Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 11 of 141
Found at i:3532817 original size:21 final size:20
Alignment explanation
Indices: 3532777--3532818 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3532767 ATTTTTTAAT
**
3532777 ATTAATATAATATATTTTTA
1 ATTAATATAATATAAATTTA
3532797 ATTAATATAAATATAAATTTA
1 ATTAATAT-AATATAAATTTA
3532818 A
1 A
3532819 AATAAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAATATAATATAAATTTA
Found at i:3533242 original size:21 final size:21
Alignment explanation
Indices: 3533204--3533243 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3533194 TCTACAATGT
*
3533204 TGTCTTGAGACATCAAGAACA
1 TGTCTTGAAACATCAAGAACA
3533225 TGTCTTGAAATCAT-AAGAA
1 TGTCTTGAAA-CATCAAGAA
3533244 TATTTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTCTTGAAACATCAAGAACA
Found at i:3534790 original size:17 final size:19
Alignment explanation
Indices: 3534747--3534789 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
3534737 GATAATGTTG
*
3534747 AAAAAATTATTTAGTTTAA
1 AAAAAATTATATAGTTTAA
3534766 AAATAAATT-TATAGTTTTAA
1 AAA-AAATTATATAG-TTTAA
3534786 AAAA
1 AAAA
3534790 TAGGATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAAAATTATATAGTTTAA
Found at i:3556393 original size:34 final size:34
Alignment explanation
Indices: 3556318--3556395 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
3556308 TCACAATGCT
* ** *
3556318 AGTATTCAGTAGGGCCTTTGCCCAATTTTAGTAAT
1 AGTA-TCAGTAGGGCCTTGGCCCAATAATAGTAAC
*
3556353 AGTATCAGTGGGGCCTTGGCCC-ATAATAGTAAC
1 AGTATCAGTAGGGCCTTGGCCCAATAATAGTAAC
3556386 AGATATCAGT
1 AG-TATCAGT
3556396 CATGCAGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 10 0.27
34 23 0.62
35 4 0.11
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (34 bp):
AGTATCAGTAGGGCCTTGGCCCAATAATAGTAAC
Found at i:3557095 original size:81 final size:80
Alignment explanation
Indices: 3556855--3557095 Score: 331
Period size: 81 Copynumber: 3.0 Consensus size: 80
3556845 GGGGTATAAT
* *
3556855 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGCTA-TTTCATTCATTCTA
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGG-TATTTTGA-TCATTTTA
*
3556919 CCCTATAGGGGTATTTC
64 CCCTATAGGGGTATTCC
*
3556936 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTAT-GGGGTATTTTGATCATTTTAC
* *
3557001 CTTATTGGGGTATTCC
65 CCTATAGGGGTATTCC
* * * * *
3557017 AGTCATTTTACCCTATAGAGGTATTTTGGTCATTTTACCCTATGTGAGTATTTTGATCATTTTAC
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATG-GGGTATTTTGATCATTTTAC
*
3557082 CCTATGGGGGTATT
65 CCTATAGGGGTATT
3557096 TTCGTAATAA
Statistics
Matches: 143, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
80 1 0.01
81 135 0.94
82 7 0.05
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (80 bp):
AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGTATTTTGATCATTTTACC
CTATAGGGGTATTCC
Found at i:3557097 original size:27 final size:27
Alignment explanation
Indices: 3556857--3557097 Score: 281
Period size: 27 Copynumber: 8.9 Consensus size: 27
3556847 GGTATAATAG
*
3556857 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTTGA
* *
3556884 TCATTTTACCCTATGGGGCTA-TTTCA
1 TCATTTTACCCTATGGGGGTATTTTGA
* * *
3556910 TTCATTCTACCCTATAGGGGTA-TTTCA
1 -TCATTTTACCCTATGGGGGTATTTTGA
*
3556937 GTCATTTTACCCTATGGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTTGA
*
3556965 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGA
* * **
3556992 TCATTTTACCTTATTGGGGTA-TTCCA
1 TCATTTTACCCTATGGGGGTATTTTGA
* * *
3557018 GTCATTTTACCCTATAGAGGTATTTTGG
1 -TCATTTTACCCTATGGGGGTATTTTGA
* *
3557046 TCATTTTACCCTATGTGAGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTTGA
3557073 TCATTTTACCCTATGGGGGTATTTT
1 TCATTTTACCCTATGGGGGTATTTT
3557098 CGTAATAAAT
Statistics
Matches: 179, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.03
27 169 0.94
28 5 0.03
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTTGA
Found at i:3559403 original size:21 final size:21
Alignment explanation
Indices: 3559365--3559406 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3559355 GAAATTAAAA
*
3559365 TGTTTTAATTTTAGTTTAATT
1 TGTTTTAATTTCAGTTTAATT
3559386 TGTTTTAATTTCCA-TTTAATT
1 TGTTTTAATTT-CAGTTTAATT
3559407 ACAAAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (21 bp):
TGTTTTAATTTCAGTTTAATT
Found at i:3563061 original size:436 final size:437
Alignment explanation
Indices: 3562238--3563111 Score: 1741
Period size: 436 Copynumber: 2.0 Consensus size: 437
3562228 GGGGATAACA
3562238 TAGGGGTGAGAAACTTATTTTATATATAAATATTAAATTTTATTTTGGGAAATAGAAAAATTAAA
1 TAGGGGTGAGAAACTTATTTTATATATAAATATTAAATTTTATTTTGGGAAATAGAAAAATTAAA
3562303 TTAGGTTGGATCACATTACAAAGTATTGGATTAAAAAGACCTAGGAAGTACTCGTAATTGGACTT
66 TTAGGTTGGATCACATTACAAAGTATTGGATTAAAAAGACCTAGGAAGTACTCGTAATTGGACTT
3562368 GATGTGAGAGAGACCCAAAAACCCCTTATAGACATGAAGGGGTCGGTAACTCTAGTAGGAATACT
131 GATGTGAGAGAGACCCAAAAACCCCTTATAGACATGAAGGGGTCGGTAACTCTAGTAGGAATACT
3562433 AGGGTGTCCCATCCACCTTAGTCCTATTCTGAGTAGGATGTTGTTTTTGTATTTGAAATAAACCA
196 AGGGTGTCCCATCCACCTTAGTCCTATTCTGAGTAGGATGTTGTTTTTGTATTTGAAATAAACCA
3562498 CTACAACTCAACAAGGGTTCTACCTTCTCTTCCTATAAATAGATGACACCGGTAGAGCTATTAAC
261 CTACAACTCAACAAGGGTTCTACCTTCTCTTCCTATAAATAGATGACACCGGTAGAGCTATTAAC
3562563 ACAACTTTGAGAGATTGTTATTCTAACAAAAAATAAAGAGAATTTATTCTCAACTATTACATATT
326 ACAACTTTGAGAGATTGTTATTCTAACAAAAAATAAAGAGAATTTATTCTCAACTATTACATATT
3562628 TTCTCAGAATAACGATTGTACCAATTTATATTAAGAAGAGAGAATTT
391 TTCTCAGAATAACGATTGTACCAATTTATATTAAGAAGAGAGAATTT
3562675 TAGGGGTGAG-AACTTATTTTATATATAAATATTAAATTTTATTTTGGGAAATAGAAAAATTAAA
1 TAGGGGTGAGAAACTTATTTTATATATAAATATTAAATTTTATTTTGGGAAATAGAAAAATTAAA
3562739 TTAGGTTGGATCACATTACAAAGTATTGGATTAAAAAGACCTAGGAAGTACTCGTAATTGGACTT
66 TTAGGTTGGATCACATTACAAAGTATTGGATTAAAAAGACCTAGGAAGTACTCGTAATTGGACTT
3562804 GATGTGAGAGAGACCCAAAAACCCCTTATAGACATGAAGGGGTCGGTAACTCTAGTAGGAATACT
131 GATGTGAGAGAGACCCAAAAACCCCTTATAGACATGAAGGGGTCGGTAACTCTAGTAGGAATACT
3562869 AGGGTGTCCCATCCACCTTAGTCCTATTCTGAGTAGGATGTTGTTTTTGTATTTGAAATAAACCA
196 AGGGTGTCCCATCCACCTTAGTCCTATTCTGAGTAGGATGTTGTTTTTGTATTTGAAATAAACCA
3562934 CTACAACTCAACAAGGGTTCTACCTTCTCTTCCTATAAATAGATGACACCGGTAGAGCTATTAAC
261 CTACAACTCAACAAGGGTTCTACCTTCTCTTCCTATAAATAGATGACACCGGTAGAGCTATTAAC
3562999 ACAACTTTGAGAGATTGTTATTCTAACAAAAAATAAAGAGAATTTATTCTCAACTATTACATATT
326 ACAACTTTGAGAGATTGTTATTCTAACAAAAAATAAAGAGAATTTATTCTCAACTATTACATATT
3563064 TTCTCAGAATAACGATTGTACCAATTTATATTAAGAAGAGAGAATTT
391 TTCTCAGAATAACGATTGTACCAATTTATATTAAGAAGAGAGAATTT
3563111 T
1 T
3563112 TATTTTTACC
Statistics
Matches: 437, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
436 427 0.98
437 10 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (437 bp):
TAGGGGTGAGAAACTTATTTTATATATAAATATTAAATTTTATTTTGGGAAATAGAAAAATTAAA
TTAGGTTGGATCACATTACAAAGTATTGGATTAAAAAGACCTAGGAAGTACTCGTAATTGGACTT
GATGTGAGAGAGACCCAAAAACCCCTTATAGACATGAAGGGGTCGGTAACTCTAGTAGGAATACT
AGGGTGTCCCATCCACCTTAGTCCTATTCTGAGTAGGATGTTGTTTTTGTATTTGAAATAAACCA
CTACAACTCAACAAGGGTTCTACCTTCTCTTCCTATAAATAGATGACACCGGTAGAGCTATTAAC
ACAACTTTGAGAGATTGTTATTCTAACAAAAAATAAAGAGAATTTATTCTCAACTATTACATATT
TTCTCAGAATAACGATTGTACCAATTTATATTAAGAAGAGAGAATTT
Found at i:3563898 original size:14 final size:14
Alignment explanation
Indices: 3563879--3563912 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3563869 TGGATTTATG
*
3563879 TTATTTCTGCCAAA
1 TTATTTCTACCAAA
3563893 TTATTTCTACCAAA
1 TTATTTCTACCAAA
3563907 TT-TTTC
1 TTATTTC
3563913 AGGATCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (14 bp):
TTATTTCTACCAAA
Found at i:3566295 original size:20 final size:20
Alignment explanation
Indices: 3566270--3566308 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3566260 AACATTCAAA
3566270 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
3566290 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
3566309 ACCATGTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:3566757 original size:20 final size:20
Alignment explanation
Indices: 3566715--3566758 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3566705 CCCTTTCCAA
* *
3566715 ATTTTCTTACTTTCATTTGC
1 ATTTTATTACTTTCATTTAC
3566735 ATTTTATTACTTTCCA-TTAC
1 ATTTTATTACTTT-CATTTAC
3566755 ATTT
1 ATTT
3566759 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTTATTACTTTCATTTAC
Found at i:3567476 original size:50 final size:49
Alignment explanation
Indices: 3567393--3567536 Score: 164
Period size: 49 Copynumber: 2.9 Consensus size: 49
3567383 GTACATCTAT
* * * *
3567393 GCTCATATGAGCT-ATGAATCGGTATGCTCTCACGAGCTATAAATTGGTAA
1 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCT-GAAATCGGTAA
*
3567443 GCTCATACGAGCTGAGAATCGGTAAGCTTTCACGAGCTGAAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
* * ** * *
3567492 GCTCATACAAGCTGAGAATTGACAAGCTCTCACAAGCTGCAATCG
1 GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCG
3567537 ATAATCCCTA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
49 47 0.58
50 33 0.41
51 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (49 bp):
GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
Found at i:3567504 original size:24 final size:24
Alignment explanation
Indices: 3567409--3567506 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 24
3567399 ATGAGCTATG
* *
3567409 AATCGGTATGCTC-TCACGAGCTATA
1 AATCGGTAAGCTCAT-ACGAGCT-GA
*
3567434 AATTGGTAAGCTCATACGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
*
3567458 GAATCGGTAAGCT-TTCACGAGCTGA
1 -AATCGGTAAGCTCAT-ACGAGCTGA
*
3567483 AATCGGTAAGCTCATACAAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
3567507 GAATTGACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
24 22 0.35
25 39 0.63
26 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:3575888 original size:37 final size:35
Alignment explanation
Indices: 3575839--3575908 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 35
3575829 TATTGAATTG
3575839 AATATTAAATTTAATTTAATATCTATATAGATATT
1 AATATTAAATTTAATTTAATATCTATATAGATATT
* *
3575874 AATATTAGATATTTAATTTAATATTTATCTAGATA
1 AATATTA-A-ATTTAATTTAATATCTATATAGATA
3575909 GTATTTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 7 0.23
36 1 0.03
37 23 0.74
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (35 bp):
AATATTAAATTTAATTTAATATCTATATAGATATT
Found at i:3578334 original size:99 final size:99
Alignment explanation
Indices: 3577972--3578872 Score: 969
Period size: 99 Copynumber: 9.1 Consensus size: 99
3577962 GGATTATTTT
* * * *
3577972 CTTCAAT-TTGTTTAATCTGCAATGTCGGGGAAACCAAATTCGCCGTTGT-GACTCCAATCTGTT
1 CTTCAATCTT-TTTAAT-TGCAATGTC-GGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTT
* * * * *
3578035 CCACTGCACTGCCAGGGAAGTAAGA-TCTGCTGTCGTAG
62 CCACTGCACCGCCAAGGAAGTAAGATTC-GCCGTTGTGG
* * *
3578073 CTTCAATATTTTAAATTGCAATGTCGGGGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTC-GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
3578138 CTGTA-C-CTAAGGAGGTAAGATTCGCCGTTGTGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
* * *
3578171 TTTCAATCTTTTTAATTCCAATGTCTGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTC-GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * * * *
3578236 CTGCATCGCTAAGGAGGTAAGATTTGCTGTTGCGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
**
3578271 CTTCAATCTTTTTAATTTTAATGTCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTTAATTGCAATGTCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
* * *
3578336 TGCACCGCTAAGGAGGTAAGATTCGCCGTTTTGG
66 TGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
*
3578370 CTTCAATCTTTTTAATTG-AATGTCGAGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCG-GGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
** * * ** *
3578434 CTATACCACCAGGGAAACAAGATTCGCTGTTGTGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
** * * * *
3578469 CTTCAATC-TTTTAATTGCAATGTTAAGGAAACCAAATCCACCGCCGTGGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATG-TCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * **
3578533 CTACACCACCAGGGAAACAAGATTCGCCGTTGTGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
*** * * *
3578568 CTTCAATC-TTTTAATTGCAATGTTAACG-AACCAGATCCACCATCGTGGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATG-TCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * ** * *
3578631 CTACACCACCAGGGAAACAAGACTCGCCGTTGAGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
*
3578666 CTTCAATC-TTTTAATTGCAATGTCGTGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCG-GGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* *
3578730 CTGCACCGCTAAGGAAGTAAGATTCGCCATTGTGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
* * *
3578765 CTTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATCTGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTC-GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * * *
3578830 CTGCACTGCC-AGGAAAATAAGATTCACTGTTGTGG
65 CTGCACCGCCAAGG-AAGTAAGATTCGCCGTTGTGG
3578865 CTTCAATC
1 CTTCAATC
3578873 CGTTCCACTG
Statistics
Matches: 704, Mismatches: 83, Indels: 27
0.86 0.10 0.03
Matches are distributed among these distances:
97 1 0.00
98 184 0.26
99 323 0.46
100 180 0.26
101 14 0.02
102 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (99 bp):
CTTCAATCTTTTTAATTGCAATGTCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
TGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
Found at i:3578422 original size:49 final size:49
Alignment explanation
Indices: 3578270--3578427 Score: 124
Period size: 49 Copynumber: 3.2 Consensus size: 49
3578260 TGCTGTTGCG
* *
3578270 GCTTCAATCTTTTTAATTTTAATGTCG-GGAAACCAGATCCGCCGTCGTA
1 GCTTCAATCTTTTTAA-TTGAATGTCGAGGAAACTAGATCCGCCGTCGTA
* ** * ** * ** * ** *
3578319 GCTTCAATCTGTTCCACTGCACCG-CTAAGG-AGGTAAGATTCGCCGTTTTG
1 GCTTCAATCTTTTTAATTG-AATGTC-GAGGAAACT-AGATCCGCCGTCGTA
3578369 GCTTCAATCTTTTTAATTGAATGTCGAGGAAACTAGATCCGCCGTCGTA
1 GCTTCAATCTTTTTAATTGAATGTCGAGGAAACTAGATCCGCCGTCGTA
3578418 GCTTCAATCT
1 GCTTCAATCT
3578428 GTTCCACTAT
Statistics
Matches: 75, Mismatches: 28, Indels: 12
0.65 0.24 0.10
Matches are distributed among these distances:
48 2 0.03
49 42 0.56
50 31 0.41
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (49 bp):
GCTTCAATCTTTTTAATTGAATGTCGAGGAAACTAGATCCGCCGTCGTA
Found at i:3578660 original size:296 final size:295
Alignment explanation
Indices: 3578072--3578872 Score: 948
Period size: 296 Copynumber: 2.7 Consensus size: 295
3578062 TGCTGTCGTA
* * * *
3578072 GCTTCAATATTTTAAATTGCAATGTCGGGGAAACCAAATCCGCCGTCGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGAGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
* * *
3578137 ACTGTACCTA-AGGAGGTAAGATTCGCCGTTGTGGTTTCAATCTTTTTAATTCCAATGTCTGGGA
66 ACTGTACC-ACAGGAAGTAAGATTCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATGT-TGGGA
* * * * ** *
3578201 AACCAGATCCACCGTCGTAGCTTCAATCTGTTCCACTGCATCGCTAAGGAGGTAAGATTTGCTGT
128 AACCAAATCCACCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCTGT
* ** *** * *
3578266 TGCGGCTTCAATCTTTTTAATTTTAATGTCGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGT
193 TGTGGCTTCAATCTTTTTAATTGCAATGTAACGAAACCAGATCCACCATCGTAGCTTCAATCTGT
* * * *** * **
3578331 TCCACTGCACCGCTAAGGAGGTAAGATTCGCCGTTTTG
258 TCCACTACACCACCAAGGAAACAAGACTCGCCGTTGAG
*
3578369 GCTTCAATCTTTTTAATTG-AATGTCGAGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGAGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
* ** * *
3578433 ACTATACCACCAGGGAAACAAGATTCGCTGTTGTGGCTTCAATCTTTTAATTGCAATGTTAAGGA
66 ACTGTACCA-CA-GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTT-GGGA
* * * * * *
3578498 AACCAAATCCACCGCCGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAACAAGATTCGCCGT
128 AACCAAATCCACCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCTGT
*
3578563 TGTGGCTTCAATC-TTTTAATTGCAATGTTAACG-AACCAGATCCACCATCGTGGCTTCAATCTG
193 TGTGGCTTCAATCTTTTTAATTGCAATG-TAACGAAACCAGATCCACCATCGTAGCTTCAATCTG
*
3578626 TTCCACTACACCACCAGGGAAACAAGACTCGCCGTTGAG
257 TTCCACTACACCACCAAGGAAACAAGACTCGCCGTTGAG
* *
3578665 GCTTCAATC-TTTTAATTGCAATGTCGTGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGAGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
* * * *
3578729 ACTGCACCGCTAAGGAAGTAAGATTCGCCATTGTGGCTTCAATCTATTTAATTGCAATGTCGGGG
66 ACTGTACCAC--AGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATGT-TGGG
** * * *
3578794 AAA-CAAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGAAAATAAGATTCACT
127 AAACCAA-ATCCACCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCT
3578858 GTTGTGGCTTCAATC
191 GTTGTGGCTTCAATC
3578873 CGTTCCACTG
Statistics
Matches: 425, Mismatches: 68, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
295 11 0.03
296 206 0.48
297 182 0.43
298 26 0.06
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (295 bp):
GCTTCAATCTTTTTAATTGCAATGTCGAGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
ACTGTACCACAGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTGGGAAAC
CAAATCCACCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCTGTTGT
GGCTTCAATCTTTTTAATTGCAATGTAACGAAACCAGATCCACCATCGTAGCTTCAATCTGTTCC
ACTACACCACCAAGGAAACAAGACTCGCCGTTGAG
Found at i:3578802 original size:50 final size:49
Alignment explanation
Indices: 3578154--3578872 Score: 242
Period size: 50 Copynumber: 14.5 Consensus size: 49
3578144 CTAAGGAGGT
* * *
3578154 AAGATTCGCCGTTGTGGTTTCAATCTTTTTAATTCCAATGTCTGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCAGGGAAAC
* * * * * ** * * ***
3578204 CAGATCCACCGTCGTAGCTTCAATCTGTTCCACTGC-ATCG-CTAAGGAGGT
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAAT-GTC-AGGGAAAC
* * * **
3578254 AAGATTTGCTGTTGCGGCTTCAATCTTTTTAATTTTAATGTC-GGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCAGGGAAAC
* * * * ** * ** * ***
3578303 CAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCG-CTAAGGAGGT
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTC-AGGGAAAC
*
3578353 AAGATTCGCCGTTTTGGCTTCAATCTTTTTAATTG-AATGTC-GAGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCAG-GGAAAC
* * * * * * * * *
3578402 TAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTATACCA--CCAGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCT-TT-TAAT-TGCAATGTCAGGGAAAC
* * *
3578452 AAGATTCGCTGTTGTGGCTTCAATCTTTTAATTGCAATGTTAAGGAAACC
1 AAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCAGGGAAA-C
* * ** ** * * ****
3578502 AA-ATCCACCGCCGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCAGGGAAAC
* **
3578551 AAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTTAACG-AAC
1 AAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCAGGGAAAC
* * * * * ** * * ****
3578599 CAGATCCACCATCGTGGCTTCAATCTGTTCCACTACACCACCAGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCAGGGAAAC
* *
3578649 AAGACTCGCCGTTGAGGCTTCAATCTTTTAATTGCAATGTC-GTGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCAG-GGAAAC
* * * ** * ** * **
3578698 CAGA-TCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACCG-CTAAGGAAGT
1 AAGATTC-GCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTC-AGGGAAAC
* *
3578748 AAGATTCGCCATTGTGGCTTCAATCTATTTAATTGCAATGTCGGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCAGGGAAAC
* * ** * * * * *
3578798 AAGA-TCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGAAAAT
1 AAGATTC-GCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCAGGGAAAC
* *
3578848 AAGATTCACTGTTGTGGCTTCAATC
1 AAGATTCGCCGTTGTGGCTTCAATC
3578873 CGTTCCACTG
Statistics
Matches: 447, Mismatches: 189, Indels: 66
0.64 0.27 0.09
Matches are distributed among these distances:
47 3 0.01
48 32 0.07
49 138 0.31
50 261 0.58
51 12 0.03
52 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (49 bp):
AAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCAGGGAAAC
Found at i:3579099 original size:167 final size:167
Alignment explanation
Indices: 3578864--3579194 Score: 466
Period size: 167 Copynumber: 2.0 Consensus size: 167
3578854 CACTGTTGTG
**
3578864 GCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCTGCTC
1 GCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCACTC
* * *
3578929 CACTTCAGCCAATTCAAGTCTTAACACCAGAGAGATAAGATTCATCGTCGTGGCTTCAATCTGCT
66 CACTTCAGCCAATCCAAGCCTTAACACCAGAGAGATAAGATTCACCGTCGTGGCTTCAATCTGCT
* * * *
3578994 TCGCTGCAATGCCAGAGAAGTAAAATTCGCCGTTACA
131 CCACTACAACGCCAGAGAAGTAAAATTCGCCGTTACA
* * *
3579031 GCTTTAATCCGTTCTACTGTAATGCCAAAGTGATAGGATTCGCTGCCCACAG-TTTCAATCCACT
1 GCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTT-AATCCACT
* ** * *
3579095 CCACTTTAGTTAATCCAAGCCTTAACACCAGGGAGATAAGATTCACCGTCGTGGCTTTAATCTGC
65 CCACTTCAGCCAATCCAAGCCTTAACACCAGAGAGATAAGATTCACCGTCGTGGCTTCAATCTGC
* * *
3579160 TCCACTATAACGCCAGGGAAGTAAGATTCGCCGTT
130 TCCACTACAACGCCAGAGAAGTAAAATTCGCCGTT
3579195 GTGGCTTCAA
Statistics
Matches: 143, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
166 3 0.02
167 140 0.98
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (167 bp):
GCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCACTC
CACTTCAGCCAATCCAAGCCTTAACACCAGAGAGATAAGATTCACCGTCGTGGCTTCAATCTGCT
CCACTACAACGCCAGAGAAGTAAAATTCGCCGTTACA
Found at i:3579216 original size:50 final size:50
Alignment explanation
Indices: 3579117--3579235 Score: 114
Period size: 50 Copynumber: 2.4 Consensus size: 50
3579107 ATCCAAGCCT
* ** *
3579117 TAACACCAGGGAGATAAGATTCACCGTCGTGGCTTTAATCTGCTCCACTA
1 TAACACCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCCACTACACTA
* * * *
3579167 TAACGCCAGGGA-AGTAAGATTCGCCGTTGTGGCTTCAATCCATTACACTA
1 TAACACCAGGGAGA-TAAGATTCACCGTCGTGGCTTCAATCCACTACACTA
* * * *
3579217 CAACATCAAGGCGATAAGA
1 TAACACCAGGGAGATAAGA
3579236 CAGATGTCTT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
49 1 0.02
50 52 0.96
51 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (50 bp):
TAACACCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCCACTACACTA
Found at i:3579406 original size:88 final size:88
Alignment explanation
Indices: 3579242--3579411 Score: 216
Period size: 88 Copynumber: 1.9 Consensus size: 88
3579232 AAGACAGATG
* ** *
3579242 TCTTCGATCTGCTTCGCTGCCAGTACAAGAAGGCAATATCTACCATTTTCAACCTACTCCACAAC
1 TCTTCGATCTACTTCGCTGCCAAAACAAGAAGACAATATCTACCATTTTCAACCTACTCCACAAC
*
3579307 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAAGGAGACAAGGCTGGTA
* * * **
3579330 TCTTCGATCTACTTCGCTGCCAAAACAGGAAGAC-ATGATCTGCTATTTTCAACCTACTCCACTG
1 TCTTCGATCTACTTCGCTGCCAAAACAAGAAGACAAT-ATCTACCATTTTCAACCTACTCCACAA
* *
3579394 CTGCTCAAGGAGATAAGG
65 CTGCCCAAGGAGACAAGG
3579412 TTGAAGTTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
87 2 0.03
88 67 0.97
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAAAACAAGAAGACAATATCTACCATTTTCAACCTACTCCACAAC
TGCCCAAGGAGACAAGGCTGGTA
Found at i:3584122 original size:23 final size:24
Alignment explanation
Indices: 3584088--3584163 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 24
3584078 TGAACAAAAT
*
3584088 ATGATTATG-AAATGAATAAAAGA
1 ATGATTATGAAAAAGAATAAAAGA
3584111 ATGATGTA-GAAAAAGAATAAAAGA
1 ATGAT-TATGAAAAAGAATAAAAGA
*
3584135 ATAATTACTCGAAAAAAGAATAAAAGA
1 ATGATTA-T-G-AAAAAGAATAAAAGA
3584162 AT
1 AT
3584164 ACTGGCTCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
23 8 0.18
24 19 0.42
26 1 0.02
27 17 0.38
ACGTcount: A:0.61, C:0.03, G:0.16, T:0.21
Consensus pattern (24 bp):
ATGATTATGAAAAAGAATAAAAGA
Found at i:3584133 original size:24 final size:25
Alignment explanation
Indices: 3584101--3584164 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 25
3584091 ATTATGAAAT
*
3584101 GAATAAAAGAATGATGTA-G-AAAAA
1 GAATAAAAGAATAAT-TACGAAAAAA
3584125 GAATAAAAGAATAATTACTCGAAAAAA
1 GAATAAAAGAATAATTA--CGAAAAAA
3584152 GAATAAAAGAATA
1 GAATAAAAGAATA
3584165 CTGGCTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 2 0.06
24 14 0.40
26 1 0.03
27 18 0.51
ACGTcount: A:0.64, C:0.03, G:0.16, T:0.17
Consensus pattern (25 bp):
GAATAAAAGAATAATTACGAAAAAA
Found at i:3584176 original size:27 final size:27
