Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_pilon, 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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 27
Found at i:2173482 original size:72 final size:72
Alignment explanation
Indices: 2173365--2173582 Score: 330
Period size: 72 Copynumber: 3.0 Consensus size: 72
2173355 TCTTTCACTT
* * * * *
2173365 CAGCTGCAGTTGCTACCCCGTCACAGTCTGTGTTTGGTAACACCAATCCGGGCCTGGTGTTTGGG
1 CAGCTGCAGTTGCTACTCCATCGCAGTCTGTGTTTGGTAACACCAATCCCGGCTTGGTGTTTGGG
2173430 TCAACTC
66 TCAACTC
2173437 CAGCTGCAGTTGCTACTCCATCGCAGTCTGTGTTTGGTAACACCAATCCCGGCTTGGTGTTTGGG
1 CAGCTGCAGTTGCTACTCCATCGCAGTCTGTGTTTGGTAACACCAATCCCGGCTTGGTGTTTGGG
2173502 TCAACTC
66 TCAACTC
* * ** *
2173509 CAGCTGCAGGTGCTACTCCATTGCAGAATGTGTTTGGCT-ACACCAGTCCCGGCTTGGTGTTTGG
1 CAGCTGCAGTTGCTACTCCATCGCAGTCTGTGTTTGG-TAACACCAATCCCGGCTTGGTGTTTGG
2173573 GTCAACTC
65 GTCAACTC
2173581 CA
1 CA
2173583 TCCAGTAATA
Statistics
Matches: 135, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
72 134 0.99
73 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (72 bp):
CAGCTGCAGTTGCTACTCCATCGCAGTCTGTGTTTGGTAACACCAATCCCGGCTTGGTGTTTGGG
TCAACTC
Found at i:2176270 original size:21 final size:21
Alignment explanation
Indices: 2176219--2176275 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2176209 CCTGACACTA
* *
2176219 TAGGTTGATCGAATTTGAGGT
1 TAGGATGATTGAATTTGAGGT
2176240 TAGGATGATTGAATTTGAGGT
1 TAGGATGATTGAATTTGAGGT
2176261 TAGGATGATTAGAAT
1 TAGGATGATT-GAAT
2176276 AGCACAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.37
Consensus pattern (21 bp):
TAGGATGATTGAATTTGAGGT
Found at i:2177537 original size:2 final size:2
Alignment explanation
Indices: 2177530--2177573 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2177520 TTGAAAGTTG
2177530 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
2177572 AT
1 AT
2177574 TTTGCATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2179015 original size:12 final size:12
Alignment explanation
Indices: 2179000--2179030 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2178990 GTTATTTAAA
*
2179000 CGGGTATCGGGT
1 CGGGTATCGGGC
2179012 CGGGTATCGGGC
1 CGGGTATCGGGC
2179024 CGGGTAT
1 CGGGTAT
2179031 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:2179095 original size:32 final size:34
Alignment explanation
Indices: 2179028--2179112 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 34
2179018 TCGGGCCGGG
2179028 TATATATATATATTTAAATTAAATATATAAATAT
1 TATATATATATATTTAAATTAAATATATAAATAT
* *
2179062 TATATATATATTTTAATTTAAATTAAATTTATTAATAT
1 TATATATATA---T-ATTTAAATTAAATATATAAATAT
2179100 TATATATATATAT
1 TATATATATATAT
2179113 ATATATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
34 12 0.27
35 1 0.02
37 1 0.02
38 31 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TATATATATATATTTAAATTAAATATATAAATAT
Found at i:2179139 original size:2 final size:2
Alignment explanation
Indices: 2179028--2179121 Score: 51
Period size: 2 Copynumber: 51.0 Consensus size: 2
2179018 TCGGGCCGGG
* * * *
2179028 TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * * *
2179068 TA TA T- TT TA -A TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2179104 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
2179122 ATTATTTTTA
Statistics
Matches: 67, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
1 8 0.12
2 59 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2179645 original size:40 final size:41
Alignment explanation
Indices: 2179577--2179653 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
2179567 TGAAAAGTAG
*
2179577 TTTTGCTTTGAGTAGATTCTACTGGATCTATATTTTTCTAC
1 TTTTGCTTTGAGTAGATTCTACTAGATCTATATTTTTCTAC
* *
2179618 TTTT-CTTTGAGTATGATT-TATTAGATCTGTATTTTT
1 TTTTGCTTTGAGTA-GATTCTACTAGATCTATATTTTT
2179654 TTCATTGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.19, C:0.10, G:0.14, T:0.56
Consensus pattern (41 bp):
TTTTGCTTTGAGTAGATTCTACTAGATCTATATTTTTCTAC
Found at i:2184788 original size:3 final size:3
Alignment explanation
Indices: 2184774--2184816 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
2184764 GAAAGTGAAC
* *
2184774 AGA AGA AAA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2184817 CAAAGACAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2184791 original size:12 final size:12
Alignment explanation
Indices: 2184774--2184822 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
2184764 GAAAGTGAAC
2184774 AGAAGAAAAAGA
1 AGAAGAAAAAGA
2184786 AGAAGAAAAAGA
1 AGAAGAAAAAGA
*
2184798 AGAAGAAGAAGA
1 AGAAGAAAAAGA
2184810 AGAAGAACAAAGA
1 AGAAGAA-AAAGA
2184823 CAGTGAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:2185289 original size:73 final size:72
Alignment explanation
Indices: 2185186--2185372 Score: 207
Period size: 73 Copynumber: 2.6 Consensus size: 72
2185176 TTGTTGATAA
* ** * * * * * *
2185186 TGTTAGTGCTAATGATGCATTGAGTAATGAAAGTGAAAAGAACAATGAGAACAAGGA-GGTGGTT
1 TGTTAGTGCCAATGATGCAAGGGGTGATGAAAGTGAAAAGAACAAAGACAACAACGATGCT-GTT
2185250 GCTGTTGT
65 GCTGTTGT
2185258 TGTTAGTGCCAGATGATGCAAGGGGTGATGAAAGTGAAAAGAACAAAGACAACAACGATGCTGTT
1 TGTTAGTGCCA-ATGATGCAAGGGGTGATGAAAGTGAAAAGAACAAAGACAACAACGATGCTGTT
2185323 GCTGTTGT
65 GCTGTTGT
** * * *
2185331 TAATAGTGCAAATGATGCACGGTGTTG-TGAAAGTGAAAAGAA
1 TGTTAGTGCCAATGATGCAAGG-GGTGATGAAAGTGAAAAGAA
2185373 GAAAAAGAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
72 35 0.36
73 61 0.62
74 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.25
Consensus pattern (72 bp):
TGTTAGTGCCAATGATGCAAGGGGTGATGAAAGTGAAAAGAACAAAGACAACAACGATGCTGTTG
CTGTTGT
Found at i:2186827 original size:15 final size:14
Alignment explanation
Indices: 2186807--2186857 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
2186797 GAGACATTAC
2186807 CCGCCCCGCATCCG
1 CCGCCCCGCATCCG
2186821 TCCGCCCCGCATCCG
1 -CCGCCCCGCATCCG
* *
2186836 CCTGCCCCACATTCG
1 CC-GCCCCGCATCCG
2186851 CCCGCCC
1 -CCGCCC
2186858 AGCTAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 2 0.06
15 28 0.88
16 2 0.06
ACGTcount: A:0.08, C:0.63, G:0.18, T:0.12
Consensus pattern (14 bp):
CCGCCCCGCATCCG
Found at i:2199983 original size:15 final size:15
Alignment explanation
Indices: 2199963--2200007 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2199953 GAGTATCATT
2199963 AATTTAATTTATAAA
1 AATTTAATTTATAAA
2199978 AATTTAAATTT-TAAAA
1 AATTT-AATTTAT-AAA
*
2199994 AATTTAATGTATAA
1 AATTTAATTTATAA
2200008 TTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTTAATTTATAAA
Found at i:2200036 original size:29 final size:28
Alignment explanation
Indices: 2199978--2200036 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
2199968 AATTTATAAA
*
2199978 AATTTAAATTTTAAAAAATTTAATGTAT
1 AATTTAAATTTTAAAAAATTTAAAGTAT
*
2200006 AATTATAAATTATTTAAAAATTTAAAG-AT
1 AATT-TAAATT-TTAAAAAATTTAAAGTAT
2200035 AA
1 AA
2200037 AATAAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 10 0.37
30 13 0.48
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
AATTTAAATTTTAAAAAATTTAAAGTAT
Found at i:2203030 original size:20 final size:21
Alignment explanation
Indices: 2202995--2203034 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2202985 AATAATCACT
2202995 AACACATATATCATATCACAA
1 AACACATATATCATATCACAA
2203016 AACACATATAT-ATATCACA
1 AACACATATATCATATCACA
2203035 TACATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
AACACATATATCATATCACAA
Found at i:2203279 original size:62 final size:63
Alignment explanation
Indices: 2203193--2203312 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
2203183 TCGACAACTG
* *
2203193 TCCATAGGTCTCAAAGAACCTAGGTAA-ACTGT-TCATATGTTCCTTAGAACATAGGTATAATA
1 TCCATAGGTCTCAAAGAACATAGGTAATACTGTCT-ATATGTTCCGTAGAACATAGGTATAATA
* * *
2203255 TCCATATGTCTCGAAAG-ACATAGGTAATTCTGTCTATATGTTCCGTAGAACATCGGTA
1 TCCATAGGTCTC-AAAGAACATAGGTAATACTGTCTATATGTTCCGTAGAACATAGGTA
2203313 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
62 20 0.40
63 29 0.58
64 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (63 bp):
TCCATAGGTCTCAAAGAACATAGGTAATACTGTCTATATGTTCCGTAGAACATAGGTATAATA
Found at i:2209324 original size:2 final size:2
Alignment explanation
Indices: 2209319--2209376 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2209309 ATATATATAT
2209319 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
2209361 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
2209377 TGGGCATTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2210592 original size:20 final size:19
Alignment explanation
Indices: 2210567--2210617 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2210557 TAATTGTTTG
2210567 AATATTATTTTAAAAAATAA
1 AATATT-TTTTAAAAAATAA
**
2210587 AATATTTTTTTTTAAAATAA
1 AATA-TTTTTTAAAAAATAA
2210607 AATATTTTTTA
1 AATATTTTTTA
2210618 TCATTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 19 0.70
21 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATTTTTTAAAAAATAA
Found at i:2210797 original size:2 final size:2
Alignment explanation
Indices: 2210790--2210840 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2210780 AATTTGTAGA
2210790 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
2210832 AG AG AG AG A
1 AG AG AG AG A
2210841 TGTTGTGAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2212651 original size:45 final size:45
Alignment explanation
Indices: 2212581--2212715 Score: 182
Period size: 46 Copynumber: 3.0 Consensus size: 45
2212571 GCAGGTCAAA
* * * *
2212581 GAGATTCAACAGGTTTTTAGGGATTTGAATATTTTTAAATTTTAG
1 GAGATTCAAAAGATTTTCAGAGATTTGAATATTTTTAAATTTTAG
* *
2212626 GAGATTCAAAAGATTTTCCGAGATTTGAATTTTTTTTAAATTTTAG
1 GAGATTCAAAAGATTTTCAGAGATTTGAA-TATTTTTAAATTTTAG
* *
2212672 GAGATTCAATAGATTTTTAGAGATTTGAATA-TTTTAAATTTTAG
1 GAGATTCAAAAGATTTTCAGAGATTTGAATATTTTTAAATTTTAG
2212716 AAATTTAGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 13 0.16
45 25 0.32
46 41 0.52
