Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 12 of 18
Found at i:4919362 original size:26 final size:25
Alignment explanation
Indices: 4919319--4919380 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
4919309 TAAAAAATAA
* *
4919319 AAATTTTTAATTTTAATTATTTTTAGT
1 AAATTTTT--TTTTAATTATTCTTAAT
* *
4919346 TAATTTTTTTTTAAATTGTTCTTAAT
1 AAATTTTTTTTT-AATTATTCTTAAT
4919372 AAATTTTTT
1 AAATTTTTT
4919381 CATATTCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 4 0.14
26 18 0.62
27 7 0.24
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (25 bp):
AAATTTTTTTTTAATTATTCTTAAT
Found at i:4925121 original size:26 final size:26
Alignment explanation
Indices: 4925089--4925141 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
4925079 GGTCCTAAAC
* *
4925089 AAGTCACCTACGTAATAATTACAACA
1 AAGTCACATACGCAATAATTACAACA
*
4925115 AAGTCACATACGCAATAGTTACAACA
1 AAGTCACATACGCAATAATTACAACA
4925141 A
1 A
4925142 GATTCCCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.09, T:0.21
Consensus pattern (26 bp):
AAGTCACATACGCAATAATTACAACA
Found at i:4931078 original size:33 final size:33
Alignment explanation
Indices: 4931034--4931132 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 33
4931024 TCAGATTATG
4931034 TTATCACATTTTAAAAAAAAAGTCAGTTTTACC
1 TTATCACATTTTAAAAAAAAAGTCAGTTTTACC
* *
4931067 TTATCATATTTTAAAAAGAAAATAAGTCAGTTTTATC
1 TTATCACATTTT--AAA-AAAA-AAGTCAGTTTTACC
*
4931104 TTAACACA-TTTAAAAAAAATTAGTCAGTT
1 TTATCACATTTTAAAAAAAA--AGTCAGTT
4931133 AATTGTATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
32 1 0.02
33 15 0.27
34 11 0.20
35 3 0.05
36 7 0.12
37 19 0.34
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (33 bp):
TTATCACATTTTAAAAAAAAAGTCAGTTTTACC
Found at i:4931896 original size:51 final size:51
Alignment explanation
Indices: 4931831--4931933 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
4931821 AGTATGTTAT
*
4931831 ATAAAGTTCAATTTAATACTTAGTACACCTTTGGTTTCAACTTAGGTTGTA
1 ATAAAGTTCAATTTAATACTTAGTACACCTTTGGCTTCAACTTAGGTTGTA
* *
4931882 ATAAGGTTCAATTTAATATTTAGTACACCTTTGGCTTCAACTTAGGTTGTA
1 ATAAAGTTCAATTTAATACTTAGTACACCTTTGGCTTCAACTTAGGTTGTA
4931933 A
1 A
4931934 GTTATAAGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (51 bp):
ATAAAGTTCAATTTAATACTTAGTACACCTTTGGCTTCAACTTAGGTTGTA
Found at i:4932670 original size:25 final size:26
Alignment explanation
Indices: 4932622--4932688 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
4932612 ATATATAAGT
*
4932622 AAATATGATTTTCATGTTGATTTT-G
1 AAATATGATTTTGATGTTGATTTTCG
* *
4932647 AAATATGATTTTGATTTTGTTTTTCG
1 AAATATGATTTTGATGTTGATTTTCG
*
4932673 -AATGTGATTGTTGATG
1 AAATATGATT-TTGATG
4932689 AATGTGTGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 29 0.83
26 6 0.17
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.52
Consensus pattern (26 bp):
AAATATGATTTTGATGTTGATTTTCG
Found at i:4933079 original size:37 final size:37
Alignment explanation
Indices: 4933009--4933107 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
4932999 ACTTCTAACT
4933009 CATGCCACTGAGGTTAATTGTGGTTTTGATTTTGACC
1 CATGCCACTGAGGTTAATTGTGGTTTTGATTTTGACC
* *
4933046 CATGCCACTGAGATTAATTGTGGTTTT-ATTTTTGACT
1 CATGCCACTGAGGTTAATTGTGGTTTTGA-TTTTGACC
* *
4933083 TATGCC-GTAGAGGTTAATTGTGGTT
1 CATGCCACT-GAGGTTAATTGTGGTT
4933108 GTAATATGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 2 0.04
37 53 0.96
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.42
Consensus pattern (37 bp):
CATGCCACTGAGGTTAATTGTGGTTTTGATTTTGACC
Found at i:4936156 original size:23 final size:22
Alignment explanation
Indices: 4936134--4936179 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
4936124 TGTTCAAATT
4936134 ATTAT-GTTG-GGAAACAAACA
1 ATTATAGTTGTGGAAACAAACA
4936154 ATTATAGTTGTTGGAAACAAACA
1 ATTATAGTTG-TGGAAACAAACA
4936177 ATT
1 ATT
4936180 GTGTCCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
23 14 0.61
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (22 bp):
ATTATAGTTGTGGAAACAAACA
Found at i:4936246 original size:18 final size:18
Alignment explanation
Indices: 4936217--4936270 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
4936207 ACAAACATGA
4936217 TTATTC-AATAATTATAT
1 TTATTCAAATAATTATAT
* *
4936234 TTATTCAAATAATTAAAAA
1 TTATTCAAATAATT-ATAT
4936253 TT-TTCAAATAATTATAT
1 TTATTCAAATAATTATAT
4936270 T
1 T
4936271 GAAAAGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 9 0.29
18 18 0.58
19 4 0.13
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTCAAATAATTATAT
Found at i:4946132 original size:21 final size:20
Alignment explanation
Indices: 4946091--4946133 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
4946081 TAAATAATAT
** *
4946091 TTATTAATATAATTAATTAA
1 TTATTAATATAAAAAACTAA
4946111 TTATTAATTATAAAAAACTAA
1 TTATTAA-TATAAAAAACTAA
4946132 TT
1 TT
4946134 TAATTTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAATATAAAAAACTAA
Found at i:4948171 original size:19 final size:18
Alignment explanation
Indices: 4948147--4948182 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4948137 ATGCTTCTTC
*
4948147 TTTTTTTTATTGTCTATTG
1 TTTTTTTAATT-TCTATTG
4948166 TTTTTTTAATTTCTATT
1 TTTTTTTAATTTCTATT
4948183 TACATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTTTAATTTCTATTG
Found at i:4959661 original size:10 final size:8
Alignment explanation
Indices: 4959636--4959661 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4959626 ACTAGCCCAC
4959636 CATGCACA
1 CATGCACA
4959644 CATGCACA
1 CATGCACA
4959652 CATGCACA
1 CATGCACA
4959660 CA
1 CA
4959662 AAAGAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (8 bp):
CATGCACA
Found at i:4969965 original size:6 final size:6
Alignment explanation
Indices: 4969954--4969980 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4969944 TTATTTTGAG
4969954 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
4969981 TTTAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:4972172 original size:26 final size:28
Alignment explanation
Indices: 4972134--4972185 Score: 65
Period size: 26 Copynumber: 1.9 Consensus size: 28
4972124 ATTACAACAT
4972134 TTTTTTAATTA-TTAGAGAATAATTATAA
1 TTTTTTAATTATTTAGA-AATAATTATAA
*
4972162 TTTTTT-A-TATTTATAAATAATTAT
1 TTTTTTAATTATTTAGAAATAATTAT
4972186 GAGCTAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.50
27 5 0.23
28 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TTTTTTAATTATTTAGAAATAATTATAA
Found at i:4976567 original size:2 final size:2
Alignment explanation
Indices: 4976555--4976594 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4976545 CTCAAGCAGC
*
4976555 TA TA TA AA 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
4976595 AGTTGACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4977385 original size:2 final size:2
Alignment explanation
Indices: 4977378--4977402 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4977368 GATCTACTAT
4977378 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4977403 TATATAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4980053 original size:2 final size:2
Alignment explanation
Indices: 4980046--4980072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4980036 TGGGAAGGAG
4980046 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
4980073 GTATTTGTAA
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:4981768 original size:2 final size:2
Alignment explanation
Indices: 4981763--4981792 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4981753 TTTTTTTTCT
*
4981763 TA TA TA CA 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
4981793 CAAATTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4982998 original size:2 final size:2
Alignment explanation
Indices: 4982991--4983020 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4982981 AACATGAGGA
4982991 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
4983021 TCAAAACAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4987856 original size:16 final size:17
Alignment explanation
Indices: 4987835--4987867 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4987825 TTAATTAATT
4987835 ATTTA-TTAATTATAAA
1 ATTTATTTAATTATAAA
*
4987851 ATTTATTTAATTTTAAA
1 ATTTATTTAATTATAAA
4987868 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTATTTAATTATAAA
Found at i:4996583 original size:12 final size:12
Alignment explanation
Indices: 4996566--4996658 Score: 53
Period size: 12 Copynumber: 7.3 Consensus size: 12
4996556 ATATCATATA
4996566 TTTTATTTTTAT
1 TTTTATTTTTAT
4996578 TTTTATTTTTAT
1 TTTTATTTTTAT
* * *
4996590 TATAATCTTATAT
1 TTTTAT-TTTTAT
*
4996603 ATTTTATTTTCAT
1 -TTTTATTTTTAT
* * *
4996616 TTGTTAATATAATT
1 TT-TTATTTTTA-T
*
4996630 TTTTATATTATAT
1 TTTTAT-TTTTAT
4996643 ATTTTA-TTTTAT
1 -TTTTATTTTTAT
4996655 TTTT
1 TTTT
4996659 TAAAAAAATA
Statistics
Matches: 60, Mismatches: 15, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
11 4 0.07
12 23 0.38
13 19 0.32
14 14 0.23
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:4996585 original size:33 final size:32
Alignment explanation
Indices: 4996563--4996652 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 32
4996553 TTAATATCAT
*
4996563 ATATTTTAT-TTTTATTTTTATTTTTATTATA
1 ATATTTTATATTTTATTTTTATTTTTAATATA
* * *
4996594 ATCTTATATATTTTATTTTCATTTGTTAATATA
1 ATATTTTATATTTTATTTTTATTT-TTAATATA
* *
4996627 ATTTTTTATATTATATATTTTATTTT
1 ATATTTTATATTTTAT-TTTTATTTT
4996653 ATTTTTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 7 0.15
32 13 0.27
33 21 0.44
34 7 0.15
