Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 84 of 113
Found at i:17581122 original size:352 final size:356
Alignment explanation
Indices: 17580301--17581180 Score: 1154
Period size: 352 Copynumber: 2.5 Consensus size: 356
17580291 CACCTTGAAC
* * *
17580301 ATATCGCCACACAAATTTTAACACAGTTATTGAAGGCGAATATCCAAGAAAGATGCCTTTAATAA
1 ATATCGCCACACAAATTCTAACACAGTTATTGAAGGTGTATATCCAAGAAAGATGCCTTTAATAA
* * * * * * *
17580366 TTCCTATCACAGTTTGTAAATAATTAGTGAAGGCGATTGCAGAA-AACAACGCCTTTAATAATTT
66 TTTCTATCACAGTTTATAAATAATTACTGAAGGAGGTTGCA-AATAACAATGCCTTCAATAATTT
* *** * *
17580430 CTCT--AAAAAAATTTTTTGAATTATTAAAGATGTCTTTTATTATGACACGTCTTCAATATACCA
130 CTCTAAAAAAAAATTTTTAG-ATTATTAAAGGCATATTTTATTATGACACGCCTTCAATATACCA
* * ** *
17580493 CGATGGTTATGGAATGTGTTTATTAGAAAAGACGCCTTTAATATACCTTTAAACTTAGTAATCCA
194 CAATGGTTATGGAAGGCATTTATTAGAAAAGACGCCTTCAATATACCTTTAAACTTA-TAATCCA
* * * *
17580558 TTATTGAAGGTGTTTATTAATAACAGACGCCTTCAAAATTTTTTCACTAAAAATTTTAAAAATTA
258 TTACTGAAGGCGTTTATTAATAACAAACGCCTTCAAAATTTTTCCACTAAAAATTTTAAAAATTA
* *
17580623 TTAAAGGCGTTTTCTACTATAAAATGCTTTTTAA
323 TTAAAGGCGTTTTCTACTATAAAATACATTTTAA
* * * *
17580657 ATA-CAGTCACACAAATTCTAACACCGTTATTAAATGTGTATATCCAAGAAAGATGCCTTTAATA
1 ATATC-GCCACACAAATTCTAACACAGTTATTGAAGGTGTATATCCAAGAAAGATGCCTTTAATA
* * *
17580721 ATTTCTATCACAGTTTATAGATAATTACTGAAGGAGGTTGCAGATAACAATACCTTCAATAATTT
65 ATTTCTATCACAGTTTATAAATAATTACTGAAGGAGGTTGCAAATAACAATGCCTTCAATAATTT
* *
17580786 -TCTTAAAAAAAAATTTTTAGATTATTAAAGGCATATTTTATTATGACATGCCTTCAATATATCA
130 CTC-TAAAAAAAAATTTTTAGATTATTAAAGGCATATTTTATTATGACACGCCTTCAATATACCA
*
17580850 CAATGGTTATGGAAGGCATTTATTAGAAAATGA-GCCTTCAATATGCCTTTAAAC-T-TAATCCA
194 CAATGGTTATGGAAGGCATTTATTAGAAAA-GACGCCTTCAATATACCTTTAAACTTATAATCCA
* *
17580912 TTACTGAAGGCGTTTGTTAATAACAAACGCCTTCAAAATTTTTCCACTAAATATTTTAAAAATTA
258 TTACTGAAGGCGTTTATTAATAACAAACGCCTTCAAAATTTTTCCACTAAAAATTTTAAAAATTA
* *
17580977 TTAAAGGCGTCTTT-TACTGTAAAATACATTTTAT
323 TTAAAGGCGT-TTTCTACTATAAAATACATTTTAA
* *
17581011 ATATCG-C-CACAAATTCTAACACTGTTATTGAAGGTGTATATCTAAGAAAGATGCCTTTAATAA
1 ATATCGCCACACAAATTCTAACACAGTTATTGAAGGTGTATATCCAAGAAAGATGCCTTTAATAA
* * * *
17581074 TTTCTATCATAATTTATATATAATTACTGAAGGTGGTTGCAAATAACAATGCCTTCAATAATTTC
66 TTTCTATCACAGTTTATAAATAATTACTGAAGGAGGTTGCAAATAACAATGCCTTCAATAATTTC
* * * *
17581139 TCAAAAAAAAAAATTTTA-ATTAGTAAAGGCATTTTTTATTAT
131 TCTAAAAAAAAATTTTTAGATTATTAAAGGCATATTTTATTAT
17581181 AAAACACTTC
Statistics
Matches: 460, Mismatches: 55, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
351 22 0.05
352 124 0.27
353 3 0.01
354 96 0.21
355 8 0.02
356 110 0.24
357 82 0.18
358 15 0.03
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (356 bp):
ATATCGCCACACAAATTCTAACACAGTTATTGAAGGTGTATATCCAAGAAAGATGCCTTTAATAA
TTTCTATCACAGTTTATAAATAATTACTGAAGGAGGTTGCAAATAACAATGCCTTCAATAATTTC
TCTAAAAAAAAATTTTTAGATTATTAAAGGCATATTTTATTATGACACGCCTTCAATATACCACA
ATGGTTATGGAAGGCATTTATTAGAAAAGACGCCTTCAATATACCTTTAAACTTATAATCCATTA
CTGAAGGCGTTTATTAATAACAAACGCCTTCAAAATTTTTCCACTAAAAATTTTAAAAATTATTA
AAGGCGTTTTCTACTATAAAATACATTTTAA
Found at i:17598590 original size:10 final size:11
Alignment explanation
Indices: 17598545--17598597 Score: 76
Period size: 11 Copynumber: 5.1 Consensus size: 11
17598535 TTTTGTTACT
17598545 TGTTTTAATTA
1 TGTTTTAATTA
17598556 TGTTTTAATTA
1 TGTTTTAATTA
17598567 TGTTTTAATT-
1 TGTTTTAATTA
17598577 T-TTTTAATT-
1 TGTTTTAATTA
*
17598586 TTTTTTAATTA
1 TGTTTTAATTA
17598597 T
1 T
17598598 CATTAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.22
10 9 0.22
11 22 0.55
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TGTTTTAATTA
Found at i:17600784 original size:34 final size:34
Alignment explanation
Indices: 17600718--17600786 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
17600708 ATGGATGCAA
**
17600718 GAACAAATACAAGCTTAACCTGGAACTTTTTTTT
1 GAACAAATACAAGCTTAACCTGGAACAGTTTTTT
* * * *
17600752 GAACAGATGCAAGCTTAACCTGGGAGAGTTTTTT
1 GAACAAATACAAGCTTAACCTGGAACAGTTTTTT
17600786 G
1 G
17600787 GCTTCCCACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (34 bp):
GAACAAATACAAGCTTAACCTGGAACAGTTTTTT
Found at i:17603291 original size:50 final size:51
Alignment explanation
Indices: 17603216--17603315 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 51
17603206 TCATACCAAA
*
17603216 GGCATTTTCATTGTTTGTTTTTATCATATGCATTTCCCATGAAACCCTAAT
1 GGCATTTTCATTATTTGTTTTTATCATATGCATTTCCCATGAAACCCTAAT
* *
17603267 GGCATTTTCGTTATTT-TTTTTATCATATGCATTTCTCATGAAACCCTAA
1 GGCATTTTCATTATTTGTTTTTATCATATGCATTTCCCATGAAACCCTAA
17603316 ACCACCATCC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 32 0.70
51 14 0.30
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (51 bp):
GGCATTTTCATTATTTGTTTTTATCATATGCATTTCCCATGAAACCCTAAT
Found at i:17603348 original size:19 final size:19
Alignment explanation
Indices: 17603307--17603376 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
17603297 ATTTCTCATG
17603307 AAACCCTAAACCACCATCC
1 AAACCCTAAACCACCATCC
* ** *
17603326 AAACTCTAAACCATTATCT
1 AAACCCTAAACCACCATCC
* * *
17603345 AAACCCTATACCA-AACCC
1 AAACCCTAAACCACCATCC
17603363 TAAACCCTAAACCA
1 -AAACCCTAAACCA
17603377 AACCTTAAAC
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 2 0.05
19 38 0.95
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (19 bp):
AAACCCTAAACCACCATCC
Found at i:17603369 original size:7 final size:7
Alignment explanation
Indices: 17603343--17603391 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
17603333 AAACCATTAT
17603343 CTAAACC
1 CTAAACC
*
17603350 CTATA-C
1 CTAAACC
17603356 C-AAACC
1 CTAAACC
17603362 CTAAACC
1 CTAAACC
17603369 CTAAA-C
1 CTAAACC
17603375 C-AAACC
1 CTAAACC
*
17603381 TTAAACC
1 CTAAACC
17603388 CTAA
1 CTAA
17603392 CCTTGATCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
5 5 0.15
6 7 0.21
7 22 0.65
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:17603377 original size:19 final size:19
Alignment explanation
Indices: 17603343--17603391 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
17603333 AAACCATTAT
*
17603343 CTAAACCCTATACCAAACC
1 CTAAACCCTAAACCAAACC
17603362 CTAAACCCTAAACCAAACC
1 CTAAACCCTAAACCAAACC
*
17603381 TTAAACCCTAA
1 CTAAACCCTAA
17603392 CCTTGATCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (19 bp):
CTAAACCCTAAACCAAACC
Found at i:17603418 original size:30 final size:31
Alignment explanation
Indices: 17603371--17603438 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
17603361 CCTAAACCCT
*
17603371 AAACCAAACCTTAAACCCTAACCTTGATCCC
1 AAACCAAACCTTAAACCCTAACCTAGATCCC
* * *
17603402 AAACCAATCC-TAAACCCTAAGCTAGATCCT
1 AAACCAAACCTTAAACCCTAACCTAGATCCC
17603432 AAACCAA
1 AAACCAA
17603439 CCAAACTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.43, C:0.35, G:0.04, T:0.18
Consensus pattern (31 bp):
AAACCAAACCTTAAACCCTAACCTAGATCCC
Found at i:17608139 original size:62 final size:61
Alignment explanation
Indices: 17608068--17608187 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 61
17608058 GATTGTTGAG
* * * ** *
17608068 CCTCTACTTAGAGGAACCTTATTTTTTTTTTAAAGTTGTTGAGTTTCTGCTTAGAGGAGCCC
1 CCTCTACTTAGAGGAACCTTATTATTTTTCT-AAGTTATTGAGCCTCTACTTAGAGGAGCCC
*
17608130 CCTCTACTTAGAGGAGCCTTATTATTTTTCTAAGTTATTGAGCCTCTACTTAGAGGAG
1 CCTCTACTTAGAGGAACCTTATTATTTTTCTAAGTTATTGAGCCTCTACTTAGAGGAG
17608188 TCTTGTTCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 23 0.45
62 28 0.55
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (61 bp):
CCTCTACTTAGAGGAACCTTATTATTTTTCTAAGTTATTGAGCCTCTACTTAGAGGAGCCC
Found at i:17608181 original size:42 final size:42
Alignment explanation
Indices: 17608130--17608402 Score: 208
Period size: 43 Copynumber: 6.4 Consensus size: 42
17608120 AGAGGAGCCC
* *
17608130 CCTCTACTTAGAGGAGCCTTATTATTTTTCTAAGTTATTGAG
1 CCTCTACTTAGAGGAGCCTTATTATTTTTCAAAGTCATTGAG
* * * *
17608172 CCTCTACTTAGAGGAGTCTTGTTCATTTTTTAAAGTCAGTGAG
1 CCTCTACTTAGAGGAGCCTTATT-ATTTTTCAAAGTCATTGAG
*
17608215 CCTCTGA-TTAGAGAAGCCTTATCTATTTTTCAAAGTCATTGAG
1 CCTCT-ACTTAGAGGAGCCTTAT-TATTTTTCAAAGTCATTGAG
* * * * * ** *
17608258 CCTCTGCTTAGAAGAGCCCTATTTATTTGTAAAAGTTGTTGAA
1 CCTCTACTTAGAGGAGCCTTA-TTATTTTTCAAAGTCATTGAG
* * * * *
17608301 CCTATGCTTAGAGGAGCTTTATTTACCTTTT-AAAGTCATTTAG
1 CCTCTACTTAGAGGAGCCTTA-TTA-TTTTTCAAAGTCATTGAG
* ** * * * *
17608344 CCTTTGTTTAGAGAAGCCTTATTTATTTTCCAAAGTCATCGAA
1 CCTCTACTTAGAGGAGCCTTA-TTATTTTTCAAAGTCATTGAG
* *
17608387 CCTCTATTTAAAGGAG
1 CCTCTACTTAGAGGAG
17608403 TTTTGTAAGT
Statistics
Matches: 181, Mismatches: 43, Indels: 13
0.76 0.18 0.05
Matches are distributed among these distances:
42 24 0.13
43 151 0.83
44 6 0.03
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (42 bp):
CCTCTACTTAGAGGAGCCTTATTATTTTTCAAAGTCATTGAG
Found at i:17609399 original size:17 final size:17
Alignment explanation
Indices: 17609377--17609416 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
17609367 GATTACTTGG
* *
17609377 TATTTTGTTTATTTATT
1 TATTTTCTTTATGTATT
17609394 TATTTTCTTTATGTATT
1 TATTTTCTTTATGTATT
17609411 TATTTT
1 TATTTT
17609417 TAAAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (17 bp):
TATTTTCTTTATGTATT
Found at i:17619817 original size:19 final size:19
Alignment explanation
Indices: 17619788--17619836 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
17619778 CTTTTTATTC
17619788 TTTTC-TTTTTTTACCTCA
1 TTTTCTTTTTTTTACCTCA
* **
17619806 TTTTCTTTTTTTTTCCTTT
1 TTTTCTTTTTTTTACCTCA
17619825 TTTTCTTTTTTT
1 TTTTCTTTTTTT
17619837 GAAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTTTTTACCTCA
Found at i:17619896 original size:21 final size:22