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.45
Consensus pattern (45 bp):
GAGATTCAAAAGATTTTCAGAGATTTGAATATTTTTAAATTTTAG
Found at i:2212898 original size:2 final size:2
Alignment explanation
Indices: 2212891--2212921 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2212881 TTTTGTGGGT
2212891 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 T
2212922 GTAATTTTAA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2222074 original size:27 final size:28
Alignment explanation
Indices: 2222026--2222079 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2222016 ATATTTAAGG
*
2222026 TATAACATATTAAATAATAAATATAATTA
1 TATAACATATTAAATAAAAAATA-AATTA
*
2222055 TATAAC-TA-TAATTAAAAAATAAATT
1 TATAACATATTAAATAAAAAATAAATT
2222080 TGGGGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 11 0.48
28 2 0.09
29 6 0.26
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (28 bp):
TATAACATATTAAATAAAAAATAAATTA
Found at i:2224347 original size:30 final size:30
Alignment explanation
Indices: 2224286--2224353 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
2224276 CAAAGGGTTG
* * **
2224286 AATTAATTTTTTAGTCGACTTCGAGTTTAT
1 AATTAATTTTTTAATCGACTTCAAGGATAT
* *
2224316 AATTGATTTTTTAATCGAGTTCAAGGATAT
1 AATTAATTTTTTAATCGACTTCAAGGATAT
*
2224346 AACTAATT
1 AATTAATT
2224354 CTAATTAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (30 bp):
AATTAATTTTTTAATCGACTTCAAGGATAT
Found at i:2226813 original size:13 final size:13
Alignment explanation
Indices: 2226792--2226836 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2226782 CCCCTAAGTG
* *
2226792 TTTAGATTTTAGT
1 TTTAAATTTTAAT
2226805 TTTAAATTTTAAAT
1 TTTAAATTTT-AAT
*
2226819 TTTAAATTTTAAA
1 TTTAAATTTTAAT
2226832 TTTAA
1 TTTAA
2226837 TTTAAGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (13 bp):
TTTAAATTTTAAT
Found at i:2226814 original size:7 final size:7
Alignment explanation
Indices: 2226804--2226834 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2226794 TAGATTTTAG
2226804 TTTTAAA
1 TTTTAAA
2226811 TTTTAAA
1 TTTTAAA
2226818 TTTTAAA
1 TTTTAAA
2226825 TTTTAAA
1 TTTTAAA
2226832 TTT
1 TTT
2226835 AATTTAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTTAAA
Found at i:2234809 original size:42 final size:42
Alignment explanation
Indices: 2234750--2234872 Score: 228
Period size: 42 Copynumber: 2.9 Consensus size: 42
2234740 AGAAGAGCCC
*
2234750 GAGAATGAACTAAGGCCTACTGATGTTGACCACCTTGAGTCT
1 GAGAATGAACTAAGGCCTGCTGATGTTGACCACCTTGAGTCT
2234792 GAGAATGAACTAAGGCCTGCTGATGTTGACCACCTTGAGTCT
1 GAGAATGAACTAAGGCCTGCTGATGTTGACCACCTTGAGTCT
*
2234834 GAGAATGAACTAAGGCCTGCTGATGTTGACCTCCTTGAG
1 GAGAATGAACTAAGGCCTGCTGATGTTGACCACCTTGAG
2234873 CAGCAAAAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (42 bp):
GAGAATGAACTAAGGCCTGCTGATGTTGACCACCTTGAGTCT
Found at i:2237292 original size:216 final size:215
Alignment explanation
Indices: 2237034--2237478 Score: 786
Period size: 216 Copynumber: 2.1 Consensus size: 215
2237024 GGTCGGGGTT
* *
2237034 GGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTTG
1 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCG
* *
2237099 GGTCGGATTAAGTCACTGTTTTTTTTAAATAAAAAT-ATTTTATTATTATTTTGGGTCGGGTCGG
66 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTT-TTATTATTTCGGGTCGGGTCGG
2237163 GTTGGATTTCTAATTCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTC
130 GTTGGATTTCTAATTCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTC
*
2237228 GGGTTTTTTAAGTGTGATATTC
195 GGG-TTTTTAACTGTGATATTC
*
2237250 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGATCGACCCGAAAATATATATAATTCAGGTCG
1 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCG
2237315 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGG
66 GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGG
2237380 TTGGATTTCTAATTCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCG
131 TTGGATTTCTAATTCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCG
2237445 GGTTTTTAACTGTGATATTC
196 GGTTTTTAACTGTGATATTC
* *
2237465 GTGTCGAG-TCGGGT
1 GGGTCGGGTTCGGGT
2237479 CGGGTTTTTT
Statistics
Matches: 220, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
214 6 0.03
215 23 0.10
216 186 0.85
217 5 0.02
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (215 bp):
GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCG
GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGG
TTGGATTTCTAATTCATATATTCGGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCG
GGTTTTTAACTGTGATATTC
Found at i:2237498 original size:38 final size:38
Alignment explanation
Indices: 2237436--2237522 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
2237426 TTTTGTTCGG
*
2237436 GTCGGGTCGGG--TTTTTAACTGTGATATTCGTGTCGA
1 GTCGGGTCGGGTTTTTTTAACTGTGATATTCGAGTCGA
* *
2237472 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGAGTCGG
1 GTCGGGTCGGGTTTTTTTAACTGTGATATTCGAGTCGA
2237510 GTCGGGTCGGGTT
1 GTCGGGTCGGGTT
2237523 CGGGTTTAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 11 0.24
38 35 0.76
ACGTcount: A:0.11, C:0.13, G:0.38, T:0.38
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAACTGTGATATTCGAGTCGA
Found at i:2240301 original size:42 final size:42
Alignment explanation
Indices: 2240255--2240375 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
2240245 CTTTTGTTGT
*
2240255 AAAAACGCTGCAATAGAGTTGACATATAGCGGCGTTTTTACA
1 AAAAACGCCGCAATAGAGTTGACATATAGCGGCGTTTTTACA
* * * * *
2240297 AAAAACACCGCAATAGAGTGGTAAAT-TAGCGGCGTTTATACC
1 AAAAACGCCGCAATAGAGTTG-ACATATAGCGGCGTTTTTACA
* * *
2240339 ACAAACGCCGCAATAGA-TTAACATATAGTGGCGTTTT
1 AAAAACGCCGCAATAGAGTTGACATATAGCGGCGTTTT
2240376 AGCCAAAATA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
40 3 0.05
41 11 0.17
42 47 0.73
43 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCAATAGAGTTGACATATAGCGGCGTTTTTACA
Found at i:2240416 original size:82 final size:82
Alignment explanation
Indices: 2240257--2240458 Score: 230
Period size: 82 Copynumber: 2.4 Consensus size: 82
2240247 TTTGTTGTAA
* * * *
2240257 AAACGCTGCAATAGAGTTGACATATAGCGGCGTTTTTACAAAAAACACCGCAATAGAGTGGTAAA
1 AAACGCCGCAATAGA-TTAACATATAGTGGCG-TTTTACAAAAAACACCACAATAGAGTGGTAAA
2240322 TTAGCGGCGTTTATACCAC
64 TTAGCGGCGTTTATACCAC
* *
2240341 AAACGCCGCAATAGATTAACATATAGTGGCGTTTTAGC-CAAAATACCACAATAGA-TCGGTAAA
1 AAACGCCGCAATAGATTAACATATAGTGGCGTTTTA-CAAAAAACACCACAATAGAGT-GGTAAA
* *
2240404 TTAGCGGTGTTTATATCAC
64 TTAGCGGCGTTTATACCAC
* * *
2240423 AAACGCCGTAATAG-TGATAATAAATAGTGGCGTTTT
1 AAACGCCGCAATAGAT--TAACATATAGTGGCGTTTT
2240459 TAGACAAACA
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
81 2 0.02
82 55 0.53
83 32 0.31
84 14 0.14
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (82 bp):
AAACGCCGCAATAGATTAACATATAGTGGCGTTTTACAAAAAACACCACAATAGAGTGGTAAATT
AGCGGCGTTTATACCAC
Found at i:2243043 original size:43 final size:43
Alignment explanation
Indices: 2242979--2243233 Score: 271
Period size: 43 Copynumber: 5.9 Consensus size: 43
2242969 ATGTAATTAG
* *
2242979 CGGCGTTTGTATCTAAAAACGCCGCTATAGATCTCAACCTTTTA
1 CGGCGTTTGT-TCAAAAAACGCCGCTATAGATCTCGACCTTTTA
* * *
2243023 CGGCGTTTATTCAAAAAACGCCGCTATAGATCT-AATCTTTTA
1 CGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTA
* * *
2243065 CGGCATTTGTTCCAATAAACGTCGCTATAGATCT-GACCTTTTA
1 CGGCGTTTGTT-CAAAAAACGCCGCTATAGATCTCGACCTTTTA
* * * * *
2243108 CGGCATTTTTTTCCAAAAATGCCGCTATAGATCTCGACCTTTTG
1 CGGC-GTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTA
* * * * *
2243152 CGGCGTTTGTTCCAAAAACACCACTATAGATCTCGACCTTCTG
1 CGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTA
* * * *
2243195 TGGCGTTTGTTCTAAAAACGCCGCTATAAATCTTGACCT
1 CGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCT
2243234 ATGGCGGCAC
Statistics
Matches: 180, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
42 17 0.09
43 137 0.76
44 26 0.14
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (43 bp):
CGGCGTTTGTTCAAAAAACGCCGCTATAGATCTCGACCTTTTA
Found at i:2255283 original size:23 final size:23
Alignment explanation
Indices: 2255257--2255301 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2255247 AATATATATT
*
2255257 TCAATTTCGACATATC-AACATGG
1 TCAATTTCCACA-ATCAAACATGG
2255280 TCAATTTCCACAATCAAACATG
1 TCAATTTCCACAATCAAACATG
2255302 ATTTCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (23 bp):
TCAATTTCCACAATCAAACATGG
Found at i:2257911 original size:44 final size:44
Alignment explanation
Indices: 2257857--2257945 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
2257847 AGTATCATAT
* *
2257857 TAATAAAATATTA-ATTATTA-AATCATATTTATTTATAATTTTAA
1 TAATAAAATATAATATTATTATAATCATA-TTA-TTATAATTATAA
* * *
2257901 TAATATAATATAATATTGTTATAATTATATTATTATAATTATAA
1 TAATAAAATATAATATTATTATAATCATATTATTATAATTATAA
2257945 T
1 T
2257946 TTTATAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
44 23 0.61
45 9 0.24
46 6 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (44 bp):
TAATAAAATATAATATTATTATAATCATATTATTATAATTATAA
Found at i:2257979 original size:28 final size:28
Alignment explanation
Indices: 2257920--2257990 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
2257910 ATAATATTGT
*
2257920 TATAATTATATTATTATAATTATAATTT
1 TATAATTATATTATTATAATTATAATTA
*
2257948 TATAATTTTATT-TTAATAATATATAA-TA
1 TATAATTATATTATT-ATAAT-TATAATTA
*
2257976 TATAA-TAAATTATTA
1 TATAATTATATTATTA
2257991 ATAAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 7 0.19
28 24 0.67
29 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TATAATTATATTATTATAATTATAATTA
Found at i:2258043 original size:27 final size:27
Alignment explanation
Indices: 2257959--2258049 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
2257949 ATAATTTTAT
* * *
2257959 TTTAATAATATATAATATATAATAAATTA
1 TTTAATAA-AAATAATAT-TATTTAATTA
*
2257988 -TTAATAAAATTAATATTATTT-ATTAA
1 TTTAATAAAAATAATATTATTTAATT-A
*
2258014 TTTCATAAAAATAATATTATTTAATTA
1 TTTAATAAAAATAATATTATTTAATTA
