Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 112 of 130
Found at i:21881904 original size:52 final size:52
Alignment explanation
Indices: 21881826--21881924 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
21881816 TCAAGCTCGC
*
21881826 CAGTCTCTTTACGTACGTAATGTATCAAAATTGTTATCAATATTTTTTTTTT
1 CAGTCTCTTCACGTACGTAATGTATCAAAATTGTTATCAATATTTTTTTTTT
21881878 CAGTCTCTTCACGTACGTAATGTATCAAAATTGTTATCAATATTTTT
1 CAGTCTCTTCACGTACGTAATGTATCAAAATTGTTATCAATATTTTT
21881925 GTTTAACTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (52 bp):
CAGTCTCTTCACGTACGTAATGTATCAAAATTGTTATCAATATTTTTTTTTT
Found at i:21889414 original size:60 final size:61
Alignment explanation
Indices: 21889332--21889454 Score: 212
Period size: 60 Copynumber: 2.0 Consensus size: 61
21889322 TACCATACTA
*
21889332 AAAAAAATTAGACACATATTTTGATCTTGTTTTAATGCTGAATTTCTAAACCATCGTATCCC
1 AAAAAAATTA-ACACATATTTTGATCTTGTTTTAAAGCTGAATTTCTAAACCATCGTATCCC
*
21889394 AAAAAAATT-ACACTTATTTTGATCTTGTTTTAAAGCTGAATTTCTAAACCATCGTATCCC
1 AAAAAAATTAACACATATTTTGATCTTGTTTTAAAGCTGAATTTCTAAACCATCGTATCCC
21889454 A
1 A
21889455 TACTAAAGAT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 50 0.85
62 9 0.15
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (61 bp):
AAAAAAATTAACACATATTTTGATCTTGTTTTAAAGCTGAATTTCTAAACCATCGTATCCC
Found at i:21893365 original size:14 final size:15
Alignment explanation
Indices: 21893342--21893379 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
21893332 ATTTAAATTA
21893342 GTTTAT-TTTTATAT
1 GTTTATATTTTATAT
21893356 -TTTATATTTTATAT
1 GTTTATATTTTATAT
21893370 GTTTAATATT
1 GTTT-ATATT
21893380 ATTTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 3 0.14
16 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
GTTTATATTTTATAT
Found at i:21893838 original size:27 final size:27
Alignment explanation
Indices: 21893791--21893843 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
21893781 TACATAAAAA
* *
21893791 TAATTTTAATAAATTTTAATAATTTAT
1 TAATTTTAATAAATATAAATAATTTAT
*
21893818 TAATTTT-ATAAATGATAAATATTTTA
1 TAATTTTAATAAAT-ATAAATAATTTA
21893844 AATTTTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATTTTAATAAATATAAATAATTTAT
Found at i:21893964 original size:21 final size:21
Alignment explanation
Indices: 21893940--21893988 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21893930 AATATATATT
*
21893940 TTAATTTCACAATTATAATAA
1 TTAATTTCACAACTATAATAA
* *
21893961 TTAATCTCATAACTATAATAA
1 TTAATTTCACAACTATAATAA
*
21893982 TAAATTT
1 TTAATTT
21893989 TTCCTCAACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAATTTCACAACTATAATAA
Found at i:21894235 original size:14 final size:16
Alignment explanation
Indices: 21894210--21894243 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
21894200 GTTGTGTACG
21894210 TGGTTTTGTCCTCGA-
1 TGGTTTTGTCCTCGAC
21894225 TGGTTTT-TCCTCGAC
1 TGGTTTTGTCCTCGAC
21894240 TGGT
1 TGGT
21894244 GAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.06, C:0.21, G:0.26, T:0.47
Consensus pattern (16 bp):
TGGTTTTGTCCTCGAC
Found at i:21894418 original size:20 final size:17
Alignment explanation
Indices: 21894393--21894434 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 17
21894383 ATAAATCAAA
21894393 TTATATATTTTTATTAATTT
1 TTATATA-TTTTA--AATTT
21894413 TTATATATTTTAAATTT
1 TTATATATTTTAAATTT
21894430 TTATA
1 TTATA
21894435 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
19 5 0.23
20 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTTTAAATTT
Found at i:21894499 original size:12 final size:13
Alignment explanation
Indices: 21894465--21894504 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
21894455 TAATTATTTA
21894465 AATATATTAAAAT
1 AATATATTAAAAT
*
21894478 -TTATATTAAAAT
1 AATATATTAAAAT
21894490 AATATA-TAAAA-
1 AATATATTAAAAT
21894501 AATA
1 AATA
21894505 AAAAACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATTAAAAT
Found at i:21900203 original size:13 final size:14
Alignment explanation
Indices: 21900187--21900218 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21900177 AAATAAATTT
21900187 ATTTTTTA-TTTAA
1 ATTTTTTACTTTAA
21900200 ATTTTTTACTTTAA
1 ATTTTTTACTTTAA
21900214 ATTTT
1 ATTTT
21900219 AAAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTACTTTAA
Found at i:21900374 original size:18 final size:17
Alignment explanation
Indices: 21900338--21900380 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
21900328 GTTTAGTAAA
*
21900338 TAAATTTATTTTTTGTT
1 TAAATTTTTTTTTTGTT
*
21900355 TAAATTTTTTATTTTTTT
1 TAAATTTTTT-TTTTGTT
21900373 TAAATTTT
1 TAAATTTT
21900381 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TAAATTTTTTTTTTGTT
Found at i:21900483 original size:35 final size:36
Alignment explanation
Indices: 21900404--21900488 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
21900394 AATATTATTT
* *
21900404 TTGTTATGAATAAACATGTTCGAACAAAAAATCATTA
1 TTGTT-TGAATAAACATGTTCAAACAAAAAATCATGA
* * * *
21900441 CTATTTGAATAAATATGTTTAAACAAAAAA-CATGA
1 TTGTTTGAATAAACATGTTCAAACAAAAAATCATGA
21900476 TTGTTTGAATAAA
1 TTGTTTGAATAAA
21900489 AAACATAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 15 0.38
36 22 0.55
37 3 0.08
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (36 bp):
TTGTTTGAATAAACATGTTCAAACAAAAAATCATGA
Found at i:21900489 original size:21 final size:21
Alignment explanation
Indices: 21900456--21900500 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21900446 TGAATAAATA
*
21900456 TGTTTAAACAAAAAACATGAT
1 TGTTTAAACAAAAAACATAAT
* *
21900477 TGTTTGAATAAAAAACATAAT
1 TGTTTAAACAAAAAACATAAT
21900498 TGT
1 TGT
21900501 CATGACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (21 bp):
TGTTTAAACAAAAAACATAAT
Found at i:21900691 original size:17 final size:18
Alignment explanation
Indices: 21900671--21900704 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21900661 ATTTGTTTTC
21900671 TTTCTT-AATTTTTCTAT
1 TTTCTTAAATTTTTCTAT
21900688 TTTCTTAAATTTTTCTA
1 TTTCTTAAATTTTTCTA
21900705 ACAATAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCTTAAATTTTTCTAT
Found at i:21909772 original size:19 final size:21
Alignment explanation
Indices: 21909742--21909780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
21909732 CACATATAAA
21909742 AATAATAAATTTA-AAATTTT
1 AATAATAAATTTATAAATTTT
21909762 AATAA-AAATTTATAAATTT
1 AATAATAAATTTATAAATTT
21909781 AACAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATAAATTTATAAATTTT
Found at i:21909787 original size:19 final size:19
Alignment explanation
Indices: 21909748--21909787 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21909738 TAAAAATAAT
*
21909748 AAATTTAAAATTTTAATAA
1 AAATTTAAAATTTTAACAA
21909767 AAATTTATAAA-TTTAACAA
1 AAATTTA-AAATTTTAACAA
21909786 AA
1 AA
21909788 TCAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTAAAATTTTAACAA
Found at i:21909843 original size:39 final size:42
Alignment explanation
Indices: 21909790--21909880 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 42
21909780 TAACAAAATC
* *
21909790 AAATAATATATTTT-ATATTTAAAATATTAATATA-AATATA
1 AAATAATATATTTTAATATTTAAAATAATAAAATATAATATA
21909830 AAATAAT-TATTTTAACAATATTTAAAATAATAAAATATAATATA
1 AAATAATATATTTT---AATATTTAAAATAATAAAATATAATATA
21909874 AATATAA
1 AA-ATAA
21909881 AAATTGTCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 6 0.14
40 7 0.16
43 18 0.42
44 8 0.19
45 4 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (42 bp):
AAATAATATATTTTAATATTTAAAATAATAAAATATAATATA
Found at i:21912656 original size:105 final size:105
Alignment explanation
Indices: 21912506--21912718 Score: 399
Period size: 105 Copynumber: 2.0 Consensus size: 105
21912496 TAGTATTTGA
*
21912506 TGATAATAAAAAAAAATTAACTCCCATCCGTAATTTATGTCATTGAATGAGTAAAAGTTTGAAAA
1 TGATAATAAAAAAAAATTAACTCCCATCCGTAATTTATGTCATTGAATGAGTAAAAGCTTGAAAA
21912571 TATATATGATTGATCTCAGCGGATAGTAGGATTGTTTGTG
66 TATATATGATTGATCTCAGCGGATAGTAGGATTGTTTGTG
*
21912611 TGATAATAAAAAAAATTTAACTCCCATCCGTAATTTATGTCATTGAATGAGTAAAAGCTTGAAAA
1 TGATAATAAAAAAAAATTAACTCCCATCCGTAATTTATGTCATTGAATGAGTAAAAGCTTGAAAA
*
21912676 TATATATGATTGATCTCAGCGGATGGTAGGATTGTTTGTG
66 TATATATGATTGATCTCAGCGGATAGTAGGATTGTTTGTG
21912716 TGA
1 TGA
21912719 CTATACAATA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (105 bp):
TGATAATAAAAAAAAATTAACTCCCATCCGTAATTTATGTCATTGAATGAGTAAAAGCTTGAAAA
TATATATGATTGATCTCAGCGGATAGTAGGATTGTTTGTG
