Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 5 of 171
Found at i:1842288 original size:27 final size:27
Alignment explanation
Indices: 1842250--1842306 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1842240 TAACCTTATA
1842250 AATCAAGCAGAGATATTATCTCTTTTC
1 AATCAAGCAGAGATATTATCTCTTTTC
1842277 AATCAAGCAGAGATATTATCTCTTTTC
1 AATCAAGCAGAGATATTATCTCTTTTC
1842304 AAT
1 AAT
1842307 AGTTCAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (27 bp):
AATCAAGCAGAGATATTATCTCTTTTC
Found at i:1850617 original size:13 final size:14
Alignment explanation
Indices: 1850590--1850618 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1850580 GTTTTGTAAT
1850590 TTTTAAATATTCAA
1 TTTTAAATATTCAA
1850604 TTTTAAAT-TTCAA
1 TTTTAAATATTCAA
1850617 TT
1 TT
1850619 AATTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAATATTCAA
Found at i:1854637 original size:14 final size:15
Alignment explanation
Indices: 1854610--1854638 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1854600 AAATTACCTA
1854610 CTAATTTTTATTTAT
1 CTAATTTTTATTTAT
1854625 CTAATTTTT-TTTAT
1 CTAATTTTTATTTAT
1854639 ACCATGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
CTAATTTTTATTTAT
Found at i:1859725 original size:72 final size:72
Alignment explanation
Indices: 1859649--1859787 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
1859639 ATGCCAAAAC
*
1859649 AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCTAACCAAGAAA
1 AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCAAACCAAGAAA
1859714 CAACAGT
66 CAACAGT
* * *
1859721 AGCAAAGCAGAGCAGCAATAGACTGCATGCTGAAACCAGAAAACAAATCCCATCAAACCAAGAAA
1 AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCAAACCAAGAAA
1859786 CA
66 CA
1859788 GCAGCCTGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.09
Consensus pattern (72 bp):
AGCAAAGCAGAGCAGCAACAGACTGCATGCTCAAACCAGAAAACAAATCCCAGCAAACCAAGAAA
CAACAGT
Found at i:1860337 original size:27 final size:28
Alignment explanation
Indices: 1860283--1860338 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1860273 GTAACAGTTT
* *
1860283 AAAAGTTTAGGTATCAATTTTGATAAAA
1 AAAAGTTTAAGTATCAATTTGGATAAAA
1860311 AAAAGTTTAAGTATCAATTTGGA-AAAA
1 AAAAGTTTAAGTATCAATTTGGATAAAA
1860338 A
1 A
1860339 TAATATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (28 bp):
AAAAGTTTAAGTATCAATTTGGATAAAA
Found at i:1860564 original size:19 final size:19
Alignment explanation
Indices: 1860529--1860571 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1860519 AGGTTGATAA
* *
1860529 TTAAATTTAAATGTTTAAT
1 TTAAATTCAAATGTTTAAG
1860548 TTAAATTCATAAT-TTTAAG
1 TTAAATTCA-AATGTTTAAG
1860567 TTAAA
1 TTAAA
1860572 GTAAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
TTAAATTCAAATGTTTAAG
Found at i:1885698 original size:10 final size:10
Alignment explanation
Indices: 1885683--1885708 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1885673 TTCGTCTCTT
1885683 TCTCTCCCTC
1 TCTCTCCCTC
1885693 TCTCTCCCTC
1 TCTCTCCCTC
1885703 TCTCTC
1 TCTCTC
1885709 TCTCCCCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (10 bp):
TCTCTCCCTC
Found at i:1885793 original size:9 final size:9
Alignment explanation
Indices: 1885779--1885822 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1885769 AGAACACGAT
1885779 GATGATGAC
1 GATGATGAC
1885788 GATGATGAC
1 GATGATGAC
* *
1885797 GACGACGAC
1 GATGATGAC
* *
1885806 GACGATGAT
1 GATGATGAC
1885815 GATGATGA
1 GATGATGA
1885823 AGGAGAAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.18
Consensus pattern (9 bp):
GATGATGAC
Found at i:1886883 original size:22 final size:23
Alignment explanation
Indices: 1886855--1886897 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1886845 CATTGTTGAA
1886855 AAAAATAAAAAAGGA-AAGCTTT
1 AAAAATAAAAAAGGAGAAGCTTT
*
1886877 AAAAATAACAAAGGAGAAGCT
1 AAAAATAAAAAAGGAGAAGCT
1886898 CTCTTCACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.63, C:0.07, G:0.16, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAAAGGAGAAGCTTT
Found at i:1888198 original size:24 final size:23
Alignment explanation
Indices: 1888152--1888199 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1888142 ATAACCATTT
* * *
1888152 AAAATTGAATGATTAATTCTAAA
1 AAAAATGAATGATTAAATATAAA
1888175 AAAAATGAATGATTAAAATATAAA
1 AAAAATGAATGATT-AAATATAAA
1888199 A
1 A
1888200 TTATCAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (23 bp):
AAAAATGAATGATTAAATATAAA
Found at i:1888700 original size:22 final size:23
Alignment explanation
Indices: 1888662--1888716 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1888652 TTTATTATTT
*
1888662 TAAAATATAAATTTTTTAAAAT-A
1 TAAAAT-TATATTTTTTAAAATAA
*
1888685 TAAAATTATATTTTTTGAAATAA
1 TAAAATTATATTTTTTAAAATAA
1888708 TAAAATTAT
1 TAAAATTAT
1888717 TAAATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAAATTATATTTTTTAAAATAA
Found at i:1889729 original size:31 final size:30
Alignment explanation
Indices: 1889669--1889741 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
1889659 TTAGAAAGAG
* *
1889669 AAAATCTCCAAAATTTTGAAACTTAAAACCC
1 AAAATCTCCAAAATTTTAAAACCTAAAA-CC
* *
1889700 AAAAATCCCCAAATTTTTAAAACCT-AAACC
1 -AAAATCTCCAAAATTTTAAAACCTAAAACC
1889730 AAAATCTCCAAA
1 AAAATCTCCAAA
1889742 CCCAAAAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.31
30 2 0.06
31 3 0.08
32 20 0.56
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.23
Consensus pattern (30 bp):
AAAATCTCCAAAATTTTAAAACCTAAAACC
Found at i:1894936 original size:48 final size:46
Alignment explanation
Indices: 1894874--1894992 Score: 127
Period size: 48 Copynumber: 2.5 Consensus size: 46
1894864 GCGCTCTCTG
*
1894874 ATTAGCA-TTGTGTGTGCTCTCTGTTTAGCACGTCTCGTG-CTCTATGTT
1 ATTAGCACTT-TGTGTGCTCTCTGTTCAGCAC-T-TCGTGACTCTATG-T
* * * *
1894922 ATTAGCACTTTGTGTGCTCTCTGATCAGTACTTTGTGTACTCTCTGT
1 ATTAGCACTTTGTGTGCTCTCTGTTCAGCACTTCGTG-ACTCTATGT
1894969 -TTAGCACTTTGTGTGCTCTCTGTT
1 ATTAGCACTTTGTGTGCTCTCTGTT
1894993 GCTCAGCACT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
46 27 0.44
47 2 0.03
48 31 0.50
49 2 0.03
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (46 bp):
ATTAGCACTTTGTGTGCTCTCTGTTCAGCACTTCGTGACTCTATGT
Found at i:1894938 original size:25 final size:24
Alignment explanation
Indices: 1894866--1895038 Score: 132
Period size: 23 Copynumber: 7.4 Consensus size: 24
1894856 ACACTAGCGC
1894866 GCTCTCTG-ATTAGCA-TTGTGTGT
1 GCTCTCTGTATTAGCACTT-TGTGT
* *
1894889 GCTCTCTGT-TTAGCACGTCT-CGT
1 GCTCTCTGTATTAGCAC-TTTGTGT
*
1894912 GCTCTATGTTATTAGCACTTTGTGT
1 GCTCTCTG-TATTAGCACTTTGTGT
* *
1894937 GCTCTCTG-ATCAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTTTGTGT
*
1894960 ACTCTCTGT-TTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTTTGTGT
*
1894983 GCTCTCTGT-TGCTCAGCAC-TTATGT
1 GCTCTCTGTAT--T-AGCACTTTGTGT
* *
1895008 GCTCTCTGT-TCAGAACTTTG-GT
1 GCTCTCTGTATTAGCACTTTGTGT
*
1895030 ACTCTCTGT
1 GCTCTCTGT
1895039 TTGTTCCGTT
Statistics
Matches: 122, Mismatches: 17, Indels: 23
0.75 0.10 0.14
Matches are distributed among these distances:
22 14 0.11
23 66 0.54
24 4 0.03
25 33 0.27
26 5 0.04
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTTTGTGT
Found at i:1894985 original size:71 final size:71
Alignment explanation
Indices: 1894866--1895040 Score: 196
Period size: 71 Copynumber: 2.5 Consensus size: 71
1894856 ACACTAGCGC
* * * *
1894866 GCTCTCTGATTAGCA-TTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCTCTATGTT-ATTAGCA
1 GCTCTCTGATCAGAACTT-TGTGTACTCTCTGTTTAGCACGTCTCGTGCTCTATGTTGATCAGCA
*
1894929 CTTTGTGT
65 C-TTATGT
* * * * *
1894937 GCTCTCTGATCAGTACTTTGTGTACTCTCTGTTTAGCAC-TTTGTGTGCTCTCTGTTGCTCAGCA
1 GCTCTCTGATCAGAACTTTGTGTACTCTCTGTTTAGCACGTCT-CGTGCTCTATGTTGATCAGCA
1895001 CTTATGT
65 CTTATGT
*
1895008 GCTCTCTGTTCAGAACTTTG-GTACTCTCTGTTT
1 GCTCTCTGATCAGAACTTTGTGTACTCTCTGTTT
1895041 GTTCCGTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
70 15 0.17
71 67 0.74
72 8 0.09
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (71 bp):
GCTCTCTGATCAGAACTTTGTGTACTCTCTGTTTAGCACGTCTCGTGCTCTATGTTGATCAGCAC
TTATGT
Found at i:1897996 original size:22 final size:23
Alignment explanation
Indices: 1897944--1898000 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1897934 GTTGGGGAAA
*
1897944 TAGTAAGCACACACAGTGCAATC
1 TAGTAGGCACACACAGTGCAATC
1897967 TAGTAGGCACACACAGTGCAATC
1 TAGTAGGCACACACAGTGCAATC
1897990 -AGTAGGCACAC
1 TAGTAGGCACAC
1898001 GAGGTGCGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (23 bp):
TAGTAGGCACACACAGTGCAATC
Found at i:1898021 original size:23 final size:23
Alignment explanation
Indices: 1897916--1898042 Score: 96
Period size: 23 Copynumber: 5.4 Consensus size: 23
