Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 62 of 109
Found at i:20168737 original size:50 final size:50
Alignment explanation
Indices: 20168662--20168802 Score: 160
Period size: 50 Copynumber: 2.8 Consensus size: 50
20168652 NNNNNNGTCG
* *
20168662 GGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACTGC-ACTTCCA
1 GGGAAGAGAGATTCACCGATGTGGCTTTAATCTACTCCACTGCAACGT-CA
* ** ** *
20168712 GGGAAGTAG-GATTCACCGCTGTGGCTTTAATCTTTTTAACTGCAACGTCG
1 GGGAAG-AGAGATTCACCGATGTGGCTTTAATCTACTCCACTGCAACGTCA
* *
20168762 GGGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACT
1 GGGAAGAGAGATTCACCGATGTGGCTTTAATCTACTCCACT
20168803 ATACCGCTAG
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 69 0.93
51 4 0.05
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (50 bp):
GGGAAGAGAGATTCACCGATGTGGCTTTAATCTACTCCACTGCAACGTCA
Found at i:20168835 original size:100 final size:99
Alignment explanation
Indices: 20168658--20169002 Score: 395
Period size: 100 Copynumber: 3.5 Consensus size: 99
20168648 NNNNNNNNNN
* ** *
20168658 GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACTGCACTTCCAGGGAAGTAGGA
1 GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACT-AACCGCCAGAGAAGTAGGA
* *
20168723 TTCACCGCTGTGGCTTTAATCTTTTTAACTGCAAC
65 TTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAAT
* *
20168758 GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACTATACCGCTAGAGAAGTAGGA
1 GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACTA-ACCGCCAGAGAAGTAGGA
* * * *
20168823 TTTGCCGTTGTGGCTTTAACCTTTTTAACTGCTATT
65 TTCGCCGCTGTGGCTTTAATCTTTTTAACTGC-AAT
* ** * * * *
20168859 GTCGGGGAAGTGAGATTTGCCGTTGTGGTTTTAATCTATTCCACGTAACCGCCAGAGAAGTAAGA
1 GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCAC-TAACCGCCAGAGAAGTAGGA
* * * *
20168924 TTCGCTGCTATAGCTTTAATCTTTTTAACTGTAAT
65 TTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAAT
* * * * *
20168959 G-CCGGGAAGCAATATTCACCGATGTGGTTTTAATCTGCTCCACT
1 GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACT
20169003 GCAACGTCAG
Statistics
Matches: 204, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
98 1 0.00
99 33 0.16
100 89 0.44
101 79 0.39
102 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (99 bp):
GTCGGGGAAGCGAGATTCACCGATGTGGCTTTAATCTACTCCACTAACCGCCAGAGAAGTAGGAT
TCGCCGCTGTGGCTTTAATCTTTTTAACTGCAAT
Found at i:20169051 original size:50 final size:50
Alignment explanation
Indices: 20168990--20169192 Score: 182
Period size: 49 Copynumber: 4.1 Consensus size: 50
20168980 ATGTGGTTTT
*
20168990 AATCTGCTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
1 AATCTGTTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
* ** * * * * *
20169040 AATCTGTTCCACTGCACCG-CCTGGAAATAAGATTCGCCGTTGTGGCCTC
1 AATCTGTTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
** * * *
20169089 AATCT-TTGGATTGCAATGTCAGGGAAGTGAGATCCG-TCGTTGTAGCTTC
1 AATCTGTTCCACTGCAACGTCAGGGAAGTAAGATCCGCT-GTTGTAGCTTC
* * * *
20169138 AATCTGTTACGCTGCACCGCTTA--GAATGTAAGATCCGCTGTTGTAGCTTC
1 AATCTGTTCCACTGCAACG-TCAGGGAA-GTAAGATCCGCTGTTGTAGCTTC
20169188 AATCT
1 AATCT
20169193 TTTGAATTGA
Statistics
Matches: 117, Mismatches: 30, Indels: 12
0.74 0.19 0.08
Matches are distributed among these distances:
48 8 0.07
49 57 0.49
50 49 0.42
51 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (50 bp):
AATCTGTTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
Found at i:20169084 original size:99 final size:98
Alignment explanation
Indices: 20168871--20169157 Score: 247
Period size: 99 Copynumber: 2.9 Consensus size: 98
20168861 CGGGGAAGTG
* * * * * * *
20168871 AGATTTGCCGTTGTGGTTTTAATCTATTCCAC-GTAACCGCCAGAGAAGTAAGATTCGCTGCTAT
1 AGATTCGCCGTTGTGGTTTTAATCT-TTCCACTGCAA-CGTCAGGGAAGTAAGATCCGCTGTTGT
* * * ** *
20168935 AGCTTTAATCTTTTTA-ACTGTAATGCCGGGAAGCA
64 AGCTTCAATC-TGTTACACTGCACCGCCGGGAAACA
* * * *
20168970 ATATTCACCGATGTGGTTTTAATCTGCTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTA
1 AGATTCGCCGTTGTGGTTTTAATCT-TTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTA
* * *
20169035 GCTTCAATCTGTTCCACTGCACCGCCTGGAAATA
65 GCTTCAATCTGTTACACTGCACCGCCGGGAAACA
** * ** * * *
20169069 AGATTCGCCGTTGTGGCCTCAATCTTTGGATTGCAATGTCAGGGAAGTGAGATCCG-TCGTTGTA
1 AGATTCGCCGTTGTGGTTTTAATCTTTCCACTGCAACGTCAGGGAAGTAAGATCCGCT-GTTGTA
*
20169133 GCTTCAATCTGTTACGCTGCACCGC
65 GCTTCAATCTGTTACACTGCACCGC
20169158 TTAGAATGTA
Statistics
Matches: 150, Mismatches: 35, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
97 1 0.01
98 57 0.38
99 89 0.59
100 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (98 bp):
AGATTCGCCGTTGTGGTTTTAATCTTTCCACTGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAG
CTTCAATCTGTTACACTGCACCGCCGGGAAACA
Found at i:20169131 original size:98 final size:99
Alignment explanation
Indices: 20169002--20169194 Score: 264
Period size: 98 Copynumber: 2.0 Consensus size: 99
20168992 TCTGCTCCAC
* *
20169002 TGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAA-
1 TGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTACACTGCACCGCCTAGAAT
* *
20169066 ATAAGATTCGCCGTTGTGGCCTCAATCTTTGGAT
66 ATAAGATCCGCCGTTGTAGCCTCAATCTTTGGAT
* * * *
20169100 TGCAATGTCAGGGAAGTGAGATCCG-TCGTTGTAGCTTCAATCTGTTACGCTGCACCGCTTAGAA
1 TGCAACGTCAGGGAAGTAAGATCCGCT-GTTGTAGCTTCAATCTGTTACACTGCACCGCCTAGAA
* * *
20169164 TGTAAGATCCGCTGTTGTAGCTTCAATCTTT
65 TATAAGATCCGCCGTTGTAGCCTCAATCTTT
20169195 TGAATTGAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
97 1 0.01
98 56 0.68
99 25 0.30
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (99 bp):
TGCAACGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTACACTGCACCGCCTAGAAT
ATAAGATCCGCCGTTGTAGCCTCAATCTTTGGAT
Found at i:20169323 original size:44 final size:45
Alignment explanation
Indices: 20169214--20169324 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 45
20169204 AACTGTTGTT
** * *
20169214 TCTTCGATCTGCTTTGCTGTTAGTACAAGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCCCTGTCAGTACAAGAAGGCAAGAGCTGCTA
* * *
20169259 TCTTC-ATTCTGC-TCCGCTGTCAGTACAGGAAGGCAAG-GCTGGTG
1 TCTTCGA-TCTGCTTCC-CTGTCAGTACAAGAAGGCAAGAGCTGCTA
20169303 TCTTCGATCTGCTTCCCTGTCA
1 TCTTCGATCTGCTTCCCTGTCA
20169325 AGGCAAGGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
44 22 0.40
45 33 0.60
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.32
Consensus pattern (45 bp):
TCTTCGATCTGCTTCCCTGTCAGTACAAGAAGGCAAGAGCTGCTA
Found at i:20169380 original size:44 final size:45
Alignment explanation
Indices: 20169332--20169558 Score: 127
Period size: 44 Copynumber: 5.2 Consensus size: 45
20169322 TCAAGGCAAG
20169332 GAGGCAAGATCTGTTGTCTTCAACCATCTCCACT-ACAACCGAGA
1 GAGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAACCGAGA
* * * * * ** *
20169376 GAGGCAAGGTTTG-TGTCTTCGACC-TGCTTCGCTGTCAA-TGCAG-
1 GAGGCAAGATCTGTTGTCTTCAACCAT-CTCCACTCACAACCG-AGA
* *
20169419 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACCGAGA
1 G-AGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAACCGAGA
* * * * * ***
20169464 GAGGCAAGGT-T-TTGTTTTCGATC-TGCTTCACTGTTAA-CGCAG-
1 GAGGCAAGATCTGTTGTCTTCAACCAT-CTCCACTCACAACCG-AGA
* * *
20169506 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACTGAGA
1 G-AGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAACCGAGA
20169551 GAGGCAAG
1 GAGGCAAG
20169559 GTTTTTGTTT
Statistics
Matches: 130, Mismatches: 36, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
42 17 0.13
43 31 0.24
44 52 0.40
45 30 0.23
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (45 bp):
GAGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAACCGAGA
Found at i:20169405 original size:88 final size:88
Alignment explanation
Indices: 20169289--20169628 Score: 479
Period size: 88 Copynumber: 3.9 Consensus size: 88
20169279 CAGTACAGGA
* * * * *
20169289 AGGCAAGGCTGGTGTCTTCGATCTGCTTCCCTGTCAAGGCAAGG-AGGCAAGATCTGTTGTCTTC
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGC-AGGAAGGCAAGATCTGTTGTCTTC
*
20169353 AACCATCTCCA-CTACAACCGAGAG
65 AACCAGCTCCATC-ACAACCGAGAG
*
20169377 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
20169442 ACCAGCTCCATCACAACCGAGAG
66 ACCAGCTCCATCACAACCGAGAG
* * * * * *
20169465 AGGCAAGGTTT-TGTTTTCGATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTTTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
*
20169529 ACCAGCTCCATCACAACTGAGAG
66 ACCAGCTCCATCACAACCGAGAG
* * * *
20169552 AGGCAAGGTTTTTGTTTTTGACCTGCTTCGCTGACAATGCAGGAAGGCAAGATCTGTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
20169617 ACCAGCTCCATC
66 ACCAGCTCCATC
20169629 NNNNNNNNNN
Statistics
Matches: 229, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
87 84 0.37
88 144 0.63
89 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (88 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
ACCAGCTCCATCACAACCGAGAG
Found at i:20169514 original size:175 final size:175
Alignment explanation
Indices: 20169305--20169628 Score: 517
Period size: 175 Copynumber: 1.9 Consensus size: 175
20169295 GGCTGGTGTC
* * *
20169305 TTCGATCTGCTTCCCTGTCAAGGCAAGGAGGCAAGATCTGTTGTCTTCAACCATCTCCA-CTACA
1 TTCGATCTGCTTCACTGTCAACGCAAGGAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC-ACA
* *
20169369 ACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
65 ACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGACAATGCAGGAAGGCAAGATCTGT
20169434 TGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTTGTT
130 TGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTTGTT
* *
20169480 TTCGATCTGCTTCACTGTTAACGC-AGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACA
1 TTCGATCTGCTTCACTGTCAACGCAAGG-AGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACA
* * * *
20169544 ACTGAGAGAGGCAAGGTTTTTGTTTTTGACCTGCTTCGCTGACAATGCAGGAAGGCAAGATCTGT
65 ACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGACAATGCAGGAAGGCAAGATCTGT
20169609 TGTCTTCAACCAGCTCCATC
130 TGTCTTCAACCAGCTCCATC
20169629 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
174 3 0.02
175 132 0.97
176 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (175 bp):
TTCGATCTGCTTCACTGTCAACGCAAGGAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAA
CCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGACAATGCAGGAAGGCAAGATCTGTT
GTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTTGTT
