Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 65 of 171
Found at i:24458577 original size:15 final size:15
Alignment explanation
Indices: 24458553--24458594 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24458543 TTTTTTTGTA
24458553 TTTT-TTGTATTGAT
1 TTTTGTTGTATTGAT
*
24458567 TTTTGTTGTATT-TT
1 TTTTGTTGTATTGAT
24458581 TTTTGTGTGTATTG
1 TTTTGT-TGTATTG
24458595 TGTGTAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.10, C:0.00, G:0.19, T:0.71
Consensus pattern (15 bp):
TTTTGTTGTATTGAT
Found at i:24459885 original size:14 final size:15
Alignment explanation
Indices: 24459856--24459900 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
24459846 AAAAAATTAT
24459856 TTTTTATTTAAATTTA
1 TTTTT-TTTAAATTTA
*
24459872 TTTTTTTTAATTTATA
1 TTTTTTTTAAATT-TA
24459888 TTTTTATTTAAAT
1 TTTTT-TTTAAAT
24459901 CTTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 12 0.48
17 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTTTAAATTTA
Found at i:24460734 original size:19 final size:18
Alignment explanation
Indices: 24460703--24460757 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
24460693 TTTTGGTTGC
* *
24460703 TGTTTTTTGCTGTTTTTA
1 TGTTTTTTACTGTTTTGA
24460721 TGTTGTTTTACTGTTTTGA
1 TGTT-TTTTACTGTTTTGA
*
24460740 TGCTTTTTTACTATTTTG
1 TG-TTTTTTACTGTTTTG
24460758 GTTGCTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 26 0.81
20 2 0.06
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.67
Consensus pattern (18 bp):
TGTTTTTTACTGTTTTGA
Found at i:24460768 original size:20 final size:19
Alignment explanation
Indices: 24460724--24460768 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
24460714 GTTTTTATGT
*
24460724 TGTTTTACTGTTTTGATGC
1 TGTTTTACTATTTTGATGC
* *
24460743 TTTTTTACTATTTTGGTTGC
1 TGTTTTACTATTTT-GATGC
24460763 TGTTTT
1 TGTTTT
24460769 CGTGTTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (19 bp):
TGTTTTACTATTTTGATGC
Found at i:24460807 original size:21 final size:21
Alignment explanation
Indices: 24460773--24460812 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24460763 TGTTTTCGTG
*
24460773 TTGTTTTCACTGTTATTTTTA
1 TTGTTTTCAATGTTATTTTTA
* *
24460794 TTGTTTTTAATGTTGTTTT
1 TTGTTTTCAATGTTATTTT
24460813 GCTTTTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.70
Consensus pattern (21 bp):
TTGTTTTCAATGTTATTTTTA
Found at i:24467172 original size:30 final size:29
Alignment explanation
Indices: 24467136--24467238 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 29
24467126 TTAAAATTTT
24467136 AATAATAAAATTATATTTTTACTCTTTAAA
1 AATAATAAAATTATA-TTTTACTCTTTAAA
* *
24467166 AATAATAAAAATT-TAATTTAATCCTTTAAA
1 AATAAT-AAAATTATATTTTACT-CTTTAAA
*
24467196 AATTATAATAA-TATATTTTA----TT-AA
1 AATAATAA-AATTATATTTTACTCTTTAAA
*
24467220 AATGATAAAATTATATTTT
1 AATAATAAAATTATATTTT
24467239 TACTATCGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.03
24 17 0.27
25 2 0.03
29 8 0.13
30 28 0.44
31 6 0.10
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.46
Consensus pattern (29 bp):
AATAATAAAATTATATTTTACTCTTTAAA
Found at i:24473796 original size:16 final size:16
Alignment explanation
Indices: 24473775--24473828 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
24473765 TTTTTAAGAA
24473775 TAAATATTTGCTTAAT
1 TAAATATTTGCTTAAT
** *
24473791 TAAATAATTTTTTTAAGAA
1 TAAAT-ATTTGCTT-A-AT
24473810 TAAATATTTGCTTAAT
1 TAAATATTTGCTTAAT
24473826 TAA
1 TAA
24473829 GTAAGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 9 0.31
17 7 0.24
18 7 0.24
19 6 0.21
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (16 bp):
TAAATATTTGCTTAAT
Found at i:24473809 original size:35 final size:35
Alignment explanation
Indices: 24473758--24473828 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
24473748 ATTTATTTGT
*
24473758 AATACTTTTTTTAAGAATAAATATTTGCTTAATTA
1 AATAATTTTTTTAAGAATAAATATTTGCTTAATTA
24473793 AATAATTTTTTTAAGAATAAATATTTGCTTAATTA
1 AATAATTTTTTTAAGAATAAATATTTGCTTAATTA
24473828 A
1 A
24473829 GTAAGATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (35 bp):
AATAATTTTTTTAAGAATAAATATTTGCTTAATTA
Found at i:24473815 original size:19 final size:19
Alignment explanation
Indices: 24473758--24473815 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
24473748 ATTTATTTGT
*
24473758 AATACTTTTTTTAAGAATA
1 AATAATTTTTTTAAGAATA
** *
24473777 AAT-ATTTGCTT-A-ATTA
1 AATAATTTTTTTAAGAATA
24473793 AATAATTTTTTTAAGAATA
1 AATAATTTTTTTAAGAATA
24473812 AATA
1 AATA
24473816 TTTGCTTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 6 0.21
17 7 0.24
18 6 0.21
19 10 0.34
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
AATAATTTTTTTAAGAATA
Found at i:24483408 original size:49 final size:49
Alignment explanation
Indices: 24483335--24483703 Score: 217
Period size: 49 Copynumber: 7.6 Consensus size: 49
24483325 TGGTACTAGA
* * * *
24483335 TTCGCCGTTGTGGCTTAAATCTTTCTCTTCATGCTTCTGAGGTATAAGG
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGAGGTATAAGG
* * *
24483384 TTCGCCATTACGACTTAAACCTTTCCCTT--TG-TATCTTCATGGTACT--GG
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCT-TC-TGA-GGTA-TAAGG
* * * * *
24483432 ATTCGCCGTTGTGACTTAAATCTTTCCCTTCATGCTTCGGATGTACAAGG
1 -TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGAGGTATAAGG
* * * * ** *
24483482 TTTGCCGTTGCGACTTAAACCTTTTTCTTTGTATTTTTC-GTGGTACT--GG
1 TTCGCCGTTGCGACTTAAACC-TTTCCCTT-CATGCTTCTGAGGTA-TAAGG
* * * * *
24483531 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTATAAGGTACAAGG
1 -TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGAGGTATAAGG
* * * * *
24483581 TTCGCCGTTGTGACTTAAACCTTT-TCTT-TTG-TATTTGTGGTACT--GG
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCT-TCTGAGGTA-TAAGG
* * * *
24483627 ATTCGTCGTTACGACTTAAATCTTTCCCTTCAT-CTTCTGAGGTACAAGG
1 -TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGAGGTATAAGG
* *
24483676 TTCGTCGTTGCGGCTTAAACCTTTCCCT
1 TTCGCCGTTGCGACTTAAACCTTTCCCT
24483704 CTATTATCTT
Statistics
Matches: 236, Mismatches: 59, Indels: 51
0.68 0.17 0.15
Matches are distributed among these distances:
46 4 0.02
47 32 0.14
48 46 0.19
49 110 0.47
50 34 0.14
51 9 0.04
52 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (49 bp):
TTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGAGGTATAAGG
Found at i:24483496 original size:98 final size:98
Alignment explanation
Indices: 24483322--24483752 Score: 555
Period size: 98 Copynumber: 4.4 Consensus size: 98
24483312 TTAAATGTCA
* * * *
24483322 TCGTGGTACTAGATTCGCCGTTGTGGCTTAAATCTTTCTCTTCATGCTTCTGAGGTATAAGGTTC
1 TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTC
* *
24483387 GCCATTACGACTTAAACCTTTCCCTTTGTATCT
66 GCCGTTGCGACTTAAACCTTTCCCTTTGTATCT
* * * * * *
24483420 TCATGGTACTGGATTCGCCGTTGTGACTTAAATCTTTCCCTTCATGCTTCGGATGTACAAGGTTT
1 TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTC
** *
24483485 GCCGTTGCGACTTAAACCTTTTTCTTTGTATTTT
66 GCCGTTGCGACTTAAACCTTTCCCTTTGTA-TCT
* *
24483519 TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTATAAGGTACAAGGTTC
1 TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTC
* * *
24483584 GCCGTTGTGACTTAAACCTTTTCTTTTGTAT-T
66 GCCGTTGCGACTTAAACCTTTCCCTTTGTATCT
* * *
24483616 T-GTGGTACTGGATTCGTCGTTACGACTTAAATCTTTCCCTTCAT-CTTCTGAGGTACAAGGTTC
1 TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTC
* *
24483679 GTCGTTGCGGCTTAAACCTTTCCCTCTAT-TATCT
66 GCCGTTGCGACTTAAACCTTTCCCT-T-TGTATCT
* * *
24483713 TCGCGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCC
1 TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
24483753 CTTCTGCATC
Statistics
Matches: 288, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
95 37 0.13
96 44 0.15
97 5 0.02
98 116 0.40
99 86 0.30
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (98 bp):
TCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTC
GCCGTTGCGACTTAAACCTTTCCCTTTGTATCT
Found at i:24489034 original size:22 final size:22
Alignment explanation
Indices: 24488977--24489034 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
24488967 AGTCAAGTGG
24488977 CTGATGTGGCGATGACGTGGCA
1 CTGATGTGGCGATGACGTGGCA
** * *
24488999 CTGACATGGTGATGATGTGGCA
1 CTGATGTGGCGATGACGTGGCA
24489021 CTGATGTGGCGATG
1 CTGATGTGGCGATG
24489035 CTGACGTGGC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.16, G:0.40, T:0.26
Consensus pattern (22 bp):
CTGATGTGGCGATGACGTGGCA
Found at i:24492179 original size:30 final size:30
Alignment explanation
Indices: 24492143--24492213 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
24492133 ACATAATCTC
**
24492143 CTGACGTGATGGTCCAGATGTATTTAAATG
1 CTGACGTGACAGTCCAGATGTATTTAAATG
* *
24492173 CTGACGTGGCAGTCTAGATGTATTTAAATG
1 CTGACGTGACAGTCCAGATGTATTTAAATG
*
24492203 CCGACGTGACA
1 CTGACGTGACA
24492214 CTATTTTGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (30 bp):
CTGACGTGACAGTCCAGATGTATTTAAATG
Found at i:24492269 original size:20 final size:20
Alignment explanation
Indices: 24492241--24492297 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
24492231 CCACATCAGC
*
24492241 AAATGATTTTAAAATTATTG
1 AAATTATTTTAAAATTATTG
*
24492261 AAATTATTTTAAAATT-TTT
1 AAATTATTTTAAAATTATTG
*
24492280 AAAAT-TTTTAAAATTATT
1 AAATTATTTTAAAATTATT
24492298 TTAAAATCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.30
19 8 0.24
20 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTG
Found at i:24492279 original size:9 final size:9
Alignment explanation
Indices: 24492247--24492304 Score: 62
Period size: 9 Copynumber: 6.0 Consensus size: 9
24492237 CAGCAAATGA
24492247 TTTTAAAAT
1 TTTTAAAAT
* *
24492256 TATTGAAATT
1 T-TTTAAAAT
24492266 ATTTTAAAAT
1 -TTTTAAAAT
24492276 TTTTAAAAT
1 TTTTAAAAT
24492285 TTTTAAAATT
1 TTTTAAAA-T
24492295 ATTTTAAAAT
1 -TTTTAAAAT
24492305 CATCATCATC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 18 0.44
10 14 0.34
11 9 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:24492293 original size:29 final size:29
Alignment explanation
Indices: 24492247--24492304 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
24492237 CAGCAAATGA
*
24492247 TTTTAAAATTATTGAAATTATTTTAAAAT
1 TTTTAAAATTATTAAAATTATTTTAAAAT
*
24492276 TTTTAAAATTTTTAAAATTATTTTAAAAT
1 TTTTAAAATTATTAAAATTATTTTAAAAT
24492305 CATCATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTAAAATTATTAAAATTATTTTAAAAT
Found at i:24492299 original size:20 final size:20
Alignment explanation
Indices: 24492241--24492304 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
24492231 CCACATCAGC
* * *
24492241 AAATGATTTTAAAATTATTG
1 AAATTATTTTAAAATTTTTA
24492261 AAATTATTTTAAAATTTTTA
1 AAATTATTTTAAAATTTTTA
24492281 AAA-T-TTTTAAAATTATTTTA
1 AAATTATTTTAAAA-T-TTTTA
24492301 AAAT
1 AAAT
24492305 CATCATCATC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 8 0.21
19 2 0.05
20 28 0.74
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATTATTTTAAAATTTTTA
Found at i:24495520 original size:25 final size:25
Alignment explanation
Indices: 24495492--24495543 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
24495482 ATTAACGTAA
* *
24495492 AGCTAAACTTAGAATTTAATAATTT
1 AGCTAAACATACAATTTAATAATTT
*
24495517 AGCTCAACATACAATTTAATAATTT
1 AGCTAAACATACAATTTAATAATTT
24495542 AG
1 AG
24495544 ATTTAGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (25 bp):
AGCTAAACATACAATTTAATAATTT
Found at i:24497811 original size:29 final size:29
Alignment explanation
Indices: 24497769--24497929 Score: 102
Period size: 30 Copynumber: 5.5 Consensus size: 29
24497759 ACCCGGGGGC
24497769 AAAATGGTAATTTTGGTGAAATCAGGGTTA
1 AAAATGGTAATTTTGGTGAAATC-GGGTTA
** *
24497799 AAAATGG-AATTTT--AAAAGATTCGGGGTA
1 AAAATGGTAATTTTGGTGAA-A-TCGGGTTA
*
24497827 AAAATGGTAATTTTTGGTGAAATTAGGGTTAA
1 AAAATGGTAA-TTTTGGTGAAA-TCGGGTT-A
* ** ** *
24497859 AAAATAG-AATTTT-AAGAGCTTCGGGGT-
1 AAAATGGTAATTTTGGTGA-AATCGGGTTA
24497886 AAAATGGTAATTTTCGGTGAAATCGGGGTTA
1 AAAATGGTAATTTT-GGTGAAATC-GGGTTA
24497917 AAAATGGT-ATTTT
1 AAAATGGTAATTTT
24497930 AGAAGCTTCG
Statistics
Matches: 98, Mismatches: 20, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
27 8 0.08
28 19 0.19
29 19 0.19
30 26 0.27
31 17 0.17
32 9 0.09
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGGGTTA
Found at i:24497860 original size:59 final size:58
Alignment explanation
Indices: 24497764--24497960 Score: 279
Period size: 59 Copynumber: 3.4 Consensus size: 58
24497754 TGGATACCCG
* *
24497764 GGGGCAAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGCTTC
* * *
24497821 GGGGTAAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAAATAGAATTTTAAGAGCTTC
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTT-AAAAATGGAATTTTAAAAGCTTC
* * * *
24497881 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGTATTTTAGAAGCTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGCTTC
24497939 GGGGGTAAAATGGTAATTTTTG
1 -GGGGTAAAATGGTAATTTTTG
24497961 AAAGTTTTAG
Statistics
