Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 88 of 117
Found at i:15994878 original size:186 final size:187
Alignment explanation
Indices: 15994577--15994920 Score: 512
Period size: 186 Copynumber: 1.8 Consensus size: 187
15994567 CAATGTAAAT
* *
15994577 CATGCAAATAAACATACAATTAAATATATAATTATGCAAATAAAAAATATATAAACCGTGCAAAT
1 CATGCAAATAAACATACAATTAAATATATAATCATGCAAATAAAAAATATATAAACCATGCAAAT
* **
15994642 AAATATGCAATTAATTATATAATTATGCAAATAGTAATATACAAATCATGCAAATAAACATAAAA
66 AAATATGCAATTAAATATATAATTATGCAAATACCAATATACAAATCATGCAAATAAACATAAAA
*
15994707 TTAAATATATAATGATACAAATAATAATACATAAATCATGCAAATAAATATATAAAAC
131 TTAAATATATAATCATACAAAT-ATAATACATAAATCATGCAAATAAATATATAAAAC
* * * *
15994765 CATGCAAATAAATATGCAATTAAATATATAATCATGTAAAT-AACAATATATAAACCATGCAAAT
1 CATGCAAATAAACATACAATTAAATATATAATCATGCAAATAAAAAATATATAAACCATGCAAAT
* * ** * **
15994829 -AATATGCAATTAAATATCTAATTATGCAAATACCAATGTATTAATCATGCAAATAAATATGCAA
66 AAATATGCAATTAAATATATAATTATGCAAATACCAATATACAAATCATGCAAATAAACATAAAA
15994893 TTAAATATATAATCATACAAATATAATA
131 TTAAATATATAATCATACAAATATAATA
15994921 TTAGTAATGC
Statistics
Matches: 139, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
185 6 0.04
186 75 0.54
187 21 0.15
188 37 0.27
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (187 bp):
CATGCAAATAAACATACAATTAAATATATAATCATGCAAATAAAAAATATATAAACCATGCAAAT
AAATATGCAATTAAATATATAATTATGCAAATACCAATATACAAATCATGCAAATAAACATAAAA
TTAAATATATAATCATACAAATATAATACATAAATCATGCAAATAAATATATAAAAC
Found at i:15995529 original size:12 final size:12
Alignment explanation
Indices: 15995505--15995538 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
15995495 ACCAATTAAA
15995505 TAAAATC-AAAT
1 TAAAATCAAAAT
15995516 TAAAATCAAAAT
1 TAAAATCAAAAT
*
15995528 TAAAATTAAAA
1 TAAAATCAAAA
15995539 CTAAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAATCAAAAT
Found at i:15995705 original size:21 final size:22
Alignment explanation
Indices: 15995680--15995723 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
15995670 ATAATTGATC
*
15995680 ATTTA-AGAATTAATTTTTAAA
1 ATTTATAGAATTAATTTTAAAA
**
15995701 ATTTATATTATTAATTTTAAAA
1 ATTTATAGAATTAATTTTAAAA
15995723 A
1 A
15995724 AATTGCTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTATAGAATTAATTTTAAAA
Found at i:16002179 original size:17 final size:16
Alignment explanation
Indices: 16002141--16002192 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
16002131 TATAGGACTT
*
16002141 GGATTTTAGGGTTTGAA
1 GGATTTTAGGATTTG-A
*
16002158 AGATTTTAGGATTTCGA
1 GGATTTTAGGATTT-GA
16002175 GGA-TTTAGGATTTAGA
1 GGATTTTAGGATTT-GA
16002191 GG
1 GG
16002193 TTTAGCGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 14 0.47
17 15 0.50
18 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.33, T:0.38
Consensus pattern (16 bp):
GGATTTTAGGATTTGA
Found at i:16002183 original size:16 final size:15
Alignment explanation
Indices: 16002162--16002197 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
16002152 TTTGAAAGAT
*
16002162 TTTAGGATTTCGAGG
1 TTTAGGATTTAGAGG
16002177 ATTTAGGATTTAGAGG
1 -TTTAGGATTTAGAGG
16002193 TTTAG
1 TTTAG
16002198 CGTTTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.25, C:0.03, G:0.31, T:0.42
Consensus pattern (15 bp):
TTTAGGATTTAGAGG
Found at i:16002304 original size:14 final size:14
Alignment explanation
Indices: 16002282--16002358 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
16002272 GTTTGGATGG
16002282 TTTAAGGTTTCAAT
1 TTTAAGGTTTCAAT
* *
16002296 TTTAGGGTTTGAGA-
1 TTTAAGGTTTCA-AT
* * *
16002310 TTTAGGGTTTTAGT
1 TTTAAGGTTTCAAT
**
16002324 TTTAAGGTTTGGAT
1 TTTAAGGTTTCAAT
16002338 GATTTAAGGTTT-AAT
1 --TTTAAGGTTTCAAT
16002353 TTTAAG
1 TTTAAG
16002359 CTTTAGGATT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
13 6 0.12
14 31 0.62
15 3 0.06
16 10 0.20
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (14 bp):
TTTAAGGTTTCAAT
Found at i:16002349 original size:30 final size:30
Alignment explanation
Indices: 16002257--16002367 Score: 120
Period size: 30 Copynumber: 3.8 Consensus size: 30
16002247 AAGGGTTTGG
* * *
16002257 GGTTTTAGTTTTATGGTTTGGATGGTTTAA
1 GGTTTTAATTTTAAGGTTTGGATGATTTAA
* * *
16002287 GGTTTCAATTTTAGGGTTT-GA-GATTTAG
1 GGTTTTAATTTTAAGGTTTGGATGATTTAA
*
16002315 GGTTTTAGTTTTAAGGTTTGGATGATTTAA
1 GGTTTTAATTTTAAGGTTTGGATGATTTAA
*
16002345 GG-TTTAATTTTAAGCTTTAGGAT
1 GGTTTTAATTTTAAGGTTT-GGAT
16002368 TTAGCATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 21 0.31
29 18 0.27
30 28 0.42
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.50
Consensus pattern (30 bp):
GGTTTTAATTTTAAGGTTTGGATGATTTAA
Found at i:16002358 original size:29 final size:29
Alignment explanation
Indices: 16002260--16002367 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 29
16002250 GGTTTGGGGT
* * *
16002260 TTTAGTTTTATGGTTTGGATGGTTTAAGG
1 TTTAATTTTAAGGTTTGGATGATTTAAGG
* *
16002289 TTTCAATTTTAGGGTTT-GA-GATTTAGGG
1 TTT-AATTTTAAGGTTTGGATGATTTAAGG
*
16002317 TTTTAGTTTTAAGGTTTGGATGATTTAAGG
1 -TTTAATTTTAAGGTTTGGATGATTTAAGG
*
16002347 TTTAATTTTAAGCTTTAGGAT
1 TTTAATTTTAAGGTTT-GGAT
16002368 TTAGCATTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
28 18 0.28
29 24 0.37
30 23 0.35
ACGTcount: A:0.22, C:0.02, G:0.26, T:0.50
Consensus pattern (29 bp):
TTTAATTTTAAGGTTTGGATGATTTAAGG
Found at i:16002384 original size:57 final size:56
Alignment explanation
Indices: 16002256--16002448 Score: 178
Period size: 58 Copynumber: 3.4 Consensus size: 56
16002246 AAAGGGTTTG
* * *
16002256 GGGTTTT-AGTTTTATGGTTTGGATGGTTTAAGGTTTCAATTTTAGGGTTT-GAGATTTA
1 GGGTTTTGA-TTTTAGGGTTTGGATGATTTAAGGTTT-AATTTTA-AGTTTAG-GATTTA
*
16002314 GGGTTTT-AGTTTTAAGGTTTGGATGATTTAAGGTTTAATTTTAAGCTTTAGGATTTA
1 GGGTTTTGA-TTTTAGGGTTTGGATGATTTAAGGTTTAATTTTAAG-TTTAGGATTTA
** ** * * *
16002371 GCATTTTGATTTTAGGGTTTAAAGGATTTAGGGTTT-AGTTTAATGTTTAGAGGATTTA
1 GGGTTTTGATTTTAGGGTTTGGATGATTTAAGGTTTAATTTTAA-GTTT--AGGATTTA
16002429 GGGTTTTGATTTTAGGGTTT
1 GGGTTTTGATTTTAGGGTTT
16002449 TAGGTTTAAG
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
56 10 0.09
57 44 0.38
58 62 0.53
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.49
Consensus pattern (56 bp):
GGGTTTTGATTTTAGGGTTTGGATGATTTAAGGTTTAATTTTAAGTTTAGGATTTA
Found at i:16002434 original size:16 final size:15
Alignment explanation
Indices: 16002381--16002434 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
16002371 GCATTTTGAT
16002381 TTTAGGGTTTAAAGGA
1 TTTAGGGTTT-AAGGA
16002397 TTTAGGGTTT-A-G-
1 TTTAGGGTTTAAGGA
**
16002409 TTTAATGTTTAGAGGA
1 TTTAGGGTTTA-AGGA
16002425 TTTAGGGTTT
1 TTTAGGGTTT
16002435 TGATTTTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 2 0.07
15 1 0.03
16 18 0.60
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (15 bp):
TTTAGGGTTTAAGGA
Found at i:16002441 original size:58 final size:57
Alignment explanation
Indices: 16002282--16002462 Score: 158
Period size: 57 Copynumber: 3.2 Consensus size: 57
16002272 GTTTGGATGG
* * * * ** *
16002282 TTTAAGGTTTCAATTTTAGGGTTT-GAGATTTAGGGTTTT-AGTTTTAAGGTTTGGATGA
1 TTTAAGGTTT-AAGTTTAAGCTTTAG-GATTTAGGGTTTTGA-TTTTAGGGTTTAAAGGA
* **
16002340 TTTAAGGTTTAATTTTAAGCTTTAGGATTTAGCATTTTGATTTTAGGGTTTAAAGGA
1 TTTAAGGTTTAAGTTTAAGCTTTAGGATTTAGGGTTTTGATTTTAGGGTTTAAAGGA
* *
16002397 TTTAGGGTTT-AGTTTAATG-TTTAGAGGATTTAGGGTTTTGATTTTAGGGTTT-TAGG-
1 TTTAAGGTTTAAGTTTAA-GCTTT--AGGATTTAGGGTTTTGATTTTAGGGTTTAAAGGA
16002453 TTTAAGGTTT
1 TTTAAGGTTT
16002463 CGATTTTAGT
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
56 18 0.17
57 48 0.46
58 38 0.37
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (57 bp):
TTTAAGGTTTAAGTTTAAGCTTTAGGATTTAGGGTTTTGATTTTAGGGTTTAAAGGA
Found at i:16002444 original size:14 final size:14
Alignment explanation
Indices: 16002425--16002476 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
16002415 GTTTAGAGGA
16002425 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
*
16002439 TTTAGGGTTTT-AGG
1 TTTAGGGTTTTGA-T
* *
16002453 TTTAAGGTTTCGAT
1 TTTAGGGTTTTGAT
*
16002467 TTTAGTGTTT
1 TTTAGGGTTT
16002477 AAAAGGTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.27, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:16002834 original size:14 final size:14
Alignment explanation
Indices: 16002803--16002843 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
16002793 ATTTTTTTTG
*
16002803 TTATTATT-TTACT
1 TTATTATTATTATT
16002816 TTATTATTATTATT
1 TTATTATTATTATT
*
16002830 TTATTTTTATTATT
1 TTATTATTATTATT
16002844 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:16003098 original size:16 final size:16
Alignment explanation
Indices: 16003062--16003091 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16003052 TAATAACAAT
16003062 TAAAAAT-AATAAATA
1 TAAAAATAAATAAATA
16003077 TAAAAATAAATAAAT
1 TAAAAATAAATAAAT
16003092 GAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATAAATAAATA
Found at i:16021435 original size:11 final size:12
Alignment explanation
Indices: 16021419--16021491 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
16021409 ATATATAAAA
16021419 AATTATTT-TTT
1 AATTATTTATTT
16021430 AATTATTTATTT
1 AATTATTTATTT
16021442 AATT-TTATATTT
1 AATTATT-TATTT
16021454 -A-TA--TATTT
1 AATTATTTATTT
16021462 ACA-TATTTATTT
1 A-ATTATTTATTT
16021474 AATT-TTATATTT
1 AATTATT-TATTT
16021486 ATATTA
1 A-ATTA
16021492 AAAAATAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
8 5 0.10
10 4 0.08
11 14 0.27
12 25 0.49
13 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:16021454 original size:16 final size:16
Alignment explanation
Indices: 16021433--16021492 Score: 77
