Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 92 of 126
Found at i:28001633 original size:41 final size:40
Alignment explanation
Indices: 28001588--28001896 Score: 257
Period size: 41 Copynumber: 7.5 Consensus size: 40
28001578 CTTTCGTGGC
* * ** *
28001588 GTTTTCAAAAAAGCGCCACTAATGTTCAGGGATTTAGCGGT
1 GTTTTC-AAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGT
* * * * * *
28001629 GTTTTTGAGAAAGCGCCGCTAATGCTTGAGGTTTTAGCGGC
1 G-TTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGT
* *
28001670 GTTTTTGAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCAT
1 G-TTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGG--T
* *
28001713 -TTTTGAAAAAGCGCCGCTAATGCTGGGGGCTTTAACGGCAT
1 GTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGG--T
*
28001754 -TTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGC
1 GTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGT
* * * *
28001793 GTTTTTCAAAAAGCGACACTAATGCTCGGGGTTTTAGCAGCGT
1 G-TTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGC-G-GT
* * * * *
28001836 -TTTTCAAAAAGCGTCACTAACGCTCGGGGTTTTAGCGGCAT
1 GTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGG--T
28001877 -TTTTCAAAAAGCGCCGCTAA
1 GTTTTCAAAAAGCGCCGCTAA
28001897 AAACACTTTA
Statistics
Matches: 230, Mismatches: 29, Indels: 18
0.83 0.10 0.06
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 222 0.97
42 5 0.02
43 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
GTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGT
Found at i:28001724 original size:82 final size:82
Alignment explanation
Indices: 28001585--28001896 Score: 365
Period size: 82 Copynumber: 3.8 Consensus size: 82
28001575 AGGCTTTCGT
* * * ** * ** * *
28001585 GGCG-TTTTCAAAAAAGCGCCACTAATGTTCAGGGATTTAGCGGTGTTTTTGAGAAAGCGCCGCT
1 GGCGTTTTTC-AAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCT
* *
28001649 AATGCTTGAGGTTTTAGC
65 AATGCTCGGGGTTTTAGC
* *
28001667 GGCGTTTTTGAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTA
1 GGCGTTTTTCAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
* * *
28001732 ATGCTGGGGGCTTTAAC
66 ATGCTCGGGGTTTTAGC
* * * * *
28001749 GGCATTTTTCAAAAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCGTTTTTCAAAAAGCGACACTA
1 GGCGTTTTTCAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
28001814 ATGCTCGGGGTTTTAGC
66 ATGCTCGGGGTTTTAGC
* * * * *
28001831 AGCGTTTTTCAAAAAGCGTCACTAACGCTCGGGGTTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
1 GGCGTTTTTCAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
28001896 A
66 A
28001897 AAACACTTTA
Statistics
Matches: 195, Mismatches: 34, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
82 191 0.98
83 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (82 bp):
GGCGTTTTTCAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCATTTTTCAAAAAGCGCCGCTA
ATGCTCGGGGTTTTAGC
Found at i:28001795 original size:123 final size:123
Alignment explanation
Indices: 28001589--28001896 Score: 364
Period size: 123 Copynumber: 2.5 Consensus size: 123
28001579 TTTCGTGGCG
* * * * * ** * *
28001589 TTTTCAAAAAAGCGCCACTAATGTTCAGGGATTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGC
1 TTTTC-AAAAAGCGCCACTAACGCTCGGGGCTTTAACGGCATTTTTCAAAAAGCGCCGCTAATGC
* * * * * * *
28001654 TTGAGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAACGCTGGGGGCTTTAGCGGCAT
65 TGGAGGCTTTAGCGGCGTTTTTCAAAAAGCGACACTAACGCTCGGGGCTTTAGCAGCAT
* * * *
28001713 TTTTGAAAAAGCGCCGCTAATGCTGGGGGCTTTAACGGCATTTTTCAAAAAGCGCCGCTAATGCT
1 TTTTCAAAAAGCGCCACTAACGCTCGGGGCTTTAACGGCATTTTTCAAAAAGCGCCGCTAATGCT
* * * *
28001778 GGGGGCTTTAGCGGCGTTTTTCAAAAAGCGACACTAATGCTCGGGGTTTTAGCAGCGT
66 GGAGGCTTTAGCGGCGTTTTTCAAAAAGCGACACTAACGCTCGGGGCTTTAGCAGCAT
* * *
28001836 TTTTCAAAAAGCGTCACTAACGCTCGGGGTTTTAGCGGCATTTTTCAAAAAGCGCCGCTAA
1 TTTTCAAAAAGCGCCACTAACGCTCGGGGCTTTAACGGCATTTTTCAAAAAGCGCCGCTAA
28001897 AAACACTTTA
Statistics
Matches: 155, Mismatches: 29, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
123 151 0.97
124 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (123 bp):
TTTTCAAAAAGCGCCACTAACGCTCGGGGCTTTAACGGCATTTTTCAAAAAGCGCCGCTAATGCT
GGAGGCTTTAGCGGCGTTTTTCAAAAAGCGACACTAACGCTCGGGGCTTTAGCAGCAT
Found at i:28002281 original size:14 final size:14
Alignment explanation
Indices: 28002262--28002298 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28002252 GAGTATGAAT
28002262 TTAGGGATTATGGA
1 TTAGGGATTATGGA
*
28002276 TTAGGGATTATGGT
1 TTAGGGATTATGGA
*
28002290 TTAAGGATT
1 TTAGGGATT
28002299 GGGATTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.41
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:28002311 original size:21 final size:21
Alignment explanation
Indices: 28002273--28002351 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
28002263 TAGGGATTAT
*
28002273 GGATTAGGGATTATGGTTTAA
1 GGATTAGGGATTAAGGTTTAA
28002294 GGATT-GGGATTTAAGGTTTAA
1 GGATTAGGGA-TTAAGGTTTAA
* * * * *
28002315 GGGTTAGGGGTTAGGGGTTAGG
1 GGATTAGGGATTAAGGTTTA-A
*
28002337 GGTTTAGGGATTAAG
1 GGATTAGGGATTAAG
28002352 AGTTAGAGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.09
21 27 0.59
22 15 0.33
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (21 bp):
GGATTAGGGATTAAGGTTTAA
Found at i:28002334 original size:14 final size:15
Alignment explanation
Indices: 28002308--28002345 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
28002298 TGGGATTTAA
*
28002308 GGTTTAAGGGTTAGG
1 GGTTTAGGGGTTAGG
28002323 GG-TTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
28002337 GGTTTAGGG
1 GGTTTAGGG
28002346 ATTAAGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.32
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:28002345 original size:8 final size:7
Alignment explanation
Indices: 28002315--28002345 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
28002305 TAAGGTTTAA
28002315 GGGTTAG
1 GGGTTAG
28002322 GGGTTAG
1 GGGTTAG
28002329 GGGTTAG
1 GGGTTAG
28002336 GGGTTTAG
1 GGG-TTAG
28002344 GG
1 GG
28002346 ATTAAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.58, T:0.29
Consensus pattern (7 bp):
GGGTTAG
Found at i:28002357 original size:14 final size:15
Alignment explanation
Indices: 28002338--28002377 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
28002328 GGGGTTAGGG
28002338 GTTTAGGGATTAAGA
1 GTTTAGGGATTAAGA
* *
28002353 G-TTAGAGATTTAGA
1 GTTTAGGGATTAAGA
28002367 GTTTAGGGATT
1 GTTTAGGGATT
28002378 CATGGGTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.38
Consensus pattern (15 bp):
GTTTAGGGATTAAGA
Found at i:28002447 original size:25 final size:25
Alignment explanation
Indices: 28002415--28002462 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28002405 AGATTAATTA
*
28002415 TTTTTTAATTTACATTTTAAATATG
1 TTTTTTAATTTACATATTAAATATG
*
28002440 TTTTTTAATTTATATATTAAATA
1 TTTTTTAATTTACATATTAAATA
28002463 ATTTCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTTTAATTTACATATTAAATATG
Found at i:28002676 original size:21 final size:20
Alignment explanation
Indices: 28002642--28002682 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28002632 GTATGGATTA
*
28002642 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
28002662 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
28002683 ATGAGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:28002832 original size:197 final size:197
Alignment explanation
Indices: 28002497--28002890 Score: 779
Period size: 197 Copynumber: 2.0 Consensus size: 197
28002487 AAGATAGTAT
28002497 CAATTTTAAAGTATTTAATTAATTATCATTATAGTTTAGGGTTTATATGGTTTACGGTATATGGT
1 CAATTTTAAAGTATTTAATTAATTATCATTATAGTTTAGGGTTTATATGGTTTACGGTATATGGT
*
28002562 TAATTTAAGATTTAAGGCCAGTTTAGGAGTTACTATTTTAAGGTTTGGGGATTATATATGGATTT
66 TAATTTAAGATTTAAGGCCAGGTTAGGAGTTACTATTTTAAGGTTTGGGGATTATATATGGATTT
28002627 AGGAAGTATGGATTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTATGAGTTAG
131 AGGAAGTATGGATTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTATGAGTTAG
28002692 GG
196 GG
28002694 CAATTTTAAAGTATTTAATTAATTATCATTATAGTTTAGGGTTTATATGGTTTACGGTATATGGT
1 CAATTTTAAAGTATTTAATTAATTATCATTATAGTTTAGGGTTTATATGGTTTACGGTATATGGT
28002759 TAATTTAAGATTTAAGGCCAGGTTAGGAGTTACTATTTTAAGGTTTGGGGATTATATATGGATTT
66 TAATTTAAGATTTAAGGCCAGGTTAGGAGTTACTATTTTAAGGTTTGGGGATTATATATGGATTT
28002824 AGGAAGTATGGATTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTATGAGTTAG
131 AGGAAGTATGGATTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTATGAGTTAG
28002889 GG
196 GG
28002891 GTTAAGGGTT
Statistics
Matches: 196, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
197 196 1.00
ACGTcount: A:0.28, C:0.03, G:0.27, T:0.41
Consensus pattern (197 bp):
CAATTTTAAAGTATTTAATTAATTATCATTATAGTTTAGGGTTTATATGGTTTACGGTATATGGT
TAATTTAAGATTTAAGGCCAGGTTAGGAGTTACTATTTTAAGGTTTGGGGATTATATATGGATTT
AGGAAGTATGGATTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTATGAGTTAG
GG
Found at i:28002873 original size:21 final size:20
Alignment explanation
Indices: 28002839--28002879 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28002829 GTATGGATTA
*
28002839 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
28002859 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
28002880 ATGAGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:28002899 original size:21 final size:21
Alignment explanation
Indices: 28002875--28002921 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28002865 TAAGGTTTAG
* *
28002875 GGGTTATGAGTTAGGGGTTAA
1 GGGTTAAGAGTTAGGGATTAA
*
28002896 GGGTTAAGAGTTAGGGATTTA
1 GGGTTAAGAGTTAGGGATTAA
28002917 GGGTT
1 GGGTT
28002922 TCAAGGGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.34
Consensus pattern (21 bp):
GGGTTAAGAGTTAGGGATTAA
Found at i:28002901 original size:14 final size:14
Alignment explanation
Indices: 28002850--28002901 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
28002840 GGATTATGGT
*
28002850 TTAAGGGTT-GGGAT
1 TTAAGGGTTAGGG-G
*
28002864 TTAAGGTTTAGGGG
1 TTAAGGGTTAGGGG
* *
28002878 TTATGAGTTAGGGG
1 TTAAGGGTTAGGGG
28002892 TTAAGGGTTA
1 TTAAGGGTTA
28002902 AGAGTTAGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 27 0.90
15 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:28004611 original size:21 final size:21
Alignment explanation
Indices: 28004585--28004639 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
28004575 AACAGCGGTG
*
28004585 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
28004606 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
28004627 GCGGTGATATTAG
1 GCGGTGAGATTAG
28004640 AAACAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:28005624 original size:21 final size:21
Alignment explanation
Indices: 28005598--28005652 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
28005588 AACAGCGGTG
*
28005598 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
28005619 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
28005640 GCGGTGATATTAG
1 GCGGTGAGATTAG
28005653 AAACAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:28013211 original size:16 final size:16
Alignment explanation
Indices: 28013192--28013228 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28013182 TTTTTAAATT
*
28013192 ACTTTTTAAGGCATGC
1 ACTTTTTAAGACATGC
28013208 ACTTTTTAAGACATGC
1 ACTTTTTAAGACATGC
28013224 ACTTT
1 ACTTT