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (32 bp):
ATATTTTATATTTTATTTTTATTTTTAATATA
Found at i:4996631 original size:45 final size:39
Alignment explanation
Indices: 4996535--4996661 Score: 118
Period size: 39 Copynumber: 3.3 Consensus size: 39
4996525 TTATATAATA
* *
4996535 TTATTT-TTAA-ATATATTTTTAATATCATATATTTTATTT
1 TTATTTGTTAATATA-ATTTTTTATATTATATATTTTA-TT
* * * * * *
4996574 TTATTT-TTATTTTTA-TTATAATCTTATATATTTTATT
1 TTATTTGTTAATATAATTTTTTATATTATATATTTTATT
4996611 TTCATTTGTTAATATAATTTTTTATATTATATATTTTATT
1 TT-ATTTGTTAATATAATTTTTTATATTATATATTTTATT
*
4996651 TTATTTTTTAA
1 TTATTTGTTAA
4996662 AAAAATAATA
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.06
38 21 0.30
39 24 0.34
40 22 0.31
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (39 bp):
TTATTTGTTAATATAATTTTTTATATTATATATTTTATT
Found at i:4997926 original size:22 final size:23
Alignment explanation
Indices: 4997877--4997928 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4997867 ATGACCATGT
*
4997877 CACATGAACCCATAATCAAATGC
1 CACATCAACCCATAATCAAATGC
*
4997900 CACATCAACCCATAAT-TAATGC
1 CACATCAACCCATAATCAAATGC
*
4997922 TACATCA
1 CACATCA
4997929 GTATACTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.42, C:0.31, G:0.06, T:0.21
Consensus pattern (23 bp):
CACATCAACCCATAATCAAATGC
Found at i:5003258 original size:16 final size:16
Alignment explanation
Indices: 5003233--5003303 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 16
5003223 GATGAAAATT
5003233 TATTAATTAATTGATA
1 TATTAATTAATTGATA
*
5003249 TATTATTTAA-T--T-
1 TATTAATTAATTGATA
5003261 TATTAATTAATTGATA
1 TATTAATTAATTGATA
* *
5003277 TATTATTTAATTTATA
1 TATTAATTAATTGATA
*
5003293 AATTAA-TAATT
1 TATTAATTAATT
5003304 TATTAATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 9 0.20
13 2 0.04
15 7 0.16
16 27 0.60
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTAATTAATTGATA
Found at i:5003268 original size:8 final size:8
Alignment explanation
Indices: 5003229--5003314 Score: 57
Period size: 8 Copynumber: 9.9 Consensus size: 8
5003219 GGAGGATGAA
5003229 AATTTATT
1 AATTTATT
*
5003237 AATTAATT
1 AATTTATT
5003245 GATATATTATTT
1 -A-AT-TTA-TT
5003257 AATTTATT
1 AATTTATT
*
5003265 AATTAATT
1 AATTTATT
5003273 GATATATTATTT
1 -A-AT-TTA-TT
5003285 AATTTA-T
1 AATTTATT
* *
5003292 AAATTAAT
1 AATTTATT
5003300 AATTTATT
1 AATTTATT
5003308 AATTTAT
1 AATTTAT
5003315 ACAGTAATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
7 6 0.10
8 30 0.48
9 8 0.13
10 8 0.13
11 6 0.10
12 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (8 bp):
AATTTATT
Found at i:5003313 original size:28 final size:28
Alignment explanation
Indices: 5003229--5003299 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
5003219 GGAGGATGAA
5003229 AATTTATTAATTAATTGATATATTATTT
1 AATTTATTAATTAATTGATATATTATTT
5003257 AATTTATTAATTAATTGATATATTATTT
1 AATTTATTAATTAATTGATATATTATTT
*
5003285 AATTTATAAATTAAT
1 AATTTATTAATTAAT
5003300 AATTTATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
AATTTATTAATTAATTGATATATTATTT
Found at i:5005083 original size:60 final size:59
Alignment explanation
Indices: 5004999--5005110 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
5004989 GTAGCCCTTA
5004999 TACTTTTATTGTGTTTAATCAAGTTTTAGTATTTTTATTTTAAACCAAATAAACTCTTG
1 TACTTTTATTGTGTTTAATCAAGTTTTAGTATTTTTATTTTAAACCAAATAAACTCTTG
* ** * *
5005058 TACTTTTATTTTGATTTAAAT-AAGTTTTTTTATTTTTATTTTGAATCAAATAA
1 TACTTTTATTGTG-TTT-AATCAAGTTTTAGTATTTTTATTTTAAACCAAATAA
5005111 GCTTTTATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 12 0.26
60 31 0.67
61 3 0.07
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.54
Consensus pattern (59 bp):
TACTTTTATTGTGTTTAATCAAGTTTTAGTATTTTTATTTTAAACCAAATAAACTCTTG
Found at i:5006753 original size:19 final size:20
Alignment explanation
Indices: 5006721--5006758 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5006711 AATTAAATCA
5006721 TAAAAATATGAATTAAAATT
1 TAAAAATATGAATTAAAATT
*
5006741 TAAAATTAT-AATTAAAAT
1 TAAAAATATGAATTAAAAT
5006759 AATTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAAAATATGAATTAAAATT
Found at i:5006800 original size:14 final size:15
Alignment explanation
Indices: 5006771--5006825 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 15
5006761 TTAATGAATT
**
5006771 TTAATATATATTAAA
1 TTAATATATAAAAAA
5006786 TTAAT-TATAAAAAA
1 TTAATATATAAAAAA
*
5006800 TT-ATAAATAAAAAA
1 TTAATATATAAAAAA
5006814 -TAATATATAAAA
1 TTAATATATAAAA
5006826 CTAAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.09
14 26 0.76
15 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATATATAAAAAA
Found at i:5007488 original size:6 final size:6
Alignment explanation
Indices: 5007477--5007507 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5007467 GTTGATTCAA
5007477 TCTGGT TCTGGT TCTGGT TCTGGT TCTGGT T
1 TCTGGT TCTGGT TCTGGT TCTGGT TCTGGT T
5007508 TTCGTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (6 bp):
TCTGGT
Found at i:5018295 original size:3 final size:3
Alignment explanation
Indices: 5018287--5018316 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5018277 AATATCGATC
*
5018287 GAA GAA GAA GAA GAA GAA GCA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5018317 CAGAGAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5023245 original size:24 final size:24
Alignment explanation
Indices: 5023200--5023245 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5023190 GCATAAAACT
* *
5023200 CCTCCATCTCCTAAGCCGAAAGCG
1 CCTCCATCTCCCAAGCCCAAAGCG
**
5023224 CCTCCATCTCCCCTGCCCAAAG
1 CCTCCATCTCCCAAGCCCAAAG
5023246 AAGAAGTCCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.22, C:0.48, G:0.13, T:0.17
Consensus pattern (24 bp):
CCTCCATCTCCCAAGCCCAAAGCG
Found at i:5035286 original size:34 final size:34
Alignment explanation
Indices: 5035239--5035326 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
5035229 ATAATATATG
* * * *
5035239 ATGACTAACTATATTCCTAGTAAATTTATGAATA
1 ATGATTAAATATATTACTAGTAAATTTATGAAGA
* * *
5035273 ATGATTAATTATATTACTAGTAAGTTTATGTAGA
1 ATGATTAAATATATTACTAGTAAATTTATGAAGA
5035307 ATGATTAAATATATTACTAG
1 ATGATTAAATATATTACTAG
5035327 CAGGTTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (34 bp):
ATGATTAAATATATTACTAGTAAATTTATGAAGA
Found at i:5037899 original size:251 final size:249
Alignment explanation
Indices: 5037263--5038782 Score: 1303
Period size: 251 Copynumber: 6.2 Consensus size: 249
5037253 TAAAAATCAT
* * * * *
5037263 TAAATTTTAAATCTTAAC-AAATATATGTGAGAGTTAACTTAATAAGTCAATTAAGTAAAAAAAA
1 TAAATTTTAAATCTTAACGTAA-ATATGTGAAAGTTAACGTAACAAGTTAATTAAGT-AAAAAAA
* * * * * *
5037327 TCTAATTTTAGTGAAAAACAAACATTTAAATTCATATTCTTGGATTAAAAGTGTTTAATAATATA
64 TCTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTTGG-CTAAAAGTGTTTAATGATAAA
* * * * *
5037392 TAAATTTTAA-TTTTAAATAAAGAGTAATAAAGATAAAATAATTATAGTGCAAAATTAACAAAGA
128 TAAATTTTAATTTTTAAATAAAAAATAATAAAGATAAAATAATTATAGTTCAAAATTGACATAGA
* * * * *
5037456 AAAATCTTGACATAAAATTGTAAGAATTGATGTAAAAACTTATAAAGGTAAAATAAC
193 TAAATCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAAGATAAAATAAC
* *
5037513 TAAATTTTAAATCTTAATGTAAATATGTGAAAGTTAA-GT--CAA-TTAAGTAA--AAAAAAA-C
1 TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAAGTTAATTAAGTAAAAAAATC
* * * * * * *
5037571 TAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTCGAACTAAAAATATTTAACGATATACA
66 TAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTTG-GCTAAAAGTGTTTAATGATAAATA
5037636 AATTTTAATTTTTAAATAAAAAATAATAAAGATAAAACTAATTATAGTTCAAAATTGACATAGAT
130 AATTTTAATTTTTAAATAAAAAATAATAAAGATAAAA-TAATTATAGTTCAAAATTGACATAGAT
* *
5037701 AAATTTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAAGATCAAATAAC
194 AAATCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAAGATAAAATAAC
* * * * * * * *
5037757 TAAAATTTAAATTTTAACATAAATGTGTGAGAGTTAACGCAACAAATTAATTAAGTAAAAAAATT
1 TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAAGTTAATTAAGTAAAAAAATC
* * *
5037822 TAATTTTAGTTAAAAACAAATATTTAAATTTATATTCTTAGGCTAAAAGTGGTTAATGATAAATA
66 TAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTT-GGCTAAAAGTGTTTAATGATAAATA
* * * *
5037887 AATTTTAATTTTTAAATAAAAAATAATAATGA-AAAA-AATTATAATTCAAAATTGACATAAATC
130 AATTTTAATTTTTAAATAAAAAATAATAAAGATAAAATAATTATAGTTCAAAATTGACATAGATA
** * * * * * * * **
5037950 AGCCTTAATATAAAACTATAAGAACTGATGTCAAAACTTATAAATG-TGGAATAAC
195 AATCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAA-GATAAAATAAC
* * * * * *
5038005 TAAATTTTAAATCTTAACGTAAATATGTGAAAATTAACATAATAAGTTAGTTAAATAACAAAATC
1 TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAAGTTAATTAAGTAAAAAAATC
* * * * * * * *
5038070 TAATTTTAATAAAAAATAAACATTTATATTTATATTATTGGGCTAAAAGTATGTAATGAT-ATTC
66 TAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTT-GGCTAAAAGTGTTTAATGATAAAT-
* * * *
5038134 AAATTTTTATTCTCAAATAAAAAATAATAAAGATAAAAATAATTATAATTCAAAATT---A-AG-
129 AAATTTTAATTTTTAAATAAAAAATAATAAAGAT-AAAATAATTATAGTTCAAAATTGACATAGA
5038194 ---A---T-A-A-AAAAC----AT--TTGACGTAAAAACTTATACAAGA-AAAATAAC
193 TAAATCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATA-AAGATAAAATAAC
** * * *
5038236 TAAATTTTAAATCTTAACGTAAACGTATGAAAGTTGACGTAACAAGTCAATTAAGTAAAAAAAAT
1 TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAAGTTAATTAAGT-AAAAAAAT
* * * * *
5038301 -TAATTTTAGTGAAAAATAAATATTTAAATTTATATTTTTGGATTAAAAGTGTTTAACGATATAC
65 CTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTTGG-CTAAAAGTGTTTAATGATAAAT
* ** * * * * * *
