Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 31 of 64
Found at i:4824045 original size:4 final size:4
Alignment explanation
Indices: 4824019--4824074 Score: 60
Period size: 4 Copynumber: 14.0 Consensus size: 4
4824009 AGAATTATAT
* * * *
4824019 TGAA TGAA T-ACA TAAA TGGA TGAA TGAA TGAA TGAA TGAG TGAA TGAG
1 TGAA TGAA TGA-A TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
4824067 TGAA TGAA
1 TGAA TGAA
4824075 CAATTGACAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 1 0.02
4 41 0.95
5 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.25
Consensus pattern (4 bp):
TGAA
Found at i:4825655 original size:16 final size:15
Alignment explanation
Indices: 4825630--4825659 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4825620 TGCATGAGAA
4825630 CTTTTTTTTTCTTTG
1 CTTTTTTTTTCTTTG
4825645 CTTTCTTTTTTCTTT
1 CTTT-TTTTTTCTTT
4825660 TTTCAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (15 bp):
CTTTTTTTTTCTTTG
Found at i:4827462 original size:15 final size:15
Alignment explanation
Indices: 4827442--4827542 Score: 61
Period size: 15 Copynumber: 6.9 Consensus size: 15
4827432 GTGTACCAAA
4827442 TTTAGGGTTTAGGAT
1 TTTAGGGTTTAGGAT
*
4827457 TTTAGGGTCTAGGAT
1 TTTAGGGTTTAGGAT
* * *
4827472 TTT-GGATTTCAAGCT
1 TTTAGGGTTT-AGGAT
* *
4827487 TTT-GGGCTTAAG-T
1 TTTAGGGTTTAGGAT
*
4827500 TTCAGGGTTTGGAGGA-
1 TTTAGGGTTT--AGGAT
4827516 TTTAGGGTTTCA--AT
1 TTTAGGGTTT-AGGAT
4827530 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
4827543 TTTATGATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
13 5 0.08
14 22 0.33
15 28 0.42
16 11 0.17
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.44
Consensus pattern (15 bp):
TTTAGGGTTTAGGAT
Found at i:4827588 original size:29 final size:29
Alignment explanation
Indices: 4827503--4827714 Score: 189
Period size: 29 Copynumber: 7.3 Consensus size: 29
4827493 CTTAAGTTTC
*
4827503 AGGGTTTGGAGGATTTAGGGTTTCAATTTT
1 AGGGTTT-GAGGTTTTAGGGTTTCAATTTT
* * * *
4827533 AGGGTTT-AGG-TTTATGATTTTAGTTTT
1 AGGGTTTGAGGTTTTAGGGTTTCAATTTT
* *
4827560 AGAGTTTGAGGTTTTAGGGTTTCGATTTT
1 AGGGTTTGAGGTTTTAGGGTTTCAATTTT
* * * *
4827589 AATGTTTTGATGG-TTTAAGGTTTTAATTTT
1 -AGGGTTTGA-GGTTTTAGGGTTTCAATTTT
** * * *
4827619 AGGGTTCAAAGTTTTAGGGTTTCGACTTTA
1 AGGGTTTGAGGTTTTAGGGTTTC-AATTTT
* * *
4827649 AGGTTTTGAGGGTTTA-GGATTCAATTTT
1 AGGGTTTGAGGTTTTAGGGTTTCAATTTT
4827677 AGGGTTTGAGGTTTTAGGGTTTCAATTTT
1 AGGGTTTGAGGTTTTAGGGTTTCAATTTT
4827706 AGGGTTTGA
1 AGGGTTTGA
4827715 AAGGTTTAAA
Statistics
Matches: 139, Mismatches: 36, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
27 19 0.14
28 25 0.18
29 51 0.37
30 42 0.30
31 2 0.01
ACGTcount: A:0.20, C:0.03, G:0.29, T:0.48
Consensus pattern (29 bp):
AGGGTTTGAGGTTTTAGGGTTTCAATTTT
Found at i:4827620 original size:59 final size:58
Alignment explanation
Indices: 4827494--4827744 Score: 240
Period size: 59 Copynumber: 4.3 Consensus size: 58
4827484 GCTTTTGGGC
* * * * *
4827494 TTAAGTTTCAGGGTTTGGAGGATTTAGGGTTTCAATTTT-AGGGTTT-AGGTTTATGATT
1 TTAA-TTTTAGGGTTT-GAGGTTTTAGGGTTTCAATTTTAAGGTTTTGAGGTTTAAGGTT
* * * *
4827552 TTAGTTTTAGAGTTTGAGGTTTTAGGGTTTCGATTTTAATGTTTTGATGGTTTAAGGTT
1 TTAATTTTAGGGTTTGAGGTTTTAGGGTTTCAATTTTAAGGTTTTGA-GGTTTAAGGTT
** * * * *
4827611 TTAATTTTAGGGTTCAAAGTTTTAGGGTTTCGACTTTAAGGTTTTGAGGGTTT-AGGAT
1 TTAATTTTAGGGTTTGAGGTTTTAGGGTTTCAATTTTAAGGTTTTGA-GGTTTAAGGTT
* * *
4827669 TCAATTTTAGGGTTTGAGGTTTTAGGGTTTCAATTTT-AGGGTTTGAAAGGTTTAAAGTT
1 TTAATTTTAGGGTTTGAGGTTTTAGGGTTTCAATTTTAAGGTTTTG--AGGTTTAAGGTT
* *
4827728 TGAGTTTTAGGGTTTGA
1 TTAATTTTAGGGTTTGA
4827745 AAAGTTTGGG
Statistics
Matches: 158, Mismatches: 29, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
56 20 0.13
57 21 0.13
58 44 0.28
59 73 0.46
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.47
Consensus pattern (58 bp):
TTAATTTTAGGGTTTGAGGTTTTAGGGTTTCAATTTTAAGGTTTTGAGGTTTAAGGTT
Found at i:4827742 original size:14 final size:14
Alignment explanation
Indices: 4827497--4827744 Score: 106
Period size: 14 Copynumber: 17.1 Consensus size: 14
4827487 TTTGGGCTTA
*
4827497 AGTTTCAGGGTTTGG
1 AGTTTTAGGGTTT-G
* *
4827512 AGGATTTAGGGTTTC
1 A-GTTTTAGGGTTTG
*
4827527 AATTTTAGGGTTT-
1 AGTTTTAGGGTTTG
* * * *
4827540 AGGTTTATGATTTT
1 AGTTTTAGGGTTTG
*
4827554 AGTTTTAGAGTTTG
1 AGTTTTAGGGTTTG
4827568 AGGTTTTAGGGTTTCG
1 A-GTTTTAGGGTTT-G
* *
4827584 A-TTTTAATGTTTTG
1 AGTTTT-AGGGTTTG
* * *
4827598 ATGGTTTAAGGTTTT
1 A-GTTTTAGGGTTTG
* **
4827613 AATTTTAGGGTTCAA
1 AGTTTTAGGGTT-TG
4827628 AGTTTTAGGGTTTCG
1 AGTTTTAGGGTTT-G
* * *
4827643 ACTTTAAGGTTTTG
1 AGTTTTAGGGTTTG
* * *
4827657 AGGGTTTA-GGATTC
1 A-GTTTTAGGGTTTG
*
4827671 AATTTTAGGGTTTG
1 AGTTTTAGGGTTTG
*
4827685 AGGTTTTAGGGTTTC
1 A-GTTTTAGGGTTTG
*
4827700 AATTTTAGGGTTTG
1 AGTTTTAGGGTTTG
* **
4827714 AAAGGTTTAAAGTTTG
1 --AGTTTTAGGGTTTG
4827730 AGTTTTAGGGTTTG
1 AGTTTTAGGGTTTG
4827744 A
1 A
4827745 AAAGTTTGGG
Statistics
Matches: 166, Mismatches: 53, Indels: 29
0.67 0.21 0.12
Matches are distributed among these distances:
13 13 0.08
14 68 0.41
15 60 0.36
16 25 0.15
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (14 bp):
AGTTTTAGGGTTTG
Found at i:4827899 original size:3 final size:3
Alignment explanation
Indices: 4827891--4827949 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
4827881 TTATGAAAAT
*
4827891 TTA TTA TTA CCTA 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
4827937 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
4827950 CCTTTTTATA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 51 0.96
4 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:4847167 original size:100 final size:100
Alignment explanation
Indices: 4846971--4847170 Score: 231
Period size: 100 Copynumber: 2.0 Consensus size: 100
4846961 GAATGCCCAC
* * * * * *
4846971 ATAGATGTGCCCTTAATGCCTTGAAAACCTTTTTTTAAAAAATCTTTTAAAGTACCCAAAATTGT
1 ATAGATGTGCCCTTAATGCCTTGAAAACCTTCTTCTAAAAAATCTTCTAAAGCACCCAAAACTAT
* * ** * * *
4847036 CAAAAAAGTTAAGAATGAGCTAGTAAGGATTCAAT
66 AAAAAAAATTAAGAACAAGCCAATAAAGATTCAAT
** *
4847071 ATAGATGTGCCCTTAATGCCTTGAAAGGC-TCTTCTAAAAAATCTTCTAAAGCACTCAAAACTAT
1 ATAGATGTGCCCTTAATGCCTTGAAAACCTTCTTCTAAAAAATCTTCTAAAGCACCCAAAACTAT
*
4847135 AAAAAAAAATTAAGGACAAGCCAATAAAGATTCAAT
66 -AAAAAAAATTAAGAACAAGCCAATAAAGATTCAAT
4847171 GTAGTTTTTT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
99 28 0.34
100 54 0.66
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (100 bp):
ATAGATGTGCCCTTAATGCCTTGAAAACCTTCTTCTAAAAAATCTTCTAAAGCACCCAAAACTAT
AAAAAAAATTAAGAACAAGCCAATAAAGATTCAAT
Found at i:4850824 original size:43 final size:45
Alignment explanation
Indices: 4850748--4850838 Score: 141
Period size: 43 Copynumber: 2.1 Consensus size: 45
4850738 AAATTTTAAA
*
4850748 ATTATGAGATATAAGATTCAATTAATTTGTTTAATGTAATATTTG
1 ATTATGAGATATAAGATTCAATTAATTTATTTAATGTAATATTTG
* *
4850793 ATTATGGGATATAA-CTT-AATTAATTTATTTAATGTAATATTTG
1 ATTATGAGATATAAGATTCAATTAATTTATTTAATGTAATATTTG
4850836 ATT
1 ATT
4850839 TTTTTTACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 28 0.65
44 2 0.05
45 13 0.30
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.48
Consensus pattern (45 bp):
ATTATGAGATATAAGATTCAATTAATTTATTTAATGTAATATTTG
Found at i:4851531 original size:21 final size:22
Alignment explanation
Indices: 4851505--4851556 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
4851495 TAAAACAGTA
4851505 ATAATAATAAA-A-TTAATTATT
1 ATAATAATAAATATTTAA-TATT
4851526 ATAATAA-AAATATTTAATATT
1 ATAATAATAAATATTTAATATT
*
4851547 ATAATGATAA
1 ATAATAATAA
4851557 GATCAAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 18 0.67
22 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATAATAAATATTTAATATT
Found at i:4851791 original size:12 final size:11
Alignment explanation
Indices: 4851744--4851791 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
4851734 TTAATGGTAA
4851744 TTATTAAATTAT
1 TTATT-AATTAT
4851756 TTATTAACTTAT
1 TTATTAA-TTAT
*
4851768 TTATGTATTTAT
1 TTAT-TAATTAT
4851780 TTATATAATTAT
1 TTAT-TAATTAT
4851792 AAAATTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTAATTAT
Found at i:4852248 original size:13 final size:13
Alignment explanation
Indices: 4852232--4852256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4852222 TTAGAACTCA
4852232 ATTTGAGAATTTG
1 ATTTGAGAATTTG
4852245 ATTTGAGAATTT
1 ATTTGAGAATTT
4852257 AAAAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
ATTTGAGAATTTG
Found at i:4853211 original size:20 final size:20
Alignment explanation
Indices: 4853188--4853245 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 20
4853178 TAAAATTAAT
4853188 ATAAATTCAAAAGTATATAA
1 ATAAATTCAAAAGTATATAA
* * *
4853208 ATAATTAATTTAAAATTATTTAA
1 AT-A--AATTCAAAAGTATATAA
*
4853231 ATTAATTCAAAAGTA
1 ATAAATTCAAAAGTA
4853246 AATGTATAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
20 12 0.41
21 1 0.03
23 16 0.55