Period size: 16 Copynumber: 3.7 Consensus size: 16
16021423 ATTTTTTAAT
16021433 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
* *
16021449 TATTTATAT-ATTTACA
1 TATTTATTTAATTT-TA
16021465 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
16021481 TATTTATATTAA
1 TATTTAT-TTAA
16021493 AAAATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.11
16 25 0.68
17 8 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATTTAATTTTA
Found at i:16021460 original size:8 final size:8
Alignment explanation
Indices: 16021433--16021489 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
16021423 ATTTTTTAAT
*
16021433 TATTTATT
1 TATTTATA
16021441 TAATTT-TA
1 T-ATTTATA
16021449 TATTTATA
1 TATTTATA
*
16021457 TATTTACA
1 TATTTATA
*
16021465 TATTTATT
1 TATTTATA
16021473 TAATTT-TA
1 T-ATTTATA
16021481 TATTTATA
1 TATTTATA
16021489 T
1 T
16021490 TAAAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
7 8 0.20
8 24 0.60
9 8 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
TATTTATA
Found at i:16021504 original size:19 final size:19
Alignment explanation
Indices: 16021480--16021530 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
16021470 ATTTAATTTT
16021480 ATATTTATATTAAAAAATA
1 ATATTTATATTAAAAAATA
* *
16021499 ATATTTTATGTTTAAAAATA
1 ATA-TTTATATTAAAAAATA
16021519 ATATTT-TATTAA
1 ATATTTATATTAA
16021531 TTTCAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 17 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATTTATATTAAAAAATA
Found at i:16030797 original size:2 final size:2
Alignment explanation
Indices: 16030790--16030827 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16030780 CAAATCTTGA
*
16030790 AT AT AT AT AT AT -T AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16030828 GTACTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16033230 original size:21 final size:22
Alignment explanation
Indices: 16033186--16033234 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
16033176 CTCAAATCTA
**
16033186 ATATTTTTAGTTTTTTAATTAT
1 ATATTTTTAGTTTTTTAAAGAT
*
16033208 ATATTTTTTG-TTTTTAAAGAT
1 ATATTTTTAGTTTTTTAAAGAT
16033229 AT-TTTT
1 ATATTTT
16033235 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 9 0.38
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
ATATTTTTAGTTTTTTAAAGAT
Found at i:16038129 original size:84 final size:83
Alignment explanation
Indices: 16037988--16038154 Score: 325
Period size: 84 Copynumber: 2.0 Consensus size: 83
16037978 TGGTTCTTGC
16037988 CAAGAACCAAATTCTCAACTTCTTGGGTATTACTTCTTATGGACAGAGAATTTAACCTTTTTTTT
1 CAAGAACCAAATTCTCAACTTCTTGGGTATTACTTCTTATGGACAGAGAATTTAACC-TTTTTTT
16038053 TTTTTCTCAGAAAACAGTG
65 TTTTTCTCAGAAAACAGTG
16038072 CAAGAACCAAATTCTCAACTTCTTGGGTATTACTTCTTATGGACAGAGAATTTAACCTTTTTTTT
1 CAAGAACCAAATTCTCAACTTCTTGGGTATTACTTCTTATGGACAGAGAATTTAACCTTTTTTTT
16038137 TTTTCTCAGAAAACAGTG
66 TTTTCTCAGAAAACAGTG
16038155 AAAATAAACC
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 26 0.31
84 57 0.69
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (83 bp):
CAAGAACCAAATTCTCAACTTCTTGGGTATTACTTCTTATGGACAGAGAATTTAACCTTTTTTTT
TTTTCTCAGAAAACAGTG
Found at i:16040713 original size:2 final size:2
Alignment explanation
Indices: 16040706--16040736 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16040696 GAGTACTGTT
16040706 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
16040737 GGAAATATTT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16043771 original size:25 final size:24
Alignment explanation
Indices: 16043742--16043788 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
16043732 ATCATAAATT
*
16043742 TTATTATAATTATGATGTAAAAAAA
1 TTATTATAATTATAAT-TAAAAAAA
16043767 TTATTATAATTATAATTAAAAA
1 TTATTATAATTATAATTAAAAA
16043789 TAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTATTATAATTATAATTAAAAAAA
Found at i:16043800 original size:25 final size:25
Alignment explanation
Indices: 16043747--16043800 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
16043737 AAATTTTATT
* * *
16043747 ATAATTATGATGTAAAAAAATTATT
1 ATAATTATAATGTAAAAAAATAATA
16043772 ATAATTATAAT-TAAAAATAATAATA
1 ATAATTATAATGTAAAAA-AATAATA
16043797 ATAA
1 ATAA
16043801 ATTTATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
ATAATTATAATGTAAAAAAATAATA
Found at i:16043847 original size:23 final size:22
Alignment explanation
Indices: 16043811--16043866 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
16043801 ATTTATGTTA
* *
16043811 ATTT-AATTTTATTAAAATTAAT
1 ATTTAAATTTAATTAAAAAT-AT
16043833 ATTTAAATTTAATTAAAAATAT
1 ATTTAAATTTAATTAAAAATAT
*
16043855 A-ATAAATTTAAT
1 ATTTAAATTTAAT
16043867 CATATCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.33
22 7 0.23
23 13 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAAATTTAATTAAAAATAT
Found at i:16050841 original size:30 final size:30
Alignment explanation
Indices: 16050807--16050873 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
16050797 AAATACTTAG
16050807 AATTAAGCTGGTTGTAATCTGTATCTCTAA
1 AATTAAGCTGGTTGTAATCTGTATCTCTAA
* *
16050837 AATTAAGCTGGTTGTAATCTGTATTTCTAG
1 AATTAAGCTGGTTGTAATCTGTATCTCTAA
16050867 AATTAAG
1 AATTAAG
16050874 AACTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (30 bp):
AATTAAGCTGGTTGTAATCTGTATCTCTAA
Found at i:16054369 original size:30 final size:30
Alignment explanation
Indices: 16054335--16054434 Score: 130
Period size: 30 Copynumber: 3.3 Consensus size: 30
16054325 GAGAAAATAC
16054335 CTAGAATTAAGCTTATTGTAATTTGTATCA
1 CTAGAATTAAGCTTATTGTAATTTGTATCA
* * *
16054365 CTAGAATTAATCTAATTGTAATTTGTATCT
1 CTAGAATTAAGCTTATTGTAATTTGTATCA
* *
16054395 CTAGAATTAAGC-TAGTTGTAATCTGTATCC
1 CTAGAATTAAGCTTA-TTGTAATTTGTATCA
*
16054425 CTAAAATTAA
1 CTAGAATTAA
16054435 AAACTAAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 1 0.02
30 60 0.98
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (30 bp):
CTAGAATTAAGCTTATTGTAATTTGTATCA
Found at i:16061088 original size:29 final size:29
Alignment explanation
Indices: 16061055--16061111 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
16061045 TTTTCTGAAC
16061055 TCGAAATTTAATTTAGTTAATTCATGCAT
1 TCGAAATTTAATTTAGTTAATTCATGCAT
* * *
16061084 TCGAAGTTTAGTTTAGTTAGTTCATGCA
1 TCGAAATTTAATTTAGTTAATTCATGCA
16061112 ATCACTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (29 bp):
TCGAAATTTAATTTAGTTAATTCATGCAT
Found at i:16061324 original size:12 final size:12
Alignment explanation
Indices: 16061307--16061331 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16061297 ACAATACTAA
16061307 TACACAAGTCAC
1 TACACAAGTCAC
16061319 TACACAAGTCAC
1 TACACAAGTCAC
16061331 T
1 T
16061332 GGTGTTTTAC
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:0.32, G:0.08, T:0.20
Consensus pattern (12 bp):
TACACAAGTCAC
Found at i:16062101 original size:27 final size:27
Alignment explanation
Indices: 16062061--16062114 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
16062051 GCCTAGCTTT
*
16062061 TAAACAGTCTTGTGAAGAAA-TTTCAGC
1 TAAACAGTCCTGTGAA-AAATTTTCAGC
16062088 TAAACAGTCCTGTGAAAAATTTTCAGC
1 TAAACAGTCCTGTGAAAAATTTTCAGC
16062115 ATTTTAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (27 bp):
TAAACAGTCCTGTGAAAAATTTTCAGC
Found at i:16062329 original size:26 final size:26
Alignment explanation
Indices: 16062293--16062349 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
16062283 ATGGGTATTG
*
16062293 ATGCAATATTGCTCCATACAAAATCA
1 ATGCAATATTGCTCCAAACAAAATCA
*
16062319 ATGCAATATTGCTCCAAACAGAATCA
1 ATGCAATATTGCTCCAAACAAAATCA
16062345 ATGCA
1 ATGCA
16062350 TAAGCTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (26 bp):
ATGCAATATTGCTCCAAACAAAATCA
Found at i:16064882 original size:16 final size:16
Alignment explanation
Indices: 16064863--16064896 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16064853 CACAATCCCC
16064863 TCTAAACCAAAAGTCA
1 TCTAAACCAAAAGTCA
16064879 TCTAAACCAAAAGTCA
1 TCTAAACCAAAAGTCA
16064895 TC
1 TC
16064897 ACCAAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.26, G:0.06, T:0.21
Consensus pattern (16 bp):
TCTAAACCAAAAGTCA
Found at i:16066321 original size:15 final size:15
Alignment explanation
Indices: 16066301--16066329 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16066291 TTAATTCATT
16066301 AATAATATATAAAAA
1 AATAATATATAAAAA
16066316 AATAATATATAAAA
1 AATAATATATAAAA
16066330 TATATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAATATATAAAAA
Found at i:16066331 original size:24 final size:24
Alignment explanation
Indices: 16066304--16066357 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16066294 ATTCATTAAT
*
16066304 AATATATAAAAAAATAATATATAA
1 AATATATAAAAAAATAATACATAA
** *
16066328 AATATATAAATTAATAATACATCA
1 AATATATAAAAAAATAATACATAA
16066352 AATATA
1 AATATA
16066358 AACTTGATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
AATATATAAAAAAATAATACATAA
Found at i:16067828 original size:31 final size:31
Alignment explanation
Indices: 16067790--16067854 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
16067780 CATTTGGAGC
*
16067790 TAACAATGATAGAATTGAGTACCAAATTAGT
1 TAACAATGATAGAATTGACTACCAAATTAGT
16067821 TAACAATGATAGAATTGACTACCAAATTAGT
1 TAACAATGATAGAATTGACTACCAAATTAGT
16067852 TAA
1 TAA
16067855 TAAATTCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (31 bp):
TAACAATGATAGAATTGACTACCAAATTAGT
Found at i:16074461 original size:15 final size:15
Alignment explanation
Indices: 16074414--16074463 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
16074404 TTAAATAATA
16074414 ATTTTATAATTTAAAT
1 ATTTTA-AATTTAAAT
* * *
16074430 A--TTATATTAAAAA
1 ATTTTAAATTTAAAT
16074443 ATTTTAAATTTAAAT