2258041 TTTGAATAA
1 TTT-AATAA
2258050 TTGATATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 30 0.59
28 14 0.27
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TTTAATAAAAATAATATTATTTAATTA
Found at i:2258136 original size:37 final size:37
Alignment explanation
Indices: 2258095--2258198 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 37
2258085 TTTTAATGTT
*
2258095 TTAATAATATTATTATTTTAATAAATAGTTAATATAA
1 TTAATAATATTATTATTTTAATAAATAATTAATATAA
2258132 TTAATATTATATTATTTCTATTTTAATAAATAATTAATATAA
1 TTAATA--ATATTA--T-TATTTTAATAAATAATTAATATAA
*
2258174 TTTATAATAATT-TTATTTTAATAAA
1 TTAATAAT-ATTATTATTTTAATAAA
2258199 ATATAATAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
37 18 0.31
38 1 0.02
39 6 0.10
40 2 0.03
41 4 0.07
42 28 0.47
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
TTAATAATATTATTATTTTAATAAATAATTAATATAA
Found at i:2258283 original size:14 final size:14
Alignment explanation
Indices: 2258240--2258284 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2258230 AATTGTAGAT
*
2258240 ATAATATTTTAAT-A
1 ATAATA-TTAAATAA
2258254 ATAATATTAACATAA
1 ATAATATTAA-ATAA
2258269 ATAATATTAAATAA
1 ATAATATTAAATAA
2258283 AT
1 AT
2258285 TATTATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 14 0.50
15 11 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATTAAATAA
Found at i:2270604 original size:27 final size:27
Alignment explanation
Indices: 2270566--2270619 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2270556 GGAGTAAGAA
2270566 TTCAAGAGTTCCCTCCATACAAAGTTT
1 TTCAAGAGTTCCCTCCATACAAAGTTT
2270593 TTCAAGAGTTCCCTCCATACAAAGTTT
1 TTCAAGAGTTCCCTCCATACAAAGTTT
2270620 CTGTGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (27 bp):
TTCAAGAGTTCCCTCCATACAAAGTTT
Found at i:2281308 original size:19 final size:19
Alignment explanation
Indices: 2281272--2281308 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2281262 TATATAATTT
**
2281272 TAATTTTTTTAATTTTAAA
1 TAATTTTTTTAAAATTAAA
2281291 TAATTTTTTTAAAATTAA
1 TAATTTTTTTAAAATTAA
2281309 CAGGTTGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTTTTTTAAAATTAAA
Found at i:2281398 original size:29 final size:29
Alignment explanation
Indices: 2281364--2281465 Score: 168
Period size: 29 Copynumber: 3.5 Consensus size: 29
2281354 GAATGAAACA
2281364 TTAGGCACCAAACTGAAACGAAATAAATG
1 TTAGGCACCAAACTGAAACGAAATAAATG
* *
2281393 TTAGGCACCAAACTAAAACGAAATAAATA
1 TTAGGCACCAAACTGAAACGAAATAAATG
*
2281422 TTAGACACCAAACTGAAACGAAATAAATG
1 TTAGGCACCAAACTGAAACGAAATAAATG
*
2281451 TTAGTCACCAAACTG
1 TTAGGCACCAAACTG
2281466 GAACCAAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.19
Consensus pattern (29 bp):
TTAGGCACCAAACTGAAACGAAATAAATG
Found at i:2289534 original size:6 final size:6
Alignment explanation
Indices: 2289516--2289548 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2289506 ATAAAATAGG
*
2289516 ATTAAA A-TAAA ATTAAA ATTAAA ATTACA ATTA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTA
2289549 TACACTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:2294823 original size:21 final size:21
Alignment explanation
Indices: 2294799--2294852 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2294789 TATCGCAAAT
2294799 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
2294820 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
2294841 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2294853 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:2294866 original size:20 final size:20
Alignment explanation
Indices: 2294841--2295138 Score: 156
Period size: 20 Copynumber: 14.9 Consensus size: 20
2294831 TAGTTGAAAA
*
2294841 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
2294861 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
2294881 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
2294901 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
2294923 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* * *
2294944 T--CGTTGCGATAGTCTACAGC
1 TCGCGTTGCGAT--TTTCCAGT
*
2294964 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
**
2294985 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAGT
2294997 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*** *
2295017 TCGCGTTGCGATAGTTGAAAAT
1 TCGCGTTGCGAT--TTTCCAGT
*
2295039 T-GCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
** ** **
2295058 TCGCGTTGCGATAGATGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
2295079 TCGCGTTACGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
2295099 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
2295121 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
2295139 AATTCGTTGC
Statistics
Matches: 211, Mismatches: 43, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
12 3 0.01
14 8 0.04
19 22 0.10
20 99 0.47
21 33 0.16
22 46 0.22
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:2294872 original size:41 final size:41
Alignment explanation
Indices: 2294820--2295113 Score: 267
Period size: 41 Copynumber: 7.4 Consensus size: 41
2294810 TAATTGAAAA
*
2294820 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
* ** **
2294861 TCGCGTTGCGAT-TTTCCAGTTCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
* * * *
2294901 TCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AGT
* * *
2294944 T--CGTTGCGATAGTCT--ACAGCTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TGAAAATC-G-CGTTGCGATTTTCC-AGT
2294985 T--CGTTGC-------GAAAATCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
* *
2295017 TCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
* *
2295058 TCGCGTTGCGATAGATGAAAATCGCGTTACGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
2295099 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
2295114 CTACAGTTGT
Statistics
Matches: 209, Mismatches: 28, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
32 3 0.01
33 14 0.07
34 7 0.03
35 3 0.01
40 34 0.16
41 130 0.62
42 15 0.07
43 3 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGT
Found at i:2294929 original size:22 final size:22
Alignment explanation
Indices: 2294904--2294975 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
2294894 TTCCAGTTCG
*
2294904 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
2294926 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
*
2294945 CGTTGCGATAGTCTACAGCTGT
1 CGTTGCGATAGTCTACAGATGT
2294967 CGTTGCGAT
1 CGTTGCGAT
2294976 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGATGT
Found at i:2294949 original size:19 final size:19
Alignment explanation
Indices: 2294925--2294993 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
2294915 TCTACAGTTG
2294925 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
2294944 TCGTTGCGATAGTCTACAGCT
1 TCGTTGCGAT--TTTCCAAAT
2294965 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2294985 TCGTTGCGA
1 TCGTTGCGA
2294994 AAATCGCGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2295084 original size:21 final size:21
Alignment explanation
Indices: 2295017--2295090 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
2295007 ATTTTCCAGT
2295017 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
2295038 TTGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
2295058 TCGCGTTGCGATAGATGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
2295079 TCGCGTTACGAT
1 TCGCGTTGCGAT
2295091 TTTCCAGTTC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2295125 original size:157 final size:156
Alignment explanation
Indices: 2294836--2295154 Score: 448
Period size: 157 Copynumber: 2.0 Consensus size: 156
2294826 TGCGATAGTT
* *** *
2294836 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCAGT
1 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTGAAAATTCGCGTTGCGATTTTCCAGT
* * * * *
2294901 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGCTG
66 TCGCGTTGCGATAGTCGAAAATCGTCGTTACGATTTTCCAAATTCGTTGCGATAGTCTACAGCTG
2294966 TCGTTGCGATTTTCCAAATTCGTTGC
131 TCGTTGCGATTTTCCAAATTCGTTGC
2294992 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATT-GCGTTGCGATTTTCCA
1 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGAT--TTGAAAATTCGCGTTGCGATTTTCCA
* *
2295056 TTTCGCGTTGCGATAGAT-GAAAATCG-CGTTACGATTTTCC-AGTTCGCGTTGCGATAGTCTAC
64 GTTCGCGTTGCGATAG-TCGAAAATCGTCGTTACGATTTTCCAAATT--CGTTGCGATAGTCTAC
*
2295118 AGTTGTCGTTGCGATTTTCCAAATTCGTTGC
126 AGCTGTCGTTGCGATTTTCCAAATTCGTTGC
2295149 GAAAAT
1 GAAAAT
2295155 TCGTTGTGAT
Statistics
Matches: 145, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
155 3 0.02
156 49 0.34
157 87 0.60
158 6 0.04
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (156 bp):
GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTGAAAATTCGCGTTGCGATTTTCCAGT
TCGCGTTGCGATAGTCGAAAATCGTCGTTACGATTTTCCAAATTCGTTGCGATAGTCTACAGCTG
TCGTTGCGATTTTCCAAATTCGTTGC
Found at i:2295147 original size:82 final size:81
Alignment explanation
Indices: 2294992--2295150 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
2294982 AATTCGTTGC
* *
2294992 GAAAATCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAT
1 GAAAATCGCGTTACGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAA
2295057 TTCGCGTTGCGATAGAT
66 TTC-CGTTGCGATAGAT
* *
2295074 GAAAATCGCGTTACGATTTTCCAGTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCC
1 GAAAATCGCGTTACGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAATTG-CGTTGCGATTTTCC
2295138 AAATT-CGTTGCGA
64 -AATTCCGTTGCGA
2295151 AAATTCGTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
82 52 0.74
83 15 0.21
84 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (81 bp):
GAAAATCGCGTTACGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTCCAA
TTCCGTTGCGATAGAT
Found at i:2295772 original size:6 final size:6
Alignment explanation
Indices: 2295756--2295788 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2295746 GTCCGTCTCG
