Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 30 of 100
Found at i:5525034 original size:19 final size:19
Alignment explanation
Indices: 5525012--5525049 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5525002 AAATTTTTTA
*
5525012 AAATAATAATAATAATAAT
1 AAATAATAACAATAATAAT
*
5525031 AAATAATCACAATAATAAT
1 AAATAATAACAATAATAAT
5525050 TAATTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAATAACAATAATAAT
Found at i:5525228 original size:50 final size:49
Alignment explanation
Indices: 5525103--5525232 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 49
5525093 TATTTAGGAT
* * * *
5525103 CTCATCAAAAAGTTGAGATGATTTTAAAATTTATTCAAAATTTTTAGGAT
1 CTCATCAAAAAGTTG-GATGATTTTAAAATTTATTAAAAATTTTGAGAAA
* *
5525153 TTCATCAAAAAGTTGGGATAATTTTAAAATTTATTAAATAAATTTTGA-AAA
1 CTCATCAAAAAGTT-GGATGATTTTAAAATTTATT-AA-AAATTTTGAGAAA
* *
5525204 CTCACCAAAAAGTTGGATGTTTTTAAAAT
1 CTCATCAAAAAGTTGGATGATTTTAAAAT
5525233 CATCTTATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 44 0.66
51 15 0.22
52 8 0.12
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (49 bp):
CTCATCAAAAAGTTGGATGATTTTAAAATTTATTAAAAATTTTGAGAAA
Found at i:5539492 original size:101 final size:101
Alignment explanation
Indices: 5539360--5539544 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
5539350 ATTTTAGCAA
* * *
5539360 CATTTCTATCTTTGAGACGCCGCTAAATTAGTGACATTTTTATGAGAAAAACGCCATTGCTATGA
1 CATTTCTATCTTTGAAACGCCACTAAATTAGTGACATTTTTATGAGAAAAACGCCATTGATATGA
**
5539425 TGGTGTTTGTAACTAAAAATGCCTCTACATTAATGG
66 TGGCATTTGTAACTAAAAATGCCTCTACATTAATGG
* * * * * *
5539461 CATTTGTATCTTTGAAACGTCATTAATTTAGTGACATTTTTATGAGAAAAACGTCATTGATTTGA
1 CATTTCTATCTTTGAAACGCCACTAAATTAGTGACATTTTTATGAGAAAAACGCCATTGATATGA
5539526 TGGCATTTGTAACTAAAAA
66 TGGCATTTGTAACTAAAAA
5539545 AGCCGTTATT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 73 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (101 bp):
CATTTCTATCTTTGAAACGCCACTAAATTAGTGACATTTTTATGAGAAAAACGCCATTGATATGA
TGGCATTTGTAACTAAAAATGCCTCTACATTAATGG
Found at i:5539665 original size:40 final size:40
Alignment explanation
Indices: 5539610--5539689 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5539600 GTATCTTTGA
5539610 GATACCGTTAATTTAATGACGTTTTTATGAGAAAAATACC
1 GATACCGTTAATTTAATGACGTTTTTATGAGAAAAATACC
5539650 GATACCGTTAATTTAATGACGTTTTTATGAGAAAAATACC
1 GATACCGTTAATTTAATGACGTTTTTATGAGAAAAATACC
5539690 ATTGCTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (40 bp):
GATACCGTTAATTTAATGACGTTTTTATGAGAAAAATACC
Found at i:5547684 original size:21 final size:20
Alignment explanation
Indices: 5547626--5547702 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
5547616 TTTTTTTATT
*
5547626 AAATAATAAATAAAATAATA
1 AAATTATAAATAAAATAATA
* *
5547646 ATATTATTAAATACAATAATA
1 AAATTA-TAAATAAAATAATA
5547667 GAAATTA-AATATAAAATATAATA
1 -AAATTATAA-AT-AAA-ATAATA
5547690 AAA-TAT-AATAAAA
1 AAATTATAAATAAAA
5547703 AAAAAACAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 8 0.17
21 18 0.39
22 10 0.22
23 6 0.13
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (20 bp):
AAATTATAAATAAAATAATA
Found at i:5547692 original size:10 final size:10
Alignment explanation
Indices: 5547677--5547702 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5547667 GAAATTAAAT
5547677 ATAAAATATA
1 ATAAAATATA
5547687 ATAAAATATA
1 ATAAAATATA
5547697 ATAAAA
1 ATAAAA
5547703 AAAAAACAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAAATATA
Found at i:5548732 original size:21 final size:21
Alignment explanation
Indices: 5548689--5548733 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5548679 TTTTAGATTT
* **
5548689 TTTTAAATATTATTTTTGTTA
1 TTTTAAATATTATTCTTAATA
*
5548710 TTTTAATTATTATTCTTAATA
1 TTTTAAATATTATTCTTAATA
5548731 TTT
1 TTT
5548734 ATGCATGTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAAATATTATTCTTAATA
Found at i:5549081 original size:18 final size:18
Alignment explanation
Indices: 5549039--5549084 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
5549029 TTGCTTATAA
*
5549039 AATAATA-AATAAAAATT
1 AATAATATAATAAAAAAT
*
5549056 AATCAATATATTAAAAAAT
1 AAT-AATATAATAAAAAAT
5549075 AATAATATAA
1 AATAATATAA
5549085 ATAAGGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 11 0.46
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAATATAATAAAAAAT
Found at i:5560293 original size:2 final size:2
Alignment explanation
Indices: 5560286--5560312 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5560276 ACTTGAAAGA
5560286 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5560313 CATTACTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5564504 original size:27 final size:27
Alignment explanation
Indices: 5564463--5564526 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
5564453 CAATTAGCTT
* *
5564463 GAAGATTTTTACAATTATCATAATTTTA
1 GAAGA-TTTTACAATGATAATAATTTTA
5564491 GAAGATTTTACAATGATAATAATTTTA
1 GAAGATTTTACAATGATAATAATTTTA
5564518 GAAGATTTT
1 GAAGATTTT
5564527 GTTAAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.44
Consensus pattern (27 bp):
GAAGATTTTACAATGATAATAATTTTA
Found at i:5565987 original size:2 final size:2
Alignment explanation
Indices: 5565982--5566007 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5565972 TGATGAGAGA
5565982 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
5566008 GTGTGTGTAT
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:5566817 original size:32 final size:30
Alignment explanation
Indices: 5566781--5566840 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
5566771 AATACATTTC
5566781 ATTTTTTATATATTAATATAAATTATAATATA
1 ATTTTTTATAT-TTAATATAAATT-TAATATA
* *
5566813 ATTTTTTATATTTTATATATATTTAATA
1 ATTTTTTATATTTAATATAAATTTAATA
5566841 AAATATGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.19
31 10 0.38
32 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTTTTATATTTAATATAAATTTAATATA
Found at i:5569415 original size:20 final size:19
Alignment explanation
Indices: 5569386--5569423 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5569376 ATCAGTTCGA
*
5569386 TTAATGTTAAATTACATTAT
1 TTAATATTAAATTA-ATTAT
5569406 TTAATATTAAATTAATTA
1 TTAATATTAAATTAATTA
5569424 AATTATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAATATTAAATTAATTAT
Found at i:5571736 original size:27 final size:27
Alignment explanation
Indices: 5571706--5571764 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
5571696 TTTAATTCAC
*
5571706 ATATATATAAAATTAAAAATAAAAATT
1 ATATATATAAAAATAAAAATAAAAATT
* * *
5571733 ATATATGTAAAAATAAATATAATAATT
1 ATATATATAAAAATAAAAATAAAAATT
5571760 ATATA
1 ATATA
5571765 AAATAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATATATAAAAATAAAAATAAAAATT
Found at i:5571802 original size:21 final size:20
Alignment explanation
Indices: 5571762--5571806 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
5571752 TAATAATTAT
5571762 ATAAAATAAATTTTAAATTTA
1 ATAAAATAAATTTT-AATTTA
*
5571783 ATAAAATATATATTTTATTTTA
1 ATAAAATA-A-ATTTTAATTTA
5571805 AT
1 AT
5571807 TTTATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAAATAAATTTTAATTTA
Found at i:5576344 original size:28 final size:28
Alignment explanation
Indices: 5576312--5576367 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
5576302 ACTTGGGTTG
5576312 AATGGTTTGTCTTTTGTTGTCTGTCAAT
1 AATGGTTTGTCTTTTGTTGTCTGTCAAT
5576340 AATGGTTTGTCTTTTGTTGTCTGTCAAT
1 AATGGTTTGTCTTTTGTTGTCTGTCAAT
5576368 CGTATGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.21, T:0.54
Consensus pattern (28 bp):
AATGGTTTGTCTTTTGTTGTCTGTCAAT
Found at i:5579780 original size:2 final size:2
Alignment explanation
Indices: 5579775--5579799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5579765 GAGAGAATAC
5579775 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5579800 AATGAGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5580017 original size:2 final size:2
Alignment explanation
Indices: 5580010--5580037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5580000 AATCCCTCTC