1897906 CGAAGTACTT
* *
1897916 AACAGTAAGCACACAAGTGTTGGGGA
1 AACAGTAAGCACACAA-AG-T-GCGA
* *
1897942 AATAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
1897964 ATCTAGTAGGCACACACAGTGC-A
1 AAC-AGTAAGCACACAAAGTGCGA
* * * *
1897987 ATCAGTAGGCACACGAGGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
1898010 AACAGTAAGCACATAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
1898033 AACAGTAAGC
1 AACAGTAAGC
1898043 GCGCTAGCGT
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.20
23 51 0.61
24 1 0.01
25 1 0.01
26 14 0.17
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.14
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:1906692 original size:1 final size:1
Alignment explanation
Indices: 1906688--1906713 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1906678 TTTTTTTTTT
1906688 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
1906714 CGCCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1913397 original size:10 final size:10
Alignment explanation
Indices: 1913379--1913415 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1913369 GTCCAATCAA
*
1913379 AAAAAAAAAG
1 AAAAGAAAAG
1913389 AAAAGAAAAG
1 AAAAGAAAAG
1913399 AAAAG-AAAG
1 AAAAGAAAAG
1913408 -AAAGAAAA
1 AAAAGAAAA
1913416 ATGAAAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
8 4 0.16
9 7 0.28
10 14 0.56
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:1913464 original size:6 final size:6
Alignment explanation
Indices: 1913453--1913482 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1913443 TTAACGGAGC
1913453 CTGAGA CTGAGA CTGAGA CTGAGA CTGAGA
1 CTGAGA CTGAGA CTGAGA CTGAGA CTGAGA
1913483 GAGCCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
CTGAGA
Found at i:1918299 original size:18 final size:16
Alignment explanation
Indices: 1918253--1918317 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
1918243 TTTATATGTA
1918253 TTTT-ATTTACTAAATT
1 TTTTAATTTA-TAAATT
1918269 TTTTAATTATTATAAACTT
1 TTTTAA-T-TTATAAA-TT
1918288 TTTATAATTTAT-AATT
1 TTT-TAATTTATAAATT
*
1918304 TTTTAATTTTTAAA
1 TTTTAATTTATAAA
1918318 ATGCTATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 7 0.17
16 11 0.26
17 3 0.07
18 9 0.21
19 9 0.21
20 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATTTATAAATT
Found at i:1918315 original size:17 final size:18
Alignment explanation
Indices: 1918258--1918319 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 18
1918248 ATGTATTTTA
1918258 TTTACTAAATTTTTTAATT
1 TTTA-TAAATTTTTTAATT
*
1918277 ATTATAAACTTTTTATAA--
1 TTTATAAA-TTTTT-TAATT
1918295 TTTAT-AATTTTTTAATT
1 TTTATAAATTTTTTAATT
1918312 TTTA-AAAT
1 TTTATAAAT
1918320 GCTATAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 3 0.08
16 5 0.14
17 9 0.25
18 8 0.22
19 8 0.22
20 3 0.08
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATAAATTTTTTAATT
Found at i:1931313 original size:29 final size:32
Alignment explanation
Indices: 1931268--1931326 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 32
1931258 AATTTTAAGT
1931268 TTAAATGTTAACATTATTA-AA-ATTATTTCG
1 TTAAATGTTAACATTATTATAATATTATTTCG
1931298 TTAAAT-TTAA-ATTTATTATAATATTATTT
1 TTAAATGTTAACA-TTATTATAATATTATTT
1931327 TATAGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 1 0.04
29 10 0.38
30 8 0.31
31 7 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (32 bp):
TTAAATGTTAACATTATTATAATATTATTTCG
Found at i:1945676 original size:16 final size:16
Alignment explanation
Indices: 1945655--1945685 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1945645 GATGGCAGGC
1945655 TTTTCTTCTCTGTTTT
1 TTTTCTTCTCTGTTTT
*
1945671 TTTTCTTCTTTGTTT
1 TTTTCTTCTCTGTTT
1945686 AATAGATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTCTTCTCTGTTTT
Found at i:1946048 original size:15 final size:14
Alignment explanation
Indices: 1946007--1946049 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1945997 GGCTCCATTG
1946007 TTTGAAAATG-ATT
1 TTTGAAAATGAATT
1946020 TTTGAAAAAT-AATT
1 TTTG-AAAATGAATT
1946034 TTTAGAAAATGAATT
1 TTT-GAAAATGAATT
1946049 T
1 T
1946050 GTTTTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.15
14 16 0.62
15 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (14 bp):
TTTGAAAATGAATT
Found at i:1948787 original size:2 final size:2
Alignment explanation
Indices: 1948780--1948830 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1948770 TTCTTTTATT
1948780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1948822 TA TA TA TA T
1 TA TA TA TA T
1948831 TAGTTAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1951659 original size:17 final size:18
Alignment explanation
Indices: 1951637--1951675 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1951627 CTGTTTGATA
1951637 TATTATTCAAAATT-AAT
1 TATTATTCAAAATTAAAT
* *
1951654 TATTATTTATAATTAAAT
1 TATTATTCAAAATTAAAT
1951672 TATT
1 TATT
1951676 TGATAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTATTCAAAATTAAAT
Found at i:1953074 original size:18 final size:18
Alignment explanation
Indices: 1953051--1953085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1953041 AAATCGAATC
* *
1953051 CTTAATTTTCCTAATTTA
1 CTTAATATTCCAAATTTA
1953069 CTTAATATTCCAAATTT
1 CTTAATATTCCAAATTT
1953086 TTATTCTCCA
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:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (18 bp):
CTTAATATTCCAAATTTA
Found at i:1954564 original size:17 final size:17
Alignment explanation
Indices: 1954542--1954589 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1954532 ATAATAAAAT
1954542 ATAATTTTATTATTT-TA
1 ATAATTTTATT-TTTATA
1954559 ATAATTTATATTTTTATA
1 ATAATTT-TATTTTTATA
1954577 A-AATTTTCATTTT
1 ATAATTTT-ATTTT
1954590 GCGTTCTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 20 0.71
18 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTTTTATA
Found at i:1963027 original size:26 final size:24
Alignment explanation
Indices: 1962998--1963049 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1962988 TATTAATATT
*
1962998 ATTAATTATATAAAATTGAACAATAA
1 ATTAATTAT-TAAAAGTGAAC-ATAA
*
1963024 ATTAATTATTATAAGTGAACATAA
1 ATTAATTATTAAAAGTGAACATAA
1963048 AT
1 AT
1963050 ATTTTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 9 0.38
26 9 0.38
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTAATTATTAAAAGTGAACATAA
Found at i:1964083 original size:2 final size:2
Alignment explanation
Indices: 1964036--1964068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1964026 CTGCCCTTAC
1964036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1964069 AATTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1981944 original size:23 final size:23
Alignment explanation
Indices: 1981870--1982083 Score: 151
Period size: 23 Copynumber: 9.5 Consensus size: 23
1981860 TAAACGGAAC
* * *
1981870 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
1981892 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1981914 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
1981940 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
1981960 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
1981979 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
1982002 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
1982025 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
1982050 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1982073 AATCAGAGAGC
1 AAACAGAGAGC
1982084 GCGCTAGTGT
Statistics
Matches: 151, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 78 0.52
24 2 0.01
25 28 0.19
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:1981978 original size:39 final size:39
Alignment explanation
Indices: 1981924--1981998 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1981914 GGGCAACAGA
*
1981924 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
1981963 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
1981999 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:1982037 original size:48 final size:46
Alignment explanation
Indices: 1981963--1982083 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
1981953 ACAAAGTACT
* * *
1981963 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
1982009 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
1982057 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
1982084 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:1986620 original size:88 final size:89
Alignment explanation
Indices: 1986504--1986734 Score: 306
Period size: 88 Copynumber: 2.6 Consensus size: 89
1986494 AAACTTTTTC
*
1986504 AAAAAAGCAATTAAGCTCCTGAATTTTTTTTGCACCCAATTGGGTACTTGAACTACCAAAATGCA
