Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 65 of 276
Found at i:20065336 original size:14 final size:14
Alignment explanation
Indices: 20065313--20065346 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20065303 GAGTTGATTT
* *
20065313 TTGAAGAATATAAA
1 TTGAAAAATAGAAA
20065327 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
20065341 TTGAAA
1 TTGAAA
20065347 TTACCTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:20065410 original size:85 final size:83
Alignment explanation
Indices: 20065283--20065478 Score: 252
Period size: 85 Copynumber: 2.3 Consensus size: 83
20065273 ACCCGAGGCT
* *
20065283 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAGAATATAAATTGAAAAATAGAAATTGAAAT
1 CAACTCACCTCTCGCAATATGAGTTGATTTATGAAGAATATAAATT---AAACAGAAATTGAAAT
*
20065348 TACCTCA-ACGTCCTGAGACC
63 TACCTCACACGCCCTGAGACC
* *
20065368 CAACTCACCTCTTGCAATATGAGTTGATTTATGAA-AAGTATAAATTAAACAGAAATTGAAATTT
1 CAACTCACCTCTCGCAATATGAGTTGATTTATGAAGAA-TATAAATTAAACAGAAATTGAAATTA
* * *
20065432 CCTCAGCATGCCCTGAGGCT
65 CCTCA-CACGCCCTGAGACC
*
20065452 CAACTCATCTCTCGCAATATGAGTTGA
1 CAACTCACCTCTCGCAATATGAGTTGA
20065479 AAATATAAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
82 21 0.21
84 36 0.37
85 41 0.42
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (83 bp):
CAACTCACCTCTCGCAATATGAGTTGATTTATGAAGAATATAAATTAAACAGAAATTGAAATTAC
CTCACACGCCCTGAGACC
Found at i:20065875 original size:162 final size:162
Alignment explanation
Indices: 20065637--20065928 Score: 559
Period size: 162 Copynumber: 1.8 Consensus size: 162
20065627 TGACCCAAGA
*
20065637 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGCATGAATTAAAGAAACAGGAATTGAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGAATGAATTAAAGAAACAGGAATTGAA
20065702 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGACAAACAG
66 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGACAAACAG
20065767 TAATTGAAAATACCTTAGTATATGAGCCGAGG
131 TAATTGAAAATACCTTAGTATATGAGCCGAGG
20065799 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-AATAGAATTAAAGAAACAGGAATTGA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGAAT-GAATTAAAGAAACAGGAATTGA
20065863 AAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGACAAACA
65 AAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGACAAACA
20065928 G
130 G
20065929 AAATAACAAC
Statistics
Matches: 128, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
161 2 0.02
162 126 0.98
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (162 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGAATGAATTAAAGAAACAGGAATTGAA
AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGACAAACAG
TAATTGAAAATACCTTAGTATATGAGCCGAGG
Found at i:20080442 original size:26 final size:26
Alignment explanation
Indices: 20080369--20080451 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
20080359 AAACAATTTG
* *
20080369 AAATAAAATAATATATAAAGTAAATTTC
1 AAAT-AAATAATATATAAAATAAA-TTA
* *
20080397 AAATAAATAATATGTTAAATAAATTA
1 AAATAAATAATATATAAAATAAATTA
* *
20080423 AAATAAATAATATACAAAATAAAATA
1 AAATAAATAATATATAAAATAAATTA
20080449 AAA
1 AAA
20080452 AGGACCCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 27 0.57
27 16 0.34
28 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAAATAATATATAAAATAAATTA
Found at i:20080760 original size:55 final size:53
Alignment explanation
Indices: 20080683--20080794 Score: 131
Period size: 55 Copynumber: 2.1 Consensus size: 53
20080673 GTGTAACTAG
*
20080683 ATAACGTATGAAAAGAAATTTAAAAT-GGATAATACATATATAATAGTTTAAAATGA
1 ATAACGTATGAAAAGAAATTTAAAATAAG-TAAT--ATATATAATAG-TTAAAATGA
* *
20080739 ATAACGTAT-AAAA-ATATTTTAAAATAAGTAATATGTATAATAGTTAAAATGA
1 ATAACGTATGAAAAGA-AATTTAAAATAAGTAATATATATAATAGTTAAAATGA
20080791 ATAA
1 ATAA
20080795 TATATGTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
52 13 0.25
53 10 0.20
54 1 0.02
55 17 0.33
56 10 0.20
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (53 bp):
ATAACGTATGAAAAGAAATTTAAAATAAGTAATATATATAATAGTTAAAATGA
Found at i:20080807 original size:27 final size:27
Alignment explanation
Indices: 20080702--20080815 Score: 83
Period size: 27 Copynumber: 4.3 Consensus size: 27
20080692 GAAAAGAAAT
* * * *
20080702 TTAAAATGGATAATACATATATAATAG
1 TTAAAATGAATAATATATGTAAAATAG
** * *
20080729 TTTAAAATGAATAACGTAT-AAAAATATT
1 -TTAAAATGAATAATATATGTAAAATA-G
*
20080757 TTAAAAT-AAGT-A-ATATGTATAATAG
1 TTAAAATGAA-TAATATATGTAAAATAG
*
20080782 TTAAAATGAATAATATATGTAAAATAT
1 TTAAAATGAATAATATATGTAAAATAG
20080809 TTAAAAT
1 TTAAAAT
20080816 CTGTAATATC
Statistics
Matches: 67, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
25 11 0.16
26 11 0.16
27 31 0.46
28 14 0.21
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.36
Consensus pattern (27 bp):
TTAAAATGAATAATATATGTAAAATAG
Found at i:20080812 original size:52 final size:53
Alignment explanation
Indices: 20080721--20080824 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 53
20080711 ATAATACATA
*
20080721 TATAATAGTTTAAAATGAATAACGTATAAAAATATTTTAAAATAAGTAATATG
1 TATAATAGTTTAAAATGAATAACATATAAAAATATTTTAAAATAAGTAATATG
* * **
20080774 TATAATAG-TTAAAATGAATAATATATGTAAAATA-TTTAAAATCTGTAATAT
1 TATAATAGTTTAAAATGAATAACATAT-AAAAATATTTTAAAATAAGTAATAT
20080825 CTTAAAGTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
52 31 0.69
53 14 0.31
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (53 bp):
TATAATAGTTTAAAATGAATAACATATAAAAATATTTTAAAATAAGTAATATG
Found at i:20082087 original size:18 final size:18
Alignment explanation
Indices: 20082064--20082104 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20082054 TACTTTTCTC
20082064 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
20082082 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
20082100 TTTCT
1 TTTCT
20082105 TTTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:20082275 original size:39 final size:40
Alignment explanation
Indices: 20082232--20082341 Score: 100
Period size: 38 Copynumber: 2.8 Consensus size: 40
20082222 TCAAATAATT
***
20082232 CGAAGTAATAGTTGACACCCAGTGTCTCATCGGCT-TAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCAAATCTAGC
** ** *
20082271 CGAAGTAA-AGTTGGTACCCAGTACCTCATCAAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCAAATCTAGC
*
20082310 CGAAGAAATA-TAGTGACACCCAGTGTCTCATC
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATC
20082342 TACTCGAGGT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
38 19 0.35
39 19 0.35
40 1 0.02
41 15 0.28
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCAAATCTAGC
Found at i:20083550 original size:23 final size:24
Alignment explanation
Indices: 20083494--20083552 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
20083484 AAATTAATTA
*
20083494 TTTTATTACAAGTGTACATATATC
1 TTTTATTACAAATGTACATATATC
20083518 TATTTATTACAAATGTACCA-ATAT-
1 T-TTTATTACAAATGTA-CATATATC
20083542 TTTTATTACAA
1 TTTTATTACAA
20083553 TTGTCATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 10 0.31
24 2 0.06
25 18 0.56
26 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTATTACAAATGTACATATATC
Found at i:20085515 original size:137 final size:136
Alignment explanation
Indices: 20085351--20085694 Score: 420
Period size: 137 Copynumber: 2.5 Consensus size: 136
20085341 CTTTGACCTG
** *** *
20085351 TTCCACTGCAACTTCAGGGAAATAAGATCCACTATCTTCAGTCTATTTCACTACTACTTCAGGAA
1 TTCCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTCAGGAA
* * * * *
20085416 GATAAGGTTTGCTATGATCTGCTCTACTGTAACTTCATAGAGATAAGATCTGTAATTTATAGCTT
66 GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTAA-TTATAGCTT
20085481 CAATCTA
130 CAATCTA
* * ** * *
20085488 TTCCACTGCAACTTCAGGGAAATAAGATTTGTTATCTTCAGTCGGCCCCACTGCAACTTCAGGGA
1 TTCCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTCAGGAA
*
20085553 GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTTATTATAGCTTC
66 GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTAATTATAGCTTC
*
20085618 AATCTG
131 AATCTA
* * * * * * *
20085624 TTCCCCCTACAACTTCAGTGAAATAAGATCTGCTATCTTCAGTCTGCTCCATTGCAACTTCAAGG
1 TT-CCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTC-AGG
20085689 -AGATAA
64 AAGATAA
20085695 GACTTGTCAT
Statistics
Matches: 178, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
136 17 0.10
137 158 0.89
138 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (136 bp):
TTCCACTGCAACTTCAGGGAAATAAGATCTGCTATCTTCAGTCTACCCCACTACAACTTCAGGAA
GATAAAGTTTGCTATGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGTAATTATAGCTTC
AATCTA
Found at i:20085695 original size:45 final size:45
Alignment explanation
Indices: 20085614--20085831 Score: 144
Period size: 45 Copynumber: 4.8 Consensus size: 45
20085604 GTTATTATAG
* * *
20085614 CTTCAATCTGTTCCCCCTACAACTTC-AGTGAAATAAGATCTGCTAT
1 CTTCAATCTGCT-CCACTACAACTTCAAG-GAGATAAGATCTGCTAT
* * *
20085660 CTTCAGTCTGCTCCATTGCAACTTCAAGGAGATAAGA-CTTGTCATAT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATC-TG-C-TAT
* * * * * * *
20085707 -TT-GATCTACTCCACTGCAACTTTAAGGAGACAAGATCTTC-AA
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATCTGCTAT
* * * * **
20085749 CTTCAATATGCTCCACTACTACTTC-AGAGAGATAAGGTTTAG-TGG
1 CTTCAATCTGCTCCACTACAACTTCAAG-GAGATAAGATCT-GCTAT
*
20085794 ATTCAATCTGCTCCACTACAACTTCAAGGAGATAAGAT
1 CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGAT
20085832 TCATCATTAC
Statistics
Matches: 131, Mismatches: 30, Indels: 23
0.71 0.16 0.12
Matches are distributed among these distances:
42 1 0.01
43 4 0.03
44 26 0.20
