Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 104 of 130
Found at i:20393221 original size:16 final size:16
Alignment explanation
Indices: 20393202--20393295 Score: 64
Period size: 16 Copynumber: 5.7 Consensus size: 16
20393192 AAATAGCATG
*
20393202 GAAAATTAAATTGTAT
1 GAAAATTAAAGTGTAT
* *
20393218 GAAAAGTAAAGTGTAA
1 GAAAATTAAAGTGTAT
* * *
20393234 GGAGATTAAAGAGTTAT
1 GAAAATTAAAGTG-TAT
* *
20393251 GAAAATTAAAGTGCAAG
1 GAAAATTAAAGTG-TAT
20393268 GAAAATTTAAAGTGCTA-
1 GAAAA-TTAAAGTG-TAT
*
20393285 GAAAAATAAAG
1 GAAAATTAAAG
20393296 AACAAGAAAG
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
16 27 0.45
17 23 0.38
18 10 0.17
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.24
Consensus pattern (16 bp):
GAAAATTAAAGTGTAT
Found at i:20393271 original size:17 final size:16
Alignment explanation
Indices: 20393251--20393295 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
20393241 AAAGAGTTAT
20393251 GAAAATTAAAGTGCAA
1 GAAAATTAAAGTGCAA
*
20393267 GGAAAATTTAAAGTGCTA
1 -GAAAA-TTAAAGTGCAA
*
20393285 GAAAAATAAAG
1 GAAAATTAAAG
20393296 AACAAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 10 0.40
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (16 bp):
GAAAATTAAAGTGCAA
Found at i:20393290 original size:18 final size:18
Alignment explanation
Indices: 20393252--20393291 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20393242 AAGAGTTATG
*
20393252 AAAA-TTAAAGTGCAAGG
1 AAAATTTAAAGTGCAAGA
*
20393269 AAAATTTAAAGTGCTAGA
1 AAAATTTAAAGTGCAAGA
20393287 AAAAT
1 AAAAT
20393292 AAAGAACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.23
Consensus pattern (18 bp):
AAAATTTAAAGTGCAAGA
Found at i:20393331 original size:16 final size:16
Alignment explanation
Indices: 20393306--20393374 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
20393296 AACAAGAAAG
20393306 TAAA-TTGCATGAATT
1 TAAAGTTGCATGAATT
*
20393321 TAAAGTTGCATAGAATAA
1 TAAAGTTGCAT-GAAT-T
*
20393339 TAAA-TTGCCTGAATT
1 TAAAGTTGCATGAATT
* * *
20393354 TAAAGTTCCATAAAAT
1 TAAAGTTGCATGAATT
20393370 TAAAG
1 TAAAG
20393375 AACAAGAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
15 8 0.19
16 22 0.51
17 9 0.21
18 4 0.09
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (16 bp):
TAAAGTTGCATGAATT
Found at i:20393384 original size:16 final size:15
Alignment explanation
Indices: 20393365--20393421 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
20393355 AAAGTTCCAT
20393365 AAAATTAAAGAACAA
1 AAAATTAAAGAACAA
* ** *
20393380 GAAAAATAAAGTTTCAT
1 -AAAATTAAAG-AACAA
*
20393397 AAATTTAAAGAACAA
1 AAAATTAAAGAACAA
20393412 AAAATTAAAG
1 AAAATTAAAG
20393422 TGCTAGAATT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
15 11 0.37
16 17 0.57
17 2 0.07
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAATTAAAGAACAA
Found at i:20393398 original size:32 final size:31
Alignment explanation
Indices: 20393354--20393422 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
20393344 TGCCTGAATT
20393354 TAAAGTTCCATAAAATTAAAGAACAAGAAAAA
1 TAAAGTTCCATAAAATTAAAGAACAA-AAAAA
* * *
20393386 TAAAGTTTCATAAATTTAAAGAACAAAAAAT
1 TAAAGTTCCATAAAATTAAAGAACAAAAAAA
20393417 TAAAGT
1 TAAAGT
20393423 GCTAGAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 10 0.29
32 24 0.71
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (31 bp):
TAAAGTTCCATAAAATTAAAGAACAAAAAAA
Found at i:20393450 original size:16 final size:16
Alignment explanation
Indices: 20393416--20393458 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
20393406 GAACAAAAAA
20393416 TTAAAGTGC-TAGAAT
1 TTAAAGTGCATAGAAT
* *
20393431 TTAAATTGCATAGTAT
1 TTAAAGTGCATAGAAT
20393447 TTAAAGTGCATA
1 TTAAAGTGCATA
20393459 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (16 bp):
TTAAAGTGCATAGAAT
Found at i:20393466 original size:16 final size:16
Alignment explanation
Indices: 20393411--20393467 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
20393401 TTAAAGAACA
20393411 AAAAATTAAAGTGC-T
1 AAAAATTAAAGTGCAT
* * *
20393426 AGAATTTAAATTGCAT
1 AAAAATTAAAGTGCAT
** *
20393442 AGTATTTAAAGTGCAT
1 AAAAATTAAAGTGCAT
20393458 AAAAATTAAA
1 AAAAATTAAA
20393468 AAAAAAAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 11 0.33
16 22 0.67
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (16 bp):
AAAAATTAAAGTGCAT
Found at i:20402194 original size:122 final size:122
Alignment explanation
Indices: 20402046--20402271 Score: 303
Period size: 122 Copynumber: 1.9 Consensus size: 122
20402036 CAGATACATG
* * * * *
20402046 GCAACATTCCTTATAAATATATGAGATTCCAA-AGAAACAGAAGTCAAAA-GTGTAAAAGAATTG
1 GCAACATTCCTCAAAAATATATGAGATT-CAACAGAAACAGAAAT-AAAATATGTAAAAGAACTG
* * * * *
20402109 AATAATTGAAGGTGATGTATGAAAATGTTCTCATTCACTTTTGAATAAAAATTTGGTGT
64 AATAATTCAAGCTAACGTATGAAAATGTTCTAATTCACTTTTGAATAAAAATTTGGTGT
* *
20402168 GCAACATTCCTCAAAAATATGTGAGATTCAACAGAAACAGAAATAAAATATGTAAAAGAACTGAG
1 GCAACATTCCTCAAAAATATATGAGATTCAACAGAAACAGAAATAAAATATGTAAAAGAACTGAA
*
20402233 TAATTCAAGCTAACGTATGAAAATTTTCTAATTCACTTT
66 TAATTCAAGCTAACGTATGAAAATGTTCTAATTCACTTT
20402272 CGGACATAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
121 7 0.08
122 82 0.92
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (122 bp):
GCAACATTCCTCAAAAATATATGAGATTCAACAGAAACAGAAATAAAATATGTAAAAGAACTGAA
TAATTCAAGCTAACGTATGAAAATGTTCTAATTCACTTTTGAATAAAAATTTGGTGT
Found at i:20402813 original size:215 final size:215
Alignment explanation
Indices: 20402442--20402875 Score: 766
Period size: 215 Copynumber: 2.0 Consensus size: 215
20402432 GCTCTCTTTA
20402442 ATGAACCATAAGTAATCTTGATTATATTGCCTAAAAAGCTGACCATCTCTTCAACATGCAAACAC
1 ATGAACCATAAGTAATCTTGATTATATTGCCTAAAAAGCTGACCATCTCTTCAACATGCAAACAC
* *
20402507 AATTCACAATCAGTTTCGTAAAACAGCAATGGCAAGAAGGAAATTGTGGAAGATAAAGCTAAGTT
66 AATTCACAATCAGTTTCGTAAAACAGCAATGGCAAGAAGGAAATAGTGGAAGAAAAAGCTAAGTT
**
20402572 CCCTTGTTTGGTACGAAGCAAATAGGAGGAATGAAGAAAAATGAGTGGATTTATACTGCCCATTG
131 CCCTTGTTTGGTACGAAGCAAATAGGAGGAATGAAGAAAAATGAGTGGATTTATACTGCCCACGG
20402637 GTACAAAATTCAATTCTTCT
196 GTACAAAATTCAATTCTTCT
20402657 ATGAACCATAAGTAATCTTGATTATATTGCCTAAAAAGCTGACCATCTCTTCAA-AGTGCAAACA
1 ATGAACCATAAGTAATCTTGATTATATTGCCTAAAAAGCTGACCATCTCTTCAACA-TGCAAACA
*
20402721 CAATTCACAATCAGTCTT-GTAAAACAGCAATGGCTAGAAGGAAATAGTGGAAGAAAAAG-TGAA
65 CAATTCACAATCAGT-TTCGTAAAACAGCAATGGCAAGAAGGAAATAGTGGAAGAAAAAGCT-AA
20402784 GTTCCCTTGTTTGGTACGAAGCAAATAGGAGGAATGAAGAAAAATGAGTGGATTTATACTGCCCA
128 GTTCCCTTGTTTGGTACGAAGCAAATAGGAGGAATGAAGAAAAATGAGTGGATTTATACTGCCCA
*
20402849 CGGGTACAAAATTCAATTCTTTT
193 CGGGTACAAAATTCAATTCTTCT
20402872 ATGA
1 ATGA
20402876 TGGGAAACAA
Statistics
Matches: 210, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
214 2 0.01
215 206 0.98
216 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (215 bp):
ATGAACCATAAGTAATCTTGATTATATTGCCTAAAAAGCTGACCATCTCTTCAACATGCAAACAC
AATTCACAATCAGTTTCGTAAAACAGCAATGGCAAGAAGGAAATAGTGGAAGAAAAAGCTAAGTT
CCCTTGTTTGGTACGAAGCAAATAGGAGGAATGAAGAAAAATGAGTGGATTTATACTGCCCACGG
GTACAAAATTCAATTCTTCT
Found at i:20403996 original size:1 final size:1
Alignment explanation
Indices: 20403990--20404014 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20403980 CTTTCTTCTC
20403990 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
20404015 CACCCATCAT
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20408241 original size:16 final size:16
Alignment explanation
Indices: 20408220--20408255 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
20408210 GAAATCATCA
*
20408220 GCTTCAAGAATGTTAG
1 GCTTCAAGAATGTAAG
20408236 GCTTCAAGAATGTAAG
1 GCTTCAAGAATGTAAG
20408252 GCTT
1 GCTT
20408256 AACAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (16 bp):
GCTTCAAGAATGTAAG
Found at i:20424304 original size:15 final size:15
Alignment explanation
Indices: 20424286--20424317 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20424276 TTTTGAAAAT
