Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 29 of 33
Found at i:5207755 original size:21 final size:21
Alignment explanation
Indices: 5207709--5207776 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
5207699 AAATATAATA
*
5207709 TATATTATTTATT-TATTT-T
1 TATATTATATATTATATTTAT
5207728 TA-A--ATATATTATATTTAT
1 TATATTATATATTATATTTAT
5207746 TATATTATAT-TTAT-TTAATAT
1 TATATTATATATTATATT--TAT
*
5207767 TTTATTATAT
1 TATATTATAT
5207777 TTTTATATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
16 6 0.15
17 5 0.12
18 4 0.10
19 5 0.12
20 4 0.10
21 16 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATATTATATATTATATTTAT
Found at i:5207766 original size:32 final size:30
Alignment explanation
Indices: 5207698--5207784 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 30
5207688 AATTTAAATA
*
5207698 TAAATATAATATATATTATT-TATTTATTTT
1 TAAATATATTATAT-TTATTATATTTATTTT
5207728 TAAATATATTATATTTATTATATTATATTTATT
1 TAAATATATTATATTTATTATATT-TA-TT-TT
*
5207761 TAATATTTTATTATATTT-TTATAT
1 TAA-A-TATATTATATTTATTATAT
5207785 CACGTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.10
30 17 0.35
31 2 0.04
32 2 0.04
33 5 0.10
34 7 0.14
35 11 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TAAATATATTATATTTATTATATTTATTTT
Found at i:5208037 original size:17 final size:18
Alignment explanation
Indices: 5208011--5208046 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5208001 TTTTTTATAT
*
5208011 TAAATTTAATAAAT-TTA
1 TAAATATAATAAATATTA
5208028 TAAATATAATAAATATTA
1 TAAATATAATAAATATTA
5208046 T
1 T
5208047 TATATTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATATAATAAATATTA
Found at i:5208945 original size:25 final size:25
Alignment explanation
Indices: 5208891--5208945 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5208881 TATTTTAACC
* **
5208891 TTAAAAATAAATTAAATAATCGTAA
1 TTAAAAATAAATAAAATAATAATAA
*
5208916 ATAAAAATAAAATAAAATAA-AATAA
1 TTAAAAAT-AAATAAAATAATAATAA
5208941 TTAAA
1 TTAAA
5208946 GATTTTTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
TTAAAAATAAATAAAATAATAATAA
Found at i:5211470 original size:34 final size:36
Alignment explanation
Indices: 5211432--5211498 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 36
5211422 GTTTGAATTT
* *
5211432 AAATTTCATAAATTTAT-AATTA-AATTTAAATAAA
1 AAATTTCATAAATTAATAAATAATAATTTAAATAAA
* *
5211466 AAATTTTATTAATTAATAAATAATAATTTAAAT
1 AAATTTCATAAATTAATAAATAATAATTTAAAT
5211499 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 14 0.52
35 4 0.15
36 9 0.33
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
AAATTTCATAAATTAATAAATAATAATTTAAATAAA
Found at i:5216093 original size:20 final size:19
Alignment explanation
Indices: 5216064--5216109 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5216054 TATAATTAAA
5216064 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAAT-TATTAT
*
5216084 TTTAATTAAAAATTATTAT
1 TTTAAATAAAAATTATTAT
5216103 TTTAAAT
1 TTTAAAT
5216110 TTAATAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:5216110 original size:20 final size:21
Alignment explanation
Indices: 5216064--5216110 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
5216054 TATAATTAAA
5216064 TTTAAA-TAAAAATATATTAT
1 TTTAAATTAAAAATATATTAT
5216084 TTT-AATTAAAAAT-TATTAT
1 TTTAAATTAAAAATATATTAT
5216103 TTTAAATT
1 TTTAAATT
5216111 TAATAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAATTAAAAATATATTAT
Found at i:5232528 original size:4 final size:4
Alignment explanation
Indices: 5232509--5232547 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
5232499 TTCTCCCTTG
*
5232509 TTTC TTTTC TTTTC TTTC TTTC TTTC TTTC TTTC CTTC T
1 TTTC -TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
5232548 GATTTTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 23 0.72
5 9 0.28
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:5239902 original size:19 final size:19
Alignment explanation
Indices: 5239851--5239904 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5239841 GTGTTTAATT
* *
5239851 TAAAATTAATTAATAATAGA
1 TAAAATT-ATAAATAATACA
*
5239871 TAAAA-TATCAAATTATACA
1 TAAAATTAT-AAATAATACA
5239890 TAAAATTATAAATAA
1 TAAAATTATAAATAA
5239905 CTTAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 2 0.07
19 18 0.64
20 8 0.29
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAATTATAAATAATACA
Found at i:5240931 original size:2 final size:2
Alignment explanation
Indices: 5240924--5240950 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5240914 AATTCTTGTG
5240924 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 A
5240951 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5240955 original size:2 final size:2
Alignment explanation
Indices: 5240950--5240985 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5240940 ATATATATAT
5240950 AG AG 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 AG AG
5240986 GGTCACATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5243217 original size:17 final size:17
Alignment explanation
Indices: 5243185--5243217 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5243175 GTTTGATTAT
5243185 AAAATTAATAAGAAAAC
1 AAAATTAATAAGAAAAC
5243202 AAAATATAATAA-AAAA
1 AAAAT-TAATAAGAAAA
5243218 AGTTACTATT
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:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATTAATAAGAAAAC
Found at i:5243218 original size:18 final size:17
Alignment explanation
Indices: 5243185--5243218 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5243175 GTTTGATTAT
*
5243185 AAAATTAATAAGAAAAC
1 AAAATTAATAAAAAAAC
5243202 AAAATATAATAAAAAAA
1 AAAAT-TAATAAAAAAA
5243219 GTTACTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATTAATAAAAAAAC
Found at i:5243448 original size:23 final size:23
Alignment explanation
Indices: 5243411--5243455 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5243401 ATATTATATA
*
5243411 TATATATATATTTATTAATTTAT
1 TATATATATAATTATTAATTTAT
*
5243434 TATATATTTAATTATTAATTTA
1 TATATATATAATTATTAATTTA
5243456 AATTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATATATAATTATTAATTTAT
Found at i:5243461 original size:13 final size:12
Alignment explanation
Indices: 5243422--5243466 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
5243412 ATATATATAT
5243422 TTATTAATTT-A
1 TTATTAATTTAA
5243433 TTA-TATATTTAA
1 TTATTA-ATTTAA
5243445 TTATTAATTTAAA
1 TTATTAATTT-AA
5243458 TTATTAATT
1 TTATTAATT
5243467 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.07
11 7 0.23
12 8 0.27
13 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTAATTTAA
Found at i:5243471 original size:13 final size:13
Alignment explanation
Indices: 5243443--5243483 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5243433 TTATATATTT
