Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 56 of 170
Found at i:16397315 original size:25 final size:25
Alignment explanation
Indices: 16397277--16397325 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
16397267 TTAAACTCTT
*
16397277 ATGAGCTTCCTGTTACATGGCTCAC
1 ATGAGCATCCTGTTACATGGCTCAC
* **
16397302 ATGAGCATCTTGTTTTATGGCTCA
1 ATGAGCATCCTGTTACATGGCTCA
16397326 AGAGAGTGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (25 bp):
ATGAGCATCCTGTTACATGGCTCAC
Found at i:16400416 original size:13 final size:13
Alignment explanation
Indices: 16400382--16400410 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16400372 TGGGTCACAC
16400382 GCCCATGTGTGTT
1 GCCCATGTGTGTT
16400395 GCCCATGTGTGTT
1 GCCCATGTGTGTT
16400408 GCC
1 GCC
16400411 GGTGTGCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.28, G:0.31, T:0.34
Consensus pattern (13 bp):
GCCCATGTGTGTT
Found at i:16401426 original size:18 final size:18
Alignment explanation
Indices: 16401403--16401443 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
16401393 TATTAACACG
*
16401403 ACACGGACTCAGACGGAT
1 ACACGGACTCAGACGAAT
16401421 ACACGGACTCAGACGAAT
1 ACACGGACTCAGACGAAT
16401439 ACACG
1 ACACG
16401444 AATCCAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.29, G:0.24, T:0.10
Consensus pattern (18 bp):
ACACGGACTCAGACGAAT
Found at i:16402093 original size:19 final size:18
Alignment explanation
Indices: 16402053--16402093 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
16402043 AAAATTACAC
*
16402053 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
16402071 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
16402090 ATTT
1 ATTT
16402094 TGCTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:16410112 original size:21 final size:20
Alignment explanation
Indices: 16410083--16410122 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
16410073 AAATCTAAAA
16410083 TATTGTAAAACACATAATTATC
1 TATTGTAAAACA-AT-ATTATC
16410105 TATT-TAAAACAATATTAT
1 TATTGTAAAACAATATTAT
16410123 ATTTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 7 0.39
22 4 0.22
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (20 bp):
TATTGTAAAACAATATTATC
Found at i:16416738 original size:23 final size:23
Alignment explanation
Indices: 16416684--16416747 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
16416674 TTTGGTGTAT
**
16416684 AATGAATTTAAACAA-AATTTTA
1 AATGAATTTAAACAATAATAATA
*
16416706 AA-AAATTTTAAACAATAATAATA
1 AATGAA-TTTAAACAATAATAATA
16416729 AATGAATTTAAACAATAAT
1 AATGAATTTAAACAATAAT
16416748 CAACAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.06
22 11 0.31
23 20 0.57
24 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (23 bp):
AATGAATTTAAACAATAATAATA
Found at i:16418092 original size:11 final size:11
Alignment explanation
Indices: 16418078--16418107 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16418068 TGGACTTTTA
16418078 TTATATTTATT
1 TTATATTTATT
*
16418089 TTATATATATT
1 TTATATTTATT
16418100 TTATATTT
1 TTATATTT
16418108 GGGTTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATTTATT
Found at i:16418686 original size:44 final size:44
Alignment explanation
Indices: 16418631--16419182 Score: 213
Period size: 44 Copynumber: 12.7 Consensus size: 44
16418621 ATTTTAACTC
* *
16418631 GCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
* * * * * *
16418675 GCTCCGCTGTAATCTCAGTGAGATAAGA--CCT-GATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
* * * * * * *
16418716 ACTCAACTGTAA-CTTTAGAGAGATAAGATCCT-TTA-TTTTAATCT
1 GCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCT
* * * *
16418760 GTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
* * * * *
16418804 GCTCCGCTGTAATCTTAGGGAGATAAGATCT-GTAATTCTTCAGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACT-A-GCTTCAATCT
** * * * * *
16418850 ATTCCATTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
* * ** ** * * *
16418891 ACTCTACTGTAA-CTTCAAAGAGATAAGATCTTTTA-TTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGAT-TACTAGCTTCAATCT
* * * *
16418935 GTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
** * * * **
16418979 TTTCCGCTGTAATCTCAGGGAGATAAGATCT-GTAATTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACT-A-GCTTCAATCT
** * * * *
16419025 ATTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
* * * * * * * *
16419066 ACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTA-TTTTAATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTA-CTAGCTTCAATCT
* * * * * *
16419110 GTTCCACTATGATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
*
16419154 GCTCCACTGTAATCTTAGGGAGATAAGAT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT
16419183 CCGCCATCTT
Statistics
Matches: 357, Mismatches: 120, Indels: 62
0.66 0.22 0.12
Matches are distributed among these distances:
40 3 0.01
41 83 0.23
42 3 0.01
43 4 0.01
44 195 0.55
45 5 0.01
46 64 0.18
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
Found at i:16418798 original size:129 final size:126
Alignment explanation
Indices: 16418554--16418831 Score: 423
Period size: 129 Copynumber: 2.2 Consensus size: 126
16418544 GTTTATTCCA
*
16418554 CTGTAATCTCAGGAAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGATAAGATCCT
1 CTGTAATCTCAGG-AGATAAGACCTGATACGATCTACTCAACTGTAACTTCAGAGATAAGATCCT
* *
16418619 TTATTTTAACTCGCTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCG
65 TTATTTTAACTCGCTCCACTGTAATCTCAGGGAAATAGGATTACTAGCTTCAATCTGCTCCG
* *
16418681 CTGTAATCTCAGTGAGATAAGACCTGATGCGATCTACTCAACTGTAACTTTAGAGAGATAAGATC
1 CTGTAATCTCAG-GAGATAAGACCTGATACGATCTACTCAACTGTAAC-TT-CAGAGATAAGATC
* *
16418746 CTTTATTTTAA-TCTGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCG
63 CTTTATTTTAACTC-GCTCCACTGTAATCTCAGGGAAATAGGATTACTAGCTTCAATCTGCTCCG
*
16418810 CTGTAATCTTAGGGAGATAAGA
1 CTGTAATCTCA-GGAGATAAGA
16418832 TCTGTAATTC
Statistics
Matches: 138, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
127 44 0.32
128 5 0.04
129 88 0.64
130 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (126 bp):
CTGTAATCTCAGGAGATAAGACCTGATACGATCTACTCAACTGTAACTTCAGAGATAAGATCCTT
TATTTTAACTCGCTCCACTGTAATCTCAGGGAAATAGGATTACTAGCTTCAATCTGCTCCG
Found at i:16418875 original size:175 final size:175
Alignment explanation
Indices: 16418681--16419183 Score: 871
Period size: 175 Copynumber: 2.9 Consensus size: 175
16418671 ATCTGCTCCG
* * *
16418681 CTGTAATCTCAGTGAGATAAGACCTGATGCGATCTACTCAACTGTAACTTTAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* *
16418746 CTTTATTTTAATCTGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCGC
66 ATTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCGC
16418811 TGTAATCTTAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
131 TGTAATCTTAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
* *
16418856 TTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* **
16418921 TTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTTTTCCGC
66 ATTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCGC
* *
16418986 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCA
131 TGTAATCTTAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
16419031 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* * *
16419096 ATTTATTTTAATCCGTTCCACTATGATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCAC
66 ATTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCGC
16419161 TGTAATCTTAGGGAGATAAGATC
131 TGTAATCTTAGGGAGATAAGATC
16419184 CGCCATCTTC
Statistics
Matches: 308, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 308 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (175 bp):
CTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
ATTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCGC
TGTAATCTTAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCA
Found at i:16428995 original size:45 final size:44
Alignment explanation
Indices: 16428942--16429039 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
16428932 TTTGGTTTGC
16428942 TGTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAA
* *
16428987 TGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAA
*
16429031 TGGAATGGA
1 TGTAATGGA
16429040 GGTGTAATAG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 1 0.02
44 24 0.49
45 24 0.49
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAA
Found at i:16429263 original size:57 final size:56
Alignment explanation
Indices: 16429156--16429270 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 56
16429146 AAAATAATAT
*
16429156 AATATAAATATTTTAATCATATTTTAACATAATTATTATTAAATATAATTTAATAAA
1 AATATAAATAATTTAATCATATTTTAACATAATTATTATT-AATATAATTTAATAAA
* * *
16429213 AATATAAATAATTTAAT-ATAATTCTTAATATAATTATTCTT-ATATGAATTTACTAAA
1 AATATAAATAATTTAATCAT-ATT-TTAACATAATTATTATTAATAT-AATTTAATAAA
16429270 A
1 A
16429271 TCATGATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
56 6 0.12
57 30 0.59
58 15 0.29
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (56 bp):
AATATAAATAATTTAATCATATTTTAACATAATTATTATTAATATAATTTAATAAA
Found at i:16432264 original size:14 final size:14
Alignment explanation
Indices: 16432245--16432272 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16432235 AGCAGAAATC
16432245 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
16432259 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
16432273 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:16432270 original size:19 final size:18
Alignment explanation
Indices: 16432248--16432292 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
16432238 AGAAATCTGG
16432248 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
16432267 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
16432284 AGAAAAGAA
1 AGAAAAGAA
16432293 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:16433772 original size:25 final size:25
Alignment explanation
Indices: 16433744--16433792 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16433734 TTTAAACTAT
16433744 AATAATAAATT-TAAACAATATTAAG
1 AATAA-AAATTATAAACAATATTAAG
* *
16433769 AATAAATATTATAAATAATATTAA
1 AATAAAAATTATAAACAATATTAA
16433793 ATACTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAAAAATTATAAACAATATTAAG
Found at i:16434948 original size:13 final size:13
Alignment explanation
Indices: 16434920--16434954 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
16434910 AGTATTGGAC
*
16434920 TTTTATTATATTTA
1 TTTTA-TATATATA
16434934 TTTTATATATATA
1 TTTTATATATATA
16434947 TTTTATAT
1 TTTTATAT
16434955 TTGGGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATATATATA
Found at i:16443656 original size:18 final size:19
Alignment explanation
Indices: 16443633--16443669 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16443623 TATAGTCAAT
*
16443633 AAAAAT-AAACATTATCTA
1 AAAAATAAAACATAATCTA
16443651 AAAAATAAAACATAATCTA
1 AAAAATAAAACATAATCTA
16443670 TCATCTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATAAAACATAATCTA
Found at i:16444021 original size:29 final size:29
Alignment explanation
Indices: 16443987--16444043 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
16443977 TAGGTTGAAA
* *
16443987 GATTGAAGATTTGAAGTTGGTTGGATAAT
1 GATTGAAGATTTAAAATTGGTTGGATAAT
*
16444016 GATTGAATATTTAAAATTGGTTGGATAA
1 GATTGAAGATTTAAAATTGGTTGGATAA
16444044 AGATCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (29 bp):
GATTGAAGATTTAAAATTGGTTGGATAAT
Found at i:16444102 original size:14 final size:15
Alignment explanation
Indices: 16444085--16444113 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16444075 CTATAATTAA
16444085 TTTAAA-TTTGATTT