Alignment explanation
Indices: 3584120--3584176 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3584110 AATGATGTAG
* *
3584120 AAAAAGAATAAAAGAATAATTACTCGA
1 AAAAAGAATAAAAGAATAATGACTCAA
* *
3584147 AAAAAGAATAAAAGAATACTGGCTCAA
1 AAAAAGAATAAAAGAATAATGACTCAA
3584174 AAA
1 AAA
3584177 TGCATACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.09, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAAAGAATAAAAGAATAATGACTCAA
Found at i:3593296 original size:50 final size:50
Alignment explanation
Indices: 3592944--3593846 Score: 381
Period size: 50 Copynumber: 18.2 Consensus size: 50
3592934 GGATTATTTT
* * * * *
3592944 CTTCAAT-TTGTTTAATCTGCAATGTC-GAGGAAACCAAATTCACCGTTGTGA
1 CTTCAATCTT-TTCAAT-TGCAATGTCAG-GGAAACCAGATCCGCCGTTGTGG
* * * * * * *** * *
3592995 CTCCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCGTCGTAG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * * *
3593045 CTTCAATATTTTAAATTGCAATGTCGGGGAATCTAGATCCGCCGTTGTAG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * ** * ** *
3593095 CTTCAATCTATTCCACTGC-ACCTAAGGAGGTA--AGATTCGCCGTTGTGG
1 CTTCAATCTTTTCAATTGCAATGTCAGG-GAAACCAGATCCGCCGTTGTGG
* * * * *
3593143 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * ** ** *
3593193 CTTCAATCTGTTCCACTGCATCAT-TAAGGAGGTA--AGATTTGCTGTTGTGG
1 CTTCAATCTTTTCAATTGCA--ATGTCAGG-GAAACCAGATCCGCCGTTGTGG
* * * *
3593243 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * * *
3593293 CTTCAAT-TTGTTCCACTATACCA--CCAGGGAAACAAGATTCGCCGTTGTGG
1 CTTCAATCTT-TT-CAAT-TGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * *
3593343 CTTCAATCTTTT-AATTGCAATGTTAAGGAACCCAGATCCACCGTCGTGG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * **** * * *
3593392 CTTCAATCTGTTCCACTACACCACCAGGGAAACAAGATTCGCCATTGTGG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * *
3593442 CTTCAATCTTTT-AATTGCAATGTTAAGGAAACCAGATCCACCGTCGTGG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * **** *
3593491 CTTCAATCTGTTCCACTACACCACCAGGGAAACAAGA-CTCGCCGTTGTGG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATC-CGCCGTTGTGG
* * * *
3593541 CTTCAATCTTTT-AATTGCAATGTTAAGGAAACCAGATCCACCGTCGTGG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * *** * * *
3593590 CTTCAATCTATTCCACTAC-ACCACAAGGGAAA-TAAAACTCGCCGTTGTGG
1 CTTCAATCTTTTCAATTGCAATGTC-AGGGAAACCAGATC-CGCCGTTGTGG
* * * *
3593640 CTTCAATCTTTT-AATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAG
1 CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * ** * *** * * *
3593689 CTTCAATCTGTTCCACTGCACCG-CTAAGGAAGTAAGATTCACCATTGTGG
1 CTTCAATCTTTTCAATTGCAATGTC-AGGGAAACCAGATCCGCCGTTGTGG
* * * *
3593739 CTTCAATCTATTT-AATTGCAATGTCGGGGAAACAAGATCCACCGTTGTAG
1 CTTCAATCT-TTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
* * * * * * * *
3593789 CTTCAATCTATTCCAA-AGCACTGCCAGGAAAACAAGATTCACCGTTGTGG
1 CTTCAATCT-TTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
3593839 CTTCAATC
1 CTTCAATC
3593847 CGTTCCACTG
Statistics
Matches: 596, Mismatches: 224, Indels: 65
0.67 0.25 0.07
Matches are distributed among these distances:
47 3 0.01
48 37 0.06
49 145 0.24
50 381 0.64
51 22 0.04
52 8 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (50 bp):
CTTCAATCTTTTCAATTGCAATGTCAGGGAAACCAGATCCGCCGTTGTGG
Found at i:3593404 original size:99 final size:99
Alignment explanation
Indices: 3592944--3593846 Score: 1042
Period size: 99 Copynumber: 9.1 Consensus size: 99
3592934 GGATTATTTT
* * * * * *
3592944 CTTCAATTTGTTTAATCTGCAATGTCGAGGAAACCAAATTCACCGTTGT-GACTCCAATCTGTTC
1 CTTCAATCT-TTTAAT-TGCAATGTCGGGGAAACCAGATCCACCGTCGTAG-CTTCAATCTGTTC
* ** * * * *
3593008 CACTGCACTGCCAGGGAAGTAAGATCCGCCGTCGTAG
63 CACTACACCACCAGGGAAATAAGATTCGCCGTTGTGG
* * * * * *
3593045 CTTCAATATTTTAAATTGCAATGTCGGGGAATCTAGATCCGCCGTTGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTT-AATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
* **
3593110 CTGCACCTA--A-GGAGGTAAGATTCGCCGTTGTGG
65 CTACACC-ACCAGGGAAATAAGATTCGCCGTTGTGG
3593143 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
* * ** * ** * *
3593208 CTGCATCATTAAGGAGGTAAGATTTGCTGTTGTGG
65 CTACACCACCAGGGAAATAAGATTCGCCGTTGTGG
* *
3593243 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATTTGTTCCA
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
* *
3593308 CTATACCACCAGGGAAACAAGATTCGCCGTTGTGG
65 CTACACCACCAGGGAAATAAGATTCGCCGTTGTGG
*** * *
3593343 CTTCAATCTTTTAATTGCAATGTTAAGGAACCCAGATCCACCGTCGTGGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
* *
3593408 TACACCACCAGGGAAACAAGATTCGCCATTGTGG
66 TACACCACCAGGGAAATAAGATTCGCCGTTGTGG
*** *
3593442 CTTCAATCTTTTAATTGCAATGTTAAGGAAACCAGATCCACCGTCGTGGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
* *
3593507 TACACCACCAGGGAAACAAGACTCGCCGTTGTGG
66 TACACCACCAGGGAAATAAGATTCGCCGTTGTGG
*** * *
3593541 CTTCAATCTTTTAATTGCAATGTTAAGGAAACCAGATCCACCGTCGTGGCTTCAATCTATTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
* * *
3593606 TACACCACAAGGGAAATAAAACTCGCCGTTGTGG
66 TACACCACCAGGGAAATAAGATTCGCCGTTGTGG
3593640 CTTCAATCTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
* * * * * * *
3593705 TGCACCGCTAAGGAAGTAAGATTCACCATTGTGG
66 TACACCACCAGGGAAATAAGATTCGCCGTTGTGG
* * *
3593739 CTTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATCCACCGTTGTAGCTTCAATCTATTCCA
1 CTTCAATCT-TTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
* ** * * *
3593804 -AAGCACTGCCAGGAAAACAAGATTCACCGTTGTGG
65 CTA-CACCACCAGGGAAATAAGATTCGCCGTTGTGG
3593839 CTTCAATC
1 CTTCAATC
3593847 CGTTCCACTG
Statistics
Matches: 714, Mismatches: 79, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
97 1 0.00
98 79 0.11
99 373 0.52
100 249 0.35
101 12 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (99 bp):
CTTCAATCTTTTAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
TACACCACCAGGGAAATAAGATTCGCCGTTGTGG
Found at i:3594073 original size:167 final size:167
Alignment explanation
Indices: 3593827--3594136 Score: 458
Period size: 167 Copynumber: 1.9 Consensus size: 167
3593817 AAAACAAGAT
* * * * *
3593827 TCACCGTTGTGGCTTCAATCCGTTCCACTGTAATGCCAGAGAGATAGGATTCGCTGCCCACAGCT
1 TCACCGTTGCGGCTTCAATCCGTTCCACTGTAATGCCAAACAGATACGATTCGCTACCCACAGCT
* ** * *
3593892 TTAATCTGCTCCACTTCAGCCAATTCAAGTCTTAACGCCAGAGAGATAAGATTCACCGTCGTGGC
66 TCAATCCACTCCACTTCAGCCAATCCAAGCCTTAACGCCAGAGAGATAAGATTCACCGTCGTGGC
3593957 TTCAATCTGCTCCGTTGCAAAGCCAGAGAAGTAAAAC
131 TTCAATCTGCTCCGTTGCAAAGCCAGAGAAGTAAAAC
* * *
3593994 TCACCGTTGCGGCTTTAATCCGTTCTACTGTAATGCCAAACTGATACGATTCGCTACCCACAGCT
1 TCACCGTTGCGGCTTCAATCCGTTCCACTGTAATGCCAAACAGATACGATTCGCTACCCACAGCT
** * *
3594059 TCAATCCACTCCACTTCAGTTAATCCAAGCCTTAACTCCAGGGAGATAAGATTCACCGTCGTGGC
66 TCAATCCACTCCACTTCAGCCAATCCAAGCCTTAACGCCAGAGAGATAAGATTCACCGTCGTGGC
*
3594124 TTTAATCTGCTCC
131 TTCAATCTGCTCC
3594137 ACTATAACGC
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
167 125 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (167 bp):
TCACCGTTGCGGCTTCAATCCGTTCCACTGTAATGCCAAACAGATACGATTCGCTACCCACAGCT
TCAATCCACTCCACTTCAGCCAATCCAAGCCTTAACGCCAGAGAGATAAGATTCACCGTCGTGGC
TTCAATCTGCTCCGTTGCAAAGCCAGAGAAGTAAAAC
Found at i:3594380 original size:88 final size:88
Alignment explanation
Indices: 3594216--3594385 Score: 241
Period size: 88 Copynumber: 1.9 Consensus size: 88
3594206 AAGACTGATG
* * *
3594216 TCTTCGATCTACTTCGCTGCTAGTACAGGAAGGCAAGATCTACCATTTTCAACCTACTCCACAAC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACCATTTTCAACCTACTCCACAAC
*
3594281 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAAGGAGACAAGGCTGGTA
* * * **
3594304 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACATGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACCATTTTCAACCTACTCCACAAC
* *
3594369 TGCTCAAGGAGATAAGG
66 TGCCCAAGGAGACAAGG
3594386 TTGAAGATTC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 71 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACCATTTTCAACCTACTCCACAAC
TGCCCAAGGAGACAAGGCTGGTA
Found at i:3600183 original size:23 final size:23
Alignment explanation
Indices: 3600138--3600193 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
3600128 ATATGAATTT
*
3600138 ATGAACAAAATATGATTATG-AA
1 ATGAATAAAATATGATTATGAAA
3600160 ATGAATAAAATAATGATGTA-GAAA
1 ATGAATAAAAT-ATGAT-TATGAAA
*
3600184 AAGAATAAAA
1 ATGAATAAAA
3600194 GAATAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 10 0.34
23 6 0.21
24 13 0.45
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.23
Consensus pattern (23 bp):
ATGAATAAAATATGATTATGAAA
Found at i:3613427 original size:20 final size:20
Alignment explanation
Indices: 3613402--3613440 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3613392 AACATTGAAA
3613402 ATACCATAATCACAA-CTAAG
1 ATACCATAA-CACAAGCTAAG
3613422 ATACCATAACACAAGCTAA
1 ATACCATAACACAAGCTAA
3613441 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.26, G:0.05, T:0.18
Consensus pattern (20 bp):
ATACCATAACACAAGCTAAG
Found at i:3614574 original size:25 final size:25
Alignment explanation
Indices: 3614535--3614601 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
3614525 TCATGTACAT
* *
3614535 GTATGCTCA-TACGAGCTGTGAATCG
1 GTATGCTCACT-CGAGCTGTAAATAG
3614560 GTATGCTCACTCGAGCTGTAAATAG
1 GTATGCTCACTCGAGCTGTAAATAG
* *
3614585 GTATGCTCTCACGAGCT
1 GTATGCTCACTCGAGCT
3614602 ACAAATCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (25 bp):
GTATGCTCACTCGAGCTGTAAATAG
Found at i:3614607 original size:25 final size:25
Alignment explanation
Indices: 3614535--3614626 Score: 67
Period size: 25 Copynumber: 3.7 Consensus size: 25
3614525 TCATGTACAT
* *** *
3614535 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTACAAATAG
* **
3614560 GTATGCTCACTCGAGCTGTAAATAG
1 GTATGCTCACACGAGCTACAAATAG
* *
3614585 GTATGCTCTCACGAGCTACAAATCG
1 GTATGCTCACACGAGCTACAAATAG
* * *
3614610 ATATGCTAATACGAGCT
1 GTATGCTCACACGAGCT
3614627 GTGGGTCGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (25 bp):
GTATGCTCACACGAGCTACAAATAG
Found at i:3617742 original size:29 final size:30
Alignment explanation
Indices: 3617710--3617813 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 30
3617700 CCTTTTCGGT
*
3617710 TATCTCAATTAAAAGGAAAG-CTTTGTGGC
1 TATCTCTATTAAAAGGAAAGACTTTGTGGC
* * * *
3617739 TATCTTTGTTAAAAGG-ATGTCTTTGTGGC
1 TATCTCTATTAAAAGGAAAGACTTTGTGGC
* *
3617768 TATTTCTACTAAAA-GAAAGACTTTGTGGC
1 TATCTCTATTAAAAGGAAAGACTTTGTGGC
* * *
3617797 AATCACTGTTAAAAGGA
1 TATCTCTATTAAAAGGA
3617814 TGCCTTTGTG
Statistics
Matches: 57, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
28 3 0.05
29 52 0.91
30 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (30 bp):
TATCTCTATTAAAAGGAAAGACTTTGTGGC
Found at i:3617820 original size:29 final size:29
Alignment explanation
Indices: 3617730--3617825 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
3617720 AAAAGGAAAG
* *
3617730 CTTTGTGGCTATCTTTGTTAAAAGGATGT
1 CTTTGTGGCTATCTCTGTTAAAAGGATGA
* ** * *
3617759 CTTTGTGGCTATTTCTACTAAAAGAAAGA
1 CTTTGTGGCTATCTCTGTTAAAAGGATGA
* * *
3617788 CTTTGTGGCAATCACTGTTAAAAGGATGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGA
3617817 CTTTGTGGC
1 CTTTGTGGC
3617826 GACACTTTGA
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (29 bp):
CTTTGTGGCTATCTCTGTTAAAAGGATGA
Found at i:3626068 original size:22 final size:21
Alignment explanation
Indices: 3626032--3626086 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3626022 CACGTAATTG
* *
3626032 AACAAAAC-AAAACAAGAACT
1 AACAAAACAAAAACAAAAACA
*
3626052 AACATAGACAAAAACAAAAACA
1 AACA-AAACAAAAACAAAAACA
3626074 AACAAAACAAAAA
1 AACAAAACAAAAA
3626087 ATTACTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 4 0.14
21 11 0.38
22 14 0.48
ACGTcount: A:0.75, C:0.18, G:0.04, T:0.04
Consensus pattern (21 bp):
AACAAAACAAAAACAAAAACA
Found at i:3628631 original size:41 final size:41
Alignment explanation
Indices: 3628503--3628643 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
3628493 CTTGGTGGAT
* *