*
5243443 AATTATTAATTTA
1 AATTATTAATTAA
5243456 AATTATTAATTAA
1 AATTATTAATTAA
* *
5243469 AATTTTTAAATAA
1 AATTATTAATTAA
5243482 AA
1 AA
5243484 AATACATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTATTAATTAA
Found at i:5244847 original size:34 final size:34
Alignment explanation
Indices: 5244801--5244985 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
5244791 GTAAAAACCA
* *
5244801 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
5244835 CCATTTAGTCAACAATGGTAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
5244869 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
*
5244903 CCATTTAATCAACAATGGTAAACTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
5244937 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
5244970 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
5244986 TCTCCCACTT
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 15 0.11
34 119 0.89
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:5249078 original size:19 final size:19
Alignment explanation
Indices: 5249051--5249113 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
5249041 TCACGTGTAC
* *
5249051 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
5249070 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
5249089 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
5249108 AGTACC
1 AGTACC
5249114 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:5249464 original size:34 final size:34
Alignment explanation
Indices: 5249418--5249600 Score: 269
Period size: 34 Copynumber: 5.4 Consensus size: 34
5249408 GTAAAAACCA
* *
5249418 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
5249452 CCATTTAGTCAACAATGGTAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
5249486 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
*
5249520 CCATTTAATCAACAATGGTAAACTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
5249554 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
5249587 CCATTTAATCAACA
1 CCATTTAATCAACA
5249601 GAAGAAGATA
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:5263429 original size:2 final size:2
Alignment explanation
Indices: 5263422--5263460 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5263412 CCGTAGCCTT
5263422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5263461 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5264707 original size:2 final size:2
Alignment explanation
Indices: 5264694--5264728 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5264684 TTCTTACGTA
* *
5264694 AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5264729 GAGCAATGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5265156 original size:20 final size:21
Alignment explanation
Indices: 5265095--5265167 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 21
5265085 CATATCATAT
*
5265095 TTATTTTAT-TATATTATATCA
1 TTATTTTATAT-TATTATATAA
*
5265116 -TATTTTATATTA-TATTTTAA
1 TTATTTTATATTATTA-TATAA
5265136 TTATTTT-TATTATTATATAA
1 TTATTTTATATTATTATATAA
*
5265156 TAATTTTATATT
1 TTATTTTATATT
5265168 TAATATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.05
20 28 0.65
21 13 0.30
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTTTATATTATTATATAA
Found at i:5265173 original size:20 final size:21
Alignment explanation
Indices: 5265117--5265178 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
5265107 ATTATATCAT
* * *
5265117 ATTTTATATTATATTTTAATT
1 ATTTTATATTATAATATAATA
*
5265138 ATTTT-TATTATTATATAATA
1 ATTTTATATTATAATATAATA
*
5265158 ATTTTATATT-TAATATTATA
1 ATTTTATATTATAATATAATA
5265178 A
1 A
5265179 AATCTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 25 0.74
21 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTATATTATAATATAATA
Found at i:5265176 original size:12 final size:12
Alignment explanation
Indices: 5265101--5265177 Score: 61
Period size: 12 Copynumber: 6.6 Consensus size: 12
5265091 ATATTTATTT
5265101 TATTATA-TT-A
1 TATTATATTTAA
* *
5265111 TATCATATTTTA
1 TATTATATTTAA
*
5265123 TATTATATTTTA
1 TATTATATTTAA
* *
5265135 -ATTATTTTTAT
1 TATTATATTTAA
*
5265146 TATTATATAATAA
1 TATTATAT-TTAA
*
5265159 TTTTATATTTAA
1 TATTATATTTAA
5265171 TATTATA
1 TATTATA
5265178 AAATCTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 6 0.12
11 10 0.19
12 27 0.52
13 9 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:5265177 original size:23 final size:22
Alignment explanation
Indices: 5265101--5265178 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
5265091 ATATTTATTT
5265101 TATT-ATATTAT-ATCATATTTTA
1 TATTAATATTATAAT-A-ATTTTA
* *
5265123 TATT-ATATTTTAATTATTTT-
1 TATTAATATTATAATAATTTTA
*
5265143 TATTATTA-TATAATAATTTTA
1 TATTAATATTATAATAATTTTA
5265164 TATTTAATATTATAA
1 TA-TTAATATTATAA
5265179 AATCTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 14 0.31
21 9 0.20
22 15 0.33
23 7 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTAATATTATAATAATTTTA
Found at i:5270750 original size:17 final size:17
Alignment explanation
Indices: 5270712--5270752 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5270702 AAAAATTTAT
* *
5270712 ATTAAAATTATATAAAT
1 ATTAAAATTATAAAAAA
*
5270729 TTTAAAATTATAAAAAA
1 ATTAAAATTATAAAAAA
5270746 ATTAAAA
1 ATTAAAA
5270753 AATAATAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAAATTATAAAAAA
Found at i:5275600 original size:2 final size:2
Alignment explanation
Indices: 5275587--5275629 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5275577 TCTTGCCATA
*
5275587 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5275629 A
1 A
5275630 AAAGGCTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5277157 original size:2 final size:2
Alignment explanation
Indices: 5277150--5277206 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
5277140 GGTTCATGAA
5277150 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5277191 AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT
5277207 TTGGTGCTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5278085 original size:2 final size:2
Alignment explanation
Indices: 5278078--5278111 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5278068 AAGATACGAG
5278078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5278112 TTAGTATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5286365 original size:16 final size:19
Alignment explanation
Indices: 5286343--5286392 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
5286333 ATTTTTATTT
5286343 TTATTTA-ATA-TAAAATA
1 TTATTTATATATTAAAATA
*
5286360 -TATTTATTTATTAAAATA
1 TTATTTATATATTAAAATA
*
5286378 TTATTTATAAATTAA
1 TTATTTATATATTAA
5286393 TTTTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.22
