Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 27 of 105
Found at i:5445008 original size:59 final size:57
Alignment explanation
Indices: 5444939--5445063 Score: 166
Period size: 59 Copynumber: 2.2 Consensus size: 57
5444929 TTTTGGAGTT
* *
5444939 TTTTTA-TTTT-AAGAAAAATTGATACTTCAAC-TTTTCTTCAAGAAATATTTTTTAAAAA
1 TTTTTATTTTTAAAG-AAAATTGATACTTCAACTTTTTC-TAAAAAAATATTTTTT--AAA
*
5444997 TTTTTATTTTTAAAGAAAATTGATACTTCAACTTTTTCTAAAAAAATATTTTTTGAA
1 TTTTTATTTTTAAAGAAAATTGATACTTCAACTTTTTCTAAAAAAATATTTTTTAAA
5445054 TTTTTATTTT
1 TTTTTATTTT
5445064 CTTCAAAAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
57 12 0.20
58 6 0.10
59 35 0.57
60 8 0.13
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (57 bp):
TTTTTATTTTTAAAGAAAATTGATACTTCAACTTTTTCTAAAAAAATATTTTTTAAA
Found at i:5445033 original size:92 final size:90
Alignment explanation
Indices: 5444754--5445017 Score: 325
Period size: 92 Copynumber: 2.9 Consensus size: 90
5444744 TTTTGATTTT
* * * * * *
5444754 TTTTTTTGTTTAAAGGAAAATCAATACTTCAACTTTTCTTCAAGAGAAACACTTTTT-AAATTTT
1 TTTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTC-A-AGAAATATTTTTTAAAATTTT
* *
5444818 ATTTTTAAGGAAAATTATTTTTTTGAG
64 ATTTTTAAAGAAAATTATTTTTTCGAG
* * *
5444845 ATTTTTTATTTTAAGAAAAATTAATACTTTAACTTTTCTTTAAGAAATATTTTTTGAAAATTTTA
1 TTTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTCAAGAAATATTTTTT-AAAATTTTA
* *
5444910 TTTTT-GAGAAAAATTATTTTTTTGGAG
65 TTTTTAAAG-AAAATTA-TTTTTTCGAG
*
5444937 TTTTTTTATTTTAAGAAAAATTGATACTTCAACTTTTCTTCAAGAAATATTTTTTAAAAATTTTT
1 TTTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTCAAGAAATATTTTTT-AAAA-TTTT
5445002 ATTTTTAAAGAAAATT
64 ATTTTTAAAGAAAATT
5445018 GATACTTCAA
Statistics
Matches: 149, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
89 11 0.07
90 2 0.01
91 54 0.36
92 64 0.43
93 16 0.11
94 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (90 bp):
TTTTTTTATTTTAAGAAAAATTAATACTTCAACTTTTCTTCAAGAAATATTTTTTAAAATTTTAT
TTTTAAAGAAAATTATTTTTTCGAG
Found at i:5449002 original size:26 final size:26
Alignment explanation
Indices: 5448968--5449025 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5448958 TTAATTAAAC
*
5448968 ATATTTTTATCT-ATTTATTTAAATGG
1 ATATTTTTATATGATTT-TTTAAATGG
* *
5448994 ATATTTTTATATGCTTTTTTAATTGG
1 ATATTTTTATATGATTTTTTAAATGG
5449020 ATATTT
1 ATATTT
5449026 AAAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.60
Consensus pattern (26 bp):
ATATTTTTATATGATTTTTTAAATGG
Found at i:5449117 original size:10 final size:9
Alignment explanation
Indices: 5449102--5449161 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
5449092 TACTCTTATC
5449102 AATTTAAAT
1 AATTTAAAT
5449111 AAATTTAAAT
1 -AATTTAAAT
*
5449121 ATTTTAAATT
1 AATTTAAA-T
*
5449131 GATTTAAAT
1 AATTTAAAT
5449140 AATATTAAAT
1 AAT-TTAAAT
**
5449150 AAAGTAAAT
1 AATTTAAAT
5449159 AAT
1 AAT
5449162 CATATATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 17 0.41
10 24 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
AATTTAAAT
Found at i:5449128 original size:19 final size:20
Alignment explanation
Indices: 5449104--5449161 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
5449094 CTCTTATCAA
5449104 TTTAAATAAATTTAAAT-AT
1 TTTAAATAAATTTAAATAAT
**
5449123 TTTAAATTGATTTAAATAAT
1 TTTAAATAAATTTAAATAAT
* *
5449143 ATTAAATAAA-GTAAATAAT
1 TTTAAATAAATTTAAATAAT
5449162 CATATATCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTAAATAAATTTAAATAAT
Found at i:5449157 original size:29 final size:29
Alignment explanation
Indices: 5449103--5449158 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5449093 ACTCTTATCA
***
5449103 ATTTAAATAAATTTAAATATTTTAAATTG
1 ATTTAAATAAATTTAAATAAAGTAAATTG
5449132 ATTTAAAT-AATATTAAATAAAGTAAAT
1 ATTTAAATAAAT-TTAAATAAAGTAAAT
5449159 AATCATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
ATTTAAATAAATTTAAATAAAGTAAATTG
Found at i:5449212 original size:18 final size:18
Alignment explanation
Indices: 5449186--5449227 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5449176 CCGTTTTTAA
5449186 ATTAATATTTGAAT-ATTT
1 ATTAATATTT-AATGATTT
*
5449204 ATTATTATTTAATGATTT
1 ATTAATATTTAATGATTT
5449222 AGTTAA
1 A-TTAA
5449228 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 14 0.70
19 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
ATTAATATTTAATGATTT
Found at i:5460916 original size:78 final size:78
Alignment explanation
Indices: 5460829--5460981 Score: 227
Period size: 78 Copynumber: 2.0 Consensus size: 78
5460819 TTGAAATATT
**
5460829 TTTAATATATTCA-GCAAAAAAAGAAATATTTTTAATATTCATATAAATAACATTTAATAATAAA
1 TTTAATATATT-AGGCAAAAAAAGAAATATTTTTAATATGAATATAAATAACATTTAATAATAAA
5460893 TAATACTATTTAAA
65 TAATACTATTTAAA
* * * *
5460907 TTTAATATATTAGGCCAAACAAGAAATATTTTTAATATGAATATCAATAATATTTAATAATAAAT
1 TTTAATATATTAGGCAAAAAAAGAAATATTTTTAATATGAATATAAATAACATTTAATAATAAAT
*
5460972 AATTCTATTT
66 AATACTATTT
5460982 TAAAATATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 1 0.01
78 66 0.99
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.40
Consensus pattern (78 bp):
TTTAATATATTAGGCAAAAAAAGAAATATTTTTAATATGAATATAAATAACATTTAATAATAAAT
AATACTATTTAAA
Found at i:5465881 original size:29 final size:29
Alignment explanation
Indices: 5465826--5465881 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5465816 ATAAAAAAAA
* *
5465826 TCATATTAAATATATAAGATATTTTAATT
1 TCATATTAAATATAAAAGATATGTTAATT
5465855 TCATATTAAATATAAAAAGA-ATGTTAA
1 TCATATTAAATAT-AAAAGATATGTTAA
5465882 AATATTATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (29 bp):
TCATATTAAATATAAAAGATATGTTAATT
Found at i:5470075 original size:32 final size:32
Alignment explanation
Indices: 5470032--5470111 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
5470022 AAAAGCATGG
* * *
5470032 TCAAAC-AATTAAAAGTCACTGCCTGGTATGG
1 TCAAACTAATTAAAAGTCACTGCATGGAATGA
* *
5470063 TTAAATTAATTAAAAGTCACTGCATGGAATGA
1 TCAAACTAATTAAAAGTCACTGCATGGAATGA
5470095 TCAAACTAATTAAAAGT
1 TCAAACTAATTAAAAGT
5470112 GATTGGGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 4 0.10
32 37 0.90
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (32 bp):
TCAAACTAATTAAAAGTCACTGCATGGAATGA
Found at i:5471217 original size:21 final size:21
Alignment explanation
Indices: 5471193--5471254 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
5471183 TACTTTTTAT
5471193 TTATAATAATATTTTTTTACG
1 TTATAATAATATTTTTTTACG
* * * *
5471214 TTATCAAT-TTAATTATTTATG
1 TTAT-AATAATATTTTTTTACG
*
5471235 TTATAATAATATGTTTTTAC
1 TTATAATAATATTTTTTTAC
5471255 ACTTGTTCTT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TTATAATAATATTTTTTTACG
Found at i:5471748 original size:20 final size:20
Alignment explanation
Indices: 5471689--5471748 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
5471679 AAAATTATTT
* *
5471689 TTTAT-TTATAATAATAATTT
1 TTTATGTTACAATAA-AATTA
* **
5471709 TTTATGTTGTCAATTTAATTA
1 TTTATGTT-ACAATAAAATTA
5471730 TTTATGTTACAATAAAATT
1 TTTATGTTACAATAAAATT
5471749 TGTTACACTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 13 0.43
21 14 0.47
22 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTATGTTACAATAAAATTA
Found at i:5471889 original size:19 final size:17
Alignment explanation
Indices: 5471862--5471927 Score: 53
Period size: 20 Copynumber: 3.5 Consensus size: 17
5471852 ATGATTATTT
*
5471862 TTATCTTTTTACTTTAATAC
1 TTAT-TTTTTA-TTTAA-AA
5471882 TTATTTTTTTATTTAAAA
1 TTA-TTTTTTATTTAAAA
5471900 TTA-TTTTTATTTATAATA
1 TTATTTTTTATTTA-AA-A
5471918 TTAATTTTTT
1 TT-ATTTTTT
5471928 TATGTTACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
16 10 0.25
17 2 0.05
18 7 0.17
19 6 0.15
20 14 0.35
21 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTTTTATTTAAAA
Found at i:5471903 original size:18 final size:19
Alignment explanation
Indices: 5471882--5471940 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 19
5471872 ACTTTAATAC
5471882 TTATTTTTTTATTTA-AAA
1 TTATTTTTTTATTTACAAA
*
5471900 TTA--TTTTTATTTATAATA
1 TTATTTTTTTATTTACAA-A
5471918 TTAATTTTTTTATGTTACAAA
1 TT-ATTTTTTTAT-TTACAAA
5471939 TT
1 TT
5471941 TATTGCGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 10 0.29
17 2 0.06
18 6 0.18
19 1 0.03
21 10 0.29
22 5 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTTTTTATTTACAAA
Found at i:5471908 original size:36 final size:39
Alignment explanation
Indices: 5471867--5471940 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 39
5471857 TATTTTTATC
5471867 TTTTTACTT-TAATACTT-ATTTTTTTAT-TTA-AAATTA
1 TTTTTACTTATAATA-TTAATTTTTTTATGTTACAAATTA
*
5471903 TTTTTATTTATAATATTAATTTTTTTATGTTACAAATT
1 TTTTTACTTATAATATTAATTTTTTTATGTTACAAATT
5471941 TATTGCGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 10 0.30
37 15 0.45
38 3 0.09
39 5 0.15
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (39 bp):
TTTTTACTTATAATATTAATTTTTTTATGTTACAAATTA
Found at i:5472364 original size:931 final size:920
Alignment explanation
Indices: 5471150--5473349 Score: 2302
Period size: 925 Copynumber: 2.4 Consensus size: 920
5471140 TTTTTTTCTT
* * * * * **
5471150 TTTTACGTTAACACTTATTTTTTGGTTTGAAATTACTTTTTATTTATAATAAT-ATTTTTTTACG
1 TTTTATGTTAAC-TTTA-TTTTT-GTTTAAAATTATTTTTTATTTGTAATAATAATTTTTTTAAA
* * * * * *
5471214 TTATCAATTTAATTATTTATGTTATAATAATATGTTTTTACACTTGTTCTTATATTTTATTATGT
63 TTA-CAACTTAATTATTTATGTTATAATAATATATTTTTA-TCTTGTTATTACATTTCATTATGT
* * * * * *
5471279 TTAAAATTATCACAATTTTTTTTTAAGGTGTTACAATACTTTTAATACACTTTATGCCAAATGAT
126 TTAGAATTATCACAACTTTTTTTAAAGGTGTTACGATACTTTTAAT-CATTTTATACCAAATGAT
* * *
5471344 ATAAATTTTATGATTATTCTCACATTTTTTACATAGACACTTATTTTTTGATT-GAATTATTTTT
190 ATAAATTTTATGATTATTCTCACATTTTTTATATA-ACACTTATTTTTTGTTTAGAATTATTATT
* * * ** * *
5471408 TATTTATAATAATAATTTTTTTTATGTTGT-TAACTTAATTATTTACGTTAAAATAA-ATTTTTT
254 TATTTGTAATAATAA-TTCTTTTATGTTGTCAAAAAT-ATTATTTATGTTACAATAATATTTTTT
* * *
5471471 ACACTTGTTCTTA-TATTTCATTACGTTTAGAATTATCACAACTATTTCTT-AGAGTATTACAAT
317 ACACTTATTCTTACT-TTTCATGACATTTAGAATTATCACAACTATTTCTTAAG-GTATTACAAT
* * * **
5471534 AGTTCTAACTT-ATTT-T-AC-AA-GGATATTAATTTTATGACTA-TAATCACCT-TTTAATGTT
380 ACTTCTAACTTAATTTATGACAAATGG-CA-TAAGTTTACAACTATTAAT-ACCTCTTT-ATGTT
* ** * **** * * *
5471592 ACT-ATATTTTTAACACATTTTATGTTAAATTATACCAATTTTATGATTATTCTCATTTTTTTTA
441 A-TGACA-TCATAACACATTTAACACCAAATAATACCAATTTT-TAATTATTCTCA-CTTTTTTA
*
5471656 CGTTAACACT-TATTTTTAGGTTTAAAATTATTTTTTATTTATAATAAT-AATTTTTTATGTTGT
502 CGTTAACA-TGTATTTTT-GGTTTAAAATTATTTTTTATTTATAATAATAAATTTTTTATATTGT
* * *
5471719 CAATTTAATTATTTATGTTACAATAAAATTTGTTACACTTATTTTTACATTTTATTATATTTAGA
565 CAACTT-A-TATTTACGTTACAATAAAATTT-TT-CACTTATTCTTACATTTTATTATATTTAGA
* * * ** *
5471784 ATTATCACAATTTTTTCTTAA-GTATTATAATACTTTAAATATATTTTATGCCAAATTATACCAA
626 ATTATCACAAGTTTTT-TTAAGGTATTACAACAC-TT--ATATATTTTACACCAAATGATACCAA
* * * * * * *
5471848 TTTTATGATTATTTTTATCTTTTTACTTTAATACTTATTTTTTTATTTAA-AATTATTTTTATTT
687 TTTTACGATTATTCTCATATTTTTACGTTAATACTTATTTTTTGATTGAATAATT-TTTTTATTT
* * * * * *
5471912 ATAATATTAATTTTTTTATGTTACAAATTTATTGCGTTTTAATAATATCTTTTACAT-TTTTTTG
751 ATAATACTAAATTTTTTACGTTACAAATTTATTACGTTTTAATAATATCTTTT-CATGTGTGTTG
*
5471976 TTACTTTTTATTACGTTTAAAATTACTACAATTTTTGTATAAAAGTGTAATGATGCTTTTAACTA
815 TTACTTTTTATTACGTTTAAAATTACTACAATTTTTGTATAAAAGTGTAATGATACTTTTAACTA
* *
5472041 TTTTACGTAAAATAATA-CTAATTTTATGATTATTCTTACCA
880 TTTTACATAAAATAATATC-AATTTTATGATTATTCTCACCA
5472082 TTTTATGTTAACTTTATTATTTGTTTAAAATTATTTTTTATTTGTAATAATAATTTTTTTAAATT
1 TTTTATGTTAACTTTATT-TTTGTTTAAAATTATTTTTTATTTGTAATAATAATTTTTTTAAATT
** * *
5472147 ACAAACTTAATTATTTACATTATAATAATATCTTTTTATGCTTGTTATTACCTTTCATTATGTTT
65 AC-AACTTAATTATTTATGTTATAATAATATATTTTTAT-CTTGTTATTACATTTCATTATGTTT
* ** * * * *
5472212 AGAATTATCATAACTTTTTTTAAATATGTTATGATACTTCTAATCATTTTACACCAAATGATATC