28013229 ATACAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (16 bp):
ACTTTTTAAGACATGC
Found at i:28014824 original size:44 final size:43
Alignment explanation
Indices: 28014743--28014979 Score: 275
Period size: 43 Copynumber: 5.5 Consensus size: 43
28014733 AAGTCATGTT
*
28014743 TTTAGCGGCGTTTGTGGTAAAAGCGTCGCTAAAGATCATGA-C
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGATCATGACC
* * *
28014785 TTCTAGCGACGTTTGTGGTAAAAAGCACCGCTAAAGATCATGACT
1 TT-TAGCGGCGTTTGTGGT-AAAAGCGCCGCTAAAGATCATGACC
* *
28014830 TTTAGTGGCGTTTGTGGTAAAAGCGCGGCTAAAGATCATGACC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGATCATGACC
* * * * * *
28014873 TTTAGCGGTGTTTGTGGAAAAAGTGCCACTAAAGACCATGATC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGATCATGACC
* *
28014916 TTTAGCGGCGTTTGATGG-AAAAGCGCCGCTAAAG-GCTATGATC
1 TTTAGCGGCGTTTG-TGGTAAAAGCGCCGCTAAAGATC-ATGACC
*
28014959 TTTAGCGGCGTTTAT-GTAAAA
1 TTTAGCGGCGTTTGTGGTAAAA
28014980 CATGCCGCTA
Statistics
Matches: 167, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.01
42 8 0.05
43 118 0.71
44 38 0.23
45 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGATCATGACC
Found at i:28015069 original size:21 final size:21
Alignment explanation
Indices: 28015043--28015100 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
28015033 AGCGGCGCTT
28015043 AAAACGCCGCTAAAAGCTTAA
1 AAAACGCCGCTAAAAGCTTAA
28015064 AAAACGCCGCTAAAAGCTTAA
1 AAAACGCCGCTAAAAGCTTAA
28015085 AAAACGCCGCTAAAAG
1 AAAACGCCGCTAAAAG
28015101 TCTCTTTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (21 bp):
AAAACGCCGCTAAAAGCTTAA
Found at i:28016912 original size:25 final size:21
Alignment explanation
Indices: 28016865--28016905 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28016855 AAAACTGGAT
28016865 TTTTGATATGACATATATATA
1 TTTTGATATGACATATATATA
28016886 TTTTGATATGACATATATAT
1 TTTTGATATGACATATATAT
28016906 GTATATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTTGATATGACATATATATA
Found at i:28030493 original size:19 final size:18
Alignment explanation
Indices: 28030452--28030494 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28030442 ACTTTTGGGG
* *
28030452 TAAAAGGCACTTTTGAGA
1 TAAAAAGCACTTTTGAAA
*
28030470 CAAAAAGCACTTTTTGAAA
1 TAAAAAGCAC-TTTTGAAA
28030489 TAAAAA
1 TAAAAA
28030495 CATTATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (18 bp):
TAAAAAGCACTTTTGAAA
Found at i:28031024 original size:33 final size:35
Alignment explanation
Indices: 28030986--28031082 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
28030976 ATGGTTATAT
28030986 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
28031019 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
*
28031054 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
28031083 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
32 7 0.14
33 25 0.49
34 5 0.10
35 11 0.22
36 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (35 bp):
TTAAATATTTAAAATATATTTTATATATTGCTTAA
Found at i:28031307 original size:13 final size:13
Alignment explanation
Indices: 28031291--28031317 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28031281 TTTCCACAGC
28031291 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
28031304 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
28031317 A
1 A
28031318 TTGTCAAACT
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:28033094 original size:387 final size:388
Alignment explanation
Indices: 28032379--28033154 Score: 1385
Period size: 387 Copynumber: 2.0 Consensus size: 388
28032369 AAATAAATAA
*
28032379 AATAAAGTTTTGGTTGAGTGGTAAACTCAAGATTTTACTAATTCAACCGCTATAAGTTTAAATCT
1 AATAAAGTTTTGGTTGAGTGGTAAACTCAAGATTTTACTAATTCAACCACTATAAGTTTAAATCT
*
28032444 CGTTATATACATATTTTTATTGGTTTTTTAAAAAAAATAAAGAGACTAAAATACGCTCAAATAAT
66 CGTTATATACATATTTTTATTGGTTTTTTAAAAAAAATAAAGAGACTAAAATACCCTCAAATAAT
* * * *
28032509 ATAACTTATTTTAATTATAGAATGATATTTTCATAATTTTTCTAATTGAGTTGGTGCTCGGTTGA
131 ATAACTTATTTTAATTATAGAATGATATTATCATAATTTTCCTAATTGAGTTGATGCTCGATTGA
*
28032574 CTCGTCGTGACACAACTCAATCGATCATATTGGTTGTATGTTGTGATAATACATGTTTAAAACTT
196 CTCGTCGTGACACAACTCAATCGATCATATTAGTTGTATGTTGTGATAATACATGTTTAAAACTT
28032639 GATTTTAACTTGATTTGAATGCCTTGTTATGACTTGTTGATATACAAATTATTGTGTTTAAGTTG
261 GATTTTAACTTGATTTGAATGCCTTGTTATGACTTGTTGATATACAAATTATTGTGTTTAAGTTG
*
28032704 GTACCAAATTGAATG-GAAAATTTGGCTTGAAAATGATCTATTTTTGTCCATACGGGCAGAGAC
326 GTACCAAATTGAATGAG-AAATGTGGCTTGAAAATGATCTATTTTTGTCCATACGGGCAGAGAC
*
28032767 AATAAAGTTTTGGTTGAGTGGTAAACTCAAGATTTTACTAATTCAACCACTATGAGTTTAAATCT
1 AATAAAGTTTTGGTTGAGTGGTAAACTCAAGATTTTACTAATTCAACCACTATAAGTTTAAATCT
*
28032832 CGTTATATATATATTTTTATTGGTTTTTT-AAAAAAATAAAGAGACTAAAATACCCTCAAATAAT
66 CGTTATATACATATTTTTATTGGTTTTTTAAAAAAAATAAAGAGACTAAAATACCCTCAAATAAT
28032896 ATAACTTATTTTAATTATAGAATGATATTATCATAATTTTCCTAATTGAGTTGATGCTCGATTGA
131 ATAACTTATTTTAATTATAGAATGATATTATCATAATTTTCCTAATTGAGTTGATGCTCGATTGA
* *
28032961 CTGGTCGTGACACAACTCAATCGATCATATTAGTTGTATGTTGTGATAATACATGTTTAAGACTT
196 CTCGTCGTGACACAACTCAATCGATCATATTAGTTGTATGTTGTGATAATACATGTTTAAAACTT
* * *
28033026 GATTTTAACTTGATTTGAATGCCTTGTTATGACTTGTTGATATGCAAATTGTTGTGTTTAGGTTG
261 GATTTTAACTTGATTTGAATGCCTTGTTATGACTTGTTGATATACAAATTATTGTGTTTAAGTTG
*
28033091 GTACCAAATTGAGTGAGAAATGTGGCTTGAAAATGATCTATTTTTGTCCATACGGGCAGAGAC
326 GTACCAAATTGAATGAGAAATGTGGCTTGAAAATGATCTATTTTTGTCCATACGGGCAGAGAC
28033154 A
1 A
28033155 CGGGCATGTG
Statistics
Matches: 371, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
387 279 0.75
388 92 0.25
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (388 bp):
AATAAAGTTTTGGTTGAGTGGTAAACTCAAGATTTTACTAATTCAACCACTATAAGTTTAAATCT
CGTTATATACATATTTTTATTGGTTTTTTAAAAAAAATAAAGAGACTAAAATACCCTCAAATAAT
ATAACTTATTTTAATTATAGAATGATATTATCATAATTTTCCTAATTGAGTTGATGCTCGATTGA
CTCGTCGTGACACAACTCAATCGATCATATTAGTTGTATGTTGTGATAATACATGTTTAAAACTT
GATTTTAACTTGATTTGAATGCCTTGTTATGACTTGTTGATATACAAATTATTGTGTTTAAGTTG
GTACCAAATTGAATGAGAAATGTGGCTTGAAAATGATCTATTTTTGTCCATACGGGCAGAGAC
Found at i:28036026 original size:29 final size:29
Alignment explanation
Indices: 28035993--28036081 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
28035983 TAATACGAGA
28035993 TTACAAAAGAACCAAATAAATGATCATGC
1 TTACAAAAGAACCAAATAAATGATCATGC
** * * *
28036022 TTACATTA-TA-C-AATAGTAAT-ATGA-GA
1 TTACAAAAGAACCAAATA--AATGATCATGC
28036048 TTACAAAAGAACCAAATAAATGATCATGC
1 TTACAAAAGAACCAAATAAATGATCATGC
28036077 TTACA
1 TTACA
28036082 TTACAGTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 11 0.26
27 8 0.19
28 8 0.19
29 16 0.37
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (29 bp):
TTACAAAAGAACCAAATAAATGATCATGC
Found at i:28036057 original size:55 final size:55
Alignment explanation
Indices: 28035976--28036084 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
28035966 ATATATATAC
28035976 ACAATAGTAATACGAGATTACAAAAGAACCAAATAAATGATCATGCTTACATTAT
1 ACAATAGTAATACGAGATTACAAAAGAACCAAATAAATGATCATGCTTACATTAT
*
28036031 ACAATAGTAATATGAGATTACAAAAGAACCAAATAAATGATCATGCTTACATTA
1 ACAATAGTAATACGAGATTACAAAAGAACCAAATAAATGATCATGCTTACATTA
28036085 CAGTTTTTCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.26
Consensus pattern (55 bp):
ACAATAGTAATACGAGATTACAAAAGAACCAAATAAATGATCATGCTTACATTAT
Found at i:28036731 original size:13 final size:11
Alignment explanation
Indices: 28036695--28036725 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28036685 CTGTCCGTAT
28036695 TAATTTTTATA
1 TAATTTTTATA
*
28036706 TTATTTTTATA
1 TAATTTTTATA
28036717 TAATTTTTA
1 TAATTTTTA
28036726 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:28038185 original size:51 final size:51
Alignment explanation
Indices: 28038099--28038388 Score: 327
Period size: 51 Copynumber: 5.7 Consensus size: 51
28038089 TATCGATGAA
* * * * *
28038099 CACGTGTGTAGTATTGTGTGAAAGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
* * * * * *
28038150 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATGTTGGT
* * * *
28038201 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
* * *
28038252 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATG--TTGGT
* ** *
28038303 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
28038353 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
28038389 TCGAATGATA
Statistics
Matches: 198, Mismatches: 35, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 43 0.22
51 153 0.77
52 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGTTGGT
Found at i:28038275 original size:102 final size:102
Alignment explanation
Indices: 28038099--28038380 Score: 440
Period size: 102 Copynumber: 2.8 Consensus size: 102
28038089 TATCGATGAA
* * *
28038099 CACGTGTGTAGTATTGTGTGAAAGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
28038164 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
28038201 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
28038266 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * *** * *
28038303 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
28038367 TATGTGAAGGCTAC
66 TAAGTGAAGGCTAC
28038381 TACGTGTATC
Statistics
Matches: 167, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 33 0.20
102 134 0.80
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:28038424 original size:101 final size:102
Alignment explanation
Indices: 28038106--28038425 Score: 302
Period size: 102 Copynumber: 3.1 Consensus size: 102
28038096 GAACACGTGT
* * * * ** *
28038106 GTAGTATTGTGTGAAAGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * * * *** * * *
28038171 AGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* ** *
28038208 GTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * *** * * *
28038273 AGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* * * *
28038310 GTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTACTATGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* *
28038374 AGGCTACTACGTGTATCG-AATGATAAAAGTAACATGG
66 AGGCTACTACGTGTACCGAAAAGAT-AAAGTAACATGG
28038411 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
28038426 AAACCCCAAA
Statistics
Matches: 193, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
100 4 0.02
101 62 0.32
102 127 0.66
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (102 bp):
GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
Found at i:28038425 original size:152 final size:153
Alignment explanation
Indices: 28038106--28038426 Score: 373
Period size: 152 Copynumber: 2.1 Consensus size: 153
28038096 GAACACGTGT
* *
28038106 GTAGTATTGTGTGAAAGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAAGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
* * * * *
28038171 AGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGA
66 AGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGA
* ** * *
28038236 ATCGATAAATGATGGTCACATGT
131 ATCGATAAATAAAAGTAACATGG
** * * * * *
28038259 GTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGTCACGTGTGTAGTACTATGT
1 GTAGTACTGTGTGAAAGCTACTACGTGTACCGATAAATG--ATGGTCACATGTGTAGTACTAAGT
*
28038322 GAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACG
64 GAAGGCTACAACGTGAACCG-AGAAACTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACG
* *
28038385 TGTATCGA-ATGATAAAAGTAACATGG
128 TGAATCGATA-AATAAAAGTAACATGG
28038411 GTAGTACTGTGTGAAA
1 GTAGTACTGTGTGAAA
28038427 AACCCCAAAT
