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 89 of 276
Found at i:27718666 original size:32 final size:31
Alignment explanation
Indices: 27718612--27718699 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 31
27718602 TGATATTGAA
* *
27718612 ATTTTAGTTTGTTGGATCTTGAAATTATTAT
1 ATTTAAGTTTGTTGGATATTGAAATTATTAT
* * *
27718643 GTCTTGAA-TTTGTTAGATATTGAATTTATTAT
1 AT-TT-AAGTTTGTTGGATATTGAAATTATTAT
*
27718675 ATTTAAGCTTGTTGGATATTGAAAT
1 ATTTAAGTTTGTTGGATATTGAAAT
27718700 GATTGACAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
30 2 0.04
31 18 0.40
32 24 0.53
33 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.51
Consensus pattern (31 bp):
ATTTAAGTTTGTTGGATATTGAAATTATTAT
Found at i:27719945 original size:17 final size:18
Alignment explanation
Indices: 27719915--27719956 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
27719905 ACAATTTAAA
27719915 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
27719933 ATATAAA-TTATTAATAT
1 ATATAAATTTATTAATAT
*
27719950 ATGTAAA
1 ATATAAA
27719957 AATAGCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:27719959 original size:19 final size:17
Alignment explanation
Indices: 27719910--27719951 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
27719900 TAAAAACAAT
* *
27719910 TTAAAATAT-AAATTTA
1 TTAATATATAAAAATTA
*
27719926 TTAATATATATAAATTA
1 TTAATATATAAAAATTA
27719943 TTAATATAT
1 TTAATATAT
27719952 GTAAAAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATATATAAAAATTA
Found at i:27720823 original size:21 final size:21
Alignment explanation
Indices: 27720799--27720840 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
27720789 TCAAACACAC
27720799 CCTAATTTAATTTTGGTTGAT
1 CCTAATTTAATTTTGGTTGAT
27720820 CCTAATTTAATTTTGGTTGAT
1 CCTAATTTAATTTTGGTTGAT
27720841 ATTATTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (21 bp):
CCTAATTTAATTTTGGTTGAT
Found at i:27721320 original size:18 final size:18
Alignment explanation
Indices: 27721299--27721338 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27721289 AATATGATGT
* *
27721299 TATAAAAAAATTAAAATA
1 TATAAAAAAACTAAAAAA
*
27721317 TATAAAAATACTAAAAAA
1 TATAAAAAAACTAAAAAA
27721335 TATA
1 TATA
27721339 TATATCAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
TATAAAAAAACTAAAAAA
Found at i:27722041 original size:23 final size:23
Alignment explanation
Indices: 27722015--27722061 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
27722005 TCCATTAATT
* *
27722015 TAAATTTACGTAAAGATAAAATC
1 TAAATTTACATAAAAATAAAATC
27722038 TAAATTTACATAAAAATAAAATC
1 TAAATTTACATAAAAATAAAATC
27722061 T
1 T
27722062 CAAAGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAATTTACATAAAAATAAAATC
Found at i:27723741 original size:7 final size:7
Alignment explanation
Indices: 27723708--27723732 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27723698 AAAAAATTTT
27723708 AAAATTC
1 AAAATTC
27723715 AAAATTC
1 AAAATTC
27723722 AAAATTC
1 AAAATTC
27723729 AAAA
1 AAAA
27723733 AATTCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:27723747 original size:22 final size:22
Alignment explanation
Indices: 27723708--27723765 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
27723698 AAAAAATTTT
*
27723708 AAAATTCAAAATTCAAAAT-TCAA
1 AAAATTCAAAA-ACAAAATAT-AA
*
27723731 AAAATTCAAAAAGAAAATATAA
1 AAAATTCAAAAACAAAATATAA
*
27723753 AAAGTTCATAAAA
1 AAAATTCA-AAAA
27723766 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAATTCAAAAACAAAATATAA
Found at i:27724741 original size:83 final size:84
Alignment explanation
Indices: 27724597--27724754 Score: 196
Period size: 83 Copynumber: 1.9 Consensus size: 84
27724587 GTCCTTAAGG
*
27724597 ATATTTTGCAGATTCATATATCACTCAGGATTCAACAAACATTTCTATTAATCAAAGGTAAACAA
1 ATATTTTGCAGATTCATATATCACTCAGGATTCAACAAACACTTCTATTAATCAAAGGTAAACAA
27724662 GGAACATGAACTTATTAGA
66 GGAACATGAACTTATTAGA
* * * ** * *
27724681 ATATTTTGCAGATT-TTCGTATC-CTTAGGATTCAACATGCACTTCTGTTAATTGAAA-GTAAAC
1 ATATTTTGCAGATTCAT-ATATCACTCAGGATTCAACAAACACTTCTATTAA-TCAAAGGTAAAC
*
27724743 AGGGAACATGAA
64 AAGGAACATGAA
27724755 AAACTTATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
83 41 0.65
84 22 0.35
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (84 bp):
ATATTTTGCAGATTCATATATCACTCAGGATTCAACAAACACTTCTATTAATCAAAGGTAAACAA
GGAACATGAACTTATTAGA
Found at i:27728937 original size:27 final size:27
Alignment explanation
Indices: 27728905--27728960 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
27728895 TGGGCTAGTA
27728905 TGAGCTTATAGTACATTCGGCTAGGCT
1 TGAGCTTATAGTACATTCGGCTAGGCT
27728932 TGAGCTTATAGTACATTCGGCTAGGCT
1 TGAGCTTATAGTACATTCGGCTAGGCT
27728959 TG
1 TG
27728961 GGTAGCCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (27 bp):
TGAGCTTATAGTACATTCGGCTAGGCT
Found at i:27733085 original size:19 final size:19
Alignment explanation
Indices: 27733061--27733103 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
27733051 AAGATCCAAC
27733061 ATTTAGAATGCAAAAATTG
1 ATTTAGAATGCAAAAATTG
*
27733080 ATTTAGAATGTAAAAATTG
1 ATTTAGAATGCAAAAATTG
27733099 ATTTA
1 ATTTA
27733104 CTTTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (19 bp):
ATTTAGAATGCAAAAATTG
Found at i:27735194 original size:21 final size:21
Alignment explanation
Indices: 27735155--27735202 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27735145 TTTGAGCAAC
* *
27735155 ACATTTTAAAAACACATT-AG
1 ACATTTTAAAAAAAAATTAAG
27735175 AACATTTTAAAAAAAAATTAAG
1 -ACATTTTAAAAAAAAATTAAG
27735197 ACATTT
1 ACATTT
27735203 GTTTACATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (21 bp):
ACATTTTAAAAAAAAATTAAG
Found at i:27736627 original size:14 final size:15
Alignment explanation
Indices: 27736608--27736637 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
27736598 TAGTTAGAAT
27736608 TCATTTTA-TAAAAA
1 TCATTTTAGTAAAAA
27736622 TCATTTTAGTAAAAA
1 TCATTTTAGTAAAAA
27736637 T
1 T
27736638 TATTAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (15 bp):
TCATTTTAGTAAAAA
Found at i:27737857 original size:17 final size:17
Alignment explanation
Indices: 27737817--27737860 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
27737807 AGGAAAAAAA
*
27737817 ATAAAAATAAAAAAGTC
1 ATAAAAATAAAAAAGAC
* * *
27737834 ATTAAAATAAATAAGAG
1 ATAAAAATAAAAAAGAC
27737851 ATAAAAATAA
1 ATAAAAATAA
27737861 CATTTTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
ATAAAAATAAAAAAGAC
Found at i:27745369 original size:18 final size:18
Alignment explanation
Indices: 27745346--27745383 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
27745336 AAACATCTGA
27745346 AAATTAATTTAAAT-AAAT
1 AAATT-ATTTAAATCAAAT
*
27745364 AAATTATTTCAATCAAAT
1 AAATTATTTAAATCAAAT
27745382 AA
1 AA
27745384 TTGTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTATTTAAATCAAAT
Found at i:27757870 original size:48 final size:48
Alignment explanation
Indices: 27757815--27758863 Score: 1938
Period size: 48 Copynumber: 21.9 Consensus size: 48
27757805 TATATATGTG
*
27757815 TGTGGTAAAGCCGAATTGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27757863 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
* * * *
27757911 TGTGATAAAGCGGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
*
27757959 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758007 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758055 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758103 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758151 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758199 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758247 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758295 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758343 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758391 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758439 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758487 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758535 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
27758583 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
*
27758631 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
*
27758679 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
*
27758727 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
* * *
27758775 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGA-ATGAGATACGTATA
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATAT-ATATGAGATATGTATA
* * * *
27758823 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
1 TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGAT
27758864 GTGTGTATAT
Statistics
Matches: 985, Mismatches: 14, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
48 984 1.00
49 1 0.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATAGCTAATGTGAAATATATATGAGATATGTATA
Found at i:27759054 original size:37 final size:37
Alignment explanation
Indices: 27759004--27759101 Score: 178
Period size: 37 Copynumber: 2.6 Consensus size: 37
27758994 GGAAATATAT
27759004 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
27759041 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
