Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 90 of 91
Found at i:35254439 original size:20 final size:19
Alignment explanation
Indices: 35254411--35254449 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
35254401 TTATTTAATT
35254411 TTAAATAAAAATATATAAAA
1 TTAAATAAAAATA-ATAAAA
* *
35254431 TTAATTAAATATAATAAAA
1 TTAAATAAAAATAATAAAA
35254450 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAATAAAAATAATAAAA
Found at i:35255405 original size:22 final size:21
Alignment explanation
Indices: 35255365--35255411 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
35255355 TTTGCAACTG
* *
35255365 TTTTCTTCCTTTTTGTTTTTT
1 TTTTCTTCCTCTTTCTTTTTT
35255386 TTTTCTATCCTCTTTCTTTTTT
1 TTTTCT-TCCTCTTTCTTTTTT
35255408 TTTT
1 TTTT
35255412 TTTTATCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTCTTCCTCTTTCTTTTTT
Found at i:35275760 original size:2 final size:2
Alignment explanation
Indices: 35275753--35275780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35275743 GGATAGGGAC
35275753 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35275781 TGAGTAGAAC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35275840 original size:2 final size:2
Alignment explanation
Indices: 35275833--35275861 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35275823 AACNCAGGAC
35275833 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
35275862 TGAGTGACAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35284046 original size:14 final size:14
Alignment explanation
Indices: 35284027--35284057 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35284017 AAAATGAAAA
*
35284027 AGAGCGAGTGAGAG
1 AGAGCGAGCGAGAG
35284041 AGAGCGAGCGAGAG
1 AGAGCGAGCGAGAG
35284055 AGA
1 AGA
35284058 AAGAGACAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.48, T:0.03
Consensus pattern (14 bp):
AGAGCGAGCGAGAG
Found at i:35284051 original size:18 final size:18
Alignment explanation
Indices: 35284028--35284062 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35284018 AAATGAAAAA
* *
35284028 GAGCGAGTGAGAGAGAGC
1 GAGCGAGAGAGAAAGAGC
35284046 GAGCGAGAGAGAAAGAG
1 GAGCGAGAGAGAAAGAG
35284063 ACAGAGTTCG
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:0.40, C:0.09, G:0.49, T:0.03
Consensus pattern (18 bp):
GAGCGAGAGAGAAAGAGC
Found at i:35296283 original size:2 final size:2
Alignment explanation
Indices: 35296278--35296304 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35296268 ATAGGATTTT
35296278 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
35296305 CTTTGAATTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35312201 original size:292 final size:292
Alignment explanation
Indices: 35311719--35312371 Score: 850
Period size: 292 Copynumber: 2.2 Consensus size: 292
35311709 AGTCATGACC
* * *
35311719 TGCAATCAATGAGGAGCCAGCCGCAGAG-GAAGTTGGAAATTCTAAATTATTACAAGAAAATAAT
1 TGCAA-CAAAGAGGAGCCAGCAGCTGAGAGAAGTTGGAAATTCTAAATTA--ACAAGAAAATAAT
* * * * *
35311783 CGGGATAAGTAAATTCAGGAAGCTATACATAAGAAGACATTGTAGTTAAAGAGTTAAATTTCACT
63 CAGGATAAGAAAATTCAAGAAGCTATACATAAGAAGACATTGTAGTTAAAGAGTTAAAATTAACT
* * * *
35311848 AACACAAAAGGCAAATTTGAGGGAATAATAAGATGTAAATAAGATGAAACAATACGATGGAACGT
128 AACACAAAAGGCAAATTTGAGGGAAGAATAAGATGAAAACAAGATGAAACAATAAGATGGAACGT
* * * ** *
35311913 GAAGACTTGATTGATTACCAGCAGCAAGGTCATGATCAGTGGA-AAGATCACTGATATCATGACT
193 AAAGACTTGATTGATTACCAGCACCAAGGTCATAATCAGT-GACAAGATCACTGATAGAAGGACT
*
35311977 ATCCAGCGCATCAAACACAGAGGCCAACTCAGGATA
257 ATACAGCGCATCAAACACAGAGGCCAACTCAGGATA
* *
35312013 TGCAGCAAAGGAGGAGCCAGCTGCTGAGAG-AGTTGGAAATTCTAAATTAACCAAGAAAATAATC
1 TGCAACAAA-GAGGAGCCAGCAGCTGAGAGAAGTTGGAAATTCTAAATTAA-CAAGAAAATAATC
* *
35312077 AGGATGAGAAAATTGAAGAAGCTATACATAAGAAGACATTGTAGTT-AAGAGTTAAAATTAACTA
64 AGGATAAGAAAATTCAAGAAGCTATACATAAGAAGACATTGTAGTTAAAGAGTTAAAATTAACTA
*
35312141 ACACAAAAGGTAAATTTGAGGGAAGAATAAGATGAAAACAAGATGAAACAATAAGATGGAACGTA
129 ACACAAAAGGCAAATTTGAGGGAAGAATAAGATGAAAACAAGATGAAACAATAAGATGGAACGTA
* * * * *
35312206 AAGTCTTGATTGATTACCGGCACCAAGGTTATAATCAGTGACAAGATCACTTATAGAAGGATTAT
194 AAGACTTGATTGATTACCAGCACCAAGGTCATAATCAGTGACAAGATCACTGATAGAAGGACTAT
** *
35312271 ATGGCGCATCAAACGCAGAGGCCAACTCAGGATA
259 ACAGCGCATCAAACACAGAGGCCAACTCAGGATA
* * * * * *
35312305 TTCAACAAAGATTGAGCCAGCAG-T-AGGAGCAGTTGGAAATCCTAAATCAACAAGAAAGTAATC
1 TGCAACAAAGA-GGAGCCAGCAGCTGA-GAGAAGTTGGAAATTCTAAATTAACAAGAAAATAATC
35312368 AGGA
64 AGGA
35312372 CGACTAAATT
Statistics
Matches: 314, Mismatches: 38, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
290 1 0.00
291 24 0.08
292 192 0.61
293 57 0.18
294 39 0.12
295 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (292 bp):
TGCAACAAAGAGGAGCCAGCAGCTGAGAGAAGTTGGAAATTCTAAATTAACAAGAAAATAATCAG
GATAAGAAAATTCAAGAAGCTATACATAAGAAGACATTGTAGTTAAAGAGTTAAAATTAACTAAC
ACAAAAGGCAAATTTGAGGGAAGAATAAGATGAAAACAAGATGAAACAATAAGATGGAACGTAAA
GACTTGATTGATTACCAGCACCAAGGTCATAATCAGTGACAAGATCACTGATAGAAGGACTATAC
AGCGCATCAAACACAGAGGCCAACTCAGGATA
Found at i:35314112 original size:2 final size:2
Alignment explanation
Indices: 35314101--35314141 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
35314091 GAAATTGATA
35314101 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35314141 A
1 A
35314142 CCTTTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35324259 original size:2 final size:2
Alignment explanation
Indices: 35324252--35324287 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35324242 GTCCACTTGG
35324252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35324288 GCAATGTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35326357 original size:10 final size:10
Alignment explanation
Indices: 35326330--35326364 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
35326320 GGTTAACAAG
35326330 AAGCCTTTAA
1 AAGCCTTTAA
35326340 AAGCCCTTTAA
1 AAG-CCTTTAA
35326351 AAGCCTTTAA
1 AAGCCTTTAA
35326361 AAGC
1 AAGC
35326365 AATCATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (10 bp):
AAGCCTTTAA
Found at i:35328689 original size:22 final size:23
Alignment explanation
Indices: 35328663--35328706 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35328653 AATAATCATA
*
35328663 AAATTTA-AAAAATTTATTATTT
1 AAATTTACAAAAATTAATTATTT
*
35328685 AAATTTACTAAAATTAATTATT
1 AAATTTACAAAAATTAATTATT
35328707 AATTAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTTACAAAAATTAATTATTT
Found at i:35328708 original size:22 final size:21
Alignment explanation
Indices: 35328646--35328708 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
35328636 GATCATAATG
* *
35328646 TTTATAAAA-TAATCATAAAA
1 TTTATAAAATTAATTATTAAA
* *
35328666 TTTAAAAAATTTATTATTTAAA
1 TTTATAAAATTAATTA-TTAAA
35328688 TTTACTAAAATTAATTATTAA
1 TTTA-TAAAATTAATTATTAA
35328709 TTAATTGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 8 0.24
21 4 0.12
22 12 0.35
23 10 0.29
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTATAAAATTAATTATTAAA
Found at i:35328767 original size:23 final size:24
Alignment explanation
Indices: 35328741--35328792 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35328731 CTAAATAAAA
*
35328741 AATTATTAT-AAAAATAAAATTAT
1 AATTATTATAAAAAATAAAAATAT
* *
35328764 AATTTTTTTAAAAAATAAAAATAT
1 AATTATTATAAAAAATAAAAATAT
35328788 -ATTAT
1 AATTAT
35328793 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTATTATAAAAAATAAAAATAT
Found at i:35328800 original size:29 final size:29
Alignment explanation
Indices: 35328748--35328804 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
35328738 AAAAATTATT
**
35328748 ATAAAAATAAAATTATAATTTTTTTAAAAA
1 ATAAAAATAAAATTATAA-AATTTTAAAAA
*
35328778 ATAAAAAT-ATATTATAAAATTTTAAAA
1 ATAAAAATAAAATTATAAAATTTTAAAA
35328805 CTTTATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 8 0.33
30 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAAAAATAAAATTATAAAATTTTAAAAA
Found at i:35330054 original size:21 final size:20
Alignment explanation
Indices: 35329992--35330059 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
35329982 CTACAAAAGC
35329992 ATAAAAATT--AATAAAT-A
1 ATAAAAATTAAAATAAATCA
* *
35330009 ATAATTAAATTAAATTAAATTA
1 ATAA--AAATTAAAATAAATCA
*
35330031 ATATAAAATTAAAATAACTCA
1 ATA-AAAATTAAAATAAATCA
35330052 ATAAAAAT
1 ATAAAAAT
35330060 AAACTAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.10
19 5 0.12
20 5 0.12
21 22 0.54
22 4 0.10
23 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAATTAAAATAAATCA
Found at i:35330071 original size:15 final size:14
Alignment explanation
Indices: 35330037--35330080 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