Statistics
Matches: 139, Mismatches: 25, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
151 2 0.01
152 68 0.49
153 68 0.49
154 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (153 bp):
GTAGTACTGTGTGAAAGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
AGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGA
ATCGATAAATAAAAGTAACATGG
Found at i:28044204 original size:21 final size:20
Alignment explanation
Indices: 28044166--28044228 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
28044156 ATTCAATTTC
28044166 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
28044183 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
28044204 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
28044223 TGCAAT
1 T-CAAT
28044229 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:28045791 original size:45 final size:45
Alignment explanation
Indices: 28045734--28045820 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
28045724 CAGATACTCG
* * *
28045734 GTGGATTCAGCACATAGCAACCGCCTTATTAATCAATAATGTCTA
1 GTGGATTCAGCACATAGCAACCACCTTACTAATAAATAATGTCTA
*
28045779 GTGGAATT-AGCACATAGCAACCACCTTACTAATAAATGATGT
1 GTGG-ATTCAGCACATAGCAACCACCTTACTAATAAATAATGT
28045821 TCGGTTCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (45 bp):
GTGGATTCAGCACATAGCAACCACCTTACTAATAAATAATGTCTA
Found at i:28045885 original size:51 final size:50
Alignment explanation
Indices: 28045820--28045963 Score: 182
Period size: 50 Copynumber: 2.9 Consensus size: 50
28045810 ATAAATGATG
*
28045820 TTCGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGATCAAAAC-T
1 TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGA-CAAAACAT
** * * ** *
28045870 ATTCGGTACGTATAGTAGCCTGCACATAGTACTACACATGCGACCTATCAT
1 -TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACAAAACAT
*
28045921 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGAC
28045964 CATCACTTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
50 41 0.52
51 38 0.48
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TTCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACAAAACAT
Found at i:28056280 original size:20 final size:20
Alignment explanation
Indices: 28056255--28056294 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28056245 CGTAAAATGA
*
28056255 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28056275 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28056295 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28056284 original size:34 final size:35
Alignment explanation
Indices: 28056240--28056306 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28056230 CAGTAAAATA
*
28056240 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
28056274 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
28056307 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:28056310 original size:14 final size:15
Alignment explanation
Indices: 28056234--28056310 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28056224 GATTGCCAGT
* *
28056234 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
28056248 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
28056262 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
28056282 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
28056297 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
28056311 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:28056908 original size:17 final size:18
Alignment explanation
Indices: 28056888--28056923 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28056878 TTGTTAGGCG
28056888 TCTGT-TTTTAATGTTGC
1 TCTGTCTTTTAATGTTGC
*
28056905 TCTGTCTTTTCATGTTGC
1 TCTGTCTTTTAATGTTGC
28056923 T
1 T
28056924 TTACAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.08, C:0.17, G:0.17, T:0.58
Consensus pattern (18 bp):
TCTGTCTTTTAATGTTGC
Found at i:28058778 original size:23 final size:25
Alignment explanation
Indices: 28058737--28058782 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
28058727 AAAAAAGCTA
28058737 AAATTAGAAAAGAAAAAAATGAAGG
1 AAATTAGAAAAGAAAAAAATGAAGG
*
28058762 AAATTA-AAAAG-ATAAAATGAA
1 AAATTAGAAAAGAAAAAAATGAA
28058783 TTTCCCCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 5 0.25
25 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (25 bp):
AAATTAGAAAAGAAAAAAATGAAGG
Found at i:28058926 original size:20 final size:20
Alignment explanation
Indices: 28058903--28058960 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
28058893 ATTTTTCTTG
28058903 TAAAAACTCAAGTTTTCCTA
1 TAAAAACTCAAGTTTTCCTA
* **
28058923 TAAAAACCCACTTAATTTCCTA
1 TAAAAACTCAAGT--TTTCCTA
*
28058945 TAAAACCTCAAGTTTT
1 TAAAAACTCAAGTTTT
28058961 TGCTTCTCTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (20 bp):
TAAAAACTCAAGTTTTCCTA
Found at i:28059228 original size:31 final size:31
Alignment explanation
Indices: 28059190--28059248 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28059180 TTAACGGTGG
28059190 GTGACTAAAATAATAAAAGAATGCAACGACA
1 GTGACTAAAATAATAAAAGAATGCAACGACA
* * *
28059221 GTGACTAAAATGATAAAAGTATGTAACG
1 GTGACTAAAATAATAAAAGAATGCAACG
28059249 GAAGTGCCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (31 bp):
GTGACTAAAATAATAAAAGAATGCAACGACA
Found at i:28060242 original size:26 final size:26
Alignment explanation
Indices: 28060193--28060243 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
28060183 ATAGCTATGA
* *
28060193 AAAATAAAAATATATTAGTTATTTTT
1 AAAATAAAAATATATTAATAATTTTT
* *
28060219 AAAATAATAATATTTTAATAATTTT
1 AAAATAAAAATATATTAATAATTTT
28060244 ATAACTGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AAAATAAAAATATATTAATAATTTTT
Found at i:28073249 original size:20 final size:21
Alignment explanation
Indices: 28073226--28073264 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28073216 AACAAATGCC
28073226 AACAAAG-AGAAAAAAATAGT
1 AACAAAGAAGAAAAAAATAGT
28073246 AACAAAGAAGAAAAAAATA
1 AACAAAGAAGAAAAAAATA
28073265 TAAACTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (21 bp):
AACAAAGAAGAAAAAAATAGT
Found at i:28073298 original size:19 final size:21
Alignment explanation
Indices: 28073274--28073319 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
28073264 ATAAACTACC
28073274 TTTGAAATCT-CT-ATTTTTG
1 TTTGAAATCTACTGATTTTTG
*
28073293 TTTGAAATTTACTGATTTTTG
1 TTTGAAATCTACTGATTTTTG
28073314 TATTGA
1 T-TTGA
28073320 TTCTCTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 8 0.35
22 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.57
Consensus pattern (21 bp):
TTTGAAATCTACTGATTTTTG
Found at i:28078563 original size:18 final size:17
Alignment explanation
Indices: 28078530--28078568 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28078520 TTGTATAAAT
28078530 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
28078548 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
28078565 TGTG
1 TGTG
28078569 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:28078821 original size:23 final size:23
Alignment explanation
Indices: 28078794--28078891 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
28078784 AGTGTTATTG
28078794 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
28078817 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28078840 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28078862 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28078885 ATCAGTG
1 ATCAGTG
28078892 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28078860 original size:45 final size:45
Alignment explanation
Indices: 28078796--28078884 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
28078786 TGTTATTGAT
* *
28078796 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
28078841 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
28078885 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:28099561 original size:15 final size:16
Alignment explanation
Indices: 28099541--28099575 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28099531 TTTTTTTAAT
28099541 TTCTAAGT-AAGGAAA
1 TTCTAAGTAAAGGAAA
*
28099556 TTCTAAGTAAAGGAAT
1 TTCTAAGTAAAGGAAA
28099572 TTCT
1 TTCT
28099576 TTTTGTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (16 bp):
TTCTAAGTAAAGGAAA
Found at i:28113815 original size:26 final size:26
Alignment explanation
Indices: 28113785--28113838 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28113775 TAGAATTATG
*
28113785 GATGCAATGTGACAATCCTAGGGAAA
1 GATGCAACGTGACAATCCTAGGGAAA
28113811 GATGCAACGTGACAATCCTAGGGAAA
1 GATGCAACGTGACAATCCTAGGGAAA
28113837 GA
1 GA
28113839 AGTTGAGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (26 bp):
GATGCAACGTGACAATCCTAGGGAAA
Found at i:28119037 original size:15 final size:14
Alignment explanation
Indices: 28119014--28119046 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28119004 TTGATTCCTA
28119014 AAAAAATGA--ATG
1 AAAAAATGATGATG
28119026 AAAAAATGATGATG
1 AAAAAATGATGATG
28119040 AAAAAAT
1 AAAAAAT
28119047 AAAAATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (14 bp):
AAAAAATGATGATG
Found at i:28120377 original size:44 final size:43
Alignment explanation
Indices: 28120314--28120778 Score: 231
Period size: 44 Copynumber: 10.2 Consensus size: 43
28120304 TCCCTAAGCA
* * *
28120314 ACAGTGGAACAGATCGAAGCCAGAATTCTTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCAAGAA-TCTTATCTCCCTGAGATT
* * * *
28120358 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGGTT
1 ACAGTGGAGCAGATTGAAGCAAG-AATCTTATCTCCCTGAGATT
* ** *
28120402 ACAGTGGAGCAGATTAAAATAAAGAATCTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATT-GAAGCAAGAATCTTATCTCCCTGAGA-TT
* * *
28120446 ACAACAGAGTAGATCACATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
1 ---AC--AGT-G----GAGCAGATTGAAGCAAG-AATCTTATCTCCCTGAGATT
* * *
28120500 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCAAG-AATCTTATCTCCCTGAGATT
* ** * ** * *
28120544 ACAATGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATT-GAAGCAAGAATCTTATCTCCCTGAGA-TT
* *
28120588 ACAGCAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
1 --A-C--AGT-G---G-AGCAGATTGAAGCAAG-AATCTTATCTCCCTGAGATT
*
28120642 ACAGTGGAGCAGATTGAAGCAAGTAATCCTATCTCCCTGAGATT
1 ACAGTGGAGCAGATTGAAGCAAG-AATCTTATCTCCCTGAGATT
* * * *
28120686 ACAGTGGAGCGGATT-AAGATAAAGGATCTTATCTCTCTGA-AGTT
1 ACAGTGGAGCAGATTGAAG--CAAGAATCTTATCTCCCTGAGA-TT
* * * * * ** *
28120730 ACAGTAGAGTAGATCGTATC--GGGTCTTATCTCCCTAAGATT
1 ACAGTGGAGCAGATTGAAGCAAGAATCTTATCTCCCTGAGATT
28120771 ACAGTGGA
1 ACAGTGGA
28120779 ATAGACCGAA
Statistics
Matches: 319, Mismatches: 68, Indels: 71
0.70 0.15 0.16
Matches are distributed among these distances:
41 23 0.07
42 1 0.00
43 5 0.02
44 197 0.62
45 15 0.05
46 1 0.00
47 3 0.01
48 2 0.01
49 10 0.03
50 2 0.01
51 3 0.01
52 1 0.00
53 9 0.03
54 45 0.14
55 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (43 bp):
ACAGTGGAGCAGATTGAAGCAAGAATCTTATCTCCCTGAGATT
Found at i:28120546 original size:98 final size:97
Alignment explanation
Indices: 28120367--28120547 Score: 231
Period size: 98 Copynumber: 1.8 Consensus size: 97
28120357 TACAGCGGAG
* * * * *
28120367 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAAAGAATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCT
*
28120432 ATCTCTCTGAAGTTACAACAGAGTAGATCACAT
65 ATCTCCCTGAAGTTACAACAGAGTAGATCACAT