27759078 TCCGGGTAAGACCCGATAACTACG
1 TCCGGGTAAGACCCGATGACTACG
27759102 CGCGGGGACT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:27761515 original size:42 final size:42
Alignment explanation
Indices: 27761456--27761543 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
27761446 GAACAAACCG
27761456 TGTGCCTCACACGGCCACCAGACACACCCATGTCATAGACCA
1 TGTGCCTCACACGGCCACCAGACACACCCATGTCATAGACCA
* * * *
27761498 TGTGCCTCACATGGCCACTAGACACACCCGTGTCATAGACCG
1 TGTGCCTCACACGGCCACCAGACACACCCATGTCATAGACCA
27761540 TGTG
1 TGTG
27761544 AAAACAGGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.25, C:0.36, G:0.20, T:0.18
Consensus pattern (42 bp):
TGTGCCTCACACGGCCACCAGACACACCCATGTCATAGACCA
Found at i:27762815 original size:41 final size:42
Alignment explanation
Indices: 27762728--27762887 Score: 200
Period size: 41 Copynumber: 3.9 Consensus size: 42
27762718 ATACTCAATA
* * *** *
27762728 TCTCGCACACTAAGTGCCAAAGCATAGCCGAAGCTATTGTAA
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATCACAG
* *
27762770 TCTCGCACACTAAGTGCC-TTTCATAGTCGAAGCTATCACAG
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATCACAG
* * *
27762811 TCTCGCACACTAAGTGTC-TTTCATAGCCGAAGCTATCTCAG
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATCACAG
27762852 TCTCGCACACTAAGTGCCATAT-ATAGCCGAAGCTAT
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTAT
27762888 TCTGATTTGC
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
41 84 0.81
42 20 0.19
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (42 bp):
TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATCACAG
Found at i:27773631 original size:40 final size:40
Alignment explanation
Indices: 27773526--27773671 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
27773516 GCTACTCGTT
*
27773526 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
27773566 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
27773606 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTTACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAG-TAACTCGCA
27773647 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27773672 CATCATTCAA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.03
40 74 0.80
41 16 0.17
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27775427 original size:37 final size:37
Alignment explanation
Indices: 27775384--27775467 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
27775374 ATTCTTACCA
27775384 TATGTTCATAGCATACCGAGATCTTTTATCATGAGTT
1 TATGTTCATAGCATACCGAGATCTTTTATCATGAGTT
27775421 TATGTTCATAGCATACCGAGATCTTTTATCATGAGTT
1 TATGTTCATAGCATACCGAGATCTTTTATCATGAGTT
*
27775458 TATGTACATA
1 TATGTTCATA
27775468 CTTGTACTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
TATGTTCATAGCATACCGAGATCTTTTATCATGAGTT
Found at i:27779545 original size:23 final size:23
Alignment explanation
Indices: 27779519--27779591 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
27779509 TTTCGAGCCA
**
27779519 TGATCGGTAAGCTCCTCCTGAGC
1 TGATCGGTAAGCTCCTAATGAGC
*
27779542 TGATAACAGTAAGCT-CTAATGAGC
1 TGAT--CGGTAAGCTCCTAATGAGC
*
27779566 TGAAACGGTAAGCTCC-AATGAGC
1 TG-ATCGGTAAGCTCCTAATGAGC
27779589 TGA
1 TGA
27779592 AAACAGTAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.02
23 21 0.51
24 10 0.24
25 9 0.22
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (23 bp):
TGATCGGTAAGCTCCTAATGAGC
Found at i:27779568 original size:24 final size:24
Alignment explanation
Indices: 27779537--27779630 Score: 109
Period size: 24 Copynumber: 3.9 Consensus size: 24
27779527 AAGCTCCTCC
27779537 TGAGCTGATAACAGTAAGCTCTAA
1 TGAGCTGATAACAGTAAGCTCTAA
* *
27779561 TGAGCTGA-AACGGTAAGCTCCAA
1 TGAGCTGATAACAGTAAGCTCTAA
* * *
27779584 TGAGCTGAAAACAGTAAGCTATTA
1 TGAGCTGATAACAGTAAGCTCTAA
*
27779608 CGAGCTGATATATCAGTAAGCTC
1 TGAGCTGATA-A-CAGTAAGCTC
27779631 ATACGAGCTG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
23 21 0.36
24 27 0.47
25 1 0.02
26 9 0.16
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (24 bp):
TGAGCTGATAACAGTAAGCTCTAA
Found at i:27779592 original size:23 final size:23
Alignment explanation
Indices: 27779537--27779603 Score: 98
Period size: 23 Copynumber: 2.8 Consensus size: 23
27779527 AAGCTCCTCC
*
27779537 TGAGCTGATAACAGTAAGCTCTAA
1 TGAGCTGA-AACAGTAAGCTCCAA
*
27779561 TGAGCTGAAACGGTAAGCTCCAA
1 TGAGCTGAAACAGTAAGCTCCAA
27779584 TGAGCTGAAAACAGTAAGCT
1 TGAGCTG-AAACAGTAAGCT
27779604 ATTACGAGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCCAA
Found at i:27779613 original size:47 final size:48
Alignment explanation
Indices: 27779523--27779615 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 48
27779513 GAGCCATGAT
** * * *
27779523 CGGTAAGCTCCTCCTGAGCTGATAACAGTAAGCTCTAATGAGCTGAAA
1 CGGTAAGCTCCTAATGAGCTGAAAACAGTAAGCTATAACGAGCTGAAA
*
27779571 CGGTAAGCTCC-AATGAGCTGAAAACAGTAAGCTATTACGAGCTGA
1 CGGTAAGCTCCTAATGAGCTGAAAACAGTAAGCTATAACGAGCTGA
27779616 TATATCAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 28 0.72
48 11 0.28
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (48 bp):
CGGTAAGCTCCTAATGAGCTGAAAACAGTAAGCTATAACGAGCTGAAA
Found at i:27788228 original size:32 final size:32
Alignment explanation
Indices: 27788186--27788246 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
27788176 ATCTATCTCA
27788186 CTCATCTAATTCAACTCGAAGAATTTCACTCG
1 CTCATCTAATTCAACTCGAAGAATTTCACTCG
*
27788218 CTCATTTAATTCAACTCGAAGAATTTCAC
1 CTCATCTAATTCAACTCGAAGAATTTCAC
27788247 CGTTTTCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (32 bp):
CTCATCTAATTCAACTCGAAGAATTTCACTCG
Found at i:27792590 original size:16 final size:17
Alignment explanation
Indices: 27792549--27792591 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
27792539 AAAACACAAA
27792549 CATGTCACACATGGTTC
1 CATGTCACACATGGTTC
* *
27792566 AAGTTTCACACATGG-TC
1 CA-TGTCACACATGGTTC
27792583 CATGTCACA
1 CATGTCACA
27792592 AAATATGGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 6 0.29
17 4 0.19
18 11 0.52
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (17 bp):
CATGTCACACATGGTTC
Found at i:27798451 original size:39 final size:39
Alignment explanation
Indices: 27798397--27798698 Score: 478
Period size: 39 Copynumber: 7.7 Consensus size: 39
27798387 TTCCAACACA
* *
27798397 AATGCCTTCAGGACTTAGCCCGGATATAAGACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* *
27798436 AATGCCTTCGGGACTTAGCCTGGATATAACACCAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* *
27798475 AATACCTTCGGGACTTAGCCCAGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* * * *
27798514 GATACCTTCGGGACTTAGCCTGGATATAACACCAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
* *
27798553 AATACCTTCGGGACTTAGCCCGAATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
*
27798592 AATGCCTTCGGGACTTAGCCCGGACATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
27798631 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
*
27798670 AATGCCTTTGGGACTTAGCCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
27798699 ATCTCACACA
Statistics
Matches: 242, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 242 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
Found at i:27802303 original size:27 final size:26
Alignment explanation
Indices: 27802273--27802371 Score: 126
Period size: 27 Copynumber: 3.7 Consensus size: 26
27802263 TTAGTTTACC
*
27802273 AAATTACCAAAATACACCTGGTTTGTA
1 AAATTACCAAAATAC-CCTGATTTGTA
* *
27802300 AAATTACCAAAATACCCTCGATTAGAA
1 AAATTACCAAAATACCCT-GATTTGTA
27802327 AAATTACCAAAATACCCCTGATTTGTA
1 AAATTACCAAAATA-CCCTGATTTGTA
**
27802354 AAATTACTGAAATACCCT
1 AAATTACCAAAATACCCT
27802372 TGTAAGGTAG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 7 0.11
27 52 0.83
28 4 0.06
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (26 bp):
AAATTACCAAAATACCCTGATTTGTA
Found at i:27802407 original size:27 final size:27
Alignment explanation
Indices: 27802351--27802414 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
27802341 CCCCTGATTT
*
27802351 GTAAAATTACTGAAATACCCTTGTAAG
1 GTAAAATTACTGAAATACCCTCGTAAG
* * **
27802378 GTAGAATTACTGAGATACCCTCGTGGG
1 GTAAAATTACTGAAATACCCTCGTAAG
27802405 GTAAAATTAC
1 GTAAAATTAC
27802415 CATTTTGCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
GTAAAATTACTGAAATACCCTCGTAAG
Found at i:27803371 original size:25 final size:25
Alignment explanation
Indices: 27803343--27803402 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
27803333 CCTGATACTG
*
27803343 ATTCTAATTCCAATTCTGTCAACTA
1 ATTCTGATTCCAATTCTGTCAACTA
** *
27803368 ATTCTGATTCTGATTCTGTCACCTA
1 ATTCTGATTCCAATTCTGTCAACTA
27803393 ATTCTGATTC
1 ATTCTGATTC
27803403 TGATTCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.43
Consensus pattern (25 bp):
ATTCTGATTCCAATTCTGTCAACTA
Found at i:27803403 original size:25 final size:25
Alignment explanation
Indices: 27803355--27803409 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
27803345 TCTAATTCCA
27803355 ATTCTGTCAACTAATTCTGATTCTG
1 ATTCTGTCAACTAATTCTGATTCTG
*
27803380 ATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGTCAACTAATTCTGATTCTG
27803405 ATTCT
1 ATTCT
