 TAGGTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (21 bp):
GTTAGGGTTTTTAATTAAATA
Found at i:5611252 original size:103 final size:102
Alignment explanation
Indices: 5611136--5611445 Score: 411
Period size: 103 Copynumber: 3.0 Consensus size: 102
5611126 TTATATAAAA
5611136 TTAAGTTAAGGGTTTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAAGTTAAGGGTTTAG-GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
5611201 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
65 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
*
5611239 TTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGG
1 TTAAGTTAAGGGTTTA-GGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
*
5611304 TTAGGGTTTTTAATT---TTAAGTTAATGGTTTAGGGTTT
65 TTAGGGTTTTTAATTAAATTAGGTTAA-GG-TTAGGGTTT
* * * *
5611341 TTAA-TTAAATTAGGTTAAGGTTTTTAATTAAATTAGGCTAAGGTTAGGGTTTTTAAGTT-AA--
1 TTAAGTT-AA--GGGTTTAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAAATT
* *
5611402 GGGTTTAGGGTTTTTAATTAAATTAGGTT-AGGGTAGGGTTT
62 AGG-TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
5611443 TTA
1 TTA
5611446 CTATCACAAG
Statistics
Matches: 186, Mismatches: 10, Indels: 23
0.85 0.05 0.11
Matches are distributed among these distances:
100 8 0.04
101 6 0.03
102 41 0.22
103 116 0.62
104 9 0.05
105 6 0.03
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (102 bp):
TTAAGTTAAGGGTTTAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGT
TAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
Found at i:5611258 original size:22 final size:20
Alignment explanation
Indices: 5611223--5611268 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
5611213 ATTAAATTAG
5611223 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
5611243 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAA-GG-TTAGGGTTTTTAA
5611265 -TTAA
1 GTTAA
5611269 ATTAGGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:5611263 original size:74 final size:74
Alignment explanation
Indices: 5611174--5611435 Score: 382
Period size: 74 Copynumber: 3.5 Consensus size: 74
5611164 AAATTAGGTT
5611174 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT
5611238 TTTAAGTTA
66 TTTAAGTTA
*
5611247 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 AGGGTTTAGGGTTTTTAATT-AA--A--TTAG-GTTAGGGTTTTTAATTAAATTAGGTTAAGGTT
*****
5611312 TTTAATTTTAAGTTA
60 AGGGTTTTTAAGTTA
* * *
5611327 ATGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTTAATTAAATTAGGCTAAGGTTAGGGTT
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT
5611392 TTTAAGTTA
66 TTTAAGTTA
5611401 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGT
5611436 AGGGTTTTTA
Statistics
Matches: 165, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
73 4 0.02
74 87 0.53
75 6 0.04
77 2 0.01
79 6 0.04
80 60 0.36
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (74 bp):
AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT
TTTAAGTTA
Found at i:5611284 original size:29 final size:29
Alignment explanation
Indices: 5611252--5611401 Score: 118
Period size: 23 Copynumber: 5.6 Consensus size: 29
5611242 AGTTAAGGGT
5611252 TTAGGGTTTTTAATTAAATTAGGTTAGAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGAG
5611281 TTAGGGTTTTTAATT-AA--A--TTAG-G
1 TTAGGGTTTTTAATTAAATTAGGTTAGAG
*
5611304 TTAGGGTTTTTAATT---TTAAGTTAATG-G
1 TTAGGGTTTTTAATTAAATTAGGTT-A-GAG
5611331 TTTAGGGTTTTTAATTAAATTAGGTT--A-
1 -TTAGGGTTTTTAATTAAATTAGGTTAGAG
*
5611358 --A-GGTTTTTAATTAAATTAGGCTA-AGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGA-G
5611384 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAA-TTAA
5611402 GGGTTTAGGG
Statistics
Matches: 101, Mismatches: 2, Indels: 35
0.73 0.01 0.25
Matches are distributed among these distances:
23 37 0.37
24 6 0.06
25 2 0.02
26 2 0.02
27 2 0.02
28 18 0.18
29 24 0.24
30 4 0.04
31 6 0.06
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGAG
Found at i:5614472 original size:19 final size:20
Alignment explanation
Indices: 5614432--5614475 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5614422 GTCTCTTTAG
* *
5614432 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
5614451 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
5614470 GCATTA
1 GCATTA