3628503 TCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAA
1 TCAGCACATAGCAACCACTTTAAATTCAGTGATACGGGGAA
* * **
3628544 TCAGCACATAGGAACCCCTTTCACAA-TCAAAGATACGGTGGAA
1 TCAGCACATAGCAACCACTTT-A-AATTCAGTGATACGG-GGAA
* * *
3628587 TCAGTACTTAGCAACCACTTTATATTCAGTGATACGGGGAA
1 TCAGCACATAGCAACCACTTTAAATTCAGTGATACGGGGAA
3628628 TCAGCACATAGCAACC
1 TCAGCACATAGCAACC
3628644 CATTTCACAA
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
41 36 0.44
42 22 0.27
43 23 0.28
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
TCAGCACATAGCAACCACTTTAAATTCAGTGATACGGGGAA
Found at i:3628637 original size:84 final size:84
Alignment explanation
Indices: 3628496--3628689 Score: 316
Period size: 84 Copynumber: 2.3 Consensus size: 84
3628486 TTCGTTACTT
* *
3628496 GGTGGATTCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGGAACCC
1 GGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
*
3628561 CTTTCACAATCAAAGATAC
66 ATTTCACAATCAAAGATAC
* * *
3628580 GGTGGAATCAGTACTTAGCAACCACTTTATATTCAGTGATACGGGGAATCAGCACATAGCAACCC
1 GGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
*
3628645 ATTTCACAATCAAATATAC
66 ATTTCACAATCAAAGATAC
*
3628664 GGTGGAATCAGCACTTAACAACCACC
1 GGTGGAATCAGCACTTAGCAACCACC
3628690 CTTAGAATCA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 100 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (84 bp):
GGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCC
ATTTCACAATCAAAGATAC
Found at i:3628699 original size:43 final size:44
Alignment explanation
Indices: 3628496--3628700 Score: 189
Period size: 43 Copynumber: 4.8 Consensus size: 44
3628486 TTCGTTACTT
* *
3628496 GGTGGATTCAGCACTTAGCAACCACC-TTA-AATTC-AGTGATAC
1 GGTGGAATCAGCACTTAGCAACCACCTTTACAA-TCAAATGATAC
* *
3628538 GG-GGAATCAGCACATAGGAACC-CCTTTCACAATCAAA-GATAC
1 GGTGGAATCAGCACTTAGCAACCACCTTT-ACAATCAAATGATAC
* * * *
3628580 GGTGGAATCAGTACTTAGCAACCA-CTTTATATTC-AGTGATAC
1 GGTGGAATCAGCACTTAGCAACCACCTTTACAATCAAATGATAC
* *
3628622 GG-GGAATCAGCACATAGCAACC-CATTTCACAATCAAAT-ATAC
1 GGTGGAATCAGCACTTAGCAACCACCTTT-ACAATCAAATGATAC
* * *
3628664 GGTGGAATCAGCACTTAACAACCACCCTTAGAATCAA
1 GGTGGAATCAGCACTTAGCAACCACCTTTACAATCAA
3628701 TAATTCAAGG
Statistics
Matches: 130, Mismatches: 21, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
40 2 0.02
41 41 0.32
42 33 0.25
43 51 0.39
44 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (44 bp):
GGTGGAATCAGCACTTAGCAACCACCTTTACAATCAAATGATAC
Found at i:3628738 original size:26 final size:26
Alignment explanation
Indices: 3628708--3628757 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3628698 CAATAATTCA
3628708 AGGAATCAACACTTAGCAACCCCTCG
1 AGGAATCAACACTTAGCAACCCCTCG
**
3628734 AGGAATCTGCACTTAGCAACCCCT
1 AGGAATCAACACTTAGCAACCCCT
3628758 TTTTATCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (26 bp):
AGGAATCAACACTTAGCAACCCCTCG
Found at i:3634570 original size:45 final size:45
Alignment explanation
Indices: 3634473--3634579 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
3634463 GTGTCATGGT
* * * *
3634473 GTCTTTCAACCATGGTTTTATTCATTTTCAATCGTGTTGCCATAGT
1 GTCTTTCAACTATGGTCTTATT-ATTTTCAATCGTGATGCCATAGC
* * *
3634519 GCCTTTCAACTATGGTCTTATT-TGTTTGATTCGTGATGCCATAGC
1 GTCTTTCAACTATGGTCTTATTAT-TTTCAATCGTGATGCCATAGC
3634564 GTCTTTCAACTATGGT
1 GTCTTTCAACTATGGT
3634580 TTTACTCGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
44 1 0.02
45 32 0.62
46 19 0.37
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.44
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTATTATTTTCAATCGTGATGCCATAGC
Found at i:3634641 original size:45 final size:45
Alignment explanation
Indices: 3634552--3634677 Score: 128
Period size: 45 Copynumber: 2.8 Consensus size: 45
3634542 GTTTGATTCG
* * ** *
3634552 TGATGCCATAGCGTCTTTCAACTATGGTTTTACTCGATAAAATCA
1 TGATGTCATAACGTCTTTCAGTTATGGTCTTACTCGATAAAATCA
* * **
3634597 TGATGTCATACCGTCTTTCAGTTATAGTCTTACTCGATGGAATCA
1 TGATGTCATAACGTCTTTCAGTTATGGTCTTACTCGATAAAATCA
** *
3634642 CAAT-TCCATAACATCTTTCAGTTATGGTCTTACTCG
1 TGATGT-CATAACGTCTTTCAGTTATGGTCTTACTCG
3634678 TTTCTGGTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 1 0.01
45 66 0.99
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (45 bp):
TGATGTCATAACGTCTTTCAGTTATGGTCTTACTCGATAAAATCA
Found at i:3634704 original size:45 final size:45
Alignment explanation
Indices: 3634655--3634763 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
3634645 TTCCATAACA
** * *
3634655 TCTTTCAGTTATGGTCTTACTC-GTTTCTGGTATGGTGCCATAGTG
1 TCTTTCAACTATGGTCTTACTCATTTTC-GATATGGTGCCATAGTG
* * * *
3634700 TCTTTCAACTATGGTCTTATTTATTTTCGATATTGTGTCATAGTG
1 TCTTTCAACTATGGTCTTACTCATTTTCGATATGGTGCCATAGTG
3634745 TCTTTCAACTATGGTCTTA
1 TCTTTCAACTATGGTCTTA
3634764 ACCATTTCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 51 0.93
46 4 0.07
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (45 bp):
TCTTTCAACTATGGTCTTACTCATTTTCGATATGGTGCCATAGTG
Found at i:3644777 original size:113 final size:113
Alignment explanation
Indices: 3644579--3644804 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
3644569 AGATCGTTGC
3644579 ACCTAGGTTCAGCTAGCTCGTACCTTTGTTTTTGAATCTGTTAAAAATTTTAGAAGTTTTCATTG
1 ACCTAGGTTCAGCTAGCTCGTACCTTTGTTTTTGAATCTGTTAAAAATTTTAGAAGTTTTCATTG
3644644 ATGAATCTTGAAGGTTTTTTTATGATAACCATGTGTTTGAAGCTTTGA
66 ATGAATCTTGAAGGTTTTTTTATGATAACCATGTGTTTGAAGCTTTGA
3644692 ACCTAGGTTCAGCTAGCTCGTACCTTTGTTTTTGAATCTGTTAAAAATTTTAGAAGTTTTCATTG
1 ACCTAGGTTCAGCTAGCTCGTACCTTTGTTTTTGAATCTGTTAAAAATTTTAGAAGTTTTCATTG
3644757 ATGAATCTTGAAGGTTTTTTTATGATAACCATGTGTTTGAAGCTTTGA
66 ATGAATCTTGAAGGTTTTTTTATGATAACCATGTGTTTGAAGCTTTGA
3644805 TTATTGTATT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (113 bp):
ACCTAGGTTCAGCTAGCTCGTACCTTTGTTTTTGAATCTGTTAAAAATTTTAGAAGTTTTCATTG
ATGAATCTTGAAGGTTTTTTTATGATAACCATGTGTTTGAAGCTTTGA
Found at i:3645332 original size:40 final size:40
Alignment explanation
Indices: 3645274--3645454 Score: 209
Period size: 40 Copynumber: 4.5 Consensus size: 40
3645264 AATTATTGAA
* * * * *
3645274 TGATTGAACTTATGTGCCCCTATTTGTACCTCGGTACCTC
1 TGATTGCACTTACGTGCCCCTGTTTGTACCTCAGTACCCC
* *
3645314 TGATTGCACTTACATGCCCCTGTTTGTACCTCAATACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACCTCAGTACCCC
* * *
3645354 TGATTGCACTTACGTGCTCCTGTTTGTACTTTAGTACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACCTCAGTACCCC
* * *
3645394 TGATTGCACTTACGTGCCTCTGTTTGTACTTCGGTACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACCTCAGTACCCC
* * **
3645434 TAAATGCACTTTTGTGCCCCT
1 TGATTGCACTTACGTGCCCCT
3645455 ATTTATACTC
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 120 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.37
Consensus pattern (40 bp):
TGATTGCACTTACGTGCCCCTGTTTGTACCTCAGTACCCC
Found at i:3645384 original size:20 final size:19
Alignment explanation
Indices: 3645351--3645424 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
3645341 ACCTCAATAC
* *
3645351 CCCTGATTGCACTTACGTG
1 CCCTGTTTGTACTTACGTG
*
3645370 CTCCTGTTTGTACTTTA-GTAC
1 C-CCTGTTTGTAC-TTACGT-G
* *
3645391 CCCTGATTGCACTTACGTG
1 CCCTGTTTGTACTTACGTG
3645410 CCTCTGTTTGTACTT
1 CC-CTGTTTGTACTT
3645425 CGGTACCCCT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
19 6 0.14
20 32 0.76
21 4 0.10
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.41
Consensus pattern (19 bp):
CCCTGTTTGTACTTACGTG
Found at i:3648942 original size:20 final size:20
Alignment explanation
Indices: 3648906--3648954 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3648896 TTTACAAACA
*
3648906 AAAATAT-AATCTTAAAAAT
1 AAAATATAAATATTAAAAAT
* *
3648925 TAAATCTAAATATTAAAAAT
1 AAAATATAAATATTAAAAAT
3648945 AAAATATAAA
1 AAAATATAAA
3648955 CATATAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATATAAATATTAAAAAT
Found at i:3655030 original size:44 final size:44
Alignment explanation
Indices: 3654956--3655117 Score: 159
Period size: 44 Copynumber: 3.7 Consensus size: 44
3654946 GATCATTTTG
* * *
3654956 ATCTGCTCCACTGCAACTTCAGGGGGATAGGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGACTTCA
* * * *
3655000 ATCTTCTCCACTACAACTTCAGGGATATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTCA
* * * *
3655044 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAT-CGA-CTTCA
*
3655089 ATCTG-TCCCACTGCAACTTCAGGGGGATA
1 ATCTGCT-CCACTGCAACTTCAGGGAGATA
3655118 AGACCTGCTT
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
43 4 0.04
44 64 0.66
45 29 0.30
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTCA
Found at i:3658967 original size:123 final size:124
Alignment explanation
Indices: 3658735--3658983 Score: 464
Period size: 123 Copynumber: 2.0 Consensus size: 124
3658725 CTTCCTACAA
3658735 AATTTTGGACTTCTTTCTGAGTGCGTGGAGGAGGTAGGTCTCGGATTGCCTTCACTTTGTCCGGG
1 AATTTTGGACTTCTTTCTGAGTGCGTGGAGGAGGTAGGTCTCGGATTGCCTTCACTTTGTCCGGG
* *
3658800 TCCACCTCAATCCCCTTTGTACTAACTATGAAGCCTAATAACTTCCCTGATCTGGCTCC
66 TCCACCTCAATCCCCTTTGTACTAACTAAGAAGCCTAATAACTTCCCTGACCTGGCTCC
3658859 AATTTTGGACTT-TTTCTGAGTGCGTGGAGGAGGTAGGTCTCGGATTGCCTTCACTTTGTCCGGG
1 AATTTTGGACTTCTTTCTGAGTGCGTGGAGGAGGTAGGTCTCGGATTGCCTTCACTTTGTCCGGG
*
3658923 TCCACCTCAATCCCCTTTGTACTAACTAAGGAGCCTAATAACTTCCCTGACCTGGCTCC
66 TCCACCTCAATCCCCTTTGTACTAACTAAGAAGCCTAATAACTTCCCTGACCTGGCTCC
3658982 AA
1 AA
3658984 ATGTGCATTT
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
123 110 0.90
124 12 0.10
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (124 bp):
AATTTTGGACTTCTTTCTGAGTGCGTGGAGGAGGTAGGTCTCGGATTGCCTTCACTTTGTCCGGG
TCCACCTCAATCCCCTTTGTACTAACTAAGAAGCCTAATAACTTCCCTGACCTGGCTCC
Found at i:3668347 original size:18 final size:18
Alignment explanation
Indices: 3668324--3668358 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3668314 GAAAAAGAAT
3668324 TAAAATAACAGT-ATGTAA
1 TAAAATAA-AGTAATGTAA
3668342 TAAAATAAAGTAATGTA
1 TAAAATAAAGTAATGTA
3668359 CATGCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAAATAAAGTAATGTAA
Found at i:3669558 original size:55 final size:55
Alignment explanation
Indices: 3669474--3669584 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
3669464 GAGCAGGGCT
3669474 GGGGACGTGGCGTGTATGGAGGCACAACAAGCAGCGGTGGCGCACGTGCGAAGGC
1 GGGGACGTGGCGTGTATGGAGGCACAACAAGCAGCGGTGGCGCACGTGCGAAGGC
3669529 GGGGACGTGGCGTGTATGGAGGCACAACAAGCAGCGGTGGCGCACGTGCGAAGGC
1 GGGGACGTGGCGTGTATGGAGGCACAACAAGCAGCGGTGGCGCACGTGCGAAGGC
3669584 G
1 G
3669585 CGCACGCGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.22, C:0.22, G:0.46, T:0.11
Consensus pattern (55 bp):
GGGGACGTGGCGTGTATGGAGGCACAACAAGCAGCGGTGGCGCACGTGCGAAGGC
Found at i:3670453 original size:17 final size:16
Alignment explanation
Indices: 3670431--3670465 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
3670421 TCAAATTTAA
3670431 TTTAATTTTTGTAGTTT
1 TTTAATTTTTGTA-TTT
3670448 TTTAATTTTTGTATTT
1 TTTAATTTTTGTATTT
3670464 TT
1 TT
3670466 AGAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTAATTTTTGTATTT
Found at i:3673383 original size:18 final size:18
Alignment explanation
Indices: 3673356--3673391 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3673346 TGGTGTGGGA
3673356 TGCCAAATCAGCATCGTT
1 TGCCAAATCAGCATCGTT
*
3673374 TGCCACATCAGCATCGTT
1 TGCCAAATCAGCATCGTT
3673392 AAAACTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.28
Consensus pattern (18 bp):
TGCCAAATCAGCATCGTT
Found at i:3676920 original size:18 final size:20
Alignment explanation
Indices: 3676892--3676946 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
3676882 AATAACAAAC
3676892 TAACA-AACTTAGCT-T-AA
1 TAACAGAACTTAGCTATCAA
3676909 TAACAGAACTTAGCTAGCTCAA
1 TAACAGAACTTAGCTA--TCAA
3676931 TAACAGAACTTAGCTA
1 TAACAGAACTTAGCTA
3676947 GCTCACTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.15
18 9 0.27
21 1 0.03
22 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (20 bp):
TAACAGAACTTAGCTATCAA
Found at i:3676932 original size:22 final size:22
Alignment explanation