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAAATTCAAAAGTATATAA
Found at i:4853217 original size:23 final size:22
Alignment explanation
Indices: 4853191--4853245 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
4853181 AATTAATATA
4853191 AATTCAAAAGTATATAAATAATT
1 AATTCAAAAGTATATAAA-AATT
* **
4853214 AATTTAAAA-T-TATTTAAATT
1 AATTCAAAAGTATATAAAAATT
4853234 AATTCAAAAGTA
1 AATTCAAAAGTA
4853246 AATGTATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 12 0.46
21 5 0.19
22 1 0.04
23 8 0.31
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
AATTCAAAAGTATATAAAAATT
Found at i:4855811 original size:2 final size:2
Alignment explanation
Indices: 4855804--4855843 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4855794 TGAAAATAAT
4855804 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4855844 GTGGATGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4862499 original size:8 final size:7
Alignment explanation
Indices: 4862473--4862498 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4862463 TTTTAATATA
4862473 AAAAATT
1 AAAAATT
4862480 AAAAATT
1 AAAAATT
4862487 AAAAATT
1 AAAAATT
4862494 AAAAA
1 AAAAA
4862499 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:4862506 original size:18 final size:18
Alignment explanation
Indices: 4862480--4862536 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
4862470 ATAAAAAATT
*
4862480 AAAAA-TTAAAAATTAAA
1 AAAAATTTAAATATTAAA
4862497 AAAAATTTAAATA-TAAA
1 AAAAATTTAAATATTAAA
*
4862514 AAAGACATTTAAGTATTAAA
1 AAA-A-ATTTAAATATTAAA
4862534 AAA
1 AAA
4862537 TATATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 12 0.35
18 7 0.21
19 8 0.24
20 7 0.21
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAAATTTAAATATTAAA
Found at i:4862514 original size:15 final size:14
Alignment explanation
Indices: 4862467--4862516 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
4862457 TTATAATTTT
4862467 AATATAAAAAATTA
1 AATATAAAAAATTA
* *
4862481 AAAATTAAAAATT-
1 AATATAAAAAATTA
*
4862494 AA-A-AAAAATTTA
1 AATATAAAAAATTA
4862506 AATATAAAAAA
1 AATATAAAAAA
4862517 GACATTTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
11 6 0.21
12 3 0.11
13 3 0.11
14 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATATAAAAAATTA
Found at i:4866915 original size:16 final size:16
Alignment explanation
Indices: 4866896--4866931 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4866886 GAAAAAGAAG
*
4866896 AAAAAATTAAAAATAA
1 AAAAAACTAAAAATAA
4866912 AAAAAACTAAAAATAA
1 AAAAAACTAAAAATAA
4866928 AAAA
1 AAAA
4866932 GTAACAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAACTAAAAATAA
Found at i:4867204 original size:34 final size:35
Alignment explanation
Indices: 4867166--4867232 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
4867156 AATTTTATAC
* * *
4867166 TTGTAAGTATAA-TTATTTTATTTTCATAAATTAT
1 TTGTAAGTACAATTTAATTTATTGTCATAAATTAT
4867200 TTGTAAGTACAATTTAATTTATTGTCATAAATT
1 TTGTAAGTACAATTTAATTTATTGTCATAAATT
4867233 TTATTTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (35 bp):
TTGTAAGTACAATTTAATTTATTGTCATAAATTAT
Found at i:4869187 original size:12 final size:12
Alignment explanation
Indices: 4869161--4869203 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
4869151 TAAATCAAAT
4869161 TTTTATATATAAA
1 TTTTATAT-TAAA
4869174 TTTTATATTAAA
1 TTTTATATTAAA
* * *
4869186 TTTTTTTTTTAA
1 TTTTATATTAAA
4869198 TTTTAT
1 TTTTAT
4869204 CAAATTATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTATATTAAA
Found at i:4870191 original size:16 final size:17
Alignment explanation
Indices: 4870152--4870195 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4870142 CAGCTTCTAG
* *
4870152 TTGTCTTCTCTTTTTTC
1 TTGTCTTTTTTTTTTTC
*
4870169 TTTTCTTTTTTTTTTTC
1 TTGTCTTTTTTTTTTTC
4870186 -TGTCTTTTTT
1 TTGTCTTTTTT
4870196 CATTGTGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (17 bp):
TTGTCTTTTTTTTTTTC
Found at i:4881533 original size:20 final size:20
Alignment explanation
Indices: 4881508--4881566 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
4881498 CAGGTCCGGG
4881508 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
4881528 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
4881548 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
4881567 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:4881622 original size:13 final size:13
Alignment explanation
Indices: 4881606--4881630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4881596 TTACCCGTAT
4881606 TTTTTATTTTTTA
1 TTTTTATTTTTTA
4881619 TTTTTATTTTTT
1 TTTTTATTTTTT
4881631 TTTCTCTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:4881878 original size:11 final size:12
Alignment explanation
Indices: 4881857--4881890 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4881847 AATTATCTAG
*
4881857 ATTTTTTTTTTA
1 ATTTTTATTTTA
4881869 A-TTTTATTTTA
1 ATTTTTATTTTA
4881880 ATTTTTATTTT
1 ATTTTTATTTT
4881891 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:4882266 original size:31 final size:31
Alignment explanation
Indices: 4882195--4882267 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
4882185 AATTTCCAGA
* *
4882195 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
*
4882226 TTTCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
4882257 TTCCGGCGACA
1 TTCCGGCGACA
4882268 GACCCAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:4882342 original size:19 final size:19
Alignment explanation
Indices: 4882318--4882362 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4882308 TCCGGCCAAT
4882318 TTCCGGCGAAATTCCCAGA
1 TTCCGGCGAAATTCCCAGA
*
4882337 TTCCGGCGAAATTTCCAGA
1 TTCCGGCGAAATTCCCAGA
*
4882356 ATCCGGC
1 TTCCGGC
4882363 ACCGGCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TTCCGGCGAAATTCCCAGA
Found at i:4882639 original size:15 final size:15
Alignment explanation
Indices: 4882606--4882649 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4882596 GCTCCAGGTT
***
4882606 TTTTTTTTTTTTTTT
1 TTTTTTTTTTTTGAA
4882621 TTTTTTTTTTTTGAA
1 TTTTTTTTTTTTGAA
*
4882636 TTTTTTTTATTTGA
1 TTTTTTTTTTTTGA
4882650 CTTTGATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.05, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTGAA
Found at i:4882643 original size:1 final size:1
Alignment explanation
Indices: 4882604--4882632 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
4882594 CCGCTCCAGG
4882604 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4882633 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4882931 original size:161 final size:161
Alignment explanation
Indices: 4882665--4883123 Score: 759
Period size: 156 Copynumber: 2.9 Consensus size: 161
4882655 ATTTTGATCT
* ** *
4882665 TGATTTT-TTTTTCTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTAAAAGTAAAAACAGTAG
1 TGATTTTGATTTT-TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAG
*
4882729 TTTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGACAA
64 TTTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAA
*
4882794 TTGAGAATAATTTCCGATAATTAATTACTTGGC
129 TTGAGAATAATTTCCGATAATTAATTAATTGGC
4882827 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
4882892 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
* *
4882957 GAGAATAATTTTCGATAATTAATTAATTGGT
131 GAGAATAATTTCCGATAATTAATTAATTGGC
* *
4882988 TGATCTTGA-----TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
*
4883048 TTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
4883113 GAGAATAATTT
131 GAGAATAATTT
4883124 TCAACAACTA
Statistics
Matches: 285, Mismatches: 11, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
156 125 0.44
161 111 0.39
162 45 0.16
163 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (161 bp):
TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
GAGAATAATTTCCGATAATTAATTAATTGGC
Found at i:4886783 original size:15 final size:15
Alignment explanation
Indices: 4886757--4886829 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
4886747 ATAGGTGAAG
*
4886757 AATGAGAAAAAAAGAT
1 AATGA-AAAAAAAGAA
*
4886773 GATGAAAAAAAAGAA
1 AATGAAAAAAAAGAA
*
4886788 AAAGAAAAAAAAGAA
1 AATGAAAAAAAAGAA
*
4886803 AGAAGAAAAAATGAA-AA
1 A-ATGAAAAAA--AAGAA
4886820 AATGAAAAAA
1 AATGAAAAAA
4886830 TGAAAAAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
15 23 0.47
16 21 0.43
17 3 0.06
18 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (15 bp):
AATGAAAAAAAAGAA
Found at i:4886796 original size:16 final size:16
Alignment explanation
Indices: 4886763--4886813 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 16
4886753 GAAGAATGAG
* *
4886763 AAAAAAAG-ATGATGA
1 AAAAAAAGAAAGAAGA
4886778 AAAAAAAGAAA-AAGA
1 AAAAAAAGAAAGAAGA
4886793 AAAAAAAGAAAGAAGA
1 AAAAAAAGAAAGAAGA
4886809 AAAAA
1 AAAAA
4886814 TGAAAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAGAAGA
Found at i:4886797 original size:8 final size:8
Alignment explanation
