Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 149 of 198
Found at i:47271667 original size:11 final size:12
Alignment explanation
Indices: 47271634--47271685 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 12
47271624 TATGTGTTAA
47271634 AAATATATTATT
1 AAATATATTATT
47271646 AAATTAGTATTATT
1 AAA-TA-TATTATT
47271660 AAAT-TATTATT
1 AAATATATTATT
*
47271671 -ATTATATT-TT
1 AAATATATTATT
47271681 AAATA
1 AAATA
47271686 AATAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 4 0.12
11 14 0.41
12 3 0.09
13 3 0.09
14 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
AAATATATTATT
Found at i:47271797 original size:3 final size:3
Alignment explanation
Indices: 47271791--47271846 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
47271781 AAGTAAATAA
47271791 TAT TAT 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
47271839 TAT TAT TA
1 TAT TAT TA
47271847 ACTAATGCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:47272105 original size:3 final size:3
Alignment explanation
Indices: 47272099--47272154 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
47272089 AATTATTACA
47272099 TAT TAT 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
47272147 TAT TAT TA
1 TAT TAT TA
47272155 ACTAATGCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:47272201 original size:17 final size:18
Alignment explanation
Indices: 47272179--47272217 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
47272169 GGAATAAAAT
*
47272179 AAAAGAATAAA-AGAAAC
1 AAAAGAAGAAATAGAAAC
47272196 AAAAGAAGAAATAGAAAC
1 AAAAGAAGAAATAGAAAC
47272214 AAAA
1 AAAA
47272218 TAGCTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAGAAGAAATAGAAAC
Found at i:47278597 original size:29 final size:30
Alignment explanation
Indices: 47278538--47278595 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
47278528 TCCGAGCCTT
*
47278538 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
47278568 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
47278596 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:47278826 original size:13 final size:13
Alignment explanation
Indices: 47278808--47278838 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47278798 TTCCAGCAAC
47278808 TATGAATTTATTT
1 TATGAATTTATTT
47278821 TATGAATTTATTT
1 TATGAATTTATTT
*
47278834 GATGA
1 TATGA
47278839 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:47279008 original size:50 final size:50
Alignment explanation
Indices: 47278933--47279175 Score: 405
Period size: 50 Copynumber: 4.8 Consensus size: 50
47278923 ATTTGGGTAA
47278933 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
47278983 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
47279033 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
47279083 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
47279133 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
47279176 TGTTATTATC
Statistics
Matches: 180, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 146 0.81
51 34 0.19
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:47281451 original size:24 final size:23
Alignment explanation
Indices: 47281406--47281483 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
47281396 ACACACCTTA
* *
47281406 GCTCTTATGAGCTTTTCGATTATG
1 GCTCTTATGAGC-TTCCCATTATG
47281430 GCTCTTCATGAGCTTCCCATTAATTG
1 GCTCTT-ATGAGCTTCCCATT-A-TG
*
47281456 GCTCTTTGTGAGCTTCCCGA-TATG
1 GCTC-TTATGAGCTTCCC-ATTATG
47281480 GCTC
1 GCTC
47281484 GCTTGAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 18 0.39
25 8 0.17
26 17 0.37
27 3 0.07
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (23 bp):
GCTCTTATGAGCTTCCCATTATG
Found at i:47285260 original size:131 final size:131
Alignment explanation
Indices: 47285038--47285373 Score: 496
Period size: 131 Copynumber: 2.6 Consensus size: 131
47285028 ATCTTTTCGG
* *
47285038 TATTCC-CTTGCTGGTCAAGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAA
1 TATTCCAC-TGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAA
* * * * *
47285102 GATGAGATTCGCCGTTTTCGATCTGCTCCGCTACTGATTAGGGAGGTAAGATCTGCAATCTCCAA
65 GATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGATTAGGGAGGCAAAATCTGCAATCTCCAA
47285167 CC
130 CC
* * * * * *
47285169 TATTCCACTGCTGGTCAGGGACATAAGACGTGTGGCTTAAACCTATTTCCTTACTCTTGGGGAAG
1 TATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAG
* *
47285234 ATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGTTTAGGGAGGCAAAATCTGCAATTTCCAAC
66 ATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGATTAGGGAGGCAAAATCTGCAATCTCCAAC
47285299 C
131 C
*
47285300 TATTCCACTGCTGTTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGG-AG
1 TATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAG
47285364 AATAAGATTC
66 -ATAAGATTC
47285374 GTCGCTTAGA
Statistics
Matches: 181, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
130 2 0.01
131 178 0.98
132 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (131 bp):
TATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAG
ATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGATTAGGGAGGCAAAATCTGCAATCTCCAAC
C
Found at i:47285398 original size:43 final size:43
Alignment explanation
Indices: 47285334--47285586 Score: 364
Period size: 43 Copynumber: 5.9 Consensus size: 43
47285324 AGGACTTGTG
* *
47285334 GCTTAAATCTGTTTCCCTACTCCTGGGG-AGAATAAGATTCGTC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAG-ATAAGATTCGCC
* * * *
47285377 GCTTAGATTTGTTTCCTTACTCCTGGGGAAAATAAGATTCTCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
* * * *
47285420 ACTTAGATCTATTTCCCTAGTTCTGGGGAAGATAAGATTCGCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
47285463 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
* * *
47285506 GCTTAGATCTGTTTCCCTACTCATTGGGAAGATAAGATTCACC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
*
47285549 GCTTAGATCTGTTTCCCTACTCTTGGGGAAGATAAGAT
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
47285587 CCGCAATATT
Statistics
Matches: 186, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 185 0.99
44 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (43 bp):
GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
Found at i:47306863 original size:17 final size:17
Alignment explanation
Indices: 47306841--47306877 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
47306831 TAAGCCACAT
47306841 ATTGATGATAACAGAAA
1 ATTGATGATAACAGAAA
*
47306858 ATTGATGATAACATAAA
1 ATTGATGATAACAGAAA
47306875 ATT
1 ATT
47306878 AAGCCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (17 bp):
ATTGATGATAACAGAAA
Found at i:47313965 original size:26 final size:27
Alignment explanation
Indices: 47313943--47313993 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
47313933 ATATAATGTT
47313943 ATTG-ATGATTTG-CGATTTTTAATTAG
1 ATTGAATGATTTGTC-ATTTTTAATTAG
47313969 ATTGAATGATTTGTCATTTTTAATT
1 ATTGAATGATTTGTCATTTTTAATT
47313994 GCAAGCAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 4 0.17
27 18 0.78
28 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (27 bp):
ATTGAATGATTTGTCATTTTTAATTAG
Found at i:47317100 original size:2 final size:2
Alignment explanation
Indices: 47317093--47317145 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
47317083 ACATATCGGG
47317093 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
47317135 GA GA GA GA GA G
1 GA GA GA GA GA G
47317146 TTATATATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47322546 original size:31 final size:30
Alignment explanation
Indices: 47322511--47322570 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
47322501 GGAGGTGGGA
*
47322511 TGGGAAGAGAGTAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAGTAAAAATTTTAGGGGAAAAG
* *
47322542 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAGTAAAAATTTTAGGGGAAAA
47322571 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAGTAAAAATTTTAGGGGAAAAG
Found at i:47322801 original size:9 final size:9
Alignment explanation
Indices: 47322784--47322820 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
47322774 TATAGTTTGA
*
47322784 TATTTGAAT
1 TATTCGAAT
47322793 TATTCGAAT
1 TATTCGAAT
*
47322802 TATTCGAGT
1 TATTCGAAT
47322811 TATTCGAAT
1 TATTCGAAT
47322820 T
1 T
47322821 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:47323763 original size:15 final size:16
Alignment explanation
Indices: 47323726--47323764 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
47323716 TTTAAATACA
*
47323726 AGTTGTTCTAAATAAT
1 AGTTATTCTAAATAAT
*
47323742 GGTTATTCTAAAT-AT
1 AGTTATTCTAAATAAT
47323757 AGTTATTC
1 AGTTATTC
47323765 CTGAAACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (16 bp):