5614476 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:5617080 original size:7 final size:8
Alignment explanation
Indices: 5617059--5617088 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5617049 TATCATGAAT
5617059 TCAAAAAA
1 TCAAAAAA
5617067 TCAAAAAA
1 TCAAAAAA
5617075 TCAAAAAAA
1 TC-AAAAAA
5617084 TCAAA
1 TCAAA
5617089 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (8 bp):
TCAAAAAA
Found at i:5619403 original size:86 final size:88
Alignment explanation
Indices: 5619200--5619463 Score: 349
Period size: 86 Copynumber: 3.0 Consensus size: 88
5619190 CAGATCAATG
*
5619200 AAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTC
1 AAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-ACACAAAGCCTTGCCTC
** * * *
5619264 TTTCGGTTG-TGATAGAGCTGGTTG
65 CATCGGTTGCAG-TGGAGCTGGTTA
*
5619288 AAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCC
1 AAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
* *
5619352 ATCGATTGCAGTGGAGCTAGTTA
66 ATCGGTTGCAGTGGAGCTGGTTA
** * *
5619375 AAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCC
1 AAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
*
5619438 ATCGGTTGCATTGGAGCTGGTTA
66 ATCGGTTGCAGTGGAGCTGGTTA
5619461 AAG
1 AAG
5619464 GTTACAGATT
Statistics
Matches: 157, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
85 3 0.02
86 79 0.50
87 28 0.18
88 47 0.30
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (88 bp):
AAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCTGGTTA
Found at i:5619701 original size:44 final size:44
Alignment explanation
Indices: 5619556--5619809 Score: 187
Period size: 44 Copynumber: 5.8 Consensus size: 44
5619546 TAAAATAAAG
* *
5619556 GATCTTATCTCTCTGAAGTTACAG-GAGAGCAGATCGCA-TCAG-
1 GATCTTATCTCCCTGAAGTTACAGTG-GAGCAGATCGAAGTCAGA
* * * * ***
5619598 G-TCTTATCTCCTTGAGGTTACAGTGGAGTAGACCGAAGAATTTCA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAG--TCAGA
* * *
5619643 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGTCAGA
* * * * *
5619687 GATCTTATCTCCCTG-AGATTGCAGCGGAGCAGATCAAAGACA-C
1 GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGTCAGA
* * * * * * *
5619730 TATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTGAAATAAAA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGTCAGA
* * *
5619774 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCG
5619810 CATCAAATTA
Statistics
Matches: 161, Mismatches: 42, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
41 28 0.17
42 2 0.01
43 30 0.19
44 67 0.42
45 1 0.01
46 33 0.20
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGTCAGA
Found at i:5619808 original size:87 final size:87
Alignment explanation
Indices: 5619648--5619808 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 87
5619638 TTTCAGATCT
* * * * * *
5619648 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTGCAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACAAAAGATCTTATCTCCCTGAGATTACAGCA
5619713 GAGCAGATCAAAGACACTATCC
66 GAGCAGATCAAAGACACTATCC
* * * *
5619735 TATCTCCCTGAAGTTACAGTGGAGCGGATTGAAATAAAAGATCTTATCTCTCTGA-AGTTACAGT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACAAAAGATCTTATCTCCCTGAGA-TTACAGC
*
5619799 AGAGTAGATC
65 AGAGCAGATC
5619809 GCATCAAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
86 1 0.02
87 61 0.98
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAACAAAAGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCAAAGACACTATCC
Found at i:5619832 original size:54 final size:54
Alignment explanation
Indices: 5619766--5619869 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
5619756 GAGCGGATTG
*
5619766 AAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAAATTA
1 AAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAATTA
* * *
5619820 AAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCATCAA
1 AAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAA
5619870 GTCTTATTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (54 bp):
AAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAAATTA
Found at i:5621701 original size:12 final size:12
Alignment explanation
Indices: 5621684--5621708 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5621674 AATCTTGTTC