128 AGAATTATCACAACTTTTTTTAAAGGTGTTACGATACTTTTAATCATTTTATACCAAATGATATA
* * *
5472277 AATTTTACGATTACTCTCACATTTTTTATATTAACACTTATTTTTTAGTTTATAATTATTATTTA
193 AATTTTATGATTATTCTCACATTTTTTATA-TAACACTTATTTTTT-GTTTAGAATTATTATTTA
* * * * *
5472342 TTTGTAATAATAATTCTTTTATGTTGCCAAGAATATTATTTATGTTACATTAATATTTTTTATAT
256 TTTGTAATAATAATTCTTTTATGTTGTCAAAAATATTATTTATGTTACAATAATATTTTTTACAC
* * * * * * *** *
5472407 TTATTCCTACTTTTTATGATATTTAGAATTATCTCAACTTTTTGTTAAGGTATTATGGTACTTTT
321 TTATTCTTACTTTTCATGACATTTAGAATTATCACAACTATTTCTTAAGGTATTACAATACTTCT
* * * *
5472472 AATTTAATTTATGCCAAATGGCATAAGTTTACAACTATTCATATCTCTTTATGTTATGACATCAT
386 AACTTAATTTATGACAAATGGCATAAGTTTACAACTATTAATACCTCTTTATGTTATGACATCAT
* * *** *
5472537 AATATATTTAACACCAAATAATTTTAATTTTTAATTATTCTCACTTTTTTACGTTAATATGTATT
451 AACACATTTAACACCAAATAATACCAATTTTTAATTATTCTCACTTTTTTACGTTAACATGTATT
*
5472602 TTTTGTTTAAAATTATTTTTTATTTATAATAATAAATTTTTTATATTGTCAACTTATATTTACGT
516 TTTGGTTTAAAATTATTTTTTATTTATAATAATAAATTTTTTATATTGTCAACTTATATTTACGT
** * ** * * *
5472667 TACAATAAAATTTTTTGCTTGTTCTTATTTTTTGTTATGTTTAGAATTATTACAAGTTTTTTTAA
581 TACAATAAAATTTTTCACTTATTCTTACATTTTATTATATTTAGAATTATCACAAGTTTTTTTAA
* * *
5472732 GGTATTACGACACTTCTATATTTTACACTAAATGATACCAATTTTACGATTATTCTCATATTTTT
646 GGTATTACAACACTTATATATTTTACACCAAATGATACCAATTTTACGATTATTCTCATATTTTT
* * * *
5472797 ACGTTAATATTTATTTTTTGATTGAATTATTTTTTTCTTTATAATACTAAATTTTTTACGTTACT
711 ACGTTAATACTTATTTTTTGATTGAATAATTTTTTTATTTATAATACTAAATTTTTTACGTTACA
* * *
5472862 AATTTATTACGTTTTAATAATATCTTTTTATGTGTGTTGTTACTTTTTATTACGTTTAGAATTAT
776 AATTTATTACGTTTTAATAATATCTTTTCATGTGTGTTGTTACTTTTTATTACGTTTAAAATTAC
* * * * * * * *
5472927 TGCAATTTTTTTCTTAAGGTTTAATGATACTTTTAACTATTTTACATTAAATATTATCAATTTTA
841 TACAATTTTTGTATAAAAGTGTAATGATACTTTTAACTATTTTACATAAAATAATATCAATTTTA
*
5472992 TGATTATTCTCACTA
906 TGATTATTCTCACCA
* * * * *
5473007 TTTTATATTAACTCTTAACTTTTTATTTAAAATTATTTTTTATTTGTAATAATAGTTCTTTTATA
1 TTTTATGTTAACT-TT-A-TTTTTGTTTAAAATTATTTTTTATTTGTAATAATAATTTTTTTAAA
* * * * **
5473072 TTGCCAACTTAATTATTTATGTTCTAATAATATATTTTTACTCTTGTTGTTACTTTTCATTA-CA
63 TT-ACAACTTAATTATTTATGTTATAATAATATATTTTTA-TCTTGTTATTACATTTCATTATGT
** * * * * *
5473136 TTAGAAACATTACAACTTTTTTCTTAAAGGTGTTACGATACTTTTAATAATTTCATATCAAATAA
126 TTAGAATTATCACAAC-TTTTT-TTAAAGGTGTTACGATACTTTTAATCATTTTATACCAAATGA
* * *
5473201 TATTAATTTTATGATTATTCTCACATTTTTTTATACTGACACTTTTTTTTTTGGTTTAGAATTAT
189 TATAAATTTTATGATTATTCTCACA-TTTTTTATA-TAACAC-TTATTTTTT-GTTTAGAATTAT
* * * * * *
5473266 TAATTATTTGCATTATTAATTCTTTTA-ATTATCAAAAATATTATTTATGTTACAATAATATTTT
250 TATTTATTTGTAATAATAATTCTTTTATGTTGTCAAAAATATTATTTATGTTACAATAATATTTT
5473330 TTACACTTATTCTTACTTTT
315 TTACACTTATTCTTACTTTT
5473350 TATTATGTTT
Statistics
Matches: 1047, Mismatches: 187, Indels: 71
0.80 0.14 0.05
Matches are distributed among these distances:
924 2 0.00
925 226 0.22
926 18 0.02
927 103 0.10
928 104 0.10
929 65 0.06
930 149 0.14
931 169 0.16
932 135 0.13
933 18 0.02
934 24 0.02
935 23 0.02
936 9 0.01
937 2 0.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (920 bp):
TTTTATGTTAACTTTATTTTTGTTTAAAATTATTTTTTATTTGTAATAATAATTTTTTTAAATTA
CAACTTAATTATTTATGTTATAATAATATATTTTTATCTTGTTATTACATTTCATTATGTTTAGA
ATTATCACAACTTTTTTTAAAGGTGTTACGATACTTTTAATCATTTTATACCAAATGATATAAAT
TTTATGATTATTCTCACATTTTTTATATAACACTTATTTTTTGTTTAGAATTATTATTTATTTGT
AATAATAATTCTTTTATGTTGTCAAAAATATTATTTATGTTACAATAATATTTTTTACACTTATT
CTTACTTTTCATGACATTTAGAATTATCACAACTATTTCTTAAGGTATTACAATACTTCTAACTT
AATTTATGACAAATGGCATAAGTTTACAACTATTAATACCTCTTTATGTTATGACATCATAACAC
ATTTAACACCAAATAATACCAATTTTTAATTATTCTCACTTTTTTACGTTAACATGTATTTTTGG
TTTAAAATTATTTTTTATTTATAATAATAAATTTTTTATATTGTCAACTTATATTTACGTTACAA
TAAAATTTTTCACTTATTCTTACATTTTATTATATTTAGAATTATCACAAGTTTTTTTAAGGTAT
TACAACACTTATATATTTTACACCAAATGATACCAATTTTACGATTATTCTCATATTTTTACGTT
AATACTTATTTTTTGATTGAATAATTTTTTTATTTATAATACTAAATTTTTTACGTTACAAATTT
ATTACGTTTTAATAATATCTTTTCATGTGTGTTGTTACTTTTTATTACGTTTAAAATTACTACAA
TTTTTGTATAAAAGTGTAATGATACTTTTAACTATTTTACATAAAATAATATCAATTTTATGATT
ATTCTCACCA
Found at i:5472814 original size:210 final size:217
Alignment explanation
Indices: 5472570--5473230 Score: 557
Period size: 210 Copynumber: 3.1 Consensus size: 217
5472560 TTAATTTTTA
*
5472570 ATTATTCTCACT-TTTTTACGTTAATATGTATTTTTTGTTTAAAATTATTTTTTATTTATAATAA
1 ATTATTCTCACTATTTTTACGTTAATATTTATTTTTTGTTTAAAATTATTTTTTATTTATAATAA
* *
5472634 TAAATTTTTTATATTGTCAACTTATATTTACGTTACAATAA-A-ATTTTT-TGCT-TGTTCTTAT
66 TAAATTTTTTATATTGACAACTTATA-TTACGTTACAATAATATATTTTTATG-TGTGTTCTTAC
* *
5472695 TTTTTGTTATGTTTAGAATTATTACAA-GTTTTT-TTAAGGTATT-ACGACACTTCT-A-TATTT
129 TTTTTATTACGTTTAGAATTATTACAATGTTTTTCTTAAGGT-TTAACGACACTTCTAACTATTT
5472755 TACACTAAATGA-TACCAATTTTACG
193 TACACTAAAT-ATTACCAATTTTACG
* * *
5472780 ATTATTCTCA-TATTTTTACGTTAATATTTATTTTTTGATT-GAATTATTTTTTTCTTTATAATA
1 ATTATTCTCACTATTTTTACGTTAATATTTATTTTTTGTTTAAAATTA-TTTTTTATTTATAATA
* ** ** * *
5472843 CTAAATTTTTTACGTT-ACTAA-TT-TATTACGTTTTAATAATATCTTTTTATGTGTGTTGTTAC
65 ATAAATTTTTTATATTGAC-AACTTATATTACGTTACAATAATATATTTTTATGTGTGTTCTTAC
* * * * *
5472905 TTTTTATTACGTTTAGAATTATTGCAATTTTTTTCTTAAGGTTTAATGATACTTTTAACTATTTT
129 TTTTTATTACGTTTAGAATTATTACAATGTTTTTCTTAAGGTTTAACGACACTTCTAACTATTTT
* * *
5472970 ACATTAAATATTATCAATTTTATG
194 ACACTAAATATTACCAATTTTACG
* * * * *
5472994 ATTATTCTCACTATTTTATA--TTAACTCTTAACTTTTTATTTAAAATTATTTTTTATTTGTAAT
1 ATTATTCTCACTATTTT-TACGTTAA-TATTTATTTTTTGTTTAAAATTATTTTTTATTTATAAT
* * * *
5473057 AAT-AGTTCTTTTATATTGCCAACTTAATTATTTATGTT-CTAATAATATATTTTTACTCT-TGT
64 AATAAATT-TTTTATATTGACAACTT-A-TA-TTACGTTAC-AATAATATATTTTTA-TGTGTGT
* * * ** * *
5473119 TGTTACTTTTCATTAC-ATTAGAAACATTACAACT-TTTTTCTTAAAGGTGTT-ACGATACTTTT
123 TCTTACTTTTTATTACGTTTAGAATTATTACAA-TGTTTTTCTT-AAGGT-TTAACGACACTTCT
* * * ** *
5473181 AA-TAATTT-CATATCAAATAATATTAATTTTATG
185 AACTATTTTACA-CT-AAATATTACCAATTTTACG
5473214 ATTATTCTCAC-ATTTTT
1 ATTATTCTCACTATTTTT
5473231 TTATACTGAC
Statistics
Matches: 370, Mismatches: 50, Indels: 54
0.78 0.11 0.11
Matches are distributed among these distances:
207 12 0.03
208 3 0.01
209 15 0.04
210 99 0.27
211 7 0.02
212 15 0.04
213 2 0.01
214 42 0.11
215 41 0.11
216 10 0.03
218 3 0.01
219 33 0.09
220 84 0.23
221 4 0.01
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.54
Consensus pattern (217 bp):
ATTATTCTCACTATTTTTACGTTAATATTTATTTTTTGTTTAAAATTATTTTTTATTTATAATAA
TAAATTTTTTATATTGACAACTTATATTACGTTACAATAATATATTTTTATGTGTGTTCTTACTT
TTTATTACGTTTAGAATTATTACAATGTTTTTCTTAAGGTTTAACGACACTTCTAACTATTTTAC
ACTAAATATTACCAATTTTACG
Found at i:5472871 original size:16 final size:17
Alignment explanation
Indices: 5472841--5472874 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5472831 TTCTTTATAA
*
5472841 TACTAAATTTTTTACGT
1 TACTAAATTTATTACGT
5472858 TACT-AATTTATTACGT
1 TACTAAATTTATTACGT
5472874 T
1 T
5472875 TTAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
TACTAAATTTATTACGT
Found at i:5472991 original size:925 final size:937
Alignment explanation
Indices: 5471628--5473781 Score: 2274
Period size: 925 Copynumber: 2.3 Consensus size: 937
5471618 AAATTATACC
* *
5471628 AATTTTATGATTATTCTCATTTTTTTTACGTTAACACTTATTTTTAGGTTTAAAATTATTTTTTA
1 AATTTTATAATTATTCTCATCTTTTTTACGTTAACACTTATTTTTAGGTTTAAAATTATTTTTTA
* * *
5471693 TTTATAATAATAATTTTTTATGTTGTCAATTTAATTATTTATGTTACAATAAAATTTGTTACACT
66 TTTATAATAATAATTTTTTATATTGTCAACTTAATTATTTACGTTACAATAAAATTTGTTACACT
* * * *
5471758 TATTTTTACATTTTATTATATTTAGAATTATCACAATTTTTTCTTAAGTATTATAATACTTTAAA
131 TATTCTTACATTTTATTATATTTAGAATTATCACAAGTTTTTCTTAAGTATTACAACACTTT-AA
** * * * * * *
5471823 TATATTTTATGCCAAATTATACCAATTTTATGATTATTTTTATCTTTTTACTTTAATACTTATTT
195 TATATTTTACACCAAATGATACCAATTTTACGATTATTCTCATATTTTTACGTTAATACTTATTT
* * * * * *
5471888 TTTTATTTAAAATTATTTTTATTTATAATATTAATTTTTTTATGTTACAAATTTATTGCGTTTTA
260 TTTGATTGAAAATTATTTTTATTTATAATACTAAATTTTTTACGTTACAAATTTATTACGTTTTA
* *
5471953 ATAATATCTTTTACATTTTTTTGTTACTTTTTATTACGTTTAAAATTACTACAATTTTTGTATAA
325 ATAATATCTTTTACATTGTGTTGTTACTTTTTATTACGTTTAAAATTACTACAATTTTTGTATAA
* * *
5472018 AAGTGTAATGATGCTTTTAACTATTTTACGTAAAATAATACTAATTTTATGATTATTCTTACCAT
390 AAGTGTAATGATACTTTTAACTATTTTACATAAAATAATACTAATTTTATGATTATTCTCACCAT
* * *
5472083 TTTATGTTAACT-TT-A-TTATTTGTTTAAAATTATTTTTTATTTGTAATAATAATTTTTTTAAA
455 TTTATATTAACTCTTAACTT-TTTATTTAAAATTATTTTTTATTTGTAATAATAATTCTTTTAAA
* *
5472145 TTACAAACTTAATTATTTACATTATAATAATATCTTTTTA-TGCTTGTTATTACCTTTCATTATG
519 TTACAAACTTAATTATTTACATTATAATAATATATTTTTACT-CTTGTTATTACCTTTCATTA-C
* ** * * * * * *
5472209 TTTAGAATTATCATAAC-TTTTT-TTAAATATGTTATGATACTTCTAATCATTTTACACCAAATG
582 ATTAGAAACATCACAACTTTTTTCTTAAAGATGTTACGATACTTCTAATAATTTCACACCAAATA
* *
5472272 ATATCAATTTTACGATTACTCTCACA-TTTTTTATATTAACAC-TTATTTTTTAGTTTATAATTA
647 ATATCAATTTTACGATTACTCTCACATTTTTTTATACTAACACTTTATTTTTTAGTTTAGAATTA
* * * * * *
5472335 TTATTTATTTGTAATAATAATTCTTTTATGTTGCCAAGAATATTATTTATGTTACATTAATATTT
712 TTAATTATTTGCAATAATAATTCTTTTA-ATTACCAAAAATATTATTTATGTTACAATAATATTT
* *
5472400 TTTATATTTATTCCTACTTTTTATGATATTTAGAATTATCTCAACTTTTTGTTAAGGTATTATGG
776 TTTACACTTATTCCTACTTTTTATGATATTTAGAATTATCTCAACTTTTTGTTAAGGTATTATGG
5472465 TACTTTTAATTTAATTTATGCCAAATGGCATAAGTTTACAACTATTCATATCTCTTTATGTTATG
841 TACTTTTAATTTAATTTATGCCAAATGGCATAAGTTTACAACTATTCATATCTCTTTATGTTATG
5472530 ACATCATAATATATTTAACACCAAATAATTTT
906 ACATCATAATATATTTAACACCAAATAATTTT
* *
5472562 AATTTT-TAATTATTCTCA-CTTTTTTACGTTAATA-TGTATTTTT-TGTTTAAAATTATTTTTT
1 AATTTTATAATTATTCTCATCTTTTTTACGTTAACACT-TATTTTTAGGTTTAAAATTATTTTTT
**
5472623 ATTTATAATAATAAATTTTTTATATTGTCAACTT-A-TATTTACGTTACAATAAAATTT-TT-TG
65 ATTTATAATAAT-AATTTTTTATATTGTCAACTTAATTATTTACGTTACAATAAAATTTGTTACA
* ** * * * *
5472684 CTTGTTCTTATTTTTTGTTATGTTTAGAATTATTACAAGTTTTT-TTAAGGTATTACGACAC-TT
129 CTTATTCTTACATTTTATTATATTTAGAATTATCACAAGTTTTTCTTAA-GTATTACAACACTTT
* * *
5472747 -CTATATTTTACACTAAATGATACCAATTTTACGATTATTCTCATATTTTTACGTTAATATTTAT
193 AATATATTTTACACCAAATGATACCAATTTTACGATTATTCTCATATTTTTACGTTAATACTTAT
* * *
5472811 TTTTTGATTGAATTATT-TTTTTCTTTATAATACTAAATTTTTTACGTTACTAATTTATTACGTT
258 TTTTTGATTGAA-AATTATTTTTATTTATAATACTAAATTTTTTACGTTACAAATTTATTACGTT
* * * * *
5472875 TTAATAATATCTTTT-TATGTGTGTTGTTACTTTTTATTACGTTTAGAATTATTGCAATTTTTTT
322 TTAATAATATCTTTTACAT-TGTGTTGTTACTTTTTATTACGTTTAAAATTACTACAATTTTTGT
* * * * * *
5472939 CTTAAGGTTTAATGATACTTTTAACTATTTTACATTAAATATTA-TCAATTTTATGATTATTCTC
386 ATAAAAGTGTAATGATACTTTTAACTATTTTACATAAAATAATACT-AATTTTATGATTATTCTC
* *
5473003 ACTATTTTATATTAACTCTTAACTTTTTATTTAAAATTATTTTTTATTTGTAATAATAGTTCTTT
450 ACCATTTTATATTAACTCTTAACTTTTTATTTAAAATTATTTTTTATTTGTAATAATAATTCTTT
* * * ** * * *
5473068 TATATTGCCAACTTAATTATTTATGTTCTAATAATATATTTTTACTCTTGTTGTTACTTTTCATT
515 TAAATTACAAACTTAATTATTTACATTATAATAATATATTTTTACTCTTGTTATTACCTTTCATT
* * * * *
5473133 ACATTAGAAACATTACAACTTTTTTCTTAAAGGTGTTACGATACTTTTAATAATTTCATATCAAA
580 ACATTAGAAACATCACAACTTTTTTCTTAAAGATGTTACGATACTTCTAATAATTTCACACCAAA
* * * * * *
5473198 TAATATTAATTTTATGATTATTCTCACATTTTTTTATACTGACACTTTTTTTTTTGGTTTAGAAT
645 TAATATCAATTTTACGATTACTCTCACATTTTTTTATACTAACACTTTATTTTTTAGTTTAGAAT
* * *
5473263 TATTAATTATTTGCATTATTAATTCTTTTAATTATCAAAAATATTATTTATGTTACAATAATATT
710 TATTAATTATTTGCAATAATAATTCTTTTAATTACCAAAAATATTATTTATGTTACAATAATATT
* * * * * * *
5473328 TTTTACACTTATTCTTACTTTTTATTATGTTTA-AGTTTATCACAA-TTCTTTGTT--GATGTTA
775 TTTTACACTTATTCCTACTTTTTATGATATTTAGA-ATTATCTCAACTT-TTTGTTAAGGTATTA
* * * * * * ** * * * *
5473389 CGATAATTTTAATCTAATTTATGTCAAGTGAAACCAATTTTACAACTATTCTTA-CAAT-TTTAC
838 TGGTACTTTTAATTTAATTTATGCCAAATGGCA-TAAGTTTACAACTATTCATATC--TCTTTAT
* * * * * *
5473452 GTTACGACACTTC-TAACACACTTT-ACGCTAAATGATTTT
900 GTTATGACA--TCATAATATA-TTTAACACCAAATAATTTT
* * ** * * * * *
5473491 AATTTAACAATTGCTCTCATTTTTTTTATGTTAGCACTTTTTTTTA--TTTAGAATTATTTTTTA