Alignment explanation
Indices: 17619870--17619911 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17619860 AAAAACTTAT
17619870 TTTTTTGAAAAAAT-AATTTAC
1 TTTTTTGAAAAAATAAATTTAC
*
17619891 TTTTTTTAAAAAATAAATTTA
1 TTTTTTGAAAAAATAAATTTA
17619912 ACTCCTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTTGAAAAAATAAATTTAC
Found at i:17619897 original size:22 final size:22
Alignment explanation
Indices: 17619869--17619911 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17619859 TAAAAACTTA
17619869 TTTTTTTGAAAAAAT-AATTTAC
1 TTTTTTT-AAAAAATAAATTTAC
17619891 TTTTTTTAAAAAATAAATTTA
1 TTTTTTTAAAAAATAAATTTA
17619912 ACTCCTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTTTAAAAAATAAATTTAC
Found at i:17620309 original size:19 final size:20
Alignment explanation
Indices: 17620285--17620355 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
17620275 AACAATCAAA
*
17620285 ATAAAA-AAATTAGTTTTTT
1 ATAAAATAAATTAATTTTTT
*
17620304 ATAAAATAATTTAATTTTTT
1 ATAAAATAAATTAATTTTTT
*
17620324 A-AAAGATATATT-ATTTTATT
1 ATAAA-ATAAATTAATTTT-TT
17620344 A-AAAGATAAATT
1 ATAAA-ATAAATT
17620356 TAAAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
ATAAAATAAATTAATTTTTT
Found at i:17622853 original size:45 final size:46
Alignment explanation
Indices: 17622760--17622857 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
17622750 ATATCTTCTC
17622760 TTTTTAATTTCTAAAATTTTTACTATTTAGGTCAATTTAGAAAATT
1 TTTTTAATTTCTAAAATTTTTACTATTTAGGTCAATTTAGAAAATT
* * * **
17622806 TTTTTAATTTCT-AAATTTTTCATTATTTGGGTCTATTTAGAATTTT
1 TTTTTAATTTCTAAAATTTTT-ACTATTTAGGTCAATTTAGAAAATT
17622852 TTTTTA
1 TTTTTA
17622858 TTTTTTATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 8 0.17
46 38 0.83
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (46 bp):
TTTTTAATTTCTAAAATTTTTACTATTTAGGTCAATTTAGAAAATT
Found at i:17623487 original size:4 final size:4
Alignment explanation
Indices: 17623478--17623526 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
17623468 AATACTTTAA
*
17623478 AAAT AAAT AAAAT AACT AAAT AAAT AAAT AAAT AAA- ATAAT AAA- AAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
17623526 A
1 A
17623527 CCAAAATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 4 0.10
4 30 0.77
5 5 0.13
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:17623507 original size:25 final size:23
Alignment explanation
Indices: 17623478--17623526 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 23
17623468 AATACTTTAA
17623478 AAATAAATAAAATAACTAAATAAAT
1 AAATAAATAAAATAA-TAAA-AAAT
17623503 AAATAAATAAAATAATAAAAAAT
1 AAATAAATAAAATAATAAAAAAT
17623526 A
1 A
17623527 CCAAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 15 0.62
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAATAAAATAATAAAAAAT
Found at i:17626980 original size:47 final size:45
Alignment explanation
Indices: 17626895--17626994 Score: 112
Period size: 47 Copynumber: 2.2 Consensus size: 45
17626885 AAATATCTTC
*
17626895 TCTTTTTAATTTCTAAAATTTTCACCATTTATGCCTATTTAGAAATT
1 TCTTTTTGATTTCTAAAATTTTCACCATTTATGCCTATTT--AAATT
* * * *
17626942 TCTTTTTGATTTCTAAATTTTTGATCATTT-TGGTCTATTTAAATT
1 TCTTTTTGATTTCTAAAATTTTCACCATTTAT-GCCTATTTAAATT
*
17626987 TTTTTTTG
1 TCTTTTTG
17626995 TTTTTTATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 12 0.26
46 1 0.02
47 33 0.72
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (45 bp):
TCTTTTTGATTTCTAAAATTTTCACCATTTATGCCTATTTAAATT
Found at i:17630665 original size:13 final size:13
Alignment explanation
Indices: 17630647--17630673 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17630637 AGATTTAAAC
17630647 AATTACAACATAT
1 AATTACAACATAT
17630660 AATTACAACATAT
1 AATTACAACATAT
17630673 A
1 A
17630674 TATGAAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AATTACAACATAT
Found at i:17638126 original size:19 final size:19
Alignment explanation
Indices: 17638094--17638230 Score: 111
Period size: 19 Copynumber: 7.1 Consensus size: 19
17638084 TTTAGAATTT
17638094 TTTTTAGAATTTTTTAGAA
1 TTTTTAGAATTTTTTAGAA
17638113 CTTTTTAGAATTTTTTAGAA
1 -TTTTTAGAATTTTTTAGAA
17638133 TTTTTCA-AATTTTTTAGAA
1 TTTTT-AGAATTTTTTAGAA
* *
17638152 -TTTTAAAATTTTTAAAGAA
1 TTTTTAGAATTTTT-TAGAA
*
17638171 TTTGTTAG-ATATCTTTA-AA
1 TTT-TTAGAAT-TTTTTAGAA
** * *
17638190 TATTTTTTATTTTTTTATAA
1 T-TTTTAGAATTTTTTAGAA
* *
17638210 TTTTCAAAATTTTTTAGAA
1 TTTTTAGAATTTTTTAGAA
17638229 TT
1 TT
17638231 AAAAAAATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.01
18 11 0.12
19 46 0.48
20 31 0.33
21 6 0.06
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.58
Consensus pattern (19 bp):
TTTTTAGAATTTTTTAGAA
Found at i:17638172 original size:29 final size:28
Alignment explanation
Indices: 17638095--17638230 Score: 98
Period size: 29 Copynumber: 4.7 Consensus size: 28
17638085 TTAGAATTTT
* * *
17638095 TTTTAGAATTTTTTAGAACTTTTTAGAA
1 TTTTAAAATTTTTAAGAATTTTTTAGAA
* *
17638123 TTTTTTAGAATTTTTCA-AATTTTTTAGAA
1 --TTTTAAAATTTTTAAGAATTTTTTAGAA
*
17638152 TTTTAAAATTTTTAAAGAATTTGTTAGATA
1 TTTTAAAATTTTT-AAGAATTTTTTAGA-A
* * *
17638182 TCTTTAAATATTTTT--TATTTTTTTATAA
1 T-TTTAAA-ATTTTTAAGAATTTTTTAGAA
*
17638210 TTTTCAAAATTTTTTAGAATT
1 TTTT-AAAATTTTTAAGAATT
17638231 AAAAAAATTA
Statistics
Matches: 87, Mismatches: 11, Indels: 17
0.76 0.10 0.15
Matches are distributed among these distances:
27 21 0.24
28 6 0.07
29 32 0.37
30 16 0.18
31 6 0.07
32 6 0.07
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (28 bp):
TTTTAAAATTTTTAAGAATTTTTTAGAA
Found at i:17638213 original size:9 final size:9
Alignment explanation
Indices: 17638094--17638223 Score: 55
Period size: 10 Copynumber: 13.6 Consensus size: 9
17638084 TTTAGAATTT
*
17638094 TTTTTAGAAT
1 TTTTTA-AAA
*
17638104 TTTTTAGAAC
1 TTTTTA-AAA
*
17638114 TTTTTAGAAT
1 TTTTTA-AAA
*
17638124 TTTTTAGAA
1 TTTTTAAAA
*
17638133 TTTTTCAAAT
1 TTTTT-AAAA
*
17638143 TTTTTAGAA
1 TTTTTAAAA
17638152 -TTTTAAAA
1 TTTTTAAAA
17638160 TTTTTAAAGAA
1 TTTTT-AA-AA
*
17638171 TTTGTTAGATA
1 TTT-TTA-AAA
*
17638182 TCTTTAAATA
1 TTTTTAAA-A
* **
17638192 TTTTTTATT
1 TTTTTAAAA
*
17638201 TTTTTATAA
1 TTTTTAAAA
*
17638210 TTTTCAAAA
1 TTTTTAAAA
17638219 TTTTT
1 TTTTT
17638224 TAGAATTAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
8 7 0.08
9 29 0.32
10 42 0.47
11 9 0.10
12 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:17638230 original size:10 final size:10
Alignment explanation
Indices: 17638083--17638155 Score: 103
Period size: 10 Copynumber: 7.2 Consensus size: 10
17638073 AGTGGAAGTG
17638083 TTTTAGAATTTT
1 TTTTAGAA--TT
17638095 TTTTAGAATT
1 TTTTAGAATT
*
17638105 TTTTAGAACT
1 TTTTAGAATT
17638115 TTTTAGAATT
1 TTTTAGAATT
17638125 TTTTAGAATT
1 TTTTAGAATT
*
17638135 TTTCA-AATT
1 TTTTAGAATT
17638144 TTTTAGAATT
1 TTTTAGAATT
17638154 TT
1 TT
17638156 AAAATTTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
9 8 0.14
10 40 0.71
12 8 0.14
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (10 bp):
TTTTAGAATT
Found at i:17638838 original size:16 final size:15
Alignment explanation
Indices: 17638812--17638841 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17638802 AATTTTCTGT
17638812 AATTTATCAATAAAA
1 AATTTATCAATAAAA
17638827 AATTTCATCAATAAA
1 AATTT-ATCAATAAA
17638842 TCCATCGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTTATCAATAAAA
Found at i:17639328 original size:3 final size:3
Alignment explanation
Indices: 17639320--17639350 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17639310 TTAAAAATAC
17639320 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17639351 GCAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17643715 original size:27 final size:26
Alignment explanation
Indices: 17643669--17643720 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
17643659 TTGGTACATC
17643669 ATATTATAATAAGATAGGATGAAATG
1 ATATTATAATAAGATAGGATGAAATG
* * *
17643695 ATATTATGAATATGATTGGATTAAAT
1 ATATTAT-AATAAGATAGGATGAAAT
17643721 AATGTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (26 bp):
ATATTATAATAAGATAGGATGAAATG
Found at i:17647384 original size:36 final size:32
Alignment explanation
Indices: 17647344--17647414 Score: 81
Period size: 36 Copynumber: 2.1 Consensus size: 32
17647334 TTTAAAATAA
17647344 TTAAAT-AGATAAAACATTATTTTTGTAATATTTTAT
1 TTAAATAAG-TAAAAC--TATTTTT-T-ATATTTTAT
*
17647380 TTAAATAAGTAAAACTATTTTTTATTTTTTAT
1 TTAAATAAGTAAAACTATTTTTTATATTTTAT
17647412 TTA
1 TTA
17647415 TGGATTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 7 0.21
36 12 0.36
37 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (32 bp):
TTAAATAAGTAAAACTATTTTTTATATTTTAT
Found at i:17648456 original size:182 final size:181
Alignment explanation
Indices: 17648062--17648469 Score: 432
Period size: 182 Copynumber: 2.2 Consensus size: 181
17648052 ATTTTTGGTC
* * * *
17648062 AAAAATACCTTGAAATAATCCCCAATAAAAAATGAAGGGGATTATTCAATGCGTTTTTGGCTAAA
1 AAAAATACCTTG-AATAATCCTCAAAAAAAAATAAAGGGGATTATTAAATGCGTTTTTGGCTAAA
* * *
17648127 AATCCCTTGAATAATCCCAAAATAAGGCAGGAGATTATTCAAAGCATTTTTTGTCAGAAAACGCC
65 AATCCCTTGAATAATCCCAAAAAAAGGCAGGAGATTATTCAAAGCATTTTTGGTCAGAAAACGAC
* * * ** *
17648192 TTAAATAATCTCTTTCAATTTTTTAAGGGATTATTCGATGCATTTTCTAGCA
130 TTAAATAACCCCATTCAATTTTTTAAAAGATTATTCGATGCACTTTCTAGCA
* ** ** *
17648244 AAAAACACCTTGAATAATCCTC-TCAAAAAATAAAGGGGATTATTGAAGATGTTTTTTTTG-TAG
1 AAAAATACCTTGAATAATCCTCAAAAAAAAATAAAGGGGATTATT-AA-ATGCGTTTTTGGCTA-
* * * **
17648307 AAAATGCTTTGAATAATCCCAAAAAAATGG-ATGAGGATTATTCAAAGTGTTTTTGGTCA-AAAA
63 AAAATCCCTTGAATAATCCCAAAAAAA-GGCAGGA-GATTATTCAAAGCATTTTTGGTCAGAAAA
* * *