35330027 ATTAATATAA
35330037 AATT-AAAATAACT
1 AATTAAAAATAACT
35330050 CAA-TAAAAATAAACT
1 -AATTAAAAAT-AACT
35330065 AATTAAAAATAACT
1 AATTAAAAATAACT
35330079 AA
1 AA
35330081 ATTCTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 15 0.56
15 11 0.41
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAATAACT
Found at i:35330083 original size:15 final size:15
Alignment explanation
Indices: 35330036--35330083 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
35330026 AATTAATATA
35330036 AAATT-AAAATAACT
1 AAATTAAAAATAACT
*
35330050 CAA-TAAAAATAAACT
1 AAATTAAAAAT-AACT
35330065 -AATTAAAAATAACT
1 AAATTAAAAATAACT
35330079 AAATT
1 AAATT
35330084 CTAGTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 1 0.03
14 13 0.45
15 15 0.52
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTAAAAATAACT
Found at i:35332191 original size:2 final size:2
Alignment explanation
Indices: 35332184--35332219 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35332174 TGAATTATCA
35332184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35332220 GAATTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35332843 original size:38 final size:38
Alignment explanation
Indices: 35332792--35332883 Score: 150
Period size: 38 Copynumber: 2.4 Consensus size: 38
35332782 TTAGAGAGAG
*
35332792 AGAGAGAGAGAGAGAAGGGGAGAGGAAAGGAAGGATAA
1 AGAGAGAGAGAGAGAAGGGGAGAGGAAAGGAAGGACAA
*
35332830 AGAGAGAGAGAGAGAAGGGGAGAGGAAAGGAAGGACAG
1 AGAGAGAGAGAGAGAAGGGGAGAGGAAAGGAAGGACAA
*
35332868 AGAGAGAAAGAG-GAAG
1 AGAGAGAGAGAGAGAAG
35332884 AGGAAAATGG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 4 0.08
38 47 0.92
ACGTcount: A:0.50, C:0.01, G:0.48, T:0.01
Consensus pattern (38 bp):
AGAGAGAGAGAGAGAAGGGGAGAGGAAAGGAAGGACAA
Found at i:35348547 original size:2 final size:2
Alignment explanation
Indices: 35348540--35348590 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
35348530 CGTATAATTT
35348540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35348582 TA TA T- TA TA
1 TA TA TA TA TA
35348591 CCTCNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35348679 original size:2 final size:2
Alignment explanation
Indices: 35348672--35348720 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
35348662 NNNNNTTTAT
35348672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35348714 TA -A TA TA
1 TA TA TA TA
35348721 CCTCTTCGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35352662 original size:2 final size:2
Alignment explanation
Indices: 35352655--35352702 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
35352645 GTAATAAGTA
35352655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35352697 AT AT AT
1 AT AT AT
35352703 GTATTTTCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35359243 original size:21 final size:21
Alignment explanation
Indices: 35359219--35359276 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
35359209 TCGCTTTCAA
*
35359219 CCTCTTGATTTCAGCTCTCAT
1 CCTCTTGTTTTCAGCTCTCAT
35359240 CCTCTTGTTTTCAGCTCTCAT
1 CCTCTTGTTTTCAGCTCTCAT
35359261 CCTCTTGTTTTCAGCT
1 CCTCTTGTTTTCAGCT
35359277 TGCAACTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.10, C:0.33, G:0.10, T:0.47
Consensus pattern (21 bp):
CCTCTTGTTTTCAGCTCTCAT
Found at i:35360535 original size:16 final size:16
Alignment explanation
Indices: 35360516--35360555 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35360506 TTAATTTAAA
*
35360516 TTATTTTAATTTTATT
1 TTATATTAATTTTATT
*
35360532 TTATATTATTTTTATT
1 TTATATTAATTTTATT
*
35360548 TTAAATTA
1 TTATATTA
35360556 CTTTAAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATTAATTTTATT
Found at i:35360539 original size:21 final size:21
Alignment explanation
Indices: 35360510--35360550 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35360500 GAGTAGTTAA
35360510 TTTAAATTATTTTAATTTTAT
1 TTTAAATTATTTTAATTTTAT
* *
35360531 TTTATATTATTTTTATTTTA
1 TTTAAATTATTTTAATTTTA
35360551 AATTACTTTA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTAAATTATTTTAATTTTAT
Found at i:35362723 original size:2 final size:2
Alignment explanation
Indices: 35362716--35362743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35362706 CTAACCCTTC
35362716 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
35362744 GTGTGTGTGT
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:35365797 original size:24 final size:24
Alignment explanation
Indices: 35365764--35365810 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
35365754 ACTTGCTATA
*
35365764 TAGAGGGTTTACCTTTTCTTTTTG
1 TAGAGAGTTTACCTTTTCTTTTTG
35365788 TAGAGAGTTTACCTTTTCTTTTT
1 TAGAGAGTTTACCTTTTCTTTTT
35365811 AGGATGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (24 bp):
TAGAGAGTTTACCTTTTCTTTTTG
Found at i:35395724 original size:17 final size:18
Alignment explanation
Indices: 35395702--35395737 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
35395692 TCAGAAAAAA
35395702 ACAGAGAGAAA-AGAAAG
1 ACAGAGAGAAAGAGAAAG
35395719 ACAGAGAGAAAGAGAAAG
1 ACAGAGAGAAAGAGAAAG
35395737 A
1 A
35395738 AACACAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.64, C:0.06, G:0.31, T:0.00
Consensus pattern (18 bp):
ACAGAGAGAAAGAGAAAG
Found at i:35397311 original size:15 final size:15
Alignment explanation
Indices: 35397291--35397327 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
35397281 AAAATAAAAC
*
35397291 TATTTTATTTTAATA
1 TATTTTATATTAATA
35397306 TATTTTATATTAAT-
1 TATTTTATATTAATA
35397320 T-TTTTATA
1 TATTTTATA
35397328 ATTCTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.33
14 1 0.05
15 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTATATTAATA
Found at i:35403085 original size:754 final size:753
Alignment explanation
Indices: 35401639--35403144 Score: 2631
Period size: 754 Copynumber: 2.0 Consensus size: 753
35401629 AATTTAAAAG
35401639 GTCATACAAGCACATGATTCCCATATCATGACTAAAGTCAATTAATTGAAAAAGAAAGGAGATAA
1 GTCATACAAGCACATGATTCCCATATCATGACTAAAGTCAATTAATTGAAAAAGAAAGGAGATAA
*
35401704 AGGTGTTAGATTGTTGCAATTGTCAAACTAGTAGTACAATACTTTTGTCTGTTCAGTTGAATTCC
66 AGGTGTTAGATTATTGCAATTGTCAAACTAGTAGTACAATACTTTTGTCTGTTCAGTTGAATTCC
* * *
35401769 TTGGTTGAATTGCTTAATACTGTCAACAGGAAAAAAGTTCTTTATGTTGTTTAGCTTGTCCCATT
131 TTGGTTGAATTGCTTAATACTGTCAACAGGAAAAAAGTTCTTCACGCTGTTTAGCTTGTCCCATT
35401834 TTATAACAAATAGAGTGTTAGTTCATAAGATAATAATTTCTAACAATCCATCCATGTGTTCTTTG
196 TTATAACAAATAGAGTGTTAGTTCATAAGATAATAATTTCTAACAATCCATCCATGTGTTCTTTG
*
35401899 ACAATTTTTTTAGTAACTGAAGGATTTTATGAGACCAATCATGTATCGTTACGTGAAATTGATGA
261 ACAATTTTTTTAGTAACTGAAGGAATTTATGAGACCAATCATGTATCGTTACGTGAAATTGATGA
*
35401964 TATAAAAAGATATAAAAATACCTTTTAAAAGAATATTGAAACTTAAATATTGACTTTTTTTTTTG
326 CATAAAAAGATATAAAAATACCTTTTAAAAGAATATTGAAACTTAAATATTGACTTTTTTTTTTG
* * *
35402029 AAAAAATTTCTATTCCTCCGAACTTGCTTTGTGATACTTTTAAATAAGTTTTGAATTTTCAACTT
391 AAAAAATTTCGATTCCTCCAAACTTGCTTTGTGAAACTTTTAAATAAGTTTTGAATTTTCAACTT
* *
35402094 TTTTTTTTCTTCAAAATTGTATAAAAAAGTTTGAAACATCACTGTATTTATAATGTTAAATAAGA
456 TTTTTTTTCTTCAAAATTATATAAAAAAGTTTGAAACATCAATGTATTTATAATGTTAAATAAGA
* * *
35402159 GATTTTTAAGAAATTTTTTTAATTTTTTATAATTAATTTATTTAATTAAAAATAAATAACAAAAT
521 GATTTTTAAGAAATATTTTTAATTTTTTATAATAAATTTAGTTAATTAAAAATAAATAACAAAAT
35402224 TTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAATATATTTTCCTTCT
586 TTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAATATATTTTCCTTCT
35402289 TTCCATTTTCCAAAAAAGAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGAAACTCA
651 TTCCATTTTCCAAAAAAGAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGAAACTCA
*
35402354 CCTGCTATCGACATCACCTATAAAAAAGTGTGCCAACT
716 CCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACT
35402392 GTCATACAAGCACATGATTCCCATATCATGACTAAAGTCAATTAATTGAAAAAGAAAGGAGATAA
1 GTCATACAAGCACATGATTCCCATATCATGACTAAAGTCAATTAATTGAAAAAGAAAGGAGATAA
*
35402457 AGGTGTTAGATTATTGCAATTGTCAAACTGGTAGTACAATACTTTTGTCTGTTCAGTTGAATTCC
66 AGGTGTTAGATTATTGCAATTGTCAAACTAGTAGTACAATACTTTTGTCTGTTCAGTTGAATTCC
*
35402522 TTGGTTGAATTGCTTAATACTGTCAACAGGAAAAAAGTTCTTCCCGCTGTTTTAGCTTGTCCCAT
131 TTGGTTGAATTGCTTAATACTGTCAACAGGAAAAAAGTTCTTCACGCTG-TTTAGCTTGTCCCAT
35402587 TTTATAACAAATAGAGTGTTAGTTCATAAGATAATAATTTCTAACAATCCATCCATGTGTTCTTT
195 TTTATAACAAATAGAGTGTTAGTTCATAAGATAATAATTTCTAACAATCCATCCATGTGTTCTTT
* * **
35402652 GACAATTTTTTTAGTAATTGAAGGAATTTATGCGATTAATCATGTATCGTTACGTGAAATTGATG
260 GACAATTTTTTTAGTAACTGAAGGAATTTATGAGACCAATCATGTATCGTTACGTGAAATTGATG
* ** *
35402717 ACATAAAAAGATATAAAATTATTTTTTAAAAGAATATTGAAACTTAAATATTGATTTTTTTTTTT
325 ACATAAAAAGATATAAAAATACCTTTTAAAAGAATATTGAAACTTAAATATTGACTTTTTTTTTT
