Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 4 of 22
Found at i:1772681 original size:23 final size:24
Alignment explanation
Indices: 1772650--1772695 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1772640 GAGTCCCGAT
1772650 TTGCATTTTTCTGT-AATGTTGAA
1 TTGCATTTTTCTGTAAATGTTGAA
*
1772673 TTGCTTTTTTCTGTAAATGTTGA
1 TTGCATTTTTCTGTAAATGTTGA
1772696 TGAGTGGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (24 bp):
TTGCATTTTTCTGTAAATGTTGAA
Found at i:1774654 original size:45 final size:45
Alignment explanation
Indices: 1774592--1774696 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
1774582 TTTTCTTTTA
* * * *
1774592 ACATGGAGTGTAGCAACCTAACCATAACGTGTCACATATTTTTGT
1 ACATGGAGTGTAACAACCTAACCATAACATGTAACATATTTCTGT
* *
1774637 ACATGGCA-TGTAACAACCTAATCATGACATGTAACATATTTCTGT
1 ACATGG-AGTGTAACAACCTAACCATAACATGTAACATATTTCTGT
*
1774682 ATAT-GATGTGTAACA
1 ACATGGA-GTGTAACA
1774697 TGTTTCTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.02
44 1 0.02
45 47 0.94
46 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (45 bp):
ACATGGAGTGTAACAACCTAACCATAACATGTAACATATTTCTGT
Found at i:1774693 original size:24 final size:24
Alignment explanation
Indices: 1774666--1774720 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1774656 AATCATGACA
*
1774666 TGTAACATATTTCTGTATATGATG
1 TGTAACATATTTCTGCATATGATG
* *
1774690 TGTAACATGTTTCTGCATATGGTG
1 TGTAACATATTTCTGCATATGATG
*
1774714 CGTAACA
1 TGTAACA
1774721 GCATGGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
TGTAACATATTTCTGCATATGATG
Found at i:1787578 original size:42 final size:43
Alignment explanation
Indices: 1787494--1787579 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
1787484 TAATAAAGAA
**
1787494 TCTGCACTTAGACTTCAAACTATGATAGAAAAATTCGCCTAAT
1 TCTGCACTTAGACTTCAAACTATGATAGAAAAATTCAACTAAT
* * *
1787537 TCTGCATTTAGTCTTC-AACTATGATAGCAAAATTCAACTAAT
1 TCTGCACTTAGACTTCAAACTATGATAGAAAAATTCAACTAAT
1787579 T
1 T
1787580 GACTAATAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 24 0.63
43 14 0.37
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (43 bp):
TCTGCACTTAGACTTCAAACTATGATAGAAAAATTCAACTAAT
Found at i:1788721 original size:2 final size:2
Alignment explanation
Indices: 1788714--1788759 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1788704 ACATGTGAAC
1788714 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
1788756 AT AT
1 AT AT
1788760 TACATAACTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1790495 original size:25 final size:25
Alignment explanation
Indices: 1790462--1790513 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1790452 GTAGGATAAT
*
1790462 ATAAGGATGCATGCTAGTATTCTCA
1 ATAAGGATGCATACTAGTATTCTCA
*
1790487 ATAAGGATGCGTACTAGTATTCTCA
1 ATAAGGATGCATACTAGTATTCTCA
1790512 AT
1 AT
1790514 GGCCATACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (25 bp):
ATAAGGATGCATACTAGTATTCTCA
Found at i:1803440 original size:19 final size:21
Alignment explanation
Indices: 1803383--1803446 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 21
1803373 CGAGAGTTAG
*
1803383 TATTATATTATAATTATT-T-A
1 TATTAT-TTTTAATTATTATAA
*
1803403 T-TTATTTTTAATTAATTATGA
1 TATTATTTTTAATT-ATTATAA
1803424 TATTATTTTT-ATT-TTATAA
1 TATTATTTTTAATTATTATAA
1803443 TATT
1 TATT
1803447 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 7 0.18
19 16 0.42
20 2 0.05
21 5 0.13
22 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTATTTTTAATTATTATAA
Found at i:1803965 original size:22 final size:22
Alignment explanation
Indices: 1803920--1803967 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1803910 GAGAAAATAT
* *
1803920 TAAAATTTAAAATTTACCTTTA
1 TAAAATTTAAAACTTACCTGTA
**
1803942 TAAAATTTAAAACTTATGTGTA
1 TAAAATTTAAAACTTACCTGTA
1803964 TAAA
1 TAAA
1803968 TTAAAGTGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATTTAAAACTTACCTGTA
Found at i:1805743 original size:33 final size:33
Alignment explanation
Indices: 1805667--1805734 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
1805657 GCCACTCCCG
* * *
1805667 ACAATCCCAACTCCAGCACCAACACCAGTTCCG
1 ACAAGCCCAACTCCAGCACCAACACCAGTACCC
**
1805700 ACAAGCCCAACTCCAGCACCAATTCCAGTACCC
1 ACAAGCCCAACTCCAGCACCAACACCAGTACCC
1805733 AC
1 AC
1805735 CATTCCAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.46, G:0.09, T:0.12
Consensus pattern (33 bp):
ACAAGCCCAACTCCAGCACCAACACCAGTACCC
Found at i:1811912 original size:2 final size:2
Alignment explanation
Indices: 1811905--1811930 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1811895 GATTCTTTCA
1811905 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
1811931 TGTTTTTATT
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:1821191 original size:41 final size:41
Alignment explanation
Indices: 1821146--1821231 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
1821136 ATTAGTATAT
1821146 TAAGTTATT-AAGTTAAATTATTAAGATATAATATATTATGA
1 TAAGTTATTGAA-TTAAATTATTAAGATATAATATATTATGA
*** *
1821187 TAAGTTATTGAATTGGGTTGTTAAGATATAATATATTATGA
1 TAAGTTATTGAATTAAATTATTAAGATATAATATATTATGA
1821228 TAAG
1 TAAG
1821232 ATTAAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (41 bp):
TAAGTTATTGAATTAAATTATTAAGATATAATATATTATGA
Found at i:1822112 original size:13 final size:13
Alignment explanation
Indices: 1822096--1822160 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
1822086 ATTTATATGA
*
1822096 AAATTTTATAAAT
1 AAATTTTAAAAAT
1822109 AAATTTTAAAAAT
1 AAATTTTAAAAAT
*
1822122 -TATTTTAAAAAAT
1 AAATTTT-AAAAAT
*
1822135 CAAATTTTAATAAT
1 -AAATTTTAAAAAT
**
1822149 TTATTTTAAAAA
1 AAATTTTAAAAA
1822161 ATTAATTAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 5 0.12
13 27 0.64
14 5 0.12
15 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:1822142 original size:27 final size:27
Alignment explanation
Indices: 1822105--1822167 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
1822095 AAAATTTTAT
1822105 AAATAAATTTTAA-AAATTATTTTAAA
1 AAATAAATTTTAATAAATTATTTTAAA
*
1822131 AAATCAAATTTTAATAATTTATTTTAAA
1 AAAT-AAATTTTAATAAATTATTTTAAA
*
1822159 AAATTAATT
1 AAATAAATT
1822168 AGTATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 13 0.39
28 16 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATAAATTTTAATAAATTATTTTAAA
Found at i:1826186 original size:27 final size:27
Alignment explanation
Indices: 1826154--1826211 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1826144 CATGATGTAT
*
1826154 TAATATATT-A-TAATAAATAATAATA
1 TAATATATTAATTATTAAATAATAATA
* *
1826179 TAATATATTAATTATTATATAATTATA
1 TAATATATTAATTATTAAATAATAATA
1826206 TAATAT
1 TAATAT
1826212 TTTTTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 9 0.32
26 1 0.04
27 18 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATATATTAATTATTAAATAATAATA
Found at i:1827117 original size:6 final size:6
Alignment explanation
Indices: 1827118--1827154 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1827108 ACCGCAACCG
1827118 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA C
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA C
1827155 CGCTCGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.35, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:1831628 original size:15 final size:15
Alignment explanation
Indices: 1831608--1831640 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1831598 TATAAATATA
*
1831608 TTTAGGGCTTTTGGC
1 TTTAGGGCTTTTAGC
1831623 TTTAGGGCTTTTAGC