1 AATTTTATAATTATTCTCATCTTTTTTACGTTAACACTTATTTTTAGGTTTAAAATTATTTTTTA
* * * * * * ** * *
5473554 TTTATATTAATAAAAATTTTTATGTTATTAACTTAATTATTTACGTTATAATAATTTTTTTTTAT
66 TTTATAATAAT--AATTTTTTATATTGTCAACTTAATTATTTACGTTACAATAA-AATTTGTTAC
* * * * * * * * * *
5473619 ACTTATAT-TTACCTTTGATTACATTTAGGATTATTATAACTTTTTCTTAAAAGTGTTACGATAC
128 ACTTAT-TCTTACATTTTATTATATTTAGAATTATCACAAGTTTTTCTT--AAGTATTACAACAC
* **** * ** * *
5473683 TTTTAA-CTATTTTATGTTAAA-AATATTAATTTTACGATTATTCTTATATTTTTACGTTAACAC
190 -TTTAATATATTTTACACCAAATGATACCAATTTTACGATTATTCTCATATTTTTACGTTAATAC
* *
5473746 TTATTTTTTGGTAT-AAGATTATTTTTTATTTATAAT
254 TTATTTTTTGAT-TGAAAATTA-TTTTTATTTATAAT
5473782 TTTTTTATAT
Statistics
Matches: 1004, Mismatches: 174, Indels: 78
0.80 0.14 0.06
Matches are distributed among these distances:
924 3 0.00
925 226 0.23
926 17 0.02
927 135 0.13
928 135 0.13
929 111 0.11
930 103 0.10
931 67 0.07
932 42 0.04
933 27 0.03
934 9 0.01
935 2 0.00
936 33 0.03
937 3 0.00
938 13 0.01
939 51 0.05
940 27 0.03
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (937 bp):
AATTTTATAATTATTCTCATCTTTTTTACGTTAACACTTATTTTTAGGTTTAAAATTATTTTTTA
TTTATAATAATAATTTTTTATATTGTCAACTTAATTATTTACGTTACAATAAAATTTGTTACACT
TATTCTTACATTTTATTATATTTAGAATTATCACAAGTTTTTCTTAAGTATTACAACACTTTAAT
ATATTTTACACCAAATGATACCAATTTTACGATTATTCTCATATTTTTACGTTAATACTTATTTT
TTGATTGAAAATTATTTTTATTTATAATACTAAATTTTTTACGTTACAAATTTATTACGTTTTAA
TAATATCTTTTACATTGTGTTGTTACTTTTTATTACGTTTAAAATTACTACAATTTTTGTATAAA
AGTGTAATGATACTTTTAACTATTTTACATAAAATAATACTAATTTTATGATTATTCTCACCATT
TTATATTAACTCTTAACTTTTTATTTAAAATTATTTTTTATTTGTAATAATAATTCTTTTAAATT
ACAAACTTAATTATTTACATTATAATAATATATTTTTACTCTTGTTATTACCTTTCATTACATTA
GAAACATCACAACTTTTTTCTTAAAGATGTTACGATACTTCTAATAATTTCACACCAAATAATAT
CAATTTTACGATTACTCTCACATTTTTTTATACTAACACTTTATTTTTTAGTTTAGAATTATTAA
TTATTTGCAATAATAATTCTTTTAATTACCAAAAATATTATTTATGTTACAATAATATTTTTTAC
ACTTATTCCTACTTTTTATGATATTTAGAATTATCTCAACTTTTTGTTAAGGTATTATGGTACTT
TTAATTTAATTTATGCCAAATGGCATAAGTTTACAACTATTCATATCTCTTTATGTTATGACATC
ATAATATATTTAACACCAAATAATTTT
Found at i:5473296 original size:16 final size:16
Alignment explanation
Indices: 5473259--5473297 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5473249 TTTTGGTTTA
5473259 GAATTATTAATTATTT
1 GAATTATTAATTATTT
* *
5473275 GCATTATTAATTCTTT
1 GAATTATTAATTATTT
*
5473291 TAATTAT
1 GAATTAT
5473298 CAAAAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (16 bp):
GAATTATTAATTATTT
Found at i:5473329 original size:220 final size:221
Alignment explanation
Indices: 5472896--5473354 Score: 479
Period size: 220 Copynumber: 2.1 Consensus size: 221
5472886 TTTTTATGTG
* ** * * *
5472896 TGTTGTTACTTTTTATTACGTTTAGAATTATTGCAATTTTTTTCTTAAGGTTTAATGATACTTTT
1 TGTTGTTACTTTTTATTACGATTAGAAACATTACAACTTTTTTCTTAAGGTTTAACGATACTTTT
* * * *
5472961 AACTATTTTACATTAAATATTATCAATTTTATGATTATTCTCACTATTTTATATTAACTCTTAAC
66 AACTAATTTACATTAAATAATATCAATTTTATGATTATTCTCACTATTTTATACTAACACTTAAC
** * * * **
5473026 TTTTTATTTAAAATTATTTTTTATTTGTAATAATAGTTCTTTTATATTGCCAACTTAATTATTTA
131 TTTTTATTTAAAATTATTAATTATTTGCAATAATAATTCTTTTATATTGCAAAAATAATTATTTA
*
5473091 TGTTCTAATAATATA-TTTTTACTCT
196 TGTTCTAATAATATATTTTTTACACT
*
5473116 TGTTGTTACTTTTCATTAC-ATTAGAAACATTACAACTTTTTTCTTAAAGGTGTT-ACGATACTT
1 TGTTGTTACTTTTTATTACGATTAGAAACATTACAACTTTTTTCTT-AAGGT-TTAACGATACTT
* * *
5473179 TTAA-TAATTT-CATATCAAATAATATTAATTTTATGATTATTCTCACATTTTTTTATACTGACA
64 TTAACTAATTTACAT-T-AAATAATATCAATTTTATGATTATTCTCAC--TATTTTATACTAACA
*** * * * * *
5473242 CTTTTTTTTTTGGTTTAGAATTATTAATTATTTGCATTATTAATTCTTTTA-ATTATCAAAAAT-
125 CTTAACTTTTT-ATTTAAAATTATTAATTATTTGCAATAATAATTCTTTTATATT-GCAAAAATA
5473305 ATTATTTATGTTAC-AAT-A-ATATTTTTTACACT
188 ATTATTTATGTT-CTAATAATATATTTTTTACACT
* *
5473337 TATTCTTACTTTTTATTA
1 TGTTGTTACTTTTTATTA
5473355 TGTTTAAGTT
Statistics
Matches: 196, Mismatches: 33, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
218 3 0.02
219 27 0.14
220 66 0.34
221 27 0.14
222 37 0.19
223 36 0.18
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.54
Consensus pattern (221 bp):
TGTTGTTACTTTTTATTACGATTAGAAACATTACAACTTTTTTCTTAAGGTTTAACGATACTTTT
AACTAATTTACATTAAATAATATCAATTTTATGATTATTCTCACTATTTTATACTAACACTTAAC
TTTTTATTTAAAATTATTAATTATTTGCAATAATAATTCTTTTATATTGCAAAAATAATTATTTA
TGTTCTAATAATATATTTTTTACACT
Found at i:5473541 original size:17 final size:16
Alignment explanation
Indices: 5473509--5473557 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
5473499 AATTGCTCTC
5473509 ATTTTTTTTATGTTAGCA
1 ATTTTTTTTAT-TTAG-A
*
5473527 CTTTTTTTTATTTAGA
1 ATTTTTTTTATTTAGA
5473543 ATTATTTTTTATTTA
1 ATT-TTTTTTATTTA
5473558 TATTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.11
17 15 0.54
18 10 0.36
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.67
Consensus pattern (16 bp):
ATTTTTTTTATTTAGA
Found at i:5474950 original size:21 final size:21
Alignment explanation
Indices: 5474926--5474974 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5474916 GATGATAATG
5474926 AAATTAATTATTATAAAAATA
1 AAATTAATTATTATAAAAATA
**
5474947 AAATTAATTATTATAATTATA
1 AAATTAATTATTATAAAAATA
5474968 AAATTAA
1 AAATTAA
5474975 AATTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTAATTATTATAAAAATA
Found at i:5475101 original size:20 final size:22
Alignment explanation
Indices: 5475055--5475109 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
5475045 TTAAAAATTT
5475055 TATTTTATAAATTATTTATATA
1 TATTTTATAAATTATTTATATA
*
5475077 TATTTTA-ATATTATTTATA-A
1 TATTTTATAAATTATTTATATA
*
5475097 TA-TTTAAAAATTA
1 TATTTTATAAATTA
5475110 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 8 0.27
21 11 0.37
22 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTTATAAATTATTTATATA
Found at i:5475162 original size:21 final size:21
Alignment explanation
Indices: 5475138--5475181 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5475128 TGATACTTAT
* *
5475138 TATTTGTTTATTATATAATAA
1 TATTTATTTATCATATAATAA
5475159 TATTTATTTATCATATAATAA
1 TATTTATTTATCATATAATAA
5475180 TA
1 TA
5475182 AAATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTTATTTATCATATAATAA
Found at i:5475214 original size:25 final size:25
Alignment explanation
Indices: 5475137--5475218 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
5475127 TTGATACTTA
* *
5475137 TTATTTGTTTATTATATAATAATAT
1 TTATTTATTTATTATATAATAAAAT
*
5475162 TTATTTA-TCA-TATAATAATAAAAT
1 TTATTTATTTATTAT-ATAATAAAAT
*
5475186 TTATTTATTTATTATATAGTAAAAT
1 TTATTTATTTATTATATAATAAAAT
5475211 TTATTTAT
1 TTATTTAT
5475219 ATTAAATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
23 3 0.06
24 18 0.37
25 25 0.51
26 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTTATTTATTATATAATAAAAT
Found at i:5475224 original size:16 final size:17
Alignment explanation
Indices: 5475192--5475224 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5475182 AAATTTATTT
5475192 ATTTATTATATAGTAAA
1 ATTTATTATATAGTAAA
*
5475209 ATTTATT-TATATTAAA
1 ATTTATTATATAGTAAA
5475225 TTATTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTTATTATATAGTAAA
Found at i:5475261 original size:7 final size:7
Alignment explanation
Indices: 5475249--5475286 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
5475239 TTAAAATTTT
5475249 AAAATAA
1 AAAATAA
5475256 AAAATAA
1 AAAATAA
5475263 AAAA-AA
1 AAAATAA
5475269 TGAAAATAA
1 --AAAATAA
5475278 AAAATAA
1 AAAATAA
5475285 AA
1 AA
5475287 GTTAAATGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 2 0.07
7 20 0.71
8 4 0.14
9 2 0.07
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:5476533 original size:20 final size:19
Alignment explanation
Indices: 5476501--5476540 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5476491 ACTTTATTTG
* *
5476501 ACTTTTTTTTTTTTTTATT
1 ACTTTTTTGTTTTTTAATT
5476520 ACTTTTTATGTTTTTTAATT
1 ACTTTTT-TGTTTTTTAATT
5476540 A
1 A
5476541 GTTAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (19 bp):
ACTTTTTTGTTTTTTAATT
Found at i:5479182 original size:23 final size:21
Alignment explanation
Indices: 5479143--5479185 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5479133 ATAACCAAAT
*
5479143 TTTTTTCTATAAAAAATAAAA
1 TTTTTTCTACAAAAAATAAAA
5479164 TTTTTTCTACAATAGAAATAAA
1 TTTTTTCTACAA-A-AAATAAA
5479186 TTTGCATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTTTTCTACAAAAAATAAAA
Found at i:5479716 original size:16 final size:18
Alignment explanation
Indices: 5479695--5479728 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5479685 CTATGAGGGC
5479695 AAAACTT-TAA-ATTTTT
1 AAAACTTATAATATTTTT
5479711 AAAACTTATAATATTTTT
1 AAAACTTATAATATTTTT
5479729 TATAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAACTTATAATATTTTT
Found at i:5480935 original size:21 final size:21
Alignment explanation
Indices: 5480911--5480962 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
5480901 ACATAATAAT
*
5480911 AATATGAATGCATGATTATTG
1 AATATGAATGCATGAATATTG
*
5480932 AATATAAATGCATGAATATTG
1 AATATGAATGCATGAATATTG
5480953 AATATGAATG
1 AATATGAATG
5480963 ACAAAGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (21 bp):
AATATGAATGCATGAATATTG
Found at i:5481113 original size:18 final size:19
Alignment explanation
Indices: 5481078--5481123 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
5481068 AGTTTAGGTT
*
5481078 TTTAGGGTTTGGGGTA-GG
1 TTTAGGGTTTAGGGTAGGG
*
5481096 TTTAGGGTTTAGGTTAGGG
1 TTTAGGGTTTAGGGTAGGG
*
5481115 TTTGGGGTT
1 TTTAGGGTT
5481124 CGGCTTAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.43
Consensus pattern (19 bp):
TTTAGGGTTTAGGGTAGGG
Found at i:5481122 original size:19 final size:19
Alignment explanation
Indices: 5481094--5481138 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5481084 GTTTGGGGTA
*
5481094 GGTTTAGGGTTTAGG-TTAG
1 GGTTT-GGGGTTAGGCTTAG
*
5481113 GGTTTGGGGTTCGGCTTAG
1 GGTTTGGGGTTAGGCTTAG
5481132 GGTTTGG
1 GGTTTGG
5481139 ATCAATTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.09, C:0.04, G:0.47, T:0.40
Consensus pattern (19 bp):
GGTTTGGGGTTAGGCTTAG
Found at i:5481225 original size:18 final size:17
Alignment explanation
Indices: 5481176--5481237 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
5481166 ACTATTTAGC
* *
5481176 TTAGGGTTTAGGTTAGT
1 TTAGGGTTAAGGTTTGT
* *
5481193 TTGGGGTTTAGGGTTTGAT
1 TTAGGG-TTAAGGTTTG-T
5481212 TTAGGGTTAAGGTTTGTT
1 TTAGGGTTAAGGTTTG-T
5481230 TTAGGGTT
1 TTAGGGTT
5481238 TTGAGTTAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 5 0.14
18 25 0.69
19 6 0.17
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (17 bp):
TTAGGGTTAAGGTTTGT
Found at i:5481301 original size:19 final size:19
Alignment explanation
Indices: 5481279--5481403 Score: 121
Period size: 19 Copynumber: 6.6 Consensus size: 19
5481269 TTAAGGTTTA
*
5481279 GTTTAGAGTTTCATGCGTG
1 GTTTAGAGTTTCATGGGTG
* *
5481298 GTTTAGAATTTGATGGGTG
1 GTTTAGAGTTTCATGGGTG
* *
5481317 GTTTA-AGGTTGCATGGTTG
1 GTTTAGA-GTTTCATGGGTG
*
5481336 GTTTAGGGTTTCATGGGTG
1 GTTTAGAGTTTCATGGGTG
*
5481355 GTTTA-AGGTTT-AGAGGGTG
1 GTTTAGA-GTTTCA-TGGGTG
*
5481374 GTTTAGAGTTTCATGGGTA
1 GTTTAGAGTTTCATGGGTG
*
5481393 GTTTAGTGTTT
1 GTTTAGAGTTT
5481404 GGAAGGTGGT
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.02
19 81 0.95
20 2 0.02
ACGTcount: A:0.17, C:0.04, G:0.36, T:0.43
Consensus pattern (19 bp):
GTTTAGAGTTTCATGGGTG
Found at i:5481389 original size:57 final size:57
Alignment explanation
Indices: 5481262--5481403 Score: 148
Period size: 57 Copynumber: 2.5 Consensus size: 57
5481252 GAGATTAAGA
*
5481262 TTAGAGTTT-AAGGTTTAGTTTAGAGTTTCATGCGTGGTTTAGAATTTGATGGGTGGT
1 TTAGAGTTTCATGG-TTAGTTTAGAGTTTCATGCGTGGTTTAGAATTTGATGGGTGGT
* * * * *
5481319 TTA-AGGTTGCATGGTTGGTTTAGGGTTTCATGGGTGGTTTA-AGGTTTAGA-GGGTGGT
1 TTAGA-GTTTCATGGTTAGTTTAGAGTTTCATGCGTGGTTTAGA-ATTT-GATGGGTGGT