Indices: 3676901--3676951 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3676891 CTAACAAACT
*
3676901 TAGCTTAATAACAGAACTTAGC
1 TAGCTCAATAACAGAACTTAGC
3676923 TAGCTCAATAACAGAACTTAGC
1 TAGCTCAATAACAGAACTTAGC
3676945 TAGCTCA
1 TAGCTCA
3676952 CTTTTTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (22 bp):
TAGCTCAATAACAGAACTTAGC
Found at i:3681964 original size:22 final size:22
Alignment explanation
Indices: 3681936--3681977 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3681926 AACTTAACTT
3681936 AATAACAAAACTTAGCTAGCTC
1 AATAACAAAACTTAGCTAGCTC
3681958 AATAACAAAACTTAGCTAGC
1 AATAACAAAACTTAGCTAGC
3681978 ACCTTTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (22 bp):
AATAACAAAACTTAGCTAGCTC
Found at i:3683164 original size:18 final size:18
Alignment explanation
Indices: 3683138--3683175 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3683128 TGGACGCGCT
*
3683138 TTCTGTTTCTTTCC-AGGG
1 TTCTATTTC-TTCCTAGGG
3683156 TTCTATTTCTTCCTAGGG
1 TTCTATTTCTTCCTAGGG
3683174 TT
1 TT
3683176 AGGGGTTTTT
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:0.08, C:0.21, G:0.18, T:0.53
Consensus pattern (18 bp):
TTCTATTTCTTCCTAGGG
Found at i:3685262 original size:20 final size:20
Alignment explanation
Indices: 3685225--3685266 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3685215 AAAATATGAG
*
3685225 AATTTTTTTATGTATTTTAT
1 AATTTTTTTATATATTTTAT
3685245 AATTTTTTTATA-ATTTTTAT
1 AATTTTTTTATATA-TTTTAT
3685265 AA
1 AA
3685267 AAATTTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
AATTTTTTTATATATTTTAT
Found at i:3685359 original size:28 final size:30
Alignment explanation
Indices: 3685288--3685370 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 30
3685278 TTTTTAGGGT
* * *
3685288 TTTTATAA-TTTTT-TACCTTTTAATAAAA
1 TTTTAAAACTTTTTATACTTTTTATTAAAA
3685316 TTTTAAAACTTTTTATA-TTTTTATTAAAA
1 TTTTAAAACTTTTTATACTTTTTATTAAAA
* * *
3685345 -TTTAATATTTTTTATACTTATTATTA
1 TTTTAAAACTTTTTATACTTTTTATTA
3685371 TTTTTTATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 21 0.46
29 23 0.50
30 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAAAACTTTTTATACTTTTTATTAAAA
Found at i:3685368 original size:29 final size:29
Alignment explanation
Indices: 3685288--3685370 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
3685278 TTTTTAGGGT
* * *
3685288 TTTTATAATTTTTTA-CCTTTTAATAAAA
1 TTTTAAAATTTTTTATACTTTTATTAAAA
* *
3685316 TTTTAAAACTTTTTATATTTTTATTAAAA
1 TTTTAAAATTTTTTATACTTTTATTAAAA
*
3685345 -TTTAATATTTTTTATACTTATTATTA
1 TTTTAAAATTTTTTATACTT-TTATTA
3685371 TTTTTTATCT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
28 29 0.64
29 16 0.36
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAATTTTTTATACTTTTATTAAAA
Found at i:3685372 original size:19 final size:17
Alignment explanation
Indices: 3685345--3685393 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
3685335 TTTATTAAAA
*
3685345 TTTAATATTTTTTATACT
1 TTTATTATTTTTTAT-CT
3685363 TATTATTATTTTTTATCT
1 T-TTATTATTTTTTATCT
*
3685381 TTTATAATTTTTT
1 TTTATTATTTTTT
3685394 TACCATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 13 0.46
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTATTTTTTATCT
Found at i:3685375 original size:20 final size:17
Alignment explanation
Indices: 3685351--3685393 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
3685341 AAAATTTAAT
*
3685351 ATTTTTTATACTTATTATT
1 ATTTTTTAT-CTT-TTATA
3685370 ATTTTTTATCTTTTATA
1 ATTTTTTATCTTTTATA
3685387 ATTTTTT
1 ATTTTTT
3685394 TACCATATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 9 0.39
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTATCTTTTATA
Found at i:3685394 original size:18 final size:20
Alignment explanation
Indices: 3685347--3685395 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
3685337 TATTAAAATT
3685347 TAATATTTTTTATACTTATTA
1 TAAT-TTTTTTATACTTATTA
*
3685368 TTA-TTTTTTAT-CTT-TTA
1 TAATTTTTTTATACTTATTA
3685385 TAATTTTTTTA
1 TAATTTTTTTA
3685396 CCATATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 8 0.32
21 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TAATTTTTTTATACTTATTA
Found at i:3694220 original size:46 final size:46
Alignment explanation
Indices: 3694168--3694260 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
3694158 ATCTCCTTAA
3694168 ACTTGAGCTGATGGTACTCAGAACGGAGATCAATTTTTGATAATAC
1 ACTTGAGCTGATGGTACTCAGAACGGAGATCAATTTTTGATAATAC
3694214 ACTTGAGCTGATGGTACTCAGAACGGAGATCAATTTTTGATAATAC
1 ACTTGAGCTGATGGTACTCAGAACGGAGATCAATTTTTGATAATAC
3694260 A
1 A
3694261 GATGCTCCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (46 bp):
ACTTGAGCTGATGGTACTCAGAACGGAGATCAATTTTTGATAATAC
Found at i:3694948 original size:14 final size:14
Alignment explanation
Indices: 3694929--3694955 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3694919 AACCCTCCTT
3694929 TAAACTTCACTAAA
1 TAAACTTCACTAAA
3694943 TAAACTTCACTAA
1 TAAACTTCACTAA
3694956 CTTTAACCGA
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAACTTCACTAAA
Found at i:3696332 original size:20 final size:20
Alignment explanation
Indices: 3696291--3696334 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3696281 TTAGATTTAG
* *
3696291 ATCATATTCAAATTAAATAT
1 ATCATACTCAAATTAAAGAT
3696311 ATCATACTC-AATTAACAGAT
1 ATCATACTCAAATTAA-AGAT
3696331 ATCA
1 ATCA
3696335 CAACGAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (20 bp):
ATCATACTCAAATTAAAGAT
Found at i:3715419 original size:28 final size:29
Alignment explanation
Indices: 3715387--3715441 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
3715377 TACTTTTACA
* *
3715387 TAACAACTAATATCTCAAA-TTCATCACT
1 TAACAACTAAAATCACAAATTTCATCACT
*
3715415 TAACATCTAAAATCACAAATTTCATCA
1 TAACAACTAAAATCACAAATTTCATCA
3715442 ATGGCAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (29 bp):
TAACAACTAAAATCACAAATTTCATCACT
Found at i:3718426 original size:7 final size:7
Alignment explanation
Indices: 3718416--3718456 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
3718406 AAATAAATAA
3718416 TATATAT
1 TATATAT
3718423 TATATAT
1 TATATAT
3718430 TATATAT
1 TATATAT
3718437 TATATAT
1 TATATAT
3718444 TATATAT
1 TATATAT
*
3718451 AATATA
1 TATATA
3718457 CTTTTTGGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:3718440 original size:21 final size:21
Alignment explanation
Indices: 3718408--3718456 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3718398 ATTAACCTAA
*
3718408 ATAA-ATAATATATATTATAT
1 ATAATATATTATATATTATAT
*
3718428 ATTATATATTATATATTATAT
1 ATAATATATTATATATTATAT
3718449 ATAATATA
1 ATAATATA
3718457 CTTTTTGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAATATATTATATATTATAT
Found at i:3721662 original size:16 final size:15
Alignment explanation
Indices: 3721637--3721669 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3721627 GTCAACAAAT
3721637 AATTTAAAAATTATA
1 AATTTAAAAATTATA
3721652 AATTATAAAAATTATA
1 AATT-TAAAAATTATA
3721668 AA
1 AA
3721670 AAAACCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTTAAAAATTATA
Found at i:3724621 original size:124 final size:123
Alignment explanation
Indices: 3724451--3724837 Score: 499
Period size: 124 Copynumber: 3.1 Consensus size: 123
3724441 GAAATAATTT
* * * * *
3724451 TTTTAGTGTCGTTTTGATTGAAAATGCCTCAAAGGTGATACATTAGTGGCGTTTTTTATAAACAC
1 TTTTAGTGGCGTTTTGACTGAAAATGCCTCAAAGGTTATACATTAGTGGCGTTTTTCATAAACGC
* * *
3724516 CGCAAAATTGCAATACCAATTCGACTTAAACGTCGTCGTTTCACTACAGAGCATTAAAC
66 CGCAAAATTACAATACCAATT-GACTTAAACGGCGTCGTTTCACTACAGAGAATTAAAC
* * * *
3724575 TTTTAGTGGCATTTTGACTGAAAAAGCCGT-AAAGGTTATACGTTAGTGGGGTTTTTCATAAACG
1 TTTTAGTGGCGTTTTGACTGAAAATGCC-TCAAAGGTTATACATTAGTGGCGTTTTTCATAAACG
* * * *
3724639 CCGTAAAATTACAATACCAAATTGACTTAAACGGCGTCGTTTCACTATAGGGAATTAAAT
65 CCGCAAAATTACAATACC-AATTGACTTAAACGGCGTCGTTTCACTACAGAGAATTAAAC
* *
3724699 TTTTAGTGGCGTTTTGACCGAAAATGCCTCAAAGGTTATACATTAGTGGCATTTTTCATAAACGC
1 TTTTAGTGGCGTTTTGACTGAAAATGCCTCAAAGGTTATACATTAGTGGCGTTTTTCATAAACGC
* * * * **
3724764 CACAAAAATACAATACCAATTTGACTTAAACGGCGTTGTTTCACGACATG-GAATTAAGT
66 CGCAAAATTACAATACCAA-TTGACTTAAACGGCGTCGTTTCACTACA-GAGAATTAAAC
3724823 TTTTAGTGGCGTTTT
1 TTTTAGTGGCGTTTT
3724838 TCATAAACGT
Statistics
Matches: 229, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
123 3 0.01
124 220 0.96
125 6 0.03
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (123 bp):
TTTTAGTGGCGTTTTGACTGAAAATGCCTCAAAGGTTATACATTAGTGGCGTTTTTCATAAACGC
CGCAAAATTACAATACCAATTGACTTAAACGGCGTCGTTTCACTACAGAGAATTAAAC
Found at i:3724885 original size:84 final size:85
Alignment explanation
Indices: 3724741--3724975 Score: 301
Period size: 84 Copynumber: 2.8 Consensus size: 85
3724731 AGGTTATACA
* * * *
3724741 TTAGTGGCATTTTTCATAAACGCCACAAAAATACAATACCAATTTGACTTAAACGGCGTTGTTTC
1 TTAGTGGCGTTTTTCATAAACGCCGCAAAATTGCAATACCAATTTGACTTAAACGGCGTTGTTTC
*
3724806 ACGACATGGAATTAAG-TTT
66 ACGACAGGGAATTAAGTTTT
* * *
3724825 TTAGTGGCGTTTTTCATAAACGTCGCAAAATTGCGATACCAATTTGACTTAAACGTCGTTGTTTC
1 TTAGTGGCGTTTTTCATAAACGCCGCAAAATTGCAATACCAATTTGACTTAAACGGCGTTGTTTC
* *
3724890 ACTATAGGGAATTAAGTTTT
66 ACGACAGGGAATTAAGTTTT
** * * * *
3724910 TTAGTGGCGTTTGCCCTAAAAACGCCGCAAAATTGCAATACCAATTTGATTTAAATGGCGTCGTT
1 TTAGTGGCGTTT-TTC-ATAAACGCCGCAAAATTGCAATACCAATTTGACTTAAACGGCGTTGTT
3724975 T
64 T
3724976 TCTTAGCCCC
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
84 71 0.55
85 15 0.12
86 1 0.01
87 42 0.33
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (85 bp):
TTAGTGGCGTTTTTCATAAACGCCGCAAAATTGCAATACCAATTTGACTTAAACGGCGTTGTTTC
ACGACAGGGAATTAAGTTTT
Found at i:3725137 original size:7 final size:7
Alignment explanation
Indices: 3725122--3725243 Score: 57
Period size: 7 Copynumber: 16.6 Consensus size: 7
3725112 AATATTTTAT
*
3725122 TTTAGGG
1 TTTAAGG
3725129 TTTAAGG
1 TTTAAGG
* *
3725136 TTTATGAT
1 TTTAAG-G
*
3725144 TTTAGGG
1 TTTAAGG
*
3725151 TGTAAGG
1 TTTAAGG
3725158 TTT-AGAG
1 TTTAAG-G
*
3725165 TTTTAGG
1 TTTAAGG
*
3725172 ATTTTAGGG
1 --TTTAAGG
*
3725181 TTTAAAG
1 TTTAAGG
*
3725188 TTTAAAGT
1 TTT-AAGG
*
3725196 TTTAGAGT
1 TTTA-AGG
3725204 TTTAAGG
1 TTTAAGG
3725211 TTTAAGG
1 TTTAAGG
* *
3725218 TTTTGAGT
1 -TTTAAGG
3725226 TTTAAGG
1 TTTAAGG
*
3725233 TTTAGGG
1 TTTAAGG
3725240 TTTA
1 TTTA
3725244 TTTTTGTATA
Statistics
Matches: 87, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
6 2 0.02
7 56 0.64
8 24 0.28
9 5 0.06
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:3725146 original size:22 final size:21
Alignment explanation
Indices: 3725120--3725171 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
3725110 AAAATATTTT
*
3725120 ATTTTAGGGTTTAAGGTTTATG
1 ATTTTAGGGTGTAAGGTTTA-G
3725142 ATTTTAGGGTGTAAGGTTTAG
1 ATTTTAGGGTGTAAGGTTTAG
3725163 AGTTTTAGG
1 A-TTTTAGG
3725172 ATTTTAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
ATTTTAGGGTGTAAGGTTTAG
Found at i:3725177 original size:30 final size:29
Alignment explanation
Indices: 3725122--3725243 Score: 122
Period size: 30 Copynumber: 4.1 Consensus size: 29
3725112 AATATTTTAT
* *
3725122 TTTAGGGTTTA-AGGTTTATGATTTTAGGG
1 TTTAAGGTTTAGAGTTTTA-GATTTTAGGG
*
3725151 TGTAAGGTTTAGAGTTTTAGGATTTTAGGG
1 TTTAAGGTTTAGAGTTTTA-GATTTTAGGG
* * *
3725181 TTTAAAGTTTAAAGTTTTAGAGTTTTAAGG
1 TTTAAGGTTTAGAGTTTTAGA-TTTTAGGG
* *
3725211 TTTAAGGTTTTGAGTTTTA-AGGTTTAGGG
1 TTTAAGGTTTAGAGTTTTAGA-TTTTAGGG
3725240 TTTA
1 TTTA
3725244 TTTTTGTATA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 23 0.29
30 55 0.71
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.48
Consensus pattern (29 bp):
TTTAAGGTTTAGAGTTTTAGATTTTAGGG
Found at i:3725225 original size:22 final size:23
Alignment explanation
Indices: 3725164--3725242 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 23
3725154 AAGGTTTAGA
* * *
3725164 GTTTTAGGATTTTAG-GGTTTAAA
1 GTTTAAGG-TTTTAGAGTTTTAAG
*
3725187 GTTTAAAGTTTTAGAGTTTTAAG
1 GTTTAAGGTTTTAGAGTTTTAAG
3725210 GTTTAAGGTTTT-GAGTTTTAAG
1 GTTTAAGGTTTTAGAGTTTTAAG
*
3725232 GTTTAGGGTTT
1 GTTTAAGGTTT