27803410 TATTTTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (25 bp):
ATTCTGTCAACTAATTCTGATTCTG
Found at i:27805540 original size:27 final size:27
Alignment explanation
Indices: 27805510--27805634 Score: 155
Period size: 27 Copynumber: 4.6 Consensus size: 27
27805500 AGTTTACCAC
*
27805510 ATTACCAAAATACCCCTGGTTTGTAAA
1 ATTACCAAAATACCCCTGATTTGTAAA
* *
27805537 ATTACCAAAATA-CCCTCGATTAGCAAA
1 ATTACCAAAATACCCCT-GATTTGTAAA
*
27805564 ATTACCAAAATATCCCT-AGTTTGTAAA
1 ATTACCAAAATACCCCTGA-TTTGTAAA
*
27805591 ATTACCAAAACACCCCTGATTTGTAAA
1 ATTACCAAAATACCCCTGATTTGTAAA
**
27805618 ATTACTGAAATACCCCT
1 ATTACCAAAATACCCCT
27805635 ATAGGGTAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
26 5 0.06
27 74 0.88
28 5 0.06
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (27 bp):
ATTACCAAAATACCCCTGATTTGTAAA
Found at i:27805574 original size:54 final size:54
Alignment explanation
Indices: 27805510--27805635 Score: 173
Period size: 54 Copynumber: 2.3 Consensus size: 54
27805500 AGTTTACCAC
* *
27805510 ATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATA-CCCTCGATTAGCAAA
1 ATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAACACCCCT-GATTAGCAAA
* * *
27805564 ATTACCAAAATATCCCTAGTTTGTAAAATTACCAAAACACCCCTGATTTGTAAA
1 ATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAACACCCCTGATTAGCAAA
**
27805618 ATTACTGAAATACCCCTA
1 ATTACCAAAATACCCCTA
27805636 TAGGGTAGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 59 0.94
55 4 0.06
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (54 bp):
ATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAACACCCCTGATTAGCAAA
Found at i:27806347 original size:27 final size:26
Alignment explanation
Indices: 27806303--27806354 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
27806293 CTCGCTGCAA
*
27806303 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
27806330 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
27806355 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:27806635 original size:6 final size:6
Alignment explanation
Indices: 27806627--27806701 Score: 57
Period size: 6 Copynumber: 12.3 Consensus size: 6
27806617 TTGTCACCTA
* * *
27806627 ATTCTA ATTCTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
27806676 ATTCTCG -TTGTG ATTCT- AGTTCTG AT
1 ATTCT-G ATTCTG ATTCTG A-TTCTG AT
27806702 AATGTTTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
5 3 0.05
6 47 0.85
7 4 0.07
8 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:27806692 original size:37 final size:37
Alignment explanation
Indices: 27806599--27806680 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
27806589 TTACCTGATA
* * *
27806599 CTGATTTTGATTCTAATTTTGTCACCTAATTCTAATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTAATT
*
27806636 CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTAATT
27806673 CTGATTCT
1 CTGATTCT
27806681 CGTTGTGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTCACCTAATTCTAATT
Found at i:27812634 original size:14 final size:15
Alignment explanation
Indices: 27812612--27812641 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
27812602 GAATATCAAA
27812612 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
27812627 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
27812641 A
1 A
27812642 AGTCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:27813201 original size:20 final size:20
Alignment explanation
Indices: 27813150--27813201 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
27813140 ACCATTTTGA
27813150 TTTCGTAAG-TTGGCCCATT
1 TTTCGTAAGTTTGGCCCATT
**
27813169 TTCTC-TATTTTTGGCCCATT
1 TT-TCGTAAGTTTGGCCCATT
27813189 TTTCGTAAGTTTG
1 TTTCGTAAGTTTG
27813202 CTCTCCTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTCGTAAGTTTGGCCCATT
Found at i:27816711 original size:55 final size:54
Alignment explanation
Indices: 27816647--27816755 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 54
27816637 GATAATAAGC
27816647 ATTAGAAATAAGTAAAATAGAAGTGAAAAGAGTAAACAAACGCTAAGGGAAAGA
1 ATTAGAAATAAGTAAAATAGAAGTGAAAAGAGTAAACAAACGCTAAGGGAAAGA
27816701 NATTAGAAATAAGTAAAATAGAAGTGAAAAGAGTAAACAAACGCTAAGGGAAAGA
1 -ATTAGAAATAAGTAAAATAGAAGTGAAAAGAGTAAACAAACGCTAAGGGAAAGA
27816756 GATTGGGAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.57, C:0.06, G:0.22, T:0.15
Consensus pattern (54 bp):
ATTAGAAATAAGTAAAATAGAAGTGAAAAGAGTAAACAAACGCTAAGGGAAAGA
Found at i:27819865 original size:45 final size:45
Alignment explanation
Indices: 27819794--27819883 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
27819784 AATTTGCTAG
27819794 TTCAGCAGGTATCGCAGGAGGCAGCTGATGGTCTT-GATTTTCAGC
1 TTCAGCAGGTATCGCAGGAGGCAGCTGATGGTCTTAG-TTTTCAGC
* * *
27819839 TTCAGCAGGTATCGCAGTAGGTAGCTGATTGTCTTAGTTTTCAGC
1 TTCAGCAGGTATCGCAGGAGGCAGCTGATGGTCTTAGTTTTCAGC
27819884 CATCTCCTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (45 bp):
TTCAGCAGGTATCGCAGGAGGCAGCTGATGGTCTTAGTTTTCAGC
Found at i:27821238 original size:15 final size:13
Alignment explanation
Indices: 27821209--27821235 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27821199 GCTCGACAAG
27821209 GACATGCCCGTGT
1 GACATGCCCGTGT
27821222 GACATGCCCGTGT
1 GACATGCCCGTGT
27821235 G
1 G
27821236 TGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GACATGCCCGTGT
Found at i:27828691 original size:43 final size:43
Alignment explanation
Indices: 27828633--27828746 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
27828623 TCATTAGGTT
* * * *
27828633 ATCGAGATGTGATTACATGTAAGACCATGTTTGGGACATTGGC
1 ATCGATATGAGATTACATGTAAGACCATGTCTGGGACAGTGGC
* * *
27828676 ATTG-TATTGAGATTACGTGTAAGACCCTGTCTGGGACAGTGGC
1 ATCGATA-TGAGATTACATGTAAGACCATGTCTGGGACAGTGGC
* *
27828719 ATCGATATGTGATAACATGTAAGACCAT
1 ATCGATATGAGATTACATGTAAGACCAT
27828747 ATCTAAGATA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 54 0.95
44 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (43 bp):
ATCGATATGAGATTACATGTAAGACCATGTCTGGGACAGTGGC
Found at i:27838135 original size:27 final size:27
Alignment explanation
Indices: 27838096--27838156 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
27838086 AATTTTGTGC
* * *
27838096 AAGA-TATATATATATAATATGATGTT
1 AAGAGTATACATATAAAATATAATGTT
27838122 AAGAGTATACATATAAAATATAATGTT
1 AAGAGTATACATATAAAATATAATGTT
*
27838149 AAAAGTAT
1 AAGAGTAT
27838157 GTATGCATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (27 bp):
AAGAGTATACATATAAAATATAATGTT
Found at i:27838486 original size:271 final size:272
Alignment explanation
Indices: 27838172--27838722 Score: 1086
Period size: 271 Copynumber: 2.0 Consensus size: 272
27838162 CATAGTGTAA
*
27838172 AAATGTATATATAATATGACATTAAAATATTTACATAACATATACATATATTGGAGATAATGATG
1 AAATCTATATATAATATGACATTAAAATATTTACATAACATATACATATATTGGAGATAATGATG
27838237 TCAAAGAAAACTATTATAATATTGCATGTATATATATCTATATGTATATTTAAGGACATATAATG
66 TCAAAGAAAACTATTATAATATTGCATGTATATATATCTATATGTATATTTAAGGACATATAATG
27838302 AGACACATATTAAAGTTAATGATAATCAACAATGATGACATAAAAACATATACATATATAACACG
131 AGACACATATTAAAGTTAATGATAATCAACAATGATGACATAAAAACATATACATATATAACACG
27838367 GCATTCACTATGTTAGCAATTATAATAGTAACGATATTAAAATACAATATAATATAACAAAAATA
196 GCATTCACTATGTTAGCAATTATAATAGTAACGATATTAAAATACAATATAATATAACAAAAATA
27838432 CATCATATATAT
261 CATCATATATAT
27838444 AAATCTAT-TATAATATGACATTAAAATATTTACATAACATATACATATATTGGAGATAATGATG
1 AAATCTATATATAATATGACATTAAAATATTTACATAACATATACATATATTGGAGATAATGATG
27838508 TCAAAGAAAACTATTATAATATTGCATGTATATATATCTATATGTATATTTAAGGACATATAATG
66 TCAAAGAAAACTATTATAATATTGCATGTATATATATCTATATGTATATTTAAGGACATATAATG
27838573 AGACACATATTAAAGTTAATGATAATCAACAATGATGACATAAAAACATATACATATATAACACG
131 AGACACATATTAAAGTTAATGATAATCAACAATGATGACATAAAAACATATACATATATAACACG
27838638 GCATTCACTATGTTAGCAATTATAATAGTAACGATATTAAAATACAATATAATATAACAAAAATA
196 GCATTCACTATGTTAGCAATTATAATAGTAACGATATTAAAATACAATATAATATAACAAAAATA
27838703 CATCATATATAT
261 CATCATATATAT
27838715 AAATCTAT
1 AAATCTAT
27838723 GTGCATAAAT
Statistics
Matches: 278, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
271 271 0.97
272 7 0.03
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (272 bp):
AAATCTATATATAATATGACATTAAAATATTTACATAACATATACATATATTGGAGATAATGATG
TCAAAGAAAACTATTATAATATTGCATGTATATATATCTATATGTATATTTAAGGACATATAATG
AGACACATATTAAAGTTAATGATAATCAACAATGATGACATAAAAACATATACATATATAACACG
GCATTCACTATGTTAGCAATTATAATAGTAACGATATTAAAATACAATATAATATAACAAAAATA
CATCATATATAT
Found at i:27838963 original size:18 final size:17
Alignment explanation
Indices: 27838942--27838975 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
27838932 ATACATTTAA
27838942 TATAACAAATATAAATAT
1 TATAACAAATA-AAATAT
27838960 TATAACAAATAAAATA
1 TATAACAAATAAAATA
27838976 CAGAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAACAAATAAAATAT
Found at i:27847137 original size:48 final size:48
Alignment explanation
Indices: 27847079--27847304 Score: 224
Period size: 48 Copynumber: 4.7 Consensus size: 48
27847069 GAGAGCCAAA
* * *
27847079 GTAAAACCATGTTTGGGACATGGCATCGGCATTGAGACGTGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACATGAGCTAGT
* ** * ** *
27847127 GTAAGACCATGTCGGGGACATGGCATCGGCACGGATATGTGAGAGCTAAT