*
20424286 AATTTTTAATTTTAA
1 AATTTTAAATTTTAA
20424301 AATTTTAAATTTTAA
1 AATTTTAAATTTTAA
20424316 AA
1 AA
20424318 AACATGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTAAATTTTAA
Found at i:20430127 original size:22 final size:22
Alignment explanation
Indices: 20430099--20430145 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
20430089 TTAATGAATC
*
20430099 AAATAATATCAC-TTTATTAATA
1 AAATAATATCACGTTTA-AAATA
20430121 AAATAATATCACGTTTAAAATA
1 AAATAATATCACGTTTAAAATA
20430143 AAA
1 AAA
20430146 ATACAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATAATATCACGTTTAAAATA
Found at i:20433186 original size:14 final size:14
Alignment explanation
Indices: 20433167--20433195 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20433157 GCATAGATGC
20433167 TGTTTGTGTGAATT
1 TGTTTGTGTGAATT
20433181 TGTTTGTGTGAATT
1 TGTTTGTGTGAATT
20433195 T
1 T
20433196 TAACAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TGTTTGTGTGAATT
Found at i:20435410 original size:15 final size:16
Alignment explanation
Indices: 20435390--20435432 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
20435380 AAATAACAAA
*
20435390 ATTAATTT-TTTAATT
1 ATTAATTTAATTAATT
20435405 ATTAATTTAATTAATT
1 ATTAATTTAATTAATT
*
20435421 -TTAATTAAATTA
1 ATTAATTTAATTA
20435433 TGAGTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAATTTAATTAATT
Found at i:20435705 original size:19 final size:19
Alignment explanation
Indices: 20435662--20435703 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
20435652 AAGTTTGATT
20435662 TTATTT-TTTAATCAAATC
1 TTATTTATTTAATCAAATC
*
20435680 TTATTTATTTATTCAAAT-
1 TTATTTATTTAATCAAATC
20435698 TTATTT
1 TTATTT
20435704 TAATATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTATTTAATCAAATC
Found at i:20435885 original size:2 final size:2
Alignment explanation
Indices: 20435878--20435903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20435868 TGCGGTTTTG
20435878 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
20435904 TTATTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20436243 original size:13 final size:14
Alignment explanation
Indices: 20436225--20436256 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20436215 TTTTAACAAA
20436225 TAAAAA-TTTATTT
1 TAAAAATTTTATTT
20436238 TAAAAATTTTATTT
1 TAAAAATTTTATTT
20436252 TAAAA
1 TAAAA
20436257 TATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAAATTTTATTT
Found at i:20440081 original size:47 final size:47
Alignment explanation
Indices: 20440003--20440097 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
20439993 TTATCACAAG
*
20440003 TACTTGGAAAATATTCACAACAGGAAATGACCCTTTTCTAAGAGTAA
1 TACTCGGAAAATATTCACAACAGGAAATGACCCTTTTCTAAGAGTAA
* * *
20440050 TACTCGGAAAATATTCACAATAGGAATTGACCCTTTTCTAAGGGTAA
1 TACTCGGAAAATATTCACAACAGGAAATGACCCTTTTCTAAGAGTAA
20440097 T
1 T
20440098 TAGCAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (47 bp):
TACTCGGAAAATATTCACAACAGGAAATGACCCTTTTCTAAGAGTAA
Found at i:20443583 original size:18 final size:19
Alignment explanation
Indices: 20443560--20443596 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20443550 TTGAAATTAA
20443560 TTATATTAA-AAATAAATT
1 TTATATTAATAAATAAATT
*
20443578 TTATATTAATTAATAAATT
1 TTATATTAATAAATAAATT
20443597 CATAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATATTAATAAATAAATT
Found at i:20444447 original size:16 final size:17
Alignment explanation
Indices: 20444415--20444459 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
20444405 GATCTCGTAG
20444415 AAAAAAATA-ATGT-GAA
1 AAAAAAATATAT-TAGAA
*
20444431 AAAGAAAT-TATTAGAA
1 AAAAAAATATATTAGAA
20444447 AAAAAAATATATT
1 AAAAAAATATATT
20444460 TTATTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 19 0.79
17 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAAAATATATTAGAA
Found at i:20446234 original size:11 final size:12
Alignment explanation
Indices: 20446217--20446249 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20446207 TAGAAAAAGT
20446217 TAGTAAAAAATA
1 TAGTAAAAAATA
*
20446229 TA-TAAAATATA
1 TAGTAAAAAATA
20446240 TAGTAAAAAA
1 TAGTAAAAAA
20446250 ATTAGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (12 bp):
TAGTAAAAAATA
Found at i:20454194 original size:38 final size:39
Alignment explanation
Indices: 20454119--20454194 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
20454109 ACTTTTAAAT
*
20454119 TTCTTTCTACTTTAAATTAGTGGTAGAGCATTCTAATAG
1 TTCTTTCTACTTTAAATTAGTGGTAGAGCATGCTAATAG
* *
20454158 TTCTTTCTACTTTAAATTATTTG-AGAGCATGCTAATA
1 TTCTTTCTACTTTAAATTAGTGGTAGAGCATGCTAATA
20454195 CTGGTATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 13 0.38
39 21 0.62
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (39 bp):
TTCTTTCTACTTTAAATTAGTGGTAGAGCATGCTAATAG
Found at i:20456385 original size:15 final size:15
Alignment explanation
Indices: 20456354--20456384 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
20456344 ATTAATTGAA
20456354 TTGATCAAATTAATT
1 TTGATCAAATTAATT
20456369 TTGATC-AATTAATT
1 TTGATCAAATTAATT
20456383 TT
1 TT
20456385 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (15 bp):
TTGATCAAATTAATT
Found at i:20458939 original size:19 final size:18
Alignment explanation
Indices: 20458908--20458943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20458898 TTTATTTTTA
*
20458908 AATAATAAGTATATATTC
1 AATAATAAATATATATTC
20458926 AATATATAAATATATATT
1 AATA-ATAAATATATATT
20458944 GTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AATAATAAATATATATTC
Found at i:20472043 original size:23 final size:25
Alignment explanation
Indices: 20472014--20472074 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
20472004 AGTCCAAAGA
20472014 AAATAATTTTTATTTAAAA-C-AAC
1 AAATAATTTTTATTTAAAATCAAAC
* * *
20472037 AATTAATCTTTCATTTAAAATCAAAT
1 AAATAAT-TTTTATTTAAAATCAAAC
20472063 AAATAATTTTTA
1 AAATAATTTTTA
20472075 AAGTAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 6 0.20
24 11 0.37
25 5 0.17
26 8 0.27
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATAATTTTTATTTAAAATCAAAC
Found at i:20472508 original size:20 final size:21
Alignment explanation
Indices: 20472478--20472517 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20472468 AAAAATTGAA
*
20472478 TGGGATTATTCAATGCATTTT
1 TGGGATTATTCAAGGCATTTT
20472499 TGGG-TTATTCAAGGCATTT
1 TGGGATTATTCAAGGCATTT
20472518 CTAATCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (21 bp):
TGGGATTATTCAAGGCATTTT
Found at i:20474702 original size:3 final size:3
Alignment explanation
Indices: 20474694--20474749 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
20474684 CATGGGGCTG
20474694 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20474741 TAT TAT TAT
1 TAT TAT TAT
20474750 GTACTTGAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20480893 original size:36 final size:35
Alignment explanation
Indices: 20480846--20480921 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 35
20480836 ACACATATCC
20480846 AAAATGACTATAATGCCTCTCCT-TCTATAATTAACT
1 AAAATGACTATAATGCCTCTCCTATC-ATAATT-ACT
* *
20480882 AAAATTACTATAATGTCTCTCCTATCATAATTACT
1 AAAATGACTATAATGCCTCTCCTATCATAATTACT
20480917 AAAAT
1 AAAAT
20480922 ACCTCTTACC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 8 0.22
36 27 0.73
37 2 0.05
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (35 bp):
AAAATGACTATAATGCCTCTCCTATCATAATTACT
Found at i:20483319 original size:2 final size:2
Alignment explanation
Indices: 20483314--20483344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20483304 AGAAAAACAA
20483314 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 A
20483345 AAGAGGGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20483728 original size:2 final size:2
Alignment explanation
Indices: 20483723--20483796 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