Found at i:20171856 original size:43 final size:42
Alignment explanation
Indices: 20171767--20171868 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
20171757 NNNNNNNNTC
* *
20171767 TGATCAAAATTTGAGCTGCTCTGATCGCCTCATCCCCCAATT
1 TGATCAAAATTTGAGCTGCTCTGATCACCTAATCCCCCAATT
* **
20171809 TGATCCAAAATTTGAG-TCGCTCTGATCACTTAATGTCCC-ATT
1 TGAT-CAAAATTTGAGCT-GCTCTGATCACCTAATCCCCCAATT
20171851 ATGATCAAAAGTTTGAGC
1 -TGATCAAAA-TTTGAGC
20171869 CGCCCTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
42 13 0.26
43 37 0.74
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (42 bp):
TGATCAAAATTTGAGCTGCTCTGATCACCTAATCCCCCAATT
Found at i:20173078 original size:6 final size:6
Alignment explanation
Indices: 20173067--20173109 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
20173057 TTGACCTCTC
20173067 CTTTTT CTTTTT CTTTTT CTTCTCTT -TTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTT-T-TT CTTTTT CTTTTT CTTTTT
20173110 TTCTATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.06
6 27 0.79
7 3 0.09
8 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:20173096 original size:25 final size:24
Alignment explanation
Indices: 20173068--20173118 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
20173058 TGACCTCTCC
*
20173068 TTTTTCTTTTTCTTTTTCTTCTCTT
1 TTTTTCTTTTTCTTTTT-TTCTATT
20173093 TTTTTCTTTTTCTTTTTTTCTATT
1 TTTTTCTTTTTCTTTTTTTCTATT
20173117 TT
1 TT
20173119 GACTTCGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTCTTTTTCTTTTTTTCTATT
Found at i:20173133 original size:1 final size:1
Alignment explanation
Indices: 20173127--20173198 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
20173117 TTGACTTCGA
* ** ** * * ** *
20173127 TTTTTTTTTTATTTTTTTTAATTTTTTGATTTTTTTTATTTTTTTTATTTTTTTTGATTTTTTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20173192 TTTTTTT
1 TTTTTTT
20173199 CTAGTTTGAA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (1 bp):
T
Found at i:20173143 original size:9 final size:9
Alignment explanation
Indices: 20173129--20173198 Score: 99
Period size: 9 Copynumber: 7.9 Consensus size: 9
20173119 GACTTCGATT
20173129 TTTTTTTTA
1 TTTTTTTTA
20173138 TTTTTTTTA
1 TTTTTTTTA
* *
20173147 ATTTTTTGA
1 TTTTTTTTA
20173156 TTTTTTTTA
1 TTTTTTTTA
20173165 TTTTTTTTA
1 TTTTTTTTA
20173174 TTTTTTTTGA
1 TTTTTTTT-A
20173184 --TTTTTTA
1 TTTTTTTTA
20173191 TTTTTTTT
1 TTTTTTTT
20173199 CTAGTTTGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
7 1 0.02
8 6 0.11
9 46 0.85
10 1 0.02
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:20173151 original size:17 final size:17
Alignment explanation
Indices: 20173131--20173198 Score: 100
Period size: 17 Copynumber: 3.9 Consensus size: 17
20173121 CTTCGATTTT
20173131 TTTTTTATTTTTTTTAA
1 TTTTTTATTTTTTTTAA
*
20173148 TTTTTTGATTTTTTTTATT
1 TTTTTT-ATTTTTTTTA-A
*
20173167 TTTTTTATTTTTTTTGA
1 TTTTTTATTTTTTTTAA
20173184 TTTTTTATTTTTTTT
1 TTTTTTATTTTTTTT
20173199 CTAGTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
17 21 0.46
18 19 0.41
19 6 0.13
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTATTTTTTTTAA
Found at i:20173159 original size:27 final size:28
Alignment explanation
Indices: 20173129--20173198 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
20173119 GACTTCGATT
20173129 TTTTTTTTATTTTTTTTA-ATTTTTTGA
1 TTTTTTTTATTTTTTTTATATTTTTTGA
*
20173156 TTTTTTTTATTTTTTTTATTTTTTTTGA
1 TTTTTTTTATTTTTTTTATATTTTTTGA
20173184 --TTTTTTATTTTTTTT
1 TTTTTTTTATTTTTTTT
20173199 CTAGTTTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 15 0.37
27 18 0.44
28 8 0.20
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (28 bp):
TTTTTTTTATTTTTTTTATATTTTTTGA
Found at i:20193399 original size:7 final size:7
Alignment explanation
Indices: 20193387--20193411 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20193377 GTTTTAGGTC
20193387 TTTTTCA
1 TTTTTCA
20193394 TTTTTCA
1 TTTTTCA
20193401 TTTTTCA
1 TTTTTCA
20193408 TTTT
1 TTTT
20193412 CACTTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:20194815 original size:64 final size:64
Alignment explanation
Indices: 20194747--20194872 Score: 252
Period size: 64 Copynumber: 2.0 Consensus size: 64
20194737 ATTCCCTGTT
20194747 ATTGCATCCTGTTTCTTTCCTTTTCTTTTTCCCATTCTTTCTCTTTACTATTGTTTTTTATTGC
1 ATTGCATCCTGTTTCTTTCCTTTTCTTTTTCCCATTCTTTCTCTTTACTATTGTTTTTTATTGC
20194811 ATTGCATCCTGTTTCTTTCCTTTTCTTTTTCCCATTCTTTCTCTTTACTATTGTTTTTTATT
1 ATTGCATCCTGTTTCTTTCCTTTTCTTTTTCCCATTCTTTCTCTTTACTATTGTTTTTTATT
20194873 TGTATTTCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.10, C:0.23, G:0.06, T:0.62
Consensus pattern (64 bp):
ATTGCATCCTGTTTCTTTCCTTTTCTTTTTCCCATTCTTTCTCTTTACTATTGTTTTTTATTGC
Found at i:20199661 original size:13 final size:13
Alignment explanation
Indices: 20199643--20199667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20199633 TAGGTTTCAA
20199643 AGAAGAAAAGAGC
1 AGAAGAAAAGAGC
20199656 AGAAGAAAAGAG
1 AGAAGAAAAGAG
20199668 AAAACCACCA
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:0.64, C:0.04, G:0.32, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAGAGC
Found at i:20206237 original size:36 final size:36
Alignment explanation
Indices: 20206189--20206558 Score: 329
Period size: 36 Copynumber: 10.1 Consensus size: 36
20206179 TAGTCAAGAC
* *
20206189 CAACCTTTAAAAAAGGTTGGGATACACTTATCTAAGG
1 CAACC-TTAAAAAAGGTTGGGATAGACTTGTCTAAGG
*
20206226 CAACCTT-AAAAAGGTTGGGATAGACCTTGTTTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGA-CTTGTCTAAGG
** *
20206262 CAACCTT-AAAAAGGTTGATATAGTCATTGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGAC-TTGTCTAAGG
* * * *
20206298 CAACTTTTAAAAACGGTTGGGATAAAGC-CGTCTAAGG
1 CAAC-CTTAAAAAAGGTTGGGATAGA-CTTGTCTAAGG
* **
20206335 CAGCCTTAAAAAA-GTTGGGATAGACATTGTCTAAAA
1 CAACCTTAAAAAAGGTTGGGATAGAC-TTGTCTAAGG
* * *
20206371 CAACCTAAAAAATAAAGGTTGGGATAGACCTATCTAAGG
1 CAACCT--TAAA-AAAGGTTGGGATAGACTTGTCTAAGG
* *
20206410 CAACCTT-AAACAGGTTGGGATAGACCTGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGACTTGTCTAAGG
*
20206445 CAACCTTAAAAAAGGTTGGAATAGACATTGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGAC-TTGTCTAAGG
* * ** * *
20206482 CAACTTTTAAAAAAGATTGGGATAGACCCGTTTAAAG
1 CAAC-CTTAAAAAAGGTTGGGATAGACTTGTCTAAGG
* * * *
20206519 CAACCTTAAAAAA-GTTGAGATAAATCTTGTCGAAAG
1 CAACCTTAAAAAAGGTTGGGATAGA-CTTGTCTAAGG
20206555 CAAC
1 CAAC
20206559 TTTTTATAAA
Statistics
Matches: 270, Mismatches: 48, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
34 1 0.00
35 66 0.24
36 100 0.37
37 41 0.15
38 34 0.13
39 16 0.06
40 12 0.04
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
CAACCTTAAAAAAGGTTGGGATAGACTTGTCTAAGG
Found at i:20206310 original size:109 final size:106
Alignment explanation
Indices: 20206193--20206542 Score: 317
Period size: 109 Copynumber: 3.2 Consensus size: 106
20206183 CAAGACCAAC
* * * *
20206193 CTTTAAAAAAGGTTGGGATACACTTATCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTTGTTT
1 CTTTAAAAAAGGTTGGGATAAAC-TGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACATTGTCT
* * * *
20206258 AAGGCAACCTTAAAAAGGTTGATATAGTCATTGTCTAAGGCAA
65 AAGGCAACCTTAAAAAGGTTGAGATAGAC-CTATCTAAGGCAA
* * * *
20206301 CTTTTAAAAACGGTTGGGATAAAGCCGTCTAAGGCAGCCTTAAAAAAGTTGGGATAGACATTGTC
1 C-TTTAAAAAAGGTTGGGATAAA-CTGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACATTGTC
** * *
20206366 TAAAACAACCTAAAAAATAAAGGTTGGGATAGACCTATCTAAGGCAA
64 TAAGGCAACCT---TAA-AAAGGTTGAGATAGACCTATCTAAGGCAA
* * * *
20206413 CCTT-AAACAGGTTGGGATAGACCTGTCTAAGGCAACCTTAAAAAAGGTTGGAATAGACATTGTC
1 CTTTAAAAAAGGTTGGGATA-AACTGTCTAAGGCAACCTT-AAAAAGGTTGGGATAGACATTGTC
* * * ** * *
20206477 TAAGGCAACTTTTAAAAAAGATTGGGATAGACCCGTTTAAAGCAA
64 TAAGGCAAC-CTT-AAAAAGGTTGAGATAGACCTATCTAAGGCAA
* *
20206522 CCTTAAAAAA-GTTGAGATAAA
1 CTTTAAAAAAGGTTGGGATAAA
20206543 TCTTGTCGAA
Statistics
Matches: 195, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
108 2 0.01
109 98 0.50
110 35 0.18
111 32 0.16
112 15 0.08
113 13 0.07
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (106 bp):
CTTTAAAAAAGGTTGGGATAAACTGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACATTGTCTA
AGGCAACCTTAAAAAGGTTGAGATAGACCTATCTAAGGCAA
Found at i:20206528 original size:184 final size:184
Alignment explanation
Indices: 20206200--20206540 Score: 533
Period size: 184 Copynumber: 1.9 Consensus size: 184
20206190 AACCTTTAAA
* *
20206200 AAAGGTTGGGATACACTTATCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTTGTTTAAGGCAA
1 AAAGGTTGGGATACACCTATCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAA
* * * *
20206265 CCTTAAAAAGGTTGATATAGTCATTGTCTAAGGCAACTTTTAAAAACGGTTGGGATAAAGCCGTC
66 CCTTAAAAAGGTTGATATAGACATTGTCTAAGGCAACTTTTAAAAAAGATTGGGATAAACCCGTC
* * *
20206330 TAAGGCAGCCTTAAAAAAGTTGGGATAGACATTGTCTAAAACAACCTAAAAAAT
131 TAAAGCAACCTTAAAAAAGTTGAGATAGACATTGTCTAAAACAACCTAAAAAAT
* *
20206384 AAAGGTTGGGATAGACCTATCTAAGGCAACCTTAAACAGGTTGGGATAGACC-TGTCTAAGGCAA
1 AAAGGTTGGGATACACCTATCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAA
*
20206448 CCTTAAAAAAGGTTGGA-ATAGACATTGTCTAAGGCAACTTTTAAAAAAGATTGGGATAGACCCG
66 CCTT-AAAAAGGTT-GATATAGACATTGTCTAAGGCAACTTTTAAAAAAGATTGGGATAAACCCG
*
20206512 TTTAAAGCAACCTTAAAAAAGTTGAGATA
129 TCTAAAGCAACCTTAAAAAAGTTGAGATA
20206541 AATCTTGTCG
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
183 15 0.11
184 125 0.88
185 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (184 bp):
AAAGGTTGGGATACACCTATCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAA
CCTTAAAAAGGTTGATATAGACATTGTCTAAGGCAACTTTTAAAAAAGATTGGGATAAACCCGTC
TAAAGCAACCTTAAAAAAGTTGAGATAGACATTGTCTAAAACAACCTAAAAAAT
Found at i:20206564 original size:74 final size:74
Alignment explanation
Indices: 20206424--20206562 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 74
20206414 CTTAAACAGG
* * * * *
20206424 TTGGGATAGACCTGTCTAAGGCAACCTTAAAAAAGGTTGGAATAGACATTGTCTAAGGCAACTTT
1 TTGGGATAGACCCGTCTAAAGCAACCTTAAAAAAGGTTGGAATAAACATTGTCGAAAGCAACTTT
20206489 TAAAAAAGA
66 TAAAAAAGA
*
20206498 TTGGGATAGACCCGTTTAAAGCAACCTTAAAAAA-GTT-GAGATAAATC-TTGTCGAAAGCAACT
1 TTGGGATAGACCCGTCTAAAGCAACCTTAAAAAAGGTTGGA-ATAAA-CATTGTCGAAAGCAACT
20206560 TTT
64 TTT
20206563 TATAAACCCG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
72 2 0.04
