Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 57 of 318
Found at i:20374010 original size:13 final size:13
Alignment explanation
Indices: 20373994--20374023 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20373984 TAGACCAAGC
20373994 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
*
20374007 TTTTCATAAGCAT
1 TTTTCAAAAGCAT
20374020 TTTT
1 TTTT
20374024 TTGCAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:20376241 original size:14 final size:14
Alignment explanation
Indices: 20376222--20376248 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20376212 GTATGGTCAG
20376222 ATATGTCGTTTCAC
1 ATATGTCGTTTCAC
20376236 ATATGTCGTTTCA
1 ATATGTCGTTTCA
20376249 ATCAGCTGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (14 bp):
ATATGTCGTTTCAC
Found at i:20380726 original size:19 final size:19
Alignment explanation
Indices: 20380698--20380734 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20380688 CTTTGAGTAG
*
20380698 AAACCAAAAACTTTAACAC
1 AAACCAAAAACTTCAACAC
*
20380717 AAACCTAAAACTTCAACA
1 AAACCAAAAACTTCAACA
20380735 ATAACAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (19 bp):
AAACCAAAAACTTCAACAC
Found at i:20383786 original size:15 final size:15
Alignment explanation
Indices: 20383748--20383803 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
20383738 ACAAAACAAT
* *
20383748 AATATAAATGACTAA
1 AATATAAATAATTAA
* *
20383763 AATAT-AATATTTCA
1 AATATAAATAATTAA
20383777 AATATAAATAATTAA
1 AATATAAATAATTAA
20383792 AATATAATATAA
1 AATATAA-ATAA
20383804 GACAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.30
15 19 0.58
16 4 0.12
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:20386119 original size:18 final size:18
Alignment explanation
Indices: 20386098--20386133 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20386088 TATTTAAATT
* *
20386098 AAAATTTCAAAATTCAAA
1 AAAATTTAAAAAATCAAA
20386116 AAAATTTAAAAAATCAAA
1 AAAATTTAAAAAATCAAA
20386134 TTAAAATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTTAAAAAATCAAA
Found at i:20395314 original size:89 final size:89
Alignment explanation
Indices: 20395162--20395330 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
20395152 CATGGCCATC
20395162 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
1 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
20395227 AAGTATATATTCTTGTAATTTATT
66 AAGTATATATTCTTGTAATTTATT
* * * * *
20395251 GTGCTTACTACCAAGGCTTGAAAATTTCCTCTAGA-TTCAATGGATTCATACTTTAAAGTTCAAT
1 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTT-AATGAACTCATACTTCAAAGCTCAAT
* * *
20395315 CATGTTTTTATTCTTG
65 CAAGTATATATTCTTG
20395331 AATCCTTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 2 0.03
89 69 0.97
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (89 bp):
GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
AAGTATATATTCTTGTAATTTATT
Found at i:20397440 original size:52 final size:48
Alignment explanation
Indices: 20397376--20397521 Score: 145
Period size: 52 Copynumber: 3.0 Consensus size: 48
20397366 AAATGTGATT
* *
20397376 TCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATACGTGC
1 TCCGTATAAGACCATAGCTGGGCTATGGCATCGGAG---TGTGATACGTGA
* * *
20397427 TACTGTATAAGACCATATCTGGGATATGGCATC--AGTGTGATACGTGA
1 T-CCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGTGATACGTGA
* * * *
20397474 TCCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTA-TGTGATATGTGA
1 TCCGTATAAGACCATAGCTGGGCTATGGCATCGG-AGTGTGATACGTGA
20397522 CTATGTGCAA
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
46 25 0.32
47 12 0.15
48 11 0.14
49 1 0.01
50 2 0.03
51 1 0.01
52 27 0.34
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (48 bp):
TCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGTGATACGTGA
Found at i:20399517 original size:13 final size:14
Alignment explanation
Indices: 20399496--20399528 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20399486 TATAATATTT
20399496 AAAAA-TATTT-AA
1 AAAAATTATTTCAA
20399508 AAAAATTATTTCAA
1 AAAAATTATTTCAA
20399522 AAAAATT
1 AAAAATT
20399529 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 5 0.26
14 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTATTTCAA
Found at i:20399540 original size:11 final size:11
Alignment explanation
Indices: 20399489--20399540 Score: 54
Period size: 10 Copynumber: 4.6 Consensus size: 11
20399479 TAAATTATAT
20399489 AATATTT-AAA
1 AATATTTAAAA
20399499 AATATTTAAAAA
1 AATATTT-AAAA
20399511 AATTATTTCAAAA
1 AA-TATTT-AAAA
20399524 AA-ATTTAAAA
1 AATATTTAAAA
*
20399534 TATATTT
1 AATATTT
20399541 TCTAAATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 12 0.33
11 8 0.22
12 5 0.14
13 11 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:20405926 original size:36 final size:36
Alignment explanation
Indices: 20405883--20405958 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
20405873 GCTTATAGGA
20405883 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
1 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
20405919 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
1 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
20405955 ATAA
1 ATAA
20405959 TATTTATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (36 bp):
ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
Found at i:20421744 original size:23 final size:22
Alignment explanation
Indices: 20421718--20421766 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
20421708 CGACTAAATC
* *
20421718 AATACATAGCATAATAAGATTTA
1 AATACATA-CATAATAAAATTAA
* *
20421741 AATATATACATTATAAAATTAA
1 AATACATACATAATAAAATTAA
20421763 AATA
1 AATA
20421767 ATTTTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (22 bp):
AATACATACATAATAAAATTAA
Found at i:20427022 original size:32 final size:32
Alignment explanation
Indices: 20426986--20427046 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
20426976 AGGCTGAACT
20426986 GAAGCTCATAAGAGCTAAAC-AGAAACCCAACG
1 GAAGCTCATAAGAGCTAAACGA-AAACCCAACG
** *
20427018 GAAGCTTGTAAGAGCTGAACGAAAACCCA
1 GAAGCTCATAAGAGCTAAACGAAAACCCA
20427047 TAAGGGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.11
Consensus pattern (32 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCAACG
Found at i:20427050 original size:21 final size:21
Alignment explanation
Indices: 20427026--20427086 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
20427016 CGGAAGCTTG
20427026 TAAGAGCTGAACGAAAACCCA
1 TAAGAGCTGAACGAAAACCCA
* * * * *
20427047 TAAGGGTTAAAC-AGAAGCTCA
1 TAAGAGCTGAACGA-AAACCCA
*
20427068 AAAGAGCTGAACGAAAACC
1 TAAGAGCTGAACGAAAACC
20427087 TATTAGGGTT
Statistics
Matches: 27, Mismatches: 11, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (21 bp):
TAAGAGCTGAACGAAAACCCA
Found at i:20430357 original size:2 final size:2
Alignment explanation
Indices: 20430350--20430375 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20430340 TTACTCCCAA
20430350 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
20430376 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20434023 original size:34 final size:34
Alignment explanation
Indices: 20433985--20434049 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
20433975 TTCGGTCAAT
* *
20433985 TTTAGTCTATGTATTTTTTAAATTTTAAAATACA
1 TTTAGTCTATGTAATATTTAAATTTTAAAATACA
* **
20434019 TTTAGTCTTTGTAATATTTGTATTTTAAAAT
1 TTTAGTCTATGTAATATTTAAATTTTAAAAT
20434050 TTCATTCCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (34 bp):
TTTAGTCTATGTAATATTTAAATTTTAAAATACA
Found at i:20441106 original size:21 final size:22
Alignment explanation