5621684 ATTTCTTTATTT
1 ATTTCTTTATTT
5621696 ATTTCTTTATTT
1 ATTTCTTTATTT
5621708 A
1 A
5621709 CATTTTCATC
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTCTTTATTT
Found at i:5623634 original size:21 final size:21
Alignment explanation
Indices: 5623608--5623648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5623598 AGACAAGCGA
* *
5623608 TACTCCACAATAGGTGGAGTG
1 TACTCCAAAAAAGGTGGAGTG
5623629 TACTCCAAAAAAGGTGGAGT
1 TACTCCAAAAAAGGTGGAGT
5623649 TTGAGCAGGT
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:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (21 bp):
TACTCCAAAAAAGGTGGAGTG
Found at i:5625811 original size:68 final size:67
Alignment explanation
Indices: 5625739--5625888 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
5625729 CATCATGTGT
* * * *
5625739 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
5625801 ATGTAG
62 ATGTAG
** * *
5625807 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
5625872 AG
66 AG
5625874 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
5625889 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:5625844 original size:64 final size:64
Alignment explanation
Indices: 5625763--5625946 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
5625753 AGACATTATG
* *
5625763 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
5625827 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
5625892 AA
63 AA
* * * *
5625894 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
5625947 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:5630275 original size:38 final size:38
Alignment explanation
Indices: 5630219--5630298 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
5630209 GATGTGTATT
* * *
5630219 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
*
5630257 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
5630295 CGGG
1 CGGG
5630299 CCTTCGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:5630415 original size:43 final size:43
Alignment explanation
Indices: 5630291--5630402 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
5630281 GCTGGTATTA
5630291 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
5630334 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
5630377 TCTTCGAGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
5630403 GTAATGCCGG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.10, C:0.28, G:0.33, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:5630800 original size:45 final size:45
Alignment explanation
Indices: 5630733--5630859 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
5630723 TTGATTTGAT
* * *
5630733 TATTCGGGCCTTT-GAGCTTAGCAGACTATAATGCCGGTGAGAT-A
1 TATTCGGG-CTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
*
5630777 CTATTCGGGCTTTCGAGCCTAGCAGGCTATAAAGCCGGTGAAATGA
1 -TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
* *
5630823 TA-TCGGGC-CTCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCGGTGA
5630860 TTTGAGAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 10 0.14
43 16 0.22
44 10 0.14
45 36 0.49
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (45 bp):
TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
Found at i:5638973 original size:12 final size:12
Alignment explanation
Indices: 5638956--5638986 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5638946 ACAAAATCGG
5638956 GTTTTCCAGGCC
1 GTTTTCCAGGCC
5638968 GTTTTCCAGGCC
1 GTTTTCCAGGCC
5638980 GTTTTCC
1 GTTTTCC
5638987 TATTGTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.32, G:0.23, T:0.39
Consensus pattern (12 bp):
GTTTTCCAGGCC
Found at i:5643848 original size:6 final size:7
Alignment explanation
Indices: 5643832--5643856 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5643822 TTATATTAAT
5643832 AAAATTA
1 AAAATTA
5643839 AAAATTA
1 AAAATTA
5643846 AAAATTA
1 AAAATTA
5643853 AAAA
1 AAAA
5643857 GATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:5649476 original size:14 final size:13
Alignment explanation
Indices: 5649455--5649499 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
5649445 TAGGTTTAAG
5649455 GGTTATGATTTAT
1 GGTTATGATTTAT
5649468 GGTTGATGATTTAT
1 GGTT-ATGATTTAT
* *
5649482 GTTTTATGATTTAG