1 TTTAAATTTTGATTT
16444099 TTTAAATTTTGATTT
1 TTTAAATTTTGATTT
16444114 ATCTAGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TTTAAATTTTGATTT
Found at i:16444333 original size:7 final size:7
Alignment explanation
Indices: 16444321--16444349 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
16444311 TCCTTCCAAG
16444321 CCCTTTC
1 CCCTTTC
16444328 CCCTTTC
1 CCCTTTC
16444335 CCCTTTC
1 CCCTTTC
16444342 CCCTTTC
1 CCCTTTC
16444349 C
1 C
16444350 ACAATTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (7 bp):
CCCTTTC
Found at i:16449074 original size:44 final size:44
Alignment explanation
Indices: 16449025--16449148 Score: 131
Period size: 45 Copynumber: 2.8 Consensus size: 44
16449015 GCCCCCAGCA
*
16449025 GTCTCCAGGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTT
1 GTCTCCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTT
* * * * * * * *
16449069 GTCTCCTCATATTGGTGGTGGAGTAGATCGAAGACAATAGATCTT
1 GTCTCCACGTACTGG-CGTGAAGTAGATCAAAGATAACAGATCTT
* * *
16449114 ATCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
1 GTCTCCACGTACTGGCGTGAAGTAGATCAAAGATA
16449149 GTAGGTCCCG
Statistics
Matches: 60, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
44 27 0.45
45 33 0.55
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (44 bp):
GTCTCCACGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTT
Found at i:16452807 original size:16 final size:15
Alignment explanation
Indices: 16452786--16452824 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
16452776 TAATTTATTA
16452786 AATAAAAATTATTTT
1 AATAAAAATTATTTT
*
16452801 AATTAAACTATTATTTT
1 AA-TAAA-AATTATTTT
16452818 AATAAAA
1 AATAAAA
16452825 TGTTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.10
16 8 0.40
17 10 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAAAAATTATTTT
Found at i:16462633 original size:27 final size:27
Alignment explanation
Indices: 16462595--16463007 Score: 138
Period size: 27 Copynumber: 15.3 Consensus size: 27
16462585 AATGGGCCAC
*
16462595 AAATGACCGAATTACTCCCGAAGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
*
16462622 AAATGACTGAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * * *
16462649 AAATTACCGAAATACCCTC-ATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* ** * * *
16462675 AAATTATTGAAATGCCCTCGATA-GGTA
1 AAATGACCGAATTACCCCCGA-AGGGTA
* * * * * *
16462702 AAATTATCGAAATACCCCTGATGGATA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * **
16462729 AAATTACCGAAATACCATC-AATGGGTA
1 AAATGACCGAATTACCCCCGAA-GGGTA
* ** * * *
16462756 AAATTACTAAAATACCCTCGATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * * *
16462783 AAATGACTGAAATATCCTCGATA-GGTA
1 AAATGACCGAATTACCCCCGA-AGGGTA
* * * ** *
16462810 AAATGACTGAAATACTCTTGATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * * * *
16462837 AAATTATCGAAATACCCTCGATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * * *
16462864 AAATTACCGAAATACCCTCGATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * * * * *
16462891 AAATTACCAAAATATCCTCGATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * * *
16462918 AAACT-ACCAAAATACCCCTGATGGGTA
1 AAA-TGACCGAATTACCCCCGAAGGGTA
* * * * *
16462945 AAATTATCGAAATACCCTCGATGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * *
16462972 AAACT-ATCGAAATA-CCCCTATAGGGTA
1 AAA-TGACCGAATTACCCCCGA-AGGGTA
16462999 AAATGACCG
1 AAATGACCG
16463008 TTATACCCCT
Statistics
Matches: 320, Mismatches: 54, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
26 29 0.09
27 288 0.90
28 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCGAAGGGTA
Found at i:16462756 original size:54 final size:54
Alignment explanation
Indices: 16462595--16463007 Score: 431
Period size: 54 Copynumber: 7.7 Consensus size: 54
16462585 AATGGGCCAC
* * * * * * * *
16462595 AAATGACCGAATTACTCCC-GAAGGGTAAAATGACTGAATTACCCCCGAAGGGTA
1 AAATTACCGAAATAC-CCCTGATGGGTAAAATTACCGAAATACCCTCGATGGGTA
* ** * *
16462649 AAATTACCGAAATA-CCCTCATGGGTAAAATTATTGAAATGCCCTCGATAGGTA
1 AAATTACCGAAATACCCCTGATGGGTAAAATTACCGAAATACCCTCGATGGGTA
* * * *
16462702 AAATTATCGAAATACCCCTGATGGATAAAATTACCGAAATACCATCAATGGGTA
1 AAATTACCGAAATACCCCTGATGGGTAAAATTACCGAAATACCCTCGATGGGTA
** * * * *
16462756 AAATTACTAAAATA-CCCTCGATGGGTAAAATGACTGAAATATCCTCGATAGGTA
1 AAATTACCGAAATACCCCT-GATGGGTAAAATTACCGAAATACCCTCGATGGGTA
* * * * *
16462810 AAATGACTGAAATACTCTTGATGGGTAAAATTATCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCCTGATGGGTAAAATTACCGAAATACCCTCGATGGGTA
* *
16462864 AAATTACCGAAATA-CCCTCGATGGGTAAAATTACCAAAATATCCTCGATGGGTA
1 AAATTACCGAAATACCCCT-GATGGGTAAAATTACCGAAATACCCTCGATGGGTA
* * *
16462918 AAACTACCAAAATACCCCTGATGGGTAAAATTATCGAAATACCCTCGATGGGTA
1 AAATTACCGAAATACCCCTGATGGGTAAAATTACCGAAATACCCTCGATGGGTA
* * *
16462972 AAACTATCGAAATACCCCT-ATAGGGTAAAATGACCG
1 AAATTACCGAAATACCCCTGAT-GGGTAAAATTACCG
16463008 TTATACCCCT
Statistics
Matches: 297, Mismatches: 55, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
52 3 0.01
53 47 0.16
54 241 0.81
55 6 0.02
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (54 bp):
AAATTACCGAAATACCCCTGATGGGTAAAATTACCGAAATACCCTCGATGGGTA
Found at i:16462808 original size:108 final size:107
Alignment explanation
Indices: 16462617--16463005 Score: 478
Period size: 108 Copynumber: 3.6 Consensus size: 107
16462607 TACTCCCGAA
* * * * *
16462617 GGGTAAAATGA-CTGAATTACCCCCGAAGGGTAAAATTACCGAAATACCCTC-ATGGGTAAAATT
1 GGGTAAAATTATC-GAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATG
* **
16462680 ATTGAAATGCCCTCGATAGGTAAAATTATCGAAATACCCCTGAT
65 ACTGAAATATCCTCGATAGGTAAAATTA-CGAAATACCCCTGAT
* * * * **
16462724 GGATAAAATTACCGAAATACCATCAATGGGTAAAATTACTAAAATACCCTCGATGGGTAAAATGA
1 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATGA
* * *
16462789 CTGAAATATCCTCGATAGGTAAAATGACTGAAATACTCTTGAT
66 CTGAAATATCCTCGATAGGTAAAATTAC-GAAATACCCCTGAT
*
16462832 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTA
1 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATGA
** * * *
16462897 CCAAAATATCCTCGATGGGTAAAACTACCAAAATACCCCTGAT
66 CTGAAATATCCTCGATAGGTAAAATTA-CGAAATACCCCTGAT
* * *
16462940 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAACTATCGAAATACCC-CTATAGGGTAAAATG
1 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGAT-GGGTAAAATG
16463004 AC
65 AC
16463006 CGTTATACCC
Statistics
Matches: 242, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
107 44 0.18
108 197 0.81
109 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (107 bp):
GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCTCGATGGGTAAAATGA
CTGAAATATCCTCGATAGGTAAAATTACGAAATACCCCTGAT
Found at i:16463017 original size:81 final size:80
Alignment explanation
Indices: 16462617--16463002 Score: 395
Period size: 81 Copynumber: 4.8 Consensus size: 80
16462607 TACTCCCGAA
* * * *
16462617 GGGTAAAATGA-CTGAATTACCCCCGAAGGGTAAAATTACCGAAATA-CCCTCATGGGTAAAATT
1 GGGTAAAATTATC-GAAATACCCTCGATGGGTAAAATTACCGAAATACCCCT-ATGGGTAAAATT
*** *
16462680 ATTGAAATGCCCTCGAT
64 ACCAAAATACCCTCGAT
* * * *
16462697 AGGTAAAATTATCGAAATACCC-CTGATGGATAAAATTACCGAAATACCATCAATGGGTAAAATT
1 GGGTAAAATTATCGAAATACCCTC-GATGGGTAAAATTACCGAAATACC-CCTATGGGTAAAATT
*
16462761 ACTAAAATACCCTCGAT
64 ACCAAAATACCCTCGAT
* * * * * * *
16462778 GGGTAAAATGA-CTGAAATATCCTCGATAGGTAAAATGACTGAAATACTCTTGATGGGTAAAATT
1 GGGTAAAATTATC-GAAATACCCTCGATGGGTAAAATTACCGAAATACCCCT-ATGGGTAAAATT
* *
16462842 ATCGAAATACCCTCGAT
64 ACCAAAATACCCTCGAT
* * * * *
16462859 GGGTAAAATTACCGAAATACCCTCGATGGGTAAAATTACCAAAATATCCTCGATGGGTAAAACTA
1 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATA-CCCCTATGGGTAAAATTA
16462924 CCAAAATACCC-CTGAT
65 CCAAAATACCCTC-GAT
* *
16462940 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAACTATCGAAATACCCCTATAGGGTAAAAT
1 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTAT-GGGTAAAAT
16463003 GACCGTTATA
Statistics
Matches: 251, Mismatches: 44, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
79 1 0.00
80 44 0.18
81 202 0.80
82 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (80 bp):
GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTATGGGTAAAATTAC
CAAAATACCCTCGAT
Found at i:16463238 original size:26 final size:26
Alignment explanation
Indices: 16463209--16463300 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
16463199 ACTATTACTA
*
16463209 GCAGCTTTGCTGTGTTACTGATATTG
1 GCAGCTTTGCTGCGTTACTGATATTG
* * * * *
16463235 GCAGCTCTGTTGCATTAATGTTATTG
1 GCAGCTTTGCTGCGTTACTGATATTG
* * *
16463261 GTAGCTTTACTGCGTTACT-ATTACTG
1 GCAGCTTTGCTGCGTTACTGA-TATTG
16463287 GCAGCTTTGCTGCG
1 GCAGCTTTGCTGCG
16463301 ATATTAGTGT
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.40
Consensus pattern (26 bp):
GCAGCTTTGCTGCGTTACTGATATTG
Found at i:16463446 original size:30 final size:30
Alignment explanation
Indices: 16463412--16463524 Score: 129
Period size: 30 Copynumber: 3.8 Consensus size: 30
16463402 ATTTGCACTA
16463412 TTACTGTATTGGGCTAAGGCCCACACTCTG
1 TTACTGTATTGGGCTAAGGCCCACACTCTG
* *
16463442 TTACTGTATTGTGCTAAGGCCCAAACTCTG
1 TTACTGTATTGGGCTAAGGCCCACACTCTG
* * *
16463472 TTACTGTATTGGGTTATGGCCCCCACAT-TG
1 TTACTGTATTGGGCTAAGGCCCACAC-TCTG
* * * *
16463502 CTACTATATAGGGCTCAGGCCCA
1 TTACTGTATTGGGCTAAGGCCCA
16463525 GACTAATTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
30 67 0.99
31 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (30 bp):
TTACTGTATTGGGCTAAGGCCCACACTCTG
Found at i:16469373 original size:24 final size:26
Alignment explanation
Indices: 16469339--16469403 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
16469329 CTCTTTATTT
*
16469339 TTTATTTAAATAATATAA-AAAATTA
1 TTTATTAAAATAATATAACAAAATTA
16469364 -TTATTAAAATAATATAACTTCAAAATTA
1 TTTATTAAAATAATATAA---CAAAATTA
16469392 TTTATTAAAATA
1 TTTATTAAAATA
16469404 CCATGAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 16 0.47
28 7 0.21
29 11 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTATTAAAATAATATAACAAAATTA
Found at i:16470369 original size:357 final size:354
Alignment explanation
Indices: 16469532--16471284 Score: 2279
Period size: 357 Copynumber: 4.9 Consensus size: 354
16469522 TAATGTGTCT
* * *
16469532 AATCACCATTTAAAATGGTAAACAGTGATTTCGTTTCTGCTTCTTCTTTTTATGAATTATAAGAG
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTT-TT-TTTTT-T-AATTATAAGAG
* * * * * * *
16469597 GAGGGCAAAACTCTTATAGCAATGCGACTAGTGCTAAATCACTATTTGAAATAATATAACTTCAA
62 GAAGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAA
* * *
16469662 AATTATTTATTAAAATAGCATGAAATGAACTGTACCAATGGGATATGCTAAATCACCATTTAAAA
127 AATTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATATGATAAATCACCATTTAAAA
* * * *
16469727 TGGTAAAAGGTGATTTCGTTTTTGCTTTTTTTTTGTTTGTTTGAATTATAAGAAGAATGCAAAAC
192 TGGTAAATGGTGATTTCATTTTTGC----TTTTT-TTT-TTTGAATTATAAGAGGAAGGCAAAAC
* *
16469792 TCTAACAGTAATGCAGT-TAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAATTATTTAT
251 TCTAACAGCAATG-AGTCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAATTATTTAT
** * *
16469856 TAAAATAGCATGGGATGAACCA-TACTAATGGGTTCTGCTA
315 TAAAATAGCATGAAATGAA-CAGTACTAATGGGATCTACTA
* *
16469896 AATCACCATTTAAAATGGTAAACGGTGATTTCGTTTTTTCTTTTTTCTTTTTAATTATAAGAGGA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGC-TTTTT-TTTTTAATTATAAGAGGA
* * *
16469961 AGGCAAAACTCTAACAACAATACGGCTAGTGCTAAATCACCATTAAAAATAGTATAACTTCAAAA
64 AGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAA
* * * *
16470026 TTATTTATTAAAGTAGCATGAAATGAACAATACTAATGGGATATGATAAATTATCATTTAAAATG
129 TTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATATGATAAATCACCATTTAAAATG
* *
16470091 GTAAATGGTGATTTCACTTTTTGCTTTTTTTTTTTGAATTATAAGAGGAGGGCAAAACTTTAACA