1 ATTTTAAATTTAAAT
16074458 ATTTTA
1 ATTTTA
16074464 TTATAATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
15 15 0.58
16 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTTAAATTTAAAT
Found at i:16075944 original size:18 final size:17
Alignment explanation
Indices: 16075921--16075957 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
16075911 TTATAAAATT
*
16075921 TTAAAATATATATATAAA
1 TTAAAAAATATATA-AAA
16075939 TTAAAAAATATATAAAA
1 TTAAAAAATATATAAAA
16075956 TT
1 TT
16075958 TGTTTCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAATATATAAAA
Found at i:16077007 original size:17 final size:16
Alignment explanation
Indices: 16076981--16077012 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
16076971 AAGATAAAAT
16076981 AAAATTATAAATAAAG
1 AAAATTATAAATAAAG
16076997 AAAATTGATAAATAAA
1 AAAATT-ATAAATAAA
16077013 TAATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAATTATAAATAAAG
Found at i:16077138 original size:5 final size:5
Alignment explanation
Indices: 16077128--16077177 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
16077118 TTATTTATTT
*
16077128 TTTTC TTTTC -TTTC -TTTC -TTTC TTTTC TTTTTC TTTTC TCTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC
16077175 TTT
1 TTT
16077178 CGTTGACTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 15 0.38
5 20 0.50
6 5 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:16077141 original size:4 final size:4
Alignment explanation
Indices: 16077129--16077178 Score: 50
Period size: 4 Copynumber: 12.0 Consensus size: 4
16077119 TATTTATTTT
16077129 TTTC TTTTC TTTC TTTC TTTC TTT- TCTT- TTTC TTTTC TCTTC TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC T-TTC TTTC -TTTC T-TTC TTTC
16077175 TTTC
1 TTTC
16077179 GTTGACTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.07
4 26 0.63
5 12 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:16077991 original size:17 final size:16
Alignment explanation
Indices: 16077969--16078003 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
16077959 TAAATTGATG
16077969 AACTATAAGCAAATATA
1 AACTATAAGCAAA-ATA
*
16077986 AACTATAATCAAAATA
1 AACTATAAGCAAAATA
16078002 AA
1 AA
16078004 GAGATAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (16 bp):
AACTATAAGCAAAATA
Found at i:16084113 original size:24 final size:24
Alignment explanation
Indices: 16084081--16084129 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16084071 AATCCTAATG
16084081 TGCTAAATTATTGATCAATATATA
1 TGCTAAATTATTGATCAATATATA
*
16084105 TGCTGAATTATTGATCAATATATA
1 TGCTAAATTATTGATCAATATATA
16084129 T
1 T
16084130 ATATCATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (24 bp):
TGCTAAATTATTGATCAATATATA
Found at i:16087436 original size:31 final size:31
Alignment explanation
Indices: 16087321--16087437 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 31
16087311 TAATAAATCT
* * **
16087321 ATTTTTAAAATGAAATGAAAATTTTTACATA
1 ATTTTTAAAATGATATGTAAATTTTTATTTA
* **
16087352 ATATTTTAAAATGATATG-GAGCTTTTATTTA
1 AT-TTTTAAAATGATATGTAAATTTTTATTTA
*** *
16087383 ATTTTTTAAACCAATATATAAATTTTTATTTA
1 A-TTTTTAAAATGATATGTAAATTTTTATTTA
*
16087415 ATTTTTAAAATTATATGTAAATT
1 ATTTTTAAAATGATATGTAAATT
16087438 AAAAAAAATT
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
31 40 0.61
32 26 0.39
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
ATTTTTAAAATGATATGTAAATTTTTATTTA
Found at i:16087623 original size:20 final size:20
Alignment explanation
Indices: 16087596--16087636 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
16087586 ATAAAAATCA
*
16087596 ATTTTTTCTTTAATTATTTTT
1 ATTTTTCCTTT-ATTATTTTT
*
16087617 ATTTTTCCTTTTTTATTTTT
1 ATTTTTCCTTTATTATTTTT
16087637 TTATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTTTCCTTTATTATTTTT
Found at i:16105805 original size:25 final size:25
Alignment explanation
Indices: 16105764--16105815 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
16105754 GAATTTGAGC
16105764 ATAAATAATCAAATTATTATTTA-AT
1 ATAAATAATCAAATTATT-TTTATAT
*
16105789 ATAAA-AATTAAACTTATTTTTATAT
1 ATAAATAATCAAA-TTATTTTTATAT
16105814 AT
1 AT
16105816 TAATTGAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAAATAATCAAATTATTTTTATAT
Found at i:16107279 original size:34 final size:34
Alignment explanation
Indices: 16107241--16107306 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
16107231 TTAAAAATTT
*
16107241 ATTTTCAA-AAAATTATATAACTTATCAAAAATGA
1 ATTTT-AAGAAAATTATAAAACTTATCAAAAATGA
* * *
16107275 ATTTTAAGAAAGTTATAAAATTTTTCAAAAAT
1 ATTTTAAGAAAATTATAAAACTTATCAAAAAT
16107307 CCATTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (34 bp):
ATTTTAAGAAAATTATAAAACTTATCAAAAATGA
Found at i:16108651 original size:10 final size:8
Alignment explanation
Indices: 16108624--16108658 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
16108614 TTATTTTTAA
16108624 ATATAAAT
1 ATATAAAT
16108632 ATATAAAT
1 ATATAAAT
16108640 ATATAATTAT
1 ATATAA--AT
16108650 ATATAAAT
1 ATATAAAT
16108658 A
1 A
16108659 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:16114207 original size:24 final size:24
Alignment explanation
Indices: 16114175--16114223 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16114165 AATCCTAATG
16114175 TGCTAAATTATTGATCAATATATA
1 TGCTAAATTATTGATCAATATATA
*
16114199 TGCTGAATTATTGATCAATATATA
1 TGCTAAATTATTGATCAATATATA
16114223 T
1 T
16114224 ATCATTGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (24 bp):
TGCTAAATTATTGATCAATATATA
Found at i:16132847 original size:50 final size:50
Alignment explanation
Indices: 16132772--16132872 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
16132762 TATATAATTG
*
16132772 TCAAGTTGAGCTTAGCCAAATTTGATTGGATAGTTCGGTTTTGGATAGGT
1 TCAAGTTGAGCTTAGCCAAATTTGATTGGATAGTTCGGTCTTGGATAGGT
16132822 TCAAGTTGAGCTTAGCCAAATTTGATTGGATAGTTCGGTCTTGGATAGGT
1 TCAAGTTGAGCTTAGCCAAATTTGATTGGATAGTTCGGTCTTGGATAGGT
16132872 T
1 T
16132873 TAGATCAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.38
Consensus pattern (50 bp):
TCAAGTTGAGCTTAGCCAAATTTGATTGGATAGTTCGGTCTTGGATAGGT
Found at i:16137672 original size:26 final size:26
Alignment explanation
Indices: 16137645--16137695 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
16137635 CTAATCAAAT
16137645 TTTTATATT-TAAAAT-TTTTTTATTA
1 TTTTA-ATTATAAAATATTTTTTATTA
16137670 TTTTAATTAATAAAATATTTTTTATT
1 TTTTAATT-ATAAAATATTTTTTATT
16137696 TGAGTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 5 0.22
26 6 0.26
27 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTAATTATAAAATATTTTTTATTA
Found at i:16138408 original size:28 final size:28
Alignment explanation
Indices: 16138377--16138449 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 28
16138367 TTTTATTAAA
16138377 TTAATTATTATTTATTATAAAAATAATT-
1 TTAATTATTATTTATTA-AAAAATAATTG
* * *
16138405 TTAATCT-TAATTAATTAAAAAATTATTG
1 TTAAT-TATTATTTATTAAAAAATAATTG
16138433 TTAATTATCTCATTTAT
1 TTAATTAT-T-ATTTAT
16138450 CTTTGGCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
27 10 0.29
28 19 0.54
29 1 0.03
30 5 0.14
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (28 bp):
TTAATTATTATTTATTAAAAAATAATTG
Found at i:16139232 original size:34 final size:33
Alignment explanation
Indices: 16139188--16139252 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
16139178 TTTAAAAATT
*
16139188 ATTTTCAGAAAATTATATAACTTATCAAAAATGA
1 ATTTTAAGAAAATTATA-AACTTATCAAAAATGA
* * *
16139222 ATTTTAAGAAAGTTATAAATTTTTCAAAAAT
1 ATTTTAAGAAAATTATAAACTTATCAAAAAT
16139253 CCATTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (33 bp):
ATTTTAAGAAAATTATAAACTTATCAAAAATGA
Found at i:16139259 original size:33 final size:33
Alignment explanation
Indices: 16139164--16139252 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
16139154 TGAATATTAT
* * * * *
16139164 AAATTTTATGATTTTTTAAAAATTATTTTCAGA
1 AAATTATATAATTTTTCAAAAATAATTTTAAGA
* *
16139197 AAATTATATAACTTATCAAAAATGAATTTTAAGA
1 AAATTATATAATTTTTCAAAAAT-AATTTTAAGA
*
16139231 AAGTTATA-AATTTTTCAAAAAT
1 AAATTATATAATTTTTCAAAAAT
16139253 CCATTTTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
33 30 0.67
34 15 0.33
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (33 bp):
AAATTATATAATTTTTCAAAAATAATTTTAAGA
Found at i:16140591 original size:10 final size:8
Alignment explanation
Indices: 16140564--16140598 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
16140554 TTATTTTTAA
16140564 ATATAAAT
1 ATATAAAT
16140572 ATATAAAT
1 ATATAAAT
16140580 ATATAATTAT
1 ATATAA--AT
16140590 ATATAAAT
1 ATATAAAT
16140598 A
1 A
16140599 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:16140605 original size:18 final size:18
Alignment explanation
Indices: 16140570--16140606 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16140560 TTAAATATAA
* *
16140570 ATATATAAATATATAATT
1 ATATATAAATAAAAAATT
16140588 ATATATAAATAAAAAATT
1 ATATATAAATAAAAAATT
16140606 A
1 A
16140607 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATAAATAAAAAATT
Found at i:16141219 original size:53 final size:51
Alignment explanation
Indices: 16141159--16141311 Score: 148
Period size: 52 Copynumber: 2.9 Consensus size: 51
16141149 TAAATAATTC
* *
16141159 CTCCTAAACAAAAGGTTTAGAAACTTAACAAAAATTTCATCTAAAAAAAGTTT
1 CTCCTAAACAAAAGGTTT-GAAACTTAA-AAAAATTTCATATAAAAAAACTTT
* * * *
16141212 CTCCTAAACAAAAGTTTTGAAGCTTTAAAAAAATTTCATTTTAAATAAACTTT
1 CTCCTAAACAAAAGGTTTGAAAC-TTAAAAAAATTTCA-TATAAAAAAACTTT
* * * *
16141265 -TCCTAAAC-TAAGGATTTGAAACTAAAAAAAAATCTCAAATAAAAAAA
1 CTCCTAAACAAAAGG-TTTGAAACT-TAAAAAAATTTCATATAAAAAAA
16141312 TTACTCTTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
