Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_pilon, 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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 30
Found at i:5397706 original size:17 final size:19
Alignment explanation
Indices: 5397670--5397706 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5397660 CATGAAATAC
5397670 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
5397689 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
5397706 A
1 A
5397707 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:5397962 original size:22 final size:24
Alignment explanation
Indices: 5397925--5397970 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5397915 TTTTAAATAA
5397925 ATAAATATTTTT-TATTATTTTTAG
1 ATAAATATTTTTAT-TTATTTTTAG
5397949 ATAAATA-TTTTATTTATTTTTA
1 ATAAATATTTTTATTTATTTTTA
5397971 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATAAATATTTTTATTTATTTTTAG
Found at i:5397962 original size:29 final size:28
Alignment explanation
Indices: 5397912--5397973 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5397902 CATTTTCTGA
5397912 TATTTTTAAATAAATAAATATTT-TTTAT
1 TATTTTTAAATAAATAAATATTTATTT-T
* **
5397940 TATTTTTAGATAAATATTTTATTTATTTT
1 TATTTTTAAATAAATA-AATATTTATTTT
5397969 TATTT
1 TATTT
5397974 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 15 0.52
29 11 0.38
30 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TATTTTTAAATAAATAAATATTTATTTT
Found at i:5397965 original size:23 final size:24
Alignment explanation
Indices: 5397925--5397970 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5397915 TTTTAAATAA
*
5397925 ATAAATATTTTTTATTATTTTTAG
1 ATAAATATTTTATATTATTTTTAG
5397949 ATAAATATTTTAT-TTATTTTTA
1 ATAAATATTTTATATTATTTTTA
5397971 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATAAATATTTTATATTATTTTTAG
Found at i:5398556 original size:28 final size:26
Alignment explanation
Indices: 5398524--5398579 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
5398514 AAATTAAAAA
5398524 TTCAT-ATATTTAATATGTACTTATTATT
1 TTCATAATATTT-ATATGTA--TATTATT
5398552 TTCATAATATTTATATGTATATTATT
1 TTCATAATATTTATATGTATATTATT
5398578 TT
1 TT
5398580 TTAAGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 9 0.33
28 12 0.44
29 6 0.22
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (26 bp):
TTCATAATATTTATATGTATATTATT
Found at i:5399141 original size:46 final size:49
Alignment explanation
Indices: 5399067--5399157 Score: 125
Period size: 46 Copynumber: 1.9 Consensus size: 49
5399057 TATTTCATTC
* * * *
5399067 TTTTTCCTAAATAAATGCATGTGAACTAGTAATCATGCGGTTAGGTTAA
1 TTTTTCCTAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGGTTAA
5399116 TTTTTCC-AAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCTAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGG
5399158 ATATATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 20 0.53
47 5 0.13
48 6 0.16
49 7 0.18
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (49 bp):
TTTTTCCTAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:5403518 original size:13 final size:14
Alignment explanation
Indices: 5403488--5403524 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5403478 AAAACAAAAC
5403488 AAAA-AAAAAAAGA
1 AAAAGAAAAAAAGA
5403501 AAAAGAAAAAAAG-
1 AAAAGAAAAAAAGA
*
5403514 GAAAGAAAAAA
1 AAAAGAAAAAA
5403525 TTAAATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:5403518 original size:19 final size:18
Alignment explanation
Indices: 5403470--5403523 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
5403460 TATACTCATT
*
5403470 CAAAAAAAAAAA-CAAAA
1 CAAAAAAAAAAAGAAAAA
5403487 CAAAAAAAAAAAGAAAAA
1 CAAAAAAAAAAAGAAAAA
* *
5403505 GAAAAAAAGGAAAGAAAAA
1 CAAAAAAA-AAAAGAAAAA
5403524 ATTAAATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 12 0.38
18 11 0.34
19 9 0.28
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAAAGAAAAA
Found at i:5407836 original size:22 final size:22
Alignment explanation
Indices: 5407811--5407887 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
5407801 ATCTACACTT
5407811 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * *
5407833 TTCAAAGATGATAGCCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* *
5407855 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
5407877 TTCAAAGATGA
1 TTCAAAGATGA
5407888 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:5408646 original size:47 final size:47
Alignment explanation
Indices: 5408581--5409229 Score: 1111
Period size: 47 Copynumber: 14.0 Consensus size: 47
5408571 CTTCGTTATC
*
5408581 AAAACCTTCGGATCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
5408628 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTAAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
5408675 AAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC--
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
5408720 AAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTC--
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
* *
5408765 AAAACCTTCGGGTCATCTATAAGCCCTTCAGTCCATGATGTTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
5408812 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
* *
5408859 AAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTT--T
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
5408904 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
5408951 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
5408998 AAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
*
5409045 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTTCATGATGTTTTC-A
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
5409091 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-A
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
* *
5409137 AAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCTTGATGTTTTC--
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
5409182 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
5409229 A
1 A
5409230 CATTTCCGTC
Statistics
Matches: 571, Mismatches: 25, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
45 171 0.30
46 89 0.16
47 311 0.54
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (47 bp):
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
Found at i:5408816 original size:92 final size:92
Alignment explanation
Indices: 5408581--5409229 Score: 1090
Period size: 92 Copynumber: 7.0 Consensus size: 92
5408571 CTTCGTTATC
*
5408581 AAAACCTTCGGATCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGTCATCT
*
5408646 GTAAGCCCTTCAGTGCATGATGTTTTAAA
65 GTAAGCCCTTCAGTGCATGATGTTTT-CA
*
5408675 AAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTG
*
5408739 TAATCCCTTCAGTGCATGATGTTTTC-
66 TAAGCCCTTCAGTGCATGATGTTTTCA
* *
5408765 AAAACCTTCGGGTCATCTATAAGCCCTTCAGTCCATGATGTTTTCAAAAAACCTTCGGGTCATCT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGTCATCT
5408830 GTAAGCCCTTCAGTGCATGATGTTTTCAA
65 GTAAGCCCTTCAGTGCATGATGTTTTC-A
* *
5408859 AAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTT-TAAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTG
5408923 TAAGCCCTTCAGTGCATGATGTTTTCAA
66 TAAGCCCTTCAGTGCATGATGTTTTC-A
* *
5408951 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAAAACCTTTGGGTCATCT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGTCATCT
5409016 GTAAGCCCTTCAGTGCATGATGTTTTCAA
65 GTAAGCCCTTCAGTGCATGATGTTTTC-A
*
5409045 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTTCATGATGTTTTCAAAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTG
5409110 TAAGCCCTTCAGTGCATGATGTTTTCA
66 TAAGCCCTTCAGTGCATGATGTTTTCA
* *
5409137 AAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTCATCTG
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTG
5409201 TAAGCCCTTCAGTGCATGATGTTTTCA
66 TAAGCCCTTCAGTGCATGATGTTTTCA
5409228 AA
1 AA
5409230 CATTTCCGTC
Statistics
Matches: 527, Mismatches: 22, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
90 42 0.08
91 48 0.09
92 219 0.42
93 45 0.09
94 173 0.33
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (92 bp):
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTG
TAAGCCCTTCAGTGCATGATGTTTTCA
Found at i:5408863 original size:139 final size:138
Alignment explanation
Indices: 5408581--5409229 Score: 1113
Period size: 139 Copynumber: 4.7 Consensus size: 138