Indices: 20441089--20441130 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20441079 ACCTAAATTT
20441089 TTAAA-TTTAAAAAATAAATAA
1 TTAAATTTTAAAAAATAAATAA
*
20441110 TTAAATTTTTAAAAATAAATA
1 TTAAATTTTAAAAAATAAATA
20441131 TATAGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAATTTTAAAAAATAAATAA
Found at i:20444609 original size:20 final size:21
Alignment explanation
Indices: 20444575--20444628 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
20444565 TGATGATATT
*
20444575 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
20444596 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
20444616 TTTTATTATTTTA
1 TTATATTATTTTA
20444629 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:20444634 original size:11 final size:11
Alignment explanation
Indices: 20444618--20444645 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20444608 ATGAGATATT
20444618 TTATTATTTTA
1 TTATTATTTTA
20444629 TTATTATTTTA
1 TTATTATTTTA
20444640 TTATTA
1 TTATTA
20444646 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:20446382 original size:25 final size:25
Alignment explanation
Indices: 20446354--20446428 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
20446344 AGATGCTTGA
20446354 GATTGCATGTTATTGATGTGAATAT
1 GATTGCATGTTATTGATGTGAATAT
*
20446379 GATTTGAATG-TA--GATGCT---TGA-
1 GA-TTGCATGTTATTGATG-TGAAT-AT
20446400 GATTGCATGTTATTGATGTGAATAT
1 GATTGCATGTTATTGATGTGAATAT
20446425 GATT
1 GATT
20446429 TGAATGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 20
0.63 0.03 0.33
Matches are distributed among these distances:
20 6 0.16
21 5 0.13
22 2 0.05
23 8 0.21
24 2 0.05
25 9 0.24
26 6 0.16
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (25 bp):
GATTGCATGTTATTGATGTGAATAT
Found at i:20446396 original size:46 final size:46
Alignment explanation
Indices: 20446343--20446435 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
20446333 ATTATATTCT
20446343 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
1 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
20446389 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
1 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
20446435 T
1 T
20446436 TCATTGTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (46 bp):
TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
Found at i:20446868 original size:46 final size:46
Alignment explanation
Indices: 20446815--20446996 Score: 249
Period size: 46 Copynumber: 4.0 Consensus size: 46
20446805 AGTGTGCTCT
*
20446815 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
20446861 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
20446907 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
20446953 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
20446997 TCATGTCAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 121 0.99
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20447717 original size:17 final size:17
Alignment explanation
Indices: 20447695--20447730 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20447685 TCCCTCTCTC
20447695 CATAGCTAGGGTTTCTT
1 CATAGCTAGGGTTTCTT
20447712 CATAGCTAGGGTTTCTT
1 CATAGCTAGGGTTTCTT
20447729 CA
1 CA
20447731 ACTTTCAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (17 bp):
CATAGCTAGGGTTTCTT
Found at i:20448496 original size:93 final size:93
Alignment explanation
Indices: 20448337--20448507 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
20448327 GGATGGTTGA
* * **
20448337 GCATCCGAACTCGTTGAGTTAAGTTCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
*
20448402 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* * *
20448430 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
20448495 TGAGTCCAAGTTC
66 TGAGTCCAAGTTC
20448508 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTACGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:20457122 original size:17 final size:17
Alignment explanation
Indices: 20457100--20457132 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20457090 TAATTAATTA
*
20457100 ATTATATTTTATTTATT
1 ATTATATTATATTTATT
20457117 ATTATATTATATTTAT
1 ATTATATTATATTTAT
20457133 CTTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATATTATATTTATT
Found at i:20460036 original size:18 final size:19
Alignment explanation
Indices: 20460002--20460037 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20459992 TTAGTCTCTC
*
20460002 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTATAAAAT
20460021 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
20460038 ATTATAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAT
Found at i:20460038 original size:19 final size:19
Alignment explanation
Indices: 20460002--20460040 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20459992 TTAGTCTCTC
*
20460002 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTAAAAAT
20460021 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TAAAAAT
20460040 T
1 T
20460041 ATAACATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:20461372 original size:18 final size:16
Alignment explanation
Indices: 20461344--20461378 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
20461334 CTAACGGCGG
20461344 AAATAATATTTATATTA
1 AAATAATATTTAT-TTA
20461361 AAATATATATTTATTTA
1 AAATA-ATATTTATTTA
20461378 A
1 A
20461379 CAATTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATAATATTTATTTA
Found at i:20461540 original size:20 final size:19
Alignment explanation
Indices: 20461495--20461549 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
20461485 TTTAATGGAA
*
20461495 AATATTTTTAATTAATTATAT
1 AATA-TTTT-ATTTATTATAT
*
20461516 TATATTTTATTTATTATTAT
1 AATATTTTATTTATTA-TAT
*
20461536 AATATTATATTTAT
1 AATATTTTATTTAT
20461550 CCTATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 19 0.66
21 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTTTATTTATTATAT
Found at i:20461605 original size:16 final size:15
Alignment explanation
Indices: 20461584--20461627 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20461574 TAAAACAAAA
*
20461584 TAAAATATTTAAATTT
1 TAAAAT-TTTAAAATT
20461600 TAAAATTTTAAAATT
1 TAAAATTTTAAAATT
*
20461615 TATAA-TTTAAAAT
1 TAAAATTTTAAAAT
20461628 CTATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 8 0.31
15 12 0.46
16 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTTAAAATT
Found at i:20461623 original size:14 final size:14
Alignment explanation
Indices: 20461590--20461636 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
20461580 AAAATAAAAT
* *
20461590 ATTTAAATTTTAAA
1 ATTTAAAATTTATA
20461604 ATTTTAAAATTTATA
1 A-TTTAAAATTTATA
*
20461619 ATTTAAAATCTAT-
1 ATTTAAAATTTATA
20461632 ATTTA
1 ATTTA
20461637 TCAAACAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 5 0.17
14 12 0.41
15 12 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTAAAATTTATA
Found at i:20461715 original size:15 final size:15
Alignment explanation
Indices: 20461692--20461733 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
20461682 ATAATTTAAA
*
20461692 TTCAGTACTTAAAAT
1 TTCAATACTTAAAAT
*
20461707 TTCAATACTTAATAT
1 TTCAATACTTAAAAT
*
20461722 TTCAACACTTAA
1 TTCAATACTTAA
20461734 TTTGTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (15 bp):
TTCAATACTTAAAAT
Found at i:20490771 original size:56 final size:56
Alignment explanation
Indices: 20490708--20490820 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
20490698 TTAATCAAAA
20490708 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
1 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