73 23 0.40
74 32 0.56
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (74 bp):
TTGGGATAGACCCGTCTAAAGCAACCTTAAAAAAGGTTGGAATAAACATTGTCGAAAGCAACTTT
TAAAAAAGA
Found at i:20209416 original size:23 final size:23
Alignment explanation
Indices: 20209373--20209416 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
20209363 AAGAAATATA
* *
20209373 TATATTTTTAAATTAAGTTAACT
1 TATATTTTAAAAGTAAGTTAACT
20209396 TATATTCTTAAAAGTAA-TTAA
1 TATATT-TTAAAAGTAAGTTAA
20209417 TATTATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (23 bp):
TATATTTTAAAAGTAAGTTAACT
Found at i:20210336 original size:140 final size:140
Alignment explanation
Indices: 20210148--20210837 Score: 745
Period size: 140 Copynumber: 5.0 Consensus size: 140
20210138 TATGACACTA
* * * **
20210148 GTCGGCATAGTGTT-AGATAAAGCCGACTCTTATTTAAACGTTGCCTTAGGTATGCATATCCTGA
1 GTCGGCATAGTGTTGA-ACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAA
* * * * * * * *
20210212 CCCTTATACAAAGAGTTGACCAAAGCATATGTTAGCAAGTTTATCCCAACATTTAGGAAAGCGTT
65 CTCTTATACAAAGAGTTGGCCAAAGTATATATTAGCAAGTCTATCCCAACACTTAGGAAAGTGTC
20210277 GGCCCAAAAGT
130 GGCCCAAAAGT
* ** * * *
20210288 ATCGGCATAGTGTTGAACAAAGCTTACTCTTAATTAAGCGTTGTCTTAGGCATGCATATCCTAAC
1 GTCGGCATAGTGTTGAACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * * *
20210353 TCGTATACAAA-AGGTTGGCCAAAGTGTATATCAACAAGTCTATCCCAACACTTAGCAAAGTGTC
66 TCTTATACAAAGA-GTTGGCCAAAGTATATATTAGCAAGTCTATCCCAACACTTAGGAAAGTGTC
* *
20210417 AGCCTAAAAGT
130 GGCCCAAAAGT
* * *
20210428 GTCGGCATAGTGTTGGACAAAGCCGACTCTTCTTTAAGCTTTGCCTTAGGCATGCATATCCCAAC
1 GTCGGCATAGTGTTGAACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * * *
20210493 TCTTATATAAAGAATTGGCCAAAGTGTATATTGGCAAGTCTATCCCAACATTTAGGAAAGTGTCG
66 TCTTATACAAAGAGTTGGCCAAAGTATATATTAGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
20210558 GCCCAAAAGT
131 GCCCAAAAGT
* * *
20210568 GTTGACATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
1 GTCGGCATAGTGTTGAACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * * *
20210633 TCTTATATAAAGAGTTGGCCAAAATGTATA-TCGACAAGTTTATCCCAACACTT-----A-----
66 TCTTATACAAAGAGTTGGCCAAAGTATATATTAG-CAAGTCTATCCCAACACTTAGGAAAGTGTC
20210687 GG----AAAGT
130 GGCCCAAAAGT
* *
20210694 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATCCCAAC
1 GTCGGCATAGTGTTGAACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * *
20210759 TCTTATAAAAAGAGTTGGCCAAAGTATAT-GTCGACAAG-CATATCCCAACATTTAGGAAAGTGT
66 TCTTATACAAAGAGTTGGCCAAAGTATATATTAG-CAAGTC-TATCCCAACACTTAGGAAAGTGT
*
20210822 -TGCTCCAAAAGT
129 CGGC-CCAAAAGT
20210834 GTCG
1 GTCG
20210838 CAGTAGGCCT
Statistics
Matches: 469, Mismatches: 61, Indels: 40
0.82 0.11 0.07
Matches are distributed among these distances:
126 113 0.24
130 2 0.00
131 1 0.00
135 2 0.00
139 3 0.01
140 346 0.74
141 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (140 bp):
GTCGGCATAGTGTTGAACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
TCTTATACAAAGAGTTGGCCAAAGTATATATTAGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
GCCCAAAAGT
Found at i:20210652 original size:280 final size:265
Alignment explanation
Indices: 20210148--20210837 Score: 862
Period size: 280 Copynumber: 2.5 Consensus size: 265
20210138 TATGACACTA
* * * * * **
20210148 GTCGGCATAGTGTTAGATAAAGCCGACTCTTATTTAAACGTTGCCTTAGGTATGCATATCCTGAC
1 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATCCCAAC
* * * * * * *
20210213 CCTTATACAAAGAGTTGACCAAAGCATATGTTAGCAAGTTTATCCCAACATTTAGGAAAGCGTTG
66 TCTTATAAAAAGAGTTGGCCAAAGTATATGTTGGCAAGTCTATCCCAACATTTAGGAAAGTG-TG
* * ** *
20210278 GCCCAAAAGTATCGGCATAGTGTTGAACAAAGCTTACTCTTAATTAAGCGTTGTCTTAGGCATGC
130 GCCCAAAAGTGTCGACATAGTGTTGAACAAAGCCGACTCTTAATTAAGCGTTGCCTTAGGCATGC
* *
20210343 ATATCCTAACTCGTATACAAAAGGTTGGCCAAAGTGTATATCAACAAGTCTATCCCAACACTTAG
195 ATATCCCAACTCGTATACAAAAGGTTGGCCAAAATGTATATCAACAAGTCTATCCCAACACTT--
20210408 CAAAGTGTCAGCCTAAAAGT
258 ---A--G---G----AAAGT
* *
20210428 GTCGGCATAGTGTTGGACAAAGCCGACTCTTCTTTAAGCTTTGCCTTAGGCATGCATATCCCAAC
1 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATCCCAAC
* * * *
20210493 TCTTATATAAAGAATTGGCCAAAGTGTATATTGGCAAGTCTATCCCAACATTTAGGAAAGTGTCG
66 TCTTATAAAAAGAGTTGGCCAAAGTATATGTTGGCAAGTCTATCCCAACATTTAGGAAAGTGT-G
* * *
20210558 GCCCAAAAGTGTTGACATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGC
130 GCCCAAAAGTGTCGACATAGTGTTGAACAAAGCCGACTCTTAATTAAGCGTTGCCTTAGGCATGC
* * * *
20210623 ATATCCCAACTCTTATA-TAAAGAGTTGGCCAAAATGTATATCGACAAGTTTATCCCAACACTTA
195 ATATCCCAACTCGTATACAAAAG-GTTGGCCAAAATGTATATCAACAAGTCTATCCCAACACTTA
20210687 GGAAAGT
259 GGAAAGT
20210694 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATCCCAAC
1 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATCCCAAC
* * *
20210759 TCTTATAAAAAGAGTTGGCCAAAGTATATGTCGACAAG-CATATCCCAACATTTAGGAAAGTGTT
66 TCTTATAAAAAGAGTTGGCCAAAGTATATGTTGGCAAGTC-TATCCCAACATTTAGGAAAGTGTG
20210823 GCTCCAAAAGTGTCG
130 GC-CCAAAAGTGTCG
20210838 CAGTAGGCCT
Statistics
Matches: 364, Mismatches: 42, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
265 3 0.01
266 134 0.37
270 1 0.00
273 1 0.00
275 1 0.00
279 5 0.01
280 219 0.60
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (265 bp):
GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATCCCAAC
TCTTATAAAAAGAGTTGGCCAAAGTATATGTTGGCAAGTCTATCCCAACATTTAGGAAAGTGTGG
CCCAAAAGTGTCGACATAGTGTTGAACAAAGCCGACTCTTAATTAAGCGTTGCCTTAGGCATGCA
TATCCCAACTCGTATACAAAAGGTTGGCCAAAATGTATATCAACAAGTCTATCCCAACACTTAGG
AAAGT
Found at i:20210793 original size:126 final size:126
Alignment explanation
Indices: 20210563--20210821 Score: 428
Period size: 126 Copynumber: 2.1 Consensus size: 126
20210553 TGTCGGCCCA
* *
20210563 AAAGTGTTGACATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
1 AAAGTGTCGACATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATC
* * **
20210628 CCAACTCTTATATAAAGAGTTGGCCAAAATGTATATCGACAAGTTTATCCCAACACTTAGG
66 CCAACTCTTATAAAAAGAGTTGGCCAAAATATATATCGACAAGCATATCCCAACACTTAGG
*
20210689 AAAGTGTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATC
1 AAAGTGTCGACATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATC
* * *
20210754 CCAACTCTTATAAAAAGAGTTGGCCAAAGTATATGTCGACAAGCATATCCCAACATTTAGG
66 CCAACTCTTATAAAAAGAGTTGGCCAAAATATATATCGACAAGCATATCCCAACACTTAGG
20210815 AAAGTGT
1 AAAGTGT
20210822 TGCTCCAAAA
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (126 bp):
AAAGTGTCGACATAGTGTTGGACAAAGCCGACTCTTATTTAAGCATTGCCTTAGGCATGCATATC
CCAACTCTTATAAAAAGAGTTGGCCAAAATATATATCGACAAGCATATCCCAACACTTAGG
Found at i:20214933 original size:20 final size:21
Alignment explanation
Indices: 20214908--20214947 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20214898 ATATTAAAAA
20214908 TAAAATAAAA-ATAAATAATC
1 TAAAATAAAACATAAATAATC
*
20214928 TAAAATAAAACATATATAAT
1 TAAAATAAAACATAAATAAT
20214948 GAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAATAAAACATAAATAATC
Found at i:20218105 original size:88 final size:89
Alignment explanation
Indices: 20217999--20218179 Score: 348
Period size: 88 Copynumber: 2.1 Consensus size: 89
20217989 ATTCACCCCA
20217999 AGTATATATTTCATTAAATAGTTTATAATAAACACTTACCTTTTTAAAAAATAATTATATAATAG
1 AGTATATATTTCATTAAATAGTTTATAATAAACACTTACCTTTTTAAAAAATAATTATATAATAG
20218064 TCACTGACATGAT-TAAAGTAGCC
66 TCACTGACATGATGTAAAGTAGCC
20218087 AGTATATATTTCATTAAATAGTTTATAATAAACACTTACCTTTTTAAAAAATAATTATATAATAG
1 AGTATATATTTCATTAAATAGTTTATAATAAACACTTACCTTTTTAAAAAATAATTATATAATAG
20218152 TCACTGACATGATGTAAAGTAGCC
66 TCACTGACATGATGTAAAGTAGCC
20218176 -GTAT
1 AGTAT
20218180 TTTTTTTTAA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
88 82 0.89
89 10 0.11
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (89 bp):
AGTATATATTTCATTAAATAGTTTATAATAAACACTTACCTTTTTAAAAAATAATTATATAATAG
TCACTGACATGATGTAAAGTAGCC
Found at i:20223980 original size:63 final size:63
Alignment explanation
Indices: 20223823--20224010 Score: 207
Period size: 63 Copynumber: 3.0 Consensus size: 63
20223813 CACACGACCT
* * *** * *
20223823 GACACATGCCCGTGTCTCTGGC-CAGTGTGGTCTTTAATAACAAATAGTGAGTCATACGGCCTG
1 GACACATGCTCGTGTCTCTAGCTC-GTGTGGTCTTTAATGGTAAATAGTGAGTCACACAGCCTG
* * ** * *
20223886 GACACATGCTGGTGTCTCTAGTTTATTTGGTCTTTAATGGTAAATAGTGAGTCACACAGCTTG
1 GACACATGCTCGTGTCTCTAGCTCGTGTGGTCTTTAATGGTAAATAGTGAGTCACACAGCCTG
* * * *
20223949 GACACATGCTTGTGTCTCTAGCTCGTGTGGTCCTTAAAGGTAAATAGTGAGTCACACGGCCT
1 GACACATGCTCGTGTCTCTAGCTCGTGTGGTCTTTAATGGTAAATAGTGAGTCACACAGCCT
20224011 AACACACAAC
Statistics
Matches: 102, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 102 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (63 bp):
GACACATGCTCGTGTCTCTAGCTCGTGTGGTCTTTAATGGTAAATAGTGAGTCACACAGCCTG
Found at i:20224564 original size:23 final size:22
Alignment explanation
Indices: 20224537--20224603 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
20224527 AGCGGAAAAT
20224537 AAAAGAGAAGCAAAGAAAAAAGC
1 AAAAGAGAAG-AAAGAAAAAAGC
20224560 AAAAG-GAAGAAA-AAGAAAA-C
1 AAAAGAGAAGAAAGAA-AAAAGC
20224580 AAAAGTAAGAAGAAAGAAAGAAAG
1 AAAAG--AGAAGAAAGAAA-AAAG
20224604 AAAGAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 8 0.22
21 7 0.19
22 4 0.11
23 13 0.35
24 5 0.14
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.01
Consensus pattern (22 bp):
AAAAGAGAAGAAAGAAAAAAGC
Found at i:20224584 original size:20 final size:20
Alignment explanation
Indices: 20224531--20224598 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
20224521 CAACCAAGCG
*
20224531 GAAAATAAAAGAGAAGCAAAGAA
1 GAAAACAAAAG-GAAG-AAA-AA
20224554 -AAAAGCAAAAGGAAGAAAAA
1 GAAAA-CAAAAGGAAGAAAAA
*
20224574 GAAAACAAAAGTAAGAAGAAA
1 GAAAACAAAAGGAAGAA-AAA
20224595 GAAA
1 GAAA
20224599 GAAAGAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 13 0.32
21 14 0.35
22 8 0.20
23 5 0.12
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.03
Consensus pattern (20 bp):
GAAAACAAAAGGAAGAAAAA
Found at i:20228870 original size:2 final size:2
Alignment explanation
Indices: 20228863--20228887 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20228853 TTGTATTAGC
20228863 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20228888 ACGAGTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20234213 original size:25 final size:24
Alignment explanation
Indices: 20234084--20234216 Score: 101