5580010 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
5580038 TAAGACTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5583073 original size:7 final size:8
Alignment explanation
Indices: 5583055--5583079 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5583045 ATTCTAATGA
5583055 TTTTATGT
1 TTTTATGT
5583063 TTTTATGT
1 TTTTATGT
5583071 TTTTATGT
1 TTTTATGT
5583079 T
1 T
5583080 GAATATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (8 bp):
TTTTATGT
Found at i:5583607 original size:18 final size:17
Alignment explanation
Indices: 5583569--5583609 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
5583559 TGGATAAATT
*
5583569 TAGAAAAAATTTCTCAC
1 TAGAGAAAATTTCTCAC
5583586 -AGAGAAAATTTCTCAC
1 TAGAGAAAATTTCTCAC
5583602 ATAGAGAA
1 -TAGAGAA
5583610 TTCTTAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 15 0.71
18 6 0.29
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (17 bp):
TAGAGAAAATTTCTCAC
Found at i:5583704 original size:8 final size:8
Alignment explanation
Indices: 5583691--5583723 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
5583681 TTTATTTAAA
5583691 ATTTTTTT
1 ATTTTTTT
5583699 ATTTTTTTT
1 A-TTTTTTT
5583708 ATTTTTTT
1 ATTTTTTT
5583716 ATTTTTTT
1 ATTTTTTT
5583724 TGTTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
ATTTTTTT
Found at i:5583706 original size:9 final size:9
Alignment explanation
Indices: 5583692--5583724 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
5583682 TTATTTAAAA
5583692 TTTTTTTAT
1 TTTTTTTAT
5583701 TTTTTTTA-
1 TTTTTTTAT
5583709 TTTTTTTAT
1 TTTTTTTAT
5583718 TTTTTTT
1 TTTTTTT
5583725 GTTTGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:5583713 original size:17 final size:17
Alignment explanation
Indices: 5583691--5583724 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5583681 TTTATTTAAA
5583691 ATTTTTTTATTTTTTTT
1 ATTTTTTTATTTTTTTT
5583708 ATTTTTTTATTTTTTTT
1 ATTTTTTTATTTTTTTT
5583725 GTTTGAAAAT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (17 bp):
ATTTTTTTATTTTTTTT
Found at i:5583820 original size:26 final size:26
Alignment explanation
Indices: 5583792--5583848 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5583782 TTAGGACAAA
*
5583792 TTTAGACAAAATTTTTCATTTAAAAAT
1 TTTAGA-AAAATTTATCATTTAAAAAT
* * *
5583819 TTTATAAAAATTTATCATTTGAAATT
1 TTTAGAAAAATTTATCATTTAAAAAT
5583845 TTTA
1 TTTA
5583849 TAAATTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTAGAAAAATTTATCATTTAAAAAT
Found at i:5583849 original size:26 final size:26
Alignment explanation
Indices: 5583799--5583852 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
5583789 AAATTTAGAC
*
5583799 AAAATTTTTCATTTAAAAATTTTATA
1 AAAATTTATCATTTAAAAATTTTATA
* *
5583825 AAAATTTATCATTTGAAATTTTTATA
1 AAAATTTATCATTTAAAAATTTTATA
5583851 AA
1 AA
5583853 TTACATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
AAAATTTATCATTTAAAAATTTTATA
Found at i:5583860 original size:25 final size:25
Alignment explanation
Indices: 5583815--5583862 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5583805 TTTCATTTAA
*
5583815 AAATTTTATAAAAATTTATCATTTG
1 AAATTTTATAAAAATTCATCATTTG
*
5583840 AAATTTT-TATAAATTACATCATT
1 AAATTTTATAAAAATT-CATCATT
5583863 GGATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (25 bp):
AAATTTTATAAAAATTCATCATTTG
Found at i:5586384 original size:2 final size:2
Alignment explanation
Indices: 5586373--5586410 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5586363 GACGAGAGAC
*
5586373 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5586411 AATGAGGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5586490 original size:2 final size:2
Alignment explanation
Indices: 5586483--5586511 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5586473 TCCATACATC
5586483 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 T
5586512 TAAGAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5597221 original size:24 final size:26
Alignment explanation
Indices: 5597194--5597242 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
5597184 ATATACATTT
5597194 AGTTTTACTT-TTAG-TTTTCCACAC
1 AGTTTTACTTCTTAGTTTTTCCACAC
*
5597218 AGTTTTATTTCTTAGTTTTTCCACA
1 AGTTTTACTTCTTAGTTTTTCCACA
5597243 AAAATCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 4 0.18
26 9 0.41
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.53
Consensus pattern (26 bp):
AGTTTTACTTCTTAGTTTTTCCACAC
Found at i:5598147 original size:15 final size:15
Alignment explanation
Indices: 5598127--5598156 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5598117 AAGAATGACC
5598127 AAATAAGATAATGGT
1 AAATAAGATAATGGT
5598142 AAATAAGATAATGGT
1 AAATAAGATAATGGT
5598157 CAGATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (15 bp):
AAATAAGATAATGGT
Found at i:5603631 original size:16 final size:17
Alignment explanation
Indices: 5603581--5603623 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
5603571 AAAAAAAAGT
*
5603581 TAAACTTAAATATAAAA
1 TAAATTTAAATATAAAA
*
5603598 TAAATTTAAATATGAAA
1 TAAATTTAAATATAAAA
5603615 T-AATTTAAA
1 TAAATTTAAA
5603624 CTTAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATATAAAA
Found at i:5605211 original size:2 final size:2
Alignment explanation
Indices: 5605204--5605240 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5605194 CATACATCTA
5605204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5605241 TAACATGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5605797 original size:15 final size:16
Alignment explanation
Indices: 5605777--5605807 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5605767 TTAAATATAT
5605777 TTTATAAAAAA-AAAA
1 TTTATAAAAAATAAAA
5605792 TTTATAAAAAATAAAA
1 TTTATAAAAAATAAAA
5605808 AATTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TTTATAAAAAATAAAA
Found at i:5605824 original size:19 final size:18
Alignment explanation
Indices: 5605782--5605818 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5605772 TATATTTTAT
5605782 AAAA-AAAAAATTTATAA
1 AAAATAAAAAATTTATAA
*
5605799 AAAATAAAAAATTTTTAA
1 AAAATAAAAAATTTATAA
5605817 AA
1 AA
5605819 TTATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAAAAAATTTATAA
Found at i:5606027 original size:20 final size:21
Alignment explanation
Indices: 5605983--5606035 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
5605973 GAGTTTTATT
5605983 TAATTTTT-AAATCGATATAG
1 TAATTTTTAAAATCGATATAG
*
5606003 AAATTTTATAAAAT-GATAT-G
1 TAATTTT-TAAAATCGATATAG
5606023 TAATTTTTTAAAA
1 TAA-TTTTTAAAA
5606036 ATATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 14 0.50
21 10 0.36
22 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (21 bp):
TAATTTTTAAAATCGATATAG
Found at i:5611441 original size:37 final size:36
Alignment explanation
Indices: 5611400--5611472 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
5611390 TATCATACTT
*
5611400 AATAATTTTAAAAAATAATTATAGATTATATATTAAA
1 AATAATTTTAAAAAATAATTATAGATAATAT-TTAAA
* *
5611437 AATAATTTTAATAAATAATTATTGATAATATTTAAA
1 AATAATTTTAAAAAATAATTATAGATAATATTTAAA
5611473 TTTAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 5 0.15
37 28 0.85
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (36 bp):
AATAATTTTAAAAAATAATTATAGATAATATTTAAA
Found at i:5611457 original size:23 final size:23
Alignment explanation
Indices: 5611431--5611503 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
5611421 TAGATTATAT
*
5611431 ATTAAAAATAATTTTAATAAATA
1 ATTATAAATAATTTTAATAAATA
** **
5611454 ATTATTGATAATATTTAA-ATTTA
1 ATTATAAATAAT-TTTAATAAATA
*
5611477 AATATAAATAATTTTAATAAATA
1 ATTATAAATAATTTTAATAAATA
5611500 ATTA
1 ATTA
5611504 CTGATAAAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 5 0.14
23 27 0.73
24 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
ATTATAAATAATTTTAATAAATA
Found at i:5611466 original size:13 final size:13
Alignment explanation
Indices: 5611400--5611502 Score: 59
Period size: 13 Copynumber: 7.5 Consensus size: 13
5611390 TATCATACTT