20490764 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
1 CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
20490820 C
1 C
20490821 TTACATATGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (56 bp):
CCTCACTCTTTTTTCACATTAATTTTTTATAAATATTATTTTATCATAACAATTTT
Found at i:20509510 original size:27 final size:27
Alignment explanation
Indices: 20509477--20509550 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
20509467 GAGGGCATGT
** *
20509477 CACAGGCGGCACCGGTGGTGGGGGTGC
1 CACAGGCGGCACCAATGGAGGGGGTGC
* * *
20509504 CAGAGGCGGCACCAATGGAGGGGTTGT
1 CACAGGCGGCACCAATGGAGGGGGTGC
20509531 CACAGGCGGCACCAATGGAG
1 CACAGGCGGCACCAATGGAG
20509551 AAGAAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.20, C:0.24, G:0.45, T:0.11
Consensus pattern (27 bp):
CACAGGCGGCACCAATGGAGGGGGTGC
Found at i:20509583 original size:14 final size:14
Alignment explanation
Indices: 20509548--20509576 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20509538 GGCACCAATG
20509548 GAGAAGAA-AAGAA
1 GAGAAGAAGAAGAA
20509561 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
20509575 GA
1 GA
20509577 ACAGAAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:20510280 original size:6 final size:6
Alignment explanation
Indices: 20510271--20510295 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20510261 TATTTTTGTT
20510271 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
20510296 AATATTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:20510303 original size:20 final size:20
Alignment explanation
Indices: 20510261--20510303 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20510251 TGGGATAGCC
* * * *
20510261 TATTTTTGTTTTTTTATTTT
1 TATTTTTATTTTTATAATAT
20510281 TATTTTTATTTTTATAATAT
1 TATTTTTATTTTTATAATAT
20510301 TAT
1 TAT
20510304 GGTAAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TATTTTTATTTTTATAATAT
Found at i:20510916 original size:24 final size:24
Alignment explanation
Indices: 20510880--20510925 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20510870 GAGAGAATTT
*
20510880 TTATTTTATTTAATATCAATATAA
1 TTATTTTATTTAAGATCAATATAA
*
20510904 TTATATTTA-TTAAGATTAATAT
1 TTAT-TTTATTTAAGATCAATAT
20510926 TAATATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTTTATTTAAGATCAATATAA
Found at i:20512093 original size:5 final size:5
Alignment explanation
Indices: 20512085--20512111 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20512075 CCCCGCCCCC
20512085 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
20512112 GCCACCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:20529999 original size:15 final size:15
Alignment explanation
Indices: 20529981--20530019 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20529971 TTATATAATC
*
20529981 AATATATTTATATTA
1 AATATATTTAAATTA
*
20529996 AATATATTAAAATTA
1 AATATATTTAAATTA
*
20530011 AATAAATTT
1 AATATATTT
20530020 TTGGTCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATTTAAATTA
Found at i:20536740 original size:13 final size:12
Alignment explanation
Indices: 20536718--20536753 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
20536708 GTTCAGCCCG
20536718 TATTAATTTTTTA
1 TATT-ATTTTTTA
20536731 TATTATTTTTTA
1 TATTATTTTTTA
*
20536743 TATAATTTTTT
1 TATTATTTTTT
20536754 TAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:20537027 original size:20 final size:21
Alignment explanation
Indices: 20536991--20537033 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
20536981 AAGATAGTGA
*
20536991 AAAAAATAACAAGAAAATAAC
1 AAAAAATAACAAGAAAAAAAC
20537012 AAAAAA-AAC-AGTAAAAAAAC
1 AAAAAATAACAAG-AAAAAAAC
20537032 AA
1 AA
20537034 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.79, C:0.09, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAATAACAAGAAAAAAAC
Found at i:20539264 original size:22 final size:21
Alignment explanation
Indices: 20539238--20539335 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
20539228 TTGTTAACTA
20539238 TTTACAATTTTTTAATAATTAT
1 TTTACAA-TTTTTAATAATTAT
*
20539260 TTTACGATTTTTAATAA-T-T
1 TTTACAATTTTTAATAATTAT
* ** * *
20539279 TTTAAAAAATTAAATAA-TGT
1 TTTACAATTTTTAATAATTAT
* * *
20539299 TTTATAACTTTTAATAATTTT
1 TTTACAATTTTTAATAATTAT
* *
20539320 TTTAAAATTTTAAATA
1 TTTACAATTTTTAATA
20539336 TTTTAAAAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
19 14 0.23
20 15 0.25
21 25 0.42
22 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTACAATTTTTAATAATTAT
Found at i:20539281 original size:10 final size:10
Alignment explanation
Indices: 20539246--20539320 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
20539236 TATTTACAAT
20539246 TTTTTAATAA
1 TTTTTAATAA
* **
20539256 TTATTTTACGA
1 TT-TTTAATAA
20539267 TTTTTAATAA
1 TTTTTAATAA
20539277 TTTTTAA-AA
1 TTTTTAATAA
** *
20539286 AATTAAATAA
1 TTTTTAATAA
20539296 TGTTTT-ATAA
1 T-TTTTAATAA
*
20539306 CTTTTAATAA
1 TTTTTAATAA
20539316 TTTTT
1 TTTTT
20539321 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
9 10 0.21
10 28 0.60
11 9 0.19
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:20539314 original size:20 final size:19
Alignment explanation
Indices: 20539268--20539358 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
20539258 ATTTTACGAT
20539268 TTTTAATAATTTTTAAAAA
1 TTTTAATAATTTTTAAAAA
* * * *
20539287 ATTAAATAATGTTTTATAAC
1 TTTTAATAAT-TTTTAAAAA
*
20539307 TTTTAATAATTTTTTTAAAA
1 TTTTAATAA-TTTTTAAAAA
*
20539327 TTTTAA-ATATTTTAAAAAAA
1 TTTTAATA-ATTTT-TAAAAA
20539347 TATTTAATAATT
1 T-TTTAATAATT
20539359 ATTACAATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
19 13 0.24
20 32 0.58
21 9 0.16
22 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTTAAAAA
Found at i:20555025 original size:16 final size:15
Alignment explanation
Indices: 20554999--20555058 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
20554989 GAGCAAAGGT
20554999 AAATATAATATTATAAA
1 AAAT-TAATATTA-AAA
20555016 AAATTAATA-TAAATA
1 AAATTAATATTAAA-A
*
20555031 AAATTAACATTAAAA
1 AAATTAATATTAAAA
20555046 TAAATTAAT-TTAA
1 -AAATTAATATTAA
20555059 CAATATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 16 0.42
16 16 0.42
17 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTAATATTAAAA
Found at i:20555042 original size:21 final size:21
Alignment explanation
Indices: 20555018--20555075 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
20555008 ATTATAAAAA
20555018 ATTAATATAAATAAAATTAAC
1 ATTAATATAAATAAAATTAAC
* * *
20555039 ATTAAAATAAATTAATTTAAC
1 ATTAATATAAATAAAATTAAC
*
20555060 AATATATAATAAATAA
1 ATTA-AT-ATAAATAA
20555076 CTTATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 21 0.72
22 1 0.03
23 7 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTAATATAAATAAAATTAAC
Found at i:20555092 original size:23 final size:23
Alignment explanation
Indices: 20555044--20555105 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
20555034 TTAACATTAA
*
20555044 AATAAATTAATTTAACAATATAT
1 AATAAATTAATTTAAAAATATAT
20555067 AATAAA-TAACTTATAAAAATAT-T
1 AATAAATTAA-TT-TAAAAATATAT
20555090 AATAACATT-ATTTAAA
1 AATAA-ATTAATTTAAA
20555106 TTACAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 7 0.21
23 16 0.47
24 10 0.29
25 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAATTAATTTAAAAATATAT
Found at i:20572500 original size:13 final size:13
Alignment explanation
Indices: 20572482--20572508 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20572472 ACAAATATCA
20572482 TACTTGTTTTGAG
1 TACTTGTTTTGAG
20572495 TACTTGTTTTGAG
1 TACTTGTTTTGAG
20572508 T
1 T
20572509 GTCTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TACTTGTTTTGAG