Found at i:21925034 original size:16 final size:15
Alignment explanation
Indices: 21925010--21925045 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
21925000 GTTTGGTTTA
21925010 TTTTGTATATATAATT
1 TTTTGTATATA-AATT
*
21925026 TTTTTTATATAAATT
1 TTTTGTATATAAATT
21925041 TTTTG
1 TTTTG
21925046 AAAGTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTGTATATAAATT
Found at i:21926053 original size:21 final size:22
Alignment explanation
Indices: 21926018--21926082 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
21926008 AATAATTTAC
*
21926018 AAAATAAATATATAATATCTTT
1 AAAATAAATAAATAATATCTTT
**
21926040 AAAA-AAATAAATAAATAAATTT
1 AAAATAAATAAAT-AATATCTTT
21926062 AAAAGTATAATAAATAATATC
1 AAAA-TA-AATAAATAATATC
21926083 ATAAAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
24 5 0.15
25 7 0.21
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATAAATAAATAATATCTTT
Found at i:21926298 original size:15 final size:17
Alignment explanation
Indices: 21926278--21926318 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
21926268 TTTTTGTTTG
21926278 AAAAAATAAA-A-TATA
1 AAAAAATAAATATTATA
21926293 AAAAAATAAATTATTATA
1 AAAAAATAAA-TATTATA
21926311 AAAAAATA
1 AAAAAATA
21926319 GAAAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.43
17 1 0.04
18 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATAAATATTATA
Found at i:21946867 original size:2 final size:2
Alignment explanation
Indices: 21946862--21946904 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
21946852 TCTCTCTCTC
* *
21946862 TA TA TA TA TA TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21946904 T
1 T
21946905 CACCTTCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21956006 original size:22 final size:22
Alignment explanation
Indices: 21955981--21956024 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21955971 TGTATATTTA
*
21955981 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
21956003 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
21956025 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:21960145 original size:22 final size:22
Alignment explanation
Indices: 21960119--21960161 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21960109 TGTATATTTA
*
21960119 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
21960141 TATTTGTATCCCTAGAATTAA
1 TATTTGTATCCCTAGAATTAA
21960162 AGACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:21960350 original size:24 final size:24
Alignment explanation
Indices: 21960301--21960351 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
21960291 AATATACATT
21960301 CAGTTTTACTCTTAGTTTTTCACA
1 CAGTTTTACTCTTAGTTTTTCACA
*
21960325 CAGTTTTATTTCTTAGTTTTTC-CA
1 CAGTTTTA-CTCTTAGTTTTTCACA
21960349 CAG
1 CAG
21960352 GCATGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (24 bp):
CAGTTTTACTCTTAGTTTTTCACA
Found at i:21971874 original size:34 final size:35
Alignment explanation
Indices: 21971836--21971905 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
21971826 CGTCTGTCGA
21971836 TGTTGCACCAGCCA-TCCCGTCGATCAAACCAGTT
1 TGTTGCACCAGCCATTCCCGTCGATCAAACCAGTT
* * * * *
21971870 TGTTGCGCCTGCCATTGCCGTCGATCAGATCAGTT
1 TGTTGCACCAGCCATTCCCGTCGATCAAACCAGTT
21971905 T
1 T
21971906 ACACCAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (35 bp):
TGTTGCACCAGCCATTCCCGTCGATCAAACCAGTT
Found at i:21975561 original size:13 final size:13
Alignment explanation
Indices: 21975543--21975567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21975533 TCGGCATACT
21975543 TGAAATATATATG
1 TGAAATATATATG
21975556 TGAAATATATAT
1 TGAAATATATAT
21975568 TTACCCTACA
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TGAAATATATATG
Found at i:21983258 original size:16 final size:15
Alignment explanation
Indices: 21983235--21983278 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
21983225 AACTTTTTAT
*
21983235 ATTTTATTTTTTAAA
1 ATTTTATTTTTAAAA
* *
21983250 ATATTTATTATAAAAA
1 AT-TTTATTTTTAAAA
21983266 ATTTTATTTTTAA
1 ATTTTATTTTTAA
21983279 TGGAATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTATTTTTAAAA
Found at i:21983946 original size:10 final size:9
Alignment explanation
Indices: 21983928--21983962 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
21983918 TGAATTTGAA
21983928 TTTTTTTTC
1 TTTTTTTTC
21983937 TTTTTCTTTC
1 TTTTT-TTTC
21983947 TTTTTTTT-
1 TTTTTTTTC
21983955 TTTTTTTT
1 TTTTTTTT
21983963 AGTTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 8 0.32
10 9 0.36
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:21985357 original size:15 final size:16
Alignment explanation
Indices: 21985334--21985374 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
21985324 ATTATATATA
21985334 AATATAATATTTTATT
1 AATATAATATTTTATT
*
21985350 AA-ATAATACTTTATT
1 AATATAATATTTTATT
21985365 AATATAATAT
1 AATATAATAT
21985375 ATATAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATAATATTTTATT
Found at i:21985598 original size:17 final size:18
Alignment explanation
Indices: 21985578--21985611 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21985568 TTATAGACTC
21985578 TATTTT-TTAAAAAAAAT
1 TATTTTATTAAAAAAAAT
21985595 TATTTTATTAAAAAAAA
1 TATTTTATTAAAAAAAA
21985612 AGAGAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTTTATTAAAAAAAAT
Found at i:21986096 original size:22 final size:22
Alignment explanation
Indices: 21986071--21986141 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
21986061 ATTGAAATAA
21986071 AATATTAAATAATAATTTTATT
1 AATATTAAATAATAATTTTATT
* *
21986093 AATA-TAATATATATAATTTAATA
1 AATATTAA-ATA-ATAATTTTATT
* *
21986116 AATAATCAAAT-AT-ATTTTTTT
1 AAT-ATTAAATAATAATTTTATT
21986137 AATAT
1 AATAT
21986142 AATTGAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 2 0.05
21 11 0.28
22 9 0.23
23 12 0.31
24 3 0.08
25 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTAAATAATAATTTTATT
Found at i:21986096 original size:27 final size:28
Alignment explanation
Indices: 21986048--21986104 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
21986038 AATTATGCAA
21986048 AAATATAATTTTTATTGAAATAAAATATT
1 AAATATAATTTTTATT-AAATAAAATATT
*
21986077 AAATAATAA-TTTTATTAATATAATATAT
1 AAAT-ATAATTTTTATTAA-ATAAAATAT
21986105 ATAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 19 0.76
30 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATATAATTTTTATTAAATAAAATATT
Found at i:21986109 original size:23 final size:24
Alignment explanation
Indices: 21986077--21986144 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 24
21986067 ATAAAATATT
21986077 AAATAATAATTTTATTAATATAAT-
1 AAAT-ATAATTTTATTAATATAATC
* *
21986101 ATATATAA-TTTAATAA-ATAATC
1 AAATATAATTTTATTAATATAATC
*
21986123 AAATAT-ATTTTTTTAATATAAT
1 AAATATAATTTTATTAATATAAT
21986145 TGAAATAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
21 6 0.17
22 18 0.50
23 9 0.25
24 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATAATTTTATTAATATAATC
Found at i:21986687 original size:13 final size:13
Alignment explanation
Indices: 21986669--21986693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21986659 AAAACAAATT
21986669 AAAAAATAAAAAC
1 AAAAAATAAAAAC
21986682 AAAAAATAAAAA
1 AAAAAATAAAAA
21986694 ATTTTAAAAT
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:0.88, C:0.04, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:21988877 original size:135 final size:132
Alignment explanation
Indices: 21988677--21989155 Score: 482
Period size: 135 Copynumber: 3.6 Consensus size: 132
21988667 ACTTTATAAC
* * * *
21988677 TTAATTAAATATTTTTTAATATTTTATACAATAATCAAAATAATTGTTACAAAATCTCTACAATA
1 TTAATTAAATGTTTCTTAATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATA
* *
21988742 TTCATAACGATAAAAAAAAAAATCATTATGAAATCTTATCATATTTGCAATAACTTTTTATAGTC
66 TTCATAAC-A-AAAAAAAAAAATCATT-TGAAATCTTATTAGATTTGCAATAACTTTTTATAGTC
21988807 ATTGT
128 ATTGT
* *
21988812 TTAATTAAATGTTTCTTAATATTTTATACAACAATCAAAATAATTATTACGAAATCTCTATAATA
1 TTAATTAAATGTTTCTTAATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATA
* * * ** *
21988877 TTCATAACAATAAAAAAATATC-GTTGCAAAATCTTATTAGATTTATAATAGCTTTTTATAGTCA
66 TTCATAACAAAAAAAAAAAATCATTTG--AAATCTTATTAGATTTGCAATAACTTTTTATAGTCA
21988941 TT-T
129 TTGT
* * *** * * * *
21988944 TGTAATTAATTTTTTAAAAAATATTTTATACAACAATTAAAATAGTCGTTACAAAATCTCTATAT
1 T-TAATTAAATGTTT-CTTAATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAA
* * * * * *
21989009 TATTCGTAAC--AACAAAAAAGTCATTTGAAAATTTTATTAGATTTGCAACAA-TTTTTATAATC
64 TATTCATAACAAAAAAAAAAAATCATTTG-AAATCTTATTAGATTTGCAATAACTTTTTATAGTC
21989071 ATTGT
128 ATTGT
* * * ** * ** * * *
21989076 CTCATTAAATGTTTCTTAATATTTTATACTATGATCAAAATAGTTGTTATGAAATTTCTATATTT
1 TTAATTAAATGTTTCTTAATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATA
*
21989141 TTAATAACAAAAAAA
66 TTCATAACAAAAAAA
21989156 TATATTAAGT
Statistics
Matches: 280, Mismatches: 56, Indels: 19
0.79 0.16 0.05
Matches are distributed among these distances:
130 45 0.16
131 25 0.09
132 35 0.12
133 58 0.21
134 50 0.18
135 67 0.24
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (132 bp):
TTAATTAAATGTTTCTTAATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATA
TTCATAACAAAAAAAAAAAATCATTTGAAATCTTATTAGATTTGCAATAACTTTTTATAGTCATT
GT
Found at i:21989003 original size:134 final size:131
Alignment explanation
Indices: 21988694--21989155 Score: 428
Period size: 133 Copynumber: 3.5 Consensus size: 131
21988684 AATATTTTTT
* *
21988694 AATATTTTATACAATAATCAAAATAATTGTTACAAAATCTCTACAATATTCATAACGATAAAAAA
1 AATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATATTCATAAC-A-AAAAAA
* * * *
21988759 AAAAATCATT-ATGAAATCTTATCATATTTGCAATAACTTTTTATAGTCATTGTTTAATTAAATG
64 AAATATC-TTGA--AAATCTTATTAGATTTACAATAACTTTTTATAGTCATTGTTTAATTAAATG
***
21988823 TTTCTT
126 TTTAAA
* * *
21988829 AATATTTTATACAACAATCAAAATAATTATTACGAAATCTCTATAATATTCATAACAATAAAAAA
1 AATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATATTCATAACAAAAAAAAA
* * * *
21988894 ATATCGTTGCAAAATCTTATTAGATTTATAATAGCTTTTTATAGTCATT-TTGTAATTAATTTTT
66 ATATC-TTG-AAAATCTTATTAGATTTACAATAACTTTTTATAGTCATTGTT-TAATTAAATGTT
21988958 TAAAA
128 T-AAA
* * * * * *
21988963 AATATTTTATACAACAATTAAAATAGTCGTTACAAAATCTCTATATTATTCGTAACAACAAAAAA
1 AATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATATTCATAACAAAAAAAAA
* * * * * * * *
21989028 GTCAT-TTGAAAATTTTATTAGATTTGCAACAA-TTTTTATAATCATTGTCTCATTAAATGTTTC
66 AT-ATCTTGAAAATCTTATTAGATTTACAATAACTTTTTATAGTCATTGTTTAATTAAATGTTTA
**
21989091 TT
130 AA
* ** * ** * * * *
21989093 AATATTTTATACTATGATCAAAATAGTTGTTATGAAATTTCTATATTTTTAATAACAAAAAAA
1 AATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATATTCATAACAAAAAAA
21989156 TATATTAAGT
Statistics
Matches: 270, Mismatches: 51, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
130 51 0.19
131 23 0.09
132 22 0.08
133 60 0.22
134 59 0.22
135 55 0.20
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (131 bp):
AATATTTTATACAACAATCAAAATAATTGTTACAAAATCTCTATAATATTCATAACAAAAAAAAA
ATATCTTGAAAATCTTATTAGATTTACAATAACTTTTTATAGTCATTGTTTAATTAAATGTTTAA
A
Found at i:21991221 original size:26 final size:25
Alignment explanation
Indices: 21991192--21991246 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
21991182 GTGCTTTCTA
*
21991192 ATATGTAAGTGGTTCTTGTCCCCAAG
1 ATAT-TAAGTGGTCCTTGTCCCCAAG
* *
21991218 ATA-TAAGTGGTCCTTGTTCCCTAG
1 ATATTAAGTGGTCCTTGTCCCCAAG
21991242 ATATT
1 ATATT
21991247 GCCTAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 21 0.84
25 1 0.04
26 3 0.12
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (25 bp):
ATATTAAGTGGTCCTTGTCCCCAAG
Found at i:21991226 original size:24 final size:24
Alignment explanation
Indices: 21991197--21991245 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
21991187 TTCTAATATG
*
21991197 TAAGTGGTTCTTGTCCCCAAGATA
1 TAAGTGGTCCTTGTCCCCAAGATA
* *
21991221 TAAGTGGTCCTTGTTCCCTAGATA
1 TAAGTGGTCCTTGTCCCCAAGATA
21991245 T
1 T
21991246 TGCCTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (24 bp):
TAAGTGGTCCTTGTCCCCAAGATA
Found at i:22002463 original size:29 final size:29
Alignment explanation
Indices: 22002421--22002479 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
22002411 TGATGACACA
22002421 AATATTAAGTGATCTATCAACATAAGCAG
1 AATATTAAGTGATCTATCAACATAAGCAG
22002450 AATATTAAGTGATCTATCAACATAAGCAG
1 AATATTAAGTGATCTATCAACATAAGCAG
22002479 A
1 A
22002480 CTTACATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (29 bp):
AATATTAAGTGATCTATCAACATAAGCAG
Found at i:22010167 original size:6 final size:6
Alignment explanation
Indices: 22010156--22010185 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
22010146 ATTATTCATG
*
22010156 CTCGAA CTCGAA CTCGAA CTCGGA CTCGAA
1 CTCGAA CTCGAA CTCGAA CTCGAA CTCGAA
22010186 ATATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (6 bp):
CTCGAA
Found at i:22011191 original size:19 final size:18
Alignment explanation
Indices: 22011158--22011195 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
22011148 GTGATTTATA
22011158 ATTTTTATATAATTTTTT
1 ATTTTTATATAATTTTTT
*
22011176 ATTTTATATGTAATTTTTT
1 ATTTT-TATATAATTTTTT
22011195 A
1 A
22011196 AATTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTATATAATTTTTT
Found at i:22011200 original size:21 final size:20
Alignment explanation
Indices: 22011152--22011200 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
22011142 TACGTAGTGA
22011152 TTTATAATTTTTATATAATTT
1 TTTA-AATTTTTATATAATTT
*
22011173 TTT--ATTTTATATGTAATTT
1 TTTAAATTTT-TATATAATTT
22011192 TTTAAATTT
1 TTTAAATTT
22011201 ATTTATTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
21 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAAATTTTTATATAATTT
Found at i:22011623 original size:30 final size:30
Alignment explanation
Indices: 22011535--22011623 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 30
22011525 TTAAATAAAA
* * **
22011535 TTTTAATTTACACACAAATAATTTTTTAAC
1 TTTTAATTTATATACAAATAAACTTTTAAC
* * *
22011565 TTTTAATTTCTAT-CAAAT-AAGTCATTAAC
1 TTTTAATTTATATACAAATAAACT-TTTAAC
*
22011594 TTTTAATTTATATATAAATAAACTTTTAAC
1 TTTTAATTTATATACAAATAAACTTTTAAC
22011624 ATAAATTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 2 0.04
29 22 0.48
30 19 0.41
31 3 0.07
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTTAATTTATATACAAATAAACTTTTAAC
Found at i:22013151 original size:2 final size:2
Alignment explanation
Indices: 22013146--22013174 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22013136 CGCGCTAGAC
22013146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22013175 TATTTATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22013316 original size:19 final size:19
Alignment explanation
Indices: 22013294--22013330 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22013284 TAATGAATAA
* *
22013294 ATAAATTTTAATTAATTTT
1 ATAAATATTAAATAATTTT
22013313 ATAAATATTAAATAATTT
1 ATAAATATTAAATAATTT
22013331 AAAACTTTTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAATATTAAATAATTTT
Found at i:22021643 original size:2 final size:2
Alignment explanation
Indices: 22021636--22021663 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22021626 ATCAAATGAA
22021636 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
22021664 GTGTTGTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22027022 original size:34 final size:35
Alignment explanation
Indices: 22026962--22027027 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
22026952 ACACTGATGA
* * *
22026962 TACTCTAGCATATGTTTAAGTTATCATGAGACTAC
1 TACTCCAGCATATGTTTAAGTGATCATAAGACTAC
22026997 TACTCCAGCATATG-TTAAGTGATCATAAGAC
1 TACTCCAGCATATGTTTAAGTGATCATAAGAC
22027028 AGATCAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (35 bp):
TACTCCAGCATATGTTTAAGTGATCATAAGACTAC
Found at i:22035034 original size:14 final size:14
Alignment explanation
Indices: 22035008--22035065 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
22034998 ACCCTCCTTT
22035008 CTTTTATATTTTTTA
1 CTTTTA-ATTTTTTA
22035023 CTTTTAATTTTTTA
1 CTTTTAATTTTTTA
* *
22035037 -TTTAAAAGTTTTTA
1 CTTT-TAATTTTTTA
*
22035051 CAATTTAATTTTTTA
1 C-TTTTAATTTTTTA
22035066 ATAAATCGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 16 0.46
15 14 0.40
16 2 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (14 bp):
CTTTTAATTTTTTA
Found at i:22035070 original size:28 final size:28
Alignment explanation
Indices: 22035017--22035070 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
22035007 TCTTTTATAT
* *
22035017 TTTTTACTTTTAATTTTTTATTTAAAAG
1 TTTTTACATTTAATTTTTTATATAAAAG
22035045 TTTTTACAATTTAATTTTTTA-ATAAA
1 TTTTTAC-ATTTAATTTTTTATATAAA
22035071 TCGAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTACATTTAATTTTTTATATAAAAG
Found at i:22035155 original size:17 final size:19
Alignment explanation