5038365 AAATTTTAATTTTTAAATAAAGAATAATAATA-ATTATTATTATTATACTTTAAAATAGATAGAG
129 AAATTTTAATTTTTAAATAAAAAATAATAA-AGA-TAAAATAATTATAGTTCAAAATTGACATAG
* * * *
5038429 ATAAATCTTGATATAAAATTGTAATAATTTACGTAAAAACTTATAAA-AGTGAAAA-AAT
192 ATAAATCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAAGA-T-AAAATAAC
* * * ** *
5038487 TAAATTTTAAATCTTAATGTAAATGTGTGAGAGTTAATATAATAAGTTAATTAAGTAAAAAAAAT
1 TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAAGTTAATTAAGT-AAAAAAAT
* * * * * * * * *
5038552 CTAATTTTAATGAAAAATAAATATTTATATTTATACTATTGAGTTAAAAATATGTAATGAT-ATT
65 CTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTTG-GCTAAAAGTGTTTAATGATAAAT
* *
5038616 CAAATTTTTA-TTTTAAATAAAAAATAATAAAGATAAAGATAATTATAGTT-AAAAGTT-ACTGT
129 -AAATTTTAATTTTTAAATAAAAAATAATAAAGATAAA-ATAATTATAGTTCAAAA-TTGAC-AT
* * * * * * * * ** *
5038678 TGA-AAAGGCTTAACGTAAAATTGTAAAAATTGAGGTAAAATCTTATAAA-AGTGGAACAAGC
190 AGATAAA-TCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAAGA-TAAAATAA-C
* * * * *
5038739 -AAATTTAAAATGTTAACGTAAATGTATGAGAGTTAACGTAACAA
1 TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAA
5038783 ATGATAATAA
Statistics
Matches: 1026, Mismatches: 187, Indels: 113
0.77 0.14 0.09
Matches are distributed among these distances:
230 2 0.00
231 159 0.15
232 11 0.01
233 1 0.00
234 1 0.00
235 2 0.00
237 5 0.00
238 1 0.00
239 2 0.00
240 1 0.00
242 63 0.06
243 34 0.03
244 105 0.10
245 5 0.00
246 6 0.01
247 8 0.01
248 203 0.20
249 5 0.00
250 61 0.06
251 287 0.28
252 63 0.06
253 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (249 bp):
TAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACGTAACAAGTTAATTAAGTAAAAAAATC
TAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTTGGCTAAAAGTGTTTAATGATAAATAA
ATTTTAATTTTTAAATAAAAAATAATAAAGATAAAATAATTATAGTTCAAAATTGACATAGATAA
ATCTTGACATAAAACTGTAATAATTGACGTAAAAACTTATAAAGATAAAATAAC
Found at i:5038927 original size:17 final size:17
Alignment explanation
Indices: 5038865--5038927 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
5038855 GTTTAAAGTA
* *
5038865 AAAAATAAAATAAAATT
1 AAAAATTAAATAAATTT
* *
5038882 AAAAGTTAAATAATTTT
1 AAAAATTAAATAAATTT
5038899 GAAAATAAATTAAATAAATTT
1 ---AA-AAATTAAATAAATTT
5038920 AAAAATTA
1 AAAAATTA
5038928 TCTATGTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 19 0.53
18 2 0.06
20 2 0.06
21 13 0.36
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAAATTAAATAAATTT
Found at i:5039437 original size:45 final size:45
Alignment explanation
Indices: 5039372--5039472 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
5039362 CTTAATGAAA
** *** *
5039372 TTACACGCCATGGTTAGGTTGTTACATGTCATGTACAAAAATATG
1 TTACACGTTATGGTTAGGTTGTTACACACCATGTACAAAAACATG
* *
5039417 TTACACGTTATGGTTTGGTTGTTATACACCATGTACAAAAACATG
1 TTACACGTTATGGTTAGGTTGTTACACACCATGTACAAAAACATG
*
5039462 TTACACATTAT
1 TTACACGTTAT
5039473 ATATAAAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (45 bp):
TTACACGTTATGGTTAGGTTGTTACACACCATGTACAAAAACATG
Found at i:5039464 original size:24 final size:24
Alignment explanation
Indices: 5039436--5039491 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5039426 ATGGTTTGGT
*
5039436 TGTTATACACCATGTACAAAAACA
1 TGTTATACACCATATACAAAAACA
* ** *
5039460 TGTTACACATTATATATAAAAACA
1 TGTTATACACCATATACAAAAACA
5039484 TGTTATAC
1 TGTTATAC
5039492 GCCACAGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (24 bp):
TGTTATACACCATATACAAAAACA
Found at i:5039561 original size:29 final size:29
Alignment explanation
Indices: 5039529--5039683 Score: 144
Period size: 29 Copynumber: 5.6 Consensus size: 29
5039519 TTATGTGAAA
5039529 AAAAAATATTATTGTTACACGTCATG-T-
1 AAAAAATATTATTGTTACACGTCATGTTG
* * *
5039556 ATAAAA-A-CA-TGTTACACGTTATGTTG
1 AAAAAATATTATTGTTACACGTCATGTTG
*
5039582 AAAAAATATTATTGTTACACGGCATGTTG
1 AAAAAATATTATTGTTACACGTCATGTTG
* *** *
5039611 AAAAAATATTATTGCTACATACCATATTG
1 AAAAAATATTATTGTTACACGTCATGTTG
* * *
5039640 AAAAAATATTATTGTTGCACATCATATT-
1 AAAAAATATTATTGTTACACGTCATGTTG
*
5039668 TAAAAATATT-TTGTTA
1 AAAAAATATTATTGTTA
5039684 TACTTTAATA
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
24 13 0.12
25 2 0.02
26 6 0.06
27 11 0.10
28 10 0.10
29 63 0.60
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (29 bp):
AAAAAATATTATTGTTACACGTCATGTTG
Found at i:5039586 original size:81 final size:85
Alignment explanation
Indices: 5039460--5039616 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 85
5039450 TACAAAAACA
* * **
5039460 TGTTACACATTATATATAAAAACATGTTATACGCCACAGTT-AAAAA-ATT-TTGTTACACGTTA
1 TGTTACACATCATATATAAAAACATGTTACACGCCACAGTTAAAAAATATTATTGTTACACGGCA
5039522 TG-TGAAAAAAAAATATTAT
66 TGTTGAAAAAAAAATATTAT
* * ** *
5039541 TGTTACACGTCATGTATAAAAACATGTTACACGTTA-TGTTGAAAAAATATTATTGTTACACGGC
1 TGTTACACATCATATATAAAAACATGTTACACGCCACAGTT-AAAAAATATTATTGTTACACGGC
5039605 ATGTTGAAAAAA
65 ATGTTGAAAAAA
5039617 TATTATTGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
80 3 0.05
81 30 0.48
82 5 0.08
83 3 0.05
84 13 0.21
85 8 0.13
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (85 bp):
TGTTACACATCATATATAAAAACATGTTACACGCCACAGTTAAAAAATATTATTGTTACACGGCA
TGTTGAAAAAAAAATATTAT
Found at i:5043420 original size:27 final size:24
Alignment explanation
Indices: 5043365--5043410 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5043355 TAATAAAATG
5043365 TTTTTGAATATGACGTGCAACATA
1 TTTTTGAATATGACGTGCAACATA
* *
5043389 TTTTTGTATATGACGTGTAACA
1 TTTTTGAATATGACGTGCAACA
5043411 ACAGTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTTTGAATATGACGTGCAACATA
Found at i:5043568 original size:45 final size:45
Alignment explanation
Indices: 5043517--5043613 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
5043507 TAACATAGCA
* *
5043517 TGTAACAACCTAACCATGACGTGTTACATATTTTTATACAT-GATG
1 TGTAACAACCTAACCATGACGTGTAACATATTTCTATACATAG-TG
* * * *
5043562 TGTAACAACTTAACCATGGCGTGTAACATGTTTCTGTACATAGTG
1 TGTAACAACCTAACCATGACGTGTAACATATTTCTATACATAGTG
5043607 TGTAACA
1 TGTAACA
5043614 TCATGATATG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (45 bp):
TGTAACAACCTAACCATGACGTGTAACATATTTCTATACATAGTG
Found at i:5059724 original size:41 final size:41
Alignment explanation
Indices: 5059644--5059724 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 41
5059634 AATCTAAATT
* * *
5059644 TATTATAACATATTATATATTAACAATCCAATCTTATAACC
1 TATTATAACATATAATATATCAACAATCCAATCTAATAACC
* * *
5059685 TATTATAATATATAATATATCAATAATTCAAT-TCAATAAC
1 TATTATAACATATAATATATCAACAATCCAATCT-AATAAC
5059725 TTAATATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (41 bp):
TATTATAACATATAATATATCAACAATCCAATCTAATAACC
Found at i:5062912 original size:35 final size:35
Alignment explanation
Indices: 5062873--5062949 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
5062863 AGTAGTATTC
* *
5062873 CACTTATTCTAATTATTTCGTGTGAAGTAATACTT
1 CACTTATTCTAATTATTTCATGTGAAGTAACACTT
* * * * * *
5062908 CACTTGTTTTAGTTGTTTTATGTGAAGTAGCACTT
1 CACTTATTCTAATTATTTCATGTGAAGTAACACTT
5062943 CACTTAT
1 CACTTAT
5062950 AATAGTTGTT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (35 bp):
CACTTATTCTAATTATTTCATGTGAAGTAACACTT
Found at i:5062956 original size:35 final size:35
Alignment explanation
Indices: 5062893--5062961 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
5062883 AATTATTTCG
* * **
5062893 TGTGAAGTAATACTTCACTTGTTTTAGTTGTTTTA
1 TGTGAAGTAACACTTCACTTATAATAGTTGTTTTA
*
5062928 TGTGAAGTAGCACTTCACTTATAATAGTTGTTTT
1 TGTGAAGTAACACTTCACTTATAATAGTTGTTTT
5062962 TATTATTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (35 bp):
TGTGAAGTAACACTTCACTTATAATAGTTGTTTTA
Found at i:5063556 original size:2 final size:2
Alignment explanation
Indices: 5063551--5063575 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5063541 TTTTTTTATG
5063551 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 T
5063576 GTTCAAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5069218 original size:2 final size:2
Alignment explanation
Indices: 5069213--5069248 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5069203 ATATAGTGAG
5069213 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
5069249 ATGTTTCTCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5076519 original size:26 final size:26
Alignment explanation
Indices: 5076483--5076532 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
5076473 AAAGGCAAAA
5076483 GCAGCCCTCAAAAGCAGCAAAAGCTT
1 GCAGCCCTCAAAAGCAGCAAAAGCTT
5076509 GCAGCCCTCAAAAGCAGCAAAAGC
1 GCAGCCCTCAAAAGCAGCAAAAGC
5076533 AAACAGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.32, G:0.20, T:0.08
Consensus pattern (26 bp):
GCAGCCCTCAAAAGCAGCAAAAGCTT
Found at i:5076604 original size:20 final size:21
Alignment explanation
Indices: 5076558--5076619 Score: 90
Period size: 20 Copynumber: 2.9 Consensus size: 21
5076548 TCACACCGAC
5076558 AAATGAAATGCAAATGTAAAAGAA
1 AAATGAAATGCAAATGT---AGAA
5076582 AAATGAAATGCAAATGT-GAA
1 AAATGAAATGCAAATGTAGAA
5076602 AAATGAAATGCAAATGTA
1 AAATGAAATGCAAATGTA
5076620 AAGGGATCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 20 0.54
24 17 0.46
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.19
Consensus pattern (21 bp):
AAATGAAATGCAAATGTAGAA
Found at i:5076803 original size:19 final size:19
Alignment explanation
Indices: 5076779--5076816 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5076769 AAATCATTTT
*
5076779 CAATTGTTTTGATTTCAAA
1 CAATTGTTCTGATTTCAAA
5076798 CAATTGTTCTGATTTCAAA
1 CAATTGTTCTGATTTCAAA
5076817 TCTATCTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (19 bp):