*
5611400 AATAATTTTAAAA
1 AATAATTTTAATA
*
5611413 AATAATTATAGAT-
1 AATAATTTTA-ATA
* *
5611426 TAT-ATATTAA-A
1 AATAATTTTAATA
5611437 AATAATTTTAATA
1 AATAATTTTAATA
*
5611450 AATAATTATTGATA
1 AATAATT-TTAATA
*
5611464 ATATTTAAATTTAAATATA
1 A-A--T-AATTT-TA-ATA
5611483 AATAATTTTAATA
1 AATAATTTTAATA
5611496 AATAATT
1 AATAATT
5611503 ACTGATAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
11 3 0.04
12 10 0.15
13 29 0.43
14 8 0.12
15 6 0.09
16 1 0.01
17 2 0.03
18 5 0.07
19 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AATAATTTTAATA
Found at i:5611486 original size:46 final size:46
Alignment explanation
Indices: 5611436--5611524 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
5611426 TATATATTAA
* *
5611436 AAATAATTTTAATAAATAATTATTGATAATATTTAAATTTAAATAT
1 AAATAATTTTAATAAATAATTACTGATAAAATTTAAATTTAAATAT
5611482 AAATAATTTTAATAAATAATTACTGATAAAATTTAAATTTAAA
1 AAATAATTTTAATAAATAATTACTGATAAAATTTAAATTTAAA
5611525 ATTTTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (46 bp):
AAATAATTTTAATAAATAATTACTGATAAAATTTAAATTTAAATAT
Found at i:5611514 original size:40 final size:43
Alignment explanation
Indices: 5611435--5611538 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 43
5611425 TTATATATTA
*
5611435 AAAATAATTTTAATAAATAATTATTGATAATATTTAAATTTAAATAT
1 AAAATAATTTTAATAAATAATTACTG--AATA--TAAATTTAAATAT
*
5611482 -AAATAATTTTAATAAATAATTACTG-ATA-AAATTTAAATTT
1 AAAATAATTTTAATAAATAATTACTGAATATAAATTTAAATAT
**
5611522 AAAATTTTTTTAATAAA
1 AAAATAATTTTAATAAA
5611539 AAATAATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
40 11 0.21
41 14 0.27
43 3 0.06
46 24 0.46
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (43 bp):
AAAATAATTTTAATAAATAATTACTGAATATAAATTTAAATAT
Found at i:5615382 original size:2 final size:2
Alignment explanation
Indices: 5615369--5615403 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5615359 CCATGGTGGA
*
5615369 GT GT GT GA GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
5615404 AGAGAGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.51, T:0.46
Consensus pattern (2 bp):
GT
Found at i:5615408 original size:2 final size:2
Alignment explanation
Indices: 5615403--5615434 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5615393 GTGTGTGTGT
5615403 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5615435 AGCCCATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5616333 original size:132 final size:132
Alignment explanation
Indices: 5616096--5616363 Score: 536
Period size: 132 Copynumber: 2.0 Consensus size: 132
5616086 CATTAAAATA
5616096 CTGTTAATGTGAACTTTGAAAGCAAGCTCACATTTATTGATGTTGGATCTCGTGTTTATCGTTAT
1 CTGTTAATGTGAACTTTGAAAGCAAGCTCACATTTATTGATGTTGGATCTCGTGTTTATCGTTAT
5616161 CTCATTTTTCAATTAGGAATTTGTTTGCAATGACCTGGATAGCTATTAAGTTATCTTGAATTATG
66 CTCATTTTTCAATTAGGAATTTGTTTGCAATGACCTGGATAGCTATTAAGTTATCTTGAATTATG
5616226 TT
131 TT
5616228 CTGTTAATGTGAACTTTGAAAGCAAGCTCACATTTATTGATGTTGGATCTCGTGTTTATCGTTAT
1 CTGTTAATGTGAACTTTGAAAGCAAGCTCACATTTATTGATGTTGGATCTCGTGTTTATCGTTAT
5616293 CTCATTTTTCAATTAGGAATTTGTTTGCAATGACCTGGATAGCTATTAAGTTATCTTGAATTATG
66 CTCATTTTTCAATTAGGAATTTGTTTGCAATGACCTGGATAGCTATTAAGTTATCTTGAATTATG
5616358 TT
131 TT
5616360 CTGT
1 CTGT
5616364 CTCTATCTTG
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 136 1.00
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.43
Consensus pattern (132 bp):
CTGTTAATGTGAACTTTGAAAGCAAGCTCACATTTATTGATGTTGGATCTCGTGTTTATCGTTAT
CTCATTTTTCAATTAGGAATTTGTTTGCAATGACCTGGATAGCTATTAAGTTATCTTGAATTATG
TT
Found at i:5622958 original size:13 final size:13
Alignment explanation
Indices: 5622940--5622964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5622930 ATGATTTTTA
5622940 ATTTTAAAAATTG
1 ATTTTAAAAATTG
5622953 ATTTTAAAAATT
1 ATTTTAAAAATT
5622965 TAAATTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATTTTAAAAATTG
Found at i:5622980 original size:16 final size:14
Alignment explanation
Indices: 5622939--5622984 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
5622929 TATGATTTTT
5622939 AATTTTAAAAATT-
1 AATTTTAAAAATTA
*
5622952 GATTTTAAAAATTTA
1 AATTTTAAAAA-TTA
5622967 AATTTTACAAAATTA
1 AATTTTA-AAAATTA
5622982 AAT
1 AAT
5622985 CAATACTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 10 0.36
14 2 0.07
15 12 0.43
16 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
AATTTTAAAAATTA
Found at i:5623776 original size:38 final size:40
Alignment explanation
Indices: 5623700--5623782 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
5623690 AAGGATAAAA
** *
5623700 ATTTTATTAATTTAATGATTAAAATTTATAATAATATTTT
1 ATTTTATTAATTTAACCATTAAAATTAATAATAATATTTT
5623740 ATTTTA-TAATTTAACCATT-AAATTAATAA-AATTATTTT
1 ATTTTATTAATTTAACCATTAAAATTAATAATAA-TATTTT
5623778 ATTTT
1 ATTTT
5623783 TCTCTCGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 2 0.05
38 20 0.51
39 11 0.28
40 6 0.15
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (40 bp):
ATTTTATTAATTTAACCATTAAAATTAATAATAATATTTT
Found at i:5623924 original size:23 final size:24
Alignment explanation
Indices: 5623898--5623943 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5623888 TTTGAACAAG
*
5623898 TCGGATTC-AAATTGTTTACTTTT
1 TCGGATACAAAATTGTTTACTTTT
*
5623921 TCGGATACAAAATTGTTTGCTTT
1 TCGGATACAAAATTGTTTACTTT
5623944 GATAAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (24 bp):
TCGGATACAAAATTGTTTACTTTT
Found at i:5624098 original size:24 final size:24
Alignment explanation
Indices: 5624071--5624116 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5624061 TAAAAATTGA
*
5624071 TAAAAGAAAGATCAAA-TAATAATT
1 TAAAA-AAAAATCAAAGTAATAATT
5624095 TAAAAAAAAATCAAAGTAATAA
1 TAAAAAAAAATCAAAGTAATAA
5624117 ATAAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (24 bp):
TAAAAAAAAATCAAAGTAATAATT
Found at i:5624121 original size:23 final size:24
Alignment explanation
Indices: 5624070--5624126 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
5624060 CTAAAAATTG
*
5624070 ATAAAAGAAAGATCAAATAATAAT
1 ATAAAAGAAAAATCAAATAATAAT
*
5624094 TTAAAA-AAAAATCAAAGTAATAA-
1 ATAAAAGAAAAATCAAA-TAATAAT
5624117 ATAAATAGAA
1 ATAAA-AGAA
5624127 TTTATCACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 13 0.48
24 12 0.44
25 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (24 bp):
ATAAAAGAAAAATCAAATAATAAT
Found at i:5632747 original size:34 final size:34
Alignment explanation
Indices: 5632637--5632750 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 34
5632627 AATTCTTGTA
* *
5632637 TATTTTTTAGAGAAACATTATAATTAATTGTTCTCTT
1 TATTTTTTA-AGAAACATT-TCATTACTTGTTCT-TT
* * *
5632674 T-TTTTTTAAAGAAGCATTTCTATTACTTATT-TTCC
1 TATTTTTT-AAGAAACATTTC-ATTACTTGTTCTT-T
5632709 TATTTTTT-AGAAACATTCTCATTACTTGTTCTTT
1 TATTTTTTAAGAAACATT-TCATTACTTGTTCTTT
5632743 TATTTTTT
1 TATTTTTT
5632751 TTAGGAGCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
34 26 0.41
35 7 0.11
36 28 0.44
37 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.56
Consensus pattern (34 bp):
TATTTTTTAAGAAACATTTCATTACTTGTTCTTT
Found at i:5632764 original size:72 final size:70
Alignment explanation
Indices: 5632637--5632789 Score: 155
Period size: 72 Copynumber: 2.1 Consensus size: 70
5632627 AATTCTTGTA
* *
5632637 TATTTTTTAGAGAAACATTATAATTAATTGTTCTCTTTTTTTTTAAAGAAGCATTTCTATTACTT
1 TATTTTTT--AGAAACATTATAATTAATTGTTCTCTTTTTTTTTAAAGAAGCATTTCCATGACTT
*
5632702 ATTTTCC
64 ATTCTCC
* * * ** * *
5632709 TATTTTTTAGAAACATTCTCATTACTTGTTCT-TTTATTTTTTTTAGGAGCACATTTCCATGATT
1 TATTTTTTAGAAACATTATAATTAATTGTTCTCTTT-TTTTTTAAAGAAG--CATTTCCATGACT
*
5632773 TATTCTCT
63 TATTCTCC
5632781 TATTTTTTA
1 TATTTTTTA
5632790 AGGGAAAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
69 3 0.04
70 31 0.46
72 33 0.49
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (70 bp):
TATTTTTTAGAAACATTATAATTAATTGTTCTCTTTTTTTTTAAAGAAGCATTTCCATGACTTAT
TCTCC
Found at i:5632805 original size:20 final size:20
Alignment explanation
Indices: 5632780--5632817 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5632770 ATTTATTCTC