AGTTATTCTAAATAAT
Found at i:47324487 original size:23 final size:23
Alignment explanation
Indices: 47324449--47324497 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
47324439 CGTCGCGATG
** **
47324449 TGAGAGAGTTTTTCATCGTGACA
1 TGAGAGAGTTCCTCATCACGACA
47324472 TGAGAGAGTTCCTCATCACGACA
1 TGAGAGAGTTCCTCATCACGACA
47324495 TGA
1 TGA
47324498 CACACTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (23 bp):
TGAGAGAGTTCCTCATCACGACA
Found at i:47326673 original size:20 final size:20
Alignment explanation
Indices: 47326648--47326695 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
47326638 TATCGATCTA
*
47326648 GTATCGATACT-TTTCTTAAG
1 GTATCGATA-TATTTCCTAAG
47326668 GTATCGATATATTTCCTAAG
1 GTATCGATATATTTCCTAAG
47326688 GTATCGAT
1 GTATCGAT
47326696 TTTCCTTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (20 bp):
GTATCGATATATTTCCTAAG
Found at i:47326701 original size:17 final size:18
Alignment explanation
Indices: 47326648--47326701 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
47326638 TATCGATCTA
*
47326648 GTATCGATACTTTTCTTAAG
1 GTATCGA-A-TTTTCCTAAG
47326668 GTATCGATATATTTCCTAAG
1 GTATCGA-AT-TTTCCTAAG
47326688 GTATCG-ATTTTCCT
1 GTATCGAATTTTCCT
47326702 TCTCCAACGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.19
18 2 0.06
19 1 0.03
20 23 0.72
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (18 bp):
GTATCGAATTTTCCTAAG
Found at i:47333468 original size:25 final size:25
Alignment explanation
Indices: 47333423--47333483 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
47333413 AAATTTTTAT
* *
47333423 TTAAAAATATTTTAAAAATTACAAA
1 TTAAAAATATTTGAAAAATTAAAAA
*
47333448 TTAAAAA-ATTTGAAATTATTAAAAA
1 TTAAAAATATTTGAAA-AATTAAAAA
*
47333473 TTTATAAATAT
1 -TTAAAAATAT
47333484 AAAATTTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 7 0.24
25 14 0.48
26 6 0.21
27 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
TTAAAAATATTTGAAAAATTAAAAA
Found at i:47336048 original size:18 final size:18
Alignment explanation
Indices: 47336025--47336064 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47336015 CAAATCTTCA
* *
47336025 GTATTTCTCTGTCTTTTC
1 GTATTTCTCTCTATTTTC
*
47336043 GTATTTCTTTCTATTTTC
1 GTATTTCTCTCTATTTTC
47336061 GTAT
1 GTAT
47336065 ATTTTTTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.62
Consensus pattern (18 bp):
GTATTTCTCTCTATTTTC
Found at i:47343318 original size:24 final size:24
Alignment explanation
Indices: 47343262--47343328 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
47343252 AAAAATATAG
* *
47343262 AAAATTATAAAATTTATTATAATGAA
1 AAAAATATAAAA--TATTAAAATGAA
47343288 AAAAATATAAAATATTAAAAT-AA
1 AAAAATATAAAATATTAAAATGAA
*
47343311 AAATAATATTAAAGTATT
1 AAA-AATA-TAAAATATT
47343329 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.14
24 12 0.33
25 8 0.22
26 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (24 bp):
AAAAATATAAAATATTAAAATGAA
Found at i:47343358 original size:9 final size:9
Alignment explanation
Indices: 47343335--47343466 Score: 65
Period size: 9 Copynumber: 14.4 Consensus size: 9
47343325 TATTTTTTTA
*
47343335 AAAAAGTAT
1 AAAAATTAT
*
47343344 ATAAATTAT
1 AAAAATTAT
47343353 AAAAA-TAT
1 AAAAATTAT
* * *
47343361 ATAAATGAA
1 AAAAATTAT
47343370 AAAAATGTA-
1 AAAAAT-TAT
*
47343379 AAAGATTAT
1 AAAAATTAT
47343388 GAAAAA-TATT
1 -AAAAATTA-T
*
47343398 TAAAA-TAT
1 AAAAATTAT
*
47343406 AGATAATTATT
1 A-AAAATTA-T
*
47343417 AAAAATAAT
1 AAAAATTAT
*
47343426 AATAATTAT
1 AAAAATTAT
47343435 AAAATATTAT
1 AAAA-ATTAT
**
47343445 AAAAAGCAT
1 AAAAATTAT
*
47343454 AAAAAATAT
1 AAAAATTAT
47343463 AAAA
1 AAAA
47343467 CAAATTAAAA
Statistics
Matches: 92, Mismatches: 22, Indels: 18
0.70 0.17 0.14
Matches are distributed among these distances:
8 10 0.11
9 58 0.63
10 22 0.24
11 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:47343361 original size:17 final size:17
Alignment explanation
Indices: 47343335--47343406 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
47343325 TATTTTTTTA
47343335 AAAAAGTATATAAATTAT
1 AAAAA-TATATAAATTAT
* *
47343353 AAAAATATATAAATGAA
1 AAAAATATATAAATTAT
* *
47343370 AAAAATGTAAAAGATTAT
1 AAAAATATATAA-ATTAT
* *
47343388 GAAAAATATTTAAAATAT
1 -AAAAATATATAAATTAT
47343406 A
1 A
47343407 GATAATTATT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
17 21 0.50
18 12 0.29
19 9 0.21
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
AAAAATATATAAATTAT
Found at i:47343365 original size:10 final size:10
Alignment explanation
Indices: 47343341--47343499 Score: 53
Period size: 9 Copynumber: 16.8 Consensus size: 10
47343331 TTTAAAAAAG
*
47343341 TATATAAAT-
1 TATAAAAATA
47343350 TATAAAAATA
1 TATAAAAATA
47343360 TAT--AAATGA
1 TATAAAAAT-A
*
47343369 -A-AAAAATG
1 TATAAAAATA
*
47343377 TA-AAAGAT-
1 TATAAAAATA
47343385 TATGAAAAATA
1 TAT-AAAAATA
*
47343396 T-TTAAAATA
1 TATAAAAATA
* * *
47343405 TAGATAATTA
1 TATAAAAATA
47343415 T-TAAAAATA
1 TATAAAAATA
*
47343424 -ATAATAAT-
1 TATAAAAATA
47343432 TAT-AAAATA
1 TATAAAAATA
*
47343441 TTATAAAAAGCA
1 -TATAAAAA-TA
47343453 TA-AAAAATA
1 TATAAAAATA
47343462 TA-AAACAA-A
1 TATAAA-AATA
47343471 T-TAAAAATA
1 TATAAAAATA
*
47343480 TATGAAAAAAA
1 TAT-AAAAATA
47343491 TTATAAAAA
1 -TATAAAAA
47343500 CCTTTTTTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 40
0.66 0.10 0.24
Matches are distributed among these distances:
8 13 0.12
9 52 0.46
10 25 0.22
11 18 0.16
12 4 0.04
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
TATAAAAATA
Found at i:47343421 original size:19 final size:19
Alignment explanation
Indices: 47343394--47343438 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
47343384 TTATGAAAAA
*
47343394 TATTTAAAAT-ATAGATAAT
1 TATTAAAAATAATA-ATAAT
47343413 TATTAAAAATAATAATAAT
1 TATTAAAAATAATAATAAT
47343432 TA-TAAAA
1 TATTAAAA
47343439 TATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TATTAAAAATAATAATAAT
Found at i:47343433 original size:16 final size:17
Alignment explanation
Indices: 47343392--47343440 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
47343382 GATTATGAAA
*
47343392 AATATTTAAAATATAGAT
1 AATAATTAAAA-ATAGAT
*
47343410 AATTATTAAAAATA-AT
1 AATAATTAAAAATAGAT
47343426 AATAATTATAAAATA
1 AATAATTA-AAAATA
47343441 TTATAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.33
17 9 0.33
18 9 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAATTAAAAATAGAT
Found at i:47343446 original size:16 final size:17
Alignment explanation
Indices: 47343397--47343446 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
47343387 TGAAAAATAT
47343397 TTAAAATATAGATAATTA
1 TTAAAATATA-ATAATTA
47343415 TTAAAAATAATAATAATTA
1 TT-AAAAT-ATAATAATTA
*
47343434 -TAAAATATTATAA
1 TTAAAATATAATAA
47343447 AAAGCATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 6 0.21
17 5 0.17
18 3 0.10
19 12 0.41
20 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAAAATATAATAATTA
Found at i:47343477 original size:20 final size:21
Alignment explanation
Indices: 47343452--47343499 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
47343442 TATAAAAAGC
47343452 ATAAAAAATAT-AAAACAAATT
1 ATAAAAAATATGAAAA-AAATT
*
47343473 A-AAAATATATGAAAAAAATT
1 ATAAAAAATATGAAAAAAATT
47343493 ATAAAAA
1 ATAAAAA
47343500 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
ATAAAAAATATGAAAAAAATT
Found at i:47345012 original size:25 final size:25
Alignment explanation
Indices: 47344966--47345013 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
47344956 TTAAATTAAA
** * *
47344966 ATAAAATTTTATATAAATTTCATCT
1 ATAAAATTAAATAAAAAATTCATCT
47344991 ATAAAATTAAATAAAAAATTCAT
1 ATAAAATTAAATAAAAAATTCAT
47345014 GTGTACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAATTAAATAAAAAATTCATCT
Found at i:47349151 original size:41 final size:41
Alignment explanation
Indices: 47349096--47349173 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
47349086 ATTATTTATA
* * *
47349096 CCCTGTATTGCACATATGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTGAATTACACATAAGTGCCCCTGTTTGTACTTCGGTAC
*
47349137 CCCTGAATTACACATAAGTGCCCTTGTTTGTACTTCG
1 CCCTGAATTACACATAAGTGCCCCTGTTTGTACTTCG
47349174 ACAACCTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (41 bp):
CCCTGAATTACACATAAGTGCCCCTGTTTGTACTTCGGTAC
Found at i:47349185 original size:41 final size:41
Alignment explanation
Indices: 47349095--47349193 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
47349085 AATTATTTAT
* * * **
47349095 ACCCTGTATTGCACATATGTGCCCCTGTTTGTACTTCGGTA
1 ACCCTGAATTACACATAAGTGCCCCTGTTTGTACTTCGACA
* *
47349136 CCCCTGAATTACACATAAGTGCCCTTGTTTGTACTTCGACA
1 ACCCTGAATTACACATAAGTGCCCCTGTTTGTACTTCGACA
* *
