Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 61 of 172
Found at i:19872424 original size:129 final size:130
Alignment explanation
Indices: 19872254--19872506 Score: 393
Period size: 129 Copynumber: 2.0 Consensus size: 130
19872244 AAAAATTTTC
* *
19872254 TTTAAAACGAAGGCAACGTTCGATGTTTGGTAACTCAGGGAATCGTGCCCTATCGTGCTGAGTTG
1 TTTAAAACGAAGGCAACGTTCGATGTTTGGCAACTCAGGGAATCGTGCCCTATCGTACTGAGTTG
*
19872319 CAATTTCCTGTTTGTTCAAAATAATAGAATAAT-CCTTTAGAATTTCACTCATG-TCTTTAAAAA
66 CAATTTCCCGTTTGTTCAAAATAATAGAAT-ATCCCTTTAGAATTTCACTCATGTTCTTTAAAAA
19872382 T
130 T
* * ** *
19872383 TTTAAAACGAAGGTAATGTTCGATGTTTGGCAACTTGGGGAATCGTGCCCTATCGTACTGGGTTG
1 TTTAAAACGAAGGCAACGTTCGATGTTTGGCAACTCAGGGAATCGTGCCCTATCGTACTGAGTTG
* *
19872448 CAATTTCCCGTTTGTTCAAAATGATCGAATATCCCTTTAGAATTTCACTCATGTTCTTT
66 CAATTTCCCGTTTGTTCAAAATAATAGAATATCCCTTTAGAATTTCACTCATGTTCTTT
19872507 GAATTCTAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 2 0.02
129 105 0.94
130 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (130 bp):
TTTAAAACGAAGGCAACGTTCGATGTTTGGCAACTCAGGGAATCGTGCCCTATCGTACTGAGTTG
CAATTTCCCGTTTGTTCAAAATAATAGAATATCCCTTTAGAATTTCACTCATGTTCTTTAAAAAT
Found at i:19875624 original size:28 final size:28
Alignment explanation
Indices: 19875574--19875670 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
19875564 GGCTGCCAGA
* **
19875574 ACAGATA-TTGTGACAGAGTCACCAAAT
1 ACAGATATTTGTGGCAGAACCACCAAAT
* **
19875601 ACAGTTATTTGTGGCAGTCCCACCAGAAT
1 ACAGATATTTGTGGCAGAACCACCA-AAT
*
19875630 -CAGATATTTGTGGCAGAACCACCAAAA
1 ACAGATATTTGTGGCAGAACCACCAAAT
19875657 ACAGATATTTGTGG
1 ACAGATATTTGTGG
19875671 TATAGCCACC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 8 0.14
28 47 0.81
29 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (28 bp):
ACAGATATTTGTGGCAGAACCACCAAAT
Found at i:19875679 original size:28 final size:28
Alignment explanation
Indices: 19875593--19875681 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
19875583 GTGACAGAGT
* * *
19875593 CACCAAATACAGTTATTTGTGGCAGT-CC
1 CACCAAAAACAGATATTTGTGGCA-TAAC
* * *
19875621 CACCAGAATCAGATATTTGTGGCAGAAC
1 CACCAAAAACAGATATTTGTGGCATAAC
* *
19875649 CACCAAAAACAGATATTTGTGGTATAGC
1 CACCAAAAACAGATATTTGTGGCATAAC
19875677 CACCA
1 CACCA
19875682 GAACACTTCC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (28 bp):
CACCAAAAACAGATATTTGTGGCATAAC
Found at i:19883446 original size:28 final size:27
Alignment explanation
Indices: 19883397--19883513 Score: 155
Period size: 28 Copynumber: 4.3 Consensus size: 27
19883387 AACATGGCTT
* *
19883397 CCAGAACAGATA-TTGTGACAGAGTCA
1 CCAGAACAGATATTTGTGGCAGAGCCA
19883423 CCAGATACAGATATTTGTGGCAGAGCCA
1 CCAGA-ACAGATATTTGTGGCAGAGCCA
*
19883451 CCAGAATCAGATATTTGTGGCAGAACCA
1 CCAGAA-CAGATATTTGTGGCAGAGCCA
* *
19883479 CCAGAAACAGATATTTATGGCATAGCCA
1 CCAG-AACAGATATTTGTGGCAGAGCCA
19883507 CCAGAAC
1 CCAGAAC
19883514 GCTTCCTCCA
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
26 5 0.06
27 11 0.14
28 63 0.78
29 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (27 bp):
CCAGAACAGATATTTGTGGCAGAGCCA
Found at i:19885797 original size:27 final size:27
Alignment explanation
Indices: 19885759--19885911 Score: 216
Period size: 27 Copynumber: 5.7 Consensus size: 27
19885749 TACCTGAACT
*
19885759 CTCATGTGATAAAATGACGATTTTGCC
1 CTCATGTGATAAAATGACGATTTTACC
19885786 CTCATGTGATAAAATGACGATTTTACC
1 CTCATGTGATAAAATGACGATTTTACC
* * *
19885813 CTTATGTGATAAAATGATGATTTTGCC
1 CTCATGTGATAAAATGACGATTTTACC
* *
19885840 CTCATGTGTTAAAATGATGATTTTACC
1 CTCATGTGATAAAATGACGATTTTACC
* * *
19885867 CTCATGTGATAAAATAATGATTTTTCC
1 CTCATGTGATAAAATGACGATTTTACC
*
19885894 TTCATGTGATAAAATGAC
1 CTCATGTGATAAAATGAC
19885912 CAAAATACCC
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 113 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (27 bp):
CTCATGTGATAAAATGACGATTTTACC
Found at i:19885921 original size:54 final size:54
Alignment explanation
Indices: 19885759--19885911 Score: 243
Period size: 54 Copynumber: 2.8 Consensus size: 54
19885749 TACCTGAACT
*
19885759 CTCATGTGATAAAATGACGATTTTGCCCTCATGTGATAAAATGACGATTTTACC
1 CTCATGTGATAAAATGATGATTTTGCCCTCATGTGATAAAATGACGATTTTACC
* * *
19885813 CTTATGTGATAAAATGATGATTTTGCCCTCATGTGTTAAAATGATGATTTTACC
1 CTCATGTGATAAAATGATGATTTTGCCCTCATGTGATAAAATGACGATTTTACC
* * *
19885867 CTCATGTGATAAAATAATGATTTTTCCTTCATGTGATAAAATGAC
1 CTCATGTGATAAAATGATGATTTTGCCCTCATGTGATAAAATGAC
19885912 CAAAATACCC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 89 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (54 bp):
CTCATGTGATAAAATGATGATTTTGCCCTCATGTGATAAAATGACGATTTTACC
Found at i:19885934 original size:81 final size:81
Alignment explanation
Indices: 19885768--19885938 Score: 184
Period size: 81 Copynumber: 2.1 Consensus size: 81
19885758 TCTCATGTGA
* * **
19885768 TAAAATGACGATTTTGCCCTCATGTGATAAAATGACGATTTTACCCTTATGTGATAAAATGATGA
1 TAAAATGACGATTTTACCCTCATGTGATAAAATAACGATTTTACCCTTATGTGATAAAATGACCA
*** * * * *
19885833 TTTTGCCCTCATGTGT
66 AAATACCCCCAAGTGG
* * *
19885849 TAAAATGATGATTTTACCCTCATGTGATAAAATAATGATTTT-TCCTTCATGTGATAAAATGACC
1 TAAAATGACGATTTTACCCTCATGTGATAAAATAACGATTTTACCCTT-ATGTGATAAAATGACC
19885913 AAAATACCCCCACAG-GG
65 AAAATACCCCCA-AGTGG
19885930 TAAAATGAC
1 TAAAATGAC
19885939 TGAAAGACCC
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
80 4 0.05
81 68 0.93
82 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (81 bp):
TAAAATGACGATTTTACCCTCATGTGATAAAATAACGATTTTACCCTTATGTGATAAAATGACCA
AAATACCCCCAAGTGG
Found at i:19885977 original size:28 final size:27
Alignment explanation
Indices: 19885903--19885993 Score: 128
Period size: 27 Copynumber: 3.3 Consensus size: 27
19885893 CTTCATGTGA
*
19885903 TAAAATGACCAAAATACCCCCACAGGG
1 TAAAATGACCAAAATACCCCCATAGGG
** *
19885930 TAAAATGACTGAAAGACCCCCATAGGG
1 TAAAATGACCAAAATACCCCCATAGGG
*
19885957 TAAAATGACCCAAAATACCCCTATAGGG
1 TAAAATGA-CCAAAATACCCCCATAGGG
19885985 TAAAATGAC
1 TAAAATGAC
19885994 TGTAATACCA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 32 0.58
28 23 0.42
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.15
Consensus pattern (27 bp):
TAAAATGACCAAAATACCCCCATAGGG
Found at i:19886000 original size:27 final size:27
Alignment explanation
Indices: 19885903--19886017 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
19885893 CTTCATGTGA
** *
19885903 TAAAATGACCAAAATACCCCCACAGGG
1 TAAAATGACTGAAATACCCCCATAGGG
*
19885930 TAAAATGACTGAAAGACCCCCATAGGG
1 TAAAATGACTGAAATACCCCCATAGGG
** *
19885957 TAAAATGACCCAAAATACCCCTATAGGG
1 TAAAATGA-CTGAAATACCCCCATAGGG
* * * *
19885985 TAAAATGACTGTAATACCACGATAAGG
1 TAAAATGACTGAAATACCCCCATAGGG
19886012 TAAAAT
1 TAAAAT
19886018 CATAGATTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
27 50 0.68
28 23 0.32
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCATAGGG
Found at i:19886014 original size:55 final size:54
Alignment explanation
Indices: 19885903--19886017 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 54
19885893 CTTCATGTGA
* *
19885903 TAAAATGACCAAAATACCCCCACAGGGTAAAATGACTGAAAGACCCCCATAGGG
1 TAAAATGACCAAAATACCCCCACAGGGTAAAATGACTGAAAGACCACCATAAGG
* * * * *
19885957 TAAAATGACCCAAAATACCCCTATAGGGTAAAATGACTGTAATACCACGATAAGG
1 TAAAATGA-CCAAAATACCCCCACAGGGTAAAATGACTGAAAGACCACCATAAGG
19886012 TAAAAT
1 TAAAAT
19886018 CATAGATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 8 0.15
55 45 0.85
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (54 bp):
TAAAATGACCAAAATACCCCCACAGGGTAAAATGACTGAAAGACCACCATAAGG
Found at i:19886388 original size:18 final size:19
Alignment explanation
Indices: 19886361--19886411 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
19886351 TATTTGCATT
19886361 CTGCACTGATTACT-ATTA
1 CTGCACTGATTACTGATTA
* * *
19886379 CTGCATTGATCA-TGGTTA
1 CTGCACTGATTACTGATTA
19886397 CTGCACTGATTACTG
1 CTGCACTGATTACTG
19886412 CAACTGCCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 1 0.04
18 23 0.88
19 2 0.08
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (19 bp):
CTGCACTGATTACTGATTA
Found at i:19895098 original size:12 final size:12
Alignment explanation
Indices: 19895083--19895108 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19895073 ATTTAACCTA
19895083 GGGTTTATATTT
1 GGGTTTATATTT
19895095 GGGTTTATATTT
1 GGGTTTATATTT
19895107 GG
1 GG
19895109 AAAAATACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (12 bp):
GGGTTTATATTT
Found at i:19895989 original size:93 final size:93
Alignment explanation
Indices: 19895830--19896000 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
19895820 GGATGGTTGA
* *
19895830 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
19895895 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
19895923 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
19895988 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
19896001 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19896003 original size:46 final size:46
Alignment explanation
Indices: 19895834--19896005 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
19895824 GGTTGAGCAT
* * *
19895834 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
19895880 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
19895925 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
19895973 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