* *
5481376 TTAGAGTTTCATGGGTAGTTTAGTGTTT
1 TTAGAGTTTCATGGTTAGTTTAGAGTTT
5481404 GGAAGGTGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
56 2 0.03
57 62 0.89
58 6 0.09
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.44
Consensus pattern (57 bp):
TTAGAGTTTCATGGTTAGTTTAGAGTTTCATGCGTGGTTTAGAATTTGATGGGTGGT
Found at i:5481412 original size:38 final size:38
Alignment explanation
Indices: 5481295--5481422 Score: 143
Period size: 38 Copynumber: 3.4 Consensus size: 38
5481285 AGTTTCATGC
* * * *
5481295 GTGGTTTAGAATTTGATGGGTGGTTTAAGG-TTGCATG
1 GTGGTTTAGAGTTTCATGGGTGGTTTAAGGTTTGGAAG
* * *
5481332 GTTGGTTTAGGGTTTCATGGGTGGTTTAAGGTTTAGAGG
1 G-TGGTTTAGAGTTTCATGGGTGGTTTAAGGTTTGGAAG
*
5481371 GTGGTTTAGAGTTTCATGGGTAGTTT-AGTGTTTGGAAG
1 GTGGTTTAGAGTTTCATGGGTGGTTTAAG-GTTTGGAAG
*
5481409 GTGGTTTAGGGTTT
1 GTGGTTTAGAGTTT
5481423 GGAATTTGAG
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
37 3 0.04
38 69 0.90
39 5 0.06
ACGTcount: A:0.16, C:0.02, G:0.39, T:0.42
Consensus pattern (38 bp):
GTGGTTTAGAGTTTCATGGGTGGTTTAAGGTTTGGAAG
Found at i:5482345 original size:11 final size:11
Alignment explanation
Indices: 5482326--5482371 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
5482316 AGAAATAGAA
5482326 AAAAT-ATATG
1 AAAATGATATG
*
5482336 AAAATGATATA
1 AAAATGATATG
5482347 AAAATGCA-ATG
1 AAAATG-ATATG
*
5482358 AAAATGCTATG
1 AAAATGATATG
5482369 AAA
1 AAA
5482372 TGCAAGAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 5 0.17
11 24 0.80
12 1 0.03
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (11 bp):
AAAATGATATG
Found at i:5482374 original size:21 final size:22
Alignment explanation
Indices: 5482333--5482380 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5482323 GAAAAAATAT
5482333 ATGAAAATGATATAAAAATGCA
1 ATGAAAATGATATAAAAATGCA
* *
5482355 ATGAAAATGCTAT-GAAATGCA
1 ATGAAAATGATATAAAAATGCA
5482376 A-GAAA
1 ATGAAA
5482381 GGAAACTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 8 0.33
22 12 0.50
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (22 bp):
ATGAAAATGATATAAAAATGCA
Found at i:5483792 original size:52 final size:51
Alignment explanation
Indices: 5483726--5483827 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 51
5483716 TTGTAAGAGC
* *
5483726 TCCTATAGACATAGGTAAGGAACTTCTAAAAAAATCTTAATAAGAAAAGTGT
1 TCCTATAAACATAGGCAAGGAACTT-TAAAAAAATCTTAATAAGAAAAGTGT
* ** **
5483778 TCCTATAAACATAGGCAAGTAACTTTTTAAAAATCTTAATTTGAAAAGTG
1 TCCTATAAACATAGGCAAGGAACTTTAAAAAAATCTTAATAAGAAAAGTG
5483828 CTCTTAAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 21 0.49
52 22 0.51
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (51 bp):
TCCTATAAACATAGGCAAGGAACTTTAAAAAAATCTTAATAAGAAAAGTGT
Found at i:5483841 original size:51 final size:52
Alignment explanation
Indices: 5483724--5483876 Score: 145
Period size: 51 Copynumber: 3.0 Consensus size: 52
5483714 TTTTGTAAGA
* ** **
5483724 GCTCCTAT-AGACATAGGTAAGGAACTTCTAAAAAAATCTTAATAAGAAAAGT
1 GCTCCTATAAGACATAGGTAAGTAACTT-TTTAAAAATCTTAATTTGAAAAGT
* *
5483776 GTTCCTATAA-ACATAGGCAAGTAACTTTTTAAAAATCTTAATTTGAAAAGT
1 GCTCCTATAAGACATAGGTAAGTAACTTTTTAAAAATCTTAATTTGAAAAGT
* * ** * *
5483827 GCTCTTA-AAGACATAAGTAAGTGGC--TTTAAAAAACTCAATTTGAAAAGT
1 GCTCCTATAAGACATAGGTAAGTAACTTTTTAAAAATCTTAATTTGAAAAGT
5483876 G
1 G
5483877 TTGCTATAGA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
49 23 0.27
50 2 0.02
51 36 0.43
52 22 0.26
53 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (52 bp):
GCTCCTATAAGACATAGGTAAGTAACTTTTTAAAAATCTTAATTTGAAAAGT
Found at i:5486968 original size:41 final size:41
Alignment explanation
Indices: 5486923--5487077 Score: 121
Period size: 41 Copynumber: 3.8 Consensus size: 41
5486913 ATTAGAGGTT
* *
5486923 TTTGGATTCACATTAGAGAAAAAAATTCACGGTTGGAAAAC
1 TTTGGATTCACAATAGAGAAAAAAATTCACAGTTGGAAAAC
* * * ** * *
5486964 TTTGGAGTCACAACAGAGTAAATGATTCATAGTTGGAAGAC
1 TTTGGATTCACAATAGAGAAAAAAATTCACAGTTGGAAAAC
* * ** * * *
5487005 TATGGATTCACAATAGAGTAAATGATTCATAGTTTGAAAGAT
1 TTTGGATTCACAATAGAGAAAAAAATTCACAGTTGGAAA-AC
* * * *
5487047 TTTAGATTCACAATAAAGTAAACAATTCACA
1 TTTGGATTCACAATAGAGAAAAAAATTCACA
5487078 ATTTAAAGGA
Statistics
Matches: 92, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 66 0.72
42 26 0.28
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (41 bp):
TTTGGATTCACAATAGAGAAAAAAATTCACAGTTGGAAAAC
Found at i:5487068 original size:42 final size:42
Alignment explanation
Indices: 5486971--5487276 Score: 182
Period size: 42 Copynumber: 7.4 Consensus size: 42
5486961 AACTTTGGAG
* * * *
5486971 TCACAACAGAGTAAATGATTCATAG-TTGGAAGACTATGGAT
1 TCACAATAGAGTAAATGATTCATAGTTTGAAAGACTCTAGAT
* *
5487012 TCACAATAGAGTAAATGATTCATAGTTTGAAAGATTTTAGAT
1 TCACAATAGAGTAAATGATTCATAGTTTGAAAGACTCTAGAT
* ** * * * * *
5487054 TCACAATAAAGTAAACAATTCACAATTT-AAAGGA-TTTTGGT
1 TCACAATAGAGTAAATGATTCATAGTTTGAAA-GACTCTAGAT
* * * * *
5487095 TCACAACT-GAGTAAATGATTCACA-CTTAAAAAACT-TTGAAT
1 TCACAA-TAGAGTAAATGATTCATAGTTTGAAAGACTCTAG-AT
* * *
5487136 TCACAACAGAGTAAACT-ATTCAAAGTTT-AAAGGACTCTGGAT
1 TCACAATAGAGTAAA-TGATTCATAGTTTGAAA-GACTCTAGAT
* * * *
5487178 TCATAGTAGAGTAAATGATTCATAGTTTG-TAGCATTCTAGAT
1 TCACAATAGAGTAAATGATTCATAGTTTGAAAG-ACTCTAGAT
* ** * * * *
5487220 TCATAGCAAAGTAAACGATTC-TCAGTTTGGAAGACTCTAGGT
1 TCACAATAGAGTAAATGATTCAT-AGTTTGAAAGACTCTAGAT
5487262 TCACAATAGAGTAAA
1 TCACAATAGAGTAAA
5487277 GGCTTTAGTT
Statistics
Matches: 209, Mismatches: 40, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
40 6 0.03
41 81 0.39
42 118 0.56
43 4 0.02
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (42 bp):
TCACAATAGAGTAAATGATTCATAGTTTGAAAGACTCTAGAT
Found at i:5487116 original size:41 final size:40
Alignment explanation
Indices: 5486962--5487199 Score: 126
Period size: 41 Copynumber: 5.8 Consensus size: 40
5486952 CGGTTGGAAA
* * * * **
5486962 ACTTTGGAGTCACAACAGAGTAAATGATTCATAGTTGGAAG
1 ACTTT-GATTCACAACTGAGTAAATGATTCACAATTTAAAG
* * *
5487003 ACTATGGATTCACAA-TAGAGTAAATGATTCATAGTTTGAAAG
1 ACT-TTGATTCACAACT-GAGTAAATGATTCACAATTT-AAAG
* * **
5487045 ATTTTAGATTCACAA-TAAAGTAAACAATTCACAATTTAAAGG
1 ACTTT-GATTCACAACT-GAGTAAATGATTCACAATTTAAA-G
* * * * *
5487087 ATTTTGGTTCACAACTGAGTAAATGATTCACACTTAAAAA
1 ACTTTGATTCACAACTGAGTAAATGATTCACAATTTAAAG
*
5487127 ACTTTGAATTCACAACAGAGTAAACT-ATTCA-AAGTTTAAAGG
1 ACTTTG-ATTCACAACTGAGTAAA-TGATTCACAA-TTTAAA-G
* * *
5487169 ACTCTGGATTCA-TAGTAGAGTAAATGATTCA
1 ACT-TTGATTCACAACT-GAGTAAATGATTCA
5487200 TAGTTTGTAG
Statistics
Matches: 155, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
40 6 0.04
41 87 0.56
42 60 0.39
43 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (40 bp):
ACTTTGATTCACAACTGAGTAAATGATTCACAATTTAAAG
Found at i:5487411 original size:18 final size:18
Alignment explanation
Indices: 5487353--5487424 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
5487343 TGAATTTAGA
5487353 AAAAGTTTTAAGATT-A-
1 AAAAGTTTTAAGATTCAT
* * *
5487369 AAAAATTTTAAGGTTCAC
1 AAAAGTTTTAAGATTCAT
5487387 AAAAGTTTTAAGATTCAT
1 AAAAGTTTTAAGATTCAT
* **
5487405 AAGAGTTCAAAGATTCAT
1 AAAAGTTTTAAGATTCAT
5487423 AA
1 AA
5487425 GAGTCAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 13 0.28
17 1 0.02
18 32 0.70
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (18 bp):
AAAAGTTTTAAGATTCAT
Found at i:5487425 original size:18 final size:17
Alignment explanation
Indices: 5487396--5487432 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
5487386 CAAAAGTTTT
5487396 AAGATTCATAAGAGTTCA
1 AAGATTCATAAGAG-TCA
5487414 AAGATTCATAAGAGTCA
1 AAGATTCATAAGAGTCA
5487431 AA
1 AA
5487433 TACCCACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (17 bp):
AAGATTCATAAGAGTCA
Found at i:5487485 original size:17 final size:17
Alignment explanation
Indices: 5487465--5487526 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
5487455 ACAAAAACCT
5487465 AAGATTCATAAATTCCA
1 AAGATTCATAAATTCCA
***
5487482 AAGATTCATAAGGACCA
1 AAGATTCATAAATTCCA
* *
5487499 AAGATCCACAAACTT-CA
1 AAGATTCATAAA-TTCCA
5487516 AAGATTCATAA
1 AAGATTCATAA
5487527 GAGTCAAGGA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (17 bp):
AAGATTCATAAATTCCA
Found at i:5487620 original size:37 final size:37
Alignment explanation
Indices: 5487579--5487692 Score: 110
Period size: 37 Copynumber: 3.2 Consensus size: 37
5487569 AAAAAATTGT
*
5487579 AAATTTCAAAGATTTGTAATAAGGGTTAGAGATTTAC
1 AAATTTCAAAGATTTGTAATAAGGGTTAAAGATTTAC
* * * *
5487616 AAATTTCAGAGA--T-TCATAAGAGTCAAAGATTTGA-
1 AAATTTCAAAGATTTGTAATAAGGGTTAAAGATTT-AC
* * * *
5487650 AAATTTCAAAGATTTGCAAGAGGGGTTAAAGATTCAC
1 AAATTTCAAAGATTTGTAATAAGGGTTAAAGATTTAC
5487687 AAATTT
1 AAATTT
5487693 TAGAGATTCG
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
34 26 0.44
35 2 0.03
36 2 0.03
37 29 0.49
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (37 bp):
AAATTTCAAAGATTTGTAATAAGGGTTAAAGATTTAC
Found at i:5487700 original size:108 final size:108
Alignment explanation
Indices: 5487506--5487705 Score: 242
Period size: 108 Copynumber: 1.9 Consensus size: 108
5487496 CCAAAGATCC
* * * *
5487506 ACAAACTTCAAAGATTCATAAGAGTCAAGGACTTGTAAATTTTAAAGTTTCGTAAGAGGGATTAA
1 ACAAACTTCAAAGATTCATAAGAGTCAAAGACTTGAAAATTTCAAAGTTTCGCAAGAGGGATTAA
** *
5487571 AAAATTGTAAATTTCAAAGATTTGTAATAAGGGTTAGAGATTT
66 AAAATTACAAATTTCAAAGATTCGTAATAAGGGTTAGAGATTT
* * * *
5487614 ACAAATTTCAGAGATTCATAAGAGTCAAAGATTTGAAAATTTCAAAGATTT-GCAAGAGGGGTT-
1 ACAAACTTCAAAGATTCATAAGAGTCAAAGACTTGAAAATTTCAAAG-TTTCGCAAGAGGGATTA
* * *
5487677 AAAGATTCACAAATTTTAGAGATTCGTAA
65 AAAAATT-ACAAATTTCAAAGATTCGTAA
5487706 ACATAAATGA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
107 6 0.08
108 67 0.88
109 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (108 bp):
ACAAACTTCAAAGATTCATAAGAGTCAAAGACTTGAAAATTTCAAAGTTTCGCAAGAGGGATTAA
AAAATTACAAATTTCAAAGATTCGTAATAAGGGTTAGAGATTT
Found at i:5489892 original size:28 final size:28
Alignment explanation
Indices: 5489861--5489919 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5489851 ATTTTTTTAA
*
5489861 TTTCATTTCATT-TTGTTTTTTTTCCTTT
1 TTTC-TTTCATTATTCTTTTTTTTCCTTT
* *
5489889 TTTCTTTTATTATTCTTTTTTTTTCTTT
1 TTTCTTTCATTATTCTTTTTTTTCCTTT
5489917 TTT
1 TTT
5489920 GCCTTGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.80
Consensus pattern (28 bp):
TTTCTTTCATTATTCTTTTTTTTCCTTT
Found at i:5490228 original size:112 final size:112
Alignment explanation
Indices: 5490105--5490340 Score: 445
Period size: 112 Copynumber: 2.1 Consensus size: 112
5490095 AATGGGGTCC
* *
5490105 TTTTTTTTTTGGTCAATGTGCCTTTAGACACTGGATAATGGTAATTTTGGGTAAAGAACTGAAAT
1 TTTTTTTTTTGGTCAATGTGCCTTTAGACACTGGATAATGATAATTTTGGGTAAAGAACTGAAAG
5490170 GTTAGTATGTTTATGGTCATTTTAAAGAATTTAGGTAGCTGTGATTT
66 GTTAGTATGTTTATGGTCATTTTAAAGAATTTAGGTAGCTGTGATTT
5490217 TTTTTTTTTTGGTCAATGTGCCTTTAGACACTGGATAATGATAATTTTGGGTAAAGAACTGAAAG
1 TTTTTTTTTTGGTCAATGTGCCTTTAGACACTGGATAATGATAATTTTGGGTAAAGAACTGAAAG
*
5490282 GTTAGTATGTTTATGGTCATTTTAAAGAATTTAGGTAGCTTTGATTT
66 GTTAGTATGTTTATGGTCATTTTAAAGAATTTAGGTAGCTGTGATTT
5490329 TTTTTTTTTTGG
1 TTTTTTTTTTGG
5490341 AGTATAGCCT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 121 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.46
Consensus pattern (112 bp):
TTTTTTTTTTGGTCAATGTGCCTTTAGACACTGGATAATGATAATTTTGGGTAAAGAACTGAAAG
GTTAGTATGTTTATGGTCATTTTAAAGAATTTAGGTAGCTGTGATTT
Found at i:5492124 original size:3 final size:3
Alignment explanation
Indices: 5492116--5492143 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5492106 ATTTTTCCTA
5492116 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5492144 TAAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5492921 original size:10 final size:10
Alignment explanation
Indices: 5492908--5492953 Score: 74
Period size: 10 Copynumber: 4.4 Consensus size: 10
5492898 AAAAAGGGGG