3725243 ATTTTTGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
22 26 0.53
23 23 0.47
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (23 bp):
GTTTAAGGTTTTAGAGTTTTAAG
Found at i:3730348 original size:43 final size:43
Alignment explanation
Indices: 3730033--3730345 Score: 301
Period size: 43 Copynumber: 7.3 Consensus size: 43
3730023 GAACGGTGCT
* * * *
3730033 TTTAGCAGCGTTTGTGATAAAAGTGCCACTAAAGATCATGTTG
1 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATGTTC
* * * * * ** *
3730076 TTTAACAGTGTTTGTAAAAAAAAAGCCGTTAAAAGG-CAT-TCTC
1 TTTAGCGGCGTTTGTGATAAAAGTGCCGCT-AAAGGTCATGT-TC
* * ** * *
3730119 TATAGTGGCGTTTGTGATAAAAGAACCGTTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATGTTC
* **
3730162 TTTAGCGGCGCTTGTGATAAAAGCACCGCT-AAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATGTTC
* * *
3730204 TTTAGTGGCGTTTGTGATAAAAGTGCCACTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATGTTC
*
3730247 TTTAGCGGCGTTTGTGAGT-AAAGTGCCGCTAAAGGTTATGTTC
1 TTTAGCGGCGTTTGTGA-TAAAAGTGCCGCTAAAGGTCATGTTC
* * * *
3730290 TTTAGCGGTGTTTTTTATAAAAGTGCCGCTAAAGTTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATGTTC
*
3730333 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
3730346 TTTCACATAA
Statistics
Matches: 220, Mismatches: 43, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
42 43 0.20
43 172 0.78
44 5 0.02
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATGTTC
Found at i:3736849 original size:32 final size:32
Alignment explanation
Indices: 3736813--3736883 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
3736803 TCTGAAATGG
*
3736813 AAATGATGGATAAATGTTGTAAGGTTGTGCTT
1 AAATGATGGATAAATGTTGTAAGGTTATGCTT
3736845 AAATGATGGATAAATGTTGTAAGGTTATGCTT
1 AAATGATGGATAAATGTTGTAAGGTTATGCTT
3736877 AAATGAT
1 AAATGAT
3736884 TATACGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (32 bp):
AAATGATGGATAAATGTTGTAAGGTTATGCTT
Found at i:3745901 original size:29 final size:27
Alignment explanation
Indices: 3745853--3745910 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
3745843 NNNNNNTTTA
3745853 TTTATTTATTTATTTATTATTTAACTAAT
1 TTTATTTATTTATTTATTATTT--CTAAT
3745882 TTTATTTATTCTCA-TT-TTATTTCTAAT
1 TTTATTTATT-T-ATTTATTATTTCTAAT
3745909 TT
1 TT
3745911 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 7 0.26
29 16 0.59
30 3 0.11
31 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATTTATTTATTTATTATTTCTAAT
Found at i:3746343 original size:144 final size:144
Alignment explanation
Indices: 3746078--3746366 Score: 517
Period size: 144 Copynumber: 2.0 Consensus size: 144
3746068 TGATAGAAAA
3746078 AAAAACATAAATATGGTGTTAAAGTAAAGGTTTCTCATGGGGAAATATTGTATTTTGACATGCTG
1 AAAAACATAAATATGGTGTTAAAGTAAAGGTTTCTCATGGGGAAATATTGTATTTTGACATGCTG
* *
3746143 ATGAAGAGAAAAGTTGAGAAAAAGAGTCAAGTGGTAGGAGAAGTAAAACGGAAGAGATTTTGATA
66 ATGAAGAGAAAAGTTGAGAAAAAGAGTCAAGTGGTAGGAGAAGTAAAAAGGAAGAGATTTTCATA
3746208 GAAAAAGAGGAAGT
131 GAAAAAGAGGAAGT
*
3746222 AAAATCATAAATATGGTGTTAAAGTAAAGGTTTCTCATGGGGAAATATTGTATTTTGACATG-TC
1 AAAAACATAAATATGGTGTTAAAGTAAAGGTTTCTCATGGGGAAATATTGTATTTTGACATGCT-
* *
3746286 GATGAATAGAAAAGTTGAGAAAAAGATTCAAGTGGTAGGAGAAGTAAAAAGGAAGAGATTTTCAT
65 GATGAAGAGAAAAGTTGAGAAAAAGAGTCAAGTGGTAGGAGAAGTAAAAAGGAAGAGATTTTCAT
3746351 AGAAAAAGAGGAAGT
130 AGAAAAAGAGGAAGT
3746366 A
1 A
3746367 CCCATGAACT
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
143 1 0.01
144 138 0.99
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (144 bp):
AAAAACATAAATATGGTGTTAAAGTAAAGGTTTCTCATGGGGAAATATTGTATTTTGACATGCTG
ATGAAGAGAAAAGTTGAGAAAAAGAGTCAAGTGGTAGGAGAAGTAAAAAGGAAGAGATTTTCATA
GAAAAAGAGGAAGT
Found at i:3746594 original size:51 final size:51
Alignment explanation
Indices: 3746530--3746647 Score: 202
Period size: 51 Copynumber: 2.3 Consensus size: 51
3746520 AATAATACAA
* *
3746530 GTGAAATACATAGAAATTTGATGTGAAAAATGAAATAGTAGAATTAATTAT
1 GTGAATTAAATAGAAATTTGATGTGAAAAATGAAATAGTAGAATTAATTAT
*
3746581 GTGAATTAAATAGAAATTTGATGTGAAAAATGAGATAGTAGAATTAATTAT
1 GTGAATTAAATAGAAATTTGATGTGAAAAATGAAATAGTAGAATTAATTAT
3746632 GTGAATTAAAT-GAAAT
1 GTGAATTAAATAGAAAT
3746648 GTGAAATAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
50 5 0.08
51 59 0.92
ACGTcount: A:0.48, C:0.01, G:0.19, T:0.32
Consensus pattern (51 bp):
GTGAATTAAATAGAAATTTGATGTGAAAAATGAAATAGTAGAATTAATTAT
Found at i:3746779 original size:19 final size:20
Alignment explanation
Indices: 3746725--3746780 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
3746715 TATAGAAGTT
* *
3746725 TACAAGAAAATATTAATAAA
1 TACAAGAATATATGAATAAA
*
3746745 TA-AAGTATATAGTGAA-AAA
1 TACAAGAATATA-TGAATAAA
3746764 TACAAGAATATATGAAT
1 TACAAGAATATATGAAT
3746781 TTTTGCAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.27
Consensus pattern (20 bp):
TACAAGAATATATGAATAAA
Found at i:3749386 original size:25 final size:25
Alignment explanation
Indices: 3749352--3749402 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3749342 ATTATCTCTA
*
3749352 AATATGATTGTATGTAAAGTGTTAT
1 AATATGATTGTATATAAAGTGTTAT
3749377 AATATGATTGTATATAAAGTGTTAT
1 AATATGATTGTATATAAAGTGTTAT
3749402 A
1 A
3749403 TGTTTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (25 bp):
AATATGATTGTATATAAAGTGTTAT
Found at i:3763563 original size:182 final size:182
Alignment explanation
Indices: 3763256--3763625 Score: 641
Period size: 182 Copynumber: 2.0 Consensus size: 182
3763246 TTTTGTTATT
*
3763256 CAAACCAACACCAAAACCTACATATTTCAAAGCCAAAAAACCAATTCACCTAACCATTTAAACAT
1 CAAACCAACACCAAAACATACATATTTCAAAGCCAAAAAACCAATTCACCTAACCATTTAAACAT
3763321 ACAACCAATATGCCATCATTGGCACCAACAATTCATCAATTCAAATCAACAACCAAATATGTTTT
66 ACAACCAATATGCCATCATTGGCACCAACAATTCATCAATTCAAATCAACAACCAAATATGTTTT
* * *
3763386 ATCCATCTAAATTCACAATTTCAAGAATTCCAATTATAACATTTTCTTACCA
131 AACCATCTAAATTCACAATTTCAAGAATGCCAATTATAACATTTGCTTACCA
* *
3763438 CAAACCAACACCAAAACATACATATTTCAAAGCCAAAAAACCAATTTACCTAATCATTTAAACAT
1 CAAACCAACACCAAAACATACATATTTCAAAGCCAAAAAACCAATTCACCTAACCATTTAAACAT
* * *
3763503 ACAACGAATATGCCCTCATTGGTACCAACAATTCATCAATTCAAATCAACAACCAAATATGTTTT
66 ACAACCAATATGCCATCATTGGCACCAACAATTCATCAATTCAAATCAACAACCAAATATGTTTT
*
3763568 AACCATCTAAATTCACAATTTTAAGAATGCCAATTATAACATTTGCTTACCA
131 AACCATCTAAATTCACAATTTCAAGAATGCCAATTATAACATTTGCTTACCA
*
3763620 GAAACC
1 CAAACC
3763626 CAAGTTTATA
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
182 177 1.00
ACGTcount: A:0.44, C:0.26, G:0.04, T:0.26
Consensus pattern (182 bp):
CAAACCAACACCAAAACATACATATTTCAAAGCCAAAAAACCAATTCACCTAACCATTTAAACAT
ACAACCAATATGCCATCATTGGCACCAACAATTCATCAATTCAAATCAACAACCAAATATGTTTT
AACCATCTAAATTCACAATTTCAAGAATGCCAATTATAACATTTGCTTACCA
Found at i:3764527 original size:46 final size:46
Alignment explanation
Indices: 3764399--3764557 Score: 158
Period size: 46 Copynumber: 3.4 Consensus size: 46
3764389 ACAGGTGAAA
** * *
3764399 ATAATAGTGTTTGGTTACCCATTTAGGTTAAACCTACACGAATAATG
1 ATAATAGTGCCTGGTCACCCATTAAGGTTAAACCTACACGAATAA-G
* * * * *
3764446 AATCATAGTGTCTGGTCAACC-GTAAGGGTTGAACCTACACGAATAAG
1 -ATAATAGTGCCTGGTCACCCATTAA-GGTTAAACCTACACGAATAAG
** **
3764493 ATAATAGTGCCTGGTCACCCATTAAGGTTAAACCTACATTAATCGG
1 ATAATAGTGCCTGGTCACCCATTAAGGTTAAACCTACACGAATAAG
*
3764539 AGAATAGTGCCTGGTCACC
1 ATAATAGTGCCTGGTCACC
3764558 TGCTAGGTTG
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 51 0.55
47 6 0.07
48 35 0.38
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (46 bp):
ATAATAGTGCCTGGTCACCCATTAAGGTTAAACCTACACGAATAAG
Found at i:3775965 original size:15 final size:17
Alignment explanation
Indices: 3775940--3775972 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3775930 TAAGTTTACT
3775940 TTTTATTTAAAAT-TAA
1 TTTTATTTAAAATATAA
3775956 TTTT-TTTAAAATATAA
1 TTTTATTTAAAATATAA
3775972 T
1 T
3775973 ACAAAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATTTAAAATATAA
Found at i:3776145 original size:31 final size:29
Alignment explanation
Indices: 3776078--3776151 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
3776068 GCCTCAGGTT
*
3776078 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
***
3776107 ACATTTTAGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
3776138 ACATTTTAGTCACT
1 ACATTTTAGTCACT
3776152 GAGTCATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 20 0.51
30 1 0.03
31 18 0.46
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:3786743 original size:13 final size:13
Alignment explanation
Indices: 3786725--3786750 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3786715 AAAGAGATTT
3786725 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
3786738 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
3786751 AAAATTAAAC
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:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:3786821 original size:19 final size:20
Alignment explanation
Indices: 3786784--3786823 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3786774 TCTTTTCGCA
* *
3786784 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
3786804 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
3786823 T
1 T
3786824 AAACACGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:3788464 original size:18 final size:19
Alignment explanation
Indices: 3788424--3788463 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
3788414 GCAAATGTTC
3788424 TTTCATTCTTTACGATTTT
1 TTTCATTCTTTACGATTTT
3788443 TTTCATTCTTT-CTGATTTT
1 TTTCATTCTTTAC-GATTTT
3788462 TT
1 TT
3788464 CTGCCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.12, C:0.15, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTCATTCTTTACGATTTT
Found at i:3789425 original size:14 final size:14
Alignment explanation
Indices: 3789408--3789457 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3789398 GAAATGAAAA
3789408 AAAATGGAAAAGTG
1 AAAATGGAAAAGTG
* *
3789422 AAAA-GAAAAAATG
1 AAAATGGAAAAGTG
3789435 AAAAATGGAAAAAGT-
1 -AAAATGG-AAAAGTG
3789450 AAAATGGA
1 AAAATGGA
3789458 GAGGCTAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 8 0.28
14 15 0.52
15 1 0.03
16 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (14 bp):
AAAATGGAAAAGTG
Found at i:3790808 original size:45 final size:45
Alignment explanation
Indices: 3790681--3791354 Score: 592
Period size: 45 Copynumber: 15.1 Consensus size: 45
3790671 GAGTAGCAGT
* * *
3790681 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGGAA-AATGC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATC-GAAGAAAGC
* * *
3790726 AGATCTTGTCTT--CAT-GTACTGGCGTGAAGTAGATCAAAGATAA-C
1 AGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGA-AAGC
* * * *
3790770 AGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCAAAAAAAGT
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
* * *
3790815 AGATCTTGTCTT--CAT-GTACTGGCGTGAAGTAGATCAAAGATAA-C
1 AGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGA-AAGC
*
3790859 AGATCTTGTCTTCCCAAACTAGTGGCGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
* * *
3790904 AGATCTTGTCTT--CAT-GTACTGGCGTGAAGTAGATCAAAGATAA-C
1 AGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGA-AAGC
* *
3790948 AGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAAC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
* *
3790993 AGATCTTGTCTT--CAT-GTATTGGCGTAAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCCATACTAGTGGCG--AAGTAGATCGAAGAAAGC
*
3791037 AGATAC-TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
1 AGAT-CTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
* * * *
3791082 AGATCTTGACTT--CAT-GTATTGGCGTGAAGTAGATCGAAGAAAGA
1 AGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGAAAGC
* *
3791126 AGATCTTGTCTT--CAT-GTATTGGCGTAAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCCATACTAGTGGCG--AAGTAGATCGAAGAAAGC
*
3791170 AGATAC-TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGC
1 AGAT-CTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
*** *
3791215 AGATCTTGTCTTCATGTA-TAG-GGCGTGAAGTAGATCAAAGACAA-C