2295756 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
2295789 ATACGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:2295952 original size:57 final size:56
Alignment explanation
Indices: 2295864--2295971 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 56
2295854 CTTTTTTTTA
*
2295864 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTTTCGCAACAATAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGAC-ACTGTAGACTATCGCAACAATAG
*
2295921 ACTATCGCAACGAATTTGGAAAATCGCAACGACATTGTAGACTATCGCAAC
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACACTGTAGACTATCGCAAC
2295972 GCGAAATGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 16 0.33
57 33 0.67
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (56 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACACTGTAGACTATCGCAACAATAG
Found at i:2296201 original size:41 final size:41
Alignment explanation
Indices: 2295921--2296184 Score: 419
Period size: 41 Copynumber: 6.5 Consensus size: 41
2295911 GCAACAATAG
* *
2295921 ACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-ATTGT-A
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA
2295960 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
2296002 ACTATCGCAACTCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
2296043 ACTATCGCAACACGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
2296084 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2296125 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2296166 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
2296185 CAATGCGAAT
Statistics
Matches: 211, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
40 11 0.05
41 195 0.92
42 5 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:2297726 original size:14 final size:16
Alignment explanation
Indices: 2297696--2297728 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2297686 TGTTTTTCTG
2297696 TTTCTTTCTGTGTTGT
1 TTTCTTTCTGTGTTGT
2297712 TTTCTTT-TG-GTTGT
1 TTTCTTTCTGTGTTGT
2297726 TTT
1 TTT
2297729 AATTAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTGTGTTGT
Found at i:2299773 original size:249 final size:249
Alignment explanation
Indices: 2299335--2299953 Score: 977
Period size: 249 Copynumber: 2.5 Consensus size: 249
2299325 AAAGACGACA
* * * ** *
2299335 ACAATGGTGAATGTAGTGTCGAACGTGTATCTACAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
1 ACAATGGTGAATATAATGTAGAACACGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
*
2299400 CCTGTGAATGAAAGTGAAAAACCTCCTCGAAAACGTAAGATAGCTAATGAAGCTCAGGGGACTAA
66 CCTGTGAATGAAAGTGAAAAACCTCCTCGAAAATGTAAGATAGCTAATGAAGCTCAGGGGACTAA
* * *
2299465 TCTGCATATTGTTGATGATCTTGAGGATGGGACTTGTAATGACGATAGCCTCGCTGCCGAACACC
131 TCTGCACATTGTTGATGATCTTGAGGATGGGACTGGTAATGACAATAGCCTCGCTGCCGAACACC
* *
2299530 CCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACGATGGTGATGAAAATG
196 CCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAACGGTGATGAAAATG
*** * *
2299584 ACAATGGTGAATATAATGTAGAGTGCGTATCTGCAAAGAGGAAGCCTTCTAAGAGTTCAAAGAAA
1 ACAATGGTGAATATAATGTAGAACACGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
* *
2299649 CCTGTGAATGAAAGTGAAAAACCTCCTCGAAAATGTAAGATAGCTAGTGAAGCTCAGGTGACTAA
66 CCTGTGAATGAAAGTGAAAAACCTCCTCGAAAATGTAAGATAGCTAATGAAGCTCAGGGGACTAA
* *
2299714 TCTGCACATTGTTGATGATCTTGAGGATGGGACTGGTAATGACAATGGCCTCGCTGCCGAGCACC
131 TCTGCACATTGTTGATGATCTTGAGGATGGGACTGGTAATGACAATAGCCTCGCTGCCGAACACC
* * *
2299779 CCTTTAGTTATGCTGTCAATGAGGATAAAGATGACAACAACGGTGATGAAAATG
196 CCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAACGGTGATGAAAATG
*
2299833 ACAATGGTGAATATAATGTAGAACATGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
1 ACAATGGTGAATATAATGTAGAACACGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
** * *
2299898 CCCATGAATGAAAGTGAGAAACCTCCTCAAAAATGTAAGATAGCTAATGAAGCTCA
66 CCTGTGAATGAAAGTGAAAAACCTCCTCGAAAATGTAAGATAGCTAATGAAGCTCA
2299954 AAAGCATAAG
Statistics
Matches: 337, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
249 337 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (249 bp):
ACAATGGTGAATATAATGTAGAACACGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
CCTGTGAATGAAAGTGAAAAACCTCCTCGAAAATGTAAGATAGCTAATGAAGCTCAGGGGACTAA
TCTGCACATTGTTGATGATCTTGAGGATGGGACTGGTAATGACAATAGCCTCGCTGCCGAACACC
CCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAACGGTGATGAAAATG
Found at i:2300771 original size:2 final size:2
Alignment explanation
Indices: 2300764--2300789 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2300754 AACGGAGTAA
2300764 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
2300790 CATAAGTTTT
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:2302220 original size:27 final size:27
Alignment explanation
Indices: 2302181--2302244 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
2302171 GTGCTTGCAG
* *
2302181 GAGGAAGTGGCAAAACCCGAGCAGGAT
1 GAGGATGTAGCAAAACCCGAGCAGGAT
*
2302208 GAGGATGTAGCAAAACCGGAGCAGGAT
1 GAGGATGTAGCAAAACCCGAGCAGGAT
2302235 GAGGATGTAG
1 GAGGATGTAG
2302245 TAATGAGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.39, T:0.11
Consensus pattern (27 bp):
GAGGATGTAGCAAAACCCGAGCAGGAT
Found at i:2303807 original size:16 final size:18
Alignment explanation
Indices: 2303767--2303807 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
2303757 CTTTTTTTAA
*
2303767 AATATTTAAATAAAAATT
1 AATATATAAATAAAAATT
2303785 AAT-TATAAA-AAAAA-T
1 AATATATAAATAAAAATT
2303800 AATATATA
1 AATATATA
2303808 TTATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 5 0.24
18 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATATAAATAAAAATT
Found at i:2304857 original size:21 final size:21
Alignment explanation
Indices: 2304786--2304901 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 21
2304776 GTTACAATGC
* **
2304786 TGACGTGACAATTCACGAGGT
1 TGACGTGACAGTTCACGATAT
* * *
2304807 TGACGTGAC-GGTCTATG-GAT
1 TGACGTGACAGTTC-ACGATAT
* *
2304827 TGATGTGACAGTTCACGATAC
1 TGACGTGACAGTTCACGATAT
*
2304848 TGACGTGACAG-TCTACGATGT
1 TGACGTGACAGTTC-ACGATAT
*
2304869 TGACGTGACAGTCCACGATAT
1 TGACGTGACAGTTCACGATAT
*
2304890 TGACGTTACAGT
1 TGACGTGACAGT
2304902 CAATCTGCCA
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 16 0.21
21 58 0.77
22 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
TGACGTGACAGTTCACGATAT
Found at i:2304902 original size:21 final size:21
Alignment explanation
Indices: 2304825--2304902 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
2304815 CGGTCTATGG
* *
2304825 ATTGATGTGACAGTTCACGAT
1 ATTGACGTGACAGTCCACGAT
* *
2304846 ACTGACGTGACAGTCTACGAT
1 ATTGACGTGACAGTCCACGAT
*
2304867 GTTGACGTGACAGTCCACGAT
1 ATTGACGTGACAGTCCACGAT
*
2304888 ATTGACGTTACAGTC
1 ATTGACGTGACAGTC
2304903 AATCTGCCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (21 bp):
ATTGACGTGACAGTCCACGAT
Found at i:2322777 original size:2 final size:2
Alignment explanation
Indices: 2322772--2322803 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2322762 CAAAAAAATA
*
2322772 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2322804 TTTAGTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2324075 original size:3 final size:3
Alignment explanation
Indices: 2324067--2324093 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2324057 TTTCTCAACA
2324067 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2324094 GCATATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2328241 original size:3 final size:3
Alignment explanation
Indices: 2328233--2328257 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2328223 GATATTCTCT
2328233 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
2328258 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2331814 original size:5 final size:5
Alignment explanation
Indices: 2331800--2331829 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2331790 TAAGGGCAAG
*
2331800 GAAGA GAAGA TAAGA GAAGA GAAGA GAAGA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA
2331830 TAAAGTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (5 bp):
GAAGA
Found at i:2332600 original size:15 final size:14
Alignment explanation
Indices: 2332560--2332606 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
2332550 TATGTGAAAA
*
2332560 TTATAGATTTAATT
1 TTATATATTTAATT
2332574 TTATAT-TTTAATT
1 TTATATATTTAATT
2332587 TTCATATATTTAATT
1 TT-ATATATTTAATT
2332602 TTATA
1 TTATA
2332607 CTTATAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 9 0.30
14 12 0.40
15 9 0.30
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:2335760 original size:16 final size:16
Alignment explanation
Indices: 2335739--2335770 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2335729 TTAATTAAAA
2335739 AAGGGAATGGGAATAG
1 AAGGGAATGGGAATAG
2335755 AAGGGAATGGGAATAG
1 AAGGGAATGGGAATAG
2335771 GTGGGTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (16 bp):
AAGGGAATGGGAATAG
Found at i:2336660 original size:23 final size:23
Alignment explanation
Indices: 2336625--2336697 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2336615 ATACTTTACA
*
2336625 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2336648 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2336671 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2336694 ATAT
1 ATAT
2336698 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2337147 original size:23 final size:23
Alignment explanation
Indices: 2337112--2337184 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2337102 ATACTTTACA
*
2337112 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2337135 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2337158 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2337181 ATAT
1 ATAT
2337185 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2337154 original size:487 final size:488
Alignment explanation
Indices: 2336223--2337324 Score: 1987
Period size: 487 Copynumber: 2.3 Consensus size: 488