*
5632780 TTATTTTTTAAGGGAAAATT
1 TTATTTTTAAAGGGAAAATT
5632800 TTATTTTTAAAGGGAAAA
1 TTATTTTTAAAGGGAAAA
5632818 ATTCCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (20 bp):
TTATTTTTAAAGGGAAAATT
Found at i:5632871 original size:36 final size:34
Alignment explanation
Indices: 5632812--5633048 Score: 160
Period size: 36 Copynumber: 6.7 Consensus size: 34
5632802 ATTTTTAAAG
*
5632812 GGAAAA-ATTCCAATTACTTATTCTGTTATTTTTTA
1 GGAAAACATTCC-ATTACTTGTTCT-TTATTTTTTA
* *
5632847 GGAAAACATTTCCATTACTTATTCTTCTA-TTTTAA
1 GGAAAACA-TTCCATTACTTGTTCTT-TATTTTTTA
* * *
5632882 GG-AAATATTCTCATGACTTGTTCTCCTATTTTTTAA
1 GGAAAACATTC-CATTACTTGTTCT-TTATTTTTT-A
*
5632918 GG-AAACACTTGCATTACTTGTTCTCTTATTTTTTA
1 GGAAAACA-TTCCATTACTTGTTCT-TTATTTTTTA
* * *
5632953 GGGAAACATTCCAATTACCTGTTATTCTA-TTTTTA
1 GGAAAACATTCC-ATTACTTGTTCTT-TATTTTTTA
* * * *
5632988 GGGAAACAATCCCATTAGTTTTTCTTTTATTTTTTA
1 GGAAAAC-ATTCCATTACTTGTTC-TTTATTTTTTA
* * *
5633024 GAAAAATACTCCTATTACTTGTTCT
1 GGAAAACATTCC-ATTACTTGTTCT
5633049 CCTATTTTAT
Statistics
Matches: 162, Mismatches: 25, Indels: 30
0.75 0.12 0.14
Matches are distributed among these distances:
33 3 0.02
34 17 0.10
35 51 0.31
36 85 0.52
37 6 0.04
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (34 bp):
GGAAAACATTCCATTACTTGTTCTTTATTTTTTA
Found at i:5633041 original size:71 final size:71
Alignment explanation
Indices: 5632900--5633056 Score: 161
Period size: 71 Copynumber: 2.2 Consensus size: 71
5632890 TCTCATGACT
* * ** ** *
5632900 TGTTCTCCTATTTTTTAAGGAAACACTTGCATTACTTGTTCTCTTATTTTTTAGGGAAACATTCC
1 TGTTATCCTA-TTTTTAAGGAAACAATCCCATTACTTGTTCTCTTATTTTTTAGAAAAACACTCC
5632965 AATTACC
65 AATTACC
* * * * * * *
5632972 TGTTATTCTATTTTTAGGGAAACAATCCCATTAGTTTTTCTTTTATTTTTTAGAAAAATACTCCT
1 TGTTATCCTATTTTTAAGGAAACAATCCCATTACTTGTTCTCTTATTTTTTAGAAAAACACTCCA
*
5633037 ATTACT
66 ATTACC
*
5633043 TGTTCTCCTATTTT
1 TGTTATCCTATTTT
5633057 ATGGCAATAC
Statistics
Matches: 68, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
71 60 0.88
72 8 0.12
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (71 bp):
TGTTATCCTATTTTTAAGGAAACAATCCCATTACTTGTTCTCTTATTTTTTAGAAAAACACTCCA
ATTACC
Found at i:5636042 original size:3 final size:3
Alignment explanation
Indices: 5636034--5636065 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5636024 TTTATTTCTT
5636034 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5636066 CTTTTACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5641568 original size:22 final size:24
Alignment explanation
Indices: 5641543--5641599 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
5641533 CGATTTTTTT
5641543 TTTATTTTTTTA-ATTA-AAATAA
1 TTTATTTTTTTATATTACAAATAA
* *
5641565 TTTAGATTTTTTATTTTACAAATAA
1 TTTA-TTTTTTTATATTACAAATAA
*
5641590 ATTATTTTTT
1 TTTATTTTTT
5641600 ATTCGAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.14
23 7 0.25
24 8 0.29
25 9 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTATTTTTTTATATTACAAATAA
Found at i:5642298 original size:4 final size:4
Alignment explanation
Indices: 5642289--5642317 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5642279 TATCATTACA
5642289 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
5642318 CTTATGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:5646372 original size:24 final size:23
Alignment explanation
Indices: 5646316--5646385 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
5646306 ATACGATATG
*
5646316 ATATAAATATAAAATTTAAAAATA
1 ATAT-AATTTAAAATTTAAAAATA
*
5646340 ATATAATTTAAAATTTTAATAATA
1 ATATAATTTAAAA-TTTAAAAATA
5646364 AT-TATATTT-AAATTTATAAAAT
1 ATATA-ATTTAAAATTTA-AAAAT
5646386 TAAAAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.10
23 17 0.43
24 19 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATAATTTAAAATTTAAAAATA
Found at i:5647157 original size:12 final size:12
Alignment explanation
Indices: 5647123--5647164 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
5647113 TAAAATTCAT
*
5647123 AAAATTTTAAAA
1 AAAATTTTAATA
5647135 AAAATGATTTAATA
1 AAAAT--TTTAATA
5647149 AAAATTTTAATA
1 AAAATTTTAATA
5647161 AAAA
1 AAAA
5647165 ATCTAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AAAATTTTAATA
Found at i:5647216 original size:37 final size:37
Alignment explanation
Indices: 5647143--5647216 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 37
5647133 AAAAAATGAT
*
5647143 TTAATAAAAATTTTAATAAAAAATCTAAACTAATAAA
1 TTAATAAAAATTTTAATAAAAAATCTAAAATAATAAA
5647180 TTAAT-AAAA-TTTAATATAAAAAT-TAATAATATATAAA
1 TTAATAAAAATTTTAATA-AAAAATCTAA-AATA-ATAAA
5647217 AAAATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 10 0.30
36 13 0.39
37 10 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (37 bp):
TTAATAAAAATTTTAATAAAAAATCTAAAATAATAAA
Found at i:5649863 original size:20 final size:20
Alignment explanation
Indices: 5649823--5649863 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5649813 ATTTAAAATT
*
5649823 TTTAAAAAATAATAAATAAA
1 TTTAAAAAATAATAAAAAAA
5649843 TTTAATAAAATAA-AAAAAAA
1 TTTAA-AAAATAATAAAAAAA
5649863 T
1 T
5649864 ATATTTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TTTAAAAAATAATAAAAAAA
Found at i:5650008 original size:22 final size:23
Alignment explanation
Indices: 5649983--5650047 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
5649973 TTTACCTCTT
5649983 TTTATAATTTTATATA-TATAAA
1 TTTATAATTTTATATATTATAAA
* *
5650005 TTTAT-ATTTGATATATTATTAA
1 TTTATAATTTTATATATTATAAA
* *
5650027 TATATAAATTTTATTTATTAT
1 TTTAT-AATTTTATATATTAT
5650048 TTGTAAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.26
22 14 0.40
24 12 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTATAATTTTATATATTATAAA
Found at i:5650708 original size:21 final size:21
Alignment explanation
Indices: 5650684--5650724 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5650674 TGGGTTTTTG
*
5650684 TTTTTCATTTGATATGTTGAC
1 TTTTTCATTTCATATGTTGAC
*
5650705 TTTTTCATTTCATATTTTGA
1 TTTTTCATTTCATATGTTGA
5650725 AAATTCTTTT
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:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (21 bp):
TTTTTCATTTCATATGTTGAC
Found at i:5659726 original size:22 final size:22
Alignment explanation
Indices: 5659701--5659803 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
5659691 CATAAATCAT
5659701 TGATAATTTAATAATTAATTAA
1 TGATAATTTAATAATTAATTAA
*
5659723 TGATAACTTAATAATT-A-T--
1 TGATAATTTAATAATTAATTAA
* *
5659741 GGATAATTTAAT-A-TAAATAA
1 TGATAATTTAATAATTAATTAA
* * * *
5659761 GTGATAATTTGATAATAAATCAT
1 -TGATAATTTAATAATTAATTAA
* *
5659784 TGATAATTTAGTAATGAATT
1 TGATAATTTAATAATTAATT
5659804 GGTGATAGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
16 1 0.02
17 2 0.03
18 11 0.18
20 1 0.02
21 11 0.18
22 32 0.52
23 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (22 bp):
TGATAATTTAATAATTAATTAA
Found at i:5659886 original size:22 final size:22
Alignment explanation
Indices: 5659861--5659935 Score: 107
Period size: 22 Copynumber: 3.4 Consensus size: 22
5659851 GATAACATAG
*
5659861 TAGTAAATATATTAA-AATATAA
1 TAGTAAAT-TATTAATAATTTAA
5659883 TAGTAAATTATTAATAATTTAA
1 TAGTAAATTATTAATAATTTAA
* *
5659905 TAATAAATTATTAATAATTTAG
1 TAGTAAATTATTAATAATTTAA
5659927 TAGTAAATT
1 TAGTAAATT
5659936 GAGAATTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.12
22 42 0.88
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TAGTAAATTATTAATAATTTAA
Found at i:5659910 original size:11 final size:11
Alignment explanation
Indices: 5659875--5659935 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
5659865 AAATATATTA
*
5659875 AAATATAATAGT
1 AAAT-TAATAAT
*
5659887 AAATTATTAAT
1 AAATTAATAAT
*
5659898 AATTTAATAAT
1 AAATTAATAAT
*
5659909 AAATTATTAAT
1 AAATTAATAAT
* * *
5659920 AATTTAGTAGT
1 AAATTAATAAT
5659931 AAATT
1 AAATT
5659936 GAGAATTTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 35 0.90
12 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
AAATTAATAAT