1 TTTAGGGCTTTTAGC
1831638 TTT
1 TTT
1831641 GTGTAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.27, T:0.52
Consensus pattern (15 bp):
TTTAGGGCTTTTAGC
Found at i:1839927 original size:86 final size:86
Alignment explanation
Indices: 1839773--1839943 Score: 290
Period size: 86 Copynumber: 2.0 Consensus size: 86
1839763 TGGTGGGGAA
*
1839773 TTTTGAAGCTTTCTTCTCAAATAAACCCTGACTTACCCCAGTAATAGATGAGTGATCTCGTTGAT
1 TTTTGAAGCTTTCTTCTCAAATAAACCCTGACTTACCCCAGTAATAGATGAGTGATCTCATTGAT
1839838 TAACAAGGAAGAATTACTGAC
66 TAACAAGGAAGAATTACTGAC
* * *
1839859 TTTTGAAGCTTTCTTCTCAAATTAACCCTTACTTACCCCAGTAATCA-ATGAGTGATCTCATTGC
1 TTTTGAAGCTTTCTTCTCAAATAAACCCTGACTTACCCCAGTAAT-AGATGAGTGATCTCATTGA
1839923 TTAACAAGGAAGAATTACTGA
65 TTAACAAGGAAGAATTACTGA
1839944 ATTTCTTGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 79 0.99
87 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (86 bp):
TTTTGAAGCTTTCTTCTCAAATAAACCCTGACTTACCCCAGTAATAGATGAGTGATCTCATTGAT
TAACAAGGAAGAATTACTGAC
Found at i:1842841 original size:16 final size:15
Alignment explanation
Indices: 1842812--1842846 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1842802 CGAAAATCAC
1842812 TATTTTTTTATTTTT
1 TATTTTTTTATTTTT
*
1842827 TATTATTTTTGTTTTT
1 TATT-TTTTTATTTTT
1842843 TATT
1 TATT
1842847 CAATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TATTTTTTTATTTTT
Found at i:1861452 original size:17 final size:17
Alignment explanation
Indices: 1861427--1861465 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1861417 AATCCTCCAT
*
1861427 TTTGGTTTCTTAGACGC
1 TTTGCTTTCTTAGACGC
1861444 TTTGCTTTCTTAGACGC
1 TTTGCTTTCTTAGACGC
1861461 TTTGC
1 TTTGC
1861466 CTAATGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (17 bp):
TTTGCTTTCTTAGACGC
Found at i:1863266 original size:15 final size:18
Alignment explanation
Indices: 1863228--1863269 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1863218 CTATGAGTAC
1863228 TTATAAATAATATATGTA
1 TTATAAATAATATATGTA
*
1863246 TAATAAATAATA-AT-T-
1 TTATAAATAATATATGTA
1863261 TTATAAATA
1 TTATAAATA
1863270 TTTACGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 1 0.05
17 2 0.09
18 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATAAATAATATATGTA
Found at i:1870431 original size:45 final size:44
Alignment explanation
Indices: 1870355--1870439 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 44
1870345 TTAAAAAAAA
*
1870355 AATTACATGATTTTGTAAACAATCAATTTTTATATTGACAAACAT
1 AATTACATGATTTTGTAAACAATCAAATTTTATATT-ACAAACAT
* *
1870400 AATTGCATGATTTTGTAAATAAT-AGAATTTTATATTACAA
1 AATTACATGATTTTGTAAACAATCA-AATTTTATATTACAA
1870440 TATTCTGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 5 0.14
45 31 0.86
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (44 bp):
AATTACATGATTTTGTAAACAATCAAATTTTATATTACAAACAT
Found at i:1873463 original size:2 final size:2
Alignment explanation
Indices: 1873452--1873481 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1873442 AAGACATAAC
1873452 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1873482 TATGATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1878253 original size:40 final size:40
Alignment explanation
Indices: 1878192--1878270 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
1878182 TTGTGAAAGG
* *
1878192 CACCAATCGTGATAAGATTAGAAACCTCACTAAGGTGAAT
1 CACCAATCGTGACAAGATTAGAAACCTCACTAAAGTGAAT
* * * *
1878232 CACCAATCTTGACAAGGTTAGAAATCTCATTAAAGTGAA
1 CACCAATCGTGACAAGATTAGAAACCTCACTAAAGTGAA
1878271 AAATAGTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (40 bp):
CACCAATCGTGACAAGATTAGAAACCTCACTAAAGTGAAT
Found at i:1885412 original size:28 final size:26
Alignment explanation
Indices: 1885349--1885415 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 26
1885339 TTAGTAAAAA
1885349 TTTAAA-TAAATTTTTTTATTTTTAT
1 TTTAAATTAAATTTTTTTATTTTTAT
1885374 TACAATT-AATTAAATTTTTATATATTTTTAT
1 T----TTAAATTAAATTTTT-T-TATTTTTAT
1885405 TTTAAATTAAA
1 TTTAAATTAAA
1885416 ATAAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
25 1 0.03
27 2 0.06
28 9 0.26
29 11 0.32
30 1 0.03
31 10 0.29
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTAAATTAAATTTTTTTATTTTTAT
Found at i:1898083 original size:19 final size:20
Alignment explanation
Indices: 1898042--1898086 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
1898032 GAAATTTTGT
*
1898042 AATATTAATTATAAATTATA
1 AATATTAATTATAAATTAAA
1898062 AATATT-ATTA-AAATTAAAA
1 AATATTAATTATAAATT-AAA
1898081 AATATT
1 AATATT
1898087 TTTTACAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATTAATTATAAATTAAA
Found at i:1898275 original size:2 final size:2
Alignment explanation
Indices: 1898268--1898294 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1898258 AAATTTGAAC
1898268 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1898295 AGAATAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1910005 original size:27 final size:27
Alignment explanation
Indices: 1909975--1910027 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1909965 CATTAAGAGT
*
1909975 ATTATACCACAAACAAAAGCAGTAGAC
1 ATTACACCACAAACAAAAGCAGTAGAC
*
1910002 ATTACACCACAACCAAAAGCAGTAGA
1 ATTACACCACAAACAAAAGCAGTAGA
1910028 TATGACAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.25, G:0.11, T:0.13
Consensus pattern (27 bp):
ATTACACCACAAACAAAAGCAGTAGAC
Found at i:1913190 original size:13 final size:13
Alignment explanation
Indices: 1913169--1913210 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1913159 ATAAAAAATA
*
1913169 TATAACATATTAT
1 TATATCATATTAT
*
1913182 TATATCATATTAA
1 TATATCATATTAT
*
1913195 TATATTATATTAT
1 TATATCATATTAT
1913208 TAT
1 TAT
1913211 TATGTGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATCATATTAT
Found at i:1913220 original size:29 final size:25
Alignment explanation
Indices: 1913176--1913234 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
1913166 ATATATAACA
1913176 TATTATTATATCATATTAATATATTATAT
1 TATTATTATATCATA-TAA-A-ATTA-AT
* *
1913205 TATTATTATGTGATATAAAATTAAT
1 TATTATTATATCATATAAAATTAAT
1913230 TATTA
1 TATTA
1913235 ATTAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.25
26 4 0.14
27 1 0.04
28 3 0.11
29 13 0.46
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
TATTATTATATCATATAAAATTAAT
Found at i:1914447 original size:16 final size:18
Alignment explanation
Indices: 1914409--1914454 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
1914399 TATTTTTTTT
*
1914409 AAATATATAAAACTAGTA
1 AAATATATAAAACTAATA
*
1914427 CAATATA-AAAAC-AATA
1 AAATATATAAAACTAATA
*
1914443 AAATAAATAAAA
1 AAATATATAAAA
1914455 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATATATAAAACTAATA
Found at i:1919820 original size:18 final size:18
Alignment explanation
Indices: 1919783--1919817 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1919773 TTTGTAGATT
1919783 TTATTTTTTATAAAGAAA
1 TTATTTTTTATAAAGAAA
1919801 TTATTTTTTA-AAAGAAA
1 TTATTTTTTATAAAGAAA
1919818 ATTTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
TTATTTTTTATAAAGAAA
Found at i:1929609 original size:57 final size:57
Alignment explanation
Indices: 1929521--1929657 Score: 229
Period size: 57 Copynumber: 2.4 Consensus size: 57
1929511 ACCAGGACAT
* * * *
1929521 TACCCACCTCCTGAGAGTAATTCACAGGTATCTTCCTCTTATCAACAATCTGCACAA
1 TACCCTCCTCCTGAAAGTAATTCACAAGTATCTTCCTCTTATCAACAACCTGCACAA
*
1929578 TACCCTCCTCCAGAAAGTAATTCACAAGTATCTTCCTCTTATCAACAACCTGCACAA