5492908 AAAAGAAAAA
1 AAAAGAAAAA
5492918 AAAAGAAAAA
1 AAAAGAAAAA
5492928 AAAAGAGAGAAA
1 AAAAGA-A-AAA
5492940 AAAAGAAAAA
1 AAAAGAAAAA
5492950 AAAA
1 AAAA
5492954 AGAGGAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 23 0.68
11 2 0.06
12 9 0.26
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:5492938 original size:24 final size:24
Alignment explanation
Indices: 5492911--5492966 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
5492901 AAGGGGGAAA
5492911 AGAAAAAAAAAGAAAAAAAAAGA-G
1 AGAAAAAAAAA-AAAAAAAAAGAGG
*
5492935 AGAAAAAAAGAAAAAAAAAAGAGG
1 AGAAAAAAAAAAAAAAAAAAGAGG
5492959 AGAAAAAA
1 AGAAAAAA
5492967 TTTTGGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AGAAAAAAAAAAAAAAAAAAGAGG
Found at i:5492940 original size:22 final size:23
Alignment explanation
Indices: 5492908--5492966 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
5492898 AAAAAGGGGG
5492908 AAAAGA-A-AAAAAAAG-AAAAA
1 AAAAGAGAGAAAAAAAGAAAAAA
5492928 AAAAGAGAGAAAAAAAGAAAAAA
1 AAAAGAGAGAAAAAAAGAAAAAA
5492951 AAAAGAGGAGAAAAAA
1 AAAAGA-GAGAAAAAA
5492967 TTTTGGTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 8 0.23
23 11 0.31
24 9 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAGAGAGAAAAAAAGAAAAAA
Found at i:5492964 original size:11 final size:11
Alignment explanation
Indices: 5492915--5492966 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
5492905 GGGAAAAGAA
*
5492915 AAAAAAAGA-A
1 AAAAAAAGAGG
5492925 AAAAAAAGAGAG
1 AAAAAAAGAG-G
**
5492937 AAAAAAAGAAA
1 AAAAAAAGAGG
5492948 AAAAAAAGAGG
1 AAAAAAAGAGG
5492959 AGAAAAAA
1 A-AAAAAA
5492967 TTTTGGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 9 0.26
11 10 0.29
12 15 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGG
Found at i:5496091 original size:48 final size:48
Alignment explanation
Indices: 5496038--5496370 Score: 278
Period size: 48 Copynumber: 6.8 Consensus size: 48
5496028 CCAAATTGAT
* * *
5496038 TTTTTTAAAAGTTTGTTACCTATTCTCATAGGAGCCTTTTCTAGATAGAT
1 TTTTTT-AAAGTTTGTTGCCTATTCTCATAGGAGCCTTTTCCAGATA-AA
* * * * * *
5496088 TTTTTTAAAATTTGTTACCTATTTTTATAGGAGCCCTTTT-TAGATAGAT
1 TTTTTTAAAGTTTGTTGCCTATTCTCATAGGAG-CCTTTTCCAGATA-AA
* **
5496137 TGTTTTTAAAGTTTGTTGCATAATT-TCATAAAAGCCTTTTCCAGATAAA
1 T-TTTTTAAAGTTTGTTGCCT-ATTCTCATAGGAGCCTTTTCCAGATAAA
* ** * * *
5496186 TTTTTTAAAGTTTGTTGCTTA-TCTTTGTAGGAGCTTTTTTCAAATAAA
1 TTTTTTAAAGTTTGTTGCCTATTC-TCATAGGAGCCTTTTCCAGATAAA
* * *
5496234 TTTTTTAAAGTTCGTTGCCTATTCTCATAAGAGCCCTTTCCAGATAAA
1 TTTTTTAAAGTTTGTTGCCTATTCTCATAGGAGCCTTTTCCAGATAAA
* * * * * * * *
5496282 TTTTTTATAGTTGGTTGCCTATTTTCATAGGATCTTTTTCCAAACAGA
1 TTTTTTAAAGTTTGTTGCCTATTCTCATAGGAGCCTTTTCCAGATAAA
* *
5496330 TTTTTTAAAGCTTGTTGTCTATAT-TCATAGGAGCCCTTTTC
1 TTTTTTAAAGTTTGTTGCCTAT-TCTCATAGGAG-CCTTTTC
5496371 AAAAGTTGAT
Statistics
Matches: 230, Mismatches: 44, Indels: 19
0.78 0.15 0.06
Matches are distributed among these distances:
46 1 0.00
47 1 0.00
48 135 0.59
49 51 0.22
50 39 0.17
51 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (48 bp):
TTTTTTAAAGTTTGTTGCCTATTCTCATAGGAGCCTTTTCCAGATAAA
Found at i:5496262 original size:96 final size:95
Alignment explanation
Indices: 5496038--5496370 Score: 330
Period size: 96 Copynumber: 3.4 Consensus size: 95
5496028 CCAAATTGAT
* * * * *
5496038 TTTTTTAAAAGTTTGTTACCTATTCTCATAGGAGCCTTTTCTAGATAGATTTTTTTAAAATTTGT
1 TTTTTT-AAAGTTTGTTGCCTATTCTCATAAGAGCCTTTTCCAGATA-AATTTTTTAAAGTTTGT
* * * *
5496103 TACCTATTTTTATAGGAGCCCTTTTT-AGATAGAT
64 TGCCTA-TTTTATAGGAG-CTTTTTTCAAATA-AA
* *
5496137 TGTTTTTAAAGTTTGTTGCATAATT-TCATAAAAGCCTTTTCCAGATAAATTTTTTAAAGTTTGT
1 T-TTTTTAAAGTTTGTTGCCT-ATTCTCATAAGAGCCTTTTCCAGATAAATTTTTTAAAGTTTGT
* *
5496201 TGCTTATCTTTGTAGGAGCTTTTTTCAAATAAA
64 TGCCTAT-TTTATAGGAGCTTTTTTCAAATAAA
* * * *
5496234 TTTTTTAAAGTTCGTTGCCTATTCTCATAAGAGCCCTTTCCAGATAAATTTTTTATAGTTGGTTG
1 TTTTTTAAAGTTTGTTGCCTATTCTCATAAGAGCCTTTTCCAGATAAATTTTTTAAAGTTTGTTG
* * * *
5496299 CCTATTTTCATAGGATCTTTTTCCAAACAGA
66 CCTATTTT-ATAGGAGCTTTTTTCAAATAAA
* * *
5496330 TTTTTTAAAGCTTGTTGTCTATAT-TCATAGGAGCCCTTTTC
1 TTTTTTAAAGTTTGTTGCCTAT-TCTCATAAGAG-CCTTTTC
5496371 AAAAGTTGAT
Statistics
Matches: 196, Mismatches: 30, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
95 6 0.03
96 102 0.52
97 16 0.08
98 32 0.16
99 32 0.16
100 8 0.04
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (95 bp):
TTTTTTAAAGTTTGTTGCCTATTCTCATAAGAGCCTTTTCCAGATAAATTTTTTAAAGTTTGTTG
CCTATTTTATAGGAGCTTTTTTCAAATAAA
Found at i:5498859 original size:15 final size:15
Alignment explanation
Indices: 5498820--5498862 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
5498810 AAAACCTAAA
5498820 AAAAATTGAAACCCC
1 AAAAATTGAAACCCC
*
5498835 -AAACTTGAAACCCC
1 AAAAATTGAAACCCC
*
5498849 AAAATTTGAAACCC
1 AAAAATTGAAACCC
5498863 TAAATTCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.49, C:0.28, G:0.07, T:0.16
Consensus pattern (15 bp):
AAAAATTGAAACCCC
Found at i:5498867 original size:14 final size:14
Alignment explanation
Indices: 5498820--5498868 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5498810 AAAACCTAAA
*
5498820 AAAAATTGAAACCC
1 AAAATTTGAAACCC
* *
5498834 CAAACTTGAAACCCC
1 AAAATTTGAAA-CCC
5498849 AAAATTTGAAACCC
1 AAAATTTGAAACCC
*
5498863 TAAATT
1 AAAATT
5498869 CCATGAAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.20
Consensus pattern (14 bp):
AAAATTTGAAACCC
Found at i:5498893 original size:14 final size:14
Alignment explanation
Indices: 5498874--5498956 Score: 70
Period size: 14 Copynumber: 6.1 Consensus size: 14
5498864 AAATTCCATG
5498874 AAACCTTAAATCCT
1 AAACCTTAAATCCT
*
5498888 AAACCTTAAACCCT
1 AAACCTTAAATCCT
*
5498902 AAATCC--AAACCCT
1 AAA-CCTTAAATCCT
5498915 AAACCTTAAA-CCTT
1 AAACCTTAAATCC-T
5498929 AAAACC-TAAAGTCC-
1 -AAACCTTAAA-TCCT
5498943 AAACCTT-AATCCT
1 AAACCTTAAATCCT
5498956 A
1 A
5498957 TGCTTAAACC
Statistics
Matches: 59, Mismatches: 1, Indels: 19
0.75 0.01 0.24
Matches are distributed among these distances:
12 5 0.08
13 20 0.34
14 25 0.42
15 7 0.12
16 2 0.03
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (14 bp):
AAACCTTAAATCCT
Found at i:5498925 original size:34 final size:33
Alignment explanation
Indices: 5498874--5498982 Score: 114
Period size: 34 Copynumber: 3.3 Consensus size: 33
5498864 AAATTCCATG
*
5498874 AAACCTTAAATCCTAAACCTTAAACCCTAAATCC
1 AAACCCTAAA-CCTAAACCTTAAACCCTAAATCC
*
5498908 AAACCCTAAACCTTAAACCTTAAAACCTAAAGTCC
1 AAACCCTAAACC-TAAACCTTAAACCCTAAA-TCC
* * **
5498943 AAACCTTAATCCT-ATGCTTAAACCCTAAA-CC
1 AAACCCTAAACCTAAACCTTAAACCCTAAATCC
*
5498974 AAACTCTAA
1 AAACCCTAA
5498983 CGTCATTCCC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 9 0.14
33 15 0.23
34 27 0.42
35 13 0.20
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (33 bp):
AAACCCTAAACCTAAACCTTAAACCCTAAATCC
Found at i:5498935 original size:8 final size:7
Alignment explanation
Indices: 5498874--5498931 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 7
5498864 AAATTCCATG
5498874 AAACCTT
1 AAACCTT
5498881 AAATCC-T
1 AAA-CCTT
5498888 AAACCTT
1 AAACCTT
*
5498895 AAACCCT
1 AAACCTT
5498902 AAATCC--
1 AAA-CCTT
*
5498908 AAACCCT
1 AAACCTT
5498915 AAACCTT
1 AAACCTT
5498922 AAACCTT
1 AAACCTT
5498929 AAA
1 AAA
5498932 ACCTAAAGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
5 2 0.05
6 5 0.11
7 33 0.75
8 4 0.09
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCTT
Found at i:5499471 original size:19 final size:20
Alignment explanation
Indices: 5499449--5499492 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5499439 AGAGAGAGAG
5499449 AAAAAAAGTT-ATTT-TTTT
1 AAAAAAAGTTGATTTGTTTT
*
5499467 AAAAAAATTTGATTTGTTTT
1 AAAAAAAGTTGATTTGTTTT
5499487 AAAAAA
1 AAAAAA
5499493 GAGAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 4 0.17
20 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (20 bp):
AAAAAAAGTTGATTTGTTTT
Found at i:5503812 original size:37 final size:36
Alignment explanation
Indices: 5503663--5503831 Score: 151
Period size: 37 Copynumber: 4.6 Consensus size: 36
5503653 ACATAAGGTA
* * *
5503663 GAATGCATATACTATCTATTAATATATGTATGAGATA
1 GAATGCATGTACTATCTATTAATATATGCATGA-ATG
* * * *
5503700 GAATGCATATACTATCTATTAACATGTACATGAAATG
1 GAATGCATGTACTATCTATTAATATATGCATG-AATG
* * **
5503737 AAATGCATGTAATA-CTATTAATAGGTGCATGGAATG
1 GAATGCATGTACTATCTATTAATATATGCAT-GAATG
**
5503773 GAATGTGTGTACTATCTATTAATATATGCATGAATTG
1 GAATGCATGTACTATCTATTAATATATGCATGAA-TG
* *
5503810 GAATACATGTACTTTCTTATTA
1 GAATGCATGTACTATC-TATTA
5503832 TTTCCAACTC
Statistics
Matches: 106, Mismatches: 21, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
36 30 0.28
37 70 0.66
38 6 0.06
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (36 bp):
GAATGCATGTACTATCTATTAATATATGCATGAATG
Found at i:5505910 original size:19 final size:19
Alignment explanation
Indices: 5505886--5505927 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
5505876 GTATGGATCA
5505886 GTTTGGGGTTTAGATTAGG
1 GTTTGGGGTTTAGATTAGG
* *
5505905 GTTTGGGGTTTGGCTTAGG
1 GTTTGGGGTTTAGATTAGG
5505924 GTTT
1 GTTT
5505928 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.02, G:0.43, T:0.45
Consensus pattern (19 bp):
GTTTGGGGTTTAGATTAGG
Found at i:5505954 original size:49 final size:49
Alignment explanation
Indices: 5505871--5505965 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 49
5505861 GAAGGTCAGT
*
5505871 TTAGGGTATGGATCAGTTTGGGGTTTAGATTAGGG-TTTGGGGTTTGGC
1 TTAGGGTATGGATCAGTTTGGGGTCTAGATTAGGGTTTTGGGGTTTGGC
* *
5505919 TTAGGGTTTAGGATTAGTTTGGGGTCTAGGA-TAGGGTTTTGGGGTTT
1 TTAGGGTAT-GGATCAGTTTGGGGTCTA-GATTAGGGTTTTGGGGTTT
5505966 TTTTTTAGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
48 8 0.20
49 21 0.51
50 12 0.29
ACGTcount: A:0.15, C:0.03, G:0.41, T:0.41
Consensus pattern (49 bp):
TTAGGGTATGGATCAGTTTGGGGTCTAGATTAGGGTTTTGGGGTTTGGC
Found at i:5505981 original size:7 final size:7
Alignment explanation
Indices: 5505969--5506047 Score: 74
Period size: 7 Copynumber: 11.7 Consensus size: 7
5505959 GGGGTTTTTT
5505969 TTTAGGG
1 TTTAGGG
5505976 TTTAGGG
1 TTTAGGG
*
5505983 TTT-GGT
1 TTTAGGG
*
5505989 TTTAAGG
1 TTTAGGG
*
5505996 TATAGGG
1 TTTAGGG
*
5506003 TATAGGG
1 TTTAGGG
*
5506010 -TTAGGT
1 TTTAGGG
5506016 TTTAGGG
1 TTTAGGG
5506023 TTTAGGG
1 TTTAGGG
*
5506030 -TTAAGG
1 TTTAGGG
*
5506036 TTTAAGG
1 TTTAGGG
5506043 TTTAG
1 TTTAG
5506048 TTTAAGGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
6 14 0.24
7 45 0.76
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:5505991 original size:20 final size:20
Alignment explanation
Indices: 5505968--5506025 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
5505958 TGGGGTTTTT
5505968 TTTTAGGGTTTAGGGTTTGG
1 TTTTAGGGTTTAGGGTTTGG
* * *
5505988 TTTTAAGGTATAGGGTATAGG
1 TTTTAGGGTTTAGGGT-TTGG
* *
5506009 -GTTAGGTTTTAGGGTTT
1 TTTTAGGGTTTAGGGTTT
5506026 AGGGTTAAGG
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 25 0.86
21 3 0.10
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (20 bp):
TTTTAGGGTTTAGGGTTTGG
Found at i:5505992 original size:13 final size:13
Alignment explanation
Indices: 5505970--5506024 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
5505960 GGGTTTTTTT
*
5505970 TTAGGGTTTAGGG
1 TTAGGTTTTAGGG
* *
5505983 TTTGGTTTTAAGG
1 TTAGGTTTTAGGG
* *
5505996 TATAGGGTATAGGG
1 T-TAGGTTTTAGGG
5506010 TTAGGTTTTAGGG
1 TTAGGTTTTAGGG
5506023 TT
1 TT
5506025 TAGGGTTAAG
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (13 bp):
TTAGGTTTTAGGG
Found at i:5506001 original size:27 final size:27
Alignment explanation
Indices: 5505971--5506045 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
5505961 GGTTTTTTTT
*
5505971 TAGGGTTTAGGGTTTGGTTTTAAGGTA
1 TAGGGTTTAGGGTTAGGTTTTAAGGTA
* * *
5505998 TAGGGTATAGGGTTAGGTTTTAGGGTT
1 TAGGGTTTAGGGTTAGGTTTTAAGGTA
* *
5506025 TAGGGTTAAGGTTTAAGGTTT