47349177 ACCTTGAATTGCACATA
1 ACCCTGAATTACACATA
47349194 CTTGCCCTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (41 bp):
ACCCTGAATTACACATAAGTGCCCCTGTTTGTACTTCGACA
Found at i:47349200 original size:41 final size:39
Alignment explanation
Indices: 47349095--47349205 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 39
47349085 AATTATTTAT
* **
47349095 ACCCTGTATTGCACATATGTGCCCCTGTTTGTACTTCGGTA
1 ACCCTGAATTGCACATAT-TG-CCCTGTTTGTACTTCGACA
* * *
47349136 CCCCTGAATTACACATAAGTGCCCTTGTTTGTACTTCGACA
1 ACCCTGAATTGCACAT-ATTGCCC-TGTTTGTACTTCGACA
*
47349177 ACCTTGAATTGCACATACTTGCCCTGTTT
1 ACCCTGAATTGCACATA-TTGCCCTGTTT
47349206 ACACTTCAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
40 9 0.16
41 47 0.82
42 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (39 bp):
ACCCTGAATTGCACATATTGCCCTGTTTGTACTTCGACA
Found at i:47350458 original size:10 final size:10
Alignment explanation
Indices: 47350430--47350472 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
47350420 ATAGAAAAAA
47350430 AATTCTTATTT
1 AATT-TTATTT
*
47350441 TA-TTTATTT
1 AATTTTATTT
47350450 AATTTTATTT
1 AATTTTATTT
47350460 AATTTTATGTT
1 AATTTTAT-TT
47350471 AA
1 AA
47350473 AGTAGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 7 0.25
10 16 0.57
11 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
AATTTTATTT
Found at i:47350771 original size:12 final size:12
Alignment explanation
Indices: 47350754--47350784 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
47350744 CAAATCCGAG
47350754 TTTAATTTCCAA
1 TTTAATTTCCAA
*
47350766 TTTAATTTCTAA
1 TTTAATTTCCAA
47350778 TTTAATT
1 TTTAATT
47350785 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTAATTTCCAA
Found at i:47368803 original size:18 final size:18
Alignment explanation
Indices: 47368779--47368822 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
47368769 GTTTAGAAAT
47368779 TATTTTTATCA-T-ATTAA
1 TATTTTTAT-AGTAATTAA
47368796 TAATTTTTATAGTAATTAA
1 T-ATTTTTATAGTAATTAA
47368815 TATTTTTA
1 TATTTTTA
47368823 AAAAGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 16 0.67
19 6 0.25
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTTTTATAGTAATTAA
Found at i:47373252 original size:90 final size:91
Alignment explanation
Indices: 47373090--47373267 Score: 229
Period size: 90 Copynumber: 2.0 Consensus size: 91
47373080 TGTTAAACCT
* * *
47373090 ATGTACCATAATAAAGCACATATTAATAGTTTAAGTACTACATATGATACTTTTAAAGTACAAGT
1 ATGTACCATAATAAAACACATATTAACAGTTTAAGTACTACATATGATACTTTTAAAATACAAGT
47373155 ACCACATT-GACATTTATGAAAGAAC
66 ACCACATTGGACATTTATGAAAGAAC
* * * *
47373180 ATGTACCATAATAAAACACATATTGACAGTTTAGGTACTATAT-TGAATA-TTTTCAAAATA-TA
1 ATGTACCATAATAAAACACATATTAACAGTTTAAGTACTACATATG-ATACTTTT-AAAATACAA
*
47373242 GATACTACATTGGACATTTATGAAAG
64 G-TACCACATTGGACATTTATGAAAG
47373268 TACAAAAACC
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
89 8 0.11
90 54 0.71
91 14 0.18
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (91 bp):
ATGTACCATAATAAAACACATATTAACAGTTTAAGTACTACATATGATACTTTTAAAATACAAGT
ACCACATTGGACATTTATGAAAGAAC
Found at i:47377505 original size:2 final size:2
Alignment explanation
Indices: 47377498--47377526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47377488 TTATTCAAAG
47377498 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 T
47377527 TGTATTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47378386 original size:42 final size:41
Alignment explanation
Indices: 47378340--47378436 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
47378330 ATACATATCT
** *
47378340 TTTACTTTGTATATTAAAGACATCATTTTTTTTATTCATAAA
1 TTTACTTTGTATATTAAAGACAT-AAATTTTTAATTCATAAA
* * *
47378382 TTTACTTTATATATTAAAGAGATAAATTTTTAATTTATAAA
1 TTTACTTTGTATATTAAAGACATAAATTTTTAATTCATAAA
* *
47378423 TTAATTTTGTATAT
1 TTTACTTTGTATAT
47378437 AATTAAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 25 0.54
42 21 0.46
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (41 bp):
TTTACTTTGTATATTAAAGACATAAATTTTTAATTCATAAA
Found at i:47378424 original size:41 final size:42
Alignment explanation
Indices: 47378340--47378424 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
47378330 ATACATATCT
* ** *
47378340 TTTACTTTGTATATTAAAGACATCATTTTTTTTATTCATAAA
1 TTTACTTTATATATTAAAGACATCAAATTTTTAATTCATAAA
* *
47378382 TTTACTTTATATATTAAAGAGAT-AAATTTTTAATTTATAAA
1 TTTACTTTATATATTAAAGACATCAAATTTTTAATTCATAAA
47378423 TT
1 TT
47378425 AATTTTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 16 0.43
42 21 0.57
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (42 bp):
TTTACTTTATATATTAAAGACATCAAATTTTTAATTCATAAA
Found at i:47380267 original size:18 final size:18
Alignment explanation
Indices: 47380240--47380275 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47380230 ACCTATTGAA
47380240 TTTATCGATACCAATTTT
1 TTTATCGATACCAATTTT
* *
47380258 TTTATTGATACCACTTTT
1 TTTATCGATACCAATTTT
47380276 GCATACTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTATCGATACCAATTTT
Found at i:47387273 original size:6 final size:6
Alignment explanation
Indices: 47387264--47387306 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
47387254 GTTAATCCTT
47387264 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA A
1 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA A
47387307 ATCACTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.00, T:0.16
Consensus pattern (6 bp):
ATCCCA
Found at i:47387801 original size:23 final size:22
Alignment explanation
Indices: 47387763--47387826 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
47387753 AATATAAACG
*
47387763 AAATTAAAATAA-AAATA-GTTT
1 AAATTAAAAAAATAAATATG-TT
47387784 AAATTAAAAAAAGTAAATATGTT
1 AAATTAAAAAAA-TAAATATGTT
* *
47387807 ATATTAAAAATATTAAATAT
1 AAATTAAAAA-AATAAATAT
47387827 CAAAATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.31
23 23 0.64
24 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
AAATTAAAAAAATAAATATGTT
Found at i:47394766 original size:23 final size:20
Alignment explanation
Indices: 47394722--47394777 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
47394712 CTTTTTTACA
*
47394722 AGAAAACCAAAAAGAAAAAAG
1 AGAAAACC-GAAAGAAAAAAG
47394743 AATGAAAACCGAAAGAAAAGAAG
1 -A-GAAAACCGAAAGAAAA-AAG
47394766 AGAAAA-CGAAAG
1 AGAAAACCGAAAG
47394778 TGGTAATCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 6 0.19
21 5 0.16
22 10 0.32
23 10 0.32
ACGTcount: A:0.70, C:0.09, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAAACCGAAAGAAAAAAG
Found at i:47398243 original size:28 final size:26
Alignment explanation
Indices: 47398189--47398243 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
47398179 AAACTCTTCT
*
47398189 AAAAGAAAAATCAAGAGAAATTCTTA
1 AAAAGAAAAATCAAGAGAAATTATTA
*
47398215 AAAAGAAAAACTCAAAGAGAACTTATTA
1 AAAAGAAAAA-TC-AAGAGAAATTATTA
47398243 A
1 A
47398244 CTCAAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 2 0.08
28 13 0.52
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (26 bp):
AAAAGAAAAATCAAGAGAAATTATTA
Found at i:47399106 original size:26 final size:27
Alignment explanation
Indices: 47399058--47399112 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
47399048 CTTAATATTT
* *
47399058 AAGTAAATATATATAATATAATAA-TA
1 AAGTAAATATATATAAAAAAATAAGTA
47399084 AAGTAAATATA-ATAAAACAAATAAGTA
1 AAGTAAATATATATAAAA-AAATAAGTA
47399111 AA
1 AA
47399113 TGAAACAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 16 0.64
27 4 0.16
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (27 bp):
AAGTAAATATATATAAAAAAATAAGTA
Found at i:47399164 original size:13 final size:14
Alignment explanation
Indices: 47399148--47399178 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
47399138 ATAAAAATTG
47399148 AGAAAG-AAAAGAA
1 AGAAAGAAAAAGAA
47399161 AGAAAGAAAAAGAA
1 AGAAAGAAAAAGAA
47399175 AGAA
1 AGAA
47399179 GGACTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAGAA
Found at i:47406672 original size:14 final size:14
Alignment explanation
Indices: 47406647--47406681 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
47406637 ATCAAAATTG
47406647 AGAAAG-AAAAGAA
1 AGAAAGAAAAAGAA
47406660 AGAAAGAAAAAGAA
1 AGAAAGAAAAAGAA
47406674 AG-AAGAAA
1 AGAAAGAAA
47406682 CGCACGACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAAGAA
Found at i:47412806 original size:23 final size:23
Alignment explanation
Indices: 47412780--47412855 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
47412770 ATAAGTGCCA
47412780 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
47412803 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
47412826 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