Found at i:5659943 original size:41 final size:41
Alignment explanation
Indices: 5659898--5659976 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
5659888 AATTATTAAT
* *
5659898 AATTTAATAATAAATTATTAATAATTTAGTAGTAAATTGAG
1 AATTTAATAACAAATTAGTAATAATTTAGTAGTAAATTGAG
* ** *
5659939 AATTTAGTTGCAAATTAGTGATAATTTAGTAGTAAATT
1 AATTTAATAACAAATTAGTAATAATTTAGTAGTAAATT
5659977 AATTAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.44, C:0.01, G:0.13, T:0.42
Consensus pattern (41 bp):
AATTTAATAACAAATTAGTAATAATTTAGTAGTAAATTGAG
Found at i:5660025 original size:11 final size:11
Alignment explanation
Indices: 5660011--5660071 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
5660001 TAAATTATCG
5660011 ATAAATTAGTA
1 ATAAATTAGTA
*
5660022 ATAAATTAATTA
1 ATAAATT-AGTA
* *
5660034 A-AATTTTGTA
1 ATAAATTAGTA
*
5660044 ATAAATTATTA
1 ATAAATTAGTA
* *
5660055 ATAACTTAGTC
1 ATAAATTAGTA
5660066 ATAAAT
1 ATAAAT
5660072 AACCAACAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
10 3 0.08
11 30 0.81
12 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (11 bp):
ATAAATTAGTA
Found at i:5660069 original size:22 final size:22
Alignment explanation
Indices: 5659999--5660160 Score: 78
Period size: 22 Copynumber: 7.4 Consensus size: 22
5659989 ATAACTTTAC
**
5659999 AATAAATTATCGATAAATTAGT
1 AATAAATTATTAATAAATTAGT
* *
5660021 AATAAATTAATTAA-AATTTTGT
1 AATAAATT-ATTAATAAATTAGT
*
5660043 AATAAATTATTAATAACTTAGT
1 AATAAATTATTAATAAATTAGT
* * ** * * *
5660065 CATAAATAACCAACAATTTAAT
1 AATAAATTATTAATAAATTAGT
* * * *
5660087 -ATAAAATCATTCATAACTTAAT
1 AAT-AAATTATTAATAAATTAGT
* *
5660109 AATAAATTATT-ATAATTTAAT
1 AATAAATTATTAATAAATTAGT
* * * * *
5660130 AATAGATCATTGATAACTTAAT
1 AATAAATTATTAATAAATTAGT
5660152 AATAAATTA
1 AATAAATTA
5660161 CCGAGGGAGT
Statistics
Matches: 109, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
21 25 0.23
22 79 0.72
23 5 0.05
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (22 bp):
AATAAATTATTAATAAATTAGT
Found at i:5660127 original size:43 final size:43
Alignment explanation
Indices: 5660011--5660160 Score: 131
Period size: 44 Copynumber: 3.4 Consensus size: 43
5660001 TAAATTATCG
* * * ** * *
5660011 ATAAATTAGTAATAAATTAATTAAAATTTTGTAATAAATTATTA
1 ATAACTTAATAATAAATT-ATTATAATTTAATAATAAATCATTC
* * * ** *
5660055 ATAACTTAGTCATAAATAACCAACAATTTAAT-ATAAAATCATTC
1 ATAACTTAATAATAAATTA-TTATAATTTAATAAT-AAATCATTC
* *
5660099 ATAACTTAATAATAAATTATTATAATTTAATAATAGATCATTG
1 ATAACTTAATAATAAATTATTATAATTTAATAATAAATCATTC
5660142 ATAACTTAATAATAAATTA
1 ATAACTTAATAATAAATTA
5660161 CCGAGGGAGT
Statistics
Matches: 85, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
43 38 0.45
44 47 0.55
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (43 bp):
ATAACTTAATAATAAATTATTATAATTTAATAATAAATCATTC
Found at i:5661736 original size:2 final size:2
Alignment explanation
Indices: 5661729--5661768 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5661719 TCGATCCATG
5661729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5661769 AAGTCAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5663075 original size:16 final size:17
Alignment explanation
Indices: 5663054--5663086 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5663044 TATGTATGCT
*
5663054 AATG-AATGCCATTTAA
1 AATGAAATGCAATTTAA
5663070 AATGAAATGCAATTTAA
1 AATGAAATGCAATTTAA
5663087 GTGTTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (17 bp):
AATGAAATGCAATTTAA
Found at i:5663366 original size:17 final size:17
Alignment explanation
Indices: 5663342--5663381 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5663332 ATTGTTATGA
5663342 GGTTTTGAATCTTT-GG
1 GGTTTTGAATCTTTAGG
*
5663358 GGATTTTGAATTTTTAGG
1 GG-TTTTGAATCTTTAGG
5663376 GGTTTT
1 GGTTTT
5663382 AAAAAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 15 0.71
18 4 0.19
ACGTcount: A:0.15, C:0.03, G:0.30, T:0.53
Consensus pattern (17 bp):
GGTTTTGAATCTTTAGG
Found at i:5664947 original size:21 final size:20
Alignment explanation
Indices: 5664900--5664948 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
5664890 AATTATTTTT
5664900 TTTAAAAAATAATAATATTA
1 TTTAAAAAATAATAATATTA
* *
5664920 TTATAAAAATTATTAATATTA
1 TT-TAAAAAATAATAATATTA
5664941 TATTAAAA
1 T-TTAAAA
5664949 TAAAAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAAAAATAATAATATTA
Found at i:5670770 original size:14 final size:15
Alignment explanation
Indices: 5670739--5670780 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
5670729 GCGATAGACG
5670739 AATAAATACTATTAAT
1 AATAAATA-TATTAAT
5670755 AATAAATATA-TAAT
1 AATAAATATATTAAT
5670769 AA-AAA-ATATTAA
1 AATAAATATATTAA
5670781 AGATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 6 0.24
14 6 0.24
15 2 0.08
16 8 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATATATTAAT
Found at i:5673289 original size:17 final size:17
Alignment explanation
Indices: 5673267--5673300 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5673257 AATTTAATTT
5673267 AAATTAACTAAAATTAA
1 AAATTAACTAAAATTAA
*
5673284 AAATTAACTGAAATTAA
1 AAATTAACTAAAATTAA
5673301 GCTACTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATTAACTAAAATTAA
Found at i:5676633 original size:19 final size:19
Alignment explanation
Indices: 5676609--5676645 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5676599 GAAAGCACTA
5676609 ATGATATATTTTAAAAGTG
1 ATGATATATTTTAAAAGTG
5676628 ATGATATATTTTAAAAGT
1 ATGATATATTTTAAAAGT
5676646 TATTATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
ATGATATATTTTAAAAGTG
Found at i:5676980 original size:32 final size:33
Alignment explanation
Indices: 5676939--5677003 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
5676929 TAAATTATAT
5676939 CATGTAATTTTTAA-ATATAATATAATATAAATA
1 CATGTAA-TTTTAATATATAATATAATATAAATA
* *
5676972 CATG-AATTTTAATATTTTATATAATATAAATA
1 CATGTAATTTTAATATATAATATAATATAAATA
5677004 TACAAATCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 6 0.21
32 19 0.66
33 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (33 bp):
CATGTAATTTTAATATATAATATAATATAAATA
Found at i:5677745 original size:17 final size:17
Alignment explanation
Indices: 5677723--5677757 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5677713 TGTTAATGTA
*
5677723 ATTATTGAAGTGATTTT
1 ATTATTAAAGTGATTTT
5677740 ATTATTAAAGTGATTTT
1 ATTATTAAAGTGATTTT
5677757 A
1 A
5677758 ACACTCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (17 bp):
ATTATTAAAGTGATTTT
Found at i:5684376 original size:16 final size:16
Alignment explanation
Indices: 5684328--5684377 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5684318 AAAATTATAT
*
5684328 TAATAATTTAAATT-A
1 TAATAATTTTAATTAA
**
5684343 T-ATAAATTTTAAAAAA
1 TAAT-AATTTTAATTAA
5684359 TAATAATTTTAATTAA
1 TAATAATTTTAATTAA
5684375 TAA
1 TAA
5684378 ACAAAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 2 0.07
15 8 0.30
16 15 0.56
17 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATTTTAATTAA
Found at i:5685247 original size:33 final size:33
Alignment explanation
Indices: 5685209--5685277 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
5685199 TTAAAATTTT
* **
5685209 AATATTTTATCAATAAATTATATAATTTTTATG
1 AATATTTTATCAACAAAACATATAATTTTTATG
*
5685242 AATATTTTATCAACAAAACATATAATTTTTGTG
1 AATATTTTATCAACAAAACATATAATTTTTATG
5685275 AAT
1 AAT
5685278 GATTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (33 bp):
AATATTTTATCAACAAAACATATAATTTTTATG
Found at i:5685293 original size:55 final size:54
Alignment explanation
Indices: 5685234--5685346 Score: 145
Period size: 55 Copynumber: 2.1 Consensus size: 54
5685224 AATTATATAA
* * * *
5685234 TTTTTATGAATATTTTATCAACAAAACATATAATTTTTGTGAATGATTAAAAATT
1 TTTTTATAAATATTTTATCAACAAAACATACAATTTTTATGAATAATT-AAAATT
* * * *
5685289 TTTTTATAAATATTTTATCAACAGATCATACGATTTTTATGGATAATTAAAATT
1 TTTTTATAAATATTTTATCAACAAAACATACAATTTTTATGAATAATTAAAATT
5685343 TTTT
1 TTTT
5685347 CCTTTATAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
54 10 0.20
55 40 0.80