1 G-GTTATGATTTAT
5649496 GGTT
1 GGTT
5649500 TGAGGTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.22
14 19 0.70
15 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (13 bp):
GGTTATGATTTAT
Found at i:5649675 original size:14 final size:14
Alignment explanation
Indices: 5649658--5649687 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5649648 GTGTTTTAAA
5649658 GTTTATTATTTAGG
1 GTTTATTATTTAGG
5649672 GTTTATTATTTAGG
1 GTTTATTATTTAGG
5649686 GT
1 GT
5649688 CTAAGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (14 bp):
GTTTATTATTTAGG
Found at i:5649727 original size:8 final size:8
Alignment explanation
Indices: 5649714--5649763 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
5649704 TAGTGATATT
5649714 AGGGTTTA
1 AGGGTTTA
5649722 AGGGTTTA
1 AGGGTTTA
5649730 A-GGTTTA
1 AGGGTTTA
5649737 AGGG-TT-
1 AGGGTTTA
5649743 AGGAGTTT-
1 AGG-GTTTA
*
5649751 AGGGGTTA
1 AGGGTTTA
5649759 AGGGT
1 AGGGT
5649764 CAATGGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 3 0.08
7 13 0.36
8 20 0.56
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (8 bp):
AGGGTTTA
Found at i:5649750 original size:15 final size:14
Alignment explanation
Indices: 5649712--5649763 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
5649702 TTTAGTGATA
5649712 TTAGGGTTTAAGGG
1 TTAGGGTTTAAGGG
*
5649726 TTTAAGGTTTAAGGG
1 -TTAGGGTTTAAGGG
*
5649741 TTAGGAGTTTAGGGG
1 TTAGG-GTTTAAGGG
5649756 TTAAGGGT
1 TT-AGGGT
5649764 CAATGGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 4 0.12
15 25 0.78
16 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (14 bp):
TTAGGGTTTAAGGG
Found at i:5649887 original size:21 final size:21
Alignment explanation
Indices: 5649862--5649920 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
5649852 GGTTAATTAA
* *
5649862 GGTTTATGGTCTAGGGTTTGG
1 GGTTTATGGTATAGGGTTTAG
* * **
5649883 GGTTTAAGGTTTATAGTTTAG
1 GGTTTATGGTATAGGGTTTAG
5649904 GGTTTATGGTATAGGGT
1 GGTTTATGGTATAGGGT
5649921 CAGGGTCTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.02, G:0.37, T:0.44
Consensus pattern (21 bp):
GGTTTATGGTATAGGGTTTAG
Found at i:5649918 original size:14 final size:14
Alignment explanation
Indices: 5649862--5649920 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
5649852 GGTTAATTAA
*
5649862 GGTTTATGGTCTAG
1 GGTTTATGGTTTAG
** *
5649876 GGTTTGGGGTTTAA
1 GGTTTATGGTTTAG
*
5649890 GGTTTATAGTTTAG
1 GGTTTATGGTTTAG
*
5649904 GGTTTATGGTATAG
1 GGTTTATGGTTTAG
5649918 GGT
1 GGT
5649921 CAGGGTCTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.17, C:0.02, G:0.37, T:0.44
Consensus pattern (14 bp):
GGTTTATGGTTTAG
Found at i:5653718 original size:32 final size:32
Alignment explanation
Indices: 5653681--5653744 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5653671 GTTTGTTTAA
5653681 AGCTGTGCATTTTGAAGTTGATGTTCAACGGC
1 AGCTGTGCATTTTGAAGTTGATGTTCAACGGC
*
5653713 AGCTGTGCATTTTTAAGTTGATGTTCAACGGC
1 AGCTGTGCATTTTGAAGTTGATGTTCAACGGC
5653745 GCAAAGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (32 bp):
AGCTGTGCATTTTGAAGTTGATGTTCAACGGC
Found at i:5655029 original size:15 final size:15
Alignment explanation
Indices: 5655009--5655037 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5654999 GGAGTAGACC
5655009 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
5655024 AGGTACGTTTTATT
1 AGGTACGTTTTATT
5655038 TCAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:5663189 original size:21 final size:21
Alignment explanation
Indices: 5663163--5663206 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5663153 TCAACTTAGA
*
5663163 GCGGAGGCAGCAGCGCGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
5663184 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
5663205 GC
1 GC
5663207 AGAGCAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.23, G:0.57, T:0.00
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:5665574 original size:18 final size:19
Alignment explanation
Indices: 5665547--5665582 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5665537 TTGTTTAGTC
*
5665547 TAAAAGCGC-TTTTGAGAT
1 TAAAACCGCTTTTTGAGAT
5665565 TAAAACCGCTTTTTGAGA
1 TAAAACCGCTTTTTGAGA
5665583 AACAATGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (19 bp):