47412849 CACTGAT
1 CACTGAT
47412856 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:47412955 original size:8 final size:8
Alignment explanation
Indices: 47412942--47412970 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
47412932 ACCCGGGACT
47412942 CACTGTAA
1 CACTGTAA
47412950 CACTGTAA
1 CACTGTAA
47412958 CACTGTAA
1 CACTGTAA
47412966 CACTG
1 CACTG
47412971 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:47413101 original size:18 final size:17
Alignment explanation
Indices: 47413075--47413113 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
47413065 ATTTTCCTTC
47413075 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
47413092 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
47413110 CACA
1 CACA
47413114 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:47415808 original size:23 final size:23
Alignment explanation
Indices: 47415781--47415827 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
47415771 ATTCTTTACT
47415781 ATATTCTCATATTA-ACTTTATAA
1 ATATTCTCATATTATA-TTTATAA
* *
47415804 ATATTCTTATTTTATATTTATAA
1 ATATTCTCATATTATATTTATAA
47415827 A
1 A
47415828 CTTCTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTCTCATATTATATTTATAA
Found at i:47424749 original size:20 final size:21
Alignment explanation
Indices: 47424707--47424760 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
47424697 TATACTGGTG
* * *
47424707 GCGGTAAGATTAGTTATTTTA
1 GCGGTGAGATTAGGTATTGTA
47424728 GCGGTGAGATT-GGTATTGTA
1 GCGGTGAGATTAGGTATTGTA
*
47424748 GCAGTGAGATTAG
1 GCGGTGAGATTAG
47424761 AAATAGCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.26, C:0.06, G:0.33, T:0.35
Consensus pattern (21 bp):
GCGGTGAGATTAGGTATTGTA
Found at i:47427218 original size:20 final size:20
Alignment explanation
Indices: 47427189--47427238 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
47427179 ATCAGCATAC
47427189 ATACAACATAGCATTTTAAA
1 ATACAACATAGCATTTTAAA
* *
47427209 ATACAGCATAGCATTTTTAA
1 ATACAACATAGCATTTTAAA
47427229 ATACAACATA
1 ATACAACATA
47427239 AAACTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (20 bp):
ATACAACATAGCATTTTAAA
Found at i:47427453 original size:29 final size:29
Alignment explanation
Indices: 47427417--47427494 Score: 156
Period size: 29 Copynumber: 2.7 Consensus size: 29
47427407 AAGAACAACT
47427417 CCGATTCTACAGAATAGCAAATAAACTCA
1 CCGATTCTACAGAATAGCAAATAAACTCA
47427446 CCGATTCTACAGAATAGCAAATAAACTCA
1 CCGATTCTACAGAATAGCAAATAAACTCA
47427475 CCGATTCTACAGAATAGCAA
1 CCGATTCTACAGAATAGCAA
47427495 GGAATCATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.21
Consensus pattern (29 bp):
CCGATTCTACAGAATAGCAAATAAACTCA
Found at i:47428168 original size:23 final size:23
Alignment explanation
Indices: 47428138--47428181 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47428128 AGTTTTTATA
47428138 TTTTTATATTTAAGAATTTAACC
1 TTTTTATATTTAAGAATTTAACC
* *
47428161 TTTTTATATTTTAGATTTTAA
1 TTTTTATATTTAAGAATTTAA
47428182 AATTTAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTTTATATTTAAGAATTTAACC
Found at i:47428619 original size:22 final size:22
Alignment explanation
Indices: 47428578--47428619 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47428568 CTTTTTATAT
**
47428578 ATATTATTATATTACTTAAAAA
1 ATATTATTATATTAAGTAAAAA
*
47428600 ATATTATTATGTTAAGTAAA
1 ATATTATTATATTAAGTAAA
47428620 CAATTAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATTATTATATTAAGTAAAAA
Found at i:47429968 original size:32 final size:33
Alignment explanation
Indices: 47429931--47430003 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
47429921 TATTATTATT
*
47429931 TAATTTAAGTTAGAGT-TAAATAGAA-AAATTAA
1 TAATTTAAGTTA-AGTATAAATAAAATAAATTAA
* * *
47429963 TAATTTAATTTAAGTATAATTAAAATAAATTAT
1 TAATTTAAGTTAAGTATAAATAAAATAAATTAA
47429996 TAATTTAA
1 TAATTTAA
47430004 TAATTTAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.09
32 18 0.51
33 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (33 bp):
TAATTTAAGTTAAGTATAAATAAAATAAATTAA
Found at i:47429998 original size:36 final size:36
Alignment explanation
Indices: 47429916--47429999 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 36
47429906 TTATTTAATT
*
47429916 TAAATTATT-ATTATTTAATTTAAGTTAGAGTTAAA
1 TAAATTATTAATAATTTAATTTAAGTTAGAGTTAAA
**
47429951 TAGAAAAATTAATAATTTAATTTAAGTATA-A-TTAAAA
1 TA-AATTATTAATAATTTAATTTAAGT-TAGAGTT-AAA
47429988 TAAATTATTAAT
1 TAAATTATTAAT
47430000 TTAATAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
35 2 0.05
36 15 0.38
37 21 0.52
38 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (36 bp):
TAAATTATTAATAATTTAATTTAAGTTAGAGTTAAA
Found at i:47430000 original size:33 final size:32
Alignment explanation
Indices: 47429925--47430004 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
47429915 TTAAATTATT
* *
47429925 ATTATTTAATTTAAGTTAGAGTTAAATAGAAAA
1 ATTA-TTAATTTAATTTAGAGTTAAATAAAAAA
* *
47429958 ATTAATAATTTAATTTA-AGTATAATTAAAATAA
1 ATTATTAATTTAATTTAGAGT-TAAATAAAA-AA
47429991 ATTATTAATTTAAT
1 ATTATTAATTTAAT
47430005 AATTTAGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 3 0.08
32 18 0.45
33 19 0.47
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (32 bp):
ATTATTAATTTAATTTAGAGTTAAATAAAAAA
Found at i:47433423 original size:41 final size:41
Alignment explanation
Indices: 47433362--47433439 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
47433352 TTTCAACAGA
47433362 TTCACCGGCATCAAGACTGCTAGACGTAAAGTCTGAAACAT
1 TTCACCGGCATCAAGACTGCTAGACGTAAAGTCTGAAACAT
*
47433403 TTCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAA
1 TTCACCGGCATCAAGACTGCTAGACGTAAAGTCTGAA
47433440 TTATCTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (41 bp):
TTCACCGGCATCAAGACTGCTAGACGTAAAGTCTGAAACAT
Found at i:47435685 original size:21 final size:21
Alignment explanation
Indices: 47435639--47435690 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
47435629 GCTACAACTT
* *
47435639 AAAGCAGATGCAGCAGCGAGG
1 AAAGCAGAGGCAGCAGCGAGA
* *
47435660 GAAGCAGAGGCAGCAGTGAGA
1 AAAGCAGAGGCAGCAGCGAGA
*
47435681 AAAGCTGAGG
1 AAAGCAGAGG
47435691 TTCAAAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.40, T:0.06
Consensus pattern (21 bp):
AAAGCAGAGGCAGCAGCGAGA
Found at i:47435728 original size:87 final size:87
Alignment explanation
Indices: 47435574--47435864 Score: 420
Period size: 87 Copynumber: 3.3 Consensus size: 87
47435564 ACTCAACTTA
* * *
47435574 AAGCGGAGGCAACATTGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
1 AAGCAGAGGCAGCAGTGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
*
47435639 AAAGCAGATGCAGCAGCGAGGG
66 AAAGCAGATGCAGCAGTGAGGG
* * *
47435661 AAGCAGAGGCAGCAGTGAGAAAAGCTGAGGTTCAAAGAAAATATGAAGAACTTCAGCTACAATTT
1 AAGCAGAGGCAGCAGTGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
* * *
47435726 AAAGCAGATACAGCAATGAGAG
66 AAAGCAGATGCAGCAGTGAGGG
* *
47435748 AAGCAGAGGCAGCAGCGAGAGAAGCTAAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
1 AAGCAGAGGCAGCAGTGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
*
47435813 AAATCAGATGCAGCAGTGAGGG
66 AAAGCAGATGCAGCAGTGAGGG
* * ** *
47435835 AAGCAAAGCCAGCAGCAAGAGAAGCAGAGG
1 AAGCAGAGGCAGCAGTGAGAGAAGCTGAGG
47435865 CTACAGCGAG
Statistics
Matches: 180, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 180 1.00
ACGTcount: A:0.43, C:0.16, G:0.28, T:0.13
Consensus pattern (87 bp):
AAGCAGAGGCAGCAGTGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
AAAGCAGATGCAGCAGTGAGGG
Found at i:47435751 original size:21 final size:21
Alignment explanation
Indices: 47435727--47435772 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
47435717 CTACAATTTA
* *
47435727 AAGCAGATACAGCAATGAGAG
1 AAGCAGAGACAGCAACGAGAG
* *
47435748 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGACAGCAACGAGAG
47435769 AAGC
1 AAGC
47435773 TAAGGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.35, T:0.04
Consensus pattern (21 bp):
AAGCAGAGACAGCAACGAGAG
Found at i:47436331 original size:43 final size:43
Alignment explanation
Indices: 47436213--47436387 Score: 176
Period size: 43 Copynumber: 4.1 Consensus size: 43
47436203 TCGTCTTCTT
* * * * *
47436213 TAGCGGCGTTTATAAAAAAGGCGACGTTAAAAGTTATGATCTA
1 TAGCGGCGTTTGTAGAAAAGGCGCCGCTAAAAGTCATGATCTA
* * * *
47436256 TAGCGGCG-TTGTGGGAGAA-GCGCCGCAAAAAGTCATGACCTA
1 TAGCGGCGTTTGT-AGAAAAGGCGCCGCTAAAAGTCATGATCTA
* *
47436298 TAGCGGCGTTTGTAGGAAAGGCGCCGCGAAAAGTCATGATCTA
1 TAGCGGCGTTTGTAGAAAAGGCGCCGCTAAAAGTCATGATCTA
** * *
47436341 TAGCAACGTTTGTA-AAAAGATCACCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTAGAAAAG-GCGCCGCTAAAAGTCATGATCTA
47436384 TAGC
1 TAGC
47436388 AATGTTTGTG
Statistics