****
35402782 TTTTAAATTTCGATTCCTCCAAACTTGCTTTGTGAAACTTTTAAATAAGTTTTGAATTTTCAACT
390 GAAAAAATTTCGATTCCTCCAAACTTGCTTTGTGAAACTTTTAAATAAGTTTTGAATTTTCAACT
35402847 TTTTTTTTTCTTCAAAATTATATAAAAAAGTTTGAAACATCAATGTATTTATAATGTTAAATAAG
455 TTTTTTTTTCTTCAAAATTATATAAAAAAGTTTGAAACATCAATGTATTTATAATGTTAAATAAG
* * *
35402912 AGA-TTTTAAGAAA-ATTTTTATTTTTTTATTATAATATTTAGTTAATTAAAAATAAATAGCAAA
520 AGATTTTTAAGAAATATTTTTAATTTTTTATAATAA-ATTTAGTTAATTAAAAATAAATAACAAA
* *
35402975 ATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAGTATATTTTTCTT
584 ATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAATATATTTTCCTT
**
35403040 CTTTCCATTTTTTTTAAAAAA-AAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGAAA
649 CTTTCCA--TTTTCCAAAAAAGAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGAAA
35403104 CTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAAC
712 CTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAAC
35403145 ATGATGAATT
Statistics
Matches: 713, Mismatches: 36, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
752 17 0.02
753 279 0.39
754 407 0.57
755 10 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (753 bp):
GTCATACAAGCACATGATTCCCATATCATGACTAAAGTCAATTAATTGAAAAAGAAAGGAGATAA
AGGTGTTAGATTATTGCAATTGTCAAACTAGTAGTACAATACTTTTGTCTGTTCAGTTGAATTCC
TTGGTTGAATTGCTTAATACTGTCAACAGGAAAAAAGTTCTTCACGCTGTTTAGCTTGTCCCATT
TTATAACAAATAGAGTGTTAGTTCATAAGATAATAATTTCTAACAATCCATCCATGTGTTCTTTG
ACAATTTTTTTAGTAACTGAAGGAATTTATGAGACCAATCATGTATCGTTACGTGAAATTGATGA
CATAAAAAGATATAAAAATACCTTTTAAAAGAATATTGAAACTTAAATATTGACTTTTTTTTTTG
AAAAAATTTCGATTCCTCCAAACTTGCTTTGTGAAACTTTTAAATAAGTTTTGAATTTTCAACTT
TTTTTTTTCTTCAAAATTATATAAAAAAGTTTGAAACATCAATGTATTTATAATGTTAAATAAGA
GATTTTTAAGAAATATTTTTAATTTTTTATAATAAATTTAGTTAATTAAAAATAAATAACAAAAT
TTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAATATATTTTCCTTCT
TTCCATTTTCCAAAAAAGAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGAAACTCA
CCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACT
Found at i:35403362 original size:224 final size:223
Alignment explanation
Indices: 35402972--35403418 Score: 885
Period size: 224 Copynumber: 2.0 Consensus size: 223
35402962 AATAAATAGC
35402972 AAAATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAGTATATTTTT
1 AAAATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAGTATATTTTT
35403037 CTTCTTTCCATTTTTTTTAAAAAAAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGA
66 CTTCTTTCCATTTTTTTTAAAAAAAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGA
35403102 AACTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACATGATGAATTTTCCACGTGGCA
131 AACTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACATGATGAATTTTCCACGTGGCA
35403167 ATAAAAGAGAAATTCACATGTCACATCA
196 ATAAAAGAGAAATTCACATGTCACATCA
35403195 NAAAATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAGTATATTTT
1 -AAAATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAGTATATTTT
35403260 TCTTCTTTCCATTTTTTTTAAAAAAAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAG
65 TCTTCTTTCCATTTTTTTTAAAAAAAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAG
35403325 AAACTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACATGATGAATTTTCCACGTGGC
130 AAACTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACATGATGAATTTTCCACGTGGC
35403390 AATAAAAGAGAAATTCACATGTCACATCA
195 AATAAAAGAGAAATTCACATGTCACATCA
35403419 TGGAGGATAA
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 223 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.31
Consensus pattern (223 bp):
AAAATTTATAGATGAATATTGATTCCCTTTAGTATAAATTTACAAATTAAAAATAGTATATTTTT
CTTCTTTCCATTTTTTTTAAAAAAAAAATCATTTTACCAATGATGTCAAAAGAGAGAAAAAGAGA
AACTCACCTGCTATCGACATCACCTATAAAAAAGTGAGCCAACATGATGAATTTTCCACGTGGCA
ATAAAAGAGAAATTCACATGTCACATCA
Found at i:35403449 original size:2 final size:2
Alignment explanation
Indices: 35403438--35403469 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
35403428 AATTCATAAC
35403438 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35403470 GCATCAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35404160 original size:4 final size:4
Alignment explanation
Indices: 35404151--35404181 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
35404141 AGGAAAAGGA
35404151 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
35404182 AGTCTGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:35405715 original size:35 final size:37
Alignment explanation
Indices: 35405675--35405749 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 37
35405665 GTCAGTGGAA
* * *
35405675 TTTGCCATTTATAGTTTCATTCTAA-TTTTCTTG-TT
1 TTTGCCAATGATAGTTTCATTCCAATTTTTCTTGCTT
*
35405710 TTTGCCAATGATAGTTTGATTCCAATTTTTCTTGCTT
1 TTTGCCAATGATAGTTTCATTCCAATTTTTCTTGCTT
35405747 TTT
1 TTT
35405750 ATGTGCATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 21 0.62
36 8 0.24
37 5 0.15
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (37 bp):
TTTGCCAATGATAGTTTCATTCCAATTTTTCTTGCTT
Found at i:35437823 original size:3 final size:3
Alignment explanation
Indices: 35437815--35437840 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35437805 ACATAAGATT
35437815 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
35437841 TTCTCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:35438015 original size:2 final size:2
Alignment explanation
Indices: 35438008--35438053 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
35437998 AGCATTTGAT
*
35438008 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35438050 TC TC
1 TC TC
35438054 CCCCTTTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35440093 original size:2 final size:2
Alignment explanation
Indices: 35440086--35440132 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
35440076 TCATTATCAA
*
35440086 TC TC TC TC TC TC TAC -C NC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35440128 TC TC T
1 TC TC T
35440133 ATATATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:35440137 original size:2 final size:2
Alignment explanation
Indices: 35440132--35440158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35440122 TCTCTCTCTC
35440132 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 T
35440159 GCTTAAGTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35446001 original size:21 final size:21
Alignment explanation
Indices: 35445977--35446016 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35445967 TATTGTCCTC
*
35445977 AGAACTCAGCTCAGATTTTGA
1 AGAAATCAGCTCAGATTTTGA
* *
35445998 AGAAATGAGCTCGGATTTT
1 AGAAATCAGCTCAGATTTT
35446017 TTGACGAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (21 bp):
AGAAATCAGCTCAGATTTTGA
Found at i:35450372 original size:18 final size:18
Alignment explanation
Indices: 35450349--35450386 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35450339 TGAAAGGTTA
35450349 TGTCTTCTAGGGACTCAT
1 TGTCTTCTAGGGACTCAT
35450367 TGTCTTCTAGGGACTCAT
1 TGTCTTCTAGGGACTCAT
35450385 TG
1 TG
35450387 CATACTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (18 bp):
TGTCTTCTAGGGACTCAT
Found at i:35451095 original size:63 final size:63
Alignment explanation
Indices: 35450996--35451120 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
35450986 TATCATAATG
35450996 TTCAAGTCTGTAAACTTGAAGTGCATTTTACTCCATTCAAGGAAGCCTGTGAAACCATGAATC
1 TTCAAGTCTGTAAACTTGAAGTGCATTTTACTCCATTCAAGGAAGCCTGTGAAACCATGAATC
* *
35451059 TTCAAGTCTGTAAACTTGAAGTGCATTTTACTCCATTCAAGGAAGCTTTTGAAACCATGAAT
1 TTCAAGTCTGTAAACTTGAAGTGCATTTTACTCCATTCAAGGAAGCCTGTGAAACCATGAAT
35451121 GAACTTAGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TTCAAGTCTGTAAACTTGAAGTGCATTTTACTCCATTCAAGGAAGCCTGTGAAACCATGAATC
Found at i:35458996 original size:2 final size:2
Alignment explanation
Indices: 35458989--35459016 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35458979 TGAGATGTAC
35458989 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35459017 TGTGTACGAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35463790 original size:24 final size:25
Alignment explanation
Indices: 35463759--35463815 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
35463749 TTTATATACT
*
35463759 TTTA-TTT-TAAAAAATATAAAAAA
1 TTTATTTTCTAAAAAATAAAAAAAA
*
35463782 TTTATTTTTCTAAAATATAAAAAAAA
1 TTTA-TTTTCTAAAAAATAAAAAAAA
35463808 TTTATTTT
1 TTTATTTT
35463816 ATTTCAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.14
25 7 0.24
26 18 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTATTTTCTAAAAAATAAAAAAAA
Found at i:35463795 original size:26 final size:26