17 2 0.07
18 7 0.26
19 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTTATATATTAAAATA
Found at i:5286384 original size:19 final size:21
Alignment explanation
Indices: 5286338--5286385 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
5286328 ATAATATTTT
5286338 TATT-TTTATTTAATATAAAA
1 TATTATTTATTTAATATAAAA
5286358 TA-TATTTATTT-AT-TAAAA
1 TATTATTTATTTAATATAAAA
5286376 TATTATTTAT
1 TATTATTTAT
5286386 AAATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATTTATTTAATATAAAA
Found at i:5286517 original size:21 final size:21
Alignment explanation
Indices: 5286464--5286510 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
5286454 TAAAAATTAA
*
5286464 AAATTAAATTAATTTTAAAATT
1 AAATTTAATT-ATTTTAAAATT
*
5286486 ATATTTAATTATTTT-AAATT
1 AAATTTAATTATTTTAAAATT
5286506 AAATT
1 AAATT
5286511 ATTATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTAATTATTTTAAAATT
Found at i:5286926 original size:17 final size:18
Alignment explanation
Indices: 5286894--5286935 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
5286884 AGCATGATAG
5286894 TAATTAAAAATAATTTTA
1 TAATTAAAAATAATTTTA
5286912 TAATTAAAAAT-ATTTTA
1 TAATTAAAAATAATTTTA
*
5286929 AAATTAA
1 TAATTAA
5286936 TAATTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATTAAAAATAATTTTA
Found at i:5291878 original size:2 final size:2
Alignment explanation
Indices: 5291871--5291899 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5291861 TCATTTTAAC
5291871 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 A
5291900 AGCATCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5291948 original size:3 final size:3
Alignment explanation
Indices: 5291942--5291967 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5291932 TATCATCATC
5291942 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
5291968 AAACTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5298908 original size:21 final size:19
Alignment explanation
Indices: 5298867--5298912 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5298857 TTCAGATTTG
* *
5298867 ATTTTTAATATTATTATTT
1 ATTTTTAATATTATAAATT
5298886 ATTTTTAATATATATAACATT
1 ATTTTTAATAT-TATAA-ATT
5298907 ATTTTT
1 ATTTTT
5298913 TTTGCAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 4 0.17
21 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTAATATTATAAATT
Found at i:5299195 original size:18 final size:19
Alignment explanation
Indices: 5299149--5299195 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
5299139 TCTTTTAAAA
5299149 AAGTAAATA-AATTTTTAT
1 AAGTAAATATAATTTTTAT
5299167 AAGT-AAT-TAATTTTT-T
1 AAGTAAATATAATTTTTAT
*
5299183 AATTAAATATAAT
1 AAGTAAATATAAT
5299196 AAAAAATGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
AAGTAAATATAATTTTTAT
Found at i:5307354 original size:3 final size:3
Alignment explanation
Indices: 5307307--5307334 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5307297 TCTAATAAAC
5307307 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5307335 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5308486 original size:21 final size:22
Alignment explanation
Indices: 5308442--5308486 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5308432 CAAATTTAAA
*
5308442 TTTTACAATAAAAATTTAAATT
1 TTTTACAATAAAAATATAAATT
*
5308464 TTTTATAATAAAAA-AT-AATT
1 TTTTACAATAAAAATATAAATT
5308484 TTT
1 TTT
5308487 AACGTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 13 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTACAATAAAAATATAAATT
Found at i:5310937 original size:18 final size:18
Alignment explanation
Indices: 5310910--5310945 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5310900 TTTCAAGGAG
5310910 TATTTTGATGT-ATTGCC
1 TATTTTGATGTCATTGCC
5310927 TATTATTGATGTCATTGCC
1 TATT-TTGATGTCATTGCC
5310946 AGCAGCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (18 bp):
TATTTTGATGTCATTGCC
Found at i:5311591 original size:18 final size:19
Alignment explanation
Indices: 5311570--5311607 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5311560 CTAATTTTCC
5311570 TATT-CTTTCACCTTTTTT
1 TATTCCTTTCACCTTTTTT
**
5311588 TATTCCTTTTTCCTTTTTT
1 TATTCCTTTCACCTTTTTT
5311607 T
1 T
5311608 TGATGTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTCCTTTCACCTTTTTT
Found at i:5313871 original size:2 final size:2
Alignment explanation
Indices: 5313864--5313894 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5313854 CTCGGTAATG
*
5313864 TC TC TC TC TC GC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5313895 TATACACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:5317930 original size:5 final size:5
Alignment explanation
Indices: 5317917--5317949 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5317907 AGGGAATTCA
*
5317917 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
5317950 CTTTAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5320409 original size:34 final size:33
Alignment explanation
Indices: 5320361--5320577 Score: 249
Period size: 34 Copynumber: 6.4 Consensus size: 33
5320351 TGGTAAAAAC
*
5320361 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
5320394 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
5320428 CATCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
5320462 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
5320496 CTCCCATTTAGTCAACAATAGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAAT-GGTAACCTACCAAAT
*
5320530 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
5320564 CACCATTTAATCAA
1 CACCATTTAATCAA
5320578 TAATTCTCCC
Statistics
Matches: 156, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 20 0.13
34 129 0.83
35 7 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:5320504 original size:102 final size:101
Alignment explanation
Indices: 5320361--5320577 Score: 326
Period size: 102 Copynumber: 2.1 Consensus size: 101
5320351 TGGTAAAAAC
* * *
5320361 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
* * *
5320426 ATCATCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
5320462 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATAGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCA
5320527 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
5320564 CACCATTTAATCAA
1 CACCATTTAATCAA
5320578 TAATTCTCCC
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 12 0.12
102 90 0.88
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:5332332 original size:3 final size:3
Alignment explanation
Indices: 5332326--5332358 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5332316 CTACTACTGT
*
5332326 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5332359 AAATGGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5334750 original size:2 final size:2