1 TAGGGTTTAGGGTT-AGGTTT
5506046 AGTTTAAGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 34 0.85
28 6 0.15
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (27 bp):
TAGGGTTTAGGGTTAGGTTTTAAGGTA
Found at i:5506028 original size:20 final size:20
Alignment explanation
Indices: 5505974--5506057 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
5505964 TTTTTTTTAG
*
5505974 GGTTTAGGGTTT-GGTTTTAA
1 GGTTTAGGGTTTAGG-GTTAA
* *
5505994 GGTATAGGGTATAGGGTT-A
1 GGTTTAGGGTTTAGGGTTAA
5506013 GGTTTTAGGGTTTAGGGTTAA
1 GG-TTTAGGGTTTAGGGTTAA
* *
5506034 GGTTTAAGGTTTA-GTTTAA
1 GGTTTAGGGTTTAGGGTTAA
5506053 GGTTT
1 GGTTT
5506058 CAAAGATGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.24
20 36 0.67
21 5 0.09
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTTAGGGTTTAGGGTTAA
Found at i:5506102 original size:18 final size:18
Alignment explanation
Indices: 5506081--5506145 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 18
5506071 GAGTTTGTTA
5506081 GGTGGTTTAGGTTTCATG
1 GGTGGTTTAGGTTTCATG
* *
5506099 GGTGGCTTAGGGTTTGGA-G
1 GGTGGTTTA-GGTTT-CATG
*
5506118 GGCGGTTTAGGATTTCATG
1 GGTGGTTTAGG-TTTCATG
5506137 GGTGGTTTA
1 GGTGGTTTA
5506146 CTGTTTGGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
18 11 0.30
19 25 0.68
20 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.43, T:0.38
Consensus pattern (18 bp):
GGTGGTTTAGGTTTCATG
Found at i:5506127 original size:19 final size:19
Alignment explanation
Indices: 5506105--5506170 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
5506095 CATGGGTGGC
*
5506105 TTAGGGTTTGGAGGGCGGT
1 TTAGGGTTTGGAGGGAGGT
* * *
5506124 TTAGGATTT-CATGGGTGGT
1 TTAGGGTTTGGA-GGGAGGT
**
5506143 TTACTGTTTGGAGGGAGGT
1 TTAGGGTTTGGAGGGAGGT
*
5506162 TTAGAGTTT
1 TTAGGGTTT
5506171 AAATGGTGGT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
18 1 0.03
19 33 0.94
20 1 0.03
ACGTcount: A:0.15, C:0.05, G:0.41, T:0.39
Consensus pattern (19 bp):
TTAGGGTTTGGAGGGAGGT
Found at i:5506152 original size:38 final size:37
Alignment explanation
Indices: 5506084--5506192 Score: 121
Period size: 38 Copynumber: 2.9 Consensus size: 37
5506074 TTTGTTAGGT
* *
5506084 GGTTTAGGTTTCATGGGTGGCTTAGGGTTTGGAGGGC
1 GGTTTAGGTTTCATGGGTGGCTTACGGTTTGGAGGGA
* *
5506121 GGTTTAGGATTTCATGGGTGGTTTACTGTTTGGAGGGA
1 GGTTTAGG-TTTCATGGGTGGCTTACGGTTTGGAGGGA
* * *
5506159 GGTTTAGAGTTTAAAT-GGTGGTTTAAGGTTTGGA
1 GGTTTAG-GTTT-CATGGGTGGCTTACGGTTTGGA
5506193 ATTAGGGGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 8 0.13
38 51 0.82
39 3 0.05
ACGTcount: A:0.17, C:0.05, G:0.40, T:0.39
Consensus pattern (37 bp):
GGTTTAGGTTTCATGGGTGGCTTACGGTTTGGAGGGA
Found at i:5506319 original size:29 final size:29
Alignment explanation
Indices: 5506283--5506345 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
5506273 AATACATGTG
5506283 ATAAAAATAAATACAAAAGTGCCATTGAT
1 ATAAAAATAAATACAAAAGTGCCATTGAT
5506312 ATAAAAATAAATACAAAAGTGCCATTGAT
1 ATAAAAATAAATACAAAAGTGCCATTGAT
5506341 A-AAAA
1 ATAAAA
5506346 TGTAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (29 bp):
ATAAAAATAAATACAAAAGTGCCATTGAT
Found at i:5506323 original size:61 final size:62
Alignment explanation
Indices: 5506205--5506324 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 62
5506195 TAGGGGTTTA
* *
5506205 ATGGGAAAATACATGTGATAAAAACAAATATAAAAGTGCCATTGATAAAAATGTAAATATTG
1 ATGGGAAAATACATGTGATAAAAACAAATACAAAAGTGCCATTGATAAAAATATAAATATTG
*
5506267 ATGGG-AAATACATGTGATAAAAATAAATACAAAAGTGCCATTGATATAAAA-ATAAATA
1 ATGGGAAAATACATGTGATAAAAACAAATACAAAAGTGCCATTGATA-AAAATATAAATA
5506325 CAAAAGTGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 45 0.83
62 9 0.17
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (62 bp):
ATGGGAAAATACATGTGATAAAAACAAATACAAAAGTGCCATTGATAAAAATATAAATATTG
Found at i:5509355 original size:3 final size:3
Alignment explanation
Indices: 5509347--5509377 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5509337 TTATATTTAC
*
5509347 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5509378 TTGCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5510212 original size:9 final size:9
Alignment explanation
Indices: 5510198--5510277 Score: 65
Period size: 9 Copynumber: 8.6 Consensus size: 9
5510188 TCATTTACAT
5510198 TTTTATTTA
1 TTTTATTTA
5510207 TTTTATTTA
1 TTTTATTTA
*
5510216 TTTAGATTT-
1 TTT-TATTTA
*
5510225 TCTTATTTA
1 TTTTATTTA
5510234 TTTTATATTTCA
1 -TTT-TATTT-A
*
5510246 TTTTATTTG
1 TTTTATTTA
5510255 TTTTATTCT-
1 TTTTATT-TA
*
5510264 TTTTATTTT
1 TTTTATTTA
5510273 TTTTA
1 TTTTA
5510278 GATTCTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
8 5 0.08
9 33 0.56
10 12 0.20
11 8 0.14
12 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:5510214 original size:21 final size:20
Alignment explanation
Indices: 5510177--5510215 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5510167 GATCGTAGGC
5510177 TTTTTTTTTTTTCATTTACA
1 TTTTTTTTTTTTCATTTACA
5510197 TTTTTATTTATTTT-ATTTA
1 TTTTT-TTT-TTTTCATTTA
5510216 TTTAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTTTTCATTTACA
Found at i:5510269 original size:18 final size:19
Alignment explanation
Indices: 5510227--5510288 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
5510217 TTAGATTTTC
* *
5510227 TTATTTATTTTATATTTCATT
1 TTATTTGTTTTA-A-TTCTTT
5510248 TTATTTGTTTT-ATTCTTT
1 TTATTTGTTTTAATTCTTT
*
5510266 TTATTTTTTTTAGATTCTTT
1 TTATTTGTTTTA-ATTCTTT
5510286 TTA
1 TTA
5510289 ATTTCATCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 15 0.42
19 1 0.03
20 10 0.28
21 10 0.28
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTTGTTTTAATTCTTT
Found at i:5517710 original size:21 final size:21
Alignment explanation
Indices: 5517686--5517728 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5517676 TAACAACTAG
5517686 GGATTTAATTTTGAAAATTTA
1 GGATTTAATTTTGAAAATTTA
5517707 GGATTTAATTTTGAAAATTTA
1 GGATTTAATTTTGAAAATTTA
5517728 G
1 G
5517729 TTAACACCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
GGATTTAATTTTGAAAATTTA
Found at i:5522396 original size:696 final size:693
Alignment explanation
Indices: 5520920--5522768 Score: 2732
Period size: 696 Copynumber: 2.7 Consensus size: 693
5520910 ATACTAAAAA
* * *
5520920 CTAAAAATGGAAGTAATGAGAGCAATTTATGAAATGTATAAAAACTATCATTTAATAAAAATTTA
1 CTAAAAATGAAAGTAATGAGAGTAATTTATGGAATGTATAAAAACTATCATTTAATAAAAATTTA
** * * *
5520985 ATTTTATTATCATTATCCCAGTAATTTC-AAA-TTCTTTTTCTTCATTTCTTTCAA-AAGTATTG
66 ATTTTATTATCATTATTACATTAATTTCAAAATTTCTTTTT-TTCATTTCTCTCAAGCA-TATTG
* * * *
5521047 AATACACATTATATTTAACTATTCTAATTATCAAGCATAAATTACTCTCAATTTAAGACACTATT
129 AATACACATTATACTTGACTATTTTAATTATCAAG-ATAAATTA-TCTCAATTTAAGATACTATT
* *
5521112 ACTCTTGATTTGGTTCTTAATTTATTTTTATTAAATTAATCATTTAAAAATAAAAATGTTAATAA
192 ACTCTTGATTTGGTTCTTAATTTA-TTTTAGTCAATTAATCATTTAAAAAT--AAATGTTAATAA
5521177 GAATCATTGAATGTGTTTTATAATAATGGAAATAAGATATTTTAAATTAAATTTATTTTACCATT
254 GAATCATTGAATGTGTTTTATAATAATGGAAATAAGATATTTTAAATTAAATTTATTTTACCATT
*** * *
5521242 AAATTCTAAATTTTAAATTTGAAGTGCATAATTAATTTTGAACACATGTTAATTTTTTAGATTGT
319 AAATTCTAAATTTTAAATTTGAAACACATAATTAATTTTGAACACATGTCAATTTTTTGGATTGT
* * * ** * *
5521307 CCAAATATAAAAAATGTAGACTATCCATATCAGACAATTTCCTTTTTTGTTAGAGGCTTAAACTT
384 CCACATATAGAAAATGTAGACTATCCACATCAGATTATTTCTTTTTTTGTTAGAGGCTTTAACTT
5521372 TTATATATTTATATAAGATTGATTTTTTTAAATTAAAAATGCATCAAATAAAATAAAAAAATGTA
449 TTATATATTTATATAAGATTGATTTTTTTAAATTAAAAATGCATCAAATAAAATAAAAAAATGTA
* * * * * * * *
5521437 TTTATTATATGACACATGACGTTTATTCATGATTGTATACATGTTAAACATAGAATATCCATAGT
514 TTTATTATATGACACAGGACATTTATTCATGATTGTATACATGTAAAAAATAAAACATCCACAAT
* * *
5521502 GAATCTTTTCTTTTCTGTTGAAGGCTTTGATTTTTATATATTTATATAAGATAAGATATAAGATT
579 GAATCTTTTCTTTTCTGTTGAAAGCTTTGATTTTTATAAATTTATATAAGATAAAATATAAGATT
* * * *
5521567 AATAAAGTGTTTAAGTTATTTACTAATTATTATAATAAGTTGACCTAAAT
644 AATAAAGTATTTAAGGTATTTAATAATTATTATAATAAATTGACCTAAAT
* * *
5521617 TTTAAAATGAAAGTAATGAGAGTAATTTATGGAATGTATAAAAACTATCATTTAATAAAATTTTA
1 CTAAAAATGAAAGTAATGAGAGTAATTTATGGAATGTATAAAAACTATCATTTAATAAAAATTTA
*
5521682 ATTTTATTATCATTATTACATTAATTTCAAAATTTCTTTTTTCCATTTCTCTCAAGCATATTGAA
66 ATTTTATTATCATTATTACATTAATTTCAAAATTTCTTTTTTTCATTTCTCTCAAGCATATTGAA
* * *
5521747 TACACATTATAGTTGACTATTTTAATTATCAAGTATAAATTATTCTCAATTTAAGATATTACTAC
131 TACACATTATACTTGACTATTTTAATTATCAAG-ATAAATTA-TCTCAATTTAAGATACTATTAC
*
5521812 TCTTGATTTGGTTCTTAATTTATTTTAGTCAATTAATTATTTAAAAATAAATGTTAATAAGAATC
194 TCTTGATTTGGTTCTTAATTTATTTTAGTCAATTAATCATTTAAAAATAAATGTTAATAAGAATC
*
5521877 ATTGAATGTGTTTTATATTAATGGAAATAAGATATTTTAAATTAAATTTATTTTACCATTAAATT
259 ATTGAATGTGTTTTATAATAATGGAAATAAGATATTTTAAATTAAATTTATTTTACCATTAAATT
5521942 CTAAATTTTAAATTTGAAACACATAATTAATTTTGAACACATGTCAATTTTTTGGATTGTCCACA
324 CTAAATTTTAAATTTGAAACACATAATTAATTTTGAACACATGTCAATTTTTTGGATTGTCCACA
* * *
5522007 TATCGAAAATGTAGACTATCTACATCAGATTATTTCTTTTTTTGTTGGA-GCTTTTAACTTTTAT
389 TATAGAAAATGTAGACTATCCACATCAGATTATTTCTTTTTTTGTTAGAGGC-TTTAACTTTTAT
*
5522071 ATATTTATATAAGATTGA-TTTTTTGAATTAAAAATGCATCAAATAAAATAAAATAAGATGTATT
453 ATATTTATATAAGATTGATTTTTTTAAATTAAAAATGCATCAAATAAAATAAAA-AA-ATGTATT
* *
5522135 TATTATATGACACAGGTCATTTATTCATGATTGTATACGTGTAAAAAATAAAACATCCACAATGA
516 TATTATATGACACAGGACATTTATTCATGATTGTATACATGTAAAAAATAAAACATCCACAATGA
*
5522200 ATCTTTTCTTTTTTGTTGAAAGCTTTGATTTTTATAAATTTATATAAGATAAAATATAAGATTAA
581 ATCTTTTCTTTTCTGTTGAAAGCTTTGATTTTTATAAATTTATATAAGATAAAATATAAGATTAA
*
5522265 T-AAGTTATTTAAGGTATTTAATATTTATTATAATAAATTGACCTAAAT
646 TAAAG-TATTTAAGGTATTTAATAATTATTATAATAAATTGACCTAAAT
* *
5522313 CTAAAAATAAAAGTAATAAGAGTAATTTATGGAATGTATAAAAACTATCATTTAATAAAAATTTA
1 CTAAAAATGAAAGTAATGAGAGTAATTTATGGAATGTATAAAAACTATCATTTAATAAAAATTTA
*
5522378 ATTTTATTATCATTATTACATTAATTTCAAAATCTCTTTTTTTTTTCATTTCTCTCAAGCATATT
66 ATTTTATTATCATTATTACATTAATTTCAAAA--T-TTCTTTTTTTCATTTCTCTCAAGCATATT
5522443 GAATACACATTATACTTGACTATTTTAATTATCAAG--------------TTTAAGATACTATTA
128 GAATACACATTATACTTGACTATTTTAATTATCAAGATAAATTATCTCAATTTAAGATACTATTA
* *
5522494 CTCTTGATTTGATTCTTAATTTATTTTAGTCAATTAGTCATTTAAAAATAAATGTTAATAAGAAT
193 CTCTTGATTTGGTTCTTAATTTATTTTAGTCAATTAATCATTTAAAAATAAATGTTAATAAGAAT
* *
5522559 C-TTGAATGTGTTTTATAATAATGGAAATAAGTTATTTTAAATTAAATTTATTTTACCATTAATT
258 CATTGAATGTGTTTTATAATAATGGAAATAAGATATTTTAAATTAAATTTATTTTACCATTAAAT
* * * *
5522623 TCTAAATTTTAAATTTGAAACATATAATTAATTTTGAATATATGTCAATTTTTTGGATTATCCAC
323 TCTAAATTTTAAATTTGAAACACATAATTAATTTTGAACACATGTCAATTTTTTGGATTGTCCAC
* * * ***
5522688 ATATTGAAAATATAGACTATCCACATCAGATTATTTCTTTTTTGGTTAGAGGCTTTGGTTTTTAT
388 ATATAGAAAATGTAGACTATCCACATCAGATTATTTCTTTTTTTGTTAGAGGCTTTAACTTTTAT
5522753 ATATTTATATAAGATT
453 ATATTTATATAAGATT
5522769 ACTCTTGATT
Statistics
Matches: 1054, Mismatches: 87, Indels: 37
0.89 0.07 0.03
Matches are distributed among these distances:
682 191 0.18
683 78 0.07
694 36 0.03
695 215 0.20
696 254 0.24
697 107 0.10
698 102 0.10
699 71 0.07
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (693 bp):
CTAAAAATGAAAGTAATGAGAGTAATTTATGGAATGTATAAAAACTATCATTTAATAAAAATTTA
ATTTTATTATCATTATTACATTAATTTCAAAATTTCTTTTTTTCATTTCTCTCAAGCATATTGAA
TACACATTATACTTGACTATTTTAATTATCAAGATAAATTATCTCAATTTAAGATACTATTACTC
TTGATTTGGTTCTTAATTTATTTTAGTCAATTAATCATTTAAAAATAAATGTTAATAAGAATCAT
TGAATGTGTTTTATAATAATGGAAATAAGATATTTTAAATTAAATTTATTTTACCATTAAATTCT
AAATTTTAAATTTGAAACACATAATTAATTTTGAACACATGTCAATTTTTTGGATTGTCCACATA
TAGAAAATGTAGACTATCCACATCAGATTATTTCTTTTTTTGTTAGAGGCTTTAACTTTTATATA
TTTATATAAGATTGATTTTTTTAAATTAAAAATGCATCAAATAAAATAAAAAAATGTATTTATTA
TATGACACAGGACATTTATTCATGATTGTATACATGTAAAAAATAAAACATCCACAATGAATCTT
TTCTTTTCTGTTGAAAGCTTTGATTTTTATAAATTTATATAAGATAAAATATAAGATTAATAAAG
TATTTAAGGTATTTAATAATTATTATAATAAATTGACCTAAAT
Found at i:5525827 original size:18 final size:19
Alignment explanation