Indices: 4886778--4886837 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
4886768 AAGATGATGA
4886778 AAAAAAAG
1 AAAAAAAG
*
4886786 AAAAAGA-
1 AAAAAAAG
4886793 AAAAAAAG
1 AAAAAAAG
*
4886801 -AAAGAAG
1 AAAAAAAG
*
4886808 AAAAAATG
1 AAAAAAAG
*
4886816 AAAAAATG
1 AAAAAAAG
*
4886824 AAAAAATG
1 AAAAAAAG
4886832 AAAAAA
1 AAAAAA
4886838 GAGATCCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
7 12 0.27
8 33 0.73
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:4886826 original size:16 final size:15
Alignment explanation
Indices: 4886786--4886839 Score: 72
Period size: 16 Copynumber: 3.5 Consensus size: 15
4886776 GAAAAAAAAG
*
4886786 AAAAAGAAAAAAAAGA
1 AAAAAG-AAAAAATGA
*
4886802 AAGAAGAAAAAATGA
1 AAAAAGAAAAAATGA
4886817 AAAAATGAAAAAATGA
1 AAAAA-GAAAAAATGA
4886833 AAAAAGA
1 AAAAAGA
4886840 GATCCAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.41
16 20 0.59
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (15 bp):
AAAAAGAAAAAATGA
Found at i:4886835 original size:15 final size:14
Alignment explanation
Indices: 4886778--4886836 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
4886768 AAGATGATGA
4886778 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
4886792 AAAAAAAAGAAAGAAG
1 -AAAAAAAGAAA-AAG
*
4886808 AAAAAATGAAAAAATG
1 AAAAAAAG-AAAAA-G
*
4886824 AAAAAATGAAAAA
1 AAAAAAAGAAAAA
4886837 AGAGATCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
15 25 0.62
16 15 0.38
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:4888134 original size:82 final size:81
Alignment explanation
Indices: 4888031--4888335 Score: 481
Period size: 82 Copynumber: 3.7 Consensus size: 81
4888021 GTCTAGGAGT
*
4888031 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTAC
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAAGTCGTGGTAC
4888096 CTCTGTTGAGAGGAGCA
65 CTCTGTTGAGAGGAGCA
*
4888113 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTAC
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCCAAAGTCGTGGTAC
4888178 CTCTGTTGAGAGGAGCA
65 CTCTGTTGAGAGGAGCA
* *
4888195 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGT--TGC
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAG-TCGTGGTAC
*
4888258 CTCTGTTTAGAGGAGCA
65 CTCTGTTGAGAGGAGCA
*
4888275 ATTTATCTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGT
1 ATTTA-CTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGT
4888336 AGAGCCTCTG
Statistics
Matches: 211, Mismatches: 8, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
80 27 0.13
81 23 0.11
82 161 0.76
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (81 bp):
ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCGTGGTACC
TCTGTTGAGAGGAGCA
Found at i:4888149 original size:40 final size:40
Alignment explanation
Indices: 4888031--4888332 Score: 412
Period size: 40 Copynumber: 7.4 Consensus size: 40
4888021 GTCTAGGAGT
4888031 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* * * *
4888071 ATTTATTTTTTCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTA-CTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
4888113 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* * *
4888153 ATTTATTTTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTA-CTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
4888195 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
4888235 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
4888275 ATTTATCTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTA-CTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
* *
4888317 ATTTATTTTTCAAAGT
1 ATTTACTTTCCAAAGT
4888333 CGTAGAGCCT
Statistics
Matches: 234, Mismatches: 16, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
40 103 0.44
41 52 0.22
42 79 0.34
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
ATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:4888230 original size:122 final size:123
Alignment explanation
Indices: 4888031--4888332 Score: 470
Period size: 122 Copynumber: 2.5 Consensus size: 123
4888021 GTCTAGGAGT
4888031 ATTTA-CTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAG-TCGTG
1 ATTTATCTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTTCAAAGTTCGT-
*
4888092 GTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
63 GTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* * * * * *
4888153 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTTCGT-TG
1 ATTTATCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTCGTGTA
*
4888217 CCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
66 CCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
4888275 ATTTATCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGT
1 ATTTATCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGT
4888333 CGTAGAGCCT
Statistics
Matches: 163, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
122 119 0.73
123 17 0.10
124 27 0.17
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (123 bp):
ATTTATCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTCGTGTA
CCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:4888519 original size:20 final size:20
Alignment explanation
Indices: 4888490--4888529 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4888480 TCCGGGCCCG
4888490 GATCAATTGGGCCTGACCCA
1 GATCAATTGGGCCTGACCCA
* *
4888510 GATCATTTGGGCCTGGCCCA
1 GATCAATTGGGCCTGACCCA
4888530 AATGGGCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
GATCAATTGGGCCTGACCCA
Found at i:4888580 original size:13 final size:13
Alignment explanation
Indices: 4888564--4888588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4888554 TTACCCGTAT
4888564 TTTTTATTTTTTA
1 TTTTTATTTTTTA
4888577 TTTTTATTTTTT
1 TTTTTATTTTTT
4888589 TTTCTCTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:4888635 original size:12 final size:14
Alignment explanation
Indices: 4888620--4888656 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4888610 TATTTATTAT
4888620 TATGTAT-TA-ATA
1 TATGTATATATATA
4888632 TATGTATATATATA
1 TATGTATATATATA
*
4888646 TATATATATAT
1 TATGTATATAT
4888657 TTTTTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:4888838 original size:11 final size:12
Alignment explanation
Indices: 4888817--4888850 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4888807 AATTATCTAG
*
4888817 ATTTTTTTTTTA
1 ATTTTTATTTTA
4888829 A-TTTTATTTTA
1 ATTTTTATTTTA
4888840 ATTTTTATTTT
1 ATTTTTATTTT
4888851 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:4889233 original size:31 final size:31
Alignment explanation
Indices: 4889166--4889238 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
4889156 AATTTCCAGA
* * *
4889166 TTCCGACGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
4889197 TTCCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
4889228 TTCCGGCGACA
1 TTCCGGCGACA
4889239 GACCCAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:4889324 original size:19 final size:19
Alignment explanation
Indices: 4889300--4889344 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4889290 TCCGGCCAAT
4889300 TTCCGGCGAAATTCCCAGA
1 TTCCGGCGAAATTCCCAGA
*
4889319 TTCCGGCGAAATTTCCAGA
1 TTCCGGCGAAATTCCCAGA
*
4889338 ATCCGGC
1 TTCCGGC
4889345 ACCGGCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TTCCGGCGAAATTCCCAGA
Found at i:4889650 original size:11 final size:11
Alignment explanation
Indices: 4889621--4889650 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4889611 TTGTTTTTTT
4889621 TTTTTTTTGAA
1 TTTTTTTTGAA
*
4889632 ATTTTTTTGAA
1 TTTTTTTTGAA
4889643 TTTTTTTT
1 TTTTTTTT
4889651 ACTTTGACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:4889892 original size:162 final size:161
Alignment explanation
Indices: 4889673--4890127 Score: 741
Period size: 155 Copynumber: 2.9 Consensus size: 161
4889663 ATTTTGATCT
* *
4889673 TGATTTT--TTTTTCTTTTTC-TTAATTAAT-CGACGACGGAGCCTCTACAAGTAAAACAGTAGT
1 TGATTTTGATTTTT-TTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGT
*
4889734 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTTCTGCTAAAAGTATTAGAGACAA
65 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAA-TTTTCTGCTAAAAGTATTAGAGTCAA
*
4889799 TTGAGAATAATTTCCGATAATTAATTACTTGGC
129 TTGAGAATAATTTCCGATAATTAATTAATTGGC
4889832 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
4889897 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTC-ATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
* *
4889961 GAGAATAATTTTCGATAATTAATTAATTGGT
131 GAGAATAATTTCCGATAATTAATTAATTGGC
* *
4889992 TGATCTTGA-----TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
*
4890052 TTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
66 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
4890117 GAGAATAATTT
131 GAGAATAATTT
4890128 TCAACAACTA
Statistics
Matches: 282, Mismatches: 9, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
155 84 0.30
156 40 0.14