194 GTAAATGGTGATTTCA-TTTTTGCTTTTTTTTTTTGAATTATAAGAGGAAGGCAAAACTCTAACA
* ** *
16470156 ACAATTTGTCTAGTGCTAAATCACCATTTAAAATAAATATAAATTCAAAATTATTTATTAAAATA
258 GCAATGAGTCTAGTGCTAAATCACCATTTAAAAT-AATATAACTTCAAAATTATTTATTAAAATA
*
16470221 CCATGAAATGAACAGTACTAATGGGATCTACTA
322 GCATGAAATGAACAGTACTAATGGGATCTACTA
*
16470254 AATCACCTTTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTTTTTTGAATTATAAGAGGAA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTTTTTT-AATTATAAGAGGAA
*
16470319 GGCAAAACTCTTACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAAT
65 GGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAAT
** * * *
16470384 TATTTATTAAAATAGTGTGAAATGAACAGTACTAATGGGATCT-ACTAAATCACCCTTTGAAATG
130 TATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATATGA-TAAATCACCATTTAAAATG
* *
16470448 GTAAATGGTGATTTCATTTTTGCTTTTTTTTTTTTTTTGCATTATAAGAGGAAGGAAAAACTCCT
194 GTAAATGGTGATTTCATTTTTGC----TTTTTTTTTTTGAATTATAAGAGGAAGGCAAAACT-CT
* * *
16470513 -ACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAATTATTTATTAAA
254 AACAGCAATGAGTCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAATTATTTATTAAA
*
16470577 ATAGCATGAAATGAACAGTACTAATGGGGTCTACTA
319 ATAGCATGAAATGAACAGTACTAATGGGATCTACTA
* * * *
16470613 AATCACCCTTTAAAATGTTAAAC----A-ATGA-TTTTG-TTTTTGTTTTTAATTATAAGAGGAA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTT-TTTTTAATTATAAGAGGAA
* * *
16470671 GGCAAAACTCTAATAGCAATGCGCCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAAT
65 GGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAAT
* * * *
16470736 TATTTATTAAAGTAGCATGAAATGAACAGTACTAATGAGATCTGCTAAATCACCATTTAAAATGG
130 TATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATATGATAAATCACCATTTAAAATGG
* * * * * *
16470801 TAAA---CGA--TGA-TTTTGCTTTTGTTTTTTT-ATTTATAAGAGGATGGAAAAATTCTAACAG
195 TAAATGGTGATTTCATTTTTGCTTTT-TTTTTTTGAATTATAAGAGGAAGGCAAAACTCTAACAG
* * *
16470859 CAATGTGTCTAGTGCTAAATCA-CATTTAAAATAATATAACTTTAAAATTATTTATTAAAATAAC
259 CAATGAGTCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAATTATTTATTAAAATAGC
* * *
16470923 ATGAAATGAATAGTACTAATGAGATCTGCTA
324 ATGAAATGAACAGTACTAATGGGATCTACTA
* * *
16470954 AATCACCCTTTAAAATGGTAAACGATGATTTCATTTTTTTCTTTTTCTTTTTAATTATAAGAGGA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCA-TTTTTGCTTTTT-TTTTTAATTATAAGAGGA
* *
16471019 AGGCAAAACTCTAACAGCAATGCGGCTAATGCTAAATCACCATTTGAAATAGTATAACTTCAAAA
64 AGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAA
* *
16471084 TTATTTATTAAAATAGTATGAAATGAATAGTACTAATGGGATATGCA-AAATCACCATTTAAAAT
129 TTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATATG-ATAAATCACCATTTAAAAT
* ** * * *
16471148 GGTAAACGGTGATTTTGTTTTTGCTTCTTTCTTTTTTTAATTATAAGAGGAGGGTAAAACTCTAA
193 GGTAAATGGTGATTTCATTTTTGCTT-TTT-TTTTTTGAATTATAAGAGGAAGGCAAAACTCTAA
* *
16471213 CAACAATGAGGCTAGTGCTAAATCACCATTT-AAATAATATAACTTCAAAATTATTTATTAAAAT
256 CAGCAATGAGTCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAATTATTTATTAAAAT
16471277 AGCATGAA
321 AGCATGAA
16471285 TCACCCTTTA
Statistics
Matches: 1230, Mismatches: 123, Indels: 79
0.86 0.09 0.06
Matches are distributed among these distances:
341 90 0.07
342 47 0.04
343 7 0.01
345 1 0.00
346 8 0.01
347 2 0.00
348 4 0.00
349 148 0.12
352 143 0.12
353 10 0.01
354 3 0.00
355 10 0.01
356 23 0.02
357 291 0.24
358 98 0.08
359 85 0.07
360 65 0.05
361 1 0.00
362 140 0.11
363 9 0.01
364 43 0.03
365 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (354 bp):
AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTTTTTTAATTATAAGAGGAAG
GCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAATT
ATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATATGATAAATCACCATTTAAAATGGT
AAATGGTGATTTCATTTTTGCTTTTTTTTTTTGAATTATAAGAGGAAGGCAAAACTCTAACAGCA
ATGAGTCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAATTATTTATTAAAATAGCAT
GAAATGAACAGTACTAATGGGATCTACTA
Found at i:16470414 original size:177 final size:177
Alignment explanation
Indices: 16469532--16471284 Score: 2248
Period size: 178 Copynumber: 9.9 Consensus size: 177
16469522 TAATGTGTCT
* * *
16469532 AATCACCATTTAAAATGGTAAACAGTGATTTCGTTTCTGCTTCTTCTTTTTATGAATTATAAGAG
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTT-TT-TTTTT-TGAATTATAAGAG
* * * * * *
16469597 GAGGGCAAAACTCTTATAGCAATGCGACTAGTGCTAAATCACTATTTGAAATAATATAACTTCAA
63 GAAGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAA
* * *
16469662 AATTATTTATTAAAATAGCATGAAATGAACTGTACCAATGGGATATGCTA
128 AATTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
* *
16469712 AATCACCATTTAAAATGGTAAAAGGTGATTTCGTTTTTGCTTTTTTTTTGTTTGTTTGAATTATA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGC-----TTTT-TTT-TTTGAATTATA
* * * * * *
16469777 AGAAGAATGCAAAACTCTAACAGTAATGCAGTTAGTGCTAAATCACCATTTAAAATAGTATAACT
59 AGAGGAAGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACT
** *
16469842 TCAAAATTATTTATTAAAATAGCATGGGATGAACCA-TACTAATGGGTTCTGCTA
124 TCAAAATTATTTATTAAAATAGCATGAAATGAA-CAGTACTAATGGGATCTGCTA
* * *
16469896 AATCACCATTTAAAATGGTAAACGGTGATTTCGTTTTTTCTTTTTTCTTTTTAATTATAAGAGGA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTT-TTTTGAATTATAAGAGGA
* * * *
16469961 AGGCAAAACTCTAACAACAATACGGCTAGTGCTAAATCACCATTAAAAATAGTATAACTTCAAAA
65 AGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAA
* * * *
16470026 TTATTTATTAAAGTAGCATGAAATGAACAATACTAATGGGATATGATA
130 TTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
* * *
16470074 AATTATCATTTAAAATGGTAAATGGTGATTTCACTTTTTGCTTTTTTTTTTTGAATTATAAGAGG
1 AATCACCATTTAAAATGGTAAACGGTGATTTCA-TTTTTGC-TTTTTTTTTTGAATTATAAGAGG
* * * ** * *
16470139 AGGGCAAAACTTTAACAACAATTTGTCTAGTGCTAAATCACCATTTAAAATAAATATAAATTCAA
64 AAGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAAT-AATATAACTTCAA
* *
16470204 AATTATTTATTAAAATACCATGAAATGAACAGTACTAATGGGATCTACTA
128 AATTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
*
16470254 AATCACCTTTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTTTTTTGAATTATAAGAGGAA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTTTTTTGAATTATAAGAGGAA
* *
16470319 GGCAAAACTCTTACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTTCAAAAT
66 GGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAAT
** *
16470384 TATTTATTAAAATAGTGTGAAATGAACAGTACTAATGGGATCTACTA
131 TATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
* * * *
16470431 AATCACCCTTTGAAATGGTAAATGGTGATTTCATTTTTGCTTTTTTTTTTTTTTTGCATTATAAG
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGC-----TTTTTTTTTTGAATTATAAG
* *
16470496 AGGAAGGAAAAACTCCT-ACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAGTATAACTT
61 AGGAAGGCAAAACT-CTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTT
* *
16470560 CAAAATTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGGTCTACTA
125 CAAAATTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
* * * *
16470613 AATCACCCTTTAAAATGTTAAAC----A-ATGA-TTTTG-TTTTTGTTTTT-AATTATAAGAGGA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTT-TTTTTGAATTATAAGAGGA
* *
16470670 AGGCAAAACTCTAATAGCAATGCGCCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAA
65 AGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAA
* *
16470735 TTATTTATTAAAGTAGCATGAAATGAACAGTACTAATGAGATCTGCTA
130 TTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
* * *
16470783 AATCACCATTTAAAATGGTAAAC---GA--TGA-TTTTGCTTTTGTTTTTTTATTTATAAGAGGA
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTT-TTTTTTGAATTATAAGAGGA
* * * * * *
16470842 TGGAAAAATTCTAACAGCAATGTGTCTAGTGCTAAATCA-CATTTAAAATAATATAACTTTAAAA
65 AGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAA
* * *
16470906 TTATTTATTAAAATAACATGAAATGAATAGTACTAATGAGATCTGCTA
130 TTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
* * *
16470954 AATCACCCTTTAAAATGGTAAACGATGATTTCATTTTTTTCTTTTTCTTTTT-AATTATAAGAGG
1 AATCACCATTTAAAATGGTAAACGGTGATTTCA-TTTTTGCTTTTT-TTTTTGAATTATAAGAGG
* * *
16471018 AAGGCAAAACTCTAACAGCAATGCGGCTAATGCTAAATCACCATTTGAAATAGTATAACTTCAAA
64 AAGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAA
* * * *
16471083 ATTATTTATTAAAATAGTATGAAATGAATAGTACTAATGGGATATGCAA
129 ATTATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
** *
16471132 AATCACCATTTAAAATGGTAAACGGTGATTTTGTTTTTGCTTCTTTCTTTTTTTAATTATAAGAG
1 AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGC-T-TTT-TTTTTTGAATTATAAGAG
* * * *
16471197 GAGGGTAAAACTCTAACAACAATGAGGCTAGTGCTAAATCACCATTT-AAATAATATAACTTCAA
63 GAAGGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAA
16471261 AATTATTTATTAAAATAGCATGAA
128 AATTATTTATTAAAATAGCATGAA
16471285 TCACCCTTTA
Statistics
Matches: 1396, Mismatches: 140, Indels: 75
0.87 0.09 0.05
Matches are distributed among these distances:
169 2 0.00
170 148 0.11
171 106 0.08
172 46 0.03
174 2 0.00
176 7 0.01
177 151 0.11
178 320 0.23
179 126 0.09
180 181 0.13
182 149 0.11
183 2 0.00
184 151 0.11
185 5 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (177 bp):
AATCACCATTTAAAATGGTAAACGGTGATTTCATTTTTGCTTTTTTTTTTGAATTATAAGAGGAA
GGCAAAACTCTAACAGCAATGCGGCTAGTGCTAAATCACCATTTAAAATAATATAACTTCAAAAT
TATTTATTAAAATAGCATGAAATGAACAGTACTAATGGGATCTGCTA
Found at i:16471466 original size:96 final size:99
Alignment explanation
Indices: 16471283--16471476 Score: 306
Period size: 96 Copynumber: 2.0 Consensus size: 99
16471273 AAATAGCATG
*
16471283 AATCACCCTTTAAAATGGGTAAACGGTGATTTCGTTTTTGCTTCTTTTTTTTGAATTATAAGAGG
1 AATCACCATTTAAAATGGGTAAACGGTGATTTCGTTTTTGCTTC-TTTTTTTGAATTATAAGAGG
* *
16471348 AAGGCAAAACTCTAATAGTAATGC-AGCTAGTGCTA
65 AAGGCAAAACTCTAACAATAATGCAAG-TAGTGCTA
16471383 AATCACCATTTAAAAT-GGTAAACGGTGATTTCGTTTTTGCTTC-TTTTTT-AATTATAAGAGGA
1 AATCACCATTTAAAATGGGTAAACGGTGATTTCGTTTTTGCTTCTTTTTTTGAATTATAAGAGGA
*
16471445 AGGCAAAAGTCTAACAATAATGCAAGTAGTGC
66 AGGCAAAACTCTAACAATAATGCAAGTAGTGC
16471477 AATTTAAACC
Statistics
Matches: 89, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
96 39 0.44
97 8 0.09
99 27 0.30
100 15 0.17
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (99 bp):
AATCACCATTTAAAATGGGTAAACGGTGATTTCGTTTTTGCTTCTTTTTTTGAATTATAAGAGGA
AGGCAAAACTCTAACAATAATGCAAGTAGTGCTA
Found at i:16472765 original size:17 final size:18
Alignment explanation
Indices: 16472733--16472766 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16472723 TAATTTTTAA
16472733 TTGTTCATTTTCATTTTG
1 TTGTTCATTTTCATTTTG
*
16472751 TTGTT-ATTTTTATTTT
1 TTGTTCATTTTCATTTT
16472767 ATTTTTATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (18 bp):
TTGTTCATTTTCATTTTG
Found at i:16472774 original size:17 final size:17
Alignment explanation
Indices: 16472727--16472774 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
16472717 ATGTTTTAAT
16472727 TTTTAATTGTTCATTTTCA
1 TTTT-ATTGTT-ATTTTCA
* *
16472746 TTTTGTTGTTATTTTTA
1 TTTTATTGTTATTTTCA
*
16472763 TTTTATTTTTAT
1 TTTTATTGTTAT
16472775 GCTATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 16 0.64
18 5 0.20
19 4 0.16
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTATTGTTATTTTCA
Found at i:16473006 original size:18 final size:19
Alignment explanation
Indices: 16472979--16473030 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
16472969 GTATATTCTA
*
16472979 TGTAAGTTATATATTATTT
1 TGTAATTTATATATTATTT
* *
16472998 TG-ACTTTAT-TTTCTATTT
1 TGTAATTTATATAT-TATTT
16473016 TGTAATTTATATATT
1 TGTAATTTATATATT
16473031 TTATGTTCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
17 2 0.08
18 12 0.48
19 9 0.36
20 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (19 bp):
TGTAATTTATATATTATTT
Found at i:16473519 original size:21 final size:21
Alignment explanation