45 79 0.60
46 18 0.14
47 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTACAACTTCAAGGAGATAAGATCTGCTAT
Found at i:20087354 original size:50 final size:46
Alignment explanation
Indices: 20087273--20087455 Score: 150
Period size: 40 Copynumber: 4.3 Consensus size: 46
20087263 AATAGGGCTT
* * *
20087273 TAGCGGCGTTTTATCAAAAAACGCCGCAAAAATTGTAAAACACATAGCAA
1 TAGCGGCGTTTTA-CCAAAAACGCCACAAAAA-T-TAAAA-ACAGAGCAA
20087323 TAGCGGCGTTTTACCAAAAACGCCAC------TAAAAACAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCACAAAAATTAAAAACAGAGCAA
*
20087363 TAGCGGCGTTTTACCAAAAACGCCAC------TAAAAATAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCACAAAAATTAAAAACAGAGCAA
*
20087403 TAGCGGCATTTTACCAAAAACGCCAC------TAAAAACAGAGCAA
1 TAGCGGCGTTTTACCAAAAACGCCACAAAAATTAAAAACAGAGCAA
*
20087443 TAGTGGCGTTTTA
1 TAGCGGCGTTTTA
20087456 GTAAAAAACG
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
40 96 0.77
41 5 0.04
49 11 0.09
50 13 0.10
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (46 bp):
TAGCGGCGTTTTACCAAAAACGCCACAAAAATTAAAAACAGAGCAA
Found at i:20087515 original size:41 final size:40
Alignment explanation
Indices: 20087308--20087490 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
20087298 GCAAAAATTG
*
20087308 TAAAACACATAGCAATAGCGGCGTTTTACCAAAAACGCCAC
1 TAAAA-ACAGAGCAATAGCGGCGTTTTACCAAAAACGCCAC
20087349 TAAAAACAGAGCAATAGCGGCGTTTTACCAAAAACGCCAC
1 TAAAAACAGAGCAATAGCGGCGTTTTACCAAAAACGCCAC
* *
20087389 TAAAAATAGAGCAATAGCGGCATTTTACCAAAAACGCCAC
1 TAAAAACAGAGCAATAGCGGCGTTTTACCAAAAACGCCAC
* ** *
20087429 TAAAAACAGAGCAATAGTGGCGTTTTAGTAAAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGTTTTA-CCAAAAACGCCAC
*
20087470 TAAAAACCAGAGCATTAGCGG
1 TAAAAA-CAGAGCAATAGCGG
20087491 GGCTTTTGGA
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
40 96 0.74
41 21 0.16
42 12 0.09
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGTTTTACCAAAAACGCCAC
Found at i:20087682 original size:7 final size:7
Alignment explanation
Indices: 20087672--20087769 Score: 61
Period size: 7 Copynumber: 13.4 Consensus size: 7
20087662 TTAATTATTA
*
20087672 TTATAGT
1 TTATGGT
20087679 TTATGGT
1 TTATGGT
20087686 TTATGGT
1 TTATGGT
* *
20087693 TTAAGAT
1 TTATGGT
*
20087700 ATATGGT
1 TTATGGT
*
20087707 TTAGGGT
1 TTATGGT
*
20087714 TTAAGGT
1 TTATGGT
20087721 TTATGAGT
1 TTATG-GT
20087729 TAACTATGGT
1 T---TATGGT
* *
20087739 TTAAGAT
1 TTATGGT
*
20087746 ATATGGT
1 TTATGGT
*
20087753 TTAGGGT
1 TTATGGT
*
20087760 TTAAGGT
1 TTATGGT
20087767 TTA
1 TTA
20087770 GGAGTTAACT
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
7 59 0.86
8 3 0.04
10 3 0.04
11 4 0.06
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.47
Consensus pattern (7 bp):
TTATGGT
Found at i:20087704 original size:21 final size:21
Alignment explanation
Indices: 20087680--20087764 Score: 98
Period size: 21 Copynumber: 3.9 Consensus size: 21
20087670 TATTATAGTT
*
20087680 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
20087701 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
*
20087722 TATGAGTTAACTATGGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
20087747 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
20087765 GTTTAGGAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 32 0.60
22 3 0.06
24 3 0.06
25 15 0.28
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:20087739 original size:46 final size:46
Alignment explanation
Indices: 20087687--20087780 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
20087677 GTTTATGGTT
*
20087687 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAAC
1 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
20087733 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
20087779 TA
1 TA
20087781 GTATTTGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (46 bp):
TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
Found at i:20090971 original size:3 final size:3
Alignment explanation
Indices: 20090963--20090999 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20090953 GCTTATTAGG
20090963 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
20091000 TACCTATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:20095639 original size:21 final size:20
Alignment explanation
Indices: 20095613--20095653 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
20095603 ATATACCTAT
* *
20095613 ATATATATTAAAGATATATAC
1 ATATATAATAAA-ACATATAC
20095634 ATATATAATAAAACATATAC
1 ATATATAATAAAACATATAC
20095654 TAAGATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATATAATAAAACATATAC
Found at i:20096020 original size:19 final size:20
Alignment explanation
Indices: 20095986--20096023 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20095976 ATAATGTATT
20095986 AATAAGAATGATAATAATAA
1 AATAAGAATGATAATAATAA
*
20096006 AATAAG-ATTATAATAATA
1 AATAAGAATGATAATAATA
20096024 GTATCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AATAAGAATGATAATAATAA
Found at i:20096234 original size:18 final size:21
Alignment explanation
Indices: 20096207--20096251 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
20096197 TAATCATGTA
20096207 AATAACAATG-AT-AAT-AAT
1 AATAACAATGAATAAATAAAT
*
20096225 AATAATAATGAATAAATAAAT
1 AATAACAATGAATAAATAAAT
20096246 AATAAC
1 AATAAC
20096252 TGTGACAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 3 0.14
21 8 0.36
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AATAACAATGAATAAATAAAT
Found at i:20102758 original size:26 final size:26
Alignment explanation
Indices: 20102721--20102803 Score: 157
Period size: 26 Copynumber: 3.2 Consensus size: 26
20102711 ATGAAATTCC
20102721 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
*
20102747 TATCATGAAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
20102773 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
20102799 TATCA
1 TATCA
20102804 ATTTATATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:20113472 original size:3 final size:3
Alignment explanation
Indices: 20113458--20113512 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
20113448 TAAAGAGCGT
*
20113458 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
20113503 TGAA TAA TAA
1 T-AA TAA TAA
20113513 CAGTAACAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 4 0.09
5 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20113659 original size:15 final size:15
Alignment explanation
Indices: 20113629--20113675 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
20113619 AATAAATAAC
*
20113629 AATTAA-TAATACTA
1 AATTAATTAATAATA
20113643 AATTAATTAATAATA
1 AATTAATTAATAATA
* *
20113658 AATAAATAAATAAATA
1 AATTAATTAAT-AATA
20113674 AA
1 AA
20113676 CATAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 6 0.21
15 16 0.57
16 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AATTAATTAATAATA
Found at i:20113661 original size:7 final size:7
Alignment explanation
Indices: 20113616--20113675 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
20113606 TAATAAGGAC
20113616 AATAATA
1 AATAATA
*
20113623 AATAACA
1 AATAATA
*
20113630 ATTAAT-
1 AATAATA
*
20113636 AATACTA
1 AATAATA
*
20113643 AATTAATT
1 AA-TAATA
20113651 AATAATA
1 AATAATA
20113658 AATAAATA
1 AAT-AATA
20113666 AATAAATA
1 AAT-AATA
20113674 AA
1 AA
20113676 CATAAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
6 4 0.10
7 19 0.45
8 19 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:20119307 original size:22 final size:22
Alignment explanation
Indices: 20119263--20119307 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
20119253 TACAGCGCTA
* *
20119263 TTTTAAGTTCTTCTATCTTCTC
1 TTTTAAGTTCTTCGATCTGCTC
20119285 TTTTAA-TTCTTCGATTCTGCTC
1 TTTTAAGTTCTTCGA-TCTGCTC
20119307 T
1 T
20119308 GACTAGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.13, C:0.22, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAAGTTCTTCGATCTGCTC
Found at i:20123275 original size:3 final size:3
Alignment explanation
Indices: 20123267--20123293 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20123257 TAAAGAGTGT
20123267 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
20123294 CGACAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20123966 original size:11 final size:10
Alignment explanation
Indices: 20123928--20123974 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
20123918 TCAAAAAAGG
20123928 TATATATTTT
1 TATATATTTT
*
20123938 T-TATTTTTT
1 TATATATTTT
20123947 TATAT-TTTT
1 TATATATTTT
20123956 TGATATATTTT
1 T-ATATATTTT
20123967 TAATATAT
1 T-ATATAT
20123975 GTATGTATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 13 0.41
10 8 0.25
11 11 0.34
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TATATATTTT
Found at i:20124430 original size:15 final size:16
Alignment explanation
Indices: 20124410--20124447 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20124400 AGGGTTAAAA
*
20124410 GGGTTTTAGGCT-GTT
1 GGGTTTTAGGATAGTT
*
20124425 GGGTTTTGGGATAGTT
1 GGGTTTTAGGATAGTT
20124441 GGGTTTT
1 GGGTTTT
20124448 GGGCAGGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.08, C:0.03, G:0.42, T:0.47
Consensus pattern (16 bp):
GGGTTTTAGGATAGTT
Found at i:20125638 original size:17 final size:17
Alignment explanation
Indices: 20125618--20125668 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
20125608 GAATAATATA
20125618 GAATAATTTAAAATAAT
1 GAATAATTTAAAATAAT
* *
20125635 GAATAGTATAAAAATGAAT
1 GAATAAT-TTAAAAT-AAT
*
20125654 -AATAACTTAAAATAA
1 GAATAATTTAAAATAA