Found at i:20594719 original size:20 final size:20
Alignment explanation
Indices: 20594691--20594729 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20594681 CGACCACGAG
20594691 CCTACCCACACGGGCGTGTC
1 CCTACCCACACGGGCGTGTC
*
20594711 CCTATCCACACGGGCGTGT
1 CCTACCCACACGGGCGTGT
20594730 GGCCCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.26, T:0.18
Consensus pattern (20 bp):
CCTACCCACACGGGCGTGTC
Found at i:20596629 original size:42 final size:42
Alignment explanation
Indices: 20596561--20596724 Score: 186
Period size: 42 Copynumber: 3.7 Consensus size: 42
20596551 CTTCGTTTTC
** * *
20596561 TCGATGCCATAGTTCAACTATAGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
20596604 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
20596645 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
*
20596694 TCGATGCTATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
20596725 GAATCACATA
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 62 0.60
43 1 0.01
45 2 0.02
48 1 0.01
49 36 0.35
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:20596706 original size:49 final size:48
Alignment explanation
Indices: 20596631--20596767 Score: 179
Period size: 49 Copynumber: 2.9 Consensus size: 48
20596621 TATGGTCTTA
*
20596631 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AAT
*
20596681 CACATATCACATATCGATGCTATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
* * * * *
20596729 CACATATCTCA-CT-GATGTCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
20596768 TACAGCAGCA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 22 0.28
47 1 0.01
48 13 0.16
49 37 0.47
50 6 0.08
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
Found at i:20596871 original size:31 final size:31
Alignment explanation
Indices: 20596836--20596984 Score: 190
Period size: 31 Copynumber: 4.8 Consensus size: 31
20596826 CTTGTCACTT
* *
20596836 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * * *
20596867 GTAGCCGGAGTTATCATTTTTCACTGGTCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
20596898 GTAGCCGGAGCTACCACTTTTCACTGATCTG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
20596929 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
20596960 GCAGCCGAAGCTATCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
20596985 TGTCATTTGT
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:20597060 original size:50 final size:50
Alignment explanation
Indices: 20596962--20597136 Score: 287
Period size: 50 Copynumber: 3.5 Consensus size: 50
20596952 CTGATCAGGC
*
20596962 AGCCGAAGCTATCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGT
* * *
20597013 AGCTGAAGCTATCACTTATCACTTTCACTTGTCCTTTATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
*
20597063 AGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
1 AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
*
20597113 AGCCGAAGCTATTACTTATCACTT
1 AGCCGAAGCTATCACTTATCACTT
20597137 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 94 0.81
51 22 0.19
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (50 bp):
AGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGT
Found at i:20597638 original size:21 final size:22
Alignment explanation
Indices: 20597611--20597667 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
20597601 ATATATTAAA
20597611 TTATTATTATTATTTATTATAG
1 TTATTATTATTATTTATTATAG
* *
20597633 TT-TTA-TATTTAATTATTATTG
1 TTATTATTA-TTATTTATTATAG
*
20597654 TTATTGTTATTATT
1 TTATTATTATTATT
20597668 ATTTAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 8 0.29
23 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTTATTATAG
Found at i:20597862 original size:15 final size:15
Alignment explanation
Indices: 20597842--20597870 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20597832 GAAATAAAAG
20597842 AAAGAAACAGAATGA
1 AAAGAAACAGAATGA
20597857 AAAGAAACAGAATG
1 AAAGAAACAGAATG
20597871 TGGAAACGAA
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:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAAACAGAATGA
Found at i:20598299 original size:23 final size:21
Alignment explanation
Indices: 20598252--20598292 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
20598242 TTTGGTTAAA
20598252 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
20598274 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
20598293 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:20598670 original size:15 final size:15
Alignment explanation
Indices: 20598622--20598671 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
20598612 TTTATCAAAT
20598622 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
20598637 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
20598652 TTATATTGATTGAAA
1 TTATATTGATTGAAA
20598667 TTATA
1 TTATA
20598672 ATATATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:20598902 original size:18 final size:18
Alignment explanation
Indices: 20598879--20598913 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20598869 TTGAATTGAA
20598879 TGAAAATGTATGAAAATG
1 TGAAAATGTATGAAAATG
*
20598897 TGAAAATGTGTGAAAAT
1 TGAAAATGTATGAAAAT
20598914 ATGTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (18 bp):
TGAAAATGTATGAAAATG
Found at i:20599208 original size:23 final size:23
Alignment explanation
Indices: 20599180--20599237 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
20599170 ATATTCCGGG
*
20599180 TGTGTTTGGGTTGGATATTCTGA
1 TGTGTTTGGGTTGAATATTCTGA
*
20599203 TGTGTTTGGGTTGAATATTCTGG
1 TGTGTTTGGGTTGAATATTCTGA
20599226 TGTGTTTGGGTT
1 TGTGTTTGGGTT
20599238 TGGGTTGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.10, C:0.03, G:0.36, T:0.50
Consensus pattern (23 bp):
TGTGTTTGGGTTGAATATTCTGA
Found at i:20599249 original size:29 final size:29
Alignment explanation
Indices: 20599206--20599264 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
20599196 ATTCTGATGT
20599206 GTTTGGGTTGAATATTCTGGTGTGTTTGG
1 GTTTGGGTTGAATATTCTGGTGTGTTTGG
*
20599235 GTTTGGGTTGGATATTCTGGTGTGTTTGG
1 GTTTGGGTTGAATATTCTGGTGTGTTTGG
20599264 G
1 G
20599265 AGGAATCGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.08, C:0.03, G:0.41, T:0.47
Consensus pattern (29 bp):
GTTTGGGTTGAATATTCTGGTGTGTTTGG
Found at i:20599390 original size:18 final size:19
Alignment explanation
Indices: 20599369--20599409 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20599359 AATGAAATGA
20599369 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
20599387 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
20599406 GAAA
1 GAAA
20599410 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:20599518 original size:17 final size:17
Alignment explanation
Indices: 20599496--20599528 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20599486 TATTGTTAAG
20599496 AAGTAAAGTGTGAATAC
1 AAGTAAAGTGTGAATAC
*
20599513 AAGTAAATTGTGAATA
1 AAGTAAAGTGTGAATA
20599529 TATTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27
Consensus pattern (17 bp):
AAGTAAAGTGTGAATAC
Found at i:20607839 original size:40 final size:40
Alignment explanation
Indices: 20607795--20607881 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
20607785 AATTCATTAC
* * * *
20607795 TTCAGTAATTTCACAGTTCAGTGCAGTACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
* **
20607835 TTCAGTAACTTCACAATTCAATTCAGTATTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
20607875 TTCAGTA
1 TTCAGTA
20607882 TTCCATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:20608694 original size:14 final size:13