159 7 0.02
160 69 0.24
161 15 0.05
162 67 0.24
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (161 bp):
TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
GAGAATAATTTCCGATAATTAATTAATTGGC
Found at i:4894129 original size:19 final size:21
Alignment explanation
Indices: 4894093--4894134 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
4894083 CGAATAAAAT
*
4894093 TATATATGTTTATTATTTTTA
1 TATATATGTTTATAATTTTTA
4894114 TATATAT-TTTA-AATTTTTA
1 TATATATGTTTATAATTTTTA
4894133 TA
1 TA
4894135 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATGTTTATAATTTTTA
Found at i:4894176 original size:20 final size:21
Alignment explanation
Indices: 4894153--4894193 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4894143 TAATTATTTT
* *
4894153 ATATTTAAATTTAT-TTAAAA
1 ATATTAAAAATTATATTAAAA
4894173 ATATTAAAAATTATATTAAAA
1 ATATTAAAAATTATATTAAAA
4894194 TAATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTAAAAATTATATTAAAA
Found at i:4894184 original size:21 final size:24
Alignment explanation
Indices: 4894159--4894206 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
4894149 TTTTATATTT
*
4894159 AAATT-TATTTAAA-AATAT-TAA
1 AAATTATATTAAAATAATATATAA
4894180 AAATTATATTAAAATAATATATAA
1 AAATTATATTAAAATAATATATAA
4894204 AAA
1 AAA
4894207 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 5 0.22
24 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATTATATTAAAATAATATATAA
Found at i:4910200 original size:13 final size:14
Alignment explanation
Indices: 4910174--4910211 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4910164 TACATACTTG
4910174 AAAAATACAAAAAT
1 AAAAATACAAAAAT
*
4910188 AAAAA-ACAGAAAT
1 AAAAATACAAAAAT
*
4910201 AATAATACAAA
1 AAAAATACAAA
4910212 GAAGAATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAATACAAAAAT
Found at i:4913368 original size:116 final size:115
Alignment explanation
Indices: 4913203--4913449 Score: 307
Period size: 116 Copynumber: 2.1 Consensus size: 115
4913193 TTAATTTTTT
* ** * * *
4913203 TTGAAAATAAATTTTTCTAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATTAATTTTTCTGAA
1 TTGAAAATAAA-ATTTAAAAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAATTTTCCTGAA
*
4913268 AAATAAAAATTTCAAAATA-ATTTCGAGGGAAAGTTAAAAATATCAATTTTCA
65 AAATAAAAATTTCAAAA-ACATTT-GAGGGAAAGTTAAAAATATCAAGTTTCA
* ** *
4913320 TTGAAAATAAAATTTAAAAAAAAAATTTTTTTTGGGAAAAGTTAAAAGTATCAATTTTCCTTAAA
1 TTGAAAATAAAATTTAAAAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAATTTTCCTGAAA
* * * * *
4913385 AATAAAATTTTCAAAAACATTTTAGGGAAAGTTGAAAGTATCAAGTTTCC
66 AATAAAAATTTCAAAAACATTTGAGGGAAAGTTAAAAATATCAAGTTTCA
*
4913435 TTGAAAATAGAATTT
1 TTGAAAATAAAATTT
4913450 CCAAATGCTT
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
115 38 0.34
116 63 0.56
117 11 0.10
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (115 bp):
TTGAAAATAAAATTTAAAAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAATTTTCCTGAAA
AATAAAAATTTCAAAAACATTTGAGGGAAAGTTAAAAATATCAAGTTTCA
Found at i:4913424 original size:55 final size:54
Alignment explanation
Indices: 4913232--4913454 Score: 194
Period size: 56 Copynumber: 3.9 Consensus size: 54
4913222 AAAAAAATAT
* * * * * *
4913232 TTTTAAGGAAAAGTTGAAAGTATTAATTTTTCTGAAAAATAAAAATTTCAAAATAA
1 TTTT-AGGGAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAATTTTCAAAA-AA
* * * * **
4913288 TTTCGAGGGAAAGTTAAAAATATCAATTTTCATTGAAAATAAAATTTAAAAAAAAAA
1 TTT-TAGGGAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAATTT--TCAAAAAA
*
4913345 TTTTTTTTGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAATTTTCAAAAACA
1 ---TTTTAGGG-AAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAATTTTCAAAAA-A
* * * * *
4913404 TTTTAGGGAAAGTTGAAAGTATCAAGTTTCCTTGAAAATAGAATTTCCAAA
1 TTTTAGGGAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAATTTTCAAA
4913455 TGCTTCAAAA
Statistics
Matches: 134, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
55 38 0.28
56 43 0.32
57 2 0.01
58 9 0.07
59 4 0.03
60 38 0.28
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (54 bp):
TTTTAGGGAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAAATTTTCAAAAAA
Found at i:4916061 original size:13 final size:13
Alignment explanation
Indices: 4916040--4916090 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
4916030 TCAAACTCCC
4916040 ATATACAACCTTA
1 ATATACAACCTTA
* *
4916053 ATATTCAACCTCCA
1 ATATACAACCT-TA
4916067 ATATACAACCTTA
1 ATATACAACCTTA
*
4916080 ATATTCAACCT
1 ATATACAACCT
4916091 CTCACAAGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATACAACCTTA
Found at i:4916070 original size:27 final size:27
Alignment explanation
Indices: 4916030--4916091 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
4916020 TTTTCAGCCC
* *
4916030 TCAAACTCCCATATACAACCTTAATAT
1 TCAACCTCCAATATACAACCTTAATAT
4916057 TCAACCTCCAATATACAACCTTAATAT
1 TCAACCTCCAATATACAACCTTAATAT
4916084 TCAACCTC
1 TCAACCTC
4916092 TCACAAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (27 bp):
TCAACCTCCAATATACAACCTTAATAT
Found at i:4917565 original size:20 final size:21
Alignment explanation
Indices: 4917542--4917587 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
4917532 AAAAGAGGAT
4917542 GAAAGAT-GAAAAAAAAAAGA
1 GAAAGATGGAAAAAAAAAAGA
*
4917562 GAAA-ATGGATAAAAAAAAGA
1 GAAAGATGGAAAAAAAAAAGA
4917582 GAAAGA
1 GAAAGA
4917588 AAAAAGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAAGATGGAAAAAAAAAAGA
Found at i:4917588 original size:24 final size:21
Alignment explanation
Indices: 4917530--4917590 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 21
4917520 AGAAAAAAGG
*
4917530 AAAAAAGAGGATGAAAGATGAAA
1 AAAAAAGA-GAAGAAA-ATGAAA
4917553 AAAAAA-AG-AGAAAATGGATAA
1 AAAAAAGAGAAGAAAAT-GA-AA
4917574 AAAAAAGAGAAAGAAAA
1 AAAAAAGAG-AAGAAAA
4917591 AAGAGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 9 0.28
22 3 0.09
23 6 0.19
24 6 0.19
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (21 bp):
AAAAAAGAGAAGAAAATGAAA
Found at i:4917592 original size:15 final size:14
Alignment explanation
Indices: 4917572--4917631 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
4917562 GAAAATGGAT
4917572 AAAAAAAAGAG-AA
1 AAAAAAAAGAGAAA
*
4917585 AGAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
* * *
4917599 ATAAAAAATATAAA
1 AAAAAAAAGAGAAA
4917613 AAATAAAAAGAGAAA
1 AAA-AAAAAGAGAAA
4917628 AAAA
1 AAAA
4917632 GAAGACTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.26
14 16 0.42
15 12 0.32
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.07
Consensus pattern (14 bp):
AAAAAAAAGAGAAA
Found at i:4917636 original size:13 final size:12
Alignment explanation
Indices: 4917572--4917633 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
4917562 GAAAATGGAT
4917572 AAAAAAAAGAGA
1 AAAAAAAAGAGA
4917584 AAGAAAAAAGAGAA
1 AA-AAAAAAGAG-A
* *
4917598 AATAAAAAATATA
1 AA-AAAAAAGAGA
*
4917611 AAAAATAAAAAGA
1 AAAAA-AAAGAGA
*
4917624 GAAAAAAAGA
1 AAAAAAAAGA
4917634 AGACTCAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
12 9 0.22
13 21 0.52
14 10 0.25
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:4918747 original size:102 final size:102
Alignment explanation
Indices: 4918571--4918774 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
4918561 GCCATATTAC
4918571 CACAATTATTTAGGACTTCATGACATCATTGACATCCGCATTACATGCATCATGTTGGCATCGTT
1 CACAATTATTTAGGACTTCATGACATCATTGACATCCGCATTACATGCATCATGTTGGCATCGTT
4918636 ACTTGAATAGTACATACACATAATTTGATGAATTAAA
66 ACTTGAATAGTACATACACATAATTTGATGAATTAAA
4918673 CACAATTATTTAGGACTTCATGACATCATTGACATCCGCATTACATGCATCATGTTGGCATCGTT
1 CACAATTATTTAGGACTTCATGACATCATTGACATCCGCATTACATGCATCATGTTGGCATCGTT
*
4918738 ACTTGAATAGTACATGCACATAATTTGATGAATTAAA
66 ACTTGAATAGTACATACACATAATTTGATGAATTAAA
4918775 ACTTTGTTTG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (102 bp):
CACAATTATTTAGGACTTCATGACATCATTGACATCCGCATTACATGCATCATGTTGGCATCGTT
ACTTGAATAGTACATACACATAATTTGATGAATTAAA
Found at i:4918940 original size:22 final size:22
Alignment explanation
Indices: 4918915--4918973 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
4918905 GAATATTTTG
*
4918915 ATGAGAATTTTTGAGTTCTC-AA
1 ATGAGAATCTTTGAGTT-TCAAA
* *
4918937 ATGAAAATCTTTGGGTTTCAAA
1 ATGAGAATCTTTGAGTTTCAAA
*
4918959 ATAAGAATCTTTGAG
1 ATGAGAATCTTTGAG
4918974 GTGTGAAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (22 bp):
ATGAGAATCTTTGAGTTTCAAA
Found at i:4919715 original size:42 final size:42
Alignment explanation
Indices: 4919563--4919767 Score: 184
Period size: 42 Copynumber: 4.9 Consensus size: 42
4919553 ATGATTGTTA
* * *
4919563 AAGAGCAATTCA-CTTTTCCAAGTTG-TGATGCCTCTGTTTAG
1 AAGAGCAATTTATTTTTTCAAAGTTGTTGA-GCCTCTGTTTAG
* * * * * *
4919604 AGGAGCAATTCACTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
1 AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTGTTTAG
**
4919646 AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTACTTAG
1 AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTGTTTAG
* * * *
4919688 AAGAGCCATTTATTTTTTCAAAGTTGTTGAACCTTTGATTAG
1 AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTGTTTAG
* * *
4919730 -AGAAGCTTTATTTATTTTTT-AAAGTCGTTGAGCTTCTG
1 AAG-AGC--AATTTATTTTTTCAAAGTTGTTGAGCCTCTG
4919768 ACTAAAGGAG
Statistics
Matches: 135, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 13 0.10
42 96 0.71
43 15 0.11
44 11 0.08
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (42 bp):
AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTGTTTAG
Found at i:4919730 original size:84 final size:84
Alignment explanation
Indices: 4919563--4919816 Score: 200
Period size: 84 Copynumber: 3.0 Consensus size: 84
4919553 ATGATTGTTA
* * * ** * * * * *
4919563 AAGAGCAATTCA-CTTTTCCAAGTTG-TGATGCCTCTGTTTAGAGGAGCAATTCACTTTTCCAAA
1 AAGAGCAATTTATTTTTTCAAAGTTGTTGA-GCCTCTACTTAGAAGAGCCATTTATTTTTTCAAA
* * * *
4919626 GTTGTGGTGCCTCTGTTTAG
65 GTTGTTGAGCCTTTGATTAG
4919646 AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTACTTAGAAGAGCCATTTATTTTTTCAAAG
1 AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTACTTAGAAGAGCCATTTATTTTTTCAAAG
*
4919711 TTGTTGAACCTTTGATTAG
66 TTGTTGAGCCTTTGATTAG
* * *
4919730 -AGAAGCTTTATTTATTTTTT-AAAGTCGTTGAGCTTCTGAC-TA-AAGGAG-C-TTTATTTATT
1 AAG-AGC--AATTTATTTTTTCAAAGTTGTTGAGCCTCT-ACTTAGAA-GAGCCATTTA-TT-TT
*
4919789 TTCCAAAGTCGTTGAGCCTTTGATTAG
59 TT-CAAAGTTGTTGAGCCTTTGATTAG
4919816 A
1 A
4919817 GGATTTTTAT
Statistics
Matches: 140, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
83 17 0.12
84 61 0.44
85 27 0.19
86 35 0.25
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (84 bp):
AAGAGCAATTTATTTTTTCAAAGTTGTTGAGCCTCTACTTAGAAGAGCCATTTATTTTTTCAAAG
TTGTTGAGCCTTTGATTAG
Found at i:4919780 original size:43 final size:43
Alignment explanation
Indices: 4919653--4919911 Score: 233
Period size: 43 Copynumber: 6.0 Consensus size: 43
4919643 TAGAAGAGCA
* * * *
4919653 ATTTATTTTTTCAAAGTTGTTGAGCCTCT-ACTTAGAAGAGC--C
1 ATTTATTTTTTCAAAGTCGTTGAG-CTTTGA-TTAGAGGAGCTTT
* * *
4919695 ATTTATTTTTTCAAAGTTGTTGAACCTTTGATTAGAGAAGCTTT
1 ATTTATTTTTTCAAAGTCGTTG-AGCTTTGATTAGAGGAGCTTT
* *
4919739 ATTTATTTTTT-AAAGTCGTTGAGCTTCTGACTAAAGGAGCTTT
1 ATTTATTTTTTCAAAGTCGTTGAGCTT-TGATTAGAGGAGCTTT
* **
4919782 ATTTA-TTTTCCAAAGTCGTTGAGCCTTTGATTAGAGGATTTTT
1 ATTTATTTTTTCAAAGTCGTTGAG-CTTTGATTAGAGGAGCTTT
* * *
4919825 ATTTA-TTTTTCAAGGTTGCTGAGCTTTTGATTAGAGGAGCTTT
1 ATTTATTTTTTCAAAGTCGTTGAGC-TTTGATTAGAGGAGCTTT
* * * *
4919868 GTTTATTTTTTTCAAAGTCGTTAAGCCTTTGTTTAGAAGAGCTT
1 ATTTA-TTTTTTCAAAGTCGTTGAG-CTTTGATTAGAGGAGCTT
4919912 AATCAAAATT
Statistics
Matches: 178, Mismatches: 28, Indels: 19
0.79 0.12 0.08
Matches are distributed among these distances:
42 42 0.24
43 92 0.52
44 14 0.08
45 29 0.16
46 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.46
Consensus pattern (43 bp):
ATTTATTTTTTCAAAGTCGTTGAGCTTTGATTAGAGGAGCTTT
Found at i:4919944 original size:8 final size:8
Alignment explanation
Indices: 4919927--4919955 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4919917 AAATTTTAAC
4919927 AAAA-AAA
1 AAAATAAA
4919934 AAAATAAA
1 AAAATAAA
4919942 AAAATAAA
1 AAAATAAA
4919950 AAAATA
1 AAAATA
4919956 TTGAGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAATAAA
Found at i:4922124 original size:56 final size:55
Alignment explanation
Indices: 4922040--4922263 Score: 197
Period size: 55 Copynumber: 4.0 Consensus size: 55
4922030 ATATAAAAAT
* * *
4922040 AAAAA-ATTTTGAGAAAAAATTAAAAGTATTAATTTTCCTTAACAATAAAAGTTTC-
1 AAAAATATTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTAA-AATAAAA-TTTCA
* * *
4922095 AAAAATATTTCGAGGAAAAGTTGAAAGTATCAA-TTTCCCTAAAACTAAAATTTTCAAAAA
1 AAAAATATTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTAAAA-TAAAA-TTTC----A
* * *
4922155 AAAAATATTTTTG-GAGAAAAGTTGAAAGTTTCAATTTTTCTTAAAATAAAATTTCA
1 AAAAATA-TTTTGAG-GAAAAGTTAAAAGTATCAATTTTCCTTAAAATAAAATTTCA
* * * *
4922211 AAAAATATTTT-AGGGAAAGTTAAAAATATCAATTTTCCTCGAAAATAGAATTT
1 AAAAATATTTTGAGGAAAAGTTAAAAGTATCAATTTTCCT-TAAAATAAAATTT
4922264 TTAAATGCTT
Statistics
Matches: 139, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
54 23 0.17
55 38 0.27
56 30 0.22
60 12 0.09
61 27 0.19
62 9 0.06
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (55 bp):
AAAAATATTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTAAAATAAAATTTCA
Found at i:4922263 original size:55 final size:56
Alignment explanation
Indices: 4922054--4922263 Score: 153
Period size: 56 Copynumber: 3.7 Consensus size: 56
4922044 AATTTTGAGA
* * * * *
4922054 AAAAATTAAAAGTATTAATTTTCCTTAACAATAAAAGTTTC-AAAAATA-TTT-CGAGG
1 AAAAGTTAAAAATATCAATTTTCCTGAA-AATAAAA-TTTCAAAAAATATTTTAGGA-G
* * * *
4922110 AAAAGTTGAAAGTATCAATTTCCCT-AAAACTAAAATTTTCAAAAAAAAAATATTTTTGGAG
1 AAAAGTTAAAAATATCAATTTTCCTGAAAA-TAAAA-TTTC----AAAAAATATTTTAGGAG
* * * * *
4922171 AAAAGTTGAAAGTTTCAATTTTTCTTAAAATAAAATTTCAAAAAATATTTTAGG-G
1 AAAAGTTAAAAATATCAATTTTCCTGAAAATAAAATTTCAAAAAATATTTTAGGAG
*
4922226 -AAAGTTAAAAATATCAATTTTCCTCGAAAATAGAATTT
1 AAAAGTTAAAAATATCAATTTTCCT-GAAAATAAAATTT
4922264 TTAAATGCTT
Statistics
Matches: 128, Mismatches: 16, Indels: 21
0.78 0.10 0.13
Matches are distributed among these distances:
54 22 0.17
55 23 0.18
56 35 0.27
60 11 0.09
61 31 0.24
62 6 0.05
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (56 bp):
AAAAGTTAAAAATATCAATTTTCCTGAAAATAAAATTTCAAAAAATATTTTAGGAG
Found at i:4922398 original size:14 final size:13
Alignment explanation
Indices: 4922367--4922402 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4922357 GTTGAATCAC
*
4922367 TATTCTTTTTTCT
1 TATTTTTTTTTCT
4922380 TATTTTTTTTTCT
1 TATTTTTTTTTCT
4922393 TGATTTTTTT
1 T-ATTTTTTT
4922403 AATGTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.81
Consensus pattern (13 bp):
TATTTTTTTTTCT
Found at i:4924688 original size:20 final size:21
Alignment explanation
Indices: 4924663--4924702 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4924653 GGCTCCTTTA
*
4924663 TCATTA-TTGCCTTCCTCTTG
1 TCATTATTTCCCTTCCTCTTG
4924683 TCATTATTTCCCTTCCTCTT
1 TCATTATTTCCCTTCCTCTT
4924703 TACAGTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.33, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTATTTCCCTTCCTCTTG
Found at i:4926193 original size:3 final size:3
Alignment explanation
Indices: 4926175--4926239 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
4926165 ATTCTGTTTA
4926175 AAT AAT AA- AACT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
4926219 AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
4926240 GAGCTAGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 3 0.05
3 54 0.95
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4926546 original size:20 final size:21
Alignment explanation
Indices: 4926507--4926552 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
4926497 TTACATTTTT
* *
4926507 ATAAATTTTAAATATAAAATC
1 ATAAATTATAAATATAAAATA
*
4926528 ATAAATTATGAAT-TAAAATA
1 ATAAATTATAAATATAAAATA
4926548 ATAAA
1 ATAAA
4926553 AATATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATTATAAATATAAAATA
Found at i:4927741 original size:16 final size:16
Alignment explanation
Indices: 4927720--4927753 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4927710 AAAGATAATT
*
4927720 AAAAAAAGAATTAAAC
1 AAAAAAAGAAATAAAC
*
4927736 AAAAAATGAAATAAAC
1 AAAAAAAGAAATAAAC
4927752 AA
1 AA
4927754 GTTGATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAAAGAAATAAAC
Found at i:4929588 original size:12 final size:12
Alignment explanation
Indices: 4929573--4929604 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
4929563 CTAAATGGCC
4929573 CAATAAAAGGCT
1 CAATAAAAGGCT
4929585 CAATAAAAGGCT
1 CAATAAAAGGCT
4929597 CAATAAAA
1 CAATAAAA
4929605 AACCTATCAT
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (12 bp):
CAATAAAAGGCT
Found at i:4929698 original size:23 final size:26
Alignment explanation
Indices: 4929668--4929721 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 26
4929658 ATAAAAAATC
4929668 AAATATAACAATAAA-A-AA-TAAAA
1 AAATATAACAATAAATATAATTAAAA
* *
4929691 AAATATAATAGTAAATATAATTAAAA
1 AAATATAACAATAAATATAATTAAAA
4929717 AAATA
1 AAATA
4929722 GTAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 13 0.50
24 1 0.04
25 2 0.08
26 10 0.38
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (26 bp):
AAATATAACAATAAATATAATTAAAA
Found at i:4929707 original size:27 final size:28
Alignment explanation
Indices: 4929648--4929700 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4929638 TTGACCATTA
4929648 AACAA-AAAAAAT-AAAAAATCA-AATAT
1 AACAATAAAAAATAAAAAAAT-ATAATAT
4929674 AACAATAAAAAATAAAAAAATATAATA
1 AACAATAAAAAATAAAAAAATATAATA
4929701 GTAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.21
27 8 0.33
28 11 0.46
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (28 bp):
AACAATAAAAAATAAAAAAATATAATAT