20125669 ATAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 2 0.07
17 12 0.44
18 10 0.37
19 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (17 bp):
GAATAATTTAAAATAAT
Found at i:20127990 original size:19 final size:20
Alignment explanation
Indices: 20127968--20128017 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
20127958 GGTCTTTTCG
* *
20127968 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGAA
20127987 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
20128007 TGAAATG-AATG
1 TGAAATGTAATG
20128018 TGAAAAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:20132279 original size:27 final size:26
Alignment explanation
Indices: 20132174--20132287 Score: 88
Period size: 27 Copynumber: 4.3 Consensus size: 26
20132164 TGAAAGAAAC
* *
20132174 TTAAAATGGATAATACATAAATAATAG
1 TTAAAATGAATAATATATAAA-AATAG
** *
20132201 TTTAAAATGAATAACGTATAAAAATAT
1 -TTAAAATGAATAATATATAAAAATAG
* *
20132228 TTCAAAAT-AAGTAATATGT-ATAATAG
1 TT-AAAATGAA-TAATATATAAAAATAG
* *
20132254 TTAAAATGAATAATATATGTAAAATAT
1 TTAAAATGAATAATATAT-AAAAATAG
20132281 TTAAAAT
1 TTAAAAT
20132288 CTGTAATATC
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
25 12 0.18
26 13 0.19
27 26 0.38
28 17 0.25
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (26 bp):
TTAAAATGAATAATATATAAAAATAG
Found at i:20132287 original size:52 final size:53
Alignment explanation
Indices: 20132194--20132296 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 53
20132184 TAATACATAA
*
20132194 ATAATAGTTTAAAATGAATAACGTATAAAAATATTTCAAAATAAGTAATATGT
1 ATAATAGTTTAAAATGAATAACATATAAAAATATTTCAAAATAAGTAATATGT
* * **
20132247 ATAATAG-TTAAAATGAATAATATATGTAAAATATTT-AAAATCTGTAATAT
1 ATAATAGTTTAAAATGAATAACATAT-AAAAATATTTCAAAATAAGTAATAT
20132297 CTTAAAGTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
52 28 0.64
53 16 0.36
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (53 bp):
ATAATAGTTTAAAATGAATAACATATAAAAATATTTCAAAATAAGTAATATGT
Found at i:20133249 original size:14 final size:14
Alignment explanation
Indices: 20133230--20133259 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20133220 AAATAATAAT
*
20133230 AAAATGAAACTAAA
1 AAAATGAAACGAAA
20133244 AAAATGAAACGAAA
1 AAAATGAAACGAAA
20133258 AA
1 AA
20133260 TGAAGAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAATGAAACGAAA
Found at i:20146988 original size:19 final size:19
Alignment explanation
Indices: 20146961--20147000 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
20146951 AAATTACATG
20146961 CGAAAGATCAGATCTGTAT
1 CGAAAGATCAGATCTGTAT
*
20146980 CGAAGGATCAGATCTGTAT
1 CGAAAGATCAGATCTGTAT
20146999 CG
1 CG
20147001 TCTAAGCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (19 bp):
CGAAAGATCAGATCTGTAT
Found at i:20148515 original size:17 final size:17
Alignment explanation
Indices: 20148493--20148610 Score: 155
Period size: 17 Copynumber: 6.6 Consensus size: 17
20148483 CTTCAATATG
20148493 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
20148510 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
20148528 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
20148545 TGCAATCTTAGATATGATA
1 --CAATCTTAGATATGATA
*
20148564 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
*
20148582 TAATCTTAGATATGATA
1 CAATCTTAGATATGATA
20148599 TGCAATCTTAGA
1 --CAATCTTAGA
20148611 AGATATGATT
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
17 32 0.36
18 31 0.35
19 26 0.29
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:20148536 original size:35 final size:35
Alignment explanation
Indices: 20148491--20148610 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 35
20148481 ATCTTCAATA
20148491 TGCAATCTTAGATATGATACAATCTTAGATATGAT
1 TGCAATCTTAGATATGATACAATCTTAGATATGAT
20148526 TGCAATCTTAGATATGATATGCAATCTTAGATATGA-
1 TGCAATCTTAGATATGATA--CAATCTTAGATATGAT
* **
20148562 TACAATCTTAGATATGATTGTAATCTTAGATATGAT
1 TGCAATCTTAGATATGA-TACAATCTTAGATATGAT
20148598 ATGCAATCTTAGA
1 -TGCAATCTTAGA
20148611 AGATATGATT
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
35 33 0.43
36 16 0.21
37 27 0.36
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (35 bp):
TGCAATCTTAGATATGATACAATCTTAGATATGAT
Found at i:20148547 original size:54 final size:54
Alignment explanation
Indices: 20148488--20148610 Score: 237
Period size: 54 Copynumber: 2.3 Consensus size: 54
20148478 ATAATCTTCA
20148488 ATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATG
1 ATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATG
*
20148542 ATATGCAATCTTAGATATGATACAATCTTAGATATGATTGTAATCTTAGATATG
1 ATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATG
20148596 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
20148611 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (54 bp):
ATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATG
Found at i:20148617 original size:17 final size:19
Alignment explanation
Indices: 20148488--20148610 Score: 195
Period size: 19 Copynumber: 6.8 Consensus size: 19
20148478 ATAATCTTCA
20148488 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
20148507 ATA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
20148524 AT-TGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
20148542 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
20148561 ATA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
20148578 AT-TGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
20148596 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
20148611 AGATATGATT
Statistics
Matches: 96, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
17 32 0.33
18 31 0.32
19 33 0.34
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:20148632 original size:23 final size:22
Alignment explanation
Indices: 20148571--20148646 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
20148561 ATACAATCTT
20148571 AGATATGA-TTGTAATCTT---
1 AGATATGATTTGTAATCTTAGA
* *
20148589 AGATATGATATGCAATCTTAGA
1 AGATATGATTTGTAATCTTAGA
20148611 AGATATGATTTTGTAATCTTAG-
1 AGATATGA-TTTGTAATCTTAGA
* *
20148633 AGATTTAATTTGTA
1 AGATATGATTTGTA
20148647 GATACCTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 8 0.17
19 8 0.17
21 6 0.13
22 14 0.30
23 11 0.23
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (22 bp):
AGATATGATTTGTAATCTTAGA
Found at i:20148636 original size:22 final size:21
Alignment explanation
Indices: 20148517--20148646 Score: 77
Period size: 19 Copynumber: 6.7 Consensus size: 21
20148507 ATACAATCTT
*
20148517 AGATATGA-TTGCAATCTT--
1 AGATATGATTTGTAATCTTAG
* *
20148535 AGATATGATATGCAATCTT--
1 AGATATGATTTGTAATCTTAG
**
20148554 AGATATGA--TACAATCTT--
1 AGATATGATTTGTAATCTTAG
20148571 AGATATGA-TTGTAATCTT--
1 AGATATGATTTGTAATCTTAG
* *
20148589 AGATATGATATGCAATCTTAG
1 AGATATGATTTGTAATCTTAG
20148610 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
* *
20148633 AGATTTAATTTGTA
1 AGATATGATTTGTA
20148647 GATACCTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
17 16 0.17
18 23 0.24
19 25 0.26
21 6 0.06
22 14 0.15
23 11 0.12
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:20151342 original size:17 final size:17
Alignment explanation
Indices: 20151320--20151353 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20151310 AATAAGCTTC
20151320 ACAACCCTTTCTCACAA
1 ACAACCCTTTCTCACAA
20151337 ACAACCCTTTCTCACAA
1 ACAACCCTTTCTCACAA
20151354 TACTTAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (17 bp):
ACAACCCTTTCTCACAA
Found at i:20162902 original size:5 final size:5
Alignment explanation
Indices: 20162892--20162919 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20162882 CCAATTAGTA
20162892 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20162920 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20183104 original size:12 final size:13
Alignment explanation
Indices: 20183067--20183101 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
20183057 CAGAAATTAT
20183067 AAAGAAAATAAAG
1 AAAGAAAATAAAG
20183080 AAAGAAATAATAAAG
1 AAAG-AA-AATAAAG
20183095 AAAGAAA
1 AAAGAAA
20183102 TAATGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 4 0.20
15 11 0.55
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:20183114 original size:14 final size:14
Alignment explanation
Indices: 20183080--20183128 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
20183070 GAAAATAAAG
**
20183080 AAAGAAATAATAAA
1 AAAGAAATAATGTA
20183094 GAAAGAAATAATGTA
1 -AAAGAAATAATGTA
* *
20183109 AAAGAAAAAAAGTA
1 AAAGAAATAATGTA
20183123 AAAGAA
1 AAAGAA
20183129 TTATATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (14 bp):
AAAGAAATAATGTA
Found at i:20183115 original size:18 final size:15
Alignment explanation
Indices: 20183073--20183105 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20183063 TTATAAAGAA
20183073 AATAAAGAAAGAAAT
1 AATAAAGAAAGAAAT
20183088 AATAAAGAAAGAAAT
1 AATAAAGAAAGAAAT
20183103 AAT
1 AAT
20183106 GTAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (15 bp):
AATAAAGAAAGAAAT
Found at i:20200420 original size:26 final size:29
Alignment explanation
Indices: 20200367--20200422 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
20200357 AGGTTTCCAT
* *
20200367 TGATGAATCTTGTGATTTTTGATGTTATA
1 TGATGAATCTTGTGAATGTTGATGTTATA
20200396 TGATGAAT-TTG-GAATGTTGAT-TTATA
1 TGATGAATCTTGTGAATGTTGATGTTATA
20200422 T
1 T
20200423 TTAAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 8 0.32
28 3 0.12
29 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (29 bp):