Alignment explanation
Indices: 20608657--20608708 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
20608647 TTCTTCTTTA
* *
20608657 CTTTGTTTTGTTT
1 CTTTATTTTATTT
20608670 CTTTATTTTATTT
1 CTTTATTTTATTT
*
20608683 CATTTCTTTTATTAT
1 C-TTTATTTTATT-T
20608698 -TTTATTTTATT
1 CTTTATTTTATT
20608709 AACTTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 10 0.30
15 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (13 bp):
CTTTATTTTATTT
Found at i:20608755 original size:19 final size:19
Alignment explanation
Indices: 20608712--20608764 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
20608702 TTTTATTAAC
20608712 TTAATAAT-AATA-ATTAT
1 TTAATAATAAATATATTAT
* *
20608729 TATTATAATAAATATCTTAT
1 T-TAATAATAAATATATTAT
*
20608749 TTAATAACAAATATAT
1 TTAATAATAAATATAT
20608765 ATATATTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 6 0.21
19 16 0.57
20 5 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATAATAAATATATTAT
Found at i:20609007 original size:20 final size:20
Alignment explanation
Indices: 20608982--20609042 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
20608972 TTATTTTTAA
*
20608982 TAATAATAATAATCATAATT
1 TAATAATAATAATAATAATT
*
20609002 TAATAAT-ATAAATTATAATT
1 TAATAATAAT-AATAATAATT
*
20609022 TGATAGAATAATAATAATAAT
1 T-A-ATAATAATAATAATAAT
20609043 GATAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 1 0.03
22 12 0.35
23 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATAATAATT
Found at i:20609194 original size:25 final size:27
Alignment explanation
Indices: 20609160--20609221 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 27
20609150 TGGCTTTAAT
*
20609160 TTAATTTAATTCATAATATGATATTTATAA
1 TTAA-TTAATTAATAATAT-AT-TTTATAA
20609190 TTAATTAATTTAATAATATATTTTATAA
1 TTAATTAA-TTAATAATATATTTTATAA
20609218 TTAA
1 TTAA
20609222 ATTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 6 0.20
30 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAATTAATTAATAATATATTTTATAA
Found at i:20609232 original size:24 final size:23
Alignment explanation
Indices: 20609191--20609245 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
20609181 TATTTATAAT
* **
20609191 TAATTAATTTAATAATATATTTTA
1 TAATTAAATTAATAATAT-TTACA
20609215 TAATTAAATT-ATATATATTTACA
1 TAATTAAATTAATA-ATATTTACA
20609238 TAATTAAA
1 TAATTAAA
20609246 ATCTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTAAATTAATAATATTTACA
Found at i:20609300 original size:16 final size:16
Alignment explanation
Indices: 20609279--20609348 Score: 104
Period size: 16 Copynumber: 4.2 Consensus size: 16
20609269 TTTGGTTCGC
*
20609279 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
20609295 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
20609311 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
20609327 TGTATATTGGATTAGAGG
1 TG--TATTGGATTAGAGG
20609345 TGTA
1 TGTA
20609349 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
16 34 0.69
18 15 0.31
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:20609322 original size:32 final size:33
Alignment explanation
Indices: 20609279--20609348 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
20609269 TTTGGTTCGC
*
20609279 TGTATTAGATTAGAGGTG-TATTGGATTAGAGG
1 TGTATTAGATTAAAGGTGATATTGGATTAGAGG
*
20609311 TGTATTGGATTAAAGGTGTATATTGGATTAGAGG
1 TGTATTAGATTAAAGGTG-ATATTGGATTAGAGG
20609345 TGTA
1 TGTA
20609349 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 16 0.47
34 18 0.53
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.39
Consensus pattern (33 bp):
TGTATTAGATTAAAGGTGATATTGGATTAGAGG
Found at i:20609591 original size:18 final size:17
Alignment explanation
Indices: 20609570--20609604 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20609560 TTATTATTAA
*
20609570 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20609588 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20609605 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20610374 original size:13 final size:13
Alignment explanation
Indices: 20610356--20610385 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20610346 TTAAAAGCTA
*
20610356 AATTCAGAAAATC
1 AATTCAGAAAAAC
20610369 AATTCAGAAAAAC
1 AATTCAGAAAAAC
20610382 AATT
1 AATT
20610386 ACATGACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:20613489 original size:71 final size:71
Alignment explanation
Indices: 20613395--20613546 Score: 261
Period size: 71 Copynumber: 2.1 Consensus size: 71
20613385 TTTAAAATAT
* *
20613395 ATTTTTAAAAAATATATTGAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATA
1 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACA-TTTTTAATA
20613460 TATTT-A
65 TATTTAA
20613466 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTAATAT
1 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTAATAT
20613531 ATTTAAA
66 ATTT-AA
20613538 ATTTTTTAA
1 ATTTTTTAA
20613547 GTTTTTTAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
70 14 0.18
71 53 0.69
72 10 0.13
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (71 bp):
ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTAATAT
ATTTAA
Found at i:20613494 original size:20 final size:20
Alignment explanation
Indices: 20613456--20613496 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20613446 AACATTTTTT
* * *
20613456 AATATATTTAATTTTTTAAA
1 AATATATTAAATATATTAAA
20613476 AATATATTAAATATATTAAA
1 AATATATTAAATATATTAAA
20613496 A
1 A
20613497 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAAATATATTAAA
Found at i:20613536 original size:18 final size:18
Alignment explanation
Indices: 20613451--20613571 Score: 65
Period size: 18 Copynumber: 6.8 Consensus size: 18
20613441 TACTTAACAT
*
20613451 TTTTTAATATATTT-AAT
1 TTTTTAATATATTTAAAA
*
20613468 TTTTTAAAAATATATT-AAA
1 TTTTT-AATATAT-TTAAAA
* *
20613487 TATATTAAAAT-TTTAAAA
1 T-TTTTAATATATTTAAAA
** * *
20613505 TTGGT--TATACTTAACA
1 TTTTTAATATATTTAAAA
20613521 TTTTTAATATATTTAAAA
1 TTTTTAATATATTTAAAA
*
20613539 TTTTTTAAGT-TTTTTAAAA
1 -TTTTTAA-TATATTTAAAA
*
20613558 TTTTAAATATATTT
1 TTTTTAATATATTT
20613572 CCCTAAACCC
Statistics
Matches: 79, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
15 2 0.03
16 8 0.10
17 10 0.13
18 30 0.38
19 25 0.32
20 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTTAATATATTTAAAA
Found at i:20615442 original size:11 final size:11
Alignment explanation
Indices: 20615428--20615452 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20615418 TAAAAAAACC
20615428 AAAAGAAAAAG
1 AAAAGAAAAAG
20615439 AAAAGAAAAAG
1 AAAAGAAAAAG
20615450 AAA
1 AAA
20615453 GTTTAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:20622049 original size:13 final size:13
Alignment explanation
Indices: 20622033--20622065 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
20622023 ATGTTAAATT
20622033 AATAAATTTAAAA
1 AATAAATTTAAAA
20622046 AATAAATTTAAAA
1 AATAAATTTAAAA
20622059 AATAAAT
1 AATAAAT
20622066 ATCTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAAATTTAAAA
Found at i:20627316 original size:21 final size:22
Alignment explanation
Indices: 20627292--20627342 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
20627282 AATCTAAAGC
20627292 CTAGA-GCACAATCAACTATAG
1 CTAGACGCACAATCAACTATAG
*
20627313 CTAGAATCCTCACAATCAACTATAG
1 CTAG-A--CGCACAATCAACTATAG
20627338 CTAGA
1 CTAGA
20627343 ATCCTCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 1 0.04
24 1 0.04
25 19 0.76
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (22 bp):
CTAGACGCACAATCAACTATAG
Found at i:20627332 original size:25 final size:25
Alignment explanation