5408571 CTTCGTTATC
*
5408581 AAAACCTTCGGATCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAACCTTCGGGTCATCT
* *
5408646 GTAAGCCCTTCAGTGCATGATGTTTTAAAAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCAT
64 GTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
5408711 GATGTTTTC-
129 GATGTTTTCA
* *
5408720 AAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTAT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGT
*
5408785 AAGCCCTTCAGTCCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
66 AAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
5408850 TGTTTTCAA
131 TGTTTTC-A
* *
5408859 AAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTTAAAACCTTCGGGTCATCTGT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGT
5408924 AAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
66 AAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
*
5408989 TATTTTCAA
131 TGTTTTC-A
*
5408998 AAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAACCTTCGGGTCATCT
*
5409063 GTAAGCCCTTCAGTTCATGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
64 GTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
5409127 GATGTTTTCA
129 GATGTTTTCA
* *
5409137 AAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGT
1 AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGT
5409202 AAGCCCTTCAGTGCATGATGTTTTCAAA
66 AAGCCCTTCAGTGCATGATGTTTTCAAA
5409230 CATTTCCGTC
Statistics
Matches: 484, Mismatches: 21, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
137 132 0.27
138 2 0.00
139 261 0.54
140 45 0.09
141 44 0.09
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (138 bp):
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGT
AAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
TGTTTTCA
Found at i:5409375 original size:21 final size:21
Alignment explanation
Indices: 5409351--5409393 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5409341 TTTTTTCATA
5409351 AATATAATA-ATAATAATTATT
1 AATATAATATAT-ATAATTATT
*
5409372 AATATAATATATATTATTATT
1 AATATAATATATATAATTATT
5409393 A
1 A
5409394 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATAATATATATAATTATT
Found at i:5409404 original size:31 final size:33
Alignment explanation
Indices: 5409366--5409427 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 33
5409356 AATAATAATA
5409366 ATTATT-AATATAATATATAT-TAT-TATTATTT
1 ATTATTAAATA-AATATATATATATATATTATTT
5409397 ATTATTAAATAAATATATATATATATATTAT
1 ATTATTAAATAAATATATATATATATATTAT
5409428 AAATTACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 15 0.54
32 7 0.25
33 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
ATTATTAAATAAATATATATATATATATTATTT
Found at i:5411172 original size:17 final size:19
Alignment explanation
Indices: 5411136--5411172 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5411126 CATGAAATAC
5411136 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
5411155 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
5411172 A
1 A
5411173 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:5411489 original size:118 final size:115
Alignment explanation
Indices: 5411304--5411515 Score: 282
Period size: 118 Copynumber: 1.8 Consensus size: 115
5411294 GAAAAATTAT
* * * * *
5411304 TATTTTTTATATTTATTTATTTTTCAATATTAAGAAAGGACAGTCTTAAAGTAACTGGATGTCCA
1 TATTTTTTATATTTATTTATTTTTAAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCA
*
5411369 TTTTCTGATATTTTTAAATAAATAAATATTTTTTATTATTTTTAGATAAA
66 TTTTCTGATATTTCTAAATAAATAAATATTTTTTATTATTTTTAGATAAA
* * * *
5411419 TATTTTATTAATATTTATTTATTTTTTAAATATTAAGAAAATAGCTGTCTTAAAGCACCTATAAG
1 TATTTT-TT-ATATTTATTTA-TTTTTAAATATTAAGAAAAGA-CAGTCTTAAAGCAACTAGAAG
*
5411484 T-CATTTTCTGATATTTCTAAGTAAATAAATAT
62 TCCATTTTCTGATATTTCTAAATAAATAAATAT
5411516 CTTATTTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
115 6 0.07
116 2 0.02
117 11 0.13
118 47 0.57
119 16 0.20
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (115 bp):
TATTTTTTATATTTATTTATTTTTAAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCA
TTTTCTGATATTTCTAAATAAATAAATATTTTTTATTATTTTTAGATAAA
Found at i:5422972 original size:22 final size:22
Alignment explanation
Indices: 5422921--5422974 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
5422911 CAACATAACT
*
5422921 ATGGTATTGATA-CCTAAGAAC
1 ATGGTATCGATACCCTAAGAAC
*
5422942 A--ATATCGATACCCTAAGAAC
1 ATGGTATCGATACCCTAAGAAC
5422962 ATGGTATCGATAC
1 ATGGTATCGATAC
5422975 TACTAACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 1 0.04
22 9 0.33
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (22 bp):
ATGGTATCGATACCCTAAGAAC
Found at i:5428052 original size:2 final size:2
Alignment explanation
Indices: 5428045--5428079 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5428035 AACCATTCAA
5428045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5428080 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5433948 original size:21 final size:21
Alignment explanation
Indices: 5433924--5433981 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
5433914 ACCTCGAGGA
5433924 AAAGGATCGATCCCTTCCCTT
1 AAAGGATCGATCCCTTCCCTT
5433945 AAAGGATCGATCCCTTCCCTT
1 AAAGGATCGATCCCTTCCCTT
*
5433966 AAAGGGTCGATCCCTT
1 AAAGGATCGATCCCTT
5433982 TGTTCCAACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGGATCGATCCCTTCCCTT
Found at i:5434639 original size:60 final size:60
Alignment explanation
Indices: 5434569--5434720 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 60
5434559 AGTTTCTAAT
* * ***
5434569 TTCGCAACGCGATAGTCAAATTCGCAACGA-GAAAGTCAAATTCGTAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCAAC-ACGAAAGTCAAATTCGCAACACAAAAGTCAAA
* * * *
5434629 TTCGTAACGCGAAAGTCAAATTTGTAACACGATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCAACACGAAAGTCAAATTCGCAACACAAAAGTCAAA
* ** *
5434689 TTCGCAAC-TGAATTTCAAATTCGCAACGCGAA
1 TTCGCAACGCGAAAGTCAAATTCGCAACACGAA
5434721 TTTAATTTCA
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 18 0.24
60 56 0.76
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (60 bp):
TTCGCAACGCGAAAGTCAAATTCGCAACACGAAAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:5434723 original size:20 final size:20
Alignment explanation
Indices: 5434525--5434721 Score: 143
Period size: 20 Copynumber: 9.9 Consensus size: 20
5434515 AAATGACCAA
5434525 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* * * *
5434544 CCAATTTCGCAAC-CCAGTTT
1 -CAAATTCGCAACGCGAATGT
*
5434564 CTAATTTCGCAACGCG-ATAGT
1 C-AAATTCGCAACGCGAAT-GT
* *
5434585 CAAATTCGCAACGAGAAAGT
1 CAAATTCGCAACGCGAATGT
* * *
5434605 CAAATTCGTAACGTGAAAGT
1 CAAATTCGCAACGCGAATGT
* *
5434625 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAATGT
* * *
5434645 CAAATTTGTAACACG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* * *
5434665 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATGT
* *
5434685 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
5434704 CAAATTCGCAACGCGAAT
1 CAAATTCGCAACGCGAAT
5434722 TTAATTTCAC
Statistics
Matches: 145, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
19 20 0.14
20 120 0.83
21 5 0.03
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATGT
Found at i:5435677 original size:24 final size:24
Alignment explanation
Indices: 5435612--5435679 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
5435602 ATGAGTACTA
* *
5435612 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* * * *
5435636 GTTAATACCCAGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
5435660 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
5435680 GATGTGATGG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:5437963 original size:18 final size:18
Alignment explanation
Indices: 5437940--5437975 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5437930 AAGCAAAAGG
*
5437940 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
5437958 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
5437976 CAACCAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:5438293 original size:20 final size:20
Alignment explanation
Indices: 5438265--5438375 Score: 114
Period size: 20 Copynumber: 5.3 Consensus size: 20
5438255 TTCCATCAAC
* *
5438265 GCGAGAGTCAAATTCGTAAT
1 GCGAAAGTCAAATTCGCAAT
5438285 GCGAAAGTCAAATTCGCAACGCTTT