2336213 TTATAATATG
2336223 TTGAAAGTGT-TCATACTTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATG
1 TTGAAAGTGTCT-ATAC-TTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATG
* *
2336287 TTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTAAAATATTAATTTAATAATTTAATTTGC
64 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
2336351 ACAAAAAATTATTTAATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
129 ACAAAAAATTATTTAATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
* *
2336416 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTATTTTTAATTTAATGATAATATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTAGTTTTAATTTAATAATAATATA
* *
2336481 TACCGTAACATAAAAAATAAATCATTAGATACATATAATTATTAAATTAATATCTTAAAACCCAC
259 TA-CGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACCCAC
* *
2336546 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAATG
323 TCAAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAATG
2336611 ATAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
388 ATAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
2336676 AGCGCTACCTATTACATCATATTTTTACCTATTATA
453 AGCGCTACCTATTACATCATATTTTTACCTATTATA
2336712 TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
2336777 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* * *
2336842 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAT
130 CAAAAAATTATTTAATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
2336907 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATT-GTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTAGTTTTAATTTAATAATAATATAT
* * * *
2336971 -CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
260 ACGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACCCACTC
2337035 AAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAATGAT
325 AAAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAATGAT
*
2337100 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
390 AAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
2337165 CGCTACCTATTACATCATATTTTTACCTATTATA
455 CGCTACCTATTACATCATATTTTTACCTATTATA
*
2337199 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
2337264 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTT
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTT
2337325 AAAAGATCCT
Statistics
Matches: 593, Mismatches: 17, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
486 57 0.10
487 287 0.48
488 53 0.09
489 35 0.06
490 161 0.27
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (488 bp):
TTGAAAGTGTCTATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTAATTATTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTAGTTTTAATTTAATAATAATATATA
CGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACCCACTCA
AAAGATAACCTTAAATTAATGTTTTCCACAATGAAAAAAGTATGGACACTTTTATAAAAATGATA
AATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
GCTACCTATTACATCATATTTTTACCTATTATA
Found at i:2337459 original size:23 final size:23
Alignment explanation
Indices: 2337424--2337496 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2337414 ATACTTTACA
*
2337424 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2337447 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2337470 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2337493 ATAT
1 ATAT
2337497 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2340601 original size:120 final size:120
Alignment explanation
Indices: 2340388--2340632 Score: 436
Period size: 120 Copynumber: 2.0 Consensus size: 120
2340378 TTTTTCTTCC
* *
2340388 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
2340453 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
2340508 ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * *
2340573 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
2340628 ATTCT
1 ATTCT
2340633 TGGTTCCGAT
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (120 bp):
ATTCTAGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:2340770 original size:303 final size:303
Alignment explanation
Indices: 2340223--2341028 Score: 1468
Period size: 303 Copynumber: 2.7 Consensus size: 303
2340213 TTAAAATTAG
*
2340223 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * * *
2340288 ATAGCAGTTATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCGATGTGTAAATGTCGA
2340353 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* *
2340418 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAATGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCAGTTATA
2340483 TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
2340526 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
2340591 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCGATATGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCGATGTGTAAATGTCGA
* *
2340656 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTTTGGACATAAAGTACCGTCACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* *
2340721 AAAAAATGTCGACATAGGTTGTAGACCTTTTCGCTAATAAAACCGGTATACTTATATCAGTTATA
196 AAAAAATGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCAGTTATA
* *
2340786 TTACAAAATTATCTAGTACATTATAATTCTGGATATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
*
2340829 CGACACAAAATTAAAAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
2340894 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCGATGTGTAAATGTCGA
2340959 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
2341024 AAAAA
196 AAAAA
2341029 GTGTGAAAAC
Statistics
Matches: 484, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
303 484 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTTGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAATGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCAGTTATA
TTACAAAATTATCTAGTACATTATAATTCTAGACATAAAGTAC
Found at i:2340913 original size:120 final size:120
Alignment explanation
Indices: 2340695--2340935 Score: 374
Period size: 120 Copynumber: 2.0 Consensus size: 120
2340685 TCTTCCATTT
* * * *
2340695 TGGACATAAAGTACCGTCACAATATTAAAAAATGTCGACATAGGTTGTAGACCTTTTCGCTAATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAATATCGACATAGGTTGTAGACCTATTCGCTAATA
*
2340760 AAACCGGTATACTTATATCAGTTATATTACAAAATTATCTAGTACATTATAATTC
66 AAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATAATTC
* * * *
2340815 TGGATATAAAGTACCGACACAAAATTAAAAAGTATCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAAAATTAAAAAATATCGACATAGGTTGTAGACCTATTCGCTAATA
* * *
2340880 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTC
66 AAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATAATTC
2340935 T
1 T
2340936 TGGTTCCGAT
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 109 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (120 bp):
TGGACATAAAGTACCGACACAAAATTAAAAAATATCGACATAGGTTGTAGACCTATTCGCTAATA
AAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATAATTC
Found at i:2342262 original size:12 final size:12
Alignment explanation
Indices: 2342231--2342288 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
2342221 CTTGTTTGGA
* *
2342231 TCATCATCATCA
1 TCATCGTCATCT
2342243 TCATCGTCATCT
1 TCATCGTCATCT
*
2342255 TCAACGTCATCT
1 TCATCGTCATCT
*
2342267 TCATCGTCAGCT
1 TCATCGTCATCT
*
2342279 TCATCTTCAT
1 TCATCGTCAT
2342289 TGACCGCTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:2342270 original size:6 final size:6
Alignment explanation
Indices: 2342231--2342288 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
2342221 CTTGTTTGGA
* * * * * * *
2342231 TCATCA TCATCA TCATCG TCATCT TCAACG TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
2342279 TCATCT TCAT
1 TCATCT TCAT
2342289 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:2344074 original size:179 final size:179
Alignment explanation
Indices: 2343787--2344642 Score: 1217
Period size: 179 Copynumber: 4.7 Consensus size: 179
2343777 AACATTAAAC
2343787 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
2343852 AAAATTACCTAATACATTATACTTATGGGTTTAGATGTTTATGGGATCGACACTTTATGGTTGCA
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTATGGTTGCA
*
2343917 CCCTGTTTTCCATTCAATCTGGACCAAAAATATCGACACAAACTACAAA
131 CCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAA
* *
2343966 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * *
2344031 AAAATTACCTATTACATTATACTTATGGGTTTCAATATTTATGGGATCAACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACAC----T-T-TATG
* ** * * ***** ** * *
2344096 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACGAACT
125 G-TTG-CACCCTGTT-TT----CC--ATT--CATTC-TGGACCAAAAAT---ATCGACACAAACT
*
2344161 AAAAA
175 ACAAA
* *
2344166 AGTATCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
2344231 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTATTGTTGCA
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTATGGTTGCA
* *
2344296 CCCTGTTTGCCATTCATTATGGACCAAAAATATCGACACAAACTACAAA
131 CCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAA
*
2344345 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
2344410 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTATGGTTGCA
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTATGGTTGCA
2344475 CCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAA
131 CCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAA
*
2344524 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
2344589 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACT
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACT
2344643 CTTTATATAT
Statistics
Matches: 599, Mismatches: 57, Indels: 42
0.86 0.08 0.06
Matches are distributed among these distances:
179 416 0.69
182 4 0.01
183 5 0.01
184 1 0.00
185 7 0.01
186 2 0.00
187 8 0.01
188 2 0.00
191 1 0.00
192 8 0.01
193 2 0.00
194 6 0.01
195 1 0.00
196 5 0.01
197 4 0.01
200 127 0.21
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (179 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTATGGTTGCA
CCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAA
Found at i:2344238 original size:200 final size:200
Alignment explanation
Indices: 2343895--2344286 Score: 676
Period size: 200 Copynumber: 2.0 Consensus size: 200
2343885 GATGTTTATG
*
2343895 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCAATCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCAAAAATATCGACACAAAC
* * * *
2343960 TACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTA
66 TAAAAAAGTATCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
2344025 GATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATATTTATGGGATCAACACTTTTTA
131 GATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATATTTATCGGATCAACACTTTTTA
2344090 TATAT
196 TATAT
* * *
2344095 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACGAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCAAAAATATCGACACAAAC
2344160 TAAAAAAGTATCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
66 TAAAAAAGTATCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
* * *
2344225 GATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTT
131 GATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATATTTATCGGATCAACACTTT
2344287 ATTGTTGCAC
Statistics
Matches: 180, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
200 180 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (200 bp):
GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCAATCTGGACCAAAAATATCGACACAAAC
TAAAAAAGTATCGAAACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
GATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATATTTATCGGATCAACACTTTTTA
TATAT
Found at i:2346785 original size:33 final size:33
Alignment explanation
Indices: 2346748--2346816 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
2346738 CATCTTAATA
*
2346748 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
2346781 TCACCCCTCAACACCTCTACTTCTTTCAGCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
2346814 TCA
1 TCA
2346817 TCTATTTTTT
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:0.23, C:0.46, G:0.01, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2349568 original size:182 final size:180
Alignment explanation
Indices: 2349082--2349553 Score: 579
Period size: 180 Copynumber: 2.6 Consensus size: 180
2349072 CATACTTACG
* * * * * * * * *
2349082 AAAGTATCGACACTTTCAATATATTCGGTATCGTTTTATCAGTTTTATCATTTTGGTACCGGTTT
1 AAAGTACCGACACATTAAATATATCCGATAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2349147 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAGCT-ATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAA-ATGATCGACACATTAT
*
2349211 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* * *
2349262 AAAGTATCGACACTTTCAATATATCCGATAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTACCGACACATTAAATATATCCGATAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
2349327 TATCATATTTTTATCTGGTATATCGTTTTGGATCTATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAATG-ATCGACACATTAT
** * *
2349392 AGGATTTAAAACTGCTTCTCTTTTAAATTCACTAAGTGTTGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * **
2349444 AAAGTACCGACACATTAAATGTATCCGGTAGCGCTTTT-CCGGTTTTATCATTTCAATACCGGTT
1 AAAGTACCGACACATTAAATATATCCGATAACG-TTTTACCGGTTTTATCATTTTGATACCGGTT
* * * * *
2349508 TTGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACACTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2349554 AATTTGGATC
Statistics
Matches: 253, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
180 102 0.40
181 57 0.23
182 90 0.36
183 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (180 bp):
AAAGTACCGACACATTAAATATATCCGATAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAATGATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:2351275 original size:21 final size:20
Alignment explanation
Indices: 2351251--2351290 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2351241 GTTAAGTGGT
*
2351251 TCGATTGAAAAAATTAAAAGA
1 TCGAATGAAAAAA-TAAAAGA
*
2351272 TCGAATGCAAAAATAAAAG
1 TCGAATGAAAAAATAAAAG
2351291 GGCTAAATAG
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:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (20 bp):
TCGAATGAAAAAATAAAAGA
Found at i:2351823 original size:32 final size:29
Alignment explanation
Indices: 2351740--2351823 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 29
2351730 TTATATTATT
2351740 ATTAAAATATTATATCTATA-ATTTTATAA
1 ATTAAAATATTATAT-TATATATTTTATAA
*
2351769 ATAAAAATATTATGATTAATATATTTTAATAA
1 ATTAAAATATTAT-ATT-ATATATTTT-ATAA
*
2351801 ATTAAATTATTATAAATTATATA
1 ATTAAAATATTAT--ATTATATA
2351824 ATTATTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 13 0.28
30 5 0.11
31 5 0.11
32 20 0.43
33 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATTAAAATATTATATTATATATTTTATAA
Found at i:2351839 original size:22 final size:20
Alignment explanation
Indices: 2351807--2351866 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
2351797 ATAAATTAAA
*
2351807 TTATTATAAATTATATAATTAT
1 TTATTAAAAATTA-ATAATT-T
2351829 TTATTAAAAA-TAATAATTT
1 TTATTAAAAATTAATAATTT
2351848 TT-TTAAAATATTAA-AATTT
1 TTATTAAAA-ATTAATAATTT
2351867 ATAATATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 6 0.17
19 9 0.26
20 9 0.26
21 2 0.06
22 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTAAAAATTAATAATTT
Found at i:2351872 original size:15 final size:15
Alignment explanation
Indices: 2351849--2351879 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2351839 TAATAATTTT
2351849 TTTAAAATATTAAAA
1 TTTAAAATATTAAAA
*
2351864 TTTATAATATTAAAA
1 TTTAAAATATTAAAA
2351879 T
1 T
2351880 AAGAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAAAATATTAAAA
Found at i:2352043 original size:23 final size:21
Alignment explanation
Indices: 2352007--2352053 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2351997 TATTATTAAA
* *
2352007 ATAAAAGTATAATATTATATATT
1 ATAAAAATAAAATA-TA-ATATT
2352030 ATAAAAATAAAATATAATATT
1 ATAAAAATAAAATATAATATT
2352051 ATA
1 ATA
2352054 TTATTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAAAATAAAATATAATATT
Found at i:2352045 original size:28 final size:29
Alignment explanation
Indices: 2351991--2352059 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
2351981 TTAATAATTC
*
2351991 ATTATATATTATTAAAATAAAAGTATAAT
1 ATTATATATTATAAAAATAAAAGTATAAT
2352020 ATTATATATTATAAAAATAAAA-TATAAT
1 ATTATATATTATAAAAATAAAAGTATAAT
2352048 ATTATATTATTA
1 ATTATA-TATTA
2352060 ACATTATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 12 0.32
29 26 0.68
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTATATATTATAAAAATAAAAGTATAAT
Found at i:2352686 original size:16 final size:15
Alignment explanation
Indices: 2352642--2352679 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2352632 AAAAAAGTTT
2352642 AAATAAA-TATTAAA
1 AAATAAATTATTAAA
2352656 AAATAAATTATTAAA
1 AAATAAATTATTAAA
*
2352671 AAATCAATT
1 AAATAAATT
2352680 TTGTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAATTATTAAA
Found at i:2356545 original size:87 final size:87
Alignment explanation
Indices: 2356399--2356648 Score: 288
Period size: 87 Copynumber: 2.9 Consensus size: 87
2356389 TTTATATCAT
* * * * *
2356399 CATTTAACAGGAAATATTATTAAGTACAAT-ATAATATTAGATAAC-ACTTATATAATGTAATAG
1 CATTTAACCGAAAATATTATAAAGTACAATAAT-ATATTAGGTAGCGA-TTATATAATGTAATAG
2356462 GTAGCGCTTATATAATAAAATAGA
64 GTAGCGCTTATATAATAAAATAGA
** * * *
2356486 CATTTAATTGAAAATATTATCAAGTACAATAATATATTAGGTAGCGTTTATATAATGTAATAAGT
1 CATTTAACCGAAAATATTATAAAGTACAATAATATATTAGGTAGCGATTATATAATGTAATAGGT
** *
2356551 AAAGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGA
* ** * * *
2356573 CTTTTAACCGGGAATATTATAAAGTACAATAACATATTAGGTAGCGATTATATTATATAATAGGT
1 CATTTAACCGAAAATATTATAAAGTACAATAATATATTAGGTAGCGATTATATAATGTAATAGGT
*
2356638 AGCGTTTATAT
66 AGCGCTTATAT
2356649 TAACTTATTT
Statistics
Matches: 136, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
87 134 0.99
88 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATAAAGTACAATAATATATTAGGTAGCGATTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGA
Found at i:2357075 original size:200 final size:199
Alignment explanation
Indices: 2356696--2357166 Score: 598
Period size: 200 Copynumber: 2.4 Consensus size: 199
2356686 ATAATATTAC
* *
2356696 AAATTTACCTATTACATTATAATTATCGGTTTCGAT-ATTTTGGGATCGATACAATTT--TAAAT
1 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAAT
*
2356758 GTATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCTACACAAACT
65 GTATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACT
* * * * * * *
2356823 TAAAACGTGTTGATACATTATGTAGACATATTTTCTTATAAAACCGGTATATTTCTA-TCGAG-T
130 TAAAACGTGTCGATACATTATATAGACATATTCTATCATAAAACAGGTATATTTATACT-G-GTT
2356886 ACATTGT
193 ACATTGT
* * *
2356893 AAATTTACCTATTACATTGTAATTATTGGTTTTGATGTTTTTGGGATCGATACTTTTAATAAATG
1 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
* * * * * ***
2356958 TATCGACACTTTATGCGTGCATCTCGTTTGACATTTATTCTTGACAAAATGTATCGACAC-TTTT
66 TATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGA-AAAAAGTATCGACACAAACT
** * *
2357022 TAAATTTGTGTCGATACATTATATCGACATATTCTATCATAAAACATGTATATTTATACTGGTTA
130 TAAA-ACGTGTCGATACATTATATAGACATATTCTATCATAAAACAGGTATATTTATACTGGTTA
2357087 CATTGT
194 CATTGT
2357093 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT-GGAGTCGATACTTTTAGA-AAA
1 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA-TCGATACTTTTA-ATAAA
2357156 TGTATCGACAC
64 TGTATCGACAC
2357167 ATATGTTTAC
Statistics
Matches: 237, Mismatches: 28, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
197 36 0.15
198 15 0.06
199 55 0.23
200 129 0.54
201 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (199 bp):
AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
TATCGACACTTTATGCGTGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTT
AAAACGTGTCGATACATTATATAGACATATTCTATCATAAAACAGGTATATTTATACTGGTTACA
TTGT
Found at i:2357724 original size:125 final size:125
Alignment explanation
Indices: 2357495--2357760 Score: 392
Period size: 125 Copynumber: 2.1 Consensus size: 125
2357485 AAAACTAATA
* * * ** **
2357495 ACAA-AATAACAAAATCGGTAGCGCTTTTACCGATTTTGTTAAGAAACTCGGTAAAATGTGAAAA
1 ACAACAATAACAAAACCGGTAGAGCTTTTACCGATTTTGTTAAGAAACCCAATAAAATGCCAAAA
* * * *
2357559 TAATAACAAAACCGGTAGAAATAATGATGTTTTCGGTAATTTTTACCGGTTTTGTTATGC
66 TAATAACAAAACCGGAAGAAATAATGATGTTTTCGATAATTTTAACCGGTTTTGTAATGC
2357619 ACAACAATAACAAAACCGGTAGAGCTTTTACCTG-TTTTGTTAAGAAACCCAATAAAATGCCAAA
1 ACAACAATAACAAAACCGGTAGAGCTTTTACC-GATTTTGTTAAGAAACCCAATAAAATGCCAAA
**
2357683 ATAATAACAAAACTTGAAGAAATAATGATGTTTTCGATAATTTTAACCGGTTTTGTAATGC
65 ATAATAACAAAACCGGAAGAAATAATGATGTTTTCGATAATTTTAACCGGTTTTGTAATGC
2357744 ACAACAATAACAAAACC
1 ACAACAATAACAAAACC
2357761 AGTACTACCT
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 4 0.03
125 122 0.96
126 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (125 bp):
ACAACAATAACAAAACCGGTAGAGCTTTTACCGATTTTGTTAAGAAACCCAATAAAATGCCAAAA
TAATAACAAAACCGGAAGAAATAATGATGTTTTCGATAATTTTAACCGGTTTTGTAATGC
Found at i:2362067 original size:21 final size:21
Alignment explanation
Indices: 2362043--2362084 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2362033 ACTCGATAAG
2362043 TTTACAAT-TAACTCTTTAATA
1 TTTA-AATATAACTCTTTAATA
* *
2362064 TTTAAATATAATTTTTTAATA
1 TTTAAATATAACTCTTTAATA
2362085 GCCACCTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAATATAACTCTTTAATA
Found at i:2366321 original size:18 final size:18
Alignment explanation
Indices: 2366298--2366341 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2366288 TTTTTCCATA
* *
2366298 AAGAAAGTCTTGATCTAT
1 AAGAAAGACTTGATCAAT
*
2366316 AAGAAACACTTGATCAAT
1 AAGAAAGACTTGATCAAT
*
2366334 AAAAAAGA
1 AAGAAAGA
2366342 TGTCAAAACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (18 bp):
AAGAAAGACTTGATCAAT
Found at i:2367092 original size:25 final size:24
Alignment explanation
Indices: 2367054--2367101 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2367044 GAAATTAGGG
** *
2367054 TTATTTTTTTAAAATATAATAATTT
1 TTATTTTTAAAAAAAATAA-AATTT
2367079 TTATTTTTAAAAAAAATAAAATT
1 TTATTTTTAAAAAAAATAAAATT
2367102 ATCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTATTTTTAAAAAAAATAAAATTT
Found at i:2367507 original size:21 final size:21
Alignment explanation
Indices: 2367456--2367508 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2367446 ATTCTGACTA
2367456 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
2367477 TCG-AGTTGCGATTTTCCTAAT
1 TCGCA-TTGCGATTTCCCAAAT
*
2367498 TCGCAATGCGA
1 TCGCATTGCGA
2367509 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2367523 original size:20 final size:20
Alignment explanation
Indices: 2367498--2367624 Score: 157
Period size: 20 Copynumber: 6.3 Consensus size: 20
2367488 TTTTCCTAAT
2367498 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
2367518 TCGCAACGCAAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2367539 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2367559 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2367579 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
2367599 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
2367619 TCGCAA
1 TCGCAA
2367625 CGAGATTCTG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 77 0.85
21 14 0.15
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2367575 original size:61 final size:60
Alignment explanation
Indices: 2367498--2367624 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 60
2367488 TTTTCCTAAT
* *
2367498 TCGCAATGCGAATACGTAAATCGCAACGCAAATTTGGAAAATCGCAATGCGATTAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATAT-GAAAATCGCAATGCGAAT-CTGTAAA
* * * *
2367559 TCGCAATGCGATTACGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATATGAAAATCGCAATGCGAATCTGTAAA
2367619 TCGCAA
1 TCGCAA
2367625 CGAGATTCTG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 27 0.46
61 31 0.53
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCAAATATGAAAATCGCAATGCGAATCTGTAAA
Found at i:2367634 original size:20 final size:20
Alignment explanation
Indices: 2367536--2367634 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
2367526 CAAATTTGGA
2367536 AAATCGCAATGCGATTAC-GT
1 AAATCGCAATGCGATT-CTGT
2367556 AAATCGCAATGCGATTAC-GT
1 AAATCGCAATGCGATT-CTGT
* *
2367576 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGATTCTGT
*
2367596 AAATCGCAATGCGAATCTGT
1 AAATCGCAATGCGATTCTGT
* *
2367616 AAATCGCAACGAGATTCTG
1 AAATCGCAATGCGATTCTG
2367635 ACTTCGCAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (20 bp):
AAATCGCAATGCGATTCTGT
Found at i:2368471 original size:24 final size:24
Alignment explanation
Indices: 2368444--2368497 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2368434 GTATTCGAAA
*
2368444 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTAGTCAATACCCGGAC
* *
2368468 TTTGATCTTAGTCAATACTCGGAT
1 TTTGATCTTAGTCAATACCCGGAC
2368492 TTTGAT
1 TTTGAT
2368498 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCGGAC
Found at i:2370962 original size:14 final size:14
Alignment explanation
Indices: 2370943--2370995 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
2370933 GAATATGACT
2370943 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2370957 ATCGCAATGCGAATGAAA
1 ATCGCAA--CG-A-GAGA
*
2370975 ATCGCAACGAGTGA
1 ATCGCAACGAGAGA
2370989 ATCGCAA
1 ATCGCAA
2370996 TGCGATTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 16 0.50
15 1 0.03
16 4 0.12
17 1 0.03
18 10 0.31
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2371036 original size:20 final size:20
Alignment explanation
Indices: 2371007--2371059 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2370997 GCGATTCTCT
*
2371007 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
2371027 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
2371047 CGTTGCGATAGTC
1 CGTTGCGATAGTC
2371060 TGTTTTGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2371176 original size:14 final size:14
Alignment explanation
Indices: 2371157--2371193 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2371147 CATTAATTAA
2371157 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2371171 ACAAATCATCTTTT
1 ACAAATCAACATTT
2371185 ACAAATCAA
1 ACAAATCAA
2371194 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2372648 original size:42 final size:42
Alignment explanation
Indices: 2372569--2372661 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2372559 CCTCTTCAAC
* * *
2372569 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
2372611 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
2372653 GATGACAGG
1 GATGACAGG
2372662 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:2373187 original size:34 final size:34
Alignment explanation
Indices: 2373140--2373293 Score: 130
Period size: 34 Copynumber: 4.4 Consensus size: 34
2373130 TGAAACTTAA
* *
2373140 AATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAATGCGAAAATGACTATCGCAACAAGAG
** * *
2373174 AATCGCAATGCG-AAATGAAAATCGCAACAACAA
1 AATCGCAATGCGAAAATGACTATCGCAACAAGAG
* * *
2373207 AATCGCAACGCGAAAATGACCATCGCAATGCAAAAATG
1 AATCGCAATGCGAAAATGACTATCGCAA--C-AAGA-G
* ** *
2373245 ACTATCACAATGCGAATTTGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAAAATGACTATCGCAACAAGAG
2373281 AATCGCAATGCGA
1 AATCGCAATGCGA
2373294 TTTTCATTTC
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
33 27 0.29
34 35 0.37
36 3 0.03
37 5 0.05
38 2 0.02
40 22 0.23
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGACTATCGCAACAAGAG
Found at i:2373233 original size:20 final size:20
Alignment explanation
Indices: 2373208--2373276 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
2373198 CAACAACAAA
*
2373208 ATCGCAACGCGAAAATGACC
1 ATCGCAACGCGAAAATGACT
* *
2373228 ATCGCAATGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
2373248 ATCACAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2373268 ATCGCAACG
1 ATCGCAACG
2373277 AGAGAATCGC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2373350 original size:20 final size:20
Alignment explanation
Indices: 2373325--2373464 Score: 166
Period size: 20 Copynumber: 7.3 Consensus size: 20
2373315 CTTTCGTTGT
** *
2373325 GATAGTCAAATTCGTATTGC
1 GATAGTCATTTTCGCATTGC
2373345 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
2373365 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
2373385 GATAGTCATTTTCGTATTGC
1 GATAGTCATTTTCGCATTGC
*
2373405 GAT--TC--TCTCG--TTGC
1 GATAGTCATTTTCGCATTGC
* * *
2373419 GATAGTCATTCTCTCGTTGC
1 GATAGTCATTTTCGCATTGC
2373439 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
2373459 GATAGT
1 GATAGT
2373465 AAACTATTCT
Statistics
Matches: 105, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
18 6 0.06
20 86 0.82
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:2375361 original size:20 final size:20
Alignment explanation
Indices: 2375338--2375392 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2375328 CTGAAACTTT
2375338 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
2375358 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
2375378 TTATCGCAACGCGAA
1 AAATCGCAACACGAA
2375393 TTTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:2375402 original size:20 final size:20
Alignment explanation
Indices: 2375360--2375432 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
2375350 GAAAATGAAA
* ** *
2375360 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAATTTGACT
2375380 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
2375400 ATCGTAACGCGAATTTAACT
1 ATCGCAACGCGAATTTGACT
2375420 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2375433 ATGAAAATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:2376043 original size:20 final size:20