Matches: 108, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
42 36 0.33
43 72 0.67
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (43 bp):
TAGCGGCGTTTGTAGAAAAGGCGCCGCTAAAAGTCATGATCTA
Found at i:47437931 original size:12 final size:12
Alignment explanation
Indices: 47437914--47437938 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47437904 TATTTGATTC
47437914 AAATTCAAATTT
1 AAATTCAAATTT
47437926 AAATTCAAATTT
1 AAATTCAAATTT
47437938 A
1 A
47437939 TTTACCTAAA
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTCAAATTT
Found at i:47445224 original size:23 final size:23
Alignment explanation
Indices: 47445181--47445225 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
47445171 TTTCTCACAT
* *
47445181 TTTCAATTCAATCATTTTCCACC
1 TTTCAATTCAATAATTATCCACC
47445204 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATT-ATCCAC
47445226 AATTCACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTCAATTCAATAATTATCCACC
Found at i:47445378 original size:3 final size:3
Alignment explanation
Indices: 47445370--47445413 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
47445360 CCACTCATTT
47445370 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47445414 CTTACCTCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47446905 original size:30 final size:31
Alignment explanation
Indices: 47446871--47446934 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
47446861 TACATTTGTC
* * *
47446871 TTAATCTAATTACTTCATTAA-AAAAATCTT
1 TTAATATAATAACTTAATTAATAAAAATCTT
* *
47446901 TTAATATAATAATTTAATTAATAAATATCTT
1 TTAATATAATAACTTAATTAATAAAAATCTT
47446932 TTA
1 TTA
47446935 CTTCAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAATATAATAACTTAATTAATAAAAATCTT
Found at i:47447092 original size:3 final size:3
Alignment explanation
Indices: 47447037--47447077 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
47447027 TTGGTTTATT
* *
47447037 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47447078 TAAAACCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:47453407 original size:22 final size:22
Alignment explanation
Indices: 47453377--47453438 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
47453367 CATATAACCT
47453377 CATTTCAATC-ATAA-TTTCTCA
1 CATTTCAATCAATAATTTTC-CA
*
47453398 CATTTTCAATTCAATCATTTTCCA
1 CA-TTTCAA-TCAATAATTTTCCA
47453422 CATTTCAATCAATAATT
1 CATTTCAATCAATAATT
47453439 AATCCACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 14 0.40
23 8 0.23
24 7 0.20
25 4 0.11
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.44
Consensus pattern (22 bp):
CATTTCAATCAATAATTTTCCA
Found at i:47453423 original size:24 final size:25
Alignment explanation
Indices: 47453380--47453434 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
47453370 ATAACCTCAT
47453380 TTCAATCATAATTTCTCACATTTTCAA
1 TTCAATCAT-ATTTCTCACA-TTTCAA
47453407 TTCAATCAT-TTTC-CACATTTCAA
1 TTCAATCATATTTCTCACATTTCAA
47453430 -TCAAT
1 TTCAAT
47453435 AATTAATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 6 0.21
24 4 0.14
25 4 0.14
27 9 0.32
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.44
Consensus pattern (25 bp):
TTCAATCATATTTCTCACATTTCAA
Found at i:47453598 original size:3 final size:3
Alignment explanation
Indices: 47453590--47453636 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
47453580 CCACTCATTT
47453590 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47453637 CTTACCTCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47454532 original size:30 final size:31
Alignment explanation
Indices: 47454498--47454561 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
47454488 TACATTTGTC
* * *
47454498 TTAATCTAATTACTTCATTAA-AAAAATCTT
1 TTAATATAATAACTTAATTAATAAAAATCTT
* *
47454528 TTAATATAATAATTTAATTAATAAATATCTT
1 TTAATATAATAACTTAATTAATAAAAATCTT
47454559 TTA
1 TTA
47454562 CTTCAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAATATAATAACTTAATTAATAAAAATCTT
Found at i:47454716 original size:3 final size:3
Alignment explanation
Indices: 47454664--47454701 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
47454654 TTGGTTTATT
*
47454664 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
47454702 TAAAACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47462360 original size:14 final size:14
Alignment explanation
Indices: 47462341--47462368 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47462331 TAAAAATTAA
47462341 AATGATTTAAATAG
1 AATGATTTAAATAG
47462355 AATGATTTAAATAG
1 AATGATTTAAATAG
47462369 GTGATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
AATGATTTAAATAG
Found at i:47462602 original size:15 final size:16
Alignment explanation
Indices: 47462578--47462622 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
47462568 TATAAAAGAG
*
47462578 AAATTTTAAAATTAAT
1 AAATTTTAAAATAAAT
*
47462594 TAA-TTTAAAGATAAAT
1 AAATTTTAAA-ATAAAT
47462610 AAATTTTAAAATA
1 AAATTTTAAAATA
47462623 TCATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATTTTAAAATAAAT
Found at i:47462743 original size:22 final size:22
Alignment explanation
Indices: 47462691--47462745 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
47462681 TATATACCAA
*
47462691 AGTTTAAAATAACTAAATAAAGT
1 AGTTTAAAATAAC-AAATAAAAT
* *
47462714 ACTGTAAAATAGA-AAATAAAAT
1 AGTTTAAAATA-ACAAATAAAAT
47462736 AGTTTAAAAT
1 AGTTTAAAAT
47462746 GTAGAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 16 0.62
23 9 0.35
24 1 0.04
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (22 bp):
AGTTTAAAATAACAAATAAAAT
Found at i:47472796 original size:13 final size:13
Alignment explanation
Indices: 47472778--47472802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47472768 ACATTCAAAT
47472778 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
47472791 TTCTCAAAAGCA
1 TTCTCAAAAGCA
47472803 ATAAAGAACT
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:47475129 original size:22 final size:24
Alignment explanation
Indices: 47475078--47475133 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
47475068 CAGGTACGGT
* * *
47475078 GTACGGGGGCGAGGGACGTGGCGC
1 GTACGGAGGCGAAGGACGTGGCCC
47475102 GTACGGAGGCGAAGG-CGT-GCCC
1 GTACGGAGGCGAAGGACGTGGCCC
47475124 GTACGGAGGC
1 GTACGGAGGC
47475134 TCGTCATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 13 0.45
23 3 0.10
24 13 0.45
ACGTcount: A:0.16, C:0.23, G:0.52, T:0.09
Consensus pattern (24 bp):
GTACGGAGGCGAAGGACGTGGCCC
Found at i:47484523 original size:171 final size:173
Alignment explanation
Indices: 47484238--47484580 Score: 582
Period size: 171 Copynumber: 2.0 Consensus size: 173
47484228 TTTGCGATAG
* * * *
47484238 TTATTCGCACTGACAATCTAGCATTCAATAATAATTGAAAGTCTAATAAATTAACTTATAAATAT
1 TTATTCGCACTGACAATCTAACATTCAATAATAATTGAAAGTCTAATAAATAAACTCATAAACAT
*
47484303 TAGCAAGAATTGTCTCAATTGCATAATCTAAATAGTTTTATTCTTAAACAAATCATT-AAAAAAT
66 TAGCAAGAATTGTCTCAATTGCATAATCTAAAAAGTTTTATTCTTAAACAAATCATTAAAAAAAT
*
47484367 AATCTC-GAAACTACAGGTTGCTTGTTGATAACTTACATGTGA
131 AATCTCAGAAACTACAGGTTGCGTGTTGATAACTTACATGTGA
47484409 TTATTCGCACTGACAATCTAACATTCAATAATAATTGAAAGTCTAATAAATAAACTCATAAACAT
1 TTATTCGCACTGACAATCTAACATTCAATAATAATTGAAAGTCTAATAAATAAACTCATAAACAT
* *
47484474 TAGCAAGAATTGTCTCGATTGCATGATCTAAAAAGTTTTATTCTTAAACAAATCATTAAAAAAAT
66 TAGCAAGAATTGTCTCAATTGCATAATCTAAAAAGTTTTATTCTTAAACAAATCATTAAAAAAAT
* *
47484539 AATCTCATAAACTATAGGTTGCGTGTTGATAACTTACATGTG
131 AATCTCAGAAACTACAGGTTGCGTGTTGATAACTTACATGTG
47484581 GATATCTTTG
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 115 0.72
172 13 0.08
173 32 0.20
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (173 bp):
TTATTCGCACTGACAATCTAACATTCAATAATAATTGAAAGTCTAATAAATAAACTCATAAACAT
TAGCAAGAATTGTCTCAATTGCATAATCTAAAAAGTTTTATTCTTAAACAAATCATTAAAAAAAT
AATCTCAGAAACTACAGGTTGCGTGTTGATAACTTACATGTGA
Found at i:47490020 original size:5 final size:6
Alignment explanation
Indices: 47490002--47490026 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47489992 TTCAACGCAC
47490002 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
47490027 CAATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:47492331 original size:11 final size:11
Alignment explanation
Indices: 47492315--47492344 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
47492305 GCAAAGTTGT
47492315 AATTAAAGCAA
1 AATTAAAGCAA
*
47492326 AATTAAAACAA
1 AATTAAAGCAA
47492337 AATTAAAG
1 AATTAAAG
47492345 GAAGAAAAAC
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:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (11 bp):
AATTAAAGCAA
Found at i:47499063 original size:2 final size:2
Alignment explanation
Indices: 47499056--47499090 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47499046 AATTTATTCA