1 GCGAAAGTCAAATTCGCAA-----T
*
5438310 GCGATAGTCAAATTCGCAAT
1 GCGAAAGTCAAATTCGCAAT
* *
5438330 GCGAAAGACAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAT
* *
5438350 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAT
5438370 GCGAAA
1 GCGAAA
5438376 TTGCAAACCG
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
20 58 0.75
25 19 0.25
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAT
Found at i:5438334 original size:45 final size:40
Alignment explanation
Indices: 5438261--5438375 Score: 149
Period size: 45 Copynumber: 2.8 Consensus size: 40
5438251 ATGTTTCCAT
* * *
5438261 CAACGCGAGAGTCAAATTCGTAATGCGAAAGTCAAATTCG
1 CAACGCGATAGTCAAATTCGCAATGCGAAAGACAAATTCG
5438301 CAACGCTTTGCGATAGTCAAATTCGCAATGCGAAAGACAAATTCG
1 CAA--C---GCGATAGTCAAATTCGCAATGCGAAAGACAAATTCG
*
5438346 CAACGCGATAGTCAAATTCGCAACGCGAAA
1 CAACGCGATAGTCAAATTCGCAATGCGAAA
5438376 TTGCAAACCG
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
40 28 0.42
42 1 0.02
43 1 0.02
45 36 0.55
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (40 bp):
CAACGCGATAGTCAAATTCGCAATGCGAAAGACAAATTCG
Found at i:5438453 original size:20 final size:22
Alignment explanation
Indices: 5438428--5438471 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
5438418 GCAACGCTTA
5438428 TTTCGCGTTGAG-AA-TTTACC
1 TTTCGCGTTGAGAAAGTTTACC
*
5438448 TTTCGCGTTGCGAAAGTTTACC
1 TTTCGCGTTGAGAAAGTTTACC
5438470 TT
1 TT
5438472 CAACATGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 2 0.10
22 8 0.38
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTCGCGTTGAGAAAGTTTACC
Found at i:5438570 original size:25 final size:25
Alignment explanation
Indices: 5438532--5438581 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5438522 AAATCAATTA
*
5438532 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
5438557 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
5438582 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:5438791 original size:25 final size:25
Alignment explanation
Indices: 5438755--5438803 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5438745 GTGTATAACA
5438755 AAACAATCTATCTCTTCCATGTGAT
1 AAACAATCTATCTCTTCCATGTGAT
*
5438780 AAACAATGTATCTCTTCCATGTGA
1 AAACAATCTATCTCTTCCATGTGA
5438804 GTACTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (25 bp):
AAACAATCTATCTCTTCCATGTGAT
Found at i:5439001 original size:24 final size:25
Alignment explanation
Indices: 5438974--5439028 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
5438964 TTTCAAATTC
*
5438974 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
*
5438998 ATTT-AAATGTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
5439022 ATTTCAA
1 ATTTCAA
5439029 TATAAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 20 0.74
25 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.45
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:5439036 original size:24 final size:24
Alignment explanation
Indices: 5438985--5439037 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5438975 TTTCATATGT
* * *
5438985 AATTGGAGTTTGAATTTAAATGTC
1 AATTTGAGTTTGAATTTAAATATA
*
5439009 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
5439033 AATTT
1 AATTT
5439038 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:5439382 original size:39 final size:39
Alignment explanation
Indices: 5439339--5439425 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
5439329 TCCGATGCTC
*
5439339 ATCAAAATCCAAAGCTTATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
5439378 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
5439417 ATCAAAATC
1 ATCAAAATC
5439426 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:5441234 original size:21 final size:21
Alignment explanation
Indices: 5441205--5441308 Score: 72
Period size: 21 Copynumber: 4.9 Consensus size: 21
5441195 GAACGGCAGG
*
5441205 TGGGACCTCTTGAACGATGATA
1 TGGG-CCTCTTGAACGATGAGA
*
5441227 TGGGCCTCTTGAACGGTG-GAA
1 TGGGCCTCTTGAACGATGAG-A
* * *
5441248 AGGGCTTCTTCG-ATGATGAGA
1 TGGGCCTCTT-GAACGATGAGA
*
5441269 TGGGCCTTTTGAACGAT-AGGA
1 TGGGCCTCTTGAACGATGA-GA
*
5441290 -GGCGCCTCTTGAATGATGA
1 TGG-GCCTCTTGAACGATGA
5441309 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.06
21 52 0.83
22 7 0.11
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (21 bp):
TGGGCCTCTTGAACGATGAGA
Found at i:5441306 original size:42 final size:41
Alignment explanation
Indices: 5441210--5441308 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
5441200 GCAGGTGGGA
* * *
5441210 CCTCTTGAACGATGATATGGGCCTCTTGAACGGTGGAAAGGG
1 CCTCTTGAATGATGAGATGGGCCTCTTGAACGATGG-AAGGG
* *
5441252 CTTCTTCG-ATGATGAGATGGGCCTTTTGAACGATAGG-AGGCG
1 CCTCTT-GAATGATGAGATGGGCCTCTTGAACGAT-GGAAGG-G
5441294 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
5441309 TAGGTGCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
41 4 0.09
42 40 0.85
43 3 0.06
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (41 bp):
CCTCTTGAATGATGAGATGGGCCTCTTGAACGATGGAAGGG
Found at i:5441482 original size:4 final size:4
Alignment explanation
Indices: 5441452--5441501 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
5441442 GGGCCACTGA
* * *
5441452 AAAT AAAT TAAT ATAT AAAT CAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5441500 AA
1 AA
5441502 TGCCAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:5443517 original size:19 final size:20
Alignment explanation
Indices: 5443461--5443518 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
5443451 TTAAATTCGA
* *
5443461 AACGTGAAAATGAAAATTGC
1 AACGCGAAAATGAAAATCGC
5443481 AACGCGAAAATGAAAATCGC
1 AACGCGAAAATGAAAATCGC
*
5443501 AACGCGAAACT-AAAATCG
1 AACGCGAAAATGAAAATCG
5443519 TGTTGCGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 7 0.20
20 28 0.80
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (20 bp):
AACGCGAAAATGAAAATCGC
Found at i:5443835 original size:22 final size:22
Alignment explanation
Indices: 5443807--5443857 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5443797 GATGAAGATA
*
5443807 GACGGATTTCATCGGAAATGGG
1 GACGGATTTCATCGGAAATGAG
** *
5443829 GACGGATTTTGTCGGAGATGAG
1 GACGGATTTCATCGGAAATGAG
5443851 GACGGAT
1 GACGGAT
5443858 GTCGCCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.39, T:0.24
Consensus pattern (22 bp):
GACGGATTTCATCGGAAATGAG
Found at i:5444041 original size:20 final size:20
Alignment explanation
Indices: 5443985--5444069 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
5443975 GCGTAAAAAC
* *
5443985 ATTTGACTTTCGCATTGCGA
1 ATTTGACTATCGCGTTGCGA
5444005 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
5444025 ATTTGACT-TCTGTGTTGCG-
1 ATTTGACTATC-GCGTTGCGA
*
5444044 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC-TA-TCGCGTTGCGA
5444065 ATTTG
1 ATTTG
5444070 GAAACTGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
18 2 0.04
19 6 0.11
20 40 0.74
21 6 0.11
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:5455504 original size:2 final size:2
Alignment explanation
Indices: 5455499--5455541 Score: 61
Period size: 2 Copynumber: 21.0 Consensus size: 2
5455489 TTTTTTAACC
5455499 AT AT AT GAT AT GAT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5455542 TTCCATGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 33 0.87
3 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5459777 original size:113 final size:112
Alignment explanation
Indices: 5459604--5459818 Score: 351
Period size: 113 Copynumber: 1.9 Consensus size: 112
5459594 CGATTTCGGG
*
5459604 GCAACAATAGTGGCGTTTTTTGAAAAAACGTCGCAATAGATCCATCTATAGTGGTGTTTATTGGA
1 GCAACAATAGTGGCGTTTTTTGAAAAAACGTCGCAATAGATCCATCTATAGTGGCGTTTATTGG-
*
5459669 AAAAACGCCACTATATATATACTTTTTTGGGATTTTTTTTGGGTCTGA
65 AAAAACGCCACTATATATATACTTTTTGGGGATTTTTTTTGGGTCTGA
* * *
5459717 GCAATAATAGTGGTGTTTATTT-AAAAAACGTCGCAATAGGTCCATCTATAGTGGCGTTTATTGG
1 GCAACAATAGTGGCGTTT-TTTGAAAAAACGTCGCAATAGATCCATCTATAGTGGCGTTTATTGG
*
5459781 AAAAACGCCACTATATATATACTTTTTGGGGCTTTTTT
65 AAAAACGCCACTATATATATACTTTTTGGGGATTTTTT
5459819 GGGGGCCCTG
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
112 36 0.38
113 56 0.59
114 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (112 bp):
GCAACAATAGTGGCGTTTTTTGAAAAAACGTCGCAATAGATCCATCTATAGTGGCGTTTATTGGA
AAAACGCCACTATATATATACTTTTTGGGGATTTTTTTTGGGTCTGA