TGATGAATCTTGTGAATGTTGATGTTATA
Found at i:20205083 original size:3 final size:3
Alignment explanation
Indices: 20205075--20205118 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
20205065 TTCCAAAAGT
20205075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20205119 GTTTAATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20205192 original size:30 final size:30
Alignment explanation
Indices: 20205158--20205229 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
20205148 CTTAAGAAAA
* * * *
20205158 AATTTCAAAAACTTTTA-TAAATTTACTTGG
1 AATTT-AAAAAATTTTAGAAAATTTAATTAG
*
20205188 AATTTTTAAAAATTTTAGAAAATTTAATTAG
1 AA-TTTAAAAAATTTTAGAAAATTTAATTAG
20205219 AATTTAAAAAA
1 AATTTAAAAAA
20205230 ATTTCATGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (30 bp):
AATTTAAAAAATTTTAGAAAATTTAATTAG
Found at i:20205544 original size:53 final size:51
Alignment explanation
Indices: 20205457--20205557 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 51
20205447 ATGGTTAACT
20205457 TTTTTAAAGAAATAAAAAATTATAAAAATAATTATTTAACTTATCAACACG
1 TTTTTAAAGAAATAAAAAATTATAAAAATAATTATTTAACTTATCAACACG
20205508 TTTTTAAAGAAATTATAAAAAATTAT-AAAATAATTATTTAACTTATCAAC
1 TTTTTAAAG-AA--ATAAAAAATTATAAAAATAATTATTTAACTTATCAAC
20205558 TTCGCCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
51 9 0.19
52 2 0.04
53 24 0.51
54 12 0.26
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (51 bp):
TTTTTAAAGAAATAAAAAATTATAAAAATAATTATTTAACTTATCAACACG
Found at i:20219430 original size:31 final size:31
Alignment explanation
Indices: 20219372--20219430 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
20219362 ATTATCATCC
* *
20219372 TTATAATCAATCAATTTTATACGTTTATACT
1 TTATAATCAATCAATTTTACACATTTATACT
*
20219403 TTATAATCATTCAAATTTT-CACATTTAT
1 TTATAATCAATC-AATTTTACACATTTAT
20219431 GCCCTGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.75
32 6 0.25
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.49
Consensus pattern (31 bp):
TTATAATCAATCAATTTTACACATTTATACT
Found at i:20229542 original size:16 final size:17
Alignment explanation
Indices: 20229506--20229544 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
20229496 TTTTAAAAGG
20229506 AAAACAAATGAATCTTA
1 AAAACAAATGAATCTTA
*
20229523 AAAACAAATGAGTCTTA
1 AAAACAAATGAATCTTA
20229540 AAAAC
1 AAAAC
20229545 TTAAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAACAAATGAATCTTA
Found at i:20235767 original size:18 final size:17
Alignment explanation
Indices: 20235729--20235768 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
20235719 TTTTGAAAAG
20235729 AAAAACAAATGAATCTT
1 AAAAACAAATGAATCTT
*
20235746 AAAAACAAATGAGTCTT
1 AAAAACAAATGAATCTT
20235763 AAAAAC
1 AAAAAC
20235769 TTAAGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAAACAAATGAATCTT
Found at i:20239906 original size:40 final size:40
Alignment explanation
Indices: 20239836--20239932 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
20239826 CCGTCTCCGT
*
20239836 CCAACCCAACACACC-A-TATGGGGATAAAATCAACCCAC
1 CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
* *
20239874 CCAACCCTACACACCAAGTATGGGGATAAAATCGACCCAT
1 CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
*
20239914 CCAGCCCTACACACCAAGT
1 CCAACCCTACACACCAAGT
20239933 GGTACTGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 14 0.26
39 1 0.02
40 38 0.72
ACGTcount: A:0.38, C:0.37, G:0.12, T:0.12
Consensus pattern (40 bp):
CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
Found at i:20247072 original size:22 final size:22
Alignment explanation
Indices: 20247041--20247094 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
20247031 TTTCACGATT
20247041 CACACGGCCTAGCCATTAAGCC
1 CACACGGCCTAGCCATTAAGCC
* *
20247063 CATACGGCCTAGCCATTGAGCC
1 CACACGGCCTAGCCATTAAGCC
20247085 CACACGGCCT
1 CACACGGCCT
20247095 GGTAATCACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.41, G:0.20, T:0.15
Consensus pattern (22 bp):
CACACGGCCTAGCCATTAAGCC
Found at i:20255582 original size:16 final size:16
Alignment explanation
Indices: 20255556--20255615 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
20255546 TCCTCCTATT
20255556 TTATT-TTTATTCTTA
1 TTATTATTTATTCTTA
20255571 TTATTATTTATTCTTA
1 TTATTATTTATTCTTA
* *
20255587 TTTTTGTTTTATT-TTA
1 TTATT-ATTTATTCTTA
20255603 TT-TTATTTTATTC
1 TTATTA-TTTATTC
20255616 CTGTTTTCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.34
16 19 0.50
17 6 0.16
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (16 bp):
TTATTATTTATTCTTA
Found at i:20255601 original size:10 final size:10
Alignment explanation
Indices: 20255552--20255614 Score: 65
Period size: 10 Copynumber: 5.9 Consensus size: 10
20255542 TGAATCCTCC
20255552 TATTTTATTTT
1 TATTTTA-TTT
20255563 TATTCTTATTAT
1 TATT-TTATT-T
20255575 TA-TTTATTCT
1 TATTTTATT-T
*
20255585 TATTTTTGTTT
1 TA-TTTTATTT
20255596 TATTTTATTT
1 TATTTTATTT
20255606 TATTTTATT
1 TATTTTATT
20255615 CCTGTTTTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 24 0.53
11 10 0.22
12 11 0.24
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (10 bp):
TATTTTATTT
Found at i:20265398 original size:12 final size:12
Alignment explanation
Indices: 20265383--20265407 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20265373 TTTTATGGAT
20265383 GATTTTTCCTTA
1 GATTTTTCCTTA
20265395 GATTTTTCCTTA
1 GATTTTTCCTTA
20265407 G
1 G
20265408 GTGAGCATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (12 bp):
GATTTTTCCTTA
Found at i:20267374 original size:7 final size:7
Alignment explanation
Indices: 20267362--20267393 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
20267352 TGCAGATCAG
*
20267362 ATCAGAT
1 ATCAGAA
20267369 ATCAGAA
1 ATCAGAA
20267376 ATCAGAA
1 ATCAGAA
20267383 ATCAGAA
1 ATCAGAA
20267390 ATCA
1 ATCA
20267394 TTCATCCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (7 bp):
ATCAGAA
Found at i:20267593 original size:237 final size:237
Alignment explanation
Indices: 20267160--20267623 Score: 675
Period size: 237 Copynumber: 2.0 Consensus size: 237
20267150 TTACTCACAA
* * *
20267160 ATCCTTAAATGTCTAGCAGTGGTCACATCGAACCCTCTGCCACACCGATCCATCTACTGCTGAGG
1 ATCCATAAATGTCCAACAGTGGTCACATCGAACCCTCTGCCACACCGATCCATCTACTGCTGAGG
* ** * *
20267225 ATTACCTGACATAAAATAAATAATGGGGTAAGTTTTTGCAAACTCAGTGTGTACATCCCCTCAAA
66 ATTACCTGACATAAAATAAATAAAGACGTAAGTTTTTCCAAACTCAGTGTGTACATCCCCACAAA
* * * *
20267290 TAGCATGCATACAAATAAATAACAGAATATAGATATTCGCCTTTAGCCTTACAAATATCACATGC
131 CAGCATGCATAAAAATAAATAACAAAATACAGATATTCGCCTTTAGCCTTACAAATATCACATGC
*
20267355 AGATCAGATCAGATATCAGA-AATCAGAAATCAGAAATCATTC
196 AGATCAAATCAGATATCAGAGAA-CAGAAATCAGAAATCATTC
* *
20267397 ATCCATAAATGTCCAACAGTGGTCACCATCGAGCCCTCTGCCATACCGATCCATCTACTGCTGAG
1 ATCCATAAATGTCCAACAGTGGTCA-CATCGAACCCTCTGCCACACCGATCCATCTACTGCTGAG
* *
20267462 GATTATCTGACATAAAATAAATAAAGACGTGAG-TTTTCCAAACTCAGTGTGTACATCCCCACAA
65 GATTACCTGACATAAAATAAATAAAGACGTAAGTTTTTCCAAACTCAGTGTGTACATCCCCACAA
* * **
20267526 ACAGCATGCATAAAAATAGATAACAAAATACAGATA-TCTGACC-TTAGCCTTACAGATATTGCA
130 ACAGCATGCATAAAAATAAATAACAAAATACAGATATTC-G-CCTTTAGCCTTACAAATATCACA
20267589 TGCAGATCAAATCAGATATCAGAGAACAGAAATCA
193 TGCAGATCAAATCAGATATCAGAGAACAGAAATCA
20267624 TGCCCACCAA
Statistics
Matches: 202, Mismatches: 21, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
236 2 0.01
237 131 0.65
238 69 0.34
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (237 bp):
ATCCATAAATGTCCAACAGTGGTCACATCGAACCCTCTGCCACACCGATCCATCTACTGCTGAGG
ATTACCTGACATAAAATAAATAAAGACGTAAGTTTTTCCAAACTCAGTGTGTACATCCCCACAAA
CAGCATGCATAAAAATAAATAACAAAATACAGATATTCGCCTTTAGCCTTACAAATATCACATGC
AGATCAAATCAGATATCAGAGAACAGAAATCAGAAATCATTC
Found at i:20267703 original size:38 final size:38
Alignment explanation
Indices: 20267661--20267751 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 38
20267651 GTCCAACCCA
**
20267661 ACACACCATGTGGGGATAAAATCGACCCACCCAGTTCT
1 ACACACCATGTGGGGATAAAATCGACCCACCCAGCCCT
* *
20267699 ACACACCAAGTATGGGGATAAAATCGACCCATCCAGCCCT
1 ACACACC-A-TGTGGGGATAAAATCGACCCACCCAGCCCT
*
20267739 ACACACCAAGTGG
1 ACACACCATGTGG
20267752 TACTGTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 10 0.22
39 2 0.04
40 33 0.73
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (38 bp):
ACACACCATGTGGGGATAAAATCGACCCACCCAGCCCT
Found at i:20267718 original size:40 final size:40
Alignment explanation
Indices: 20267671--20267749 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
20267661 ACACACCATG
**
20267671 TGGGGATAAAATCGACCCACCCAGTTCTACACACCAAGTA
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
*
20267711 TGGGGATAAAATCGACCCATCCAGCCCTACACACCAAGT
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
20267750 GGTACTGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
Found at i:20269169 original size:20 final size:20
Alignment explanation
Indices: 20269136--20269212 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
20269126 GTTCAAAAGA
*
20269136 TAAT-AAAT-AAAATAAATC
1 TAATAAAATAAAAATAAAAC
20269154 TAATAAAATAAAAATAAAAC
1 TAATAAAATAAAAATAAAAC
20269174 -AACTAAAATAAAAAATAAAA-
1 TAA-TAAAAT-AAAAATAAAAC
*
20269194 -AACTAAAATAAAACTAAAA
1 TAA-TAAAATAAAAATAAAA
20269213 TTAGTGGTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
18 4 0.08
19 15 0.28
20 24 0.45
21 10 0.19
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (20 bp):
TAATAAAATAAAAATAAAAC
Found at i:20272903 original size:30 final size:30
Alignment explanation
Indices: 20272867--20272923 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20272857 ATGACCATGA