1 AAAAAAGCAATTAAGCTCCT-AA-TTTTTTTGCACTCAATTGGGTACTTGAACTACCAAAATGCA
1986569 T-AAAAAAACCCTCAAAC-TTAAAAA
64 TCAAAAAAACCCTCAAACTTTAAAAA
* * * * ** *
1986593 AAAAAAGCAATTAAGCCCCTATATTTTTTTACACTAAATCGGGTACTTGAACTATTAAAATGTAT
1 AAAAAAGCAATTAAGCTCCTA-ATTTTTTTGCACTCAATTGGGTACTTGAACTACCAAAATGCAT
*
1986658 CAAAAAAGCCCTCAAACTTTTTAAAAA
65 CAAAAAAACCCTCAAAC--TTTAAAAA
*
1986685 AAAAAA-CAATTAAGCTCCTGATTTTTTTGCACTCAATTGGGTACTTGAAC
1 AAAAAAGCAATTAAGCTCCTAATTTTTTTGCACTCAATTGGGTACTTGAAC
1986735 CATCTTTAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
88 36 0.29
89 35 0.28
90 27 0.22
91 12 0.10
92 13 0.11
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (89 bp):
AAAAAAGCAATTAAGCTCCTAATTTTTTTGCACTCAATTGGGTACTTGAACTACCAAAATGCATC
AAAAAAACCCTCAAACTTTAAAAA
Found at i:1986853 original size:29 final size:29
Alignment explanation
Indices: 1986821--1986954 Score: 123
Period size: 30 Copynumber: 4.6 Consensus size: 29
1986811 AATAAAAAAA
1986821 AATAAAAATTATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAAATTATTAAATTTT
* *
1986850 AATAAAAACTATAAAAAATATTTAAATTTT
1 AATAAAAATTATAAAAATTA-TTAAATTTT
* * *
1986880 ATTAAAAATTAGAACAAATTA-TAAATTAT
1 AATAAAAATTATAA-AAATTATTAAATTTT
* *
1986909 -ATAGAAA-TATAGAAAATTTTATAAAATTTT
1 AATAAAAATTATA-AAAA--TTATTAAATTTT
*
1986939 AA-GAAAATTATAAAAA
1 AATAAAAATTATAAAAA
1986955 ATGTAAAAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
27 6 0.07
28 6 0.07
29 28 0.34
30 33 0.40
31 10 0.12
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (29 bp):
AATAAAAATTATAAAAATTATTAAATTTT
Found at i:1986955 original size:10 final size:10
Alignment explanation
Indices: 1986796--1986966 Score: 58
Period size: 10 Copynumber: 17.7 Consensus size: 10
1986786 GACATGTGAC
*
1986796 AAAAAATGAT
1 AAAAAATTAT
1986806 AAAAAA--AT
1 AAAAAATTAT
**
1986814 AAAAAAAAAT
1 AAAAAATTAT
1986824 -AAAAATTAT
1 AAAAAATTAT
1986833 -AAAAATTAT
1 AAAAAATTAT
* **
1986842 TAAATTTTA-
1 AAAAAATTAT
*
1986851 ATAAAAACTAT
1 A-AAAAATTAT
1986862 AAAAAA-TATT
1 AAAAAATTA-T
* **
1986872 TAAATTTTAT
1 AAAAAATTAT
* *
1986882 TAAAAATTAG
1 AAAAAATTAT
*
1986892 AACAAATTAT
1 AAAAAATTAT
1986902 ---AAATTAT
1 AAAAAATTAT
*
1986909 ATAGAAA-TAT
1 A-AAAAATTAT
* *
1986919 AGAAAATTTT
1 AAAAAATTAT
* *
1986929 ATAAAATTTT
1 AAAAAATTAT
1986939 AAGAAAATTAT
1 AA-AAAATTAT
1986950 AAAAAATGTA-
1 AAAAAAT-TAT
1986960 AAAAAAT
1 AAAAAAT
1986967 AAAATTCATA
Statistics
Matches: 124, Mismatches: 23, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.06
8 8 0.06
9 21 0.17
10 71 0.57
11 17 0.14
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:1987221 original size:19 final size:19
Alignment explanation
Indices: 1987178--1987224 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1987168 TTTTATGATT
1987178 TTTTTATAATTTTTATAAA
1 TTTTTATAATTTTTATAAA
**
1987197 AGTTTATAATTTTT-TATAA
1 TTTTTATAATTTTTATA-AA
1987216 TTTTTATAA
1 TTTTTATAA
1987225 AAAATTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAA
Found at i:1987240 original size:29 final size:28
Alignment explanation
Indices: 1987178--1987271 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 28
1987168 TTTTATGATT
1987178 TTTTTATAATTTTTATAAAAGTTTATAA
1 TTTTTATAATTTTTATAAAAGTTTATAA
* *
1987206 TTTTTTATAATTTTTATAAAAAATTTTCTAA
1 -TTTTTATAATTTTTAT--AAAAGTTTATAA
*
1987237 TTTTTAT-ATTTTAATTAAAA-TTTAATAA
1 TTTTTATAATTTTTA-TAAAAGTTT-ATAA
*
1987265 ATTTTAT
1 TTTTTAT
1987272 TTATTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.05
28 13 0.23
29 22 0.39
30 8 0.14
31 10 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTTTATAATTTTTATAAAAGTTTATAA
Found at i:1987639 original size:89 final size:88
Alignment explanation
Indices: 1987451--1987641 Score: 226
Period size: 88 Copynumber: 2.2 Consensus size: 88
1987441 AATTAGGGGC
*
1987451 TTAATTTTTTTTTTGAAAAAGTTTGAGGATATTTTTAATGCATTTTGAAAGTTTAAGTACCCAAT
1 TTAATTTTTTTTTTGAAAAAGTTTGAGGATATTTTTAATGCATTTTGAAAGTTCAAGTACCCAAT
*
1987516 TGAGTGAAAAAAAAGGCAGGAGT
66 TGAATGAAAAAAAAGGCAGGAGT
* * * * * * *
1987539 TTAATTTTTTTTTTGAAAACGTTTGAGAGTCTTTTTTTTATGTATTTTG-GAGTTCAAGTACCTA
1 TTAATTTTTTTTTTGAAAAAGTTTGAG-G-ATATTTTTAATGCATTTTGAAAGTTCAAGTACCCA
* *
1987603 ATTGAATGCAAAGAAA-GCA-GAGGT
64 ATTGAATGAAAAAAAAGGCAGGA-GT
1987627 TTAATTGTTTTTTTT
1 TTAATT-TTTTTTTT
1987642 TTAAATTTGA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
87 2 0.02
88 37 0.42
89 34 0.39
90 15 0.17
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.44
Consensus pattern (88 bp):
TTAATTTTTTTTTTGAAAAAGTTTGAGGATATTTTTAATGCATTTTGAAAGTTCAAGTACCCAAT
TGAATGAAAAAAAAGGCAGGAGT
Found at i:1995127 original size:22 final size:22
Alignment explanation
Indices: 1995077--1995127 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1995067 ATCATTTTGC
*
1995077 TATTATTTTATTATTATTATTT
1 TATTATTTTATAATTATTATTT
*
1995099 TGA-TATTTTATAATTCTTATTT
1 T-ATTATTTTATAATTATTATTT
1995121 TATTATT
1 TATTATT
1995128 AACTTTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTATTTTATAATTATTATTT
Found at i:1998083 original size:29 final size:31
Alignment explanation
Indices: 1998014--1998083 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
1998004 AATGCTTCAA
*
1998014 GTATACATTTGAACCACAATTAAAATTTTAT
1 GTATACAATTGAACCACAATTAAAATTTTAT
* * *
1998045 GTGTATAATTGTACC-CAATTAAAA-TTTAT
1 GTATACAATTGAACCACAATTAAAATTTTAT
1998074 GTATACAATT
1 GTATACAATT
1998084 ACACATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 13 0.39
30 9 0.27
31 11 0.33
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (31 bp):
GTATACAATTGAACCACAATTAAAATTTTAT
Found at i:2003837 original size:28 final size:28
Alignment explanation
Indices: 2003788--2003844 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2003778 AAATTACGGG
* *
2003788 TGTAATGTTATACATAAAATTTTATTTA
1 TGTAATGTTATAAATAAAATTTTAATTA
* * *
2003816 TGTAATTTTATAAATGAGATTTTAATTA
1 TGTAATGTTATAAATAAAATTTTAATTA
2003844 T
1 T
2003845 TTTATATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.51
Consensus pattern (28 bp):
TGTAATGTTATAAATAAAATTTTAATTA
Found at i:2009162 original size:14 final size:16
Alignment explanation
Indices: 2009130--2009163 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2009120 AGAATACGCC
2009130 AAATGAGACAGACAAG
1 AAATGAGACAGACAAG
2009146 AAATGAGACA-A-AAG
1 AAATGAGACAGACAAG
2009160 AAAT
1 AAAT
2009164 ACTGTCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.62, C:0.09, G:0.21, T:0.09
Consensus pattern (16 bp):
AAATGAGACAGACAAG
Found at i:2013847 original size:18 final size:17
Alignment explanation
Indices: 2013815--2013848 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2013805 TAATCTTTTA
*
2013815 TTTCTTTTTTCTTATTT
1 TTTCTTTTTTATTATTT
2013832 TTTCTTTTTTAATTATT
1 TTTCTTTTTT-ATTATT
2013849 CGTATCAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTTATTATTT
Found at i:2029474 original size:22 final size:21
Alignment explanation
Indices: 2029433--2029475 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2029423 AATTTTAAAA
*
2029433 TTTTAAAATTATATTTTTATT
1 TTTTAAAATTATATTATTATT
2029454 TTTTAAAAATTA-ATTAATTATT
1 TTTT-AAAATTATATT-ATTATT
2029476 AACACATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAAATTATATTATTATT
Found at i:2049529 original size:3 final size:3
Alignment explanation
Indices: 2049521--2049551 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2049511 AGTTGAAAAC
2049521 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2049552 AAATATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2059230 original size:89 final size:89
Alignment explanation
Indices: 2059040--2059265 Score: 269
Period size: 89 Copynumber: 2.5 Consensus size: 89
2059030 TTGATGTTTT
* * * * **
2059040 TTATCAAACATGAATGATAATTGGAATTGATCTCATCTCTTTTTTTTTTTTTTTTTTTTACTGTC
1 TTATCAAACGTGAATCATAGTTGGAATTGATCT-ATCTCCTTTTTTTTTTTTTTTTAATACTGTC
* *
2059105 TAACATTTTTTCAAGAATTAAAAGC
65 TAACATTTTTTCAAAAATCAAAAGC
* *
2059130 TTATCAAACGTGAATTATAGTTGGGATTGATCTATCTCCTTTTTTTTTTTTTTTTAAT-CTGTCT
1 TTATCAAACGTGAATCATAGTTGGAATTGATCTATCTCCTTTTTTTTTTTTTTTTAATACTGTCT
* * *
2059194 AGCTCTTTTTTCAAAAATCAAAGGC
66 AAC-ATTTTTTCAAAAATCAAAAGC
* *
2059219 TTATCACACGTGAATCATAGTTGAAATTGAT-T-TCTCTCTTTTTTTTT
1 TTATCAAACGTGAATCATAGTTGGAATTGATCTATCTC-CTTTTTTTTT
2059266 AACTGTCTAT
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
87 4 0.03
88 19 0.16
89 66 0.56
90 29 0.25
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.50
Consensus pattern (89 bp):
TTATCAAACGTGAATCATAGTTGGAATTGATCTATCTCCTTTTTTTTTTTTTTTTAATACTGTCT
AACATTTTTTCAAAAATCAAAAGC
Found at i:2077366 original size:17 final size:19
Alignment explanation