Period size: 25 Copynumber: 5.3 Consensus size: 24
20234074 CAACTAGTAT
*
20234084 GAGCTTACC-AATTTACAGCTCATGA
1 GAGCTTACCGTATTT-CAGCTCA-GA
20234109 GAGCTTACCG-ATTCTCAGCTC-GTA
1 GAGCTTACCGTATT-TCAGCTCAG-A
**
20234133 TGAGCTTACCGTATTTCAGCTTGGA
1 -GAGCTTACCGTATTTCAGCTCAGA
* *** *
20234158 TAAGCTTATTTTATTTCAGCTCGGA
1 -GAGCTTACCGTATTTCAGCTCAGA
20234183 GGAGCTTACCGTATTTCAGCTCAGA
1 -GAGCTTACCGTATTTCAGCTCAGA
20234208 GAAGCTTAC
1 G-AGCTTAC
20234217 AAATTATGGC
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 81 0.91
26 5 0.06
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (24 bp):
GAGCTTACCGTATTTCAGCTCAGA
Found at i:20249889 original size:21 final size:21
Alignment explanation
Indices: 20249843--20249895 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20249833 GGGTACATGG
* * *
20249843 CCGTTTAACTGAGGGACACGC
1 CCGTGTAACTGAGGGAAACAC
*
20249864 CCGTGTGACTGAGGGAAACAC
1 CCGTGTAACTGAGGGAAACAC
*
20249885 TCGTGTAACTG
1 CCGTGTAACTG
20249896 GGTTACACGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.21
Consensus pattern (21 bp):
CCGTGTAACTGAGGGAAACAC
Found at i:20253887 original size:18 final size:18
Alignment explanation
Indices: 20253866--20253910 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
20253856 AACATTTATC
* *
20253866 ATTTCTTGAATTTTTAAA
1 ATTTCTTAAAATTTTAAA
*
20253884 ATTTTTTAAAATTTTAAA
1 ATTTCTTAAAATTTTAAA
20253902 ATATTCTTA
1 AT-TTCTTA
20253911 TGAATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTCTTAAAATTTTAAA
Found at i:20261525 original size:12 final size:12
Alignment explanation
Indices: 20261508--20261532 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20261498 TATATTTACA
20261508 AAATGTATAAAT
1 AAATGTATAAAT
20261520 AAATGTATAAAT
1 AAATGTATAAAT
20261532 A
1 A
20261533 TAATATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AAATGTATAAAT
Found at i:20261680 original size:9 final size:9
Alignment explanation
Indices: 20261666--20261697 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
20261656 AAAAGTTATG
20261666 AAAATAAAA
1 AAAATAAAA
20261675 AAAAT-AAA
1 AAAATAAAA
20261683 AAAATAAAA
1 AAAATAAAA
20261692 AAAATA
1 AAAATA
20261698 TGTACATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAA
Found at i:20261771 original size:3 final size:3
Alignment explanation
Indices: 20261763--20261797 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
20261753 TATGTATAGA
*
20261763 AAT AAT AAT AAT AAT AAT AAT AAAT AAT GAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
20261798 CTATTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20263064 original size:10 final size:10
Alignment explanation
Indices: 20263033--20263079 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
20263023 TACAAATTAG
20263033 ATATATAAAA
1 ATATATAAAA
*
20263043 ATAGA-AATAA
1 ATATATAA-AA
20263053 ATATATAAAA
1 ATATATAAAA
20263063 AT-TCATAAAA
1 ATAT-ATAAAA
20263073 ATATATA
1 ATATATA
20263080 TAATCTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 3 0.10
10 25 0.81
11 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
ATATATAAAA
Found at i:20263074 original size:20 final size:20
Alignment explanation
Indices: 20263022--20263079 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
20263012 TTAAATGTAT
*
20263022 ATACAAATTAGATATATAAAA
1 ATACAAA-TAAATATATAAAA
*
20263043 ATAGAAATAAATATATAAAA
1 ATACAAATAAATATATAAAA
*
20263063 ATTCATAA-AAATATATA
1 ATACA-AATAAATATATA
20263080 TAATCTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 24 0.75
21 8 0.25
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
ATACAAATAAATATATAAAA
Found at i:20263109 original size:18 final size:20
Alignment explanation
Indices: 20263069--20263112 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
20263059 AAAAATTCAT
*
20263069 AAAAATATATATAATCTAGA
1 AAAAAAATATATAATCTAGA
*
20263089 AAAAAAATATA-AAT-TATA
1 AAAAAAATATATAATCTAGA
20263107 AAAAAA
1 AAAAAA
20263113 TTTACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 3 0.14
20 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAATATATAATCTAGA
Found at i:20263185 original size:11 final size:11
Alignment explanation
Indices: 20263169--20263194 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20263159 ATATTATTAG
20263169 AAAAAATTGTA
1 AAAAAATTGTA
20263180 AAAAAATTGTA
1 AAAAAATTGTA
20263191 AAAA
1 AAAA
20263195 TTATTTANNN
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAAAATTGTA
Found at i:20263304 original size:21 final size:22
Alignment explanation
Indices: 20263260--20263304 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20263250 ATATAATTTT
* *
20263260 TTATAAAATTTTAAAATATATA
1 TTATAAAATTCTAAAATAGATA
*
20263282 TTATAAAATTCT-AAATAGGTA
1 TTATAAAATTCTAAAATAGATA
20263303 TT
1 TT
20263305 CTAATAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TTATAAAATTCTAAAATAGATA
Found at i:20266394 original size:20 final size:21
Alignment explanation
Indices: 20266347--20266394 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
20266337 TTGACTTGTT
20266347 TTAAAA-TAGTTTTAACTCAA
1 TTAAAATTAGTTTTAACTCAA
**
20266367 TTAAAATTA-TTTTAACTTGA
1 TTAAAATTAGTTTTAACTCAA
20266387 TTAAAATT
1 TTAAAATT
20266395 TGATTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAAAATTAGTTTTAACTCAA
Found at i:20269091 original size:15 final size:14
Alignment explanation
Indices: 20269067--20269097 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
20269057 TTATCACTAT
20269067 TATTATATTATATA
1 TATTATATTATATA
20269081 TATTATCATTATATA
1 TATTAT-ATTATATA
20269096 TA
1 TA
20269098 CTTTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATATTATATA
Found at i:20274136 original size:7 final size:7
Alignment explanation
Indices: 20274111--20274152 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
20274101 AGTGATGTGA
20274111 AAAAATG
1 AAAAATG
20274118 AAAAGATG
1 AAAA-ATG
20274126 -AAAATG
1 AAAAATG
20274132 AAAAATG
1 AAAAATG
20274139 AAAAA-G
1 AAAAATG
20274145 TAAAAATG
1 -AAAAATG
20274153 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:20274150 original size:21 final size:21
Alignment explanation
Indices: 20274111--20274152 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20274101 AGTGATGTGA
*
20274111 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
20274132 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
20274153 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:20276313 original size:132 final size:132
Alignment explanation
Indices: 20275573--20276279 Score: 1195
Period size: 132 Copynumber: 5.4 Consensus size: 132
20275563 NNNNNNNNNN
* * ***
20275573 ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTAGTTGGC
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACT-TCCCTAGGCAGC
* * * *
20275637 AGTGGAATAGATTGAATATTTCAGATCTTGTCTCTCTAAGCAGTAGTGGAGCATATCAAAGATGA
65 AGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
20275702 CAG
130 CAG
20275705 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCT-GAGCAGC
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAG-GCAGC
*
20275769 AGTGGAATAGATTGAATATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
65 AGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG
20275834 CAG
130 CAG
*
20275837 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAGGCAGCG
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAGGCAGCA
20275902 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20275967 AG
131 AG
*
20275969 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAGGCAGCG
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAGGCAGCA
20276034 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
66 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
20276099 AG
131 AG
* *
20276101 ATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAGGCCAGTAATTCTACTTCCCTGGGCAGCA
1 ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAGGCAGCA
* *
20276166 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGG-
66 GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
*
20276230 TG
131 AG
* *
20276232 AATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT
1 -ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATT
20276280 ATATCTCCCT
Statistics
Matches: 552, Mismatches: 19, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
131 2 0.00
132 548 0.99
133 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTAATTCTACTTCCCTAGGCAGCA
GTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGC
AG
Found at i:20276413 original size:100 final size:100
Alignment explanation
Indices: 20276295--20276588 Score: 401
Period size: 100 Copynumber: 2.9 Consensus size: 100
20276285 TCCCTGGGCG
* * *
20276295 GCAGTAGAACAAATTGAAGCTACGACGGCGAATCTGGTTTCCCTGATATTGCCATTAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGAATCTGGTTTCCCTGATATTGCAATTAAAAAGATT
* * * *
20276360 GAAGCCACAACGGTGGATCTTACTTCCTTAGCAGT
66 GAAGCCACAACGGCGAATCTTACTTCCCTAACAGT
*
20276395 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGAATCTGGTTTCCCTGATATTGCAATTAAAAAGATT
** * *
20276460 GAAGCCACAACAACAAATCTTACTTCCCTAACGGT
66 GAAGCCACAACGGCGAATCTTACTTCCCTAACAGT
* * * * * * *
20276495 GCAGTGGATCAGATCGAAGCTACAACGGCGAATCTGG-CTCCTCCGACATTGCAATTAAAAATAT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGAATCTGGTTTCC-CTGATATTGCAATTAAAAAGAT
20276559 TGAAGCCACAACGGCGAATCTTACTTCCCT
65 TGAAGCCACAACGGCGAATCTTACTTCCCT
20276589 GGCGGNNNNN
Statistics
Matches: 170, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
99 3 0.02
100 167 0.98
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (100 bp):
GCAGTGGAACAGATTGAAGCTACGACGGCGAATCTGGTTTCCCTGATATTGCAATTAAAAAGATT
GAAGCCACAACGGCGAATCTTACTTCCCTAACAGT
Found at i:20276459 original size:50 final size:50
Alignment explanation
Indices: 20276307--20276464 Score: 165
Period size: 50 Copynumber: 3.2 Consensus size: 50
20276297 AGTAGAACAA
* *
20276307 ATTGAAGCTACGACGGCGAATCTGGTTTCCCTGATATTGCCATTAAAAAG
1 ATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAG
* * * *** * * * * ** *
20276357 ATTGAAGCCACAACGGTGGATCTTACTT-CCTTAGCAGTGCAGTGGAACAG
1 ATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TATTGCAATTAAAAAG
20276407 ATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAG
1 ATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAG
20276457 ATTGAAGC
1 ATTGAAGC
20276465 CACAACAACA
Statistics
Matches: 78, Mismatches: 28, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
49 4 0.05
50 70 0.90
51 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (50 bp):
ATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAG
Found at i:20276905 original size:44 final size:44
Alignment explanation
Indices: 20276847--20276960 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
20276837 CAGATTTTAC
* * *
20276847 CTCCCTGAAGTTGCATTGGAGCAGATTAAAGCCAATA-ATC-CTAT
1 CTCCTTGAAGTTGCAATGGAGCAGATTAAAACC-ATAGATCTC-AT
**
20276891 CTCCTTGAAGTTGCAATGGAGTGGATTAAAACCATAGATCTCAT
1 CTCCTTGAAGTTGCAATGGAGCAGATTAAAACCATAGATCTCAT
* **
20276935 CTCTTTGAAGTTGCAACAGAGCAGAT
1 CTCCTTGAAGTTGCAATGGAGCAGAT
20276961 CGCATCATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
43 3 0.05
44 54 0.93
45 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
CTCCTTGAAGTTGCAATGGAGCAGATTAAAACCATAGATCTCAT
Found at i:20279979 original size:11 final size:12
Alignment explanation
Indices: 20279964--20279992 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
20279954 TGGGGGGGAG
20279964 CATTTTTCTTTT
1 CATTTTTCTTTT
20279976 -ATTTTTCTTTT
1 CATTTTTCTTTT
20279987 CATTTT
1 CATTTT
20279993 CATTTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (12 bp):
CATTTTTCTTTT
Found at i:20280840 original size:15 final size:15
Alignment explanation
Indices: 20280822--20280854 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20280812 TTATCTTTAC
20280822 TATTGTTATTATTAT
1 TATTGTTATTATTAT
20280837 TATTGTTATTATTAT
1 TATTGTTATTATTAT
20280852 TAT
1 TAT
20280855 CTTAGCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TATTGTTATTATTAT
Found at i:20282632 original size:21 final size:19
Alignment explanation
Indices: 20282604--20282643 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
20282594 CGGAAAATGA
20282604 TTTCGGAAAAATAATTTACT
1 TTTCGG-AAAATAATTTACT
*
20282624 TTTCTGGAAAATGATTTACT
1 TTTC-GGAAAATAATTTACT
20282644 GAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (19 bp):
TTTCGGAAAATAATTTACT
Found at i:20285175 original size:3 final size:3
Alignment explanation
Indices: 20285167--20285191 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20285157 TATATAACTT
20285167 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
20285192 CAAATAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:20286235 original size:29 final size:29
Alignment explanation
Indices: 20286176--20286232 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
20286166 TAACTTACTT
20286176 TTTTAATATTAAAAATATTTTCTATTAAA
1 TTTTAATATTAAAAATATTTTCTATTAAA
* *
20286205 TTTT-ATATTTAAATTATTTT-TAGTTAAA
1 TTTTAATATTAAAAATATTTTCTA-TTAAA
20286233 ATTAAATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 19 0.76
29 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTTAATATTAAAAATATTTTCTATTAAA
Found at i:20293578 original size:45 final size:45
Alignment explanation
Indices: 20293529--20293622 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
20293519 TTAATTCGAC
20293529 AAATTTACTAGACCAATCTCTAATATATTTTTATATTTTCTCTGT
1 AAATTTACTAGACCAATCTCTAATATATTTTTATATTTTCTCTGT
20293574 AAATTTACTAGACCAATCTCTAATATATTTTTATATTTTCTCTGT
1 AAATTTACTAGACCAATCTCTAATATATTTTTATATTTTCTCTGT
20293619 AAAT
1 AAAT
20293623 GTTCATATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (45 bp):
AAATTTACTAGACCAATCTCTAATATATTTTTATATTTTCTCTGT
Found at i:20294136 original size:21 final size:21
Alignment explanation
Indices: 20294112--20294159 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
20294102 ACGTTAGTTC
20294112 TTTCTTCTTTAATATTTTTTA
1 TTTCTTCTTTAATATTTTTTA
*
20294133 TTTCTTCTTTAATCTTTTTTA
1 TTTCTTCTTTAATATTTTTTA
20294154 TTTCTT
1 TTTCTT
20294160 TCTTCTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTCTTCTTTAATATTTTTTA
Found at i:20306378 original size:54 final size:52
Alignment explanation
Indices: 20306291--20306486 Score: 153
Period size: 54 Copynumber: 3.6 Consensus size: 52
20306281 ATCAGTAGAC
* * * *
20306291 CACAAGATTATGAAAATCTTGTAAGTACAAGGTTACGATATTAACTCAACGAA
1 CACAAGATTCT-AAAATCTTGGAAGTGCAAGGTTACGATATTAAATCAACGAA
* * **
20306344 TCACAAGATTCTAATAATTTTGGAAGTGCAAGGTTACGATCTTAAATCAGTGAA
1 -CACAAGATTCTAA-AATCTTGGAAGTGCAAGGTTACGATATTAAATCAACGAA
** * * ***
20306398 CTGTAAGATTCTAAAAATCTTAGAAGTGCAAGGTTGCGAT-TGTAAATCGGTGAA
1 C-ACAAGATTCT-AAAATCTTGGAAGTGCAAGGTTACGATAT-TAAATCAACGAA
*
20306452 C-CGTAAGATTCTAAAAATCATGGAAGTGCAAGGTT
1 CAC--AAGATTCT-AAAATCTTGGAAGTGCAAGGTT
20306487 GTGATTGTAA
Statistics
Matches: 119, Mismatches: 17, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
53 4 0.03
54 113 0.95
55 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (52 bp):
CACAAGATTCTAAAATCTTGGAAGTGCAAGGTTACGATATTAAATCAACGAA
Found at i:20306487 original size:54 final size:54
Alignment explanation
Indices: 20306348--20306631 Score: 240
Period size: 54 Copynumber: 5.3 Consensus size: 54
20306338 AACGAATCAC
* * * * * *
20306348 AAGATTCTAATAATTTTGGAAGTGCAAGGTTACGATCT-TAAATCAGTGAACTGT
1 AAGATTCTAAAAATCTTGGAAGTGCAAGGTTGCGAT-TGTAAATCGGTAAACCGT
* *
20306402 AAGATTCTAAAAATCTTAGAAGTGCAAGGTTGCGATTGTAAATCGGTGAACCGT
1 AAGATTCTAAAAATCTTGGAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCGT
* * *
20306456 AAGATTCTAAAAATCATGGAAGTGCAAGGTTGTGATTGTAAA----AAAACCAG-
1 AAGATTCTAAAAATCTTGGAAGTGCAAGGTTGCGATTGTAAATCGGTAAACC-GT
* * * * ** * * * *
20306506 AAGTTTCTGAAAATCGTGTAAGTATAGGGTTGCAATTGTAAATTGGCAAACCGT
1 AAGATTCTAAAAATCTTGGAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCGT
* * * ***
20306560 AAGATTCTAAAAATCTTGAAACTGCAAGGTTGTGATTGTAAATCAACAAACCCG-
1 AAGATTCTAAAAATCTTGGAAGTGCAAGGTTGCGATTGTAAATCGGTAAA-CCGT
20306614 AAGATTCTGAAAAATCTT
1 AAGATTCT-AAAAATCTT
20306632 ATAAGTATAG
Statistics
Matches: 187, Mismatches: 34, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
50 37 0.20
51 1 0.01
53 2 0.01
54 135 0.72
55 12 0.06
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (54 bp):
AAGATTCTAAAAATCTTGGAAGTGCAAGGTTGCGATTGTAAATCGGTAAACCGT
Found at i:20306558 original size:104 final size:108
Alignment explanation
Indices: 20306402--20306671 Score: 334
Period size: 104 Copynumber: 2.5 Consensus size: 108
20306392 AGTGAACTGT
* * ** * * **
20306402 AAGATTCT-AAAAATCTTAGAAGTGCAAGGTTGCGATTGTAAATCGGTGAACCGTAAGATTCTAA
1 AAGATTCTGAAAAATCGTATAAGTATAGGGTTGCAATTGTAAATCGGCAAACCGTAAGATTCTAA
* *
20306466 AAATCATGGAAGTGCAAGGTTGTGATTGT-AA-AA-AAACCAG
66 AAATCATGAAACTGCAAGGTTGTGATTGTAAACAACAAACCAG
* * *
20306506 AAGTTTCTG-AAAATCGTGTAAGTATAGGGTTGCAATTGTAAATTGGCAAACCGTAAGATTCTAA
1 AAGATTCTGAAAAATCGTATAAGTATAGGGTTGCAATTGTAAATCGGCAAACCGTAAGATTCTAA
* *
20306570 AAATCTTGAAACTGCAAGGTTGTGATTGTAAATCAACAAACCCG
66 AAATCATGAAACTGCAAGGTTGTGATTGTAAA-CAACAAACCAG
* * *
20306614 AAGATTCTGAAAAATCTTATAAGTATAGGGTTGCAATCGTAAATCGACAAACCGTAAG
1 AAGATTCTGAAAAATCGTATAAGTATAGGGTTGCAATTGTAAATCGGCAAACCGTAAG
20306672 TGGTTACTAC
Statistics
Matches: 139, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
104 78 0.56
105 2 0.01
107 2 0.01
108 14 0.10
109 43 0.31
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (108 bp):
AAGATTCTGAAAAATCGTATAAGTATAGGGTTGCAATTGTAAATCGGCAAACCGTAAGATTCTAA
AAATCATGAAACTGCAAGGTTGTGATTGTAAACAACAAACCAG
Found at i:20306656 original size:55 final size:55
Alignment explanation
Indices: 20306499--20306666 Score: 164
Period size: 54 Copynumber: 3.1 Consensus size: 55
20306489 GATTGTAAAA
* * * * * *
20306499 AAACCAGAAGTTTCTG-AAAATCGTGTAAGTATAGGGTTGCAATTGTAAATTGGC
1 AAACCCGAAGATTCTGAAAAATCTTATAAGTATAGGGTTGCAATTGTAAATCGAC
* ** * ** *
20306553 AAA-CCGTAAGATTCT-AAAAATCTTGA-AACTGCAAGGTTGTGATTGTAAATCAAC
1 AAACCCG-AAGATTCTGAAAAATCTT-ATAAGTATAGGGTTGCAATTGTAAATCGAC
*
20306607 AAACCCGAAGATTCTGAAAAATCTTATAAGTATAGGGTTGCAATCGTAAATCGAC
1 AAACCCGAAGATTCTGAAAAATCTTATAAGTATAGGGTTGCAATTGTAAATCGAC
20306662 AAACC
1 AAACC
20306667 GTAAGTGGTT
Statistics
Matches: 87, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
53 2 0.02
54 48 0.55
55 37 0.43
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (55 bp):
AAACCCGAAGATTCTGAAAAATCTTATAAGTATAGGGTTGCAATTGTAAATCGAC
Found at i:20308116 original size:16 final size:16
Alignment explanation
Indices: 20308095--20308128 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20308085 CTTCAACCTC
*
20308095 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
20308111 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
20308127 TC
1 TC
20308129 CTCTCCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:20308743 original size:18 final size:18
Alignment explanation
Indices: 20308720--20308757 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
20308710 CTATCTGCTG
20308720 TTGTTTAAAGTTGTGCAT
1 TTGTTTAAAGTTGTGCAT
*
20308738 TTGTTTAAATTTGTGCAT
1 TTGTTTAAAGTTGTGCAT
20308756 TT
1 TT
20308758 TTTCAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.55
Consensus pattern (18 bp):
TTGTTTAAAGTTGTGCAT
Found at i:20310293 original size:34 final size:35
Alignment explanation
Indices: 20310227--20310293 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20310217 CAAACACCAG
20310227 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
20310262 AAAATATTTTCTAG-AAATTATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
20310294 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:20311374 original size:18 final size:18
Alignment explanation
Indices: 20311348--20311382 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20311338 TAATTTTTGT
20311348 ACTCAAGCTCGAACTCGA
1 ACTCAAGCTCGAACTCGA
* *
20311366 ACTCGAGCTCGAGCTCG
1 ACTCAAGCTCGAACTCG
20311383 GCTCAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
ACTCAAGCTCGAACTCGA
Found at i:20311480 original size:23 final size:23
Alignment explanation
Indices: 20311450--20311501 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
20311440 NNNNNNATAT
20311450 ATATATATATATATATCAGGGTG
1 ATATATATATATATATCAGGGTG
20311473 ATATATATATATATATCAGGGTG
1 ATATATATATATATATCAGGGTG
20311496 ATATAT
1 ATATAT
20311502 GCACGGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (23 bp):
ATATATATATATATATCAGGGTG
Found at i:20312929 original size:18 final size:18
Alignment explanation