CAATTGTTCTGATTTCAAA
Found at i:5076883 original size:2 final size:2
Alignment explanation
Indices: 5076876--5076910 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5076866 CTGGACACAT
5076876 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 T
5076911 GCTTAAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5084562 original size:2 final size:2
Alignment explanation
Indices: 5084555--5084593 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5084545 CTCTTTTCAA
5084555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5084594 AGAAGAGGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5085191 original size:64 final size:64
Alignment explanation
Indices: 5085084--5085229 Score: 195
Period size: 64 Copynumber: 2.3 Consensus size: 64
5085074 TCATTGTATT
* * *
5085084 TTTTCAATGCATTTTGCATGCATGTTCTTAATTTCCTTGTCCAAGGAAAAAACAGCATTT-TCCA
1 TTTTCAAAGCATTTTGCATGCACGTTCTTAATTTCCTTGTCCAAGGAAAAAACAAC-TTTGTCCA
* * * * *
5085148 TTTTCAAAGCATTTTGCATGTACGTTTTTAATTTCTTTTTCCAAGGAAAAAACAACTTTGTGCA
1 TTTTCAAAGCATTTTGCATGCACGTTCTTAATTTCCTTGTCCAAGGAAAAAACAACTTTGTCCA
*
5085212 TTTTCAACGCATTTTGCA
1 TTTTCAAAGCATTTTGCA
5085230 CGCATATTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 3 0.04
64 69 0.96
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (64 bp):
TTTTCAAAGCATTTTGCATGCACGTTCTTAATTTCCTTGTCCAAGGAAAAAACAACTTTGTCCA
Found at i:5110401 original size:21 final size:20
Alignment explanation
Indices: 5110373--5110412 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5110363 TAAATATATG
5110373 AAAATATTATAAAAATAAAA
1 AAAATATTATAAAAATAAAA
*
5110393 AAAATTATTATTAAAATAAA
1 AAAA-TATTATAAAAATAAA
5110413 TAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATATTATAAAAATAAAA
Found at i:5115678 original size:13 final size:13
Alignment explanation
Indices: 5115660--5115702 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
5115650 CATCAGTGTC
5115660 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
5115673 AAAAAAGGAAGGAAA
1 AAAAAA-GAA-GAAA
*
5115688 AAAAGAGAGAGAAA
1 AAAAAAGA-AGAAA
5115702 A
1 A
5115703 TAGTTCTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.23
14 10 0.38
15 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:5116255 original size:17 final size:17
Alignment explanation
Indices: 5116230--5116263 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5116220 TGCTTCTTTG
*
5116230 TAAGTTAGAAAATTTTC
1 TAAGCTAGAAAATTTTC
5116247 TAAGCTAGAAAATTTTC
1 TAAGCTAGAAAATTTTC
5116264 CAAATTTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (17 bp):
TAAGCTAGAAAATTTTC
Found at i:5120944 original size:24 final size:25
Alignment explanation
Indices: 5120907--5120958 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
5120897 ACCACTAGAG
5120907 AAAGAAAAATAG-AAGAAAGAAAAAC
1 AAAGAAAAATAGAAAG-AAGAAAAAC
*
5120932 AAAGAAAAA-AGAAAGAAGGAAAAC
1 AAAGAAAAATAGAAAGAAGAAAAAC
5120956 AAA
1 AAA
5120959 ATTCCACTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (25 bp):
AAAGAAAAATAGAAAGAAGAAAAAC
Found at i:5121170 original size:34 final size:34
Alignment explanation
Indices: 5121106--5121171 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
5121096 CCTGGTATAG
**
5121106 TTGCTGTCGGTTAGGAAGGGTAGAGCTGGGGTAT
1 TTGCTGTCGGTTAGGAAGGAAAGAGCTGGGGTAT
5121140 TTGCTGTCGGTTA-GAGAGGAAAG-GCTTGGGGT
1 TTGCTGTCGGTTAGGA-AGGAAAGAGC-TGGGGT
5121172 TAGAATCGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.18, C:0.09, G:0.44, T:0.29
Consensus pattern (34 bp):
TTGCTGTCGGTTAGGAAGGAAAGAGCTGGGGTAT
Found at i:5130144 original size:38 final size:36
Alignment explanation
Indices: 5130073--5130144 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 36
5130063 TGAAATAGAG
* *
5130073 TTCAATACAATGTGTTTTATGGATCAAGTACAACTT
1 TTCAATACAATGTGTTTTATGGATAAAGCACAACTT
* *
5130109 TTCAATACAATGCCTTTTTTATGGTTAAAGCACAAC
1 TTCAATACAATG--TGTTTTATGGATAAAGCACAAC
5130145 CACTCTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 12 0.40
38 18 0.60
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (36 bp):
TTCAATACAATGTGTTTTATGGATAAAGCACAACTT
Found at i:5130383 original size:24 final size:24
Alignment explanation
Indices: 5130349--5130397 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5130339 TGGAAGACTT
* *
5130349 AAATGCCAGAAGAGAGGTAAAAAG
1 AAATGCAAGAACAGAGGTAAAAAG
*
5130373 AAATGCAAGAACAGAGGTATAAAG
1 AAATGCAAGAACAGAGGTAAAAAG
5130397 A
1 A
5130398 GTATTGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.08, G:0.27, T:0.10
Consensus pattern (24 bp):
AAATGCAAGAACAGAGGTAAAAAG
Found at i:5140755 original size:18 final size:18
Alignment explanation
Indices: 5140732--5140778 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
5140722 TTACTTATGT
5140732 GTGTGTGTGTGCGCGCAC
1 GTGTGTGTGTGCGCGCAC
5140750 GTGTGTGTGTGCGCGCAC
1 GTGTGTGTGTGCGCGCAC
5140768 GTGTGTGTGTG
1 GTGTGTGTGTG
5140779 AGAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.04, C:0.17, G:0.47, T:0.32
Consensus pattern (18 bp):
GTGTGTGTGTGCGCGCAC
Found at i:5152864 original size:27 final size:28
Alignment explanation
Indices: 5152834--5152903 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
5152824 AACGATATTG
**
5152834 AAAATGTAGTTGTTATTCGGCATGTT-A
1 AAAATGTAGTTGTTATAAGGCATGTTGA
* * *
5152861 AAAATTTAATTGTTATAAGTCATGTTGA
1 AAAATGTAGTTGTTATAAGGCATGTTGA
5152889 AAAATGTAGTTGTTA
1 AAAATGTAGTTGTTA
5152904 CATGTCATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (28 bp):
AAAATGTAGTTGTTATAAGGCATGTTGA
Found at i:5152901 original size:28 final size:28
Alignment explanation
Indices: 5152834--5152916 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
5152824 AACGATATTG
** *
5152834 AAAATGTAGTTGTTATTCGGCATGTT-A
1 AAAATGTAGTTGTTATAAGTCATGTTGA
* *
5152861 AAAATTTAATTGTTATAAGTCATGTTGA
1 AAAATGTAGTTGTTATAAGTCATGTTGA
* *
5152889 AAAATGTAGTTGTTACATGTCATGTTGA
1 AAAATGTAGTTGTTATAAGTCATGTTGA
5152917 GATTCAGTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 21 0.46
28 25 0.54
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (28 bp):
AAAATGTAGTTGTTATAAGTCATGTTGA
Found at i:5153029 original size:27 final size:27
Alignment explanation
Indices: 5152999--5153066 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
5152989 GTCATGTTAT
*
5152999 AAATTTAGTTATTACATGCGATGATGA
1 AAATTTAGTTATTACATGCCATGATGA
* * * *
5153026 AAATATAGTTGTTACATTCCATGTTGA
1 AAATTTAGTTATTACATGCCATGATGA
*
5153053 AGATTTAGTTATTA
1 AAATTTAGTTATTA
5153067 TAAAGCAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (27 bp):
AAATTTAGTTATTACATGCCATGATGA
Found at i:5163169 original size:17 final size:17
Alignment explanation
Indices: 5163149--5163181 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5163139 TTCTTGATAA
5163149 AATAA-AACTCTTTATTG
1 AATAATAACT-TTTATTG
5163166 AATAATAACTTTTATT
1 AATAATAACTTTTATT
5163182 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (17 bp):
AATAATAACTTTTATTG
Found at i:5163484 original size:29 final size:28
Alignment explanation
Indices: 5163333--5163487 Score: 170
Period size: 29 Copynumber: 5.4 Consensus size: 28
5163323 TCTTGTCTTT
*
5163333 AATTAAGACAAAAATATTTTATCTTATCTA
1 AATTAAGACAAAAATATTTT-T-TTGTCTA
* * * * *
5163363 AATTGAGACAAATATGTTTTCTTATCTA
1 AATTAAGACAAAAATATTTTTTTGTCTA
*
5163391 GATTAAGACAAAAAATATTTTTTTGTCTTA
1 AATTAAGAC-AAAAATATTTTTTTGTC-TA
*
5163421 AATTAA-A-AAAAATATTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTTTTGTCTA
*
5163447 AATTAAGACCAAATATATTTTTTTGTCTA
1 AATTAAGA-CAAAAATATTTTTTTGTCTA
5163476 AATTAAGACAAA
1 AATTAAGACAAA
5163488 CATGTTAAAG
Statistics
Matches: 106, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.08
27 17 0.16
28 18 0.17
29 39 0.37
30 24 0.23
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (28 bp):
AATTAAGACAAAAATATTTTTTTGTCTA
Found at i:5170197 original size:15 final size:15
Alignment explanation
Indices: 5170177--5170207 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5170167 AGAATGTCGA
*
5170177 CTCAAACACAGCAGC
1 CTCAAACACAACAGC
5170192 CTCAAACACAACAGC
1 CTCAAACACAACAGC
5170207 C
1 C
5170208 CGTTGTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.42, G:0.10, T:0.06
Consensus pattern (15 bp):
CTCAAACACAACAGC
Found at i:5170606 original size:33 final size:33
Alignment explanation
Indices: 5170496--5170645 Score: 122
Period size: 33 Copynumber: 4.5 Consensus size: 33
5170486 AAGGGTTCAA
* * * * *
5170496 AATGCCCGGAAATGGAGATCCCAGAGGGTTCAG
1 AATGCCTGGAAATGGGGATCCCACAGGATTTAG
* * ** **
5170529 AATTCCT-GAACATGGGGATCCTAGGGGAACTAG
1 AATGCCTGGAA-ATGGGGATCCCACAGGATTTAG
* * *
5170562 AGTGCCAGGAAATGGGGATCCCGCAGGATTTAG
1 AATGCCTGGAAATGGGGATCCCACAGGATTTAG
* *
5170595 AATGCCTGGAAATGGGGATCCCACGGGATTCAG
1 AATGCCTGGAAATGGGGATCCCACAGGATTTAG
* *
5170628 AATGCCTCGACATGGGGA
1 AATGCCTGGAAATGGGGA
5170646 CATCAAAGGT
Statistics
Matches: 90, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
32 3 0.03
33 84 0.93
34 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.33, T:0.18
Consensus pattern (33 bp):
AATGCCTGGAAATGGGGATCCCACAGGATTTAG
Found at i:5179392 original size:30 final size:30
Alignment explanation
Indices: 5179356--5179449 Score: 179
Period size: 30 Copynumber: 3.1 Consensus size: 30
5179346 GCTAGGAGAT
*
5179356 GGTGGTGATTGCTGCTTAGGAGGGCTAGGA
1 GGTGGTGATTTCTGCTTAGGAGGGCTAGGA
5179386 GGTGGTGATTTCTGCTTAGGAGGGCTAGGA
1 GGTGGTGATTTCTGCTTAGGAGGGCTAGGA
5179416 GGTGGTGATTTCTGCTTAGGAGGGCTAGGA
1 GGTGGTGATTTCTGCTTAGGAGGGCTAGGA
5179446 GGTG
1 GGTG