1 GTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACAT--GAGCTAGT
* * * *
27847177 GTAAGACCATGTCTGGGACATGGCGTCGGCCTCAATGATA-AT-AGTTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGG---CATTGAGACATGAGCTAGT
* * *
27847226 GTAAGACCATGTTTGGGACATGGCATCGAC-TTGAGACATGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACATGAGCTAGT
*
27847273 GTAAGACCATGTCTGGGATATGGCATCGGCAT
1 GTAAGACCATGTCTGGGACATGGCATCGGCAT
27847305 CATACCCTAT
Statistics
Matches: 145, Mismatches: 25, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
45 4 0.03
46 3 0.02
47 32 0.22
48 34 0.23
49 31 0.21
50 34 0.23
52 1 0.01
53 6 0.04
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACATGAGCTAGT
Found at i:27847194 original size:98 final size:95
Alignment explanation
Indices: 27847067--27847304 Score: 239
Period size: 98 Copynumber: 2.5 Consensus size: 95
27847057 CAACCACATT
* * * *
27847067 ATGAGAGCCAAAGTAAAACCATGTTTGGGACATGGCATCGGCATTGAGACGTGAGCTAGTGTAAG
1 ATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA-AT-AGCTAGTGTAAG
* *
27847132 ACCATGTCGGGGACATGGCATCGGCAC-GGATAT
64 ACCATGTCGGGGACATGGCATC-G-ACTGGAGAC
* * * * * *
27847165 GTGAGAGCTAATGTAAGACCATGTCTGGGACATGGCGTCGGCCTCAATGATAATAGTTAGTGTAA
1 ATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGG---CATTGAGAATAGCTAGTGTAA
** *
27847230 GACCATGTTTGGGACATGGCATCGACTTGAGAC
63 GACCATGTCGGGGACATGGCATCGACTGGAGAC
* *
27847263 AT--GAGCCAGTGTAAGACCATGTCTGGGATATGGCATCGGCAT
1 ATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCAT
27847305 CATACCCTAT
Statistics
Matches: 115, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
93 2 0.02
96 33 0.29
97 2 0.02
98 40 0.35
99 31 0.27
100 1 0.01
101 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (95 bp):
ATGAGAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAATAGCTAGTGTAAGAC
CATGTCGGGGACATGGCATCGACTGGAGAC
Found at i:27847243 original size:49 final size:50
Alignment explanation
Indices: 27847079--27847303 Score: 178
Period size: 49 Copynumber: 4.6 Consensus size: 50
27847069 GAGAGCCAAA
* * * * *
27847079 GTAAAACCATGTTTGGGACATGGCATCGGCATTG-AGACGT--GAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCA-CGCATATGTAAGAGCTAGT
* * * *
27847127 GTAAGACCATGTCGGGGACATGGCATCGGCACGGATATGTGAGAGCTAAT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACGCATATGTAAGAGCTAGT
* * * *
27847177 GTAAGACCATGTCTGGGACATGGCGTCGGC-CTCA-ATGATAATAGTTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACGCATATG-TAAGAGCTAGT
* * ** * * * *
27847226 GTAAGACCATGTTTGGGACATGGCATCGACTTG-AGA--CATGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACGCATATGTAAGAGCTAGT
*
27847273 GTAAGACCATGTCTGGGATATGGCATCGGCA
1 GTAAGACCATGTCTGGGACATGGCATCGGCA
27847304 TCATACCCTA
Statistics
Matches: 142, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
47 34 0.24
48 35 0.25
49 37 0.26
50 36 0.25
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCACGCATATGTAAGAGCTAGT
Found at i:27857989 original size:17 final size:18
Alignment explanation
Indices: 27857954--27857991 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27857944 CTTTAGGATT
27857954 TATTTTTTTTCCTTCTTC
1 TATTTTTTTTCCTTCTTC
27857972 TATTTTTTATT-CTT-TTC
1 TATTTTTT-TTCCTTCTTC
27857989 TAT
1 TAT
27857992 CCTTCTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 11 0.58
19 2 0.11
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTTTTCCTTCTTC
Found at i:27861405 original size:48 final size:46
Alignment explanation
Indices: 27861258--27861428 Score: 156
Period size: 48 Copynumber: 3.6 Consensus size: 46
27861248 TGAGGCAAAC
*
27861258 GCCATGTCCCAGACATGGTCTTACACTAGCTCCCGCAT-ATCCGTGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCT--CTCATAAT--GTG-CGAT
* *
27861308 GCCATATCCTC-GACATGGTCTTACACTAGATCT-AGTCTCAATGT-CGAT
1 GCCATGTCC-CAGACATGGTCTTACACTAGCTCTCA---T-AATGTGCGAT
*
27861356 GCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGT-GC-GAT
27861404 G-CATGTCCCAGACAT-GTCTTACACT
1 GCCATGTCCCAGACATGGTCTTACACT
27861429 CACTCACAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 26
0.76 0.04 0.19
Matches are distributed among these distances:
45 5 0.05
46 11 0.11
47 17 0.16
48 37 0.36
49 1 0.01
50 30 0.29
51 1 0.01
52 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGCGAT
Found at i:27864479 original size:28 final size:28
Alignment explanation
Indices: 27864447--27864513 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
27864437 TATAGTTTGT
* *
27864447 ACACTTAGTGCTCAATATTTAA-ACTCGC
1 ACACTTAGTGCTCAATA-ATAACACTCAC
* *
27864475 ACACTTAGTGCTCGATAATAACATTCAC
1 ACACTTAGTGCTCAATAATAACACTCAC
27864503 ACACTTAGTGC
1 ACACTTAGTGC
27864514 AAGATTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 3 0.09
28 31 0.91
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
ACACTTAGTGCTCAATAATAACACTCAC
Found at i:27871356 original size:59 final size:59
Alignment explanation
Indices: 27871264--27871381 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
27871254 ACTATAAACA
*
27871264 AATACACATAATTTAAGCATCACAAATAAAGGAAAACTTAAATCACAACCAAACATAAC
1 AATACACATAATTTAAGCATCACAAATAAAGGAAAACTCAAATCACAACCAAACATAAC
27871323 AATACACATAATTTAAGCATCACAAATAAAGGAAAACTCAAATCACAACCAAACATAAC
1 AATACACATAATTTAAGCATCACAAATAAAGGAAAACTCAAATCACAACCAAACATAAC
27871382 GAAACTTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (59 bp):
AATACACATAATTTAAGCATCACAAATAAAGGAAAACTCAAATCACAACCAAACATAAC
Found at i:27872111 original size:28 final size:28
Alignment explanation
Indices: 27872079--27872145 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
27872069 TATAGTTTGT
* *
27872079 ACACTTAGTGCTCAATATTTAA-ACTCGC
1 ACACTTAGTGCTCAATA-ATAACACTCAC
* *
27872107 ACACTTAGTGCTCGATAATAACATTCAC
1 ACACTTAGTGCTCAATAATAACACTCAC
27872135 ACACTTAGTGC
1 ACACTTAGTGC
27872146 AAGATTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 3 0.09
28 31 0.91
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
ACACTTAGTGCTCAATAATAACACTCAC
Found at i:27879684 original size:28 final size:28
Alignment explanation
Indices: 27879652--27879718 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
27879642 TATAGTTTGT
* *
27879652 ACACTTAGTGCTCAATATTTAA-ACTCGC
1 ACACTTAGTGCTCAATA-ATAACACTCAC
* *
27879680 ACACTTAGTGCTCGATAATAACATTCAC
1 ACACTTAGTGCTCAATAATAACACTCAC
27879708 ACACTTAGTGC
1 ACACTTAGTGC
27879719 AAGATTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 3 0.09
28 31 0.91
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
ACACTTAGTGCTCAATAATAACACTCAC
Found at i:27894838 original size:22 final size:21
Alignment explanation
Indices: 27894813--27894853 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
27894803 TCAAATTGGT
27894813 CACACAAGCATGTTGCCCCTCC
1 CACACAAGCATG-TGCCCCTCC
**
27894835 CACACGGGCATGTGCCCCT
1 CACACAAGCATGTGCCCCT
27894854 GTGTCAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.17
Consensus pattern (21 bp):
CACACAAGCATGTGCCCCTCC
Found at i:27899161 original size:16 final size:16
Alignment explanation
Indices: 27899131--27899160 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27899121 TGCTATTAAT
27899131 TTATTAAAATAAAAAC
1 TTATTAAAATAAAAAC
27899147 TTATT-AAATAAAAA
1 TTATTAAAATAAAAA
27899161 ATGATCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TTATTAAAATAAAAAC
Found at i:27902624 original size:17 final size:17
Alignment explanation
Indices: 27902602--27902636 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
27902592 TCCCCTTTAA
27902602 TTAGCTTCTAGCAAATT
1 TTAGCTTCTAGCAAATT
27902619 TTAGCTTCTAGCAAATT
1 TTAGCTTCTAGCAAATT
27902636 T
1 T
27902637 AAGTATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (17 bp):
TTAGCTTCTAGCAAATT
Found at i:27908506 original size:43 final size:45
Alignment explanation
Indices: 27908454--27908577 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 45
27908444 TGTAGCGCCT
*
27908454 GAGCTCGTTGAGAGGTCTGAGTTCATTATGGATGC-G-AGCATCC
1 GAGCTCGTTGAGAGGTCTGAGTTCATTATGGATGCAGTAACATCC
* * * *
27908497 GAGCTCGTTGAGATGTCTAAGTTCATAATGCGATTCATGTAACATCC
1 GAGCTCGTTGAGAGGTCTGAGTTCATTATG-GATGCA-GTAACATCC
* *
27908544 GAGCTCATTGAGAGGTCCGAGTTCATTATGGATG
1 GAGCTCGTTGAGAGGTCTGAGTTCATTATGGATG
27908578 TATACATGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
43 27 0.41
44 4 0.06
46 4 0.06
47 31 0.47
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (45 bp):
GAGCTCGTTGAGAGGTCTGAGTTCATTATGGATGCAGTAACATCC
Found at i:27913444 original size:48 final size:48
Alignment explanation
Indices: 27913305--27913512 Score: 239
Period size: 48 Copynumber: 4.4 Consensus size: 48
27913295 TAGGGTTATG
* * *
27913305 TGTGATCCCATATAAGACCATGTCTGGGACATGGCTTTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCGATA
* ** * * * *
27913353 TGTAATTTCGTATAAGACCATAG-CTAGG-C-T---ATCGACATCGATA
1 TGTGATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGACATCGATA
* *
27913396 TGTGATCCCATGTAAGACCATGTCTGGGACATGTCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCGATA
* *
27913444 TGTGATCCCATGTAAGACCATGTCTGGGGCATGGCGTTGACATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCGATA
27913492 TGTGATCCCATGTAAGACCAT