47499056 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 A
47499091 AGAAAAGGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47504682 original size:40 final size:40
Alignment explanation
Indices: 47504635--47504780 Score: 177
Period size: 40 Copynumber: 3.6 Consensus size: 40
47504625 AGTGTATGAT
**
47504635 TGCACATACGTGCCTTTGTTTATACTTCGGTACCCCTAAA
1 TGCACATACGTGCCCCTGTTTATACTTCGGTACCCCTAAA
* * **
47504675 TGCACATACGTGCCCCTGTTTGTACTTTGGTACCTTTGAAA
1 TGCACATACGTGCCCCTGTTTATACTTCGGTACCCCT-AAA
* * *
47504716 -GCACATATGTGCCCCTATTTGTACTTCGGTACCCCTAAA
1 TGCACATACGTGCCCCTGTTTATACTTCGGTACCCCTAAA
* *
47504755 TGCACATATGTGCCACTGTTTATACT
1 TGCACATACGTGCCCCTGTTTATACT
47504781 CTGGTAACTC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.03
40 84 0.93
41 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (40 bp):
TGCACATACGTGCCCCTGTTTATACTTCGGTACCCCTAAA
Found at i:47505535 original size:80 final size:80
Alignment explanation
Indices: 47505401--47505568 Score: 255
Period size: 80 Copynumber: 2.1 Consensus size: 80
47505391 AGGGGCTGTC
* * * * *
47505401 ACACGGTCGTGTAAGGCACACGGCTTGGCGACACTACCGTGTGTCATCTGAAAATTTCTTAGGGT
1 ACACGGCCGTGTAAGGCACACGGCCTGGCGACACGACCATGTGTCATCTAAAAATTTCTTAGGGT
*
47505466 TCAAGTTAGTGAGTT
66 TCAAGTCAGTGAGTT
* * *
47505481 GCACGGCCGTGTGAGGCACACGGCCTGGCGACACGACCATGTGTTATCTAAAAATTTCTTAGGGT
1 ACACGGCCGTGTAAGGCACACGGCCTGGCGACACGACCATGTGTCATCTAAAAATTTCTTAGGGT
47505546 TCAAGTCAGTGAGTT
66 TCAAGTCAGTGAGTT
47505561 ACACGGCC
1 ACACGGCC
47505569 TGGCACATGG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
ACACGGCCGTGTAAGGCACACGGCCTGGCGACACGACCATGTGTCATCTAAAAATTTCTTAGGGT
TCAAGTCAGTGAGTT
Found at i:47506110 original size:28 final size:29
Alignment explanation
Indices: 47506079--47506137 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
47506069 TTTAAATAGC
*
47506079 ATAA-AAATAAATTAATTTA-CAAAATGAT
1 ATAAGAAATAAATT-ATTTATCAAAATAAT
**
47506107 ATAAGTTATAAATTATTTATCAAAATAAT
1 ATAAGAAATAAATTATTTATCAAAATAAT
47506136 AT
1 AT
47506138 GGAAGGTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
ATAAGAAATAAATTATTTATCAAAATAAT
Found at i:47507586 original size:28 final size:28
Alignment explanation
Indices: 47507541--47507609 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
47507531 GTAAATTAAA
*
47507541 AAAAAACATGT-AAGGTAA-AAGCTAAATT
1 AAAAAACAT-TAAATGTAAGAA-CTAAATT
*
47507569 AAAAAATATTAAATGTAAGAACTAAATT
1 AAAAAACATTAAATGTAAGAACTAAATT
47507597 AAAAAACATTAAA
1 AAAAAACATTAAA
47507610 ATTAAATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.03
28 33 0.92
29 2 0.06
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (28 bp):
AAAAAACATTAAATGTAAGAACTAAATT
Found at i:47507936 original size:19 final size:19
Alignment explanation
Indices: 47507909--47507950 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
47507899 TTCTCCCATC
*
47507909 GCTGGTTCTTTATTCCTCT
1 GCTGATTCTTTATTCCTCT
*
47507928 GCTGATTCTTTGTTCCTCT
1 GCTGATTCTTTATTCCTCT
47507947 GCTG
1 GCTG
47507951 GTGCTGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.05, C:0.26, G:0.19, T:0.50
Consensus pattern (19 bp):
GCTGATTCTTTATTCCTCT
Found at i:47507955 original size:25 final size:25
Alignment explanation
Indices: 47507927--47507975 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
47507917 TTTATTCCTC
47507927 TGCTGATTCTTTGTTCCTCTGCTGG
1 TGCTGATTCTTTGTTCCTCTGCTGG
* *
47507952 TGCTGGTTCTTTGTTCCTTTGCTG
1 TGCTGATTCTTTGTTCCTCTGCTG
47507976 CTTCTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.02, C:0.22, G:0.24, T:0.51
Consensus pattern (25 bp):
TGCTGATTCTTTGTTCCTCTGCTGG
Found at i:47507980 original size:19 final size:19
Alignment explanation
Indices: 47507952--47507988 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
47507942 CCTCTGCTGG
*
47507952 TGCTGGTTCTTTGTTCCTT
1 TGCTGCTTCTTTGTTCCTT
47507971 TGCTGCTTCTTTGTTCCT
1 TGCTGCTTCTTTGTTCCT
47507989 CTTCTCCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.19, T:0.57
Consensus pattern (19 bp):
TGCTGCTTCTTTGTTCCTT
Found at i:47508936 original size:67 final size:66
Alignment explanation
Indices: 47508808--47508936 Score: 206
Period size: 67 Copynumber: 1.9 Consensus size: 66
47508798 AAAGGAGAAG
*
47508808 GAAAATTTTCAGAAACATTTGGAAAACAAATTGAGTACTAATTGAAAAAGCTAAATGGAACACAT
1 GAAAATTTTCAGAAACATTTGGAAAACAAATTGAGTACTAATTG-AAAAGCTAAATAGAACACAT
47508873 TA
65 TA
*
47508875 GAAAATTTTCAGAAACATTTGGAAAACAAATTGAGTACTAATTG-CAAGCTAATAATAGAACA
1 GAAAATTTTCAGAAACATTTGGAAAACAAATTGAGTACTAATTGAAAAGCT-A-AATAGAACA
47508937 TTCAAATCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
65 5 0.09
66 1 0.02
67 52 0.90
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (66 bp):
GAAAATTTTCAGAAACATTTGGAAAACAAATTGAGTACTAATTGAAAAGCTAAATAGAACACATT
A
Found at i:47510738 original size:18 final size:18
Alignment explanation
Indices: 47510715--47510762 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
47510705 AAAATATAAG
* *
47510715 AAATGATGTTCACGTTTT
1 AAATGATGTTCACATTTC
47510733 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
47510751 AAATGATGTTCA
1 AAATGATGTTCA
47510763 AATTGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:47511341 original size:72 final size:72
Alignment explanation
Indices: 47511187--47511359 Score: 224
Period size: 72 Copynumber: 2.4 Consensus size: 72
47511177 AACAACAATG
* * * * * *
47511187 CTAAACTAGTTTTATCAATAGTTATTTGTGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTA
1 CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTTA
47511252 TTTATGT
66 TTTATGT
* * *
47511259 GT-AATCTAGTTTTATTAAAAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTT
1 CTAAAT-TAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTT
*
47511323 ATTT-TTT
65 ATTTATGT
47511330 ACTAAATTAGTTTTATCAATAGTTGTTTAT
1 -CTAAATTAGTTTTATCAATAGTTGTTTAT
47511360 ATGTGATTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
71 4 0.05
72 78 0.92
73 3 0.04
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.54
Consensus pattern (72 bp):
CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTTA
TTTATGT
Found at i:47521983 original size:23 final size:23
Alignment explanation
Indices: 47521949--47522016 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
47521939 TACGCAACTA
47521949 AGGCTTAGCAG-ATCATGCCACAC
1 AGGCTTAGCAGAAT-ATGCCACAC
47521972 AGGCTTTA-CAGAATATGCCACAC
1 AGGC-TTAGCAGAATATGCCACAC
** **
47521995 AGGCCAAATAGAATATGCCACA
1 AGGCTTAGCAGAATATGCCACA
47522017 AAAGCCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.03
23 33 0.85
24 5 0.13
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (23 bp):
AGGCTTAGCAGAATATGCCACAC
Found at i:47522023 original size:23 final size:23
Alignment explanation
Indices: 47521981--47522116 Score: 130
Period size: 23 Copynumber: 5.9 Consensus size: 23
47521971 CAGGCTTTAC
*
47521981 AGAATATGCCACACAGGCCAAAT
1 AGAATATGCCACAAAGGCCAAAT
*
47522004 AGAATATGCCACAAAAGCCAAAT
1 AGAATATGCCACAAAGGCCAAAT
* * * *
47522027 GGATTACGCCGCAAAGGCCAAAT
1 AGAATATGCCACAAAGGCCAAAT
*
47522050 AGAATATGCCACAAAGGCCAAAC
1 AGAATATGCCACAAAGGCCAAAT
* * * * *
47522073 ATAAT-TCACCGCAAAAGCCAAAC
1 AGAATAT-GCCACAAAGGCCAAAT
* *
47522096 AGATTACGCCACAAAGGCCAA
1 AGAATATGCCACAAAGGCCAA
47522117 CCAGAATGCA
Statistics
Matches: 89, Mismatches: 22, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
22 1 0.01
23 88 0.99
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.12
Consensus pattern (23 bp):
AGAATATGCCACAAAGGCCAAAT
Found at i:47522059 original size:69 final size:69
Alignment explanation
Indices: 47521981--47522116 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 69
47521971 CAGGCTTTAC
* * * ** *
47521981 AGAATATGCCACACAGGCCAAATAGAATAT-GCCACAAAAGCCAAATGGATTACGCCGCAAAGGC
1 AGAATATGCCACAAAGGCCAAACAGAAT-TCACCACAAAAGCCAAACAGATTACGCCACAAAGGC
47522045 CAAAT
65 CAAAT
* *
47522050 AGAATATGCCACAAAGGCCAAACATAATTCACCGCAAAAGCCAAACAGATTACGCCACAAAGGCC
1 AGAATATGCCACAAAGGCCAAACAGAATTCACCACAAAAGCCAAACAGATTACGCCACAAAGGCC
47522115 AA
66 AA
47522117 CCAGAATGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 57 0.98
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.12
Consensus pattern (69 bp):
AGAATATGCCACAAAGGCCAAACAGAATTCACCACAAAAGCCAAACAGATTACGCCACAAAGGCC
AAAT
Found at i:47522085 original size:46 final size:46
Alignment explanation
Indices: 47521995--47522136 Score: 153
Period size: 46 Copynumber: 3.1 Consensus size: 46
47521985 TATGCCACAC
* * *
47521995 AGGCCAAATAGAATATGCCACAAAAGCC-AA-ATGGATTACGCCGCAA
1 AGGCCAAATAGAATATGCCACAAAGGCCAAACAT-AATT-CACCGCAA
47522041 AGGCCAAATAGAATATGCCACAAAGGCCAAACATAATTCACCGCAA