Found at i:5462646 original size:21 final size:21
Alignment explanation
Indices: 5462620--5462664 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5462610 GATTTCTGGG
* *
5462620 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
5462641 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
5462662 CAA
1 CAA
5462665 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:5463549 original size:32 final size:32
Alignment explanation
Indices: 5463496--5463590 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
5463486 GTCGAGGGTT
*
5463496 TACCTATGTTCT-ACGGAACATATGGACAGTTT
1 TACCTATGTTCTAAC-GAACATATGGACAGTTA
**
5463528 TACCTAT-TTCTTTCGAGACATATGGACAG-TA
1 TACCTATGTTCTAACGA-ACATATGGACAGTTA
*
5463559 TACCTATGTTCTAAGGAACATATGGACAGTTA
1 TACCTATGTTCTAACGAACATATGGACAGTTA
5463591 CCGAGGATCT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (32 bp):
TACCTATGTTCTAACGAACATATGGACAGTTA
Found at i:5463580 original size:31 final size:30
Alignment explanation
Indices: 5463495--5463592 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
5463485 AGTCGAGGGT
*
5463495 TTACCTATGTTCTACGGAACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAG
***
5463525 TTTTACCTAT-TTCTTTCGAGACATATGGACAG
1 --TTACCTATGTTCTAAGGA-ACATATGGACAG
5463557 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAG
5463588 TTACC
1 TTACC
5463593 GAGGATCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
30 5 0.09
31 26 0.46
32 26 0.46
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (30 bp):
TTACCTATGTTCTAAGGAACATATGGACAG
Found at i:5463706 original size:29 final size:30
Alignment explanation
Indices: 5463581--5463703 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
5463571 AAGGAACATA
5463581 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
5463611 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
5463641 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
5463671 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
5463700 TGGA
1 TGGA
5463704 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:5463988 original size:6 final size:6
Alignment explanation
Indices: 5463974--5464045 Score: 117
Period size: 6 Copynumber: 12.0 Consensus size: 6
5463964 GTATGTGTGG
*
5463974 ATATGT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
5464022 ATATAT ATATAT CTATAT CTATAT
1 ATATAT ATATAT ATATAT ATATAT
5464046 GAAAGGTGCA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:5463990 original size:8 final size:8
Alignment explanation
Indices: 5463974--5464045 Score: 117
Period size: 8 Copynumber: 9.0 Consensus size: 8
5463964 GTATGTGTGG
*
5463974 ATATGTAT
1 ATATATAT
5463982 ATATATAT
1 ATATATAT
5463990 ATATATAT
1 ATATATAT
5463998 ATATATAT
1 ATATATAT
5464006 ATATATAT
1 ATATATAT
5464014 ATATATAT
1 ATATATAT
5464022 ATATATAT
1 ATATATAT
*
5464030 ATATCTAT
1 ATATATAT
*
5464038 ATCTATAT
1 ATATATAT
5464046 GAAAGGTGCA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 60 1.00
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (8 bp):
ATATATAT
Found at i:5467601 original size:21 final size:21
Alignment explanation
Indices: 5467575--5467619 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5467565 GATTTCTGGG
* *
5467575 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
5467596 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
5467617 CAA
1 CAA
5467620 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:5468492 original size:32 final size:32
Alignment explanation
Indices: 5468450--5468545 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
5468440 GAGTCGAGGG
*
5468450 TTTACATATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
5468482 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
5468513 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
5468545 T
1 T
5468546 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:5468522 original size:31 final size:30
Alignment explanation
Indices: 5468451--5468548 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 30
5468441 AGTCGAGGGT
*
5468451 TTACATATGTTCT-ACGGAACATATGGACAG
1 TTACCTATGTTCTAAC-GAACATATGGACAG
**
5468481 TTTTACCTATG-TCTTTCGAGACATATGGACAG
1 --TTACCTATGTTCTAACGA-ACATATGGACAG
*
5468513 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
5468544 TTACC
1 TTACC
5468549 GAGGATCTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
30 5 0.09
31 26 0.46
32 26 0.46
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:5468662 original size:29 final size:30
Alignment explanation
Indices: 5468537--5468659 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
5468527 AAGGAACATA
5468537 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
5468567 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
5468597 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
5468627 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
5468656 TGGA
1 TGGA
5468660 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:5468942 original size:2 final size:2
Alignment explanation
Indices: 5468932--5468995 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
5468922 GTATGTGTGG
*
5468932 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5468974 AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5468996 GAAAGGTGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5471391 original size:31 final size:31
Alignment explanation
Indices: 5471350--5471409 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
5471340 AAGAGTTTGT
*
5471350 GAGTTTCTAGTGAGAAGGACATATTGAATAG
1 GAGTTCCTAGTGAGAAGGACATATTGAATAG
5471381 GAGTTCCTAGTGAGAAGGACATATTGAAT
1 GAGTTCCTAGTGAGAAGGACATATTGAAT
5471410 TCATCGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.28
Consensus pattern (31 bp):
GAGTTCCTAGTGAGAAGGACATATTGAATAG
Found at i:5473558 original size:12 final size:12
Alignment explanation
Indices: 5473543--5473571 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5473533 AAAATAGAAA
5473543 TAAAATTAAAAT
1 TAAAATTAAAAT
5473555 TAAAATTAAAAT
1 TAAAATTAAAAT
5473567 TAAAA
1 TAAAA
5473572 ACATAAAATA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAAAAT
Found at i:5473589 original size:12 final size:11
Alignment explanation
Indices: 5473528--5473590 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 11
5473518 TACAAAACAC
5473528 AAATAAAAATA
1 AAATAAAAATA
*
5473539 GAAATAAAATTA
1 -AAATAAAAATA
*
5473551 AAATTAAAATTA
1 AAA-TAAAAATA
5473563 AAATTAAAAACATA
1 AAA-T-AAAA-ATA
5473577 AAATAATAAATA
1 AAATAA-AAATA
5473589 AA
1 AA
5473591 GTAGTAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
11 3 0.07
12 30 0.67
13 7 0.16
14 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5475245 original size:10 final size:11
Alignment explanation
Indices: 5475230--5475267 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
5475220 AATTATAATT
5475230 TATAATAT-TA
1 TATAATATATA
5475240 TATAATATATA
1 TATAATATATA
5475251 TAT-ATATATA
1 TATAATATATA
5475261 TTATAAT
1 -TATAAT
5475268 TTGGACGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
11 8 0.32
12 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATAATATATA
Found at i:5475245 original size:17 final size:17
Alignment explanation
Indices: 5475223--5475265 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5475213 AAATTGTAAT
*
5475223 TATAATTTATA-ATATTA
1 TATAATATATATATA-TA
5475240 TATAATATATATATATA
1 TATAATATATATATATA
*
5475257 TATATTATA
1 TATAATATA
5475266 ATTTGGACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATATATATATA
Found at i:5477341 original size:7 final size:7
Alignment explanation
Indices: 5477322--5477356 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
5477312 CCTTAAACAT
5477322 TTTTTTC
1 TTTTTTC
*
5477329 TCTTTTTG
1 T-TTTTTC
5477337 TTTTTTC
1 TTTTTTC
5477344 TTTTTTC
1 TTTTTTC
5477351 TTTTTT
1 TTTTTT
5477357 TCCTGACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:5477357 original size:15 final size:15
Alignment explanation
Indices: 5477321--5477358 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5477311 ACCTTAAACA
5477321 TTTTTTTCTCTTTTT
1 TTTTTTTCTCTTTTT
*
5477336 GTTTTTTCT-TTTTT
1 TTTTTTTCTCTTTTT
5477350 CTTTTTTTC
1 -TTTTTTTC
5477359 CTGACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTCTTTTT
Found at i:5480883 original size:20 final size:20