17648370 CGATTTGAATAACCCCATTCAATTTTTTAAAAGATTATTC-ATGGCACTTT-TAGCC
126 CGACTTAAATAACCCCATTCAATTTTTTAAAAGATTATTCGAT-GCACTTTCTAGCA
* * * *
17648425 AGAAATACCTTGAATAATCTTCAAAAAAAAATAAAAGAGATTATT
1 AAAAATACCTTGAATAATCCTCAAAAAAAAATAAAGGGGATTATT
17648470 CAAGGTATTT
Statistics
Matches: 186, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
180 19 0.10
181 37 0.20
182 107 0.58
183 23 0.12
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (181 bp):
AAAAATACCTTGAATAATCCTCAAAAAAAAATAAAGGGGATTATTAAATGCGTTTTTGGCTAAAA
ATCCCTTGAATAATCCCAAAAAAAGGCAGGAGATTATTCAAAGCATTTTTGGTCAGAAAACGACT
TAAATAACCCCATTCAATTTTTTAAAAGATTATTCGATGCACTTTCTAGCA
Found at i:17648687 original size:63 final size:60
Alignment explanation
Indices: 17648517--17648689 Score: 161
Period size: 61 Copynumber: 2.8 Consensus size: 60
17648507 TTAATTTTTG
* * *
17648517 CCTTGAATAATCCTAAAAAAAAATGGAAGAGGATTATTCAAGGC-TTTTTTGACCAAAAACA
1 CCTTGAATAATCCAAAAAAAAAAAGG-A-AGGATTATTCAAGGCATTTTTAGACCAAAAACA
* ** ** * ***
17648578 CCTTAAATAATTTTAAAAAAAATTA-GAGAGGATTATTGAAGGCATTTTTAGTGGAAAAACA
1 CCTTGAATAA-TCCAAAAAAAAAAAGGA-AGGATTATTCAAGGCATTTTTAGACCAAAAACA
17648639 CCTTTGAATAATCCAAAAAAAAAAAGGAACGTGATTATTCAAGGCATTTTT
1 CC-TTGAATAATCCAAAAAAAAAAAGGAA-G-GATTATTCAAGGCATTTTT
17648690 TGCCAGAAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
60 16 0.18
61 36 0.41
62 18 0.20
63 18 0.20
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (60 bp):
CCTTGAATAATCCAAAAAAAAAAAGGAAGGATTATTCAAGGCATTTTTAGACCAAAAACA
Found at i:17649965 original size:34 final size:34
Alignment explanation
Indices: 17649922--17649991 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
17649912 GTAACAGCAC
17649922 TTTCTACTATAAACG-CTACTAAATTTAGTGGTGT
1 TTTCTACTATAAACGTCT-CTAAATTTAGTGGTGT
* * *
17649956 TTTCTACTATAAATGTCTTTAAATTTTGTGGTGT
1 TTTCTACTATAAACGTCTCTAAATTTAGTGGTGT
17649990 TT
1 TT
17649992 ATAATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 30 0.94
35 2 0.06
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (34 bp):
TTTCTACTATAAACGTCTCTAAATTTAGTGGTGT
Found at i:17650593 original size:30 final size:30
Alignment explanation
Indices: 17650558--17650614 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
17650548 AAAAATTTAC
17650558 GTAAGACATTGAAAATTCAAACAACTTCAT
1 GTAAGACATTGAAAATTCAAACAACTTCAT
* *
17650588 GTAAGATATTGAAAATTCAGACAACTT
1 GTAAGACATTGAAAATTCAAACAACTT
17650615 TTTATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (30 bp):
GTAAGACATTGAAAATTCAAACAACTTCAT
Found at i:17651421 original size:59 final size:60
Alignment explanation
Indices: 17651357--17651528 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 60
17651347 AGGGAAAATA
* * * * *
17651357 TTTTTTGGAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAC-CTT
1 TTTTTTGGAAACTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCT-AAAAACACAT
** * * *
17651417 TTTTTTTTAAA-TTTATTTTTAAGGAAACTTGATACTTTTAACTTTTCCTAAAAACAAAATTCAT
1 TTTTTTGGAAACTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAC---A--CAT
* *
17651481 TTTATTGGAAACTTTATTTTCAAGGAAAATTGATTCTTTCAACTTTTC
1 TTTTTTGGAAACTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTC
17651529 TTCGAGAATA
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
58 6 0.07
59 31 0.35
60 9 0.10
64 10 0.11
65 32 0.36
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.47
Consensus pattern (60 bp):
TTTTTTGGAAACTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAACACAT
Found at i:17654004 original size:20 final size:20
Alignment explanation
Indices: 17653976--17654018 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
17653966 AAAAGAAAAT
17653976 AAATCATAAA-ATAAAAATAA
1 AAATCATAAATAT-AAAATAA
* *
17653996 AAATGATAAATATGAAATAA
1 AAATCATAAATATAAAATAA
17654016 AAA
1 AAA
17654019 AATCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATCATAAATATAAAATAA
Found at i:17654221 original size:14 final size:14
Alignment explanation
Indices: 17654184--17654222 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17654174 ACTCAACTGG
17654184 ATTTTTTTTTACCC
1 ATTTTTTTTTACCC
* *
17654198 ATTTTGTTTTACCT
1 ATTTTTTTTTACCC
*
17654212 TTTTTTTTTTA
1 ATTTTTTTTTA
17654223 AATTTTGATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.72
Consensus pattern (14 bp):
ATTTTTTTTTACCC
Found at i:17654374 original size:98 final size:98
Alignment explanation
Indices: 17654211--17654460 Score: 368
Period size: 98 Copynumber: 2.6 Consensus size: 98
17654201 TTGTTTTACC
17654211 TTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAA
1 TTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAA
**
17654276 ACAAAGCT-TCTCTAAACA-AAGGTATTTTTT-T
66 ACAAAGCTCTCT-TAAACAGAAGCAATTTTTTGT
* *
17654307 TTTACTTTTTTTTAAAATTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAATAT
1 TTT--TTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACAT
17654372 AAACAAAGCTCTCTTAAACAGAAGCAATTTTTTGT
64 AAACAAAGCTCTCTTAAACAGAAGCAATTTTTTGT
* *
17654407 TTTTTTTATTTT---TTTTTATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA
1 TTTTTTT-TTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGA
17654461 AAAGTAAATT
Statistics
Matches: 141, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
96 42 0.30
98 78 0.55
99 17 0.12
100 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (98 bp):
TTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAA
ACAAAGCTCTCTTAAACAGAAGCAATTTTTTGT
Found at i:17654546 original size:41 final size:41
Alignment explanation
Indices: 17654430--17654653 Score: 342
Period size: 41 Copynumber: 5.5 Consensus size: 41
17654420 TTTTATCAAA
* *
17654430 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
17654471 GCTCCTCTAAACA-AGACACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
17654511 GCTCATCTAAACAGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
17654552 GCTCCTCTAAATAGAGGCATCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* *
17654594 GCTCCTCTAAATAGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
17654635 GCTCCTCTAAACAGAGGCA
1 GCTCCTCTAAACAGAGGCA
17654654 ACAAAACTTT
Statistics
Matches: 166, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 35 0.21
41 92 0.55
42 39 0.23
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:17654613 original size:83 final size:82
Alignment explanation
Indices: 17654430--17654653 Score: 360
Period size: 83 Copynumber: 2.7 Consensus size: 82
17654420 TTTTATCAAA
* * * *
17654430 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACA-AGACACCACG
1 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
17654494 ACTTTGGAAAGTAAATT
66 ACTTTGGAAAGTAAATT
* * *
17654511 GCTCATCTAAACAGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCATCACG
1 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
17654576 ACTTTGAGAAAGTAAATT
66 ACTTTG-GAAAGTAAATT
*
17654594 GCTCCTCTAAATAGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
1 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
17654654 ACAAAACTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
81 49 0.37
82 14 0.11
83 68 0.52
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGGAAAGTAAATT
Found at i:17654663 original size:41 final size:41
Alignment explanation
Indices: 17654430--17654679 Score: 324
Period size: 41 Copynumber: 6.1 Consensus size: 41
17654420 TTTTATCAAA
*
17654430 GCTCCTCTAAACAGAGGC-TCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAA-GACTTTGAAAAGTAAATT
* * *
17654471 GCTCCTCTAAACA-AGACACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATT
* *
17654511 GCTCATCTAAACAGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATT
* * *
17654552 GCTCCTCTAAATAGAGGCATCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGA-AAAGTAAATT
* *
17654594 GCTCCTCTAAATAGAGGCACCATGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATT
* * * * *
17654635 GCTCCTCTAAACAGAGGCAACAAAACTTTAAAAAATAAATG
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATT
17654676 GCTC
1 GCTC
17654680 ATTGACAATC
Statistics
Matches: 185, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 32 0.17
41 114 0.62
42 39 0.21
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATT
Found at i:17654663 original size:124 final size:122
Alignment explanation
Indices: 17654430--17654679 Score: 358
Period size: 124 Copynumber: 2.0 Consensus size: 122
17654420 TTTTATCAAA
17654430 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAGACACCACGA
1 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAGACACCACGA
* * ** * * *
17654495 CTTTGGAAAGTAAATTGCTCATCTAAACAGAGGCACCATGACTTTGAAAAGTAAATT
66 CTTTGAAAAGTAAATTGCTCATCTAAACAGAGGCAACAAAACTTTAAAAAATAAATG
* * *
17654552 GCTCCTCTAAATAGAGGCATC-ACGACTTTGAGAAAGTAAATTGCTCCTCTAAATAGAGGCACCA
1 GCTCCTCTAAACAGAGGC-TCAACGACTTTGA-AAAGTAAATTGCTCCTCTAAACA-AGACACCA
* *
17654616 TGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACAAAACTTTAAAAAATAAATG
63 CGACTTTGAAAAGTAAATTGCTCATCTAAACAGAGGCAACAAAACTTTAAAAAATAAATG
17654676 GCTC
1 GCTC
17654680 ATTGACAATC
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 27 0.24
123 24 0.21
124 62 0.55
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (122 bp):
GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAGACACCACGA
CTTTGAAAAGTAAATTGCTCATCTAAACAGAGGCAACAAAACTTTAAAAAATAAATG
Found at i:17655776 original size:62 final size:63
Alignment explanation
Indices: 17655663--17655785 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 63
17655653 GCTTATCAGC
* *
17655663 ACTAACCATTTCAAAATAAATTTCATCTTCTGTCACTTGGTCATCGTTTATAAGCTTCTCAAT
1 ACTAACCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCGTTTATAAGCTTCTCAAT
*
17655726 ACTAGCCATTTCAAAACAAATTTCATCATC-GTCACTTGGTCATCGTTTATAAGCTTCTCA
1 ACTAACCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCGTTTATAAGCTTCTCA
17655786 GCACCAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 30 0.53
63 27 0.47
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (63 bp):
ACTAACCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCGTTTATAAGCTTCTCAAT
Found at i:17656517 original size:12 final size:12
Alignment explanation
Indices: 17656487--17656536 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
17656477 CATTTTTTCA
* *
17656487 TTTTTTCCTTCT
1 TTTTTTCTTTTT
*
17656499 TTCTTTCTTTTT
1 TTTTTTCTTTTT
17656511 TTTTTTC--TTT
1 TTTTTTCTTTTT
17656521 TTTTTTCTTTTT
1 TTTTTTCTTTTT
17656533 TTTT
1 TTTT
17656537 CATCATCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 10 0.31
12 22 0.69
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:17656527 original size:22 final size:23
Alignment explanation
Indices: 17656487--17656536 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
17656477 CATTTTTTCA
17656487 TTTTTTCCTTCTTTCTTTCTTTT
1 TTTTTTCCTTCTTTCTTTCTTTT
* *
17656510 TTTTTTTCTT-TTTTTTTCTTTT
1 TTTTTTCCTTCTTTCTTTCTTTT
17656532 TTTTT
1 TTTTT
17656537 CATCATCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTCCTTCTTTCTTTCTTTT
Found at i:17656534 original size:8 final size:8
Alignment explanation
Indices: 17656479--17656534 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
17656469 TTGAATCTCA
*
17656479 TTTTTTCA
1 TTTTTTCT
*
17656487 TTTTTTCC
1 TTTTTTCT
*
17656495 TTCTTTCT
1 TTTTTTCT
17656503 TTCTTTT-T
1 TT-TTTTCT
17656511 TTTTTTCTTT
1 TTTTTTC--T
17656521 TTTTTTCT
1 TTTTTTCT
17656529 TTTTTT
1 TTTTTT
17656535 TTCATCATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 4 0.10
8 25 0.62
9 3 0.08
10 8 0.20
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:17660607 original size:118 final size:121
Alignment explanation
Indices: 17660465--17660701 Score: 336
Period size: 118 Copynumber: 2.0 Consensus size: 121
17660455 ATGTGCAGGG
* * *
17660465 AAAAATATTTTTTGGAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCT-CAAAAAC
1 AAAAATACTTTTTGGAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAAA
* *
17660529 CCCTTTTTTTTGAAAA-TTTATTTTTAAAGAAAATTGATACTTTCAACTTTTTCCC
66 CCCATTTTTTTGAAAACTTTATTTTCAAAGAAAATTGATACTTTCAACTTTTTCCC
* *
17660584 AAAAATACTTTTT-GAAACTTTAATTTCGAGGAAAATTGATAGTTTCAACTTTTCCTAAAAAAAA
1 AAAAATACTTTTTGGAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCT--AAAAAA
** * *
17660648 AATTCATTTTTTTGAAAACTTTATTTTCAAGGAAAATTGATACTTTTAACTTTT
64 AACCCATTTTTTTGAAAACTTTATTTTCAAAGAAAATTGATACTTTCAACTTTT
17660702 CCTCGAGAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
118 41 0.40
119 12 0.12
121 18 0.17
122 32 0.31
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.43
Consensus pattern (121 bp):
AAAAATACTTTTTGGAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAAA
CCCATTTTTTTGAAAACTTTATTTTCAAAGAAAATTGATACTTTCAACTTTTTCCC
Found at i:17663169 original size:20 final size:20
Alignment explanation
Indices: 17663141--17663183 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
17663131 AAAAGAAAAT
17663141 AAATAATAAA-ATAAAAATAA
1 AAATAATAAATAT-AAAATAA
* *
17663161 AAATGATAAATATGAAATAA
1 AAATAATAAATATAAAATAA
17663181 AAA
1 AAA
17663184 AATCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAATAAATATAAAATAA
Found at i:17664102 original size:16 final size:17
Alignment explanation
Indices: 17664083--17664124 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
17664073 CTTGTATATA
17664083 TCTTTATT-TTTATTTG
1 TCTTTATTCTTTATTTG
17664099 TCTTTATTCTTTATTT-
1 TCTTTATTCTTTATTTG
*
17664115 TATTTATTCT
1 TCTTTATTCT
17664125 ATTTTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (17 bp):
TCTTTATTCTTTATTTG
Found at i:17669133 original size:5 final size:5
Alignment explanation
Indices: 17669123--17669246 Score: 56
Period size: 5 Copynumber: 22.8 Consensus size: 5
17669113 AAAAATCCAG
* * *
17669123 ATAAA ATAAA ATAAA ATAATA A-AGATA ATTAA ATAAA ACAAA ATAAG
1 ATAAA ATAAA ATAAA ATAA-A ATA-A-A ATAAA ATAAA ATAAA ATAAA
* *
17669170 ATAAA GA-ATAG ATAAA GATAAAA ATAAA ATAAA ATATATA TATATA AT-AA
1 ATAAA -ATA-AA ATAAA -AT-AAA ATAAA ATAAA ATA-A-A -ATAAA ATAAA
*
17669220 ATGAA ATAAA GATAAA GATAAGA ATAA
1 ATAAA ATAAA -ATAAA -ATAA-A ATAA
17669247 TGGTAAATAC
Statistics
Matches: 94, Mismatches: 11, Indels: 27
0.71 0.08 0.20
Matches are distributed among these distances:
4 3 0.03
5 53 0.56
6 30 0.32
7 5 0.05
8 3 0.03
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:17669170 original size:23 final size:22
Alignment explanation
Indices: 17669131--17669173 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17669121 AGATAAAATA
* *
17669131 AAATAAAATAATAAAGATAATT
1 AAATAAAACAAAAAAGATAATT
17669153 AAATAAAACAAAATAAGATAA
1 AAATAAAACAAAA-AAGATAA
17669174 AGAATAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (22 bp):
AAATAAAACAAAAAAGATAATT
Found at i:17669191 original size:32 final size:29
Alignment explanation
Indices: 17669121--17669202 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 29
17669111 AAAAAAATCC
17669121 AGATAAAATAAAATAAAAT-AATAAAGAT
1 AGATAAAATAAAATAAAATAAATAAAGAT
* *
17669149 A-ATTAAATAAAACAAAATAAGATAAAGAAT
1 AGATAAAATAAAATAAAATAA-ATAAAG-AT
17669179 AGATAAAGATAAAAATAAAATAAA
1 AGATAAA-AT-AAAATAAAATAAA
17669203 ATATATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 15 0.34
28 2 0.05
29 6 0.14
30 3 0.07
31 4 0.09
32 3 0.07
33 11 0.25
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (29 bp):
AGATAAAATAAAATAAAATAAATAAAGAT
Found at i:17669691 original size:20 final size:20
Alignment explanation
Indices: 17669662--17669703 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
17669652 ATTTGTAAAA
**
17669662 TTTTTAAGATTCGCAAGATT
1 TTTTTAAGATTCAAAAGATT
*
17669682 TTTTTTAGATTCAAAAGATT
1 TTTTTAAGATTCAAAAGATT
17669702 TT
1 TT
17669704 CAAATTTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTTTAAGATTCAAAAGATT
Found at i:17669727 original size:17 final size:18
Alignment explanation
Indices: 17669702--17669786 Score: 75
Period size: 17 Copynumber: 4.8 Consensus size: 18
17669692 TCAAAAGATT
*
17669702 TTCAAATTTGCAAGAA-C
1 TTCAGATTTGCAAGAATC
* * *
17669719 TTGAGATTTACAAGAATA
1 TTCAGATTTGCAAGAATC
* * *
17669737 TTCAGGTTTGCAAAAATTT
1 TTCAGATTTGCAAGAA-TC
17669756 TTCAGATTTGCAAGAA-C
1 TTCAGATTTGCAAGAATC
*
17669773 TTGAGATTTGCAAG
1 TTCAGATTTGCAAG
17669787 GATTTAAAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
17 26 0.49
18 12 0.23
19 15 0.28
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (18 bp):
TTCAGATTTGCAAGAATC
Found at i:17669855 original size:25 final size:27
Alignment explanation
Indices: 17669794--17669855 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
17669784 AAGGATTTAA
*
17669794 AAAATTCACATTCAAGAGATTTGCATCC
1 AAAATTCA-ATTCAAGAGATTCGCATCC
* *
17669822 AAAGTTCAATTC-AGGGATTCGCAT-C
1 AAAATTCAATTCAAGAGATTCGCATCC
17669847 AAAATTCAA
1 AAAATTCAA
17669856 AGATTCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 9 0.30
26 10 0.33
27 4 0.13
28 7 0.23
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (27 bp):
AAAATTCAATTCAAGAGATTCGCATCC
Found at i:17669902 original size:22 final size:23
Alignment explanation
Indices: 17669854--17669902 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
17669844 ATCAAAATTC
* *
17669854 AAAGATTCACATTCAACAATTTT
1 AAAGATTCACATCCAACAACTTT
*
17669877 AAAGATTCACATCCAA-GACTTT
1 AAAGATTCACATCCAACAACTTT
17669899 AAAG
1 AAAG
17669903 CTCACATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (23 bp):
AAAGATTCACATCCAACAACTTT
Found at i:17670036 original size:22 final size:21
Alignment explanation
Indices: 17669997--17670056 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
17669987 TGGTGTTTCA
*
17669997 CATCCAATACTTCAAAGGTTCT
1 CATCCAAAACTTCAAAGGTT-T
* *
17670019 CATTCAAAACTTCTAAGGTTT
1 CATCCAAAACTTCAAAGGTTT
*
17670040 CATCCAAAATTTCAAAG
1 CATCCAAAACTTCAAAG
17670057 ATCTTAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (21 bp):
CATCCAAAACTTCAAAGGTTT
Found at i:17670192 original size:69 final size:67
Alignment explanation
Indices: 17670051--17670226 Score: 205
Period size: 69 Copynumber: 2.6 Consensus size: 67
17670041 ATCCAAAATT
* * * *
17670051 TCAAAGATCTTAATTAAAAAAACTTTGAAGATTCA--CATAAAATTTCAAGATTCTCATTTAAAA
1 TCAAAGATTTTCATTAAAAAAACTTTGAGGATTCACTCAAAAAATTTCAAGATTCTCATTTAAAA
17670114 AC
66 AC
* *
17670116 TCAAAGATTTTCATTCAAAAAAACTTTGAGGATTCACCTCAAAAAATTTTCAAGCTTTTCATTT-
1 TCAAAGATTTTCATT-AAAAAAACTTTGAGGATTCA-CTCAAAAAA-TTTCAAGATTCTCATTTA
17670180 AAAAC
63 AAAAC
* ** *
17670185 TCAAAGATTCTCATTTGAAAAACTTTGAGAATTCACATCAAA
1 TCAAAGATTTTCATTAAAAAAACTTTGAGGATTCAC-TCAAA
17670227 GATTCTAATT
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
65 13 0.14
66 19 0.20
67 1 0.01
68 22 0.23
69 25 0.26
70 15 0.16
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (67 bp):
TCAAAGATTTTCATTAAAAAAACTTTGAGGATTCACTCAAAAAATTTCAAGATTCTCATTTAAAA
AC
Found at i:17671522 original size:6 final size:7
Alignment explanation
Indices: 17671484--17671570 Score: 81
Period size: 8 Copynumber: 12.0 Consensus size: 7
17671474 CTTCTTTTCA
17671484 CATTTTT
1 CATTTTT
17671491 CATTTTT
1 CATTTTT
*
17671498 --TTTTA
1 CATTTTT
17671503 C-TTTTT
1 CATTTTT
*
17671509 TACTTTTT
1 CA-TTTTT
17671517 CATTTTT
1 CATTTTT
17671524 CATTTTT
1 CATTTTT
17671531 CATTTTTTT
1 CA--TTTTT
17671540 CACTTTTT
1 CA-TTTTT
17671548 CATTTCTT
1 CATTT-TT
17671556 CATTTCTT
1 CATTT-TT