Indices: 2077330--2077369 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2077320 TAATTTTAGC
2077330 ATTTGCTTAATATATTTTG
1 ATTTGCTTAATATATTTTG
*
2077349 ATTTTCTTAAT-T-TTTTG
1 ATTTGCTTAATATATTTTG
2077366 ATTT
1 ATTT
2077370 ACTGATCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (19 bp):
ATTTGCTTAATATATTTTG
Found at i:2088198 original size:14 final size:14
Alignment explanation
Indices: 2088179--2088207 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2088169 ATAGTTACGA
2088179 TAACTCGTGAAAAT
1 TAACTCGTGAAAAT
2088193 TAACTCGTGAAAAT
1 TAACTCGTGAAAAT
2088207 T
1 T
2088208 TTCGACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (14 bp):
TAACTCGTGAAAAT
Found at i:2098596 original size:23 final size:23
Alignment explanation
Indices: 2098560--2098604 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2098550 AGGTCTGAAC
* *
2098560 TATTAAAATGTAATTTTATCATA
1 TATTAAAATATAATTCTATCATA
*
2098583 TATTAATATATAATTCTATCAT
1 TATTAAAATATAATTCTATCAT
2098605 TTTGAAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTAAAATATAATTCTATCATA
Found at i:2111206 original size:21 final size:22
Alignment explanation
Indices: 2111166--2111206 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2111156 GGGATATGGA
* *
2111166 CTTTTTTTTTTTTTCCTTATAG
1 CTTTGTTTTTTTTTCATTATAG
2111188 CTTTGTTTTTTTTT-ATTAT
1 CTTTGTTTTTTTTTCATTAT
2111207 TATTATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (22 bp):
CTTTGTTTTTTTTTCATTATAG
Found at i:2121852 original size:28 final size:30
Alignment explanation
Indices: 2121815--2121870 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2121805 TGATATAACA
*
2121815 TTAATAATTTTAGATA-TAA-TTAAAATATT
1 TTAATAATTTAAGA-ACTAATTTAAAATATT
2121844 TTAA-AATTTAAGAACTAATTTAAAATA
1 TTAATAATTTAAGAACTAATTTAAAATA
2121871 AGAGTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.04
28 11 0.46
29 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (30 bp):
TTAATAATTTAAGAACTAATTTAAAATATT
Found at i:2123530 original size:31 final size:28
Alignment explanation
Indices: 2123494--2123575 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 28
2123484 AATTAGATCA
*
2123494 AAATTAAAATTTTATATATACATTTGAACT
1 AAATTAAAATTTTATATATA-ATTT-AACC
* *
2123524 ATAATTAAAGTTTCATATGTATAATTTAACC
1 A-AATTAAAATTT--TATATATAATTTAACC
* *
2123555 AAATTTAAATTTCATATATAA
1 AAATTAAAATTTTATATATAA
2123576 AATTATCCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.17
30 10 0.24
31 14 0.33
32 4 0.10
33 7 0.17
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATTAAAATTTTATATATAATTTAACC
Found at i:2125364 original size:15 final size:15
Alignment explanation
Indices: 2125344--2125372 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2125334 TCGTCTTCAG
2125344 CCTCTCCTTCATCTC
1 CCTCTCCTTCATCTC
2125359 CCTCTCCTTCATCT
1 CCTCTCCTTCATCT
2125373 TCTTTGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (15 bp):
CCTCTCCTTCATCTC
Found at i:2133158 original size:20 final size:22
Alignment explanation
Indices: 2133133--2133175 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2133123 GAATTACTCG
*
2133133 ATTTTTCTTT-TA-AAAAATAT
1 ATTTTTATTTATATAAAAATAT
2133153 ATTTTTATTTATATAAAAATAT
1 ATTTTTATTTATATAAAAATAT
2133175 A
1 A
2133176 ATAGTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTATTTATATAAAAATAT
Found at i:2133320 original size:28 final size:26
Alignment explanation
Indices: 2133268--2133320 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2133258 GCAATAGATT
*
2133268 TGATTAAATAAGTTTTTTTTGGAAAC
1 TGATTAAATAAGTTTTTTATGGAAAC
2133294 TGATTAAATAAGTATTTTTATGCGAAA
1 TGATTAAATAAGT-TTTTTATG-GAAA
2133321 ATTTATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.54
27 7 0.29
28 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (26 bp):
TGATTAAATAAGTTTTTTATGGAAAC
Found at i:2138155 original size:5 final size:5
Alignment explanation
Indices: 2138148--2138191 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
2138138 CTCACAGCTT
* *
2138148 CCCTT CCCTT CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCT
1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCT
2138192 TCTTCCTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (5 bp):
CCCTC
Found at i:2144280 original size:3 final size:3
Alignment explanation
Indices: 2144266--2144307 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2144256 CTCTGTAGCT
* *
2144266 GAA GAC GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GCA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2144308 TAAAAGAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.05, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2146920 original size:19 final size:18
Alignment explanation
Indices: 2146883--2146919 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2146873 TTTTAAAATA
2146883 TATAAATTTTTGAATTTT
1 TATAAATTTTTGAATTTT
2146901 TATAAATATTTTG-ATTTT
1 TATAAAT-TTTTGAATTTT
2146919 T
1 T
2146920 TTTTGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATAAATTTTTGAATTTT
Found at i:2151295 original size:2 final size:2
Alignment explanation
Indices: 2151288--2151314 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2151278 TCAGCTAGCG
2151288 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2151315 TCGGTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2154092 original size:134 final size:134
Alignment explanation
Indices: 2153852--2154119 Score: 502
Period size: 134 Copynumber: 2.0 Consensus size: 134
2153842 CCCAGAAAAA
2153852 AAAGTATAGTTTCTTTTTTAGTTAAACAATTTCATGAGCCAAAACCCATTCCTTCAACAACCCAA
1 AAAGTATAGTTTCTTTTTTAGTTAAACAATTTCATGAGCCAAAACCCATTCCTTCAACAACCCAA
2153917 TCACCGACTAAGCTTTGATCTGGGTTTCTTTTAGTATATCAGCTAATAATGTGATGTGAGAGGTT
66 TCACCGACTAAGCTTTGATCTGGGTTTCTTTTAGTATATCAGCTAATAATGTGATGTGAGAGGTT
2153982 TTGG
131 TTGG
*
2153986 AAAGTAT-GATTTCTTTTTTAGTTAAACAATTTCATGAGCCAAAACCCATTCCTTCAACAACTCA
1 AAAGTATAG-TTTCTTTTTTAGTTAAACAATTTCATGAGCCAAAACCCATTCCTTCAACAACCCA
*
2154050 ATCACCGACTAAGCTTTGATCTGGGTTTCTTTTAGTATATCAGTTAATAATGTGATGTGAGAGGT
65 ATCACCGACTAAGCTTTGATCTGGGTTTCTTTTAGTATATCAGCTAATAATGTGATGTGAGAGGT
2154115 TTTGG
130 TTTGG
2154120 GTTTTGATTC
Statistics
Matches: 131, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
133 1 0.01
134 130 0.99
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (134 bp):
AAAGTATAGTTTCTTTTTTAGTTAAACAATTTCATGAGCCAAAACCCATTCCTTCAACAACCCAA
TCACCGACTAAGCTTTGATCTGGGTTTCTTTTAGTATATCAGCTAATAATGTGATGTGAGAGGTT
TTGG
Found at i:2154600 original size:18 final size:17
Alignment explanation
Indices: 2154573--2154606 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2154563 AAATATTTTA
2154573 TTATTTTTTAATTTAAT
1 TTATTTTTTAATTTAAT
*
2154590 TTATGTTTTTACTTTAA
1 TTAT-TTTTTAATTTAA
2154607 ATTTTTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTTTTTAATTTAAT
Found at i:2156241 original size:30 final size:31
Alignment explanation
Indices: 2156177--2156244 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
2156167 ACAACAAGAG
* *
2156177 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACTTTTCGATAACTTGAGT
*
2156208 GACTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGATAACTTGAGT
2156238 GACTGTT
1 GACTGTT
2156245 GTGTTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 14 0.42
31 14 0.42
32 5 0.15
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.46
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTGAGT
Found at i:2160341 original size:24 final size:24
Alignment explanation
Indices: 2160313--2160375 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
2160303 AAAAATAATC
2160313 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* * *
2160337 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
*
2160361 TTTGAGTTAAACTCT
1 TTTCAGTTAAACTCT
2160376 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:2160874 original size:21 final size:21
Alignment explanation
Indices: 2160844--2160890 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2160834 ATCTGTGGCA
2160844 AGTTCGGATGATGGCAATTCT
1 AGTTCGGATGATGGCAATTCT
* *
2160865 AGTTCTGATGATGGTAATTCT
1 AGTTCGGATGATGGCAATTCT
2160886 AGTTC
1 AGTTC
2160891 AGACCGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (21 bp):
AGTTCGGATGATGGCAATTCT
Found at i:2162263 original size:24 final size:24
Alignment explanation
Indices: 2162236--2162290 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2162226 AATCTTTCAG
*
2162236 TTAAACTATATTTAATTGTTTTAA
1 TTAAACTATATTTAATTGTTTGAA
* * * *
2162260 TTAAATTCTATTTATTTGTTTGAG
1 TTAAACTATATTTAATTGTTTGAA
2162284 TTAAACT
1 TTAAACT
2162291 CTTATTAGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (24 bp):