Found at i:4929865 original size:2 final size:2
Alignment explanation
Indices: 4929858--4929899 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4929848 AACAAATCTT
4929858 TA TA TA 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
4929900 AAGAGAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4930170 original size:2 final size:2
Alignment explanation
Indices: 4930163--4930202 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4930153 AACAAAGCCT
4930163 TA TA 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
4930203 AAGAGAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4930196 original size:305 final size:303
Alignment explanation
Indices: 4929703--4930312 Score: 1089
Period size: 303 Copynumber: 2.0 Consensus size: 303
4929693 ATATAATAGT
* *
4929703 AAATATAATTAAAAAAATAGTAATAAAAATACTAAAAATAATAAGAAAAAGAGCTTGCCCATAAA
1 AAATATAATTAAAAAAATAGTAATAAAAATACCAAAAATAATAAGAAAAAAAGCTTGCCCATAAA
*
4929768 AAAAGAATGAAAAATGATTAAAAAAGTAAAAAATAAGCTTAAAGCTAAAAATGGCCTAAATGGCT
66 AAAAGAATGAAAAATGATTAAAAAAGTAAAAAATAAGCTTAAAACTAAAAATGGCCTAAATGGCT
* *
4929833 AAAGCTTACAACCCAAACAAATCTTTATATATATATATATATATATATATATATATATATATATA
131 AAAGCTTACAACCCAAACAAAGC-CT-TATATATATATATATATATATATATATATATATATATA
*
4929898 TAAAGAGAGAAAGCCCACTTGGCTTACAGCTTAGTATGCATGAAAATCATATAAAAAAAGCTAAT
194 TAAAGAGAGAAAGCCCACTTGGCTTACAGCTTAGTATGCATGAAAATCATATAAAAAAAACTAAT
*
4929963 GAAAAGCCATGCATAGGGCATGCAAAAGCAACTAAAAAAATTGAAA
259 GAAAACCCATGCATAGGGCATGCAAAAGCAACTAAAAAAATT-AAA
*
4930009 AAATATAATT-AAAAAATAGTAATAAAAATACCAAAAATAATAAGAAAAAAAGCTTGGCCATAAA
1 AAATATAATTAAAAAAATAGTAATAAAAATACCAAAAATAATAAGAAAAAAAGCTTGCCCAT-AA
4930073 AAAAAGAATGAAAAATGATTAAAAAA-TAAAAAATAAGCTTAAAACTAAAAATGGCCTAAATGGC
65 AAAAAGAATGAAAAATGATTAAAAAAGTAAAAAATAAGCTTAAAACTAAAAATGGCCTAAATGGC
4930137 TAAAGCTTACAACCCAAACAAAGCCTTATATATATATATATATATATATATATATATATATATAT
130 TAAAGCTTACAACCCAAACAAAGCCTTATATATATATATATATATATATATATATATATATATAT
4930202 AAAGAGAGAAAGCCCACTTGGCTTACAGCTTAGTATGCATGAAAATCATATAAAAAAAACTAATG
195 AAAGAGAGAAAGCCCACTTGGCTTACAGCTTAGTATGCATGAAAATCATATAAAAAAAACTAATG
*
4930267 AAAACCCATGCATAGGGCATGCAAAAGCAGCTAAAAAAATTAAA
260 AAAACCCATGCATAGGGCATGCAAAAGCAACTAAAAAAATTAAA
4930311 AA
1 AA
4930313 GTAGTTGGAA
Statistics
Matches: 294, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
302 5 0.02
303 142 0.48
304 1 0.00
305 108 0.37
306 38 0.13
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (303 bp):
AAATATAATTAAAAAAATAGTAATAAAAATACCAAAAATAATAAGAAAAAAAGCTTGCCCATAAA
AAAAGAATGAAAAATGATTAAAAAAGTAAAAAATAAGCTTAAAACTAAAAATGGCCTAAATGGCT
AAAGCTTACAACCCAAACAAAGCCTTATATATATATATATATATATATATATATATATATATATA
AAGAGAGAAAGCCCACTTGGCTTACAGCTTAGTATGCATGAAAATCATATAAAAAAAACTAATGA
AAACCCATGCATAGGGCATGCAAAAGCAACTAAAAAAATTAAA
Found at i:4930825 original size:19 final size:20
Alignment explanation
Indices: 4930793--4930830 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4930783 TGAAAAATGA
4930793 AAACCAACAGAAAAAGAAAG
1 AAACCAACAGAAAAAGAAAG
4930813 AAACCAACA-AAAAAGAAA
1 AAACCAACAGAAAAAGAAA
4930831 CAGAGGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.16, G:0.11, T:0.00
Consensus pattern (20 bp):
AAACCAACAGAAAAAGAAAG
Found at i:4931439 original size:3 final size:3
Alignment explanation
Indices: 4931427--4931477 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
4931417 TGAATGTTTA
4931427 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4931474 TAT T
1 TAT T
4931478 TTAATTGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:4931874 original size:20 final size:20
Alignment explanation
Indices: 4931849--4931888 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4931839 AACCCTAAAA
*
4931849 TGAAAGCCCTAGGTAAAACC
1 TGAAAGCCCTAAGTAAAACC
*
4931869 TGAAAGCTCTAAGTAAAACC
1 TGAAAGCCCTAAGTAAAACC
4931889 CTAAACTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
TGAAAGCCCTAAGTAAAACC
Found at i:4932139 original size:20 final size:19
Alignment explanation
Indices: 4932112--4932152 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
4932102 TTTTTTAATC
4932112 TAAAAATAATAAAAT-TAAA
1 TAAAAATAA-AAAATATAAA
4932131 TAAAGAATAAAAAATATAAA
1 TAAA-AATAAAAAATATAAA
4932151 TA
1 TA
4932153 GGATCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAATAAAAAATATAAA
Found at i:4935577 original size:17 final size:18
Alignment explanation
Indices: 4935536--4935577 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4935526 GGTCTACTTT
*
4935536 AAGAAAGACATTTTTGGG
1 AAGAATGACATTTTTGGG
*
4935554 AAAAATGACA-TTTTGGG
1 AAGAATGACATTTTTGGG
*
4935571 GAGAATG
1 AAGAATG
4935578 GATGCAAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.40, C:0.05, G:0.29, T:0.26
Consensus pattern (18 bp):
AAGAATGACATTTTTGGG
Found at i:4943438 original size:34 final size:35
Alignment explanation
Indices: 4943389--4943486 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
4943379 CCTTATTTAC
* * *
4943389 TAACTTATGGTTCAGTCCCGATCATCTTT-TTTTT
1 TAACTTGTGGCTCAGTCCCAATCATCTTTGTTTTT
* * *
4943423 TGACTTGTGGCTCAGTCCCTATCATTTTTGTTTTT
1 TAACTTGTGGCTCAGTCCCAATCATCTTTGTTTTT
* *
4943458 TAACTTGTGGCTCAATCACAATCATCTTT
1 TAACTTGTGGCTCAGTCCCAATCATCTTT
4943487 ATTTCCTGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 24 0.45
35 29 0.55
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (35 bp):
TAACTTGTGGCTCAGTCCCAATCATCTTTGTTTTT
Found at i:4943662 original size:35 final size:34
Alignment explanation
Indices: 4943623--4943743 Score: 80
Period size: 35 Copynumber: 3.4 Consensus size: 34
4943613 TCGGTCGCCT
4943623 TTATTCCTTAACTTGCAACTCAGTCTCGATCATCC
1 TTATTCCTTAACTTGCAACTCAGTC-CGATCATCC
* ** * * **
4943658 TTATTTTCTTAACTTATAAGTCAGTCCCAGTCATTT
1 TTA-TTCCTTAACTTGCAACTCAGTCCGA-TCATCC
** * * *
4943694 TTATTTTTTGACTTGCAATTTAGTCCCGATCATCC
1 TTATTCCTTAACTTGCAACTCAGT-CCGATCATCC
* *
4943729 ATATTCCTTGACTTG
1 TTATTCCTTAACTTG
4943744 TGATTCAATC
Statistics
Matches: 64, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
35 36 0.56
36 28 0.44
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (34 bp):
TTATTCCTTAACTTGCAACTCAGTCCGATCATCC
Found at i:4943810 original size:70 final size:70
Alignment explanation
Indices: 4943687--4943823 Score: 159
Period size: 70 Copynumber: 2.0 Consensus size: 70
4943677 GTCAGTCCCA
* * * * *
4943687 GTCATTTTTATTTTTTGACTTGCAATTTAGTCCCGATCATCCATATTCCTTGACTTGTGATTCAA
1 GTCATCTTTATTTTTTGACTTGCAACTTAGTCCCGATCATCCATAGTACTTGACTTATGATTCAA
4943752 TCATG
66 TCATG
* * ** * *
4943757 GTCATCTTTATTTTTTGACTTGCAGCTTAGTCCTTG-TCATCTTTAGTATTTGACTTATGGTTCA
1 GTCATCTTTATTTTTTGACTTGCAACTTAGTCC-CGATCATCCATAGTACTTGACTTATGATTCA
4943821 ATC
65 ATC
4943824 CCAATCATCT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
70 54 0.98
71 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (70 bp):
GTCATCTTTATTTTTTGACTTGCAACTTAGTCCCGATCATCCATAGTACTTGACTTATGATTCAA
TCATG
Found at i:4944698 original size:13 final size:13
Alignment explanation
Indices: 4944678--4944707 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
4944668 TGATAGCAAG
4944678 CAAAAAAAAAAGAA
1 CAAAAAAAAAA-AA
4944692 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
4944705 CAA
1 CAA
4944708 TAGGAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:4945587 original size:3 final size:3
Alignment explanation
Indices: 4945579--4945656 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
4945569 TTGAATAGCT
4945579 TTA TTA TTA -TA TTA 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 TTA
* *
4945626 TTA TTA TTA TTA TTA TTG TTA -TA TGA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4945657 TTTGCTTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4946105 original size:26 final size:26
Alignment explanation
Indices: 4946033--4946087 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
4946023 AAATTTGAAA
4946033 AAACCTTA-AGTAAAACCCTAAAATG
1 AAACCTTATAGTAAAACCCTAAAATG
**
4946058 AAACCTTATAGTAAAATTCTAAAATG
1 AAACCTTATAGTAAAACCCTAAAATG
4946084 AAAC
1 AAAC
4946088 TTTAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (26 bp):
AAACCTTATAGTAAAACCCTAAAATG
Found at i:4946182 original size:20 final size:19
Alignment explanation
Indices: 4946152--4946198 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4946142 ATGAAACCTG
*
4946152 AAACTCTAGGTGAAATCCA
1 AAACCCTAGGTGAAATCCA
*
4946171 AAAGCCCTAGGTGAAATCCT
1 AAA-CCCTAGGTGAAATCCA
4946191 AAACCCTA
1 AAACCCTA
4946199 AACGAAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (19 bp):
AAACCCTAGGTGAAATCCA
Found at i:4950082 original size:18 final size:18
Alignment explanation
Indices: 4950056--4950093 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4950046 CAATATCAAA
* *
4950056 ACATTATCAGATTTTCAT
1 ACATCATCAAATTTTCAT
4950074 ACATCATCAAATTTTCAT
1 ACATCATCAAATTTTCAT
4950092 AC
1 AC
4950094 CAATGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (18 bp):
ACATCATCAAATTTTCAT