Indices: 16473495--16473534 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16473485 CAAAATAACG
**
16473495 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTAACTTTTAACTTGA
16473516 TAGTTTTAACTTTTAACTT
1 TAGTTTTAACTTTTAACTT
16473535 TAGAAAAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.10, T:0.55
Consensus pattern (21 bp):
TAGTTTTAACTTTTAACTTGA
Found at i:16473919 original size:18 final size:19
Alignment explanation
Indices: 16473898--16473933 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16473888 TTTTAAAAAA
16473898 TATAAAT-TTTAGAATTTC
1 TATAAATATTTAGAATTTC
*
16473916 TATAAATATTTTGAATTT
1 TATAAATATTTAGAATTT
16473934 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (19 bp):
TATAAATATTTAGAATTTC
Found at i:16473933 original size:19 final size:18
Alignment explanation
Indices: 16473898--16473946 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
16473888 TTTTAAAAAA
*
16473898 TATAAAT-TTTAGAATTT
1 TATAAATATTTTGAATTT
16473915 CTATAAATATTTTGAATTT
1 -TATAAATATTTTGAATTT
*
16473934 TAAAAATTATTTT
1 TATAAA-TATTTT
16473947 CAAAAGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:16473940 original size:18 final size:21
Alignment explanation
Indices: 16473903--16473946 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
16473893 AAAAATATAA
*
16473903 ATTTTAGAATTTCTATAAA-T
1 ATTTTAGAATTTCTAAAAATT
16473923 ATTTT-GAATTT-TAAAAATT
1 ATTTTAGAATTTCTAAAAATT
16473942 ATTTT
1 ATTTT
16473947 CAAAAGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTTTAGAATTTCTAAAAATT
Found at i:16475183 original size:43 final size:43
Alignment explanation
Indices: 16475126--16475482 Score: 430
Period size: 43 Copynumber: 8.3 Consensus size: 43
16475116 TTTTAGAAAT
* *
16475126 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
**
16475169 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * * *
16475212 AAACGCCGCTAAATACCATGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
*
16475255 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * *
16475298 AAACGCCACTAAATACCATGACCATTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * *
16475341 AAACGCCGCTATAA-ACCATGACCATTAGTGACGCTTTT-CCAA
1 AAACGCCGCTA-AAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* ** * * * **
16475383 CAAACGCCACTATTGACCATGACCTTTAGTGGCACTGTTCCCTC
1 -AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * * * *
16475427 AAACGCCGCCATAGACTATGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
16475470 AAACGCCGCTAAA
1 AAACGCCGCTAAA
16475483 AACATAATCT
Statistics
Matches: 272, Mismatches: 38, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
42 4 0.01
43 264 0.97
44 4 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
Found at i:16480244 original size:34 final size:34
Alignment explanation
Indices: 16480202--16480269 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
16480192 TGCCCGTAAA
16480202 AAAATTATTTTATTTGGAATAAAACGACACTGTT
1 AAAATTATTTTATTTGGAATAAAACGACACTGTT
16480236 AAAATTATTTTATTTGGAATAAAACGACACTGTT
1 AAAATTATTTTATTTGGAATAAAACGACACTGTT
16480270 TTATTATGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (34 bp):
AAAATTATTTTATTTGGAATAAAACGACACTGTT
Found at i:16481378 original size:29 final size:29
Alignment explanation
Indices: 16481335--16481390 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
16481325 CCGAATCTCT
* *
16481335 AAACCCTAAATCACTAACTCCC-AAACCCC
1 AAACCCCAAACCACTAAC-CCCTAAACCCC
16481364 AAACCCCAAACCACTAACCCCTAAACC
1 AAACCCCAAACCACTAACCCCTAAACC
16481391 TTATTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.43, C:0.46, G:0.00, T:0.11
Consensus pattern (29 bp):
AAACCCCAAACCACTAACCCCTAAACCCC
Found at i:16481470 original size:89 final size:89
Alignment explanation
Indices: 16481332--16481534 Score: 280
Period size: 89 Copynumber: 2.2 Consensus size: 89
16481322 ACCCCGAATC
* * *
16481332 TCTAAACCCTAAATCACTAACTCCCAAACCCCAAACCCCAAACCACTAACCCCTAAACCTTATTT
1 TCTAAACCCTAAA-CCCTAA--CCC-GACCCCAAACCCCAAACCACTAACCCCTAAACATTATTT
16481397 AATATATAAATTAAAAAACACTAATTAA
62 AATATATAAATTAAAAAACACTAATTAA
* * * * *
16481425 TTTAAATCCTAAACCCTAACCCGACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATA
1 TCTAAACCCTAAACCCTAACCCGACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATA
*
16481490 TATAAATTAAAATACACTAATTAA
66 TATAAATTAAAAAACACTAATTAA
*
16481514 TCTAAACCCTAAACCTTAACC
1 TCTAAACCCTAAACCCTAACC
16481535 TAACACCGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
89 79 0.81
90 3 0.03
92 5 0.05
93 11 0.11
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (89 bp):
TCTAAACCCTAAACCCTAACCCGACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATA
TATAAATTAAAAAACACTAATTAA
Found at i:16481575 original size:21 final size:20
Alignment explanation
Indices: 16481551--16481608 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
16481541 CGAATCCATA
*
16481551 AACCCTAAATCCTTAACTCTT
1 AACCCTAAA-CCTTAACCCTT
* *
16481572 AACCTCTAACCCCTAACCCTT
1 AACC-CTAAACCTTAACCCTT
16481593 AACCCATAAACCTTAA
1 AACCC-TAAACCTTAA
16481609 ATCACAACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 25 0.83
22 4 0.13
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (20 bp):
AACCCTAAACCTTAACCCTT
Found at i:16481645 original size:14 final size:15
Alignment explanation
Indices: 16481628--16481660 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
16481618 CTTAAATCAG
16481628 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
16481642 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
16481657 AATC
1 AATC
16481661 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:16482119 original size:41 final size:41
Alignment explanation
Indices: 16482060--16482177 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 41
16482050 AAATGTTTTT
*
16482060 GCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* ** ** * *
16482101 GCGGCGCTTATTGGAAAACGCCGCTAAAGATCTGAGCTTTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
16482142 GCGGCGCTTTTTTTAAAAACGACGCTAAAGCCCCGA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGCCCCGA
16482178 AAGGTAGAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
41 40 0.66
42 21 0.34
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:16482278 original size:39 final size:39
Alignment explanation
Indices: 16482235--16482346 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 39
16482225 TCAAAAAACA
*
16482235 CCGCTAATGCTC-ATTTTTAACGGCGCTTTTTTGAAAGCG
1 CCGCTAATGCTCAATTTTTAGCGGCG-TTTTTTGAAAGCG
* * * * * *
16482274 CCGCTAATGCTCGATCTTTAGTGGCATTTTACCT-AATGCG
1 CCGCTAATGCTCAATTTTTAGCGGCGTTTT--TTGAAAGCG
16482314 CCGCTAATGCTCAATTTTTAGCGGCGTTTTTTG
1 CCGCTAATGCTCAATTTTTAGCGGCGTTTTTTG
16482347 TACAAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
38 1 0.02
39 16 0.28
40 40 0.69
41 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (39 bp):
CCGCTAATGCTCAATTTTTAGCGGCGTTTTTTGAAAGCG
Found at i:16487565 original size:26 final size:26
Alignment explanation
Indices: 16487536--16487690 Score: 145
Period size: 26 Copynumber: 6.0 Consensus size: 26
16487526 CTTTTGTGGC
*
16487536 ATTCTATATGATAGCCTTTATGGTGT
1 ATTCTGTATGATAGCCTTTATGGTGT
* * **
16487562 ATTCTGTATGATAACCTTTTTGGCAT
1 ATTCTGTATGATAGCCTTTATGGTGT
* *
16487588 ATT-TGCATGATAGACTTTATGGTGT
1 ATTCTGTATGATAGCCTTTATGGTGT
*
16487613 ATTTTGTATGATAGCCTTTATGGCT-T
1 ATTCTGTATGATAGCCTTTATGG-TGT
* * * *
16487639 ATTTTGTATGGTAGCCTTTGTAGTGT
1 ATTCTGTATGATAGCCTTTATGGTGT
* * *
16487665 ATTCAGTATG-TTGCCTTTGTGGTGT
1 ATTCTGTATGATAGCCTTTATGGTGT
16487690 A
1 A
16487691 ACCTATTTGA
Statistics
Matches: 106, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
25 34 0.32
26 71 0.67
27 1 0.01
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (26 bp):
ATTCTGTATGATAGCCTTTATGGTGT
Found at i:16487606 original size:51 final size:52
Alignment explanation
Indices: 16487543--16487674 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 52
16487533 GGCATTCTAT
*
16487543 ATGATAGCCTTTATGGTGTATTCTGTATGATAACCTTTTTGGCATA-TTTGC
1 ATGATAGCCTTTATGGTGTATTCTGTATGATAACCTTTATGGCATATTTTGC
* * * * *
16487594 ATGATAGACTTTATGGTGTATTTTGTATGATAGCCTTTATGGCTTATTTTGT
1 ATGATAGCCTTTATGGTGTATTCTGTATGATAACCTTTATGGCATATTTTGC
* * * *
16487646 ATGGTAGCCTTTGTAGTGTATTCAGTATG
1 ATGATAGCCTTTATGGTGTATTCTGTATG
16487675 TTGCCTTTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 41 0.60
52 27 0.40
ACGTcount: A:0.21, C:0.11, G:0.22, T:0.46
Consensus pattern (52 bp):
ATGATAGCCTTTATGGTGTATTCTGTATGATAACCTTTATGGCATATTTTGC
Found at i:16494295 original size:10 final size:11
Alignment explanation
Indices: 16494280--16494369 Score: 53
Period size: 11 Copynumber: 8.0 Consensus size: 11
16494270 TACAGTGCAT
16494280 AATAAAAT-AA
1 AATAAAATAAA
16494290 AATAAAATAAA
1 AATAAAATAAA
*
16494301 AATAAAAACAAA
1 AAT-AAAATAAA
* *
16494313 AACAAAAACAAA
1 AA-TAAAATAAA
*
16494325 AACAAAA-ACAA
1 AATAAAATA-AA
16494336 AA-AAAATATAA
1 AATAAAATA-AA
*
16494347 AA-AATATAAA
1 AATAAAATAAA
16494357 ATATAAAACTAAA
1 A-ATAAAA-TAAA
16494370 TGAAACCACT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
10 16 0.24
11 24 0.36
12 22 0.33
13 4 0.06
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:16494304 original size:6 final size:6
Alignment explanation
Indices: 16494283--16494369 Score: 63
Period size: 6 Copynumber: 14.3 Consensus size: 6
16494273 AGTGCATAAT
* * * *
16494283 AAAAT- AAAAT- AAAATA AAAATA AAAACA AAAACA AAAACA AAAACA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
16494329 AAAACA AAAA-A AATATAA AAAATA TAAAATA TAAAACTA AA
1 AAAATA AAAATA AAAAT-A AAAATA -AAAATA -AAAA-TA AA
16494370 TGAAACCACT
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
5 14 0.19
6 40 0.54
7 18 0.24
8 2 0.03
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:16494313 original size:12 final size:12
Alignment explanation
Indices: 16494293--16494338 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
16494283 AAAATAAAAT
* *
16494293 AAAATAAAAATA
1 AAAACAAAAACA
16494305 AAAACAAAAACA
1 AAAACAAAAACA
16494317 AAAACAAAAACA
1 AAAACAAAAACA
16494329 AAAACAAAAA
1 AAAACAAAAA
16494339 AAATATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.85, C:0.11, G:0.00, T:0.04
Consensus pattern (12 bp):
AAAACAAAAACA
Found at i:16494350 original size:18 final size:18
Alignment explanation
Indices: 16494293--16494338 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
16494283 AAAATAAAAT
* *
16494293 AAAATAAAAATAAAAACA
1 AAAACAAAAACAAAAACA
16494311 AAAACAAAAACAAAAACA
1 AAAACAAAAACAAAAACA
16494329 AAAACAAAAA
1 AAAACAAAAA
16494339 AAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.85, C:0.11, G:0.00, T:0.04
Consensus pattern (18 bp):
AAAACAAAAACAAAAACA
Found at i:16495678 original size:22 final size:21
Alignment explanation
Indices: 16495651--16495718 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
16495641 AGGCCACTTT
16495651 TTTTTTTCAAATATTTTCATTC
1 TTTTTTTCAAATATTTTC-TTC
** *
16495673 TTTTTTTCCTATTTTTTCTT-
1 TTTTTTTCAAATATTTTCTTC
*
16495693 TTTTTTTCAAA-ATTTTGTTC
1 TTTTTTTCAAATATTTTCTTC
16495713 TTTTTT
1 TTTTTT
16495719 AAAATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.16
20 15 0.39
21 2 0.05
22 15 0.39
ACGTcount: A:0.15, C:0.12, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTTTTCAAATATTTTCTTC
Found at i:16495698 original size:20 final size:21
Alignment explanation
Indices: 16495649--16495708 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
16495639 GCAGGCCACT
16495649 TTTTTTTTTCAAATATTTTCA
1 TTTTTTTTTCAAATATTTTCA
** *
16495670 TTCTTTTTTTCCTATTTTTTC-
1 TT-TTTTTTTCAAATATTTTCA