51 11 0.13
52 40 0.48
53 32 0.39
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (51 bp):
CTCCTAAACAAAAGGTTTGAAACTTAAAAAAATTTCATATAAAAAAACTTT
Found at i:16141226 original size:17 final size:17
Alignment explanation
Indices: 16141185--16141228 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
16141175 TTAGAAACTT
*
16141185 AACAAAAATTTCATCTA
1 AACAAAAGTTTCATCTA
16141202 AA-AAAAGTTTC-TCCTA
1 AACAAAAGTTTCAT-CTA
16141218 AACAAAAGTTT
1 AACAAAAGTTT
16141229 TGAAGCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 10 0.42
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.30
Consensus pattern (17 bp):
AACAAAAGTTTCATCTA
Found at i:16142488 original size:15 final size:16
Alignment explanation
Indices: 16142465--16142508 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
16142455 TATCTACCCA
16142465 TAAAAAATTTAATATT
1 TAAAAAATTTAATATT
* *
16142481 TTAAAATTATTAATATT
1 TAAAAAAT-TTAATATT
16142498 TAAAAAATTTA
1 TAAAAAATTTA
16142509 TCTACCCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAAATTTAATATT
Found at i:16144684 original size:51 final size:50
Alignment explanation
Indices: 16144606--16144766 Score: 150
Period size: 52 Copynumber: 3.1 Consensus size: 50
16144596 TGAAATTTTT
*
16144606 AAAAAAA--TCACATCTAAACAATTTCTCCTAAACAAAGGTTTCGAAACTTA
1 AAAAAAATTTCAC-TCTAAAAAATTTCTCCTAAACAAAGGTTT-GAAACTTA
* * *
16144656 ACAAAAATTT-ACTCTAAAAAAGTTTCTCCTAAACAAAAGTTTTGAAGCTTTA
1 AAAAAAATTTCACTCTAAAAAA-TTTCTCCTAAAC-AAAGGTTTGAAAC-TTA
* * * *
16144708 AAAAAAATTTCATTTTAAAAATACTTT-TCCTAAACTAAGGATTTGAAACTAA
1 AAAAAAATTTCACTCTAAAAA-A-TTTCTCCTAAACAAAGG-TTTGAAACTTA
16144760 AAAAAAA
1 AAAAAAA
16144767 ATCTCAAATA
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
50 14 0.15
51 18 0.20
52 32 0.35
53 23 0.25
54 4 0.04
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (50 bp):
AAAAAAATTTCACTCTAAAAAATTTCTCCTAAACAAAGGTTTGAAACTTA
Found at i:16144712 original size:50 final size:50
Alignment explanation
Indices: 16144603--16144713 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 50
16144593 TTTTGAAATT
* *
16144603 TTTAAAAAAATCACATCTAAACAATTTCTCCTAAACAAAGGTTTCGAAAC
1 TTTAAAAAAATCACATCTAAAAAATTTCTCCTAAACAAAAGTTTCGAAAC
* * *
16144653 -TTAACAAAAATTTAC-TCTAAAAAAGTTTCTCCTAAACAAAAGTTTTGAAGC
1 TTTAA-AAAAA-TCACATCTAAAAAA-TTTCTCCTAAACAAAAGTTTCGAAAC
16144704 TTTAAAAAAA
1 TTTAAAAAAA
16144714 ATTTCATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
49 4 0.08
50 13 0.25
51 31 0.60
52 4 0.08
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (50 bp):
TTTAAAAAAATCACATCTAAAAAATTTCTCCTAAACAAAAGTTTCGAAAC
Found at i:16144753 original size:53 final size:51
Alignment explanation
Indices: 16144594--16144768 Score: 151
Period size: 53 Copynumber: 3.4 Consensus size: 51
16144584 NNNNNNNNNT
* * * *
16144594 TTTGAAATTTTTAAAAAAA-TCACATCTAAACAA-TTTCTCCTAAACAAAGG
1 TTTGAAACTTTAAAAAAAATTTAC-TCTAAAAAACTTTCTCCTAAACAAAGG
* * *
16144644 TTTCGAAAC-TTAACAAAAATTTACTCTAAAAAAGTTTCTCCTAAACAAAAGT
1 TTT-GAAACTTTAAAAAAAATTTACTCTAAAAAACTTTCTCCTAAAC-AAAGG
* * * *
16144696 TTTGAAGCTTTAAAAAAAATTTCATTTTAAAAATACTTT-TCCTAAACTAAGG
1 TTTGAAACTTTAAAAAAAATTT-ACTCTAAAAA-ACTTTCTCCTAAACAAAGG
**
16144748 ATTTGAAACTAAAAAAAAAAT
1 -TTTGAAACTTTAAAAAAAAT
16144769 CTCAAATAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
50 19 0.19
51 23 0.23
52 22 0.22
53 33 0.33
54 4 0.04
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (51 bp):
TTTGAAACTTTAAAAAAAATTTACTCTAAAAAACTTTCTCCTAAACAAAGG
Found at i:16146135 original size:18 final size:16
Alignment explanation
Indices: 16146106--16146149 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 16
16146096 TCTACCCATA
16146106 AAAAAATTTAATATTT
1 AAAAAATTTAATATTT
16146122 AAAAAATTAGTAATATTT
1 AAAAAATT--TAATATTT
16146140 AAAAAATTTA
1 AAAAAATTTA
16146150 TCTATCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.38
18 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAAAATTTAATATTT
Found at i:16146491 original size:17 final size:17
Alignment explanation
Indices: 16146469--16146501 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16146459 ATAAAATTAA
16146469 TCAC-TTAACTGAAAATG
1 TCACTTTAACT-AAAATG
16146486 TCACTTTAACTAAAAT
1 TCACTTTAACTAAAAT
16146502 AAACTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (17 bp):
TCACTTTAACTAAAATG
Found at i:16152241 original size:14 final size:17
Alignment explanation
Indices: 16152209--16152241 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
16152199 GATCTAATGT
16152209 AAATTATTCTAAGTAAA
1 AAATTATTCTAAGTAAA
16152226 AAATTA-TC-AAGTAAA
1 AAATTATTCTAAGTAAA
16152241 A
1 A
16152242 TAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
AAATTATTCTAAGTAAA
Found at i:16152810 original size:538 final size:531
Alignment explanation
Indices: 16151782--16152851 Score: 1601
Period size: 538 Copynumber: 2.0 Consensus size: 531
16151772 ATACCCCTAT
* **
16151782 AAATTTCTAAATTAACTAATTGATCCTTAAATATTGATAACCTTTATTAATTTATTTAAATTTAA
1 AAATTTCTAAATTAACAAATTGATAATTAAATATTGATAACCTTTATTAATTTATTTAAATTTAA
*
16151847 TTTAAACAAACTAAAATTAAAAATAGAGTTTATGTAAAATTAAATTATTTAAAATTTTAATTTTA
66 TTTAAACAAACTAAAATTAAAAATAGAGTTTATGTAAAATTAAATTATTTAAAATTTTAATTCTA
* * *
16151912 AAAGTATTAAAAGTGATTGTCTAAAATATCTTTACTAAATGTTTTTATATGAATTTTTTATTATT
131 AAAGCATTAAAAGTGATTGCCTAAAATATCCTTACTAAATGTTTTTATATGAATTTTTTATTATT
* * *
16151977 AGACTCTTTCTTTTTGTAATTAAGCTAAAAAAAAAAAATACTAAAAGTGATTGATTAAAATACTT
196 AGACTCTTTCCTTTTATAATTAAGCT----AAAAAAAATACTAAAAGTGATTGATTAAAATACTC
*
16152042 TTAATAAAATTTTAATTTAAAAAATATTAAAAAATTATTAATCAAAATATCATTAGTAATTTTTT
257 TTAATAAAATTTTAATTTAAAAAATATTAAAAAATGATTAATCAAAATATCATTAGTAATTTTTT
*** *
16152107 TAAAAATTTTAATTTAAATGACTTTTTTTTATTATAAGACTCTTTTTATAAGCAAAATGATTTTT
322 TAAAAATTTTAATTTAAATGAAAATTTTTTATTATAAGACTCTTTTTATAAGCAAAATGATCTTT
* * * * *
16152172 CACATTAAATAATCTAGGTGGTTGAATGATCTAATGTAAATTATTCTAAGTAAAAAATTATCAAG
387 CACATCAAATAATCTAGGTGATTAAATGATCTAATATAAATTATTCTAAGTAAAAAACTATCAAG
**
16152237 TAAAATAAAATTAATTGTTTTTGGTGATTTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTT
452 TAAAATAAAATTAATTGTTTTTGGTGAAGTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTT
16152302 AAAATTATGTATATA
517 AAAATTATGTATATA
* *
16152317 AAATTT-TAAATTAACAAATTTATAATTAAATA-TGTATAACTTTTATTAATTTATTTAAATTTA
1 AAATTTCTAAATTAACAAATTGATAATTAAATATTG-ATAACCTTTATTAATTTATTTAAATTTA
* * *
16152380 ATTTAAATAAACTAAAATTAAAAATAGAGTTTATGTAAAATTAATTTTTTTTTAAATTTTAAATT
65 ATTTAAACAAACTAAAATTAAAAATAGAGTTTATGTAAAATTAA------ATT--A-TTTAAAAT
*
16152445 TTTAATTCTAAAAGCATTAAAAGTGATTGCCTAAAATATCCTTACTAATTGTTTTTATATGAATT
121 TTTAATTCTAAAAGCATTAAAAGTGATTGCCTAAAATATCCTTACTAAATGTTTTTATATGAA-T
*
16152510 TTTTTATTATTAGACTCTTTCCTTTTATAATT-AGACT-AAAAAAATATTAAAAGTGATTGATTA
185 TTTTTATTATTAGACTCTTTCCTTTTATAATTAAG-CTAAAAAAAATACTAAAAGTGATTGATTA
* * * *
16152573 AAATACTCTTAATAAAATTTTAATTTAAAAAATGTT-AAAAGTGATTGATCAAAATGTCATTAGT
249 AAATACTCTTAATAAAATTTTAATTTAAAAAATATTAAAAAATGATTAATCAAAATATCATTAGT
* * * *
16152637 AATTTTTTTAGAAATTTTAATTTAAATGAAAATTTTTTATTATTAGATTCTTTTTATAAGTAAAA
314 AATTTTTTTAAAAATTTTAATTTAAATGAAAATTTTTTATTATAAGACTCTTTTTATAAGCAAAA
* *
16152702 TGATCTTTCACATCAAATAATCTAGGTGATTAAATGATCTAATATGAATTATTCTGAGTAAAAAA
379 TGATCTTTCACATCAAATAATCTAGGTGATTAAATGATCTAATATAAATTATTCTAAGTAAAAAA
*
16152767 CTATTAAGTAAAATAAAATTAATTGTTTTTGGTGAAGTCTTTCAAGGTAAGATTTTATTTTATTT
444 CTATCAAGTAAAATAAAATTAATTGTTTTTGGTGAAGTCTTTCAAGGTAAGATTTTATTTTATTT
16152832 TATTTTTTAAAATTATGTAT
509 TATTTTTTAAAATTATGTAT
16152852 TTATATAATA
Statistics
Matches: 483, Mismatches: 40, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
533 2 0.00
534 92 0.19
535 6 0.01
538 221 0.46
539 59 0.12
540 2 0.00
542 1 0.00
543 67 0.14
544 33 0.07
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (531 bp):
AAATTTCTAAATTAACAAATTGATAATTAAATATTGATAACCTTTATTAATTTATTTAAATTTAA
TTTAAACAAACTAAAATTAAAAATAGAGTTTATGTAAAATTAAATTATTTAAAATTTTAATTCTA
AAAGCATTAAAAGTGATTGCCTAAAATATCCTTACTAAATGTTTTTATATGAATTTTTTATTATT
AGACTCTTTCCTTTTATAATTAAGCTAAAAAAAATACTAAAAGTGATTGATTAAAATACTCTTAA
TAAAATTTTAATTTAAAAAATATTAAAAAATGATTAATCAAAATATCATTAGTAATTTTTTTAAA
AATTTTAATTTAAATGAAAATTTTTTATTATAAGACTCTTTTTATAAGCAAAATGATCTTTCACA
TCAAATAATCTAGGTGATTAAATGATCTAATATAAATTATTCTAAGTAAAAAACTATCAAGTAAA
ATAAAATTAATTGTTTTTGGTGAAGTCTTTCAAGGTAAGATTTTATTTTATTTTATTTTTTAAAA
TTATGTATATA
Found at i:16155357 original size:22 final size:22
Alignment explanation
Indices: 16155327--16155389 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
16155317 TAATAATCAT
* *
16155327 CAATAATTTAGTAGTAAATTAA
1 CAATAATTTAGTAATAAATGAA
** *
16155349 TGATAATTTAATAATAAATGAA
1 CAATAATTTAGTAATAAATGAA
*
16155371 CAATAATTTAGTGATAAAT
1 CAATAATTTAGTAATAAAT
16155390 AATTTATAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (22 bp):
CAATAATTTAGTAATAAATGAA
Found at i:16155549 original size:22 final size:22
Alignment explanation
Indices: 16155524--16155598 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
16155514 AAAAAATAAG
*
16155524 TGATAATTTAGTAGTTAATTAT
1 TGATAATTTAGTAGTTAATTAA
* * *
16155546 TGATAACTTAGTA-ATAATCAA
1 TGATAATTTAGTAGTTAATTAA
* * *
16155567 TGATAATTTAATAGTAAATTAG
1 TGATAATTTAGTAGTTAATTAA
*
16155589 TAATAATTTA
1 TGATAATTTA
16155599 ATACTATATC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 16 0.39
22 25 0.61
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (22 bp):
TGATAATTTAGTAGTTAATTAA
Found at i:16155825 original size:21 final size:21
Alignment explanation
Indices: 16155796--16155897 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 21
16155786 GATTCAATCC