TAAAACCGCTTTTTGAGAT
Found at i:5666306 original size:129 final size:128
Alignment explanation
Indices: 5665977--5666299 Score: 391
Period size: 129 Copynumber: 2.5 Consensus size: 128
5665967 CATTTATTCC
* * * * *
5665977 AACGAAAAATCAAAACCCAGCACGGTAGGGCACGATTTCTCGAATTCCCAAACATTGAACATTGC
1 AACGAGAAATCGAAACCCAGCACGGTAGGGCACGA-TTCTCAAATTTCCAAACATTAAACATTGC
* * * *
5666042 CTTGTTTTAGAA--TTTAAAGAATACGAATGAAATTCTAAAAGAATATTTGATGATTTTGGATA
65 CTTGTTTTAGAATTTTTAAAGAATACGAATGAAATTCTAAAAGAAGATTCGATGATTTTGAACA
* * * * *
5666104 AACGAGAAATCGAAACCCAGCACGATAAGGCACGGTTCCCCAAATTTCCAAGCATTAAACATTGC
1 AACGAGAAATCGAAACCCAGCACGGTAGGGCACGATT-CTCAAATTTCCAAACATTAAACATTGC
* * * *
5666169 CTTGTTTTAGAATTTTTAAAGAA-AGCGAGTGAAATTCTAAAGGAAGGTTCGATTATTTTGAACA
65 CTTGTTTTAGAATTTTTAAAGAATA-CGAATGAAATTCTAAAAGAAGATTCGATGATTTTGAACA
* * ** *
5666233 AACGGGAAATCGAAACCCAGCACGGTAGGGCACGATTCTCAAATTTTCAAACACCAAACATTACC
1 AACGAGAAATCGAAACCCAGCACGGTAGGGCACGATTCTCAAATTTCCAAACATTAAACATTGCC
5666298 TT
66 TT
5666300 CATTTTAAGG
Statistics
Matches: 164, Mismatches: 28, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
126 2 0.01
127 64 0.39
128 25 0.15
129 73 0.45
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (128 bp):
AACGAGAAATCGAAACCCAGCACGGTAGGGCACGATTCTCAAATTTCCAAACATTAAACATTGCC
TTGTTTTAGAATTTTTAAAGAATACGAATGAAATTCTAAAAGAAGATTCGATGATTTTGAACA
Found at i:5670080 original size:131 final size:130
Alignment explanation
Indices: 5669847--5670084 Score: 350
Period size: 131 Copynumber: 1.8 Consensus size: 130
5669837 TAATTATTCA
* * * * * *
5669847 TTTAAAAATTCTTTAAAACGAAGGCAATACTCGATGTTTGGCAATTCGAGAATCGTGCCCTATTG
1 TTTAAAAACTCTTTAAAACGAAGGAAATACTCGACGTTTGGAAATTCGAGAATAGTGCCCTATCG
* *
5669912 TGCTGGGTTGCGATTTCTCATTTGTTCAAAACAATCAAATATCTCTTTAAAATTTCACTCATGTC
66 TGCTGAGTTGCGATTTCCCATTTGTTCAAAACAATCAAATATCTCTTTAAAATTTCACTCATGTC
**
5669977 TTTAAAAACTCTTTAAAACGAAGGAAATGTTCGACGTTTGGAAATTCGGAGAATAGTGCCCTATC
1 TTTAAAAACTCTTTAAAACGAAGGAAATACTCGACGTTTGGAAATTC-GAGAATAGTGCCCTATC
* * *
5670042 GTGCTGAGTTTCGATTTCCCGTTTGTTCAAAATAATCAAATAT
65 GTGCTGAGTTGCGATTTCCCATTTGTTCAAAACAATCAAATAT
5670085 TCCTTTGGAA
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 41 0.44
131 53 0.56
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (130 bp):
TTTAAAAACTCTTTAAAACGAAGGAAATACTCGACGTTTGGAAATTCGAGAATAGTGCCCTATCG
TGCTGAGTTGCGATTTCCCATTTGTTCAAAACAATCAAATATCTCTTTAAAATTTCACTCATGTC
Found at i:5672828 original size:51 final size:51
Alignment explanation
Indices: 5672746--5672865 Score: 188
Period size: 51 Copynumber: 2.4 Consensus size: 51
5672736 CTCAAACTTA
* *
5672746 CTTCATACTTCATCCGGAATTATTACCTTGTTGCTCTAACTTTAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTTAACAAGAG
*
5672797 CTTCATATTTCATCCGGAATAATT-CCTTTGTTGCTCTAGCTTTAACAAGAG
1 CTTCATATTTCATCCGGAATAATTACC-TTGTTGCTCTAACTTTAACAAGAG
*
5672848 CTTCATATTTTATCCGGA
1 CTTCATATTTCATCCGGA
5672866 TAACTTAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 2 0.03
51 62 0.97
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (51 bp):
CTTCATATTTCATCCGGAATAATTACCTTGTTGCTCTAACTTTAACAAGAG
Found at i:5677813 original size:23 final size:23
Alignment explanation
Indices: 5677786--5677830 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5677776 AGATTTTTTC
5677786 TAAATATTATCACTAAATAATTT
1 TAAATATTATCACTAAATAATTT
5677809 TAAATATTATCACTAAATAATT
1 TAAATATTATCACTAAATAATT
5677831 CAAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTT
Found at i:5677836 original size:23 final size:23
Alignment explanation
Indices: 5677787--5677836 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
5677777 GATTTTTTCT
**
5677787 AAATATTATCACTAAATAATTTT
1 AAATATTATCACTAAATAATTCA
5677810 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATTCA
5677833 AAAT
1 AAAT
5677837 TTAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCA
Found at i:5685740 original size:37 final size:37
Alignment explanation
Indices: 5685689--5685763 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
5685679 CATCATATTC
* *
5685689 ATTGTTTTTATGACCAGTTTCCATAATATAATTTATA
1 ATTGTTATTATGACCAATTTCCATAATATAATTTATA
*
5685726 ATTGTTATTGTGACCAATTTCCATAATATAATTTATA
1 ATTGTTATTATGACCAATTTCCATAATATAATTTATA