Found at i:4954097 original size:93 final size:93
Alignment explanation
Indices: 4953938--4954125 Score: 331
Period size: 93 Copynumber: 2.0 Consensus size: 93
4953928 TTATGAAAGG
* *
4953938 CAAACTGCCCCAGAATTTAGGCATAAGATTTAAGGCAACTAGATAAGAGTAATATCACCATAACC
1 CAAACTCCCCCAGAATTTAGGCATAAGATTTAAGGCAACTAGACAAGAGTAATATCACCATAACC
4954003 ATCAATATATCCATCAATATCAAAACAT
66 ATCAATATATCCATCAATATCAAAACAT
* *
4954031 CAAACTCCCCCTGAATTTAGGCATAAGATTTAAGGCAACTAGACAAGAGTAATATCATCATAACC
1 CAAACTCCCCCAGAATTTAGGCATAAGATTTAAGGCAACTAGACAAGAGTAATATCACCATAACC
*
4954096 ATCAATATATCCATCAATATCAAAGCAT
66 ATCAATATATCCATCAATATCAAAACAT
4954124 CA
1 CA
4954126 TTATCAATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (93 bp):
CAAACTCCCCCAGAATTTAGGCATAAGATTTAAGGCAACTAGACAAGAGTAATATCACCATAACC
ATCAATATATCCATCAATATCAAAACAT
Found at i:4966753 original size:27 final size:27
Alignment explanation
Indices: 4966723--4966777 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
4966713 TGATATAAGA
*
4966723 TAACCATCATGTAGGA-CAACCGAGTGC
1 TAACCATCACGTAGGATC-ACCGAGTGC
*
4966750 TAACTATCACGTAGGATCACCGAGTGC
1 TAACCATCACGTAGGATCACCGAGTGC
4966777 T
1 T
4966778 TACAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (27 bp):
TAACCATCACGTAGGATCACCGAGTGC
Found at i:4972100 original size:14 final size:15
Alignment explanation
Indices: 4972081--4972109 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4972071 TTGACAACTT
4972081 TTTATGATT-TTCAC
1 TTTATGATTGTTCAC
4972095 TTTATGATTGTTCAC
1 TTTATGATTGTTCAC
4972110 AATAAAATTT
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:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (15 bp):
TTTATGATTGTTCAC
Found at i:4973033 original size:30 final size:30
Alignment explanation
Indices: 4972997--4973055 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4972987 TTAAGCCTTC
4972997 TTTAATATTGATCTCTAAATCACGCTAATT
1 TTTAATATTGATCTCTAAATCACGCTAATT
4973027 TTTAATATTGATCTCTAAATCACGCTAAT
1 TTTAATATTGATCTCTAAATCACGCTAAT
4973056 CAGAAGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTAATATTGATCTCTAAATCACGCTAATT
Found at i:4974685 original size:29 final size:28
Alignment explanation
Indices: 4974638--4974700 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
4974628 GTTCAATTTT
* *
4974638 TTTTATTTTTTTATATATTATTTATATCA
1 TTTTATTTTATTATATATTACTTATA-CA
4974667 TTTTAGTTTTATTAT-TATTACTTATACA
1 TTTTA-TTTTATTATATATTACTTATACA
4974695 TGTTTA
1 T-TTTA
4974701 ATACCTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 19 0.63
30 8 0.27
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTATTTTATTATATATTACTTATACA
Found at i:4974744 original size:3 final size:3
Alignment explanation
Indices: 4974738--4974765 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4974728 TTGTTGTTTT
4974738 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4974766 ATAAATAAAT
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):
ATA
Found at i:4974770 original size:4 final size:4
Alignment explanation
Indices: 4974761--4974796 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
4974751 TAATAATAAT
4974761 AATA AATA AATA AATA AATA AATA AA-A AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA A
4974797 GGAGTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:4975432 original size:21 final size:22
Alignment explanation
Indices: 4975399--4975460 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
4975389 CCAAGCTTTA
*
4975399 AAACCCTTAAAACCCTAAGA-TC
1 AAACCC-TAAAACCCTAAAACTC
4975421 AAACCCTAAAACCCTTAAAACTC
1 AAACCCTAAAACCC-TAAAACTC
4975444 AAA-CC-AAAACCCTAAAA
1 AAACCCTAAAACCCTAAAA
4975461 TCCAAAACTC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 5 0.14
21 15 0.41
22 12 0.32
23 5 0.14
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.15
Consensus pattern (22 bp):
AAACCCTAAAACCCTAAAACTC
Found at i:4975468 original size:21 final size:22
Alignment explanation
Indices: 4975406--4975468 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
4975396 TTAAAACCCT
* *
4975406 TAAAACCCTAAGAT-CAAACCC
1 TAAAACCCTAAAATCCAAAACC
4975427 TAAAACCCTTAAAA-CTC-AAACC
1 TAAAACCC-TAAAATC-CAAAACC
4975449 -AAAACCCTAAAATCCAAAAC
1 TAAAACCCTAAAATCCAAAAC
4975469 TCCAAAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
20 6 0.17
21 20 0.57
22 8 0.23
23 1 0.03
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.14
Consensus pattern (22 bp):
TAAAACCCTAAAATCCAAAACC
Found at i:4982342 original size:12 final size:12
Alignment explanation
Indices: 4982325--4982349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4982315 TAGATAAATT
4982325 AAGTTTGTGTTC
1 AAGTTTGTGTTC
4982337 AAGTTTGTGTTC
1 AAGTTTGTGTTC
4982349 A
1 A
4982350 CGGAGTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (12 bp):
AAGTTTGTGTTC
Found at i:4983116 original size:62 final size:61
Alignment explanation
Indices: 4983044--4983181 Score: 165
Period size: 61 Copynumber: 2.2 Consensus size: 61
4983034 TCATGTATCT
* * *
4983044 AAATTATTATAATGCCTTT-TTACCATAATTATGAAAATACCACTCTTT-TTC-ATAATTAATCA
1 AAATTATTATAAT-ACTTTCCTACCATAATTAT-AAAA-A-CACTCTTTCTACTATAATTAATCA
*
4983106 AAATTATTATAATACTTTCCTACCATAATTATAAAAATACTCTTTCTACTATAATTAATCA
1 AAATTATTATAATACTTTCCTACCATAATTATAAAAACACTCTTTCTACTATAATTAATCA
* *
4983167 AAATTACTACAATAC
1 AAATTATTATAATAC
4983182 CCTTCATACA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
59 7 0.10
60 3 0.04
61 32 0.48
62 25 0.37
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (61 bp):
AAATTATTATAATACTTTCCTACCATAATTATAAAAACACTCTTTCTACTATAATTAATCA
Found at i:4983136 original size:25 final size:26
Alignment explanation
Indices: 4983107--4983162 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
4983097 AATTAATCAA
* *
4983107 AATTATTATAATACT-TTCCTACCAT
1 AATTATAAAAATACTCTTCCTACCAT
* *
4983132 AATTATAAAAATACTCTTTCTACTAT
1 AATTATAAAAATACTCTTCCTACCAT
4983158 AATTA
1 AATTA
4983163 ATCAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTATAAAAATACTCTTCCTACCAT
Found at i:4987306 original size:55 final size:55
Alignment explanation
Indices: 4987220--4987323 Score: 172
Period size: 55 Copynumber: 1.9 Consensus size: 55
4987210 ACAACTCGCC
*
4987220 CAATCATCTAAACTAACGTCTTATCAGCACATCATCTCATAATAATTTACTCCTT
1 CAATCATCTAAACTAACGTCTTATCAACACATCATCTCATAATAATTTACTCCTT
* * *
4987275 CAATCATTTAAATTAACGTCTTATCAACACATCTTCTCATAATAATTTA
1 CAATCATCTAAACTAACGTCTTATCAACACATCATCTCATAATAATTTA
4987324 ACTTATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (55 bp):
CAATCATCTAAACTAACGTCTTATCAACACATCATCTCATAATAATTTACTCCTT
Found at i:4988599 original size:2 final size:2
Alignment explanation
Indices: 4988587--4988618 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4988577 AATTATGCAG
4988587 AT AT A- 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 A
4988619 GTAAGAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4991494 original size:18 final size:18
Alignment explanation
Indices: 4991471--4991520 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 18
4991461 GACAACTTAA
4991471 TAACATGTGAATAATACG
1 TAACATGTGAATAATACG
* * *
4991489 TAACAT-T-CATAACATG
1 TAACATGTGAATAATACG
*
4991505 TTACATGTGAATAATA
1 TAACATGTGAATAATA
4991521 TGTTGTCTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
16 11 0.46
17 2 0.08
18 11 0.46
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (18 bp):
TAACATGTGAATAATACG
Found at i:4991523 original size:18 final size:18
Alignment explanation
Indices: 4991473--4991524 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
4991463 CAACTTAATA
* *
4991473 ACATGTGAATAATACGTA
1 ACATGTGAATAATATGTT
* *
4991491 ACAT-T-CATAACATGTT
1 ACATGTGAATAATATGTT
4991507 ACATGTGAATAATATGTT
1 ACATGTGAATAATATGTT
4991525 GTCTTTGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 11 0.42
17 2 0.08
18 13 0.50
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (18 bp):
ACATGTGAATAATATGTT
Found at i:4991946 original size:73 final size:72
Alignment explanation
Indices: 4991821--4991956 Score: 166
Period size: 73 Copynumber: 1.9 Consensus size: 72
4991811 AATGTTATCT
* ** * *
4991821 TTGTTGAAACTATAGAATTATGAAAATATAATTTCAATATTTACTACATTTTTTTATTTTAAAAG
1 TTGTTGAAACTATAGAATTATGAAAATATAATTTCAACATACACCACA-TTTTTTATCTTAAAAG
4991886 CACAATAC
65 CACAATAC
* * * *
4991894 TTGTTGGAACTATATAATTATGAAAATATAGTTTTAACATACACCA-AGTTTTTTATCTTAAAA
1 TTGTTGAAACTATAGAATTATGAAAATATAATTTCAACATACACCACA-TTTTTTATCTTAAAA
4991957 ATATAGTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
72 15 0.28
73 38 0.72
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (72 bp):
TTGTTGAAACTATAGAATTATGAAAATATAATTTCAACATACACCACATTTTTTATCTTAAAAGC
ACAATAC
Found at i:4992070 original size:69 final size:72
Alignment explanation
Indices: 4991909--4992074 Score: 187
Period size: 72 Copynumber: 2.3 Consensus size: 72
4991899 GGAACTATAT
* * * *
4991909 AATTATGAAAATATAGTTTTAACATACACCAAGTTTTTTATCTTAAAAATATAGTTTTTGTTAAA