Matches: 123, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
57 4 0.03
58 29 0.24
59 65 0.53
60 25 0.20
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGCTTC
Found at i:24497897 original size:28 final size:27
Alignment explanation
Indices: 24497866--24497958 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 27
24497856 TAAAAAATAG
24497866 AATTTTAAGAGCTTCGGGGTAAAATGGT
1 AATTTT-AGAGCTTCGGGGTAAAATGGT
* * **
24497894 AATTTTCGGTGAAATCGGGGTTAAAAATGGT
1 AATTTT-AGAG-CTTCGGGG-T-AAAATGGT
24497925 -ATTTTAGAAGCTTCGGGGGTAAAATGGT
1 AATTTTAG-AGCTTC-GGGGTAAAATGGT
24497953 AATTTT
1 AATTTT
24497959 TGAAAGTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
28 16 0.32
29 15 0.30
30 11 0.22
31 8 0.16
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (27 bp):
AATTTTAGAGCTTCGGGGTAAAATGGT
Found at i:24497995 original size:30 final size:30
Alignment explanation
Indices: 24497940--24498137 Score: 301
Period size: 30 Copynumber: 6.6 Consensus size: 30
24497930 AGAAGCTTCG
*
24497940 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
* *
24497969 AGGGTCTAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
24497999 GGGGTCAAAATGTAATTTTGGAAACGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
24498029 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
24498059 GGGGTCAAAATGTAACTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
24498089 GGGGTCAAAATATAATTTTGGGAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
24498119 GGGGTCAAAATGTAATTTT
1 GGGGTCAAAATGTAATTTT
24498138 TGGACAATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
29 13 0.08
30 140 0.92
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:24498407 original size:162 final size:162
Alignment explanation
Indices: 24498234--24498558 Score: 460
Period size: 162 Copynumber: 2.0 Consensus size: 162
24498224 ATTTGAAAAT
*
24498234 CTTGAAAAAATT-TTGGACCAATTTT-GTAATT-AATTAAAAGTCGATTTAAGGATTAAATTAAA
1 CTTGAAAAAATTATTGGACC-ATTTTCGTAATTAAAAT-AAAGTCGATTT-AGGATTAAATTAAA
* *
24498296 ACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGACACGTGGCAACCTCT
63 ACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAA-ATGACACGTGGCAACCTAT
** **
24498361 AGTGTAGTCAAACAGTCAAAGGACTAGTTTATAAAC
127 AGTACAGTCAAACAGTCAAAGGACTAAATTATAAAC
* * *
24498397 CTTG-AAAAATTATTGGGCCATTTTCGTAATTAAAATAAAGTTGATTTGGGATTAAATTAAAACA
1 CTTGAAAAAATTATTGGACCATTTTCGTAATTAAAATAAAGTCGATTTAGGATTAAATTAAAACA
* ** *
24498461 AATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGTCTATGGTA
66 AATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAATGACACGTGGCAACCTATAGTA
24498526 CAGTCAAACAGTCAAAGGACTAAATTATAAAC
131 CAGTCAAACAGTCAAAGGACTAAATTATAAAC
24498558 C
1 C
24498559 AATTAAAATT
Statistics
Matches: 145, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
161 48 0.33
162 68 0.47
163 26 0.18
164 3 0.02
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (162 bp):
CTTGAAAAAATTATTGGACCATTTTCGTAATTAAAATAAAGTCGATTTAGGATTAAATTAAAACA
AATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAATGACACGTGGCAACCTATAGTA
CAGTCAAACAGTCAAAGGACTAAATTATAAAC
Found at i:24498626 original size:161 final size:161
Alignment explanation
Indices: 24498281--24498629 Score: 384
Period size: 161 Copynumber: 2.2 Consensus size: 161
24498271 AAGTCGATTT
*
24498281 AAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
1 AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
* ** ** **
24498346 CACGTGGCAACCTCTAGTGTAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATT
66 CACGTGGCAACCTATAGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACA
** * * * * *
24498411 GGGCCATTTTCGTAATTAAAATAAAGTTGATT
130 GGGAAAATTGCATAATTAAAATAAAGTAGATA
** *
24498443 TGGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAA-ATGA
1 AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
** *
24498507 CACGTGGCAGTCTATGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCAATT-AAAATTAC
66 CACGTGGCAACCTATAGTACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
*
24498571 AGGGTAAAATTGCAAATAATT-AAA-AATGTAGA-A
129 AGGG-AAAATTGC--ATAATTAAAATAAAGTAGATA
* * *
24498604 AAGGACTAAATTGAAGCAAATAAAAA
1 AAGGATTAAATTAAAACAAATAAAAA
24498630 TGCGGAAGGA
Statistics
Matches: 155, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
161 79 0.51
162 66 0.43
163 5 0.03
164 5 0.03
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.23
Consensus pattern (161 bp):
AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
CACGTGGCAACCTATAGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAG
GGAAAATTGCATAATTAAAATAAAGTAGATA
Found at i:24500138 original size:6 final size:6
Alignment explanation
Indices: 24500122--24500210 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
24500112 TTAAATTTTT
**
24500122 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
24500172 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
24500211 ATCAATTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 48 0.69
7 5 0.07
8 6 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:24500159 original size:11 final size:11
Alignment explanation
Indices: 24500143--24500193 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
24500133 AATTTAAATT
*
24500143 TAAATTTAAGG
1 TAAATTTAAGA
24500154 TAAATTTAA-A
1 TAAATTTAAGA
* **
24500164 T-AATTAAATT
1 TAAATTTAAGA
24500174 TAAATTTAAGA
1 TAAATTTAAGA
24500185 TAAATTTAA
1 TAAATTTAA
24500194 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:24500195 original size:37 final size:38
Alignment explanation
Indices: 24500134--24500210 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
24500124 TATAATTTAA
*
24500134 ATTTAAATTTAAATTTAAGGTAAATTTAAATAA-TTAA
1 ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
**
24500171 ATTTAAATTTAAGA-TAAATTTAAATTTAAATAAATTTAA
1 ATTTAAATTTAA-ATTAAAGGTAAATTTAAAT-AATTTAA
24500210 A
1 A
24500211 ATCAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 26 0.76
38 3 0.09
39 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (38 bp):
ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
Found at i:24500212 original size:17 final size:16
Alignment explanation
Indices: 24500122--24500210 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
24500112 TTAAATTTTT
24500122 TTTATAATTTAAATTTAAA
1 TTTA-AATTTAAA--TAAA
*
24500141 TTTAAATTTAAGGTAAA
1 TTTAAATTTAA-ATAAA
*
24500158 TTTAAA--TAATTAAA
1 TTTAAATTTAAATAAA
24500172 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
24500189 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
24500205 TTTAAA
1 TTTAAA
24500211 ATCAATTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 14 0.22
17 25 0.40
18 7 0.11
19 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:24500595 original size:68 final size:68
Alignment explanation
Indices: 24500509--24501017 Score: 838
Period size: 68 Copynumber: 7.4 Consensus size: 68
24500499 AAGACTTCGC
* * * * *
24500509 TATCCAACTTTACTTCAATTTCAAGAGGATGACATTGCCCTTACTTCAATTTCAAAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
24500574 GTGT
65 GTGT
* *
24500578 TATCCACTCTGCTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGAC
1 TATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
*
24500643 ATGT
65 GTGT
*
24500647 TATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
24500712 TGT
66 TGT
* * *
24500715 TATCCACTCTACTTCAATTTCAAGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAAACA
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
24500780 TGT
66 TGT
24500783 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
24500848 TGT
66 TGT
* * * *
24500851 TATCCACTTTACTTCAATTTCGAGGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAAAC
1 TATCCACTCTACTTCAATTTC-AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
*
24500916 ATGT
65 GTGT
24500920 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
24500985 TGT
66 TGT
24500988 TATCCACTCTACTTCAATTTCAAGGGGATG
1 TATCCACTCTACTTCAATTTCAAGGGGATG
24501018 TGTTATCCAC
Statistics
Matches: 409, Mismatches: 29, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
68 280 0.68
69 129 0.32
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (68 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
TGT
Found at i:24500731 original size:137 final size:136
Alignment explanation
Indices: 24500509--24501021 Score: 884
Period size: 137 Copynumber: 3.8 Consensus size: 136
24500499 AAGACTTCGC
* * * *
24500509 TATCCAACTTTACTTCAATTTCAAGAGGATGACATTGCCCTTACTTCAATTTCAAAGATGAAGAC
1 TATCC-ACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGAC
* * *
24500574 GTGTTATCCACTCTGCTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGA
65 GTGTTATCCACTCTACTTCAATTTC-AAGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGA
*
24500639 AGACATGT
129 AAACATGT
24500647 TATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACG
24500712 TGTTATCCACTCTACTTCAATTTCAAGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAA
66 TGTTATCCACTCTACTTCAATTTCAAGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAA
24500777 ACATGT
131 ACATGT
*
24500783 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACG
* *
24500848 TGTTATCCACTTTACTTCAATTTCGAGGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAA
66 TGTTATCCACTCTACTTCAATTTC-AAGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAA
24500913 AACATGT
130 AACATGT
*
24500920 TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACG
1 TATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACG
24500985 TGTTATCCACTCTACTTCAATTTCAAGGGGATG-TGTT
66 TGTTATCCACTCTACTTCAATTTCAAGGGGATGATGTT
24501022 ATCCACTCTT
Statistics
Matches: 361, Mismatches: 13, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
135 4 0.01
136 139 0.39
137 213 0.59
138 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (136 bp):
TATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGAAGACG
TGTTATCCACTCTACTTCAATTTCAAGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGAAA
ACATGT
Found at i:24501006 original size:273 final size:273
Alignment explanation
Indices: 24500509--24501021 Score: 893
Period size: 273 Copynumber: 1.9 Consensus size: 273
24500499 AAGACTTCGC
*
24500509 TATCCAACTTTACTTCAATTTCAAGAGGATGACATTGCCCTTACTTCAATTTCAAAGATGAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACATTGCCCTTACTTCAATTTCAAAGATGAAGAC
* *
24500574 GTGTTATCCACTCTGCTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCGGAGATGA
66 GTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
24500639 AGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGA
131 AAACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGA
24500704 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGATGTTGCTCTTACTTCAATTTCAG
196 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG-TGTTGCTCTTACTTCAATTTCAG
24500769 AGATGAAAACATGT
260 AGATGAAAACATGT
* * * *
24500783 TATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGAC
1 TATCCAACTCTACTTCAATTTCAAGAGGATGACATTGCCCTTACTTCAATTTCAAAGATGAAGAC
* * * *
24500847 GTGTTATCCACTTTACTTCAATTTCGAGGGGGATGATGTTGCTCTTACTTCAATTTCAGAGATGA
66 GTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
24500912 AAACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
131 AAACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGA
24500977 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGTGTT
196 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGTGTT
24501022 ATCCACTCTT
Statistics
Matches: 226, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
272 4 0.02
273 217 0.96
274 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (273 bp):
TATCCAACTCTACTTCAATTTCAAGAGGATGACATTGCCCTTACTTCAATTTCAAAGATGAAGAC
GTGTTATCCACTCTACTTCAATTTCAAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AAACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGA
TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGTGTTGCTCTTACTTCAATTTCAGA
GATGAAAACATGT
Found at i:24513032 original size:58 final size:58
Alignment explanation
Indices: 24512954--24513144 Score: 246
Period size: 58 Copynumber: 3.3 Consensus size: 58
24512944 TAAATGATGA
* *
24512954 AATC-GGGTAAAAAACGGGACTTATGGATACCCGGGGGCAAAATGGTAATTTT-GGTG
1 AATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
24513010 TAATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
1 -AATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
* * * *
24513069 AGATTCGGGGTTAAAAA-TGGAATTTTGGA-AGCTTCGGGGGTAAAATGGTAATTTTCGGTG
1 A-A-TCGGGGTTAAAAACGGGACTTATGGATA-C-CCGGGGGTAAAATGGTAATTTTCGGTG
24513129 AAATCGGGGTTAAAAA
1 -AATCGGGGTTAAAAA
24513145 TGAAATTTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
57 4 0.03
58 48 0.40
59 28 0.23
60 40 0.33
61 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.32, T:0.27
Consensus pattern (58 bp):
AATCGGGGTTAAAAACGGGACTTATGGATACCCGGGGGTAAAATGGTAATTTTCGGTG
Found at i:24513046 original size:29 final size:29