19896006 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 60 0.56
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:19899005 original size:182 final size:182
Alignment explanation
Indices: 19898689--19899063 Score: 506
Period size: 182 Copynumber: 2.1 Consensus size: 182
19898679 GAATCAAAAT
* * * * *
19898689 AGGGACACACGATTGTGTCCCAACCCGTGTCCTCACCCGTGTAACTCACTAAGTAGGGTCACAAT
1 AGGGACACACGATCGTGTCCCAACCCATGTCCTCACCAGTGTAACTCACTAAATAGGGTCACAAG
* * * *
19898754 GTCATGCCATTCGCCCATGTGCCAGGCTGTGTAACTCTCGAAATAGCCCCACACGCCTGTGCTCC
66 GCCATGCCATTCGCCCATGTGCCAGGCTGTGTAACTCTCGAAATAACCCCACAAGCCTATGC-CC
* *
19898819 AGGCCATGTGTTAGGCCATGTAACTGCCTGACTTGTGTGCAATAAAACCTACA
130 AGGCCATGTGTTAGGCCATGTAACTACCTGACTTGTATGCAATAAAACCTACA
*** *
19898872 AGGGACACACGATCGTGTCCCAACCCATGTCCTCA-CAGTGTAACTCACTAAATAGGGTTGTACG
1 AGGGACACACGATCGTGTCCCAACCCATGTCCTCACCAGTGTAACTCACTAAATAGGGTCACAAG
* *
19898936 GCCATGTCTCA-T-GCCCGTGTGCCAGGCTGTGTAACTCTTGAAATAACCCCACAAGCCCATATG
66 GCCATG-C-CATTCGCCCATGTGCCAGGCTGTGTAACTCTCGAAATAACCCCACAAG-CC-TATG
* *
19898999 -CCAGGCCATGTGTTAGGCCATGTTACTACCTGACTTGTATGCAATAAGACCTACA
127 CCCAGGCCATGTGTTAGGCCATGTAACTACCTGACTTGTATGCAATAAAACCTACA
19899054 AGGGACACAC
1 AGGGACACAC
19899064 AGCTGAGTCA
Statistics
Matches: 169, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
182 127 0.75
183 37 0.22
184 5 0.03
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.23
Consensus pattern (182 bp):
AGGGACACACGATCGTGTCCCAACCCATGTCCTCACCAGTGTAACTCACTAAATAGGGTCACAAG
GCCATGCCATTCGCCCATGTGCCAGGCTGTGTAACTCTCGAAATAACCCCACAAGCCTATGCCCA
GGCCATGTGTTAGGCCATGTAACTACCTGACTTGTATGCAATAAAACCTACA
Found at i:19900354 original size:43 final size:43
Alignment explanation
Indices: 19900305--19900455 Score: 151
Period size: 43 Copynumber: 3.5 Consensus size: 43
19900295 GGTTATCGAG
* * *
19900305 ATGTGATTACAAGTAAGACCATGTCTGGGTCATTGGCATTG-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCAATGTT
* *
19900347 ATTGTGATTACATGTAAGACAATGCCTGGGACATTGGCAATGTT
1 A-TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAATGTT
* * * * * ** *
19900391 ATATGATTTCATGTAAGACCCTGTCTAGGACAGTGGCACCGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCAATGTT
* *
19900434 ATGTGGTAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
19900456 ATCTAGGATA
Statistics
Matches: 87, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
42 1 0.01
43 84 0.97
44 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCAATGTT
Found at i:19903663 original size:17 final size:17
Alignment explanation
Indices: 19903624--19903664 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19903614 AAAGTATATC
*
19903624 TGATAAAGCCCGATTAA
1 TGATAAAGCCCGATAAA
* *
19903641 TAATAATGCCCGATAAA
1 TGATAAAGCCCGATAAA
19903658 TGATAAA
1 TGATAAA
19903665 TGTTAAAAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
TGATAAAGCCCGATAAA
Found at i:19910425 original size:23 final size:23
Alignment explanation
Indices: 19910382--19910426 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
19910372 TGGAACTCTA
19910382 CTTTTTCACTTATTACGATTAAGC
1 CTTTTTCACTTATTAC-ATTAAGC
19910406 CTTTTTCACTTAATTA-ATTAA
1 CTTTTTCACTT-ATTACATTAA
19910427 ACAAACATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (23 bp):
CTTTTTCACTTATTACATTAAGC
Found at i:19914375 original size:20 final size:20
Alignment explanation
Indices: 19914352--19914400 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
19914342 AGCTCCGTCC
*
19914352 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAACTCATTTG
***
19914372 AGCTCGTTTCAACTCATTTG
1 AGCTCAACTCAACTCATTTG
19914392 AGCTCAACT
1 AGCTCAACT
19914401 GGGCTTACTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAACTCATTTG
Found at i:19925517 original size:22 final size:22
Alignment explanation
Indices: 19925489--19925530 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19925479 TGATATTTGC
19925489 AAAAATTGAT-TTATTTTTTAAG
1 AAAAATTGATATT-TTTTTTAAG
19925511 AAAAATTGATATTTTTTTTA
1 AAAAATTGATATTTTTTTTA
19925531 TATTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
AAAAATTGATATTTTTTTTAAG
Found at i:19925991 original size:26 final size:26
Alignment explanation
Indices: 19925934--19925993 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
19925924 ATTGTAATAT
* *
19925934 ATATTTATTATTAAAATATTAAGATAA
1 ATATTT-TTAATAAAATATTAACATAA
*
19925961 ATATTTTTAATAATATATTAACA-AA
1 ATATTTTTAATAAAATATTAACATAA
19925986 ATTATTTT
1 A-TATTTT
19925994 AAATTTAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.10
26 20 0.69
27 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATATTTTTAATAAAATATTAACATAA
Found at i:19926052 original size:18 final size:18
Alignment explanation
Indices: 19926014--19926049 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19926004 TTATTATTGT
*
19926014 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
19926032 TAAAATATTAATATTAAA
1 TAAAAT-TTAATATTAAA
19926050 TAATTAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:19927329 original size:52 final size:52
Alignment explanation
Indices: 19927251--19927354 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
19927241 AATATGAACC
19927251 GGATACTTCTATATATATATATATATATATATAGAAGTCGAAGCCACTCGGT
1 GGATACTTCTATATATATATATATATATATATAGAAGTCGAAGCCACTCGGT
*
19927303 GGATACTTCTATATATATATATATATATATATAGAAGTCGAAGCCATTCGGT
1 GGATACTTCTATATATATATATATATATATATAGAAGTCGAAGCCACTCGGT
19927355 TTGTGGCACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (52 bp):
GGATACTTCTATATATATATATATATATATATAGAAGTCGAAGCCACTCGGT
Found at i:19937643 original size:3 final size:3
Alignment explanation
Indices: 19937635--19937673 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
19937625 CTCATAATCA
* *
19937635 TCT TCT TCT TCT TTT TCT TAT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
19937674 ACAAAAAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:19937889 original size:2 final size:2
Alignment explanation
Indices: 19937884--19937917 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19937874 CTCTAAATTA
* *
19937884 TC TC TC CC TC TA TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19937918 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:19938868 original size:13 final size:13
Alignment explanation
Indices: 19938846--19938896 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
19938836 TTTAGCAATG
*
19938846 CTTTTGAAAAGTA
1 CTTTTAAAAAGTA
*
19938859 CTTTTAAAAAGTG
1 CTTTTAAAAAGTA
* *
19938872 CTGTGAAAAAGTA
1 CTTTTAAAAAGTA
*
19938885 CTTTTAAGAAGT
1 CTTTTAAAAAGT
19938897 GTTTTTGAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (13 bp):
CTTTTAAAAAGTA
Found at i:19938873 original size:26 final size:26
Alignment explanation
Indices: 19938844--19938909 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
19938834 AGTTTAGCAA
19938844 TGCTTTTGAAAAGTACTTTTAAAAAG
1 TGCTTTTGAAAAGTACTTTTAAAAAG
* *
19938870 TGC-TGTGAAAAAGTACTTTTAAGAAG
1 TGCTTTTG-AAAAGTACTTTTAAAAAG
*
19938896 TGTTTTTGAAAAGT
1 TGCTTTTGAAAAGT
19938910 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 3 0.09
26 28 0.82
27 3 0.09
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTTAAAAAG
Found at i:19941410 original size:53 final size:53
Alignment explanation
Indices: 19941230--19941436 Score: 216
Period size: 53 Copynumber: 3.8 Consensus size: 53
19941220 ATTAGACTTT
* * * *
19941230 AAGGATACCAAGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
19941284 AAGGAAATCATATAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
19941339 AAAGATTCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
19941392 AAGGATACCACGTAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
19941437 TAAAAAGGAA
Statistics
Matches: 122, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
53 45 0.37
54 38 0.31
55 39 0.32
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:19943585 original size:28 final size:29
Alignment explanation
Indices: 19943528--19943585 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
19943518 TACAGGGGTT
19943528 TTCACACGGCCTGGCACACGCCCGTGTCC
1 TTCACACGGCCTGGCACACGCCCGTGTCC
*
19943557 TTCACACGGCCAT-G-ACATGCCCGTGTCC
1 TTCACACGGCC-TGGCACACGCCCGTGTCC
19943585 T
1 T
19943586 AGCCCGTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.52
29 12 0.44
30 1 0.04
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (29 bp):
TTCACACGGCCTGGCACACGCCCGTGTCC
Found at i:19948797 original size:17 final size:17
Alignment explanation
Indices: 19948775--19948808 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19948765 AATTACCCTA
19948775 AAAATTAATCTAAGTGT
1 AAAATTAATCTAAGTGT
19948792 AAAATTAATCTAAGTGT
1 AAAATTAATCTAAGTGT
19948809 GCTTACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
AAAATTAATCTAAGTGT
Found at i:19953852 original size:26 final size:26
Alignment explanation
Indices: 19953823--19953982 Score: 275
Period size: 26 Copynumber: 6.2 Consensus size: 26
19953813 TGGTACAAAT
19953823 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
19953849 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19953875 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
19953901 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19953927 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
19953953 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