5179450 ACTGGGATGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.16, C:0.10, G:0.46, T:0.29
Consensus pattern (30 bp):
GGTGGTGATTTCTGCTTAGGAGGGCTAGGA
Found at i:5182301 original size:158 final size:158
Alignment explanation
Indices: 5182008--5182324 Score: 440
Period size: 158 Copynumber: 2.0 Consensus size: 158
5181998 TTTTTTTCTC
* ** *
5182008 CAAACTAAATAAGTGTACTAAACAAAGTGAAAATCTAATGCTATGTTTTCTTTCTACTTTGTCTA
1 CAAACTAAATAAGTATACTAAACAAAGCAAAAAACTAATGCTATGTTTTCTTTCTACTTTGTCTA
* *
5182073 TTTATACTGATGAATCTGAAAACTTATATTTAAATTGTTAATGAATTTTTATGTCACAAATTTAC
66 TTTATACTGATGAATCTGAAAACTTATATTTAAATTGTTAATAAAATTTTATGTCACAAATTTAC
*
5182138 CTAATGTGAAAATTTAATATTGATTTTT
131 CTAATGTGAAAATTTAATATTAATTTTT
* * *
5182166 CAAACTAAATAAGTATACTAAACAAAGCAAAAAACTTATGTTAAT-TTTTCATTT-TATTTTGTC
1 CAAACTAAATAAGTATACTAAACAAAGCAAAAAACTAATGCT-ATGTTTTC-TTTCTACTTTGTC
* * * *
5182229 TATTTATATTGGTGAATCTGAAAACTTATATTTAAATTGTTAATAAAATTTTATGTTATAAATTT
64 TATTTATACTGATGAATCTGAAAACTTATATTTAAATTGTTAATAAAATTTTATGTCACAAATTT
*** *
5182294 GGGTAATGTGAAAATTTAATGTTAATTTTT
129 ACCTAATGTGAAAATTTAATATTAATTTTT
5182324 C
1 C
5182325 TTTCTATTTT
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
158 134 0.96
159 5 0.04
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (158 bp):
CAAACTAAATAAGTATACTAAACAAAGCAAAAAACTAATGCTATGTTTTCTTTCTACTTTGTCTA
TTTATACTGATGAATCTGAAAACTTATATTTAAATTGTTAATAAAATTTTATGTCACAAATTTAC
CTAATGTGAAAATTTAATATTAATTTTT
Found at i:5184367 original size:26 final size:25
Alignment explanation
Indices: 5184312--5184368 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
5184302 TATGGATAAA
* *
5184312 TTATATATATAATATTTATACAATT
1 TTATATACATAATATTCATACAATT
*
5184337 ATATATACATATATATTCATA-ACATT
1 TTATATACATA-ATATTCATACA-ATT
5184363 TTATAT
1 TTATAT
5184369 TACGAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATATACATAATATTCATACAATT
Found at i:5184657 original size:15 final size:15
Alignment explanation
Indices: 5184622--5184670 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5184612 TCTTCTAAAT
* * *
5184622 ATATATAAAAATATC
1 ATATATATATATATA
5184637 ATATATATTAGTATATA
1 ATATATA-TA-TATATA
5184654 ATATATATATATATA
1 ATATATATATATATA
5184669 AT
1 AT
5184671 TAGTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 15 0.52
16 3 0.10
17 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:5184668 original size:17 final size:17
Alignment explanation
Indices: 5184619--5184668 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5184609 AACTCTTCTA
* *
5184619 AATATATATAAAAATAT
1 AATATATATATATATAT
*
5184636 CATATATAT-TAGTATAT
1 AATATATATATA-TATAT
5184653 AATATATATATATATA
1 AATATATATATATATA
5184669 ATTAGTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.04
17 24 0.89
18 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:5202434 original size:14 final size:15
Alignment explanation
Indices: 5202409--5202437 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5202399 CTGATTTATA
5202409 TATTTATTTAAATTT
1 TATTTATTTAAATTT
5202424 TATTT-TTTAAATTT
1 TATTTATTTAAATTT
5202438 AAATTATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTATTTAAATTT
Found at i:5203810 original size:27 final size:27
Alignment explanation
Indices: 5203772--5203828 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
5203762 CATACAGAGT
5203772 CTTGCTGGAACTCACACTGCTTAATTG
1 CTTGCTGGAACTCACACTGCTTAATTG
5203799 CTTGCTGGAACTCACACTGCTTAATTG
1 CTTGCTGGAACTCACACTGCTTAATTG
5203826 CTT
1 CTT
5203829 ATTACATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (27 bp):
CTTGCTGGAACTCACACTGCTTAATTG
Found at i:5203840 original size:27 final size:27
Alignment explanation
Indices: 5203780--5203834 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5203770 GTCTTGCTGG
* **
5203780 AACTCACACTGCTTAATTGCTTGCTGG
1 AACTCACACTGCTTAATTGCTTACTAC
*
5203807 AACTCACACTGCTTAATTGCTTATTAC
1 AACTCACACTGCTTAATTGCTTACTAC
5203834 A
1 A
5203835 TATCACCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (27 bp):
AACTCACACTGCTTAATTGCTTACTAC
Found at i:5211813 original size:15 final size:18
Alignment explanation
Indices: 5211774--5211814 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
5211764 TATATTTTAG
5211774 TATTTTAATAGTATTGAA
1 TATTTTAATAGTATTGAA
*
5211792 TAATTTAA-A-TATT-AA
1 TATTTTAATAGTATTGAA
5211807 TATTTTAA
1 TATTTTAA
5211815 GTTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 1 0.05
18 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TATTTTAATAGTATTGAA
Found at i:5217474 original size:17 final size:18
Alignment explanation
Indices: 5217438--5217475 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5217428 TTCATATTAA
5217438 GCCAAATAGTCGAGATAG
1 GCCAAATAGTCGAGATAG
* *
5217456 GCCAAGTAGTCTA-ATAG
1 GCCAAATAGTCGAGATAG
5217473 GCC
1 GCC
5217476 GAACATAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (18 bp):
GCCAAATAGTCGAGATAG
Found at i:5218403 original size:12 final size:12
Alignment explanation
Indices: 5218386--5218417 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5218376 TAAAGAGTAT
5218386 GAGAGGGACTAG
1 GAGAGGGACTAG
5218398 GAGAGGGACTAG
1 GAGAGGGACTAG
5218410 GAGAGGGA
1 GAGAGGGA
5218418 ATAAAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.53, T:0.06
Consensus pattern (12 bp):
GAGAGGGACTAG
Found at i:5230390 original size:21 final size:20
Alignment explanation
Indices: 5230364--5230405 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5230354 TAATTTAAAA
5230364 TAAAATAACATACAATTTAAC
1 TAAAATAACATA-AATTTAAC
*
5230385 TAAAATAACTTAAA-TTAAC
1 TAAAATAACATAAATTTAAC
5230404 TA
1 TA
5230406 TTCAGTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATAACATAAATTTAAC
Found at i:5232134 original size:21 final size:21
Alignment explanation
Indices: 5232110--5232150 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5232100 AACACAATAA
* *
5232110 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
5232131 AAAGTATATATATATATATT
1 AAAGTAAATATATATATATT
5232151 AAAAATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:5232367 original size:343 final size:340
Alignment explanation
Indices: 5231716--5232834 Score: 1245
Period size: 343 Copynumber: 3.3 Consensus size: 340
5231706 TATCTTAAAC
*
5231716 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACAC--AATAAAAAGTAAATATATT
* * * * * *
5231781 TATATTT-AA--A-ATGTGTATATACTAAAAGTATTTTAGTATATATACAATAGTAATTAAATTT
64 TATATTTAAAGTATATATATATATATTAAAAATATTTTA-TATATAT--AATAATAATTATATTT
* * ** *
5231842 CTTTTAAATGAGCCCAATGTATATAAAGCATATATATTAAAAGACATTACAAGTCAATTAATAAT
126 CTTATAAATGA-ACCAACATATATAAAGTATATATATTAAAAGACATTACAAGT-AATTAATAAT
* * * * **
5231907 CATAGTTCCATTAATTAATTCAATTAACTATATGAAATTGTCCTTAATTACATGAAATTAAAAAA
189 AATAGTTTCATCAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTACATGAAATTAAAAAA
** * * * *
5231972 ATAACTAAATTTCAAAACTATTCTAATCTCACAACTTCCCTTTAGATTTATATATTATAGGTTTA
254 ATAACTAGGTTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAGGTTTATATATTATAAGTTTA
5232037 TATAAAAAAAGATATATATATATT
319 TATAAAAAAAG-TATA-ATATATT
* *
5232061 GTAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAATAAAAAGTAAATATGTTTA
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAATAAAAAGTAAATATATTTA
*
5232126 TATTTAAAGTATATATATATATATTAAAAATATTTTA-ATATAT-ATAATAATTATATTCCTTAT
66 TATTTAAAGTATATATATATATATTAAAAATATTTTATATATATAATAATAATTATATTTCTTAT
* *
5232189 AAATGAACCTAACATATATAGAGTATATATATTAAAAGGCATTACAAGCTAA-TAATAATAATAG
131 AAATGAACC-AACATATATAAAGTATATATATTAAAAGACATTACAAG-TAATTAATAATAATAG
* * *
5232253 TTTCATCAATTAATTTAATTAACTATATGAGTTTGCCCTTAATTACTTTAAATTTAAAAAAAATA
194 TTTCATCAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTACATGAAA-TT-AAAAAAATA
* *
5232318 ACTAGGTTTCAAAACTATTATAATCTCATAACTTCTCTTTAGGTTTATATATTATAAGTTTATAT
257 ACTAGGTTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAGGTTTATATATTATAAGTTTATAT
* *
5232383 AAATAAAGGTA-CATATATT
322 AAA-AAAAGTATAATATATT
* * *
5232402 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATATTAAAACAAAATAGAAAGTAAATATATT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTT--AACACAATAAAAAGTAAATATATT
*
5232467 TATATTTAAAGTATATATATA-CTA--AAAAAT-TTTAGTATATGTATAATAATAATTATTATTA
64 TATATTTAAAGTATATATATATATATTAAAAATATTT--TATA--TAT-ATAATAA-TA--ATTA
* * * * *
5232528 TATTTCTTATAAATTAA-C-ACAATATATAAACTACAAATATTAAAAGACATTAGAAGTTAATTA
121 TATTTCTTATAAATGAACCAAC-ATATATAAAGTATATATATTAAAAGACATTACAAG-TAATTA
* * *
5232591 ATAATTATAGTTTCATGAATTAATTTAATTAACTATATG-GATTTGTCCTTAATTTCATGAAATT
184 ATAATAATAGTTTCATCAATTAATTTAATTAACTATATGAG-TTTGTCCTTAATTACATGAAATT
** ** * * * * * *
5232655 AACCAAATAGTTAGG-TTAAAAATTATTCTAATCTCAAAAGTTCTCTTTAAGTATATAT-TTCTA
248 AAAAAAATAACTAGGTTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAGGTTTATATATTATA
* *
5232718 AGTTTATA-AATAACAGTATAA-ATATT
313 AGTTTATATAAAAAAAGTATAATATATT
* *
5232744 ATAATTAATAATTTTATATA-TTATAATTTTTATAATGTTAACATAA-AATAGGAAGTAAATATA
1 ATAATTAATAATTTTATA-AGTTATAATTTTTGTAATGTTAACACAATAA-A--AAGTAAATATA
*
5232807 TTTATATTAAAAGTATATATATATATAT
62 TTTATATTTAAAGTATATATATATATAT
5232835 ATAATAGTAA
Statistics
Matches: 665, Mismatches: 78, Indels: 63
0.83 0.10 0.08
Matches are distributed among these distances:
339 4 0.01
340 13 0.02
341 103 0.15
342 140 0.21
343 145 0.22
344 21 0.03
345 87 0.13
346 18 0.03
347 58 0.09
348 57 0.09
349 19 0.03
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (340 bp):
ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAATAAAAAGTAAATATATTTA
TATTTAAAGTATATATATATATATTAAAAATATTTTATATATATAATAATAATTATATTTCTTAT