Indices: 5525801--5525836 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5525791 TACATTTATA
*
5525801 TATTTAAAATAA-AATTTG
1 TATTAAAAATAATAATTTG
5525819 TATTAAAAATAATAATTT
1 TATTAAAAATAATAATTT
5525837 TATATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TATTAAAAATAATAATTTG
Found at i:5526335 original size:22 final size:22
Alignment explanation
Indices: 5526309--5526352 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5526299 TAGTAGATTT
5526309 AGATTTGATTTGTTATATAAGA
1 AGATTTGATTTGTTATATAAGA
5526331 AGATTTGATTTGTTATATAAGA
1 AGATTTGATTTGTTATATAAGA
5526353 TATGATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (22 bp):
AGATTTGATTTGTTATATAAGA
Found at i:5532434 original size:19 final size:21
Alignment explanation
Indices: 5532412--5532450 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
5532402 AGAAGAAAAA
5532412 AAAGTAAAAA-AAA-AAAAGC
1 AAAGTAAAAATAAATAAAAGC
5532431 AAAGTAAAAATAAATAAAAG
1 AAAGTAAAAATAAATAAAAG
5532451 AATAAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAGTAAAAATAAATAAAAGC
Found at i:5536746 original size:153 final size:153
Alignment explanation
Indices: 5536578--5537037 Score: 785
Period size: 153 Copynumber: 3.0 Consensus size: 153
5536568 TGAGGAAATG
* * *
5536578 AATGAAAAAGATGAGATGCGATAACAAGTCAAGTTTTTAGAAAGAATAAATGTCAAAAAACTTTA
1 AATGAAAAAGATGAGATACGATAACAAGTCGAGTTTTTAGAAAGAATAAATGTAAAAAAACTTTA
*
5536643 AAAGAGATGAGATTTAAGTCTAGTTCAGCTAGCATTAATGAGAATTAAACCTAGTTTAGTTGGCA
66 AAAGAGATGAGATTTAAGTCTAGTTTAGCTAGCATTAATGAGAATTAAACCTAGTTTAGTTGGCA
*
5536708 CCAATAAGAATTAAGCCTAGTTT
131 CCAATGAGAATTAAGCCTAGTTT
5536731 AATGAAAAAGATGAGATACGATAACAAGTCGAGTTTTTAGAAAGAATAAATGTAAAAAAACTTTA
1 AATGAAAAAGATGAGATACGATAACAAGTCGAGTTTTTAGAAAGAATAAATGTAAAAAAACTTTA
* *
5536796 AAAGAAATGAGATTGAAGTCTAGTTTAGCTAGCATTAATGAGAATTAAACCTAGTTTAGTTGGCA
66 AAAGAGATGAGATTTAAGTCTAGTTTAGCTAGCATTAATGAGAATTAAACCTAGTTTAGTTGGCA
5536861 CCAATGAGAATTAAGCCTAGTTT
131 CCAATGAGAATTAAGCCTAGTTT
* *
5536884 AATGAAAAAGATGAGATATGATAACAAATCGAGTTTTTAGAAAGAATAAATGTAAAAAAACTTTA
1 AATGAAAAAGATGAGATACGATAACAAGTCGAGTTTTTAGAAAGAATAAATGTAAAAAAACTTTA
* * * * * *
5536949 AAAGAGACGAGATTTAAGTCCAATTTAGCTAGCATTAATAAGAATTAAACTTAATTTAGTTGGCA
66 AAAGAGATGAGATTTAAGTCTAGTTTAGCTAGCATTAATGAGAATTAAACCTAGTTTAGTTGGCA
5537014 CCAATGAGAATTAAGCCTAGTTT
131 CCAATGAGAATTAAGCCTAGTTT
5537037 A
1 A
5537038 GCTGGCACCA
Statistics
Matches: 290, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
153 290 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (153 bp):
AATGAAAAAGATGAGATACGATAACAAGTCGAGTTTTTAGAAAGAATAAATGTAAAAAAACTTTA
AAAGAGATGAGATTTAAGTCTAGTTTAGCTAGCATTAATGAGAATTAAACCTAGTTTAGTTGGCA
CCAATGAGAATTAAGCCTAGTTT
Found at i:5536850 original size:31 final size:31
Alignment explanation
Indices: 5536815--5536884 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
5536805 AGATTGAAGT
**
5536815 CTAGTTTAGCTAGCATTAATGAGAATTAAAC
1 CTAGTTTAGCTAGCACCAATGAGAATTAAAC
* * *
5536846 CTAGTTTAGTTGGCACCAATGAGAATTAAGC
1 CTAGTTTAGCTAGCACCAATGAGAATTAAAC
5536877 CTAGTTTA
1 CTAGTTTA
5536885 ATGAAAAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (31 bp):
CTAGTTTAGCTAGCACCAATGAGAATTAAAC
Found at i:5537024 original size:31 final size:31
Alignment explanation
Indices: 5536957--5537199 Score: 202
Period size: 31 Copynumber: 7.8 Consensus size: 31
5536947 TAAAAGAGAC
* * **
5536957 GAGATTTAAGTCC-AATTTAGCTAGCATTAAT
1 GAGAATTAAG-CCTAATTTAGCTGGCACCAAT
* * * *
5536988 AAGAATTAAACTTAATTTAGTTGGCACCAAT
1 GAGAATTAAGCCTAATTTAGCTGGCACCAAT
*
5537019 GAGAATTAAGCCTAGTTTAGCTGGCACCAAT
1 GAGAATTAAGCCTAATTTAGCTGGCACCAAT
* * * * ***
5537050 GAAAATTAAACCTAGTTTAGTTAATACCAAT
1 GAGAATTAAGCCTAATTTAGCTGGCACCAAT
* *
5537081 GAGAATTAAGCCTAATTTAGCTGACACCGAT
1 GAGAATTAAGCCTAATTTAGCTGGCACCAAT
* **
5537112 GAGAATTAAGCCTAATTTAGTTGGCATTAAT
1 GAGAATTAAGCCTAATTTAGCTGGCACCAAT
* * * *
5537143 GGGATTTAAG-CTCAATTTAACTGACACCAAT
1 GAGAATTAAGCCT-AATTTAGCTGGCACCAAT
* * *
5537174 GAGATTTAAACTTAATTTAGCTGGCA
1 GAGAATTAAGCCTAATTTAGCTGGCA
5537200 TCGAGATTTT
Statistics
Matches: 166, Mismatches: 43, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
30 3 0.02
31 162 0.98
32 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (31 bp):
GAGAATTAAGCCTAATTTAGCTGGCACCAAT
Found at i:5537060 original size:62 final size:62
Alignment explanation
Indices: 5536989--5537199 Score: 244
Period size: 62 Copynumber: 3.4 Consensus size: 62
5536979 AGCATTAATA
* * *
5536989 AGAATTAAACTTAATTTAGTTGGCACCAATGAGAATTAAGCCTAGTTTAGCTGGCACCAATG
1 AGAATTAAACCTAATTTAGTTGGCACCAATGAGAATTAAGCCTAATTTAGCTGACACCAATG
* * *** *
5537051 AAAATTAAACCTAGTTTAGTTAATACCAATGAGAATTAAGCCTAATTTAGCTGACACCGATG
1 AGAATTAAACCTAATTTAGTTGGCACCAATGAGAATTAAGCCTAATTTAGCTGACACCAATG
* ** * * *
5537113 AGAATTAAGCCTAATTTAGTTGGCATTAATGGGATTTAAG-CTCAATTTAACTGACACCAATG
1 AGAATTAAACCTAATTTAGTTGGCACCAATGAGAATTAAGCCT-AATTTAGCTGACACCAATG
* * *
5537175 AGATTTAAACTTAATTTAGCTGGCA
1 AGAATTAAACCTAATTTAGTTGGCA
5537200 TCGAGATTTT
Statistics
Matches: 123, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
61 2 0.02
62 121 0.98
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (62 bp):
AGAATTAAACCTAATTTAGTTGGCACCAATGAGAATTAAGCCTAATTTAGCTGACACCAATG
Found at i:5537242 original size:93 final size:94
Alignment explanation
Indices: 5536989--5537252 Score: 212
Period size: 93 Copynumber: 2.8 Consensus size: 94
5536979 AGCATTAATA
* * * * * * * **
5536989 AGAATTAAACTTAATTTAGTTGGCACCAATGAGAATTAAGCCTAGTTTAGCTGGCACCAATGA-A
1 AGAATTAAACCTAATTTAGCTGACACCGATGAGAATTAAGCCTAATTAAGTTGGCATTAATGAGA
** * * * ** * *
5537053 AATTAAACCTAGTTTAGTTAATACCAATG
66 TTTTAAGCCCAATTTAACTGACACCAATG
* * *
5537082 AGAATTAAGCCTAATTTAGCTGACACCGATGAGAATTAAGCCTAATTTAGTTGGCATTAATGGGA
1 AGAATTAAACCTAATTTAGCTGACACCGATGAGAATTAAGCCTAATTAAGTTGGCATTAATGAGA
*
5537147 -TTTAAGCTCAATTTAACTGACACCAATG
66 TTTTAAGCCCAATTTAACTGACACCAATG
* * * * *** *
5537175 AGATTTAAACTTAATTTAGCTGGCATCGA-GATTTTTAAGTCC-AATTAAGTTGGCATTAGTTGA
1 AGAATTAAACCTAATTTAGCTGACACCGATGAGAATTAAG-CCTAATTAAGTTGGCATTA-ATGA
5537238 GATTTTAAGCCCAAT
64 GATTTTAAGCCCAAT
5537253 AAAGTTGGCA
Statistics
Matches: 136, Mismatches: 31, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
92 22 0.16
93 102 0.75
94 12 0.09
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (94 bp):
AGAATTAAACCTAATTTAGCTGACACCGATGAGAATTAAGCCTAATTAAGTTGGCATTAATGAGA
TTTTAAGCCCAATTTAACTGACACCAATG
Found at i:5537252 original size:33 final size:34
Alignment explanation
Indices: 5537202--5537268 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
5537192 AGCTGGCATC
* * *
5537202 GAGATTTTTAAGTCCAATTAAGTTGGCATTAGTT
1 GAGATTTTTAAGCCCAATAAAGTTGGCACTAGTT
5537236 GAGA-TTTTAAGCCCAATAAAGTTGGCACTAGTT
1 GAGATTTTTAAGCCCAATAAAGTTGGCACTAGTT
5537269 AAGGAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (34 bp):
GAGATTTTTAAGCCCAATAAAGTTGGCACTAGTT
Found at i:5537804 original size:22 final size:22
Alignment explanation
Indices: 5537761--5537808 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5537751 TTTAAAAAAT
*
5537761 GATTTGTAAGGCCTTTAGGTAA
1 GATTTGTAAGGCCTTTAAGTAA
*
5537783 GATTTGTAA-GTCTTTCAAGTAA
1 GATTTGTAAGGCCTTT-AAGTAA
5537805 -ATTT
1 GATTT
5537809 TTAAAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (22 bp):
GATTTGTAAGGCCTTTAAGTAA
Found at i:5539628 original size:248 final size:248
Alignment explanation
Indices: 5539190--5539688 Score: 971
Period size: 248 Copynumber: 2.0 Consensus size: 248
5539180 AGAGGAACCT
5539190 CAGTGAAAAATAGTAAAAAAATGAAAAGAAAGGGGGAGTCTTTTGGGGTTTTTGGTTTGGAGTTT
1 CAGTGAAAAATAGTAAAAAAATGAAAAGAAAGGGGGAGTCTTTTGGGGTTTTTGGTTTGGAGTTT
5539255 CGAGGTCGAGTTTATGGAAGGAAGAAAGAAACGGGTAAAAGAAAGGCATAGTAAAAAATAGTGGC
66 CGAGGTCGAGTTTATGGAAGGAAGAAAGAAACGGGTAAAAGAAAGGCATAGTAAAAAATAGTGGC
5539320 GTTTGAGCGATGGCGGGGAAGATTTTGGGGTGTTCATGCCGTGGTTTTAGGGGTAGGTCTAAGCT
131 GTTTGAGCGATGGCGGGGAAGATTTTGGGGTGTTCATGCCGTGGTTTTAGGGGTAGGTCTAAGCT
5539385 GTTGTAAAGCTATTTGCGAAAAACCAAGGCTGGATTTGAGAATAGGGGGTTTG
196 GTTGTAAAGCTATTTGCGAAAAACCAAGGCTGGATTTGAGAATAGGGGGTTTG
5539438 CAGTGAAAAATAGTAAAAAAATGAAAAGAAAGGGGGAGTCTTTTGGGGTTTTTGGTTTGGAGTTT
1 CAGTGAAAAATAGTAAAAAAATGAAAAGAAAGGGGGAGTCTTTTGGGGTTTTTGGTTTGGAGTTT
*
5539503 CGAGGTCGAGTTTATGGAAGGAAGAAAGAAACGGGTAAAAGAAGGGCATAGTAAAAAATAGTGGC
66 CGAGGTCGAGTTTATGGAAGGAAGAAAGAAACGGGTAAAAGAAAGGCATAGTAAAAAATAGTGGC
*
5539568 GTTTGAGCGATGGCGGGGGAGATTTTGGGGTGTTCATGCCGTGGTTTTAGGGGTAGGTCTAAGCT
131 GTTTGAGCGATGGCGGGGAAGATTTTGGGGTGTTCATGCCGTGGTTTTAGGGGTAGGTCTAAGCT
*
5539633 GTTGTAAGGCTATTTGCGAAAAACCAAGGCTGGATTTGAGAATAGGGGGTTTG
196 GTTGTAAAGCTATTTGCGAAAAACCAAGGCTGGATTTGAGAATAGGGGGTTTG
5539686 CAG
1 CAG
5539689 GAGCCTTCAA
Statistics
Matches: 248, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 248 1.00
ACGTcount: A:0.31, C:0.08, G:0.35, T:0.26
Consensus pattern (248 bp):
CAGTGAAAAATAGTAAAAAAATGAAAAGAAAGGGGGAGTCTTTTGGGGTTTTTGGTTTGGAGTTT
CGAGGTCGAGTTTATGGAAGGAAGAAAGAAACGGGTAAAAGAAAGGCATAGTAAAAAATAGTGGC
GTTTGAGCGATGGCGGGGAAGATTTTGGGGTGTTCATGCCGTGGTTTTAGGGGTAGGTCTAAGCT
GTTGTAAAGCTATTTGCGAAAAACCAAGGCTGGATTTGAGAATAGGGGGTTTG
Found at i:5541078 original size:19 final size:19
Alignment explanation
Indices: 5541049--5541085 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5541039 ATTTTTTTAG
5541049 AAATAAAAAATAATATTTTT
1 AAATAAAAAATAAT-TTTTT
5541069 AAAT-AAAAATAATTTTT
1 AAATAAAAAATAATTTTT
5541086 GAGACTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAAAAAATAATTTTTT
Found at i:5542452 original size:15 final size:15
Alignment explanation
Indices: 5542432--5542475 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
5542422 TTTATATAGT
5542432 TTAATATATATACTA
1 TTAATATATATACTA
5542447 TTAATATAGTTTATACTA
1 TTAATATA---TATACTA
5542465 TTAATAT-TATA
1 TTAATATATATA
5542476 AGGTAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
18 14 0.54
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (15 bp):
TTAATATATATACTA
Found at i:5548284 original size:19 final size:20
Alignment explanation
Indices: 5548257--5548297 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5548247 TTTTTTGCTT
5548257 AAAACGCCTTTAATA-TTCC
1 AAAACGCCTTTAATATTTCC
*
5548276 AAAATGCCTTTAATATTTCC
1 AAAACGCCTTTAATATTTCC
5548296 AA
1 AA
5548298 TGATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAACGCCTTTAATATTTCC
Found at i:5551745 original size:12 final size:12
Alignment explanation
Indices: 5551728--5551752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5551718 TCGTACAAAA
5551728 ACACCATTCAGC
1 ACACCATTCAGC
5551740 ACACCATTCAGC
1 ACACCATTCAGC
5551752 A
1 A
5551753 ATGTGCTAAG
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:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (12 bp):
ACACCATTCAGC
Found at i:5553006 original size:51 final size:51
Alignment explanation
Indices: 5552910--5553014 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
5552900 CTTTTTATAA
* *
5552910 CCATCGTGCTATATTAAAGGTATTTATAATAAAAGACGTCTTTAATAAT-C
1 CCATCGTGCTATATTAAAGGCATTTATAATAAAAGACGCCTTTAATAATGC
* *
5552960 CCATCGTAG-TATATTGAAGGCATTTTATAGTAGAAA-ACGCCTTTAATAATGC
1 CCATCGT-GCTATATTAAAGGCA-TTTATAATA-AAAGACGCCTTTAATAATGC
5553012 CCA
1 CCA
5553015 AAATTTTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
50 18 0.38
51 22 0.47
52 7 0.15
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (51 bp):
CCATCGTGCTATATTAAAGGCATTTATAATAAAAGACGCCTTTAATAATGC
Found at i:5562058 original size:29 final size:29
Alignment explanation
Indices: 5561999--5562058 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
5561989 TAAGTTTAGT
* * *
5561999 AAAGTATTTAATACAGTATTTGAATTTTA
1 AAAGTATTTAATACAGTATTTAAACTATA
* **
5562028 AAAGTTTTTAATATGGTATTTAAACTATA
1 AAAGTATTTAATACAGTATTTAAACTATA
5562057 AA
1 AA
5562059 TATGTTAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (29 bp):