Alignment explanation
Indices: 24512958--24513053 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 29
24512948 TGATGAAATC
*
24512958 GGGTAAAAAACGGGACTTATGGATACCCG
1 GGGTTAAAAACGGGACTTATGGATACCCG
** * * * * * **
24512987 GGG-GCAAAATGGTAATTTTGGTGTAATCG
1 GGGTTAAAAACGGGACTTATGG-ATACCCG
24513016 GGGTTAAAAACGGGACTTATGGATACCCG
1 GGGTTAAAAACGGGACTTATGGATACCCG
*
24513045 GGGGTAAAA
1 GGGTTAAAA
24513054 TGGTAATTTT
Statistics
Matches: 46, Mismatches: 19, Indels: 4
0.67 0.28 0.06
Matches are distributed among these distances:
28 12 0.26
29 22 0.48
30 12 0.26
ACGTcount: A:0.32, C:0.12, G:0.33, T:0.22
Consensus pattern (29 bp):
GGGTTAAAAACGGGACTTATGGATACCCG
Found at i:24513079 original size:30 final size:30
Alignment explanation
Indices: 24513045--24513209 Score: 125
Period size: 29 Copynumber: 5.7 Consensus size: 30
24513035 TGGATACCCG
24513045 GGGGT-AAAATGGTAATTTTCGGTGAGATTC
1 GGGGTAAAAATGGTAATTTT-GGTGAGATTC
* *
24513075 GGGGTTAAAAATGG-AATTTTGG-AAGCTTC
1 GGGG-TAAAAATGGTAATTTTGGTGAGATTC
*
24513104 GGGGGT-AAAATGGTAATTTTCGGTGA-AATC
1 -GGGGTAAAAATGGTAATTTT-GGTGAGATTC
* * * *
24513134 GGGGTTAAAAAT-GAAATTTTAG-AAGCTTC
1 GGGG-TAAAAATGGTAATTTTGGTGAGATTC
* * *
24513163 GGGGT-CAAATGGTATTTTTGGTGA-AATC
1 GGGGTAAAAATGGTAATTTTGGTGAGATTC
24513191 GGGGTAAAAATGG-AATTTT
1 GGGGTAAAAATGGTAATTTT
24513210 AAAAGATTTG
Statistics
Matches: 104, Mismatches: 19, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
27 4 0.04
28 28 0.27
29 30 0.29
30 22 0.21
31 13 0.12
32 7 0.07
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (30 bp):
GGGGTAAAAATGGTAATTTTGGTGAGATTC
Found at i:24513160 original size:59 final size:59
Alignment explanation
Indices: 24512985--24513238 Score: 295
Period size: 59 Copynumber: 4.4 Consensus size: 59
24512975 TATGGATACC
* * * * * * *
24512985 CGGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTTAAAAACGGGACTTATGGATA-C-C
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAA-TGGAATTTTAGA-AGCTT
* *
24513043 CGGGGGTAAAATGGTAATTTTCGGTGAGATTCGGGGTTAAAAATGGAATTTTGGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGA-AATCGGGGTTAAAAATGGAATTTTAGAAGCTT
*
24513103 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* * * *
24513162 C-GGGGTCAAATGGT-ATTTTTGGTGAAATCGGGG-TAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
* *
24513218 TGGGGGTAAATTGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
24513239 TTGAAAGTTT
Statistics
Matches: 172, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
56 20 0.12
57 29 0.17
58 38 0.22
59 44 0.26
60 41 0.24
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:24513267 original size:30 final size:29
Alignment explanation
Indices: 24513242--24513448 Score: 216
Period size: 29 Copynumber: 7.2 Consensus size: 29
24513232 TAATTTTTTG
24513242 AAAGTTTTTAGGGTAAAATGTAA-TTTGGA
1 AAAG-TTTTAGGGTAAAATGTAATTTTGGA
24513271 AAAGTTTTA-GGTCAAAATGTAATTTTGGA
1 AAAGTTTTAGGGT-AAAATGTAATTTTGGA
*
24513300 AAAGTTTTAGGGTTAAAATATAATTTTGG-
1 AAAGTTTTAGGG-TAAAATGTAATTTTGGA
* *
24513329 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTAGGGT-AAAATGTAATTTTGGA
*
24513359 AAAGTTTT-GGGATTAAAATATAATTTTGGA
1 AAAGTTTTAGGG--TAAAATGTAATTTTGGA
* *
24513389 AAAGTCTT-GGGTCAAAATAT-ATTTTGG-
1 AAAGTTTTAGGGT-AAAATGTAATTTTGGA
*
24513416 -AAGTTTT-GGGTTAAAATATAATTTTGGA
1 AAAGTTTTAGGG-TAAAATGTAATTTTGGA
24513444 AAAGT
1 AAAGT
24513449 ATTGGGGGCA
Statistics
Matches: 161, Mismatches: 4, Indels: 26
0.84 0.02 0.14
Matches are distributed among these distances:
26 16 0.10
27 11 0.07
28 23 0.14
29 59 0.37
30 50 0.31
31 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.39
Consensus pattern (29 bp):
AAAGTTTTAGGGTAAAATGTAATTTTGGA
Found at i:24513357 original size:59 final size:58
Alignment explanation
Indices: 24513242--24513502 Score: 313
Period size: 59 Copynumber: 4.5 Consensus size: 58
24513232 TAATTTTTTG
* * *
24513242 AAAGTTTTTAGGG-TAAAATGTAA-TTTGGAAAAGTTTTAGGTCAAAATGTAATTTTGGA
1 AAAG-TTTT-GGGTTAAAATATAATTTTGGAAAAGTTTTGGGTCAAAATATAATTTTGGA
24513300 AAAGTTTTAGGGTTAAAATATAATTTTGG-AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTT-GGGTTAAAATATAATTTTGGAAAAGTTTT-GGGTCAAAATATAATTTTGGA
*
24513359 AAAGTTTTGGGATTAAAATATAATTTTGGAAAAGTCTTGGGTCAAAATAT-ATTTTGG-
1 AAAGTTTTGGG-TTAAAATATAATTTTGGAAAAGTTTTGGGTCAAAATATAATTTTGGA
* *
24513416 -AAGTTTTGGGTTAAAATATAATTTTGGAAAAGTATTGGGGGCAAAATATAA-TTT-GA
1 AAAGTTTTGGGTTAAAATATAATTTTGGAAAAGT-TTTGGGTCAAAATATAATTTTGGA
* * *
24513472 AAAATTTCGGGTTTAAAAGATAATTTCTGGA
1 AAAGTTTTGGG-TTAAAATATAATTT-TGGA
24513503 CAATTTAGGG
Statistics
Matches: 182, Mismatches: 10, Indels: 21
0.85 0.05 0.10
Matches are distributed among these distances:
55 24 0.13
56 25 0.14
57 17 0.09
58 44 0.24
59 65 0.36
60 7 0.04
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (58 bp):
AAAGTTTTGGGTTAAAATATAATTTTGGAAAAGTTTTGGGTCAAAATATAATTTTGGA
Found at i:24513475 original size:29 final size:30
Alignment explanation
Indices: 24513242--24513469 Score: 276
Period size: 30 Copynumber: 7.9 Consensus size: 30
24513232 TAATTTTTTG
* *
24513242 AAAGTTTTTAGGGT-AAAATGTAA-TTTGGA
1 AAAG-TTTTGGGGTCAAAATATAATTTTGGA
* *
24513271 AAAGTTTT-AGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
24513300 AAAGTTTTAGGGTTAAAATATAATTTTGG-
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
24513329 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
24513359 AAAGTTTTGGGATTAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
*
24513389 AAAGTCTT-GGGTCAAAATAT-ATTTTGG-
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
*
24513416 -AAGTTTT-GGGTTAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTGGA
* *
24513444 AAAGTATTGGGGGCAAAATATAATTT
1 AAAGTTTTGGGGTCAAAATATAATTT
24513470 GAAAAATTTC
Statistics
Matches: 175, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
26 17 0.10
27 10 0.06
28 20 0.11
29 61 0.35
30 67 0.38
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATATAATTTTGGA
Found at i:24514278 original size:18 final size:19
Alignment explanation
Indices: 24514255--24514290 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24514245 TCTCTGTTCT
*
24514255 TTCTTTCTTC-TATTTTTG
1 TTCTTTATTCTTATTTTTG
24514273 TTCTTTATTCTTATTTTT
1 TTCTTTATTCTTATTTTT
24514291 CTGTTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.75
Consensus pattern (19 bp):
TTCTTTATTCTTATTTTTG
Found at i:24514295 original size:21 final size:23
Alignment explanation
Indices: 24514247--24514295 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
24514237 CCTTTCTCTC
* *
24514247 TCTGTTCTTTCTTTCTTCTATTT
1 TCTGTTCTTTCATTCTTATATTT
24514270 T-TGTTCTTT-ATTCTTAT-TTT
1 TCTGTTCTTTCATTCTTATATTT
24514290 TCTGTT
1 TCTGTT
24514296 TTATGTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.17
21 10 0.43
22 8 0.35
23 1 0.04
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.71
Consensus pattern (23 bp):
TCTGTTCTTTCATTCTTATATTT
Found at i:24515366 original size:6 final size:6
Alignment explanation
Indices: 24515357--24515434 Score: 65
Period size: 6 Copynumber: 13.2 Consensus size: 6
24515347 TTTTAATTTT
* *
24515357 ATTTAA ATTTTAA ATTCAA A-TTAA ATTCAAA TATTTAA ATTTAA ATTTAA
1 ATTTAA A-TTTAA ATTTAA ATTTAA ATT-TAA -ATTTAA ATTTAA ATTTAA
* *
24515407 A-ATAA ATCTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
24515435 ATCAATTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 4 0.07
5 8 0.14
6 33 0.57
7 10 0.17
8 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:24515403 original size:31 final size:30
Alignment explanation
Indices: 24515356--24515425 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
24515346 CTTTTAATTT
*
24515356 TATTTAAATTTTAAATTCAAATTAAATTCAAA
1 TATTTAAA-TTTAAATTCAAAATAAA-TCAAA
* *
24515388 TATTTAAATTTAAATTTAAAATAAATCTAA
1 TATTTAAATTTAAATTCAAAATAAATCAAA
24515418 -ATTTAAAT
1 TATTTAAAT
24515426 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 4 0.11
31 15 0.43
32 8 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (30 bp):
TATTTAAATTTAAATTCAAAATAAATCAAA
Found at i:24515436 original size:17 final size:17
Alignment explanation
Indices: 24515392--24515434 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
24515382 TTCAAATATT
24515392 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
24515409 TAAATCTAAATTT-AAA
1 TAAATTTAAATTTAAAA
24515425 TAAATTTAAA
1 TAAATTTAAA
24515435 ATCAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:24516026 original size:69 final size:69
Alignment explanation
Indices: 24515753--24516364 Score: 837
Period size: 69 Copynumber: 9.0 Consensus size: 69
24515743 GGAAATGATC
* * *
24515753 TTGCTCTTACTTTCAATTTCAGAGATGATGACGT-TTATCC-ACTCTACTTCAATTTCGAGGGGA
1 TTGCTCTTAC-TTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGA
24515816 TGACG
65 TGACG
* * * *
24515821 TTGTTCTTGCTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTTTTCAATTTC-AGAG
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTAC---TTCAATTTCAAGAG
24515885 GATGACG
63 GATGACG
*
24515892 TTGCTCTTACTTCAATTTCAGAGAT-AAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
24515956 GACG
66 GACG
*
24515960 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATTCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
24516025 GACG
66 GACG
* * *
24516029 TTGCTCTTACTTCAATTTCAGAGGTAAAGACGTATTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
24516094 GACG
66 GACG
* *
24516098 TTGCTCTTACTTCAATTTCAGAGATGGAGACGTGATATCCAACTCTACTTCAATTTC-AGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
24516162 GAC-
66 GACG
* * *
24516165 --G----T--TTCAATTTTAGAGATAAAGAC-TATTATCC-ACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
24516220 GACG
66 GACG
* *
24516224 TCGCTCTTACTTCAATTTCAGAGATGGAGACGTGTTATCC-ACTCTACTTCATTCAATTTCAAGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTA---C-TTCAATTTCAAGA
24516288 GGATGACG
62 GGATGACG
* *
24516296 TTGCTCTTACTTCAATTTCAGAGATGGAGACGTGTTATCCAACTCTACTTCAA-TTCGAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
24516360 GACG
66 GACG
24516364 T
1 T
24516365 CGGTGACCTG
Statistics
Matches: 491, Mismatches: 30, Indels: 46
0.87 0.05 0.08
Matches are distributed among these distances:
57 16 0.03
58 16 0.03
59 18 0.04
61 2 0.00
65 2 0.00
67 48 0.10
68 87 0.18
69 170 0.35
70 23 0.05
71 34 0.07
72 69 0.14
73 6 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:24516078 original size:38 final size:36
Alignment explanation
Indices: 24515830--24516159 Score: 186
Period size: 38 Copynumber: 9.4 Consensus size: 36
24515820 GTTGTTCTTG
*
24515830 CTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTA
1 CTTCAATTTCAGAGGT-AAGACGT-ATATCCAACTCTA
* * *
24515868 CTTTTTCAATTTCAGAGG-ATGACG--T-TGC-TCT-TA
1 C---TTCAATTTCAGAGGTAAGACGTATATCCAACTCTA
*
24515901 CTTCAATTTCAGAGATAAGACGTGATATCCAACTCTA
1 CTTCAATTTCAGAGGTAAGACGT-ATATCCAACTCTA
* * *
24515938 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTC-AGAGGTAAGACGTATATCCAACTCTA
* * *
24515969 CTTCAATTTCAGAGATGAAGACGTGTTATTCAACTCTA
1 CTTCAATTTCAGAGGT-AAGACGT-ATATCCAACTCTA
* * *
24516007 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTC-AGAGGTAAGACGTATATCCAACTCTA
24516038 CTTCAATTTCAGAGGTAAAGACGTATTATCCAACTCTA
1 CTTCAATTTCAGAGGT-AAGACGTA-TATCCAACTCTA
* * *
24516076 CTTCAATTTCAAGAGG-ATGACG--T-TGC-TCT-TA
1 CTTCAATTTC-AGAGGTAAGACGTATATCCAACTCTA
* *
24516107 CTTCAATTTCAGAGATGGAGACGTGATATCCAACTCTA
1 CTTCAATTTCAGAGGT-AAGACGT-ATATCCAACTCTA
24516145 CTTCAATTTCAGAGG
1 CTTCAATTTCAGAGG
24516160 ATGACGTTTC
Statistics
Matches: 223, Mismatches: 32, Indels: 74
0.68 0.10 0.22
Matches are distributed among these distances:
30 26 0.12
31 41 0.18
32 20 0.09
33 9 0.04
34 6 0.03
35 7 0.03
36 9 0.04
37 33 0.15
38 45 0.20
39 14 0.06
41 13 0.06
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (36 bp):
CTTCAATTTCAGAGGTAAGACGTATATCCAACTCTA
Found at i:24516288 original size:72 final size:72
Alignment explanation
Indices: 24516167--24516347 Score: 273
Period size: 72 Copynumber: 2.6 Consensus size: 72
24516157 AGGATGACGT
* ** *
24516167 TTCAATTTTAGAGATAAAGAC-TATTATCCACTCTA---C-TTCAATTTCAAGAGGATGACGTCG
1 TTCAATTTCAGAGATGGAGACGTGTTATCCACTCTACTTCATTCAATTTCAAGAGGATGACGTCG
24516227 CTCTTAC
66 CTCTTAC
*
24516234 TTCAATTTCAGAGATGGAGACGTGTTATCCACTCTACTTCATTCAATTTCAAGAGGATGACGTTG
1 TTCAATTTCAGAGATGGAGACGTGTTATCCACTCTACTTCATTCAATTTCAAGAGGATGACGTCG
24516299 CTCTTAC
66 CTCTTAC
24516306 TTCAATTTCAGAGATGGAGACGTGTTATCCAACTCTACTTCA
1 TTCAATTTCAGAGATGGAGACGTGTTATCC-ACTCTACTTCA
24516348 ATTCGAGAGG
Statistics
Matches: 103, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
67 18 0.17
68 13 0.13
71 1 0.01
72 60 0.58
73 11 0.11
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (72 bp):
TTCAATTTCAGAGATGGAGACGTGTTATCCACTCTACTTCATTCAATTTCAAGAGGATGACGTCG
CTCTTAC
Found at i:24528429 original size:29 final size:29
Alignment explanation
Indices: 24528397--24528557 Score: 118