AAATGAACCAACATATATAAAGTATATATATTAAAAGACATTACAAGTAATTAATAATAATAGTT
TCATCAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTACATGAAATTAAAAAAATAACTA
GGTTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAGGTTTATATATTATAAGTTTATATAAAA
AAAGTATAATATATT
Found at i:5232769 original size:15 final size:16
Alignment explanation
Indices: 5232742--5232777 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5232732 AGTATAAATA
5232742 TTATA-ATTAATAATT
1 TTATATATTAATAATT
5232757 TTATATATT-ATAATT
1 TTATATATTAATAATT
5232772 TT-TATA
1 TTATATA
5232778 ATGTTAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 13 0.65
16 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATATTAATAATT
Found at i:5232802 original size:342 final size:335
Alignment explanation
Indices: 5231716--5232829 Score: 1271
Period size: 342 Copynumber: 3.3 Consensus size: 335
5231706 TATCTTAAAC
5231716 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
* * * * * * * *
5231781 TATATTTAAAATGTGTATATACTAAAAGTATTTTAGTATATATACAATAGTAATTAAATTTCTTT
66 TATATTTAAAGTATATATATACTAAAA-AATTTTAGTATATATATAATAATAATTATATTTCTTA
* * *
5231846 TAAATGAGCCCAATGTATATAAAGC-ATATATATTAAAAGACATTACAAGTCAATTAATAATCAT
130 TAAATGA-ACCAA--TATATAAA-CTATATATATTAAAAGACATTACAAGTTAATTAATAATAAT
* * * * *
5231910 AGTTCCATTAATTAATTCAATTAACTATATGAAATTGTCCTTAATTACATGAAATTAAAAAAATA
191 AGTTTCATCAATTAATTTAATTAACTATATGGATTTGTCCTTAATTACATGAAATTAAAAAAATA
* ** * * *
5231975 ACTAAATTTCAAAACTATTCTAATCTCACAACTTCCCTTT-AGATTTATATATTATAGGTTTATA
256 A-TTAGGTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAAG-TTTATATATTATAAG-TT-TA
*
5232039 TAAAAAAAGATATATATATATT
317 TAAATAAAG-TATA-A-ATATT
* * *
5232061 GTAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACAC--AATAAAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
* *
5232124 TATATTTAAAGTATATATATATATATTAAAAATATTT--TA-ATATAT-ATAATAATTATATTCC
66 TATATTTAAAGTATATATATA-CTA--AAAAAT-TTTAGTATATATATAATAATAATTATATTTC
* * * *
5232185 TTATAAATGAACCTAACATATATAGAGTATATATATTAAAAGGCATTACAAGCTAA-TAATAATA
127 TTATAAATGAACC--A-ATATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATA
* * *
5232249 ATAGTTTCATCAATTAATTTAATTAACTATAT-GAGTTTGCCCTTAATTACTTTAAATTTAAAAA
189 ATAGTTTCATCAATTAATTTAATTAACTATATGGA-TTTGTCCTTAATTACATGAAA-TT-AAAA
* * * *
5232313 AAATAACTAGGTTTCAAAACTATTATAATCTCATAACTTCTCTTTAGGTTTATATATTATAAGTT
251 AAATAATTAGG-TTCAAAACTATTCTAATCTCAAAACTTCTCTTTAAGTTTATATATTATAAG-T
* *
5232378 TATATAAATAAAGGTACATATATT
314 T-TATAAATAAA-GTATAAATATT
* *
5232402 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATATTAAAACAAAATAGAAAGTAAATATATT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
5232467 TATATTTAAAGTATATATATACTAAAAAATTTTAGTATATGTATAATAATAATTATTATTATATT
66 TATATTTAAAGTATATATATACTAAAAAATTTTAGTATA--TAT-ATAATAA-TA--ATTATATT
* * * * *
5232532 TCTTATAAATTAACACAATATATAAACTACAAATATTAAAAGACATTAGAAGTTAATTAATAATT
125 TCTTATAAATGAAC-CAATATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATA
* * **
5232597 ATAGTTTCATGAATTAATTTAATTAACTATATGGATTTGTCCTTAATTTCATGAAATTAACCAAA
189 ATAGTTTCATCAATTAATTTAATTAACTATATGGATTTGTCCTTAATTACATGAAATTAAAAAAA
* * * * * *
5232662 TAGTTAGGTTAAAAATTATTCTAATCTCAAAAGTTCTCTTTAAGTATATAT-TTCTAAGTTTATA
254 TAATTAGGTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAAGTTTATATATTATAAGTTTATA
5232726 AATAACAGTATAAATATT
319 AATAA-AGTATAAATATT
* * *
5232744 ATAATTAATAATTTTATATA-TTATAATTTTTATAATGTTAACATAAAATAGGAAGTAAATATAT
1 ATAATTAATAATTTTATA-AGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATAT
*
5232808 TTATATTAAAAGTATATATATA
65 TTATATTTAAAGTATATATATA
5232830 TATATATAAT
Statistics
Matches: 657, Mismatches: 81, Indels: 65
0.82 0.10 0.08
Matches are distributed among these distances:
339 3 0.00
340 7 0.01
341 103 0.16
342 156 0.24
343 153 0.23
344 16 0.02
345 83 0.13
346 21 0.03
347 36 0.05
348 56 0.09
349 22 0.03
350 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (335 bp):
ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
TATATTTAAAGTATATATATACTAAAAAATTTTAGTATATATATAATAATAATTATATTTCTTAT
AAATGAACCAATATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATAATAGTTT
CATCAATTAATTTAATTAACTATATGGATTTGTCCTTAATTACATGAAATTAAAAAAATAATTAG
GTTCAAAACTATTCTAATCTCAAAACTTCTCTTTAAGTTTATATATTATAAGTTTATAAATAAAG
TATAAATATT
Found at i:5232826 original size:21 final size:21
Alignment explanation
Indices: 5232796--5232851 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
5232786 ATAAAATAGG
5232796 AAGTAAATATATTTATAT-TAA
1 AAGT-AATATATTTATATATAA
*
5232817 AAGTATATATATATATATATAA
1 AAGTA-ATATATTTATATATAA
*
5232839 TAGTAATTATATT
1 AAGTAA-TATATT
5232852 CCTTTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 16 0.55
22 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
AAGTAATATATTTATATATAA
Found at i:5241354 original size:21 final size:21
Alignment explanation
Indices: 5241329--5241371 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5241319 GGTACGTATA
5241329 TTGTTTTAATTAAGATAAGAG
1 TTGTTTTAATTAAGATAAGAG
* *
5241350 TTGTTTTAATTTATATAAGAG
1 TTGTTTTAATTAAGATAAGAG
5241371 T
1 T
5241372 ATTTATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (21 bp):
TTGTTTTAATTAAGATAAGAG
Found at i:5244727 original size:39 final size:40
Alignment explanation
Indices: 5244669--5244748 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
5244659 GCATTGTGAA
** *
5244669 AACACCAATTATGGTGAGGTTAG-AAGCCCCACTAAGGTG
1 AACACCAATTATGACGAGGTTAGAAAACCCCACTAAGGTG
* *
5244708 AACACCAATTTTGACGAGGTTAGAAAATCCCACTAAGGTG
1 AACACCAATTATGACGAGGTTAGAAAACCCCACTAAGGTG
5244748 A
1 A
5244749 GTAATGGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (40 bp):
AACACCAATTATGACGAGGTTAGAAAACCCCACTAAGGTG
Found at i:5245668 original size:14 final size:14
Alignment explanation
Indices: 5245642--5245678 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
5245632 AGTTTCTCAA
5245642 ACTTTTG-TTGACC
1 ACTTTTGTTTGACC
5245655 ACTTTTGTTTGACC
1 ACTTTTGTTTGACC
5245669 A--TTTGTTTGA
1 ACTTTTGTTTGA
5245679 GGGTGACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 7 0.30
14 7 0.30
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (14 bp):
ACTTTTGTTTGACC
Found at i:5247791 original size:43 final size:43
Alignment explanation
Indices: 5247744--5247886 Score: 171
Period size: 43 Copynumber: 3.3 Consensus size: 43
5247734 GCTATATAAA
*
5247744 TTTAAAATGAATAAGCTCTTCATCTGGAATAAGATTACGTAAC
1 TTTAAAAGGAATAAGCTCTTCATCTGGAATAAGATTACGTAAC
* * * *
5247787 TTTAAAAGGAATAAGCTCTTCATCTGGAATGAGGTTGCATAAC
1 TTTAAAAGGAATAAGCTCTTCATCTGGAATAAGATTACGTAAC
* * *
5247830 TTTAAAAGGAAAATAAGCTCCTCATCTAGAATAA-AGCTACGTAAC
1 TTTAAAAGG--AATAAGCTCTTCATCTGGAATAAGA-TTACGTAAC
*
5247875 TTCAAAAGGAAT
1 TTTAAAAGGAAT
5247887 CTTTAATGCA
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
43 50 0.60
45 34 0.40
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (43 bp):
TTTAAAAGGAATAAGCTCTTCATCTGGAATAAGATTACGTAAC
Found at i:5247862 original size:88 final size:86
Alignment explanation
Indices: 5247689--5247886 Score: 218
Period size: 88 Copynumber: 2.3 Consensus size: 86
5247679 TTGAAATGAG
* * * *
5247689 GCTACGTAACTTTAACGTAGGAATAAATTCCTCATCTAGAATGAGGCTATATAAATTTAAAATGA
1 GCTACGTAACTTTAA--AAGGAATAAACTCCTCATCTAGAATGAGGCTACATAAATTTAAAAGGA
* *
5247754 ATAAGCTCTTCATCTGGAAT-AA
64 ATAAGCTCCTCATCTAGAATAAA
* * * * * * *
5247776 GATTACGTAACTTTAAAAGGAATAAGCTCTTCATCTGGAATGAGGTTGCATAACTTTAAAAGGAA
1 G-CTACGTAACTTTAAAAGGAATAAACTCCTCATCTAGAATGAGGCTACATAAATTTAAAAGG--
5247841 AATAAGCTCCTCATCTAGAATAAA
63 AATAAGCTCCTCATCTAGAATAAA
*
5247865 GCTACGTAACTTCAAAAGGAAT
1 GCTACGTAACTTTAAAAGGAAT
5247887 CTTTAATGCA
Statistics
Matches: 92, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
86 37 0.40
87 1 0.01
88 51 0.55
89 3 0.03
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (86 bp):
GCTACGTAACTTTAAAAGGAATAAACTCCTCATCTAGAATGAGGCTACATAAATTTAAAAGGAAT
AAGCTCCTCATCTAGAATAAA
Found at i:5247875 original size:45 final size:43
Alignment explanation
Indices: 5247683--5247886 Score: 167
Period size: 43 Copynumber: 4.7 Consensus size: 43
5247673 CCTCAATTGA
* * * **
5247683 AATGAGGCTACGTAACTTTAACGTAGGAATAAATTCCTCATCTAG
1 AATGAAGCTACATAACTTTAA--AAGGAATAAGCTCCTCATCTAG
* * * * * *
5247728 AATGAGGCTATATAAATTTAAAATGAATAAGCTCTTCATCTGG
1 AATGAAGCTACATAACTTTAAAAGGAATAAGCTCCTCATCTAG
* * * *
5247771 AAT-AAGATTACGTAACTTTAAAAGGAATAAGCTCTTCATCTGG
1 AATGAAG-CTACATAACTTTAAAAGGAATAAGCTCCTCATCTAG
* * *
5247814 AATGAGGTTGCATAACTTTAAAAGGAAAATAAGCTCCTCATCTAG
1 AATGAAGCTACATAACTTTAAAAGG--AATAAGCTCCTCATCTAG
* * *
5247859 AATAAAGCTACGTAACTTCAAAAGGAAT
1 AATGAAGCTACATAACTTTAAAAGGAAT
5247887 CTTTAATGCA
Statistics
Matches: 129, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
42 2 0.02
43 72 0.56
44 2 0.02
45 53 0.41
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (43 bp):
AATGAAGCTACATAACTTTAAAAGGAATAAGCTCCTCATCTAG
Found at i:5253869 original size:31 final size:31
Alignment explanation
Indices: 5253829--5253901 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
5253819 CTCTCAACCG
* * *
5253829 TCTTTCTCTCAGCAGCTCTTCCTCTTTTCCC
1 TCTTTCTCTCAGCAGCTATTCCTCCTCTCCC
* *
5253860 TGTTTCTCTCAGCCGCTATTCCTCCTCTCCC
1 TCTTTCTCTCAGCAGCTATTCCTCCTCTCCC
5253891 TCTTTCTCTCA
1 TCTTTCTCTCA
5253902 ACCGGCTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.07, C:0.42, G:0.07, T:0.44
Consensus pattern (31 bp):
TCTTTCTCTCAGCAGCTATTCCTCCTCTCCC
Found at i:5253960 original size:77 final size:78
Alignment explanation