TTAAACTATATTTAATTGTTTGAA
Found at i:2167997 original size:7 final size:7
Alignment explanation
Indices: 2167985--2168015 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2167975 TAAGGGGGTT
2167985 TATACTG
1 TATACTG
2167992 TATACTG
1 TATACTG
2167999 TATACTG
1 TATACTG
*
2168006 TATAATG
1 TATACTG
2168013 TAT
1 TAT
2168016 TATAGTCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (7 bp):
TATACTG
Found at i:2168284 original size:2 final size:2
Alignment explanation
Indices: 2168279--2168328 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2168269 TATATAGAAT
2168279 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2168321 AG AG -G AG A
1 AG AG AG AG A
2168329 TATTATGGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2185298 original size:25 final size:26
Alignment explanation
Indices: 2185270--2185318 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2185260 ATTCTTATTT
2185270 AATAAAT-TGCT-CATTTGATTAAAAA
1 AATAAATATGCTGC-TTTGATTAAAAA
*
2185295 AATAAATATGTTGCTTTGATTAAA
1 AATAAATATGCTGCTTTGATTAAA
2185319 TAATCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (26 bp):
AATAAATATGCTGCTTTGATTAAAAA
Found at i:2187476 original size:11 final size:11
Alignment explanation
Indices: 2187462--2187558 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 11
2187452 CAAATACCTC
2187462 TAAAATAATAA
1 TAAAATAATAA
2187473 TAAAATTAATAA
1 TAAAA-TAATAA
2187485 TAAAAT-ATAAA
1 TAAAATAAT-AA
* * *
2187496 TTATATAATAT
1 TAAAATAATAA
*
2187507 TAAAACAATAA
1 TAAAATAATAA
* *
2187518 CAACTAAATAATGA
1 -TA--AAATAATAA
**
2187532 TAGTATAATAA
1 TAAAATAATAA
**
2187543 CGAAATAATAA
1 TAAAATAATAA
2187554 TAAAA
1 TAAAA
2187559 CTATGAAAAA
Statistics
Matches: 60, Mismatches: 20, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
10 2 0.03
11 36 0.60
12 14 0.23
13 1 0.02
14 7 0.12
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2187484 original size:12 final size:12
Alignment explanation
Indices: 2187462--2187490 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2187452 CAAATACCTC
2187462 TAAAA-TAATAA
1 TAAAATTAATAA
2187473 TAAAATTAATAA
1 TAAAATTAATAA
2187485 TAAAAT
1 TAAAAT
2187491 ATAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:2187503 original size:19 final size:18
Alignment explanation
Indices: 2187465--2187505 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
2187455 ATACCTCTAA
2187465 AATAATAATAAAATTAAT
1 AATAATAATAAAATTAAT
2187483 AATAA-AATATAAATTATAT
1 AATAATAATA-AAATTA-AT
2187502 AATA
1 AATA
2187506 TTAAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATAATAAAATTAAT
Found at i:2189751 original size:822 final size:822
Alignment explanation
Indices: 2188168--2189817 Score: 3282
Period size: 822 Copynumber: 2.0 Consensus size: 822
2188158 AGTAATTTTA
*
2188168 GTATGATAGTGTTTTAACTAAGTATGATGATTAAATTGCATAAGTGATAAAAGTGCAATTTATAA
1 GTATGATAGTGTTTTAACTAAGTATGATGACTAAATTGCATAAGTGATAAAAGTGCAATTTATAA
2188233 AGGGATTTTTAATTGAAATTAAAAGGGAGGACCAAAGGGGCAAATTTCCCCTTTAAACCCTTAGT
66 AGGGATTTTTAATTGAAATTAAAAGGGAGGACCAAAGGGGCAAATTTCCCCTTTAAACCCTTAGT
2188298 GTCGTTAGGTGATTATGTGTGTGGGTTAAAAATTTTGCTTAAATTTTATAATTAAAAGAAATTAA
131 GTCGTTAGGTGATTATGTGTGTGGGTTAAAAATTTTGCTTAAATTTTATAATTAAAAGAAATTAA
2188363 ATAAAACAAAGAAAAAGAAAGACAATGATGATTATAAGTATGGGTTGTTAAGAGAAGAGGGAAAT
196 ATAAAACAAAGAAAAAGAAAGACAATGATGATTATAAGTATGGGTTGTTAAGAGAAGAGGGAAAT
2188428 ATCTTCCTTCCATTTTCAGCTGTACATGAAACAGAGAGGGAGAAAAGAGAAAGAAAAAGGTTGAG
261 ATCTTCCTTCCATTTTCAGCTGTACATGAAACAGAGAGGGAGAAAAGAGAAAGAAAAAGGTTGAG
2188493 TTCTAATTAGGTTCAAGATGTAAGTCTAATTAAGTCTTTTTCTCATAATTTTTATGTTTTTGAAA
326 TTCTAATTAGGTTCAAGATGTAAGTCTAATTAAGTCTTTTTCTCATAATTTTTATGTTTTTGAAA
2188558 TCTTGGTGCCTCCCCCTTCATGACTCATGCCGTAGTTTTCGTTATTATTGGAAATATTATATACC
391 TCTTGGTGCCTCCCCCTTCATGACTCATGCCGTAGTTTTCGTTATTATTGGAAATATTATATACC
2188623 ACCATTGTTGGGTTCTTAGAGCTCTAATGATAATTTGGTGTATTTTGGAGCTAGATGTGAAAAAG
456 ACCATTGTTGGGTTCTTAGAGCTCTAATGATAATTTGGTGTATTTTGGAGCTAGATGTGAAAAAG
2188688 AAATAAATGGTGAGATAAATTGCTAACCTTATTAGTATAAGGGTCAAATTGAGAAGTTTGGTAAG
521 AAATAAATGGTGAGATAAATTGCTAACCTTATTAGTATAAGGGTCAAATTGAGAAGTTTGGTAAG
2188753 TTATTGTAAAAATGAGAAAATAGGGAATTAAATTTAGTTAAAACAAAAAGGATGTGTTTTAACGA
586 TTATTGTAAAAATGAGAAAATAGGGAATTAAATTTAGTTAAAACAAAAAGGATGTGTTTTAACGA
2188818 AATATATTGTATGTTTAATTTCATAGCTAACGTCGACTCGAATTCCTCCAAAAGGAAGGGCAAAG
651 AATATATTGTATGTTTAATTTCATAGCTAACGTCGACTCGAATTCCTCCAAAAGGAAGGGCAAAG
2188883 ACAAAGTTGACAATGAGTAGCTCAGAAATTACTATTGGTGTTTCTACAACTTTAACTAGTTTATT
716 ACAAAGTTGACAATGAGTAGCTCAGAAATTACTATTGGTGTTTCTACAACTTTAACTAGTTTATT
2188948 AAATCGTCAAATTATAATTAATTGCTCAAAGTAGAAATCAAG
781 AAATCGTCAAATTATAATTAATTGCTCAAAGTAGAAATCAAG
2188990 GTATGATAGTGTTTTAACTAAGTATGATGACTAAATTGCATAAGTGATAAAAGTGCAATTTATAA
1 GTATGATAGTGTTTTAACTAAGTATGATGACTAAATTGCATAAGTGATAAAAGTGCAATTTATAA
*
2189055 AGGGATTTTTAATTGAAATTAAAAGGGAGGACCAATGGGGCAAATTTCCCCTTTAAACCCTTAGT
66 AGGGATTTTTAATTGAAATTAAAAGGGAGGACCAAAGGGGCAAATTTCCCCTTTAAACCCTTAGT
2189120 GTCGTTAGGTGATTATGTGTGTGGGTTAAAAATTTTGCTTAAATTTTATAATTAAAAGAAATTAA
131 GTCGTTAGGTGATTATGTGTGTGGGTTAAAAATTTTGCTTAAATTTTATAATTAAAAGAAATTAA
2189185 ATAAAACAAAGAAAAAGAAAGACAATGATGATTATAAGTATGGGTTGTTAAGAGAAGAGGGAAAT
196 ATAAAACAAAGAAAAAGAAAGACAATGATGATTATAAGTATGGGTTGTTAAGAGAAGAGGGAAAT
2189250 ATCTTCCTTCCATTTTCAGCTGTACATGAAACAGAGAGGGAGAAAAGAGAAAGAAAAAGGTTGAG
261 ATCTTCCTTCCATTTTCAGCTGTACATGAAACAGAGAGGGAGAAAAGAGAAAGAAAAAGGTTGAG
2189315 TTCTAATTAGGTTCAAGATGTAAGTCTAATTAAGTCTTTTTCTCATAATTTTTATGTTTTTGAAA
326 TTCTAATTAGGTTCAAGATGTAAGTCTAATTAAGTCTTTTTCTCATAATTTTTATGTTTTTGAAA
2189380 TCTTGGTGCCTCCCCCTTCATGACTCATGCCGTAGTTTTCGTTATTATTGGAAATATTATATACC
391 TCTTGGTGCCTCCCCCTTCATGACTCATGCCGTAGTTTTCGTTATTATTGGAAATATTATATACC
2189445 ACCATTGTTGGGTTCTTAGAGCTCTAATGATAATTTGGTGTATTTTGGAGCTAGATGTGAAAAAG
456 ACCATTGTTGGGTTCTTAGAGCTCTAATGATAATTTGGTGTATTTTGGAGCTAGATGTGAAAAAG
2189510 AAATAAATGGTGAGATAAATTGCTAACCTTATTAGTATAAGGGTCAAATTGAGAAGTTTGGTAAG
521 AAATAAATGGTGAGATAAATTGCTAACCTTATTAGTATAAGGGTCAAATTGAGAAGTTTGGTAAG
2189575 TTATTGTAAAAATGAGAAAATAGGGAATTAAATTTAGTTAAAACAAAAAGGATGTGTTTTAACGA
586 TTATTGTAAAAATGAGAAAATAGGGAATTAAATTTAGTTAAAACAAAAAGGATGTGTTTTAACGA
2189640 AATATATTGTATGTTTAATTTCATAGCTAACGTCGACTCGAATTCCTCCAAAAGGAAGGGCAAAG
651 AATATATTGTATGTTTAATTTCATAGCTAACGTCGACTCGAATTCCTCCAAAAGGAAGGGCAAAG
2189705 ACAAAGTTGACAATGAGTAGCTCAGAAATTACTATTGGTGTTTCTACAACTTTAACTAGTTTATT
716 ACAAAGTTGACAATGAGTAGCTCAGAAATTACTATTGGTGTTTCTACAACTTTAACTAGTTTATT
2189770 AAATCGTCAAATTATAATTAATTGCTCAAAGTAGAAATCAAG
781 AAATCGTCAAATTATAATTAATTGCTCAAAGTAGAAATCAAG
2189812 GTATGA
1 GTATGA
2189818 GATTCTCTAC
Statistics
Matches: 826, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
822 826 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (822 bp):
GTATGATAGTGTTTTAACTAAGTATGATGACTAAATTGCATAAGTGATAAAAGTGCAATTTATAA
AGGGATTTTTAATTGAAATTAAAAGGGAGGACCAAAGGGGCAAATTTCCCCTTTAAACCCTTAGT
GTCGTTAGGTGATTATGTGTGTGGGTTAAAAATTTTGCTTAAATTTTATAATTAAAAGAAATTAA
ATAAAACAAAGAAAAAGAAAGACAATGATGATTATAAGTATGGGTTGTTAAGAGAAGAGGGAAAT
ATCTTCCTTCCATTTTCAGCTGTACATGAAACAGAGAGGGAGAAAAGAGAAAGAAAAAGGTTGAG
TTCTAATTAGGTTCAAGATGTAAGTCTAATTAAGTCTTTTTCTCATAATTTTTATGTTTTTGAAA
TCTTGGTGCCTCCCCCTTCATGACTCATGCCGTAGTTTTCGTTATTATTGGAAATATTATATACC
ACCATTGTTGGGTTCTTAGAGCTCTAATGATAATTTGGTGTATTTTGGAGCTAGATGTGAAAAAG
AAATAAATGGTGAGATAAATTGCTAACCTTATTAGTATAAGGGTCAAATTGAGAAGTTTGGTAAG
TTATTGTAAAAATGAGAAAATAGGGAATTAAATTTAGTTAAAACAAAAAGGATGTGTTTTAACGA
AATATATTGTATGTTTAATTTCATAGCTAACGTCGACTCGAATTCCTCCAAAAGGAAGGGCAAAG
ACAAAGTTGACAATGAGTAGCTCAGAAATTACTATTGGTGTTTCTACAACTTTAACTAGTTTATT
AAATCGTCAAATTATAATTAATTGCTCAAAGTAGAAATCAAG
Found at i:2195290 original size:20 final size:19
Alignment explanation
Indices: 2195257--2195295 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2195247 GTTTATTAAA
*
2195257 TTTTTAATTAATACTGTTTT
1 TTTTTAAATAATACT-TTTT
*
2195277 TTTTTAAATGATACTTTTT
1 TTTTTAAATAATACTTTTT
2195296 AGGGCGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTAAATAATACTTTTT
Found at i:2199439 original size:15 final size:15
Alignment explanation
Indices: 2199430--2199480 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2199420 GTCATCATCC
2199430 TCATCCTCATCCTCA
1 TCATCCTCATCCTCA
* * *
2199445 TCATCTTCATCAAT-T
1 TCATCCTCATC-CTCA
*
2199460 TCATCTTCATCCTCA
1 TCATCCTCATCCTCA
2199475 TCATCC
1 TCATCC
2199481 AACTCAAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (15 bp):
TCATCCTCATCCTCA
Found at i:2199494 original size:30 final size:29
Alignment explanation
Indices: 2199429--2199495 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
2199419 CGTCATCATC