1 TGTGATCCCATGTAAGACCAT
27913513 ATCCAAGATT
Statistics
Matches: 133, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.01
43 30 0.23
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 97 0.73
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCGATA
Found at i:27913460 original size:91 final size:93
Alignment explanation
Indices: 27913305--27913512 Score: 262
Period size: 91 Copynumber: 2.2 Consensus size: 93
27913295 TAGGGTTATG
* * ** *
27913305 TGTGATCCCATATAAGACCATGTCTGGGACATGGCTTTGGCATCGATATGTAATTTCGTATAAGA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTAATCCCATATAAGA
27913370 CCATAG-CT-AGGCTAT-C-GACATCGATA
66 CCAT-GTCTGAGGC-ATGCTGACATCGATA
* * *
27913396 TGTGATCCCATGTAAGACCATGTCTGGGACATGTCATTGGCATCGATATGTGATCCCATGTAAGA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTAATCCCATATAAGA
*
27913461 CCATGTCTGGGGCATGGCGTTGACATCGATA
66 CCATGTCTGAGGCAT-GC--TGACATCGATA
27913492 TGTGATCCCATGTAAGACCAT
1 TGTGATCCCATGTAAGACCAT
27913513 ATCCAAGATT
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
90 1 0.01
91 65 0.64
92 3 0.03
93 1 0.01
96 31 0.31
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (93 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTAATCCCATATAAGA
CCATGTCTGAGGCATGCTGACATCGATA
Found at i:27921692 original size:16 final size:15
Alignment explanation
Indices: 27921668--27921697 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27921658 AACTATTTTA
27921668 TTACAAATTTCACTC
1 TTACAAATTTCACTC
27921683 TTACATAATTTCACT
1 TTACA-AATTTCACT
27921698 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:27921966 original size:50 final size:50
Alignment explanation
Indices: 27921912--27922089 Score: 207
Period size: 49 Copynumber: 3.5 Consensus size: 50
27921902 GTACGCATAA
* * * * *
27921912 TAGCCTGCACTTAGTATTACACATGCGACCTAACTATCTGGTACATGTAG
1 TAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAG
*
27921962 TAGCCTACACTTAGTACTACAC-TCGTGA-CTAACCATCTGATACACGTAG
1 TAGCCTGCACTTAGTACTACACAT-GTGACCTAACCATCTGATACACGTAG
* * * *
27922011 TAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTAAACACATAG
1 TAGCCTGCACTTAGTACTACACATGTGACCT--AACCATCTGATACACGTAG
**
27922063 TAGCCTGCACAGAGTACTACACATGTG
1 TAGCCTGCACTTAGTACTACACATGTG
27922090 TTCTCACAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 44 0.40
50 25 0.23
52 40 0.37
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
TAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAG
Found at i:27948504 original size:45 final size:45
Alignment explanation
Indices: 27948432--27948518 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
27948422 CCAAAACATG
* * * *
27948432 TGTCACATACATCATGAACTCATACCACAACTCAATTAGTTCGAA
1 TGTCACATACATCATGAAATCAGACCACAACTAAATGAGTTCGAA
* *
27948477 TGTCACATATATCATGAAATCCGACCACAACTAAATGAGTTC
1 TGTCACATACATCATGAAATCAGACCACAACTAAATGAGTTC
27948519 AGATCACATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.26
Consensus pattern (45 bp):
TGTCACATACATCATGAAATCAGACCACAACTAAATGAGTTCGAA
Found at i:27959313 original size:5 final size:5
Alignment explanation
Indices: 27959303--27959330 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27959293 GGTTTTACTT
27959303 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
27959331 GGTTAAGTTT
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:27961139 original size:29 final size:29
Alignment explanation
Indices: 27961089--27961170 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
27961079 GTGACAGAGT
*
27961089 CACCAGATACAGATAT-TTTGTGGCAGTGC
1 CACCAGA-ACAGATATATTTGTGGCAGGGC
*
27961118 CACCAGAACAGATATATATGTGGCAGGGC
1 CACCAGAACAGATATATTTGTGGCAGGGC
* *
27961147 CACCAAAATAGATA-ATTTGTGGCA
1 CACCAGAACAGATATATTTGTGGCA
27961171 TAGCCACTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
28 17 0.36
29 30 0.64
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (29 bp):
CACCAGAACAGATATATTTGTGGCAGGGC
Found at i:27961333 original size:28 final size:28
Alignment explanation
Indices: 27961286--27961353 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
27961276 AAATTAACCT
*
27961286 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTCATTTTGCATACA
27961314 TAGGGGTATAATGG-CAATTTTGCATACA
1 TAGGGGTATAATGGTC-ATTTTGCATACA
27961342 TAGGGGTATAAT
1 TAGGGGTATAAT
27961354 AGTACATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAATGGTCATTTTGCATACA
Found at i:27965186 original size:52 final size:52
Alignment explanation
Indices: 27965108--27965213 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
27965098 TATTAAAATG
27965108 ATAGTTTGGTCGGCTCAGCAAGTATGCTAGGGAGTGTGTCTCCTCCAAAGAT
1 ATAGTTTGGTCGGCTCAGCAAGTATGCTAGGGAGTGTGTCTCCTCCAAAGAT
27965160 ATAGTTTGGTCGGCTCAGCAAGTATGCTAGGGAGTGTGTCTCCTCCAAAGAT
1 ATAGTTTGGTCGGCTCAGCAAGTATGCTAGGGAGTGTGTCTCCTCCAAAGAT
27965212 AT
1 AT
27965214 TATGTGTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (52 bp):
ATAGTTTGGTCGGCTCAGCAAGTATGCTAGGGAGTGTGTCTCCTCCAAAGAT
Found at i:27976730 original size:22 final size:22
Alignment explanation
Indices: 27976685--27976732 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
27976675 CCTGAGCTGA
* *
27976685 TGAACAGTAAGCTCTATTGGGC
1 TGAACAGTAAACTCTATTGAGC
27976707 TGAACAGTAAACTCT-TTCGAGC
1 TGAACAGTAAACTCTATT-GAGC
27976729 TGAA
1 TGAA
27976733 TTGGTAAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (22 bp):
TGAACAGTAAACTCTATTGAGC
Found at i:27981808 original size:49 final size:49
Alignment explanation
Indices: 27981746--27981841 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
27981736 TCTTTGATTT
* *
27981746 AGGTATGTAATTTGTTCTATTTTTGACAATTTTTATGTTTTTGAGATGA
1 AGGTATGTAATTTGTTCGATTTTTGACAATTTTTACGTTTTTGAGATGA
*
27981795 AGGTATGTAATTTGTTCGATTTTTGATAATTTTTACGTTTTTGAGAT
1 AGGTATGTAATTTGTTCGATTTTTGACAATTTTTACGTTTTTGAGAT
27981842 CACTTCGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.24, C:0.04, G:0.19, T:0.53
Consensus pattern (49 bp):
AGGTATGTAATTTGTTCGATTTTTGACAATTTTTACGTTTTTGAGATGA
Found at i:27984039 original size:41 final size:43
Alignment explanation
Indices: 27983939--27984093 Score: 190
Period size: 43 Copynumber: 3.7 Consensus size: 43
27983929 TGTGTTCTTG
** * * *
27983939 TGTAAGACCACATTTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACA
*
27983982 TGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATT-CA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACA
** *
27984023 TGTAAGAACC-TGTCTGGGACAGCGGCATCGATATGTGATTGCA
1 TGTAAG-ACCATGTCTGGGACATTGGCATCGATATGTGATTACA
*
27984066 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
27984094 TGTACGATAT
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
41 25 0.26
42 22 0.23
43 49 0.51
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACA
Found at i:27993014 original size:15 final size:15
Alignment explanation
Indices: 27992994--27993024 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27992984 TGAATTTGAT
*
27992994 GTTATTTTGGTTATG
1 GTTATTTTAGTTATG
27993009 GTTATTTTAGTTATG
1 GTTATTTTAGTTATG
27993024 G
1 G
27993025 ATTGGTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (15 bp):
GTTATTTTAGTTATG
Found at i:28002333 original size:41 final size:43
Alignment explanation
Indices: 28002241--28002395 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 43
28002231 TGTATTCTCG
* *
28002241 TGTAAGATCACATCTGAGACATTGGCATCGATATGTGATTACA
1 TGTAAGACCACATCTGGGACATTGGCATCGATATGTGATTACA
* ** * * *
28002284 CGTAAGACCATGTCTGGGACATTGGAATCG-TATTTGATT-CG
1 TGTAAGACCACATCTGGGACATTGGCATCGATATGTGATTACA
* * *
28002325 TGTAAGACC-CTATCTAGGACAGTGGCATCGATATGTGATTGCA
1 TGTAAGACCAC-ATCTGGGACATTGGCATCGATATGTGATTACA
* * *
28002368 TGTAAGACCACGTTTGGGACGTTGGCAT
1 TGTAAGACCACATCTGGGACATTGGCAT
28002396 TGCACAATAT
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 24 0.28
42 16 0.18
43 46 0.53
44 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACATCTGGGACATTGGCATCGATATGTGATTACA
Found at i:28003249 original size:8 final size:8
Alignment explanation
Indices: 28003236--28003274 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
28003226 ATGGCTTATA
28003236 TATATATT
1 TATATATT
28003244 TATATATAT
1 TATATAT-T
*
28003253 AACTATATT
1 TA-TATATT
28003262 TATATATT
1 TATATATT
28003270 TATAT
1 TATAT
28003275 GTGAATCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 18 0.67
9 4 0.15
10 5 0.19
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (8 bp):
TATATATT
Found at i:28013024 original size:11 final size:11
Alignment explanation
Indices: 28013008--28013032 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28012998 TTATGTATTT
28013008 AAAGCCATGCG
1 AAAGCCATGCG
28013019 AAAGCCATGCG
1 AAAGCCATGCG
28013030 AAA
1 AAA
28013033 ATGGCTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (11 bp):
AAAGCCATGCG
Found at i:28016877 original size:11 final size:11
Alignment explanation
Indices: 28016861--28016910 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
28016851 ATATATGAAT
28016861 ATATCATGTGC
1 ATATCATGTGC
*
28016872 ATATCA--TAC
1 ATATCATGTGC
28016881 ATATCATGTGC
1 ATATCATGTGC
*
28016892 CTATCATGT-C
1 ATATCATGTGC
*