* *
20272867 CACACGGG-GATGTGGTTTGCCTGTGTGCCT
1 CACACGGGCG-TGTGGTTTACCCGTGTGCCT
20272897 CACACGGGCGTGTGGTTTACCCGTGTG
1 CACACGGGCGTGTGGTTTACCCGTGTG
20272924 GTTGTGCCTA
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:0.11, C:0.25, G:0.37, T:0.28
Consensus pattern (30 bp):
CACACGGGCGTGTGGTTTACCCGTGTGCCT
Found at i:20273454 original size:17 final size:18
Alignment explanation
Indices: 20273404--20273455 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
20273394 ATAATGAAAT
*
20273404 AACAAT-AATAATAATCAA
1 AACAATAAAAAATAAT-AA
*
20273422 AACAATAAAACA-AATAA
1 AACAATAAAAAATAATAA
20273439 AA-AATAAAAAATAATAA
1 AACAATAAAAAATAATAA
20273456 TAAGATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.28
17 9 0.31
18 9 0.31
19 3 0.10
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (18 bp):
AACAATAAAAAATAATAA
Found at i:20273520 original size:47 final size:43
Alignment explanation
Indices: 20273404--20273521 Score: 116
Period size: 47 Copynumber: 2.7 Consensus size: 43
20273394 ATAATGAAAT
* * *
20273404 AACAATAATAATAATCA-AAACAATAAAACAAATAAAAAATAA
1 AACAATAATAATAATGATAAACAATAAAACAAAGAAAAAAAAA
* *
20273446 AA-AATAATAATAA-GATAATGATAATAAAACTAAGAAAAATAAAA
1 AACAATAATAATAATGATAA--ACAATAAAACAAAGAAAAA-AAAA
20273490 CAACCAATAATAATAATGATAAACAGATAAAA
1 -AA-CAATAATAATAATGATAAACA-ATAAAA
20273522 ATGCACTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
40 1 0.02
41 13 0.21
42 2 0.03
43 16 0.26
44 3 0.05
45 2 0.03
46 2 0.03
47 17 0.28
48 5 0.08
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (43 bp):
AACAATAATAATAATGATAAACAATAAAACAAAGAAAAAAAAA
Found at i:20275638 original size:20 final size:20
Alignment explanation
Indices: 20275615--20275673 Score: 118
Period size: 20 Copynumber: 3.0 Consensus size: 20
20275605 ATGAATTTAT
20275615 CAACTTTAATAAGTACATAC
1 CAACTTTAATAAGTACATAC
20275635 CAACTTTAATAAGTACATAC
1 CAACTTTAATAAGTACATAC
20275655 CAACTTTAATAAGTACATA
1 CAACTTTAATAAGTACATA
20275674 GCCATAGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
CAACTTTAATAAGTACATAC
Found at i:20279882 original size:14 final size:14
Alignment explanation
Indices: 20279863--20279889 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20279853 TTCATTTGAT
20279863 CTCATCCATCATCC
1 CTCATCCATCATCC
20279877 CTCATCCATCATC
1 CTCATCCATCATC
20279890 ATTCTGTCTA
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:0.48, G:0.00, T:0.30
Consensus pattern (14 bp):
CTCATCCATCATCC
Found at i:20283011 original size:24 final size:24
Alignment explanation
Indices: 20282979--20283026 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
20282969 TACATACATA
* *
20282979 TATATATATATCCTTTAGCCAAAT
1 TATATATATATCATTCAGCCAAAT
20283003 TATATATATATCATTCAGCCAAAT
1 TATATATATATCATTCAGCCAAAT
20283027 CAACCAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (24 bp):
TATATATATATCATTCAGCCAAAT
Found at i:20283554 original size:36 final size:36
Alignment explanation
Indices: 20283514--20283585 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
20283504 TTCCATTTGC
*
20283514 ATCATACATAATTTATATAATATTTCAAATAACTAT
1 ATCATACATAATTTATATAACATTTCAAATAACTAT
*
20283550 ATCATACATAATTTATATCACATTTCAAATAACTAT
1 ATCATACATAATTTATATAACATTTCAAATAACTAT
20283586 CTTACATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (36 bp):
ATCATACATAATTTATATAACATTTCAAATAACTAT
Found at i:20284594 original size:12 final size:12
Alignment explanation
Indices: 20284577--20284603 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20284567 TTCTAAAATC
20284577 TTTTATTTTTCT
1 TTTTATTTTTCT
20284589 TTTTATTTTTCT
1 TTTTATTTTTCT
20284601 TTT
1 TTT
20284604 CTTTGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTCT
Found at i:20303459 original size:38 final size:38
Alignment explanation
Indices: 20303411--20303488 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
20303401 ATTACTTACA
*
20303411 AACAACCATATAATAATCATTTAGGAATTTAATTTATC
1 AACAACCATATAATAATCATTTAGAAATTTAATTTATC
*
20303449 AACAACCATATAATAATCGTTTAGAAATTTAATTTATC
1 AACAACCATATAATAATCATTTAGAAATTTAATTTATC
20303487 AA
1 AA
20303489 ATAGCCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (38 bp):
AACAACCATATAATAATCATTTAGAAATTTAATTTATC
Found at i:20304678 original size:12 final size:12
Alignment explanation
Indices: 20304638--20304676 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
20304628 CCCTGTGAGT
20304638 TTTTCTTTTTTC
1 TTTTCTTTTTTC
20304650 TTTTCTTTTTTCC
1 TTTTCTTTTTT-C
20304663 TTTT-TTTTTT-
1 TTTTCTTTTTTC
20304673 TTTT
1 TTTT
20304677 TTGGAGGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
12 17 0.65
13 5 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:20310004 original size:28 final size:28
Alignment explanation
Indices: 20309963--20310018 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
20309953 AGTTCATGTT
*
20309963 CATAGTCTCGTGATTACCTTTAGCACAG
1 CATAGTCTCATGATTACCTTTAGCACAG
20309991 CATAGTCTCATGATTACCTTTAGCACAG
1 CATAGTCTCATGATTACCTTTAGCACAG
20310019 ATGAATAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (28 bp):
CATAGTCTCATGATTACCTTTAGCACAG
Found at i:20310351 original size:7 final size:7
Alignment explanation
Indices: 20310339--20310368 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
20310329 GACAGAGAAT
20310339 GTGAAGA
1 GTGAAGA
20310346 GTGAAGA
1 GTGAAGA
20310353 GTGAAGA
1 GTGAAGA
20310360 GTGAAGA
1 GTGAAGA
20310367 GT
1 GT
20310369 AGGGTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (7 bp):
GTGAAGA
Found at i:20312382 original size:21 final size:18
Alignment explanation
Indices: 20312352--20312397 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
20312342 ATTTGTCTTT
*
20312352 TTTTAATTTAATATTTTTGAG
1 TTTTATTTTAA-ATTTTT--G
20312373 TTTTATTTTAAATTTTTG
1 TTTTATTTTAAATTTTTG
20312391 TTTTATT
1 TTTTATT
20312398 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
20 6 0.25
21 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTATTTTAAATTTTTG
Found at i:20312387 original size:20 final size:21
Alignment explanation
Indices: 20312352--20312390 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20312342 ATTTGTCTTT
20312352 TTTTAATTTAATATTTTTGAG
1 TTTTAATTTAATATTTTTGAG
*
20312373 TTTTATTTTAA-ATTTTTG
1 TTTTAATTTAATATTTTTG
20312391 TTTTATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTTAATTTAATATTTTTGAG
Found at i:20315268 original size:12 final size:13
Alignment explanation
Indices: 20315245--20315270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20315235 AAAATTTTAA
20315245 AATTTTTAAAAAT
1 AATTTTTAAAAAT
20315258 AATTTTTAAAAAT
1 AATTTTTAAAAAT
20315271 GTTATAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:20315296 original size:17 final size:17
Alignment explanation
Indices: 20315276--20315313 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20315266 AAAATGTTAT
20315276 AAATTAGAAAAACA-TAA
1 AAATTA-AAAAACATTAA
*
20315293 AAATTATAAAACATTAA
1 AAATTAAAAAACATTAA
20315310 AAAT
1 AAAT
20315314 ACATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATTAAAAAACATTAA
Found at i:20317041 original size:22 final size:22
Alignment explanation
Indices: 20317015--20317056 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20317005 AACGAATCTA
**
20317015 GTTAATGGCCGACAGATCAAAT
1 GTTAATGGAAGACAGATCAAAT
20317037 GTTAATGGAAGACAGATCAA
1 GTTAATGGAAGACAGATCAA
20317057 CAAAAGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (22 bp):
GTTAATGGAAGACAGATCAAAT
Found at i:20318167 original size:19 final size:20
Alignment explanation
Indices: 20318145--20318192 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
20318135 CTAGACATCC
20318145 TTAAATTATTATCTTT-ATT
1 TTAAATTATTATCTTTAATT
20318164 TTAAATTA--ATCTTTAAATT
1 TTAAATTATTATCTTT-AATT
*
20318183 TTAAAATATT
1 TTAAATTATT
20318193 TTAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 6 0.25
19 18 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTATTATCTTTAATT
Found at i:20318208 original size:28 final size:30
Alignment explanation
Indices: 20318160--20318215 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
20318150 TTATTATCTT
*
20318160 TATTTTAAATTAATCTTTAAATT-TTAAAA
1 TATTTTAAATTAATCTCTAAATTATTAAAA
20318189 TATTTT-AATTATATC-CTAAATTATTAA
1 TATTTTAAATTA-ATCTCTAAATTATTAA
20318216 TATTATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTTAAATTAATCTCTAAATTATTAAAA
Found at i:20323728 original size:48 final size:47
Alignment explanation
Indices: 20323616--20323758 Score: 169
Period size: 48 Copynumber: 3.0 Consensus size: 47
20323606 ACGGATGAAG
* *
20323616 TAGTCGGTAGTTTATCTACACGACCAGTGGTTCATCCACAACGCATTT
1 TAGTCGGTAG-TTATCTACACGACTAGTGGTTCATCCACAACGTATTT
*** * * *
20323664 TAGTCAACAGTCTATCTGCACAACTAGTGGTTCATCCACAATGTATTT
1 TAGTCGGTAGT-TATCTACACGACTAGTGGTTCATCCACAACGTATTT
* *
20323712 TAGTTGGTAGCTTATCTACATGACTAGTGGTTCATCCACAACGTATT
1 TAGTCGGTAG-TTATCTACACGACTAGTGGTTCATCCACAACGTATT
20323759 AGTAGTTTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
47 1 0.01
48 75 0.97
49 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (47 bp):
TAGTCGGTAGTTATCTACACGACTAGTGGTTCATCCACAACGTATTT
Found at i:20324258 original size:17 final size:15
Alignment explanation
Indices: 20324220--20324260 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
20324210 TATTAAGAAG
*
20324220 TATTTTAGATTTTTT
1 TATTTGAGATTTTTT
20324235 TATTTGAGATTTTTGT
1 TATTTGAGATTTTT-T
20324251 TAATTTGAGA
1 T-ATTTGAGA
20324261 ACTGTATCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (15 bp):