Alignment explanation
Indices: 5480835--5480876 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5480825 GAAGGAACAA
5480835 AGAAGATATGTGTGTAAGAG
1 AGAAGATATGTGTGTAAGAG
5480855 AGAAGATATGTGTGTAAGAG
1 AGAAGATATGTGTGTAAGAG
5480875 AG
1 AG
5480877 GAAATATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (20 bp):
AGAAGATATGTGTGTAAGAG
Found at i:5480999 original size:60 final size:60
Alignment explanation
Indices: 5480899--5481015 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
5480889 ACGAAATAGT
*
5480899 AAAGAATTAAAATTGAAAGAAAATGGAAATGAAGTACTGGAATGAAGAAAACAGATATTC
1 AAAGAAATAAAATTGAAAGAAAATGGAAATGAAGTACTGGAATGAAGAAAACAGATATTC
* * * *
5480959 AAAGAAATAAATTTGAAAGAAAATGGAAATTAAGTGCTGGAATGAAGAAAATAGATA
1 AAAGAAATAAAATTGAAAGAAAATGGAAATGAAGTACTGGAATGAAGAAAACAGATA
5481016 ATAAATTCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (60 bp):
AAAGAAATAAAATTGAAAGAAAATGGAAATGAAGTACTGGAATGAAGAAAACAGATATTC
Found at i:5488058 original size:3 final size:3
Alignment explanation
Indices: 5488050--5488105 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
5488040 ATGAAAAAAG
* *
5488050 TAA TAA TAA TAAA TAAA CAA GAA TGAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
5488097 TAA TAA TAA
1 TAA TAA TAA
5488106 ACGAAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.04
3 36 0.77
4 9 0.19
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5488317 original size:31 final size:30
Alignment explanation
Indices: 5488240--5488318 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
5488230 AAAAAATGAG
* *
5488240 AATAAAA-AATAATAAAAAATATATAATTA
1 AATAAAATAATAATAATAAATACATAATTA
* *
5488269 AATATAGATAATAATAATAAATACATTATTTA
1 AATA-AAATAATAATAATAAATACA-TAATTA
5488301 AATAAAATAATAATAATA
1 AATAAAATAATAATAATA
5488319 GAAAGAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 4 0.10
30 2 0.05
31 27 0.64
32 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (30 bp):
AATAAAATAATAATAATAAATACATAATTA
Found at i:5489410 original size:7 final size:8
Alignment explanation
Indices: 5489397--5489459 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 8
5489387 TAAAATTGTA
5489397 ATTATAAT
1 ATTATAAT
5489405 -TTATAAT
1 ATTATAAT
5489412 ATTAT-AT
1 ATTATAAT
*
5489419 AATAT-AT
1 ATTATAAT
5489426 ATTAT-AT
1 ATTATAAT
*
5489433 AATATATAT
1 ATTATA-AT
5489442 ATATATATAT
1 AT-TATA-AT
5489452 ATTATAAT
1 ATTATAAT
5489460 TTGGACGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
7 25 0.53
8 6 0.13
9 7 0.15
10 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
ATTATAAT
Found at i:5489425 original size:2 final size:2
Alignment explanation
Indices: 5489406--5489457 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
5489396 AATTATAATT
5489406 TA TA -A TA T- TA TA TA -A TA TA TA T- TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5489443 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
5489458 ATTTGGACGG
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
1 6 0.14
2 38 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5489426 original size:24 final size:23
Alignment explanation
Indices: 5489395--5489459 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
5489385 AATAAAATTG
5489395 TAAT-TATAATTTATAATATTATA
1 TAATATATAATTTATAATA-TATA
5489418 TAATATAT-ATTATATAATATATA
1 TAATATATAATT-TATAATATATA
5489441 T-ATATATATATATTATAAT
1 TAATATATA-AT-TTATAAT
5489460 TTGGACGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 18 0.49
25 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATATAATTTATAATATATA
Found at i:5489429 original size:14 final size:14
Alignment explanation
Indices: 5489410--5489457 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
5489400 ATAATTTATA
5489410 ATATTATATAATAT
1 ATATTATATAATAT
5489424 ATATTATATAATAT
1 ATATTATATAATAT
5489438 ATA-TATAT-ATAT
1 ATATTATATAATAT
5489450 ATATTATA
1 ATATTATA
5489458 ATTTGGACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.21
13 9 0.27
14 17 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTATATAATAT
Found at i:5489675 original size:14 final size:15
Alignment explanation
Indices: 5489651--5489681 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5489641 CTAAAACCTC
5489651 TAAAGATAATAATTA
1 TAAAGATAATAATTA
5489666 TAAA-ATAATAATTA
1 TAAAGATAATAATTA
5489680 TA
1 TA
5489682 CTTTGACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TAAAGATAATAATTA
Found at i:5493601 original size:22 final size:21
Alignment explanation
Indices: 5493576--5493617 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
5493566 TATAAAAAAT
5493576 TATTTTTATTAAATATTTTTAG
1 TATTTTTATTAAAT-TTTTTAG
*
5493598 TATTTTTATTTAATTTTTTA
1 TATTTTTATTAAATTTTTTA
5493618 AATAATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTAG
Found at i:5500713 original size:22 final size:21
Alignment explanation
Indices: 5500645--5500715 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
5500635 TGATCAACAA
** *
5500645 ATTCGCAACGCAAACTCCAAT
1 ATTCGCAACGCAATTTCCCAT
* *
5500666 -TTCGCAACACAATTT-CCAA
1 ATTCGCAACGCAATTTCCCAT
5500685 ATTCGCAACGCGAATTTCCCAT
1 ATTCGCAACGC-AATTTCCCAT
5500707 ATTCGCAAC
1 ATTCGCAAC
5500716 TCAGTTTTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.05
20 21 0.52
21 5 0.12
22 12 0.30
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (21 bp):
ATTCGCAACGCAATTTCCCAT
Found at i:5500729 original size:42 final size:41
Alignment explanation
Indices: 5500642--5500741 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
5500632 AAATGATCAA
*
5500642 CAAATTCGCAACGC-AAACTCCAATTTCGCAACACAATTTC
1 CAAATTCGCAACGCGAATCTCCAATTTCGCAACACAATTTC
* * * * *
5500682 CAAATTCGCAACGCGAATTTCCCATATTCGCAACTCAGTTTT
1 CAAATTCGCAACGCGAATCTCCAAT-TTCGCAACACAATTTC
* *
5500724 GAAATTCGCAACGTGAAT
1 CAAATTCGCAACGCGAAT
5500742 ATGTAAATCG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
40 14 0.28
41 7 0.14
42 29 0.58
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATCTCCAATTTCGCAACACAATTTC
Found at i:5500752 original size:20 final size:20
Alignment explanation
Indices: 5500729--5500795 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
5500719 GTTTTGAAAT
* *
5500729 TCGCAACGTGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
* *
5500749 TCGCAACACAAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
* *
5500769 TCGCAATGCGAATTTGTAAT
1 TCGCAACGCGAATTTGTAAA
5500789 TCGCAAC
1 TCGCAAC
5500796 ACAGAAGTCA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:5500773 original size:40 final size:40
Alignment explanation
Indices: 5500667--5500798 Score: 106
Period size: 40 Copynumber: 3.2 Consensus size: 40
5500657 AACTCCAATT
* * ** *
5500667 TCGCAACAC-AATTTCCAAATTCGCAACGCGAATTTCCCATAT
1 TCGCAACACAAATTT-GAAATTCGCAACGCGAATAT-GTA-AA
* ** *
5500709 TCGCAACTCAGTTTTGAAATTCGCAACGTGAATATGTAAA
1 TCGCAACACAAATTTGAAATTCGCAACGCGAATATGTAAA
* * *
5500749 TCGCAACACAAATTTGTAAA-TCGCAATGCGAATTTGTAAT
1 TCGCAACACAAATTTG-AAATTCGCAACGCGAATATGTAAA
5500789 TCGCAACACA
1 TCGCAACACA
5500799 GAAGTCAAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
40 40 0.56
41 4 0.06
42 25 0.35
43 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (40 bp):
TCGCAACACAAATTTGAAATTCGCAACGCGAATATGTAAA
Found at i:5500990 original size:22 final size:22
Alignment explanation
Indices: 5500965--5501012 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5500955 CTCTCTACGA
* *
5500965 CGACATCCGTCCCCATCTCCGG
1 CGACATCCATCCCCATATCCGG
*
5500987 CGACATCCATCCCTATATCCGG
1 CGACATCCATCCCCATATCCGG
5501009 CGAC
1 CGAC
5501013 CCCCTCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.46, G:0.17, T:0.19
Consensus pattern (22 bp):
CGACATCCATCCCCATATCCGG
Found at i:5501375 original size:20 final size:20
Alignment explanation
Indices: 5501352--5501390 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5501342 TTTGAAACTT
5501352 AAATTCGCAACACGAAAATA
1 AAATTCGCAACACGAAAATA
5501372 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
5501391 TGCAACAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATA
Found at i:5501397 original size:14 final size:15
Alignment explanation
Indices: 5501371--5501404 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5501361 ACACGAAAAT
*
5501371 AAAATTCGCAACACG
1 AAAATTCGCAACAAG
5501386 AAAATT-GCAACAAG
1 AAAATTCGCAACAAG
5501400 AAAAT