1 TACCCTCCTCCTGAAAGTAATTCACAAGTATCTTCCTCTTATCAACAACCTGCACAA
1929635 TACCCTCCTCCTGAAAGTAATTC
1 TACCCTCCTCCTGAAAGTAATTC
1929658 TCAGCTGCAC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
57 74 1.00
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.28
Consensus pattern (57 bp):
TACCCTCCTCCTGAAAGTAATTCACAAGTATCTTCCTCTTATCAACAACCTGCACAA
Found at i:1929644 original size:29 final size:28
Alignment explanation
Indices: 1929554--1929644 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 28
1929544 ACAGGTATCT
1929554 TCCTCTTATCAACAATCTGCACAATACCC
1 TCCTCTTATCAACAA-CTGCACAATACCC
* ** * * * *
1929583 TCCTC-CAGAAAGTAA-TTCACAAGTATCT
1 TCCTCTTATCAA-CAACTGCACAA-TACCC
1929611 TCCTCTTATCAACAACCTGCACAATACCC
1 TCCTCTTATCAACAA-CTGCACAATACCC
1929640 TCCTC
1 TCCTC
1929645 CTGAAAGTAA
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
27 6 0.14
28 13 0.30
29 18 0.42
30 6 0.14
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.27
Consensus pattern (28 bp):
TCCTCTTATCAACAACTGCACAATACCC
Found at i:1960954 original size:15 final size:14
Alignment explanation
Indices: 1960934--1960973 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1960924 TAATATAAAA
*
1960934 TAATTAATAATATTT
1 TAATTAATAATA-AT
1960949 TAATTAATAATAAT
1 TAATTAATAATAAT
*
1960963 TAATTATTAAT
1 TAATTAATAAT
1960974 TATCAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTAATAATAAT
Found at i:1961077 original size:21 final size:19
Alignment explanation
Indices: 1961044--1961083 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
1961034 ATCAACACTT
1961044 ATTTAAATTTTTTTAAATA
1 ATTTAAATTTTTTTAAATA
1961063 ATTTAAAAGTTTTTTTAAATA
1 ATTT-AAA-TTTTTTTAAATA
1961084 TTATACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTAAATTTTTTTAAATA
Found at i:1964192 original size:2 final size:2
Alignment explanation
Indices: 1964185--1964222 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1964175 GGGCTTAATA
1964185 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
1964223 TGCCATTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1965159 original size:14 final size:14
Alignment explanation
Indices: 1965140--1965171 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1965130 GTGGACACAT
1965140 AGAGAGGGAGAAAG
1 AGAGAGGGAGAAAG
*
1965154 AGAGAGGGAGAGAG
1 AGAGAGGGAGAAAG
1965168 AGAG
1 AGAG
1965172 GAATGAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (14 bp):
AGAGAGGGAGAAAG
Found at i:1973155 original size:31 final size:30
Alignment explanation
Indices: 1973120--1973181 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
1973110 TTTAAATAAA
*
1973120 TTATTAAATT-ATTTAAATAAATTTTTATTTT
1 TTATTAAATTCAATT-AA-AAATTTTTATTTT
* *
1973151 TTATTACATTCAATTAAAATTTTTTATTTT
1 TTATTAAATTCAATTAAAAATTTTTATTTT
1973181 T
1 T
1973182 AATTTATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.48
31 11 0.41
32 3 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TTATTAAATTCAATTAAAAATTTTTATTTT
Found at i:1973199 original size:29 final size:29
Alignment explanation
Indices: 1973134--1973200 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1973124 TAAATTATTT
*
1973134 AAATAAA-TTTTTATTTTTTATTACATTC
1 AAATAAATTTTTTATTTTTAATTACATTC
* *
1973162 AATTAAAATTTTTTATTTTTAATT-TATATC
1 AAAT-AAATTTTTTATTTTTAATTACAT-TC
1973192 AAATAAATT
1 AAATAAATT
1973201 CTTATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.09
29 10 0.31
30 19 0.59
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATAAATTTTTTATTTTTAATTACATTC
Found at i:1976211 original size:16 final size:16
Alignment explanation
Indices: 1976190--1976221 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1976180 ATGGTGATCT
*
1976190 TTTGGTGGCTGGCATG
1 TTTGGTGGCTAGCATG
1976206 TTTGGTGGCTAGCATG
1 TTTGGTGGCTAGCATG
1976222 CCACATGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.41, T:0.38
Consensus pattern (16 bp):
TTTGGTGGCTAGCATG
Found at i:1983999 original size:26 final size:26
Alignment explanation
Indices: 1983969--1984018 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1983959 ACACCAGATT
1983969 TTATATGAAAAG-TAATAATAAAATAA
1 TTATAT-AAAAGATAATAATAAAATAA
*
1983995 TTATATAAATGATAATAATAAAAT
1 TTATATAAAAGATAATAATAAAAT
1984019 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATATAAAAGATAATAATAAAATAA
Found at i:1986241 original size:38 final size:38
Alignment explanation
Indices: 1986199--1986272 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
1986189 TGGACAAACC
1986199 TTAAGACTTTGCGTAGCCTAATTTCTAGGCACACAACT
1 TTAAGACTTTGCGTAGCCTAATTTCTAGGCACACAACT
1986237 TTAAGACTTTGCGTAGCCTAATTTCTAGGCACACAA
1 TTAAGACTTTGCGTAGCCTAATTTCTAGGCACACAA
1986273 ATTAATCGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (38 bp):
TTAAGACTTTGCGTAGCCTAATTTCTAGGCACACAACT
Found at i:1989587 original size:28 final size:28
Alignment explanation
Indices: 1989556--1989620 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1989546 AAAATTATTT
*
1989556 TAAAAAATCATTTAAAAGATATAT-AT-AA
1 TAAAAAA-AATTTAAAA-ATATATAATAAA
*
1989584 TAAATAAAAATTTTAAAATATATAATAAA
1 TAAA-AAAAATTTAAAAATATATAATAAA
1989613 TAAAAAAA
1 TAAAAAAA
1989621 TAAAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 17 0.53
29 9 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (28 bp):
TAAAAAAAATTTAAAAATATATAATAAA
Found at i:1989606 original size:29 final size:28
Alignment explanation
Indices: 1989557--1989620 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1989547 AAATTATTTT
1989557 AAAAAATCATTTAAAAGATAT-ATATAATAA
1 AAAAAAT--TTTAAAAGATATAATA-AATAA
*
1989587 ATAAAAATTTTAAAATATATAATAAATAA
1 A-AAAAATTTTAAAAGATATAATAAATAA
1989616 AAAAA
1 AAAAA
1989621 TAAAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 4 0.13
29 17 0.55
30 4 0.13
31 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAAATTTTAAAAGATATAATAAATAA
Found at i:1989626 original size:25 final size:25
Alignment explanation
Indices: 1989576--1989626 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1989566 TTTAAAAGAT
** *
1989576 ATATATAATAAATAAAAATTTTAAA
1 ATATATAATAAATAAAAAAATAAAA
1989601 ATATATAATAAATAAAAAAATAAAA
1 ATATATAATAAATAAAAAAATAAAA
1989626 A
1 A
1989627 ATTTTGGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
ATATATAATAAATAAAAAAATAAAA
Found at i:1991872 original size:24 final size:24
Alignment explanation
Indices: 1991840--1991891 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1991830 AAAATAAAAG
*
1991840 TTTATTTA-TATTTGACATAATTTA
1 TTTACTTATTATTTG-CATAATTTA
*
1991864 TTTACTTATTATTTGTATAATTTA
1 TTTACTTATTATTTGCATAATTTA
1991888 TTTA
1 TTTA
1991892 TTTGTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTACTTATTATTTGCATAATTTA
Found at i:1999434 original size:16 final size:16
Alignment explanation
Indices: 1999413--1999446 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1999403 CTAATATATT
*
1999413 TTAAGTATATTATTAA
1 TTAAGTATACTATTAA
*
1999429 TTAAGTTTACTATTAA
1 TTAAGTATACTATTAA
1999445 TT
1 TT
1999447 TTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATACTATTAA
Found at i:2021780 original size:21 final size:21
Alignment explanation
Indices: 2021756--2021798 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2021746 TCACAGCAAA
2021756 GCATCAAAGCTGTGTTGTGAT
1 GCATCAAAGCTGTGTTGTGAT
*
2021777 GCATCGAAGCTGTGTTGTGAT
1 GCATCAAAGCTGTGTTGTGAT
2021798 G
1 G
2021799 TGTAAACCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.33
Consensus pattern (21 bp):