17671564 CATTTTT
1 CATTTTT
17671571 TTTTATTTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
5 4 0.06
6 4 0.06
7 26 0.38
8 28 0.41
9 7 0.10
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:17671529 original size:40 final size:40
Alignment explanation
Indices: 17671484--17671570 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 40
17671474 CTTCTTTTCA
* *
17671484 CATTTTTCATTTTTTTTTACTTTTTTACTTT-TTCATTT-TT
1 CATTTTTCA-TTTTTTTCACTTTTTCA-TTTCTTCATTTCTT
17671524 CATTTTTCATTTTTTTCACTTTTTCATTTCTTCATTTCTT
1 CATTTTTCATTTTTTTCACTTTTTCATTTCTTCATTTCTT
17671564 CATTTTT
1 CATTTTT
17671571 TTTTATTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 3 0.07
39 22 0.51
40 18 0.42
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (40 bp):
CATTTTTCATTTTTTTCACTTTTTCATTTCTTCATTTCTT
Found at i:17672425 original size:17 final size:16
Alignment explanation
Indices: 17672390--17672431 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
17672380 AAATTTAAAA
17672390 ATGGGAATAAAAAGAC
1 ATGGGAATAAAAAGAC
17672406 ATGGGAAATAACAAAG-C
1 ATGGG-AATAA-AAAGAC
17672423 AT-GGAATAA
1 ATGGGAATAA
17672432 TGGCTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
17 8 0.33
18 4 0.17
ACGTcount: A:0.55, C:0.07, G:0.24, T:0.14
Consensus pattern (16 bp):
ATGGGAATAAAAAGAC
Found at i:17672552 original size:23 final size:22
Alignment explanation
Indices: 17672509--17672552 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17672499 ATAAAATCTT
*
17672509 ATTACTTAAAAGAAATTTTAAC
1 ATTACTTAAAAGAAATATTAAC
*
17672531 ATTACTCTAAAAGAGATATTAA
1 ATTACT-TAAAAGAAATATTAA
17672553 AATGATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (22 bp):
ATTACTTAAAAGAAATATTAAC
Found at i:17673144 original size:246 final size:246
Alignment explanation
Indices: 17672709--17673193 Score: 684
Period size: 246 Copynumber: 2.0 Consensus size: 246
17672699 AATGCAAGGT
17672709 AAATTTTTATATAATAACCCACATCCCATTATGGTAATAGCATGTGGCATTAACATCATACCATT
1 AAATTTTTATATAATAACCCACATCCCATTATGGTAATAGCATGTGGCATTAACATCATACCATT
* * * * * * *
17672774 TGGGATAGGGTGACTTTAATAGTTCTAGAATAATTGGTGACACCAAATTATTCTTAACTAGTTTT
66 TGAGATAAGGTGACTTTAATAGCTCTAGAATAACTGATGACACCAAATCATTCTTAACTAGTTCT
* *
17672839 GGGAATAATTCAGTGTAAGTCATAAGGATAGGATCAATGTGGGCCCTTTCTTAGTTATTCTAAGA
131 GGAAATAATTCAGTGTAAGTCATAAGGATAGGATCAATGTGAGCCCTTTCTTAGTTATTCTAAGA
* *
17672904 TCTCCTTAAACCACTCATTTAGTTGTTAGGCCTTGAAGCTGATAAGATGAC
196 TCTCCGTAAACCACTCACTTAGTTGTTAGGCCTTGAAGCTGATAAGATGAC
* * * * * * * *
17672955 AAATTTTTATATAATGACTCACATCTCATTATGGTAATTGTATGTGGTATTAGCATCATATCATT
1 AAATTTTTATATAATAACCCACATCCCATTATGGTAATAGCATGTGGCATTAACATCATACCATT
*
17673020 TGAGATAAGGTGGCTTTAATAGCTCTAGAATAACTGATGACACCAAATCATTCTTAACTAGTTCT
66 TGAGATAAGGTGACTTTAATAGCTCTAGAATAACTGATGACACCAAATCATTCTTAACTAGTTCT
* * * * * *
17673085 GGAAATAACTT-AGTGTAAGTTATGATGATAGGATTAATGTGAGCCCTTTCTTGGTTATTCTGAG
131 GGAAATAA-TTCAGTGTAAGTCATAAGGATAGGATCAATGTGAGCCCTTTCTTAGTTATTCTAAG
* * * *
17673149 ATCTTCGTAAATCACTCGCTTGGTTGTTAGGCCTTGAAGCTGATA
195 ATCTCCGTAAACCACTCACTTAGTTGTTAGGCCTTGAAGCTGATA
17673194 TAGTGATATG
Statistics
Matches: 208, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
246 206 0.99
247 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (246 bp):
AAATTTTTATATAATAACCCACATCCCATTATGGTAATAGCATGTGGCATTAACATCATACCATT
TGAGATAAGGTGACTTTAATAGCTCTAGAATAACTGATGACACCAAATCATTCTTAACTAGTTCT
GGAAATAATTCAGTGTAAGTCATAAGGATAGGATCAATGTGAGCCCTTTCTTAGTTATTCTAAGA
TCTCCGTAAACCACTCACTTAGTTGTTAGGCCTTGAAGCTGATAAGATGAC
Found at i:17676231 original size:13 final size:14
Alignment explanation
Indices: 17676197--17676229 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
17676187 TCACACCAAA
17676197 ATTTTTTAAGTTAT
1 ATTTTTTAAGTTAT
17676211 ATTTTTTAA-TTA-
1 ATTTTTTAAGTTAT
17676223 ATTTTTT
1 ATTTTTT
17676230 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 3 0.16
14 9 0.47
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
ATTTTTTAAGTTAT
Found at i:17676237 original size:7 final size:8
Alignment explanation
Indices: 17676223--17676250 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
17676213 TTTTTAATTA
17676223 ATTTTTTT
1 ATTTTTTT
17676231 ATTTTTTT
1 ATTTTTTT
17676239 ATTTTTTT
1 ATTTTTTT
17676247 ATTT
1 ATTT
17676251 AAGAAAAAAT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
ATTTTTTT
Found at i:17676251 original size:20 final size:20
Alignment explanation
Indices: 17676210--17676251 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
17676200 TTTTAAGTTA
17676210 TATTTTTTAATTAATTTT-TT
1 TATTTTTTAATT-ATTTTATT
* *
17676230 TATTTTTTTATTTTTTTATT
1 TATTTTTTAATTATTTTATT
17676250 TA
1 TA
17676252 AGAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTTAATTATTTTATT
Found at i:17678231 original size:17 final size:17
Alignment explanation
Indices: 17678209--17678242 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17678199 CATGTTTCGT
17678209 TTACCTTCTAAAATTGA
1 TTACCTTCTAAAATTGA
*
17678226 TTACCTTCTAGAATTGA
1 TTACCTTCTAAAATTGA
17678243 CTTGGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
TTACCTTCTAAAATTGA
Found at i:17680385 original size:23 final size:22
Alignment explanation
Indices: 17680355--17680397 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
17680345 CTTGTCATTT
17680355 TAGAATTTCTTTTAGAGTAATGC
1 TAGAATTTCTTTTA-AGTAATGC
17680378 TAGAATTTCTTTTAAGTAAT
1 TAGAATTTCTTTTAAGTAAT
17680398 AATATTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (22 bp):
TAGAATTTCTTTTAAGTAATGC
Found at i:17681393 original size:19 final size:19
Alignment explanation
Indices: 17681362--17681399 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17681352 GTGAAATATG
*
17681362 AAAAAAGTAAAAAGTAAAA
1 AAAAAAGTAAAAAGGAAAA
17681381 AAAAAAG-AGAAAAGGAAAA
1 AAAAAAGTA-AAAAGGAAAA
17681400 CTTAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAAGTAAAAAGGAAAA
Found at i:17682882 original size:32 final size:32
Alignment explanation
Indices: 17682827--17682914 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
17682817 ATTTTTGACT
* * * * *
17682827 TTGGCTCAATCTGGTCTCATTCATCTTTAACC
1 TTGGTTCAATCTAGTCACTTTCATCTTCAACC
*
17682859 TTGGTTCAATCTAGTCACTTTCATCTTCGACC
1 TTGGTTCAATCTAGTCACTTTCATCTTCAACC
* *
17682891 TTAGTTCAATCCAAGTCA-TTTCAT
1 TTGGTTCAAT-CTAGTCACTTTCAT
17682915 TTTTTGATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 41 0.87
33 6 0.13
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (32 bp):
TTGGTTCAATCTAGTCACTTTCATCTTCAACC
Found at i:17683458 original size:6 final size:5
Alignment explanation
Indices: 17683412--17683483 Score: 51
Period size: 5 Copynumber: 14.0 Consensus size: 5
17683402 ATCTCTATTC
* *
17683412 TTTAT TTTA- TTGAT TTTACT TTGAT TTTGAT TTT-T TCTTAT CTTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTT-AT TTTAT T-TTAT -TTTAT
*
17683459 TTTAT TTGA- TTTAT TTTAT TGTTAT
1 TTTAT TTTAT TTTAT TTTAT T-TTAT
17683484 AAAAAAAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
4 8 0.15
5 26 0.49
6 18 0.34
7 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:17685025 original size:3 final size:3
Alignment explanation
Indices: 17685017--17685073 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
17685007 GTTTTGAAAT
* * *
17685017 ATA ATA ATA ATA GTA GTA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17685065 ATA ATA ATA
1 ATA ATA ATA
17685074 TTATTATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17685078 original size:3 final size:3
Alignment explanation
Indices: 17685072--17685103 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17685062 ATAATAATAA
17685072 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17685104 ATAAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17689023 original size:120 final size:121
Alignment explanation
Indices: 17688899--17689152 Score: 277
Period size: 121 Copynumber: 2.1 Consensus size: 121
17688889 ATTATCCTAT
* * * *
17688899 AATATATTGGTATGATTTTA-TGAAAAT-TATTTCTTT-TCTAAAAATTAATTTTTATTTAAAAA
1 AATATGTTGGTAAGACTTTATTG-AAATCTATTT-TTTCTCTAAAAATTAATTTTT-TATAAAAA
* * *
17688961 A-TCATAAAA-TTTCTTAATATATT-AGTAAAACCTTATCTTAAAAATCAAATTGCCTTCC
63 ATTAATAAAATTTTC-CAATATATTGA-TAAAACCTTATCTTAAAAATCAAATCGCCTTCC
* ** *
17689019 AATATGTTGGTAAGGCTTTATTGAAATCTATTTTTTCTCTTGAAATTTATTTTTTATAAAAAATT
1 AATATGTTGGTAAGACTTTATTGAAATCTATTTTTTCTCTAAAAATTAATTTTTTATAAAAAATT
* * * * *
17689084 AATAAGATTTTCCAATATGTTGATAAAACCTTATTTTAAAAATCCAATCGTCTTCC
66 AATAAAATTTTCCAATATATTGATAAAACCTTATCTTAAAAATCAAATCGCCTTCC
17689140 AATATGTTGGTAA
1 AATATGTTGGTAA
17689153 AGCATTTTAT
Statistics
Matches: 112, Mismatches: 16, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
120 31 0.28
121 76 0.68
122 5 0.04
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (121 bp):
AATATGTTGGTAAGACTTTATTGAAATCTATTTTTTCTCTAAAAATTAATTTTTTATAAAAAATT
AATAAAATTTTCCAATATATTGATAAAACCTTATCTTAAAAATCAAATCGCCTTCC
Found at i:17689340 original size:4 final size:4
Alignment explanation
Indices: 17689331--17689397 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
17689321 AAATATTTAC
** * * *
17689331 AAAT AAAT AAAT GCAT AAAT -AGT CAAAT AAAT AAAAT AAAA AAAT AAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT
*
17689380 AAAT AAAT AAAT AGAT AA
1 AAAT AAAT AAAT AAAT AA
17689398 TTATGATAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 2 0.04
4 40 0.83
5 6 0.12
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:17691001 original size:22 final size:22
Alignment explanation
Indices: 17690956--17691001 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
17690946 TTTTTTTGAG