1 AAAAT
5501405 GAAAATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.15
Consensus pattern (15 bp):
AAAATTCGCAACAAG
Found at i:5501501 original size:20 final size:20
Alignment explanation
Indices: 5501433--5501503 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
5501423 TTAGTTTCGC
* *
5501433 GTTGCGATTTTCATTTTTGC
1 GTTGCGAATTTCATTTTTGT
* *
5501453 GTTGCGAATTTTATTTTCGT
1 GTTGCGAATTTCATTTTTGT
* *
5501473 ATTGTGAATTTCATTTTTGT
1 GTTGCGAATTTCATTTTTGT
5501493 GTTGCGAATTT
1 GTTGCGAATTT
5501504 AAGTTTCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.55
Consensus pattern (20 bp):
GTTGCGAATTTCATTTTTGT
Found at i:5503059 original size:42 final size:42
Alignment explanation
Indices: 5503000--5503098 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
5502990 ACCCCCACTT
* * *
5503000 CGAGAGCCATCACCTGATCGAGCCAATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCAATTATACACCTCCACAC
* * *
5503042 CGAGAGTCATCACCTGATCGAGCCGATTATACACCTCCACAT
1 CGAGAGCCATCACCTGATCGAGCCAATTATACACCTCCACAC
5503084 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
5503099 ATTCCATCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCAATTATACACCTCCACAC
Found at i:5503265 original size:21 final size:21
Alignment explanation
Indices: 5503213--5503265 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5503203 GTTAGGGGAG
*
5503213 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * *
5503234 TTGCGTAATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
*
5503255 TTATGTGATGA
1 TTACGTGATGA
5503266 CAATGGTGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:5503334 original size:63 final size:63
Alignment explanation
Indices: 5503251--5503391 Score: 153
Period size: 63 Copynumber: 2.2 Consensus size: 63
5503241 ATGAGGTCGG
* * * * *
5503251 TACTTTATGTGATGACAATGGTGCATGGCGTGGTGAGGTA-CGGT-CTTTATGTGGTGAGGTAAT
1 TACTTTACGCGATGAAAATGGTGCATGACGTGGTGAGGTATC--TACTTTACGTGGTGAGGT-AT
5503314 -
63 C
* * *
5503314 TATTTTACGCGATGAAAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTGGTGAGGTATC
1 TACTTTACGCGATGAAAATGGTGCATGACGTGGTGAGGTATCTACTTTACGTGGTGAGGTATC
*
5503377 TACTTTACGTGATGA
1 TACTTTACGCGATGA
5503392 GGTAGCCGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
62 3 0.05
63 61 0.94
64 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.36
Consensus pattern (63 bp):
TACTTTACGCGATGAAAATGGTGCATGACGTGGTGAGGTATCTACTTTACGTGGTGAGGTATC
Found at i:5503361 original size:21 final size:21
Alignment explanation
Indices: 5503337--5503395 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
5503327 GAAAATGGTG
5503337 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGGTGAGGTATCTA
5503358 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGGTGAGGTATCTA
*
5503379 CTTTACGTGATGAGGTA
1 CTTTACGTGGTGAGGTA
5503396 GCCGTTCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.37
Consensus pattern (21 bp):
CTTTACGTGGTGAGGTATCTA
Found at i:5503724 original size:21 final size:21
Alignment explanation
Indices: 5503698--5503767 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
5503688 CTGTCATCAA
*
5503698 TCAAGAGGCCATTCCTATCGT
1 TCAAGAGGCCCTTCCTATCGT
*
5503719 TCAAGAGGCCCCT-CTCATCGT
1 TCAAGAGGCCCTTCCT-ATCGT
*
5503740 TCAAGAGGCCCCTTCC-ACCGT
1 TCAAGAGG-CCCTTCCTATCGT
5503761 TCAAGAG
1 TCAAGAG
5503768 CCCGATTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.05
21 35 0.83
22 4 0.10
23 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGAGGCCCTTCCTATCGT
Found at i:5505334 original size:20 final size:20
Alignment explanation
Indices: 5505323--5505457 Score: 198
Period size: 20 Copynumber: 6.8 Consensus size: 20
5505313 TTTCGCGTTT
5505323 TGAATTTGACTTTCGCAACG
1 TGAATTTGACTTTCGCAACG
5505343 TGAATTTGACTTTCGCAACG
1 TGAATTTGACTTTCGCAACG
5505363 TGAATTTGACTTTCGCAACG
1 TGAATTTGACTTTCGCAACG
*
5505383 CGAATTTGACTTTCGCAACG
1 TGAATTTGACTTTCGCAACG
* ** *
5505403 CGAATTTGACAATCACAACG
1 TGAATTTGACTTTCGCAACG
**
5505423 TGAATTTGACTTTCGCATTG
1 TGAATTTGACTTTCGCAACG
*
5505443 CGAATTTGACTTTCG
1 TGAATTTGACTTTCG
5505458 TGTTGCGAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (20 bp):
TGAATTTGACTTTCGCAACG
Found at i:5505378 original size:60 final size:60
Alignment explanation
Indices: 5505306--5505457 Score: 214
Period size: 60 Copynumber: 2.5 Consensus size: 60
5505296 TCGCGTTGCG
* * ** * ** *
5505306 ATTTTACTTTCGCGTTTTGAATTTGACTTTCGCAACGTGAATTTGACTTTCGCAACGTGA
1 ATTTGACTTTCGCATTGCGAATTTGACTTTCGCAACGCGAATTTGACAATCACAACGTGA
**
5505366 ATTTGACTTTCGCAACGCGAATTTGACTTTCGCAACGCGAATTTGACAATCACAACGTGA
1 ATTTGACTTTCGCATTGCGAATTTGACTTTCGCAACGCGAATTTGACAATCACAACGTGA
5505426 ATTTGACTTTCGCATTGCGAATTTGACTTTCG
1 ATTTGACTTTCGCATTGCGAATTTGACTTTCG
5505458 TGTTGCGAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (60 bp):
ATTTGACTTTCGCATTGCGAATTTGACTTTCGCAACGCGAATTTGACAATCACAACGTGA
Found at i:5505463 original size:20 final size:20
Alignment explanation
Indices: 5505294--5505468 Score: 136
Period size: 20 Copynumber: 8.8 Consensus size: 20
5505284 TTATTGTGAT
* *
5505294 TTTCGCGTTGCG-ATTTTAC
1 TTTCGCATTGCGAATTTGAC
* **
5505313 TTTCGCGTTTTGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
** *
5505333 TTTCGCAACGTGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
** *
5505353 TTTCGCAACGTGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
**
5505373 TTTCGCAACGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
**
5505393 TTTCGCAACGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
** * ** *
5505413 AATCACAACGTGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
5505433 TTTCGCATTGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
**
5505453 TTTCGTGTTGCGAATT
1 TTTCGCATTGCGAATT
5505469 CAAGGAAAAC
Statistics
Matches: 135, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
19 10 0.07
20 125 0.93
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTGAC
Found at i:5509030 original size:20 final size:21
Alignment explanation
Indices: 5509007--5509050 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5508997 TTGCGATTTA
5509007 GAAAATCT-TGTTGC-AAAAAG
1 GAAAAT-TGTGTTGCGAAAAAG
*
5509027 GAAACTTGTGTTGCGAAAAAG
1 GAAAATTGTGTTGCGAAAAAG
5509048 GAA
1 GAA
5509051 TTCGCGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.52
21 9 0.43
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (21 bp):
GAAAATTGTGTTGCGAAAAAG
Found at i:5509169 original size:21 final size:22
Alignment explanation
Indices: 5509117--5509169 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
5509107 CAGAAACTGA
* *
5509117 GTTGCAAATTTTGGAAATTTGC
1 GTTGCAAAATTTGGAAATATGC
* *
5509139 GTTGC-GAATTTGGAAA-ATGT
1 GTTGCAAAATTTGGAAATATGC
5509159 GTTGCAAAATT
1 GTTGCAAAATT
5509170 GGAGTACACG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.28
21 13 0.52
22 5 0.20
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (22 bp):
GTTGCAAAATTTGGAAATATGC
Found at i:5510874 original size:19 final size:19
Alignment explanation
Indices: 5510831--5510874 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5510821 AAATGACCAA
*
5510831 CAAATTCGCAACACGATCT
1 CAAATTCGCAACACGAACT
**
5510850 CAAATTCGCAATGCGAACT
1 CAAATTCGCAACACGAACT
*
5510869 CCAATT
1 CAAATT
5510875 TTGCAACTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:5511071 original size:40 final size:38
Alignment explanation
Indices: 5510955--5511103 Score: 104
Period size: 40 Copynumber: 3.7 Consensus size: 38
5510945 CAGTTTCTGC
* *
5510955 AATCGCAACGCGAATTTTTTTCTCGCAACGCGA-TTTCCA
1 AATCGCAACACGAATTTTTTT-TCGCAAC-CAATTTTCCA
* * * *
5510994 AATTCGCAACAC-AAGTTTCCTTTTCACAACAAGATTTTCTA
1 AA-TCGCAACACGAA-TTT-TTTTTCGCAACCA-ATTTTCCA
*
5511035 AATCGCAACACGAATTTTGTTTTCGCAACTCAATTTTCGA
1 AATCGCAACACGAATTTT-TTTTCGCAAC-CAATTTTCCA
* * * *
5511075 ATTTGCAACATGAATTTTAATTTCGCAAC
1 AATCGCAACACGAATTTT-TTTTCGCAAC
5511104 AGCTTTTATT
Statistics
Matches: 87, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
39 4 0.05
40 70 0.80
41 13 0.15
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (38 bp):
AATCGCAACACGAATTTTTTTTCGCAACCAATTTTCCA
Found at i:5511091 original size:21 final size:20
Alignment explanation
Indices: 5511037--5511104 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
5511027 ATTTTCTAAA
* **
5511037 TCGCAACACGAATTTTGTTT
1 TCGCAACATGAATTTTAATT
*