20483713 TCCCCCCTCG
20483723 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20483765 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20483797 ATATATTATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20483801 original size:2 final size:2
Alignment explanation
Indices: 20483796--20483836 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
20483786 TCTCTCTCTC
20483796 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA 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
20483837 CTCTTAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20484423 original size:21 final size:21
Alignment explanation
Indices: 20484399--20484443 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20484389 GTTATTGTTG
* *
20484399 TAATGAGATTAGATATTA-TAA
1 TAATAAGATTA-AAATTATTAA
20484420 TAATAAGATTAAAATTATTAA
1 TAATAAGATTAAAATTATTAA
20484441 TAA
1 TAA
20484444 GATATGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (21 bp):
TAATAAGATTAAAATTATTAA
Found at i:20487672 original size:18 final size:18
Alignment explanation
Indices: 20487639--20487711 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
20487629 CATTTGTTTT
**
20487639 TGATACATTTAAGGTGGA
1 TGATACATTTGTGGTGGA
*
20487657 TGATATATTTGTGGTGGGA
1 TGATACATTTGTGGT-GGA
**
20487676 -GATACATTTGTGGTAAA
1 TGATACATTTGTGGTGGA
*
20487693 AGATACATTTGTGGTGGA
1 TGATACATTTGTGGTGGA
20487711 T
1 T
20487712 AATAACTACA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
17 1 0.02
18 40 0.91
19 3 0.07
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (18 bp):
TGATACATTTGTGGTGGA
Found at i:20492031 original size:28 final size:27
Alignment explanation
Indices: 20491971--20492031 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
20491961 TGACAATAAT
20491971 ATAAATTCCAAAACAACAAAAAAATTA
1 ATAAATTCCAAAACAACAAAAAAATTA
* * *
20491998 TTAAATTTCAAAACAA-AATCATAAATTA
1 ATAAATTCCAAAACAACAA--AAAAATTA
20492026 ATAAAT
1 ATAAAT
20492032 AACAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
28 12 0.43
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (27 bp):
ATAAATTCCAAAACAACAAAAAAATTA
Found at i:20492562 original size:21 final size:21
Alignment explanation
Indices: 20492536--20492582 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
20492526 ATTCTACATA
*
20492536 AATTTTACAAGAAAGAAAGGT
1 AATTTTACAAGAAAGAAACGT
20492557 AATTTTACAAGAAAGAAACGT
1 AATTTTACAAGAAAGAAACGT
20492578 AATTT
1 AATTT
20492583 AACTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (21 bp):
AATTTTACAAGAAAGAAACGT
Found at i:20493551 original size:17 final size:17
Alignment explanation
Indices: 20493531--20493564 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20493521 ATAATAAATA
*
20493531 ATAACTAATAAATAATT
1 ATAAATAATAAATAATT
*
20493548 ATAAATAATAATTAATT
1 ATAAATAATAAATAATT
20493565 TTTATATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAATAATAAATAATT
Found at i:20494405 original size:3 final size:3
Alignment explanation
Indices: 20494397--20494421 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20494387 AGTAAATAAG
20494397 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
20494422 GTTGTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20496206 original size:37 final size:37
Alignment explanation
Indices: 20496156--20496233 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
20496146 TCCACTGTCC
*
20496156 AATAAACATTCTCATTGTCTTAGCACTTTAAAGTATG
1 AATAAACATTCTCATTGTCTAAGCACTTTAAAGTATG
*
20496193 AATAAACATTCTCATTTTCTAAGCACTTTAAAGTATG
1 AATAAACATTCTCATTGTCTAAGCACTTTAAAGTATG
20496230 AATA
1 AATA
20496234 CAGCAGTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
AATAAACATTCTCATTGTCTAAGCACTTTAAAGTATG
Found at i:20499340 original size:8 final size:8
Alignment explanation
Indices: 20499327--20499360 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
20499317 AGAGGGGAAA
20499327 ATCTCAAT
1 ATCTCAAT
*
20499335 ATCTCAAC
1 ATCTCAAT
20499343 ATCTCAAT
1 ATCTCAAT
*
20499351 AACTCAAT
1 ATCTCAAT
20499359 AT
1 AT
20499361 TCAGCATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (8 bp):
ATCTCAAT
Found at i:20502546 original size:22 final size:21
Alignment explanation
Indices: 20502525--20502572 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
20502515 AAATTTTTAT
*
20502525 TAATTTTTTTAATGACAATTA
1 TAATTTTTTTAATAACAATTA
*
20502546 TAATATTTTTTAATAATAATTA
1 TAAT-TTTTTTAATAACAATTA
20502568 TAATT
1 TAATT
20502573 ATTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATTTTTTTAATAACAATTA
Found at i:20503278 original size:18 final size:18
Alignment explanation
Indices: 20503255--20503292 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20503245 TAAATAATAT
20503255 ATAAAAATAAAAAATAAA
1 ATAAAAATAAAAAATAAA
* *
20503273 ATAAAAATAATAAATTAA
1 ATAAAAATAAAAAATAAA
20503291 AT
1 AT
20503293 TAAATCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATAAAAAATAAA
Found at i:20503788 original size:41 final size:43
Alignment explanation
Indices: 20503742--20503822 Score: 114
Period size: 41 Copynumber: 1.9 Consensus size: 43
20503732 AAATTTTATA
20503742 AAAATTAA-AAAATATATATTTTATA-TTTA-ATATATTAACAT
1 AAAATTAATAAAATA-ATATTTTATATTTTACATATATTAACAT
* *
20503783 AAAATTAATATAATAATTTTTTATATTTTACATATATTAA
1 AAAATTAATAAAATAATATTTTATATTTTACATATATTAA
20503823 ACACGACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 17 0.49
42 9 0.26
43 9 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (43 bp):
AAAATTAATAAAATAATATTTTATATTTTACATATATTAACAT
Found at i:20504751 original size:11 final size:11
Alignment explanation
Indices: 20504731--20504773 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
20504721 TTATTTTTTT
20504731 AATATAAAATA
1 AATATAAAATA
20504742 AATATTAAATATA
1 AATA-TAAA-ATA
*
20504755 AAAATAAAATA
1 AATATAAAATA
20504766 AA-ATAAAA
1 AATATAAAA
20504774 AGCCATCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 6 0.21
11 9 0.31
12 8 0.28
13 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATATAAAATA
Found at i:20504754 original size:18 final size:16
Alignment explanation
Indices: 20504731--20504773 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
20504721 TTATTTTTTT
20504731 AATATAAAATAAATATTA
1 AATATAAAATAAA-A-TA
20504749 AATATAAAAATAAAATA
1 AATAT-AAAATAAAATA
20504766 AA-ATAAAA
1 AATATAAAA
20504774 AGCCATCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 2 0.08
17 4 0.17
18 6 0.25
19 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATATAAAATAAAATA
Found at i:20505666 original size:18 final size:19
Alignment explanation
Indices: 20505643--20505678 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20505633 AATATACTTA
*
20505643 TTTTATAA-GTAAATTAAT
1 TTTTATAATATAAATTAAT
20505661 TTTTATAATATAAATTAA
1 TTTTATAATATAAATTAA
20505679 GTAAATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTATAATATAAATTAAT
Found at i:20506017 original size:17 final size:17
Alignment explanation
Indices: 20505983--20506016 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20505973 AAATAATTTA
*
20505983 TCATTTAGTAGTTTTTT
1 TCATTTAATAGTTTTTT
20506000 TCATTTAATA-TTTTTT
1 TCATTTAATAGTTTTTT
20506016 T
1 T
20506017 TTCATGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (17 bp):
TCATTTAATAGTTTTTT
Found at i:20506725 original size:23 final size:22
Alignment explanation
Indices: 20506693--20506752 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
20506683 TTTGATAAAT
*
20506693 TAAATCAATAAATATAAAATTAA
1 TAAATTAATAAATATAAAATT-A
*
20506716 TAAATTAATAAATACTACAATTA
1 TAAATTAATAAATA-TAAAATTA
20506739 T-AATT-ATAAA-ATAA
1 TAAATTAATAAATATAA
20506753 TTGATTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 5 0.15
22 4 0.12
23 15 0.45
24 6 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATTAATAAATATAAAATTA
Found at i:20506790 original size:15 final size:14
Alignment explanation