Indices: 22035103--22035161 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
22035093 CTTGATATAA
*
22035103 AAATAATTTAATACAT-TTT
1 AAATAATTTTATA-ATATTT
*
22035122 CAATAATTTTATAATA-TT
1 AAATAATTTTATAATATTT
*
22035140 AAATAA-TTTATTATATTT
1 AAATAATTTTATAATATTT
22035158 AAAT
1 AAAT
22035162 TTTAATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.24
18 15 0.44
19 11 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATTTTATAATATTT
Found at i:22039894 original size:21 final size:21
Alignment explanation
Indices: 22039870--22039918 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
22039860 TAAAATTTTT
*
22039870 TTAT-TATTTTTTATTATTTAA
1 TTATATATATTTTA-TATTTAA
22039891 TTATATATATTTTATATTTACA
1 TTATATATATTTTATATTTA-A
22039913 TT-TATA
1 TTATATA
22039919 AAATAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATATATTTTATATTTAA
Found at i:22039995 original size:17 final size:19
Alignment explanation
Indices: 22039918--22039992 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
22039908 TTACATTTAT
*
22039918 AAAATAACATTTTATATCTTAA
1 AAAATAATATTTTATA--TT-A
22039940 AAAATAATATTTTATATTA
1 AAAATAATATTTTATATTA
22039959 AAAATAATATTTTATATTA
1 AAAATAATATTTTATATTA
22039978 AAAATAATATTTTAT
1 AAAATAATATTTTAT
22039993 TAATTTCTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 35 0.67
20 2 0.04
22 15 0.29
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATAATATTTTATATTA
Found at i:22045998 original size:2 final size:2
Alignment explanation
Indices: 22045991--22046023 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22045981 TCACAAGGAA
22045991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22046024 AAACATACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22046200 original size:2 final size:2
Alignment explanation
Indices: 22046193--22046227 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22046183 ATCCCTACAA
22046193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22046228 ATCAAAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22051938 original size:122 final size:122
Alignment explanation
Indices: 22051780--22052019 Score: 453
Period size: 122 Copynumber: 2.0 Consensus size: 122
22051770 AGACAATTTA
* *
22051780 TTCATTTAACTGTTTTCTATGTTCTTTTTAACTTCATTCAGCCAATATAAGAAATCAGAGACCTA
1 TTCATTTAACTGTTTTCCAAGTTCTTTTTAACTTCATTCAGCCAATATAAGAAATCAGAGACCTA
*
22051845 AGAAGATGAAGATCACCTTCCAGGGGAAGAAAGTCGATTTATGTGTTATACAACTTG
66 AGAAGATGAAGATCACCTTCCAGGGGAAAAAAGTCGATTTATGTGTTATACAACTTG
22051902 TTCATTTAACTGTTTTCCAAGTTCTTTTTAACTTCATTCAGCCAATATAAGAAATCAGAGACCTA
1 TTCATTTAACTGTTTTCCAAGTTCTTTTTAACTTCATTCAGCCAATATAAGAAATCAGAGACCTA
22051967 AGAAGATGAAGATCACCTTCCAGGGGAAAAAAGTCGATTTATGTGTTATACAA
66 AGAAGATGAAGATCACCTTCCAGGGGAAAAAAGTCGATTTATGTGTTATACAA
22052020 TGATTTCCTG
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 115 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (122 bp):
TTCATTTAACTGTTTTCCAAGTTCTTTTTAACTTCATTCAGCCAATATAAGAAATCAGAGACCTA
AGAAGATGAAGATCACCTTCCAGGGGAAAAAAGTCGATTTATGTGTTATACAACTTG
Found at i:22053206 original size:3 final size:3
Alignment explanation
Indices: 22053198--22053238 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
22053188 AGAAAGGAAT
*
22053198 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22053239 TTATTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:22054069 original size:3 final size:3
Alignment explanation
Indices: 22054061--22054090 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
22054051 ATTAAATTAA
*
22054061 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22054091 TTTAAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:22054545 original size:18 final size:18
Alignment explanation
Indices: 22054524--22054605 Score: 53
Period size: 18 Copynumber: 4.7 Consensus size: 18
22054514 TAATATTTAT
22054524 AAAATTAATAAATAATTA
1 AAAATTAATAAATAATTA
* * * *
22054542 AAAAATATTAAATTATTT
1 AAAATTAATAAATAATTA
* **
22054560 TATGTTAA-ATAATAATT-
1 AAAATTAATA-AATAATTA
**
22054577 TTA-TTAATAAATAATTA
1 AAAATTAATAAATAATTA
22054594 AAAATTAATAAA
1 AAAATTAATAAA
22054606 AATAATAGTA
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
16 11 0.24
17 4 0.09
18 31 0.67
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
AAAATTAATAAATAATTA
Found at i:22054753 original size:7 final size:7
Alignment explanation
Indices: 22054741--22054779 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
22054731 AAAGAATAAA
22054741 ATTTATT
1 ATTTATT
22054748 ATTTATT
1 ATTTATT
*
22054755 AGTTCATT
1 A-TTTATT
22054763 ATTTATT
1 ATTTATT
22054770 AATTTATT
1 -ATTTATT
22054778 AT
1 AT
22054780 ATAATAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (7 bp):
ATTTATT
Found at i:22054778 original size:15 final size:15
Alignment explanation
Indices: 22054740--22054779 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
22054730 AAAAGAATAA
22054740 AATTTATTATTTATT
1 AATTTATTATTTATT
* *
22054755 AGTTCATTATTTATT
1 AATTTATTATTTATT
22054770 AATTTATTAT
1 AATTTATTAT
22054780 ATAATAGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
AATTTATTATTTATT
Found at i:22055245 original size:26 final size:27
Alignment explanation
Indices: 22055202--22055254 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
22055192 TATAATTAAA
22055202 AAATAAATTTGATAAAAAATT-ATATT
1 AAATAAATTTGATAAAAAATTAATATT
** *
22055228 AAATAAATTTTTTTAAAAATTAATATT
1 AAATAAATTTGATAAAAAATTAATATT
22055255 TGAATTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AAATAAATTTGATAAAAAATTAATATT
Found at i:22056218 original size:26 final size:25
Alignment explanation
Indices: 22056167--22056219 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
22056157 ATATTAATTA
* * *
22056167 AATATTTAAAATTTATTTTTATATT
1 AATATTTAAAATATATTTTAAGATT
22056192 AATATTTTAAAATATATTTTAAGATT
1 AATA-TTTAAAATATATTTTAAGATT
22056218 AA
1 AA
22056220 AAAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATTTAAAATATATTTTAAGATT
Found at i:22061913 original size:3 final size:3
Alignment explanation
Indices: 22061905--22061932 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
22061895 GGCAACTCAG
22061905 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22061933 GAAAAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22069484 original size:25 final size:24
Alignment explanation
Indices: 22069433--22069499 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
22069423 CAAGATAATA
* *
22069433 ATTTTTAATTATTTATTAATATTT
1 ATTTATAAATATTTATTAATATTT
*
22069457 ATTTATAAATATTTTTTAAATATTT
1 ATTTATAAATATTTATT-AATATTT
*
22069482 ATTTATAAAAATATTATT
1 ATTTATAAATAT-TTATT
22069500 TGATATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 14 0.39
25 18 0.50
26 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTATAAATATTTATTAATATTT
Found at i:22074291 original size:3 final size:3
Alignment explanation
Indices: 22074283--22074311 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
22074273 GAGGTTGATG
22074283 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
22074312 ATCCTCCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:22076542 original size:21 final size:21
Alignment explanation
Indices: 22076518--22076558 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22076508 TTTTTTTAAT
*
22076518 TTATCAAA-ATAAATTCAAATA
1 TTAT-AAATATAAAATCAAATA
22076539 TTATAAATATAAAATCAAAT
1 TTATAAATATAAAATCAAAT
22076559 CAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
TTATAAATATAAAATCAAATA
Found at i:22076578 original size:26 final size:26
Alignment explanation
Indices: 22076523--22076571 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
22076513 TTAATTTATC
22076523 AAAATAAATTCAAATATTATAAATAT
1 AAAATAAATTCAAATATTATAAATAT
22076549 AAAATCAAA-TCAAAT-TTA-AAATA
1 AAAAT-AAATTCAAATATTATAAATA
22076572 AATAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 3 0.14
26 11 0.50
27 3 0.14
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAATAAATTCAAATATTATAAATAT
Found at i:22077837 original size:14 final size:14
Alignment explanation
Indices: 22077820--22077846 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22077810 TAAATTTTGA
22077820 ATATATATTTTTAG
1 ATATATATTTTTAG
22077834 ATATATATTTTTA
1 ATATATATTTTTA
22077847 ATAAAAATAT
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:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