16495691 TTTTTTTTTCAAA-ATTTT
1 TTTTTTTTTCAAATATTTT
16495709 GTTCTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.12
20 9 0.28
21 4 0.12
22 15 0.47
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTTTTCAAATATTTTCA
Found at i:16499614 original size:16 final size:17
Alignment explanation
Indices: 16499593--16499634 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
16499583 GAAAAGAAGC
*
16499593 AAAAAAAAG-TTCGAGT
1 AAAAAAAAGTTTCGAAT
16499609 AAAAAAAAGTTTCGAAT
1 AAAAAAAAGTTTCGAAT
16499626 ATAAAAAAA
1 A-AAAAAAA
16499635 AGTGTGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 7 0.30
18 7 0.30
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (17 bp):
AAAAAAAAGTTTCGAAT
Found at i:16499615 original size:17 final size:17
Alignment explanation
Indices: 16499593--16499637 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
16499583 GAAAAGAAGC
*
16499593 AAAAAAAAGTTCG-AGT
1 AAAAAAAAGTTCGAATT
16499609 AAAAAAAAGTTTCGAATAT
1 AAAAAAAAG-TTCGAAT-T
16499628 AAAAAAAAGT
1 AAAAAAAAGT
16499638 GTGCAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 2 0.08
19 10 0.40
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (17 bp):
AAAAAAAAGTTCGAATT
Found at i:16499648 original size:19 final size:19
Alignment explanation
Indices: 16499608--16499652 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16499598 AAAGTTCGAG
* *
16499608 TAAAAAAAAGTTTCGAATA
1 TAAAAAAAAGTTGCGAAAA
16499627 TAAAAAAAAGTGTGC-AAAA
1 TAAAAAAAAGT-TGCGAAAA
16499646 TAAAAAA
1 TAAAAAA
16499653 GTGAAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.20
Consensus pattern (19 bp):
TAAAAAAAAGTTGCGAAAA
Found at i:16500770 original size:18 final size:17
Alignment explanation
Indices: 16500747--16500799 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
16500737 AAGACACGAG
16500747 TGAAAAAGAAAGAGGGCT
1 TGAAAAAGAAAGA-GGCT
16500765 TGAAAAAGAAACGA-G--
1 TGAAAAAGAAA-GAGGCT
16500780 TGAAAAAGAAAGAGAGCT
1 TGAAAAAGAAAGAG-GCT
16500798 TG
1 TG
16500800 CATGAGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.07
15 11 0.37
16 1 0.03
17 1 0.03
18 13 0.43
19 2 0.07
ACGTcount: A:0.53, C:0.06, G:0.30, T:0.11
Consensus pattern (17 bp):
TGAAAAAGAAAGAGGCT
Found at i:16500790 original size:15 final size:15
Alignment explanation
Indices: 16500732--16500790 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 15
16500722 GTGTTGTTGT
*
16500732 TGAAAAAGACACGAG
1 TGAAAAAGAAACGAG
16500747 TGAAAAAGAAA-GAGGG
1 TGAAAAAGAAACGA--G
16500763 CTTGAAAAAGAAACGAG
1 --TGAAAAAGAAACGAG
16500780 TGAAAAAGAAA
1 TGAAAAAGAAA
16500791 GAGAGCTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.05
15 21 0.55
16 1 0.03
17 1 0.03
18 11 0.29
19 2 0.05
ACGTcount: A:0.58, C:0.07, G:0.27, T:0.08
Consensus pattern (15 bp):
TGAAAAAGAAACGAG
Found at i:16500809 original size:33 final size:33
Alignment explanation
Indices: 16500731--16500799 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
16500721 AGTGTTGTTG
* *
16500731 TTGAAAAAGACACGAGTGAAAAAGAAAGAGGGC
1 TTGAAAAAGAAACGAGTGAAAAAGAAAGAGAGC
16500764 TTGAAAAAGAAACGAGTGAAAAAGAAAGAGAGC
1 TTGAAAAAGAAACGAGTGAAAAAGAAAGAGAGC
16500797 TTG
1 TTG
16500800 CATGAGAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.07, G:0.29, T:0.12
Consensus pattern (33 bp):
TTGAAAAAGAAACGAGTGAAAAAGAAAGAGAGC
Found at i:16500815 original size:33 final size:33
Alignment explanation
Indices: 16500731--16500816 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
16500721 AGTGTTGTTG
* * *
16500731 TTGAAAAAGACACGAGTGAAAAAGAAAGAGGGC
1 TTGAAAAAGAAACAAGTGAAAAAGAAAGAGAGC
*
16500764 TTGAAAAAGAAACGAGTGAAAAAGAAAGAGAGC
1 TTGAAAAAGAAACAAGTGAAAAAGAAAGAGAGC
* **
16500797 TTGCATGAGAAACAAGTGAA
1 TTGAAAAAGAAACAAGTGAA
16500817 GAGAGTAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (33 bp):
TTGAAAAAGAAACAAGTGAAAAAGAAAGAGAGC
Found at i:16506707 original size:27 final size:28
Alignment explanation
Indices: 16506658--16506712 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
16506648 ATGTATGGAT
*
16506658 AACATGAAGTCTTATGGTCAAAGTATGA
1 AACATGAAGTCTTATGGTCAAAGGATGA
*
16506686 AACATGAA-TCTTGA-GGTTAAAGGATGA
1 AACATGAAGTCTT-ATGGTCAAAGGATGA
16506713 TTGTGTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (28 bp):
AACATGAAGTCTTATGGTCAAAGGATGA
Found at i:16506999 original size:53 final size:52
Alignment explanation
Indices: 16506916--16507066 Score: 189
Period size: 53 Copynumber: 2.9 Consensus size: 52
16506906 GGCGCTAAAG
* * * * *
16506916 GACCATA-CCTGTAAGACCGTAACTGATGGGTTGTGGGATCATATGAAA-AGTA
1 GACCATATCGTGTAAGACTGTAACTGGTGGGTTATGGCATCATATGAAATA--A
*
16506968 GACCATATCGTGTAAGACTGTAATTGGTGGGTTATGGCATCATATCGAAATAA
1 GACCATATCGTGTAAGACTGTAACTGGTGGGTTATGGCATCATAT-GAAATAA
* *
16507021 GACCATATCGTGTAAGACTATAACTGGTGGGTTATGGTATCATATG
1 GACCATATCGTGTAAGACTGTAACTGGTGGGTTATGGCATCATATG
16507067 GGAAAAAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
52 8 0.09
53 74 0.85
54 4 0.05
55 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (52 bp):
GACCATATCGTGTAAGACTGTAACTGGTGGGTTATGGCATCATATGAAATAA
Found at i:16507390 original size:57 final size:57
Alignment explanation
Indices: 16507281--16507391 Score: 127
Period size: 57 Copynumber: 1.9 Consensus size: 57
16507271 AAGAGGACAA
* * ** * * *
16507281 CCTTTGTGGCAAAACTCTAGAAAGGTAAGTCTTTGAGTTGAATCTGTTAAAGGATAG
1 CCTTTGTGGCAAAACCCTAGAAAGGTAAGCCTTTGAGTCAAACCTCTCAAAGGATAG
16507338 CCTTTGTGGCAAAACCCTAGAAAGGTAAGCCCTTATG-G-CAAACCTCTCAAAGGA
1 CCTTTGTGGCAAAACCCTAGAAAGGTAAG-CCTT-TGAGTCAAACCTCTCAAAGGA
16507392 ACTCCTGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
57 39 0.87
58 4 0.09
59 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (57 bp):
CCTTTGTGGCAAAACCCTAGAAAGGTAAGCCTTTGAGTCAAACCTCTCAAAGGATAG
Found at i:16507488 original size:28 final size:28
Alignment explanation
Indices: 16507281--16507506 Score: 118
Period size: 28 Copynumber: 7.9 Consensus size: 28
16507271 AAGAGGACAA
* *
16507281 CCTTTGTGGCAAAACTCTAGAAAGGTAAG
1 CCTTTGTGGCAAATCTCT-GAAAGGAAAG
* * *** * * *
16507310 TCTTTGAGTTGAATCTGTTAAAGGATAG
1 CCTTTGTGGCAAATCTCTGAAAGGAAAG
* * *
16507338 CCTTTGTGGCAAAACCCTAGAAAGGTAAG
1 CCTTTGTGGCAAATCTCT-GAAAGGAAAG
* * * * **
16507367 CCCTTATGGCAAACCTCTCAAAGGAACT
1 CCTTTGTGGCAAATCTCTGAAAGGAAAG
* * *
16507395 CCTGTGTGGCAAATCGCTAAAAGGAAAAG
1 CCTTTGTGGCAAATCTCTGAAAGG-AAAG
* * *
16507424 CCTTTGTTGC-GATCTCTGTCAAAAGAAAG
1 CCTTTGTGGCAAATCTCTG--AAAGGAAAG
*
16507453 -CTTCTGTGGCAAA-CTCTAGAAAGGAAAT
1 CCTT-TGTGGCAAATCTCT-GAAAGGAAAG
16507481 CCTTTGTGG-AAATCTCTGTAAAGGAA
1 CCTTTGTGGCAAATCTCTG-AAAGGAA
16507507 GCTTTCGTGG
Statistics
Matches: 140, Mismatches: 47, Indels: 21
0.67 0.23 0.10
Matches are distributed among these distances:
27 4 0.03
28 72 0.51
29 58 0.41
30 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (28 bp):
CCTTTGTGGCAAATCTCTGAAAGGAAAG
Found at i:16519200 original size:25 final size:25
Alignment explanation
Indices: 16519146--16519200 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
16519136 AACTAACATC
* * *
16519146 ACAAACCACAAATTATCATCAATGT
1 ACAAAACACAAATAATCAACAATGT
16519171 A-AAAACACAAAATAATCAACAAT-T
1 ACAAAACAC-AAATAATCAACAATGT
16519195 ACAAAA
1 ACAAAA
16519201 ATTCAAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.60, C:0.20, G:0.02, T:0.18
Consensus pattern (25 bp):
ACAAAACACAAATAATCAACAATGT
Found at i:16519645 original size:13 final size:13
Alignment explanation
Indices: 16519627--16519651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16519617 TCAAATGATC
16519627 AAATTTTCACACG
1 AAATTTTCACACG
16519640 AAATTTTCACAC
1 AAATTTTCACAC
16519652 ATATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:16525917 original size:41 final size:41
Alignment explanation
Indices: 16525835--16525943 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 41
16525825 AACCTGATTC
* *
16525835 AATTCACCGGCAATT-AGCCTGCTAGACTTAAAGTCCAAATT
1 AATTCACCGGC-ATTAAGCCAGCTAGACATAAAGTCCAAATT
* * * **
16525876 ATTTCACCGACATTAAGCCAGCTGGACATAAAGTCTGAATT
1 AATTCACCGGCATTAAGCCAGCTAGACATAAAGTCCAAATT
* * *
16525917 AAATCACCGGCCTTAAGCCTGCTAGAC
1 AATTCACCGGCATTAAGCCAGCTAGAC
16525944 TTTAAGTTTG
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 3 0.06
41 51 0.94
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (41 bp):
AATTCACCGGCATTAAGCCAGCTAGACATAAAGTCCAAATT
Found at i:16527614 original size:13 final size:13
Alignment explanation
Indices: 16527596--16527620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16527586 TCAAACGATC
16527596 AAATTTTCACACG
1 AAATTTTCACACG
16527609 AAATTTTCACAC
1 AAATTTTCACAC
16527621 ATATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:16528386 original size:27 final size:27
Alignment explanation
Indices: 16528351--16528523 Score: 185
Period size: 27 Copynumber: 6.4 Consensus size: 27
16528341 TGGAAGTCTT
16528351 TGGCAATCTAT-AATATAGAAGCCTTTG
1 TGGCAATCTATGAA-ATAGAAGCCTTTG
*
16528378 TGGCAATCTATGAAGTAGAAGCCTTTG
1 TGGCAATCTATGAAATAGAAGCCTTTG
*
16528405 TGGCAAT-TATGAAAT-GTAAGACTTTG
1 TGGCAATCTATGAAATAG-AAGCCTTTG
* * * *
16528431 TGACAATCTCTGAAATGGAAACCTTTG
1 TGGCAATCTATGAAATAGAAGCCTTTG
* *
16528458 TGGAAATCTATGATATTA-AAGCCTTTG
1 TGGCAATCTATGA-AATAGAAGCCTTTG
*
16528485 TGGAAATCTATGAAATTA-AAGCCTTTG
1 TGGCAATCTATGAAA-TAGAAGCCTTTG
*
16528512 TGGCGATCTATG
1 TGGCAATCTATG
16528524 GAAAGGAACA
Statistics
Matches: 124, Mismatches: 16, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
25 1 0.01
26 22 0.18
27 96 0.77
28 5 0.04
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (27 bp):
TGGCAATCTATGAAATAGAAGCCTTTG
Found at i:16528459 original size:80 final size:82
Alignment explanation
Indices: 16528372--16528543 Score: 219
Period size: 80 Copynumber: 2.1 Consensus size: 82
16528362 AATATAGAAG
*
16528372 CCTTTGTGGCAATCTATGA-AGTAGAAGCCTTTGTGGCAAT-TATGAAATGT-AAGACTTTGTGA
1 CCTTTGTGGCAATCTATGATAGTA-AAGCCTTTGTGGAAATCTATGAAAT-TAAAGACTTTGTGA
*
16528434 CAATCTCT-GAAATGGAA-A
64 CAATCTATGGAAA-GGAACA
* * * * *
16528452 CCTTTGTGGAAATCTATGATATTAAAGCCTTTGTGGAAATCTATGAAATTAAAGCCTTTGTGGCG
1 CCTTTGTGGCAATCTATGATAGTAAAGCCTTTGTGGAAATCTATGAAATTAAAGACTTTGTGACA
16528517 ATCTATGGAAAGGAACA
66 ATCTATGGAAAGGAACA
16528534 CCTTTGTGGC
1 CCTTTGTGGC
16528544 GCACTCTACA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
80 34 0.43
81 31 0.39
82 14 0.18
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (82 bp):
CCTTTGTGGCAATCTATGATAGTAAAGCCTTTGTGGAAATCTATGAAATTAAAGACTTTGTGACA
ATCTATGGAAAGGAACA
Found at i:16528640 original size:27 final size:27
Alignment explanation
Indices: 16528610--16528681 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
16528600 ACCTTGAATG
16528610 AGAAGAATGGTAAGTATGACCAACCCT
1 AGAAGAATGGTAAGTATGACCAACCCT
* * * * *
16528637 AGAAGAATGATATGTATGGCTAACTCT
1 AGAAGAATGGTAAGTATGACCAACCCT
*
16528664 -GAAGAATTGTAAGTATGA
1 AGAAGAATGGTAAGTATGA
16528682 TAAACCTCGA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (27 bp):
AGAAGAATGGTAAGTATGACCAACCCT
Found at i:16528698 original size:53 final size:53
Alignment explanation
Indices: 16528611--16528857 Score: 175
Period size: 53 Copynumber: 4.9 Consensus size: 53
16528601 CCTTGAATGA
* * *
16528611 GAAGAATGGTAAGTATGACCAACCCTAGAA-GAATGATATGTATGGCTAACTCT
1 GAAGAATTGTAAGTATGA-CAAACCTCGAAGGAATGATATGTATGGCTAACTCT
* * *
16528664 GAAGAATTGTAAGTATGATAAACCTCGAAGGAATGATATGTGTGGCGAACAT-T
1 GAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTATGGCTAAC-TCT
* * * * * *
16528717 GAAGGAATAGTACGTATGGCAAACTTTGAAGGAAT-AGTACGTATGGC-AAGCTCT
1 GAA-GAATTGTAAGTATGACAAACCTCGAAGGAATGA-TATGTATGGCTAA-CTCT
** * *
16528771 GAAGAA-ACT--GT-T------CCGC-AAGAAATG-TATGTATGGCTAACTCT