Alignment explanation
Indices: 5334738--5334785 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
5334728 ATCAAAATCT
5334738 TA TA T- TA 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
5334779 TA -A TA TA
1 TA TA TA TA
5334786 ACGTTTGGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5341437 original size:13 final size:13
Alignment explanation
Indices: 5341402--5341431 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5341392 GAGTGGGGCA
*
5341402 TTTTCTTTTTCTT
1 TTTTCTTTTTTTT
5341415 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
5341428 TTTT
1 TTTT
5341432 TGTTTTCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:5341989 original size:32 final size:31
Alignment explanation
Indices: 5341938--5341998 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
5341928 TATTTTATAT
*
5341938 TTATATAAATATTTTTATATTAATAACATTTA
1 TTATATAAATATTTATATATTAAT-ACATTTA
*
5341970 TTATATAAAT-TTTGATATATTTATACATT
1 TTATATAAATATTT-ATATATTAATACATT
5341999 CATTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (31 bp):
TTATATAAATATTTATATATTAATACATTTA
Found at i:5348208 original size:3 final size:3
Alignment explanation
Indices: 5348200--5348225 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5348190 TTAAAAAAGA
5348200 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
5348226 CTTTCCCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5348274 original size:2 final size:2
Alignment explanation
Indices: 5348267--5348292 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5348257 GAAAAGGAAA
5348267 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
5348293 TGTCGGATTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5349103 original size:16 final size:15
Alignment explanation
Indices: 5349076--5349115 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5349066 AAGTAAATAA
5349076 AGTATTTTAAATTTT
1 AGTATTTTAAATTTT
5349091 AGTATTATTAAA-TTT
1 AGTATT-TTAAATTTT
*
5349106 AATATTTTAA
1 AGTATTTTAA
5349116 TGTTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
AGTATTTTAAATTTT
Found at i:5349112 original size:30 final size:31
Alignment explanation
Indices: 5349078--5349140 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5349068 GTAAATAAAG
5349078 TATTTTAAAT-TTTAGT-ATTATTAAATT-TAA
1 TATTTT-AATGTTTA-TAATTATTAAATTATAA
*
5349108 TATTTTAATGTTTATAATTTTTAAATTATAA
1 TATTTTAATGTTTATAATTATTAAATTATAA
5349139 TA
1 TA
5349141 AATAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.14
30 20 0.69
31 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTTTAATGTTTATAATTATTAAATTATAA
Found at i:5349186 original size:20 final size:20
Alignment explanation
Indices: 5349131--5349192 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
5349121 ATAATTTTTA
5349131 AATTATAATA-AATAAAAAAT
1 AATTA-AATATAATAAAAAAT
* *
5349151 AATTAATTATATTAAAAAAT
1 AATTAAATATAATAAAAAAT
* *
5349171 -TTTAAATATTAATAAAATAT
1 AATTAAATA-TAATAAAAAAT
5349191 AA
1 AA
5349193 ATGCATCATG
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAAATATAATAAAAAAT
Found at i:5349670 original size:15 final size:14
Alignment explanation
Indices: 5349646--5349695 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
5349636 AGTAAATGAA
5349646 ATATA-TTTAATTT
1 ATATATTTTAATTT
5349659 ATATATTATTAAATTT
1 ATATATT-TT-AATTT
*
5349675 A-ATATTTTAGTTT
1 ATATATTTTAATTT
5349688 -TATATTTT
1 ATATATTTT
5349696 TAAAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 16 0.50
14 3 0.09
15 7 0.22
16 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
ATATATTTTAATTT
Found at i:5349691 original size:28 final size:32
Alignment explanation
Indices: 5349645--5349708 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 32
5349635 TAGTAAATGA
5349645 AATATATTTAATTTATATATTATT-AAATT-T
1 AATATATTTAATTTATATATTATTAAAATTAT
* *
5349675 AATAT-TTTAGTTT-TATATTTTTAAAATTAT
1 AATATATTTAATTTATATATTATTAAAATTAT
5349705 AATA
1 AATA
5349709 AATAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 12 0.40
30 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
AATATATTTAATTTATATATTATTAAAATTAT
Found at i:5351749 original size:10 final size:10
Alignment explanation
Indices: 5351712--5351746 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5351702 ATGTTCATAT
5351712 ATTAAATTTA
1 ATTAAATTTA
*
5351722 ATTAAATTAA
1 ATTAAATTTA
*
5351732 ATTAATTTTA
1 ATTAAATTTA
5351742 ATTAA
1 ATTAA
5351747 TTTGTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATTAAATTTA
Found at i:5355037 original size:3 final size:3
Alignment explanation
Indices: 5355029--5355105 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
5355019 TTTTGCTGAC
5355029 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5355077 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5355106 AAGAGTTTCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5358316 original size:2 final size:2
Alignment explanation
Indices: 5358309--5358342 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5358299 AAAATAAATG
5358309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5358343 TTACCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5358861 original size:4 final size:4
Alignment explanation
Indices: 5358852--5358884 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
5358842 AATCTACCAA
*
5358852 ATTT ATTT ATTT ATTT ATTT ATTT ATTT CTTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
5358885 AAATAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:5359199 original size:2 final size:2
Alignment explanation
Indices: 5359192--5359222 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5359182 GGCTTATTTA
5359192 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
5359223 CATTTAGTTT
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:5359979 original size:28 final size:27
Alignment explanation
Indices: 5359925--5359990 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
5359915 ATTACCTATT
*
5359925 TGTTTGTTAAAAATGATGATTATTTTG
1 TGTTTGTCAAAAATGATGATTATTTTG
* *
5359952 TGTTTGTCAAAAATTATGATT-TTTTT
1 TGTTTGTCAAAAATGATGATTATTTTG
5359978 TGAATTTGTCAAA
1 TG--TTTGTCAAA
5359991 TATGGAGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.18
27 19 0.56
28 9 0.26
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATGATTATTTTG
Found at i:5366701 original size:23 final size:25
Alignment explanation
Indices: 5366662--5366707 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
5366652 TATAATTTAC
*
5366662 ATTTTTACTTATTATAA-ATAAATA
1 ATTTTTACTTATAATAACATAAATA
5366686 ATTTTTAC-TATAATAACATAAA
1 ATTTTTACTTATAATAACATAAA
5366708 AATAGCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTTTACTTATAATAACATAAATA
Found at i:5373025 original size:2 final size:2
Alignment explanation
Indices: 5373018--5373045 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5373008 TTAAGTTTGA
5373018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5373046 TCATAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5373701 original size:74 final size:74
Alignment explanation
Indices: 5373579--5373728 Score: 225
Period size: 74 Copynumber: 2.0 Consensus size: 74
5373569 ATAGATATAA
*
5373579 TGAAACATGAAATTCCCTTTTTCGATGCATTTCACCATCTGAAAGGAACC-TTGAGGAGAATGCA
1 TGAAACATGAAATT-CCTTTTTCGATGCATTTCACCATCTGAAAGGAACCTTTG-GGAGAATCCA
5373643 CTACCCAAGAG
64 CTACCCAAGAG
*
5373654 TGAAACATGAAATT-CTTTTTACGATGCATTTCACCGTCT-AGAAGGAACCTTTGGGAGAATCCA
1 TGAAACATGAAATTCCTTTTT-CGATGCATTTCACCATCTGA-AAGGAACCTTTGGGAGAATCCA
5373717 CTACCCAAGAG
64 CTACCCAAGAG
5373728 T
1 T
5373729 TCAATGGAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
73 7 0.10
74 46 0.66
75 17 0.24
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (74 bp):
TGAAACATGAAATTCCTTTTTCGATGCATTTCACCATCTGAAAGGAACCTTTGGGAGAATCCACT
ACCCAAGAG
Found at i:5377567 original size:78 final size:78
Alignment explanation
Indices: 5377438--5377592 Score: 292
Period size: 78 Copynumber: 2.0 Consensus size: 78
5377428 TGCTTGAGGA
*
5377438 TTGTTTCATAATGGTCCTAGGTCTGACTTGCTGAAATGGCTTCATAATATGAAGATAAACCTAGT
1 TTGTTTCATAATGGTCCTAGGTCTGACTTGCTGAAATGGCTTCACAATATGAAGATAAACCTAGT
5377503 TCATATAGGTCAC
66 TCATATAGGTCAC
*
5377516 TTGTTTCATAATGGTCCTAGGTCTGACTTGCTGAAATGGCTTCACAGTATGAAGATAAACCTAGT
1 TTGTTTCATAATGGTCCTAGGTCTGACTTGCTGAAATGGCTTCACAATATGAAGATAAACCTAGT
5377581 TCATATAGGTCA
66 TCATATAGGTCA
5377593 TTATTGCCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (78 bp):
TTGTTTCATAATGGTCCTAGGTCTGACTTGCTGAAATGGCTTCACAATATGAAGATAAACCTAGT
TCATATAGGTCAC
Found at i:5381507 original size:2 final size:2
Alignment explanation
Indices: 5381500--5381536 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5381490 CGTATGTGTT
5381500 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5381537 TGGAGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5383549 original size:21 final size:22
Alignment explanation
Indices: 5383505--5383551 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5383495 CCAACAATTA
* *
5383505 AAAAAAAAAAAAGAATAACTCC
1 AAAAAAAAAAAACAATAACACC
*
5383527 AAAAAAAAAAAACCATAA-ACC
1 AAAAAAAAAAAACAATAACACC
5383548 AAAA
1 AAAA
5383552 CCAAATAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.77, C:0.15, G:0.02, T:0.06
Consensus pattern (22 bp):
AAAAAAAAAAAACAATAACACC
Found at i:5383692 original size:18 final size:18
Alignment explanation
Indices: 5383669--5383714 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5383659 CACTAAAACA
*
5383669 AGAACCTGAAACAGAACC
1 AGAACCGGAAACAGAACC
* *
5383687 AGAACCGGAAGCGGAACC
1 AGAACCGGAAACAGAACC
5383705 AGAACCGGAA
1 AGAACCGGAA
5383715 CATGAACCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.26, T:0.02
Consensus pattern (18 bp):
AGAACCGGAAACAGAACC
Found at i:5383721 original size:18 final size:17
Alignment explanation
Indices: 5383678--5383722 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
5383668 AAGAACCTGA
5383678 AACAGAACCAGAACCGG
1 AACAGAACCAGAACCGG
*
5383695 AAGCGGAACCAGAACCGG
1 AA-CAGAACCAGAACCGG
5383713 AACATGAACC
1 AACA-GAACC
5383723 TGCATTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.44, C:0.29, G:0.24, T:0.02
Consensus pattern (17 bp):
AACAGAACCAGAACCGG
Found at i:5384680 original size:16 final size:18
Alignment explanation
Indices: 5384654--5384690 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
5384644 TTTATTGGGA
5384654 TTTTCCTTTTTTTATT-T
1 TTTTCCTTTTTTTATTCT
5384671 TTTTCC-TTTTTTATTCT
1 TTTTCCTTTTTTTATTCT
5384688 TTT
1 TTT
5384691 GGGATGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCCTTTTTTTATTCT
Found at i:5395187 original size:2 final size:2
Alignment explanation
Indices: 5395175--5395211 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
5395165 GATTGAGCTG
5395175 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5395212 GCTGCATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5406470 original size:2 final size:2
Alignment explanation
Indices: 5406463--5406488 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5406453 TGGAAGATCT
5406463 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
5406489 GGAGGGAGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5406781 original size:24 final size:26
Alignment explanation
Indices: 5406722--5406812 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 26
5406712 TCTCCATTCA
* *
5406722 TATTATTTAT-AACTTATAATGCATTTT
1 TATT-TTTATAAATTTATAAT-TATTTT
*
5406749 TATTGTTATAAA-TTA-AATTATTTT
1 TATTTTTATAAATTTATAATTATTTT
*
5406773 TATTTTTATTAAAATTTATAATTTTTTAT
1 TATTTTTA-T-AAATTTATAATTATTT-T
5406802 TATTTTTATAA
1 TATTTTTATAA
5406813 TAATTTTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 12 0.22
25 4 0.07
26 10 0.19
27 11 0.20
28 8 0.15
29 9 0.17
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTTTATAAATTTATAATTATTTT
Found at i:5406805 original size:29 final size:32
Alignment explanation
Indices: 5406762--5406835 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 32
5406752 TGTTATAAAT
*
5406762 TAAATTATTT-TTATTTTTATTAA-AA-TTT-A
1 TAAATTTTTTATTATTTTTA-TAATAATTTTGA
5406791 T-AATTTTTTATTATTTTTATAATAATTTTGA
1 TAAATTTTTTATTATTTTTATAATAATTTTGA
5406822 TAAATTTTTTATTA
1 TAAATTTTTTATTA
5406836 ATCTTTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 10 0.26
29 12 0.31
30 3 0.08
31 2 0.05
32 12 0.31
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (32 bp):
TAAATTTTTTATTATTTTTATAATAATTTTGA
Found at i:5406852 original size:32 final size:31
Alignment explanation
Indices: 5406762--5406835 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
5406752 TGTTATAAAT
* *
5406762 TAAATTATTT-TTATTTTTATTAA-AATTT-A
1 TAAATTTTTTATTATTTTTA-TAATATTTTGA
5406791 T-AATTTTTTATTATTTTTATAATAATTTTGA
1 TAAATTTTTTATTATTTTTATAAT-ATTTTGA
5406822 TAAATTTTTTATTA
1 TAAATTTTTTATTA
5406836 ATCTTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 10 0.26
29 10 0.26
30 4 0.11
31 2 0.05
32 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (31 bp):
TAAATTTTTTATTATTTTTATAATATTTTGA
Found at i:5406968 original size:19 final size:18
Alignment explanation
Indices: 5406946--5406987 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5406936 ACCTTTAAAA
*
5406946 ATTTTTCATAATATTTAAT
1 ATTTTTAATAAT-TTTAAT
*
5406965 ATTTGTAATAATTTTAAT
1 ATTTTTAATAATTTTAAT
5406983 ATTTT
1 ATTTT
5406988 ATAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTTAATAATTTTAAT
Found at i:5407233 original size:1 final size:1
Alignment explanation
Indices: 5407229--5407254 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5407219 TCCTTCTAGG
5407229 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5407255 CCAGTTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5411241 original size:16 final size:17
Alignment explanation
Indices: 5411210--5411242 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5411200 ATTATGTTTA
5411210 TATTTAAAATTTTAATT
1 TATTTAAAATTTTAATT
*
5411227 TATTTAATA-TTTAATT
1 TATTTAAAATTTTAATT
5411243 ATAAGTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTAAAATTTTAATT
Found at i:5411519 original size:39 final size:39
Alignment explanation
Indices: 5411465--5411543 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
5411455 ATTGACCAAT
*
5411465 GCTCGAATCAAATAATAACAAGTAATTATTATAAAGTAA
1 GCTCGAATCAAATAATAACAAGTAATTATTATAAAATAA
5411504 GCTCGAATCAAATAATAACAAGTAATTATTATAAAATAA
1 GCTCGAATCAAATAATAACAAGTAATTATTATAAAATAA
5411543 G
1 G
5411544 TTGTTTGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (39 bp):
GCTCGAATCAAATAATAACAAGTAATTATTATAAAATAA
Found at i:5412113 original size:27 final size:28
Alignment explanation
Indices: 5412080--5412145 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
5412070 GTCACCTATT
5412080 TATTTGTCAAAAATGAT-GGTTATTTTG
1 TATTTGTCAAAAATGATAGGTTATTTTG
* * *
5412107 TGTTTGTCAAAAATGATAGTTTTTTTTG
1 TATTTGTCAAAAATGATAGGTTATTTTG
5412135 TATTTGTCAAA
1 TATTTGTCAAA
5412146 TATGGAGGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.50
Consensus pattern (28 bp):
TATTTGTCAAAAATGATAGGTTATTTTG
Found at i:5412194 original size:24 final size:25
Alignment explanation
Indices: 5412135--5412204 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
5412125 GTTTTTTTTG
*
5412135 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
5412160 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
5412184 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
5412205 AATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 17 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:5416714 original size:28 final size:27
Alignment explanation
Indices: 5416659--5416729 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
5416649 GCCACCCATT
*
5416659 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTAGTTATTTTG
*
5416686 TGTTTGTCAAAAATGGTAGTT-TCCTTTG
1 TATTTGTCAAAAATGGTAGTTAT--TTTG
*
5416714 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
5416730 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.50
28 18 0.47
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTAGTTATTTTG
Found at i:5416748 original size:25 final size:24
Alignment explanation
Indices: 5416714--5416777 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
5416704 GTTTCCTTTG
5416714 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGAGGCTTG-T
*
5416739 TATTTGTCAAAATTGGTGGCTTGT
1 TATTTGTCAAAATTGGAGGCTTGT
*
5416763 TGTTTGTCAAAATTG
1 TATTTGTCAAAATTG
5416778 ATGGCTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 15 0.42
25 17 0.47
26 4 0.11
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (24 bp):
TATTTGTCAAAATTGGAGGCTTGT
Found at i:5416773 original size:24 final size:25
Alignment explanation
Indices: 5416714--5416783 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
5416704 GTTTCCTTTG
*
5416714 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
5416739 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
* *
5416763 TGTTTGTCAAAATTGATGGCT
1 TATTTGTCAAAATTGGTGGCT
5416784 AATTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 20 0.49
25 17 0.41
26 4 0.10
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:5419391 original size:14 final size:16
Alignment explanation
Indices: 5419356--5419395 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
5419346 TTTTTACTGA
5419356 ATTTAATATTAATATTT
1 ATTTAAT-TTAATATTT
5419373 ATTTAATTTAAT-TTT
1 ATTTAATTTAATATTT
5419388 -TTTAATTT
1 ATTTAATTT
5419396 TATCTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 3 0.13
16 5 0.22
17 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAATTTAATATTT
Found at i:5419631 original size:30 final size:31
Alignment explanation
Indices: 5419597--5419656 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5419587 AACGATATAA
*
5419597 ATAATT-TAATTTATTAATAA-TAAAAATTTC
1 ATAATTATAATTTAATAA-AATTAAAAATTTC
*
5419627 ATAATTATCATTTAATAAAATTAAAAATTT
1 ATAATTATAATTTAATAAAATTAAAAATTT
5419657 GTGATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
ATAATTATAATTTAATAAAATTAAAAATTTC
Found at i:5421297 original size:15 final size:13
Alignment explanation
Indices: 5421268--5421306 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
5421258 TTTTAAGTTA
5421268 TTTATTTTAAAAT
1 TTTATTTTAAAAT
5421281 TTTATTTATATAAAT
1 TTTATTT-TA-AAAT
5421296 TTTAATTTTAA
1 TTT-ATTTTAA
5421307 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.30
14 3 0.13
15 9 0.39
16 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTTTAAAAT
Found at i:5421330 original size:39 final size:37
Alignment explanation
Indices: 5421255--5421330 Score: 89
Period size: 39 Copynumber: 2.0 Consensus size: 37
5421245 ATTTATTCAA
* **
5421255 AAATTTTAAGTTATTTATTTTAAAATTTTATTTATAT
1 AAATTTTAAGTTATTTATTTTAAAATTATAAATATAT
* *
5421292 AAATTTTAATTTTAATTTATTTTATAATTATAAATATAT
1 AAATTTTAA-GTT-ATTTATTTTAAAATTATAAATATAT
5421331 TTTATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 9 0.28
38 2 0.06
39 21 0.66
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (37 bp):
AAATTTTAAGTTATTTATTTTAAAATTATAAATATAT
Found at i:5421350 original size:22 final size:24
Alignment explanation
Indices: 5421279--5421339 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
5421269 TTATTTTAAA
* * *
5421279 ATTTTATTTATATAAATTTTAATTTT
1 ATTTTATTT-TAT-AATTATAAATAT
*
5421305 AATTTATTTTATAATTATAAATAT
1 ATTTTATTTTATAATTATAAATAT
5421329 ATTTTATTTTA
1 ATTTTATTTTA
5421340 AATGTAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 19 0.63
25 3 0.10
26 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATTTTATAATTATAAATAT
Found at i:5428641 original size:18 final size:18
Alignment explanation
Indices: 5428620--5428657 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5428610 ATTTATTTAC
5428620 TTAAATAATAA-AATTATA
1 TTAAATAATAATAA-TATA
*
5428638 TTAAATTATAATAATATA
1 TTAAATAATAATAATATA
5428656 TT
1 TT
5428658 TTATCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATAATAATAATATA
Found at i:5428757 original size:20 final size:20
Alignment explanation
Indices: 5428734--5428771 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5428724 ATAATTTTTT