Period size: 29 Copynumber: 5.4 Consensus size: 29
24528387 CCCGAGGGGC
24528397 AAAATGGTAATTTTGGTGAAATCAGGGTTA
1 AAAATGG-AATTTTGGTGAAATCAGGGTTA
** *
24528427 AAAATGGAATTTT--AAAATATTC-GGGGTA
1 AAAATGGAATTTTGGTGAA-A-TCAGGGTTA
*
24528455 AAAATGGTAATTTTCGATGAAATCAGGGTTAA
1 AAAATGG-AATTTT-GGTGAAATCAGGGTT-A
* ** *
24528487 AAAATGGAATTTTAG-GAGCTTC-GGGGT-
1 AAAATGGAATTTTGGTGA-AATCAGGGTTA
*
24528514 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCAGGGTTA
24528545 AAAATGGAATTTT
1 AAAATGGAATTTT
24528558 AGAAGCTTCG
Statistics
Matches: 102, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
27 9 0.09
28 15 0.15
29 31 0.30
30 19 0.19
31 18 0.18
32 10 0.10
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGTGAAATCAGGGTTA
Found at i:24528476 original size:59 final size:59
Alignment explanation
Indices: 24528392--24528647 Score: 374
Period size: 59 Copynumber: 4.4 Consensus size: 59
24528382 GGATACCCGA
* * **
24528392 GGGGCAAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAATATTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTCG
* * *
24528449 GGGGTAAAAATGGTAATTTTCGATGAAATCAGGGTTAAAAAATGGAATTTTAGGAGCTTC-
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTT-AAAAATGGAATTTTAGAAGCTTCG
*
24528509 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTCG
* **
24528568 GGGGTAAAATGGTAATTTTTGGTAAAATTGGGGTTAAAAATGGAATTTTAGAAGCTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTCG
24528627 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
24528648 AAAGTTTTAG
Statistics
Matches: 182, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
57 4 0.02
58 32 0.18
59 122 0.67
60 24 0.13
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTCG
Found at i:24528568 original size:29 final size:30
Alignment explanation
Indices: 24528421--24528645 Score: 173
Period size: 29 Copynumber: 7.7 Consensus size: 30
24528411 GGTGAAATCA
* *
24528421 GGGTTAAAAATGG-AATTTTAAAATATTCG
1 GGGTTAAAAATGGTAATTTTAGAAGATTCG
* * * *
24528450 GGG-TAAAAATGGTAATTTTCGATGAAATCA
1 GGGTTAAAAATGGTAATTTTAGAAG-ATTCG
* *
24528480 GGGTTAAAAAATGG-AATTTTAGGAGCTTCG
1 GGGTT-AAAAATGGTAATTTTAGAAGATTCG
* ** *
24528510 GGG-T-AAAATGGTAATTTTTGGTGAAATCG
1 GGGTTAAAAATGGTAATTTTAGAAG-ATTCG
*
24528539 GGGTTAAAAATGG-AATTTTAGAAGCTTCG
1 GGGTTAAAAATGGTAATTTTAGAAGATTCG
* * *
24528568 GGGGT-AAAATGGTAATTTTTGGTAAAATT-G
1 GGGTTAAAAATGGTAA-TTTTAG-AAGATTCG
*
24528598 GGGTTAAAAATGG-AATTTTAGAAGCTTCG
1 GGGTTAAAAATGGTAATTTTAGAAGATTCG
*
24528627 GGGGT-AAAATGGTAATTTT
1 GGGTTAAAAATGGTAATTTT
24528646 TGAAAGTTTT
Statistics
Matches: 152, Mismatches: 30, Indels: 28
0.72 0.14 0.13
Matches are distributed among these distances:
27 7 0.05
28 36 0.24
29 42 0.28
30 32 0.21
31 27 0.18
32 8 0.05
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (30 bp):
GGGTTAAAAATGGTAATTTTAGAAGATTCG
Found at i:24528682 original size:30 final size:30
Alignment explanation
Indices: 24528627--24528768 Score: 171
Period size: 30 Copynumber: 4.7 Consensus size: 30
24528617 AGAAGCTTCG
*
24528627 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
* *
24528656 AGGGTCTAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
24528686 GGGGTCAAAATGTAACTTCGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* ** *
24528716 GGGGCCAAAAAATAATTTTGGGAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
24528746 GGGGTCAAAATGTAATTTCTGGA
1 GGGGTCAAAATGTAATTT-TGGA
24528769 CAATTTAGGG
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
29 13 0.14
30 77 0.83
31 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.35
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:24528780 original size:60 final size:60
Alignment explanation
Indices: 24528668--24528780 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
24528658 GGTCTAAATG
*
24528668 TAATTTTGGAAAAGTTTTGGGGTCAAAATGTAACTTCGGAAAAGTTTTGGGGCCAAAAAA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATGTAACTTCGGAAAAGTTTAGGGGCCAAAAAA
* * *
24528728 TAATTTTGGGAAAGTTTTGGGGTCAAAATGTAATTTCTGGACAA-TTTAGGGGC
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATGTAACTTC-GGAAAAGTTTAGGGGC
24528781 TTACAAAGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (60 bp):
TAATTTTGGAAAAGTTTTGGGGTCAAAATGTAACTTCGGAAAAGTTTAGGGGCCAAAAAA
Found at i:24529085 original size:162 final size:162
Alignment explanation
Indices: 24528861--24529185 Score: 492
Period size: 162 Copynumber: 2.0 Consensus size: 162
24528851 ATTTGAAAAT
* * *
24528861 CTTGAAAAATTTTTGGACCAATTTTGTAATTAATTAAAAGTCGATTTAAGGATTAAATTAAAACA
1 CTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
* *
24528926 AATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGACACGTGGCAACCTCTGGT
66 AATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAA-ATGACACGTGGCAACCTATGGT
* **
24528991 GCAGTCAAACAGTCAAAGGACTAGTTTATAAAC
130 ACAGTCAAACAGTCAAAGGACTAAATTATAAAC
* * *
24529024 CTTGAAAAATTATTGGGCCAATTTCGTAATTAAA-ATAAAGTTGATTT-GGGATTAAATTAAAAC
1 CTTGAAAAATTATTGGACCAATTTCGTAATTAAATA-AAAGTCGATTTAAGGATTAAATTAAAAC
* **
24529087 AAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAAATGACACGTGGCAGTCTATGGT
65 AAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAATGACACGTGGCAACCTATGGT
24529152 ACAGTCAAACAGTCAAAGGACTAAATTATAAAC
130 ACAGTCAAACAGTCAAAGGACTAAATTATAAAC
24529185 C
1 C
24529186 AATTAAAATT
Statistics
Matches: 147, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
161 50 0.34
162 57 0.39
163 40 0.27
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (162 bp):
CTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACA
AATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAATGACACGTGGCAACCTATGGTA
CAGTCAAACAGTCAAAGGACTAAATTATAAAC
Found at i:24529253 original size:161 final size:161
Alignment explanation
Indices: 24528908--24529256 Score: 411
Period size: 161 Copynumber: 2.2 Consensus size: 161
24528898 AAGTCGATTT
*
24528908 AAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
1 AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
* * ** **
24528973 CACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATT
66 CACGTGGCAACCTATGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACA
* * * ** *
24529038 GGGCCAATTTCGTAATTAAAATAAAGTTGATT
130 GGGCAAATTGCATAATTAAAATAAAGCAGATA
** *
24529070 TGGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATGCAGAAATAATCCAAAAA-ATGA
1 AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
**
24529134 CACGTGGCAGTCTATGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCAATT-AAAATTAC
66 CACGTGGCAACCTATGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
*
24529198 AGGGCAAAATTGCAAATAATT-AAA-AATGCAGA-A
129 AGGGC-AAATTGC--ATAATTAAAATAAAGCAGATA
* * *
24529231 AAGGACTAAATTGAAGCAAATAAAAA
1 AAGGATTAAATTAAAACAAATAAAAA
24529257 TGCGGAAGGA
Statistics
Matches: 158, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
161 82 0.52
162 66 0.42
163 5 0.03
164 5 0.03
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.22
Consensus pattern (161 bp):
AAGGATTAAATTAAAACAAATAAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAGATGA
CACGTGGCAACCTATGGTACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAG
GGCAAATTGCATAATTAAAATAAAGCAGATA
Found at i:24529672 original size:14 final size:13
Alignment explanation
Indices: 24529645--24529685 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
24529635 CGTCCCTCTC
*
24529645 TCTTCTCTTCTTT
1 TCTTCTCTTTTTT
24529658 TCTTCTTCTTTTTT
1 TCTTC-TCTTTTTT
*
24529672 TCTTCCCTTTTTT
1 TCTTCTCTTTTTT
24529685 T
1 T
24529686 TCTCTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTTCTCTTTTTT
Found at i:24530768 original size:6 final size:6
Alignment explanation
Indices: 24530752--24530840 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
24530742 TTAAATTTTT
**
24530752 TTTATAA TTTAAA TTTAAA TTTAAA TTT-AA GGTAAA TTTAAA TAATTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
24530802 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA --TAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
24530841 ATCAATTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 48 0.69
7 5 0.07
8 6 0.09
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:24530789 original size:11 final size:11
Alignment explanation
Indices: 24530773--24530823 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
24530763 AATTTAAATT
*
24530773 TAAATTTAAGG
1 TAAATTTAAGA
24530784 TAAATTTAA-A
1 TAAATTTAAGA
* **
24530794 T-AATTAAATT
1 TAAATTTAAGA
24530804 TAAATTTAAGA
1 TAAATTTAAGA
24530815 TAAATTTAA
1 TAAATTTAA
24530824 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 24 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (11 bp):
TAAATTTAAGA
Found at i:24530825 original size:37 final size:38
Alignment explanation
Indices: 24530764--24530840 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
24530754 TATAATTTAA
*
24530764 ATTTAAATTTAAATTTAAGGTAAATTTAAATAA-TTAA
1 ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
**
24530801 ATTTAAATTTAAGA-TAAATTTAAATTTAAATAAATTTAA
1 ATTTAAATTTAA-ATTAAAGGTAAATTTAAAT-AATTTAA
24530840 A
1 A
24530841 ATCAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 26 0.76
38 3 0.09
39 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (38 bp):
ATTTAAATTTAAATTAAAGGTAAATTTAAATAATTTAA
Found at i:24530842 original size:17 final size:16
Alignment explanation
Indices: 24530752--24530840 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
24530742 TTAAATTTTT
24530752 TTTATAATTTAAATTTAAA
1 TTTA-AATTTAAA--TAAA
*
24530771 TTTAAATTTAAGGTAAA
1 TTTAAATTTAA-ATAAA
*
24530788 TTTAAA--TAATTAAA
1 TTTAAATTTAAATAAA
24530802 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
24530819 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
24530835 TTTAAA
1 TTTAAA
24530841 ATCAATTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 14 0.22
17 25 0.40
18 7 0.11
19 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:24531286 original size:30 final size:29
Alignment explanation
Indices: 24531252--24531530 Score: 91
Period size: 29 Copynumber: 9.5 Consensus size: 29
24531242 TACCCGAGGG
24531252 CAAAATAGTAATTTTTAGTAAAATTGGGGT
1 CAAAATAGTAATTTTTAG-AAAATTGGGGT
* **
24531282 CAAAA-A-TAAAATTTTAGAGAGTTTAGGGGT
1 CAAAATAGT-AATTTTTAGA-AAATT-GGGGT
* * * * *
24531312 -AAAATGGTAATTTTTGGTGAAATCGAGGTT
1 CAAAATAGTAATTTTTAG-AAAATTG-GGGT
* * *
24531342 TAAAAT-GGAA-TTTTAGAAAGTTCAGGGGT
1 CAAAATAGTAATTTTTAGAAAATT--GGGGT
* * *
24531371 -AAAATGGTGATTTTGGT-G-AAATCGGGGGT
1 CAAAATAGTAATTTT--TAGAAAAT-TGGGGT
* * *
24531400 AAAAAT-GGAATTTTGTA-AAACTTGAGGGT
1 CAAAATAGTAATTTT-TAGAAAATTG-GGGT
*
24531429 CAAAATA-TAATTTTTAGAAAGTTTTGGGGT
1 CAAAATAGTAATTTTTAGAAA--ATTGGGGT
* * **
24531459 TAAAATA-TAATTTTAAAGAAGTTTGGGGT
1 CAAAATAGTAATTTT-TAGAAAATTGGGGT
*
24531488 CAAAAT-GTAATTTTTAGAAAGTTTTGGGGT
1 CAAAATAGTAATTTTTAGAAA--ATTGGGGT
24531518 CAAAATA-TAATTT
1 CAAAATAGTAATTT
24531531 CAAAAAAGTT
Statistics
Matches: 187, Mismatches: 34, Indels: 56
0.68 0.12 0.20
Matches are distributed among these distances:
28 19 0.10
29 79 0.42
30 74 0.40
31 14 0.07
32 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
CAAAATAGTAATTTTTAGAAAATTGGGGT
Found at i:24531398 original size:29 final size:29
Alignment explanation
Indices: 24531307--24531414 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 29
24531297 AGAGAGTTTA
24531307 GGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCG
** * *
24531337 AGGTTTAAAATGG-AATTTT--AGAAAGTTCA
1 -GGGGTAAAATGGTAATTTTGGTGAAA--TCG
*
24531366 GGGGTAAAATGGTGATTTTGGTGAAATCG
1 GGGGTAAAATGGTAATTTTGGTGAAATCG
24531395 GGGGTAAAAATGG-AATTTTG
1 GGGGT-AAAATGGTAATTTTG
24531415 TAAAACTTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.07
28 10 0.16
29 24 0.39
30 9 0.15
31 14 0.23
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCG
Found at i:24531413 original size:58 final size:59
Alignment explanation
Indices: 24531253--24531413 Score: 191
Period size: 59 Copynumber: 2.7 Consensus size: 59
24531243 ACCCGAGGGC
* * * * ** * *
24531253 AAAATAGTAATTTTTAGTAAAAT-TGGGGTCAAAAATAAAATTTTAGAGAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGGT-AAAAATGGAATTTTAGAAAGTTCAGGGGT
* * *
24531312 AAAATGGTAATTTTTGGTGAAATCGAGGTTTAAAATGGAATTTTAGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGGTAAAAATGGAATTTTAGAAAGTTCAGGGGT
*
24531371 AAAATGGTGA-TTTTGGTGAAATCGGGGGTAAAAATGGAATTTT
1 AAAATGGTAATTTTTGGTGAAATCGGGGGTAAAAATGGAATTTT
24531414 GTAAAACTTG
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 30 0.35
59 53 0.62
60 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGGTAAAAATGGAATTTTAGAAAGTTCAGGGGT
Found at i:24531442 original size:58 final size:58
Alignment explanation
Indices: 24531291--24531442 Score: 148
Period size: 58 Copynumber: 2.6 Consensus size: 58
24531281 TCAAAAATAA
* * * * * *
24531291 AATTTTAGAGAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTTAAAATGG
1 AATTTTAGAAACTTCAGGGGTAAAATGATAA-TTTTGGTGAAATCGAGGGTAAAAATGG
* * * *
24531350 AATTTTAGAAAGTTCAGGGGTAAAATGGTGATTTTGGTGAAATCGGGGGTAAAAATGG
1 AATTTTAGAAACTTCAGGGGTAAAATGATAATTTTGGTGAAATCGAGGGTAAAAATGG
*
24531408 AATTTT-GTAAAACTTGA-GGGTCAAAAT-ATAATTTT
1 AATTTTAG--AAACTTCAGGGGT-AAAATGATAATTTT
24531443 TAGAAAGTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 40 0.50
59 39 0.49
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
AATTTTAGAAACTTCAGGGGTAAAATGATAATTTTGGTGAAATCGAGGGTAAAAATGG
Found at i:24531539 original size:30 final size:30
Alignment explanation
Indices: 24531425--24531652 Score: 228
Period size: 30 Copynumber: 7.6 Consensus size: 30
24531415 TAAAACTTGA
*
24531425 GGGTCAAAATATAATTTTTAGAAAGTTTTG
1 GGGTCAAAATATAATTTTTAAAAAGTTTTG
*
24531455 GGGTTAAAATATAA-TTTTAAAGAAG-TTTG
1 GGGTCAAAATATAATTTTTAAA-AAGTTTTG
* *
24531484 GGGTCAAAATGTAATTTTTAGAAAGTTTTG
1 GGGTCAAAATATAATTTTTAAAAAGTTTTG
** **
24531514 GGGTCAAAATATAATTTCAAAAAAGTTTAA
1 GGGTCAAAATATAATTTTTAAAAAGTTTTG
* * *
24531544 GGGTTAAAATTTAATTTTTAGAAAGTTTTG
1 GGGTCAAAATATAATTTTTAAAAAGTTTTG
** ** *
24531574 GCATCAAAATATAATTTTGGAGAAG-TTTG
1 GGGTCAAAATATAATTTTTAAAAAGTTTTG
* *
24531603 GAGGTCAAAATGTAATTTTTAAAAAGTTTTTA
1 G-GGTCAAAATATAATTTTTAAAAAG-TTTTG
* *
24531635 GGGTTAAGATATAATTTT
1 GGGTCAAAATATAATTTT
24531653 ATGAAGTTTG
Statistics
Matches: 156, Mismatches: 36, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
29 30 0.19
30 108 0.69
31 14 0.09
32 4 0.03
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTTAAAAAGTTTTG
Found at i:24531659 original size:60 final size:60
Alignment explanation
Indices: 24531426--24531662 Score: 282
Period size: 60 Copynumber: 4.0 Consensus size: 60
24531416 AAAACTTGAG
* * *
24531426 GGTCAAAATATAATTTTTAGAAAGTTTTGGGGTTAAAATATAATTTTAAAGAAGTTTGG-
1 GGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAGAAGTTTGGA
** * *
24531485 GGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTCAAAAAAGTTT-AA
1 GGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAGAAGTTTGGA
* * ** *
24531544 GGGTTAAAATTTAATTTTTAGAAAGTTTTGGCATCAAAATATAATTTTGGAGAAGTTTGGA
1 -GGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAGAAGTTTGGA
* * * * *
24531605 GGTCAAAATGTAATTTTTAAAAAGTTTTTAGGGTTAAGATATAATTTT-ATGAAGTTTG
1 GGTCAAAATGTAATTTTTAGAAAG-TTTTGGGGTCAAAATATAATTTTGAAGAAGTTTG
24531663 AGGGTCGAAA
Statistics
Matches: 150, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
59 53 0.35
60 78 0.52
61 19 0.13
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39
Consensus pattern (60 bp):
GGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGAAGAAGTTTGGA
Found at i:24533056 original size:12 final size:12
Alignment explanation
Indices: 24533039--24533095 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
24533029 ATAAATGTAT
24533039 TTTAAATTTAAA
1 TTTAAATTTAAA
24533051 TTTAAATTTAAA
1 TTTAAATTTAAA
* * *
24533063 -ATAAACTTAAT
1 TTTAAATTTAAA
*
24533074 TTTAAA-ATAAA
1 TTTAAATTTAAA
24533085 TTTAAACTTTA
1 TTTAAA-TTTA
24533096 TTGGGCCCGG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 17 0.49
12 16 0.46
13 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:24533064 original size:7 final size:6
Alignment explanation
Indices: 24533039--24533095 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
24533029 ATAAATGTAT
* * * *
24533039 TTTAAA TTTAAA TTTAAA TTTAAA -ATAAA CTTAAT TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
24533085 TTTAAA CTTTA
1 TTTAAA -TTTA
24533096 TTGGGCCCGG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
5 8 0.20
6 29 0.71
7 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:24533067 original size:17 final size:17
Alignment explanation
Indices: 24533047--24533095 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
24533037 ATTTTAAATT
24533047 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
24533064 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
24533081 TAAATTTAAACTTTA
1 TAAATTTAAA-TTTA
24533096 TTGGGCCCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:24546109 original size:59 final size:59
Alignment explanation
Indices: 24546010--24546175 Score: 203
Period size: 59 Copynumber: 2.8 Consensus size: 59
24546000 TGGATACCCG
* * * * *
24546010 GGGGCAAAATAGTAATTTTTGGTAAAATAGGGGTCAAAAATGAAATTTTAGAGAGTT-T
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTTAGAAAGTTCA
* ** *
24546068 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTTAAAATGGAATTTTAGAAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTTAGAAAGTTCA
*
24546128 GGGGTAAAATGGTGA-TTTTGGTAAAATCGAGGG-CAAAAATGAAATTTT
1 GGGGTAAAATGGTAATTTTTGGTAAAATCG-GGGTCAAAAATGAAATTTT
24546176 GTAAAACTTG
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 26 0.29
59 64 0.70
60 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTTAGAAAGTTCA
Found at i:24546196 original size:59 final size:59
Alignment explanation
Indices: 24546009--24546204 Score: 179
Period size: 59 Copynumber: 3.3 Consensus size: 59
24545999 TTGGATACCC
* * * * **
24546009 GGGGGCAAAATAGTAATTTTTGGTAAAATAGGGGTCAAAAATGAAATTTTAG-AGAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTT-GTAAAACTT
* * ** * *
24546068 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTTAAAATGGAA-TTT-TAGAAAGTT
1 GGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTTGTA-AAACTT
* *
24546126 CAGGGGTAAAATGGTGA-TTTTGGTAAAATCGAGGG-CAAAAATGAAATTTTGTAAAACTT
1 -GGGGGTAAAATGGTAATTTTTGGTAAAATCG-GGGTCAAAAATGAAATTTTGTAAAACTT
24546185 GGGGGTCAAAAT-GTAATTTT
1 GGGGGT-AAAATGGTAATTTT
24546205 CAAAAAGTTT
Statistics
Matches: 108, Mismatches: 21, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
57 1 0.01
58 35 0.32
59 70 0.65
60 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTTGTAAAACTT
Found at i:24546210 original size:29 final size:30
Alignment explanation
Indices: 24546163--24546264 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 30
24546153 ATCGAGGGCA
* **
24546163 AAAATGAAATTTTGTAAAA-CTTGGGGGTC
1 AAAATGTAATTTTCAAAAAGCTTGGGGGTC
* *
24546192 AAAATGTAATTTTCAAAAAGTTTTGGGGTC
1 AAAATGTAATTTTCAAAAAGCTTGGGGGTC
* * * * **
24546222 AAAATATAATTTTTAGAAAGTTTTAGGGTC
1 AAAATGTAATTTTCAAAAAGCTTGGGGGTC
*
24546252 AAAATATAATTTT
1 AAAATGTAATTTT
24546265 AGAGAAGTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
29 16 0.25
30 47 0.75
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTCAAAAAGCTTGGGGGTC
Found at i:24546324 original size:30 final size:30
Alignment explanation
Indices: 24546187--24546311 Score: 139
Period size: 30 Copynumber: 4.2 Consensus size: 30
24546177 TAAAACTTGG
* * *
24546187 GGGTCAAAATGTAATTTTCA-AAAAGTTTTG-
1 GGGTCAAAATATAATTTT-AGAGAAG-TTCGA
**
24546217 GGGTCAAAATATAATTTTTAGA-AAGTTTTA
1 GGGTCAAAATATAA-TTTTAGAGAAGTTCGA
24546247 GGGTCAAAATATAATTTTAGAGAAGTTCGA
1 GGGTCAAAATATAATTTTAGAGAAGTTCGA
* *
24546277 GGGTTAAATTATAATTTTAGAGAAGTTCGA
1 GGGTCAAAATATAATTTTAGAGAAGTTCGA
24546307 GGGTC
1 GGGTC
24546312 GAAACATTAT
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
29 10 0.12
30 69 0.82
31 5 0.06
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTAGAGAAGTTCGA
Found at i:24546641 original size:33 final size:29
Alignment explanation
Indices: 24546572--24546655 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 29
24546562 GTTAAAGGAT
*
24546572 TAAATTGAAAAGTAATT-AAAATAATAAGGC
1 TAAATT-AAAA-TAATTAAAAATAAAAAGGC
24546602 TAAATTAAAATTAATTAAAAATATGAAAAGAGC
1 TAAATTAAAA-TAATTAAAAATA--AAAAG-GC
*
24546635 TAAATTAAAACAATTAAAAAT
1 TAAATTAAAATAATTAAAAAT
24546656 GCGGAAGGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.19
30 12 0.26
32 14 0.30
33 12 0.26
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (29 bp):
TAAATTAAAATAATTAAAAATAAAAAGGC
Found at i:24547778 original size:17 final size:17
Alignment explanation
Indices: 24547758--24547806 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
24547748 AAATGTATTT
24547758 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
24547775 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
24547792 TAAATTTAAACTTTA
1 TAAATTTAAA-TTTA
24547807 TTGGGCCCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:24548346 original size:24 final size:23
Alignment explanation
Indices: 24548313--24548392 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
24548303 AACATCCAAA
* *
24548313 CAACCAAAATAACAACCAAAACAG
1 CAACAAAAATAACAA-AAAAACAG
* * *
24548337 CAGCAAAAATAATAGAAAAAATAG
1 CAACAAAAATAACA-AAAAAACAG
*
24548361 CAACAAAAATAACAATAAAAACAA
1 CAACAAAAATAACAA-AAAAACAG
*
24548385 CACCAAAA
1 CAACAAAA
24548393 TAGTAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.02
24 42 0.95
25 1 0.02
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (23 bp):
CAACAAAAATAACAAAAAAACAG
Found at i:24548368 original size:12 final size:12
Alignment explanation
Indices: 24548311--24548392 Score: 58
Period size: 12 Copynumber: 6.8 Consensus size: 12
24548301 ATAACATCCA
*
24548311 AACAACCAAAAT
1 AACAACAAAAAT
* *
24548323 AACAACCAAAAC
1 AACAACAAAAAT
* *
24548335 AGCAGCAAAAAT
1 AACAACAAAAAT
*
24548347 AATAGA-AAAAAT
1 AACA-ACAAAAAT
*
24548359 AGCAACAAAAAT
1 AACAACAAAAAT
* *
24548371 AACAATAAAAAC
1 AACAACAAAAAT
*
24548383 AACACCAAAA
1 AACAACAAAA
24548393 TAGTAAAAAA
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
11 1 0.02
12 52 0.98
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:24548466 original size:22 final size:22
Alignment explanation
Indices: 24548410--24548471 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
24548400 AAAAAGCATT
**
24548410 AAAATAGCAACCAAAACAGTAA
1 AAAATAGCAACCAAAACAACAA
* * *
24548432 AAACACAAC-ACCAAAATAACAA
1 AAA-ATAGCAACCAAAACAACAA
24548454 AAAATAGCAACCAAAACA
1 AAAATAGCAACCAAAACA
24548472 GCACCAAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
21 3 0.10
22 24 0.80
23 3 0.10
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.06
Consensus pattern (22 bp):
AAAATAGCAACCAAAACAACAA
Found at i:24548478 original size:55 final size:54
Alignment explanation
Indices: 24548377--24548482 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 54
24548367 AAATAACAAT
** ** *
24548377 AAAAACAACACCAAAATAGTAAAAAAAAGCATTAAAATAGCAACCAAAACAGTA
1 AAAAACAACACCAAAATAACAAAAAAAAGCACCAAAACAGCAACCAAAACAGTA
*
24548431 AAAACACAACACCAAAATAACAAAAAATAGCAACCAAAACAGC-ACCAAAACA
1 AAAA-ACAACACCAAAATAACAAAAAAAAGC-ACCAAAACAGCAACCAAAACA
24548483 ATAATATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 4 0.09
55 32 0.73
56 8 0.18
ACGTcount: A:0.65, C:0.22, G:0.06, T:0.08
Consensus pattern (54 bp):
AAAAACAACACCAAAATAACAAAAAAAAGCACCAAAACAGCAACCAAAACAGTA
Found at i:24549382 original size:21 final size:23
Alignment explanation
Indices: 24549337--24549384 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
24549327 AATTCCAATT
24549337 AAAAATAAATTTTATTTGCTTTTCA
1 AAAAATAAATTTTATTTG--TTTCA
24549362 AAAAATAAATTTT-TTTG-TTCA
1 AAAAATAAATTTTATTTGTTTCA
24549383 AA
1 AA
24549385 TAATTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
24 4 0.17
25 13 0.57
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (23 bp):
AAAAATAAATTTTATTTGTTTCA
Found at i:24549718 original size:15 final size:15
Alignment explanation
Indices: 24549681--24549723 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24549671 CGGTTGAATT
24549681 AAATTTTTTT-ACAA
1 AAATTTTTTTGACAA
* *
24549695 AAATATTTTTTGATAG
1 AAAT-TTTTTTGACAA
24549711 AAATTTTTTTGAC
1 AAATTTTTTTGAC
24549724 TAATTGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (15 bp):
AAATTTTTTTGACAA
Found at i:24550589 original size:50 final size:50
Alignment explanation
Indices: 24550513--24550652 Score: 140
Period size: 51 Copynumber: 2.8 Consensus size: 50
24550503 CACGACCAGA
* **
24550513 CACACGGGCATGTGTTTAGGCCGTGTAACTCACTATTTATG-TATTAAGGT
1 CACACAGGCATGTGTGCAGGCCGTGTAACTCACTATTT-TGATATTAAGGT
* * *
24550563 TACACAGGCATGTGTGCAGGCTGTGTAACTCATTATTTTGAATATTAAGGT
1 CACACAGGCATGTGTGCAGGCCGTGTAACTCACTATTTTG-ATATTAAGGT
* * * * *
24550614 CACAC-GGACGTGTGTCCAGGCCATGTAACTTACCATTTT
1 CACACAGG-CATGTGTGCAGGCCGTGTAACTCACTATTTT
24550653 TAATATTTGG
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
49 2 0.03
50 34 0.47
51 37 0.51
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
CACACAGGCATGTGTGCAGGCCGTGTAACTCACTATTTTGATATTAAGGT
Found at i:24550634 original size:51 final size:50
Alignment explanation
Indices: 24550513--24550643 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
24550503 CACGACCAGA
* **
24550513 CACACGGGCATGTGTTTAGGCCGTGTAACTCACTATTTATGTATTAAGGT
1 CACACAGGCATGTGTCCAGGCCGTGTAACTCACTATTTATGTATTAAGGT
* * * *
24550563 TACACAGGCATGTGTGCAGGCTGTGTAACTCATTATTT-TGAATATTAAGGT
1 CACACAGGCATGTGTCCAGGCCGTGTAACTCACTATTTATG--TATTAAGGT
* *
24550614 CACAC-GGACGTGTGTCCAGGCCATGTAACT
1 CACACAGG-CATGTGTCCAGGCCGTGTAACT
24550644 TACCATTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.03
50 34 0.51