1 GAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTATGGCTAACTCT
* *
16528812 GAAGAATTGTAAGTGTGACAAACCTCGAAGGAATGATATGTGTGGC
1 GAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTATGGC
16528858 AAACATTAAA
Statistics
Matches: 149, Mismatches: 25, Indels: 40
0.70 0.12 0.19
Matches are distributed among these distances:
41 19 0.13
42 9 0.06
43 1 0.01
44 2 0.01
45 1 0.01
49 1 0.01
50 2 0.01
51 3 0.02
52 17 0.11
53 55 0.37
54 39 0.26
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (53 bp):
GAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTATGGCTAACTCT
Found at i:16528773 original size:27 final size:27
Alignment explanation
Indices: 16528650--16528774 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
16528640 AGAATGATAT
* * *
16528650 GTATGGCTAACTCTGAA-GAATTGTAA
1 GTATGGCAAACTCTGAAGGAATAGTAC
** *
16528676 GTATGATAAAC-CTCGAAGGAAT-GATAT
1 GTATGGCAAACTCT-GAAGGAATAG-TAC
* *
16528703 GTGTGGCGAACAT-TGAAGGAATAGTAC
1 GTATGGCAAAC-TCTGAAGGAATAGTAC
*
16528730 GTATGGCAAACTTTGAAGGAATAGTAC
1 GTATGGCAAACTCTGAAGGAATAGTAC
*
16528757 GTATGGCAAGCTCTGAAG
1 GTATGGCAAACTCTGAAG
16528775 AAACTGTTCC
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
25 2 0.03
26 13 0.16
27 62 0.78
28 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (27 bp):
GTATGGCAAACTCTGAAGGAATAGTAC
Found at i:16528884 original size:27 final size:27
Alignment explanation
Indices: 16528854--16528913 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
16528844 ATGATATGTG
16528854 TGGCAAACATTAAAGGAATAGTACGTA
1 TGGCAAACATTAAAGGAATAGTACGTA
* * *
16528881 TGGCGAACTTTGAAGGAATAGTACGTA
1 TGGCAAACATTAAAGGAATAGTACGTA
16528908 TGGCAA
1 TGGCAA
16528914 GCTCTGAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (27 bp):
TGGCAAACATTAAAGGAATAGTACGTA
Found at i:16528907 original size:148 final size:148
Alignment explanation
Indices: 16528642--16528943 Score: 532
Period size: 148 Copynumber: 2.0 Consensus size: 148
16528632 ACCCTAGAAG
*
16528642 AATGATATGTATGGCTAACTCTGAAGAATTGTAAGTATGATAAACCTCGAAGGAATGATATGTGT
1 AATG-TATGTATGGCTAACTCTGAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTGT
* *
16528707 GGCGAACATTGAAGGAATAGTACGTATGGCAAACTTTGAAGGAATAGTACGTATGGCAAGCTCTG
65 GGCAAACATTAAAGGAATAGTACGTATGGCAAACTTTGAAGGAATAGTACGTATGGCAAGCTCTG
*
16528772 AAGAAACTGTTCCGCAAGA
130 AAGAAAATGTTCCGCAAGA
*
16528791 AATGTATGTATGGCTAACTCTGAAGAATTGTAAGTGTGACAAACCTCGAAGGAATGATATGTGTG
1 AATGTATGTATGGCTAACTCTGAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTGTG
*
16528856 GCAAACATTAAAGGAATAGTACGTATGGCGAACTTTGAAGGAATAGTACGTATGGCAAGCTCTGA
66 GCAAACATTAAAGGAATAGTACGTATGGCAAACTTTGAAGGAATAGTACGTATGGCAAGCTCTGA
*
16528921 AGAAAATGTTCTGCAAGA
131 AGAAAATGTTCCGCAAGA
16528939 AATGT
1 AATGT
16528944 CGTGGCGTAT
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
148 142 0.97
149 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (148 bp):
AATGTATGTATGGCTAACTCTGAAGAATTGTAAGTATGACAAACCTCGAAGGAATGATATGTGTG
GCAAACATTAAAGGAATAGTACGTATGGCAAACTTTGAAGGAATAGTACGTATGGCAAGCTCTGA
AGAAAATGTTCCGCAAGA
Found at i:16528921 original size:27 final size:27
Alignment explanation
Indices: 16528866--16528922 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
16528856 GCAAACATTA
*
16528866 AAGGAATAGTACGTATGGCGAACTTTG
1 AAGGAATAGTACGTATGGCGAACTCTG
16528893 AAGGAATAGTACGTATGGC-AAGCTCTG
1 AAGGAATAGTACGTATGGCGAA-CTCTG
16528920 AAG
1 AAG
16528923 AAAATGTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (27 bp):
AAGGAATAGTACGTATGGCGAACTCTG
Found at i:16531024 original size:17 final size:16
Alignment explanation
Indices: 16531002--16531046 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
16530992 TAGAATCAGG
*
16531002 TTGAGAAAATTATTTAA
1 TTGAG-AAATTAATTAA
16531019 TTGAGAAATTAATTAA
1 TTGAGAAATTAATTAA
16531035 TT-A-AAATTAATT
1 TTGAGAAATTAATT
16531047 TATGATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 12 0.44
17 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
TTGAGAAATTAATTAA
Found at i:16546543 original size:21 final size:21
Alignment explanation
Indices: 16546517--16546556 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16546507 TCAAACAATG
*
16546517 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTGACTTTTAACTTGA
16546538 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
16546557 TAGATAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTGA
Found at i:16546981 original size:19 final size:20
Alignment explanation
Indices: 16546938--16547003 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
16546928 AAAAATGCAA
*
16546938 ATTTTAGAACTTTTATAAA-T
1 ATTTT-GAACTTTTAAAAATT
16546958 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAACTTTTAAAAATT
* *
16546977 ATTTTGAATTTTTTAAAATT
1 ATTTTGAACTTTTAAAAATT
16546997 ATTTTGA
1 ATTTTGA
16547004 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.19
19 12 0.29
20 22 0.52
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTTTGAACTTTTAAAAATT
Found at i:16547011 original size:21 final size:20
Alignment explanation
Indices: 16546948--16547009 Score: 85
Period size: 19 Copynumber: 3.2 Consensus size: 20
16546938 ATTTTAGAAC
16546948 TTTTATAAA-TATTTTGAA-T
1 TTTTA-AAATTATTTTGAATT
*
16546967 TTTAAAAATTATTTTGAATT
1 TTTTAAAATTATTTTGAATT
16546987 TTTTAAAATTATTTTG-ATT
1 TTTTAAAATTATTTTGAATT
16547006 TTTT
1 TTTT
16547010 TTTTTGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.08
19 20 0.51
20 16 0.41
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTAAAATTATTTTGAATT
Found at i:16547105 original size:9 final size:9
Alignment explanation
Indices: 16547091--16547139 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
16547081 TACTCATCTG
*
16547091 TTATTCAAA
1 TTATTCGAA
*
16547100 TTATTCGAG
1 TTATTCGAA
16547109 TTATTCGAA
1 TTATTCGAA
*
16547118 TTATTCGAG
1 TTATTCGAA
*
16547127 TTATTCAAA
1 TTATTCGAA
16547136 TTAT
1 TTAT
16547140 AAAAATTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:16547113 original size:18 final size:18
Alignment explanation
Indices: 16547090--16547139 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
16547080 ATACTCATCT
16547090 GTTATTCAAATTATTCGA
1 GTTATTCAAATTATTCGA
*
16547108 GTTATTCGAATTATTCGA
1 GTTATTCAAATTATTCGA
16547126 GTTATTCAAATTAT
1 GTTATTCAAATTAT
16547140 AAAAATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (18 bp):
GTTATTCAAATTATTCGA
Found at i:16552326 original size:2 final size:2
Alignment explanation
Indices: 16552321--16552345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16552311 AATATATACG
16552321 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
16552346 GAGAATGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16555272 original size:17 final size:18
Alignment explanation
Indices: 16555239--16555272 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16555229 TATTTAGACT
16555239 TTTATCCAACACTTATAG
1 TTTATCCAACACTTATAG
*
16555257 TTTATCTAAC-CTTATA
1 TTTATCCAACACTTATA
16555273 ACAACTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTATCCAACACTTATAG
Found at i:16560386 original size:17 final size:18
Alignment explanation
Indices: 16560364--16560407 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
16560354 TAATTTAATT
16560364 AATTAAATTA-ATTTCTC
1 AATTAAATTATATTTCTC
*
16560381 AATTAAATTATTTTTCTC
1 AATTAAATTATATTTCTC
*
16560399 AATCAAATT
1 AATTAAATT
16560408 CTAATTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAAATTATATTTCTC
Found at i:16565104 original size:100 final size:100
Alignment explanation
Indices: 16564931--16565131 Score: 357
Period size: 100 Copynumber: 2.0 Consensus size: 100
16564921 TTTTGATCTT
*
16564931 AAATGTGGCTAAATAGGAGACTTTATCTCTACGTACTCCTTTAGAAAATTGGATTGTCAACAATG
1 AAATGTGGCTAAATAGGAGACTTCATCTCTACGTACTCCTTTAGAAAATTGGATTGTCAACAATG
16564996 TTTTTCCCTCCATGTTTCTCTTCCTTGTCATTCTC
66 TTTTTCCCTCCATGTTTCTCTTCCTTGTCATTCTC
* * *
16565031 AAATGTGGCTAAATAGGAGACTTCATCTCTATGTATTCCTTTAGCAAATTGGATTGTCAACAATG
1 AAATGTGGCTAAATAGGAGACTTCATCTCTACGTACTCCTTTAGAAAATTGGATTGTCAACAATG
*
16565096 TTTTTCCCTCCATGTTTCTGTTCCTTGTCATTCTC
66 TTTTTCCCTCCATGTTTCTCTTCCTTGTCATTCTC
16565131 A
1 A
16565132 CCATGCATTG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (100 bp):
AAATGTGGCTAAATAGGAGACTTCATCTCTACGTACTCCTTTAGAAAATTGGATTGTCAACAATG
TTTTTCCCTCCATGTTTCTCTTCCTTGTCATTCTC
Found at i:16566813 original size:21 final size:22
Alignment explanation
Indices: 16566787--16566827 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16566777 ATGGGTAATC
16566787 TATGAC-ACAAGTCTCGAGACA
1 TATGACTACAAGTCTCGAGACA
* *
16566808 TATGACTATATGTCTCGAGA
1 TATGACTACAAGTCTCGAGA
16566828 TATCAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
TATGACTACAAGTCTCGAGACA
Found at i:16568510 original size:31 final size:31
Alignment explanation
Indices: 16568470--16568543 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
16568460 ACTGTTGTGC
* *
16568470 TACACTTTCATATTACATTATAAATCATGAAT
1 TACACTTTCATATGACACTATAAATCATG-AT
*
16568502 T-CACTTTCACATGACACTATAAATCATGAT
1 TACACTTTCATATGACACTATAAATCATGAT
*
16568532 TACTCTTTCATA
1 TACACTTTCATA
16568544 AAACACTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 3 0.08
31 32 0.89
32 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.39
Consensus pattern (31 bp):
TACACTTTCATATGACACTATAAATCATGAT
Found at i:16570584 original size:15 final size:15
Alignment explanation
Indices: 16570566--16570597 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16570556 CATTTTACTA
*
16570566 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
16570581 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
16570596 TT
1 TT
16570598 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:16571539 original size:28 final size:27
Alignment explanation
Indices: 16571499--16571591 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 27
16571489 ACTGCACTAT
16571499 ACTGTTACTGTATTGGGCTAAGGTCCAC
1 ACTGTTACTGTATTGGGCTAAGG-CCAC
*
16571527 ACTGTTACTGTATTAGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGG-CCAC
* *
16571555 ACTATTACTGTATCGGGCTAAGGCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCAC
16571582 ACTG-TACTGT
1 ACTGTTACTGT
16571592 TACTGAATAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 6 0.10
27 7 0.12
28 46 0.78
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (27 bp):
ACTGTTACTGTATTGGGCTAAGGCCAC
Found at i:16572969 original size:37 final size:36
Alignment explanation
Indices: 16572915--16572992 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 36
16572905 TTATTCTAGA
*
16572915 ATTAATATTATTTTAATAGT-TTAATATTAAATTTAAT
1 ATTAATATTATCTTAATAGTATT-ATATT-AATTTAAT
*
16572952 -TTAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 ATTAATA-TTATCTTAATAGTATTATATTAATTTAAT
16572988 ATTAA
1 ATTAA
16572993 AGTGATTATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
36 14 0.39
37 20 0.56
38 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
ATTAATATTATCTTAATAGTATTATATTAATTTAAT
Found at i:16577312 original size:41 final size:41
Alignment explanation
Indices: 16577262--16577488 Score: 375
Period size: 41 Copynumber: 5.5 Consensus size: 41
16577252 GACTTTAAGT
*
16577262 CTAGCAGGCTAAGAGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
16577303 CTAGTAGGCTAAGAGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
16577344 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
16577385 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
16577426 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
16577467 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