* *
2199429 CTCATCCTCATCCTCATCATCTTCATCAAT
1 CTCATCTTCATCCTCATCATC-TCATCAAG
*
2199459 TTCATCTTCATCCTCATCATC-CAACTCAAG
1 CTCATCTTCATCCTCATCATCTC-A-TCAAG
2199489 CTCATCT
1 CTCATCT
2199496 CCCTGAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 29 0.94
ACGTcount: A:0.24, C:0.39, G:0.01, T:0.36
Consensus pattern (29 bp):
CTCATCTTCATCCTCATCATCTCATCAAG
Found at i:2203923 original size:20 final size:20
Alignment explanation
Indices: 2203898--2203949 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2203888 ATTAATTATT
*
2203898 TATAAAATTTAATTTGAATA
1 TATAAAATATAATTTGAATA
* *
2203918 TATAAACTATATTTTGAATA
1 TATAAAATATAATTTGAATA
*
2203938 T-TAATATATAAT
1 TATAAAATATAAT
2203950 AAAAATATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TATAAAATATAATTTGAATA
Found at i:2207839 original size:30 final size:30
Alignment explanation
Indices: 2207803--2207863 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2207793 GATATACTCT
2207803 TAGATGATGCTATAGTATCAGAAAAAAAGG
1 TAGATGATGCTATAGTATCAGAAAAAAAGG
* * *
2207833 TAGATGATGCTGTGGTATCAGGAAAAAAGG
1 TAGATGATGCTATAGTATCAGAAAAAAAGG
2207863 T
1 T
2207864 GGAGGAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.28, T:0.25
Consensus pattern (30 bp):
TAGATGATGCTATAGTATCAGAAAAAAAGG
Found at i:2212891 original size:155 final size:155
Alignment explanation
Indices: 2212609--2212919 Score: 527
Period size: 155 Copynumber: 2.0 Consensus size: 155
2212599 TAATGTATTG
*
2212609 TCAAAACAAAATTTAATACTAAGGAAAAACATACGAAAACAGTAGTACGGATATACAAATCATTA
1 TCAAAACAAAATTTAATACTAAGGAAAAACATACGAAAACAGTAGTACGGATACACAAATCATTA
*
2212674 CATCTTATACAGGATCCTAGGGTCAGTGAAAATGAAAGTTATCGCCTTAAGCGCTAAAACAAACA
66 CATCTTATACAGGATCCTAGGGTCAGTAAAAATGAAAGTTATCGCCTTAAGCGCTAAAACAAACA
2212739 ACATCGAGATATGAATCTTGTCATT
131 ACATCGAGATATGAATCTTGTCATT
* *
2212764 TCAAAATAAAATTTAATACTAAGGAAAAACATACGAAAACAGTGGTACGGATACACAAATCATTA
1 TCAAAACAAAATTTAATACTAAGGAAAAACATACGAAAACAGTAGTACGGATACACAAATCATTA
* * *
2212829 CATCTTATACGGGA-CTCTAGGGTCAGTAAAAATGAAAGTTGTCGCCTTGAA-CGCTAAGACAAA
66 CATCTTATACAGGATC-CTAGGGTCAGTAAAAATGAAAGTTATCGCCTT-AAGCGCTAAAACAAA
2212892 CAACATCGAGATATGAATCTTGTCATT
129 CAACATCGAGATATGAATCTTGTCATT
2212919 T
1 T
2212920 AAGTTATTGG
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
154 1 0.01
155 144 0.98
156 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.25
Consensus pattern (155 bp):
TCAAAACAAAATTTAATACTAAGGAAAAACATACGAAAACAGTAGTACGGATACACAAATCATTA
CATCTTATACAGGATCCTAGGGTCAGTAAAAATGAAAGTTATCGCCTTAAGCGCTAAAACAAACA
ACATCGAGATATGAATCTTGTCATT
Found at i:2218196 original size:17 final size:16
Alignment explanation
Indices: 2218154--2218196 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2218144 TTATTTTCCA
* *
2218154 TATTTGTTATTTCTGT
1 TATTTGTTATTACTAT
2218170 TATTTAGTTATTACTAT
1 TATTT-GTTATTACTAT
2218187 TAGTTTGTTA
1 TA-TTTGTTA
2218197 ATTAGAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 15 0.65
18 3 0.13
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (16 bp):
TATTTGTTATTACTAT
Found at i:2222660 original size:17 final size:16
Alignment explanation
Indices: 2222633--2222675 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
2222623 TTATTTTCCA
*
2222633 TATTTGTTATTTCTGT
1 TATTTGTTATTACTGT
2222649 TATTTAGTTATTACTGT
1 TATTT-GTTATTACTGT
2222666 TAGTTTGTTA
1 TA-TTTGTTA
2222676 ATTAGAGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.63
Consensus pattern (16 bp):
TATTTGTTATTACTGT
Found at i:2227185 original size:33 final size:32
Alignment explanation
Indices: 2227124--2227186 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
2227114 TAATACAATG
*
2227124 AATATATTAAAAATATTAAAATAAATATTTCTC
1 AATAAATTAAAAATATTAAAAT-AATATTTCTC
2227157 AATAAATTACAAATATATTAAAAT-ATATTT
1 AATAAATTA-AAA-ATATTAAAATAATATTT
2227187 ATACTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 14 0.52
34 3 0.11
35 10 0.37
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAAATTAAAAATATTAAAATAATATTTCTC
Found at i:2227209 original size:11 final size:11
Alignment explanation
Indices: 2227202--2227232 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
2227192 TAAATAACAC
2227202 TAAAATAATAA
1 TAAAATAATAA
2227213 TAAAATTAATAA
1 TAAAA-TAATAA
2227225 TAAAATAA
1 TAAAATAA
2227233 GAGTTATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2228503 original size:15 final size:16
Alignment explanation
Indices: 2228483--2228512 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2228473 AATTTAAAAA
2228483 TTTTAAT-TTTTTTAT
1 TTTTAATATTTTTTAT
2228498 TTTTAATATTTTTTA
1 TTTTAATATTTTTTA
2228513 AAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTAATATTTTTTAT
Found at i:2228625 original size:18 final size:19
Alignment explanation
Indices: 2228602--2228639 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2228592 TTTTGGGATG
*
2228602 ATTTAATAAACAT-TATAA
1 ATTTAAAAAACATATATAA
*
2228620 ATTTAAAAAATATATATAA
1 ATTTAAAAAACATATATAA
2228639 A
1 A
2228640 AAACTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTAAAAAACATATATAA
Found at i:2259247 original size:151 final size:151
Alignment explanation
Indices: 2259078--2259349 Score: 445
Period size: 151 Copynumber: 1.8 Consensus size: 151
2259068 AGTCACTAAA
* * *
2259078 GATTCCAATATCTTTTTTCCGTTAAGTTTTTTTGGGTTAATGGGTTTCAAAGATTCAAGCTTTGA
1 GATTCCAATATCTTTTTTCAGTTAAGTTTTTTTGGATTAATGAGTTTCAAAGATTCAAGCTTTGA
* * * *
2259143 GACAGATTTGTAATTAAAGATATTGGAATTAAAAGGGAAGAAGATGAAAATGAAGAAGAGAGGTG
66 GACAGATTTGTAACTAAAGATATTAGAATCAAAAAGGAAGAAGATGAAAATGAAGAAGAGAGGTG
2259208 TGTGGAAGATTCAATATCTTT
131 TGTGGAAGATTCAATATCTTT
* *
2259229 GATTCCAATATTTTTTTTCAGTTAAGTTTTTTTGGATTAATGAGTTTCAAAGATTTAAGCTTTGA
1 GATTCCAATATCTTTTTTCAGTTAAGTTTTTTTGGATTAATGAGTTTCAAAGATTCAAGCTTTGA
* *
2259294 GATAGATTTGTAACTAAAGATATTAGAATCAAAAAGGAAGAAGATGAAGATGAAGA
66 GACAGATTTGTAACTAAAGATATTAGAATCAAAAAGGAAGAAGATGAAAATGAAGA
2259350 TGAAGATGAA
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 110 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (151 bp):
GATTCCAATATCTTTTTTCAGTTAAGTTTTTTTGGATTAATGAGTTTCAAAGATTCAAGCTTTGA
GACAGATTTGTAACTAAAGATATTAGAATCAAAAAGGAAGAAGATGAAAATGAAGAAGAGAGGTG
TGTGGAAGATTCAATATCTTT
Found at i:2259344 original size:6 final size:6
Alignment explanation
Indices: 2259333--2259361 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2259323 CAAAAAGGAA
2259333 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
2259362 AGAAAGGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:2263152 original size:19 final size:20
Alignment explanation
Indices: 2263111--2263152 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2263101 ATTTTCGTTA
**
2263111 AAAAATAAAATTTGATTTTT
1 AAAAATAAAATTTGATTACT
2263131 AAAAA-AAAATTTGATTACT
1 AAAAATAAAATTTGATTACT
2263150 AAA
1 AAA
2263153 TTTTGATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAAATAAAATTTGATTACT
Found at i:2264262 original size:5 final size:5
Alignment explanation
Indices: 2264252--2264294 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
2264242 CCATTCTTGT
*
2264252 TAAAA TAAAA TACAA T--AA TAAAA TAAAA TAAAA TAAAA GTAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -TAAA
2264295 GTTTAAATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
3 3 0.09
5 27 0.79
6 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:2264275 original size:18 final size:18
Alignment explanation
Indices: 2264252--2264287 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2264242 CCATTCTTGT
*
2264252 TAAAATAAAATACAATAA
1 TAAAATAAAATAAAATAA
2264270 TAAAATAAAATAAAATAA
1 TAAAATAAAATAAAATAA
2264288 AAGTAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAATAAAATAAAATAA
Found at i:2265230 original size:16 final size:17
Alignment explanation
Indices: 2265209--2265241 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2265199 TAAAATTTAT
*
2265209 TTTTATTAATT-TAAAA
1 TTTTATAAATTATAAAA
2265225 TTTTATAAATTATAAAA
1 TTTTATAAATTATAAAA
2265242 AAAAAAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTATAAATTATAAAA
Found at i:2272799 original size:19 final size:18
Alignment explanation
Indices: 2272777--2272827 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2272767 CTAAAAAAAT
2272777 AAATAATAATTTTTGTAAA
1 AAATAATAATTTTT-TAAA
* *
2272796 AAATAAAAATTCTTTAAA
1 AAATAATAATTTTTTAAA
*
2272814 AAA-AGTAATTTTTT
1 AAATAATAATTTTTT
2272828 TCTTTACTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 12 0.44
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (18 bp):
AAATAATAATTTTTTAAA
Found at i:2272950 original size:18 final size:19
Alignment explanation