GCATCAAAGCTGTGTTGTGAT
Found at i:2029973 original size:3 final size:3
Alignment explanation
Indices: 2029965--2029989 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2029955 TTACAGATAT
2029965 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
2029990 ATATACACAC
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:2035233 original size:20 final size:20
Alignment explanation
Indices: 2035210--2035249 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2035200 ACAAAGGACC
* *
2035210 AAGTGACAAAAACTAAACTG
1 AAGTCACAAAAACCAAACTG
*
2035230 AAGTCACAACAACCAAACTG
1 AAGTCACAAAAACCAAACTG
2035250 CACACTGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.12, T:0.12
Consensus pattern (20 bp):
AAGTCACAAAAACCAAACTG
Found at i:2043551 original size:2 final size:2
Alignment explanation
Indices: 2043544--2043570 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2043534 TGTTTGCTAC
2043544 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2043571 TCAGAGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2046488 original size:15 final size:16
Alignment explanation
Indices: 2046468--2046505 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2046458 AGTTTAGTAT
2046468 ATTATTAG-AAATACG
1 ATTATTAGAAAATACG
*
2046483 ATTATT-GAAAATATG
1 ATTATTAGAAAATACG
2046498 ATTATTAG
1 ATTATTAG
2046506 GTATATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (16 bp):
ATTATTAGAAAATACG
Found at i:2046526 original size:15 final size:15
Alignment explanation
Indices: 2046468--2046526 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2046458 AGTTTAGTAT
*
2046468 ATTATT-AGAAATACG
1 ATTATTGAG-AATATG
*
2046483 ATTATTGAAAATATG
1 ATTATTGAGAATATG
*
2046498 ATTATT-AGGTATATG
1 ATTATTGA-GAATATG
*
2046513 ATTGTTGAGAATAT
1 ATTATTGAGAATAT
2046527 AACTTTGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 1 0.03
15 32 0.91
16 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.41
Consensus pattern (15 bp):
ATTATTGAGAATATG
Found at i:2046782 original size:21 final size:21
Alignment explanation
Indices: 2046744--2046784 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2046734 AATTTTAAGC
2046744 CATTAAAATAATAAATAATAA
1 CATTAAAATAATAAATAATAA
*
2046765 CATTGAAA-AATAACATAATA
1 CATTAAAATAATAA-ATAATA
2046785 TTTTTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (21 bp):
CATTAAAATAATAAATAATAA
Found at i:2046942 original size:20 final size:20
Alignment explanation
Indices: 2046917--2046954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2046907 AATTTTATCA
*
2046917 ATAAATCATATTATCTATTG
1 ATAAATCATACTATCTATTG
*
2046937 ATAAATTATACTATCTAT
1 ATAAATCATACTATCTAT
2046955 CAATAGATAA
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:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (20 bp):
ATAAATCATACTATCTATTG
Found at i:2063905 original size:2 final size:2
Alignment explanation
Indices: 2063898--2063923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2063888 GGAAGCATAC
2063898 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
2063924 TCCTTAATTA
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:2076781 original size:2 final size:2
Alignment explanation
Indices: 2076774--2076804 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2076764 TGAAACAATA
2076774 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2076805 GAAAGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2077021 original size:5 final size:5
Alignment explanation
Indices: 2077011--2077038 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2077001 GATAGTAACA
2077011 CCCCT CCCCT CCCCT CCCCT CCCCT CCC
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCC
2077039 TTACCCACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (5 bp):
CCCCT
Found at i:2080773 original size:3 final size:3
Alignment explanation
Indices: 2080767--2080801 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2080757 TTTTTTGGCT
2080767 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2080802 TCTTAAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2085122 original size:3 final size:3
Alignment explanation
Indices: 2085114--2085140 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2085104 CCCTATAGAA
2085114 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2085141 GATGTGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2095106 original size:26 final size:27
Alignment explanation
Indices: 2095074--2095135 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
2095064 AAAATAATGT
2095074 ATTTAATTAAA-AATAAA-AATATAAAA
1 ATTTAATTAAACAATAAATAA-ATAAAA
2095100 ATTTAATTAAACGTAATAAATAAATAAAA
1 ATTTAATTAAAC--AATAAATAAATAAAA
2095129 ATTTAAT
1 ATTTAAT
2095136 CGAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 11 0.34
29 19 0.59
30 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
ATTTAATTAAACAATAAATAAATAAAA
Found at i:2097303 original size:27 final size:26
Alignment explanation
Indices: 2097247--2097313 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
2097237 TAATTTTAAC
* * **
2097247 TTTTCTCATATAACATCTTATAATTTT
1 TTTTCTAAT-TAACAACTTATAATAAT
2097274 TTTTCTAATTAACAACTTATGAATAAT
1 TTTTCTAATTAACAACTTAT-AATAAT
*
2097301 TTTT-TAATCAACA
1 TTTTCTAATTAACA
2097314 CCATGTAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.49
Consensus pattern (26 bp):
TTTTCTAATTAACAACTTATAATAAT
Found at i:2111080 original size:2 final size:2
Alignment explanation
Indices: 2111073--2111116 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2111063 AGAATATGAT
*
2111073 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2111114 TA T
1 TA T
2111117 TGAATGTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2117204 original size:23 final size:20
Alignment explanation
Indices: 2117166--2117224 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 20
2117156 TGCCTTTTTC
2117166 AAAATTTAGACATTATATTTAGA
1 AAAATTTA-A-ATTATATTTA-A
*
2117189 AAATATCTTAAATTATTTTTAA
1 AAA-AT-TTAAATTATATTTAA
2117211 AAAATTTAAATTAT
1 AAAATTTAAATTAT
2117225 TATTAATCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 9 0.27
21 2 0.06
22 4 0.12
23 12 0.36
24 3 0.09
25 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAATTTAAATTATATTTAA
Found at i:2117221 original size:20 final size:20
Alignment explanation
Indices: 2117166--2117230 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
2117156 TGCCTTTTTC
*
2117166 AAAATTTAGACATTATATTTAGA
1 AAAATTTA-A-ATTATTTTTA-A
2117189 AAATATCTTAAATTATTTTTAA
1 AAA-AT-TTAAATTATTTTTAA
*
2117211 AAAATTTAAATTATTATTAA
1 AAAATTTAAATTATTTTTAA
2117231 TCGAAACAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 14 0.37
21 2 0.05
22 4 0.11
23 12 0.32
24 3 0.08
25 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATTTAAATTATTTTTAA
Found at i:2121949 original size:2 final size:2
Alignment explanation
Indices: 2121944--2121972 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2121934 TTACCCATAG
2121944 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 A
2121973 AAATAGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2122076 original size:16 final size:17
Alignment explanation
Indices: 2122048--2122079 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2122038 AGGTTGAAGG
2122048 AATAAAAATAATTATTA
1 AATAAAAATAATTATTA
2122065 AATAAAAA-AATTATT
1 AATAAAAATAATTATT
2122080 TTGAGGGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAAATAATTATTA
Found at i:2133301 original size:9 final size:9
Alignment explanation
Indices: 2133290--2133331 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
2133280 TCAGGACTCA
*
2133290 CTGGAGGAA
1 CTGGAGGAG
2133299 CTGGAGGAG
1 CTGGAGGAG
2133308 CTGGAGGAG
1 CTGGAGGAG
2133317 CTGGAGGAG
1 CTGGAGGAG
2133326 CTGGAG
1 CTGGAG
2133332 CATTGTCCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (9 bp):
CTGGAGGAG
Found at i:2139856 original size:23 final size:21
Alignment explanation
Indices: 2139823--2139864 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
2139813 TTATAACTTA
*
2139823 TTAAATTAATTTTTTATTATT
1 TTAAATTAATTTATTATTATT
2139844 TTAAATCTAAATTTATTATTA
1 TTAAAT-T-AATTTATTATTA
2139865 ATAATTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAATTAATTTATTATTATT
Found at i:2147853 original size:24 final size:24
Alignment explanation
Indices: 2147826--2147875 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2147816 GTAGTTTCAT
2147826 AAATGTGTAAAATAAA-ATTTTAAA
1 AAAT-TGTAAAATAAATATTTTAAA
*
2147850 AAATTTTAAAATAAATATTTTAAA
1 AAATTGTAAAATAAATATTTTAAA
2147874 AA
1 AA
2147876 TTATGGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATTGTAAAATAAATATTTTAAA
Found at i:2147915 original size:16 final size:17
Alignment explanation
Indices: 2147883--2147921 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2147873 AAATTATGGG
2147883 TATTTAATTTTAAAATT
1 TATTTAATTTTAAAATT
**
2147900 T-TTTAATTTTTTAATT
1 TATTTAATTTTAAAATT
2147916 TATTTA
1 TATTTA
2147922 TTAATAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTAATTTTAAAATT
Found at i:2157121 original size:3 final size:3
Alignment explanation
Indices: 2157113--2157138 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2157103 AATGGGTTTC
2157113 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2157139 TATTTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2178765 original size:42 final size:41
Alignment explanation
Indices: 2178712--2178810 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
2178702 AAAGTTAATT
* *
2178712 CCTTTCATAATACAACTGTTCCTAAACAATTATATTTAATAA
1 CCTTTCATAATACAACTGTTCATAAA-AATTATATTTAACAA
* * *
2178754 TCTTTTATAATACAACTGTTTATAAAAATTATATTTAACAA
1 CCTTTCATAATACAACTGTTCATAAAAATTATATTTAACAA
*
2178795 CCTTTCATAGTACAAC
1 CCTTTCATAATACAAC
2178811 AATTTAAAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 27 0.55
42 22 0.45
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.39
Consensus pattern (41 bp):
CCTTTCATAATACAACTGTTCATAAAAATTATATTTAACAA
Found at i:2179782 original size:4 final size:4
Alignment explanation
Indices: 2179773--2179797 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2179763 ACTGAGGTAT
2179773 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
2179798 GATTGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2180905 original size:5 final size:5
Alignment explanation
Indices: 2180897--2181007 Score: 54
Period size: 5 Copynumber: 22.4 Consensus size: 5
2180887 TTATATTATA
* ** * * * *
2180897 TATTT TATTT TAATT TATTT TA-CC TATAT TATATA AATTT TATTT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT
*
2180946 TGTTT TATTT TATTT TAATTT T-TTAT T-TTT TATTAT ATATTT TATTT
1 TATTT TATTT TATTT T-ATTT TATT-T TATTT TATT-T -TATTT TATTT
*
2180993 TA-AT T-TTT TATTT TA
1 TATTT TATTT TATTT TA
2181008 ATTATAATAG
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
4 13 0.16
5 54 0.68
6 9 0.11
7 4 0.05
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:2180944 original size:7 final size:7
Alignment explanation
Indices: 2180934--2181006 Score: 59
Period size: 7 Copynumber: 11.3 Consensus size: 7
2180924 ATTATATAAA
2180934 TTTTATT
1 TTTTATT
*
2180941 TTTTATG
1 TTTTATT
2180948 TTTTA--
1 TTTTATT
2180953 TTTTA-T
1 TTTTATT
*
2180959 TTTAATT
1 TTTTATT
2180966 TTTTATT
1 TTTTATT
2180973 TTTTA--
1 TTTTATT
* *
2180978 TTATATA
1 TTTTATT
2180985 TTTTA-T
1 TTTTATT
*
2180991 TTTAATT
1 TTTTATT
2180998 TTTTATT
1 TTTTATT
2181005 TT
1 TT
2181007 AATTATAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
5 9 0.17
6 8 0.15
7 36 0.68
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTATT
Found at i:2180953 original size:25 final size:25
Alignment explanation
Indices: 2180925--2180993 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
2180915 TTTACCTATA
*
2180925 TTATATAAATTTTATTTTTTATGTT
1 TTATATATATTTTATTTTTTATGTT
* *
2180950 TTAT-TTTATTTTAATTTTTTATTTT
1 TTATATATATTTT-ATTTTTTATGTT
2180975 TTATTATATATTTTATTTT
1 TTA-TATATATTTTATTTT
2180994 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.16
25 18 0.49
26 6 0.16
27 7 0.19
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (25 bp):
TTATATATATTTTATTTTTTATGTT
Found at i:2180970 original size:32 final size:32
Alignment explanation
Indices: 2180934--2181006 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
2180924 ATTATATAAA
*
2180934 TTTTATTTTTTATGT-TTTATTTTATTTTAATT
1 TTTTATTTTTTAT-TATATATTTTATTTTAATT
2180966 TTTTATTTTTTATTATATATTTTATTTTAATT
1 TTTTATTTTTTATTATATATTTTATTTTAATT
2180998 TTTTATTTT
1 TTTTATTTT
2181007 AATTATAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTTATTTTTTATTATATATTTTATTTTAATT
Found at i:2180998 original size:25 final size:26
Alignment explanation
Indices: 2180890--2181004 Score: 76
Period size: 25 Copynumber: 4.2 Consensus size: 26
2180880 NNNNNNTTTA
2180890 TATTATATATTTTATTTTAATTTATTTTACCT
1 TATTATATATTTTA-TTT--TTTATTTT---T
* *
2180922 ATATTATATAAATTT-TATTTTTTATGTTT
1 -TATTATAT-ATTTTAT-TTT-TTATTTTT
2180951 TATT-T-TATTTTAATTTTTTATTTTT
1 TATTATATATTTT-ATTTTTTATTTTT
*
2180976 TATTATATATTTTA-TTTTAATTTTT
1 TATTATATATTTTATTTTTTATTTTT
2181001 TATT
1 TATT
2181005 TTAATTATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
25 29 0.41
26 6 0.09
27 8 0.11
28 4 0.06
29 1 0.01
31 1 0.01
32 7 0.10
33 10 0.14
34 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (26 bp):
TATTATATATTTTATTTTTTATTTTT
Found at i:2210514 original size:30 final size:28
Alignment explanation
Indices: 2210466--2210537 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
2210456 TTATATATAC
*
2210466 AGATATAATGAGTTTTTTTTTTTTGAAG
1 AGATATAATGAGTTTTTTTTTTTTTAAG
2210494 AGATATAATGAGTTTTTTTTTTTTTAAG
1 AGATATAATGAGTTTTTTTTTTTTTAAG
*
2210522 AGAGATAATGAGTTTT
1 AGATATAATGAGTTTT
2210538 GTAATATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (28 bp):
AGATATAATGAGTTTTTTTTTTTTTAAG
Found at i:2211031 original size:20 final size:18
Alignment explanation
Indices: 2211011--2211092 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 18
2211001 TATTAATATG
2211011 TTATAATATATATAGTAATGTT
1 TTATAATATATATA-TAA---T
*
2211033 TTGTAATATATA-AT-AT
1 TTATAATATATATATAAT
2211049 TATATACATATATATATTAA-
1 T-TATA-ATATATATA-TAAT
*
2211069 TTATAATATATATTTAAT
1 TTATAATATATATATAAT
2211087 TTATAA
1 TTATAA
2211093 ATAAGTATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
16 2 0.04
17 6 0.12
18 21 0.41
19 6 0.12
20 3 0.06
21 2 0.04
22 11 0.22
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (18 bp):
TTATAATATATATATAAT
Found at i:2211189 original size:14 final size:16
Alignment explanation
Indices: 2211170--2211206 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2211160 TAACTTAGTT
2211170 TTTATAA-TA-TATTA
1 TTTATAATTAGTATTA
2211184 TTTATAATTAGTTATTA
1 TTTATAATTAG-TATTA
2211201 TTTATA
1 TTTATA
2211207 CAAGTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