19953979 TGAT
1 TGAT
19953983 GAGCATTTCA
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 125 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:19955617 original size:27 final size:26
Alignment explanation
Indices: 19955579--19955717 Score: 170
Period size: 27 Copynumber: 5.2 Consensus size: 26
19955569 GAAACGTCCC
*
19955579 GGTGGCTATGCCACAATTATCTGATCT
1 GGTGGCTCTGCCAC-ATTATCTGATCT
* *
19955606 GGTGGTTCTGCCACATATATCTGTTCT
1 GGTGGCTCTGCCACAT-TATCTGATCT
*
19955633 GGTGGCTATGCCACGATTATCTGATCT
1 GGTGGCTCTGCCAC-ATTATCTGATCT
*
19955660 GGTGGCTCTGCCACATATATCTGTTCT
1 GGTGGCTCTGCCACAT-TATCTGATCT
* *
19955687 GGTGGCTTTGCCACAATATCTGTATCT
1 GGTGGCTCTGCCACATTATCTG-ATCT
19955714 GGTG
1 GGTG
19955718 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.10
27 85 0.88
28 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (26 bp):
GGTGGCTCTGCCACATTATCTGATCT
Found at i:19955661 original size:54 final size:53
Alignment explanation
Indices: 19955579--19955717 Score: 224
Period size: 54 Copynumber: 2.6 Consensus size: 53
19955569 GAAACGTCCC
*
19955579 GGTGGCTATGCCACAATTATCTGATCTGGTGGTTCTGCCACATATATCTGTTCT
1 GGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
19955633 GGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
1 GGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
* *
19955687 GGTGGCTTTGCCACAATATCTGTATCTGGTG
1 GGTGGCTATGCCACATTATCTG-ATCTGGTG
19955718 ACTTCGTCAC
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 7 0.09
54 73 0.91
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (53 bp):
GGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCT
Found at i:19955728 original size:27 final size:27
Alignment explanation
Indices: 19955579--19955735 Score: 150
Period size: 27 Copynumber: 5.8 Consensus size: 27
19955569 GAAACGTCCC
19955579 GGTGGCTAT-GCCACAATTATCTG-ATCT
1 GGTGGCT-TCGCCACAA-TATCTGTATCT
19955606 GGTGG-TTCTGCCACATATATCTGT-TCT
1 GGTGGCTTC-GCCACA-ATATCTGTATCT
*
19955633 GGTGGCTAT-GCCACGATTATCTG-ATCT
1 GGTGGCT-TCGCCAC-AATATCTGTATCT
19955660 GGTGGC-TCTGCCACATATATCTGT-TCT
1 GGTGGCTTC-GCCACA-ATATCTGTATCT
*
19955687 GGTGGCTTTGCCACAATATCTGTATCT
1 GGTGGCTTCGCCACAATATCTGTATCT
* *
19955714 GGTGACTTCGTCACAATATCTG
1 GGTGGCTTCGCCACAATATCTG
19955736 GCAGCCTCGC
Statistics
Matches: 110, Mismatches: 6, Indels: 28
0.76 0.04 0.19
Matches are distributed among these distances:
25 2 0.02
26 10 0.09
27 93 0.85
28 4 0.04
29 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
GGTGGCTTCGCCACAATATCTGTATCT
Found at i:19957985 original size:20 final size:21
Alignment explanation
Indices: 19957962--19958008 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
19957952 GGTTCAAGTT
19957962 ATTTTCT-AGAAAATCAATCC
1 ATTTTCTCAGAAAATCAATCC
**
19957982 ATTTT-TCAGAAAATTGATCC
1 ATTTTCTCAGAAAATCAATCC
19958002 ATTTTCT
1 ATTTTCT
19958009 TAAAGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (21 bp):
ATTTTCTCAGAAAATCAATCC
Found at i:19964734 original size:39 final size:39
Alignment explanation
Indices: 19964691--19964776 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
19964681 TTTAGTTATT
* *
19964691 TTAGTTTGTGTCTTTAATTATGTCATAGTTTGAACATCA
1 TTAGTATGAGTCTTTAATTATGTCATAGTTTGAACATCA
19964730 TTAGTATGAGTCTTTAATTATGTCATAGTTTGAACATCA
1 TTAGTATGAGTCTTTAATTATGTCATAGTTTGAACATCA
*
19964769 TTAATATG
1 TTAGTATG
19964777 TGTTCTGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (39 bp):
TTAGTATGAGTCTTTAATTATGTCATAGTTTGAACATCA
Found at i:19964913 original size:52 final size:50
Alignment explanation
Indices: 19964793--19964915 Score: 183
Period size: 50 Copynumber: 2.4 Consensus size: 50
19964783 GCATTTAGTA
*
19964793 AAGTCATGCATTATGTAACTCTCATGTAAGTTAAGTTTGCATCATAAATT
1 AAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCATCATAAATT
* * *
19964843 ATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATT
1 AAGTCATGCATTATGTAACTCCCATGTAAGTT-AAGTTTGCATCA-TAAATT
*
19964895 AAGTCATGCATTAAGTAACTC
1 AAGTCATGCATTATGTAACTC
19964916 ATTTGTTCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
50 28 0.44
51 12 0.19
52 24 0.38
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (50 bp):
AAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCATCATAAATT
Found at i:19968898 original size:76 final size:76
Alignment explanation
Indices: 19968796--19968965 Score: 214
Period size: 76 Copynumber: 2.2 Consensus size: 76
19968786 GGTTTTTCTA
* * * * * * **
19968796 ACTAATGTTGGGCACACATTTAATATCGTTAGTTTATTCGATTAGCGCTTGGTGCAAATCCTTGT
1 ACTAGTGTTGGGCACACATTTAATATCGTCAGTTTATCCGACTAGCACTGGGCACAAATCCTTGT
19968861 CGGGTTATCCG
66 CGGGTTATCCG
* * * *
19968872 ACTAGTGTTGGGCACATATTTAATATCGTCAGTTTATCCGACTAGTACTGGGCACAAATCTTTTT
1 ACTAGTGTTGGGCACACATTTAATATCGTCAGTTTATCCGACTAGCACTGGGCACAAATCCTTGT
*
19968937 TGGGTTATCCG
66 CGGGTTATCCG
*
19968948 GCTAGTGTTGGGCACACA
1 ACTAGTGTTGGGCACACA
19968966 CATTTAATTT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
ACTAGTGTTGGGCACACATTTAATATCGTCAGTTTATCCGACTAGCACTGGGCACAAATCCTTGT
CGGGTTATCCG
Found at i:19982373 original size:28 final size:28
Alignment explanation
Indices: 19982289--19982374 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 28
19982279 TAAAAAATTT
*
19982289 ATAGTTGAGTGACTAAAAAAGAAGCAAACA-C
1 ATAGTTGAGTGAC-CAAAAA-AAG-AAA-ATC
* * * *
19982320 ATAGTTGGGTTATCAATTAAAA-AAAATC
1 ATAGTTGAGTGACCAA-AAAAAGAAAATC
19982348 ATAGTTGAGTGACCAAAAAAAGAAAAT
1 ATAGTTGAGTGACCAAAAAAAGAAAAT
19982375 AACCCATAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
27 5 0.12
28 22 0.51
30 4 0.09
31 12 0.28
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.22
Consensus pattern (28 bp):
ATAGTTGAGTGACCAAAAAAAGAAAATC
Found at i:19982383 original size:60 final size:59
Alignment explanation
Indices: 19982274--19982389 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
19982264 GTTAGGTGAC
* * * * * *
19982274 CAATTTAAAAAATTTATAGTTGAGTGACTAAAAAAGAAGCAAACACATAGTTGGGTTAT
1 CAATTAAAAAAAATCATAGTTGAGTGACAAAAAAAGAAGAAAACACATAGTCGGGTTAT
*
19982333 CAATTAAAAAAAATCATAGTTGAGTGACCAAAAAAAGAA-AATAACCCATAGTCGGGT
1 CAATTAAAAAAAATCATAGTTGAGTGA-CAAAAAAAGAAGAA-AACACATAGTCGGGT
19982390 ACCTATGGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 25 0.52
60 23 0.48
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.24
Consensus pattern (59 bp):
CAATTAAAAAAAATCATAGTTGAGTGACAAAAAAAGAAGAAAACACATAGTCGGGTTAT
Found at i:19983397 original size:31 final size:30
Alignment explanation
Indices: 19983357--19983424 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
19983347 TTTATAAAAT
* *
19983357 AGTCATTGAATTATTTAAAAGTTTTTATTGA
1 AGTCATTGAACTATTCAAAA-TTTTTATTGA
* * *
19983388 AGTCGTTGAACTATTCGAAATTTTTATTTA
1 AGTCATTGAACTATTCAAAATTTTTATTGA
*
19983418 AATCATT
1 AGTCATT
19983425 AGGCTGTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (30 bp):
AGTCATTGAACTATTCAAAATTTTTATTGA
Found at i:19985167 original size:17 final size:16
Alignment explanation
Indices: 19985137--19985178 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19985127 AATATGTGTT
*
19985137 TAAA-AATAACATATAA
1 TAAATAATAAAATAT-A
19985153 TAAATAATAAAATATA
1 TAAATAATAAAATATA
*
19985169 TTAATAATAA
1 TAAATAATAA
19985179 TACATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATAATAAAATATA
Found at i:20000507 original size:5 final size:5
Alignment explanation
Indices: 20000497--20000535 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
20000487 GTCAAAGATG
* *
20000497 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TCAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
20000536 TGTTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:20001191 original size:25 final size:26
Alignment explanation
Indices: 20001103--20001193 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 26
20001093 TACCCATTAT
* *
20001103 TGGCTCACATGAGCTT-CC-TAAATA
1 TGGCTCACATGAGCTTCCCGTATACA
**
20001127 TGGCTCTTATGAGCTTCCCGTTATACA
1 TGGCTCACATGAGCTTCCCG-TATACA
* * *
20001154 -GTC-CAGATAAGCTTCCCGT-TACA
1 TGGCTCACATGAGCTTCCCGTATACA
20001177 TGGCTCACATGAGCTTC
1 TGGCTCACATGAGCTTC
20001194 TTGTTATATG
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 4 0.08
24 17 0.33
25 24 0.47
26 2 0.04
27 4 0.08
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (26 bp):
TGGCTCACATGAGCTTCCCGTATACA
Found at i:20006812 original size:42 final size:42
Alignment explanation
Indices: 20006763--20006856 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
20006753 AGACTATATG
* * *
20006763 TAAGACCATATATGGGAAATGGCATCTATATGAGACTTTGTA
1 TAAGACCATATATGGGAAATGACATCAATATGAGACTTCGTA
* * * *
20006805 TAAGACCATATCTGGGATATGACATCAATATGGGACTTCGTG
1 TAAGACCATATATGGGAAATGACATCAATATGAGACTTCGTA
20006847 TAAGACCATA
1 TAAGACCATA
20006857 GCTAGGCTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (42 bp):
TAAGACCATATATGGGAAATGACATCAATATGAGACTTCGTA
Found at i:20010001 original size:20 final size:20
Alignment explanation
Indices: 20009964--20010001 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20009954 TGATGGGGAG
*
20009964 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
20009984 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
20010002 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:20011949 original size:46 final size:46
Alignment explanation
Indices: 20011897--20012216 Score: 570