5428734 TATAATTTTGATAACTTTGA
1 TATAATTTTGATAACTTTGA
* *
5428754 TATATTTTTGCTAACTTT
1 TATAATTTTGATAACTTT
5428772 TAAAATAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (20 bp):
TATAATTTTGATAACTTTGA
Found at i:5428854 original size:43 final size:43
Alignment explanation
Indices: 5428807--5428905 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
5428797 GTAATTTGTA
* *
5428807 ATAATTTTATTAACATATATAATAGTTTTTAGTAACATTTCAT
1 ATAATTTTATTAACATATATAATAATTTTTAATAACATTTCAT
* * * * *
5428850 ATAATTTTAATAATATCTATAATAATTTTTAATACCATTTGAT
1 ATAATTTTATTAACATATATAATAATTTTTAATAACATTTCAT
5428893 ATAATTTTATTAA
1 ATAATTTTATTAA
5428906 GAAAAAAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (43 bp):
ATAATTTTATTAACATATATAATAATTTTTAATAACATTTCAT
Found at i:5428857 original size:22 final size:22
Alignment explanation
Indices: 5428800--5428900 Score: 84
Period size: 22 Copynumber: 4.7 Consensus size: 22
5428790 TTTTAATGTA
* *
5428800 ATTTGTAATAA-TTTTATTAAC
1 ATTTATAATAATTTTTAATAAC
* * *
5428821 ATATATAATAGTTTTTAGTAAC
1 ATTTATAATAATTTTTAATAAC
*
5428843 ATTTCAT-ATAA-TTTTAATAAT
1 ATTT-ATAATAATTTTTAATAAC
* *
5428864 ATCTATAATAATTTTTAATACC
1 ATTTATAATAATTTTTAATAAC
5428886 ATTTGAT-ATAATTTT
1 ATTT-ATAATAATTTT
5428901 ATTAAGAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.03
21 23 0.37
22 34 0.54
23 4 0.06
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTATAATAATTTTTAATAAC
Found at i:5430532 original size:21 final size:21
Alignment explanation
Indices: 5430508--5430550 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5430498 GATTTATGTT
5430508 TTTTAAAATTTTTAAAAATAA
1 TTTTAAAATTTTTAAAAATAA
** *
5430529 TTTTTTATTTTTTAAAAATAA
1 TTTTAAAATTTTTAAAAATAA
5430550 T
1 T
5430551 GCATTGTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAAATTTTTAAAAATAA
Found at i:5437752 original size:2 final size:2
Alignment explanation
Indices: 5437745--5437793 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
5437735 GGTATGAAAA
* * * *
5437745 AT AT AT AT AT AT AT AT AT AC AC AC AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5437787 AT AT AT A
1 AT AT AT A
5437794 AATGTATGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:5437792 original size:14 final size:14
Alignment explanation
Indices: 5437745--5437793 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
5437735 GGTATGAAAA
*
5437745 ATATATATATATAT
1 ATATATACATATAT
* *
5437759 ATATACACACATAT
1 ATATATACATATAT
5437773 ATATATACATATAT
1 ATATATACATATAT
5437787 ATATATA
1 ATATATA
5437794 AATGTATGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:5437997 original size:15 final size:16
Alignment explanation
Indices: 5437955--5437997 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
5437945 TAATTTTAAA
*
5437955 AAATATTTAATATATT
1 AAATATTTAAAATATT
*
5437971 AAAAATTT-AAATATT
1 AAATATTTAAAATATT
5437986 -AATATTTAAAAT
1 AAATATTTAAAAT
5437998 TTTTATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 6 0.26
15 10 0.43
16 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTTAAAATATT
Found at i:5438340 original size:2 final size:2
Alignment explanation
Indices: 5438322--5438366 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
5438312 CATTCATACG
* * *
5438322 TA TA CA TA TA TA AA TA TA TA AA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5438363 TA TA
1 TA TA
5438367 GTTGTTAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5444959 original size:3 final size:3
Alignment explanation
Indices: 5444941--5444997 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
5444931 TCTCCTGTTT
*
5444941 TTA TTT TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5444987 TTA TTA TTA TT
1 TTA TTA TTA TT
5444998 TCTTTCAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5445240 original size:18 final size:18
Alignment explanation
Indices: 5445217--5445276 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
5445207 TCAATAACTG
*
5445217 ATTTTTTAAGAATTTTAA
1 ATTTTTTAAGAATTATAA
*
5445235 ATTTTTTAAAAATTATAA
1 ATTTTTTAAGAATTATAA
**
5445253 ATTTTTTAAGAATGGTAA
1 ATTTTTTAAGAATTATAA
5445271 ATTTTT
1 ATTTTT
5445277 ATGATCATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (18 bp):
ATTTTTTAAGAATTATAA
Found at i:5445292 original size:17 final size:18
Alignment explanation
Indices: 5445217--5445292 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
5445207 TCAATAACTG
**
5445217 ATTTTTTAAGAATTTTAA
1 ATTTTTTAAGAATCATAA
* *
5445235 ATTTTTTAAAAATTATAA
1 ATTTTTTAAGAATCATAA
**
5445253 ATTTTTTAAGAATGGTAA
1 ATTTTTTAAGAATCATAA
*
5445271 A-TTTTTATG-ATCATAA
1 ATTTTTTAAGAATCATAA
5445287 ATTTTT
1 ATTTTT
5445293 AATTCTAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
16 6 0.12
17 11 0.22
18 32 0.65
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (18 bp):
ATTTTTTAAGAATCATAA
Found at i:5448046 original size:18 final size:18
Alignment explanation
Indices: 5448023--5448097 Score: 114
Period size: 18 Copynumber: 4.2 Consensus size: 18
5448013 TAATCACAAA
*
5448023 TTTTAAAAATTATAGATT
1 TTTTAAAAATTATAAATT
*
5448041 TTTTAAAAATTTTAAATT
1 TTTTAAAAATTATAAATT
* *
5448059 TTTTAATAATCATAAATT
1 TTTTAAAAATTATAAATT
5448077 TTTTAAAAATTATAAATT
1 TTTTAAAAATTATAAATT
5448095 TTT
1 TTT
5448098 GTAATTATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (18 bp):
TTTTAAAAATTATAAATT
Found at i:5448103 original size:16 final size:16
Alignment explanation
Indices: 5448084--5448114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5448074 ATTTTTTAAA
5448084 AATTATAAATTTTTGT
1 AATTATAAATTTTTGT
*
5448100 AATTATAGATTTTTG
1 AATTATAAATTTTTG
5448115 ACTCAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
AATTATAAATTTTTGT
Found at i:5455463 original size:4 final size:4
Alignment explanation
Indices: 5455454--5455481 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5455444 CAATCTATAC
5455454 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
5455482 ATATATACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:5461681 original size:5 final size:5
Alignment explanation
Indices: 5461665--5461700 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
5461655 GATTGCAGCT
* *
5461665 AATTC AATTA AACTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA A
5461701 TTCTATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (5 bp):
AATTA
Found at i:5462787 original size:27 final size:27
Alignment explanation
Indices: 5462757--5462876 Score: 92
Period size: 25 Copynumber: 4.5 Consensus size: 27
5462747 ATGTTATACG
5462757 ATTATATAATATAAAAATAAATAAAAT
1 ATTATATAATATAAAAATAAATAAAAT
* *
5462784 ATTATAT--TATATAAATAAATAATAT
1 ATTATATAATATAAAAATAAATAAAAT
* *
5462809 A-AATATAATAT--TAATAAATAAATAT
1 ATTATATAATATAAAAATAAATAAA-AT
* *