28016902 AAATCATGT
1 ATATCATGT
28016911 ATATCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
9 8 0.25
10 8 0.25
11 16 0.50
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATATCATGTGC
Found at i:28016886 original size:20 final size:20
Alignment explanation
Indices: 28016861--28016898 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28016851 ATATATGAAT
28016861 ATATCATGTGCATATCATAC
1 ATATCATGTGCATATCATAC
*
28016881 ATATCATGTGCCTATCAT
1 ATATCATGTGCATATCAT
28016899 GTCAAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
ATATCATGTGCATATCATAC
Found at i:28024350 original size:24 final size:24
Alignment explanation
Indices: 28024304--28024376 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 24
28024294 ACTTTATCAT
** *
28024304 ATAACTGGAGGCCTAGCCTCTTTTA
1 ATAACTGG-GGCAAAGCCCCTTTTA
**
28024329 ATAACTGGGGCAAAGCCCCTTTCG
1 ATAACTGGGGCAAAGCCCCTTTTA
* *
28024353 GTAAACTGGGGCAAAGCCCTTTTT
1 AT-AACTGGGGCAAAGCCCCTTTT
28024377 TACTTCCTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 12 0.31
25 27 0.69
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (24 bp):
ATAACTGGGGCAAAGCCCCTTTTA
Found at i:28024437 original size:11 final size:11
Alignment explanation
Indices: 28024421--28024470 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
28024411 ATATATGAAT
28024421 ATATCATGTGC
1 ATATCATGTGC
*
28024432 ATATCA--TAC
1 ATATCATGTGC
28024441 ATATCATGTGC
1 ATATCATGTGC
28024452 ATATCATGT-C
1 ATATCATGTGC
*
28024462 AAATCATGT
1 ATATCATGT
28024471 ATATCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 8 0.24
10 9 0.26
11 17 0.50
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (11 bp):
ATATCATGTGC
Found at i:28024446 original size:20 final size:20
Alignment explanation
Indices: 28024421--28024458 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28024411 ATATATGAAT
28024421 ATATCATGTGCATATCATAC
1 ATATCATGTGCATATCATAC
28024441 ATATCATGTGCATATCAT
1 ATATCATGTGCATATCAT
28024459 GTCAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
ATATCATGTGCATATCATAC
Found at i:28026724 original size:21 final size:21
Alignment explanation
Indices: 28026700--28026744 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
28026690 ATATTCCTTC
* *
28026700 CATTTAATTCAGTCCAAATTT
1 CATTCAATTCAGTCCAAAATT
28026721 CATTCAATTCAGTCCAAAATT
1 CATTCAATTCAGTCCAAAATT
28026742 CAT
1 CAT
28026745 ACTTTTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (21 bp):
CATTCAATTCAGTCCAAAATT
Found at i:28029578 original size:48 final size:48
Alignment explanation
Indices: 28029462--28029780 Score: 395
Period size: 48 Copynumber: 6.6 Consensus size: 48
28029452 GAGATCCCGA
* * * * * * * * *
28029462 GTAAGACCGTGTCTAGGACATGGCATCAGCATCCGAGATGAGAGTCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCGT-TGATATGTGTGCCAGT
* * * * * * * * *
28029511 TTAAGACCTTGTCTAGGACATGGAATCGGCGTTTATTTATGTGCTAGC
1 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCAGT
*
28029559 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCATT
1 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCAGT
*
28029607 GTAAGACCATGTCTGGGACATGGCATCGGCGTGGATATGTGTGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCAGT
**
28029655 GTAAGACCATGTCTGGGACATGGCATCACCGTTGATATGTGTGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCAGT
* * * *
28029703 GTAAGACCATGTTTGGGACATGGCATCAGCGATGATATGTGTGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCAGT
28029751 GTAAGACCATGTCTGGGACATGGCATCGGC
1 GTAAGACCATGTCTGGGACATGGCATCGGC
28029781 ATCGGTATGA
Statistics
Matches: 234, Mismatches: 36, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
48 207 0.88
49 27 0.12
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCAGT
Found at i:28029804 original size:48 final size:46
Alignment explanation
Indices: 28029512--28029822 Score: 236
Period size: 48 Copynumber: 6.5 Consensus size: 46
28029502 AGAGTCAGTT
* * * * * *
28029512 TAAGACCTTGTCTAGGACATGGAATCGGCGTTTATTTATGTGC-TAGCG
1 TAAGACCATGTCTGGGACATGGCATCGGCG-TGA--TATGTGCTTCGTG
* *
28029560 TAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTG-TGCCATTG
1 TAAGACCATGTCTGGGACATGGCATCGGCG-TGATATGTGCT-TC-GTG
*
28029608 TAAGACCATGTCTGGGACATGGCATCGGCGTGGATATGTG-TGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCGT-GATATGTGCT-TC-GTG
** *
28029656 TAAGACCATGTCTGGGACATGGCATCACCGTTGATATGTG-TGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCG-TGATATGTGCT-TC-GTG
* * *
28029704 TAAGACCATGTTTGGGACATGGCATCAGCGATGATATGTG-TGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCG-TGATATGTGCT--TCGTG
* * * *
28029752 TAAGACCATGTCTGGGACATGGCATCGGCATCGGTATGAGACTTCGTA
1 TAAGACCATGTCTGGGACATGGCATCGGCGT-GATATGTG-CTTCGTG
* * *
28029800 TAAGACCATATCTTGGATATGGC
1 TAAGACCATGTCTGGGACATGGC
28029823 TTCGATATGT
Statistics
Matches: 227, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
46 6 0.03
47 2 0.01
48 217 0.96
49 1 0.00
50 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (46 bp):
TAAGACCATGTCTGGGACATGGCATCGGCGTGATATGTGCTTCGTG
Found at i:28029804 original size:96 final size:94
Alignment explanation
Indices: 28029462--28029822 Score: 332
Period size: 96 Copynumber: 3.8 Consensus size: 94
28029452 GAGATCCCGA
* * * * * *
28029462 GTAAGACCGTGTCTAGGACATGGCATCAGCATCCGAGATGAGAGTCAGTTTAAGACCTTGTCTAG
1 GTAAGACCATGTCTGGGACATGGCATCAGCAT-CGATATGAGATTCAG-TTAAGACCATGTCTGG
* * * * *
28029527 GACATGGAATCGGCGTTTATTTATGTGCTAGC
64 GACATGGCATCGGCG-TGATATGTGTGCTAGT
* * * * * *
28029559 GTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTG-TGCCATTGTAAGACCATGTCTGG
1 GTAAGACCATGTCTGGGACATGGCATCAGCATCGATATGAGAT-TCAGT-TAAGACCATGTCTGG
*
28029623 GACATGGCATCGGCGTGGATATGTGTGCCAGT
64 GACATGGCATCGGCGT-GATATGTGTGCTAGT
* * * * * *
28029655 GTAAGACCATGTCTGGGACATGGCATCACCGTTGATATGTG-TGCCAGTGTAAGACCATGTTTGG
1 GTAAGACCATGTCTGGGACATGGCATCAGCATCGATATGAGAT-TCAGT-TAAGACCATGTCTGG
*
28029719 GACATGGCATCAGCGATGATATGTGTGCTAGT
64 GACATGGCATCGGCG-TGATATGTGTGCTAGT
* * * *
28029751 GTAAGACCATGTCTGGGACATGGCATCGGCATCGGTATGAGACTTC-GTATAAGACCATATCTTG
1 GTAAGACCATGTCTGGGACATGGCATCAGCATCGATATGAGA-TTCAGT-TAAGACCATGTCTGG
*
28029815 GATATGGC
64 GACATGGC
28029823 TTCGATATGT
Statistics
Matches: 222, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
95 2 0.01
96 189 0.85
97 30 0.14
98 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (94 bp):
GTAAGACCATGTCTGGGACATGGCATCAGCATCGATATGAGATTCAGTTAAGACCATGTCTGGGA
CATGGCATCGGCGTGATATGTGTGCTAGT
Found at i:28029804 original size:144 final size:144
Alignment explanation
Indices: 28029462--28029822 Score: 406
Period size: 144 Copynumber: 2.5 Consensus size: 144
28029452 GAGATCCCGA
* * * * * *
28029462 GTAAGACCGTGTCTAGGACATGGCATCAGCATCCGAG-ATGAGAGTCAGTTTAAGACCTTGTCTA
1 GTAAGACCATGTCTGGGACATGGCATCGGCAT-CG-GTATGAGATTCAGTATAAGACCATGTCTA
* ** * * * * *
28029526 GGACATGGAATCGGCGTTTATTTATGTGCTAGCGTAAGACCATGTCTGGGACATGGCATCGGCGT
64 GGACATGGCATCACCGTTGATATATGTGCCAGCGTAAGACCATGTCTGGGACATGGCATCAGCGA
*
28029591 TGATATGTGTGCCATT
129 TGATATGTGTGCCAGT
* * * * *
28029607 GTAAGACCATGTCTGGGACATGGCATCGGCGT-GGATATGTG-TGCCAGTGTAAGACCATGTCTG
1 GTAAGACCATGTCTGGGACATGGCATCGGCATCGG-TATGAGAT-TCAGTATAAGACCATGTCTA
* * *
28029670 GGACATGGCATCACCGTTGATATGTGTGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCGA
64 GGACATGGCATCACCGTTGATATATGTGCCAGCGTAAGACCATGTCTGGGACATGGCATCAGCGA
*
28029735 TGATATGTGTGCTAGT
129 TGATATGTGTGCCAGT
* *
28029751 GTAAGACCATGTCTGGGACATGGCATCGGCATCGGTATGAGACTTC-GTATAAGACCATATCTTG
1 GTAAGACCATGTCTGGGACATGGCATCGGCATCGGTATGAGA-TTCAGTATAAGACCATGTCTAG
*
28029815 GATATGGC
65 GACATGGC
28029823 TTCGATATGT
Statistics
Matches: 180, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
142 1 0.01
143 1 0.01
144 146 0.81
145 31 0.17
146 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (144 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCATCGGTATGAGATTCAGTATAAGACCATGTCTAGG
ACATGGCATCACCGTTGATATATGTGCCAGCGTAAGACCATGTCTGGGACATGGCATCAGCGATG
ATATGTGTGCCAGT
Found at i:28032683 original size:16 final size:19
Alignment explanation
Indices: 28032648--28032684 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
28032638 TCTAATACTG
28032648 TTTTACTACTAATGTTCAC
1 TTTTACTACTAATGTTCAC
28032667 TTTTAC-AC-AAT-TTCAC
1 TTTTACTACTAATGTTCAC
28032683 TT
1 TT
28032685 AATCCATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 2 0.11
19 6 0.33
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTTACTACTAATGTTCAC
Found at i:28032963 original size:49 final size:49
Alignment explanation
Indices: 28032889--28033083 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 49
28032879 GTCGAAGCTA
* * *
28032889 TCTGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG
* * *
28032938 TCTGGTATACATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAACAG
** * * *
28032988 TCTAATTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAG
1 TCT-GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG
* * *
28033037 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
28033084 TCACAATAGA
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
48 2 0.02
49 38 0.32
50 4 0.03