ATATATATTTTTAG
Found at i:22077904 original size:27 final size:28
Alignment explanation
Indices: 22077851--22077908 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
22077841 TTTTTAATAA
* *
22077851 AAATATTAATTAAATTTTATTATTAAAT
1 AAATATCAATTAAATTTAATTATTAAAT
22077879 AAATATCAA-TAAATTTAAATTA-TAAAT
1 AAATATCAATTAAATTT-AATTATTAAAT
22077906 AAA
1 AAA
22077909 ATTTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATATCAATTAAATTTAATTATTAAAT
Found at i:22077910 original size:28 final size:29
Alignment explanation
Indices: 22077850--22077910 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
22077840 ATTTTTAATA
* *
22077850 AAAATATTAATTAAATTTTATTATTAAAT
1 AAAATATCAATTAAATTTAATTATTAAAT
22077879 -AAATATCAA-TAAATTTAAATTA-TAAAT
1 AAAATATCAATTAAATTT-AATTATTAAAT
22077906 AAAAT
1 AAAAT
22077911 TTTTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATATCAATTAAATTTAATTATTAAAT
Found at i:22079236 original size:17 final size:17
Alignment explanation
Indices: 22079214--22079246 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22079204 TAATGAATTG
22079214 ATGAACTATAAGCAAAT
1 ATGAACTATAAGCAAAT
*
22079231 ATGAACTATAATCAAA
1 ATGAACTATAAGCAAA
22079247 ATAAAGAGAT
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:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (17 bp):
ATGAACTATAAGCAAAT
Found at i:22084944 original size:22 final size:21
Alignment explanation
Indices: 22084894--22084949 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
22084884 GTCGCATTTC
*
22084894 CTTTATTAATAACTTTTAAAG
1 CTTTATTAATAAATTTTAAAG
* *
22084915 ATTCATTATATAAATTTTATAA-
1 CTTTATTA-ATAAATTTTA-AAG
22084937 CTTTATTAATAAA
1 CTTTATTAATAAA
22084950 GAATATGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 11 0.39
22 15 0.54
23 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
CTTTATTAATAAATTTTAAAG
Found at i:22089081 original size:16 final size:13
Alignment explanation
Indices: 22089056--22089100 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 13
22089046 TCAAAATGTT
22089056 AATTTTTAAAGTTA
1 AATTTTTAAA-TTA
22089070 AATTAATTTAAATTTA
1 AATT--TTTAAA-TTA
22089086 AATTTTTAAATTA
1 AATTTTTAAATTA
22089099 AA
1 AA
22089101 AAATTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.18
14 10 0.36
16 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
AATTTTTAAATTA
Found at i:22090822 original size:90 final size:90
Alignment explanation
Indices: 22090669--22090848 Score: 342
Period size: 90 Copynumber: 2.0 Consensus size: 90
22090659 AATCTTTCGT
* *
22090669 GGCATTTTAAATTCTGTATTAAAAAATAAAACTCACACAAACCCATACACACATACAGGGAGAGA
1 GGCATTTTAAATTCTGCATTAAAAAATAAAACTCACACAAACCCATACACACATACAAGGAGAGA
22090734 ATGCACATACGTACCACTGAGACTA
66 ATGCACATACGTACCACTGAGACTA
22090759 GGCATTTTAAATTCTGCATTAAAAAATAAAACTCACACAAACCCATACACACATACAAGGAGAGA
1 GGCATTTTAAATTCTGCATTAAAAAATAAAACTCACACAAACCCATACACACATACAAGGAGAGA
22090824 ATGCACATACGTACCACTGAGACTA
66 ATGCACATACGTACCACTGAGACTA
22090849 AGTTATGATT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.21
Consensus pattern (90 bp):
GGCATTTTAAATTCTGCATTAAAAAATAAAACTCACACAAACCCATACACACATACAAGGAGAGA
ATGCACATACGTACCACTGAGACTA
Found at i:22099307 original size:49 final size:53
Alignment explanation
Indices: 22099253--22099363 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 53
22099243 ATTATTAATA
*
22099253 ATTTTTTTAATAA-AT-TAT-TAAGGATGTA-TGATATTAAAATAATTTTTAT
1 ATTTTTTTAATAATATATATGTAAGAATGTATTGATATTAAAATAATTTTTAT
* * *
22099302 GTTTTTATAATAATATATATGAGTAAGAATGTATTTATATTAAAATAATTTTTAT
1 ATTTTTTTAATAATATATAT--GTAAGAATGTATTGATATTAAAATAATTTTTAT
22099357 ATTTTTT
1 ATTTTTT
22099364 AATTCTTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
49 11 0.22
50 2 0.04
51 3 0.06
54 9 0.18
55 25 0.50
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (53 bp):
ATTTTTTTAATAATATATATGTAAGAATGTATTGATATTAAAATAATTTTTAT
Found at i:22102880 original size:28 final size:27
Alignment explanation
Indices: 22102849--22102902 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
22102839 TAGTAAAATG
22102849 AAGCACATAAAAATAAAATGAAGCAAGC
1 AAGCACATAAAAA-AAAATGAAGCAAGC
* * *
22102877 AAGCACATTATAAAAAATGAATCAAG
1 AAGCACATAAAAAAAAATGAAGCAAG
22102903 AATCTTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (27 bp):
AAGCACATAAAAAAAAATGAAGCAAGC
Found at i:22104142 original size:16 final size:16
Alignment explanation
Indices: 22104102--22104144 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
22104092 TTTAATTTTT
* *
22104102 TATTTATATATTTATA
1 TATTTATATTTTTAAA
* *
22104118 TAATGATATTTTTAAA
1 TATTTATATTTTTAAA
22104134 TATTTATATTT
1 TATTTATATTT
22104145 CAAAAATAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTATATTTTTAAA
Found at i:22104162 original size:21 final size:21
Alignment explanation
Indices: 22104132--22104192 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
22104122 GATATTTTTA
22104132 AATA-TTTATATTTCAAAAAT
1 AATATTTTATATTTCAAAAAT
*
22104152 AATATTTTATATTTTAAAAAAT
1 AATATTTTATA-TTTCAAAAAT
22104174 AATATTTTATTAATTTCAA
1 AATATTTTA-T-ATTTCAA
22104193 TCGGGATCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 18 0.51
23 6 0.17
24 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTTATATTTCAAAAAT
Found at i:22110818 original size:17 final size:16
Alignment explanation
Indices: 22110785--22110819 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
22110775 AAAAACCATT
*
22110785 TAAATTATTTAACCAA
1 TAAATTATTTAAACAA
22110801 TAAATTATTTCAAACAA
1 TAAATTATTT-AAACAA
22110818 TA
1 TA
22110820 TTTTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTATTTAAACAA
Found at i:22111440 original size:19 final size:19
Alignment explanation
Indices: 22111381--22111441 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 19
22111371 TTCTCAAAAT
22111381 TAATTATAATTA-TTTTA-A
1 TAATT-TAATTATTTTTATA
22111399 TAGA-TTAATT-TTATTT-T-
1 TA-ATTTAATTATT-TTTATA
22111416 TAATTTAATTATTTTTATA
1 TAATTTAATTATTTTTATA
22111435 TAATTTA
1 TAATTTA
22111442 TAATATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
16 1 0.03
17 17 0.49
18 9 0.26
19 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TAATTTAATTATTTTTATA
Found at i:22113540 original size:21 final size:22
Alignment explanation
Indices: 22113515--22113573 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
22113505 TTATAGTCAA
*
22113515 TTATAATTTTTAATTAAT-CAT
1 TTATATTTTTTAATTAATGCAT
* *
22113536 TTATATTTTTTAATTTTATGTAT
1 TTATATTTTTTAA-TTAATGCAT
22113559 TTATATTTTTTAATT
1 TTATATTTTTTAATT
22113574 TTTTCATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.36
22 6 0.18
23 15 0.45
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATATTTTTTAATTAATGCAT
Found at i:22127353 original size:16 final size:16
Alignment explanation
Indices: 22127329--22127361 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22127319 TTGGATCTTT
*
22127329 TTTTTTTATCATTTCA
1 TTTTATTATCATTTCA
22127345 TTTTATTATCATTTCA
1 TTTTATTATCATTTCA
22127361 T
1 T
22127362 AAATTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTATCATTTCA
Found at i:22128802 original size:3 final size:3
Alignment explanation
Indices: 22128794--22128819 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22128784 GGCCATTACT
22128794 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
22128820 CAGAGGCAGC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:22135061 original size:16 final size:16
Alignment explanation
Indices: 22135040--22135070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22135030 AATAAACTCG
22135040 AAATAATTCAAATTTA
1 AAATAATTCAAATTTA
*
22135056 AAATAATTTAAATTT
1 AAATAATTCAAATTT
22135071 TTTCGAATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAATTCAAATTTA
Found at i:22137474 original size:30 final size:30
Alignment explanation
Indices: 22137438--22137521 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
22137428 TATTTTGTAT
*
22137438 AAATTAAAGATTAAGAATTTATTTGCATAC
1 AAATTAAAGATTAAGAATTTATTTGAATAC
* *
22137468 AAATTAAAGGTTAA-AATTTTATTTGAATGC
1 AAATTAAAGATTAAGAA-TTTATTTGAATAC
*
22137498 AAATTAAAAATTAAG-ATCTTATTT
1 AAATTAAAGATTAAGAAT-TTATTT
22137522 AAGTATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
29 3 0.07
30 43 0.93
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (30 bp):
AAATTAAAGATTAAGAATTTATTTGAATAC
Found at i:22137793 original size:27 final size:26
Alignment explanation