* **
28120465 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATCC
28120529 TATCTCCCTG-AGATTACAA
64 TATCTCCCTGAAG-TTACAA
28120548 TGGAGTGGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
97 4 0.06
98 64 0.90
99 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (97 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAACAGAGTAGATCACAT
Found at i:28120688 original size:98 final size:98
Alignment explanation
Indices: 28120509--28120689 Score: 222
Period size: 98 Copynumber: 1.8 Consensus size: 98
28120499 TACAGCGGAG
* * ** * * *
28120509 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAATGGAGTGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAATGGAGCAGATTAAAAGAAAGAATCCT
*
28120574 ATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
66 ATCTCCCTGAAGTTACAGCAGAGTAGATCGCAT
* * * *
28120607 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-GAAGCAAGTAATCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAATGGAGCAGATTAAAAGAAAG-AATCC
28120671 TATCTCCCTG-AGATTACAG
65 TATCTCCCTGAAG-TTACAG
28120690 TGGAGCGGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
97 7 0.10
98 62 0.90
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (98 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAATGGAGCAGATTAAAAGAAAGAATCCT
ATCTCCCTGAAGTTACAGCAGAGTAGATCGCAT
Found at i:28120745 original size:142 final size:142
Alignment explanation
Indices: 28120323--28120745 Score: 729
Period size: 142 Copynumber: 3.0 Consensus size: 142
28120313 AACAGTGGAA
* *
28120323 CAGATCGAAGCCAGAATTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* * * *
28120388 ATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAAAGAATCTTATCTCTCTGAAGTTACAACAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
*
28120453 AGTAGATCACAT
131 AGTAGATCGCAT
28120465 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
28120530 ATCTCCCTGAGATTACAATGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
28120595 AGTAGATCGCAT
131 AGTAGATCGCAT
* *
28120607 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
28120672 ATCTCCCTGAGATTACAGTGGAGCGGATTAAGATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
28120737 AGTAGATCG
131 AGTAGATCG
28120746 TATCGGGTCT
Statistics
Matches: 266, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 266 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
AGTAGATCGCAT
Found at i:28126785 original size:67 final size:67
Alignment explanation
Indices: 28126712--28126847 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
28126702 CTGTCATACG
*
28126712 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTAAAATTTATGGACTGGCTCGAGCACTGCT
1 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTAAAATTTATGGACTGACTCGAGCACTGCT
28126777 CA
66 CA
*
28126779 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTGAAATTTATGGACTGACTCGAGCACTGCT
1 TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTAAAATTTATGGACTGACTCGAGCACTGCT
28126844 CA
66 CA
28126846 TA
1 TA
28126848 CTCTCACAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (67 bp):
TAGAAGTGTTGGTGCTGAAAAAACAATAGACTTGTTAAAATTTATGGACTGACTCGAGCACTGCT
CA
Found at i:28127768 original size:30 final size:31
Alignment explanation
Indices: 28127703--28127774 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
28127693 ACAATTGAAT
*
28127703 CAAAATCAAAGTTTTATGTGTATATTTCAAC
1 CAAAATCAAAGTTTTATGTGTATATTGCAAC
28127734 CAAAATCAAA-TTTTAATGTGTATAGTTGC-A-
1 CAAAATCAAAGTTTT-ATGTGTATA-TTGCAAC
28127764 CAAAATCAAAG
1 CAAAATCAAAG
28127775 ATTATGTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 14 0.38
31 20 0.54
32 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
CAAAATCAAAGTTTTATGTGTATATTGCAAC
Found at i:28129419 original size:2 final size:2
Alignment explanation
Indices: 28129412--28129436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28129402 CTTTGAGCCT
28129412 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28129437 TTCCATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28129475 original size:18 final size:18
Alignment explanation
Indices: 28129452--28129497 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
28129442 TAATTGGATG
*
28129452 CTTAAATATGTTTTAAAA
1 CTTAAATATGTTGTAAAA
*
28129470 CTTAAATATGTTGTAACA
1 CTTAAATATGTTGTAAAA
*
28129488 CATAAATATG
1 CTTAAATATG
28129498 GGGTGGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (18 bp):
CTTAAATATGTTGTAAAA
Found at i:28130062 original size:9 final size:9
Alignment explanation
Indices: 28130048--28130085 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
28130038 TGACCAGCCA
28130048 AAAAATATT
1 AAAAATATT
28130057 AAAAATA-T
1 AAAAATATT
*
28130065 AAAAGTTATT
1 AAAA-ATATT
28130075 AAAAATATT
1 AAAAATATT
28130084 AA
1 AA
28130086 GATTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.20
9 15 0.60
10 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATATT
Found at i:28143751 original size:19 final size:19
Alignment explanation
Indices: 28143723--28143765 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28143713 GAGGTATCAT
28143723 AATTTCTAAT-AGATACCAA
1 AATTTCTAATCA-ATACCAA
*
28143742 AATTTTTAATCAATACC-A
1 AATTTCTAATCAATACCAA
28143760 AATTTC
1 AATTTC
28143766 CAACGCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTTCTAATCAATACCAA
Found at i:28144939 original size:21 final size:22
Alignment explanation
Indices: 28144915--28144961 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
28144905 TATCATGATT
*
28144915 TAAAACCTTAAAAAAT-TTATA
1 TAAAACCATAAAAAATATTATA
*
28144936 TAAAATCATAAAAAATATTATA
1 TAAAACCATAAAAAATATTATA
28144958 -AAAA
1 TAAAA
28144962 TATTTTGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAACCATAAAAAATATTATA
Found at i:28144962 original size:21 final size:21
Alignment explanation
Indices: 28144923--28144962 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28144913 TTTAAAACCT
28144923 TAAAAAATTTATATAAAATCA
1 TAAAAAATTTATATAAAATCA
28144944 TAAAAAATATTATA-AAAAT
1 TAAAAAAT-TTATATAAAAT
28144963 ATTTTGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATTTATATAAAATCA
Found at i:28146103 original size:15 final size:15
Alignment explanation
Indices: 28146058--28146104 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
28146048 CGTCCGGCCC
28146058 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
*
28146073 TAAA-CAAAACAT--A
1 AAAACCAAAA-ATAAA
28146086 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
28146101 AAAA
1 AAAA
28146105 AATTCAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 6 0.23
14 10 0.38
15 10 0.38
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAACCAAAAATAAA
Found at i:28147438 original size:17 final size:20
Alignment explanation
Indices: 28147416--28147453 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28147406 CTTTATTTAC
28147416 TAAAT-CTT-TTATTT-TTT
1 TAAATCCTTGTTATTTATTT
28147433 TAAATCCTTGTTATTTATTT
1 TAAATCCTTGTTATTTATTT
28147453 T
1 T
28147454 CTTTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 6 0.33
20 4 0.22
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (20 bp):
TAAATCCTTGTTATTTATTT
Found at i:28147487 original size:15 final size:16
Alignment explanation
Indices: 28147455--28147495 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
28147445 ATTTATTTTC
*
28147455 TTTATTATTATGCATT
1 TTTATTATTATCCATT
*
28147471 TTTATT-TTATCC-CT
1 TTTATTATTATCCATT
28147485 TTTATTATTAT
1 TTTATTATTAT
28147496 TATTTCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTATCCATT
Found at i:28147645 original size:12 final size:12
Alignment explanation
Indices: 28147630--28147654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28147620 TCTTTTTTAT
28147630 TTTATTTATTCA
1 TTTATTTATTCA
28147642 TTTATTTATTCA
1 TTTATTTATTCA
28147654 T
1 T
28147655 CTATCATGTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:28153269 original size:28 final size:28
Alignment explanation
Indices: 28153237--28153292 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28153227 AAACCCGTGG
*
28153237 CTTTTCCCTATAAAGATAGCAAAAGGGT
1 CTTTTCCCTACAAAGATAGCAAAAGGGT
28153265 CTTTTCCCTACAAAGATAGCAAAAGGGT
1 CTTTTCCCTACAAAGATAGCAAAAGGGT
28153293 TCCATAGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (28 bp):
CTTTTCCCTACAAAGATAGCAAAAGGGT
Found at i:28158968 original size:17 final size:17
Alignment explanation
Indices: 28158946--28158998 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
28158936 TAATATTAGT
28158946 TTATTAATATTTTATTA
1 TTATTAATATTTTATTA
***
28158963 TTATTAGCCTTTTATTA
1 TTATTAATATTTTATTA
* *
28158980 TTATTACTA-TATATTA
1 TTATTAATATTTTATTA
28158996 TTA
1 TTA
28158999 CTCTTATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATTAATATTTTATTA
Found at i:28158984 original size:28 final size:28
Alignment explanation
Indices: 28158945--28159011 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
28158935 TTAATATTAG
* *
28158945 TTTATTAATATT-TTAT-TATTATTAGCCT
1 TTTATTATTATTACTATATATTATTA--CT
28158973 TTTATTATTATTACTATATATTATTACT
1 TTTATTATTATTACTATATATTATTACT
*
28159001 CTTATTATTAT
1 TTTATTATTAT
28159012 AGATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 23 0.68
29 3 0.09
30 8 0.24
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTATTATTATTACTATATATTATTACT
Found at i:28158996 original size:13 final size:12
Alignment explanation
Indices: 28158975--28159010 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
28158965 ATTAGCCTTT
28158975 TATTATTATTAC
1 TATTATTATTAC
28158987 TATATATTATTAC
1 TAT-TATTATTAC
*
28159000 TCTTATTATTA
1 TATTATTATTA
28159011 TAGATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:28159027 original size:22 final size:21
Alignment explanation
Indices: 28158948--28159027 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
28158938 ATATTAGTTT
*
28158948 ATTAATATTTTATTATTATTAG
1 ATTATTATTTTATTATTA-TAG
* * *
28158970 CCTT-TTATTATTATTACTATAT
1 -ATTATTATT-TTATTATTATAG
*
28158992 ATTATTACTCTTATTATTATAG
1 ATTATTA-TTTTATTATTATAG
28159014 ATTATTATATTTAT
1 ATTATTAT-TTTAT
28159028 CATATTTTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
21 3 0.07
22 30 0.68
23 11 0.25
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (21 bp):
ATTATTATTTTATTATTATAG
Found at i:28159175 original size:23 final size:24
Alignment explanation
Indices: 28159134--28159179 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28159124 GTATTATAAA
28159134 TTTTTTGTGTATTATTATATTAAG
1 TTTTTTGTGTATTATTATATTAAG
28159158 TTTTTATGT-TATTA-TATATTAA
1 TTTTT-TGTGTATTATTATATTAA
28159180 TATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 10 0.48
25 3 0.14
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (24 bp):
TTTTTTGTGTATTATTATATTAAG
Found at i:28165892 original size:50 final size:50
Alignment explanation
Indices: 28165836--28166318 Score: 372
Period size: 50 Copynumber: 9.7 Consensus size: 50
28165826 GCAGTGGAAC
* * * *
28165836 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** ** *
28165886 ATATTAAAGCTACAACAGCGAATCTTAC-TCCCC-AGGTGATGCAGTGGAAC
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACAT--TGCAGTTAAAA
* * * *
28165936 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** ** *
28165986 ATATTAAAGCTACAACAGCGAATCTTAC-TCCCC-AGGTGATGCAGTGGAAC
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACAT--TGCAGTTAAAA