Indices: 5253800--5253949 Score: 223
Period size: 77 Copynumber: 1.9 Consensus size: 78
5253790 TTTTTCTCTC
* * * * * *
5253800 TTCCTCCTTTTCCCTTTTTCTCTCAACCGTCTTTCTCTCAGCAGCTCTTCCTCTTTTCCCTGTTT
1 TTCCTCCTTCTCCCTCTTTCTCTCAACCGGCTTTCTCTCAGCAGCTCTGCCTCCTTTCCCTATTT
5253865 CTCTCAGCCGCTA
66 CTCTCAGCCGCTA
5253878 TTCCTCC-TCTCCCTCTTTCTCTCAACCGGCTTTCTCTCAGCCA-CTCTGCCTCCTTTCCCTATT
1 TTCCTCCTTCTCCCTCTTTCTCTCAACCGGCTTTCTCTCAG-CAGCTCTGCCTCCTTTCCCTATT
5253941 TCTCTCAGC
65 TCTCTCAGC
5253950 TGTTTTTCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 56 0.86
78 9 0.14
ACGTcount: A:0.08, C:0.43, G:0.07, T:0.42
Consensus pattern (78 bp):
TTCCTCCTTCTCCCTCTTTCTCTCAACCGGCTTTCTCTCAGCAGCTCTGCCTCCTTTCCCTATTT
CTCTCAGCCGCTA
Found at i:5254899 original size:27 final size:26
Alignment explanation
Indices: 5254846--5254903 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
5254836 TTTTTATTTT
* * *
5254846 ATTTTTTTAAAAGTTAATAATTTATA
1 ATTTATTTAAAAATTAATAATTGATA
5254872 ATTTATTTAAAATATTAATAATTGATA
1 ATTTATTTAAAA-ATTAATAATTGATA
5254899 ATTTA
1 ATTTA
5254904 AATATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTTATTTAAAAATTAATAATTGATA
Found at i:5254915 original size:114 final size:116
Alignment explanation
Indices: 5254708--5254925 Score: 334
Period size: 114 Copynumber: 1.9 Consensus size: 116
5254698 CATTATAATA
*
5254708 TATACTTATTTATTTTTATTTTATTTTATTTTAAAATATTAATAATATATAGTTATTTAAAATAT
1 TATAATTATTTATTTTTATTTTATTTTATTTTAAAATATTAATAATATATAGTTATTTAAAATAT
*
5254773 TAATAATTGATCAGTTAAATATTGATATTTTATTTATAATCTAAAGGTTAT
66 TAATAATTGATAAGTTAAATATTGATATTTTATTTATAATCTAAAGGTTAT
* * *
5254824 TATAATTATTTATTTTTATTTTA-TTT-TTTTAAAA-GTTAATAATTTATAATTTATTTAAAATA
1 TATAATTATTTATTTTTATTTTATTTTATTTTAAAATATTAATAATATAT-AGTTATTTAAAATA
* * *
5254886 TTAATAATTGATAATTTAAATATTTATATTTTGTTTATAA
65 TTAATAATTGATAAGTTAAATATTGATATTTTATTTATAA
5254926 GTTAATCAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
113 11 0.12
114 57 0.61
115 3 0.03
116 22 0.24
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (116 bp):
TATAATTATTTATTTTTATTTTATTTTATTTTAAAATATTAATAATATATAGTTATTTAAAATAT
TAATAATTGATAAGTTAAATATTGATATTTTATTTATAATCTAAAGGTTAT
Found at i:5254958 original size:114 final size:115
Alignment explanation
Indices: 5254724--5254962 Score: 265
Period size: 114 Copynumber: 2.1 Consensus size: 115
5254714 TATTTATTTT
*
5254724 TATTTTATTTTATTTTAAAATATTAATAATATATAGTTATTTAAAATATTAATAATTGATCAGTT
1 TATTTTA-TTTATTTTAAAATATTAATAATATATAGTTATTTAAAATATTAATAATTGATAAGTT
* ** **
5254789 AAATATTGATATTTTATTTATAATCTAAAGGTTATTATAATTATTTATTTT
65 AAATATTGATATTTTATTTATAATCTAAAGGTTATCATAATTAAATATTAA
* * * *
5254840 TATTTTATTT-TTTTAAAA-GTTAATAATTTATAATTTATTTAAAATATTAATAATTGATAATTT
1 TATTTTATTTATTTTAAAATATTAATAATATAT-AGTTATTTAAAATATTAATAATTGATAAGTT
* * *
5254903 AAATATTTATATTTTGTTTATAAGT-TAATCA-G-TATCAT-TTTGAAATATTAA
65 AAATATTGATATTTTATTTATAA-TCTAA--AGGTTATCATAATT-AAATATTAA
5254954 TATTTTATT
1 TATTTTATT
5254963 ATAAATTTAA
Statistics
Matches: 105, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
113 13 0.12
114 79 0.75
115 5 0.05
116 8 0.08
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (115 bp):
TATTTTATTTATTTTAAAATATTAATAATATATAGTTATTTAAAATATTAATAATTGATAAGTTA
AATATTGATATTTTATTTATAATCTAAAGGTTATCATAATTAAATATTAA
Found at i:5255077 original size:42 final size:41
Alignment explanation
Indices: 5255017--5255130 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 41
5255007 TTTTTTGATA
* * *
5255017 TTAAA-ATTTATAATTTATTTAAAATATTGATAATTGAA-AAT
1 TTAAATATTAATATTTTATTTAAAAT-TTAATAATT-AACAAT
* * *
5255058 TTAAATATTAATATTTTATTTATAATTTAATCATTAACATT
1 TTAAATATTAATATTTTATTTAAAATTTAATAATTAACAAT
*
5255099 TTGAGATATTAATATTTTATTTATAAATTTAA
1 TT-AAATATTAATATTTTATTTA-AAATTTAA
5255131 ATATTTGTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.03
41 16 0.26
42 36 0.59
43 7 0.11
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (41 bp):
TTAAATATTAATATTTTATTTAAAATTTAATAATTAACAAT
Found at i:5255192 original size:20 final size:20
Alignment explanation
Indices: 5255176--5255247 Score: 62
Period size: 22 Copynumber: 3.6 Consensus size: 20
5255166 TTTTTTAATA
5255176 TTAAAAT-TT-ATAATTTAT
1 TTAAAATGTTAATAATTTAT
5255194 TTAAAATGTTAATAATTGATAAT
1 TTAAAATGTTAATAATT--T-AT
* *
5255217 TT-AAATGTCAATATTTTAT
1 TTAAAATGTTAATAATTTAT
*
5255236 TTACAAT-TTAAT
1 TTAAAATGTTAAT
5255248 CATAAGCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
18 7 0.16
19 10 0.23
20 10 0.23
22 13 0.30
23 4 0.09
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (20 bp):
TTAAAATGTTAATAATTTAT
Found at i:5255288 original size:316 final size:313
Alignment explanation
Indices: 5254832--5255441 Score: 804
Period size: 316 Copynumber: 1.9 Consensus size: 313
5254822 ATTATAATTA
5254832 TTTATTTTTATTTTATTTTTTTAAAAGTTAATAATTTATAATTTATTTAAAATATTAATAATTGA
1 TTTATTTTTATTTTATTTTTTTAAAAGTTAATAATTTATAATTTATTTAAAATATTAATAATTGA
** * * * *
5254897 TAATTTAAATATTTATATTTTGTTTATAAGTTAATCAGTATCATTTTGAAATATTAATATTTTAT
66 TAATTTAAATATCAATATTTTATTTACAAGTTAATCAGTAGCATTTTGAAATATTAATACTTTAT
* * * *
5254962 TATAAATTTAAATGTTATTATAATTATTTGTTTTTATTTTATTTATTTTTTGATATTAA-AATTT
131 TATAAATTTAAATGTTATTATAATTATTTATTTTTA-TTT-TTCA------AATATTAATAATTA
* * * * *
5255026 ATAATTTATTTAAAATATTGATAATTGAAAATTTAAATATTAATATTTTATTTATAATTTAATCA
188 ATAATTTAATGAAAATATTAATAATCGAAAATTTAAATATTAATATTTTATTTATAATTGAATCA
* * *
5255091 TTAACATTTTGAGA-TATTAATATTTTATTTATAAATTTAAATATTTGTATGATTATTTGTT
253 TTAACATTTT-AAACTATTAATATTTTAGTGATAAATTTAAATATTTGTATGATTATTTGTT
* *
5255152 TTTA-TTTTATTTTA-TTTTTTAATA-TTAA-AATTTATAATTTATTTAAAATGTTAATAATTGA
1 TTTATTTTTATTTTATTTTTTTAAAAGTTAATAATTTATAATTTATTTAAAATATTAATAATTGA
* * * *
5255213 TAATTTAAATGTCAATATTTTATTTACAATTTAATCA-TAAGCATTTTTAAATATTAATCCTTTA
66 TAATTTAAATATCAATATTTTATTTACAAGTTAATCAGT-AGCATTTTGAAATATTAATACTTTA
*
5255277 TT-TATAATTTAAATGTTATTATGATTATTTATTTTTATTTTTCAAATATTAATAATTAATAATT
130 TTATA-AATTTAAATGTTATTATAATTATTTATTTTTATTTTTCAAATATTAATAATTAATAATT
* * *
5255341 TAATGAAAATATTAATAATCGATAATTTAGATATTAATATTTTATTTGTAATTGAATCATTAACA
194 TAATGAAAATATTAATAATCGAAAATTTAAATATTAATATTTTATTTATAATTGAATCATTAACA
*
5255406 TTTTAAACTATTAATATTTTAGTGGTAAATTTAAAT
259 TTTTAAACTATTAATATTTTAGTGATAAATTTAAAT
5255442 GTTATTAGGA
Statistics
Matches: 257, Mismatches: 29, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
308 9 0.04
309 96 0.37
314 3 0.01
315 6 0.02
316 116 0.45
317 4 0.02
318 9 0.04
319 10 0.04
320 4 0.02
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (313 bp):
TTTATTTTTATTTTATTTTTTTAAAAGTTAATAATTTATAATTTATTTAAAATATTAATAATTGA
TAATTTAAATATCAATATTTTATTTACAAGTTAATCAGTAGCATTTTGAAATATTAATACTTTAT
TATAAATTTAAATGTTATTATAATTATTTATTTTTATTTTTCAAATATTAATAATTAATAATTTA
ATGAAAATATTAATAATCGAAAATTTAAATATTAATATTTTATTTATAATTGAATCATTAACATT
TTAAACTATTAATATTTTAGTGATAAATTTAAATATTTGTATGATTATTTGTT
Found at i:5255501 original size:150 final size:146
Alignment explanation
Indices: 5255156--5255504 Score: 371
Period size: 150 Copynumber: 2.3 Consensus size: 146
5255146 TTTGTTTTTA
** *
5255156 TTTTATTTTATTTTTTAATATTAAAATTTATAATTTATTTAAAATGTTAATAATTGATAATTTAA
1 TTTTATTTTATTTTGAAATATTAAAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAA
* * * ** *
5255221 ATGTCAATATTTTATTTACAATTTAATCA-TAAGCATTTTTAAATATTAATCCTTTATTTATAAT
66 ATATTAATATTTTATTTATAATTTAATCATTAA-CA-TTTTAAATATTAATATTTTATATA-AAT
5255285 TTAAATGTTATTATGAT--
128 TTAAATGTTATTATGATAG
* * * * *
5255302 TATTTATTTTTATTTTTCAAATATTAATAATTAATAATTTAATGAAAATATTAATAATCGATAAT
1 T-TTTA-TTTTA-TTTTGAAATATTAA-AATTTATAATTTATTTAAAATATTAATAATTGATAAT
* * * *
5255367 TTAGATATTAATATTTTATTTGTAATTGAATCATTAACATTTTAAACTATTAATATTTTAGTGGT
62 TTAAATATTAATATTTTATTTATAATTTAATCATTAACATTTTAAA-TATTAATATTTTA-T-AT
*
5255432 AAATTTAAATGTTATTAGGATAG
124 AAATTTAAATGTTATTATGATAG
* * * *
5255455 TTTTATTTTATTTTGAAATATTAATAATATGTAATATATTTCAAATATTA
1 TTTTATTTTATTTTGAAATATTAA-AATTTATAATTTATTTAAAATATTA
5255505 CCAGTGATTC
Statistics
Matches: 168, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
146 1 0.01
147 4 0.02
148 5 0.03
149 19 0.11
150 104 0.62
151 28 0.17
152 6 0.04
153 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (146 bp):
TTTTATTTTATTTTGAAATATTAAAATTTATAATTTATTTAAAATATTAATAATTGATAATTTAA
ATATTAATATTTTATTTATAATTTAATCATTAACATTTTAAATATTAATATTTTATATAAATTTA
AATGTTATTATGATAG
Found at i:5257612 original size:21 final size:22
Alignment explanation
Indices: 5257570--5257612 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5257560 AGTAACAGAA
*
5257570 GGCAGAAAAACATAAGAGATTG
1 GGCAGAAAAACATAAGAAATTG
5257592 GGCAGAAATAA-A-AAGAAATTG
1 GGCAGAAA-AACATAAGAAATTG
5257613 AATTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 9 0.47
23 2 0.11
ACGTcount: A:0.53, C:0.07, G:0.26, T:0.14
Consensus pattern (22 bp):
GGCAGAAAAACATAAGAAATTG
Found at i:5272930 original size:2 final size:2
Alignment explanation
Indices: 5272925--5272962 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5272915 GTGTGTGTGT
*
5272925 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5272963 TCGTGATTTG
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:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5273462 original size:57 final size:57
Alignment explanation
Indices: 5273398--5273506 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
5273388 TTAAAAAGTA
*
5273398 ATTAAATAAATAAAAGTTATTATGTAATTTAATTAAATACTTAATTTTGGAATTTTT
1 ATTAAATAAATAAAAGTTATTATGTAATTTAATTAAATACATAATTTTGGAATTTTT
* ** * * *