1 AGGCCAAATAGAATATGCCACAAAGGCCAAACATAATTCACCGCAA
* * * * * * * *
47522087 AAGCCAAACAGATTACGCCACAAAGGCCAACCAGAATGCACCACAA
1 AGGCCAAATAGAATATGCCACAAAGGCCAAACATAATTCACCGCAA
47522133 AGGC
1 AGGC
47522137 TTTGTTTGGA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 75 0.91
47 5 0.06
48 2 0.02
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (46 bp):
AGGCCAAATAGAATATGCCACAAAGGCCAAACATAATTCACCGCAA
Found at i:47522121 original size:23 final size:23
Alignment explanation
Indices: 47521979--47522136 Score: 111
Period size: 23 Copynumber: 6.9 Consensus size: 23
47521969 CACAGGCTTT
* * *
47521979 ACAGAATATGCCACACAGGCCAA
1 ACAGATTACGCCACAAAGGCCAA
* * * *
47522002 ATAGAATATGCCACAAAAGCCAA
1 ACAGATTACGCCACAAAGGCCAA
** *
47522025 ATGGATTACGCCGCAAAGGCCAA
1 ACAGATTACGCCACAAAGGCCAA
* * *
47522048 ATAGAATATGCCACAAAGGCCAA
1 ACAGATTACGCCACAAAGGCCAA
* * * *
47522071 ACATAATT-CACCGCAAAAGCCAA
1 ACA-GATTACGCCACAAAGGCCAA
47522094 ACAGATTACGCCACAAAGGCCAA
1 ACAGATTACGCCACAAAGGCCAA
* * * *
47522117 CCAGAATGCACCACAAAGGC
1 ACAGATTACGCCACAAAGGC
47522137 TTTGTTTGGA
Statistics
Matches: 106, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
22 3 0.03
23 101 0.95
24 2 0.02
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (23 bp):
ACAGATTACGCCACAAAGGCCAA
Found at i:47525230 original size:23 final size:22
Alignment explanation
Indices: 47525187--47525230 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
47525177 TTCTAAGTCG
47525187 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
47525210 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
47525231 TTAATCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:47525483 original size:51 final size:49
Alignment explanation
Indices: 47525370--47525559 Score: 182
Period size: 51 Copynumber: 3.8 Consensus size: 49
47525360 ATATTCGGTT
* * * * *
47525370 CACATAGTAGCCTACACATAGTACTACGCATGTGACTATTACCATCTGATA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCA--AACATCTGGTA
* * * *
47525421 CATATAATAGCCTACACATAGTACTACACACGTGATCGAAACTATCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGA-CCAAAC-ATCTGGTA
* * * * * *
47525472 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCAAACA-TCTGGTA
* *
47525522 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCA
47525560 TCACTTTCAC
Statistics
Matches: 113, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.01
50 44 0.39
51 66 0.58
52 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (49 bp):
CACATAGTAGCCTACACATAGTACTACACACGTGACCAAACATCTGGTA
Found at i:47525553 original size:101 final size:101
Alignment explanation
Indices: 47525372--47525556 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 101
47525362 ATTCGGTTCA
* * *
47525372 CATAGTAGCCTACACATAGTACTACGCATGTGACTATTACCATCTGATACATATAATAGCCTACA
1 CATAGTAGCCTACACATAGTACTACACATGCGACTATTA-CATCTGATACACATAATAGCCTACA
47525437 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * * *
47525474 CATAGTAGCCTGCACATAGTACTACACATGCGACCTA-T-CATTCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTACACATAGTACTACACATGCGA-CTATTACA-TCTGATACACATAATAGCCTAC
47525537 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
47525557 CCATCACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 2 0.03
101 37 0.51
102 31 0.42
103 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACTATTACATCTGATACACATAATAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:47531731 original size:45 final size:46
Alignment explanation
Indices: 47531657--47531769 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 46
47531647 TAGTGTCATG
* * *
47531657 GTGTCTTTCAACCATGGTCTTATTTA-TTTTCGTCTTGATGCCATA
1 GTGTCTTTCAACCATGGTCTTATTCATTTTTCATCGTGATGCCATA
* * *
47531702 GTG-CATTTCAACCATAGTCTTATTCATTTTTCATCGTGTTTCCATA
1 GTGTC-TTTCAACCATGGTCTTATTCATTTTTCATCGTGATGCCATA
47531748 GTGTCTTTCAACCATGGTCTTA
1 GTGTCTTTCAACCATGGTCTTA
47531770 CTCGATAGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
44 1 0.02
45 22 0.38
46 34 0.59
47 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.45
Consensus pattern (46 bp):
GTGTCTTTCAACCATGGTCTTATTCATTTTTCATCGTGATGCCATA
Found at i:47531858 original size:45 final size:44
Alignment explanation
Indices: 47531743--47531905 Score: 125
Period size: 45 Copynumber: 3.6 Consensus size: 44
47531733 CATCGTGTTT
* * *
47531743 CCATAGTGTCTTTCAACCATGGTCTTACTCGATAGAACT-GTA-ATG
1 CCATAGTGTCTTTCAACTATGGTCTTACTCGAT---TCTGGTATGTG
** **
47531788 CCATAACGTCTTTCAGTTATGGTCTTACTCGATTCTGGTATGGTG
1 CCATAGTGTCTTTCAACTATGGTCTTACTCGATTCTGGTAT-GTG
* **
47531833 CCATAGTGTCTTTCAACTATAGTCTTA-TTTATTTTCTGGTATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTACTCGA--TTCTGGTAT-GTG
** *
47531879 TTATAGTGTCTTTCAACTATGATCTTA
1 CCATAGTGTCTTTCAACTATGGTCTTA
47531906 ATCATTTTCC
Statistics
Matches: 94, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 52 0.55
46 35 0.37
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (44 bp):
CCATAGTGTCTTTCAACTATGGTCTTACTCGATTCTGGTATGTG
Found at i:47531905 original size:46 final size:46
Alignment explanation
Indices: 47531820--47531914 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
47531810 TCTTACTCGA
* * *
47531820 TTCTGGTATGGTGCCATAGTGTCTTTCAACTATAGTCTTATTTATT
1 TTCTGGTATAGTGCCATAGTGTCTTTCAACTATAGTCTTAATCATT
**
47531866 TTCTGGTATAGTGTTATAGTGTCTTTCAACTAT-GATCTTAATCATT
1 TTCTGGTATAGTGCCATAGTGTCTTTCAACTATAG-TCTTAATCATT
47531912 TTC
1 TTC
47531915 CTTCAAGCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.02
46 42 0.98
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (46 bp):
TTCTGGTATAGTGCCATAGTGTCTTTCAACTATAGTCTTAATCATT
Found at i:47533473 original size:61 final size:60
Alignment explanation
Indices: 47533331--47533491 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 60
47533321 AGTAGGTTAT
47533331 ATATTATTTTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGATATTAA
1 ATATTATTTT-T-ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAGAATGATATTAA
* * *
47533394 ATAATA-TATTA-TTTTATTAAATTATATTTAATAATAATTATGTTAA-AAT-ATGATTAA
1 ATATTATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATGAT-ATTAA
* * *
47533451 ATTATTTATTTTTATTTTTATTAAAATATACTTAGTAATAA
1 A-TA-TTATTTTTATTTTTATTAAATTATATTTAATAATAA
47533492 ACTTATTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
56 2 0.02
57 9 0.11
58 21 0.25
59 12 0.14
60 9 0.11
61 24 0.29
62 2 0.02
63 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (60 bp):
ATATTATTTTTATTTTTATTAAATTATATTTAATAATAATTATATTAAGAATGATATTAA
Found at i:47536683 original size:16 final size:15
Alignment explanation
Indices: 47536662--47536709 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
47536652 GTAGTATTTC
47536662 TTTAAATTAATTATAT
1 TTTAAATTAATT-TAT
47536678 TTTAAATATCATATTTAT
1 TTTAAAT-T-A-ATTTAT
47536696 TATTAAATTAATTT
1 T-TTAAATTAATTT
47536710 TTTAAACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 11 0.39
17 2 0.07
18 6 0.21
19 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAATTAATTTAT
Found at i:47546921 original size:13 final size:13
Alignment explanation
Indices: 47546898--47546948 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
47546888 TTTAGCGTTG
*
47546898 CTTTTGCAAAGTA
1 CTTTTGAAAAGTA
* *
47546911 CTTTTAAAAAGTG
1 CTTTTGAAAAGTA
*
47546924 CTTTTGAGAAGTA
1 CTTTTGAAAAGTA
47546937 CTTTTGAAAAGT
1 CTTTTGAAAAGT
47546949 TTGGTTTAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:47546925 original size:26 final size:26
Alignment explanation
Indices: 47546896--47546948 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
47546886 AATTTAGCGT
47546896 TGCTTTTGCA-AAGTACTTTTAAAAAG
1 TGCTTTTG-AGAAGTACTTTTAAAAAG
*
47546922 TGCTTTTGAGAAGTACTTTTGAAAAG
1 TGCTTTTGAGAAGTACTTTTAAAAAG
47546948 T
1 T
47546949 TTGGTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (26 bp):
TGCTTTTGAGAAGTACTTTTAAAAAG
Found at i:47550796 original size:26 final size:26
Alignment explanation
Indices: 47550767--47550819 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
47550757 TTTAAAAGAA
47550767 TGTTTTTTTTTATTTTGCTCATTTAT
1 TGTTTTTTTTTATTTTGCTCATTTAT
47550793 TGTTTTTTTTTATTTTGCTCATTTAT
1 TGTTTTTTTTTATTTTGCTCATTTAT
47550819 T
1 T
47550820 TGATACTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.08, G:0.08, T:0.74
Consensus pattern (26 bp):
TGTTTTTTTTTATTTTGCTCATTTAT
Found at i:47558228 original size:50 final size:50
Alignment explanation
Indices: 47558174--47558580 Score: 268
Period size: 50 Copynumber: 8.2 Consensus size: 50
47558164 GTAGTGGAAT
*
47558174 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * ** * ** ** * * ** *
47558224 AGATTGATGCTTCAACAACGAATCTTACTTT-CCTGACGGTGTAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTT-GTTTCCCCAACATTGCAATTAAAA