*
16155796 CAAACCAAAAAAAAAAAATAA
1 CAAAACAAAAAAAAAAAATAA
16155817 CAAAACAAAAAAAAATAAA-AA
1 CAAAACAAAAAAAAA-AAATAA
* *
16155838 TAAAAACAAAAACAACAAAAAACAA
1 -CAAAAC-AAAA-AA-AAAAAATAA
*
16155863 CAAAA-AATAAACAAAAAATAA
1 CAAAACAA-AAAAAAAAAATAA
*
16155884 -ACACACAAAAAAAA
1 CA-AAACAAAAAAAA
16155898 CACAAAAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
20 1 0.02
21 31 0.48
22 13 0.20
23 6 0.09
24 9 0.14
25 5 0.08
ACGTcount: A:0.81, C:0.14, G:0.00, T:0.05
Consensus pattern (21 bp):
CAAAACAAAAAAAAAAAATAA
Found at i:16155837 original size:11 final size:11
Alignment explanation
Indices: 16155804--16155884 Score: 60
Period size: 11 Copynumber: 7.3 Consensus size: 11
16155794 CCCAAACCAA
16155804 AAAAAAAAAAT
1 AAAAAAAAAAT
16155815 AACAAAACAAAA-
1 AA-AAAA-AAAAT
16155827 AAAAATAAAAAT
1 AAAAA-AAAAAT
16155839 AAAAACAAAAA-
1 AAAAA-AAAAAT
* *
16155850 CAACAAAAAA-
1 AAAAAAAAAAT
* *
16155860 CAACAAAAAAT
1 AAAAAAAAAAT
*
16155871 AAACAAAAAAT
1 AAAAAAAAAAT
16155882 AAA
1 AAA
16155885 CACACAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
10 15 0.25
11 25 0.41
12 17 0.28
13 4 0.07
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:16155868 original size:37 final size:36
Alignment explanation
Indices: 16155802--16155905 Score: 99
Period size: 36 Copynumber: 2.9 Consensus size: 36
16155792 ATCCCAAACC
*
16155802 AAAAAAAAAAAATAACAAAACAA-AA-AAAAATAAAA
1 AAAAAAAAAAAACAACAAAA-AACAACAAAAATAAAA
*
16155837 ATAAAAACAAAAACAACAAAAAACAACAAAAAATAAACA
1 A-AAAAAAAAAAACAACAAAAAACAAC-AAAAATAAA-A
* *
16155876 AAAAATAAACACACAA-AAAAAAC-ACAAAAA
1 AAAAA-AAAAAAACAACAAAAAACAACAAAAA
16155906 AGGAAAGAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
35 3 0.05
36 24 0.41
37 2 0.03
38 20 0.34
39 9 0.16
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.05
Consensus pattern (36 bp):
AAAAAAAAAAAACAACAAAAAACAACAAAAATAAAA
Found at i:16155874 original size:24 final size:23
Alignment explanation
Indices: 16155845--16155906 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
16155835 AAATAAAAAC
16155845 AAAAACAACAAAAAACA-ACAAAA
1 AAAAACAACAAAAAACACAC-AAA
*
16155868 AATAAACAAAAAATAAACACACAAA
1 AA-AAACAACAAA-AAACACACAAA
16155893 AAAAAC-ACAAAAAA
1 AAAAACAACAAAAAA
16155907 GGAAAGAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 3 0.09
23 6 0.18
24 13 0.38
25 10 0.29
26 2 0.06
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (23 bp):
AAAAACAACAAAAAACACACAAA
Found at i:16155885 original size:11 final size:10
Alignment explanation
Indices: 16155801--16155906 Score: 81
Period size: 10 Copynumber: 9.8 Consensus size: 10
16155791 AATCCCAAAC
16155801 CAAAAAAAAA
1 CAAAAAAAAA
16155811 -AAATAACAAAA
1 CAAA-AA-AAAA
16155822 CAAAAAAAAA
1 CAAAAAAAAA
*
16155832 TAAAAATAAAA
1 CAAAAA-AAAA
*
16155843 -ACAAAAACAA
1 CA-AAAAAAAA
*
16155853 CAAAAAACAA
1 CAAAAAAAAA
16155863 CAAAAAATAAA
1 CAAAAAA-AAA
16155874 CAAAAAATAAACA
1 C-AAAAA-AAA-A
16155887 CACAAAAAAAA
1 CA-AAAAAAAA
16155898 CACAAAAAA
1 CA-AAAAAA
16155907 GGAAAGAGGG
Statistics
Matches: 82, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
9 3 0.04
10 30 0.37
11 28 0.34
12 14 0.17
13 7 0.09
ACGTcount: A:0.82, C:0.13, G:0.00, T:0.05
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:16155897 original size:1 final size:1
Alignment explanation
Indices: 16155802--16155880 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
16155792 ATCCCAAACC
* * * * * * * * * *
16155802 AAAAAAAAAAAATAACAAAACAAAAAAAAATAAAAATAAAAACAAAAACAACAAAAAACAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
16155867 AAATAAACAAAAAA
1 AAAAAAAAAAAAAA
16155881 TAAACACACA
Statistics
Matches: 54, Mismatches: 24, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:16155906 original size:37 final size:38
Alignment explanation
Indices: 16155802--16155906 Score: 112
Period size: 38 Copynumber: 2.8 Consensus size: 38
16155792 ATCCCAAACC
* *
16155802 AAAAA-AAAAA-AATAACAAAACAAAAAAAAATAAAAAT
1 AAAAACAAAAACAACAA-AAAACAACAAAAAATAAAAAT
*
16155839 AAAAACAAAAACAACAAAAAACAACAAAAAATAAACA-
1 AAAAACAAAAACAACAAAAAACAACAAAAAATAAAAAT
*
16155876 AAAAATAAACACACAA-AAAAAAC-ACAAAAAA
1 AAAAACAAA-A-ACAACAAAAAACAACAAAAAA
16155907 GGAAAGAGGG
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
37 21 0.35
38 31 0.52
39 8 0.13
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.05
Consensus pattern (38 bp):
AAAAACAAAAACAACAAAAAACAACAAAAAATAAAAAT
Found at i:16156602 original size:144 final size:142
Alignment explanation
Indices: 16156373--16156745 Score: 421
Period size: 144 Copynumber: 2.6 Consensus size: 142
16156363 GCTTTCTATG
* * * * *
16156373 GGGTATTTTCATAATTTGACCTTTCCGAA-CTCAGATTTTCATGAACTTTTTAGATCTTAATTTC
1 GGGTATTTTCATAATTTGACCTTTTC-AAGCTCAAATTTTCATGAAATTTTCAAATCTT-ATTTC
* * * *
16156437 ATAATATTTCATTATTTTTGGTGCATTTGAAATCACAACAGTATCCCGAGAAG-TGTGAAATTA-
64 ATAATATTTCATAATTTTTGGTGCATTTGAAATCACAACAATA-CCCCAAAAGATGTGAAATTAT
* **
16156500 CGAAAATA-TCTTTATA
128 C-AAAATACCCCATA-A
* * *
16156516 GGAGTATTTTCATAATTTGGCCTTTTCAAGCTCAAATTTTTATAAAAATTTTCAAATCTTATTTC
1 GG-GTATTTTCATAATTTGACCTTTTCAAGCTCAAATTTTCAT-GAAATTTTCAAATCTTATTTC
* * *
16156581 ATAATATTTTATAATTTTTGGTGCATTTGAAATCATAGCAATACCCCAAAAGATGTGAAATTATC
64 ATAATATTTCATAATTTTTGGTGCATTTGAAATCACAACAATACCCCAAAAGATGTGAAATTATC
16156646 AAAATACCCCATAA
129 AAAATACCCCATAA
* * * *
16156660 GGGTATTTTCATAATTTGACATTTTCAAGCTCAAATTTTCATGAAACTTTCAAAATCTAAATTTT
1 GGGTATTTTCATAATTTGACCTTTTCAAGCTCAAATTTTCATGAAATTTTC-AAATCT-TATTTC
*
16156725 ATAATATTTCATGAGTTTTTG
64 ATAATATTTCAT-AATTTTTG
16156746 TGTTTTAAAA
Statistics
Matches: 194, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
142 7 0.04
143 54 0.28
144 110 0.57
145 23 0.12
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (142 bp):
GGGTATTTTCATAATTTGACCTTTTCAAGCTCAAATTTTCATGAAATTTTCAAATCTTATTTCAT
AATATTTCATAATTTTTGGTGCATTTGAAATCACAACAATACCCCAAAAGATGTGAAATTATCAA
AATACCCCATAA
Found at i:16161428 original size:3 final size:3
Alignment explanation
Indices: 16161420--16161450 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16161410 ATGAAATTTA
16161420 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
16161451 GCACCCACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:16168303 original size:19 final size:19
Alignment explanation
Indices: 16168279--16168317 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16168269 AGTATTTGTT
16168279 ATATTAACATAATATT-TTA
1 ATATTAA-ATAATATTATTA
*
16168298 ATATTAAATATTATTATTA
1 ATATTAAATAATATTATTA
16168317 A
1 A
16168318 AATATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTAAATAATATTATTA
Found at i:16168360 original size:25 final size:26
Alignment explanation
Indices: 16168332--16168414 Score: 100
Period size: 25 Copynumber: 3.2 Consensus size: 26
16168322 TAATTATTTG
16168332 TTAATTTTAATAATTTTAATAATA-A
1 TTAATTTTAATAATTTTAATAATAGA
*
16168357 TTAATTTCAATATATTTTAATAATAGA
1 TTAATTTTAATA-ATTTTAATAATAGA
*
16168384 -TAATTTTTAAT-ATTTTAATAATTATA
1 TTAA-TTTTAATAATTTTAATAA-TAGA
16168410 TTAAT
1 TTAAT
16168415 ATTATTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
25 21 0.42
26 19 0.38
27 10 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TTAATTTTAATAATTTTAATAATAGA
Found at i:16168580 original size:19 final size:19
Alignment explanation
Indices: 16168556--16168660 Score: 74
Period size: 19 Copynumber: 5.3 Consensus size: 19
16168546 CATTAGCTGG
16168556 TTTATTC-TTTATTCTTTAT
1 TTTATTCATTTATT-TTTAT
16168575 TTTATTCATTTATTTTTATT
1 TTTATTCATTTATTTTTA-T
* *
16168595 TTTATTGTCCTATTATCTTTAT
1 TTTA-T-TCAT-TTATTTTTAT
* *
16168617 TTT-TATC-TTTAATTTAAT
1 TTTAT-TCATTTATTTTTAT
16168635 TTTATCTCATTTA-TTTTAT
1 TTTAT-TCATTTATTTTTAT
16168654 TATTATT
1 T-TTATT
16168661 GTTTATCATT
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
18 10 0.14
19 22 0.31
20 22 0.31
21 1 0.01
22 7 0.10
23 8 0.11
ACGTcount: A:0.21, C:0.09, G:0.01, T:0.70
Consensus pattern (19 bp):
TTTATTCATTTATTTTTAT
Found at i:16168588 original size:13 final size:12
Alignment explanation
Indices: 16168563--16168600 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
16168553 TGGTTTATTC
16168563 TTTATTCTTTAT
1 TTTATTCTTTAT
16168575 TTTATTCATTTATT
1 TTTATTC-TTTA-T
16168589 TTTATT-TTTAT
1 TTTATTCTTTAT
16168600 T
1 T
16168601 GTCCTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 11 0.46
13 4 0.17
14 7 0.29
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTCTTTAT
Found at i:16168597 original size:20 final size:19
Alignment explanation
Indices: 16168556--16168666 Score: 77
Period size: 20 Copynumber: 5.6 Consensus size: 19
16168546 CATTAGCTGG
16168556 TTTATTCTTTATTCTTTA-T
1 TTTATTCTTTATT-TTTATT
16168575 TTTATTCATTTATTTTTATT
1 TTTATTC-TTTATTTTTATT
*
16168595 TTTATTGTCCTATTATCTTTATT
1 TTTA-T-T-CT-TTATTTTTATT
* *
16168618 TTTA-TCTTTA-ATTTAAT
1 TTTATTCTTTATTTTTATT
16168635 TTTATCTCATTTA-TTTTATT
1 TTTAT-TC-TTTATTTTTATT
* *
16168655 ATTATTGTTTAT
1 TTTATTCTTTAT
16168667 CATTAAACAA
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
17 9 0.12
18 7 0.09
19 16 0.21
20 25 0.33
21 1 0.01
22 2 0.03
23 15 0.20
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTATTCTTTATTTTTATT
Found at i:16168933 original size:14 final size:14
Alignment explanation
Indices: 16168914--16168947 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16168904 TCTTTATATG
*
16168914 ATTTAAGATTTAGC
1 ATTTAAAATTTAGC
*
16168928 ATTTAAAATTTAGG
1 ATTTAAAATTTAGC
16168942 ATTTAA
1 ATTTAA
16168948 CATCTAGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (14 bp):
ATTTAAAATTTAGC
Found at i:16169513 original size:58 final size:57