5685763 A
1 A
5685764 ATTTACTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (37 bp):
ATTGTTATTATGACCAATTTCCATAATATAATTTATA
Found at i:5686748 original size:38 final size:38
Alignment explanation
Indices: 5686704--5686778 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
5686694 CCAAACTAAA
*
5686704 CAAATAACTACCCATAAACCCAACAGACCCCAAACCCC
1 CAAATAACTACCCATAAACCCAACAGACCCAAAACCCC
5686742 CAAATAACTACCCATAAACCCAACAGACCCAAAACCC
1 CAAATAACTACCCATAAACCCAACAGACCCAAAACCC
5686779 ACTAAAGACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.47, C:0.43, G:0.03, T:0.08
Consensus pattern (38 bp):
CAAATAACTACCCATAAACCCAACAGACCCAAAACCCC
Found at i:5688383 original size:22 final size:22
Alignment explanation
Indices: 5688349--5688392 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5688339 CTAACATGTA
*
5688349 TATATATACTATATATTTTTAT
1 TATATATACTATACATTTTTAT
*
5688371 TATAT-TACATATACGTTTTTAT
1 TATATATAC-TATACATTTTTAT
5688393 ATGTACGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TATATATACTATACATTTTTAT
Found at i:5701284 original size:38 final size:37
Alignment explanation
Indices: 5701241--5701323 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 37
5701231 AAACCCCCAA
5701241 ACCCAAACTAAACAAATAACTACCCATAAACCCAACAG
1 ACCCAAAC-AAACAAATAACTACCCATAAACCCAACAG
***
5701279 ACCCAAAACCCCCAAATAACTACCCATAAACCCAACAG
1 ACCC-AAACAAACAAATAACTACCCATAAACCCAACAG
5701317 ACCCAAA
1 ACCCAAA
5701324 GCCCACTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
37 3 0.07
38 34 0.83
39 4 0.10
ACGTcount: A:0.51, C:0.39, G:0.02, T:0.08
Consensus pattern (37 bp):
ACCCAAACAAACAAATAACTACCCATAAACCCAACAG
Found at i:5702937 original size:17 final size:17
Alignment explanation
Indices: 5702915--5702948 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5702905 TGTAATGTTT
5702915 TTTGTATTGTTATTATC
1 TTTGTATTGTTATTATC
5702932 TTTGTATTGTTATTATC
1 TTTGTATTGTTATTATC
5702949 GTTATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTGTATTGTTATTATC
Found at i:5703055 original size:22 final size:22
Alignment explanation
Indices: 5702997--5703064 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
5702987 GCTTTCATCA
*
5702997 TTATTAT-TATTACTA-ACATGT
1 TTATTATATA-TACTATACATTT
* *
5703018 ATA-TATATATACTATATATTT
1 TTATTATATATACTATACATTT
*
5703039 TTATTATAT-TACGTATACGTTT
1 TTATTATATATAC-TATACATTT
5703061 TTAT
1 TTAT
5703065 ATGTACGCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 8 0.22
21 13 0.35
22 16 0.43
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.54
Consensus pattern (22 bp):
TTATTATATATACTATACATTT
Found at i:5714934 original size:12 final size:12
Alignment explanation
Indices: 5714917--5714946 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5714907 TCTTTCAAAA
5714917 AAATTTTGCTAC
1 AAATTTTGCTAC
5714929 AAATTTTGCTAC
1 AAATTTTGCTAC
5714941 AAATTT
1 AAATTT
5714947 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (12 bp):
AAATTTTGCTAC
Found at i:5715799 original size:4 final size:4
Alignment explanation
Indices: 5715790--5715816 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5715780 CAAACACAAA
5715790 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
5715817 AACTTTGGGA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5722934 original size:41 final size:41
Alignment explanation
Indices: 5722877--5722958 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
5722867 ATGGATGTTT
5722877 TGTTGATTGTGCCTTGTATTTGATCTGTTTGAATAAAATTC
1 TGTTGATTGTGCCTTGTATTTGATCTGTTTGAATAAAATTC
5722918 TGTTGATTGTGCCTTGTATTTGATCTGTTTGAATAAAATTC
1 TGTTGATTGTGCCTTGTATTTGATCTGTTTGAATAAAATTC
5722959 CAACATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.49
Consensus pattern (41 bp):
TGTTGATTGTGCCTTGTATTTGATCTGTTTGAATAAAATTC
Found at i:5724033 original size:45 final size:45
Alignment explanation
Indices: 5723982--5724141 Score: 119
Period size: 45 Copynumber: 3.4 Consensus size: 45
5723972 TCCCTGACTA
*
5723982 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
* * * * * * *
5724027 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCATGTGACTAT--
1 CAGTGGAATACATTGAAG--C--CGAT---A-ACTCTATCTCCCTGT-A-TTTGG
*
5724080 -AGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