16577489 ATATGTTAAA
Statistics
Matches: 176, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 1 0.01
41 175 0.99
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:16590556 original size:18 final size:18
Alignment explanation
Indices: 16590533--16590586 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
16590523 ATTTTAAAAA
16590533 TAATATTATTTAATAGTT
1 TAATATTATTTAATAGTT
*
16590551 TAATATTAAATTAA-A-TT
1 TAATATT-ATTTAATAGTT
16590568 TAATAATTATCTTAATAGT
1 TAAT-ATTAT-TTAATAGT
16590587 ATTTTAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.24
18 15 0.52
19 6 0.21
20 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATATTATTTAATAGTT
Found at i:16594335 original size:18 final size:20
Alignment explanation
Indices: 16594312--16594352 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
16594302 TTTTGATTTG
16594312 TTTTTTTGAAT-TTTTG-AA
1 TTTTTTTGAATCTTTTGTAA
*
16594330 TTTTTTTGATTCTTTTGTAA
1 TTTTTTTGAATCTTTTGTAA
16594350 TTT
1 TTT
16594353 CTGTTGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 5 0.25
20 5 0.25
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTTTTTGAATCTTTTGTAA
Found at i:16597777 original size:22 final size:22
Alignment explanation
Indices: 16597751--16597804 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
16597741 AAAGACTTGA
*
16597751 GTTAAGTTTAAAGGAAAC-TCTT
1 GTTAAGTTAAAAGGAAACAT-TT
*
16597773 GTTAAGTTAAAAGGACACATTT
1 GTTAAGTTAAAAGGAAACATTT
16597795 GTTAAGTTAA
1 GTTAAGTTAA
16597805 GGGAGAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (22 bp):
GTTAAGTTAAAAGGAAACATTT
Found at i:16598808 original size:60 final size:60
Alignment explanation
Indices: 16598712--16598959 Score: 266
Period size: 60 Copynumber: 4.1 Consensus size: 60
16598702 AAAGGACATG
* *
16598712 CTTTGTGGCAAGTACTGAACGTAAAGGATACCTTTGTGGCAAAAATCTGGACAGGAAAGC
1 CTTTGTGGCGAGTACTGAATGTAAAGGATACCTTTGTGGCAAAAATCTGGACAGGAAAGC
* * * *
16598772 CTTTGTAGCGAGTACTGAATGTAAAGGATGCATTTGTGGAAAAAATCTGGACAAGG-AAGC
1 CTTTGTGGCGAGTACTGAATGTAAAGGATACCTTTGTGGCAAAAATCTGGAC-AGGAAAGC
* * ** * * *
16598832 CTTTGTGGTGAGTACTGAATGCAAAGGATGGCTTTGTGG-AAAACCTCTGGATAGGAAAGT
1 CTTTGTGGCGAGTACTGAATGTAAAGGATACCTTTGTGGCAAAA-ATCTGGACAGGAAAGC
* * * * * * * * *
16598892 CTTTGTGGCGACTATTAAATGAAAAGGACACCTTTGTGGCAAAACTCTAGAAAGGTAAGC
1 CTTTGTGGCGAGTACTGAATGTAAAGGATACCTTTGTGGCAAAAATCTGGACAGGAAAGC
16598952 CTTTGTGG
1 CTTTGTGG
16598960 AAACCTCTGT
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
59 7 0.04
60 144 0.91
61 7 0.04
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (60 bp):
CTTTGTGGCGAGTACTGAATGTAAAGGATACCTTTGTGGCAAAAATCTGGACAGGAAAGC
Found at i:16608039 original size:22 final size:21
Alignment explanation
Indices: 16608008--16608078 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
16607998 CTGCAAAGGC
* *
16608008 GGCTTACAAAATATACCAAAAA
1 GGCTAACAAAATAT-CCATAAA
*
16608030 GGCTAGCAAAAT-TCCATAAA
1 GGCTAACAAAATATCCATAAA
*
16608050 GGCTAACAAACTATGCCATAAA
1 GGCTAACAAAATAT-CCATAAA
16608072 GGC-AACA
1 GGCTAACA
16608079 TATGAAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 16 0.38
21 6 0.14
22 20 0.48
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (21 bp):
GGCTAACAAAATATCCATAAA
Found at i:16608052 original size:20 final size:21
Alignment explanation
Indices: 16608027--16608078 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
16608017 AATATACCAA
* *
16608027 AAAGGCTAGCAAA-ATTCCAT
1 AAAGGCTAACAAACATGCCAT
16608047 AAAGGCTAACAAACTATGCCAT
1 AAAGGCTAACAAAC-ATGCCAT
16608069 AAAGGC-AACA
1 AAAGGCTAACA
16608079 TATGAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAGGCTAACAAACATGCCAT
Found at i:16611514 original size:50 final size:50
Alignment explanation
Indices: 16611434--16611674 Score: 218
Period size: 50 Copynumber: 4.8 Consensus size: 50
16611424 ATTTGGGTAA
* * *
16611434 AGAGATCCCATGTAAGACCATGTCTAGGACATGGTGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * *
16611484 AGAGGTCCCATGTAAGACTATATCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * * * * *
16611534 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * * * *
16611584 AGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGCAGTACAAGA--
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA--CCAAGATG
** * *
16611634 A-AAATCCCATGTAAGACCGTGTCTGGGACATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
16611675 TGTTATTATC
Statistics
Matches: 158, Mismatches: 31, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
49 35 0.22
50 120 0.76
52 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:16614094 original size:213 final size:212
Alignment explanation
Indices: 16613853--16614238 Score: 550
Period size: 213 Copynumber: 1.8 Consensus size: 212
16613843 GGCTCTTGCC
16613853 TATTTTACAACGATATTATTGAGGAATCTATTCTCATACATCATTACAAATTTTTT-AATGGATT
1 TATTTTACAACGATATTATTGAGGAATCTATTCTCATACATCATTAC-AATTTTTTGAATGG-TT
* * * *
16613917 -TGAAGATGGATGTAAATAAAAACTTCAAAATTTTAAAA-TGAAAACTTA-ATTTTTTGCATACT
64 ACGAAGATGAATGTAAATAAAAACTT-AAAATTTTAAAACAG-AAACTTATATTTTTTGCAAACT
*
16613979 AAATTATTTTGAAGAGATTGTTGGAGAGAAAAA-TTACTCAAGAGAATTTTGGGAAAATTGAGAC
127 AAATTATTTT-AAGAGATTGTTGGAGA-AAAAATTTACTCAAAAGAATTTTGGGAAAATTGAGAC
16614043 CTCTCTTATAGAGAGTTTTTCCA
190 CTCTCTTATAGAGAGTTTTTCCA
*
16614066 TATTTTACATCGATATTATT-AGGGAATCTATTCTCATACATCATTACAATTTTTTGAATGGTTA
1 TATTTTACAACGATATTATTGA-GGAATCTATTCTCATACATCATTACAATTTTTTGAATGGTTA
* * * *
16614130 CGAGGATTAATGTAAATAAAAACTTAAAATTTTAAAACAGAAACTTATTCTTTTTTGCAAATTAA
65 CGAAGATGAATGTAAATAAAAACTTAAAATTTTAAAACAGAAACTTA-TATTTTTTGCAAACTAA
* *
16614195 ATTCTTTTAAGAGATTGTTGTAGAAAAAATTTACTCAAAAGAAT
129 ATTATTTTAAGAGATTGTTGGAGAAAAAATTTACTCAAAAGAAT
16614239 GCTGAGAAAA
Statistics
Matches: 154, Mismatches: 12, Indels: 14
0.86 0.07 0.08
Matches are distributed among these distances:
212 35 0.23
213 99 0.64
214 20 0.13
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (212 bp):
TATTTTACAACGATATTATTGAGGAATCTATTCTCATACATCATTACAATTTTTTGAATGGTTAC
GAAGATGAATGTAAATAAAAACTTAAAATTTTAAAACAGAAACTTATATTTTTTGCAAACTAAAT
TATTTTAAGAGATTGTTGGAGAAAAAATTTACTCAAAAGAATTTTGGGAAAATTGAGACCTCTCT
TATAGAGAGTTTTTCCA
Found at i:16616678 original size:28 final size:28
Alignment explanation
Indices: 16616621--16616736 Score: 123
Period size: 28 Copynumber: 4.2 Consensus size: 28
16616611 TATACAGTAG
16616621 CAGT-ACAGTGT--GCCTTAGCCCAA-A
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
* *
16616645 GCAGTAACAATGTAGGCCTTAGCCCAATA
1 -CAGTAACAGTGTGGGCCTTAGCCCAATA
* * * *
16616674 TAGTAATAGTGTGGGCCGTAGCCCAGTA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
* *
16616702 TAGTAATAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
16616730 CAGTAAC
1 CAGTAAC
16616737 CGGTACAGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
25 4 0.05
26 6 0.08
28 65 0.86
29 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:16617136 original size:27 final size:26
Alignment explanation
Indices: 16617106--16617419 Score: 267
Period size: 27 Copynumber: 11.7 Consensus size: 26
16617096 TACCCTATTG
*
16617106 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCC-TCGA
* * *
16617133 GGGTATTTC-AGTGATTTTACCTTTCGG
1 GGGTATTTCGA-TCATTTTACC-CTCGA
* *
16617160 GGGTATTTCAATCATTTTACCCTTCGG
1 GGGTATTTCGATCATTTTACCC-TCGA
* * ** *
16617187 GGGTATTTTGGTCATTTTATTCTCTGG
1 GGGTATTTCGATCATTTTACCCTC-GA
* *
16617214 GGGTATTTCGATTATTTTACCCTCTAA
1 GGGTATTTCGATCATTTTACCCTC-GA
*
16617241 GGGTATTTC-ATTCATTTTACCCTCAA
1 GGGTATTTCGA-TCATTTTACCCTCGA
*
16617267 GGGTATTTCGATCATTTTACCCTCTA
1 GGGTATTTCGATCATTTTACCCTCGA
* *
16617293 GGGGTATTT-TAGTAATTTTACCCTCTGA
1 -GGGTATTTCGA-TCATTTTACCCTC-GA
* * *
16617321 GGATACTTCGATCATTTTACCCTCTGG
1 GGGTATTTCGATCATTTTACCCTC-GA
*
16617348 GGGTATTTC-AGTCATTTTACCCTCCGG
1 GGGTATTTCGA-TCATTTTACCCT-CGA
* *
16617375 GGGTATTTCGATCACTTTACCCTCCA
1 GGGTATTTCGATCATTTTACCCTCGA
16617401 GGGGTATTTCGATCATTTT
1 -GGGTATTTCGATCATTTT
16617420 CCCATGAATT
Statistics
Matches: 238, Mismatches: 34, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
26 31 0.13
27 202 0.85
28 5 0.02
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (26 bp):
GGGTATTTCGATCATTTTACCCTCGA
Found at i:16617150 original size:54 final size:52
Alignment explanation
Indices: 16617088--16617419 Score: 299
Period size: 54 Copynumber: 6.2 Consensus size: 52
16617078 GAGGTATAAT
*
16617088 AGTCATTTTACCCTATTGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTC
1 AGTCATTTTACCCT-TTGGGGTATTTCGATCATTTTACCC-TCGAGGGTATTTC
* * * *
16617142 AGTGATTTTA-CCTTTCGGGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTT
1 AGTCATTTTACCCTTT--GGGGTATTTCGATCATTTTACCC-TCGAGGGTATTTC
* ** * * *
16617196 GGTCATTTTATTCTCTGGGGGTATTTCGATTATTTTACCCTCTAAGGGTATTTC
1 AGTCATTTTACCCT-TTGGGGTATTTCGATCATTTTACCCTC-GAGGGTATTTC
* *** * *
16617250 ATTCATTTTACCCTCAAGGGTATTTCGATCATTTTACCCTCTAGGGGTATTTT
1 AGTCATTTTACCCTTTGGGGTATTTCGATCATTTTACCCTCGA-GGGTATTTC
* * * * *
16617303 AGTAATTTTACCCTCTGAGGATACTTCGATCATTTTACCCTCTGGGGGTATTTC
1 AGTCATTTTACCCTTTG-GGGTATTTCGATCATTTTACCCTC-GAGGGTATTTC
** * *
16617357 AGTCATTTTACCCTCCGGGGGTATTTCGATCACTTTACCCTCCAGGGGTATTTC
1 AGTCATTTTACCCT-TTGGGGTATTTCGATCATTTTACCCTCGA-GGGTATTTC
16617411 -GATCATTTT
1 AG-TCATTTT
16617420 CCCATGAATT
Statistics
Matches: 227, Mismatches: 40, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
52 3 0.01
53 50 0.22
54 169 0.74
55 4 0.02
56 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (52 bp):
AGTCATTTTACCCTTTGGGGTATTTCGATCATTTTACCCTCGAGGGTATTTC
Found at i:16617200 original size:81 final size:79
Alignment explanation
Indices: 16617090--16617419 Score: 297
Period size: 81 Copynumber: 4.1 Consensus size: 79
16617080 GGTATAATAG
** *
16617090 TCATTTTACCCTATTGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTC-AGTGATTTTA-C
1 TCATTTTACCCT-CGGGGGTATTTCGGTCATTTTACCC-TCGAGGGTATTTCGA-TAATTTTACC
* **
16617153 CTTTCGGGGGTATTTCAA
63 CTCT-AAGGGTATTTCAA
* ** * *
16617171 TCATTTTACCCTTCGGGGGTATTTTGGTCATTTTATTCTCTGGGGGTATTTCGATTATTTTACCC
1 TCATTTTACCC-TCGGGGGTATTTCGGTCATTTTACCCTC-GAGGGTATTTCGATAATTTTACCC
*
16617236 TCTAAGGGTATTTCAT
64 TCTAAGGGTATTTCAA
** * * *
16617252 TCATTTTACCCTCAAGGGTATTTCGATCATTTTACCCTCTAGGGGTATTT-TAGTAATTTTACCC
1 TCATTTTACCCTCGGGGGTATTTCGGTCATTTTACCCTCGA-GGGTATTTCGA-TAATTTTACCC
* * * *
16617316 TCTGAGGATACTTCGA
64 TCTAAGGGTATTTCAA
* * * *
16617332 TCATTTTACCCTCTGGGGGTATTTCAGTCATTTTACCCTCCGGGGGTATTTCGATCACTTTACCC
1 TCATTTTACCCTC-GGGGGTATTTCGGTCATTTTACCCT-CGAGGGTATTTCGATAATTTTACCC
* * *
16617397 TCCAGGGGTATTTCGA
64 TCTAAGGGTATTTCAA
16617413 TCATTTT
1 TCATTTT
16617420 CCCATGAATT
Statistics
Matches: 200, Mismatches: 40, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
79 1 0.00
80 66 0.33
81 125 0.62
82 8 0.04
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (79 bp):
TCATTTTACCCTCGGGGGTATTTCGGTCATTTTACCCTCGAGGGTATTTCGATAATTTTACCCTC
TAAGGGTATTTCAA
Found at i:16624439 original size:28 final size:28
Alignment explanation
Indices: 16624385--16624507 Score: 158
Period size: 28 Copynumber: 4.4 Consensus size: 28
16624375 AAGCCCTATA
16624385 CAATAGCAGT-ATAGTGTGGGCCTTAGCC
1 CAATA-CAGTAATAGTGTGGGCCTTAGCC
* * * *
16624413 CAAAACAATAACAATGTGGGCCTTAGCC
1 CAATACAGTAATAGTGTGGGCCTTAGCC
*
16624441 CAATACAGCAATAGTGTGGGCCTTAGCC
1 CAATACAGTAATAGTGTGGGCCTTAGCC
* *
16624469 CAGTACAGTAATAGTGTGAGCCTTAGCC
1 CAATACAGTAATAGTGTGGGCCTTAGCC
*
16624497 CAATATAGTAA
1 CAATACAGTAA
16624508 CCAGTACAGT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
27 3 0.04
28 77 0.96
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (28 bp):