TATTTGAGATTTTTT
Found at i:20324745 original size:14 final size:15
Alignment explanation
Indices: 20324715--20324750 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
20324705 ACTCACTATT
*
20324715 TGTTTGCCAGTAAAA
1 TGTTTTCCAGTAAAA
20324730 TGTTTTCCAG-AAAA
1 TGTTTTCCAGTAAAA
20324744 TGTTTTC
1 TGTTTTC
20324751 TGGAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (15 bp):
TGTTTTCCAGTAAAA
Found at i:20324771 original size:20 final size:20
Alignment explanation
Indices: 20324746--20324792 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
20324736 CCAGAAAATG
*
20324746 TTTTCTGGAAAATTATTTAC
1 TTTTCTGGAAAATGATTTAC
20324766 TTTTCT-GAAAATGATTTAC
1 TTTTCTGGAAAATGATTTAC
20324785 TTTTCTGG
1 TTTTCTGG
20324793 TGTTTGGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTTCTGGAAAATGATTTAC
Found at i:20324896 original size:20 final size:19
Alignment explanation
Indices: 20324871--20324909 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
20324861 TTGTTTTTAC
20324871 ATATATTAATAAATTTATAT
1 ATATATTAATAAA-TTATAT
20324891 ATATATTAATAAATTATAT
1 ATATATTAATAAATTATAT
20324910 TTTAAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATTAATAAATTATAT
Found at i:20325363 original size:12 final size:12
Alignment explanation
Indices: 20325346--20325371 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20325336 CAATTCTTGT
20325346 ATGCCTACAAAA
1 ATGCCTACAAAA
20325358 ATGCCTACAAAA
1 ATGCCTACAAAA
20325370 AT
1 AT
20325372 CAACTCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (12 bp):
ATGCCTACAAAA
Found at i:20327338 original size:9 final size:9
Alignment explanation
Indices: 20327324--20327350 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
20327314 ATTTGGAAAC
20327324 TATACAAAA
1 TATACAAAA
20327333 TATACAAAA
1 TATACAAAA
20327342 TATACAAAA
1 TATACAAAA
20327351 AATTTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
TATACAAAA
Found at i:20328762 original size:72 final size:72
Alignment explanation
Indices: 20328645--20328791 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
20328635 ATGTTTGTGC
*
20328645 ACTCTTTCATCTTGATCCTATACTTTGGAAATTGGTTAGCCACATGGATCCTTAGATAACCTTAA
1 ACTCTTTCATCTTGATCCTATACTTTGGAAATTGGATAGCCACATGGATCCTTAGATAACCTTAA
20328710 GAATTGT
66 GAATTGT
20328717 ACTCTTTCATCTTGATCCTATACTTTGGAAATTGGATAGCCACATGGATCCTTAGATAACCTTAA
1 ACTCTTTCATCTTGATCCTATACTTTGGAAATTGGATAGCCACATGGATCCTTAGATAACCTTAA
20328782 GAATTGT
66 GAATTGT
20328789 ACT
1 ACT
20328792 TAAGACAATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (72 bp):
ACTCTTTCATCTTGATCCTATACTTTGGAAATTGGATAGCCACATGGATCCTTAGATAACCTTAA
GAATTGT
Found at i:20330907 original size:22 final size:22
Alignment explanation
Indices: 20330864--20330919 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
20330854 TAGTCATATA
* * *
20330864 ATAAATTATTAATATAAAAAAT
1 ATAATTTATTATTTTAAAAAAT
*
20330886 ATAATTTATTATTTTAATAAAT
1 ATAATTTATTATTTTAAAAAAT
*
20330908 -T-ATTTAATATTT
1 ATAATTTATTATTT
20330920 CAATTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
22 18 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTTATTATTTTAAAAAAT
Found at i:20330943 original size:13 final size:14
Alignment explanation
Indices: 20330927--20330968 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
20330917 TTTCAATTTT
20330927 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
20330940 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
20330955 ATTTTAAATAATAT
1 ATTTT-AATAATAT
20330969 TATTGACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:20330953 original size:16 final size:16
Alignment explanation
Indices: 20330931--20330967 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20330921 AATTTTATTT
20330931 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
20330948 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
20330963 TAATA
1 TAATA
20330968 TTATTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:20331546 original size:14 final size:14
Alignment explanation
Indices: 20331511--20331549 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20331501 CCAGAAAAAT
*
20331511 AAATCATATTCCAG
1 AAATCATTTTCCAG
20331525 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
20331539 AAGTCATTTTC
1 AAATCATTTTC
20331550 AGTGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:20338264 original size:22 final size:22
Alignment explanation
Indices: 20338236--20338278 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20338226 ACATTAACTG
20338236 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
20338258 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
20338279 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:20340742 original size:22 final size:22
Alignment explanation
Indices: 20340714--20340756 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20340704 AGGGGGAGTG
20340714 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
20340736 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
20340757 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:20355650 original size:128 final size:128
Alignment explanation
Indices: 20355454--20355692 Score: 318
Period size: 128 Copynumber: 1.9 Consensus size: 128
20355444 GACTAATATG
* * * * * * * *
20355454 TCATCTATCAAGTCCAATTGAGGAGATGTTTTGTCTTAGGCATTGGAGTGGATGACTCCTAGAAG
1 TCATCTATCAAGTCCAATTGAGGAGATGTTTTGTCATAGACATTAGAGCGAAAGACTCCCAAAAG
* * *
20355519 ATAAAGACTTAGATGTGACTAACTAGACTGATAGTACATCGAACTAGACTCAAGAAGAATAGA
66 ATAAAGACATAGATGCGACTAACTAGACTGACAGTACATCGAACTAGACTCAAGAAGAATAGA
* * *
20355582 TCATGTATCAAGTCCAATTGGGGATATGTTTTGTCAT-GCACATTAGAGCGAAAGACTCCCAAAA
1 TCATCTATCAAGTCCAATTGAGGAGATGTTTTGTCATAG-ACATTAGAGCGAAAGACTCCCAAAA
* *
20355646 GATAAAGACATAGATGCGACTGACTAGACTGACAGTACATCGGACTA
65 GATAAAGACATAGATGCGACTAACTAGACTGACAGTACATCGAACTA
20355693 TACCCAAGGT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
127 1 0.01
128 93 0.99
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (128 bp):
TCATCTATCAAGTCCAATTGAGGAGATGTTTTGTCATAGACATTAGAGCGAAAGACTCCCAAAAG
ATAAAGACATAGATGCGACTAACTAGACTGACAGTACATCGAACTAGACTCAAGAAGAATAGA
Found at i:20355729 original size:22 final size:22
Alignment explanation
Indices: 20355701--20355744 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20355691 TATACCCAAG
20355701 GTGTGGATTTATTCACTTGTGA
1 GTGTGGATTTATTCACTTGTGA
20355723 GTGTGGATTTATTCACTTGTGA
1 GTGTGGATTTATTCACTTGTGA
20355745 CGTTCAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45
Consensus pattern (22 bp):
GTGTGGATTTATTCACTTGTGA
Found at i:20366052 original size:19 final size:20
Alignment explanation
Indices: 20366028--20366069 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
20366018 GTAATTAGGT
* *
20366028 AATTTAGTAAATAAAT-TAA
1 AATTTAATAAAAAAATCTAA
20366047 AATTTAATAAAAAAATCTAA
1 AATTTAATAAAAAAATCTAA
20366067 AAT
1 AAT
20366070 CATCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATTTAATAAAAAAATCTAA
Found at i:20370190 original size:38 final size:38
Alignment explanation
Indices: 20370158--20370323 Score: 253
Period size: 38 Copynumber: 4.4 Consensus size: 38
20370148 GCAGGCTATA
* *
20370158 TGCTGG-AATTATATCCGGGTTAAATCTCGCAGGCTTTG
1 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
*
20370196 TACTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
20370234 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* *
20370272 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* *
20370310 TGCTAGTATTATAT
1 TGCTGGTAATATAT
20370324 TCGAGCCTTC
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 117 0.98
39 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (38 bp):
TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:20370369 original size:43 final size:43
Alignment explanation
Indices: 20370321--20370432 Score: 188
Period size: 43 Copynumber: 2.6 Consensus size: 43
20370311 GCTAGTATTA
* * *
20370321 TATTCGAGCCTTCGTGCCTAACAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
*
20370364 TATTCGGGCCTTCATGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
20370407 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
20370433 GTAATGCTGG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.13, C:0.27, G:0.30, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
Found at i:20370829 original size:45 final size:45
Alignment explanation
Indices: 20370762--20370888 Score: 131
Period size: 45 Copynumber: 2.9 Consensus size: 45
20370752 TTGATTTGAT
* * *
20370762 TATTCGGGCATTT-GAGCTTAGCAGACTATAATGCTGGTGAGAT-A
1 TATTCGGGC-TTTCGAGCCTAGCAGACTATAATGCCGGTGAAATGA
*
20370806 CTATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAAATGA
1 -TATTCGGGCTTTCGAGCCTAGCAGACTATAATGCCGGTGAAATGA
* *
20370852 TATT-GGGC-CTCGAGCCTAGCA-AGCGA-AATGCCGGTGA
1 TATTCGGGCTTTCGAGCCTAGCAGA-CTATAATGCCGGTGA
20370889 TTTGAGAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 7 0.10
45 39 0.54
46 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (45 bp):
TATTCGGGCTTTCGAGCCTAGCAGACTATAATGCCGGTGAAATGA
Found at i:20374320 original size:16 final size:16
Alignment explanation
Indices: 20374299--20374330 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20374289 GTATATATAA
20374299 GGAAAGAAAGATGAAG
1 GGAAAGAAAGATGAAG
20374315 GGAAAGAAAGATGAAG
1 GGAAAGAAAGATGAAG
20374331 AATTATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (16 bp):
GGAAAGAAAGATGAAG
Found at i:20376079 original size:57 final size:56
Alignment explanation