Indices: 20627298--20627358 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
20627288 AAGCCTAGAG
20627298 CACAATCAACTATAGCTAGAATCCT
1 CACAATCAACTATAGCTAGAATCCT
20627323 CACAATCAACTATAGCTAGAATCCT
1 CACAATCAACTATAGCTAGAATCCT
20627348 CACAATCAACT
1 CACAATCAACT
20627359 TGTCTCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.23
Consensus pattern (25 bp):
CACAATCAACTATAGCTAGAATCCT
Found at i:20630011 original size:3 final size:3
Alignment explanation
Indices: 20630003--20630029 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20629993 CCACTTTGAT
20630003 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
20630030 TCTGAATATG
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20631883 original size:4 final size:4
Alignment explanation
Indices: 20631874--20631898 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20631864 GAAGAAGAAG
20631874 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
20631899 CAAATCTGAA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:20637963 original size:18 final size:18
Alignment explanation
Indices: 20637933--20637971 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20637923 TTAAAACTTG
20637933 AAAAATGAATAATTA-AA
1 AAAAATGAATAATTATAA
*
20637950 AAAAATTAATTAATTATAA
1 AAAAATGAA-TAATTATAA
20637969 AAA
1 AAA
20637972 GTGTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAATGAATAATTATAA
Found at i:20647933 original size:20 final size:20
Alignment explanation
Indices: 20647904--20647971 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
20647894 AAAAATATAT
*
20647904 CAAATTTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
*
20647924 CAAATCTTCATTATCCG-ATTGCA
1 CAAATCTTCATAATCCGCA----A
*
20647947 CCAATCTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
20647967 CAAAT
1 CAAAT
20647972 TGATGCCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.03
20 20 0.53
23 16 0.42
24 1 0.03
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (20 bp):
CAAATCTTCATAATCCGCAA
Found at i:20652934 original size:21 final size:22
Alignment explanation
Indices: 20652908--20652949 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20652898 ATCCTAGTCA
20652908 AGATTTAC-TCTT-AACTTTTAC
1 AGATTT-CTTCTTAAACTTTTAC
20652929 AGATTTCTTCTTAAACTTTTA
1 AGATTTCTTCTTAAACTTTTA
20652950 TTCAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (22 bp):
AGATTTCTTCTTAAACTTTTAC
Found at i:20653725 original size:105 final size:105
Alignment explanation
Indices: 20653607--20653816 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
20653597 AACAAATTAA
20653607 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
1 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
20653672 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
66 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
*
20653712 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGTCT
1 ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
20653777 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
66 CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
20653817 GAGGTGAAGA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (105 bp):
ACCAATAATTACATTTAGTTATGAACATATATATATTATATTGATGTTAAATCATGGCATTGCCT
CTGTATAATGGTTTTAATATTATAAGTAAGGTTAATTTAT
Found at i:20653915 original size:43 final size:43
Alignment explanation
Indices: 20653854--20653940 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
20653844 TTCTGTTCAC
20653854 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
*
20653897 ATTCTCCATTGATTTTGTAGGATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
20653940 A
1 A
20653941 ATTACATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (43 bp):
ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
Found at i:20665709 original size:27 final size:25
Alignment explanation
Indices: 20665644--20665710 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
20665634 ATTTATTTAT
*
20665644 TATTTATAATGTTAATCATTTAAATA
1 TATTTATAAT-TTAATAATTTAAATA
20665670 TGATTTATTAATTTAATAATTTAAAACTA
1 T-ATTTA-TAATTTAATAATTT-AAA-TA
*
20665699 TATTTACAATTT
1 TATTTATAATTT
20665711 TAACAGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 12 0.34
29 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (25 bp):
TATTTATAATTTAATAATTTAAATA
Found at i:20668768 original size:13 final size:13
Alignment explanation
Indices: 20668750--20668774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20668740 AATAAATATC
20668750 ATTTTAATTTTTA
1 ATTTTAATTTTTA
20668763 ATTTTAATTTTT
1 ATTTTAATTTTT
20668775 CACTCCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:20669094 original size:65 final size:65
Alignment explanation
Indices: 20668985--20669107 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
20668975 TGTATTCTCC
* * * *
20668985 AACTGATCTAGTAGTCCCTCTACTGTTTCTAGGCAATTCTCAGCAATTTCGAGTTCTGCACTCTT
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
* *
20669050 AACTAATCTAATAGTCTCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGGGTTCTG
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTG
20669108 TGCCTTTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (65 bp):
AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
Found at i:20677981 original size:31 final size:31
Alignment explanation
Indices: 20677943--20678005 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
20677933 TACAGATTGT
20677943 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
20677974 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
20678005 A
1 A
20678006 TAATAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (31 bp):
AAATGGCAAAAGAATTGACCTTCCCTTGAGA
Found at i:20688808 original size:47 final size:49
Alignment explanation
Indices: 20688695--20688874 Score: 164
Period size: 47 Copynumber: 3.8 Consensus size: 49
20688685 TGTAACCCGC
* * * * * **
20688695 CCATAAGTGAACTCGGACTCAACTCAATGAGCTC--A-GGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
* *
20688741 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
*
20688791 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATT-CACAT
*
20688835 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
20688875 TCAACCATCC
Statistics
Matches: 110, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.05
45 1 0.01
46 33 0.30
47 57 0.52
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:20688863 original size:94 final size:93
Alignment explanation
Indices: 20688703--20688874 Score: 265
Period size: 94 Copynumber: 1.8 Consensus size: 93
20688693 GCCCATAAGT
* * **
20688703 GAACTCGGACTCAACTCAATGAGCTCAGGCGTTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAGTGAACTCAGACTCAACTCAA
20688768 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
20688796 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCCACATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATT-CACATCCATAAGTGAACTCAGACTCAACTC
20688860 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
20688875 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
92 2 0.03
93 27 0.38
94 42 0.59
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:20690178 original size:6 final size:6
Alignment explanation
Indices: 20690167--20690191 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20690157 ATATTACAAG
20690167 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
20690192 CGGTACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:20690236 original size:47 final size:47
Alignment explanation
Indices: 20690179--20690285 Score: 178
Period size: 47 Copynumber: 2.3 Consensus size: 47