Indices: 20506770--20506803 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20506760 TCTAATCAAT
20506770 TATTTGATACATTTA
1 TATTTGAT-CATTTA
*
20506785 TATTTGATTATTTA
1 TATTTGATCATTTA
20506799 TATTT
1 TATTT
20506804 TTATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (14 bp):
TATTTGATCATTTA
Found at i:20506809 original size:15 final size:15
Alignment explanation
Indices: 20506780--20506817 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20506770 TATTTGATAC
20506780 ATTTATA-TTTGATT
1 ATTTATATTTTGATT
*
20506794 ATTTATATTTTTATT
1 ATTTATATTTTGATT
*
20506809 ATTAATATT
1 ATTTATATT
20506818 AAATCACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
ATTTATATTTTGATT
Found at i:20506914 original size:23 final size:24
Alignment explanation
Indices: 20506882--20506927 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
20506872 ATTTGAAAAT
20506882 TAAATCAATAAATA-TAGAATTAA
1 TAAATCAATAAATACTAGAATTAA
* *
20506905 TAAATTAATAAATACTATAATTA
1 TAAATCAATAAATACTAGAATTA
20506928 CAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAATCAATAAATACTAGAATTAA
Found at i:20506937 original size:189 final size:188
Alignment explanation
Indices: 20506596--20506983 Score: 541
Period size: 189 Copynumber: 2.0 Consensus size: 188
20506586 AAATTTTAAA
*
20506596 TTGATTATGTTTATATTTTTATTATTAACCTTAAATCACTCTCAATTCAATTAATATTAAAGTAT
1 TTGATTA-GTTTATATTTTTATTATTAACATTAAATCACTCTCAATTCAATTAATATTAAAGTAT
20506661 TAAAATTTTTTTAAAAATTTAATTTGATAAATTAAATCAATAAATATAAAATTAATAAATTAATA
65 TAAAA---TTTTAAAAATTTAATTTGATAAATTAAATCAATAAATATAAAATTAATAAATTAATA
* * *
20506726 AATACTACAATTATAATTATAAAATAATTGATTCTCTAATCAATTATTTGATACATTTATAT
127 AATACTACAATTACAATTATAAAATAATTAATTATCTAATCAATTATTTGATACATTTATAT
* * *
20506788 TTGATTA-TTTATATTTTTATTATTAATATTAAATCACTCTCAATTTAATTGATATTAAAAAGTA
1 TTGATTAGTTTATATTTTTATTATTAACATTAAATCACTCTCAATTCAATTAATATT--AAAGTA
* *
20506852 -TCAAA-TTTAAAAATTTTGTAATTTGA-AAATTAAATCAATAAATATAGAATTAATAAATTAAT
64 TTAAAATTTTAAAAA--TT-TAATTTGATAAATTAAATCAATAAATATAAAATTAATAAATTAAT
* * * * *
20506914 AAATACTATAATTACAATTATAAAATAGTTAATTATTTAATCAATTATTTGATATATTTATGT
126 AAATACTACAATTACAATTATAAAATAATTAATTATCTAATCAATTATTTGATACATTTATAT
20506977 TTGATTA
1 TTGATTA
20506984 AATATAGTAT
Statistics
Matches: 177, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
187 8 0.05
189 99 0.56
190 53 0.30
191 4 0.02
192 13 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (188 bp):
TTGATTAGTTTATATTTTTATTATTAACATTAAATCACTCTCAATTCAATTAATATTAAAGTATT
AAAATTTTAAAAATTTAATTTGATAAATTAAATCAATAAATATAAAATTAATAAATTAATAAATA
CTACAATTACAATTATAAAATAATTAATTATCTAATCAATTATTTGATACATTTATAT
Found at i:20507292 original size:12 final size:12
Alignment explanation
Indices: 20507277--20507306 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20507267 TTTGAGTAAT
20507277 TGATGTATTTCA
1 TGATGTATTTCA
20507289 TGATGTATTTCA
1 TGATGTATTTCA
20507301 TG-TGTA
1 TGATGTA
20507307 AATATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (12 bp):
TGATGTATTTCA
Found at i:20507683 original size:20 final size:21
Alignment explanation
Indices: 20507642--20507683 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20507632 ATTCACTCAC
* *
20507642 AATTTTTATTATTTCAATATT
1 AATTTTTATAATTTCAAAATT
20507663 AATTTTTATAATTT-AAAATT
1 AATTTTTATAATTTCAAAATT
20507683 A
1 A
20507684 TCTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTTATAATTTCAAAATT
Found at i:20508101 original size:31 final size:32
Alignment explanation
Indices: 20508031--20508106 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
20508021 AATTTCATTT
* *
20508031 GATTTCATTT-AGTAAAATATTAATAAACGTTT
1 GATTTCATTTGA-TAAAATATTAATAAACGATG
**
20508063 GATTTCATTTGATAAAATATTAATGCAC-ATG
1 GATTTCATTTGATAAAATATTAATAAACGATG
20508094 GATTTCATTTGAT
1 GATTTCATTTGAT
20508107 TTCATTTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 14 0.36
32 24 0.62
33 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (32 bp):
GATTTCATTTGATAAAATATTAATAAACGATG
Found at i:20512027 original size:21 final size:21
Alignment explanation
Indices: 20511996--20512045 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
20511986 AAAACAACAA
* *
20511996 AAAAATTATAAATT-TCAAAT
1 AAAAATCATAAATTAACAAAT
20512016 ACAAAATCATAAATTAACAAAT
1 A-AAAATCATAAATTAACAAAT
20512038 AAAAATCA
1 AAAAATCA
20512046 AATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.73
22 6 0.23
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATCATAAATTAACAAAT
Found at i:20512790 original size:28 final size:27
Alignment explanation
Indices: 20512730--20512790 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
20512720 TGACAATAAT
20512730 ATAAATTCCAAAACAACAAAAAAATTA
1 ATAAATTCCAAAACAACAAAAAAATTA
* * *
20512757 TTAAATTTCAAAACAA-AATCATAAATTA
1 ATAAATTCCAAAACAACAA--AAAAATTA
20512785 ATAAAT
1 ATAAAT
20512791 AACAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
28 12 0.43
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (27 bp):
ATAAATTCCAAAACAACAAAAAAATTA
Found at i:20513318 original size:21 final size:21
Alignment explanation
Indices: 20513292--20513338 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
20513282 ATTCTACATA
*
20513292 AATTTTACAAGAAAGAAAGGT
1 AATTTTACAAGAAAGAAACGT
20513313 AATTTTACAAGAAAGAAACGT
1 AATTTTACAAGAAAGAAACGT
20513334 AATTT
1 AATTT
20513339 AACTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (21 bp):
AATTTTACAAGAAAGAAACGT
Found at i:20514302 original size:17 final size:17
Alignment explanation
Indices: 20514270--20514319 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
20514260 ATTTATATTT
20514270 TAATAAAT-AT-AATAA
1 TAATAAATAATAAATAA
*
20514285 TAATAACTAATAAATAA
1 TAATAAATAATAAATAA
* *
20514302 TTATAAATAATAATTAA
1 TAATAAATAATAAATAA
20514319 T
1 T
20514320 TTTTATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 20 0.69
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATAAATAATAAATAA
Found at i:20514316 original size:13 final size:12
Alignment explanation
Indices: 20514270--20514317 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
20514260 ATTTATATTT
*
20514270 TAATAAATATAA
1 TAATAATTATAA
*
20514282 TAATAATAACTAA
1 TAATAATTA-TAA
20514295 TAAATAATTATAAA
1 T-AATAATTAT-AA
20514309 TAATAATTA
1 TAATAATTA
20514318 ATTTTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 7 0.23
13 13 0.43
14 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:20516964 original size:37 final size:37
Alignment explanation
Indices: 20516914--20516991 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
20516904 TCCACTGTCC
*
20516914 AATAAACATTCTCATTGTCTTAGCACTTTAAAGTATG
1 AATAAACATTCTCATTGTCTAAGCACTTTAAAGTATG
*
20516951 AATAAACATTCTCATTTTCTAAGCACTTTAAAGTATG
1 AATAAACATTCTCATTGTCTAAGCACTTTAAAGTATG
20516988 AATA
1 AATA
20516992 CAGCAGTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
AATAAACATTCTCATTGTCTAAGCACTTTAAAGTATG
Found at i:20523302 original size:23 final size:23
Alignment explanation
Indices: 20523272--20523318 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
20523262 TTTTTTATTA
*
20523272 ATTTTTTTAATGACAATTATAAT
1 ATTTTTTTAATAACAATTATAAT
*
20523295 ATTTTTTTAATAATAATTATAAT
1 ATTTTTTTAATAACAATTATAAT
20523318 A
1 A
20523319 ATTATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTTTTAATAACAATTATAAT
Found at i:20523419 original size:24 final size:24
Alignment explanation
Indices: 20523392--20523437 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20523382 TATGTGATAA
20523392 AAAATATATAA-AAATAATATAATT
1 AAAATATATAATAAA-AATATAATT
* *
20523416 AAAATTTTTAATAAAAATATAA
1 AAAATATATAATAAAAATATAA
20523438 AAGTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATATATAATAAAAATATAATT
Found at i:20523941 original size:17 final size:18
Alignment explanation
Indices: 20523919--20523957 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