Indices: 20376010--20376146 Score: 166
Period size: 56 Copynumber: 2.4 Consensus size: 56
20376000 GTTAAAGTCT
* ** * *
20376010 GGATTTAGCCTGGATTGGTAATCCAGATTAAGCTCTTTAGAGTATTTGTCACAGAAA
1 GGATTTAGCCTGGACTGGTAATCCAGACAAAGCTC-TTAGAGCATATGTCACAGAAA
* * **
20376067 GGATTTAGCCTGGACTGGTAATCCTGACAAAGCTCTTAGAGCATATGTTACAGGCA
1 GGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTAGAGCATATGTCACAGAAA
* *
20376123 GGATTTAGCATGAACTGGTAATCC
1 GGATTTAGCCTGGACTGGTAATCC
20376147 TGTTGTATGA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 38 0.55
57 31 0.45
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (56 bp):
GGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTAGAGCATATGTCACAGAAA
Found at i:20376140 original size:56 final size:56
Alignment explanation
Indices: 20375966--20376148 Score: 179
Period size: 57 Copynumber: 3.3 Consensus size: 56
20375956 GATTCAGCTC
* * ** * * * *
20375966 GGACGGGTAATCCTAAGTAAGC-CTTTGAGCATATGTTAAAGTCTGGATTTAGCCT
1 GGACTGGTAATCCTGACAAAGCTCTTAGAGCATATGTTACAGACAGGATTTAGCCT
* * ** * * * *
20376021 GGATTGGTAATCCAGATTAAGCTCTTTAGAGTATTTGTCACAGAAAGGATTTAGCCT
1 GGACTGGTAATCCTGACAAAGCTC-TTAGAGCATATGTTACAGACAGGATTTAGCCT
* *
20376078 GGACTGGTAATCCTGACAAAGCTCTTAGAGCATATGTTACAGGCAGGATTTAGCAT
1 GGACTGGTAATCCTGACAAAGCTCTTAGAGCATATGTTACAGACAGGATTTAGCCT
*
20376134 GAACTGGTAATCCTG
1 GGACTGGTAATCCTG
20376149 TTGTATGATA
Statistics
Matches: 102, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
55 17 0.17
56 41 0.40
57 44 0.43
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (56 bp):
GGACTGGTAATCCTGACAAAGCTCTTAGAGCATATGTTACAGACAGGATTTAGCCT
Found at i:20377185 original size:25 final size:26
Alignment explanation
Indices: 20377137--20377185 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
20377127 TAAATAAAAT
*
20377137 TTAATATTAATATAATCACTTTAATA
1 TTAATATTAATAAAATCACTTTAATA
20377163 TTAA-ATTAATAAAAT-ACTGTTAA
1 TTAATATTAATAAAATCACT-TTAA
20377186 AATAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (26 bp):
TTAATATTAATAAAATCACTTTAATA
Found at i:20377196 original size:31 final size:30
Alignment explanation
Indices: 20377161--20377270 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 30
20377151 ATCACTTTAA
20377161 TATTAAATTAATAAAATACTGTTAAAATAAG
1 TATTAAATTAATAAAATACT-TTAAAATAAG
* * * *
20377192 TATTAAAGTAAATTTAATATTACTATAACTACTTTAA-
1 TATTAAA-TTAA--TAA-AATACTTTAA--A--ATAAG
*
20377229 TATTAAATTAATAAAATACTATTAAGATAAG
1 TATTAAATTAATAAAATACT-TTAAAATAAG
20377260 TATTAAATTAA
1 TATTAAATTAA
20377271 ATTTAATATT
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
30 3 0.05
31 18 0.30
32 3 0.05
33 5 0.08
34 12 0.20
35 5 0.08
36 4 0.07
37 7 0.12
38 3 0.05
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (30 bp):
TATTAAATTAATAAAATACTTTAAAATAAG
Found at i:20377206 original size:68 final size:67
Alignment explanation
Indices: 20377125--20377282 Score: 246
Period size: 68 Copynumber: 2.3 Consensus size: 67
20377115 CAAGATAAAC
*
20377125 ATTAAATAAAATTTAATATTAATATAA-TCACTTTAATATTAAATTAATAAAATACTGTTAAAAT
1 ATTAAAT-AAATTTAATATTAATATAACT-ACTTTAATATTAAATTAATAAAATACTATTAAAAT
20377189 AAGT
64 AAGT
* *
20377193 ATTAAAGTAAATTTAATATTACTATAACTACTTTAATATTAAATTAATAAAATACTATTAAGATA
1 ATTAAA-TAAATTTAATATTAATATAACTACTTTAATATTAAATTAATAAAATACTATTAAAATA
20377258 AGT
65 AGT
20377261 ATTAAATTAAATTTAATATTAA
1 ATTAAA-TAAATTTAATATTAA
20377283 ATTATTAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
68 81 0.98
69 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (67 bp):
ATTAAATAAATTTAATATTAATATAACTACTTTAATATTAAATTAATAAAATACTATTAAAATAA
GT
Found at i:20385527 original size:32 final size:32
Alignment explanation
Indices: 20385491--20385556 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
20385481 TAATAACATG
20385491 TTATCCAACACTATTGATGATAAATATTTATA
1 TTATCCAACACTATTGATGATAAATATTTATA
20385523 TTATCCAACACTATTGATGATAAATATTTATA
1 TTATCCAACACTATTGATGATAAATATTTATA
20385555 TT
1 TT
20385557 TCAAGCTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (32 bp):
TTATCCAACACTATTGATGATAAATATTTATA
Found at i:20390596 original size:39 final size:40
Alignment explanation
Indices: 20390512--20390596 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
20390502 ACTTAATTCA
* *
20390512 CCAGCATCAAGCCTGCGGGACTTTAAACCCCGATACAATC
1 CCAGCATCAAGCCAGCGGGACTCTAAACCCCGATACAATC
* * *
20390552 CCAGCATGAAGCCAGCGGGTCTCT-AACCCGGATACAATC
1 CCAGCATCAAGCCAGCGGGACTCTAAACCCCGATACAATC
*
20390591 TCAGCA
1 CCAGCA
20390597 CAATTAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 19 0.49
40 20 0.51
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.16
Consensus pattern (40 bp):
CCAGCATCAAGCCAGCGGGACTCTAAACCCCGATACAATC
Found at i:20390829 original size:22 final size:22
Alignment explanation
Indices: 20390803--20390872 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
20390793 TTTCACATTC
20390803 ATCACATTGGCCATTCGACCTT
1 ATCACATTGGCCATTCGACCTT
* * *
20390825 ATCACATGTATGCACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGACCTT
*
20390849 CATCACATTGGCCATTCGATCTT
1 -ATCACATTGGCCATTCGACCTT
20390872 A
1 A
20390873 AGCTAGATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
22 12 0.33
23 6 0.17
24 7 0.19
25 11 0.31
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:20390867 original size:47 final size:47
Alignment explanation
Indices: 20390664--20390872 Score: 244
Period size: 47 Copynumber: 4.5 Consensus size: 47
20390654 TGCACACTTT
* * *
20390664 TCACAATTGGTCATTCGACCTTATCACA--TATTCACTTACACATAT-A
1 TCAC-ATTGGCCATTCGACCTTATCACATGTATGCACTTTCACAT-TCA
** * * *
20390710 TCACATTAACCATTCGGCCTTATCACATGTATGTATTTTCACATTCA
1 TCACATTGGCCATTCGACCTTATCACATGTATGCACTTTCACATTCA
* * * * **
20390757 TCACATTGGCCCTTCGGCCTTATCACGTATACACACTTTCACATTCA
1 TCACATTGGCCATTCGACCTTATCACATGTATGCACTTTCACATTCA
20390804 TCACATTGGCCATTCGACCTTATCACATGTATGCACTTTCACATTCA
1 TCACATTGGCCATTCGACCTTATCACATGTATGCACTTTCACATTCA
*
20390851 TCACATTGGCCATTCGATCTTA
1 TCACATTGGCCATTCGACCTTA
20390873 AGCTAGATAT
Statistics
Matches: 136, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
45 19 0.14
46 5 0.04
47 112 0.82
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGACCTTATCACATGTATGCACTTTCACATTCA
Found at i:20392103 original size:377 final size:377
Alignment explanation
Indices: 20391409--20392159 Score: 1475
Period size: 377 Copynumber: 2.0 Consensus size: 377
20391399 TTTACATTAA
20391409 TAACACCATATCAACAATGTATAATGCCGACCCCTTTAAACCAATTATCCATACAAATATTATTT
1 TAACACCATATCAACAATGTATAATGCCGACCCCTTTAAACCAATTATCCATACAAATATTATTT
20391474 GTACACATTTCCTTACCTAAATTTCACATTCGGCAACCACTTAATCAACTTAACAAATTTTCTAT
66 GTACACATTTCCTTACCTAAATTTCACATTCGGCAACCACTTAATCAACTTAACAAATTTTCTAT
20391539 ACTTCAAAACCACAAGTAAATATCATAATTTGTATCATTACATCGATTAAACTAAATCATGCATT
131 ACTTCAAAACCACAAGTAAATATCATAATTTGTATCATTACATCGATTAAACTAAATCATGCATT
*
20391604 AGCTTTTAGCACATTCGGCCATTAAAGAGACAACCCAATTAACATTCAAACCTTTTTAAGCTTAG
196 AGCTTTTAGCACATTCGGCCATTAAAGAGACAACCCAATTAACATTCAAACCTTTATAAGCTTAG
20391669 ATTTCCCAAGGCCGAATATCACATAAAAACCTTTAATACACATGCAAAGTTTACACTTTAACTAA
261 ATTTCCCAAGGCCGAATATCACATAAAAACCTTTAATACACATGCAAAGTTTACACTTTAACTAA
20391734 TTATACATATACTAATAAACCGAATATTATTTAAACAACCATTTGAATATAT
326 TTATACATATACTAATAAACCGAATATTATTTAAACAACCATTTGAATATAT
20391786 TAACACCATATCAACAATGTATAATGCCGACCCCTTTAAACCAATTATCCATACAAATATTATTT
1 TAACACCATATCAACAATGTATAATGCCGACCCCTTTAAACCAATTATCCATACAAATATTATTT
20391851 GTACACATTTCCTTACCTAAATTTCACATTCGGCAACCACTTAATCAACTTAACAAATTTTCTAT
66 GTACACATTTCCTTACCTAAATTTCACATTCGGCAACCACTTAATCAACTTAACAAATTTTCTAT
20391916 ACTTCAAAACCACAAGTAAATATCATAATTTGTATCATTACATCGATTAAACTAAATCATGCATT
131 ACTTCAAAACCACAAGTAAATATCATAATTTGTATCATTACATCGATTAAACTAAATCATGCATT
20391981 AGCTTTTAGCACATTCGGCCATTAAAGAGACAACCCAATTAACATTCAAACCTTTATAAGCTTAG
196 AGCTTTTAGCACATTCGGCCATTAAAGAGACAACCCAATTAACATTCAAACCTTTATAAGCTTAG
*
20392046 ATTTCCCAAGGCTGAATATCACATAAAAACCTTTAATACACATGCAAAGTTTACACTTTAACTAA
261 ATTTCCCAAGGCCGAATATCACATAAAAACCTTTAATACACATGCAAAGTTTACACTTTAACTAA
*
20392111 TTATGCATATACTAATAAACCGAATATTATTTAAACAACCATTTGAATA
326 TTATACATATACTAATAAACCGAATATTATTTAAACAACCATTTGAATA
20392160 ATTCTTTATC
Statistics
Matches: 371, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
377 371 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (377 bp):
TAACACCATATCAACAATGTATAATGCCGACCCCTTTAAACCAATTATCCATACAAATATTATTT
GTACACATTTCCTTACCTAAATTTCACATTCGGCAACCACTTAATCAACTTAACAAATTTTCTAT
ACTTCAAAACCACAAGTAAATATCATAATTTGTATCATTACATCGATTAAACTAAATCATGCATT
AGCTTTTAGCACATTCGGCCATTAAAGAGACAACCCAATTAACATTCAAACCTTTATAAGCTTAG
ATTTCCCAAGGCCGAATATCACATAAAAACCTTTAATACACATGCAAAGTTTACACTTTAACTAA
TTATACATATACTAATAAACCGAATATTATTTAAACAACCATTTGAATATAT
Found at i:20393588 original size:476 final size:474
Alignment explanation
Indices: 20392666--20393625 Score: 1758
Period size: 476 Copynumber: 2.0 Consensus size: 474
20392656 ATTTTAGCAC
* *
20392666 ATATTTGGCTAATATATAAATATATGCTATCAATTTAATTACAATTATAAATTTTCAACTCAAAC
1 ATATTCGGCTAATATAGAAATATATGCTATCAATTTAATTACAATTATAAATTTTCAACTCAAAC
20392731 TCATTCTTTACCTCGTCTTTCACCTTAATTCAAATTCGGCAAGTATATAAACATATATTAGCAAT
66 TCATTCTTTACCTCGTCTTTCACCTTAATTCAAATTCGGCAAGTATATAAACATATATTAGCAAT
20392796 TTAATTATAGCATTCCACAATTAAGCACAAGTTTCATACTTCACTTTAATAACCGAATGATATTT
131 TTAATTATAGCATTCCACAATTAAGCACAAGTTTCATACTTCACTTTAATAACCGAATGATATTT
20392861 TACTCAAACTTGCCCCTCATAGCAAATTTAATTAGTCTATCCTCATCCATAAACACTTATCATCA
196 TACTCAAACTTGCCCCTCATAGCAAATTTAATTAGTCTATCCTCATCCATAAACACTTATCATCA