17 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATAATTAGTATTA
Found at i:2213276 original size:16 final size:16
Alignment explanation
Indices: 2213229--2213277 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 16
2213219 GAATAATTAC
2213229 AAGAATTGTCATTGAT
1 AAGAATTGTCATTGAT
2213245 AAGTTATATCTGTCATTGAT
1 AAG--A-AT-TGTCATTGAT
2213265 AAGAATTGTCATT
1 AAGAATTGTCATT
2213278 TAATACATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 10 0.34
17 2 0.07
18 2 0.07
19 2 0.07
20 13 0.45
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (16 bp):
AAGAATTGTCATTGAT
Found at i:2229132 original size:15 final size:17
Alignment explanation
Indices: 2229100--2229155 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
2229090 CCAGCAGTTT
2229100 CAACATCACCAACCGCAA
1 CAACATCACCAA-CGCAA
2229118 CAACATCACC-A-GCAA
1 CAACATCACCAACGCAA
* *
2229133 CAACAGCATCAACAGCAA
1 CAACATCACCAAC-GCAA
2229151 CAACA
1 CAACA
2229156 GTGGCTCAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 12 0.36
16 1 0.03
17 1 0.03
18 19 0.58
ACGTcount: A:0.48, C:0.39, G:0.07, T:0.05
Consensus pattern (17 bp):
CAACATCACCAACGCAA
Found at i:2229139 original size:9 final size:9
Alignment explanation
Indices: 2229127--2229156 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2229117 ACAACATCAC
2229127 CAGCAACAA
1 CAGCAACAA
*
2229136 CAGCATCAA
1 CAGCAACAA
2229145 CAGCAACAA
1 CAGCAACAA
2229154 CAG
1 CAG
2229157 TGGCTCAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (9 bp):
CAGCAACAA
Found at i:2229156 original size:18 final size:18
Alignment explanation
Indices: 2229115--2229156 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2229105 TCACCAACCG
* *
2229115 CAACAACATCACCAGCAA
1 CAACAGCATCAACAGCAA
2229133 CAACAGCATCAACAGCAA
1 CAACAGCATCAACAGCAA
2229151 CAACAG
1 CAACAG
2229157 TGGCTCAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.36, G:0.10, T:0.05
Consensus pattern (18 bp):
CAACAGCATCAACAGCAA
Found at i:2252935 original size:28 final size:27
Alignment explanation
Indices: 2252915--2252988 Score: 130
Period size: 28 Copynumber: 2.7 Consensus size: 27
2252905 ATTATCTATT
2252915 AATAACAATTTCTTTTTCATTTTTTTA
1 AATAACAATTTCTTTTTCATTTTTTTA
2252942 CAATAACAATTTCTTTTTCATTTTTTTA
1 -AATAACAATTTCTTTTTCATTTTTTTA
2252970 CAATAACAATTTCTTTTTC
1 -AATAACAATTTCTTTTTC
2252989 GTATATTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (27 bp):
AATAACAATTTCTTTTTCATTTTTTTA
Found at i:2265318 original size:81 final size:81
Alignment explanation
Indices: 2265147--2265342 Score: 207
Period size: 81 Copynumber: 2.4 Consensus size: 81
2265137 TAACAAAATT
* * * * *
2265147 TTTTAAACATGGTGTGTAACAATAATATTTTTTTTCAATATGGCACGTAATAACCTTTTTTTAAC
1 TTTTATACATGATGTGTAACAATAATATTTTTTTTCAATATAGCACATAACAACCTTTTTTTAAC
** *
2265212 CATGGCATGTAACCTG
66 CATAACATGTAACATG
*
2265228 TTTTATACATGATGTGTAACAAT-ATAATTTTTTTTCAATATAGCATATAACAACC-TTTTTTAA
1 TTTTATACATGATGTGTAACAATAAT-ATTTTTTTTCAATATAGCACATAACAACCTTTTTTTAA
* * * *
2265291 TCATAACGTGTGATATG
65 CCATAACATGTAACATG
* ** *
2265308 TTTTTGTACATGACCTGTACCAATAATATTTTTTT
1 -TTTTATACATGATGTGTAACAATAATATTTTTTT
2265343 CAACATGACG
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
80 20 0.21
81 73 0.77
82 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (81 bp):
TTTTATACATGATGTGTAACAATAATATTTTTTTTCAATATAGCACATAACAACCTTTTTTTAAC
CATAACATGTAACATG
Found at i:2265370 original size:21 final size:21
Alignment explanation
Indices: 2265346--2265410 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
2265336 TTTTTTTCAA
*
2265346 CATGACGTATAACATCATGTG
1 CATGACGTGTAACATCATGTG
* *
2265367 CATGGCGTGTAACATTATGTG
1 CATGACGTGTAACATCATGTG
* * *
2265388 CACGACATGTAACATCTTGTG
1 CATGACGTGTAACATCATGTG
2265409 CA
1 CA
2265411 CTTGATAGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
CATGACGTGTAACATCATGTG
Found at i:2271400 original size:4 final size:4
Alignment explanation
Indices: 2271391--2271422 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
2271381 ATCAATTCCC
2271391 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
2271423 ACGAACACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2274679 original size:30 final size:30
Alignment explanation
Indices: 2274639--2274712 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
2274629 GGCTCAGGTC
* ***
2274639 GGCACGGGGAATCGGGACTCGTGGGCGGGG
1 GGCAGGGGGAATCGGGACTCGTGGGAAAGG
2274669 GGCAGGGGGAATCGGGACTCGTGGGAAAGG
1 GGCAGGGGGAATCGGGACTCGTGGGAAAGG
2274699 GGC-GGGGGAATCGG
1 GGCAGGGGGAATCGG
2274713 TAGGAGTGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 11 0.28
30 29 0.73
ACGTcount: A:0.18, C:0.16, G:0.57, T:0.09
Consensus pattern (30 bp):
GGCAGGGGGAATCGGGACTCGTGGGAAAGG
Found at i:2275157 original size:24 final size:22
Alignment explanation
Indices: 2275130--2275174 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2275120 ACAATGCATT
2275130 TATTTGCTTCATCTCTTTTTATTA
1 TATTTG-TTC-TCTCTTTTTATTA
*
2275154 TATTTGTTCTTTCTTTTTATT
1 TATTTGTTCTCTCTTTTTATT
2275175 TTAATTTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 3 0.15
24 6 0.30
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTTGTTCTCTCTTTTTATTA
Found at i:2290908 original size:15 final size:16
Alignment explanation
Indices: 2290860--2290909 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
2290850 CTTTTTTTCT
* *
2290860 AATACAAAAAATATTA
1 AATAAAAAAAATAATA
* *
2290876 AGT-AAAAAATTAATA
1 AATAAAAAAAATAATA
2290891 AATAAAAAAAATAA-A
1 AATAAAAAAAATAATA
2290906 AATA
1 AATA
2290910 TCAACCAAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AATAAAAAAAATAATA
Found at i:2294913 original size:25 final size:25
Alignment explanation
Indices: 2294885--2294958 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
2294875 TTGATAAATG
2294885 ATATTTTAATTAAATTAATTATTAA
1 ATATTTTAATTAAATTAATTATTAA
***
2294910 ATATAAAAATTAAATTAATTTATTTAA
1 ATATTTTAATTAAATTAA-TTA-TTAA
* *
2294937 AT-TTTTAAAT-AATTTATTATTA
1 ATATTTTAATTAAATTAATTATTA
2294959 TTTTTAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 3 0.08
24 3 0.08
25 20 0.51
26 7 0.18
27 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTTTAATTAAATTAATTATTAA
Found at i:2294937 original size:21 final size:21
Alignment explanation
Indices: 2294913--2294954 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2294903 TTATTAAATA
2294913 TAAA-AATTAAATTAATTTATT
1 TAAATAATTAAA-TAATTTATT
**
2294934 TAAATTTTTAAATAATTTATT
1 TAAATAATTAAATAATTTATT
2294955 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATAATTAAATAATTTATT
Found at i:2294961 original size:21 final size:21
Alignment explanation
Indices: 2294919--2294968 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
2294909 AATATAAAAA
2294919 TTAAATTAATTTATTTAAATTT
1 TTAAA-TAATTTATTTAAATTT
*
2294941 TTAAATAATTTA-TTATTATTT
1 TTAAATAATTTATTTA-AATTT
2294962 TTAAATA
1 TTAAATA
2294969 TTACCATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.69
22 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATAATTTATTTAAATTT
Found at i:2297455 original size:39 final size:39
Alignment explanation
Indices: 2297412--2297489 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
2297402 AATGAGAAAG
2297412 AAAATTGACTCAAAG-AGTATGAA-AAATTTAAAAATTTTA
1 AAAATTGACTCAAAGAAGT-T-AACAAATTTAAAAATTTTA
*
2297451 AAAATTGACTCAAGGAAGTTAACTAAATTTAAAAATTTT
1 AAAATTGACTCAAAGAAGTTAAC-AAATTTAAAAATTTT
2297490 GGTGGGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 2 0.06