Period size: 46 Copynumber: 7.0 Consensus size: 46
20011887 AGTGTGCTCT
20011897 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20011943 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20011989 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20012035 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20012081 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20012127 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
20012173 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20012217 TCATGTCAAA
Statistics
Matches: 267, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
45 1 0.00
46 266 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20014413 original size:40 final size:40
Alignment explanation
Indices: 20014314--20014442 Score: 141
Period size: 41 Copynumber: 3.2 Consensus size: 40
20014304 AACACTTCTT
* * * * * *
20014314 TTTCATTCGTTGTCCTTTTTGAATAACATCCTTTTTAACA
1 TTTCATTTGTTATCCTTTTCGGATAACTTCCTTTTCAACA
* *
20014354 TTTTCATTTGTTATTCTTTTCGGATAACTTCCTTGTCAACA
1 -TTTCATTTGTTATCCTTTTCGGATAACTTCCTTTTCAACA
* * *
20014395 TTTCATTTGTTATCCTTTTCGGATCACTTTCTTTTCAAGCT
1 TTTCATTTGTTATCCTTTTCGGATAACTTCCTTTTCAA-CA
20014436 TTTCATT
1 TTTCATT
20014443 GATTTAGAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 34 0.46
41 40 0.54
ACGTcount: A:0.19, C:0.20, G:0.09, T:0.53
Consensus pattern (40 bp):
TTTCATTTGTTATCCTTTTCGGATAACTTCCTTTTCAACA
Found at i:20016074 original size:68 final size:69
Alignment explanation
Indices: 20015955--20016086 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 69
20015945 TAAATTAAAA
* * *
20015955 AATACATTTAATTCATTCATATTTTTATATATAAAAATATTTATAGATAATATAATTTAGTGCAC
1 AATACATTTAATTAATTCATATTTTTATATATAAAAATATTTATACATAATATAAATTAGTGCAC
20016020 ATAT
66 ATAT
* * *
20016024 AATA-ATTTAATTAATTTATATTTTTATCTAT-AAAATATTT-TACCCTTAATATAAATTAGTGC
1 AATACATTTAATTAATTCATATTTTTATATATAAAAATATTTATA--CATAATATAAATTAGTGC
20016086 A
64 A
20016087 TTGGATTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 2 0.04
67 9 0.16
68 40 0.73
69 4 0.07
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (69 bp):
AATACATTTAATTAATTCATATTTTTATATATAAAAATATTTATACATAATATAAATTAGTGCAC
ATAT
Found at i:20017024 original size:21 final size:21
Alignment explanation
Indices: 20016998--20017053 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
20016988 AATGATTTAT
*
20016998 TAGGTTCAAGTGGTAAGACCC
1 TAGGTTCAAGTGGTAAAACCC
* *
20017019 TAGGTTCAAGAGGTAAAACTC
1 TAGGTTCAAGTGGTAAAACCC
20017040 TAAGG-TCAAGTGGT
1 T-AGGTTCAAGTGGT
20017054 TTTAGAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (21 bp):
TAGGTTCAAGTGGTAAAACCC
Found at i:20017752 original size:30 final size:30
Alignment explanation
Indices: 20017716--20017775 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
20017706 GGCTGTAATG
20017716 AATGCCATGAATATTCAGCTAGCATGAGTT
1 AATGCCATGAATATTCAGCTAGCATGAGTT
*
20017746 AATGCCATGAATATTCAGTTAGCATGAGTT
1 AATGCCATGAATATTCAGCTAGCATGAGTT
20017776 TGCATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (30 bp):
AATGCCATGAATATTCAGCTAGCATGAGTT
Found at i:20021209 original size:20 final size:20
Alignment explanation
Indices: 20021179--20021223 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
20021169 CTGTTTTGTT
*
20021179 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTATATTAAA
* *
20021198 ATGGGCCCAACTATGTTAAT
1 ATGGGCCCAACTATATTAAA
20021218 ATGGGC
1 ATGGGC
20021224 AAGGCCCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTATATTAAA
Found at i:20023643 original size:18 final size:18
Alignment explanation
Indices: 20023575--20023762 Score: 101
Period size: 18 Copynumber: 10.0 Consensus size: 18
20023565 AACTGGAAAG
*
20023575 ATTGACTGTTACTGAATA
1 ATTGATTGTTACTGAATA
* * *
20023593 ATTTAATTGTTTCTGTAT-
1 A-TTGATTGTTACTGAATA
*
20023611 ATCTGATTTTTACTGAATA
1 AT-TGATTGTTACTGAATA
*
20023630 ATTGACTGTTACTGGATAACCGATCA
1 ATTGATTGTTACT-G---A---AT-A
* *
20023656 ATTGATTGATACTCAATA
1 ATTGATTGTTACTGAATA
* * *
20023674 ACTGATTATTATTGAATA
1 ATTGATTGTTACTGAATA
20023692 ATTGATTGTTACTGAATA
1 ATTGATTGTTACTGAATA
* *
20023710 ACTGACTGTTACTGAATA
1 ATTGATTGTTACTGAATA
* * * *
20023728 AATAATTGTT-CTGATTG
1 ATTGATTGTTACTGAATA
* *
20023745 ACTGATTGTTAATGAATA
1 ATTGATTGTTACTGAATA
20023763 TTACTAATTG
Statistics
Matches: 125, Mismatches: 33, Indels: 24
0.69 0.18 0.13
Matches are distributed among these distances:
17 14 0.11
18 78 0.62
19 17 0.14
22 2 0.02
25 2 0.02
26 12 0.10
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (18 bp):
ATTGATTGTTACTGAATA
Found at i:20023710 original size:36 final size:36
Alignment explanation
Indices: 20023655--20023762 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
20023645 ATAACCGATC
* * * *
20023655 AATTGATTGATACTCAATAACTGATTATTATTGAAT
1 AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
* *
20023691 AATTGATTGTTACTGAATAACTGACTGTTACTGAAT
1 AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
* * * *
20023727 AAATAATTGTT-CTGATTGACTGATTGTTAATGAAT
1 AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
20023762 A
1 A
20023763 TTACTAATTG
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 21 0.34
36 40 0.66
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (36 bp):
AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
Found at i:20030417 original size:46 final size:46
Alignment explanation
Indices: 20030357--20030532 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
20030347 TATTTGGGCA
*
20030357 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
20030403 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* *
20030448 CATCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
20030496 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20030533 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 61 0.57
47 26 0.24
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:20030464 original size:93 final size:93
Alignment explanation
Indices: 20030353--20030525 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
20030343 CGGATATTTG
* *
20030353 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
20030418 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
20030446 GGCATCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
20030511 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
20030526 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:20033226 original size:20 final size:21
Alignment explanation
Indices: 20033201--20033241 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20033191 AATACATGAG
20033201 TATTTTG-ATGTTTGATGATA
1 TATTTTGAATGTTTGATGATA
20033221 TATTTTGAATGTTTGATGATA
1 TATTTTGAATGTTTGATGATA
20033242 GTTATACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TATTTTGAATGTTTGATGATA
Found at i:20063028 original size:48 final size:48
Alignment explanation
Indices: 20062960--20063325 Score: 545
Period size: 48 Copynumber: 7.6 Consensus size: 48
20062950 GTAAATTGTA
* * * * ** *
20062960 GATGCCATGTCTCAGACATGGTCTTACATTGGCTCACAT-GTCAAGGTA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGTC
* *
20063008 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
*
20063056 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
* * *
20063104 GATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
*
20063152 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
* * *
20063200 GATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
*
20063248 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
*
20063296 GATGTCATGTCCCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
20063326 AGCACACATA
Statistics
Matches: 287, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
48 286 1.00
49 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTC
Found at i:20063124 original size:96 final size:96
Alignment explanation
Indices: 20062960--20063328 Score: 643
Period size: 96 Copynumber: 3.8 Consensus size: 96
20062950 GTAAATTGTA
* * * ** * *
20062960 GATGCCATGT-CTCAGACATGGTCTTACATTGGCTCACAT-GTCAAGGTAGATGCCATGTCCCAG
1 GATGCCATGTCCT-AGACATGGTCTTACACTGGCTCTCATAAT-GTGGTCGATGTCATGTCCCAG
20063023 ACATGGTCTTACACTAGCTCTCATAATGTGGCC
64 ACATGGTCTTACACTAGCTCTCATAATGTGGCC
20063056 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
20063121 ATGGTCTTACACTAGCTCTCATAATGTGGCC
66 ATGGTCTTACACTAGCTCTCATAATGTGGCC
20063152 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
20063217 ATGGTCTTACACTAGCTCTCATAATGTGGCC
66 ATGGTCTTACACTAGCTCTCATAATGTGGCC
20063248 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
20063313 ATGGTCTTACACTAGC
66 ATGGTCTTACACTAGC
20063329 ACACATATCA
Statistics
Matches: 264, Mismatches: 7, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
96 261 0.99
97 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (96 bp):
GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGTCATGTCCCAGAC
ATGGTCTTACACTAGCTCTCATAATGTGGCC
Found at i:20067840 original size:40 final size:40
Alignment explanation
Indices: 20067772--20067849 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
20067762 AAGTTCCATA
**
20067772 TATATAGCCAAAGCTATTCCAATTCGCACACCAAGTGCTT
1 TATATAGCCAAAGCTATTCCAAAACGCACACCAAGTGCTT
*
20067812 TATATAGCCAAAGCTA-TCTCAAAACGCACACTAAGTGC
1 TATATAGCCAAAGCTATTC-CAAAACGCACACCAAGTGC
20067850 CAAACATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (40 bp):