20523909 AATCGAATTA
*
20523919 TATATATATTT-TATTTT
1 TATATATATTTAAATTTT
20523936 TATATATATTTAAATTTT
1 TATATATATTTAAATTTT
20523954 TATA
1 TATA
20523958 AAATCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATATATTTAAATTTT
Found at i:20524533 original size:41 final size:43
Alignment explanation
Indices: 20524487--20524567 Score: 114
Period size: 41 Copynumber: 1.9 Consensus size: 43
20524477 AAATTTTATA
20524487 AAAATTAA-AAAATATATATTTTATA-TTTA-ATATATTAACAT
1 AAAATTAATAAAATA-ATATTTTATATTTTACATATATTAACAT
* *
20524528 AAAATTAATATAATAATTTTTTATATTTTACATATATTAA
1 AAAATTAATAAAATAATATTTTATATTTTACATATATTAA
20524568 ACACGACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 17 0.49
42 9 0.26
43 9 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (43 bp):
AAAATTAATAAAATAATATTTTATATTTTACATATATTAACAT
Found at i:20525449 original size:10 final size:10
Alignment explanation
Indices: 20525436--20525460 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20525426 TTTGATGAAA
20525436 TTTTTTTTAT
1 TTTTTTTTAT
20525446 TTTTTTTTAT
1 TTTTTTTTAT
20525456 TTTTT
1 TTTTT
20525461 AATAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:20525487 original size:21 final size:19
Alignment explanation
Indices: 20525463--20525501 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
20525453 TATTTTTTAA
20525463 TAAAAATAAATATTAAAATAT
1 TAAAAATAAA-A-TAAAATAT
20525484 TAAAAATAAAATAAAATA
1 TAAAAATAAAATAAAATA
20525502 AAAAGCATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAAAATAAAATAT
Found at i:20526751 original size:17 final size:17
Alignment explanation
Indices: 20526717--20526750 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20526707 AAATAATTTA
*
20526717 TCATTTAGTAGTTTTTT
1 TCATTTAATAGTTTTTT
20526734 TCATTTAATA-TTTTTT
1 TCATTTAATAGTTTTTT
20526750 T
1 T
20526751 TTCATGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (17 bp):
TCATTTAATAGTTTTTT
Found at i:20527632 original size:23 final size:24
Alignment explanation
Indices: 20527596--20527641 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
20527586 TTTGACAAAT
* *
20527596 TAAATCAATCAATA-TAGAATTAA
1 TAAATCAATAAATACTACAATTAA
*
20527619 TAAATTAATAAATACTACAATTA
1 TAAATCAATAAATACTACAATTA
20527642 TAATTATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAATCAATAAATACTACAATTAA
Found at i:20527693 original size:15 final size:14
Alignment explanation
Indices: 20527673--20527706 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20527663 TCTAATCAAT
20527673 TATTTGATACATTTA
1 TATTTGAT-CATTTA
*
20527688 TATTTGATTATTTA
1 TATTTGATCATTTA
20527702 TATTT
1 TATTT
20527707 TTATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (14 bp):
TATTTGATCATTTA
Found at i:20527712 original size:15 final size:15
Alignment explanation
Indices: 20527683--20527720 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20527673 TATTTGATAC
20527683 ATTTATA-TTTGATT
1 ATTTATATTTTGATT
*
20527697 ATTTATATTTTTATT
1 ATTTATATTTTGATT
*
20527712 ATTAATATT
1 ATTTATATT
20527721 AAATCACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
ATTTATATTTTGATT
Found at i:20527725 original size:190 final size:191
Alignment explanation
Indices: 20527499--20527887 Score: 586
Period size: 190 Copynumber: 2.0 Consensus size: 191
20527489 AAATTTTAAA
* *
20527499 TTGATTATGTTTATGTTTTTATTATTAACCTTAAATCACTCTCAATTTAATTAATATT-AAAGTA
1 TTGATTA-GTTTATATTTTTATTATTAACATTAAATCACTCTCAATTTAATTAATATTAAAAGTA
*
20527563 TTAAAAATTTTAAAAAAATT-TAATTTGACAAATTAAATCAATCAATATAGAATTAATAAATTAA
65 -TAAAAA-TTTAAAAAAATTGTAATTTGACAAATTAAATCAATAAATATAGAATTAATAAATTAA
* * *
20527627 TAAATACTACAATTATAATTATAAAATAATTGATTCTCTAATCAATTATTTGATACATTTATAT
128 TAAATACTACAATTACAATTATAAAATAATTAATTATCTAATCAATTATTTGATACATTTATAT
* *
20527691 TTGATTA-TTTATATTTTTATTATTAATATTAAATCACTCTCAATTTAATTGATATTAAAAGTAT
1 TTGATTAGTTTATATTTTTATTATTAACATTAAATCACTCTCAATTTAATTAATATTAAAAGTAT
* **
20527755 ACAAATTTAAAAATTTTGTAATTTGACAAATTAAATCAATAAATATAGAATTAATAAATTAATAA
66 AAAAATTTAAAAAAATTGTAATTTGACAAATTAAATCAATAAATATAGAATTAATAAATTAATAA
* * * * *
20527820 ATACTATAATTACAATTATAAAATAGTTAATTATTTAATCAATTATTTGATATATTTATGT
131 ATACTACAATTACAATTATAAAATAATTAATTATCTAATCAATTATTTGATACATTTATAT
20527881 TTGATTA
1 TTGATTA
20527888 AATATAGTAT
Statistics
Matches: 179, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
189 10 0.06
190 156 0.87
191 6 0.03
192 7 0.04
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (191 bp):
TTGATTAGTTTATATTTTTATTATTAACATTAAATCACTCTCAATTTAATTAATATTAAAAGTAT
AAAAATTTAAAAAAATTGTAATTTGACAAATTAAATCAATAAATATAGAATTAATAAATTAATAA
ATACTACAATTACAATTATAAAATAATTAATTATCTAATCAATTATTTGATACATTTATAT
Found at i:20527818 original size:23 final size:24
Alignment explanation
Indices: 20527786--20527831 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
20527776 TTTGACAAAT
20527786 TAAATCAATAAATA-TAGAATTAA
1 TAAATCAATAAATACTAGAATTAA
* *
20527809 TAAATTAATAAATACTATAATTA
1 TAAATCAATAAATACTAGAATTA
20527832 CAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAATCAATAAATACTAGAATTAA
Found at i:20528608 original size:20 final size:21
Alignment explanation
Indices: 20528567--20528608 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20528557 ATTCACTCAC
* *
20528567 AATTTTTATTATTTCAATATT
1 AATTTTTATAATTTCAAAATT
20528588 AATTTTTATAATTT-AAAATT
1 AATTTTTATAATTTCAAAATT
20528608 A
1 A
20528609 TCTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTTATAATTTCAAAATT
Found at i:20531926 original size:10 final size:10
Alignment explanation
Indices: 20531908--20531937 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20531898 GAACCCGAAA
20531908 TTTTCAAAAT
1 TTTTCAAAAT
*
20531918 TTTTTAAAAT
1 TTTTCAAAAT
20531928 TTTTCAAAAT
1 TTTTCAAAAT
20531938 GAAGTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTCAAAAT
Found at i:20539503 original size:26 final size:27
Alignment explanation
Indices: 20539472--20539524 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
20539462 GTTTGGTTTG
20539472 AGAAAAT-ATTTTCTATTTTC-ATTTTT
1 AGAAAATAATTTT-TATTTTCTATTTTT
20539498 AGAAAATAATTTTTATTTTCTATTTTT
1 AGAAAATAATTTTTATTTTCTATTTTT
20539525 TGAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (27 bp):
AGAAAATAATTTTTATTTTCTATTTTT
Found at i:20539758 original size:7 final size:7
Alignment explanation
Indices: 20539748--20539806 Score: 55
Period size: 7 Copynumber: 7.6 Consensus size: 7
20539738 ATGTTTTCTG
20539748 TTTTTAT
1 TTTTTAT
20539755 TTTTTAT
1 TTTTTAT
20539762 TTTTTAAAT
1 TTTTT--AT
20539771 TAATTTTCAT
1 T--TTTT-AT
20539781 TTTTTAT
1 TTTTTAT
20539788 TTTTTGAT
1 TTTTT-AT
*
20539796 TTTTGAT
1 TTTTTAT
20539803 TTTT
1 TTTT
20539807 GAAAAACATG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
7 25 0.56
8 10 0.22
9 3 0.07
10 3 0.07
11 4 0.09
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTAT
Found at i:20540155 original size:2 final size:2
Alignment explanation
Indices: 20540144--20540177 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20540134 CAAACAACCG
*
20540144 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20540178 GAAATAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20540346 original size:62 final size:63
Alignment explanation
Indices: 20540249--20540372 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 63
20540239 GAGATGCATG
20540249 GCTTCACAACACTAAAAAGTCTTCCTCGTAATATGAAGCTATAGTTGTATGTCTT-AGAGTAT
1 GCTTCACAACACTAAAAAGTCTTCCTCGTAATATGAAGCTATAGTTGTATGTCTTAAGAGTAT
*
20540311 GCTTCACAACACTAAAAAGTCTTCTTCGTAATATGAAGCTATAGTTGTATGTCTTAAGAGTA
1 GCTTCACAACACTAAAAAGTCTTCCTCGTAATATGAAGCTATAGTTGTATGTCTTAAGAGTA
20540373 ACAAGTGAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 54 0.90
63 6 0.10
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (63 bp):
GCTTCACAACACTAAAAAGTCTTCCTCGTAATATGAAGCTATAGTTGTATGTCTTAAGAGTAT
Found at i:20541232 original size:31 final size:30