* * * *
28166036 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAA
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** *
28166086 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCC-GAC-ATTGCAGTTAAAA
* * *
28166136 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * ** * * * ** *
28166186 AGATTATAGCTACAACACCGAATCTTAC-TCCCCAAGCGA-CGCAATGGAAC
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGA-C-ATTGCAGTTAAAA
* * *
28166236 AGATTAAAGCAACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
28166286 AGATTAAAGCTACAAT-AGTGAATCTTACTTCCC
1 AGATTAAAGCTAC-ATCAGTGAATCTTACTTCCC
28166319 AGGCGGTGTA
Statistics
Matches: 323, Mismatches: 93, Indels: 34
0.72 0.21 0.08
Matches are distributed among these distances:
48 4 0.01
49 23 0.07
50 267 0.83
51 25 0.08
52 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCTACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:28166341 original size:50 final size:50
Alignment explanation
Indices: 28165810--28166368 Score: 330
Period size: 50 Copynumber: 11.2 Consensus size: 50
28165800 AATGCCAGTT
* *
28165810 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATC
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAAT-AGTGAATC
* * * * ** * * * *
28165860 TTGCTTCCCCGAC-ATTGTAGTTAAAAATATTAAAGCTACAACAGCGAATC
1 TTACTTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
* * * *
28165910 TTACTCCCCAGGTGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATC
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAAT-AGTGAATC
* * * * ** * * * *
28165960 TTGCTTCCCCGAC-ATTGTAGTTAAAAATATTAAAGCTACAACAGCGAATC
1 TTACTTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
* * * *
28166010 TTACTCCCCAGGTGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATC
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAAT-AGTGAATC
* * ** * * *
28166060 TTGCTTCCCCA-AC-ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
1 TTACTT-CCCAGGCGA-TGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
* *
28166110 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCAC-ATCAGTGAATC
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAAT-AGTGAATC
* * * * ** * * * **
28166160 TTGCTTCCCCGAC-ATTGCAATTAAAAAGATTATAGCTACAACACCGAATC
1 TTACTTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
* * * * * *
28166210 TTACTCCCCAAGCGACGCAATGGAACAGATTAAAGCAAC-ATCGGTGAATC
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAAT-AGTGAATC
* * * ** *
28166260 TTGCTTCCCCGAC-ATTGCAGTTAAAAAGATTAAAGCTACAATAGTGAATC
1 TTACTTCCCAGGCGA-TGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
* * * * *
28166310 TTACTTCCCAGGCGGTGTAGTGGAACTGATTAAAGCTACAGTAGCGAATC
1 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
*
28166360 TTATTTCCC
1 TTACTTCCC
28166369 CGACATCAGT
Statistics
Matches: 362, Mismatches: 126, Indels: 42
0.68 0.24 0.08
Matches are distributed among these distances:
49 13 0.04
50 335 0.93
51 14 0.04
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (50 bp):
TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCTACAATAGTGAATC
Found at i:28166374 original size:100 final size:100
Alignment explanation
Indices: 28165810--28166345 Score: 874
Period size: 100 Copynumber: 5.4 Consensus size: 100
28165800 AATGCCAGTT
*
28165810 TTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
28165875 TGTAGTTAAAAATATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
*
28165910 TTACTCCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
28165975 TGTAGTTAAAAATATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
28166010 TTACTCCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCAACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
28166075 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
*
28166110 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* * *
28166175 TGCAATTAAAAAGATTATAGCTACAACACCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * *
28166210 TTACTCCCCAAGCGACGCAATGGAACAGATTAAAGCAACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
* *
28166275 TGCAGTTAAAAAGATTAAAGCTACAATAGTGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * *
28166310 TTACTTCCCAGGCGGTGTAGTGGAACTGATTAAAGC
1 TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGC
28166346 TACAGTAGCG
Statistics
Matches: 408, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 408 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (100 bp):
TTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
Found at i:28170987 original size:23 final size:23
Alignment explanation
Indices: 28170954--28170998 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28170944 CATGTTAAAG
*
28170954 CTACAAATCTTATCTCCCTGAAA
1 CTACAAATCTTATCCCCCTGAAA
*
28170977 CTACAAGTCTTATCCCCCTGAA
1 CTACAAATCTTATCCCCCTGAA
28170999 GTTGCAGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.07, T:0.29
Consensus pattern (23 bp):
CTACAAATCTTATCCCCCTGAAA
Found at i:28171040 original size:44 final size:44
Alignment explanation
Indices: 28170977--28171230 Score: 192
Period size: 44 Copynumber: 5.6 Consensus size: 44
28170967 CTCCCTGAAA
* *
28170977 CTACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGCTGATTAAAG
1 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * * *
28171021 CTACAAGTTTTATCTCCCTGAAGTTACAATGGAGCAGATTGAAG
1 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * * * * * *
28171065 CGACAAATCCTATGC-CTCTGAATTTGTAGTGG-GTCAGATTAAAT
1 CTACAAGTCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTAAAG
* *
28171109 CTACCATAGCCAGTCTTATTTCCCTGAAGTAGCAGTGGAGCAGATTAAAG
1 CTA-C--A---AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * * *
28171159 CTACAAATCATATCTCCCTGAAGTTGCAGCGGAGTAGATTGAAA-
1 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAG
* * *
28171203 CTACGATTCCTATAC-CCCTGAAGTTGCA
1 CTACAAGTCTTAT-CTCCCTGAAGTTGCA
28171231 ATGGGTTAGA
Statistics
Matches: 163, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
43 1 0.01
44 121 0.74
45 6 0.04
47 2 0.01
49 1 0.01
50 31 0.19
51 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
Found at i:28171198 original size:94 final size:94
Alignment explanation
Indices: 28171030--28171206 Score: 209
Period size: 94 Copynumber: 1.9 Consensus size: 94
28171020 GCTACAAGTT
* * * * * *
28171030 TTATCTCCCTGAAGTTACAATGGAGCAGATTGAAGCGACAAATCCTATGCCTCTGAATTTGTAGT
1 TTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCGACAAATCATATGCCCCTGAAGTTGCAGC
28171095 GGGTCAGATT-AAATCTACCATAGCCAGTC
66 GGGTCAGATTGAAA-CTACCATAGCCAGTC
* * *
28171124 TTATTTCCCTGAAG-TAGCAGTGGAGCAGATTAAAGCTACAAATCATAT-CTCCCTGAAGTTGCA
1 TTATCTCCCTGAAGTTA-CAATGGAGCAGATTAAAGCGACAAATCATATGC-CCCTGAAGTTGCA
28171187 GCGGAGT-AGATTGAAACTAC
64 GCGG-GTCAGATTGAAACTAC
28171207 GATTCCTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
93 3 0.04
94 62 0.89
95 5 0.07
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (94 bp):
TTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCGACAAATCATATGCCCCTGAAGTTGCAGC
GGGTCAGATTGAAACTACCATAGCCAGTC
Found at i:28171236 original size:138 final size:138
Alignment explanation
Indices: 28170982--28171236 Score: 330
Period size: 138 Copynumber: 1.8 Consensus size: 138
28170972 TGAAACTACA
* * * **
28170982 AGTCTTATCCCCCTGAAGTTGCAGTGGAGCTGATTAAAGCTACAAGTTTTATCTCCCTGAAGTTA
1 AGTCTTATCCCCCTGAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTA
* * * * * * *
28171047 CAATGGAGCAGATTGAAGCGACAAATCCTATGCCTCTGAATTTGTAGTGGGTCAGATTAAATCTA
66 CAACGGAGCAGATTGAAACGACAAATCCTATACCCCTGAAGTTGCAATGGGTCAGATTAAATCTA
28171112 CCATAGCC
131 CCATAGCC
** *
28171120 AGTCTTATTTCCCTGAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTG
1 AGTCTTATCCCCCTGAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTA
* * * * *
28171185 CAGCGGAGTAGATTGAAACTACGATTCCTATACCCCTGAAGTTGCAATGGGT
66 CAACGGAGCAGATTGAAACGACAAATCCTATACCCCTGAAGTTGCAATGGGT
28171237 TAGAATGAGA
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
138 97 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (138 bp):
AGTCTTATCCCCCTGAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTA
CAACGGAGCAGATTGAAACGACAAATCCTATACCCCTGAAGTTGCAATGGGTCAGATTAAATCTA
CCATAGCC
Found at i:28171429 original size:15 final size:14
Alignment explanation
Indices: 28171391--28171436 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
28171381 CGTTCGGCCC
28171391 AAAACCAAAAATAA
1 AAAACCAAAAATAA
*
28171405 ATAAA--TAAAATATA
1 A-AAACCAAAAATA-A
28171419 AAAACCAAAAATAA
1 AAAACCAAAAATAA
28171433 AAAA
1 AAAA
28171437 ATCCAAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 9 0.35
14 8 0.31
15 9 0.35
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACCAAAAATAA
Found at i:28171432 original size:13 final size:13
Alignment explanation
Indices: 28171391--28171435 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
28171381 CGTTCGGCCC
28171391 AAAACCAAAAATA
1 AAAACCAAAAATA
**
28171404 AATAAATAAAATATA
1 AA-AACCAAAA-ATA
28171419 AAAACCAAAAATA
1 AAAACCAAAAATA
28171432 AAAA
1 AAAA
28171436 AATCCAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAACCAAAAATA
Found at i:28171437 original size:15 final size:15
Alignment explanation
Indices: 28171391--28171442 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
28171381 CGTTCGGCCC
28171391 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
* * *
28171406 TAAA--TAAAATATA
1 AAAACCAAAAATAAA
28171419 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
28171434 AAAATCCAA
1 AAAA-CCAA
28171443 GTTCATTTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 10 0.36
15 14 0.50
16 4 0.14
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCAAAAATAAA
Found at i:28172820 original size:15 final size:16
Alignment explanation
Indices: 28172788--28172828 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
28172778 ATTTATTTTC
*
28172788 TTTATTATTATGCATT
1 TTTATTATTATCCATT
*
28172804 TTTATT-TTATCC-CT
1 TTTATTATTATCCATT
28172818 TTTATTATTAT
1 TTTATTATTAT
28172829 TATTATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTATCCATT
Found at i:28172984 original size:12 final size:12
Alignment explanation
Indices: 28172967--28172991 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28172957 CCTTTTTTAT
28172967 TTTATTTATTCA
1 TTTATTTATTCA
28172979 TTTATTTATTCA
1 TTTATTTATTCA
28172991 T
1 T
28172992 CTATCATGTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:28173746 original size:17 final size:16
Alignment explanation
Indices: 28173724--28173763 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
28173714 TAACTGCTTA
*
28173724 TATTTTTCTCTATTGTG
1 TATTTTTCTCTATT-TC
*
28173741 TATTTTTCTTTATTTC
1 TATTTTTCTCTATTTC
28173757 TATTTTT
1 TATTTTT
28173764 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.72
Consensus pattern (16 bp):
TATTTTTCTCTATTTC
Found at i:28173760 original size:16 final size:16
Alignment explanation
Indices: 28173724--28173786 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
28173714 TAACTGCTTA
* *
28173724 TATTTTTCTCTATTGTG
1 TATTTTTCTTTATT-TC
28173741 TATTTTTCTTTATTTC
1 TATTTTTCTTTATTTC
*
28173757 TATTTTT-TTTATTTT
1 TATTTTTCTTTATTTC
* *
28173772 TATGTTTGTTTATTT
1 TATTTTTCTTTATTT
28173787 TTTTTACTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
15 13 0.32
16 15 0.37
17 13 0.32