*
17690956 ATTATACCTAGAGGTCTTAAAA
1 ATTATACCTAGAGATCTTAAAA
* *
17690978 ATTATACCTAGAGATTTTACAA
1 ATTATACCTAGAGATCTTAAAA
17691000 AT
1 AT
17691002 CATGCACGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
ATTATACCTAGAGATCTTAAAA
Found at i:17691028 original size:22 final size:23
Alignment explanation
Indices: 17690996--17691116 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 23
17690986 TAGAGATTTT
* *
17690996 ACAAATCATGCACGGAGGTCATG
1 ACAAATTATGCTCGGAGGTCATG
* * *
17691019 A-AAATTATGCTCGAAGG-CTTT
1 ACAAATTATGCTCGGAGGTCATG
*
17691040 ACAAATTATGCTCGGAGGTC-TT
1 ACAAATTATGCTCGGAGGTCATG
* * * * *
17691062 ACAAATCATGTTTGAAGGTCTTG
1 ACAAATTATGCTCGGAGGTCATG
* * * *
17691085 A-GAATTATGCTCGAAGG-CCTT
1 ACAAATTATGCTCGGAGGTCATG
17691106 ACAAATTATGC
1 ACAAATTATGC
17691117 CTAAAGGCCT
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
21 6 0.08
22 66 0.87
23 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (23 bp):
ACAAATTATGCTCGGAGGTCATG
Found at i:17691123 original size:22 final size:22
Alignment explanation
Indices: 17691020--17691354 Score: 229
Period size: 22 Copynumber: 15.2 Consensus size: 22
17691010 GAGGTCATGA
*
17691020 AAATTATGCTCGAAGG-CTTTAC
1 AAATTATGCTTGAAGGTC-TTAC
* *
17691042 AAATTATGCTCGGAGGTCTTAC
1 AAATTATGCTTGAAGGTCTTAC
* *
17691064 AAATCATGTTTGAAGGTCTTGA-
1 AAATTATGCTTGAAGGTCTT-AC
* * *
17691086 GAATTATGCTCGAAGGCCTTAC
1 AAATTATGCTTGAAGGTCTTAC
* * *
17691108 AAATTATGCCTAAAGGCCTT-C
1 AAATTATGCTTGAAGGTCTTAC
*
17691129 AAAATTATGCTTTG-AGGCCTTAC
1 -AAATTATGC-TTGAAGGTCTTAC
* * *
17691152 AAATTATGTTTGGAGGTCTTAT
1 AAATTATGCTTGAAGGTCTTAC
* *
17691174 AAATCATG-TCTAAAGGTCTTGA-
1 AAATTATGCT-TGAAGGTCTT-AC
* *
17691196 AAATTATGCTTGAAGGCCTTAT
1 AAATTATGCTTGAAGGTCTTAC
* * *
17691218 AAATTATGTTTGGAGGTCTTAA
1 AAATTATGCTTGAAGGTCTTAC
* *
17691240 AAATTATGCCTGAAGGTCTTAA
1 AAATTATGCTTGAAGGTCTTAC
*** *
17691262 AAATTATGCCCAAAAGTCTTAC
1 AAATTATGCTTGAAGGTCTTAC
17691284 AAATTATGCTTAGAA-GTCTTAC
1 AAATTATGCTT-GAAGGTCTTAC
* * *
17691306 AAATAATAT-CATGGAGGCCTTAC
1 AAAT--TATGCTTGAAGGTCTTAC
*
17691329 AAATTATGCTGTG-ATGTCTTAC
1 AAATTATGCT-TGAAGGTCTTAC
17691351 AAAT
1 AAAT
17691355 CATTTCTTAT
Statistics
Matches: 251, Mismatches: 45, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
21 10 0.04
22 216 0.86
23 22 0.09
24 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (22 bp):
AAATTATGCTTGAAGGTCTTAC
Found at i:17692295 original size:10 final size:10
Alignment explanation
Indices: 17692282--17692324 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
17692272 ATTTTAATCT
17692282 TTTTTTTTCA
1 TTTTTTTTCA
17692292 -TTTTTTT-A
1 TTTTTTTTCA
*
17692300 TTTTTTTTCC
1 TTTTTTTTCA
*
17692310 TTTTTTTTCG
1 TTTTTTTTCA
17692320 TTTTT
1 TTTTT
17692325 CCATATTCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 1 0.03
9 14 0.48
10 14 0.48
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:17692305 original size:18 final size:18
Alignment explanation
Indices: 17692282--17692316 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17692272 ATTTTAATCT
17692282 TTTTTTTTCATTTTTTTA
1 TTTTTTTTCATTTTTTTA
*
17692300 TTTTTTTTCCTTTTTTT
1 TTTTTTTTCATTTTTTT
17692317 TCGTTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTTCATTTTTTTA
Found at i:17695120 original size:61 final size:61
Alignment explanation
Indices: 17695052--17695182 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
17695042 CATAAAAATT
* * * * *
17695052 TAATGATGGATGGATTG-ACAATTGACTACATGAATGGATGCATGACTTAATGTTTACCTCA
1 TAATGATGCATGGA-TGAACAAATAACTACATGAATAGATGCATGACGTAATGTTTACCTCA
* * * *
17695113 TAATGATGCATGGATGAACAAATAATTACATGAATAGATGCATGAGGTAATGTTTGCCTTA
1 TAATGATGCATGGATGAACAAATAACTACATGAATAGATGCATGACGTAATGTTTACCTCA
*
17695174 TAATAATGC
1 TAATGATGC
17695183 TTGAATGATG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 2 0.03
61 57 0.97
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (61 bp):
TAATGATGCATGGATGAACAAATAACTACATGAATAGATGCATGACGTAATGTTTACCTCA
Found at i:17696654 original size:121 final size:120
Alignment explanation
Indices: 17696484--17696745 Score: 307
Period size: 121 Copynumber: 2.2 Consensus size: 120
17696474 AATTATCTTT
* *
17696484 CAATATGTTGGT-AGGATTTTATTTAAATTATTTCTTTTCTAAAAATTAATTTTTATTTAAAAAA
1 CAATATGTTGGTAAGGATTTTATTAAAATTATTTCTTTTCTAAAAATTAATTTTT-TATAAAAAA
* * *
17696548 -CATAAGGTTTTTCCAATATGTTGGTAAAACCTTATCATAAAAATCAAATTGCCTTC
65 TAATAAGG-TTCTCCAATATATTGGTAAAACCTTATCATAAAAATCAAATTGCCTTC
* * *
17696604 CAGTATGTTAGTAAGG-TTTTATTAAAAATTATTT-TTTCTCTTAAAATTAATTTTTTATAAAAA
1 CAATATGTTGGTAAGGATTTTATT-AAAATTATTTCTTT-TCTAAAAATTAATTTTTTATAAAAA
* * * ** *
17696667 ATTAATAATGTTCTCTAATATATTGTTAAAACCTTATTTTAAAAATCAAATTGTCTTC
64 A-TAATAAGGTTCTCCAATATATTGGTAAAACCTTATCATAAAAATCAAATTGCCTTC
* *
17696725 CAATATATTGGTAAGGCTTTT
1 CAATATGTTGGTAAGGATTTT
17696746 TATTTTATTA
Statistics
Matches: 119, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
120 28 0.24
121 82 0.69
122 9 0.08
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.45
Consensus pattern (120 bp):
CAATATGTTGGTAAGGATTTTATTAAAATTATTTCTTTTCTAAAAATTAATTTTTTATAAAAAAT
AATAAGGTTCTCCAATATATTGGTAAAACCTTATCATAAAAATCAAATTGCCTTC
Found at i:17696816 original size:56 final size:59
Alignment explanation
Indices: 17696748--17696870 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 59
17696738 AGGCTTTTTA
* * * * * *
17696748 TTTTATTAAAACAATT-TATTAA-A-AATTTGAATCTTCGAATATGTTGGTAAAATTCT
1 TTTTATTTAAACAATTATATTAAGAGAATATGAACCCTCCAATATGTTAGTAAAATTCT
* **
17696804 TTTTATTTAAACAATTATTTTAAGAGAATATGAACCCTCCAATATGTTAGTAAGGTTCT
1 TTTTATTTAAACAATTATATTAAGAGAATATGAACCCTCCAATATGTTAGTAAAATTCT
17696863 TTTTATTT
1 TTTTATTT
17696871 TATTTAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
56 15 0.27
57 5 0.09
58 1 0.02
59 34 0.62
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (59 bp):
TTTTATTTAAACAATTATATTAAGAGAATATGAACCCTCCAATATGTTAGTAAAATTCT
Found at i:17698203 original size:3 final size:3
Alignment explanation
Indices: 17698195--17698219 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17698185 ATGTGCATAT
17698195 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
17698220 ATTTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17699125 original size:17 final size:17
Alignment explanation
Indices: 17699103--17699158 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
17699093 TTTTCTTTTT
17699103 TTTTTGTTTATTTTCTA
1 TTTTTGTTTATTTTCTA
17699120 TTTTTGATTT-TTTTCTA
1 TTTTTG-TTTATTTTCTA
17699137 -TTTT-TTTACTTTTCTA
1 TTTTTGTTTA-TTTTCTA
17699153 CTTTTT
1 -TTTTT
17699159 TATATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.09
16 11 0.32
17 13 0.38
18 7 0.21
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTGTTTATTTTCTA
Found at i:17699166 original size:17 final size:16
Alignment explanation
Indices: 17699111--17699166 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
17699101 TTTTTTTGTT
*
17699111 TATTTTCTATTTTTGA
1 TATTTTCTATTTTTTA
*
17699127 TTTTTTTCTATTTTTT-
1 -TATTTTCTATTTTTTA
17699143 TACTTTTCTACTTTTTTA
1 TA-TTTTCTA-TTTTTTA
17699161 TATTTT
1 TATTTT
17699167 TATATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.03
16 7 0.21
17 23 0.70
18 2 0.06
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (16 bp):
TATTTTCTATTTTTTA
Found at i:17701068 original size:10 final size:10
Alignment explanation
Indices: 17701041--17701074 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
17701031 TGAAAAAAGG
*
17701041 TTTAATTATT
1 TTTATTTATT
17701051 TGTTATTTATT
1 T-TTATTTATT
17701062 TTTATTTATT
1 TTTATTTATT
17701072 TTT
1 TTT
17701075 TGTGAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTATTTATT
Found at i:17702831 original size:43 final size:41
Alignment explanation
Indices: 17702782--17702911 Score: 113
Period size: 40 Copynumber: 3.2 Consensus size: 41
17702772 TGACTTTTGG
* * * *
17702782 AAATAAATTAAGCTTCTCTAAATAGAGGCACCACAACTTTGAA
1 AAATAAA-TAAGCTCCTCTAAACA-AAGCACCACAACTTTAAA
*
17702825 AAATAAA-ATGCTCCTCTAAACAAAGCACCACAACTTTAAA
1 AAATAAATAAGCTCCTCTAAACAAAGCACCACAACTTTAAA
* * * * * *
17702865 AAATAAAT--GCTCTTTTAAACAGAGGTACCATAACTTTAGA
1 AAATAAATAAGCTCCTCTAAACA-AAGCACCACAACTTTAAA
17702905 AAATAAA
1 AAATAAA
17702912 AGTTTCCCTA
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 11 0.15
40 44 0.59
41 12 0.16
43 7 0.09
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (41 bp):
AAATAAATAAGCTCCTCTAAACAAAGCACCACAACTTTAAA
Found at i:17702884 original size:39 final size:40
Alignment explanation
Indices: 17702797--17702911 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 40
17702787 AATTAAGCTT
* * *
17702797 CTCTAAATAGAGGCACCACAACTTTGAAAAATAAAATGCTC
1 CTCTAAACAGAAGCACCACAACTTTAAAAAAT-AAATGCTC
17702838 CTCTAAACA-AAGCACCACAACTTTAAAAAATAAATGCTC
1 CTCTAAACAGAAGCACCACAACTTTAAAAAATAAATGCTC
* * * * * *
17702877 TTTTAAACAGAGGTACCATAACTTTAGAAAATAAA
1 CTCTAAACAGAAGCACCACAACTTTAAAAAATAAA
17702912 AGTTTCCCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 15 0.23
40 41 0.64
41 8 0.12
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (40 bp):
CTCTAAACAGAAGCACCACAACTTTAAAAAATAAATGCTC
Found at i:17703410 original size:21 final size:22
Alignment explanation
Indices: 17703384--17703429 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
17703374 AACTCAAAAC
17703384 TCAAAGATTCTCATTTGAA-AT
1 TCAAAGATTCTCATTTGAAGAT
17703405 TCAAAGATTCTCATTTGAAGAT
1 TCAAAGATTCTCATTTGAAGAT
17703427 TCA
1 TCA
17703430 CAATCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (22 bp):
TCAAAGATTCTCATTTGAAGAT