51 73 0.61
52 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (49 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG
Found at i:28033068 original size:102 final size:100
Alignment explanation
Indices: 28032900--28033087 Score: 261
Period size: 102 Copynumber: 1.9 Consensus size: 100
28032890 CTGGTACGCA
* * *
28032900 TAGTAGCCTACACTTAGTACTACACATGCGACCAACAGTCTGGTATACATAGTAGCCTGCACTTA
1 TAGTAGCCTACACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
*
28032965 GTACTACACACGTGACCTCACCATCTAATTACACG
66 GTACTACACACGCGACCTCACCATCTAATTACACG
* * * *
28033000 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTACACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTGCAC
*
28033064 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
28033088 AATAGATCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
99 4 0.05
100 29 0.38
102 43 0.57
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (100 bp):
TAGTAGCCTACACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATTACACG
Found at i:28037363 original size:44 final size:42
Alignment explanation
Indices: 28037284--28037394 Score: 113
Period size: 44 Copynumber: 2.6 Consensus size: 42
28037274 ATTCAATATG
** *
28037284 TGATTTC-GTGTAAGACCACATCTAGGGCATTGGCATCG-ACTT
1 TGATTTCAGTGTAAGACCATGTCT-GGGCATCGGCATCGTA-TT
28037326 ATGATTT-ATGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
1 -TGATTTCA-GTGTAAGACCATGTCTGGG-CATCGGCATCGTATT
*
28037370 TGATTTCA-TGTAAGACCCTGTCTGG
1 TGATTTCAGTGTAAGACCATGTCTGG
28037395 AACAGTGGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
42 16 0.27
43 15 0.25
44 27 0.46
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATTTCAGTGTAAGACCATGTCTGGGCATCGGCATCGTATT
Found at i:28037392 original size:42 final size:43
Alignment explanation
Indices: 28037336--28037430 Score: 113
Period size: 42 Copynumber: 2.2 Consensus size: 43
28037326 ATGATTTATG
* * *
28037336 TGTAAGACCATGTCTGGGACA-TCGGCATCG-TATTTGATTTCA
1 TGTAAGACCATGTCTGGAACAGT-GGCATCGATATTCGATTACA
* * *
28037378 TGTAAGACCCTGTCTGGAACAGTGGTATCGATATTCGGTTACA
1 TGTAAGACCATGTCTGGAACAGTGGCATCGATATTCGATTACA
28037421 TGTAAGACCA
1 TGTAAGACCA
28037431 CGTTTGGGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 25 0.57
43 19 0.43
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGAACAGTGGCATCGATATTCGATTACA
Found at i:28045195 original size:19 final size:19
Alignment explanation
Indices: 28045171--28045210 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28045161 TGAAAATGTG
*
28045171 TAAGTTATGTCTATAAATT
1 TAAGTTATGCCTATAAATT
*
28045190 TAAGTTATGCCTATGAATT
1 TAAGTTATGCCTATAAATT
28045209 TA
1 TA
28045211 TGATAACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (19 bp):
TAAGTTATGCCTATAAATT
Found at i:28052772 original size:37 final size:37
Alignment explanation
Indices: 28052731--28052879 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
28052721 ACCTTTAGCT
* * * *
28052731 CGGACGAAATCTACACACGAAGTTATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
* *
28052768 CGGACAAAATCCCCATACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
*
28052805 CGGGCAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
* * * *
28052842 CGGACATACTCTCCAGACGTAGTCATCGGGTCTCACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
28052879 C
1 C
28052880 AGAATATATT
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (37 bp):
CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:28053100 original size:47 final size:47
Alignment explanation
Indices: 28053047--28053512 Score: 691
Period size: 47 Copynumber: 9.9 Consensus size: 47
28053037 TCACACTAGT
* * * *
28053047 CATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
*
28053094 CATTCGGCCTTATCACACATATGCATGCTT-ACATTCATCACATTGGC
1 CATTCGGCCTTATCACATATATGCATG-TTCACATTCATCACATTGGC
* *
28053141 CATTCGGCCTTATCATATATATGCATGCTCACATTCATCACATTGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* *
28053188 CATTCGGCCTCATCACATATATGCATGTTCACATTCATCACATAGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* *
28053235 CATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* *
28053282 CATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* *
28053329 CATTCGGCCTCATCACATATATGCATGTTCACATTCATCACATAGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* *
28053376 CATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* * * * *
28053423 CATTCAGCCTTATCACACATATGCATGCTCACATTTATCAAATTGGC
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* **
28053470 CATTCGGCCTTATCACATATATACACATTCACATTCATCACAT
1 CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
28053513 AAAATCCTAA
Statistics
Matches: 374, Mismatches: 43, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
46 1 0.00
47 371 0.99
48 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
Found at i:28053156 original size:25 final size:25
Alignment explanation
Indices: 28053085--28053156 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 25
28053075 TCATATTCAC
28053085 CACATTGGCCATTCGGCCTTATCA-
1 CACATTGGCCATTCGGCCTTATCAT
* *** *
28053109 CACATAT-G-CATGCTTACAT-TCAT
1 CACAT-TGGCCATTCGGCCTTATCAT
28053132 CACATTGGCCATTCGGCCTTATCAT
1 CACATTGGCCATTCGGCCTTATCAT
28053157 ATATATGCAT
Statistics
Matches: 33, Mismatches: 10, Indels: 9
0.63 0.19 0.17
Matches are distributed among these distances:
22 4 0.12
23 12 0.36
24 12 0.36
25 5 0.15
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (25 bp):
CACATTGGCCATTCGGCCTTATCAT
Found at i:28056681 original size:19 final size:19
Alignment explanation
Indices: 28056657--28056694 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28056647 ACCTATCAGG
*
28056657 AGAAAATAAAAGAAAAATT
1 AGAAAAGAAAAGAAAAATT
*
28056676 AGAAAAGAAAATAAAAATT
1 AGAAAAGAAAAGAAAAATT
28056695 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (19 bp):
AGAAAAGAAAAGAAAAATT
Found at i:28061788 original size:19 final size:19
Alignment explanation
Indices: 28061766--28061810 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
28061756 AAGTAGAAAT
* *
28061766 AAATATAAAAAATTCATAA
1 AAATATAAAAAATCCAGAA
* *
28061785 AAATATATATAATCCAGAA
1 AAATATAAAAAATCCAGAA
28061804 AAATATA
1 AAATATA
28061811 TATTATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATAAAAAATCCAGAA
Found at i:28061822 original size:17 final size:18
Alignment explanation
Indices: 28061783--28061828 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
28061773 AAAAATTCAT
*
28061783 AAAAATATATATAATCCAG
1 AAAAATATATATAAT-CAA
*
28061802 AAAAATATATATTAT-AA
1 AAAAATATATATAATCAA
28061819 AAAAAT-TATA
1 AAAAATATATA
28061829 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
19 14 0.56
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATATATATAATCAA
Found at i:28062123 original size:33 final size:31
Alignment explanation
Indices: 28062071--28062131 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
28062061 TTTTATACAT
* * *
28062071 TATTTTGACTTTTTTTAAAATTTATAATTATA
1 TATTTTGAATTTTATTAAAAATTA-AATTATA
28062103 TATTTTAGAATTTTATTAAAAATTAAATT
1 TATTTT-GAATTTTATTAAAAATTAAATT
28062132 TTCTAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 10 0.40
33 15 0.60
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (31 bp):
TATTTTGAATTTTATTAAAAATTAAATTATA
Found at i:28064321 original size:22 final size:23
Alignment explanation
Indices: 28064278--28064321 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28064268 AAATTATGCC
* *
28064278 AGTAAAAATGTAGACAAGTCGCT
1 AGTAAAAATATAGACAAATCGCT
*
28064301 AGTAAAAATAT-GATAAATCGC
1 AGTAAAAATATAGACAAATCGC
28064322 CATTCCCCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (23 bp):
AGTAAAAATATAGACAAATCGCT
Found at i:28076909 original size:14 final size:14
Alignment explanation
Indices: 28076883--28076922 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
28076873 GTTTAAAGAC
*
28076883 TTTTAT-TTATTAT
1 TTTTATCTTTTTAT
28076896 TTTTATCTTTTTAT
1 TTTTATCTTTTTAT
28076910 TTTTATCTTTTTA
1 TTTTATCTTTTTA
28076923 AAACTACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATCTTTTTAT
Found at i:28076950 original size:11 final size:11
Alignment explanation
Indices: 28076931--28076965 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28076921 TAAAACTACC
28076931 TTTTATTTTAT
1 TTTTATTTTAT
*
28076942 TTTTCTTTTAT
1 TTTTATTTTAT
*
28076953 TTTAATTTTAT
1 TTTTATTTTAT
28076964 TT
1 TT
28076966 CATCCTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:28076951 original size:16 final size:17
Alignment explanation
Indices: 28076930--28076961 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28076920 TTAAAACTAC
28076930 CTTTTATTTT-ATTTTT
1 CTTTTATTTTAATTTTT
28076946 CTTTTATTTTAATTTT
1 CTTTTATTTTAATTTT
28076962 ATTTCATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
CTTTTATTTTAATTTTT
Found at i:28081220 original size:28 final size:28
Alignment explanation
Indices: 28081188--28081262 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
28081178 ATTGCATGGC
28081188 TATGAATGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
28081216 TATGAATGTGATTGGGGCAGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