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.75
Consensus pattern (16 bp):
TATTTTTCTTTATTTC
Found at i:28173787 original size:16 final size:15
Alignment explanation
Indices: 28173744--28173788 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28173734 TATTGTGTAT
* *
28173744 TTTTCTTTATTTCTA
1 TTTTGTTTATTTTTA
*
28173759 TTTTTTTTATTTTTA
1 TTTTGTTTATTTTTA
28173774 TGTTTGTTTATTTTT
1 T-TTTGTTTATTTTT
28173789 TTTACTACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.80
Consensus pattern (15 bp):
TTTTGTTTATTTTTA
Found at i:28174714 original size:3 final size:3
Alignment explanation
Indices: 28174706--28174860 Score: 310
Period size: 3 Copynumber: 51.7 Consensus size: 3
28174696 TATACATTTC
28174706 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28174754 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28174802 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28174850 ATT ATT ATT AT
1 ATT ATT ATT AT
28174861 CATCATCATT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 152 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28177268 original size:19 final size:19
Alignment explanation
Indices: 28177232--28177331 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 19
28177222 AATAGGGGAA
28177232 ACTGGCACACATAA-TGCAT
1 ACTGGCACACA-AAGTGCAT
*
28177251 ACTGGCACACGAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * *
28177270 CCTGACATACAAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * * * * *
28177289 ATTGACGCACGAAGCGTAT
1 ACTGGCACACAAAGTGCAT
28177308 -CTTGGCACACAAAGTGCAT
1 AC-TGGCACACAAAGTGCAT
28177327 ACTGG
1 ACTGG
28177332 GAAAATTAGT
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
18 2 0.03
19 57 0.95
20 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (19 bp):
ACTGGCACACAAAGTGCAT
Found at i:28177288 original size:38 final size:38
Alignment explanation
Indices: 28177237--28177331 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
28177227 GGGAAACTGG
*
28177237 CACACATAA-TGCATACTGGCACACGAAGTGCATCCTGA
1 CACACA-AAGTGCATACTGGCACACGAAGCGCATCCTGA
* * * * * * *
28177275 CATACAAAGTGCATATTGACGCACGAAGCGTATCTTGG
1 CACACAAAGTGCATACTGGCACACGAAGCGCATCCTGA
28177313 CACACAAAGTGCATACTGG
1 CACACAAAGTGCATACTGG
28177332 GAAAATTAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
37 2 0.04
38 43 0.96
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (38 bp):
CACACAAAGTGCATACTGGCACACGAAGCGCATCCTGA
Found at i:28187552 original size:9 final size:9
Alignment explanation
Indices: 28187538--28187704 Score: 53
Period size: 9 Copynumber: 18.1 Consensus size: 9
28187528 TTTTAGTACG
28187538 ATAATTTTT
1 ATAATTTTT
28187547 ATAATTTTCTTTT
1 ATAA--TT--TTT
28187560 ATGAATTTTAT
1 AT-AATTTT-T
*
28187571 ATATTTTTT
1 ATAATTTTT
* *
28187580 ACATTTTTT
1 ATAATTTTT
*
28187589 ATACTTTTCTT
1 ATA-ATTT-TT
* *
28187600 ACGAATTTAT
1 A-TAATTTTT
*
28187610 A-AAATTTT
1 ATAATTTTT
28187618 AT-ATTTTT
1 ATAATTTTT
* *
28187626 CCTATATTTCT
1 -ATA-ATTTTT
28187637 ATAATTTTT
1 ATAATTTTT
*
28187646 ATGATTTTT
1 ATAATTTTT
28187655 ATAA-TTTT
1 ATAATTTTT
28187663 -T--TTTTT
1 ATAATTTTT
*
28187669 A-AA-TTTA
1 ATAATTTTT
*
28187676 ATTATTTTT
1 ATAATTTTT
*
28187685 ATAAATTTT
1 ATAATTTTT
28187694 ATTAATTTTT
1 A-TAATTTTT
28187704 A
1 A
28187705 CTTTTTATCC
Statistics
Matches: 117, Mismatches: 21, Indels: 39
0.66 0.12 0.22
Matches are distributed among these distances:
6 4 0.03
7 5 0.04
8 16 0.14
9 43 0.37
10 23 0.20
11 16 0.14
12 3 0.03
13 5 0.04
14 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:28187704 original size:19 final size:18
Alignment explanation
Indices: 28187656--28187704 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28187646 ATGATTTTTA
* *
28187656 TAATTTTTTTTTTAAATT
1 TAATTATTTTTATAAATT
28187674 TAATTATTTTTATAAATT
1 TAATTATTTTTATAAATT
*
28187692 TTATTAATTTTTA
1 TAATT-ATTTTTA
28187705 CTTTTTATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATTATTTTTATAAATT
Found at i:28193891 original size:14 final size:14
Alignment explanation
Indices: 28193868--28193901 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28193858 TGGTATGAGT
28193868 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
28193881 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
28193895 TTATAGG
1 TTATAGG
28193902 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:28197862 original size:89 final size:87
Alignment explanation
Indices: 28197389--28197958 Score: 305
Period size: 84 Copynumber: 6.6 Consensus size: 87
28197379 ACTACTGCTT
* *
28197389 AGGGAGATAAGA-TCTGCTTACTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAG-A--
1 AGGGAGATAAGACT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATC
* *
28197450 TAC-GATCTGCTCTCTGCAACTTC
65 TTCAG-TCTGCTCACTGCAACTTC
* * * * ** * *
28197473 AGAGAGATAAGATCTGAGATT--TTAATCCACTCC-CTGCAACTTCAGGGAGAT-AGAATTGTCG
1 AGGGAGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CA
* * *
28197534 GCTTTAATCTGCTCCACTGCAACTTC
63 TCTTCAGTCTGCT-CACTGCAACTTC
* *
28197560 AGGGAGATAAGATTTGC-CATCTTCAGTCTGC-CTCACTGCAACTTC-GGGAGGATAAGACTTGC
1 AGGGAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC
* *
28197622 TTACTT-AGTTTGCTCCACTGCAACTTC
62 AT-CTTCAGTCTGCT-CACTGCAACTTC
* * * * * ** *
28197649 AGGGAGATAAGACTAG-ATAC-GA-TCTACT-CTCTGCAACTTCAGAAAGATAAGA-TCTGAGAT
1 AGGGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TG-CAT
* * * ** *
28197709 -TTTAATCCGCTTCACCACAACTTT
64 CTTCAGTCTGC-TCACTGCAACTTC
* * * *
28197733 AGGGAGATAGGA-TTGTCAGTT--TTAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTC
1 AGGGAGATAAGACTTG-C--TTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-C
28197795 ATCTTCAGTCTGCCTCACTGCAACTTC
62 ATCTTCAGTCTG-CTCACTGCAACTTC
*
28197822 A-GGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-AT-
1 AGGGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATC
* * * * *
28197884 GTGA-TCCGCTCTCTGCAATTTC
65 TTCAGTCTGCTCACTGCAACTTC
* * * * *
28197906 AGAGAGATAAGATCTGGGATT--TTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 AGGGAGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
28197959 GGATCCCGGC
Statistics
Matches: 369, Mismatches: 76, Indels: 82
0.70 0.14 0.16
Matches are distributed among these distances:
82 5 0.01
83 22 0.06
84 114 0.31
85 16 0.04
86 19 0.05
87 35 0.09
88 37 0.10
89 108 0.29
90 13 0.04
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (87 bp):
AGGGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCT
TCAGTCTGCTCACTGCAACTTC
Found at i:28197951 original size:44 final size:44
Alignment explanation
Indices: 28197389--28197963 Score: 340
Period size: 44 Copynumber: 13.3 Consensus size: 44
28197379 ACTACTGCTT
* * *
28197389 AGGGAGATAAGATCT--GCTTACTTAGTCTGCTCCACTACAACTTC
1 AGGGAGATAAGATCTGAGATT--TTAATCTGCTCCACTGCAACTTC
*** *
28197433 AGGGAGATAAGA-CT-AGA-TACGATCTGCT-CTCTGCAACTTC
1 AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
* **
28197473 AGAGAGATAAGATCTGAGATTTTAATCCACTCC-CTGCAACTTC
1 AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
* **
28197516 AGGGAGAT-AGAAT-TGTCGGCTTTAATCTGCTCCACTGCAACTTC
1 AGGGAGATAAG-ATCTG-AGATTTTAATCTGCTCCACTGCAACTTC
* ** * *
28197560 AGGGAGATAAGATTTGCCATCTTCAGTCTGC-CTCACTGCAACTTC
1 AGGGAGATAAGATCTGAGAT-TTTAATCTGCTC-CACTGCAACTTC
* * * *
28197605 -GGGAGGATAAGA-CT-TGCTTACTTAGTTTGCTCCACTGCAACTTC
1 AGGGA-GATAAGATCTGAGATT--TTAATCTGCTCCACTGCAACTTC
*** * *
28197649 AGGGAGATAAGA-CT-AGA-TACGATCTACT-CTCTGCAACTTC
1 AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
** * * ** *
28197689 AGAAAGATAAGATCTGAGATTTTAATCCGCTTCACCACAACTTT
1 AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
* *
28197733 AGGGAGATAGGAT-TGTCAG-TTTTAATCTGCTCTACTGCAACTTC
1 AGGGAGATAAGATCTG--AGATTTTAATCTGCTCCACTGCAACTTC
* ** * *
28197777 AGGGAGATAAGATTTGTCATCTTCAGTCTGC-CTCACTGCAACTTC
1 AGGGAGATAAGATCTGAGAT-TTTAATCTGCTC-CACTGCAACTTC
* * *
28197822 A-GGAGGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTC
1 AGGGA-GATAAGATCTGAGATT--TTAATCTGCTCCACTGCAACTTC
* * * * *
28197866 AGGGAGATAAGA-CT-AGA-TGTGATCCGCT-CTCTGCAATTTC
1 AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
* * *
28197906 AGAGAGATAAGATCTGGGATTTTAATCCGCTCCACTGCAACTTC
1 AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
*
28197950 AGGGAGATAGGATC
1 AGGGAGATAAGATC
28197964 CCGGCCACTA
Statistics
Matches: 410, Mismatches: 85, Indels: 72
0.72 0.15 0.13
Matches are distributed among these distances:
40 63 0.15
41 22 0.05
42 14 0.03
43 62 0.15
44 178 0.43
45 71 0.17
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGAGATTTTAATCTGCTCCACTGCAACTTC
Found at i:28197978 original size:217 final size:217
Alignment explanation
Indices: 28197394--28197962 Score: 935
Period size: 217 Copynumber: 2.6 Consensus size: 217
28197384 TGCTTAGGGA
*
28197394 GATAAGA-TCTGCTTACTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGATACGATCT
1 GATAAGACT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCT
*
28197458 GCTCTCTGCAACTTCAGAGAGATAAGATCTGAGATTTTAATCCACTCC-CTGCAACTTCAGGGAG
65 GCTCTCTGCAACTTCAGAGAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAG
*
28197522 ATAGAATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGT
130 ATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGT
*
28197587 CTGCCTCACTGCAACTTCGGGAG
195 CTGCCTCACTGCAACTTCAGGAG
* *
28197610 GATAAGACTTGCTTACTTAGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTA
1 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTG
* * ** *
28197675 CTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTTAATCCGCTTCACCACAACTTTAGGGAGA
66 CTCTCTGCAACTTCAGAGAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
* * * *
28197740 TAGGATTGTCAGTTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTC
131 TAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTC
28197805 TGCCTCACTGCAACTTCAGGAG
196 TGCCTCACTGCAACTTCAGGAG
** *
28197827 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCCG
1 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTG
* *
28197892 CTCTCTGCAATTTCAGAGAGATAAGATCTGGGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
66 CTCTCTGCAACTTCAGAGAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
28197957 TAGGAT
131 TAGGAT
28197963 CCCGGCCACT
Statistics
Matches: 324, Mismatches: 27, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
216 104 0.32
217 220 0.68
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (217 bp):
GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTG
CTCTCTGCAACTTCAGAGAGATAAGATCTGAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
TAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTC
TGCCTCACTGCAACTTCAGGAG
Found at i:28209706 original size:121 final size:121
Alignment explanation
Indices: 28209498--28209738 Score: 455
Period size: 121 Copynumber: 2.0 Consensus size: 121
28209488 TACGTATGAG
28209498 GAAGGATTAGCACCCTCATTACGCCCAAAAAATTGGTACCTAGTTAATTAATTAGTGTCTTAAGG
1 GAAGGATTAGCACCCTCATTACGCCCAAAAAATTGGTACCTAGTTAATTAATTAGTGTCTTAAGG
*
28209563 TTGAGAATTTAGAAAAAACGTAATCCTTAGCAAAACTTAAAAGGCTACGTATTAAA
66 TCGAGAATTTAGAAAAAACGTAATCCTTAGCAAAACTTAAAAGGCTACGTATTAAA
28209619 GAAGGATTAGCACCCTCATTACGCCCAAAAAATTGGTACCTAGTTAATTAATTAGTGTCTTAAGG
1 GAAGGATTAGCACCCTCATTACGCCCAAAAAATTGGTACCTAGTTAATTAATTAGTGTCTTAAGG
* *
28209684 TCGAGAATTTGGAAAAACCGTAATCCTTAGCAAAACTTAAAAGGCTACGTATTAA