5511057 TCGCAAC-TCAATTTTCGAATT
1 TCGCAACATGAATTTT--AATT
5511078 T-GCAACATGAATTTTAATT
1 TCGCAACATGAATTTTAATT
5511097 TCGCAACA
1 TCGCAACA
5511105 GCTTTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 11 0.28
20 18 0.46
21 10 0.26
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (20 bp):
TCGCAACATGAATTTTAATT
Found at i:5512067 original size:24 final size:24
Alignment explanation
Indices: 5512040--5512095 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
5512030 CAGTATTTAA
5512040 AATTTGATCTTGGTCAATACCCGG
1 AATTTGATCTTGGTCAATACCCGG
*
5512064 AATTTGATCTTGGTCAATACTCGG
1 AATTTGATCTTGGTCAATACCCGG
*
5512088 ATTTTGAT
1 AATTTGAT
5512096 GATGTTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
AATTTGATCTTGGTCAATACCCGG
Found at i:5514391 original size:18 final size:18
Alignment explanation
Indices: 5514365--5514400 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5514355 AAACAAAAGG
*
5514365 AAATAAAAATCGCAATCA
1 AAATAAAAATCCCAATCA
*
5514383 AAATCAAAATCCCAATCA
1 AAATAAAAATCCCAATCA
5514401 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.22, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAAAATCCCAATCA
Found at i:5516108 original size:21 final size:21
Alignment explanation
Indices: 5516084--5516160 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
5516074 ATGAATCGGG
* *
5516084 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
5516105 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
5516126 CTCTTGAACGATAAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
5516147 CTCTTGAACGATGA
1 CTCTTGAACGATGA
5516161 CAGGTGAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:5516577 original size:21 final size:21
Alignment explanation
Indices: 5516487--5516602 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 21
5516477 AGAACCATTG
* * * *
5516487 TCATCGCGTAAAACATCTACC
1 TCATCACGTAAAGCACCGACC
*
5516508 TCACCACGTAAAG-ACCGTACC
1 TCATCACGTAAAGCACCG-ACC
** * **
5516529 TCATCACGCCATGCACC-ATTA
1 TCATCACGTAAAGCACCGA-CC
* *
5516550 TCGTCACGTAAAGTACCGACC
1 TCATCACGTAAAGCACCGACC
** *
5516571 TCATCACACAAAGCACTGACC
1 TCATCACGTAAAGCACCGACC
5516592 TCATCACGTAA
1 TCATCACGTAA
5516603 CTCCCCTAAC
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 3 0.05
21 59 0.89
22 4 0.06
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (21 bp):
TCATCACGTAAAGCACCGACC
Found at i:5516792 original size:42 final size:42
Alignment explanation
Indices: 5516717--5516815 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
5516707 GTGATGGAAT
* * * *
5516717 AGGTGATGACTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTGGAGCTGTAGAATCGGCTCGATC
* *
5516759 AGGTGATGGCTCTGGGTGTTGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTGGAGCTGTAGAATCGGCTCGATC
5516801 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
5516816 AAGTGGGGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTGGAGCTGTAGAATCGGCTCGATC
Found at i:5518754 original size:22 final size:22
Alignment explanation
Indices: 5518729--5518775 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5518719 ATAGAGGGGG
*
5518729 GTCGCCGGATATAGGG-ACGGAT
1 GTCGCCGGAGAT-GGGTACGGAT
*
5518751 GTCGCTGGAGATGGGTACGGAT
1 GTCGCCGGAGATGGGTACGGAT
5518773 GTC
1 GTC
5518776 TCCGTAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.19, C:0.17, G:0.43, T:0.21
Consensus pattern (22 bp):
GTCGCCGGAGATGGGTACGGAT
Found at i:5524008 original size:29 final size:29
Alignment explanation
Indices: 5523953--5524009 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
5523943 ATGCCCGTTT
*
5523953 TTCCAGTATAGTGTCTAACATTTATTTCA
1 TTCCAGTATAGTGCCTAACATTTATTTCA
* *
5523982 TTCCAGT-TTGTGCCTAACGTTTCATTTC
1 TTCCAGTATAGTGCCTAACATTT-ATTTC
5524010 GTTACATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (29 bp):
TTCCAGTATAGTGCCTAACATTTATTTCA
Found at i:5525895 original size:22 final size:22
Alignment explanation
Indices: 5525868--5525909 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5525858 GATGATATTA
5525868 TATATT-TTTATTCAATTTAATT
1 TATATTATTT-TTCAATTTAATT
*
5525890 TATATTATTTTTCTATTTAA
1 TATATTATTTTTCAATTTAA
5525910 ATTAATGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTATTTTTCAATTTAATT
Found at i:5526828 original size:30 final size:31
Alignment explanation
Indices: 5526788--5526860 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
5526778 AATGGATTTA
* *
5526788 TTTA-GTGACCAAATTATAAA-TTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAACTTT-GAAAAG
*
5526818 TTT-GGTGACCAAAGTGTAAACTTTGAAAAG
1 TTTAGGTGACCAAAGTATAAACTTTGAAAAG
5526848 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
5526861 ATGTAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 32 0.86
31 5 0.14
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAACTTTGAAAAG
Found at i:5531768 original size:32 final size:31
Alignment explanation
Indices: 5531732--5531795 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
5531722 TACTTATTAG
* *
5531732 TTTTAATTGATTTTTAAAACATTTAAAATTGA
1 TTTTAATTGATTTTTAAAA-ATGTAAAAGTGA
5531764 TTTTAATTGATTTTTAAAAATGTAAAAGTGA
1 TTTTAATTGATTTTTAAAAATGTAAAAGTGA
5531795 T
1 T
5531796 ACTTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (31 bp):
TTTTAATTGATTTTTAAAAATGTAAAAGTGA
Found at i:5533528 original size:29 final size:28
Alignment explanation
Indices: 5533495--5533560 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 28
5533485 TTTAATAGTT
5533495 AATTATATACTTCACTTTAAATAAGTATA
1 AATTATATACTT-ACTTTAAATAAGTATA
5533524 AA-T-TATA--TACTTTAAATAAGTATA
1 AATTATATACTTACTTTAAATAAGTATA
5533548 AATTATATACTTA
1 AATTATATACTTA
5533561 TTTCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
24 18 0.55
25 2 0.06
26 4 0.12
27 4 0.12
28 3 0.09
29 2 0.06
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (28 bp):
AATTATATACTTACTTTAAATAAGTATA
Found at i:5533537 original size:24 final size:24
Alignment explanation
Indices: 5533508--5533559 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
5533498 TATATACTTC
5533508 ACTTTAAATAAGTATAAATTATAT
1 ACTTTAAATAAGTATAAATTATAT
5533532 ACTTTAAATAAGTATAAATTATAT
1 ACTTTAAATAAGTATAAATTATAT
5533556 ACTT
1 ACTT
5533560 ATTTCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (24 bp):
ACTTTAAATAAGTATAAATTATAT
Found at i:5534068 original size:85 final size:85
Alignment explanation
Indices: 5533907--5534120 Score: 254
Period size: 85 Copynumber: 2.5 Consensus size: 85
5533897 AATGACGTGT
* * *
5533907 GCTTCAATGACACGCAATGTAAGTCATATATACGTGTCATAAATTTATGACACACAAATGTGAGT
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGCGTGTCATAAATTTATGACACACAAATGTGAGT
*
5533972 CAAGAAGATTTACGACGGGG
66 CAAGAAGATTTACGACCGGG
* * *
5533992 GCTTCAATGACGCTCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGCGTGTCATAAATTTATGACACACAAATGTGAGT
*** * *
5534057 CATCTTA-ATTTATGACCGTG
66 CA-AGAAGATTTACGACCGGG
* *
5534077 TCTTCAATGACGCGCAATG--AGCATCATAAATGCGCGTCATAAAT
1 GCTTCAATGACGCGCAATGTAAG--TCATAAATGCGTGTCATAAAT
5534121 GTGCGTCATA
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
83 2 0.02
85 108 0.97
86 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATAAATGCGTGTCATAAATTTATGACACACAAATGTGAGT
CAAGAAGATTTACGACCGGG
Found at i:5534116 original size:13 final size:13
Alignment explanation
Indices: 5534100--5534154 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
5534090 GCAATGAGCA
5534100 TCATAAATGCGCG
1 TCATAAATGCGCG
*
5534113 TCATAAATGTGCG
1 TCATAAATGCGCG
**
5534126 TCATAAATGCATG
1 TCATAAATGCGCG
*
5534139 TCATAAATACGCG
1 TCATAAATGCGCG
5534152 TCA
1 TCA
5534155 AAGATTCATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:5534121 original size:26 final size:26
Alignment explanation
Indices: 5534092--5534146 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5534082 AATGACGCGC
*
5534092 AATGAGCATCATAAATGCGCGTCATA
1 AATGAGCATCATAAATGCACGTCATA
* * *
5534118 AATGTGCGTCATAAATGCATGTCATA
1 AATGAGCATCATAAATGCACGTCATA
5534144 AAT
1 AAT
5534147 ACGCGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (26 bp):
AATGAGCATCATAAATGCACGTCATA
Found at i:5535026 original size:9 final size:9
Alignment explanation
Indices: 5535009--5535062 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 9
5534999 AATTCCATTA
5535009 CTGGAATTT
1 CTGGAATTT
*
5535018 CTTGAATTT
1 CTGGAATTT
* *