TATATAGCCAAAGCTATTCCAAAACGCACACCAAGTGCTT
Found at i:20072882 original size:21 final size:20
Alignment explanation
Indices: 20072853--20072891 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
20072843 TACATGAGTA
20072853 TTTGATGTTTGATGATAGAT
1 TTTGATGTTTGATGATAGAT
20072873 TTTGAATGTTTGATGATAG
1 TTTG-ATGTTTGATGATAG
20072892 TTATACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (20 bp):
TTTGATGTTTGATGATAGAT
Found at i:20078877 original size:13 final size:13
Alignment explanation
Indices: 20078859--20078888 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20078849 TCAAAACTAT
*
20078859 TTAACATCTAAGC
1 TTAACATCCAAGC
20078872 TTAACATCCAAGC
1 TTAACATCCAAGC
20078885 TTAA
1 TTAA
20078889 TCCCTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACATCCAAGC
Found at i:20079081 original size:23 final size:23
Alignment explanation
Indices: 20079055--20079100 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20079045 GGGATATTAG
*
20079055 ATATTTACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
20079078 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
20079101 TCAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
ATATTGACTAGTTATATACGAAC
Found at i:20082588 original size:35 final size:35
Alignment explanation
Indices: 20082444--20082611 Score: 126
Period size: 35 Copynumber: 4.8 Consensus size: 35
20082434 TCTTTCGAGA
*
20082444 TGACACCATGAT-GATGGTATATAGGTCCTTCAGGG
1 TGACACCAT-ATAAATGGTATATAGGTCCTTCAGGG
* ** * * * *
20082479 CGACACTGTGTAAACGGCATATAGGTCTTTC-GAGG
1 TGACACCATATAAATGGTATATAGGTCCTTCAG-GG
* * * * * * * *
20082514 CGACACCGTGTAAATAG-ATGTAAGTCTTTCATGG
1 TGACACCATATAAATGGTATATAGGTCCTTCAGGG
20082548 TGACACCATATAAATGGTATATAGGTCCTTCAGGG
1 TGACACCATATAAATGGTATATAGGTCCTTCAGGG
* * *
20082583 TGACACCCTATAAATGATATATAAGTCCT
1 TGACACCATATAAATGGTATATAGGTCCT
20082612 ACGGGGGGGC
Statistics
Matches: 104, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
34 28 0.27
35 76 0.73
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (35 bp):
TGACACCATATAAATGGTATATAGGTCCTTCAGGG
Found at i:20092450 original size:12 final size:12
Alignment explanation
Indices: 20092433--20092461 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20092423 AAACCAGTTC
20092433 ATTCAGTTCACG
1 ATTCAGTTCACG
20092445 ATTCAGTTCACG
1 ATTCAGTTCACG
20092457 ATTCA
1 ATTCA
20092462 TGATTTAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (12 bp):
ATTCAGTTCACG
Found at i:20094844 original size:21 final size:21
Alignment explanation
Indices: 20094805--20094845 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20094795 TCGATGACAG
* **
20094805 TGGTGGCTATTGGTTGTCCAA
1 TGGTGGCTAGTGGAGGTCCAA
20094826 TGGTGGCTAGTGGAGGTCCA
1 TGGTGGCTAGTGGAGGTCCA
20094846 GCGGTGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.39, T:0.32
Consensus pattern (21 bp):
TGGTGGCTAGTGGAGGTCCAA
Found at i:20103589 original size:46 final size:47
Alignment explanation
Indices: 20103509--20103675 Score: 148
Period size: 46 Copynumber: 3.6 Consensus size: 47
20103499 ATGTCTCAGG
* * *
20103509 CATGTCCTAGACATGTCTTACACTAGCTTACGTCTCGAGGCCGAAG-
1 CATGTCCCAGACATGTCTTACACTAGCCTACGTCTCAAGGCCGAAGC
* * * * *
20103555 TATGTCCCAGACATTTTTTACACTAGCACT-CGTCTCAATGCCGATGC
1 CATGTCCCAGACATGTCTTACACTAGC-CTACGTCTCAAGGCCGAAGC
* * *
20103602 CATGTCCCAGACATGGTCTTACACT-GGCT-C-TCTTAATGTGGCCGATG-
1 CATGTCCCAGACAT-GTCTTACACTAGCCTACGTCTCAA---GGCCGAAGC
20103649 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
20103676 TCATAATAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
45 5 0.05
46 49 0.49
47 30 0.30
48 15 0.15
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCCTACGTCTCAAGGCCGAAGC
Found at i:20108997 original size:15 final size:15
Alignment explanation
Indices: 20108975--20109043 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
20108965 GTATATTGGG
20108975 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
20108990 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
20109005 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
20109020 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
20109035 TTTCTTTAT
1 TTTCTTTAT
20109044 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:20109044 original size:30 final size:29
Alignment explanation
Indices: 20108970--20109057 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
20108960 ATATCGTATA
* * * *
20108970 TTGGGTTTCTTTATCCTGGATCTCTTTAT
1 TTGGATTTCTTTATTCTGGATTTCTCTAT
*
20108999 TCTGGATTTCTTTATTCTGGGTTTCTCTAT
1 T-TGGATTTCTTTATTCTGGATTTCTCTAT
*
20109029 CTTGGATTTCTTTATTC-GGTTTTCT-TAT
1 -TTGGATTTCTTTATTCTGGATTTCTCTAT
20109057 T
1 T
20109058 ATCTTTGTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 3 0.06
29 8 0.16
30 38 0.75
31 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.58
Consensus pattern (29 bp):
TTGGATTTCTTTATTCTGGATTTCTCTAT
Found at i:20112102 original size:63 final size:63
Alignment explanation
Indices: 20112023--20112175 Score: 306
Period size: 63 Copynumber: 2.4 Consensus size: 63
20112013 GAAGTCATGA
20112023 TTTATTAGAAATAAACGGCATAGTCATGAATAAATTGTTCAAAGATTCCTTATTGAGTCTAGT
1 TTTATTAGAAATAAACGGCATAGTCATGAATAAATTGTTCAAAGATTCCTTATTGAGTCTAGT
20112086 TTTATTAGAAATAAACGGCATAGTCATGAATAAATTGTTCAAAGATTCCTTATTGAGTCTAGT
1 TTTATTAGAAATAAACGGCATAGTCATGAATAAATTGTTCAAAGATTCCTTATTGAGTCTAGT
20112149 TTTATTAGAAATAAACGGCATAGTCAT
1 TTTATTAGAAATAAACGGCATAGTCAT
20112176 TGAAACTCTG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (63 bp):
TTTATTAGAAATAAACGGCATAGTCATGAATAAATTGTTCAAAGATTCCTTATTGAGTCTAGT
Found at i:20116001 original size:28 final size:27
Alignment explanation
Indices: 20115937--20116088 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
20115927 TTATTAAGTC
* *
20115937 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
20115964 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
20115992 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
20116019 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
20116047 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
20116074 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20116089 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20116021 original size:55 final size:55
Alignment explanation
Indices: 20115937--20116113 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
20115927 TTATTAAGTC
* * *
20115937 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
20115992 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
20116047 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
20116103 CGCACACTTAG
1 CGCACACTTAG
20116114 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:20135535 original size:42 final size:43
Alignment explanation
Indices: 20135476--20135571 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 43
20135466 TGAGATTTAT
* * *
20135476 GTGTAAGACCATGTCTGGGACATTGGCATC-ATATCTG-ATTTC
1 GTGTAAGACCATATCTGGGACAGTGGCATCGATA-CTGAATTAC
*
20135518 GTGTAAGACCCTATCTGGGACAGTGGCATCGATACTGAATTAC
1 GTGTAAGACCATATCTGGGACAGTGGCATCGATACTGAATTAC
*
20135561 ATGTAAGACCA
1 GTGTAAGACCA
20135572 CGTCCGGGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATATCTGGGACAGTGGCATCGATACTGAATTAC
Found at i:20135581 original size:43 final size:42
Alignment explanation
Indices: 20135477--20135589 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
20135467 GAGATTTATG
* * * *
20135477 TGTAAGACCATGTCTGGGACATTGGCATCATATCTGATTTCG
1 TGTAAGACCACGTCTGGGACAGTGGCATCATATCTGATTACA
*
20135519 TGTAAGACC-CTATCTGGGACAGTGGCATCGATA-CTGAATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATC-ATATCTG-ATTACA
*
20135562 TGTAAGACCACGTCCGGGAC-GTTGGCAT
1 TGTAAGACCACGTCTGGGACAG-TGGCAT
20135590 TGTACGCGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 29 0.49
43 29 0.49
44 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCATATCTGATTACA
Found at i:20142778 original size:29 final size:29
Alignment explanation
Indices: 20142712--20142802 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 29
20142702 AAGTCTACAT
* * *
20142712 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCTATTAGGCCCAAATC
*
20142740 TCATTCATATGGCCTATTAGGCCCAAATC
1 ACATTCATATGGCCTATTAGGCCCAAATC
20142769 ACATTCATATGGCCTATCT-GGCCCAAATC
1 ACATTCATATGGCCTAT-TAGGCCCAAATC
20142798 A-ATTC
1 ACATTC
20142803 CAAGCCATGT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 24 0.43
29 31 0.55
30 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCTATTAGGCCCAAATC
Found at i:20146884 original size:43 final size:42
Alignment explanation
Indices: 20146832--20146990 Score: 139
Period size: 43 Copynumber: 3.8 Consensus size: 42
20146822 ATATGTTTTC
* *
20146832 TCGTGTAAGATCACGTCTGGGACGTTAGCATTGGTATGTGAT
1 TCGTGTAAGACCACGTCTGGGACGTTGGCATTGGTATGTGAT
* * * *
20146874 TACGTGTAAGACCATGTCTGGGACATCT-GCA-TCGTATTTGAT
1 T-CGTGTAAGACCACGTCTGGGACGT-TGGCATTGGTATGTGAT
* *
20146916 TCGTGTAAGACCCAAC--CTGGGACAG-TGGCATCGATATGTGAT
1 TCGTGTAAGA-CC-ACGTCTGGGAC-GTTGGCATTGGTATGTGAT
* *
20146958 TGCATGTAAGACCACGTCTGGAACGTTGGCATT
1 T-CGTGTAAGACCACGTCTGGGACGTTGGCATT
20146991 ATACGATATG
Statistics
Matches: 92, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
40 1 0.01
41 21 0.23
42 24 0.26
43 45 0.49
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGGGACGTTGGCATTGGTATGTGAT