66 TCGAGAATTTAGAAAAAACGTAATCCTTAGCAAAACTTAAAAGGCTACGTATTAA
28209739 GACCCTTATT
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (121 bp):
GAAGGATTAGCACCCTCATTACGCCCAAAAAATTGGTACCTAGTTAATTAATTAGTGTCTTAAGG
TCGAGAATTTAGAAAAAACGTAATCCTTAGCAAAACTTAAAAGGCTACGTATTAAA
Found at i:28210013 original size:98 final size:98
Alignment explanation
Indices: 28209844--28210040 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
28209834 GTGCAATAAA
* *
28209844 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACGATT
1 ACTTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATT
28209909 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
*
28209942 ACTTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATT
28210007 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
28210040 A
1 A
28210041 TTATTTTTAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACATTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:28213402 original size:7 final size:7
Alignment explanation
Indices: 28213390--28213485 Score: 86
Period size: 7 Copynumber: 13.4 Consensus size: 7
28213380 AATGCACCAC
28213390 AAACCCT
1 AAACCCT
28213397 AAACCCT
1 AAACCCT
*
28213404 AAAACCTT
1 -AAACCCT
28213412 AAACCCT
1 AAACCCT
28213419 -AACCCT
1 AAACCCT
28213425 AAAACCCT
1 -AAACCCT
* *
28213433 AAGCACT
1 AAACCCT
**
28213440 AAACATT
1 AAACCCT
28213447 AAACCCT
1 AAACCCT
**
28213454 ATAATTCT
1 A-AACCCT
28213462 AAACCCT
1 AAACCCT
*
28213469 AAACTCT
1 AAACCCT
28213476 AAACCCT
1 AAACCCT
28213483 AAA
1 AAA
28213486 ATTAATAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
6 6 0.08
7 48 0.68
8 17 0.24
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:28213414 original size:8 final size:8
Alignment explanation
Indices: 28213390--28213434 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
28213380 AATGCACCAC
28213390 AAACCCT-
1 AAACCCTA
28213397 AAACCCTA
1 AAACCCTA
*
28213405 AAA-CCTT
1 AAACCCTA
28213412 AAACCCT-
1 AAACCCTA
28213419 -AACCCTA
1 AAACCCTA
28213426 AAACCCTA
1 AAACCCTA
28213434 A
1 A
28213435 GCACTAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
6 6 0.18
7 13 0.39
8 14 0.42
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16
Consensus pattern (8 bp):
AAACCCTA
Found at i:28213451 original size:29 final size:29
Alignment explanation
Indices: 28213390--28213486 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
28213380 AATGCACCAC
*
28213390 AAACCCT-AAACCCTAAA-ACCTTAAACCCT
1 AAACCCTAAAACCCTAAACA-C-TAAACTCT
*
28213419 -AACCCTAAAACCCTAAGCACTAAACAT-T
1 AAACCCTAAAACCCTAAACACTAAAC-TCT
* ** *
28213447 AAACCCTATAATTCTAAACCCTAAACTCT
1 AAACCCTAAAACCCTAAACACTAAACTCT
28213476 AAACCCTAAAA
1 AAACCCTAAAA
28213487 TTAATAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 13 0.24
29 41 0.75
30 1 0.02
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (29 bp):
AAACCCTAAAACCCTAAACACTAAACTCT
Found at i:28221555 original size:20 final size:19
Alignment explanation
Indices: 28221514--28221566 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
28221504 TTGAGAACTT
28221514 TTTGAG-AATTGTGAGAAA
1 TTTGAGAAATTGTGAGAAA
28221532 TTTGAGAAATTAG-GAGAGAA
1 TTTGAGAAATT-GTGAGA-AA
*
28221552 TTTGTGAAAATTGTG
1 TTTGAG-AAATTGTG
28221567 TGTGTGTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 8 0.28
20 9 0.31
21 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (19 bp):
TTTGAGAAATTGTGAGAAA
Found at i:28241305 original size:45 final size:46
Alignment explanation
Indices: 28241239--28241357 Score: 159
Period size: 45 Copynumber: 2.6 Consensus size: 46
28241229 AAGGAGAAGG
**
28241239 GACCAAGGTGAAAACTTGCAAAGGGCACTTTGAGTCCT-AAAAAGA
1 GACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCTAAAAAAGA
* *
28241284 GACCAAGGTGAAAACCCGCAAATGGCGCTTTGAGTCCTAAAAAAAAGA
1 GACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCT--AAAAAAGA
* *
28241332 GGCCAAGGTGAAAACCCTCAAAGGGC
1 GACCAAGGTGAAAACCCGCAAAGGGC
28241358 GCCTTGAGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
45 34 0.53
48 30 0.47
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (46 bp):
GACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCTAAAAAAGA
Found at i:28241346 original size:48 final size:45
Alignment explanation
Indices: 28241239--28241365 Score: 164
Period size: 48 Copynumber: 2.8 Consensus size: 45
28241229 AAGGAGAAGG
** *
28241239 GACCAAGGTGAAAACTTGCAAAGGGCACTTTGAGTCCTAAAAAGA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAGA
*
28241284 GACCAAGGTGAAAACCCGCAAATGGCGCTTTGAGTCCTAAAAAAAAGA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCT---AAAAAGA
* * *
28241332 GGCCAAGGTGAAAACCCTCAAAGGGCGCCTTGAG
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAG
28241366 ACCAAAGGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
45 34 0.48
48 37 0.52
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (45 bp):
GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAGA
Found at i:28242220 original size:24 final size:24
Alignment explanation
Indices: 28242184--28242235 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
28242174 ATGTCCCAAA
* *
28242184 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTAGATTGAACCTTAAAG
28242208 ATTACAGTAGATTGAACCTTAAAG
1 ATTACAGTAGATTGAACCTTAAAG
28242232 ATTA
1 ATTA
28242236 TAGTGGGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (24 bp):
ATTACAGTAGATTGAACCTTAAAG
Found at i:28242585 original size:51 final size:50
Alignment explanation
Indices: 28242530--28242697 Score: 202
Period size: 51 Copynumber: 3.4 Consensus size: 50
28242520 CCCTGACATG
* *
28242530 GCAGTGGAACAGATTAAAGTTGAAGGCAGCGAATCTTATCTCCCTGGCGTT
1 GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTAT-TCCCTGGCGTT
* *
28242581 GCA---G--TAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCTTGGCGTT
1 GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTA-TTCCCTGGCGTT
* * *
28242627 GCACTGGAATAGATTAAAGCTGAAGGCAGCGAACCTTATTTCCTGAGCGTT
1 GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTCCCTG-GCGTT
*
28242678 GCAGTGAAATAGATTAAAGC
1 GCAGTGGAATAGATTAAAGC
28242698 CACAAATTAT
Statistics
Matches: 100, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
46 39 0.39
47 1 0.01
48 1 0.01
49 1 0.01
50 5 0.05
51 53 0.53
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (50 bp):
GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTCCCTGGCGTT
Found at i:28242611 original size:46 final size:45
Alignment explanation
Indices: 28242540--28242682 Score: 169
Period size: 46 Copynumber: 3.0 Consensus size: 45
28242530 GCAGTGGAAC
*
28242540 AGATTAAAGTTGAAGGCAGCGAATCTTATCTCCCTGGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTAT-TCCCTGGCGTTGCAGT
* *
28242586 AGATTAAAGCTGAAGGCAGCAAATCTTATTTCCTTGGCGTTGCACTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTA-TTCCCTGGCGTTGCA---G--T
* *
28242637 AGATTAAAGCTGAAGGCAGCGAACCTTATTTCCTGAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTCCCTG-GCGTTGCAGT
28242683 GAAATAGATT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
46 40 0.48
47 1 0.01
48 1 0.01
49 1 0.01
50 5 0.06
51 35 0.42
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (45 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTCCCTGGCGTTGCAGT
Found at i:28244233 original size:14 final size:13
Alignment explanation
Indices: 28244216--28244267 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 13
28244206 ATTAATTTAA
28244216 TATTATTATTATGT
1 TATTATTATTAT-T
28244230 TATTATT-TTACCTT
1 TATTATTATTA--TT
28244244 TATTATTCATATATT
1 TATTATT-AT-TATT
28244259 TATTATTAT
1 TATTATTAT
28244268 CATAACTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.09
14 17 0.52
15 10 0.30
16 1 0.03
17 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:28245617 original size:23 final size:23
Alignment explanation
Indices: 28245572--28245673 Score: 71
Period size: 23 Copynumber: 4.5 Consensus size: 23
28245562 TTATAGAAAC
* **
28245572 TTAAAACATGCTTTGGATGACAT
1 TTAAAACATACTTTGGACAACAT
*
28245595 TTAAAACATATTTTGGACAACAT
1 TTAAAACATACTTTGGACAACAT
* * * * *
28245618 TCAAACCTTACTTT-GCCAGCAT
1 TTAAAACATACTTTGGACAACAT
* * * *
28245640 TTGAAACATACTTTTGCCAGCAT
1 TTAAAACATACTTTGGACAACAT
*
28245663 TTAAAGCATAC
1 TTAAAACATAC
28245674 CAAATGTTAT
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
22 16 0.26
23 46 0.74
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (23 bp):
TTAAAACATACTTTGGACAACAT
Found at i:28247096 original size:23 final size:24
Alignment explanation
Indices: 28247065--28247112 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28247055 TAGTGGATAA
*
28247065 TTGCTCATTT-GGTCCCTCCTATT
1 TTGCCCATTTAGGTCCCTCCTATT
28247088 TTGCCCATTTAGGTCCCTCCTATT
1 TTGCCCATTTAGGTCCCTCCTATT
28247112 T
1 T
28247113 ATTTCTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.46
Consensus pattern (24 bp):
TTGCCCATTTAGGTCCCTCCTATT
Found at i:28253216 original size:111 final size:111
Alignment explanation
Indices: 28253021--28253241 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
28253011 ATATAATCAA
* *
28253021 AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATTATTTTTCATTACTGTAGGAGCCAT
1 AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATCACTTTTCATTACTGTAGGAGCCAT
*
28253086 TATTAATATTCAATACAGAACCATCTAATTAAGCAATGAATATCCAT
66 TATTAATATTCAATACAGAACCATCT-ATTAAGCAATGAACATCCAT
* *
28253133 AATATCTTAAAAGCTTGAAGAAG-AAAAAAGAACAATAGTCACTTTTCATTACTGTAGGAGCCAT
1 AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATCACTTTTCATTACTGTAGGAGCCAT
28253197 TATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATCCA
66 TATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATCCA
28253242 ATAAACACCA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
110 18 0.17
111 63 0.61
112 23 0.22
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (111 bp):
AATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATCACTTTTCATTACTGTAGGAGCCAT
TATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATCCAT
Found at i:28256333 original size:19 final size:20
Alignment explanation
Indices: 28256311--28256406 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 20
28256301 AAACAATTCA
*
28256311 AAAATAATTTTCAAAAA-TT
1 AAAATAATTTTAAAAAATTT
*
28256330 AAAATTA-TTTATAAAAATTT
1 AAAATAATTTTA-AAAAATTT
28256350 CAAAATTTATATTTTAAAAAA-TT
1 -AAAA--TA-ATTTTAAAAAATTT
*
28256373 ATAAA-AATTCTAAAAAATTT
1 A-AAATAATTTTAAAAAATTT
*
28256393 AAAA-AAATTTAAAA
1 AAAATAATTTTAAAA
28256407 TTTTAAGAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.05
19 32 0.52
20 6 0.10
21 4 0.06
22 1 0.02
23 6 0.10
24 6 0.10
25 4 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTAAAAAATTT
Found at i:28256379 original size:10 final size:9
Alignment explanation
Indices: 28256362--28256406 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 9
28256352 AAATTTATAT
28256362 TTTAAAAAA
1 TTTAAAAAA
28256371 -TTATAAAAA
1 TTTA-AAAAA
28256380 TTCTAAAAAA
1 TT-TAAAAAA
28256390 TTTAAAAAAA
1 TTT-AAAAAA
28256400 TTTAAAA
1 TTTAAAA
28256407 TTTTAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.09
9 10 0.31
10 17 0.53
11 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:28259053 original size:105 final size:106
Alignment explanation
Indices: 28258933--28259143 Score: 352
Period size: 105 Copynumber: 2.0 Consensus size: 106