51 31 0.46
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (50 bp):
CACACAGGCATGTGTCCAGGCCGTGTAACTCACTATTTATGTATTAAGGT
Found at i:24551691 original size:6 final size:7
Alignment explanation
Indices: 24551658--24551701 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
24551648 AGAGTGTTAC
24551658 AACCTTA
1 AACCTTA
*
24551665 AACCTAA
1 AACCTTA
*
24551672 AACCCTA
1 AACCTTA
24551679 AACCTTA
1 AACCTTA
24551686 AA-CTTA
1 AACCTTA
*
24551692 AATCTTA
1 AACCTTA
24551699 AAC
1 AAC
24551702 ATTGAACCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (7 bp):
AACCTTA
Found at i:24553133 original size:19 final size:21
Alignment explanation
Indices: 24553111--24553149 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24553101 TTTGATTCGA
24553111 AAAATTCG-A-TAAATAATTC
1 AAAATTCGAATTAAATAATTC
*
24553130 AAAATTTGAATTAAATAATT
1 AAAATTCGAATTAAATAATT
24553150 TGAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATTCGAATTAAATAATTC
Found at i:24557297 original size:23 final size:23
Alignment explanation
Indices: 24557228--24557421 Score: 198
Period size: 23 Copynumber: 8.3 Consensus size: 23
24557218 ACGGAACAAG
* *
24557228 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
*
24557249 CAGAGAGCACA-TAAGTGCTGGGAAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
24557274 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
24557297 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
24557320 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
24557343 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
24557366 CAGAGAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
24557391 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
24557414 CAGAGAGC
1 CAGAGAGC
24557422 GCGCTAGTGT
Statistics
Matches: 148, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.10
23 95 0.64
24 2 0.01
25 29 0.20
26 7 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:24557347 original size:69 final size:69
Alignment explanation
Indices: 24557228--24557421 Score: 225
Period size: 69 Copynumber: 2.8 Consensus size: 69
24557218 ACGGAACAAG
* *
24557228 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGAAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--GAAACAGAGAGCACACAAAGT
24557291 GCTAAA
64 GCTAAA
*
24557297 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAAACAGAGAGCACACAAAGTG
*
24557361 CTAAT
65 CTAAA
* * * * *
24557366 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCT-AAACAGAGAGC
1 CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAAACAGAGAGC
24557422 GCGCTAGTGT
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
69 53 0.49
70 11 0.10
71 37 0.34
72 8 0.07
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (69 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAAACAGAGAGCACACAAAGTGC
TAAA
Found at i:24564689 original size:23 final size:23
Alignment explanation
Indices: 24564620--24564813 Score: 198
Period size: 23 Copynumber: 8.3 Consensus size: 23
24564610 ACGGAACAAG
* *
24564620 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
*
24564641 CAGAGAGCACA-TAAGTGCTGGGAAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
24564666 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
24564689 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
24564712 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
24564735 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
24564758 CAGAGAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
24564783 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
24564806 CAGAGAGC
1 CAGAGAGC
24564814 GCGCTAGTGT
Statistics
Matches: 148, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.10
23 95 0.64
24 2 0.01
25 29 0.20
26 7 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:24564739 original size:69 final size:69
Alignment explanation
Indices: 24564620--24564813 Score: 225
Period size: 69 Copynumber: 2.8 Consensus size: 69
24564610 ACGGAACAAG
* *
24564620 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGAAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--GAAACAGAGAGCACACAAAGT
24564683 GCTAAA
64 GCTAAA
*
24564689 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAAACAGAGAGCACACAAAGTG
*
24564753 CTAAT
65 CTAAA
* * * * *
24564758 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCT-AAACAGAGAGC
1 CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAAACAGAGAGC
24564814 GCGCTAGTGT
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
69 53 0.49
70 11 0.10
71 37 0.34
72 8 0.07
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (69 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAAACAGAGAGCACACAAAGTGC
TAAA
Found at i:24567876 original size:69 final size:69
Alignment explanation
Indices: 24567765--24567908 Score: 234
Period size: 69 Copynumber: 2.1 Consensus size: 69
24567755 AATCAACATC
* * *
24567765 CCAATCCTTGAATAAAGAGTAATGTCAAACTGCTAATTATCATCCCAGTATGTGGGATCCCACCA
1 CCAATCCTTGAATAAAGAGCAATGTCAAACTGCTAACTATCATCCCAGTATGTGGGATACCACCA
24567830 CCAT
66 CCAT
* * *
24567834 CCAATCCTTGAATGAAGAGCAATGTCGAACTGCTAACTATCATCCCAGTATTTGGGATACCACCA
1 CCAATCCTTGAATAAAGAGCAATGTCAAACTGCTAACTATCATCCCAGTATGTGGGATACCACCA
24567899 CCAT
66 CCAT
24567903 CCAATC
1 CCAATC
24567909 TTTTACCACT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (69 bp):
CCAATCCTTGAATAAAGAGCAATGTCAAACTGCTAACTATCATCCCAGTATGTGGGATACCACCA
CCAT
Found at i:24571494 original size:30 final size:30
Alignment explanation
Indices: 24571468--24571749 Score: 273
Period size: 30 Copynumber: 9.4 Consensus size: 30
24571458 CCAAAAATGG
* *
24571468 TATTTTGACCCAAAAACTTTTTAAAAATT-
1 TATTTTAACCCCAAAACTTTTTAAAAATTA
** ** *
24571497 TCATTTTAACCCTTAAACTTTTCCAAAATCA
1 T-ATTTTAACCCCAAAACTTTTTAAAAATTA
*
24571528 TATTTTGACCCCAAAACTTTTTAAAAATTA
1 TATTTTAACCCCAAAACTTTTTAAAAATTA
* * **
24571558 CATTTTAACCCCTAAACTTTTCCAAAATTA
1 TATTTTAACCCCAAAACTTTTTAAAAATTA
*
24571588 TATTTTAACCCTAAAACTTTTTAAAAATTA
1 TATTTTAACCCCAAAACTTTTTAAAAATTA
* **
24571618 CATTTTAACCCTC-AAACTTTTCCAAAATTA
1 TATTTTAACCC-CAAAACTTTTTAAAAATTA
* *
24571648 TATTTTAACCTCAAAACTTTCTAAAAATTA
1 TATTTTAACCCCAAAACTTTTTAAAAATTA
* * * **
24571678 CATTTTGACCCCCTAAACTTTTCCAAAATTA
1 TATTTT-AACCCCAAAACTTTTTAAAAATTA
* *
24571709 TATTTTGACCCCAAAACTTTCT-AAAATTA
1 TATTTTAACCCCAAAACTTTTTAAAAATTA
* *
24571738 CATTTTTACCCC
1 TATTTTAACCCC
24571750 TAGTTTTCCA
Statistics
Matches: 202, Mismatches: 46, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
29 19 0.09
30 159 0.79
31 24 0.12
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTTTAACCCCAAAACTTTTTAAAAATTA
Found at i:24571525 original size:60 final size:60
Alignment explanation
Indices: 24571446--24571751 Score: 429
Period size: 60 Copynumber: 5.1 Consensus size: 60
24571436 GCCCTAGAAG
* ** * *
24571446 CCCCTAAAC-TATCCAAAAATGGTATTTTGACCCAAAAACTTTTTAAAAATTTCATTTTAA
1 CCCCTAAACTTTTCC-AAAATTATATTTTGACCCCAAAACTTTTTAAAAATTACATTTTAA
* *
24571506 CCCTTAAACTTTTCCAAAATCATATTTTGACCCCAAAACTTTTTAAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTACATTTTAA
* *
24571566 CCCCTAAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTACATTTTAA
* * * *
24571626 -CCCTCAAACTTTTCCAAAATTATATTTTAACCTCAAAACTTTCTAAAAATTACATTTTGAC
1 CCCCT-AAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTACATTTT-AA
* *
24571687 CCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTCT-AAAATTACATTTTTA
1 CCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTACATTTTAA
24571746 CCCCTA
1 CCCCTA
24571752 GTTTTCCATA
Statistics
Matches: 224, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
59 10 0.04
60 168 0.75
61 42 0.19
62 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (60 bp):
CCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTTAAAAATTACATTTTAA
Found at i:24571605 original size:90 final size:88
Alignment explanation
Indices: 24571481--24571751 Score: 305
Period size: 90 Copynumber: 3.0 Consensus size: 88
24571471 TTTGACCCAA
* *
24571481 AAACTTTTTAAAAATT-TCATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCAAAAC
1 AAACTTTTCAAAAATTAT-ATTTTAACCC-TAAACTTTTCCAAAATTATATTTTGACCCCAAAAC
24571545 TTTTTAAAAATTACATTTTAACCCCT
64 TTTTT-AAAATTACATTTTAACCCCT
* ** * *
24571571 AAACTTTTCCAAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTAACCCTC-AAAC
1 AAACTTTTCAAAAATTATATTTTAACCCT-AAACTTTTCCAAAATTATATTTTGACCC-CAAAAC
* * * *
24571635 TTTTCCAAAATTATATTTTAACCTCA
64 TTTT-TAAAATTACATTTTAACCCCT
* *
24571661 AAAC-TTTCTAAAAATTACATTTTGACCCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAA
1 AAACTTTTC-AAAAATTATATTTT-A-ACCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAA
* *
24571725 CTTTCTAAAATTACATTTTTACCCCT
63 CTTTTTAAAATTACATTTTAACCCCT
24571751 A
1 A
24571752 GTTTTCCATA
Statistics
Matches: 149, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
89 5 0.03
90 106 0.71
91 34 0.23
92 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (88 bp):
AAACTTTTCAAAAATTATATTTTAACCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTT
TTTAAAATTACATTTTAACCCCT
Found at i:24571817 original size:59 final size:59
Alignment explanation
Indices: 24571754--24571890 Score: 184
Period size: 59 Copynumber: 2.3 Consensus size: 59
24571744 TACCCCTAGT
* *
24571754 TTTCCATAATTCCATTTTTAACCTCGATTTTACCAAAAACTACTATTTTACCCCCGAAC
1 TTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAACTACCATTTTACCCCCGAAC
* * * ** * *
24571813 TTTCCAAAATTCCATTTTTGACGTCGATTTTACTAAAATTTACCATTTTATCCTCGAAC
1 TTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAACTACCATTTTACCCCCGAAC
24571872 TTTCCAAAATTACCATTTT
1 TTTCCAAAATT-CCATTTT
24571891 ACCCCCGAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 61 0.90
60 7 0.10
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (59 bp):
TTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAACTACCATTTTACCCCCGAAC
Found at i:24571887 original size:29 final size:29
Alignment explanation
Indices: 24571551--24571968 Score: 161
Period size: 30 Copynumber: 14.1 Consensus size: 29
24571541 AAACTTTTTA
*
24571551 AAAATTA-CATTTTAACCC-CTAAACTTTTCC
1 AAAATTACCATTTT-ACCCTC-GAAC-TTTCC
* ** **
24571581 AAAATTA-TATTTTAACCCTAAAACTTTTTA
1 AAAATTACCATTTT-ACCCTCGAAC-TTTCC
*
24571611 AAAATTA-CATTTTAACCCTCAAACTTTTCC
1 AAAATTACCATTTT-ACCCTCGAAC-TTTCC
* * * *
24571641 AAAATTA-TATTTTAACCTCAAAACTTTCTA
1 AAAATTACCATTTTACCCTC-GAACTTTC-C
* *
24571671 AAAATTA-CATTTTGACCCCCTAAACTTTTCC
1 AAAATTACCATTTT-ACCCTC-GAAC-TTTCC
* * *
24571702 AAAATTA-TATTTTGACCC-CAAAACTTTCT
1 AAAATTACCATTTT-ACCCTC-GAACTTTCC
* **
24571731 AAAATTA-CATTTTTACCC-CTAGTTTTCC
1 AAAATTACCA-TTTTACCCTCGAACTTTCC
* * *
24571759 ATAATT-CCATTTTTAACCTCG-ATTTTACC
1 AAAATTACCA-TTTTACCCTCGAACTTT-CC
* * *
24571788 AAAAACTACTATTTTACCCCCGAACTTTCC
1 -AAAATTACCATTTTACCCTCGAACTTTCC
* * *
24571818 AAAATT-CCATTTTTGA-CGTCG-ATTTTACT
1 AAAATTACCA-TTTT-ACCCTCGAACTTT-CC
*
24571847 AAAATTTACCATTTTATCCTCGAACTTTCC
1 AAAA-TTACCATTTTACCCTCGAACTTTCC
* *
24571877 AAAATTACCATTTTACCCCCGAACTTTCT
1 AAAATTACCATTTTACCCTCGAACTTTCC
* *
24571906 AAAATT-CCATCTTTAACCCT--AATTTTAGCA
1 AAAATTACCAT-TTT-ACCCTCGAACTTT--CC
* *
24571936 AAAATTACCATATTACCCTCAAACTTTCC
1 AAAATTACCATTTTACCCTCGAACTTTCC
24571965 AAAA
1 AAAA
24571969 CCCTCTTTTT
Statistics
Matches: 310, Mismatches: 52, Indels: 53
0.75 0.13 0.13
Matches are distributed among these distances:
28 39 0.13
29 88 0.28
30 132 0.43
31 47 0.15
32 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACTTTCC
Found at i:24571889 original size:147 final size:145
Alignment explanation
Indices: 24571723--24572011 Score: 325
Period size: 147 Copynumber: 2.0 Consensus size: 145
24571713 TTGACCCCAA
* * ** * * *
24571723 AACTTTCTAAAATTACATTTTTA-CCCCTAGTTTTCCATAATTCCATTTTTAA-CCTCGATTTTA
1 AACTTTCCAAAATTACA-TTTTACCCCCGAACTTTCCAAAATTCCATCTTTAACCCT-AATTTTA
* * * * * * *
24571786 CCAAAAACTACTATTTTACCCCCGAACTTTCCAAAATTCC-ATTTTTGACGTCGATTTT-ACTAA
64 CCAAAAACTACCATATTACCCCCAAACTTTCCAAAA-CCCTATTTTTGACCT-AATTTTAACCAA
24571849 AATTTACCATTTTATCCTCG
127 AA-TTACCATTTTATCCTCG
* *
24571869 AACTTTCCAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATCTTTAACCCTAATTTTAG
1 AACTTTCCAAAATTA-CATTTTACCCCCGAACTTTCCAAAATTCCATCTTTAACCCTAATTTTAC
* * *
24571934 CAAAAATTACCATATTACCCTCAAACTTTCCAAAACCCTCTTTTTGACCTAATTTTAACCAAAAT
65 CAAAAACTACCATATTACCCCCAAACTTTCCAAAACCCTATTTTTGACCTAATTTTAACCAAAAT
24571999 TACCATTTTATCC
130 TACCATTTTATCC
24572012 CCGGGTATCC
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
146 40 0.34
147 76 0.64
148 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.38
Consensus pattern (145 bp):
AACTTTCCAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCATCTTTAACCCTAATTTTACC
AAAAACTACCATATTACCCCCAAACTTTCCAAAACCCTATTTTTGACCTAATTTTAACCAAAATT
ACCATTTTATCCTCG
Found at i:24571903 original size:88 final size:88
Alignment explanation