Alignment explanation
Indices: 35463766--35463815 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
35463756 ACTTTTATTT
*
35463766 TAAAAAATATAAAAAATTTATTTTTC
1 TAAAAAATAAAAAAAATTTATTTTTC
*
35463792 TAAAATATAAAAAAAATTTATTTT
1 TAAAAAATAAAAAAAATTTATTTT
35463816 ATTTCAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAAAATAAAAAAAATTTATTTTTC
Found at i:35465858 original size:21 final size:20
Alignment explanation
Indices: 35465818--35465863 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
35465808 ATTTAGCTGC
*
35465818 TAGGCTTTTTCTCATGGA-T
1 TAGGCTTTTTCACATGGATT
35465837 TAGGCTTTTATCACATTGGATT
1 TAGGCTTTT-TCACA-TGGATT
35465859 TAGGC
1 TAGGC
35465864 CTCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 4 0.17
21 4 0.17
22 6 0.26
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (20 bp):
TAGGCTTTTTCACATGGATT
Found at i:35486335 original size:22 final size:22
Alignment explanation
Indices: 35486309--35486350 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
35486299 TGTTTCATAA
35486309 TTTAAAAT-AATGAAAAAAATAT
1 TTTAAAATAAAT-AAAAAAATAT
35486331 TTTAAAATAAATAAAAAAAT
1 TTTAAAATAAATAAAAAAAT
35486351 CACATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TTTAAAATAAATAAAAAAATAT
Found at i:35491483 original size:21 final size:21
Alignment explanation
Indices: 35491459--35491500 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35491449 TATTTAATTA
*
35491459 ATTATATCATATATT-ATATTT
1 ATTATATAAT-TATTAATATTT
35491480 ATTATATAATTATTAATATTT
1 ATTATATAATTATTAATATTT
35491501 TATGTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATATAATTATTAATATTT
Found at i:35498871 original size:91 final size:92
Alignment explanation
Indices: 35498716--35498899 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 92
35498706 CTGTTGTTTT
35498716 TATTGTTATTATTATTTATTACTTAAACCTTAATTAATCTCAAAAAATTACAAATTTTTAAATAT
1 TATTGTTATTATTATTTATTACTTAAACCTTAATTAATCTCAAAAAATTACAAATTTTTAAATAT
35498781 TATTAGCTTTAAAAAAGGG-AAGAAGA
66 TATTAGCTTTAAAAAAGGGAAAGAAGA
35498807 TATTGTTATTATTATTTATTACTTAAACCTTAATTAATCTCAAAAAATTACAAATTTTTAAATAT
1 TATTGTTATTATTATTTATTACTTAAACCTTAATTAATCTCAAAAAATTACAAATTTTTAAATAT
35498872 TATTAGCTTTAAAAAAGGGAAAGAAGA
66 TATTAGCTTTAAAAAAGGGAAAGAAGA
35498899 T
1 T
35498900 GTTGATTTGA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 84 0.91
92 8 0.09
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (92 bp):
TATTGTTATTATTATTTATTACTTAAACCTTAATTAATCTCAAAAAATTACAAATTTTTAAATAT
TATTAGCTTTAAAAAAGGGAAAGAAGA
Found at i:35499643 original size:23 final size:23
Alignment explanation
Indices: 35499613--35499658 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35499603 TTATTAATGA
35499613 AAAAAGGTAAAGACATTAGAAAT
1 AAAAAGGTAAAGACATTAGAAAT
35499636 AAAAAGGTAAAGACATTAGAAAT
1 AAAAAGGTAAAGACATTAGAAAT
35499659 TCTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAAAGGTAAAGACATTAGAAAT
Found at i:35501055 original size:18 final size:18
Alignment explanation
Indices: 35501003--35501093 Score: 51
Period size: 18 Copynumber: 4.7 Consensus size: 18
35500993 ATTAGAAATT
*
35501003 AAAATAAAATATAATATAA
1 AAAATAAAAAATAA-ATAA
* **
35501022 AAATTATATTAA-AAATAA
1 AAAATA-AAAAATAAATAA
35501040 AAAATAAAAAATAAATAA
1 AAAATAAAAAATAAATAA
*
35501058 GATTATAATAAAAAATGAAA-AT
1 -A--A-AATAAAAAAT-AAATAA
35501080 AAAATANAAAAATA
1 AAAATA-AAAAATA
35501094 TATTTAAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
17 3 0.05
18 20 0.36
19 15 0.27
20 2 0.04
21 2 0.04
22 11 0.20
23 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATAAAAAATAAATAA
Found at i:35501079 original size:35 final size:36
Alignment explanation
Indices: 35500998--35501083 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
35500988 TAAGAATTAG
* * *
35500998 AAATTAAAATAAAATATAATATAAAAATTATATTAA
1 AAATAAAAATAAAAAATAATATAAAAATTATATAAA
*
35501034 AAATAAAAAATAAAAAATAA-AT-AAGATTATAATAAA
1 AAAT-AAAAATAAAAAATAATATAAAAATTAT-ATAAA
*
35501070 AAATGAAAATAAAA
1 AAATAAAAATAAAA
35501084 TANAAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 16 0.37
36 14 0.33
37 13 0.30
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (36 bp):
AAATAAAAATAAAAAATAATATAAAAATTATATAAA
Found at i:35510450 original size:3 final size:3
Alignment explanation
Indices: 35510442--35510479 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
35510432 ATCAAATCCA
*
35510442 TCC TCC TCC TCC TCC TCC TCC TCC TTC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
35510480 GACCGCCGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:35514359 original size:2 final size:2
Alignment explanation
Indices: 35514317--35514347 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35514307 ATTACAAGAC
35514317 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
35514348 GAAGGCAGAG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35521847 original size:3 final size:3
Alignment explanation
Indices: 35521839--35521867 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35521829 TCAAAGTTCA
35521839 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
35521868 TCAACATTTT
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35543845 original size:2 final size:2
Alignment explanation
Indices: 35543838--35543891 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
35543828 GAATTGAAGC
35543838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35543880 AT AT GT AT AT AT
1 AT AT AT AT AT AT
35543892 GTTGTACTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35548019 original size:33 final size:33
Alignment explanation
Indices: 35547975--35548042 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
35547965 AGCTTTTCTT
**
35547975 AAAGCT-TTTTTTTAAAATATTACTCTTAAAAAA
1 AAAGCTATTTTTAAAAAATATT-CTCTTAAAAAA
35548008 AAAGCTATTTTTAAAAAATATTCTCTTAAAAAA
1 AAAGCTATTTTTAAAAAATATTCTCTTAAAAAA
35548041 AA
1 AA
35548043 TTATTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 19 0.59
34 13 0.41
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (33 bp):
AAAGCTATTTTTAAAAAATATTCTCTTAAAAAA
Found at i:35548437 original size:2 final size:2
Alignment explanation
Indices: 35548430--35548456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35548420 GTTAAAATTC
35548430 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
35548457 AACAGGAAGA
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:35549742 original size:16 final size:17
Alignment explanation
Indices: 35549712--35549753 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
35549702 CATGTCACAT
35549712 CATGATATATCAATGACA
1 CATGATATA-CAATGACA
*
35549730 CATGATATA-AATGATA
1 CATGATATACAATGACA
*
35549746 AATGATAT
1 CATGATAT
35549754 TTTGAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (17 bp):
CATGATATACAATGACA
Found at i:35556684 original size:2 final size:2
Alignment explanation
Indices: 35556677--35556701 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35556667 CCCCCATATC
35556677 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
35556702 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:35557082 original size:2 final size:2
Alignment explanation
Indices: 35557075--35557102 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35557065 AAAAGGTAAA
35557075 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35557103 CTAAAGAAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35557309 original size:3 final size:3
Alignment explanation
Indices: 35557296--35557343 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
35557286 AGAGCGAGAG
*
35557296 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
35557343 A
1 A
35557344 AGAGATAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35577512 original size:2 final size:2
Alignment explanation
Indices: 35577505--35577545 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
35577495 GAGATCAGGN
35577505 AT AT 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 AT AT
35577546 TCCCCAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35578492 original size:21 final size:21
Alignment explanation
Indices: 35578450--35578489 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35578440 CTAATATTTA
*
35578450 TAATATATGTTATCACATAAT
1 TAATATATGTTATCAAATAAT
*
35578471 TAATATAT-TTATTAAATAA
1 TAATATATGTTATCAAATAA
35578490 ATTTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
TAATATATGTTATCAAATAAT
Found at i:35606617 original size:2 final size:2
Alignment explanation
Indices: 35606610--35606638 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35606600 TCTGCTCTTT