28258923 CCTAGAAAAT
* ** *
28258933 ATTTTGGCTTTGCCCCTCATGATGTCCTAAACTATTTCACAAAGAAAATTGAAATGTAGAAGAGA
1 ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
*
28258998 A-GGGGAAAAGAGTTTTTAATTAGTGCAAGTAGAGTGATAA
66 AGGGGGAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
28259038 ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
1 ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
* *
28259103 AGGGGGAAAAGAGTTTTTGATTGGTGCAAGCAGAGTGATAA
66 AGGGGGAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
28259144 GAGAAAGCCA
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
105 62 0.63
106 36 0.37
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (106 bp):
ATTTTGGCTTTGCCCCTCATGACGTCAAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
AGGGGGAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
Found at i:28260060 original size:126 final size:125
Alignment explanation
Indices: 28259822--28260387 Score: 787
Period size: 126 Copynumber: 4.5 Consensus size: 125
28259812 AAAATTAAAG
* * * * * * *
28259822 CAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* *
28259887 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAGCGCTTCAAC
66 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAC
* * * *
28259947 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGTCCTCGTAGACGCTCTTTTGCTACAGTTGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* * *
28260012 TCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTCAAG
66 TCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTCAAC
* *
28260074 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* * * * *
28260139 TCCTGAAAAAATAATTTTGAGTTGACGTTGCTGAGCAAATAATATAAAATAACGCTGCAAC
66 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCTTCAAC
* *
28260200 CAGGATGCTATT-TGAGAAAAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAG
1 CAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
* * * * *
28260264 GTCTTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTAG
65 GTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAC
*
28260324 CAGGATGCTATATGAGAAGAATTTGTGAAATCGCGCCCAT-GTGGACGCGCTTTTGCTACAGTAG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCC-TCGTGGACGCGCTTTTGCTACAGTAG
28260388 CATGTTTGGG
Statistics
Matches: 390, Mismatches: 45, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
123 1 0.00
124 64 0.16
125 69 0.18
126 176 0.45
127 80 0.21
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (125 bp):
CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAC
Found at i:28263588 original size:21 final size:21
Alignment explanation
Indices: 28263562--28264208 Score: 575
Period size: 21 Copynumber: 30.7 Consensus size: 21
28263552 TCAAATTATA
28263562 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
28263583 TTTAAGTTAAGTGTTAGGGCTT
1 TTTAAGTTAAGGGTTAGGG-TT
* ** *
28263605 TTT-ATTTAAGGGTTACAGCT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
28263625 TTAAAGTTAAGGTTTTAGGGTA
1 TTTAAGTTAAGG-GTTAGGGTT
* *
28263647 TTTAATTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
28263669 TTTAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
28263690 TTTAAGTTAAGGGTTTAGGGTA
1 TTTAAGTTAAGGG-TTAGGGTT
* * * *
28263712 TTTAATTTAATGGTCTATGATT
1 TTTAAGTTAAGGGT-TAGGGTT
28263734 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
28263756 TTAAAGTTAAGGATTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* ***
28263777 TTTAATTTAAGGGTTACAATT
1 TTTAAGTTAAGGGTTAGGGTT
28263798 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
28263820 TTAAAGTTAAGGGTCATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
28263841 TTTAGGTTTAGGGTTTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTT
28263863 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
* *
28263884 TTT-A--T--GGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
28263900 TTTAATTTAAGGGTTTACGATT
1 TTTAAGTTAAGGG-TTAGGGTT
*
28263922 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGG-GTTAGGGTT
*
28263944 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* **
28263965 TTTAATTTAAGGGTTATAGTT
1 TTTAAGTTAAGGGTTAGGGTT
28263986 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* ***
28264008 TTAAAGTTAAAAATTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
28264028 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
28264050 TTTAAGTCAAGGATTTAGGGTT
1 TTTAAGTTAAGG-GTTAGGGTT
28264072 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
28264093 TTTAAATTAAGGGTTTAGGG--
1 TTTAAGTTAAGGG-TTAGGGTT
* **
28264113 -TT---TTAAGGTTTAAAGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
28264130 TTTAATTTAAGGGGTTAGAGTT
1 TTTAAGTTAA-GGGTTAGGGTT
28264152 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
28264173 TTTAAGTTTAGGGTTAGGGGT
1 TTTAAGTTAAGGGTTAGGGTT
*
28264194 TTTAGGTTAAGGGTT
1 TTTAAGTTAAGGGTT
28264209 TAAGGTTTGT
Statistics
Matches: 500, Mismatches: 97, Indels: 58
0.76 0.15 0.09
Matches are distributed among these distances:
15 9 0.02
16 12 0.02
17 1 0.00
18 3 0.01
19 3 0.01
20 14 0.03
21 229 0.46
22 228 0.46
23 1 0.00
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:28263657 original size:22 final size:21
Alignment explanation
Indices: 28263562--28264216 Score: 512
Period size: 22 Copynumber: 31.0 Consensus size: 21
28263552 TCAAATTATA
*
28263562 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGTTTAGGGTT
28263583 TTTAAGTTAA-GTGTTAGGGCTT
1 TTTAAGTTAAGGT-TTAGGG-TT
* * ** *
28263605 TTT-ATTTAAGGGTTACAGCT
1 TTTAAGTTAAGGTTTAGGGTT
* *
28263625 TTAAAGTTAAGGTTTTAGGGTA
1 TTTAAGTTAAGG-TTTAGGGTT
* *
28263647 TTTAATTTAAGGGTTTAGTGTT
1 TTTAAGTTAA-GGTTTAGGGTT
* *
28263669 TTTAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGTTTAGGGTT
*
28263690 TTTAAGTTAAGGGTTTAGGGTA
1 TTTAAGTTAA-GGTTTAGGGTT
* * * *
28263712 TTTAATTTAATGGTCTATGATT
1 TTTAAGTTAA-GGTTTAGGGTT
28263734 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAA-GGTTTAGGGTT
* *
28263756 TTAAAGTTAAGGATTAGGGTT
1 TTTAAGTTAAGGTTTAGGGTT
* * ***
28263777 TTTAATTTAAGGGTTACAATT
1 TTTAAGTTAAGGTTTAGGGTT
28263798 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAA-GGTTTAGGGTT
* * * *
28263820 TTAAAGTTAAGGGTCATGGTT
1 TTTAAGTTAAGGTTTAGGGTT
* * *
28263841 TTTAGGTTTAGGGTTTAGAGTT
1 TTTAAG-TTAAGGTTTAGGGTT
28263863 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAA-GGTTTAGGGTT
*
28263884 TTT-A--T--GGTTTAAGGTT
1 TTTAAGTTAAGGTTTAGGGTT
* * *
28263900 TTTAATTTAAGGGTTTACGATT
1 TTTAAGTTAA-GGTTTAGGGTT
28263922 TTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGG-TTTAGGGTT
* *
28263944 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGTTTAGGGTT
* * **
28263965 TTTAATTTAAGGGTTATAGTT
1 TTTAAGTTAAGGTTTAGGGTT
28263986 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAA-GGTTTAGGGTT
* ***
28264008 TTAAAGTTAAAAATTAGGG-T
1 TTTAAGTTAAGGTTTAGGGTT
28264028 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAA-GGTTTAGGGTT
*
28264050 TTTAAGTCAAGGATTTAGGGTT
1 TTTAAGTTAAGG-TTTAGGGTT
*
28264072 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGTTTAGGGTT
*
28264093 TTTAAATTAAGGGTTTAGGG--
1 TTTAAGTTAA-GGTTTAGGGTT
**
28264113 -TT---TTAAGGTTTAAAGTT
1 TTTAAGTTAAGGTTTAGGGTT
* * *
28264130 TTTAATTTAAGGGGTTAGAGTT
1 TTTAAGTTAA-GGTTTAGGGTT
*
28264152 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGTTTAGGGTT
* * *
28264173 TTTAAGTTTAGGGTTAGGGGT
1 TTTAAGTTAAGGTTTAGGGTT
* *
28264194 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAA-GGTTTAGGGTT
28264216 T
1 T
28264217 GTCAATTAAA
Statistics
Matches: 500, Mismatches: 103, Indels: 61
0.75 0.16 0.09
Matches are distributed among these distances:
15 15 0.03
16 8 0.02
17 1 0.00
18 3 0.01
19 3 0.01
20 15 0.03
21 212 0.42
22 241 0.48
23 2 0.00
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGTTTAGGGTT
Found at i:28263657 original size:43 final size:42
Alignment explanation
Indices: 28263562--28264208 Score: 568
Period size: 43 Copynumber: 15.4 Consensus size: 42
28263552 TCAAATTATA
28263562 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GTGTTAGGGCTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGT-TTAGGG-TT
* ** * * *
28263605 TTT-ATTTAAGGGTTACAGCTTTAAAGTTAAGGTTTTAGGGTA
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG-TTTAGGGTT
* * * *
28263647 TTTAATTTAAGGGTTTAGTGTTTTTAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* * * * *
28263690 TTTAAGTTAAGGGTTTAGGGTATTTAATTTAATGGTCTATGATT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* *
28263734 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGATTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* ***
28263777 TTTAATTTAAGGGTTACAATTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* * * * * *
28263820 TTAAAGTTAAGGGTCATGGTTTTTAGGTTTAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAG-TTAAGGTTTAGGGTT
*
28263863 TTTAAGTTAAGGGTTTAGGG-TTTT-A--T--GGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* * *
28263900 TTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGTTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG-TTTAGGGTT
* * * **
28263944 TTAAAGTTAAGGGTTAGGGTTTTTAATTTAAGGGTTATAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTAGGGTT
* ***
28263986 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAATTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGTTTAGGGTT
*
28264028 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTCAAGGATTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG-TTTAGGGTT
*
28264072 TTTAAGTTAAGGGTTAGGGTTTTTAAATTAAGGGTTTAGGG--
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* ** * * *
28264113 -TT---TTAAGGTTTAAAGTTTTTAATTTAAGGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
* * *
28264152 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTTAGGGTTAGGGGT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTAGGGTT
*
28264194 TTTAGGTTAAGGGTT
1 TTTAAGTTAAGGGTT
28264209 TAAGGTTTGT
Statistics
Matches: 488, Mismatches: 91, Indels: 51
0.77 0.14 0.08
Matches are distributed among these distances:
37 55 0.11
38 4 0.01
39 2 0.00
40 4 0.01
41 1 0.00
42 112 0.23
43 216 0.44
44 94 0.19
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTAGGGTT
Found at i:28265459 original size:7 final size:7
Alignment explanation
Indices: 28265449--28265474 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28265439 TTATATACAT
28265449 AATACTA
1 AATACTA
28265456 AATACTA
1 AATACTA
28265463 AATACTA
1 AATACTA
28265470 AATAC
1 AATAC
28265475 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:28266494 original size:59 final size:58
Alignment explanation
Indices: 28266341--28266496 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 58
28266331 ATATTATGAT
* *
28266341 TTTTATT-AATTCATATTTTAAAAATAAT-TATATTAAGAATGTTATTAAATTATATATTA
1 TTTTATTAAATT-ATA-TTTAATAATAATCTATATTAA-AATATTATTAAATTATATATTA
* *
28266400 TTTTATTAAATTGTATTTAATAATAA-CTATTTTAAAATATTATTAAATTATATCATTA
1 TTTTATTAAATTATATTTAATAATAATCTATATTAAAATATTATTAAATTATAT-ATTA
*
28266458 CTTTTATTAAATTATATTTAGTAATAATCT-TATTAAAAT
1 -TTTTATTAAATTATATTTAATAATAATCTATATTAAAAT
28266497 TTAATAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
57 17 0.20
58 21 0.25
59 41 0.48
60 6 0.07
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATCTATATTAAAATATTATTAAATTATATATTA
Done.