5535027 ATGGAATTA
1 CTGGAATTT
*
5535036 CTTGAATTT
1 CTGGAATTT
*
5535045 ATGGAATTT
1 CTGGAATTT
5535054 CTGGAATTT
1 CTGGAATTT
5535063 TTGGTATTTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (9 bp):
CTGGAATTT
Found at i:5535035 original size:27 final size:27
Alignment explanation
Indices: 5535005--5535061 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5534995 TAATAATTCC
* *
5535005 ATTACTGGAATTTCTTGAATTTATGGA
1 ATTACTGGAATTTATGGAATTTATGGA
* *
5535032 ATTACTTGAATTTATGGAATTTCTGGA
1 ATTACTGGAATTTATGGAATTTATGGA
5535059 ATT
1 ATT
5535062 TTTGGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (27 bp):
ATTACTGGAATTTATGGAATTTATGGA
Found at i:5535071 original size:18 final size:18
Alignment explanation
Indices: 5535010--5535062 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5535000 ATTCCATTAC
5535010 TGGAATTTCTTGAATTTA
1 TGGAATTTCTTGAATTTA
*
5535028 TGGAATTACTTGAATTTA
1 TGGAATTTCTTGAATTTA
*
5535046 TGGAATTTCTGGAATTT
1 TGGAATTTCTTGAATTT
5535063 TTGGTATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (18 bp):
TGGAATTTCTTGAATTTA
Found at i:5535896 original size:33 final size:33
Alignment explanation
Indices: 5535859--5535923 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5535849 ATATGAAAAG
5535859 GATCTATGAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
*
5535892 GATCTATGAGATCATACAAGAATGTTATACAA
1 GATCTATGAGATCATACAAGAATGTTACACAA
5535924 GCTACATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAT
Found at i:5536178 original size:20 final size:20
Alignment explanation
Indices: 5536153--5536198 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5536143 CCTTCGGGAT
*
5536153 AATTTATATGTCGTT-GTGGG
1 AATTTATATG-CCTTAGTGGG
5536173 AATTTATATGCCTTAGTGGG
1 AATTTATATGCCTTAGTGGG
5536193 AATTTA
1 AATTTA
5536199 AATGAGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (20 bp):
AATTTATATGCCTTAGTGGG
Found at i:5536612 original size:18 final size:18
Alignment explanation
Indices: 5536589--5536688 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 18
5536579 AATGGGTTCA
5536589 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
** *
5536607 TGATAAT-A-ACAGATAT
1 TGATAATGATATTGATGT
*
5536623 CATGATAATGATATTTATGT
1 --TGATAATGATATTGATGT
* ** **
5536643 TGAGAATGATAGAGATCA
1 TGATAATGATATTGATGT
*
5536661 TGATAACGATATTGATGT
1 TGATAATGATATTGATGT
5536679 TGATAATGAT
1 TGATAATGAT
5536689 GGTATTTATG
Statistics
Matches: 58, Mismatches: 20, Indels: 8
0.67 0.23 0.09
Matches are distributed among these distances:
16 5 0.09
17 1 0.02
18 47 0.81
19 1 0.02
20 4 0.07
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:5536687 original size:36 final size:36
Alignment explanation
Indices: 5536586--5536688 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
5536576 TTAAATGGGT
* * *
5536586 TCATGATAATGATATTGATGTTGATAATAACAGATA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
* *
5536622 TCATGATAATGATATTTATGTTGAGAATGATAGAGA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
*
5536658 TCATGATAACGATATTGATGTTGATAATGAT
1 TCATGATAATGATATTGATGTTGATAATGAT
5536689 GGTATTTATG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (36 bp):
TCATGATAATGATATTGATGTTGATAATGATAGAGA
Found at i:5538926 original size:10 final size:10
Alignment explanation
Indices: 5538901--5538941 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
5538891 AAGGCGTAAT
5538901 AAGAAAAA-G
1 AAGAAAAATG
*
5538910 AAAAAAAATG
1 AAGAAAAATG
5538920 AAGAAAAAATG
1 AAG-AAAAATG
5538931 AAGAAAAATG
1 AAGAAAAATG
5538941 A
1 A
5538942 GATATGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 7 0.25
10 11 0.39
11 10 0.36
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (10 bp):
AAGAAAAATG
Found at i:5538928 original size:11 final size:11
Alignment explanation
Indices: 5538904--5538938 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
5538894 GCGTAATAAG
5538904 AAAAA-GAA-A
1 AAAAATGAAGA
5538913 AAAAATGAAGA
1 AAAAATGAAGA
5538924 AAAAATGAAGA
1 AAAAATGAAGA
5538935 AAAA
1 AAAA
5538939 TGAGATATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.21
10 3 0.12
11 16 0.67
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (11 bp):
AAAAATGAAGA
Found at i:5539931 original size:17 final size:17
Alignment explanation
Indices: 5539883--5539933 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
5539873 AGTTTAAAGA
*
5539883 CATAAATGGTATTTTTTC
1 CATAAATGG-ATTTATTC
* *
5539901 CA-AAAAGAATTTTATTC
1 CATAAATGGA-TTTATTC
5539918 CATAAATGGATTTATT
1 CATAAATGGATTTATT
5539934 TAGTGACCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
16 1 0.04
17 18 0.69
18 7 0.27
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (17 bp):
CATAAATGGATTTATTC
Found at i:5540989 original size:30 final size:31
Alignment explanation
Indices: 5540947--5541014 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
5540937 ACAAGCTCTT
* * *
5540947 AAAAA-TTCAGGGATGATTTTATAATTTT-C
1 AAAAAGTTCAGGGATCAATTCATAATTTTGC
* *
5540976 AAAAAGTTGAGGGATCAATTCATAATTTTGG
1 AAAAAGTTCAGGGATCAATTCATAATTTTGC
5541007 AAAAAGTT
1 AAAAAGTT
5541015 AGGAATAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 5 0.16
30 19 0.59
31 8 0.25
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (31 bp):
AAAAAGTTCAGGGATCAATTCATAATTTTGC
Found at i:5541242 original size:9 final size:9
Alignment explanation
Indices: 5541222--5541271 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
5541212 CCATTACTGA
*
5541222 AATTTCTTG
1 AATTTCTGG
*
5541231 AATTTATGG
1 AATTTCTGG
*
5541240 AATTTCTTG
1 AATTTCTGG
*
5541249 AGTTTCTGG
1 AATTTCTGG
5541258 AATTTCTGG
1 AATTTCTGG
5541267 AATTT
1 AATTT
5541272 TTGGTATTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (9 bp):
AATTTCTGG
Found at i:5541280 original size:18 final size:18
Alignment explanation
Indices: 5541222--5541271 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
5541212 CCATTACTGA
5541222 AATTTCTTGAATTTATGG
1 AATTTCTTGAATTTATGG
* *
5541240 AATTTCTTGAGTTTCTGG
1 AATTTCTTGAATTTATGG
*
5541258 AATTTCTGGAATTT
1 AATTTCTTGAATTT
5541272 TTGGTATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (18 bp):
AATTTCTTGAATTTATGG
Found at i:5542293 original size:20 final size:20
Alignment explanation
Indices: 5542270--5542317 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
5542260 CCTTCGGGAT
*
5542270 AATTTATATGCCTTTGTGGG
1 AATTTATATGCCTTAGTGGG
5542290 AATTTATATGCCTTAGTGGG
1 AATTTATATGCCTTAGTGGG
5542310 AATTTATA
1 AATTTATA
5542318 CGAGCTGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (20 bp):
AATTTATATGCCTTAGTGGG
Found at i:5542717 original size:18 final size:18
Alignment explanation
Indices: 5542694--5542793 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 18
5542684 AATGGGTTCA
5542694 TGATAATGATATTGATGT
1 TGATAATGATATTGATGT
* *
5542712 TGATAAT-A-ATAGATAT
1 TGATAATGATATTGATGT
* *
5542728 CAGGATAATGATATTTATGT
1 --TGATAATGATATTGATGT
* ** **
5542748 TGAGAATGATAGAGATCA
1 TGATAATGATATTGATGT
*
5542766 TGATAACGATATTGATGT
1 TGATAATGATATTGATGT
5542784 TGATAATGAT
1 TGATAATGAT
5542794 GGTATTTATG
Statistics
Matches: 58, Mismatches: 20, Indels: 8
0.67 0.23 0.09
Matches are distributed among these distances:
16 6 0.10
17 1 0.02
18 45 0.78
19 1 0.02
20 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (18 bp):
TGATAATGATATTGATGT
Found at i:5542792 original size:36 final size:36
Alignment explanation
Indices: 5542691--5542793 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
5542681 TTAAATGGGT
* *
5542691 TCATGATAATGATATTGATGTTGATAATAATAGATA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
* * *
5542727 TCAGGATAATGATATTTATGTTGAGAATGATAGAGA
1 TCATGATAATGATATTGATGTTGATAATGATAGAGA
*
5542763 TCATGATAACGATATTGATGTTGATAATGAT
1 TCATGATAATGATATTGATGTTGATAATGAT
5542794 GGTATTTATG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (36 bp):
TCATGATAATGATATTGATGTTGATAATGATAGAGA
Found at i:5544531 original size:12 final size:12
Alignment explanation
Indices: 5544514--5544538 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5544504 GAAGTGCTAG
5544514 GAAGGTTTACAA
1 GAAGGTTTACAA
5544526 GAAGGTTTACAA
1 GAAGGTTTACAA
5544538 G
1 G
5544539 CTAAAGACAC
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:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (12 bp):
GAAGGTTTACAA
Done.