Alignment explanation
Indices: 16169449--16169891 Score: 481
Period size: 58 Copynumber: 7.7 Consensus size: 57
16169439 TTGTGCAGGA
* *
16169449 AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAGAAAACTTTAATCTTGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAGAAAA-TTTAATTTTAAGG
* * * **
16169507 AAAATTGATACTTTCAACTTTTCCCCAAAATATCTTTTA-AAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAGAAAATTTAATTTTAAGG
* *
16169563 AAAATTGATACTTTCAAC-TTTTCCTCAAAA-ACTTTTTTTTGAAAATTTACTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCC-CAAAATA--TTTTTTAGAAAATTTAATTTTAAGG
* ** *
16169621 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTTCCC-AAAATATTTTTTAGAAAA-TTTAATTTTAAGG
* * *
16169679 AAAATTGATACTTTCAAC-TTTTCCTCAAAA-ACCTGTTTTA-AAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCC-CAAAATA--TTTTTTAGAAAATTTAATTTTAAGG
* * *
16169736 AAAATTGATACTTTCAACTTTTTCTCAAAA-ACGCTTTTTAGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAATA--TTTTTTAGAAAATTTAATTTTAAGG
* * *
16169794 AAAATTGATACTTTCAAC-TTTTCCTCAAAATTTTTTTTTTTGAAAATTTACTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCC-CAAAA--TATTTTTTAGAAAATTTAATTTTAAGG
*
16169853 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTT
1 AAAATTGATACTTTCAAC-TTTTTCCCAAAATATTTTTT
16169892 TTTGGATTTT
Statistics
Matches: 331, Mismatches: 34, Indels: 40
0.82 0.08 0.10
Matches are distributed among these distances:
55 6 0.02
56 35 0.11
57 67 0.20
58 163 0.49
59 49 0.15
60 5 0.02
61 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAGAAAATTTAATTTTAAGG
Found at i:16169754 original size:115 final size:116
Alignment explanation
Indices: 16169447--16169891 Score: 564
Period size: 115 Copynumber: 3.9 Consensus size: 116
16169437 TTTTGTGCAG
* * *
16169447 GAAAAATTGATACTTTCAACTTTTTCC-CAAAATA--TTTTTTAGAAAACTTTAATCTTGAGGAA
1 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAATACTTTTTTTA-AAAA-TTTACTTTTAAGGAA
*
16169509 AATTGATACTTTCAACTTTTCCCC-AAAATATCTTTT-AAAACTTTAATTTCGA
63 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGA
* *
16169561 GGAAAATTGATACTTTCAACTTTTCCTCAAAA-ACTTTTTTTTGAAAATTTACTTTTAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAATAC-TTTTTTTAAAAATTTACTTTTAAGGAAAA
16169625 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGA
65 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGA
* * * *
16169677 GAAAAATTGATACTTTCAACTTTTCCTCAAAA-ACCTGTTTTAAAAATTTATTTTTAAGAAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAATACTTTTTTTAAAAATTTACTTTTAAGGAAAAT
* * ** * * **
16169741 TGATACTTTCAACTTTTTCTCAAAAACGCTTTTTAGAAAA-TTTATTTTTAA
66 TGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGAAAACTTTAATTTCGA
* ** *
16169792 GGAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTTTGAAAATTTACTTTTAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAA-TACTTTTTTTAAAAATTTACTTTTAAGGAAAA
**
16169857 TTGATACTTTCAACTTTTTTCCAAAAATATTTTTT
65 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
16169892 TTTGGATTTT
Statistics
Matches: 289, Mismatches: 33, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
113 7 0.02
114 60 0.21
115 103 0.36
116 70 0.24
117 49 0.17
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (116 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAATACTTTTTTTAAAAATTTACTTTTAAGGAAAAT
TGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGA
Found at i:16169755 original size:173 final size:171
Alignment explanation
Indices: 16169449--16169874 Score: 588
Period size: 173 Copynumber: 2.5 Consensus size: 171
16169439 TTGTGCAGGA
*
16169449 AAAATTGATACTTTCAACTTTTTCCC-AAAATATTTTTTAGAAAACTTTAATCTTGAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAAACTTTAAT-TTGAGGAAAATT
* * *
16169513 GATACTTTCAACTTTTCCCCAAAATATCTTTTAAAACTTTAATTTCGAGGAAAATTGATACTTTC
64 GATACTTTCAACTTTTCCCCAAAATATCTTTTAAAAATTTAATTTCAAGAAAAATTGATACTTTC
** *
16169578 AACTTTTCCTCAAAAACTTTTTTTTGAAAATTTACTTTTAAGG
129 AACTTTTCCTCAAAAACGCTTTTTAGAAAATTTACTTTTAAGG
*
16169621 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTT-GAGGAAAATTG
* * * *
16169686 ATACTTTCAACTTTTCCTCAAAA-ACCTGTTTTAAAAATTTATTTTTAAGAAAAATTGATACTTT
65 ATACTTTCAACTTTTCCCCAAAATA--TCTTTTAAAAATTTAATTTCAAGAAAAATTGATACTTT
* *
16169750 CAACTTTTTCTCAAAAACGCTTTTTAGAAAATTTATTTTTAAGG
128 CAACTTTTCCTCAAAAACGCTTTTTAGAAAATTTACTTTTAAGG
* * * * *
16169794 AAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTTTGAAAA-TTTACTTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCAAAA--ATATTTTTTGAAAACTTTA-ATTTGAGGAAAAT
16169858 TGATACTTTCAACTTTT
63 TGATACTTTCAACTTTT
16169875 TTCCAAAAAT
Statistics
Matches: 227, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
171 3 0.01
172 69 0.30
173 112 0.49
174 28 0.12
175 15 0.07
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (171 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTGAGGAAAATTGA
TACTTTCAACTTTTCCCCAAAATATCTTTTAAAAATTTAATTTCAAGAAAAATTGATACTTTCAA
CTTTTCCTCAAAAACGCTTTTTAGAAAATTTACTTTTAAGG
Found at i:16169917 original size:5 final size:5
Alignment explanation
Indices: 16169909--16170029 Score: 56
Period size: 5 Copynumber: 23.6 Consensus size: 5
16169899 TTTATTTAAA
* *
16169909 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AGAAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT A-AAAT
* *
16169954 AAAAT AAAA- AATAA- AAAA- ACAAAG AAAAGT AAAACA AAAAT AAAAAT
1 AAAAT AAAAT AA-AAT AAAAT A-AAAT AAAA-T AAAA-T AAAAT -AAAAT
* * *
16170001 AAAAT AAAGAT AAAAG AATAT TAAAT AAA
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAA
16170030 CCTAATCTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
3 3 0.03
4 6 0.07
5 56 0.62
6 22 0.24
7 4 0.04
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:16169917 original size:7 final size:7
Alignment explanation
Indices: 16169907--16169971 Score: 53
Period size: 7 Copynumber: 8.9 Consensus size: 7
16169897 ATTTTATTTA
16169907 AAAAAAT
1 AAAAAAT
16169914 AAAATAAT
1 AAAA-AAT
16169922 AAAACAA-
1 AAAA-AAT
16169929 AATAAAAGT
1 AA-AAAA-T
*
16169938 -GAAAAT
1 AAAAAAT
*
16169944 AAAAAGAA
1 AAAAA-AT
16169952 AAAAAAT
1 AAAAAAT
16169959 AAAAAAT
1 AAAAAAT
16169966 AAAAAA
1 AAAAAA
16169972 ACAAAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.02
7 29 0.62
8 17 0.36
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:16169953 original size:6 final size:6
Alignment explanation
Indices: 16169908--16170015 Score: 68
Period size: 6 Copynumber: 18.7 Consensus size: 6
16169898 TTTTATTTAA
* * *
16169908 AAAAAT -AAAAT AATAAA- ACAAAAT AAAAGT GAAAAT AAAAAG AAAAA-
1 AAAAAT AAAAAT AA-AAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * *
16169955 AAATA- AAAAAT AAAAA- AACAAAG AAAAGT -AAAAC AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
16170001 -AAAAT AAAGAT AAAA
1 AAAAAT AAAAAT AAAA
16170016 GAATATTAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
5 23 0.29
6 49 0.62
7 7 0.09
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:16170008 original size:22 final size:21
Alignment explanation
Indices: 16169906--16170015 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 21
16169896 GATTTTATTT
*
16169906 AAAAAAATAAAATAATAAAACAA
1 AAAAAAAT-AAA-AATAAAATAA
* *
16169929 AATAAAAGTGAAAATAAAA-AGA
1 AAAAAAA-TAAAAATAAAATA-A
*
16169951 AAAAAAATAAAAAATAAAAAAA
1 AAAAAAAT-AAAAATAAAATAA
16169973 CAAAGAAAAGTAAAACA-AAAATAA
1 -AAA-AAAA-TAAAA-ATAAAATAA
*
16169997 AAATAAAATAAAGATAAAA
1 AAA-AAAATAAAAATAAAA
16170016 GAATATTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
21 3 0.04
22 32 0.45
23 19 0.27
24 15 0.21
25 2 0.03
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAAAATAAAAATAAAATAA
Found at i:16170559 original size:14 final size:13
Alignment explanation
Indices: 16170530--16170569 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
16170520 AATTTTCCAG
16170530 AAATTTCCAAAAA
1 AAATTTCCAAAAA
*
16170543 AAATTTCACAGAAA
1 AAATTTC-CAAAAA
*
16170557 AAATCTCCAAAAA
1 AAATTTCCAAAAA
16170570 TTTCTCCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.60, C:0.17, G:0.03, T:0.20
Consensus pattern (13 bp):
AAATTTCCAAAAA
Found at i:16170870 original size:20 final size:20
Alignment explanation
Indices: 16170835--16170896 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
16170825 TAAATCAAAA
* *
16170835 AAAATAAAAAAAAGATAAAT
1 AAAATAAATAACAGATAAAT
16170855 AAAA-AAATTAACAGATAAATT
1 AAAATAAA-TAACAGATAAA-T
16170876 AAAATTAAATAACAGATAAAT
1 AAAA-TAAATAACAGATAAAT
16170897 TATAACATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 3 0.08
20 13 0.36
21 6 0.17
22 11 0.31
23 3 0.08
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAAATAACAGATAAAT
Found at i:16170874 original size:12 final size:12
Alignment explanation
Indices: 16170859--16170898 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
16170849 ATAAATAAAA
16170859 AAATTAACAGAT
1 AAATTAACAGAT
16170871 AAATTAA-A-ATT
1 AAATTAACAGA-T
16170882 AAA-TAACAGAT
1 AAATTAACAGAT
16170893 AAATTA
1 AAATTA
16170899 TAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTAACAGAT
Found at i:16170891 original size:22 final size:21
Alignment explanation
Indices: 16170847--16170898 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
16170837 AATAAAAAAA
16170847 AGATAAA-TAAAAAAATTAAC
1 AGATAAATTAAAAAAATTAAC
16170867 AGATAAATTAAAATTAAA-TAAC
1 AGATAAATTAAAA--AAATTAAC
16170889 AGATAAATTA
1 AGATAAATTA
16170899 TAACATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.24
21 5 0.17
22 14 0.48
23 3 0.10
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (21 bp):
AGATAAATTAAAAAAATTAAC
Found at i:16171023 original size:6 final size:6