1 AATTTTGAAAATATAGTTTCAACATACACCAAGTTTTTTATCATAAAAATATAGTCTTTGTTAAA
**
4991974 ATTTTAG
66 ATTACAG
* * * * *
4991981 AATTTTGAAAATTTATTTTCAACAT-CTACTATGTTTTTTATCATAAAAA-A-A-TCTTTGTTGA
1 AATTTTGAAAATATAGTTTCAACATAC-ACCAAGTTTTTTATCATAAAAATATAGTCTTTGTTAA
4992042 AATTACAG
65 AATTACAG
*
4992050 AATTTTTAAAATATAGTTTCAACAT
1 AATTTTGAAAATATAGTTTCAACAT
4992075 TCACAGCATT
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
69 36 0.46
70 1 0.01
71 2 0.03
72 40 0.51
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (72 bp):
AATTTTGAAAATATAGTTTCAACATACACCAAGTTTTTTATCATAAAAATATAGTCTTTGTTAAA
ATTACAG
Found at i:4992393 original size:72 final size:71
Alignment explanation
Indices: 4992267--4992431 Score: 217
Period size: 72 Copynumber: 2.3 Consensus size: 71
4992257 ATTCTAAAAT
* ** *
4992267 CTACATCTTTATCTTAAAAATGAGATCGTTATTAAAATTATAGAATTTTGAAAATCTAATTTT-A
1 CTACATTTTTATCTTAAAAATGAGATCGTTATTAAAATTATAGAATTTCAAAAATAT-ATTTTAA
4992331 ACATTCA
65 ACATTCA
** * *
4992338 CTACATTTTTTAT-TATAAAAATGAGATTTTTGTTAAAATTTTAGAATTTCAAAAATATATTTTA
1 CTACA-TTTTTATCT-TAAAAATGAGATCGTTATTAAAATTATAGAATTTCAAAAATATATTTTA
4992402 AACATTCA
64 AACATTCA
4992410 CTACATTTTTATCTTAAAAATG
1 CTACATTTTTATCTTAAAAATG
4992432 CAATACTTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 26 0.32
72 56 0.68
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.44
Consensus pattern (71 bp):
CTACATTTTTATCTTAAAAATGAGATCGTTATTAAAATTATAGAATTTCAAAAATATATTTTAAA
CATTCA
Found at i:4992442 original size:71 final size:70
Alignment explanation
Indices: 4992267--4992451 Score: 214
Period size: 72 Copynumber: 2.6 Consensus size: 70
4992257 ATTCTAAAAT
* * ** *
4992267 CTACATCTTTATCTTAAAAATGAGATCGTTATTAAAATTATAGAATTTTGAAAATCTAATTTTAA
1 CTACATTTTTATCTTAAAAATGAGATC-TTGTTAAAATTATAGAATTTCAAAAATATAATTTTAA
4992332 CATTCA
65 CATTCA
* *
4992338 CTACATTTTTTAT-TATAAAAATGAGATTTTTGTTAAAATTTTAGAATTTCAAAAATAT-ATTTT
1 CTACA-TTTTTATCT-TAAAAATGAGA-TCTTGTTAAAATTATAGAATTTCAAAAATATAATTTT
4992401 AAACATTCA
63 -AACATTCA
*
4992410 CTACATTTTTATCTTAAAAATGCA-ATACTTGTTGAAATTATA
1 CTACATTTTTATCTTAAAAATG-AGAT-CTTGTTAAAATTATA
4992452 AATAATAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
70 1 0.01
71 39 0.40
72 56 0.58
73 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (70 bp):
CTACATTTTTATCTTAAAAATGAGATCTTGTTAAAATTATAGAATTTCAAAAATATAATTTTAAC
ATTCA
Found at i:5003177 original size:53 final size:53
Alignment explanation
Indices: 5003099--5003207 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 53
5003089 GGTTTTAGAG
* * *
5003099 TTTAGGGCTTAGGATTTTAATGTTTAAGATTTTATGG-TTTAGAATTTTAAGGT
1 TTTAGGGCTTAAGATTTTAATGTTTAAGATTTT-GGGTTTTAAAATTTTAAGGT
* * *
5003152 TTTAGGGGTTAAGATTTTAGA-GTTTAGGATTTTGGGTTTTAAAATTTTAGGGT
1 TTTAGGGCTTAAGATTTTA-ATGTTTAAGATTTTGGGTTTTAAAATTTTAAGGT
5003205 TTT
1 TTT
5003208 TCATATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
52 2 0.04
53 45 0.94
54 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.50
Consensus pattern (53 bp):
TTTAGGGCTTAAGATTTTAATGTTTAAGATTTTGGGTTTTAAAATTTTAAGGT
Found at i:5004561 original size:22 final size:22
Alignment explanation
Indices: 5004535--5004576 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5004525 ACTACTTAGA
5004535 AAGAAA-AAAAAAAGTAAAATGC
1 AAGAAAGAAAAAAAG-AAAATGC
*
5004557 AAGAAAGTAAAAAAGAAAAT
1 AAGAAAGAAAAAAAGAAAAT
5004577 TTTGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (22 bp):
AAGAAAGAAAAAAAGAAAATGC
Found at i:5006034 original size:13 final size:13
Alignment explanation
Indices: 5006016--5006040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5006006 TTATTTTCTT
5006016 TTTCATTCTTTTG
1 TTTCATTCTTTTG
5006029 TTTCATTCTTTT
1 TTTCATTCTTTT
5006041 TTCAAGCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTCATTCTTTTG
Found at i:5010396 original size:7 final size:7
Alignment explanation
Indices: 5010384--5010408 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5010374 TGCACCCATT
5010384 TTTTTTC
1 TTTTTTC
5010391 TTTTTTC
1 TTTTTTC
5010398 TTTTTTC
1 TTTTTTC
5010405 TTTT
1 TTTT
5010409 CTTTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:5010464 original size:13 final size:13
Alignment explanation
Indices: 5010448--5010472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5010438 TGCTTTTCTT
5010448 TGCTATTTTTTTG
1 TGCTATTTTTTTG
5010461 TGCTATTTTTTT
1 TGCTATTTTTTT
5010473 AATTCTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.72
Consensus pattern (13 bp):
TGCTATTTTTTTG
Found at i:5011580 original size:34 final size:33
Alignment explanation
Indices: 5011542--5011622 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
5011532 AAATGTCACT
* * *
5011542 ATTTAGCAGCGTTTGTATTTAAAAAATACTGTTA
1 ATTTAGTAGCGTTTGTA-TAAAAAAATACTGCTA
* * *
5011576 ATTTAGTGGTGTTTGTATAAAAAAATGCTGCTA
1 ATTTAGTAGCGTTTGTATAAAAAAATACTGCTA
*
5011609 ATATAGTAGCGTTT
1 ATTTAGTAGCGTTT
5011623 ATATGATAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (33 bp):
ATTTAGTAGCGTTTGTATAAAAAAATACTGCTA
Found at i:5013231 original size:160 final size:162
Alignment explanation
Indices: 5013049--5013342 Score: 382
Period size: 160 Copynumber: 1.8 Consensus size: 162
5013039 AACCAAAGAC
* * ****
5013049 AAGTTTAATATCATGGATTGAAGCCATCCAAACTATTAAAAGCCATCCAA-AAGTTTAATT-TGT
1 AAGTTTAATATCATGGATTGAAGCCATCCAAACTATTAAAAGACA-ACAATAACAACAATTATGT
* * *
5013112 ATTTTTGCC-TTTAAAAGACA-AAAATAGTCCTAAATAGATGTAAACGATAAC-TTTTTCATACA
65 ATTTTTACCAATTAAAAG-CATAAAA-AGTCCTAAATAGATGTAAACAATAACTTTTTTCATACA
5013174 TATCAACCGTAGAAATCAAGTTTAATCATTCAGAA
128 TATCAACCGTAGAAATCAAGTTTAATCATTCAGAA
* * * * * *
5013209 AAGTTTAATATCATGTATTGAAGCTATCCAAATTGTTAAAATAGAACAATAACAACAATTATGTA
1 AAGTTTAATATCATGGATTGAAGCCATCCAAACTATTAAAAGACAACAATAACAACAATTATGTA
*
5013274 TTTTTACCAATTAACAGCATAAAAAGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATAT
66 TTTTTACCAATTAAAAGCATAAAAAGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATAT
5013339 CAAC
131 CAAC
5013343 TATGGCAACT
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
159 3 0.03
160 44 0.39
161 38 0.34
162 28 0.25
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (162 bp):
AAGTTTAATATCATGGATTGAAGCCATCCAAACTATTAAAAGACAACAATAACAACAATTATGTA
TTTTTACCAATTAAAAGCATAAAAAGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATAT
CAACCGTAGAAATCAAGTTTAATCATTCAGAA
Found at i:5013325 original size:161 final size:163
Alignment explanation
Indices: 5013132--5013423 Score: 412
Period size: 162 Copynumber: 1.8 Consensus size: 163
5013122 TTAAAAGACA
* *
5013132 AAAATAGTCCTAAATAGATGTAAACGATAAC-TTTTTCATACATATCAACCGTAGAAA-TCAAGT
1 AAAATAGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATATCAACCATAGAAACT-AAGT
* * * * *
5013195 TTAAT-CATTCAGAAAAGTTTAATATCATGTATTGAAGCTATCCAAATTGTTAAAATAGAACAAT
65 TTAATAC-TTCAGAAAAGTTTAACATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAAT
5013259 AACAACAATTATGTATTTTTACCAATTAACAGCAT
129 AACAACAATTATGTATTTTTACCAATTAACAGCAT
* * *
5013294 AAAA-AGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATATCAACTATGGCAACTAAGTT
1 AAAATAGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATATCAACCATAGAAACTAAGTT
** * *
5013358 TAATACTTTGGATAAGTTTAACATCATGTATTGAAACTATGAAAACTATTAAAATAGAACAATAA
66 TAATACTTCAGAAAAGTTTAACATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAA
5013423 C
131 C
5013424 TGTTAATTTG
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
161 25 0.22
162 86 0.76
163 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (163 bp):
AAAATAGTCCTAAATAGATGTAAACAATAACTTTTTTCATACATATCAACCATAGAAACTAAGTT
TAATACTTCAGAAAAGTTTAACATCATGTATTGAAACTATCAAAACTATTAAAATAGAACAATAA
CAACAATTATGTATTTTTACCAATTAACAGCAT
Found at i:5021100 original size:28 final size:28
Alignment explanation
Indices: 5021065--5021130 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
5021055 TTGTTTATTG
*
5021065 AATGGTATTGTATGATATTGTTTTGCTA
1 AATGGTATTGTATGATATTGGTTTGCTA
*
5021093 AATGGTATTGTATGATATTGGTTTGCTG
1 AATGGTATTGTATGATATTGGTTTGCTA
5021121 AATGGT-TTGT
1 AATGGTATTGT
5021131 TGAATGATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.48
Consensus pattern (28 bp):
AATGGTATTGTATGATATTGGTTTGCTA
Found at i:5021128 original size:12 final size:12
Alignment explanation
Indices: 5021111--5021200 Score: 58
Period size: 12 Copynumber: 7.3 Consensus size: 12
5021101 TGTATGATAT
5021111 TGGTTTGCTGAA
1 TGGTTTGCTGAA
*
5021123 TGGTTTGTTGAA
1 TGGTTTGCTGAA
*
5021135 TGATGTTT-TTGAA
1 TG--GTTTGCTGAA
*
5021148 TGGTTTCCTGAA
1 TGGTTTGCTGAA
**
5021160 TGGTATTTTTGAA
1 TGGT-TTGCTGAA
* * *
5021173 -GATATTACTGAT
1 TGGT-TTGCTGAA
5021185 TGGTTTGCTGAA
1 TGGTTTGCTGAA
5021197 TGGT
1 TGGT
5021201 GTTTCTATAC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
11 4 0.06
12 39 0.63
13 15 0.24
14 4 0.06
ACGTcount: A:0.20, C:0.06, G:0.28, T:0.47
Consensus pattern (12 bp):
TGGTTTGCTGAA
Done.