Indices: 24571789--24571969 Score: 231
Period size: 88 Copynumber: 2.1 Consensus size: 88
24571779 GATTTTACCA
* * * * * *
24571789 AAAACTACTATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGA-CGTCGATTTTA-CTAAAAT
1 AAAACTACCATTTTACCCCCGAACTTTCCAAAATTCCATCTTTAACCCT-AATTTTAGC-AAAAA
* * *
24571852 TTACCATTTTATCCTCGAACTTTCC
64 TTACCATATTACCCTCAAACTTTCC
* *
24571877 AAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATCTTTAACCCTAATTTTAGCAAAAATT
1 AAAACTACCATTTTACCCCCGAACTTTCCAAAATTCCATCTTTAACCCTAATTTTAGCAAAAATT
24571942 ACCATATTACCCTCAAACTTTCC
66 ACCATATTACCCTCAAACTTTCC
24571965 AAAAC
1 AAAAC
24571970 CCTCTTTTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
88 76 0.96
89 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (88 bp):
AAAACTACCATTTTACCCCCGAACTTTCCAAAATTCCATCTTTAACCCTAATTTTAGCAAAAATT
ACCATATTACCCTCAAACTTTCC
Found at i:24571908 original size:59 final size:59
Alignment explanation
Indices: 24571663--24571911 Score: 160
Period size: 59 Copynumber: 4.2 Consensus size: 59
24571653 TAACCTCAAA
* * *
24571663 ACTTT-CTAAAAATTA-CATTTTGACCCCCTAAACTTTTCCAAAATT--ATATTTTGACCCCAAA
1 ACTTTACTAAAATTTACCATTTT-ACCCCC-GAAC-TTTCCAAAATTCCAT-TTTTGACCCC--G
* ** * * *
24571724 ACTTT-CTAAAA-TTA-CATTTTTA-CCCCTAGTTTTCCATAATTCCATTTTTAACCTCG
1 ACTTTACTAAAATTTACCA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCG
* * ** * **
24571780 ATTTTACCAAAAACTACTATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACGTCG
1 ACTTTACTAAAATTTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCG
* * *
24571839 ATTTTACTAAAATTTACCATTTTATCCTCGAACTTTCCAAAATTACCA-TTTT-ACCCCCG
1 ACTTTACTAAAATTTACCATTTTACCCCCGAACTTTCCAAAATT-CCATTTTTGA-CCCCG
24571898 AACTTT-CTAAAATT
1 -ACTTTACTAAAATT
24571912 CCATCTTTAA
Statistics
Matches: 152, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
56 4 0.03
57 15 0.10
58 17 0.11
59 88 0.58
60 13 0.09
61 15 0.10
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
ACTTTACTAAAATTTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCG
Found at i:24571940 original size:59 final size:57
Alignment explanation
Indices: 24571877--24572014 Score: 152
Period size: 59 Copynumber: 2.4 Consensus size: 57
24571867 CGAACTTTCC
* *
24571877 AAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATC-TTTAACCCTAATTTTAGCA
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAA--CCATCTTTTAA-CCTAATTTTAACA
* * * * * *
24571936 AAAATTACCATATTACCCTCAAACTTTCCAAAACCCTCTTTTTGACCTAATTTTAACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAACCATC-TTTTAACCTAATTTTAACA
*
24571994 AAAATTACCATTTTATCCCCG
1 AAAATTACCATTTTACCCCCG
24572015 GGTATCCAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
57 4 0.06
58 28 0.43
59 33 0.51
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAACCATCTTTTAACCTAATTTTAACA
Found at i:24583929 original size:92 final size:92
Alignment explanation
Indices: 24583798--24584485 Score: 1081
Period size: 92 Copynumber: 7.5 Consensus size: 92
24583788 TCAAACATAG
* * *
24583798 CAAGTCTTCATCTCTCTGAAGTTGTCGTAAGAGCAAGATGAAGCTTC-AACTATCAAATCTTATC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAAC-ATCAAATCTTATC
*
24583862 CTCTTGAAGTTGCAGTAAAGTCGGATAA
65 CTCTTGAAGTTGCAGTAAAGTTGGATAA
* *
24583890 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCTTATCC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
24583955 TCTTGAAGTTGCAGTAAAGTTGGATAA
66 TCTTGAAGTTGCAGTAAAGTTGGATAA
* * *
24583982 CAAGCCTTTATCTCTTTGAAATTGTACTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
*
24584047 TCTTGAAGTTGCAGTAAAGCTGGATAA
66 TCTTGAAGTTGCAGTAAAGTTGGATAA
* *
24584074 CAAGCCTTTATCTCTCTAAAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
* *
24584139 TCTTGAAGCTGTAGTAAAGTTGGATAA
66 TCTTGAAGTTGCAGTAAAGTTGGATAA
* * *
24584166 CAAGACTTTATCTCTCTGAAGTTGTAGCAAGAGCAAGATGAAGCTTCAAACATCAATTCTTATCC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
24584231 TCTTGAAGTTGCAGTAAAGTTGGATAA
66 TCTTGAAGTTGCAGTAAAGTTGGATAA
* *
24584258 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAAATCTTATCC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
*
24584323 TCTTGAAGCTGCAGTAAAGTTGGATAA
66 TCTTGAAGTTGCAGTAAAGTTGGATAA
* * * * *
24584350 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGAAAGATGAAGTTTCAAACGTCGATTCTTATCC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
* *
24584415 TCTTGAAGTTGCAGTAAAGTTAGATAG
66 TCTTGAAGTTGCAGTAAAGTTGGATAA
* * * *
24584442 CAAGTCTTTATCTCTCCGAAGTTGTAGTAAGAACAAGATAAAGC
1 CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
24584486 CTCGACATCA
Statistics
Matches: 547, Mismatches: 48, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
92 544 0.99
93 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (92 bp):
CAAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCC
TCTTGAAGTTGCAGTAAAGTTGGATAA
Found at i:24584149 original size:52 final size:51
Alignment explanation
Indices: 24584092--24584339 Score: 148
Period size: 52 Copynumber: 5.2 Consensus size: 51
24584082 TATCTCTCTA
24584092 AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAAATCTTATCCTCTTG
1 AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATC-AATCTTATCCTCTTG
*** *
24584144 AAGCTGTAGTAA-AGTTGGAT-AA----C-AAGA-C--T-TTAT-CTCTCTG
1 AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATCTTATCCTCT-TG
* *
24584184 AAGTTGTAGCAAGAGCAAGATGAAGCTTCAAACATCAATTCTTATCCTCTTG
1 AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAA-TCTTATCCTCTTG
* * *** *
24584236 AAGTTGCAGTAA-AGTTGGAT-AA----C-AA-GTC--T-TTAT-CTCTCTG
1 AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATCTTATCCTCT-TG
* *
24584276 AAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAAATCTTATCCTCTTG
1 AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATC-AATCTTATCCTCTTG
*
24584328 AAGCTGCAGTAA
1 AAGCTGTAGTAA
24584340 AGTTGGATAA
Statistics
Matches: 144, Mismatches: 24, Indels: 56
0.64 0.11 0.25
Matches are distributed among these distances:
39 8 0.06
40 33 0.23
41 12 0.08
42 4 0.03
44 3 0.02
45 5 0.03
46 3 0.02
47 5 0.03
48 3 0.02
50 4 0.03
51 12 0.08
52 44 0.31
53 8 0.06
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (51 bp):
AAGCTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATCTTATCCTCTTG
Found at i:24584192 original size:40 final size:40
Alignment explanation
Indices: 24584133--24584287 Score: 98
Period size: 40 Copynumber: 3.6 Consensus size: 40
24584123 ACATCAAATC
*
24584133 TTATCCTCTTGAAGCTGTAGTAAAGTTGGATAACAAGACT
1 TTATCCTCTTGAAGTTGTAGTAAAGTTGGATAACAAGACT
* *** *
24584173 TTAT-CTCTCTGAAGTTGTAGCAAGAGCAAGATGAAGCTTCAAACATCAATT
1 TTATCCTCT-TGAAGTTGTAGTAA-AGTTGGAT-AA----C-AAGA-C---T
* *
24584224 CTTATCCTCTTGAAGTTGCAGTAAAGTTGGATAACAAGTCT
1 -TTATCCTCTTGAAGTTGTAGTAAAGTTGGATAACAAGACT
24584265 TTAT-CTCTCTGAAGTTGTAGTAA
1 TTATCCTCT-TGAAGTTGTAGTAA
24584288 GAGCAAGATG
Statistics
Matches: 86, Mismatches: 14, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
39 8 0.09
40 33 0.38
41 6 0.07
42 2 0.02
44 1 0.01
45 2 0.02
46 2 0.02
47 3 0.03
48 1 0.01
50 2 0.02
51 6 0.07
52 16 0.19
53 4 0.05
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTGTAGTAAAGTTGGATAACAAGACT
Found at i:24584788 original size:17 final size:16
Alignment explanation
Indices: 24584752--24584806 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
24584742 GAATTTGTTC
*
24584752 TAAAATTAAATTTA-T
1 TAAATTTAAATTTATT
24584767 TAAATTTAAATTTAATT
1 TAAATTTAAATTT-ATT
*
24584784 TAAATTTAAAATTATT
1 TAAATTTAAATTTATT
24584800 ATAAATT
1 -TAAATT
24584807 CAATTGAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 12 0.34
16 4 0.11
17 19 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTTAAATTTATT
Found at i:24586654 original size:30 final size:30
Alignment explanation
Indices: 24586619--24586838 Score: 225
Period size: 30 Copynumber: 7.4 Consensus size: 30
24586609 CTAGAAATGG
*
24586619 TATTTTGACCCTAAAACTTTTTGAAAATTA
1 TATTTTAACCCTAAAACTTTTTGAAAATTA
* **
24586649 CATTTTAACCCCT-AAACTTTTCT-AAAACCA
1 TATTTTAA-CCCTAAAACTTTT-TGAAAATTA
*
24586679 TATTTTTAACCCTAAATCTTTTTGAAAATTA
1 TA-TTTTAACCCTAAAACTTTTTGAAAATTA
**
24586710 TATTTTAAGCCCT-AAACTTTTCCAAAATTA
1 TATTTTAA-CCCTAAAACTTTTTGAAAATTA
*
24586740 TATTTTAACCTTAAAAC-TTTTGAAAATTA
1 TATTTTAACCCTAAAACTTTTTGAAAATTA
* * **
24586769 CATTTTAACCCTTAAACTTTTCCAAAATTA
1 TATTTTAACCCTAAAACTTTTTGAAAATTA
* *
24586799 TATTTAAACCCTAAAACTTTCT-AAAATTA
1 TATTTTAACCCTAAAACTTTTTGAAAATTA
* *
24586828 CATTTTTACCC
1 TATTTTAACCC
24586839 CCAAGTTTTC
Statistics
Matches: 155, Mismatches: 27, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
29 42 0.27
30 84 0.54
31 29 0.19
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.41
Consensus pattern (30 bp):
TATTTTAACCCTAAAACTTTTTGAAAATTA
Found at i:24586785 original size:59 final size:59
Alignment explanation
Indices: 24586619--24586838 Score: 300
Period size: 59 Copynumber: 3.7 Consensus size: 59
24586609 CTAGAAATGG
* * **
24586619 TATTTTGACCCTAAAACTTTTTGAAAATTACATTTTAACCCCTAAACTTTTCTAAAACCA
1 TATTTTAACCCTAAAACTTTTTGAAAATTACATTTTAA-CCCTAAACTTTTCCAAAATTA
* *
24586679 TATTTTTAACCCTAAATCTTTTTGAAAATTATATTTTAAGCCCTAAACTTTTCCAAAATTA
1 TA-TTTTAACCCTAAAACTTTTTGAAAATTACATTTTAA-CCCTAAACTTTTCCAAAATTA
*
24586740 TATTTTAACCTTAAAAC-TTTTGAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
1 TATTTTAACCCTAAAACTTTTTGAAAATTACATTTTAACCC-TAAACTTTTCCAAAATTA
* * *
24586799 TATTTAAACCCTAAAACTTTCT-AAAATTACATTTTTACCC
1 TATTTTAACCCTAAAACTTTTTGAAAATTACATTTTAACCC
24586839 CCAAGTTTTC
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 3 0.02
59 69 0.48
60 18 0.13
61 53 0.37
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.41
Consensus pattern (59 bp):
TATTTTAACCCTAAAACTTTTTGAAAATTACATTTTAACCCTAAACTTTTCCAAAATTA
Found at i:24586884 original size:88 final size:87
Alignment explanation
Indices: 24586792--24586975 Score: 208
Period size: 88 Copynumber: 2.1 Consensus size: 87
24586782 AAACTTTTCC
* ** *
24586792 AAAATTATATTTAAACCCTAAAACTTTCTAAAATTA-CATTTTTACCCCCAAGTTTTCCATAATT
1 AAAATTATATTTAAACCCT-AAACTTTCCAAAATTACCA-TTTTACCCCCAAACTTTCCAAAATT
* *
24586856 CCATTTTTAAACCTGATTTTACCA
64 CCATCTTTAAACCCGATTTTACCA
* * * * * *
24586880 AAAATTACCATTTTACCCCTGAACTTTCCAAAATTACCATTTTACCCCTAAACTTTCTAAAATTC
1 AAAATTA-TATTTAAACCCTAAACTTTCCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC
* *
24586945 CATCTTTGACCCCGATTTTACCA
65 CATCTTTAAACCCGATTTTACCA
24586968 AAAATTAT
1 AAAATTAT
24586976 CATATTACCA
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
88 68 0.86
89 11 0.14
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (87 bp):
AAAATTATATTTAAACCCTAAACTTTCCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCC
ATCTTTAAACCCGATTTTACCA
Found at i:24586922 original size:29 final size:29
Alignment explanation
Indices: 24586762--24587001 Score: 122
Period size: 29 Copynumber: 8.2 Consensus size: 29
24586752 AAAACTTTTG
* *
24586762 AAAATTA-CATTTTAACCCTTAAACTTTTCC
1 AAAATTACCATTTT-ACCCCTGAAC-TTTCC
* * * * *
24586792 AAAATTA-TATTTAAACCCTAAAACTTTCT
1 AAAATTACCATTTTACCCCT-GAACTTTCC
* *
24586821 AAAATTA-CATTTTTACCCC-CAAGTTTTCC
1 AAAATTACCA-TTTTACCCCTGAA-CTTTCC
* ** *
24586850 ATAATT-CCATTTTTAAACCTG-ATTTTACC
1 AAAATTACCA-TTTTACCCCTGAACTTT-CC
24586879 AAAAATTACCATTTTACCCCTGAACTTTCC
1 -AAAATTACCATTTTACCCCTGAACTTTCC
* *
24586909 AAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATTACCATTTTACCCCTGAACTTTCC
*
24586938 AAAATT-CCATCTTTGACCCC-G-ATTTTACC
1 AAAATTACCAT-TTT-ACCCCTGAACTTT-CC
* * *
24586967 AAAAATTATCATATTA-CCATCGAACTTTCC
1 -AAAATTACCATTTTACCCCT-GAACTTTCC
24586997 AAAAT
1 AAAAT
24587002 CTCATTTTTG
Statistics
Matches: 165, Mismatches: 28, Indels: 35
0.72 0.12 0.15
Matches are distributed among these distances:
28 16 0.10
29 81 0.49
30 54 0.33
31 14 0.08
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTGAACTTTCC
Found at i:24586972 original size:59 final size:59
Alignment explanation
Indices: 24586907--24587044 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 59
24586897 CCTGAACTTT
* * *
24586907 CCAAAATTACCATTTTACCCCT-AAACTTTCTAAAAT-TCCATCTTTGACCCCGATTT-TA
1 CCAAAATTACCATTTTACCCCTCAAACTTTCCAAAATCT-CATCTTTGA-CCCAATTTCAA
* * * * *
24586965 CCAAAAATTATCATATTA-CCATCGAACTTTCCAAAATCTCATTTTTGACCCAATTTCAA
1 CC-AAAATTACCATTTTACCCCTCAAACTTTCCAAAATCTCATCTTTGACCCAATTTCAA
24587024 CCAAAATTACCATTTTACCCC
1 CCAAAATTACCATTTTACCCC
24587045 CGGGTATCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
58 25 0.39
59 38 0.59
60 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAATTACCATTTTACCCCTCAAACTTTCCAAAATCTCATCTTTGACCCAATTTCAA
Found at i:24586984 original size:88 final size:88
Alignment explanation
Indices: 24586813--24587015 Score: 232
Period size: 88 Copynumber: 2.3 Consensus size: 88
24586803 TAAACCCTAA
* ** * * *
24586813 AACTTTCTAAAATTACATTTTTACCCCCAAGTTTTCCATAATTCCATTTTTAAACCTGATTTTAC