1 AGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAGA-AAGC
* * * * * **
3791260 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATTGAAGTTAGC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
* *
3791305 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGT
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
3791350 AGATC
1 AGATC
3791355 GAAGAAACTA
Statistics
Matches: 518, Mismatches: 67, Indels: 88
0.77 0.10 0.13
Matches are distributed among these distances:
42 30 0.06
43 19 0.04
44 180 0.35
45 239 0.46
46 18 0.03
47 32 0.06
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (45 bp):
AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAGC
Found at i:3790832 original size:89 final size:89
Alignment explanation
Indices: 3790681--3791354 Score: 744
Period size: 89 Copynumber: 7.6 Consensus size: 89
3790671 GAGTAGCAGT
* * * *
3790681 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGGAAAATGCAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAAAAAGCAGATCTTGTCTTCATGTACT
*
3790746 GGCGTGAAGTAGATCAAAGATAAC
66 GGCGTGAAGTAGATCGAAGATAAC
* * *
3790770 AGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCAAAAAAAGTAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAAAAAGCAGATCTTGTCTTCATGTACT
*
3790835 GGCGTGAAGTAGATCAAAGATAAC
66 GGCGTGAAGTAGATCGAAGATAAC
* *
3790859 AGATCTTGTCTTCCCAAACTAGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAAAAAGCAGATCTTGTCTTCATGTACT
*
3790924 GGCGTGAAGTAGATCAAAGATAAC
66 GGCGTGAAGTAGATCGAAGATAAC
* *
3790948 AGATCTTATCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAAA-CAGATCTTGTCTTCATGTAT
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAA-AAAAGCAGATCTTGTCTTCATGTAC
*
3791012 TGGCGTAAAGTAGATCGAAGA-AAGC
65 TGGCGTGAAGTAGATCGAAGATAA-C
* * * *
3791037 AGATAC-TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGACTTCATGTAT
1 AGAT-CTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAAAAAGCAGATCTTGTCTTCATGTAC
*
3791101 TGGCGTGAAGTAGATCGAAGA-AAGA
65 TGGCGTGAAGTAGATCGAAGATAA-C
* * * ***
3791126 AGATCTTGTCTT--CAT-GTATTGGCGTAAAGTAGATCGAAGAAAGCAGATAC-TGTCTTCCCAT
1 AGATCTTGTCTTCCCATACTAGTGGCG--AAGTAGATCGAAAAAAGCAGAT-CTTGTCTTCATGT
* *
3791187 ACTGGTGGCGAAGTAGATCGAAGA-AAGC
63 ACTGG-CGTGAAGTAGATCGAAGATAA-C
*** * ***
3791215 AGATCTTGTCTTCATGTA-TAG-GGCGTGAAGTAGATC-AAAGACAA-CAGATCTTGTCTCCCCA
1 AGATCTTGTCTTCCCATACTAGTGGC--GAAGTAGATCGAAA-A-AAGCAGATCTTGTCTTCATG
* * * * *
3791276 TACTGGTGGTGGAGTAGATTGAAGTTAGC
62 TACTGG-CGTGAAGTAGATCGAAGATAAC
* * *
3791305 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGTAGATC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAAAAAGCAGATC
3791355 GAAGAAACTA
Statistics
Matches: 512, Mismatches: 51, Indels: 43
0.84 0.08 0.07
Matches are distributed among these distances:
86 6 0.01
87 3 0.01
88 39 0.08
89 366 0.71
90 84 0.16
91 10 0.02
92 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (89 bp):
AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAAAAAGCAGATCTTGTCTTCATGTACT
GGCGTGAAGTAGATCGAAGATAAC
Found at i:3791351 original size:14 final size:14
Alignment explanation
Indices: 3791332--3791368 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3791322 ACTGGTGGCG
3791332 AAGTAGATCGAAGA
1 AAGTAGATCGAAGA
3791346 AAGTAGATCGAAGA
1 AAGTAGATCGAAGA
*
3791360 AACTAGATC
1 AAGTAGATC
3791369 TTGTCTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.24, T:0.16
Consensus pattern (14 bp):
AAGTAGATCGAAGA
Found at i:3795046 original size:29 final size:29
Alignment explanation
Indices: 3795013--3795285 Score: 199
Period size: 29 Copynumber: 9.4 Consensus size: 29
3795003 TTTGTAATCT
*
3795013 TCCCTTTTCATATTCGATGGTCGAAACCA
1 TCCCTTTTCATATTCGATGGTCGAAACTA
* *
3795042 TCCCTTTTCATATTCGATGGTTGAAACCA
1 TCCCTTTTCATATTCGATGGTCGAAACTA
* * * ** *
3795071 TCCCTTTTCATTAATCAATGTTCGTCACCA
1 TCCCTTTTCA-TATTCGATGGTCGAAACTA
* * *
3795101 TCCCTTTTCATAATCGATAG-CTGAAGCTA
1 TCCCTTTTCATATTCGATGGTC-GAAACTA
* * * * *
3795130 TCCCTTTTCACATTTGATAGCCGAAGCTA
1 TCCCTTTTCATATTCGATGGTCGAAACTA
* ** *
3795159 TCCCTTTTCATATTTGATGGTCGTTACCA
1 TCCCTTTTCATATTCGATGGTCGAAACTA
* * * **
3795188 CCCCTTTTCATGTTTGATGGTCGTCACTA
1 TCCCTTTTCATATTCGATGGTCGAAACTA
* * * *
3795217 TCCATTTTCATAATCGATAG-CCAAAGCTA
1 TCCCTTTTCATATTCGATGGTCGAAA-CTA
* * * *
3795246 TCCCTTTTTATATTCGATAGCCGAAGCTA
1 TCCCTTTTCATATTCGATGGTCGAAACTA
3795275 TCCCTTTTCAT
1 TCCCTTTTCAT
3795286 TATCTGAGGG
Statistics
Matches: 196, Mismatches: 43, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.02
29 166 0.85
30 27 0.14
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (29 bp):
TCCCTTTTCATATTCGATGGTCGAAACTA
Found at i:3795265 original size:116 final size:116
Alignment explanation
Indices: 3795013--3795285 Score: 350
Period size: 116 Copynumber: 2.3 Consensus size: 116
3795003 TTTGTAATCT
* * * * * *
3795013 TCCCTTTTCATATTCGATGGTCGAAACCATCCCTTTTCATATTCGATGGTTGAAACCATCCCTTT
1 TCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGAAACCACCCCTTT
* * **
3795078 TCATTAATCAATGTTCGTCACCATCCCTTTTCATAATCGATAGCTGAAGCTA
66 TCATT-ATCAATGGTCGTCACCATCCATTTTCATAATCGATAGCCAAAGCTA
* * * **
3795130 TCCCTTTTCACATTTGATAGCCGAAGCTATCCCTTTTCATATTTGATGGTCGTTACCACCCCTTT
1 TCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGAAACCACCCCTTT
** *
3795195 TCATGT-TTGATGGTCGTCACTATCCATTTTCATAATCGATAGCCAAAGCTA
66 TCAT-TATCAATGGTCGTCACCATCCATTTTCATAATCGATAGCCAAAGCTA
*
3795246 TCCCTTTTTATATTCGATAGCCGAAGCTATCCCTTTTCAT
1 TCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCAT
3795286 TATCTGAGGG
Statistics
Matches: 134, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
116 75 0.56
117 58 0.43
118 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (116 bp):
TCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCGATGGTCGAAACCACCCCTTT
TCATTATCAATGGTCGTCACCATCCATTTTCATAATCGATAGCCAAAGCTA
Found at i:3808206 original size:25 final size:25
Alignment explanation
Indices: 3808146--3808206 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
3808136 CTCCTAAATT
*
3808146 TTAATTTAATTATCTAAATTTTCAA
1 TTAATTAAATTATCTAAATTTTCAA
* *
3808171 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAA-ATTTTCA-A
3808196 TTAATTAAATT
1 TTAATTAAATT
3808207 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAATTAAATTATCTAAATTTTCAA
Found at i:3808716 original size:17 final size:17
Alignment explanation
Indices: 3808694--3808727 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3808684 CAGGTTCTAA
3808694 GTGGATTGTGTCAAAGC
1 GTGGATTGTGTCAAAGC
3808711 GTGGATTGTGTCAAAGC
1 GTGGATTGTGTCAAAGC
3808728 AAGGAATCCA
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:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (17 bp):
GTGGATTGTGTCAAAGC
Found at i:3820498 original size:25 final size:25
Alignment explanation
Indices: 3820464--3820558 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
3820454 TCATATACAT
3820464 GTATGCTCACACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGTGAATCG
* * *
3820489 GTATGCTCACTCGAGTTGT-AGATCA
1 GTATGCTCACACGAGCTGTGA-ATCG
* * * * *
3820514 ATATGCTCTCACGTGCTATAAATCG
1 GTATGCTCACACGAGCTGTGAATCG
*
3820539 GTATGCTCTCACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
3820559 GAGTATTCGC
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
24 1 0.02
25 52 0.96
26 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCG
Found at i:3826898 original size:26 final size:24
Alignment explanation
Indices: 3826861--3826914 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
3826851 CTTTCCACTT
3826861 ATATATTCTAAATAAT-AAATAATAAA
1 ATATATTCTAAA-AATCAAAT--TAAA
3826887 ATATCATT-TAAAAATCAAATTAAA
1 ATAT-ATTCTAAAAATCAAATTAAA
3826911 ATAT
1 ATAT
3826915 TAATAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 8 0.31
25 3 0.12
26 12 0.46
27 3 0.12
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATATTCTAAAAATCAAATTAAA
Found at i:3829431 original size:43 final size:42
Alignment explanation
Indices: 3829311--3829439 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 42
3829301 CTCGGTGGAT
* *
3829311 TCAACACTTAGCAACCA-CATTAAATTCAGTGATACAGGGAA
1 TCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
* * *
3829352 TCAGCACATAGCAACC-CCTTTCACAA-TCAAAT-ATACGGTGGAA
1 TCAACACTTAGCAACCACCTTT-A-AATTC-AGTGATACGG-GGAA
*
3829395 TCAACACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
3829437 TCA
1 TCA
3829440 GCACACAGCA
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
41 17 0.24
42 18 0.25
43 31 0.44
44 5 0.07
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (42 bp):
TCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAA
Found at i:3829524 original size:74 final size:74
Alignment explanation
Indices: 3829376--3829517 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
3829366 CCCCTTTCAC
* * * * *
3829376 AATCAAATATACGGTGGAATCAACACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAG
1 AATCAAATATACAGTGGAATCAACACTTAGCAACCACCTTTAGAATCAATAATACGGGGAATCAG
3829441 CACACAGCA
66 CACACAGCA
* **
3829450 AATCAAATATACAGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTTGGGGAATCAG
1 AATCAAATATACAGTGGAATCAACACTTAGCAACCACCTTTAGAATCAATAATACGGGGAATCAG
3829515 CAC
66 CAC
3829518 TTAGCAACCC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.23
Consensus pattern (74 bp):
AATCAAATATACAGTGGAATCAACACTTAGCAACCACCTTTAGAATCAATAATACGGGGAATCAG
CACACAGCA
Found at i:3840146 original size:30 final size:31
Alignment explanation
Indices: 3840089--3840146 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
3840079 TCAAAATGAA
* **
3840089 TAAATTGAATAAAATGAATTATTTTATTGTC
1 TAAATTGAATAAAATGAATGAAATTATTGTC
*
3840120 TAAATT-AATAAATTGAATGAAATTATT
1 TAAATTGAATAAAATGAATGAAATTATT
3840147 AATTTAGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 17 0.74
31 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (31 bp):
TAAATTGAATAAAATGAATGAAATTATTGTC
Found at i:3844040 original size:322 final size:322
Alignment explanation
Indices: 3843455--3844103 Score: 1262
Period size: 322 Copynumber: 2.0 Consensus size: 322
3843445 CCATATAATG
*
3843455 CCAATAAGAGGATATCATTTATCCATGTCTCATGCTATGGATTTCGGTATCATGAATAAAGCTAT
1 CCAATAAGAGGATATCATTTATCCATGTCTCATGCTATGGATTCCGGTATCATGAATAAAGCTAT
3843520 GTACTGTAGAAGTCGTACACCCAATGCAATAGTTTTCGGTTCCTTATCTATTAGAACTCAGGCTT
66 GTACTGTAGAAGTCGTACACCCAATGCAATAGTTTTCGGTTCCTTATCTATTAGAACTCAGGCTT
3843585 TTACTTAAATTAAATTGTATGAGTCACGATACATGGTCCCCCATCCACCTAGATTTAAGTATGTC
131 TTACTTAAATTAAATTGTATGAGTCACGATACATGGTCCCCCATCCACCTAGATTTAAGTATGTC
3843650 ACACTATGAACATCACAAGTGAATAAGTCCATAAAAAAATTTAGGATCTATTCTGCTTAGGTCCT
196 ACACTATGAACATCACAAGTGAATAAGTCCATAAAAAAATTTAGGATCTATTCTGCTTAGGTCCT
3843715 ATCCATTATACTATTAGTCCGTCAGTCTTATCTATGTCTCTATCTTTTGGGAGTCATCCGCA
261 ATCCATTATACTATTAGTCCGTCAGTCTTATCTATGTCTCTATCTTTTGGGAGTCATCCGCA
*
3843777 CCAATAAGAGGATATCATTTATCCATGTCTCATGCTATGGATTCCTGTATCATGAATAAAGCTAT
1 CCAATAAGAGGATATCATTTATCCATGTCTCATGCTATGGATTCCGGTATCATGAATAAAGCTAT
3843842 GTACTGTAGAAGTCGTACACCCAATGCAATAGTTTTCGGTTCCTTATCTATTAGAACTCAGGCTT
66 GTACTGTAGAAGTCGTACACCCAATGCAATAGTTTTCGGTTCCTTATCTATTAGAACTCAGGCTT
*
3843907 TTACTTAAATTAAATTGTTTGAGTCACGATACATGGTCCCCCATCCACCTAGATTTAAGTATGTC
131 TTACTTAAATTAAATTGTATGAGTCACGATACATGGTCCCCCATCCACCTAGATTTAAGTATGTC
3843972 ACACTATGAACATCACAAGTGAATAAGTCCATAAAAAAATTTAGGATCTATTCTGCTTAGGTCCT
196 ACACTATGAACATCACAAGTGAATAAGTCCATAAAAAAATTTAGGATCTATTCTGCTTAGGTCCT
*
3844037 ATCCATTGTACTATTAGTCCGTCAGTCTTATCTATGTCTCTATCTTTTGGGAGTCATCCGCA
261 ATCCATTATACTATTAGTCCGTCAGTCTTATCTATGTCTCTATCTTTTGGGAGTCATCCGCA
3844099 CCAAT
1 CCAAT
3844104 GCTTAAGACA
Statistics
Matches: 323, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
322 323 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (322 bp):
CCAATAAGAGGATATCATTTATCCATGTCTCATGCTATGGATTCCGGTATCATGAATAAAGCTAT
GTACTGTAGAAGTCGTACACCCAATGCAATAGTTTTCGGTTCCTTATCTATTAGAACTCAGGCTT
TTACTTAAATTAAATTGTATGAGTCACGATACATGGTCCCCCATCCACCTAGATTTAAGTATGTC