35606610 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35606639 GCCCTTCCCC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35610511 original size:9 final size:9
Alignment explanation
Indices: 35610474--35610508 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
35610464 ATTATGCCTA
35610474 CCCAAATGC
1 CCCAAATGC
35610483 CCCAAATGC
1 CCCAAATGC
*
35610492 CCCAAATGT
1 CCCAAATGC
35610501 CCCAAATG
1 CCCAAATG
35610509 TCCAAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.34, C:0.40, G:0.11, T:0.14
Consensus pattern (9 bp):
CCCAAATGC
Found at i:35613549 original size:17 final size:17
Alignment explanation
Indices: 35613529--35613572 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
35613519 AACTTGACTC
35613529 AATTTAA-AGTAATTTTA
1 AATTTAATA-TAATTTTA
35613546 AATTTAATATAATTTTA
1 AATTTAATATAATTTTA
35613563 AATTTTAATA
1 AA-TTTAATA
35613573 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTAATATAATTTTA
Found at i:35614112 original size:21 final size:22
Alignment explanation
Indices: 35614065--35614112 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
35614055 ATACAGAATT
* *
35614065 AATAATTTTTTCTTATACTCAA
1 AATAATTTTCTCTTAAACTCAA
35614087 AATAATTTTCT-TTAAACT-AA
1 AATAATTTTCTCTTAAACTCAA
35614107 ATATAA
1 A-ATAA
35614113 AACGTAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 10 0.43
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATTTTCTCTTAAACTCAA
Found at i:35614295 original size:16 final size:15
Alignment explanation
Indices: 35614276--35614305 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
35614266 TTTTAAATTT
35614276 TTAAAAATTAAAATCA
1 TTAAAAA-TAAAATCA
35614292 TTAAAAATAAAATC
1 TTAAAAATAAAATC
35614306 CACATAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAATAAAATCA
Found at i:35615271 original size:23 final size:23
Alignment explanation
Indices: 35615234--35615277 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35615224 CTTTTCTTAT
*
35615234 TTATTATTTTATTAAATAAAATA
1 TTATTATTTCATTAAATAAAATA
* *
35615257 TTATTATTTCGTTAATTAAAA
1 TTATTATTTCATTAAATAAAA
35615278 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTATTTCATTAAATAAAATA
Found at i:35622966 original size:54 final size:54
Alignment explanation
Indices: 35622899--35623003 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
35622889 TCATTTGAGC
35622899 TAGGCACTGCCAATTTTTACTGAAAGAAGCTCTTTGGAACTAATAGGCCTTAAA
1 TAGGCACTGCCAATTTTTACTGAAAGAAGCTCTTTGGAACTAATAGGCCTTAAA
35622953 TAGGCACTGCCAATTTTTACTGAAAGAAGCTCTTTGGAACTAATAGGCCTT
1 TAGGCACTGCCAATTTTTACTGAAAGAAGCTCTTTGGAACTAATAGGCCTT
35623004 TTTAAGGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
TAGGCACTGCCAATTTTTACTGAAAGAAGCTCTTTGGAACTAATAGGCCTTAAA
Found at i:35623642 original size:28 final size:28
Alignment explanation
Indices: 35623601--35623656 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
35623591 CCATTTCATG
*
35623601 TTTTCACAGAAACGAATTGTATGTAGAA
1 TTTTCACAGAAACGAATTGCATGTAGAA
35623629 TTTTCACA-ATAACGAATTGCATGTAGAA
1 TTTTCACAGA-AACGAATTGCATGTAGAA
35623657 GCAACTACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (28 bp):
TTTTCACAGAAACGAATTGCATGTAGAA
Found at i:35624780 original size:29 final size:30
Alignment explanation
Indices: 35624722--35624783 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
35624712 CTTGTTAGGT
* *
35624722 ATAATTACAAAGGAAAATTTAGGGATAAAA
1 ATAATTACAAAGGAAAATTTAGAGAGAAAA
*
35624752 ATAATTATAAA-GAAAATTT-GAAGAGAAAA
1 ATAATTACAAAGGAAAATTTAG-AGAGAAAA
35624781 ATA
1 ATA
35624784 GATGTTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 17 0.61
30 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.15, T:0.24
Consensus pattern (30 bp):
ATAATTACAAAGGAAAATTTAGAGAGAAAA
Found at i:35631651 original size:2 final size:2
Alignment explanation
Indices: 35631646--35631676 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35631636 TTTTTATTAT
35631646 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35631677 CTTATTGTGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35639708 original size:27 final size:27
Alignment explanation
Indices: 35639674--35639738 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
35639664 CAATTTTAAA
* *
35639674 TTTT-TAAAAAGTTAAATTAATTGAAT
1 TTTTATAAAAAATGAAATTAATTGAAT
*
35639700 TTTTATAAAAAATGAAATTGATTGAAT
1 TTTTATAAAAAATGAAATTAATTGAAT
*
35639727 TATTA-AAAAAAT
1 TTTTATAAAAAAT
35639739 AAAGACGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (27 bp):
TTTTATAAAAAATGAAATTAATTGAAT
Found at i:35640094 original size:119 final size:119
Alignment explanation
Indices: 35639951--35640363 Score: 474
Period size: 119 Copynumber: 3.5 Consensus size: 119
35639941 AAATTATTCT
*
35639951 TCTTAATCAATTTAATACCAAAATTGAAAAAATTAATTCAAATTAACCGAATTCAATAAAGTATC
1 TCTTAATCAA-TTAATACCAAAATTGAAAAAATTAATT-AAATTAACCGAATTCAATAAAATATC
* * * **
35640016 ATATTAAATAGAAGCAAAATCAATCTCGAGCTTAAAAACAAATTAATAGAGTT-AG
64 ATATTAAATAGAACCAAAATCAATCTCAAGCTTAAAAACAAACTAATAGAGTTCCC
* ** **
35640071 TCTTAATCAATTAATACCAAAATTGAAAAAATTAATATGAATTAACTAAATTCAATAAAATATTT
1 TCTTAATCAATTAATACCAAAATTGAAAAAATTAAT-TAAATTAACCGAATTCAATAAAATATCA
* * * * *
35640136 TATTAATTTGAACCAAAATCAATCTCAATCTTAGAAACAAACAAATAG-GTTCCC
65 TATTAAATAGAACCAAAATCAATCTCAAGCTTAAAAACAAACTAATAGAGTTCCC
* *
35640190 TCTTAATCAATTAATACCAAGA-T-CAAAAA--AATT-AATT---CGAATTCAATAAAATATCAT
1 TCTTAATCAATTAATACCAAAATTGAAAAAATTAATTAAATTAACCGAATTCAATAAAATATCAT
* * * *
35640247 ATTAAATTA-AATCAAAATCAATCTTAAGTTTACAAACAAACTAAT--AGTTCCC
66 ATTAAA-TAGAACCAAAATCAATCTCAAGCTTAAAAACAAACTAATAGAGTTCCC
* *
35640299 TCTTAATCAATTAATACCAAAATTAAAAAAATTAATCTAAATTGACCGAATTCAATAAAATATCA
1 TCTTAATCAATTAATACCAAAATTGAAAAAATTAAT-TAAATTAACCGAATTCAATAAAATATCA
35640364 AGACATTTAA
Statistics
Matches: 248, Mismatches: 32, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
109 27 0.11
110 52 0.21
111 6 0.02
113 7 0.03
114 2 0.01
115 7 0.03
117 5 0.02
118 23 0.09
119 108 0.44
120 11 0.04
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (119 bp):
TCTTAATCAATTAATACCAAAATTGAAAAAATTAATTAAATTAACCGAATTCAATAAAATATCAT
ATTAAATAGAACCAAAATCAATCTCAAGCTTAAAAACAAACTAATAGAGTTCCC
Found at i:35640328 original size:110 final size:109
Alignment explanation
Indices: 35640119--35640334 Score: 310
Period size: 110 Copynumber: 2.0 Consensus size: 109
35640109 GAATTAACTA
** * * *
35640119 AATTCAATAAAATATTTTATTAATTTGAACCAAAATCAATCTCAATCTTAGAAACAAACAAATAG
1 AATTCAATAAAATATCATATTAAATTAAACCAAAATCAATCTCAATCTTACAAACAAACAAATAG
*
35640184 GTTCCCTCTTAATCAATTAATACCAAGATCAAAAAAATTAATTCG
66 GTTCCCTCTTAATCAATTAATACCAAAAT-AAAAAAATTAATTCG
* * *
35640229 AATTCAATAAAATATCATATTAAATTAAATCAAAATCAATCTTAAGT-TTACAAACAAACTAATA
1 AATTCAATAAAATATCATATTAAATTAAACCAAAATCAATCTCAA-TCTTACAAACAAACAAATA
35640293 -GTTCCCTCTTAATCAATTAATACCAAAATTAAAAAAATTAAT
65 GGTTCCCTCTTAATCAATTAATACCAAAA-TAAAAAAATTAAT
35640335 CTAAATTGAC
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
109 39 0.41
110 55 0.58
111 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (109 bp):
AATTCAATAAAATATCATATTAAATTAAACCAAAATCAATCTCAATCTTACAAACAAACAAATAG
GTTCCCTCTTAATCAATTAATACCAAAATAAAAAAATTAATTCG
Found at i:35641636 original size:138 final size:137
Alignment explanation
Indices: 35641370--35641619 Score: 306
Period size: 138 Copynumber: 1.8 Consensus size: 137
35641360 CCCAAGTTTA
* *
35641370 AAAAACGAGTTAATAGATTCCTTCCTAATGGATTAATAACAAAATAAAAAAGAATTAATTGAATT
1 AAAAACAAGTTAATAGATTCCCTCCTAATGGATTAATAACAAAATAAAAAAGAATTAATTGAATT
* * * ** * *
35641435 CAATAAATATCATATTAAATTGACTTAAATCAATCTCAAGCTTAAAAACAAACTAATAATTAATC
66 CAATAAAAATAATATTAAATTGAATTAAATCAAAATCAAGCTCAAAAACAAAC-AACAATTAATC
35641500 TCAAGCTT
130 TCAAGCTT
* * * *
35641508 AAAAACAAGTTAATAGATTCCCTCTTAATTGATTAATACCAAAATCAAAAA-AATTAATCTGAAT
1 AAAAACAAGTTAATAGATTCCCTCCTAATGGATTAATAACAAAATAAAAAAGAATTAAT-TGAAT
* * *
35641572 TCAATAAAAAATAAATGTTAAATT-AATTAAATTAAAATCAATCTCAAA
65 TCAAT-AAAAAT-AATATTAAATTGAATTAAATCAAAATCAAGCTCAAA
35641620 CTTAAAAACA
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
137 7 0.07
138 55 0.59
139 23 0.24
140 9 0.10
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.30
Consensus pattern (137 bp):
AAAAACAAGTTAATAGATTCCCTCCTAATGGATTAATAACAAAATAAAAAAGAATTAATTGAATT
CAATAAAAATAATATTAAATTGAATTAAATCAAAATCAAGCTCAAAAACAAACAACAATTAATCT
CAAGCTT
Found at i:35659223 original size:21 final size:21
Alignment explanation
Indices: 35659189--35659262 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
35659179 ATGGAAGGGA
*
35659189 TGGAACAGTGGAAGGATCAAT
1 TGGAGCAGTGGAAGGATCAAT
* *