Alignment explanation
Indices: 20541167--20541235 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
20541157 TTTGAATTTG
*
20541167 ATATTAAAAATTAATATAGTTATGTAATAT
1 ATATTAAAAATTAATATAGTTATGTAATAC
*
20541197 ATATTAAAATTTAAATATA-TATAT-TAAATAC
1 ATATTAAAAATT-AATATAGT-TATGT-AATAC
20541228 ATATTAAA
1 ATATTAAA
20541236 TGTGTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (30 bp):
ATATTAAAAATTAATATAGTTATGTAATAC
Found at i:20543825 original size:52 final size:51
Alignment explanation
Indices: 20543731--20543833 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
20543721 TATAAGCATA
*
20543731 CAAACTTACTTATTAAGATTCATTTCTTCTTAAAATTATTCTTCTGCAAGT
1 CAAACTTACTTATTAAGAATCATTTCTTCTTAAAATTATTCTTCTGCAAGT
* * * *
20543782 CAAACTTACCTT-TTAAGAATCTTTTTTCTCTTAAAATTCTTCTTTTGCAAGT
1 CAAACTTA-CTTATTAAGAATCATTTCT-TCTTAAAATTATTCTTCTGCAAGT
20543834 TTTCCTATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 20 0.44
52 25 0.56
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (51 bp):
CAAACTTACTTATTAAGAATCATTTCTTCTTAAAATTATTCTTCTGCAAGT
Found at i:20545477 original size:13 final size:13
Alignment explanation
Indices: 20545459--20545497 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
20545449 TAATTTTTTA
20545459 ATTTTTATATATT
1 ATTTTTATATATT
20545472 ATTTTTATATGATT
1 ATTTTTATAT-ATT
*
20545486 -TTTTAATATATT
1 ATTTTTATATATT
20545498 TAAATAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 3 0.12
13 18 0.75
14 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
ATTTTTATATATT
Found at i:20548500 original size:4 final size:4
Alignment explanation
Indices: 20548488--20548533 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
20548478 AATAAATAAG
* * * *
20548488 CATA TATA CATA CATA CATA CATA CATA CATA TATA TATA TATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
20548534 CACACACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (4 bp):
CATA
Found at i:20555785 original size:12 final size:12
Alignment explanation
Indices: 20555768--20555792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20555758 ATACAATCAA
20555768 TAAAGAGTTATG
1 TAAAGAGTTATG
20555780 TAAAGAGTTATG
1 TAAAGAGTTATG
20555792 T
1 T
20555793 GATATTTGAA
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:0.00, G:0.24, T:0.36
Consensus pattern (12 bp):
TAAAGAGTTATG
Found at i:20555930 original size:16 final size:17
Alignment explanation
Indices: 20555893--20555930 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
20555883 ATCAGTTCGA
* *
20555893 TTTTATAATTAGATCAG
1 TTTTACAATTAAATCAG
20555910 TTTTACAATTAAATC-G
1 TTTTACAATTAAATCAG
20555926 TTTTA
1 TTTTA
20555931 AATCGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (17 bp):
TTTTACAATTAAATCAG
Found at i:20556312 original size:16 final size:15
Alignment explanation
Indices: 20556287--20556322 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
20556277 CATAATTAAA
20556287 AATAATTATAAAAAT
1 AATAATTATAAAAAT
*
20556302 AATAATATATAAAACT
1 AATAAT-TATAAAAAT
20556318 AATAA
1 AATAA
20556323 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATTATAAAAAT
Found at i:20556329 original size:16 final size:16
Alignment explanation
Indices: 20556294--20556343 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
20556284 AAAAATAATT
* *
20556294 ATAAAAATAATAATAT
1 ATAAAAATAATAAAAA
*
20556310 ATAAAACTAATAAAAA
1 ATAAAAATAATAAAAA
20556326 ATAAAATATTAATAAAAA
1 ATAAAA-A-TAATAAAAA
20556344 CGATTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 19 0.68
18 9 0.32
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATAATAAAAA
Found at i:20556344 original size:28 final size:29
Alignment explanation
Indices: 20556283--20556344 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 29
20556273 ATACCATAAT
20556283 TAAAAA-TAATTATAAAAATAATAATATA
1 TAAAAACTAATTATAAAAATAATAATATA
20556311 T-AAAACTAA-TA-AAAAATAA-AATATTAA
1 TAAAAACTAATTATAAAAATAATAATA-T-A
20556338 TAAAAAC
1 TAAAAAC
20556345 GATTAATCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
25 4 0.13
26 9 0.30
27 8 0.27
28 9 0.30
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (29 bp):
TAAAAACTAATTATAAAAATAATAATATA
Found at i:20563330 original size:25 final size:25
Alignment explanation
Indices: 20563302--20563368 Score: 109
Period size: 25 Copynumber: 2.6 Consensus size: 25
20563292 TATTTATATA
20563302 ATTATTAAAATATT-AAAATATATTT
1 ATTATTAAAATATTAAAAAT-TATTT
20563327 ATTATTAAAATATTAAAAATTATTT
1 ATTATTAAAATATTAAAAATTATTT
20563352 ATTATTAAAATTATTAA
1 ATTATTAAAA-TATTAA
20563369 TATTAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 29 0.73
26 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTATTAAAATATTAAAAATTATTT
Found at i:20563418 original size:14 final size:15
Alignment explanation
Indices: 20563395--20563423 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20563385 CATTTTAATC
20563395 AAAATATTTAATATT
1 AAAATATTTAATATT
20563410 AAAAT-TTTAATATT
1 AAAATATTTAATATT
20563424 GATAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATATTTAATATT
Found at i:20563756 original size:17 final size:16
Alignment explanation
Indices: 20563736--20563790 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
20563726 TTAAAAATGT
20563736 TAATATTATTAAAATAA
1 TAATATTATT-AAATAA
20563753 TAATATTGTATTAAATAA
1 TAATA-T-TATTAAATAA
*
20563771 TATTAATTATTAAATAA
1 TAAT-ATTATTAAATAA
20563788 TAA
1 TAA
20563791 GAAATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 17 0.52
18 11 0.33
19 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATATTATTAAATAA
Found at i:20563798 original size:17 final size:17
Alignment explanation
Indices: 20563761--20563799 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
20563751 AATAATATTG
** *
20563761 TATTAAATAATATTAAT
1 TATTAAATAATAAGAAA
20563778 TATTAAATAATAAGAAA
1 TATTAAATAATAAGAAA
20563795 TATTA
1 TATTA
20563800 TTTACAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATTAAATAATAAGAAA
Found at i:20572636 original size:10 final size:10
Alignment explanation
Indices: 20572621--20572645 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20572611 ATTCAAATAA
20572621 TATTTTTCTT
1 TATTTTTCTT
20572631 TATTTTTCTT
1 TATTTTTCTT
20572641 TATTT
1 TATTT
20572646 ATTATTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTCTT
Found at i:20572711 original size:34 final size:31
Alignment explanation
Indices: 20572642--20572770 Score: 103
Period size: 30 Copynumber: 4.3 Consensus size: 31
20572632 ATTTTTCTTT
*
20572642 ATTTA-TTATTAGTTTATTGT-ATAATAATAA
1 ATTTATTTATTA-TTTATTATCATAATAATAA
20572672 A---ATTTATTATTTATTAGCTCATAATAATAA
1 ATTTATTTATTATTTATTA--TCATAATAATAA
* *
20572702 TTCTTATTTATTA-TTATTATTATAATAATAA
1 AT-TTATTTATTATTTATTATCATAATAATAA
* *
20572733 ATTTATTTATTATATTA-AATTA-AATAATAA
1 ATTTATTTATTAT-TTATTATCATAATAATAA
*
20572763 AATTATTT
1 ATTTATTT
20572771 CATAATTTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
27 7 0.08
28 6 0.07
29 1 0.01
30 36 0.43
31 16 0.19
32 3 0.04
33 6 0.07
34 8 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
ATTTATTTATTATTTATTATCATAATAATAA
Found at i:20572759 original size:61 final size:64
Alignment explanation
Indices: 20572640--20572762 Score: 157
Period size: 61 Copynumber: 2.0 Consensus size: 64
20572630 TTATTTTTCT
**
20572640 TTATTTATTATTAGTTTATTGTATAATAATAAAATTTATTATTTATTAGCTCATAATAATAATTC
1 TTATTTATTATTAG-TTATTGTATAATAATAAAATTTATTATTTATTAAATCATAATAATAATTC
*
20572705 TTATTTATTATTA-TTA-T-TATAATAAT-AAATTTATTTATTATATTAAATTA-AATAATAA
1 TTATTTATTATTAGTTATTGTATAATAATAAAATTTA-TTATT-TATTAAATCATAATAATAA
20572763 AATTATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
60 7 0.13
61 22 0.42
62 8 0.15
63 3 0.06
65 13 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (64 bp):
TTATTTATTATTAGTTATTGTATAATAATAAAATTTATTATTTATTAAATCATAATAATAATTC
Found at i:20576889 original size:34 final size:36