Indices: 2272927--2272963 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2272917 AATAATACTC
2272927 TGATAACA-ACAAAAATAT
1 TGATAACATACAAAAATAT
*
2272945 TGATAACATATAAAAATAT
1 TGATAACATACAAAAATAT
2272964 ACCAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (19 bp):
TGATAACATACAAAAATAT
Found at i:2278328 original size:6 final size:6
Alignment explanation
Indices: 2278297--2278381 Score: 65
Period size: 6 Copynumber: 15.0 Consensus size: 6
2278287 GATTTTCAAG
* * * *
2278297 TTTAAA ATTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
* *
2278343 TTTAAA TTT-AC TTTAAA TTTAAA TTT-GA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2278382 AATAATATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
4 4 0.07
5 12 0.20
6 43 0.70
7 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2278331 original size:17 final size:16
Alignment explanation
Indices: 2278304--2278381 Score: 95
Period size: 17 Copynumber: 4.7 Consensus size: 16
2278294 AAGTTTAAAA
*
2278304 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
*
2278321 TTAGATTTAAATTTAT
1 TTAAATTTAAATTTAT
2278337 CTTAAATTTAAATTTACT
1 -TTAAATTTAAATTTA-T
2278355 TTAAATTTAAATTTGA-
1 TTAAATTTAAATTT-AT
2278371 TTAAATTTAAA
1 TTAAATTTAAA
2278382 AATAATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
16 16 0.29
17 37 0.67
18 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:2280296 original size:30 final size:30
Alignment explanation
Indices: 2280260--2280573 Score: 443
Period size: 30 Copynumber: 10.4 Consensus size: 30
2280250 AAATTATCCA
*
2280260 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
2280290 AAAATTACATTTTGACCCCAAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
2280320 AAAATTATC-TTTTGAACCTAAAACTTTTCC
1 AAAATTA-CATTTTGACCCCAAAACTTTTCC
*
2280350 AAAATTATATTTTGACCCCAAAACTTTTTCC
1 AAAATTACATTTTGACCCCAAAAC-TTTTCC
**
2280381 AAAATTACATTTTGACCCCAAATTTTTTTCC
1 AAAATTACATTTTGACCCCAAA-ACTTTTCC
**
2280412 AAAATTACATTTTGACCCCAAAACTTTTTA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* **
2280442 AAAATTATATTTTGACCTTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
2280472 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
2280502 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
2280532 AAAATTATATTTTGACCCCAAAAC-TTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
2280561 AAAATTACCATTT
1 AAAATTA-CATTT
2280574 CACACTCAAA
Statistics
Matches: 253, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.04
30 186 0.74
31 56 0.22
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:2282991 original size:34 final size:33
Alignment explanation
Indices: 2282944--2283016 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
2282934 TATTGAAAAT
*
2282944 ATTTATATCAATATTTTAATG-ATAAATATATATTAA
1 ATTTATA-CAATATTTTAAAGTA-AAATATA-ATT-A
2282980 ATTTATA-AATATTTTAAAGTAAAATATAATTA
1 ATTTATACAATATTTTAAAGTAAAATATAATTA
2283012 ATTTA
1 ATTTA
2283017 ATTATATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 6 0.17
33 3 0.09
34 18 0.51
35 1 0.03
36 7 0.20
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (33 bp):
ATTTATACAATATTTTAAAGTAAAATATAATTA
Found at i:2285185 original size:19 final size:18
Alignment explanation
Indices: 2285161--2285196 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2285151 AAAGCCTTGT
*
2285161 TATTTTATTTAATTTTTTA
1 TATTTTAATT-ATTTTTTA
2285180 TATTTTAATTATTTTTT
1 TATTTTAATTATTTTTT
2285197 CCCCAGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTTTAATTATTTTTTA
Found at i:2287934 original size:2 final size:2
Alignment explanation
Indices: 2287927--2287986 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2287917 TGCTGGAAGA
2287927 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2287969 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
2287987 GTGTTATATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2309093 original size:38 final size:38
Alignment explanation
Indices: 2309042--2309117 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
2309032 TAGGCTGCAA
*
2309042 ATTATTGCCATGATGCTAAGCATCAGCTACAGAGACTG
1 ATTATTGCCATGATGCTAAGCATCAGCTAAAGAGACTG
* **
2309080 ATTATTGCCATGATGCTAGGCATTGGCTAAAGAGACTG
1 ATTATTGCCATGATGCTAAGCATCAGCTAAAGAGACTG
2309118 CAAAAGCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (38 bp):
ATTATTGCCATGATGCTAAGCATCAGCTAAAGAGACTG
Found at i:2313885 original size:2 final size:2
Alignment explanation
Indices: 2313878--2313943 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
2313868 TAAATTATCA
2313878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2313920 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
2313944 CAAAATTTCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2325323 original size:2 final size:2
Alignment explanation
Indices: 2325316--2325350 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2325306 ATATTTACTT
2325316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2325351 TTGTAATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2331214 original size:17 final size:16
Alignment explanation
Indices: 2331174--2331215 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
2331164 ATAAAGAAAT
2331174 AAATTAAAAGAAAAAA
1 AAATTAAAAGAAAAAA
2331190 AAAGTTAAAAGAGAAAAA
1 AAA-TTAAAAGA-AAAAA
*
2331208 GAATTAAA
1 AAATTAAA
2331216 TTACTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 13 0.57
18 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (16 bp):
AAATTAAAAGAAAAAA
Found at i:2332514 original size:21 final size:23
Alignment explanation
Indices: 2332488--2332533 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2332478 TCATTAAGTT
*
2332488 ATTTTCA-T-TTTAAATATATTG
1 ATTTTCACTGTTTAAAAATATTG
*
2332509 ATTTTCACTGTTTAAAAATTTTG
1 ATTTTCACTGTTTAAAAATATTG
2332532 AT
1 AT
2332534 GAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTTTCACTGTTTAAAAATATTG
Found at i:2335151 original size:59 final size:59
Alignment explanation
Indices: 2335108--2335397 Score: 404
Period size: 59 Copynumber: 4.9 Consensus size: 59
2335098 GAAATTTTAA
* * * * *
2335108 GGTTAAAAATGGGATTTTAGAAAGTTCAGGGATAAAATGGTAATTTTCGATGAAATCGG
1 GGTTAAAAATGGGATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTGGGTGAAATCGG
* *
2335167 GGTT-AAAATGGGATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTGGGTGAAATCGA
1 GGTTAAAAATGGGATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTGGGTGAAATCGG
2335225 GGTTAAAAATGGGATTTTGGAAGGTTC-GAGGGTAAAATGGTAATTTTGGGTGAAATCGG
1 GGTTAAAAATGGGATTTTGGAAGGTTCAG-GGGTAAAATGGTAATTTTGGGTGAAATCGG
* * * **
2335284 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGATAAATTTTGGGTGAAATTAG
1 GGTTAAAAATGGGATTTTGGAAGGTTCAGGGGTAAAATGGT-AATTTTGGGTGAAATCGG
* * *
2335344 GGTTAAAAGTGGGATTTTGGAAGGTTCGGGGGTAAAATGGTAAATTTTAGGTGA
1 GGTTAAAAATGGGATTTTGGAAGGTTCAGGGGTAAAATGGT-AATTTTGGGTGA
2335398 TATTAGGGTA
Statistics
Matches: 208, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
58 52 0.25
59 91 0.44
60 65 0.31
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (59 bp):
GGTTAAAAATGGGATTTTGGAAGGTTCAGGGGTAAAATGGTAATTTTGGGTGAAATCGG
Found at i:2335153 original size:29 final size:28
Alignment explanation
Indices: 2335113--2335212 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 28
2335103 TTTAAGGTTA
* *
2335113 AAAATGGGATTTTAGAAAGTTCAGGGAT
1 AAAATGGAATTTTAGAAAGTTCGGGGAT
*
2335141 AAAATGGTAATTTTCGATGAAA--TCGGGGTT
1 AAAATGG-AATTTT--A-GAAAGTTCGGGGAT
* * * *
2335171 AAAATGGGATTTTGGAAGGTTCGGGGGT
1 AAAATGGAATTTTAGAAAGTTCGGGGAT
2335199 AAAATGGTAATTTT
1 AAAATGG-AATTTT
2335213 GGGTGAAATC
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
26 3 0.05
28 21 0.37
29 15 0.26
30 13 0.23
31 1 0.02
32 4 0.07
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTAGAAAGTTCGGGGAT
Found at i:2335228 original size:117 final size:116
Alignment explanation
Indices: 2335074--2335391 Score: 401
Period size: 117 Copynumber: 2.7 Consensus size: 116
2335064 TTTTTGACTC
* *
2335074 TCGGGGGTAAACAT-GTAATTTT-GG-GAAATTTTAAGGTTAAAAATGGGATTTTAGAAAGTTCA
1 TCGGGGGTAAA-ATGGTAATTTTGGGTGAAA---TAAGGTTAAAAATGGGATTTTGGAAGGTTCA
*
2335136 GGGATAAAATGGTAATTTTCGATGAAATCGGGGTT-AAAATGGGATTTTGGAAGGT
62 GGG-TAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGGATTTTGGAAAGT
*
2335191 TCGGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAGGTTCGAGG
1 TCGGGGGTAAAATGGTAATTTTGGGTGAAAT-AAGGTTAAAAATGGGATTTTGGAAGGTTC-AGG
* *
2335256 GTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGT
64 GTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGGATTTTGGAAAGT
** * * * *
2335309 TTAGGGGTAAAATGATAAATTTTGGGTGAAATTAGGGTTAAAAGTGGGATTTTGGAAGGTTCGGG