CAATACAGTAATAGTGTGGGCCTTAGCC
Found at i:16624880 original size:27 final size:27
Alignment explanation
Indices: 16624850--16625135 Score: 133
Period size: 27 Copynumber: 10.6 Consensus size: 27
16624840 TATCTCTTAA
16624850 GGGTATAAT-AGTCATTTTACCCTAT-GG
1 GGGTAT-ATCAGTCATTTTACCCT-TCGG
*
16624877 GGGTATTTCAGTCATTTTACCCTTCGG
1 GGGTATATCAGTCATTTTACCCTTCGG
* * * *
16624904 GGGTATTTCGGTCGTTTTACCC-TCTGA
1 GGGTATATCAGTCATTTTACCCTTC-GG
* * * * * *
16624931 GGGTTTTTAAGTTATTTTACCCTCCGA
1 GGGTATATCAGTCATTTTACCCTTCGG
* ** *
16624958 GGGTATTTTGGTCATTTTACCCTTTGG
1 GGGTATATCAGTCATTTTACCCTTCGG
* *
16624985 GGGTATTTCAGTTATTTT-CCC-TCTGG
1 GGGTATATCAGTCATTTTACCCTTC-GG
* * *
16625011 GGGTATTTCAGCCATTTTACCC-TCTTG
1 GGGTATATCAGTCATTTTACCCTTC-GG
* **
16625038 AGGTACT-TTGGTCATTTTA-CCTTCTGG
1 GGGTA-TATCAGTCATTTTACCCTTC-GG
* * * *
16625065 GGGTATTTCGGTCATTTTATCCTTCAG
1 GGGTATATCAGTCATTTTACCCTTCGG
* * *
16625092 GGGTACT-TC-GTTCATTTTACACTCCGA
1 GGGTA-TATCAG-TCATTTTACCCTTCGG
* *
16625119 GGGTCTTTCAGTCATTT
1 GGGTATATCAGTCATTT
16625136 GCCCACGAAT
Statistics
Matches: 207, Mismatches: 38, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.00
26 30 0.14
27 167 0.81
28 9 0.04
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGTATATCAGTCATTTTACCCTTCGG
Found at i:16624922 original size:54 final size:55
Alignment explanation
Indices: 16624860--16625083 Score: 253
Period size: 54 Copynumber: 4.2 Consensus size: 55
16624850 GGGTATAATA
*
16624860 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTTC-GGGGGTATTTCG
1 GTCATTTTACCCTCTGGGGGTATTTCAGTCATTTTACCCTTCTGGGGGTATTTCG
* * * * * * * *
16624914 GTCGTTTTACCCTCTGAGGGTTTTTAAGTTATTTTACCC-TCCGAGGGTATTTTG
1 GTCATTTTACCCTCTGGGGGTATTTCAGTCATTTTACCCTTCTGGGGGTATTTCG
* * *
16624968 GTCATTTTACCCTTTGGGGGTATTTCAGTTATTTT-CCC-TCTGGGGGTATTTCA
1 GTCATTTTACCCTCTGGGGGTATTTCAGTCATTTTACCCTTCTGGGGGTATTTCG
* * * *
16625021 GCCATTTTACCCTCTTGAGGTACTTT-GGTCATTTTA-CCTTCTGGGGGTATTTCG
1 GTCATTTTACCCTCTGGGGGTA-TTTCAGTCATTTTACCCTTCTGGGGGTATTTCG
16625075 GTCATTTTA
1 GTCATTTTA
16625084 TCCTTCAGGG
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
53 43 0.30
54 98 0.70
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (55 bp):
GTCATTTTACCCTCTGGGGGTATTTCAGTCATTTTACCCTTCTGGGGGTATTTCG
Found at i:16625050 original size:80 final size:81
Alignment explanation
Indices: 16624887--16625083 Score: 256
Period size: 80 Copynumber: 2.4 Consensus size: 81
16624877 GGGTATTTCA
* * * **
16624887 GTCATTTTACCCTTCGGGGGTATTTCGGTCGTTTTACCCTCTGAGGGTTTTTAAGTTATTTTACC
1 GTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCCTCTGAGGGTATTTAAGCCATTTTACC
*
16624952 CTCCGAGGGTATTTTG
66 CTCCGAGGGTACTTTG
* * * *
16624968 GTCATTTTACCCTTTGGGGGTATTTCAGTTATTTT-CCCTCTGGGGGTATTTCAGCCATTTTACC
1 GTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCCTCTGAGGGTATTTAAGCCATTTTACC
*
16625032 CTCTTGA-GGTACTTTG
66 CTC-CGAGGGTACTTTG
16625048 GTCATTTTA-CCTTCTGGGGGTATTTCGGTCATTTTA
1 GTCATTTTACCCTT-TGGGGGTATTTCGGTCATTTTA
16625084 TCCTTCAGGG
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
79 4 0.04
80 63 0.63
81 33 0.33
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (81 bp):
GTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACCCTCTGAGGGTATTTAAGCCATTTTACC
CTCCGAGGGTACTTTG
Found at i:16625095 original size:107 final size:108
Alignment explanation
Indices: 16624860--16625135 Score: 276
Period size: 107 Copynumber: 2.6 Consensus size: 108
16624850 GGGTATAATA
* * * * *
16624860 GTCATTTTACCCTAT-GGGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCGGTCGTTTTAC
1 GTCATTTTACCCT-TCAGGGGTATTTCAGTTATTTTACCCTTCGGGGGTATTTCAGCCATTTTAC
* * *
16624924 CCTCTGAGGGTTTTTAAGTTATTTTACCCTCCGAGGGTATTTTG
65 CCTCTGAGGGTCTTTAAGTCATTTTACCCTCCGAGGGTATTTCG
**
16624968 GTCATTTTACCCTTTGGGGGTATTTCAGTTATTTT-CCC-TCTGGGGGTATTTCAGCCATTTTAC
1 GTCATTTTACCCTTCAGGGGTATTTCAGTTATTTTACCCTTC-GGGGGTATTTCAGCCATTTTAC
* * * *
16625031 CCTCTTGA-GGTACTTT-GGTCATTTTACCTTCTGGGGGTATTTCG
65 CCTC-TGAGGGT-CTTTAAGTCATTTTACCCTCCGAGGGTATTTCG
* * * * * * *
16625075 GTCATTTTATCCTTCAGGGGTACTTC-GTTCATTTTACACTCCGAGGGTCTTTCAGTCATTT
1 GTCATTTTACCCTTCAGGGGTATTTCAGTT-ATTTTACCCTTCGGGGGTATTTCAGCCATTT
16625136 GCCCACGAAT
Statistics
Matches: 141, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
106 5 0.04
107 79 0.56
108 56 0.40
109 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (108 bp):
GTCATTTTACCCTTCAGGGGTATTTCAGTTATTTTACCCTTCGGGGGTATTTCAGCCATTTTACC
CTCTGAGGGTCTTTAAGTCATTTTACCCTCCGAGGGTATTTCG
Found at i:16625107 original size:54 final size:53
Alignment explanation
Indices: 16624860--16625135 Score: 220
Period size: 54 Copynumber: 5.1 Consensus size: 53
16624850 GGGTATAATA
* *
16624860 GTCATTTTACCCTATGGGGGTATTTCAG-TCATTTTACCCT-TCGGGGGTATTTCG
1 GTCATTTTACCCTCT-GGGGTACTTC-GTTCATTTTACCCTCT-GGGGGTATTTCG
* ** * * * *
16624914 GTCGTTTTACCCTCTGAGGGTTTTTAAGTT-ATTTTACCCTCCGAGGGTATTTTG
1 GTCATTTTACCCTCTG-GGGTACTT-CGTTCATTTTACCCTCTGGGGGTATTTCG
* * *
16624968 GTCATTTTACCCTTTGGGGGTATTTCAGTT-ATTTT-CCCTCTGGGGGTATTTCA
1 GTCATTTTACCCTCT-GGGGTACTTC-GTTCATTTTACCCTCTGGGGGTATTTCG
* * * * *
16625021 GCCATTTTACCCTCTTGAGGTACTTTGGTCATTTTACCTTCTGGGGGTATTTCG
1 GTCATTTTACCCTC-TGGGGTACTTCGTTCATTTTACCCTCTGGGGGTATTTCG
* * * * * * *
16625075 GTCATTTTATCCTTCAGGGGTACTTCGTTCATTTTACACTCCGAGGGTCTTTCA
1 GTCATTTTA-CCCTCTGGGGTACTTCGTTCATTTTACCCTCTGGGGGTATTTCG
16625129 GTCATTT
1 GTCATTT
16625136 GCCCACGAAT
Statistics
Matches: 177, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
52 2 0.01
53 39 0.22
54 130 0.73
55 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (53 bp):
GTCATTTTACCCTCTGGGGTACTTCGTTCATTTTACCCTCTGGGGGTATTTCG
Found at i:16625852 original size:12 final size:13
Alignment explanation
Indices: 16625828--16625866 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16625818 GAAGACAGGT
*
16625828 AGAAGAAATGAAA
1 AGAAGAAAAGAAA
16625841 AG-AGAAAAGAAA
1 AGAAGAAAAGAAA
*
16625853 AGAAGAGAAGAAA
1 AGAAGAAAAGAAA
16625866 A
1 A
16625867 AAAAGAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (13 bp):
AGAAGAAAAGAAA
Found at i:16625852 original size:17 final size:18
Alignment explanation
Indices: 16625830--16625872 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
16625820 AGACAGGTAG
*
16625830 AAGAAATGAAAAG-AGAA
1 AAGAAAAGAAAAGAAGAA
*
16625847 AAGAAAAGAAGAGAAGAA
1 AAGAAAAGAAAAGAAGAA
16625865 AA-AAAAGA
1 AAGAAAAGA
16625873 GGGTTCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (18 bp):
AAGAAAAGAAAAGAAGAA
Found at i:16629352 original size:76 final size:78
Alignment explanation
Indices: 16629112--16629365 Score: 386
Period size: 78 Copynumber: 3.3 Consensus size: 78
16629102 AAAGTATATA
16629112 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
16629177 GTATAAGTTCTTG
66 GTATAAGTTCTTG
*
16629190 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
* *
16629255 GTATAAGTTTTTT
66 GTATAAGTTCTTG
* * * * *
16629268 AATTGAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-AA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
* * *
16629331 ATACAAGTACTTG
66 GTATAAGTTCTTG
*
16629344 AATTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
16629366 GTAAATACTT
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
76 44 0.27
77 2 0.01
78 115 0.71
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
GTATAAGTTCTTG
Found at i:16629417 original size:154 final size:153
Alignment explanation
Indices: 16629112--16629401 Score: 356
Period size: 154 Copynumber: 1.9 Consensus size: 153
16629102 AAAGTATATA
* * *
16629112 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* * * * * * *
16629177 GTATAAGTTCTTGAATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATA
66 ATACAAGTACTTGAATTGAATTAAAAGTATGAATTATAAATATGTATA---GAGATTCGAACATA
* * *
16629242 TATGTATATACATGTATAAGTTTTTT
128 GATGTACAAACATGTATAAGTTTTTT
* *
16629268 AATTGAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-AA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
* *
16629331 ATACAAGTACTTGAATTGAATTAAAAGTATGAATTGTAAATACT-TATA-AGATTCGAACATGGA
66 ATACAAGTACTTGAATTGAATTAAAAGTATGAATTATAAATA-TGTATAGAGATTCGAACATAGA
16629394 T-TACAAAC
130 TGTACAAAC
16629402 TTCTTGAGGT
Statistics
Matches: 116, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
149 5 0.04
150 12 0.10
154 55 0.47
155 3 0.03
156 41 0.35
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (153 bp):
AATTGAATTAAAGGTATGAATTTTACATATGTATATGTGAGATTCGAATATAGATGTATATACAT
ATACAAGTACTTGAATTGAATTAAAAGTATGAATTATAAATATGTATAGAGATTCGAACATAGAT
GTACAAACATGTATAAGTTTTTT
Found at i:16629753 original size:35 final size:33
Alignment explanation
Indices: 16629711--16629908 Score: 158
Period size: 35 Copynumber: 5.9 Consensus size: 33
16629701 ATTTATATCT
16629711 TATTTGATAAGTATATATATGCATTCGGTTAT-A-
1 TATTTGAT-AG-ATATATATGCATTCGGTTATAAG
* *
16629744 TACCTTTGAT-G-TGTATATGCATTCGATTATAAG
1 TA--TTTGATAGATATATATGCATTCGGTTATAAG
* * *
16629777 TATTTGATAGGTATATATGCATTCGGTTGT-AT
1 TATTTGATAGATATATATGCATTCGGTTATAAG
* *
16629809 TCATTTGAT-G-TGTATATGCATTCGATTATAAG
1 T-ATTTGATAGATATATATGCATTCGGTTATAAG
* *
16629841 TAGTTGATAAGTATATTTATGCATTCGGTTATAAG
1 TATTTGAT-AG-ATATATATGCATTCGGTTATAAG
* * *
16629876 TATTTGATGAGTATATACATACATTTGGTTATA
1 TATTTGAT-AG-ATATATATGCATTCGGTTATA
16629909 TACATTCGAT
Statistics
Matches: 133, Mismatches: 20, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
31 45 0.34
32 7 0.05
33 29 0.22
35 52 0.39
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (33 bp):
TATTTGATAGATATATATGCATTCGGTTATAAG
Found at i:16629791 original size:66 final size:66
Alignment explanation
Indices: 16629711--16629891 Score: 260
Period size: 64 Copynumber: 2.8 Consensus size: 66
16629701 ATTTATATCT
*
16629711 TATTTGATAAGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
16629776 G
66 G
* * *
16629777 TATTTGAT-AG-GTATATATGCATTCGGTTGTATTCATTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
16629840 G
66 G
* * * *
16629841 TAGTTGATAAGTATATTTATGCATTCGGTTATA-AGTATTTGATGAGTATAT
1 TATTTGATAAGTATATATATGCATTCGGTTATATA-CATTTGATGTGTATAT
16629892 ACATACATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
64 57 0.56
65 4 0.04
66 40 0.40
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (66 bp):
TATTTGATAAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
G
Found at i:16629848 original size:31 final size:31
Alignment explanation
Indices: 16629726--16629891 Score: 149
Period size: 31 Copynumber: 5.2 Consensus size: 31
16629716 GATAAGTATA
*
16629726 TATATGCATTCGGTTAT-A-TACCTTTGATGTG
1 TATATGCATTCGATTATAAGTA--TTTGATGTG
*
16629757 TATATGCATTCGATTATAAGTATTTGATAGGTA
1 TATATGCATTCGATTATAAGTATTTGAT--GTG
* * *
16629790 TATATGCATTCGGTTGT-ATTCATTTGATGTG
1 TATATGCATTCGATTATAAGT-ATTTGATGTG
* *
16629821 TATATGCATTCGATTATAAGTAGTTGATAAGTA
1 TATATGCATTCGATTATAAGTATTTGAT--GTG
* *
16629854 TATTTATGCATTCGGTTATAAGTATTTGATGAG
1 TA--TATGCATTCGATTATAAGTATTTGATGTG
16629887 TATAT
1 TATAT
16629892 ACATACATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
31 48 0.44
32 5 0.05
33 33 0.30
35 24 0.22
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (31 bp):
TATATGCATTCGATTATAAGTATTTGATGTG
Found at i:16636340 original size:13 final size:13
Alignment explanation
Indices: 16636322--16636363 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
16636312 TGAGTGAAAA
16636322 TTCTCTTTGAGTT
1 TTCTCTTTGAGTT
** *
16636335 TTCTCTAAGAATT
1 TTCTCTTTGAGTT
16636348 TTCTC-TTGAGTT
1 TTCTCTTTGAGTT
16636360 TTCT
1 TTCT
16636364 TTAGAAGTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (13 bp):
TTCTCTTTGAGTT
Done.