Indices: 20312906--20312958 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
20312896 GGTTGAATCA
20312906 TTTTAATATATTTTTTAT
1 TTTTAATATATTTTTTAT
20312924 TTTTAA-A-ATTTTTATGAT
1 TTTTAATATATTTTT-T-AT
20312942 TTTTAAT-TATTTATTTA
1 TTTTAATATATTT-TTTA
20312959 GTTATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 15 0.50
19 5 0.17
20 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTAATATATTTTTTAT
Found at i:20314337 original size:3 final size:3
Alignment explanation
Indices: 20314329--20314449 Score: 72
Period size: 3 Copynumber: 39.7 Consensus size: 3
20314319 TATAGTCTCG
* * *
20314329 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TCA -AA CTAA TTA GTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA
* * *
20314373 TTA TCA TTA TTA -TA TTTA TTA TTA TCA TTA TTA TT- GTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* *
20314418 TTA TTA CTTA CCTTA CTA TTA TTA TTT TTA TT
1 TTA TTA -TTA --TTA TTA TTA TTA TTA TTA TT
20314450 TACCCATTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
2 8 0.09
3 71 0.76
4 11 0.12
5 4 0.04
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:20314538 original size:30 final size:28
Alignment explanation
Indices: 20314496--20314559 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
20314486 ATAATGCACG
*
20314496 TACATA-TTTTTATAACTCATTTATATATA
1 TACATACTTTTTATAA-T-ATATATATATA
20314525 TACATACTTTTTATAATATATATATATA
1 TACATACTTTTTATAATATATATATATA
*
20314553 TATATAC
1 TACATAC
20314560 ACATCTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 16 0.50
29 7 0.22
30 9 0.28
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (28 bp):
TACATACTTTTTATAATATATATATATA
Found at i:20320810 original size:44 final size:43
Alignment explanation
Indices: 20320747--20320938 Score: 149
Period size: 44 Copynumber: 4.5 Consensus size: 43
20320737 GCTACAATCC
20320747 TATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAACGGA-TAAAACCATAGATCT
* * * * *** *
20320791 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAACGGATAAAACCATAGATCT
**** * * ** *
20320832 TATCTCCCT-AAGAAATAGTGGAGCGGACAGAAAAAATCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAACGGATA-AAACCAT-AGATCT
20320875 TATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAACGGA-TAAAACCATAGATCT
* *
20320919 TATCGCTCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGT
20320939 AGAGCAGATC
Statistics
Matches: 108, Mismatches: 33, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
40 12 0.11
41 13 0.12
42 2 0.02
43 17 0.16
44 63 0.58
45 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAACGGATAAAACCATAGATCT
Found at i:20320969 original size:128 final size:128
Alignment explanation
Indices: 20320741--20321025 Score: 561
Period size: 128 Copynumber: 2.2 Consensus size: 128
20320731 AGTAAAGCTA
*
20320741 CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCTCTCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCGCTCTGAAGTT
20320806 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
66 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
20320869 CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCGCTCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCGCTCTGAAGTT
20320934 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
66 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
20320997 CAATCCTATCTCCCTGAAGTTGCAGTGGA
1 CAATCCTATCTCCCTGAAGTTGCAGTGGA
20321026 GCAGACTGAA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 156 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (128 bp):
CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCGCTCTGAAGTT
GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
Found at i:20321058 original size:128 final size:128
Alignment explanation
Indices: 20320741--20321206 Score: 510
Period size: 128 Copynumber: 3.6 Consensus size: 128
20320731 AGTAAAGCTA
* * * * *
20320741 CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCTCTCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAACCATAGATCCTAACTCCCTGAAGTT
20320806 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
66 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
* * * * * *
20320869 CAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCATAGATCTTATCGCTCTGAAGTT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAACCATAGATCCTAACTCCCTGAAGTT
20320934 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
66 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
* * * *
20320997 CAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTA-ATCCTAACTCCCTGAAGT
1 CAATCCTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAACCA-TAGATCCTAACTCCCTGAAGT
* * * * **** * *
20321061 TGCAGTGGAGCAGA-CTGAAGCTACTAA-TCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAA
65 TGCAGTAGAGCAGATC-GCA--T-C-AAGTCTTATCTCCCT-AAGAAATAGTGGAGCGGACAGAA
***
20321124 GCTA-
124 AAAAT
* * * * *
20321128 CTAATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTA-ATCCTAACTCCCTGAAG
1 C-AATCCTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAACCA-TAGATCCTAACTCCCTGAAG
*
20321192 TTGCAGTGGAGCAGA
64 TTGCAGTAGAGCAGA
20321207 CTGAAGCTAC
Statistics
Matches: 305, Mismatches: 25, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
127 1 0.00
128 193 0.63
129 2 0.01
130 1 0.00
131 12 0.04
132 96 0.31
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (128 bp):
CAATCCTATCTCCCTGAAGTTGCAGTGGAACAGACTAAAACCATAGATCCTAACTCCCTGAAGTT
GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCGGACAGAAAAAAT
Found at i:20321313 original size:44 final size:44
Alignment explanation
Indices: 20320998--20321291 Score: 570
Period size: 44 Copynumber: 6.7 Consensus size: 44
20320988 AGAAAAAATC
*
20320998 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
20321042 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
20321086 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
20321130 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
20321174 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
20321218 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
*
20321262 AATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 AATCCTAACTCCCTGAAGTTGCAGTGGAGC
20321292 GGGTTAAAAT
Statistics
Matches: 248, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 248 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (44 bp):
AATCCTAACTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACT
Found at i:20322887 original size:3 final size:3
Alignment explanation
Indices: 20322879--20322973 Score: 111
Period size: 3 Copynumber: 30.7 Consensus size: 3
20322869 TTTAGTCCCG
*
20322879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
20322927 TTA TT- GTA TTTA TTA TTA TTA CTTA CCTTA CTA TTA TTA TTT TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA -TTA --TTA TTA TTA TTA TTA TTA TT
20322974 TACCCATTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 70 0.88
4 5 0.06
5 4 0.05
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:20323087 original size:16 final size:17
Alignment explanation
Indices: 20323061--20323221 Score: 75
Period size: 17 Copynumber: 9.6 Consensus size: 17
20323051 ATATATATAC
20323061 ATACTTATATAACTTT-T
1 ATACTTATATAA-TTTAT
20323078 ATACTT-TATAATTTAT
1 ATACTTATATAATTTAT
* **
20323094 ATACATATATACATACAT
1 ATACTTATATA-ATTTAT
* * * *
20323112 ACATTTTTATAATATAT
1 ATACTTATATAATTTAT
** *
20323129 ATACACATTTAATTATAT
1 ATACTTATATAATT-TAT
* * *
20323147 ATACATACATATATTT-G
1 ATACTTATATA-ATTTAT
* *
20323164 AT--TTATAT-ATATAC
1 ATACTTATATAATTTAT
* *
20323178 ATACTTATATATTTTTT
1 ATACTTATATAATTTAT
20323195 ATACTT-TATAATTTAT
1 ATACTTATATAATTTAT
*
20323211 ATACATATATA
1 ATACTTATATA
20323222 CATACATACA
Statistics
Matches: 104, Mismatches: 30, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
13 3 0.03
14 2 0.02
15 7 0.07
16 30 0.29
17 36 0.35
18 23 0.22
19 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (17 bp):
ATACTTATATAATTTAT
Found at i:20323146 original size:117 final size:119
Alignment explanation
Indices: 20323004--20323250 Score: 426
Period size: 117 Copynumber: 2.1 Consensus size: 119
20322994 AGATTTTGTT
* *
20323004 ATATATATACATACTTATATATATATATACATACATACCTTTGATTTATATATATACATACTTAT
1 ATATATATACACACTTATATATATATATACATACATACATTTGATTTATATATATACATACTTAT
20323069 ATAACTTTTATACTTTATAATTTATATACATATATACATACATACATTTTTATA
66 ATAACTTTTATACTTTATAATTTATATACATATATACATACATACATTTTTATA
* *
20323123 ATATATATACACATTTA-AT-TATATATACATACATATATTTGATTTATATATATACATACTTAT
1 ATATATATACACACTTATATATATATATACATACATACATTTGATTTATATATATACATACTTAT
**
20323186 ATATTTTTTATACTTTATAATTTATATACATATATACATACATACATTTTTATA
66 ATAACTTTTATACTTTATAATTTATATACATATATACATACATACATTTTTATA
20323240 ATATATATACA
1 ATATATATACA
20323251 TATGCACGTA
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
117 105 0.86
118 2 0.02
119 15 0.12
ACGTcount: A:0.42, C:0.11, G:0.01, T:0.47
Consensus pattern (119 bp):
ATATATATACACACTTATATATATATATACATACATACATTTGATTTATATATATACATACTTAT
ATAACTTTTATACTTTATAATTTATATACATATATACATACATACATTTTTATA
Found at i:20323195 original size:27 final size:26
Alignment explanation
Indices: 20323142--20323197 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
20323132 CACATTTAAT
20323142 TATATATACATACATATATTTGATTTA
1 TATATATACATACATATATTT-ATTTA
20323169 TATATATACATACTTATATATTT-TTTA
1 TATATATACATAC--ATATATTTATTTA
20323196 TA
1 TA
20323198 CTTTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 19 0.70
29 8 0.30
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (26 bp):
TATATATACATACATATATTTATTTA
Found at i:20323200 original size:17 final size:17
Alignment explanation
Indices: 20323178--20323221 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
20323168 ATATATATAC
* *
20323178 ATACTTATATATTTTTT
1 ATACTTATATAATTTAT
20323195 ATACTT-TATAATTTAT
1 ATACTTATATAATTTAT
*
20323211 ATACATATATA
1 ATACTTATATA
20323222 CATACATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (17 bp):
ATACTTATATAATTTAT
Found at i:20323268 original size:33 final size:34
Alignment explanation
Indices: 20323199--20323273 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
20323189 TTTTTTATAC
* *
20323199 TTTATAATTTATATACATATATACATACATACATT
1 TTTATAATATATATACATATACACATACATA-ATT