5273455 ATTAAATATATAGGATTTATTATGTAATTTAGTTAGATACATAATTTTGGAA
1 ATTAAATAAATAAAAGTTATTATGTAATTTAATTAAATACATAATTTTGGAA
5273507 ATTTAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (57 bp):
ATTAAATAAATAAAAGTTATTATGTAATTTAATTAAATACATAATTTTGGAATTTTT
Found at i:5280181 original size:16 final size:16
Alignment explanation
Indices: 5280160--5280190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5280150 GTGAGTTTTT
*
5280160 TTTGTTCATTGATTTG
1 TTTGTTCATTAATTTG
5280176 TTTGTTCATTAATTT
1 TTTGTTCATTAATTT
5280191 TTTTTAATAT
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:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (16 bp):
TTTGTTCATTAATTTG
Found at i:5282369 original size:16 final size:16
Alignment explanation
Indices: 5282348--5282378 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5282338 CACTCAAAAC
5282348 AAATAATATATTAATA
1 AAATAATATATTAATA
*
5282364 AAATAATATTTTAAT
1 AAATAATATATTAAT
5282379 TATTATCAAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAATATATTAATA
Found at i:5283660 original size:3 final size:3
Alignment explanation
Indices: 5283652--5283688 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5283642 TAGATATCTA
5283652 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5283689 TTACTTGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5284466 original size:40 final size:40
Alignment explanation
Indices: 5284396--5284481 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
5284386 AAAGGAAGCA
*
5284396 AAATTAAAATAAAATATATAATATACAAAAT-TATATTAAG
1 AAATGAAAATAAAATATATAATATACAAAATATAT-TTAAG
* * *
5284436 AAATGAAAATACAATATATGATATTA-AAAATATATTTTAG
1 AAATGAAAATAAAATATATAATA-TACAAAATATATTTAAG
5284476 AAATGA
1 AAATGA
5284482 TATTATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
40 35 0.88
41 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (40 bp):
AAATGAAAATAAAATATATAATATACAAAATATATTTAAG
Found at i:5286122 original size:3 final size:3
Alignment explanation
Indices: 5286114--5286141 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5286104 GATATCTACA
5286114 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5286142 TATTTTACTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5286431 original size:18 final size:18
Alignment explanation
Indices: 5286398--5286440 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5286388 TCCCAAACTC
5286398 TTTTTTTCAAGTTTAATT
1 TTTTTTTCAAGTTTAATT
5286416 TTTTTCTTCAAG-TTAATT
1 TTTTT-TTCAAGTTTAATT
5286434 TTTTTTT
1 TTTTTTT
5286441 TACTTCCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.08
18 16 0.67
19 6 0.25
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTTTCAAGTTTAATT
Found at i:5295655 original size:9 final size:9
Alignment explanation
Indices: 5295641--5295670 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5295631 CACTTGTTTG
5295641 CTCTAAAAT
1 CTCTAAAAT
5295650 CTCTAAAAT
1 CTCTAAAAT
5295659 GCTCTAAAAT
1 -CTCTAAAAT
5295669 CT
1 CT
5295671 TCAAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.33
Consensus pattern (9 bp):
CTCTAAAAT
Found at i:5295665 original size:10 final size:10
Alignment explanation
Indices: 5295639--5295668 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5295629 TTCACTTGTT
5295639 TGCTCTAAAA
1 TGCTCTAAAA
5295649 T-CTCTAAAA
1 TGCTCTAAAA
5295658 TGCTCTAAAA
1 TGCTCTAAAA
5295668 T
1 T
5295669 CTTCAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (10 bp):
TGCTCTAAAA
Found at i:5305680 original size:27 final size:27
Alignment explanation
Indices: 5305578--5305682 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
5305568 CAAAATATAT
*
5305578 AAATAATGTATTATTTT-ACTGAAAGTA
1 AAATAATATATTATTTTGA-TGAAAGTA
* * * * *
5305605 AAACAGTGTATTATTTTGATAAAAATA
1 AAATAATATATTATTTTGATGAAAGTA
*
5305632 AAATAATATATTATTTTAATGAAAGTA
1 AAATAATATATTATTTTGATGAAAGTA
*
5305659 AAATAATTTATT-TTTTGGATGAAA
1 AAATAATATATTATTTT-GATGAAA
5305683 AGAAAGCTTG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 4 0.06
27 59 0.92
28 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (27 bp):
AAATAATATATTATTTTGATGAAAGTA
Found at i:5308893 original size:62 final size:62
Alignment explanation
Indices: 5308817--5308936 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
5308807 TGAGTTGGTC
* * *
5308817 TTTGATTTTCCCAAGCAAAATATATTTTACCGTTATAAACTAAAATATTATAGAATCAAACT
1 TTTGATTCTCCCAAGCAAAATATATTCTACCGTTATAAACTAAAATATTACAGAATCAAACT
* * * * *
5308879 TTTGATTCTGCCAAGCAAAATATATTCTGCTGTTATAAACTAAATTGTTACAGAATCA
1 TTTGATTCTCCCAAGCAAAATATATTCTACCGTTATAAACTAAAATATTACAGAATCA
5308937 GAGTTTTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (62 bp):
TTTGATTCTCCCAAGCAAAATATATTCTACCGTTATAAACTAAAATATTACAGAATCAAACT
Found at i:5315349 original size:15 final size:15
Alignment explanation
Indices: 5315329--5315358 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5315319 TGGACAATTG
*
5315329 TTTAGGTTGTTCCTC
1 TTTAGGATGTTCCTC
5315344 TTTAGGATGTTCCTC
1 TTTAGGATGTTCCTC
5315359 ATTAATCGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (15 bp):
TTTAGGATGTTCCTC
Found at i:5324269 original size:40 final size:40
Alignment explanation
Indices: 5324180--5324261 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
5324170 TCACTGCGAT
5324180 ATAAGATTGCAATGCAATCACATTACAGCCAAGGGATGTA
1 ATAAGATTGCAATGCAATCACATTACAGCCAAGGGATGTA
*
5324220 ATAAGATTGCAATGCAATCACATTACAGCTAAGGGATGTA
1 ATAAGATTGCAATGCAATCACATTACAGCCAAGGGATGTA
5324260 AT
1 AT
5324262 GTGATTGCGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (40 bp):
ATAAGATTGCAATGCAATCACATTACAGCCAAGGGATGTA
Found at i:5324396 original size:15 final size:15
Alignment explanation
Indices: 5324376--5324407 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5324366 TACTGTTATA
5324376 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
5324391 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
5324406 AT
1 AT
5324408 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:5324433 original size:26 final size:25
Alignment explanation
Indices: 5324394--5324567 Score: 90
Period size: 26 Copynumber: 6.6 Consensus size: 25
5324384 AAAAAATATT
* *
5324394 AAAATAAAATATATAATATAAGAATCA
1 AAAATTAAA-ATATAATATAA-AATAA
*
5324421 AAAATTAAAATATAATATAATATAA
1 AAAATTAAAATATAATATAAAATAA
*
5324446 AAAATTAAAAT-TTATATAATATAGGTAAA
1 AAAATTAAAATATAATATAA-A-A--T-AA
*
5324475 ACAAATTAAAATAAAATATATAATATAA
1 A-AAATTAAAATATAATATA-AA-ATAA
*
5324503 AAAATATATTAAAGA-AATA-AAAATAA
1 AAAAT-TA--AAATATAATATAAAATAA
* *
5324529 AATATATAAGATTATAATA-ATAAAT-A
1 AAAAT-TAA-AATATAATATA-AAATAA
5324555 AAAA-TAAAATATA
1 AAAATTAAAATATA
5324568 TGACATTAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
23 5 0.04
24 11 0.09
25 16 0.13
26 32 0.27
27 18 0.15
28 7 0.06
29 8 0.07
30 14 0.12
31 8 0.07
32 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (25 bp):
AAAATTAAAATATAATATAAAATAA
Found at i:5324462 original size:24 final size:25
Alignment explanation
Indices: 5324375--5324468 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
5324365 ATACTGTTAT
*
5324375 AATTAAAATA-AA-A-AATAT-TAA
1 AATTAAAATATAATATAATATAAAA
* * *
5324396 AATAAAATATATAATATAAGAATCAAA
1 AATTAAA-ATATAATATAA-TATAAAA
5324423 AATTAAAATATAATATAATATAAAA
1 AATTAAAATATAATATAATATAAAA
*
5324448 AATTAAAAT-TTATATAATATA
1 AATTAAAATATAATATAATATA
5324469 GGTAAAACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
21 6 0.10
22 3 0.05
23 2 0.03
24 12 0.20
25 16 0.27
26 13 0.22
27 8 0.13
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (25 bp):
AATTAAAATATAATATAATATAAAA
Found at i:5324533 original size:33 final size:33
Alignment explanation
Indices: 5324483--5324567 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
5324473 AAACAAATTA
* *
5324483 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAA-ATAAAATATAAAAAATTATAAT-AAG
* * *
5324517 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATAAAAAATTATAATAAG
5324550 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
5324568 TGACATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAAAATTATAATAAG
Found at i:5324566 original size:57 final size:57
Alignment explanation
Indices: 5324503--5324682 Score: 179
Period size: 57 Copynumber: 3.2 Consensus size: 57
5324493 TATAATATAA
*
5324503 AAAATATATTAAAGAAATAAAAATAAAATATATAAGATTATAATAATAAATAAAAAT
1 AAAATATATTAAATAAATAAAAATAAAATATATAAGATTATAATAATAAATAAAAAT
* * * ** * * * * *
5324560 AAAATATATGACATTAAA-AATATATTTAAGACATGATATTAT-ATAA-AAATTAATAAT
1 AAAATATATTA-AATAAATAA-AAATAAAATATATAAGATTATAATAATAAA-TAAAAAT
* *
5324617 AAAAAATA-TAAATATATTAAAAATAAAATATATAAGATTATAATAATAAATAAAAAT
1 AAAATATATTAAATA-AATAAAAATAAAATATATAAGATTATAATAATAAATAAAAAT
5324674 AAAATATAT
1 AAAATATAT
5324683 GACATTAAAA
Statistics
Matches: 91, Mismatches: 24, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
55 3 0.03
56 19 0.21
57 48 0.53
58 21 0.23
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (57 bp):
AAAATATATTAAATAAATAAAAATAAAATATATAAGATTATAATAATAAATAAAAAT
Found at i:5324626 original size:24 final size:24
Alignment explanation
Indices: 5324599--5324666 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
5324589 GACATGATAT
5324599 TATATAAAAATTAATAATAAAAAA
1 TATATAAAAATTAATAATAAAAAA
* *
5324623 TATA-AATATATTAA-AA-ATAAAA
1 TATATAA-AAATTAATAATAAAAAA
* *
5324645 TATATAAGATTATAATAATAAA
1 TATATAAAAAT-TAATAATAAA
5324667 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
24 12 0.36
25 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
TATATAAAAATTAATAATAAAAAA
Done.