20690169 CAGTAACAGT
* *
20690179 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATTCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* *
20690226 AACAGTAACAGTACGGTACACGGAGTACCTCATTGGAACAAATCCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
20690273 AACAGTAACAGTA
1 AACAGTAACAGTA
20690286 ATGGTAGCAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:20691407 original size:20 final size:18
Alignment explanation
Indices: 20691371--20691415 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
20691361 AAACCTTGAA
20691371 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
20691389 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
20691409 -TTTCCCT
1 TTTTCCCT
20691416 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:20691635 original size:16 final size:15
Alignment explanation
Indices: 20691603--20691637 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
20691593 TTTTTATTAT
*
20691603 ATAATATATTATTTA
1 ATAATATATTATATA
20691618 ATAATATACTTATATA
1 ATAATATA-TTATATA
20691634 ATAA
1 ATAA
20691638 GTAAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATATTATATA
Found at i:20711317 original size:74 final size:74
Alignment explanation
Indices: 20711196--20711340 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 74
20711186 CTTCAGTCAA
20711196 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
20711261 GTCATTCAG
66 GTCATTCAG
*
20711270 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
20711335 GTCATT
66 GTCATT
20711341 ATAAGGGTAC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (74 bp):
AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
GTCATTCAG
Found at i:20714415 original size:18 final size:18
Alignment explanation
Indices: 20714392--20714426 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20714382 TGTAATATCA
* *
20714392 ATTAATTTTTTTATTTTT
1 ATTAATTATTATATTTTT
20714410 ATTAATTATTATATTTT
1 ATTAATTATTATATTTT
20714427 AATTCCATAT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTAATTATTATATTTTT
Found at i:20720825 original size:19 final size:17
Alignment explanation
Indices: 20720803--20720838 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
20720793 ATGAAAATTT
20720803 AAAATTTATAAAATATTAA
1 AAAATTTA-AAAA-ATTAA
20720822 AAAATTTAAAAAATTAA
1 AAAATTTAAAAAATTAA
20720839 GATTAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTTAAAAAATTAA
Found at i:20720833 original size:10 final size:9
Alignment explanation
Indices: 20720803--20720836 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
20720793 ATGAAAATTT
*
20720803 AAAATTTAT
1 AAAATTTAA
20720812 AAAATATTAA
1 AAAAT-TTAA
20720822 AAAATTTAA
1 AAAATTTAA
20720831 AAAATT
1 AAAATT
20720837 AAGATTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTTAA
Found at i:20721170 original size:14 final size:16
Alignment explanation
Indices: 20721142--20721174 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
20721132 TTACGGTAAT
20721142 AAAAATATAATATTTA
1 AAAAATATAATATTTA
20721158 AAAAAT-TAA-ATTTA
1 AAAAATATAATATTTA
20721172 AAA
1 AAA
20721175 TTTTATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATAATATTTA
Found at i:20721516 original size:85 final size:85
Alignment explanation
Indices: 20721373--20721537 Score: 330
Period size: 85 Copynumber: 1.9 Consensus size: 85
20721363 CCAGAATCAA
20721373 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
1 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
20721438 ATTAGTCCCAAAAACGATTC
66 ATTAGTCCCAAAAACGATTC
20721458 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
1 TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
20721523 ATTAGTCCCAAAAAC
66 ATTAGTCCCAAAAAC
20721538 ACGAGGGCCA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (85 bp):
TGGTATGATAATGATAGCAGAAAGGAAATATAAATTGAATTAAAACAGCCATGAGTACGGACATT
ATTAGTCCCAAAAACGATTC
Found at i:20729569 original size:18 final size:19
Alignment explanation
Indices: 20729548--20729586 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20729538 ATTTTGGATT
*
20729548 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
20729566 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
20729585 TT
1 TT
20729587 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:20738007 original size:11 final size:11
Alignment explanation
Indices: 20737993--20738037 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
20737983 AGATAAATAT
20737993 TATTTTATTAA
1 TATTTTATTAA
*
20738004 TATTTTAATATGA
1 TATTTT-AT-TAA
*
20738017 TATTTTATTAT
1 TATTTTATTAA
20738028 TATTTTATTA
1 TATTTTATTA
20738038 GTTTATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:20738106 original size:3 final size:3
Alignment explanation
Indices: 20738098--20738131 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20738088 AACTAAAGTG
20738098 AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
20738132 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20739425 original size:62 final size:62
Alignment explanation
Indices: 20739358--20739492 Score: 252
Period size: 62 Copynumber: 2.2 Consensus size: 62
20739348 TCATTGTATG
20739358 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
*
20739420 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATCTCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
20739482 AAAATTCGATG
1 AAAATT-GATG
20739493 GATCTCTGAA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 67 0.94
63 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (62 bp):
AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
Found at i:20739867 original size:46 final size:46
Alignment explanation
Indices: 20739797--20740111 Score: 398
Period size: 46 Copynumber: 6.8 Consensus size: 46
20739787 GCTCTCTGAA
* * *
20739797 ATGAAATGTGTAAGACCATTGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
20739843 ATGAAATGTGTAAGACCAGGGTTGAAAGATGCCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * **
20739889 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGCCAATGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
20739935 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
20739981 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
20740027 ATGAAAAGAATAAGACCCTGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
20740073 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
20740112 TCAATGTCAA
Statistics
Matches: 240, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 239 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:20743076 original size:11 final size:11
Alignment explanation
Indices: 20743062--20743106 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
20743052 AGATAAATAT
20743062 TATTTTATTAA
1 TATTTTATTAA
*
20743073 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
20743086 TATTTTATTAT
1 TATTTTATTAA
20743097 TATTTTATTA
1 TATTTTATTA
20743107 GTATATGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:20744760 original size:21 final size:21
Alignment explanation
Indices: 20744736--20744807 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
20744726 CTCTCTGAAA
20744736 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
20744757 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
20744781 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
20744803 TGAAA
1 TGAAA
20744808 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:20744787 original size:46 final size:46
Alignment explanation
Indices: 20744735--20745095 Score: 474
Period size: 46 Copynumber: 7.8 Consensus size: 46
20744725 GCTCTCTGAA