AAAGTATTTAATACAGTATTTAAACTATA
Found at i:5563377 original size:22 final size:22
Alignment explanation
Indices: 5563350--5563395 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5563340 AAAATTTTTT
*
5563350 TAAAAACAATTAGATATATTTAG
1 TAAAAA-AATGAGATATATTTAG
* *
5563373 TAAAAAAATGAGGTGTATTTAG
1 TAAAAAAATGAGATATATTTAG
5563395 T
1 T
5563396 TCTGTCCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (22 bp):
TAAAAAAATGAGATATATTTAG
Found at i:5567695 original size:24 final size:23
Alignment explanation
Indices: 5567657--5567702 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
5567647 CTCAACTTTC
*
5567657 TCATTTGTTATTTTTTTTATTTTG
1 TCATTTGTTAGTTTTTTT-TTTTG
*
5567681 TCATTTTTTAGTTTTTTTTTTT
1 TCATTTGTTAGTTTTTTTTTTT
5567703 AAATTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (23 bp):
TCATTTGTTAGTTTTTTTTTTTG
Found at i:5568480 original size:26 final size:26
Alignment explanation
Indices: 5568437--5568486 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5568427 CACAATGAGC
*
5568437 TTTTTTTTTTTTTGTTCACTTTTAAA
1 TTTTTTTTTCTTTGTTCACTTTTAAA
*
5568463 TTTTTTTTCTCTTT-TTCATTTTTA
1 TTTTTTTT-TCTTTGTTCACTTTTA
5568487 GTTTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCTTTGTTCACTTTTAAA
Found at i:5568492 original size:26 final size:25
Alignment explanation
Indices: 5568437--5568506 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 25
5568427 CACAATGAGC
5568437 TTTTTTTTTT-TTTGTTCACTTTTAAA
1 TTTTTTTTTTCTTT-TTCACTTTT-AA
* * *
5568463 TTTTTTTTCTCTTTTTCATTTTTAG
1 TTTTTTTTTTCTTTTTCACTTTTAA
5568488 TTTTTCATTTTATCTTTTT
1 TTTTT--TTTT-TCTTTTT
5568507 AATAAAAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 6 0.17
26 17 0.47
27 6 0.17
28 7 0.19
ACGTcount: A:0.11, C:0.10, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTTTTTTTTCTTTTTCACTTTTAA
Found at i:5568959 original size:12 final size:12
Alignment explanation
Indices: 5568919--5568959 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5568909 TTTATTGCTA
*
5568919 TTTTTCTTTCTT
1 TTTTTCTTTTTT
* *
5568931 TCTTTCTTTTTC
1 TTTTTCTTTTTT
5568943 TTTTTCTTTTTT
1 TTTTTCTTTTTT
5568955 TTTTT
1 TTTTT
5568960 TCGTTTACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:5577660 original size:64 final size:64
Alignment explanation
Indices: 5577559--5577678 Score: 222
Period size: 64 Copynumber: 1.9 Consensus size: 64
5577549 TTCTATACAA
*
5577559 CTGTAATTTACACCTAACTCACAAAGTAAACCAATTTTTATCTCCTTTCTTGATTTTATATAAC
1 CTGTAATTTACACCTAACTCACAAAGTAAACCAATTTTTATCTCCATTCTTGATTTTATATAAC
*
5577623 CTGTAATTTACACCTAACTCATAAAGTAAACCAATTTTTATCTCCATTCTTGATTT
1 CTGTAATTTACACCTAACTCACAAAGTAAACCAATTTTTATCTCCATTCTTGATTT
5577679 CAAACCAGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (64 bp):
CTGTAATTTACACCTAACTCACAAAGTAAACCAATTTTTATCTCCATTCTTGATTTTATATAAC
Found at i:5582296 original size:22 final size:21
Alignment explanation
Indices: 5582250--5582296 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
5582240 AAATCGAATT
5582250 ATATATTTTTATTAGTTTTAAA
1 ATATATTTTTATTA-TTTTAAA
5582272 ATATATTTTATATT-TTTATAAA
1 ATATATTTT-TATTATTT-TAAA
5582294 ATA
1 ATA
5582297 AAATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.13
22 16 0.70
23 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATATTTTTATTATTTTAAA
Found at i:5583329 original size:18 final size:18
Alignment explanation
Indices: 5583306--5583340 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5583296 ACTGAAACTG
5583306 CAAAAG-CAAAAGTAAAAA
1 CAAAAGCCAAAAG-AAAAA
5583324 CAAAAGCCAAAAGAAAA
1 CAAAAGCCAAAAGAAAA
5583341 GATAAGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.71, C:0.14, G:0.11, T:0.03
Consensus pattern (18 bp):
CAAAAGCCAAAAGAAAAA
Found at i:5590810 original size:1 final size:1
Alignment explanation
Indices: 5590804--5590828 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5590794 AAAAGCCATT
5590804 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
5590829 GCGGGCCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:5597702 original size:19 final size:19
Alignment explanation
Indices: 5597680--5597729 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5597670 TTTTTGACAT
*
5597680 TTTTTATTATTTTATAAAA
1 TTTTTATTATATTATAAAA
** *
5597699 TTTTTAAAAAATTATAAAA
1 TTTTTATTATATTATAAAA
*
5597718 ATTTTATTATAT
1 TTTTTATTATAT
5597730 ATTTCATTAT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTATTATATTATAAAA
Found at i:5597705 original size:201 final size:203
Alignment explanation
Indices: 5597333--5597705 Score: 443
Period size: 202 Copynumber: 1.8 Consensus size: 203
5597323 GGAAAAATTT
* * * * * **
5597333 TTTTTATTATATTGAAGTTTTTATATAAATATTCCAATGCATTGGTAATATTTAAAAAAATCTTC
1 TTTTTATTATATTAAAATTTTTATATAAATATTCAAATACACTGGTAATATTTAAAAAAAAATTC
* * * * *
5597398 TCACCTAGGGATTTCGTAAAGCATCACTACTTAAATACTTTTAAAATCCCATCATTGGATAAAAT
66 TCACATAGAGATTTCGTAAAGAATCACTACTGAAATACCTTTAAAATCCCATCATTGGATAAAAT
* * * ** *
5597463 TTCATTTTTTTCTCATTTTTATTGCTTTATTTTAGTTTTTAATTAATTTTTATTTATTATTAACG
131 TTCACTTTTTTCACATTTTTATTACTTTATTAAAATTTTTAATTAATTTTTATTTATTATTAACG
5597528 AAAGAAAA
196 AAAGAAAA
* *
5597536 TTTTTATTGTATTAAAATTTTT-TATAAATACTT-AAATACACTGGTAGTATTTAAAAAAAAATT
1 TTTTTATTATATTAAAATTTTTATATAAATA-TTCAAATACACTGGTAATATTTAAAAAAAAATT
* * *
5597599 TTCACATAGAGATTTCGT-AAGAATCACTACTCGAAATACCTTT-GAATCTCATCATTGGATAAA
65 CTCACATAGAGATTTCGTAAAGAATCACTACT-GAAATACCTTTAAAATCCCATCATTGGATAAA
* *
5597662 ATTTTC-CTTTTTTGACATTTTTTATTATTTTA-TAAAATTTTTAA
129 A-TTTCACTTTTTTCACA-TTTTTATTACTTTATTAAAATTTTTAA
5597706 AAAATTATAA
Statistics
Matches: 141, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
201 48 0.34
202 72 0.51
203 21 0.15
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (203 bp):
TTTTTATTATATTAAAATTTTTATATAAATATTCAAATACACTGGTAATATTTAAAAAAAAATTC
TCACATAGAGATTTCGTAAAGAATCACTACTGAAATACCTTTAAAATCCCATCATTGGATAAAAT
TTCACTTTTTTCACATTTTTATTACTTTATTAAAATTTTTAATTAATTTTTATTTATTATTAACG
AAAGAAAA
Found at i:5597925 original size:12 final size:12
Alignment explanation
Indices: 5597908--5597936 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5597898 AACCGGACCA
5597908 ATCAATGATTCG
1 ATCAATGATTCG
5597920 ATCAATGATTCG
1 ATCAATGATTCG
5597932 ATCAA
1 ATCAA
5597937 CACCTGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (12 bp):
ATCAATGATTCG
Found at i:5598141 original size:26 final size:26
Alignment explanation
Indices: 5598105--5598174 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
5598095 TCCTTATGGC
5598105 TCAAAACGACATCATTTTAATCTTTA
1 TCAAAACGACATCATTTTAATCTTTA
*
5598131 TCAAAACGACATCGTTTTAATCTTTA
1 TCAAAACGACATCATTTTAATCTTTA
* *
5598157 TTAAAACGACGTCATTTT
1 TCAAAACGACATCATTTT
5598175 GGTTCCAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (26 bp):
TCAAAACGACATCATTTTAATCTTTA
Found at i:5598719 original size:23 final size:23
Alignment explanation
Indices: 5598689--5598733 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5598679 TAGAGCTTTC
5598689 TGGGATTCAAATCCCATATTTTT
1 TGGGATTCAAATCCCATATTTTT
*
5598712 TGGGATTCGAATCCCATATTTT
1 TGGGATTCAAATCCCATATTTT
5598734 CCATTGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (23 bp):
TGGGATTCAAATCCCATATTTTT
Found at i:5598903 original size:27 final size:27
Alignment explanation
Indices: 5598872--5598926 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
5598862 GAAGAAGAAG
5598872 AAAAAAGAAAGA-AAGAAAAAAAATAAT
1 AAAAAAGAAA-ATAAGAAAAAAAATAAT
* * *
5598899 AAAAAATAAAATAATAAAAATAATAAT
1 AAAAAAGAAAATAAGAAAAAAAATAAT
5598926 A
1 A
5598927 CTAAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (27 bp):
AAAAAAGAAAATAAGAAAAAAAATAAT
Found at i:5598909 original size:15 final size:15
Alignment explanation
Indices: 5598887--5598932 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
5598877 AGAAAGAAAG
5598887 AAAA-AAAATAATAA
1 AAAATAAAATAATAA
5598901 AAAATAAAATAAT-A
1 AAAATAAAATAATAA
*
5598915 AAAATAATAATACTAA
1 AAAATAA-AATAATAA
5598931 AA
1 AA
5598933 CAAAATGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 12 0.43
15 13 0.46
16 3 0.11
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAATAA
Found at i:5599289 original size:48 final size:47
Alignment explanation
Indices: 5599228--5599517 Score: 286
Period size: 48 Copynumber: 6.1 Consensus size: 47
5599218 AAGGCTTCTT
* *
5599228 TCAGCATAGGCTCAACAACTTTAAAACTTCATCTTGAAAAGGCTCCTC
1 TCAGCAGA-GCTCAACAACTTTAAAACTTCATCTTGAAAAAGCTCCTC
* * * * *
5599276 TTAGCAAATGCTCAACAGCTTTAAAACTTCACCTTGAAAAAACTCCTC
1 TCAGCAGA-GCTCAACAACTTTAAAACTTCATCTTGAAAAAGCTCCTC
* ** *
5599324 TAAGCAGAGACTCAACAACTTTAAAAAAATCATCTTGAAAAAGCTCATC
1 TCAGCAGAG-CTCAACAACTTT-AAAACTTCATCTTGAAAAAGCTCCTC
* * *
5599373 TCAGTAGAGGCTCAACAACTTTAAAACCTCACCTTGAAAAAGCTCCTC
1 TCAGCAGA-GCTCAACAACTTTAAAACTTCATCTTGAAAAAGCTCCTC
* * **
5599421 TTAGTAGAATTTCAACAACTTTAAAA--T-AT-TTGAAAAAGGCTCCTC
1 TCAGCAG-AGCTCAACAACTTTAAAACTTCATCTTGAAAAA-GCTCCTC
5599466 TCAGCAGAGACTCAACAACTTTAAAA-TATCATCTTGAAAAAG-TCCTC
1 TCAGCAGAG-CTCAACAACTTTAAAACT-TCATCTTGAAAAAGCTCCTC
5599513 GTCAG
1 -TCAG
5599518 TCAACTGCTT
Statistics
Matches: 202, Mismatches: 29, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
44 9 0.04
45 28 0.14
46 1 0.00
47 7 0.03
48 108 0.53
49 48 0.24
50 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (47 bp):
TCAGCAGAGCTCAACAACTTTAAAACTTCATCTTGAAAAAGCTCCTC
Found at i:5599386 original size:97 final size:96
Alignment explanation
Indices: 5599238--5599506 Score: 316
Period size: 97 Copynumber: 2.8 Consensus size: 96
5599228 TCAGCATAGG
** * * * * *
5599238 CTCAACAACTTTAAAACTTCATCTTGAAAAGGCTCCTCTTAGCAAATGCTCAACAGCTTTAAAAC
1 CTCAACAACTTTAAAAAATCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAC
5599303 TTCACCTTGAAAAAACTCCTCTAAGCAGAGA-
66 TTCACCTTGAAAAAACTCCTCTAAGCAGA-AT
* *
5599334 CTCAACAACTTTAAAAAAATCATCTTGAAAAAGCTCATCTCAGTAGAGGCTCAACAACTTTAAAA
1 CTCAACAACTTT-AAAAAATCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
* * * *
5599399 CCTCACCTTGAAAAAGCTCCTCTTAGTAGAAT
65 CTTCACCTTGAAAAAACTCCTCTAAGCAGAAT
* *
5599431 TTCAACAACTTT--AAAAT-AT-TTGAAAAAGGCTCCTCTCAGCAGAGACTCAACAACTTTAAAA
1 CTCAACAACTTTAAAAAATCATCTTGAAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
*
5599492 -TATCATCTTGAAAAA
65 CT-TCACCTTGAAAAA
5599507 GTCCTCGTCA
Statistics
Matches: 150, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
92 8 0.05
93 44 0.29
94 5 0.03
96 13 0.09
97 80 0.53
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.26
Consensus pattern (96 bp):
CTCAACAACTTTAAAAAATCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAC
TTCACCTTGAAAAAACTCCTCTAAGCAGAAT
Found at i:5599443 original size:145 final size:141
Alignment explanation
Indices: 5599235--5599507 Score: 388
Period size: 145 Copynumber: 1.9 Consensus size: 141
5599225 CTTTCAGCAT
* * * *
5599235 AGGCTCAACAACTTTAAAACTTCATCTTGAAAAGGCTCCTCTTAGCAAATGCTCAACAGCTTTAA
1 AGGCTCAACAACTTTAAAACCTCACCTTGAAAAAGCTCCTCTTAGCAAATGCTCAACAACTTTAA
5599300 AACTTCACCTTGAAAAA-ACTCCTCTAAGCAGAGACTCAACAACTTTAAAAAAATCATCTTGAAA
66 AA--T-A-CTTGAAAAAGACTCCTCTAAGCAGAGACTCAACAACTTT-AAAAAATCATCTTGAAA
5599364 AAGCTCATCTCAGTAG
126 AAGCTCATCTCAGTAG
* *
5599380 AGGCTCAACAACTTTAAAACCTCACCTTGAAAAAGCTCCTCTTAGTAGAAT-TTCAACAACTTTA
1 AGGCTCAACAACTTTAAAACCTCACCTTGAAAAAGCTCCTCTTAGCA-AATGCTCAACAACTTTA
* * * *
5599444 AAATATTTGAAAAAGGCTCCTCTCAGCAGAGACTCAACAACTTTAAAATATCATCTTGAAAAAG
65 AAATACTTGAAAAAGACTCCTCTAAGCAGAGACTCAACAACTTTAAAAAATCATCTTGAAAAAG
5599508 TCCTCGTCAG
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
141 27 0.23
142 28 0.24
143 1 0.01
145 57 0.49
146 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (141 bp):
AGGCTCAACAACTTTAAAACCTCACCTTGAAAAAGCTCCTCTTAGCAAATGCTCAACAACTTTAA
AATACTTGAAAAAGACTCCTCTAAGCAGAGACTCAACAACTTTAAAAAATCATCTTGAAAAAGCT
CATCTCAGTAG
Done.