Found at i:17704592 original size:13 final size:13
Alignment explanation
Indices: 17704574--17704598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17704564 TTTTTCCATT
17704574 TTTATTTATTTTA
1 TTTATTTATTTTA
17704587 TTTATTTATTTT
1 TTTATTTATTTT
17704599 GTTTTTTTCC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:17704996 original size:27 final size:27
Alignment explanation
Indices: 17704942--17704996 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17704932 ATGTATGGCA
* * * * *
17704942 TTTTTCTTTCTTTTTTTTTTTACTTTT
1 TTTTTCTTTCTATATTTTATGACCTTT
17704969 TTTTTCTTTCTATATTTTATGACCTTT
1 TTTTTCTTTCTATATTTTATGACCTTT
17704996 T
1 T
17704997 GTGATCTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTTCTTTCTATATTTTATGACCTTT
Found at i:17708570 original size:17 final size:17
Alignment explanation
Indices: 17708548--17708580 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17708538 ATTTTTTTTA
17708548 ATTATTTATTATTTGTT
1 ATTATTTATTATTTGTT
*
17708565 ATTATTTATTTTTTGT
1 ATTATTTATTATTTGT
17708581 GAAAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (17 bp):
ATTATTTATTATTTGTT
Found at i:17708833 original size:25 final size:25
Alignment explanation
Indices: 17708781--17708833 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
17708771 TCACCTAGAG
*
17708781 ATTTCTTAAGAATTCACCATTTGAA
1 ATTTCTTAAGAATTCACCATTGGAA
* *
17708806 ATTTC-TAAGAATTTATCATTGGATA
1 ATTTCTTAAGAATTCACCATTGGA-A
17708831 ATT
1 ATT
17708834 ATCAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTTCTTAAGAATTCACCATTGGAA
Found at i:17709047 original size:18 final size:20
Alignment explanation
Indices: 17709024--17709066 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
17709014 TTTTATTAAA
17709024 TCTTTTT-TATTTT-TTTAT
1 TCTTTTTGTATTTTCTTTAT
*
17709042 TCTTTTTGTTTTTTCTTTAT
1 TCTTTTTGTATTTTCTTTAT
17709062 T-TTTT
1 TCTTTT
17709067 GTTTGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (20 bp):
TCTTTTTGTATTTTCTTTAT
Found at i:17709565 original size:22 final size:23
Alignment explanation
Indices: 17709528--17709570 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
17709518 GTAGATCTCC
17709528 CTTTCTTCCCTTTCTCTTTCTTT
1 CTTTCTTCCCTTTCTCTTTCTTT
*
17709551 CTTT-TTCTCTTTCTCTTTCT
1 CTTTCTTCCCTTTCTCTTTCT
17709571 AGAATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (23 bp):
CTTTCTTCCCTTTCTCTTTCTTT
Found at i:17712594 original size:10 final size:10
Alignment explanation
Indices: 17712581--17712613 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
17712571 AAAAATGATG
17712581 AAAAAAAGAA
1 AAAAAAAGAA
17712591 AAAAAAAGAA
1 AAAAAAAGAA
17712601 AAAAAAATGAA
1 AAAAAAA-GAA
17712612 AA
1 AA
17712614 TGAAAGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:17712595 original size:11 final size:11
Alignment explanation
Indices: 17712581--17712613 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17712571 AAAAATGATG
17712581 AAAAAAAG-AA
1 AAAAAAAGAAA
17712591 AAAAAAAGAAA
1 AAAAAAAGAAA
*
17712602 AAAAAATGAAA
1 AAAAAAAGAAA
17712613 A
1 A
17712614 TGAAAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:17714095 original size:45 final size:45
Alignment explanation
Indices: 17714021--17714155 Score: 141
Period size: 45 Copynumber: 3.1 Consensus size: 45
17714011 AAAAAGAACC
* * *
17714021 TTTGAAATTTTAGATGTGAATCCCAAAATTTTTTGAATAAGAATT
1 TTTGAAATTTTGGATATGAATCCCTAAATTTTTTGAATAAGAATT
* * *
17714066 TTTGAAATTTTGGATATGAATCCTTAAATTTCTTGAATAA-AAAT
1 TTTGAAATTTTGGATATGAATCCCTAAATTTTTTGAATAAGAATT
* * * * * *
17714110 TTT-AACTTTTGGGTTTAAATCCCTAAA-TTTTCGAATGAGAATT
1 TTTGAAATTTTGGATATGAATCCCTAAATTTTTTGAATAAGAATT
17714153 TTT
1 TTT
17714156 TAATTTTAGA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 8 0.11
43 25 0.34
44 6 0.08
45 35 0.47
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (45 bp):
TTTGAAATTTTGGATATGAATCCCTAAATTTTTTGAATAAGAATT
Found at i:17714304 original size:17 final size:17
Alignment explanation
Indices: 17714282--17714464 Score: 69
Period size: 17 Copynumber: 10.4 Consensus size: 17
17714272 ATAAAAATTA
17714282 TTGTGAACCTGAATTTC
1 TTGTGAACCTGAATTTC
*
17714299 TTGTGAACCTGATTTTC
1 TTGTGAACCTGAATTTC
** ** ** *
17714316 TTGCAAAATTGAAGCTA
1 TTGTGAACCTGAATTTC
* * *
17714333 TTGCGAATCTTTGAATTTT
1 TTGTGAA-C-CTGAATTTC
**
17714352 TTGTGAATTTTTGAATTTC
1 TTGTGAA--CCTGAATTTC
** *
17714371 TTACGAACCTAAATTTC
1 TTGTGAACCTGAATTTC
* * **
17714388 TTGCGAAACTGAAGCTC
1 TTGTGAACCTGAATTTC
* * *
17714405 TTATGAATCTTTGAAATTC
1 TTGTGAA-C-CTGAATTTC
*
17714424 TTGTGAACCTGAATTTT
1 TTGTGAACCTGAATTTC
** *
17714441 TTACGAACATGAATTTC
1 TTGTGAACCTGAATTTC
17714458 TTGTGAA
1 TTGTGAA
17714465 TTTTTTAAGT
Statistics
Matches: 118, Mismatches: 43, Indels: 10
0.69 0.25 0.06
Matches are distributed among these distances:
17 79 0.67
18 1 0.01
19 37 0.31
20 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (17 bp):
TTGTGAACCTGAATTTC
Found at i:17714413 original size:72 final size:70
Alignment explanation
Indices: 17714276--17714460 Score: 208
Period size: 72 Copynumber: 2.6 Consensus size: 70
17714266 ACAATGATAA
* ** * * *
17714276 AAATTATTGTGAACCTGAATTTCTTGTGAACCTGATTTTCTTGCAAAATTGAAGCTATTGCGAAT
1 AAATTCTTGTGAACCTGAATTTCTTACGAACCTGAATTTCTTGCAAAACTGAAGCTATTACGAAT
17714341 CTTTG
66 CTTTG
* * ** * * * *
17714346 AATTTTTTGTGAATTTTTGAATTTCTTACGAACCTAAATTTCTTGCGAAACTGAAGCTCTTATGA
1 AAATTCTTGTGAA--CCTGAATTTCTTACGAACCTGAATTTCTTGCAAAACTGAAGCTATTACGA
17714411 ATCTTTG
64 ATCTTTG
* *
17714418 AAATTCTTGTGAACCTGAATTTTTTACGAACATGAATTTCTTG
1 AAATTCTTGTGAACCTGAATTTCTTACGAACCTGAATTTCTTG
17714461 TGAATTTTTT
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
70 36 0.39
72 57 0.61
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (70 bp):
AAATTCTTGTGAACCTGAATTTCTTACGAACCTGAATTTCTTGCAAAACTGAAGCTATTACGAAT
CTTTG
Found at i:17714465 original size:53 final size:53
Alignment explanation
Indices: 17714344--17714483 Score: 129
Period size: 53 Copynumber: 2.6 Consensus size: 53
17714334 TGCGAATCTT
* * * *
17714344 TGAATTTTTTGTGAATTTTTGAATTTCTTACGAACCTAAATTTCTTGCGAAAC
1 TGAATTTCTTGTGAATCTTTGAAATTCTTACGAACCTAAATTTCTTACGAAAC
** * ** * *
17714397 TGAAGCTCTTATGAATCTTTGAAATTCTTGTGAACCTGAATTTTTTACG-AAC
1 TGAATTTCTTGTGAATCTTTGAAATTCTTACGAACCTAAATTTCTTACGAAAC
* * * *
17714449 ATGAATTTCTTGTGAATTTTTTAAGTTTTTACGAA
1 -TGAATTTCTTGTGAATCTTTGAAATTCTTACGAA
17714484 TCTTTCAATT
Statistics
Matches: 66, Mismatches: 20, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
52 3 0.05
53 63 0.95
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (53 bp):
TGAATTTCTTGTGAATCTTTGAAATTCTTACGAACCTAAATTTCTTACGAAAC
Found at i:17714515 original size:17 final size:18
Alignment explanation
Indices: 17714490--17714525 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17714480 CGAATCTTTC
*
17714490 AATTGTTGTGAA-CTAAA
1 AATTCTTGTGAATCTAAA
17714507 AATTCTTGTGAATCTAAA
1 AATTCTTGTGAATCTAAA
17714525 A
1 A
17714526 GTTTTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (18 bp):
AATTCTTGTGAATCTAAA
Found at i:17714654 original size:16 final size:16
Alignment explanation
Indices: 17714630--17714660 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17714620 AACTCTTAAG
17714630 AATTATTACAAATCTA
1 AATTATTACAAATCTA
*
17714646 AATTTTTACAAATCT
1 AATTATTACAAATCT
17714661 TCCCTTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTATTACAAATCTA
Found at i:17714799 original size:18 final size:18
Alignment explanation
Indices: 17714778--17714828 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
17714768 TCTTAAGTCA
*
17714778 TTTACGAATTTGAAAATC
1 TTTACGAATTTGAAAACC
* * *
17714796 TTTATGAATCTGGAAACC
1 TTTACGAATTTGAAAACC
17714814 TTTACGAATCTTGAA
1 TTTACGAAT-TTGAA
17714829 TCTTTGCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
TTTACGAATTTGAAAACC
Found at i:17716203 original size:17 final size:16
Alignment explanation
Indices: 17716156--17716211 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
17716146 TGTCTTTTTC
17716156 TTTTTTTGTTTATTT-T
1 TTTTTTTGTTT-TTTAT
17716172 TTGTTTTTGATTTTTTCTAT
1 TT-TTTTTG--TTTTT-TAT
17716192 TTTTTTTGTTTTTATAT
1 TTTTTTTGTTTTT-TAT
17716209 TTT
1 TTT
17716212 AATATTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 2 0.06
17 17 0.50
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.82
Consensus pattern (16 bp):
TTTTTTTGTTTTTTAT
Found at i:17716217 original size:25 final size:25
Alignment explanation
Indices: 17716168--17716218 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
17716158 TTTTTGTTTA
**
17716168 TTTTTTGTTTTTGATTTTTTCTATT
1 TTTTTTGTTTTTGATTTTTAATATT
17716193 TTTTTTGTTTTT-ATATTTTAATATT
1 TTTTTTGTTTTTGAT-TTTTAATATT
17716218 T
1 T
17716219 ATTACTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (25 bp):
TTTTTTGTTTTTGATTTTTAATATT
Found at i:17716336 original size:21 final size:20
Alignment explanation
Indices: 17716316--17716363 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
17716306 ATAAAGTTTA
*
17716316 ATATATTTGCATGATATTTT
1 ATATATTTGCATGATAATTT
*
17716336 ATATTAATTGCATGATAATTT
1 ATA-TATTTGCATGATAATTT
17716357 ATATATT
1 ATATATT
17716364 ATATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (20 bp):
ATATATTTGCATGATAATTT
Found at i:17716393 original size:29 final size:28
Alignment explanation
Indices: 17716334--17716395 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
17716324 GCATGATATT
*
17716334 TTATATTAATTGCATGATAATTTATATA
1 TTATATTAATTGCATGATAATTTATACA
* *
17716362 TTATATTTATTTGCATGATAAGTTT-TGCA
1 TTATA-TTAATTGCATGATAA-TTTATACA
17716391 TTATA
1 TTATA
17716396 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.17