1 AACTTTCCAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATCTTTAAACCCGATTTTAC
* *
24586878 CAAAAATTACCATTTTACC-CCTG
66 CAAAAATTACCATATTACCATC-G
* * * *
24586901 AACTTTCCAAAATTACCA-TTTTACCCCTAAACTTTCTAAAATTCCATCTTTGACCCCGATTTTA
1 AACTTTCCAAAATTA-CATTTTTACCCCCAAACTTTCCAAAATTCCATCTTTAAACCCGATTTTA
*
24586965 CCAAAAATTATCATATTACCATCG
65 CCAAAAATTACCATATTACCATCG
24586989 AACTTTCCAAAATCT-CATTTTTGACCC
1 AACTTTCCAAAAT-TACATTTTT-ACCC
24587016 AATTTCAACC
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
87 2 0.02
88 87 0.90
89 8 0.08
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (88 bp):
AACTTTCCAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATCTTTAAACCCGATTTTAC
CAAAAATTACCATATTACCATCG
Found at i:24590579 original size:29 final size:28
Alignment explanation
Indices: 24590549--24590766 Score: 159
Period size: 29 Copynumber: 7.5 Consensus size: 28
24590539 ATCGATGTTA
*
24590549 AAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGAATTTTAGAAGATTCGGGGGT
* *
24590577 AAAATGGTAATTTTTGATGAGA-TCGGGGTT
1 AAAATGG-AATTTTAGA--AGATTCGGGGGT
* * *
24590607 AAAAATGGAATTTTGGAAGCTTCAGGGGT
1 -AAAATGGAATTTTAGAAGATTCGGGGGT
* * * * * *
24590636 AAAATGCTAATTTTCGATGAAATCGAGGTT
1 AAAATG-GAATTTTAGAAG-ATTCGGGGGT
* *
24590666 AAAAAAGGAATTTTAGAAGTTTCGGGGGT
1 -AAAATGGAATTTTAGAAGATTCGGGGGT
* * * * *
24590695 CAAATGGTAATTTTTGATGAAATCGGGGTT
1 AAAATGG-AATTTTAGAAG-ATTCGGGGGT
*
24590725 AAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGAATTTTAGAAGATTCGGGGGT
24590753 AAAATGGTAATTTT
1 AAAATGG-AATTTT
24590767 TGAAAGTTTT
Statistics
Matches: 143, Mismatches: 36, Indels: 21
0.71 0.18 0.10
Matches are distributed among these distances:
28 35 0.24
29 51 0.36
30 42 0.29
31 15 0.10
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTAGAAGATTCGGGGGT
Found at i:24590610 original size:30 final size:30
Alignment explanation
Indices: 24590569--24590769 Score: 141
Period size: 30 Copynumber: 6.8 Consensus size: 30
24590559 TTTAAAAGAT
24590569 TCGGGGGTAAAATGGTAATTTTTGATGAGA
1 TCGGGGGTAAAATGGTAATTTTTGATGAGA
* * *
24590599 TCGGGGTTAAAAATGG-AATTTTGGA--AGCT
1 TCGGGGGT-AAAATGGTAATTTTTGATGAG-A
* * * *
24590628 TCAGGGGTAAAATGCTAATTTTCGATGAAA
1 TCGGGGGTAAAATGGTAATTTTTGATGAGA
* * * * *
24590658 TCGAGGTTAAAAAAGG-AATTTTAGA--AGTT
1 TCGGGGGT-AAAATGGTAATTTTTGATGAG-A
* *
24590687 TCGGGGGTCAAATGGTAATTTTTGATGAAA
1 TCGGGGGTAAAATGGTAATTTTTGATGAGA
* **
24590717 TCGGGGTTAAAATGG-AA-TTTT-AAAAGA
1 TCGGGGGTAAAATGGTAATTTTTGATGAGA
24590744 TTCGGGGGTAAAATGGTAATTTTTGA
1 -TCGGGGGTAAAATGGTAATTTTTGA
24590770 AAGTTTTGGG
Statistics
Matches: 127, Mismatches: 30, Indels: 27
0.69 0.16 0.15
Matches are distributed among these distances:
27 3 0.02
28 32 0.25
29 32 0.25
30 45 0.35
31 15 0.12
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (30 bp):
TCGGGGGTAAAATGGTAATTTTTGATGAGA
Found at i:24590618 original size:59 final size:59
Alignment explanation
Indices: 24590512--24590769 Score: 349
Period size: 59 Copynumber: 4.4 Consensus size: 59
24590502 TATGGATACC
* * * *
24590512 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGATGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
* * ** *
24590570 CGGGGGTAAAATGGTAATTTTTGATGAGATCGGGGTTAAAAATGGAATTTTGGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
* * * * * *
24590629 CAGGGGTAAAATGCTAATTTTCGATGAAATCGAGGTTAAAAAAGGAATTTTAGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
* *
24590688 CGGGGGTCAAATGGTAATTTTTGATGAAATCGGGGTT-AAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
24590746 CGGGGGTAAAATGGTAATTTTTGA
1 CGGGGGTAAAATGGTAATTTTTGA
24590770 AAGTTTTGGG
Statistics
Matches: 173, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
58 57 0.33
59 116 0.67
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTAAAAGATT
Found at i:24590803 original size:30 final size:30
Alignment explanation
Indices: 24590760--24590979 Score: 327
Period size: 30 Copynumber: 7.3 Consensus size: 30
24590750 GGTAAAATGG
* *
24590760 TAATTTTTG-AAAGTTTTGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
24590789 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
24590819 TAATTTTGGAAAAGTTTTGGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
24590849 TAATTTTGGAAAAGTCTTGGGGTCAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
* *
24590879 TAATTTTGGAAAAGTTTTAGGGTTAAAATA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
*
24590909 TAATTTTGGAAAAGTATTAGGGGT-AAAATA
1 TAATTTTGGAAAAGT-TTTGGGGTCAAAATA
* *
24590939 TAATTTTGAAAAAGTTTTGGGGTCAAAAGA
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATA
24590969 TAATTTCTGGA
1 TAATTT-TGGA
24590980 CAATTTAGAG
Statistics
Matches: 173, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.09
30 149 0.86
31 9 0.05
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTTGGGGTCAAAATA
Found at i:24591783 original size:18 final size:17
Alignment explanation
Indices: 24591742--24591790 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
24591732 CCTCTTTTTC
*
24591742 CTTTCTTCTCTTCTGTTT
1 CTTTCTT-TCTTCTATTT
24591760 CTTTCTTTCTTCTATTT
1 CTTTCTTTCTTCTATTT
* *
24591777 TTGTTCTTTATTCT
1 CT-TTCTTTCTTCT
24591791 TTATTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.69
Consensus pattern (17 bp):
CTTTCTTTCTTCTATTT
Found at i:24591803 original size:22 final size:23
Alignment explanation
Indices: 24591752--24591803 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
24591742 CTTTCTTCTC
*
24591752 TTCTGTTTCTTTCTTTCTTCTATT
1 TTCTG-TTCTTTCATTCTTCTATT
24591776 TT-TGTTCTTT-ATTCTT-TATTT
1 TTCTGTTCTTTCATTCTTCTA-TT
24591797 TTCTGTT
1 TTCTGTT
24591804 TTATGTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 9 0.36
22 10 0.40
23 2 0.08
24 2 0.08
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (23 bp):
TTCTGTTCTTTCATTCTTCTATT
Found at i:24592897 original size:6 final size:6
Alignment explanation
Indices: 24592878--24592954 Score: 81
Period size: 6 Copynumber: 13.2 Consensus size: 6
24592868 TTTAATTTTT
*
24592878 ATTTAA ATTTAA ATTCAA A-TTAA ATTTAAA TATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA -ATTTAA ATTTAA ATTTAA
* *
24592927 A-ATAA ATCTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
24592955 ATCAATTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.07
5 8 0.13
6 40 0.67
7 4 0.07
8 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:24592900 original size:17 final size:17
Alignment explanation
Indices: 24592880--24592964 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
24592870 TAATTTTTAT
24592880 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTCAAA
*
24592897 TTAAATTTAAA-T--AT
1 TTAAATTTAAATTCAAA
*
24592911 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* * *
24592928 ATAAATCTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
24592945 -TAAATTTAAAATCAAT
1 TTAAATTTAAATTCAAA
24592961 TTAA
1 TTAA
24592965 CTCAAAAGTC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 13 0.23
17 30 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAATTCAAA
Found at i:24592912 original size:31 final size:31
Alignment explanation
Indices: 24592877--24592939 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
24592867 TTTTAATTTT
* *
24592877 TATTTAAATTTAAATTCAAATTAAATTTAAA
1 TATTTAAATTTAAATTCAAAATAAATCTAAA
*
24592908 TATTTAAATTTAAATTTAAAATAAATCTAAA
1 TATTTAAATTTAAATTCAAAATAAATCTAAA
24592939 T
1 T
24592940 TTAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAATTCAAAATAAATCTAAA
Found at i:24593423 original size:69 final size:69
Alignment explanation
Indices: 24593273--24594091 Score: 1263
Period size: 69 Copynumber: 12.0 Consensus size: 69
24593263 GGAAATGATC
* * *
24593273 TTGCTCTTACTTCAATTTCAGAGATGATGACGT-ATTATCC-ACTCTACTTCAATTTCGAGGGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
*
24593336 TGACA
65 TGACG
* * *
24593341 TTGTTCTTGCTTCAATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24593406 GACG
66 GACG
24593410 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24593475 GACG
66 GACG
* *
24593479 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATTCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24593544 GACG
66 GACG
* * *
24593548 TTGCTCTTACTTCAATTTCAGAGGTAAAGACAT-ATTATCCAACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
24593612 TGACG
65 TGACG
24593617 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24593682 GACG
66 GACG
* *
24593686 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATTCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24593751 GACG
66 GACG
* * *
24593755 TTGCTCTTACTTCAATTTCAGAGGTAAAGACAT-ATTATCCAACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
24593819 TGACG
65 TGACG
24593824 TTGCTCTTACTTCAATTTCAGAGAT-AGAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGATGA-AGACGTGATATCCAACTCTACTTCAATTTCAAGAGGA
24593888 TGAC-
65 TGACG
*
24593892 --G----T--TTCAATTTCAGAGATAAAGACGT-ATTATCCAACTCTACTTCAATTTCAAGAGGA
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGA-TATCCAACTCTACTTCAATTTCAAGAGGA
24593948 TGACG
65 TGACG
* * *
24593953 TCGCTCTTACTTCAATTTCAGAGATGGAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24594018 GACG
66 GACG
* * * *
24594022 TCGCTCTTACTTCAATTTCAGAGATGGAGACGTGTTATCCAACTCTACTTCAATTTCGAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
24594087 GACG
66 GACG
24594091 T
1 T
24594092 CGGTGACCTG
Statistics
Matches: 699, Mismatches: 33, Indels: 37
0.91 0.04 0.05
Matches are distributed among these distances:
59 1 0.00
60 54 0.08
61 1 0.00
62 1 0.00
63 1 0.00
66 1 0.00
67 1 0.00
68 35 0.05
69 602 0.86
70 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:24605855 original size:58 final size:58
Alignment explanation
Indices: 24605788--24606078 Score: 258
Period size: 58 Copynumber: 5.0 Consensus size: 58
24605778 TGATAAATGA
* * * *
24605788 TGAAATCGGGGTGAAAAATGGGACTTATGGATACCCGGGGGCAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTA-GGATACTCGGGGGTAAAATGGTAATTTTTGG
* * ** * *
24605846 TGTAATCGGGGTTTAAAAT-GGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGGAA--TTAGGATACTCGGGGGTAAAATGGTAATTTTTGG
*
24605905 TGAAATCGGGGTTAAAAA-CGGAATTAGGA-AGCTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTAGGATA-C-TCGGGGGTAAAATGGTAATTTTTGG
* *
24605963 TGAAATCGGGGTT-AAAAT-GGAATTTTA-GA-AGCTTCGAGGGTCAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGGAA--TTAGGATA-C-TCGGGGGTAAAATGGTAATTTTTGG
* ** * *
24606021 TGAAATCAGGGTTAAAAAT-GGAATTTTAAAATATTCGGGGGTAAAATGGTAGTTTTTG
1 TGAAATCGGGGTTAAAAATGGGAA--TTAGGATACTCGGGGGTAAAATGGTAATTTTTG
24606079 AAAGTTTTGG
Statistics
Matches: 198, Mismatches: 23, Indels: 23
0.81 0.09 0.09
Matches are distributed among these distances:
56 1 0.01
57 15 0.08
58 113 0.57
59 67 0.34
60 1 0.01
61 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (58 bp):
TGAAATCGGGGTTAAAAATGGGAATTAGGATACTCGGGGGTAAAATGGTAATTTTTGG
Found at i:24605864 original size:30 final size:28
Alignment explanation
Indices: 24605830--24606047 Score: 119
Period size: 30 Copynumber: 7.5 Consensus size: 28
24605820 ACCCGGGGGC
*
24605830 AAAATGGTAATTTTGGTGTAATCGGGGTTT
1 AAAATGG-AATTTTGGTGAAATCGGGG-TT
** *
24605860 AAAATGGAATTTT--AAAAGATTCGGGGGT
1 AAAATGGAATTTTGGTGAA-A-TCGGGGTT
24605888 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
* * * *
24605918 AAAAACGGAA--TTAG-GAAGCTTCGGGGGT
1 -AAAATGGAATTTTGGTGAA--ATCGGGGTT
24605946 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
* *
24605976 AAAATGGAATTTT--AGAAGCTTCGAGGG-T
1 AAAATGGAATTTTGGTGAA--ATCG-GGGTT
* *
24606004 CAAATGGTAATTTTTGGTGAAATCAGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
24606034 AAAAATGGAATTTT
1 -AAAATGGAATTTT
24606048 AAAATATTCG
Statistics
Matches: 143, Mismatches: 22, Indels: 47
0.67 0.10 0.22
Matches are distributed among these distances:
26 6 0.04
27 10 0.07
28 32 0.22
29 28 0.20
30 43 0.30
31 16 0.11
32 8 0.06
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGGGGTT
Found at i:24606068 original size:59 final size:59
Alignment explanation
Indices: 24605823--24606078 Score: 358
Period size: 58 Copynumber: 4.4 Consensus size: 59
24605813 TATGGATACC
* * *
24605823 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTTAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * *
24605881 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGGAA--TTAGGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AAAGATT
* *
24605939 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * * *
24605997 CGAGGGTCAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAATATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
24606056 CGGGGGTAAAATGGTAGTTTTTG
1 CGGGGGTAAAATGGTAATTTTTG
24606079 AAAGTTTTGG
Statistics
Matches: 177, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
57 11 0.06
58 99 0.56
59 67 0.38
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.32
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Done.