Alignment explanation
Indices: 16171012--16171102 Score: 60
Period size: 6 Copynumber: 14.0 Consensus size: 6
16171002 AATACCTAAG
* *
16171012 ATAAAA ATAAAA GAAAAAA ATATATAA A-ACAATA ATAATA ATAAAA ATAAAA
1 ATAAAA ATAAAA -ATAAAA ATA-A-AA ATA-AA-A ATAAAA ATAAAA ATAAAA
*
16171064 AT-AAA ATAAAA ATGTAAAA TACAAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA A--TAAAA -A-TAAAA ATAAAA ATAAAA
16171103 TAGACTTACC
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 5 0.07
6 37 0.54
7 12 0.18
8 13 0.19
9 1 0.01
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:16171073 original size:34 final size:34
Alignment explanation
Indices: 16171012--16171104 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 34
16171002 AATACCTAAG
* * *
16171012 ATAAAAATAAAAGAAAAAAAT-ATATAAAACA-ATA
1 ATAATAATAAAA-ATAAAAATAAAATAAAA-ATATA
*
16171046 ATAATAATAAAAATAAAAATAAAATAAAAATGTA
1 ATAATAATAAAAATAAAAATAAAATAAAAATATA
16171080 A-AATACA-AAAAATAAAAATAAAATA
1 ATAATA-ATAAAAATAAAAATAAAATA
16171105 GACTTACCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
33 30 0.58
34 22 0.42
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (34 bp):
ATAATAATAAAAATAAAAATAAAATAAAAATATA
Found at i:16171265 original size:1 final size:1
Alignment explanation
Indices: 16171261--16171324 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
16171251 ATTTTTTTAA
* * * * * * * *
16171261 TTTTTTTATTTTTTTTATTTTTTTTATTTTTTTGTTTTTTTATTTATTTTGTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16171325 GACCAAAGCT
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.08, C:0.00, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:16171271 original size:17 final size:16
Alignment explanation
Indices: 16171249--16171324 Score: 89
Period size: 17 Copynumber: 4.5 Consensus size: 16
16171239 GATATTTTCA
*
16171249 TTATTTTTTTAATTTTT
1 TTATTTTTTT-GTTTTT
*
16171266 TTATTTTTTTTATTTTTT
1 TTA-TTTTTTT-GTTTTT
16171284 TTATTTTTTTGTTTTT
1 TTATTTTTTTGTTTTT
16171300 TTATTTATTTTGTTTTT
1 TTATTT-TTTTGTTTTT
*
16171317 TTGTTTTT
1 TTATTTTT
16171325 GACCAAAGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
16 13 0.24
17 25 0.46
18 16 0.30
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.86
Consensus pattern (16 bp):
TTATTTTTTTGTTTTT
Found at i:16171275 original size:8 final size:8
Alignment explanation
Indices: 16171249--16171324 Score: 89
Period size: 9 Copynumber: 9.0 Consensus size: 8
16171239 GATATTTTCA
16171249 TTATTTTT
1 TTATTTTT
16171257 TTAATTTTT
1 TT-ATTTTT
16171266 TTATTTTTT
1 TTA-TTTTT
16171275 TTATTTTTT
1 TTA-TTTTT
16171284 TTATTTTT
1 TTATTTTT
*
16171292 TTGTTTTT
1 TTATTTTT
16171300 TTATTTATT
1 TTATTT-TT
*
16171309 TTGTTTTT
1 TTATTTTT
*
16171317 TTGTTTTT
1 TTATTTTT
16171325 GACCAAAGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
8 30 0.48
9 32 0.52
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.86
Consensus pattern (8 bp):
TTATTTTT
Found at i:16171290 original size:25 final size:23
Alignment explanation
Indices: 16171252--16171324 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
16171242 ATTTTCATTA
*
16171252 TTTTTTTAATTTTTTTATTTTTTT
1 TTTTTTTTATTTTTTT-TTTTTTT
* * *
16171276 TATTTTTT-TTATTTTTTTGTTT
1 TTTTTTTTATTTTTTTTTTTTTT
* * *
16171298 TTTTATTTATTTTGTTTTTTTGT
1 TTTTTTTTATTTTTTTTTTTTTT
16171321 TTTT
1 TTTT
16171325 GACCAAAGCT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
22 12 0.32
23 20 0.53
24 6 0.16
ACGTcount: A:0.10, C:0.00, G:0.04, T:0.86
Consensus pattern (23 bp):
TTTTTTTTATTTTTTTTTTTTTT
Found at i:16171557 original size:124 final size:124
Alignment explanation
Indices: 16171369--16171710 Score: 469
Period size: 124 Copynumber: 2.8 Consensus size: 124
16171359 TTAAGAAACA
* * *** * ***
16171369 TAAATGGCTCCTCTAATCAGAGGCTTAACGACTTTAGAAAA-TAAATTACTCCTCTAATTTGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGG
* * *
16171433 CTCAACGACTTTGGAAAAATAAATTGCTCCTCTAA-ACAGAGGCACCACGACTTTGAAAAG
65 CACCACGACTTTGGAAAAGTAAATTGCTCCTCTAATA-AGAGGCACCACGACTTTGAAAAG
*
16171493 TAAATTGCTCCTCTAAACA-ATGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 TAAATTGCTCCTCTAAACAGA-GGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
*
16171557 CACCACGACTTT-GAAAAGTAAATTGCTTCTCTAATAAGAGGCACCACGACTTTGAAAAG
65 CACCACGACTTTGGAAAAGTAAATTGCTCCTCTAATAAGAGGCACCACGACTTTGAAAAG
* *
16171616 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTTTAAACAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
16171681 CACCACGACTTTGG-AAAGTAAATTGCTCCT
65 CACCACGACTTTGGAAAAGTAAATTGCTCCT
16171711 TGACAATCAT
Statistics
Matches: 194, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
123 78 0.40
124 115 0.59
125 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (124 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC
ACCACGACTTTGGAAAAGTAAATTGCTCCTCTAATAAGAGGCACCACGACTTTGAAAAG
Found at i:16171711 original size:41 final size:41
Alignment explanation
Indices: 16171369--16171710 Score: 445
Period size: 41 Copynumber: 8.3 Consensus size: 41
16171359 TTAAGAAACA
* * *** * *
16171369 TAAATGGCTCCTCTAATCAGAGGCTTAACGACTTTAGAAAA
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
* *** * * *
16171410 TAAATTACTCCTCTAATTTGAGGCTCAACGACTTTGGAAAAA
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAG
*
16171452 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
* *
16171493 TAAATTGCTCCTCTAAACA-ATGGCACCATGACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGA-GGCACCACGACTTTGGAAAG
*
16171534 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
* *
16171575 TAAATTGCTTCTCTAATA-AGAGGCACCACGACTTTGAAAAG
1 TAAATTGCTCCTCTAA-ACAGAGGCACCACGACTTTGGAAAG
16171616 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAG
*
16171658 TAAATTGCTCCTTTAAACAGAGGCACCACGACTTTGGAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
16171699 TAAATTGCTCCT
1 TAAATTGCTCCT
16171711 TGACAATCAT
Statistics
Matches: 275, Mismatches: 20, Indels: 12
0.90 0.07 0.04
Matches are distributed among these distances:
40 2 0.01
41 198 0.72
42 75 0.27
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (41 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
Found at i:16172740 original size:8 final size:8
Alignment explanation
Indices: 16172723--16172773 Score: 77
Period size: 8 Copynumber: 6.5 Consensus size: 8
16172713 CATTCACTTC
*
16172723 TTTTCTTT
1 TTTTCATT
*
16172731 TTTTTATT
1 TTTTCATT
16172739 TTTT-ATT
1 TTTTCATT
16172746 TTTTCATT
1 TTTTCATT
16172754 TTTTCATT
1 TTTTCATT
16172762 TTTTCATT
1 TTTTCATT
16172770 TTTT
1 TTTT
16172774 TTCAAGCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
7 7 0.17
8 33 0.82
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCATT
Found at i:16181646 original size:57 final size:58
Alignment explanation
Indices: 16181429--16181726 Score: 316
Period size: 57 Copynumber: 5.1 Consensus size: 58
16181419 AAGAAAAGAA
* * * *
16181429 TTTTTTT-AAAGATTTATTTTTAAGGAAAATTGATACTTTTAACTTTTCCTAAAAAAATCTT
1 TTTTTTTGAAACA-TTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAA-C-C
* * * * **
16181490 TTTTTTTGAAA-ATTTATTTTTACGAAAAATTGATACTTTCAATTTTTCCCCAAAAATA
1 TTTTTTTGAAACA-TTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACC
* * ** * *
16181548 TTTTTTTGAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCTCGAAAACC
1 TTTTTTTGAAACATTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACC
* *
16181606 TTTTTTAGAAA-ATTATTTTTAAGGAAAATTGATACCTTCAACTTTTCCTCAAAAACC
1 TTTTTTTGAAACATTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACC
** * **
16181663 -TTTTTTGAAAGTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
1 TTTTTTTGAAACATTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACC
16181720 TTTTTTT
1 TTTTTTT
16181727 TTGGATTTTA
Statistics
Matches: 201, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
56 9 0.04
57 80 0.40
58 63 0.31
60 5 0.02
61 41 0.20
62 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (58 bp):
TTTTTTTGAAACATTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACC
Found at i:16181752 original size:5 final size:5
Alignment explanation
Indices: 16181744--16181828 Score: 52
Period size: 5 Copynumber: 16.6 Consensus size: 5
16181734 TTATTTAAAG
* *
16181744 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AATAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AA-AAT
* *
16181789 AAAAT AAAGA- AAAGT AAAACA AAAAT AAAAAT AAAAT AAA
1 AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAA
16181829 GATAGAAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
3 3 0.05
4 2 0.03
5 40 0.63
6 14 0.22
7 4 0.06
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:16181786 original size:37 final size:35
Alignment explanation
Indices: 16181744--16181827 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 35
16181734 TTATTTAAAG
**
16181744 AAAATAAAATAATAAA-ACAAAATAAAAGTGAAAATAA
1 AAAATAAAATAATAAAGA-AAAATAAAA-CAAAAAT-A
* *
16181781 AAAATAAAAAAATAAAGAAAAGTAAAACAAAAATA
1 AAAATAAAATAATAAAGAAAAATAAAACAAAAATA
16181816 AAAATAAAATAA
1 AAAATAAAATAA
16181828 AGATAGAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 12 0.29
36 5 0.12
37 23 0.56
38 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (35 bp):
AAAATAAAATAATAAAGAAAAATAAAACAAAAATA
Found at i:16181812 original size:29 final size:31
Alignment explanation
Indices: 16181749--16181819 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
16181739 TAAAGAAAAT
*
16181749 AAAATAATAAAACAAAATAAAAGTGAAAATAA
1 AAAATAA-AAAACAAAAGAAAAGTGAAAATAA
*
16181781 AAAATAAAAAA-ATAAAGAAAAGT-AAAA-CA
1 AAAATAAAAAACA-AAAGAAAAGTGAAAATAA
16181810 AAAATAAAAA
1 AAAATAAAAA