Found at i:20146936 original size:41 final size:43
Alignment explanation
Indices: 20146865--20146970 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 43
20146855 GTTAGCATTG
** *
20146865 GTATGTGATTACGTGTAAGA-CCATGTCTGGGACA-TCTGCATC
1 GTATGTGATTACGTGTAAGACCCATACCTGGGACAGT-GGCATC
*
20146907 GTATTTGATT-CGTGTAAGACCCA-ACCTGGGACAGTGGCATC
1 GTATGTGATTACGTGTAAGACCCATACCTGGGACAGTGGCATC
* *
20146948 GATATGTGATTGCATGTAAGACC
1 G-TATGTGATTACGTGTAAGACC
20146971 ACGTCTGGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
41 23 0.43
42 21 0.39
43 10 0.19
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
GTATGTGATTACGTGTAAGACCCATACCTGGGACAGTGGCATC
Found at i:20151671 original size:48 final size:49
Alignment explanation
Indices: 20151614--20151791 Score: 188
Period size: 48 Copynumber: 3.7 Consensus size: 49
20151604 TACGAGATGT
*
20151614 GTCAGTGTAAGACTATGTCTGGGACATGGCATCGGCACGT-G-TAGAGATA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-C-TCGATAGAGATA
* ***
20151663 -TCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGATA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAGAGATA
* * **
20151711 GTCAGTGTAAGACCATGTTTGGGACATGGCATC-GACTTAAT-G-GATAA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAGAGAT-A
* *
20151758 GCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCG
20151792 ACATTACACC
Statistics
Matches: 110, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
46 4 0.04
47 33 0.30
48 43 0.39
49 30 0.27
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (49 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAGAGATA
Found at i:20152426 original size:36 final size:36
Alignment explanation
Indices: 20152386--20152457 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
20152376 ATAATTACCC
* *
20152386 TAAATTTTCTTTCTCTCTATGCTTATTTGTACTTTA
1 TAAATTTTCTTTCTCTCCACGCTTATTTGTACTTTA
*
20152422 TAAATTTTCTTTCTCTCCACGCTTATTTGTGCTTTA
1 TAAATTTTCTTTCTCTCCACGCTTATTTGTACTTTA
20152458 CTCAGACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (36 bp):
TAAATTTTCTTTCTCTCCACGCTTATTTGTACTTTA
Found at i:20163407 original size:34 final size:34
Alignment explanation
Indices: 20163364--20163432 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
20163354 GCTTGTCAAC
20163364 ACTACAAGGAATGAAAAGGAGAAAGTAAGCATAA
1 ACTACAAGGAATGAAAAGGAGAAAGTAAGCATAA
**
20163398 ACTACAAGGAATGAAAAGGAGGGAGTAAGCATAA
1 ACTACAAGGAATGAAAAGGAGAAAGTAAGCATAA
20163432 A
1 A
20163433 TGCTTAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.54, C:0.09, G:0.26, T:0.12
Consensus pattern (34 bp):
ACTACAAGGAATGAAAAGGAGAAAGTAAGCATAA
Found at i:20163930 original size:46 final size:46
Alignment explanation
Indices: 20163764--20163939 Score: 164
Period size: 46 Copynumber: 3.8 Consensus size: 46
20163754 TGTAACCCGC
* * * * *
20163764 CCATAAGCGAACTCGAACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTTGCAT
* * * * *
20163810 CCATGAGTAAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
20163860 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
20163903 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
20163940 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 8 0.08
44 1 0.01
45 2 0.02
46 56 0.53
47 27 0.26
49 1 0.01
50 6 0.06
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:20163935 original size:93 final size:93
Alignment explanation
Indices: 20163773--20163942 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
20163763 CCCATAAGCG
* * *
20163773 AACTCGAACTCAACTCAACGAGCTCAGGCGTTCGCATCCATGAGTAAACTCGGACTCAACTCAAT
1 AACTCGAACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTAAACTCGGACTCAACTCAAC
20163838 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
* * * *
20163866 AACTCGGACTCAACTCAACGAGTTC-GGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCGAACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
20163930 CGAGTTCGGATGC
65 CGAGTTCGGATGC
20163943 TCAACCATCC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCGAACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTAAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:20166350 original size:233 final size:233
Alignment explanation
Indices: 20165943--20166419 Score: 945
Period size: 233 Copynumber: 2.0 Consensus size: 233
20165933 TCGTCGAAAG
20165943 GTAGTAACATCAAATCAACCAGAAAACATGAATCTCGAATCATCAACGGGCAATTCTTACACACT
1 GTAGTAACATCAAATCAACCAGAAAACATGAATCTCGAATCATCAACGGGCAATTCTTACACACT
20166008 TTGTCAACCAGAACACACCGACCCAGGGGGATTCATACTCGAATTACAAACTCAGTAGACTCAAC
66 TTGTCAACCAGAACACACCGACCCAGGGGGATTCATACTCGAATTACAAACTCAGTAGACTCAAC
20166073 AGGCAAAGTCTTAGTGGATACTAATGTTTCACACATATATGAATGAGTCAAACCAGGATCAATCA
131 AGGCAAAGTCTTAGTGGATACTAATGTTTCACACATATATGAATGAGTCAAACCAGGATCAATCA
20166138 ATGCAATAACACTAGTATCATAAAGAGTGAAAGTACCA
196 ATGCAATAACACTAGTATCATAAAGAGTGAAAGTACCA
20166176 GTAGTAACATCAAATCAACCAGAAAACATGAATCTCGAATCATCAACGGGCAATTCTTACACACT
1 GTAGTAACATCAAATCAACCAGAAAACATGAATCTCGAATCATCAACGGGCAATTCTTACACACT
*
20166241 TTGTCAACCAGAACACACCGACCCAGGGGGTTTCATACTCGAATTACAAACTCAGTAGACTCAAC
66 TTGTCAACCAGAACACACCGACCCAGGGGGATTCATACTCGAATTACAAACTCAGTAGACTCAAC
20166306 AGGCAAAGTCTTAGTGGATACTAATGTTTCACACATATATGAATGAGTCAAACCAGGATCAATCA
131 AGGCAAAGTCTTAGTGGATACTAATGTTTCACACATATATGAATGAGTCAAACCAGGATCAATCA
20166371 ATGCAATAACACTAGTATCATAAAGAGTGAAAGTACCA
196 ATGCAATAACACTAGTATCATAAAGAGTGAAAGTACCA
20166409 GTAGTAACATC
1 GTAGTAACATC
20166420 TGGGGAAGAA
Statistics
Matches: 243, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 243 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (233 bp):
GTAGTAACATCAAATCAACCAGAAAACATGAATCTCGAATCATCAACGGGCAATTCTTACACACT
TTGTCAACCAGAACACACCGACCCAGGGGGATTCATACTCGAATTACAAACTCAGTAGACTCAAC
AGGCAAAGTCTTAGTGGATACTAATGTTTCACACATATATGAATGAGTCAAACCAGGATCAATCA
ATGCAATAACACTAGTATCATAAAGAGTGAAAGTACCA
Found at i:20180799 original size:29 final size:29
Alignment explanation
Indices: 20180766--20180839 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
20180756 GTTGTGAGAT
* *
20180766 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
20180795 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
20180824 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
20180840 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:20183117 original size:40 final size:39
Alignment explanation
Indices: 20183073--20183193 Score: 109
Period size: 39 Copynumber: 3.1 Consensus size: 39
20183063 ACTAGGCAAA
* * *
20183073 AAGCTTATAAAATCTGATCCA-ACTGAAATACGCCAAACAG
1 AAGCTCATAAAAGCTGATCCACA-TGAAACACGCC-AACAG
* * *
20183113 AAGCTCATAAGAGCTGGTCCACATGAAACACGCCAATAG
1 AAGCTCATAAAAGCTGATCCACATGAAACACGCCAACAG
* * ** *
20183152 AAGCTCATAAGAGCTGGTCCACCCGAATCACGCCGAACAG
1 AAGCTCATAAAAGCTGATCCACATGAAACACGCC-AACAG
20183192 AA
1 AA
20183194 AGTATAACAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 35 0.51
40 33 0.48
41 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (39 bp):
AAGCTCATAAAAGCTGATCCACATGAAACACGCCAACAG
Found at i:20183161 original size:39 final size:40
Alignment explanation
Indices: 20183096--20183193 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 40
20183086 CTGATCCAAC
*
20183096 TGAAATACGCCAAACAGAAGCTCATAAGAGCTGGTCCACA
1 TGAAACACGCCAAACAGAAGCTCATAAGAGCTGGTCCACA
* *
20183136 TGAAACACGCC-AATAGAAGCTCATAAGAGCTGGTCCACC
1 TGAAACACGCCAAACAGAAGCTCATAAGAGCTGGTCCACA
* * *
20183175 CGAATCACGCCGAACAGAA
1 TGAAACACGCCAAACAGAA
20183194 AGTATAACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 35 0.69
40 16 0.31
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.13
Consensus pattern (40 bp):
TGAAACACGCCAAACAGAAGCTCATAAGAGCTGGTCCACA
Found at i:20186195 original size:38 final size:38
Alignment explanation
Indices: 20186144--20186224 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
20186134 ATATTTGATG
* * *
20186144 TATATCCGGGTTAAATCCCGAAGGCTTCGTGCTGGTAT
1 TATATCCGAGTTAAATCCCGAAGGCCTAGTGCTGGTAT
*
20186182 TATATCCGAGTTAAATCCCGTAGGCCTAGTGCTGGTAT
1 TATATCCGAGTTAAATCCCGAAGGCCTAGTGCTGGTAT
20186220 TATAT
1 TATAT
20186225 TCGGGCCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (38 bp):
TATATCCGAGTTAAATCCCGAAGGCCTAGTGCTGGTAT
Found at i:20189722 original size:40 final size:40
Alignment explanation
Indices: 20189663--20189836 Score: 280
Period size: 40 Copynumber: 4.4 Consensus size: 40
20189653 CGGGTGTAAC
*
20189663 AACCAGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
** *
20189703 AACTAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
*
20189743 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
20189783 AA-CCGCACGAATGCCTTCGGGACTTAACCC-AGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGA-TTATAAT
20189822 AACCCGCACGAATGC
1 AACCCGCACGAATGC
20189837 TATGCACATA
Statistics
Matches: 127, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
39 37 0.29
40 90 0.71
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAAT
Found at i:20189824 original size:79 final size:80
Alignment explanation
Indices: 20189663--20189836 Score: 305
Period size: 79 Copynumber: 2.2 Consensus size: 80
20189653 CGGGTGTAAC
*
20189663 AACCAGCACGAATGCCTTCGGGACTTAACCCGATTATAATAACTAGCACGAATGCCTTCGGGACT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAATAACTAGCACGAATGCCTTCGGGACT
*
20189728 TAACCCGGTTATAAT
66 TAACCCAGTTATAAT
* *