39 15 0.43
40 18 0.51
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.32
Consensus pattern (39 bp):
AAAATTGACTCAAAGAAGTTAACAAATTTAAAAATTTTA
Found at i:2298010 original size:42 final size:43
Alignment explanation
Indices: 2297963--2298046 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
2297953 TTAATTAACT
* *
2297963 CAAAATAAAAGTATAAGAGCTTA-TTGA-TTCAAAATAAAAGTC
1 CAAAATAAAAGTATAAAAACTTATTTGACTT-AAAATAAAAGTC
* *
2298005 CAAAATAAAATTATAAAAATTTATTTGACTTAAAATAAAAGT
1 CAAAATAAAAGTATAAAAACTTATTTGACTTAAAATAAAAGT
2298047 ATTTAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 19 0.53
43 15 0.42
44 2 0.06
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (43 bp):
CAAAATAAAAGTATAAAAACTTATTTGACTTAAAATAAAAGTC
Found at i:2303781 original size:26 final size:27
Alignment explanation
Indices: 2303745--2303795 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2303735 TCTAAAACTT
*
2303745 TATCAGCTCTCAGCA-TATTCCCAATA
1 TATCAGCTCTCAGCACAATTCCCAATA
*
2303771 TATCCGCTCTCAGCACAATTCCCAA
1 TATCAGCTCTCAGCACAATTCCCAA
2303796 CAATATGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.35, G:0.08, T:0.27
Consensus pattern (27 bp):
TATCAGCTCTCAGCACAATTCCCAATA
Found at i:2320783 original size:12 final size:12
Alignment explanation
Indices: 2320752--2320784 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2320742 GTAAAATATC
*
2320752 TATAATTTTTTT
1 TATAATTTTATT
2320764 TA-AATTTTATT
1 TATAATTTTATT
2320775 TATAATTTTA
1 TATAATTTTA
2320785 CGCGAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATAATTTTATT
Found at i:2329363 original size:30 final size:32
Alignment explanation
Indices: 2329329--2329397 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
2329319 TCAATTTAGT
2329329 TTTTTTTA-TTTAAAA-TTATAATAATTTAAA
1 TTTTTTTATTTTAAAATTTATAATAATTTAAA
**
2329359 -TTTTTTATTTTAAAATTTATTTTAATTTAAA
1 TTTTTTTATTTTAAAATTTATAATAATTTAAA
2329390 TTTTTTTA
1 TTTTTTTA
2329398 ACGATATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.21
30 7 0.21
31 13 0.38
32 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTTTTTTATTTTAAAATTTATAATAATTTAAA
Found at i:2329398 original size:15 final size:15
Alignment explanation
Indices: 2329350--2329398 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
2329340 AAAATTATAA
2329350 TAATTTAAA-TTTTT
1 TAATTTAAATTTTTT
*
2329364 TATTTTAAAATTTATTT
1 TAATTT-AAATTT-TTT
2329381 TAATTTAAATTTTTT
1 TAATTTAAATTTTTT
2329396 TAA
1 TAA
2329399 CGATATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 5 0.17
15 9 0.30
16 8 0.27
17 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAATTTAAATTTTTT
Found at i:2330282 original size:15 final size:15
Alignment explanation
Indices: 2330262--2330291 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2330252 TTCAAGTTAT
2330262 ATTTTTTACATTGAA
1 ATTTTTTACATTGAA
*
2330277 ATTTTTTGCATTGAA
1 ATTTTTTACATTGAA
2330292 TACTATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (15 bp):
ATTTTTTACATTGAA
Found at i:2340245 original size:15 final size:15
Alignment explanation
Indices: 2340225--2340281 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
2340215 ATTTCAATGC
2340225 AATGTGATT-CTAAGT
1 AATGTGATTAC-AAGT
2340240 AATGTGATTACAAGT
1 AATGTGATTACAAGT
* *
2340255 AATGTGATTGCAAGC
1 AATGTGATTACAAGT
2340270 AATGTGATTACA
1 AATGTGATTACA
2340282 GAAAAATAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 37 0.97
16 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:2340261 original size:30 final size:30
Alignment explanation
Indices: 2340225--2340281 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2340215 ATTTCAATGC
*
2340225 AATGTGATT-CTAAGTAATGTGATTACAAGT
1 AATGTGATTGC-AAGCAATGTGATTACAAGT
2340255 AATGTGATTGCAAGCAATGTGATTACA
1 AATGTGATTGCAAGCAATGTGATTACA
2340282 GAAAAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (30 bp):
AATGTGATTGCAAGCAATGTGATTACAAGT
Found at i:2340520 original size:19 final size:19
Alignment explanation
Indices: 2340498--2340569 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
2340488 ATCATATATT
2340498 TATTTTTATTTAATTATAA
1 TATTTTTATTTAATTATAA
*
2340517 TATTTTATATTT-ATTTTAA
1 TATTTT-TATTTAATTATAA
* * *
2340536 TATATTATATTTTTATTATTA
1 TAT-TTTTA-TTTAATTATAA
*
2340557 -ATTTTTATATAAT
1 TATTTTTATTTAAT
2340570 ATCATTTCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 4 0.10
19 21 0.50
20 12 0.29
21 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATTTAATTATAA
Found at i:2340867 original size:77 final size:81
Alignment explanation
Indices: 2340694--2340868 Score: 182
Period size: 84 Copynumber: 2.1 Consensus size: 81
2340684 TTTCTTAATA
** * * * *
2340694 TATTTTTAATATCATATATTTTATTTTTATTTTTTATTATAATATTTTATATTTTATTTTTAATA
1 TATTTTTAATATCA-ATATTTTAAATATATTTTATATCATAATATTTTATATTTTATTATTAATA
2340759 TATTTATATTATATTAT
65 TATTTATATTATATTAT
2340776 TAATTTTATATAATATC-ATATTTTAAATATATTTTAATATCAT-ATATTTTAT-TTTTATTATT
1 T-A-TTT-T-TAATATCAATATTTTAAATATATTTT-ATATCATAATATTTTATATTTTATTATT
*
2340838 ATTATAATTT-TA-TATATT-T
61 AATAT-ATTTATATTATATTAT
2340857 TATTTTTAATAT
1 TATTTTTAATAT
2340869 ATTTATATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
77 6 0.08
78 1 0.01
79 3 0.04
80 1 0.01
81 2 0.03
82 7 0.09
83 16 0.20
84 31 0.39
85 6 0.08
86 7 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (81 bp):
TATTTTTAATATCAATATTTTAAATATATTTTATATCATAATATTTTATATTTTATTATTAATAT
ATTTATATTATATTAT
Found at i:2340896 original size:109 final size:111
Alignment explanation
Indices: 2340427--2341079 Score: 947
Period size: 110 Copynumber: 6.0 Consensus size: 111
2340417 ATATAAGTTT
*
2340427 ATATATATTATATTTTTTATTATTAATTTTTATATAATAGCATTTCTTAAATAT-TTTTAATATC
1 ATATAT-TTATA-TTTTTATTATTAATTTTTATATAATATCATTT-TTAAATATATTTTAATATC
2340491 ATATA-TTTATTTTTATTTA--ATTATAATATTTTATA-TTTA-TTTTA
63 ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTA
*
2340535 ATATA-TTATATTTTTATTATTAATTTTTATATAATATCATTTCTAAATATATTTTAATATCATA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTAATATCATA
*
2340599 TATTTTATTTTTATTTATTATTTTAATATTTTATATTTTATTTTTA
66 TATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTA
2340645 ATATATTTATA-TTTTATTATTAATTTTTATATAATATCATTTCTT-AATATATTTTTAATATCA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTT-TTAAATATA-TTTTAATATCA
*
2340708 TATATTTTATTTTTATTTTTTATTATAATATTTTATATTTTATTTTTA
64 TATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTA
*
2340756 ATATATTTATA-TTATATTATTAA-TTTTATATAATATCATATTTTAAATATATTTTAATATCAT
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTTTAAATATATTTTAATATCAT
2340819 ATATTTTATTTTTA-TTATTATTATAAT-TTTATATATTTTATTTTTA
65 ATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATTTTTA
* *
2340865 ATATATTTATATTTTTATTA-TAA-TTTTATATAATATTATTTTTTAAATATATTTTTAATGTCA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCA-TTTTTAAATATA-TTTTAATATCA
*
2340928 TCTATTTTA-TTTTA-TT-TTATTA-AATATTTTATATTTTATTTTTAA
64 TATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTT-A
* *
2340973 ATATATTTATATTTATATTATTAATTTTTATATAAT-TCATATTTTAAATATATTTTAATGTCAT
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTTTAAATATATTTTAATATCAT
2341037 ATATTTTATTTTTATTTATTA-TATAAT-TTATTATA-TTTATTTT
65 ATATTTTATTTTTATTTATTATTATAATATT-TTATATTTTATTTT
2341080 AATTGTTTTA
Statistics
Matches: 505, Mismatches: 15, Indels: 48
0.89 0.03 0.08
Matches are distributed among these distances:
104 7 0.01
105 46 0.09
106 19 0.04
107 17 0.03