*
5724124 CAGTGGAATAGATTGAAG
1 CAGTGGAATACATTGAAG
5724142 ATTGCAGATC
Statistics
Matches: 84, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 11 0.13
45 32 0.38
47 1 0.01
48 3 0.04
49 3 0.04
50 1 0.01
52 16 0.19
53 11 0.13
54 1 0.01
55 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
CAGTGGAATACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
Found at i:5724112 original size:97 final size:95
Alignment explanation
Indices: 5723948--5724143 Score: 356
Period size: 97 Copynumber: 2.0 Consensus size: 95
5723938 ACAGCGAAGC
5723948 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
5724013 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGTATTTGGCAGTGGAATAGATTGA
* *
5724043 AGATCAAAGATGGCAGATTTTACCTCCATGTGACTATAGTGGAGTACATTGAAGCCGATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCC--CTGACTACAGTGGAGTACATTGAAGCCGATAACTCT
5724108 ATCTCCCTGTATTTGGCAGTGGAATAGATTGA
64 ATCTCCCTGTATTTGGCAGTGGAATAGATTGA
5724140 AGAT
1 AGAT
5724144 TGCAGATCTT
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
95 27 0.28
97 70 0.72
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGTATTTGGCAGTGGAATAGATTGA
Found at i:5733131 original size:20 final size:20
Alignment explanation
Indices: 5733095--5733132 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5733085 ATACTTTACT
*
5733095 TTAATTTATAGCTCATACAA
1 TTAATTTATAGCACATACAA
5733115 TTAATTTA-AGTCACATAC
1 TTAATTTATAG-CACATAC
5733133 TTTCATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (20 bp):
TTAATTTATAGCACATACAA
Found at i:5733467 original size:38 final size:38
Alignment explanation
Indices: 5733423--5733545 Score: 185
Period size: 38 Copynumber: 3.2 Consensus size: 38
5733413 ACTTTAAGCT
* * *
5733423 CGGATATAATACCAGCACTAAGCTTGCAGGATTTAACC
1 CGGATATATTACCAGCACTAAGCCTGCGGGATTTAACC
*
5733461 CGGATATATTACCAGCACGAAGCCTGCGGGATTTAACC
1 CGGATATATTACCAGCACTAAGCCTGCGGGATTTAACC
*
5733499 CGGATATATTACCAGCA-TGAAGCCTGCGGGACTTAACC
1 CGGATATATTACCAGCACT-AAGCCTGCGGGATTTAACC
5733537 CGGATATAT
1 CGGATATAT
5733546 ATCGAGTGCT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (38 bp):
CGGATATATTACCAGCACTAAGCCTGCGGGATTTAACC
Found at i:5744384 original size:56 final size:56
Alignment explanation
Indices: 5744324--5744431 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
5744314 AAATCGTACT
* *
5744324 TAATATTAAAGTCATAATTATTAACCTAACAAATGATCTGACCCATAAACAGTATC
1 TAATATTAAAATCATAATTATAAACCTAACAAATGATCTGACCCATAAACAGTATC
* * * * *
5744380 TAATATTAAAATTATAATTATAAACTTAACAGATGATCTGACTCATGAACAG
1 TAATATTAAAATCATAATTATAAACCTAACAAATGATCTGACCCATAAACAG
5744432 AATTTATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.31
Consensus pattern (56 bp):
TAATATTAAAATCATAATTATAAACCTAACAAATGATCTGACCCATAAACAGTATC
Found at i:5749200 original size:28 final size:27
Alignment explanation
Indices: 5749159--5749221 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
5749149 TTTAAATAAA
*
5749159 TTTTATCAAAATTT-TCAATTTATATATT
1 TTTTAT-AATATTTATC-ATTTATATATT
* *
5749187 TTTCTATAATATTTATCGTTTTTATATT
1 TTT-TATAATATTTATCATTTATATATT
5749215 TTTTATA
1 TTTTATA
5749222 TTTTTTCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 4 0.13
28 21 0.70
29 5 0.17
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTATAATATTTATCATTTATATATT
Found at i:5749331 original size:20 final size:20
Alignment explanation
Indices: 5749297--5749339 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5749287 TAATTTAATA
*
5749297 TTTACTAATCATATATATCT
1 TTTACTAATCATATATATAT
5749317 TTTAC-AATCATTATATATAT
1 TTTACTAATCA-TATATATAT
5749337 TTT
1 TTT
5749340 TGTTAATTTT
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:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTACTAATCATATATATAT
Found at i:5750459 original size:18 final size:18
Alignment explanation
Indices: 5750436--5750477 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5750426 TTCAAGGTGT
5750436 AATTAATTTAAATTT-TAA
1 AATTAA-TTAAATTTATAA
*
5750454 AATTAATTAAATTTATTA
1 AATTAATTAAATTTATAA
5750472 AATTAA
1 AATTAA
5750478 AAATCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAAATTTATAA
Found at i:5754356 original size:12 final size:12
Alignment explanation