1 TCGGGGGTAAAATGGT-AATTTTGGGTGAAA-TAAGGTTAAAAATGGGATTTTGGAAGGTTC-AG
2335374 GGTAAAATGGTAAATTTT
63 GGTAAAATGGT-AATTTT
2335392 AGGTGATATT
Statistics
Matches: 179, Mismatches: 13, Indels: 15
0.86 0.06 0.07
Matches are distributed among these distances:
116 3 0.02
117 74 0.41
118 38 0.21
119 57 0.32
120 7 0.04
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (116 bp):
TCGGGGGTAAAATGGTAATTTTGGGTGAAATAAGGTTAAAAATGGGATTTTGGAAGGTTCAGGGT
AAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGGATTTTGGAAAGT
Found at i:2335301 original size:30 final size:29
Alignment explanation
Indices: 2335140--2335304 Score: 129
Period size: 30 Copynumber: 5.6 Consensus size: 29
2335130 AGTTCAGGGA
* *
2335140 TAAAATGGTAATTTTCGATGAAATCGGGGT
1 TAAAATGG-GATTTTGGATGAAATCGGGGT
* ** *
2335170 TAAAATGGGATTTTGGAAG-GTTCGGGGG
1 TAAAATGGGATTTTGGATGAAATCGGGGT
* * *
2335198 TAAAATGGTAATTTTGGGTGAAATCGAGGT
1 TAAAATGG-GATTTTGGATGAAATCGGGGT
* **
2335228 TAAAAATGGGATTTTGGAAG-GTTCGAGGG-
1 T-AAAATGGGATTTTGGATGAAATCG-GGGT
* *
2335257 TAAAATGGTAATTTTGGGTGAAATCGGGGT
1 TAAAATGG-GATTTTGGATGAAATCGGGGT
2335287 TAAAAATGGGATTTTGGA
1 T-AAAATGGGATTTTGGA
2335305 AAGTTTAGGG
Statistics
Matches: 101, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
28 21 0.21
29 31 0.31
30 35 0.35
31 14 0.14
ACGTcount: A:0.32, C:0.04, G:0.33, T:0.32
Consensus pattern (29 bp):
TAAAATGGGATTTTGGATGAAATCGGGGT
Found at i:2335359 original size:60 final size:59
Alignment explanation
Indices: 2335077--2335406 Score: 375
Period size: 59 Copynumber: 5.6 Consensus size: 59
2335067 TTGACTCTCG
* *
2335077 GGGGTAAACAT-GTAATTTT-GG-GAAATTTTAAGGTTAAAAATGGGATTTTAGAAAGTTCA
1 GGGGTAAA-ATGGTAATTTTGGGTGAAA--TTAGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * * ** * *
2335136 GGGATAAAATGGTAATTTTCGATGAAATCGGGGTT-AAAATGGGATTTTGGAAGGTTCG
1 GGGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCA
* *
2335194 GGGGTAAAATGGTAATTTTGGGTGAAA-TCGAGGTTAAAAATGGGATTTTGGAAGGTTC-
1 GGGGTAAAATGGTAATTTTGGGTGAAATTAG-GGTTAAAAATGGGATTTTGGAAAGTTCA
** *
2335252 GAGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTA
1 G-GGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCA
* * * *
2335312 GGGGTAAAATGATAAATTTTGGGTGAAATTAGGGTTAAAAGTGGGATTTTGGAAGGTTCG
1 GGGGTAAAATGGT-AATTTTGGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCA
* *
2335372 GGGGTAAAATGGTAAATTTTAGGTGATATTAGGGT
1 GGGGTAAAATGGT-AATTTTGGGTGAAATTAGGGT
2335407 AAGTCTTGAA
Statistics
Matches: 235, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.00
58 51 0.22
59 104 0.44
60 75 0.32
61 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTGGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCA
Found at i:2335361 original size:30 final size:29
Alignment explanation
Indices: 2335198--2335363 Score: 78
Period size: 31 Copynumber: 5.6 Consensus size: 29
2335188 GGTTCGGGGG
* *
2335198 TAAAATGGTAATTTTGGGTGAAA-TCGAGGT
1 TAAAATGG-GATTTTGGGTGAAATTAG-GGT
*
2335228 TAAAAATGGGATTTT--G-GAAGGTTCGAGGG-
1 T-AAAATGGGATTTTGGGTGAA-ATT--AGGGT
* **
2335257 TAAAATGGTAATTTTGGGTGAAATCGGGGT
1 TAAAATGG-GATTTTGGGTGAAATTAGGGT
*
2335287 TAAAAATGGGATTTT--G-GAAAGTTTAGGGG
1 T-AAAATGGGATTTTGGGTGAAA--TTAGGGT
**
2335316 TAAAATGATAAATTTTGGGTGAAATTAGGGT
1 TAAAATG--GGATTTTGGGTGAAATTAGGGT
2335347 TAAAAGTGGGATTTTGG
1 TAAAA-TGGGATTTTGG
2335364 AAGGTTCGGG
Statistics
Matches: 101, Mismatches: 16, Indels: 38
0.65 0.10 0.25
Matches are distributed among these distances:
27 7 0.07
28 15 0.15
29 15 0.15
30 26 0.26
31 28 0.28
32 6 0.06
33 4 0.04
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.33
Consensus pattern (29 bp):
TAAAATGGGATTTTGGGTGAAATTAGGGT
Found at i:2337365 original size:17 final size:17
Alignment explanation
Indices: 2337345--2337407 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
2337335 TTTTAAATGT
2337345 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
2337362 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
2337378 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
2337395 ACTT-AATTTAAAA
1 ATTTAAATTTAAAA
2337408 TCCAAGTTGG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:2337391 original size:27 final size:27
Alignment explanation
Indices: 2337329--2337400 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
2337319 TTTAAGTTTC
* * **
2337329 AAATTATTTTAAATGTATTTAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
**
2337356 AAACAAATTTAAATTTAAATAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
* *
2337383 AAATTAATTCAAACTTAA
1 AAATTAATTTAAATTTAA
2337401 TTTAAAATCC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (27 bp):
AAATTAATTTAAATTTAAATAAATTTA
Found at i:2345156 original size:19 final size:19
Alignment explanation
Indices: 2345128--2345184 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
2345118 ATTTAAAGAA
*
2345128 TATAATTTTTTATGATTTT
1 TATAAATTTTTATGATTTT
2345147 TATAAATTTTTAT-ATTTT
1 TATAAATTTTTATGATTTT
*
2345165 T-TATA-TTTTATGATTTT
1 TATAAATTTTTATGATTTT
2345182 TAT
1 TAT
2345185 TTTTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 6 0.18
17 9 0.26
18 7 0.21
19 12 0.35
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TATAAATTTTTATGATTTT
Found at i:2345192 original size:35 final size:36
Alignment explanation
Indices: 2345130--2345209 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 36
2345120 TTAAAGAATA
*
2345130 TAATTTTTTATGATTTTTATAAATTTTTAT-ATTTT
1 TAATATTTTATGATTTTTATAAATTTTTATAATTTT
* *** *
2345165 TTATATTTTATGATTTTTATTTTTTTTTCTAATTTT
1 TAATATTTTATGATTTTTATAAATTTTTATAATTTT
2345201 TAATATTTT
1 TAATATTTT
2345210 TATTAAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 24 0.65
36 13 0.35
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (36 bp):
TAATATTTTATGATTTTTATAAATTTTTATAATTTT
Found at i:2345240 original size:9 final size:9
Alignment explanation
Indices: 2345128--2345265 Score: 79
Period size: 9 Copynumber: 15.1 Consensus size: 9
2345118 ATTTAAAGAA
2345128 TATAATTTTT
1 TATAA-TTTT
*
2345138 TATGATTTT
1 TATAATTTT
2345147 TATAAATTTT
1 TAT-AATTTT
*
2345157 TATATTTTT
1 TATAATTTT
2345166 TAT-A-TTT
1 TATAATTTT
*
2345173 TATGATTTT
1 TATAATTTT
**
2345182 TATTTTTTTT
1 TA-TAATTTT
*
2345192 TCTAATTTT
1 TATAATTTT
2345201 TA-ATATTTT
1 TATA-ATTTT
**
2345210 TATTAAAAATT
1 TA-T-AATTTT
* *
2345221 AATAATATT
1 TATAATTTT
2345230 TATAATTTT
1 TATAATTTT
*
2345239 TATTGATTTT
1 TA-TAATTTT
2345249 T-T-ATTTT
1 TATAATTTT
2345256 TATAATTTT
1 TATAATTTT
2345265 T
1 T
2345266 TGTCACATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 23
0.71 0.12 0.16
Matches are distributed among these distances:
7 12 0.12
8 4 0.04
9 53 0.53
10 26 0.26
11 4 0.04
12 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (9 bp):
TATAATTTT
Found at i:2345262 original size:26 final size:25
Alignment explanation
Indices: 2345142--2345265 Score: 81
Period size: 26 Copynumber: 4.6 Consensus size: 25
2345132 ATTTTTTATG
2345142 ATTTTTATAAATTTTTA-TATTTTTT
1 ATTTTTAT-AATTTTTATTATTTTTT
* *
2345167 ATATTTTATGATTTTTATTTTTTTTTCT
1 AT-TTTTATAATTTTTA-TTATTTTT-T
** *
2345195 AATTTTTA-ATATTTTTATTAAAAATTAATA
1 -ATTTTTATA-ATTTTTATT----ATTTTTT
*
2345225 ATATTTATAATTTTTATTGATTTTTT
1 ATTTTTATAATTTTTATT-ATTTTTT
2345251 ATTTTTATAATTTTT
1 ATTTTTATAATTTTT
2345266 TGTCACATAT
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
25 9 0.12
26 24 0.32
27 8 0.11
28 13 0.17
29 17 0.23
30 1 0.01
31 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTTATAATTTTTATTATTTTTT
Found at i:2345263 original size:16 final size:17
Alignment explanation
Indices: 2345234--2345266 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2345224 AATATTTATA
*
2345234 ATTTTTATTGATTTTTT
1 ATTTTTATTAATTTTTT
2345251 ATTTTTA-TAATTTTTT
1 ATTTTTATTAATTTTTT
2345267 GTCACATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTTTATTAATTTTTT
Found at i:2347326 original size:14 final size:15
Alignment explanation
Indices: 2347305--2347338 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2347295 ATTGTTTGGA
* *
2347305 TAAAAAATTAATACT
1 TAAAAATTTAACACT
2347320 TAAAAATTTAACACT
1 TAAAAATTTAACACT
2347335 TAAA
1 TAAA
2347339 TTTCTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAATTTAACACT
Found at i:2356805 original size:15 final size:15
Alignment explanation
Indices: 2356773--2356823 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
2356763 AGCATTTAAA
* *
2356773 TTTTCAATACTTAAT
1 TTTTCAACACTTATT
2356788 TTTTCAACACTTATT
1 TTTTCAACACTTATT
* *
2356803 TTTTCAGCAGTTATT
1 TTTTCAACACTTATT
2356818 TTTTCA
1 TTTTCA
2356824 GTTTATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (15 bp):
TTTTCAACACTTATT
Done.