108 72 0.14
109 98 0.19
110 142 0.28
111 104 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (111 bp):
ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTAATATCATA
TATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTA
Found at i:2340914 original size:46 final size:43
Alignment explanation
Indices: 2340491--2340918 Score: 163
Period size: 43 Copynumber: 10.2 Consensus size: 43
2340481 TTTTAATATC
*
2340491 ATATATTTATTTTTATTTAATTATAATATTT-TATAT-TTA-TTTTA
1 ATATATTTA-TATTA-TT-ATTATAAT-TTTATATATATTATTTTTA
* * *
2340535 ATATA-TTATATTTTTATTATTAATTTTTATATAATATCATTTCTAA
1 ATATATTTATATTATTATTA-TAA-TTTTATAT-ATATTATTT-TTA
* * *
2340581 ATATATTTTAATATCATATATT-TTATTTT-TATTTATTA-TTTTA
1 ATATA-TTT-ATATTAT-TATTATAATTTTATATATATTATTTTTA
* * *
2340624 ATAT-TTTATATT-TTATTTTTAATATATT-TATATTTTATTATTA
1 ATATATTTATATTATTA-TTATAAT-T-TTATATATATTATTTTTA
*
2340667 AT-T-TTTATA-TA--A-TATCATTTCT-TA-ATA-TATTTTTA
1 ATATATTTATATTATTATTATAATTT-TATATATATTATTTTTA
* * * * *
2340702 ATATCATATATTTTATTTTTAT-TTTTTAT-TATAATA-TTTT-
1 ATAT-ATTTATATTATTATTATAATTTTATATATATTATTTTTA
* *
2340742 ATAT-TTTAT-TT-TTAATAT-A-TTTATATTATATTATTAATTTT
1 ATATATTTATATTATTATTATAATTTTATA-TATATTATT--TTTA
* * *
2340783 ATATAATATCATATT-TTA-AATATATTTTA-ATATCA-TATATTT-
1 ATAT-AT-TTATATTATTATTATA-ATTTTATATAT-ATTATTTTTA
*
2340825 -TAT-TTT-TATTATTATTATAATTTTATATATTTTATTTTTA
1 ATATATTTATATTATTATTATAATTTTATATATATTATTTTTA
*
2340865 ATATATTTATATTTTTATTATAATTTTATATAATATTATTTTTTAA
1 ATATATTTATATTATTATTATAATTTTATAT-ATATTA-TTTTT-A
2340911 ATATATTT
1 ATATATTT
2340919 TTAATGTCAT
Statistics
Matches: 294, Mismatches: 37, Indels: 104
0.68 0.09 0.24
Matches are distributed among these distances:
35 14 0.05
36 9 0.03
37 16 0.05
38 25 0.09
39 19 0.06
40 20 0.07
41 34 0.12
42 31 0.11
43 42 0.14
44 19 0.06
45 22 0.07
46 22 0.07
47 8 0.03
48 4 0.01
49 5 0.02
50 4 0.01
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (43 bp):
ATATATTTATATTATTATTATAATTTTATATATATTATTTTTA
Found at i:2340963 original size:24 final size:24
Alignment explanation
Indices: 2340935--2341005 Score: 89
Period size: 23 Copynumber: 3.1 Consensus size: 24
2340925 TCATCTATTT
2340935 TATTTTATTTTATTAAATATTTTA
1 TATTTTATTTTATTAAATATTTTA
2340959 TATTTTA-TTT-TTAAATATATTTA
1 TATTTTATTTTATTAAATAT-TTTA
*
2340982 TA-TTTATATTATT-AAT-TTTTA
1 TATTTTATTTTATTAAATATTTTA
2341003 TAT
1 TAT
2341006 AATTCATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
21 6 0.14
22 13 0.31
23 14 0.33
24 9 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTATTTTATTAAATATTTTA
Found at i:2340994 original size:46 final size:45
Alignment explanation
Indices: 2340933--2341027 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 45
2340923 TGTCATCTAT
* *
2340933 TTTATTTTATTTTATTAAATATTTTATAT-TTTAT-TTTTAAATATA
1 TTTATTTTATATTATT-AAT-TTTTATATATTCATATTTTAAATATA
2340978 TTTATATTTATATTATTAATTTTTATATAATTCATATTTTAAATATA
1 TTTAT-TTTATATTATTAATTTTTATAT-ATTCATATTTTAAATATA
2341025 TTT
1 TTT
2341028 TAATGTCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
44 8 0.18
45 8 0.18
46 14 0.32
47 14 0.32
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (45 bp):
TTTATTTTATATTATTAATTTTTATATATTCATATTTTAAATATA
Found at i:2341066 original size:22 final size:21
Alignment explanation
Indices: 2341035--2341077 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2341025 TTTTAATGTC
* *
2341035 ATATATTTTATTTTTATTTATT
1 ATATAATTTA-TTATATTTATT
2341057 ATATAATTTATTATATTTATT
1 ATATAATTTATTATATTTATT
2341078 TTAATTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATAATTTATTATATTTATT
Found at i:2341151 original size:25 final size:25
Alignment explanation
Indices: 2341107--2341175 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
2341097 TATATAAATG
*
2341107 TTAATTTTTTATATTTTATTTTAT-T
1 TTAA-TTTTTATATTTTATTATATAT
2341132 TTAATTTTTAT-TCTTATATTATATAT
1 TTAATTTTTATAT-TT-TATTATATAT
*
2341158 TT-ATTTTAATATTTTATT
1 TTAATTTTTATATTTTATT
2341176 TTAATTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 1 0.03
24 13 0.34
25 20 0.53
26 4 0.11
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (25 bp):
TTAATTTTTATATTTTATTATATAT
Found at i:2341186 original size:19 final size:18
Alignment explanation
Indices: 2341117--2341189 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 18
2341107 TTAATTTTTT
*
2341117 ATATTTTATTTTATTTTA
1 ATATTTTATTTTATTATA
2341135 AT-TTTTATTCTTA-TAT-
1 ATATTTTATT-TTATTATA
* *
2341151 -TA-TATA-TTTATTTTA
1 ATATTTTATTTTATTATA
2341166 ATATTTTATTTTAATTATA
1 ATATTTTATTTT-ATTATA
2341185 ATATT
1 ATATT
2341190 ATTAATATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 4 0.10
16 2 0.05
17 12 0.29
18 8 0.19
19 10 0.24
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTTATTTTATTATA
Found at i:2364389 original size:19 final size:21
Alignment explanation
Indices: 2364365--2364403 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2364355 CCGGCTAGGG
2364365 AGAGGGG-G-GCGCGTGAGAC
1 AGAGGGGTGAGCGCGTGAGAC
2364384 AGAGGGGTGAGCGCGTGAGA
1 AGAGGGGTGAGCGCGTGAGA
2364404 GTTAGGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.23, C:0.13, G:0.56, T:0.08
Consensus pattern (21 bp):
AGAGGGGTGAGCGCGTGAGAC
Found at i:2365023 original size:15 final size:15
Alignment explanation
Indices: 2364999--2365032 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2364989 TTTTAAAAAA
2364999 TTAATAATTTAAA-T
1 TTAATAATTTAAACT
2365013 TTAATTAATTTAAACT
1 TTAA-TAATTTAAACT
2365029 TTAA
1 TTAA
2365033 ATTCGAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 9 0.50
16 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAATTTAAACT
Found at i:2381463 original size:20 final size:20
Alignment explanation
Indices: 2381438--2381477 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2381428 ATTTCTTCTA
2381438 CCATGGAAAGTGTAGATAGG
1 CCATGGAAAGTGTAGATAGG
2381458 CCATGGAAAGTGTAGATAGG
1 CCATGGAAAGTGTAGATAGG
2381478 ACTGGTAGGA
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:0.35, T:0.20
Consensus pattern (20 bp):
CCATGGAAAGTGTAGATAGG
Found at i:2389206 original size:11 final size:11
Alignment explanation
Indices: 2389154--2389205 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
2389144 TGTTTTTTTG
2389154 CATATTTTTAA
1 CATATTTTTAA
*
2389165 CACATTTTTAA
1 CATATTTTTAA
* *
2389176 TATGTTTTTAA
1 CATATTTTTAA
*
2389187 TATATTTTTAA
1 CATATTTTTAA
2389198 CAT-TTTTT
1 CATATTTTT
2389206 TTGCACGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 5 0.14
11 30 0.86
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (11 bp):
CATATTTTTAA
Found at i:2390346 original size:10 final size:11
Alignment explanation
Indices: 2390322--2390359 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2390312 TTTTAGTACA
*
2390322 TTTTAACATGT
1 TTTTAACATAT
*
2390333 TTTTCACATAT
1 TTTTAACATAT
2390344 TTTTAACATAT
1 TTTTAACATAT
2390355 TTTTA
1 TTTTA
2390360 TACGTTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (11 bp):
TTTTAACATAT
Found at i:2391298 original size:30 final size:30
Alignment explanation
Indices: 2391238--2391298 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
2391228 TTCATAAAAT
* *
2391238 ACATGTATATAAATTAAAAAATATATATAA
1 ACATGTATAAAAATTAAAAAATATAAATAA
* *
2391268 ACATGTATAAAAATGTATAATAT-TAAATAA
1 ACATGTATAAAAAT-TAAAAAATATAAATAA
2391298 A
1 A
2391299 AATTATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (30 bp):
ACATGTATAAAAATTAAAAAATATAAATAA
Done.