Alignment explanation
Indices: 20576831--20576900 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
20576821 TCTTATGTTA
*
20576831 AAAAAAAATGTATTGTGAGAAAATTTT-CATTAATT
1 AAAAAAAATGTACTGTGAGAAAATTTTCCATTAATT
20576866 AAAAAAAATGTACTGTGAG-AAATTTTCCATTAATT
1 AAAAAAAATGTACTGTGAGAAAATTTTCCATTAATT
20576901 TGATTGGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 7 0.21
35 26 0.79
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (36 bp):
AAAAAAAATGTACTGTGAGAAAATTTTCCATTAATT
Found at i:20577598 original size:2 final size:2
Alignment explanation
Indices: 20577591--20577622 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20577581 TGCAAAGCAC
20577591 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20577623 CTTTCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20589513 original size:7 final size:7
Alignment explanation
Indices: 20589490--20589541 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
20589480 AAAATTAAAT
20589490 AAAATAGA
1 AAAATA-A
20589498 AAAATAA
1 AAAATAA
*
20589505 AATA-AA
1 AAAATAA
20589511 AAAATAA
1 AAAATAA
20589518 AAAATAA
1 AAAATAA
**
20589525 AAAGGAA
1 AAAATAA
*
20589532 AAAAGAA
1 AAAATAA
20589539 AAA
1 AAA
20589542 CCTATAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
6 5 0.13
7 27 0.71
8 6 0.16
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.10
Consensus pattern (7 bp):
AAAATAA
Found at i:20589526 original size:13 final size:13
Alignment explanation
Indices: 20589486--20589541 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
20589476 TAAGAAAATT
*
20589486 AAATAAAATAGAA
1 AAATAAAAAAGAA
20589499 AAATAAAATAA-AA
1 AAATAAAA-AAGAA
*
20589512 AAATAAAAAATAA
1 AAATAAAAAAGAA
*
20589525 AAAGGAAAAAAGAA
1 AAA-TAAAAAAGAA
20589539 AAA
1 AAA
20589542 CCTATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 2 0.05
13 23 0.62
14 12 0.32
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (13 bp):
AAATAAAAAAGAA
Found at i:20589821 original size:20 final size:19
Alignment explanation
Indices: 20589780--20589825 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
20589770 TTTGACATTG
*
20589780 AAAAATTCAAATGGTGCAA
1 AAAAATTCAAATGGTCCAA
* *
20589799 AAAAATTCAAATTGTTCCCA
1 AAAAATTCAAA-TGGTCCAA
20589819 AAAAATT
1 AAAAATT
20589826 AAAGGACCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (19 bp):
AAAAATTCAAATGGTCCAA
Found at i:20596412 original size:145 final size:145
Alignment explanation
Indices: 20596130--20596530 Score: 330
Period size: 145 Copynumber: 2.8 Consensus size: 145
20596120 GATTTTAAAA
* * * * * ** * *
20596130 CACCAAAAATCATGAACTATTATAAGATTATGATCTGAAAG-GTTTCATGAAATTCTGAGCTAGG
1 CACCAAAAATCATGAAATATTACAAAAGTAAGATCTGAAAGAGTTTCACAAAAATCTGAGCT-CG
* * * *
20596194 AAAA-GCTAGATTACGAAAATACCTCTATGAGGGTATTTT-AGTAATTTCACACTTCTTGAGATA
65 AAAAGGCCAAATTACAAAAATACC-CTATAAGGGTATTTTGA-TAATTTCACACTTCTTGAGATA
* *
20596257 CTACTGTGATTCTAAACT-
128 CCACTATGATTCTAAA-TG
* * * * *
20596275 CACCAAAAATTATGAAATGTTACAAAAGTGAGATCTGAAA-AGTTTCACAAAATTTTGAGCTCGA
1 CACCAAAAATCATGAAATATTACAAAAGTAAGATCTGAAAGAGTTTCACAAAAATCTGAGCTCGA
* * * *
20596339 GAAGGCCAAATTACAAAAATACCCATATAAGGGTATTTTGATAATTTCATACTT-TTCGGGTTAC
66 AAAGGCCAAATTACAAAAATACCC-TATAAGGGTATTTTGATAATTTCACACTTCTT-GAGATAC
* *
20596403 CGCTATGATTTTAAATG
129 CACTATGATTCTAAATG
** * ** * * * * *
20596420 CGTCAAAAATCATGAAATATTATAGGATTAAGGTCTGAAAGATTTTTATAAAAATCTGAGCTCGA
1 CACCAAAAATCATGAAATATTACAAAAGTAAGATCTGAAAGAGTTTCACAAAAATCTGAGCTCGA
* **
20596485 AAAGGTCAAATTA-TGAAATACCCCTTATAAGGGTATTTTGATAATT
66 AAAGGCCAAATTACAAAAATA-CCC-TATAAGGGTATTTTGATAATT
20596531 CAACCTTTCT
Statistics
Matches: 204, Mismatches: 44, Indels: 15
0.78 0.17 0.06
Matches are distributed among these distances:
144 8 0.04
145 141 0.69
146 55 0.27
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (145 bp):
CACCAAAAATCATGAAATATTACAAAAGTAAGATCTGAAAGAGTTTCACAAAAATCTGAGCTCGA
AAAGGCCAAATTACAAAAATACCCTATAAGGGTATTTTGATAATTTCACACTTCTTGAGATACCA
CTATGATTCTAAATG
Found at i:20596770 original size:13 final size:13
Alignment explanation
Indices: 20596752--20596785 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
20596742 TATGAGTCTA
20596752 AAATGGTCATTGT
1 AAATGGTCATTGT
20596765 AAATGGTCATTGT
1 AAATGGTCATTGT
20596778 AAATGGTC
1 AAATGGTC
20596786 TTAGCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (13 bp):
AAATGGTCATTGT
Found at i:20597117 original size:67 final size:67
Alignment explanation
Indices: 20597036--20597223 Score: 268
Period size: 67 Copynumber: 2.8 Consensus size: 67
20597026 TTAAATCTCA
* * * *
20597036 AAAACTTTTTGAATGCTCCTCTAATTAGAGGCCATGAAACTTTGAATTTAAAATGTTTTACGAAT
1 AAAAC-TTTTGAATGCTCATCCAATTAAAGGCCATGAAACTTTGAATTTAAAATGTTTTACAAAT
20597101 CAC
65 CAC
* * *
20597104 AAAACTTTTGAATGCTCATCCAGTCAAAGGGCATGAAACTTTGAATTTAAAATGTTTTACAAATC
1 AAAACTTTTGAATGCTCATCCAATTAAAGGCCATGAAACTTTGAATTTAAAATGTTTTACAAATC
20597169 AC
66 AC
* * * *
20597171 AAAAATTTTGAATGCTCTTCCAATTAAAGGTCATGAAATTTTGAATTTAAAAT
1 AAAACTTTTGAATGCTCATCCAATTAAAGGCCATGAAACTTTGAATTTAAAAT
20597224 ATTTAGAGAT
Statistics
Matches: 107, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 102 0.95
68 5 0.05
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (67 bp):
AAAACTTTTGAATGCTCATCCAATTAAAGGCCATGAAACTTTGAATTTAAAATGTTTTACAAATC
AC
Found at i:20597372 original size:22 final size:22
Alignment explanation
Indices: 20597321--20597372 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20597311 AATGTTTTGT
20597321 TCGAAGGTCTTGAAAATTATGC
1 TCGAAGGTCTTGAAAATTATGC
*
20597343 -CCAGAGGTCTT-AAAGATTATGC
1 TCGA-AGGTCTTGAAA-ATTATGC
20597365 TCGAAGGT
1 TCGAAGGT
20597373 GTTAGGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 5 0.20
22 18 0.72
23 2 0.08
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (22 bp):
TCGAAGGTCTTGAAAATTATGC
Found at i:20597477 original size:22 final size:22
Alignment explanation
Indices: 20597445--20597498 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
20597435 TAAAATGTTT
*
20597445 TGCCTGAAGGTATTAAAAATTA
1 TGCCTGAAGGTATTAAAAATAA
* * *
20597467 TGCCTGGAGGTTTTAAAGATAA
1 TGCCTGAAGGTATTAAAAATAA
*
20597489 TGCCCGAAGG
1 TGCCTGAAGG
20597499 CCCGTAGGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (22 bp):
TGCCTGAAGGTATTAAAAATAA
Found at i:20597484 original size:127 final size:126
Alignment explanation
Indices: 20597259--20597498 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 126
20597249 TACAAATCTC
* * *
20597259 AAAATCTTTAAATGCTCATCGAATCAGAAGCCATAAAACTTTGAAATATTAAAATGTTTTGTTCG
1 AAAATCTTTAAATGCTCATCGAATCAGAAGCCATAAAACTTTAAAAAATTAAAATGTTTTGCTCG
* * * *
20597324 AAGGTCTTGAAAATTATGCCCAGAGGTCTTAAAGATTATGCTCGAAGGTGTTAGGGATTTT
66 AAGGTATTAAAAATTATGCCCAGAGGTCTTAAAGATAATGCCCGAAGGTGTTAGGGATTTT
* *
20597385 AAAATCTTTGAATGCTCATTC-AATCA-AAGGCCATGAAACTTTTAAAAAATTAAAATGTTTTGC
1 AAAATCTTTAAATGCTCA-TCGAATCAGAA-GCCATAAAAC-TTTAAAAAATTAAAATGTTTTGC
** *
20597448 -CTGAAGGTATTAAAAATTATGCCTGGAGGTTTTAAAGATAATGCCCGAAGG
63 TC-GAAGGTATTAAAAATTATGCCCAGAGGTCTTAAAGATAATGCCCGAAGG
20597499 CCCGTAGGTC
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
125 2 0.02
126 32 0.33
127 64 0.65
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (126 bp):
AAAATCTTTAAATGCTCATCGAATCAGAAGCCATAAAACTTTAAAAAATTAAAATGTTTTGCTCG
AAGGTATTAAAAATTATGCCCAGAGGTCTTAAAGATAATGCCCGAAGGTGTTAGGGATTTT
Found at i:20597629 original size:69 final size:70
Alignment explanation
Indices: 20597518--20597649 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 70
20597508 CTTAGAGATT
* * *
20597518 TCAAAATCTTTGAATGCTCCTCCAATTAGAGACCATGAAACTTTGAATA-TTTAAAATGTTTTAT
1 TCAAAATCTTTGAATGCTCATCCAATTAGAGACCATGAAACTTTAAAAATTTTAAAATGTTTTAT
20597582 AAATC
66 AAATC
*
20597587 TCAAAA-CTTTTGAATGCTCATCCAATTAGAGGCCATGAAACTTTAAAAATTTTAAAATGTTTT
1 TCAAAATC-TTTGAATGCTCATCCAATTAGAGACCATGAAACTTTAAAAATTTTAAAATGTTTT