5462834 ATTA-A-AATATATAACATAAATTATAAT
1 ATTATATAATATA-AAAATAAA-TAAAAT
5462861 ATATATATAAATATAA
1 AT-TATAT-AATATAA
5462877 CGTTAATATT
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
24 18 0.25
25 21 0.29
26 4 0.06
27 16 0.22
28 5 0.07
29 1 0.01
30 1 0.01
31 6 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTATATAATATAAAAATAAATAAAAT
Found at i:5462841 original size:29 final size:28
Alignment explanation
Indices: 5462757--5462844 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 28
5462747 ATGTTATACG
*
5462757 ATTATATAATATAAAAATAAATAAAATATTAT
1 ATTATATAA-AT--AAAT-AATAAAATATAAT
5462789 ATTATATAAATAAATAATATAAATATAAT
1 ATTATATAAATAAATAATA-AAATATAAT
5462818 ATTA-ATAAATAAATATATTAAAATATA
1 ATTATATAAATAAATA-A-TAAAATATA
5462845 TAACATAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
28 15 0.29
29 24 0.46
30 2 0.04
31 2 0.04
32 9 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTATATAAATAAATAATAAAATATAAT
Found at i:5463191 original size:13 final size:13
Alignment explanation
Indices: 5463173--5463198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5463163 CCATCGAAAT
5463173 AAATAAAAATAAA
1 AAATAAAAATAAA
5463186 AAATAAAAATAAA
1 AAATAAAAATAAA
5463199 TATCTCATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:5465335 original size:22 final size:21
Alignment explanation
Indices: 5465301--5465341 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5465291 TTTATTTTTT
*
5465301 AAAATTTAATTTTAAAAATAA
1 AAAATGTAATTTTAAAAATAA
*
5465322 AAAATGTATATTTTATAAAT
1 AAAATGTA-ATTTTAAAAAT
5465342 TATATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAATGTAATTTTAAAAATAA
Found at i:5465482 original size:2 final size:2
Alignment explanation
Indices: 5465431--5465464 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5465421 GAGGACCCTT
*
5465431 TA TA TA TA TA TA CA 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
5465465 GTTACATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5467395 original size:30 final size:30
Alignment explanation
Indices: 5467323--5467395 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
5467313 CATCTTAAAT
* * *
5467323 ATTTATTTTTAAATAAATTTTTTCTATTTTT
1 ATTTA-TTTTAAACAAATTTTTTATATTTTG
* *
5467354 A-TTATAATTAAACAAGTTTTTTATATTTTG
1 ATTTAT-TTTAAACAAATTTTTTATATTTTG
5467384 ATTTATTTTAAA
1 ATTTATTTTAAA
5467396 TAGGACTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.82
31 5 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTATTTTAAACAAATTTTTTATATTTTG
Found at i:5467617 original size:10 final size:11
Alignment explanation
Indices: 5467585--5467629 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
5467575 TTAAGTACAT
5467585 TATAAATATAA
1 TATAAATATAA
5467596 TATAAAAAATATAA
1 TAT---AAATATAA
5467610 T-TAAATATAA
1 TATAAATATAA
5467620 TATAAATATA
1 TATAAATATA
5467630 TAAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.30
11 11 0.37
13 1 0.03
14 9 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TATAAATATAA
Found at i:5467633 original size:19 final size:20
Alignment explanation
Indices: 5467585--5467636 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 20
5467575 TTAAGTACAT
5467585 TATAAATATAATATAAAAAATA
1 TATAAATATAATAT--AAAATA
5467607 TAATTAAATATAATAT-AAATA
1 T-A-TAAATATAATATAAAATA
5467628 TATAAATAT
1 TATAAATAT
5467637 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 7 0.25
20 1 0.04
21 6 0.21
22 1 0.04
23 1 0.04
24 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAATATAATATAAAATA
Found at i:5467649 original size:18 final size:18
Alignment explanation
Indices: 5467623--5467681 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
5467613 AATATAATAT
*
5467623 AAATATATAAATATTTTA
1 AAATTTATAAATATTTTA
*
5467641 AAATTTATATA-ATTTT-
1 AAATTTATAAATATTTTA
* *
5467657 -AA-TTATTAATATATTA
1 AAATTTATAAATATTTTA
5467673 AAATTTATA
1 AAATTTATA
5467682 TAAAAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
17 7 0.23
18 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTTATAAATATTTTA
Found at i:5467651 original size:20 final size:19
Alignment explanation
Indices: 5467626--5467694 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
5467616 ATAATATAAA
5467626 TATATAAATATTTTAAAATT
1 TATAT-AATATTTTAAAATT
5467646 TATAT-A-ATTTT--AA-T
1 TATATAATATTTTAAAATT
*
5467660 TAT-TAATATATTAAAATT
1 TATATAATATTTTAAAATT
*
5467678 TATATAAAAATTTTAAA
1 TATAT-AATATTTTAAA
5467695 TATAATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.13
15 6 0.15
17 7 0.18
18 5 0.13
19 1 0.03
20 14 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATAATATTTTAAAATT
Found at i:5467655 original size:17 final size:17
Alignment explanation
Indices: 5467635--5467684 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5467625 ATATATAAAT
5467635 ATTTTAAAATTTATATA
1 ATTTTAAAATTTATATA
5467652 ATTTT--AA-TTAT-TA
1 ATTTTAAAATTTATATA
5467665 ATATATTAAAATTTATATA
1 AT-T-TTAAAATTTATATA
5467684 A
1 A
5467685 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 4 0.15
17 7 0.26
18 4 0.15
19 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTAAAATTTATATA
Found at i:5467674 original size:32 final size:32
Alignment explanation
Indices: 5467614--5467710 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 32
5467604 ATATAATTAA
* * * *
5467614 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATTTTAAT-TATTAATATATTAAAATTT
5467647 ATATAATTTTAATTATTAATATATTAAAATTT
1 ATATAATTTTAATTATTAATATATTAAAATTT
*
5467679 ATATAAAAATTTTAAATA-TAATTATATTAAAA
1 ATAT---AATTTTAATTATTAA-TATATTAAAA
5467711 AATATATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
32 21 0.38
33 11 0.20
34 3 0.05
35 20 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATAATTTTAATTATTAATATATTAAAATTT
Found at i:5467722 original size:37 final size:35
Alignment explanation
Indices: 5467622--5467723 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 35
5467612 AAATATAATA
* *
5467622 TAAATATATAAATATTTTAAAAT-T-TAT-ATAATTT
1 TAAATAT-T-AATATATTAAAATATATATAAAAATTT
* *
5467656 TAATTATTAATATATTAAAATTTATATAAAAATTT
1 TAAATATTAATATATTAAAATATATATAAAAATTT
* *
5467691 TAAATA-TAATTATATTAAAAAATATATATAAAT
1 TAAATATTAA-TATATTAAAATATATATAAAAAT
5467724 ATTGATAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
32 12 0.21
33 2 0.04
34 12 0.21
35 31 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TAAATATTAATATATTAAAATATATATAAAAATTT
Found at i:5470767 original size:5 final size:5
Alignment explanation
Indices: 5470757--5470783 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5470747 AACTATCAAT
5470757 ATATC ATATC ATATC ATATC ATATC AT
1 ATATC ATATC ATATC ATATC ATATC AT
5470784 CAGCTTCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Done.