Indices: 22137742--22137803 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
22137732 TTTTTCAATA
*
22137742 AATTTTT-TTTAATCGTAATTGTAAT
1 AATTTTTATTTAATCGCAATTGTAAT
*
22137767 AATTTTTATTTCAATTGCAATTGTAAT
1 AATTTTTATTT-AATCGCAATTGTAAT
*
22137794 AATTATTATT
1 AATTTTTATT
22137804 ATTATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 7 0.22
26 3 0.09
27 22 0.69
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (26 bp):
AATTTTTATTTAATCGCAATTGTAAT
Found at i:22140549 original size:17 final size:18
Alignment explanation
Indices: 22140524--22140561 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
22140514 TTGACATGTA
*
22140524 TTTTAATTTTTAAT-TAT
1 TTTTAATTTTAAATATAT
*
22140541 TTTTTATTTTAAATATAT
1 TTTTAATTTTAAATATAT
22140559 TTT
1 TTT
22140562 AAGAGATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTAAATATAT
Found at i:22143031 original size:17 final size:17
Alignment explanation
Indices: 22143011--22143045 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22143001 ATAATTTTTA
*
22143011 TAATATTATATTTAAAT
1 TAATATTATATTCAAAT
*
22143028 TAATTTTATATTCAAAT
1 TAATATTATATTCAAAT
22143045 T
1 T
22143046 GGACTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATATTATATTCAAAT
Found at i:22143252 original size:39 final size:39
Alignment explanation
Indices: 22143207--22143283 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
22143197 ATTTTATATT
*
22143207 TAAATTAGATTCTTT-CACTTATTATTAATTAATTTTAAG
1 TAAATTAGA-CCTTTACACTTATTATTAATTAATTTTAAG
* *
22143246 TAAATTAGACCTTTATATTTATTATTAATTAATTTTAA
1 TAAATTAGACCTTTACACTTATTATTAATTAATTTTAA
22143284 ATTAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (39 bp):
TAAATTAGACCTTTACACTTATTATTAATTAATTTTAAG
Found at i:22156667 original size:23 final size:23
Alignment explanation
Indices: 22156620--22156668 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
22156610 TAAACAGTTT
* * *
22156620 AACTATAGTTAACTACCTATTTA
1 AACTATAGTTAACAACCAATATA
22156643 AACTATAGTTAACAACCAATATA
1 AACTATAGTTAACAACCAATATA
22156666 AAC
1 AAC
22156669 CATATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AACTATAGTTAACAACCAATATA
Found at i:22159607 original size:11 final size:11
Alignment explanation
Indices: 22159590--22159625 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
22159580 AAATATCATA
22159590 AGAGATTTGTT
1 AGAGATTTGTT
* *
22159601 TGAGATTTATT
1 AGAGATTTGTT
22159612 AGAGATTTGTT
1 AGAGATTTGTT
22159623 AGA
1 AGA
22159626 TATTACTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:22159715 original size:52 final size:52
Alignment explanation
Indices: 22159647--22159802 Score: 185
Period size: 52 Copynumber: 3.0 Consensus size: 52
22159637 GGACAAGAAA
*
22159647 ACTTACAAAAGAAGAATTCTAAGAAAAAGATA-ATTCTTAATAGGTAAGTTTG
1 ACTTACAAGAGAAGAATTCTAAGAAAAAGA-AGATTCTTAATAGGTAAGTTTG
* * *
22159699 ATTTGCAAGAGAAGAATTCTAA-AAGGAAA-AAGATTCTTAATAGGCAAGTTTG
1 ACTTACAAGAGAAGAATTCTAAGAA--AAAGAAGATTCTTAATAGGTAAGTTTG
** *
22159751 ACTTACAAGAGAAGAATTCTAAG-AGGAGAAAGATTCTTAATAGGTAATTTTG
1 ACTTACAAGAGAAGAATTCTAAGAAAAAG-AAGATTCTTAATAGGTAAGTTTG
22159803 TATGGTTATA
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
50 1 0.01
51 3 0.03
52 81 0.92
53 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (52 bp):
ACTTACAAGAGAAGAATTCTAAGAAAAAGAAGATTCTTAATAGGTAAGTTTG
Found at i:22160434 original size:49 final size:50
Alignment explanation
Indices: 22160341--22160449 Score: 114
Period size: 49 Copynumber: 2.2 Consensus size: 50
22160331 AATGTTTGAA
* * *
22160341 ACGTGAGAAGAGTTGAAGATTCAAGATGTGGAAAGGGCCGAAGGTTCGAG
1 ACGTGAGAAGAGCTGAAGATTCAAGATGTGGAAAGAGCCAAAGGTTCGAG
* * * **
22160391 ACGTG-GAAGAGCTGAA-AGTTCGAGATGTGGGAAGAGCTAAAGGTTTAAG
1 ACGTGAGAAGAGCTGAAGA-TTCAAGATGTGGAAAGAGCCAAAGGTTCGAG
*
22160440 ATGTGAGAAG
1 ACGTGAGAAG
22160450 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
48 1 0.02
49 38 0.79
50 9 0.19
ACGTcount: A:0.35, C:0.08, G:0.38, T:0.19
Consensus pattern (50 bp):
ACGTGAGAAGAGCTGAAGATTCAAGATGTGGAAAGAGCCAAAGGTTCGAG
Found at i:22160441 original size:25 final size:25
Alignment explanation
Indices: 22160347--22160449 Score: 77
Period size: 25 Copynumber: 4.2 Consensus size: 25
22160337 TGAAACGTGA
*
22160347 GAAGAGTTG-AAGATTCAAGATGTGG
1 GAAGAGCTGAAAG-TTCAAGATGTGG
* * * * * *
22160372 AAAGGGCCGAAGGTTCGAGACGT-G
1 GAAGAGCTGAAAGTTCAAGATGTGG
*
22160396 GAAGAGCTGAAAGTTCGAGATGTGG
1 GAAGAGCTGAAAGTTCAAGATGTGG
* *
22160421 GAAGAGCT-AAAGGTTTAAGATGTGA
1 GAAGAGCTGAAA-GTTCAAGATGTGG
22160446 GAAG
1 GAAG
22160450 TGCATGGTTT
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
24 22 0.37
25 36 0.60
26 2 0.03
ACGTcount: A:0.35, C:0.08, G:0.38, T:0.19
Consensus pattern (25 bp):
GAAGAGCTGAAAGTTCAAGATGTGG
Found at i:22160711 original size:12 final size:12
Alignment explanation
Indices: 22160694--22160737 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
22160684 TATCATTAAG
22160694 AGATTTGTTTGA
1 AGATTTGTTTGA
*
22160706 AGATTTGTTAG-
1 AGATTTGTTTGA
22160717 AGATTTGTTTGA
1 AGATTTGTTTGA
*
22160729 CG-TTTGTTT
1 AGATTTGTTT
22160738 AAATAGTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.52
Consensus pattern (12 bp):
AGATTTGTTTGA
Found at i:22160722 original size:23 final size:22
Alignment explanation
Indices: 22160692--22160736 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
22160682 AATATCATTA
22160692 AGAGATTTGTTTGAAGATTTGTT
1 AGAGATTTGTTTGAAG-TTTGTT
*
22160715 AGAGATTTGTTTGACGTTTGTT
1 AGAGATTTGTTTGAAGTTTGTT
22160737 TAAATAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAAGTTTGTT
Found at i:22160884 original size:52 final size:51
Alignment explanation
Indices: 22160796--22160920 Score: 128
Period size: 52 Copynumber: 2.4 Consensus size: 51
22160786 GGAGAAAGAT
** * *
22160796 GATTCTTATATAGGTTAGTTTGACGTAAAGATAAGAATGCTAA-AGGA-AAGG
1 GATTCTTA-ATAGGCAAGTTTGACGTAAAGAGAAGAATGCTAAGAGGAGAA-A
* * *
22160847 GATTCTTACATAGGCAAGTTTGACTTACAGGAGAAGAATTCTAAGAGGAGAAA
1 GATTCTTA-ATAGGCAAGTTTGACGTA-AAGAGAAGAATGCTAAGAGGAGAAA
*
22160900 GATTCCTAATAGGCAAGTTTG
1 GATTCTTAATAGGCAAGTTTG
22160921 TATGGTTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
51 23 0.37
52 26 0.42
53 11 0.18
54 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (51 bp):
GATTCTTAATAGGCAAGTTTGACGTAAAGAGAAGAATGCTAAGAGGAGAAA
Found at i:22163194 original size:30 final size:31
Alignment explanation
Indices: 22163152--22163219 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
22163142 ATTTTTTAAA
* *
22163152 AATTTA-TTTATTAATAAGATAATATTATTT
1 AATTTATTTTATTAATAAAATAATATCATTT
22163182 -ATTTATTTTATTAATAAAATAATATCATTT
1 AATTTATTTTATTAATAAAATAATATCATTT
22163212 AATTTATT
1 AATTTATT
22163220 AATAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 5 0.15
30 22 0.65
31 7 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (31 bp):
AATTTATTTTATTAATAAAATAATATCATTT
Found at i:22163334 original size:26 final size:26
Alignment explanation
Indices: 22163295--22163355 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 26
22163285 TGATATTTTT
*
22163295 TTAAAAATAATATAATAATTTATGATATA
1 TTAATAAT-ATATAAT-ATTTAT-ATATA
22163324 TTAATAATATATAATATTTATATATA
1 TTAATAATATATAATATTTATATATA
22163350 TTAATA
1 TTAATA
22163356 CGCTATCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 11 0.35
27 6 0.19
28 7 0.23
29 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TTAATAATATATAATATTTATATATA
Found at i:22163354 original size:16 final size:16
Alignment explanation
Indices: 22163301--22163355 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
22163291 TTTTTTAAAA
*
22163301 ATAATA-TAATAATTT
1 ATAATATTAATAATAT
22163316 ATGATATATTAATAATAT
1 AT-A-ATATTAATAATAT
*
22163334 ATAATATTTAT-ATAT
1 ATAATATTAATAATAT
22163349 ATTAATA
1 A-TAATA
22163356 CGCTATCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 7 0.21
16 13 0.38
17 4 0.12
18 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATAATATTAATAATAT
Found at i:22168208 original size:16 final size:17
Alignment explanation
Indices: 22168178--22168217 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
22168168 AAAATAAATA
22168178 ATAAAAAATTAATTAAT
1 ATAAAAAATTAATTAAT
22168195 ATAAAAAATT-ATTAAT
1 ATAAAAAATTAATTAAT
22168211 A-AAAAAA
1 ATAAAAAA
22168218 GTTTACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAAAATTAATTAAT
Found at i:22168904 original size:14 final size:15
Alignment explanation