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (54 bp):
TTTTTATAAATATTTTATCAACAAAACATACAATTTTTATGAATAATTAAAATT
Found at i:5687969 original size:2 final size:2
Alignment explanation
Indices: 5687962--5687988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5687952 CAATACATAC
5687962 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5687989 AAGAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5688165 original size:2 final size:2
Alignment explanation
Indices: 5688158--5688188 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5688148 ATCTTTACTC
5688158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5688189 CCTTCTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5690073 original size:11 final size:12
Alignment explanation
Indices: 5690057--5690089 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5690047 ATACGATGAT
5690057 ATGATACAAA-A
1 ATGATACAAATA
*
5690068 ATGATATAAATA
1 ATGATACAAATA
5690080 ATGATACAAA
1 ATGATACAAA
5690090 GATAACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (12 bp):
ATGATACAAATA
Found at i:5691488 original size:21 final size:20
Alignment explanation
Indices: 5691449--5691488 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5691439 ATCAAAGACT
*
5691449 AATAAATCAAAATATAATTG
1 AATAAATCAAAATAAAATTG
*
5691469 AATAAATTCAAATTAAAATT
1 AATAAA-TCAAAATAAAATT
5691489 TGAACCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AATAAATCAAAATAAAATTG
Found at i:5693716 original size:3 final size:3
Alignment explanation
Indices: 5693710--5693738 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5693700 TGTTCTTGAC
5693710 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
5693739 ACGTTGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:5693771 original size:14 final size:14
Alignment explanation
Indices: 5693752--5693779 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5693742 TTGGGTACTG
5693752 GTGTTCAATAAAAA
1 GTGTTCAATAAAAA
5693766 GTGTTCAATAAAAA
1 GTGTTCAATAAAAA
5693780 TGCAGTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
GTGTTCAATAAAAA
Found at i:5707320 original size:20 final size:20
Alignment explanation
Indices: 5707295--5707332 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5707285 ATGATAAGTT
5707295 GTAAGGTTTCACTCAACCGG
1 GTAAGGTTTCACTCAACCGG
5707315 GTAAGGTTTCACTCAACC
1 GTAAGGTTTCACTCAACC
5707333 AGGACTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
GTAAGGTTTCACTCAACCGG
Found at i:5713861 original size:22 final size:22
Alignment explanation
Indices: 5713833--5713877 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5713823 AAAATAGCAC
5713833 GTGTTAGGAATCTCAACTATTA
1 GTGTTAGGAATCTCAACTATTA
5713855 GTGTTAGGAATCTCAACTATTA
1 GTGTTAGGAATCTCAACTATTA
5713877 G
1 G
5713878 ATTACAACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (22 bp):
GTGTTAGGAATCTCAACTATTA
Found at i:5713924 original size:11 final size:11
Alignment explanation
Indices: 5713892--5713924 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5713882 CAACGTTTTC
*
5713892 CTTTCTTTCCC
1 CTTTCTTTCCT
5713903 CTTTCTTTCCT
1 CTTTCTTTCCT
5713914 CTTTCTTTCCT
1 CTTTCTTTCCT
5713925 TCCTGCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (11 bp):
CTTTCTTTCCT
Found at i:5716798 original size:27 final size:27
Alignment explanation
Indices: 5716754--5716807 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
5716744 TTCAAATTAA
* * * * *
5716754 ATTAATTATATTATATTTTTTATTTTT
1 ATTAATTAAATCAAATTTATTAATTTT
5716781 ATTAATTAAATCAAATTTATTAATTTT
1 ATTAATTAAATCAAATTTATTAATTTT
5716808 CAAAGTAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTAATTAAATCAAATTTATTAATTTT
Found at i:5716863 original size:17 final size:17
Alignment explanation
Indices: 5716851--5716883 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5716841 AATTAAATGA
5716851 TAAA-TATA-TTTAAAT
1 TAAATTATATTTTAAAT
5716866 TAAATTATATTTTAAAT
1 TAAATTATATTTTAAAT
5716883 T
1 T
5716884 TTTAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTATATTTTAAAT
Found at i:5721044 original size:63 final size:63
Alignment explanation
Indices: 5720893--5721021 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 63
5720883 TGATAGATAC
* * *
5720893 GATTCTTTAGGAGATTCAGAAACAGGAGAAAGAGATATTGGAGCCAAAGCAGGTACTGGAGAT
1 GATTCTGTAGGAGATTCAGAAACAGGAGAAAAAGATATAGGAGCCAAAGCAGGTACTGGAGAT
* * * *
5720956 GATTCTGTAGGAGATTCAGAAACAGGGGAAAAAGATGTAGGAGGCAAGGCAGGTACTGGAGAT
1 GATTCTGTAGGAGATTCAGAAACAGGAGAAAAAGATATAGGAGCCAAAGCAGGTACTGGAGAT
5721019 GAT
1 GAT
5721022 GTTGTGGGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.37, C:0.10, G:0.33, T:0.19
Consensus pattern (63 bp):
GATTCTGTAGGAGATTCAGAAACAGGAGAAAAAGATATAGGAGCCAAAGCAGGTACTGGAGAT
Found at i:5721078 original size:63 final size:63
Alignment explanation
Indices: 5721011--5721143 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 63
5721001 AAGGCAGGTA
* * * * * *
5721011 CTGGAGATGATG-TTGTGGGAGGTTTTGCAACAGGACCATGATGCTTGGGAGAGTATGCTGGTC
1 CTGGAGATGATGCTT-TGGGAGGTTCTACAACAGGACCACGATGCTTGGGAGAGTAAGCAGGCC
* *
5721074 CTGGAGTTGATGCTTTGGGAGGTTCTACAACAGGGCCACGATGCTTGGGAGAGTAAGCAGGCC
1 CTGGAGATGATGCTTTGGGAGGTTCTACAACAGGACCACGATGCTTGGGAGAGTAAGCAGGCC
5721137 CTGGAGA
1 CTGGAGA
5721144 GAGAAAGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
63 58 0.97
64 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.25
Consensus pattern (63 bp):
CTGGAGATGATGCTTTGGGAGGTTCTACAACAGGACCACGATGCTTGGGAGAGTAAGCAGGCC
Found at i:5722562 original size:13 final size:13
Alignment explanation
Indices: 5722544--5722568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5722534 AAGAAATTTG
5722544 ATAAATAAAACAA
1 ATAAATAAAACAA
5722557 ATAAATAAAACA
1 ATAAATAAAACA
5722569 CAAATGGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAATAAAACAA
Found at i:5726624 original size:21 final size:22
Alignment explanation
Indices: 5726582--5726634 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
5726572 CTTGAAATTA
5726582 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
5726604 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
5726625 ATAAATATAT
1 ATAAA-ATAT
5726635 AATTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:5726916 original size:29 final size:28
Alignment explanation
Indices: 5726852--5726916 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
5726842 TTAAATGTTT
5726852 AAATAATTAAAATAAATTTAAAAATTAA
1 AAATAATTAAAATAAATTTAAAAATTAA
* *
5726880 ATCA-AATTAATAATAATATTT-TAAATTAA
1 A-AATAATTAA-AATAA-ATTTAAAAATTAA
5726909 AAATAATT
1 AAATAATT
5726917 TATATTTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
28 8 0.27
29 18 0.60
30 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAATTAAAATAAATTTAAAAATTAA
Found at i:5727191 original size:18 final size:18
Alignment explanation
Indices: 5727155--5727188 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5727145 TGGACTTTGA
*
5727155 ATTTTGGAGGAGGAGAAG
1 ATTTTGGAGAAGGAGAAG
5727173 ATTTTGGA-AAGGAGAA
1 ATTTTGGAGAAGGAGAA
5727189 AGACATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (18 bp):
ATTTTGGAGAAGGAGAAG
Found at i:5727447 original size:21 final size:21
Alignment explanation
Indices: 5727408--5727447 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5727398 TGATTGTTAT
*
5727408 AAGAAAAGAGTGAATTTATAA
1 AAGAAAAGAGAGAATTTATAA
5727429 AAGAAAAGA-AGAATATTAT
1 AAGAAAAGAGAGAAT-TTAT
5727448 TATAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (21 bp):
AAGAAAAGAGAGAATTTATAA
Found at i:5728880 original size:12 final size:12
Alignment explanation
Indices: 5728863--5728893 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5728853 TCCCCCTTGA
5728863 CTTCCTTCTTCT
1 CTTCCTTCTTCT
5728875 CTTCCTTCTTCT
1 CTTCCTTCTTCT
5728887 CTTCCTT
1 CTTCCTT
5728894 ACCATCCTTC
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:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
CTTCCTTCTTCT
Found at i:5729622 original size:17 final size:15
Alignment explanation