Alignment explanation
Indices: 2376018--2376091 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
2376008 GCGCTATGTA
2376018 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* **
2376038 AATCGCATTGCGATTTTCCA
1 AATCGCATTGCGATTTACGT
* *
2376058 AATTCGCGTTACGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
2376079 ATTCGCATTGCGA
1 AATCGCATTGCGA
2376092 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:2376684 original size:4 final size:4
Alignment explanation
Indices: 2376677--2376701 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2376667 TTCTTCTTTC
2376677 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
2376702 ATTATTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:2391009 original size:31 final size:31
Alignment explanation
Indices: 2390942--2391017 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2390932 AAGTCTCAGA
* * *
2390942 GGTTATAAAATGGTCATTAAACTTCCTAAGT
1 GGTTACAAAATGGTCATTAAACTTACTAACT
*
2390973 GGTTACAAAATGGTCATTAAACTTATTGAACT
1 GGTTACAAAATGGTCATTAAACTTACT-AACT
2391005 -GTTACAAAATGGT
1 GGTTACAAAATGGT
2391018 TTAATGACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 37 0.93
32 3 0.08
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (31 bp):
GGTTACAAAATGGTCATTAAACTTACTAACT
Found at i:2395008 original size:109 final size:109
Alignment explanation
Indices: 2394867--2395068 Score: 300
Period size: 109 Copynumber: 1.9 Consensus size: 109
2394857 AGGTTGCGCC
* * *
2394867 TAAAATATTACCAAAATTTAAGATGATAGAGCATTGGATTTT-TCCACGATAATAAAATAAGTTA
1 TAAAATATTACCAAAATTTAAGATGATAGAGCAGTAGATTTTCT-CACGATAAGAAAATAAGTTA
2394931 AAA-ACTAAAAATGTTATGAATATATATAAGAAATACGGTTATGCT
65 AAATA-TAAAAATGTTATGAATATATATAAGAAATACGGTTATGCT
* * * *
2394976 TAAAATGTTACCAAAGTTTAAGCTGATGGAGCAGTAGATTTTCTCACGATAAGAAAATAAGTTAA
1 TAAAATATTACCAAAATTTAAGATGATAGAGCAGTAGATTTTCTCACGATAAGAAAATAAGTTAA
*
2395041 AATATGAAAATGTTATGAATATATATAA
66 AATATAAAAATGTTATGAATATATATAA
2395069 AAAAATAAGG
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
109 81 0.98
110 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (109 bp):
TAAAATATTACCAAAATTTAAGATGATAGAGCAGTAGATTTTCTCACGATAAGAAAATAAGTTAA
AATATAAAAATGTTATGAATATATATAAGAAATACGGTTATGCT
Found at i:2395096 original size:26 final size:24
Alignment explanation
Indices: 2395056--2395105 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2395046 GAAAATGTTA
2395056 TGAATATATATAAAAAAATAAGGT
1 TGAATATATATAAAAAAATAAGGT
2395080 TGAATATATATAAAAAAATAAGGT
1 TGAATATATATAAAAAAATAAGGT
2395104 TG
1 TG
2395106 CGCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (24 bp):
TGAATATATATAAAAAAATAAGGT
Found at i:2395357 original size:20 final size:20
Alignment explanation
Indices: 2395332--2395372 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2395322 TTATAAAAAA
*
2395332 TTCAAAAGTATAGATATTTT
1 TTCAAAAATATAGATATTTT
*
2395352 TTCAAAAATATCGATATTTT
1 TTCAAAAATATAGATATTTT
2395372 T
1 T
2395373 GAATTTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (20 bp):
TTCAAAAATATAGATATTTT
Found at i:2396302 original size:64 final size:62
Alignment explanation
Indices: 2396221--2396363 Score: 207
Period size: 64 Copynumber: 2.3 Consensus size: 62
2396211 CATTTTTCTA
*
2396221 AAAGTATCA-ATACTTTTAACTTTGAAAGTTAAAATAACATTTTTCATATTTTTTTTAAAATTAG
1 AAAGTAT-AGATACTTTTAACTTTAAAAGTTAAAATAACA-TTTTC-TATTTTTTTTAAAATTAG
* * *
2396285 AAAGTATAGATACTTTTAACTTTAAAAGTTAAAATATCATTTTCTATTTTTTTTTAAATTCG
1 AAAGTATAGATACTTTTAACTTTAAAAGTTAAAATAACATTTTCTATTTTTTTTAAAATTAG
*
2396347 AAAGTATCGATACTTTT
1 AAAGTATAGATACTTTT
2396364 GGAAAAATAT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
62 32 0.44
63 6 0.08
64 35 0.48
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (62 bp):
AAAGTATAGATACTTTTAACTTTAAAAGTTAAAATAACATTTTCTATTTTTTTTAAAATTAG
Found at i:2396613 original size:77 final size:77
Alignment explanation
Indices: 2396435--2396755 Score: 357
Period size: 77 Copynumber: 4.2 Consensus size: 77
2396425 CGCAACTTGC
* * * *
2396435 TTTCTTAGTGAACCA-AACATTATTGTGTGCAACCCATTTTATTAATAAAAATATTAACATT--A
1 TTTCTTAGTGAACCATGACATTCTTGAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
* *
2396497 GATCACAACCTA
66 TATCACAACATA
* * *
2396509 TTTCTTAGTGAACTGA-GACATTCTTGAGCGCAACCCATTTTATAAATAAAAATATTAACATTTC
1 TTTCTTAGTGAAC-CATGACATTCTTGAGCGCAACCCATTTTATTAATAAAAATATTAACATTCC
2396573 ATATCACAACATA
65 ATATCACAACATA
* * * * * * *
2396586 TTTTTTAGTGAACCATGACATTGTTGAGCGTAATCTATTTTATTAATAAAAAAATTAATATTCCA
1 TTTCTTAGTGAACCATGACATTCTTGAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
* *
2396651 TATCGCAACCTA
66 TATCACAACATA
* * *
2396663 TTTCTTAGTGAACAATGACATTCTT-AGGCACAACCCATTTTATTAATAAAAGTATTAACATTCC
1 TTTCTTAGTGAACCATGACATTCTTGA-GCGCAACCCATTTTATTAATAAAAATATTAACATTCC
* *
2396727 AAAT-AGCAACATG
65 ATATCA-CAACATA
*
2396740 TTTCTTAATGAACCAT
1 TTTCTTAGTGAACCAT
2396756 TATATTTTTA
Statistics
Matches: 205, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
74 13 0.06
75 42 0.20
76 2 0.01
77 148 0.72
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (77 bp):
TTTCTTAGTGAACCATGACATTCTTGAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCA
TATCACAACATA
Found at i:2396959 original size:76 final size:77
Alignment explanation
Indices: 2396877--2397039 Score: 220
Period size: 76 Copynumber: 2.1 Consensus size: 77
2396867 TTTTAGGTGT
* * * * * *
2396877 AACCTATTTTATTATTAAAAATATTAAGATTCCATATCAC-ACCTATATATTAGTGAACCATGAC
1 AACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACATATATATTAGTGAACCATAAC
*
2396941 ATTCTTGGGCGC
66 ATTATTGGGCGC
* * *
2396953 AACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACATATTTCTTAGTGAACTATAAC
1 AACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACATATATATTAGTGAACCATAAC
2397018 ATTATTGGGCGC
66 ATTATTGGGCGC
2397030 AACCTTATTT
1 AACC-TATTT
2397040 CTGATATATA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
76 36 0.48
77 34 0.45
78 5 0.07
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (77 bp):
AACCTATTTTATTAATAAAAATATTAACATTACAAATCACAACATATATATTAGTGAACCATAAC
ATTATTGGGCGC
Found at i:2397678 original size:50 final size:50
Alignment explanation
Indices: 2397612--2397734 Score: 147
Period size: 50 Copynumber: 2.5 Consensus size: 50
2397602 GCAGGAAAGT
* * * *
2397612 GCGCCCCCTGAACCGCGCTATATGCTGATTTGGCTCCACGTGGATATAGC
1 GCGCCCCCTGACCCGCGCTATACGCTGATCTGGCACCACGTGGATATAGC
* * * * * *
2397662 GCGCGCCCTGCCCCGCGATATACGGTGATCTGGCACCACGTGGGTATAGT
1 GCGCCCCCTGACCCGCGCTATACGCTGATCTGGCACCACGTGGATATAGC
*
2397712 GCGCCCCCTGATCCGCGCTATAC
1 GCGCCCCCTGACCCGCGCTATAC
2397735 CTGGATATCT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.21
Consensus pattern (50 bp):
GCGCCCCCTGACCCGCGCTATACGCTGATCTGGCACCACGTGGATATAGC
Found at i:2397870 original size:10 final size:10
Alignment explanation
Indices: 2397855--2397889 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2397845 TTTATCACAC
2397855 CAAATTCTCT
1 CAAATTCTCT
2397865 CAAATTCTCT
1 CAAATTCTCT
2397875 -AAATTTCTCT
1 CAAA-TTCTCT
2397885 CAAAT
1 CAAAT
2397890 ATTCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2397894 original size:12 final size:12
Alignment explanation
Indices: 2397858--2397896 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 12
2397848 ATCACACCAA
2397858 ATTCTCTC-AA-
1 ATTCTCTCAAAT
2397868 ATTCTCT-AAAT
1 ATTCTCTCAAAT
2397879 -TTCTCTCAAAT
1 ATTCTCTCAAAT
2397890 ATTCTCT
1 ATTCTCT
2397897 TTTTAAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 15 0.60
11 4 0.16
12 6 0.24
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTCTCTCAAAT
Found at i:2398213 original size:111 final size:111
Alignment explanation
Indices: 2398027--2398240 Score: 401
Period size: 111 Copynumber: 1.9 Consensus size: 111
2398017 ATATATCTAT
* *
2398027 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
2398092 TGATTGATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
2398138 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
2398203 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
2398241 TTTTTGTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (111 bp):
ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:2400142 original size:9 final size:9
Alignment explanation
Indices: 2400125--2400177 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
2400115 ACCTGCTCAA
2400125 GACGACGAT
1 GACGACGAT
*
2400134 GATGACGAT
1 GACGACGAT
* *
2400143 GACGATGGT
1 GACGACGAT
2400152 GACGACGAT
1 GACGACGAT
*
2400161 GATGACGAT
1 GACGACGAT
*
2400170 GACAACGA
1 GACGACGA
2400178 GGAGTCAGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.15
Consensus pattern (9 bp):
GACGACGAT
Found at i:2400398 original size:35 final size:33
Alignment explanation
Indices: 2400359--2400443 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
2400349 ATATTTTAGT
2400359 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
2400394 TAATTTGGTTATCATTTACCATTTTATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
2400429 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
2400444 TAAATATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:2404111 original size:50 final size:51
Alignment explanation
Indices: 2404024--2404156 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 51
2404014 CCCCTACGTG
* *
2404024 GCGTATAGCGC-GTATCAGGGGGCGCGCTATACC-CCACGTGTAC-CC-AGTCA
1 GCGTATAGCGCGGT-TCAGGGGGCGCGCT-TTCCTCCACGTG-ACGCCAAATCA
* *
2404074 GCGTATAACGCGGTTCAGGGGGCGCGCTTTCCTCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGTTCAGGGGGCGCGCTTTCCTCCACGTGACGCCAAATCA
* * *
2404125 GCATATAGCGCGGTTCAAGGGG-GCACTTTCCT
1 GCGTATAGCGCGGTTCAGGGGGCGCGCTTTCCT
2404157 GCTAAGGGTG
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
49 4 0.06
50 42 0.59
51 25 0.35
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.20
Consensus pattern (51 bp):
GCGTATAGCGCGGTTCAGGGGGCGCGCTTTCCTCCACGTGACGCCAAATCA
Done.