35659210 TAGAGCAGTTGAA-GAGTCAAT
1 TGGAGCAGTGGAAGGA-TCAAT
*
35659231 TGGAGCCA-TGGAAGAATCAAT
1 TGGAG-CAGTGGAAGGATCAAT
35659252 TGGAGCAGTGG
1 TGGAGCAGTGG
35659263 TTGCATCAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.09
21 36 0.84
22 3 0.07
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.20
Consensus pattern (21 bp):
TGGAGCAGTGGAAGGATCAAT
Found at i:35675048 original size:12 final size:12
Alignment explanation
Indices: 35675031--35675056 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35675021 CCTGATTTTT
35675031 CTTCAGCTTCTC
1 CTTCAGCTTCTC
35675043 CTTCAGCTTCTC
1 CTTCAGCTTCTC
35675055 CT
1 CT
35675057 GGTTCAGTTC
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:0.08, C:0.42, G:0.08, T:0.42
Consensus pattern (12 bp):
CTTCAGCTTCTC
Found at i:35681623 original size:4 final size:4
Alignment explanation
Indices: 35681614--35681643 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35681604 AAGCTAAACA
*
35681614 ATAC ATAC ATAC ATAC ATAC ATGC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
35681644 GTACACACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:35682322 original size:72 final size:71
Alignment explanation
Indices: 35682191--35682325 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 71
35682181 CCATCTCACG
* * * *
35682191 ATCAGCTTTATAGGTATGCCATTTTTATGCAGGTTTTATTGTCAAGCGTATACCTGCCAACTCGA
1 ATCAGCTTTACAGGTATGCCATTTTTATGCAGGCTCTATTGTCAAGCATATACCTGCCAACTCGA
35682256 ATCATA
66 ATCATA
* *
35682262 ATCAGCTTTACAGGTATGCTATTTTTTATGCAGGCTCTATTTTCGAA-CATATACCTGCCAACTC
1 ATCAGCTTTACAGGTATGCCA-TTTTTATGCAGGCTCTATTGTC-AAGCATATACCTGCCAACTC
35682326 AGTTCATCCA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
71 19 0.34
72 35 0.62
73 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (71 bp):
ATCAGCTTTACAGGTATGCCATTTTTATGCAGGCTCTATTGTCAAGCATATACCTGCCAACTCGA
ATCATA
Found at i:35691091 original size:19 final size:19
Alignment explanation
Indices: 35691063--35691105 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
35691053 ATAAATAAAT
*
35691063 CATAAGAAAAAGA-AATACA
1 CATAAAAAAAAGATAATA-A
35691082 CATAAAAAAAAAGATAATAA
1 CAT-AAAAAAAAGATAATAA
35691102 CATA
1 CATA
35691106 TAGATAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (19 bp):
CATAAAAAAAAGATAATAA
Found at i:35691617 original size:261 final size:255
Alignment explanation
Indices: 35691022--35691955 Score: 1144
Period size: 261 Copynumber: 3.6 Consensus size: 255
35691012 ATACTCGCAG
* * * * * * * *
35691022 AAGAAACACGTGTACATTAAAATTCTAATATATAAATAAAT-CATAAGAAAAAGAAATACACATA
1 AAGAAACACGTGCACATTAAAATTTTAAAAAATAAATATATAAATAAAAAAAAGAAACACACATA
* * * * * *
35691086 AAAAAAAAGATAATAACATATAGATAGTATAACAAAACTCGATAAATTCGATAGAGATACCAAAG
66 AAGAAAAAGAGAATAACATATAGATAGTACAATAAAACTCGACAAACTCGATAGAGATACCAAAG
* * * *
35691151 TGCAAAGTACAAAAAGA-TTTGTAAAGAATGCTCGAGCGAGCAGGCAATCAATATATTCCCGAGC
131 TGCAAAGTGCAAAAAGACCTCG-AAAGAATGCTCGAGCGAGCAAGCAATCAATATATTCCCGAGC
* *
35691215 TTGCCTTTCACTCGACCTCATCCTTCGTCAACAAATGAATATA-GATACTC-ACATTCACAA
195 TTGCCTTTCACTCGACCTCATCCTTCGTCAGCAAATGAATATACAATACTCTACATTCAC-A
* ** *
35691275 AAGAAACATGTGCATGTTAAAATTTTATAAAATTAAATATATAAATAAAAAGAAAAAGAAACACA
1 AAGAAACACGTGCACATTAAAATTTTA-AAAAATAAATATATAAAT--AAA-AAAAAGAAACACA
* * *
35691340 AATAAAGAAAAAAAAGAGAATAATATATAGATAGTACAATAAAACTCGATAAACTCGATAGAGAT
62 CATAAAG---AAAAAGAGAATAACATATAGATAGTACAATAAAACTCGACAAACTCGATAGAGAT
* * *
35691405 ACCAAAGTGCAAAGTGCAAAAAGACCTAGAAAGAATGCTCGAGTGAGCAAGCAATCGATATATTC
124 ACCAAAGTGCAAAGTGCAAAAAGACCTCGAAAGAATGCTCGAGCGAGCAAGCAATCAATATATTC
** * * *
35691470 TTGAGCTTGCCTTTCACTCAACCTCATCCTTCATCAGTAAATGAATATACATAATACATACTAAC
189 CCGAGCTTGCCTTTCACTCGACCTCATCCTTCGTCAGCAAATGAATATAC--AATAC-T-CT-AC
35691535 ATTCACA
249 ATTCACA
*
35691542 ATAGAAACATGTGCACATTAAAATTTTAAAAAATAAATATATAAATAAAAAAAAAGAAACACACA
1 A-AGAAACACGTGCACATTAAAATTTTAAAAAATAAATATATAAAT-AAAAAAAAGAAACACACA
* * * * * *
35691607 -AAAGAAAAAGATAATAACATAAAGATAGTACAATAAAGCTTGACAAACTCAATAGAGATATCAA
64 TAAAGAAAAAGAGAATAACATATAGATAGTACAATAAAACTCGACAAACTCGATAGAGATACCAA
* * *
35691671 AGTGCAAAGTGCAAAAGGACCTCGAAAGAATGCTCGAGCGAGCAAGCAATCTATATATTCCCAAG
129 AGTGCAAAGTGCAAAAAGACCTCGAAAGAATGCTCGAGCGAGCAAGCAATCAATATATTCCCGAG
*
35691736 CTTGCCTTTCACTCGACCTCATCCTTCGTCGGCAAATGAATATAC-ATACT-TACATTCACA
194 CTTGCCTTTCACTCGACCTCATCCTTCGTCAGCAAATGAATATACAATACTCTACATTCACA
* * * * *
35691796 GAAGAAATACGTACACATTGAAATTTTAAAAAATAAATATATAAATAAAAAAAATAAACACACAC
1 -AAGAAACACGTGCACATTAAAATTTTAAAAAATAAATATATAAATAAAAAAAAGAAACACACAT
* * * * * *
35691861 AAAGAAAAAGAGAATGATATATAAATAGTATAATAAAGCTCGACAAACTGGATAGAGATACCAAA
65 AAAGAAAAAGAGAATAACATATAGATAGTACAATAAAACTCGACAAACTCGATAGAGATACCAAA
*
35691926 GTGCAAAGTGCAAAAGGACCTCGAAAGAAT
130 GTGCAAAGTGCAAAAAGACCTCGAAAGAAT
35691956 ACCAAATTGG
Statistics
Matches: 592, Mismatches: 70, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
253 39 0.07
254 144 0.24
255 4 0.01
257 3 0.01
258 21 0.04
261 300 0.51
262 2 0.00
264 8 0.01
265 15 0.03
266 5 0.01
267 19 0.03
268 32 0.05
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (255 bp):
AAGAAACACGTGCACATTAAAATTTTAAAAAATAAATATATAAATAAAAAAAAGAAACACACATA
AAGAAAAAGAGAATAACATATAGATAGTACAATAAAACTCGACAAACTCGATAGAGATACCAAAG
TGCAAAGTGCAAAAAGACCTCGAAAGAATGCTCGAGCGAGCAAGCAATCAATATATTCCCGAGCT
TGCCTTTCACTCGACCTCATCCTTCGTCAGCAAATGAATATACAATACTCTACATTCACA
Found at i:35695200 original size:27 final size:26
Alignment explanation
Indices: 35695170--35695232 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 26
35695160 CCCTTTTTTG
* *
35695170 CTTTTTTTTTCTTTATTCTCTTATTTC
1 CTTTTTTTTTCTTTACTC-CTCATTTC
* **
35695197 CTTTATTCATCTTTACTCCTCATTTC
1 CTTTTTTTTTCTTTACTCCTCATTTC
*
35695223 TTTTTTTTTT
1 CTTTTTTTTT
35695233 TATTTATTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.70
Consensus pattern (26 bp):
CTTTTTTTTTCTTTACTCCTCATTTC
Found at i:35698930 original size:30 final size:30
Alignment explanation
Indices: 35698893--35699117 Score: 193
Period size: 30 Copynumber: 7.5 Consensus size: 30
35698883 GCTTCTACTT
* * *
35698893 GTGGTCTGCACTTCCTTTTCTGCCGAAATC
1 GTGGTCTGCACTTCCTTGTCTGCGGAACTC
* * * **
35698923 ATGGTCTGCAGTTGCTTGTCTGTTGAACTC
1 GTGGTCTGCACTTCCTTGTCTGCGGAACTC
* * * * * *
35698953 ATGGTTTGCACATCCTTCTTTGCGGTAGC-C
1 GTGGTCTGCACTTCCTTGTCTGCGG-AACTC
* *
35698983 GTGGTCTGCACTTCCTTGTCAGCTGAACTC
1 GTGGTCTGCACTTCCTTGTCTGCGGAACTC
* * *
35699013 GTGGGT-TGCACTTCCTTGTCTGAGGAAATT
1 GT-GGTCTGCACTTCCTTGTCTGCGGAACTC
*
35699043 GTGGTCTGCGCTTCCTTGTCTGCGGAACTC
1 GTGGTCTGCACTTCCTTGTCTGCGGAACTC
* * * *
35699073 GTGGTTTGCACTTCCTTGTCCGTGGAAGTC
1 GTGGTCTGCACTTCCTTGTCTGCGGAACTC
*
35699103 GTGCTCTGCACTTCC
1 GTGGTCTGCACTTCC
35699118 CTCTTGGCTG
Statistics
Matches: 151, Mismatches: 40, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
29 5 0.03
30 141 0.93
31 5 0.03
ACGTcount: A:0.12, C:0.26, G:0.26, T:0.36
Consensus pattern (30 bp):
GTGGTCTGCACTTCCTTGTCTGCGGAACTC
Found at i:35699137 original size:45 final size:45
Alignment explanation
Indices: 35699086--35699212 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
35699076 GTTTGCACTT
*
35699086 CCTTGTCCG-TGGAAGTCGTGCTCTGCACTTCCCTCTTGGCTGAAA
1 CCTTGTCCGCT-GAACTCGTGCTCTGCACTTCCCTCTTGGCTGAAA
* ** * * *
35699131 CCTTGTCTGCTGAACTTTTGGTCTGCACTTCCTTCTTGGCTGGAA
1 CCTTGTCCGCTGAACTCGTGCTCTGCACTTCCCTCTTGGCTGAAA
* * * * * *
35699176 GCTTGTCTGCTGCACTTGTGGTCTGCACTTCCTTCTT
1 CCTTGTCCGCTGAACTCGTGCTCTGCACTTCCCTCTT
35699213 TGTGGAACTC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 70 0.99
46 1 0.01
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.38
Consensus pattern (45 bp):
CCTTGTCCGCTGAACTCGTGCTCTGCACTTCCCTCTTGGCTGAAA
Found at i:35699251 original size:30 final size:30
Alignment explanation
Indices: 35699177--35699257 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
35699167 TGGCTGGAAG
* *
35699177 CTTGTCTGCTGCACTTGTGGTCTGCACTTC
1 CTTGTCTGCTGAACTTGTGGTCTCCACTTC
* * * *
35699207 CTTCTTTG-TGGAACTCGTGGTGTCCACTTC
1 CTTGTCTGCT-GAACTTGTGGTCTCCACTTC
35699237 CTTGTCTGCTGAACTTGTGGT
1 CTTGTCTGCTGAACTTGTGGT
35699258 TTGCGGTTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 1 0.03
30 38 0.95
31 1 0.03
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.41
Consensus pattern (30 bp):
CTTGTCTGCTGAACTTGTGGTCTCCACTTC
Found at i:35710053 original size:7 final size:7
Alignment explanation
Indices: 35710035--35710098 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 7
35710025 TAATAAAAAT
35710035 ATTTTAAA
1 ATTTT-AA
35710043 ATTTTAA
1 ATTTTAA
35710050 ATTTTAA
1 ATTTTAA
***
35710057 AAAATAA