Indices: 22168879--22168909 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
22168869 CTCTTGTCAC
22168879 CACTGTTATTTATCA
1 CACTGTTATTTATCA
22168894 CACTG-TATTTATCA
1 CACTGTTATTTATCA
22168908 CA
1 CA
22168910 TAATGGGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (15 bp):
CACTGTTATTTATCA
Found at i:22176520 original size:30 final size:30
Alignment explanation
Indices: 22176484--22176540 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
22176474 ACAATGTGTC
*
22176484 TAGGGAAGATGA-ATTAGAATATGATAGGGT
1 TAGGGAAGATGACA-TAGAAAATGATAGGGT
*
22176514 TAGGGAAGGTGACATAGAAAATGATAG
1 TAGGGAAGATGACATAGAAAATGATAG
22176541 AGTCAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.23
Consensus pattern (30 bp):
TAGGGAAGATGACATAGAAAATGATAGGGT
Found at i:22180995 original size:22 final size:23
Alignment explanation
Indices: 22180968--22181011 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
22180958 TTTATCTTAG
22180968 ATTTTTTTATTTCAT-ATTTATC
1 ATTTTTTTATTTCATGATTTATC
*
22180990 ATTTTTTTATTTTATGATTTAT
1 ATTTTTTTATTTCATGATTTAT
22181012 TTTCTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTTTTTATTTCATGATTTATC
Found at i:22181009 original size:16 final size:17
Alignment explanation
Indices: 22180973--22181019 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
22180963 CTTAGATTTT
*
22180973 TTTATTTCATATTTATCA
1 TTTATTTTAT-TTTATCA
*
22180991 TTT-TTTTATTTTATGA
1 TTTATTTTATTTTATCA
*
22181007 TTTATTTTCTTTT
1 TTTATTTTATTTT
22181020 TCTTTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 9 0.36
17 13 0.52
18 3 0.12
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTATTTTATTTTATCA
Found at i:22181019 original size:22 final size:21
Alignment explanation
Indices: 22180968--22181025 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
22180958 TTTATCTTAG
22180968 ATTTTTTTATTTCATATTTAT
1 ATTTTTTTATTTCATATTTAT
*
22180989 CATTTTTTTATTTTATGATTTAT
1 -ATTTTTTTATTTCAT-ATTTAT
* *
22181012 TTTCTTTTTCTTTC
1 ATT-TTTTTATTTC
22181026 TTTTGATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTTTTTATTTCATATTTAT
Found at i:22182372 original size:81 final size:81
Alignment explanation
Indices: 22182213--22182388 Score: 228
Period size: 81 Copynumber: 2.2 Consensus size: 81
22182203 CTGTCAATGG
* * * * *
22182213 CCAGCCTTGGCACCAAGTTCGGGTACGTCATCTCAAAAATAATAGAGACTTTGGGGTCTACCTAA
1 CCAGCCTTGGCACCAAGTTCAGGCACGTCATATCAAAAATAATAGAGACCTTGGGGTCTACCCAA
* *
22182278 TATTTTTTATTTTTTC
66 TATTTCTGATTTTTTC
* * *
22182294 CCAGCCTTGGCACCAAGTTCAGGCACGTCATATCAGAAATAATAGAGACCTT-GTGTCTGCCCAA
1 CCAGCCTTGGCACCAAGTTCAGGCACGTCATATCAAAAATAATAGAGACCTTGGGGTCTACCCAA
*
22182358 TATTTCTGATTTTTTTT
66 TATTTCTGA-TTTTTTC
*
22182375 CCAGCCATGGCACC
1 CCAGCCTTGGCACC
22182389 GCAACGCCAC
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
80 16 0.20
81 66 0.80
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (81 bp):
CCAGCCTTGGCACCAAGTTCAGGCACGTCATATCAAAAATAATAGAGACCTTGGGGTCTACCCAA
TATTTCTGATTTTTTC
Found at i:22183605 original size:44 final size:46
Alignment explanation
Indices: 22183546--22183643 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 46
22183536 AAATTTTCAA
22183546 AAAAAAAAGTTTTTGA-AGAAAAG-TGAAAAGTATCAATTTTCCTTG-
1 AAAAAAAAGTTTTTGAGA-AAAAGTTG-AAAGTATCAATTTTCCTTGC
* *
22183591 AAAATAAA-TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGC
1 AAAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGC
22183636 AAAAAAAA
1 AAAAAAAA
22183644 AAAACAATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 30 0.64
45 17 0.36
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (46 bp):
AAAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGC
Found at i:22184145 original size:32 final size:32
Alignment explanation
Indices: 22184103--22184164 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
22184093 TTATGACAAT
* *
22184103 AATCATACAAATAAATATATTAATAATCATAC
1 AATCACACAAATAAATAAATTAATAATCATAC
*
22184135 AATCACACAAATACATAAATTAATAATCAT
1 AATCACACAAATAAATAAATTAATAATCAT
22184165 GCAAATGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (32 bp):
AATCACACAAATAAATAAATTAATAATCATAC
Found at i:22184218 original size:41 final size:41
Alignment explanation
Indices: 22184173--22184477 Score: 265
Period size: 41 Copynumber: 7.5 Consensus size: 41
22184163 ATGCAAATGG
*
22184173 ACATGCAATTAAATATATAATCATGCAATTAACAATGTAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* * * *
22184214 ACATGTAATTAAATATCTAATCATACAATTAACAATGTAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
*
22184255 ACATGCAAATAAATATATAA-CATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* *
22184295 TCATGCAAATAAATA-ATAATCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* * *
22184335 TCATGCAATTAACA-ATATAAAACATGCAATT-A-AATATATTA
1 ACATGCAATTAA-ATATAT-AATCATGCAATTAACAATATA-AA
* * * *
22184376 TCATGCAATTAACA-ACATAAAACATGCAACT-A-AATATATAA
1 ACATGCAATTAA-ATATAT-AATCATGCAATTAACAATATA-AA
* * *
22184417 TCATGCAATTAACA-ATATAAAACATGCAACT-A-AATATATAA
1 ACATGCAATTAA-ATATAT-AATCATGCAATTAACAATATA-AA
*
22184458 TCATGCAATTAACA-ATATAA
1 ACATGCAATTAA-ATATATAA
22184478 AATGTGCAAC
Statistics
Matches: 243, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
39 4 0.02
40 72 0.30
41 156 0.64
42 11 0.05
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.28
Consensus pattern (41 bp):
ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
Found at i:22184223 original size:21 final size:21
Alignment explanation
Indices: 22184173--22184560 Score: 287
Period size: 21 Copynumber: 19.0 Consensus size: 21
22184163 ATGCAAATGG
22184173 ACATGCAATT-A-AATATATAA
1 ACATGCAATTAACAATATA-AA
* *
22184193 TCATGCAATTAACAATGTAAA
1 ACATGCAATTAACAATATAAA
* *
22184214 ACATGTAATT-A-AATATCTAA
1 ACATGCAATTAACAATAT-AAA
* * *
22184234 TCATACAATTAACAATGTAAA
1 ACATGCAATTAACAATATAAA
* *
22184255 ACATGCAAAT-A-AATATATA
1 ACATGCAATTAACAATATAAA
22184274 ACATGCAATTAACAATATAAA
1 ACATGCAATTAACAATATAAA
* *
22184295 TCATGCAAAT-A-AATA-ATAA
1 ACATGCAATTAACAATATA-AA
*
22184314 TCATGCAATTAACAATATAAA
1 ACATGCAATTAACAATATAAA
*
22184335 TCATGCAATTAACAATATAAA
1 ACATGCAATTAACAATATAAA
*
22184356 ACATGCAATT-A-AATATATTA
1 ACATGCAATTAACAATATA-AA
* *
22184376 TCATGCAATTAACAACATAAA
1 ACATGCAATTAACAATATAAA
*
22184397 ACATGCAACT-A-AATATATAA
1 ACATGCAATTAACAATATA-AA
*
22184417 TCATGCAATTAACAATATAAA
1 ACATGCAATTAACAATATAAA
*
22184438 ACATGCAACT-A-AATATATAA
1 ACATGCAATTAACAATATA-AA
*
22184458 TCATGCAATTAACAATATAAA
1 ACATGCAATTAACAATATAAA
** *
22184479 ATGTGCAACT-A-AATATATAA
1 ACATGCAATTAACAATATA-AA
* * *
22184499 TCAAGCAATTAACAATATATGA
1 ACATGCAATTAACAATATA-AA
*
22184521 A-ATGCCATT-A-AATATATAA
1 ACATGCAATTAACAATATA-AA
*
22184540 TCATGCAATTACACAA-ATAAA
1 ACATGCAATTA-ACAATATAAA
22184561 TAAATTGATA
Statistics
Matches: 290, Mismatches: 51, Indels: 53
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.00
19 65 0.22
20 72 0.25
21 111 0.38
22 39 0.13
23 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (21 bp):
ACATGCAATTAACAATATAAA
Found at i:22184478 original size:41 final size:41
Alignment explanation
Indices: 22184266--22184560 Score: 361
Period size: 41 Copynumber: 7.2 Consensus size: 41
22184256 CATGCAAATA
* *
22184266 AATATATAACATGCAATTAACA-ATATAAATCATGCAAAT-A-
1 AATATAAAACATGCAATTAA-ATATAT-AATCATGCAATTAAC
*
22184306 AATA-ATAATCATGCAATTAACA-ATATAAATCATGCAATTAAC
1 AATATA-AAACATGCAATTAA-ATATAT-AATCATGCAATTAAC
*
22184348 AATATAAAACATGCAATTAAATATATTATCATGCAATTAAC
1 AATATAAAACATGCAATTAAATATATAATCATGCAATTAAC
* *
22184389 AACATAAAACATGCAACTAAATATATAATCATGCAATTAAC
1 AATATAAAACATGCAATTAAATATATAATCATGCAATTAAC
*
22184430 AATATAAAACATGCAACTAAATATATAATCATGCAATTAAC
1 AATATAAAACATGCAATTAAATATATAATCATGCAATTAAC
** * *
22184471 AATATAAAATGTGCAACTAAATATATAATCAAGCAATTAAC
1 AATATAAAACATGCAATTAAATATATAATCATGCAATTAAC
* *
22184512 AATATATGAA-ATGCCATTAAATATATAATCATGCAATTACAC
1 AATATA-AAACATGCAATTAAATATATAATCATGCAATTA-AC
22184554 AA-ATAAA
1 AATATAAA
22184561 TAAATTGATA
Statistics
Matches: 230, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.00
40 35 0.15
41 166 0.72
42 27 0.12
43 1 0.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (41 bp):
AATATAAAACATGCAATTAAATATATAATCATGCAATTAAC
Found at i:22184627 original size:20 final size:20
Alignment explanation
Indices: 22184558--22184631 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