Indices: 5729600--5729647 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
5729590 AATTTGACTT
5729600 TTATTTTGTATTTTATA
1 TTATTTT-TATTTT-TA
5729617 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
*
5729632 TTTTTATTTTATTTTT
1 -TTAT-TTTTATTTTT
5729648 TTTCTTTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:5729627 original size:23 final size:23
Alignment explanation
Indices: 5729598--5729647 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5729588 TCAATTTGAC
5729598 TTTTATTTTGTA-TTTTATATTAT
1 TTTTATTTT-TATTTTTATATTAT
*
5729621 TTTTATTTTTATTTTTATTTTAT
1 TTTTATTTTTATTTTTATATTAT
5729644 TTTT
1 TTTT
5729648 TTTCTTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTATTTTTATTTTTATATTAT
Found at i:5729628 original size:6 final size:6
Alignment explanation
Indices: 5729598--5729647 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
5729588 TCAATTTGAC
*
5729598 TTTTAT TTTGTA- TTTTA- TATTAT TTTTAT TTTTAT TTTTA- TTTTAT
1 TTTTAT TTT-TAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
5729644 TTTT
1 TTTT
5729648 TTTCTTTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 11 0.28
6 26 0.67
7 2 0.05
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:5729685 original size:4 final size:4
Alignment explanation
Indices: 5729676--5729899 Score: 87
Period size: 4 Copynumber: 57.2 Consensus size: 4
5729666 TATGTATCTA
* * * * * *
5729676 TTAT TTAT TTAT TTA- TTAT TACTAT GTAT TAAT ATAT GTAT ATCT TTAT
1 TTAT TTAT TTAT TTAT TTAT T--TAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
5729725 TTAT TTAT TTAT TTAT TT-T CTAT GTTA- ATAT TTAT ATAT GTTTT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT -TTAT TTAT
* * *
5729773 TTAT CTAG TTAT ATAT TTA- TTA- TTAT ATTA- TTAT TTA- TTA- TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT
* * * *
5729816 TTAT TTTT TTAT TTAT CTTGT AATAT TT-T TTAT TTAT CTTA- TTAT TTTT
1 TTAT TTAT TTAT TTAT -TTAT -TTAT TTAT TTAT TTAT -TTAT TTAT TTAT
* * * * *
5729865 TTAA TTAT CTGT TAAT TTTT TTA- TTAT TT-T TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
5729900 CGTTTATCTG
Statistics
Matches: 160, Mismatches: 43, Indels: 34
0.68 0.18 0.14
Matches are distributed among these distances:
3 37 0.23
4 105 0.66
5 15 0.09
6 3 0.02
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:5729725 original size:45 final size:45
Alignment explanation
Indices: 5729670--5729776 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
5729660 GTATCTTATG
*
5729670 TATCTATTATTTATTTATTTA-TTA-TTACTATGTATTAATATATGTA
1 TATCT-TTATTTATTTATTTATTTATTTACTATG--TTAATATATATA
* *
5729716 TATCTTTATTTATTTATTTATTTATTTTCTATGTTAATATTTATA
1 TATCTTTATTTATTTATTTATTTATTTACTATGTTAATATATATA
*
5729761 TATGTTT-TTTATTTAT
1 TATCTTTATTTATTTAT
5729777 CTAGTTATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
44 9 0.16
45 31 0.56
46 8 0.15
47 7 0.13
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (45 bp):
TATCTTTATTTATTTATTTATTTATTTACTATGTTAATATATATA
Found at i:5729803 original size:27 final size:25
Alignment explanation
Indices: 5729769--5729820 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
5729759 TATATGTTTT
5729769 TTATTTATCTAGTTATATATTTATTA
1 TTATTTAT-TAGTTATATATTTATTA
*
5729795 TTATATTATTATTTAT-TA-TTATTA
1 TTAT-TTATTAGTTATATATTTATTA
5729819 TT
1 TT
5729821 TTTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.33
25 2 0.08
26 10 0.42
27 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATTTATTAGTTATATATTTATTA
Found at i:5729815 original size:21 final size:21
Alignment explanation
Indices: 5729789--5729831 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5729779 AGTTATATAT
5729789 TTATTATTATATTATTATTTA
1 TTATTATTATATTATTATTTA
* *
5729810 TTATTATTATTTTTTTATTTA
1 TTATTATTATATTATTATTTA
5729831 T
1 T
5729832 CTTGTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTATTATTATATTATTATTTA
Found at i:5729886 original size:41 final size:42
Alignment explanation
Indices: 5729803--5729889 Score: 126
Period size: 41 Copynumber: 2.1 Consensus size: 42
5729793 TATTATATTA
*
5729803 TTATTTATTATTATTATTTTTTTATTTATCTTGTAATATTTT
1 TTATTTATTATTATTATTTTTTTAATTATCTTGTAATATTTT
*
5729845 TTATTTA-TCTTATTATTTTTTTAATTATC-TGTTAAT-TTTT
1 TTATTTATTATTATTATTTTTTTAATTATCTTG-TAATATTTT
5729885 TTATT
1 TTATT
5729890 ATTTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 11 0.26
41 24 0.57
42 7 0.17
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.71
Consensus pattern (42 bp):
TTATTTATTATTATTATTTTTTTAATTATCTTGTAATATTTT
Found at i:5729938 original size:20 final size:20
Alignment explanation
Indices: 5729890--5729939 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
5729880 TTTTTTTATT
*
5729890 ATTTTTTATTCGTTTATCTG
1 ATTTTTTTTTCGTTTATCTG
5729910 ATTTTTTTTT-GTTTATCTG
1 ATTTTTTTTTCGTTTATCTG
5729929 ATTTTTTTTTC
1 ATTTTTTTTTC
5729940 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (20 bp):
ATTTTTTTTTCGTTTATCTG
Found at i:5729949 original size:53 final size:53
Alignment explanation
Indices: 5729848--5729948 Score: 125
Period size: 52 Copynumber: 1.9 Consensus size: 53
5729838 ATATTTTTTA
*
5729848 TTTATCTTATTATTTTTTTAATTATCTGTTAATTTTTTTATTATTTTTTATTCG
1 TTTATCTGATTATTTTTTTAATTATCTGTT-ATTTTTTTATTATTTTTTATTCG
** * *
5729902 TTTATCTGATT-TTTTTTTGTTTATCTGATT-TTTTTTTCTTTTTTTTT
1 TTTATCTGATTATTTTTTTAATTATCTG-TTATTTTTTTATTATTTTTT
5729949 TTGGGTTGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 15 0.37
53 14 0.34
54 12 0.29
ACGTcount: A:0.15, C:0.06, G:0.05, T:0.74
Consensus pattern (53 bp):
TTTATCTGATTATTTTTTTAATTATCTGTTATTTTTTTATTATTTTTTATTCG
Found at i:5730834 original size:5 final size:5
Alignment explanation
Indices: 5730817--5730893 Score: 61
Period size: 5 Copynumber: 14.8 Consensus size: 5
5730807 TTTAATGTTC
*
5730817 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- TTTTA TTTTCA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTT-A
*
5730866 CTTTTA TTTT- GTTT- TTTTA TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5730894 CTTTAAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
4 10 0.16
5 26 0.43
6 21 0.34
7 4 0.07
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5730837 original size:6 final size:6
Alignment explanation
Indices: 5730817--5730893 Score: 56
Period size: 6 Copynumber: 13.5 Consensus size: 6
5730807 TTTAATGTTC
* * *
5730817 TTTTAT CTTTA- TTTTAT TTTTAT TTTT-G TTTTA- CTTT-T TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
5730861 TTTCAC TTTTAT TTTGTTT TTTTA- TTTTAT TTT
1 TTTTAT TTTTAT TTT-TAT TTTTAT TTTTAT TTT
5730894 CTTTAAATAA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
5 19 0.35
6 30 0.56
7 5 0.09
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:5730837 original size:17 final size:16
Alignment explanation
Indices: 5730816--5730897 Score: 75
Period size: 17 Copynumber: 5.2 Consensus size: 16
5730806 ATTTAATGTT
5730816 CTTTTATCTTTATTTTA
1 CTTTTAT-TTTATTTTA
* *
5730833 TTTTTATTTTTGTTTTA
1 CTTTTA-TTTTATTTTA
5730850 CTTTT-TTTTATTTTCA
1 CTTTTATTTTATTTT-A
*
5730866 CTTTTATTTT-GTTT-
1 CTTTTATTTTATTTTA
5730880 -TTTTATTTTATTTT-
1 CTTTTATTTTATTTTA
5730894 CTTT
1 CTTT
5730898 AAATAAAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
13 9 0.17
14 3 0.06
15 11 0.20
16 9 0.17
17 21 0.39
18 1 0.02
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (16 bp):
CTTTTATTTTATTTTA
Found at i:5730848 original size:11 final size:10
Alignment explanation
Indices: 5730824--5730893 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 10
5730814 TTCTTTTATC
5730824 TTTATTTTATT
1 TTTATTTT-TT
5730835 TTTATTTTTGT
1 TTTATTTTT-T
*
5730846 TTTACTTTTT
1 TTTATTTTTT
*
5730856 TTTATTTTCACT
1 TTTATTTT--TT
*
5730868 TTTA-TTTTG
1 TTTATTTTTT
*
5730877 TTT-TTTTAT
1 TTTATTTTTT
5730886 TTTATTTT
1 TTTATTTT
5730894 CTTTAAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
9 9 0.19
10 13 0.28
11 20 0.43
12 5 0.11
ACGTcount: A:0.13, C:0.04, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:5730898 original size:27 final size:28