ACACTATGAACATCACAAGTGAATAAGTCCATAAAAAAATTTAGGATCTATTCTGCTTAGGTCCT
ATCCATTATACTATTAGTCCGTCAGTCTTATCTATGTCTCTATCTTTTGGGAGTCATCCGCA
Found at i:3854971 original size:19 final size:21
Alignment explanation
Indices: 3854949--3854987 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
3854939 CTGATAAACA
3854949 ATTTCA-TTGCAT-TTAGTTT
1 ATTTCATTTGCATATTAGTTT
3854968 ATTTCATTTGCATATTAGTT
1 ATTTCATTTGCATATTAGTT
3854988 GTTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
ATTTCATTTGCATATTAGTTT
Found at i:3863806 original size:12 final size:12
Alignment explanation
Indices: 3863789--3863813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3863779 CTCACACGCT
3863789 CATGTGCCAGGC
1 CATGTGCCAGGC
3863801 CATGTGCCAGGC
1 CATGTGCCAGGC
3863813 C
1 C
3863814 GTGTAACATT
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:0.36, G:0.32, T:0.16
Consensus pattern (12 bp):
CATGTGCCAGGC
Found at i:3866759 original size:8 final size:8
Alignment explanation
Indices: 3866746--3866781 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
3866736 TATTTATGAA
3866746 AAAATTAC
1 AAAATTAC
3866754 AAAATTAC
1 AAAATTAC
*
3866762 AAAATTAT
1 AAAATTAC
*
3866770 AAAATTAT
1 AAAATTAC
3866778 AAAA
1 AAAA
3866782 CAACCTTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATTAC
Found at i:3869319 original size:27 final size:26
Alignment explanation
Indices: 3869289--3869387 Score: 110
Period size: 26 Copynumber: 3.7 Consensus size: 26
3869279 AGGCCCATTC
*
3869289 TTTCAGAGAATGCCATGAAA-GCTTTCA
1 TTTCAGA-AATGCCA-CAAAGGCTTTCA
* *
3869316 TTTCAGATATGCCACAAAGGCTTCCA
1 TTTCAGAAATGCCACAAAGGCTTTCA
*
3869342 TTTCAGATATGCCACAAAGGCTTTCA
1 TTTCAGAAATGCCACAAAGGCTTTCA
* *
3869368 TTTCATAGATTGCCACAAAG
1 TTTCAGA-AATGCCACAAAG
3869388 ATATCCATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
25 3 0.05
26 43 0.68
27 17 0.27
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (26 bp):
TTTCAGAAATGCCACAAAGGCTTTCA
Found at i:3869338 original size:26 final size:26
Alignment explanation
Indices: 3869309--3869387 Score: 124
Period size: 26 Copynumber: 3.0 Consensus size: 26
3869299 TGCCATGAAA
3869309 GCTTTCATTTCAGATATGCCACAAAG
1 GCTTTCATTTCAGATATGCCACAAAG
*
3869335 GCTTCCATTTCAGATATGCCACAAAG
1 GCTTTCATTTCAGATATGCCACAAAG
3869361 GCTTTCATTTCATAGAT-TGCCACAAAG
1 GCTTTCATTTC--AGATATGCCACAAAG
3869388 ATATCCATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
26 35 0.71
27 10 0.20
28 4 0.08
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (26 bp):
GCTTTCATTTCAGATATGCCACAAAG
Found at i:3869396 original size:27 final size:28
Alignment explanation
Indices: 3869320--3869424 Score: 139
Period size: 27 Copynumber: 3.9 Consensus size: 28
3869310 CTTTCATTTC
3869320 AGATATGCCACAAAGGCTTCCATTTC--
1 AGATATGCCACAAAGGCTTCCATTTCAT
*
3869346 AGATATGCCACAAAGGCTTTCATTTCAT
1 AGATATGCCACAAAGGCTTCCATTTCAT
*
3869374 AGAT-TGCCACAAA-GATATCCATTTCAT
1 AGATATGCCACAAAGGCT-TCCATTTCAT
*
3869401 AGATA-GCCACAAGGGCTTCCATTT
1 AGATATGCCACAAAGGCTTCCATTT
3869425 TTTGGTGTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
26 27 0.39
27 36 0.52
28 6 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (28 bp):
AGATATGCCACAAAGGCTTCCATTTCAT
Found at i:3870368 original size:112 final size:112
Alignment explanation
Indices: 3870171--3870396 Score: 434
Period size: 112 Copynumber: 2.0 Consensus size: 112
3870161 GCGTTAACCC
3870171 GATTACTTTTTCATAATACATTACCAAGCTCATTTCCTTAACAATTCATCCTTTCTATGACAATT
1 GATTACTTTTTCATAATACATTACCAAGCTCATTTCCTTAACAATTCATCCTTTCTATGACAATT
3870236 CCTTATAATAATCCAATACCTGCTACGCACCTACTTTTACACACCAA
66 CCTTATAATAATCCAATACCTGCTACGCACCTACTTTTACACACCAA
* *
3870283 GATTACTTTTTCATACTACATTAGCAAGCTCATTTCCTTAACAATTCATCCTTTCTATGACAATT
1 GATTACTTTTTCATAATACATTACCAAGCTCATTTCCTTAACAATTCATCCTTTCTATGACAATT
3870348 CCTTATAATAATCCAATACCTGCTACGCACCTACTTTTACACACCAA
66 CCTTATAATAATCCAATACCTGCTACGCACCTACTTTTACACACCAA
3870395 GA
1 GA
3870397 GCATTAGTTG
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (112 bp):
GATTACTTTTTCATAATACATTACCAAGCTCATTTCCTTAACAATTCATCCTTTCTATGACAATT
CCTTATAATAATCCAATACCTGCTACGCACCTACTTTTACACACCAA
Found at i:3870860 original size:7 final size:7
Alignment explanation
Indices: 3870848--3870927 Score: 142
Period size: 7 Copynumber: 11.4 Consensus size: 7
3870838 ATATAACTCT
3870848 TTTCTTC
1 TTTCTTC
3870855 TTTCTTC
1 TTTCTTC
3870862 TTTCTTC
1 TTTCTTC
3870869 TTTCTTC
1 TTTCTTC
3870876 TTTCTTC
1 TTTCTTC
3870883 TTTCTTC
1 TTTCTTC
3870890 TTTCTTC
1 TTTCTTC
3870897 TTTCTTC
1 TTTCTTC
3870904 TTTCTTC
1 TTTCTTC
*
3870911 TTTCATC
1 TTTCTTC
*
3870918 TTTCATC
1 TTTCTTC
3870925 TTT
1 TTT
3870928 TAACCTTTAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 72 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTCTTC
Found at i:3873377 original size:22 final size:21
Alignment explanation
Indices: 3873352--3873415 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 21
3873342 TACAAATTAA
*
3873352 ATCTCTAAGATTTCACAATCAT
1 ATCTCTAAGATTGCA-AATCAT
*
3873374 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTGCAAATCAT
* *
3873396 A--TCTAAGATTACATATCAT
1 ATCTCTAAGATTGCAAATCAT
3873415 A
1 A
3873416 ACTAAGACTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 18 0.47
22 9 0.24
23 11 0.29
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (21 bp):
ATCTCTAAGATTGCAAATCAT
Found at i:3873381 original size:23 final size:22
Alignment explanation
Indices: 3873355--3873399 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
3873345 AAATTAAATC
*
3873355 TCTAAGATTTCACAATCATATCT
1 TCTAAGATTGCA-AATCATATCT
*
3873378 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCAAATCATATCT
3873400 AAGATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (22 bp):
TCTAAGATTGCAAATCATATCT
Found at i:3873402 original size:19 final size:19
Alignment explanation
Indices: 3873378--3873431 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
3873368 AATCATATCT
3873378 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
3873397 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
* *
3873416 ACTAAGACTGCATATC
1 TCTAAGATTGCATATC
3873432 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3874038 original size:45 final size:45
Alignment explanation
Indices: 3873989--3874278 Score: 185
Period size: 45 Copynumber: 6.6 Consensus size: 45
3873979 TTAGTCTACC
* * *
3873989 CCACTGCAATTTCAGAGG-GATAAGACTTGATTTCTTGAGTCTGGT
1 CCACTGCAACTTCAG-GGAGATAAGACTCGATTTCTTGAGTCTGCT
* * *
3874034 CCACTGCAACTTAAGGGAGATAAGACTCGCTTTCTTGGGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTGCT
*
3874079 CCACTGCAACTTCAGGGAGATAAGAC-CAGA-TGC--GA-TCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTC-GATTTCTTGAGTCTGCT
* ** * * **
3874120 -CTCTGCAACTTCAGAAAGATAAGA-TCTG-TGAT-TTGAATCCACT
1 CCACTGCAACTTCAGGGAGATAAGACTC-GAT-TTCTTGAGTCTGCT
* * ** *
3874163 CCACTGCAACTTCAGGGAGATAATATTC-ACAATCTTCAGTCTGC-
1 CCACTGCAACTTCAGGGAGATAAGACTCGA-TTTCTTGAGTCTGCT
* * * * *
3874207 CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTACTT-AGTCTGCT
1 C-CACTGCAACTTCAGGGA-GATAAGACTCGATTTCTTGAGTCTGCT
* *
3874252 CCACTACAACTTCAGAGAGATAAGACT
1 CCACTGCAACTTCAGGGAGATAAGACT
3874279 AGATACGATC
Statistics
Matches: 189, Mismatches: 38, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
40 23 0.12
41 6 0.03
42 3 0.02
43 4 0.02
44 59 0.31
45 94 0.50
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTGCT
Found at i:3874177 original size:84 final size:83
Alignment explanation
Indices: 3874077--3874360 Score: 277
Period size: 84 Copynumber: 3.3 Consensus size: 83
3874067 CTTGGGTCTG
*
3874077 CTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAGAAAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACCAGAT-CGATCTGCTCTCTACAACTTCAGAAAGATAA
*
3874142 GATCTGTGATTTGAATCCA
65 GATCTGTGATTTTAATCCA
* * * *
3874161 CTCCACTGCAACTTCAGGGAGATAATATTCACA-ATCTTCAGTCTGCCTCACTACAACTTCAGGA
1 CTCCACTGCAACTTCAGGGAGATAAGA--C-CAGATC--GA-TCTG-CTCTCTACAACTTCAGAA
* * * * **
3874225 GGATAAG-GCT-TGCTTACTTAGTCTG
59 AGATAAGATCTGTGATT--TTAATCCA
* * * * *
3874250 CTCCACTACAACTTCAGAGAGATAAGACTAGATACGATCTGCTCTCTACAACTTTAGAGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACCAGAT-CGATCTGCTCTCTACAACTTCAGAAAGATAA
*
3874315 GATGTGTGATTTTAATCCA
65 GATCTGTGATTTTAATCCA
*
3874334 CTCCACTGCGACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
3874361 TTATTCGCTT
Statistics
Matches: 156, Mismatches: 31, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
84 75 0.48
85 6 0.04
86 9 0.06
87 10 0.06
88 7 0.04
89 49 0.31
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (83 bp):
CTCCACTGCAACTTCAGGGAGATAAGACCAGATCGATCTGCTCTCTACAACTTCAGAAAGATAAG
ATCTGTGATTTTAATCCA
Found at i:3874819 original size:44 final size:44
Alignment explanation
Indices: 3874769--3874890 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
3874759 ATCTGCTATT
* *
3874769 TTCAACCTACTCCACTGTTGCTCAGGGAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTGCTGCTCAGGGAGATAGGACTT-ACAATC
* **
3874813 TTCAACCTATTCCACTGCTGACT-AGGGAGAGAATACTTACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGGGAGATAGGACTTACAATC
3874857 TTCAACCTATTCCACTGCTGC-CAAGGGAGATAGG
1 TTCAACCTATTCCACTGCTGCTC-AGGGAGATAGG
3874891 GCTGGGGTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 61 0.92
45 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGCTCAGGGAGATAGGACTTACAATC
Found at i:3875009 original size:88 final size:88
Alignment explanation
Indices: 3874890--3875640 Score: 1378
Period size: 88 Copynumber: 8.5 Consensus size: 88
3874880 AGGGAGATAG
* * *
3874890 GGCTGGGGTCATCGATCTGCTTCGCTATCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3874955 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
3874978 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3875043 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
3875066 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3875131 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
3875154 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3875219 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
3875242 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3875307 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
3875330 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3875395 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
3875418 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG-TAATTTTTAACCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT-ATTTTTAACCTG
** *
3875482 CTCCATTGCAACCCAGGGAGGCAA
65 CTCCGCTACAACCCAGGGAGGCAA
* * *
3875506 GGCTGGTATCTTCGATCTGTTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3875571 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGGGAGGCAA
* * *
3875594 GGCTGGTGTCTTCGATCTGCTTCACTTTCGGTGCAGGTAGGCAAGAT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGAT
3875641 GTGTTATCTT
Statistics
Matches: 644, Mismatches: 17, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
87 1 0.00
88 642 1.00
89 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTACAACCCAGGGAGGCAA
Found at i:3876987 original size:14 final size:15
Alignment explanation
Indices: 3876964--3876996 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3876954 ATCGACGCTT
3876964 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
3876978 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
3876993 TTCC
1 TTCC
3876997 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:3884229 original size:19 final size:19
Alignment explanation
Indices: 3884161--3884220 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
3884151 NNNNNNNNNN
*
3884161 AGATTGCATATCATATCTA
1 AGATTACATATCATATCTA
3884180 AGATTACATATCATATCTA
1 AGATTACATATCATATCTA
3884199 AGATTACATATCATATCTA
1 AGATTACATATCATATCTA
3884218 AGA
1 AGA
3884221 CTGCATATCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (19 bp):
AGATTACATATCATATCTA
Done.