* *
47558274 AGATTGAAGCTACGACGACGAATCTTGTTT-CCCAACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* ** *** * * * * *
47558323 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACA
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAAT-TAAAA
* *
47558374 TG-TTGAAGCTACAATGGCGAATCTTGTTT-CCCAACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * ** *** * * ** *
47558422 AGATTGAAGAC-GCAACGGTGAATTTTACTTCCCTGGCATTGTAGTGGAAC
1 AGATTGAAG-CTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* *
47558472 AGATTGAAGCTACGATGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * * * * *
47558522 AGATTGAAGCCATAATGGCGAATCTTATTTCCCCGACATT-CTAGTTAAAC
1 AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGC-AATTAAAA
47558572 AGATTGAAG
1 AGATTGAAG
47558581 ATGGCGAATC
Statistics
Matches: 257, Mismatches: 92, Indels: 16
0.70 0.25 0.04
Matches are distributed among these distances:
48 4 0.02
49 67 0.26
50 179 0.70
51 7 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:47558367 original size:99 final size:100
Alignment explanation
Indices: 47558124--47558554 Score: 607
Period size: 99 Copynumber: 4.3 Consensus size: 100
47558114 ACAGTGGAGC
* * * * *
47558124 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTAGCGGTGTAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGA
47558189 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* ** ** * * *
47558224 AGATTGATGCTTCAACAACGAATCTTACTTTCCTGACGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGA
*
47558289 CGACGAATCTTGTTT-CCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
*
47558323 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACATG-TTGAAGCTACA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACA-GATTGAAGCTACG
*
47558387 ATGGCGAATCTTGTTT-CCCAACATTGCAATTAAAA
65 ACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * * *
47558422 AGATTGAAGACGCAACGGTGAATTTTACTTCCCTGGCATTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGA
*
47558487 TGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * *
47558522 AGATTGAAGCCATAATGGCGAATCTTATTTCCC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCC
47558555 CGACATTCTA
Statistics
Matches: 293, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
98 1 0.00
99 177 0.60
100 115 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGA
CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:47558509 original size:199 final size:199
Alignment explanation
Indices: 47558124--47558554 Score: 616
Period size: 199 Copynumber: 2.2 Consensus size: 199
47558114 ACAGTGGAGC
* * * * *
47558124 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTAGCGGTGTAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGTAGTGGAACAGATTGAAGCTACAA
* *
47558189 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGATGCTTCAACAACGAATCTTACTT
66 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCTGCAACAACGAATCTTACTT
* *
47558254 TCCTGACGGTGTAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCAACATTGCAATT
131 CCCTGACAGTGTAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCAACATTGCAATT
47558319 AAAA
196 AAAA
*
47558323 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACATG-TTGAAGCTACA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGTAGTGGAACA-GATTGAAGCTACA
* *** *
47558387 ATGGCGAATCTTGTTT-CCCAACATTGCAATTAAAAAGATTGAAGAC-GCAACGGTGAATTTTAC
65 ACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAG-CTGCAACAACGAATCTTAC
* * * *
47558450 TTCCCTGGCATTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTTGTTTCCCCAACATTGCA
129 TTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTT-CCCAACATTGCA
47558515 ATTAAAA
193 ATTAAAA
* * *
47558522 AGATTGAAGCCATAATGGCGAATCTTATTTCCC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCC
47558555 CGACATTCTA
Statistics
Matches: 207, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
198 85 0.41
199 121 0.58
200 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (199 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCAGTGTAGTGGAACAGATTGAAGCTACAA
CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCTGCAACAACGAATCTTACTT
CCCTGACAGTGTAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCAACATTGCAATT
AAAA
Found at i:47558647 original size:44 final size:43
Alignment explanation
Indices: 47558587--47558911 Score: 204
Period size: 44 Copynumber: 7.5 Consensus size: 43
47558577 GAAGATGGCG
* *
47558587 AATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* * * * **
47558631 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTATAGTGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
* * * * *
47558674 AGATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T--CGCATCT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-AT
* * *
47558715 AGTCTTATCTCCCTGAAGTTGCAGGGGAGCAGACTGAGTAAGC-A-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCAAT
* * * *
47558759 AGTCTTATC-CTCCTGAAGTTGTAGTGGGGCAGACTGAAGATGGC-A-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAA-A--GCAAT
*
47558804 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* * * * *
47558848 AATCCTATCTCCCTGAAGTTGCAATAGAGCGGATTAAAAC-A-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
* * *
47558889 GATCTTATCTCTCTAAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
47558912 TGAGAGTAGA
Statistics
Matches: 221, Mismatches: 43, Indels: 37
0.73 0.14 0.12
Matches are distributed among these distances:
40 22 0.10
41 28 0.13
42 4 0.02
43 13 0.06
44 121 0.55
45 30 0.14
46 1 0.00
47 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
Found at i:47560645 original size:27 final size:24
Alignment explanation
Indices: 47560570--47560646 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 24
47560560 AATTTCAATA
47560570 ATGTAATTATTATTTTTTTATATAT
1 ATGTAATT-TTATTTTTTTATATAT
*
47560595 ATGTAATTTTTTTTATAATTTATATAT
1 ATGTAATTTTATTT-T--TTTATATAT
47560622 ATGTATATATTTA-TTTTTTATATAT
1 ATGTA-AT-TTTATTTTTTTATATAT
47560647 GTACATGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
24 5 0.11
25 18 0.40
27 15 0.33
28 4 0.09
29 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
ATGTAATTTTATTTTTTTATATAT
Found at i:47562429 original size:29 final size:29
Alignment explanation
Indices: 47562368--47562429 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
47562358 TTTTTTACTT
** *
47562368 TTCCCTCAAAACTTTTACTCCTTTCCACT
1 TTCCCTCAAAACTTTTACTCCCCTCCACC
47562397 TTCCCTCCAAAACTTTTACTCCCCTCC-CC
1 TTCCCT-CAAAACTTTTACTCCCCTCCACC
47562426 TTCC
1 TTCC
47562430 AACCCTCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.37
Consensus pattern (29 bp):
TTCCCTCAAAACTTTTACTCCCCTCCACC
Found at i:47562545 original size:30 final size:31
Alignment explanation
Indices: 47562511--47562570 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
47562501 AAACCTTTTA
*
47562511 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
47562541 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
47562571 TCCACCTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:47563838 original size:8 final size:8
Alignment explanation
Indices: 47563825--47563852 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
47563815 TAATTAGAAT
47563825 ATATTTAA
1 ATATTTAA
47563833 ATATTTAA
1 ATATTTAA
47563841 ATATTTAA
1 ATATTTAA
47563849 ATAT
1 ATAT
47563853 AATAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTTAA
Found at i:47568054 original size:22 final size:23
Alignment explanation
Indices: 47568028--47568071 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
47568018 TTTAAAATAT
*
47568028 ATATAATCTTAATC-TAATATTA
1 ATATAATATTAATCTTAATATTA
*
47568050 ATATAATATTCATCTTAATATT
1 ATATAATATTAATCTTAATATT
47568072 TTCGTCGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATAATATTAATCTTAATATTA
Found at i:47573487 original size:63 final size:63
Alignment explanation
Indices: 47573358--47573512 Score: 181
Period size: 63 Copynumber: 2.5 Consensus size: 63
47573348 CAGTACACAT
* * * * *
47573358 AATCATTCCCTGCATCAACACATACAACACCGATTTATTTTACATGAGCACCATATCACGCAC
1 AATCATTCCCTGCACCAACACATTCATCACCGATTTATTTCACATAAGCACCATATCACGCAC
* *
47573421 AATCGTTCCCTGCACCAACACATTCATCACC-ACTTTATTTCACATAAGCACCAT-TACATG-AG
1 AATCATTCCCTGCACCAACACATTCATCACCGA-TTTATTTCACATAAGCACCATAT-CACGCA-
47573483 C
63 C
* *
47573484 AATCTTTCCCTGCACCAGCACATTCATCA
1 AATCATTCCCTGCACCAACACATTCATCA
47573513 TAAGTTTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
62 3 0.04
63 77 0.96
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (63 bp):
AATCATTCCCTGCACCAACACATTCATCACCGATTTATTTCACATAAGCACCATATCACGCAC
Done.