Alignment explanation
Indices: 5730824--5730898 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 28
5730814 TTCTTTTATC
*
5730824 TTTATTTTATTTT-TAT-TTTTGTTTTA
1 TTTATTTTATTTTCTTTATTTTGTTTTA
*
5730850 CTTTTTTTTATTTTCACTTTTATTTTGTTTT-
1 -TTTATTTTATTTT--C-TTTATTTTGTTTTA
5730881 TTTATTTTATTTTCTTTA
1 TTTATTTTATTTTCTTTA
5730899 AATAAAACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
27 16 0.40
28 1 0.03
30 12 0.30
31 2 0.05
32 9 0.22
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (28 bp):
TTTATTTTATTTTCTTTATTTTGTTTTA
Found at i:5731094 original size:16 final size:17
Alignment explanation
Indices: 5731065--5731097 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5731055 TGAAAGTATC
*
5731065 AATTTTTCTTAAAAATA
1 AATTTTTCTAAAAAATA
5731082 AATTTTT-TAAAAAATA
1 AATTTTTCTAAAAAATA
5731098 TTTTGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTTCTAAAAAATA
Found at i:5731277 original size:177 final size:179
Alignment explanation
Indices: 5730911--5731603 Score: 876
Period size: 177 Copynumber: 3.9 Consensus size: 179
5730901 TAAAACCTAA
* *
5730911 AAAAAAATATTTTTGGAGAAAAGTTAAAAGTATCAA-TTTTCTTTAAAAATAAATTTTC-AAAAA
1 AAAAAAATATTTTGGGAGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTTCAAAAAA
* * * * * *
5730974 A-AAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAGGAATCCAAAAAAAAA
66 ATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TCAAAATCAAAGATTTC--AAAAGAA
*
5731038 TATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTT-
128 TATTTTTGGGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAATTTTTC
* *
5731089 TAAAAAATATTTTGGGA-AAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAATTTTTAAAAAA
1 AAAAAAATATTTTGGGAGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTTCAAAAAA
* *
5731152 ATAAATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCAAAATTAAAG-TTTCAAAAGAATAT
66 ATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATCAAAGATTTCAAAAGAATAT
* * *
5731216 TTTCGGAAAAAAGTTAAAAGTATTAATTTTTCTTAAAAATAAATTTTTCC
131 TTTTGGGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAATTTTT-C
* * *
5731266 AAAACAATATTTTTGGAGAAAAGTTGAAAGTATC-ACTTTTCTTTAAAAATAAATTTTCAAAAAA
1 AAAAAAATATTTTGGGAGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTTCAAAAAA
* * * * * *
5731330 GT--TTTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAAATCAAAGTTTTCAAAA-AATA
66 ATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTC-AAAATCAAAGATTTCAAAAGAATA
* *
5731392 TTTTTGGGGAAAAGTTGAAAGTATTAATTTTCCTTAAAAATAAA-TTTTC
130 TTTTTGGGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAATTTTTC
* ** * *
5731441 AAAAAAAGTTTTTTTTGAGGAAAAATTGAAAGTATCAA-TTTTCCTTAAAAATAAATTTTCAAAA
1 AAAAAAA-TATTTTGGGA-GAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTTCAAAA
* *
5731505 AAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAA-AGTTTCAAAAGAA
64 AAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATCAAAGA-TTTCAAAAGAA
* *
5731569 TATTTTTGAGG-AAAAGTTGAAAATATCAATTTTTC
128 TATTTTTG-GGAAAAAGTTGAAAGTATTAATTTTTC
5731604 CTGCACAAAA
Statistics
Matches: 449, Mismatches: 49, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
175 60 0.13
176 43 0.10
177 150 0.33
178 97 0.22
179 97 0.22
180 2 0.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (179 bp):
AAAAAAATATTTTGGGAGAAAAGTTGAAAGTATCAATTTTTCTTTAAAAATAAATTTTCAAAAAA
ATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATCAAAGATTTCAAAAGAATAT
TTTTGGGAAAAAGTTGAAAGTATTAATTTTTCTTAAAAATAAATTTTTC
Found at i:5731509 original size:355 final size:354
Alignment explanation
Indices: 5730911--5731574 Score: 1037
Period size: 355 Copynumber: 1.9 Consensus size: 354
5730901 TAAAACCTAA
5730911 AAAAAAATATTTTTGGAGAAAAGTTAAAAGTATCAATTTTCTTTAAAAATAAATTTTCAAAAAAA
1 AAAAAAATATTTTTGGAGAAAAGTTAAAAGTATCAATTTTCTTTAAAAATAAATTTTCAAAAAAA
* * * *
5730976 AGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAGGAATCCAAAAAAAAATAT
66 AGTTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGAATCC--AAAAAAATAT
* **
5731041 TTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTTAAAAAATATTTTGGGA
129 TTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATATTTTGGGA
* *
5731106 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAAAAATAAATTTTTGAGGAAAAG
194 AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATAAATTTTTGAGGAAAAG
5731171 TTGAAAATATCAATTTTCCTCAAAATT-AAAGTTTCAAAAGAATATTTTCGGAAAAAAGTTAAAA
259 TTGAAAATATCAATTTTCCTCAAAATTAAAAGTTTCAAAAGAATATTTTCGGAAAAAAGTTAAAA
5731235 GTATTAATTTTTCTTAAAAATAAATTTTTCC
324 GTATTAATTTTTCTTAAAAATAAATTTTTCC
* * * *
5731266 AAAACAATATTTTTGGAGAAAAGTTGAAAGTATCACTTTTCTTTAAAAATAAATTTTCAAAAAAG
1 AAAAAAATATTTTTGGAGAAAAGTTAAAAGTATCAATTTTCTTTAAAAATAAATTTTCAAAAAAA
** * ** *
5731331 TTTTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAAATCAAAGTTTTC-AAAAAATATTT
66 AGTTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGAATCCAAAAAAATATTT
* * *
5731395 TTGGGGAAAAGTTGAAAGTATTAATTTTCCTTAAAAATAAATTTTCAAAAAAAGTTTTTTTTGAG
131 TTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA---TATTTTG-G
5731460 GAAAAA-TTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATAAATTTTTGAGGAAA
192 GAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATAAATTTTTGAGGAAA
* *
5731524 AGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTCAAAAGAATATTTT
257 AGTTGAAAATATCAATTTTCCTCAAAATTAAAAGTTTCAAAAGAATATTTT
5731575 TGAGGAAAAG
Statistics
Matches: 280, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
352 59 0.21
355 193 0.69
356 28 0.10
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (354 bp):
AAAAAAATATTTTTGGAGAAAAGTTAAAAGTATCAATTTTCTTTAAAAATAAATTTTCAAAAAAA
AGTTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGAATCCAAAAAAATATTT
TTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATATTTTGGGAAA
AAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAATAAATTTTTGAGGAAAAGTT
GAAAATATCAATTTTCCTCAAAATTAAAAGTTTCAAAAGAATATTTTCGGAAAAAAGTTAAAAGT
ATTAATTTTTCTTAAAAATAAATTTTTCC
Found at i:5731604 original size:60 final size:58
Alignment explanation
Indices: 5730911--5731601 Score: 761
Period size: 60 Copynumber: 11.7 Consensus size: 58
5730901 TAAAACCTAA
* *
5730911 AAAAAAATATTTTTG-GAGAAAAGTTAAAAGTATCAATTTTCTTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
5730969 AAAAAAA-AGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAGGA-ATCC
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AA--ATTTTC
* *
5731029 AAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTT
1 --AAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
5731089 TAAAAAATA-TTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTT
1 AAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * *
5731146 AAAAAAATAAATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCAAAATTAAAGTTTC
1 AAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * * *
5731206 AAAAGAATATTTTCG-GAAAAAAGTTAAAAGTATTAATTTTTCTTAAAAATAAATTTTTCC
1 AAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTT-C
* * *
5731266 AAAACAATATTTTTG-GAGAAAAGTTGAAAGTATCACTTTTCTTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * * * **
5731324 AAAAAAGTTTTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAAATCAAAGTTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTTC
* *
5731384 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATTAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
5731441 AAAAAAAGTTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
** * *
5731501 AAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTC
1 AAAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* *
5731562 AAAAGAATATTTTTGAGGAAAAGTTGAAAATATCAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
5731602 TCCTGCACAA
Statistics
Matches: 540, Mismatches: 67, Indels: 51
0.82 0.10 0.08
Matches are distributed among these distances:
57 62 0.11
58 135 0.25
59 87 0.16
60 191 0.35
61 21 0.04
62 43 0.08
63 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Done.