22184548 TTACACAAAT
*
22184558 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
*
22184578 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
*
22184598 AAATAAATTAATAGTCATGC
1 AAATAAATTAATAATCATGC
*
22184618 AAATATATTAATAA
1 AAATAAATTAATAA
22184632 ATCACACAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:22184649 original size:41 final size:40
Alignment explanation
Indices: 22184558--22184650 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
22184548 TTACACAAAT
* * * **
22184558 AAATAAATTGATAATCATGCAAATAAATTGATAATCATGC
1 AAATAAATTAATAGTCATGCAAATAAATTAATAATCACAC
*
22184598 AAATAAATTAATAGTCATGCAAATATATTAATAAATCACAC
1 AAATAAATTAATAGTCATGCAAATAAATTAAT-AATCACAC
* *
22184639 AATTATATTAAT
1 AAATAAATTAAT
22184651 CATACAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 28 0.64
41 16 0.36
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (40 bp):
AAATAAATTAATAGTCATGCAAATAAATTAATAATCACAC
Found at i:22184812 original size:12 final size:12
Alignment explanation
Indices: 22184793--22184822 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
22184783 TAAAAATTAC
22184793 AAAAAGAAAGAA
1 AAAAAGAAAGAA
*
22184805 AGAAAGAAAGAA
1 AAAAAGAAAGAA
22184817 AAAAAG
1 AAAAAG
22184823 CAAGCATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:22185895 original size:43 final size:42
Alignment explanation
Indices: 22185628--22186268 Score: 586
Period size: 43 Copynumber: 15.1 Consensus size: 42
22185618 TTTTTTTTTT
* * *
22185628 AAATGCTCTCCCACAATTGATGCTTTGAAAGTTTTTGAAAAATA
1 AAATGCTC-CCCACAATTGAGGCTTTGAAA-CTTTTAAAAAATA
* * *
22185672 AAATGTTCCCCCATAACTGAGGCTTTGAAACTTTT-AAAAATA
1 AAATGCT-CCCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* *
22185714 AAATGCT-CCCACAACTGAGGCTTTGAAAC-TTTGAAAAATA
1 AAATGCTCCCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * * * *
22185754 AAATGCTCCCCTACAACTAAGGCTTTGGAAGTTTT-GAAAATA
1 AAATGCTCCCC-ACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * *
22185796 AAATACTCTTCCACAATTGAGGCTTTG-AAC-TTTGAAAAATA
1 AAATGCTC-CCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
*
22185837 AAATGCTCCCTCATAATTGAGGCTTTGAAACTTTTAAAAAATA
1 AAATGCTCCC-CACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * * *
22185880 AAATGCTACCCCATAACTGAGGCTTTGGAAC-ATTAGAAAAATA
1 AAATGCT-CCCCACAATTGAGGCTTTGAAACTTTTA-AAAAATA
* * * *
22185923 AAATGCTCTCTCACAATTGAAGCTTTGGAACTTTT-GAAAATA
1 AAATGCTC-CCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* *
22185965 AAATACTCCCCACAATTGAGGCTTTGAAAC-TTTGAAAAATA
1 AAATGCTCCCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* ** ** *
22186006 AAATGCACCTTTACAGCTAAGGCTTT-AGAACTTTTAAAAAATA
1 AAATGCTCC-CCACAATTGAGGCTTTGA-AACTTTTAAAAAATA
*
22186049 AAATGCTCTCCCACAATTGAGGCTTTGAAACTTTGAAAAAATA
1 AAATGCTC-CCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * * *
22186092 AAATGTTCTCCCACAATTGAGGCATTGAGACTTTGAAAAAATA
1 AAATGCTC-CCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * *
22186135 AAATGCTCCCCCACAACTGAGGCATTGAAACTTTTCAAAAATA
1 AAATGCT-CCCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * * * * *
22186178 AAATACTCCTCTATAACTGAAGCTTTGAAACTTTGAAAAAATA
1 AAATGCTCC-CCACAATTGAGGCTTTGAAACTTTTAAAAAATA
* * *
22186221 AAATGTTCCCCTAC-ATCTAAGG-TTTTAGAACTTTTAAAAAATA
1 AAATGCTCCCC-ACAAT-TGAGGCTTTGA-AACTTTTAAAAAATA
22186264 AAATG
1 AAATG
22186269 AGATCATTCT
Statistics
Matches: 498, Mismatches: 74, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.01
40 42 0.08
41 66 0.13
42 97 0.19
43 257 0.52
44 32 0.06
45 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (42 bp):
AAATGCTCCCCACAATTGAGGCTTTGAAACTTTTAAAAAATA
Found at i:22185967 original size:169 final size:168
Alignment explanation
Indices: 22185628--22186268 Score: 728
Period size: 169 Copynumber: 3.8 Consensus size: 168
22185618 TTTTTTTTTT
* * * * *
22185628 AAATGCTCTCCCACAATTGATGCTTTGAAAGTTTTTGAAAAATAAAATGTTCCCCCATAACTGAG
1 AAATACTCTCCCACAATTGAGGCTTTGAAA--CTTTGAAAAATAAAATGCTCCCTCATAACTGAG
22185693 GCTTTGAAACTTTT-AAAAATAAAATGCT-CCCACAACTGAGGCTTTGAAACTTTGAAAAATAAA
64 GCTTTGAAACTTTTAAAAAATAAAATGCTCCCCACAACTGAGGCTTTGAAACTTTGAAAAATAAA
* *
22185756 ATGCTC-CCCTACAACT-AAGGCTTTGGAAGTTTTGAAAATA
129 ATGCTCTCCC-ACAATTGAA-GCTTTGGAACTTTTGAAAATA
* *
22185796 AAATACTCTTCCACAATTGAGGCTTTG-AACTTTGAAAAATAAAATGCTCCCTCATAATTGAGGC
1 AAATACTCTCCCACAATTGAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCTCATAACTGAGGC
* * *
22185860 TTTGAAACTTTTAAAAAATAAAATGCTACCCCATAACTGAGGCTTTGGAACATTAGAAAAATAAA
66 TTTGAAACTTTTAAAAAATAAAATGCT-CCCCACAACTGAGGCTTTGAAAC-TTTGAAAAATAAA
*
22185925 ATGCTCTCTCACAATTGAAGCTTTGGAACTTTTGAAAATA
129 ATGCTCTCCCACAATTGAAGCTTTGGAACTTTTGAAAATA
* * * * * *
22185965 AAATACTC-CCCACAATTGAGGCTTTGAAACTTTGAAAAATAAAATGCACCTTTACAGCTAAGGC
1 AAATACTCTCCCACAATTGAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCTCATAACTGAGGC
*
22186029 TTT-AGAACTTTTAAAAAATAAAATGCTCTCCCACAATTGAGGCTTTGAAACTTTGAAAAAATAA
66 TTTGA-AACTTTTAAAAAATAAAATGCTC-CCCACAACTGAGGCTTTGAAACTTTG-AAAAATAA
* * *
22186093 AATGTTCTCCCACAATTGAGGCATT-GAGAC-TTTGAAAAAATA
128 AATGCTCTCCCACAATTGAAGCTTTGGA-ACTTTTG--AAAATA
* * * * * * *
22186135 AAATGCTCCCCCACAACTGAGGCATTGAAACTTTTCAAAAATAAAATACT-CCTCTATAACTGAA
1 AAATACTCTCCCACAATTGAGGCTTTGAAAC-TTTGAAAAATAAAATGCTCCCTC-ATAACTGAG
* * * * * *
22186199 GCTTTGAAACTTTGAAAAAATAAAATGTTCCCCTACATCTAAGG-TTTTAGAACTTTTAAAAAAT
64 GCTTTGAAACTTTTAAAAAATAAAATGCTCCCC-ACAACTGAGGCTTTGA-AAC-TTTGAAAAAT
22186263 AAAATG
126 AAAATG
22186269 AGATCATTCT
Statistics
Matches: 405, Mismatches: 48, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
165 43 0.11
166 14 0.03
167 2 0.00
168 72 0.18
169 156 0.39
170 17 0.04
171 29 0.07
172 68 0.17
173 4 0.01
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (168 bp):
AAATACTCTCCCACAATTGAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCTCATAACTGAGGC
TTTGAAACTTTTAAAAAATAAAATGCTCCCCACAACTGAGGCTTTGAAACTTTGAAAAATAAAAT
GCTCTCCCACAATTGAAGCTTTGGAACTTTTGAAAATA
Found at i:22187208 original size:16 final size:17
Alignment explanation
Indices: 22187179--22187210 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
22187169 AATTTGACTT
22187179 TTATTTTGTATTTTATA
1 TTATTTTGTATTTTATA
22187196 TTATTTT-TATTTTAT
1 TTATTTTGTATTTTAT
22187211 TTTTTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TTATTTTGTATTTTATA
Found at i:22187245 original size:4 final size:4
Alignment explanation
Indices: 22187226--22187458 Score: 88
Period size: 4 Copynumber: 57.2 Consensus size: 4
22187216 CCCTTTGTAT
* * *
22187226 TTTA TGTA TTTA -TTA TTTA TTTA TTTA -TTA TTACTA TTTA TTAA TATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA
* * * * *
22187274 TTTA TATC TTTA TTTA TTT- TTT- TTCTG TTAATA TTTA TATA TAT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT--TA TTTA TTTA TTTA TTTA
* * * *
22187322 TTTA TCTA GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA TTATT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TT-TA
* * * *
22187369 TTTA TTTT TTTA TTTA TCTTG TAATA TTT- TTTA TTTA TCTTA TTT- TTATT
1 TTTA TTTA TTTA TTTA T-TTA T-TTA TTTA TTTA TTTA T-TTA TTTA TT-TA
* * * * * *
22187419 TTTA ATTA TCTG TTAA TTTT TTTA TTT- TTTA TTTG TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
22187459 CTGATTTTTT
Statistics
Matches: 169, Mismatches: 42, Indels: 36
0.68 0.17 0.15
Matches are distributed among these distances:
3 24 0.14
4 112 0.66
5 23 0.14
6 10 0.06
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:22187265 original size:21 final size:21
Alignment explanation
Indices: 22187239--22187406 Score: 78
Period size: 21 Copynumber: 7.7 Consensus size: 21
22187229 ATGTATTTAT
22187239 TATTTATTTATTTATTATTAC
1 TATTTATTTATTTATTATTAC
* *
22187260 TATTTATTAATATATT-TATATC
1 TATTTATTTATTTATTAT-TA-C
* * *
22187282 TTTATTTATTT-TTTTTCTGTTAA
1 --TATTTATTTATTTAT-TATTAC
*
22187305 TATTTATATATATT-TTATTTATC
1 TATTTATTTAT-TTATTA-TTA-C
* *
22187328 TAGTTATATATTTATTATTA-
1 TATTTATTTATTTATTATTAC
**
22187348 TATTATAATTTATTTATTATTTT
1 TATT-T-ATTTATTTATTATTAC
* *
22187371 TATTTTTTTATTTATCT-TGTAA
1 TATTTATTTATTTAT-TAT-TAC
22187393 TATTT-TTTATTTAT
1 TATTTATTTATTTAT
22187407 CTTATTTTTA
Statistics
Matches: 115, Mismatches: 16, Indels: 32
0.71 0.10 0.20
Matches are distributed among these distances:
20 4 0.03
21 45 0.39
22 32 0.28
23 22 0.19
24 11 0.10
25 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTATTTATTTATTATTAC
Done.