20189743 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAATAAC-CGCACGAATGCCTTCGGGACT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAATAACTAGCACGAATGCCTTCGGGACT
20189807 TAACCCAGTTATAAT
66 TAACCCAGTTATAAT
20189822 AACCCGCACGAATGC
1 AACCCGCACGAATGC
20189837 TATGCACATA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 49 0.54
80 41 0.46
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (80 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGATTATAATAACTAGCACGAATGCCTTCGGGACT
TAACCCAGTTATAAT
Found at i:20193022 original size:42 final size:42
Alignment explanation
Indices: 20192901--20193022 Score: 129
Period size: 43 Copynumber: 2.9 Consensus size: 42
20192891 TATCGTACTA
* * * *
20192901 ATGCCATATCCTAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATACCCCAGATATGGTCTTACACGTAATCTCATATCG
* * **
20192943 ATCCCAATAGCCCACCTATGGTCTTACACG-AAGTCTCATATCG
1 ATGCC-ATACCCCAGATATGGTCTTACACGTAA-TCTCATATCG
* *
20192986 ATGCCATACCCCAGATATAGTCTTGCACGTAATCTCA
1 ATGCCATACCCCAGATATGGTCTTACACGTAATCTCA
20193023 GTAACCCTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 30 0.47
43 34 0.53
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATACCCCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:20200741 original size:19 final size:20
Alignment explanation
Indices: 20200706--20200743 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20200696 GTTTTTTTAT
20200706 TATATTATGATTTTATAACA
1 TATATTATGATTTTATAACA
*
20200726 TATATTATTA-TTTATAAC
1 TATATTATGATTTTATAAC
20200744 CTTTATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TATATTATGATTTTATAACA
Found at i:20204834 original size:15 final size:15
Alignment explanation
Indices: 20204816--20204846 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20204806 AATAATGTTA
20204816 TAACTCAAACTTCTT
1 TAACTCAAACTTCTT
20204831 TAACTCAAACTTCTT
1 TAACTCAAACTTCTT
20204846 T
1 T
20204847 GCAGGAGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (15 bp):
TAACTCAAACTTCTT
Found at i:20206145 original size:28 final size:28
Alignment explanation
Indices: 20206114--20206209 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
20206104 TATAGTCTCT
*
20206114 TTTATTTTATTTCATTATTATTCATT-TC
1 TTTATTTTATTT-ATTATTATTTATTATC
* * *
20206142 TTTATTTTCTTTATT-TCATTTATTAGC
1 TTTATTTTATTTATTATTATTTATTATC
* *
20206169 TTTTATTTTCTTTATTTATTATTTATTCTC
1 -TTTATTTTATTTA-TTATTATTTATTATC
20206199 TTTATTTTATT
1 TTTATTTTATT
20206210 CTCAGTTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
26 7 0.12
27 4 0.07
28 24 0.43
29 12 0.21
30 9 0.16
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.71
Consensus pattern (28 bp):
TTTATTTTATTTATTATTATTTATTATC
Found at i:20206146 original size:15 final size:13
Alignment explanation
Indices: 20206114--20206209 Score: 59
Period size: 15 Copynumber: 6.8 Consensus size: 13
20206104 TATAGTCTCT
20206114 TTTATTTTATTTC
1 TTTATTTTATTTC
*
20206127 ATTATTATTCATTTC
1 TTTATT-TT-ATTTC
* *
20206142 TTTATTTTCTTTA
1 TTTATTTTATTTC
*
20206155 TTTCA-TTTATTAGC
1 TTT-ATTTTATT-TC
* *
20206169 TTTTATTTTCTTTA
1 -TTTATTTTATTTC
20206183 TTTATTATTTATTCTC
1 TTTA-T-TTTATT-TC
20206199 TTTATTTTATT
1 TTTATTTTATT
20206210 CTCAGTTTAC
Statistics
Matches: 62, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
13 20 0.32
14 13 0.21
15 24 0.39
16 5 0.08
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.71
Consensus pattern (13 bp):
TTTATTTTATTTC
Found at i:20206152 original size:9 final size:9
Alignment explanation
Indices: 20206138--20206206 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
20206128 TTATTATTCA
20206138 TTTCTTTAT
1 TTTCTTTAT
20206147 TTTCTTTA-
1 TTTCTTTAT
20206155 TTTCATTTAT
1 TTTC-TTTAT
**
20206165 TAGCTTTTAT
1 TTTC-TTTAT
20206175 TTTCTTTATT
1 TTTCTTTA-T
*
20206185 TATTATTTAT
1 T-TTCTTTAT
*
20206195 TCTCTTTAT
1 TTTCTTTAT
20206204 TTT
1 TTT
20206207 ATTCTCAGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
8 4 0.09
9 24 0.51
10 13 0.28
11 6 0.13
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTCTTTAT
Found at i:20213221 original size:46 final size:46
Alignment explanation
Indices: 20213168--20213343 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
20213158 TATTTGGGCA
*
20213168 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
20213214 TCCGAACTCGTTGAGTTAAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
20213261 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
20213307 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20213344 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.58
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:20213323 original size:93 final size:93
Alignment explanation
Indices: 20213164--20213335 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
20213154 GGGATATTTG
* * * * *
20213164 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCATTGAG
20213229 TTAAGTCCGAGTTCGTGAGATGTAACTA
66 TTAAGTCCGAGTTCGTGAGATGTAACTA
* *
20213257 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCATTGAG
*
20213322 TTGAGTCCGAGTTC
66 TTAAGTCCGAGTTC
20213336 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCATTGAG
TTAAGTCCGAGTTCGTGAGATGTAACTA
Found at i:20216216 original size:50 final size:50
Alignment explanation
Indices: 20216141--20216424 Score: 239
Period size: 50 Copynumber: 5.6 Consensus size: 50
20216131 TTGGTATGCA
* * * *
20216141 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACTCG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGGTACACG
* ** * * ** *
20216191 TAGTAGCCTGCACTTAGCACTACACACGTGATCGAAGTTAA-CGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAATCTGGTACACG
* * * * * *
20216242 TATTAGCCTGCACTTAGTCCTACACACGTGACTTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGGTACACG
* ** * * * *
20216292 TAGTATCCTGCACTTAGTACTACACACGTGATCGAAGTTAAT-GGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAATCTGGTACACG
***
20216343 TAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGGTACACG
* * *
20216393 AAGTAGCCTACACTTAGTACTACACACTTGAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGAC
20216425 TCACAACGGA
Statistics
Matches: 177, Mismatches: 51, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
49 5 0.03
50 98 0.55
51 69 0.39
52 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAATCTGGTACACG
Found at i:20216257 original size:51 final size:51
Alignment explanation
Indices: 20216191--20216368 Score: 191
Period size: 51 Copynumber: 3.5 Consensus size: 51
20216181 CTAGTACTCG
*
20216191 TAGTAGCCTGCACTTAGCACTACACACGTGATCGAAGTTAACGGGTATGCA
1 TAGTAGCCTGCACTTAGCACTACACACGTGATCGAAGTTAACGGGTACGCA
* * ** * * * * *
20216242 TATTAGCCTGCACTTAGTC-CTACACACGTGA-CTTAA-CCATCTGATACACG
1 TAGTAGCCTGCACTTAG-CACTACACACGTGATC-GAAGTTAACGGGTACGCA
* * *
20216292 TAGTATCCTGCACTTAGTACTACACACGTGATCGAAGTTAATGGGTACGCA
1 TAGTAGCCTGCACTTAGCACTACACACGTGATCGAAGTTAACGGGTACGCA
*
20216343 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGCACTACACA
20216369 TACGACCTAT
Statistics
Matches: 99, Mismatches: 23, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
50 36 0.36
51 62 0.63
52 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACTTAGCACTACACACGTGATCGAAGTTAACGGGTACGCA
Found at i:20216302 original size:101 final size:101
Alignment explanation
Indices: 20216133--20216419 Score: 414
Period size: 101 Copynumber: 2.8 Consensus size: 101
20216123 GAAGCTCTTT
*
20216133 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT-AGTACTCGTAGTAG
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGA-TACACGTAGTAG
*
20216197 CCTGCACTTAGCACTACACACGTGATCGAAGTTAACG
65 CCTGCACTTAGTACTACACACGTGATCGAAGTTAACG
* * * * * * * *
20216234 GGTATGCATATTAGCCTGCACTTAGTCCTACACACGTGACTTAACCATCTGATACACGTAGTATC
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGC
*
20216299 CTGCACTTAGTACTACACACGTGATCGAAGTTAATG
66 CTGCACTTAGTACTACACACGTGATCGAAGTTAACG
* * * *
20216335 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACGACCTATCAATCTGGTACACGAAGTAGC
1 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGC
*
20216400 CTACACTTAGTACTACACAC
66 CTGCACTTAGTACTACACAC
20216420 TTGACTCACA
Statistics
Matches: 161, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
101 160 0.99
102 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (101 bp):
GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACGTAGTAGC
CTGCACTTAGTACTACACACGTGATCGAAGTTAACG
Found at i:20216801 original size:19 final size:20
Alignment explanation
Indices: 20216773--20216819 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
20216763 AAGAACATGT
20216773 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
20216794 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
20216813 TATATAT
1 TATATAT
20216820 ACTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:20220820 original size:28 final size:28
Alignment explanation
Indices: 20220758--20220827 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
20220748 TGATTTTAGT
* * *
20220758 GGTAAGCTATGAAAAGAATAGTCATTGT
1 GGTAAACTATGAAAAGAATAGCCATTGC
* *
20220786 GGCAAACTATGAAAAGAATAGCCTTTGC
1 GGTAAACTATGAAAAGAATAGCCATTGC
*
20220814 GGTAAACTCTGAAA
1 GGTAAACTATGAAA
20220828 GGGATGCCTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (28 bp):
GGTAAACTATGAAAAGAATAGCCATTGC
Found at i:20225345 original size:27 final size:27
Alignment explanation