* *
20323234 TTTATAATATATATACATATGCACGTACAT-ATT
1 TTTATAATATATATACATATACACATACATAATT
20323267 TTTATAA
1 TTTATAA
20323274 CTCATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 10 0.28
35 26 0.72
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (34 bp):
TTTATAATATATATACATATACACATACATAATT
Found at i:20325735 original size:17 final size:17
Alignment explanation
Indices: 20325713--20325746 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20325703 GTGAGTTTCA
*
20325713 AATATAATTATCTTATT
1 AATATAAATATCTTATT
*
20325730 AATATAAATATTTTATT
1 AATATAAATATCTTATT
20325747 TTTTTATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATAAATATCTTATT
Found at i:20329990 original size:2 final size:2
Alignment explanation
Indices: 20329983--20330008 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20329973 TACCCATAAA
20329983 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20330009 CACTTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20331473 original size:24 final size:24
Alignment explanation
Indices: 20331427--20331473 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20331417 CATGTCAATG
*
20331427 AAAAATTTTAAAAATATAGAAAAT
1 AAAAATTTTAAAAATATAAAAAAT
*
20331451 AAAAATATTT-AAAATCTAAAAAA
1 AAAAAT-TTTAAAAATATAAAAAA
20331474 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAAATTTTAAAAATATAAAAAAT
Found at i:20331556 original size:54 final size:55
Alignment explanation
Indices: 20331497--20331606 Score: 213
Period size: 54 Copynumber: 2.0 Consensus size: 55
20331487 TCATAACAAT
20331497 TCAAAAAAAATTGATTGTCCCCGCTCCATTATATTAAATTATT-TTTTACCCATA
1 TCAAAAAAAATTGATTGTCCCCGCTCCATTATATTAAATTATTATTTTACCCATA
20331551 TCAAAAAAAATTGATTGTCCCCGCTCCATTATATTAAATTATTATTTTACCCATA
1 TCAAAAAAAATTGATTGTCCCCGCTCCATTATATTAAATTATTATTTTACCCATA
20331606 T
1 T
20331607 ATATTTAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 43 0.78
55 12 0.22
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.39
Consensus pattern (55 bp):
TCAAAAAAAATTGATTGTCCCCGCTCCATTATATTAAATTATTATTTTACCCATA
Found at i:20339099 original size:18 final size:18
Alignment explanation
Indices: 20339058--20339099 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
20339048 GTTAACTCTG
*
20339058 GTATCTGTTAATCTTTCT
1 GTATCTGATAATCTTTCT
*
20339076 -TATCTGATATTCTTTCT
1 GTATCTGATAATCTTTCT
20339093 GTATCTG
1 GTATCTG
20339100 GCTATGGGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (18 bp):
GTATCTGATAATCTTTCT
Found at i:20349943 original size:24 final size:25
Alignment explanation
Indices: 20349916--20349987 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
20349906 GGATGTTCCG
20349916 AAGAGCTAT-TAACGGGAAGCTCTC
1 AAGAGCTATATAACGGGAAGCTCTC
* * * *
20349940 AAGAACCATATAACAGGAAGCT-TG
1 AAGAGCTATATAACGGGAAGCTCTC
*
20349964 AGAGAGCT-TATAACGGGATGCTCT
1 A-AGAGCTATATAACGGGAAGCTCT
20349988 TTCGAGCTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
24 21 0.57
25 16 0.43
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (25 bp):
AAGAGCTATATAACGGGAAGCTCTC
Found at i:20365821 original size:20 final size:20
Alignment explanation
Indices: 20365796--20365835 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20365786 ATATTTAAAT
20365796 ATGCGTATAATACATGTATG
1 ATGCGTATAATACATGTATG
20365816 ATGCGTATAATACATGTATG
1 ATGCGTATAATACATGTATG
20365836 GCTGGCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
ATGCGTATAATACATGTATG
Found at i:20369692 original size:13 final size:13
Alignment explanation
Indices: 20369661--20369712 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
20369651 GTGCGAATCC
*
20369661 AAATTAA-TATTT
1 AAATTAACTAATT
*
20369673 TAATTAACTAATT
1 AAATTAACTAATT
*
20369686 AAATTAACTAACCT
1 AAATTAACTAA-TT
20369700 AAATTAATCTAAT
1 AAATTAA-CTAAT
20369713 GGACTCTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 6 0.19
13 14 0.44
14 8 0.25
15 4 0.12
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAACTAATT
Found at i:20380299 original size:13 final size:12
Alignment explanation
Indices: 20380281--20380358 Score: 74
Period size: 13 Copynumber: 6.5 Consensus size: 12
20380271 TAGATTTTTC
20380281 TAAATATTATCA
1 TAAATATTATCA
*
20380293 TTAAATAAT-TC-
1 -TAAATATTATCA
20380304 TAAATATTATCA
1 TAAATATTATCA
20380316 TTAAATATTATCA
1 -TAAATATTATCA
*
20380329 CTAAATAAT-TC-
1 -TAAATATTATCA
20380340 TAAATATTATCA
1 TAAATATTATCA
20380352 CTAAATA
1 -TAAATA
20380359 AGTCAAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 14 0.26
11 4 0.07
12 4 0.07
13 32 0.59
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATATTATCA
Found at i:20380304 original size:23 final size:23
Alignment explanation
Indices: 20380278--20380322 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
20380268 AGTTAGATTT
20380278 TTCTAAATATTATCATTAAATAA
1 TTCTAAATATTATCATTAAATAA
20380301 TTCTAAATATTATCATTAAATA
1 TTCTAAATATTATCATTAAATA
20380323 TTATCACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
TTCTAAATATTATCATTAAATAA
Found at i:20380321 original size:36 final size:36
Alignment explanation
Indices: 20380280--20380358 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
20380270 TTAGATTTTT
*
20380280 CTAAATATTATCATTAAATAATTCTAAATATTATCA
1 CTAAATATTATCACTAAATAATTCTAAATATTATCA
*
20380316 TTAAATATTATCACTAAATAATTCTAAATATTATCA
1 CTAAATATTATCACTAAATAATTCTAAATATTATCA
20380352 CTAAATA
1 CTAAATA
20380359 AGTCAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (36 bp):
CTAAATATTATCACTAAATAATTCTAAATATTATCA
Found at i:20380367 original size:23 final size:23
Alignment explanation
Indices: 20380318--20380367 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
20380308 TATTATCATT
* *
20380318 AAATATTATCACTAAATAATTCT
1 AAATATTATCACTAAATAAGTCA
20380341 AAATATTATCACTAAATAAGTCA
1 AAATATTATCACTAAATAAGTCA
20380364 AAAT
1 AAAT
20380368 TTAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAAGTCA
Found at i:20382495 original size:15 final size:15
Alignment explanation
Indices: 20382475--20382531 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
20382465 ATTCAATATT
20382475 AATATTTTAATAATA
1 AATATTTTAATAATA
*
20382490 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
20382509 AATATATTAATAATA
1 AATATTTTAATAATA
*
20382524 AATGTTTT
1 AATATTTT
20382532 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:20386384 original size:22 final size:22
Alignment explanation
Indices: 20386333--20386384 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
20386323 TTTACCCATT
* *
20386333 TAATTATTTCATTTTAATCAAT
1 TAATTATTTCATCTTAATCAAG
* *
20386355 TAAATATTTCA-CTTAATTAGAG
1 TAATTATTTCATCTTAATCA-AG
20386377 TAATTATT
1 TAATTATT
20386385 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (22 bp):
TAATTATTTCATCTTAATCAAG
Found at i:20388074 original size:13 final size:13
Alignment explanation
Indices: 20388056--20388080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20388046 TAAGTTATAT
20388056 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20388069 GTGTGAAAATTT
1 GTGTGAAAATTT
20388081 GATCGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20390071 original size:41 final size:41
Alignment explanation
Indices: 20390008--20390103 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
20389998 TTCAAGCTTA
* * *
20390008 AAGTCTAGCAGGCTTAAGGCCGGT-AATGTAAGTCGGACTTT
1 AAGTCCAGCAGGCTTAAGGCCGGTGAA-ATAAGTCGAACTTT
* * *
20390049 ATGTCCAGCAGGCTTAATGCCGGTGAAATAATTCGAACTTT
1 AAGTCCAGCAGGCTTAAGGCCGGTGAAATAAGTCGAACTTT
*
20390090 AAGTCTAGCAGGCT
1 AAGTCCAGCAGGCT
20390104 AATTGCTGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (41 bp):
AAGTCCAGCAGGCTTAAGGCCGGTGAAATAAGTCGAACTTT
Found at i:20409118 original size:13 final size:11
Alignment explanation
Indices: 20409085--20409112 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20409075 ATATTTTTTA
20409085 TTTTTTAAAAT
1 TTTTTTAAAAT
20409096 TTTTTTAAAAT
1 TTTTTTAAAAT
20409107 TTTTTT
1 TTTTTT
20409113 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:20415744 original size:13 final size:13
Alignment explanation
Indices: 20415726--20415799 Score: 103
Period size: 13 Copynumber: 5.7 Consensus size: 13
20415716 CTCAAATTTT
*
20415726 TCAAAAGCACTCC
1 TCAAAAGCACTTC
20415739 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
20415752 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
20415765 TCCACAGCACTTC
1 TCAAAAGCACTTC
*
20415778 TCAAAAGCACTTA
1 TCAAAAGCACTTC
20415791 TCAAAAGCA
1 TCAAAAGCA
20415800 ATGAAAAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.39, C:0.31, G:0.08, T:0.22
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:20422508 original size:20 final size:20
Alignment explanation
Indices: 20422473--20422510 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20422463 AGAGAAAGAG
* *
20422473 AAAAAAAAAGATAAAAGATA
1 AAAAAAAAAAAGAAAAGATA
20422493 AAAAAAAAAAAGAAAAGA
1 AAAAAAAAAAAGAAAAGA
20422511 AAAGGAGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAAGATA
Found at i:20423161 original size:17 final size:17
Alignment explanation
Indices: 20423115--20423161 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
20423105 CATTCGCAAT
20423115 AAAATTACAAAAACTTTA
1 AAAATT-CAAAAACTTTA
*
20423133 AAAATTCCAAAA-TATTA
1 AAAATTCAAAAACT-TTA
*
20423150 TAAATTCAAAAA
1 AAAATTCAAAAA
20423162 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 18 0.72
18 6 0.24
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATTCAAAAACTTTA
Found at i:20423413 original size:3 final size:3
Alignment explanation
Indices: 20423405--20423429 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20423395 CCATGAAAAG
20423405 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
20423430 AAGGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20430774 original size:25 final size:25
Alignment explanation
Indices: 20430708--20430781 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
20430698 AGCCCTCTCT
*
20430708 CGAGCCATATAACGGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTCATC
* * * *
20430733 TGAGCCATGTAAAGGGAAGCTTATC
1 CGAGCCATATAACGGGAAGCTCATC
* *
20430758 CGGGCTATATAACGGGAAGCTCAT
1 CGAGCCATATAACGGGAAGCTCAT
20430782 AAGATCCATA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCTCATC
Found at i:20431121 original size:17 final size:17
Alignment explanation
Indices: 20431096--20431138 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
20431086 GCTATGGTGT
20431096 GTCCACAACATAAGCAA
1 GTCCACAACATAAGCAA
* *
20431113 GTCCGCAACATAAGCAT
1 GTCCACAACATAAGCAA
*
20431130 GACCACAAC
1 GTCCACAAC
20431139 CAATACGGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.33, G:0.14, T:0.12
Consensus pattern (17 bp):
GTCCACAACATAAGCAA
Found at i:20435592 original size:23 final size:23
Alignment explanation
Indices: 20435516--20435592 Score: 57
Period size: 25 Copynumber: 3.2 Consensus size: 23
20435506 CTCGAGCCAT
* * *
20435516 ATAACGGAAAGCTCATATGAGCC
1 ATAACGGGAAGCTCATAAGAGTC
* *
20435539 ATGTAAAGGGAAGCTTATCCAAGATGT-
1 A--TAACGGGAAGCTCAT--AAGA-GTC
20435566 ATAACGGGAAGCTCATAAGAGTC
1 ATAACGGGAAGCTCATAAGAGTC
20435589 ATAA
1 ATAA
20435593 TTAGGAAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
22 2 0.05
23 9 0.22
25 25 0.61
27 4 0.10
28 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (23 bp):
ATAACGGGAAGCTCATAAGAGTC
Found at i:20435729 original size:25 final size:26
Alignment explanation
Indices: 20435701--20435758 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
20435691 GAGAAACTCT
20435701 AAAGAGCAATT-ATTAGGAAGCTCAC
1 AAAGAGCAATTAATTAGGAAGCTCAC
** *
20435726 AAAGAGCCTTTAATTTGGAAGCTCAC
1 AAAGAGCAATTAATTAGGAAGCTCAC
*
20435752 GAAGAGC
1 AAAGAGC
20435759 CAAATGTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (26 bp):
AAAGAGCAATTAATTAGGAAGCTCAC
Found at i:20436272 original size:21 final size:21
Alignment explanation
Indices: 20436248--20436287 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20436238 GAAAATTTAG
*
20436248 CTCAATTTAATACAATTCATA
1 CTCAATTCAATACAATTCATA
*
20436269 CTCAATTCAATCCAATTCA
1 CTCAATTCAATACAATTCA
20436288 CATCTTAGGC
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:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCAATTCAATACAATTCATA
Found at i:20437472 original size:37 final size:37
Alignment explanation
Indices: 20437422--20438303 Score: 1719
Period size: 37 Copynumber: 23.8 Consensus size: 37
20437412 TTAAAANNNN
20437422 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437459 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437496 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437533 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437570 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437607 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437644 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437681 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437718 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437755 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437792 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437829 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437866 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437903 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437940 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20437977 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20438014 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20438051 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20438088 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20438125 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20438162 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
20438199 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
*
20438236 TATCTGATCAAGAAACAAAGTGATAAGTGGCTACACT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
****
20438273 TATCTGATCAAGTGGTAAAGTGATAAGTGGT
1 TATCTGATCAAGAAACAAAGTGATAAGTGGT
20438304 AGCCTAGCTA
Statistics
Matches: 839, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 839 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (37 bp):
TATCTGATCAAGAAACAAAGTGATAAGTGGTTACACT
Found at i:20441576 original size:28 final size:28
Alignment explanation
Indices: 20441509--20441570 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
20441499 GCTGATGGAC
*
20441509 AGAGAG-GAAGGAGAACGACTGCTGTGA
1 AGAGAGTGAAGGAGAACGACTGCTATGA
20441536 AGAGAGTGAAGGAGAACGACTGCTATGA
1 AGAGAGTGAAGGAGAACGACTGCTATGA
*
20441564 TGAGAGT
1 AGAGAGT
20441571 AGAGGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.37, C:0.10, G:0.39, T:0.15
Consensus pattern (28 bp):
AGAGAGTGAAGGAGAACGACTGCTATGA
Found at i:20443699 original size:27 final size:27
Alignment explanation
Indices: 20443668--20443733 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
20443658 TGTAAATTAA
* * * *
20443668 TGTTTAATGTCTTGACGAGCTACCCCG
1 TGTTTAATATCCTGACAAACTACCCCG
*
20443695 TGTTTATTATCCTGACAAACTACCCCG
1 TGTTTAATATCCTGACAAACTACCCCG
*
20443722 TGTTTACTATCC
1 TGTTTAATATCC
20443734 CGGTAGACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (27 bp):
TGTTTAATATCCTGACAAACTACCCCG
Found at i:20445881 original size:22 final size:21
Alignment explanation
Indices: 20445856--20445923 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
20445846 ATATAATAGT
*
20445856 AAAATGGAAACAAAACAACATC
1 AAAATGGAAAC-AAACAACAAC
* *
20445878 AAAATGGCATCAAACAACAAC
1 AAAATGGAAACAAACAACAAC
20445899 AAAAT--AACATCAAACAACAAC
1 AAAATGGAA-A-CAAACAACAAC
20445920 AAAA
1 AAAA
20445924 ACTAGCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
21 29 0.74
22 9 0.23
ACGTcount: A:0.65, C:0.21, G:0.06, T:0.09
Consensus pattern (21 bp):
AAAATGGAAACAAACAACAAC
Found at i:20445894 original size:21 final size:21
Alignment explanation
Indices: 20445868--20445923 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
20445858 AATGGAAACA
* **
20445868 AAACAACATCAAAATGGCATC
1 AAACAACAACAAAATAACATC
20445889 AAACAACAACAAAATAACATC
1 AAACAACAACAAAATAACATC
20445910 AAACAACAACAAAA
1 AAACAACAACAAAA
20445924 ACTAGCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.64, C:0.23, G:0.04, T:0.09
Consensus pattern (21 bp):
AAACAACAACAAAATAACATC
Found at i:20446524 original size:16 final size:16
Alignment explanation
Indices: 20446503--20446536 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20446493 TTAAGTTGAG
*
20446503 AAAATTATTTAATTAA
1 AAAATTAATTAATTAA
20446519 AAAATTAATTAATTAA
1 AAAATTAATTAATTAA
20446535 AA
1 AA
20446537 TTAATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTAATTAATTAA
Found at i:20446549 original size:14 final size:14
Alignment explanation
Indices: 20446503--20446542 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
20446493 TTAAGTTGAG
*
20446503 AAAATTATTTAATT
1 AAAATTAATTAATT
20446517 AAAAAATTAATTAATT
1 --AAAATTAATTAATT
20446533 AAAATTAATT
1 AAAATTAATT
20446543 TGATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
16 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTAATTAATT
Found at i:20451119 original size:45 final size:45
Alignment explanation
Indices: 20451032--20451120 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
20451022 TAATTTCTAA
* * *
20451032 AAACTTTTGAAAATTAATAAAATAAATTAAAAATTAATAAAATAC
1 AAACTTTTGAAAATTAATAAAAGAAAGTAAAAATTAAAAAAATAC
20451077 AAACTTTTAGAAAATT-ATAAAAGAAAGTAAAAA-TACAAAAAATA
1 AAACTTTT-GAAAATTAATAAAAGAAAGTAAAAATTA-AAAAAATA
20451121 TATATAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 2 0.05
45 30 0.77
46 7 0.18
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (45 bp):
AAACTTTTGAAAATTAATAAAAGAAAGTAAAAATTAAAAAAATAC
Found at i:20451149 original size:20 final size:19
Alignment explanation
Indices: 20451095--20451155 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
20451085 AGAAAATTAT
* *
20451095 AAAAGAAA-GTAAAAATAC
1 AAAAGAAATTTAAAAATTC
* *
20451113 AAAA-AATATATATAAATTC
1 AAAAGAA-ATTTAAAAATTC
20451132 TAAAAGAAATTTAAAAATTC
1 -AAAAGAAATTTAAAAATTC
20451152 AAAA
1 AAAA
20451156 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.06
18 5 0.15
19 11 0.32
20 14 0.41
21 2 0.06
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAGAAATTTAAAAATTC
Found at i:20451448 original size:35 final size:34
Alignment explanation
Indices: 20451395--20451466 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
20451385 TTTTAACTCT
* *
20451395 TTTTTCTTTTTTAATTTTG-AATATTTTAGAAAATA
1 TTTTTCTTTTTGAATTTTGTAAT-TATT-GAAAATA
20451430 TTTTT-TTTTTGAATTTTTGTAATTATTGAAAATA
1 TTTTTCTTTTTGAA-TTTTGTAATTATTGAAAATA
20451464 TTT
1 TTT
20451467 AATTGTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 17 0.52
35 13 0.39
36 3 0.09
ACGTcount: A:0.29, C:0.01, G:0.07, T:0.62
Consensus pattern (34 bp):
TTTTTCTTTTTGAATTTTGTAATTATTGAAAATA
Found at i:20470038 original size:23 final size:23
Alignment explanation
Indices: 20470012--20470058 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20470002 TTTAAATTTT
20470012 GAATTATTTAGTGATAATAATTA
1 GAATTATTTAGTGATAATAATTA
*
20470035 GAATTATTTAGTGATAATATTTA
1 GAATTATTTAGTGATAATAATTA
20470058 G
1 G
20470059 TGATAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (23 bp):
GAATTATTTAGTGATAATAATTA
Found at i:20470057 original size:13 final size:13
Alignment explanation
Indices: 20470016--20470094 Score: 71
Period size: 13 Copynumber: 6.5 Consensus size: 13
20470006 AATTTTGAAT
20470016 TATTTAGTGATAA
1 TATTTAGTGATAA
* *
20470029 TAATTA--GA-AT
1 TATTTAGTGATAA
20470039 TATTTAGTGATAA
1 TATTTAGTGATAA
20470052 TATTTAGTGATAA
1 TATTTAGTGATAA
* *
20470065 TATCTA--GA-AT
1 TATTTAGTGATAA
*
20470075 TATTTAGTAATAA
1 TATTTAGTGATAA
20470088 TATTTAG
1 TATTTAG
20470095 GAAAAATCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
10 12 0.24
11 4 0.08
12 3 0.06
13 32 0.63
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.46
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:20470063 original size:36 final size:36
Alignment explanation
Indices: 20470016--20470094 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
20470006 AATTTTGAAT
*
20470016 TATTTAGTGATAATAAT-TAGAATTATTTAGTGATAA
1 TATTTAGTGATAAT-ATCTAGAATTATTTAGTAATAA
20470052 TATTTAGTGATAATATCTAGAATTATTTAGTAATAA
1 TATTTAGTGATAATATCTAGAATTATTTAGTAATAA
20470088 TATTTAG
1 TATTTAG
20470095 GAAAAATCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 2 0.05
36 39 0.95
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.46
Consensus pattern (36 bp):
TATTTAGTGATAATATCTAGAATTATTTAGTAATAA
Done.