*
28081244 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
28081263 AAAGGGGCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:28090030 original size:40 final size:40
Alignment explanation
Indices: 28089993--28090085 Score: 152
Period size: 40 Copynumber: 2.3 Consensus size: 40
28089983 GCTACTCGTT
*
28089993 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
28090033 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
28090073 CAAATGCCTTCGG
1 CAAATGCCTTCGG
28090086 ATCTTAGTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 48 0.96
41 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28092617 original size:35 final size:35
Alignment explanation
Indices: 28092541--28092657 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
28092531 AGTCCAACTA
* *
28092541 AAACACACCAGATGCTCATAAGAGCCAATCCAAACG
1 AAACACACCA-ATGCTCATAAGAGCTAATCCAACCG
* **
28092577 AAACACACCAATACTCATAAGAGCTAATTTAACCG
1 AAACACACCAATGCTCATAAGAGCTAATCCAACCG
* *
28092612 GAACACACCAATGCTCATAAGAGCTAGTCCAACCG
1 AAACACACCAATGCTCATAAGAGCTAATCCAACCG
28092647 AAACACACCAA
1 AAACACACCAA
28092658 ACAGAGAGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
35 60 0.86
36 10 0.14
ACGTcount: A:0.44, C:0.30, G:0.12, T:0.14
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCAACCG
Found at i:28095075 original size:26 final size:30
Alignment explanation
Indices: 28095018--28095078 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 30
28095008 GCTATAAAGT
28095018 TTGGGTTTCAAAATTATATTTTGGAAAGAA
1 TTGGGTTTCAAAATTATATTTTGGAAAGAA
* *
28095048 TTGGTTTTC-AAA-TAT-TTTTGGATA-AA
1 TTGGGTTTCAAAATTATATTTTGGAAAGAA
28095074 TTGGG
1 TTGGG
28095079 AAGTATGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 3 0.11
29 3 0.11
30 8 0.29
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (30 bp):
TTGGGTTTCAAAATTATATTTTGGAAAGAA
Found at i:28097774 original size:13 final size:13
Alignment explanation
Indices: 28097756--28097780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28097746 TGTATATATA
28097756 AAAAAGGAAAAAT
1 AAAAAGGAAAAAT
28097769 AAAAAGGAAAAA
1 AAAAAGGAAAAA
28097781 AGAAATAAAG
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAAGGAAAAAT
Found at i:28099866 original size:46 final size:46
Alignment explanation
Indices: 28099814--28099949 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
28099804 GCTCTCTGAT
* * *
28099814 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
28099860 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
28099906 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
28099950 TCAAAGATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 77 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:28107318 original size:18 final size:18
Alignment explanation
Indices: 28107295--28107330 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28107285 TAACATATAA
28107295 AAGTATATAATACATACC
1 AAGTATATAATACATACC
28107313 AAGTATATAATACATACC
1 AAGTATATAATACATACC
28107331 TGACCAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (18 bp):
AAGTATATAATACATACC
Found at i:28107523 original size:39 final size:39
Alignment explanation
Indices: 28107461--28107583 Score: 167
Period size: 39 Copynumber: 3.1 Consensus size: 39
28107451 CCAAATAGCA
*
28107461 TGCGGGACTTTAAGCCCTGATATAATACCAGCATAAAGCC
1 TGCGGGACTTT-AGCCCGGATATAATACCAGCATAAAGCC
* * *
28107501 TGCGGGGCTTTAGCCCGGATATAACACCAGCACAAATGCC
1 TGCGGGACTTTAGCCCGGATATAATACCAGCATAAA-GCC
* *
28107541 TTCGAGAC-TTAGCCCGGATATAATACCAGCATAAAGCC
1 TGCGGGACTTTAGCCCGGATATAATACCAGCATAAAGCC
28107579 TGCGG
1 TGCGG
28107584 ACCTCATGTC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
38 6 0.08
39 47 0.66
40 18 0.25
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (39 bp):
TGCGGGACTTTAGCCCGGATATAATACCAGCATAAAGCC
Found at i:28107597 original size:39 final size:37
Alignment explanation
Indices: 28107474--28107601 Score: 123
Period size: 39 Copynumber: 3.3 Consensus size: 37
28107464 GGGACTTTAA
* * *
28107474 GCCCTGATATAATACCAGCATAAAGCCTGCGGGGCTTT
1 GCCCGGATATAATACCAGCATAAAGCCTGC-GGACTAT
* * *
28107512 AGCCCGGATATAACACCAGCACAAATGCCTTCGAGACT-T
1 -GCCCGGATATAATACCAGCATAAA-GCCTGCG-GACTAT
28107551 AGCCCGGATATAATACCAGCATAAAGCCTGCGGACCTCAT
1 -GCCCGGATATAATACCAGCATAAAGCCTGCGGA-CT-AT
*
28107591 GTCCGGATATA
1 GCCCGGATATA
28107602 TTTCTAGTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
37 2 0.03
38 8 0.11
39 56 0.75
40 9 0.12
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.20
Consensus pattern (37 bp):
GCCCGGATATAATACCAGCATAAAGCCTGCGGACTAT
Found at i:28116397 original size:40 final size:39
Alignment explanation
Indices: 28116338--28116415 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
28116328 CACTTGTTGG
* *
28116338 CATGTCAGACATTTTCCTACAAACTCCGTTACTTCTCGC
1 CATGTAAGACATTTCCCTACAAACTCCGTTACTTCTCGC
*
28116377 NCATGTAAGACATTTCCCTACAAACTCTGTTACTTCTCG
1 -CATGTAAGACATTTCCCTACAAACTCCGTTACTTCTCG
28116416 TTTAAGTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.33
Consensus pattern (39 bp):
CATGTAAGACATTTCCCTACAAACTCCGTTACTTCTCGC
Found at i:28130600 original size:43 final size:43
Alignment explanation
Indices: 28130540--28130630 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
28130530 CTTTGAGTTC
* * *
28130540 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
28130582 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
28130625 ATTACC
1 ATTACC
28130631 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:28131452 original size:42 final size:43
Alignment explanation
Indices: 28131333--28131487 Score: 123
Period size: 43 Copynumber: 3.6 Consensus size: 43
28131323 AAAATGCAGT
* * * ** * * *
28131333 TAAAAGTCATGTTTTATAGCGGTATTTATGGGAAAAACGCCAC
1 TAAAGGTCATATTCTATAGCGACATTTATAGGAAAAGCGCCGC
* * * **
28131376 TAAAGGTTATAATCTATAGCGACATTTAT-GGGAAAGCGTTGC
1 TAAAGGTCATATTCTATAGCGACATTTATAGGAAAAGCGCCGC
* * * * *
28131418 TAGAGGTCATATTCTATAGCGCCGTTTGTAGGAAAAGTGCCGC
1 TAAAGGTCATATTCTATAGCGACATTTATAGGAAAAGCGCCGC
* *
28131461 TAAAGGTCATGTTCTATAGCGGCATTT
1 TAAAGGTCATATTCTATAGCGACATTT
28131488 TTCCATATAA
Statistics
Matches: 85, Mismatches: 26, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
42 31 0.36
43 54 0.64
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATATTCTATAGCGACATTTATAGGAAAAGCGCCGC
Found at i:28132223 original size:21 final size:21
Alignment explanation
Indices: 28132199--28132242 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
28132189 ACTTGTTATT
28132199 ACCCTTTGAACCTTGAAACTA
1 ACCCTTTGAACCTTGAAACTA
*
28132220 ACCCTTTGAATCTTGAAACTA
1 ACCCTTTGAACCTTGAAACTA
28132241 AC
1 AC
28132243 TTTTGGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (21 bp):
ACCCTTTGAACCTTGAAACTA
Found at i:28139338 original size:21 final size:20
Alignment explanation
Indices: 28139288--28139341 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
28139278 TTCACTTGAG
28139288 TTAAAAAT-TTTCAATCGAT
1 TTAAAAATGTTTCAATCGAT
* *
28139307 TCAAAACTGTTTCAATCGATT
1 TTAAAAATGTTTCAATCGA-T
*
28139328 TTAAAATTGTTTCA
1 TTAAAAATGTTTCA
28139342 CTTGAGATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 6 0.21
20 10 0.34
21 13 0.45
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (20 bp):
TTAAAAATGTTTCAATCGAT
Found at i:28139464 original size:14 final size:15
Alignment explanation
Indices: 28139429--28139458 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28139419 GAGACTTTAA
28139429 AAAACTTTTTACTTT
1 AAAACTTTTTACTTT
28139444 AAAACTTTTTACTTT
1 AAAACTTTTTACTTT
28139459 GAACTTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAACTTTTTACTTT
Found at i:28139502 original size:18 final size:18
Alignment explanation
Indices: 28139468--28139502 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28139458 TGAACTTCAT
28139468 CAATCCTTAGTTCAAAAA
1 CAATCCTTAGTTCAAAAA
*
28139486 CAATCTTTA-TTCAAAAA
1 CAATCCTTAGTTCAAAAA
28139503 TATTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (18 bp):
CAATCCTTAGTTCAAAAA
Found at i:28141589 original size:20 final size:20
Alignment explanation
Indices: 28141544--28141594 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28141534 CATTTATAGA
**
28141544 TAAGTATCGATATTTTTTCT
1 TAAGTATCGATAAATTTTCT
* *
28141564 TTAGTATCGATAAATTTTGT
1 TAAGTATCGATAAATTTTCT
*
28141584 TAAGTACCGAT
1 TAAGTATCGAT
28141595 TTGAAAGTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TAAGTATCGATAAATTTTCT
Found at i:28162764 original size:42 final size:43
Alignment explanation
Indices: 28162662--28162773 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 43
28162652 CACAAGGCCA
*
28162662 AGACACACGCCTGTGT-TCTAGGCCGTGTAGCACACACGGCTG
1 AGACACACGCCTGTGTCTCTAGCCCGTGTAGCACACACGGCTG
** *
28162704 AGACACACGCCTACGTCTCTA-CCCGTGTAGCACACATGGCTG
1 AGACACACGCCTGTGTCTCTAGCCCGTGTAGCACACACGGCTG
* *
28162746 AGACACACACCTGTGTCTCT-GCTCGTGT
1 AGACACACGCCTGTGTCTCTAGCCCGTGT
28162774 GCTTAATTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 56 0.93
43 4 0.07
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (43 bp):
AGACACACGCCTGTGTCTCTAGCCCGTGTAGCACACACGGCTG
Done.