20392926 AAACATCCACAATCTAATCCTTGAAGCCATGACCGAATGCTTTATGAAATAAATTCACAAAAATT
261 AAACATCCACAATCTAATCCTTGAAGCCATGACCGAATGCTTTATGAAATAAATTCACAAAAATT
20392991 AACATATGGGTCATGTTGTGAGCTTCAAAACTAACAACATTTCGCAAAAATTAAAAATAAAATAC
326 AACATATGGGTCATGTTGTGAGCTTCAAAACTAACAACATTTCGCAAAAATTAAAAATAAAATAC
*
20393056 ATGAAATCTCACCTTAATTCCCAACACCAATGCCTTTGGTGTTCTTTCCTTTCTTTCTTGCTTAG
391 ATGAAATCTCACCTTAATTCCCAACACCAATGCC--TGGTGTCCTTTCCTTTCTTTCTTGCTTAG
20393121 TTACAGCAATAAGAGAAAACT
454 TTACAGCAATAAGAGAAAACT
20393142 ATATTCGGCTAATATAGAAATATATGCTATCAATTTAATTACAATTATAAATTTTCAACTCAAAC
1 ATATTCGGCTAATATAGAAATATATGCTATCAATTTAATTACAATTATAAATTTTCAACTCAAAC
20393207 TCATTCTTTACCTCGTCTTTCACCTTAATTCAAATTCGGCAAGTATATAAACATATATTAGCAAT
66 TCATTCTTTACCTCGTCTTTCACCTTAATTCAAATTCGGCAAGTATATAAACATATATTAGCAAT
20393272 TTAATTATAGCATTCCACAATTAAGCACAAGTTTCATACTTCACTTTAATAACCGAATGATATTT
131 TTAATTATAGCATTCCACAATTAAGCACAAGTTTCATACTTCACTTTAATAACCGAATGATATTT
20393337 TACTCAAACTTGCCCCTCATAGCAAATTTAATTAGTCTATCCTCATCCATAAACACTTATCATCA
196 TACTCAAACTTGCCCCTCATAGCAAATTTAATTAGTCTATCCTCATCCATAAACACTTATCATCA
20393402 AAACATCCACAATCTAATCCTTGAAGCCATGACCGAATGCTTTATGAAATAAATTCACAAAAATT
261 AAACATCCACAATCTAATCCTTGAAGCCATGACCGAATGCTTTATGAAATAAATTCACAAAAATT
20393467 AACATATGGGTCATGTTGTGAGCTTCAAAACTAACAACATTTCGCAAAAATTAAAAATAAAATAC
326 AACATATGGGTCATGTTGTGAGCTTCAAAACTAACAACATTTCGCAAAAATTAAAAATAAAATAC
*
20393532 ATGAAATCTCACCTTAATTCCCAACACCAAGTGACCGAGTGCCTTTGGTGTTCTTTCCTTTCTTT
391 ATGAAATCTCACCTTAATTCCCAACACC-----A---A-TGCC--TGGTGTCCTTTCCTTTCTTT
*
20393597 CTTGCTTAGTTACGGCAATAAGAGAAAAC
445 CTTGCTTAGTTACAGCAATAAGAGAAAAC
20393626 AAAGAGAAAA
Statistics
Matches: 472, Mismatches: 3, Indels: 9
0.98 0.01 0.02
Matches are distributed among these distances:
476 416 0.88
481 1 0.00
484 1 0.00
485 54 0.11
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (474 bp):
ATATTCGGCTAATATAGAAATATATGCTATCAATTTAATTACAATTATAAATTTTCAACTCAAAC
TCATTCTTTACCTCGTCTTTCACCTTAATTCAAATTCGGCAAGTATATAAACATATATTAGCAAT
TTAATTATAGCATTCCACAATTAAGCACAAGTTTCATACTTCACTTTAATAACCGAATGATATTT
TACTCAAACTTGCCCCTCATAGCAAATTTAATTAGTCTATCCTCATCCATAAACACTTATCATCA
AAACATCCACAATCTAATCCTTGAAGCCATGACCGAATGCTTTATGAAATAAATTCACAAAAATT
AACATATGGGTCATGTTGTGAGCTTCAAAACTAACAACATTTCGCAAAAATTAAAAATAAAATAC
ATGAAATCTCACCTTAATTCCCAACACCAATGCCTGGTGTCCTTTCCTTTCTTTCTTGCTTAGTT
ACAGCAATAAGAGAAAACT
Found at i:20405441 original size:18 final size:19
Alignment explanation
Indices: 20405393--20405442 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
20405383 TAATTTTCTA
20405393 TTTAATATATATAAATTGT
1 TTTAATATATATAAATTGT
* *
20405412 TTTTATA-ATATATATT-T
1 TTTAATATATATAAATTGT
*
20405429 TTTAATATTTATAA
1 TTTAATATATATAA
20405443 TATAATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.28
18 12 0.48
19 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAATATATATAAATTGT
Found at i:20408121 original size:18 final size:18
Alignment explanation
Indices: 20408090--20408127 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
20408080 ATATCATATT
20408090 TTATAGTACAAATTATAA
1 TTATAGTACAAATTATAA
*
20408108 TTATA-TACATAATTTTAA
1 TTATAGTACA-AATTATAA
20408126 TT
1 TT
20408128 CTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATAGTACAAATTATAA
Found at i:20412732 original size:30 final size:30
Alignment explanation
Indices: 20412697--20412773 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
20412687 ACACAAATTC
**
20412697 TTAAGAAAAGAATTATTCTTAACACATAGG
1 TTAAGAAAAGAATTATTCACAACACATAGG
* **
20412727 TTAAGAAAAGAATGATTCACAACACATATT
1 TTAAGAAAAGAATTATTCACAACACATAGG
*
20412757 TTAAGAAAAGATTTATT
1 TTAAGAAAAGAATTATT
20412774 GATCACAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (30 bp):
TTAAGAAAAGAATTATTCACAACACATAGG
Found at i:20419066 original size:405 final size:396
Alignment explanation
Indices: 20418115--20419521 Score: 1390
Period size: 405 Copynumber: 3.6 Consensus size: 396
20418105 CAGTGTGGGA
* *
20418115 CTGCCTGTTCTTGAAGCAAGATCAGTAGAAGATATTGATTTGGCATTTAAGCAACTTCATGAAGG
1 CTGCCTGTTCTTGAAGCAAGATCAGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * * * *
20418180 AGCTGATTTTGAGGAAGTAATTCTTCCAAGGATGATTAAGAATCAGCCGGATCATGCAGATACGA
66 AG-TGATGTTGAGGAAGTAATTCTTCCAAGCATGATTGAGAATCAGCCGGATCATGAAGATAC-C
* * ** * *
20418245 AC-TCGGATTTACCTGTTGTCGAGGTGAGATCTCTGGAGGATATACATAATGCTTTGC-T-ACAG
129 ACTTC-AAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCATAAAAG
*
20418307 GACCCAGAACCTAATCTAGCTCAGCTGCCACATTCCACAGACTTGAGGAATGGATCATCAGAAGT
193 GA-CCAGAACCTAATCTAGCTGAGCTGCCACA-TCCACAGACTTGAGGAATGGATCATCAGAAGT
* * * * * *
20418372 AGAGCAGCATGTTATTGTTTCTTCTGAAGAGATTGAAGTTAGTAATGCTGTCTCTGGTATTGAAG
256 AGAGCAGCATGATGTGGTTTCTTCT-AAGAGATTGAAGTTGGCAATGCAGTCTCTGGTATTGAAG
** * * * * * *
20418437 AAGGTTTTGATAATGCTGCTGGTGAACCCAAAAATGAAGAAGAAATAGAAGAACTAAAGACAGAA
320 AACATCTTCAGAATGCTCCTGGTGAACCAAAAAAAGAAGAAGAAATAGAAGAACTAAAGACAGAA
*
20418502 ACCAATGTGGAG
385 ACCAATGCGGAG
* *
20418514 TTACCTGTTCTTGAAGCAAGATCAGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
1 CTGCCTGTTCTTGAAGCAAGATCAGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * *
20418579 AGTGGATGTTGAGGAAGTAATTCTTCCAAGTATGATTGAGAATCTGCCAGATCAT-ACAGATACC
66 AGT-GATGTTGAGGAAGTAATTCTTCCAAGCATGATTGAGAATCAGCCGGATCATGA-AGATACC
* *
20418643 ACTTCAGAATTTCCTGTTGTCGAGGCAATATCTCTGGATGG-TATACATAATGCTTT-CATAAAA
129 ACTTCA-AATTACCTGTTGTCGAGGCAAGATCTCTGGA-GGATATACATAATGCTTTCCATAAAA
* * * *
20418706 GGACCGGAACCTAATCCAGCTGAGCTGCCACATACAGCAGACTTGAGGCATGGATCATCAGAAGT
192 GGACCAGAACCTAATCTAGCTGAGCTGCCACATCCA-CAGACTTGAGGAATGGATCATCAGAAGT
*
20418771 AGAGCAGCATGATGTGGTTTGTTCTAATGAGATTGAAGTTGGCCAA-GCAGTCTCTGGCT-TTGA
256 AGAGCAGCATGATGTGGTTTCTTCTAA-GAGATTGAAGTTGG-CAATGCAGTCTCTGG-TATTGA
* *
20418834 AGAACATCTTCAGAACGTTGCTCCTGGTGAACCAAAAAAAGAATATGAAGAAATAGAAGAATTGA
318 AGAACATCTTCAGAA---TGCTCCTGGTGAACCAAAAAAAG-A-A-GAAGAAATAGAAGAACTAA
** *
20418899 AGATGGAGACCAATGCGGAG
377 AGACAGAAACCAATGCGGAG
* * *
20418919 CTGCCTGTTCTGGATGCAAGATCGGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
1 CTGCCTGTTCTTGAAGCAAGATCAGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * * * * * *
20418984 TGTAGATGTTGAGGAAGTAGTACTTGCAAGCATGATTGAGGATCAGCTGGATCATGAAGATTCCA
66 AGT-GATGTTGAGGAAGTAATTCTTCCAAGCATGATTGAGAATCAGCCGGATCATGAAGATACCA
20419049 CTTCAAAGTTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCA-AAAAGG
130 CTTCAAA-TTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCATAAAAGG
* * * * * * * *
20419113 TCCAGAACCTAATCTGGCCGAGCTGCCACTTTCCACAGACTTGAGAAATGGATTATCAGAAATGG
194 ACCAGAACCTAATCTAGCTGAGCTGCCAC-ATCCACAGACTTGAGGAATGGATCATCAGAAGTAG
* **
20419178 AGCAGCATGATGCGGTTTCTAATAAAGAGATTGAAGTT-G-AA---A---------A-T--AG--
258 AGCAGCATGATGTGGTTTCTTCT-AAGAGATTGAAGTTGGCAATGCAGTCTCTGGTATTGAAGAA
* * * * * * **
20419224 -----TCAGAATGCTGCC-AGTGAACCAAAAAATGACCATGAAGAAACAGAGGAAATGAAGATGG
322 CATCTTCAGAATGCT-CCTGGTGAACCAAAAAAAGA--A-GAAGAAATAGAAGAACTAAAGACAG
* *
20419283 AGACCAATGCAGAG
383 AAACCAATGCGGAG
* * * *
20419297 CTGCCTGTTCTTGAAGCAAGATCACTGGAAGACATTGATTTGGCTTTTAAGCAACTTCATGGAGG
1 CTGCCTGTTCTTGAAGCAAGATCAGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
* * * * * *
20419362 AGTTGATGTTGAGGAAGTAATTCTTACAAGCATGATTGAGACTCAGCAGGGTGATGCAGATACCA
66 AG-TGATGTTGAGGAAGTAATTCTTCCAAGCATGATTGAGAATCAGCCGGATCATGAAGATACCA
* * * * * * * * * *
20419427 ATTCGGATTTACCAGTTGTTGAGGCGAGATCTCTGGAGGATATACAGAGTGCTTTTCA-ACAAGG
130 CTTC-AAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCATAAAAGG
* * * *
20419491 CCCTGAATCTAATCTAGCTGAGGTGCCACAT
194 ACCAGAACCTAATCTAGCTGAGCTGCCACAT
20419522 TCCTCAGGAG
Statistics
Matches: 860, Mismatches: 120, Indels: 78
0.81 0.11 0.07
Matches are distributed among these distances:
377 2 0.00
378 240 0.28
379 4 0.00
381 6 0.01
388 2 0.00
390 1 0.00
398 9 0.01
399 270 0.31
400 11 0.01
402 22 0.03
403 1 0.00
404 6 0.01
405 278 0.32
406 8 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (396 bp):
CTGCCTGTTCTTGAAGCAAGATCAGTTGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGG
AGTGATGTTGAGGAAGTAATTCTTCCAAGCATGATTGAGAATCAGCCGGATCATGAAGATACCAC
TTCAAATTACCTGTTGTCGAGGCAAGATCTCTGGAGGATATACATAATGCTTTCCATAAAAGGAC
CAGAACCTAATCTAGCTGAGCTGCCACATCCACAGACTTGAGGAATGGATCATCAGAAGTAGAGC
AGCATGATGTGGTTTCTTCTAAGAGATTGAAGTTGGCAATGCAGTCTCTGGTATTGAAGAACATC
TTCAGAATGCTCCTGGTGAACCAAAAAAAGAAGAAGAAATAGAAGAACTAAAGACAGAAACCAAT
GCGGAG
Found at i:20422313 original size:20 final size:20
Alignment explanation
Indices: 20422267--20422313 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20422257 TTGTACGAGA
20422267 TTGCACTTCGGTGCCCCTAT
1 TTGCACTTCGGTGCCCCTAT
* * * *
20422287 TTACACTTTGGTGTCCCTGT
1 TTGCACTTCGGTGCCCCTAT
20422307 TTGCACT
1 TTGCACT
20422314 ATAGTGCTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCCTAT
Found at i:20423644 original size:22 final size:23
Alignment explanation
Indices: 20423591--20423693 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
20423581 AAAGATGGAT
20423591 AATGAAGATTCTCTGCAATGAAC
1 AATGAAGATTCTCTGCAATGAAC
* *
20423614 AGTGAAGATTTTCTGCAA-GAAC
1 AATGAAGATTCTCTGCAATGAAC
* * *
20423636 AATGGAGATTCTCTACAATGATC
1 AATGAAGATTCTCTGCAATGAAC
* * * * *
20423659 AGTAAAGATTCGCTACAATAAAC
1 AATGAAGATTCTCTGCAATGAAC
20423682 AATGAAGATTCT
1 AATGAAGATTCT
20423694 TCGTAAAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
22 18 0.29
23 45 0.71
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (23 bp):
AATGAAGATTCTCTGCAATGAAC
Done.