** * * *
20744735 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
**
20744781 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** * *
20744827 ATGAAAAAAATAAGACCATGGTTGAGAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** *
20744873 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCTGA-GTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGC-AACGTGAC
20744919 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * *
20744965 ATGAAATGAATAAGATCATGGTTGAAAGAGACCATGACAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
20745011 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * * *
20745057 A-GAAAATGAGTAAGATCATAGTTGAAAGAAACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
20745096 TCAATGTCAA
Statistics
Matches: 279, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
45 2 0.01
46 276 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:20754597 original size:46 final size:46
Alignment explanation
Indices: 20754545--20754722 Score: 286
Period size: 46 Copynumber: 3.9 Consensus size: 46
20754535 GTGCTCTCTA
*
20754545 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
20754591 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
20754637 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* * * * *
20754683 ACA-GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20754723 TCATGTCAAA
Statistics
Matches: 125, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 33 0.26
46 92 0.74
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:20754743 original size:45 final size:45
Alignment explanation
Indices: 20754557--20754745 Score: 146
Period size: 46 Copynumber: 4.2 Consensus size: 45
20754547 ATGAAATGTG
* * * * * ***
20754557 TAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACA-GAAATAAA
* * * * ***
20754603 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACA-GAAATAAA
* * * *
20754649 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAAATAAA
* * *
20754694 TAAGACCATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAA
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAA-ATAAA
20754739 TAAGACC
1 TAAGACC
20754746 GTGGATGGGA
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 2 0.02
45 49 0.37
46 80 0.61
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAAATAAA
Found at i:20755964 original size:43 final size:41
Alignment explanation
Indices: 20755887--20755966 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
20755877 TGGTAGAATG
20755887 TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
1 TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
* * *
20755928 TACATGTTTAGAGTCATTGTTGTC-GGGCCACTCGGGGTG
1 TACATG-TT-GAGTCATCGTT-TCTGGGCAACCCGGGGTG
20755967 ACAAATCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 6 0.18
42 2 0.06
43 23 0.70
44 2 0.06
ACGTcount: A:0.16, C:0.19, G:0.33, T:0.33
Consensus pattern (41 bp):
TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
Found at i:20758591 original size:18 final size:18
Alignment explanation
Indices: 20758570--20758612 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20758560 GAACAATTAT
* * *
20758570 TTATTCAGTAACAGTCAG
1 TTATTCAGCAACAATCAA
*
20758588 TTATTCGGCAACAATCAA
1 TTATTCAGCAACAATCAA
20758606 TTATTCA
1 TTATTCA
20758613 ATAATAACTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATTCAGCAACAATCAA
Found at i:20758778 original size:18 final size:18
Alignment explanation
Indices: 20758655--20758819 Score: 113
Period size: 18 Copynumber: 9.2 Consensus size: 18
20758645 ATTGGCTATC
20758655 CAGTAACAGTCAATTATT
1 CAGTAACAGTCAATTATT
* *
20758673 TAGTAA-AATCAGA-TATT
1 CAGTAACAGTCA-ATTATT
* * *
20758690 CAGTAGCAATTAAGTTATT
1 CAGTAACAGTCAA-TTATT
* * *
20758709 CAGTGACAATCAGTTATT
1 CAGTAACAGTCAATTATT
* *
20758727 CAGTAA-TGATCATTTATT
1 CAGTAACAG-TCAATTATT
*
20758745 CAGTAATA-TCCAATTATT
1 CAGTAACAGT-CAATTATT
* *
20758763 CAGTAACAGTCTATTATC
1 CAGTAACAGTCAATTATT
** *
20758781 CAGTTTCGGTCAATTATT
1 CAGTAACAGTCAATTATT
*
20758799 CAGTAACAGTAAATTATT
1 CAGTAACAGTCAATTATT
20758817 CAG
1 CAG
20758820 AAATAATCAG
Statistics
Matches: 112, Mismatches: 27, Indels: 16
0.72 0.17 0.10
Matches are distributed among these distances:
17 14 0.12
18 84 0.75
19 14 0.12
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (18 bp):
CAGTAACAGTCAATTATT
Found at i:20758834 original size:36 final size:36
Alignment explanation
Indices: 20758655--20758834 Score: 134
Period size: 36 Copynumber: 5.0 Consensus size: 36
20758645 ATTGGCTATC
* *
20758655 CAGTAACAGTCAATTATTTAGTAA-AATCAGATATT
1 CAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
* * * * *
20758690 CAGTAGCAATTAAGTTATTCAGTGACAATCAGTTATT
1 CAGTAACAGTCAA-TTATTCAGTAATAATCAGTTATT
* * *
20758727 CAGTAA-TGATCATTTATTCAGTAAT-ATCCAATTATT
1 CAGTAACAG-TCAATTATTCAGTAATAAT-CAGTTATT
* * * ** *
20758763 CAGTAACAGTCTATTATCCAGT-TTCGGTCAATTATT
1 CAGTAACAGTCAATTATTCAGTAAT-AATCAGTTATT
* *
20758799 CAGTAACAGTAAATTATTCAGAAATAATCAGTTATT
1 CAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
20758835 TTATATATTT
Statistics
Matches: 109, Mismatches: 28, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
35 13 0.12
36 76 0.70
37 20 0.18
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (36 bp):
CAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
Found at i:20762479 original size:45 final size:44
Alignment explanation
Indices: 20762370--20762482 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 44
20762360 AAATTCTGAA
* * *
20762370 CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAA-TGTAACAGTATTCAACACACAAAGTGCCGAAT
* * * *
20762415 CAATAACGGTAAATATAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGT-AATGTAACAGTATTCAACACACAAAGTGCCGAAT
*
20762460 CGGTAACAGTAATGGTAACAGTA
1 CAGTAACAGTAAT-GTAACAGTA
20762483 ACAGTAGTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
44 3 0.05
45 50 0.91
46 2 0.04
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (44 bp):
CAGTAACAGTAATGTAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:20762485 original size:51 final size:48
Alignment explanation
Indices: 20762368--20762505 Score: 124
Period size: 45 Copynumber: 2.9 Consensus size: 48
20762358 ACAAATTCTG
* * * *
20762368 AACAGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATC
1 AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
*
20762416 -A-A-TAACGGTAA-ATATAACAGTATTCGACACACAAAGTGCCGAATC
1 AACAGTAACGGTAACA-GTAACAGTATTCGACACACAAAGTGCCGAATC
* * * *
20762461 GGTAACAGTAATGGTAACAGTAACAGTAGTCGGCACA-TAAGTGCC
1 ---AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCC
20762506 TAATGAGTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
44 1 0.01
45 36 0.50
46 1 0.01
47 1 0.01
49 1 0.01
50 8 0.11
51 23 0.32
52 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (48 bp):
AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
Found at i:20763443 original size:31 final size:32
Alignment explanation
Indices: 20763387--20763449 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
20763377 CACACTTGTC
*
20763387 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
20763419 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
20763450 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:20763594 original size:16 final size:15
Alignment explanation
Indices: 20763568--20763597 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20763558 ATTTATTTCA
20763568 TAATATAATTAATAT
1 TAATATAATTAATAT
20763583 TAATATTAATTAATA
1 TAATA-TAATTAATA
20763598 ATTATAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATAATTAATAT
Done.