16181820 TAAAATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 11 0.31
30 5 0.14
31 13 0.36
32 7 0.19
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.13
Consensus pattern (31 bp):
AAAATAAAAAACAAAAGAAAAGTGAAAATAA
Found at i:16181830 original size:32 final size:33
Alignment explanation
Indices: 16181744--16181830 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 33
16181734 TTATTTAAAG
* * *
16181744 AAAATAAAATAATAAAACAAAATAAAAGTGAAAATA
1 AAAAT-AAA-AATAAAA-TAAAGAAAAGTGAAAACA
*
16181780 AAAA-ATAAA-AAAATAAAGAAAAGT-AAAACA
1 AAAATAAAAATAAAATAAAGAAAAGTGAAAACA
16181810 AAAATAAAAATAAAATAAAGA
1 AAAATAAAAATAAAATAAAGA
16181831 TAGAAGAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 9 0.20
31 13 0.30
32 14 0.32
33 2 0.05
34 2 0.05
36 4 0.09
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (33 bp):
AAAATAAAAATAAAATAAAGAAAAGTGAAAACA
Found at i:16182765 original size:22 final size:21
Alignment explanation
Indices: 16182718--16182770 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
16182708 TAAAAAAAAT
16182718 CAGATAAA-TAAAAAAATTAA
1 CAGATAAATTAAAAAAATTAA
*
16182738 CTGATAAATTAAAATTAAA-TAA
1 CAGATAAATTAAAA--AAATTAA
16182760 CAGATAAATTA
1 CAGATAAATTA
16182771 TAACATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.25
21 5 0.18
22 13 0.46
23 3 0.11
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (21 bp):
CAGATAAATTAAAAAAATTAA
Found at i:16182908 original size:12 final size:13
Alignment explanation
Indices: 16182886--16182986 Score: 56
Period size: 11 Copynumber: 8.2 Consensus size: 13
16182876 ATAAATACCT
16182886 AAGATAAAAATAA
1 AAGATAAAAATAA
16182899 AAGA-AAAAAT-A
1 AAGATAAAAATAA
* *
16182910 TATATATAAAATAA
1 AAGATA-AAAATAA
*
16182924 TA-ATAAAAATAA
1 AAGATAAAAATAA
*
16182936 AA-AT-AAAATAG
1 AAGATAAAAATAA
16182947 AA-AT-AAAATAA
1 AAGATAAAAATAA
*
16182958 AA-ATGTAAAATACA
1 AAGAT-AAAAATA-A
* *
16182972 AAAATAAAATTAA
1 AAGATAAAAATAA
16182985 AA
1 AA
16182987 AAAAAAGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
11 23 0.31
12 17 0.23
13 21 0.28
14 11 0.15
15 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (13 bp):
AAGATAAAAATAA
Found at i:16182937 original size:43 final size:44
Alignment explanation
Indices: 16182889--16182997 Score: 112
Period size: 47 Copynumber: 2.4 Consensus size: 44
16182879 AATACCTAAG
* * *
16182889 ATAAAAATAAAAGAAAAAATATATATATAAAAT-AATAATAAAA
1 ATAAAAATAAAAGAAAAAATAAAAATATAAAATAAAAAATAAAA
*
16182932 ATAAAAATAAAATAGAAATAAAATAAAAATGTAAAATACAAAAATAAAA
1 ATAAAAAT-AAA-AG-AA-AAAATAAAAATATAAAATA-AAAAATAAAA
* *
16182981 TTAAAAAAAAAAGAAAA
1 ATAAAAATAAAAGAAAA
16182998 TAGACTTACC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
43 8 0.15
44 3 0.06
45 4 0.07
46 4 0.07
47 17 0.31
48 3 0.06
49 15 0.28
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (44 bp):
ATAAAAATAAAAGAAAAAATAAAAATATAAAATAAAAAATAAAA
Found at i:16182938 original size:31 final size:29
Alignment explanation
Indices: 16182857--16182961 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 29
16182847 AATAAATAGC
* *
16182857 AATAATAA-ATAAATAAATAATAAATACCTAA
1 AATAATAATAAAAATAAA-AAT-AATA-ATAA
* *
16182888 GATAAAAATAAAAGA-AAAAATATATATATAA
1 AATAATAATAAAA-ATAAAAATA-ATA-ATAA
16182919 AATAATAATAAAAATAAAAATAA-AATAGA
1 AATAATAATAAAAATAAAAATAATAATA-A
16182948 AATAA-AATAAAAAT
1 AATAATAATAAAAAT
16182962 GTAAAATACA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
28 12 0.19
29 7 0.11
30 3 0.05
31 33 0.53
32 6 0.10
33 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (29 bp):
AATAATAATAAAAATAAAAATAATAATAA
Found at i:16182960 original size:17 final size:17
Alignment explanation
Indices: 16182857--16182999 Score: 85
Period size: 18 Copynumber: 7.9 Consensus size: 17
16182847 AATAAATAGC
16182857 AATAATAAAT-AAATAAA
1 AATAA-AAATAAAATAAA
* *
16182874 TAATAAATACCTAAGATAAA
1 -AATAAA-A-ATAAAATAAA
* *
16182894 AATAAAAGAAAAAATATA
1 AATAAAA-ATAAAATAAA
*
16182912 TATATAAAATAATAATAAA
1 AATA-AAAATAA-AATAAA
*
16182931 AATAAAAATAAAATAGA
1 AATAAAAATAAAATAAA
16182948 AAT-AAAATAAAAATGTAAA
1 AATAAAAAT-AAAA--TAAA
*
16182967 ATACAAAAATAAAATTAAA
1 A-ATAAAAATAAAA-TAAA
*
16182986 AA-AAAAAGAAAATA
1 AATAAAAATAAAATA
16183000 GACTTACCTA
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
16 7 0.07
17 22 0.22
18 27 0.27
19 27 0.27
20 11 0.11
21 5 0.05
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.21
Consensus pattern (17 bp):
AATAAAAATAAAATAAA
Found at i:16182974 original size:7 final size:6
Alignment explanation
Indices: 16182889--16182997 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
16182879 AATACCTAAG
* * *
16182889 ATAAAA ATAAAA GA-AAAA ATATAT ATATAAA ATAATA ATAAAA ATAAAA
1 ATAAAA ATAAAA -ATAAAA ATAAAA ATA-AAA ATAAAA ATAAAA ATAAAA
* * *
16182938 AT-AAA ATAGAA AT-AAA ATAAAA ATGTAAAA TACAAAA ATAAAA TTAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA A--TAAAA -ATAAAA ATAAAA ATAAAA
*
16182987 A-AAAA AGAAAA
1 ATAAAA ATAAAA
16182998 TAGACTTACC
Statistics
Matches: 82, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
5 15 0.18
6 52 0.63
7 9 0.11
8 5 0.06
9 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:16182986 original size:32 final size:30
Alignment explanation
Indices: 16182940--16182999 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 30
16182930 AAATAAAAAT
*
16182940 AAAATAGAAATAAAATAAAAATGTAAAATACA
1 AAAATAGAAATAAAA-AAAAAAG-AAAATACA
16182972 AAAATA-AAATTAAAAAAAAAAGAAAATA
1 AAAATAGAAA-TAAAAAAAAAAGAAAATA
16183000 GACTTACCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 9 0.35
32 11 0.42
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (30 bp):
AAAATAGAAATAAAAAAAAAAGAAAATACA
Found at i:16184706 original size:18 final size:18
Alignment explanation
Indices: 16184683--16184785 Score: 50
Period size: 18 Copynumber: 5.6 Consensus size: 18
16184673 CAATTGGCTT
16184683 TTATTTTTATTTTTTTTA
1 TTATTTTTATTTTTTTTA
* *
16184701 TTATTTGTCTA-TTTATTAA
1 TTATTT-T-TATTTTTTTTA
*
16184720 TATATATTTA-TTTTTTTA
1 T-TATTTTTATTTTTTTTA
** *
16184738 TCTATTAATATTTTTATTA
1 T-TATTTTTATTTTTTTTA
* * *
16184757 TT-TATCTACTTTTATTTA
1 TTATTTTTA-TTTTTTTTA
*
16184775 TTATTATTATT
1 TTATTTTTATT
16184786 ATTTATCTAT
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
17 3 0.05
18 32 0.52
19 20 0.33
20 6 0.10
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (18 bp):
TTATTTTTATTTTTTTTA
Found at i:16184730 original size:26 final size:24
Alignment explanation
Indices: 16184701--16184755 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
16184691 ATTTTTTTTA
*
16184701 TTATTTGTCTATTTATTAATATATAT
1 TTATTTGTCTATCTATTAATAT-T-T
* *
16184727 TTATTTTTTTATCTATTAATATTT
1 TTATTTGTCTATCTATTAATATTT
16184751 TTATT
1 TTATT
16184756 ATTTATCTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 1 0.04
26 19 0.73
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATTTGTCTATCTATTAATATTT
Found at i:16184769 original size:17 final size:16
Alignment explanation
Indices: 16184681--16184811 Score: 74
Period size: 17 Copynumber: 8.0 Consensus size: 16
16184671 CCCAATTGGC
* *
16184681 TTTTATT-TTTATTTT
1 TTTTATTATTTATCTA
*
16184696 TTTTATTATTTGTCTA
1 TTTTATTATTTATCTA
*
16184712 -TTTATTAATATATATTTA
1 TTTTATT-AT-T-TATCTA
* * *
16184730 TTTTTTTATCTATTAATA
1 TTTTATTATTTA-T-CTA
16184748 TTTTTATTATTTATCTA
1 -TTTTATTATTTATCTA
*
16184765 -CTT-TTATTTAT-TA
1 TTTTATTATTTATCTA
16184778 TTATTATTATTTATCTA
1 TT-TTATTATTTATCTA
*
16184795 TTTCTTTTATTTATCTA
1 TTT-TATTATTTATCTA
16184812 ATAATTTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
13 2 0.02
14 8 0.09
15 17 0.19
16 18 0.20
17 20 0.22
18 9 0.10
19 15 0.17
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.69
Consensus pattern (16 bp):
TTTTATTATTTATCTA
Found at i:16184777 original size:33 final size:33
Alignment explanation
Indices: 16184733--16184834 Score: 98
Period size: 33 Copynumber: 3.0 Consensus size: 33
16184723 ATATTTATTT
* *
16184733 TTTTATCTATTAATATTTTTA-TTATTTATCTAC
1 TTTTATTTATTAATATTTTTATTTATCTAT-TAC
* * *
16184766 TTTTATTTATTATTATTATTATTTATCTATTTC
1 TTTTATTTATTAATATTTTTATTTATCTATTAC
*
16184799 TTTTATTTATCTAATAATTTTTTTTGTTATCTATTA
1 TTTTATTTAT-TAAT-A-TTTTTAT-TTATCTATTA
16184835 ATATATTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
33 30 0.55
34 10 0.18
35 1 0.02
36 5 0.09
37 9 0.16
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (33 bp):
TTTTATTTATTAATATTTTTATTTATCTATTAC
Found at i:16184787 original size:30 final size:31
Alignment explanation
Indices: 16184746--16184808 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 31
16184736 TATCTATTAA
*
16184746 TATTTTTATTATTTATCTA-CTTTTATTTAT
1 TATTATTATTATTTATCTATCTTTTATTTAT
16184776 TATTATTATTATTTATCTATTTCTTTTATTTAT
1 TATTATTATTATTTATCTA--TCTTTTATTTAT
16184809 CTAATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 18 0.62
33 11 0.38
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (31 bp):
TATTATTATTATTTATCTATCTTTTATTTAT
Found at i:16184791 original size:53 final size:52
Alignment explanation
Indices: 16184695--16184796 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 52
16184685 ATTTTTATTT
*
16184695 TTTTTATTATTTGTCTATTTATTAATATATATTTATTTTTTTATCTATTAATA
1 TTTTTATTATTTATCTATTTATT-ATATATATTTATTTTTTTATCTATTAATA
16184748 TTTTTATTATTTATCTACTTTTATT-TAT-TA-TTATTATTATTTATCTATT
1 TTTTTATTATTTATCTA--TTTATTATATATATTTATT-TT-TTTATCTATT
16184797 TCTTTTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
51 5 0.11
52 4 0.09
53 29 0.66
55 6 0.14
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (52 bp):
TTTTTATTATTTATCTATTTATTATATATATTTATTTTTTTATCTATTAATA
Done.