29 21 0.72
30 3 0.10
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (28 bp):
TTATATTAATTGCATGATAATTTATACA
Found at i:17717284 original size:19 final size:19
Alignment explanation
Indices: 17717250--17717290 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
17717240 ATTTTCAAAG
17717250 ATTTTCCTGACAAAATTATA
1 ATTTTCCTGACAAAATT-TA
17717270 ATTTTCCTG-CAAAATTTA
1 ATTTTCCTGACAAAATTTA
17717288 ATT
1 ATT
17717291 ATTTAAACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 7 0.33
20 9 0.43
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTTTCCTGACAAAATTTA
Found at i:17721703 original size:16 final size:16
Alignment explanation
Indices: 17721682--17721713 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17721672 AAAAAGAAAA
17721682 AGAGAGGCTTTTTTTT
1 AGAGAGGCTTTTTTTT
17721698 AGAGAGGCTTTTTTTT
1 AGAGAGGCTTTTTTTT
17721714 GTCTAAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
AGAGAGGCTTTTTTTT
Found at i:17727944 original size:2 final size:2
Alignment explanation
Indices: 17727937--17727984 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
17727927 AAGTTGGCAA
17727937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17727979 AT AT AT
1 AT AT AT
17727985 TGAAATAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17729255 original size:18 final size:17
Alignment explanation
Indices: 17729232--17729265 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17729222 CTTTTAGAAA
17729232 ATATTTTATAAAAAATAT
1 ATATTTT-TAAAAAATAT
*
17729250 ATATTTTTCAAAAATA
1 ATATTTTTAAAAAATA
17729266 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTTTTAAAAAATAT
Found at i:17730998 original size:63 final size:63
Alignment explanation
Indices: 17730911--17731059 Score: 210
Period size: 63 Copynumber: 2.4 Consensus size: 63
17730901 ACAGTTCTAG
* * *
17730911 TCCAACCCAAACTCTTATCTTAAGAATCTCATTCTAACAAAAACTCTAT-TCAATGAGTCTAAA
1 TCCAACCAAAACTCTTATCCTAAGAATCTCAGTCTAACAAAAACTCTATCT-AATGAGTCTAAA
* * * * *
17730974 TCGAACCAAAACTTTTATCCTAAGAATCTTAGTCTAACCAAAACTCTATCTAATGAGTCTTAA
1 TCCAACCAAAACTCTTATCCTAAGAATCTCAGTCTAACAAAAACTCTATCTAATGAGTCTAAA
17731037 TCCAACCAAAACTCTTATCCTAA
1 TCCAACCAAAACTCTTATCCTAA
17731060 TAGTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
63 74 0.99
64 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (63 bp):
TCCAACCAAAACTCTTATCCTAAGAATCTCAGTCTAACAAAAACTCTATCTAATGAGTCTAAA
Found at i:17731079 original size:63 final size:63
Alignment explanation
Indices: 17730911--17731083 Score: 188
Period size: 63 Copynumber: 2.7 Consensus size: 63
17730901 ACAGTTCTAG
* * * * * *
17730911 TCCAACCCAAACTCTTATCTTAAGAATCTCATTCTAACAAAAACTCTATTCAATGAGTCTAAA
1 TCCAACCAAAACTCTTATCCTAAGAATCTTAATCCAACCAAAACTCTATTCAATGAGTCTAAA
* * * * *
17730974 TCGAACCAAAACTTTTATCCTAAGAATCTTAGTCTAACCAAAACTCTA-TCTAATGAGTCTTAA
1 TCCAACCAAAACTCTTATCCTAAGAATCTTAATCCAACCAAAACTCTATTC-AATGAGTCTAAA
* * *
17731037 TCCAACCAAAACTCTTATCCTAATAGT-TTCAATCCAATCAAAACTCT
1 TCCAACCAAAACTCTTATCCTAAGAATCTT-AATCCAACCAAAACTCT
17731084 TATCCCAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
62 4 0.04
63 89 0.96
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (63 bp):
TCCAACCAAAACTCTTATCCTAAGAATCTTAATCCAACCAAAACTCTATTCAATGAGTCTAAA
Found at i:17731088 original size:32 final size:33
Alignment explanation
Indices: 17730911--17731088 Score: 156
Period size: 32 Copynumber: 5.6 Consensus size: 33
17730901 ACAGTTCTAG
* * * * *
17730911 TCCAACCCAAACTCTTATCTTAA-GAATCTCAT
1 TCCAACCAAAACTCTTATCCTAATGAGTCTTAA
* * * *
17730943 TCTAACAAAAACTC-TATTC-AATGAGTCTAAA
1 TCCAACCAAAACTCTTATCCTAATGAGTCTTAA
* * * *
17730974 TCGAACCAAAACTTTTATCCTAA-GAATCTTAG
1 TCCAACCAAAACTCTTATCCTAATGAGTCTTAA
*
17731006 TCTAACCAAAACTC-TAT-CTAATGAGTCTTAA
1 TCCAACCAAAACTCTTATCCTAATGAGTCTTAA
17731037 TCCAACCAAAACTCTTATCCTAAT-AGT-TTCAA
1 TCCAACCAAAACTCTTATCCTAATGAGTCTT-AA
*
17731069 TCCAATCAAAACTCTTATCC
1 TCCAACCAAAACTCTTATCC
17731089 CAAAAAGTCG
Statistics
Matches: 118, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
30 6 0.05
31 45 0.38
32 60 0.51
33 7 0.06
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (33 bp):
TCCAACCAAAACTCTTATCCTAATGAGTCTTAA
Found at i:17735572 original size:76 final size:76
Alignment explanation
Indices: 17735446--17735599 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
17735436 TTTGGTTTGT
*
17735446 TAATCACAACTAGGTTTGGGAGTTCAGCTACATGTGGGAAATATTTTAGACTCCCACAATGCCAT
1 TAATCACAACTAGGTTTGGGAGTTCAGCTACATGTGGGAAAGATTTTAGACTCCCACAATGCCAT
17735511 CCATAGGATGG
66 CCATAGGATGG
17735522 TAATCACAACTAGGTTTGGGAGTTCAGCTACATGTGGGAAAGATTTTAGACTCCCACAATGCCAT
1 TAATCACAACTAGGTTTGGGAGTTCAGCTACATGTGGGAAAGATTTTAGACTCCCACAATGCCAT
17735587 CCATAGGATGG
66 CCATAGGATGG
17735598 TA
1 TA
17735600 CCAAATAGTT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (76 bp):
TAATCACAACTAGGTTTGGGAGTTCAGCTACATGTGGGAAAGATTTTAGACTCCCACAATGCCAT
CCATAGGATGG
Found at i:17736250 original size:194 final size:196
Alignment explanation
Indices: 17736050--17736408 Score: 442
Period size: 194 Copynumber: 1.8 Consensus size: 196
17736040 TTGTTATCGA
* * * * *
17736050 TTGAAAACAAATGTCAATTACTATTATTAAAA-TTTTATCTAAAATTTCTACCATTTTGA-AAAT
1 TTGAAAACAAATGACAATTACTATTATAAAAATTTTTAACTAAAATTCCCACC-TTTTGAGAAA-
*
17736113 ATTTA-AAGGAAAACTTATTACTTAAAAA-TTTCT-AAGAAATCAACCATTCTTGA-TTTTCAAA
64 ATTTAGAA-GAAAACTTATCA-TTAAAAATTTTCTAAAGAAATCAACCATTCTTGATTTTTCAAA
* * *
17736174 ATTTCATCATCAGATAATTTTCACTTATTTCTAATAATGTAGAGTCTCCTCATTTATTATTATAA
127 ATATCATCATCAGATAATTATCACTTATTTCCAATAATGTAGAGTCTCCTCATTTATTATTATAA
17736239 TTCAT
192 TTCAT
* * * * * * *
17736244 TTGAAAATAAGTGACAATTATTTTTATAAAAATTTTTAACTAAACTTCCCACCTTTTTAGAGAAT
1 TTGAAAACAAATGACAATTACTATTATAAAAATTTTTAACTAAAATTCCCACCTTTTGAGAAAAT
* * *
17736309 TTAGAAGAAAATTTCTCATTAAAAATTTTCTAAAGAAATCAACCATTCTTGATTTTTTTAAAATA
66 TTAGAAGAAAACTTATCATTAAAAATTTTCTAAAGAAATCAACCATTCTTGA-TTTTTCAAAATA
* *
17736374 TCATCATTAGATAATTATCATTTATTTCCAATAAT
130 TCATCATCAGATAATTATCACTTATTTCCAATAAT
17736409 AAAAATTTTA
Statistics
Matches: 137, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
193 7 0.05
194 50 0.36
195 40 0.29
197 40 0.29
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (196 bp):
TTGAAAACAAATGACAATTACTATTATAAAAATTTTTAACTAAAATTCCCACCTTTTGAGAAAAT
TTAGAAGAAAACTTATCATTAAAAATTTTCTAAAGAAATCAACCATTCTTGATTTTTCAAAATAT
CATCATCAGATAATTATCACTTATTTCCAATAATGTAGAGTCTCCTCATTTATTATTATAATTCA
T
Found at i:17736476 original size:197 final size:197
Alignment explanation
Indices: 17736132--17736564 Score: 446
Period size: 197 Copynumber: 2.2 Consensus size: 197
17736122 AAAACTTATT
* * *
17736132 ACTTAAAAATTTCT-AAGAAATCAACCATTCTTGA--TTTTCAAAATTTCATCATCAGATAATTT
1 ACTTAAAAATTTCTAAAGAAATCAACCATTCTTGATTTTTTTAAAATATCATCATCAGATAATTA
* ** * * * * *
17736194 TCACTTATTTCTAATAATGTAGAGTCTCCTCATTTATTATTATAATTCATTTGAAAATAAGTGAC
66 TCACTTATTTCCAATAATAAAAAGTCTACTCATTTATTATTATAACTCATTTGAAAATAAATGAA
* * * * * *
17736259 AATTATTTTTATAAAAATTTTTAACTAAACTTCCCAC-CTTTTTAGAGAATTTAGAAGAAAATTT
131 AATAATTTTTATAAAAATTTTCAACTAAACTTCCCACAATTTTGA-AGAATTTAAAAGAAAATTC
17736323 CTC
195 CTC
*
17736326 A-TTAAAAATTTTCTAAAGAAATCAACCATTCTTGATTTTTTTAAAATATCATCATTAGATAATT
1 ACTTAAAAA-TTTCTAAAGAAATCAACCATTCTTGATTTTTTTAAAATATCATCATCAGATAATT
* * * * * ** * * *
17736390 ATCATTTATTTCCAATAATAAAAATTTTATTTATTT-TTATTATTCCTCCTTTTAATATAAATGA
65 ATCACTTATTTCCAATAATAAAAAGTCTACTCATTTATTATTATAACTCATTTGAAAATAAATGA
* ** * * **
17736454 AAATAATTTTTTCTTGAAATTTTCCACTATACTTTTCACAATTTTGAAGAATTTAAAAGAAAATT
130 AAATAA-TTTTTATAAAAATTTTCAACTAAACTTCCCACAATTTTGAAGAATTTAAAAGAAAATT
*
17736519 CCTT
194 CCTC
* * *
17736523 ACTTAGAAATTTCTAAAGGAATCAACCATTCTTAATTTTTTT
1 ACTTAAAAATTTCTAAAGAAATCAACCATTCTTGATTTTTTT
17736565 TAGAATTTCA
Statistics
Matches: 193, Mismatches: 39, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
193 7 0.04
194 6 0.03
195 20 0.10
196 25 0.13
197 124 0.64
198 11 0.06
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (197 bp):
ACTTAAAAATTTCTAAAGAAATCAACCATTCTTGATTTTTTTAAAATATCATCATCAGATAATTA
TCACTTATTTCCAATAATAAAAAGTCTACTCATTTATTATTATAACTCATTTGAAAATAAATGAA
AATAATTTTTATAAAAATTTTCAACTAAACTTCCCACAATTTTGAAGAATTTAAAAGAAAATTCC
TC
Found at i:17736685 original size:20 final size:22
Alignment explanation
Indices: 17736657--17736697 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
17736647 ATCTTAACAA
*
17736657 TTATTATTTTT-TTAA-CTAAC
1 TTATAATTTTTATTAATCTAAC
17736677 TTATAATTTTTATTAATCTAA
1 TTATAATTTTTATTAATCTAA
17736698 AATTTATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATAATTTTTATTAATCTAAC
Found at i:17743333 original size:18 final size:18
Alignment explanation
Indices: 17743312--17743360 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
17743302 ATATATCAAT
*
17743312 AGATAAATAAAAATGGAA
1 AGATAAATAAAAATGCAA
*
17743330 AGATAAATTAAAA-GCAA
1 AGATAAATAAAAATGCAA
* *
17743347 AAATGAATAAAAAT
1 AGATAAATAAAAAT
17743361 TATAAAGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.18
Consensus pattern (18 bp):
AGATAAATAAAAATGCAA
Found at i:17744937 original size:21 final size:21
Alignment explanation
Indices: 17744905--17744964 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
17744895 AGAGTTGAAA
*
17744905 TTTTTT-GACACTAAAATACT
1 TTTTTTCGTCACTAAAATACT
17744925 TTTTTTCGTCACTAAAATACT
1 TTTTTTCGTCACTAAAATACT
* **
17744946 ATTTTTCGTTGCTAAAATA
1 TTTTTTCGTCACTAAAATA
17744965 TATTACCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 6 0.17
21 29 0.83
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTTTCGTCACTAAAATACT
Done.