1 ATTTTAA
35710064 ATTTTAA
1 ATTTTAA
*
35710071 ATCTTAA
1 ATTTTAA
35710078 ATTTTAA
1 ATTTTAA
*
35710085 ATTTTGA
1 ATTTTAA
35710092 ATTTTAA
1 ATTTTAA
35710099 TGCGAGATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
7 41 0.89
8 5 0.11
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (7 bp):
ATTTTAA
Found at i:35710122 original size:2 final size:2
Alignment explanation
Indices: 35710117--35710153 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35710107 TTTTTAACAT
35710117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35710154 TATTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35720083 original size:24 final size:24
Alignment explanation
Indices: 35720056--35720101 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
35720046 AGCAACAACA
35720056 AACAA-ATCAGGAAAAGCAGCAGCC
1 AACAAGATCA-GAAAAGCAGCAGCC
* *
35720080 AACAAGTTCAGAAAATCAGCAG
1 AACAAGATCAGAAAAGCAGCAG
35720102 AAAACGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.50, C:0.22, G:0.20, T:0.09
Consensus pattern (24 bp):
AACAAGATCAGAAAAGCAGCAGCC
Found at i:35720117 original size:24 final size:25
Alignment explanation
Indices: 35720061--35720118 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
35720051 CAACAAACAA
35720061 ATCAGGAAAAGCAGCAGCCAACAAGT
1 ATCAGGAAAAGCAGCAG-CAACAAGT
*
35720087 -TCA-GAAAATCAGCAG-AA-AACGT
1 ATCAGGAAAAGCAGCAGCAACAA-GT
35720109 ATCAGGAAAA
1 ATCAGGAAAA
35720119 CCAACGGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 2 0.07
22 4 0.14
23 3 0.11
24 16 0.57
25 3 0.11
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (25 bp):
ATCAGGAAAAGCAGCAGCAACAAGT
Found at i:35724457 original size:17 final size:17
Alignment explanation
Indices: 35724431--35724482 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
35724421 TCCTAGATAA
*
35724431 TTTTTACTTCTTCACTT
1 TTTTTTCTTCTTCACTT
*
35724448 TTTTTTCTTCTCCA-TT
1 TTTTTTCTTCTTCACTT
* *
35724464 CTTTTTCTTTTTC-CTT
1 TTTTTTCTTCTTCACTT
35724480 TTT
1 TTT
35724483 ATTTACTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTCTTCTTCACTT
Found at i:35725953 original size:14 final size:15
Alignment explanation
Indices: 35725934--35725968 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
35725924 TTTCTTATAA
35725934 ATTAATTTAA-ATTT
1 ATTAATTTAATATTT
*
35725948 ATTAATTTAATTTTT
1 ATTAATTTAATATTT
35725963 ATTAAT
1 ATTAAT
35725969 AATTTACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTAATTTAATATTT
Found at i:35725953 original size:34 final size:32
Alignment explanation
Indices: 35725883--35725974 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 32
35725873 CTTACCAATA
* *
35725883 TTAA-TTAATTATTATACATATAATTTAAAATT
1 TTAATTTAATTTTTATAAAT-TAATTTAAAATT
* *
35725915 TTAATTTATTTTCTTATAAATTAATTTAAATTT
1 TTAATTTAATTT-TTATAAATTAATTTAAAATT
*
35725948 ATTAATTTAATTTTTATTAA-TAATTTA
1 -TTAATTTAATTTTTATAAATTAATTTA
35725975 CATAAAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 11 0.22
33 22 0.43
34 18 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (32 bp):
TTAATTTAATTTTTATAAATTAATTTAAAATT
Found at i:35728300 original size:33 final size:33
Alignment explanation
Indices: 35728252--35729013 Score: 909
Period size: 33 Copynumber: 23.1 Consensus size: 33
35728242 GTCTGATTCG
* *
35728252 TTTGAAGCT-CTAGATGCTTGATTTGAATCCTCT
1 TTTGAAGCTGC-AGATGCTTGACTTGAACCCTCT
* *
35728285 TTGGAAGCTGCAGATGCTTGACTTGAAACCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728318 TTTGAAGCTGCAGATGCTTGATTTAAATCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* *
35728351 TTTGAAGCTGCAGATGCTTGACTGGAAACCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728384 TTTGAAGCTGCAGATGCTTGATTTGGATCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728417 TTTGAAGCTGCTGATCCTTCACTTGAACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* *
35728450 TTTGAAGCTGCAGATGCTTGAATTGAATCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
** *
35728483 TTTGAAGCTATAGATGCTTGACTTGAAACCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728516 TTTGAAGCTGCAGATGCTTGATTTGGATCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728549 TTTGAAGCTGCTGATCCTTCACTTGAACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728582 TTTGAGGCTGCAGATGCTTGAATTGAATCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
** *
35728615 TTTGAAGCTATAGATGCTTGACTTGAAACCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
*
35728648 TTTGAAGCTGCAGATGCTTGACTTGAAACCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* *
35728681 TTTGAAGCTGCAGATGCTTGAATTGGACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * * *
35728714 TTCGAAGCTGCTGATGCTTCATTTGAACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728747 TTTGAAGCTGCAGATGCTTGAATTGGACCCTCA
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* *
35728780 TTTGAAGCTGCAGATGCTTGAATTGGACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* *
35728813 TTTGAAGCTGCAGATGCTTCATTTGAACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * *
35728846 TTTGAAGCTGCAGGTGCTTGAGTTGGACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
*
35728879 TTTGAAGCTGCAGATGCTTGGA-TTCG-GCCCTCT
1 TTTGAAGCTGCAGATGCTT-GACTT-GAACCCTCT
* * * *
35728912 TCTGAAGCTGTAGATGCTTGACTTGAAACCTCA
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* ** * *
35728945 TTTGAAGCCGTGGATGCTTGAGTTGGACCCTCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
* * * *
35728978 TTTGATGCTGCAGGTGCTTGAATTGAACCATCT
1 TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
35729011 TTT
1 TTT
35729014 TGTTTCTTTT
Statistics
Matches: 626, Mismatches: 98, Indels: 10
0.85 0.13 0.01
Matches are distributed among these distances:
32 3 0.00
33 619 0.99
34 4 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (33 bp):
TTTGAAGCTGCAGATGCTTGACTTGAACCCTCT
Found at i:35732346 original size:8 final size:8
Alignment explanation
Indices: 35732318--35732360 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
35732308 TCAAAAAAAA
35732318 AATTTAAT
1 AATTTAAT
35732326 AATTTTAATT
1 AA-TTTAA-T
35732336 AATTTAAT
1 AATTTAAT
*
35732344 AATTTTAT
1 AATTTAAT
35732352 ATATTTAAT
1 A-ATTTAAT
35732361 TATAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 11 0.37
9 16 0.53
10 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
AATTTAAT
Found at i:35732710 original size:28 final size:26
Alignment explanation
Indices: 35732667--35732730 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
35732657 AAAGATTTAA
35732667 ATTT-TATTTATATAATATATTTGTTT
1 ATTTATATTTATATAATATATTT-TTT
* *
35732693 ATTTATATTTGATGTAATTTATTTTTT
1 ATTTATATTT-ATATAATATATTTTTT
*
35732720 ATAATATATTT
1 AT-TTATATTT
35732731 TTATTATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.12
27 10 0.31
28 18 0.56
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (26 bp):
ATTTATATTTATATAATATATTTTTT
Found at i:35746245 original size:24 final size:24
Alignment explanation
Indices: 35746214--35746265 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
35746204 CAGAATTTGG
*
35746214 ATCTCATTTTGCAGAAAAGAAGCT
1 ATCTCATTTTGCAAAAAAGAAGCT
35746238 ATCTCATTTTGCAAAAAAGAAGCT
1 ATCTCATTTTGCAAAAAAGAAGCT
35746262 ATCT
1 ATCT
35746266 TTTCCAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (24 bp):
ATCTCATTTTGCAAAAAAGAAGCT
Found at i:35753730 original size:23 final size:23
Alignment explanation
Indices: 35753678--35753731 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
35753668 TTCATCTGTT
35753678 ATGCTTTC-GATTTCTCTTTCTC
1 ATGCTTTCAGATTTCTCTTTCTC
* * *
35753700 ACGTTTTCAGATTTCTCTTTCTT
1 ATGCTTTCAGATTTCTCTTTCTC
*
35753723 GTGCTTTCA
1 ATGCTTTCA
35753732 AGACACCAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.11, C:0.24, G:0.11, T:0.54
Consensus pattern (23 bp):
ATGCTTTCAGATTTCTCTTTCTC
Found at i:35754599 original size:17 final size:18
Alignment explanation
Indices: 35754577--35754610 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35754567 CACTGGAAAG
*
35754577 AAAAAATTTG-AATAAAC
1 AAAAAAGTTGAAATAAAC
35754594 AAAAAAGTTGAAATAAA
1 AAAAAAGTTGAAATAAA
35754611 AAGCTCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (18 bp):
AAAAAAGTTGAAATAAAC
Found at i:35757614 original size:19 final size:19
Alignment explanation
Indices: 35757586--35757623 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35757576 ATAGGTATAA
*
35757586 TATTTTAAAAAATTTAAAT
1 TATTTAAAAAAATTTAAAT
*
35757605 TATTTAAAAAATTTTAAAT
1 TATTTAAAAAAATTTAAAT
35757624 AAGTCTTTAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAAAAAAATTTAAAT
Found at i:35758035 original size:16 final size:16