Indices: 5754339--5754364 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5754329 AAATGGGGGC
5754339 AATATATATATA
1 AATATATATATA
5754351 AATATATATATA
1 AATATATATATA
5754363 AA
1 AA
5754365 CTGGAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATATATA
Found at i:5754404 original size:5 final size:6
Alignment explanation
Indices: 5754389--5754442 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
5754379 GGTAAGTTGC
* * *
5754389 TTTTTA TTTTTA TTTTTG TTCTTA TTTTTA TATTTTA TATTTTC TTTTCTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA T-TTTTA TTTT-TA
5754440 TTT
1 TTT
5754443 CAAGTCAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
6 24 0.60
7 16 0.40
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5766126 original size:30 final size:30
Alignment explanation
Indices: 5766092--5766150 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5766082 TTTAATAAGC
*
5766092 AAATA-CTTCTAAAATAATAATAAAATTAAT
1 AAATACCTT-TAAAATAATAACAAAATTAAT
5766122 AAATACCTTTAAAATAATAACAAAATTAA
1 AAATACCTTTAAAATAATAACAAAATTAA
5766151 CAATAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (30 bp):
AAATACCTTTAAAATAATAACAAAATTAAT
Found at i:5772548 original size:3 final size:3
Alignment explanation
Indices: 5772542--5772663 Score: 75
Period size: 3 Copynumber: 40.3 Consensus size: 3
5772532 TAATATTATC
* * * * * *
5772542 AAT AAT AAT AGT AAT AGT AAA AAT ACT AAT AAT AAT GAA- AAA AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * * * * * * *
5772587 AAT AAT AAT AAT AAT AAT AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5772635 AAT AAG AAT AAT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
5772664 GCAAAAACAT
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.02
3 96 0.93
4 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.11, T:0.22
Consensus pattern (3 bp):
AAT
Found at i:5784647 original size:68 final size:68
Alignment explanation
Indices: 5784538--5784756 Score: 420
Period size: 68 Copynumber: 3.2 Consensus size: 68
5784528 TAGTATTCTT
5784538 CAACCGTATACCCCATAGCTTTGACAGTCGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
1 CAACCGTATACCCCATAGCTTTGACAGTCGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
5784603 TGC
66 TGC
5784606 CAACCGTATACCCCATAGCTTTGACAGTCGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
1 CAACCGTATACCCCATAGCTTTGACAGTCGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
5784671 TGC
66 TGC
*
5784674 CAACCGTATACCCCATAGCTTTGACAGTTGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
1 CAACCGTATACCCCATAGCTTTGACAGTCGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
5784739 TGC
66 TGC
*
5784742 CAACCATATACCCCA
1 CAACCGTATACCCCA
5784757 ATGAAGCAGG
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 149 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (68 bp):
CAACCGTATACCCCATAGCTTTGACAGTCGAGCAATAATAGCATGATTTGGACGCAAGACTTTGT
TGC
Found at i:5792695 original size:3 final size:3
Alignment explanation
Indices: 5792683--5792853 Score: 335
Period size: 3 Copynumber: 57.3 Consensus size: 3
5792673 CTTGTATGTT
5792683 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5792730 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5792778 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5792826 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5792854 ACAATTAAAA
Statistics
Matches: 167, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.01
3 165 0.99
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5793270 original size:11 final size:12
Alignment explanation
Indices: 5793254--5793284 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5793244 AAGAGGAAAG
5793254 AAAAAAAAA-TA
1 AAAAAAAAAGTA
5793265 AAAAAAAAAGTA
1 AAAAAAAAAGTA
5793277 AAAAAAAA
1 AAAAAAAA
5793285 CTCCCTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAGTA
Found at i:5793492 original size:7 final size:8
Alignment explanation
Indices: 5793464--5793492 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5793454 AATAGATGAA
5793464 AAAAAAGT
1 AAAAAAGT
5793472 AAAAAAGT
1 AAAAAAGT
5793480 AAAAAA-T
1 AAAAAAGT
5793487 AAAAAA
1 AAAAAA
5793493 ACGATTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (8 bp):
AAAAAAGT
Done.