20597650 GCAAATGATT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
68 1 0.02
69 43 0.75
70 13 0.23
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (70 bp):
TCAAAATCTTTGAATGCTCATCCAATTAGAGACCATGAAACTTTAAAAATTTTAAAATGTTTTAT
AAATC
Found at i:20598464 original size:42 final size:44
Alignment explanation
Indices: 20598405--20598505 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
20598395 AAATGTAAGT
*
20598405 GATGCAAATGCAAATATCTTTTTTC-T-TGATACAGATGCAAGA
1 GATGCAAATGCAAATATCTTTTTCCTTATGATACAGATGCAAGA
* *
20598447 GATGCAAATGCAAATATCTTTTTCCTTATGATGCAGATGCAAGT
1 GATGCAAATGCAAATATCTTTTTCCTTATGATACAGATGCAAGA
* *
20598491 GGTGCAAATGTAAAT
1 GATGCAAATGCAAAT
20598506 TTTTTCTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 24 0.46
43 1 0.02
44 27 0.52
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (44 bp):
GATGCAAATGCAAATATCTTTTTCCTTATGATACAGATGCAAGA
Found at i:20598499 original size:44 final size:43
Alignment explanation
Indices: 20598392--20598551 Score: 163
Period size: 42 Copynumber: 3.8 Consensus size: 43
20598382 CAGATACAAG
* * *
20598392 TGCAAATGTAAGTGATGCAAATGCAAATATCTTTTTTC-T-TGA
1 TGCAGATGCAAGTGATGCAAATGCAAATAT-TTTTTCCTTATGA
* *
20598434 TACAGATGCAAGAGATGCAAATGCAAATATCTTTTTCCTTATGA
1 TGCAGATGCAAGTGATGCAAATGCAAATAT-TTTTTCCTTATGA
* *
20598478 TGCAGATGCAAGTGGTGCAAATG-TAA-ATTTTTT-CTTAT-A
1 TGCAGATGCAAGTGATGCAAATGCAAATATTTTTTCCTTATGA
* * *
20598517 TGCAGATACAAGTGATGTAAAAGCAAAT-TTTTTTC
1 TGCAGATGCAAGTGATGCAAATGCAAATATTTTTTC
20598552 ATGATGTAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
39 20 0.20
40 13 0.13
41 5 0.05
42 35 0.35
43 3 0.03
44 23 0.23
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (43 bp):
TGCAGATGCAAGTGATGCAAATGCAAATATTTTTTCCTTATGA
Found at i:20598529 original size:39 final size:40
Alignment explanation
Indices: 20598401--20598557 Score: 122
Period size: 39 Copynumber: 3.8 Consensus size: 40
20598391 GTGCAAATGT
* * * *
20598401 AAGTGATGCAAATGCAAATATCTTTT-TTCTTGATACAGATGC
1 AAGTGATGCAAAAGCAAAT-T-TTTTCTT-ATGATGCAGATAC
* * *
20598443 AAGAGATGCAAATGCAAATATCTTTTTCCTTATGATGCAGATGC
1 AAGTGATGCAAAAGC-AA-AT-TTTTT-CTTATGATGCAGATAC
* * *
20598487 AAGTGGTGCAAATGTAAATTTTTTCTTAT-ATGCAGATAC
1 AAGTGATGCAAAAGCAAATTTTTTCTTATGATGCAGATAC
* *
20598526 AAGTGATGTAAAAGCAAATTTTTT-TCATGATG
1 AAGTGATGCAAAAGCAAATTTTTTCTTATGATG
20598558 TAAATATAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.33
40 5 0.05
41 5 0.05
42 16 0.16
43 8 0.08
44 26 0.27
45 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (40 bp):
AAGTGATGCAAAAGCAAATTTTTTCTTATGATGCAGATAC
Found at i:20598606 original size:37 final size:38
Alignment explanation
Indices: 20598565--20598642 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
20598555 ATGTAAATAT
*
20598565 AAATTTTCTT-TTGATGCAGATGCAAGTGATGC-AATGC
1 AAATTTT-TTCTTGATACAGATGCAAGTGATGCAAATGC
* **
20598602 AAATTTTTTCTTGATACAGGTGTTAGTGATGCAAATGC
1 AAATTTTTTCTTGATACAGATGCAAGTGATGCAAATGC
20598640 AAA
1 AAA
20598643 CGTCTATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 2 0.06
37 25 0.71
38 8 0.23
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (38 bp):
AAATTTTTTCTTGATACAGATGCAAGTGATGCAAATGC
Found at i:20598653 original size:101 final size:101
Alignment explanation
Indices: 20598466--20598655 Score: 224
Period size: 101 Copynumber: 1.9 Consensus size: 101
20598456 GCAAATATCT
* *
20598466 TTTTCCTTATGATGCAGATGCAAGTGGTGCAAATGTAAATTTTTTCTTATATGCAGATACAAGTG
1 TTTTCCTTATGATGCAGATGCAAGTGATGCAAATGCAAATTTTTTCTTATA-GCAGATACAAGTG
* * *
20598531 ATGTAAAAGCAAATTTTTTTCATGATGTAAATATAAA
65 ATGCAAAAGCAAATCTATTTCATGATGTAAATATAAA
* * ***
20598568 TTTT-CTTTTGATGCAGATGCAAGTGATGC-AATGCAAATTTTTTCTTGATA-CAGGTGTTAGTG
1 TTTTCCTTATGATGCAGATGCAAGTGATGCAAATGCAAATTTTTTCTT-ATAGCAGATACAAGTG
*
20598630 ATGCAAATGCAAACGTCTATTTCATG
65 ATGCAAAAGCAAA--TCTATTTCATG
20598656 GTGCAAATGC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
99 19 0.26
100 16 0.22
101 35 0.47
102 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (101 bp):
TTTTCCTTATGATGCAGATGCAAGTGATGCAAATGCAAATTTTTTCTTATAGCAGATACAAGTGA
TGCAAAAGCAAATCTATTTCATGATGTAAATATAAA
Found at i:20598903 original size:39 final size:40
Alignment explanation
Indices: 20598860--20598941 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 40
20598850 AATGTGTTGG
* *
20598860 ATGCAAATACGACTATCTTTTT-TTATGATGCAGATGTGA
1 ATGCAAATACGAATATCTTTTTATTATGATGCAGATGCGA
* * * *
20598899 ATGCAAATATGAATGTCTTTTTATTGTGATGTAGATGCGA
1 ATGCAAATACGAATATCTTTTTATTATGATGCAGATGCGA
20598939 ATG
1 ATG
20598942 ATGCAAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (40 bp):
ATGCAAATACGAATATCTTTTTATTATGATGCAGATGCGA
Found at i:20599049 original size:34 final size:33
Alignment explanation
Indices: 20599003--20599098 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
20598993 TTTTTATGTC
* *
20599003 AGATAAATTAAGCTTAAAATCTTCATCAAAGGCT
1 AGATAAACTAAGCTT-AAATTTTCATCAAAGGCT
* *
20599037 AGATAAACTAAGCTTAAATTTTCAGT-AACGGTT
1 AGATAAACTAAGCTTAAATTTTCA-TCAAAGGCT
*
20599070 TGATAAACTAAGCTTAAATTTTCATCAAA
1 AGATAAACTAAGCTTAAATTTTCATCAAA
20599099 TGCCTGCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 1 0.02
33 38 0.70
34 15 0.28
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (33 bp):
AGATAAACTAAGCTTAAATTTTCATCAAAGGCT
Found at i:20599216 original size:33 final size:33
Alignment explanation
Indices: 20599132--20599216 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
20599122 ATTTTTAGGA
* *
20599132 GCCAGCTAAGCTAGGCTTAAAATTTTACCTAGG
1 GCCAGCTAAACTAGGCTTAAAATTTTACCTAAG
* * * *
20599165 GCTAGTTAAATTAAGCTTAAAATTTTACCTAAG
1 GCCAGCTAAACTAGGCTTAAAATTTTACCTAAG
*
20599198 GCCAACTAAACTAGGCTTA
1 GCCAGCTAAACTAGGCTTA
20599217 TGTGCCAGCT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (33 bp):
GCCAGCTAAACTAGGCTTAAAATTTTACCTAAG
Found at i:20599806 original size:12 final size:12
Alignment explanation
Indices: 20599789--20599813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20599779 CCCTAAAGCC
20599789 ATTTTTTTTATT
1 ATTTTTTTTATT
20599801 ATTTTTTTTATT
1 ATTTTTTTTATT
20599813 A
1 A
20599814 ACACTCCATG
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTTATT
Found at i:20600201 original size:10 final size:9
Alignment explanation
Indices: 20600148--20600232 Score: 59
Period size: 10 Copynumber: 9.0 Consensus size: 9
20600138 CACTCATTCA
20600148 TTTCTTTTT
1 TTTCTTTTT
20600157 CTTTCTTTTAT
1 -TTTCTTTT-T
20600168 TCTTCCTTTTT
1 T-TT-CTTTTT
20600179 TTTCATTTTT
1 TTTC-TTTTT
20600189 TTTCTTTTCT
1 TTTCTTTT-T
20600199 TTT-TGTTTT
1 TTTCT-TTTT
** *
20600208 TGCCTTGTT
1 TTTCTTTTT
20600217 TTT-TTTTT
1 TTTCTTTTT
20600225 TTT-TTTTT
1 TTTCTTTTT
20600233 GCTTTTGGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
8 12 0.19
9 12 0.19
10 28 0.45
11 5 0.08
12 5 0.08
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:20601585 original size:25 final size:25
Alignment explanation
Indices: 20601548--20601602 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
20601538 AAACTCAAAA
** *
20601548 TTTTTTCTTTTTTTTTTTTTTTTGC
1 TTTTTTCCCTTTTTTTTGTTTTTGC
20601573 TTTTTTCCCTTTTTTTTGTTTTTGC
1 TTTTTTCCCTTTTTTTTGTTTTTGC
20601598 TTTTT
1 TTTTT
20601603 GTTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (25 bp):
TTTTTTCCCTTTTTTTTGTTTTTGC
Found at i:20601610 original size:25 final size:23
Alignment explanation
Indices: 20601549--20601613 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
20601539 AACTCAAAAT
20601549 TTTTTCTTTTTTTTTTTTTTTTGC
1 TTTTT-TTTTTTTTTTTTTTTTGC
* *
20601573 TTTTTTCCCTTTTTTTTGTTTTTGC
1 TTTTTT--TTTTTTTTTTTTTTTGC
*
20601598 TTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTT
20601614 AGAGTACCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 9 0.26
24 5 0.15
25 20 0.59
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (23 bp):
TTTTTTTTTTTTTTTTTTTTTGC
Done.