Alignment explanation
Indices: 35758010--35758040 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35758000 ATTTATACTC
35758010 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
35758026 ATTAATAATTTAATA
1 ATTAAAAATTTAATA
35758041 AGGTAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:35758070 original size:16 final size:15
Alignment explanation
Indices: 35758044--35758135 Score: 75
Period size: 16 Copynumber: 6.1 Consensus size: 15
35758034 TTTAATAAGG
*
35758044 TAAACATTAATATTT
1 TAAATATTAATATTT
35758059 TGAAATATTAATATTT
1 T-AAATATTAATATTT
*
35758075 T--AT-TT-ATAATT
1 TAAATATTAATATTT
*
35758086 TAAATATTATTATGATT
1 TAAATATTAATAT--TT
*
35758103 AAAATATTAATATTT
1 TAAATATTAATATTT
*
35758118 TAAAATATTAATTTTT
1 T-AAATATTAATATTT
35758134 TA
1 TA
35758136 TAATTTATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.10
12 2 0.03
13 4 0.07
14 2 0.03
15 6 0.10
16 28 0.46
17 13 0.21
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (15 bp):
TAAATATTAATATTT
Found at i:35769894 original size:48 final size:48
Alignment explanation
Indices: 35769822--35769916 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
35769812 AAATAAAGCA
*
35769822 TTGGTTTTCCAATCCCTGATATGCTCTGGGTAAATTTAGTTCTTGTAT
1 TTGGTTTTCCAATCCCTGACATGCTCTGGGTAAATTTAGTTCTTGTAT
35769870 TTGGTTTTCCAATCCCTGACATGCTCTGGGTAAATTTAGTTCTTGTA
1 TTGGTTTTCCAATCCCTGACATGCTCTGGGTAAATTTAGTTCTTGTA
35769917 GTTGAGGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (48 bp):
TTGGTTTTCCAATCCCTGACATGCTCTGGGTAAATTTAGTTCTTGTAT
Found at i:35771369 original size:17 final size:18
Alignment explanation
Indices: 35771347--35771380 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35771337 CCACTAGAAA
35771347 AAAAAAATTG-AATAAAC
1 AAAAAAATTGAAATAAAC
*
35771364 AAAAAAGTTGAAATAAA
1 AAAAAAATTGAAATAAA
35771381 AAGCTCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAAAAATTGAAATAAAC
Found at i:35776499 original size:29 final size:29
Alignment explanation
Indices: 35776440--35776501 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
35776430 ATTTTGAAAT
* *
35776440 TTTATTAATATAAAATAAAAACTATGATA
1 TTTATTAATATAAAATAAAAAATAAGATA
35776469 TTTA-TAATATGAAAATAAAAAAATAAG-TA
1 TTTATTAATAT-AAAAT-AAAAAATAAGATA
35776498 TTTA
1 TTTA
35776502 AAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.21
29 15 0.52
30 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (29 bp):
TTTATTAATATAAAATAAAAAATAAGATA
Found at i:35777623 original size:22 final size:21
Alignment explanation
Indices: 35777593--35777636 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 21
35777583 AAAATTTATT
35777593 GTTAT-ACACTATACTTAAAAA
1 GTTATAACACTATA-TTAAAAA
35777614 GTTATTACACACTATATTAAAAA
1 GTTA-TA-ACACTATATTAAAAA
35777637 AAATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 1 0.05
23 7 0.35
24 8 0.40
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (21 bp):
GTTATAACACTATATTAAAAA
Found at i:35777645 original size:26 final size:26
Alignment explanation
Indices: 35777554--35777646 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 26
35777544 TCAATTATAA
* *
35777554 AAAAAAAAGATATTACAC-GTCATATT
1 AAAAAAAATATATTACACACT-ATATT
* * *
35777580 AAAAAAATTTATTGTTATACACTATACTT
1 AAAAAAA-ATA-TATTACACACTATA-TT
*
35777609 --AAAAAGT-TATTACACACTATATT
1 AAAAAAAATATATTACACACTATATT
35777632 AAAAAAAATATATTA
1 AAAAAAAATATATTA
35777647 TTATTACATG
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
23 2 0.04
24 12 0.24
25 6 0.12
26 13 0.25
27 6 0.12
28 9 0.18
29 3 0.06
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAAAAAATATATTACACACTATATT
Found at i:35777746 original size:31 final size:31
Alignment explanation
Indices: 35777709--35777767 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
35777699 GTCACGTGTT
*
35777709 ATGTTGAAAAAAAATATTATTGTTACACGTC
1 ATGTTGAAAAAAAATATTATTATTACACGTC
35777740 ATGTTGAAAAAAAATATTATTATTACAC
1 ATGTTGAAAAAAAATATTATTATTACAC
35777768 ACAATGTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (31 bp):
ATGTTGAAAAAAAATATTATTATTACACGTC
Found at i:35777781 original size:31 final size:31
Alignment explanation
Indices: 35777715--35777781 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
35777705 TGTTATGTTG
* * **
35777715 AAAAAAAATATTATTGTTACACGTCATGTTG
1 AAAAAAAATATTATTATTACACGACATGTAC
35777746 AAAAAAAATATTATTATTACAC-ACAATGTAC
1 AAAAAAAATATTATTATTACACGAC-ATGTAC
35777777 AAAAA
1 AAAAA
35777782 CATATTACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAAAAAATATTATTATTACACGACATGTAC
Found at i:35798961 original size:36 final size:36
Alignment explanation
Indices: 35798920--35798992 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
35798910 AGCATGACAG
* *
35798920 TAGGTATGCATGAATAACTGATGAGTTTAGGATAAA
1 TAGGTATGCATGAATAACTGATGAGTCTACGATAAA
35798956 TAGGTATGCATGAATAACTGATGAGTCTACGATAAA
1 TAGGTATGCATGAATAACTGATGAGTCTACGATAAA
35798992 T
1 T
35798993 TCAGAAGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (36 bp):
TAGGTATGCATGAATAACTGATGAGTCTACGATAAA
Found at i:35806121 original size:64 final size:64
Alignment explanation
Indices: 35806020--35806152 Score: 221
Period size: 64 Copynumber: 2.1 Consensus size: 64
35806010 TGGAGTACGA
* * *
35806020 CTTGAACATAGTTTTACCATTTCCCTGAGGAAAGAAAAAGTGATTCCCGGTCTGCCAAATGGGT
1 CTTGAACACAGTTTCACCATTTCCCTGAGGAAAGAAAAAGTGATTCCCGGTCGGCCAAATGGGT
* *
35806084 CTTGAACACAGTTTCACCATTTCCCTGCGGAAAGAAAAAGTGATTCCTGGTCGGCCAAATGGGT
1 CTTGAACACAGTTTCACCATTTCCCTGAGGAAAGAAAAAGTGATTCCCGGTCGGCCAAATGGGT
35806148 CTTGA
1 CTTGA
35806153 CTAACAAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (64 bp):
CTTGAACACAGTTTCACCATTTCCCTGAGGAAAGAAAAAGTGATTCCCGGTCGGCCAAATGGGT
Found at i:35819794 original size:2 final size:2
Alignment explanation
Indices: 35819789--35819819 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35819779 AGAAAAAAAT
35819789 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35819820 ATTTAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35838352 original size:6 final size:6
Alignment explanation
Indices: 35838336--35838365 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35838326 ACCCTCCTGT
*
35838336 CTGTTC TTGTTC CTGTTC CTGTTC CTGTTC
1 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC
35838366 GGCCCGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.17, T:0.53
Consensus pattern (6 bp):
CTGTTC
Found at i:35842018 original size:11 final size:11
Alignment explanation
Indices: 35842002--35842026 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35841992 AATCAACCAG
35842002 GGAACAGGACA
1 GGAACAGGACA
35842013 GGAACAGGACA
1 GGAACAGGACA
35842024 GGA
1 GGA
35842027 GTTGGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.40, T:0.00
Consensus pattern (11 bp):
GGAACAGGACA
Found at i:35847285 original size:14 final size:14
Alignment explanation
Indices: 35847266--35847296 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35847256 AGTTGTTTGG
*
35847266 TAAATTTTTTTTTA
1 TAAATTCTTTTTTA
35847280 TAAATTCTTTTTTA
1 TAAATTCTTTTTTA
35847294 TAA
1 TAA
35847297 GTTATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TAAATTCTTTTTTA
Found at i:35855961 original size:51 final size:51
Alignment explanation
Indices: 35855885--35856010 Score: 175
Period size: 51 Copynumber: 2.5 Consensus size: 51
35855875 CCCACCACCT
* *
35855885 GGACCACCGCCACCTGGGCATGGCGGCTTCGG-TTTCTCACTTGGACCGCCA
1 GGACCACCACCACCTGGGCATGGCGGCTTCGGCTTTC-CACGTGGACCGCCA
35855936 GGACCACCACCACCTGGGC-TCGGCGGCTTCGGCTTTCCACGTGGACCGCCA
1 GGACCACCACCACCTGGGCAT-GGCGGCTTCGGCTTTCCACGTGGACCGCCA
* **
35855987 CGACCACCACCACAGGGGCATGGC
1 GGACCACCACCACCTGGGCATGGC
35856011 TTTTTCCCTG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.01
51 61 0.91
52 5 0.07
ACGTcount: A:0.16, C:0.40, G:0.29, T:0.15
Consensus pattern (51 bp):
GGACCACCACCACCTGGGCATGGCGGCTTCGGCTTTCCACGTGGACCGCCA
Found at i:35869863 original size:2 final size:2
Alignment explanation
Indices: 35869856--35869894 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
35869846 TTTACCACCA
*
35869856 CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
35869895 ACACACACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:35875341 original size:18 final size:19
Alignment explanation
Indices: 35875305--35875342 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35875295 TATGAATTTT
*
35875305 TTTTATTTTTTATATATTA
1 TTTTATTTTTAATATATTA
35875324 TTTTATTTTTAATA-ATTA
1 TTTTATTTTTAATATATTA
35875342 T
1 T
35875343 CTTTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTTTTAATATATTA
Done.