Indices: 20225289--20225346 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
20225279 GCAATCATAG
* *
20225289 AGTCCACCGGGACAATAAACATAAGGT
1 AGTCCACCGGGACAATAAAAATAAGAT
* *
20225316 AGTCCACTGGGACAGTAAAAAT-AGAAT
1 AGTCCACCGGGACAATAAAAATAAG-AT
20225343 AGTC
1 AGTC
20225347 TGTCAAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (27 bp):
AGTCCACCGGGACAATAAAAATAAGAT
Found at i:20232190 original size:56 final size:56
Alignment explanation
Indices: 20232123--20232236 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
20232113 AATGATTGAA
20232123 AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
1 AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
*
20232179 AAATGACAAATGGTTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
1 AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
20232235 AA
1 AA
20232237 TGATAAGTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (56 bp):
AAATGACAAATGATTCACTAGATTTACTCATTGGAGTATTAGGTGCTTCTTAGTTT
Found at i:20232337 original size:100 final size:99
Alignment explanation
Indices: 20232212--20232410 Score: 326
Period size: 100 Copynumber: 2.0 Consensus size: 99
20232202 TTACTCATTG
* * * *
20232212 GAGTATTAGGTGCTTCTTAGTTTAATGATAAGTTTGATTTAAGATTAATTTAGTCATTTTGAATA
1 GAGTATTAGGTACTTCTTAGCTTAATGATAAGTTTGATTTAAGATTAATTTAATCACTTTGAATA
20232277 TTTATTTAATAAAATAAATAATGATTCTAAAATA
66 TTTATTTAATAAAATAAATAATGATTCTAAAATA
* *
20232311 GAGTATTAGGTACTTTCTTAGCTTAATGATAAGTTTGATTTAGGGTTAATTTAATCACTTTGAAT
1 GAGTATTAGGTAC-TTCTTAGCTTAATGATAAGTTTGATTTAAGATTAATTTAATCACTTTGAAT
*
20232376 ATTTATTTAATAGAATAAATAATGATTCTAAAATA
65 ATTTATTTAATAAAATAAATAATGATTCTAAAATA
20232411 AAGCTAAATT
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 12 0.13
100 80 0.87
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.44
Consensus pattern (99 bp):
GAGTATTAGGTACTTCTTAGCTTAATGATAAGTTTGATTTAAGATTAATTTAATCACTTTGAATA
TTTATTTAATAAAATAAATAATGATTCTAAAATA
Found at i:20235450 original size:5 final size:5
Alignment explanation
Indices: 20235440--20235475 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
20235430 GGAGTTGTGA
20235440 AAAAT AAAAT AAAAT AAAAT -AAA- AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20235476 GAACACATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:20239906 original size:12 final size:12
Alignment explanation
Indices: 20239889--20239913 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20239879 TGTGAAAAAT
20239889 AAAATAAAATAA
1 AAAATAAAATAA
20239901 AAAATAAAATAA
1 AAAATAAAATAA
20239913 A
1 A
20239914 GAACACACAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:20247390 original size:4 final size:4
Alignment explanation
Indices: 20247381--20247409 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
20247371 AAAAAAAGTA
20247381 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
20247410 TGCAAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:20250766 original size:21 final size:21
Alignment explanation
Indices: 20250724--20250777 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20250714 TTCTCATTTT
* * *
20250724 CAGCAACTTCTTCTTTTTCAG
1 CAGCAACTTCCTCTTCTGCAG
20250745 C-GACAACTTCCTCTTCTGCAG
1 CAG-CAACTTCCTCTTCTGCAG
20250766 CAGCAACTTCCT
1 CAGCAACTTCCT
20250778 TCTCAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.33
Consensus pattern (21 bp):
CAGCAACTTCCTCTTCTGCAG
Found at i:20257653 original size:27 final size:27
Alignment explanation
Indices: 20257623--20257799 Score: 113
Period size: 27 Copynumber: 6.5 Consensus size: 27
20257613 ATATTGAGCC
* * * *
20257623 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCCACACAATCAAAT
**
20257650 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACACAATCAAAT
* * **
20257677 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCCACACAAT-CAAAT
* *** *
20257705 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACACAATCAAAT
* * **
20257732 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CACAATCAAAT
* * * *
20257759 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCACACAATCAAAT
*
20257786 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
20257800 TGTACAATTT
Statistics
Matches: 122, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 97 0.80
28 24 0.20
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (27 bp):
CGCACACTTAGTGCCACACAATCAAAT
Found at i:20257715 original size:55 final size:55
Alignment explanation
Indices: 20257623--20257799 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 55
20257613 ATATTGAGCC
* * * * *
20257623 CGCACACTCAGTGCTATACA-AT-CAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCAT-CATATCCATCTCGCACACTTAGTGCCACATAGTCAAAT
* * *
20257677 CGCACACTTAGTGCCA-CATAGTCCATCTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCATCATA-TCCATCTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
20257732 CGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCATCATATCCATCTCGCACACTTAGTGCCACATAGTCAAAT
*
20257786 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
20257800 TGTACAATTT
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.55
55 43 0.42
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCCATCATATCCATCTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:20257762 original size:82 final size:81
Alignment explanation
Indices: 20257644--20257799 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
20257634 TGCTATACAA
* * * **
20257644 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCCACATAGTCCATCTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGT-CAAATCGCA
20257709 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20257726 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
20257790 CCCTTAGTGC
65 CACTTAGTGC
20257800 TGTACAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.29
82 45 0.71
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20262164 original size:40 final size:40
Alignment explanation
Indices: 20262110--20262302 Score: 271
Period size: 40 Copynumber: 4.8 Consensus size: 40
20262100 GGATATAGCT
*
20262110 ACTCGCCCAAATGCCTTCGGGACTTAGCCCGGTCATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA
*
20262150 ACTCGCACAAATGCCTTCGGGACTTAACCCGGTCATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA
* * *
20262190 ACTCGCACAAATGCCTTCGGGACTTAACCCAGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA
* *** *
20262230 ACTCGCACAATTGCCTTCGGGACTTAGCCC-AAAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCA-TAGTA
*
20262270 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGT
20262303 TATTATCCGA
Statistics
Matches: 137, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 136 0.99
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTCATAGTA
Found at i:20266581 original size:18 final size:17
Alignment explanation
Indices: 20266552--20266593 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
20266542 TAATTATTAG
20266552 TTTTATTATTATGTTT-A
1 TTTTATTATTAT-TTTCA
*
20266569 TTTCTATTTTTATTTTCA
1 TTT-TATTATTATTTTCA
20266587 TTTTATT
1 TTTTATT
20266594 GTACTCTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTATTATTATTTTCA
Found at i:20270210 original size:13 final size:13
Alignment explanation
Indices: 20270192--20270216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20270182 ACAAACGATA
20270192 AAATTTTCACACG
1 AAATTTTCACACG
20270205 AAATTTTCACAC
1 AAATTTTCACAC
20270217 ATATAAATTA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:20285015 original size:13 final size:13
Alignment explanation
Indices: 20284997--20285021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20284987 ACAAACGATA
20284997 AAATTTTCACACG
1 AAATTTTCACACG
20285010 AAATTTTCACAC
1 AAATTTTCACAC
20285022 ATAGAAATTA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:20286826 original size:18 final size:18
Alignment explanation
Indices: 20286803--20286838 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20286793 TCCAAGGAGG
*
20286803 AGTGTTATAATTTCTTAT
1 AGTGTTATAATATCTTAT
20286821 AGTGTTATAATATCTTAT
1 AGTGTTATAATATCTTAT
20286839 TAAGTAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
AGTGTTATAATATCTTAT
Found at i:20287479 original size:35 final size:35
Alignment explanation
Indices: 20287402--20287471 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
20287392 ATTTTCTAGT
20287402 GGGTCTTTCTAATTTGATCAAAAACCCTTTTTTTC
1 GGGTCTTTCTAATTTGATCAAAAACCCTTTTTTTC
20287437 GGGTCTTTCTAATTTGATCAAAAACCCTTTTTTTC
1 GGGTCTTTCTAATTTGATCAAAAACCCTTTTTTTC
20287472 TTTTCTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (35 bp):
GGGTCTTTCTAATTTGATCAAAAACCCTTTTTTTC
Found at i:20300327 original size:4 final size:4
Alignment explanation
Indices: 20300313--20300349 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
20300303 TTACTACTAA
*
20300313 TATG AATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
20300350 TTTTTTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:20303589 original size:20 final size:20
Alignment explanation
Indices: 20303529--20303580 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
20303519 CTCACTTCTC
20303529 CCACGCCCGTGTATGTATGT
1 CCACGCCCGTGTATGTATGT
*
20303549 CCACGCCCGTGTATGAATGT
1 CCACGCCCGTGTATGTATGT
20303569 CCACGCCCGTGT
1 CCACGCCCGTGT
20303581 TTTTTTGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (20 bp):
CCACGCCCGTGTATGTATGT
Done.